Multiple sequence alignment - TraesCS3D01G441700

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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 TraesCS3D01G441700 chr3D 100.000 3288 0 0 1 3288 551987077 551983790 0.000000e+00 6072.0
1 TraesCS3D01G441700 chr3D 100.000 29 0 0 587 615 527207731 527207703 2.000000e-03 54.7
2 TraesCS3D01G441700 chr3A 84.393 3351 250 131 1 3249 688679494 688676315 0.000000e+00 3038.0
3 TraesCS3D01G441700 chr3B 89.418 1408 82 35 911 2288 732432655 732431285 0.000000e+00 1712.0
4 TraesCS3D01G441700 chr3B 83.964 555 37 16 2238 2746 732431279 732430731 4.930000e-133 484.0
5 TraesCS3D01G441700 chr3B 91.176 204 11 4 3049 3249 732430433 732430234 1.500000e-68 270.0
6 TraesCS3D01G441700 chr3B 90.173 173 8 7 732 897 732432804 732432634 1.990000e-52 217.0
7 TraesCS3D01G441700 chr3B 86.538 208 10 4 2814 3012 732430700 732430502 2.570000e-51 213.0
8 TraesCS3D01G441700 chr2B 77.847 483 82 19 2771 3241 793499916 793499447 3.230000e-70 276.0
9 TraesCS3D01G441700 chr2B 88.976 127 8 1 993 1113 402089069 402089195 5.680000e-33 152.0
10 TraesCS3D01G441700 chr5D 80.000 140 16 7 488 620 218259580 218259446 3.490000e-15 93.5
11 TraesCS3D01G441700 chr5D 87.931 58 2 4 563 615 57074226 57074169 2.740000e-06 63.9
12 TraesCS3D01G441700 chr5D 93.182 44 2 1 576 619 298277589 298277547 2.740000e-06 63.9
13 TraesCS3D01G441700 chr7D 78.571 126 16 10 500 615 605785909 605785785 4.550000e-09 73.1
14 TraesCS3D01G441700 chr1D 78.632 117 18 6 506 615 411125655 411125771 1.640000e-08 71.3
15 TraesCS3D01G441700 chr5B 85.294 68 3 6 552 612 616731565 616731632 2.740000e-06 63.9
16 TraesCS3D01G441700 chr5B 86.000 50 5 2 576 623 563165532 563165483 6.000000e-03 52.8
17 TraesCS3D01G441700 chr4B 100.000 28 0 0 585 612 659479873 659479900 6.000000e-03 52.8


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 TraesCS3D01G441700 chr3D 551983790 551987077 3287 True 6072.0 6072 100.0000 1 3288 1 chr3D.!!$R2 3287
1 TraesCS3D01G441700 chr3A 688676315 688679494 3179 True 3038.0 3038 84.3930 1 3249 1 chr3A.!!$R1 3248
2 TraesCS3D01G441700 chr3B 732430234 732432804 2570 True 579.2 1712 88.2538 732 3249 5 chr3B.!!$R1 2517

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
987 1019 0.393402 TCCATCAGCAAGCAAGCGAT 60.393 50.0 0.0 0.0 40.15 4.58 F
2102 2167 0.178861 AAAGGAGCAGGAGAAGGGGA 60.179 55.0 0.0 0.0 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2111 2176 0.034670 CCCTCCTCCTGCTCCTTTTG 60.035 60.0 0.00 0.0 0.0 2.44 R
3103 3326 0.105593 ACCAGTATCATCAGCTGCGG 59.894 55.0 9.47 3.2 0.0 5.69 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 1.445582 AAGGACGCCGACACGAATC 60.446 57.895 0.00 0.00 36.70 2.52
37 38 5.452777 CGACACGAATCTAGATAGAATGCA 58.547 41.667 5.46 0.00 35.69 3.96
48 49 7.923888 TCTAGATAGAATGCATCTGTTTTTGC 58.076 34.615 0.00 0.00 39.30 3.68
55 56 2.867368 TGCATCTGTTTTTGCTTTGCTG 59.133 40.909 0.00 0.00 39.60 4.41
56 57 2.222445 GCATCTGTTTTTGCTTTGCTGG 59.778 45.455 0.00 0.00 35.95 4.85
78 79 1.884067 GCTGGCAGTTTTGGAGCTAGT 60.884 52.381 17.16 0.00 38.85 2.57
80 81 3.003480 CTGGCAGTTTTGGAGCTAGTAC 58.997 50.000 6.28 0.00 32.94 2.73
104 105 2.158813 ACGAACAATGAACTGGACACCT 60.159 45.455 0.00 0.00 0.00 4.00
149 153 5.931724 TGTGAAATTTCGATAGCTGAAGTCA 59.068 36.000 13.34 0.00 0.00 3.41
165 169 5.316167 TGAAGTCAGGTTTGATGTAAGCAT 58.684 37.500 0.00 0.00 35.39 3.79
190 194 4.508861 TGTCGGCTTGTTAAGTGTAAGAAC 59.491 41.667 0.00 0.00 0.00 3.01
217 221 5.105595 GGTAGCTCTTTGAAATGAAGGCATT 60.106 40.000 0.00 0.00 46.35 3.56
251 255 2.687700 TCTTGCCAGAGAAGATGAGC 57.312 50.000 0.00 0.00 0.00 4.26
252 256 1.904537 TCTTGCCAGAGAAGATGAGCA 59.095 47.619 0.00 0.00 0.00 4.26
264 268 4.765856 AGAAGATGAGCATGCACTCTTTTT 59.234 37.500 21.98 9.11 37.58 1.94
279 284 6.974622 GCACTCTTTTTGAAAATGAAGTCTCA 59.025 34.615 7.51 0.00 35.56 3.27
350 355 3.604582 CACCATTCTCTGAGGTTTCTCC 58.395 50.000 4.59 0.00 39.23 3.71
384 389 8.029642 TCGTGATCAATTTTCTTTCTAGAACC 57.970 34.615 4.18 0.00 40.04 3.62
425 430 7.086376 CAGTAGCAGTTGCATCTGTTATTTTT 58.914 34.615 22.50 8.57 45.16 1.94
465 470 5.249780 TCTTTTCAATAAGGGTGTGGCTA 57.750 39.130 0.00 0.00 0.00 3.93
466 471 5.253330 TCTTTTCAATAAGGGTGTGGCTAG 58.747 41.667 0.00 0.00 0.00 3.42
467 472 3.644966 TTCAATAAGGGTGTGGCTAGG 57.355 47.619 0.00 0.00 0.00 3.02
470 475 3.332485 TCAATAAGGGTGTGGCTAGGTTT 59.668 43.478 0.00 0.00 0.00 3.27
472 477 2.767644 AAGGGTGTGGCTAGGTTTTT 57.232 45.000 0.00 0.00 0.00 1.94
473 478 1.995376 AGGGTGTGGCTAGGTTTTTG 58.005 50.000 0.00 0.00 0.00 2.44
474 479 1.497286 AGGGTGTGGCTAGGTTTTTGA 59.503 47.619 0.00 0.00 0.00 2.69
475 480 1.886542 GGGTGTGGCTAGGTTTTTGAG 59.113 52.381 0.00 0.00 0.00 3.02
476 481 2.488347 GGGTGTGGCTAGGTTTTTGAGA 60.488 50.000 0.00 0.00 0.00 3.27
478 483 3.477530 GTGTGGCTAGGTTTTTGAGACT 58.522 45.455 0.00 0.00 0.00 3.24
479 484 3.883489 GTGTGGCTAGGTTTTTGAGACTT 59.117 43.478 0.00 0.00 0.00 3.01
