Multiple sequence alignment - TraesCS3B01G457700

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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 TraesCS3B01G457700 chr3B 100.000 3080 0 0 1 3080 700074329 700071250 0.000000e+00 5688
1 TraesCS3B01G457700 chr3B 89.278 1315 120 10 852 2164 700234692 700235987 0.000000e+00 1628
2 TraesCS3B01G457700 chr3D 93.289 1520 83 9 704 2217 529496797 529495291 0.000000e+00 2224
3 TraesCS3B01G457700 chr3D 88.824 1190 96 15 898 2087 529503848 529502696 0.000000e+00 1426
4 TraesCS3B01G457700 chr3D 84.725 563 43 16 1 544 529497332 529496794 9.790000e-145 523
5 TraesCS3B01G457700 chr3D 87.441 422 22 11 2338 2730 529493615 529493196 1.010000e-124 457
6 TraesCS3B01G457700 chr3D 96.000 250 9 1 2831 3080 529487401 529487153 3.700000e-109 405
7 TraesCS3B01G457700 chr3D 95.349 86 4 0 2728 2813 529487897 529487812 1.490000e-28 137
8 TraesCS3B01G457700 chr3A 93.833 1427 76 5 704 2128 663442100 663440684 0.000000e+00 2137
9 TraesCS3B01G457700 chr3A 89.446 1336 121 9 819 2148 663452127 663450806 0.000000e+00 1668
10 TraesCS3B01G457700 chr3A 85.775 471 45 6 1 449 663456366 663455896 2.150000e-131 479
11 TraesCS3B01G457700 chr3A 91.051 257 14 3 2829 3080 663439884 663439632 3.800000e-89 339
12 TraesCS3B01G457700 chr3A 88.971 272 26 3 182 449 663442438 663442167 1.770000e-87 333
13 TraesCS3B01G457700 chr3A 89.922 129 13 0 704 832 663455840 663455712 1.900000e-37 167
14 TraesCS3B01G457700 chr7D 84.347 1118 164 9 972 2083 624769085 624770197 0.000000e+00 1085
15 TraesCS3B01G457700 chr7D 93.750 176 10 1 543 717 312574292 312574117 2.360000e-66 263
16 TraesCS3B01G457700 chr4A 84.057 1129 156 13 971 2081 604105236 604104114 0.000000e+00 1066
17 TraesCS3B01G457700 chr5B 83.319 1145 163 18 973 2094 710608479 710609618 0.000000e+00 1031
18 TraesCS3B01G457700 chr5D 83.393 1126 133 21 984 2095 560224868 560225953 0.000000e+00 994
19 TraesCS3B01G457700 chr5D 95.210 167 8 0 541 707 5112352 5112186 6.550000e-67 265
20 TraesCS3B01G457700 chr2D 82.823 1077 146 21 1028 2081 13770230 13771290 0.000000e+00 928
21 TraesCS3B01G457700 chr2D 89.394 198 18 2 543 740 593801760 593801566 2.370000e-61 246
22 TraesCS3B01G457700 chr2A 81.673 1124 148 39 995 2087 15959782 15960878 0.000000e+00 881
23 TraesCS3B01G457700 chr2A 95.758 165 7 0 543 707 469790200 469790036 1.820000e-67 267
24 TraesCS3B01G457700 chr7A 94.152 171 9 1 541 710 443397798 443397628 3.050000e-65 259
25 TraesCS3B01G457700 chr7A 91.444 187 11 5 524 707 709731046 709731230 5.100000e-63 252
26 TraesCS3B01G457700 chr6B 92.265 181 12 2 543 723 639991656 639991478 3.940000e-64 255
27 TraesCS3B01G457700 chr4D 92.614 176 13 0 540 715 327965888 327965713 1.420000e-63 254
28 TraesCS3B01G457700 chr5A 91.758 182 12 3 527 707 367790062 367790241 1.830000e-62 250


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 TraesCS3B01G457700 chr3B 700071250 700074329 3079 True 5688.000000 5688 100.0000 1 3080 1 chr3B.!!$R1 3079
1 TraesCS3B01G457700 chr3B 700234692 700235987 1295 False 1628.000000 1628 89.2780 852 2164 1 chr3B.!!$F1 1312
2 TraesCS3B01G457700 chr3D 529502696 529503848 1152 True 1426.000000 1426 88.8240 898 2087 1 chr3D.!!$R1 1189
3 TraesCS3B01G457700 chr3D 529493196 529497332 4136 True 1068.000000 2224 88.4850 1 2730 3 chr3D.!!$R3 2729
4 TraesCS3B01G457700 chr3D 529487153 529487897 744 True 271.000000 405 95.6745 2728 3080 2 chr3D.!!$R2 352
5 TraesCS3B01G457700 chr3A 663439632 663442438 2806 True 936.333333 2137 91.2850 182 3080 3 chr3A.!!$R1 2898
6 TraesCS3B01G457700 chr3A 663450806 663456366 5560 True 771.333333 1668 88.3810 1 2148 3 chr3A.!!$R2 2147
7 TraesCS3B01G457700 chr7D 624769085 624770197 1112 False 1085.000000 1085 84.3470 972 2083 1 chr7D.!!$F1 1111
8 TraesCS3B01G457700 chr4A 604104114 604105236 1122 True 1066.000000 1066 84.0570 971 2081 1 chr4A.!!$R1 1110
9 TraesCS3B01G457700 chr5B 710608479 710609618 1139 False 1031.000000 1031 83.3190 973 2094 1 chr5B.!!$F1 1121
10 TraesCS3B01G457700 chr5D 560224868 560225953 1085 False 994.000000 994 83.3930 984 2095 1 chr5D.!!$F1 1111
11 TraesCS3B01G457700 chr2D 13770230 13771290 1060 False 928.000000 928 82.8230 1028 2081 1 chr2D.!!$F1 1053
12 TraesCS3B01G457700 chr2A 15959782 15960878 1096 False 881.000000 881 81.6730 995 2087 1 chr2A.!!$F1 1092

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
890 4514 0.038599 TGCCTGTCAGCAATCATGGT 59.961 50.0 0.0 0.0 40.56 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2730 8252 0.035881 TGCCTCAGCTTCTTCTGTGG 59.964 55.0 7.33 7.33 45.62 4.17 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
29 34 8.523915 TTGCACAATAGAATAGTGGATGATTT 57.476 30.769 0.00 0.00 41.72 2.17
