Multiple sequence alignment - TraesCS3D01G218600

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G218600 chr3D 100.000 2363 0 0 1 2363 297719616 297717254 0.000000e+00 4364.0
1 TraesCS3D01G218600 chr3D 92.857 42 2 1 1494 1535 143948410 143948370 2.540000e-05 60.2
2 TraesCS3D01G218600 chr3A 92.831 1883 106 13 493 2363 394721598 394719733 0.000000e+00 2702.0
3 TraesCS3D01G218600 chr3A 90.309 485 47 0 1 485 394722146 394721662 9.210000e-179 636.0
4 TraesCS3D01G218600 chr3A 97.143 35 1 0 1498 1532 458683803 458683769 2.540000e-05 60.2
5 TraesCS3D01G218600 chr3B 91.547 1396 89 16 645 2038 392839445 392838077 0.000000e+00 1897.0
6 TraesCS3D01G218600 chr3B 90.928 485 44 0 1 485 392850572 392850088 0.000000e+00 652.0
7 TraesCS3D01G218600 chr3B 89.583 48 4 1 1485 1531 137746770 137746817 2.540000e-05 60.2
8 TraesCS3D01G218600 chr5A 100.000 35 0 0 1499 1533 621019694 621019660 5.450000e-07 65.8
9 TraesCS3D01G218600 chr7A 97.368 38 0 1 1494 1531 424976358 424976394 1.960000e-06 63.9
10 TraesCS3D01G218600 chr5D 97.297 37 1 0 1496 1532 480838760 480838724 1.960000e-06 63.9
11 TraesCS3D01G218600 chr4A 91.489 47 1 3 1485 1531 364000390 364000347 7.050000e-06 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G218600 chr3D 297717254 297719616 2362 True 4364 4364 100.000 1 2363 1 chr3D.!!$R2 2362
1 TraesCS3D01G218600 chr3A 394719733 394722146 2413 True 1669 2702 91.570 1 2363 2 chr3A.!!$R2 2362
2 TraesCS3D01G218600 chr3B 392838077 392839445 1368 True 1897 1897 91.547 645 2038 1 chr3B.!!$R1 1393

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
72 73 0.033366 TCATGTGGGCGATATGGACG 59.967 55.0 6.41 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 2090 0.250684 TTCATCTTGCGGCACCTTCA 60.251 50.0 0.05 0.0 0.0 3.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.607661 TGTGACGCACGGGTAGCA 61.608 61.111 0.00 0.00 37.14 3.49
35 36 0.395311 CGGGTAGCAGAGGTAGACCA 60.395 60.000 0.66 0.00 38.89 4.02
48 49 2.633488 GTAGACCAGGCCAAGATTGTC 58.367 52.381 5.01 1.72 0.00 3.18
72 73 0.033366 TCATGTGGGCGATATGGACG 59.967 55.000 6.41 0.00 0.00 4.79
74 75 0.468226 ATGTGGGCGATATGGACGTT 59.532 50.000 0.00 0.00 0.00 3.99
115 116 9.574458 CAGATGATAAAGTAAGTATGGATACGG 57.426 37.037 0.00 0.00 38.28 4.02
132 133 3.261981 ACGGTTCAGTCTTTGAAGTGT 57.738 42.857 0.00 0.00 46.09 3.55
