Multiple sequence alignment - TraesCS5B01G271400

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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 TraesCS5B01G271400 chr5B 100.000 5477 0 0 1 5477 457119784 457125260 0.000000e+00 10115.0
1 TraesCS5B01G271400 chr5B 85.714 364 30 5 570 915 457049365 457049724 1.120000e-96 364.0
2 TraesCS5B01G271400 chr5B 86.713 143 7 7 447 582 457018659 457018796 1.230000e-31 148.0
3 TraesCS5B01G271400 chr5D 89.357 3796 230 102 7 3708 381020739 381024454 0.000000e+00 4612.0
4 TraesCS5B01G271400 chr5D 89.399 1764 127 31 3728 5476 381024440 381026158 0.000000e+00 2167.0
5 TraesCS5B01G271400 chr5D 89.344 122 5 3 6 127 380852392 380852505 4.420000e-31 147.0
6 TraesCS5B01G271400 chr5D 92.958 71 4 1 442 511 380852758 380852828 9.710000e-18 102.0
7 TraesCS5B01G271400 chr5A 89.904 1763 114 33 3728 5477 481892025 481893736 0.000000e+00 2211.0
8 TraesCS5B01G271400 chr5A 92.774 1467 82 14 1929 3377 481890080 481891540 0.000000e+00 2100.0
9 TraesCS5B01G271400 chr5A 83.683 1575 117 68 102 1612 481888309 481889807 0.000000e+00 1356.0
10 TraesCS5B01G271400 chr5A 91.667 360 18 6 3361 3708 481891680 481892039 6.380000e-134 488.0
11 TraesCS5B01G271400 chr5A 92.821 195 14 0 1743 1937 481889859 481890053 3.230000e-72 283.0
12 TraesCS5B01G271400 chr5A 90.909 77 5 2 14 88 481888244 481888320 9.710000e-18 102.0
13 TraesCS5B01G271400 chr7A 76.580 269 47 14 3411 3676 232588176 232588431 3.440000e-27 134.0
14 TraesCS5B01G271400 chr7B 90.816 98 9 0 3411 3508 179256329 179256232 1.240000e-26 132.0
15 TraesCS5B01G271400 chr7D 89.796 98 10 0 3411 3508 220276441 220276538 5.760000e-25 126.0
16 TraesCS5B01G271400 chr1A 95.082 61 3 0 2915 2975 333536584 333536644 4.520000e-16 97.1


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 TraesCS5B01G271400 chr5B 457119784 457125260 5476 False 10115.0 10115 100.000 1 5477 1 chr5B.!!$F3 5476
1 TraesCS5B01G271400 chr5D 381020739 381026158 5419 False 3389.5 4612 89.378 7 5476 2 chr5D.!!$F2 5469
2 TraesCS5B01G271400 chr5A 481888244 481893736 5492 False 1090.0 2211 90.293 14 5477 6 chr5A.!!$F1 5463

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
90 92 0.179032 AAGGAACATCACCACACGCA 60.179 50.000 0.00 0.00 0.00 5.24 F
1627 1754 0.181114 ACCTGCGTGTATGCATGGAT 59.819 50.000 10.16 4.68 45.26 3.41 F
1804 1932 0.948678 TCCTTGTGTGCCGTTTTAGC 59.051 50.000 0.00 0.00 0.00 3.09 F
2730 2915 1.146041 TATTGATGAGGGCGCGCTT 59.854 52.632 32.29 19.89 0.00 4.68 F
3380 3565 1.174783 AAGATGCAAGGCTTCAGCTG 58.825 50.000 7.63 7.63 41.70 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2157 0.035630 AGTGCCTTCTGTGGAGCATC 60.036 55.0 0.00 0.00 37.60 3.91 R
2912 3097 0.319555 CTTCGAAGCCGGTCTTGACA 60.320 55.0 13.09 0.00 34.56 3.58 R
3764 4122 0.526954 CGCAGCCTGGCAATTCATTC 60.527 55.0 22.65 0.00 0.00 2.67 R
4010 4368 0.391927 CGGAATGGTGAAGGGCGTAA 60.392 55.0 0.00 0.00 0.00 3.18 R
