Multiple sequence alignment - TraesCS7A01G551200

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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 TraesCS7A01G551200 chr7A 100.000 4029 0 0 1 4029 724962683 724966711 0.000000e+00 7441.0
1 TraesCS7A01G551200 chr7A 96.933 163 3 2 462 624 729274221 729274061 5.130000e-69 272.0
2 TraesCS7A01G551200 chr7D 92.949 2879 129 42 625 3482 628215370 628212545 0.000000e+00 4124.0
3 TraesCS7A01G551200 chr7D 94.549 477 16 5 1 473 628215819 628215349 0.000000e+00 728.0
4 TraesCS7A01G551200 chr7D 90.617 373 35 0 3657 4029 628212439 628212067 2.800000e-136 496.0
5 TraesCS7A01G551200 chr7D 95.000 40 2 0 3036 3075 418918987 418919026 3.360000e-06 63.9
6 TraesCS7A01G551200 chr7B 93.776 2619 93 36 625 3204 730813651 730816238 0.000000e+00 3869.0
7 TraesCS7A01G551200 chr7B 93.697 476 19 6 1 473 730813205 730813672 0.000000e+00 702.0
8 TraesCS7A01G551200 chr7B 89.572 374 37 2 3657 4029 730817041 730817413 1.310000e-129 473.0
9 TraesCS7A01G551200 chr7B 96.085 281 8 2 3204 3482 730816668 730816947 4.750000e-124 455.0
10 TraesCS7A01G551200 chr7B 96.914 162 4 1 463 624 152466576 152466736 1.850000e-68 270.0
11 TraesCS7A01G551200 chr3D 90.781 1844 127 18 2224 4029 29707392 29705554 0.000000e+00 2423.0
12 TraesCS7A01G551200 chr3D 90.062 322 19 5 1453 1763 29708212 29707893 4.850000e-109 405.0
13 TraesCS7A01G551200 chr3D 94.595 222 12 0 1997 2218 29707725 29707504 1.070000e-90 344.0
14 TraesCS7A01G551200 chr3A 89.402 1840 132 25 2224 4029 40365114 40363304 0.000000e+00 2259.0
15 TraesCS7A01G551200 chr3A 86.307 482 38 11 1402 1868 40365992 40365524 2.160000e-137 499.0
16 TraesCS7A01G551200 chr3A 92.164 268 19 2 1953 2218 40365496 40365229 1.060000e-100 377.0
17 TraesCS7A01G551200 chr3B 90.502 1674 107 28 2224 3867 50938689 50937038 0.000000e+00 2163.0
18 TraesCS7A01G551200 chr3B 89.053 475 45 4 3560 4029 50933446 50932974 2.090000e-162 582.0
19 TraesCS7A01G551200 chr3B 86.278 532 44 20 2999 3523 50933958 50933449 5.890000e-153 551.0
20 TraesCS7A01G551200 chr3B 87.313 402 24 5 2605 3001 50937041 50936662 6.180000e-118 435.0
21 TraesCS7A01G551200 chr3B 95.113 266 13 0 1953 2218 50939066 50938801 1.730000e-113 420.0
22 TraesCS7A01G551200 chr3B 95.041 121 6 0 1483 1603 50939458 50939338 1.480000e-44 191.0
23 TraesCS7A01G551200 chr6B 97.531 162 3 1 465 625 159404775 159404936 3.970000e-70 276.0
24 TraesCS7A01G551200 chr6A 98.089 157 3 0 468 624 447173314 447173470 1.430000e-69 274.0
25 TraesCS7A01G551200 chr2B 97.500 160 4 0 465 624 67298302 67298143 1.430000e-69 274.0
26 TraesCS7A01G551200 chr4A 96.914 162 5 0 463 624 443844765 443844926 5.130000e-69 272.0
27 TraesCS7A01G551200 chr2A 96.933 163 3 2 464 624 90524555 90524393 5.130000e-69 272.0
28 TraesCS7A01G551200 chr2A 96.933 163 3 2 464 624 362436659 362436497 5.130000e-69 272.0
29 TraesCS7A01G551200 chr4B 96.894 161 4 1 464 624 634327588 634327429 6.640000e-68 268.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G551200 chr7A 724962683 724966711 4028 False 7441.000000 7441 100.000000 1 4029 1 chr7A.!!$F1 4028
1 TraesCS7A01G551200 chr7D 628212067 628215819 3752 True 1782.666667 4124 92.705000 1 4029 3 chr7D.!!$R1 4028
2 TraesCS7A01G551200 chr7B 730813205 730817413 4208 False 1374.750000 3869 93.282500 1 4029 4 chr7B.!!$F2 4028
3 TraesCS7A01G551200 chr3D 29705554 29708212 2658 True 1057.333333 2423 91.812667 1453 4029 3 chr3D.!!$R1 2576
4 TraesCS7A01G551200 chr3A 40363304 40365992 2688 True 1045.000000 2259 89.291000 1402 4029 3 chr3A.!!$R1 2627
5 TraesCS7A01G551200 chr3B 50932974 50939458 6484 True 723.666667 2163 90.550000 1483 4029 6 chr3B.!!$R1 2546

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
629 634 0.033796 ATGGTCACAAGGCATGGGAG 60.034 55.0 0.00 0.00 43.77 4.30 F
1262 1304 0.175760 TCTTCACTAGGCCACATCGC 59.824 55.0 5.01 0.00 0.00 4.58 F
1481 1524 0.251354 AATGTGCTCGAGCCTGATGT 59.749 50.0 33.23 11.88 41.18 3.06 F
1841 1905 1.166531 ACTGCTGCCGTCCTTCAAAC 61.167 55.0 0.00 0.00 0.00 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2030 3.877559 CCCTGCACAATACAGATTCTGA 58.122 45.455 20.33 4.65 37.32 3.27 R
2295 2508 4.222114 GTTGCTTTCTCACATCTTTTCCG 58.778 43.478 0.00 0.00 0.00 4.30 R
2599 2836 4.329392 TCGTGGTGTCAGTCATTAGTCTA 58.671 43.478 0.00 0.00 0.00 2.59 R
3820 8435 0.941463 CGTGAGCAGCGAAGTGAACT 60.941 55.000 0.00 0.00 0.00 3.01 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
95 96 1.756375 GCAACGGCGCAGAGTCATAG 61.756 60.000 16.26 1.57 0.00 2.23
96 97 0.179137 CAACGGCGCAGAGTCATAGA 60.179 55.000 16.26 0.00 0.00 1.98
97 98 0.101399 AACGGCGCAGAGTCATAGAG 59.899 55.000 16.26 0.00 0.00 2.43
98 99 1.032657 ACGGCGCAGAGTCATAGAGT 61.033 55.000 16.26 0.00 0.00 3.24
99 100 0.945099 CGGCGCAGAGTCATAGAGTA 59.055 55.000 10.83 0.00 0.00 2.59
150 151 5.104693 ACCACTTGTGTATATCCGATTCCAA 60.105 40.000 0.00 0.00 0.00 3.53
182 183 3.069443 GGAGAGTGATCCAGTCAAGATCC 59.931 52.174 4.81 0.00 39.56 3.36
