Multiple sequence alignment - TraesCS5D01G235600

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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 TraesCS5D01G235600 chr5D 100.000 2801 0 0 1 2801 344467414 344470214 0.000000e+00 5173.0
1 TraesCS5D01G235600 chr5D 91.822 807 62 4 1808 2614 455808276 455809078 0.000000e+00 1122.0
2 TraesCS5D01G235600 chr5D 79.882 676 53 44 755 1403 344447266 344446647 4.320000e-113 418.0
3 TraesCS5D01G235600 chr5D 75.845 207 37 8 1152 1350 452493814 452494015 2.970000e-15 93.5
4 TraesCS5D01G235600 chr5D 97.368 38 1 0 2764 2801 62678538 62678575 6.480000e-07 65.8
5 TraesCS5D01G235600 chr5B 87.423 1296 78 27 556 1805 407615803 407614547 0.000000e+00 1411.0
6 TraesCS5D01G235600 chr5B 79.942 688 41 53 751 1403 407622041 407622666 1.550000e-112 416.0
7 TraesCS5D01G235600 chr5B 93.846 195 11 1 356 549 407616096 407615902 2.730000e-75 292.0
8 TraesCS5D01G235600 chr5B 90.256 195 18 1 160 354 407616399 407616206 1.290000e-63 254.0
9 TraesCS5D01G235600 chr3B 91.256 812 59 5 1806 2614 225175052 225175854 0.000000e+00 1096.0
10 TraesCS5D01G235600 chr3B 93.023 43 3 0 2759 2801 735109425 735109383 2.330000e-06 63.9
11 TraesCS5D01G235600 chr7D 90.977 809 72 1 1808 2616 453287457 453288264 0.000000e+00 1088.0
12 TraesCS5D01G235600 chr6D 90.909 814 67 4 1807 2617 184811872 184812681 0.000000e+00 1086.0
13 TraesCS5D01G235600 chr6D 90.122 820 74 7 1799 2617 347168057 347168870 0.000000e+00 1059.0
14 TraesCS5D01G235600 chr6B 89.988 809 77 4 1806 2612 82047219 82046413 0.000000e+00 1042.0
15 TraesCS5D01G235600 chr4D 90.518 791 69 5 1804 2592 380345465 380346251 0.000000e+00 1040.0
16 TraesCS5D01G235600 chr4D 89.396 811 78 5 1808 2614 483459482 483458676 0.000000e+00 1014.0
17 TraesCS5D01G235600 chr4A 89.429 823 79 7 1804 2622 688337615 688336797 0.000000e+00 1031.0
18 TraesCS5D01G235600 chr4A 74.534 161 35 5 183 341 214878875 214879031 6.480000e-07 65.8
19 TraesCS5D01G235600 chr5A 83.893 1012 77 50 617 1598 447552492 447551537 0.000000e+00 887.0
20 TraesCS5D01G235600 chr5A 88.390 534 39 8 600 1124 447625786 447625267 3.060000e-174 621.0
21 TraesCS5D01G235600 chr5A 88.961 462 37 4 88 547 447626422 447625973 2.440000e-155 558.0
22 TraesCS5D01G235600 chr5A 81.053 665 55 32 751 1383 447630752 447631377 5.460000e-127 464.0
23 TraesCS5D01G235600 chr5A 88.070 285 12 3 1129 1404 447624426 447624155 4.500000e-83 318.0
24 TraesCS5D01G235600 chr5A 87.636 275 30 4 277 549 447552797 447552525 1.620000e-82 316.0
25 TraesCS5D01G235600 chr5A 85.427 199 17 7 1611 1805 447551139 447550949 2.200000e-46 196.0
26 TraesCS5D01G235600 chr5A 78.659 164 27 4 1149 1304 571425326 571425489 4.940000e-18 102.0
27 TraesCS5D01G235600 chr5A 90.385 52 4 1 291 341 236122740 236122689 1.800000e-07 67.6
28 TraesCS5D01G235600 chr2D 75.000 152 34 4 183 333 237748119 237748267 1.800000e-07 67.6
29 TraesCS5D01G235600 chr2D 95.238 42 2 0 2760 2801 534482805 534482846 1.800000e-07 67.6
30 TraesCS5D01G235600 chr2D 95.238 42 2 0 2760 2801 537188190 537188149 1.800000e-07 67.6
31 TraesCS5D01G235600 chr3D 92.857 42 3 0 2760 2801 7970653 7970612 8.380000e-06 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 TraesCS5D01G235600 chr5D 344467414 344470214 2800 False 5173.000000 5173 100.000000 1 2801 1 chr5D.!!$F2 2800
1 TraesCS5D01G235600 chr5D 455808276 455809078 802 False 1122.000000 1122 91.822000 1808 2614 1 chr5D.!!$F4 806
2 TraesCS5D01G235600 chr5D 344446647 344447266 619 True 418.000000 418 79.882000 755 1403 1 chr5D.!!$R1 648
3 TraesCS5D01G235600 chr5B 407614547 407616399 1852 True 652.333333 1411 90.508333 160 1805 3 chr5B.!!$R1 1645
4 TraesCS5D01G235600 chr5B 407622041 407622666 625 False 416.000000 416 79.942000 751 1403 1 chr5B.!!$F1 652
5 TraesCS5D01G235600 chr3B 225175052 225175854 802 False 1096.000000 1096 91.256000 1806 2614 1 chr3B.!!$F1 808
6 TraesCS5D01G235600 chr7D 453287457 453288264 807 False 1088.000000 1088 90.977000 1808 2616 1 chr7D.!!$F1 808
7 TraesCS5D01G235600 chr6D 184811872 184812681 809 False 1086.000000 1086 90.909000 1807 2617 1 chr6D.!!$F1 810
8 TraesCS5D01G235600 chr6D 347168057 347168870 813 False 1059.000000 1059 90.122000 1799 2617 1 chr6D.!!$F2 818
9 TraesCS5D01G235600 chr6B 82046413 82047219 806 True 1042.000000 1042 89.988000 1806 2612 1 chr6B.!!$R1 806
10 TraesCS5D01G235600 chr4D 380345465 380346251 786 False 1040.000000 1040 90.518000 1804 2592 1 chr4D.!!$F1 788
11 TraesCS5D01G235600 chr4D 483458676 483459482 806 True 1014.000000 1014 89.396000 1808 2614 1 chr4D.!!$R1 806
12 TraesCS5D01G235600 chr4A 688336797 688337615 818 True 1031.000000 1031 89.429000 1804 2622 1 chr4A.!!$R1 818
13 TraesCS5D01G235600 chr5A 447624155 447626422 2267 True 499.000000 621 88.473667 88 1404 3 chr5A.!!$R3 1316
14 TraesCS5D01G235600 chr5A 447550949 447552797 1848 True 466.333333 887 85.652000 277 1805 3 chr5A.!!$R2 1528
15 TraesCS5D01G235600 chr5A 447630752 447631377 625 False 464.000000 464 81.053000 751 1383 1 chr5A.!!$F1 632

