Multiple sequence alignment - TraesCS2B01G327900

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 TraesCS2B01G327900 chr2B 100.000 3578 0 0 1 3578 470056710 470060287 0.000000e+00 6608
1 TraesCS2B01G327900 chr2B 92.697 534 38 1 1 533 17178211 17177678 0.000000e+00 769
2 TraesCS2B01G327900 chr2B 89.720 535 52 3 1 533 758664534 758665067 0.000000e+00 680
3 TraesCS2B01G327900 chr2B 97.222 72 1 1 2936 3007 470059606 470059676 1.740000e-23 121
4 TraesCS2B01G327900 chr2B 97.222 72 1 1 2897 2967 470059645 470059716 1.740000e-23 121
5 TraesCS2B01G327900 chr2D 88.392 2214 157 53 718 2877 396660154 396662321 0.000000e+00 2573
6 TraesCS2B01G327900 chr2D 90.000 580 20 18 2975 3517 396662368 396662946 0.000000e+00 715
7 TraesCS2B01G327900 chr2A 87.720 1531 91 42 703 2190 534623499 534624975 0.000000e+00 1696
8 TraesCS2B01G327900 chr2A 95.372 605 20 4 2974 3578 534625721 534626317 0.000000e+00 955
9 TraesCS2B01G327900 chr2A 87.811 763 48 15 2184 2919 534624995 534625739 0.000000e+00 852
10 TraesCS2B01G327900 chr4B 95.506 534 22 2 1 533 616136670 616136138 0.000000e+00 852
11 TraesCS2B01G327900 chr4B 89.907 535 51 3 1 533 46943673 46943140 0.000000e+00 686
12 TraesCS2B01G327900 chr5B 92.467 531 39 1 4 533 680778939 680778409 0.000000e+00 758
13 TraesCS2B01G327900 chr6B 91.978 536 39 4 1 533 658283449 658282915 0.000000e+00 749
14 TraesCS2B01G327900 chr6B 100.000 40 0 0 2348 2387 353181440 353181479 1.380000e-09 75
15 TraesCS2B01G327900 chr3B 91.386 534 45 1 1 533 744975025 744975558 0.000000e+00 730
16 TraesCS2B01G327900 chr3B 89.346 535 54 3 1 533 790573145 790572612 0.000000e+00 669
17 TraesCS2B01G327900 chr7B 90.093 535 50 3 1 533 658458207 658457674 0.000000e+00 691
18 TraesCS2B01G327900 chr1A 92.045 88 7 0 1132 1219 8247510 8247597 1.350000e-24 124
19 TraesCS2B01G327900 chr1D 92.771 83 6 0 1137 1219 6774749 6774831 1.740000e-23 121
20 TraesCS2B01G327900 chr1B 91.566 83 7 0 1137 1219 9072901 9072819 8.120000e-22 115


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 TraesCS2B01G327900 chr2B 470056710 470060287 3577 False 2283.333333 6608 98.148 1 3578 3 chr2B.!!$F2 3577
1 TraesCS2B01G327900 chr2B 17177678 17178211 533 True 769.000000 769 92.697 1 533 1 chr2B.!!$R1 532
2 TraesCS2B01G327900 chr2B 758664534 758665067 533 False 680.000000 680 89.720 1 533 1 chr2B.!!$F1 532
3 TraesCS2B01G327900 chr2D 396660154 396662946 2792 False 1644.000000 2573 89.196 718 3517 2 chr2D.!!$F1 2799
4 TraesCS2B01G327900 chr2A 534623499 534626317 2818 False 1167.666667 1696 90.301 703 3578 3 chr2A.!!$F1 2875
5 TraesCS2B01G327900 chr4B 616136138 616136670 532 True 852.000000 852 95.506 1 533 1 chr4B.!!$R2 532
6 TraesCS2B01G327900 chr4B 46943140 46943673 533 True 686.000000 686 89.907 1 533 1 chr4B.!!$R1 532
7 TraesCS2B01G327900 chr5B 680778409 680778939 530 True 758.000000 758 92.467 4 533 1 chr5B.!!$R1 529
8 TraesCS2B01G327900 chr6B 658282915 658283449 534 True 749.000000 749 91.978 1 533 1 chr6B.!!$R1 532
9 TraesCS2B01G327900 chr3B 744975025 744975558 533 False 730.000000 730 91.386 1 533 1 chr3B.!!$F1 532
10 TraesCS2B01G327900 chr3B 790572612 790573145 533 True 669.000000 669 89.346 1 533 1 chr3B.!!$R1 532
11 TraesCS2B01G327900 chr7B 658457674 658458207 533 True 691.000000 691 90.093 1 533 1 chr7B.!!$R1 532

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
590 593 0.038892 GGGAACGTAGTCACAGCGAA 60.039 55.0 0.0 0.0 45.0 4.7 F
1846 1911 0.103208 CAAGCAGCTACTACCGAGGG 59.897 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 2367 0.466739 TCAGCATAGGCCTGCAATGG 60.467 55.0 17.99 3.69 44.77 3.16 R
3394 3556 0.247460 CAGCGAACCATGGAGAGTGA 59.753 55.0 21.47 0.00 0.00 3.41 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
53 55 1.407618 GCGGAACACCTTCCACTTTTT 59.592 47.619 0.61 0.00 45.99 1.94
445 448 1.478916 TCGTCGCCATTAATCACCTCA 59.521 47.619 0.00 0.00 0.00 3.86
533 536 1.002921 ATCCGACCCACCCTGATCA 59.997 57.895 0.00 0.00 0.00 2.92
534 537 0.620410 ATCCGACCCACCCTGATCAA 60.620 55.000 0.00 0.00 0.00 2.57
535 538 1.078426 CCGACCCACCCTGATCAAC 60.078 63.158 0.00 0.00 0.00 3.18
536 539 1.078426 CGACCCACCCTGATCAACC 60.078 63.158 0.00 0.00 0.00 3.77
537 540 1.078426 GACCCACCCTGATCAACCG 60.078 63.158 0.00 0.00 0.00 4.44
538 541 2.272146 CCCACCCTGATCAACCGG 59.728 66.667 0.00 0.00 0.00 5.28
539 542 2.602676 CCCACCCTGATCAACCGGT 61.603 63.158 0.00 0.00 0.00 5.28
540 543 1.377202 CCACCCTGATCAACCGGTG 60.377 63.158 21.44 21.44 44.47 4.94
541 544 1.377202 CACCCTGATCAACCGGTGG 60.377 63.158 20.95 4.63 41.75 4.61
542 545 2.438434 CCCTGATCAACCGGTGGC 60.438 66.667 8.52 0.00 0.00 5.01
543 546 2.438434 CCTGATCAACCGGTGGCC 60.438 66.667 8.52 0.00 0.00 5.36
544 547 2.350895 CTGATCAACCGGTGGCCA 59.649 61.111 8.52 0.00 0.00 5.36
545 548 1.303236 CTGATCAACCGGTGGCCAA 60.303 57.895 8.52 0.00 0.00 4.52
546 549 1.303236 TGATCAACCGGTGGCCAAG 60.303 57.895 8.52 4.38 0.00 3.61