480 485 4.023963 GTGTGGCTAGGTTTTTGAGACTTC 60.024 45.833 0.00 0.00 0.00 3.01
481 486 3.186613 GTGGCTAGGTTTTTGAGACTTCG 59.813 47.826 0.00 0.00 0.00 3.79
482 487 2.159824 GGCTAGGTTTTTGAGACTTCGC 59.840 50.000 0.00 0.00 0.00 4.70
483 488 2.159827 GCTAGGTTTTTGAGACTTCGCG 60.160 50.000 0.00 0.00 0.00 5.87
486 501 1.398578 GGTTTTTGAGACTTCGCGAGC 60.399 52.381 9.59 2.99 0.00 5.03
494 509 0.737715 GACTTCGCGAGCCAAGTGAT 60.738 55.000 15.43 0.00 32.83 3.06
498 513 0.737367 TCGCGAGCCAAGTGATTGAG 60.737 55.000 3.71 0.00 0.00 3.02
504 519 3.059120 CGAGCCAAGTGATTGAGCATATG 60.059 47.826 0.00 0.00 0.00 1.78
513 528 8.403236 CAAGTGATTGAGCATATGAAAAGATGA 58.597 33.333 6.97 0.00 0.00 2.92
514 529 8.515695 AGTGATTGAGCATATGAAAAGATGAA 57.484 30.769 6.97 0.00 0.00 2.57
515 530 8.963725 AGTGATTGAGCATATGAAAAGATGAAA 58.036 29.630 6.97 0.00 0.00 2.69
516 531 9.234384 GTGATTGAGCATATGAAAAGATGAAAG 57.766 33.333 6.97 0.00 0.00 2.62
517 532 9.181061 TGATTGAGCATATGAAAAGATGAAAGA 57.819 29.630 6.97 0.00 0.00 2.52
614 629 6.116680 CAGTTGACTGAGATTTAGCAATCC 57.883 41.667 5.19 0.00 46.59 3.01
678 693 7.184022 AGGGGAATTCAGTAAATTAGGTACAGT 59.816 37.037 7.93 0.00 37.70 3.55
679 694 8.488668 GGGGAATTCAGTAAATTAGGTACAGTA 58.511 37.037 7.93 0.00 37.70 2.74
680 695 9.543783 GGGAATTCAGTAAATTAGGTACAGTAG 57.456 37.037 7.93 0.00 37.70 2.57
692 707 9.482175 AATTAGGTACAGTAGATCTCAAGAGTT 57.518 33.333 0.00 0.00 0.00 3.01
694 709 7.868906 AGGTACAGTAGATCTCAAGAGTTAC 57.131 40.000 0.00 0.00 0.00 2.50
695 710 7.635648 AGGTACAGTAGATCTCAAGAGTTACT 58.364 38.462 0.00 0.00 0.00 2.24
697 712 8.400186 GGTACAGTAGATCTCAAGAGTTACTTC 58.600 40.741 0.00 0.00 36.61 3.01
698 713 7.399245 ACAGTAGATCTCAAGAGTTACTTCC 57.601 40.000 0.00 0.00 36.61 3.46
699 714 7.179269 ACAGTAGATCTCAAGAGTTACTTCCT 58.821 38.462 0.00 0.00 36.61 3.36
700 715 7.672239 ACAGTAGATCTCAAGAGTTACTTCCTT 59.328 37.037 0.00 0.00 36.61 3.36
701 716 8.188139 CAGTAGATCTCAAGAGTTACTTCCTTC 58.812 40.741 0.00 0.00 36.61 3.46
703 718 7.790782 AGATCTCAAGAGTTACTTCCTTCTT 57.209 36.000 0.00 0.00 36.61 2.52
704 719 8.201242 AGATCTCAAGAGTTACTTCCTTCTTT 57.799 34.615 0.00 0.00 36.61 2.52
705 720 9.315363 AGATCTCAAGAGTTACTTCCTTCTTTA 57.685 33.333 0.00 0.00 36.61 1.85
720 735 7.504924 TCCTTCTTTAATTTTTCTTGAGCGA 57.495 32.000 0.00 0.00 0.00 4.93
721 736 7.936584 TCCTTCTTTAATTTTTCTTGAGCGAA 58.063 30.769 0.00 0.00 0.00 4.70
723 738 9.196552 CCTTCTTTAATTTTTCTTGAGCGAAAT 57.803 29.630 0.00 0.00 33.33 2.17
726 741 8.901748 TCTTTAATTTTTCTTGAGCGAAATTCG 58.098 29.630 11.47 11.47 43.89 3.34
753 768 1.661509 GCTTTTGTCTGGCAACGGC 60.662 57.895 0.00 0.00 45.18 5.68
760 775 0.594796 GTCTGGCAACGGCACAAAAG 60.595 55.000 0.00 0.00 45.18 2.27
768 783 3.564511 CAACGGCACAAAAGGTAATCAG 58.435 45.455 0.00 0.00 0.00 2.90
909 935 1.438469 TCCTCCATCCATCCATCCAC 58.562 55.000 0.00 0.00 0.00 4.02
958 988 1.144913 CTCTCCTCCCTCCGAATCTCT 59.855 57.143 0.00 0.00 0.00 3.10
987 1019 0.393402 TCCATCAGCAAGCAAGCGAT 60.393 50.000 0.00 0.00 40.15 4.58
991 1023 2.821366 AGCAAGCAAGCGATCCCG 60.821 61.111 0.00 0.00 40.15 5.14
1383 1430 1.709994 CCCCCATCCTGTAAGCTCCC 61.710 65.000 0.00 0.00 0.00 4.30
1389 1436 0.978146 TCCTGTAAGCTCCCCTCTGC 60.978 60.000 0.00 0.00 0.00 4.26
1393 1440 0.689412 GTAAGCTCCCCTCTGCCTCT 60.689 60.000 0.00 0.00 0.00 3.69
1394 1441 0.689080 TAAGCTCCCCTCTGCCTCTG 60.689 60.000 0.00 0.00 0.00 3.35
1395 1442 2.364842 GCTCCCCTCTGCCTCTGA 60.365 66.667 0.00 0.00 0.00 3.27
1403 1452 3.160269 CCCTCTGCCTCTGATTTTTGTT 58.840 45.455 0.00 0.00 0.00 2.83
1404 1453 3.192212 CCCTCTGCCTCTGATTTTTGTTC 59.808 47.826 0.00 0.00 0.00 3.18
1405 1454 3.192212 CCTCTGCCTCTGATTTTTGTTCC 59.808 47.826 0.00 0.00 0.00 3.62
1408 1457 4.520492 TCTGCCTCTGATTTTTGTTCCTTC 59.480 41.667 0.00 0.00 0.00 3.46
1409 1458 4.473444 TGCCTCTGATTTTTGTTCCTTCT 58.527 39.130 0.00 0.00 0.00 2.85
1410 1459 4.520492 TGCCTCTGATTTTTGTTCCTTCTC 59.480 41.667 0.00 0.00 0.00 2.87
1416 1465 6.488006 TCTGATTTTTGTTCCTTCTCTTCTGG 59.512 38.462 0.00 0.00 0.00 3.86
1423 1472 4.020573 TGTTCCTTCTCTTCTGGCGAATTA 60.021 41.667 0.00 0.00 0.00 1.40
1424 1473 5.119694 GTTCCTTCTCTTCTGGCGAATTAT 58.880 41.667 0.00 0.00 0.00 1.28
1425 1474 5.359194 TCCTTCTCTTCTGGCGAATTATT 57.641 39.130 0.00 0.00 0.00 1.40
1426 1475 5.745227 TCCTTCTCTTCTGGCGAATTATTT 58.255 37.500 0.00 0.00 0.00 1.40
1427 1476 5.586243 TCCTTCTCTTCTGGCGAATTATTTG 59.414 40.000 0.00 0.00 0.00 2.32
1428 1477 5.220931 CCTTCTCTTCTGGCGAATTATTTGG 60.221 44.000 0.00 0.00 0.00 3.28
1429 1478 5.097742 TCTCTTCTGGCGAATTATTTGGA 57.902 39.130 0.00 0.00 0.00 3.53
1430 1479 5.684704 TCTCTTCTGGCGAATTATTTGGAT 58.315 37.500 0.00 0.00 0.00 3.41
1431 1480 5.760253 TCTCTTCTGGCGAATTATTTGGATC 59.240 40.000 0.00 0.00 0.00 3.36
1436 1485 3.181453 TGGCGAATTATTTGGATCCCGTA 60.181 43.478 9.90 0.00 0.00 4.02
1437 1486 3.816523 GGCGAATTATTTGGATCCCGTAA 59.183 43.478 9.90 6.19 0.00 3.18
1438 1487 4.319984 GGCGAATTATTTGGATCCCGTAAC 60.320 45.833 9.90 0.00 0.00 2.50