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
670 932 0.035915 GGAAGGCAGGACCAGTTCTC 60.036 60.0 0.0 0.0 43.14 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2666 4246 0.101759 TCGGGATCTTAAGCCGTTCG 59.898 55.0 16.45 8.6 0.0 3.95 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
22 23 5.565592 TGAAATTTTCATGCGATGCTACT 57.434 34.783 7.74 0.00 34.08 2.57
23 24 6.676237 TGAAATTTTCATGCGATGCTACTA 57.324 33.333 7.74 0.00 34.08 1.82
24 25 7.263100 TGAAATTTTCATGCGATGCTACTAT 57.737 32.000 7.74 0.00 34.08 2.12
25 26 7.706159 TGAAATTTTCATGCGATGCTACTATT 58.294 30.769 7.74 0.00 34.08 1.73
26 27 8.190122 TGAAATTTTCATGCGATGCTACTATTT 58.810 29.630 7.74 0.00 34.08 1.40
27 28 9.663904 GAAATTTTCATGCGATGCTACTATTTA 57.336 29.630 4.25 0.00 0.00 1.40
29 30 9.616634 AATTTTCATGCGATGCTACTATTTATG 57.383 29.630 0.00 0.00 0.00 1.90
30 31 7.728847 TTTCATGCGATGCTACTATTTATGT 57.271 32.000 0.00 0.00 0.00 2.29
31 32 6.951256 TCATGCGATGCTACTATTTATGTC 57.049 37.500 0.00 0.00 0.00 3.06
32 33 6.691508 TCATGCGATGCTACTATTTATGTCT 58.308 36.000 0.00 0.00 0.00 3.41
33 34 7.154656 TCATGCGATGCTACTATTTATGTCTT 58.845 34.615 0.00 0.00 0.00 3.01
34 35 7.657354 TCATGCGATGCTACTATTTATGTCTTT 59.343 33.333 0.00 0.00 0.00 2.52
35 36 7.177498 TGCGATGCTACTATTTATGTCTTTG 57.823 36.000 0.00 0.00 0.00 2.77
36 37 6.202762 TGCGATGCTACTATTTATGTCTTTGG 59.797 38.462 0.00 0.00 0.00 3.28
37 38 6.202954 GCGATGCTACTATTTATGTCTTTGGT 59.797 38.462 0.00 0.00 0.00 3.67
38 39 7.254795 GCGATGCTACTATTTATGTCTTTGGTT 60.255 37.037 0.00 0.00 0.00 3.67
39 40 8.612619 CGATGCTACTATTTATGTCTTTGGTTT 58.387 33.333 0.00 0.00 0.00 3.27
51 52 9.581289 TTATGTCTTTGGTTTAAAGGAATGAGA 57.419 29.630 0.00 0.00 44.75 3.27
52 53 7.272037 TGTCTTTGGTTTAAAGGAATGAGAC 57.728 36.000 0.00 0.00 44.75 3.36
53 54 6.831353 TGTCTTTGGTTTAAAGGAATGAGACA 59.169 34.615 11.75 11.75 44.75 3.41
54 55 7.340743 TGTCTTTGGTTTAAAGGAATGAGACAA 59.659 33.333 12.72 0.00 44.75 3.18
55 56 8.194769 GTCTTTGGTTTAAAGGAATGAGACAAA 58.805 33.333 0.00 0.00 44.75 2.83
56 57 8.413229 TCTTTGGTTTAAAGGAATGAGACAAAG 58.587 33.333 0.00 0.00 44.75 2.77
57 58 7.889873 TTGGTTTAAAGGAATGAGACAAAGA 57.110 32.000 0.00 0.00 0.00 2.52
58 59 7.889873 TGGTTTAAAGGAATGAGACAAAGAA 57.110 32.000 0.00 0.00 0.00 2.52
59 60 7.940850 TGGTTTAAAGGAATGAGACAAAGAAG 58.059 34.615 0.00 0.00 0.00 2.85
60 61 7.777910 TGGTTTAAAGGAATGAGACAAAGAAGA 59.222 33.333 0.00 0.00 0.00 2.87
61 62 8.630037 GGTTTAAAGGAATGAGACAAAGAAGAA 58.370 33.333 0.00 0.00 0.00 2.52
64 65 6.830873 AAGGAATGAGACAAAGAAGAATGG 57.169 37.500 0.00 0.00 0.00 3.16
65 66 6.131972 AGGAATGAGACAAAGAAGAATGGA 57.868 37.500 0.00 0.00 0.00 3.41
66 67 6.179040 AGGAATGAGACAAAGAAGAATGGAG 58.821 40.000 0.00 0.00 0.00 3.86
67 68 5.163673 GGAATGAGACAAAGAAGAATGGAGC 60.164 44.000 0.00 0.00 0.00 4.70
68 69 3.329386 TGAGACAAAGAAGAATGGAGCG 58.671 45.455 0.00 0.00 0.00 5.03
69 70 3.006859 TGAGACAAAGAAGAATGGAGCGA 59.993 43.478 0.00 0.00 0.00 4.93
70 71 3.997021 GAGACAAAGAAGAATGGAGCGAA 59.003 43.478 0.00 0.00 0.00 4.70
71 72 3.999663 AGACAAAGAAGAATGGAGCGAAG 59.000 43.478 0.00 0.00 0.00 3.79
85 86 2.513159 CGAAGCAACGGAGAAACGA 58.487 52.632 0.00 0.00 37.61 3.85
86 87 0.856641 CGAAGCAACGGAGAAACGAA 59.143 50.000 0.00 0.00 37.61 3.85
92 93 3.564225 AGCAACGGAGAAACGAAGAATTT 59.436 39.130 0.00 0.00 37.61 1.82
93 94 3.664025 GCAACGGAGAAACGAAGAATTTG 59.336 43.478 0.00 0.00 37.61 2.32
105 106 5.762045 ACGAAGAATTTGAACATCCAACTG 58.238 37.500 0.00 0.00 32.44 3.16
107 108 6.207417 ACGAAGAATTTGAACATCCAACTGAT 59.793 34.615 0.00 0.00 32.44 2.90
111 112 7.405292 AGAATTTGAACATCCAACTGATCCTA 58.595 34.615 0.00 0.00 0.00 2.94
114 115 8.599624 ATTTGAACATCCAACTGATCCTATTT 57.400 30.769 0.00 0.00 0.00 1.40
154 157 8.779303 TGCATGAAGAACGAGACTAAATTTTTA 58.221 29.630 0.00 0.00 0.00 1.52
172 175 8.920509 AATTTTTAGTCGCATAATAACAACCC 57.079 30.769 0.00 0.00 0.00 4.11
197 200 7.667219 CCATCTAGCTATAAATTTCCATGTGGT 59.333 37.037 0.00 0.00 36.34 4.16
198 201 9.071276 CATCTAGCTATAAATTTCCATGTGGTT 57.929 33.333 0.00 0.00 36.34 3.67
199 202 9.646522 ATCTAGCTATAAATTTCCATGTGGTTT 57.353 29.630 0.00 0.00 36.34 3.27
200 203 8.902806 TCTAGCTATAAATTTCCATGTGGTTTG 58.097 33.333 0.00 0.00 36.34 2.93
201 204 7.716799 AGCTATAAATTTCCATGTGGTTTGA 57.283 32.000 0.00 0.00 36.34 2.69
202 205 7.547227 AGCTATAAATTTCCATGTGGTTTGAC 58.453 34.615 0.00 0.00 36.34 3.18
203 206 7.397192 AGCTATAAATTTCCATGTGGTTTGACT 59.603 33.333 0.00 0.00 36.34 3.41
204 207 8.034804 GCTATAAATTTCCATGTGGTTTGACTT 58.965 33.333 0.00 0.00 36.34 3.01
205 208 9.927668 CTATAAATTTCCATGTGGTTTGACTTT 57.072 29.630 0.00 0.00 36.34 2.66
206 209 6.923928 AAATTTCCATGTGGTTTGACTTTG 57.076 33.333 0.00 0.00 36.34 2.77
207 210 5.867903 ATTTCCATGTGGTTTGACTTTGA 57.132 34.783 0.00 0.00 36.34 2.69
264 278 2.461300 TTCCCATGAACCAAACACCA 57.539 45.000 0.00 0.00 0.00 4.17
273 287 3.056465 TGAACCAAACACCAAAGTTGACC 60.056 43.478 0.00 0.00 0.00 4.02