4960 5335 0.391130 ATGCATTTTGCTGCTGCCTG 60.391 50.0 13.47 6.64 45.31 4.85 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
24 25 1.241315 AACGATGGAAAAGGCGGTGG 61.241 55.000 0.00 0.00 0.00 4.61
26 27 1.001393 GATGGAAAAGGCGGTGGGA 60.001 57.895 0.00 0.00 0.00 4.37
76 78 5.164954 CGTTTCCACAAGAAAAACAAGGAA 58.835 37.500 0.00 0.00 45.93 3.36
85 87 5.262588 AGAAAAACAAGGAACATCACCAC 57.737 39.130 0.00 0.00 0.00 4.16
86 88 4.709397 AGAAAAACAAGGAACATCACCACA 59.291 37.500 0.00 0.00 0.00 4.17
87 89 4.385358 AAAACAAGGAACATCACCACAC 57.615 40.909 0.00 0.00 0.00 3.82
88 90 1.593196 ACAAGGAACATCACCACACG 58.407 50.000 0.00 0.00 0.00 4.49
89 91 0.238289 CAAGGAACATCACCACACGC 59.762 55.000 0.00 0.00 0.00 5.34
90 92 0.179032 AAGGAACATCACCACACGCA 60.179 50.000 0.00 0.00 0.00 5.24
91 93 0.603707 AGGAACATCACCACACGCAG 60.604 55.000 0.00 0.00 0.00 5.18
99 101 0.601046 CACCACACGCAGTCACTCAT 60.601 55.000 0.00 0.00 41.61 2.90
127 137 1.915266 CTCACTCACCTGCCCTCCA 60.915 63.158 0.00 0.00 0.00 3.86
131 141 1.062488 ACTCACCTGCCCTCCAAACT 61.062 55.000 0.00 0.00 0.00 2.66
134 144 0.675633 CACCTGCCCTCCAAACTTTG 59.324 55.000 0.00 0.00 0.00 2.77
135 145 1.115326 ACCTGCCCTCCAAACTTTGC 61.115 55.000 0.00 0.00 0.00 3.68
139 149 1.133325 TGCCCTCCAAACTTTGCCTTA 60.133 47.619 0.00 0.00 0.00 2.69
140 150 1.967779 GCCCTCCAAACTTTGCCTTAA 59.032 47.619 0.00 0.00 0.00 1.85
141 151 2.367241 GCCCTCCAAACTTTGCCTTAAA 59.633 45.455 0.00 0.00 0.00 1.52
142 152 3.181459 GCCCTCCAAACTTTGCCTTAAAA 60.181 43.478 0.00 0.00 0.00 1.52
143 153 4.684757 GCCCTCCAAACTTTGCCTTAAAAA 60.685 41.667 0.00 0.00 0.00 1.94
162 172 4.048470 GAACCAGCCCTCCCACCC 62.048 72.222 0.00 0.00 0.00 4.61
239 249 6.980978 TCATTCTCGTATCTTCTCCATCAAAC 59.019 38.462 0.00 0.00 0.00 2.93
275 295 1.903877 ATTAGCCAGCGCAGTGAGGT 61.904 55.000 11.47 0.00 37.52 3.85
294 314 5.131142 TGAGGTAGGAGAGGGATTTCATTTC 59.869 44.000 0.00 0.00 0.00 2.17
295 315 5.039645 AGGTAGGAGAGGGATTTCATTTCA 58.960 41.667 0.00 0.00 0.00 2.69
296 316 5.674035 AGGTAGGAGAGGGATTTCATTTCAT 59.326 40.000 0.00 0.00 0.00 2.57
297 317 6.161170 AGGTAGGAGAGGGATTTCATTTCATT 59.839 38.462 0.00 0.00 0.00 2.57
298 318 6.836007 GGTAGGAGAGGGATTTCATTTCATTT 59.164 38.462 0.00 0.00 0.00 2.32
299 319 7.013750 GGTAGGAGAGGGATTTCATTTCATTTC 59.986 40.741 0.00 0.00 0.00 2.17
300 320 6.496743 AGGAGAGGGATTTCATTTCATTTCA 58.503 36.000 0.00 0.00 0.00 2.69
301 321 7.130775 AGGAGAGGGATTTCATTTCATTTCAT 58.869 34.615 0.00 0.00 0.00 2.57
302 322 7.622479 AGGAGAGGGATTTCATTTCATTTCATT 59.378 33.333 0.00 0.00 0.00 2.57
303 323 8.262933 GGAGAGGGATTTCATTTCATTTCATTT 58.737 33.333 0.00 0.00 0.00 2.32
352 372 1.853963 TGCTTCCTCTCTACTCACCC 58.146 55.000 0.00 0.00 0.00 4.61
415 440 1.623542 GGCTTAGCCTTTCCCTCCGA 61.624 60.000 17.16 0.00 46.69 4.55
484 513 1.208293 CCTTCCTTTCTCCTTCTCCCG 59.792 57.143 0.00 0.00 0.00 5.14
608 642 3.599285 TACCGTCGGCAGCAAAGGG 62.599 63.158 12.28 0.00 0.00 3.95
610 644 2.978010 CGTCGGCAGCAAAGGGTT 60.978 61.111 0.00 0.00 0.00 4.11
