Multiple sequence alignment - TraesCS2D01G209800

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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 TraesCS2D01G209800 chr2D 100.000 4055 0 0 1 4055 165486585 165482531 0.000000e+00 7489
1 TraesCS2D01G209800 chr2D 88.781 1649 100 42 681 2319 165333137 165334710 0.000000e+00 1941
2 TraesCS2D01G209800 chr2D 92.103 1013 64 10 2315 3316 165340076 165341083 0.000000e+00 1413
3 TraesCS2D01G209800 chr2D 95.726 234 7 2 442 673 165491480 165491712 1.380000e-99 374
4 TraesCS2D01G209800 chr2A 92.799 2222 122 12 1834 4055 185269395 185271578 0.000000e+00 3182
5 TraesCS2D01G209800 chr2A 92.062 2066 128 21 1213 3263 185364742 185362698 0.000000e+00 2874
6 TraesCS2D01G209800 chr2A 90.893 1120 67 17 680 1795 185264404 185265492 0.000000e+00 1471
7 TraesCS2D01G209800 chr2A 87.090 488 33 14 681 1157 185365226 185364758 3.590000e-145 525
8 TraesCS2D01G209800 chr2B 92.919 2076 96 15 998 3070 232291521 232289494 0.000000e+00 2972
9 TraesCS2D01G209800 chr2B 92.378 1863 93 24 995 2857 232261313 232263126 0.000000e+00 2608
10 TraesCS2D01G209800 chr2B 91.800 1061 73 8 2866 3924 232264237 232265285 0.000000e+00 1465
11 TraesCS2D01G209800 chr2B 90.647 278 12 6 680 947 232291806 232291533 1.390000e-94 357
12 TraesCS2D01G209800 chr2B 91.327 196 8 5 680 871 232257508 232257698 4.020000e-65 259
13 TraesCS2D01G209800 chr2B 86.188 181 19 5 3088 3267 232289170 232288995 1.490000e-44 191
14 TraesCS2D01G209800 chr2B 93.750 96 6 0 3960 4055 232265483 232265578 1.170000e-30 145
15 TraesCS2D01G209800 chr7D 82.625 2118 300 45 996 3081 149086009 149083928 0.000000e+00 1810
16 TraesCS2D01G209800 chr7D 84.679 1201 168 13 1860 3055 149181891 149183080 0.000000e+00 1184
17 TraesCS2D01G209800 chr7D 96.302 676 21 1 2 673 46784311 46784986 0.000000e+00 1107
18 TraesCS2D01G209800 chr7D 84.293 764 83 21 996 1753 149181076 149181808 0.000000e+00 712
19 TraesCS2D01G209800 chr7A 81.734 2157 318 55 996 3123 149862953 149860844 0.000000e+00 1731
20 TraesCS2D01G209800 chr7A 85.988 992 139 0 1852 2843 150022491 150023482 0.000000e+00 1062
21 TraesCS2D01G209800 chr7A 96.567 233 6 1 443 673 25053284 25053052 6.360000e-103 385
22 TraesCS2D01G209800 chr7A 95.473 243 8 2 442 682 732735450 732735691 6.360000e-103 385
23 TraesCS2D01G209800 chr7A 95.690 232 7 2 442 673 25057945 25058173 1.780000e-98 370
24 TraesCS2D01G209800 chr7B 85.887 992 140 0 1852 2843 111943049 111944040 0.000000e+00 1057
25 TraesCS2D01G209800 chr7B 90.841 535 49 0 1219 1753 111942447 111942981 0.000000e+00 717
26 TraesCS2D01G209800 chr3A 81.841 1206 197 18 1860 3053 608195757 608194562 0.000000e+00 994
27 TraesCS2D01G209800 chr3B 80.526 1217 205 22 1860 3053 618155765 618154558 0.000000e+00 905
28 TraesCS2D01G209800 chr5B 78.543 1235 214 27 1854 3061 679312541 679313751 0.000000e+00 765
29 TraesCS2D01G209800 chr5B 84.149 776 85 19 996 1753 679310915 679311670 0.000000e+00 717
30 TraesCS2D01G209800 chr5A 95.851 241 8 1 443 681 519535969 519536209 4.910000e-104 388
31 TraesCS2D01G209800 chr5A 96.137 233 7 1 443 673 374082143 374082375 2.960000e-101 379
32 TraesCS2D01G209800 chr5A 95.726 234 8 1 442 673 374050350 374050117 3.830000e-100 375
33 TraesCS2D01G209800 chr5A 95.299 234 9 1 442 673 519530515 519530282 1.780000e-98 370


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 TraesCS2D01G209800 chr2D 165482531 165486585 4054 True 7489.000000 7489 100.00000 1 4055 1 chr2D.!!$R1 4054
1 TraesCS2D01G209800 chr2D 165333137 165334710 1573 False 1941.000000 1941 88.78100 681 2319 1 chr2D.!!$F1 1638
2 TraesCS2D01G209800 chr2D 165340076 165341083 1007 False 1413.000000 1413 92.10300 2315 3316 1 chr2D.!!$F2 1001
3 TraesCS2D01G209800 chr2A 185264404 185271578 7174 False 2326.500000 3182 91.84600 680 4055 2 chr2A.!!$F1 3375
4 TraesCS2D01G209800 chr2A 185362698 185365226 2528 True 1699.500000 2874 89.57600 681 3263 2 chr2A.!!$R1 2582
5 TraesCS2D01G209800 chr2B 232288995 232291806 2811 True 1173.333333 2972 89.91800 680 3267 3 chr2B.!!$R1 2587
6 TraesCS2D01G209800 chr2B 232257508 232265578 8070 False 1119.250000 2608 92.31375 680 4055 4 chr2B.!!$F1 3375
7 TraesCS2D01G209800 chr7D 149083928 149086009 2081 True 1810.000000 1810 82.62500 996 3081 1 chr7D.!!$R1 2085
8 TraesCS2D01G209800 chr7D 46784311 46784986 675 False 1107.000000 1107 96.30200 2 673 1 chr7D.!!$F1 671
9 TraesCS2D01G209800 chr7D 149181076 149183080 2004 False 948.000000 1184 84.48600 996 3055 2 chr7D.!!$F2 2059
10 TraesCS2D01G209800 chr7A 149860844 149862953 2109 True 1731.000000 1731 81.73400 996 3123 1 chr7A.!!$R2 2127
11 TraesCS2D01G209800 chr7A 150022491 150023482 991 False 1062.000000 1062 85.98800 1852 2843 1 chr7A.!!$F2 991
12 TraesCS2D01G209800 chr7B 111942447 111944040 1593 False 887.000000 1057 88.36400 1219 2843 2 chr7B.!!$F1 1624
13 TraesCS2D01G209800 chr3A 608194562 608195757 1195 True 994.000000 994 81.84100 1860 3053 1 chr3A.!!$R1 1193
