Multiple sequence alignment - TraesCS2A01G045100

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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 TraesCS2A01G045100 chr2A 100.000 5617 0 0 1 5617 17742815 17737199 0.000000e+00 10373.0
1 TraesCS2A01G045100 chr2D 91.082 4250 179 80 626 4746 15734798 15730620 0.000000e+00 5565.0
2 TraesCS2A01G045100 chr2D 89.803 814 28 23 4776 5572 15730623 15729848 0.000000e+00 992.0
3 TraesCS2A01G045100 chr2D 93.669 537 16 5 1 523 15735558 15735026 0.000000e+00 787.0
4 TraesCS2A01G045100 chr2D 93.600 125 7 1 3430 3554 607600291 607600168 9.610000e-43 185.0
5 TraesCS2A01G045100 chr2D 85.039 127 19 0 1440 1566 160801416 160801290 4.570000e-26 130.0
6 TraesCS2A01G045100 chr2B 91.451 2433 110 40 2323 4662 27898299 27895872 0.000000e+00 3251.0
7 TraesCS2A01G045100 chr2B 86.322 987 54 44 701 1654 27899798 27898860 0.000000e+00 1000.0
8 TraesCS2A01G045100 chr2B 76.747 916 74 67 4675 5494 27895728 27894856 3.170000e-102 383.0
9 TraesCS2A01G045100 chr2B 82.891 339 33 13 1705 2034 27898842 27898520 1.190000e-71 281.0
10 TraesCS2A01G045100 chr2B 82.353 204 15 10 2088 2277 27898495 27898299 2.090000e-34 158.0
11 TraesCS2A01G045100 chr1B 78.426 686 53 54 1705 2366 50129518 50128904 5.350000e-95 359.0
12 TraesCS2A01G045100 chr1B 89.177 231 21 2 3324 3554 83213094 83212868 9.210000e-73 285.0
13 TraesCS2A01G045100 chr1B 92.523 107 3 5 1535 1639 50129639 50129536 1.260000e-31 148.0
14 TraesCS2A01G045100 chr1B 93.750 96 4 2 3188 3283 83213183 83213090 5.870000e-30 143.0
15 TraesCS2A01G045100 chr1B 82.099 162 17 6 3824 3985 83212832 83212683 1.640000e-25 128.0
16 TraesCS2A01G045100 chr1B 89.655 58 2 1 4310 4367 83212671 83212618 2.810000e-08 71.3
17 TraesCS2A01G045100 chr5B 78.240 625 44 45 4678 5247 325918038 325918625 3.270000e-82 316.0
18 TraesCS2A01G045100 chr5B 87.931 116 13 1 4023 4137 319313590 319313705 9.820000e-28 135.0
19 TraesCS2A01G045100 chr5B 84.375 96 11 3 2678 2773 13377725 13377816 2.160000e-14 91.6
20 TraesCS2A01G045100 chrUn 89.140 221 21 3 266 484 171049248 171049467 7.170000e-69 272.0
21 TraesCS2A01G045100 chrUn 88.636 220 24 1 266 484 189398003 189398222 3.340000e-67 267.0
22 TraesCS2A01G045100 chr6D 88.636 220 24 1 266 484 124523043 124523262 3.340000e-67 267.0
23 TraesCS2A01G045100 chr4D 88.636 220 24 1 266 484 398041402 398041183 3.340000e-67 267.0
24 TraesCS2A01G045100 chr4D 87.069 232 29 1 266 496 241278881 241278650 1.550000e-65 261.0
25 TraesCS2A01G045100 chr3B 87.500 232 28 1 266 496 368735730 368735961 3.340000e-67 267.0
26 TraesCS2A01G045100 chr3B 81.212 165 24 5 3239 3399 127309194 127309355 5.910000e-25 126.0
27 TraesCS2A01G045100 chr3B 92.157 51 4 0 3061 3111 143573203 143573153 7.810000e-09 73.1
28 TraesCS2A01G045100 chr1D 88.636 220 24 1 266 484 185774916 185775135 3.340000e-67 267.0
29 TraesCS2A01G045100 chr1D 88.636 220 24 1 266 484 351008704 351008485 3.340000e-67 267.0
30 TraesCS2A01G045100 chr5A 91.870 123 10 0 4001 4123 367753951 367754073 7.480000e-39 172.0
31 TraesCS2A01G045100 chr5A 91.200 125 11 0 3999 4123 367753838 367753962 2.690000e-38 171.0
32 TraesCS2A01G045100 chr7A 85.039 127 19 0 1440 1566 172420029 172419903 4.570000e-26 130.0
33 TraesCS2A01G045100 chr6A 83.465 127 21 0 1440 1566 523827010 523827136 9.890000e-23 119.0
34 TraesCS2A01G045100 chr3D 95.556 45 2 0 3061 3105 92868701 92868745 7.810000e-09 73.1
35 TraesCS2A01G045100 chr3D 95.556 45 2 0 3061 3105 92880260 92880304 7.810000e-09 73.1
36 TraesCS2A01G045100 chr7D 91.667 48 4 0 3236 3283 523826456 523826503 3.630000e-07 67.6
37 TraesCS2A01G045100 chr7B 100.000 28 0 0 5077 5104 219622038 219622065 1.000000e-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 TraesCS2A01G045100 chr2A 17737199 17742815 5616 True 10373.0 10373 100.0000 1 5617 1 chr2A.!!$R1 5616
1 TraesCS2A01G045100 chr2D 15729848 15735558 5710 True 2448.0 5565 91.5180 1 5572 3 chr2D.!!$R3 5571
2 TraesCS2A01G045100 chr2B 27894856 27899798 4942 True 1014.6 3251 83.9528 701 5494 5 chr2B.!!$R1 4793
3 TraesCS2A01G045100 chr1B 50128904 50129639 735 True 253.5 359 85.4745 1535 2366 2 chr1B.!!$R1 831
4 TraesCS2A01G045100 chr5B 325918038 325918625 587 False 316.0 316 78.2400 4678 5247 1 chr5B.!!$F3 569

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
551 566 0.037882 CAAGAGACTCGCAGGCAAGA 60.038 55.000 0.00 0.00 0.00 3.02 F
1595 1787 0.104356 TCCTCCCCACCAAGGTAACA 60.104 55.000 0.00 0.00 41.41 2.41 F
1700 1899 0.043053 CGAATGCAGCACGATTACCG 60.043 55.000 0.00 0.00 45.44 4.02 F
1955 2170 0.109532 TCCGTGCCACCTTTTCATCA 59.890 50.000 0.00 0.00 0.00 3.07 F
2053 2268 0.684479 TCCATGGACACCGGAGAGAG 60.684 60.000 11.44 0.00 0.00 3.20 F
2238 2503 0.824109 AGTTGCTTCGGATCGGATCA 59.176 50.000 18.99 3.15 0.00 2.92 F
2451 2765 0.944386 GTTTTCTCTTGCAGGCACGA 59.056 50.000 0.00 0.00 0.00 4.35 F
2691 3005 1.674651 CAGGACCTCCGACGACTCA 60.675 63.158 0.00 0.00 42.08 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1841 0.106419 GGGACTGACTCGAGGAGGAT 60.106 60.000 18.41 0.0 33.35 3.24 R
3060 3389 0.536915 GCAGCTTCTCCCCCATCATC 60.537 60.000 0.00 0.0 0.00 2.92 R
