Multiple sequence alignment - TraesCS3D01G324400

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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 TraesCS3D01G324400 chr3D 100.000 6941 0 0 1 6941 437488218 437495158 0.000000e+00 12818.0
1 TraesCS3D01G324400 chr3D 94.325 511 4 2 1684 2169 585010873 585011383 0.000000e+00 760.0
2 TraesCS3D01G324400 chr3D 88.298 188 17 3 528 710 550509616 550509429 3.260000e-53 220.0
3 TraesCS3D01G324400 chr3A 96.619 2100 55 6 2174 4258 575495169 575497267 0.000000e+00 3470.0
4 TraesCS3D01G324400 chr3A 95.254 927 30 5 4386 5301 575497603 575498526 0.000000e+00 1456.0
5 TraesCS3D01G324400 chr3A 91.996 912 41 13 6051 6941 575499563 575500463 0.000000e+00 1251.0
6 TraesCS3D01G324400 chr3A 94.648 710 34 3 5316 6021 575498736 575499445 0.000000e+00 1098.0
7 TraesCS3D01G324400 chr3A 89.729 886 36 27 808 1676 575494323 575495170 0.000000e+00 1081.0
8 TraesCS3D01G324400 chr3A 95.165 393 18 1 1 392 575493756 575494148 2.750000e-173 619.0
9 TraesCS3D01G324400 chr3A 98.667 75 1 0 391 465 575494107 575494181 4.370000e-27 134.0
10 TraesCS3D01G324400 chr3B 92.674 1447 73 11 2174 3618 572746339 572747754 0.000000e+00 2054.0
11 TraesCS3D01G324400 chr3B 94.978 896 34 7 6051 6941 572750230 572751119 0.000000e+00 1395.0
12 TraesCS3D01G324400 chr3B 85.307 1334 149 27 3889 5189 572748011 572749330 0.000000e+00 1334.0
13 TraesCS3D01G324400 chr3B 90.023 882 49 23 807 1678 572745490 572746342 0.000000e+00 1105.0
14 TraesCS3D01G324400 chr3B 92.760 663 41 5 5325 5984 572749431 572750089 0.000000e+00 952.0
15 TraesCS3D01G324400 chr3B 90.840 393 29 3 3 391 572744929 572745318 2.870000e-143 520.0
16 TraesCS3D01G324400 chr3B 85.294 204 22 7 541 740 576481097 576480898 3.280000e-48 204.0
17 TraesCS3D01G324400 chr3B 90.476 126 4 3 391 510 572745278 572745401 7.210000e-35 159.0
18 TraesCS3D01G324400 chr4D 93.690 523 8 2 1675 2172 273155249 273155771 0.000000e+00 760.0
19 TraesCS3D01G324400 chr4D 93.164 512 10 2 1682 2169 222689843 222689333 0.000000e+00 728.0
20 TraesCS3D01G324400 chr4D 91.945 509 17 1 1683 2167 455285290 455284782 0.000000e+00 691.0
21 TraesCS3D01G324400 chr4D 90.588 170 12 2 545 710 93336682 93336851 9.060000e-54 222.0
22 TraesCS3D01G324400 chr5D 93.398 515 8 3 1683 2173 515248814 515248302 0.000000e+00 739.0
23 TraesCS3D01G324400 chr5D 92.481 266 13 3 1922 2180 369035911 369035646 2.360000e-99 374.0
24 TraesCS3D01G324400 chr5D 88.649 185 16 3 543 722 117350617 117350433 3.260000e-53 220.0
25 TraesCS3D01G324400 chr7D 93.204 515 10 2 1682 2172 95570168 95569655 0.000000e+00 734.0
26 TraesCS3D01G324400 chr7D 94.400 250 12 2 1929 2177 236679049 236679297 3.930000e-102 383.0
27 TraesCS3D01G324400 chr7D 87.764 237 5 2 1683 1895 76473367 76473131 8.930000e-64 255.0
28 TraesCS3D01G324400 chr7D 95.333 150 7 0 1673 1822 506880548 506880697 9.000000e-59 239.0
29 TraesCS3D01G324400 chr1D 92.913 508 10 3 1680 2163 419724169 419723664 0.000000e+00 715.0
30 TraesCS3D01G324400 chr1D 87.764 237 4 7 1684 1895 460167190 460166954 3.210000e-63 254.0
31 TraesCS3D01G324400 chr1D 90.116 172 12 3 540 707 199866832 199867002 1.170000e-52 219.0
32 TraesCS3D01G324400 chr2D 88.655 238 3 2 1682 1895 36217067 36217304 1.150000e-67 268.0
33 TraesCS3D01G324400 chr2A 91.071 168 12 3 545 709 422098835 422098668 2.520000e-54 224.0
34 TraesCS3D01G324400 chr1A 91.515 165 10 2 547 707 586112413 586112577 2.520000e-54 224.0
35 TraesCS3D01G324400 chr5B 89.266 177 15 2 536 708 687987899 687987723 1.170000e-52 219.0
36 TraesCS3D01G324400 chr5B 100.000 28 0 0 5979 6006 693086910 693086937 1.300000e-02 52.8
37 TraesCS3D01G324400 chr7A 89.266 177 13 4 539 710 320981344 320981169 4.220000e-52 217.0
38 TraesCS3D01G324400 chr7A 100.000 30 0 0 5979 6008 501077687 501077716 1.000000e-03 56.5
39 TraesCS3D01G324400 chr7A 100.000 28 0 0 5979 6006 300320863 300320836 1.300000e-02 52.8
40 TraesCS3D01G324400 chr6D 86.207 145 12 3 6023 6162 454000910 454001051 4.340000e-32 150.0
41 TraesCS3D01G324400 chr7B 100.000 29 0 0 5979 6007 254488512 254488484 3.000000e-03 54.7
42 TraesCS3D01G324400 chr4A 100.000 28 0 0 5979 6006 731341906 731341879 1.300000e-02 52.8
43 TraesCS3D01G324400 chr1B 100.000 28 0 0 5979 6006 510917921 510917948 1.300000e-02 52.8


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 TraesCS3D01G324400 chr3D 437488218 437495158 6940 False 12818.000000 12818 100.000000 1 6941 1 chr3D.!!$F1 6940
1 TraesCS3D01G324400 chr3D 585010873 585011383 510 False 760.000000 760 94.325000 1684 2169 1 chr3D.!!$F2 485
2 TraesCS3D01G324400 chr3A 575493756 575500463 6707 False 1301.285714 3470 94.582571 1 6941 7 chr3A.!!$F1 6940
3 TraesCS3D01G324400 chr3B 572744929 572751119 6190 False 1074.142857 2054 91.008286 3 6941 7 chr3B.!!$F1 6938
4 TraesCS3D01G324400 chr4D 273155249 273155771 522 False 760.000000 760 93.690000 1675 2172 1 chr4D.!!$F2 497
5 TraesCS3D01G324400 chr4D 222689333 222689843 510 True 728.000000 728 93.164000 1682 2169 1 chr4D.!!$R1 487
6 TraesCS3D01G324400 chr4D 455284782 455285290 508 True 691.000000 691 91.945000 1683 2167 1 chr4D.!!$R2 484