14 TraesCS2D01G209800 chr3B 618154558 618155765 1207 True 905.000000 905 80.52600 1860 3053 1 chr3B.!!$R1 1193
15 TraesCS2D01G209800 chr5B 679310915 679313751 2836 False 741.000000 765 81.34600 996 3061 2 chr5B.!!$F1 2065

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
476 477 0.041312 TTTCTGCAAAGAAGACGCGC 60.041 50.0 5.73 0.00 0.0 6.86 F
543 544 0.108377 ATGCCAGCACGTCGTATGAA 60.108 50.0 10.48 1.06 0.0 2.57 F
1882 10119 0.235926 GACACGTTCAAGCTGAAGGC 59.764 55.0 14.42 0.00 43.7 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1828 6197 0.165944 GTGCACGGTAAGCATGACAC 59.834 55.0 0.00 0.0 44.79 3.67 R
2228 10486 0.242825 CGTTGAACCTCGGCAGAGTA 59.757 55.0 13.02 0.0 42.86 2.59 R
3144 12814 1.238439 CAAGACCCGCACACTGATTT 58.762 50.0 0.00 0.0 0.00 2.17 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
68 69 2.020720 TCGGTTTGCAACAACATGAGT 58.979 42.857 0.00 0.00 0.00 3.41
76 77 2.698803 CAACAACATGAGTCGGATCCA 58.301 47.619 13.41 0.00 0.00 3.41
89 90 1.668419 GGATCCAGTGAACATTCCGG 58.332 55.000 6.95 0.00 0.00 5.14
92 93 0.109532 TCCAGTGAACATTCCGGCAA 59.890 50.000 0.00 0.00 0.00 4.52
107 108 1.278127 CGGCAACTCCTCCTCCTAAAA 59.722 52.381 0.00 0.00 0.00 1.52
179 180 5.596361 AGACAGATCTGTTACCTCATAGTGG 59.404 44.000 28.46 0.00 45.05 4.00
311 312 2.027625 GCCACCTAGTGCACACGTC 61.028 63.158 21.04 0.00 36.20 4.34
385 386 1.304134 GCGATTTGGGAACAGGGGT 60.304 57.895 0.00 0.00 44.54 4.95
423 424 2.359230 GCCACTGTCAGCAGGGTC 60.359 66.667 12.46 1.09 44.44 4.46
449 450 2.278854 TGCGTAAATAGTAAACGGGCC 58.721 47.619 0.00 0.00 37.12 5.80
450 451 2.278854 GCGTAAATAGTAAACGGGCCA 58.721 47.619 4.39 0.00 37.12 5.36
451 452 2.677337 GCGTAAATAGTAAACGGGCCAA 59.323 45.455 4.39 0.00 37.12 4.52
452 453 3.242511 GCGTAAATAGTAAACGGGCCAAG 60.243 47.826 4.39 0.00 37.12 3.61
453 454 3.310501 CGTAAATAGTAAACGGGCCAAGG 59.689 47.826 4.39 0.00 33.13 3.61
454 455 2.430248 AATAGTAAACGGGCCAAGGG 57.570 50.000 4.39 0.00 0.00 3.95
455 456 0.549469 ATAGTAAACGGGCCAAGGGG 59.451 55.000 4.39 0.00 37.18 4.79
456 457 0.841594 TAGTAAACGGGCCAAGGGGT 60.842 55.000 4.39 0.00 36.17 4.95
457 458 1.228644 GTAAACGGGCCAAGGGGTT 60.229 57.895 4.39 0.00 36.17 4.11
458 459 0.828762 GTAAACGGGCCAAGGGGTTT 60.829 55.000 4.39 8.03 36.62 3.27
459 460 0.105607 TAAACGGGCCAAGGGGTTTT 60.106 50.000 4.39 0.00 34.68 2.43
460 461 1.404479 AAACGGGCCAAGGGGTTTTC 61.404 55.000 4.39 0.00 36.17 2.29
461 462 2.117423 CGGGCCAAGGGGTTTTCT 59.883 61.111 4.39 0.00 36.17 2.52
462 463 2.275380 CGGGCCAAGGGGTTTTCTG 61.275 63.158 4.39 0.00 36.17 3.02
463 464 2.583441 GGGCCAAGGGGTTTTCTGC 61.583 63.158 4.39 0.00 36.17 4.26
464 465 1.836604 GGCCAAGGGGTTTTCTGCA 60.837 57.895 0.00 0.00 36.17 4.41
465 466 1.406860 GGCCAAGGGGTTTTCTGCAA 61.407 55.000 0.00 0.00 36.17 4.08
466 467 0.467804 GCCAAGGGGTTTTCTGCAAA 59.532 50.000 0.00 0.00 36.17 3.68
467 468 1.541015 GCCAAGGGGTTTTCTGCAAAG 60.541 52.381 0.00 0.00 36.17 2.77
468 469 2.038659 CCAAGGGGTTTTCTGCAAAGA 58.961 47.619 0.00 0.00 0.00 2.52
469 470 2.433970 CCAAGGGGTTTTCTGCAAAGAA 59.566 45.455 0.00 0.00 0.00 2.52
470 471 3.493176 CCAAGGGGTTTTCTGCAAAGAAG 60.493 47.826 0.00 0.00 0.00 2.85
471 472 3.312736 AGGGGTTTTCTGCAAAGAAGA 57.687 42.857 0.00 0.00 0.00 2.87
472 473 2.959030 AGGGGTTTTCTGCAAAGAAGAC 59.041 45.455 1.89 1.89 33.69 3.01
473 474 2.287608 GGGGTTTTCTGCAAAGAAGACG 60.288 50.000 4.08 0.00 34.81 4.18
474 475 2.385315 GGTTTTCTGCAAAGAAGACGC 58.615 47.619 4.08 0.00 34.81 5.19
475 476 2.036933 GTTTTCTGCAAAGAAGACGCG 58.963 47.619 3.53 3.53 0.00 6.01
476 477 0.041312 TTTCTGCAAAGAAGACGCGC 60.041 50.000 5.73 0.00 0.00 6.86
477 478 2.158058 TTCTGCAAAGAAGACGCGCG 62.158 55.000 30.96 30.96 0.00 6.86
478 479 4.368808 TGCAAAGAAGACGCGCGC 62.369 61.111 32.58 23.91 0.00 6.86
501 502 4.918201 GCCGGGCGGAATCAGAGG 62.918 72.222 1.81 0.00 37.50 3.69
502 503 4.918201 CCGGGCGGAATCAGAGGC 62.918 72.222 0.00 0.00 37.50 4.70
503 504 3.854669 CGGGCGGAATCAGAGGCT 61.855 66.667 0.00 0.00 0.00 4.58
504 505 2.203126 GGGCGGAATCAGAGGCTG 60.203 66.667 0.00 0.00 0.00 4.85
505 506 2.899339 GGCGGAATCAGAGGCTGC 60.899 66.667 0.00 0.00 0.00 5.25
506 507 2.899339 GCGGAATCAGAGGCTGCC 60.899 66.667 11.65 11.65 0.00 4.85
507 508 2.586245 CGGAATCAGAGGCTGCCA 59.414 61.111 22.65 0.00 0.00 4.92
508 509 1.523258 CGGAATCAGAGGCTGCCAG 60.523 63.158 22.65 10.42 0.00 4.85
509 510 1.823041 GGAATCAGAGGCTGCCAGC 60.823 63.158 22.65 8.55 41.46 4.85
510 511 2.124819 AATCAGAGGCTGCCAGCG 60.125 61.111 22.65 8.19 43.62 5.18
511 512 3.694058 AATCAGAGGCTGCCAGCGG 62.694 63.158 22.65 12.96 43.62 5.52
529 530 2.123769 GCCAGGTATGCCATGCCA 60.124 61.111 14.55 0.00 37.52 4.92
530 531 2.198287 GCCAGGTATGCCATGCCAG 61.198 63.158 14.55 5.90 37.52 4.85
531 532 2.198287 CCAGGTATGCCATGCCAGC 61.198 63.158 14.55 0.00 37.52 4.85
532 533 1.454295 CAGGTATGCCATGCCAGCA 60.454 57.895 14.55 0.00 45.94 4.41
533 534 1.454479 AGGTATGCCATGCCAGCAC 60.454 57.895 14.55 0.00 44.40 4.40
534 535 2.717485 GTATGCCATGCCAGCACG 59.283 61.111 0.00 0.00 44.40 5.34
