Multiple sequence alignment - TraesCS7D01G218700

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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 TraesCS7D01G218700 chr7D 100.000 4902 0 0 1 4902 179489630 179484729 0.000000e+00 9053.0
1 TraesCS7D01G218700 chr7D 75.556 855 185 21 2343 3182 17859596 17860441 2.750000e-107 399.0
2 TraesCS7D01G218700 chr7D 90.909 198 12 3 4499 4696 486166391 486166582 1.350000e-65 261.0
3 TraesCS7D01G218700 chr7B 96.230 3793 87 10 748 4502 145679891 145676117 0.000000e+00 6161.0
4 TraesCS7D01G218700 chr7B 88.778 401 22 4 1 394 145680441 145680057 2.070000e-128 470.0
5 TraesCS7D01G218700 chr7B 92.473 186 10 1 4717 4902 145676130 145675949 3.760000e-66 263.0
6 TraesCS7D01G218700 chr7A 90.537 1416 82 23 690 2057 183839845 183838434 0.000000e+00 1825.0
7 TraesCS7D01G218700 chr7A 89.070 1107 100 10 2095 3190 183838450 183837354 0.000000e+00 1354.0
8 TraesCS7D01G218700 chr7A 92.453 477 19 7 198 666 183840307 183839840 0.000000e+00 665.0
9 TraesCS7D01G218700 chr7A 88.616 448 40 9 3478 3917 183837223 183836779 7.220000e-148 534.0
10 TraesCS7D01G218700 chr7A 92.952 227 8 3 198 417 183840372 183840597 1.700000e-84 324.0
11 TraesCS7D01G218700 chr7A 73.998 823 177 27 2343 3139 17347210 17348021 2.870000e-77 300.0
12 TraesCS7D01G218700 chr7A 85.238 210 24 6 4294 4498 183834739 183834532 4.970000e-50 209.0
13 TraesCS7D01G218700 chr3A 86.238 1119 127 18 2095 3190 702579917 702578803 0.000000e+00 1188.0
14 TraesCS7D01G218700 chr3A 85.906 447 60 3 1604 2050 702580351 702579908 1.600000e-129 473.0
15 TraesCS7D01G218700 chr3A 86.543 431 55 3 3441 3869 702578734 702578305 5.740000e-129 472.0
16 TraesCS7D01G218700 chr3A 84.163 221 28 4 4505 4724 570310725 570310939 1.790000e-49 207.0
17 TraesCS7D01G218700 chr3A 89.565 115 12 0 4615 4729 269217019 269216905 3.950000e-31 147.0
18 TraesCS7D01G218700 chr3D 86.109 1123 127 19 2095 3190 570043417 570042297 0.000000e+00 1182.0
19 TraesCS7D01G218700 chr3D 86.728 437 53 5 3441 3873 570042228 570041793 9.540000e-132 481.0
20 TraesCS7D01G218700 chr3D 85.906 447 60 3 1604 2050 570043851 570043408 1.600000e-129 473.0
21 TraesCS7D01G218700 chr3D 86.441 177 13 4 4497 4672 209682077 209682243 3.010000e-42 183.0
22 TraesCS7D01G218700 chr3B 88.318 856 95 3 2321 3175 756677055 756676204 0.000000e+00 1022.0
23 TraesCS7D01G218700 chr3B 87.561 410 49 2 3435 3843 756676094 756675686 1.600000e-129 473.0
24 TraesCS7D01G218700 chr3B 87.554 233 19 3 4497 4729 296186608 296186830 1.350000e-65 261.0
25 TraesCS7D01G218700 chr3B 83.815 173 28 0 1872 2044 756677439 756677267 1.090000e-36 165.0
26 TraesCS7D01G218700 chr4A 76.601 812 164 20 2343 3139 715745331 715744531 1.630000e-114 424.0
27 TraesCS7D01G218700 chr4A 75.966 828 174 20 2342 3155 715817734 715818550 2.120000e-108 403.0
28 TraesCS7D01G218700 chr4A 84.163 221 28 4 4505 4724 682738397 682738611 1.790000e-49 207.0
29 TraesCS7D01G218700 chrUn 81.218 394 55 10 1075 1456 468676744 468676358 2.870000e-77 300.0
30 TraesCS7D01G218700 chrUn 87.619 105 13 0 1069 1173 90516624 90516728 6.660000e-24 122.0
31 TraesCS7D01G218700 chr1B 88.462 234 22 2 4497 4730 87973167 87972939 1.340000e-70 278.0
32 TraesCS7D01G218700 chr4D 84.681 235 29 4 4497 4730 943244 943016 1.370000e-55 228.0
33 TraesCS7D01G218700 chr1A 84.375 224 28 4 4505 4727 64694359 64694142 3.840000e-51 213.0
34 TraesCS7D01G218700 chr4B 83.772 228 29 4 4505 4731 640809800 640810020 4.970000e-50 209.0
35 TraesCS7D01G218700 chr2B 97.222 36 1 0 1388 1423 26507737 26507772 1.470000e-05 62.1
36 TraesCS7D01G218700 chr2A 97.222 36 1 0 1388 1423 16830304 16830339 1.470000e-05 62.1


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 TraesCS7D01G218700 chr7D 179484729 179489630 4901 True 9053.000000 9053 100.000000 1 4902 1 chr7D.!!$R1 4901
1 TraesCS7D01G218700 chr7D 17859596 17860441 845 False 399.000000 399 75.556000 2343 3182 1 chr7D.!!$F1 839
2 TraesCS7D01G218700 chr7B 145675949 145680441 4492 True 2298.000000 6161 92.493667 1 4902 3 chr7B.!!$R1 4901
3 TraesCS7D01G218700 chr7A 183834532 183840307 5775 True 917.400000 1825 89.182800 198 4498 5 chr7A.!!$R1 4300
4 TraesCS7D01G218700 chr7A 17347210 17348021 811 False 300.000000 300 73.998000 2343 3139 1 chr7A.!!$F1 796
5 TraesCS7D01G218700 chr3A 702578305 702580351 2046 True 711.000000 1188 86.229000 1604 3869 3 chr3A.!!$R2 2265
6 TraesCS7D01G218700 chr3D 570041793 570043851 2058 True 712.000000 1182 86.247667 1604 3873 3 chr3D.!!$R1 2269
7 TraesCS7D01G218700 chr3B 756675686 756677439 1753 True 553.333333 1022 86.564667 1872 3843 3 chr3B.!!$R1 1971
8 TraesCS7D01G218700 chr4A 715744531 715745331 800 True 424.000000 424 76.601000 2343 3139 1 chr4A.!!$R1 796
9 TraesCS7D01G218700 chr4A 715817734 715818550 816 False 403.000000 403 75.966000 2342 3155 1 chr4A.!!$F2 813

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
60 61 0.038744 CCATTCTGCTCCAAGGGTGT 59.961 55.000 0.00 0.00 0.00 4.16 F
952 967 0.179032 ACCACAACTTCACATCGCCA 60.179 50.000 0.00 0.00 0.00 5.69 F
1061 1076 0.321671 CCAGAGAAGCAAAGTCCGGA 59.678 55.000 0.00 0.00 0.00 5.14 F
1158 1173 1.413767 CGACTGTGACGTATGCAGCC 61.414 60.000 11.77 2.59 33.87 4.85 F
