Multiple sequence alignment - TraesCS6B01G416000

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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 TraesCS6B01G416000 chr6B 100.000 2899 0 0 1 2899 688371234 688374132 0.000000e+00 5354.0
1 TraesCS6B01G416000 chr6B 95.181 83 4 0 652 734 85703638 85703720 6.520000e-27 132.0
2 TraesCS6B01G416000 chr6B 91.489 94 8 0 641 734 458503577 458503484 2.340000e-26 130.0
3 TraesCS6B01G416000 chr6D 90.533 1088 55 20 740 1825 453021370 453022411 0.000000e+00 1395.0
4 TraesCS6B01G416000 chr6D 86.156 679 57 20 4 650 453020692 453021365 0.000000e+00 699.0
5 TraesCS6B01G416000 chr6D 82.990 582 75 16 2337 2899 453023453 453024029 3.330000e-139 505.0
6 TraesCS6B01G416000 chr6D 81.902 326 25 16 1901 2201 453022846 453023162 8.020000e-61 244.0
7 TraesCS6B01G416000 chr6D 91.753 97 8 0 645 741 7985337 7985433 5.040000e-28 135.0
8 TraesCS6B01G416000 chr6D 94.253 87 4 1 652 738 299191345 299191260 6.520000e-27 132.0
9 TraesCS6B01G416000 chr6D 91.304 92 7 1 652 743 9406774 9406684 1.090000e-24 124.0
10 TraesCS6B01G416000 chr6A 87.933 895 59 13 740 1634 599059189 599060034 0.000000e+00 1009.0
11 TraesCS6B01G416000 chr6A 83.022 695 66 27 4 650 599058171 599058861 1.500000e-162 582.0
12 TraesCS6B01G416000 chr6A 92.593 324 17 4 1584 1907 599072842 599073158 2.630000e-125 459.0
13 TraesCS6B01G416000 chr6A 81.849 584 66 17 2337 2893 599073805 599074375 3.410000e-124 455.0
14 TraesCS6B01G416000 chr6A 80.256 390 49 17 1972 2342 599060679 599061059 4.760000e-68 268.0
15 TraesCS6B01G416000 chr6A 87.500 248 11 6 1973 2204 599073273 599073516 4.760000e-68 268.0
16 TraesCS6B01G416000 chr6A 93.671 79 5 0 740 818 599058866 599058944 5.070000e-23 119.0
17 TraesCS6B01G416000 chr1B 94.186 86 5 0 652 737 510799176 510799091 6.520000e-27 132.0
18 TraesCS6B01G416000 chr2D 92.222 90 6 1 649 737 612817261 612817350 3.030000e-25 126.0
19 TraesCS6B01G416000 chr2D 88.889 63 7 0 1326 1388 577338085 577338023 8.610000e-11 78.7
20 TraesCS6B01G416000 chr4B 90.323 93 9 0 642 734 631527868 631527776 3.920000e-24 122.0
21 TraesCS6B01G416000 chr4B 88.119 101 11 1 644 744 52864305 52864206 5.070000e-23 119.0
22 TraesCS6B01G416000 chr2B 89.231 65 7 0 1324 1388 694275494 694275430 6.660000e-12 82.4
23 TraesCS6B01G416000 chr2A 89.231 65 7 0 1324 1388 715415863 715415799 6.660000e-12 82.4
24 TraesCS6B01G416000 chr3B 100.000 28 0 0 1434 1461 435961889 435961916 5.000000e-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 TraesCS6B01G416000 chr6B 688371234 688374132 2898 False 5354.00 5354 100.00000 1 2899 1 chr6B.!!$F2 2898
1 TraesCS6B01G416000 chr6D 453020692 453024029 3337 False 710.75 1395 85.39525 4 2899 4 chr6D.!!$F2 2895
2 TraesCS6B01G416000 chr6A 599058171 599061059 2888 False 494.50 1009 86.22050 4 2342 4 chr6A.!!$F1 2338
3 TraesCS6B01G416000 chr6A 599072842 599074375 1533 False 394.00 459 87.31400 1584 2893 3 chr6A.!!$F2 1309

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
784 831 0.102844 TTGCACAAACAAGCCTCTGC 59.897 50.0 0.0 0.0 37.95 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2547 3523 0.107703 CCAAATGACTGAGCCGGCTA 60.108 55.0 32.97 14.88 0.0 3.93 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
35 36 2.751436 CTGGCCACATTCCCACCG 60.751 66.667 0.00 0.00 0.00 4.94
75 76 1.831652 AACAGAACCAGGGCCTCTCG 61.832 60.000 0.95 0.00 0.00 4.04
164 165 4.766404 AGATTAAGGCAACAAACTTCCG 57.234 40.909 0.00 0.00 41.41 4.30
166 167 1.611519 TAAGGCAACAAACTTCCGGG 58.388 50.000 0.00 0.00 41.41 5.73
170 171 1.956802 CAACAAACTTCCGGGCCTC 59.043 57.895 0.84 0.00 0.00 4.70
301 330 3.855255 TGTCACCAGGAAGATGAAACA 57.145 42.857 0.00 0.00 0.00 2.83
305 334 2.227388 CACCAGGAAGATGAAACACTGC 59.773 50.000 0.00 0.00 0.00 4.40
330 359 2.575532 TGTCCTTGGTTGCTCTTTGAG 58.424 47.619 0.00 0.00 0.00 3.02
357 386 4.081087 TGGTTCCTAAGGTATGTGAGCTTC 60.081 45.833 0.00 0.00 42.29 3.86
374 404 3.118884 AGCTTCATTTCATTGATGGTGGC 60.119 43.478 0.00 0.00 32.34 5.01
377 407 5.581126 TTCATTTCATTGATGGTGGCTAC 57.419 39.130 0.00 0.00 0.00 3.58
399 429 7.813148 GCTACTTTGTCTGAATCTACTTGTGTA 59.187 37.037 0.00 0.00 0.00 2.90
415 445 4.492494 TGTGTATGGCAGACAGATTGAT 57.508 40.909 16.33 0.00 0.00 2.57
416 446 4.193865 TGTGTATGGCAGACAGATTGATG 58.806 43.478 16.33 0.00 0.00 3.07
417 447 3.562973 GTGTATGGCAGACAGATTGATGG 59.437 47.826 16.33 0.00 0.00 3.51
418 448 3.200605 TGTATGGCAGACAGATTGATGGT 59.799 43.478 11.51 0.00 0.00 3.55
