Multiple sequence alignment - TraesCS6B01G081400

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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 TraesCS6B01G081400 chr6B 100.000 3738 0 0 1 3738 57727698 57723961 0.000000e+00 6903.0
1 TraesCS6B01G081400 chr6B 78.719 968 165 24 1132 2078 57452842 57453789 3.190000e-170 608.0
2 TraesCS6B01G081400 chr6B 83.227 626 99 3 1132 1757 57910584 57909965 1.510000e-158 569.0
3 TraesCS6B01G081400 chr6B 97.222 180 5 0 3559 3738 57703471 57703292 4.690000e-79 305.0
4 TraesCS6B01G081400 chr6B 72.774 977 228 27 1130 2098 81667894 81666948 2.820000e-76 296.0
5 TraesCS6B01G081400 chr6B 72.539 965 216 34 1130 2083 80207638 80208564 6.150000e-68 268.0
6 TraesCS6B01G081400 chr6B 72.539 965 216 34 1130 2083 80682774 80683700 6.150000e-68 268.0
7 TraesCS6B01G081400 chr6B 83.152 184 21 5 3279 3461 57454111 57454285 3.860000e-35 159.0
8 TraesCS6B01G081400 chr6B 76.628 261 43 9 3205 3459 80685462 80685710 1.090000e-25 128.0
9 TraesCS6B01G081400 chr6B 80.357 168 20 7 1400 1556 63989496 63989661 8.480000e-22 115.0
10 TraesCS6B01G081400 chr6A 94.183 997 55 1 1175 2171 32796694 32795701 0.000000e+00 1517.0
11 TraesCS6B01G081400 chr6A 90.855 667 34 13 2167 2826 32795587 32794941 0.000000e+00 869.0
12 TraesCS6B01G081400 chr6A 91.130 575 44 2 1 574 32797934 32797366 0.000000e+00 773.0
13 TraesCS6B01G081400 chr6A 90.869 449 29 9 3053 3491 32794918 32794472 3.220000e-165 592.0
14 TraesCS6B01G081400 chr6A 84.979 486 63 6 1143 1626 32865391 32864914 5.610000e-133 484.0
15 TraesCS6B01G081400 chr6A 83.084 467 71 5 1640 2104 32860254 32859794 5.770000e-113 418.0
16 TraesCS6B01G081400 chr6A 93.200 250 17 0 682 931 32797368 32797119 5.900000e-98 368.0
17 TraesCS6B01G081400 chr6A 83.436 326 53 1 1767 2091 32850909 32850584 6.070000e-78 302.0
18 TraesCS6B01G081400 chr6A 94.505 182 8 1 3559 3738 32793696 32793515 2.840000e-71 279.0
19 TraesCS6B01G081400 chr6A 81.346 327 61 0 1735 2061 32328184 32328510 2.210000e-67 267.0
20 TraesCS6B01G081400 chr6A 92.391 184 10 1 957 1136 32797042 32796859 3.700000e-65 259.0
21 TraesCS6B01G081400 chr6A 79.667 300 40 11 3141 3429 47142291 47142580 2.950000e-46 196.0
22 TraesCS6B01G081400 chr6A 86.139 101 11 1 3362 3459 46765813 46765913 5.110000e-19 106.0
23 TraesCS6B01G081400 chr6A 100.000 49 0 0 3511 3559 32793935 32793887 1.430000e-14 91.6
24 TraesCS6B01G081400 chr6D 93.416 972 64 0 1184 2155 29932720 29933691 0.000000e+00 1441.0
25 TraesCS6B01G081400 chr6D 88.268 1074 64 27 2462 3490 29934070 29935126 0.000000e+00 1229.0
26 TraesCS6B01G081400 chr6D 85.795 887 123 1 1184 2070 29875414 29876297 0.000000e+00 937.0
27 TraesCS6B01G081400 chr6D 86.949 567 31 5 386 931 29931779 29932323 6.910000e-167 597.0
28 TraesCS6B01G081400 chr6D 90.407 344 25 6 1 343 29931440 29931776 2.650000e-121 446.0
29 TraesCS6B01G081400 chr6D 95.720 257 7 3 2167 2423 29933815 29934067 9.660000e-111 411.0
30 TraesCS6B01G081400 chr6D 77.877 669 137 9 1442 2104 31266525 31265862 4.500000e-109 405.0
31 TraesCS6B01G081400 chr6D 85.196 358 52 1 1735 2091 29876407 29876764 2.120000e-97 366.0
32 TraesCS6B01G081400 chr6D 90.659 182 15 1 3559 3738 29935546 29935727 1.340000e-59 241.0
33 TraesCS6B01G081400 chr6D 83.696 184 20 5 3279 3461 30076931 30076757 8.310000e-37 165.0
34 TraesCS6B01G081400 chr6D 96.154 78 3 0 957 1034 29932636 29932713 1.090000e-25 128.0
35 TraesCS6B01G081400 chrUn 82.270 141 23 2 1403 1542 103309790 103309651 1.820000e-23 121.0
36 TraesCS6B01G081400 chrUn 79.762 168 21 10 1400 1556 102663458 102663623 3.950000e-20 110.0
37 TraesCS6B01G081400 chrUn 73.065 323 56 20 1261 1560 112304195 112303881 6.650000e-13 86.1
38 TraesCS6B01G081400 chrUn 83.562 73 12 0 1488 1560 102522093 102522021 6.700000e-08 69.4


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 TraesCS6B01G081400 chr6B 57723961 57727698 3737 True 6903.000000 6903 100.000000 1 3738 1 chr6B.!!$R2 3737
1 TraesCS6B01G081400 chr6B 57909965 57910584 619 True 569.000000 569 83.227000 1132 1757 1 chr6B.!!$R3 625
2 TraesCS6B01G081400 chr6B 57452842 57454285 1443 False 383.500000 608 80.935500 1132 3461 2 chr6B.!!$F3 2329
3 TraesCS6B01G081400 chr6B 81666948 81667894 946 True 296.000000 296 72.774000 1130 2098 1 chr6B.!!$R4 968
4 TraesCS6B01G081400 chr6B 80207638 80208564 926 False 268.000000 268 72.539000 1130 2083 1 chr6B.!!$F2 953
5 TraesCS6B01G081400 chr6A 32793515 32797934 4419 True 593.575000 1517 93.391625 1 3738 8 chr6A.!!$R4 3737
6 TraesCS6B01G081400 chr6D 29875414 29876764 1350 False 651.500000 937 85.495500 1184 2091 2 chr6D.!!$F1 907
7 TraesCS6B01G081400 chr6D 29931440 29935727 4287 False 641.857143 1441 91.653286 1 3738 7 chr6D.!!$F2 3737
8 TraesCS6B01G081400 chr6D 31265862 31266525 663 True 405.000000 405 77.877000 1442 2104 1 chr6D.!!$R2 662