170 171 2.359975 GTTGGAGCTTCCGGTGGG 60.360 66.667 0.00 0.00 40.17 4.61
172 173 1.923395 TTGGAGCTTCCGGTGGGAT 60.923 57.895 0.00 0.00 43.41 3.85
188 189 2.310647 TGGGATAAACCAAGACCCTTCC 59.689 50.000 0.00 0.00 40.98 3.46
203 204 1.251251 CTTCCTGGCTTTGGTTGGAG 58.749 55.000 0.00 0.00 0.00 3.86
210 211 4.986708 TTTGGTTGGAGGCCGCCC 62.987 66.667 24.15 16.49 0.00 6.13
242 243 3.548014 CGGGTGAAAATCAATACCGATGC 60.548 47.826 11.58 0.00 40.52 3.91
251 252 1.854743 CAATACCGATGCGAGTGTCTG 59.145 52.381 0.00 0.00 0.00 3.51
252 253 1.389555 ATACCGATGCGAGTGTCTGA 58.610 50.000 0.00 0.00 0.00 3.27
264 265 3.363378 CGAGTGTCTGATGTGTTGAAAGC 60.363 47.826 0.00 0.00 0.00 3.51
279 280 2.056906 AAAGCAAGAGTGGAGCCGGT 62.057 55.000 1.90 0.00 0.00 5.28
310 311 7.620880 AGCAAGAACACCTACTACATTCATTA 58.379 34.615 0.00 0.00 0.00 1.90
314 315 8.135382 AGAACACCTACTACATTCATTACTGT 57.865 34.615 0.00 0.00 0.00 3.55
315 316 8.251721 AGAACACCTACTACATTCATTACTGTC 58.748 37.037 0.00 0.00 0.00 3.51
326 327 4.737855 TCATTACTGTCTGGAGTAAGCC 57.262 45.455 0.00 0.00 40.81 4.35
360 361 0.739462 TTGACCGCTTACTGCCGATG 60.739 55.000 0.00 0.00 38.78 3.84
370 371 0.108138 ACTGCCGATGCTACAACTCC 60.108 55.000 0.00 0.00 38.71 3.85
373 374 1.009829 GCCGATGCTACAACTCCAAG 58.990 55.000 0.00 0.00 33.53 3.61
403 404 3.062234 GTGATTTTCGCTAAACTCCGAGG 59.938 47.826 0.00 0.00 34.68 4.63
410 411 2.352421 CGCTAAACTCCGAGGTCTTTCA 60.352 50.000 0.00 0.00 0.00 2.69
411 412 2.994578 GCTAAACTCCGAGGTCTTTCAC 59.005 50.000 0.00 0.00 0.00 3.18
414 415 0.882474 ACTCCGAGGTCTTTCACGAG 59.118 55.000 0.00 0.00 0.00 4.18
426 427 4.935808 GTCTTTCACGAGTGGTAATGGAAT 59.064 41.667 3.19 0.00 0.00 3.01
440 441 8.474025 GTGGTAATGGAATATGATTGTTTGGAA 58.526 33.333 0.00 0.00 0.00 3.53
446 447 6.071447 TGGAATATGATTGTTTGGAAGTGGTG 60.071 38.462 0.00 0.00 0.00 4.17
449 450 7.722949 ATATGATTGTTTGGAAGTGGTGAAT 57.277 32.000 0.00 0.00 0.00 2.57
452 453 6.303054 TGATTGTTTGGAAGTGGTGAATCTA 58.697 36.000 0.00 0.00 0.00 1.98
454 455 6.573664 TTGTTTGGAAGTGGTGAATCTATG 57.426 37.500 0.00 0.00 0.00 2.23
460 461 6.173339 TGGAAGTGGTGAATCTATGAAACTC 58.827 40.000 0.00 0.00 0.00 3.01
462 463 4.184629 AGTGGTGAATCTATGAAACTCGC 58.815 43.478 0.00 0.00 0.00 5.03
463 464 3.932710 GTGGTGAATCTATGAAACTCGCA 59.067 43.478 0.00 0.00 0.00 5.10