303 317 9.985318 CTCTCATGTTCACAAATTCTCTATTTC 57.015 33.333 0.00 0.00 34.19 2.17
320 334 0.804364 TTCGCACATGCATTCCTGTC 59.196 50.000 0.00 0.00 42.21 3.51
339 354 6.214615 TCCTGTCCTATCCATGTGTTTTTCTA 59.785 38.462 0.00 0.00 0.00 2.10
354 477 7.707035 TGTGTTTTTCTATTGCCACGTTTTTAT 59.293 29.630 0.00 0.00 0.00 1.40
381 504 2.301346 ACAAACCAAAGGAGCACTGAG 58.699 47.619 0.00 0.00 0.00 3.35
497 621 1.070134 TCAGTTCGAAGACCTTGGGTG 59.930 52.381 0.00 0.00 35.25 4.61
549 673 0.748005 CCCCGTAATCTTGCACCCTG 60.748 60.000 0.00 0.00 0.00 4.45
550 674 1.376609 CCCGTAATCTTGCACCCTGC 61.377 60.000 0.00 0.00 45.29 4.85
634 892 8.303876 TCATATAAACATGCGCTACTCTATCAA 58.696 33.333 9.73 0.00 0.00 2.57
641 899 5.718649 TGCGCTACTCTATCAATTGAAAC 57.281 39.130 13.09 0.00 0.00 2.78
642 900 5.419542 TGCGCTACTCTATCAATTGAAACT 58.580 37.500 13.09 0.00 0.00 2.66
643 901 5.520288 TGCGCTACTCTATCAATTGAAACTC 59.480 40.000 13.09 0.00 0.00 3.01
644 902 5.331905 GCGCTACTCTATCAATTGAAACTCG 60.332 44.000 13.09 9.05 0.00 4.18
645 903 5.971792 CGCTACTCTATCAATTGAAACTCGA 59.028 40.000 13.09 4.13 0.00 4.04
646 904 6.141527 CGCTACTCTATCAATTGAAACTCGAG 59.858 42.308 13.09 11.84 0.00 4.04
647 905 7.197017 GCTACTCTATCAATTGAAACTCGAGA 58.803 38.462 21.68 7.59 0.00 4.04
648 906 7.166804 GCTACTCTATCAATTGAAACTCGAGAC 59.833 40.741 21.68 10.48 0.00 3.36
652 910 3.575630 TCAATTGAAACTCGAGACTCGG 58.424 45.455 23.92 16.57 40.88 4.63
653 911 3.254903 TCAATTGAAACTCGAGACTCGGA 59.745 43.478 23.92 10.37 40.88 4.55
664 926 2.203788 ACTCGGAAGGCAGGACCA 60.204 61.111 0.00 0.00 43.14 4.02
669 931 1.831652 CGGAAGGCAGGACCAGTTCT 61.832 60.000 0.00 0.00 43.14 3.01
670 932 0.035915 GGAAGGCAGGACCAGTTCTC 60.036 60.000 0.00 0.00 43.14 2.87
688 950 1.098712 TCACTGTTGGGTTTGACCGC 61.099 55.000 0.00 0.00 39.83 5.68
709 971 0.671251 GGCGACATCCAGAGGAGTAG 59.329 60.000 0.00 0.00 34.05 2.57
712 974 2.291190 GCGACATCCAGAGGAGTAGTAC 59.709 54.545 0.00 0.00 34.05 2.73
715 977 4.751098 CGACATCCAGAGGAGTAGTACTAC 59.249 50.000 23.03 23.03 34.05 2.73
721 983 7.123355 TCCAGAGGAGTAGTACTACTAGTTC 57.877 44.000 30.80 25.45 40.14 3.01
776 1047 2.945668 GAGAGCAACCCGAGCAATATTT 59.054 45.455 0.00 0.00 0.00 1.40
789 1060 5.687285 CGAGCAATATTTTAATCCTTGCACC 59.313 40.000 17.60 11.38 43.49 5.01
824 1098 4.057428 GCACGGAGCAGGTCGAGT 62.057 66.667 0.00 0.00 44.79 4.18
979 1284 1.418755 GCCGTTATATAAGCGCGCC 59.581 57.895 30.33 10.31 0.00 6.53
1076 1387 2.826488 CCTCTCAGGGAAGGAAGAGAA 58.174 52.381 0.00 0.00 36.76 2.87
1077 1388 2.765699 CCTCTCAGGGAAGGAAGAGAAG 59.234 54.545 0.00 0.00 36.76 2.85
1078 1389 3.565449 CCTCTCAGGGAAGGAAGAGAAGA 60.565 52.174 0.00 0.00 36.76 2.87
1079 1390 3.701040 CTCTCAGGGAAGGAAGAGAAGAG 59.299 52.174 0.00 0.00 36.76 2.85
1080 1391 3.335183 TCTCAGGGAAGGAAGAGAAGAGA 59.665 47.826 0.00 0.00 34.45 3.10
1093 1406 3.006752 AGAGAAGAGACTGCTTGGTGAAG 59.993 47.826 0.00 0.00 0.00 3.02
1124 1438 0.247736 GTGTGATCAAGAGCTCGGGT 59.752 55.000 8.37 0.19 0.00 5.28
1253 2408 1.418908 CCACCACCAAGACCCTCTGT 61.419 60.000 0.00 0.00 0.00 3.41
1468 2644 0.248539 GCGATCGTTTCCGAGCTACT 60.249 55.000 17.81 0.00 46.84 2.57
1469 2645 1.003116 GCGATCGTTTCCGAGCTACTA 60.003 52.381 17.81 0.00 46.84 1.82
1470 2646 2.906153 CGATCGTTTCCGAGCTACTAG 58.094 52.381 7.03 0.00 46.84 2.57
1471 2647 2.287373 CGATCGTTTCCGAGCTACTAGT 59.713 50.000 7.03 0.00 46.84 2.57
1472 2648 3.492383 CGATCGTTTCCGAGCTACTAGTA 59.508 47.826 7.03 1.89 46.84 1.82
1473 2649 4.376210 CGATCGTTTCCGAGCTACTAGTAG 60.376 50.000 23.25 23.25 46.84 2.57
1625 3194 1.000827 TGTTTTGGCTACCGTGCAATG 60.001 47.619 0.00 0.00 34.04 2.82
1660 3229 5.586243 TGTGTTTTGAGGAGAAACTTCTGAG 59.414 40.000 0.00 0.00 37.73 3.35
1672 3241 5.163152 AGAAACTTCTGAGGAATGGAACAGT 60.163 40.000 0.00 0.00 37.85 3.55
1673 3242 6.635875 AGAAACTTCTGAGGAATGGAACAGTT 60.636 38.462 0.00 0.00 37.85 3.16
1706 3275 6.729690 TCATGAAACTCTCCAAATGGTTTT 57.270 33.333 0.00 0.00 32.95 2.43
1711 3280 7.164803 TGAAACTCTCCAAATGGTTTTGTTTT 58.835 30.769 0.00 0.00 40.55 2.43
1713 3282 5.348164 ACTCTCCAAATGGTTTTGTTTTCG 58.652 37.500 0.00 0.00 40.55 3.46
1753 3322 1.760192 AATGCTCAGGATGTCCTTGC 58.240 50.000 13.70 13.70 46.09 4.01
1760 3329 0.530650 AGGATGTCCTTGCATACGCG 60.531 55.000 3.53 3.53 46.09 6.01
1761 3330 0.529773 GGATGTCCTTGCATACGCGA 60.530 55.000 15.93 0.00 42.97 5.87
1768 3337 3.554324 GTCCTTGCATACGCGATTTCTAA 59.446 43.478 15.93 0.00 42.97 2.10
1770 3339 4.814234 TCCTTGCATACGCGATTTCTAAAT 59.186 37.500 15.93 0.00 42.97 1.40
1878 3451 4.689812 CGTCCTATAGCATACAGACTACGT 59.310 45.833 0.00 0.00 0.00 3.57
1896 3469 2.168313 ACGTCATGTCACCTCATGCATA 59.832 45.455 0.00 0.00 43.18 3.14
1897 3470 3.181462 ACGTCATGTCACCTCATGCATAT 60.181 43.478 0.00 0.00 43.18 1.78
1905 3478 5.013391 TGTCACCTCATGCATATATGTGGAT 59.987 40.000 14.14 0.43 41.82 3.41
1906 3479 5.942236 GTCACCTCATGCATATATGTGGATT 59.058 40.000 14.14 0.00 41.82 3.01
1908 3481 7.005902 TCACCTCATGCATATATGTGGATTTT 58.994 34.615 14.14 0.00 41.82 1.82