535 536 2.114670 GTATGCCATGCCAGCACGT 61.115 57.895 0.00 0.00 44.40 4.49
536 537 1.819208 TATGCCATGCCAGCACGTC 60.819 57.895 0.00 0.00 44.40 4.34
539 540 2.125713 CCATGCCAGCACGTCGTA 60.126 61.111 0.00 0.00 0.00 3.43
540 541 1.521457 CCATGCCAGCACGTCGTAT 60.521 57.895 0.00 0.00 0.00 3.06
541 542 1.637934 CATGCCAGCACGTCGTATG 59.362 57.895 0.00 0.00 0.00 2.39
542 543 0.805711 CATGCCAGCACGTCGTATGA 60.806 55.000 10.48 0.00 0.00 2.15
543 544 0.108377 ATGCCAGCACGTCGTATGAA 60.108 50.000 10.48 1.06 0.00 2.57
544 545 0.735978 TGCCAGCACGTCGTATGAAG 60.736 55.000 10.48 0.00 0.00 3.02
545 546 1.421410 GCCAGCACGTCGTATGAAGG 61.421 60.000 10.48 4.71 0.00 3.46
546 547 1.421410 CCAGCACGTCGTATGAAGGC 61.421 60.000 10.48 3.55 0.00 4.35
547 548 0.735978 CAGCACGTCGTATGAAGGCA 60.736 55.000 0.00 0.00 0.00 4.75
548 549 0.458543 AGCACGTCGTATGAAGGCAG 60.459 55.000 0.00 0.60 0.00 4.85
549 550 0.457853 GCACGTCGTATGAAGGCAGA 60.458 55.000 0.00 0.00 0.00 4.26
550 551 1.269166 CACGTCGTATGAAGGCAGAC 58.731 55.000 0.00 0.00 33.00 3.51
556 557 2.622064 GTATGAAGGCAGACGGGATT 57.378 50.000 0.00 0.00 0.00 3.01
557 558 2.919228 GTATGAAGGCAGACGGGATTT 58.081 47.619 0.00 0.00 0.00 2.17
558 559 1.755179 ATGAAGGCAGACGGGATTTG 58.245 50.000 0.00 0.00 0.00 2.32
559 560 0.400213 TGAAGGCAGACGGGATTTGT 59.600 50.000 0.00 0.00 0.00 2.83
560 561 0.804989 GAAGGCAGACGGGATTTGTG 59.195 55.000 0.00 0.00 0.00 3.33
561 562 0.400213 AAGGCAGACGGGATTTGTGA 59.600 50.000 0.00 0.00 0.00 3.58
562 563 0.321653 AGGCAGACGGGATTTGTGAC 60.322 55.000 0.00 0.00 0.00 3.67
563 564 1.305930 GGCAGACGGGATTTGTGACC 61.306 60.000 0.00 0.00 0.00 4.02
569 570 2.018542 CGGGATTTGTGACCGTATGT 57.981 50.000 0.00 0.00 42.53 2.29
570 571 1.663643 CGGGATTTGTGACCGTATGTG 59.336 52.381 0.00 0.00 42.53 3.21
571 572 1.400494 GGGATTTGTGACCGTATGTGC 59.600 52.381 0.00 0.00 0.00 4.57
572 573 2.080693 GGATTTGTGACCGTATGTGCA 58.919 47.619 0.00 0.00 0.00 4.57
573 574 2.159572 GGATTTGTGACCGTATGTGCAC 60.160 50.000 10.75 10.75 0.00 4.57
574 575 0.862490 TTTGTGACCGTATGTGCACG 59.138 50.000 13.13 0.00 41.59 5.34
575 576 0.249531 TTGTGACCGTATGTGCACGT 60.250 50.000 17.19 17.19 40.31 4.49
576 577 0.597072 TGTGACCGTATGTGCACGTA 59.403 50.000 14.85 14.85 40.31 3.57
577 578 1.000496 TGTGACCGTATGTGCACGTAA 60.000 47.619 20.12 1.77 40.31 3.18
578 579 2.060284 GTGACCGTATGTGCACGTAAA 58.940 47.619 20.12 0.00 40.31 2.01
579 580 2.060284 TGACCGTATGTGCACGTAAAC 58.940 47.619 20.12 10.84 40.31 2.01
580 581 1.058129 GACCGTATGTGCACGTAAACG 59.942 52.381 21.91 21.91 46.33 3.60
581 582 0.246989 CCGTATGTGCACGTAAACGC 60.247 55.000 22.97 10.55 44.43 4.84
582 583 0.435388 CGTATGTGCACGTAAACGCA 59.565 50.000 20.12 0.00 44.43 5.24
583 584 1.136584 CGTATGTGCACGTAAACGCAA 60.137 47.619 20.12 0.00 44.43 4.85
584 585 2.492001 GTATGTGCACGTAAACGCAAG 58.508 47.619 20.12 0.00 44.43 4.01
585 586 5.460942 CGTATGTGCACGTAAACGCAAGT 62.461 47.826 20.12 0.00 45.15 3.16
599 600 1.963747 GCAAGTTATGCGACCACAAC 58.036 50.000 0.00 0.00 46.87 3.32
600 601 1.724654 GCAAGTTATGCGACCACAACG 60.725 52.381 0.00 0.00 46.87 4.10
601 602 1.795872 CAAGTTATGCGACCACAACGA 59.204 47.619 0.00 0.00 33.66 3.85
602 603 2.380084 AGTTATGCGACCACAACGAT 57.620 45.000 0.00 0.00 33.66 3.73
603 604 1.999735 AGTTATGCGACCACAACGATG 59.000 47.619 0.00 0.00 33.66 3.84
604 605 1.730064 GTTATGCGACCACAACGATGT 59.270 47.619 0.00 0.00 41.61 3.06
605 606 2.924926 GTTATGCGACCACAACGATGTA 59.075 45.455 0.00 0.00 37.82 2.29
606 607 2.309528 ATGCGACCACAACGATGTAT 57.690 45.000 0.00 0.00 37.82 2.29
607 608 2.087501 TGCGACCACAACGATGTATT 57.912 45.000 0.00 0.00 37.82 1.89
608 609 2.418692 TGCGACCACAACGATGTATTT 58.581 42.857 0.00 0.00 37.82 1.40
609 610 2.809119 TGCGACCACAACGATGTATTTT 59.191 40.909 0.00 0.00 37.82 1.82
610 611 3.160545 GCGACCACAACGATGTATTTTG 58.839 45.455 0.00 0.00 37.82 2.44
611 612 3.160545 CGACCACAACGATGTATTTTGC 58.839 45.455 0.00 0.00 37.82 3.68
612 613 3.364465 CGACCACAACGATGTATTTTGCA 60.364 43.478 0.00 0.00 37.82 4.08
613 614 4.541779 GACCACAACGATGTATTTTGCAA 58.458 39.130 0.00 0.00 37.82 4.08
614 615 4.545610 ACCACAACGATGTATTTTGCAAG 58.454 39.130 0.00 0.00 37.82 4.01
615 616 4.037446 ACCACAACGATGTATTTTGCAAGT 59.963 37.500 0.00 0.00 37.82 3.16
616 617 4.981674 CCACAACGATGTATTTTGCAAGTT 59.018 37.500 0.00 0.00 37.82 2.66
617 618 5.461737 CCACAACGATGTATTTTGCAAGTTT 59.538 36.000 0.00 0.00 37.82 2.66
618 619 6.019156 CCACAACGATGTATTTTGCAAGTTTT 60.019 34.615 0.00 0.00 37.82 2.43
619 620 7.168302 CCACAACGATGTATTTTGCAAGTTTTA 59.832 33.333 0.00 0.00 37.82 1.52
620 621 8.207252 CACAACGATGTATTTTGCAAGTTTTAG 58.793 33.333 0.00 0.00 37.82 1.85
621 622 6.927933 ACGATGTATTTTGCAAGTTTTAGC 57.072 33.333 0.00 0.00 0.00 3.09
622 623 6.442952 ACGATGTATTTTGCAAGTTTTAGCA 58.557 32.000 0.00 0.00 39.32 3.49
623 624 6.362283 ACGATGTATTTTGCAAGTTTTAGCAC 59.638 34.615 0.00 0.00 41.05 4.40
624 625 6.582295 CGATGTATTTTGCAAGTTTTAGCACT 59.418 34.615 0.00 0.00 41.05 4.40