612 646 1.024579 CGTCGGCAGCAAAGGGTTAT 61.025 55.000 0.00 0.00 0.00 1.89
614 648 1.132453 GTCGGCAGCAAAGGGTTATTC 59.868 52.381 0.00 0.00 0.00 1.75
625 663 5.567423 GCAAAGGGTTATTCAGTTGCTCATT 60.567 40.000 0.00 0.00 38.60 2.57
649 687 2.027751 GTGATCCGTAGCCGCCTC 59.972 66.667 0.00 0.00 0.00 4.70
690 754 2.042259 CATTGCTCTTGGCTGCCGA 61.042 57.895 14.98 11.82 42.39 5.54
712 776 2.347490 GCCTTCTTCCTGTCGCCA 59.653 61.111 0.00 0.00 0.00 5.69
730 794 2.560105 GCCAACATCCAAGAAAGCTTCT 59.440 45.455 0.00 0.00 43.15 2.85
831 896 2.063979 CCATGGACGGCTGACCCTA 61.064 63.158 5.56 0.00 0.00 3.53
903 983 1.951130 CGCCTGGACGGATTCATCG 60.951 63.158 0.00 0.00 33.16 3.84
988 1084 3.986006 AGGTTTCTCGCCGACGCA 61.986 61.111 0.00 0.00 39.84 5.24
1020 1117 2.206536 GGAGAGGGCCTGGAGATCG 61.207 68.421 12.95 0.00 0.00 3.69
1135 1250 3.010584 ACCTCCTTGCCAATTACAGACAT 59.989 43.478 0.00 0.00 0.00 3.06
1148 1263 7.148239 CCAATTACAGACATAGTTTCCTCCAAC 60.148 40.741 0.00 0.00 0.00 3.77
1170 1285 8.437742 CCAACACTTCAATTGCTATTTTCATTC 58.562 33.333 0.00 0.00 0.00 2.67
1171 1286 8.980610 CAACACTTCAATTGCTATTTTCATTCA 58.019 29.630 0.00 0.00 0.00 2.57
1176 1291 9.582431 CTTCAATTGCTATTTTCATTCATCAGT 57.418 29.630 0.00 0.00 0.00 3.41
1255 1373 3.943269 ACATGGACCCATATAGGAGGA 57.057 47.619 0.55 0.00 41.22 3.71
1258 1376 5.173246 ACATGGACCCATATAGGAGGAAAT 58.827 41.667 0.55 0.00 41.22 2.17
1259 1377 5.251700 ACATGGACCCATATAGGAGGAAATC 59.748 44.000 0.55 0.00 41.22 2.17
1260 1378 4.838403 TGGACCCATATAGGAGGAAATCA 58.162 43.478 0.00 0.00 41.22 2.57
1261 1379 5.424068 TGGACCCATATAGGAGGAAATCAT 58.576 41.667 0.00 0.00 41.22 2.45
1262 1380 5.488919 TGGACCCATATAGGAGGAAATCATC 59.511 44.000 0.00 0.00 41.22 2.92
1274 1392 3.991367 GGAAATCATCCTTATCGTCCGT 58.009 45.455 0.00 0.00 45.56 4.69
1275 1393 3.741344 GGAAATCATCCTTATCGTCCGTG 59.259 47.826 0.00 0.00 45.56 4.94
1276 1394 4.500887 GGAAATCATCCTTATCGTCCGTGA 60.501 45.833 0.00 0.00 45.56 4.35
1277 1395 4.665833 AATCATCCTTATCGTCCGTGAA 57.334 40.909 0.00 0.00 0.00 3.18
1278 1396 3.710326 TCATCCTTATCGTCCGTGAAG 57.290 47.619 0.00 0.00 0.00 3.02
1283 1406 4.885413 TCCTTATCGTCCGTGAAGAAAAA 58.115 39.130 5.37 0.00 0.00 1.94
1284 1407 4.687483 TCCTTATCGTCCGTGAAGAAAAAC 59.313 41.667 5.37 0.00 0.00 2.43
1317 1440 5.321959 TGTGAAGAAACACTGCAAATTGA 57.678 34.783 0.00 0.00 40.87 2.57
1322 1445 2.490328 AACACTGCAAATTGACACCG 57.510 45.000 0.00 0.00 0.00 4.94
1337 1461 6.395426 TTGACACCGAACTTAAACTCTAGA 57.605 37.500 0.00 0.00 0.00 2.43
1338 1462 6.010294 TGACACCGAACTTAAACTCTAGAG 57.990 41.667 18.49 18.49 0.00 2.43
1344 1468 5.447548 CCGAACTTAAACTCTAGAGACTCCG 60.448 48.000 26.57 15.48 0.00 4.63
1345 1469 5.447548 CGAACTTAAACTCTAGAGACTCCGG 60.448 48.000 26.57 12.79 0.00 5.14
1479 1603 2.651105 TACGCGCCAACCATCCTCA 61.651 57.895 5.73 0.00 0.00 3.86
1507 1631 5.011090 TCTCATTCATCTCCTTTACACCG 57.989 43.478 0.00 0.00 0.00 4.94
1614 1741 1.071471 AGACCCACTTTCACCTGCG 59.929 57.895 0.00 0.00 0.00 5.18
