Multiple sequence alignment - TraesCS6B01G366300

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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 TraesCS6B01G366300 chr6B 100.000 3074 0 0 1 3074 638956534 638953461 0.000000e+00 5677.0
1 TraesCS6B01G366300 chr6B 83.946 299 25 13 1 290 639147282 639146998 6.540000e-67 265.0
2 TraesCS6B01G366300 chr6B 88.732 71 2 2 340 405 639146929 639146860 7.060000e-12 82.4
3 TraesCS6B01G366300 chr6D 94.054 2405 118 11 520 2921 423654986 423657368 0.000000e+00 3626.0
4 TraesCS6B01G366300 chr6D 87.984 258 17 7 1 252 423654382 423654631 3.000000e-75 292.0
5 TraesCS6B01G366300 chr6D 98.701 154 2 0 2921 3074 215405491 215405338 1.090000e-69 274.0
6 TraesCS6B01G366300 chr6A 93.152 1212 61 9 937 2139 568047735 568046537 0.000000e+00 1759.0
7 TraesCS6B01G366300 chr6A 91.736 363 19 5 533 894 568048097 568047745 7.660000e-136 494.0
8 TraesCS6B01G366300 chr6A 98.052 154 3 0 2921 3074 282934353 282934200 5.050000e-68 268.0
9 TraesCS6B01G366300 chr6A 77.804 419 35 30 1 405 553546964 553546590 4.020000e-49 206.0
10 TraesCS6B01G366300 chr6A 77.590 415 43 27 1 405 568272147 568271773 4.020000e-49 206.0
11 TraesCS6B01G366300 chr6A 92.063 126 7 2 2356 2481 568045020 568044898 1.130000e-39 174.0
12 TraesCS6B01G366300 chr6A 75.540 417 42 27 3 405 553468036 553467666 1.910000e-32 150.0
13 TraesCS6B01G366300 chr6A 75.300 417 45 30 3 405 553454050 553453678 2.470000e-31 147.0
14 TraesCS6B01G366300 chr6A 92.157 51 3 1 356 406 568295380 568295331 1.530000e-08 71.3
15 TraesCS6B01G366300 chr7B 83.824 408 36 16 1 386 593129133 593129532 8.100000e-96 361.0
16 TraesCS6B01G366300 chr7B 86.598 97 12 1 413 509 477429730 477429825 4.190000e-19 106.0
17 TraesCS6B01G366300 chr1B 76.734 692 104 34 1322 1987 42309673 42309013 1.770000e-87 333.0
18 TraesCS6B01G366300 chr1B 98.710 155 1 1 2921 3074 243511498 243511344 1.090000e-69 274.0
19 TraesCS6B01G366300 chr1B 98.026 152 3 0 2923 3074 251103647 251103496 6.540000e-67 265.0
20 TraesCS6B01G366300 chr1B 97.403 154 4 0 2921 3074 244498935 244498782 2.350000e-66 263.0
21 TraesCS6B01G366300 chr1B 87.037 108 11 3 412 518 336394276 336394381 5.380000e-23 119.0
22 TraesCS6B01G366300 chr1B 83.178 107 18 0 412 518 403994584 403994478 7.010000e-17 99.0
23 TraesCS6B01G366300 chr1B 88.060 67 8 0 1921 1987 514308020 514308086 2.540000e-11 80.5
24 TraesCS6B01G366300 chrUn 100.000 154 0 0 2921 3074 191288852 191288699 5.020000e-73 285.0
25 TraesCS6B01G366300 chr4B 99.351 154 1 0 2921 3074 304043869 304043716 2.330000e-71 279.0
26 TraesCS6B01G366300 chr4B 86.111 108 14 1 412 518 11583849 11583742 6.970000e-22 115.0
27 TraesCS6B01G366300 chr7D 96.753 154 5 0 2921 3074 268887378 268887531 1.090000e-64 257.0
28 TraesCS6B01G366300 chr7D 86.111 108 13 2 412 518 15027092 15026986 6.970000e-22 115.0
29 TraesCS6B01G366300 chr7D 86.111 108 14 1 412 519 631836209 631836315 6.970000e-22 115.0
30 TraesCS6B01G366300 chr1A 96.104 154 6 0 2921 3074 250267496 250267343 5.090000e-63 252.0
31 TraesCS6B01G366300 chr2D 87.850 107 13 0 412 518 616614217 616614323 3.220000e-25 126.0
32 TraesCS6B01G366300 chr2B 86.916 107 14 0 412 518 41377324 41377430 1.500000e-23 121.0
33 TraesCS6B01G366300 chr2B 86.916 107 14 0 412 518 800998025 800998131 1.500000e-23 121.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G366300 chr6B 638953461 638956534 3073 True 5677 5677 100.000 1 3074 1 chr6B.!!$R1 3073
1 TraesCS6B01G366300 chr6D 423654382 423657368 2986 False 1959 3626 91.019 1 2921 2 chr6D.!!$F1 2920
2 TraesCS6B01G366300 chr6A 568044898 568048097 3199 True 809 1759 92.317 533 2481 3 chr6A.!!$R7 1948
3 TraesCS6B01G366300 chr1B 42309013 42309673 660 True 333 333 76.734 1322 1987 1 chr1B.!!$R1 665

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
621 797 1.261619 GCGCGATCTTTGGGTATCTTG 59.738 52.381 12.10 0.0 0.00 3.02 F
929 1106 1.795768 AACTCCGTACTACGTCGTGA 58.204 50.000 8.47 0.0 40.58 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 1608 2.048127 GGCAAGAGAAGCGACGGT 60.048 61.111 0.0 0.0 0.0 4.83 R
2770 4282 0.893727 ACACATGGTTCCTTTCGGCC 60.894 55.000 0.0 0.0 0.0 6.13 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
31 32 3.520290 CAGAGTTGCACCTAATCCGTA 57.480 47.619 0.00 0.00 0.00 4.02
32 33 3.857052 CAGAGTTGCACCTAATCCGTAA 58.143 45.455 0.00 0.00 0.00 3.18
36 37 4.251268 AGTTGCACCTAATCCGTAACTTC 58.749 43.478 0.00 0.00 32.60 3.01
47 48 4.145365 TCCGTAACTTCCCAATGGTATG 57.855 45.455 0.00 0.00 0.00 2.39
55 56 2.634600 TCCCAATGGTATGTTACACGC 58.365 47.619 0.00 0.00 0.00 5.34
59 60 3.266636 CAATGGTATGTTACACGCCTCA 58.733 45.455 8.15 0.00 0.00 3.86
66 67 3.066291 TGTTACACGCCTCATTCCAAT 57.934 42.857 0.00 0.00 0.00 3.16
70 71 1.812571 ACACGCCTCATTCCAATGAAC 59.187 47.619 3.64 0.00 44.20 3.18
100 101 6.751514 AATATTTCATCGCAAACAGTACCA 57.248 33.333 0.00 0.00 0.00 3.25
157 158 3.762779 GGTAGTTTTGCTAGCAATGCAG 58.237 45.455 29.72 4.14 45.01 4.41