7 TraesCS3D01G324400 chr5D 515248302 515248814 512 True 739.000000 739 93.398000 1683 2173 1 chr5D.!!$R3 490
8 TraesCS3D01G324400 chr7D 95569655 95570168 513 True 734.000000 734 93.204000 1682 2172 1 chr7D.!!$R2 490
9 TraesCS3D01G324400 chr1D 419723664 419724169 505 True 715.000000 715 92.913000 1680 2163 1 chr1D.!!$R1 483

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
486 497 0.692476 ATGTTGGCTGGAGCTGTGTA 59.308 50.000 0.00 0.00 41.70 2.90 F
2236 2301 0.595095 GCAGCTGTTGTTTCTCCTGG 59.405 55.000 16.64 0.00 0.00 4.45 F
3599 3666 0.868406 GAGCAGCATATTGTACCGGC 59.132 55.000 0.00 0.00 0.00 6.13 F
3982 4098 0.387239 GTTGCTGCGAATTGGGTGAC 60.387 55.000 0.00 0.00 0.00 3.67 F
4566 4909 1.601759 ACCTGAAGCATGCGCAACT 60.602 52.632 17.11 13.04 42.27 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 2402 0.252197 GGTTGAGCCGTGTAATCCCT 59.748 55.0 0.00 0.0 0.00 4.20 R
3895 4011 0.751643 GTGTTGGCAGGTGTCAAGGT 60.752 55.0 0.00 0.0 40.68 3.50 R
5535 6093 0.034337 TCGGCTAAGCGTTTTGACCT 59.966 50.0 0.00 0.0 0.00 3.85 R
5623 6182 2.128771 AGCGCAATACAGGTTCCAAT 57.871 45.0 11.47 0.0 0.00 3.16 R
6293 6952 0.181587 TTGAGGTTGGCAAAGACGGA 59.818 50.0 0.00 0.0 0.00 4.69 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
211 212 1.004918 CTCGTTCCTCTGGCCGTTT 60.005 57.895 0.00 0.00 0.00 3.60
375 380 2.280797 GCTGGAGGCGTTGTGTGA 60.281 61.111 0.00 0.00 0.00 3.58
379 384 1.598130 GGAGGCGTTGTGTGAAGCT 60.598 57.895 0.00 0.00 0.00 3.74
380 385 1.166531 GGAGGCGTTGTGTGAAGCTT 61.167 55.000 0.00 0.00 0.00 3.74
381 386 1.508632 GAGGCGTTGTGTGAAGCTTA 58.491 50.000 0.00 0.00 0.00 3.09
382 387 1.461127 GAGGCGTTGTGTGAAGCTTAG 59.539 52.381 0.00 0.00 0.00 2.18
383 388 1.070134 AGGCGTTGTGTGAAGCTTAGA 59.930 47.619 0.00 0.00 0.00 2.10
384 389 2.076863 GGCGTTGTGTGAAGCTTAGAT 58.923 47.619 0.00 0.00 0.00 1.98
385 390 3.056107 AGGCGTTGTGTGAAGCTTAGATA 60.056 43.478 0.00 0.00 0.00 1.98
386 391 3.871594 GGCGTTGTGTGAAGCTTAGATAT 59.128 43.478 0.00 0.00 0.00 1.63
387 392 5.047847 GGCGTTGTGTGAAGCTTAGATATA 58.952 41.667 0.00 0.00 0.00 0.86
388 393 5.696724 GGCGTTGTGTGAAGCTTAGATATAT 59.303 40.000 0.00 0.00 0.00 0.86
389 394 6.866770 GGCGTTGTGTGAAGCTTAGATATATA 59.133 38.462 0.00 0.00 0.00 0.86
390 395 7.545965 GGCGTTGTGTGAAGCTTAGATATATAT 59.454 37.037 0.00 0.00 0.00 0.86
391 396 8.376203 GCGTTGTGTGAAGCTTAGATATATATG 58.624 37.037 0.00 0.00 0.00 1.78
392 397 8.376203 CGTTGTGTGAAGCTTAGATATATATGC 58.624 37.037 0.00 7.05 0.00 3.14
393 398 9.429359 GTTGTGTGAAGCTTAGATATATATGCT 57.571 33.333 10.96 10.96 37.66 3.79
394 399 9.645059 TTGTGTGAAGCTTAGATATATATGCTC 57.355 33.333 15.67 10.88 35.70 4.26
395 400 8.253810 TGTGTGAAGCTTAGATATATATGCTCC 58.746 37.037 15.67 6.42 35.70 4.70
396 401 8.253810 GTGTGAAGCTTAGATATATATGCTCCA 58.746 37.037 15.67 8.71 35.70 3.86
397 402 8.815912 TGTGAAGCTTAGATATATATGCTCCAA 58.184 33.333 15.67 4.92 35.70 3.53
398 403 9.311916 GTGAAGCTTAGATATATATGCTCCAAG 57.688 37.037 15.67 0.00 35.70 3.61
399 404 7.984050 TGAAGCTTAGATATATATGCTCCAAGC 59.016 37.037 15.67 15.84 42.82 4.01
400 405 7.673641 AGCTTAGATATATATGCTCCAAGCT 57.326 36.000 18.41 18.41 42.97 3.74
401 406 7.499292 AGCTTAGATATATATGCTCCAAGCTG 58.501 38.462 21.06 0.00 43.21 4.24
402 407 6.705381 GCTTAGATATATATGCTCCAAGCTGG 59.295 42.308 16.11 0.00 42.97 4.85
403 408 7.418368 GCTTAGATATATATGCTCCAAGCTGGA 60.418 40.741 16.11 0.00 45.98 3.86
412 417 3.052082 CAAGCTGGAGGCGTGGTG 61.052 66.667 0.00 0.00 44.53 4.17
413 418 3.832237 CAAGCTGGAGGCGTGGTGT 62.832 63.158 0.00 0.00 44.53 4.16
416 421 3.625897 CTGGAGGCGTGGTGTGGA 61.626 66.667 0.00 0.00 0.00 4.02
417 422 3.596066 CTGGAGGCGTGGTGTGGAG 62.596 68.421 0.00 0.00 0.00 3.86
418 423 3.626924 GGAGGCGTGGTGTGGAGT 61.627 66.667 0.00 0.00 0.00 3.85
486 497 0.692476 ATGTTGGCTGGAGCTGTGTA 59.308 50.000 0.00 0.00 41.70 2.90
488 499 1.905894 TGTTGGCTGGAGCTGTGTATA 59.094 47.619 0.00 0.00 41.70 1.47
510 521 9.804758 GTATAAAATGTAAGCTGTCTACTGAGT 57.195 33.333 0.00 0.00 0.00 3.41
511 522 8.709386 ATAAAATGTAAGCTGTCTACTGAGTG 57.291 34.615 0.00 0.00 0.00 3.51
512 523 5.984695 AATGTAAGCTGTCTACTGAGTGA 57.015 39.130 0.00 0.00 0.00 3.41
513 524 5.574891 ATGTAAGCTGTCTACTGAGTGAG 57.425 43.478 0.00 0.00 0.00 3.51
559 572 9.498176 TTCTGTAGTAAAATACTCCCTTTGTTC 57.502 33.333 0.00 0.00 40.14 3.18
560 573 8.098912 TCTGTAGTAAAATACTCCCTTTGTTCC 58.901 37.037 0.00 0.00 40.14 3.62
561 574 7.747690 TGTAGTAAAATACTCCCTTTGTTCCA 58.252 34.615 0.00 0.00 40.14 3.53
562 575 8.219178 TGTAGTAAAATACTCCCTTTGTTCCAA 58.781 33.333 0.00 0.00 40.14 3.53
563 576 9.070179 GTAGTAAAATACTCCCTTTGTTCCAAA 57.930 33.333 0.00 0.00 40.14 3.28
564 577 8.721133 AGTAAAATACTCCCTTTGTTCCAAAT 57.279 30.769 0.00 0.00 32.47 2.32
565 578 9.816787 AGTAAAATACTCCCTTTGTTCCAAATA 57.183 29.630 0.00 0.00 32.47 1.40
569 582 9.942850 AAATACTCCCTTTGTTCCAAATATTTG 57.057 29.630 19.40 19.40 37.90 2.32
570 583 6.994421 ACTCCCTTTGTTCCAAATATTTGT 57.006 33.333 23.24 1.17 36.45 2.83
571 584 6.993079 ACTCCCTTTGTTCCAAATATTTGTC 58.007 36.000 23.24 14.75 36.45 3.18
572 585 6.782494 ACTCCCTTTGTTCCAAATATTTGTCT 59.218 34.615 23.24 0.00 36.45 3.41