3135 3464 1.066587 GAAGGCGACGATGGAGAGG 59.933 63.158 0.00 0.0 0.00 3.69 R
3918 4271 1.950973 GCGAGGAGGTGGAGGAGTTC 61.951 65.000 0.00 0.0 0.00 3.01 R
3919 4272 1.985116 GCGAGGAGGTGGAGGAGTT 60.985 63.158 0.00 0.0 0.00 3.01 R
3922 4275 2.363018 CTGCGAGGAGGTGGAGGA 60.363 66.667 0.00 0.0 0.00 3.71 R
4358 4717 1.467035 GCTCGTTACAGATCGACCGTT 60.467 52.381 0.00 0.0 32.65 4.44 R
4631 5030 0.240945 GGACCATTCAACCACAAGCG 59.759 55.000 0.00 0.0 0.00 4.68 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
116 117 1.276421 AGACGTGATTGAGTTGGGGAG 59.724 52.381 0.00 0.00 0.00 4.30
119 120 1.276421 CGTGATTGAGTTGGGGAGTCT 59.724 52.381 0.00 0.00 0.00 3.24
141 142 6.823689 GTCTGAAATCCCATTACATGTGTAGT 59.176 38.462 9.11 0.00 0.00 2.73
145 146 7.551262 TGAAATCCCATTACATGTGTAGTGTAC 59.449 37.037 9.11 0.00 36.77 2.90
162 163 5.726397 AGTGTACCGCTCATAACATTACAA 58.274 37.500 0.00 0.00 0.00 2.41
173 174 7.645340 GCTCATAACATTACAAATCAAATCGCT 59.355 33.333 0.00 0.00 0.00 4.93
182 183 1.386533 ATCAAATCGCTGAGGGCTTG 58.613 50.000 0.00 0.00 39.13 4.01
183 184 1.138247 CAAATCGCTGAGGGCTTGC 59.862 57.895 0.00 0.00 39.13 4.01
184 185 1.001641 AAATCGCTGAGGGCTTGCT 60.002 52.632 0.00 0.00 39.13 3.91
185 186 0.610232 AAATCGCTGAGGGCTTGCTT 60.610 50.000 0.00 0.00 39.13 3.91
265 267 0.390866 ACCGTAGCTCTCGTCGAGAA 60.391 55.000 24.29 8.62 42.62 2.87
310 312 0.673644 GTGAGACGGAACACCCATGG 60.674 60.000 4.14 4.14 34.14 3.66
366 368 5.598005 TGTGTCCAGAAAAAGATCCAAACAT 59.402 36.000 0.00 0.00 0.00 2.71
380 382 7.861629 AGATCCAAACATGTAAGAATCTACCA 58.138 34.615 0.00 0.00 0.00 3.25
388 390 8.668510 ACATGTAAGAATCTACCATAAAGCAG 57.331 34.615 0.00 0.00 0.00 4.24
412 414 4.032558 GGTTTCTACTCGTTATTGCTTCCG 59.967 45.833 0.00 0.00 0.00 4.30
416 418 1.436983 CTCGTTATTGCTTCCGCCCC 61.437 60.000 0.00 0.00 34.43 5.80
418 420 1.101049 CGTTATTGCTTCCGCCCCAT 61.101 55.000 0.00 0.00 34.43 4.00
502 517 2.044860 GCGTGGATAATCTTCGTCGAG 58.955 52.381 0.00 0.00 0.00 4.04
523 538 6.362551 TCGAGAAGAGACTTGTATTGAAAACG 59.637 38.462 0.00 0.00 0.00 3.60
524 539 6.362551 CGAGAAGAGACTTGTATTGAAAACGA 59.637 38.462 0.00 0.00 0.00 3.85
525 540 7.409874 CGAGAAGAGACTTGTATTGAAAACGAG 60.410 40.741 0.00 0.00 34.94 4.18
526 541 7.434492 AGAAGAGACTTGTATTGAAAACGAGA 58.566 34.615 0.00 0.00 33.33 4.04
527 542 7.926555 AGAAGAGACTTGTATTGAAAACGAGAA 59.073 33.333 0.00 0.00 33.33 2.87
528 543 8.433421 AAGAGACTTGTATTGAAAACGAGAAA 57.567 30.769 0.00 0.00 33.33 2.52
529 544 7.852516 AGAGACTTGTATTGAAAACGAGAAAC 58.147 34.615 0.00 0.00 33.33 2.78
531 546 6.477688 AGACTTGTATTGAAAACGAGAAACGA 59.522 34.615 0.00 0.00 45.77 3.85
532 547 6.416514 ACTTGTATTGAAAACGAGAAACGAC 58.583 36.000 0.00 0.00 45.77 4.34
533 548 5.970140 TGTATTGAAAACGAGAAACGACA 57.030 34.783 0.00 0.00 45.77 4.35
534 549 6.347270 TGTATTGAAAACGAGAAACGACAA 57.653 33.333 0.00 0.00 45.77 3.18
535 550 6.415702 TGTATTGAAAACGAGAAACGACAAG 58.584 36.000 0.00 0.00 45.77 3.16
536 551 5.728351 ATTGAAAACGAGAAACGACAAGA 57.272 34.783 0.00 0.00 45.77 3.02
537 552 4.772046 TGAAAACGAGAAACGACAAGAG 57.228 40.909 0.00 0.00 45.77 2.85
538 553 4.426416 TGAAAACGAGAAACGACAAGAGA 58.574 39.130 0.00 0.00 45.77 3.10
539 554 4.266976 TGAAAACGAGAAACGACAAGAGAC 59.733 41.667 0.00 0.00 45.77 3.36
540 555 3.712091 AACGAGAAACGACAAGAGACT 57.288 42.857 0.00 0.00 45.77 3.24
541 556 3.270962 ACGAGAAACGACAAGAGACTC 57.729 47.619 0.00 0.00 45.77 3.36
542 557 2.235020 CGAGAAACGACAAGAGACTCG 58.765 52.381 0.00 0.00 45.77 4.18
543 558 1.980156 GAGAAACGACAAGAGACTCGC 59.020 52.381 0.00 0.00 32.98 5.03
544 559 1.337071 AGAAACGACAAGAGACTCGCA 59.663 47.619 0.00 0.00 32.98 5.10
545 560 1.716581 GAAACGACAAGAGACTCGCAG 59.283 52.381 0.00 0.00 32.98 5.18
546 561 0.039074 AACGACAAGAGACTCGCAGG 60.039 55.000 0.00 0.00 32.98 4.85
547 562 1.803519 CGACAAGAGACTCGCAGGC 60.804 63.158 0.00 0.00 0.00 4.85
548 563 1.290324 GACAAGAGACTCGCAGGCA 59.710 57.895 0.00 0.00 0.00 4.75
549 564 0.319900 GACAAGAGACTCGCAGGCAA 60.320 55.000 0.00 0.00 0.00 4.52
550 565 0.320247 ACAAGAGACTCGCAGGCAAG 60.320 55.000 0.00 0.00 0.00 4.01
551 566 0.037882 CAAGAGACTCGCAGGCAAGA 60.038 55.000 0.00 0.00 0.00 3.02
552 567 0.246086 AAGAGACTCGCAGGCAAGAG 59.754 55.000 0.00 3.00 40.16 2.85
553 568 0.610509 AGAGACTCGCAGGCAAGAGA 60.611 55.000 10.14 0.00 37.87 3.10
554 569 0.459489 GAGACTCGCAGGCAAGAGAT 59.541 55.000 10.14 0.23 37.87 2.75
555 570 0.459489 AGACTCGCAGGCAAGAGATC 59.541 55.000 10.14 0.00 37.87 2.75
556 571 0.174389 GACTCGCAGGCAAGAGATCA 59.826 55.000 10.14 0.00 37.87 2.92
557 572 0.829333 ACTCGCAGGCAAGAGATCAT 59.171 50.000 10.14 0.00 37.87 2.45
558 573 2.034878 ACTCGCAGGCAAGAGATCATA 58.965 47.619 10.14 0.00 37.87 2.15
559 574 2.432146 ACTCGCAGGCAAGAGATCATAA 59.568 45.455 10.14 0.00 37.87 1.90
560 575 3.118629 ACTCGCAGGCAAGAGATCATAAA 60.119 43.478 10.14 0.00 37.87 1.40
561 576 3.198068 TCGCAGGCAAGAGATCATAAAC 58.802 45.455 0.00 0.00 0.00 2.01
562 577 2.289002 CGCAGGCAAGAGATCATAAACC 59.711 50.000 0.00 0.00 0.00 3.27
563 578 2.620585 GCAGGCAAGAGATCATAAACCC 59.379 50.000 0.00 0.00 0.00 4.11
564 579 3.217626 CAGGCAAGAGATCATAAACCCC 58.782 50.000 0.00 0.00 0.00 4.95
