| Legend : | mRNA | The GenBank/DDBJ/EMBL accession. |
| Method | The method or program, or GOLD. | |
| #Exon | The number of exons in the alignment. | |
| Length | The length of the cDNA to be aligned; i.e. the length of the accession minus the eventual poly A and vector. | |
| From | The first base aligned, in coordinate on the accession as it is in GenBank. | |
| Aligned | The total number of bases aligned, not the last base of the alignment! | |
| #err | The number of point differences from the genome, as measured by Smith Waterman. | |
| Chrom | The chromosome number (or NT_ contig if unmapped). | |
| from | The beginning of the alignment on the genome, in basepairs, calling 1 the first base. | |
| to | The end of the alignemnt. If End < From, the cDNA aligns on the minus strand. |
| mRNA | Method | #Exon | Length | From | Aligned | #err | Chrom | from | to |
| AB011103 | Gold_bad | 2 | 6927 | 1 | 585 | 0 | 2 | 149843588 | 149890566 |
| AB011103 | Gold_partial | 23 | 6927 | 658 | 6270 | 5 | 2 | 149996341 | 150085818 |
| AB014562 | Gold_bad | 1 | 5253 | 91 | 77 | 1 | 9 | 91680377 | 91680454 |
| AB014562 | Gold_partial | 22 | 5253 | 163 | 5091 | 6 | 9 | 91733685 | 91783274 |
| AB023181 | Gold_bad | 1 | 5007 | 1 | 133 | 0 | 20 | 35609732 | 35609865 |
| AB023181 | Gold_excellent | 12 | 5007 | 129 | 4879 | 5 | 20 | 35680873 | 35842465 |
| AB033050 | Gold_bad | 1 | 4860 | 4759 | 47 | 1 | 10 | 80419049 | 80419003 |
| AB033050 | Gold_bad | 1 | 4860 | 4801 | 60 | 0 | 10 | 80418903 | 80418962 |
| AB033050 | Gold_excellent | 19 | 4860 | 1 | 4753 | 2 | 10 | 80348028 | 80418867 |
| AB046778 | Gold_bad | 1 | 5950 | 26 | 56 | 0 | 11 | 68109883 | 68109938 |
| AB046778 | Gold_bad | 1 | 5950 | 79 | 49 | 0 | 11 | 68109984 | 68109936 |
| AB046778 | Gold_excellent | 12 | 5950 | 137 | 5814 | 5 | 11 | 68112575 | 68150862 |
| AK000473 | Gold_bad | 1 | 594 | 421 | 174 | 0 | 11 | 68929206 | 68929380 |
| AK000473 | Gold_excellent | 1 | 594 | 1 | 424 | 0 | 11 | 68836982 | 68837406 |
| AK024951 | Gold_bad | 1 | 3501 | 2414 | 1088 | 2 | 12 | 7058860 | 7057773 |
| AK024951 | Gold_partial | 5 | 3501 | 1 | 2104 | 6 | 12 | 7136178 | 7132346 |
| AK056288 | Gold_bad | 1 | 2451 | 1 | 48 | 0 | 18 | 70414097 | 70414145 |
| AK056288 | Gold_excellent | 1 | 2451 | 43 | 2409 | 1 | 18 | 70469896 | 70472304 |
| AK056485 | Gold_bad | 3 | 2956 | 1 | 329 | 0 | 5 | 91579427 | 91685527 |
| AK056485 | Gold_good | 2 | 2956 | 329 | 2628 | 12 | 5 | 91810698 | 91816424 |
| AK074131 | Gold_bad | 6 | 4683 | 1 | 1223 | 0 | 2 | 109609518 | 109687346 |
| AK074131 | Gold_partial | 1 | 4683 | 1554 | 3130 | 1 | 2 | 109871328 | 109874457 |
| AK090416 | Gold_bad | 2 | 5215 | 1 | 452 | 0 | 9 | 132651878 | 132654265 |
| AK090416 | Gold_excellent | 1 | 5215 | 451 | 4765 | 16 | 9 | 132732801 | 132737565 |
| AK094079 | Gold_bad | 3 | 2668 | 1 | 261 | 0 | 1 | 91289995 | 91280788 |
| AK094079 | Gold_excellent | 18 | 2668 | 262 | 2407 | 3 | 1 | 91257124 | 91193123 |
| AK097782 | Gold_bad | 1 | 2914 | 481 | 83 | 0 | 15 | 78349796 | 78349714 |
| AK097782 | Gold_bad | 3 | 2914 | 220 | 268 | 1 | 15 | 78296016 | 78288074 |
| AK097782 | Gold_partial | 3 | 2914 | 561 | 2354 | 2 | 15 | 78296014 | 78285992 |
| AK123443 | Gold_bad | 2 | 1464 | 1 | 207 | 0 | 22 | 47184393 | 47184627 |
| AK123443 | Gold_excellent | 3 | 1464 | 204 | 1261 | 1 | 22 | 47265401 | 47369195 |
| AK124241 | Gold_bad | 1 | 2142 | 1771 | 372 | 0 | 19 | 53247337 | 53246966 |
| AK124241 | Gold_partial | 5 | 2142 | 1 | 1299 | 0 | 19 | 53268120 | 53248057 |
| AK125256 | Gold_bad | 1 | 1526 | 1 | 268 | 0 | 22 | 47184359 | 47184627 |
| AK125256 | Gold_excellent | 3 | 1526 | 265 | 1262 | 1 | 22 | 47265401 | 47369196 |