192 193 3.276857 CAGTCAAGATCCCACTTCCATG 58.723 50.000 0.00 0.00 0.00 3.66
229 230 6.203145 CAGCAAGATCATTGTCCAGAATCTAG 59.797 42.308 0.00 0.00 0.00 2.43
236 237 8.905660 ATCATTGTCCAGAATCTAGAGAATTG 57.094 34.615 0.00 0.00 0.00 2.32
241 244 8.327941 TGTCCAGAATCTAGAGAATTGTTTTG 57.672 34.615 0.00 0.00 0.00 2.44
306 311 0.729140 GCGATTCACGTGCCTTTTGG 60.729 55.000 11.67 0.00 44.60 3.28
307 312 0.591170 CGATTCACGTGCCTTTTGGT 59.409 50.000 11.67 0.00 38.42 3.67
359 364 5.006386 ACCTACAGGAAAAGAGCATCAAAG 58.994 41.667 1.29 0.00 36.53 2.77
362 367 6.655003 CCTACAGGAAAAGAGCATCAAAGTTA 59.345 38.462 0.00 0.00 35.28 2.24
387 392 4.968259 TCTCCAAGCAAGCACTAAAAGTA 58.032 39.130 0.00 0.00 0.00 2.24
463 468 1.285078 GGCCAAACTGGGAGTTATCCT 59.715 52.381 0.00 0.00 45.85 3.24
464 469 2.369394 GCCAAACTGGGAGTTATCCTG 58.631 52.381 0.00 0.00 45.85 3.86
465 470 2.026262 GCCAAACTGGGAGTTATCCTGA 60.026 50.000 0.00 0.00 45.85 3.86
466 471 3.561313 GCCAAACTGGGAGTTATCCTGAA 60.561 47.826 0.00 0.00 45.85 3.02
467 472 4.662278 CCAAACTGGGAGTTATCCTGAAA 58.338 43.478 0.00 0.00 45.85 2.69
468 473 4.702131 CCAAACTGGGAGTTATCCTGAAAG 59.298 45.833 0.00 0.00 45.85 2.62
469 474 5.514834 CCAAACTGGGAGTTATCCTGAAAGA 60.515 44.000 0.00 0.00 45.85 2.52
470 475 5.843019 AACTGGGAGTTATCCTGAAAGAA 57.157 39.130 0.00 0.00 45.85 2.52
471 476 5.843019 ACTGGGAGTTATCCTGAAAGAAA 57.157 39.130 0.00 0.00 45.85 2.52
472 477 6.200878 ACTGGGAGTTATCCTGAAAGAAAA 57.799 37.500 0.00 0.00 45.85 2.29
473 478 6.610830 ACTGGGAGTTATCCTGAAAGAAAAA 58.389 36.000 0.00 0.00 45.85 1.94
496 501 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
497 502 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
498 503 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
499 504 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
500 505 1.538047 CAACCTGGTGCATGTAGCTT 58.462 50.000 14.15 0.00 45.94 3.74
501 506 1.470098 CAACCTGGTGCATGTAGCTTC 59.530 52.381 14.15 0.00 45.94 3.86
502 507 0.035056 ACCTGGTGCATGTAGCTTCC 60.035 55.000 14.15 0.00 45.94 3.46
503 508 1.091771 CCTGGTGCATGTAGCTTCCG 61.092 60.000 14.15 0.85 45.94 4.30
504 509 1.709147 CTGGTGCATGTAGCTTCCGC 61.709 60.000 14.15 0.00 45.94 5.54
506 511 1.026718 GGTGCATGTAGCTTCCGCTT 61.027 55.000 5.68 0.00 46.47 4.68
507 512 0.097674 GTGCATGTAGCTTCCGCTTG 59.902 55.000 0.00 0.00 46.47 4.01
508 513 1.063166 GCATGTAGCTTCCGCTTGC 59.937 57.895 0.00 0.00 46.47 4.01
509 514 1.349627 CATGTAGCTTCCGCTTGCG 59.650 57.895 8.14 8.14 46.47 4.85
510 515 2.464459 ATGTAGCTTCCGCTTGCGC 61.464 57.895 9.71 0.00 46.47 6.09
511 516 3.118454 GTAGCTTCCGCTTGCGCA 61.118 61.111 5.66 5.66 46.47 6.09
512 517 2.815211 TAGCTTCCGCTTGCGCAG 60.815 61.111 11.31 6.32 46.47 5.18
524 529 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
525 530 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
526 531 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
527 532 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
528 533 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
529 534 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
530 535 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
531 536 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
532 537 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
533 538 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
534 539 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
535 540 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
536 541 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
537 542 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
538 543 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
539 544 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
540 545 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
541 546 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
542 547 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
552 557 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
553 558 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
554 559 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
555 560 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
556 561 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
557 562 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
558 563 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
559 564 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
560 565 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
561 566 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
562 567 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
563 568 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
564 569 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
565 570 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
566 571 1.497161 AGTACGCAGCCTTTCCCTAT 58.503 50.000 0.00 0.00 0.00 2.57
567 572 2.674420 AGTACGCAGCCTTTCCCTATA 58.326 47.619 0.00 0.00 0.00 1.31
568 573 3.240302 AGTACGCAGCCTTTCCCTATAT 58.760 45.455 0.00 0.00 0.00 0.86