573 586 7.290014 ACTCCCTTTGTTCCAAATATTTGTCTT 59.710 33.333 23.24 0.00 36.45 3.01
574 587 8.028652 TCCCTTTGTTCCAAATATTTGTCTTT 57.971 30.769 23.24 0.00 36.45 2.52
575 588 9.148879 TCCCTTTGTTCCAAATATTTGTCTTTA 57.851 29.630 23.24 6.48 36.45 1.85
576 589 9.942850 CCCTTTGTTCCAAATATTTGTCTTTAT 57.057 29.630 23.24 0.00 36.45 1.40
594 607 9.996554 TGTCTTTATAGAGATTTCAACAAGTGA 57.003 29.630 0.00 0.00 0.00 3.41
602 615 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
603 616 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
604 617 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
605 618 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
606 619 5.456548 TCAACAAGTGACTACATACGGAA 57.543 39.130 0.00 0.00 0.00 4.30
607 620 5.224888 TCAACAAGTGACTACATACGGAAC 58.775 41.667 0.00 0.00 0.00 3.62
608 621 4.859304 ACAAGTGACTACATACGGAACA 57.141 40.909 0.00 0.00 0.00 3.18
609 622 5.204409 ACAAGTGACTACATACGGAACAA 57.796 39.130 0.00 0.00 0.00 2.83
610 623 5.603596 ACAAGTGACTACATACGGAACAAA 58.396 37.500 0.00 0.00 0.00 2.83
611 624 6.050432 ACAAGTGACTACATACGGAACAAAA 58.950 36.000 0.00 0.00 0.00 2.44
612 625 6.708949 ACAAGTGACTACATACGGAACAAAAT 59.291 34.615 0.00 0.00 0.00 1.82
613 626 6.721571 AGTGACTACATACGGAACAAAATG 57.278 37.500 0.00 0.00 0.00 2.32
614 627 6.460781 AGTGACTACATACGGAACAAAATGA 58.539 36.000 0.00 0.00 0.00 2.57
615 628 6.590292 AGTGACTACATACGGAACAAAATGAG 59.410 38.462 0.00 0.00 0.00 2.90
616 629 6.367969 GTGACTACATACGGAACAAAATGAGT 59.632 38.462 0.00 0.00 0.00 3.41
617 630 6.367695 TGACTACATACGGAACAAAATGAGTG 59.632 38.462 0.00 0.00 0.00 3.51
618 631 6.460781 ACTACATACGGAACAAAATGAGTGA 58.539 36.000 0.00 0.00 0.00 3.41
619 632 6.932400 ACTACATACGGAACAAAATGAGTGAA 59.068 34.615 0.00 0.00 0.00 3.18
620 633 6.817765 ACATACGGAACAAAATGAGTGAAT 57.182 33.333 0.00 0.00 0.00 2.57
621 634 6.842163 ACATACGGAACAAAATGAGTGAATC 58.158 36.000 0.00 0.00 0.00 2.52
622 635 6.655003 ACATACGGAACAAAATGAGTGAATCT 59.345 34.615 0.00 0.00 0.00 2.40
623 636 7.822334 ACATACGGAACAAAATGAGTGAATCTA 59.178 33.333 0.00 0.00 0.00 1.98
624 637 8.830580 CATACGGAACAAAATGAGTGAATCTAT 58.169 33.333 0.00 0.00 0.00 1.98
626 639 8.964476 ACGGAACAAAATGAGTGAATCTATAT 57.036 30.769 0.00 0.00 0.00 0.86
627 640 9.396022 ACGGAACAAAATGAGTGAATCTATATT 57.604 29.630 0.00 0.00 0.00 1.28
702 715 8.943909 AAAGACTTATATTTAGGAACGGAGTG 57.056 34.615 0.00 0.00 45.00 3.51
720 733 5.307204 GGAGTGAGTATATCGGACTGTACT 58.693 45.833 0.00 0.16 0.00 2.73
721 734 5.179742 GGAGTGAGTATATCGGACTGTACTG 59.820 48.000 0.00 0.00 0.00 2.74
722 735 5.682659 AGTGAGTATATCGGACTGTACTGT 58.317 41.667 4.92 4.92 0.00 3.55
723 736 6.824553 AGTGAGTATATCGGACTGTACTGTA 58.175 40.000 5.27 0.00 0.00 2.74
724 737 6.705381 AGTGAGTATATCGGACTGTACTGTAC 59.295 42.308 10.98 10.98 0.00 2.90
725 738 6.705381 GTGAGTATATCGGACTGTACTGTACT 59.295 42.308 17.98 7.55 0.00 2.73
726 739 6.704937 TGAGTATATCGGACTGTACTGTACTG 59.295 42.308 19.36 19.36 0.00 2.74
735 748 5.452917 GGACTGTACTGTACTGGTTCAGTTT 60.453 44.000 23.12 9.38 42.59 2.66
757 770 6.647212 TTCAGCTGAACTTGTATTATCACG 57.353 37.500 25.16 0.00 0.00 4.35
758 771 4.566759 TCAGCTGAACTTGTATTATCACGC 59.433 41.667 15.67 0.00 0.00 5.34
762 775 5.276868 GCTGAACTTGTATTATCACGCGATT 60.277 40.000 15.93 0.00 32.73 3.34
765 778 9.124807 CTGAACTTGTATTATCACGCGATTATA 57.875 33.333 15.93 4.29 32.73 0.98
768 781 7.950236 ACTTGTATTATCACGCGATTATAAGC 58.050 34.615 15.93 10.60 32.73 3.09
770 783 7.506296 TGTATTATCACGCGATTATAAGCAG 57.494 36.000 15.93 0.00 32.73 4.24
771 784 7.088272 TGTATTATCACGCGATTATAAGCAGT 58.912 34.615 15.93 0.00 32.73 4.40
772 785 5.822584 TTATCACGCGATTATAAGCAGTG 57.177 39.130 15.93 15.85 38.35 3.66
773 786 3.430333 TCACGCGATTATAAGCAGTGA 57.570 42.857 15.93 18.89 41.04 3.41
774 787 3.372060 TCACGCGATTATAAGCAGTGAG 58.628 45.455 15.93 9.64 39.71 3.51
775 788 2.097202 CACGCGATTATAAGCAGTGAGC 60.097 50.000 15.93 4.49 46.19 4.26
786 799 2.259505 GCAGTGAGCAAGCAGAATTC 57.740 50.000 0.00 0.00 44.79 2.17
787 800 1.538512 GCAGTGAGCAAGCAGAATTCA 59.461 47.619 8.44 0.00 44.79 2.57
789 802 2.812591 CAGTGAGCAAGCAGAATTCAGT 59.187 45.455 8.44 0.00 0.00 3.41
790 803 3.072944 AGTGAGCAAGCAGAATTCAGTC 58.927 45.455 8.44 0.00 0.00 3.51
791 804 3.072944 GTGAGCAAGCAGAATTCAGTCT 58.927 45.455 8.44 0.00 0.00 3.24
793 806 3.244318 TGAGCAAGCAGAATTCAGTCTGA 60.244 43.478 8.44 0.00 46.76 3.27
794 807 3.748083 AGCAAGCAGAATTCAGTCTGAA 58.252 40.909 17.46 17.46 46.76 3.02
795 808 4.139786 AGCAAGCAGAATTCAGTCTGAAA 58.860 39.130 18.93 3.54 46.76 2.69
796 809 4.023365 AGCAAGCAGAATTCAGTCTGAAAC 60.023 41.667 18.93 15.09 46.76 2.78
797 810 4.461405 CAAGCAGAATTCAGTCTGAAACG 58.539 43.478 18.93 8.95 46.76 3.60
798 811 3.070018 AGCAGAATTCAGTCTGAAACGG 58.930 45.455 18.93 16.00 46.76 4.44
800 813 2.807967 CAGAATTCAGTCTGAAACGGCA 59.192 45.455 18.93 0.00 46.76 5.69
801 814 3.438087 CAGAATTCAGTCTGAAACGGCAT 59.562 43.478 18.93 0.00 46.76 4.40
802 815 4.074970 AGAATTCAGTCTGAAACGGCATT 58.925 39.130 18.93 7.85 40.12 3.56
803 816 4.520492 AGAATTCAGTCTGAAACGGCATTT 59.480 37.500 18.93 7.15 40.12 2.32