1621 1748 1.135972 CACTTTCACCTGCGTGTATGC 60.136 52.381 0.00 0.00 41.09 3.14
1627 1754 0.181114 ACCTGCGTGTATGCATGGAT 59.819 50.000 10.16 4.68 45.26 3.41
1804 1932 0.948678 TCCTTGTGTGCCGTTTTAGC 59.051 50.000 0.00 0.00 0.00 3.09
1886 2014 6.623767 GCCTGTGAGTAAATTGGATTTGTCTC 60.624 42.308 10.53 10.53 36.29 3.36
1887 2015 6.430925 CCTGTGAGTAAATTGGATTTGTCTCA 59.569 38.462 13.60 13.60 39.59 3.27
1909 2037 8.455682 TCTCACAAACTTTTCGACATTTTTACT 58.544 29.630 0.00 0.00 0.00 2.24
1985 2148 4.512571 CACATATTGCAGACCATCAATCGA 59.487 41.667 0.00 0.00 34.95 3.59
1994 2157 2.606725 GACCATCAATCGAGACAGCAAG 59.393 50.000 0.00 0.00 0.00 4.01
2078 2241 3.379057 GGAAAACAACGGAAAGGACTCAA 59.621 43.478 0.00 0.00 0.00 3.02
2103 2266 3.133183 GGCCACTTCAAAGGTTTGGTTTA 59.867 43.478 0.00 0.00 38.66 2.01
2121 2284 2.512692 TACTGCAAATCCTGGCACAT 57.487 45.000 0.00 0.00 38.20 3.21
2168 2336 6.464895 TTTTGTGTTTTGTTGAAGCTGAAG 57.535 33.333 0.00 0.00 0.00 3.02
2172 2340 5.633182 TGTGTTTTGTTGAAGCTGAAGAAAC 59.367 36.000 0.00 0.00 0.00 2.78
2181 2349 4.934001 TGAAGCTGAAGAAACTATGCAGAG 59.066 41.667 6.84 6.84 0.00 3.35
2183 2351 4.502962 AGCTGAAGAAACTATGCAGAGAC 58.497 43.478 16.75 6.13 0.00 3.36
2184 2352 4.222588 AGCTGAAGAAACTATGCAGAGACT 59.777 41.667 16.75 8.35 0.00 3.24
2256 2433 7.823635 TCCATGAGTAGTCTAAGTAGGGTAAT 58.176 38.462 0.00 0.00 0.00 1.89
2263 2440 8.555729 AGTAGTCTAAGTAGGGTAATACACACT 58.444 37.037 0.00 0.00 45.34 3.55
2264 2441 9.183368 GTAGTCTAAGTAGGGTAATACACACTT 57.817 37.037 12.54 12.54 37.80 3.16
2265 2442 8.661752 AGTCTAAGTAGGGTAATACACACTTT 57.338 34.615 12.96 0.19 37.80 2.66
2275 2452 9.411189 AGGGTAATACACACTTTTAGAAAAACA 57.589 29.630 0.00 0.00 37.80 2.83
2276 2453 9.454585 GGGTAATACACACTTTTAGAAAAACAC 57.545 33.333 0.00 0.00 0.00 3.32
2277 2454 9.161684 GGTAATACACACTTTTAGAAAAACACG 57.838 33.333 0.00 0.00 0.00 4.49
2279 2456 5.632244 ACACACTTTTAGAAAAACACGGT 57.368 34.783 0.00 0.00 0.00 4.83
2280 2457 6.740411 ACACACTTTTAGAAAAACACGGTA 57.260 33.333 0.00 0.00 0.00 4.02
2301 2481 6.296026 GGTAGCACCACTAATCCATGAAATA 58.704 40.000 0.00 0.00 38.42 1.40
2362 2542 1.821136 GAAAAGTGAGGAAGGCATGGG 59.179 52.381 0.00 0.00 0.00 4.00
2371 2551 1.341383 GGAAGGCATGGGTGTTCATCT 60.341 52.381 0.00 0.00 0.00 2.90
2383 2563 3.000727 GTGTTCATCTGTACCTTTCGGG 58.999 50.000 0.00 0.00 41.89 5.14
2616 2798 3.069729 GGTACATAACTCAGGGTGCTAGG 59.930 52.174 0.00 0.00 0.00 3.02
2628 2813 1.757118 GGTGCTAGGCAGATGAGTACA 59.243 52.381 0.00 0.00 40.08 2.90
2632 2817 4.272018 GTGCTAGGCAGATGAGTACATTTG 59.728 45.833 0.00 0.00 40.08 2.32
2634 2819 5.163269 TGCTAGGCAGATGAGTACATTTGAT 60.163 40.000 0.00 0.00 39.85 2.57
2658 2843 5.482006 TCATGACAACAGTATGAAGTCCAG 58.518 41.667 0.00 0.00 40.67 3.86
2679 2864 7.824289 GTCCAGTATGCTAAGATTAATGCCATA 59.176 37.037 0.00 0.00 31.97 2.74
2730 2915 1.146041 TATTGATGAGGGCGCGCTT 59.854 52.632 32.29 19.89 0.00 4.68
2734 2919 4.760047 ATGAGGGCGCGCTTCGTT 62.760 61.111 32.29 16.43 41.07 3.85