625 626 7.748683 CGATGTATTTTGCAAGTTTTAGCACTA 59.251 33.333 0.00 0.00 41.05 2.74
626 627 9.405587 GATGTATTTTGCAAGTTTTAGCACTAA 57.594 29.630 0.00 0.00 41.05 2.24
627 628 9.757227 ATGTATTTTGCAAGTTTTAGCACTAAA 57.243 25.926 0.00 0.00 41.05 1.85
628 629 9.587772 TGTATTTTGCAAGTTTTAGCACTAAAA 57.412 25.926 10.74 10.74 41.05 1.52
631 632 6.523676 TTGCAAGTTTTAGCACTAAAATGC 57.476 33.333 22.69 22.69 43.82 3.56
632 633 5.595885 TGCAAGTTTTAGCACTAAAATGCA 58.404 33.333 25.64 25.64 46.94 3.96
633 634 5.461737 TGCAAGTTTTAGCACTAAAATGCAC 59.538 36.000 25.64 13.61 45.75 4.57
634 635 6.902466 TGCAAGTTTTAGCACTAAAATGCACA 60.902 34.615 25.64 16.68 45.75 4.57
635 636 8.163768 TGCAAGTTTTAGCACTAAAATGCACAT 61.164 33.333 25.64 7.11 45.75 3.21
641 642 2.916716 GCACTAAAATGCACATCCAACG 59.083 45.455 0.00 0.00 45.39 4.10
642 643 2.916716 CACTAAAATGCACATCCAACGC 59.083 45.455 0.00 0.00 0.00 4.84
643 644 2.556189 ACTAAAATGCACATCCAACGCA 59.444 40.909 0.00 0.00 40.50 5.24
644 645 2.522836 AAAATGCACATCCAACGCAA 57.477 40.000 0.00 0.00 39.48 4.85
645 646 2.068837 AAATGCACATCCAACGCAAG 57.931 45.000 0.00 0.00 39.48 4.01
661 662 4.732285 CGCAAGTTTTGTGACTGATAGT 57.268 40.909 0.00 0.00 43.66 2.12
662 663 4.457810 CGCAAGTTTTGTGACTGATAGTG 58.542 43.478 0.00 0.00 43.66 2.74
663 664 4.211164 CGCAAGTTTTGTGACTGATAGTGA 59.789 41.667 0.00 0.00 43.66 3.41
664 665 5.106948 CGCAAGTTTTGTGACTGATAGTGAT 60.107 40.000 0.00 0.00 43.66 3.06
665 666 6.090763 CGCAAGTTTTGTGACTGATAGTGATA 59.909 38.462 0.00 0.00 43.66 2.15
666 667 7.201556 CGCAAGTTTTGTGACTGATAGTGATAT 60.202 37.037 0.00 0.00 43.66 1.63
667 668 8.454106 GCAAGTTTTGTGACTGATAGTGATATT 58.546 33.333 0.00 0.00 0.00 1.28
670 671 9.601217 AGTTTTGTGACTGATAGTGATATTACC 57.399 33.333 0.00 0.00 0.00 2.85
671 672 9.601217 GTTTTGTGACTGATAGTGATATTACCT 57.399 33.333 0.00 0.00 0.00 3.08
672 673 9.817809 TTTTGTGACTGATAGTGATATTACCTC 57.182 33.333 0.00 0.00 0.00 3.85
673 674 8.533569 TTGTGACTGATAGTGATATTACCTCA 57.466 34.615 0.00 0.00 0.00 3.86
674 675 8.533569 TGTGACTGATAGTGATATTACCTCAA 57.466 34.615 0.00 0.00 0.00 3.02
675 676 9.147732 TGTGACTGATAGTGATATTACCTCAAT 57.852 33.333 0.00 0.00 0.00 2.57
676 677 9.988815 GTGACTGATAGTGATATTACCTCAATT 57.011 33.333 0.00 0.00 0.00 2.32
699 700 0.257039 AACCAGAGGTGATGGATGGC 59.743 55.000 0.00 0.00 40.51 4.40
738 741 2.033550 CGCTCGACTCCAAAGCTATAGT 59.966 50.000 0.84 0.00 33.83 2.12
833 852 2.372504 TCAAAGAAATGGGACGGTGGTA 59.627 45.455 0.00 0.00 0.00 3.25
834 853 2.484742 AAGAAATGGGACGGTGGTAC 57.515 50.000 0.00 0.00 0.00 3.34
835 854 0.248289 AGAAATGGGACGGTGGTACG 59.752 55.000 0.00 0.00 40.31 3.67
939 4479 3.829026 CTCACCTAGCCATACATCTGCTA 59.171 47.826 0.00 0.00 36.57 3.49
961 4501 3.181477 ACTCAAGAGCTCATCAAGATCGG 60.181 47.826 17.77 0.00 45.33 4.18
985 4528 3.525862 AGCTAGCTGATTAGGGCCTAAT 58.474 45.455 33.51 33.51 39.09 1.73
1091 4637 1.554392 GCACAGAGCATCACTAGACG 58.446 55.000 0.00 0.00 44.79 4.18
1113 4659 7.705325 AGACGCTACGATTTCAATGTAAGTATT 59.295 33.333 0.00 0.00 0.00 1.89
1161 4711 1.731700 CTCTGCATGCATTTCCGGG 59.268 57.895 22.97 4.90 0.00 5.73
1165 4715 2.102749 CATGCATTTCCGGGCGTG 59.897 61.111 0.00 4.74 40.26 5.34
1169 4719 4.114997 CATTTCCGGGCGTGCACC 62.115 66.667 12.15 3.87 0.00 5.01
1189 4749 3.220110 CCTGATTTCTCACATGGATGGG 58.780 50.000 0.00 0.00 0.00 4.00
1190 4750 3.220110 CTGATTTCTCACATGGATGGGG 58.780 50.000 0.00 0.00 0.00 4.96
1191 4751 2.582172 TGATTTCTCACATGGATGGGGT 59.418 45.455 0.00 0.00 0.00 4.95
1192 4752 3.011595 TGATTTCTCACATGGATGGGGTT 59.988 43.478 0.00 0.00 0.00 4.11
1604 5183 3.959975 TTGCGCCGCACAAGGAAC 61.960 61.111 13.21 0.00 38.71 3.62
1652 5231 2.264480 CGGACACGGAGGCATTGA 59.736 61.111 0.00 0.00 36.18 2.57
1736 5315 1.524961 CCTGGGCCGCTATACAACA 59.475 57.895 0.00 0.00 0.00 3.33
1779 6012 0.671472 TCACTCTGTGCTTCCATGCG 60.671 55.000 0.00 0.00 32.98 4.73
1795 6163 3.370978 CCATGCGTCTTAATCGTCAAAGT 59.629 43.478 0.00 0.00 0.00 2.66
1796 6164 4.326205 CATGCGTCTTAATCGTCAAAGTG 58.674 43.478 3.01 0.00 0.00 3.16
1798 6166 3.427528 TGCGTCTTAATCGTCAAAGTGTC 59.572 43.478 3.01 0.00 0.00 3.67
1803 6172 7.464178 GCGTCTTAATCGTCAAAGTGTCATAAT 60.464 37.037 3.01 0.00 0.00 1.28
1804 6173 8.380644 CGTCTTAATCGTCAAAGTGTCATAATT 58.619 33.333 0.00 0.00 0.00 1.40
1805 6174 9.478019 GTCTTAATCGTCAAAGTGTCATAATTG 57.522 33.333 0.00 0.00 0.00 2.32
1806 6175 8.175069 TCTTAATCGTCAAAGTGTCATAATTGC 58.825 33.333 0.00 0.00 0.00 3.56
1807 6176 5.878332 ATCGTCAAAGTGTCATAATTGCA 57.122 34.783 0.00 0.00 0.00 4.08
1809 6178 5.448438 TCGTCAAAGTGTCATAATTGCAAC 58.552 37.500 0.00 0.00 0.00 4.17
1810 6179 5.008118 TCGTCAAAGTGTCATAATTGCAACA 59.992 36.000 0.00 0.00 0.00 3.33
1815 6184 6.826893 AAGTGTCATAATTGCAACAACAAC 57.173 33.333 0.00 0.00 31.03 3.32
1818 6187 6.815641 AGTGTCATAATTGCAACAACAACAAA 59.184 30.769 0.00 0.00 31.03 2.83
1819 6188 7.332926 AGTGTCATAATTGCAACAACAACAAAA 59.667 29.630 0.00 0.00 31.03 2.44
1821 6190 8.333908 TGTCATAATTGCAACAACAACAAAATC 58.666 29.630 0.00 0.00 31.03 2.17
