Multiple sequence alignment - TraesCS5A01G236500

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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 TraesCS5A01G236500 chr5A 100.000 3779 0 0 1 3779 452108183 452111961 0.000000e+00 6979.0
1 TraesCS5A01G236500 chr5A 98.256 172 2 1 3414 3584 651496990 651496819 2.210000e-77 300.0
2 TraesCS5A01G236500 chr5B 95.943 2317 63 11 1034 3321 414827854 414830168 0.000000e+00 3729.0
3 TraesCS5A01G236500 chr5B 87.740 938 66 23 88 992 414826638 414827559 0.000000e+00 1050.0
4 TraesCS5A01G236500 chr5B 95.000 200 9 1 3580 3779 414830181 414830379 2.830000e-81 313.0
5 TraesCS5A01G236500 chr5B 84.158 101 14 2 3652 3750 485912169 485912069 3.110000e-16 97.1
6 TraesCS5A01G236500 chr5D 95.282 2268 78 11 1076 3321 351785775 351788035 0.000000e+00 3568.0
7 TraesCS5A01G236500 chr5D 86.356 623 59 21 89 691 351774331 351774947 0.000000e+00 656.0
8 TraesCS5A01G236500 chr5D 90.127 395 25 4 1 386 351784573 351784962 5.640000e-138 501.0
9 TraesCS5A01G236500 chr5D 90.780 282 15 6 791 1072 351775116 351775386 2.140000e-97 366.0
10 TraesCS5A01G236500 chr5D 96.045 177 7 0 3580 3756 351788047 351788223 4.780000e-74 289.0
11 TraesCS5A01G236500 chr5D 93.023 86 4 2 3321 3406 428386499 428386582 1.430000e-24 124.0
12 TraesCS5A01G236500 chr5D 77.564 156 27 6 3578 3729 141424780 141424931 1.870000e-13 87.9
13 TraesCS5A01G236500 chr5D 100.000 28 0 0 3711 3738 488862389 488862416 7.000000e-03 52.8
14 TraesCS5A01G236500 chr2D 98.810 168 1 1 3415 3581 516708309 516708476 7.940000e-77 298.0
15 TraesCS5A01G236500 chr2D 79.503 161 24 9 3581 3737 430625665 430625510 5.160000e-19 106.0
16 TraesCS5A01G236500 chr6B 86.219 283 28 9 3416 3694 711383847 711383572 2.850000e-76 296.0
17 TraesCS5A01G236500 chr6B 91.765 85 7 0 3321 3405 693099135 693099219 6.630000e-23 119.0
18 TraesCS5A01G236500 chr6B 76.331 169 27 12 3591 3750 668909489 668909653 1.130000e-10 78.7
19 TraesCS5A01G236500 chr4D 98.235 170 2 1 3413 3581 477898790 477898959 2.850000e-76 296.0
20 TraesCS5A01G236500 chr4D 95.580 181 5 3 3418 3597 13359916 13360094 1.720000e-73 287.0
21 TraesCS5A01G236500 chr4D 91.111 90 7 1 3317 3406 303843466 303843554 1.840000e-23 121.0
22 TraesCS5A01G236500 chr4D 83.019 106 14 4 3648 3750 503174930 503175034 4.020000e-15 93.5
23 TraesCS5A01G236500 chr4D 81.188 101 15 4 3595 3694 19406215 19406312 1.130000e-10 78.7
24 TraesCS5A01G236500 chr4A 97.126 174 3 2 3409 3581 670838282 670838454 3.690000e-75 292.0
25 TraesCS5A01G236500 chr1D 96.089 179 3 2 3404 3581 206955712 206955537 4.780000e-74 289.0
26 TraesCS5A01G236500 chr1D 83.000 100 16 1 3652 3750 317590806 317590905 5.200000e-14 89.8
27 TraesCS5A01G236500 chr1D 91.304 46 4 0 1158 1203 426595153 426595198 3.150000e-06 63.9
28 TraesCS5A01G236500 chr7D 95.082 183 6 3 3418 3599 381458552 381458372 6.180000e-73 285.0
29 TraesCS5A01G236500 chr4B 91.748 206 14 2 3378 3582 323794456 323794659 2.220000e-72 283.0
30 TraesCS5A01G236500 chr4B 92.391 92 4 3 3316 3405 315723269 315723359 1.100000e-25 128.0
31 TraesCS5A01G236500 chr4B 86.301 73 10 0 3669 3741 666798525 666798453 3.130000e-11 80.5
32 TraesCS5A01G236500 chr2B 93.182 88 4 1 3320 3405 733151092 733151179 1.100000e-25 128.0
33 TraesCS5A01G236500 chr2B 81.132 159 24 6 3581 3737 508959544 508959390 5.130000e-24 122.0
34 TraesCS5A01G236500 chr7A 90.323 93 7 2 3317 3409 290616136 290616046 1.840000e-23 121.0
35 TraesCS5A01G236500 chr3B 91.860 86 6 1 3320 3405 380679547 380679463 6.630000e-23 119.0
36 TraesCS5A01G236500 chr3A 91.860 86 6 1 3320 3405 65949494 65949410 6.630000e-23 119.0
37 TraesCS5A01G236500 chr3A 79.612 103 19 2 3590 3690 552211834 552211936 5.240000e-09 73.1
38 TraesCS5A01G236500 chr3A 100.000 30 0 0 1174 1203 498229371 498229400 5.270000e-04 56.5
39 TraesCS5A01G236500 chr3D 80.503 159 26 5 3581 3737 400694547 400694392 2.380000e-22 117.0
40 TraesCS5A01G236500 chr3D 90.110 91 6 2 3316 3405 523900136 523900048 8.580000e-22 115.0
41 TraesCS5A01G236500 chr6A 80.247 162 25 6 3580 3738 446898074 446898231 8.580000e-22 115.0
42 TraesCS5A01G236500 chr2A 84.466 103 15 1 3652 3753 161954741 161954843 2.400000e-17 100.0
43 TraesCS5A01G236500 chrUn 83.036 112 10 6 3302 3405 95593860 95593970 4.020000e-15 93.5
44 TraesCS5A01G236500 chrUn 92.857 42 2 1 3650 3690 84239984 84239943 4.080000e-05 60.2
45 TraesCS5A01G236500 chr1B 86.047 86 12 0 3652 3737 429700149 429700234 4.020000e-15 93.5
46 TraesCS5A01G236500 chr1A 83.168 101 14 3 3652 3750 544041363 544041264 5.200000e-14 89.8
47 TraesCS5A01G236500 chr1A 91.304 46 4 0 1158 1203 521639874 521639919 3.150000e-06 63.9
48 TraesCS5A01G236500 chr6D 88.732 71 8 0 3652 3722 90113132 90113202 1.870000e-13 87.9
49 TraesCS5A01G236500 chr6D 83.117 77 12 1 3615 3690 451186842 451186918 6.770000e-08 69.4


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 TraesCS5A01G236500 chr5A 452108183 452111961 3778 False 6979.000000 6979 100.000000 1 3779 1 chr5A.!!$F1 3778
1 TraesCS5A01G236500 chr5B 414826638 414830379 3741 False 1697.333333 3729 92.894333 88 3779 3 chr5B.!!$F1 3691