569 574 3.646637 AGTACGCAGCCTTTCCCTATATT 59.353 43.478 0.00 0.00 0.00 1.28
570 575 3.577805 ACGCAGCCTTTCCCTATATTT 57.422 42.857 0.00 0.00 0.00 1.40
571 576 3.477530 ACGCAGCCTTTCCCTATATTTC 58.522 45.455 0.00 0.00 0.00 2.17
572 577 3.136626 ACGCAGCCTTTCCCTATATTTCT 59.863 43.478 0.00 0.00 0.00 2.52
573 578 3.499918 CGCAGCCTTTCCCTATATTTCTG 59.500 47.826 0.00 0.00 0.00 3.02
574 579 4.464947 GCAGCCTTTCCCTATATTTCTGT 58.535 43.478 0.00 0.00 0.00 3.41
575 580 5.621193 GCAGCCTTTCCCTATATTTCTGTA 58.379 41.667 0.00 0.00 0.00 2.74
576 581 6.062095 GCAGCCTTTCCCTATATTTCTGTAA 58.938 40.000 0.00 0.00 0.00 2.41
577 582 6.205658 GCAGCCTTTCCCTATATTTCTGTAAG 59.794 42.308 0.00 0.00 0.00 2.34
578 583 7.509546 CAGCCTTTCCCTATATTTCTGTAAGA 58.490 38.462 0.00 0.00 44.68 2.10
590 595 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
591 596 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
592 597 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
593 598 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
594 599 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
595 600 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
596 601 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
597 602 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
598 603 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
599 604 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
600 605 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
601 606 2.749800 GCTGTTTCCAGGACTTGAACCT 60.750 50.000 0.00 0.00 39.22 3.50
602 607 3.496160 GCTGTTTCCAGGACTTGAACCTA 60.496 47.826 0.00 0.00 39.22 3.08
603 608 4.807643 GCTGTTTCCAGGACTTGAACCTAT 60.808 45.833 0.00 0.00 39.22 2.57
604 609 4.651778 TGTTTCCAGGACTTGAACCTATG 58.348 43.478 0.00 0.00 35.84 2.23
605 610 4.349636 TGTTTCCAGGACTTGAACCTATGA 59.650 41.667 0.00 0.00 35.84 2.15
606 611 4.553330 TTCCAGGACTTGAACCTATGAC 57.447 45.455 0.00 0.00 35.84 3.06
607 612 2.838202 TCCAGGACTTGAACCTATGACC 59.162 50.000 0.00 0.00 35.84 4.02
608 613 2.840651 CCAGGACTTGAACCTATGACCT 59.159 50.000 0.00 0.00 35.84 3.85
609 614 3.118592 CCAGGACTTGAACCTATGACCTC 60.119 52.174 0.00 0.00 35.84 3.85
610 615 3.515502 CAGGACTTGAACCTATGACCTCA 59.484 47.826 0.00 0.00 35.84 3.86
611 616 4.163078 CAGGACTTGAACCTATGACCTCAT 59.837 45.833 0.00 0.00 40.22 2.90
612 617 4.163078 AGGACTTGAACCTATGACCTCATG 59.837 45.833 0.00 0.00 37.15 3.07
613 618 4.446371 GACTTGAACCTATGACCTCATGG 58.554 47.826 0.00 0.00 37.15 3.66
623 628 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
624 629 0.700564 ACCTCATGGTCACAAGGCAT 59.299 50.000 0.00 0.00 44.78 4.40
625 630 1.100510 CCTCATGGTCACAAGGCATG 58.899 55.000 0.00 0.00 0.00 4.06
626 631 1.100510 CTCATGGTCACAAGGCATGG 58.899 55.000 0.00 0.00 0.00 3.66
627 632 0.323633 TCATGGTCACAAGGCATGGG 60.324 55.000 0.00 0.00 0.00 4.00
628 633 0.323633 CATGGTCACAAGGCATGGGA 60.324 55.000 0.00 0.00 39.84 4.37
629 634 0.033796 ATGGTCACAAGGCATGGGAG 60.034 55.000 0.00 0.00 43.77 4.30
630 635 1.380302 GGTCACAAGGCATGGGAGT 59.620 57.895 0.00 0.00 43.77 3.85
631 636 0.251341 GGTCACAAGGCATGGGAGTT 60.251 55.000 0.00 0.00 43.77 3.01
632 637 1.004277 GGTCACAAGGCATGGGAGTTA 59.996 52.381 0.00 0.00 43.77 2.24
633 638 2.357154 GGTCACAAGGCATGGGAGTTAT 60.357 50.000 0.00 0.00 43.77 1.89
634 639 2.945668 GTCACAAGGCATGGGAGTTATC 59.054 50.000 0.00 0.00 43.77 1.75
635 640 2.092429 TCACAAGGCATGGGAGTTATCC 60.092 50.000 0.00 0.00 45.85 2.59
759 764 2.916934 AGGTAATGGCCTGGTAAGTGAA 59.083 45.455 3.32 0.00 37.50 3.18
760 765 3.332485 AGGTAATGGCCTGGTAAGTGAAA 59.668 43.478 3.32 0.00 37.50 2.69
761 766 3.442625 GGTAATGGCCTGGTAAGTGAAAC 59.557 47.826 3.32 0.00 0.00 2.78
762 767 2.969821 ATGGCCTGGTAAGTGAAACA 57.030 45.000 3.32 0.00 41.43 2.83
796 801 7.885922 ACTCTCTGACAGAAGAATAACAGACTA 59.114 37.037 16.62 0.00 32.31 2.59
814 819 3.348236 CAGAGCACCTGGTTGCAC 58.652 61.111 18.81 14.14 45.62 4.57
828 838 3.753797 TGGTTGCACGCAATAATGTAAGA 59.246 39.130 7.85 0.00 38.28 2.10
830 840 4.378978 GGTTGCACGCAATAATGTAAGACA 60.379 41.667 7.85 0.00 38.28 3.41
876 886 1.203364 TCTCCCCTTCAGCCTTCTTCT 60.203 52.381 0.00 0.00 0.00 2.85
877 887 1.632920 CTCCCCTTCAGCCTTCTTCTT 59.367 52.381 0.00 0.00 0.00 2.52
878 888 1.630878 TCCCCTTCAGCCTTCTTCTTC 59.369 52.381 0.00 0.00 0.00 2.87
927 937 6.228258 GGAGAAGTATCAGGTAAACACACAA 58.772 40.000 0.00 0.00 0.00 3.33
928 938 6.147328 GGAGAAGTATCAGGTAAACACACAAC 59.853 42.308 0.00 0.00 0.00 3.32
929 939 5.995897 AGAAGTATCAGGTAAACACACAACC 59.004 40.000 0.00 0.00 0.00 3.77
931 941 5.876357 AGTATCAGGTAAACACACAACCAT 58.124 37.500 0.00 0.00 35.64 3.55
962 972 0.744281 ACGGTTGCAAAACAAGGGAG 59.256 50.000 0.00 0.00 39.50 4.30
978 988 5.946377 ACAAGGGAGTTATTTAGAAGCAAGG 59.054 40.000 0.00 0.00 0.00 3.61
981 991 5.489278 AGGGAGTTATTTAGAAGCAAGGAGT 59.511 40.000 0.00 0.00 0.00 3.85
984 994 7.496263 GGGAGTTATTTAGAAGCAAGGAGTAAG 59.504 40.741 0.00 0.00 0.00 2.34
985 995 7.496263 GGAGTTATTTAGAAGCAAGGAGTAAGG 59.504 40.741 0.00 0.00 0.00 2.69