162 163 3.837213 TTTGCTAGCAATGCAGTTCTC 57.163 42.857 29.72 0.00 41.71 2.87
170 171 2.354199 GCAATGCAGTTCTCTTAGCCTC 59.646 50.000 0.00 0.00 0.00 4.70
175 176 1.825474 CAGTTCTCTTAGCCTCCGGAA 59.175 52.381 5.23 0.00 0.00 4.30
262 432 7.147637 ACACAGTAATTGTTTTATGGTTGGGTT 60.148 33.333 0.00 0.00 38.16 4.11
281 451 6.953101 TGGGTTGCTTAGATTTACTACATGA 58.047 36.000 0.00 0.00 0.00 3.07
299 469 6.735678 ACATGATAATTCGTTTACTGCACA 57.264 33.333 0.00 0.00 0.00 4.57
315 485 3.976169 TGCACATTGCTTCACTTTTACC 58.024 40.909 0.00 0.00 45.31 2.85
332 502 6.323739 ACTTTTACCATCAATGAAGTGGTTGT 59.676 34.615 13.09 6.04 43.44 3.32
337 507 5.816777 ACCATCAATGAAGTGGTTGTTTTTG 59.183 36.000 2.84 0.00 43.44 2.44
373 548 1.453900 CGGTTTAATTTGTTGGTGCGC 59.546 47.619 0.00 0.00 0.00 6.09
375 550 2.121009 GTTTAATTTGTTGGTGCGCGT 58.879 42.857 8.43 0.00 0.00 6.01
494 669 5.856126 CTTTGACCAAAGCTAATACGTGA 57.144 39.130 9.25 0.00 40.94 4.35
495 670 6.236017 CTTTGACCAAAGCTAATACGTGAA 57.764 37.500 9.25 0.00 40.94 3.18
496 671 5.856126 TTGACCAAAGCTAATACGTGAAG 57.144 39.130 0.00 0.00 0.00 3.02
497 672 4.890088 TGACCAAAGCTAATACGTGAAGT 58.110 39.130 0.00 0.00 0.00 3.01
498 673 6.028146 TGACCAAAGCTAATACGTGAAGTA 57.972 37.500 0.00 0.00 40.03 2.24
499 674 6.457355 TGACCAAAGCTAATACGTGAAGTAA 58.543 36.000 0.00 0.00 39.04 2.24
500 675 6.930164 TGACCAAAGCTAATACGTGAAGTAAA 59.070 34.615 0.00 0.00 39.04 2.01
501 676 7.604927 TGACCAAAGCTAATACGTGAAGTAAAT 59.395 33.333 0.00 0.00 39.04 1.40
502 677 8.331730 ACCAAAGCTAATACGTGAAGTAAATT 57.668 30.769 0.00 0.00 39.04 1.82
503 678 9.439500 ACCAAAGCTAATACGTGAAGTAAATTA 57.561 29.630 0.00 0.00 39.04 1.40
508 683 9.962759 AGCTAATACGTGAAGTAAATTAAAACG 57.037 29.630 0.00 0.00 39.04 3.60
509 684 9.202545 GCTAATACGTGAAGTAAATTAAAACGG 57.797 33.333 0.00 0.00 39.04 4.44
512 687 6.232139 ACGTGAAGTAAATTAAAACGGAGG 57.768 37.500 0.00 0.00 0.00 4.30
513 688 5.179929 ACGTGAAGTAAATTAAAACGGAGGG 59.820 40.000 0.00 0.00 0.00 4.30
514 689 5.409214 CGTGAAGTAAATTAAAACGGAGGGA 59.591 40.000 0.00 0.00 0.00 4.20
515 690 6.401796 CGTGAAGTAAATTAAAACGGAGGGAG 60.402 42.308 0.00 0.00 0.00 4.30
516 691 6.429078 GTGAAGTAAATTAAAACGGAGGGAGT 59.571 38.462 0.00 0.00 0.00 3.85
517 692 7.603784 GTGAAGTAAATTAAAACGGAGGGAGTA 59.396 37.037 0.00 0.00 0.00 2.59
518 693 7.603784 TGAAGTAAATTAAAACGGAGGGAGTAC 59.396 37.037 0.00 0.00 0.00 2.73
519 694 7.250032 AGTAAATTAAAACGGAGGGAGTACT 57.750 36.000 0.00 0.00 0.00 2.73
520 695 7.101700 AGTAAATTAAAACGGAGGGAGTACTG 58.898 38.462 0.00 0.00 0.00 2.74
521 696 5.494390 AATTAAAACGGAGGGAGTACTGT 57.506 39.130 0.00 0.00 0.00 3.55
522 697 6.610075 AATTAAAACGGAGGGAGTACTGTA 57.390 37.500 0.00 0.00 0.00 2.74
523 698 6.803366 ATTAAAACGGAGGGAGTACTGTAT 57.197 37.500 0.00 0.00 0.00 2.29
524 699 4.467198 AAAACGGAGGGAGTACTGTATG 57.533 45.455 0.00 0.00 0.00 2.39
525 700 2.822707 ACGGAGGGAGTACTGTATGT 57.177 50.000 0.00 0.00 0.00 2.29
526 701 2.376109 ACGGAGGGAGTACTGTATGTG 58.624 52.381 0.00 0.00 0.00 3.21
527 702 2.291411 ACGGAGGGAGTACTGTATGTGT 60.291 50.000 0.00 0.00 0.00 3.72
528 703 2.358267 CGGAGGGAGTACTGTATGTGTC 59.642 54.545 0.00 0.00 0.00 3.67
529 704 3.362706 GGAGGGAGTACTGTATGTGTCA 58.637 50.000 0.00 0.00 0.00 3.58
530 705 3.130693 GGAGGGAGTACTGTATGTGTCAC 59.869 52.174 0.00 0.00 0.00 3.67
531 706 3.097614 AGGGAGTACTGTATGTGTCACC 58.902 50.000 0.00 0.00 0.00 4.02
552 728 5.998363 CACCCCTTATTGCTTCTATTCTACC 59.002 44.000 0.00 0.00 0.00 3.18
621 797 1.261619 GCGCGATCTTTGGGTATCTTG 59.738 52.381 12.10 0.00 0.00 3.02
635 811 5.010282 GGGTATCTTGCAAGGAAAGAAAGA 58.990 41.667 25.73 3.89 37.22 2.52
724 901 2.505982 CCGCCTGATGGTACCCTG 59.494 66.667 10.07 0.00 35.27 4.45
745 922 5.280113 CCTGGATGAAAAACAAATCCACCAT 60.280 40.000 0.00 0.00 43.85 3.55
748 925 7.385267 TGGATGAAAAACAAATCCACCATTAG 58.615 34.615 0.00 0.00 43.85 1.73
749 926 6.818142 GGATGAAAAACAAATCCACCATTAGG 59.182 38.462 0.00 0.00 39.79 2.69
750 927 6.985653 TGAAAAACAAATCCACCATTAGGA 57.014 33.333 0.00 0.00 39.97 2.94
751 928 7.366847 TGAAAAACAAATCCACCATTAGGAA 57.633 32.000 0.00 0.00 38.93 3.36
752 929 7.441017 TGAAAAACAAATCCACCATTAGGAAG 58.559 34.615 0.00 0.00 38.93 3.46
753 930 6.358974 AAAACAAATCCACCATTAGGAAGG 57.641 37.500 0.00 0.00 38.93 3.46
764 941 2.775032 TTAGGAAGGTCCGTGCACGC 62.775 60.000 33.17 20.26 42.75 5.34
919 1096 1.864176 CGGGCAACAAACTCCGTAC 59.136 57.895 0.00 0.00 37.92 3.67
929 1106 1.795768 AACTCCGTACTACGTCGTGA 58.204 50.000 8.47 0.00 40.58 4.35
963 1140 4.036804 TGTGCGGCGCCATGTTTC 62.037 61.111 30.82 10.45 0.00 2.78
984 1161 4.214310 TCTCTTTTCAAATCAAGCCACCA 58.786 39.130 0.00 0.00 0.00 4.17
1143 1326 2.742372 GCAACCATGTCTCCGCGT 60.742 61.111 4.92 0.00 0.00 6.01
1578 1771 2.650778 CTTTGCAACCGGAAGCCC 59.349 61.111 9.46 0.00 0.00 5.19
2126 2336 3.317430 TGATCGTGTGATGGATCTCTCAG 59.683 47.826 0.00 0.00 39.77 3.35
2160 2370 2.310327 ATTGAGCGTGCGGATGCCTA 62.310 55.000 18.21 4.05 41.78 3.93
2161 2371 2.962253 GAGCGTGCGGATGCCTAC 60.962 66.667 18.21 6.18 41.78 3.18