1988 3561 7.175816 TGAAGATCCGTTTTCACCATTAAATCA 59.824 33.333 0.00 0.00 0.00 2.57
2124 3697 6.092670 CCGAAGTTGTCATGATATGTTTCAGT 59.907 38.462 0.00 0.00 0.00 3.41
2200 3773 3.960571 AGAAACTAGACTTGCCATGCAT 58.039 40.909 0.00 0.00 38.76 3.96
2298 3872 9.087424 GAAAAACTAAAATTGCCATGATCTACC 57.913 33.333 0.00 0.00 0.00 3.18
2356 3930 4.391830 CACTATGACAACTGCGGTGTAAAT 59.608 41.667 0.00 0.00 0.00 1.40
2432 4012 3.839293 AGTTTTGAAGATCTCGTCGAGG 58.161 45.455 21.63 0.00 0.00 4.63
2581 4161 4.088762 GCGTGTGGGTGATGTGCG 62.089 66.667 0.00 0.00 0.00 5.34
2617 4197 2.291190 TGGGCGTTAGTTTTTCCGAAAG 59.709 45.455 0.00 0.00 0.00 2.62
2622 4202 5.970612 GGCGTTAGTTTTTCCGAAAGTTTAA 59.029 36.000 0.00 0.00 0.00 1.52
2623 4203 6.141211 GGCGTTAGTTTTTCCGAAAGTTTAAG 59.859 38.462 0.00 0.00 0.00 1.85
2624 4204 6.344468 GCGTTAGTTTTTCCGAAAGTTTAAGC 60.344 38.462 0.00 0.00 0.00 3.09
2625 4205 6.908820 CGTTAGTTTTTCCGAAAGTTTAAGCT 59.091 34.615 0.00 0.00 0.00 3.74
2626 4206 7.430211 CGTTAGTTTTTCCGAAAGTTTAAGCTT 59.570 33.333 3.48 3.48 0.00 3.74
2627 4207 9.079833 GTTAGTTTTTCCGAAAGTTTAAGCTTT 57.920 29.630 16.13 16.13 40.94 3.51
2628 4208 7.520119 AGTTTTTCCGAAAGTTTAAGCTTTG 57.480 32.000 20.34 12.62 38.64 2.77
2629 4209 7.094631 AGTTTTTCCGAAAGTTTAAGCTTTGT 58.905 30.769 20.34 0.00 38.64 2.83
2630 4210 8.245491 AGTTTTTCCGAAAGTTTAAGCTTTGTA 58.755 29.630 20.34 4.54 38.64 2.41
2631 4211 8.862074 GTTTTTCCGAAAGTTTAAGCTTTGTAA 58.138 29.630 20.34 9.60 38.64 2.41
2632 4212 8.983307 TTTTCCGAAAGTTTAAGCTTTGTAAA 57.017 26.923 20.34 13.96 38.64 2.01
2633 4213 8.623310 TTTCCGAAAGTTTAAGCTTTGTAAAG 57.377 30.769 20.34 7.60 38.64 1.85
2634 4214 7.556733 TCCGAAAGTTTAAGCTTTGTAAAGA 57.443 32.000 20.34 7.96 38.64 2.52
2635 4215 8.161699 TCCGAAAGTTTAAGCTTTGTAAAGAT 57.838 30.769 20.34 0.00 38.64 2.40
2636 4216 9.275398 TCCGAAAGTTTAAGCTTTGTAAAGATA 57.725 29.630 20.34 0.00 38.64 1.98
2637 4217 9.887406 CCGAAAGTTTAAGCTTTGTAAAGATAA 57.113 29.630 20.34 4.33 38.64 1.75
2656 4236 7.555306 AGATAAGAAGGAAAAATTACGCTCC 57.445 36.000 0.00 0.00 0.00 4.70
2657 4237 7.339482 AGATAAGAAGGAAAAATTACGCTCCT 58.661 34.615 0.00 0.00 40.10 3.69
2658 4238 5.629079 AAGAAGGAAAAATTACGCTCCTG 57.371 39.130 0.00 0.00 38.34 3.86
2659 4239 4.906618 AGAAGGAAAAATTACGCTCCTGA 58.093 39.130 0.00 0.00 38.34 3.86
2660 4240 5.501156 AGAAGGAAAAATTACGCTCCTGAT 58.499 37.500 0.00 0.00 38.34 2.90
2661 4241 5.355350 AGAAGGAAAAATTACGCTCCTGATG 59.645 40.000 0.00 0.00 38.34 3.07
2662 4242 3.378427 AGGAAAAATTACGCTCCTGATGC 59.622 43.478 0.00 0.00 36.92 3.91
2663 4243 3.489229 GGAAAAATTACGCTCCTGATGCC 60.489 47.826 0.00 0.00 0.00 4.40
2664 4244 2.717639 AAATTACGCTCCTGATGCCT 57.282 45.000 0.00 0.00 0.00 4.75
2665 4245 2.246719 AATTACGCTCCTGATGCCTC 57.753 50.000 0.00 0.00 0.00 4.70
2666 4246 0.394565 ATTACGCTCCTGATGCCTCC 59.605 55.000 0.00 0.00 0.00 4.30
2667 4247 2.016393 TTACGCTCCTGATGCCTCCG 62.016 60.000 0.00 0.00 0.00 4.63
2668 4248 2.904178 TACGCTCCTGATGCCTCCGA 62.904 60.000 0.00 0.00 0.00 4.55
2669 4249 2.903357 GCTCCTGATGCCTCCGAA 59.097 61.111 0.00 0.00 0.00 4.30
2670 4250 1.522580 GCTCCTGATGCCTCCGAAC 60.523 63.158 0.00 0.00 0.00 3.95
2671 4251 1.227089 CTCCTGATGCCTCCGAACG 60.227 63.158 0.00 0.00 0.00 3.95
2672 4252 2.202932 CCTGATGCCTCCGAACGG 60.203 66.667 6.94 6.94 0.00 4.44
2678 4258 3.795638 GCCTCCGAACGGCTTAAG 58.204 61.111 8.48 0.00 44.17 1.85
2679 4259 1.217244 GCCTCCGAACGGCTTAAGA 59.783 57.895 6.67 0.00 44.17 2.10
2680 4260 0.179081 GCCTCCGAACGGCTTAAGAT 60.179 55.000 6.67 0.00 44.17 2.40
2681 4261 1.854227 CCTCCGAACGGCTTAAGATC 58.146 55.000 6.67 0.00 34.68 2.75
2682 4262 1.538419 CCTCCGAACGGCTTAAGATCC 60.538 57.143 6.67 0.00 34.68 3.36
2683 4263 0.462789 TCCGAACGGCTTAAGATCCC 59.537 55.000 6.67 0.00 34.68 3.85
2684 4264 0.874607 CCGAACGGCTTAAGATCCCG 60.875 60.000 15.78 15.78 46.97 5.14
2685 4265 0.101759 CGAACGGCTTAAGATCCCGA 59.898 55.000 22.00 0.00 44.55 5.14
2686 4266 1.854227 GAACGGCTTAAGATCCCGAG 58.146 55.000 22.00 0.00 44.55 4.63
2687 4267 1.407979 GAACGGCTTAAGATCCCGAGA 59.592 52.381 22.00 0.00 44.55 4.04
2688 4268 1.705873 ACGGCTTAAGATCCCGAGAT 58.294 50.000 22.00 2.36 44.55 2.75
2689 4269 1.341531 ACGGCTTAAGATCCCGAGATG 59.658 52.381 22.00 0.00 44.55 2.90
2690 4270 1.802069 GGCTTAAGATCCCGAGATGC 58.198 55.000 6.67 0.00 30.90 3.91
2691 4271 1.070758 GGCTTAAGATCCCGAGATGCA 59.929 52.381 6.67 0.00 30.90 3.96
2692 4272 2.411904 GCTTAAGATCCCGAGATGCAG 58.588 52.381 6.67 0.00 30.90 4.41
2693 4273 2.036475 GCTTAAGATCCCGAGATGCAGA 59.964 50.000 6.67 0.00 30.90 4.26
2694 4274 3.860378 GCTTAAGATCCCGAGATGCAGAG 60.860 52.174 6.67 0.00 30.90 3.35
2695 4275 2.079170 AAGATCCCGAGATGCAGAGA 57.921 50.000 0.00 0.00 30.90 3.10
2696 4276 1.619654 AGATCCCGAGATGCAGAGAG 58.380 55.000 0.00 0.00 30.90 3.20
2697 4277 1.133513 AGATCCCGAGATGCAGAGAGT 60.134 52.381 0.00 0.00 30.90 3.24
2698 4278 2.107378 AGATCCCGAGATGCAGAGAGTA 59.893 50.000 0.00 0.00 30.90 2.59
2699 4279 1.681538 TCCCGAGATGCAGAGAGTAC 58.318 55.000 0.00 0.00 0.00 2.73