2085 2144 1.766059 TGTCCCAGACACTGTGGCT 60.766 57.895 11.16 11.16 34.86 4.75 F
3364 3507 0.620556 GGTCATCTGGGCAAGAAGGA 59.379 55.000 0.00 0.00 38.79 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1047 1062 0.591659 GGTTGTCCGGACTTTGCTTC 59.408 55.000 33.39 15.44 0.00 3.86 R
2085 2144 0.614697 TCTTGTCCATGAGAGCCCGA 60.615 55.000 0.00 0.00 0.00 5.14 R
2863 2990 2.229792 TGACCAAACTTGTCATCTGCC 58.770 47.619 0.00 0.00 0.00 4.85 R
3219 3362 2.810164 AGTCTTCCTCTTTAGGCGAGT 58.190 47.619 0.00 0.00 43.31 4.18 R
3558 3719 0.391661 GAGGATTGAGTCGCCTGCAA 60.392 55.000 3.98 0.00 30.70 4.08 R
4537 6420 0.030297 ATCTGGATGGAGCAGGGAGT 60.030 55.000 0.00 0.00 0.00 3.85 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
30 31 1.406539 GGTGCTTCATGGCCTTATGTG 59.593 52.381 3.32 0.00 0.00 3.21
56 57 2.490165 CAGCCATTCTGCTCCAAGG 58.510 57.895 0.00 0.00 40.32 3.61
57 58 1.035932 CAGCCATTCTGCTCCAAGGG 61.036 60.000 0.00 0.00 40.32 3.95
58 59 1.000396 GCCATTCTGCTCCAAGGGT 60.000 57.895 0.00 0.00 0.00 4.34
59 60 1.318158 GCCATTCTGCTCCAAGGGTG 61.318 60.000 0.00 0.00 0.00 4.61
60 61 0.038744 CCATTCTGCTCCAAGGGTGT 59.961 55.000 0.00 0.00 0.00 4.16
61 62 1.171308 CATTCTGCTCCAAGGGTGTG 58.829 55.000 0.00 0.00 0.00 3.82
62 63 0.038744 ATTCTGCTCCAAGGGTGTGG 59.961 55.000 0.00 0.00 40.33 4.17
63 64 2.034687 CTGCTCCAAGGGTGTGGG 59.965 66.667 0.00 0.00 39.34 4.61
64 65 2.449518 TGCTCCAAGGGTGTGGGA 60.450 61.111 0.00 0.00 39.34 4.37
66 67 3.081554 CTCCAAGGGTGTGGGAGG 58.918 66.667 0.00 0.00 43.59 4.30
67 68 2.531685 TCCAAGGGTGTGGGAGGG 60.532 66.667 0.00 0.00 39.34 4.30
77 78 1.059584 TGTGGGAGGGAGTTTCTGCA 61.060 55.000 0.00 0.00 0.00 4.41
110 111 2.303600 ACCAGTGACCTTATTTACGGCA 59.696 45.455 0.00 0.00 0.00 5.69
135 136 1.271001 TGGAACTGCAGTGTCATCCTG 60.271 52.381 27.49 0.00 0.00 3.86
144 145 1.153309 TGTCATCCTGGCAGCATCG 60.153 57.895 9.56 0.00 0.00 3.84
163 164 1.608590 CGCTTCCAAACATGGTGAGTT 59.391 47.619 0.00 0.00 0.00 3.01
182 183 1.827399 TTTCCCTCACAGTCGCTCCC 61.827 60.000 0.00 0.00 0.00 4.30
194 195 3.521796 GCTCCCGAAATGCCAGCC 61.522 66.667 0.00 0.00 0.00 4.85
251 252 9.569167 CATAACATATTTCATTCATCAGCATCC 57.431 33.333 0.00 0.00 0.00 3.51
364 372 3.861276 TGAATGATTGAAGCTTGCCTG 57.139 42.857 2.10 0.00 0.00 4.85
415 423 6.767524 ACCAAGTCTAATTTGTTCACACAA 57.232 33.333 0.00 0.00 41.39 3.33
441 449 7.510549 ACAAACTAAGCATTGTACTGTTCAT 57.489 32.000 0.00 0.00 37.96 2.57
442 450 7.940850 ACAAACTAAGCATTGTACTGTTCATT 58.059 30.769 0.00 0.00 37.96 2.57
452 460 2.183478 ACTGTTCATTCATCGCACCA 57.817 45.000 0.00 0.00 0.00 4.17
480 488 4.758674 GCATGAGTATACCCGTGTAGTCTA 59.241 45.833 8.23 0.00 30.76 2.59
486 494 7.875041 TGAGTATACCCGTGTAGTCTAACTATC 59.125 40.741 0.00 0.00 32.65 2.08
516 524 9.123902 CATAAACTCTGGGACAATTTGATGATA 57.876 33.333 2.79 0.00 38.70 2.15
519 527 6.666678 ACTCTGGGACAATTTGATGATACAT 58.333 36.000 2.79 0.00 38.70 2.29
599 608 8.862325 TTTATAAATCACAGTATATGCAGGGG 57.138 34.615 0.00 0.00 0.00 4.79
600 609 6.702449 ATAAATCACAGTATATGCAGGGGA 57.298 37.500 0.00 0.00 0.00 4.81
601 610 5.387113 AAATCACAGTATATGCAGGGGAA 57.613 39.130 0.00 0.00 0.00 3.97
607 616 4.475016 ACAGTATATGCAGGGGAAGAAGTT 59.525 41.667 0.00 0.00 0.00 2.66
666 675 5.987098 AGATGCTGAATGTGAATACTGACT 58.013 37.500 0.00 0.00 0.00 3.41
667 676 6.413052 AGATGCTGAATGTGAATACTGACTT 58.587 36.000 0.00 0.00 0.00 3.01
668 677 6.538021 AGATGCTGAATGTGAATACTGACTTC 59.462 38.462 0.00 0.00 0.00 3.01
669 678 5.798132 TGCTGAATGTGAATACTGACTTCT 58.202 37.500 0.00 0.00 0.00 2.85
670 679 6.233434 TGCTGAATGTGAATACTGACTTCTT 58.767 36.000 0.00 0.00 0.00 2.52
671 680 6.369890 TGCTGAATGTGAATACTGACTTCTTC 59.630 38.462 0.00 0.00 0.00 2.87
672 681 6.369890 GCTGAATGTGAATACTGACTTCTTCA 59.630 38.462 0.00 0.00 0.00 3.02
673 682 7.095060 GCTGAATGTGAATACTGACTTCTTCAA 60.095 37.037 0.00 0.00 32.21 2.69
674 683 8.315391 TGAATGTGAATACTGACTTCTTCAAG 57.685 34.615 0.00 0.00 32.21 3.02
675 684 7.933577 TGAATGTGAATACTGACTTCTTCAAGT 59.066 33.333 0.00 0.00 46.21 3.16
694 703 3.971245 GTCCTCAAGACCTCAACTGAT 57.029 47.619 0.00 0.00 39.84 2.90
709 718 4.644234 TCAACTGATGAAGAGTGCCAAAAA 59.356 37.500 0.00 0.00 34.30 1.94
721 730 6.116126 AGAGTGCCAAAAAGTATGTAGATCC 58.884 40.000 0.00 0.00 0.00 3.36
751 760 3.732721 GCACAGCTGAAAAGATTGTTCAC 59.267 43.478 23.35 0.00 31.78 3.18
778 787 3.998341 GCCCGTTAAGTTGTCATACAAGA 59.002 43.478 0.00 0.00 39.00 3.02
779 788 4.453136 GCCCGTTAAGTTGTCATACAAGAA 59.547 41.667 0.00 0.00 39.00 2.52
907 922 1.143684 GGATGCCATACAGACCCACAT 59.856 52.381 0.00 0.00 0.00 3.21
928 943 7.880195 CCACATGGCTATATAACTAAGAGCTTT 59.120 37.037 0.00 0.00 33.57 3.51
952 967 0.179032 ACCACAACTTCACATCGCCA 60.179 50.000 0.00 0.00 0.00 5.69
1036 1051 3.355378 CAAGTAGCATCCCACAATCCAA 58.645 45.455 0.00 0.00 0.00 3.53
1041 1056 1.134907 GCATCCCACAATCCAAAGCAG 60.135 52.381 0.00 0.00 0.00 4.24
1047 1062 1.201647 CACAATCCAAAGCAGCCAGAG 59.798 52.381 0.00 0.00 0.00 3.35
1061 1076 0.321671 CCAGAGAAGCAAAGTCCGGA 59.678 55.000 0.00 0.00 0.00 5.14
1143 1158 2.031163 GCCACTCTGGTTGCGACT 59.969 61.111 3.59 0.00 40.46 4.18
1158 1173 1.413767 CGACTGTGACGTATGCAGCC 61.414 60.000 11.77 2.59 33.87 4.85