1451 1500 3.528594 CGTAACGGATCTGACTCGG 57.471 57.895 9.00 1.45 0.00 4.63
1452 1501 1.012086 CGTAACGGATCTGACTCGGA 58.988 55.000 9.00 0.00 0.00 4.55
1453 1502 1.267932 CGTAACGGATCTGACTCGGAC 60.268 57.143 9.00 0.00 0.00 4.79
1454 1503 1.065251 GTAACGGATCTGACTCGGACC 59.935 57.143 9.00 0.00 0.00 4.46
1455 1504 0.323542 AACGGATCTGACTCGGACCT 60.324 55.000 9.00 0.00 0.00 3.85
1456 1505 1.032657 ACGGATCTGACTCGGACCTG 61.033 60.000 9.00 0.00 0.00 4.00
1458 1507 1.064946 GATCTGACTCGGACCTGCG 59.935 63.158 0.00 0.00 0.00 5.18
1459 1508 2.343163 GATCTGACTCGGACCTGCGG 62.343 65.000 0.00 0.00 0.00 5.69
1460 1509 4.135153 CTGACTCGGACCTGCGGG 62.135 72.222 11.02 11.02 38.88 6.13
1469 1518 4.643795 ACCTGCGGGTGAATCATG 57.356 55.556 18.90 0.00 45.43 3.07
1495 1547 3.260100 AGAAGGTGGTGCTGGGGG 61.260 66.667 0.00 0.00 0.00 5.40
1599 1651 2.560119 CCTCATCTCCTCGGCCTCG 61.560 68.421 0.00 0.00 37.82 4.63
1737 1789 0.250901 TGCCCCTGTTGAAGAAGCTC 60.251 55.000 0.00 0.00 0.00 4.09
1739 1791 1.818642 CCCCTGTTGAAGAAGCTCAG 58.181 55.000 0.00 0.00 0.00 3.35
1741 1793 1.818642 CCTGTTGAAGAAGCTCAGGG 58.181 55.000 7.35 0.00 41.10 4.45
1773 1825 4.410400 GCCAACCTCAGGGTCCGG 62.410 72.222 0.00 0.00 46.67 5.14
2053 2112 1.003355 CTTCAAGGAGGCTGCCGAA 60.003 57.895 13.96 9.26 0.00 4.30
2056 2115 0.179004 TCAAGGAGGCTGCCGAAAAA 60.179 50.000 13.96 0.00 0.00 1.94
2083 2148 4.648762 CAGGAGAAGAAGGAGAATGAGCTA 59.351 45.833 0.00 0.00 0.00 3.32
2100 2165 2.998316 CTAAAGGAGCAGGAGAAGGG 57.002 55.000 0.00 0.00 0.00 3.95
2102 2167 0.178861 AAAGGAGCAGGAGAAGGGGA 60.179 55.000 0.00 0.00 0.00 4.81
2103 2168 0.178861 AAGGAGCAGGAGAAGGGGAA 60.179 55.000 0.00 0.00 0.00 3.97
2111 2176 0.544223 GGAGAAGGGGAAGAAGGAGC 59.456 60.000 0.00 0.00 0.00 4.70
2113 2178 1.630878 GAGAAGGGGAAGAAGGAGCAA 59.369 52.381 0.00 0.00 0.00 3.91
2114 2179 2.040412 GAGAAGGGGAAGAAGGAGCAAA 59.960 50.000 0.00 0.00 0.00 3.68
2115 2180 2.447047 AGAAGGGGAAGAAGGAGCAAAA 59.553 45.455 0.00 0.00 0.00 2.44
2116 2181 2.593925 AGGGGAAGAAGGAGCAAAAG 57.406 50.000 0.00 0.00 0.00 2.27
2120 2185 1.815613 GGAAGAAGGAGCAAAAGGAGC 59.184 52.381 0.00 0.00 0.00 4.70
2122 2187 2.197283 AGAAGGAGCAAAAGGAGCAG 57.803 50.000 0.00 0.00 0.00 4.24
2125 2190 0.327591 AGGAGCAAAAGGAGCAGGAG 59.672 55.000 0.00 0.00 0.00 3.69
2129 2194 0.679321 GCAAAAGGAGCAGGAGGAGG 60.679 60.000 0.00 0.00 0.00 4.30
2130 2195 0.034670 CAAAAGGAGCAGGAGGAGGG 60.035 60.000 0.00 0.00 0.00 4.30
2132 2197 2.125066 AAAGGAGCAGGAGGAGGGGA 62.125 60.000 0.00 0.00 0.00 4.81
2133 2198 2.041265 GGAGCAGGAGGAGGGGAA 59.959 66.667 0.00 0.00 0.00 3.97
2143 2208 2.115427 GAGGAGGGGAAGAAGGAGAAG 58.885 57.143 0.00 0.00 0.00 2.85
2156 2221 1.290732 AGGAGAAGGAGGAAGAGGAGG 59.709 57.143 0.00 0.00 0.00 4.30
2157 2222 1.289530 GGAGAAGGAGGAAGAGGAGGA 59.710 57.143 0.00 0.00 0.00 3.71
2158 2223 2.666317 GAGAAGGAGGAAGAGGAGGAG 58.334 57.143 0.00 0.00 0.00 3.69
2159 2224 2.243736 GAGAAGGAGGAAGAGGAGGAGA 59.756 54.545 0.00 0.00 0.00 3.71
2160 2225 2.657459 AGAAGGAGGAAGAGGAGGAGAA 59.343 50.000 0.00 0.00 0.00 2.87
2161 2226 2.846665 AGGAGGAAGAGGAGGAGAAG 57.153 55.000 0.00 0.00 0.00 2.85
2162 2227 1.290732 AGGAGGAAGAGGAGGAGAAGG 59.709 57.143 0.00 0.00 0.00 3.46
2163 2228 1.289530 GGAGGAAGAGGAGGAGAAGGA 59.710 57.143 0.00 0.00 0.00 3.36
2164 2229 2.666317 GAGGAAGAGGAGGAGAAGGAG 58.334 57.143 0.00 0.00 0.00 3.69
2166 2231 2.657459 AGGAAGAGGAGGAGAAGGAGAA 59.343 50.000 0.00 0.00 0.00 2.87
2178 2243 2.837591 AGAAGGAGAAGGAGAAGAAGGC 59.162 50.000 0.00 0.00 0.00 4.35
2281 2346 2.666190 GTCTCGCAGTTGCAGGCA 60.666 61.111 4.84 0.00 42.21 4.75
2288 2353 1.135315 CGCAGTTGCAGGCACAATAAT 60.135 47.619 4.84 0.00 42.21 1.28
2289 2354 2.533266 GCAGTTGCAGGCACAATAATC 58.467 47.619 0.00 0.00 41.59 1.75
2290 2355 2.094597 GCAGTTGCAGGCACAATAATCA 60.095 45.455 0.00 0.00 41.59 2.57
2291 2356 3.614630 GCAGTTGCAGGCACAATAATCAA 60.615 43.478 0.00 0.00 41.59 2.57
2292 2357 3.922240 CAGTTGCAGGCACAATAATCAAC 59.078 43.478 0.00 0.00 34.31 3.18
2293 2358 3.828451 AGTTGCAGGCACAATAATCAACT 59.172 39.130 0.00 0.00 38.15 3.16
2294 2359 3.853831 TGCAGGCACAATAATCAACTG 57.146 42.857 0.00 0.00 0.00 3.16
2295 2360 3.156293 TGCAGGCACAATAATCAACTGT 58.844 40.909 0.00 0.00 0.00 3.55
2299 2364 4.154015 CAGGCACAATAATCAACTGTTCGA 59.846 41.667 0.00 0.00 0.00 3.71
2300 2365 4.759693 AGGCACAATAATCAACTGTTCGAA 59.240 37.500 0.00 0.00 0.00 3.71
2301 2366 5.415701 AGGCACAATAATCAACTGTTCGAAT 59.584 36.000 0.00 0.00 0.00 3.34
2302 2367 5.512788 GGCACAATAATCAACTGTTCGAATG 59.487 40.000 0.00 0.00 0.00 2.67
2320 2446 0.733150 TGATCGTCGCGATTCTGTCT 59.267 50.000 14.06 0.00 47.00 3.41
2367 2498 0.672342 GCATGATCTGCCCATGTTCC 59.328 55.000 0.00 0.00 45.66 3.62
2453 2587 1.423921 AGAAAACATGGTTCCCGGTCT 59.576 47.619 0.00 0.00 0.00 3.85
2455 2589 0.768622 AAACATGGTTCCCGGTCTCA 59.231 50.000 0.00 0.00 0.00 3.27
2461 2595 1.592223 GTTCCCGGTCTCAGGAGTG 59.408 63.158 0.00 0.00 32.57 3.51