2700 4280 0.671251 CCCGAGATGCAGAGAGTACC 59.329 60.000 0.00 0.00 0.00 3.34
2701 4281 0.671251 CCGAGATGCAGAGAGTACCC 59.329 60.000 0.00 0.00 0.00 3.69
2702 4282 1.686355 CGAGATGCAGAGAGTACCCT 58.314 55.000 0.00 0.00 0.00 4.34
2703 4283 1.336440 CGAGATGCAGAGAGTACCCTG 59.664 57.143 0.00 0.00 0.00 4.45
2704 4284 2.383855 GAGATGCAGAGAGTACCCTGT 58.616 52.381 0.00 0.00 33.19 4.00
2705 4285 2.360801 GAGATGCAGAGAGTACCCTGTC 59.639 54.545 0.00 1.69 33.19 3.51
2706 4286 2.103373 GATGCAGAGAGTACCCTGTCA 58.897 52.381 0.00 7.69 33.49 3.58
2707 4287 1.257743 TGCAGAGAGTACCCTGTCAC 58.742 55.000 8.64 0.00 33.49 3.67
2708 4288 0.533032 GCAGAGAGTACCCTGTCACC 59.467 60.000 8.64 0.00 33.49 4.02
2709 4289 1.924731 CAGAGAGTACCCTGTCACCA 58.075 55.000 0.00 0.00 33.49 4.17
2710 4290 1.546476 CAGAGAGTACCCTGTCACCAC 59.454 57.143 0.00 0.00 33.49 4.16
2711 4291 1.429687 AGAGAGTACCCTGTCACCACT 59.570 52.381 0.00 0.00 33.49 4.00
2712 4292 1.819903 GAGAGTACCCTGTCACCACTC 59.180 57.143 0.00 0.00 36.67 3.51
2713 4293 1.147191 AGAGTACCCTGTCACCACTCA 59.853 52.381 0.00 0.00 38.45 3.41
2714 4294 2.180276 GAGTACCCTGTCACCACTCAT 58.820 52.381 0.00 0.00 36.48 2.90
2715 4295 1.902508 AGTACCCTGTCACCACTCATG 59.097 52.381 0.00 0.00 0.00 3.07
2716 4296 1.899814 GTACCCTGTCACCACTCATGA 59.100 52.381 0.00 0.00 0.00 3.07
2717 4297 0.687354 ACCCTGTCACCACTCATGAC 59.313 55.000 0.00 0.00 45.58 3.06
2718 4298 0.979665 CCCTGTCACCACTCATGACT 59.020 55.000 6.68 0.00 45.58 3.41
2719 4299 1.066573 CCCTGTCACCACTCATGACTC 60.067 57.143 6.68 0.00 45.58 3.36
2720 4300 1.620323 CCTGTCACCACTCATGACTCA 59.380 52.381 6.68 0.00 45.58 3.41
2721 4301 2.611473 CCTGTCACCACTCATGACTCAC 60.611 54.545 6.68 0.00 45.58 3.51
2722 4302 1.344438 TGTCACCACTCATGACTCACC 59.656 52.381 6.68 0.00 45.58 4.02
2723 4303 1.620819 GTCACCACTCATGACTCACCT 59.379 52.381 0.00 0.00 42.68 4.00
2724 4304 1.620323 TCACCACTCATGACTCACCTG 59.380 52.381 0.00 0.00 0.00 4.00
2725 4305 1.345741 CACCACTCATGACTCACCTGT 59.654 52.381 0.00 0.00 0.00 4.00
2726 4306 1.345741 ACCACTCATGACTCACCTGTG 59.654 52.381 0.00 0.00 0.00 3.66
2727 4307 1.345741 CCACTCATGACTCACCTGTGT 59.654 52.381 7.86 0.00 0.00 3.72
2728 4308 2.224378 CCACTCATGACTCACCTGTGTT 60.224 50.000 7.86 0.00 0.00 3.32
2729 4309 3.470709 CACTCATGACTCACCTGTGTTT 58.529 45.455 0.00 0.00 0.00 2.83
2730 4310 3.879295 CACTCATGACTCACCTGTGTTTT 59.121 43.478 0.00 0.00 0.00 2.43
2731 4311 4.336433 CACTCATGACTCACCTGTGTTTTT 59.664 41.667 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.566008 AAATAGTAGCATCGCATGAAAATTTC 57.434 30.769 0.00 0.00 0.00 2.17
4 5 8.786898 ACATAAATAGTAGCATCGCATGAAAAT 58.213 29.630 0.00 0.00 0.00 1.82
5 6 8.153479 ACATAAATAGTAGCATCGCATGAAAA 57.847 30.769 0.00 0.00 0.00 2.29
7 8 7.154656 AGACATAAATAGTAGCATCGCATGAA 58.845 34.615 0.00 0.00 0.00 2.57
8 9 6.691508 AGACATAAATAGTAGCATCGCATGA 58.308 36.000 0.00 0.00 0.00 3.07
9 10 6.957984 AGACATAAATAGTAGCATCGCATG 57.042 37.500 0.00 0.00 0.00 4.06
10 11 7.095060 CCAAAGACATAAATAGTAGCATCGCAT 60.095 37.037 0.00 0.00 0.00 4.73
11 12 6.202762 CCAAAGACATAAATAGTAGCATCGCA 59.797 38.462 0.00 0.00 0.00 5.10
12 13 6.202954 ACCAAAGACATAAATAGTAGCATCGC 59.797 38.462 0.00 0.00 0.00 4.58
13 14 7.715265 ACCAAAGACATAAATAGTAGCATCG 57.285 36.000 0.00 0.00 0.00 3.84
25 26 9.581289 TCTCATTCCTTTAAACCAAAGACATAA 57.419 29.630 0.00 0.00 45.62 1.90
26 27 9.010029 GTCTCATTCCTTTAAACCAAAGACATA 57.990 33.333 0.00 0.00 45.62 2.29
27 28 7.505585 TGTCTCATTCCTTTAAACCAAAGACAT 59.494 33.333 0.00 0.00 45.62 3.06
28 29 6.831353 TGTCTCATTCCTTTAAACCAAAGACA 59.169 34.615 0.00 0.00 45.62 3.41
29 30 7.272037 TGTCTCATTCCTTTAAACCAAAGAC 57.728 36.000 0.00 0.00 45.62 3.01
30 31 7.889873 TTGTCTCATTCCTTTAAACCAAAGA 57.110 32.000 0.00 0.00 45.62 2.52
31 32 8.413229 TCTTTGTCTCATTCCTTTAAACCAAAG 58.587 33.333 0.00 0.00 42.90 2.77
32 33 8.299990 TCTTTGTCTCATTCCTTTAAACCAAA 57.700 30.769 0.00 0.00 0.00 3.28
33 34 7.889873 TCTTTGTCTCATTCCTTTAAACCAA 57.110 32.000 0.00 0.00 0.00 3.67
34 35 7.777910 TCTTCTTTGTCTCATTCCTTTAAACCA 59.222 33.333 0.00 0.00 0.00 3.67
35 36 8.166422 TCTTCTTTGTCTCATTCCTTTAAACC 57.834 34.615 0.00 0.00 0.00 3.27
38 39 8.796475 CCATTCTTCTTTGTCTCATTCCTTTAA 58.204 33.333 0.00 0.00 0.00 1.52
39 40 8.163408 TCCATTCTTCTTTGTCTCATTCCTTTA 58.837 33.333 0.00 0.00 0.00 1.85
40 41 7.006509 TCCATTCTTCTTTGTCTCATTCCTTT 58.993 34.615 0.00 0.00 0.00 3.11
41 42 6.546484 TCCATTCTTCTTTGTCTCATTCCTT 58.454 36.000 0.00 0.00 0.00 3.36
42 43 6.131972 TCCATTCTTCTTTGTCTCATTCCT 57.868 37.500 0.00 0.00 0.00 3.36
43 44 5.163673 GCTCCATTCTTCTTTGTCTCATTCC 60.164 44.000 0.00 0.00 0.00 3.01
44 45 5.447010 CGCTCCATTCTTCTTTGTCTCATTC 60.447 44.000 0.00 0.00 0.00 2.67
45 46 4.394300 CGCTCCATTCTTCTTTGTCTCATT 59.606 41.667 0.00 0.00 0.00 2.57
46 47 3.937706 CGCTCCATTCTTCTTTGTCTCAT 59.062 43.478 0.00 0.00 0.00 2.90
47 48 3.006859 TCGCTCCATTCTTCTTTGTCTCA 59.993 43.478 0.00 0.00 0.00 3.27
48 49 3.589988 TCGCTCCATTCTTCTTTGTCTC 58.410 45.455 0.00 0.00 0.00 3.36
