Multiple sequence alignment - TraesCS1B01G068500

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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 TraesCS1B01G068500 chr1B 100.000 3029 0 0 1 3029 53246502 53249530 0.000000e+00 5594.0
1 TraesCS1B01G068500 chr1B 80.791 177 34 0 491 667 686827441 686827617 4.070000e-29 139.0
2 TraesCS1B01G068500 chr1D 92.345 1450 59 18 924 2366 34943127 34944531 0.000000e+00 2015.0
3 TraesCS1B01G068500 chr1D 94.131 443 17 5 668 1105 211216338 211215900 0.000000e+00 665.0
4 TraesCS1B01G068500 chr1D 94.970 338 13 2 2693 3029 34944898 34945232 7.440000e-146 527.0
5 TraesCS1B01G068500 chr1D 93.117 247 12 2 244 489 211216573 211216331 1.030000e-94 357.0
6 TraesCS1B01G068500 chr1D 100.000 58 0 0 1103 1160 211215923 211215866 1.150000e-19 108.0
7 TraesCS1B01G068500 chr1A 88.466 789 58 12 1535 2316 33372441 33373203 0.000000e+00 922.0
8 TraesCS1B01G068500 chr1A 87.755 539 35 9 924 1458 33371712 33372223 4.320000e-168 601.0
9 TraesCS1B01G068500 chr1A 93.629 361 22 1 2670 3029 33373462 33373822 3.440000e-149 538.0
10 TraesCS1B01G068500 chr1A 83.871 341 36 9 156 489 565236290 565236618 1.050000e-79 307.0
11 TraesCS1B01G068500 chr1A 87.611 226 19 7 668 893 33371510 33371726 1.390000e-63 254.0
12 TraesCS1B01G068500 chr1A 81.991 211 23 10 668 878 565236611 565236806 6.720000e-37 165.0
13 TraesCS1B01G068500 chr4D 92.623 488 30 3 3 489 189517732 189518214 0.000000e+00 697.0
14 TraesCS1B01G068500 chr4D 92.551 443 24 5 668 1105 189518207 189518645 7.130000e-176 627.0
15 TraesCS1B01G068500 chr4D 96.552 58 2 0 1103 1160 189518622 189518679 2.490000e-16 97.1
16 TraesCS1B01G068500 chrUn 93.023 473 27 3 18 489 104824783 104825250 0.000000e+00 686.0
17 TraesCS1B01G068500 chr7D 93.023 473 27 3 18 489 569721682 569721215 0.000000e+00 686.0
18 TraesCS1B01G068500 chr7D 93.483 445 17 7 668 1105 569721222 569720783 0.000000e+00 651.0
19 TraesCS1B01G068500 chr7D 100.000 58 0 0 1103 1160 569720806 569720749 1.150000e-19 108.0
20 TraesCS1B01G068500 chr6B 91.543 473 34 3 18 489 501361816 501361349 0.000000e+00 647.0
21 TraesCS1B01G068500 chr6B 89.868 454 25 9 668 1105 501361356 501360908 5.670000e-157 564.0
22 TraesCS1B01G068500 chr6B 91.379 174 15 0 491 664 500892029 500892202 3.900000e-59 239.0
23 TraesCS1B01G068500 chr6B 100.000 58 0 0 1103 1160 501360931 501360874 1.150000e-19 108.0
24 TraesCS1B01G068500 chr2B 90.682 440 27 7 670 1105 216213115 216213544 9.420000e-160 573.0
25 TraesCS1B01G068500 chr2B 100.000 58 0 0 1103 1160 216213521 216213578 1.150000e-19 108.0
26 TraesCS1B01G068500 chr3B 84.320 338 34 10 159 489 806385241 806384916 2.270000e-81 313.0
27 TraesCS1B01G068500 chr3B 84.071 339 34 10 159 489 220473272 220472946 2.930000e-80 309.0
28 TraesCS1B01G068500 chr6A 83.578 341 37 9 156 489 596280439 596280767 4.910000e-78 302.0
29 TraesCS1B01G068500 chr6A 90.395 177 16 1 491 667 561448650 561448825 6.530000e-57 231.0
30 TraesCS1B01G068500 chr6A 87.931 174 20 1 494 667 561605241 561605069 1.420000e-48 204.0
31 TraesCS1B01G068500 chr6A 81.991 211 23 10 668 878 596280760 596280955 6.720000e-37 165.0
32 TraesCS1B01G068500 chr5B 95.288 191 7 2 485 674 92194178 92193989 4.910000e-78 302.0
33 TraesCS1B01G068500 chr5B 94.915 177 8 1 491 667 550223140 550223315 2.970000e-70 276.0
34 TraesCS1B01G068500 chr5B 81.991 211 23 11 668 878 253037453 253037258 6.720000e-37 165.0
35 TraesCS1B01G068500 chr6D 90.805 174 16 0 494 667 322589003 322588830 1.820000e-57 233.0
36 TraesCS1B01G068500 chr6D 88.950 181 19 1 488 667 369706959 369706779 3.930000e-54 222.0
37 TraesCS1B01G068500 chr3D 79.775 178 36 0 491 668 593042732 593042909 2.450000e-26 130.0


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 TraesCS1B01G068500 chr1B 53246502 53249530 3028 False 5594.000000 5594 100.000000 1 3029 1 chr1B.!!$F1 3028
1 TraesCS1B01G068500 chr1D 34943127 34945232 2105 False 1271.000000 2015 93.657500 924 3029 2 chr1D.!!$F1 2105
2 TraesCS1B01G068500 chr1D 211215866 211216573 707 True 376.666667 665 95.749333 244 1160 3 chr1D.!!$R1 916
3 TraesCS1B01G068500 chr1A 33371510 33373822 2312 False 578.750000 922 89.365250 668 3029 4 chr1A.!!$F1 2361
4 TraesCS1B01G068500 chr1A 565236290 565236806 516 False 236.000000 307 82.931000 156 878 2 chr1A.!!$F2 722
5 TraesCS1B01G068500 chr4D 189517732 189518679 947 False 473.700000 697 93.908667 3 1160 3 chr4D.!!$F1 1157
6 TraesCS1B01G068500 chr7D 569720749 569721682 933 True 481.666667 686 95.502000 18 1160 3 chr7D.!!$R1 1142
7 TraesCS1B01G068500 chr6B 501360874 501361816 942 True 439.666667 647 93.803667 18 1160 3 chr6B.!!$R1 1142