1822 6191 7.526850 GTCATAATTGCAACAACAACAAAATCG 59.473 33.333 0.00 0.00 31.03 3.34
1823 6192 5.793026 AATTGCAACAACAACAAAATCGT 57.207 30.435 0.00 0.00 31.03 3.73
1824 6193 4.831741 TTGCAACAACAACAAAATCGTC 57.168 36.364 0.00 0.00 0.00 4.20
1825 6194 3.838120 TGCAACAACAACAAAATCGTCA 58.162 36.364 0.00 0.00 0.00 4.35
1828 6197 5.164012 TGCAACAACAACAAAATCGTCAAAG 60.164 36.000 0.00 0.00 0.00 2.77
1829 6198 5.164002 GCAACAACAACAAAATCGTCAAAGT 60.164 36.000 0.00 0.00 0.00 2.66
1830 6199 6.232788 CAACAACAACAAAATCGTCAAAGTG 58.767 36.000 0.00 0.00 0.00 3.16
1831 6200 5.465935 ACAACAACAAAATCGTCAAAGTGT 58.534 33.333 0.00 0.00 0.00 3.55
1882 10119 0.235926 GACACGTTCAAGCTGAAGGC 59.764 55.000 14.42 0.00 43.70 4.35
1979 10216 0.671796 ACACACTCACCATCGTCGAA 59.328 50.000 0.00 0.00 0.00 3.71
2007 10244 3.561503 GCAGTTTATGTCAAACCGTTCC 58.438 45.455 0.00 0.00 0.00 3.62
2045 10282 4.631740 TCTCCGGGCCAGACCACA 62.632 66.667 4.39 0.00 42.05 4.17
2526 10784 1.303074 GGGTCAAACTTCCCGGTCC 60.303 63.158 0.00 0.00 33.97 4.46
2606 10864 1.079819 GACCAAGCTGCTCGTGCTA 60.080 57.895 11.19 0.00 40.22 3.49
2914 12278 6.149633 TGTACTCATACGTGTGATATGCATC 58.850 40.000 15.75 0.00 33.60 3.91
3007 12371 2.037367 TGCTAGACGGGAGCCTGT 59.963 61.111 0.00 0.00 39.30 4.00
3156 12826 8.942669 TTTTTAGTGTATTAAATCAGTGTGCG 57.057 30.769 0.00 0.00 0.00 5.34
3235 12906 8.499162 ACAATGTTTTGACTCTTCTCGAATAAG 58.501 33.333 1.58 1.58 36.64 1.73
3258 12929 5.295292 AGCAATGACTTCAATAGAATGTCCG 59.705 40.000 0.00 0.00 34.15 4.79
3384 13056 7.880160 AATAGCATGATTGGCTAAACTTACA 57.120 32.000 0.00 0.00 46.03 2.41
3712 13385 5.243507 AGAACATGCCATGTGTGATTTGTAA 59.756 36.000 11.79 0.00 44.07 2.41
3836 13509 4.339814 TCATCCAAGTGTGGGTTGTTAAAC 59.660 41.667 0.00 0.00 46.01 2.01
3838 13511 2.683867 CCAAGTGTGGGTTGTTAAACGA 59.316 45.455 0.00 0.00 41.77 3.85
3925 13598 2.547826 GTGGTAGTAGTGATTTCCCGC 58.452 52.381 0.00 0.00 0.00 6.13
3936 13609 2.550699 ATTTCCCGCGGCATCCTCAA 62.551 55.000 22.85 0.00 0.00 3.02
3962 13797 3.965379 TTTTGCGGGTATCAGACACTA 57.035 42.857 0.00 0.00 0.00 2.74
3971 13806 5.005394 CGGGTATCAGACACTAAAATTGTCG 59.995 44.000 0.00 0.00 46.73 4.35
4009 13844 2.092103 AGAGGCTCTCTCGTTGGTAGAT 60.092 50.000 12.24 0.00 46.82 1.98
4020 13855 4.936891 TCGTTGGTAGATGATCATGACAG 58.063 43.478 14.30 4.47 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.528600 TGGGATGGAAGAATGAGGTAAAA 57.471 39.130 0.00 0.00 0.00 1.52
68 69 2.691409 GGAATGTTCACTGGATCCGA 57.309 50.000 7.39 0.00 0.00 4.55
76 77 1.523758 GAGTTGCCGGAATGTTCACT 58.476 50.000 5.05 0.00 0.00 3.41
89 90 4.589908 TGATTTTTAGGAGGAGGAGTTGC 58.410 43.478 0.00 0.00 0.00 4.17
92 93 9.997172 AAATAATTGATTTTTAGGAGGAGGAGT 57.003 29.630 0.00 0.00 33.77 3.85
119 120 7.172703 ACGATTTGTTACCCTACTTTTTCTCAG 59.827 37.037 0.00 0.00 0.00 3.35
130 131 6.938507 AGTTCATGTACGATTTGTTACCCTA 58.061 36.000 0.00 0.00 0.00 3.53
179 180 2.990066 ATCACTGGGGATCGAAGAAC 57.010 50.000 0.00 0.00 43.58 3.01
385 386 0.038251 CTCTGTACAGCTGACCGCAA 60.038 55.000 23.35 0.00 42.61 4.85
445 446 2.583441 GCAGAAAACCCCTTGGCCC 61.583 63.158 0.00 0.00 33.59 5.80
449 450 3.384467 TCTTCTTTGCAGAAAACCCCTTG 59.616 43.478 0.00 0.00 38.63 3.61
450 451 3.384789 GTCTTCTTTGCAGAAAACCCCTT 59.615 43.478 0.00 0.00 38.63 3.95
451 452 2.959030 GTCTTCTTTGCAGAAAACCCCT 59.041 45.455 0.00 0.00 38.63 4.79
452 453 2.287608 CGTCTTCTTTGCAGAAAACCCC 60.288 50.000 0.00 0.00 38.63 4.95
453 454 2.858646 GCGTCTTCTTTGCAGAAAACCC 60.859 50.000 0.00 0.00 38.63 4.11
454 455 2.385315 GCGTCTTCTTTGCAGAAAACC 58.615 47.619 0.00 0.00 38.63 3.27
455 456 2.036933 CGCGTCTTCTTTGCAGAAAAC 58.963 47.619 0.00 0.00 38.63 2.43
456 457 1.596954 GCGCGTCTTCTTTGCAGAAAA 60.597 47.619 8.43 0.00 38.63 2.29
457 458 0.041312 GCGCGTCTTCTTTGCAGAAA 60.041 50.000 8.43 0.00 38.63 2.52
458 459 1.569493 GCGCGTCTTCTTTGCAGAA 59.431 52.632 8.43 0.00 36.62 3.02
459 460 2.657757 CGCGCGTCTTCTTTGCAGA 61.658 57.895 24.19 0.00 0.00 4.26
460 461 2.202096 CGCGCGTCTTCTTTGCAG 60.202 61.111 24.19 0.00 0.00 4.41
461 462 4.368808 GCGCGCGTCTTCTTTGCA 62.369 61.111 32.35 0.00 0.00 4.08
484 485 4.918201 CCTCTGATTCCGCCCGGC 62.918 72.222 0.00 0.00 34.68 6.13
485 486 4.918201 GCCTCTGATTCCGCCCGG 62.918 72.222 0.00 0.00 0.00 5.73
486 487 3.854669 AGCCTCTGATTCCGCCCG 61.855 66.667 0.00 0.00 0.00 6.13
487 488 2.203126 CAGCCTCTGATTCCGCCC 60.203 66.667 0.00 0.00 32.44 6.13
488 489 2.899339 GCAGCCTCTGATTCCGCC 60.899 66.667 0.00 0.00 32.44 6.13
489 490 2.899339 GGCAGCCTCTGATTCCGC 60.899 66.667 3.29 0.00 32.44 5.54
490 491 1.523258 CTGGCAGCCTCTGATTCCG 60.523 63.158 14.15 0.00 32.44 4.30
491 492 1.823041 GCTGGCAGCCTCTGATTCC 60.823 63.158 28.87 0.00 34.48 3.01
492 493 2.178890 CGCTGGCAGCCTCTGATTC 61.179 63.158 32.08 3.38 38.18 2.52
493 494 2.124819 CGCTGGCAGCCTCTGATT 60.125 61.111 32.08 0.00 38.18 2.57
494 495 4.172512 CCGCTGGCAGCCTCTGAT 62.173 66.667 32.08 0.00 38.18 2.90
513 514 2.198287 GCTGGCATGGCATACCTGG 61.198 63.158 23.59 10.93 36.63 4.45