986 996 8.147244 AGTTATTTAGAAGCAAGGAGTAAGGA 57.853 34.615 0.00 0.00 0.00 3.36
987 997 8.603304 AGTTATTTAGAAGCAAGGAGTAAGGAA 58.397 33.333 0.00 0.00 0.00 3.36
988 998 8.666573 GTTATTTAGAAGCAAGGAGTAAGGAAC 58.333 37.037 0.00 0.00 0.00 3.62
1041 1051 2.046507 CAGGCTCACCCTCAGCAC 60.047 66.667 0.00 0.00 44.09 4.40
1094 1106 5.044846 AGTTCCATAGCAGGTACAGGATTTT 60.045 40.000 0.00 0.00 31.98 1.82
1102 1114 6.016555 AGCAGGTACAGGATTTTATTTGGTT 58.983 36.000 0.00 0.00 0.00 3.67
1106 1118 8.531146 CAGGTACAGGATTTTATTTGGTTTCAT 58.469 33.333 0.00 0.00 0.00 2.57
1108 1120 9.366216 GGTACAGGATTTTATTTGGTTTCATTC 57.634 33.333 0.00 0.00 0.00 2.67
1114 1126 9.317936 GGATTTTATTTGGTTTCATTCATCCTC 57.682 33.333 0.00 0.00 0.00 3.71
1115 1127 8.931385 ATTTTATTTGGTTTCATTCATCCTCG 57.069 30.769 0.00 0.00 0.00 4.63
1121 1133 2.218953 TTCATTCATCCTCGCGGTAC 57.781 50.000 6.13 0.00 0.00 3.34
1139 1158 4.138290 GGTACTCCGATCTGAATCTCTGA 58.862 47.826 0.00 0.00 0.00 3.27
1145 1164 6.322456 ACTCCGATCTGAATCTCTGAATTGTA 59.678 38.462 0.00 0.00 0.00 2.41
1158 1177 8.856490 TCTCTGAATTGTAAGCTTTTGTTTTC 57.144 30.769 3.20 3.29 0.00 2.29
1165 1184 9.575783 AATTGTAAGCTTTTGTTTTCGAGTTTA 57.424 25.926 3.20 0.00 0.00 2.01
1168 1187 5.500645 AGCTTTTGTTTTCGAGTTTAGCT 57.499 34.783 0.00 0.00 0.00 3.32
1173 1192 6.920569 TTTGTTTTCGAGTTTAGCTCTTCT 57.079 33.333 0.00 0.00 41.98 2.85
1174 1193 6.526566 TTGTTTTCGAGTTTAGCTCTTCTC 57.473 37.500 0.00 0.00 41.98 2.87
1175 1194 5.597806 TGTTTTCGAGTTTAGCTCTTCTCA 58.402 37.500 0.00 0.00 41.98 3.27
1187 1206 7.667575 TTAGCTCTTCTCACTCCTGAATTAT 57.332 36.000 0.00 0.00 0.00 1.28
1191 1210 7.289782 AGCTCTTCTCACTCCTGAATTATATGT 59.710 37.037 0.00 0.00 0.00 2.29
1194 1213 8.138074 TCTTCTCACTCCTGAATTATATGTTCG 58.862 37.037 0.00 0.00 0.00 3.95
1195 1214 7.582667 TCTCACTCCTGAATTATATGTTCGA 57.417 36.000 0.00 0.00 0.00 3.71
1198 1217 7.782049 TCACTCCTGAATTATATGTTCGAAGT 58.218 34.615 0.00 0.00 0.00 3.01
1199 1218 7.921214 TCACTCCTGAATTATATGTTCGAAGTC 59.079 37.037 0.00 0.00 0.00 3.01
1200 1219 7.706607 CACTCCTGAATTATATGTTCGAAGTCA 59.293 37.037 0.00 0.00 0.00 3.41
1211 1253 3.871006 TGTTCGAAGTCATATGTCATGCC 59.129 43.478 0.00 0.00 0.00 4.40
1219 1261 4.581824 AGTCATATGTCATGCCAACATTCC 59.418 41.667 1.90 0.00 38.31 3.01
1220 1262 4.338964 GTCATATGTCATGCCAACATTCCA 59.661 41.667 1.90 0.00 38.31 3.53
1229 1271 6.265196 GTCATGCCAACATTCCAATCCTAATA 59.735 38.462 0.00 0.00 32.87 0.98
1230 1272 7.011994 TCATGCCAACATTCCAATCCTAATAT 58.988 34.615 0.00 0.00 32.87 1.28
1231 1273 6.899393 TGCCAACATTCCAATCCTAATATC 57.101 37.500 0.00 0.00 0.00 1.63
1243 1285 6.769822 CCAATCCTAATATCACTGCTCACTTT 59.230 38.462 0.00 0.00 0.00 2.66
1251 1293 4.937201 TCACTGCTCACTTTCTTCACTA 57.063 40.909 0.00 0.00 0.00 2.74
1262 1304 0.175760 TCTTCACTAGGCCACATCGC 59.824 55.000 5.01 0.00 0.00 4.58
1268 1310 2.942376 CACTAGGCCACATCGCAAATTA 59.058 45.455 5.01 0.00 0.00 1.40
1270 1312 3.815401 ACTAGGCCACATCGCAAATTATC 59.185 43.478 5.01 0.00 0.00 1.75
1271 1313 2.936202 AGGCCACATCGCAAATTATCT 58.064 42.857 5.01 0.00 0.00 1.98
1272 1314 3.290710 AGGCCACATCGCAAATTATCTT 58.709 40.909 5.01 0.00 0.00 2.40
1273 1315 4.460263 AGGCCACATCGCAAATTATCTTA 58.540 39.130 5.01 0.00 0.00 2.10
1274 1316 4.516698 AGGCCACATCGCAAATTATCTTAG 59.483 41.667 5.01 0.00 0.00 2.18
1275 1317 4.515191 GGCCACATCGCAAATTATCTTAGA 59.485 41.667 0.00 0.00 0.00 2.10
1276 1318 5.334414 GGCCACATCGCAAATTATCTTAGAG 60.334 44.000 0.00 0.00 0.00 2.43
1277 1319 5.466728 GCCACATCGCAAATTATCTTAGAGA 59.533 40.000 0.00 0.00 0.00 3.10
1278 1320 6.017934 GCCACATCGCAAATTATCTTAGAGAA 60.018 38.462 0.00 0.00 0.00 2.87
1279 1321 7.571026 CCACATCGCAAATTATCTTAGAGAAG 58.429 38.462 0.00 0.00 0.00 2.85
1280 1322 7.068341 CACATCGCAAATTATCTTAGAGAAGC 58.932 38.462 0.00 0.00 32.21 3.86
1281 1323 6.203723 ACATCGCAAATTATCTTAGAGAAGCC 59.796 38.462 0.00 0.00 32.21 4.35
1282 1324 5.918608 TCGCAAATTATCTTAGAGAAGCCT 58.081 37.500 0.00 0.00 32.21 4.58
1283 1325 7.050970 TCGCAAATTATCTTAGAGAAGCCTA 57.949 36.000 0.00 0.00 32.21 3.93
1284 1326 7.671302 TCGCAAATTATCTTAGAGAAGCCTAT 58.329 34.615 0.00 0.00 32.21 2.57
1285 1327 8.150945 TCGCAAATTATCTTAGAGAAGCCTATT 58.849 33.333 0.00 0.00 32.21 1.73
1286 1328 8.439286 CGCAAATTATCTTAGAGAAGCCTATTC 58.561 37.037 0.00 0.00 32.21 1.75
1287 1329 8.726068 GCAAATTATCTTAGAGAAGCCTATTCC 58.274 37.037 0.00 0.00 32.21 3.01
1288 1330 9.225436 CAAATTATCTTAGAGAAGCCTATTCCC 57.775 37.037 0.00 0.00 32.21 3.97
1289 1331 8.511748 AATTATCTTAGAGAAGCCTATTCCCA 57.488 34.615 0.00 0.00 32.21 4.37
1317 1359 8.738106 TGCAGAATAACAATGATGTATGTTCAA 58.262 29.630 0.00 0.00 39.40 2.69
1328 1370 5.409520 TGATGTATGTTCAACTGCTGTTCTC 59.590 40.000 5.94 1.29 33.52 2.87
1333 1375 2.880890 GTTCAACTGCTGTTCTCCATGT 59.119 45.455 5.94 0.00 33.52 3.21
1481 1524 0.251354 AATGTGCTCGAGCCTGATGT 59.749 50.000 33.23 11.88 41.18 3.06
1582 1629 6.146837 GTCAATGTAGGAGATATGCACATGAC 59.853 42.308 0.00 0.00 30.55 3.06
1771 1829 9.855021 AGACATAAAATCCCATTTTTAGAAACG 57.145 29.630 0.00 0.00 42.13 3.60