8 TraesCS1B01G068500 chr6A 596280439 596280955 516 False 233.500000 302 82.784500 156 878 2 chr6A.!!$F2 722

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
804 822 0.178932 TGGTGCTATCGGCCCTCTAT 60.179 55.0 0.0 0.0 40.92 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2605 2903 0.03213 GATGATCGCGCCACTCCTAA 59.968 55.0 0.0 0.0 0.0 2.69 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
53 54 1.012486 CCCTAGTTCGTCGTTGTGGC 61.012 60.000 0.00 0.00 0.00 5.01
64 65 2.938798 TTGTGGCAGGGTAGGGGG 60.939 66.667 0.00 0.00 0.00 5.40
86 87 2.626683 CCCCCAAATTAGCCCTTCATGT 60.627 50.000 0.00 0.00 0.00 3.21
145 146 1.803519 GGATCGATCGATGCGGCTC 60.804 63.158 33.86 19.12 33.57 4.70
149 150 2.360542 CGATCGATGCGGCTCTTCG 61.361 63.158 10.26 6.45 41.88 3.79
185 186 5.011586 GGGGTTAATTAGCCAGTGTTGTTA 58.988 41.667 18.80 0.00 46.65 2.41
223 224 7.386848 GTCAGGATGCGTAATAAGGCTAAAATA 59.613 37.037 0.00 0.00 37.40 1.40
254 255 2.023673 TGCACTTGGTTTGGTTCAGAG 58.976 47.619 0.00 0.00 0.00 3.35
286 287 4.577988 TTCTCCCCGATTGGTTAATCAA 57.422 40.909 3.09 3.09 42.27 2.57
335 340 6.179756 TGATTAGTACATGCATGTTTCACCT 58.820 36.000 35.45 23.24 41.97 4.00
478 484 6.122964 GCCCTGTTTATTTTAGTCAGAGGAT 58.877 40.000 0.00 0.00 0.00 3.24
481 487 7.995488 CCCTGTTTATTTTAGTCAGAGGATCAT 59.005 37.037 0.00 0.00 37.82 2.45
482 488 8.834465 CCTGTTTATTTTAGTCAGAGGATCATG 58.166 37.037 0.00 0.00 37.82 3.07
483 489 9.388506 CTGTTTATTTTAGTCAGAGGATCATGT 57.611 33.333 0.00 0.00 37.82 3.21
484 490 9.383519 TGTTTATTTTAGTCAGAGGATCATGTC 57.616 33.333 0.00 0.00 37.82 3.06
485 491 9.606631 GTTTATTTTAGTCAGAGGATCATGTCT 57.393 33.333 0.00 0.00 37.82 3.41
486 492 9.605275 TTTATTTTAGTCAGAGGATCATGTCTG 57.395 33.333 11.08 11.08 41.44 3.51
487 493 6.857437 TTTTAGTCAGAGGATCATGTCTGA 57.143 37.500 14.49 14.49 45.54 3.27
492 498 3.321396 TCAGAGGATCATGTCTGATGAGC 59.679 47.826 14.49 0.00 43.41 4.26
493 499 2.296752 AGAGGATCATGTCTGATGAGCG 59.703 50.000 0.00 0.00 42.27 5.03
494 500 1.343789 AGGATCATGTCTGATGAGCGG 59.656 52.381 0.00 0.00 42.27 5.52
495 501 1.146637 GATCATGTCTGATGAGCGGC 58.853 55.000 0.00 0.00 42.27 6.53
496 502 0.599466 ATCATGTCTGATGAGCGGCG 60.599 55.000 0.51 0.51 40.66 6.46
497 503 2.107750 ATGTCTGATGAGCGGCGG 59.892 61.111 9.78 0.00 0.00 6.13
498 504 2.426406 ATGTCTGATGAGCGGCGGA 61.426 57.895 9.78 0.00 0.00 5.54
499 505 2.279120 GTCTGATGAGCGGCGGAG 60.279 66.667 9.78 0.00 0.00 4.63
518 524 4.803426 CAGCTCGGCCGGTGAGAC 62.803 72.222 27.83 16.67 35.43 3.36
527 533 2.742372 CGGTGAGACGGGGCAAAG 60.742 66.667 0.00 0.00 0.00 2.77
528 534 2.430367 GGTGAGACGGGGCAAAGT 59.570 61.111 0.00 0.00 0.00 2.66
529 535 1.671379 GGTGAGACGGGGCAAAGTC 60.671 63.158 0.00 0.00 37.63 3.01
530 536 1.671379 GTGAGACGGGGCAAAGTCC 60.671 63.158 3.24 0.00 38.08 3.85
531 537 2.144078 TGAGACGGGGCAAAGTCCA 61.144 57.895 3.24 0.08 38.08 4.02
532 538 1.072505 GAGACGGGGCAAAGTCCAA 59.927 57.895 3.24 0.00 38.08 3.53
533 539 0.955919 GAGACGGGGCAAAGTCCAAG 60.956 60.000 3.24 0.00 38.08 3.61
534 540 1.072505 GACGGGGCAAAGTCCAAGA 59.927 57.895 0.00 0.00 0.00 3.02
535 541 1.228154 ACGGGGCAAAGTCCAAGAC 60.228 57.895 0.00 0.00 0.00 3.01
536 542 2.325082 CGGGGCAAAGTCCAAGACG 61.325 63.158 0.00 0.00 37.67 4.18
537 543 2.626780 GGGGCAAAGTCCAAGACGC 61.627 63.158 0.00 0.00 37.67 5.19
538 544 1.600916 GGGCAAAGTCCAAGACGCT 60.601 57.895 0.00 0.00 37.67 5.07
539 545 1.578206 GGGCAAAGTCCAAGACGCTC 61.578 60.000 0.00 0.00 37.67 5.03
540 546 1.578206 GGCAAAGTCCAAGACGCTCC 61.578 60.000 0.00 0.00 37.67 4.70
541 547 0.603975 GCAAAGTCCAAGACGCTCCT 60.604 55.000 0.00 0.00 37.67 3.69
542 548 1.151668 CAAAGTCCAAGACGCTCCTG 58.848 55.000 0.00 0.00 37.67 3.86
543 549 0.603975 AAAGTCCAAGACGCTCCTGC 60.604 55.000 0.00 0.00 37.67 4.85
544 550 2.435059 GTCCAAGACGCTCCTGCC 60.435 66.667 0.00 0.00 35.36 4.85
545 551 3.706373 TCCAAGACGCTCCTGCCC 61.706 66.667 0.00 0.00 35.36 5.36
557 563 4.341502 CTGCCCGCCGGTTGTTTG 62.342 66.667 1.90 0.00 0.00 2.93
562 568 3.679738 CGCCGGTTGTTTGCCCAT 61.680 61.111 1.90 0.00 0.00 4.00
563 569 2.048316 GCCGGTTGTTTGCCCATG 60.048 61.111 1.90 0.00 0.00 3.66
564 570 2.048316 CCGGTTGTTTGCCCATGC 60.048 61.111 0.00 0.00 38.26 4.06
574 580 3.462427 TGCCCATGCAAAATGATGC 57.538 47.368 0.00 0.00 46.66 3.91
575 581 0.906066 TGCCCATGCAAAATGATGCT 59.094 45.000 0.00 0.00 46.66 3.79
576 582 1.279558 TGCCCATGCAAAATGATGCTT 59.720 42.857 0.00 0.00 46.66 3.91
577 583 1.668751 GCCCATGCAAAATGATGCTTG 59.331 47.619 0.00 10.30 46.54 4.01
580 586 2.627945 CATGCAAAATGATGCTTGGCT 58.372 42.857 0.00 0.00 46.54 4.75
