Multiple sequence alignment - TraesCS3A01G340000

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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 TraesCS3A01G340000 chr3A 100.000 4500 0 0 1 4500 587395690 587400189 0.000000e+00 8311.0
1 TraesCS3A01G340000 chr3A 100.000 2144 0 0 4795 6938 587400484 587402627 0.000000e+00 3960.0
2 TraesCS3A01G340000 chr3A 95.082 122 4 2 505 625 572598403 572598283 2.550000e-44 191.0
3 TraesCS3A01G340000 chr3A 93.333 75 2 2 6202 6275 80090880 80090952 2.650000e-19 108.0
4 TraesCS3A01G340000 chr3A 89.231 65 6 1 4335 4399 346425573 346425636 5.770000e-11 80.5
5 TraesCS3A01G340000 chr3D 97.997 2147 27 4 4795 6938 445631087 445633220 0.000000e+00 3712.0
6 TraesCS3A01G340000 chr3D 91.192 2509 157 18 610 3082 445626729 445629209 0.000000e+00 3350.0
7 TraesCS3A01G340000 chr3D 94.003 1434 61 13 3079 4500 445629302 445630722 0.000000e+00 2148.0
8 TraesCS3A01G340000 chr3D 88.538 506 56 1 1 506 445626227 445626730 4.600000e-171 612.0
9 TraesCS3A01G340000 chr3D 97.391 115 3 0 497 611 26258690 26258804 5.490000e-46 196.0
10 TraesCS3A01G340000 chr3D 97.368 114 3 0 498 611 350668382 350668495 1.970000e-45 195.0
11 TraesCS3A01G340000 chr3D 85.057 87 10 2 6202 6288 424659654 424659571 1.240000e-12 86.1
12 TraesCS3A01G340000 chr3D 83.696 92 11 3 6189 6280 434025882 434025795 4.460000e-12 84.2
13 TraesCS3A01G340000 chr3D 83.516 91 11 4 6190 6280 19306648 19306562 1.600000e-11 82.4
14 TraesCS3A01G340000 chr3B 96.717 2132 47 8 4811 6938 584543694 584545806 0.000000e+00 3528.0
15 TraesCS3A01G340000 chr3B 92.332 2517 134 19 610 3082 584539459 584541960 0.000000e+00 3524.0
16 TraesCS3A01G340000 chr3B 93.952 1389 66 8 3079 4457 584542051 584543431 0.000000e+00 2084.0
17 TraesCS3A01G340000 chr3B 92.773 512 30 5 1 509 584538957 584539464 0.000000e+00 734.0
18 TraesCS3A01G340000 chr4D 98.214 112 2 0 503 614 211385439 211385328 5.490000e-46 196.0
19 TraesCS3A01G340000 chr4D 96.522 115 4 0 505 619 415293008 415293122 2.550000e-44 191.0
20 TraesCS3A01G340000 chr5A 97.345 113 3 0 499 611 492896373 492896261 7.100000e-45 193.0
21 TraesCS3A01G340000 chr2D 96.522 115 4 0 505 619 349931344 349931230 2.550000e-44 191.0
22 TraesCS3A01G340000 chr2D 93.548 124 7 1 505 628 638351426 638351548 4.270000e-42 183.0
23 TraesCS3A01G340000 chr1A 91.111 135 9 2 481 612 279202692 279202826 5.530000e-41 180.0
24 TraesCS3A01G340000 chr5D 88.462 78 7 1 6202 6279 134780580 134780505 7.410000e-15 93.5
25 TraesCS3A01G340000 chr7B 88.462 78 2 3 6202 6279 329083580 329083650 3.450000e-13 87.9
26 TraesCS3A01G340000 chr4A 83.871 93 11 3 6187 6279 285485363 285485451 1.240000e-12 86.1


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 TraesCS3A01G340000 chr3A 587395690 587402627 6937 False 6135.5 8311 100.0000 1 6938 2 chr3A.!!$F3 6937
1 TraesCS3A01G340000 chr3D 445626227 445633220 6993 False 2455.5 3712 92.9325 1 6938 4 chr3D.!!$F3 6937
2 TraesCS3A01G340000 chr3B 584538957 584545806 6849 False 2467.5 3528 93.9435 1 6938 4 chr3B.!!$F1 6937

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
520 523 0.038744 AGTTACTCCCTCCGTTCCGA 59.961 55.000 0.00 0.00 0.00 4.55 F
521 524 0.890683 GTTACTCCCTCCGTTCCGAA 59.109 55.000 0.00 0.00 0.00 4.30 F
1597 1610 0.173481 AGCTGACATATCGCGTGTGT 59.827 50.000 5.77 9.79 34.56 3.72 F
2957 3005 0.107848 ACCCCCGTGAATAAGCGAAG 60.108 55.000 0.00 0.00 0.00 3.79 F
3343 3492 0.250727 TTGACCCAAGCTACACTGGC 60.251 55.000 0.00 0.00 0.00 4.85 F
3740 3890 0.843309 TGTTGACTTCAGCCCAGGAA 59.157 50.000 0.00 0.00 0.00 3.36 F
3750 3900 1.484240 CAGCCCAGGAACTCCTCTAAG 59.516 57.143 0.00 0.00 46.65 2.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1337 1349 0.830648 TAGCTCCCGTTCCTGGATTG 59.169 55.000 0.0 0.0 0.00 2.67 R
2287 2318 0.884704 GCAAAAGGGAGTGCGAGACA 60.885 55.000 0.0 0.0 0.00 3.41 R
3038 3087 0.250901 GTGGGAGGCTGAAAAGAGCA 60.251 55.000 0.0 0.0 41.08 4.26 R
4027 4177 1.812571 ACAATAAGGACAAAGCCAGCG 59.187 47.619 0.0 0.0 0.00 5.18 R
5149 5375 4.080863 AGACCCAATTGCGATCTTAAGTCT 60.081 41.667 0.0 0.0 0.00 3.24 R
5819 6045 2.158986 CCTCTACCTGTTGCATCTCCAG 60.159 54.545 0.0 0.0 0.00 3.86 R
5952 6178 9.507329 AAACAATGAGTAGAGATAAGCAAGAAA 57.493 29.630 0.0 0.0 0.00 2.52 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
26 27 3.395639 TGCCTGTCTTTGTTACTAACCG 58.604 45.455 0.00 0.00 0.00 4.44
70 71 2.564947 GGTACCTGATAGCTCCTCCATG 59.435 54.545 4.06 0.00 0.00 3.66
98 99 2.356135 CAATTGGGTAGACTTGTCCCG 58.644 52.381 0.00 0.00 43.75 5.14
133 134 4.447290 TCGAGATTGTTTCTGGTTTGACA 58.553 39.130 0.00 0.00 33.74 3.58
506 509 5.495502 CAATTCGGTGGCGTTAATAGTTAC 58.504 41.667 0.00 0.00 0.00 2.50
507 510 4.454728 TTCGGTGGCGTTAATAGTTACT 57.545 40.909 0.00 0.00 0.00 2.24
508 511 4.032703 TCGGTGGCGTTAATAGTTACTC 57.967 45.455 0.00 0.00 0.00 2.59
509 512 3.118542 CGGTGGCGTTAATAGTTACTCC 58.881 50.000 0.00 0.00 0.00 3.85
510 513 3.461061 GGTGGCGTTAATAGTTACTCCC 58.539 50.000 0.00 0.00 0.00 4.30
511 514 3.133542 GGTGGCGTTAATAGTTACTCCCT 59.866 47.826 0.00 0.00 0.00 4.20
512 515 4.366586 GTGGCGTTAATAGTTACTCCCTC 58.633 47.826 0.00 0.00 0.00 4.30