1456 1474 2.234908 ACAACCATCTACTCCTCAGTGC 59.765 50.000 0.00 0.00 33.62 4.40
1461 1479 3.317711 CCATCTACTCCTCAGTGCTAGTG 59.682 52.174 0.00 0.00 33.62 2.74
1466 1484 2.560542 ACTCCTCAGTGCTAGTGTCTTG 59.439 50.000 0.00 0.00 0.00 3.02
1546 1597 1.981495 AGAGTACAGAAGGCAAGGCTT 59.019 47.619 8.74 8.74 0.00 4.35
1581 1632 3.522750 ACAAGGATCCTGAGAAGCAAGAT 59.477 43.478 17.02 0.00 30.35 2.40
2028 2087 5.939883 TGCATACATATTTCTACAGATGGCC 59.060 40.000 0.00 0.00 0.00 5.36
2071 2130 1.993370 CGAACAAGAAGGATCGTGTCC 59.007 52.381 0.00 2.00 45.70 4.02
2085 2144 1.766059 TGTCCCAGACACTGTGGCT 60.766 57.895 11.16 11.16 34.86 4.75
2095 2154 3.385384 CTGTGGCTCGGGCTCTCA 61.385 66.667 7.48 3.71 38.73 3.27
2713 2823 4.154195 GTCCTTGTGTATGTGGTGATTCAC 59.846 45.833 8.34 8.34 38.09 3.18
2863 2990 2.046892 CCAGGTGGCTTCTGGTCG 60.047 66.667 15.36 0.00 44.97 4.79
3232 3375 3.430333 GAGGAAGACTCGCCTAAAGAG 57.570 52.381 0.00 0.00 41.27 2.85
3233 3376 2.100087 GAGGAAGACTCGCCTAAAGAGG 59.900 54.545 0.00 0.00 40.29 3.69
3234 3377 4.187176 GAGGAAGACTCGCCTAAAGAGGA 61.187 52.174 0.00 0.00 39.96 3.71
3235 3378 5.648446 GAGGAAGACTCGCCTAAAGAGGAA 61.648 50.000 0.00 0.00 39.96 3.36
3236 3379 7.398380 GAGGAAGACTCGCCTAAAGAGGAAG 62.398 52.000 0.00 0.00 39.96 3.46
3252 3395 6.441088 AGAGGAAGACTTGGACTTAAATGT 57.559 37.500 0.00 0.00 0.00 2.71
3259 3402 4.344104 ACTTGGACTTAAATGTCATGGGG 58.656 43.478 0.00 0.00 38.61 4.96
3308 3451 6.068010 AGTCAAGTTTCACCATTCCATGTTA 58.932 36.000 0.00 0.00 0.00 2.41
3317 3460 2.355197 CATTCCATGTTAGTGGTGCGA 58.645 47.619 0.00 0.00 40.27 5.10
3364 3507 0.620556 GGTCATCTGGGCAAGAAGGA 59.379 55.000 0.00 0.00 38.79 3.36
3558 3719 4.158394 GCAGGACAACAACAATGGACATAT 59.842 41.667 0.00 0.00 0.00 1.78
3566 3727 1.677576 ACAATGGACATATTGCAGGCG 59.322 47.619 0.00 0.00 40.80 5.52
3579 3740 1.227089 CAGGCGACTCAATCCTCCG 60.227 63.158 0.00 0.00 40.21 4.63
3670 3831 2.673368 CGTCATTGTCTTGCTACTTCCC 59.327 50.000 0.00 0.00 0.00 3.97
3942 5262 4.935205 TGACGTGATCCTTTATCTGGTTTG 59.065 41.667 0.00 0.00 35.45 2.93
4433 6313 4.720649 TCAGAGGACTTCACCTAATTCG 57.279 45.455 0.00 0.00 40.73 3.34
4449 6329 6.318900 ACCTAATTCGATGGAAAGGAATTGAC 59.681 38.462 13.41 0.00 39.82 3.18
4502 6385 6.779860 AGGAAATTAAGAACTGGCACTTAGA 58.220 36.000 0.00 0.00 31.66 2.10
4503 6386 6.881602 AGGAAATTAAGAACTGGCACTTAGAG 59.118 38.462 0.00 0.00 31.66 2.43
4504 6387 6.403746 GGAAATTAAGAACTGGCACTTAGAGC 60.404 42.308 0.00 0.00 31.66 4.09
4512 6395 2.755929 GCACTTAGAGCCTGTTCGG 58.244 57.895 0.00 0.00 0.00 4.30
4522 6405 4.020617 CTGTTCGGCAGGCCTCCA 62.021 66.667 0.00 1.39 41.42 3.86
4523 6406 4.329545 TGTTCGGCAGGCCTCCAC 62.330 66.667 0.00 3.60 0.00 4.02
4524 6407 4.021925 GTTCGGCAGGCCTCCACT 62.022 66.667 0.00 0.00 0.00 4.00
4525 6408 3.706373 TTCGGCAGGCCTCCACTC 61.706 66.667 0.00 0.00 0.00 3.51
4530 6413 3.721706 CAGGCCTCCACTCCCCAC 61.722 72.222 0.00 0.00 0.00 4.61
4531 6414 3.947041 AGGCCTCCACTCCCCACT 61.947 66.667 0.00 0.00 0.00 4.00
4532 6415 2.936032 GGCCTCCACTCCCCACTT 60.936 66.667 0.00 0.00 0.00 3.16
4533 6416 2.539081 GGCCTCCACTCCCCACTTT 61.539 63.158 0.00 0.00 0.00 2.66
4534 6417 1.460699 GCCTCCACTCCCCACTTTT 59.539 57.895 0.00 0.00 0.00 2.27
4535 6418 0.609406 GCCTCCACTCCCCACTTTTC 60.609 60.000 0.00 0.00 0.00 2.29
4536 6419 0.771127 CCTCCACTCCCCACTTTTCA 59.229 55.000 0.00 0.00 0.00 2.69
4537 6420 1.144913 CCTCCACTCCCCACTTTTCAA 59.855 52.381 0.00 0.00 0.00 2.69
4538 6421 2.230660 CTCCACTCCCCACTTTTCAAC 58.769 52.381 0.00 0.00 0.00 3.18
4539 6422 1.850345 TCCACTCCCCACTTTTCAACT 59.150 47.619 0.00 0.00 0.00 3.16
4540 6423 2.158667 TCCACTCCCCACTTTTCAACTC 60.159 50.000 0.00 0.00 0.00 3.01
4541 6424 2.230660 CACTCCCCACTTTTCAACTCC 58.769 52.381 0.00 0.00 0.00 3.85
4542 6425 1.145119 ACTCCCCACTTTTCAACTCCC 59.855 52.381 0.00 0.00 0.00 4.30
4543 6426 1.425448 CTCCCCACTTTTCAACTCCCT 59.575 52.381 0.00 0.00 0.00 4.20
4544 6427 1.144913 TCCCCACTTTTCAACTCCCTG 59.855 52.381 0.00 0.00 0.00 4.45
4545 6428 0.961753 CCCACTTTTCAACTCCCTGC 59.038 55.000 0.00 0.00 0.00 4.85
4546 6429 1.479389 CCCACTTTTCAACTCCCTGCT 60.479 52.381 0.00 0.00 0.00 4.24
4547 6430 1.882623 CCACTTTTCAACTCCCTGCTC 59.117 52.381 0.00 0.00 0.00 4.26
4548 6431 1.882623 CACTTTTCAACTCCCTGCTCC 59.117 52.381 0.00 0.00 0.00 4.70
4549 6432 1.494721 ACTTTTCAACTCCCTGCTCCA 59.505 47.619 0.00 0.00 0.00 3.86
4550 6433 2.108952 ACTTTTCAACTCCCTGCTCCAT 59.891 45.455 0.00 0.00 0.00 3.41
4551 6434 2.496899 TTTCAACTCCCTGCTCCATC 57.503 50.000 0.00 0.00 0.00 3.51
4552 6435 0.620556 TTCAACTCCCTGCTCCATCC 59.379 55.000 0.00 0.00 0.00 3.51
4553 6436 0.547471 TCAACTCCCTGCTCCATCCA 60.547 55.000 0.00 0.00 0.00 3.41
4554 6437 0.107312 CAACTCCCTGCTCCATCCAG 60.107 60.000 0.00 0.00 0.00 3.86
4555 6438 0.252881 AACTCCCTGCTCCATCCAGA 60.253 55.000 0.00 0.00 32.03 3.86
4556 6439 0.030297 ACTCCCTGCTCCATCCAGAT 60.030 55.000 0.00 0.00 32.03 2.90
4557 6440 0.397187 CTCCCTGCTCCATCCAGATG 59.603 60.000 0.40 0.40 38.51 2.90
4558 6441 1.228184 CCCTGCTCCATCCAGATGC 60.228 63.158 1.92 0.00 37.49 3.91
4559 6442 1.597302 CCTGCTCCATCCAGATGCG 60.597 63.158 1.92 0.00 37.49 4.73
4560 6443 1.597302 CTGCTCCATCCAGATGCGG 60.597 63.158 1.92 0.00 37.49 5.69