2 TraesCS5A01G236500 chr5D 351784573 351788223 3650 False 1452.666667 3568 93.818000 1 3756 3 chr5D.!!$F5 3755
3 TraesCS5A01G236500 chr5D 351774331 351775386 1055 False 511.000000 656 88.568000 89 1072 2 chr5D.!!$F4 983

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
413 425 0.173708 CTCTTCTTTCCCGTCCTCCG 59.826 60.000 0.0 0.00 0.0 4.63 F
1790 2159 1.452833 GGGCTTCACCTGGATCAGC 60.453 63.158 0.0 3.92 39.1 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2171 2541 1.214175 TCAAACTTGGTGAGCTTGGGA 59.786 47.619 0.0 0.0 33.28 4.37 R
3565 3967 2.108970 GATGTTACTCCCTCCGTTCCT 58.891 52.381 0.0 0.0 0.00 3.36 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
21 22 0.756903 ATTCGATCCCACCCTAACCG 59.243 55.000 0.00 0.00 0.00 4.44
56 57 9.371136 GTTTCTGTCCATTTTTCTTTCTTTCTT 57.629 29.630 0.00 0.00 0.00 2.52
57 58 9.942850 TTTCTGTCCATTTTTCTTTCTTTCTTT 57.057 25.926 0.00 0.00 0.00 2.52
58 59 9.586435 TTCTGTCCATTTTTCTTTCTTTCTTTC 57.414 29.630 0.00 0.00 0.00 2.62
59 60 8.971073 TCTGTCCATTTTTCTTTCTTTCTTTCT 58.029 29.630 0.00 0.00 0.00 2.52
75 76 6.882610 TTCTTTCTAGTGTTTCACATGCAT 57.117 33.333 0.00 0.00 36.74 3.96
144 146 0.320771 AGGAGGCACAACTAGTTGCG 60.321 55.000 30.97 24.27 44.03 4.85
151 153 2.843077 CACAACTAGTTGCGCAGATTG 58.157 47.619 30.97 17.94 44.03 2.67
188 190 4.948847 TGATTCGACATCCTAACATCCAG 58.051 43.478 0.00 0.00 0.00 3.86
215 217 0.894642 TCCACCGACATGACACCGTA 60.895 55.000 0.00 0.00 0.00 4.02
222 224 3.795101 CCGACATGACACCGTATTCTTAC 59.205 47.826 0.00 0.00 0.00 2.34
342 352 5.924254 CCTTATTCATATCCGCTTTGTCGTA 59.076 40.000 0.00 0.00 0.00 3.43
354 364 4.418392 GCTTTGTCGTACGATCTCCTTTA 58.582 43.478 22.57 0.99 0.00 1.85
361 371 5.908499 GTCGTACGATCTCCTTTATCACTTC 59.092 44.000 22.57 0.00 0.00 3.01
410 420 2.452505 CTCTCTCTTCTTTCCCGTCCT 58.547 52.381 0.00 0.00 0.00 3.85
413 425 0.173708 CTCTTCTTTCCCGTCCTCCG 59.826 60.000 0.00 0.00 0.00 4.63
422 434 2.273179 CCGTCCTCCGACTTCCACA 61.273 63.158 0.00 0.00 39.56 4.17
448 460 3.315142 GATCTGCCGCCACTGGTGA 62.315 63.158 10.43 0.00 34.74 4.02
457 469 1.609208 GCCACTGGTGACATCAAGTT 58.391 50.000 1.93 0.00 41.51 2.66
465 477 3.007940 TGGTGACATCAAGTTGGGACTAG 59.992 47.826 2.34 0.00 32.50 2.57
481 493 6.252995 TGGGACTAGTTGATTAGGCATTTTT 58.747 36.000 0.00 0.00 29.77 1.94
503 515 2.915659 AGTCCAAGACACGCCGGA 60.916 61.111 5.05 0.00 34.60 5.14
523 535 4.517285 GGAGTTGAACATCTGGCTATCAA 58.483 43.478 0.00 0.00 0.00 2.57
544 556 3.497031 GCCGTTGAGGTTAGCCGC 61.497 66.667 0.00 0.00 43.70 6.53
603 615 7.421684 AGAATTCCTTTTGAGGGGATATTCAA 58.578 34.615 0.65 0.00 34.92 2.69
609 621 8.539544 TCCTTTTGAGGGGATATTCAATTTTTC 58.460 33.333 0.00 0.00 33.68 2.29
614 626 9.723601 TTGAGGGGATATTCAATTTTTCTTTTG 57.276 29.630 0.00 0.00 0.00 2.44
615 627 9.099071 TGAGGGGATATTCAATTTTTCTTTTGA 57.901 29.630 0.00 0.00 0.00 2.69
616 628 9.591792 GAGGGGATATTCAATTTTTCTTTTGAG 57.408 33.333 0.00 0.00 33.68 3.02
617 629 9.325248 AGGGGATATTCAATTTTTCTTTTGAGA 57.675 29.630 0.00 0.00 33.68 3.27
618 630 9.591792 GGGGATATTCAATTTTTCTTTTGAGAG 57.408 33.333 0.00 0.00 33.68 3.20
626 638 9.669353 TCAATTTTTCTTTTGAGAGAGAATTCG 57.331 29.630 0.00 0.00 32.40 3.34
627 639 9.669353 CAATTTTTCTTTTGAGAGAGAATTCGA 57.331 29.630 0.00 0.00 32.40 3.71
628 640 9.670719 AATTTTTCTTTTGAGAGAGAATTCGAC 57.329 29.630 0.00 0.00 32.40 4.20
629 641 6.453643 TTTCTTTTGAGAGAGAATTCGACG 57.546 37.500 0.00 0.00 32.40 5.12
630 642 5.122512 TCTTTTGAGAGAGAATTCGACGT 57.877 39.130 0.00 0.00 0.00 4.34
631 643 5.529791 TCTTTTGAGAGAGAATTCGACGTT 58.470 37.500 0.00 0.00 0.00 3.99
632 644 5.983720 TCTTTTGAGAGAGAATTCGACGTTT 59.016 36.000 0.00 0.00 0.00 3.60
633 645 6.479001 TCTTTTGAGAGAGAATTCGACGTTTT 59.521 34.615 0.00 0.00 0.00 2.43
634 646 7.650504 TCTTTTGAGAGAGAATTCGACGTTTTA 59.349 33.333 0.00 0.00 0.00 1.52
635 647 7.884816 TTTGAGAGAGAATTCGACGTTTTAT 57.115 32.000 0.00 0.00 0.00 1.40
636 648 7.884816 TTGAGAGAGAATTCGACGTTTTATT 57.115 32.000 0.00 0.00 0.00 1.40
637 649 7.884816 TGAGAGAGAATTCGACGTTTTATTT 57.115 32.000 0.00 0.00 0.00 1.40
638 650 8.306680 TGAGAGAGAATTCGACGTTTTATTTT 57.693 30.769 0.00 0.00 0.00 1.82
639 651 9.414295 TGAGAGAGAATTCGACGTTTTATTTTA 57.586 29.630 0.00 0.00 0.00 1.52
640 652 9.888637 GAGAGAGAATTCGACGTTTTATTTTAG 57.111 33.333 0.00 0.00 0.00 1.85
643 655 9.211485 AGAGAATTCGACGTTTTATTTTAGGAA 57.789 29.630 0.00 0.00 0.00 3.36
667 679 5.758924 AGCATTCCACGTTTTCTTTAGAAC 58.241 37.500 0.00 0.00 33.13 3.01
700 763 4.000988 TGAGAAGGCATTCGGTAGTTTTC 58.999 43.478 5.31 0.00 40.58 2.29
701 764 4.254492 GAGAAGGCATTCGGTAGTTTTCT 58.746 43.478 5.31 0.00 40.58 2.52
704 767 5.181433 AGAAGGCATTCGGTAGTTTTCTTTC 59.819 40.000 5.31 0.00 40.58 2.62
741 804 2.544480 GCATTCGGTAGCCAGTTTTC 57.456 50.000 0.00 0.00 0.00 2.29
857 965 1.681264 CAAAACAGCGAAGGAAACCCT 59.319 47.619 0.00 0.00 34.97 4.34
916 1033 5.276820 CCGAGCACCAAACTTGAAAATTTTC 60.277 40.000 21.60 21.60 37.69 2.29
1006 1123 2.410322 ATTCCCCACAAGCAGACGCA 62.410 55.000 0.00 0.00 42.27 5.24
1007 1124 3.052082 CCCCACAAGCAGACGCAG 61.052 66.667 0.00 0.00 42.27 5.18