513 516 3.385755 TGGCGTTAATAGTTACTCCCTCC 59.614 47.826 0.00 0.00 0.00 4.30
514 517 3.551659 GGCGTTAATAGTTACTCCCTCCG 60.552 52.174 0.00 0.00 0.00 4.63
515 518 3.067320 GCGTTAATAGTTACTCCCTCCGT 59.933 47.826 0.00 0.00 0.00 4.69
516 519 4.440663 GCGTTAATAGTTACTCCCTCCGTT 60.441 45.833 0.00 0.00 0.00 4.44
517 520 5.277047 CGTTAATAGTTACTCCCTCCGTTC 58.723 45.833 0.00 0.00 0.00 3.95
518 521 5.595885 GTTAATAGTTACTCCCTCCGTTCC 58.404 45.833 0.00 0.00 0.00 3.62
519 522 1.755179 TAGTTACTCCCTCCGTTCCG 58.245 55.000 0.00 0.00 0.00 4.30
520 523 0.038744 AGTTACTCCCTCCGTTCCGA 59.961 55.000 0.00 0.00 0.00 4.55
521 524 0.890683 GTTACTCCCTCCGTTCCGAA 59.109 55.000 0.00 0.00 0.00 4.30
522 525 1.479730 GTTACTCCCTCCGTTCCGAAT 59.520 52.381 0.00 0.00 0.00 3.34
523 526 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
524 527 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
525 528 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
526 529 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
527 530 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
528 531 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
529 532 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
530 533 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
531 534 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
532 535 2.030007 TCCGTTCCGAATTACTTGTCGT 60.030 45.455 0.00 0.00 35.48 4.34
533 536 3.190327 TCCGTTCCGAATTACTTGTCGTA 59.810 43.478 0.00 0.00 35.48 3.43
534 537 3.545078 CCGTTCCGAATTACTTGTCGTAG 59.455 47.826 0.00 0.00 35.48 3.51
535 538 3.545078 CGTTCCGAATTACTTGTCGTAGG 59.455 47.826 0.00 0.00 35.48 3.18
536 539 4.488879 GTTCCGAATTACTTGTCGTAGGT 58.511 43.478 0.00 0.00 35.48 3.08
537 540 5.640732 GTTCCGAATTACTTGTCGTAGGTA 58.359 41.667 0.00 0.00 35.48 3.08
538 541 6.268566 GTTCCGAATTACTTGTCGTAGGTAT 58.731 40.000 0.00 0.00 35.48 2.73
539 542 5.824429 TCCGAATTACTTGTCGTAGGTATG 58.176 41.667 0.00 0.00 35.48 2.39
540 543 4.980434 CCGAATTACTTGTCGTAGGTATGG 59.020 45.833 0.00 0.00 35.48 2.74
541 544 5.221106 CCGAATTACTTGTCGTAGGTATGGA 60.221 44.000 0.00 0.00 35.48 3.41
542 545 6.444633 CGAATTACTTGTCGTAGGTATGGAT 58.555 40.000 0.00 0.00 32.61 3.41
543 546 6.362551 CGAATTACTTGTCGTAGGTATGGATG 59.637 42.308 0.00 0.00 32.61 3.51
544 547 6.726490 ATTACTTGTCGTAGGTATGGATGT 57.274 37.500 0.00 0.00 0.00 3.06
545 548 7.828508 ATTACTTGTCGTAGGTATGGATGTA 57.171 36.000 0.00 0.00 0.00 2.29
546 549 7.828508 TTACTTGTCGTAGGTATGGATGTAT 57.171 36.000 0.00 0.00 0.00 2.29
547 550 6.328641 ACTTGTCGTAGGTATGGATGTATC 57.671 41.667 0.00 0.00 0.00 2.24
548 551 6.069331 ACTTGTCGTAGGTATGGATGTATCT 58.931 40.000 0.00 0.00 0.00 1.98
549 552 7.229308 ACTTGTCGTAGGTATGGATGTATCTA 58.771 38.462 0.00 0.00 0.00 1.98
550 553 7.390996 ACTTGTCGTAGGTATGGATGTATCTAG 59.609 40.741 0.00 0.00 0.00 2.43
551 554 7.012661 TGTCGTAGGTATGGATGTATCTAGA 57.987 40.000 0.00 0.00 0.00 2.43
552 555 7.631007 TGTCGTAGGTATGGATGTATCTAGAT 58.369 38.462 10.73 10.73 0.00 1.98
553 556 7.553044 TGTCGTAGGTATGGATGTATCTAGATG 59.447 40.741 15.79 0.00 0.00 2.90
554 557 7.553402 GTCGTAGGTATGGATGTATCTAGATGT 59.447 40.741 15.79 1.25 0.00 3.06
555 558 8.765517 TCGTAGGTATGGATGTATCTAGATGTA 58.234 37.037 15.79 4.44 0.00 2.29
556 559 9.562408 CGTAGGTATGGATGTATCTAGATGTAT 57.438 37.037 15.79 9.11 0.00 2.29
585 588 8.311395 AGTTCTAGATACATCCATTTCTGTGA 57.689 34.615 0.00 0.00 0.00 3.58
586 589 8.200792 AGTTCTAGATACATCCATTTCTGTGAC 58.799 37.037 0.00 0.00 0.00 3.67
587 590 6.739112 TCTAGATACATCCATTTCTGTGACG 58.261 40.000 0.00 0.00 0.00 4.35
588 591 5.598416 AGATACATCCATTTCTGTGACGA 57.402 39.130 0.00 0.00 0.00 4.20
589 592 5.595885 AGATACATCCATTTCTGTGACGAG 58.404 41.667 0.00 0.00 0.00 4.18
590 593 3.685139 ACATCCATTTCTGTGACGAGT 57.315 42.857 0.00 0.00 0.00 4.18
591 594 4.801330 ACATCCATTTCTGTGACGAGTA 57.199 40.909 0.00 0.00 0.00 2.59
592 595 5.147330 ACATCCATTTCTGTGACGAGTAA 57.853 39.130 0.00 0.00 0.00 2.24
593 596 5.734720 ACATCCATTTCTGTGACGAGTAAT 58.265 37.500 0.00 0.00 0.00 1.89
594 597 6.173339 ACATCCATTTCTGTGACGAGTAATT 58.827 36.000 0.00 0.00 0.00 1.40
595 598 6.655003 ACATCCATTTCTGTGACGAGTAATTT 59.345 34.615 0.00 0.00 0.00 1.82
596 599 6.480524 TCCATTTCTGTGACGAGTAATTTG 57.519 37.500 0.00 0.00 0.00 2.32
597 600 5.411361 TCCATTTCTGTGACGAGTAATTTGG 59.589 40.000 0.00 0.00 0.00 3.28
598 601 5.411361 CCATTTCTGTGACGAGTAATTTGGA 59.589 40.000 0.00 0.00 0.00 3.53
599 602 6.072728 CCATTTCTGTGACGAGTAATTTGGAA 60.073 38.462 0.00 0.00 0.00 3.53
600 603 5.917541 TTCTGTGACGAGTAATTTGGAAC 57.082 39.130 0.00 0.00 0.00 3.62
601 604 3.985279 TCTGTGACGAGTAATTTGGAACG 59.015 43.478 0.00 0.00 0.00 3.95
602 605 3.061322 TGTGACGAGTAATTTGGAACGG 58.939 45.455 0.00 0.00 0.00 4.44
603 606 3.243805 TGTGACGAGTAATTTGGAACGGA 60.244 43.478 0.00 0.00 0.00 4.69
604 607 3.367025 GTGACGAGTAATTTGGAACGGAG 59.633 47.826 0.00 0.00 0.00 4.63
605 608 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
606 609 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
607 610 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
608 611 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