2464 2598 2.681778 CCGGTCTCAGGAGTGGCT 60.682 66.667 0.00 0.00 0.00 4.75
2547 2682 2.959465 AAAAACTCTGACCCAGGAGG 57.041 50.000 0.00 0.00 43.78 4.30
2557 2692 4.169452 CCAGGAGGGATGGTCCAA 57.831 61.111 0.00 0.00 38.64 3.53
2559 2694 0.621571 CCAGGAGGGATGGTCCAAGA 60.622 60.000 0.00 0.00 38.64 3.02
2560 2695 0.543749 CAGGAGGGATGGTCCAAGAC 59.456 60.000 0.00 0.00 38.64 3.01
2585 2723 2.589014 AGGTACATCGAAAACGACGAC 58.411 47.619 0.00 0.00 42.37 4.34
2590 2728 0.518636 ATCGAAAACGACGACGAGGA 59.481 50.000 15.32 3.91 42.37 3.71
2591 2729 0.110509 TCGAAAACGACGACGAGGAG 60.111 55.000 15.32 1.61 42.66 3.69
2609 2764 1.410882 GAGGCGTCCTATCTTTCAGCT 59.589 52.381 0.00 0.00 31.76 4.24
2612 2767 2.362717 GGCGTCCTATCTTTCAGCTAGT 59.637 50.000 0.00 0.00 0.00 2.57
2614 2769 4.434520 GCGTCCTATCTTTCAGCTAGTTT 58.565 43.478 0.00 0.00 0.00 2.66
2617 2772 5.044558 GTCCTATCTTTCAGCTAGTTTCGG 58.955 45.833 0.00 0.00 0.00 4.30
2626 2781 1.069668 AGCTAGTTTCGGTCCAAACGT 59.930 47.619 9.75 0.00 40.60 3.99
2633 2788 2.241880 CGGTCCAAACGTGTCGCTT 61.242 57.895 0.00 0.00 0.00 4.68
2637 2792 0.462225 TCCAAACGTGTCGCTTTCCA 60.462 50.000 0.00 0.00 0.00 3.53
2760 2929 3.653009 GTTCACGCAGCAGCAGCA 61.653 61.111 10.77 0.00 45.49 4.41
2795 2971 2.257371 CGTTCCTTCCTGCGTCGA 59.743 61.111 0.00 0.00 0.00 4.20
2806 2982 1.006571 TGCGTCGAGTCCTTGTTCC 60.007 57.895 0.00 0.00 0.00 3.62
2809 2985 1.872653 GCGTCGAGTCCTTGTTCCTTT 60.873 52.381 0.00 0.00 0.00 3.11
2810 2986 2.059541 CGTCGAGTCCTTGTTCCTTTC 58.940 52.381 0.00 0.00 0.00 2.62
2927 3112 2.356793 GAGGCGGCGGATGATCAG 60.357 66.667 9.78 0.00 0.00 2.90
2954 3139 2.261671 GACAAGAAGGCGCCTCGA 59.738 61.111 32.93 0.00 0.00 4.04
2956 3141 2.048222 CAAGAAGGCGCCTCGACA 60.048 61.111 32.93 0.00 37.34 4.35
2957 3142 1.667830 CAAGAAGGCGCCTCGACAA 60.668 57.895 32.93 0.00 37.34 3.18
2960 3145 4.394712 AAGGCGCCTCGACAAGGG 62.395 66.667 32.93 0.00 46.32 3.95
3012 3200 2.202623 GCCTCACCGTCGCTGTAG 60.203 66.667 0.00 0.00 0.00 2.74
3015 3203 1.136984 CTCACCGTCGCTGTAGGTC 59.863 63.158 0.00 0.00 35.85 3.85
3016 3204 2.181021 CACCGTCGCTGTAGGTCC 59.819 66.667 0.00 0.00 35.85 4.46
3019 3207 2.754658 CGTCGCTGTAGGTCCCCT 60.755 66.667 0.00 0.00 37.71 4.79
3020 3208 2.772691 CGTCGCTGTAGGTCCCCTC 61.773 68.421 0.00 0.00 34.61 4.30
3021 3209 2.043248 TCGCTGTAGGTCCCCTCC 60.043 66.667 0.00 0.00 34.61 4.30
3022 3210 2.363795 CGCTGTAGGTCCCCTCCA 60.364 66.667 0.00 0.00 34.61 3.86
3024 3212 2.722201 GCTGTAGGTCCCCTCCACG 61.722 68.421 0.00 0.00 34.61 4.94
3025 3213 2.038329 TGTAGGTCCCCTCCACGG 59.962 66.667 0.00 0.00 34.61 4.94
3040 3256 2.372504 TCCACGGGTGTTTAATTCCTCA 59.627 45.455 0.00 0.00 0.00 3.86
3041 3257 2.486592 CCACGGGTGTTTAATTCCTCAC 59.513 50.000 0.00 0.00 0.00 3.51
3046 3266 3.763057 GGTGTTTAATTCCTCACCCAGT 58.237 45.455 12.11 0.00 42.90 4.00
3047 3267 3.506067 GGTGTTTAATTCCTCACCCAGTG 59.494 47.826 12.11 0.00 42.90 3.66
3066 3286 2.481952 GTGAGTTTCATGTCTGCCTGAC 59.518 50.000 0.00 0.00 45.54 3.51
3079 3302 0.178990 GCCTGACCCAAGTTCCAACT 60.179 55.000 0.00 0.00 42.04 3.16
3083 3306 1.283613 TGACCCAAGTTCCAACTGTGT 59.716 47.619 0.00 0.00 39.66 3.72
3084 3307 2.291282 TGACCCAAGTTCCAACTGTGTT 60.291 45.455 0.00 0.00 39.66 3.32
3085 3308 2.357952 GACCCAAGTTCCAACTGTGTTC 59.642 50.000 0.00 0.00 39.66 3.18
3093 3316 1.928503 TCCAACTGTGTTCGTTCGTTC 59.071 47.619 0.00 0.00 0.00 3.95
3094 3317 1.331680 CCAACTGTGTTCGTTCGTTCG 60.332 52.381 0.00 0.00 0.00 3.95
3095 3318 1.322338 CAACTGTGTTCGTTCGTTCGT 59.678 47.619 2.67 0.00 0.00 3.85
3098 3321 0.915904 TGTGTTCGTTCGTTCGTGTC 59.084 50.000 2.67 0.00 0.00 3.67
3099 3322 1.194495 GTGTTCGTTCGTTCGTGTCT 58.806 50.000 2.67 0.00 0.00 3.41
3100 3323 1.072348 GTGTTCGTTCGTTCGTGTCTG 60.072 52.381 2.67 0.00 0.00 3.51
3101 3324 0.111835 GTTCGTTCGTTCGTGTCTGC 60.112 55.000 2.67 0.00 0.00 4.26
3102 3325 1.533988 TTCGTTCGTTCGTGTCTGCG 61.534 55.000 2.67 0.00 0.00 5.18
3103 3326 2.167918 GTTCGTTCGTGTCTGCGC 59.832 61.111 0.00 0.00 0.00 6.09
3104 3327 3.033764 TTCGTTCGTGTCTGCGCC 61.034 61.111 4.18 0.00 0.00 6.53
3249 3472 0.252284 TCCCACTCTCCCTCAAGGTC 60.252 60.000 0.00 0.00 36.75 3.85
3250 3473 1.268283 CCCACTCTCCCTCAAGGTCC 61.268 65.000 0.00 0.00 36.75 4.46
3251 3474 1.268283 CCACTCTCCCTCAAGGTCCC 61.268 65.000 0.00 0.00 36.75 4.46
3252 3475 1.081277 ACTCTCCCTCAAGGTCCCC 59.919 63.158 0.00 0.00 36.75 4.81
3253 3476 1.690985 CTCTCCCTCAAGGTCCCCC 60.691 68.421 0.00 0.00 36.75 5.40
3254 3477 2.184631 TCTCCCTCAAGGTCCCCCT 61.185 63.158 0.00 0.00 45.63 4.79
3262 3485 4.252493 AGGTCCCCCTTCTGAACC 57.748 61.111 0.00 0.00 38.13 3.62
3263 3486 1.541620 AGGTCCCCCTTCTGAACCC 60.542 63.158 0.00 0.00 38.13 4.11
3264 3487 1.541620 GGTCCCCCTTCTGAACCCT 60.542 63.158 0.00 0.00 0.00 4.34
3265 3488 0.253020 GGTCCCCCTTCTGAACCCTA 60.253 60.000 0.00 0.00 0.00 3.53
3266 3489 0.910338 GTCCCCCTTCTGAACCCTAC 59.090 60.000 0.00 0.00 0.00 3.18
3267 3490 0.797579 TCCCCCTTCTGAACCCTACT 59.202 55.000 0.00 0.00 0.00 2.57