1036 1405 2.584418 CGCCTGCTGATCTGACCG 60.584 66.667 3.42 0.00 0.00 4.79
1361 1730 3.338250 TTCTCCATGGCCCGCCTT 61.338 61.111 6.96 0.00 36.94 4.35
1680 2049 1.988063 CGATGTATCCATCCAGCTCG 58.012 55.000 0.00 0.00 43.87 5.03
1790 2159 1.452833 GGGCTTCACCTGGATCAGC 60.453 63.158 0.00 3.92 39.10 4.26
1917 2286 7.222611 GTCATAACTTTGCAAGATTGTGTTGTT 59.777 33.333 16.02 7.96 0.00 2.83
1955 2325 5.270083 TGTGTCGTGAATTGTGATGAAAAC 58.730 37.500 0.00 0.00 0.00 2.43
2171 2541 1.737793 GTCGATTTCTTCAACGGCCAT 59.262 47.619 2.24 0.00 0.00 4.40
2270 2640 1.226379 CACGCCGCCTTTATTGCTG 60.226 57.895 0.00 0.00 0.00 4.41
2275 2653 1.069906 GCCGCCTTTATTGCTGTATCG 60.070 52.381 0.00 0.00 0.00 2.92
2404 2782 3.267860 CGCTCGCCTCTCAATGCC 61.268 66.667 0.00 0.00 0.00 4.40
2414 2792 2.613977 CCTCTCAATGCCGAACAGAAGT 60.614 50.000 0.00 0.00 0.00 3.01
2451 2829 2.472861 CGCTTGTGAAGTACAGTGTCAG 59.527 50.000 0.00 0.00 41.10 3.51
2455 2833 2.224042 TGTGAAGTACAGTGTCAGGCTG 60.224 50.000 8.58 8.58 39.67 4.85
2461 2839 2.025969 CAGTGTCAGGCTGCAGTCG 61.026 63.158 16.64 9.67 0.00 4.18
2499 2877 3.697542 TCACAGATGAAGAATTGCCATGG 59.302 43.478 7.63 7.63 0.00 3.66
2509 2887 0.686441 ATTGCCATGGTGCTGCTGAT 60.686 50.000 14.67 0.00 0.00 2.90
2589 2967 4.104102 TGAATAAAAGGAGACCCTGTGTGT 59.896 41.667 0.00 0.00 43.48 3.72
2677 3056 3.562973 GTCATTACTGGAGGATGCATGTG 59.437 47.826 2.46 0.00 34.26 3.21
2707 3086 6.294176 CCTCTTGAATAACTTTGGAGTTGTGG 60.294 42.308 2.25 0.00 45.46 4.17
2716 3095 4.638865 ACTTTGGAGTTGTGGTGTTTAGTC 59.361 41.667 0.00 0.00 29.87 2.59
2737 3116 7.441890 AGTCGATTGATATTCATCTAGTCGT 57.558 36.000 0.00 0.00 34.56 4.34
3120 3509 8.472413 CCATTGAGATGACTTTTACATTCCATT 58.528 33.333 0.00 0.00 35.16 3.16
3174 3563 8.746922 TCGTGAATTTAGTACGTTTCTGTTAT 57.253 30.769 0.00 0.00 38.80 1.89
3175 3564 8.853345 TCGTGAATTTAGTACGTTTCTGTTATC 58.147 33.333 0.00 0.00 38.80 1.75
3176 3565 8.857216 CGTGAATTTAGTACGTTTCTGTTATCT 58.143 33.333 0.00 0.00 33.48 1.98
3186 3585 4.319177 GTTTCTGTTATCTGTGGTCTGCT 58.681 43.478 0.00 0.00 0.00 4.24
3202 3601 7.179160 TGTGGTCTGCTATGAGTATATGCTTAT 59.821 37.037 3.65 3.65 0.00 1.73
3204 3603 6.915300 GGTCTGCTATGAGTATATGCTTATCG 59.085 42.308 1.28 0.00 0.00 2.92
3325 3727 9.801873 TTTAAGTTTGACCACGTATATACTACC 57.198 33.333 11.05 0.00 0.00 3.18
3326 3728 7.651027 AAGTTTGACCACGTATATACTACCT 57.349 36.000 11.05 0.00 0.00 3.08
3327 3729 7.269477 AGTTTGACCACGTATATACTACCTC 57.731 40.000 11.05 1.93 0.00 3.85
3328 3730 6.264067 AGTTTGACCACGTATATACTACCTCC 59.736 42.308 11.05 0.00 0.00 4.30
3329 3731 4.318332 TGACCACGTATATACTACCTCCG 58.682 47.826 11.05 0.00 0.00 4.63
3330 3732 4.202357 TGACCACGTATATACTACCTCCGT 60.202 45.833 11.05 0.00 0.00 4.69
3331 3733 4.319177 ACCACGTATATACTACCTCCGTC 58.681 47.826 11.05 0.00 0.00 4.79
3332 3734 3.686726 CCACGTATATACTACCTCCGTCC 59.313 52.174 11.05 0.00 0.00 4.79
3333 3735 3.686726 CACGTATATACTACCTCCGTCCC 59.313 52.174 11.05 0.00 0.00 4.46
3334 3736 3.327757 ACGTATATACTACCTCCGTCCCA 59.672 47.826 11.05 0.00 0.00 4.37
3335 3737 4.202461 ACGTATATACTACCTCCGTCCCAA 60.202 45.833 11.05 0.00 0.00 4.12
3336 3738 4.761739 CGTATATACTACCTCCGTCCCAAA 59.238 45.833 11.05 0.00 0.00 3.28
3337 3739 5.241506 CGTATATACTACCTCCGTCCCAAAA 59.758 44.000 11.05 0.00 0.00 2.44
3338 3740 6.071728 CGTATATACTACCTCCGTCCCAAAAT 60.072 42.308 11.05 0.00 0.00 1.82
3339 3741 7.121168 CGTATATACTACCTCCGTCCCAAAATA 59.879 40.741 11.05 0.00 0.00 1.40
3340 3742 7.860649 ATATACTACCTCCGTCCCAAAATAA 57.139 36.000 0.00 0.00 0.00 1.40
3341 3743 4.482952 ACTACCTCCGTCCCAAAATAAG 57.517 45.455 0.00 0.00 0.00 1.73
3342 3744 3.842436 ACTACCTCCGTCCCAAAATAAGT 59.158 43.478 0.00 0.00 0.00 2.24
3343 3745 3.067684 ACCTCCGTCCCAAAATAAGTG 57.932 47.619 0.00 0.00 0.00 3.16
3344 3746 2.374170 ACCTCCGTCCCAAAATAAGTGT 59.626 45.455 0.00 0.00 0.00 3.55
3345 3747 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
3346 3748 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
3347 3749 4.324267 CTCCGTCCCAAAATAAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
3348 3750 5.484715 CTCCGTCCCAAAATAAGTGTCTTA 58.515 41.667 0.00 0.00 0.00 2.10
3349 3751 5.867330 TCCGTCCCAAAATAAGTGTCTTAA 58.133 37.500 0.00 0.00 0.00 1.85
3350 3752 5.702209 TCCGTCCCAAAATAAGTGTCTTAAC 59.298 40.000 0.00 0.00 0.00 2.01
3351 3753 5.106436 CCGTCCCAAAATAAGTGTCTTAACC 60.106 44.000 0.00 0.00 0.00 2.85
3352 3754 5.704053 CGTCCCAAAATAAGTGTCTTAACCT 59.296 40.000 0.00 0.00 0.00 3.50
3353 3755 6.206048 CGTCCCAAAATAAGTGTCTTAACCTT 59.794 38.462 0.00 0.00 0.00 3.50
3354 3756 7.388500 CGTCCCAAAATAAGTGTCTTAACCTTA 59.612 37.037 0.00 0.00 0.00 2.69
3355 3757 8.727910 GTCCCAAAATAAGTGTCTTAACCTTAG 58.272 37.037 0.00 0.00 0.00 2.18
3356 3758 8.442374 TCCCAAAATAAGTGTCTTAACCTTAGT 58.558 33.333 0.00 0.00 0.00 2.24
3357 3759 9.729281 CCCAAAATAAGTGTCTTAACCTTAGTA 57.271 33.333 0.00 0.00 0.00 1.82
3362 3764 9.716531 AATAAGTGTCTTAACCTTAGTACAACC 57.283 33.333 0.00 0.00 0.00 3.77
3363 3765 6.990908 AGTGTCTTAACCTTAGTACAACCT 57.009 37.500 0.00 0.00 0.00 3.50