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
624 626 0.033503 TCTGCCCACATCTCGTAGGA 60.034 55.0 0.00 0.00 0.00 2.94 F
652 654 0.038744 CCCCACTCAAGACATGCCTT 59.961 55.0 0.00 0.00 0.00 4.35 F
664 666 0.179156 CATGCCTTGTCATGTTCGCC 60.179 55.0 0.00 0.00 39.10 5.54 F
2066 3082 0.747255 ACTCCAGGTACTAGCATGCG 59.253 55.0 13.01 0.84 36.02 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1456 2015 2.033448 CCCGTTGCTGCCTACCAA 59.967 61.111 0.0 0.0 0.00 3.67 R
2631 3775 1.448540 GCTCCATCGTGTCCACCAG 60.449 63.158 0.0 0.0 0.00 4.00 R
2661 3805 0.606401 ATCCACCAACGGCTCACAAG 60.606 55.000 0.0 0.0 0.00 3.16 R
3050 4218 0.393537 AAGAGAATCCAGCCCAAGCG 60.394 55.000 0.0 0.0 39.63 4.68 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
66 68 2.269023 TGAGGGAGCCTTCTGATTCAA 58.731 47.619 0.21 0.00 31.76 2.69
69 71 2.025510 AGGGAGCCTTCTGATTCAAAGG 60.026 50.000 16.78 16.78 44.10 3.11
113 115 1.343465 ACTACCACTCCAACAGTTCCG 59.657 52.381 0.00 0.00 30.26 4.30
122 124 6.016943 CCACTCCAACAGTTCCGTTAAATTTA 60.017 38.462 0.00 0.00 30.26 1.40
124 126 8.079809 CACTCCAACAGTTCCGTTAAATTTATT 58.920 33.333 0.00 0.00 30.26 1.40
182 184 1.363246 GTCCCCTTCTTCTGTCCCTT 58.637 55.000 0.00 0.00 0.00 3.95
183 185 1.003696 GTCCCCTTCTTCTGTCCCTTG 59.996 57.143 0.00 0.00 0.00 3.61
209 211 1.073444 CTGATCCACCATAGCTGCCAT 59.927 52.381 0.00 0.00 0.00 4.40
262 264 3.771577 CTTCAGTAGTTGGAAGGGTGT 57.228 47.619 0.00 0.00 37.46 4.16
263 265 4.884668 CTTCAGTAGTTGGAAGGGTGTA 57.115 45.455 0.00 0.00 37.46 2.90
343 345 6.096705 TCCCAAAATATTTCATCGTGCATTCT 59.903 34.615 0.10 0.00 0.00 2.40
376 378 5.703130 GTCTCCCATTACCATCATTTCTAGC 59.297 44.000 0.00 0.00 0.00 3.42
380 382 5.416952 CCCATTACCATCATTTCTAGCATCC 59.583 44.000 0.00 0.00 0.00 3.51
382 384 6.491062 CCATTACCATCATTTCTAGCATCCAA 59.509 38.462 0.00 0.00 0.00 3.53
395 397 6.052360 TCTAGCATCCAAATTACGTGCATTA 58.948 36.000 0.00 0.00 38.23 1.90
423 425 9.013229 TCAAAGCATCATAATTATTATTCCGCT 57.987 29.630 0.00 1.23 0.00 5.52
450 452 3.537580 CCATTAAACCGCCAGCTACTAA 58.462 45.455 0.00 0.00 0.00 2.24
451 453 3.311596 CCATTAAACCGCCAGCTACTAAC 59.688 47.826 0.00 0.00 0.00 2.34
469 471 4.992951 ACTAACAGGAATTACGTCAACACC 59.007 41.667 0.00 0.00 0.00 4.16
470 472 2.774687 ACAGGAATTACGTCAACACCC 58.225 47.619 0.00 0.00 0.00 4.61
471 473 2.105134 ACAGGAATTACGTCAACACCCA 59.895 45.455 0.00 0.00 0.00 4.51
472 474 3.244770 ACAGGAATTACGTCAACACCCAT 60.245 43.478 0.00 0.00 0.00 4.00
473 475 4.020039 ACAGGAATTACGTCAACACCCATA 60.020 41.667 0.00 0.00 0.00 2.74
474 476 4.938832 CAGGAATTACGTCAACACCCATAA 59.061 41.667 0.00 0.00 0.00 1.90
515 517 1.867233 CCTGTATCTTCAATTCCCGCG 59.133 52.381 0.00 0.00 0.00 6.46
531 533 1.807886 GCGCCTCTACCTCTTTCGA 59.192 57.895 0.00 0.00 0.00 3.71
558 560 2.744202 CCACCGAAGTTTCCATCAGAAG 59.256 50.000 0.00 0.00 35.40 2.85
572 574 4.318332 CATCAGAAGCTTGTACACCTTCA 58.682 43.478 25.60 13.93 37.91 3.02
573 575 3.995199 TCAGAAGCTTGTACACCTTCAG 58.005 45.455 25.60 20.82 37.91 3.02
574 576 3.070018 CAGAAGCTTGTACACCTTCAGG 58.930 50.000 25.60 17.79 37.91 3.86
575 577 2.972713 AGAAGCTTGTACACCTTCAGGA 59.027 45.455 25.60 0.06 37.91 3.86
576 578 2.841442 AGCTTGTACACCTTCAGGAC 57.159 50.000 0.00 0.00 38.94 3.85
577 579 1.348036 AGCTTGTACACCTTCAGGACC 59.652 52.381 0.00 0.00 38.94 4.46
578 580 1.071699 GCTTGTACACCTTCAGGACCA 59.928 52.381 0.00 0.00 38.94 4.02
579 581 2.290323 GCTTGTACACCTTCAGGACCAT 60.290 50.000 0.00 0.00 38.94 3.55
580 582 3.338249 CTTGTACACCTTCAGGACCATG 58.662 50.000 0.00 0.00 38.94 3.66
581 583 2.615391 TGTACACCTTCAGGACCATGA 58.385 47.619 0.00 0.00 38.94 3.07
582 584 2.301870 TGTACACCTTCAGGACCATGAC 59.698 50.000 0.00 0.00 38.94 3.06
583 585 0.693049 ACACCTTCAGGACCATGACC 59.307 55.000 0.00 0.00 38.94 4.02
584 586 0.692476 CACCTTCAGGACCATGACCA 59.308 55.000 0.00 0.00 38.94 4.02
585 587 0.693049 ACCTTCAGGACCATGACCAC 59.307 55.000 0.00 0.00 38.94 4.16
586 588 0.035056 CCTTCAGGACCATGACCACC 60.035 60.000 10.59 1.61 37.39 4.61
587 589 0.692476 CTTCAGGACCATGACCACCA 59.308 55.000 10.59 0.00 0.00 4.17
588 590 0.400213 TTCAGGACCATGACCACCAC 59.600 55.000 10.59 0.00 0.00 4.16
589 591 0.473694 TCAGGACCATGACCACCACT 60.474 55.000 10.59 0.00 0.00 4.00
590 592 0.401738 CAGGACCATGACCACCACTT 59.598 55.000 10.59 0.00 0.00 3.16
591 593 0.693049 AGGACCATGACCACCACTTC 59.307 55.000 10.59 0.00 0.00 3.01
592 594 0.322546 GGACCATGACCACCACTTCC 60.323 60.000 0.00 0.00 0.00 3.46
593 595 0.693049 GACCATGACCACCACTTCCT 59.307 55.000 0.00 0.00 0.00 3.36
594 596 0.693049 ACCATGACCACCACTTCCTC 59.307 55.000 0.00 0.00 0.00 3.71
595 597 0.391661 CCATGACCACCACTTCCTCG 60.392 60.000 0.00 0.00 0.00 4.63
596 598 0.608130 CATGACCACCACTTCCTCGA 59.392 55.000 0.00 0.00 0.00 4.04