4561 6444 2.036428 CTGCTCCATCCAGATGCGGA 62.036 60.000 1.92 0.00 40.07 5.54
4562 6445 1.301558 GCTCCATCCAGATGCGGAG 60.302 63.158 8.87 8.87 38.83 4.63
4594 6477 2.917363 GCACTTTTGCTACTCCGAAAC 58.083 47.619 0.00 0.00 46.17 2.78
4595 6478 2.289547 GCACTTTTGCTACTCCGAAACA 59.710 45.455 0.00 0.00 46.17 2.83
4596 6479 3.058224 GCACTTTTGCTACTCCGAAACAT 60.058 43.478 0.00 0.00 46.17 2.71
4597 6480 4.556699 GCACTTTTGCTACTCCGAAACATT 60.557 41.667 0.00 0.00 46.17 2.71
4598 6481 4.911610 CACTTTTGCTACTCCGAAACATTG 59.088 41.667 0.00 0.00 0.00 2.82
4599 6482 4.023193 ACTTTTGCTACTCCGAAACATTGG 60.023 41.667 0.00 0.00 0.00 3.16
4600 6483 1.448985 TGCTACTCCGAAACATTGGC 58.551 50.000 0.00 0.00 0.00 4.52
4601 6484 0.733150 GCTACTCCGAAACATTGGCC 59.267 55.000 0.00 0.00 0.00 5.36
4602 6485 1.679032 GCTACTCCGAAACATTGGCCT 60.679 52.381 3.32 0.00 0.00 5.19
4603 6486 2.419574 GCTACTCCGAAACATTGGCCTA 60.420 50.000 3.32 0.00 0.00 3.93
4604 6487 2.109425 ACTCCGAAACATTGGCCTAC 57.891 50.000 3.32 0.00 0.00 3.18
4605 6488 1.349688 ACTCCGAAACATTGGCCTACA 59.650 47.619 3.32 0.00 0.00 2.74
4606 6489 2.224670 ACTCCGAAACATTGGCCTACAA 60.225 45.455 3.32 0.00 44.54 2.41
4607 6490 2.420022 CTCCGAAACATTGGCCTACAAG 59.580 50.000 3.32 0.00 43.48 3.16
4608 6491 1.135402 CCGAAACATTGGCCTACAAGC 60.135 52.381 3.32 0.00 43.48 4.01
4617 6500 4.148825 CCTACAAGCCGCTCCGCT 62.149 66.667 0.00 0.00 42.22 5.52
4618 6501 2.583593 CTACAAGCCGCTCCGCTC 60.584 66.667 0.00 0.00 38.44 5.03
4619 6502 4.143333 TACAAGCCGCTCCGCTCC 62.143 66.667 0.00 0.00 38.44 4.70
4628 6511 4.200283 CTCCGCTCCGCTCCACTC 62.200 72.222 0.00 0.00 0.00 3.51
4643 6526 3.136750 CTCCGGGAGAGCATGGAG 58.863 66.667 19.57 0.00 41.82 3.86
4644 6527 3.157252 TCCGGGAGAGCATGGAGC 61.157 66.667 0.00 0.00 46.19 4.70
4653 6536 3.354678 GCATGGAGCCAACGTGTT 58.645 55.556 0.00 0.00 37.23 3.32
4654 6537 1.210155 GCATGGAGCCAACGTGTTC 59.790 57.895 0.00 0.00 37.23 3.18
4655 6538 1.497278 CATGGAGCCAACGTGTTCG 59.503 57.895 0.00 0.00 43.34 3.95
4656 6539 1.671054 ATGGAGCCAACGTGTTCGG 60.671 57.895 0.00 0.00 41.85 4.30
4657 6540 2.280592 GGAGCCAACGTGTTCGGT 60.281 61.111 0.00 0.00 41.85 4.69
4664 6547 2.967740 AACGTGTTCGGTGTCACTC 58.032 52.632 2.35 0.00 41.85 3.51
4665 6548 0.529119 AACGTGTTCGGTGTCACTCC 60.529 55.000 2.35 0.00 41.85 3.85
4667 6550 2.028484 TGTTCGGTGTCACTCCGC 59.972 61.111 13.62 1.28 46.49 5.54
4668 6551 2.028484 GTTCGGTGTCACTCCGCA 59.972 61.111 13.62 0.00 46.49 5.69
4669 6552 2.022129 GTTCGGTGTCACTCCGCAG 61.022 63.158 13.62 0.00 46.49 5.18
4670 6553 3.858868 TTCGGTGTCACTCCGCAGC 62.859 63.158 13.62 0.00 46.49 5.25
4671 6554 4.363990 CGGTGTCACTCCGCAGCT 62.364 66.667 5.16 0.00 41.48 4.24
4672 6555 2.970639 GGTGTCACTCCGCAGCTA 59.029 61.111 2.35 0.00 0.00 3.32
4673 6556 1.446272 GGTGTCACTCCGCAGCTAC 60.446 63.158 2.35 0.00 0.00 3.58
4674 6557 1.587054 GTGTCACTCCGCAGCTACT 59.413 57.895 0.00 0.00 0.00 2.57
4675 6558 0.456995 GTGTCACTCCGCAGCTACTC 60.457 60.000 0.00 0.00 0.00 2.59
4676 6559 1.139947 GTCACTCCGCAGCTACTCC 59.860 63.158 0.00 0.00 0.00 3.85
4677 6560 1.304134 TCACTCCGCAGCTACTCCA 60.304 57.895 0.00 0.00 0.00 3.86
4678 6561 1.140589 CACTCCGCAGCTACTCCAG 59.859 63.158 0.00 0.00 0.00 3.86
4686 6569 3.461773 GCTACTCCAGCCGCTCCA 61.462 66.667 0.00 0.00 45.23 3.86
4687 6570 2.811101 CTACTCCAGCCGCTCCAG 59.189 66.667 0.00 0.00 0.00 3.86
4688 6571 2.759973 TACTCCAGCCGCTCCAGG 60.760 66.667 0.00 0.00 0.00 4.45
4689 6572 3.296842 TACTCCAGCCGCTCCAGGA 62.297 63.158 0.00 0.00 0.00 3.86
4690 6573 3.847602 CTCCAGCCGCTCCAGGAG 61.848 72.222 12.81 12.81 41.43 3.69
4708 6591 4.504916 CGGAGCTGCGGAGTGGAG 62.505 72.222 21.08 0.00 39.42 3.86
4709 6592 4.154347 GGAGCTGCGGAGTGGAGG 62.154 72.222 5.62 0.00 36.36 4.30
4711 6594 3.386237 AGCTGCGGAGTGGAGGTC 61.386 66.667 5.62 0.00 43.97 3.85
4712 6595 3.386237 GCTGCGGAGTGGAGGTCT 61.386 66.667 5.62 0.00 36.36 3.85
4713 6596 2.575993 CTGCGGAGTGGAGGTCTG 59.424 66.667 0.00 0.00 31.26 3.51
4714 6597 3.655810 CTGCGGAGTGGAGGTCTGC 62.656 68.421 0.00 0.00 45.17 4.26
4715 6598 4.459089 GCGGAGTGGAGGTCTGCC 62.459 72.222 0.00 0.00 39.98 4.85
4716 6599 4.135153 CGGAGTGGAGGTCTGCCG 62.135 72.222 0.00 0.00 40.50 5.69
4717 6600 2.680352 GGAGTGGAGGTCTGCCGA 60.680 66.667 0.00 0.00 40.50 5.54
4718 6601 2.283529 GGAGTGGAGGTCTGCCGAA 61.284 63.158 0.00 0.00 40.50 4.30
4719 6602 1.079750 GAGTGGAGGTCTGCCGAAC 60.080 63.158 0.00 0.00 40.50 3.95
4720 6603 1.816863 GAGTGGAGGTCTGCCGAACA 61.817 60.000 0.00 0.00 40.50 3.18
4733 6616 2.743636 CCGAACAGGCTCTTAGTTGA 57.256 50.000 0.00 0.00 0.00 3.18
4734 6617 3.040147 CCGAACAGGCTCTTAGTTGAA 57.960 47.619 0.00 0.00 0.00 2.69
4735 6618 2.737252 CCGAACAGGCTCTTAGTTGAAC 59.263 50.000 0.00 0.00 0.00 3.18
4736 6619 3.555168 CCGAACAGGCTCTTAGTTGAACT 60.555 47.826 2.37 2.37 0.00 3.01
4737 6620 3.430218 CGAACAGGCTCTTAGTTGAACTG 59.570 47.826 8.33 0.00 0.00 3.16
4738 6621 3.409026 ACAGGCTCTTAGTTGAACTGG 57.591 47.619 8.33 1.02 0.00 4.00
4751 6634 5.513233 AGTTGAACTGGCCTGATGAAATAT 58.487 37.500 17.64 0.00 0.00 1.28
4760 6643 8.439971 ACTGGCCTGATGAAATATAATTACAGA 58.560 33.333 17.64 0.00 0.00 3.41
4767 6650 9.851686 TGATGAAATATAATTACAGAAGGCAGT 57.148 29.630 0.00 0.00 0.00 4.40