419 449 2.118313 TGGCAGACAGATTGATGGTG 57.882 50.000 0.00 0.00 0.00 4.17
421 451 1.340405 GGCAGACAGATTGATGGTGGT 60.340 52.381 0.00 0.00 0.00 4.16
422 452 2.092968 GGCAGACAGATTGATGGTGGTA 60.093 50.000 0.00 0.00 0.00 3.25
423 453 2.939103 GCAGACAGATTGATGGTGGTAC 59.061 50.000 0.00 0.00 0.00 3.34
425 455 4.836825 CAGACAGATTGATGGTGGTACTT 58.163 43.478 0.00 0.00 0.00 2.24
426 456 5.248640 CAGACAGATTGATGGTGGTACTTT 58.751 41.667 0.00 0.00 0.00 2.66
427 457 5.352569 CAGACAGATTGATGGTGGTACTTTC 59.647 44.000 0.00 0.00 0.00 2.62
429 459 5.819991 ACAGATTGATGGTGGTACTTTCAT 58.180 37.500 0.00 0.00 0.00 2.57
430 460 6.248433 ACAGATTGATGGTGGTACTTTCATT 58.752 36.000 0.00 0.00 0.00 2.57
431 461 6.151648 ACAGATTGATGGTGGTACTTTCATTG 59.848 38.462 0.00 0.00 0.00 2.82
459 505 7.383029 TGAATTGTTTCAATCTGTTCATTCTGC 59.617 33.333 0.00 0.00 38.90 4.26
469 515 8.403236 CAATCTGTTCATTCTGCTAATTCATCA 58.597 33.333 0.00 0.00 0.00 3.07
475 521 9.362539 GTTCATTCTGCTAATTCATCATTTGTT 57.637 29.630 0.00 0.00 0.00 2.83
476 522 9.932207 TTCATTCTGCTAATTCATCATTTGTTT 57.068 25.926 0.00 0.00 0.00 2.83
493 539 8.739039 TCATTTGTTTTCTACACATTATCTGGG 58.261 33.333 0.00 0.00 36.21 4.45
496 542 6.774673 TGTTTTCTACACATTATCTGGGTCA 58.225 36.000 0.00 0.00 41.86 4.02
503 549 5.930135 ACACATTATCTGGGTCAATCCTAC 58.070 41.667 0.00 0.00 36.50 3.18
530 577 7.500992 TGGAATGTAGAGATATCTCAACCAAC 58.499 38.462 29.83 19.64 45.21 3.77
534 581 7.482169 TGTAGAGATATCTCAACCAACACTT 57.518 36.000 29.83 11.25 45.21 3.16
559 606 2.236766 CAAATCCATGAGCCCCTGATC 58.763 52.381 0.00 0.00 0.00 2.92
570 617 1.004080 CCCTGATCCATAGCAGCGG 60.004 63.158 0.00 0.00 37.82 5.52
571 618 1.750930 CCTGATCCATAGCAGCGGT 59.249 57.895 0.00 0.00 37.82 5.68
573 620 1.067283 CCTGATCCATAGCAGCGGTAG 60.067 57.143 0.00 0.00 37.82 3.18
577 624 3.005472 TGATCCATAGCAGCGGTAGTTAC 59.995 47.826 0.00 0.00 0.00 2.50
583 630 1.278127 AGCAGCGGTAGTTACCAACAT 59.722 47.619 8.91 0.00 46.80 2.71
586 633 3.063045 GCAGCGGTAGTTACCAACATTAC 59.937 47.826 8.91 0.00 46.80 1.89
591 638 5.220719 GCGGTAGTTACCAACATTACATTCC 60.221 44.000 8.91 0.00 46.80 3.01
608 655 6.061231 ACATTCCGAAGAAAACTTTCAGAC 57.939 37.500 5.07 0.00 39.61 3.51
621 668 1.305201 TTCAGACGGGCTGTTTTCAC 58.695 50.000 11.30 0.00 45.14 3.18
650 697 9.701355 GTTGTTTCTATTCATTTTTGTTTGGTG 57.299 29.630 0.00 0.00 0.00 4.17
651 698 7.914465 TGTTTCTATTCATTTTTGTTTGGTGC 58.086 30.769 0.00 0.00 0.00 5.01
653 700 7.945033 TTCTATTCATTTTTGTTTGGTGCTC 57.055 32.000 0.00 0.00 0.00 4.26
654 701 6.454795 TCTATTCATTTTTGTTTGGTGCTCC 58.545 36.000 0.00 0.00 0.00 4.70
655 702 3.467374 TCATTTTTGTTTGGTGCTCCC 57.533 42.857 1.59 0.00 0.00 4.30
656 703 3.037549 TCATTTTTGTTTGGTGCTCCCT 58.962 40.909 1.59 0.00 0.00 4.20
657 704 3.069443 TCATTTTTGTTTGGTGCTCCCTC 59.931 43.478 1.59 0.00 0.00 4.30
658 705 2.452600 TTTTGTTTGGTGCTCCCTCT 57.547 45.000 1.59 0.00 0.00 3.69
659 706 1.691196 TTTGTTTGGTGCTCCCTCTG 58.309 50.000 1.59 0.00 0.00 3.35
660 707 0.550914 TTGTTTGGTGCTCCCTCTGT 59.449 50.000 1.59 0.00 0.00 3.41
661 708 1.429930 TGTTTGGTGCTCCCTCTGTA 58.570 50.000 1.59 0.00 0.00 2.74
662 709 1.771854 TGTTTGGTGCTCCCTCTGTAA 59.228 47.619 1.59 0.00 0.00 2.41
663 710 2.173782 TGTTTGGTGCTCCCTCTGTAAA 59.826 45.455 1.59 0.00 0.00 2.01
664 711 2.552743 GTTTGGTGCTCCCTCTGTAAAC 59.447 50.000 1.59 1.73 0.00 2.01
665 712 1.429930 TGGTGCTCCCTCTGTAAACA 58.570 50.000 1.59 0.00 0.00 2.83
666 713 1.771854 TGGTGCTCCCTCTGTAAACAA 59.228 47.619 1.59 0.00 0.00 2.83
667 714 2.173782 TGGTGCTCCCTCTGTAAACAAA 59.826 45.455 1.59 0.00 0.00 2.83
668 715 3.181434 TGGTGCTCCCTCTGTAAACAAAT 60.181 43.478 1.59 0.00 0.00 2.32
669 716 4.042311 TGGTGCTCCCTCTGTAAACAAATA 59.958 41.667 1.59 0.00 0.00 1.40
670 717 5.193679 GGTGCTCCCTCTGTAAACAAATAT 58.806 41.667 0.00 0.00 0.00 1.28
671 718 6.069905 TGGTGCTCCCTCTGTAAACAAATATA 60.070 38.462 1.59 0.00 0.00 0.86
672 719 6.826741 GGTGCTCCCTCTGTAAACAAATATAA 59.173 38.462 0.00 0.00 0.00 0.98
673 720 7.012421 GGTGCTCCCTCTGTAAACAAATATAAG 59.988 40.741 0.00 0.00 0.00 1.73
674 721 7.769044 GTGCTCCCTCTGTAAACAAATATAAGA 59.231 37.037 0.00 0.00 0.00 2.10
675 722 7.987458 TGCTCCCTCTGTAAACAAATATAAGAG 59.013 37.037 0.00 0.00 0.00 2.85
676 723 7.041712 GCTCCCTCTGTAAACAAATATAAGAGC 60.042 40.741 0.00 0.00 33.56 4.09
677 724 7.857456 TCCCTCTGTAAACAAATATAAGAGCA 58.143 34.615 0.00 0.00 0.00 4.26
678 725 7.769044 TCCCTCTGTAAACAAATATAAGAGCAC 59.231 37.037 0.00 0.00 0.00 4.40