597 599 0.608640 ATGACCACCACTTCCTCGAC 59.391 55.000 0.00 0.00 0.00 4.20
598 600 1.292541 GACCACCACTTCCTCGACC 59.707 63.158 0.00 0.00 0.00 4.79
599 601 1.152312 ACCACCACTTCCTCGACCT 60.152 57.895 0.00 0.00 0.00 3.85
600 602 1.186267 ACCACCACTTCCTCGACCTC 61.186 60.000 0.00 0.00 0.00 3.85
601 603 0.900647 CCACCACTTCCTCGACCTCT 60.901 60.000 0.00 0.00 0.00 3.69
602 604 0.244994 CACCACTTCCTCGACCTCTG 59.755 60.000 0.00 0.00 0.00 3.35
603 605 1.216710 CCACTTCCTCGACCTCTGC 59.783 63.158 0.00 0.00 0.00 4.26
604 606 1.536073 CCACTTCCTCGACCTCTGCA 61.536 60.000 0.00 0.00 0.00 4.41
605 607 0.534412 CACTTCCTCGACCTCTGCAT 59.466 55.000 0.00 0.00 0.00 3.96
606 608 0.820871 ACTTCCTCGACCTCTGCATC 59.179 55.000 0.00 0.00 0.00 3.91
607 609 1.110442 CTTCCTCGACCTCTGCATCT 58.890 55.000 0.00 0.00 0.00 2.90
608 610 0.820226 TTCCTCGACCTCTGCATCTG 59.180 55.000 0.00 0.00 0.00 2.90
609 611 1.227205 CCTCGACCTCTGCATCTGC 60.227 63.158 0.00 0.00 42.50 4.26
610 612 1.227205 CTCGACCTCTGCATCTGCC 60.227 63.158 0.00 0.00 41.18 4.85
611 613 2.202987 CGACCTCTGCATCTGCCC 60.203 66.667 0.00 0.00 41.18 5.36
612 614 2.993008 GACCTCTGCATCTGCCCA 59.007 61.111 0.00 0.00 41.18 5.36
613 615 1.451028 GACCTCTGCATCTGCCCAC 60.451 63.158 0.00 0.00 41.18 4.61
614 616 2.189191 GACCTCTGCATCTGCCCACA 62.189 60.000 0.00 0.00 41.18 4.17
615 617 1.226542 CCTCTGCATCTGCCCACAT 59.773 57.895 0.00 0.00 41.18 3.21
616 618 0.818445 CCTCTGCATCTGCCCACATC 60.818 60.000 0.00 0.00 41.18 3.06
617 619 0.180642 CTCTGCATCTGCCCACATCT 59.819 55.000 0.00 0.00 41.18 2.90
618 620 0.179702 TCTGCATCTGCCCACATCTC 59.820 55.000 0.00 0.00 41.18 2.75
619 621 1.153309 TGCATCTGCCCACATCTCG 60.153 57.895 0.00 0.00 41.18 4.04
620 622 1.153289 GCATCTGCCCACATCTCGT 60.153 57.895 0.00 0.00 34.31 4.18
621 623 0.104855 GCATCTGCCCACATCTCGTA 59.895 55.000 0.00 0.00 34.31 3.43
622 624 1.871408 GCATCTGCCCACATCTCGTAG 60.871 57.143 0.00 0.00 34.31 3.51
623 625 1.043816 ATCTGCCCACATCTCGTAGG 58.956 55.000 0.00 0.00 0.00 3.18
624 626 0.033503 TCTGCCCACATCTCGTAGGA 60.034 55.000 0.00 0.00 0.00 2.94
625 627 1.043816 CTGCCCACATCTCGTAGGAT 58.956 55.000 0.00 0.00 0.00 3.24
626 628 2.158519 TCTGCCCACATCTCGTAGGATA 60.159 50.000 0.00 0.00 0.00 2.59
627 629 2.628178 CTGCCCACATCTCGTAGGATAA 59.372 50.000 0.00 0.00 0.00 1.75
628 630 3.035363 TGCCCACATCTCGTAGGATAAA 58.965 45.455 0.00 0.00 0.00 1.40
629 631 3.452990 TGCCCACATCTCGTAGGATAAAA 59.547 43.478 0.00 0.00 0.00 1.52
630 632 4.102524 TGCCCACATCTCGTAGGATAAAAT 59.897 41.667 0.00 0.00 0.00 1.82
631 633 5.063880 GCCCACATCTCGTAGGATAAAATT 58.936 41.667 0.00 0.00 0.00 1.82
632 634 6.183361 TGCCCACATCTCGTAGGATAAAATTA 60.183 38.462 0.00 0.00 0.00 1.40
633 635 6.147328 GCCCACATCTCGTAGGATAAAATTAC 59.853 42.308 0.00 0.00 0.00 1.89
634 636 6.649557 CCCACATCTCGTAGGATAAAATTACC 59.350 42.308 0.00 0.00 0.00 2.85
635 637 6.649557 CCACATCTCGTAGGATAAAATTACCC 59.350 42.308 0.00 0.00 0.00 3.69
636 638 6.649557 CACATCTCGTAGGATAAAATTACCCC 59.350 42.308 0.00 0.00 0.00 4.95
637 639 6.328148 ACATCTCGTAGGATAAAATTACCCCA 59.672 38.462 0.00 0.00 0.00 4.96
638 640 6.165700 TCTCGTAGGATAAAATTACCCCAC 57.834 41.667 0.00 0.00 0.00 4.61
639 641 5.901276 TCTCGTAGGATAAAATTACCCCACT 59.099 40.000 0.00 0.00 0.00 4.00
640 642 6.041296 TCTCGTAGGATAAAATTACCCCACTC 59.959 42.308 0.00 0.00 0.00 3.51
641 643 5.662208 TCGTAGGATAAAATTACCCCACTCA 59.338 40.000 0.00 0.00 0.00 3.41
642 644 6.156602 TCGTAGGATAAAATTACCCCACTCAA 59.843 38.462 0.00 0.00 0.00 3.02
643 645 6.482308 CGTAGGATAAAATTACCCCACTCAAG 59.518 42.308 0.00 0.00 0.00 3.02
644 646 6.652205 AGGATAAAATTACCCCACTCAAGA 57.348 37.500 0.00 0.00 0.00 3.02
645 647 6.424032 AGGATAAAATTACCCCACTCAAGAC 58.576 40.000 0.00 0.00 0.00 3.01
646 648 6.011981 AGGATAAAATTACCCCACTCAAGACA 60.012 38.462 0.00 0.00 0.00 3.41
647 649 6.833933 GGATAAAATTACCCCACTCAAGACAT 59.166 38.462 0.00 0.00 0.00 3.06
648 650 5.982890 AAAATTACCCCACTCAAGACATG 57.017 39.130 0.00 0.00 0.00 3.21
649 651 2.489938 TTACCCCACTCAAGACATGC 57.510 50.000 0.00 0.00 0.00 4.06
650 652 0.618458 TACCCCACTCAAGACATGCC 59.382 55.000 0.00 0.00 0.00 4.40
651 653 1.136329 ACCCCACTCAAGACATGCCT 61.136 55.000 0.00 0.00 0.00 4.75
652 654 0.038744 CCCCACTCAAGACATGCCTT 59.961 55.000 0.00 0.00 0.00 4.35
653 655 1.171308 CCCACTCAAGACATGCCTTG 58.829 55.000 15.00 15.00 43.58 3.61
654 656 1.546323 CCCACTCAAGACATGCCTTGT 60.546 52.381 19.57 0.61 42.95 3.16
663 665 3.317608 CATGCCTTGTCATGTTCGC 57.682 52.632 0.00 0.00 39.10 4.70
664 666 0.179156 CATGCCTTGTCATGTTCGCC 60.179 55.000 0.00 0.00 39.10 5.54
665 667 1.647545 ATGCCTTGTCATGTTCGCCG 61.648 55.000 0.00 0.00 0.00 6.46
666 668 2.325082 GCCTTGTCATGTTCGCCGT 61.325 57.895 0.00 0.00 0.00 5.68
667 669 1.787847 CCTTGTCATGTTCGCCGTC 59.212 57.895 0.00 0.00 0.00 4.79
668 670 1.416049 CTTGTCATGTTCGCCGTCG 59.584 57.895 0.00 0.00 0.00 5.12