2162 2372 4.873129 AGCGTGCGGATGCCTACG 62.873 66.667 18.21 0.00 41.78 3.51
2199 2409 8.230486 GTCAATCTAAAGTTGTCCTACACATTG 58.770 37.037 0.00 0.00 33.90 2.82
2212 2422 4.164221 CCTACACATTGGTTCCATCCTAGT 59.836 45.833 0.00 0.00 0.00 2.57
2286 3474 4.552166 GCACTTTTGCTAACTTGAGTGA 57.448 40.909 12.62 0.00 46.17 3.41
2301 3489 3.942829 TGAGTGAGAAACAAGGCATAGG 58.057 45.455 0.00 0.00 0.00 2.57
2311 3499 5.841957 AACAAGGCATAGGAACATCATTC 57.158 39.130 0.00 0.00 0.00 2.67
2340 3528 6.260936 ACTTAGGCTATCATCACATTTTTCCG 59.739 38.462 0.00 0.00 0.00 4.30
2343 3531 4.335315 GGCTATCATCACATTTTTCCGACA 59.665 41.667 0.00 0.00 0.00 4.35
2350 3538 8.956533 TCATCACATTTTTCCGACATCTATTA 57.043 30.769 0.00 0.00 0.00 0.98
2351 3539 9.559732 TCATCACATTTTTCCGACATCTATTAT 57.440 29.630 0.00 0.00 0.00 1.28
2382 3892 8.106462 TCAAAGGTCATTTATTGTGTGAGGATA 58.894 33.333 0.00 0.00 0.00 2.59
2543 4053 6.608808 AGGAAGCATTAAGGAGCAACATATTT 59.391 34.615 0.00 0.00 0.00 1.40
2554 4064 9.515226 AAGGAGCAACATATTTACAAACTCTAA 57.485 29.630 0.00 0.00 0.00 2.10
2615 4125 2.031683 GCCACCATAACGTGTATCAAGC 59.968 50.000 0.00 0.00 31.47 4.01
2621 4131 2.450609 AACGTGTATCAAGCGTCCTT 57.549 45.000 0.00 0.00 37.92 3.36
2631 4141 8.609176 GTGTATCAAGCGTCCTTCATAATTTTA 58.391 33.333 0.00 0.00 0.00 1.52
2646 4158 8.818141 TCATAATTTTATAGACTCTTGAGGCG 57.182 34.615 2.55 0.00 0.00 5.52
2649 4161 7.721286 AATTTTATAGACTCTTGAGGCGATG 57.279 36.000 8.95 0.00 0.00 3.84
2675 4187 6.090088 TGCAAACACAAAATCGCCATAAATAC 59.910 34.615 0.00 0.00 0.00 1.89
2677 4189 7.359598 GCAAACACAAAATCGCCATAAATACAA 60.360 33.333 0.00 0.00 0.00 2.41
2685 4197 8.920509 AAATCGCCATAAATACAACCTAAAAC 57.079 30.769 0.00 0.00 0.00 2.43
2702 4214 4.350368 AAAACAAATTCATGTGGGTCCC 57.650 40.909 0.00 0.00 32.81 4.46
2703 4215 2.692709 ACAAATTCATGTGGGTCCCA 57.307 45.000 6.47 6.47 30.82 4.37
2728 4240 4.124238 TGTCTTTGGTTAACAAGACCTCG 58.876 43.478 24.84 2.51 40.82 4.63
2754 4266 9.495572 GTCCTCCCTCATCTTATATAACAAAAG 57.504 37.037 0.00 0.00 0.00 2.27
2809 4321 4.096984 GTGTCTCATATGGGCCAAAAGAAG 59.903 45.833 11.89 5.09 0.00 2.85
2810 4322 3.067320 GTCTCATATGGGCCAAAAGAAGC 59.933 47.826 11.89 0.66 0.00 3.86
2847 4359 0.960364 TTGAAAGACCCATGAGCCGC 60.960 55.000 0.00 0.00 0.00 6.53
2848 4360 1.078143 GAAAGACCCATGAGCCGCT 60.078 57.895 0.00 0.00 0.00 5.52
2929 4441 9.917129 TTCAACTATTATTCTACTCGTTGAACA 57.083 29.630 9.73 0.00 41.87 3.18
2930 4442 9.350357 TCAACTATTATTCTACTCGTTGAACAC 57.650 33.333 0.00 0.00 37.08 3.32
2931 4443 9.135843 CAACTATTATTCTACTCGTTGAACACA 57.864 33.333 0.00 0.00 33.94 3.72
2932 4444 9.701098 AACTATTATTCTACTCGTTGAACACAA 57.299 29.630 0.00 0.00 0.00 3.33
2933 4445 9.701098 ACTATTATTCTACTCGTTGAACACAAA 57.299 29.630 0.00 0.00 0.00 2.83
2934 4446 9.953825 CTATTATTCTACTCGTTGAACACAAAC 57.046 33.333 0.00 0.00 0.00 2.93
2935 4447 4.765281 TTCTACTCGTTGAACACAAACG 57.235 40.909 2.45 2.45 0.00 3.60
2936 4448 4.031418 TCTACTCGTTGAACACAAACGA 57.969 40.909 10.54 10.54 0.00 3.85
2937 4449 4.422840 TCTACTCGTTGAACACAAACGAA 58.577 39.130 11.89 0.00 32.10 3.85
2938 4450 3.651562 ACTCGTTGAACACAAACGAAG 57.348 42.857 11.89 8.88 32.10 3.79
2940 4452 4.175516 ACTCGTTGAACACAAACGAAGTA 58.824 39.130 11.89 0.00 45.00 2.24
2941 4453 4.032104 ACTCGTTGAACACAAACGAAGTAC 59.968 41.667 11.89 0.00 45.00 2.73
2942 4454 3.000872 TCGTTGAACACAAACGAAGTACG 60.001 43.478 8.77 0.00 45.00 3.67
2943 4455 3.024313 GTTGAACACAAACGAAGTACGC 58.976 45.455 0.00 0.00 45.00 4.42
2944 4456 1.255859 TGAACACAAACGAAGTACGCG 59.744 47.619 3.53 3.53 45.00 6.01
2945 4457 1.518102 GAACACAAACGAAGTACGCGA 59.482 47.619 15.93 0.00 45.00 5.87
2946 4458 1.558741 ACACAAACGAAGTACGCGAA 58.441 45.000 15.93 0.00 45.00 4.70
2947 4459 1.519758 ACACAAACGAAGTACGCGAAG 59.480 47.619 15.93 0.00 45.00 3.79
2948 4460 1.519758 CACAAACGAAGTACGCGAAGT 59.480 47.619 15.93 0.00 45.00 3.01
2949 4461 2.034339 CACAAACGAAGTACGCGAAGTT 60.034 45.455 15.93 1.43 45.00 2.66
2950 4462 2.034339 ACAAACGAAGTACGCGAAGTTG 60.034 45.455 15.93 16.36 45.00 3.16
2951 4463 0.505655 AACGAAGTACGCGAAGTTGC 59.494 50.000 15.93 0.00 45.00 4.17
2952 4464 0.595567 ACGAAGTACGCGAAGTTGCA 60.596 50.000 15.93 0.00 46.94 4.08
2953 4465 0.091344 CGAAGTACGCGAAGTTGCAG 59.909 55.000 15.93 0.00 34.51 4.41
2954 4466 0.179248 GAAGTACGCGAAGTTGCAGC 60.179 55.000 15.93 0.00 34.15 5.25
2955 4467 0.600255 AAGTACGCGAAGTTGCAGCT 60.600 50.000 15.93 0.00 34.15 4.24
2956 4468 0.242825 AGTACGCGAAGTTGCAGCTA 59.757 50.000 15.93 0.00 34.15 3.32
2957 4469 1.135083 AGTACGCGAAGTTGCAGCTAT 60.135 47.619 15.93 0.00 34.15 2.97
2958 4470 1.005975 GTACGCGAAGTTGCAGCTATG 60.006 52.381 15.93 0.17 34.15 2.23
2959 4471 1.349627 CGCGAAGTTGCAGCTATGG 59.650 57.895 2.53 0.00 34.15 2.74
2960 4472 1.063166 GCGAAGTTGCAGCTATGGC 59.937 57.895 2.53 4.07 39.06 4.40
2961 4473 1.349627 CGAAGTTGCAGCTATGGCG 59.650 57.895 2.53 2.19 44.37 5.69
2962 4474 1.083806 CGAAGTTGCAGCTATGGCGA 61.084 55.000 2.53 0.00 44.37 5.54
2963 4475 1.086696 GAAGTTGCAGCTATGGCGAA 58.913 50.000 2.53 0.00 44.37 4.70