805 818 4.647424 TTCAGTCTGAAACGGCATTTTT 57.353 36.364 13.00 0.00 32.71 1.94
806 819 3.963665 TCAGTCTGAAACGGCATTTTTG 58.036 40.909 0.00 0.00 0.00 2.44
807 820 3.380004 TCAGTCTGAAACGGCATTTTTGT 59.620 39.130 0.00 0.00 0.00 2.83
808 821 4.111916 CAGTCTGAAACGGCATTTTTGTT 58.888 39.130 0.00 0.00 0.00 2.83
809 822 4.207019 CAGTCTGAAACGGCATTTTTGTTC 59.793 41.667 0.00 0.00 0.00 3.18
810 823 4.097892 AGTCTGAAACGGCATTTTTGTTCT 59.902 37.500 0.00 0.00 0.00 3.01
811 824 4.441087 GTCTGAAACGGCATTTTTGTTCTC 59.559 41.667 0.00 0.00 0.00 2.87
812 825 4.338118 TCTGAAACGGCATTTTTGTTCTCT 59.662 37.500 0.00 0.00 0.00 3.10
813 826 4.358851 TGAAACGGCATTTTTGTTCTCTG 58.641 39.130 0.00 0.00 0.00 3.35
814 827 4.142271 TGAAACGGCATTTTTGTTCTCTGT 60.142 37.500 0.00 0.00 0.00 3.41
815 828 3.354089 ACGGCATTTTTGTTCTCTGTG 57.646 42.857 0.00 0.00 0.00 3.66
818 831 2.796593 GGCATTTTTGTTCTCTGTGTGC 59.203 45.455 0.00 0.00 0.00 4.57
836 849 1.206115 GCCGCACAAAAGAAACGTGG 61.206 55.000 0.00 0.00 0.00 4.94
898 924 2.631545 ACTACTTGTTTAGTCAGGCCGT 59.368 45.455 0.00 0.00 38.33 5.68
922 948 5.236695 TCCAGACTTATCTATCTCACGTTCG 59.763 44.000 0.00 0.00 32.25 3.95
1043 1075 3.114065 GCTACCGTGTTATCTTCTTCCG 58.886 50.000 0.00 0.00 0.00 4.30
1130 1163 3.064324 GCCATGGTTTGCTCCGCT 61.064 61.111 14.67 0.00 0.00 5.52
1329 1362 7.041712 GGAGGAAGAAAATCGAGGTAATTGATC 60.042 40.741 0.00 0.00 30.03 2.92
1347 1380 2.695759 CGCTCTGCACTCTCTCCGT 61.696 63.158 0.00 0.00 0.00 4.69
1385 1418 4.440808 TCTGACCCCCTCCAATTAGTTAA 58.559 43.478 0.00 0.00 0.00 2.01
1420 1453 3.507162 TTCCTGTGTGGTTCATGTGAT 57.493 42.857 0.00 0.00 37.07 3.06
1457 1494 9.188588 CCATGATGCTTTACTGCAAATTAATAG 57.811 33.333 0.00 0.00 46.61 1.73
1506 1543 4.319549 GGACTTCCATTTCTTCGTGTTGTC 60.320 45.833 0.00 0.00 35.64 3.18
1525 1562 3.257375 TGTCGAGTAAGCACCAAGTGTAT 59.743 43.478 0.00 0.00 35.75 2.29
1526 1563 4.460034 TGTCGAGTAAGCACCAAGTGTATA 59.540 41.667 0.00 0.00 35.75 1.47
1589 1626 3.251729 TCTGAGAACAGCATTTGTCTTGC 59.748 43.478 0.00 0.00 43.17 4.01
1632 1669 4.325972 TCAAGCTCTGTTGTGATGCATTA 58.674 39.130 0.00 0.00 0.00 1.90
1649 1686 6.588719 TGCATTATTTTCCTTGCTGTAACT 57.411 33.333 0.00 0.00 36.10 2.24
1650 1687 7.695480 TGCATTATTTTCCTTGCTGTAACTA 57.305 32.000 0.00 0.00 36.10 2.24
1651 1688 7.761409 TGCATTATTTTCCTTGCTGTAACTAG 58.239 34.615 0.00 0.00 36.10 2.57
1652 1689 7.148086 TGCATTATTTTCCTTGCTGTAACTAGG 60.148 37.037 0.00 0.00 36.10 3.02
1664 1701 5.154932 GCTGTAACTAGGTGCTACGATATG 58.845 45.833 0.00 0.00 0.00 1.78
1678 1715 3.141398 ACGATATGTGCCTGCCATAAAG 58.859 45.455 0.00 5.14 0.00 1.85
2236 2301 0.595095 GCAGCTGTTGTTTCTCCTGG 59.405 55.000 16.64 0.00 0.00 4.45
2328 2393 1.069823 CAGCTAGCCGACCAGATTGAT 59.930 52.381 12.13 0.00 0.00 2.57
2337 2402 4.262463 GCCGACCAGATTGATAAGGATGTA 60.262 45.833 0.00 0.00 0.00 2.29
2361 2426 2.335316 TTACACGGCTCAACCTGTTT 57.665 45.000 0.00 0.00 35.61 2.83
2441 2506 9.620259 TTAAATTTGGTTCTTATTGTTTTGCCT 57.380 25.926 0.00 0.00 0.00 4.75
2569 2634 5.621228 CGTGAGTTATTTCTTGTGCTTGTTC 59.379 40.000 0.00 0.00 0.00 3.18
2779 2846 8.245195 TGTACCAACTTATCAGCTGTATGATA 57.755 34.615 14.67 1.13 40.40 2.15
3305 3372 7.120726 ACTGATAAGCACTTTTGGGTATGTAAC 59.879 37.037 0.00 0.00 0.00 2.50
3599 3666 0.868406 GAGCAGCATATTGTACCGGC 59.132 55.000 0.00 0.00 0.00 6.13
3657 3769 2.040178 AGTCCCTACTCCATTAAGGCG 58.960 52.381 0.00 0.00 37.29 5.52
3662 3774 2.093658 CCTACTCCATTAAGGCGTGTGT 60.094 50.000 0.00 0.00 35.70 3.72
3671 3783 2.271821 AAGGCGTGTGTGTGTTTTTC 57.728 45.000 0.00 0.00 0.00 2.29
3727 3841 7.994911 TGTCATTGTATATCAGAAGAAGGCATT 59.005 33.333 0.00 0.00 0.00 3.56
3758 3872 3.975035 GCAAAGTAGAAGGCAAACGAAAG 59.025 43.478 0.00 0.00 0.00 2.62
3788 3902 4.162320 ACTGATACAAAGCAGCCTAGCTAA 59.838 41.667 0.00 0.00 45.89 3.09
3885 4001 1.274703 ACAGGGCATGGAGTGGTAGG 61.275 60.000 3.46 0.00 0.00 3.18
3936 4052 1.075536 CAAAGCTTAGTTCCCCCAGGT 59.924 52.381 0.00 0.00 0.00 4.00
3939 4055 0.696501 GCTTAGTTCCCCCAGGTTGA 59.303 55.000 0.00 0.00 0.00 3.18
3982 4098 0.387239 GTTGCTGCGAATTGGGTGAC 60.387 55.000 0.00 0.00 0.00 3.67
4038 4154 6.763135 TGTTACAATCCTGATAGCACATTCTC 59.237 38.462 0.00 0.00 0.00 2.87
4125 4257 4.342092 AGAAATGCCAGGCCACATTAATAC 59.658 41.667 9.64 9.99 35.49 1.89
4200 4332 4.838423 TGGACCAGAAAGAGTGAAGTATCA 59.162 41.667 0.00 0.00 0.00 2.15
4237 4370 7.067615 TGTTTCAACCTATTGACAGTTGCTTAA 59.932 33.333 0.00 0.00 44.66 1.85
4268 4484 5.220854 GGTTTAGCTGATACATCGCAATTGT 60.221 40.000 7.40 0.00 0.00 2.71
4270 4486 2.615447 AGCTGATACATCGCAATTGTGG 59.385 45.455 18.51 6.45 0.00 4.17
4351 4568 5.474876 GCAAATATCCACTTTCATAGAGGGG 59.525 44.000 0.00 0.00 39.14 4.79
4506 4849 5.114764 TGCAGATTGTCCAAGATATTCCA 57.885 39.130 0.00 0.00 0.00 3.53
4566 4909 1.601759 ACCTGAAGCATGCGCAACT 60.602 52.632 17.11 13.04 42.27 3.16
4762 5107 6.412362 AATGATCTAGGTATGGAGTGTGAC 57.588 41.667 0.00 0.00 0.00 3.67
4778 5123 7.654520 TGGAGTGTGACTACAATAACTTGTTAC 59.345 37.037 0.00 0.00 43.05 2.50
4789 5134 8.792830 ACAATAACTTGTTACATGCTATCACT 57.207 30.769 0.00 0.00 43.05 3.41
4855 5200 7.996644 TGGAGAACATTTAGTAAAACTGGTTCT 59.003 33.333 22.05 22.05 41.54 3.01