669 671 2.548587 CTTGTCATGTTCGCCGTCGC 62.549 60.000 0.00 0.00 35.26 5.19
670 672 3.849953 GTCATGTTCGCCGTCGCC 61.850 66.667 0.00 0.00 35.26 5.54
671 673 4.063967 TCATGTTCGCCGTCGCCT 62.064 61.111 0.00 0.00 35.26 5.52
672 674 2.202690 CATGTTCGCCGTCGCCTA 60.203 61.111 0.00 0.00 35.26 3.93
673 675 2.104331 ATGTTCGCCGTCGCCTAG 59.896 61.111 0.00 0.00 35.26 3.02
674 676 4.789075 TGTTCGCCGTCGCCTAGC 62.789 66.667 0.00 0.00 35.26 3.42
675 677 4.789075 GTTCGCCGTCGCCTAGCA 62.789 66.667 0.00 0.00 35.26 3.49
676 678 4.492160 TTCGCCGTCGCCTAGCAG 62.492 66.667 0.00 0.00 35.26 4.24
679 681 4.874977 GCCGTCGCCTAGCAGACC 62.875 72.222 9.33 0.00 32.00 3.85
680 682 4.554363 CCGTCGCCTAGCAGACCG 62.554 72.222 9.33 5.83 32.00 4.79
729 862 5.554437 TTCATACTTCACTTGGTACCACA 57.446 39.130 16.04 5.34 0.00 4.17
801 934 4.361451 ACATTCATTTTAGCTCGCAAGG 57.639 40.909 0.00 0.00 38.47 3.61
839 972 6.423905 CCTCGAGAATTTCTAAACACAGTTGA 59.576 38.462 15.71 0.00 0.00 3.18
884 1017 5.919348 ATTTCTCCCATGGATCTACACAT 57.081 39.130 15.22 0.00 0.00 3.21
887 1020 2.304180 CTCCCATGGATCTACACATCCC 59.696 54.545 15.22 0.00 41.78 3.85
923 1056 6.756299 TCATGCAACAATTGTCTATTAGCA 57.244 33.333 12.39 14.61 34.41 3.49
937 1070 6.436218 TGTCTATTAGCATATACACATCCCGT 59.564 38.462 0.00 0.00 0.00 5.28
938 1071 7.612633 TGTCTATTAGCATATACACATCCCGTA 59.387 37.037 0.00 0.00 0.00 4.02
939 1072 8.464404 GTCTATTAGCATATACACATCCCGTAA 58.536 37.037 0.00 0.00 0.00 3.18
940 1073 9.197306 TCTATTAGCATATACACATCCCGTAAT 57.803 33.333 0.00 0.00 0.00 1.89
941 1074 9.817809 CTATTAGCATATACACATCCCGTAATT 57.182 33.333 0.00 0.00 0.00 1.40
944 1077 9.811995 TTAGCATATACACATCCCGTAATTATC 57.188 33.333 0.00 0.00 0.00 1.75
1015 1439 3.071206 AGATGACGACGGCCAGCT 61.071 61.111 2.24 0.88 0.00 4.24
1086 1510 1.051812 AAGATCCCCTCGTATGCAGG 58.948 55.000 0.00 0.00 0.00 4.85
1121 1545 2.890474 CGCCTCCGTGGTATGCAC 60.890 66.667 0.00 0.00 38.35 4.57
1172 1650 1.792006 GGTTTCTTCATCGACCACGT 58.208 50.000 0.00 0.00 40.69 4.49
1485 2044 1.450312 CAACGGGAAGCAGCCTAGG 60.450 63.158 3.67 3.67 0.00 3.02
1584 2143 4.808895 GGTTTGTTCATTTTCAGGTCCAAC 59.191 41.667 0.00 0.00 0.00 3.77
1757 2767 3.695606 GCGAGCAGAGGGTGGTGA 61.696 66.667 0.00 0.00 36.87 4.02
1787 2797 6.990939 GGTTTCCTCTTCTTATACGGCTTTAT 59.009 38.462 0.00 0.00 0.00 1.40
1813 2823 4.162040 CAATTATGGAGTCTGAAGCCCT 57.838 45.455 0.00 0.00 0.00 5.19
2014 3027 4.340950 ACAAGCTCTCTAAGACTAGCATCC 59.659 45.833 0.00 0.00 37.44 3.51
2066 3082 0.747255 ACTCCAGGTACTAGCATGCG 59.253 55.000 13.01 0.84 36.02 4.73
2105 3122 6.917217 TGGCAAAACAGAGTTAATTTTTGG 57.083 33.333 7.53 0.00 38.71 3.28
2132 3149 2.032799 TGTTGTTCACATTCTTCCGTGC 59.967 45.455 0.00 0.00 33.03 5.34
2144 3161 1.123756 CTTCCGTGCGAAGTTAACGAC 59.876 52.381 0.00 0.00 42.74 4.34
2161 3178 9.189723 AGTTAACGACTTTAAGTAGTTGTCATC 57.810 33.333 25.96 14.57 42.57 2.92
2387 3529 8.786898 TGCTAATAATCTGAAATCCATAACAGC 58.213 33.333 0.00 0.00 0.00 4.40
2443 3585 2.598565 TCACTTGCAGTAGAGTCCTGT 58.401 47.619 0.00 0.00 32.41 4.00
2453 3595 2.246719 AGAGTCCTGTTGCAAGTGAC 57.753 50.000 0.00 7.10 0.00 3.67
2454 3596 1.486310 AGAGTCCTGTTGCAAGTGACA 59.514 47.619 19.35 7.13 0.00 3.58
2455 3597 2.092968 AGAGTCCTGTTGCAAGTGACAA 60.093 45.455 19.35 0.00 0.00 3.18
2456 3598 2.017049 AGTCCTGTTGCAAGTGACAAC 58.983 47.619 19.35 9.99 46.05 3.32
2457 3599 2.017049 GTCCTGTTGCAAGTGACAACT 58.983 47.619 14.71 0.00 46.03 3.16
2458 3600 2.016318 TCCTGTTGCAAGTGACAACTG 58.984 47.619 0.00 14.16 46.03 3.16
2459 3601 2.016318 CCTGTTGCAAGTGACAACTGA 58.984 47.619 0.00 4.23 46.03 3.41
2460 3602 2.620115 CCTGTTGCAAGTGACAACTGAT 59.380 45.455 0.00 0.00 46.03 2.90
2464 3606 4.881273 TGTTGCAAGTGACAACTGATAAGT 59.119 37.500 0.00 0.00 46.03 2.24
2477 3619 7.916552 ACAACTGATAAGTTCATTTATACCGC 58.083 34.615 0.00 0.00 32.72 5.68
2526 3670 7.538334 TCATTTCATCGTTTCAAATTACAGCTG 59.462 33.333 13.48 13.48 0.00 4.24
2544 3688 7.178712 ACAGCTGCGAGTTTATGTTAATATC 57.821 36.000 15.27 0.00 0.00 1.63
2551 3695 8.761497 TGCGAGTTTATGTTAATATCTAGTTGC 58.239 33.333 0.00 0.00 0.00 4.17
2573 3717 4.392940 CTGCCTCCTTGTATCTATTTGGG 58.607 47.826 0.00 0.00 0.00 4.12
2574 3718 3.138283 TGCCTCCTTGTATCTATTTGGGG 59.862 47.826 0.00 0.00 0.00 4.96
2631 3775 6.644592 TCTTATGTTTGTAAAACAGGCATTGC 59.355 34.615 10.90 0.00 33.18 3.56
2661 3805 3.123621 CACGATGGAGCTAAAGTTGTGAC 59.876 47.826 0.00 0.00 0.00 3.67
2669 3813 3.561725 AGCTAAAGTTGTGACTTGTGAGC 59.438 43.478 10.62 10.62 45.18 4.26
2697 3841 1.421410 GATGACACGATGGGCACGAC 61.421 60.000 0.00 0.00 34.70 4.34
2698 3842 3.179265 GACACGATGGGCACGACG 61.179 66.667 3.17 3.17 34.70 5.12
2699 3843 3.620300 GACACGATGGGCACGACGA 62.620 63.158 11.29 0.00 34.70 4.20
2700 3844 3.179265 CACGATGGGCACGACGAC 61.179 66.667 11.29 0.00 34.70 4.34