609 612 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
610 613 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
684 688 8.725148 GCACAAATAGAACTATAATGGATCAGG 58.275 37.037 0.00 0.00 0.00 3.86
692 696 6.102897 ACTATAATGGATCAGGTACACAGC 57.897 41.667 0.00 0.00 0.00 4.40
695 699 1.937191 TGGATCAGGTACACAGCAGA 58.063 50.000 0.00 0.00 0.00 4.26
751 755 1.829222 TGGAGAAATAGGTCCCACGAC 59.171 52.381 0.00 0.00 38.38 4.34
838 842 9.508642 CCTCCTTTCTTGGATTAATACTTATCC 57.491 37.037 0.00 0.00 35.30 2.59
968 973 1.936547 GCCTCTCTAATGTTCGCTTGG 59.063 52.381 0.00 0.00 0.00 3.61
974 979 4.624024 TCTCTAATGTTCGCTTGGTAAACG 59.376 41.667 0.00 0.00 0.00 3.60
1120 1125 9.778741 AAATGTTAGAACTCAACTTATCAGTCA 57.221 29.630 0.00 0.00 30.45 3.41
1275 1283 7.447594 AGTCATTGCTTCCTCAATTTCAAAAT 58.552 30.769 0.00 0.00 34.68 1.82
1337 1349 6.146898 ACAAAAACATGCGGTAACAGATAAC 58.853 36.000 0.00 0.00 0.00 1.89
1521 1533 5.940192 CTGTAAGAACAGCAACCATACAA 57.060 39.130 0.00 0.00 46.28 2.41
1522 1534 5.931532 CTGTAAGAACAGCAACCATACAAG 58.068 41.667 0.00 0.00 46.28 3.16
1589 1602 3.879892 GACAGGGGAAAAGCTGACATATC 59.120 47.826 0.00 0.00 0.00 1.63
1590 1603 2.874701 CAGGGGAAAAGCTGACATATCG 59.125 50.000 0.00 0.00 0.00 2.92
1591 1604 1.604278 GGGGAAAAGCTGACATATCGC 59.396 52.381 0.00 0.00 0.00 4.58
1597 1610 0.173481 AGCTGACATATCGCGTGTGT 59.827 50.000 5.77 9.79 34.56 3.72
1631 1644 3.131755 GGAATTTGCTAGGATGCAGCTTT 59.868 43.478 0.22 0.00 44.27 3.51
1688 1701 4.081752 AGACAGCTCACATTCCTGTAAGAG 60.082 45.833 0.00 0.00 39.72 2.85
1705 1718 7.857885 CCTGTAAGAGTTCACTGAAATTTCAAC 59.142 37.037 20.82 15.64 33.77 3.18
1717 1732 7.752239 CACTGAAATTTCAACGCAGATCTTTAT 59.248 33.333 20.82 0.00 36.64 1.40
1726 1741 7.909267 TCAACGCAGATCTTTATTGACATTAG 58.091 34.615 7.80 0.00 0.00 1.73
1735 1750 9.374960 GATCTTTATTGACATTAGTTGATTCGC 57.625 33.333 0.00 0.00 0.00 4.70
1748 1763 4.504461 AGTTGATTCGCGAGATGATACAAC 59.496 41.667 9.59 16.87 41.60 3.32
1827 1849 2.551459 CAGAACTTGGCCTTCTCACAAG 59.449 50.000 3.32 0.00 45.27 3.16
1919 1941 1.129811 GGTTGGATAAACTTGTCGCCG 59.870 52.381 0.00 0.00 38.92 6.46
1954 1976 7.441017 TGTAAGTACTAAAATGTTGTACCCGT 58.559 34.615 0.00 0.00 37.76 5.28
1960 1982 6.168389 ACTAAAATGTTGTACCCGTTCTAGG 58.832 40.000 0.00 0.00 0.00 3.02
2025 2048 1.477377 CGGCTCATCCATCCATCCAAA 60.477 52.381 0.00 0.00 34.01 3.28
2075 2098 0.682209 CAGGCCCAATGGACAGAAGG 60.682 60.000 0.00 0.00 45.14 3.46
2082 2105 2.232208 CCAATGGACAGAAGGCTTTTCC 59.768 50.000 0.00 8.75 0.00 3.13
2100 2123 2.134354 TCCATGCCAATATGACCCTCA 58.866 47.619 0.00 0.00 0.00 3.86
2116 2139 3.519510 ACCCTCATACATGTGTAAGCAGT 59.480 43.478 9.11 0.00 33.76 4.40
2117 2140 4.714802 ACCCTCATACATGTGTAAGCAGTA 59.285 41.667 9.11 0.00 33.76 2.74
2150 2173 4.318332 CACTTGCTAATGTCCTCTGTTCA 58.682 43.478 0.00 0.00 0.00 3.18
2151 2174 4.153117 CACTTGCTAATGTCCTCTGTTCAC 59.847 45.833 0.00 0.00 0.00 3.18
2157 2180 4.630644 AATGTCCTCTGTTCACTCATGT 57.369 40.909 0.00 0.00 0.00 3.21
2174 2205 6.580041 CACTCATGTCATCTAACTTGTTTTGC 59.420 38.462 0.00 0.00 0.00 3.68
2188 2219 6.449698 ACTTGTTTTGCTAATCATTGTCAGG 58.550 36.000 0.00 0.00 0.00 3.86
2196 2227 5.300034 TGCTAATCATTGTCAGGCTATTTGG 59.700 40.000 0.00 0.00 0.00 3.28
2226 2257 1.295020 CTTACTGGACCAATCCCCCA 58.705 55.000 0.00 0.00 45.59 4.96
2230 2261 0.929244 CTGGACCAATCCCCCAATCT 59.071 55.000 0.00 0.00 45.59 2.40
2264 2295 8.144155 TGTCGAAACACTTCAAATTATGTACA 57.856 30.769 0.00 0.00 0.00 2.90
2325 2356 8.116136 CCTTTTGCACAGTTTTATTGACTTTTC 58.884 33.333 0.00 0.00 0.00 2.29
2329 2360 8.770438 TGCACAGTTTTATTGACTTTTCTTTT 57.230 26.923 0.00 0.00 0.00 2.27
2330 2361 8.655092 TGCACAGTTTTATTGACTTTTCTTTTG 58.345 29.630 0.00 0.00 0.00 2.44
2331 2362 8.655970 GCACAGTTTTATTGACTTTTCTTTTGT 58.344 29.630 0.00 0.00 0.00 2.83
2339 2370 5.216566 TGACTTTTCTTTTGTCGACTGTG 57.783 39.130 17.92 4.72 33.81 3.66
2341 2372 3.438781 ACTTTTCTTTTGTCGACTGTGCA 59.561 39.130 17.92 0.00 0.00 4.57
2343 2374 5.295787 ACTTTTCTTTTGTCGACTGTGCATA 59.704 36.000 17.92 0.00 0.00 3.14
2344 2375 5.940192 TTTCTTTTGTCGACTGTGCATAT 57.060 34.783 17.92 0.00 0.00 1.78
2366 2397 2.730382 TCAGCCGACTAGACCATAACA 58.270 47.619 0.00 0.00 0.00 2.41
2374 2405 6.038271 GCCGACTAGACCATAACAAATTCAAT 59.962 38.462 0.00 0.00 0.00 2.57
2477 2511 7.723616 TGTTTCTTCTTCCTTCCAAATGATGTA 59.276 33.333 0.00 0.00 0.00 2.29
2485 2519 8.537728 TTCCTTCCAAATGATGTAGCAAATAT 57.462 30.769 0.00 0.00 0.00 1.28
2522 2556 2.027100 AGGAGCCTAGCAAGTAACCAAC 60.027 50.000 0.00 0.00 0.00 3.77
2526 2560 3.072476 AGCCTAGCAAGTAACCAACTGAA 59.928 43.478 0.00 0.00 38.88 3.02
2531 2565 2.567985 CAAGTAACCAACTGAACGGGT 58.432 47.619 0.00 0.00 38.88 5.28
2533 2567 1.142474 GTAACCAACTGAACGGGTCG 58.858 55.000 0.00 0.00 32.67 4.79
2548 2582 2.523168 TCGGTGCCAGACCTCACA 60.523 61.111 0.00 0.00 43.55 3.58
2577 2611 8.311109 TGCAACTAATCTCACTTATGTGTAAGA 58.689 33.333 8.46 5.79 44.14 2.10
2638 2672 5.890334 TGTTGTCTCAACACAATTTTCTCC 58.110 37.500 10.63 0.00 38.53 3.71
2657 2691 2.362369 CCGGACAGGGACATGAGCT 61.362 63.158 0.00 0.00 35.97 4.09
2663 2697 3.388024 GGACAGGGACATGAGCTACAATA 59.612 47.826 0.00 0.00 0.00 1.90