465 466 5.065218 GTGGTGAATCTATGAAACTCGCAAT 59.935 40.000 0.00 0.00 0.00 3.56
471 472 9.330063 TGAATCTATGAAACTCGCAATAATTCT 57.670 29.630 0.00 0.00 0.00 2.40
473 474 7.394870 TCTATGAAACTCGCAATAATTCTCG 57.605 36.000 0.00 0.00 0.00 4.04
475 476 3.682377 TGAAACTCGCAATAATTCTCGCA 59.318 39.130 0.00 0.00 0.00 5.10
485 486 6.399459 CGCAATAATTCTCGCACTCTCTTATC 60.399 42.308 0.00 0.00 0.00 1.75
486 487 6.422100 GCAATAATTCTCGCACTCTCTTATCA 59.578 38.462 0.00 0.00 0.00 2.15
488 489 3.406728 TTCTCGCACTCTCTTATCACG 57.593 47.619 0.00 0.00 0.00 4.35
489 490 1.064208 TCTCGCACTCTCTTATCACGC 59.936 52.381 0.00 0.00 0.00 5.34
516 573 3.073274 ACTAGAAATGCCAACACTCCC 57.927 47.619 0.00 0.00 0.00 4.30
553 610 5.681880 CAAAATTTGCATGCACACTAAAGG 58.318 37.500 22.58 2.39 0.00 3.11
554 611 4.605640 AATTTGCATGCACACTAAAGGT 57.394 36.364 22.58 1.07 0.00 3.50
560 617 2.254546 TGCACACTAAAGGTCACTGG 57.745 50.000 0.00 0.00 0.00 4.00
566 623 4.398044 CACACTAAAGGTCACTGGTTGTTT 59.602 41.667 0.00 0.00 0.00 2.83
590 647 2.565834 TGAACTCCCCCTAGTTTCTTCG 59.434 50.000 0.00 0.00 39.78 3.79
593 650 1.207329 CTCCCCCTAGTTTCTTCGTGG 59.793 57.143 0.00 0.00 0.00 4.94
595 652 0.392595 CCCCTAGTTTCTTCGTGGCC 60.393 60.000 0.00 0.00 0.00 5.36
597 654 0.739813 CCTAGTTTCTTCGTGGCCCG 60.740 60.000 0.00 3.30 38.13 6.13
616 673 2.237066 TGTTATGGCTGATCGCGCG 61.237 57.895 26.76 26.76 40.44 6.86
652 710 6.243148 TGGTTGATAAAGTCCTAAGTTTCCC 58.757 40.000 0.00 0.00 30.64 3.97
655 713 4.778958 TGATAAAGTCCTAAGTTTCCCGGA 59.221 41.667 0.73 0.00 30.64 5.14
853 915 4.457466 ACGGGATTTCCAATTTATAGCGT 58.543 39.130 0.00 0.00 37.91 5.07
1129 1191 1.078143 GGGCACAAGAAGGAGCGAT 60.078 57.895 0.00 0.00 0.00 4.58
1131 1193 1.202698 GGGCACAAGAAGGAGCGATAT 60.203 52.381 0.00 0.00 0.00 1.63
1233 1295 1.149148 GCGAACCACTCAACTTCTCC 58.851 55.000 0.00 0.00 0.00 3.71
1413 1475 6.975197 GTGTGATCCCATCATATATACTCGTG 59.025 42.308 0.00 0.00 42.04 4.35
1414 1476 6.889722 TGTGATCCCATCATATATACTCGTGA 59.110 38.462 0.00 0.00 42.04 4.35
1449 1511 6.995091 ACTAGGAATATGAAAATGGCTGTCTC 59.005 38.462 0.00 0.00 0.00 3.36
1458 1520 1.800805 ATGGCTGTCTCGTGAAAGTG 58.199 50.000 6.54 0.00 30.25 3.16
1474 1538 6.846283 CGTGAAAGTGTGAAAAGTTCTGATAC 59.154 38.462 0.00 0.00 0.00 2.24
1500 1564 8.137437 CGAGGAGAAAATGCCAATGTTATTATT 58.863 33.333 0.00 0.00 0.00 1.40