4784 6667 2.734079 GCAGTTTCTAGTGACTCTGCAC 59.266 50.000 15.64 0.00 42.81 4.57
4842 6725 9.702494 AGTACTGACTGTAGTGTTAATTTTACC 57.298 33.333 0.00 0.00 33.81 2.85
4880 6763 5.297029 GCAGACCTGTTTAATCATTCTACCC 59.703 44.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.214589 CAGAATGGCTGCAACTGCC 59.785 57.895 8.48 8.48 46.46 4.85
52 53 1.427072 AACTCCCTCCCACACCCTTG 61.427 60.000 0.00 0.00 0.00 3.61
53 54 0.701310 AAACTCCCTCCCACACCCTT 60.701 55.000 0.00 0.00 0.00 3.95
54 55 1.072930 AAACTCCCTCCCACACCCT 60.073 57.895 0.00 0.00 0.00 4.34
55 56 1.134438 AGAAACTCCCTCCCACACCC 61.134 60.000 0.00 0.00 0.00 4.61
56 57 0.036875 CAGAAACTCCCTCCCACACC 59.963 60.000 0.00 0.00 0.00 4.16
57 58 0.606673 GCAGAAACTCCCTCCCACAC 60.607 60.000 0.00 0.00 0.00 3.82
58 59 1.059584 TGCAGAAACTCCCTCCCACA 61.060 55.000 0.00 0.00 0.00 4.17
59 60 0.322008 CTGCAGAAACTCCCTCCCAC 60.322 60.000 8.42 0.00 0.00 4.61
60 61 1.492133 CCTGCAGAAACTCCCTCCCA 61.492 60.000 17.39 0.00 0.00 4.37
61 62 1.301293 CCTGCAGAAACTCCCTCCC 59.699 63.158 17.39 0.00 0.00 4.30
62 63 0.322008 CACCTGCAGAAACTCCCTCC 60.322 60.000 17.39 0.00 0.00 4.30
63 64 0.322008 CCACCTGCAGAAACTCCCTC 60.322 60.000 17.39 0.00 0.00 4.30
64 65 1.763770 CCACCTGCAGAAACTCCCT 59.236 57.895 17.39 0.00 0.00 4.20
65 66 1.303643 CCCACCTGCAGAAACTCCC 60.304 63.158 17.39 0.00 0.00 4.30
66 67 0.178990 AACCCACCTGCAGAAACTCC 60.179 55.000 17.39 0.00 0.00 3.85
67 68 1.239347 GAACCCACCTGCAGAAACTC 58.761 55.000 17.39 0.00 0.00 3.01
110 111 1.973515 TGACACTGCAGTTCCATCTCT 59.026 47.619 18.94 0.00 0.00 3.10
124 125 0.107312 GATGCTGCCAGGATGACACT 60.107 55.000 2.44 0.00 39.69 3.55
126 127 1.153309 CGATGCTGCCAGGATGACA 60.153 57.895 2.44 0.00 39.69 3.58
144 145 3.733443 AAACTCACCATGTTTGGAAGC 57.267 42.857 0.00 0.00 46.92 3.86
163 164 1.671742 GGAGCGACTGTGAGGGAAA 59.328 57.895 0.00 0.00 0.00 3.13
174 175 2.435938 TGGCATTTCGGGAGCGAC 60.436 61.111 0.00 0.00 0.00 5.19
175 176 2.125147 CTGGCATTTCGGGAGCGA 60.125 61.111 0.00 0.00 0.00 4.93
176 177 3.880846 GCTGGCATTTCGGGAGCG 61.881 66.667 0.00 0.00 0.00 5.03
182 183 2.180017 GCACAGGCTGGCATTTCG 59.820 61.111 20.34 0.00 36.96 3.46
194 195 1.137404 GGCGTAATGCTTGGCACAG 59.863 57.895 0.00 0.00 43.04 3.66
251 252 0.892358 AGGCCAGTGCAACATGTCAG 60.892 55.000 5.01 0.00 41.43 3.51
364 372 4.953579 ACCTTCATAGTCTTCTCTCTGACC 59.046 45.833 0.00 0.00 34.02 4.02
415 423 7.767261 TGAACAGTACAATGCTTAGTTTGTTT 58.233 30.769 7.70 0.00 37.29 2.83
417 425 6.935741 TGAACAGTACAATGCTTAGTTTGT 57.064 33.333 0.00 7.57 39.32 2.83
418 426 8.075574 TGAATGAACAGTACAATGCTTAGTTTG 58.924 33.333 0.00 0.00 0.00 2.93
441 449 1.402613 CATGCTGAATGGTGCGATGAA 59.597 47.619 0.00 0.00 32.10 2.57
442 450 1.018910 CATGCTGAATGGTGCGATGA 58.981 50.000 0.00 0.00 32.10 2.92
452 460 3.388024 ACACGGGTATACTCATGCTGAAT 59.612 43.478 0.00 0.00 0.00 2.57
516 524 7.391148 AAAACGCCTTGAAATATGACTATGT 57.609 32.000 0.00 0.00 0.00 2.29
519 527 8.231837 GTGTAAAAACGCCTTGAAATATGACTA 58.768 33.333 0.00 0.00 0.00 2.59
599 608 7.201741 GCTTATTCCCATTCCAGTAACTTCTTC 60.202 40.741 0.00 0.00 0.00 2.87
600 609 6.603599 GCTTATTCCCATTCCAGTAACTTCTT 59.396 38.462 0.00 0.00 0.00 2.52
601 610 6.069381 AGCTTATTCCCATTCCAGTAACTTCT 60.069 38.462 0.00 0.00 0.00 2.85
607 616 5.071788 CCTACAGCTTATTCCCATTCCAGTA 59.928 44.000 0.00 0.00 0.00 2.74
666 675 3.967326 TGAGGTCTTGAGGACTTGAAGAA 59.033 43.478 0.00 0.00 43.97 2.52
667 676 3.576861 TGAGGTCTTGAGGACTTGAAGA 58.423 45.455 0.00 0.00 43.97 2.87
668 677 4.061596 GTTGAGGTCTTGAGGACTTGAAG 58.938 47.826 0.00 0.00 43.97 3.02
669 678 3.711704 AGTTGAGGTCTTGAGGACTTGAA 59.288 43.478 0.00 0.00 43.97 2.69
670 679 3.070159 CAGTTGAGGTCTTGAGGACTTGA 59.930 47.826 0.00 0.00 43.97 3.02
671 680 3.070159 TCAGTTGAGGTCTTGAGGACTTG 59.930 47.826 0.00 0.00 43.97 3.16
672 681 3.309296 TCAGTTGAGGTCTTGAGGACTT 58.691 45.455 0.00 0.00 43.97 3.01
673 682 2.964209 TCAGTTGAGGTCTTGAGGACT 58.036 47.619 0.00 0.00 43.97 3.85
674 683 3.259374 TCATCAGTTGAGGTCTTGAGGAC 59.741 47.826 0.00 0.00 43.79 3.85
675 684 3.510459 TCATCAGTTGAGGTCTTGAGGA 58.490 45.455 0.00 0.00 0.00 3.71
676 685 3.969287 TCATCAGTTGAGGTCTTGAGG 57.031 47.619 0.00 0.00 0.00 3.86
677 686 5.144692 TCTTCATCAGTTGAGGTCTTGAG 57.855 43.478 0.00 0.00 35.27 3.02
678 687 4.590647 ACTCTTCATCAGTTGAGGTCTTGA 59.409 41.667 0.00 0.00 35.27 3.02
679 688 4.689812 CACTCTTCATCAGTTGAGGTCTTG 59.310 45.833 0.00 0.00 35.27 3.02
680 689 4.802248 GCACTCTTCATCAGTTGAGGTCTT 60.802 45.833 0.00 0.00 35.27 3.01
681 690 3.306641 GCACTCTTCATCAGTTGAGGTCT 60.307 47.826 0.00 0.00 35.27 3.85
682 691 2.999355 GCACTCTTCATCAGTTGAGGTC 59.001 50.000 0.00 0.00 35.27 3.85
683 692 2.289945 GGCACTCTTCATCAGTTGAGGT 60.290 50.000 0.00 0.00 35.27 3.85
684 693 2.289882 TGGCACTCTTCATCAGTTGAGG 60.290 50.000 0.00 0.00 35.27 3.86
685 694 3.049708 TGGCACTCTTCATCAGTTGAG 57.950 47.619 0.00 0.00 35.27 3.02
686 695 3.490439 TTGGCACTCTTCATCAGTTGA 57.510 42.857 0.00 0.00 0.00 3.18
687 696 4.572985 TTTTGGCACTCTTCATCAGTTG 57.427 40.909 0.00 0.00 0.00 3.16
688 697 4.646492 ACTTTTTGGCACTCTTCATCAGTT 59.354 37.500 0.00 0.00 0.00 3.16
689 698 4.210331 ACTTTTTGGCACTCTTCATCAGT 58.790 39.130 0.00 0.00 0.00 3.41