581 587 2.373540 TGCAAAATGATGCTTGGCTC 57.626 45.000 4.79 0.00 46.54 4.70
582 588 1.897133 TGCAAAATGATGCTTGGCTCT 59.103 42.857 4.79 0.00 46.54 4.09
583 589 2.300723 TGCAAAATGATGCTTGGCTCTT 59.699 40.909 4.79 0.00 46.54 2.85
584 590 2.928116 GCAAAATGATGCTTGGCTCTTC 59.072 45.455 0.00 0.00 43.06 2.87
585 591 3.615592 GCAAAATGATGCTTGGCTCTTCA 60.616 43.478 0.00 0.00 43.06 3.02
586 592 4.755411 CAAAATGATGCTTGGCTCTTCAT 58.245 39.130 0.00 0.00 0.00 2.57
587 593 5.175859 CAAAATGATGCTTGGCTCTTCATT 58.824 37.500 8.86 8.86 36.10 2.57
588 594 6.334989 CAAAATGATGCTTGGCTCTTCATTA 58.665 36.000 12.50 0.00 34.77 1.90
589 595 6.534475 AAATGATGCTTGGCTCTTCATTAA 57.466 33.333 12.50 0.00 34.77 1.40
590 596 6.726490 AATGATGCTTGGCTCTTCATTAAT 57.274 33.333 11.32 0.00 34.43 1.40
591 597 6.726490 ATGATGCTTGGCTCTTCATTAATT 57.274 33.333 0.00 0.00 0.00 1.40
592 598 7.828508 ATGATGCTTGGCTCTTCATTAATTA 57.171 32.000 0.00 0.00 0.00 1.40
593 599 7.031226 TGATGCTTGGCTCTTCATTAATTAC 57.969 36.000 0.00 0.00 0.00 1.89
594 600 6.830324 TGATGCTTGGCTCTTCATTAATTACT 59.170 34.615 0.00 0.00 0.00 2.24
595 601 7.992608 TGATGCTTGGCTCTTCATTAATTACTA 59.007 33.333 0.00 0.00 0.00 1.82
596 602 8.752005 ATGCTTGGCTCTTCATTAATTACTAA 57.248 30.769 0.00 0.00 0.00 2.24
597 603 8.752005 TGCTTGGCTCTTCATTAATTACTAAT 57.248 30.769 0.00 0.00 0.00 1.73
598 604 8.623903 TGCTTGGCTCTTCATTAATTACTAATG 58.376 33.333 0.00 0.00 45.77 1.90
617 623 7.713750 ACTAATGATCAAAGAAGAATGCATGG 58.286 34.615 13.73 0.00 0.00 3.66
618 624 4.380841 TGATCAAAGAAGAATGCATGGC 57.619 40.909 0.00 0.00 0.00 4.40
619 625 3.764972 TGATCAAAGAAGAATGCATGGCA 59.235 39.130 0.00 0.00 44.86 4.92
620 626 3.581024 TCAAAGAAGAATGCATGGCAC 57.419 42.857 0.00 0.00 43.04 5.01
621 627 2.892215 TCAAAGAAGAATGCATGGCACA 59.108 40.909 0.00 0.00 43.04 4.57
732 746 7.873719 TCTTTTACCAAGTCAAATGTTCTGA 57.126 32.000 0.00 0.00 0.00 3.27
735 749 8.925161 TTTTACCAAGTCAAATGTTCTGAAAG 57.075 30.769 0.00 0.00 0.00 2.62
764 778 1.852633 TAGTTCTGCTCTAGCTGGCA 58.147 50.000 0.00 3.43 42.66 4.92
765 779 1.202330 AGTTCTGCTCTAGCTGGCAT 58.798 50.000 10.40 0.00 42.66 4.40
766 780 2.392662 AGTTCTGCTCTAGCTGGCATA 58.607 47.619 10.40 2.66 42.66 3.14
793 811 3.370840 ACATCAATGTGGTGGTGCTAT 57.629 42.857 0.00 0.00 40.03 2.97
804 822 0.178932 TGGTGCTATCGGCCCTCTAT 60.179 55.000 0.00 0.00 40.92 1.98
816 834 2.223994 GGCCCTCTATACCGACAAGAAC 60.224 54.545 0.00 0.00 0.00 3.01
828 846 8.758633 ATACCGACAAGAACATATATTAGCAC 57.241 34.615 0.00 0.00 0.00 4.40
863 881 7.168219 ACAGTACATCATGTGTTTAGTGGAAT 58.832 34.615 0.00 0.00 42.29 3.01
908 926 6.287589 AGATTTCTGTCCTGTAATTCGAGT 57.712 37.500 0.00 0.00 0.00 4.18
1101 1128 2.862780 AGGTTACCCTCCACAGCAA 58.137 52.632 0.00 0.00 35.62 3.91
1102 1129 0.693049 AGGTTACCCTCCACAGCAAG 59.307 55.000 0.00 0.00 35.62 4.01
1103 1130 0.322546 GGTTACCCTCCACAGCAAGG 60.323 60.000 0.00 0.00 0.00 3.61
1104 1131 0.690762 GTTACCCTCCACAGCAAGGA 59.309 55.000 0.00 0.00 34.35 3.36
1111 1138 0.690762 TCCACAGCAAGGAGGTTACC 59.309 55.000 0.00 0.00 0.00 2.85
1112 1139 0.322546 CCACAGCAAGGAGGTTACCC 60.323 60.000 0.00 0.00 0.00 3.69
1113 1140 0.693049 CACAGCAAGGAGGTTACCCT 59.307 55.000 0.00 0.00 46.66 4.34
1121 1148 4.660521 AGGTTACCCTCCACAGCA 57.339 55.556 0.00 0.00 35.62 4.41
1254 1281 2.748798 GCTCCTCTCCAACATCATGCAT 60.749 50.000 0.00 0.00 0.00 3.96
1287 1314 1.001020 TCATGGTGGTGGTCATGGC 60.001 57.895 0.00 0.00 40.63 4.40
1407 1455 1.078214 TCCACAGCAGCATGGCTAC 60.078 57.895 10.32 0.00 43.68 3.58
1507 1555 2.381911 CAAAGCCATCATAGCACCCTT 58.618 47.619 0.00 0.00 0.00 3.95
1516 1564 3.873910 TCATAGCACCCTTTCTGTTAGC 58.126 45.455 0.00 0.00 0.00 3.09
1662 1710 7.174253 TGAGTGGTGGTTTATCTTGATGTTAAC 59.826 37.037 0.00 0.00 0.00 2.01
1666 1714 6.248631 GTGGTTTATCTTGATGTTAACGAGC 58.751 40.000 0.26 0.00 0.00 5.03
1685 1733 1.365699 CCCCAAGTTCGGTTGTATCG 58.634 55.000 0.00 0.00 0.00 2.92
1776 2001 4.147587 GGAGGCATGGGCATGGGT 62.148 66.667 0.00 0.00 43.71 4.51
1794 2019 4.119363 GGCATGCTGGCTGGAGGA 62.119 66.667 18.92 0.00 40.14 3.71
1863 2088 3.068881 CACGGTGGAGGTGGACAT 58.931 61.111 0.00 0.00 0.00 3.06
2032 2261 5.625150 AGTTCAAGAAGTGGAAGTAATGCT 58.375 37.500 0.00 0.00 0.00 3.79
2040 2269 2.611292 GTGGAAGTAATGCTGCTAGCTG 59.389 50.000 17.23 16.92 42.97 4.24
2104 2333 0.526662 ACTCTTCGTGTAGGCTTCCG 59.473 55.000 0.00 0.00 0.00 4.30
2188 2418 0.394488 TCGATCTCGTGGAGCTTCCT 60.394 55.000 0.00 0.00 40.80 3.36
2190 2420 1.676529 CGATCTCGTGGAGCTTCCTTA 59.323 52.381 0.00 0.00 37.46 2.69
2195 2425 2.996621 CTCGTGGAGCTTCCTTACTTTG 59.003 50.000 0.00 0.00 37.46 2.77