679 726 7.770897 CCCTCTGTAAACAAATATAAGAGCACT 59.229 37.037 0.00 0.00 0.00 4.40
680 727 9.167311 CCTCTGTAAACAAATATAAGAGCACTT 57.833 33.333 1.05 1.05 39.81 3.16
707 754 7.988904 ATCACTAAAGTAGTTATCTGAACGC 57.011 36.000 0.00 0.00 36.76 4.84
708 755 7.154435 TCACTAAAGTAGTTATCTGAACGCT 57.846 36.000 0.00 0.00 36.76 5.07
709 756 7.249147 TCACTAAAGTAGTTATCTGAACGCTC 58.751 38.462 0.00 0.00 36.76 5.03
710 757 7.120873 TCACTAAAGTAGTTATCTGAACGCTCT 59.879 37.037 0.00 0.00 36.76 4.09
711 758 7.755822 CACTAAAGTAGTTATCTGAACGCTCTT 59.244 37.037 0.00 0.00 36.76 2.85
712 759 8.954350 ACTAAAGTAGTTATCTGAACGCTCTTA 58.046 33.333 0.00 0.00 34.86 2.10
713 760 9.953697 CTAAAGTAGTTATCTGAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
724 771 8.336498 TCTGAACGCTCTTATATTTCTTTACG 57.664 34.615 0.00 0.00 0.00 3.18
725 772 7.434307 TCTGAACGCTCTTATATTTCTTTACGG 59.566 37.037 0.00 0.00 0.00 4.02
726 773 7.259882 TGAACGCTCTTATATTTCTTTACGGA 58.740 34.615 0.00 0.00 0.00 4.69
727 774 7.434307 TGAACGCTCTTATATTTCTTTACGGAG 59.566 37.037 0.00 0.00 0.00 4.63
728 775 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
729 776 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
730 777 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
731 778 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
732 779 7.471679 GCTCTTATATTTCTTTACGGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
733 780 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
734 781 9.425248 TCTTATATTTCTTTACGGAGGGAGTAA 57.575 33.333 0.00 0.00 32.84 2.24
738 785 7.625828 ATTTCTTTACGGAGGGAGTAATTTG 57.374 36.000 0.00 0.00 34.50 2.32
747 794 6.120220 CGGAGGGAGTAATTTGTAAAGGATT 58.880 40.000 0.00 0.00 0.00 3.01
784 831 0.102844 TTGCACAAACAAGCCTCTGC 59.897 50.000 0.00 0.00 37.95 4.26
834 1204 2.510613 ACAAAGTAAATGTGGGGTCGG 58.489 47.619 0.00 0.00 0.00 4.79
835 1205 1.816224 CAAAGTAAATGTGGGGTCGGG 59.184 52.381 0.00 0.00 0.00 5.14
856 1226 5.482006 GGGTGATTCTTCCTTTTGATTTGG 58.518 41.667 0.00 0.00 0.00 3.28
858 1228 6.239572 GGGTGATTCTTCCTTTTGATTTGGAA 60.240 38.462 0.00 0.00 38.10 3.53
883 1253 2.140717 ACCTTTCTTCTGTTAACGCCG 58.859 47.619 0.26 0.00 0.00 6.46
886 1256 3.122445 CCTTTCTTCTGTTAACGCCGTAC 59.878 47.826 0.26 0.00 0.00 3.67
926 1296 5.070981 TGAAGGCTTATATCAAGAGGTGGAG 59.929 44.000 0.00 0.00 0.00 3.86
929 1299 3.904339 GCTTATATCAAGAGGTGGAGGGA 59.096 47.826 0.00 0.00 0.00 4.20
957 1327 6.441088 AAGACTTAAGTTGTGGATTCCTCT 57.559 37.500 10.02 0.00 0.00 3.69
1076 1446 6.414732 GCCAAGCATCCAGTATATATACCAA 58.585 40.000 17.52 5.76 33.79 3.67
1077 1447 6.316390 GCCAAGCATCCAGTATATATACCAAC 59.684 42.308 17.52 0.00 33.79 3.77
1078 1448 6.823689 CCAAGCATCCAGTATATATACCAACC 59.176 42.308 17.52 4.18 33.79 3.77
1079 1449 7.394016 CAAGCATCCAGTATATATACCAACCA 58.606 38.462 17.52 0.81 33.79 3.67
1080 1450 6.947464 AGCATCCAGTATATATACCAACCAC 58.053 40.000 17.52 5.99 33.79 4.16
1081 1451 6.070194 AGCATCCAGTATATATACCAACCACC 60.070 42.308 17.52 3.82 33.79 4.61
1082 1452 5.988310 TCCAGTATATATACCAACCACCG 57.012 43.478 17.52 0.00 33.79 4.94
1090 1460 5.680594 ATATACCAACCACCGTTCTACAA 57.319 39.130 0.00 0.00 0.00 2.41
1123 1493 5.652014 CCTAAATTCTAACCAGCCACAATGA 59.348 40.000 0.00 0.00 0.00 2.57
1124 1494 6.152661 CCTAAATTCTAACCAGCCACAATGAA 59.847 38.462 0.00 0.00 0.00 2.57
1125 1495 6.610075 AAATTCTAACCAGCCACAATGAAT 57.390 33.333 0.00 0.00 0.00 2.57
1126 1496 6.610075 AATTCTAACCAGCCACAATGAATT 57.390 33.333 0.00 0.00 0.00 2.17
1127 1497 7.716799 AATTCTAACCAGCCACAATGAATTA 57.283 32.000 0.00 0.00 33.09 1.40
1128 1498 7.716799 ATTCTAACCAGCCACAATGAATTAA 57.283 32.000 0.00 0.00 0.00 1.40
1129 1499 7.716799 TTCTAACCAGCCACAATGAATTAAT 57.283 32.000 0.00 0.00 0.00 1.40
1130 1500 7.716799 TCTAACCAGCCACAATGAATTAATT 57.283 32.000 0.00 0.00 0.00 1.40
1157 1527 5.443185 AATCACCTCAACAATGTTCACAG 57.557 39.130 0.00 0.00 0.00 3.66
1161 1531 3.446873 ACCTCAACAATGTTCACAGCAAA 59.553 39.130 0.00 0.00 0.00 3.68
1182 1552 4.864916 ACATCATGAACATGCGTAGAAC 57.135 40.909 0.00 0.00 38.65 3.01
1185 1555 4.456280 TCATGAACATGCGTAGAACTCT 57.544 40.909 9.59 0.00 38.65 3.24
1193 1563 4.402793 ACATGCGTAGAACTCTACCAGAAT 59.597 41.667 10.57 0.00 44.46 2.40
1206 1576 5.994250 TCTACCAGAATATGAAAAGCTGCT 58.006 37.500 0.00 0.00 0.00 4.24
1207 1577 4.978083 ACCAGAATATGAAAAGCTGCTG 57.022 40.909 1.35 0.00 0.00 4.41
1208 1578 3.129988 ACCAGAATATGAAAAGCTGCTGC 59.870 43.478 1.35 7.62 40.05 5.25
