Multiple sequence alignment - TraesCS2D01G061700

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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 TraesCS2D01G061700 chr2D 100.000 4853 0 0 1 4853 25355737 25350885 0.000000e+00 8962
1 TraesCS2D01G061700 chr2D 84.038 2318 344 12 1331 3644 615063362 615061067 0.000000e+00 2207
2 TraesCS2D01G061700 chr2D 83.604 616 77 18 1 610 25680746 25681343 1.530000e-154 556
3 TraesCS2D01G061700 chr2D 89.346 413 44 0 3206 3618 25352502 25352090 2.000000e-143 520
4 TraesCS2D01G061700 chr2D 89.346 413 44 0 3236 3648 25352532 25352120 2.000000e-143 520
5 TraesCS2D01G061700 chr2A 96.372 3528 124 3 1159 4685 27969937 27966413 0.000000e+00 5803
6 TraesCS2D01G061700 chr2A 84.809 2508 356 12 1135 3637 745267086 745264599 0.000000e+00 2497
7 TraesCS2D01G061700 chr2A 92.157 408 32 0 3206 3613 27967860 27967453 1.170000e-160 577
8 TraesCS2D01G061700 chr2A 87.500 416 52 0 3236 3651 27967890 27967475 9.450000e-132 481
9 TraesCS2D01G061700 chr2A 90.769 325 12 6 801 1125 27970685 27970379 7.510000e-113 418
10 TraesCS2D01G061700 chr2A 94.012 167 9 1 4686 4852 27966308 27966143 8.060000e-63 252
11 TraesCS2D01G061700 chr2B 95.038 2479 123 0 1173 3651 41147452 41144974 0.000000e+00 3897
12 TraesCS2D01G061700 chr2B 95.934 1648 57 5 3206 4853 41145329 41143692 0.000000e+00 2663
13 TraesCS2D01G061700 chr2B 84.298 2592 376 18 1054 3637 749421609 749419041 0.000000e+00 2503
14 TraesCS2D01G061700 chr2B 92.327 404 31 0 3215 3618 41145290 41144887 4.210000e-160 575
15 TraesCS2D01G061700 chr2B 89.091 440 48 0 3212 3651 41145353 41144914 9.180000e-152 547
16 TraesCS2D01G061700 chr2B 88.596 228 13 12 906 1132 41148085 41147870 1.040000e-66 265
17 TraesCS2D01G061700 chr2B 92.105 76 5 1 791 866 41148165 41148091 6.640000e-19 106
18 TraesCS2D01G061700 chr4A 90.741 108 10 0 3 110 699002749 699002642 1.410000e-30 145
19 TraesCS2D01G061700 chr6A 89.815 108 10 1 1 107 454677965 454678072 2.360000e-28 137
20 TraesCS2D01G061700 chr5B 90.385 104 10 0 4 107 220033107 220033210 2.360000e-28 137
21 TraesCS2D01G061700 chr6D 89.423 104 11 0 4 107 90111150 90111253 1.100000e-26 132
22 TraesCS2D01G061700 chr6D 88.785 107 12 0 4 110 391925985 391925879 1.100000e-26 132
23 TraesCS2D01G061700 chr6B 88.785 107 12 0 4 110 585524840 585524734 1.100000e-26 132
24 TraesCS2D01G061700 chr3B 89.423 104 11 0 4 107 33114059 33114162 1.100000e-26 132
25 TraesCS2D01G061700 chr4B 89.320 103 11 0 4 106 600920075 600919973 3.940000e-26 130
26 TraesCS2D01G061700 chr5D 87.963 108 13 0 4 111 371860610 371860717 1.420000e-25 128
27 TraesCS2D01G061700 chr1D 91.463 82 7 0 4246 4327 378099498 378099579 3.970000e-21 113


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 TraesCS2D01G061700 chr2D 25350885 25355737 4852 True 3334.000000 8962 92.897333 1 4853 3 chr2D.!!$R2 4852
1 TraesCS2D01G061700 chr2D 615061067 615063362 2295 True 2207.000000 2207 84.038000 1331 3644 1 chr2D.!!$R1 2313
2 TraesCS2D01G061700 chr2D 25680746 25681343 597 False 556.000000 556 83.604000 1 610 1 chr2D.!!$F1 609
3 TraesCS2D01G061700 chr2A 745264599 745267086 2487 True 2497.000000 2497 84.809000 1135 3637 1 chr2A.!!$R1 2502
4 TraesCS2D01G061700 chr2A 27966143 27970685 4542 True 1506.200000 5803 92.162000 801 4852 5 chr2A.!!$R2 4051
5 TraesCS2D01G061700 chr2B 749419041 749421609 2568 True 2503.000000 2503 84.298000 1054 3637 1 chr2B.!!$R1 2583
6 TraesCS2D01G061700 chr2B 41143692 41148165 4473 True 1342.166667 3897 92.181833 791 4853 6 chr2B.!!$R2 4062

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
691 695 0.171231 GCAGCGAGGAATGGTTTTCC 59.829 55.000 0.00 0.0 38.86 3.13 F
884 888 0.179000 CAGAGAACCATCGGGGGAAG 59.821 60.000 0.07 0.0 42.91 3.46 F
2641 3458 0.178973 TGAGTTCCGGGAGTCTGTCA 60.179 55.000 18.69 0.0 0.00 3.58 F
2757 3574 1.371183 CCCTCGCACTTCACCTCAA 59.629 57.895 0.00 0.0 0.00 3.02 F
3579 4609 2.194056 CAGCAGCCTGGGTATGGG 59.806 66.667 0.00 0.0 35.38 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1604 2421 1.003442 AGCATCTCCTGGTAGGCCA 59.997 57.895 5.01 0.00 43.73 5.36 R
2841 3658 0.037975 CACCATTGCCAGGCTGAAAC 60.038 55.000 17.94 5.61 0.00 2.78 R
3570 4600 1.064017 GCTTGATGAACCCCATACCCA 60.064 52.381 0.00 0.00 35.17 4.51 R
3579 4609 1.136147 CTGCTGCGCTTGATGAACC 59.864 57.895 9.73 0.00 0.00 3.62 R
4518 5549 2.600420 CGTCGACCATCATCTGTTTCAG 59.400 50.000 10.58 0.00 0.00 3.02 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
25 26 4.405756 ACTCCCTCCGATCCATATTACT 57.594 45.455 0.00 0.00 0.00 2.24
34 35 3.921021 CGATCCATATTACTTGTCGCTCC 59.079 47.826 0.00 0.00 0.00 4.70
38 39 3.245284 CCATATTACTTGTCGCTCCAACG 59.755 47.826 0.00 0.00 0.00 4.10