92 102 2.191513 AGCCTATTAGCGCCGACGA 61.192 57.895 2.29 0.00 43.93 4.20
95 105 1.344942 CCTATTAGCGCCGACGATGC 61.345 60.000 2.29 0.00 43.93 3.91
96 106 1.344942 CTATTAGCGCCGACGATGCC 61.345 60.000 2.29 0.00 43.93 4.40
120 130 8.133627 GCCTACATATCAAAATATGCATGATCC 58.866 37.037 10.16 0.00 45.88 3.36
135 145 4.580167 GCATGATCCCAAATAGTTGCTACA 59.420 41.667 0.00 0.00 33.01 2.74
228 251 2.180946 AGATCCTGGCATCACCACTA 57.819 50.000 0.00 0.00 46.36 2.74
260 283 3.305950 CGCATTGCTCCTAGCTATTCTCT 60.306 47.826 7.12 0.00 42.97 3.10
278 301 5.428496 TCTCTTCTGCATGTTCAGTTTTG 57.572 39.130 0.00 0.00 35.63 2.44
288 311 1.866601 GTTCAGTTTTGCACAATGGGC 59.133 47.619 0.00 0.00 0.00 5.36
289 312 1.117994 TCAGTTTTGCACAATGGGCA 58.882 45.000 5.86 5.86 40.00 5.36
310 333 1.408969 TCAAAAACAAGGTGCTCCCC 58.591 50.000 0.00 0.00 0.00 4.81
319 342 2.203294 GTGCTCCCCACAAACCGT 60.203 61.111 0.00 0.00 44.06 4.83
320 343 2.203280 TGCTCCCCACAAACCGTG 60.203 61.111 0.00 0.00 45.92 4.94
356 380 1.924524 AGAAAACGCCGACGATACATG 59.075 47.619 0.00 0.00 43.93 3.21
357 381 1.921887 GAAAACGCCGACGATACATGA 59.078 47.619 0.00 0.00 43.93 3.07
437 463 8.740123 TGACCATAAACTTGTTCTTAGTTTGA 57.260 30.769 10.35 0.00 43.58 2.69
438 464 9.349713 TGACCATAAACTTGTTCTTAGTTTGAT 57.650 29.630 10.35 0.29 43.58 2.57
440 466 9.349713 ACCATAAACTTGTTCTTAGTTTGATCA 57.650 29.630 10.35 0.00 43.58 2.92
444 470 7.823745 AACTTGTTCTTAGTTTGATCATGGT 57.176 32.000 0.00 0.00 32.06 3.55
445 471 7.823745 ACTTGTTCTTAGTTTGATCATGGTT 57.176 32.000 0.00 0.00 0.00 3.67
446 472 8.237811 ACTTGTTCTTAGTTTGATCATGGTTT 57.762 30.769 0.00 0.00 0.00 3.27
447 473 8.695456 ACTTGTTCTTAGTTTGATCATGGTTTT 58.305 29.630 0.00 0.00 0.00 2.43
448 474 9.533253 CTTGTTCTTAGTTTGATCATGGTTTTT 57.467 29.630 0.00 0.00 0.00 1.94
479 505 0.392863 GATGGGGGTTTTTGGCATGC 60.393 55.000 9.90 9.90 0.00 4.06
510 536 4.522789 TCTTTGCCCACCTAGTTCATTTTC 59.477 41.667 0.00 0.00 0.00 2.29
517 543 3.081804 ACCTAGTTCATTTTCCTTGCCG 58.918 45.455 0.00 0.00 0.00 5.69
535 561 2.417243 GCCGGTGCTTGCTAAATCATTT 60.417 45.455 1.90 0.00 33.53 2.32
536 562 3.181397 CCGGTGCTTGCTAAATCATTTG 58.819 45.455 0.00 0.00 0.00 2.32
538 564 3.853671 CGGTGCTTGCTAAATCATTTGAC 59.146 43.478 0.00 0.00 0.00 3.18
539 565 4.379813 CGGTGCTTGCTAAATCATTTGACT 60.380 41.667 0.00 0.00 0.00 3.41
540 566 5.163764 CGGTGCTTGCTAAATCATTTGACTA 60.164 40.000 0.00 0.00 0.00 2.59
541 567 6.261118 GGTGCTTGCTAAATCATTTGACTAG 58.739 40.000 0.00 0.00 0.00 2.57
542 568 6.127897 GGTGCTTGCTAAATCATTTGACTAGT 60.128 38.462 0.00 0.00 0.00 2.57
543 569 7.065803 GGTGCTTGCTAAATCATTTGACTAGTA 59.934 37.037 0.00 0.00 0.00 1.82
544 570 7.905493 GTGCTTGCTAAATCATTTGACTAGTAC 59.095 37.037 0.00 0.00 0.00 2.73
545 571 7.824289 TGCTTGCTAAATCATTTGACTAGTACT 59.176 33.333 0.00 0.00 0.00 2.73
546 572 8.331742 GCTTGCTAAATCATTTGACTAGTACTC 58.668 37.037 0.00 0.00 0.00 2.59
547 573 8.718102 TTGCTAAATCATTTGACTAGTACTCC 57.282 34.615 0.00 0.00 0.00 3.85
548 574 7.272978 TGCTAAATCATTTGACTAGTACTCCC 58.727 38.462 0.00 0.00 0.00 4.30
549 575 7.125811 TGCTAAATCATTTGACTAGTACTCCCT 59.874 37.037 0.00 0.00 0.00 4.20
550 576 7.988028 GCTAAATCATTTGACTAGTACTCCCTT 59.012 37.037 0.00 0.00 0.00 3.95
551 577 9.535878 CTAAATCATTTGACTAGTACTCCCTTC 57.464 37.037 0.00 0.00 0.00 3.46
552 578 5.578005 TCATTTGACTAGTACTCCCTTCG 57.422 43.478 0.00 0.00 0.00 3.79
553 579 5.014858 TCATTTGACTAGTACTCCCTTCGT 58.985 41.667 0.00 0.00 0.00 3.85
554 580 5.479375 TCATTTGACTAGTACTCCCTTCGTT 59.521 40.000 0.00 0.00 0.00 3.85
555 581 5.382618 TTTGACTAGTACTCCCTTCGTTC 57.617 43.478 0.00 0.00 0.00 3.95
556 582 3.350833 TGACTAGTACTCCCTTCGTTCC 58.649 50.000 0.00 0.00 0.00 3.62
557 583 2.687425 GACTAGTACTCCCTTCGTTCCC 59.313 54.545 0.00 0.00 0.00 3.97
558 584 2.042162 ACTAGTACTCCCTTCGTTCCCA 59.958 50.000 0.00 0.00 0.00 4.37
559 585 2.019807 AGTACTCCCTTCGTTCCCAA 57.980 50.000 0.00 0.00 0.00 4.12
560 586 2.332117 AGTACTCCCTTCGTTCCCAAA 58.668 47.619 0.00 0.00 0.00 3.28
561 587 2.910977 AGTACTCCCTTCGTTCCCAAAT 59.089 45.455 0.00 0.00 0.00 2.32
562 588 4.098894 AGTACTCCCTTCGTTCCCAAATA 58.901 43.478 0.00 0.00 0.00 1.40
563 589 4.720273 AGTACTCCCTTCGTTCCCAAATAT 59.280 41.667 0.00 0.00 0.00 1.28
564 590 5.901276 AGTACTCCCTTCGTTCCCAAATATA 59.099 40.000 0.00 0.00 0.00 0.86
565 591 5.906772 ACTCCCTTCGTTCCCAAATATAT 57.093 39.130 0.00 0.00 0.00 0.86
566 592 5.621193 ACTCCCTTCGTTCCCAAATATATG 58.379 41.667 0.00 0.00 0.00 1.78
567 593 5.132144 ACTCCCTTCGTTCCCAAATATATGT 59.868 40.000 0.00 0.00 0.00 2.29
568 594 5.617252 TCCCTTCGTTCCCAAATATATGTC 58.383 41.667 0.00 0.00 0.00 3.06
569 595 5.368523 TCCCTTCGTTCCCAAATATATGTCT 59.631 40.000 0.00 0.00 0.00 3.41