49 50 3.685139 TCGCTCCATTCTTCTTTGTCT 57.315 42.857 0.00 0.00 0.00 3.41
50 51 3.425492 GCTTCGCTCCATTCTTCTTTGTC 60.425 47.826 0.00 0.00 0.00 3.18
51 52 2.485814 GCTTCGCTCCATTCTTCTTTGT 59.514 45.455 0.00 0.00 0.00 2.83
52 53 2.485426 TGCTTCGCTCCATTCTTCTTTG 59.515 45.455 0.00 0.00 0.00 2.77
53 54 2.783135 TGCTTCGCTCCATTCTTCTTT 58.217 42.857 0.00 0.00 0.00 2.52
54 55 2.479566 TGCTTCGCTCCATTCTTCTT 57.520 45.000 0.00 0.00 0.00 2.52
55 56 2.079925 GTTGCTTCGCTCCATTCTTCT 58.920 47.619 0.00 0.00 0.00 2.85
56 57 1.201965 CGTTGCTTCGCTCCATTCTTC 60.202 52.381 0.00 0.00 0.00 2.87
57 58 0.798776 CGTTGCTTCGCTCCATTCTT 59.201 50.000 0.00 0.00 0.00 2.52
58 59 1.021390 CCGTTGCTTCGCTCCATTCT 61.021 55.000 0.00 0.00 0.00 2.40
59 60 1.019278 TCCGTTGCTTCGCTCCATTC 61.019 55.000 0.00 0.00 0.00 2.67
60 61 1.003839 TCCGTTGCTTCGCTCCATT 60.004 52.632 0.00 0.00 0.00 3.16
61 62 1.448540 CTCCGTTGCTTCGCTCCAT 60.449 57.895 0.00 0.00 0.00 3.41
62 63 2.048222 CTCCGTTGCTTCGCTCCA 60.048 61.111 0.00 0.00 0.00 3.86
63 64 0.949105 TTTCTCCGTTGCTTCGCTCC 60.949 55.000 0.00 0.00 0.00 4.70
64 65 0.164002 GTTTCTCCGTTGCTTCGCTC 59.836 55.000 0.00 0.00 0.00 5.03
65 66 1.557443 CGTTTCTCCGTTGCTTCGCT 61.557 55.000 0.00 0.00 0.00 4.93
66 67 1.154654 CGTTTCTCCGTTGCTTCGC 60.155 57.895 0.00 0.00 0.00 4.70
67 68 0.856641 TTCGTTTCTCCGTTGCTTCG 59.143 50.000 0.00 0.00 0.00 3.79
68 69 2.132762 TCTTCGTTTCTCCGTTGCTTC 58.867 47.619 0.00 0.00 0.00 3.86
69 70 2.234300 TCTTCGTTTCTCCGTTGCTT 57.766 45.000 0.00 0.00 0.00 3.91
70 71 2.234300 TTCTTCGTTTCTCCGTTGCT 57.766 45.000 0.00 0.00 0.00 3.91
71 72 3.537793 AATTCTTCGTTTCTCCGTTGC 57.462 42.857 0.00 0.00 0.00 4.17
72 73 5.090652 TCAAATTCTTCGTTTCTCCGTTG 57.909 39.130 0.00 0.00 0.00 4.10
73 74 5.065474 TGTTCAAATTCTTCGTTTCTCCGTT 59.935 36.000 0.00 0.00 0.00 4.44
74 75 4.573201 TGTTCAAATTCTTCGTTTCTCCGT 59.427 37.500 0.00 0.00 0.00 4.69
75 76 5.090652 TGTTCAAATTCTTCGTTTCTCCG 57.909 39.130 0.00 0.00 0.00 4.63
76 77 6.086871 GGATGTTCAAATTCTTCGTTTCTCC 58.913 40.000 0.00 0.00 0.00 3.71
77 78 6.668323 TGGATGTTCAAATTCTTCGTTTCTC 58.332 36.000 0.00 0.00 0.00 2.87
78 79 6.633500 TGGATGTTCAAATTCTTCGTTTCT 57.367 33.333 0.00 0.00 0.00 2.52
79 80 6.918022 AGTTGGATGTTCAAATTCTTCGTTTC 59.082 34.615 0.00 0.00 0.00 2.78
80 81 6.697019 CAGTTGGATGTTCAAATTCTTCGTTT 59.303 34.615 0.00 0.00 0.00 3.60
81 82 6.039270 TCAGTTGGATGTTCAAATTCTTCGTT 59.961 34.615 0.00 0.00 0.00 3.85
82 83 5.530915 TCAGTTGGATGTTCAAATTCTTCGT 59.469 36.000 0.00 0.00 0.00 3.85
83 84 6.000891 TCAGTTGGATGTTCAAATTCTTCG 57.999 37.500 0.00 0.00 0.00 3.79
84 85 7.031975 GGATCAGTTGGATGTTCAAATTCTTC 58.968 38.462 0.00 0.00 36.00 2.87
85 86 6.723052 AGGATCAGTTGGATGTTCAAATTCTT 59.277 34.615 0.00 0.00 36.00 2.52
86 87 6.251471 AGGATCAGTTGGATGTTCAAATTCT 58.749 36.000 0.00 0.00 36.00 2.40
114 115 5.595885 TCTTCATGCACGGAAATTTGAAAA 58.404 33.333 0.00 0.00 0.00 2.29
121 124 2.416547 CTCGTTCTTCATGCACGGAAAT 59.583 45.455 0.00 0.00 36.06 2.17
126 129 1.702886 AGTCTCGTTCTTCATGCACG 58.297 50.000 0.00 0.00 36.68 5.34
127 130 5.786401 ATTTAGTCTCGTTCTTCATGCAC 57.214 39.130 0.00 0.00 0.00 4.57
154 157 5.036117 AGATGGGTTGTTATTATGCGACT 57.964 39.130 0.00 0.00 0.00 4.18
172 175 8.627208 ACCACATGGAAATTTATAGCTAGATG 57.373 34.615 4.53 0.00 38.94 2.90
189 192 5.599732 TCAAATCAAAGTCAAACCACATGG 58.400 37.500 0.00 0.00 42.17 3.66
197 200 5.766150 ACCACGATCAAATCAAAGTCAAA 57.234 34.783 0.00 0.00 0.00 2.69
198 201 5.766150 AACCACGATCAAATCAAAGTCAA 57.234 34.783 0.00 0.00 0.00 3.18
199 202 7.447374 AATAACCACGATCAAATCAAAGTCA 57.553 32.000 0.00 0.00 0.00 3.41
200 203 7.640240 GCTAATAACCACGATCAAATCAAAGTC 59.360 37.037 0.00 0.00 0.00 3.01
201 204 7.120579 TGCTAATAACCACGATCAAATCAAAGT 59.879 33.333 0.00 0.00 0.00 2.66
202 205 7.471721 TGCTAATAACCACGATCAAATCAAAG 58.528 34.615 0.00 0.00 0.00 2.77
203 206 7.384439 TGCTAATAACCACGATCAAATCAAA 57.616 32.000 0.00 0.00 0.00 2.69
204 207 6.993786 TGCTAATAACCACGATCAAATCAA 57.006 33.333 0.00 0.00 0.00 2.57
205 208 7.566760 AATGCTAATAACCACGATCAAATCA 57.433 32.000 0.00 0.00 0.00 2.57
206 209 8.345565 AGAAATGCTAATAACCACGATCAAATC 58.654 33.333 0.00 0.00 0.00 2.17
207 210 8.225603 AGAAATGCTAATAACCACGATCAAAT 57.774 30.769 0.00 0.00 0.00 2.32
273 287 8.545229 AGAGAATTTGTGAACATGAGAGTTAG 57.455 34.615 0.00 0.00 0.00 2.34
303 317 1.430632 GGACAGGAATGCATGTGCG 59.569 57.895 0.00 0.00 45.83 5.34
320 334 6.096705 TGGCAATAGAAAAACACATGGATAGG 59.903 38.462 0.00 0.00 0.00 2.57
339 354 9.915629 TTTGTAAGATTATAAAAACGTGGCAAT 57.084 25.926 0.00 0.00 0.00 3.56
354 477 6.206634 CAGTGCTCCTTTGGTTTGTAAGATTA 59.793 38.462 0.00 0.00 0.00 1.75
358 481 3.882888 TCAGTGCTCCTTTGGTTTGTAAG 59.117 43.478 0.00 0.00 0.00 2.34
361 484 2.301346 CTCAGTGCTCCTTTGGTTTGT 58.699 47.619 0.00 0.00 0.00 2.83
381 504 1.338020 ACAAAGCAGTGGCAAAGCTAC 59.662 47.619 14.32 0.00 44.61 3.58
497 621 0.613012 ATGAACCCAGCTGCCCTTTC 60.613 55.000 8.66 7.92 0.00 2.62
553 677 3.930229 TCGCACGTGCATAAGAAAGTATT 59.070 39.130 37.03 0.00 42.21 1.89