52 53 3.306364 GCTCCAACGGATGTATCTAGCAT 60.306 47.826 0.00 0.00 0.00 3.79
63 64 8.598924 CGGATGTATCTAGCATTGAAATATGTC 58.401 37.037 0.00 0.00 0.00 3.06
99 100 8.070171 CCATTTGAACGACAAGTATTATGGATC 58.930 37.037 15.44 0.00 41.04 3.36
100 101 7.548196 TTTGAACGACAAGTATTATGGATCC 57.452 36.000 4.20 4.20 39.77 3.36
101 102 5.286438 TGAACGACAAGTATTATGGATCCG 58.714 41.667 7.39 0.00 0.00 4.18
110 111 7.403231 ACAAGTATTATGGATCCGAGGGAATAT 59.597 37.037 7.39 0.00 34.34 1.28
120 121 6.480320 GGATCCGAGGGAATATAATGAAATCG 59.520 42.308 0.00 0.00 34.34 3.34
126 127 8.955002 CGAGGGAATATAATGAAATCGTATACG 58.045 37.037 19.23 19.23 41.45 3.06
134 135 4.472691 TGAAATCGTATACGTACCGAGG 57.527 45.455 23.67 6.39 40.80 4.63
145 146 1.738030 CGTACCGAGGTGATTTCCCAC 60.738 57.143 4.80 0.00 36.37 4.61
150 151 2.552155 CCGAGGTGATTTCCCACTCAAA 60.552 50.000 0.00 0.00 37.24 2.69
160 161 5.845391 TTTCCCACTCAAACAAACTAAGG 57.155 39.130 0.00 0.00 0.00 2.69
164 165 3.380004 CCACTCAAACAAACTAAGGCACA 59.620 43.478 0.00 0.00 0.00 4.57
175 176 2.677836 ACTAAGGCACACATATGTTGCG 59.322 45.455 24.07 17.32 36.72 4.85
183 184 1.946081 CACATATGTTGCGTATGGGCA 59.054 47.619 5.37 0.00 42.12 5.36
292 295 7.111353 TGGAAACACGAAAAACAAAGAAAAG 57.889 32.000 0.00 0.00 33.40 2.27
294 297 7.438459 TGGAAACACGAAAAACAAAGAAAAGAA 59.562 29.630 0.00 0.00 33.40 2.52
295 298 8.277018 GGAAACACGAAAAACAAAGAAAAGAAA 58.723 29.630 0.00 0.00 0.00 2.52
296 299 9.639636 GAAACACGAAAAACAAAGAAAAGAAAA 57.360 25.926 0.00 0.00 0.00 2.29
297 300 9.989869 AAACACGAAAAACAAAGAAAAGAAAAA 57.010 22.222 0.00 0.00 0.00 1.94
322 325 6.790232 AGGGAAGTGTTGAAATTGAAAAGA 57.210 33.333 0.00 0.00 0.00 2.52
325 328 7.549134 AGGGAAGTGTTGAAATTGAAAAGAAAC 59.451 33.333 0.00 0.00 0.00 2.78
328 331 8.791327 AAGTGTTGAAATTGAAAAGAAACCAT 57.209 26.923 0.00 0.00 0.00 3.55
330 333 9.313118 AGTGTTGAAATTGAAAAGAAACCATAC 57.687 29.630 0.00 0.00 0.00 2.39
339 342 8.485976 TTGAAAAGAAACCATACAACCAAAAG 57.514 30.769 0.00 0.00 0.00 2.27
341 344 8.314751 TGAAAAGAAACCATACAACCAAAAGAA 58.685 29.630 0.00 0.00 0.00 2.52
342 345 9.325198 GAAAAGAAACCATACAACCAAAAGAAT 57.675 29.630 0.00 0.00 0.00 2.40
345 348 8.934023 AGAAACCATACAACCAAAAGAATAGA 57.066 30.769 0.00 0.00 0.00 1.98
346 349 8.793592 AGAAACCATACAACCAAAAGAATAGAC 58.206 33.333 0.00 0.00 0.00 2.59
405 408 6.780522 ACTAAAAAGGCAGAAACCAGGAAATA 59.219 34.615 0.00 0.00 0.00 1.40
406 409 6.493189 AAAAAGGCAGAAACCAGGAAATAA 57.507 33.333 0.00 0.00 0.00 1.40
407 410 6.686484 AAAAGGCAGAAACCAGGAAATAAT 57.314 33.333 0.00 0.00 0.00 1.28
408 411 5.921962 AAGGCAGAAACCAGGAAATAATC 57.078 39.130 0.00 0.00 0.00 1.75
409 412 4.934356 AGGCAGAAACCAGGAAATAATCA 58.066 39.130 0.00 0.00 0.00 2.57
410 413 5.332743 AGGCAGAAACCAGGAAATAATCAA 58.667 37.500 0.00 0.00 0.00 2.57
411 414 5.779771 AGGCAGAAACCAGGAAATAATCAAA 59.220 36.000 0.00 0.00 0.00 2.69
412 415 6.269769 AGGCAGAAACCAGGAAATAATCAAAA 59.730 34.615 0.00 0.00 0.00 2.44
413 416 6.934083 GGCAGAAACCAGGAAATAATCAAAAA 59.066 34.615 0.00 0.00 0.00 1.94
417 420 9.546428 AGAAACCAGGAAATAATCAAAAACAAG 57.454 29.630 0.00 0.00 0.00 3.16
418 421 9.541143 GAAACCAGGAAATAATCAAAAACAAGA 57.459 29.630 0.00 0.00 0.00 3.02
420 423 9.546428 AACCAGGAAATAATCAAAAACAAGAAG 57.454 29.630 0.00 0.00 0.00 2.85
438 441 9.533253 AACAAGAAGAAACACAAATAAGAATGG 57.467 29.630 0.00 0.00 0.00 3.16
439 442 8.143835 ACAAGAAGAAACACAAATAAGAATGGG 58.856 33.333 0.00 0.00 0.00 4.00
454 457 2.819477 TGGGAAAACCACTGGCAAG 58.181 52.632 0.00 0.00 46.80 4.01
455 458 1.367471 GGGAAAACCACTGGCAAGC 59.633 57.895 0.00 0.00 39.85 4.01
456 459 1.367471 GGAAAACCACTGGCAAGCC 59.633 57.895 3.61 3.61 0.00 4.35
457 460 1.398958 GGAAAACCACTGGCAAGCCA 61.399 55.000 13.93 13.93 45.02 4.75
466 470 1.603171 TGGCAAGCCAGCGAAATGA 60.603 52.632 10.24 0.00 41.89 2.57
472 476 2.768492 GCCAGCGAAATGAGCCCAG 61.768 63.158 0.00 0.00 34.64 4.45
483 487 4.942363 AATGAGCCCAGCCATATAGAAT 57.058 40.909 0.00 0.00 0.00 2.40
487 491 4.080695 TGAGCCCAGCCATATAGAATCATC 60.081 45.833 0.00 0.00 0.00 2.92
491 495 5.248640 CCCAGCCATATAGAATCATCGTTT 58.751 41.667 0.00 0.00 0.00 3.60
492 496 5.707298 CCCAGCCATATAGAATCATCGTTTT 59.293 40.000 0.00 0.00 0.00 2.43
493 497 6.128172 CCCAGCCATATAGAATCATCGTTTTC 60.128 42.308 0.00 0.00 0.00 2.29
494 498 6.401474 CCAGCCATATAGAATCATCGTTTTCG 60.401 42.308 0.00 0.00 45.64 3.46
538 542 3.886550 GAAGGCCAACCCACCCTGG 62.887 68.421 5.01 0.00 36.11 4.45
542 546 2.938798 CCAACCCACCCTGGCCTA 60.939 66.667 3.32 0.00 35.79 3.93
545 549 2.238701 AACCCACCCTGGCCTAAGG 61.239 63.158 3.32 2.51 35.79 2.69
565 569 2.339769 GGTAGCTCCCCCATTACTCAT 58.660 52.381 0.00 0.00 0.00 2.90
567 571 2.196742 AGCTCCCCCATTACTCATGA 57.803 50.000 0.00 0.00 34.31 3.07
582 586 3.317711 ACTCATGAGATTGCGGAGTCTAG 59.682 47.826 29.27 0.00 33.84 2.43