1841 1905 1.166531 ACTGCTGCCGTCCTTCAAAC 61.167 55.000 0.00 0.00 0.00 2.93
1937 2001 2.160219 GTGAGCACAATCAGCATCGAAA 59.840 45.455 0.00 0.00 0.00 3.46
1966 2030 3.445096 GCTCCAAACATAAGCATGAACCT 59.555 43.478 0.00 0.00 36.06 3.50
2472 2709 9.453572 CCATTCAGTATACTATAATGTGCCAAT 57.546 33.333 24.57 4.66 31.67 3.16
2498 2735 5.663456 ACACAGTGCAGACAATTTTTCATT 58.337 33.333 0.00 0.00 0.00 2.57
2599 2836 5.011533 AGTTGAAGCGAAGGATATAGCTGAT 59.988 40.000 0.00 0.00 40.17 2.90
2735 2972 6.958193 CGAAGTGAGCATAAAATCTTTGACTC 59.042 38.462 0.00 0.00 0.00 3.36
2743 2980 7.330208 AGCATAAAATCTTTGACTCAATTGCAC 59.670 33.333 0.00 0.00 0.00 4.57
3033 3275 1.594194 CCAATGCGCACCTAAAGGCA 61.594 55.000 14.90 0.00 39.32 4.75
3461 4144 0.744414 TCTTCAATAGGCTGGTGCGC 60.744 55.000 0.00 0.00 40.82 6.09
3543 4226 7.333323 TCCAGAGCATACCATAATATGATGTG 58.667 38.462 1.10 0.00 40.23 3.21
3590 4300 9.561069 GTATGGATATATGTATGGACCATTTCC 57.439 37.037 13.40 8.47 46.13 3.13
3613 4323 5.935789 CCAGAAATCTTTCCAAAATGCACAT 59.064 36.000 0.00 0.00 37.92 3.21
3620 4330 5.769662 TCTTTCCAAAATGCACATGAGTACT 59.230 36.000 0.00 0.00 0.00 2.73
3706 4416 8.988064 TTAGCTTTATTATAGGAATCTCAGCG 57.012 34.615 0.00 0.00 0.00 5.18
3750 8362 5.892568 AGAACTGTGAAGCCTAGTATTACG 58.107 41.667 0.00 0.00 0.00 3.18
3754 8366 2.101917 GTGAAGCCTAGTATTACGCCCA 59.898 50.000 0.00 0.00 0.00 5.36
3765 8377 6.920569 AGTATTACGCCCAAATAGTTGAAG 57.079 37.500 4.10 0.00 36.83 3.02
3766 8378 5.820947 AGTATTACGCCCAAATAGTTGAAGG 59.179 40.000 4.10 0.00 36.83 3.46
3783 8395 3.181455 TGAAGGCTACAGTTTCTCTTGCA 60.181 43.478 0.00 0.00 0.00 4.08
3788 8400 5.104776 AGGCTACAGTTTCTCTTGCATGATA 60.105 40.000 2.33 0.00 0.00 2.15
3801 8413 7.281774 TCTCTTGCATGATATTGTTCTTCCTTC 59.718 37.037 2.33 0.00 0.00 3.46
3803 8415 6.932356 TGCATGATATTGTTCTTCCTTCTC 57.068 37.500 0.00 0.00 0.00 2.87
3820 8435 1.966354 TCTCTGCTTCTTCTCTGCACA 59.034 47.619 0.00 0.00 32.91 4.57
3827 8442 3.726607 CTTCTTCTCTGCACAGTTCACT 58.273 45.455 0.00 0.00 0.00 3.41
3914 8529 2.978156 AAACAATCTGGGGAGCTCAA 57.022 45.000 17.19 0.00 0.00 3.02
3916 8531 2.725221 ACAATCTGGGGAGCTCAATC 57.275 50.000 17.19 4.66 0.00 2.67
3922 8537 3.911719 GGGGAGCTCAATCCACAAT 57.088 52.632 17.19 0.00 42.83 2.71
3936 8551 3.877559 TCCACAATTACTGCTGGAGATG 58.122 45.455 2.24 0.00 33.14 2.90
3939 8554 4.012374 CACAATTACTGCTGGAGATGGTT 58.988 43.478 2.24 0.00 0.00 3.67
4005 8620 3.005791 CACACAGTAGATCAGACCACACA 59.994 47.826 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 3.274288 CCTGGTCTTTCCAAGCATACTC 58.726 50.000 0.00 0.00 46.59 2.59
96 97 3.356529 CCTGGTCTTTCCAAGCATACT 57.643 47.619 0.00 0.00 46.59 2.12
150 151 3.052566 TGGATCACTCTCCTGTACTGGAT 60.053 47.826 20.52 6.03 36.20 3.41
217 218 7.627300 GCCAAAACAATTCTCTAGATTCTGGAC 60.627 40.741 0.00 0.00 0.00 4.02
359 364 3.077359 AGTGCTTGCTTGGAGATGTAAC 58.923 45.455 0.00 0.00 0.00 2.50
362 367 3.423539 TTAGTGCTTGCTTGGAGATGT 57.576 42.857 0.00 0.00 0.00 3.06
387 392 3.869246 CCACGATTAACGCCAACTCTATT 59.131 43.478 0.00 0.00 46.94 1.73
473 478 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
474 479 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
475 480 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
476 481 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
477 482 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
478 483 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
479 484 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
480 485 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
481 486 1.470098 GAAGCTACATGCACCAGGTTG 59.530 52.381 11.80 0.00 45.94 3.77
482 487 1.614317 GGAAGCTACATGCACCAGGTT 60.614 52.381 7.88 7.88 45.94 3.50
483 488 0.035056 GGAAGCTACATGCACCAGGT 60.035 55.000 0.00 0.00 45.94 4.00
484 489 1.091771 CGGAAGCTACATGCACCAGG 61.092 60.000 0.00 0.00 45.94 4.45
485 490 2.387309 CGGAAGCTACATGCACCAG 58.613 57.895 0.00 0.00 45.94 4.00
486 491 4.615901 CGGAAGCTACATGCACCA 57.384 55.556 0.00 0.00 45.94 4.17
507 512 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
508 513 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
509 514 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
510 515 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
511 516 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
512 517 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
513 518 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
514 519 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
515 520 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
516 521 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
517 522 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
518 523 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
519 524 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
520 525 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
521 526 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