1209 1579 3.490419 CCAGAATATGAAAAGCTGCTGCC 60.490 47.826 12.44 0.00 40.80 4.85
1210 1580 2.692041 AGAATATGAAAAGCTGCTGCCC 59.308 45.455 12.44 0.00 40.80 5.36
1216 1587 1.200948 GAAAAGCTGCTGCCCAGTTAG 59.799 52.381 12.44 0.00 43.71 2.34
1218 1589 0.035630 AAGCTGCTGCCCAGTTAGAG 60.036 55.000 12.44 0.00 43.71 2.43
1232 1603 6.142817 CCCAGTTAGAGAAAATTGTGAAACG 58.857 40.000 0.00 0.00 42.39 3.60
1283 1655 3.071786 TGGTGTTGTAAAATGTGTGCG 57.928 42.857 0.00 0.00 0.00 5.34
1321 1693 1.447838 CGTGCGGGTAGTTGCAGAT 60.448 57.895 0.00 0.00 42.68 2.90
1456 1832 4.683942 CGCCATTTCCATTTCCATTTCCAT 60.684 41.667 0.00 0.00 0.00 3.41
1457 1833 5.195185 GCCATTTCCATTTCCATTTCCATT 58.805 37.500 0.00 0.00 0.00 3.16
1458 1834 5.653330 GCCATTTCCATTTCCATTTCCATTT 59.347 36.000 0.00 0.00 0.00 2.32
1459 1835 6.183360 GCCATTTCCATTTCCATTTCCATTTC 60.183 38.462 0.00 0.00 0.00 2.17
1460 1836 6.319405 CCATTTCCATTTCCATTTCCATTTCC 59.681 38.462 0.00 0.00 0.00 3.13
1461 1837 6.445451 TTTCCATTTCCATTTCCATTTCCA 57.555 33.333 0.00 0.00 0.00 3.53
1492 1868 0.298707 CAATTCTCCATCGTGACGCG 59.701 55.000 3.53 3.53 43.01 6.01
1626 2002 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1627 2003 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1628 2004 2.018086 AGGAGGAGGAGGAGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
1629 2005 2.612251 GAGGAGGAGGAGGAGGGG 59.388 72.222 0.00 0.00 0.00 4.79
1630 2006 3.039526 AGGAGGAGGAGGAGGGGG 61.040 72.222 0.00 0.00 0.00 5.40
1631 2007 3.036959 GGAGGAGGAGGAGGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
1923 2658 4.778415 CGCTGCTCGCTGGTACGT 62.778 66.667 0.00 0.00 36.13 3.57
1941 2676 3.351020 CGTACATACGGGGAGAAGAAG 57.649 52.381 3.47 0.00 45.30 2.85
2058 2824 0.899019 ACGTTGTTTGTTTTGGGCCT 59.101 45.000 4.53 0.00 0.00 5.19
2062 2828 0.107945 TGTTTGTTTTGGGCCTGTGC 60.108 50.000 4.53 0.00 0.00 4.57
2076 2842 1.227823 TGTGCTTGGAACCGACTGG 60.228 57.895 0.00 0.00 42.84 4.00
2091 2857 3.247648 CCGACTGGTTTTAGAAGTGTGTG 59.752 47.826 0.00 0.00 0.00 3.82
2159 2940 9.199982 GCTTAGCGTGTGTTATTATCCTTATTA 57.800 33.333 0.00 0.00 0.00 0.98
2240 3024 5.362105 AAGTTCACCTATATTTGGGCGTA 57.638 39.130 0.51 0.00 0.00 4.42
2259 3043 6.091437 GGCGTATCTATAACTCGCTTATTGT 58.909 40.000 7.69 0.00 45.01 2.71
2272 3056 3.119884 CGCTTATTGTGAGGTGCATTTCA 60.120 43.478 0.00 0.00 0.00 2.69
2285 3069 1.394917 GCATTTCACGCTCACCTACAG 59.605 52.381 0.00 0.00 0.00 2.74
2290 3074 0.599991 CACGCTCACCTACAGCACAA 60.600 55.000 0.00 0.00 36.61 3.33
2291 3075 0.321671 ACGCTCACCTACAGCACAAT 59.678 50.000 0.00 0.00 36.61 2.71
2292 3076 0.723414 CGCTCACCTACAGCACAATG 59.277 55.000 0.00 0.00 36.61 2.82
2311 3095 4.927782 GACATATGGGCCGGCGCA 62.928 66.667 43.00 43.00 42.90 6.09
2347 3321 1.002684 CGGTAGCGTCTCACATCTACC 60.003 57.143 6.07 7.11 44.61 3.18
2356 3330 6.258727 AGCGTCTCACATCTACCATTAATTTG 59.741 38.462 0.00 0.00 0.00 2.32
2361 3335 5.645929 TCACATCTACCATTAATTTGCACGT 59.354 36.000 0.00 0.00 0.00 4.49
2362 3336 5.965334 CACATCTACCATTAATTTGCACGTC 59.035 40.000 0.00 0.00 0.00 4.34
2363 3337 5.880332 ACATCTACCATTAATTTGCACGTCT 59.120 36.000 0.00 0.00 0.00 4.18
2364 3338 7.011016 CACATCTACCATTAATTTGCACGTCTA 59.989 37.037 0.00 0.00 0.00 2.59
2367 3341 5.950758 ACCATTAATTTGCACGTCTACAA 57.049 34.783 0.00 0.00 0.00 2.41
2372 3346 7.360522 CCATTAATTTGCACGTCTACAAGTGTA 60.361 37.037 0.00 0.00 40.26 2.90
2391 3365 4.030306 GTGTATCTAGTGTTGTTCGCTTCG 59.970 45.833 0.00 0.00 38.01 3.79
2421 3395 9.553064 GATCATTGTCTATATGAGAAGTGGTTT 57.447 33.333 0.00 0.00 35.63 3.27
2434 3408 7.004086 TGAGAAGTGGTTTGATGGTTAAGAAT 58.996 34.615 0.00 0.00 0.00 2.40
2450 3426 6.374333 GGTTAAGAATGCAGTGATACTTCCAA 59.626 38.462 0.00 0.00 0.00 3.53
2456 3432 3.245229 TGCAGTGATACTTCCAACCCATT 60.245 43.478 0.00 0.00 0.00 3.16
2486 3462 0.521735 CCCTAGGTTTGACGCTTTGC 59.478 55.000 8.29 0.00 0.00 3.68
2501 3477 3.363378 CGCTTTGCTATCTCATAAAGGCG 60.363 47.826 0.00 0.00 32.30 5.52
2503 3479 4.380531 CTTTGCTATCTCATAAAGGCGGA 58.619 43.478 0.00 0.00 0.00 5.54
2509 3485 3.917329 TCTCATAAAGGCGGACTATCG 57.083 47.619 0.00 0.00 0.00 2.92
2525 3501 0.613260 ATCGCTCAGCAAGGGTAACA 59.387 50.000 0.00 0.00 38.97 2.41
2534 3510 1.129811 GCAAGGGTAACATTTCCGTCG 59.870 52.381 0.00 0.00 39.57 5.12
2561 3537 3.826754 CGCTAGCCGGCTCAGTCA 61.827 66.667 36.73 15.02 0.00 3.41
2578 3554 6.621596 GCTCAGTCATTTGGAAGTGTTCATAC 60.622 42.308 0.00 0.00 0.00 2.39
2585 3561 4.665833 TGGAAGTGTTCATACGGATAGG 57.334 45.455 0.00 0.00 0.00 2.57