3364 3766 7.370905 AGTGTCTTAACCTTAGTACAACCTT 57.629 36.000 0.00 0.00 0.00 3.50
3365 3767 8.482852 AGTGTCTTAACCTTAGTACAACCTTA 57.517 34.615 0.00 0.00 0.00 2.69
3366 3768 8.583296 AGTGTCTTAACCTTAGTACAACCTTAG 58.417 37.037 0.00 0.00 0.00 2.18
3367 3769 8.363390 GTGTCTTAACCTTAGTACAACCTTAGT 58.637 37.037 0.00 0.00 0.00 2.24
3368 3770 9.586732 TGTCTTAACCTTAGTACAACCTTAGTA 57.413 33.333 0.00 0.00 0.00 1.82
3369 3771 9.847706 GTCTTAACCTTAGTACAACCTTAGTAC 57.152 37.037 0.00 0.00 41.59 2.73
3370 3772 9.586732 TCTTAACCTTAGTACAACCTTAGTACA 57.413 33.333 6.30 0.00 43.24 2.90
3374 3776 8.255111 ACCTTAGTACAACCTTAGTACAAAGT 57.745 34.615 6.30 0.00 43.24 2.66
3375 3777 8.708378 ACCTTAGTACAACCTTAGTACAAAGTT 58.292 33.333 6.30 0.00 43.24 2.66
3376 3778 8.985805 CCTTAGTACAACCTTAGTACAAAGTTG 58.014 37.037 13.32 13.32 43.24 3.16
3377 3779 9.754382 CTTAGTACAACCTTAGTACAAAGTTGA 57.246 33.333 18.83 5.96 43.24 3.18
3378 3780 9.754382 TTAGTACAACCTTAGTACAAAGTTGAG 57.246 33.333 18.83 0.00 43.24 3.02
3379 3781 8.015185 AGTACAACCTTAGTACAAAGTTGAGA 57.985 34.615 18.83 8.28 43.24 3.27
3380 3782 7.924947 AGTACAACCTTAGTACAAAGTTGAGAC 59.075 37.037 18.83 15.76 43.24 3.36
3381 3783 6.646267 ACAACCTTAGTACAAAGTTGAGACA 58.354 36.000 18.83 0.00 0.00 3.41
3382 3784 6.537660 ACAACCTTAGTACAAAGTTGAGACAC 59.462 38.462 18.83 0.00 0.00 3.67
3383 3785 6.481434 ACCTTAGTACAAAGTTGAGACACT 57.519 37.500 0.00 0.00 0.00 3.55
3384 3786 6.885922 ACCTTAGTACAAAGTTGAGACACTT 58.114 36.000 0.00 0.00 38.74 3.16
3385 3787 8.015185 ACCTTAGTACAAAGTTGAGACACTTA 57.985 34.615 0.00 0.00 35.87 2.24
3386 3788 8.648693 ACCTTAGTACAAAGTTGAGACACTTAT 58.351 33.333 0.00 0.00 35.87 1.73
3387 3789 9.490379 CCTTAGTACAAAGTTGAGACACTTATT 57.510 33.333 0.00 0.00 35.87 1.40
3391 3793 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
3392 3794 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
3393 3795 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
3394 3796 7.287696 ACAAAGTTGAGACACTTATTTTGGGAT 59.712 33.333 0.00 0.00 35.87 3.85
3395 3797 6.824305 AGTTGAGACACTTATTTTGGGATG 57.176 37.500 0.00 0.00 0.00 3.51
3396 3798 6.542821 AGTTGAGACACTTATTTTGGGATGA 58.457 36.000 0.00 0.00 0.00 2.92
3397 3799 7.004086 AGTTGAGACACTTATTTTGGGATGAA 58.996 34.615 0.00 0.00 0.00 2.57
3398 3800 7.175641 AGTTGAGACACTTATTTTGGGATGAAG 59.824 37.037 0.00 0.00 0.00 3.02
3399 3801 5.945784 TGAGACACTTATTTTGGGATGAAGG 59.054 40.000 0.00 0.00 0.00 3.46
3400 3802 5.264395 AGACACTTATTTTGGGATGAAGGG 58.736 41.667 0.00 0.00 0.00 3.95
3401 3803 5.015178 AGACACTTATTTTGGGATGAAGGGA 59.985 40.000 0.00 0.00 0.00 4.20
3402 3804 5.264395 ACACTTATTTTGGGATGAAGGGAG 58.736 41.667 0.00 0.00 0.00 4.30
3403 3805 5.222337 ACACTTATTTTGGGATGAAGGGAGT 60.222 40.000 0.00 0.00 0.00 3.85
3404 3806 6.011981 ACACTTATTTTGGGATGAAGGGAGTA 60.012 38.462 0.00 0.00 0.00 2.59
3431 3833 5.548181 AAATATTCTACTCCCTCCGTTCC 57.452 43.478 0.00 0.00 0.00 3.62
3432 3834 2.850695 ATTCTACTCCCTCCGTTCCT 57.149 50.000 0.00 0.00 0.00 3.36
3433 3835 3.967467 ATTCTACTCCCTCCGTTCCTA 57.033 47.619 0.00 0.00 0.00 2.94
3434 3836 3.744940 TTCTACTCCCTCCGTTCCTAA 57.255 47.619 0.00 0.00 0.00 2.69
3435 3837 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
3436 3838 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
3437 3839 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
3438 3840 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
3439 3841 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
3440 3842 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3441 3843 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3442 3844 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3443 3845 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3444 3846 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3445 3847 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3446 3848 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3447 3849 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
3448 3850 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
3449 3851 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
3450 3852 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
3451 3853 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
3464 3866 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
3465 3867 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
3466 3868 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
3467 3869 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
3468 3870 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
3469 3871 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
3470 3872 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
3471 3873 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
3472 3874 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
3474 3876 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
3475 3877 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
3476 3878 7.375834 AGATTTCAACAAGTGACTACATACGA 58.624 34.615 0.00 0.00 35.39 3.43
3477 3879 7.870954 AGATTTCAACAAGTGACTACATACGAA 59.129 33.333 0.00 0.00 35.39 3.85