591 595 2.298610 TGCGGAGTCTAGTCATAGTGG 58.701 52.381 0.00 0.00 0.00 4.00
593 597 2.550606 GCGGAGTCTAGTCATAGTGGAG 59.449 54.545 0.00 0.00 0.00 3.86
603 607 5.939764 AGTCATAGTGGAGAAGTTATGCA 57.060 39.130 0.00 0.00 0.00 3.96
610 614 5.072741 AGTGGAGAAGTTATGCACACAATT 58.927 37.500 21.86 0.45 41.04 2.32
611 615 5.048504 AGTGGAGAAGTTATGCACACAATTG 60.049 40.000 21.86 3.24 41.04 2.32
612 616 4.826733 TGGAGAAGTTATGCACACAATTGT 59.173 37.500 4.92 4.92 35.84 2.71
613 617 5.048782 TGGAGAAGTTATGCACACAATTGTC 60.049 40.000 8.48 0.00 31.66 3.18
614 618 5.182001 GGAGAAGTTATGCACACAATTGTCT 59.818 40.000 8.48 0.00 31.66 3.41
615 619 6.371548 GGAGAAGTTATGCACACAATTGTCTA 59.628 38.462 8.48 0.00 31.66 2.59
616 620 7.094805 GGAGAAGTTATGCACACAATTGTCTAA 60.095 37.037 8.48 0.00 31.66 2.10
617 621 7.810658 AGAAGTTATGCACACAATTGTCTAAG 58.189 34.615 8.48 0.00 31.66 2.18
618 622 7.661437 AGAAGTTATGCACACAATTGTCTAAGA 59.339 33.333 8.48 0.00 31.66 2.10
619 623 7.744087 AGTTATGCACACAATTGTCTAAGAA 57.256 32.000 8.48 0.00 31.66 2.52
620 624 8.165239 AGTTATGCACACAATTGTCTAAGAAA 57.835 30.769 8.48 0.00 31.66 2.52
621 625 8.629158 AGTTATGCACACAATTGTCTAAGAAAA 58.371 29.630 8.48 0.00 31.66 2.29
622 626 9.243637 GTTATGCACACAATTGTCTAAGAAAAA 57.756 29.630 8.48 0.00 31.66 1.94
623 627 7.935338 ATGCACACAATTGTCTAAGAAAAAG 57.065 32.000 8.48 0.00 31.66 2.27
624 628 6.862209 TGCACACAATTGTCTAAGAAAAAGT 58.138 32.000 8.48 0.00 31.66 2.66
625 629 7.319646 TGCACACAATTGTCTAAGAAAAAGTT 58.680 30.769 8.48 0.00 31.66 2.66
626 630 8.462811 TGCACACAATTGTCTAAGAAAAAGTTA 58.537 29.630 8.48 0.00 31.66 2.24
627 631 8.958043 GCACACAATTGTCTAAGAAAAAGTTAG 58.042 33.333 8.48 0.00 31.66 2.34
628 632 9.450807 CACACAATTGTCTAAGAAAAAGTTAGG 57.549 33.333 8.48 0.00 31.66 2.69
629 633 8.135529 ACACAATTGTCTAAGAAAAAGTTAGGC 58.864 33.333 8.48 0.00 33.48 3.93
630 634 8.352942 CACAATTGTCTAAGAAAAAGTTAGGCT 58.647 33.333 8.48 0.00 33.93 4.58
631 635 8.568794 ACAATTGTCTAAGAAAAAGTTAGGCTC 58.431 33.333 4.92 0.00 33.93 4.70
632 636 8.787852 CAATTGTCTAAGAAAAAGTTAGGCTCT 58.212 33.333 0.00 0.00 33.93 4.09
633 637 7.964604 TTGTCTAAGAAAAAGTTAGGCTCTC 57.035 36.000 0.00 0.00 33.93 3.20
634 638 7.062749 TGTCTAAGAAAAAGTTAGGCTCTCA 57.937 36.000 0.00 0.00 33.93 3.27
635 639 7.680730 TGTCTAAGAAAAAGTTAGGCTCTCAT 58.319 34.615 0.00 0.00 33.93 2.90
636 640 8.157476 TGTCTAAGAAAAAGTTAGGCTCTCATT 58.843 33.333 0.00 0.00 33.93 2.57
637 641 9.654663 GTCTAAGAAAAAGTTAGGCTCTCATTA 57.345 33.333 0.00 0.00 30.75 1.90
638 642 9.877178 TCTAAGAAAAAGTTAGGCTCTCATTAG 57.123 33.333 0.00 0.00 0.00 1.73
639 643 9.660180 CTAAGAAAAAGTTAGGCTCTCATTAGT 57.340 33.333 0.00 0.00 0.00 2.24
640 644 8.926092 AAGAAAAAGTTAGGCTCTCATTAGTT 57.074 30.769 0.00 0.00 0.00 2.24
641 645 8.329203 AGAAAAAGTTAGGCTCTCATTAGTTG 57.671 34.615 0.00 0.00 0.00 3.16
642 646 8.157476 AGAAAAAGTTAGGCTCTCATTAGTTGA 58.843 33.333 0.00 0.00 0.00 3.18
669 673 9.869844 GTTCTTTTATATCATTCTGTCATTCCG 57.130 33.333 0.00 0.00 0.00 4.30
670 674 9.613428 TTCTTTTATATCATTCTGTCATTCCGT 57.387 29.630 0.00 0.00 0.00 4.69
673 677 8.534333 TTTATATCATTCTGTCATTCCGTAGC 57.466 34.615 0.00 0.00 0.00 3.58
674 678 3.885724 TCATTCTGTCATTCCGTAGCA 57.114 42.857 0.00 0.00 0.00 3.49
675 679 3.785486 TCATTCTGTCATTCCGTAGCAG 58.215 45.455 0.00 0.00 0.00 4.24
676 680 2.010145 TTCTGTCATTCCGTAGCAGC 57.990 50.000 0.00 0.00 0.00 5.25
677 681 0.179137 TCTGTCATTCCGTAGCAGCG 60.179 55.000 0.00 0.00 0.00 5.18
678 682 0.179137 CTGTCATTCCGTAGCAGCGA 60.179 55.000 1.45 0.00 0.00 4.93
679 683 0.179137 TGTCATTCCGTAGCAGCGAG 60.179 55.000 1.45 0.00 0.00 5.03
680 684 0.872021 GTCATTCCGTAGCAGCGAGG 60.872 60.000 1.45 0.00 0.00 4.63
681 685 1.035385 TCATTCCGTAGCAGCGAGGA 61.035 55.000 2.90 2.90 0.00 3.71
682 686 0.179111 CATTCCGTAGCAGCGAGGAA 60.179 55.000 17.56 17.56 37.94 3.36
683 687 0.753262 ATTCCGTAGCAGCGAGGAAT 59.247 50.000 19.74 19.74 37.94 3.01
684 688 0.179111 TTCCGTAGCAGCGAGGAATG 60.179 55.000 13.12 0.00 37.94 2.67
685 689 1.592669 CCGTAGCAGCGAGGAATGG 60.593 63.158 1.45 0.00 0.00 3.16
686 690 1.141881 CGTAGCAGCGAGGAATGGT 59.858 57.895 0.00 0.00 0.00 3.55
687 691 0.460284 CGTAGCAGCGAGGAATGGTT 60.460 55.000 0.00 0.00 0.00 3.67
688 692 1.739067 GTAGCAGCGAGGAATGGTTT 58.261 50.000 0.00 0.00 0.00 3.27
689 693 2.084546 GTAGCAGCGAGGAATGGTTTT 58.915 47.619 0.00 0.00 0.00 2.43
690 694 1.168714 AGCAGCGAGGAATGGTTTTC 58.831 50.000 0.00 0.00 0.00 2.29
691 695 0.171231 GCAGCGAGGAATGGTTTTCC 59.829 55.000 0.00 0.00 38.86 3.13
700 704 5.728637 AGGAATGGTTTTCCTTTCATCAC 57.271 39.130 12.55 0.00 46.21 3.06
701 705 5.397360 AGGAATGGTTTTCCTTTCATCACT 58.603 37.500 12.55 1.61 46.21 3.41
702 706 5.840693 AGGAATGGTTTTCCTTTCATCACTT 59.159 36.000 12.55 0.00 46.21 3.16