2664 2698 4.502259 GGACAGGGACATGAGCTACAATAG 60.502 50.000 0.00 0.00 0.00 1.73
2732 2766 3.809832 CCTGAACACCTTGTGAGTTGTAG 59.190 47.826 0.49 0.00 36.96 2.74
2743 2777 3.130516 TGTGAGTTGTAGGAGGATTAGCG 59.869 47.826 0.00 0.00 0.00 4.26
2752 2786 2.832129 AGGAGGATTAGCGAAGTGAACA 59.168 45.455 0.00 0.00 0.00 3.18
2777 2811 9.869757 CATTAAATGGGTTTAGTAAGGGAAAAG 57.130 33.333 0.00 0.00 31.81 2.27
2781 2815 3.245514 GGGTTTAGTAAGGGAAAAGGCCT 60.246 47.826 0.00 0.00 0.00 5.19
2783 2817 5.191426 GGTTTAGTAAGGGAAAAGGCCTAG 58.809 45.833 5.16 0.00 0.00 3.02
2784 2818 5.191426 GTTTAGTAAGGGAAAAGGCCTAGG 58.809 45.833 5.16 3.67 0.00 3.02
2785 2819 2.930653 AGTAAGGGAAAAGGCCTAGGT 58.069 47.619 5.16 0.00 0.00 3.08
2786 2820 4.084466 AGTAAGGGAAAAGGCCTAGGTA 57.916 45.455 5.16 0.00 0.00 3.08
2787 2821 4.642938 AGTAAGGGAAAAGGCCTAGGTAT 58.357 43.478 5.16 0.00 0.00 2.73
2788 2822 5.796191 AGTAAGGGAAAAGGCCTAGGTATA 58.204 41.667 5.16 0.00 0.00 1.47
2789 2823 5.845065 AGTAAGGGAAAAGGCCTAGGTATAG 59.155 44.000 5.16 0.00 0.00 1.31
2790 2824 4.297427 AGGGAAAAGGCCTAGGTATAGT 57.703 45.455 5.16 0.00 0.00 2.12
2795 2829 5.546887 GGAAAAGGCCTAGGTATAGTGGTAT 59.453 44.000 5.16 0.00 0.00 2.73
2818 2852 1.064758 TGAAGGGTGAGTGCACAAACT 60.065 47.619 21.04 6.67 46.96 2.66
2830 2864 5.928976 AGTGCACAAACTATATCAGCCATA 58.071 37.500 21.04 0.00 0.00 2.74
2845 2879 5.684704 TCAGCCATAAATAGAACCTTCAGG 58.315 41.667 0.00 0.00 42.17 3.86
2880 2928 6.040166 ACTCTTGCAATGTGTGAAAAGATCTT 59.960 34.615 0.88 0.88 33.46 2.40
2885 2933 5.159209 CAATGTGTGAAAAGATCTTGAGGC 58.841 41.667 9.17 1.34 0.00 4.70
2886 2934 4.090761 TGTGTGAAAAGATCTTGAGGCT 57.909 40.909 9.17 0.00 0.00 4.58
2892 2940 5.295540 GTGAAAAGATCTTGAGGCTGTATCC 59.704 44.000 9.17 0.00 0.00 2.59
2907 2955 7.414266 AGGCTGTATCCATGACTGATATAGTA 58.586 38.462 12.47 0.00 40.53 1.82
2917 2965 8.456471 CCATGACTGATATAGTATTTGCAATGG 58.544 37.037 0.00 0.00 40.53 3.16
2919 2967 7.226441 TGACTGATATAGTATTTGCAATGGCT 58.774 34.615 0.00 1.07 40.53 4.75
2940 2988 4.083271 GCTCTTGAGTGTACAAAATCCACC 60.083 45.833 0.00 0.00 0.00 4.61
2954 3002 1.817941 CCACCCCCGTGAATAAGCG 60.818 63.158 0.00 0.00 43.14 4.68
2956 3004 0.391927 CACCCCCGTGAATAAGCGAA 60.392 55.000 0.00 0.00 43.14 4.70
2957 3005 0.107848 ACCCCCGTGAATAAGCGAAG 60.108 55.000 0.00 0.00 0.00 3.79
2958 3006 0.107848 CCCCCGTGAATAAGCGAAGT 60.108 55.000 0.00 0.00 0.00 3.01
2965 3013 4.259970 CCGTGAATAAGCGAAGTGATTCTG 60.260 45.833 0.00 0.00 31.03 3.02
2972 3020 5.456192 AAGCGAAGTGATTCTGAATAACG 57.544 39.130 11.35 9.75 0.00 3.18
2975 3023 5.408604 AGCGAAGTGATTCTGAATAACGTTT 59.591 36.000 5.91 2.86 0.00 3.60
3002 3051 8.964476 TTCTCTGGTTGGATAATTACAGATTC 57.036 34.615 0.00 0.00 34.81 2.52
3007 3056 6.265196 TGGTTGGATAATTACAGATTCATGGC 59.735 38.462 0.00 0.00 0.00 4.40
3013 3062 7.831193 GGATAATTACAGATTCATGGCTGGTAT 59.169 37.037 13.22 5.72 36.47 2.73
3014 3063 8.798859 ATAATTACAGATTCATGGCTGGTATC 57.201 34.615 13.22 0.00 36.47 2.24
3015 3064 3.498774 ACAGATTCATGGCTGGTATCC 57.501 47.619 13.22 0.00 36.47 2.59
3022 3071 2.364324 TCATGGCTGGTATCCGTCTTAC 59.636 50.000 0.00 0.00 0.00 2.34
3092 3237 4.566004 TGTAATTTCCTCAAGACCTCACG 58.434 43.478 0.00 0.00 0.00 4.35
3094 3239 2.526304 TTTCCTCAAGACCTCACGTG 57.474 50.000 9.94 9.94 0.00 4.49
3115 3261 9.459276 CACGTGCTTTATTTACATTTAATTTGC 57.541 29.630 0.82 0.00 0.00 3.68
3137 3283 5.863397 TGCATTGTTTTAGCTGCAAATAGAC 59.137 36.000 1.02 0.00 41.33 2.59
3138 3284 5.289434 GCATTGTTTTAGCTGCAAATAGACC 59.711 40.000 1.02 0.00 34.77 3.85
3139 3285 5.385509 TTGTTTTAGCTGCAAATAGACCC 57.614 39.130 1.02 0.00 0.00 4.46
3140 3286 4.662278 TGTTTTAGCTGCAAATAGACCCT 58.338 39.130 1.02 0.00 0.00 4.34
3142 3288 6.242396 TGTTTTAGCTGCAAATAGACCCTTA 58.758 36.000 1.02 0.00 0.00 2.69
3143 3289 6.150474 TGTTTTAGCTGCAAATAGACCCTTAC 59.850 38.462 1.02 0.00 0.00 2.34
3144 3290 5.693769 TTAGCTGCAAATAGACCCTTACT 57.306 39.130 1.02 0.00 0.00 2.24
3145 3291 4.576330 AGCTGCAAATAGACCCTTACTT 57.424 40.909 1.02 0.00 0.00 2.24
3146 3292 4.265073 AGCTGCAAATAGACCCTTACTTG 58.735 43.478 1.02 0.00 0.00 3.16
3147 3293 4.019321 AGCTGCAAATAGACCCTTACTTGA 60.019 41.667 1.02 0.00 0.00 3.02
3148 3294 4.095036 GCTGCAAATAGACCCTTACTTGAC 59.905 45.833 0.00 0.00 0.00 3.18
3149 3295 4.250464 TGCAAATAGACCCTTACTTGACG 58.750 43.478 0.00 0.00 0.00 4.35
3157 3303 8.757982 ATAGACCCTTACTTGACGTCTAATTA 57.242 34.615 17.92 5.57 38.98 1.40
3158 3304 7.472334 AGACCCTTACTTGACGTCTAATTAA 57.528 36.000 17.92 12.09 32.15 1.40
3162 3308 7.101700 CCCTTACTTGACGTCTAATTAAACCT 58.898 38.462 17.92 0.00 0.00 3.50
3190 3336 9.912634 AATGTACCAACAATTTTATGTCTTCTG 57.087 29.630 0.00 0.00 39.58 3.02
3196 3342 8.918658 CCAACAATTTTATGTCTTCTGATGTTG 58.081 33.333 0.00 0.00 41.96 3.33
3227 3373 7.227314 TGGTATTTTAATGCAGATCACTAGCTG 59.773 37.037 0.00 0.00 42.20 4.24
3233 3379 4.056092 TGCAGATCACTAGCTGAGAATG 57.944 45.455 0.00 0.00 41.85 2.67
3235 3381 3.391965 CAGATCACTAGCTGAGAATGCC 58.608 50.000 0.00 0.00 41.85 4.40
3242 3388 0.700564 AGCTGAGAATGCCCTTGGAA 59.299 50.000 0.00 0.00 0.00 3.53
3243 3389 1.287146 AGCTGAGAATGCCCTTGGAAT 59.713 47.619 0.00 0.00 0.00 3.01