690 699 4.843220 ACTTTTTGGCACTCTTCATCAG 57.157 40.909 0.00 0.00 0.00 2.90
691 700 5.769662 ACATACTTTTTGGCACTCTTCATCA 59.230 36.000 0.00 0.00 0.00 3.07
692 701 6.259550 ACATACTTTTTGGCACTCTTCATC 57.740 37.500 0.00 0.00 0.00 2.92
693 702 7.168219 TCTACATACTTTTTGGCACTCTTCAT 58.832 34.615 0.00 0.00 0.00 2.57
694 703 6.530120 TCTACATACTTTTTGGCACTCTTCA 58.470 36.000 0.00 0.00 0.00 3.02
709 718 3.711190 TGCACACATGGGATCTACATACT 59.289 43.478 0.00 0.00 0.00 2.12
721 730 0.669619 TTTCAGCTGTGCACACATGG 59.330 50.000 17.42 7.51 41.01 3.66
751 760 2.422597 TGACAACTTAACGGGCATCAG 58.577 47.619 0.00 0.00 0.00 2.90
778 787 3.117131 AGTTGTTCCCTTGTCTTCCCATT 60.117 43.478 0.00 0.00 0.00 3.16
779 788 2.447047 AGTTGTTCCCTTGTCTTCCCAT 59.553 45.455 0.00 0.00 0.00 4.00
907 922 9.363401 TCTGTAAAGCTCTTAGTTATATAGCCA 57.637 33.333 0.00 0.00 33.63 4.75
928 943 3.649073 CGATGTGAAGTTGTGGTCTGTA 58.351 45.455 0.00 0.00 0.00 2.74
952 967 0.038159 CGAAGAAGACGCCTTGAGGT 60.038 55.000 0.00 0.00 37.57 3.85
1036 1051 1.245732 CTTTGCTTCTCTGGCTGCTT 58.754 50.000 0.00 0.00 0.00 3.91
1041 1056 1.301677 CCGGACTTTGCTTCTCTGGC 61.302 60.000 0.00 0.00 0.00 4.85
1047 1062 0.591659 GGTTGTCCGGACTTTGCTTC 59.408 55.000 33.39 15.44 0.00 3.86
1143 1158 2.125713 CCGGCTGCATACGTCACA 60.126 61.111 0.50 0.00 0.00 3.58
1189 1207 2.806745 CGAAGTGTCCATCCTGTGTGTT 60.807 50.000 0.00 0.00 0.00 3.32
1466 1484 7.646061 GACATATATGATGTAGGCGAAGACGC 61.646 46.154 19.63 6.05 46.96 5.19
1525 1576 1.552792 AGCCTTGCCTTCTGTACTCTC 59.447 52.381 0.00 0.00 0.00 3.20
1546 1597 3.055530 GGATCCTTGTCTTGCTTCTCAGA 60.056 47.826 3.84 0.00 0.00 3.27
1581 1632 2.567615 GTCTTGCTTCTCAGGGTCCTTA 59.432 50.000 0.00 0.00 0.00 2.69
1747 1806 2.225242 TGTGGTCCTGCATAATTGGGTT 60.225 45.455 0.00 0.00 0.00 4.11
2028 2087 3.754850 TCTTGTTCATGGCTTCAGTGATG 59.245 43.478 0.00 0.00 0.00 3.07
2071 2130 2.047844 CCGAGCCACAGTGTCTGG 60.048 66.667 0.00 0.00 35.51 3.86
2085 2144 0.614697 TCTTGTCCATGAGAGCCCGA 60.615 55.000 0.00 0.00 0.00 5.14
2095 2154 4.080299 GTCCCAACTATCCTTCTTGTCCAT 60.080 45.833 0.00 0.00 0.00 3.41
2863 2990 2.229792 TGACCAAACTTGTCATCTGCC 58.770 47.619 0.00 0.00 0.00 4.85
3219 3362 2.810164 AGTCTTCCTCTTTAGGCGAGT 58.190 47.619 0.00 0.00 43.31 4.18
3223 3366 3.262151 AGTCCAAGTCTTCCTCTTTAGGC 59.738 47.826 0.00 0.00 43.31 3.93
3224 3367 5.491323 AAGTCCAAGTCTTCCTCTTTAGG 57.509 43.478 0.00 0.00 45.21 2.69
3225 3368 8.940952 CATTTAAGTCCAAGTCTTCCTCTTTAG 58.059 37.037 0.00 0.00 0.00 1.85
3226 3369 8.437575 ACATTTAAGTCCAAGTCTTCCTCTTTA 58.562 33.333 0.00 0.00 0.00 1.85
3227 3370 7.290813 ACATTTAAGTCCAAGTCTTCCTCTTT 58.709 34.615 0.00 0.00 0.00 2.52
3228 3371 6.842676 ACATTTAAGTCCAAGTCTTCCTCTT 58.157 36.000 0.00 0.00 0.00 2.85
3229 3372 6.043243 TGACATTTAAGTCCAAGTCTTCCTCT 59.957 38.462 0.00 0.00 37.73 3.69
3230 3373 6.231211 TGACATTTAAGTCCAAGTCTTCCTC 58.769 40.000 0.00 0.00 37.73 3.71
3231 3374 6.187727 TGACATTTAAGTCCAAGTCTTCCT 57.812 37.500 0.00 0.00 37.73 3.36
3232 3375 6.127897 CCATGACATTTAAGTCCAAGTCTTCC 60.128 42.308 0.00 0.00 37.73 3.46
3233 3376 6.127897 CCCATGACATTTAAGTCCAAGTCTTC 60.128 42.308 0.00 0.00 37.73 2.87
3234 3377 5.711976 CCCATGACATTTAAGTCCAAGTCTT 59.288 40.000 0.00 0.00 37.73 3.01
3235 3378 5.256474 CCCATGACATTTAAGTCCAAGTCT 58.744 41.667 0.00 0.00 37.73 3.24
3236 3379 4.399303 CCCCATGACATTTAAGTCCAAGTC 59.601 45.833 0.00 0.00 37.73 3.01
3237 3380 4.344104 CCCCATGACATTTAAGTCCAAGT 58.656 43.478 0.00 0.00 37.73 3.16
3238 3381 3.701040 CCCCCATGACATTTAAGTCCAAG 59.299 47.826 0.00 0.00 37.73 3.61
3239 3382 3.076785 ACCCCCATGACATTTAAGTCCAA 59.923 43.478 0.00 0.00 37.73 3.53
3240 3383 2.652348 ACCCCCATGACATTTAAGTCCA 59.348 45.455 0.00 0.00 37.73 4.02
3308 3451 2.663196 GGTAGGCTTCGCACCACT 59.337 61.111 0.00 0.00 32.32 4.00
3349 3492 3.203710 TGATGATTCCTTCTTGCCCAGAT 59.796 43.478 0.00 0.00 0.00 2.90
3364 3507 5.012458 TGGTTCAGAAGACTCACTGATGATT 59.988 40.000 11.38 0.00 41.71 2.57
3558 3719 0.391661 GAGGATTGAGTCGCCTGCAA 60.392 55.000 3.98 0.00 30.70 4.08
3566 3727 2.796383 CGATGTCACGGAGGATTGAGTC 60.796 54.545 0.00 0.00 0.00 3.36
3670 3831 1.268539 GGGAACTTGTGCTTGTTCACG 60.269 52.381 7.91 0.00 42.91 4.35
3942 5262 9.013490 CATAGCACTTGCAGTTCAATAAATTAC 57.987 33.333 3.62 0.00 45.16 1.89
4095 5423 4.178540 CACAAATGGCTGGCAATTCTAAG 58.821 43.478 8.35 0.00 0.00 2.18
4170 5507 2.229792 CCAAAGCTCCACACTAGCAAA 58.770 47.619 0.00 0.00 42.62 3.68
4266 6082 8.073768 AGTTTATTTACACCAATGAAACAGACG 58.926 33.333 0.00 0.00 0.00 4.18
4433 6313 7.785033 ACCATATTTGTCAATTCCTTTCCATC 58.215 34.615 0.00 0.00 0.00 3.51
4449 6329 9.586732 TTCAAGGATCCCTTTATACCATATTTG 57.413 33.333 8.55 1.13 41.69 2.32
4505 6388 4.020617 TGGAGGCCTGCCGAACAG 62.021 66.667 22.95 0.00 46.77 3.16
4506 6389 4.329545 GTGGAGGCCTGCCGAACA 62.330 66.667 22.95 0.00 41.95 3.18
4507 6390 3.959991 GAGTGGAGGCCTGCCGAAC 62.960 68.421 22.95 13.48 41.95 3.95
4513 6396 3.721706 GTGGGGAGTGGAGGCCTG 61.722 72.222 12.00 0.00 0.00 4.85
4514 6397 3.507143 AAGTGGGGAGTGGAGGCCT 62.507 63.158 3.86 3.86 0.00 5.19
4515 6398 2.081585 AAAAGTGGGGAGTGGAGGCC 62.082 60.000 0.00 0.00 0.00 5.19
4516 6399 0.609406 GAAAAGTGGGGAGTGGAGGC 60.609 60.000 0.00 0.00 0.00 4.70