3478 3880 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
3479 3881 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
3480 3882 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
3481 3883 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
3482 3884 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
3483 3885 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
3484 3886 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
3485 3887 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
3486 3888 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
3487 3889 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
3488 3890 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
3489 3891 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
3490 3892 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
3491 3893 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
3492 3894 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
3493 3895 6.913170 ACATACGAAGCAAAATGAGTGAATT 58.087 32.000 0.00 0.00 0.00 2.17
3494 3896 7.370383 ACATACGAAGCAAAATGAGTGAATTT 58.630 30.769 0.00 0.00 0.00 1.82
3495 3897 8.511321 ACATACGAAGCAAAATGAGTGAATTTA 58.489 29.630 0.00 0.00 0.00 1.40
3496 3898 8.788813 CATACGAAGCAAAATGAGTGAATTTAC 58.211 33.333 0.00 0.00 0.00 2.01
3497 3899 6.734137 ACGAAGCAAAATGAGTGAATTTACA 58.266 32.000 2.93 0.00 0.00 2.41
3498 3900 6.636850 ACGAAGCAAAATGAGTGAATTTACAC 59.363 34.615 2.93 0.00 40.60 2.90
3531 3933 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
3533 3935 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
3534 3936 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
3535 3937 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
3536 3938 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
3537 3939 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
3538 3940 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
3539 3941 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
3540 3942 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
3541 3943 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
3542 3944 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
3543 3945 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
3544 3946 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
3545 3947 5.163794 CCGTATGTGGTAGTCCATTTGAAAC 60.164 44.000 0.00 0.00 46.20 2.78
3546 3948 5.642063 CGTATGTGGTAGTCCATTTGAAACT 59.358 40.000 0.00 0.00 46.20 2.66
3547 3949 6.183360 CGTATGTGGTAGTCCATTTGAAACTC 60.183 42.308 0.00 0.00 46.20 3.01
3548 3950 5.304686 TGTGGTAGTCCATTTGAAACTCT 57.695 39.130 0.00 0.00 46.20 3.24
3549 3951 6.428083 TGTGGTAGTCCATTTGAAACTCTA 57.572 37.500 0.00 0.00 46.20 2.43
3550 3952 6.833041 TGTGGTAGTCCATTTGAAACTCTAA 58.167 36.000 0.00 0.00 46.20 2.10
3551 3953 7.284074 TGTGGTAGTCCATTTGAAACTCTAAA 58.716 34.615 0.00 0.00 46.20 1.85
3552 3954 7.776030 TGTGGTAGTCCATTTGAAACTCTAAAA 59.224 33.333 0.00 0.00 46.20 1.52
3553 3955 8.626526 GTGGTAGTCCATTTGAAACTCTAAAAA 58.373 33.333 0.00 0.00 46.20 1.94
3554 3956 8.846211 TGGTAGTCCATTTGAAACTCTAAAAAG 58.154 33.333 0.00 0.00 39.03 2.27
3555 3957 9.063615 GGTAGTCCATTTGAAACTCTAAAAAGA 57.936 33.333 0.00 0.00 0.00 2.52
3556 3958 9.880064 GTAGTCCATTTGAAACTCTAAAAAGAC 57.120 33.333 0.00 0.00 0.00 3.01
3557 3959 8.519799 AGTCCATTTGAAACTCTAAAAAGACA 57.480 30.769 0.00 0.00 30.54 3.41
3558 3960 8.966868 AGTCCATTTGAAACTCTAAAAAGACAA 58.033 29.630 0.00 0.00 30.54 3.18
3559 3961 9.581099 GTCCATTTGAAACTCTAAAAAGACAAA 57.419 29.630 0.00 0.00 0.00 2.83
3575 3977 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
3576 3978 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3577 3979 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3578 3980 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.202430 ACATATTTCGGTTAGGGTGGGATC 60.202 45.833 0.00 0.00 0.00 3.36
7 8 3.720002 ACATATTTCGGTTAGGGTGGGAT 59.280 43.478 0.00 0.00 0.00 3.85
21 22 9.696917 AGAAAAATGGACAGAAACACATATTTC 57.303 29.630 0.00 0.00 38.62 2.17
144 146 8.915871 ATCAATGTGTTGTATTAACAATCTGC 57.084 30.769 0.00 0.00 46.84 4.26
151 153 9.210426 GATGTCGAATCAATGTGTTGTATTAAC 57.790 33.333 0.00 0.00 36.69 2.01
188 190 0.659427 CATGTCGGTGGATCATGCAC 59.341 55.000 0.00 0.00 38.03 4.57
222 224 9.438291 GTTGGTATTGTGAATTTATGATTCTCG 57.562 33.333 5.56 0.00 0.00 4.04
322 332 3.734231 CGTACGACAAAGCGGATATGAAT 59.266 43.478 10.44 0.00 35.12 2.57
342 352 3.388350 GGGGAAGTGATAAAGGAGATCGT 59.612 47.826 0.00 0.00 0.00 3.73
354 364 3.790089 AAGACGAAAAGGGGAAGTGAT 57.210 42.857 0.00 0.00 0.00 3.06
361 371 0.881796 GCCAGAAAGACGAAAAGGGG 59.118 55.000 0.00 0.00 0.00 4.79
410 420 1.361271 GTGACGTGTGGAAGTCGGA 59.639 57.895 0.00 0.00 40.05 4.55
413 425 2.029828 AGATCTGTGACGTGTGGAAGTC 60.030 50.000 0.00 0.00 37.85 3.01
422 434 2.125912 GCGGCAGATCTGTGACGT 60.126 61.111 23.38 0.00 0.00 4.34
448 460 4.974645 TCAACTAGTCCCAACTTGATGT 57.025 40.909 0.00 0.00 36.92 3.06
457 469 5.450818 AAATGCCTAATCAACTAGTCCCA 57.549 39.130 0.00 0.00 0.00 4.37