2766 3910 3.873952 GGTTGAGCAGGTAAGCTTATCTG 59.126 47.826 33.40 33.40 46.75 2.90
2785 3929 1.210931 CGGCATGCAAGTTCAGGTG 59.789 57.895 21.36 0.00 0.00 4.00
2812 3956 6.843208 TGAACTGTTTAACGAAAATGTGTCA 58.157 32.000 0.00 0.00 0.00 3.58
2826 3970 9.787532 CGAAAATGTGTCACCTTCATTATTAAT 57.212 29.630 0.00 0.00 32.52 1.40
2887 4031 9.295825 TCATTTTCTCTAAAATACCTTGCTCAA 57.704 29.630 0.00 0.00 42.18 3.02
2937 4081 3.198068 TGCTTTCATGTATCGCTTCCTC 58.802 45.455 0.00 0.00 0.00 3.71
2938 4082 3.198068 GCTTTCATGTATCGCTTCCTCA 58.802 45.455 0.00 0.00 0.00 3.86
2964 4108 2.086610 TTTTCTCAAGGCCCTGCTTT 57.913 45.000 0.00 0.00 0.00 3.51
2982 4132 6.239008 CCTGCTTTCTCAACAGTTTTCCATTA 60.239 38.462 0.00 0.00 0.00 1.90
3005 4155 2.541120 CGCCATGCCTTGAGCTAGC 61.541 63.158 6.62 6.62 44.23 3.42
3022 4172 1.029947 AGCTTGGCGGGGAATTTACG 61.030 55.000 0.00 0.00 0.00 3.18
3034 4184 4.201881 GGGGAATTTACGCATGTTCTACAC 60.202 45.833 0.00 0.00 0.00 2.90
3069 4237 0.393537 CGCTTGGGCTGGATTCTCTT 60.394 55.000 0.00 0.00 36.09 2.85
3074 4244 0.820226 GGGCTGGATTCTCTTTTGCC 59.180 55.000 0.00 0.00 38.28 4.52
3091 4261 1.767681 TGCCTTTTGTCCTTGCCATTT 59.232 42.857 0.00 0.00 0.00 2.32
3168 4339 5.163478 GCCTTTTATGGATGAGAATGCTGTT 60.163 40.000 0.00 0.00 0.00 3.16
3177 4348 4.488126 TGAGAATGCTGTTGTGTTAAGC 57.512 40.909 0.00 0.00 37.46 3.09
3209 4386 4.890158 TGACATACTTCCTCTGCTTTGA 57.110 40.909 0.00 0.00 0.00 2.69
3265 4442 4.374689 TCTTGTAATTGGGTGCTGGTAA 57.625 40.909 0.00 0.00 0.00 2.85
3269 4446 4.667573 TGTAATTGGGTGCTGGTAAATGA 58.332 39.130 0.00 0.00 0.00 2.57
3272 4449 6.545666 TGTAATTGGGTGCTGGTAAATGATAG 59.454 38.462 0.00 0.00 0.00 2.08
3274 4451 2.849943 TGGGTGCTGGTAAATGATAGGT 59.150 45.455 0.00 0.00 0.00 3.08
3276 4453 4.475381 TGGGTGCTGGTAAATGATAGGTTA 59.525 41.667 0.00 0.00 0.00 2.85
3277 4454 5.133660 TGGGTGCTGGTAAATGATAGGTTAT 59.866 40.000 0.00 0.00 0.00 1.89
3278 4455 5.473504 GGGTGCTGGTAAATGATAGGTTATG 59.526 44.000 0.00 0.00 0.00 1.90
3279 4456 6.296026 GGTGCTGGTAAATGATAGGTTATGA 58.704 40.000 0.00 0.00 0.00 2.15
3280 4457 6.942576 GGTGCTGGTAAATGATAGGTTATGAT 59.057 38.462 0.00 0.00 0.00 2.45
3322 4500 2.881734 TCTGAGTGAGTGTGATCTGGT 58.118 47.619 0.00 0.00 0.00 4.00
3349 4527 3.118956 CGCCTTACCTGAGTGAAATCTCT 60.119 47.826 0.00 0.00 35.68 3.10
3376 4563 8.319057 TGTATAATGAGTACCTTCATGTTCCT 57.681 34.615 0.00 0.00 37.83 3.36
3397 4585 8.669243 GTTCCTTTAGTACAGATTTCTGAATGG 58.331 37.037 14.29 9.15 46.59 3.16
3457 4646 7.898636 TCCCATTAAAACTTCTATGGACCAAAT 59.101 33.333 0.00 0.00 39.93 2.32
3473 4662 5.278660 GGACCAAATGGAATCATACTGCATC 60.279 44.000 6.42 0.00 38.94 3.91
3475 4664 5.895534 ACCAAATGGAATCATACTGCATCTT 59.104 36.000 6.42 0.00 38.94 2.40
3491 4680 8.693120 ACTGCATCTTTTATCATCATCTCATT 57.307 30.769 0.00 0.00 0.00 2.57
3492 4681 9.132923 ACTGCATCTTTTATCATCATCTCATTT 57.867 29.630 0.00 0.00 0.00 2.32
3493 4682 9.967346 CTGCATCTTTTATCATCATCTCATTTT 57.033 29.630 0.00 0.00 0.00 1.82
3659 5558 2.192263 GAGAGAATCCCCACCTCACTT 58.808 52.381 0.00 0.00 33.66 3.16
3690 5591 6.851318 TGGGTGGATGATTCACATATGTAAT 58.149 36.000 8.32 8.82 39.56 1.89
3712 5613 9.583765 GTAATTATCTCTCGGTTATATGGTTCC 57.416 37.037 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.141909 AGAGCAATGAAAACCATGATATGAATG 58.858 33.333 0.00 0.00 35.24 2.67
13 15 3.379372 CCGAGAGCAATGAAAACCATGAT 59.621 43.478 0.00 0.00 35.24 2.45
66 68 2.143876 ACCAGTGCAAGTTCAACCTT 57.856 45.000 0.00 0.00 0.00 3.50
69 71 5.238583 AGATAGTACCAGTGCAAGTTCAAC 58.761 41.667 0.00 0.00 0.00 3.18
122 124 6.349363 CCCTCTAGAAAAGCGCAAACTAAAAT 60.349 38.462 11.47 0.00 0.00 1.82
124 126 4.454504 CCCTCTAGAAAAGCGCAAACTAAA 59.545 41.667 11.47 0.00 0.00 1.85
127 129 2.427506 CCCTCTAGAAAAGCGCAAACT 58.572 47.619 11.47 5.89 0.00 2.66
182 184 3.264193 AGCTATGGTGGATCAGTTTGACA 59.736 43.478 0.00 0.00 0.00 3.58
183 185 3.624861 CAGCTATGGTGGATCAGTTTGAC 59.375 47.826 0.00 0.00 0.00 3.18
262 264 4.518278 ATGGTGACCCAGCAATACAATA 57.482 40.909 0.00 0.00 46.15 1.90
263 265 2.897271 TGGTGACCCAGCAATACAAT 57.103 45.000 0.00 0.00 38.96 2.71
343 345 6.157820 TGATGGTAATGGGAGACAAGATGTTA 59.842 38.462 0.00 0.00 0.00 2.41
376 378 7.984002 TTGAATAATGCACGTAATTTGGATG 57.016 32.000 0.00 0.00 0.00 3.51
380 382 7.275697 TGCTTTGAATAATGCACGTAATTTG 57.724 32.000 0.00 0.00 40.67 2.32
382 384 7.257003 TGATGCTTTGAATAATGCACGTAATT 58.743 30.769 0.00 0.00 45.85 1.40
423 425 0.328592 TGGCGGTTTAATGGGCTGTA 59.671 50.000 0.00 0.00 0.00 2.74
450 452 2.105134 TGGGTGTTGACGTAATTCCTGT 59.895 45.455 0.00 0.00 0.00 4.00
451 453 2.773487 TGGGTGTTGACGTAATTCCTG 58.227 47.619 0.00 0.00 0.00 3.86
469 471 1.963515 GGCAAGGGCTTATGGTTATGG 59.036 52.381 0.00 0.00 40.87 2.74
470 472 1.963515 GGGCAAGGGCTTATGGTTATG 59.036 52.381 0.00 0.00 40.87 1.90
471 473 1.478654 CGGGCAAGGGCTTATGGTTAT 60.479 52.381 0.00 0.00 40.87 1.89