570 596 6.062095 CCCTTCGTTCCCAAATATATGTCTT 58.938 40.000 0.00 0.00 0.00 3.01
571 597 6.546034 CCCTTCGTTCCCAAATATATGTCTTT 59.454 38.462 0.00 0.00 0.00 2.52
572 598 7.068226 CCCTTCGTTCCCAAATATATGTCTTTT 59.932 37.037 0.00 0.00 0.00 2.27
573 599 8.466798 CCTTCGTTCCCAAATATATGTCTTTTT 58.533 33.333 0.00 0.00 0.00 1.94
576 602 9.893634 TCGTTCCCAAATATATGTCTTTTTAGA 57.106 29.630 0.00 0.00 0.00 2.10
588 614 6.808008 TGTCTTTTTAGAGATTCCAGCAAG 57.192 37.500 0.00 0.00 0.00 4.01
589 615 6.299141 TGTCTTTTTAGAGATTCCAGCAAGT 58.701 36.000 0.00 0.00 0.00 3.16
590 616 6.428159 TGTCTTTTTAGAGATTCCAGCAAGTC 59.572 38.462 0.00 0.00 0.00 3.01
591 617 6.428159 GTCTTTTTAGAGATTCCAGCAAGTCA 59.572 38.462 0.00 0.00 0.00 3.41
592 618 6.428159 TCTTTTTAGAGATTCCAGCAAGTCAC 59.572 38.462 0.00 0.00 0.00 3.67
593 619 5.489792 TTTAGAGATTCCAGCAAGTCACT 57.510 39.130 0.00 0.00 0.00 3.41
594 620 6.605471 TTTAGAGATTCCAGCAAGTCACTA 57.395 37.500 0.00 0.00 0.00 2.74
595 621 4.464069 AGAGATTCCAGCAAGTCACTAC 57.536 45.455 0.00 0.00 0.00 2.73
596 622 3.834813 AGAGATTCCAGCAAGTCACTACA 59.165 43.478 0.00 0.00 0.00 2.74
597 623 4.469227 AGAGATTCCAGCAAGTCACTACAT 59.531 41.667 0.00 0.00 0.00 2.29
598 624 5.658634 AGAGATTCCAGCAAGTCACTACATA 59.341 40.000 0.00 0.00 0.00 2.29
599 625 5.665459 AGATTCCAGCAAGTCACTACATAC 58.335 41.667 0.00 0.00 0.00 2.39
600 626 3.503827 TCCAGCAAGTCACTACATACG 57.496 47.619 0.00 0.00 0.00 3.06
601 627 2.165641 TCCAGCAAGTCACTACATACGG 59.834 50.000 0.00 0.00 0.00 4.02
602 628 2.165641 CCAGCAAGTCACTACATACGGA 59.834 50.000 0.00 0.00 0.00 4.69
603 629 3.439293 CAGCAAGTCACTACATACGGAG 58.561 50.000 0.00 0.00 0.00 4.63
604 630 2.159226 AGCAAGTCACTACATACGGAGC 60.159 50.000 0.00 0.00 0.00 4.70
605 631 2.416836 GCAAGTCACTACATACGGAGCA 60.417 50.000 0.00 0.00 0.00 4.26
606 632 3.845178 CAAGTCACTACATACGGAGCAA 58.155 45.455 0.00 0.00 0.00 3.91
607 633 4.242475 CAAGTCACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
608 634 4.530710 AGTCACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
609 635 5.086104 AGTCACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
610 636 4.870426 AGTCACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
611 637 4.868171 GTCACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
612 638 5.005779 GTCACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
613 639 4.870426 CACTACATACGGAGCAAAATGAGT 59.130 41.667 0.00 0.00 0.00 3.41
614 640 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
615 641 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
616 642 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
617 643 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
618 644 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
619 645 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
620 646 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
621 647 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
622 648 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
623 649 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
637 663 9.860650 AGTGAATCTACACTCTAGAATATGTCT 57.139 33.333 7.12 0.00 46.36 3.41
648 674 9.168451 ACTCTAGAATATGTCTACATACATCCG 57.832 37.037 4.98 3.03 41.15 4.18
649 675 9.168451 CTCTAGAATATGTCTACATACATCCGT 57.832 37.037 4.98 0.00 41.15 4.69
662 688 5.838529 CATACATCCGTATGTTGTAGTCCA 58.161 41.667 0.00 0.00 46.70 4.02
663 689 6.455647 CATACATCCGTATGTTGTAGTCCAT 58.544 40.000 0.00 0.00 46.70 3.41
664 690 5.353394 ACATCCGTATGTTGTAGTCCATT 57.647 39.130 0.00 0.00 44.07 3.16
665 691 5.741011 ACATCCGTATGTTGTAGTCCATTT 58.259 37.500 0.00 0.00 44.07 2.32
666 692 5.584649 ACATCCGTATGTTGTAGTCCATTTG 59.415 40.000 0.00 0.00 44.07 2.32
667 693 5.408880 TCCGTATGTTGTAGTCCATTTGA 57.591 39.130 0.00 0.00 0.00 2.69
668 694 5.795972 TCCGTATGTTGTAGTCCATTTGAA 58.204 37.500 0.00 0.00 0.00 2.69
669 695 6.231951 TCCGTATGTTGTAGTCCATTTGAAA 58.768 36.000 0.00 0.00 0.00 2.69
670 696 6.882140 TCCGTATGTTGTAGTCCATTTGAAAT 59.118 34.615 0.00 0.00 0.00 2.17
671 697 6.966632 CCGTATGTTGTAGTCCATTTGAAATG 59.033 38.462 10.84 10.84 0.00 2.32
672 698 7.361713 CCGTATGTTGTAGTCCATTTGAAATGT 60.362 37.037 15.93 1.43 0.00 2.71
673 699 7.692291 CGTATGTTGTAGTCCATTTGAAATGTC 59.308 37.037 15.93 9.10 0.00 3.06
674 700 7.765695 ATGTTGTAGTCCATTTGAAATGTCT 57.234 32.000 15.93 14.81 0.00 3.41
675 701 8.862325 ATGTTGTAGTCCATTTGAAATGTCTA 57.138 30.769 15.93 13.97 0.00 2.59
676 702 8.684386 TGTTGTAGTCCATTTGAAATGTCTAA 57.316 30.769 15.93 4.89 0.00 2.10
677 703 9.126151 TGTTGTAGTCCATTTGAAATGTCTAAA 57.874 29.630 15.93 10.39 0.00 1.85
678 704 9.959749 GTTGTAGTCCATTTGAAATGTCTAAAA 57.040 29.630 15.93 14.59 0.00 1.52
683 709 9.136323 AGTCCATTTGAAATGTCTAAAAAGACT 57.864 29.630 15.93 14.21 39.41 3.24