4856 5201 8.504815 GGAGAACATTTAGTAAAACTGGTTCTC 58.495 37.037 28.55 28.55 45.77 2.87
5015 5360 6.373774 ACATTCTCTTGCTGAACTAAATCTGG 59.626 38.462 0.00 0.00 0.00 3.86
5121 5471 7.212274 CCTCAGAAAATTATATTTTGCCCTGG 58.788 38.462 2.37 0.00 0.00 4.45
5154 5504 7.757624 GTCGATTAGATGAGTCTTTTTGAGAGT 59.242 37.037 0.00 0.00 40.81 3.24
5191 5541 7.687941 ATTTTAGCTGTGTAGTTAGCATTGT 57.312 32.000 0.00 0.00 42.29 2.71
5194 5544 7.827819 TTAGCTGTGTAGTTAGCATTGTAAG 57.172 36.000 0.00 0.00 42.29 2.34
5262 5626 6.017934 CGTATTTAAGGTGTGAGATTCCATGG 60.018 42.308 4.97 4.97 0.00 3.66
5300 5664 5.869649 AACAATCAGGGCAAATATAACCC 57.130 39.130 0.00 0.00 44.62 4.11
5302 5666 3.542969 ATCAGGGCAAATATAACCCCC 57.457 47.619 4.40 0.00 45.48 5.40
5305 5669 2.223174 AGGGCAAATATAACCCCCTGT 58.777 47.619 0.00 0.00 44.23 4.00
5306 5670 2.590137 AGGGCAAATATAACCCCCTGTT 59.410 45.455 0.00 0.00 44.23 3.16
5307 5671 2.698274 GGGCAAATATAACCCCCTGTTG 59.302 50.000 0.00 0.00 37.83 3.33
5308 5672 3.628769 GGGCAAATATAACCCCCTGTTGA 60.629 47.826 0.00 0.00 37.83 3.18
5309 5673 3.383505 GGCAAATATAACCCCCTGTTGAC 59.616 47.826 0.00 0.00 37.83 3.18
5310 5674 4.278310 GCAAATATAACCCCCTGTTGACT 58.722 43.478 0.00 0.00 37.83 3.41
5311 5675 5.442391 GCAAATATAACCCCCTGTTGACTA 58.558 41.667 0.00 0.00 37.83 2.59
5312 5676 6.068670 GCAAATATAACCCCCTGTTGACTAT 58.931 40.000 0.00 0.00 37.83 2.12
5313 5677 6.549736 GCAAATATAACCCCCTGTTGACTATT 59.450 38.462 0.00 0.00 37.83 1.73
5314 5678 7.255486 GCAAATATAACCCCCTGTTGACTATTC 60.255 40.741 0.00 0.00 37.83 1.75
5335 5893 4.565022 TCAACACTCGTATCTGCATTTGA 58.435 39.130 0.00 0.00 0.00 2.69
5358 5916 8.477984 TGAAATTTGGAAATGCATTTAGTAGC 57.522 30.769 24.15 11.46 0.00 3.58
5372 5930 8.405531 TGCATTTAGTAGCCAAACTATTTGATC 58.594 33.333 2.86 0.00 43.26 2.92
5461 6019 3.258228 TGCGTTTGTGTATGACGATGAT 58.742 40.909 0.00 0.00 38.99 2.45
5683 6242 2.817396 GGTGCAGAGGCTCGCTTC 60.817 66.667 24.21 18.34 41.91 3.86
5904 6465 8.755018 CACCATCAAGTTTGTTGATAAGAAAAC 58.245 33.333 0.06 0.00 37.06 2.43
5906 6467 9.185192 CCATCAAGTTTGTTGATAAGAAAACTC 57.815 33.333 0.06 0.00 40.91 3.01
5984 6545 3.244112 CCTCCGTCCCATAATGGTCTTAC 60.244 52.174 0.00 0.00 35.17 2.34
5985 6546 3.376636 TCCGTCCCATAATGGTCTTACA 58.623 45.455 0.00 0.00 35.17 2.41
5986 6547 3.971305 TCCGTCCCATAATGGTCTTACAT 59.029 43.478 0.00 0.00 35.17 2.29
5987 6548 4.410883 TCCGTCCCATAATGGTCTTACATT 59.589 41.667 0.00 0.00 43.13 2.71
6021 6585 7.612633 GGAGGGAGTATTTCAGTAGGTATCTAG 59.387 44.444 0.00 0.00 0.00 2.43
6048 6690 0.872388 CGCCAGGTTTGGTTCTACAC 59.128 55.000 0.00 0.00 46.80 2.90
6049 6691 1.812324 CGCCAGGTTTGGTTCTACACA 60.812 52.381 0.00 0.00 46.80 3.72
6073 6731 4.379499 GGAATCAACGTTGACTTCCAATCC 60.379 45.833 36.15 27.67 40.54 3.01
6182 6840 3.078837 TGACGCCCTTGAAATCTAAACC 58.921 45.455 0.00 0.00 0.00 3.27
6186 6844 1.749063 CCCTTGAAATCTAAACCGGGC 59.251 52.381 6.32 0.00 0.00 6.13
6187 6845 2.620627 CCCTTGAAATCTAAACCGGGCT 60.621 50.000 6.32 0.00 0.00 5.19
6201 6859 1.003233 GGGCTGCGGAGAAGAAACT 60.003 57.895 8.65 0.00 0.00 2.66
6214 6873 6.818644 CGGAGAAGAAACTAATCAAATCCAGA 59.181 38.462 0.00 0.00 0.00 3.86
6293 6952 4.049393 GCCACTGACTGCGAACTT 57.951 55.556 0.00 0.00 0.00 2.66
6305 6964 1.503818 GCGAACTTCCGTCTTTGCCA 61.504 55.000 0.00 0.00 0.00 4.92
6306 6965 0.941542 CGAACTTCCGTCTTTGCCAA 59.058 50.000 0.00 0.00 0.00 4.52
6857 7533 2.676748 TCCTTTTTGTGGCCAGTTGAT 58.323 42.857 5.11 0.00 0.00 2.57
6865 7541 2.027653 TGTGGCCAGTTGATGACGATTA 60.028 45.455 5.11 0.00 0.00 1.75
6897 7573 2.874648 TAACATGCGAGCCCTGCTGG 62.875 60.000 1.89 1.89 39.88 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
171 172 4.500116 GGCTCCCTCTGTCGTCGC 62.500 72.222 0.00 0.00 0.00 5.19
369 374 8.253810 GGAGCATATATATCTAAGCTTCACACA 58.746 37.037 0.00 0.00 31.61 3.72
379 384 7.978099 TCCAGCTTGGAGCATATATATCTAA 57.022 36.000 2.47 0.00 42.67 2.10
395 400 3.052082 CACCACGCCTCCAGCTTG 61.052 66.667 0.00 0.00 40.35 4.01
396 401 3.560251 ACACCACGCCTCCAGCTT 61.560 61.111 0.00 0.00 40.39 3.74
397 402 4.320456 CACACCACGCCTCCAGCT 62.320 66.667 0.00 0.00 40.39 4.24
399 404 3.596066 CTCCACACCACGCCTCCAG 62.596 68.421 0.00 0.00 0.00 3.86
400 405 3.625897 CTCCACACCACGCCTCCA 61.626 66.667 0.00 0.00 0.00 3.86
401 406 2.676163 AAACTCCACACCACGCCTCC 62.676 60.000 0.00 0.00 0.00 4.30
402 407 0.034337 TAAACTCCACACCACGCCTC 59.966 55.000 0.00 0.00 0.00 4.70
403 408 0.034896 CTAAACTCCACACCACGCCT 59.965 55.000 0.00 0.00 0.00 5.52
404 409 0.034337 TCTAAACTCCACACCACGCC 59.966 55.000 0.00 0.00 0.00 5.68
405 410 2.094762 ATCTAAACTCCACACCACGC 57.905 50.000 0.00 0.00 0.00 5.34
406 411 8.520351 TCATATATATCTAAACTCCACACCACG 58.480 37.037 0.00 0.00 0.00 4.94
486 497 8.531982 TCACTCAGTAGACAGCTTACATTTTAT 58.468 33.333 0.00 0.00 0.00 1.40
488 499 6.759272 TCACTCAGTAGACAGCTTACATTTT 58.241 36.000 0.00 0.00 0.00 1.82
510 521 6.775594 ATATACAGTAGTTCACACTGCTCA 57.224 37.500 2.51 0.00 43.61 4.26
511 522 7.433719 CAGAATATACAGTAGTTCACACTGCTC 59.566 40.741 2.51 0.00 43.61 4.26
512 523 7.093727 ACAGAATATACAGTAGTTCACACTGCT 60.094 37.037 2.51 0.00 46.17 4.24