703 707 6.327365 AGGAATGGTTTTCCTTTCATCACTTT 59.673 34.615 12.55 0.00 46.21 2.66
704 708 7.147497 AGGAATGGTTTTCCTTTCATCACTTTT 60.147 33.333 12.55 0.00 46.21 2.27
705 709 7.790823 AATGGTTTTCCTTTCATCACTTTTG 57.209 32.000 0.00 0.00 41.38 2.44
706 710 6.293004 TGGTTTTCCTTTCATCACTTTTGT 57.707 33.333 0.00 0.00 41.38 2.83
707 711 6.706295 TGGTTTTCCTTTCATCACTTTTGTT 58.294 32.000 0.00 0.00 41.38 2.83
708 712 7.841956 TGGTTTTCCTTTCATCACTTTTGTTA 58.158 30.769 0.00 0.00 41.38 2.41
709 713 7.762159 TGGTTTTCCTTTCATCACTTTTGTTAC 59.238 33.333 0.00 0.00 41.38 2.50
710 714 7.979537 GGTTTTCCTTTCATCACTTTTGTTACT 59.020 33.333 0.00 0.00 36.94 2.24
711 715 9.020813 GTTTTCCTTTCATCACTTTTGTTACTC 57.979 33.333 0.00 0.00 0.00 2.59
712 716 7.873719 TTCCTTTCATCACTTTTGTTACTCA 57.126 32.000 0.00 0.00 0.00 3.41
713 717 8.463930 TTCCTTTCATCACTTTTGTTACTCAT 57.536 30.769 0.00 0.00 0.00 2.90
714 718 7.874940 TCCTTTCATCACTTTTGTTACTCATG 58.125 34.615 0.00 0.00 0.00 3.07
715 719 7.502226 TCCTTTCATCACTTTTGTTACTCATGT 59.498 33.333 0.00 0.00 0.00 3.21
716 720 7.592533 CCTTTCATCACTTTTGTTACTCATGTG 59.407 37.037 0.00 0.00 0.00 3.21
717 721 7.800155 TTCATCACTTTTGTTACTCATGTGA 57.200 32.000 0.94 0.00 36.46 3.58
718 722 7.800155 TCATCACTTTTGTTACTCATGTGAA 57.200 32.000 0.94 0.00 36.05 3.18
719 723 8.219546 TCATCACTTTTGTTACTCATGTGAAA 57.780 30.769 0.94 0.00 36.05 2.69
720 724 8.681806 TCATCACTTTTGTTACTCATGTGAAAA 58.318 29.630 0.94 0.00 36.05 2.29
721 725 8.745837 CATCACTTTTGTTACTCATGTGAAAAC 58.254 33.333 0.94 6.34 36.05 2.43
722 726 7.821652 TCACTTTTGTTACTCATGTGAAAACA 58.178 30.769 12.90 12.90 32.67 2.83
723 727 7.967854 TCACTTTTGTTACTCATGTGAAAACAG 59.032 33.333 14.99 9.88 33.98 3.16
724 728 7.967854 CACTTTTGTTACTCATGTGAAAACAGA 59.032 33.333 14.99 10.98 33.98 3.41
725 729 8.519526 ACTTTTGTTACTCATGTGAAAACAGAA 58.480 29.630 14.99 15.28 33.98 3.02
726 730 8.909708 TTTTGTTACTCATGTGAAAACAGAAG 57.090 30.769 14.99 0.00 33.98 2.85
727 731 6.618287 TGTTACTCATGTGAAAACAGAAGG 57.382 37.500 12.90 0.00 30.93 3.46
728 732 6.353323 TGTTACTCATGTGAAAACAGAAGGA 58.647 36.000 12.90 0.00 30.93 3.36
729 733 6.998074 TGTTACTCATGTGAAAACAGAAGGAT 59.002 34.615 12.90 0.00 30.93 3.24
730 734 7.502226 TGTTACTCATGTGAAAACAGAAGGATT 59.498 33.333 12.90 0.00 30.93 3.01
748 752 8.851960 GAAGGATTCGTTTTTCTGTAACTTTT 57.148 30.769 0.00 0.00 34.17 2.27
749 753 9.297586 GAAGGATTCGTTTTTCTGTAACTTTTT 57.702 29.630 0.00 0.00 34.17 1.94
774 778 9.627123 TTTTGAATGAGAAAGAAAGAGGTTAGA 57.373 29.630 0.00 0.00 0.00 2.10
775 779 8.839310 TTGAATGAGAAAGAAAGAGGTTAGAG 57.161 34.615 0.00 0.00 0.00 2.43
776 780 8.195165 TGAATGAGAAAGAAAGAGGTTAGAGA 57.805 34.615 0.00 0.00 0.00 3.10
777 781 8.651389 TGAATGAGAAAGAAAGAGGTTAGAGAA 58.349 33.333 0.00 0.00 0.00 2.87
778 782 9.665719 GAATGAGAAAGAAAGAGGTTAGAGAAT 57.334 33.333 0.00 0.00 0.00 2.40
783 787 9.936759 AGAAAGAAAGAGGTTAGAGAATAAGTG 57.063 33.333 0.00 0.00 0.00 3.16
784 788 9.157104 GAAAGAAAGAGGTTAGAGAATAAGTGG 57.843 37.037 0.00 0.00 0.00 4.00
785 789 6.645306 AGAAAGAGGTTAGAGAATAAGTGGC 58.355 40.000 0.00 0.00 0.00 5.01
786 790 5.360649 AAGAGGTTAGAGAATAAGTGGCC 57.639 43.478 0.00 0.00 0.00 5.36
787 791 4.362677 AGAGGTTAGAGAATAAGTGGCCA 58.637 43.478 0.00 0.00 0.00 5.36
788 792 4.407296 AGAGGTTAGAGAATAAGTGGCCAG 59.593 45.833 5.11 0.00 0.00 4.85
789 793 4.362677 AGGTTAGAGAATAAGTGGCCAGA 58.637 43.478 5.11 0.00 0.00 3.86
880 884 1.221840 CCACAGAGAACCATCGGGG 59.778 63.158 0.00 0.00 44.81 5.73
881 885 1.221840 CACAGAGAACCATCGGGGG 59.778 63.158 0.00 0.00 42.91 5.40
882 886 1.080354 ACAGAGAACCATCGGGGGA 59.920 57.895 0.07 0.00 42.91 4.81
883 887 0.546747 ACAGAGAACCATCGGGGGAA 60.547 55.000 0.07 0.00 42.91 3.97
884 888 0.179000 CAGAGAACCATCGGGGGAAG 59.821 60.000 0.07 0.00 42.91 3.46
885 889 0.983378 AGAGAACCATCGGGGGAAGG 60.983 60.000 0.07 0.00 42.91 3.46
886 890 0.981277 GAGAACCATCGGGGGAAGGA 60.981 60.000 0.07 0.00 42.91 3.36
969 974 1.229984 AGAACCCTTCCCTCCCCTG 60.230 63.158 0.00 0.00 0.00 4.45
1026 1031 3.213402 CTCCTCCGCCGTCTCCTC 61.213 72.222 0.00 0.00 0.00 3.71
1320 2137 2.283966 ACCACCTCCTCCCTCGTG 60.284 66.667 0.00 0.00 0.00 4.35
1452 2269 3.240606 CTTCACCTGCAACGCCGTG 62.241 63.158 0.00 0.00 31.79 4.94
2214 3031 2.352030 CGGCTGCTTCAACAACATCATT 60.352 45.455 0.00 0.00 0.00 2.57
2412 3229 1.068434 CACGGCCCAAAGTTCAACATT 59.932 47.619 0.00 0.00 0.00 2.71
2445 3262 8.110860 TCAATAGAATGTTTGAAGGACTTTCC 57.889 34.615 0.00 0.00 33.86 3.13
2458 3275 4.676951 TTTCCCAAGCTGGCCGGG 62.677 66.667 15.02 10.31 41.76 5.73
2538 3355 4.039124 ACAACCACATTTGAAATCCTGGTC 59.961 41.667 14.20 0.00 30.54 4.02
2613 3430 1.760480 GGCAAGGGGTGGTGTTGTT 60.760 57.895 0.00 0.00 0.00 2.83