684 710 9.750125 GTCCATTTGAAATGTCTAAAAAGACTT 57.250 29.630 15.93 0.00 39.41 3.01
702 728 9.868160 AAAAGACTTATATTTAGGATTGGAGGG 57.132 33.333 0.00 0.00 0.00 4.30
800 828 3.422343 CGAAGACATTGACGCTTTGAGAC 60.422 47.826 0.00 0.00 0.00 3.36
859 4483 2.167693 TCAGCAAATCGGGATAGACGTT 59.832 45.455 0.00 0.00 0.00 3.99
890 4514 0.038599 TGCCTGTCAGCAATCATGGT 59.961 50.000 0.00 0.00 40.56 3.55
932 4561 1.828832 CGACTACATCGCTCACTTCC 58.171 55.000 0.00 0.00 45.52 3.46
933 4562 1.534175 CGACTACATCGCTCACTTCCC 60.534 57.143 0.00 0.00 45.52 3.97
944 4573 1.225983 CACTTCCCCCACACACACA 59.774 57.895 0.00 0.00 0.00 3.72
1369 5035 1.589716 GCCGTACTACACCCGTGACT 61.590 60.000 0.96 0.00 0.00 3.41
1413 5079 0.586802 GCAACTTCGACCTGTTCCAC 59.413 55.000 0.00 0.00 0.00 4.02
1488 5163 2.674754 GCACCCGAGGAAATCCCA 59.325 61.111 0.00 0.00 37.41 4.37
1518 5193 1.675641 GGCCATCGCACCAGAGTTT 60.676 57.895 0.00 0.00 36.38 2.66
1521 5196 1.503542 CATCGCACCAGAGTTTGCC 59.496 57.895 0.00 0.00 35.14 4.52
1641 5319 4.172512 CTGAGCCTCGCCTGCCAT 62.173 66.667 0.00 0.00 0.00 4.40
1698 5376 1.003355 CACCACCAAGCACTCCGAT 60.003 57.895 0.00 0.00 0.00 4.18
2040 5751 2.907179 GCACTACAGGGCCAAGGGT 61.907 63.158 6.18 0.28 0.00 4.34
2087 5802 8.138074 CGAACACTTCAGGATCTAATGAATCTA 58.862 37.037 8.36 0.00 35.04 1.98
2088 5803 9.995003 GAACACTTCAGGATCTAATGAATCTAT 57.005 33.333 8.36 0.00 35.04 1.98
2090 5805 9.995003 ACACTTCAGGATCTAATGAATCTATTC 57.005 33.333 8.36 0.00 35.04 1.75
2097 5812 7.038659 GGATCTAATGAATCTATTCTCACCCG 58.961 42.308 4.45 0.00 37.67 5.28
2102 5817 4.380531 TGAATCTATTCTCACCCGAATGC 58.619 43.478 4.45 0.00 37.67 3.56
2108 5823 0.810648 TCTCACCCGAATGCATTTGC 59.189 50.000 19.70 4.69 42.50 3.68
2119 5834 2.658373 TGCATTTGCTGTGCTTATGG 57.342 45.000 3.94 0.00 42.92 2.74
2214 6124 1.019673 CACTCTTCCCAATGGCGATG 58.980 55.000 0.00 0.00 0.00 3.84
2229 6193 4.633175 TGGCGATGTTAACTTACAGTTGA 58.367 39.130 7.22 0.00 39.11 3.18
2230 6194 4.688879 TGGCGATGTTAACTTACAGTTGAG 59.311 41.667 7.22 0.00 39.11 3.02
2232 6196 4.435651 GCGATGTTAACTTACAGTTGAGGC 60.436 45.833 7.22 0.00 39.11 4.70
2246 6210 7.195374 ACAGTTGAGGCTAGGAAAACATATA 57.805 36.000 0.00 0.00 0.00 0.86
2248 6212 7.092846 ACAGTTGAGGCTAGGAAAACATATACT 60.093 37.037 0.00 0.00 0.00 2.12
2250 6214 8.422566 AGTTGAGGCTAGGAAAACATATACTAC 58.577 37.037 0.00 0.00 0.00 2.73
2251 6215 8.422566 GTTGAGGCTAGGAAAACATATACTACT 58.577 37.037 0.00 0.00 0.00 2.57
2253 6217 9.298250 TGAGGCTAGGAAAACATATACTACTAG 57.702 37.037 0.00 0.00 0.00 2.57
2280 6245 2.106338 TGAACTGGAAATCACAGGCAGA 59.894 45.455 0.00 0.00 40.23 4.26
2281 6246 3.245016 TGAACTGGAAATCACAGGCAGAT 60.245 43.478 0.00 0.00 40.23 2.90
2302 6267 6.429385 CAGATATCTCCTACAAATTGAAGGGC 59.571 42.308 1.03 0.00 0.00 5.19
2303 6268 4.591321 ATCTCCTACAAATTGAAGGGCA 57.409 40.909 0.00 0.00 0.00 5.36
2304 6269 4.380843 TCTCCTACAAATTGAAGGGCAA 57.619 40.909 0.00 0.00 41.53 4.52
2305 6270 4.079253 TCTCCTACAAATTGAAGGGCAAC 58.921 43.478 0.00 0.00 39.78 4.17
2306 6271 3.826157 CTCCTACAAATTGAAGGGCAACA 59.174 43.478 0.00 0.00 39.78 3.33
2307 6272 4.415596 TCCTACAAATTGAAGGGCAACAT 58.584 39.130 0.00 0.00 39.78 2.71
2308 6273 5.575157 TCCTACAAATTGAAGGGCAACATA 58.425 37.500 0.00 0.00 39.78 2.29
2309 6274 6.013379 TCCTACAAATTGAAGGGCAACATAA 58.987 36.000 0.00 0.00 39.78 1.90
2310 6275 6.071616 TCCTACAAATTGAAGGGCAACATAAC 60.072 38.462 0.00 0.00 39.78 1.89
2311 6276 4.893608 ACAAATTGAAGGGCAACATAACC 58.106 39.130 0.00 0.00 39.78 2.85
2312 6277 4.346418 ACAAATTGAAGGGCAACATAACCA 59.654 37.500 0.00 0.00 39.78 3.67
2313 6278 5.163258 ACAAATTGAAGGGCAACATAACCAA 60.163 36.000 0.00 0.00 39.78 3.67
2314 6279 5.559148 AATTGAAGGGCAACATAACCAAA 57.441 34.783 0.00 0.00 39.78 3.28
2315 6280 5.760484 ATTGAAGGGCAACATAACCAAAT 57.240 34.783 0.00 0.00 39.78 2.32
2316 6281 4.533919 TGAAGGGCAACATAACCAAATG 57.466 40.909 0.00 0.00 39.74 2.32
2317 6282 3.260380 TGAAGGGCAACATAACCAAATGG 59.740 43.478 0.00 0.00 39.20 3.16
2318 6283 1.554617 AGGGCAACATAACCAAATGGC 59.445 47.619 0.00 0.00 37.11 4.40
2329 6294 7.096551 ACATAACCAAATGGCAAGTTATTCAC 58.903 34.615 10.84 0.00 39.32 3.18
2340 6305 7.026562 TGGCAAGTTATTCACAATTTCATACG 58.973 34.615 0.00 0.00 0.00 3.06
2358 7852 0.605589 CGAGAGCTGGGACTGAAACT 59.394 55.000 0.00 0.00 0.00 2.66
2409 7903 5.997129 TGATGACTTTCTTCAGCATGTACAA 59.003 36.000 0.00 0.00 36.99 2.41
2432 7926 9.926158 ACAAACAGATAGAGATACATGATGATC 57.074 33.333 0.00 0.00 0.00 2.92
2452 7946 6.914259 TGATCTTGTACACTGAGTTACTGAG 58.086 40.000 0.00 0.00 0.00 3.35
2487 7988 5.555966 TGCGTGGCCAATAATAATCTCATA 58.444 37.500 7.24 0.00 0.00 2.15
2492 7993 7.550551 CGTGGCCAATAATAATCTCATATCACT 59.449 37.037 7.24 0.00 0.00 3.41