2596 3572 4.770010 TCATACGGATAGGATGTATGTGCA 59.230 41.667 10.37 0.00 43.63 4.57
2598 3574 4.623932 ACGGATAGGATGTATGTGCATT 57.376 40.909 0.00 0.00 0.00 3.56
2606 3587 4.139786 GGATGTATGTGCATTCATGAGGT 58.860 43.478 8.63 0.00 30.49 3.85
2640 3621 9.506018 TGCATATAGTTTATGAGCATATGTGTT 57.494 29.630 4.29 0.00 33.86 3.32
2651 3632 7.075674 TGAGCATATGTGTTTGTTCTGTATG 57.924 36.000 4.29 0.00 0.00 2.39
2662 3643 9.221775 GTGTTTGTTCTGTATGTCTACAAAAAG 57.778 33.333 0.00 0.00 39.53 2.27
2694 3686 6.551736 AGTATGTTTTCAACCGTCAATATGC 58.448 36.000 0.00 0.00 0.00 3.14
2696 3688 5.188327 TGTTTTCAACCGTCAATATGCAA 57.812 34.783 0.00 0.00 0.00 4.08
2705 3708 2.285026 CGTCAATATGCAAGTCGGTTCG 60.285 50.000 0.00 0.00 0.00 3.95
2709 3712 4.214545 TCAATATGCAAGTCGGTTCGTTTT 59.785 37.500 0.00 0.00 0.00 2.43
2710 3713 4.759516 ATATGCAAGTCGGTTCGTTTTT 57.240 36.364 0.00 0.00 0.00 1.94
2860 3868 9.743057 TTACACAATTTTAAGAAATCACACCTG 57.257 29.630 0.00 0.00 34.44 4.00
2861 3869 8.006298 ACACAATTTTAAGAAATCACACCTGA 57.994 30.769 0.00 0.00 34.44 3.86
2862 3870 8.641541 ACACAATTTTAAGAAATCACACCTGAT 58.358 29.630 0.00 0.00 38.94 2.90
2869 3877 6.748333 AAGAAATCACACCTGATACATGTG 57.252 37.500 9.11 0.00 44.14 3.21
2873 3881 3.272581 TCACACCTGATACATGTGCATG 58.727 45.455 9.11 10.31 42.80 4.06
2893 3901 6.017852 TGCATGTCGTGTAAAGTTATTCACAA 60.018 34.615 0.00 0.00 0.00 3.33
2894 3902 6.519761 GCATGTCGTGTAAAGTTATTCACAAG 59.480 38.462 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.302949 GTGGGAATGTGGCCAGCTA 59.697 57.895 5.11 0.00 0.00 3.32
24 25 2.914908 GCGCAAACGGTGGGAATGT 61.915 57.895 0.30 0.00 42.76 2.71
25 26 2.126502 GCGCAAACGGTGGGAATG 60.127 61.111 0.30 0.00 42.76 2.67
35 36 1.797025 AACTAGTCTGGAGCGCAAAC 58.203 50.000 11.47 0.00 0.00 2.93
75 76 1.909532 CGTTTCGACACGTACCAGATC 59.090 52.381 15.68 0.00 35.34 2.75
164 165 4.157660 GGGGGAAATGGGAGGCCC 62.158 72.222 0.00 0.00 45.71 5.80
166 167 1.685765 GTTGGGGGAAATGGGAGGC 60.686 63.158 0.00 0.00 0.00 4.70
170 171 1.304891 TCCTAGTTGGGGGAAATGGG 58.695 55.000 0.00 0.00 36.20 4.00
301 330 2.233271 CAACCAAGGACAATCAGCAGT 58.767 47.619 0.00 0.00 0.00 4.40
305 334 2.787994 AGAGCAACCAAGGACAATCAG 58.212 47.619 0.00 0.00 0.00 2.90
330 359 5.758784 GCTCACATACCTTAGGAACCAATAC 59.241 44.000 4.77 0.00 0.00 1.89
357 386 5.587388 AAGTAGCCACCATCAATGAAATG 57.413 39.130 0.00 0.00 0.00 2.32
374 404 9.862371 ATACACAAGTAGATTCAGACAAAGTAG 57.138 33.333 0.00 0.00 32.86 2.57
377 407 7.413438 GCCATACACAAGTAGATTCAGACAAAG 60.413 40.741 0.00 0.00 32.86 2.77
399 429 2.651455 CACCATCAATCTGTCTGCCAT 58.349 47.619 0.00 0.00 0.00 4.40
426 456 9.414295 GAACAGATTGAAACAATTCATCAATGA 57.586 29.630 12.28 0.00 44.70 2.57
427 457 9.198837 TGAACAGATTGAAACAATTCATCAATG 57.801 29.630 12.28 5.88 44.70 2.82
429 459 9.767228 AATGAACAGATTGAAACAATTCATCAA 57.233 25.926 9.74 0.00 44.70 2.57
430 460 9.414295 GAATGAACAGATTGAAACAATTCATCA 57.586 29.630 9.74 7.82 44.70 3.07
431 461 9.635520 AGAATGAACAGATTGAAACAATTCATC 57.364 29.630 9.74 6.09 44.70 2.92
469 515 8.650143 ACCCAGATAATGTGTAGAAAACAAAT 57.350 30.769 0.00 0.00 40.63 2.32
475 521 7.054124 GGATTGACCCAGATAATGTGTAGAAA 58.946 38.462 0.00 0.00 0.00 2.52
476 522 6.386927 AGGATTGACCCAGATAATGTGTAGAA 59.613 38.462 0.00 0.00 40.05 2.10
503 549 7.674120 TGGTTGAGATATCTCTACATTCCATG 58.326 38.462 33.51 0.00 45.92 3.66
525 572 6.186957 TCATGGATTTGCTATAAGTGTTGGT 58.813 36.000 0.00 0.00 0.00 3.67
530 577 4.217118 GGGCTCATGGATTTGCTATAAGTG 59.783 45.833 0.00 0.00 0.00 3.16
534 581 2.988859 AGGGGCTCATGGATTTGCTATA 59.011 45.455 0.00 0.00 0.00 1.31
559 606 2.150397 GGTAACTACCGCTGCTATGG 57.850 55.000 0.00 0.00 36.50 2.74
570 617 7.546667 TCTTCGGAATGTAATGTTGGTAACTAC 59.453 37.037 0.00 0.00 43.07 2.73
571 618 7.613585 TCTTCGGAATGTAATGTTGGTAACTA 58.386 34.615 0.00 0.00 37.61 2.24
573 620 6.730960 TCTTCGGAATGTAATGTTGGTAAC 57.269 37.500 0.00 0.00 0.00 2.50
577 624 6.677913 AGTTTTCTTCGGAATGTAATGTTGG 58.322 36.000 0.00 0.00 33.58 3.77
583 630 7.517734 CGTCTGAAAGTTTTCTTCGGAATGTAA 60.518 37.037 6.21 0.00 39.48 2.41
586 633 5.140177 CGTCTGAAAGTTTTCTTCGGAATG 58.860 41.667 6.21 0.00 39.48 2.67
591 638 2.349532 GCCCGTCTGAAAGTTTTCTTCG 60.350 50.000 6.21 7.54 39.48 3.79
608 655 1.134175 ACAACTTGTGAAAACAGCCCG 59.866 47.619 0.00 0.00 0.00 6.13
650 697 7.041712 GCTCTTATATTTGTTTACAGAGGGAGC 60.042 40.741 0.00 0.00 33.61 4.70
651 698 7.987458 TGCTCTTATATTTGTTTACAGAGGGAG 59.013 37.037 0.00 0.00 0.00 4.30