472 474 0.106918 CGGGCAAGGGCTTATGGTTA 60.107 55.000 0.00 0.00 40.87 2.85
473 475 1.379843 CGGGCAAGGGCTTATGGTT 60.380 57.895 0.00 0.00 40.87 3.67
474 476 2.275418 CGGGCAAGGGCTTATGGT 59.725 61.111 0.00 0.00 40.87 3.55
531 533 3.433306 TGGAAACTTCGGTGGATTCAT 57.567 42.857 0.00 0.00 0.00 2.57
558 560 1.071699 TGGTCCTGAAGGTGTACAAGC 59.928 52.381 0.00 0.00 36.34 4.01
572 574 0.693049 GAAGTGGTGGTCATGGTCCT 59.307 55.000 8.76 0.00 0.00 3.85
573 575 0.322546 GGAAGTGGTGGTCATGGTCC 60.323 60.000 0.00 0.00 0.00 4.46
574 576 0.693049 AGGAAGTGGTGGTCATGGTC 59.307 55.000 0.00 0.00 0.00 4.02
575 577 0.693049 GAGGAAGTGGTGGTCATGGT 59.307 55.000 0.00 0.00 0.00 3.55
576 578 0.391661 CGAGGAAGTGGTGGTCATGG 60.392 60.000 0.00 0.00 0.00 3.66
577 579 0.608130 TCGAGGAAGTGGTGGTCATG 59.392 55.000 0.00 0.00 0.00 3.07
578 580 0.608640 GTCGAGGAAGTGGTGGTCAT 59.391 55.000 0.00 0.00 0.00 3.06
579 581 1.469335 GGTCGAGGAAGTGGTGGTCA 61.469 60.000 0.00 0.00 0.00 4.02
580 582 1.186267 AGGTCGAGGAAGTGGTGGTC 61.186 60.000 0.00 0.00 0.00 4.02
581 583 1.152312 AGGTCGAGGAAGTGGTGGT 60.152 57.895 0.00 0.00 0.00 4.16
582 584 0.900647 AGAGGTCGAGGAAGTGGTGG 60.901 60.000 0.00 0.00 0.00 4.61
583 585 0.244994 CAGAGGTCGAGGAAGTGGTG 59.755 60.000 0.00 0.00 0.00 4.17
584 586 1.536943 GCAGAGGTCGAGGAAGTGGT 61.537 60.000 0.00 0.00 0.00 4.16
585 587 1.216710 GCAGAGGTCGAGGAAGTGG 59.783 63.158 0.00 0.00 0.00 4.00
586 588 0.534412 ATGCAGAGGTCGAGGAAGTG 59.466 55.000 0.00 0.00 0.00 3.16
587 589 0.820871 GATGCAGAGGTCGAGGAAGT 59.179 55.000 0.00 0.00 0.00 3.01
588 590 1.110442 AGATGCAGAGGTCGAGGAAG 58.890 55.000 0.00 0.00 0.00 3.46
589 591 0.820226 CAGATGCAGAGGTCGAGGAA 59.180 55.000 0.00 0.00 0.00 3.36
590 592 1.670949 GCAGATGCAGAGGTCGAGGA 61.671 60.000 0.00 0.00 41.59 3.71
591 593 1.227205 GCAGATGCAGAGGTCGAGG 60.227 63.158 0.00 0.00 41.59 4.63
592 594 1.227205 GGCAGATGCAGAGGTCGAG 60.227 63.158 7.19 0.00 44.36 4.04
593 595 2.725312 GGGCAGATGCAGAGGTCGA 61.725 63.158 7.19 0.00 44.36 4.20
594 596 2.202987 GGGCAGATGCAGAGGTCG 60.203 66.667 7.19 0.00 44.36 4.79
595 597 1.451028 GTGGGCAGATGCAGAGGTC 60.451 63.158 7.19 0.00 44.36 3.85
596 598 1.569030 ATGTGGGCAGATGCAGAGGT 61.569 55.000 7.19 0.00 44.36 3.85
597 599 0.818445 GATGTGGGCAGATGCAGAGG 60.818 60.000 7.19 0.00 44.36 3.69
598 600 0.180642 AGATGTGGGCAGATGCAGAG 59.819 55.000 7.19 0.00 44.36 3.35
599 601 0.179702 GAGATGTGGGCAGATGCAGA 59.820 55.000 7.19 0.00 44.36 4.26
600 602 1.158484 CGAGATGTGGGCAGATGCAG 61.158 60.000 7.19 0.00 44.36 4.41
601 603 1.153309 CGAGATGTGGGCAGATGCA 60.153 57.895 7.19 0.00 44.36 3.96
602 604 0.104855 TACGAGATGTGGGCAGATGC 59.895 55.000 0.00 0.00 41.14 3.91
603 605 1.269988 CCTACGAGATGTGGGCAGATG 60.270 57.143 0.00 0.00 42.84 2.90
604 606 1.043816 CCTACGAGATGTGGGCAGAT 58.956 55.000 0.00 0.00 42.84 2.90
605 607 2.504920 CCTACGAGATGTGGGCAGA 58.495 57.895 0.00 0.00 42.84 4.26
610 612 6.649557 GGGTAATTTTATCCTACGAGATGTGG 59.350 42.308 0.00 0.00 31.02 4.17
611 613 6.649557 GGGGTAATTTTATCCTACGAGATGTG 59.350 42.308 0.00 0.00 34.26 3.21
612 614 6.328148 TGGGGTAATTTTATCCTACGAGATGT 59.672 38.462 0.00 0.00 34.26 3.06
613 615 6.649557 GTGGGGTAATTTTATCCTACGAGATG 59.350 42.308 0.98 0.00 35.99 2.90
614 616 6.557633 AGTGGGGTAATTTTATCCTACGAGAT 59.442 38.462 9.62 0.00 46.51 2.75
615 617 5.901276 AGTGGGGTAATTTTATCCTACGAGA 59.099 40.000 9.62 0.00 46.51 4.04
616 618 6.170846 AGTGGGGTAATTTTATCCTACGAG 57.829 41.667 9.62 0.00 46.51 4.18
617 619 5.662208 TGAGTGGGGTAATTTTATCCTACGA 59.338 40.000 9.62 0.45 46.51 3.43
618 620 5.920903 TGAGTGGGGTAATTTTATCCTACG 58.079 41.667 9.62 0.00 46.51 3.51
619 621 7.498239 GTCTTGAGTGGGGTAATTTTATCCTAC 59.502 40.741 7.79 7.79 43.48 3.18
620 622 7.183112 TGTCTTGAGTGGGGTAATTTTATCCTA 59.817 37.037 0.00 0.00 34.26 2.94
621 623 6.011981 TGTCTTGAGTGGGGTAATTTTATCCT 60.012 38.462 0.00 0.00 34.26 3.24
622 624 6.184789 TGTCTTGAGTGGGGTAATTTTATCC 58.815 40.000 0.00 0.00 32.98 2.59
623 625 7.682021 GCATGTCTTGAGTGGGGTAATTTTATC 60.682 40.741 0.00 0.00 0.00 1.75
624 626 6.096846 GCATGTCTTGAGTGGGGTAATTTTAT 59.903 38.462 0.00 0.00 0.00 1.40
625 627 5.417580 GCATGTCTTGAGTGGGGTAATTTTA 59.582 40.000 0.00 0.00 0.00 1.52
626 628 4.220602 GCATGTCTTGAGTGGGGTAATTTT 59.779 41.667 0.00 0.00 0.00 1.82
627 629 3.763897 GCATGTCTTGAGTGGGGTAATTT 59.236 43.478 0.00 0.00 0.00 1.82
628 630 3.356290 GCATGTCTTGAGTGGGGTAATT 58.644 45.455 0.00 0.00 0.00 1.40
629 631 2.357154 GGCATGTCTTGAGTGGGGTAAT 60.357 50.000 0.00 0.00 0.00 1.89
630 632 1.004277 GGCATGTCTTGAGTGGGGTAA 59.996 52.381 0.00 0.00 0.00 2.85
631 633 0.618458 GGCATGTCTTGAGTGGGGTA 59.382 55.000 0.00 0.00 0.00 3.69
632 634 1.136329 AGGCATGTCTTGAGTGGGGT 61.136 55.000 0.00 0.00 0.00 4.95
633 635 0.038744 AAGGCATGTCTTGAGTGGGG 59.961 55.000 12.78 0.00 0.00 4.96