3268 3491 1.153565 TCCCCCTTCTGAACCCTACTT 59.846 52.381 0.00 0.00 0.00 2.24
3269 3492 1.560146 CCCCCTTCTGAACCCTACTTC 59.440 57.143 0.00 0.00 0.00 3.01
3270 3493 1.560146 CCCCTTCTGAACCCTACTTCC 59.440 57.143 0.00 0.00 0.00 3.46
3271 3494 2.552367 CCCTTCTGAACCCTACTTCCT 58.448 52.381 0.00 0.00 0.00 3.36
3272 3495 2.913617 CCCTTCTGAACCCTACTTCCTT 59.086 50.000 0.00 0.00 0.00 3.36
3273 3496 3.055021 CCCTTCTGAACCCTACTTCCTTC 60.055 52.174 0.00 0.00 0.00 3.46
3274 3497 3.055021 CCTTCTGAACCCTACTTCCTTCC 60.055 52.174 0.00 0.00 0.00 3.46
3275 3498 3.562108 TCTGAACCCTACTTCCTTCCT 57.438 47.619 0.00 0.00 0.00 3.36
3276 3499 3.870559 TCTGAACCCTACTTCCTTCCTT 58.129 45.455 0.00 0.00 0.00 3.36
3277 3500 3.583086 TCTGAACCCTACTTCCTTCCTTG 59.417 47.826 0.00 0.00 0.00 3.61
3278 3501 3.323775 TGAACCCTACTTCCTTCCTTGT 58.676 45.455 0.00 0.00 0.00 3.16
3279 3502 3.326880 TGAACCCTACTTCCTTCCTTGTC 59.673 47.826 0.00 0.00 0.00 3.18
3280 3503 2.267192 ACCCTACTTCCTTCCTTGTCC 58.733 52.381 0.00 0.00 0.00 4.02
3281 3504 2.157989 ACCCTACTTCCTTCCTTGTCCT 60.158 50.000 0.00 0.00 0.00 3.85
3282 3505 2.237392 CCCTACTTCCTTCCTTGTCCTG 59.763 54.545 0.00 0.00 0.00 3.86
3283 3506 2.907042 CCTACTTCCTTCCTTGTCCTGT 59.093 50.000 0.00 0.00 0.00 4.00
3284 3507 3.055747 CCTACTTCCTTCCTTGTCCTGTC 60.056 52.174 0.00 0.00 0.00 3.51
3285 3508 2.408565 ACTTCCTTCCTTGTCCTGTCA 58.591 47.619 0.00 0.00 0.00 3.58
3286 3509 2.370189 ACTTCCTTCCTTGTCCTGTCAG 59.630 50.000 0.00 0.00 0.00 3.51
3287 3510 2.398754 TCCTTCCTTGTCCTGTCAGA 57.601 50.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.632136 TTCGTGTCGGCGTCCTTGTT 62.632 55.000 6.85 0.00 0.00 2.83
24 25 7.928103 AGCAAAAACAGATGCATTCTATCTAG 58.072 34.615 0.00 0.00 44.95 2.43
37 38 3.460103 CACCAGCAAAGCAAAAACAGAT 58.540 40.909 0.00 0.00 0.00 2.90
48 49 1.741327 AACTGCCAGCACCAGCAAAG 61.741 55.000 0.00 0.00 45.49 2.77
55 56 1.662044 CTCCAAAACTGCCAGCACC 59.338 57.895 0.00 0.00 0.00 5.01
56 57 1.006922 GCTCCAAAACTGCCAGCAC 60.007 57.895 0.00 0.00 0.00 4.40
78 79 3.737266 GTCCAGTTCATTGTTCGTTCGTA 59.263 43.478 0.00 0.00 0.00 3.43
80 81 2.542178 TGTCCAGTTCATTGTTCGTTCG 59.458 45.455 0.00 0.00 0.00 3.95
104 105 7.726216 TCACATCTCTTCTCAAGACAACTTAA 58.274 34.615 0.00 0.00 34.70 1.85
149 153 4.816385 CCGACATATGCTTACATCAAACCT 59.184 41.667 1.58 0.00 37.74 3.50
152 156 4.450976 AGCCGACATATGCTTACATCAAA 58.549 39.130 1.58 0.00 37.74 2.69
156 160 3.808728 ACAAGCCGACATATGCTTACAT 58.191 40.909 1.58 0.00 45.59 2.29
165 169 6.028146 TCTTACACTTAACAAGCCGACATA 57.972 37.500 0.00 0.00 0.00 2.29
190 194 5.295540 GCCTTCATTTCAAAGAGCTACCTAG 59.704 44.000 0.00 0.00 0.00 3.02
239 243 2.767394 AGAGTGCATGCTCATCTTCTCT 59.233 45.455 20.33 15.23 37.94 3.10
240 244 3.182341 AGAGTGCATGCTCATCTTCTC 57.818 47.619 20.33 13.50 37.94 2.87
241 245 3.630892 AAGAGTGCATGCTCATCTTCT 57.369 42.857 20.33 10.98 37.94 2.85
242 246 4.698583 AAAAGAGTGCATGCTCATCTTC 57.301 40.909 23.52 13.29 37.94 2.87
243 247 4.521639 TCAAAAAGAGTGCATGCTCATCTT 59.478 37.500 20.33 20.14 37.94 2.40
244 248 4.077108 TCAAAAAGAGTGCATGCTCATCT 58.923 39.130 20.33 15.61 37.94 2.90
245 249 4.430137 TCAAAAAGAGTGCATGCTCATC 57.570 40.909 20.33 13.58 37.94 2.92
246 250 4.859304 TTCAAAAAGAGTGCATGCTCAT 57.141 36.364 20.33 5.46 37.94 2.90
247 251 4.652421 TTTCAAAAAGAGTGCATGCTCA 57.348 36.364 20.33 0.00 37.94 4.26
248 252 5.693104 TCATTTTCAAAAAGAGTGCATGCTC 59.307 36.000 20.33 15.94 35.82 4.26
249 253 5.603596 TCATTTTCAAAAAGAGTGCATGCT 58.396 33.333 20.33 0.00 0.00 3.79
250 254 5.910637 TCATTTTCAAAAAGAGTGCATGC 57.089 34.783 11.82 11.82 0.00 4.06
251 255 7.437267 AGACTTCATTTTCAAAAAGAGTGCATG 59.563 33.333 0.00 0.00 0.00 4.06
252 256 7.495055 AGACTTCATTTTCAAAAAGAGTGCAT 58.505 30.769 0.00 0.00 0.00 3.96
279 284 0.323178 CTGCCTCACTGCCTCCAAAT 60.323 55.000 0.00 0.00 0.00 2.32
350 355 5.523916 AGAAAATTGATCACGAGATAACCGG 59.476 40.000 0.00 0.00 33.72 5.28
399 404 1.446907 ACAGATGCAACTGCTACTGC 58.553 50.000 22.56 0.00 43.02 4.40
442 447 4.479158 AGCCACACCCTTATTGAAAAGAA 58.521 39.130 0.00 0.00 0.00 2.52
443 448 4.112634 AGCCACACCCTTATTGAAAAGA 57.887 40.909 0.00 0.00 0.00 2.52
445 450 4.202631 ACCTAGCCACACCCTTATTGAAAA 60.203 41.667 0.00 0.00 0.00 2.29
446 451 3.332485 ACCTAGCCACACCCTTATTGAAA 59.668 43.478 0.00 0.00 0.00 2.69
447 452 2.916934 ACCTAGCCACACCCTTATTGAA 59.083 45.455 0.00 0.00 0.00 2.69
448 453 2.557869 ACCTAGCCACACCCTTATTGA 58.442 47.619 0.00 0.00 0.00 2.57
449 454 3.366052 AACCTAGCCACACCCTTATTG 57.634 47.619 0.00 0.00 0.00 1.90
450 455 4.397919 AAAACCTAGCCACACCCTTATT 57.602 40.909 0.00 0.00 0.00 1.40
451 456 4.086457 CAAAAACCTAGCCACACCCTTAT 58.914 43.478 0.00 0.00 0.00 1.73
452 457 3.138653 TCAAAAACCTAGCCACACCCTTA 59.861 43.478 0.00 0.00 0.00 2.69
453 458 2.091555 TCAAAAACCTAGCCACACCCTT 60.092 45.455 0.00 0.00 0.00 3.95
454 459 1.497286 TCAAAAACCTAGCCACACCCT 59.503 47.619 0.00 0.00 0.00 4.34
455 460 1.886542 CTCAAAAACCTAGCCACACCC 59.113 52.381 0.00 0.00 0.00 4.61