2867 3052 6.266103 CCATCCAAGCAACATAATGTTCCTAT 59.734 38.462 0.00 0.00 38.77 2.57
2912 3097 2.481441 TGGCATCTCACAGGAGGTATT 58.519 47.619 0.00 0.00 41.69 1.89
2946 3131 3.992260 TCGAAGCATTCTAGCCTAGTC 57.008 47.619 0.00 0.00 44.75 2.59
3087 3272 1.442184 CGAGTCCGTGACTTCACCG 60.442 63.158 7.80 0.00 43.53 4.94
3120 3305 5.926542 TGTTTCATCTTCAAGTACCTTCTCG 59.073 40.000 0.00 0.00 0.00 4.04
3377 3562 5.182760 AGTTAAGAAAGATGCAAGGCTTCAG 59.817 40.000 0.00 0.00 35.57 3.02
3379 3564 1.817447 GAAAGATGCAAGGCTTCAGCT 59.183 47.619 10.45 10.38 41.70 4.24
3380 3565 1.174783 AAGATGCAAGGCTTCAGCTG 58.825 50.000 7.63 7.63 41.70 4.24
3511 3859 4.875536 ACGCTTTAGTCATGCATGTATTGA 59.124 37.500 25.43 4.57 0.00 2.57
3519 3867 5.994054 AGTCATGCATGTATTGATCTACACC 59.006 40.000 25.43 0.00 34.59 4.16
3524 3872 6.128486 TGCATGTATTGATCTACACCCAAAT 58.872 36.000 0.00 0.00 34.59 2.32
3525 3873 7.286313 TGCATGTATTGATCTACACCCAAATA 58.714 34.615 0.00 0.00 34.59 1.40
3526 3874 7.228507 TGCATGTATTGATCTACACCCAAATAC 59.771 37.037 0.00 0.00 34.59 1.89
3527 3875 7.228507 GCATGTATTGATCTACACCCAAATACA 59.771 37.037 11.26 11.26 34.59 2.29
3528 3876 9.288576 CATGTATTGATCTACACCCAAATACAT 57.711 33.333 13.77 13.77 34.59 2.29
3529 3877 9.866655 ATGTATTGATCTACACCCAAATACATT 57.133 29.630 13.77 4.22 34.59 2.71
3532 3880 7.801716 TTGATCTACACCCAAATACATTAGC 57.198 36.000 0.00 0.00 0.00 3.09
3533 3881 6.894682 TGATCTACACCCAAATACATTAGCA 58.105 36.000 0.00 0.00 0.00 3.49
3633 3990 4.792068 CTTTTCTGGCCTATGGGATACAA 58.208 43.478 3.32 0.00 39.74 2.41
3642 3999 5.279809 GGCCTATGGGATACAAGATAAACGA 60.280 44.000 0.00 0.00 39.74 3.85
3666 4023 5.186603 ACTGAAGAGCACTGACATGATTCTA 59.813 40.000 0.00 0.00 0.00 2.10
3705 4063 7.826918 AGCCTAGTCTTATTTCTACTCGAAT 57.173 36.000 0.00 0.00 0.00 3.34
3706 4064 7.878036 AGCCTAGTCTTATTTCTACTCGAATC 58.122 38.462 0.00 0.00 0.00 2.52
3707 4065 7.722285 AGCCTAGTCTTATTTCTACTCGAATCT 59.278 37.037 0.00 0.00 0.00 2.40
3708 4066 8.354426 GCCTAGTCTTATTTCTACTCGAATCTT 58.646 37.037 0.00 0.00 0.00 2.40
3764 4122 2.256391 TGCCTGAGCATTTGAACCG 58.744 52.632 0.00 0.00 46.52 4.44
3773 4131 5.162794 TGAGCATTTGAACCGAATGAATTG 58.837 37.500 10.27 0.00 37.41 2.32
3774 4132 3.928375 AGCATTTGAACCGAATGAATTGC 59.072 39.130 10.27 0.00 37.41 3.56
3813 4171 2.427095 GGGTGGTGAATCAGTAAATGCC 59.573 50.000 0.00 0.00 0.00 4.40
3904 4262 6.219473 ACAATACGCAAAACATGAAATTCCA 58.781 32.000 0.00 0.00 0.00 3.53
3943 4301 5.373222 ACACACTAACAAGCATTACCTTCA 58.627 37.500 0.00 0.00 0.00 3.02
3988 4346 1.892329 GCCAGCAAAAAGATCCCTGGA 60.892 52.381 9.02 0.00 44.50 3.86
4128 4486 0.106268 TGCCATTGTCCACACCTTGT 60.106 50.000 0.00 0.00 0.00 3.16
4136 4496 0.468226 TCCACACCTTGTCCTGTGTC 59.532 55.000 0.00 0.00 43.52 3.67
4147 4507 2.069273 GTCCTGTGTCAAATCTCACCG 58.931 52.381 0.00 0.00 34.14 4.94
4159 4519 2.920724 TCTCACCGTGAAATTCACCA 57.079 45.000 19.16 1.77 44.20 4.17
4211 4571 3.957586 CCACCACCAGCTGGAGCA 61.958 66.667 39.19 0.00 43.95 4.26