565 580 2.175715 AGGCAAGAGATCATAAACCCCC 59.824 50.000 0.00 0.00 0.00 5.40
587 602 3.391382 CCTCCTCCCCACACCGTC 61.391 72.222 0.00 0.00 0.00 4.79
588 603 3.760035 CTCCTCCCCACACCGTCG 61.760 72.222 0.00 0.00 0.00 5.12
591 606 3.760035 CTCCCCACACCGTCGGAG 61.760 72.222 20.51 13.51 36.23 4.63
592 607 4.608774 TCCCCACACCGTCGGAGT 62.609 66.667 20.51 14.32 0.00 3.85
593 608 3.622826 CCCCACACCGTCGGAGTT 61.623 66.667 20.51 0.00 0.00 3.01
594 609 2.357034 CCCACACCGTCGGAGTTG 60.357 66.667 20.51 12.21 0.00 3.16
595 610 2.420043 CCACACCGTCGGAGTTGT 59.580 61.111 20.51 9.42 0.00 3.32
596 611 1.954146 CCACACCGTCGGAGTTGTG 60.954 63.158 20.51 20.76 34.92 3.33
597 612 1.954146 CACACCGTCGGAGTTGTGG 60.954 63.158 20.51 0.00 33.07 4.17
598 613 3.041940 CACCGTCGGAGTTGTGGC 61.042 66.667 20.51 0.00 0.00 5.01
599 614 4.309950 ACCGTCGGAGTTGTGGCC 62.310 66.667 20.51 0.00 0.00 5.36
604 619 2.897207 CGGAGTTGTGGCCGGATA 59.103 61.111 5.05 0.00 43.67 2.59
605 620 1.219664 CGGAGTTGTGGCCGGATAA 59.780 57.895 5.05 0.00 43.67 1.75
606 621 0.810031 CGGAGTTGTGGCCGGATAAG 60.810 60.000 5.05 0.00 43.67 1.73
607 622 0.463833 GGAGTTGTGGCCGGATAAGG 60.464 60.000 5.05 0.00 0.00 2.69
608 623 0.463833 GAGTTGTGGCCGGATAAGGG 60.464 60.000 5.05 0.00 0.00 3.95
609 624 1.453197 GTTGTGGCCGGATAAGGGG 60.453 63.158 5.05 0.00 0.00 4.79
610 625 1.616930 TTGTGGCCGGATAAGGGGA 60.617 57.895 5.05 0.00 0.00 4.81
611 626 1.208844 TTGTGGCCGGATAAGGGGAA 61.209 55.000 5.05 0.00 0.00 3.97
612 627 1.148498 GTGGCCGGATAAGGGGAAG 59.852 63.158 5.05 0.00 0.00 3.46
613 628 1.003704 TGGCCGGATAAGGGGAAGA 59.996 57.895 5.05 0.00 0.00 2.87
614 629 0.622154 TGGCCGGATAAGGGGAAGAA 60.622 55.000 5.05 0.00 0.00 2.52
615 630 0.179026 GGCCGGATAAGGGGAAGAAC 60.179 60.000 5.05 0.00 0.00 3.01
616 631 0.532196 GCCGGATAAGGGGAAGAACG 60.532 60.000 5.05 0.00 0.00 3.95
617 632 0.106149 CCGGATAAGGGGAAGAACGG 59.894 60.000 0.00 0.00 0.00 4.44
618 633 1.117150 CGGATAAGGGGAAGAACGGA 58.883 55.000 0.00 0.00 0.00 4.69
619 634 1.068741 CGGATAAGGGGAAGAACGGAG 59.931 57.143 0.00 0.00 0.00 4.63
620 635 1.202663 GGATAAGGGGAAGAACGGAGC 60.203 57.143 0.00 0.00 0.00 4.70
621 636 0.464452 ATAAGGGGAAGAACGGAGCG 59.536 55.000 0.00 0.00 0.00 5.03
622 637 1.610554 TAAGGGGAAGAACGGAGCGG 61.611 60.000 0.00 0.00 0.00 5.52
623 638 4.468689 GGGGAAGAACGGAGCGGG 62.469 72.222 0.00 0.00 0.00 6.13
624 639 4.468689 GGGAAGAACGGAGCGGGG 62.469 72.222 0.00 0.00 0.00 5.73
780 921 6.978080 GTGTTCAAAAGAGGAGCAACAAATTA 59.022 34.615 0.00 0.00 0.00 1.40
781 922 6.978080 TGTTCAAAAGAGGAGCAACAAATTAC 59.022 34.615 0.00 0.00 0.00 1.89
782 923 6.959639 TCAAAAGAGGAGCAACAAATTACT 57.040 33.333 0.00 0.00 0.00 2.24
811 952 2.360475 GAGGTGCAGGAAGTGGGC 60.360 66.667 0.00 0.00 0.00 5.36
840 981 2.031516 CGTGGCAAGTGAGCTCAGG 61.032 63.158 18.89 11.10 34.17 3.86
842 983 2.149383 TGGCAAGTGAGCTCAGGGT 61.149 57.895 18.89 1.42 34.17 4.34
847 988 0.901124 AAGTGAGCTCAGGGTAGCAG 59.099 55.000 18.89 0.00 45.30 4.24
916 1064 4.082190 TGACGAGCAGCACTAAATTACTCT 60.082 41.667 0.00 0.00 0.00 3.24
938 1086 0.596083 CATGGAAGCTCGCTCGTAGG 60.596 60.000 0.00 0.00 0.00 3.18
940 1088 2.278923 GAAGCTCGCTCGTAGGCC 60.279 66.667 0.00 0.00 0.00 5.19
941 1089 4.194720 AAGCTCGCTCGTAGGCCG 62.195 66.667 0.00 0.00 38.13 6.13
1141 1327 1.077334 TCTTTCTCTCCCCGGAGACTT 59.923 52.381 9.47 0.00 45.26 3.01
1155 1341 1.601759 GACTTTGAGCCAGCCAGCA 60.602 57.895 0.00 0.00 34.23 4.41
1156 1342 1.584380 GACTTTGAGCCAGCCAGCAG 61.584 60.000 0.00 0.00 34.23 4.24
1158 1344 2.759641 CTTTGAGCCAGCCAGCAGGA 62.760 60.000 5.10 0.00 36.89 3.86
1159 1345 3.557903 TTGAGCCAGCCAGCAGGAC 62.558 63.158 5.10 0.00 36.89 3.85
1160 1346 4.792804 GAGCCAGCCAGCAGGACC 62.793 72.222 5.10 0.00 36.89 4.46
1167 1353 2.579201 CCAGCAGGACCACGGTAG 59.421 66.667 0.00 0.00 36.89 3.18
1373 1559 1.604378 CTTCTTCTCCGGCATGGGT 59.396 57.895 0.00 0.00 38.76 4.51
1595 1787 0.104356 TCCTCCCCACCAAGGTAACA 60.104 55.000 0.00 0.00 41.41 2.41
1597 1789 0.322546 CTCCCCACCAAGGTAACAGC 60.323 60.000 0.00 0.00 41.41 4.40
1598 1790 1.304134 CCCCACCAAGGTAACAGCC 60.304 63.158 0.00 0.00 41.41 4.85
1599 1791 1.674322 CCCACCAAGGTAACAGCCG 60.674 63.158 0.00 0.00 41.41 5.52
1600 1792 1.373435 CCACCAAGGTAACAGCCGA 59.627 57.895 0.00 0.00 41.41 5.54
1601 1793 0.953960 CCACCAAGGTAACAGCCGAC 60.954 60.000 0.00 0.00 41.41 4.79
1638 1832 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
1647 1841 2.038975 CCTCCCTCCCCGTCTTCA 59.961 66.667 0.00 0.00 0.00 3.02
1656 1850 1.736586 CCCGTCTTCATCCTCCTCG 59.263 63.158 0.00 0.00 0.00 4.63
1698 1897 0.304705 CCCGAATGCAGCACGATTAC 59.695 55.000 6.97 0.00 0.00 1.89
1699 1898 0.304705 CCGAATGCAGCACGATTACC 59.695 55.000 6.97 0.00 0.00 2.85
1700 1899 0.043053 CGAATGCAGCACGATTACCG 60.043 55.000 0.00 0.00 45.44 4.02
1776 1975 0.915364 ATTTCCCAGTGGAGGAGAGC 59.085 55.000 11.95 0.00 43.07 4.09
1778 1977 0.252881 TTCCCAGTGGAGGAGAGCAT 60.253 55.000 11.95 0.00 43.07 3.79
1797 2007 1.391577 TGGGATCAATCATTGCCACG 58.608 50.000 0.00 0.00 0.00 4.94
1902 2112 1.970917 CTAACGGCAGCAGCTTTCCG 61.971 60.000 24.35 24.35 46.61 4.30
1916 2126 0.909623 TTTCCGATCCCCACTTCTCC 59.090 55.000 0.00 0.00 0.00 3.71