481 493 1.305201 GGCGTGTCTTGGACTCAAAA 58.695 50.000 0.00 0.00 33.15 2.44
503 515 5.171339 ACTTGATAGCCAGATGTTCAACT 57.829 39.130 0.00 0.00 0.00 3.16
523 535 1.080025 GCTAACCTCAACGGCGACT 60.080 57.895 16.62 0.00 35.61 4.18
544 556 3.201708 AGGATGAAGAAGGGGTTGATGAG 59.798 47.826 0.00 0.00 0.00 2.90
603 615 8.012241 CGTCGAATTCTCTCTCAAAAGAAAAAT 58.988 33.333 3.52 0.00 35.29 1.82
609 621 5.830900 AACGTCGAATTCTCTCTCAAAAG 57.169 39.130 0.00 0.00 0.00 2.27
614 626 9.888637 CTAAAATAAAACGTCGAATTCTCTCTC 57.111 33.333 0.00 0.00 0.00 3.20
615 627 8.870879 CCTAAAATAAAACGTCGAATTCTCTCT 58.129 33.333 0.00 0.00 0.00 3.10
616 628 8.866956 TCCTAAAATAAAACGTCGAATTCTCTC 58.133 33.333 0.00 0.00 0.00 3.20
617 629 8.767478 TCCTAAAATAAAACGTCGAATTCTCT 57.233 30.769 0.00 0.00 0.00 3.10
618 630 9.815936 TTTCCTAAAATAAAACGTCGAATTCTC 57.184 29.630 0.00 0.00 0.00 2.87
619 631 9.821662 CTTTCCTAAAATAAAACGTCGAATTCT 57.178 29.630 0.00 0.00 0.00 2.40
620 632 8.572976 GCTTTCCTAAAATAAAACGTCGAATTC 58.427 33.333 0.00 0.00 0.00 2.17
621 633 8.077386 TGCTTTCCTAAAATAAAACGTCGAATT 58.923 29.630 0.00 0.00 0.00 2.17
623 635 6.957150 TGCTTTCCTAAAATAAAACGTCGAA 58.043 32.000 0.00 0.00 0.00 3.71
624 636 6.542574 TGCTTTCCTAAAATAAAACGTCGA 57.457 33.333 0.00 0.00 0.00 4.20
625 637 7.007995 GGAATGCTTTCCTAAAATAAAACGTCG 59.992 37.037 21.16 0.00 46.80 5.12
626 638 8.169839 GGAATGCTTTCCTAAAATAAAACGTC 57.830 34.615 21.16 0.00 46.80 4.34
643 655 6.206498 GTTCTAAAGAAAACGTGGAATGCTT 58.794 36.000 0.00 0.00 35.58 3.91
667 679 1.901650 GCCTTCTCAAACGTGGCTCG 61.902 60.000 7.50 7.50 46.00 5.03
700 763 5.413833 TGCCTAATGCTCAGAAGAAAGAAAG 59.586 40.000 0.00 0.00 42.00 2.62
701 764 5.316167 TGCCTAATGCTCAGAAGAAAGAAA 58.684 37.500 0.00 0.00 42.00 2.52
704 767 5.503683 CGAATGCCTAATGCTCAGAAGAAAG 60.504 44.000 0.00 0.00 42.00 2.62
734 797 4.543692 CTGCATTCTTCTGTGGAAAACTG 58.456 43.478 0.00 0.00 0.00 3.16
741 804 1.651240 CCGGCTGCATTCTTCTGTGG 61.651 60.000 0.50 0.00 0.00 4.17
837 945 1.681264 AGGGTTTCCTTCGCTGTTTTG 59.319 47.619 0.00 0.00 41.56 2.44
838 946 2.067365 AGGGTTTCCTTCGCTGTTTT 57.933 45.000 0.00 0.00 41.56 2.43
857 965 1.270041 GCGAGTTTGAAATGGGGCAAA 60.270 47.619 0.00 0.00 0.00 3.68
987 1104 1.675641 GCGTCTGCTTGTGGGGAAT 60.676 57.895 0.00 0.00 38.39 3.01
1012 1129 1.812922 GATCAGCAGGCGAGTGTGG 60.813 63.158 0.00 0.00 0.00 4.17
1401 1770 2.583593 GTCCATCCGCAGCTCGAC 60.584 66.667 7.07 0.00 41.67 4.20
1680 2049 3.275338 GCACCGCTGGAGCATAGC 61.275 66.667 10.92 0.00 39.08 2.97
1917 2286 3.687212 ACGACACAATTTATTGCATCCGA 59.313 39.130 2.46 0.00 41.38 4.55
1955 2325 1.338107 TATACACCCTCCCTGCATCG 58.662 55.000 0.00 0.00 0.00 3.84
2171 2541 1.214175 TCAAACTTGGTGAGCTTGGGA 59.786 47.619 0.00 0.00 33.28 4.37
2404 2782 2.748605 AGAGTGCTCAACTTCTGTTCG 58.251 47.619 1.82 0.00 40.07 3.95
2414 2792 2.462456 AGCGATTCAAGAGTGCTCAA 57.538 45.000 1.82 0.00 0.00 3.02
2451 2829 1.153289 ATGACCATCGACTGCAGCC 60.153 57.895 15.27 0.16 0.00 4.85
2455 2833 0.179111 TTCGGATGACCATCGACTGC 60.179 55.000 4.15 0.00 38.69 4.40
2461 2839 3.068732 TCTGTGAGATTCGGATGACCATC 59.931 47.826 1.50 1.50 37.11 3.51
2499 2877 4.413087 CTCAAAGAAATCATCAGCAGCAC 58.587 43.478 0.00 0.00 0.00 4.40
2632 3011 5.221682 ACAACAATCAAAATCAGGGAATGCA 60.222 36.000 0.00 0.00 0.00 3.96
2634 3013 6.457355 TGACAACAATCAAAATCAGGGAATG 58.543 36.000 0.00 0.00 0.00 2.67
2677 3056 5.497474 TCCAAAGTTATTCAAGAGGGCTAC 58.503 41.667 0.00 0.00 0.00 3.58
2716 3095 6.863645 ACCAACGACTAGATGAATATCAATCG 59.136 38.462 0.00 0.00 38.77 3.34
2737 3116 6.826231 TCAACAAGTTCTAGTCATCAAACCAA 59.174 34.615 0.00 0.00 0.00 3.67
3120 3509 9.995003 ATCTAAATTGTTCCAAAATAAACAGCA 57.005 25.926 0.00 0.00 36.78 4.41
3150 3539 8.857216 AGATAACAGAAACGTACTAAATTCACG 58.143 33.333 0.00 0.00 41.32 4.35
3164 3553 4.319177 AGCAGACCACAGATAACAGAAAC 58.681 43.478 0.00 0.00 0.00 2.78
3174 3563 5.047731 GCATATACTCATAGCAGACCACAGA 60.048 44.000 0.00 0.00 0.00 3.41
3175 3564 5.047448 AGCATATACTCATAGCAGACCACAG 60.047 44.000 0.00 0.00 0.00 3.66
3176 3565 4.835056 AGCATATACTCATAGCAGACCACA 59.165 41.667 0.00 0.00 0.00 4.17
3202 3601 2.158711 TCCGTAGAGATTTCCCTAGCGA 60.159 50.000 0.00 0.00 0.00 4.93
3204 3603 4.875561 ATTCCGTAGAGATTTCCCTAGC 57.124 45.455 0.00 0.00 0.00 3.42
3313 3715 3.942829 TGGGACGGAGGTAGTATATACG 58.057 50.000 7.23 0.00 0.00 3.06
3321 3723 4.189231 CACTTATTTTGGGACGGAGGTAG 58.811 47.826 0.00 0.00 0.00 3.18
3322 3724 3.583966 ACACTTATTTTGGGACGGAGGTA 59.416 43.478 0.00 0.00 0.00 3.08
3323 3725 2.374170 ACACTTATTTTGGGACGGAGGT 59.626 45.455 0.00 0.00 0.00 3.85
3324 3726 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3325 3727 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
3326 3728 4.360951 AAGACACTTATTTTGGGACGGA 57.639 40.909 0.00 0.00 0.00 4.69
3327 3729 5.106436 GGTTAAGACACTTATTTTGGGACGG 60.106 44.000 0.00 0.00 0.00 4.79
3328 3730 5.704053 AGGTTAAGACACTTATTTTGGGACG 59.296 40.000 0.00 0.00 0.00 4.79
3329 3731 7.520451 AAGGTTAAGACACTTATTTTGGGAC 57.480 36.000 0.00 0.00 0.00 4.46
3330 3732 8.442374 ACTAAGGTTAAGACACTTATTTTGGGA 58.558 33.333 0.00 0.00 0.00 4.37