457 462 3.477530 AGTCTCAAAAACCTAGCCACAC 58.522 45.455 0.00 0.00 0.00 3.82
458 463 3.857157 AGTCTCAAAAACCTAGCCACA 57.143 42.857 0.00 0.00 0.00 4.17
459 464 3.186613 CGAAGTCTCAAAAACCTAGCCAC 59.813 47.826 0.00 0.00 0.00 5.01
461 466 2.159824 GCGAAGTCTCAAAAACCTAGCC 59.840 50.000 0.00 0.00 0.00 3.93
465 470 2.135933 CTCGCGAAGTCTCAAAAACCT 58.864 47.619 11.33 0.00 0.00 3.50
466 471 1.398578 GCTCGCGAAGTCTCAAAAACC 60.399 52.381 11.33 0.00 0.00 3.27
467 472 1.398578 GGCTCGCGAAGTCTCAAAAAC 60.399 52.381 11.33 0.00 0.00 2.43
470 475 0.249699 TTGGCTCGCGAAGTCTCAAA 60.250 50.000 11.33 0.00 0.00 2.69
472 477 1.080501 CTTGGCTCGCGAAGTCTCA 60.081 57.895 11.33 1.21 0.00 3.27
473 478 1.080434 ACTTGGCTCGCGAAGTCTC 60.080 57.895 11.33 0.00 40.12 3.36
474 479 1.373497 CACTTGGCTCGCGAAGTCT 60.373 57.895 11.33 0.00 41.77 3.24
475 480 0.737715 ATCACTTGGCTCGCGAAGTC 60.738 55.000 11.33 6.75 41.77 3.01
476 481 0.320771 AATCACTTGGCTCGCGAAGT 60.321 50.000 11.33 12.58 43.87 3.01
478 483 0.320334 TCAATCACTTGGCTCGCGAA 60.320 50.000 11.33 0.00 32.95 4.70
479 484 0.737367 CTCAATCACTTGGCTCGCGA 60.737 55.000 9.26 9.26 32.95 5.87
480 485 1.712081 CTCAATCACTTGGCTCGCG 59.288 57.895 0.00 0.00 32.95 5.87
481 486 1.300971 TGCTCAATCACTTGGCTCGC 61.301 55.000 0.00 0.00 32.81 5.03
482 487 1.376543 ATGCTCAATCACTTGGCTCG 58.623 50.000 0.00 0.00 32.81 5.03
483 488 4.132336 TCATATGCTCAATCACTTGGCTC 58.868 43.478 0.00 0.00 32.81 4.70
486 501 7.092137 TCTTTTCATATGCTCAATCACTTGG 57.908 36.000 0.00 0.00 32.95 3.61
591 606 5.879223 AGGATTGCTAAATCTCAGTCAACTG 59.121 40.000 3.69 3.69 41.74 3.16
592 607 5.879223 CAGGATTGCTAAATCTCAGTCAACT 59.121 40.000 0.00 0.00 41.74 3.16
593 608 5.645497 ACAGGATTGCTAAATCTCAGTCAAC 59.355 40.000 0.00 0.00 41.74 3.18
594 609 5.809001 ACAGGATTGCTAAATCTCAGTCAA 58.191 37.500 0.00 0.00 41.74 3.18
595 610 5.426689 ACAGGATTGCTAAATCTCAGTCA 57.573 39.130 0.00 0.00 41.74 3.41
647 662 9.831682 ACCTAATTTACTGAATTCCCCTAAAAA 57.168 29.630 2.27 0.00 38.80 1.94
678 693 8.887264 AAGAAGGAAGTAACTCTTGAGATCTA 57.113 34.615 4.49 0.00 36.40 1.98
679 694 7.790782 AAGAAGGAAGTAACTCTTGAGATCT 57.209 36.000 0.00 0.00 36.40 2.75
680 695 9.930693 TTAAAGAAGGAAGTAACTCTTGAGATC 57.069 33.333 4.49 0.00 36.40 2.75
694 709 8.076178 TCGCTCAAGAAAAATTAAAGAAGGAAG 58.924 33.333 0.00 0.00 0.00 3.46
695 710 7.936584 TCGCTCAAGAAAAATTAAAGAAGGAA 58.063 30.769 0.00 0.00 0.00 3.36
697 712 8.574196 TTTCGCTCAAGAAAAATTAAAGAAGG 57.426 30.769 0.00 0.00 37.20 3.46
700 715 8.901748 CGAATTTCGCTCAAGAAAAATTAAAGA 58.098 29.630 5.78 0.00 42.52 2.52
727 742 0.239347 CCAGACAAAAGCTTCGCCAG 59.761 55.000 0.00 0.00 0.00 4.85
728 743 1.795170 GCCAGACAAAAGCTTCGCCA 61.795 55.000 0.00 0.00 0.00 5.69
729 744 1.081175 GCCAGACAAAAGCTTCGCC 60.081 57.895 0.00 0.00 0.00 5.54
730 745 0.030638 TTGCCAGACAAAAGCTTCGC 59.969 50.000 0.00 0.00 34.56 4.70
731 746 1.758783 GTTGCCAGACAAAAGCTTCG 58.241 50.000 0.00 0.00 40.82 3.79
732 747 1.600413 CCGTTGCCAGACAAAAGCTTC 60.600 52.381 0.00 0.00 40.82 3.86
733 748 0.385390 CCGTTGCCAGACAAAAGCTT 59.615 50.000 0.00 0.00 40.82 3.74
734 749 2.032981 CCGTTGCCAGACAAAAGCT 58.967 52.632 0.00 0.00 40.82 3.74
735 750 1.661509 GCCGTTGCCAGACAAAAGC 60.662 57.895 0.00 0.00 40.82 3.51
736 751 0.594796 GTGCCGTTGCCAGACAAAAG 60.595 55.000 0.00 0.00 40.82 2.27
753 768 2.420022 CGGGCTCTGATTACCTTTTGTG 59.580 50.000 0.00 0.00 0.00 3.33
760 775 0.946221 CGATGCGGGCTCTGATTACC 60.946 60.000 0.00 0.00 0.00 2.85
851 867 4.941873 GTCGGAGTTTAAAATGTGGAGGAT 59.058 41.667 0.00 0.00 0.00 3.24
931 958 1.135960 GGAGGGAGGAGAGATTTGGG 58.864 60.000 0.00 0.00 0.00 4.12
958 988 1.144716 GCTGATGGATGGAGACGCA 59.855 57.895 0.00 0.00 0.00 5.24
991 1023 4.129148 GAGGGCCATGGGTGGGAC 62.129 72.222 15.13 0.00 46.14 4.46
1130 1168 3.406361 CGTCGTTGCGCTGCTTCT 61.406 61.111 9.73 0.00 0.00 2.85
1383 1430 3.192212 GGAACAAAAATCAGAGGCAGAGG 59.808 47.826 0.00 0.00 0.00 3.69
1389 1436 6.714356 AGAAGAGAAGGAACAAAAATCAGAGG 59.286 38.462 0.00 0.00 0.00 3.69
1393 1440 5.010012 GCCAGAAGAGAAGGAACAAAAATCA 59.990 40.000 0.00 0.00 0.00 2.57
1394 1441 5.465051 GCCAGAAGAGAAGGAACAAAAATC 58.535 41.667 0.00 0.00 0.00 2.17
1395 1442 4.022849 CGCCAGAAGAGAAGGAACAAAAAT 60.023 41.667 0.00 0.00 0.00 1.82
1403 1452 5.359194 AATAATTCGCCAGAAGAGAAGGA 57.641 39.130 0.00 0.00 40.09 3.36
1404 1453 5.220931 CCAAATAATTCGCCAGAAGAGAAGG 60.221 44.000 0.00 0.00 40.09 3.46
1405 1454 5.586243 TCCAAATAATTCGCCAGAAGAGAAG 59.414 40.000 0.00 0.00 40.09 2.85
1408 1457 5.049129 GGATCCAAATAATTCGCCAGAAGAG 60.049 44.000 6.95 0.00 40.09 2.85
1409 1458 4.821805 GGATCCAAATAATTCGCCAGAAGA 59.178 41.667 6.95 0.00 40.09 2.87
1410 1459 4.022849 GGGATCCAAATAATTCGCCAGAAG 60.023 45.833 15.23 0.00 40.09 2.85
1416 1465 4.609783 CGTTACGGGATCCAAATAATTCGC 60.610 45.833 15.23 0.00 0.00 4.70
1436 1485 0.323542 AGGTCCGAGTCAGATCCGTT 60.324 55.000 0.00 0.00 0.00 4.44
1437 1486 1.032657 CAGGTCCGAGTCAGATCCGT 61.033 60.000 0.00 0.00 0.00 4.69