2641 3458 0.178973 TGAGTTCCGGGAGTCTGTCA 60.179 55.000 18.69 0.00 0.00 3.58
2757 3574 1.371183 CCCTCGCACTTCACCTCAA 59.629 57.895 0.00 0.00 0.00 3.02
3579 4609 2.194056 CAGCAGCCTGGGTATGGG 59.806 66.667 0.00 0.00 35.38 4.00
3580 4610 3.099170 AGCAGCCTGGGTATGGGG 61.099 66.667 0.00 0.00 0.00 4.96
3581 4611 3.420482 GCAGCCTGGGTATGGGGT 61.420 66.667 0.00 0.00 0.00 4.95
3902 4933 6.777580 CCAAATATACCCCAAGTTAATGAGCT 59.222 38.462 0.00 0.00 0.00 4.09
3989 5020 6.696583 TGTGTGCAACTGTTTGATCTTATTTG 59.303 34.615 0.00 0.00 38.04 2.32
4328 5359 6.094048 TGGAGTACCTTGTACGTAGTATGAAC 59.906 42.308 0.00 0.00 40.49 3.18
4444 5475 7.174253 TGTTTAAAATGACGCCAGAACTAGAAT 59.826 33.333 0.00 0.00 0.00 2.40
4454 5485 4.096532 GCCAGAACTAGAATTTAAGCCCAC 59.903 45.833 0.00 0.00 0.00 4.61
4518 5549 1.401539 GCCGTTGCCAAATCTTCTGTC 60.402 52.381 0.00 0.00 0.00 3.51
4560 5591 5.302360 ACGCCACTACAATCTTACTTTTGA 58.698 37.500 0.00 0.00 0.00 2.69
4602 5633 7.619050 ACATGGCTGATGATCTTACTATAAGG 58.381 38.462 0.00 0.00 35.80 2.69
4842 5977 2.811514 GCCCGATGCCAGGATGAGA 61.812 63.158 0.00 0.00 39.69 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.531753 AGTAATATGGATCGGAGGGAGTA 57.468 43.478 0.00 0.00 0.00 2.59
25 26 0.604073 TACATCCGTTGGAGCGACAA 59.396 50.000 0.00 0.00 34.05 3.18
34 35 6.603237 TTTCAATGCTAGATACATCCGTTG 57.397 37.500 0.00 0.00 0.00 4.10
38 39 9.664332 AGACATATTTCAATGCTAGATACATCC 57.336 33.333 0.00 0.00 0.00 3.51
63 64 6.902224 TGTCGTTCAAATGGATGTGTATAG 57.098 37.500 0.00 0.00 0.00 1.31
68 69 4.488126 ACTTGTCGTTCAAATGGATGTG 57.512 40.909 0.00 0.00 35.48 3.21
70 71 7.857389 CCATAATACTTGTCGTTCAAATGGATG 59.143 37.037 13.21 7.28 39.71 3.51
71 72 7.773224 TCCATAATACTTGTCGTTCAAATGGAT 59.227 33.333 15.29 1.21 40.51 3.41
73 74 7.315247 TCCATAATACTTGTCGTTCAAATGG 57.685 36.000 12.71 12.71 39.17 3.16
99 100 9.245962 GTATACGATTTCATTATATTCCCTCGG 57.754 37.037 0.00 0.00 0.00 4.63
100 101 8.955002 CGTATACGATTTCATTATATTCCCTCG 58.045 37.037 20.58 0.00 43.02 4.63
101 102 9.798994 ACGTATACGATTTCATTATATTCCCTC 57.201 33.333 30.77 0.00 43.02 4.30
126 127 1.553704 AGTGGGAAATCACCTCGGTAC 59.446 52.381 0.00 0.00 38.34 3.34
132 133 3.593442 TGTTTGAGTGGGAAATCACCT 57.407 42.857 0.00 0.00 38.34 4.00
134 135 5.262588 AGTTTGTTTGAGTGGGAAATCAC 57.737 39.130 0.00 0.00 37.89 3.06
145 146 4.630894 TGTGTGCCTTAGTTTGTTTGAG 57.369 40.909 0.00 0.00 0.00 3.02
150 151 5.564651 GCAACATATGTGTGCCTTAGTTTGT 60.565 40.000 22.14 0.00 38.92 2.83
164 165 2.158827 TCTGCCCATACGCAACATATGT 60.159 45.455 1.41 1.41 38.56 2.29
175 176 2.803451 GATCGATCGATCTGCCCATAC 58.197 52.381 38.45 18.34 45.42 2.39
251 253 9.243637 CGTGTTTCCATCTTTTATTTCTTTTCA 57.756 29.630 0.00 0.00 0.00 2.69
252 254 9.458374 TCGTGTTTCCATCTTTTATTTCTTTTC 57.542 29.630 0.00 0.00 0.00 2.29
295 298 8.628630 TTTTCAATTTCAACACTTCCCTTTTT 57.371 26.923 0.00 0.00 0.00 1.94
296 299 8.100164 TCTTTTCAATTTCAACACTTCCCTTTT 58.900 29.630 0.00 0.00 0.00 2.27
297 300 7.619965 TCTTTTCAATTTCAACACTTCCCTTT 58.380 30.769 0.00 0.00 0.00 3.11
300 303 7.201609 GGTTTCTTTTCAATTTCAACACTTCCC 60.202 37.037 0.00 0.00 0.00 3.97
301 304 7.333174 TGGTTTCTTTTCAATTTCAACACTTCC 59.667 33.333 0.00 0.00 0.00 3.46
302 305 8.250538 TGGTTTCTTTTCAATTTCAACACTTC 57.749 30.769 0.00 0.00 0.00 3.01
315 318 7.841956 TCTTTTGGTTGTATGGTTTCTTTTCA 58.158 30.769 0.00 0.00 0.00 2.69
322 325 8.472007 TGTCTATTCTTTTGGTTGTATGGTTT 57.528 30.769 0.00 0.00 0.00 3.27
325 328 9.927668 ATTTTGTCTATTCTTTTGGTTGTATGG 57.072 29.630 0.00 0.00 0.00 2.74
376 379 6.070481 TCCTGGTTTCTGCCTTTTTAGTTTTT 60.070 34.615 0.00 0.00 0.00 1.94
387 390 4.934356 TGATTATTTCCTGGTTTCTGCCT 58.066 39.130 0.00 0.00 0.00 4.75
392 395 9.541143 TCTTGTTTTTGATTATTTCCTGGTTTC 57.459 29.630 0.00 0.00 0.00 2.78
412 415 9.533253 CCATTCTTATTTGTGTTTCTTCTTGTT 57.467 29.630 0.00 0.00 0.00 2.83
413 416 8.143835 CCCATTCTTATTTGTGTTTCTTCTTGT 58.856 33.333 0.00 0.00 0.00 3.16
417 420 9.541143 TTTTCCCATTCTTATTTGTGTTTCTTC 57.459 29.630 0.00 0.00 0.00 2.87
418 421 9.325198 GTTTTCCCATTCTTATTTGTGTTTCTT 57.675 29.630 0.00 0.00 0.00 2.52
420 423 7.713073 TGGTTTTCCCATTCTTATTTGTGTTTC 59.287 33.333 0.00 0.00 38.72 2.78
438 441 1.367471 GGCTTGCCAGTGGTTTTCC 59.633 57.895 11.74 4.04 41.14 3.13
439 442 0.032540 CTGGCTTGCCAGTGGTTTTC 59.967 55.000 28.08 0.00 33.53 2.29
447 450 1.153901 CATTTCGCTGGCTTGCCAG 60.154 57.895 30.97 30.97 40.47 4.85
454 457 2.751436 TGGGCTCATTTCGCTGGC 60.751 61.111 0.00 0.00 0.00 4.85
455 458 2.768492 GCTGGGCTCATTTCGCTGG 61.768 63.158 0.00 0.00 0.00 4.85
456 459 2.768492 GGCTGGGCTCATTTCGCTG 61.768 63.158 0.00 0.00 0.00 5.18
457 460 2.439156 GGCTGGGCTCATTTCGCT 60.439 61.111 0.00 0.00 0.00 4.93
458 461 0.819259 TATGGCTGGGCTCATTTCGC 60.819 55.000 0.00 0.00 0.00 4.70