653 700 7.770897 AGTGCTCTTATATTTGTTTACAGAGGG 59.229 37.037 0.00 0.00 0.00 4.30
654 701 8.723942 AGTGCTCTTATATTTGTTTACAGAGG 57.276 34.615 0.00 0.00 0.00 3.69
681 728 9.680315 GCGTTCAGATAACTACTTTAGTGATAT 57.320 33.333 0.00 0.00 39.39 1.63
682 729 8.900781 AGCGTTCAGATAACTACTTTAGTGATA 58.099 33.333 0.00 0.00 39.39 2.15
683 730 7.773149 AGCGTTCAGATAACTACTTTAGTGAT 58.227 34.615 0.00 0.00 39.39 3.06
684 731 7.120873 AGAGCGTTCAGATAACTACTTTAGTGA 59.879 37.037 1.01 0.00 39.39 3.41
685 732 7.251994 AGAGCGTTCAGATAACTACTTTAGTG 58.748 38.462 1.01 0.00 39.39 2.74
686 733 7.393841 AGAGCGTTCAGATAACTACTTTAGT 57.606 36.000 1.01 0.00 41.73 2.24
687 734 9.953697 ATAAGAGCGTTCAGATAACTACTTTAG 57.046 33.333 1.01 0.00 0.00 1.85
698 745 8.969267 CGTAAAGAAATATAAGAGCGTTCAGAT 58.031 33.333 1.01 0.00 0.00 2.90
699 746 7.434307 CCGTAAAGAAATATAAGAGCGTTCAGA 59.566 37.037 1.01 0.00 0.00 3.27
700 747 7.434307 TCCGTAAAGAAATATAAGAGCGTTCAG 59.566 37.037 1.01 0.00 0.00 3.02
701 748 7.259882 TCCGTAAAGAAATATAAGAGCGTTCA 58.740 34.615 1.01 0.00 0.00 3.18
702 749 7.096147 CCTCCGTAAAGAAATATAAGAGCGTTC 60.096 40.741 0.00 0.00 0.00 3.95
703 750 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
704 751 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
705 752 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
706 753 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
707 754 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
708 755 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
712 759 9.338622 CAAATTACTCCCTCCGTAAAGAAATAT 57.661 33.333 0.00 0.00 31.36 1.28
713 760 8.323567 ACAAATTACTCCCTCCGTAAAGAAATA 58.676 33.333 0.00 0.00 31.36 1.40
714 761 7.173032 ACAAATTACTCCCTCCGTAAAGAAAT 58.827 34.615 0.00 0.00 31.36 2.17
715 762 6.536447 ACAAATTACTCCCTCCGTAAAGAAA 58.464 36.000 0.00 0.00 31.36 2.52
716 763 6.117975 ACAAATTACTCCCTCCGTAAAGAA 57.882 37.500 0.00 0.00 31.36 2.52
717 764 5.750352 ACAAATTACTCCCTCCGTAAAGA 57.250 39.130 0.00 0.00 31.36 2.52
718 765 7.065443 CCTTTACAAATTACTCCCTCCGTAAAG 59.935 40.741 0.00 0.00 41.77 1.85
719 766 6.880529 CCTTTACAAATTACTCCCTCCGTAAA 59.119 38.462 0.00 0.00 31.36 2.01
720 767 6.213195 TCCTTTACAAATTACTCCCTCCGTAA 59.787 38.462 0.00 0.00 0.00 3.18
721 768 5.721000 TCCTTTACAAATTACTCCCTCCGTA 59.279 40.000 0.00 0.00 0.00 4.02
722 769 4.533311 TCCTTTACAAATTACTCCCTCCGT 59.467 41.667 0.00 0.00 0.00 4.69
723 770 5.093849 TCCTTTACAAATTACTCCCTCCG 57.906 43.478 0.00 0.00 0.00 4.63
724 771 6.183360 GCAATCCTTTACAAATTACTCCCTCC 60.183 42.308 0.00 0.00 0.00 4.30
725 772 6.377146 TGCAATCCTTTACAAATTACTCCCTC 59.623 38.462 0.00 0.00 0.00 4.30
726 773 6.252995 TGCAATCCTTTACAAATTACTCCCT 58.747 36.000 0.00 0.00 0.00 4.20
727 774 6.524101 TGCAATCCTTTACAAATTACTCCC 57.476 37.500 0.00 0.00 0.00 4.30
728 775 7.702348 GTGATGCAATCCTTTACAAATTACTCC 59.298 37.037 0.00 0.00 44.73 3.85
729 776 8.243426 TGTGATGCAATCCTTTACAAATTACTC 58.757 33.333 0.00 0.00 44.73 2.59
730 777 8.121305 TGTGATGCAATCCTTTACAAATTACT 57.879 30.769 0.00 0.00 44.73 2.24
731 778 8.931385 ATGTGATGCAATCCTTTACAAATTAC 57.069 30.769 0.00 0.00 44.73 1.89
732 779 9.941325 AAATGTGATGCAATCCTTTACAAATTA 57.059 25.926 0.00 0.00 44.73 1.40
733 780 8.851541 AAATGTGATGCAATCCTTTACAAATT 57.148 26.923 0.00 0.00 44.73 1.82
734 781 8.095792 TGAAATGTGATGCAATCCTTTACAAAT 58.904 29.630 0.00 0.00 44.73 2.32
735 782 7.440198 TGAAATGTGATGCAATCCTTTACAAA 58.560 30.769 0.00 0.00 44.73 2.83
736 783 6.990798 TGAAATGTGATGCAATCCTTTACAA 58.009 32.000 0.00 0.00 44.73 2.41
737 784 6.587206 TGAAATGTGATGCAATCCTTTACA 57.413 33.333 0.00 0.00 44.73 2.41
738 785 7.546667 ACAATGAAATGTGATGCAATCCTTTAC 59.453 33.333 0.00 0.00 44.73 2.01
747 794 4.211584 GTGCAAACAATGAAATGTGATGCA 59.788 37.500 13.69 13.69 46.17 3.96
777 824 1.337071 CCAATGTCATCATGCAGAGGC 59.663 52.381 0.00 0.00 41.68 4.70
834 1204 6.345096 TCCAAATCAAAAGGAAGAATCACC 57.655 37.500 0.00 0.00 0.00 4.02
835 1205 8.661352 TTTTCCAAATCAAAAGGAAGAATCAC 57.339 30.769 0.00 0.00 41.97 3.06
856 1226 7.325338 GGCGTTAACAGAAGAAAGGTTATTTTC 59.675 37.037 6.39 0.00 37.34 2.29
858 1228 6.567132 CGGCGTTAACAGAAGAAAGGTTATTT 60.567 38.462 6.39 0.00 0.00 1.40
912 1282 3.199442 TGTTCCCTCCACCTCTTGATA 57.801 47.619 0.00 0.00 0.00 2.15
926 1296 5.358725 TCCACAACTTAAGTCTTTTGTTCCC 59.641 40.000 8.95 0.00 29.65 3.97
929 1299 7.342026 AGGAATCCACAACTTAAGTCTTTTGTT 59.658 33.333 8.95 1.09 29.65 2.83