513 524 7.036220 ACAGAATATACAGTAGTTCACACTGC 58.964 38.462 2.51 0.00 45.96 4.40
568 581 9.996554 TCACTTGTTGAAATCTCTATAAAGACA 57.003 29.630 0.00 0.00 0.00 3.41
576 589 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
577 590 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
578 591 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
579 592 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
580 593 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
581 594 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
582 595 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
583 596 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
584 597 5.221283 TGTTCCGTATGTAGTCACTTGTTGA 60.221 40.000 0.00 0.00 0.00 3.18
585 598 4.986034 TGTTCCGTATGTAGTCACTTGTTG 59.014 41.667 0.00 0.00 0.00 3.33
586 599 5.204409 TGTTCCGTATGTAGTCACTTGTT 57.796 39.130 0.00 0.00 0.00 2.83
587 600 4.859304 TGTTCCGTATGTAGTCACTTGT 57.141 40.909 0.00 0.00 0.00 3.16
588 601 6.533819 TTTTGTTCCGTATGTAGTCACTTG 57.466 37.500 0.00 0.00 0.00 3.16
589 602 6.932400 TCATTTTGTTCCGTATGTAGTCACTT 59.068 34.615 0.00 0.00 0.00 3.16
590 603 6.460781 TCATTTTGTTCCGTATGTAGTCACT 58.539 36.000 0.00 0.00 0.00 3.41
591 604 6.367969 ACTCATTTTGTTCCGTATGTAGTCAC 59.632 38.462 0.00 0.00 0.00 3.67
592 605 6.367695 CACTCATTTTGTTCCGTATGTAGTCA 59.632 38.462 0.00 0.00 0.00 3.41
593 606 6.588756 TCACTCATTTTGTTCCGTATGTAGTC 59.411 38.462 0.00 0.00 0.00 2.59
594 607 6.460781 TCACTCATTTTGTTCCGTATGTAGT 58.539 36.000 0.00 0.00 0.00 2.73
595 608 6.961359 TCACTCATTTTGTTCCGTATGTAG 57.039 37.500 0.00 0.00 0.00 2.74
596 609 7.822334 AGATTCACTCATTTTGTTCCGTATGTA 59.178 33.333 0.00 0.00 0.00 2.29
597 610 6.655003 AGATTCACTCATTTTGTTCCGTATGT 59.345 34.615 0.00 0.00 0.00 2.29
598 611 7.076842 AGATTCACTCATTTTGTTCCGTATG 57.923 36.000 0.00 0.00 0.00 2.39
599 612 8.964476 ATAGATTCACTCATTTTGTTCCGTAT 57.036 30.769 0.00 0.00 0.00 3.06
601 614 8.964476 ATATAGATTCACTCATTTTGTTCCGT 57.036 30.769 0.00 0.00 0.00 4.69
675 688 9.955102 ACTCCGTTCCTAAATATAAGTCTTTTT 57.045 29.630 0.00 0.00 0.00 1.94
676 689 9.379791 CACTCCGTTCCTAAATATAAGTCTTTT 57.620 33.333 0.00 0.00 0.00 2.27
677 690 8.755977 TCACTCCGTTCCTAAATATAAGTCTTT 58.244 33.333 0.00 0.00 0.00 2.52
678 691 8.302515 TCACTCCGTTCCTAAATATAAGTCTT 57.697 34.615 0.00 0.00 0.00 3.01
679 692 7.560626 ACTCACTCCGTTCCTAAATATAAGTCT 59.439 37.037 0.00 0.00 0.00 3.24
680 693 7.714703 ACTCACTCCGTTCCTAAATATAAGTC 58.285 38.462 0.00 0.00 0.00 3.01
681 694 7.657023 ACTCACTCCGTTCCTAAATATAAGT 57.343 36.000 0.00 0.00 0.00 2.24
685 698 8.675504 CGATATACTCACTCCGTTCCTAAATAT 58.324 37.037 0.00 0.00 0.00 1.28
686 699 7.120285 CCGATATACTCACTCCGTTCCTAAATA 59.880 40.741 0.00 0.00 0.00 1.40
687 700 6.072064 CCGATATACTCACTCCGTTCCTAAAT 60.072 42.308 0.00 0.00 0.00 1.40
688 701 5.240183 CCGATATACTCACTCCGTTCCTAAA 59.760 44.000 0.00 0.00 0.00 1.85
689 702 4.758674 CCGATATACTCACTCCGTTCCTAA 59.241 45.833 0.00 0.00 0.00 2.69
690 703 4.040829 TCCGATATACTCACTCCGTTCCTA 59.959 45.833 0.00 0.00 0.00 2.94
691 704 3.147629 CCGATATACTCACTCCGTTCCT 58.852 50.000 0.00 0.00 0.00 3.36
692 705 3.058363 GTCCGATATACTCACTCCGTTCC 60.058 52.174 0.00 0.00 0.00 3.62
693 706 3.814283 AGTCCGATATACTCACTCCGTTC 59.186 47.826 0.00 0.00 0.00 3.95
694 707 3.564644 CAGTCCGATATACTCACTCCGTT 59.435 47.826 0.00 0.00 0.00 4.44
695 708 3.139850 CAGTCCGATATACTCACTCCGT 58.860 50.000 0.00 0.00 0.00 4.69
696 709 3.139850 ACAGTCCGATATACTCACTCCG 58.860 50.000 0.00 0.00 0.00 4.63
697 710 5.179742 CAGTACAGTCCGATATACTCACTCC 59.820 48.000 0.00 0.00 0.00 3.85
698 711 5.759273 ACAGTACAGTCCGATATACTCACTC 59.241 44.000 0.00 0.00 0.00 3.51
699 712 5.682659 ACAGTACAGTCCGATATACTCACT 58.317 41.667 0.00 0.00 0.00 3.41
700 713 6.705381 AGTACAGTACAGTCCGATATACTCAC 59.295 42.308 13.37 0.00 0.00 3.51
701 714 6.704937 CAGTACAGTACAGTCCGATATACTCA 59.295 42.308 13.37 0.00 0.00 3.41
702 715 6.147492 CCAGTACAGTACAGTCCGATATACTC 59.853 46.154 13.37 0.00 0.00 2.59
720 733 3.133901 TCAGCTGAAACTGAACCAGTACA 59.866 43.478 15.67 3.99 44.62 2.90
721 734 3.728845 TCAGCTGAAACTGAACCAGTAC 58.271 45.455 15.67 0.00 44.62 2.73
735 748 4.566759 GCGTGATAATACAAGTTCAGCTGA 59.433 41.667 13.74 13.74 0.00 4.26
757 770 3.605692 GCTTGCTCACTGCTTATAATCGC 60.606 47.826 0.00 0.00 43.37 4.58
758 771 3.557185 TGCTTGCTCACTGCTTATAATCG 59.443 43.478 0.00 0.00 43.37 3.34
762 775 3.893326 TCTGCTTGCTCACTGCTTATA 57.107 42.857 0.00 0.00 43.37 0.98
765 778 1.906990 ATTCTGCTTGCTCACTGCTT 58.093 45.000 0.00 0.00 43.37 3.91
768 781 2.812591 ACTGAATTCTGCTTGCTCACTG 59.187 45.455 11.86 0.00 0.00 3.66
770 783 3.072944 AGACTGAATTCTGCTTGCTCAC 58.927 45.455 11.86 0.00 0.00 3.51
771 784 3.072211 CAGACTGAATTCTGCTTGCTCA 58.928 45.455 11.86 0.00 36.83 4.26
772 785 3.332919 TCAGACTGAATTCTGCTTGCTC 58.667 45.455 11.86 2.64 42.52 4.26
773 786 3.413846 TCAGACTGAATTCTGCTTGCT 57.586 42.857 11.86 2.81 42.52 3.91
774 787 4.225208 GTTTCAGACTGAATTCTGCTTGC 58.775 43.478 18.38 0.73 42.52 4.01
775 788 4.461405 CGTTTCAGACTGAATTCTGCTTG 58.539 43.478 18.38 10.31 42.52 4.01