514 515 1.454295 TGCTGGCATGGCATACCTG 60.454 57.895 23.59 17.16 36.63 4.00
515 516 1.454479 GTGCTGGCATGGCATACCT 60.454 57.895 23.59 0.00 41.86 3.08
516 517 2.837883 CGTGCTGGCATGGCATACC 61.838 63.158 23.59 9.95 41.86 2.73
517 518 2.051804 GACGTGCTGGCATGGCATAC 62.052 60.000 23.59 21.54 40.55 2.39
518 519 1.819208 GACGTGCTGGCATGGCATA 60.819 57.895 23.59 12.19 40.55 3.14
519 520 3.136123 GACGTGCTGGCATGGCAT 61.136 61.111 23.59 7.28 40.55 4.40
522 523 1.521457 ATACGACGTGCTGGCATGG 60.521 57.895 11.56 7.26 37.27 3.66
523 524 0.805711 TCATACGACGTGCTGGCATG 60.806 55.000 11.56 12.54 38.78 4.06
524 525 0.108377 TTCATACGACGTGCTGGCAT 60.108 50.000 11.56 0.00 0.00 4.40
525 526 0.735978 CTTCATACGACGTGCTGGCA 60.736 55.000 11.56 0.00 0.00 4.92
526 527 1.421410 CCTTCATACGACGTGCTGGC 61.421 60.000 11.56 0.00 0.00 4.85
527 528 1.421410 GCCTTCATACGACGTGCTGG 61.421 60.000 11.56 6.84 0.00 4.85
528 529 0.735978 TGCCTTCATACGACGTGCTG 60.736 55.000 11.56 8.34 0.00 4.41
529 530 0.458543 CTGCCTTCATACGACGTGCT 60.459 55.000 11.56 0.00 0.00 4.40
530 531 0.457853 TCTGCCTTCATACGACGTGC 60.458 55.000 11.56 4.68 0.00 5.34
531 532 1.269166 GTCTGCCTTCATACGACGTG 58.731 55.000 11.56 0.00 0.00 4.49
532 533 0.179171 CGTCTGCCTTCATACGACGT 60.179 55.000 5.52 5.52 42.95 4.34
533 534 0.866061 CCGTCTGCCTTCATACGACG 60.866 60.000 0.00 0.00 42.95 5.12
534 535 0.527817 CCCGTCTGCCTTCATACGAC 60.528 60.000 5.06 0.00 42.95 4.34
535 536 0.681887 TCCCGTCTGCCTTCATACGA 60.682 55.000 5.06 0.00 42.95 3.43
536 537 0.389391 ATCCCGTCTGCCTTCATACG 59.611 55.000 0.00 0.00 40.90 3.06
537 538 2.614057 CAAATCCCGTCTGCCTTCATAC 59.386 50.000 0.00 0.00 0.00 2.39
538 539 2.238646 ACAAATCCCGTCTGCCTTCATA 59.761 45.455 0.00 0.00 0.00 2.15
539 540 1.004745 ACAAATCCCGTCTGCCTTCAT 59.995 47.619 0.00 0.00 0.00 2.57
540 541 0.400213 ACAAATCCCGTCTGCCTTCA 59.600 50.000 0.00 0.00 0.00 3.02
541 542 0.804989 CACAAATCCCGTCTGCCTTC 59.195 55.000 0.00 0.00 0.00 3.46
542 543 0.400213 TCACAAATCCCGTCTGCCTT 59.600 50.000 0.00 0.00 0.00 4.35
543 544 0.321653 GTCACAAATCCCGTCTGCCT 60.322 55.000 0.00 0.00 0.00 4.75
544 545 1.305930 GGTCACAAATCCCGTCTGCC 61.306 60.000 0.00 0.00 0.00 4.85
545 546 1.635663 CGGTCACAAATCCCGTCTGC 61.636 60.000 0.00 0.00 37.00 4.26
546 547 2.456000 CGGTCACAAATCCCGTCTG 58.544 57.895 0.00 0.00 37.00 3.51
550 551 1.663643 CACATACGGTCACAAATCCCG 59.336 52.381 0.00 0.00 46.93 5.14
551 552 1.400494 GCACATACGGTCACAAATCCC 59.600 52.381 0.00 0.00 0.00 3.85
552 553 2.080693 TGCACATACGGTCACAAATCC 58.919 47.619 0.00 0.00 0.00 3.01
553 554 2.473868 CGTGCACATACGGTCACAAATC 60.474 50.000 18.64 0.00 40.22 2.17
554 555 1.463056 CGTGCACATACGGTCACAAAT 59.537 47.619 18.64 0.00 40.22 2.32
555 556 0.862490 CGTGCACATACGGTCACAAA 59.138 50.000 18.64 0.00 40.22 2.83
556 557 2.523179 CGTGCACATACGGTCACAA 58.477 52.632 18.64 0.00 40.22 3.33
557 558 4.253442 CGTGCACATACGGTCACA 57.747 55.556 18.64 0.00 40.22 3.58
563 564 7.551062 TAACTTGCGTTTACGTGCACATACG 62.551 44.000 18.64 19.09 41.57 3.06
564 565 2.096614 ACTTGCGTTTACGTGCACATAC 60.097 45.455 18.64 7.53 41.57 2.39
565 566 2.136728 ACTTGCGTTTACGTGCACATA 58.863 42.857 18.64 2.14 41.57 2.29
566 567 0.941542 ACTTGCGTTTACGTGCACAT 59.058 45.000 18.64 3.45 41.57 3.21
567 568 0.727970 AACTTGCGTTTACGTGCACA 59.272 45.000 18.64 0.00 41.57 4.57
568 569 2.649140 TAACTTGCGTTTACGTGCAC 57.351 45.000 6.82 6.82 41.57 4.57
569 570 2.663334 GCATAACTTGCGTTTACGTGCA 60.663 45.455 0.00 0.00 42.54 4.57
570 571 1.902504 GCATAACTTGCGTTTACGTGC 59.097 47.619 0.00 0.00 42.54 5.34
581 582 1.795872 TCGTTGTGGTCGCATAACTTG 59.204 47.619 0.00 0.00 0.00 3.16
582 583 2.157834 TCGTTGTGGTCGCATAACTT 57.842 45.000 0.00 0.00 0.00 2.66
583 584 1.999735 CATCGTTGTGGTCGCATAACT 59.000 47.619 0.00 0.00 0.00 2.24
584 585 1.730064 ACATCGTTGTGGTCGCATAAC 59.270 47.619 0.00 0.00 33.85 1.89
585 586 2.087501 ACATCGTTGTGGTCGCATAA 57.912 45.000 0.00 0.00 33.85 1.90
586 587 2.943449 TACATCGTTGTGGTCGCATA 57.057 45.000 9.39 0.00 36.53 3.14
587 588 2.309528 ATACATCGTTGTGGTCGCAT 57.690 45.000 9.39 0.00 36.53 4.73
588 589 2.087501 AATACATCGTTGTGGTCGCA 57.912 45.000 9.39 0.00 36.53 5.10
589 590 3.160545 CAAAATACATCGTTGTGGTCGC 58.839 45.455 9.39 0.00 36.53 5.19
590 591 3.160545 GCAAAATACATCGTTGTGGTCG 58.839 45.455 9.39 0.00 36.53 4.79
591 592 4.153958 TGCAAAATACATCGTTGTGGTC 57.846 40.909 9.39 0.00 36.53 4.02
592 593 4.037446 ACTTGCAAAATACATCGTTGTGGT 59.963 37.500 9.39 0.00 36.53 4.16
593 594 4.545610 ACTTGCAAAATACATCGTTGTGG 58.454 39.130 9.39 0.00 36.53 4.17
594 595 6.509317 AAACTTGCAAAATACATCGTTGTG 57.491 33.333 9.39 0.00 36.53 3.33
595 596 7.096230 GCTAAAACTTGCAAAATACATCGTTGT 60.096 33.333 0.00 4.29 39.98 3.32
596 597 7.096271 TGCTAAAACTTGCAAAATACATCGTTG 60.096 33.333 0.00 0.00 36.15 4.10
597 598 6.920758 TGCTAAAACTTGCAAAATACATCGTT 59.079 30.769 0.00 0.00 36.15 3.85
598 599 6.362283 GTGCTAAAACTTGCAAAATACATCGT 59.638 34.615 0.00 0.00 41.10 3.73
599 600 6.582295 AGTGCTAAAACTTGCAAAATACATCG 59.418 34.615 0.00 0.00 41.10 3.84