547 550 2.676471 ATCAACCGGTGGCCAAGC 60.676 61.111 8.52 0.00 0.00 4.01
563 566 2.512286 GCGCCAGCAGCAGATGTA 60.512 61.111 0.00 0.00 44.04 2.29
564 567 2.532256 GCGCCAGCAGCAGATGTAG 61.532 63.158 0.00 0.00 44.04 2.74
565 568 1.142531 CGCCAGCAGCAGATGTAGA 59.857 57.895 0.00 0.00 44.04 2.59
566 569 0.460811 CGCCAGCAGCAGATGTAGAA 60.461 55.000 0.00 0.00 44.04 2.10
567 570 1.297664 GCCAGCAGCAGATGTAGAAG 58.702 55.000 0.00 0.00 42.97 2.85
568 571 1.950828 CCAGCAGCAGATGTAGAAGG 58.049 55.000 0.00 0.00 0.00 3.46
569 572 1.209019 CCAGCAGCAGATGTAGAAGGT 59.791 52.381 0.00 0.00 0.00 3.50
570 573 2.355513 CCAGCAGCAGATGTAGAAGGTT 60.356 50.000 0.00 0.00 0.00 3.50
571 574 2.676839 CAGCAGCAGATGTAGAAGGTTG 59.323 50.000 0.00 0.00 0.00 3.77
572 575 2.012673 GCAGCAGATGTAGAAGGTTGG 58.987 52.381 0.00 0.00 0.00 3.77
573 576 2.636830 CAGCAGATGTAGAAGGTTGGG 58.363 52.381 0.00 0.00 0.00 4.12
574 577 2.237143 CAGCAGATGTAGAAGGTTGGGA 59.763 50.000 0.00 0.00 0.00 4.37
575 578 2.912956 AGCAGATGTAGAAGGTTGGGAA 59.087 45.455 0.00 0.00 0.00 3.97
576 579 3.010420 GCAGATGTAGAAGGTTGGGAAC 58.990 50.000 0.00 0.00 0.00 3.62
577 580 3.262420 CAGATGTAGAAGGTTGGGAACG 58.738 50.000 0.00 0.00 0.00 3.95
578 581 2.904434 AGATGTAGAAGGTTGGGAACGT 59.096 45.455 0.00 0.00 0.00 3.99
579 582 4.081862 CAGATGTAGAAGGTTGGGAACGTA 60.082 45.833 0.00 0.00 0.00 3.57
580 583 3.947910 TGTAGAAGGTTGGGAACGTAG 57.052 47.619 0.00 0.00 0.00 3.51
582 585 3.256631 TGTAGAAGGTTGGGAACGTAGTC 59.743 47.826 0.00 0.00 45.00 2.59
583 586 2.322658 AGAAGGTTGGGAACGTAGTCA 58.677 47.619 0.00 0.00 45.00 3.41
584 587 2.036862 AGAAGGTTGGGAACGTAGTCAC 59.963 50.000 0.00 0.00 45.00 3.67
585 588 1.416243 AGGTTGGGAACGTAGTCACA 58.584 50.000 0.00 0.00 45.00 3.58
586 589 1.343465 AGGTTGGGAACGTAGTCACAG 59.657 52.381 0.00 0.00 45.00 3.66
587 590 1.145803 GTTGGGAACGTAGTCACAGC 58.854 55.000 0.00 0.00 45.00 4.40
588 591 0.319211 TTGGGAACGTAGTCACAGCG 60.319 55.000 0.00 0.00 45.00 5.18
589 592 1.174078 TGGGAACGTAGTCACAGCGA 61.174 55.000 0.00 0.00 45.00 4.93
590 593 0.038892 GGGAACGTAGTCACAGCGAA 60.039 55.000 0.00 0.00 45.00 4.70
591 594 1.058404 GGAACGTAGTCACAGCGAAC 58.942 55.000 0.00 0.00 45.00 3.95
592 595 1.335689 GGAACGTAGTCACAGCGAACT 60.336 52.381 0.00 0.00 45.00 3.01
593 596 1.977412 GAACGTAGTCACAGCGAACTC 59.023 52.381 0.00 0.00 45.00 3.01
594 597 0.110328 ACGTAGTCACAGCGAACTCG 60.110 55.000 0.00 0.00 29.74 4.18
604 607 3.832171 CGAACTCGCAGCTCACGC 61.832 66.667 0.73 0.00 0.00 5.34
629 632 2.846918 GTGTGTCGCACGAGAAGC 59.153 61.111 0.00 0.00 38.45 3.86
647 650 2.028484 GTGAGTCGCACGGGAACA 59.972 61.111 0.00 0.00 37.83 3.18
648 651 1.374252 GTGAGTCGCACGGGAACAT 60.374 57.895 0.00 0.00 37.83 2.71
649 652 1.080093 TGAGTCGCACGGGAACATC 60.080 57.895 0.00 0.00 0.00 3.06
650 653 1.810030 GAGTCGCACGGGAACATCC 60.810 63.158 0.00 0.00 35.23 3.51
651 654 2.047655 GTCGCACGGGAACATCCA 60.048 61.111 0.00 0.00 38.64 3.41
652 655 2.100631 GTCGCACGGGAACATCCAG 61.101 63.158 0.00 0.00 38.64 3.86
653 656 2.819595 CGCACGGGAACATCCAGG 60.820 66.667 0.00 0.00 38.64 4.45
654 657 3.134127 GCACGGGAACATCCAGGC 61.134 66.667 0.00 0.00 38.64 4.85
655 658 2.438434 CACGGGAACATCCAGGCC 60.438 66.667 0.00 0.00 38.64 5.19
656 659 2.933287 ACGGGAACATCCAGGCCA 60.933 61.111 5.01 0.00 38.64 5.36
657 660 2.308722 ACGGGAACATCCAGGCCAT 61.309 57.895 5.01 0.00 38.64 4.40
658 661 1.526917 CGGGAACATCCAGGCCATC 60.527 63.158 5.01 0.00 38.64 3.51
659 662 1.152673 GGGAACATCCAGGCCATCC 60.153 63.158 5.01 0.26 38.64 3.51
660 663 1.649271 GGGAACATCCAGGCCATCCT 61.649 60.000 5.01 0.00 45.66 3.24
661 664 0.179006 GGAACATCCAGGCCATCCTC 60.179 60.000 5.01 0.00 41.93 3.71
662 665 0.842635 GAACATCCAGGCCATCCTCT 59.157 55.000 5.01 0.00 41.93 3.69
663 666 0.842635 AACATCCAGGCCATCCTCTC 59.157 55.000 5.01 0.00 41.93 3.20
664 667 1.059006 ACATCCAGGCCATCCTCTCC 61.059 60.000 5.01 0.00 41.93 3.71
665 668 1.058428 CATCCAGGCCATCCTCTCCA 61.058 60.000 5.01 0.00 41.93 3.86
666 669 0.327867 ATCCAGGCCATCCTCTCCAA 60.328 55.000 5.01 0.00 41.93 3.53
667 670 0.549902 TCCAGGCCATCCTCTCCAAA 60.550 55.000 5.01 0.00 41.93 3.28
668 671 0.332632 CCAGGCCATCCTCTCCAAAA 59.667 55.000 5.01 0.00 41.93 2.44
669 672 1.272648 CCAGGCCATCCTCTCCAAAAA 60.273 52.381 5.01 0.00 41.93 1.94
695 698 6.077202 AGGACAACCTTAGTAGTAGTAGCT 57.923 41.667 0.00 0.00 45.36 3.32
696 699 7.205515 AGGACAACCTTAGTAGTAGTAGCTA 57.794 40.000 0.00 0.00 45.36 3.32
697 700 7.053498 AGGACAACCTTAGTAGTAGTAGCTAC 58.947 42.308 16.43 16.43 45.36 3.58
698 701 7.092489 AGGACAACCTTAGTAGTAGTAGCTACT 60.092 40.741 28.50 28.50 45.30 2.57
699 702 8.207545 GGACAACCTTAGTAGTAGTAGCTACTA 58.792 40.741 26.36 26.36 46.84 1.82
742 745 7.340487 GTCATCATGAATCCTAAAGAAAAGGGT 59.660 37.037 0.00 0.00 34.66 4.34
883 897 4.428209 CACTAGTGCACTCCAGAGTTATG 58.572 47.826 25.56 6.23 40.20 1.90
898 912 4.079253 GAGTTATGACCTTTTTCTGCCCA 58.921 43.478 0.00 0.00 0.00 5.36
995 1013 0.196118 TTCCTTTGGGGAGGAGGAGT 59.804 55.000 0.00 0.00 46.09 3.85