1955 2170 0.109532 TCCGTGCCACCTTTTCATCA 59.890 50.000 0.00 0.00 0.00 3.07
2002 2217 1.192793 GACGAGATCTTCTTTCGGCG 58.807 55.000 0.00 0.00 38.58 6.46
2043 2258 5.136828 ACACTACAAACAAATCCATGGACA 58.863 37.500 18.99 0.00 0.00 4.02
2053 2268 0.684479 TCCATGGACACCGGAGAGAG 60.684 60.000 11.44 0.00 0.00 3.20
2120 2371 4.539726 CAATCTCATCATTTGGGGGAAGA 58.460 43.478 0.00 0.00 0.00 2.87
2122 2373 4.240881 TCTCATCATTTGGGGGAAGAAG 57.759 45.455 0.00 0.00 0.00 2.85
2163 2419 2.868583 CAATCGTGCGATGGAAGAAGAT 59.131 45.455 7.89 0.00 34.70 2.40
2168 2427 1.139654 TGCGATGGAAGAAGATGAGGG 59.860 52.381 0.00 0.00 0.00 4.30
2184 2444 1.003696 GAGGGTAAAAGGCTGCTCTGT 59.996 52.381 0.00 0.00 0.00 3.41
2186 2446 2.158460 AGGGTAAAAGGCTGCTCTGTTT 60.158 45.455 0.00 0.00 0.00 2.83
2187 2447 3.073946 AGGGTAAAAGGCTGCTCTGTTTA 59.926 43.478 0.00 0.00 0.00 2.01
2190 2450 2.959465 AAAGGCTGCTCTGTTTACCT 57.041 45.000 0.00 0.00 0.00 3.08
2192 2452 2.959465 AGGCTGCTCTGTTTACCTTT 57.041 45.000 0.00 0.00 0.00 3.11
2193 2453 4.367039 AAGGCTGCTCTGTTTACCTTTA 57.633 40.909 0.00 0.00 33.82 1.85
2196 2456 6.062258 AGGCTGCTCTGTTTACCTTTATTA 57.938 37.500 0.00 0.00 0.00 0.98
2237 2502 1.941325 AAGTTGCTTCGGATCGGATC 58.059 50.000 9.54 9.54 0.00 3.36
2238 2503 0.824109 AGTTGCTTCGGATCGGATCA 59.176 50.000 18.99 3.15 0.00 2.92
2239 2504 1.202463 AGTTGCTTCGGATCGGATCAG 60.202 52.381 18.99 15.15 0.00 2.90
2240 2505 1.111277 TTGCTTCGGATCGGATCAGA 58.889 50.000 18.99 17.18 0.00 3.27
2241 2506 1.111277 TGCTTCGGATCGGATCAGAA 58.889 50.000 25.06 25.06 40.35 3.02
2274 2550 3.565764 ATCCCGATTCTGATTTGAGCA 57.434 42.857 0.00 0.00 0.00 4.26
2275 2551 2.910199 TCCCGATTCTGATTTGAGCAG 58.090 47.619 0.00 0.00 34.71 4.24
2276 2552 1.332997 CCCGATTCTGATTTGAGCAGC 59.667 52.381 0.00 0.00 33.45 5.25
2296 2572 4.096231 CAGCAACCGTCCAATGATTCAATA 59.904 41.667 0.00 0.00 0.00 1.90
2298 2574 4.587306 CAACCGTCCAATGATTCAATACG 58.413 43.478 0.00 0.00 0.00 3.06
2299 2575 2.612212 ACCGTCCAATGATTCAATACGC 59.388 45.455 0.00 0.00 0.00 4.42
2302 2578 4.457810 CGTCCAATGATTCAATACGCATC 58.542 43.478 0.00 0.00 0.00 3.91
2345 2634 3.180613 GCCCAAAAAGAACGAACGAAAA 58.819 40.909 0.14 0.00 0.00 2.29
2367 2656 1.839994 TCTTTTCCTCATCCCGATGCT 59.160 47.619 0.00 0.00 38.65 3.79
2368 2657 2.158900 TCTTTTCCTCATCCCGATGCTC 60.159 50.000 0.00 0.00 38.65 4.26
2407 2706 6.469782 TTTTCATGGAAAGTGCTCTTCTTT 57.530 33.333 0.74 0.00 37.75 2.52
2411 2710 5.593909 TCATGGAAAGTGCTCTTCTTTTTCA 59.406 36.000 0.74 0.00 35.62 2.69
2451 2765 0.944386 GTTTTCTCTTGCAGGCACGA 59.056 50.000 0.00 0.00 0.00 4.35
2691 3005 1.674651 CAGGACCTCCGACGACTCA 60.675 63.158 0.00 0.00 42.08 3.41
2724 3041 4.980805 GTGACGACCAAGGCCGCA 62.981 66.667 0.00 0.00 0.00 5.69
2838 3155 4.808238 GACGACGACGAGGGCGAC 62.808 72.222 15.32 2.84 42.66 5.19
3060 3389 4.087892 CTGGACGTGAGCCAGGGG 62.088 72.222 12.81 0.00 45.50 4.79
3321 3653 2.074967 CAAGGCCACCAAGGTCCTA 58.925 57.895 5.01 0.00 45.84 2.94
3969 4328 2.028484 GACCTGTTCGTGGCGACA 59.972 61.111 0.00 0.00 34.89 4.35
4173 4532 3.310860 GACGCCAACATCCCGGTCT 62.311 63.158 0.00 0.00 0.00 3.85
4227 4586 4.851214 GGCGGAGGAGGAGGAGCT 62.851 72.222 0.00 0.00 0.00 4.09
4308 4667 1.753930 TCATGCGCAAGTCCATGAAT 58.246 45.000 17.11 0.00 43.34 2.57
4585 4984 7.664318 TCCTTTCCTTCTTGTTAATTACTCCAC 59.336 37.037 0.00 0.00 0.00 4.02
4724 5266 6.541934 TCCAGCATAGATAGATGGATGAAG 57.458 41.667 0.00 0.00 45.80 3.02
4743 5285 5.736040 GAAGCATTCGTTGAATCAAGTTG 57.264 39.130 0.00 0.00 34.17 3.16
4744 5286 3.568538 AGCATTCGTTGAATCAAGTTGC 58.431 40.909 0.00 3.83 28.87 4.17
4745 5287 3.004629 AGCATTCGTTGAATCAAGTTGCA 59.995 39.130 16.31 0.00 28.87 4.08
4746 5288 3.362831 GCATTCGTTGAATCAAGTTGCAG 59.637 43.478 0.00 0.00 28.87 4.41
4747 5289 4.539870 CATTCGTTGAATCAAGTTGCAGT 58.460 39.130 0.00 0.00 28.87 4.40
4748 5290 3.878086 TCGTTGAATCAAGTTGCAGTC 57.122 42.857 0.00 0.00 0.00 3.51
4749 5291 2.548057 TCGTTGAATCAAGTTGCAGTCC 59.452 45.455 0.00 0.00 0.00 3.85
4750 5292 2.290367 CGTTGAATCAAGTTGCAGTCCA 59.710 45.455 0.00 0.00 0.00 4.02
4751 5293 3.607775 CGTTGAATCAAGTTGCAGTCCAG 60.608 47.826 0.00 0.00 0.00 3.86
4752 5294 2.507484 TGAATCAAGTTGCAGTCCAGG 58.493 47.619 0.00 0.00 0.00 4.45
4753 5295 2.106338 TGAATCAAGTTGCAGTCCAGGA 59.894 45.455 0.00 0.00 0.00 3.86
4754 5296 2.486472 ATCAAGTTGCAGTCCAGGAG 57.514 50.000 0.00 0.00 0.00 3.69
4755 5297 1.423584 TCAAGTTGCAGTCCAGGAGA 58.576 50.000 0.00 0.00 0.00 3.71
4756 5298 1.768275 TCAAGTTGCAGTCCAGGAGAA 59.232 47.619 0.00 0.00 0.00 2.87
4757 5299 2.149578 CAAGTTGCAGTCCAGGAGAAG 58.850 52.381 0.00 0.00 0.00 2.85
4758 5300 0.036022 AGTTGCAGTCCAGGAGAAGC 59.964 55.000 0.00 0.00 0.00 3.86
4759 5301 0.036022 GTTGCAGTCCAGGAGAAGCT 59.964 55.000 8.69 0.00 0.00 3.74
4760 5302 0.322975 TTGCAGTCCAGGAGAAGCTC 59.677 55.000 8.69 0.00 0.00 4.09
4761 5303 0.543883 TGCAGTCCAGGAGAAGCTCT 60.544 55.000 8.69 0.00 0.00 4.09
4762 5304 0.175531 GCAGTCCAGGAGAAGCTCTC 59.824 60.000 0.00 0.00 42.66 3.20
4763 5305 1.851304 CAGTCCAGGAGAAGCTCTCT 58.149 55.000 11.38 5.82 42.95 3.10
4769 5311 4.804496 GAGAAGCTCTCTCCGCAC 57.196 61.111 12.34 0.00 44.39 5.34