3331 3733 8.631480 ACTAAGGTTAAGACACTTATTTTGGG 57.369 34.615 0.00 0.00 0.00 4.12
3336 3738 9.716531 GGTTGTACTAAGGTTAAGACACTTATT 57.283 33.333 0.00 0.00 0.00 1.40
3337 3739 9.097946 AGGTTGTACTAAGGTTAAGACACTTAT 57.902 33.333 0.00 0.00 0.00 1.73
3338 3740 8.482852 AGGTTGTACTAAGGTTAAGACACTTA 57.517 34.615 0.00 0.00 0.00 2.24
3339 3741 7.370905 AGGTTGTACTAAGGTTAAGACACTT 57.629 36.000 0.00 0.00 0.00 3.16
3340 3742 6.990908 AGGTTGTACTAAGGTTAAGACACT 57.009 37.500 0.00 0.00 0.00 3.55
3341 3743 8.363390 ACTAAGGTTGTACTAAGGTTAAGACAC 58.637 37.037 0.00 0.00 0.00 3.67
3342 3744 8.482852 ACTAAGGTTGTACTAAGGTTAAGACA 57.517 34.615 0.00 0.00 0.00 3.41
3343 3745 9.847706 GTACTAAGGTTGTACTAAGGTTAAGAC 57.152 37.037 0.00 0.00 37.76 3.01
3344 3746 9.586732 TGTACTAAGGTTGTACTAAGGTTAAGA 57.413 33.333 0.00 0.00 40.44 2.10
3348 3750 8.708378 ACTTTGTACTAAGGTTGTACTAAGGTT 58.292 33.333 19.08 8.32 46.97 3.50
3349 3751 8.255111 ACTTTGTACTAAGGTTGTACTAAGGT 57.745 34.615 19.08 11.91 46.97 3.50
3350 3752 8.985805 CAACTTTGTACTAAGGTTGTACTAAGG 58.014 37.037 19.08 11.49 46.97 2.69
3352 3754 9.754382 CTCAACTTTGTACTAAGGTTGTACTAA 57.246 33.333 19.08 6.61 40.44 2.24
3353 3755 9.135189 TCTCAACTTTGTACTAAGGTTGTACTA 57.865 33.333 19.08 6.87 40.44 1.82
3354 3756 7.924947 GTCTCAACTTTGTACTAAGGTTGTACT 59.075 37.037 19.08 0.00 40.44 2.73
3355 3757 7.707893 TGTCTCAACTTTGTACTAAGGTTGTAC 59.292 37.037 19.08 18.93 40.27 2.90
3356 3758 7.707893 GTGTCTCAACTTTGTACTAAGGTTGTA 59.292 37.037 19.08 11.57 0.00 2.41
3357 3759 6.537660 GTGTCTCAACTTTGTACTAAGGTTGT 59.462 38.462 19.08 0.00 0.00 3.32
3358 3760 6.761714 AGTGTCTCAACTTTGTACTAAGGTTG 59.238 38.462 19.08 18.65 0.00 3.77
3359 3761 6.885922 AGTGTCTCAACTTTGTACTAAGGTT 58.114 36.000 19.08 9.89 0.00 3.50
3360 3762 6.481434 AGTGTCTCAACTTTGTACTAAGGT 57.519 37.500 19.08 11.48 0.00 3.50
3361 3763 9.490379 AATAAGTGTCTCAACTTTGTACTAAGG 57.510 33.333 19.08 4.85 40.77 2.69
3365 3767 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
3366 3768 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
3367 3769 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
3368 3770 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
3369 3771 7.038154 TCCCAAAATAAGTGTCTCAACTTTG 57.962 36.000 0.00 0.00 40.77 2.77
3370 3772 7.505585 TCATCCCAAAATAAGTGTCTCAACTTT 59.494 33.333 0.00 0.00 40.77 2.66
3371 3773 7.004086 TCATCCCAAAATAAGTGTCTCAACTT 58.996 34.615 0.00 0.00 42.89 2.66
3372 3774 6.542821 TCATCCCAAAATAAGTGTCTCAACT 58.457 36.000 0.00 0.00 0.00 3.16
3373 3775 6.817765 TCATCCCAAAATAAGTGTCTCAAC 57.182 37.500 0.00 0.00 0.00 3.18
3374 3776 6.434028 CCTTCATCCCAAAATAAGTGTCTCAA 59.566 38.462 0.00 0.00 0.00 3.02
3375 3777 5.945784 CCTTCATCCCAAAATAAGTGTCTCA 59.054 40.000 0.00 0.00 0.00 3.27
3376 3778 5.358160 CCCTTCATCCCAAAATAAGTGTCTC 59.642 44.000 0.00 0.00 0.00 3.36
3377 3779 5.015178 TCCCTTCATCCCAAAATAAGTGTCT 59.985 40.000 0.00 0.00 0.00 3.41
3378 3780 5.261216 TCCCTTCATCCCAAAATAAGTGTC 58.739 41.667 0.00 0.00 0.00 3.67
3379 3781 5.222337 ACTCCCTTCATCCCAAAATAAGTGT 60.222 40.000 0.00 0.00 0.00 3.55
3380 3782 5.264395 ACTCCCTTCATCCCAAAATAAGTG 58.736 41.667 0.00 0.00 0.00 3.16
3381 3783 5.536497 ACTCCCTTCATCCCAAAATAAGT 57.464 39.130 0.00 0.00 0.00 2.24
3382 3784 6.900194 TCTACTCCCTTCATCCCAAAATAAG 58.100 40.000 0.00 0.00 0.00 1.73
3383 3785 6.901615 TCTACTCCCTTCATCCCAAAATAA 57.098 37.500 0.00 0.00 0.00 1.40
3384 3786 6.901615 TTCTACTCCCTTCATCCCAAAATA 57.098 37.500 0.00 0.00 0.00 1.40
3385 3787 5.796502 TTCTACTCCCTTCATCCCAAAAT 57.203 39.130 0.00 0.00 0.00 1.82
3386 3788 5.592587 TTTCTACTCCCTTCATCCCAAAA 57.407 39.130 0.00 0.00 0.00 2.44
3387 3789 5.592587 TTTTCTACTCCCTTCATCCCAAA 57.407 39.130 0.00 0.00 0.00 3.28
3388 3790 5.592587 TTTTTCTACTCCCTTCATCCCAA 57.407 39.130 0.00 0.00 0.00 4.12
3417 3819 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
3418 3820 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
3419 3821 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3420 3822 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3421 3823 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3422 3824 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3423 3825 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3424 3826 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
3425 3827 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
3438 3840 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
3439 3841 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
3440 3842 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
3441 3843 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
3442 3844 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
3443 3845 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
3444 3846 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
3445 3847 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
3446 3848 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
3447 3849 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
3448 3850 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