1024 1049 1.940613 GCAACGAGTTGTGAGTTCCTT 59.059 47.619 16.14 0.00 42.31 3.36
1069 1094 6.039493 TGGTTTTGTTTCCGTGTATGTACATT 59.961 34.615 14.77 0.00 38.63 2.71
1087 1112 2.296073 TTTCCCGTTAATTGCCTGGT 57.704 45.000 0.00 0.00 0.00 4.00
1163 1188 1.903183 ACTACCTGTTCAAGCTCCTCC 59.097 52.381 0.00 0.00 0.00 4.30
1180 1205 2.725008 CTGATCGGCGACTCCTCC 59.275 66.667 13.76 0.00 0.00 4.30
1225 1250 2.221055 CCGTTTCTCCGTGAGTTTCTTG 59.779 50.000 1.60 0.00 0.00 3.02
1226 1251 2.221055 CGTTTCTCCGTGAGTTTCTTGG 59.779 50.000 1.60 0.00 0.00 3.61
1230 1255 2.298163 TCTCCGTGAGTTTCTTGGTACC 59.702 50.000 4.43 4.43 0.00 3.34
1255 1282 2.285024 CCTTGGCAATGTGGGTGGG 61.285 63.158 0.00 0.00 0.00 4.61
1256 1283 1.533753 CTTGGCAATGTGGGTGGGT 60.534 57.895 0.00 0.00 0.00 4.51
1257 1284 1.818959 CTTGGCAATGTGGGTGGGTG 61.819 60.000 0.00 0.00 0.00 4.61
1258 1285 2.996734 GGCAATGTGGGTGGGTGG 60.997 66.667 0.00 0.00 0.00 4.61
1259 1286 2.117206 GCAATGTGGGTGGGTGGA 59.883 61.111 0.00 0.00 0.00 4.02
1260 1287 1.978617 GCAATGTGGGTGGGTGGAG 60.979 63.158 0.00 0.00 0.00 3.86
1280 1307 3.499737 GACTGACCAATGGCGCCG 61.500 66.667 23.90 10.06 0.00 6.46
1298 1325 2.803451 CCGTCTTCCTTCTCAAGATCG 58.197 52.381 0.00 0.00 32.50 3.69
1300 1327 2.189342 GTCTTCCTTCTCAAGATCGCG 58.811 52.381 0.00 0.00 32.50 5.87
1402 1429 1.082756 CGGCGTTGACTTTGTGAGC 60.083 57.895 0.00 0.00 0.00 4.26
1418 1476 3.773667 TGTGAGCCTTGATGATTCTCTCT 59.226 43.478 0.00 0.00 0.00 3.10
1420 1478 3.067883 TGAGCCTTGATGATTCTCTCTCG 59.932 47.826 0.00 0.00 0.00 4.04
1421 1479 2.134346 GCCTTGATGATTCTCTCTCGC 58.866 52.381 0.00 0.00 0.00 5.03
1422 1480 2.224018 GCCTTGATGATTCTCTCTCGCT 60.224 50.000 0.00 0.00 0.00 4.93
1423 1481 3.005261 GCCTTGATGATTCTCTCTCGCTA 59.995 47.826 0.00 0.00 0.00 4.26
1424 1482 4.545610 CCTTGATGATTCTCTCTCGCTAC 58.454 47.826 0.00 0.00 0.00 3.58
1425 1483 4.278170 CCTTGATGATTCTCTCTCGCTACT 59.722 45.833 0.00 0.00 0.00 2.57
1426 1484 5.221224 CCTTGATGATTCTCTCTCGCTACTT 60.221 44.000 0.00 0.00 0.00 2.24
1427 1485 6.016693 CCTTGATGATTCTCTCTCGCTACTTA 60.017 42.308 0.00 0.00 0.00 2.24
1428 1486 6.552859 TGATGATTCTCTCTCGCTACTTAG 57.447 41.667 0.00 0.00 0.00 2.18
1429 1487 6.058833 TGATGATTCTCTCTCGCTACTTAGT 58.941 40.000 0.00 0.00 0.00 2.24
1430 1488 7.217906 TGATGATTCTCTCTCGCTACTTAGTA 58.782 38.462 0.00 0.00 0.00 1.82
1431 1489 6.847956 TGATTCTCTCTCGCTACTTAGTAC 57.152 41.667 0.00 0.00 0.00 2.73
1432 1490 6.584488 TGATTCTCTCTCGCTACTTAGTACT 58.416 40.000 0.00 0.00 0.00 2.73
1433 1491 6.480651 TGATTCTCTCTCGCTACTTAGTACTG 59.519 42.308 5.39 0.00 0.00 2.74
1434 1492 5.341872 TCTCTCTCGCTACTTAGTACTGT 57.658 43.478 5.39 0.00 0.00 3.55
1435 1493 6.462552 TCTCTCTCGCTACTTAGTACTGTA 57.537 41.667 5.39 0.00 0.00 2.74
1436 1494 6.272318 TCTCTCTCGCTACTTAGTACTGTAC 58.728 44.000 9.93 9.93 0.00 2.90
1437 1495 5.039984 TCTCTCGCTACTTAGTACTGTACG 58.960 45.833 11.97 7.19 0.00 3.67
1438 1496 3.553511 TCTCGCTACTTAGTACTGTACGC 59.446 47.826 11.97 7.58 0.00 4.42
1439 1497 3.261580 TCGCTACTTAGTACTGTACGCA 58.738 45.455 11.97 2.16 0.00 5.24
1440 1498 3.062639 TCGCTACTTAGTACTGTACGCAC 59.937 47.826 11.97 0.00 0.00 5.34
1463 1521 5.946377 ACTTTCTCATCCTATGTTTGGTTCC 59.054 40.000 0.00 0.00 0.00 3.62
1464 1522 5.512942 TTCTCATCCTATGTTTGGTTCCA 57.487 39.130 0.00 0.00 0.00 3.53
1465 1523 5.715439 TCTCATCCTATGTTTGGTTCCAT 57.285 39.130 0.00 0.00 0.00 3.41
1467 1525 5.887598 TCTCATCCTATGTTTGGTTCCATTG 59.112 40.000 0.00 0.00 0.00 2.82
1468 1526 5.825532 TCATCCTATGTTTGGTTCCATTGA 58.174 37.500 0.00 0.00 0.00 2.57
1469 1527 6.434302 TCATCCTATGTTTGGTTCCATTGAT 58.566 36.000 0.00 0.00 0.00 2.57
1470 1528 6.896860 TCATCCTATGTTTGGTTCCATTGATT 59.103 34.615 0.00 0.00 0.00 2.57
1471 1529 6.528537 TCCTATGTTTGGTTCCATTGATTG 57.471 37.500 0.00 0.00 0.00 2.67
1472 1530 6.252233 TCCTATGTTTGGTTCCATTGATTGA 58.748 36.000 0.00 0.00 0.00 2.57
1473 1531 6.896860 TCCTATGTTTGGTTCCATTGATTGAT 59.103 34.615 0.00 0.00 0.00 2.57
1474 1532 7.399765 TCCTATGTTTGGTTCCATTGATTGATT 59.600 33.333 0.00 0.00 0.00 2.57
1475 1533 7.493320 CCTATGTTTGGTTCCATTGATTGATTG 59.507 37.037 0.00 0.00 0.00 2.67
1476 1534 6.416631 TGTTTGGTTCCATTGATTGATTGA 57.583 33.333 0.00 0.00 0.00 2.57
1621 1686 4.133013 ACGTAAGGGATATGTTGTCACC 57.867 45.455 0.00 0.00 46.39 4.02
1627 1692 3.053395 AGGGATATGTTGTCACCTGCAAT 60.053 43.478 0.00 0.00 0.00 3.56
1629 1694 3.002656 GGATATGTTGTCACCTGCAATCG 59.997 47.826 0.00 0.00 0.00 3.34
1659 1724 7.710475 ACTTTTTGTGTATTGGAAATGAACTGG 59.290 33.333 0.00 0.00 0.00 4.00
1673 1738 1.893137 GAACTGGTTCCCCATCAAACC 59.107 52.381 2.35 0.00 44.29 3.27
1703 1768 5.527951 TCACAAACATACAAACTGCATTCC 58.472 37.500 0.00 0.00 0.00 3.01
1751 1816 1.061131 CAGAAACCGTAATGCTCGCAG 59.939 52.381 0.00 0.00 0.00 5.18
1774 1839 6.942005 CAGTCTCATCTCATATCAGTACCTCT 59.058 42.308 0.00 0.00 0.00 3.69
1782 1847 7.212976 TCTCATATCAGTACCTCTTTGCATTC 58.787 38.462 0.00 0.00 0.00 2.67
1846 1911 0.103208 CAAGCAGCTACTACCGAGGG 59.897 60.000 0.00 0.00 0.00 4.30