4770 5312 2.188912 GAGAAGCTCTCTCCGCACT 58.811 57.895 12.34 0.00 44.39 4.40
4771 5313 0.179140 GAGAAGCTCTCTCCGCACTG 60.179 60.000 12.34 0.00 44.39 3.66
4772 5314 1.809209 GAAGCTCTCTCCGCACTGC 60.809 63.158 0.00 0.00 0.00 4.40
4773 5315 2.498291 GAAGCTCTCTCCGCACTGCA 62.498 60.000 1.11 0.00 0.00 4.41
4774 5316 2.778309 AAGCTCTCTCCGCACTGCAC 62.778 60.000 1.11 0.00 0.00 4.57
4802 5372 5.362430 ACCATACACCAATTTCACTGTTGTT 59.638 36.000 0.00 0.00 0.00 2.83
4803 5373 5.691305 CCATACACCAATTTCACTGTTGTTG 59.309 40.000 0.00 0.00 0.00 3.33
4804 5374 4.122143 ACACCAATTTCACTGTTGTTGG 57.878 40.909 0.00 0.00 43.75 3.77
4805 5375 2.865551 CACCAATTTCACTGTTGTTGGC 59.134 45.455 2.57 0.00 42.31 4.52
4806 5376 2.765699 ACCAATTTCACTGTTGTTGGCT 59.234 40.909 2.57 0.00 42.31 4.75
4807 5377 3.125316 CCAATTTCACTGTTGTTGGCTG 58.875 45.455 0.00 0.00 33.66 4.85
4808 5378 3.181477 CCAATTTCACTGTTGTTGGCTGA 60.181 43.478 0.00 0.00 33.66 4.26
4811 5381 1.608055 TCACTGTTGTTGGCTGATGG 58.392 50.000 0.00 0.00 0.00 3.51
4819 5389 0.598065 GTTGGCTGATGGTGGTTGTC 59.402 55.000 0.00 0.00 0.00 3.18
4838 5412 3.579586 TGTCGATCATCCATCCATCATCA 59.420 43.478 0.00 0.00 0.00 3.07
4839 5413 4.182339 GTCGATCATCCATCCATCATCAG 58.818 47.826 0.00 0.00 0.00 2.90
4840 5414 2.937149 CGATCATCCATCCATCATCAGC 59.063 50.000 0.00 0.00 0.00 4.26
4842 5416 3.697619 TCATCCATCCATCATCAGCTC 57.302 47.619 0.00 0.00 0.00 4.09
4844 5418 3.008049 TCATCCATCCATCATCAGCTCTG 59.992 47.826 0.00 0.00 0.00 3.35
4845 5419 1.071857 TCCATCCATCATCAGCTCTGC 59.928 52.381 0.00 0.00 0.00 4.26
4875 5449 1.423845 CGTTACAGTCGGCCAATGC 59.576 57.895 2.24 0.00 0.00 3.56
4918 5502 3.716195 CCTGGTGGGTGCCGATCA 61.716 66.667 0.00 0.00 0.00 2.92
4919 5503 2.124983 CTGGTGGGTGCCGATCAG 60.125 66.667 0.00 0.00 0.00 2.90
4920 5504 2.606213 TGGTGGGTGCCGATCAGA 60.606 61.111 0.00 0.00 0.00 3.27
4950 5534 4.832248 ACCTGAACTACCACACATACATG 58.168 43.478 0.00 0.00 0.00 3.21
4951 5535 3.623060 CCTGAACTACCACACATACATGC 59.377 47.826 0.00 0.00 0.00 4.06
4952 5536 4.507710 CTGAACTACCACACATACATGCT 58.492 43.478 0.00 0.00 0.00 3.79
4953 5537 4.503910 TGAACTACCACACATACATGCTC 58.496 43.478 0.00 0.00 0.00 4.26
4954 5538 4.222810 TGAACTACCACACATACATGCTCT 59.777 41.667 0.00 0.00 0.00 4.09
4955 5539 4.128925 ACTACCACACATACATGCTCTG 57.871 45.455 0.00 0.00 0.00 3.35
4975 5576 4.421515 CCTGACCCTGGCCTGCAG 62.422 72.222 6.78 6.78 0.00 4.41
5030 5651 2.674852 CAAAGTGATGGTGAGTGATCCG 59.325 50.000 0.00 0.00 0.00 4.18
5077 5724 3.005684 TGTGCTTTGCATTAGGGTCAAAG 59.994 43.478 8.96 8.96 45.56 2.77
5078 5725 3.255642 GTGCTTTGCATTAGGGTCAAAGA 59.744 43.478 15.51 1.72 45.61 2.52
5079 5726 4.082026 GTGCTTTGCATTAGGGTCAAAGAT 60.082 41.667 15.51 0.00 45.61 2.40
5080 5727 5.125417 GTGCTTTGCATTAGGGTCAAAGATA 59.875 40.000 15.51 3.66 45.61 1.98
5081 5728 5.357878 TGCTTTGCATTAGGGTCAAAGATAG 59.642 40.000 15.51 0.00 45.61 2.08
5082 5729 5.590259 GCTTTGCATTAGGGTCAAAGATAGA 59.410 40.000 15.51 0.00 45.61 1.98
5083 5730 6.264067 GCTTTGCATTAGGGTCAAAGATAGAT 59.736 38.462 15.51 0.00 45.61 1.98
5084 5731 7.572523 TTTGCATTAGGGTCAAAGATAGATG 57.427 36.000 0.00 0.00 0.00 2.90
5090 5737 7.798710 TTAGGGTCAAAGATAGATGGATAGG 57.201 40.000 0.00 0.00 0.00 2.57
5149 5796 1.664321 GATTGGCTGCAGCAAGGGAG 61.664 60.000 37.63 0.24 44.36 4.30
5256 5932 8.688151 TCATCACATCAATTCATTGCAAAGATA 58.312 29.630 1.71 0.00 37.68 1.98
5293 5981 1.133699 TCCTCTTGCCCTTATGCATGG 60.134 52.381 10.16 2.93 41.70 3.66
5432 6123 3.086600 CCTCTGGCAGGGAGGGAC 61.087 72.222 17.99 0.00 44.71 4.46
5513 6219 1.597302 CAGGGCGCAGATCTCCATG 60.597 63.158 10.83 0.00 0.00 3.66
5516 6222 1.596477 GGCGCAGATCTCCATGGTC 60.596 63.158 12.58 1.67 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 142 6.819146 TGATTTGTAATGTTATGAGCGGTACA 59.181 34.615 0.00 0.00 0.00 2.90
145 146 7.112009 CGATTTGATTTGTAATGTTATGAGCGG 59.888 37.037 0.00 0.00 0.00 5.52
173 174 0.391661 GTCGATGAAGCAAGCCCTCA 60.392 55.000 0.00 0.00 0.00 3.86
182 183 1.059264 GTGTAAGCACGTCGATGAAGC 59.941 52.381 12.58 14.45 35.75 3.86
265 267 1.622811 CCACTCTTCTCCAACAGAGCT 59.377 52.381 0.00 0.00 42.90 4.09
310 312 4.398319 ACTATTGGTATTACATGGCCTGC 58.602 43.478 3.32 0.00 0.00 4.85
324 326 1.071699 ACAGGCACGTCAACTATTGGT 59.928 47.619 0.00 0.00 0.00 3.67
366 368 6.157994 ACCCTGCTTTATGGTAGATTCTTACA 59.842 38.462 0.00 0.00 0.00 2.41
380 382 4.820894 ACGAGTAGAAACCCTGCTTTAT 57.179 40.909 0.00 0.00 37.98 1.40
388 390 4.331992 GGAAGCAATAACGAGTAGAAACCC 59.668 45.833 0.00 0.00 0.00 4.11
412 414 2.057137 TTAGCTGTCATCAATGGGGC 57.943 50.000 0.00 0.00 0.00 5.80
418 420 8.450964 GCTTTTAGTAACATTAGCTGTCATCAA 58.549 33.333 0.00 0.00 36.98 2.57
502 517 7.639162 TCTCGTTTTCAATACAAGTCTCTTC 57.361 36.000 0.00 0.00 0.00 2.87
523 538 1.980156 GCGAGTCTCTTGTCGTTTCTC 59.020 52.381 0.00 0.00 38.48 2.87
524 539 1.337071 TGCGAGTCTCTTGTCGTTTCT 59.663 47.619 0.00 0.00 38.48 2.52
525 540 1.716581 CTGCGAGTCTCTTGTCGTTTC 59.283 52.381 0.00 0.00 38.48 2.78
526 541 1.603172 CCTGCGAGTCTCTTGTCGTTT 60.603 52.381 0.00 0.00 38.48 3.60
527 542 0.039074 CCTGCGAGTCTCTTGTCGTT 60.039 55.000 0.00 0.00 38.48 3.85