3449 3851 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
3450 3852 7.541091 TCGTATGTAGTCACTTGTTGAAATCTC 59.459 37.037 0.00 0.00 35.39 2.75
3451 3853 7.375834 TCGTATGTAGTCACTTGTTGAAATCT 58.624 34.615 0.00 0.00 35.39 2.40
3452 3854 7.576750 TCGTATGTAGTCACTTGTTGAAATC 57.423 36.000 0.00 0.00 35.39 2.17
3453 3855 7.360101 GCTTCGTATGTAGTCACTTGTTGAAAT 60.360 37.037 0.00 0.00 35.39 2.17
3454 3856 6.073980 GCTTCGTATGTAGTCACTTGTTGAAA 60.074 38.462 0.00 0.00 35.39 2.69
3455 3857 5.404366 GCTTCGTATGTAGTCACTTGTTGAA 59.596 40.000 0.00 0.00 35.39 2.69
3456 3858 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
3457 3859 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
3458 3860 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
3459 3861 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
3460 3862 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
3461 3863 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
3462 3864 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
3463 3865 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
3464 3866 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
3465 3867 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
3466 3868 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
3467 3869 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
3468 3870 7.609760 ATTCACTCATTTTGCTTCGTATGTA 57.390 32.000 0.00 0.00 0.00 2.29
3469 3871 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
3470 3872 7.801547 AAATTCACTCATTTTGCTTCGTATG 57.198 32.000 0.00 0.00 0.00 2.39
3471 3873 8.511321 TGTAAATTCACTCATTTTGCTTCGTAT 58.489 29.630 0.00 0.00 0.00 3.06
3472 3874 7.801315 GTGTAAATTCACTCATTTTGCTTCGTA 59.199 33.333 0.00 0.00 35.68 3.43
3473 3875 6.636850 GTGTAAATTCACTCATTTTGCTTCGT 59.363 34.615 0.00 0.00 35.68 3.85
3474 3876 6.857964 AGTGTAAATTCACTCATTTTGCTTCG 59.142 34.615 0.00 0.00 44.07 3.79
3505 3907 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
3507 3909 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
3508 3910 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
3509 3911 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
3510 3912 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
3511 3913 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
3512 3914 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
3513 3915 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
3514 3916 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
3515 3917 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
3516 3918 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
3529 3931 9.063615 TCTTTTTAGAGTTTCAAATGGACTACC 57.936 33.333 0.00 0.00 0.00 3.18
3530 3932 9.880064 GTCTTTTTAGAGTTTCAAATGGACTAC 57.120 33.333 0.00 0.00 0.00 2.73
3531 3933 9.621629 TGTCTTTTTAGAGTTTCAAATGGACTA 57.378 29.630 0.00 0.00 0.00 2.59
3532 3934 8.519799 TGTCTTTTTAGAGTTTCAAATGGACT 57.480 30.769 0.00 0.00 0.00 3.85
3533 3935 9.581099 TTTGTCTTTTTAGAGTTTCAAATGGAC 57.419 29.630 0.00 0.00 0.00 4.02
3549 3951 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
3550 3952 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
3551 3953 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3552 3954 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3553 3955 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3554 3956 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3555 3957 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3556 3958 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3557 3959 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3558 3960 6.384886 TGTTACTCCCTCCGTTCCTAAATATT 59.615 38.462 0.00 0.00 0.00 1.28
3559 3961 5.901276 TGTTACTCCCTCCGTTCCTAAATAT 59.099 40.000 0.00 0.00 0.00 1.28
3560 3962 5.271598 TGTTACTCCCTCCGTTCCTAAATA 58.728 41.667 0.00 0.00 0.00 1.40
3561 3963 4.098894 TGTTACTCCCTCCGTTCCTAAAT 58.901 43.478 0.00 0.00 0.00 1.40
3562 3964 3.509442 TGTTACTCCCTCCGTTCCTAAA 58.491 45.455 0.00 0.00 0.00 1.85
3563 3965 3.173953 TGTTACTCCCTCCGTTCCTAA 57.826 47.619 0.00 0.00 0.00 2.69
3564 3966 2.905415 TGTTACTCCCTCCGTTCCTA 57.095 50.000 0.00 0.00 0.00 2.94
3565 3967 2.108970 GATGTTACTCCCTCCGTTCCT 58.891 52.381 0.00 0.00 0.00 3.36
3566 3968 2.108970 AGATGTTACTCCCTCCGTTCC 58.891 52.381 0.00 0.00 0.00 3.62
3567 3969 4.996788 TTAGATGTTACTCCCTCCGTTC 57.003 45.455 0.00 0.00 0.00 3.95
3568 3970 5.012354 TGTTTTAGATGTTACTCCCTCCGTT 59.988 40.000 0.00 0.00 0.00 4.44
3569 3971 4.529377 TGTTTTAGATGTTACTCCCTCCGT 59.471 41.667 0.00 0.00 0.00 4.69
3570 3972 5.080969 TGTTTTAGATGTTACTCCCTCCG 57.919 43.478 0.00 0.00 0.00 4.63
3571 3973 6.650120 TGATGTTTTAGATGTTACTCCCTCC 58.350 40.000 0.00 0.00 0.00 4.30
3572 3974 8.561738 TTTGATGTTTTAGATGTTACTCCCTC 57.438 34.615 0.00 0.00 0.00 4.30
3573 3975 9.533831 AATTTGATGTTTTAGATGTTACTCCCT 57.466 29.630 0.00 0.00 0.00 4.20
3690 4092 4.097286 TGTCCCAAGTCAAGCAACTTTAAC 59.903 41.667 0.00 0.00 37.38 2.01


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

AutoCloner maintained by Alex Coulton.