600 601 7.873739 AGTGCTAAAACTTGCAAAATACATC 57.126 32.000 0.00 0.00 41.10 3.06
601 602 9.757227 TTTAGTGCTAAAACTTGCAAAATACAT 57.243 25.926 0.00 0.00 41.10 2.29
602 603 9.587772 TTTTAGTGCTAAAACTTGCAAAATACA 57.412 25.926 11.71 0.00 39.34 2.29
605 606 8.069574 GCATTTTAGTGCTAAAACTTGCAAAAT 58.930 29.630 23.79 7.46 44.68 1.82
606 607 7.065085 TGCATTTTAGTGCTAAAACTTGCAAAA 59.935 29.630 26.48 14.43 46.57 2.44
607 608 6.536582 TGCATTTTAGTGCTAAAACTTGCAAA 59.463 30.769 26.48 14.87 46.57 3.68
608 609 6.045318 TGCATTTTAGTGCTAAAACTTGCAA 58.955 32.000 26.48 17.45 46.57 4.08
609 610 5.461737 GTGCATTTTAGTGCTAAAACTTGCA 59.538 36.000 25.69 25.69 46.94 4.08
610 611 5.461737 TGTGCATTTTAGTGCTAAAACTTGC 59.538 36.000 22.87 22.87 44.68 4.01
611 612 7.148755 GGATGTGCATTTTAGTGCTAAAACTTG 60.149 37.037 16.42 13.43 44.68 3.16
612 613 6.868339 GGATGTGCATTTTAGTGCTAAAACTT 59.132 34.615 16.42 6.03 44.68 2.66
613 614 6.015519 TGGATGTGCATTTTAGTGCTAAAACT 60.016 34.615 16.42 6.47 44.68 2.66
614 615 6.155827 TGGATGTGCATTTTAGTGCTAAAAC 58.844 36.000 16.42 7.85 44.68 2.43
615 616 6.338214 TGGATGTGCATTTTAGTGCTAAAA 57.662 33.333 16.42 16.42 45.56 1.52
616 617 5.973899 TGGATGTGCATTTTAGTGCTAAA 57.026 34.783 0.00 0.68 45.27 1.85
617 618 5.618863 CGTTGGATGTGCATTTTAGTGCTAA 60.619 40.000 0.00 0.00 45.27 3.09
618 619 4.142708 CGTTGGATGTGCATTTTAGTGCTA 60.143 41.667 0.00 0.00 45.27 3.49
619 620 3.366273 CGTTGGATGTGCATTTTAGTGCT 60.366 43.478 0.00 0.00 45.27 4.40
620 621 2.916716 CGTTGGATGTGCATTTTAGTGC 59.083 45.455 0.00 0.00 45.25 4.40
621 622 2.916716 GCGTTGGATGTGCATTTTAGTG 59.083 45.455 0.00 0.00 0.00 2.74
622 623 2.556189 TGCGTTGGATGTGCATTTTAGT 59.444 40.909 0.00 0.00 32.86 2.24
623 624 3.214697 TGCGTTGGATGTGCATTTTAG 57.785 42.857 0.00 0.00 32.86 1.85
624 625 3.005261 ACTTGCGTTGGATGTGCATTTTA 59.995 39.130 0.00 0.00 38.60 1.52
625 626 2.224018 ACTTGCGTTGGATGTGCATTTT 60.224 40.909 0.00 0.00 38.60 1.82
626 627 1.340889 ACTTGCGTTGGATGTGCATTT 59.659 42.857 0.00 0.00 38.60 2.32
627 628 0.961019 ACTTGCGTTGGATGTGCATT 59.039 45.000 0.00 0.00 38.60 3.56
628 629 0.961019 AACTTGCGTTGGATGTGCAT 59.039 45.000 0.00 0.00 38.60 3.96
629 630 0.743688 AAACTTGCGTTGGATGTGCA 59.256 45.000 0.00 0.00 36.72 4.57
630 631 1.522258 CAAAACTTGCGTTGGATGTGC 59.478 47.619 0.00 0.00 32.65 4.57
631 632 2.535166 CACAAAACTTGCGTTGGATGTG 59.465 45.455 0.00 0.00 37.03 3.21
632 633 2.425312 TCACAAAACTTGCGTTGGATGT 59.575 40.909 0.00 0.00 32.65 3.06
633 634 2.788786 GTCACAAAACTTGCGTTGGATG 59.211 45.455 0.00 0.00 32.65 3.51
634 635 2.687935 AGTCACAAAACTTGCGTTGGAT 59.312 40.909 0.00 0.00 32.65 3.41
635 636 2.088423 AGTCACAAAACTTGCGTTGGA 58.912 42.857 0.00 0.00 32.65 3.53
636 637 2.159448 TCAGTCACAAAACTTGCGTTGG 60.159 45.455 0.00 0.00 32.65 3.77
637 638 3.129852 TCAGTCACAAAACTTGCGTTG 57.870 42.857 0.00 0.00 32.65 4.10
638 639 4.574828 ACTATCAGTCACAAAACTTGCGTT 59.425 37.500 0.00 0.00 34.03 4.84
639 640 4.024893 CACTATCAGTCACAAAACTTGCGT 60.025 41.667 0.00 0.00 0.00 5.24
640 641 4.211164 TCACTATCAGTCACAAAACTTGCG 59.789 41.667 0.00 0.00 0.00 4.85
641 642 5.673337 TCACTATCAGTCACAAAACTTGC 57.327 39.130 0.00 0.00 0.00 4.01
644 645 9.601217 GGTAATATCACTATCAGTCACAAAACT 57.399 33.333 0.00 0.00 0.00 2.66
645 646 9.601217 AGGTAATATCACTATCAGTCACAAAAC 57.399 33.333 0.00 0.00 0.00 2.43
646 647 9.817809 GAGGTAATATCACTATCAGTCACAAAA 57.182 33.333 0.00 0.00 0.00 2.44
647 648 8.977412 TGAGGTAATATCACTATCAGTCACAAA 58.023 33.333 0.00 0.00 0.00 2.83
648 649 8.533569 TGAGGTAATATCACTATCAGTCACAA 57.466 34.615 0.00 0.00 0.00 3.33
649 650 8.533569 TTGAGGTAATATCACTATCAGTCACA 57.466 34.615 0.00 0.00 0.00 3.58
650 651 9.988815 AATTGAGGTAATATCACTATCAGTCAC 57.011 33.333 0.00 0.00 0.00 3.67
669 670 6.350445 CCATCACCTCTGGTTTTTAATTGAGG 60.350 42.308 0.00 0.00 44.61 3.86
670 671 6.434028 TCCATCACCTCTGGTTTTTAATTGAG 59.566 38.462 0.00 0.00 31.02 3.02
671 672 6.310941 TCCATCACCTCTGGTTTTTAATTGA 58.689 36.000 0.00 0.00 31.02 2.57
672 673 6.588719 TCCATCACCTCTGGTTTTTAATTG 57.411 37.500 0.00 0.00 31.02 2.32
673 674 6.155049 CCATCCATCACCTCTGGTTTTTAATT 59.845 38.462 0.00 0.00 31.02 1.40
674 675 5.658190 CCATCCATCACCTCTGGTTTTTAAT 59.342 40.000 0.00 0.00 31.02 1.40
675 676 5.016173 CCATCCATCACCTCTGGTTTTTAA 58.984 41.667 0.00 0.00 31.02 1.52
676 677 4.599041 CCATCCATCACCTCTGGTTTTTA 58.401 43.478 0.00 0.00 31.02 1.52
677 678 3.434309 CCATCCATCACCTCTGGTTTTT 58.566 45.455 0.00 0.00 31.02 1.94
678 679 2.885554 GCCATCCATCACCTCTGGTTTT 60.886 50.000 0.00 0.00 31.02 2.43
699 700 3.389741 GAAAGCCAGTGCATTCGTG 57.610 52.632 0.00 0.00 41.13 4.35
833 852 0.804989 GTACCACCAGCTACGTACGT 59.195 55.000 25.98 25.98 0.00 3.57
834 853 0.804364 TGTACCACCAGCTACGTACG 59.196 55.000 15.01 15.01 35.01 3.67
835 854 1.466360 CGTGTACCACCAGCTACGTAC 60.466 57.143 0.00 0.00 33.29 3.67
836 855 0.804364 CGTGTACCACCAGCTACGTA 59.196 55.000 0.00 0.00 0.00 3.57
898 4436 3.511146 TGAGGATGGAATGCTTTTGTTCC 59.489 43.478 0.00 0.00 45.52 3.62