2199 2429 2.639839 TGGAGCTTCCTTACTTTGCTCT 59.360 45.455 12.06 0.00 46.39 4.09
2200 2430 3.838317 TGGAGCTTCCTTACTTTGCTCTA 59.162 43.478 12.06 4.49 46.39 2.43
2220 2452 7.158021 GCTCTATATGATTTGGCACTCTAGTT 58.842 38.462 0.00 0.00 0.00 2.24
2291 2523 1.065491 TGGTGCTATGCTTACCCTGTG 60.065 52.381 0.00 0.00 33.51 3.66
2295 2527 1.959042 CTATGCTTACCCTGTGCTGG 58.041 55.000 0.00 0.00 0.00 4.85
2317 2549 4.320202 GGTGCTGTTCATATGTCGTTGTTT 60.320 41.667 1.90 0.00 0.00 2.83
2343 2575 3.668447 TGAGGCATCTTGTTCTCTGAAC 58.332 45.455 0.00 3.74 0.00 3.18
2367 2599 1.274728 TGTTGTGTTTGCTTTGCTGGT 59.725 42.857 0.00 0.00 0.00 4.00
2390 2624 2.892852 CAATTGCTCCTCCTGACCAAAA 59.107 45.455 0.00 0.00 0.00 2.44
2391 2625 2.746279 TTGCTCCTCCTGACCAAAAA 57.254 45.000 0.00 0.00 0.00 1.94
2398 2632 3.117701 TCCTCCTGACCAAAAACATGTGA 60.118 43.478 0.00 0.00 0.00 3.58
2401 2635 3.631686 TCCTGACCAAAAACATGTGACAG 59.368 43.478 0.00 2.39 0.00 3.51
2407 2641 5.546526 ACCAAAAACATGTGACAGTTTTGT 58.453 33.333 22.09 14.69 44.54 2.83
2410 2644 6.073331 CCAAAAACATGTGACAGTTTTGTTGT 60.073 34.615 22.09 8.27 44.54 3.32
2411 2645 6.464895 AAAACATGTGACAGTTTTGTTGTG 57.535 33.333 18.27 1.49 43.88 3.33
2413 2647 4.732784 ACATGTGACAGTTTTGTTGTGAC 58.267 39.130 0.00 0.00 37.76 3.67
2415 2649 5.645929 ACATGTGACAGTTTTGTTGTGACTA 59.354 36.000 0.00 0.00 37.76 2.59
2416 2650 6.150307 ACATGTGACAGTTTTGTTGTGACTAA 59.850 34.615 0.00 0.00 37.76 2.24
2417 2651 6.561737 TGTGACAGTTTTGTTGTGACTAAA 57.438 33.333 0.00 0.00 37.76 1.85
2418 2652 6.375377 TGTGACAGTTTTGTTGTGACTAAAC 58.625 36.000 8.01 8.01 45.58 2.01
2426 2676 5.986501 TTGTTGTGACTAAACCCAAAAGT 57.013 34.783 0.00 0.00 0.00 2.66
2428 2678 4.767928 TGTTGTGACTAAACCCAAAAGTGT 59.232 37.500 0.00 0.00 0.00 3.55
2439 2689 1.406614 CCAAAAGTGTGGGCAAGCAAA 60.407 47.619 0.00 0.00 34.77 3.68
2444 2732 0.249447 GTGTGGGCAAGCAAAACCTC 60.249 55.000 0.00 0.00 0.00 3.85
2446 2734 0.249447 GTGGGCAAGCAAAACCTCAC 60.249 55.000 0.00 0.00 0.00 3.51
2451 2739 1.134848 GCAAGCAAAACCTCACCAACA 60.135 47.619 0.00 0.00 0.00 3.33
2454 2742 4.190772 CAAGCAAAACCTCACCAACATTT 58.809 39.130 0.00 0.00 0.00 2.32
2461 2749 3.074412 ACCTCACCAACATTTTAGAGCG 58.926 45.455 0.00 0.00 0.00 5.03
2462 2750 2.159517 CCTCACCAACATTTTAGAGCGC 60.160 50.000 0.00 0.00 0.00 5.92
2463 2751 2.744202 CTCACCAACATTTTAGAGCGCT 59.256 45.455 11.27 11.27 0.00 5.92
2477 2765 2.802816 AGAGCGCTCTGTTACAAACTTG 59.197 45.455 37.86 0.00 38.75 3.16
2478 2766 2.544267 GAGCGCTCTGTTACAAACTTGT 59.456 45.455 29.88 0.07 44.86 3.16
2480 2768 3.377172 AGCGCTCTGTTACAAACTTGTTT 59.623 39.130 2.64 0.00 42.35 2.83
2498 2786 8.237811 ACTTGTTTTGATCCTGTAAAGAACAT 57.762 30.769 0.00 0.00 37.50 2.71
2516 2804 4.882671 ACATATTGAACTGTTCGATGCC 57.117 40.909 26.31 1.24 35.44 4.40
2522 2810 2.226200 TGAACTGTTCGATGCCACATTG 59.774 45.455 15.18 0.00 0.00 2.82
2526 2814 1.952990 TGTTCGATGCCACATTGTGTT 59.047 42.857 15.34 0.38 0.00 3.32
2527 2815 2.360483 TGTTCGATGCCACATTGTGTTT 59.640 40.909 15.34 0.03 0.00 2.83
2528 2816 2.702898 TCGATGCCACATTGTGTTTG 57.297 45.000 15.34 1.96 0.00 2.93
2530 2818 2.226200 TCGATGCCACATTGTGTTTGAG 59.774 45.455 15.34 4.63 0.00 3.02
2531 2819 2.226200 CGATGCCACATTGTGTTTGAGA 59.774 45.455 15.34 0.00 0.00 3.27
2535 2833 1.069022 CCACATTGTGTTTGAGAGCGG 60.069 52.381 15.34 0.00 0.00 5.52
2546 2844 2.010145 TGAGAGCGGTAATCTTGCAC 57.990 50.000 0.00 0.00 0.00 4.57
2550 2848 1.060937 GCGGTAATCTTGCACAGCG 59.939 57.895 0.00 0.00 35.17 5.18
2571 2869 3.122948 CGGTGTTACAATCGGTTTCAGAG 59.877 47.826 0.00 0.00 0.00 3.35
2575 2873 1.160137 ACAATCGGTTTCAGAGCAGC 58.840 50.000 0.00 0.00 0.00 5.25
2577 2875 1.741706 CAATCGGTTTCAGAGCAGCAT 59.258 47.619 0.00 0.00 0.00 3.79
2582 2880 2.938451 CGGTTTCAGAGCAGCATTGATA 59.062 45.455 0.00 0.00 0.00 2.15
2597 2895 4.149571 GCATTGATATCTAGACGCACTGTG 59.850 45.833 2.76 2.76 0.00 3.66
2598 2896 4.983671 TTGATATCTAGACGCACTGTGT 57.016 40.909 9.86 0.00 0.00 3.72
2599 2897 4.983671 TGATATCTAGACGCACTGTGTT 57.016 40.909 9.86 0.00 0.00 3.32
2618 2916 1.153353 TTTTTCTTAGGAGTGGCGCG 58.847 50.000 0.00 0.00 0.00 6.86
2619 2917 0.319083 TTTTCTTAGGAGTGGCGCGA 59.681 50.000 12.10 0.00 0.00 5.87
2620 2918 0.535335 TTTCTTAGGAGTGGCGCGAT 59.465 50.000 12.10 0.00 0.00 4.58
2621 2919 0.102481 TTCTTAGGAGTGGCGCGATC 59.898 55.000 12.10 0.51 0.00 3.69
2622 2920 1.035385 TCTTAGGAGTGGCGCGATCA 61.035 55.000 12.10 3.94 0.00 2.92
2623 2921 0.032678 CTTAGGAGTGGCGCGATCAT 59.967 55.000 12.10 1.42 0.00 2.45
2625 2923 1.806461 TAGGAGTGGCGCGATCATCC 61.806 60.000 12.10 11.71 0.00 3.51
2627 2925 1.663074 GAGTGGCGCGATCATCCTC 60.663 63.158 12.10 7.47 0.00 3.71