4243 4603 0.605319 GTTCATCCAGGCCAACGTCA 60.605 55.000 5.01 0.00 0.00 4.35
4503 4868 3.922190 CGGTTTTCGGTTTCGGTTT 57.078 47.368 0.00 0.00 36.95 3.27
4504 4869 2.191815 CGGTTTTCGGTTTCGGTTTT 57.808 45.000 0.00 0.00 36.95 2.43
4505 4870 1.847390 CGGTTTTCGGTTTCGGTTTTG 59.153 47.619 0.00 0.00 36.95 2.44
4522 4887 4.281182 GGTTTTGGGTTTTGGGTTTTGTTT 59.719 37.500 0.00 0.00 0.00 2.83
4632 5004 2.506957 GGTTTTGGGGCTGGGTGTG 61.507 63.158 0.00 0.00 0.00 3.82
4651 5023 0.883833 GCTGGTGGTCTGAATTGTGG 59.116 55.000 0.00 0.00 0.00 4.17
4664 5036 5.707298 TCTGAATTGTGGAACCTTCTCATTC 59.293 40.000 0.00 0.00 34.36 2.67
4673 5047 1.980765 ACCTTCTCATTCTGCCTGTGA 59.019 47.619 0.00 0.00 0.00 3.58
4681 5055 2.472695 TTCTGCCTGTGATGTGTACC 57.527 50.000 0.00 0.00 0.00 3.34
4682 5056 1.347062 TCTGCCTGTGATGTGTACCA 58.653 50.000 0.00 0.00 0.00 3.25
4687 5061 2.688507 CCTGTGATGTGTACCACTCAC 58.311 52.381 14.51 14.51 39.96 3.51
4689 5063 3.579709 CTGTGATGTGTACCACTCACTC 58.420 50.000 18.62 5.08 40.08 3.51
4696 5070 2.029828 GTGTACCACTCACTCCAGTCAG 60.030 54.545 0.00 0.00 33.59 3.51
4716 5090 1.202110 GCTGTGCATCCAGAATTGACG 60.202 52.381 8.43 0.00 34.23 4.35
4722 5096 2.938451 GCATCCAGAATTGACGTGATGA 59.062 45.455 11.20 0.00 33.20 2.92
4725 5099 4.001618 TCCAGAATTGACGTGATGACAA 57.998 40.909 0.00 0.00 36.70 3.18
4727 5101 4.392754 TCCAGAATTGACGTGATGACAATG 59.607 41.667 0.00 0.00 41.13 2.82
4728 5102 4.437794 CCAGAATTGACGTGATGACAATGG 60.438 45.833 0.00 0.00 41.13 3.16
4729 5103 3.127548 AGAATTGACGTGATGACAATGGC 59.872 43.478 0.00 0.40 41.13 4.40
4730 5104 1.889545 TTGACGTGATGACAATGGCA 58.110 45.000 0.00 0.00 0.00 4.92
4731 5105 2.112380 TGACGTGATGACAATGGCAT 57.888 45.000 0.00 0.00 0.00 4.40
4732 5106 2.009051 TGACGTGATGACAATGGCATC 58.991 47.619 21.56 21.56 41.87 3.91
4741 5115 4.771590 TGACAATGGCATCAGAGAAAAC 57.228 40.909 0.00 0.00 0.00 2.43
4743 5117 4.828939 TGACAATGGCATCAGAGAAAACTT 59.171 37.500 0.00 0.00 0.00 2.66
4746 5120 5.302568 ACAATGGCATCAGAGAAAACTTTCA 59.697 36.000 0.00 0.00 39.61 2.69
4751 5125 5.334724 GGCATCAGAGAAAACTTTCAGTCTG 60.335 44.000 12.13 12.13 39.19 3.51
4752 5126 5.334724 GCATCAGAGAAAACTTTCAGTCTGG 60.335 44.000 15.79 7.14 38.75 3.86
4753 5127 4.130118 TCAGAGAAAACTTTCAGTCTGGC 58.870 43.478 15.79 0.00 38.75 4.85
4757 5131 3.885901 AGAAAACTTTCAGTCTGGCCTTC 59.114 43.478 3.32 0.00 39.61 3.46
4758 5132 1.884235 AACTTTCAGTCTGGCCTTCG 58.116 50.000 3.32 0.00 0.00 3.79
4774 5148 2.739913 CCTTCGCCACACTTCGAAATTA 59.260 45.455 0.00 0.00 42.99 1.40
4777 5151 3.655486 TCGCCACACTTCGAAATTAAGA 58.345 40.909 0.00 0.00 0.00 2.10
4831 5206 5.550290 AGTAATTTGGCTTTTCATTGTGGG 58.450 37.500 0.00 0.00 0.00 4.61
4832 5207 4.703379 AATTTGGCTTTTCATTGTGGGA 57.297 36.364 0.00 0.00 0.00 4.37
4834 5209 2.380064 TGGCTTTTCATTGTGGGAGT 57.620 45.000 0.00 0.00 0.00 3.85
4840 5215 4.380233 GCTTTTCATTGTGGGAGTGATCTG 60.380 45.833 0.00 0.00 0.00 2.90
4841 5216 3.354948 TTCATTGTGGGAGTGATCTGG 57.645 47.619 0.00 0.00 0.00 3.86