2493 7994 8.887717 GTGGCCAATAATAATCTCATATCACTC 58.112 37.037 7.24 0.00 0.00 3.51
2494 7995 8.829746 TGGCCAATAATAATCTCATATCACTCT 58.170 33.333 0.61 0.00 0.00 3.24
2495 7996 9.323985 GGCCAATAATAATCTCATATCACTCTC 57.676 37.037 0.00 0.00 0.00 3.20
2500 8021 7.403312 AATAATCTCATATCACTCTCCTCCG 57.597 40.000 0.00 0.00 0.00 4.63
2542 8063 2.125106 CAGGCTTGGCGTACCTCC 60.125 66.667 0.00 0.00 36.63 4.30
2548 8069 0.953960 CTTGGCGTACCTCCCACAAC 60.954 60.000 0.00 0.00 36.63 3.32
2572 8093 8.715191 ACATTCTGAACAGAGATTATGAGTTC 57.285 34.615 16.19 0.00 38.88 3.01
2597 8118 6.902948 CGTCGTTGAGAAAGACAAAAACAATA 59.097 34.615 0.00 0.00 39.43 1.90
2660 8182 5.520376 AATCAAACCTTGTGACTTTCTGG 57.480 39.130 0.00 0.00 0.00 3.86
2667 8189 4.136796 CCTTGTGACTTTCTGGTCATTCA 58.863 43.478 0.70 0.00 46.04 2.57
2678 8200 1.068541 TGGTCATTCACACTCTCGTCG 60.069 52.381 0.00 0.00 0.00 5.12
2679 8201 1.068472 GGTCATTCACACTCTCGTCGT 60.068 52.381 0.00 0.00 0.00 4.34
2687 8209 2.848887 CACACTCTCGTCGTGAATCATC 59.151 50.000 8.11 0.00 36.29 2.92
2693 8215 1.135517 TCGTCGTGAATCATCAGCGAA 60.136 47.619 0.00 0.00 39.23 4.70
2694 8216 1.253800 CGTCGTGAATCATCAGCGAAG 59.746 52.381 0.00 0.00 39.23 3.79
2730 8252 2.376165 GGGTCCTGAGGGGTTAGGC 61.376 68.421 0.00 0.00 34.00 3.93
2760 8282 0.746659 GCTGAGGCAAAAACACCTGT 59.253 50.000 0.00 0.00 36.05 4.00
2795 8317 0.455633 GTCTGCAGCAGCGAAAATGG 60.456 55.000 18.43 0.00 46.23 3.16
2805 8327 1.474077 AGCGAAAATGGGCTGCTTTAG 59.526 47.619 0.00 0.00 38.27 1.85
2813 8335 1.133637 TGGGCTGCTTTAGTTGGTGAA 60.134 47.619 0.00 0.00 0.00 3.18
2814 8336 1.960689 GGGCTGCTTTAGTTGGTGAAA 59.039 47.619 0.00 0.00 0.00 2.69
2816 8338 3.381045 GGCTGCTTTAGTTGGTGAAAAC 58.619 45.455 0.00 0.00 0.00 2.43
2817 8339 3.068165 GGCTGCTTTAGTTGGTGAAAACT 59.932 43.478 0.00 0.00 42.89 2.66
2818 8340 4.290969 GCTGCTTTAGTTGGTGAAAACTC 58.709 43.478 0.00 0.00 40.77 3.01
2821 8343 6.274157 TGCTTTAGTTGGTGAAAACTCAAA 57.726 33.333 0.00 0.00 40.77 2.69
2822 8344 6.872920 TGCTTTAGTTGGTGAAAACTCAAAT 58.127 32.000 0.00 0.00 40.77 2.32
2823 8345 7.327214 TGCTTTAGTTGGTGAAAACTCAAATT 58.673 30.769 0.00 0.00 40.77 1.82
2826 8348 8.925161 TTTAGTTGGTGAAAACTCAAATTCAG 57.075 30.769 0.00 0.00 40.77 3.02
2827 8349 6.530019 AGTTGGTGAAAACTCAAATTCAGT 57.470 33.333 0.00 0.00 35.44 3.41
2893 8818 2.582728 TGCTGTTGGTTGCAAGAAAG 57.417 45.000 0.00 0.00 36.15 2.62
2952 8882 6.632909 TGATTAATATAGGGCAATTGCATGC 58.367 36.000 30.32 11.82 45.67 4.06
3068 8998 1.214424 GGCAACTCTTATTAGGGCCCA 59.786 52.381 27.56 3.72 35.93 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 71 1.340248 GCGCTAATAGGCTGGAGTACA 59.660 52.381 0.00 0.00 0.00 2.90
92 102 8.584063 TCATGCATATTTTGATATGTAGGCAT 57.416 30.769 0.00 0.00 42.95 4.40
95 105 8.627403 GGGATCATGCATATTTTGATATGTAGG 58.373 37.037 0.00 5.80 36.98 3.18
96 106 9.181061 TGGGATCATGCATATTTTGATATGTAG 57.819 33.333 0.00 0.00 36.98 2.74
197 220 3.266772 TGCCAGGATCTAAACCTTGTGAT 59.733 43.478 0.00 0.00 35.35 3.06
228 251 0.674895 GAGCAATGCGAGGAGGTGTT 60.675 55.000 0.00 0.00 0.00 3.32
260 283 3.797451 TGCAAAACTGAACATGCAGAA 57.203 38.095 7.27 0.00 43.32 3.02
278 301 2.877168 TGTTTTTGAATGCCCATTGTGC 59.123 40.909 0.00 0.00 0.00 4.57
288 311 3.392882 GGGAGCACCTTGTTTTTGAATG 58.607 45.455 0.00 0.00 35.85 2.67
289 312 2.368548 GGGGAGCACCTTGTTTTTGAAT 59.631 45.455 0.00 0.00 40.03 2.57
319 342 0.105224 TCTTCTTTTCGACGTGCCCA 59.895 50.000 0.00 0.00 0.00 5.36
320 343 1.223187 TTCTTCTTTTCGACGTGCCC 58.777 50.000 0.00 0.00 0.00 5.36
328 351 2.295696 GTCGGCGTTTTCTTCTTTTCG 58.704 47.619 6.85 0.00 0.00 3.46
329 352 2.033492 TCGTCGGCGTTTTCTTCTTTTC 60.033 45.455 10.18 0.00 39.49 2.29
332 356 1.792006 ATCGTCGGCGTTTTCTTCTT 58.208 45.000 10.18 0.00 39.49 2.52
356 380 3.541632 TCCAACACACAACCTTCTTCTC 58.458 45.455 0.00 0.00 0.00 2.87
357 381 3.644966 TCCAACACACAACCTTCTTCT 57.355 42.857 0.00 0.00 0.00 2.85
445 471 3.503227 CCCCCATCAAACTCCCCTAAAAA 60.503 47.826 0.00 0.00 0.00 1.94
446 472 2.043801 CCCCCATCAAACTCCCCTAAAA 59.956 50.000 0.00 0.00 0.00 1.52
447 473 1.643811 CCCCCATCAAACTCCCCTAAA 59.356 52.381 0.00 0.00 0.00 1.85
448 474 1.304891 CCCCCATCAAACTCCCCTAA 58.695 55.000 0.00 0.00 0.00 2.69
449 475 0.122435 ACCCCCATCAAACTCCCCTA 59.878 55.000 0.00 0.00 0.00 3.53
450 476 0.780090 AACCCCCATCAAACTCCCCT 60.780 55.000 0.00 0.00 0.00 4.79
451 477 0.116342 AAACCCCCATCAAACTCCCC 59.884 55.000 0.00 0.00 0.00 4.81
452 478 2.024176 AAAACCCCCATCAAACTCCC 57.976 50.000 0.00 0.00 0.00 4.30
453 479 2.038426 CCAAAAACCCCCATCAAACTCC 59.962 50.000 0.00 0.00 0.00 3.85
454 480 2.549992 GCCAAAAACCCCCATCAAACTC 60.550 50.000 0.00 0.00 0.00 3.01
455 481 1.419762 GCCAAAAACCCCCATCAAACT 59.580 47.619 0.00 0.00 0.00 2.66