779 792 2.807967 TGCCGTTTCAGACTGAATTCTG 59.192 45.455 18.38 10.51 43.93 3.02
780 793 3.126001 TGCCGTTTCAGACTGAATTCT 57.874 42.857 18.38 0.00 36.11 2.40
781 794 4.425577 AATGCCGTTTCAGACTGAATTC 57.574 40.909 18.38 13.15 36.11 2.17
782 795 4.853924 AAATGCCGTTTCAGACTGAATT 57.146 36.364 18.38 6.22 36.11 2.17
783 796 4.853924 AAAATGCCGTTTCAGACTGAAT 57.146 36.364 18.38 0.00 36.11 2.57
784 797 4.142271 ACAAAAATGCCGTTTCAGACTGAA 60.142 37.500 13.99 13.99 34.03 3.02
785 798 3.380004 ACAAAAATGCCGTTTCAGACTGA 59.620 39.130 0.00 0.00 0.00 3.41
786 799 3.705604 ACAAAAATGCCGTTTCAGACTG 58.294 40.909 0.00 0.00 0.00 3.51
787 800 4.097892 AGAACAAAAATGCCGTTTCAGACT 59.902 37.500 0.00 0.00 0.00 3.24
789 802 4.338118 AGAGAACAAAAATGCCGTTTCAGA 59.662 37.500 0.00 0.00 0.00 3.27
790 803 4.442073 CAGAGAACAAAAATGCCGTTTCAG 59.558 41.667 0.00 0.00 0.00 3.02
791 804 4.142271 ACAGAGAACAAAAATGCCGTTTCA 60.142 37.500 0.00 0.00 0.00 2.69
793 806 4.111916 CACAGAGAACAAAAATGCCGTTT 58.888 39.130 0.00 0.00 0.00 3.60
794 807 3.130340 ACACAGAGAACAAAAATGCCGTT 59.870 39.130 0.00 0.00 0.00 4.44
795 808 2.687935 ACACAGAGAACAAAAATGCCGT 59.312 40.909 0.00 0.00 0.00 5.68
796 809 3.044986 CACACAGAGAACAAAAATGCCG 58.955 45.455 0.00 0.00 0.00 5.69
797 810 2.796593 GCACACAGAGAACAAAAATGCC 59.203 45.455 0.00 0.00 0.00 4.40
798 811 2.796593 GGCACACAGAGAACAAAAATGC 59.203 45.455 0.00 0.00 0.00 3.56
800 813 2.543653 GCGGCACACAGAGAACAAAAAT 60.544 45.455 0.00 0.00 0.00 1.82
801 814 1.202245 GCGGCACACAGAGAACAAAAA 60.202 47.619 0.00 0.00 0.00 1.94
802 815 0.380378 GCGGCACACAGAGAACAAAA 59.620 50.000 0.00 0.00 0.00 2.44
803 816 0.746204 TGCGGCACACAGAGAACAAA 60.746 50.000 0.00 0.00 0.00 2.83
805 818 2.503546 TGCGGCACACAGAGAACA 59.496 55.556 0.00 0.00 0.00 3.18
813 826 0.920664 GTTTCTTTTGTGCGGCACAC 59.079 50.000 33.44 17.35 44.47 3.82
814 827 0.524392 CGTTTCTTTTGTGCGGCACA 60.524 50.000 30.40 30.40 43.02 4.57
815 828 0.524604 ACGTTTCTTTTGTGCGGCAC 60.525 50.000 25.55 25.55 34.56 5.01
818 831 1.206115 GCCACGTTTCTTTTGTGCGG 61.206 55.000 0.00 0.00 32.32 5.69
898 924 5.236695 CGAACGTGAGATAGATAAGTCTGGA 59.763 44.000 0.00 0.00 35.87 3.86
922 948 3.184178 CGACATGTGTTTGGAATTTTGGC 59.816 43.478 1.15 0.00 0.00 4.52
984 1010 2.665185 GCGACGGGTTTGAGCAGT 60.665 61.111 0.00 0.00 0.00 4.40
1043 1075 1.491668 GGGGGAGGAAGAAGAGACTC 58.508 60.000 0.00 0.00 0.00 3.36
1067 1099 1.377333 CTGAGAAACGGGGAAGGGC 60.377 63.158 0.00 0.00 0.00 5.19
1130 1163 0.743688 GGCTCTGCGAGAGAAGATGA 59.256 55.000 14.86 0.00 46.96 2.92
1261 1294 0.963962 TCTTACGCTTGGAGACCGTT 59.036 50.000 0.00 0.00 36.51 4.44
1329 1362 2.101965 CGGAGAGAGTGCAGAGCG 59.898 66.667 0.00 0.00 0.00 5.03
1347 1380 3.932710 GGTCAGAAATCACAGATAACGCA 59.067 43.478 0.00 0.00 0.00 5.24
1385 1418 2.332654 GGAAATTGCGCCGGTGACT 61.333 57.895 21.76 0.00 0.00 3.41
1463 1500 5.776716 AGTCCATGATTGTTGTCCAGAATTT 59.223 36.000 0.00 0.00 0.00 1.82
1464 1501 5.327732 AGTCCATGATTGTTGTCCAGAATT 58.672 37.500 0.00 0.00 0.00 2.17
1465 1502 4.927049 AGTCCATGATTGTTGTCCAGAAT 58.073 39.130 0.00 0.00 0.00 2.40
1506 1543 5.588240 TGATATACACTTGGTGCTTACTCG 58.412 41.667 0.00 0.00 36.98 4.18
1589 1626 9.443283 GCTTGAAGCAATTCACTATGTTATAAG 57.557 33.333 13.09 0.00 41.89 1.73
1590 1627 9.177608 AGCTTGAAGCAATTCACTATGTTATAA 57.822 29.630 20.45 0.00 45.56 0.98
1601 1638 3.633525 ACAACAGAGCTTGAAGCAATTCA 59.366 39.130 20.45 0.00 45.56 2.57
1632 1669 4.459337 GCACCTAGTTACAGCAAGGAAAAT 59.541 41.667 0.00 0.00 33.16 1.82
1649 1686 2.296190 CAGGCACATATCGTAGCACCTA 59.704 50.000 0.00 0.00 0.00 3.08
1650 1687 1.069204 CAGGCACATATCGTAGCACCT 59.931 52.381 0.00 0.00 0.00 4.00
1651 1688 1.502231 CAGGCACATATCGTAGCACC 58.498 55.000 0.00 0.00 0.00 5.01
1652 1689 0.861837 GCAGGCACATATCGTAGCAC 59.138 55.000 0.00 0.00 0.00 4.40
1664 1701 4.261801 TCTCTTTACTTTATGGCAGGCAC 58.738 43.478 0.00 0.00 0.00 5.01
1694 1731 4.294347 TGGAAACTTGAGGGACCAAAAAT 58.706 39.130 0.00 0.00 0.00 1.82
2328 2393 3.322828 GCCGTGTAATCCCTACATCCTTA 59.677 47.826 0.00 0.00 42.50 2.69
2337 2402 0.252197 GGTTGAGCCGTGTAATCCCT 59.748 55.000 0.00 0.00 0.00 4.20
2361 2426 4.720046 TGGTACATACTTTGCAAGGTGAA 58.280 39.130 23.17 5.54 0.00 3.18
2441 2506 8.492415 AAATGCTATACAGGTCTAGGTCAATA 57.508 34.615 0.00 0.00 0.00 1.90
3305 3372 9.801873 CCCTTTAATGTCAAAACAATGTATAGG 57.198 33.333 0.00 0.00 39.30 2.57
3599 3666 2.762887 TGCTTCACATACCTCTCCTCTG 59.237 50.000 0.00 0.00 0.00 3.35
3657 3769 6.183309 AGAGAAGAAGAAAAACACACACAC 57.817 37.500 0.00 0.00 0.00 3.82
3727 3841 5.744171 TGCCTTCTACTTTGCATCATCTTA 58.256 37.500 0.00 0.00 0.00 2.10
3758 3872 4.378874 GGCTGCTTTGTATCAGTTTCAGTC 60.379 45.833 0.00 0.00 33.09 3.51
3788 3902 5.417580 TGCTGTCTAGTTGTTTTTGTTTCCT 59.582 36.000 0.00 0.00 0.00 3.36
3895 4011 0.751643 GTGTTGGCAGGTGTCAAGGT 60.752 55.000 0.00 0.00 40.68 3.50
3936 4052 4.719273 AGGAAAGGTTTTGGTGGATTTCAA 59.281 37.500 0.00 0.00 0.00 2.69
3939 4055 4.294347 TCAGGAAAGGTTTTGGTGGATTT 58.706 39.130 0.00 0.00 0.00 2.17
3982 4098 4.571984 TCATGCCAGTATCACAGAAAATCG 59.428 41.667 0.00 0.00 0.00 3.34
4038 4154 3.211045 TGAAGTTCTTTTGGGAAGACCG 58.789 45.455 4.17 0.00 44.64 4.79