554 678 3.517602 TCGCACGTGCATAAGAAAGTAT 58.482 40.909 37.03 0.00 42.21 2.12
634 892 3.367498 CCTTCCGAGTCTCGAGTTTCAAT 60.367 47.826 23.74 0.00 43.74 2.57
641 899 1.431440 CTGCCTTCCGAGTCTCGAG 59.569 63.158 23.74 13.28 43.74 4.04
642 900 2.046864 CCTGCCTTCCGAGTCTCGA 61.047 63.158 23.74 7.04 43.74 4.04
643 901 2.046864 TCCTGCCTTCCGAGTCTCG 61.047 63.158 15.53 15.53 40.07 4.04
644 902 1.513622 GTCCTGCCTTCCGAGTCTC 59.486 63.158 0.00 0.00 0.00 3.36
645 903 1.985116 GGTCCTGCCTTCCGAGTCT 60.985 63.158 0.00 0.00 0.00 3.24
646 904 2.232298 CTGGTCCTGCCTTCCGAGTC 62.232 65.000 0.00 0.00 38.35 3.36
647 905 2.203788 TGGTCCTGCCTTCCGAGT 60.204 61.111 0.00 0.00 38.35 4.18
648 906 1.831652 AACTGGTCCTGCCTTCCGAG 61.832 60.000 0.00 0.00 38.35 4.63
652 910 0.687354 TGAGAACTGGTCCTGCCTTC 59.313 55.000 0.00 0.00 38.35 3.46
653 911 0.398318 GTGAGAACTGGTCCTGCCTT 59.602 55.000 0.00 0.00 38.35 4.35
664 926 3.279434 GTCAAACCCAACAGTGAGAACT 58.721 45.455 0.00 0.00 0.00 3.01
669 931 1.098712 GCGGTCAAACCCAACAGTGA 61.099 55.000 0.00 0.00 33.75 3.41
670 932 1.358759 GCGGTCAAACCCAACAGTG 59.641 57.895 0.00 0.00 33.75 3.66
688 950 3.144120 CTCCTCTGGATGTCGCCGG 62.144 68.421 0.00 0.00 35.54 6.13
697 959 6.671340 TGAACTAGTAGTACTACTCCTCTGGA 59.329 42.308 33.47 16.74 44.58 3.86
709 971 6.822506 ACGTAAAGTCGTGAACTAGTAGTAC 58.177 40.000 2.50 0.00 42.56 2.73
712 974 6.473521 CCTACGTAAAGTCGTGAACTAGTAG 58.526 44.000 0.00 0.00 43.93 2.57
715 977 4.094212 GCCTACGTAAAGTCGTGAACTAG 58.906 47.826 0.00 0.00 43.93 2.57
721 983 1.468736 GGGAGCCTACGTAAAGTCGTG 60.469 57.143 0.00 0.00 43.93 4.35
776 1047 1.948611 GCTCACGGGTGCAAGGATTAA 60.949 52.381 6.88 0.00 33.80 1.40
824 1098 0.038890 TTGGAATTGGATGGACGCCA 59.961 50.000 1.01 1.01 38.19 5.69
911 1208 1.673808 GGTAGGGACGTAGGGTGCAG 61.674 65.000 0.00 0.00 39.01 4.41
944 1249 4.517703 CGAGACGAGACGCCGGTC 62.518 72.222 1.90 0.00 43.76 4.79
979 1284 4.410400 GTTCTGGAGGTGCGGGGG 62.410 72.222 0.00 0.00 0.00 5.40
994 1299 5.737063 GCTTGATTGATGTGTTTGTGAGGTT 60.737 40.000 0.00 0.00 0.00 3.50
1040 1346 0.667993 GAGGCCGAGACTGATCAGAG 59.332 60.000 29.27 15.57 0.00 3.35
1076 1387 1.000283 CGACTTCACCAAGCAGTCTCT 60.000 52.381 0.00 0.00 35.70 3.10
1077 1388 1.423395 CGACTTCACCAAGCAGTCTC 58.577 55.000 0.00 0.00 35.70 3.36
1078 1389 0.601311 GCGACTTCACCAAGCAGTCT 60.601 55.000 0.00 0.00 35.70 3.24
1079 1390 0.601311 AGCGACTTCACCAAGCAGTC 60.601 55.000 0.00 0.00 34.68 3.51
1080 1391 0.882042 CAGCGACTTCACCAAGCAGT 60.882 55.000 0.00 0.00 32.09 4.40
1093 1406 0.438830 GATCACACGAAACCAGCGAC 59.561 55.000 0.00 0.00 0.00 5.19
1124 1438 2.435805 GCTCACCATCTCCAACTCCATA 59.564 50.000 0.00 0.00 0.00 2.74
1373 2540 4.974438 TTCTGGTGGGCGAGGGGT 62.974 66.667 0.00 0.00 0.00 4.95
1468 2644 3.190079 CACGCACCGAGTACTACTACTA 58.810 50.000 0.00 0.00 32.96 1.82
1469 2645 2.005451 CACGCACCGAGTACTACTACT 58.995 52.381 0.00 0.00 35.77 2.57
1470 2646 1.530646 GCACGCACCGAGTACTACTAC 60.531 57.143 0.00 0.00 0.00 2.73
1471 2647 0.729116 GCACGCACCGAGTACTACTA 59.271 55.000 0.00 0.00 0.00 1.82
1472 2648 0.959372 AGCACGCACCGAGTACTACT 60.959 55.000 0.00 0.00 0.00 2.57
1473 2649 0.797249 CAGCACGCACCGAGTACTAC 60.797 60.000 0.00 0.00 0.00 2.73
1625 3194 1.109296 CAAAACACAAGCACGTACGC 58.891 50.000 16.72 0.00 0.00 4.42
1660 3229 7.601856 TGATATGAACAAAACTGTTCCATTCC 58.398 34.615 13.81 2.93 45.41 3.01
1833 3406 2.355115 GGCGGGTTTGACTCCCAT 59.645 61.111 1.91 0.00 44.81 4.00
2050 3623 7.860373 GTGCAATAGACATGACAACTTTTAACA 59.140 33.333 0.00 0.00 0.00 2.41
2241 3815 7.387948 GTGTCAATTCCAGTACTTTGACTATGT 59.612 37.037 26.67 0.00 45.12 2.29
2264 3838 5.694458 GGCAATTTTAGTTTTTCGATGGTGT 59.306 36.000 0.00 0.00 0.00 4.16
2267 3841 6.589523 TCATGGCAATTTTAGTTTTTCGATGG 59.410 34.615 0.00 0.00 0.00 3.51
2332 3906 1.070134 ACACCGCAGTTGTCATAGTGT 59.930 47.619 0.00 0.00 32.42 3.55
2346 3920 3.315191 AGTTGCCATGATATTTACACCGC 59.685 43.478 0.00 0.00 0.00 5.68
2356 3930 2.533916 TGCCCAAAAGTTGCCATGATA 58.466 42.857 0.00 0.00 0.00 2.15
2432 4012 3.119779 TCCGTTTTCACCATTAAATCCGC 60.120 43.478 0.00 0.00 0.00 5.54
2630 4210 8.459635 GGAGCGTAATTTTTCCTTCTTATCTTT 58.540 33.333 0.00 0.00 0.00 2.52
2631 4211 7.829706 AGGAGCGTAATTTTTCCTTCTTATCTT 59.170 33.333 0.00 0.00 36.69 2.40
2632 4212 7.281100 CAGGAGCGTAATTTTTCCTTCTTATCT 59.719 37.037 0.00 0.00 37.97 1.98
2633 4213 7.280205 TCAGGAGCGTAATTTTTCCTTCTTATC 59.720 37.037 0.00 0.00 37.97 1.75
2634 4214 7.110155 TCAGGAGCGTAATTTTTCCTTCTTAT 58.890 34.615 0.00 0.00 37.97 1.73
2635 4215 6.469410 TCAGGAGCGTAATTTTTCCTTCTTA 58.531 36.000 0.00 0.00 37.97 2.10
2636 4216 5.313712 TCAGGAGCGTAATTTTTCCTTCTT 58.686 37.500 0.00 0.00 37.97 2.52
2637 4217 4.906618 TCAGGAGCGTAATTTTTCCTTCT 58.093 39.130 0.00 0.00 37.97 2.85
2638 4218 5.573146 CATCAGGAGCGTAATTTTTCCTTC 58.427 41.667 0.00 0.00 37.97 3.46
2639 4219 4.142381 GCATCAGGAGCGTAATTTTTCCTT 60.142 41.667 0.00 0.00 37.97 3.36
2640 4220 3.378427 GCATCAGGAGCGTAATTTTTCCT 59.622 43.478 0.00 0.00 40.63 3.36