4517 6400 0.771127 TGAAAAGTGGGGAGTGGAGG 59.229 55.000 0.00 0.00 0.00 4.30
4518 6401 2.158608 AGTTGAAAAGTGGGGAGTGGAG 60.159 50.000 0.00 0.00 0.00 3.86
4519 6402 1.850345 AGTTGAAAAGTGGGGAGTGGA 59.150 47.619 0.00 0.00 0.00 4.02
4520 6403 2.230660 GAGTTGAAAAGTGGGGAGTGG 58.769 52.381 0.00 0.00 0.00 4.00
4521 6404 2.230660 GGAGTTGAAAAGTGGGGAGTG 58.769 52.381 0.00 0.00 0.00 3.51
4522 6405 1.145119 GGGAGTTGAAAAGTGGGGAGT 59.855 52.381 0.00 0.00 0.00 3.85
4523 6406 1.425448 AGGGAGTTGAAAAGTGGGGAG 59.575 52.381 0.00 0.00 0.00 4.30
4524 6407 1.144913 CAGGGAGTTGAAAAGTGGGGA 59.855 52.381 0.00 0.00 0.00 4.81
4525 6408 1.620822 CAGGGAGTTGAAAAGTGGGG 58.379 55.000 0.00 0.00 0.00 4.96
4526 6409 0.961753 GCAGGGAGTTGAAAAGTGGG 59.038 55.000 0.00 0.00 0.00 4.61
4527 6410 1.882623 GAGCAGGGAGTTGAAAAGTGG 59.117 52.381 0.00 0.00 0.00 4.00
4528 6411 1.882623 GGAGCAGGGAGTTGAAAAGTG 59.117 52.381 0.00 0.00 0.00 3.16
4529 6412 1.494721 TGGAGCAGGGAGTTGAAAAGT 59.505 47.619 0.00 0.00 0.00 2.66
4530 6413 2.276732 TGGAGCAGGGAGTTGAAAAG 57.723 50.000 0.00 0.00 0.00 2.27
4531 6414 2.555227 GGATGGAGCAGGGAGTTGAAAA 60.555 50.000 0.00 0.00 0.00 2.29
4532 6415 1.004745 GGATGGAGCAGGGAGTTGAAA 59.995 52.381 0.00 0.00 0.00 2.69
4533 6416 0.620556 GGATGGAGCAGGGAGTTGAA 59.379 55.000 0.00 0.00 0.00 2.69
4534 6417 0.547471 TGGATGGAGCAGGGAGTTGA 60.547 55.000 0.00 0.00 0.00 3.18
4535 6418 0.107312 CTGGATGGAGCAGGGAGTTG 60.107 60.000 0.00 0.00 0.00 3.16
4536 6419 0.252881 TCTGGATGGAGCAGGGAGTT 60.253 55.000 0.00 0.00 0.00 3.01
4537 6420 0.030297 ATCTGGATGGAGCAGGGAGT 60.030 55.000 0.00 0.00 0.00 3.85
4538 6421 0.397187 CATCTGGATGGAGCAGGGAG 59.603 60.000 2.88 0.00 35.24 4.30
4539 6422 1.703014 GCATCTGGATGGAGCAGGGA 61.703 60.000 11.82 0.00 39.16 4.20
4540 6423 1.228184 GCATCTGGATGGAGCAGGG 60.228 63.158 11.82 0.00 39.16 4.45
4541 6424 1.597302 CGCATCTGGATGGAGCAGG 60.597 63.158 11.82 0.00 39.16 4.85
4542 6425 1.597302 CCGCATCTGGATGGAGCAG 60.597 63.158 11.82 0.00 39.16 4.24
4543 6426 2.036428 CTCCGCATCTGGATGGAGCA 62.036 60.000 11.82 0.00 39.16 4.26
4544 6427 1.301558 CTCCGCATCTGGATGGAGC 60.302 63.158 11.82 0.00 39.16 4.70
4545 6428 1.301558 GCTCCGCATCTGGATGGAG 60.302 63.158 11.82 11.21 39.16 3.86
4546 6429 2.824546 GCTCCGCATCTGGATGGA 59.175 61.111 11.82 1.97 39.16 3.41
4547 6430 2.664185 CGCTCCGCATCTGGATGG 60.664 66.667 11.82 3.27 39.16 3.51
4564 6447 4.030452 AAAAGTGCTGCTCCGCGC 62.030 61.111 0.00 0.00 40.58 6.86
4565 6448 2.127118 CAAAAGTGCTGCTCCGCG 60.127 61.111 0.00 0.00 0.00 6.46
4575 6458 4.749245 ATGTTTCGGAGTAGCAAAAGTG 57.251 40.909 0.00 0.00 0.00 3.16
4576 6459 4.023193 CCAATGTTTCGGAGTAGCAAAAGT 60.023 41.667 0.00 0.00 0.00 2.66
4577 6460 4.475944 CCAATGTTTCGGAGTAGCAAAAG 58.524 43.478 0.00 0.00 0.00 2.27
4578 6461 3.305064 GCCAATGTTTCGGAGTAGCAAAA 60.305 43.478 0.00 0.00 0.00 2.44
4579 6462 2.227865 GCCAATGTTTCGGAGTAGCAAA 59.772 45.455 0.00 0.00 0.00 3.68
4580 6463 1.810151 GCCAATGTTTCGGAGTAGCAA 59.190 47.619 0.00 0.00 0.00 3.91
4581 6464 1.448985 GCCAATGTTTCGGAGTAGCA 58.551 50.000 0.00 0.00 0.00 3.49
4582 6465 0.733150 GGCCAATGTTTCGGAGTAGC 59.267 55.000 0.00 0.00 0.00 3.58
4583 6466 2.403252 AGGCCAATGTTTCGGAGTAG 57.597 50.000 5.01 0.00 0.00 2.57
4584 6467 2.568062 TGTAGGCCAATGTTTCGGAGTA 59.432 45.455 5.01 0.00 0.00 2.59
4585 6468 1.349688 TGTAGGCCAATGTTTCGGAGT 59.650 47.619 5.01 0.00 0.00 3.85
4586 6469 2.107950 TGTAGGCCAATGTTTCGGAG 57.892 50.000 5.01 0.00 0.00 4.63
4587 6470 2.432444 CTTGTAGGCCAATGTTTCGGA 58.568 47.619 5.01 0.00 31.20 4.55
4588 6471 1.135402 GCTTGTAGGCCAATGTTTCGG 60.135 52.381 5.01 0.00 31.20 4.30
4589 6472 2.262572 GCTTGTAGGCCAATGTTTCG 57.737 50.000 5.01 0.00 31.20 3.46
4622 6505 2.060383 CATGCTCTCCCGGAGTGGA 61.060 63.158 14.36 13.36 43.62 4.02
4623 6506 2.503061 CATGCTCTCCCGGAGTGG 59.497 66.667 14.36 9.56 43.62 4.00
4624 6507 2.025767 CTCCATGCTCTCCCGGAGTG 62.026 65.000 14.36 12.86 43.62 3.51
4625 6508 1.760086 CTCCATGCTCTCCCGGAGT 60.760 63.158 14.36 0.00 43.62 3.85
4626 6509 3.136750 CTCCATGCTCTCCCGGAG 58.863 66.667 8.30 8.30 44.49 4.63
4627 6510 3.157252 GCTCCATGCTCTCCCGGA 61.157 66.667 0.73 0.00 38.95 5.14
4628 6511 4.247380 GGCTCCATGCTCTCCCGG 62.247 72.222 0.00 0.00 42.39 5.73
4629 6512 3.035173 TTGGCTCCATGCTCTCCCG 62.035 63.158 0.00 0.00 42.39 5.14
4630 6513 1.452833 GTTGGCTCCATGCTCTCCC 60.453 63.158 0.00 0.00 42.39 4.30
4631 6514 1.817099 CGTTGGCTCCATGCTCTCC 60.817 63.158 0.00 0.00 42.39 3.71
4632 6515 1.078848 ACGTTGGCTCCATGCTCTC 60.079 57.895 0.00 0.00 42.39 3.20
4633 6516 1.376424 CACGTTGGCTCCATGCTCT 60.376 57.895 0.00 0.00 42.39 4.09
4634 6517 1.237285 AACACGTTGGCTCCATGCTC 61.237 55.000 0.00 0.00 42.39 4.26
4635 6518 1.228245 AACACGTTGGCTCCATGCT 60.228 52.632 0.00 0.00 42.39 3.79
4636 6519 1.210155 GAACACGTTGGCTCCATGC 59.790 57.895 0.00 0.00 41.94 4.06
4637 6520 1.497278 CGAACACGTTGGCTCCATG 59.503 57.895 0.00 0.00 0.00 3.66
4638 6521 1.671054 CCGAACACGTTGGCTCCAT 60.671 57.895 0.00 0.00 0.00 3.41
4639 6522 2.280524 CCGAACACGTTGGCTCCA 60.281 61.111 0.00 0.00 0.00 3.86
4640 6523 2.280592 ACCGAACACGTTGGCTCC 60.281 61.111 0.00 0.00 0.00 4.70