456 482 1.141858 TGCCAAAAACCCCCATCAAAC 59.858 47.619 0.00 0.00 0.00 2.93
457 483 1.511613 TGCCAAAAACCCCCATCAAA 58.488 45.000 0.00 0.00 0.00 2.69
458 484 1.350351 CATGCCAAAAACCCCCATCAA 59.650 47.619 0.00 0.00 0.00 2.57
459 485 0.982704 CATGCCAAAAACCCCCATCA 59.017 50.000 0.00 0.00 0.00 3.07
460 486 0.392863 GCATGCCAAAAACCCCCATC 60.393 55.000 6.36 0.00 0.00 3.51
461 487 1.684629 GCATGCCAAAAACCCCCAT 59.315 52.632 6.36 0.00 0.00 4.00
462 488 2.524204 GGCATGCCAAAAACCCCCA 61.524 57.895 32.08 0.00 35.81 4.96
463 489 2.350895 GGCATGCCAAAAACCCCC 59.649 61.111 32.08 0.00 35.81 5.40
464 490 3.155750 TGGCATGCCAAAAACCCC 58.844 55.556 36.95 7.44 44.12 4.95
479 505 0.037046 GGTGGGCAAAGAAGCATTGG 60.037 55.000 0.00 0.00 35.83 3.16
510 536 1.523154 TTTAGCAAGCACCGGCAAGG 61.523 55.000 0.00 0.00 44.61 3.61
517 543 5.064441 AGTCAAATGATTTAGCAAGCACC 57.936 39.130 0.00 0.00 28.98 5.01
535 561 3.350833 GGAACGAAGGGAGTACTAGTCA 58.649 50.000 0.00 0.00 0.00 3.41
536 562 2.687425 GGGAACGAAGGGAGTACTAGTC 59.313 54.545 0.00 0.00 0.00 2.59
538 564 2.731572 TGGGAACGAAGGGAGTACTAG 58.268 52.381 0.00 0.00 0.00 2.57
539 565 2.905415 TGGGAACGAAGGGAGTACTA 57.095 50.000 0.00 0.00 0.00 1.82
540 566 2.019807 TTGGGAACGAAGGGAGTACT 57.980 50.000 0.00 0.00 0.00 2.73
541 567 2.845363 TTTGGGAACGAAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
542 568 6.328148 ACATATATTTGGGAACGAAGGGAGTA 59.672 38.462 0.00 0.00 37.08 2.59
543 569 5.132144 ACATATATTTGGGAACGAAGGGAGT 59.868 40.000 0.00 0.00 37.08 3.85
544 570 5.621193 ACATATATTTGGGAACGAAGGGAG 58.379 41.667 0.00 0.00 37.08 4.30
545 571 5.368523 AGACATATATTTGGGAACGAAGGGA 59.631 40.000 0.00 0.00 37.08 4.20
546 572 5.621193 AGACATATATTTGGGAACGAAGGG 58.379 41.667 0.00 0.00 37.08 3.95
547 573 7.568199 AAAGACATATATTTGGGAACGAAGG 57.432 36.000 0.00 0.00 37.08 3.46
550 576 9.893634 TCTAAAAAGACATATATTTGGGAACGA 57.106 29.630 0.00 0.00 0.00 3.85
562 588 9.118300 CTTGCTGGAATCTCTAAAAAGACATAT 57.882 33.333 0.00 0.00 0.00 1.78
563 589 8.103305 ACTTGCTGGAATCTCTAAAAAGACATA 58.897 33.333 0.00 0.00 0.00 2.29
564 590 6.944862 ACTTGCTGGAATCTCTAAAAAGACAT 59.055 34.615 0.00 0.00 0.00 3.06
565 591 6.299141 ACTTGCTGGAATCTCTAAAAAGACA 58.701 36.000 0.00 0.00 0.00 3.41
566 592 6.428159 TGACTTGCTGGAATCTCTAAAAAGAC 59.572 38.462 0.00 0.00 0.00 3.01
567 593 6.428159 GTGACTTGCTGGAATCTCTAAAAAGA 59.572 38.462 0.00 0.00 0.00 2.52
568 594 6.429385 AGTGACTTGCTGGAATCTCTAAAAAG 59.571 38.462 0.00 0.00 0.00 2.27
569 595 6.299141 AGTGACTTGCTGGAATCTCTAAAAA 58.701 36.000 0.00 0.00 0.00 1.94
570 596 5.869579 AGTGACTTGCTGGAATCTCTAAAA 58.130 37.500 0.00 0.00 0.00 1.52
571 597 5.489792 AGTGACTTGCTGGAATCTCTAAA 57.510 39.130 0.00 0.00 0.00 1.85
572 598 5.480422 TGTAGTGACTTGCTGGAATCTCTAA 59.520 40.000 0.00 0.00 0.00 2.10
573 599 5.016831 TGTAGTGACTTGCTGGAATCTCTA 58.983 41.667 0.00 0.00 0.00 2.43
574 600 3.834813 TGTAGTGACTTGCTGGAATCTCT 59.165 43.478 0.00 0.00 0.00 3.10
575 601 4.193826 TGTAGTGACTTGCTGGAATCTC 57.806 45.455 0.00 0.00 0.00 2.75
576 602 4.833478 ATGTAGTGACTTGCTGGAATCT 57.167 40.909 0.00 0.00 0.00 2.40
577 603 4.504461 CGTATGTAGTGACTTGCTGGAATC 59.496 45.833 0.00 0.00 0.00 2.52
578 604 4.433615 CGTATGTAGTGACTTGCTGGAAT 58.566 43.478 0.00 0.00 0.00 3.01
579 605 3.368013 CCGTATGTAGTGACTTGCTGGAA 60.368 47.826 0.00 0.00 0.00 3.53
580 606 2.165641 CCGTATGTAGTGACTTGCTGGA 59.834 50.000 0.00 0.00 0.00 3.86
581 607 2.165641 TCCGTATGTAGTGACTTGCTGG 59.834 50.000 0.00 0.00 0.00 4.85
582 608 3.439293 CTCCGTATGTAGTGACTTGCTG 58.561 50.000 0.00 0.00 0.00 4.41
583 609 2.159226 GCTCCGTATGTAGTGACTTGCT 60.159 50.000 0.00 0.00 0.00 3.91
584 610 2.194271 GCTCCGTATGTAGTGACTTGC 58.806 52.381 0.00 0.00 0.00 4.01
585 611 3.503827 TGCTCCGTATGTAGTGACTTG 57.496 47.619 0.00 0.00 0.00 3.16
586 612 4.530710 TTTGCTCCGTATGTAGTGACTT 57.469 40.909 0.00 0.00 0.00 3.01
587 613 4.530710 TTTTGCTCCGTATGTAGTGACT 57.469 40.909 0.00 0.00 0.00 3.41
588 614 4.868171 TCATTTTGCTCCGTATGTAGTGAC 59.132 41.667 0.00 0.00 0.00 3.67
589 615 5.079689 TCATTTTGCTCCGTATGTAGTGA 57.920 39.130 0.00 0.00 0.00 3.41
590 616 4.870426 ACTCATTTTGCTCCGTATGTAGTG 59.130 41.667 0.00 0.00 0.00 2.74
591 617 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
592 618 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
593 619 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
594 620 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
595 621 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
596 622 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
597 623 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
598 624 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
599 625 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