1876 1941 4.022416 GGCATCATCGTAAGTCTCATCTCT 60.022 45.833 0.00 0.00 39.48 3.10
1880 1945 4.576873 TCATCGTAAGTCTCATCTCTCCAC 59.423 45.833 0.00 0.00 39.48 4.02
1885 1950 4.323569 AAGTCTCATCTCTCCACCTGTA 57.676 45.455 0.00 0.00 0.00 2.74
1921 1986 0.250989 TTCCCAGCTTTTACCCACCG 60.251 55.000 0.00 0.00 0.00 4.94
1924 1989 1.175983 CCAGCTTTTACCCACCGCAA 61.176 55.000 0.00 0.00 0.00 4.85
1933 1998 1.213537 CCCACCGCAATTCAGCAAG 59.786 57.895 0.00 0.00 0.00 4.01
1939 2004 0.704551 CGCAATTCAGCAAGCGTTTC 59.295 50.000 0.00 0.00 44.67 2.78
1945 2010 0.306533 TCAGCAAGCGTTTCGTTTCC 59.693 50.000 0.00 0.00 0.00 3.13
1946 2011 0.307760 CAGCAAGCGTTTCGTTTCCT 59.692 50.000 0.00 0.00 0.00 3.36
1947 2012 1.021968 AGCAAGCGTTTCGTTTCCTT 58.978 45.000 0.00 0.00 0.00 3.36
1948 2013 1.120437 GCAAGCGTTTCGTTTCCTTG 58.880 50.000 0.00 0.00 36.78 3.61
1949 2014 1.268335 GCAAGCGTTTCGTTTCCTTGA 60.268 47.619 0.00 0.00 36.00 3.02
2122 2187 2.159819 CTGCCGTAGCACAGGTCACT 62.160 60.000 0.00 0.00 46.52 3.41
2123 2188 1.004918 GCCGTAGCACAGGTCACTT 60.005 57.895 0.00 0.00 39.53 3.16
2137 2202 3.072622 AGGTCACTTTTCCAACTACCCTC 59.927 47.826 0.00 0.00 0.00 4.30
2143 2208 2.561478 TTCCAACTACCCTCTTGCAC 57.439 50.000 0.00 0.00 0.00 4.57
2158 2226 3.759086 TCTTGCACTCGAGATACTGACTT 59.241 43.478 21.68 0.00 0.00 3.01
2171 2239 9.217278 CGAGATACTGACTTATAAACTAGGCTA 57.783 37.037 0.00 0.00 0.00 3.93
2177 2245 8.852135 ACTGACTTATAAACTAGGCTATGTCTC 58.148 37.037 0.00 0.00 0.00 3.36
2178 2246 8.179509 TGACTTATAAACTAGGCTATGTCTCC 57.820 38.462 0.00 0.00 0.00 3.71
2208 2301 6.071221 CCTGTGGAAAATGAATCAATTCCTCA 60.071 38.462 22.97 22.82 41.51 3.86
2210 2303 7.909518 TGTGGAAAATGAATCAATTCCTCATT 58.090 30.769 22.97 1.92 41.51 2.57
2220 2313 3.378112 TCAATTCCTCATTTGTCGATGCC 59.622 43.478 0.00 0.00 0.00 4.40
2244 2337 7.635587 GCCGATATTGTTTTGTTGCATATTTTG 59.364 33.333 0.00 0.00 0.00 2.44
2252 2345 8.547069 TGTTTTGTTGCATATTTTGTTAAGCTC 58.453 29.630 0.00 0.00 0.00 4.09
2257 2350 6.890663 TGCATATTTTGTTAAGCTCAATGC 57.109 33.333 0.00 0.00 43.29 3.56
2258 2351 5.811613 TGCATATTTTGTTAAGCTCAATGCC 59.188 36.000 7.21 0.00 44.23 4.40
2259 2352 5.811613 GCATATTTTGTTAAGCTCAATGCCA 59.188 36.000 0.00 0.00 44.23 4.92
2260 2353 6.313411 GCATATTTTGTTAAGCTCAATGCCAA 59.687 34.615 0.00 0.00 44.23 4.52
2261 2354 7.011669 GCATATTTTGTTAAGCTCAATGCCAAT 59.988 33.333 0.00 0.00 44.23 3.16
2262 2355 6.730960 ATTTTGTTAAGCTCAATGCCAATG 57.269 33.333 0.00 0.00 44.23 2.82
2263 2356 3.235157 TGTTAAGCTCAATGCCAATGC 57.765 42.857 0.00 0.00 44.23 3.56
2318 2411 5.841237 TGAGATGGGTATTCCTTTCCTAGAG 59.159 44.000 0.00 0.00 36.20 2.43
2333 2426 6.665992 TTCCTAGAGACAAGTGCTAAAGAA 57.334 37.500 0.00 0.00 0.00 2.52
2345 2438 7.039504 ACAAGTGCTAAAGAATCCATCAATGTT 60.040 33.333 0.00 0.00 0.00 2.71
2392 2485 3.870419 GCAGCAATCAAGAAGAGGTAGAG 59.130 47.826 0.00 0.00 0.00 2.43
2403 2496 4.780021 AGAAGAGGTAGAGGAGCAAATGAA 59.220 41.667 0.00 0.00 0.00 2.57
2407 2500 4.837972 AGGTAGAGGAGCAAATGAACTTC 58.162 43.478 0.00 0.00 0.00 3.01
2412 2505 2.887152 AGGAGCAAATGAACTTCCACAC 59.113 45.455 0.00 0.00 0.00 3.82
2418 2511 7.145932 AGCAAATGAACTTCCACACTATTAC 57.854 36.000 0.00 0.00 0.00 1.89
2419 2512 6.942576 AGCAAATGAACTTCCACACTATTACT 59.057 34.615 0.00 0.00 0.00 2.24
2423 2516 9.574516 AAATGAACTTCCACACTATTACTTTCT 57.425 29.630 0.00 0.00 0.00 2.52
2427 2520 9.485206 GAACTTCCACACTATTACTTTCTGTTA 57.515 33.333 0.00 0.00 0.00 2.41
2511 2615 2.122768 AGGAAGGCCTCTAATCTGGTG 58.877 52.381 5.23 0.00 42.19 4.17
2579 2683 1.068748 CAGCTGCTGTTCAACATGACC 60.069 52.381 21.21 0.00 0.00 4.02
2605 2709 0.249398 CGGACTTGTGGGAGGGTAAG 59.751 60.000 0.00 0.00 0.00 2.34
2616 2720 1.619363 AGGGTAAGGCATCCCAGCA 60.619 57.895 12.72 0.00 45.64 4.41
2626 2730 0.814410 CATCCCAGCAGCACAGCTAG 60.814 60.000 0.00 0.00 44.54 3.42
2672 2776 4.439305 GCATCTGCCAAATGTGAACTTA 57.561 40.909 0.00 0.00 34.31 2.24
2675 2779 6.563422 GCATCTGCCAAATGTGAACTTATTA 58.437 36.000 0.00 0.00 34.31 0.98
2680 2784 7.665559 TCTGCCAAATGTGAACTTATTACTTCT 59.334 33.333 0.00 0.00 0.00 2.85
2683 2787 9.129209 GCCAAATGTGAACTTATTACTTCTTTC 57.871 33.333 0.00 0.00 0.00 2.62
2758 2862 4.604043 CGCATGTTCGTATCGATCTTTCAC 60.604 45.833 0.00 0.00 35.23 3.18
2797 2901 4.436584 CGAAATCATGTCAGGAAACTCTGC 60.437 45.833 0.00 0.00 40.21 4.26
2805 2909 1.394917 CAGGAAACTCTGCGATTTCGG 59.605 52.381 1.75 0.00 40.21 4.30
2824 2928 2.271800 GGTGGTTCTCTAATCAGCACG 58.728 52.381 0.00 0.00 42.56 5.34
2825 2929 2.094182 GGTGGTTCTCTAATCAGCACGA 60.094 50.000 0.00 0.00 42.56 4.35
2840 2944 3.612860 CAGCACGACAACCAGAGTTATAC 59.387 47.826 0.00 0.00 33.27 1.47
2848 2952 7.147794 ACGACAACCAGAGTTATACCATATCAA 60.148 37.037 0.00 0.00 33.27 2.57
2914 3040 7.831691 AGCTTGTACAGATACAGATACAGAT 57.168 36.000 0.00 0.00 42.29 2.90
2915 3041 7.656412 AGCTTGTACAGATACAGATACAGATG 58.344 38.462 0.00 0.00 42.29 2.90
2916 3042 6.364706 GCTTGTACAGATACAGATACAGATGC 59.635 42.308 0.00 0.00 42.29 3.91