1060 1430 5.396485 ACGGTGGTTGGTATATATACTGGA 58.604 41.667 19.78 6.18 33.81 3.86
1064 1434 7.885297 TGTAGAACGGTGGTTGGTATATATAC 58.115 38.462 13.60 13.60 36.24 1.47
1067 1437 6.788598 TTGTAGAACGGTGGTTGGTATATA 57.211 37.500 0.00 0.00 36.24 0.86
1069 1439 5.187381 TGATTGTAGAACGGTGGTTGGTATA 59.813 40.000 0.00 0.00 36.24 1.47
1070 1440 4.020039 TGATTGTAGAACGGTGGTTGGTAT 60.020 41.667 0.00 0.00 36.24 2.73
1071 1441 3.324268 TGATTGTAGAACGGTGGTTGGTA 59.676 43.478 0.00 0.00 36.24 3.25
1072 1442 2.105134 TGATTGTAGAACGGTGGTTGGT 59.895 45.455 0.00 0.00 36.24 3.67
1076 1446 4.007659 GGATTTGATTGTAGAACGGTGGT 58.992 43.478 0.00 0.00 0.00 4.16
1077 1447 3.377172 GGGATTTGATTGTAGAACGGTGG 59.623 47.826 0.00 0.00 0.00 4.61
1078 1448 3.377172 GGGGATTTGATTGTAGAACGGTG 59.623 47.826 0.00 0.00 0.00 4.94
1079 1449 3.265995 AGGGGATTTGATTGTAGAACGGT 59.734 43.478 0.00 0.00 0.00 4.83
1080 1450 3.886123 AGGGGATTTGATTGTAGAACGG 58.114 45.455 0.00 0.00 0.00 4.44
1081 1451 6.995511 TTTAGGGGATTTGATTGTAGAACG 57.004 37.500 0.00 0.00 0.00 3.95
1082 1452 9.190317 AGAATTTAGGGGATTTGATTGTAGAAC 57.810 33.333 0.00 0.00 0.00 3.01
1090 1460 6.551227 GCTGGTTAGAATTTAGGGGATTTGAT 59.449 38.462 0.00 0.00 0.00 2.57
1129 1499 9.906660 GTGAACATTGTTGAGGTGATTAATTAA 57.093 29.630 6.80 0.00 0.00 1.40
1130 1500 9.072375 TGTGAACATTGTTGAGGTGATTAATTA 57.928 29.630 6.80 0.00 0.00 1.40
1137 1507 2.618241 GCTGTGAACATTGTTGAGGTGA 59.382 45.455 6.80 0.00 0.00 4.02
1142 1512 4.446994 TGTTTGCTGTGAACATTGTTGA 57.553 36.364 6.80 0.00 32.44 3.18
1143 1513 4.804665 TGATGTTTGCTGTGAACATTGTTG 59.195 37.500 6.80 0.00 45.11 3.33
1150 1520 4.609947 TGTTCATGATGTTTGCTGTGAAC 58.390 39.130 0.00 8.61 43.32 3.18
1157 1527 2.598589 ACGCATGTTCATGATGTTTGC 58.401 42.857 15.74 3.42 0.00 3.68
1161 1531 4.507710 AGTTCTACGCATGTTCATGATGT 58.492 39.130 15.74 14.06 0.00 3.06
1182 1552 6.018098 CAGCAGCTTTTCATATTCTGGTAGAG 60.018 42.308 0.00 0.00 34.26 2.43
1185 1555 4.336433 GCAGCAGCTTTTCATATTCTGGTA 59.664 41.667 0.00 0.00 37.91 3.25
1193 1563 1.272092 ACTGGGCAGCAGCTTTTCATA 60.272 47.619 0.00 0.00 41.70 2.15
1206 1576 4.724399 TCACAATTTTCTCTAACTGGGCA 58.276 39.130 0.00 0.00 0.00 5.36
1207 1577 5.705609 TTCACAATTTTCTCTAACTGGGC 57.294 39.130 0.00 0.00 0.00 5.36
1208 1578 6.017440 TCGTTTCACAATTTTCTCTAACTGGG 60.017 38.462 0.00 0.00 0.00 4.45
1209 1579 6.954944 TCGTTTCACAATTTTCTCTAACTGG 58.045 36.000 0.00 0.00 0.00 4.00
1210 1580 8.835467 TTTCGTTTCACAATTTTCTCTAACTG 57.165 30.769 0.00 0.00 0.00 3.16
1216 1587 6.198966 ACTGCATTTCGTTTCACAATTTTCTC 59.801 34.615 0.00 0.00 0.00 2.87
1218 1589 6.272698 ACTGCATTTCGTTTCACAATTTTC 57.727 33.333 0.00 0.00 0.00 2.29
1232 1603 4.886579 ACTTTCCATTCCAACTGCATTTC 58.113 39.130 0.00 0.00 0.00 2.17
1283 1655 1.627879 CACACAACAACACACAAGGC 58.372 50.000 0.00 0.00 0.00 4.35
1321 1693 1.762460 GATCTCCGGCTCCTTGGGA 60.762 63.158 0.00 0.00 0.00 4.37
1456 1832 2.940994 TTGGAGATTCACGGTGGAAA 57.059 45.000 8.50 0.00 0.00 3.13
1457 1833 3.009033 AGAATTGGAGATTCACGGTGGAA 59.991 43.478 8.50 2.10 0.00 3.53
1458 1834 2.571653 AGAATTGGAGATTCACGGTGGA 59.428 45.455 8.50 0.00 0.00 4.02
1459 1835 2.939103 GAGAATTGGAGATTCACGGTGG 59.061 50.000 8.50 0.00 0.00 4.61
1460 1836 2.939103 GGAGAATTGGAGATTCACGGTG 59.061 50.000 0.56 0.56 0.00 4.94
1461 1837 2.571653 TGGAGAATTGGAGATTCACGGT 59.428 45.455 2.07 0.00 0.00 4.83
1670 2046 2.362632 CCCTTCCCTCTCGTCCGT 60.363 66.667 0.00 0.00 0.00 4.69
1922 2657 2.694109 AGCTTCTTCTCCCCGTATGTAC 59.306 50.000 0.00 0.00 0.00 2.90
1923 2658 3.028094 AGCTTCTTCTCCCCGTATGTA 57.972 47.619 0.00 0.00 0.00 2.29
2039 2805 0.899019 AGGCCCAAAACAAACAACGT 59.101 45.000 0.00 0.00 0.00 3.99
2058 2824 1.227823 CCAGTCGGTTCCAAGCACA 60.228 57.895 0.00 0.00 0.00 4.57
2076 2842 5.086058 CACACACACACACACTTCTAAAAC 58.914 41.667 0.00 0.00 0.00 2.43
2086 2852 3.194062 CATCTACACACACACACACACA 58.806 45.455 0.00 0.00 0.00 3.72
2087 2853 3.001228 CACATCTACACACACACACACAC 59.999 47.826 0.00 0.00 0.00 3.82
2088 2854 3.194062 CACATCTACACACACACACACA 58.806 45.455 0.00 0.00 0.00 3.72
2089 2855 2.543848 CCACATCTACACACACACACAC 59.456 50.000 0.00 0.00 0.00 3.82
2091 2857 3.106242 TCCACATCTACACACACACAC 57.894 47.619 0.00 0.00 0.00 3.82
2208 2990 9.474920 CAAATATAGGTGAACTTTTTGCTCAAA 57.525 29.630 0.00 0.00 0.00 2.69
2210 2992 7.309744 CCCAAATATAGGTGAACTTTTTGCTCA 60.310 37.037 0.00 0.00 0.00 4.26
2212 2994 6.574269 GCCCAAATATAGGTGAACTTTTTGCT 60.574 38.462 0.00 0.00 0.00 3.91