2964 4476 0.804989 AAGTTGCAGCTATGGCGAAC 59.195 50.000 2.53 0.64 44.37 3.95
2965 4477 0.036010 AGTTGCAGCTATGGCGAACT 60.036 50.000 0.00 9.36 44.37 3.01
2966 4478 0.804989 GTTGCAGCTATGGCGAACTT 59.195 50.000 0.00 0.00 44.37 2.66
2967 4479 1.200020 GTTGCAGCTATGGCGAACTTT 59.800 47.619 0.00 0.00 44.37 2.66
2968 4480 1.533625 TGCAGCTATGGCGAACTTTT 58.466 45.000 0.00 0.00 44.37 2.27
2969 4481 2.705730 TGCAGCTATGGCGAACTTTTA 58.294 42.857 0.00 0.00 44.37 1.52
2970 4482 3.078097 TGCAGCTATGGCGAACTTTTAA 58.922 40.909 0.00 0.00 44.37 1.52
2971 4483 3.694072 TGCAGCTATGGCGAACTTTTAAT 59.306 39.130 0.00 0.00 44.37 1.40
2972 4484 4.201910 TGCAGCTATGGCGAACTTTTAATC 60.202 41.667 0.00 0.00 44.37 1.75
2973 4485 4.035675 GCAGCTATGGCGAACTTTTAATCT 59.964 41.667 0.00 0.00 44.37 2.40
2974 4486 5.236478 GCAGCTATGGCGAACTTTTAATCTA 59.764 40.000 0.00 0.00 44.37 1.98
2975 4487 6.238374 GCAGCTATGGCGAACTTTTAATCTAA 60.238 38.462 0.00 0.00 44.37 2.10
2976 4488 7.678690 GCAGCTATGGCGAACTTTTAATCTAAA 60.679 37.037 0.00 0.00 44.37 1.85
2977 4489 7.640240 CAGCTATGGCGAACTTTTAATCTAAAC 59.360 37.037 0.00 0.00 44.37 2.01
2978 4490 7.335924 AGCTATGGCGAACTTTTAATCTAAACA 59.664 33.333 0.00 0.00 44.37 2.83
2979 4491 7.966204 GCTATGGCGAACTTTTAATCTAAACAA 59.034 33.333 0.00 0.00 0.00 2.83
2980 4492 9.834628 CTATGGCGAACTTTTAATCTAAACAAA 57.165 29.630 0.00 0.00 0.00 2.83
2982 4494 8.342725 TGGCGAACTTTTAATCTAAACAAAAC 57.657 30.769 0.00 0.00 0.00 2.43
2983 4495 7.435784 TGGCGAACTTTTAATCTAAACAAAACC 59.564 33.333 0.00 0.00 0.00 3.27
2984 4496 7.095940 GGCGAACTTTTAATCTAAACAAAACCC 60.096 37.037 0.00 0.00 0.00 4.11
2985 4497 7.095940 GCGAACTTTTAATCTAAACAAAACCCC 60.096 37.037 0.00 0.00 0.00 4.95
2986 4498 7.921745 CGAACTTTTAATCTAAACAAAACCCCA 59.078 33.333 0.00 0.00 0.00 4.96
2987 4499 8.951787 AACTTTTAATCTAAACAAAACCCCAC 57.048 30.769 0.00 0.00 0.00 4.61
2988 4500 7.502696 ACTTTTAATCTAAACAAAACCCCACC 58.497 34.615 0.00 0.00 0.00 4.61
2989 4501 7.346175 ACTTTTAATCTAAACAAAACCCCACCT 59.654 33.333 0.00 0.00 0.00 4.00
2990 4502 7.678207 TTTAATCTAAACAAAACCCCACCTT 57.322 32.000 0.00 0.00 0.00 3.50
2991 4503 5.545063 AATCTAAACAAAACCCCACCTTG 57.455 39.130 0.00 0.00 0.00 3.61
2992 4504 4.252570 TCTAAACAAAACCCCACCTTGA 57.747 40.909 0.00 0.00 0.00 3.02
2993 4505 4.810345 TCTAAACAAAACCCCACCTTGAT 58.190 39.130 0.00 0.00 0.00 2.57
2994 4506 4.830600 TCTAAACAAAACCCCACCTTGATC 59.169 41.667 0.00 0.00 0.00 2.92
2995 4507 2.765689 ACAAAACCCCACCTTGATCA 57.234 45.000 0.00 0.00 0.00 2.92
2996 4508 3.039252 ACAAAACCCCACCTTGATCAA 57.961 42.857 8.12 8.12 0.00 2.57
2997 4509 3.586429 ACAAAACCCCACCTTGATCAAT 58.414 40.909 8.96 0.00 0.00 2.57
2998 4510 4.746466 ACAAAACCCCACCTTGATCAATA 58.254 39.130 8.96 0.00 0.00 1.90
2999 4511 5.151454 ACAAAACCCCACCTTGATCAATAA 58.849 37.500 8.96 0.00 0.00 1.40
3000 4512 5.604650 ACAAAACCCCACCTTGATCAATAAA 59.395 36.000 8.96 0.00 0.00 1.40
3001 4513 6.165577 CAAAACCCCACCTTGATCAATAAAG 58.834 40.000 8.96 0.00 0.00 1.85
3002 4514 3.365472 ACCCCACCTTGATCAATAAAGC 58.635 45.455 8.96 0.00 0.00 3.51
3003 4515 3.011708 ACCCCACCTTGATCAATAAAGCT 59.988 43.478 8.96 0.00 0.00 3.74
3004 4516 4.026052 CCCCACCTTGATCAATAAAGCTT 58.974 43.478 8.96 0.00 0.00 3.74
3005 4517 4.467438 CCCCACCTTGATCAATAAAGCTTT 59.533 41.667 17.30 17.30 0.00 3.51
3006 4518 5.394553 CCCCACCTTGATCAATAAAGCTTTC 60.395 44.000 16.57 0.13 0.00 2.62
3007 4519 5.185635 CCCACCTTGATCAATAAAGCTTTCA 59.814 40.000 16.57 3.26 0.00 2.69
3008 4520 6.127253 CCCACCTTGATCAATAAAGCTTTCAT 60.127 38.462 16.57 2.62 0.00 2.57
3009 4521 6.976925 CCACCTTGATCAATAAAGCTTTCATC 59.023 38.462 16.57 12.96 0.00 2.92
3010 4522 7.147949 CCACCTTGATCAATAAAGCTTTCATCT 60.148 37.037 16.57 0.00 0.00 2.90
3011 4523 8.248945 CACCTTGATCAATAAAGCTTTCATCTT 58.751 33.333 16.57 2.83 0.00 2.40
3012 4524 9.466497 ACCTTGATCAATAAAGCTTTCATCTTA 57.534 29.630 16.57 0.00 0.00 2.10
3020 4532 9.882996 CAATAAAGCTTTCATCTTATATTCGCA 57.117 29.630 16.57 0.00 0.00 5.10
3026 4538 8.887717 AGCTTTCATCTTATATTCGCAATATCC 58.112 33.333 5.13 0.00 35.72 2.59
3027 4539 8.668353 GCTTTCATCTTATATTCGCAATATCCA 58.332 33.333 5.13 0.00 35.72 3.41
3029 4541 9.942850 TTTCATCTTATATTCGCAATATCCAGA 57.057 29.630 5.13 8.05 35.72 3.86
3045 4557 9.674824 CAATATCCAGATTGCAATCTTAGTTTC 57.325 33.333 34.17 11.44 42.96 2.78
3046 4558 9.638176 AATATCCAGATTGCAATCTTAGTTTCT 57.362 29.630 34.17 18.43 42.96 2.52
3047 4559 7.951347 ATCCAGATTGCAATCTTAGTTTCTT 57.049 32.000 34.17 12.08 42.96 2.52
3048 4560 7.149569 TCCAGATTGCAATCTTAGTTTCTTG 57.850 36.000 34.17 21.47 42.96 3.02
3049 4561 5.803967 CCAGATTGCAATCTTAGTTTCTTGC 59.196 40.000 34.17 8.35 42.96 4.01
3050 4562 6.349944 CCAGATTGCAATCTTAGTTTCTTGCT 60.350 38.462 34.17 10.69 42.96 3.91
3051 4563 7.088905 CAGATTGCAATCTTAGTTTCTTGCTT 58.911 34.615 34.17 10.27 42.96 3.91
3052 4564 7.061905 CAGATTGCAATCTTAGTTTCTTGCTTG 59.938 37.037 34.17 17.46 42.96 4.01
3053 4565 5.772825 TGCAATCTTAGTTTCTTGCTTGT 57.227 34.783 7.52 0.00 43.33 3.16