1438 1487 1.730487 CAGGTCCGAGTCAGATCCG 59.270 63.158 0.00 0.00 0.00 4.18
1454 1503 1.825191 CCCCATGATTCACCCGCAG 60.825 63.158 0.00 0.00 0.00 5.18
1455 1504 2.275089 CCCCATGATTCACCCGCA 59.725 61.111 0.00 0.00 0.00 5.69
1456 1505 3.219198 GCCCCATGATTCACCCGC 61.219 66.667 0.00 0.00 0.00 6.13
1458 1507 1.456331 CCTGCCCCATGATTCACCC 60.456 63.158 0.00 0.00 0.00 4.61
1459 1508 1.456331 CCCTGCCCCATGATTCACC 60.456 63.158 0.00 0.00 0.00 4.02
1460 1509 0.466922 CTCCCTGCCCCATGATTCAC 60.467 60.000 0.00 0.00 0.00 3.18
1461 1510 0.624206 TCTCCCTGCCCCATGATTCA 60.624 55.000 0.00 0.00 0.00 2.57
1463 1512 0.554792 CTTCTCCCTGCCCCATGATT 59.445 55.000 0.00 0.00 0.00 2.57
1464 1513 1.358830 CCTTCTCCCTGCCCCATGAT 61.359 60.000 0.00 0.00 0.00 2.45
1465 1514 2.002977 CCTTCTCCCTGCCCCATGA 61.003 63.158 0.00 0.00 0.00 3.07
1466 1515 2.311854 ACCTTCTCCCTGCCCCATG 61.312 63.158 0.00 0.00 0.00 3.66
1467 1516 2.128226 ACCTTCTCCCTGCCCCAT 59.872 61.111 0.00 0.00 0.00 4.00
1468 1517 2.935481 CACCTTCTCCCTGCCCCA 60.935 66.667 0.00 0.00 0.00 4.96
1469 1518 3.732849 CCACCTTCTCCCTGCCCC 61.733 72.222 0.00 0.00 0.00 5.80
1737 1789 3.000819 TGGTGGACGTAGGCCCTG 61.001 66.667 0.00 0.00 0.00 4.45
1739 1791 4.446413 CGTGGTGGACGTAGGCCC 62.446 72.222 0.00 0.00 43.50 5.80
2047 2106 0.396435 TCTCCTGCTCTTTTTCGGCA 59.604 50.000 0.00 0.00 34.66 5.69
2053 2112 3.906846 TCTCCTTCTTCTCCTGCTCTTTT 59.093 43.478 0.00 0.00 0.00 2.27
2056 2115 2.917713 TCTCCTTCTTCTCCTGCTCT 57.082 50.000 0.00 0.00 0.00 4.09
2083 2148 0.178861 TCCCCTTCTCCTGCTCCTTT 60.179 55.000 0.00 0.00 0.00 3.11
2096 2161 2.491640 CCTTTTGCTCCTTCTTCCCCTT 60.492 50.000 0.00 0.00 0.00 3.95
2098 2163 1.075536 TCCTTTTGCTCCTTCTTCCCC 59.924 52.381 0.00 0.00 0.00 4.81
2100 2165 1.815613 GCTCCTTTTGCTCCTTCTTCC 59.184 52.381 0.00 0.00 0.00 3.46
2102 2167 2.512705 CTGCTCCTTTTGCTCCTTCTT 58.487 47.619 0.00 0.00 0.00 2.52
2103 2168 1.271817 CCTGCTCCTTTTGCTCCTTCT 60.272 52.381 0.00 0.00 0.00 2.85
2111 2176 0.034670 CCCTCCTCCTGCTCCTTTTG 60.035 60.000 0.00 0.00 0.00 2.44
2113 2178 1.617839 CCCCTCCTCCTGCTCCTTT 60.618 63.158 0.00 0.00 0.00 3.11
2114 2179 2.041928 CCCCTCCTCCTGCTCCTT 59.958 66.667 0.00 0.00 0.00 3.36
2115 2180 2.543978 CTTCCCCTCCTCCTGCTCCT 62.544 65.000 0.00 0.00 0.00 3.69
2116 2181 2.041265 TTCCCCTCCTCCTGCTCC 59.959 66.667 0.00 0.00 0.00 4.70
2120 2185 0.043334 TCCTTCTTCCCCTCCTCCTG 59.957 60.000 0.00 0.00 0.00 3.86
2122 2187 0.340208 TCTCCTTCTTCCCCTCCTCC 59.660 60.000 0.00 0.00 0.00 4.30
2125 2190 1.208706 CCTTCTCCTTCTTCCCCTCC 58.791 60.000 0.00 0.00 0.00 4.30
2129 2194 2.255770 TCCTCCTTCTCCTTCTTCCC 57.744 55.000 0.00 0.00 0.00 3.97
2130 2195 3.445987 TCTTCCTCCTTCTCCTTCTTCC 58.554 50.000 0.00 0.00 0.00 3.46
2132 2197 3.078305 TCCTCTTCCTCCTTCTCCTTCTT 59.922 47.826 0.00 0.00 0.00 2.52
2133 2198 2.657459 TCCTCTTCCTCCTTCTCCTTCT 59.343 50.000 0.00 0.00 0.00 2.85
2143 2208 1.289530 TCCTTCTCCTCCTCTTCCTCC 59.710 57.143 0.00 0.00 0.00 4.30
2156 2221 3.118775 GCCTTCTTCTCCTTCTCCTTCTC 60.119 52.174 0.00 0.00 0.00 2.87
2157 2222 2.837591 GCCTTCTTCTCCTTCTCCTTCT 59.162 50.000 0.00 0.00 0.00 2.85
2158 2223 2.569404 TGCCTTCTTCTCCTTCTCCTTC 59.431 50.000 0.00 0.00 0.00 3.46
2159 2224 2.571202 CTGCCTTCTTCTCCTTCTCCTT 59.429 50.000 0.00 0.00 0.00 3.36
2160 2225 2.187100 CTGCCTTCTTCTCCTTCTCCT 58.813 52.381 0.00 0.00 0.00 3.69
2161 2226 2.168313 CTCTGCCTTCTTCTCCTTCTCC 59.832 54.545 0.00 0.00 0.00 3.71
2162 2227 2.418609 GCTCTGCCTTCTTCTCCTTCTC 60.419 54.545 0.00 0.00 0.00 2.87
2163 2228 1.554617 GCTCTGCCTTCTTCTCCTTCT 59.445 52.381 0.00 0.00 0.00 2.85
2164 2229 1.406751 GGCTCTGCCTTCTTCTCCTTC 60.407 57.143 0.73 0.00 46.69 3.46
2166 2231 2.295904 GGCTCTGCCTTCTTCTCCT 58.704 57.895 0.73 0.00 46.69 3.69
2200 2265 4.767255 CACAGGCTCTCCCACGCC 62.767 72.222 0.00 0.00 46.65 5.68
2292 2357 4.863520 AATCGCGACGATCATTCGAACAG 61.864 47.826 12.93 0.00 46.30 3.16
2293 2358 3.046328 AATCGCGACGATCATTCGAACA 61.046 45.455 12.93 0.00 46.30 3.18
2294 2359 1.517276 AATCGCGACGATCATTCGAAC 59.483 47.619 12.93 0.88 46.30 3.95
2295 2360 1.779157 GAATCGCGACGATCATTCGAA 59.221 47.619 12.93 0.00 46.30 3.71
2299 2364 2.120232 GACAGAATCGCGACGATCATT 58.880 47.619 12.93 0.00 46.30 2.57
2300 2365 1.335182 AGACAGAATCGCGACGATCAT 59.665 47.619 12.93 2.90 46.30 2.45
2301 2366 0.733150 AGACAGAATCGCGACGATCA 59.267 50.000 12.93 0.00 46.30 2.92
2302 2367 1.116436 CAGACAGAATCGCGACGATC 58.884 55.000 12.93 10.83 46.30 3.69
2320 2446 1.860326 CATGCATCACTACGAATCGCA 59.140 47.619 1.15 0.00 33.49 5.10
2367 2498 6.515272 AACACCAATAATTTGAGCCTACTG 57.485 37.500 0.00 0.00 34.60 2.74
2420 2552 9.612620 GAACCATGTTTTCTTCAACTGTAATAG 57.387 33.333 0.00 0.00 0.00 1.73
2453 2587 0.830648 CGGGAAATAGCCACTCCTGA 59.169 55.000 0.00 0.00 37.77 3.86
2455 2589 0.326238 TCCGGGAAATAGCCACTCCT 60.326 55.000 0.00 0.00 0.00 3.69
2461 2595 3.945981 TTTTTGTTCCGGGAAATAGCC 57.054 42.857 11.82 0.00 0.00 3.93
2486 2621 0.371645 GCTGAATTTCCTGAGCGACG 59.628 55.000 0.00 0.00 0.00 5.12