2213 2995 5.580691 GCCCAAATATAGGTGAACTTTTTGC 59.419 40.000 0.00 0.00 0.00 3.68
2214 2996 5.804979 CGCCCAAATATAGGTGAACTTTTTG 59.195 40.000 0.00 0.00 35.58 2.44
2215 2997 5.479027 ACGCCCAAATATAGGTGAACTTTTT 59.521 36.000 6.86 0.00 37.10 1.94
2217 2999 4.595986 ACGCCCAAATATAGGTGAACTTT 58.404 39.130 6.86 0.00 37.10 2.66
2218 3000 4.230745 ACGCCCAAATATAGGTGAACTT 57.769 40.909 6.86 0.00 37.10 2.66
2219 3001 3.926058 ACGCCCAAATATAGGTGAACT 57.074 42.857 6.86 0.00 37.10 3.01
2221 3003 5.818678 AGATACGCCCAAATATAGGTGAA 57.181 39.130 6.86 0.00 37.10 3.18
2222 3004 8.472413 GTTATAGATACGCCCAAATATAGGTGA 58.528 37.037 6.86 0.00 37.10 4.02
2224 3006 8.605325 AGTTATAGATACGCCCAAATATAGGT 57.395 34.615 0.00 0.00 0.00 3.08
2225 3007 7.861372 CGAGTTATAGATACGCCCAAATATAGG 59.139 40.741 0.00 0.00 0.00 2.57
2226 3008 7.378995 GCGAGTTATAGATACGCCCAAATATAG 59.621 40.741 0.00 0.00 42.79 1.31
2227 3009 7.198390 GCGAGTTATAGATACGCCCAAATATA 58.802 38.462 0.00 0.00 42.79 0.86
2228 3010 6.040878 GCGAGTTATAGATACGCCCAAATAT 58.959 40.000 0.00 0.00 42.79 1.28
2229 3011 5.404946 GCGAGTTATAGATACGCCCAAATA 58.595 41.667 0.00 0.00 42.79 1.40
2230 3012 4.243270 GCGAGTTATAGATACGCCCAAAT 58.757 43.478 0.00 0.00 42.79 2.32
2231 3013 3.645884 GCGAGTTATAGATACGCCCAAA 58.354 45.455 0.00 0.00 42.79 3.28
2240 3024 7.148641 CACCTCACAATAAGCGAGTTATAGAT 58.851 38.462 0.00 0.00 30.55 1.98
2272 3056 0.321671 ATTGTGCTGTAGGTGAGCGT 59.678 50.000 0.00 0.00 39.47 5.07
2285 3069 0.318107 GCCCATATGTCGCATTGTGC 60.318 55.000 1.24 0.00 40.69 4.57
2290 3074 2.032528 CCGGCCCATATGTCGCAT 59.967 61.111 12.56 0.00 0.00 4.73
2291 3075 4.927782 GCCGGCCCATATGTCGCA 62.928 66.667 18.11 0.00 0.00 5.10
2319 3103 0.867753 GAGACGCTACCGCATGAGTG 60.868 60.000 0.00 0.00 38.22 3.51
2322 3106 1.138883 GTGAGACGCTACCGCATGA 59.861 57.895 0.00 0.00 38.22 3.07
2330 3114 6.650427 ATTAATGGTAGATGTGAGACGCTA 57.350 37.500 0.00 0.00 0.00 4.26
2347 3321 6.370593 ACACTTGTAGACGTGCAAATTAATG 58.629 36.000 0.00 0.00 34.58 1.90
2356 3330 5.029014 CACTAGATACACTTGTAGACGTGC 58.971 45.833 0.00 0.00 33.69 5.34
2361 3335 7.303261 CGAACAACACTAGATACACTTGTAGA 58.697 38.462 0.00 0.00 33.69 2.59
2362 3336 6.033619 GCGAACAACACTAGATACACTTGTAG 59.966 42.308 0.00 0.00 33.69 2.74
2363 3337 5.860182 GCGAACAACACTAGATACACTTGTA 59.140 40.000 0.00 0.00 33.69 2.41
2364 3338 4.684703 GCGAACAACACTAGATACACTTGT 59.315 41.667 0.00 0.00 35.19 3.16
2367 3341 4.785511 AGCGAACAACACTAGATACACT 57.214 40.909 0.00 0.00 0.00 3.55
2372 3346 3.299340 ACGAAGCGAACAACACTAGAT 57.701 42.857 0.00 0.00 0.00 1.98
2396 3370 9.334947 CAAACCACTTCTCATATAGACAATGAT 57.665 33.333 0.00 0.00 33.08 2.45
2404 3378 9.613428 TTAACCATCAAACCACTTCTCATATAG 57.387 33.333 0.00 0.00 0.00 1.31
2421 3395 6.653020 AGTATCACTGCATTCTTAACCATCA 58.347 36.000 0.00 0.00 0.00 3.07
2434 3408 1.702401 TGGGTTGGAAGTATCACTGCA 59.298 47.619 0.00 0.00 0.00 4.41
2450 3426 4.168088 CCTAGGGTTTGATTCCTAATGGGT 59.832 45.833 0.00 0.00 35.45 4.51
2486 3462 5.574082 CGATAGTCCGCCTTTATGAGATAG 58.426 45.833 0.00 0.00 0.00 2.08
2501 3477 0.249657 CCCTTGCTGAGCGATAGTCC 60.250 60.000 0.00 0.00 39.35 3.85
2503 3479 1.776662 TACCCTTGCTGAGCGATAGT 58.223 50.000 0.00 0.85 39.35 2.12
2509 3485 2.164422 GGAAATGTTACCCTTGCTGAGC 59.836 50.000 0.00 0.00 0.00 4.26
2515 3491 2.690786 TCGACGGAAATGTTACCCTTG 58.309 47.619 0.00 0.00 0.00 3.61
2516 3492 3.622166 ATCGACGGAAATGTTACCCTT 57.378 42.857 0.00 0.00 0.00 3.95
2517 3493 3.492137 GCTATCGACGGAAATGTTACCCT 60.492 47.826 0.00 0.00 0.00 4.34
2525 3501 1.583054 GCCTTGCTATCGACGGAAAT 58.417 50.000 0.00 0.00 0.00 2.17
2547 3523 0.107703 CCAAATGACTGAGCCGGCTA 60.108 55.000 32.97 14.88 0.00 3.93
2561 3537 6.055588 CCTATCCGTATGAACACTTCCAAAT 58.944 40.000 0.00 0.00 0.00 2.32
2578 3554 4.568956 TGAATGCACATACATCCTATCCG 58.431 43.478 0.00 0.00 0.00 4.18
2585 3561 4.818005 TCACCTCATGAATGCACATACATC 59.182 41.667 0.00 0.00 33.02 3.06
2640 3621 8.999431 GGATCTTTTTGTAGACATACAGAACAA 58.001 33.333 0.00 0.00 42.72 2.83
2682 3674 1.066430 ACCGACTTGCATATTGACGGT 60.066 47.619 15.48 15.48 45.51 4.83
2683 3675 1.651987 ACCGACTTGCATATTGACGG 58.348 50.000 14.55 14.55 43.61 4.79
2864 3872 3.811722 ACTTTACACGACATGCACATG 57.188 42.857 9.06 9.06 44.15 3.21
2869 3877 5.922546 TGTGAATAACTTTACACGACATGC 58.077 37.500 0.00 0.00 36.25 4.06
2873 3881 8.831000 AAAACTTGTGAATAACTTTACACGAC 57.169 30.769 0.00 0.00 36.25 4.34


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

AutoCloner maintained by Alex Coulton.