2628 2926 2.663188 GTGGCGCGATCATCCTCC 60.663 66.667 12.10 0.00 0.00 4.30
2629 2927 2.839632 TGGCGCGATCATCCTCCT 60.840 61.111 12.10 0.00 0.00 3.69
2630 2928 2.356793 GGCGCGATCATCCTCCTG 60.357 66.667 12.10 0.00 0.00 3.86
2632 2930 1.663074 GCGCGATCATCCTCCTGAC 60.663 63.158 12.10 0.00 0.00 3.51
2634 2932 0.387202 CGCGATCATCCTCCTGACTT 59.613 55.000 0.00 0.00 0.00 3.01
2645 2998 3.014110 TCCTCCTGACTTCTTAATCCCCT 59.986 47.826 0.00 0.00 0.00 4.79
2649 3002 4.016105 TCCTGACTTCTTAATCCCCTCTCT 60.016 45.833 0.00 0.00 0.00 3.10
2651 3004 5.396213 CCTGACTTCTTAATCCCCTCTCTTG 60.396 48.000 0.00 0.00 0.00 3.02
2653 3006 6.261435 TGACTTCTTAATCCCCTCTCTTGTA 58.739 40.000 0.00 0.00 0.00 2.41
2654 3007 6.381420 TGACTTCTTAATCCCCTCTCTTGTAG 59.619 42.308 0.00 0.00 0.00 2.74
2655 3008 6.503944 ACTTCTTAATCCCCTCTCTTGTAGA 58.496 40.000 0.00 0.00 0.00 2.59
2686 3039 6.939627 TGATACTGTTTAATAAATGTCGCCG 58.060 36.000 0.00 0.00 0.00 6.46
2688 3041 5.464965 ACTGTTTAATAAATGTCGCCGAG 57.535 39.130 0.00 0.00 0.00 4.63
2724 3077 2.106683 GCCCAGAATTGACGGACGG 61.107 63.158 0.00 0.00 0.00 4.79
2730 3083 3.262420 CAGAATTGACGGACGGAATTCT 58.738 45.455 19.53 19.53 43.86 2.40
2744 3097 4.022068 ACGGAATTCTGCATGAAAACATGT 60.022 37.500 14.40 0.00 38.29 3.21
2768 3121 1.946768 CTCAGCCCAAACGACTTTGAA 59.053 47.619 0.36 0.00 39.43 2.69
2771 3124 2.875933 CAGCCCAAACGACTTTGAAGTA 59.124 45.455 0.00 0.00 39.43 2.24
2820 3174 5.414144 TGTCATTGTCACACAGAAAACAGAA 59.586 36.000 0.00 0.00 0.00 3.02
2841 3195 1.181098 GGTTGCTTGTCTGGCCATGT 61.181 55.000 5.51 0.00 0.00 3.21
2850 3205 1.043116 TCTGGCCATGTCTAGTCGGG 61.043 60.000 5.51 0.00 0.00 5.14
2935 3290 2.046892 ATGCTGCTGACGGTGGAC 60.047 61.111 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.741525 CAACCAGCCAACCAACCAG 59.258 57.895 0.00 0.00 0.00 4.00
1 2 1.760086 CCAACCAGCCAACCAACCA 60.760 57.895 0.00 0.00 0.00 3.67
12 13 0.817634 TTCTCACGGCAACCAACCAG 60.818 55.000 0.00 0.00 0.00 4.00
14 15 0.741915 TTTTCTCACGGCAACCAACC 59.258 50.000 0.00 0.00 0.00 3.77
16 17 0.741915 GGTTTTCTCACGGCAACCAA 59.258 50.000 0.00 0.00 38.89 3.67
64 65 0.325203 TGAAGGGCTAATTTGGGGGC 60.325 55.000 0.00 0.00 0.00 5.80
65 66 2.041701 CATGAAGGGCTAATTTGGGGG 58.958 52.381 0.00 0.00 0.00 5.40
66 67 2.431782 CACATGAAGGGCTAATTTGGGG 59.568 50.000 0.00 0.00 0.00 4.96
86 87 0.320683 CTCGGGCATGACTTGTCACA 60.321 55.000 5.53 0.00 0.00 3.58
123 124 1.284982 CCGCATCGATCGATCCAACC 61.285 60.000 27.20 12.15 31.62 3.77
145 146 1.000163 CCCCATGACCGATCTACGAAG 60.000 57.143 0.00 0.00 45.77 3.79
149 150 4.618920 ATTAACCCCATGACCGATCTAC 57.381 45.455 0.00 0.00 0.00 2.59
185 186 3.745480 CGCATCCTGACACCTAATTCCAT 60.745 47.826 0.00 0.00 0.00 3.41
254 255 1.092348 CGGGGAGAATTTTCGGGTTC 58.908 55.000 0.00 0.00 0.00 3.62
286 287 1.134128 TGAAGGGCGCACATACATGAT 60.134 47.619 14.57 0.00 0.00 2.45
291 292 1.094785 AACATGAAGGGCGCACATAC 58.905 50.000 14.57 2.63 0.00 2.39
297 298 2.423538 ACTAATCAAACATGAAGGGCGC 59.576 45.455 0.00 0.00 0.00 6.53
298 299 4.634004 TGTACTAATCAAACATGAAGGGCG 59.366 41.667 0.00 0.00 0.00 6.13
376 381 1.067635 GTGACCAAACCATGTCCATGC 60.068 52.381 1.64 0.00 37.49 4.06
478 484 1.227060 CGCCGCTCATCAGACATGA 60.227 57.895 0.00 0.00 40.50 3.07
481 487 3.068064 TCCGCCGCTCATCAGACA 61.068 61.111 0.00 0.00 0.00 3.41
482 488 2.279120 CTCCGCCGCTCATCAGAC 60.279 66.667 0.00 0.00 0.00 3.51
483 489 4.212913 GCTCCGCCGCTCATCAGA 62.213 66.667 0.00 0.00 0.00 3.27
501 507 4.803426 GTCTCACCGGCCGAGCTG 62.803 72.222 30.73 18.55 34.23 4.24
510 516 2.742372 CTTTGCCCCGTCTCACCG 60.742 66.667 0.00 0.00 0.00 4.94
511 517 1.671379 GACTTTGCCCCGTCTCACC 60.671 63.158 0.00 0.00 0.00 4.02
512 518 1.671379 GGACTTTGCCCCGTCTCAC 60.671 63.158 0.00 0.00 0.00 3.51
513 519 1.701031 TTGGACTTTGCCCCGTCTCA 61.701 55.000 0.00 0.00 0.00 3.27
514 520 0.955919 CTTGGACTTTGCCCCGTCTC 60.956 60.000 0.00 0.00 0.00 3.36
515 521 1.073199 CTTGGACTTTGCCCCGTCT 59.927 57.895 0.00 0.00 0.00 4.18
516 522 1.072505 TCTTGGACTTTGCCCCGTC 59.927 57.895 0.00 0.00 0.00 4.79
517 523 1.228154 GTCTTGGACTTTGCCCCGT 60.228 57.895 0.00 0.00 0.00 5.28
518 524 2.325082 CGTCTTGGACTTTGCCCCG 61.325 63.158 0.00 0.00 0.00 5.73
519 525 2.626780 GCGTCTTGGACTTTGCCCC 61.627 63.158 0.00 0.00 0.00 5.80
520 526 1.578206 GAGCGTCTTGGACTTTGCCC 61.578 60.000 0.00 0.00 0.00 5.36
521 527 1.578206 GGAGCGTCTTGGACTTTGCC 61.578 60.000 0.00 0.00 0.00 4.52
522 528 0.603975 AGGAGCGTCTTGGACTTTGC 60.604 55.000 0.00 0.00 0.00 3.68
523 529 1.151668 CAGGAGCGTCTTGGACTTTG 58.848 55.000 0.00 0.00 0.00 2.77
524 530 0.603975 GCAGGAGCGTCTTGGACTTT 60.604 55.000 0.00 0.00 0.00 2.66