600 626 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
601 627 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
611 637 9.860650 AGACATATTCTAGAGTGTAGATTCACT 57.139 33.333 0.00 0.00 41.09 3.41
622 648 9.168451 CGGATGTATGTAGACATATTCTAGAGT 57.832 37.037 5.69 0.00 40.18 3.24
623 649 9.168451 ACGGATGTATGTAGACATATTCTAGAG 57.832 37.037 5.69 0.00 40.18 2.43
640 666 6.665992 ATGGACTACAACATACGGATGTAT 57.334 37.500 15.10 8.21 45.93 2.29
641 667 6.474140 AATGGACTACAACATACGGATGTA 57.526 37.500 15.10 0.00 45.93 2.29
643 669 5.815222 TCAAATGGACTACAACATACGGATG 59.185 40.000 5.94 5.94 39.16 3.51
644 670 5.984725 TCAAATGGACTACAACATACGGAT 58.015 37.500 0.00 0.00 0.00 4.18
645 671 5.408880 TCAAATGGACTACAACATACGGA 57.591 39.130 0.00 0.00 0.00 4.69
646 672 6.489127 TTTCAAATGGACTACAACATACGG 57.511 37.500 0.00 0.00 0.00 4.02
647 673 7.526608 ACATTTCAAATGGACTACAACATACG 58.473 34.615 14.70 0.00 0.00 3.06
648 674 8.730680 AGACATTTCAAATGGACTACAACATAC 58.269 33.333 14.70 0.00 0.00 2.39
649 675 8.862325 AGACATTTCAAATGGACTACAACATA 57.138 30.769 14.70 0.00 0.00 2.29
650 676 7.765695 AGACATTTCAAATGGACTACAACAT 57.234 32.000 14.70 0.00 0.00 2.71
651 677 8.684386 TTAGACATTTCAAATGGACTACAACA 57.316 30.769 14.70 1.25 0.00 3.33
652 678 9.959749 TTTTAGACATTTCAAATGGACTACAAC 57.040 29.630 14.70 0.00 0.00 3.32
657 683 9.136323 AGTCTTTTTAGACATTTCAAATGGACT 57.864 29.630 14.70 14.18 41.02 3.85
658 684 9.750125 AAGTCTTTTTAGACATTTCAAATGGAC 57.250 29.630 14.70 8.92 41.02 4.02
676 702 9.868160 CCCTCCAATCCTAAATATAAGTCTTTT 57.132 33.333 0.00 0.00 0.00 2.27
677 703 9.237706 TCCCTCCAATCCTAAATATAAGTCTTT 57.762 33.333 0.00 0.00 0.00 2.52
678 704 8.814448 TCCCTCCAATCCTAAATATAAGTCTT 57.186 34.615 0.00 0.00 0.00 3.01
679 705 8.019652 ACTCCCTCCAATCCTAAATATAAGTCT 58.980 37.037 0.00 0.00 0.00 3.24
680 706 8.208575 ACTCCCTCCAATCCTAAATATAAGTC 57.791 38.462 0.00 0.00 0.00 3.01
681 707 9.684702 TTACTCCCTCCAATCCTAAATATAAGT 57.315 33.333 0.00 0.00 0.00 2.24
686 712 9.237706 AGATTTTACTCCCTCCAATCCTAAATA 57.762 33.333 0.00 0.00 0.00 1.40
687 713 8.119062 AGATTTTACTCCCTCCAATCCTAAAT 57.881 34.615 0.00 0.00 0.00 1.40
688 714 7.525158 AGATTTTACTCCCTCCAATCCTAAA 57.475 36.000 0.00 0.00 0.00 1.85
689 715 7.183839 TCAAGATTTTACTCCCTCCAATCCTAA 59.816 37.037 0.00 0.00 0.00 2.69
690 716 6.676632 TCAAGATTTTACTCCCTCCAATCCTA 59.323 38.462 0.00 0.00 0.00 2.94
691 717 5.492524 TCAAGATTTTACTCCCTCCAATCCT 59.507 40.000 0.00 0.00 0.00 3.24
692 718 5.590663 GTCAAGATTTTACTCCCTCCAATCC 59.409 44.000 0.00 0.00 0.00 3.01
693 719 5.590663 GGTCAAGATTTTACTCCCTCCAATC 59.409 44.000 0.00 0.00 0.00 2.67
694 720 5.015178 TGGTCAAGATTTTACTCCCTCCAAT 59.985 40.000 0.00 0.00 0.00 3.16
695 721 4.352595 TGGTCAAGATTTTACTCCCTCCAA 59.647 41.667 0.00 0.00 0.00 3.53
696 722 3.913799 TGGTCAAGATTTTACTCCCTCCA 59.086 43.478 0.00 0.00 0.00 3.86
697 723 4.569719 TGGTCAAGATTTTACTCCCTCC 57.430 45.455 0.00 0.00 0.00 4.30
698 724 6.894339 TTTTGGTCAAGATTTTACTCCCTC 57.106 37.500 0.00 0.00 0.00 4.30
699 725 9.547279 AATATTTTGGTCAAGATTTTACTCCCT 57.453 29.630 0.00 0.00 0.00 4.20
767 793 3.942115 TCAATGTCTTCGGTTGTGTTTGA 59.058 39.130 0.00 0.00 0.00 2.69
859 4483 2.163613 CTGACAGGCAGTGTATACGTCA 59.836 50.000 0.00 3.27 40.56 4.35
890 4514 5.505159 CGTGGCTCTTTACTGATCGTACATA 60.505 44.000 0.00 0.00 0.00 2.29
932 4561 1.974265 TTGTGTATGTGTGTGTGGGG 58.026 50.000 0.00 0.00 0.00 4.96
933 4562 2.948979 AGTTTGTGTATGTGTGTGTGGG 59.051 45.455 0.00 0.00 0.00 4.61
944 4573 7.390440 TCGATCCTTTGAATTCAGTTTGTGTAT 59.610 33.333 8.41 0.00 0.00 2.29
1376 5042 2.675423 TCTGGTACCTCACGCGCT 60.675 61.111 14.36 0.00 0.00 5.92
1473 5148 2.666098 CGGTGGGATTTCCTCGGGT 61.666 63.158 0.00 0.00 36.20 5.28
1509 5184 3.570212 AGCCCGGCAAACTCTGGT 61.570 61.111 13.15 0.00 0.00 4.00
1641 5319 3.773404 GGGCACGCCGGGTAGTAA 61.773 66.667 2.18 0.00 36.85 2.24
1698 5376 2.203788 ACGGTGAGGAAGCTGGGA 60.204 61.111 0.00 0.00 0.00 4.37
2062 5773 9.995003 ATAGATTCATTAGATCCTGAAGTGTTC 57.005 33.333 8.42 2.97 35.04 3.18
2087 5802 2.159198 GCAAATGCATTCGGGTGAGAAT 60.159 45.455 13.38 0.00 41.12 2.40
2088 5803 1.202114 GCAAATGCATTCGGGTGAGAA 59.798 47.619 13.38 0.00 41.59 2.87
2089 5804 0.810648 GCAAATGCATTCGGGTGAGA 59.189 50.000 13.38 0.00 41.59 3.27
2090 5805 0.813184 AGCAAATGCATTCGGGTGAG 59.187 50.000 13.38 0.00 45.16 3.51
2091 5806 0.527113 CAGCAAATGCATTCGGGTGA 59.473 50.000 26.52 0.00 45.16 4.02
2097 5812 3.554324 CCATAAGCACAGCAAATGCATTC 59.446 43.478 13.38 0.67 45.92 2.67
2102 5817 2.478370 CCGACCATAAGCACAGCAAATG 60.478 50.000 0.00 0.00 0.00 2.32
2108 5823 3.270027 TGAATTCCGACCATAAGCACAG 58.730 45.455 2.27 0.00 0.00 3.66
2119 5834 1.014352 CCCCGAACATGAATTCCGAC 58.986 55.000 0.00 0.00 0.00 4.79