4107 4239 1.210722 TCGTATTAATGTGGCCTGGCA 59.789 47.619 22.05 1.21 0.00 4.92
4162 4294 6.157862 TCTGGTCCAGGATATCATAGATGA 57.842 41.667 19.11 0.00 35.13 2.92
4170 4302 4.651503 TCACTCTTTCTGGTCCAGGATATC 59.348 45.833 19.11 0.00 31.51 1.63
4200 4332 4.724279 AGGTTGAAACAGGGTTCAGTAT 57.276 40.909 0.00 0.00 38.69 2.12
4237 4370 7.228507 TGCGATGTATCAGCTAAACCAATTATT 59.771 33.333 0.00 0.00 0.00 1.40
4305 4521 3.804036 TCGAACACAGTTGAACAAGGAT 58.196 40.909 0.00 0.00 0.00 3.24
4306 4522 3.194861 CTCGAACACAGTTGAACAAGGA 58.805 45.455 0.00 0.00 0.00 3.36
4566 4909 9.899661 ATACATATTACCTTGTAAACTTCAGCA 57.100 29.630 0.00 0.00 32.46 4.41
4594 4937 8.069574 GCATGCACTTTTAAGTTAAGCAAATTT 58.930 29.630 14.21 0.00 38.44 1.82
4597 4940 6.279882 AGCATGCACTTTTAAGTTAAGCAAA 58.720 32.000 21.98 0.00 38.44 3.68
4600 4943 6.769608 AAAGCATGCACTTTTAAGTTAAGC 57.230 33.333 21.98 0.00 36.47 3.09
4601 4944 8.579682 AGAAAAGCATGCACTTTTAAGTTAAG 57.420 30.769 21.98 0.00 46.99 1.85
4602 4945 8.940768 AAGAAAAGCATGCACTTTTAAGTTAA 57.059 26.923 21.98 0.00 46.99 2.01
4604 4947 8.817100 GTTAAGAAAAGCATGCACTTTTAAGTT 58.183 29.630 21.98 13.86 46.99 2.66
4606 4949 8.351495 TGTTAAGAAAAGCATGCACTTTTAAG 57.649 30.769 21.98 0.00 46.99 1.85
4778 5123 9.702494 TTGAAGATACATCTAAGTGATAGCATG 57.298 33.333 0.00 0.00 35.76 4.06
4818 5163 7.620880 ACTAAATGTTCTCCAGCAACATACTA 58.379 34.615 0.29 0.00 42.47 1.82
5015 5360 7.968956 GCTAGAATAAGGCTACTTTGGAAAAAC 59.031 37.037 0.00 0.00 38.14 2.43
5111 5461 4.617200 CCCAAGACCAGGGCAAAA 57.383 55.556 0.00 0.00 39.96 2.44
5121 5471 4.339814 AGACTCATCTAATCGACCCAAGAC 59.660 45.833 0.00 0.00 31.46 3.01
5168 5518 8.610248 TTACAATGCTAACTACACAGCTAAAA 57.390 30.769 0.00 0.00 38.63 1.52
5172 5522 4.631813 GCTTACAATGCTAACTACACAGCT 59.368 41.667 0.00 0.00 38.63 4.24
5191 5541 6.110411 ACAGAAAAGCACTTAGGTAGCTTA 57.890 37.500 12.57 0.00 46.95 3.09
5194 5544 4.315803 TGACAGAAAAGCACTTAGGTAGC 58.684 43.478 0.00 0.00 0.00 3.58
5305 5669 5.805486 GCAGATACGAGTGTTGAATAGTCAA 59.195 40.000 0.56 0.56 41.57 3.18
5306 5670 5.105917 TGCAGATACGAGTGTTGAATAGTCA 60.106 40.000 0.00 0.00 0.00 3.41
5307 5671 5.340803 TGCAGATACGAGTGTTGAATAGTC 58.659 41.667 0.00 0.00 0.00 2.59
5308 5672 5.324784 TGCAGATACGAGTGTTGAATAGT 57.675 39.130 0.00 0.00 0.00 2.12
5309 5673 6.834959 AATGCAGATACGAGTGTTGAATAG 57.165 37.500 0.00 0.00 0.00 1.73
5310 5674 6.816140 TCAAATGCAGATACGAGTGTTGAATA 59.184 34.615 0.00 0.00 0.00 1.75
5311 5675 5.643348 TCAAATGCAGATACGAGTGTTGAAT 59.357 36.000 0.00 0.00 0.00 2.57
5312 5676 4.994217 TCAAATGCAGATACGAGTGTTGAA 59.006 37.500 0.00 0.00 0.00 2.69
5313 5677 4.565022 TCAAATGCAGATACGAGTGTTGA 58.435 39.130 0.00 0.00 0.00 3.18
5314 5678 4.926860 TCAAATGCAGATACGAGTGTTG 57.073 40.909 0.00 0.00 0.00 3.33
5335 5893 7.393216 TGGCTACTAAATGCATTTCCAAATTT 58.607 30.769 27.28 5.42 0.00 1.82
5358 5916 4.457603 TGTTGTCCCGATCAAATAGTTTGG 59.542 41.667 2.92 0.00 40.98 3.28
5461 6019 5.883115 TGACACAAAAACATCCTTGTAGTCA 59.117 36.000 12.16 12.16 39.04 3.41
5533 6091 2.070783 CGGCTAAGCGTTTTGACCTTA 58.929 47.619 0.00 0.00 0.00 2.69
5535 6093 0.034337 TCGGCTAAGCGTTTTGACCT 59.966 50.000 0.00 0.00 0.00 3.85
5623 6182 2.128771 AGCGCAATACAGGTTCCAAT 57.871 45.000 11.47 0.00 0.00 3.16
5904 6465 4.214758 ACCGTTTCCCTTTACAAAATCGAG 59.785 41.667 0.00 0.00 0.00 4.04
5906 6467 4.492791 ACCGTTTCCCTTTACAAAATCG 57.507 40.909 0.00 0.00 0.00 3.34
5984 6545 2.124560 ACTCCCTCCCTCCCATAATG 57.875 55.000 0.00 0.00 0.00 1.90
5985 6546 4.526991 AATACTCCCTCCCTCCCATAAT 57.473 45.455 0.00 0.00 0.00 1.28
5986 6547 4.240323 GAAATACTCCCTCCCTCCCATAA 58.760 47.826 0.00 0.00 0.00 1.90
5987 6548 3.211232 TGAAATACTCCCTCCCTCCCATA 59.789 47.826 0.00 0.00 0.00 2.74
5989 6550 1.368203 TGAAATACTCCCTCCCTCCCA 59.632 52.381 0.00 0.00 0.00 4.37
6048 6690 3.138304 TGGAAGTCAACGTTGATTCCTG 58.862 45.455 37.69 18.73 40.94 3.86
6049 6691 3.485463 TGGAAGTCAACGTTGATTCCT 57.515 42.857 37.69 28.62 40.94 3.36
6073 6731 6.928520 AGCTTTGTTTTCTTATGGAATGGAG 58.071 36.000 0.00 0.00 33.53 3.86
6182 6840 2.047274 TTTCTTCTCCGCAGCCCG 60.047 61.111 0.00 0.00 0.00 6.13
6186 6844 5.862924 TTTGATTAGTTTCTTCTCCGCAG 57.137 39.130 0.00 0.00 0.00 5.18
6187 6845 5.354234 GGATTTGATTAGTTTCTTCTCCGCA 59.646 40.000 0.00 0.00 0.00 5.69
6201 6859 6.471233 ACGATGACTCTCTGGATTTGATTA 57.529 37.500 0.00 0.00 0.00 1.75
6293 6952 0.181587 TTGAGGTTGGCAAAGACGGA 59.818 50.000 0.00 0.00 0.00 4.69
6305 6964 2.430367 GCCACCGGAGTTGAGGTT 59.570 61.111 9.46 0.00 39.00 3.50
6306 6965 3.637273 GGCCACCGGAGTTGAGGT 61.637 66.667 9.46 0.00 42.34 3.85
6336 7004 1.296715 CGGTTGTGAAGGAGGAGGG 59.703 63.158 0.00 0.00 0.00 4.30
6454 7122 0.980423 GTCCTTCTCCTTCCAGCACT 59.020 55.000 0.00 0.00 0.00 4.40
6833 7502 1.043022 CTGGCCACAAAAAGGAAGCT 58.957 50.000 0.00 0.00 0.00 3.74
6837 7506 2.151502 TCAACTGGCCACAAAAAGGA 57.848 45.000 0.00 0.00 0.00 3.36
6840 7509 2.223688 CGTCATCAACTGGCCACAAAAA 60.224 45.455 0.00 0.00 0.00 1.94
6857 7533 0.457166 CCTCACGCCGTTAATCGTCA 60.457 55.000 0.00 0.00 36.73 4.35
6865 7541 0.672401 CATGTTACCCTCACGCCGTT 60.672 55.000 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.