4845 5220 0.994247 TGTGGGAGTGATCTGGCAAT 59.006 50.000 0.00 0.00 0.00 3.56
4847 5222 1.065199 GTGGGAGTGATCTGGCAATGA 60.065 52.381 0.00 0.00 0.00 2.57
4853 5228 4.197750 GAGTGATCTGGCAATGATGAAGT 58.802 43.478 0.00 0.00 0.00 3.01
4862 5237 3.181493 GGCAATGATGAAGTAAGTGGCAG 60.181 47.826 0.00 0.00 0.00 4.85
4863 5238 3.181493 GCAATGATGAAGTAAGTGGCAGG 60.181 47.826 0.00 0.00 0.00 4.85
4865 5240 3.616956 TGATGAAGTAAGTGGCAGGAG 57.383 47.619 0.00 0.00 0.00 3.69
4877 5252 1.301716 GCAGGAGTGCGGAGTTGAA 60.302 57.895 0.00 0.00 40.71 2.69
4879 5254 1.813513 CAGGAGTGCGGAGTTGAAAT 58.186 50.000 0.00 0.00 0.00 2.17
4880 5255 2.935238 GCAGGAGTGCGGAGTTGAAATA 60.935 50.000 0.00 0.00 40.71 1.40
4881 5256 3.334691 CAGGAGTGCGGAGTTGAAATAA 58.665 45.455 0.00 0.00 0.00 1.40
4882 5257 3.751175 CAGGAGTGCGGAGTTGAAATAAA 59.249 43.478 0.00 0.00 0.00 1.40
4883 5258 4.396166 CAGGAGTGCGGAGTTGAAATAAAT 59.604 41.667 0.00 0.00 0.00 1.40
4884 5259 5.584649 CAGGAGTGCGGAGTTGAAATAAATA 59.415 40.000 0.00 0.00 0.00 1.40
4885 5260 6.093495 CAGGAGTGCGGAGTTGAAATAAATAA 59.907 38.462 0.00 0.00 0.00 1.40
4886 5261 6.657541 AGGAGTGCGGAGTTGAAATAAATAAA 59.342 34.615 0.00 0.00 0.00 1.40
4887 5262 7.339466 AGGAGTGCGGAGTTGAAATAAATAAAT 59.661 33.333 0.00 0.00 0.00 1.40
4888 5263 8.617809 GGAGTGCGGAGTTGAAATAAATAAATA 58.382 33.333 0.00 0.00 0.00 1.40
4889 5264 9.997482 GAGTGCGGAGTTGAAATAAATAAATAA 57.003 29.630 0.00 0.00 0.00 1.40
4930 5305 1.301293 GCTCAACCCAGGGAGGAAG 59.699 63.158 14.54 5.03 41.22 3.46
4931 5306 1.492993 GCTCAACCCAGGGAGGAAGT 61.493 60.000 14.54 0.00 41.22 3.01
4933 5308 2.266279 CTCAACCCAGGGAGGAAGTTA 58.734 52.381 14.54 0.00 41.22 2.24
4935 5310 0.992695 AACCCAGGGAGGAAGTTAGC 59.007 55.000 14.54 0.00 41.22 3.09
4936 5311 0.914902 ACCCAGGGAGGAAGTTAGCC 60.915 60.000 14.54 0.00 41.22 3.93
4938 5313 0.543749 CCAGGGAGGAAGTTAGCCAG 59.456 60.000 0.00 0.00 41.22 4.85
4939 5314 1.280457 CAGGGAGGAAGTTAGCCAGT 58.720 55.000 0.00 0.00 0.00 4.00
4940 5315 1.630878 CAGGGAGGAAGTTAGCCAGTT 59.369 52.381 0.00 0.00 0.00 3.16
4941 5316 1.630878 AGGGAGGAAGTTAGCCAGTTG 59.369 52.381 0.00 0.00 0.00 3.16
4942 5317 1.351350 GGGAGGAAGTTAGCCAGTTGT 59.649 52.381 0.00 0.00 0.00 3.32
4943 5318 2.615747 GGGAGGAAGTTAGCCAGTTGTC 60.616 54.545 0.00 0.00 0.00 3.18
4944 5319 2.038557 GGAGGAAGTTAGCCAGTTGTCA 59.961 50.000 0.00 0.00 0.00 3.58
4945 5320 3.330267 GAGGAAGTTAGCCAGTTGTCAG 58.670 50.000 0.00 0.00 0.00 3.51
4946 5321 1.807142 GGAAGTTAGCCAGTTGTCAGC 59.193 52.381 0.00 0.00 0.00 4.26
4960 5335 1.227943 TCAGCAACACCAGGCAGTC 60.228 57.895 0.00 0.00 0.00 3.51
4972 5347 2.981909 GCAGTCAGGCAGCAGCAA 60.982 61.111 2.65 0.00 44.61 3.91
5055 5430 5.361427 TGAATCAATTGCAAAGCATATGGG 58.639 37.500 1.71 0.00 38.76 4.00
5113 5488 9.216117 GACAGTTGATGTTTGGTAATAGTAACT 57.784 33.333 0.00 0.00 44.17 2.24
5140 5515 7.928706 AGACGACATAGGAATTATTTGAAGAGG 59.071 37.037 0.00 0.00 0.00 3.69
5203 5578 0.727398 GACGTGTTTGGCTATGGCTC 59.273 55.000 0.00 0.00 38.73 4.70