522 527 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
523 528 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
524 529 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
525 530 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
526 531 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
531 536 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
532 537 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
533 538 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
534 539 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
535 540 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
536 541 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
537 542 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
538 543 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
539 544 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
540 545 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
541 546 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
542 547 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
543 548 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
544 549 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
545 550 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
546 551 2.148446 TAGGGAAAGGCTGCGTACTA 57.852 50.000 0.00 0.00 0.00 1.82
547 552 1.497161 ATAGGGAAAGGCTGCGTACT 58.503 50.000 0.00 0.00 0.00 2.73
548 553 3.679824 ATATAGGGAAAGGCTGCGTAC 57.320 47.619 0.00 0.00 0.00 3.67
549 554 4.347000 AGAAATATAGGGAAAGGCTGCGTA 59.653 41.667 0.00 0.00 0.00 4.42
550 555 3.136626 AGAAATATAGGGAAAGGCTGCGT 59.863 43.478 0.00 0.00 0.00 5.24
551 556 3.499918 CAGAAATATAGGGAAAGGCTGCG 59.500 47.826 0.00 0.00 0.00 5.18
552 557 4.464947 ACAGAAATATAGGGAAAGGCTGC 58.535 43.478 0.00 0.00 0.00 5.25
553 558 7.509546 TCTTACAGAAATATAGGGAAAGGCTG 58.490 38.462 0.00 0.00 0.00 4.85
554 559 7.202139 CCTCTTACAGAAATATAGGGAAAGGCT 60.202 40.741 0.00 0.00 0.00 4.58
555 560 6.937465 CCTCTTACAGAAATATAGGGAAAGGC 59.063 42.308 0.00 0.00 0.00 4.35
556 561 6.937465 GCCTCTTACAGAAATATAGGGAAAGG 59.063 42.308 0.00 0.00 0.00 3.11
557 562 7.659390 CAGCCTCTTACAGAAATATAGGGAAAG 59.341 40.741 0.00 0.00 0.00 2.62
558 563 7.127339 ACAGCCTCTTACAGAAATATAGGGAAA 59.873 37.037 0.00 0.00 0.00 3.13
559 564 6.615726 ACAGCCTCTTACAGAAATATAGGGAA 59.384 38.462 0.00 0.00 0.00 3.97
560 565 6.143915 ACAGCCTCTTACAGAAATATAGGGA 58.856 40.000 0.00 0.00 0.00 4.20
561 566 6.426646 ACAGCCTCTTACAGAAATATAGGG 57.573 41.667 0.00 0.00 0.00 3.53
562 567 7.442666 GGAAACAGCCTCTTACAGAAATATAGG 59.557 40.741 0.00 0.00 0.00 2.57
563 568 7.987458 TGGAAACAGCCTCTTACAGAAATATAG 59.013 37.037 0.00 0.00 35.01 1.31
564 569 7.857456 TGGAAACAGCCTCTTACAGAAATATA 58.143 34.615 0.00 0.00 35.01 0.86
565 570 6.721318 TGGAAACAGCCTCTTACAGAAATAT 58.279 36.000 0.00 0.00 35.01 1.28
566 571 6.121776 TGGAAACAGCCTCTTACAGAAATA 57.878 37.500 0.00 0.00 35.01 1.40
567 572 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
568 573 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
582 587 4.349636 TCATAGGTTCAAGTCCTGGAAACA 59.650 41.667 0.00 0.00 36.60 2.83
583 588 4.695928 GTCATAGGTTCAAGTCCTGGAAAC 59.304 45.833 0.00 0.00 36.60 2.78
584 589 4.263331 GGTCATAGGTTCAAGTCCTGGAAA 60.263 45.833 0.00 0.00 36.60 3.13
585 590 3.263425 GGTCATAGGTTCAAGTCCTGGAA 59.737 47.826 0.00 0.00 36.60 3.53
586 591 2.838202 GGTCATAGGTTCAAGTCCTGGA 59.162 50.000 0.00 0.00 36.60 3.86
587 592 2.840651 AGGTCATAGGTTCAAGTCCTGG 59.159 50.000 0.00 0.00 36.60 4.45
588 593 3.515502 TGAGGTCATAGGTTCAAGTCCTG 59.484 47.826 0.00 0.00 36.60 3.86
589 594 3.791320 TGAGGTCATAGGTTCAAGTCCT 58.209 45.455 0.00 0.00 38.91 3.85
590 595 4.446371 CATGAGGTCATAGGTTCAAGTCC 58.554 47.826 0.00 0.00 34.26 3.85
591 596 4.446371 CCATGAGGTCATAGGTTCAAGTC 58.554 47.826 0.00 0.00 34.26 3.01
592 597 4.494091 CCATGAGGTCATAGGTTCAAGT 57.506 45.455 0.00 0.00 34.26 3.16
606 611 1.100510 CATGCCTTGTGACCATGAGG 58.899 55.000 0.00 0.00 38.84 3.86
607 612 1.100510 CCATGCCTTGTGACCATGAG 58.899 55.000 0.00 0.00 38.84 2.90
608 613 0.323633 CCCATGCCTTGTGACCATGA 60.324 55.000 0.00 0.00 38.84 3.07
609 614 0.323633 TCCCATGCCTTGTGACCATG 60.324 55.000 0.00 0.00 36.87 3.66
610 615 0.033796 CTCCCATGCCTTGTGACCAT 60.034 55.000 0.00 0.00 0.00 3.55
611 616 1.379916 CTCCCATGCCTTGTGACCA 59.620 57.895 0.00 0.00 0.00 4.02
612 617 0.251341 AACTCCCATGCCTTGTGACC 60.251 55.000 0.00 0.00 0.00 4.02
613 618 2.489938 TAACTCCCATGCCTTGTGAC 57.510 50.000 0.00 0.00 0.00 3.67
614 619 2.092429 GGATAACTCCCATGCCTTGTGA 60.092 50.000 0.00 0.00 35.28 3.58
615 620 2.092212 AGGATAACTCCCATGCCTTGTG 60.092 50.000 0.00 0.00 43.21 3.33
616 621 2.092212 CAGGATAACTCCCATGCCTTGT 60.092 50.000 0.00 0.00 43.21 3.16
617 622 2.173356 TCAGGATAACTCCCATGCCTTG 59.827 50.000 0.00 0.00 43.21 3.61
618 623 2.492025 TCAGGATAACTCCCATGCCTT 58.508 47.619 0.00 0.00 43.21 4.35
619 624 2.196742 TCAGGATAACTCCCATGCCT 57.803 50.000 0.00 0.00 43.21 4.75
620 625 3.117888 TCTTTCAGGATAACTCCCATGCC 60.118 47.826 0.00 0.00 43.21 4.40