2641 4221 3.489229 GGCATCAGGAGCGTAATTTTTCC 60.489 47.826 0.00 0.00 0.00 3.13
2642 4222 3.378427 AGGCATCAGGAGCGTAATTTTTC 59.622 43.478 0.00 0.00 0.00 2.29
2643 4223 3.356290 AGGCATCAGGAGCGTAATTTTT 58.644 40.909 0.00 0.00 0.00 1.94
2644 4224 2.945668 GAGGCATCAGGAGCGTAATTTT 59.054 45.455 0.00 0.00 0.00 1.82
2645 4225 2.565841 GAGGCATCAGGAGCGTAATTT 58.434 47.619 0.00 0.00 0.00 1.82
2646 4226 1.202698 GGAGGCATCAGGAGCGTAATT 60.203 52.381 0.00 0.00 0.00 1.40
2647 4227 0.394565 GGAGGCATCAGGAGCGTAAT 59.605 55.000 0.00 0.00 0.00 1.89
2648 4228 1.823295 GGAGGCATCAGGAGCGTAA 59.177 57.895 0.00 0.00 0.00 3.18
2649 4229 2.490148 CGGAGGCATCAGGAGCGTA 61.490 63.158 0.00 0.00 0.00 4.42
2650 4230 3.842923 CGGAGGCATCAGGAGCGT 61.843 66.667 0.00 0.00 0.00 5.07
2651 4231 3.081311 TTCGGAGGCATCAGGAGCG 62.081 63.158 0.00 0.00 0.00 5.03
2652 4232 1.522580 GTTCGGAGGCATCAGGAGC 60.523 63.158 0.00 0.00 0.00 4.70
2653 4233 1.227089 CGTTCGGAGGCATCAGGAG 60.227 63.158 0.00 0.00 0.00 3.69
2654 4234 2.721167 CCGTTCGGAGGCATCAGGA 61.721 63.158 5.19 0.00 0.00 3.86
2655 4235 2.202932 CCGTTCGGAGGCATCAGG 60.203 66.667 5.19 0.00 0.00 3.86
2662 4242 1.538419 GGATCTTAAGCCGTTCGGAGG 60.538 57.143 15.69 0.00 0.00 4.30
2663 4243 1.538419 GGGATCTTAAGCCGTTCGGAG 60.538 57.143 15.69 3.54 0.00 4.63
2664 4244 0.462789 GGGATCTTAAGCCGTTCGGA 59.537 55.000 15.69 0.00 0.00 4.55
2665 4245 0.874607 CGGGATCTTAAGCCGTTCGG 60.875 60.000 10.77 6.90 0.00 4.30
2666 4246 0.101759 TCGGGATCTTAAGCCGTTCG 59.898 55.000 16.45 8.60 0.00 3.95
2667 4247 1.407979 TCTCGGGATCTTAAGCCGTTC 59.592 52.381 16.45 3.79 0.00 3.95
2668 4248 1.481871 TCTCGGGATCTTAAGCCGTT 58.518 50.000 16.45 0.00 0.00 4.44
2669 4249 1.341531 CATCTCGGGATCTTAAGCCGT 59.658 52.381 16.45 0.00 0.00 5.68
2670 4250 1.937108 GCATCTCGGGATCTTAAGCCG 60.937 57.143 12.31 12.31 0.00 5.52
2671 4251 1.070758 TGCATCTCGGGATCTTAAGCC 59.929 52.381 0.00 0.00 0.00 4.35
2672 4252 2.036475 TCTGCATCTCGGGATCTTAAGC 59.964 50.000 0.00 0.00 0.00 3.09
2673 4253 3.571828 TCTCTGCATCTCGGGATCTTAAG 59.428 47.826 0.00 0.00 0.00 1.85
2674 4254 3.566351 TCTCTGCATCTCGGGATCTTAA 58.434 45.455 0.00 0.00 0.00 1.85
2675 4255 3.153130 CTCTCTGCATCTCGGGATCTTA 58.847 50.000 0.00 0.00 0.00 2.10
2676 4256 1.962807 CTCTCTGCATCTCGGGATCTT 59.037 52.381 0.00 0.00 0.00 2.40
2677 4257 1.133513 ACTCTCTGCATCTCGGGATCT 60.134 52.381 0.00 0.00 0.00 2.75
2678 4258 1.327303 ACTCTCTGCATCTCGGGATC 58.673 55.000 0.00 0.00 0.00 3.36
2679 4259 2.235016 GTACTCTCTGCATCTCGGGAT 58.765 52.381 0.00 0.00 0.00 3.85
2680 4260 1.681538 GTACTCTCTGCATCTCGGGA 58.318 55.000 0.00 0.00 0.00 5.14
2681 4261 0.671251 GGTACTCTCTGCATCTCGGG 59.329 60.000 0.00 0.00 0.00 5.14
2682 4262 0.671251 GGGTACTCTCTGCATCTCGG 59.329 60.000 0.00 0.00 0.00 4.63
2683 4263 1.336440 CAGGGTACTCTCTGCATCTCG 59.664 57.143 0.00 0.00 0.00 4.04
2684 4264 2.360801 GACAGGGTACTCTCTGCATCTC 59.639 54.545 0.00 0.00 34.57 2.75
2685 4265 2.291865 TGACAGGGTACTCTCTGCATCT 60.292 50.000 0.00 0.00 34.57 2.90
2686 4266 2.103373 TGACAGGGTACTCTCTGCATC 58.897 52.381 0.00 0.00 34.57 3.91
2687 4267 1.827969 GTGACAGGGTACTCTCTGCAT 59.172 52.381 0.00 0.00 34.57 3.96
2688 4268 1.257743 GTGACAGGGTACTCTCTGCA 58.742 55.000 0.00 0.00 34.57 4.41
2689 4269 0.533032 GGTGACAGGGTACTCTCTGC 59.467 60.000 0.00 0.00 34.57 4.26
2690 4270 1.546476 GTGGTGACAGGGTACTCTCTG 59.454 57.143 0.00 1.06 44.46 3.35
2691 4271 1.429687 AGTGGTGACAGGGTACTCTCT 59.570 52.381 0.00 0.00 44.46 3.10
2692 4272 1.819903 GAGTGGTGACAGGGTACTCTC 59.180 57.143 0.00 0.00 44.46 3.20
2693 4273 1.147191 TGAGTGGTGACAGGGTACTCT 59.853 52.381 0.00 0.00 44.46 3.24
2694 4274 1.629043 TGAGTGGTGACAGGGTACTC 58.371 55.000 0.00 0.00 44.46 2.59
2695 4275 1.902508 CATGAGTGGTGACAGGGTACT 59.097 52.381 0.00 0.00 44.46 2.73
2696 4276 1.899814 TCATGAGTGGTGACAGGGTAC 59.100 52.381 0.00 0.00 44.46 3.34
2697 4277 1.899814 GTCATGAGTGGTGACAGGGTA 59.100 52.381 0.00 0.00 44.13 3.69
2698 4278 0.687354 GTCATGAGTGGTGACAGGGT 59.313 55.000 0.00 0.00 44.13 4.34
2699 4279 0.979665 AGTCATGAGTGGTGACAGGG 59.020 55.000 1.14 0.00 46.46 4.45
2700 4280 1.620323 TGAGTCATGAGTGGTGACAGG 59.380 52.381 8.05 0.00 46.46 4.00
2701 4281 2.611473 GGTGAGTCATGAGTGGTGACAG 60.611 54.545 8.05 0.00 46.46 3.51
2702 4282 1.344438 GGTGAGTCATGAGTGGTGACA 59.656 52.381 8.05 0.00 46.46 3.58
2703 4283 1.620819 AGGTGAGTCATGAGTGGTGAC 59.379 52.381 8.05 0.00 44.85 3.67
2704 4284 1.620323 CAGGTGAGTCATGAGTGGTGA 59.380 52.381 8.05 0.00 0.00 4.02
2705 4285 1.345741 ACAGGTGAGTCATGAGTGGTG 59.654 52.381 8.05 2.46 0.00 4.17
2706 4286 1.345741 CACAGGTGAGTCATGAGTGGT 59.654 52.381 8.05 0.00 0.00 4.16
2707 4287 1.345741 ACACAGGTGAGTCATGAGTGG 59.654 52.381 8.05 0.00 31.37 4.00
2708 4288 2.827800 ACACAGGTGAGTCATGAGTG 57.172 50.000 8.05 15.78 31.37 3.51
2709 4289 3.845781 AAACACAGGTGAGTCATGAGT 57.154 42.857 1.67 1.67 33.63 3.41


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

AutoCloner maintained by Alex Coulton.