3264 3410 6.266558 GGAATCTCACTGACTATGACTGGTAT 59.733 42.308 0.00 0.00 0.00 2.73
3265 3411 6.892658 ATCTCACTGACTATGACTGGTATC 57.107 41.667 0.00 0.00 0.00 2.24
3267 3413 6.187682 TCTCACTGACTATGACTGGTATCAA 58.812 40.000 0.00 0.00 30.82 2.57
3343 3492 0.250727 TTGACCCAAGCTACACTGGC 60.251 55.000 0.00 0.00 0.00 4.85
3363 3512 4.065789 GGCAGCCTAATGTAAGTATCACC 58.934 47.826 3.29 0.00 0.00 4.02
3369 3518 6.013639 AGCCTAATGTAAGTATCACCCCATAC 60.014 42.308 0.00 0.00 0.00 2.39
3387 3537 6.435277 CCCCATACGGTATACTGTACAACTAT 59.565 42.308 23.70 8.00 40.20 2.12
3388 3538 7.310664 CCCATACGGTATACTGTACAACTATG 58.689 42.308 23.70 17.71 40.20 2.23
3453 3603 1.453762 GGGAATCCTGCATGCTCAGC 61.454 60.000 20.33 0.00 32.87 4.26
3454 3604 1.453762 GGAATCCTGCATGCTCAGCC 61.454 60.000 20.33 8.99 32.87 4.85
3462 3612 2.226674 CTGCATGCTCAGCCAATATCAG 59.773 50.000 20.33 0.00 0.00 2.90
3471 3621 4.334552 TCAGCCAATATCAGTTTCTGCAA 58.665 39.130 0.00 0.00 0.00 4.08
3484 3634 4.363138 GTTTCTGCAAACTCAAGGAAAGG 58.637 43.478 0.00 0.00 39.17 3.11
3492 3642 1.143684 ACTCAAGGAAAGGCAGCAAGA 59.856 47.619 0.00 0.00 0.00 3.02
3493 3643 2.224967 ACTCAAGGAAAGGCAGCAAGAT 60.225 45.455 0.00 0.00 0.00 2.40
3494 3644 2.422832 CTCAAGGAAAGGCAGCAAGATC 59.577 50.000 0.00 0.00 0.00 2.75
3510 3660 4.770010 GCAAGATCCATACTCTACTAGCCT 59.230 45.833 0.00 0.00 0.00 4.58
3520 3670 1.152312 TACTAGCCTAGGCCCCTGC 60.152 63.158 30.42 4.01 43.17 4.85
3532 3682 1.224592 CCCCTGCGGTGCTATTTCT 59.775 57.895 0.00 0.00 0.00 2.52
3538 3688 1.032114 GCGGTGCTATTTCTTGCCCT 61.032 55.000 0.00 0.00 0.00 5.19
3609 3759 3.442996 CCTTCGAGGGTGTGATGAC 57.557 57.895 5.19 0.00 0.00 3.06
3719 3869 2.886523 CCAAGATCAGTTGCACTTTCCA 59.113 45.455 0.00 0.00 0.00 3.53
3740 3890 0.843309 TGTTGACTTCAGCCCAGGAA 59.157 50.000 0.00 0.00 0.00 3.36
3750 3900 1.484240 CAGCCCAGGAACTCCTCTAAG 59.516 57.143 0.00 0.00 46.65 2.18
5103 5329 6.490566 AACAAGGACATACGATTTAACCAC 57.509 37.500 0.00 0.00 0.00 4.16
5149 5375 5.397899 GGGATACAGTTGGATTGGATGAAGA 60.398 44.000 0.00 0.00 39.74 2.87
5206 5432 3.181493 GGCATACCTTCATGAACTTGCTG 60.181 47.826 18.79 9.82 0.00 4.41
5819 6045 5.628193 CAGCATCTTTGTCAACTGAACATTC 59.372 40.000 0.00 0.00 0.00 2.67
5952 6178 7.266905 ACCAAAGTAGGAACTATGTATTGGT 57.733 36.000 0.00 0.00 45.60 3.67
6003 6229 3.609853 GTGCATGGTCCAAGTGAATAGA 58.390 45.455 0.00 0.00 0.00 1.98
6110 6336 9.357652 GCAAATTGCTTTCTTAAGATATGACAA 57.642 29.630 11.19 7.53 40.96 3.18
6223 6449 9.286170 TCTGTATAAGAGCGTTTAGATCACTAT 57.714 33.333 0.00 0.00 37.82 2.12
6275 6501 8.980481 TGCTCTTATATTTCTTTAAAGAGGGG 57.020 34.615 17.05 6.17 42.13 4.79
6341 6569 5.075493 GTTCCAATCCATCATCAAGCCTAT 58.925 41.667 0.00 0.00 0.00 2.57
6388 6617 5.641636 TCGTTCATCCGATTTCTGATTTGAA 59.358 36.000 0.00 0.00 30.63 2.69
6402 6631 8.675705 TTCTGATTTGAATAATTAGCGGATGA 57.324 30.769 0.00 0.00 0.00 2.92
6571 6802 2.696707 AGTGAGGTCGTAAAGTGGTTGA 59.303 45.455 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.312443 CTTCCTGCGGTTAGTAACAAAGA 58.688 43.478 14.81 1.67 0.00 2.52
70 71 3.421844 AGTCTACCCAATTGGCAAGTTC 58.578 45.455 19.75 13.84 37.83 3.01
98 99 3.189287 ACAATCTCGATGGTTGTTCTTGC 59.811 43.478 7.44 0.00 32.53 4.01
107 108 3.703001 ACCAGAAACAATCTCGATGGT 57.297 42.857 0.00 0.00 35.73 3.55
133 134 3.118112 CCTCCACAGCAGATCAAGGTAAT 60.118 47.826 0.00 0.00 0.00 1.89
280 281 8.914011 GCAACTTTCTTCCTATTAACCCAATAT 58.086 33.333 0.00 0.00 0.00 1.28
359 361 1.576356 GGCTGAACTAATCTGGCTCG 58.424 55.000 2.40 0.00 45.46 5.03
435 438 2.092968 ACATACCACCGTGATGCTGATT 60.093 45.455 0.00 0.00 0.00 2.57
446 449 3.452755 TCTTGATGCTACATACCACCG 57.547 47.619 0.00 0.00 0.00 4.94
450 453 7.880195 AGAACCATAATCTTGATGCTACATACC 59.120 37.037 0.00 0.00 0.00 2.73
512 515 3.500982 TACGACAAGTAATTCGGAACGG 58.499 45.455 0.00 0.00 42.34 4.44
513 516 3.545078 CCTACGACAAGTAATTCGGAACG 59.455 47.826 0.00 0.00 44.64 3.95
514 517 4.488879 ACCTACGACAAGTAATTCGGAAC 58.511 43.478 0.00 0.00 39.63 3.62
515 518 4.789012 ACCTACGACAAGTAATTCGGAA 57.211 40.909 0.00 0.00 39.63 4.30
516 519 5.221106 CCATACCTACGACAAGTAATTCGGA 60.221 44.000 0.00 0.00 39.63 4.55
517 520 4.980434 CCATACCTACGACAAGTAATTCGG 59.020 45.833 0.00 0.00 39.63 4.30
518 521 5.824429 TCCATACCTACGACAAGTAATTCG 58.176 41.667 0.00 0.00 41.14 3.34
519 522 7.208080 ACATCCATACCTACGACAAGTAATTC 58.792 38.462 0.00 0.00 34.45 2.17
520 523 7.120923 ACATCCATACCTACGACAAGTAATT 57.879 36.000 0.00 0.00 34.45 1.40
521 524 6.726490 ACATCCATACCTACGACAAGTAAT 57.274 37.500 0.00 0.00 34.45 1.89
522 525 7.722728 AGATACATCCATACCTACGACAAGTAA 59.277 37.037 0.00 0.00 34.45 2.24
523 526 7.229308 AGATACATCCATACCTACGACAAGTA 58.771 38.462 0.00 0.00 0.00 2.24
524 527 6.069331 AGATACATCCATACCTACGACAAGT 58.931 40.000 0.00 0.00 0.00 3.16
525 528 6.576662 AGATACATCCATACCTACGACAAG 57.423 41.667 0.00 0.00 0.00 3.16
526 529 7.455891 TCTAGATACATCCATACCTACGACAA 58.544 38.462 0.00 0.00 0.00 3.18
527 530 7.012661 TCTAGATACATCCATACCTACGACA 57.987 40.000 0.00 0.00 0.00 4.35
528 531 7.553402 ACATCTAGATACATCCATACCTACGAC 59.447 40.741 4.54 0.00 0.00 4.34