1604 1671 2.158652 AGATGGGACGACGATCCTCTAA 60.159 50.000 0.00 0.00 38.95 2.10
1622 1690 8.281212 TCCTCTAATTTTTATTTGCCAGTCTC 57.719 34.615 0.00 0.00 0.00 3.36
1646 1714 7.427214 TCGTGGACGATGTAATTGATGTAATA 58.573 34.615 0.00 0.00 44.22 0.98
1734 1802 4.265073 AGCAAATTCAAGTAATCTCGGCT 58.735 39.130 0.00 0.00 0.00 5.52
1745 1813 6.161855 AGTAATCTCGGCTATCAAATCACA 57.838 37.500 0.00 0.00 0.00 3.58
1777 1845 5.847304 ACGAGCTAGATTGCTTCAATGATA 58.153 37.500 0.00 0.00 44.17 2.15
1912 1980 7.148423 TGCCGAATATCATCATGCAATTAGTAC 60.148 37.037 0.00 0.00 0.00 2.73
1929 1997 2.945576 CGCATTGCATGTTCGCGG 60.946 61.111 6.13 0.00 42.13 6.46
1975 2043 5.838955 TCTTCTTGATCCCTACCTACTCAA 58.161 41.667 0.00 0.00 0.00 3.02
2022 2090 3.181445 TGCCCTTCACAATTCACACTAGT 60.181 43.478 0.00 0.00 0.00 2.57
2078 2146 5.591643 TTTCTCGTGAAACAACTATGAGC 57.408 39.130 8.50 0.00 37.27 4.26
2092 2160 6.761714 ACAACTATGAGCGGGTTATTTCTTAG 59.238 38.462 0.00 0.00 0.00 2.18
2171 2240 8.792633 CACAGAAAAAGAGGGTAATGTTATTCA 58.207 33.333 0.00 0.00 0.00 2.57
2194 2263 1.671379 GTTCCAAGCCCGGACTCAC 60.671 63.158 0.73 0.00 33.75 3.51
2224 2293 4.410400 CCACCGCCCTCCTCCAAC 62.410 72.222 0.00 0.00 0.00 3.77
2331 2400 4.342378 CGTTCTTTCCTCATCTCCATCCTA 59.658 45.833 0.00 0.00 0.00 2.94
2351 2420 7.469537 TCCTATAAATCTGCTACTAGCCTTC 57.530 40.000 5.58 0.00 41.51 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.404843 CCTGGTCTACCTCTGCTACC 58.595 60.000 0.02 0.00 36.82 3.18
19 20 0.747852 GCCTGGTCTACCTCTGCTAC 59.252 60.000 0.02 0.00 36.82 3.58
24 25 0.413832 TCTTGGCCTGGTCTACCTCT 59.586 55.000 3.32 0.00 36.82 3.69
62 63 3.159353 TGTTCCTCAACGTCCATATCG 57.841 47.619 0.00 0.00 34.95 2.92
72 73 7.798596 ATCATCTGTGATATTGTTCCTCAAC 57.201 36.000 0.00 0.00 43.18 3.18
74 75 9.551734 CTTTATCATCTGTGATATTGTTCCTCA 57.448 33.333 0.00 0.00 44.53 3.86
112 113 3.261981 ACACTTCAAAGACTGAACCGT 57.738 42.857 0.00 0.00 39.20 4.83
115 116 9.134734 CTCTCTAATACACTTCAAAGACTGAAC 57.865 37.037 0.00 0.00 39.20 3.18
132 133 8.758829 TCCAACAATGCTAAAGTCTCTCTAATA 58.241 33.333 0.00 0.00 0.00 0.98
170 171 3.621558 CCAGGAAGGGTCTTGGTTTATC 58.378 50.000 0.00 0.00 44.24 1.75
188 189 2.278330 GGCCTCCAACCAAAGCCAG 61.278 63.158 0.00 0.00 43.32 4.85
210 211 2.725203 TTTTCACCCGGTCCTGCTCG 62.725 60.000 0.00 0.00 0.00 5.03