525 531 1.004440 GCAGGAGCGTCTTGGACTT 60.004 57.895 0.00 0.00 0.00 3.01
526 532 2.659610 GCAGGAGCGTCTTGGACT 59.340 61.111 0.00 0.00 0.00 3.85
527 533 2.435059 GGCAGGAGCGTCTTGGAC 60.435 66.667 0.00 0.00 43.41 4.02
528 534 3.706373 GGGCAGGAGCGTCTTGGA 61.706 66.667 0.00 0.00 43.41 3.53
540 546 4.341502 CAAACAACCGGCGGGCAG 62.342 66.667 31.78 20.91 36.48 4.85
545 551 3.679738 ATGGGCAAACAACCGGCG 61.680 61.111 0.00 0.00 0.00 6.46
546 552 2.048316 CATGGGCAAACAACCGGC 60.048 61.111 0.00 0.00 0.00 6.13
547 553 2.048316 GCATGGGCAAACAACCGG 60.048 61.111 0.00 0.00 40.72 5.28
557 563 1.668751 CAAGCATCATTTTGCATGGGC 59.331 47.619 0.00 0.00 45.23 5.36
560 566 2.607635 GAGCCAAGCATCATTTTGCATG 59.392 45.455 0.00 0.00 45.23 4.06
561 567 2.500098 AGAGCCAAGCATCATTTTGCAT 59.500 40.909 0.00 0.00 45.23 3.96
562 568 1.897133 AGAGCCAAGCATCATTTTGCA 59.103 42.857 0.00 0.00 45.23 4.08
563 569 2.667473 AGAGCCAAGCATCATTTTGC 57.333 45.000 0.00 0.00 43.09 3.68
564 570 4.182693 TGAAGAGCCAAGCATCATTTTG 57.817 40.909 0.00 0.00 0.00 2.44
565 571 5.416271 AATGAAGAGCCAAGCATCATTTT 57.584 34.783 8.52 0.00 36.20 1.82
566 572 6.534475 TTAATGAAGAGCCAAGCATCATTT 57.466 33.333 15.53 5.80 38.50 2.32
567 573 6.726490 ATTAATGAAGAGCCAAGCATCATT 57.274 33.333 15.00 15.00 39.71 2.57
568 574 6.726490 AATTAATGAAGAGCCAAGCATCAT 57.274 33.333 0.00 0.00 32.83 2.45
569 575 6.830324 AGTAATTAATGAAGAGCCAAGCATCA 59.170 34.615 0.00 0.00 0.00 3.07
570 576 7.269477 AGTAATTAATGAAGAGCCAAGCATC 57.731 36.000 0.00 0.00 0.00 3.91
571 577 8.752005 TTAGTAATTAATGAAGAGCCAAGCAT 57.248 30.769 0.00 0.00 0.00 3.79
572 578 8.752005 ATTAGTAATTAATGAAGAGCCAAGCA 57.248 30.769 0.00 0.00 30.74 3.91
591 597 8.843262 CCATGCATTCTTCTTTGATCATTAGTA 58.157 33.333 0.00 0.00 0.00 1.82
592 598 7.683704 GCCATGCATTCTTCTTTGATCATTAGT 60.684 37.037 0.00 0.00 0.00 2.24
593 599 6.641314 GCCATGCATTCTTCTTTGATCATTAG 59.359 38.462 0.00 0.00 0.00 1.73
594 600 6.097129 TGCCATGCATTCTTCTTTGATCATTA 59.903 34.615 0.00 0.00 31.71 1.90
595 601 5.105106 TGCCATGCATTCTTCTTTGATCATT 60.105 36.000 0.00 0.00 31.71 2.57
596 602 4.404394 TGCCATGCATTCTTCTTTGATCAT 59.596 37.500 0.00 0.00 31.71 2.45
597 603 3.764972 TGCCATGCATTCTTCTTTGATCA 59.235 39.130 0.00 0.00 31.71 2.92
598 604 4.110482 GTGCCATGCATTCTTCTTTGATC 58.890 43.478 0.00 0.00 41.91 2.92
599 605 3.512329 TGTGCCATGCATTCTTCTTTGAT 59.488 39.130 0.00 0.00 41.91 2.57
600 606 2.892215 TGTGCCATGCATTCTTCTTTGA 59.108 40.909 0.00 0.00 41.91 2.69
601 607 3.250744 CTGTGCCATGCATTCTTCTTTG 58.749 45.455 0.00 0.00 41.91 2.77
602 608 2.353406 GCTGTGCCATGCATTCTTCTTT 60.353 45.455 0.00 0.00 41.91 2.52
603 609 1.203994 GCTGTGCCATGCATTCTTCTT 59.796 47.619 0.00 0.00 41.91 2.52
604 610 0.815734 GCTGTGCCATGCATTCTTCT 59.184 50.000 0.00 0.00 41.91 2.85
605 611 3.340727 GCTGTGCCATGCATTCTTC 57.659 52.632 0.00 0.00 41.91 2.87
656 662 0.036952 AATCAGACACAGTGGCGGAG 60.037 55.000 15.02 2.93 31.94 4.63
657 663 0.320683 CAATCAGACACAGTGGCGGA 60.321 55.000 12.07 12.07 33.24 5.54
658 664 1.915614 GCAATCAGACACAGTGGCGG 61.916 60.000 5.31 2.12 0.00 6.13
659 665 0.952497 AGCAATCAGACACAGTGGCG 60.952 55.000 5.31 0.00 0.00 5.69
660 666 1.068748 CAAGCAATCAGACACAGTGGC 60.069 52.381 5.31 0.45 0.00 5.01
661 667 1.068748 GCAAGCAATCAGACACAGTGG 60.069 52.381 5.31 0.00 0.00 4.00
662 668 1.605232 TGCAAGCAATCAGACACAGTG 59.395 47.619 0.00 0.00 0.00 3.66
663 669 1.605710 GTGCAAGCAATCAGACACAGT 59.394 47.619 0.00 0.00 0.00 3.55
664 670 1.399343 CGTGCAAGCAATCAGACACAG 60.399 52.381 0.00 0.00 0.00 3.66
665 671 0.587768 CGTGCAAGCAATCAGACACA 59.412 50.000 0.00 0.00 0.00 3.72
666 672 0.727122 GCGTGCAAGCAATCAGACAC 60.727 55.000 20.14 0.00 37.05 3.67
742 756 3.198635 TGCCAGCTAGAGCAGAACTAATT 59.801 43.478 4.01 0.00 45.16 1.40
804 822 7.014905 AGGTGCTAATATATGTTCTTGTCGGTA 59.985 37.037 0.00 0.00 0.00 4.02
828 846 7.041721 ACACATGATGTACTGTATGTAACAGG 58.958 38.462 0.00 0.00 46.56 4.00
849 867 5.301551 AGCACATGAAATTCCACTAAACACA 59.698 36.000 0.00 0.00 0.00 3.72
1106 1133 0.690762 TCCTTGCTGTGGAGGGTAAC 59.309 55.000 0.00 0.00 33.73 2.50
1107 1134 1.668826 ATCCTTGCTGTGGAGGGTAA 58.331 50.000 0.00 0.00 36.99 2.85
1108 1135 2.116238 GTATCCTTGCTGTGGAGGGTA 58.884 52.381 0.00 0.00 36.99 3.69
1109 1136 0.912486 GTATCCTTGCTGTGGAGGGT 59.088 55.000 0.00 0.00 36.99 4.34
1110 1137 0.181350 GGTATCCTTGCTGTGGAGGG 59.819 60.000 0.00 0.00 36.99 4.30
1111 1138 0.181350 GGGTATCCTTGCTGTGGAGG 59.819 60.000 0.00 0.00 36.99 4.30
1112 1139 0.179073 CGGGTATCCTTGCTGTGGAG 60.179 60.000 0.00 0.00 36.99 3.86
1113 1140 1.904771 CGGGTATCCTTGCTGTGGA 59.095 57.895 0.00 0.00 38.06 4.02