2917 3043 6.959639 TGTACAGATACAGATACAGATGCA 57.040 37.500 0.00 0.00 36.34 3.96
2918 3044 6.974965 TGTACAGATACAGATACAGATGCAG 58.025 40.000 0.00 0.00 36.34 4.41
2919 3045 6.547510 TGTACAGATACAGATACAGATGCAGT 59.452 38.462 0.00 0.00 36.34 4.40
2920 3046 6.477053 ACAGATACAGATACAGATGCAGTT 57.523 37.500 0.00 0.00 0.00 3.16
2921 3047 6.882656 ACAGATACAGATACAGATGCAGTTT 58.117 36.000 0.00 0.00 0.00 2.66
2922 3048 7.334090 ACAGATACAGATACAGATGCAGTTTT 58.666 34.615 0.00 0.00 0.00 2.43
2923 3049 7.826252 ACAGATACAGATACAGATGCAGTTTTT 59.174 33.333 0.00 0.00 0.00 1.94
2950 3076 8.547481 TTTTGAGGGATACAGATACAGATACA 57.453 34.615 0.00 0.00 39.74 2.29
2951 3077 7.767250 TTGAGGGATACAGATACAGATACAG 57.233 40.000 0.00 0.00 39.74 2.74
2952 3078 7.091533 TGAGGGATACAGATACAGATACAGA 57.908 40.000 0.00 0.00 39.74 3.41
2953 3079 7.703755 TGAGGGATACAGATACAGATACAGAT 58.296 38.462 0.00 0.00 39.74 2.90
2954 3080 7.613411 TGAGGGATACAGATACAGATACAGATG 59.387 40.741 0.00 0.00 39.74 2.90
2955 3081 6.379703 AGGGATACAGATACAGATACAGATGC 59.620 42.308 0.00 0.00 39.74 3.91
2956 3082 6.153510 GGGATACAGATACAGATACAGATGCA 59.846 42.308 0.00 0.00 39.74 3.96
2957 3083 7.257003 GGATACAGATACAGATACAGATGCAG 58.743 42.308 0.00 0.00 0.00 4.41
2958 3084 7.121907 GGATACAGATACAGATACAGATGCAGA 59.878 40.741 0.00 0.00 0.00 4.26
2959 3085 6.914654 ACAGATACAGATACAGATGCAGAT 57.085 37.500 0.00 0.00 0.00 2.90
2960 3086 7.300556 ACAGATACAGATACAGATGCAGATT 57.699 36.000 0.00 0.00 0.00 2.40
2961 3087 7.733969 ACAGATACAGATACAGATGCAGATTT 58.266 34.615 0.00 0.00 0.00 2.17
2962 3088 8.209584 ACAGATACAGATACAGATGCAGATTTT 58.790 33.333 0.00 0.00 0.00 1.82
2963 3089 9.053840 CAGATACAGATACAGATGCAGATTTTT 57.946 33.333 0.00 0.00 0.00 1.94
3122 3255 3.568853 AGATAACTTGGATAGGTCGGTCG 59.431 47.826 0.00 0.00 0.00 4.79
3154 3287 1.950909 CGAGTACTCCTCTCCATGGTC 59.049 57.143 17.23 0.00 38.11 4.02
3169 3302 1.301293 GGTCAGCTGGAGGGGAAAG 59.699 63.158 15.13 0.00 0.00 2.62
3267 3429 4.825422 TCGACAGATGCTGATCTTCTTTT 58.175 39.130 0.82 0.00 36.75 2.27
3355 3517 2.668550 AAACCCGAACTGGCGAGC 60.669 61.111 0.00 0.00 35.87 5.03
3393 3555 7.166691 TGGTTGTTTAGGCTAGAAGTAGTAG 57.833 40.000 0.00 0.00 0.00 2.57
3394 3556 6.723052 TGGTTGTTTAGGCTAGAAGTAGTAGT 59.277 38.462 0.00 0.00 0.00 2.73
3398 3560 7.173722 TGTTTAGGCTAGAAGTAGTAGTCACT 58.826 38.462 0.00 0.00 38.91 3.41
3447 3609 0.458260 GCATCATCATGTTGCTGCCA 59.542 50.000 17.79 0.00 39.34 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
219 221 1.066587 GCTCCAAGAGATCGACCGG 59.933 63.158 0.00 0.00 0.00 5.28
267 269 2.187685 CAGCAGATGTGGGCGCTA 59.812 61.111 7.64 0.00 32.29 4.26
543 546 3.132139 ATCTGCTGCTGGCGCTTG 61.132 61.111 7.64 0.90 45.43 4.01
544 547 2.526450 TACATCTGCTGCTGGCGCTT 62.526 55.000 7.64 0.00 45.43 4.68
545 548 2.919960 CTACATCTGCTGCTGGCGCT 62.920 60.000 7.64 0.00 45.43 5.92
546 549 2.512286 TACATCTGCTGCTGGCGC 60.512 61.111 0.00 0.00 45.43 6.53
547 550 0.460811 TTCTACATCTGCTGCTGGCG 60.461 55.000 6.69 1.22 45.43 5.69
548 551 1.297664 CTTCTACATCTGCTGCTGGC 58.702 55.000 6.69 0.00 42.22 4.85
549 552 1.209019 ACCTTCTACATCTGCTGCTGG 59.791 52.381 6.69 0.00 0.00 4.85
550 553 2.676839 CAACCTTCTACATCTGCTGCTG 59.323 50.000 0.00 0.00 0.00 4.41
551 554 2.355513 CCAACCTTCTACATCTGCTGCT 60.356 50.000 0.00 0.00 0.00 4.24
552 555 2.012673 CCAACCTTCTACATCTGCTGC 58.987 52.381 0.00 0.00 0.00 5.25
553 556 2.237143 TCCCAACCTTCTACATCTGCTG 59.763 50.000 0.00 0.00 0.00 4.41
554 557 2.551270 TCCCAACCTTCTACATCTGCT 58.449 47.619 0.00 0.00 0.00 4.24
555 558 3.010420 GTTCCCAACCTTCTACATCTGC 58.990 50.000 0.00 0.00 0.00 4.26
556 559 3.262420 CGTTCCCAACCTTCTACATCTG 58.738 50.000 0.00 0.00 0.00 2.90
557 560 2.904434 ACGTTCCCAACCTTCTACATCT 59.096 45.455 0.00 0.00 0.00 2.90
558 561 3.329929 ACGTTCCCAACCTTCTACATC 57.670 47.619 0.00 0.00 0.00 3.06
559 562 3.836562 ACTACGTTCCCAACCTTCTACAT 59.163 43.478 0.00 0.00 0.00 2.29
560 563 3.233507 ACTACGTTCCCAACCTTCTACA 58.766 45.455 0.00 0.00 0.00 2.74
561 564 3.256631 TGACTACGTTCCCAACCTTCTAC 59.743 47.826 0.00 0.00 0.00 2.59
562 565 3.256631 GTGACTACGTTCCCAACCTTCTA 59.743 47.826 0.00 0.00 0.00 2.10
563 566 2.036862 GTGACTACGTTCCCAACCTTCT 59.963 50.000 0.00 0.00 0.00 2.85
564 567 2.224113 TGTGACTACGTTCCCAACCTTC 60.224 50.000 0.00 0.00 0.00 3.46
565 568 1.764134 TGTGACTACGTTCCCAACCTT 59.236 47.619 0.00 0.00 0.00 3.50
566 569 1.343465 CTGTGACTACGTTCCCAACCT 59.657 52.381 0.00 0.00 0.00 3.50
567 570 1.792006 CTGTGACTACGTTCCCAACC 58.208 55.000 0.00 0.00 0.00 3.77
568 571 1.145803 GCTGTGACTACGTTCCCAAC 58.854 55.000 0.00 0.00 0.00 3.77
569 572 0.319211 CGCTGTGACTACGTTCCCAA 60.319 55.000 0.00 0.00 0.00 4.12
570 573 1.174078 TCGCTGTGACTACGTTCCCA 61.174 55.000 0.00 0.00 0.00 4.37
571 574 0.038892 TTCGCTGTGACTACGTTCCC 60.039 55.000 0.00 0.00 0.00 3.97
572 575 1.058404 GTTCGCTGTGACTACGTTCC 58.942 55.000 0.00 0.00 0.00 3.62
573 576 1.977412 GAGTTCGCTGTGACTACGTTC 59.023 52.381 0.00 0.00 0.00 3.95