634 636 1.171308 CAAGGCATGTCTTGAGTGGG 58.829 55.000 31.82 6.32 44.98 4.61
635 637 1.901591 ACAAGGCATGTCTTGAGTGG 58.098 50.000 39.24 18.26 44.98 4.00
646 648 1.647545 CGGCGAACATGACAAGGCAT 61.648 55.000 0.00 0.00 0.00 4.40
647 649 2.324330 CGGCGAACATGACAAGGCA 61.324 57.895 0.00 0.00 0.00 4.75
648 650 2.240612 GACGGCGAACATGACAAGGC 62.241 60.000 16.62 0.00 0.00 4.35
649 651 1.787847 GACGGCGAACATGACAAGG 59.212 57.895 16.62 0.00 0.00 3.61
650 652 1.416049 CGACGGCGAACATGACAAG 59.584 57.895 16.62 0.00 40.82 3.16
651 653 2.663478 GCGACGGCGAACATGACAA 61.663 57.895 18.90 0.00 40.82 3.18
652 654 3.109547 GCGACGGCGAACATGACA 61.110 61.111 18.90 0.00 40.82 3.58
653 655 2.877360 TAGGCGACGGCGAACATGAC 62.877 60.000 18.90 0.00 41.24 3.06
654 656 2.607668 CTAGGCGACGGCGAACATGA 62.608 60.000 18.90 0.00 41.24 3.07
655 657 2.202690 TAGGCGACGGCGAACATG 60.203 61.111 18.90 0.00 41.24 3.21
656 658 2.104331 CTAGGCGACGGCGAACAT 59.896 61.111 18.90 0.00 41.24 2.71
657 659 4.789075 GCTAGGCGACGGCGAACA 62.789 66.667 18.90 0.00 41.24 3.18
658 660 4.789075 TGCTAGGCGACGGCGAAC 62.789 66.667 18.90 6.17 41.24 3.95
659 661 4.492160 CTGCTAGGCGACGGCGAA 62.492 66.667 18.90 7.52 41.24 4.70
662 664 4.874977 GGTCTGCTAGGCGACGGC 62.875 72.222 14.41 14.41 34.70 5.68
663 665 4.554363 CGGTCTGCTAGGCGACGG 62.554 72.222 0.00 0.00 34.70 4.79
665 667 4.129737 TGCGGTCTGCTAGGCGAC 62.130 66.667 5.01 0.00 46.63 5.19
666 668 3.826754 CTGCGGTCTGCTAGGCGA 61.827 66.667 5.01 0.00 46.63 5.54
667 669 3.649277 AACTGCGGTCTGCTAGGCG 62.649 63.158 0.00 0.00 46.63 5.52
668 670 2.103042 CAACTGCGGTCTGCTAGGC 61.103 63.158 0.00 0.00 46.63 3.93
669 671 2.103042 GCAACTGCGGTCTGCTAGG 61.103 63.158 19.33 0.00 46.63 3.02
670 672 2.103042 GGCAACTGCGGTCTGCTAG 61.103 63.158 23.13 3.61 46.63 3.42
671 673 2.047274 GGCAACTGCGGTCTGCTA 60.047 61.111 23.13 0.00 46.63 3.49
672 674 4.254709 TGGCAACTGCGGTCTGCT 62.255 61.111 23.13 0.00 46.63 4.24
673 675 4.030452 GTGGCAACTGCGGTCTGC 62.030 66.667 18.74 18.74 46.70 4.26
674 676 3.357079 GGTGGCAACTGCGGTCTG 61.357 66.667 0.00 0.84 43.26 3.51
675 677 2.902423 TTTGGTGGCAACTGCGGTCT 62.902 55.000 3.27 0.00 43.26 3.85
676 678 2.406452 CTTTGGTGGCAACTGCGGTC 62.406 60.000 3.27 0.00 43.26 4.79
677 679 2.441164 TTTGGTGGCAACTGCGGT 60.441 55.556 3.27 0.00 43.26 5.68
678 680 1.526575 ATCTTTGGTGGCAACTGCGG 61.527 55.000 3.27 0.00 43.26 5.69
679 681 1.131126 CTATCTTTGGTGGCAACTGCG 59.869 52.381 3.27 0.00 43.26 5.18
680 682 1.474077 CCTATCTTTGGTGGCAACTGC 59.526 52.381 3.27 0.00 41.14 4.40
681 683 3.071874 TCCTATCTTTGGTGGCAACTG 57.928 47.619 3.27 0.00 37.61 3.16
729 862 5.325239 CATTACAAAAGGGGAAGAGAAGGT 58.675 41.667 0.00 0.00 0.00 3.50
775 908 6.247727 TGCGAGCTAAAATGAATGTTAACA 57.752 33.333 11.41 11.41 0.00 2.41
801 934 6.442513 AATTCTCGAGGTCCAAATCAAATC 57.557 37.500 13.56 0.00 0.00 2.17
839 972 6.855763 TTCTGGAGGTGCAAATCAAATTAT 57.144 33.333 0.00 0.00 0.00 1.28
846 979 4.142293 GGAGAAATTCTGGAGGTGCAAATC 60.142 45.833 0.00 0.00 0.00 2.17
852 985 3.285484 CATGGGAGAAATTCTGGAGGTG 58.715 50.000 0.00 0.00 0.00 4.00
884 1017 5.482163 TGCATGATCAGATAATTACGGGA 57.518 39.130 0.09 0.00 0.00 5.14
887 1020 8.898792 CAATTGTTGCATGATCAGATAATTACG 58.101 33.333 0.09 0.00 0.00 3.18
927 1060 6.479972 TCTTGAGATAATTACGGGATGTGT 57.520 37.500 0.00 0.00 0.00 3.72
931 1064 7.967908 AGTGATTCTTGAGATAATTACGGGAT 58.032 34.615 0.00 0.00 29.60 3.85
933 1066 7.169982 GTGAGTGATTCTTGAGATAATTACGGG 59.830 40.741 0.00 0.00 29.60 5.28
934 1067 7.706607 TGTGAGTGATTCTTGAGATAATTACGG 59.293 37.037 0.00 0.00 29.60 4.02
937 1070 9.809096 GAGTGTGAGTGATTCTTGAGATAATTA 57.191 33.333 0.00 0.00 0.00 1.40
938 1071 8.316946 TGAGTGTGAGTGATTCTTGAGATAATT 58.683 33.333 0.00 0.00 0.00 1.40
939 1072 7.763528 GTGAGTGTGAGTGATTCTTGAGATAAT 59.236 37.037 0.00 0.00 0.00 1.28
940 1073 7.093354 GTGAGTGTGAGTGATTCTTGAGATAA 58.907 38.462 0.00 0.00 0.00 1.75
941 1074 6.209391 TGTGAGTGTGAGTGATTCTTGAGATA 59.791 38.462 0.00 0.00 0.00 1.98
943 1076 4.342092 TGTGAGTGTGAGTGATTCTTGAGA 59.658 41.667 0.00 0.00 0.00 3.27
944 1077 4.625028 TGTGAGTGTGAGTGATTCTTGAG 58.375 43.478 0.00 0.00 0.00 3.02
997 1421 2.842394 AAGCTGGCCGTCGTCATCTG 62.842 60.000 0.00 0.00 0.00 2.90
1015 1439 3.771160 GAGGAGGCGGCGGAGAAA 61.771 66.667 9.78 0.00 0.00 2.52
1456 2015 2.033448 CCCGTTGCTGCCTACCAA 59.967 61.111 0.00 0.00 0.00 3.67
1490 2049 2.434359 AGTAAACGCAGGCGAGCC 60.434 61.111 21.62 5.89 42.83 4.70
1757 2767 5.070580 CCGTATAAGAAGAGGAAACCCATCT 59.929 44.000 0.00 0.00 0.00 2.90
1787 2797 2.115427 TCAGACTCCATAATTGGGCGA 58.885 47.619 0.00 0.00 43.81 5.54
2014 3027 6.528537 TTCAAATGGATGGTACCAAGAATG 57.471 37.500 20.76 13.17 43.47 2.67
2066 3082 5.637006 TTTGCCATATCCACAGTGTAAAC 57.363 39.130 0.00 0.00 0.00 2.01
2144 3161 7.981789 TGCTATGAGGATGACAACTACTTAAAG 59.018 37.037 0.00 0.00 0.00 1.85