4641 6524 1.828331 GACACCGAACACGTTGGCTC 61.828 60.000 0.00 0.00 0.00 4.70
4642 6525 1.885850 GACACCGAACACGTTGGCT 60.886 57.895 0.00 0.00 0.00 4.75
4643 6526 2.174969 TGACACCGAACACGTTGGC 61.175 57.895 0.00 0.00 0.00 4.52
4644 6527 0.808453 AGTGACACCGAACACGTTGG 60.808 55.000 0.84 0.00 41.22 3.77
4645 6528 0.575390 GAGTGACACCGAACACGTTG 59.425 55.000 0.84 0.00 41.22 4.10
4646 6529 0.529119 GGAGTGACACCGAACACGTT 60.529 55.000 0.84 0.00 41.22 3.99
4647 6530 1.066918 GGAGTGACACCGAACACGT 59.933 57.895 0.84 0.00 41.22 4.49
4648 6531 3.932289 GGAGTGACACCGAACACG 58.068 61.111 0.84 0.00 41.22 4.49
4655 6538 1.446272 GTAGCTGCGGAGTGACACC 60.446 63.158 5.62 0.00 0.00 4.16
4656 6539 0.456995 GAGTAGCTGCGGAGTGACAC 60.457 60.000 5.62 0.00 0.00 3.67
4657 6540 1.595993 GGAGTAGCTGCGGAGTGACA 61.596 60.000 5.62 0.00 0.00 3.58
4658 6541 1.139947 GGAGTAGCTGCGGAGTGAC 59.860 63.158 5.62 3.98 0.00 3.67
4659 6542 1.304134 TGGAGTAGCTGCGGAGTGA 60.304 57.895 5.62 0.00 0.00 3.41
4660 6543 1.140589 CTGGAGTAGCTGCGGAGTG 59.859 63.158 5.62 0.00 29.37 3.51
4661 6544 3.609703 CTGGAGTAGCTGCGGAGT 58.390 61.111 5.62 0.00 29.37 3.85
4670 6553 2.790791 CCTGGAGCGGCTGGAGTAG 61.791 68.421 7.50 0.00 0.00 2.57
4671 6554 2.759973 CCTGGAGCGGCTGGAGTA 60.760 66.667 7.50 0.00 0.00 2.59
4672 6555 4.704103 TCCTGGAGCGGCTGGAGT 62.704 66.667 7.50 0.00 0.00 3.85
4673 6556 3.847602 CTCCTGGAGCGGCTGGAG 61.848 72.222 17.36 17.36 39.87 3.86
4691 6574 4.504916 CTCCACTCCGCAGCTCCG 62.505 72.222 0.00 0.00 0.00 4.63
4692 6575 4.154347 CCTCCACTCCGCAGCTCC 62.154 72.222 0.00 0.00 0.00 4.70
4693 6576 3.363844 GACCTCCACTCCGCAGCTC 62.364 68.421 0.00 0.00 0.00 4.09
4694 6577 3.386237 GACCTCCACTCCGCAGCT 61.386 66.667 0.00 0.00 0.00 4.24
4695 6578 3.386237 AGACCTCCACTCCGCAGC 61.386 66.667 0.00 0.00 0.00 5.25
4696 6579 2.575993 CAGACCTCCACTCCGCAG 59.424 66.667 0.00 0.00 0.00 5.18
4697 6580 3.695606 GCAGACCTCCACTCCGCA 61.696 66.667 0.00 0.00 0.00 5.69
4698 6581 4.459089 GGCAGACCTCCACTCCGC 62.459 72.222 0.00 0.00 0.00 5.54
4699 6582 4.135153 CGGCAGACCTCCACTCCG 62.135 72.222 0.00 0.00 0.00 4.63
4700 6583 2.283529 TTCGGCAGACCTCCACTCC 61.284 63.158 0.00 0.00 0.00 3.85
4701 6584 1.079750 GTTCGGCAGACCTCCACTC 60.080 63.158 0.00 0.00 0.00 3.51
4702 6585 1.837051 TGTTCGGCAGACCTCCACT 60.837 57.895 0.00 0.00 0.00 4.00
4703 6586 2.741092 TGTTCGGCAGACCTCCAC 59.259 61.111 0.00 0.00 0.00 4.02
4714 6597 2.737252 GTTCAACTAAGAGCCTGTTCGG 59.263 50.000 0.00 0.00 0.00 4.30
4715 6598 3.430218 CAGTTCAACTAAGAGCCTGTTCG 59.570 47.826 0.00 0.00 0.00 3.95
4716 6599 3.748568 CCAGTTCAACTAAGAGCCTGTTC 59.251 47.826 0.00 0.00 0.00 3.18
4717 6600 3.744660 CCAGTTCAACTAAGAGCCTGTT 58.255 45.455 0.00 0.00 0.00 3.16
4718 6601 2.551071 GCCAGTTCAACTAAGAGCCTGT 60.551 50.000 0.00 0.00 0.00 4.00
4719 6602 2.079925 GCCAGTTCAACTAAGAGCCTG 58.920 52.381 0.00 0.00 0.00 4.85
4720 6603 1.003696 GGCCAGTTCAACTAAGAGCCT 59.996 52.381 11.15 0.00 36.22 4.58
4721 6604 1.003696 AGGCCAGTTCAACTAAGAGCC 59.996 52.381 5.01 10.65 39.49 4.70
4722 6605 2.079925 CAGGCCAGTTCAACTAAGAGC 58.920 52.381 5.01 0.00 0.00 4.09
4723 6606 3.685139 TCAGGCCAGTTCAACTAAGAG 57.315 47.619 5.01 0.00 0.00 2.85
4724 6607 3.582647 TCATCAGGCCAGTTCAACTAAGA 59.417 43.478 5.01 0.00 0.00 2.10
4725 6608 3.942829 TCATCAGGCCAGTTCAACTAAG 58.057 45.455 5.01 0.00 0.00 2.18
4726 6609 4.365514 TTCATCAGGCCAGTTCAACTAA 57.634 40.909 5.01 0.00 0.00 2.24
4727 6610 4.365514 TTTCATCAGGCCAGTTCAACTA 57.634 40.909 5.01 0.00 0.00 2.24
4728 6611 2.957402 TTCATCAGGCCAGTTCAACT 57.043 45.000 5.01 0.00 0.00 3.16
4729 6612 5.841957 ATATTTCATCAGGCCAGTTCAAC 57.158 39.130 5.01 0.00 0.00 3.18
4730 6613 8.537728 AATTATATTTCATCAGGCCAGTTCAA 57.462 30.769 5.01 0.00 0.00 2.69
4731 6614 9.066892 GTAATTATATTTCATCAGGCCAGTTCA 57.933 33.333 5.01 0.00 0.00 3.18
4732 6615 9.066892 TGTAATTATATTTCATCAGGCCAGTTC 57.933 33.333 5.01 0.00 0.00 3.01
4733 6616 8.995027 TGTAATTATATTTCATCAGGCCAGTT 57.005 30.769 5.01 0.00 0.00 3.16
4734 6617 8.439971 TCTGTAATTATATTTCATCAGGCCAGT 58.560 33.333 5.01 0.00 0.00 4.00
4735 6618 8.853077 TCTGTAATTATATTTCATCAGGCCAG 57.147 34.615 5.01 0.00 0.00 4.85
4736 6619 9.288576 CTTCTGTAATTATATTTCATCAGGCCA 57.711 33.333 5.01 0.00 0.00 5.36
4737 6620 8.734386 CCTTCTGTAATTATATTTCATCAGGCC 58.266 37.037 0.00 0.00 0.00 5.19
4738 6621 8.239998 GCCTTCTGTAATTATATTTCATCAGGC 58.760 37.037 10.26 10.26 0.00 4.85
4751 6634 7.817962 GTCACTAGAAACTGCCTTCTGTAATTA 59.182 37.037 0.00 0.00 36.34 1.40
4760 6643 3.556004 GCAGAGTCACTAGAAACTGCCTT 60.556 47.826 4.42 0.00 43.24 4.35
4767 6650 7.939784 TTATAGAGTGCAGAGTCACTAGAAA 57.060 36.000 0.00 0.00 46.40 2.52
4819 6702 8.426489 TCTGGTAAAATTAACACTACAGTCAGT 58.574 33.333 0.00 0.00 0.00 3.41
4820 6703 8.827177 TCTGGTAAAATTAACACTACAGTCAG 57.173 34.615 0.00 0.00 0.00 3.51
4821 6704 8.644216 TCTCTGGTAAAATTAACACTACAGTCA 58.356 33.333 0.00 0.00 0.00 3.41
4822 6705 9.654663 ATCTCTGGTAAAATTAACACTACAGTC 57.345 33.333 0.00 0.00 0.00 3.51
4837 6720 5.926542 GTCTGCGCATTATATCTCTGGTAAA 59.073 40.000 12.24 0.00 0.00 2.01
4842 6725 3.925299 CAGGTCTGCGCATTATATCTCTG 59.075 47.826 12.24 6.87 0.00 3.35


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

AutoCloner maintained by Alex Coulton.