529 532 7.631007 ACATCTAGATACATCCATACCTACGA 58.369 38.462 4.54 0.00 0.00 3.43
530 533 7.867305 ACATCTAGATACATCCATACCTACG 57.133 40.000 4.54 0.00 0.00 3.51
559 562 9.421399 TCACAGAAATGGATGTATCTAGAACTA 57.579 33.333 0.00 0.00 0.00 2.24
560 563 8.200792 GTCACAGAAATGGATGTATCTAGAACT 58.799 37.037 0.00 0.00 0.00 3.01
561 564 7.168302 CGTCACAGAAATGGATGTATCTAGAAC 59.832 40.741 0.00 0.00 0.00 3.01
562 565 7.068226 TCGTCACAGAAATGGATGTATCTAGAA 59.932 37.037 0.00 0.00 0.00 2.10
563 566 6.546034 TCGTCACAGAAATGGATGTATCTAGA 59.454 38.462 0.00 0.00 0.00 2.43
564 567 6.739112 TCGTCACAGAAATGGATGTATCTAG 58.261 40.000 0.00 0.00 0.00 2.43
565 568 6.321435 ACTCGTCACAGAAATGGATGTATCTA 59.679 38.462 0.00 0.00 0.00 1.98
566 569 5.127845 ACTCGTCACAGAAATGGATGTATCT 59.872 40.000 0.00 0.00 0.00 1.98
567 570 5.352284 ACTCGTCACAGAAATGGATGTATC 58.648 41.667 0.00 0.00 0.00 2.24
568 571 5.344743 ACTCGTCACAGAAATGGATGTAT 57.655 39.130 0.00 0.00 0.00 2.29
569 572 4.801330 ACTCGTCACAGAAATGGATGTA 57.199 40.909 0.00 0.00 0.00 2.29
570 573 3.685139 ACTCGTCACAGAAATGGATGT 57.315 42.857 0.00 0.00 0.00 3.06
571 574 6.668541 AATTACTCGTCACAGAAATGGATG 57.331 37.500 0.00 0.00 0.00 3.51
572 575 6.094048 CCAAATTACTCGTCACAGAAATGGAT 59.906 38.462 0.00 0.00 0.00 3.41
573 576 5.411361 CCAAATTACTCGTCACAGAAATGGA 59.589 40.000 0.00 0.00 0.00 3.41
574 577 5.411361 TCCAAATTACTCGTCACAGAAATGG 59.589 40.000 0.00 0.00 0.00 3.16
575 578 6.480524 TCCAAATTACTCGTCACAGAAATG 57.519 37.500 0.00 0.00 0.00 2.32
576 579 6.347402 CGTTCCAAATTACTCGTCACAGAAAT 60.347 38.462 0.00 0.00 0.00 2.17
577 580 5.050634 CGTTCCAAATTACTCGTCACAGAAA 60.051 40.000 0.00 0.00 0.00 2.52
578 581 4.446385 CGTTCCAAATTACTCGTCACAGAA 59.554 41.667 0.00 0.00 0.00 3.02
579 582 3.985279 CGTTCCAAATTACTCGTCACAGA 59.015 43.478 0.00 0.00 0.00 3.41
580 583 3.122948 CCGTTCCAAATTACTCGTCACAG 59.877 47.826 0.00 0.00 0.00 3.66
581 584 3.061322 CCGTTCCAAATTACTCGTCACA 58.939 45.455 0.00 0.00 0.00 3.58
582 585 3.319755 TCCGTTCCAAATTACTCGTCAC 58.680 45.455 0.00 0.00 0.00 3.67
583 586 3.581755 CTCCGTTCCAAATTACTCGTCA 58.418 45.455 0.00 0.00 0.00 4.35
584 587 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
585 588 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
586 589 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
587 590 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
588 591 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
589 592 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
590 593 3.118519 GCTACTCCCTCCGTTCCAAATTA 60.119 47.826 0.00 0.00 0.00 1.40
591 594 2.355818 GCTACTCCCTCCGTTCCAAATT 60.356 50.000 0.00 0.00 0.00 1.82
592 595 1.209747 GCTACTCCCTCCGTTCCAAAT 59.790 52.381 0.00 0.00 0.00 2.32
593 596 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
594 597 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
595 598 0.683504 GAGCTACTCCCTCCGTTCCA 60.684 60.000 0.00 0.00 0.00 3.53
596 599 0.396001 AGAGCTACTCCCTCCGTTCC 60.396 60.000 0.00 0.00 0.00 3.62
597 600 1.476477 AAGAGCTACTCCCTCCGTTC 58.524 55.000 0.00 0.00 0.00 3.95
598 601 2.822707 TAAGAGCTACTCCCTCCGTT 57.177 50.000 0.00 0.00 0.00 4.44
599 602 2.657143 CTTAAGAGCTACTCCCTCCGT 58.343 52.381 0.00 0.00 0.00 4.69
600 603 1.338655 GCTTAAGAGCTACTCCCTCCG 59.661 57.143 6.67 0.00 45.65 4.63
684 688 6.000891 TGTTTGATTTGATCTGCTGTGTAC 57.999 37.500 0.00 0.00 0.00 2.90
719 723 7.136822 ACCTATTTCTCCATACATTAGCACA 57.863 36.000 0.00 0.00 0.00 4.57
838 842 5.163844 GCAAGTATCATCATAGAGCATGCAG 60.164 44.000 21.98 4.13 34.35 4.41
968 973 0.860533 TGCGGCAACTGTACGTTTAC 59.139 50.000 0.00 0.00 32.27 2.01
974 979 0.941542 TTGAAGTGCGGCAACTGTAC 59.058 50.000 3.23 0.00 0.00 2.90
1148 1156 2.871096 TACCAGGTTTCAGCGGATTT 57.129 45.000 0.00 0.00 0.00 2.17
1325 1337 5.293569 CGTTCCTGGATTGTTATCTGTTACC 59.706 44.000 0.00 0.00 0.00 2.85
1337 1349 0.830648 TAGCTCCCGTTCCTGGATTG 59.169 55.000 0.00 0.00 0.00 2.67
1353 1365 7.926555 TCTGTAGATAATTTTGTAGGCTGTAGC 59.073 37.037 0.00 0.00 41.14 3.58
1512 1524 8.697507 AAGAAGAAGAATGTTCTTGTATGGTT 57.302 30.769 10.22 0.00 44.77 3.67
1521 1533 6.717084 CCTAACCCAAAGAAGAAGAATGTTCT 59.283 38.462 0.00 0.00 40.64 3.01
1522 1534 6.490381 ACCTAACCCAAAGAAGAAGAATGTTC 59.510 38.462 0.00 0.00 0.00 3.18
1604 1617 4.343231 TGCATCCTAGCAAATTCCTGAAA 58.657 39.130 0.00 0.00 42.46 2.69
1616 1629 2.216898 CCAGTAAAGCTGCATCCTAGC 58.783 52.381 1.02 0.00 43.71 3.42
1619 1632 3.009033 TGTTACCAGTAAAGCTGCATCCT 59.991 43.478 1.02 0.00 43.71 3.24
1631 1644 4.422057 TCTCTTGTGGGATGTTACCAGTA 58.578 43.478 0.00 0.00 39.00 2.74
1688 1701 4.597079 TCTGCGTTGAAATTTCAGTGAAC 58.403 39.130 19.64 14.22 38.61 3.18
1705 1718 7.909267 TCAACTAATGTCAATAAAGATCTGCG 58.091 34.615 0.00 0.00 0.00 5.18
1717 1732 4.490743 TCTCGCGAATCAACTAATGTCAA 58.509 39.130 11.33 0.00 0.00 3.18
1726 1741 4.504461 AGTTGTATCATCTCGCGAATCAAC 59.496 41.667 11.33 15.31 33.87 3.18
1735 1750 8.864069 AGAGTAAATTGAGTTGTATCATCTCG 57.136 34.615 0.00 0.00 34.14 4.04
1748 1763 5.059833 GGCCCTGTATGAGAGTAAATTGAG 58.940 45.833 0.00 0.00 0.00 3.02
1827 1849 3.394719 GACAAGTCCAACCAAGAGAGAC 58.605 50.000 0.00 0.00 0.00 3.36