220 221 3.548014 GCATCGGTATTGATTTTCACCCG 60.548 47.826 0.00 0.00 35.17 5.28
224 225 4.033932 CACTCGCATCGGTATTGATTTTCA 59.966 41.667 0.00 0.00 0.00 2.69
242 243 3.363378 GCTTTCAACACATCAGACACTCG 60.363 47.826 0.00 0.00 0.00 4.18
251 252 3.565482 TCCACTCTTGCTTTCAACACATC 59.435 43.478 0.00 0.00 0.00 3.06
252 253 3.554934 TCCACTCTTGCTTTCAACACAT 58.445 40.909 0.00 0.00 0.00 3.21
264 265 2.046892 CCACCGGCTCCACTCTTG 60.047 66.667 0.00 0.00 0.00 3.02
279 280 2.438021 AGTAGGTGTTCTTGCTTGACCA 59.562 45.455 0.00 0.00 0.00 4.02
310 311 2.921834 TAGGGCTTACTCCAGACAGT 57.078 50.000 0.00 0.00 0.00 3.55
314 315 4.078805 TGTTAGGATAGGGCTTACTCCAGA 60.079 45.833 7.49 0.00 0.00 3.86
315 316 4.223953 TGTTAGGATAGGGCTTACTCCAG 58.776 47.826 7.49 0.00 0.00 3.86
326 327 3.997021 GCGGTCAATGATGTTAGGATAGG 59.003 47.826 0.00 0.00 0.00 2.57
370 371 1.750778 CGAAAATCACCCCATCCCTTG 59.249 52.381 0.00 0.00 0.00 3.61
373 374 0.395724 AGCGAAAATCACCCCATCCC 60.396 55.000 0.00 0.00 0.00 3.85
403 404 3.921677 TCCATTACCACTCGTGAAAGAC 58.078 45.455 0.00 0.00 0.00 3.01
410 411 6.591935 ACAATCATATTCCATTACCACTCGT 58.408 36.000 0.00 0.00 0.00 4.18
411 412 7.496529 AACAATCATATTCCATTACCACTCG 57.503 36.000 0.00 0.00 0.00 4.18
414 415 8.006298 TCCAAACAATCATATTCCATTACCAC 57.994 34.615 0.00 0.00 0.00 4.16
426 427 6.947733 AGATTCACCACTTCCAAACAATCATA 59.052 34.615 0.00 0.00 0.00 2.15
440 441 4.184629 GCGAGTTTCATAGATTCACCACT 58.815 43.478 0.00 0.00 0.00 4.00
446 447 9.804547 GAGAATTATTGCGAGTTTCATAGATTC 57.195 33.333 0.00 0.00 0.00 2.52
449 450 6.074302 GCGAGAATTATTGCGAGTTTCATAGA 60.074 38.462 0.00 0.00 0.00 1.98
452 453 4.332543 TGCGAGAATTATTGCGAGTTTCAT 59.667 37.500 7.76 0.00 31.72 2.57
454 455 4.022475 GTGCGAGAATTATTGCGAGTTTC 58.978 43.478 7.76 0.00 31.72 2.78
460 461 3.119291 AGAGAGTGCGAGAATTATTGCG 58.881 45.455 7.76 0.00 31.72 4.85
462 463 7.357941 CGTGATAAGAGAGTGCGAGAATTATTG 60.358 40.741 0.00 0.00 0.00 1.90
463 464 6.638873 CGTGATAAGAGAGTGCGAGAATTATT 59.361 38.462 0.00 0.00 0.00 1.40
465 466 5.511571 CGTGATAAGAGAGTGCGAGAATTA 58.488 41.667 0.00 0.00 0.00 1.40
471 472 0.100682 GGCGTGATAAGAGAGTGCGA 59.899 55.000 0.00 0.00 0.00 5.10
473 474 1.929836 CAAGGCGTGATAAGAGAGTGC 59.070 52.381 0.00 0.00 0.00 4.40
475 476 4.463186 AGTTACAAGGCGTGATAAGAGAGT 59.537 41.667 7.60 0.00 0.00 3.24