3054 4566 6.147864 TGCAATCTTAGTTTCTTGCTTGTT 57.852 33.333 7.52 0.00 43.33 2.83
3055 4567 6.208644 TGCAATCTTAGTTTCTTGCTTGTTC 58.791 36.000 7.52 0.00 43.33 3.18
3056 4568 6.039717 TGCAATCTTAGTTTCTTGCTTGTTCT 59.960 34.615 7.52 0.00 43.33 3.01
3057 4569 6.920210 GCAATCTTAGTTTCTTGCTTGTTCTT 59.080 34.615 0.00 0.00 40.55 2.52
3058 4570 7.114106 GCAATCTTAGTTTCTTGCTTGTTCTTC 59.886 37.037 0.00 0.00 40.55 2.87
3059 4571 6.287107 TCTTAGTTTCTTGCTTGTTCTTCG 57.713 37.500 0.00 0.00 0.00 3.79
3060 4572 5.815740 TCTTAGTTTCTTGCTTGTTCTTCGT 59.184 36.000 0.00 0.00 0.00 3.85
3061 4573 4.965119 AGTTTCTTGCTTGTTCTTCGTT 57.035 36.364 0.00 0.00 0.00 3.85
3062 4574 5.310720 AGTTTCTTGCTTGTTCTTCGTTT 57.689 34.783 0.00 0.00 0.00 3.60
3063 4575 5.095490 AGTTTCTTGCTTGTTCTTCGTTTG 58.905 37.500 0.00 0.00 0.00 2.93
3064 4576 3.065019 TCTTGCTTGTTCTTCGTTTGC 57.935 42.857 0.00 0.00 0.00 3.68
3065 4577 2.682856 TCTTGCTTGTTCTTCGTTTGCT 59.317 40.909 0.00 0.00 0.00 3.91
3066 4578 2.755836 TGCTTGTTCTTCGTTTGCTC 57.244 45.000 0.00 0.00 0.00 4.26
3067 4579 1.003972 TGCTTGTTCTTCGTTTGCTCG 60.004 47.619 0.00 0.00 0.00 5.03
3068 4580 1.663494 CTTGTTCTTCGTTTGCTCGC 58.337 50.000 0.00 0.00 0.00 5.03
3069 4581 1.003972 CTTGTTCTTCGTTTGCTCGCA 60.004 47.619 0.00 0.00 0.00 5.10
3070 4582 0.581529 TGTTCTTCGTTTGCTCGCAG 59.418 50.000 0.00 0.00 0.00 5.18
3071 4583 0.110644 GTTCTTCGTTTGCTCGCAGG 60.111 55.000 0.00 0.00 0.00 4.85
3072 4584 0.249699 TTCTTCGTTTGCTCGCAGGA 60.250 50.000 0.00 0.00 0.00 3.86
3073 4585 0.249699 TCTTCGTTTGCTCGCAGGAA 60.250 50.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 6.183360 CGTGTAACATACCATTGGGAAGTTAC 60.183 42.308 27.92 27.92 42.48 2.50
31 32 4.698304 CGTGTAACATACCATTGGGAAGTT 59.302 41.667 12.87 12.87 35.74 2.66
32 33 4.258543 CGTGTAACATACCATTGGGAAGT 58.741 43.478 7.78 0.00 35.74 3.01
36 37 1.673920 GGCGTGTAACATACCATTGGG 59.326 52.381 7.78 0.00 35.74 4.12
47 48 3.006940 TCATTGGAATGAGGCGTGTAAC 58.993 45.455 0.00 0.00 40.32 2.50
55 56 5.637006 TTAAACCGTTCATTGGAATGAGG 57.363 39.130 2.46 4.58 45.35 3.86
66 67 6.843208 TGCGATGAAATATTTAAACCGTTCA 58.157 32.000 0.00 10.15 0.00 3.18
70 71 7.272515 ACTGTTTGCGATGAAATATTTAAACCG 59.727 33.333 14.78 12.25 0.00 4.44
123 124 4.558496 GCAAAACTACCTGCAATGTTAGCA 60.558 41.667 0.00 0.00 38.48 3.49
124 125 3.920412 GCAAAACTACCTGCAATGTTAGC 59.080 43.478 0.00 0.00 38.48 3.09
152 153 1.137872 CGGAGGCTAAGAGAACTGCAT 59.862 52.381 0.00 0.00 0.00 3.96
170 171 9.116067 TGTTATTTCCATAAACTTCTATTCCGG 57.884 33.333 0.00 0.00 0.00 5.14
235 242 7.506261 ACCCAACCATAAAACAATTACTGTGTA 59.494 33.333 0.00 0.00 38.67 2.90
236 243 6.325286 ACCCAACCATAAAACAATTACTGTGT 59.675 34.615 0.00 0.00 38.67 3.72
255 425 7.335924 TCATGTAGTAAATCTAAGCAACCCAAC 59.664 37.037 0.00 0.00 0.00 3.77
295 465 3.976169 TGGTAAAAGTGAAGCAATGTGC 58.024 40.909 0.00 0.00 45.46 4.57
299 469 7.230849 TCATTGATGGTAAAAGTGAAGCAAT 57.769 32.000 0.00 0.00 0.00 3.56
315 485 6.313411 ACACAAAAACAACCACTTCATTGATG 59.687 34.615 0.00 0.00 0.00 3.07
337 507 2.019951 CCGTCACACGTGCCTACAC 61.020 63.158 17.22 4.22 40.58 2.90
373 548 0.597118 TTTACGTTCCGACCACCACG 60.597 55.000 0.00 0.00 38.62 4.94
375 550 2.547299 ATTTTACGTTCCGACCACCA 57.453 45.000 0.00 0.00 0.00 4.17
452 627 9.730420 GTCAAAGTGAAGCTTTATAAAGTTTGA 57.270 29.630 26.09 24.12 44.95 2.69
453 628 8.968242 GGTCAAAGTGAAGCTTTATAAAGTTTG 58.032 33.333 26.09 22.74 44.95 2.93
454 629 8.691797 TGGTCAAAGTGAAGCTTTATAAAGTTT 58.308 29.630 22.61 22.61 44.95 2.66
455 630 8.232913 TGGTCAAAGTGAAGCTTTATAAAGTT 57.767 30.769 22.94 16.35 44.95 2.66
456 631 7.817418 TGGTCAAAGTGAAGCTTTATAAAGT 57.183 32.000 22.94 7.45 44.95 2.66
457 632 9.185192 CTTTGGTCAAAGTGAAGCTTTATAAAG 57.815 33.333 19.08 19.08 44.95 1.85
473 648 5.761234 ACTTCACGTATTAGCTTTGGTCAAA 59.239 36.000 0.00 0.00 0.00 2.69
474 649 5.302360 ACTTCACGTATTAGCTTTGGTCAA 58.698 37.500 0.00 0.00 0.00 3.18
475 650 4.890088 ACTTCACGTATTAGCTTTGGTCA 58.110 39.130 0.00 0.00 0.00 4.02
476 651 6.956299 TTACTTCACGTATTAGCTTTGGTC 57.044 37.500 0.00 0.00 0.00 4.02
477 652 7.916914 ATTTACTTCACGTATTAGCTTTGGT 57.083 32.000 0.00 0.00 0.00 3.67
482 657 9.962759 CGTTTTAATTTACTTCACGTATTAGCT 57.037 29.630 0.00 0.00 0.00 3.32
483 658 9.202545 CCGTTTTAATTTACTTCACGTATTAGC 57.797 33.333 0.00 0.00 0.00 3.09
486 661 8.445493 CCTCCGTTTTAATTTACTTCACGTATT 58.555 33.333 0.00 0.00 0.00 1.89
487 662 7.064966 CCCTCCGTTTTAATTTACTTCACGTAT 59.935 37.037 0.00 0.00 0.00 3.06
488 663 6.368516 CCCTCCGTTTTAATTTACTTCACGTA 59.631 38.462 0.00 0.00 0.00 3.57
489 664 5.179929 CCCTCCGTTTTAATTTACTTCACGT 59.820 40.000 0.00 0.00 0.00 4.49
490 665 5.409214 TCCCTCCGTTTTAATTTACTTCACG 59.591 40.000 0.00 0.00 0.00 4.35
491 666 6.429078 ACTCCCTCCGTTTTAATTTACTTCAC 59.571 38.462 0.00 0.00 0.00 3.18
492 667 6.536447 ACTCCCTCCGTTTTAATTTACTTCA 58.464 36.000 0.00 0.00 0.00 3.02
493 668 7.821359 AGTACTCCCTCCGTTTTAATTTACTTC 59.179 37.037 0.00 0.00 0.00 3.01
494 669 7.605309 CAGTACTCCCTCCGTTTTAATTTACTT 59.395 37.037 0.00 0.00 0.00 2.24