466 470 3.118482 CGATGATTCTATATGGCTGGGCT 60.118 47.826 0.00 0.00 0.00 5.19
472 476 6.145534 TGTCGAAAACGATGATTCTATATGGC 59.854 38.462 0.00 0.00 0.00 4.40
483 487 5.064198 ACAAAGTTCTTGTCGAAAACGATGA 59.936 36.000 0.00 0.00 32.41 2.92
487 491 5.566016 TCAAACAAAGTTCTTGTCGAAAACG 59.434 36.000 0.00 0.00 32.41 3.60
491 495 6.090129 CCTTTCAAACAAAGTTCTTGTCGAA 58.910 36.000 0.00 0.00 0.00 3.71
492 496 5.392595 CCCTTTCAAACAAAGTTCTTGTCGA 60.393 40.000 0.00 0.00 0.00 4.20
493 497 4.798387 CCCTTTCAAACAAAGTTCTTGTCG 59.202 41.667 0.00 0.00 0.00 4.35
494 498 5.109210 CCCCTTTCAAACAAAGTTCTTGTC 58.891 41.667 0.00 0.00 0.00 3.18
495 499 4.081142 CCCCCTTTCAAACAAAGTTCTTGT 60.081 41.667 0.00 0.00 0.00 3.16
496 500 4.161377 TCCCCCTTTCAAACAAAGTTCTTG 59.839 41.667 0.00 0.00 0.00 3.02
545 549 1.802553 TGAGTAATGGGGGAGCTACC 58.197 55.000 6.36 6.36 38.08 3.18
565 569 2.723273 TGACTAGACTCCGCAATCTCA 58.277 47.619 0.00 0.00 0.00 3.27
567 571 4.277174 CACTATGACTAGACTCCGCAATCT 59.723 45.833 0.00 0.00 0.00 2.40
582 586 5.292101 GTGTGCATAACTTCTCCACTATGAC 59.708 44.000 0.00 0.00 0.00 3.06
591 595 6.246420 AGACAATTGTGTGCATAACTTCTC 57.754 37.500 17.58 0.00 38.41 2.87
593 597 7.806690 TCTTAGACAATTGTGTGCATAACTTC 58.193 34.615 17.58 0.00 38.41 3.01
603 607 8.135529 GCCTAACTTTTTCTTAGACAATTGTGT 58.864 33.333 17.58 15.25 42.10 3.72
610 614 7.062749 TGAGAGCCTAACTTTTTCTTAGACA 57.937 36.000 0.00 0.00 0.00 3.41
611 615 8.554835 AATGAGAGCCTAACTTTTTCTTAGAC 57.445 34.615 0.00 0.00 0.00 2.59
612 616 9.877178 CTAATGAGAGCCTAACTTTTTCTTAGA 57.123 33.333 0.00 0.00 0.00 2.10
613 617 9.660180 ACTAATGAGAGCCTAACTTTTTCTTAG 57.340 33.333 0.00 0.00 0.00 2.18
615 619 8.787852 CAACTAATGAGAGCCTAACTTTTTCTT 58.212 33.333 0.00 0.00 0.00 2.52
616 620 8.157476 TCAACTAATGAGAGCCTAACTTTTTCT 58.843 33.333 0.00 0.00 33.04 2.52
617 621 8.324163 TCAACTAATGAGAGCCTAACTTTTTC 57.676 34.615 0.00 0.00 33.04 2.29
643 647 9.869844 CGGAATGACAGAATGATATAAAAGAAC 57.130 33.333 0.00 0.00 39.69 3.01
644 648 9.613428 ACGGAATGACAGAATGATATAAAAGAA 57.387 29.630 0.00 0.00 39.69 2.52
647 651 8.988934 GCTACGGAATGACAGAATGATATAAAA 58.011 33.333 0.00 0.00 39.69 1.52
648 652 8.147704 TGCTACGGAATGACAGAATGATATAAA 58.852 33.333 0.00 0.00 39.69 1.40
649 653 7.666623 TGCTACGGAATGACAGAATGATATAA 58.333 34.615 0.00 0.00 39.69 0.98
650 654 7.227049 TGCTACGGAATGACAGAATGATATA 57.773 36.000 0.00 0.00 39.69 0.86
651 655 6.101650 TGCTACGGAATGACAGAATGATAT 57.898 37.500 0.00 0.00 39.69 1.63
652 656 5.529581 TGCTACGGAATGACAGAATGATA 57.470 39.130 0.00 0.00 39.69 2.15
653 657 4.375272 CTGCTACGGAATGACAGAATGAT 58.625 43.478 0.00 0.00 39.69 2.45
654 658 3.785486 CTGCTACGGAATGACAGAATGA 58.215 45.455 0.00 0.00 39.69 2.57
655 659 2.286294 GCTGCTACGGAATGACAGAATG 59.714 50.000 0.00 0.00 46.00 2.67
656 660 2.555199 GCTGCTACGGAATGACAGAAT 58.445 47.619 0.00 0.00 0.00 2.40
657 661 1.735700 CGCTGCTACGGAATGACAGAA 60.736 52.381 0.00 0.00 0.00 3.02
658 662 0.179137 CGCTGCTACGGAATGACAGA 60.179 55.000 0.00 0.00 0.00 3.41
659 663 0.179137 TCGCTGCTACGGAATGACAG 60.179 55.000 0.00 0.00 0.00 3.51
660 664 0.179137 CTCGCTGCTACGGAATGACA 60.179 55.000 0.00 0.00 0.00 3.58
661 665 0.872021 CCTCGCTGCTACGGAATGAC 60.872 60.000 0.00 0.00 0.00 3.06
662 666 1.035385 TCCTCGCTGCTACGGAATGA 61.035 55.000 0.00 0.00 0.00 2.57
663 667 0.179111 TTCCTCGCTGCTACGGAATG 60.179 55.000 9.20 0.00 31.00 2.67
664 668 0.753262 ATTCCTCGCTGCTACGGAAT 59.247 50.000 16.23 16.23 40.46 3.01
665 669 0.179111 CATTCCTCGCTGCTACGGAA 60.179 55.000 13.78 13.78 39.62 4.30
666 670 1.437573 CATTCCTCGCTGCTACGGA 59.562 57.895 0.00 0.00 0.00 4.69
667 671 1.592669 CCATTCCTCGCTGCTACGG 60.593 63.158 0.00 0.00 0.00 4.02
668 672 0.460284 AACCATTCCTCGCTGCTACG 60.460 55.000 0.00 0.00 0.00 3.51
669 673 1.739067 AAACCATTCCTCGCTGCTAC 58.261 50.000 0.00 0.00 0.00 3.58
670 674 2.356135 GAAAACCATTCCTCGCTGCTA 58.644 47.619 0.00 0.00 0.00 3.49
671 675 1.168714 GAAAACCATTCCTCGCTGCT 58.831 50.000 0.00 0.00 0.00 4.24
672 676 0.171231 GGAAAACCATTCCTCGCTGC 59.829 55.000 0.00 0.00 35.73 5.25
673 677 1.826385 AGGAAAACCATTCCTCGCTG 58.174 50.000 3.92 0.00 45.32 5.18
679 683 5.728637 AGTGATGAAAGGAAAACCATTCC 57.271 39.130 0.00 0.00 38.86 3.01
680 684 7.495606 ACAAAAGTGATGAAAGGAAAACCATTC 59.504 33.333 0.00 0.00 0.00 2.67
681 685 7.337938 ACAAAAGTGATGAAAGGAAAACCATT 58.662 30.769 0.00 0.00 0.00 3.16
682 686 6.888105 ACAAAAGTGATGAAAGGAAAACCAT 58.112 32.000 0.00 0.00 0.00 3.55
683 687 6.293004 ACAAAAGTGATGAAAGGAAAACCA 57.707 33.333 0.00 0.00 0.00 3.67
684 688 7.979537 AGTAACAAAAGTGATGAAAGGAAAACC 59.020 33.333 0.00 0.00 0.00 3.27
685 689 8.926715 AGTAACAAAAGTGATGAAAGGAAAAC 57.073 30.769 0.00 0.00 0.00 2.43
686 690 8.744652 TGAGTAACAAAAGTGATGAAAGGAAAA 58.255 29.630 0.00 0.00 0.00 2.29