485 486 3.181510 GGCATTTCTAGTTACAAGGCGTG 60.182 47.826 0.00 0.00 0.00 5.34
486 487 3.007635 GGCATTTCTAGTTACAAGGCGT 58.992 45.455 0.00 0.00 0.00 5.68
488 489 4.217550 TGTTGGCATTTCTAGTTACAAGGC 59.782 41.667 0.00 0.00 0.00 4.35
489 490 5.473504 AGTGTTGGCATTTCTAGTTACAAGG 59.526 40.000 0.00 0.00 0.00 3.61
530 587 5.236911 ACCTTTAGTGTGCATGCAAATTTTG 59.763 36.000 24.58 10.05 0.00 2.44
549 606 4.277476 TCATCAAACAACCAGTGACCTTT 58.723 39.130 0.00 0.00 0.00 3.11
550 607 3.897239 TCATCAAACAACCAGTGACCTT 58.103 40.909 0.00 0.00 0.00 3.50
551 608 3.576078 TCATCAAACAACCAGTGACCT 57.424 42.857 0.00 0.00 0.00 3.85
552 609 3.632145 AGTTCATCAAACAACCAGTGACC 59.368 43.478 0.00 0.00 40.56 4.02
553 610 4.261197 GGAGTTCATCAAACAACCAGTGAC 60.261 45.833 0.00 0.00 40.56 3.67
554 611 3.882888 GGAGTTCATCAAACAACCAGTGA 59.117 43.478 0.00 0.00 40.56 3.41
560 617 2.876581 AGGGGGAGTTCATCAAACAAC 58.123 47.619 0.00 0.00 40.56 3.32
566 623 3.803340 AGAAACTAGGGGGAGTTCATCA 58.197 45.455 0.00 0.00 38.75 3.07
595 652 1.821241 CGCGATCAGCCATAACACGG 61.821 60.000 0.00 0.00 44.76 4.94
597 654 1.276844 GCGCGATCAGCCATAACAC 59.723 57.895 12.10 0.00 44.76 3.32
623 680 8.706322 AACTTAGGACTTTATCAACCAATGTT 57.294 30.769 0.00 0.00 34.14 2.71
853 915 9.627123 CAACTAAATCTTTCCCAGTAATGGATA 57.373 33.333 11.65 0.00 0.00 2.59
1107 1169 1.172812 GCTCCTTCTTGTGCCCGTTT 61.173 55.000 0.00 0.00 0.00 3.60
1218 1280 0.393077 CACCGGAGAAGTTGAGTGGT 59.607 55.000 9.46 0.00 0.00 4.16
1233 1295 1.518572 GTCGTAGTGGATGGCACCG 60.519 63.158 0.00 0.00 0.00 4.94
1338 1400 2.354305 GTTGGACACGCGACGACT 60.354 61.111 15.93 0.00 0.00 4.18
1413 1475 4.649674 TCATATTCCTAGTCACCACACCTC 59.350 45.833 0.00 0.00 0.00 3.85
1414 1476 4.620723 TCATATTCCTAGTCACCACACCT 58.379 43.478 0.00 0.00 0.00 4.00
1449 1511 5.216566 TCAGAACTTTTCACACTTTCACG 57.783 39.130 0.00 0.00 0.00 4.35
1458 1520 5.710984 TCTCCTCGTATCAGAACTTTTCAC 58.289 41.667 0.00 0.00 0.00 3.18
1474 1538 3.855689 AACATTGGCATTTTCTCCTCG 57.144 42.857 0.00 0.00 0.00 4.63
1569 1636 7.115947 CGTCGTCCCATCTATAAAAGGAATTAC 59.884 40.741 0.00 0.00 0.00 1.89
1578 1645 4.404640 AGGATCGTCGTCCCATCTATAAA 58.595 43.478 9.39 0.00 39.17 1.40
1581 1648 2.040545 AGAGGATCGTCGTCCCATCTAT 59.959 50.000 9.64 0.00 42.67 1.98