1114 1141 1.819632 GCGGGTATCCTTGCTGTGG 60.820 63.158 0.00 0.00 0.00 4.17
1115 1142 1.819632 GGCGGGTATCCTTGCTGTG 60.820 63.158 0.00 0.00 0.00 3.66
1116 1143 1.995626 AGGCGGGTATCCTTGCTGT 60.996 57.895 0.00 0.00 0.00 4.40
1117 1144 1.524621 CAGGCGGGTATCCTTGCTG 60.525 63.158 0.00 0.00 0.00 4.41
1118 1145 2.911143 CAGGCGGGTATCCTTGCT 59.089 61.111 0.00 0.00 0.00 3.91
1119 1146 2.902343 GCAGGCGGGTATCCTTGC 60.902 66.667 0.00 0.00 0.00 4.01
1120 1147 1.819632 GTGCAGGCGGGTATCCTTG 60.820 63.158 0.00 0.00 0.00 3.61
1121 1148 2.590092 GTGCAGGCGGGTATCCTT 59.410 61.111 0.00 0.00 0.00 3.36
1188 1215 1.612442 TCCAGGTGCAGGAGGGTAC 60.612 63.158 0.00 0.00 0.00 3.34
1254 1281 3.490031 ATGAGCACCGGCAACACCA 62.490 57.895 0.00 0.00 44.61 4.17
1458 1506 9.163899 CAGATCCTTATCAATATCAATGACTGG 57.836 37.037 0.00 0.00 34.28 4.00
1507 1555 7.865385 GTGGAAATGTAAATGTTGCTAACAGAA 59.135 33.333 7.58 0.00 45.95 3.02
1516 1564 9.734620 ATATCAATCGTGGAAATGTAAATGTTG 57.265 29.630 0.00 0.00 0.00 3.33
1558 1606 9.836076 CTAAATGCATATCAATCCAACACATAG 57.164 33.333 0.00 0.00 0.00 2.23
1565 1613 8.467963 ACACATCTAAATGCATATCAATCCAA 57.532 30.769 0.00 0.00 36.26 3.53
1662 1710 2.032071 AACCGAACTTGGGGCTCG 59.968 61.111 0.00 0.00 0.00 5.03
1666 1714 1.066716 TCGATACAACCGAACTTGGGG 60.067 52.381 0.00 0.00 32.64 4.96
1676 1724 5.408604 AGAATGACACAAGTTCGATACAACC 59.591 40.000 0.00 0.00 0.00 3.77
1685 1733 4.818534 TGCTGAAGAATGACACAAGTTC 57.181 40.909 0.00 0.00 0.00 3.01
1721 1946 5.509501 CCACTGTGACCTGCAAAAACAATAT 60.510 40.000 9.86 0.00 0.00 1.28
1732 1957 1.376037 GGCTACCACTGTGACCTGC 60.376 63.158 9.86 7.78 0.00 4.85
1776 2001 4.435970 CCTCCAGCCAGCATGCCA 62.436 66.667 15.66 0.00 31.97 4.92
1831 2056 3.423154 GTGGCCGCCGTGAGAAAG 61.423 66.667 4.45 0.00 0.00 2.62
1863 2088 1.637035 CCCATCATGCCTCCCATCATA 59.363 52.381 0.00 0.00 29.71 2.15
2040 2269 0.253044 TCAGCCATGGTGAAGCTACC 59.747 55.000 14.67 0.00 37.11 3.18
2075 2304 6.856135 CCTACACGAAGAGTTTAGGTTTTT 57.144 37.500 0.00 0.00 44.43 1.94
2104 2333 1.133606 TCCCTGACCAAACCAAGTTCC 60.134 52.381 0.00 0.00 0.00 3.62
2188 2418 7.775093 AGTGCCAAATCATATAGAGCAAAGTAA 59.225 33.333 0.00 0.00 0.00 2.24
2190 2420 6.125029 AGTGCCAAATCATATAGAGCAAAGT 58.875 36.000 0.00 0.00 0.00 2.66
2195 2425 6.696411 ACTAGAGTGCCAAATCATATAGAGC 58.304 40.000 0.00 0.00 0.00 4.09
2199 2429 6.202762 CGCAAACTAGAGTGCCAAATCATATA 59.797 38.462 14.12 0.00 37.47 0.86
2200 2430 5.008019 CGCAAACTAGAGTGCCAAATCATAT 59.992 40.000 14.12 0.00 37.47 1.78
2220 2452 3.926527 GTCATATCTTGTCACAGACGCAA 59.073 43.478 0.00 0.00 34.95 4.85
2246 2478 9.743057 CAGACAGAATTCAGGTACTTATTAGAG 57.257 37.037 8.44 0.00 34.60 2.43
2247 2479 8.696374 CCAGACAGAATTCAGGTACTTATTAGA 58.304 37.037 8.44 0.00 34.60 2.10
2291 2523 1.328680 CGACATATGAACAGCACCAGC 59.671 52.381 10.38 0.00 42.56 4.85
2295 2527 4.404507 AACAACGACATATGAACAGCAC 57.595 40.909 10.38 0.00 0.00 4.40
2317 2549 4.758674 CAGAGAACAAGATGCCTCAGAAAA 59.241 41.667 0.00 0.00 0.00 2.29
2324 2556 3.558746 CCAGTTCAGAGAACAAGATGCCT 60.559 47.826 11.92 0.00 0.00 4.75
2333 2565 3.270877 ACACAACACCAGTTCAGAGAAC 58.729 45.455 1.77 1.77 35.28 3.01
2335 2567 3.627395 AACACAACACCAGTTCAGAGA 57.373 42.857 0.00 0.00 35.28 3.10
2343 2575 1.660104 GCAAAGCAAACACAACACCAG 59.340 47.619 0.00 0.00 0.00 4.00
2367 2599 0.322816 GGTCAGGAGGAGCAATTGCA 60.323 55.000 30.89 5.95 45.16 4.08
2375 2609 3.254166 CACATGTTTTTGGTCAGGAGGAG 59.746 47.826 0.00 0.00 0.00 3.69
2377 2611 3.004734 GTCACATGTTTTTGGTCAGGAGG 59.995 47.826 0.00 0.00 0.00 4.30
2390 2624 5.048083 AGTCACAACAAAACTGTCACATGTT 60.048 36.000 0.00 0.00 34.74 2.71
2391 2625 4.458989 AGTCACAACAAAACTGTCACATGT 59.541 37.500 0.00 0.00 0.00 3.21
2398 2632 4.767928 TGGGTTTAGTCACAACAAAACTGT 59.232 37.500 0.00 0.00 33.40 3.55
2401 2635 6.647481 ACTTTTGGGTTTAGTCACAACAAAAC 59.353 34.615 0.00 0.00 34.29 2.43
2407 2641 4.158764 CCACACTTTTGGGTTTAGTCACAA 59.841 41.667 0.00 0.00 30.69 3.33
2426 2676 0.685785 TGAGGTTTTGCTTGCCCACA 60.686 50.000 0.00 0.00 0.00 4.17
2428 2678 1.398958 GGTGAGGTTTTGCTTGCCCA 61.399 55.000 0.00 0.00 0.00 5.36
2439 2689 3.502211 CGCTCTAAAATGTTGGTGAGGTT 59.498 43.478 0.00 0.00 0.00 3.50
2444 2732 2.744202 AGAGCGCTCTAAAATGTTGGTG 59.256 45.455 37.61 0.00 38.35 4.17
2446 2734 2.744202 ACAGAGCGCTCTAAAATGTTGG 59.256 45.455 37.74 23.95 37.98 3.77
2451 2739 5.701290 AGTTTGTAACAGAGCGCTCTAAAAT 59.299 36.000 37.74 28.02 37.98 1.82
2454 2742 4.252971 AGTTTGTAACAGAGCGCTCTAA 57.747 40.909 37.74 25.27 37.98 2.10
2461 2749 6.417930 GGATCAAAACAAGTTTGTAACAGAGC 59.582 38.462 0.00 0.00 45.83 4.09
2462 2750 7.645340 CAGGATCAAAACAAGTTTGTAACAGAG 59.355 37.037 0.00 0.00 45.83 3.35