495 670 7.101700 CAGTACTCCCTCCGTTTTAATTTACT 58.898 38.462 0.00 0.00 0.00 2.24
496 671 6.875726 ACAGTACTCCCTCCGTTTTAATTTAC 59.124 38.462 0.00 0.00 0.00 2.01
497 672 7.008021 ACAGTACTCCCTCCGTTTTAATTTA 57.992 36.000 0.00 0.00 0.00 1.40
498 673 5.872963 ACAGTACTCCCTCCGTTTTAATTT 58.127 37.500 0.00 0.00 0.00 1.82
499 674 5.494390 ACAGTACTCCCTCCGTTTTAATT 57.506 39.130 0.00 0.00 0.00 1.40
500 675 6.155737 ACATACAGTACTCCCTCCGTTTTAAT 59.844 38.462 0.00 0.00 0.00 1.40
501 676 5.481473 ACATACAGTACTCCCTCCGTTTTAA 59.519 40.000 0.00 0.00 0.00 1.52
502 677 5.018809 ACATACAGTACTCCCTCCGTTTTA 58.981 41.667 0.00 0.00 0.00 1.52
503 678 3.836562 ACATACAGTACTCCCTCCGTTTT 59.163 43.478 0.00 0.00 0.00 2.43
504 679 3.194968 CACATACAGTACTCCCTCCGTTT 59.805 47.826 0.00 0.00 0.00 3.60
505 680 2.758979 CACATACAGTACTCCCTCCGTT 59.241 50.000 0.00 0.00 0.00 4.44
506 681 2.291411 ACACATACAGTACTCCCTCCGT 60.291 50.000 0.00 0.00 0.00 4.69
507 682 2.358267 GACACATACAGTACTCCCTCCG 59.642 54.545 0.00 0.00 0.00 4.63
508 683 3.130693 GTGACACATACAGTACTCCCTCC 59.869 52.174 0.00 0.00 0.00 4.30
509 684 3.130693 GGTGACACATACAGTACTCCCTC 59.869 52.174 8.08 0.00 0.00 4.30
510 685 3.097614 GGTGACACATACAGTACTCCCT 58.902 50.000 8.08 0.00 0.00 4.20
511 686 2.167900 GGGTGACACATACAGTACTCCC 59.832 54.545 8.08 0.00 34.69 4.30
512 687 2.167900 GGGGTGACACATACAGTACTCC 59.832 54.545 8.08 0.00 0.00 3.85
513 688 3.097614 AGGGGTGACACATACAGTACTC 58.902 50.000 8.08 0.00 34.58 2.59
514 689 3.185880 AGGGGTGACACATACAGTACT 57.814 47.619 8.08 0.00 34.58 2.73
515 690 3.975168 AAGGGGTGACACATACAGTAC 57.025 47.619 8.08 0.00 34.58 2.73
516 691 5.628200 GCAATAAGGGGTGACACATACAGTA 60.628 44.000 8.08 0.00 34.58 2.74
517 692 4.843728 CAATAAGGGGTGACACATACAGT 58.156 43.478 8.08 0.00 34.58 3.55
518 693 3.627577 GCAATAAGGGGTGACACATACAG 59.372 47.826 8.08 0.00 34.58 2.74
519 694 3.265737 AGCAATAAGGGGTGACACATACA 59.734 43.478 8.08 0.00 34.58 2.29
520 695 3.886123 AGCAATAAGGGGTGACACATAC 58.114 45.455 8.08 0.00 34.58 2.39
521 696 4.227300 AGAAGCAATAAGGGGTGACACATA 59.773 41.667 8.08 0.00 34.58 2.29
522 697 3.010584 AGAAGCAATAAGGGGTGACACAT 59.989 43.478 8.08 0.00 34.58 3.21
523 698 2.375174 AGAAGCAATAAGGGGTGACACA 59.625 45.455 8.08 0.00 34.58 3.72
524 699 3.073274 AGAAGCAATAAGGGGTGACAC 57.927 47.619 0.00 0.00 0.00 3.67
525 700 5.191722 AGAATAGAAGCAATAAGGGGTGACA 59.808 40.000 0.00 0.00 0.00 3.58
526 701 5.685728 AGAATAGAAGCAATAAGGGGTGAC 58.314 41.667 0.00 0.00 0.00 3.67
527 702 5.975988 AGAATAGAAGCAATAAGGGGTGA 57.024 39.130 0.00 0.00 0.00 4.02
528 703 5.998363 GGTAGAATAGAAGCAATAAGGGGTG 59.002 44.000 0.00 0.00 0.00 4.61
529 704 5.073280 GGGTAGAATAGAAGCAATAAGGGGT 59.927 44.000 0.00 0.00 0.00 4.95
530 705 5.561679 GGGTAGAATAGAAGCAATAAGGGG 58.438 45.833 0.00 0.00 0.00 4.79
531 706 5.238583 CGGGTAGAATAGAAGCAATAAGGG 58.761 45.833 0.00 0.00 0.00 3.95
621 797 0.523519 CCGCCTCTTTCTTTCCTTGC 59.476 55.000 0.00 0.00 0.00 4.01
698 875 2.897350 ATCAGGCGGCGCTAAAGC 60.897 61.111 32.30 14.71 37.78 3.51
724 901 6.818142 CCTAATGGTGGATTTGTTTTTCATCC 59.182 38.462 0.00 0.00 0.00 3.51
745 922 1.290955 CGTGCACGGACCTTCCTAA 59.709 57.895 31.15 0.00 33.30 2.69
748 925 4.980805 TGCGTGCACGGACCTTCC 62.981 66.667 37.47 20.74 40.23 3.46
749 926 3.414700 CTGCGTGCACGGACCTTC 61.415 66.667 37.47 21.45 40.23 3.46
788 965 2.182537 ACGTACGGCCGTGGAATC 59.817 61.111 40.02 21.72 40.08 2.52
806 983 3.591254 AAAGGAGCGTGACGAGCCC 62.591 63.158 10.10 5.86 34.64 5.19
903 1080 1.723003 CGTAGTACGGAGTTTGTTGCC 59.277 52.381 15.02 0.00 37.78 4.52
919 1096 0.522180 AAGCAGAGGTCACGACGTAG 59.478 55.000 0.00 0.00 0.00 3.51
963 1140 4.279169 TCTGGTGGCTTGATTTGAAAAGAG 59.721 41.667 0.00 0.00 0.00 2.85
984 1161 1.079819 CATTCGTGCGGAGGTGTCT 60.080 57.895 0.00 0.00 0.00 3.41
1076 1259 2.529389 GGTGGACTGGTGGGAGGT 60.529 66.667 0.00 0.00 0.00 3.85
1425 1608 2.048127 GGCAAGAGAAGCGACGGT 60.048 61.111 0.00 0.00 0.00 4.83
1778 1985 4.864334 CTCCATGGCCGTGCTCCC 62.864 72.222 20.27 0.00 0.00 4.30
2160 2370 3.827008 AGATTGACATGCCATCTACGT 57.173 42.857 0.00 0.00 0.00 3.57
2161 2371 5.755375 ACTTTAGATTGACATGCCATCTACG 59.245 40.000 8.07 6.19 0.00 3.51
2162 2372 7.066284 ACAACTTTAGATTGACATGCCATCTAC 59.934 37.037 8.07 0.00 0.00 2.59
2173 2383 7.907214 ATGTGTAGGACAACTTTAGATTGAC 57.093 36.000 0.00 0.00 38.36 3.18
2199 2409 4.187506 AGAGGAGTACTAGGATGGAACC 57.812 50.000 0.00 0.00 0.00 3.62
2212 2422 3.136443 CACATTTGGGCCATAGAGGAGTA 59.864 47.826 7.26 0.00 41.22 2.59
2274 3462 4.816385 TGCCTTGTTTCTCACTCAAGTTAG 59.184 41.667 0.00 0.00 37.45 2.34
2286 3474 4.922206 TGATGTTCCTATGCCTTGTTTCT 58.078 39.130 0.00 0.00 0.00 2.52
2301 3489 3.944015 AGCCTAAGTGCAGAATGATGTTC 59.056 43.478 0.00 0.00 39.69 3.18
2311 3499 4.063998 TGTGATGATAGCCTAAGTGCAG 57.936 45.455 0.00 0.00 0.00 4.41
2340 3528 8.492673 TGACCTTTGACACAATAATAGATGTC 57.507 34.615 0.00 0.00 41.51 3.06
2350 3538 7.652909 CACACAATAAATGACCTTTGACACAAT 59.347 33.333 0.00 0.00 0.00 2.71