2555 2690 7.811759 CGTTTTCGATGTACCTACAGGTCTTG 61.812 46.154 3.65 0.00 45.81 3.02
2556 2691 5.848880 CGTTTTCGATGTACCTACAGGTCTT 60.849 44.000 3.65 0.00 45.81 3.01
2557 2692 4.380233 CGTTTTCGATGTACCTACAGGTCT 60.380 45.833 3.65 0.00 45.81 3.85
2585 2723 1.001158 GAAAGATAGGACGCCTCCTCG 60.001 57.143 7.61 0.00 44.59 4.63
2590 2728 1.490574 AGCTGAAAGATAGGACGCCT 58.509 50.000 3.87 3.87 34.07 5.52
2598 2753 4.464951 TGGACCGAAACTAGCTGAAAGATA 59.535 41.667 0.00 0.00 34.07 1.98
2609 2764 2.472816 GACACGTTTGGACCGAAACTA 58.527 47.619 13.91 0.00 34.26 2.24
2612 2767 1.764180 GCGACACGTTTGGACCGAAA 61.764 55.000 0.00 0.00 0.00 3.46
2614 2769 2.632136 AAGCGACACGTTTGGACCGA 62.632 55.000 0.00 0.00 0.00 4.69
2617 2772 0.041576 GGAAAGCGACACGTTTGGAC 60.042 55.000 0.00 0.00 29.69 4.02
2626 2781 4.361253 GCTCACTGGAAAGCGACA 57.639 55.556 0.00 0.00 0.00 4.35
2633 2788 1.112916 TCACCACTCGCTCACTGGAA 61.113 55.000 0.00 0.00 0.00 3.53
2637 2792 0.900182 TGGATCACCACTCGCTCACT 60.900 55.000 0.00 0.00 41.77 3.41
2773 2942 2.357034 GCAGGAAGGAACGTGCGA 60.357 61.111 0.00 0.00 40.70 5.10
2781 2950 2.341101 GGACTCGACGCAGGAAGGA 61.341 63.158 0.00 0.00 0.00 3.36
2795 2971 5.373812 TCAAGAAGAAAGGAACAAGGACT 57.626 39.130 0.00 0.00 0.00 3.85
2806 2982 2.359900 CCCCGTCCATCAAGAAGAAAG 58.640 52.381 0.00 0.00 0.00 2.62
2809 2985 1.910580 GCCCCCGTCCATCAAGAAGA 61.911 60.000 0.00 0.00 0.00 2.87
2810 2986 1.452108 GCCCCCGTCCATCAAGAAG 60.452 63.158 0.00 0.00 0.00 2.85
2905 3090 4.240103 CATCCGCCGCCTCATGGA 62.240 66.667 0.00 0.00 34.57 3.41
2927 3112 2.049802 TTCTTGTCGCCGTCGTCC 60.050 61.111 0.00 0.00 36.96 4.79
2975 3163 3.271014 CGGAAGACGTCGAGGGAA 58.729 61.111 10.46 0.00 37.93 3.97
3019 3207 2.372504 TGAGGAATTAAACACCCGTGGA 59.627 45.455 0.00 0.00 34.19 4.02
3020 3208 2.486592 GTGAGGAATTAAACACCCGTGG 59.513 50.000 0.00 0.00 34.19 4.94
3021 3209 2.486592 GGTGAGGAATTAAACACCCGTG 59.513 50.000 13.20 0.00 44.59 4.94
3022 3210 2.786777 GGTGAGGAATTAAACACCCGT 58.213 47.619 13.20 0.00 44.59 5.28
3026 3214 4.394729 TCACTGGGTGAGGAATTAAACAC 58.605 43.478 0.00 0.00 37.67 3.32
3040 3256 2.811873 GCAGACATGAAACTCACTGGGT 60.812 50.000 0.00 0.00 0.00 4.51
3041 3257 1.808945 GCAGACATGAAACTCACTGGG 59.191 52.381 0.00 0.00 0.00 4.45
3045 3265 2.481952 GTCAGGCAGACATGAAACTCAC 59.518 50.000 5.03 0.00 46.77 3.51
3046 3266 2.771089 GTCAGGCAGACATGAAACTCA 58.229 47.619 5.03 0.00 46.77 3.41
3066 3286 1.333619 CGAACACAGTTGGAACTTGGG 59.666 52.381 0.00 0.00 37.08 4.12
3079 3302 0.915904 GACACGAACGAACGAACACA 59.084 50.000 11.97 0.00 37.03 3.72
3083 3306 1.533988 CGCAGACACGAACGAACGAA 61.534 55.000 11.97 0.00 37.03 3.85
3084 3307 2.007114 CGCAGACACGAACGAACGA 61.007 57.895 11.97 0.00 37.03 3.85
3085 3308 2.459904 CGCAGACACGAACGAACG 59.540 61.111 0.14 0.00 39.31 3.95
3099 3322 3.444014 TATCATCAGCTGCGGCGCA 62.444 57.895 34.06 34.06 44.37 6.09
3100 3323 2.662857 TATCATCAGCTGCGGCGC 60.663 61.111 27.44 27.44 44.37 6.53
3101 3324 1.300465 AGTATCATCAGCTGCGGCG 60.300 57.895 12.87 0.51 44.37 6.46
3102 3325 1.226686 CCAGTATCATCAGCTGCGGC 61.227 60.000 10.33 10.33 39.06 6.53
3103 3326 0.105593 ACCAGTATCATCAGCTGCGG 59.894 55.000 9.47 3.20 0.00 5.69
3104 3327 1.215244 CACCAGTATCATCAGCTGCG 58.785 55.000 9.47 2.31 0.00 5.18
3234 3457 4.899243 GGGACCTTGAGGGAGAGT 57.101 61.111 1.54 0.00 40.27 3.24
3249 3472 1.560146 GAAGTAGGGTTCAGAAGGGGG 59.440 57.143 0.00 0.00 0.00 5.40
3250 3473 1.560146 GGAAGTAGGGTTCAGAAGGGG 59.440 57.143 0.00 0.00 0.00 4.79
3251 3474 2.552367 AGGAAGTAGGGTTCAGAAGGG 58.448 52.381 0.00 0.00 0.00 3.95
3252 3475 3.055021 GGAAGGAAGTAGGGTTCAGAAGG 60.055 52.174 0.00 0.00 0.00 3.46
3253 3476 3.841255 AGGAAGGAAGTAGGGTTCAGAAG 59.159 47.826 0.00 0.00 0.00 2.85
3254 3477 3.870559 AGGAAGGAAGTAGGGTTCAGAA 58.129 45.455 0.00 0.00 0.00 3.02
3255 3478 3.562108 AGGAAGGAAGTAGGGTTCAGA 57.438 47.619 0.00 0.00 0.00 3.27
3256 3479 3.328050 ACAAGGAAGGAAGTAGGGTTCAG 59.672 47.826 0.00 0.00 0.00 3.02
3257 3480 3.323775 ACAAGGAAGGAAGTAGGGTTCA 58.676 45.455 0.00 0.00 0.00 3.18
3258 3481 3.307550 GGACAAGGAAGGAAGTAGGGTTC 60.308 52.174 0.00 0.00 0.00 3.62
3259 3482 2.643304 GGACAAGGAAGGAAGTAGGGTT 59.357 50.000 0.00 0.00 0.00 4.11
3260 3483 2.157989 AGGACAAGGAAGGAAGTAGGGT 60.158 50.000 0.00 0.00 0.00 4.34
3261 3484 2.237392 CAGGACAAGGAAGGAAGTAGGG 59.763 54.545 0.00 0.00 0.00 3.53
3262 3485 2.907042 ACAGGACAAGGAAGGAAGTAGG 59.093 50.000 0.00 0.00 0.00 3.18
3263 3486 3.578716 TGACAGGACAAGGAAGGAAGTAG 59.421 47.826 0.00 0.00 0.00 2.57
3264 3487 3.578716 CTGACAGGACAAGGAAGGAAGTA 59.421 47.826 0.00 0.00 0.00 2.24
3265 3488 2.370189 CTGACAGGACAAGGAAGGAAGT 59.630 50.000 0.00 0.00 0.00 3.01
3266 3489 2.634940 TCTGACAGGACAAGGAAGGAAG 59.365 50.000 1.81 0.00 0.00 3.46
3267 3490 2.689658 TCTGACAGGACAAGGAAGGAA 58.310 47.619 1.81 0.00 0.00 3.36
3268 3491 2.398754 TCTGACAGGACAAGGAAGGA 57.601 50.000 1.81 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.