2241 3377 9.104965 GTTGGTTCAGGCTAACTTTAAATTTTT 57.895 29.630 0.00 0.00 0.00 1.94
2258 3395 3.713858 TTGACATTGCAGTTGGTTCAG 57.286 42.857 4.06 0.00 0.00 3.02
2345 3487 9.820725 GATTATTAGCAAGATCAGCAGAGATAT 57.179 33.333 11.97 0.08 0.00 1.63
2387 3529 8.903570 TTATTTGTAAATTGCATACCAAGTCG 57.096 30.769 0.00 0.00 36.76 4.18
2443 3585 5.588246 TGAACTTATCAGTTGTCACTTGCAA 59.412 36.000 0.00 0.00 43.79 4.08
2453 3595 7.042992 TCGCGGTATAAATGAACTTATCAGTTG 60.043 37.037 6.13 0.00 45.31 3.16
2455 3597 6.509656 TCGCGGTATAAATGAACTTATCAGT 58.490 36.000 6.13 0.00 42.53 3.41
2456 3598 7.402811 TTCGCGGTATAAATGAACTTATCAG 57.597 36.000 6.13 0.00 42.53 2.90
2457 3599 7.773864 TTTCGCGGTATAAATGAACTTATCA 57.226 32.000 6.13 0.00 43.67 2.15
2497 3641 9.398170 CTGTAATTTGAAACGATGAAATGAACT 57.602 29.630 0.00 0.00 0.00 3.01
2526 3670 8.979574 AGCAACTAGATATTAACATAAACTCGC 58.020 33.333 0.00 0.00 0.00 5.03
2544 3688 3.133721 AGATACAAGGAGGCAGCAACTAG 59.866 47.826 0.00 0.00 0.00 2.57
2551 3695 4.392940 CCCAAATAGATACAAGGAGGCAG 58.607 47.826 0.00 0.00 0.00 4.85
2573 3717 5.670485 ACCAATGACTTTCCAAAGAAAACC 58.330 37.500 6.05 0.00 41.40 3.27
2574 3718 6.593770 ACAACCAATGACTTTCCAAAGAAAAC 59.406 34.615 6.05 0.00 41.40 2.43
2631 3775 1.448540 GCTCCATCGTGTCCACCAG 60.449 63.158 0.00 0.00 0.00 4.00
2661 3805 0.606401 ATCCACCAACGGCTCACAAG 60.606 55.000 0.00 0.00 0.00 3.16
2669 3813 0.391130 ATCGTGTCATCCACCAACGG 60.391 55.000 0.00 0.00 41.26 4.44
2697 3841 4.856487 ACTGAACAATTGTTTTGTGTGTCG 59.144 37.500 24.02 8.53 38.56 4.35
2698 3842 6.704512 AACTGAACAATTGTTTTGTGTGTC 57.295 33.333 24.02 10.08 38.56 3.67
2699 3843 7.598278 TCTAACTGAACAATTGTTTTGTGTGT 58.402 30.769 24.02 13.41 38.56 3.72
2700 3844 8.633075 ATCTAACTGAACAATTGTTTTGTGTG 57.367 30.769 24.02 18.43 38.56 3.82
2743 3887 2.380084 TAAGCTTACCTGCTCAACCG 57.620 50.000 0.86 0.00 43.24 4.44
2766 3910 2.180017 CCTGAACTTGCATGCCGC 59.820 61.111 16.68 0.22 42.89 6.53
2768 3912 0.242017 GACACCTGAACTTGCATGCC 59.758 55.000 16.68 0.00 0.00 4.40
2780 3924 4.116961 TCGTTAAACAGTTCAGACACCTG 58.883 43.478 0.00 0.00 41.74 4.00
2785 3929 6.964934 ACACATTTTCGTTAAACAGTTCAGAC 59.035 34.615 0.00 0.00 0.00 3.51
2798 3942 5.514274 AATGAAGGTGACACATTTTCGTT 57.486 34.783 6.97 11.34 36.64 3.85
2826 3970 8.851541 ATTTTGGTAACCGAGAAATGTTACTA 57.148 30.769 11.09 4.06 43.91 1.82
2828 3972 8.806177 AAATTTTGGTAACCGAGAAATGTTAC 57.194 30.769 0.00 0.00 43.78 2.50
2840 3984 9.710900 AAATGATCTCTTGAAATTTTGGTAACC 57.289 29.630 0.00 0.00 0.00 2.85
2873 4017 4.402474 GGGCAATAGTTGAGCAAGGTATTT 59.598 41.667 0.00 0.00 0.00 1.40
2878 4022 1.474077 GTGGGCAATAGTTGAGCAAGG 59.526 52.381 0.00 0.00 0.00 3.61
2937 4081 4.280174 CAGGGCCTTGAGAAAATATCCATG 59.720 45.833 9.80 0.00 0.00 3.66
2938 4082 4.477249 CAGGGCCTTGAGAAAATATCCAT 58.523 43.478 9.80 0.00 0.00 3.41
2964 4108 5.468746 CGAAGGTAATGGAAAACTGTTGAGA 59.531 40.000 0.00 0.00 0.00 3.27
2982 4132 1.377725 CTCAAGGCATGGCGAAGGT 60.378 57.895 14.30 0.00 0.00 3.50
3005 4155 1.309499 TGCGTAAATTCCCCGCCAAG 61.309 55.000 12.05 0.00 46.44 3.61
3050 4218 0.393537 AAGAGAATCCAGCCCAAGCG 60.394 55.000 0.00 0.00 39.63 4.68
3051 4219 1.844687 AAAGAGAATCCAGCCCAAGC 58.155 50.000 0.00 0.00 35.29 4.01
3064 4232 3.181476 GCAAGGACAAAAGGCAAAAGAGA 60.181 43.478 0.00 0.00 0.00 3.10
3065 4233 3.126073 GCAAGGACAAAAGGCAAAAGAG 58.874 45.455 0.00 0.00 0.00 2.85
3069 4237 1.198713 TGGCAAGGACAAAAGGCAAA 58.801 45.000 0.00 0.00 33.37 3.68
3074 4244 6.690530 TGAATCTAAATGGCAAGGACAAAAG 58.309 36.000 0.00 0.00 0.00 2.27
3091 4261 3.263170 TGGCTGCAAGGTAGTTGAATCTA 59.737 43.478 0.50 0.00 38.60 1.98
3168 4339 2.823924 TTCTGCTACCGCTTAACACA 57.176 45.000 0.00 0.00 36.97 3.72
3177 4348 4.051922 GGAAGTATGTCATTCTGCTACCG 58.948 47.826 0.00 0.00 0.00 4.02
3280 4457 9.581289 TCAGATCCTAATTTTTAGTCAAACCAA 57.419 29.630 0.00 0.00 0.00 3.67
3291 4469 7.453393 TCACACTCACTCAGATCCTAATTTTT 58.547 34.615 0.00 0.00 0.00 1.94
3322 4500 2.250031 TCACTCAGGTAAGGCGGTAAA 58.750 47.619 0.00 0.00 0.00 2.01
3349 4527 9.391006 GGAACATGAAGGTACTCATTATACAAA 57.609 33.333 0.00 0.00 38.49 2.83
3376 4563 7.685481 TGGTCCATTCAGAAATCTGTACTAAA 58.315 34.615 10.06 0.00 44.12 1.85
3379 4566 5.762179 TGGTCCATTCAGAAATCTGTACT 57.238 39.130 10.06 0.00 44.12 2.73
3457 4646 8.929260 ATGATAAAAGATGCAGTATGATTCCA 57.071 30.769 0.00 0.00 39.69 3.53
3636 5535 2.573915 GTGAGGTGGGGATTCTCTCTTT 59.426 50.000 0.00 0.00 0.00 2.52
3637 5536 2.192263 GTGAGGTGGGGATTCTCTCTT 58.808 52.381 0.00 0.00 0.00 2.85
3659 5558 3.826157 GTGAATCATCCACCCAACTTTGA 59.174 43.478 0.00 0.00 0.00 2.69
3690 5591 7.606135 TTGGAACCATATAACCGAGAGATAA 57.394 36.000 0.00 0.00 0.00 1.75
3712 5613 8.991243 ACCATACACAGATTGAAAAATGATTG 57.009 30.769 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.