687 691 8.287439 TGAGTAACAAAAGTGATGAAAGGAAA 57.713 30.769 0.00 0.00 0.00 3.13
688 692 7.873719 TGAGTAACAAAAGTGATGAAAGGAA 57.126 32.000 0.00 0.00 0.00 3.36
689 693 7.502226 ACATGAGTAACAAAAGTGATGAAAGGA 59.498 33.333 0.00 0.00 0.00 3.36
690 694 7.592533 CACATGAGTAACAAAAGTGATGAAAGG 59.407 37.037 0.00 0.00 34.29 3.11
691 695 8.344831 TCACATGAGTAACAAAAGTGATGAAAG 58.655 33.333 0.00 0.00 35.55 2.62
692 696 8.219546 TCACATGAGTAACAAAAGTGATGAAA 57.780 30.769 0.00 0.00 35.55 2.69
693 697 7.800155 TCACATGAGTAACAAAAGTGATGAA 57.200 32.000 0.00 0.00 35.55 2.57
694 698 7.800155 TTCACATGAGTAACAAAAGTGATGA 57.200 32.000 0.00 0.00 38.04 2.92
695 699 8.745837 GTTTTCACATGAGTAACAAAAGTGATG 58.254 33.333 0.00 0.00 38.04 3.07
696 700 8.465999 TGTTTTCACATGAGTAACAAAAGTGAT 58.534 29.630 0.00 0.00 38.04 3.06
697 701 7.821652 TGTTTTCACATGAGTAACAAAAGTGA 58.178 30.769 0.00 0.00 37.21 3.41
698 702 7.967854 TCTGTTTTCACATGAGTAACAAAAGTG 59.032 33.333 0.00 0.00 33.31 3.16
699 703 8.050778 TCTGTTTTCACATGAGTAACAAAAGT 57.949 30.769 0.00 0.00 33.31 2.66
700 704 8.909708 TTCTGTTTTCACATGAGTAACAAAAG 57.090 30.769 0.00 0.00 33.31 2.27
701 705 7.973388 CCTTCTGTTTTCACATGAGTAACAAAA 59.027 33.333 0.00 0.28 33.31 2.44
702 706 7.338196 TCCTTCTGTTTTCACATGAGTAACAAA 59.662 33.333 0.00 4.71 33.31 2.83
703 707 6.826231 TCCTTCTGTTTTCACATGAGTAACAA 59.174 34.615 0.00 0.00 33.31 2.83
704 708 6.353323 TCCTTCTGTTTTCACATGAGTAACA 58.647 36.000 0.00 6.57 32.96 2.41
705 709 6.861065 TCCTTCTGTTTTCACATGAGTAAC 57.139 37.500 0.00 2.04 30.39 2.50
706 710 7.095229 CGAATCCTTCTGTTTTCACATGAGTAA 60.095 37.037 0.00 0.00 30.39 2.24
707 711 6.368791 CGAATCCTTCTGTTTTCACATGAGTA 59.631 38.462 0.00 0.00 30.39 2.59
708 712 5.180117 CGAATCCTTCTGTTTTCACATGAGT 59.820 40.000 0.00 0.00 30.39 3.41
709 713 5.180117 ACGAATCCTTCTGTTTTCACATGAG 59.820 40.000 0.00 0.00 30.39 2.90
710 714 5.063204 ACGAATCCTTCTGTTTTCACATGA 58.937 37.500 0.00 0.00 30.39 3.07
711 715 5.362556 ACGAATCCTTCTGTTTTCACATG 57.637 39.130 0.00 0.00 30.39 3.21
712 716 6.391227 AAACGAATCCTTCTGTTTTCACAT 57.609 33.333 0.00 0.00 34.91 3.21
713 717 5.828299 AAACGAATCCTTCTGTTTTCACA 57.172 34.783 0.00 0.00 34.91 3.58
714 718 6.972901 AGAAAAACGAATCCTTCTGTTTTCAC 59.027 34.615 17.61 14.69 41.14 3.18
715 719 6.972328 CAGAAAAACGAATCCTTCTGTTTTCA 59.028 34.615 17.61 0.00 41.14 2.69
716 720 7.381744 CAGAAAAACGAATCCTTCTGTTTTC 57.618 36.000 15.71 14.04 41.14 2.29
721 725 7.190920 AGTTACAGAAAAACGAATCCTTCTG 57.809 36.000 8.69 8.69 46.62 3.02
722 726 7.803279 AAGTTACAGAAAAACGAATCCTTCT 57.197 32.000 0.00 0.00 32.00 2.85
723 727 8.851960 AAAAGTTACAGAAAAACGAATCCTTC 57.148 30.769 0.00 0.00 32.00 3.46
748 752 9.627123 TCTAACCTCTTTCTTTCTCATTCAAAA 57.373 29.630 0.00 0.00 0.00 2.44
749 753 9.277783 CTCTAACCTCTTTCTTTCTCATTCAAA 57.722 33.333 0.00 0.00 0.00 2.69
750 754 8.651389 TCTCTAACCTCTTTCTTTCTCATTCAA 58.349 33.333 0.00 0.00 0.00 2.69
751 755 8.195165 TCTCTAACCTCTTTCTTTCTCATTCA 57.805 34.615 0.00 0.00 0.00 2.57
752 756 9.665719 ATTCTCTAACCTCTTTCTTTCTCATTC 57.334 33.333 0.00 0.00 0.00 2.67
757 761 9.936759 CACTTATTCTCTAACCTCTTTCTTTCT 57.063 33.333 0.00 0.00 0.00 2.52
758 762 9.157104 CCACTTATTCTCTAACCTCTTTCTTTC 57.843 37.037 0.00 0.00 0.00 2.62
759 763 7.608376 GCCACTTATTCTCTAACCTCTTTCTTT 59.392 37.037 0.00 0.00 0.00 2.52
760 764 7.106890 GCCACTTATTCTCTAACCTCTTTCTT 58.893 38.462 0.00 0.00 0.00 2.52
761 765 6.352308 GGCCACTTATTCTCTAACCTCTTTCT 60.352 42.308 0.00 0.00 0.00 2.52
762 766 5.818336 GGCCACTTATTCTCTAACCTCTTTC 59.182 44.000 0.00 0.00 0.00 2.62
763 767 5.250774 TGGCCACTTATTCTCTAACCTCTTT 59.749 40.000 0.00 0.00 0.00 2.52
764 768 4.783227 TGGCCACTTATTCTCTAACCTCTT 59.217 41.667 0.00 0.00 0.00 2.85
765 769 4.362677 TGGCCACTTATTCTCTAACCTCT 58.637 43.478 0.00 0.00 0.00 3.69
766 770 4.406003 TCTGGCCACTTATTCTCTAACCTC 59.594 45.833 0.00 0.00 0.00 3.85
767 771 4.362677 TCTGGCCACTTATTCTCTAACCT 58.637 43.478 0.00 0.00 0.00 3.50
768 772 4.755266 TCTGGCCACTTATTCTCTAACC 57.245 45.455 0.00 0.00 0.00 2.85
769 773 6.038714 CCAATTCTGGCCACTTATTCTCTAAC 59.961 42.308 0.00 0.00 35.39 2.34
770 774 6.122277 CCAATTCTGGCCACTTATTCTCTAA 58.878 40.000 0.00 0.00 35.39 2.10
771 775 5.397899 CCCAATTCTGGCCACTTATTCTCTA 60.398 44.000 0.00 0.00 41.99 2.43
772 776 4.530875 CCAATTCTGGCCACTTATTCTCT 58.469 43.478 0.00 0.00 35.39 3.10
773 777 3.633986 CCCAATTCTGGCCACTTATTCTC 59.366 47.826 0.00 0.00 41.99 2.87
774 778 3.011708 ACCCAATTCTGGCCACTTATTCT 59.988 43.478 0.00 0.00 41.99 2.40
775 779 3.365472 ACCCAATTCTGGCCACTTATTC 58.635 45.455 0.00 0.00 41.99 1.75
776 780 3.473113 ACCCAATTCTGGCCACTTATT 57.527 42.857 0.00 0.00 41.99 1.40
777 781 3.099141 CAACCCAATTCTGGCCACTTAT 58.901 45.455 0.00 0.00 41.99 1.73