574 577 1.662309 CGAGTTCGCTGTGACTACGTT 60.662 52.381 0.00 0.00 0.00 3.99
575 578 0.110328 CGAGTTCGCTGTGACTACGT 60.110 55.000 0.00 0.00 0.00 3.57
576 579 2.626648 CGAGTTCGCTGTGACTACG 58.373 57.895 0.00 0.00 0.00 3.51
612 615 2.846918 GCTTCTCGTGCGACACAC 59.153 61.111 9.95 0.00 46.45 3.82
630 633 1.352156 GATGTTCCCGTGCGACTCAC 61.352 60.000 0.00 0.00 42.23 3.51
631 634 1.080093 GATGTTCCCGTGCGACTCA 60.080 57.895 0.00 0.00 0.00 3.41
632 635 1.810030 GGATGTTCCCGTGCGACTC 60.810 63.158 0.00 0.00 0.00 3.36
633 636 2.264794 GGATGTTCCCGTGCGACT 59.735 61.111 0.00 0.00 0.00 4.18
634 637 2.047655 TGGATGTTCCCGTGCGAC 60.048 61.111 0.00 0.00 35.03 5.19
635 638 2.264480 CTGGATGTTCCCGTGCGA 59.736 61.111 0.00 0.00 35.03 5.10
636 639 2.819595 CCTGGATGTTCCCGTGCG 60.820 66.667 0.00 0.00 35.03 5.34
637 640 3.134127 GCCTGGATGTTCCCGTGC 61.134 66.667 0.00 0.00 35.03 5.34
638 641 2.438434 GGCCTGGATGTTCCCGTG 60.438 66.667 0.00 0.00 35.03 4.94
639 642 2.270874 GATGGCCTGGATGTTCCCGT 62.271 60.000 3.32 0.00 35.03 5.28
640 643 1.526917 GATGGCCTGGATGTTCCCG 60.527 63.158 3.32 0.00 35.03 5.14
641 644 1.152673 GGATGGCCTGGATGTTCCC 60.153 63.158 3.32 0.00 35.03 3.97
642 645 1.925888 AGGATGGCCTGGATGTTCC 59.074 57.895 3.32 0.00 44.90 3.62
671 674 7.555914 GTAGCTACTACTACTAAGGTTGTCCTT 59.444 40.741 16.88 4.90 43.07 3.36
672 675 7.053498 GTAGCTACTACTACTAAGGTTGTCCT 58.947 42.308 16.88 0.00 41.45 3.85
673 676 7.258022 GTAGCTACTACTACTAAGGTTGTCC 57.742 44.000 16.88 0.00 39.57 4.02
684 687 7.222872 TCCATCACCTTAGTAGCTACTACTAC 58.777 42.308 29.18 3.38 45.56 2.73
685 688 7.384524 TCCATCACCTTAGTAGCTACTACTA 57.615 40.000 29.18 16.98 44.35 1.82
687 690 6.570764 GCATCCATCACCTTAGTAGCTACTAC 60.571 46.154 29.18 12.07 38.43 2.73
688 691 5.477291 GCATCCATCACCTTAGTAGCTACTA 59.523 44.000 26.36 26.36 37.73 1.82
689 692 4.282195 GCATCCATCACCTTAGTAGCTACT 59.718 45.833 28.50 28.50 40.24 2.57
690 693 4.282195 AGCATCCATCACCTTAGTAGCTAC 59.718 45.833 16.43 16.43 0.00 3.58
691 694 4.483950 AGCATCCATCACCTTAGTAGCTA 58.516 43.478 0.00 0.00 0.00 3.32
692 695 3.312890 AGCATCCATCACCTTAGTAGCT 58.687 45.455 0.00 0.00 0.00 3.32
693 696 3.760580 AGCATCCATCACCTTAGTAGC 57.239 47.619 0.00 0.00 0.00 3.58
694 697 5.431765 ACAAAGCATCCATCACCTTAGTAG 58.568 41.667 0.00 0.00 0.00 2.57
695 698 5.045942 TGACAAAGCATCCATCACCTTAGTA 60.046 40.000 0.00 0.00 0.00 1.82
696 699 4.263462 TGACAAAGCATCCATCACCTTAGT 60.263 41.667 0.00 0.00 0.00 2.24
697 700 4.264253 TGACAAAGCATCCATCACCTTAG 58.736 43.478 0.00 0.00 0.00 2.18
698 701 4.299586 TGACAAAGCATCCATCACCTTA 57.700 40.909 0.00 0.00 0.00 2.69
699 702 3.159213 TGACAAAGCATCCATCACCTT 57.841 42.857 0.00 0.00 0.00 3.50
700 703 2.885135 TGACAAAGCATCCATCACCT 57.115 45.000 0.00 0.00 0.00 4.00
701 704 3.018856 TGATGACAAAGCATCCATCACC 58.981 45.455 0.00 0.00 43.10 4.02
841 854 1.079127 AAACTGATCTCCCGGTGCG 60.079 57.895 0.00 0.00 0.00 5.34
874 888 4.156739 GGGCAGAAAAAGGTCATAACTCTG 59.843 45.833 0.00 0.00 33.54 3.35
883 897 2.795329 TCTCATGGGCAGAAAAAGGTC 58.205 47.619 0.00 0.00 0.00 3.85
898 912 1.836802 GGTGGAGAAGAGGCTTCTCAT 59.163 52.381 28.33 3.88 45.01 2.90
995 1013 1.164411 CAACTCGTTGCCCATGCTTA 58.836 50.000 0.00 0.00 38.71 3.09
1024 1049 0.722848 GGCGCGAAAATAGAAACGGA 59.277 50.000 12.10 0.00 0.00 4.69
1069 1094 1.889829 CAACCAGGCAATTAACGGGAA 59.110 47.619 5.05 0.00 0.00 3.97
1087 1112 2.170397 TCAGTTCACCAGAGCAGAACAA 59.830 45.455 0.00 0.00 43.00 2.83
1163 1188 2.725008 GGAGGAGTCGCCGATCAG 59.275 66.667 0.00 0.00 43.43 2.90
1225 1250 1.272807 TGCCAAGGAGTAGTGGTACC 58.727 55.000 4.43 4.43 37.23 3.34
1226 1251 3.270877 CATTGCCAAGGAGTAGTGGTAC 58.729 50.000 0.00 0.00 37.23 3.34
1230 1255 2.086869 CCACATTGCCAAGGAGTAGTG 58.913 52.381 0.00 0.00 0.00 2.74
1280 1307 2.189342 CGCGATCTTGAGAAGGAAGAC 58.811 52.381 0.00 0.00 32.30 3.01
1298 1325 1.174712 AGGACCATGCCATTATGCGC 61.175 55.000 0.00 0.00 0.00 6.09
1300 1327 1.985473 TCAGGACCATGCCATTATGC 58.015 50.000 0.00 0.00 0.00 3.14
1402 1429 3.731652 AGCGAGAGAGAATCATCAAGG 57.268 47.619 0.00 0.00 37.82 3.61
1418 1476 3.062639 GTGCGTACAGTACTAAGTAGCGA 59.937 47.826 9.10 0.00 32.41 4.93
1420 1478 4.612932 AGTGCGTACAGTACTAAGTAGC 57.387 45.455 6.38 4.38 44.08 3.58
1421 1479 6.840075 AGAAAGTGCGTACAGTACTAAGTAG 58.160 40.000 6.38 0.00 45.18 2.57
1422 1480 6.427853 TGAGAAAGTGCGTACAGTACTAAGTA 59.572 38.462 6.38 0.00 45.18 2.24
1423 1481 5.240183 TGAGAAAGTGCGTACAGTACTAAGT 59.760 40.000 6.38 0.00 45.18 2.24
1424 1482 5.696822 TGAGAAAGTGCGTACAGTACTAAG 58.303 41.667 6.38 0.00 45.18 2.18
1425 1483 5.694231 TGAGAAAGTGCGTACAGTACTAA 57.306 39.130 6.38 0.00 45.18 2.24
1426 1484 5.163683 GGATGAGAAAGTGCGTACAGTACTA 60.164 44.000 6.38 0.00 45.18 1.82
1428 1486 3.858238 GGATGAGAAAGTGCGTACAGTAC 59.142 47.826 6.38 0.00 35.57 2.73
1429 1487 3.762288 AGGATGAGAAAGTGCGTACAGTA 59.238 43.478 6.38 0.00 0.00 2.74
1430 1488 2.563179 AGGATGAGAAAGTGCGTACAGT 59.437 45.455 6.38 0.00 0.00 3.55