2351 3539 6.977502 CACACAATAAATGACCTTTGACACAA 59.022 34.615 0.00 0.00 0.00 3.33
2352 3540 6.319911 TCACACAATAAATGACCTTTGACACA 59.680 34.615 0.00 0.00 0.00 3.72
2399 3909 9.173939 CGGAATTGCTTATATCATTGAAAGAAC 57.826 33.333 0.00 0.00 0.00 3.01
2402 3912 9.903682 ATTCGGAATTGCTTATATCATTGAAAG 57.096 29.630 0.00 0.00 0.00 2.62
2506 4016 6.705381 CCTTAATGCTTCCTGATAGAAGTGAG 59.295 42.308 3.47 0.00 44.27 3.51
2584 4094 3.181449 ACGTTATGGTGGCTGCCAATATA 60.181 43.478 25.23 20.34 42.48 0.86
2621 4131 8.638873 TCGCCTCAAGAGTCTATAAAATTATGA 58.361 33.333 0.00 0.00 0.00 2.15
2631 4141 2.223923 GCACATCGCCTCAAGAGTCTAT 60.224 50.000 0.00 0.00 32.94 1.98
2649 4161 1.565305 TGGCGATTTTGTGTTTGCAC 58.435 45.000 0.00 0.00 45.44 4.57
2675 4187 6.287525 ACCCACATGAATTTGTTTTAGGTTG 58.712 36.000 0.00 0.00 0.00 3.77
2677 4189 5.011635 GGACCCACATGAATTTGTTTTAGGT 59.988 40.000 0.00 0.00 0.00 3.08
2685 4197 4.255301 CAAATGGGACCCACATGAATTTG 58.745 43.478 17.78 17.14 35.80 2.32
2702 4214 6.805713 AGGTCTTGTTAACCAAAGACAAATG 58.194 36.000 27.12 3.41 39.39 2.32
2703 4215 6.238648 CGAGGTCTTGTTAACCAAAGACAAAT 60.239 38.462 27.12 18.00 39.39 2.32
2728 4240 9.495572 CTTTTGTTATATAAGATGAGGGAGGAC 57.504 37.037 0.00 0.00 0.00 3.85
2754 4266 2.035321 TCGGCCCAAAGTTTGAATTCAC 59.965 45.455 17.33 0.00 0.00 3.18
2761 4273 1.036707 TCCTTTCGGCCCAAAGTTTG 58.963 50.000 19.80 8.73 32.26 2.93
2768 4280 1.304052 CATGGTTCCTTTCGGCCCA 60.304 57.895 0.00 0.00 36.07 5.36
2770 4282 0.893727 ACACATGGTTCCTTTCGGCC 60.894 55.000 0.00 0.00 0.00 6.13
2791 4303 3.098774 TGCTTCTTTTGGCCCATATGA 57.901 42.857 3.65 0.00 0.00 2.15
2809 4321 4.199310 TCAAGCTAAGTATGACCCATTGC 58.801 43.478 0.00 0.00 0.00 3.56
2810 4322 6.599244 TCTTTCAAGCTAAGTATGACCCATTG 59.401 38.462 0.00 0.00 0.00 2.82
2921 4433 3.266067 CGTACTTCGTTTGTGTTCAACG 58.734 45.455 0.00 0.00 32.93 4.10
2922 4434 3.024313 GCGTACTTCGTTTGTGTTCAAC 58.976 45.455 0.00 0.00 42.13 3.18
2923 4435 2.285141 CGCGTACTTCGTTTGTGTTCAA 60.285 45.455 0.00 0.00 42.13 2.69
2924 4436 1.255859 CGCGTACTTCGTTTGTGTTCA 59.744 47.619 0.00 0.00 42.13 3.18
2925 4437 1.518102 TCGCGTACTTCGTTTGTGTTC 59.482 47.619 5.77 0.00 42.13 3.18
2926 4438 1.558741 TCGCGTACTTCGTTTGTGTT 58.441 45.000 5.77 0.00 42.13 3.32
2927 4439 1.519758 CTTCGCGTACTTCGTTTGTGT 59.480 47.619 5.77 0.00 42.13 3.72
2928 4440 1.519758 ACTTCGCGTACTTCGTTTGTG 59.480 47.619 5.77 0.00 42.13 3.33
2929 4441 1.843992 ACTTCGCGTACTTCGTTTGT 58.156 45.000 5.77 0.00 42.13 2.83
2930 4442 2.546665 CAACTTCGCGTACTTCGTTTG 58.453 47.619 5.77 0.00 42.13 2.93
2931 4443 1.071041 GCAACTTCGCGTACTTCGTTT 60.071 47.619 5.77 0.00 42.13 3.60
2932 4444 0.505655 GCAACTTCGCGTACTTCGTT 59.494 50.000 5.77 0.00 42.13 3.85
2933 4445 0.595567 TGCAACTTCGCGTACTTCGT 60.596 50.000 5.77 0.00 42.13 3.85
2934 4446 0.091344 CTGCAACTTCGCGTACTTCG 59.909 55.000 5.77 0.00 43.12 3.79
2935 4447 0.179248 GCTGCAACTTCGCGTACTTC 60.179 55.000 5.77 0.00 33.35 3.01
2936 4448 0.600255 AGCTGCAACTTCGCGTACTT 60.600 50.000 5.77 0.00 33.35 2.24
2937 4449 0.242825 TAGCTGCAACTTCGCGTACT 59.757 50.000 5.77 0.00 33.35 2.73
2938 4450 1.005975 CATAGCTGCAACTTCGCGTAC 60.006 52.381 5.77 0.00 33.35 3.67
2939 4451 1.277326 CATAGCTGCAACTTCGCGTA 58.723 50.000 5.77 0.00 33.35 4.42
2940 4452 1.361668 CCATAGCTGCAACTTCGCGT 61.362 55.000 5.77 0.00 33.35 6.01
2941 4453 1.349627 CCATAGCTGCAACTTCGCG 59.650 57.895 0.00 0.00 33.35 5.87
2942 4454 1.063166 GCCATAGCTGCAACTTCGC 59.937 57.895 1.02 0.00 35.50 4.70
2943 4455 1.083806 TCGCCATAGCTGCAACTTCG 61.084 55.000 1.02 0.00 36.60 3.79
2944 4456 1.086696 TTCGCCATAGCTGCAACTTC 58.913 50.000 1.02 0.00 36.60 3.01
2945 4457 0.804989 GTTCGCCATAGCTGCAACTT 59.195 50.000 1.02 0.00 36.60 2.66
2946 4458 0.036010 AGTTCGCCATAGCTGCAACT 60.036 50.000 1.02 0.00 36.60 3.16
2947 4459 0.804989 AAGTTCGCCATAGCTGCAAC 59.195 50.000 1.02 0.00 36.60 4.17
2948 4460 1.533625 AAAGTTCGCCATAGCTGCAA 58.466 45.000 1.02 0.00 36.60 4.08
2949 4461 1.533625 AAAAGTTCGCCATAGCTGCA 58.466 45.000 1.02 0.00 36.60 4.41
2950 4462 3.757745 TTAAAAGTTCGCCATAGCTGC 57.242 42.857 0.00 0.00 36.60 5.25
2951 4463 5.741388 AGATTAAAAGTTCGCCATAGCTG 57.259 39.130 0.00 0.00 36.60 4.24
2952 4464 7.335924 TGTTTAGATTAAAAGTTCGCCATAGCT 59.664 33.333 0.00 0.00 36.60 3.32
2953 4465 7.469260 TGTTTAGATTAAAAGTTCGCCATAGC 58.531 34.615 0.00 0.00 0.00 2.97
2954 4466 9.834628 TTTGTTTAGATTAAAAGTTCGCCATAG 57.165 29.630 0.00 0.00 0.00 2.23
2956 4468 8.974408 GTTTTGTTTAGATTAAAAGTTCGCCAT 58.026 29.630 0.00 0.00 0.00 4.40
2957 4469 7.435784 GGTTTTGTTTAGATTAAAAGTTCGCCA 59.564 33.333 0.00 0.00 0.00 5.69
2958 4470 7.095940 GGGTTTTGTTTAGATTAAAAGTTCGCC 60.096 37.037 0.00 0.00 0.00 5.54
2959 4471 7.095940 GGGGTTTTGTTTAGATTAAAAGTTCGC 60.096 37.037 0.00 0.00 0.00 4.70
2960 4472 7.921745 TGGGGTTTTGTTTAGATTAAAAGTTCG 59.078 33.333 0.00 0.00 0.00 3.95
2961 4473 9.037737 GTGGGGTTTTGTTTAGATTAAAAGTTC 57.962 33.333 0.00 0.00 0.00 3.01
2962 4474 7.988599 GGTGGGGTTTTGTTTAGATTAAAAGTT 59.011 33.333 0.00 0.00 0.00 2.66