528 543 1.581954 CCTGCGAGTCTCTTGTCGT 59.418 57.895 0.00 0.00 38.48 4.34
529 544 1.803519 GCCTGCGAGTCTCTTGTCG 60.804 63.158 0.00 0.00 39.25 4.35
530 545 0.319900 TTGCCTGCGAGTCTCTTGTC 60.320 55.000 0.00 0.00 0.00 3.18
531 546 0.320247 CTTGCCTGCGAGTCTCTTGT 60.320 55.000 0.00 0.00 0.00 3.16
532 547 0.037882 TCTTGCCTGCGAGTCTCTTG 60.038 55.000 6.29 0.00 0.00 3.02
533 548 0.246086 CTCTTGCCTGCGAGTCTCTT 59.754 55.000 6.29 0.00 0.00 2.85
534 549 0.610509 TCTCTTGCCTGCGAGTCTCT 60.611 55.000 6.29 0.00 0.00 3.10
535 550 0.459489 ATCTCTTGCCTGCGAGTCTC 59.541 55.000 6.29 0.00 0.00 3.36
536 551 0.459489 GATCTCTTGCCTGCGAGTCT 59.541 55.000 6.29 0.00 0.00 3.24
537 552 0.174389 TGATCTCTTGCCTGCGAGTC 59.826 55.000 6.29 0.00 0.00 3.36
538 553 0.829333 ATGATCTCTTGCCTGCGAGT 59.171 50.000 6.29 0.00 0.00 4.18
539 554 2.808523 TATGATCTCTTGCCTGCGAG 57.191 50.000 0.00 0.00 0.00 5.03
540 555 3.198068 GTTTATGATCTCTTGCCTGCGA 58.802 45.455 0.00 0.00 0.00 5.10
541 556 2.289002 GGTTTATGATCTCTTGCCTGCG 59.711 50.000 0.00 0.00 0.00 5.18
542 557 2.620585 GGGTTTATGATCTCTTGCCTGC 59.379 50.000 0.00 0.00 0.00 4.85
543 558 3.217626 GGGGTTTATGATCTCTTGCCTG 58.782 50.000 0.00 0.00 0.00 4.85
544 559 2.175715 GGGGGTTTATGATCTCTTGCCT 59.824 50.000 0.00 0.00 0.00 4.75
545 560 2.587522 GGGGGTTTATGATCTCTTGCC 58.412 52.381 0.00 0.00 0.00 4.52
570 585 3.391382 GACGGTGTGGGGAGGAGG 61.391 72.222 0.00 0.00 0.00 4.30
571 586 3.760035 CGACGGTGTGGGGAGGAG 61.760 72.222 0.00 0.00 0.00 3.69
574 589 3.760035 CTCCGACGGTGTGGGGAG 61.760 72.222 14.79 0.00 40.05 4.30
575 590 4.608774 ACTCCGACGGTGTGGGGA 62.609 66.667 20.10 0.00 32.22 4.81
576 591 3.622826 AACTCCGACGGTGTGGGG 61.623 66.667 21.32 5.50 32.22 4.96
577 592 2.357034 CAACTCCGACGGTGTGGG 60.357 66.667 21.32 13.23 32.61 4.61
578 593 1.954146 CACAACTCCGACGGTGTGG 60.954 63.158 21.32 20.37 29.35 4.17
579 594 1.954146 CCACAACTCCGACGGTGTG 60.954 63.158 22.66 22.66 29.35 3.82
580 595 2.420043 CCACAACTCCGACGGTGT 59.580 61.111 15.58 15.58 0.00 4.16
581 596 3.041940 GCCACAACTCCGACGGTG 61.042 66.667 14.79 14.46 0.00 4.94
582 597 4.309950 GGCCACAACTCCGACGGT 62.310 66.667 14.79 0.00 0.00 4.83
587 602 0.810031 CTTATCCGGCCACAACTCCG 60.810 60.000 2.24 0.00 44.89 4.63
588 603 0.463833 CCTTATCCGGCCACAACTCC 60.464 60.000 2.24 0.00 0.00 3.85
589 604 0.463833 CCCTTATCCGGCCACAACTC 60.464 60.000 2.24 0.00 0.00 3.01
590 605 1.607612 CCCTTATCCGGCCACAACT 59.392 57.895 2.24 0.00 0.00 3.16
591 606 1.453197 CCCCTTATCCGGCCACAAC 60.453 63.158 2.24 0.00 0.00 3.32
592 607 1.208844 TTCCCCTTATCCGGCCACAA 61.209 55.000 2.24 0.00 0.00 3.33
593 608 1.616930 TTCCCCTTATCCGGCCACA 60.617 57.895 2.24 0.00 0.00 4.17
594 609 1.148498 CTTCCCCTTATCCGGCCAC 59.852 63.158 2.24 0.00 0.00 5.01
595 610 0.622154 TTCTTCCCCTTATCCGGCCA 60.622 55.000 2.24 0.00 0.00 5.36
596 611 0.179026 GTTCTTCCCCTTATCCGGCC 60.179 60.000 0.00 0.00 0.00 6.13
597 612 0.532196 CGTTCTTCCCCTTATCCGGC 60.532 60.000 0.00 0.00 0.00 6.13
598 613 0.106149 CCGTTCTTCCCCTTATCCGG 59.894 60.000 0.00 0.00 0.00 5.14
599 614 1.068741 CTCCGTTCTTCCCCTTATCCG 59.931 57.143 0.00 0.00 0.00 4.18
600 615 1.202663 GCTCCGTTCTTCCCCTTATCC 60.203 57.143 0.00 0.00 0.00 2.59
601 616 1.538419 CGCTCCGTTCTTCCCCTTATC 60.538 57.143 0.00 0.00 0.00 1.75
602 617 0.464452 CGCTCCGTTCTTCCCCTTAT 59.536 55.000 0.00 0.00 0.00 1.73
603 618 1.610554 CCGCTCCGTTCTTCCCCTTA 61.611 60.000 0.00 0.00 0.00 2.69
604 619 2.663196 CGCTCCGTTCTTCCCCTT 59.337 61.111 0.00 0.00 0.00 3.95
605 620 3.391382 CCGCTCCGTTCTTCCCCT 61.391 66.667 0.00 0.00 0.00 4.79
606 621 4.468689 CCCGCTCCGTTCTTCCCC 62.469 72.222 0.00 0.00 0.00 4.81
607 622 4.468689 CCCCGCTCCGTTCTTCCC 62.469 72.222 0.00 0.00 0.00 3.97
608 623 2.646117 GATCCCCGCTCCGTTCTTCC 62.646 65.000 0.00 0.00 0.00 3.46
609 624 1.227292 GATCCCCGCTCCGTTCTTC 60.227 63.158 0.00 0.00 0.00 2.87
610 625 2.901042 GATCCCCGCTCCGTTCTT 59.099 61.111 0.00 0.00 0.00 2.52
611 626 3.528370 CGATCCCCGCTCCGTTCT 61.528 66.667 0.00 0.00 0.00 3.01
623 638 3.334463 GCTTTCCGGATGCGATCC 58.666 61.111 8.71 5.39 46.22 3.36
636 776 1.133730 TGAAACCCTAACCACCGCTTT 60.134 47.619 0.00 0.00 0.00 3.51
637 777 0.475044 TGAAACCCTAACCACCGCTT 59.525 50.000 0.00 0.00 0.00 4.68
780 921 4.080863 CCTGCACCTCTCTTTATTGGTAGT 60.081 45.833 0.00 0.00 0.00 2.73
781 922 4.162320 TCCTGCACCTCTCTTTATTGGTAG 59.838 45.833 0.00 0.00 0.00 3.18
782 923 4.101114 TCCTGCACCTCTCTTTATTGGTA 58.899 43.478 0.00 0.00 0.00 3.25
840 981 0.822164 TACGGGAAAGCTCTGCTACC 59.178 55.000 0.00 0.35 38.25 3.18
842 983 5.546621 ATTATTACGGGAAAGCTCTGCTA 57.453 39.130 0.00 0.00 38.25 3.49
847 988 3.004419 GGCCAATTATTACGGGAAAGCTC 59.996 47.826 0.00 0.00 0.00 4.09
883 1028 1.067669 GCTGCTCGTCATGTGATAGGA 59.932 52.381 0.00 0.00 0.00 2.94
916 1064 1.032794 ACGAGCGAGCTTCCATGATA 58.967 50.000 0.00 0.00 0.00 2.15
944 1092 2.376222 ATAATGGGGAGGGGGAGGGG 62.376 65.000 0.00 0.00 0.00 4.79
947 1095 3.005529 AGTTATAATGGGGAGGGGGAG 57.994 52.381 0.00 0.00 0.00 4.30
948 1096 3.332968 GAAGTTATAATGGGGAGGGGGA 58.667 50.000 0.00 0.00 0.00 4.81
958 1127 6.423182 TGGACTTTGGAGGGAAGTTATAATG 58.577 40.000 0.00 0.00 37.46 1.90