1431 1489 3.238108 AGGATGAGAAAGTGCGTACAG 57.762 47.619 6.38 0.00 0.00 2.74
1432 1490 4.159693 ACATAGGATGAGAAAGTGCGTACA 59.840 41.667 6.38 0.00 0.00 2.90
1433 1491 4.683832 ACATAGGATGAGAAAGTGCGTAC 58.316 43.478 0.00 0.00 0.00 3.67
1434 1492 5.339008 AACATAGGATGAGAAAGTGCGTA 57.661 39.130 0.00 0.00 0.00 4.42
1435 1493 3.895232 ACATAGGATGAGAAAGTGCGT 57.105 42.857 0.00 0.00 0.00 5.24
1436 1494 4.201851 CCAAACATAGGATGAGAAAGTGCG 60.202 45.833 0.00 0.00 0.00 5.34
1437 1495 4.702131 ACCAAACATAGGATGAGAAAGTGC 59.298 41.667 0.00 0.00 0.00 4.40
1438 1496 6.127897 GGAACCAAACATAGGATGAGAAAGTG 60.128 42.308 0.00 0.00 0.00 3.16
1439 1497 5.946377 GGAACCAAACATAGGATGAGAAAGT 59.054 40.000 0.00 0.00 0.00 2.66
1440 1498 5.945784 TGGAACCAAACATAGGATGAGAAAG 59.054 40.000 0.00 0.00 0.00 2.62
1463 1521 5.173131 CACGTGCATCATCAATCAATCAATG 59.827 40.000 0.82 0.00 0.00 2.82
1464 1522 5.163591 ACACGTGCATCATCAATCAATCAAT 60.164 36.000 17.22 0.00 0.00 2.57
1465 1523 4.156373 ACACGTGCATCATCAATCAATCAA 59.844 37.500 17.22 0.00 0.00 2.57
1467 1525 4.033019 CACACGTGCATCATCAATCAATC 58.967 43.478 17.22 0.00 0.00 2.67
1468 1526 4.023739 CACACGTGCATCATCAATCAAT 57.976 40.909 17.22 0.00 0.00 2.57
1469 1527 3.474693 CACACGTGCATCATCAATCAA 57.525 42.857 17.22 0.00 0.00 2.57
1532 1593 6.769822 AGGGATTAATCACTTACAATCTGCAG 59.230 38.462 14.73 7.63 37.20 4.41
1621 1686 4.104776 ACACAAAAAGTTGACGATTGCAG 58.895 39.130 0.00 0.00 38.20 4.41
1627 1692 6.438259 TTCCAATACACAAAAAGTTGACGA 57.562 33.333 0.00 0.00 38.20 4.20
1629 1694 8.641499 TCATTTCCAATACACAAAAAGTTGAC 57.359 30.769 0.00 0.00 38.20 3.18
1659 1724 1.257750 GCAGGGGTTTGATGGGGAAC 61.258 60.000 0.00 0.00 0.00 3.62
1673 1738 4.022068 AGTTTGTATGTTTGTGATGCAGGG 60.022 41.667 0.00 0.00 0.00 4.45
1703 1768 0.673437 AATTGTTTCCACCGGCAGTG 59.327 50.000 0.00 0.00 46.83 3.66
1751 1816 7.759489 AAGAGGTACTGATATGAGATGAGAC 57.241 40.000 0.00 0.00 41.55 3.36
1774 1839 2.100584 GTCCCACTGTTGTGAATGCAAA 59.899 45.455 0.00 0.00 46.55 3.68
1782 1847 0.747644 TGCTGTGTCCCACTGTTGTG 60.748 55.000 3.71 0.00 43.45 3.33
1846 1911 0.529773 TTACGATGATGCCGTGAGCC 60.530 55.000 0.00 0.00 42.71 4.70
1855 1920 5.240403 TGGAGAGATGAGACTTACGATGATG 59.760 44.000 0.00 0.00 0.00 3.07
1876 1941 5.723672 TTTGTTGTTGTTTTACAGGTGGA 57.276 34.783 0.00 0.00 0.00 4.02
1901 1966 1.615919 CGGTGGGTAAAAGCTGGGAAT 60.616 52.381 0.00 0.00 0.00 3.01
1903 1968 1.377229 CGGTGGGTAAAAGCTGGGA 59.623 57.895 0.00 0.00 0.00 4.37
1904 1969 2.340328 GCGGTGGGTAAAAGCTGGG 61.340 63.158 0.00 0.00 0.00 4.45
1905 1970 1.175983 TTGCGGTGGGTAAAAGCTGG 61.176 55.000 0.00 0.00 0.00 4.85
1908 1973 1.271102 TGAATTGCGGTGGGTAAAAGC 59.729 47.619 0.00 0.00 0.00 3.51
1921 1986 0.704551 CGAAACGCTTGCTGAATTGC 59.295 50.000 0.00 0.00 0.00 3.56
1924 1989 2.604614 GGAAACGAAACGCTTGCTGAAT 60.605 45.455 0.00 0.00 0.00 2.57
1933 1998 2.223180 ACAACTCAAGGAAACGAAACGC 60.223 45.455 0.00 0.00 0.00 4.84
1935 2000 5.686834 GGATACAACTCAAGGAAACGAAAC 58.313 41.667 0.00 0.00 0.00 2.78
1946 2011 7.981789 GTCATAGACAATCTGGATACAACTCAA 59.018 37.037 0.00 0.00 38.28 3.02
1947 2012 7.124147 TGTCATAGACAATCTGGATACAACTCA 59.876 37.037 0.00 0.00 43.07 3.41
1948 2013 7.492524 TGTCATAGACAATCTGGATACAACTC 58.507 38.462 0.00 0.00 43.07 3.01
1949 2014 7.423844 TGTCATAGACAATCTGGATACAACT 57.576 36.000 0.00 0.00 43.07 3.16
2062 2127 2.371841 AGCCAGATCACACTTGTTACCA 59.628 45.455 0.00 0.00 0.00 3.25
2122 2187 3.117663 AGTGCAAGAGGGTAGTTGGAAAA 60.118 43.478 0.00 0.00 0.00 2.29
2123 2188 2.441750 AGTGCAAGAGGGTAGTTGGAAA 59.558 45.455 0.00 0.00 0.00 3.13
2137 2202 3.773860 AGTCAGTATCTCGAGTGCAAG 57.226 47.619 13.13 1.59 0.00 4.01
2143 2208 8.231837 GCCTAGTTTATAAGTCAGTATCTCGAG 58.768 40.741 5.93 5.93 0.00 4.04
2177 2245 4.955450 TGATTCATTTTCCACAGGGTATGG 59.045 41.667 0.00 0.00 38.71 2.74
2178 2246 6.528537 TTGATTCATTTTCCACAGGGTATG 57.471 37.500 0.00 0.00 34.93 2.39
2244 2337 2.187707 CGCATTGGCATTGAGCTTAAC 58.812 47.619 13.23 0.00 44.79 2.01
2252 2345 1.350319 GCATTGCGCATTGGCATTG 59.650 52.632 27.90 11.94 43.52 2.82
2274 2367 0.466739 TCAGCATAGGCCTGCAATGG 60.467 55.000 17.99 3.69 44.77 3.16
2277 2370 0.547553 TCATCAGCATAGGCCTGCAA 59.452 50.000 17.99 4.97 44.77 4.08
2318 2411 6.500684 TTGATGGATTCTTTAGCACTTGTC 57.499 37.500 0.00 0.00 0.00 3.18
2333 2426 3.053095 AGGCCTCTTCAACATTGATGGAT 60.053 43.478 0.00 0.29 37.00 3.41
2392 2485 2.887152 AGTGTGGAAGTTCATTTGCTCC 59.113 45.455 5.01 0.00 0.00 4.70
2407 2500 9.226606 TCCAAATAACAGAAAGTAATAGTGTGG 57.773 33.333 0.00 0.00 0.00 4.17
2418 2511 7.977853 AGCATAAGCATTCCAAATAACAGAAAG 59.022 33.333 0.00 0.00 45.49 2.62
2419 2512 7.760794 CAGCATAAGCATTCCAAATAACAGAAA 59.239 33.333 0.00 0.00 45.49 2.52
2423 2516 6.772360 TCAGCATAAGCATTCCAAATAACA 57.228 33.333 0.00 0.00 45.49 2.41
2427 2520 6.474140 TTCATCAGCATAAGCATTCCAAAT 57.526 33.333 0.00 0.00 45.49 2.32
2511 2615 1.252904 TTGGCTGGCCTTTCATCTGC 61.253 55.000 13.05 0.00 36.94 4.26