2963 4475 7.346175 AGGTGGGGTTTTGTTTAGATTAAAAGT 59.654 33.333 0.00 0.00 0.00 2.66
2964 4476 7.732025 AGGTGGGGTTTTGTTTAGATTAAAAG 58.268 34.615 0.00 0.00 0.00 2.27
2965 4477 7.678207 AGGTGGGGTTTTGTTTAGATTAAAA 57.322 32.000 0.00 0.00 0.00 1.52
2966 4478 7.344871 TCAAGGTGGGGTTTTGTTTAGATTAAA 59.655 33.333 0.00 0.00 0.00 1.52
2967 4479 6.839657 TCAAGGTGGGGTTTTGTTTAGATTAA 59.160 34.615 0.00 0.00 0.00 1.40
2968 4480 6.374588 TCAAGGTGGGGTTTTGTTTAGATTA 58.625 36.000 0.00 0.00 0.00 1.75
2969 4481 5.212745 TCAAGGTGGGGTTTTGTTTAGATT 58.787 37.500 0.00 0.00 0.00 2.40
2970 4482 4.810345 TCAAGGTGGGGTTTTGTTTAGAT 58.190 39.130 0.00 0.00 0.00 1.98
2971 4483 4.252570 TCAAGGTGGGGTTTTGTTTAGA 57.747 40.909 0.00 0.00 0.00 2.10
2972 4484 4.586841 TGATCAAGGTGGGGTTTTGTTTAG 59.413 41.667 0.00 0.00 0.00 1.85
2973 4485 4.547671 TGATCAAGGTGGGGTTTTGTTTA 58.452 39.130 0.00 0.00 0.00 2.01
2974 4486 3.379452 TGATCAAGGTGGGGTTTTGTTT 58.621 40.909 0.00 0.00 0.00 2.83
2975 4487 3.039252 TGATCAAGGTGGGGTTTTGTT 57.961 42.857 0.00 0.00 0.00 2.83
2976 4488 2.765689 TGATCAAGGTGGGGTTTTGT 57.234 45.000 0.00 0.00 0.00 2.83
2977 4489 5.736951 TTATTGATCAAGGTGGGGTTTTG 57.263 39.130 14.54 0.00 0.00 2.44
2978 4490 5.279960 GCTTTATTGATCAAGGTGGGGTTTT 60.280 40.000 14.54 0.00 0.00 2.43
2979 4491 4.222810 GCTTTATTGATCAAGGTGGGGTTT 59.777 41.667 14.54 0.00 0.00 3.27
2980 4492 3.769300 GCTTTATTGATCAAGGTGGGGTT 59.231 43.478 14.54 0.00 0.00 4.11
2981 4493 3.011708 AGCTTTATTGATCAAGGTGGGGT 59.988 43.478 14.54 5.83 29.56 4.95
2982 4494 3.635591 AGCTTTATTGATCAAGGTGGGG 58.364 45.455 14.54 3.41 29.56 4.96
2983 4495 5.185635 TGAAAGCTTTATTGATCAAGGTGGG 59.814 40.000 12.68 4.40 31.15 4.61
2984 4496 6.271488 TGAAAGCTTTATTGATCAAGGTGG 57.729 37.500 12.68 5.72 31.15 4.61
2985 4497 7.769220 AGATGAAAGCTTTATTGATCAAGGTG 58.231 34.615 12.68 5.39 31.15 4.00
2986 4498 7.951347 AGATGAAAGCTTTATTGATCAAGGT 57.049 32.000 12.68 2.55 32.04 3.50
2994 4506 9.882996 TGCGAATATAAGATGAAAGCTTTATTG 57.117 29.630 12.68 2.82 41.66 1.90
3000 4512 8.887717 GGATATTGCGAATATAAGATGAAAGCT 58.112 33.333 0.00 0.00 34.31 3.74
3001 4513 8.668353 TGGATATTGCGAATATAAGATGAAAGC 58.332 33.333 0.00 0.00 34.31 3.51
3003 4515 9.942850 TCTGGATATTGCGAATATAAGATGAAA 57.057 29.630 0.00 0.00 34.31 2.69
3019 4531 9.674824 GAAACTAAGATTGCAATCTGGATATTG 57.325 33.333 36.16 24.00 44.67 1.90
3020 4532 9.638176 AGAAACTAAGATTGCAATCTGGATATT 57.362 29.630 36.16 26.49 44.67 1.28
3021 4533 9.638176 AAGAAACTAAGATTGCAATCTGGATAT 57.362 29.630 36.16 24.43 44.67 1.63
3022 4534 8.896744 CAAGAAACTAAGATTGCAATCTGGATA 58.103 33.333 36.16 24.87 44.67 2.59
3023 4535 7.630082 GCAAGAAACTAAGATTGCAATCTGGAT 60.630 37.037 36.16 25.07 44.67 3.41
3024 4536 6.349611 GCAAGAAACTAAGATTGCAATCTGGA 60.350 38.462 36.16 26.51 44.67 3.86
3025 4537 5.803967 GCAAGAAACTAAGATTGCAATCTGG 59.196 40.000 36.16 30.91 44.67 3.86
3026 4538 6.866179 GCAAGAAACTAAGATTGCAATCTG 57.134 37.500 36.16 27.46 44.67 2.90
3032 4544 6.442112 AGAACAAGCAAGAAACTAAGATTGC 58.558 36.000 0.65 0.65 46.50 3.56
3033 4545 7.322222 CGAAGAACAAGCAAGAAACTAAGATTG 59.678 37.037 0.00 0.00 0.00 2.67
3034 4546 7.012421 ACGAAGAACAAGCAAGAAACTAAGATT 59.988 33.333 0.00 0.00 0.00 2.40
3035 4547 6.483640 ACGAAGAACAAGCAAGAAACTAAGAT 59.516 34.615 0.00 0.00 0.00 2.40
3036 4548 5.815740 ACGAAGAACAAGCAAGAAACTAAGA 59.184 36.000 0.00 0.00 0.00 2.10
3037 4549 6.049263 ACGAAGAACAAGCAAGAAACTAAG 57.951 37.500 0.00 0.00 0.00 2.18
3038 4550 6.431198 AACGAAGAACAAGCAAGAAACTAA 57.569 33.333 0.00 0.00 0.00 2.24
3039 4551 6.255215 CAAACGAAGAACAAGCAAGAAACTA 58.745 36.000 0.00 0.00 0.00 2.24
3040 4552 4.965119 AACGAAGAACAAGCAAGAAACT 57.035 36.364 0.00 0.00 0.00 2.66
3041 4553 4.259411 GCAAACGAAGAACAAGCAAGAAAC 60.259 41.667 0.00 0.00 0.00 2.78
3042 4554 3.857093 GCAAACGAAGAACAAGCAAGAAA 59.143 39.130 0.00 0.00 0.00 2.52
3043 4555 3.128589 AGCAAACGAAGAACAAGCAAGAA 59.871 39.130 0.00 0.00 0.00 2.52
3044 4556 2.682856 AGCAAACGAAGAACAAGCAAGA 59.317 40.909 0.00 0.00 0.00 3.02
3045 4557 3.038710 GAGCAAACGAAGAACAAGCAAG 58.961 45.455 0.00 0.00 0.00 4.01
3046 4558 2.538737 CGAGCAAACGAAGAACAAGCAA 60.539 45.455 0.00 0.00 35.09 3.91
3047 4559 1.003972 CGAGCAAACGAAGAACAAGCA 60.004 47.619 0.00 0.00 35.09 3.91
3048 4560 1.663494 CGAGCAAACGAAGAACAAGC 58.337 50.000 0.00 0.00 35.09 4.01
3049 4561 1.003972 TGCGAGCAAACGAAGAACAAG 60.004 47.619 0.00 0.00 35.09 3.16
3050 4562 1.003972 CTGCGAGCAAACGAAGAACAA 60.004 47.619 0.00 0.00 40.98 2.83
3051 4563 0.581529 CTGCGAGCAAACGAAGAACA 59.418 50.000 0.00 0.00 40.98 3.18
3052 4564 0.110644 CCTGCGAGCAAACGAAGAAC 60.111 55.000 7.38 0.00 40.98 3.01
3053 4565 0.249699 TCCTGCGAGCAAACGAAGAA 60.250 50.000 7.38 0.00 40.98 2.52
3054 4566 0.249699 TTCCTGCGAGCAAACGAAGA 60.250 50.000 7.38 0.00 40.98 2.87
3055 4567 2.234613 TTCCTGCGAGCAAACGAAG 58.765 52.632 0.00 0.00 38.52 3.79
3056 4568 4.447544 TTCCTGCGAGCAAACGAA 57.552 50.000 0.00 0.00 35.09 3.85


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

AutoCloner maintained by Alex Coulton.