621 626 4.156455 TCTTTCAGGATAACTCCCATGC 57.844 45.455 0.00 0.00 43.21 4.06
622 627 7.651027 ATTTTCTTTCAGGATAACTCCCATG 57.349 36.000 0.00 0.00 43.21 3.66
623 628 8.560903 AGTATTTTCTTTCAGGATAACTCCCAT 58.439 33.333 0.00 0.00 43.21 4.00
624 629 7.928873 AGTATTTTCTTTCAGGATAACTCCCA 58.071 34.615 0.00 0.00 43.21 4.37
625 630 9.901172 TTAGTATTTTCTTTCAGGATAACTCCC 57.099 33.333 0.00 0.00 43.21 4.30
665 670 4.020573 CAGGTACCCTTGACTTGTGTGATA 60.021 45.833 8.74 0.00 0.00 2.15
729 734 1.220749 GCCATTACCTGCCGTCTCA 59.779 57.895 0.00 0.00 0.00 3.27
745 750 1.534729 CCTGTTTCACTTACCAGGCC 58.465 55.000 0.00 0.00 38.19 5.19
759 764 1.346068 GTCAGAGAGTTCCAGCCTGTT 59.654 52.381 0.00 0.00 0.00 3.16
760 765 0.972883 GTCAGAGAGTTCCAGCCTGT 59.027 55.000 0.00 0.00 0.00 4.00
761 766 0.972134 TGTCAGAGAGTTCCAGCCTG 59.028 55.000 0.00 0.00 0.00 4.85
762 767 1.203112 TCTGTCAGAGAGTTCCAGCCT 60.203 52.381 0.00 0.00 0.00 4.58
764 769 2.560542 TCTTCTGTCAGAGAGTTCCAGC 59.439 50.000 2.12 0.00 30.18 4.85
765 770 4.862902 TTCTTCTGTCAGAGAGTTCCAG 57.137 45.455 2.12 0.00 30.18 3.86
796 801 1.526917 GTGCAACCAGGTGCTCTGT 60.527 57.895 9.42 0.00 45.17 3.41
811 816 4.330074 AGAGTGTCTTACATTATTGCGTGC 59.670 41.667 0.00 0.00 0.00 5.34
812 817 5.348724 ACAGAGTGTCTTACATTATTGCGTG 59.651 40.000 0.00 0.00 0.00 5.34
813 818 5.348724 CACAGAGTGTCTTACATTATTGCGT 59.651 40.000 0.00 0.00 0.00 5.24
814 819 5.220472 CCACAGAGTGTCTTACATTATTGCG 60.220 44.000 0.00 0.00 0.00 4.85
828 838 1.825281 GAGCAGAGCCCACAGAGTGT 61.825 60.000 0.00 0.00 0.00 3.55
830 840 2.289532 GGAGCAGAGCCCACAGAGT 61.290 63.158 0.00 0.00 0.00 3.24
876 886 7.442969 CCGTACATGCCTTTGTATTTATAGGAA 59.557 37.037 0.00 0.00 34.76 3.36
877 887 6.932400 CCGTACATGCCTTTGTATTTATAGGA 59.068 38.462 0.00 0.00 34.76 2.94
878 888 6.148811 CCCGTACATGCCTTTGTATTTATAGG 59.851 42.308 0.00 0.00 34.76 2.57
927 937 2.032634 CGTGCGCCTTGTGTATGGT 61.033 57.895 4.18 0.00 0.00 3.55
928 938 2.749865 CCGTGCGCCTTGTGTATGG 61.750 63.158 4.18 0.00 0.00 2.74
929 939 1.573829 AACCGTGCGCCTTGTGTATG 61.574 55.000 4.18 0.00 0.00 2.39
931 941 2.109387 AACCGTGCGCCTTGTGTA 59.891 55.556 4.18 0.00 0.00 2.90
951 961 7.833285 TGCTTCTAAATAACTCCCTTGTTTT 57.167 32.000 0.00 0.00 0.00 2.43
962 972 8.666573 GTTCCTTACTCCTTGCTTCTAAATAAC 58.333 37.037 0.00 0.00 0.00 1.89
978 988 2.615747 GGCTTCAGGTGGTTCCTTACTC 60.616 54.545 0.00 0.00 45.67 2.59
981 991 1.440618 TGGCTTCAGGTGGTTCCTTA 58.559 50.000 0.00 0.00 45.67 2.69
984 994 0.251341 ACATGGCTTCAGGTGGTTCC 60.251 55.000 0.00 0.00 33.82 3.62
985 995 0.883833 CACATGGCTTCAGGTGGTTC 59.116 55.000 0.00 0.00 45.95 3.62
986 996 3.040965 CACATGGCTTCAGGTGGTT 57.959 52.632 0.00 0.00 45.95 3.67
987 997 4.828409 CACATGGCTTCAGGTGGT 57.172 55.556 0.00 0.00 45.95 4.16
1053 1063 2.383368 ACTCATCTCTGTTGAGCAGC 57.617 50.000 0.78 0.00 43.57 5.25
1094 1106 4.035091 CGCGAGGATGAATGAAACCAAATA 59.965 41.667 0.00 0.00 0.00 1.40
1121 1133 5.599732 ACAATTCAGAGATTCAGATCGGAG 58.400 41.667 0.00 0.00 37.37 4.63
1137 1156 7.254852 ACTCGAAAACAAAAGCTTACAATTCA 58.745 30.769 0.00 0.00 0.00 2.57
1139 1158 8.474006 AAACTCGAAAACAAAAGCTTACAATT 57.526 26.923 0.00 0.00 0.00 2.32
1145 1164 5.891451 AGCTAAACTCGAAAACAAAAGCTT 58.109 33.333 0.00 0.00 34.26 3.74
1158 1177 8.226994 TTCAGGAGTGAGAAGAGCTAAACTCG 62.227 46.154 0.00 0.00 41.48 4.18
1165 1184 7.289782 ACATATAATTCAGGAGTGAGAAGAGCT 59.710 37.037 0.00 0.00 32.98 4.09
1168 1187 8.138074 CGAACATATAATTCAGGAGTGAGAAGA 58.862 37.037 0.00 0.00 32.98 2.87
1173 1192 7.782049 ACTTCGAACATATAATTCAGGAGTGA 58.218 34.615 0.00 0.00 0.00 3.41
1174 1193 7.706607 TGACTTCGAACATATAATTCAGGAGTG 59.293 37.037 0.00 0.00 0.00 3.51
1175 1194 7.782049 TGACTTCGAACATATAATTCAGGAGT 58.218 34.615 0.00 4.34 0.00 3.85
1187 1206 5.696270 GGCATGACATATGACTTCGAACATA 59.304 40.000 10.38 9.99 34.27 2.29
1191 1210 4.135747 TGGCATGACATATGACTTCGAA 57.864 40.909 10.38 0.00 0.00 3.71
1194 1213 5.762825 ATGTTGGCATGACATATGACTTC 57.237 39.130 10.38 0.00 36.04 3.01
1195 1214 5.068198 GGAATGTTGGCATGACATATGACTT 59.932 40.000 10.38 0.00 36.76 3.01
1198 1217 4.534797 TGGAATGTTGGCATGACATATGA 58.465 39.130 10.38 0.00 36.76 2.15
1199 1218 4.922471 TGGAATGTTGGCATGACATATG 57.078 40.909 0.00 0.00 36.76 1.78
1200 1219 5.011329 GGATTGGAATGTTGGCATGACATAT 59.989 40.000 0.00 0.00 36.76 1.78
1204 1246 2.762327 AGGATTGGAATGTTGGCATGAC 59.238 45.455 0.00 0.00 35.15 3.06
1211 1253 7.230108 AGCAGTGATATTAGGATTGGAATGTTG 59.770 37.037 0.00 0.00 0.00 3.33
1219 1261 7.714377 AGAAAGTGAGCAGTGATATTAGGATTG 59.286 37.037 0.00 0.00 0.00 2.67
1220 1262 7.800092 AGAAAGTGAGCAGTGATATTAGGATT 58.200 34.615 0.00 0.00 0.00 3.01
1229 1271 4.348863 AGTGAAGAAAGTGAGCAGTGAT 57.651 40.909 0.00 0.00 0.00 3.06
1230 1272 3.827008 AGTGAAGAAAGTGAGCAGTGA 57.173 42.857 0.00 0.00 0.00 3.41
1231 1273 3.993081 CCTAGTGAAGAAAGTGAGCAGTG 59.007 47.826 0.00 0.00 0.00 3.66
1243 1285 0.175760 GCGATGTGGCCTAGTGAAGA 59.824 55.000 3.32 0.00 0.00 2.87
1251 1293 2.936202 AGATAATTTGCGATGTGGCCT 58.064 42.857 3.32 0.00 0.00 5.19