| AK126616 | Gold_bad | 1 | 2716 | 2379 | 58 | 1 | 5 | 177498208 | 177498265 |
| AK126616 | Gold_bad | 1 | 2716 | 2522 | 195 | 1 | Y | 1114572 | 1114378 |
| AK126616 | Gold_partial | 1 | 2716 | 1 | 1911 | 24 | 5 | 177490358 | 177492269 |
| AL137570 | Gold_bad | 1 | 659 | 1 | 186 | 0 | 15 | 46887435 | 46887620 |
| AL137570 | Gold_bad | 1 | 659 | 182 | 53 | 0 | 15 | 46887656 | 46887604 |
| AL137570 | Gold_excellent | 1 | 659 | 234 | 426 | 0 | 15 | 46887632 | 46888058 |
| AL157463 | Gold_bad | 1 | 2377 | 1 | 132 | 0 | 10 | 6897160 | 6897029 |
| AL157463 | Gold_bad | 1 | 2377 | 133 | 36 | 0 | 10 | 6896991 | 6897026 |
| AL157463 | Gold_good | 1 | 2377 | 169 | 2209 | 17 | 10 | 6897016 | 6894793 |
| AL831825 | Gold_bad | 1 | 3596 | 1 | 136 | 0 | 2 | 109687210 | 109687346 |
| AL831825 | Gold_partial | 1 | 3596 | 467 | 3130 | 3 | 2 | 109871328 | 109874457 |
| AL832820 | Gold_bad | 1 | 2022 | 1 | 422 | 0 | 17 | 45992425 | 45992004 |
| AL832820 | Gold_bad | 1 | 2022 | 419 | 168 | 0 | 17 | 45991947 | 45992115 |
| AL832820 | Gold_excellent | 1 | 2022 | 585 | 1438 | 8 | 17 | 45991949 | 45990509 |
| BC002721 | Gold_bad | 2 | 1403 | 1 | 594 | 0 | 2 | 149843579 | 149890566 |
| BC002721 | Gold_partial | 8 | 1403 | 667 | 737 | 0 | 2 | 149996341 | 150021101 |
| BC008064 | Gold_bad | 3 | 1902 | 1 | 328 | 0 | X | 42546507 | 42583615 |
| BC008064 | Gold_partial | 9 | 1902 | 790 | 1113 | 0 | X | 42636593 | 42650040 |
| BC008431 | Gold_bad | 1 | 826 | 1 | 58 | 0 | 5 | 155163573 | 155163631 |
| BC008431 | Gold_excellent | 8 | 826 | 56 | 770 | 1 | 5 | 155278248 | 156002862 |
| BC017298 | Gold_bad | 2 | 1376 | 1 | 567 | 0 | 2 | 149843606 | 149890566 |
| BC017298 | Gold_partial | 8 | 1376 | 640 | 737 | 0 | 2 | 149996341 | 150021088 |
| BC018349 | Gold_bad | 3 | 3557 | 1 | 352 | 0 | 7 | 50093126 | 50112153 |
| BC018349 | Gold_excellent | 4 | 3557 | 352 | 3206 | 1 | 7 | 50185979 | 50212005 |
| BC025961 | Gold_bad | 2 | 1403 | 1 | 594 | 0 | 2 | 149843579 | 149890566 |
| BC025961 | Gold_partial | 8 | 1403 | 667 | 737 | 0 | 2 | 149996341 | 150021101 |
| BC033587 | Gold_bad | 1 | 3468 | 1 | 208 | 0 | 12 | 107921565 | 107921358 |
| BC033587 | Gold_partial | 8 | 3468 | 941 | 2528 | 3 | 12 | 107835197 | 107807128 |
| BC035220 | Gold_bad | 1 | 2496 | 1405 | 1092 | 0 | 12 | 7058863 | 7057772 |
| BC035220 | Gold_partial | 7 | 2496 | 1 | 1098 | 2 | 12 | 7136184 | 7132346 |
| BC039396 | Gold_bad | 1 | 1485 | 1 | 226 | 0 | 22 | 47097534 | 47097760 |
| BC039396 | Gold_excellent | 3 | 1485 | 225 | 1260 | 2 | 22 | 47265403 | 47369195 |
| BC041688 | Gold_bad | 3 | 3329 | 1 | 1114 | 0 | 8 | 21668285 | 21654423 |
| BC041688 | Gold_excellent | 6 | 3329 | 1112 | 2218 | 1 | 8 | 21618730 | 21559805 |
| BC053933 | Gold_bad | 1 | 3328 | 810 | 132 | 0 | 19 | 14368154 | 14368285 |
| BC053933 | Gold_bad | 5 | 3328 | 4 | 806 | 1 | 19 | 14750348 | 14744154 |
| BC053933 | Gold_excellent | 10 | 3328 | 942 | 2385 | 4 | 19 | 14738193 | 14707390 |
| BC063827 | Gold_bad | 1 | 5515 | 1 | 190 | 0 | 9 | 132661250 | 132661440 |
| BC063827 | Gold_excellent | 9 | 5515 | 190 | 5326 | 8 | 9 | 132732802 | 132771754 |
| BC064594 | Gold_bad | 3 | 1808 | 1 | 369 | 0 | 7 | 50089125 | 50112153 |
| BC064594 | Gold_excellent | 1 | 1808 | 369 | 1440 | 0 | 7 | 50177452 | 50178892 |
| BX649037 | Gold_bad | 2 | 1926 | 1 | 102 | 0 | 1 | 91284807 | 91280788 |
| BX649037 | Gold_good | 17 | 1926 | 103 | 1824 | 10 | 1 | 91257124 | 91194544 |
| D63487 | Gold_bad | 1 | 3394 | 2778 | 43 | 1 | 22 | 41794129 | 41794172 |
| D63487 | Gold_bad | 1 | 3394 | 2820 | 575 | 0 | 22 | 41794144 | 41793570 |
| D63487 | Gold_partial | 13 | 3394 | 1 | 1767 | 0 | 22 | 41814000 | 41795721 |