1897 1919 2.433436 GCGACAAGTTTATCCAACCCT 58.567 47.619 0.00 0.00 35.77 4.34
1919 1941 9.191995 ACATTTTAGTACTTACAAATGCTTTGC 57.808 29.630 22.57 0.00 44.39 3.68
2025 2048 5.239525 GGTTCTCGCTAAAATGGCTATTGAT 59.760 40.000 0.00 0.00 0.00 2.57
2075 2098 3.493176 GGGTCATATTGGCATGGAAAAGC 60.493 47.826 0.00 0.00 0.00 3.51
2082 2105 4.654915 TGTATGAGGGTCATATTGGCATG 58.345 43.478 0.14 0.00 40.97 4.06
2095 2118 4.142609 ACTGCTTACACATGTATGAGGG 57.857 45.455 0.00 0.00 0.00 4.30
2116 2139 7.388776 GGACATTAGCAAGTGCAGATGAATATA 59.611 37.037 19.40 0.00 45.16 0.86
2117 2140 6.206243 GGACATTAGCAAGTGCAGATGAATAT 59.794 38.462 19.40 3.83 45.16 1.28
2134 2157 5.728471 ACATGAGTGAACAGAGGACATTAG 58.272 41.667 0.00 0.00 0.00 1.73
2150 2173 6.488006 AGCAAAACAAGTTAGATGACATGAGT 59.512 34.615 0.00 0.00 0.00 3.41
2151 2174 6.906659 AGCAAAACAAGTTAGATGACATGAG 58.093 36.000 0.00 0.00 0.00 2.90
2157 2180 9.844790 CAATGATTAGCAAAACAAGTTAGATGA 57.155 29.630 0.00 0.00 0.00 2.92
2174 2205 5.300034 TGCCAAATAGCCTGACAATGATTAG 59.700 40.000 0.00 0.00 0.00 1.73
2196 2227 2.683362 GGTCCAGTAAGGCTATTGTTGC 59.317 50.000 0.00 0.00 37.29 4.17
2226 2257 2.814336 GTTTCGACAAGCCCAAGAGATT 59.186 45.455 0.00 0.00 0.00 2.40
2230 2261 1.134220 AGTGTTTCGACAAGCCCAAGA 60.134 47.619 0.00 0.00 0.00 3.02
2275 2306 4.074970 AGTGCGAGACAAATGAGGATTTT 58.925 39.130 0.00 0.00 28.65 1.82
2280 2311 1.363744 GGAGTGCGAGACAAATGAGG 58.636 55.000 0.00 0.00 0.00 3.86
2287 2318 0.884704 GCAAAAGGGAGTGCGAGACA 60.885 55.000 0.00 0.00 0.00 3.41
2291 2322 1.153066 TGTGCAAAAGGGAGTGCGA 60.153 52.632 0.00 0.00 43.93 5.10
2325 2356 5.688823 TGAAATATGCACAGTCGACAAAAG 58.311 37.500 19.50 7.04 0.00 2.27
2329 2360 2.672874 GCTGAAATATGCACAGTCGACA 59.327 45.455 19.50 0.00 34.60 4.35
2330 2361 2.030946 GGCTGAAATATGCACAGTCGAC 59.969 50.000 7.70 7.70 34.60 4.20
2331 2362 2.279741 GGCTGAAATATGCACAGTCGA 58.720 47.619 0.00 0.00 34.60 4.20
2332 2363 2.744787 GGCTGAAATATGCACAGTCG 57.255 50.000 0.00 0.00 34.60 4.18
2339 2370 3.060602 GGTCTAGTCGGCTGAAATATGC 58.939 50.000 0.00 0.00 0.00 3.14
2341 2372 6.041637 TGTTATGGTCTAGTCGGCTGAAATAT 59.958 38.462 0.00 0.00 0.00 1.28
2343 2374 4.161565 TGTTATGGTCTAGTCGGCTGAAAT 59.838 41.667 0.00 0.00 0.00 2.17
2344 2375 3.512329 TGTTATGGTCTAGTCGGCTGAAA 59.488 43.478 0.00 0.00 0.00 2.69
2454 2488 6.375455 GCTACATCATTTGGAAGGAAGAAGAA 59.625 38.462 0.00 0.00 0.00 2.52
2457 2491 5.569355 TGCTACATCATTTGGAAGGAAGAA 58.431 37.500 0.00 0.00 0.00 2.52
2499 2533 1.134371 GGTTACTTGCTAGGCTCCTGG 60.134 57.143 0.00 0.00 0.00 4.45
2507 2541 3.432252 CCGTTCAGTTGGTTACTTGCTAG 59.568 47.826 0.00 0.00 33.85 3.42
2522 2556 4.308458 TGGCACCGACCCGTTCAG 62.308 66.667 0.00 0.00 0.00 3.02
2621 2655 2.228822 CCGGGGAGAAAATTGTGTTGAG 59.771 50.000 0.00 0.00 0.00 3.02
2657 2691 5.312895 TCCTGAGCTTGCAAAACTATTGTA 58.687 37.500 0.00 0.00 0.00 2.41
2687 2721 1.153901 TCGACGTCGAAAGCCATCC 60.154 57.895 36.25 0.00 46.30 3.51
2732 2766 3.247006 TGTTCACTTCGCTAATCCTCC 57.753 47.619 0.00 0.00 0.00 4.30
2752 2786 9.042450 CCTTTTCCCTTACTAAACCCATTTAAT 57.958 33.333 0.00 0.00 29.82 1.40
2777 2811 5.824421 TCAGTATACCACTATACCTAGGCC 58.176 45.833 9.30 0.00 36.74 5.19
2781 2815 7.074109 TCACCCTTCAGTATACCACTATACCTA 59.926 40.741 0.00 0.00 36.74 3.08
2783 2817 6.073314 TCACCCTTCAGTATACCACTATACC 58.927 44.000 0.00 0.00 36.74 2.73
2784 2818 6.776603 ACTCACCCTTCAGTATACCACTATAC 59.223 42.308 0.00 0.00 34.98 1.47
2785 2819 6.776116 CACTCACCCTTCAGTATACCACTATA 59.224 42.308 0.00 0.00 34.98 1.31
2786 2820 5.598830 CACTCACCCTTCAGTATACCACTAT 59.401 44.000 0.00 0.00 34.98 2.12
2787 2821 4.954202 CACTCACCCTTCAGTATACCACTA 59.046 45.833 0.00 0.00 34.98 2.74
2788 2822 3.769844 CACTCACCCTTCAGTATACCACT 59.230 47.826 0.00 0.00 38.32 4.00
2789 2823 3.679083 GCACTCACCCTTCAGTATACCAC 60.679 52.174 0.00 0.00 0.00 4.16
2790 2824 2.500098 GCACTCACCCTTCAGTATACCA 59.500 50.000 0.00 0.00 0.00 3.25
2795 2829 1.419381 TGTGCACTCACCCTTCAGTA 58.581 50.000 19.41 0.00 42.46 2.74
2880 2928 7.969130 ACTATATCAGTCATGGATACAGCCTCA 60.969 40.741 0.00 0.00 42.64 3.86
2886 2934 9.875691 GCAAATACTATATCAGTCATGGATACA 57.124 33.333 0.00 0.00 45.55 2.29
2892 2940 7.966753 GCCATTGCAAATACTATATCAGTCATG 59.033 37.037 1.71 0.00 36.68 3.07
2907 2955 2.895404 ACACTCAAGAGCCATTGCAAAT 59.105 40.909 1.71 0.00 41.13 2.32
2917 2965 4.083271 GGTGGATTTTGTACACTCAAGAGC 60.083 45.833 0.00 0.00 41.73 4.09
2919 2967 4.394729 GGGTGGATTTTGTACACTCAAGA 58.605 43.478 0.00 0.00 42.22 3.02
2940 2988 1.006832 CACTTCGCTTATTCACGGGG 58.993 55.000 0.00 0.00 0.00 5.73
2975 3023 9.753674 AATCTGTAATTATCCAACCAGAGAAAA 57.246 29.630 7.15 0.00 32.96 2.29
2978 3026 8.089625 TGAATCTGTAATTATCCAACCAGAGA 57.910 34.615 7.15 0.00 32.96 3.10
2979 3027 8.781196 CATGAATCTGTAATTATCCAACCAGAG 58.219 37.037 7.15 0.00 32.96 3.35
3002 3051 2.365617 AGTAAGACGGATACCAGCCATG 59.634 50.000 0.00 0.00 0.00 3.66
3007 3056 2.361438 GTCCCAGTAAGACGGATACCAG 59.639 54.545 0.00 0.00 0.00 4.00
3013 3062 2.440409 GTACTGTCCCAGTAAGACGGA 58.560 52.381 5.71 0.00 46.55 4.69
3014 3063 1.475682 GGTACTGTCCCAGTAAGACGG 59.524 57.143 5.71 0.00 46.55 4.79