1262 1304 9.225436 GGGAATAGGCTTCTCTAAGATAATTTG 57.775 37.037 0.00 0.00 34.37 2.32
1268 1310 6.746614 GCAATGGGAATAGGCTTCTCTAAGAT 60.747 42.308 0.00 0.00 34.37 2.40
1270 1312 4.759183 GCAATGGGAATAGGCTTCTCTAAG 59.241 45.833 0.00 0.00 35.68 2.18
1271 1313 4.165950 TGCAATGGGAATAGGCTTCTCTAA 59.834 41.667 0.00 0.00 0.00 2.10
1272 1314 3.716353 TGCAATGGGAATAGGCTTCTCTA 59.284 43.478 0.00 0.00 0.00 2.43
1273 1315 2.511218 TGCAATGGGAATAGGCTTCTCT 59.489 45.455 0.00 0.00 0.00 3.10
1274 1316 2.883386 CTGCAATGGGAATAGGCTTCTC 59.117 50.000 0.00 0.00 0.00 2.87
1275 1317 2.511218 TCTGCAATGGGAATAGGCTTCT 59.489 45.455 0.00 0.00 0.00 2.85
1276 1318 2.936202 TCTGCAATGGGAATAGGCTTC 58.064 47.619 0.00 0.00 0.00 3.86
1277 1319 3.386932 TTCTGCAATGGGAATAGGCTT 57.613 42.857 0.00 0.00 0.00 4.35
1278 1320 3.607490 ATTCTGCAATGGGAATAGGCT 57.393 42.857 0.00 0.00 31.38 4.58
1279 1321 4.584325 TGTTATTCTGCAATGGGAATAGGC 59.416 41.667 6.32 5.33 36.30 3.93
1280 1322 6.713762 TTGTTATTCTGCAATGGGAATAGG 57.286 37.500 6.32 0.00 36.30 2.57
1281 1323 7.944061 TCATTGTTATTCTGCAATGGGAATAG 58.056 34.615 14.63 0.00 46.94 1.73
1282 1324 7.894753 TCATTGTTATTCTGCAATGGGAATA 57.105 32.000 14.63 2.82 46.94 1.75
1283 1325 6.795144 TCATTGTTATTCTGCAATGGGAAT 57.205 33.333 14.63 4.54 46.94 3.01
1284 1326 6.154877 ACATCATTGTTATTCTGCAATGGGAA 59.845 34.615 14.63 0.00 46.94 3.97
1285 1327 5.657745 ACATCATTGTTATTCTGCAATGGGA 59.342 36.000 14.63 0.83 46.94 4.37
1286 1328 5.909477 ACATCATTGTTATTCTGCAATGGG 58.091 37.500 14.63 10.82 46.94 4.00
1287 1329 8.139350 ACATACATCATTGTTATTCTGCAATGG 58.861 33.333 14.63 5.21 46.94 3.16
1289 1331 9.740239 GAACATACATCATTGTTATTCTGCAAT 57.260 29.630 0.00 0.00 36.25 3.56
1306 1348 4.697352 GGAGAACAGCAGTTGAACATACAT 59.303 41.667 0.00 0.00 38.30 2.29
1308 1350 4.065088 TGGAGAACAGCAGTTGAACATAC 58.935 43.478 0.00 0.00 38.30 2.39
1317 1359 3.012518 GCAATACATGGAGAACAGCAGT 58.987 45.455 0.00 0.00 0.00 4.40
1319 1361 3.070476 TGCAATACATGGAGAACAGCA 57.930 42.857 0.00 0.00 0.00 4.41
1328 1370 2.346766 TGTAGGCCTGCAATACATGG 57.653 50.000 22.42 0.00 0.00 3.66
1805 1863 5.743872 GCAGCAGTTTAACCATTGTAATAGC 59.256 40.000 0.00 0.00 0.00 2.97
1966 2030 3.877559 CCCTGCACAATACAGATTCTGA 58.122 45.455 20.33 4.65 37.32 3.27
2295 2508 4.222114 GTTGCTTTCTCACATCTTTTCCG 58.778 43.478 0.00 0.00 0.00 4.30
2472 2709 4.717233 AAAATTGTCTGCACTGTGTTCA 57.283 36.364 9.86 0.00 0.00 3.18
2599 2836 4.329392 TCGTGGTGTCAGTCATTAGTCTA 58.671 43.478 0.00 0.00 0.00 2.59
3033 3275 4.785376 TCTTTCTTCCTATTTGAGGCTCCT 59.215 41.667 12.86 0.00 46.25 3.69
3163 3405 8.632906 ATTTGACTTGATCTGTCTCTGAATTT 57.367 30.769 16.32 0.00 35.63 1.82
3224 3896 9.973246 CAACATGAAGTCTGTAAATACACATAC 57.027 33.333 0.00 0.00 31.93 2.39
3431 4112 6.201806 CCAGCCTATTGAAGAAAAGAGATACG 59.798 42.308 0.00 0.00 0.00 3.06
3435 4116 5.248640 CACCAGCCTATTGAAGAAAAGAGA 58.751 41.667 0.00 0.00 0.00 3.10
3461 4144 5.413309 ACTAGAAACCTCTGAATGACCAG 57.587 43.478 0.00 0.00 32.70 4.00
3517 4200 7.494952 CACATCATATTATGGTATGCTCTGGAG 59.505 40.741 3.89 0.00 33.15 3.86
3543 4226 6.137618 ATACAACTGTATCTGCAGAGTGCAC 61.138 44.000 22.96 9.40 41.78 4.57
3581 4286 5.982890 TGGAAAGATTTCTGGAAATGGTC 57.017 39.130 12.51 7.25 40.77 4.02
3590 4300 6.647481 TCATGTGCATTTTGGAAAGATTTCTG 59.353 34.615 5.37 0.00 37.35 3.02
3613 4323 1.339055 GCAATCCTGTGCCAGTACTCA 60.339 52.381 0.00 0.00 38.66 3.41
3634 4344 7.765819 TGGTGATGTGTAACTTCTCATCTTATG 59.234 37.037 0.00 0.00 41.21 1.90
3692 4402 6.265649 ACTTGTATACACGCTGAGATTCCTAT 59.734 38.462 4.68 0.00 0.00 2.57
3694 4404 4.402793 ACTTGTATACACGCTGAGATTCCT 59.597 41.667 4.68 0.00 0.00 3.36
3706 4416 9.857957 AGTTCTTTCTAGCTTACTTGTATACAC 57.142 33.333 4.68 0.00 0.00 2.90
3750 8362 3.352648 TGTAGCCTTCAACTATTTGGGC 58.647 45.455 5.33 5.33 39.27 5.36
3754 8366 7.454225 AGAGAAACTGTAGCCTTCAACTATTT 58.546 34.615 0.00 0.00 0.00 1.40
3765 8377 3.338249 TCATGCAAGAGAAACTGTAGCC 58.662 45.455 0.00 0.00 0.00 3.93
3766 8378 6.857777 ATATCATGCAAGAGAAACTGTAGC 57.142 37.500 0.00 0.00 0.00 3.58
3783 8395 6.897986 AGCAGAGAAGGAAGAACAATATCAT 58.102 36.000 0.00 0.00 0.00 2.45
3788 8400 5.240013 AGAAGCAGAGAAGGAAGAACAAT 57.760 39.130 0.00 0.00 0.00 2.71
3801 8413 2.339418 CTGTGCAGAGAAGAAGCAGAG 58.661 52.381 4.50 0.00 42.08 3.35
3803 8415 2.166821 ACTGTGCAGAGAAGAAGCAG 57.833 50.000 19.13 5.73 39.21 4.24
3820 8435 0.941463 CGTGAGCAGCGAAGTGAACT 60.941 55.000 0.00 0.00 0.00 3.01
3849 8464 5.844004 AGAACAATTACTAGGTGGATAGCG 58.156 41.667 0.00 0.00 0.00 4.26
3914 8529 4.458397 CATCTCCAGCAGTAATTGTGGAT 58.542 43.478 0.00 0.00 36.81 3.41
3916 8531 2.947652 CCATCTCCAGCAGTAATTGTGG 59.052 50.000 0.00 0.00 32.51 4.17
3922 8537 5.086104 GTTCTAACCATCTCCAGCAGTAA 57.914 43.478 0.00 0.00 0.00 2.24
3936 8551 0.036875 AGGCACTGCTGGTTCTAACC 59.963 55.000 4.87 4.87 44.22 2.85
3939 8554 0.036732 CCAAGGCACTGCTGGTTCTA 59.963 55.000 0.00 0.00 40.86 2.10


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

AutoCloner maintained by Alex Coulton.