939 4479 3.181477 CCGATCTTGATGAGCTCTTGAGT 60.181 47.826 16.19 0.00 0.00 3.41
961 4501 1.233919 GCCCTAATCAGCTAGCTTGC 58.766 55.000 16.46 12.54 0.00 4.01
975 4515 3.309556 CCAGGGTTTTCAATTAGGCCCTA 60.310 47.826 0.00 0.00 44.00 3.53
985 4528 1.479368 GCCATGGCCAGGGTTTTCAA 61.479 55.000 35.31 0.00 34.16 2.69
1027 4570 0.814812 GCCATGAGGAGAGAGCAAGC 60.815 60.000 0.00 0.00 36.89 4.01
1068 4614 1.479730 CTAGTGATGCTCTGTGCCTGA 59.520 52.381 0.00 0.00 42.00 3.86
1113 4659 9.020731 AGATGAATGTGGACGTGTATACATATA 57.979 33.333 9.18 0.00 33.70 0.86
1118 4664 6.089551 GCATAGATGAATGTGGACGTGTATAC 59.910 42.308 0.00 0.00 0.00 1.47
1120 4666 4.991056 GCATAGATGAATGTGGACGTGTAT 59.009 41.667 0.00 0.00 0.00 2.29
1161 4711 0.166814 GTGAGAAATCAGGTGCACGC 59.833 55.000 11.45 3.85 0.00 5.34
1165 4715 2.715046 TCCATGTGAGAAATCAGGTGC 58.285 47.619 0.00 0.00 0.00 5.01
1167 4717 3.372349 CCCATCCATGTGAGAAATCAGGT 60.372 47.826 0.00 0.00 0.00 4.00
1169 4719 3.220110 CCCCATCCATGTGAGAAATCAG 58.780 50.000 0.00 0.00 0.00 2.90
1190 4750 4.274950 TCAAGGTTTGGAAGACGATCAAAC 59.725 41.667 8.98 8.98 45.38 2.93
1191 4751 4.456535 TCAAGGTTTGGAAGACGATCAAA 58.543 39.130 0.00 0.00 0.00 2.69
1192 4752 4.079980 TCAAGGTTTGGAAGACGATCAA 57.920 40.909 0.00 0.00 0.00 2.57
1604 5183 0.811915 TCGCCGAAGAGAAGAGGAAG 59.188 55.000 0.00 0.00 0.00 3.46
1779 6012 9.478019 CAATTATGACACTTTGACGATTAAGAC 57.522 33.333 0.00 0.00 0.00 3.01
1795 6163 7.601073 TTTTGTTGTTGTTGCAATTATGACA 57.399 28.000 0.59 3.13 0.00 3.58
1796 6164 7.526850 CGATTTTGTTGTTGTTGCAATTATGAC 59.473 33.333 0.59 0.30 0.00 3.06
1798 6166 7.343691 ACGATTTTGTTGTTGTTGCAATTATG 58.656 30.769 0.59 0.00 0.00 1.90
1803 6172 4.237724 TGACGATTTTGTTGTTGTTGCAA 58.762 34.783 0.00 0.00 0.00 4.08
1804 6173 3.838120 TGACGATTTTGTTGTTGTTGCA 58.162 36.364 0.00 0.00 0.00 4.08
1805 6174 4.831741 TTGACGATTTTGTTGTTGTTGC 57.168 36.364 0.00 0.00 0.00 4.17
1806 6175 6.128956 ACACTTTGACGATTTTGTTGTTGTTG 60.129 34.615 0.00 0.00 0.00 3.33
1807 6176 5.923684 ACACTTTGACGATTTTGTTGTTGTT 59.076 32.000 0.00 0.00 0.00 2.83
1809 6178 5.570973 TGACACTTTGACGATTTTGTTGTTG 59.429 36.000 0.00 0.00 0.00 3.33
1810 6179 5.704888 TGACACTTTGACGATTTTGTTGTT 58.295 33.333 0.00 0.00 0.00 2.83
1815 6184 4.539870 AGCATGACACTTTGACGATTTTG 58.460 39.130 0.00 0.00 0.00 2.44
1818 6187 4.154195 GGTAAGCATGACACTTTGACGATT 59.846 41.667 0.00 0.00 0.00 3.34
1819 6188 3.684788 GGTAAGCATGACACTTTGACGAT 59.315 43.478 0.00 0.00 0.00 3.73
1821 6190 2.159841 CGGTAAGCATGACACTTTGACG 60.160 50.000 0.00 0.00 0.00 4.35
1822 6191 2.806244 ACGGTAAGCATGACACTTTGAC 59.194 45.455 0.00 0.00 0.00 3.18
1823 6192 2.805671 CACGGTAAGCATGACACTTTGA 59.194 45.455 0.00 0.00 0.00 2.69
1824 6193 2.665519 GCACGGTAAGCATGACACTTTG 60.666 50.000 0.00 0.00 0.00 2.77
1825 6194 1.535462 GCACGGTAAGCATGACACTTT 59.465 47.619 0.00 0.00 0.00 2.66
1828 6197 0.165944 GTGCACGGTAAGCATGACAC 59.834 55.000 0.00 0.00 44.79 3.67
1829 6198 0.953471 GGTGCACGGTAAGCATGACA 60.953 55.000 11.45 0.00 44.79 3.58
1830 6199 1.644786 GGGTGCACGGTAAGCATGAC 61.645 60.000 11.45 0.00 44.79 3.06
1831 6200 1.376683 GGGTGCACGGTAAGCATGA 60.377 57.895 11.45 0.00 44.79 3.07
1882 10119 3.190535 CAGGTATGTTTTTCCTGGTTCCG 59.809 47.826 0.00 0.00 43.30 4.30
1979 10216 2.717580 TGACATAAACTGCGTCGACT 57.282 45.000 14.70 0.00 32.17 4.18
2007 10244 6.239008 GGAGAGATTATCAGAGTCTTGACAGG 60.239 46.154 3.49 0.00 0.00 4.00
2228 10486 0.242825 CGTTGAACCTCGGCAGAGTA 59.757 55.000 13.02 0.00 42.86 2.59
2526 10784 1.815003 GTTGAATTGTGAGAGGGGCAG 59.185 52.381 0.00 0.00 0.00 4.85
2606 10864 2.029964 ACCGACGCGTTGAATGGT 59.970 55.556 27.96 19.42 0.00 3.55
2914 12278 2.102420 TGAACCATACACCTGCGGATAG 59.898 50.000 0.00 0.00 0.00 2.08
3007 12371 1.293498 GGAGCAGCTTCTGGTTCGA 59.707 57.895 0.00 0.00 42.53 3.71
3144 12814 1.238439 CAAGACCCGCACACTGATTT 58.762 50.000 0.00 0.00 0.00 2.17
3156 12826 7.979537 AGAAAACACAAGAAAATTACAAGACCC 59.020 33.333 0.00 0.00 0.00 4.46
3235 12906 5.294306 TCGGACATTCTATTGAAGTCATTGC 59.706 40.000 15.45 0.00 35.44 3.56
3437 13109 6.202937 TGGTTCAAAACAAATACTTGTAGCG 58.797 36.000 0.00 0.00 45.25 4.26
3551 13224 7.039363 AGGTGTTGATGGAAATAAATCGGAAAA 60.039 33.333 0.00 0.00 0.00 2.29
3712 13385 1.952990 TGCACACATTCAACCGTCATT 59.047 42.857 0.00 0.00 0.00 2.57
3870 13543 4.202111 GCCACTGTAAACACAAAATCACCT 60.202 41.667 0.00 0.00 0.00 4.00
3906 13579 1.135527 CGCGGGAAATCACTACTACCA 59.864 52.381 0.00 0.00 0.00 3.25
3945 13618 3.965379 TTTTAGTGTCTGATACCCGCA 57.035 42.857 0.57 0.00 0.00 5.69
3946 13619 4.634443 ACAATTTTAGTGTCTGATACCCGC 59.366 41.667 0.57 0.00 0.00 6.13
3947 13620 5.005394 CGACAATTTTAGTGTCTGATACCCG 59.995 44.000 0.57 0.00 42.68 5.28
3962 13797 3.435105 TGCAAGTGCTTCGACAATTTT 57.565 38.095 4.69 0.00 42.66 1.82
4009 13844 4.508551 AAGTATTGGCCTGTCATGATCA 57.491 40.909 3.32 0.00 0.00 2.92
4020 13855 7.041107 TCATTAGCAATTTGAAAGTATTGGCC 58.959 34.615 0.00 0.00 33.41 5.36


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

AutoCloner maintained by Alex Coulton.