2592 2696 1.279025 GGATGCCTTACCCTCCCACA 61.279 60.000 0.00 0.00 0.00 4.17
2594 2698 1.696314 GGGATGCCTTACCCTCCCA 60.696 63.158 0.00 0.00 45.66 4.37
2605 2709 3.138798 CTGTGCTGCTGGGATGCC 61.139 66.667 0.00 0.00 0.00 4.40
2616 2720 0.906756 TCCTGGAAGCTAGCTGTGCT 60.907 55.000 20.16 1.15 43.32 4.40
2626 2730 3.287867 TTCATCCTGATTCCTGGAAGC 57.712 47.619 17.46 17.46 42.56 3.86
2683 2787 5.610398 AGCTAAAAATGTGTTCCAAAAGGG 58.390 37.500 0.00 0.00 38.37 3.95
2697 2801 5.712152 ACAGTTTGCAGCTAGCTAAAAAT 57.288 34.783 18.86 16.72 45.94 1.82
2758 2862 4.571984 TGATTTCGACATATGTTGCTCCAG 59.428 41.667 17.10 1.38 0.00 3.86
2797 2901 4.430007 TGATTAGAGAACCACCGAAATCG 58.570 43.478 0.00 0.00 39.44 3.34
2805 2909 2.924290 GTCGTGCTGATTAGAGAACCAC 59.076 50.000 0.00 0.00 0.00 4.16
2824 2928 7.441458 GGTTGATATGGTATAACTCTGGTTGTC 59.559 40.741 0.00 0.00 36.92 3.18
2825 2929 7.092623 TGGTTGATATGGTATAACTCTGGTTGT 60.093 37.037 0.00 0.00 36.92 3.32
2840 2944 6.097356 GCAGATTGCAATATGGTTGATATGG 58.903 40.000 29.64 6.31 44.26 2.74
2924 3050 8.988060 TGTATCTGTATCTGTATCCCTCAAAAA 58.012 33.333 0.00 0.00 0.00 1.94
2925 3051 8.547481 TGTATCTGTATCTGTATCCCTCAAAA 57.453 34.615 0.00 0.00 0.00 2.44
2926 3052 8.004801 TCTGTATCTGTATCTGTATCCCTCAAA 58.995 37.037 0.00 0.00 0.00 2.69
2927 3053 7.526918 TCTGTATCTGTATCTGTATCCCTCAA 58.473 38.462 0.00 0.00 0.00 3.02
2928 3054 7.091533 TCTGTATCTGTATCTGTATCCCTCA 57.908 40.000 0.00 0.00 0.00 3.86
2929 3055 7.416213 GCATCTGTATCTGTATCTGTATCCCTC 60.416 44.444 0.00 0.00 0.00 4.30
2930 3056 6.379703 GCATCTGTATCTGTATCTGTATCCCT 59.620 42.308 0.00 0.00 0.00 4.20
2931 3057 6.153510 TGCATCTGTATCTGTATCTGTATCCC 59.846 42.308 0.00 0.00 0.00 3.85
2932 3058 7.121907 TCTGCATCTGTATCTGTATCTGTATCC 59.878 40.741 0.00 0.00 0.00 2.59
2933 3059 8.049655 TCTGCATCTGTATCTGTATCTGTATC 57.950 38.462 0.00 0.00 0.00 2.24
2934 3060 8.592529 ATCTGCATCTGTATCTGTATCTGTAT 57.407 34.615 0.00 0.00 0.00 2.29
2935 3061 8.414629 AATCTGCATCTGTATCTGTATCTGTA 57.585 34.615 0.00 0.00 0.00 2.74
2936 3062 6.914654 ATCTGCATCTGTATCTGTATCTGT 57.085 37.500 0.00 0.00 0.00 3.41
2937 3063 8.604640 AAAATCTGCATCTGTATCTGTATCTG 57.395 34.615 0.00 0.00 0.00 2.90
2964 3090 8.988060 TGTATCTGTATCTGTATCCCTCAAAAA 58.012 33.333 0.00 0.00 0.00 1.94
2965 3091 8.547481 TGTATCTGTATCTGTATCCCTCAAAA 57.453 34.615 0.00 0.00 0.00 2.44
2966 3092 8.004801 TCTGTATCTGTATCTGTATCCCTCAAA 58.995 37.037 0.00 0.00 0.00 2.69
2967 3093 7.526918 TCTGTATCTGTATCTGTATCCCTCAA 58.473 38.462 0.00 0.00 0.00 3.02
2968 3094 7.091533 TCTGTATCTGTATCTGTATCCCTCA 57.908 40.000 0.00 0.00 0.00 3.86
2969 3095 7.416213 GCATCTGTATCTGTATCTGTATCCCTC 60.416 44.444 0.00 0.00 0.00 4.30
2970 3096 6.379703 GCATCTGTATCTGTATCTGTATCCCT 59.620 42.308 0.00 0.00 0.00 4.20
2971 3097 6.153510 TGCATCTGTATCTGTATCTGTATCCC 59.846 42.308 0.00 0.00 0.00 3.85
2972 3098 7.121907 TCTGCATCTGTATCTGTATCTGTATCC 59.878 40.741 0.00 0.00 0.00 2.59
2973 3099 8.049655 TCTGCATCTGTATCTGTATCTGTATC 57.950 38.462 0.00 0.00 0.00 2.24
2974 3100 8.592529 ATCTGCATCTGTATCTGTATCTGTAT 57.407 34.615 0.00 0.00 0.00 2.29
2975 3101 8.414629 AATCTGCATCTGTATCTGTATCTGTA 57.585 34.615 0.00 0.00 0.00 2.74
2976 3102 6.914654 ATCTGCATCTGTATCTGTATCTGT 57.085 37.500 0.00 0.00 0.00 3.41
2977 3103 8.496751 CAAAATCTGCATCTGTATCTGTATCTG 58.503 37.037 0.00 0.00 0.00 2.90
2978 3104 8.209584 ACAAAATCTGCATCTGTATCTGTATCT 58.790 33.333 0.00 0.00 0.00 1.98
2979 3105 8.375608 ACAAAATCTGCATCTGTATCTGTATC 57.624 34.615 0.00 0.00 0.00 2.24
2980 3106 8.743085 AACAAAATCTGCATCTGTATCTGTAT 57.257 30.769 0.00 0.00 0.00 2.29
2981 3107 8.453320 CAAACAAAATCTGCATCTGTATCTGTA 58.547 33.333 0.00 0.00 0.00 2.74
2982 3108 7.040201 ACAAACAAAATCTGCATCTGTATCTGT 60.040 33.333 0.00 0.00 0.00 3.41
2983 3109 7.310664 ACAAACAAAATCTGCATCTGTATCTG 58.689 34.615 0.00 0.00 0.00 2.90
2984 3110 7.458409 ACAAACAAAATCTGCATCTGTATCT 57.542 32.000 0.00 0.00 0.00 1.98
2985 3111 8.454106 AGTACAAACAAAATCTGCATCTGTATC 58.546 33.333 0.00 0.00 0.00 2.24
2986 3112 8.340618 AGTACAAACAAAATCTGCATCTGTAT 57.659 30.769 0.00 0.00 0.00 2.29
3037 3170 2.862536 CGTCTCATAGCCTTGTGTGATG 59.137 50.000 0.00 0.00 0.00 3.07
3122 3255 2.159407 GGAGTACTCGTGTAGCCTGAAC 60.159 54.545 16.56 0.00 0.00 3.18
3154 3287 1.676967 GCACTTTCCCCTCCAGCTG 60.677 63.158 6.78 6.78 0.00 4.24
3169 3302 2.355756 AGATTGCATGATGTTACCGCAC 59.644 45.455 0.00 0.00 31.10 5.34
3196 3329 8.712103 AGATTCATCATCTTTCAGATTGGACTA 58.288 33.333 0.00 0.00 39.47 2.59
3267 3429 5.127845 TGCCACTTCATGTTGTAAAAAGGAA 59.872 36.000 0.00 0.00 30.28 3.36
3355 3517 6.316390 CCTAAACAACCAACCTATCAAGCTAG 59.684 42.308 0.00 0.00 0.00 3.42
3393 3555 0.247736 AGCGAACCATGGAGAGTGAC 59.752 55.000 21.47 0.62 0.00 3.67
3394 3556 0.247460 CAGCGAACCATGGAGAGTGA 59.753 55.000 21.47 0.00 0.00 3.41
3398 3560 0.250234 CTTCCAGCGAACCATGGAGA 59.750 55.000 21.47 0.16 46.01 3.71
3447 3609 0.616111 AGAGCGGGATTCTGGACACT 60.616 55.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.