778 782 2.524306 CAACCCAATTCTGGCCACTTA 58.476 47.619 0.00 0.00 41.99 2.24
779 783 1.341080 CAACCCAATTCTGGCCACTT 58.659 50.000 0.00 0.00 41.99 3.16
780 784 0.542702 CCAACCCAATTCTGGCCACT 60.543 55.000 0.00 0.00 41.99 4.00
781 785 0.541764 TCCAACCCAATTCTGGCCAC 60.542 55.000 0.00 0.00 41.99 5.01
782 786 0.189574 TTCCAACCCAATTCTGGCCA 59.810 50.000 4.71 4.71 41.99 5.36
783 787 0.897621 CTTCCAACCCAATTCTGGCC 59.102 55.000 0.00 0.00 41.99 5.36
784 788 0.897621 CCTTCCAACCCAATTCTGGC 59.102 55.000 0.00 0.00 41.99 4.85
785 789 2.603075 TCCTTCCAACCCAATTCTGG 57.397 50.000 0.00 0.00 43.10 3.86
786 790 2.232208 GCTTCCTTCCAACCCAATTCTG 59.768 50.000 0.00 0.00 0.00 3.02
787 791 2.529632 GCTTCCTTCCAACCCAATTCT 58.470 47.619 0.00 0.00 0.00 2.40
788 792 1.202348 CGCTTCCTTCCAACCCAATTC 59.798 52.381 0.00 0.00 0.00 2.17
789 793 1.203001 TCGCTTCCTTCCAACCCAATT 60.203 47.619 0.00 0.00 0.00 2.32
880 884 3.165875 CCCTTTCCTTTCCTTTCCTTCC 58.834 50.000 0.00 0.00 0.00 3.46
881 885 3.165875 CCCCTTTCCTTTCCTTTCCTTC 58.834 50.000 0.00 0.00 0.00 3.46
882 886 2.158158 CCCCCTTTCCTTTCCTTTCCTT 60.158 50.000 0.00 0.00 0.00 3.36
883 887 1.433199 CCCCCTTTCCTTTCCTTTCCT 59.567 52.381 0.00 0.00 0.00 3.36
884 888 1.149288 ACCCCCTTTCCTTTCCTTTCC 59.851 52.381 0.00 0.00 0.00 3.13
885 889 2.158370 TCACCCCCTTTCCTTTCCTTTC 60.158 50.000 0.00 0.00 0.00 2.62
886 890 1.863581 TCACCCCCTTTCCTTTCCTTT 59.136 47.619 0.00 0.00 0.00 3.11
1009 1014 3.213402 GAGGAGACGGCGGAGGAG 61.213 72.222 13.24 0.00 0.00 3.69
1010 1015 4.816984 GGAGGAGACGGCGGAGGA 62.817 72.222 13.24 0.00 0.00 3.71
1011 1016 4.824515 AGGAGGAGACGGCGGAGG 62.825 72.222 13.24 0.00 0.00 4.30
1012 1017 3.213402 GAGGAGGAGACGGCGGAG 61.213 72.222 13.24 0.00 0.00 4.63
1013 1018 4.816984 GGAGGAGGAGACGGCGGA 62.817 72.222 13.24 0.00 0.00 5.54
1014 1019 4.824515 AGGAGGAGGAGACGGCGG 62.825 72.222 13.24 0.00 0.00 6.13
1015 1020 3.213402 GAGGAGGAGGAGACGGCG 61.213 72.222 4.80 4.80 0.00 6.46
1016 1021 2.835895 GGAGGAGGAGGAGACGGC 60.836 72.222 0.00 0.00 0.00 5.68
1017 1022 2.517402 CGGAGGAGGAGGAGACGG 60.517 72.222 0.00 0.00 0.00 4.79
1018 1023 3.213402 GCGGAGGAGGAGGAGACG 61.213 72.222 0.00 0.00 0.00 4.18
1019 1024 2.835895 GGCGGAGGAGGAGGAGAC 60.836 72.222 0.00 0.00 0.00 3.36
1020 1025 4.507916 CGGCGGAGGAGGAGGAGA 62.508 72.222 0.00 0.00 0.00 3.71
1021 1026 4.824515 ACGGCGGAGGAGGAGGAG 62.825 72.222 13.24 0.00 0.00 3.69
1022 1027 4.816984 GACGGCGGAGGAGGAGGA 62.817 72.222 13.24 0.00 0.00 3.71
1023 1028 4.824515 AGACGGCGGAGGAGGAGG 62.825 72.222 13.24 0.00 0.00 4.30
1024 1029 3.213402 GAGACGGCGGAGGAGGAG 61.213 72.222 13.24 0.00 0.00 3.69
1025 1030 4.816984 GGAGACGGCGGAGGAGGA 62.817 72.222 13.24 0.00 0.00 3.71
1026 1031 4.824515 AGGAGACGGCGGAGGAGG 62.825 72.222 13.24 0.00 0.00 4.30
1092 1109 3.828023 GTTGGGGTGGTGGTGGGT 61.828 66.667 0.00 0.00 0.00 4.51
1094 1111 4.614036 GGGTTGGGGTGGTGGTGG 62.614 72.222 0.00 0.00 0.00 4.61
1604 2421 1.003442 AGCATCTCCTGGTAGGCCA 59.997 57.895 5.01 0.00 43.73 5.36
1721 2538 1.003839 CGGTGGTACATGCTGTGGT 60.004 57.895 0.00 0.00 44.52 4.16
1953 2770 1.819632 GGCGGGCGTCATCTTGAAT 60.820 57.895 0.00 0.00 0.00 2.57
2230 3047 1.453379 CCTCTGCAAGCATCCCCTG 60.453 63.158 0.00 0.00 0.00 4.45
2412 3229 7.656948 CCTTCAAACATTCTATTGAAAAAGCCA 59.343 33.333 2.99 0.00 42.96 4.75
2445 3262 3.944250 ATCAACCCGGCCAGCTTGG 62.944 63.158 2.24 0.00 41.55 3.61
2458 3275 2.821969 ACACCTTCAAGGCATCATCAAC 59.178 45.455 2.20 0.00 39.63 3.18
2641 3458 4.326826 TCGGCATTCTTGAAAATCTCACT 58.673 39.130 0.00 0.00 32.21 3.41
2670 3487 5.541845 TCAAAAGCTTTCTCGATCTCTTCA 58.458 37.500 13.10 0.00 0.00 3.02
2747 3564 1.676967 GGCAGCCCTTGAGGTGAAG 60.677 63.158 0.00 0.00 37.44 3.02
2757 3574 2.363406 GCAAATCCTGGCAGCCCT 60.363 61.111 9.64 0.00 0.00 5.19
2841 3658 0.037975 CACCATTGCCAGGCTGAAAC 60.038 55.000 17.94 5.61 0.00 2.78
3570 4600 1.064017 GCTTGATGAACCCCATACCCA 60.064 52.381 0.00 0.00 35.17 4.51
3579 4609 1.136147 CTGCTGCGCTTGATGAACC 59.864 57.895 9.73 0.00 0.00 3.62
3580 4610 1.513586 GCTGCTGCGCTTGATGAAC 60.514 57.895 9.73 0.00 0.00 3.18
3581 4611 2.693762 GGCTGCTGCGCTTGATGAA 61.694 57.895 9.73 0.00 40.82 2.57
3902 4933 1.945580 TAGGGACACATGCAGTACCA 58.054 50.000 19.32 5.80 42.76 3.25
3989 5020 5.099042 ACATAAACATCAGTGGGGTCTAC 57.901 43.478 0.00 0.00 0.00 2.59
4444 5475 6.040391 GCCAATAACAGATATGTGGGCTTAAA 59.960 38.462 14.72 0.00 35.35 1.52
4454 5485 5.009310 ACATGCAGTGCCAATAACAGATATG 59.991 40.000 13.72 7.34 0.00 1.78
4518 5549 2.600420 CGTCGACCATCATCTGTTTCAG 59.400 50.000 10.58 0.00 0.00 3.02
4560 5591 4.763793 GCCATGTATCCAATAGACAGCATT 59.236 41.667 0.00 0.00 31.63 3.56
4752 5887 9.225436 TGTCTTATATAGCAAACATCAAACACA 57.775 29.630 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.