2463 2751 7.122055 ACAGGATCAAAACAAGTTTGTAACAGA 59.878 33.333 0.00 0.00 45.83 3.41
2480 2768 9.739276 AGTTCAATATGTTCTTTACAGGATCAA 57.261 29.630 0.00 0.00 40.83 2.57
2498 2786 3.669536 TGTGGCATCGAACAGTTCAATA 58.330 40.909 13.82 0.00 0.00 1.90
2500 2788 1.960417 TGTGGCATCGAACAGTTCAA 58.040 45.000 13.82 0.00 0.00 2.69
2502 2790 2.226437 ACAATGTGGCATCGAACAGTTC 59.774 45.455 2.85 2.85 0.00 3.01
2504 2792 1.536766 CACAATGTGGCATCGAACAGT 59.463 47.619 5.29 0.00 0.00 3.55
2516 2804 1.603802 ACCGCTCTCAAACACAATGTG 59.396 47.619 12.40 12.40 39.75 3.21
2522 2810 3.424962 GCAAGATTACCGCTCTCAAACAC 60.425 47.826 0.00 0.00 0.00 3.32
2526 2814 2.289382 TGTGCAAGATTACCGCTCTCAA 60.289 45.455 0.00 0.00 0.00 3.02
2527 2815 1.275010 TGTGCAAGATTACCGCTCTCA 59.725 47.619 0.00 0.00 0.00 3.27
2528 2816 1.929836 CTGTGCAAGATTACCGCTCTC 59.070 52.381 0.00 0.00 0.00 3.20
2530 2818 0.375106 GCTGTGCAAGATTACCGCTC 59.625 55.000 0.00 0.00 0.00 5.03
2531 2819 1.361668 CGCTGTGCAAGATTACCGCT 61.362 55.000 0.00 0.00 0.00 5.52
2535 2833 1.156736 ACACCGCTGTGCAAGATTAC 58.843 50.000 8.32 0.00 46.86 1.89
2546 2844 1.153353 AACCGATTGTAACACCGCTG 58.847 50.000 0.00 0.00 0.00 5.18
2550 2848 3.120304 GCTCTGAAACCGATTGTAACACC 60.120 47.826 0.00 0.00 0.00 4.16
2553 2851 3.424962 GCTGCTCTGAAACCGATTGTAAC 60.425 47.826 0.00 0.00 0.00 2.50
2571 2869 3.122613 GTGCGTCTAGATATCAATGCTGC 59.877 47.826 5.32 0.00 0.00 5.25
2575 2873 5.284864 ACACAGTGCGTCTAGATATCAATG 58.715 41.667 5.32 13.79 0.00 2.82
2577 2875 4.983671 ACACAGTGCGTCTAGATATCAA 57.016 40.909 5.32 0.00 0.00 2.57
2599 2897 1.153353 CGCGCCACTCCTAAGAAAAA 58.847 50.000 0.00 0.00 0.00 1.94
2605 2903 0.032130 GATGATCGCGCCACTCCTAA 59.968 55.000 0.00 0.00 0.00 2.69
2610 2908 2.419198 GAGGATGATCGCGCCACT 59.581 61.111 0.00 0.00 0.00 4.00
2611 2909 2.663188 GGAGGATGATCGCGCCAC 60.663 66.667 0.00 0.00 0.00 5.01
2612 2910 2.839632 AGGAGGATGATCGCGCCA 60.840 61.111 0.00 1.58 0.00 5.69
2613 2911 2.356793 CAGGAGGATGATCGCGCC 60.357 66.667 0.00 0.00 0.00 6.53
2614 2912 1.663074 GTCAGGAGGATGATCGCGC 60.663 63.158 0.00 0.00 0.00 6.86
2615 2913 0.387202 AAGTCAGGAGGATGATCGCG 59.613 55.000 0.00 0.00 0.00 5.87
2617 2915 5.521906 TTAAGAAGTCAGGAGGATGATCG 57.478 43.478 0.00 0.00 0.00 3.69
2618 2916 6.463360 GGATTAAGAAGTCAGGAGGATGATC 58.537 44.000 0.00 0.00 0.00 2.92
2619 2917 5.309282 GGGATTAAGAAGTCAGGAGGATGAT 59.691 44.000 0.00 0.00 0.00 2.45
2620 2918 4.656112 GGGATTAAGAAGTCAGGAGGATGA 59.344 45.833 0.00 0.00 0.00 2.92
2621 2919 4.202409 GGGGATTAAGAAGTCAGGAGGATG 60.202 50.000 0.00 0.00 0.00 3.51
2622 2920 3.977326 GGGGATTAAGAAGTCAGGAGGAT 59.023 47.826 0.00 0.00 0.00 3.24
2623 2921 3.014110 AGGGGATTAAGAAGTCAGGAGGA 59.986 47.826 0.00 0.00 0.00 3.71
2625 2923 4.294347 AGAGGGGATTAAGAAGTCAGGAG 58.706 47.826 0.00 0.00 0.00 3.69
2627 2925 4.294347 AGAGAGGGGATTAAGAAGTCAGG 58.706 47.826 0.00 0.00 0.00 3.86
2628 2926 5.188751 ACAAGAGAGGGGATTAAGAAGTCAG 59.811 44.000 0.00 0.00 0.00 3.51
2629 2927 5.094387 ACAAGAGAGGGGATTAAGAAGTCA 58.906 41.667 0.00 0.00 0.00 3.41
2630 2928 5.685520 ACAAGAGAGGGGATTAAGAAGTC 57.314 43.478 0.00 0.00 0.00 3.01
2645 2998 9.647918 AACAGTATCAATATCCTCTACAAGAGA 57.352 33.333 5.50 0.00 45.07 3.10
2660 3013 8.067784 CGGCGACATTTATTAAACAGTATCAAT 58.932 33.333 0.00 0.00 0.00 2.57
2661 3014 7.278203 TCGGCGACATTTATTAAACAGTATCAA 59.722 33.333 4.99 0.00 0.00 2.57
2662 3015 6.757478 TCGGCGACATTTATTAAACAGTATCA 59.243 34.615 4.99 0.00 0.00 2.15
2663 3016 7.169035 TCGGCGACATTTATTAAACAGTATC 57.831 36.000 4.99 0.00 0.00 2.24
2664 3017 6.202188 CCTCGGCGACATTTATTAAACAGTAT 59.798 38.462 4.99 0.00 0.00 2.12
2665 3018 5.521010 CCTCGGCGACATTTATTAAACAGTA 59.479 40.000 4.99 0.00 0.00 2.74
2666 3019 4.331717 CCTCGGCGACATTTATTAAACAGT 59.668 41.667 4.99 0.00 0.00 3.55
2667 3020 4.331717 ACCTCGGCGACATTTATTAAACAG 59.668 41.667 4.99 0.00 0.00 3.16
2668 3021 4.255301 ACCTCGGCGACATTTATTAAACA 58.745 39.130 4.99 0.00 0.00 2.83
2673 3026 5.883503 TTTTAACCTCGGCGACATTTATT 57.116 34.783 4.99 0.00 0.00 1.40
2702 3055 0.690192 TCCGTCAATTCTGGGCTTGA 59.310 50.000 0.00 0.00 0.00 3.02
2802 3156 2.675844 CCGTTCTGTTTTCTGTGTGACA 59.324 45.455 0.00 0.00 0.00 3.58
2803 3157 2.676342 ACCGTTCTGTTTTCTGTGTGAC 59.324 45.455 0.00 0.00 0.00 3.67
2820 3174 2.594592 GGCCAGACAAGCAACCGT 60.595 61.111 0.00 0.00 0.00 4.83
2841 3195 0.107312 CTCCGTCTTCCCCGACTAGA 60.107 60.000 0.00 0.00 0.00 2.43
2935 3290 2.440796 AACATGCTCATGGGGGCG 60.441 61.111 13.69 0.00 42.91 6.13


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

AutoCloner maintained by Alex Coulton.