1141 1327 3.251509 TCCTGCTGGCTGGCTCAA 61.252 61.111 12.65 0.00 35.38 3.02
1155 1341 2.362120 CGTCCCTACCGTGGTCCT 60.362 66.667 0.00 0.00 0.00 3.85
1156 1342 3.455469 CCGTCCCTACCGTGGTCC 61.455 72.222 0.00 0.00 0.00 4.46
1158 1344 2.362120 CTCCGTCCCTACCGTGGT 60.362 66.667 0.00 0.00 0.00 4.16
1159 1345 3.145551 CCTCCGTCCCTACCGTGG 61.146 72.222 0.00 0.00 0.00 4.94
1160 1346 2.044650 TCCTCCGTCCCTACCGTG 60.045 66.667 0.00 0.00 0.00 4.94
1161 1347 2.274760 CTCCTCCGTCCCTACCGT 59.725 66.667 0.00 0.00 0.00 4.83
1163 1349 2.838693 GGCTCCTCCGTCCCTACC 60.839 72.222 0.00 0.00 0.00 3.18
1597 1789 3.600410 AATGGGGGCTTTGGGTCGG 62.600 63.158 0.00 0.00 0.00 4.79
1598 1790 1.191489 AAAATGGGGGCTTTGGGTCG 61.191 55.000 0.00 0.00 0.00 4.79
1599 1791 1.003118 GAAAAATGGGGGCTTTGGGTC 59.997 52.381 0.00 0.00 0.00 4.46
1600 1792 1.064003 GAAAAATGGGGGCTTTGGGT 58.936 50.000 0.00 0.00 0.00 4.51
1601 1793 1.278985 GAGAAAAATGGGGGCTTTGGG 59.721 52.381 0.00 0.00 0.00 4.12
1638 1832 0.752009 TCGAGGAGGATGAAGACGGG 60.752 60.000 0.00 0.00 0.00 5.28
1647 1841 0.106419 GGGACTGACTCGAGGAGGAT 60.106 60.000 18.41 0.00 33.35 3.24
1656 1850 1.370587 CCTCGTCTCGGGACTGACTC 61.371 65.000 14.69 0.00 40.10 3.36
1679 1878 0.304705 GTAATCGTGCTGCATTCGGG 59.695 55.000 5.27 0.00 0.00 5.14
1700 1899 0.249911 AGAGACAAGCAACACGGGAC 60.250 55.000 0.00 0.00 0.00 4.46
1701 1900 0.468226 AAGAGACAAGCAACACGGGA 59.532 50.000 0.00 0.00 0.00 5.14
1702 1901 2.069273 CTAAGAGACAAGCAACACGGG 58.931 52.381 0.00 0.00 0.00 5.28
1703 1902 1.461127 GCTAAGAGACAAGCAACACGG 59.539 52.381 0.00 0.00 38.63 4.94
1738 1937 2.031163 GGAATGGGGATCGCCGAG 59.969 66.667 22.58 0.00 33.83 4.63
1776 1975 2.287970 CGTGGCAATGATTGATCCCATG 60.288 50.000 9.76 8.52 0.00 3.66
1778 1977 1.391577 CGTGGCAATGATTGATCCCA 58.608 50.000 9.76 4.12 0.00 4.37
1797 2007 3.942115 GGATTAGGACAAAACAGAGGAGC 59.058 47.826 0.00 0.00 0.00 4.70
1902 2112 2.084546 CAAAACGGAGAAGTGGGGATC 58.915 52.381 0.00 0.00 0.00 3.36
1916 2126 6.245296 CACGGAATGAAAAACAAAACAAAACG 59.755 34.615 0.00 0.00 0.00 3.60
1955 2170 6.363882 GGAATGATGGAAAGGAGAAGAAGAT 58.636 40.000 0.00 0.00 0.00 2.40
2043 2258 3.551846 GAGATCTTTCTCTCTCTCCGGT 58.448 50.000 0.00 0.00 44.29 5.28
2053 2268 6.329496 ACATCAAGTTCGAGAGATCTTTCTC 58.671 40.000 11.20 6.78 45.22 2.87
2120 2371 5.631119 TGCATCCATCATCATCATCTTCTT 58.369 37.500 0.00 0.00 0.00 2.52
2122 2373 5.959618 TTGCATCCATCATCATCATCTTC 57.040 39.130 0.00 0.00 0.00 2.87
2163 2419 1.003580 CAGAGCAGCCTTTTACCCTCA 59.996 52.381 0.00 0.00 0.00 3.86
2168 2427 4.072839 AGGTAAACAGAGCAGCCTTTTAC 58.927 43.478 0.00 0.00 33.66 2.01
2187 2447 8.960591 CCATCTTTCACTTCACATAATAAAGGT 58.039 33.333 0.00 0.00 0.00 3.50
2190 2450 8.112822 TCCCCATCTTTCACTTCACATAATAAA 58.887 33.333 0.00 0.00 0.00 1.40
2192 2452 7.206789 TCCCCATCTTTCACTTCACATAATA 57.793 36.000 0.00 0.00 0.00 0.98
2193 2453 6.078456 TCCCCATCTTTCACTTCACATAAT 57.922 37.500 0.00 0.00 0.00 1.28
2196 2456 4.387026 TTCCCCATCTTTCACTTCACAT 57.613 40.909 0.00 0.00 0.00 3.21
2237 2502 3.134458 GGGATAAAGCTGATCCGTTCTG 58.866 50.000 17.60 0.00 43.43 3.02
2238 2503 2.224066 CGGGATAAAGCTGATCCGTTCT 60.224 50.000 17.60 0.00 43.43 3.01
2239 2504 2.135933 CGGGATAAAGCTGATCCGTTC 58.864 52.381 17.60 7.04 43.43 3.95
2240 2505 1.760613 TCGGGATAAAGCTGATCCGTT 59.239 47.619 17.60 0.00 43.43 4.44
2241 2506 1.410004 TCGGGATAAAGCTGATCCGT 58.590 50.000 17.60 0.00 43.43 4.69
2274 2550 2.198827 TGAATCATTGGACGGTTGCT 57.801 45.000 0.00 0.00 0.00 3.91
2275 2551 3.508744 ATTGAATCATTGGACGGTTGC 57.491 42.857 0.00 0.00 0.00 4.17
2276 2552 4.587306 CGTATTGAATCATTGGACGGTTG 58.413 43.478 0.00 0.00 0.00 3.77
2296 2572 1.806623 GCAGTAGGATTTCGGATGCGT 60.807 52.381 6.49 0.00 0.00 5.24
2298 2574 1.869767 CTGCAGTAGGATTTCGGATGC 59.130 52.381 5.25 0.00 0.00 3.91
2299 2575 1.869767 GCTGCAGTAGGATTTCGGATG 59.130 52.381 16.64 0.00 0.00 3.51
2302 2578 2.474816 GTAGCTGCAGTAGGATTTCGG 58.525 52.381 16.64 0.00 0.00 4.30
2345 2634 3.117738 AGCATCGGGATGAGGAAAAGATT 60.118 43.478 12.66 0.00 41.20 2.40
2367 2656 6.579666 ATGAAAAACATGAGCTAAAGCAGA 57.420 33.333 0.00 0.00 39.71 4.26
2398 2687 4.321527 CCCACTCCATTGAAAAAGAAGAGC 60.322 45.833 0.00 0.00 0.00 4.09
2407 2706 4.111255 TCAATCACCCACTCCATTGAAA 57.889 40.909 0.00 0.00 33.34 2.69
2411 2710 2.421952 CCGATCAATCACCCACTCCATT 60.422 50.000 0.00 0.00 0.00 3.16
2574 2888 3.385384 CAGACCGGGCAGCAGAGA 61.385 66.667 11.69 0.00 0.00 3.10
2724 3041 3.246112 TACACCTTGGGCACGCCT 61.246 61.111 8.20 0.00 36.10 5.52
2781 3098 2.975799 TTGAACCCGCTGCCGTTC 60.976 61.111 16.30 16.30 39.07 3.95
3033 3362 4.640855 ACGTCCAGCACCGTCACG 62.641 66.667 0.00 0.00 36.54 4.35
3060 3389 0.536915 GCAGCTTCTCCCCCATCATC 60.537 60.000 0.00 0.00 0.00 2.92
3135 3464 1.066587 GAAGGCGACGATGGAGAGG 59.933 63.158 0.00 0.00 0.00 3.69
3391 3732 3.411418 GATCGCCGTGCTTCCTCGA 62.411 63.158 0.00 0.00 0.00 4.04
3591 3944 2.125912 ATGACCACGCTGACGAGC 60.126 61.111 0.00 0.00 43.93 5.03
3918 4271 1.950973 GCGAGGAGGTGGAGGAGTTC 61.951 65.000 0.00 0.00 0.00 3.01
3919 4272 1.985116 GCGAGGAGGTGGAGGAGTT 60.985 63.158 0.00 0.00 0.00 3.01
3920 4273 2.363147 GCGAGGAGGTGGAGGAGT 60.363 66.667 0.00 0.00 0.00 3.85