2195 6105 1.019673 CATCGCCATTGGGAAGAGTG 58.980 55.000 4.53 0.00 36.96 3.51
2246 6210 8.812972 TGATTTCCAGTTCATGTTACTAGTAGT 58.187 33.333 8.14 8.14 0.00 2.73
2248 6212 8.590204 TGTGATTTCCAGTTCATGTTACTAGTA 58.410 33.333 0.00 0.00 0.00 1.82
2250 6214 7.065085 CCTGTGATTTCCAGTTCATGTTACTAG 59.935 40.741 0.00 0.00 0.00 2.57
2251 6215 6.878923 CCTGTGATTTCCAGTTCATGTTACTA 59.121 38.462 0.00 0.00 0.00 1.82
2253 6217 5.619981 GCCTGTGATTTCCAGTTCATGTTAC 60.620 44.000 0.00 0.00 0.00 2.50
2280 6245 6.266131 TGCCCTTCAATTTGTAGGAGATAT 57.734 37.500 20.23 0.00 37.12 1.63
2281 6246 5.708736 TGCCCTTCAATTTGTAGGAGATA 57.291 39.130 20.23 4.29 37.12 1.98
2302 6267 7.601886 TGAATAACTTGCCATTTGGTTATGTTG 59.398 33.333 0.00 0.00 35.76 3.33
2303 6268 7.602265 GTGAATAACTTGCCATTTGGTTATGTT 59.398 33.333 0.00 5.74 35.76 2.71
2304 6269 7.096551 GTGAATAACTTGCCATTTGGTTATGT 58.903 34.615 0.00 0.00 35.76 2.29
2305 6270 7.095910 TGTGAATAACTTGCCATTTGGTTATG 58.904 34.615 0.00 0.00 35.76 1.90
2306 6271 7.238486 TGTGAATAACTTGCCATTTGGTTAT 57.762 32.000 0.00 0.00 36.72 1.89
2307 6272 6.656632 TGTGAATAACTTGCCATTTGGTTA 57.343 33.333 0.00 0.00 37.57 2.85
2308 6273 5.543507 TGTGAATAACTTGCCATTTGGTT 57.456 34.783 0.00 0.00 37.57 3.67
2309 6274 5.543507 TTGTGAATAACTTGCCATTTGGT 57.456 34.783 0.00 0.00 37.57 3.67
2310 6275 7.172875 TGAAATTGTGAATAACTTGCCATTTGG 59.827 33.333 0.00 0.00 38.53 3.28
2311 6276 8.085720 TGAAATTGTGAATAACTTGCCATTTG 57.914 30.769 0.00 0.00 0.00 2.32
2312 6277 8.851541 ATGAAATTGTGAATAACTTGCCATTT 57.148 26.923 0.00 0.00 0.00 2.32
2313 6278 9.369904 GTATGAAATTGTGAATAACTTGCCATT 57.630 29.630 0.00 0.00 0.00 3.16
2314 6279 7.701924 CGTATGAAATTGTGAATAACTTGCCAT 59.298 33.333 0.00 0.00 0.00 4.40
2315 6280 7.026562 CGTATGAAATTGTGAATAACTTGCCA 58.973 34.615 0.00 0.00 0.00 4.92
2316 6281 7.247728 TCGTATGAAATTGTGAATAACTTGCC 58.752 34.615 0.00 0.00 0.00 4.52
2317 6282 8.175069 TCTCGTATGAAATTGTGAATAACTTGC 58.825 33.333 0.00 0.00 0.00 4.01
2318 6283 9.694520 CTCTCGTATGAAATTGTGAATAACTTG 57.305 33.333 0.00 0.00 0.00 3.16
2329 6294 3.557595 GTCCCAGCTCTCGTATGAAATTG 59.442 47.826 0.00 0.00 0.00 2.32
2340 6305 1.620819 TCAGTTTCAGTCCCAGCTCTC 59.379 52.381 0.00 0.00 0.00 3.20
2358 7852 1.066858 GGTCTGTCTCGCCTGAAATCA 60.067 52.381 0.00 0.00 0.00 2.57
2432 7926 6.073327 TCACTCAGTAACTCAGTGTACAAG 57.927 41.667 0.00 0.00 38.94 3.16
2433 7927 5.507482 GCTCACTCAGTAACTCAGTGTACAA 60.507 44.000 0.00 0.00 38.94 2.41
2435 7929 4.216687 AGCTCACTCAGTAACTCAGTGTAC 59.783 45.833 5.49 0.29 38.94 2.90
2438 7932 3.932545 AGCTCACTCAGTAACTCAGTG 57.067 47.619 0.00 0.00 39.18 3.66
2452 7946 2.089854 CCACGCATGGTTAGCTCAC 58.910 57.895 0.00 0.00 41.64 3.51
2487 7988 1.456705 GGAGGCGGAGGAGAGTGAT 60.457 63.158 0.00 0.00 0.00 3.06
2500 8021 3.257127 GATATAGGCATATCTCCGGAGGC 59.743 52.174 30.80 24.29 39.86 4.70
2515 8036 2.037772 ACGCCAAGCCTGAAGATATAGG 59.962 50.000 0.00 0.00 37.14 2.57
2542 8063 5.954296 AATCTCTGTTCAGAATGTTGTGG 57.046 39.130 4.09 0.00 37.40 4.17
2548 8069 7.490725 ACGAACTCATAATCTCTGTTCAGAATG 59.509 37.037 4.09 5.25 37.46 2.67
2572 8093 4.643953 TGTTTTTGTCTTTCTCAACGACG 58.356 39.130 0.00 0.00 0.00 5.12
2606 8127 6.769822 AGCACCTCAGTATTCCATTTTATCTG 59.230 38.462 0.00 0.00 0.00 2.90
2678 8200 0.302890 CGGCTTCGCTGATGATTCAC 59.697 55.000 0.00 0.00 37.02 3.18
2679 8201 2.681660 CGGCTTCGCTGATGATTCA 58.318 52.632 0.00 0.00 37.02 2.57
2705 8227 1.685820 CCCTCAGGACCCCTTGAAC 59.314 63.158 0.00 0.00 33.47 3.18
2730 8252 0.035881 TGCCTCAGCTTCTTCTGTGG 59.964 55.000 7.33 7.33 45.62 4.17
2760 8282 8.972458 TGCTGCAGACCTTGTAAATATATTTA 57.028 30.769 20.43 12.90 0.00 1.40
2795 8317 3.068165 AGTTTTCACCAACTAAAGCAGCC 59.932 43.478 0.00 0.00 35.10 4.85
2805 8327 6.329496 TGACTGAATTTGAGTTTTCACCAAC 58.671 36.000 0.00 0.00 31.71 3.77
2813 8335 6.263842 TGATTGCTCTGACTGAATTTGAGTTT 59.736 34.615 0.00 0.00 0.00 2.66
2814 8336 5.766670 TGATTGCTCTGACTGAATTTGAGTT 59.233 36.000 0.00 0.00 0.00 3.01
2816 8338 5.874895 TGATTGCTCTGACTGAATTTGAG 57.125 39.130 0.00 0.00 0.00 3.02
2817 8339 5.766670 AGTTGATTGCTCTGACTGAATTTGA 59.233 36.000 0.00 0.00 0.00 2.69
2818 8340 5.856986 CAGTTGATTGCTCTGACTGAATTTG 59.143 40.000 0.00 0.00 37.93 2.32
2821 8343 4.903054 TCAGTTGATTGCTCTGACTGAAT 58.097 39.130 2.32 0.00 39.79 2.57
2822 8344 4.341366 TCAGTTGATTGCTCTGACTGAA 57.659 40.909 2.32 0.00 39.79 3.02
2827 8349 5.737860 ACATATGTCAGTTGATTGCTCTGA 58.262 37.500 1.41 0.00 36.12 3.27
2893 8818 9.807649 ATGCTATTTCACCAAAATCAAATAGTC 57.192 29.630 10.45 5.53 39.49 2.59
2930 8855 5.185635 ACGCATGCAATTGCCCTATATTAAT 59.814 36.000 26.94 8.05 39.52 1.40


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

AutoCloner maintained by Alex Coulton.