3015 3064 1.475682 GGGTACTGTCCCAGTAAGACG 59.524 57.143 5.71 0.00 46.55 4.18
3030 3079 2.164422 GGCTGAAAAGAGCATTGGGTAC 59.836 50.000 0.00 0.00 41.08 3.34
3038 3087 0.250901 GTGGGAGGCTGAAAAGAGCA 60.251 55.000 0.00 0.00 41.08 4.26
3114 3260 5.289434 GGTCTATTTGCAGCTAAAACAATGC 59.711 40.000 0.00 0.00 39.14 3.56
3115 3261 5.807011 GGGTCTATTTGCAGCTAAAACAATG 59.193 40.000 0.00 0.00 0.00 2.82
3119 3265 5.644977 AAGGGTCTATTTGCAGCTAAAAC 57.355 39.130 0.00 0.00 0.00 2.43
3124 3270 4.019321 TCAAGTAAGGGTCTATTTGCAGCT 60.019 41.667 0.00 0.00 0.00 4.24
3126 3272 4.330074 CGTCAAGTAAGGGTCTATTTGCAG 59.670 45.833 0.00 0.00 0.00 4.41
3135 3281 7.063898 GGTTTAATTAGACGTCAAGTAAGGGTC 59.936 40.741 19.50 10.29 0.00 4.46
3137 3283 7.101700 AGGTTTAATTAGACGTCAAGTAAGGG 58.898 38.462 19.50 0.00 0.00 3.95
3138 3284 8.543862 AAGGTTTAATTAGACGTCAAGTAAGG 57.456 34.615 19.50 0.00 0.00 2.69
3142 3288 9.498176 ACATTAAGGTTTAATTAGACGTCAAGT 57.502 29.630 19.50 11.51 0.00 3.16
3145 3291 9.369904 GGTACATTAAGGTTTAATTAGACGTCA 57.630 33.333 19.50 0.00 0.00 4.35
3146 3292 9.369904 TGGTACATTAAGGTTTAATTAGACGTC 57.630 33.333 7.70 7.70 0.00 4.34
3147 3293 9.723601 TTGGTACATTAAGGTTTAATTAGACGT 57.276 29.630 0.00 0.00 39.30 4.34
3148 3294 9.977762 GTTGGTACATTAAGGTTTAATTAGACG 57.022 33.333 0.00 0.00 39.30 4.18
3190 3336 9.289303 CTGCATTAAAATACCAGTTACAACATC 57.711 33.333 0.00 0.00 0.00 3.06
3196 3342 8.893727 AGTGATCTGCATTAAAATACCAGTTAC 58.106 33.333 0.00 0.00 0.00 2.50
3202 3348 7.442364 TCAGCTAGTGATCTGCATTAAAATACC 59.558 37.037 0.00 0.00 0.00 2.73
3227 3373 2.948315 GTGAGATTCCAAGGGCATTCTC 59.052 50.000 0.00 0.00 0.00 2.87
3233 3379 1.280421 AGTCAGTGAGATTCCAAGGGC 59.720 52.381 0.00 0.00 0.00 5.19
3235 3381 5.128499 AGTCATAGTCAGTGAGATTCCAAGG 59.872 44.000 0.00 0.00 0.00 3.61
3242 3388 6.368805 TGATACCAGTCATAGTCAGTGAGAT 58.631 40.000 0.00 0.00 0.00 2.75
3243 3389 5.755849 TGATACCAGTCATAGTCAGTGAGA 58.244 41.667 0.00 0.00 0.00 3.27
3264 3410 1.403679 CAACCCGCAGTTTTGAGTTGA 59.596 47.619 0.00 0.00 36.18 3.18
3265 3411 1.134175 ACAACCCGCAGTTTTGAGTTG 59.866 47.619 0.00 0.00 36.18 3.16
3267 3413 1.470051 AACAACCCGCAGTTTTGAGT 58.530 45.000 0.00 0.00 36.18 3.41
3307 3456 8.731275 TTGGGTCAACTGTAATAATACTGATG 57.269 34.615 2.19 1.23 36.06 3.07
3311 3460 6.958767 AGCTTGGGTCAACTGTAATAATACT 58.041 36.000 0.00 0.00 32.98 2.12
3312 3461 7.767198 TGTAGCTTGGGTCAACTGTAATAATAC 59.233 37.037 0.00 0.00 0.00 1.89
3315 3464 5.935789 GTGTAGCTTGGGTCAACTGTAATAA 59.064 40.000 0.00 0.00 0.00 1.40
3318 3467 3.389983 AGTGTAGCTTGGGTCAACTGTAA 59.610 43.478 0.00 0.00 0.00 2.41
3321 3470 2.146342 CAGTGTAGCTTGGGTCAACTG 58.854 52.381 0.00 0.00 0.00 3.16
3322 3471 1.072331 CCAGTGTAGCTTGGGTCAACT 59.928 52.381 0.00 0.00 0.00 3.16
3343 3492 4.102524 TGGGGTGATACTTACATTAGGCTG 59.897 45.833 0.00 0.00 0.00 4.85
3363 3512 5.779529 AGTTGTACAGTATACCGTATGGG 57.220 43.478 5.82 0.00 40.75 4.00
3369 3518 4.980434 GCCACATAGTTGTACAGTATACCG 59.020 45.833 0.00 0.00 33.76 4.02
3387 3537 1.073025 GGGTGAGACACATGCCACA 59.927 57.895 0.00 0.00 35.86 4.17
3388 3538 0.322816 ATGGGTGAGACACATGCCAC 60.323 55.000 0.00 0.00 41.44 5.01
3450 3600 4.707030 TTGCAGAAACTGATATTGGCTG 57.293 40.909 2.81 0.00 32.44 4.85
3462 3612 4.363138 CCTTTCCTTGAGTTTGCAGAAAC 58.637 43.478 0.00 0.00 41.69 2.78
3471 3621 1.959282 CTTGCTGCCTTTCCTTGAGTT 59.041 47.619 0.00 0.00 0.00 3.01
3483 3633 2.926778 AGAGTATGGATCTTGCTGCC 57.073 50.000 0.00 0.00 0.00 4.85
3484 3634 4.599047 AGTAGAGTATGGATCTTGCTGC 57.401 45.455 0.00 0.00 0.00 5.25
3492 3642 4.325501 GGCCTAGGCTAGTAGAGTATGGAT 60.326 50.000 32.18 0.00 41.60 3.41
3493 3643 3.010361 GGCCTAGGCTAGTAGAGTATGGA 59.990 52.174 32.18 0.00 41.60 3.41
3494 3644 3.358118 GGCCTAGGCTAGTAGAGTATGG 58.642 54.545 32.18 3.72 41.60 2.74
3520 3670 2.325583 TAGGGCAAGAAATAGCACCG 57.674 50.000 0.00 0.00 33.76 4.94
3562 3712 1.070309 CAAGCGCAGTTCTGTGAAGTC 60.070 52.381 11.47 0.14 0.00 3.01
3609 3759 1.228675 AAGGCAGGTGCTTGGAAGG 60.229 57.895 1.26 0.00 41.70 3.46
3719 3869 1.425066 TCCTGGGCTGAAGTCAACATT 59.575 47.619 0.00 0.00 0.00 2.71
3740 3890 7.732222 ACTTCAATCTGAATCTTAGAGGAGT 57.268 36.000 0.00 0.00 35.59 3.85
3774 3924 2.489329 CGATTGAAGCCCATTTCACTGT 59.511 45.455 0.00 0.00 36.84 3.55
4027 4177 1.812571 ACAATAAGGACAAAGCCAGCG 59.187 47.619 0.00 0.00 0.00 5.18
4109 4259 3.809832 CCAAATGGATTAGTAGTCCGCTG 59.190 47.826 7.17 4.42 38.64 5.18
5103 5329 5.363939 CCTCCTTTACCTGAAGATTAGCAG 58.636 45.833 0.00 0.00 0.00 4.24
5149 5375 4.080863 AGACCCAATTGCGATCTTAAGTCT 60.081 41.667 0.00 0.00 0.00 3.24
5819 6045 2.158986 CCTCTACCTGTTGCATCTCCAG 60.159 54.545 0.00 0.00 0.00 3.86
5952 6178 9.507329 AAACAATGAGTAGAGATAAGCAAGAAA 57.493 29.630 0.00 0.00 0.00 2.52
6275 6501 7.121315 ACAATGTTCTTCCTTTTAGCAGATACC 59.879 37.037 0.00 0.00 0.00 2.73
6341 6569 6.368791 CGATTCAAGTCAGTGAAGGATGTTTA 59.631 38.462 0.00 0.00 40.72 2.01
6388 6617 7.716998 ACTGTTGAGATTTCATCCGCTAATTAT 59.283 33.333 0.00 0.00 32.27 1.28
6499 6730 2.871096 TTAACCTCAACGGCCAATCT 57.129 45.000 2.24 0.00 35.61 2.40
6571 6802 2.034066 CAGACCACCCGCCAATGT 59.966 61.111 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.