3922 4275 2.363018 CTGCGAGGAGGTGGAGGA 60.363 66.667 0.00 0.00 0.00 3.71
3923 4276 4.154347 GCTGCGAGGAGGTGGAGG 62.154 72.222 0.00 0.00 0.00 4.30
4358 4717 1.467035 GCTCGTTACAGATCGACCGTT 60.467 52.381 0.00 0.00 32.65 4.44
4469 4853 1.293498 CAGCAGCACCTCTAACCGT 59.707 57.895 0.00 0.00 0.00 4.83
4473 4857 0.329261 AATGGCAGCAGCACCTCTAA 59.671 50.000 2.65 0.00 44.61 2.10
4631 5030 0.240945 GGACCATTCAACCACAAGCG 59.759 55.000 0.00 0.00 0.00 4.68
4724 5266 3.307674 TGCAACTTGATTCAACGAATGC 58.692 40.909 0.00 4.85 31.89 3.56
4742 5284 0.543883 AGAGCTTCTCCTGGACTGCA 60.544 55.000 11.63 0.00 0.00 4.41
4743 5285 0.175531 GAGAGCTTCTCCTGGACTGC 59.824 60.000 0.00 0.00 37.55 4.40
4744 5286 1.750778 GAGAGAGCTTCTCCTGGACTG 59.249 57.143 12.34 0.00 44.42 3.51
4745 5287 2.143876 GAGAGAGCTTCTCCTGGACT 57.856 55.000 12.34 0.00 44.42 3.85
4753 5295 1.889454 CAGTGCGGAGAGAGCTTCT 59.111 57.895 0.00 0.00 39.43 2.85
4754 5296 1.809209 GCAGTGCGGAGAGAGCTTC 60.809 63.158 0.00 0.00 35.28 3.86
4755 5297 2.264166 GCAGTGCGGAGAGAGCTT 59.736 61.111 0.00 0.00 35.28 3.74
4756 5298 2.993840 TGCAGTGCGGAGAGAGCT 60.994 61.111 11.20 0.00 35.28 4.09
4757 5299 2.813042 GTGCAGTGCGGAGAGAGC 60.813 66.667 11.20 0.00 0.00 4.09
4758 5300 1.445754 CAGTGCAGTGCGGAGAGAG 60.446 63.158 8.96 0.00 0.00 3.20
4759 5301 2.653115 CAGTGCAGTGCGGAGAGA 59.347 61.111 8.96 0.00 0.00 3.10
4760 5302 3.117171 GCAGTGCAGTGCGGAGAG 61.117 66.667 29.43 0.00 32.74 3.20
4766 5308 1.236616 TGTATGGTGCAGTGCAGTGC 61.237 55.000 34.65 34.65 40.08 4.40
4767 5309 0.518636 GTGTATGGTGCAGTGCAGTG 59.481 55.000 20.42 17.56 40.08 3.66
4768 5310 0.606401 GGTGTATGGTGCAGTGCAGT 60.606 55.000 20.42 10.39 40.08 4.40
4769 5311 0.606130 TGGTGTATGGTGCAGTGCAG 60.606 55.000 20.42 0.00 40.08 4.41
4770 5312 0.179006 TTGGTGTATGGTGCAGTGCA 60.179 50.000 15.37 15.37 35.60 4.57
4771 5313 1.176527 ATTGGTGTATGGTGCAGTGC 58.823 50.000 8.58 8.58 0.00 4.40
4772 5314 3.255395 TGAAATTGGTGTATGGTGCAGTG 59.745 43.478 0.00 0.00 0.00 3.66
4773 5315 3.255642 GTGAAATTGGTGTATGGTGCAGT 59.744 43.478 0.00 0.00 0.00 4.40
4774 5316 3.507233 AGTGAAATTGGTGTATGGTGCAG 59.493 43.478 0.00 0.00 0.00 4.41
4802 5372 1.302431 CGACAACCACCATCAGCCA 60.302 57.895 0.00 0.00 0.00 4.75
4803 5373 0.392998 ATCGACAACCACCATCAGCC 60.393 55.000 0.00 0.00 0.00 4.85
4804 5374 1.009829 GATCGACAACCACCATCAGC 58.990 55.000 0.00 0.00 0.00 4.26
4805 5375 2.385013 TGATCGACAACCACCATCAG 57.615 50.000 0.00 0.00 0.00 2.90
4806 5376 2.419990 GGATGATCGACAACCACCATCA 60.420 50.000 0.00 0.00 40.52 3.07
4807 5377 2.213499 GGATGATCGACAACCACCATC 58.787 52.381 8.65 0.00 40.52 3.51
4808 5378 1.559219 TGGATGATCGACAACCACCAT 59.441 47.619 11.16 0.00 44.53 3.55
4819 5389 2.937149 GCTGATGATGGATGGATGATCG 59.063 50.000 0.00 0.00 30.87 3.69
4838 5412 1.532523 GGCAGAAGAAAAGCAGAGCT 58.467 50.000 0.00 0.00 42.56 4.09
4839 5413 0.167689 CGGCAGAAGAAAAGCAGAGC 59.832 55.000 0.00 0.00 0.00 4.09
4840 5414 1.517242 ACGGCAGAAGAAAAGCAGAG 58.483 50.000 0.00 0.00 0.00 3.35
4842 5416 2.548057 TGTAACGGCAGAAGAAAAGCAG 59.452 45.455 0.00 0.00 0.00 4.24
4844 5418 2.548480 ACTGTAACGGCAGAAGAAAAGC 59.452 45.455 10.17 0.00 39.62 3.51
4845 5419 3.120991 CGACTGTAACGGCAGAAGAAAAG 60.121 47.826 10.17 0.00 39.62 2.27
4868 5442 2.362120 AGCAGGGTGAGCATTGGC 60.362 61.111 0.00 0.00 41.61 4.52
4917 5501 4.021104 TGGTAGTTCAGGTTCAGTGATCTG 60.021 45.833 14.41 14.41 42.54 2.90
4918 5502 4.021016 GTGGTAGTTCAGGTTCAGTGATCT 60.021 45.833 0.00 0.00 0.00 2.75
4919 5503 4.246458 GTGGTAGTTCAGGTTCAGTGATC 58.754 47.826 0.00 0.00 0.00 2.92
4920 5504 3.646162 TGTGGTAGTTCAGGTTCAGTGAT 59.354 43.478 0.00 0.00 0.00 3.06
4950 5534 2.664081 CCAGGGTCAGGGTCAGAGC 61.664 68.421 0.00 0.00 0.00 4.09
4951 5535 2.664081 GCCAGGGTCAGGGTCAGAG 61.664 68.421 0.00 0.00 0.00 3.35
4952 5536 2.607750 GCCAGGGTCAGGGTCAGA 60.608 66.667 0.00 0.00 0.00 3.27
4953 5537 3.721706 GGCCAGGGTCAGGGTCAG 61.722 72.222 0.00 0.00 0.00 3.51
4954 5538 4.270153 AGGCCAGGGTCAGGGTCA 62.270 66.667 5.01 0.00 0.00 4.02
4955 5539 3.721706 CAGGCCAGGGTCAGGGTC 61.722 72.222 5.01 0.00 0.00 4.46
4975 5576 4.308526 CCTCACACAGGCACCATC 57.691 61.111 0.00 0.00 34.56 3.51
5030 5651 2.427232 AACACACAAGATGCATGCAC 57.573 45.000 25.37 16.77 0.00 4.57
5082 5729 9.134504 CCCCTATCTATCTATCTACCTATCCAT 57.865 40.741 0.00 0.00 0.00 3.41
5083 5730 8.312606 TCCCCTATCTATCTATCTACCTATCCA 58.687 40.741 0.00 0.00 0.00 3.41
5084 5731 8.760362 TCCCCTATCTATCTATCTACCTATCC 57.240 42.308 0.00 0.00 0.00 2.59
5149 5796 0.176449 GCCTTTGCAATGGACATCCC 59.824 55.000 30.10 11.16 37.47 3.85
5256 5932 3.209612 AGAGGAGGAGGAGGAATGATCTT 59.790 47.826 0.00 0.00 0.00 2.40
5293 5981 2.814336 CAGGAAGGAACTGTTGTTAGGC 59.186 50.000 0.00 0.00 40.86 3.93
5360 6051 2.069273 GTGCACTGTGGCTACTGTAAG 58.931 52.381 10.32 3.17 36.93 2.34
5388 6079 4.320456 CAGAGGCGCCACTGTGGT 62.320 66.667 36.72 13.82 40.46 4.16
5389 6080 3.832237 AACAGAGGCGCCACTGTGG 62.832 63.158 45.68 28.34 44.68 4.17
5428 6119 0.685097 TACCTGCAACAGTGAGTCCC 59.315 55.000 0.00 0.00 0.00 4.46
5429 6120 1.344763 AGTACCTGCAACAGTGAGTCC 59.655 52.381 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.