1604 1671 4.764823 TCCACGAGACTGGCAAATAAAAAT 59.235 37.500 0.00 0.00 0.00 1.82
1622 1690 5.959652 TTACATCAATTACATCGTCCACG 57.040 39.130 0.00 0.00 41.45 4.94
1705 1773 8.017373 CGAGATTACTTGAATTTGCTCTTTTGA 58.983 33.333 0.00 0.00 0.00 2.69
1710 1778 4.333926 GCCGAGATTACTTGAATTTGCTCT 59.666 41.667 0.00 0.00 0.00 4.09
1711 1779 4.333926 AGCCGAGATTACTTGAATTTGCTC 59.666 41.667 0.00 0.00 0.00 4.26
1719 1787 6.701841 GTGATTTGATAGCCGAGATTACTTGA 59.298 38.462 0.00 0.00 0.00 3.02
1734 1802 4.880696 TCGTTGGATGCATGTGATTTGATA 59.119 37.500 2.46 0.00 0.00 2.15
1745 1813 3.136763 CAATCTAGCTCGTTGGATGCAT 58.863 45.455 0.00 0.00 0.00 3.96
1777 1845 2.731217 GTGAAAACATGTTGAGCGCTT 58.269 42.857 13.26 0.76 0.00 4.68
1862 1930 7.035612 CAGGATTTTGTTTAGGAAAGGTATGC 58.964 38.462 0.00 0.00 0.00 3.14
1865 1933 5.479027 GGCAGGATTTTGTTTAGGAAAGGTA 59.521 40.000 0.00 0.00 0.00 3.08
1921 1989 1.153353 GAAAGGATTCACCGCGAACA 58.847 50.000 8.23 0.00 44.74 3.18
1924 1992 1.134907 GTAGGAAAGGATTCACCGCGA 60.135 52.381 8.23 0.00 44.74 5.87
1929 1997 4.470304 AGTAGGGTGTAGGAAAGGATTCAC 59.530 45.833 0.00 0.00 37.29 3.18
2022 2090 0.250684 TTCATCTTGCGGCACCTTCA 60.251 50.000 0.05 0.00 0.00 3.02
2092 2160 9.366216 GGACAAATAACCCATTGATAGTTTTTC 57.634 33.333 0.00 0.00 0.00 2.29
2139 2208 9.975218 ACATTACCCTCTTTTTCTGTGTTATAT 57.025 29.630 0.00 0.00 0.00 0.86
2171 2240 1.841556 TCCGGGCTTGGAACAGACT 60.842 57.895 0.00 0.00 42.39 3.24
2194 2263 2.711922 CGGTGGGAGAAGACTCGGG 61.712 68.421 0.00 0.00 43.44 5.14
2198 2267 3.003763 GGGCGGTGGGAGAAGACT 61.004 66.667 0.00 0.00 0.00 3.24
2199 2268 3.003763 AGGGCGGTGGGAGAAGAC 61.004 66.667 0.00 0.00 0.00 3.01
2224 2293 2.545532 GGAGTCATCATCAGAAGAGCCG 60.546 54.545 0.00 0.00 0.00 5.52
2254 2323 3.574284 TCGGGAACAAAATGCTCAATG 57.426 42.857 0.00 0.00 0.00 2.82
2264 2333 2.961531 TGGGAAGAATCGGGAACAAA 57.038 45.000 0.00 0.00 0.00 2.83
2268 2337 6.665680 TGAAAATTATTGGGAAGAATCGGGAA 59.334 34.615 0.00 0.00 0.00 3.97
2272 2341 8.844244 AGATCTGAAAATTATTGGGAAGAATCG 58.156 33.333 0.00 0.00 0.00 3.34
2300 2369 5.859495 AGATGAGGAAAGAACGAAAAGACT 58.141 37.500 0.00 0.00 0.00 3.24
2301 2370 5.120986 GGAGATGAGGAAAGAACGAAAAGAC 59.879 44.000 0.00 0.00 0.00 3.01
2331 2400 5.366768 TGTGGAAGGCTAGTAGCAGATTTAT 59.633 40.000 23.24 1.38 44.75 1.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.