5204 5579 0.324943 ACGTGTTTGGCTATGGCTCT 59.675 50.000 0.00 0.00 38.73 4.09
5206 5581 1.131126 CGTGTTTGGCTATGGCTCTTG 59.869 52.381 0.00 0.00 38.73 3.02
5208 5583 2.558359 GTGTTTGGCTATGGCTCTTGTT 59.442 45.455 0.00 0.00 38.73 2.83
5209 5584 2.819608 TGTTTGGCTATGGCTCTTGTTC 59.180 45.455 0.00 0.00 38.73 3.18
5312 5687 2.575532 TGCACTCCTTTGAACTTGAGG 58.424 47.619 0.00 0.00 0.00 3.86
5339 5714 1.548582 CCCTGGAGCTTGGATGTGTTT 60.549 52.381 0.00 0.00 0.00 2.83
5360 5735 1.766143 GCTGATACGCCTGCTTTCCG 61.766 60.000 0.00 0.00 0.00 4.30
5385 5760 1.148949 TTGTTGAGCCTGCAGAGCA 59.851 52.632 23.46 12.85 36.92 4.26
5404 5779 4.236935 AGCAATTTCAAGGTACGCATTTG 58.763 39.130 0.00 0.00 0.00 2.32
5405 5780 3.367630 GCAATTTCAAGGTACGCATTTGG 59.632 43.478 0.00 0.00 0.00 3.28
5406 5781 4.804108 CAATTTCAAGGTACGCATTTGGA 58.196 39.130 0.00 0.00 0.00 3.53
5414 5789 4.997565 AGGTACGCATTTGGATCAAAATG 58.002 39.130 25.44 25.44 46.03 2.32
5420 5795 3.869065 CATTTGGATCAAAATGCTGGCT 58.131 40.909 20.09 0.00 39.83 4.75
5421 5796 4.258543 CATTTGGATCAAAATGCTGGCTT 58.741 39.130 20.09 0.00 39.83 4.35
5422 5797 3.598019 TTGGATCAAAATGCTGGCTTC 57.402 42.857 0.00 0.00 0.00 3.86
5424 5799 2.898612 TGGATCAAAATGCTGGCTTCAA 59.101 40.909 0.00 0.00 0.00 2.69
5425 5800 3.056393 TGGATCAAAATGCTGGCTTCAAG 60.056 43.478 0.00 0.00 0.00 3.02
5426 5801 3.194116 GGATCAAAATGCTGGCTTCAAGA 59.806 43.478 0.00 0.00 0.00 3.02
5429 5804 4.084287 TCAAAATGCTGGCTTCAAGAGAT 58.916 39.130 0.00 0.00 0.00 2.75
5430 5805 4.082408 TCAAAATGCTGGCTTCAAGAGATG 60.082 41.667 0.00 0.00 0.00 2.90
5431 5806 2.054232 ATGCTGGCTTCAAGAGATGG 57.946 50.000 0.00 0.00 0.00 3.51
5432 5807 0.986527 TGCTGGCTTCAAGAGATGGA 59.013 50.000 0.00 0.00 0.00 3.41
5433 5808 1.562942 TGCTGGCTTCAAGAGATGGAT 59.437 47.619 0.00 0.00 0.00 3.41
5434 5809 2.025605 TGCTGGCTTCAAGAGATGGATT 60.026 45.455 0.00 0.00 0.00 3.01
5462 5837 9.979578 AAGAAAAATATGTATGTTCACAGCAAA 57.020 25.926 0.00 0.00 0.00 3.68
5470 5845 3.358707 TGTTCACAGCAAAAGCAGATG 57.641 42.857 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.315901 CGCCTTTTCCATCGTTTGTTC 58.684 47.619 0.00 0.00 0.00 3.18
1 2 1.000717 CCGCCTTTTCCATCGTTTGTT 60.001 47.619 0.00 0.00 0.00 2.83
2 3 0.596082 CCGCCTTTTCCATCGTTTGT 59.404 50.000 0.00 0.00 0.00 2.83
3 4 0.596082 ACCGCCTTTTCCATCGTTTG 59.404 50.000 0.00 0.00 0.00 2.93
4 5 0.596082 CACCGCCTTTTCCATCGTTT 59.404 50.000 0.00 0.00 0.00 3.60
5 6 1.241315 CCACCGCCTTTTCCATCGTT 61.241 55.000 0.00 0.00 0.00 3.85
24 25 2.857744 CGACCGGAGCCACCTATCC 61.858 68.421 9.46 0.00 36.31 2.59
26 27 2.838225 CCGACCGGAGCCACCTAT 60.838 66.667 9.46 0.00 37.50 2.57
76 78 0.880278 GTGACTGCGTGTGGTGATGT 60.880 55.000 0.00 0.00 0.00 3.06
85 87 2.738314 TGAATGAATGAGTGACTGCGTG 59.262 45.455 0.00 0.00 0.00 5.34
86 88 2.998670 CTGAATGAATGAGTGACTGCGT 59.001 45.455 0.00 0.00 0.00 5.24
87 89 2.222976 GCTGAATGAATGAGTGACTGCG 60.223 50.000 0.00 0.00 0.00 5.18
88 90 2.097142 GGCTGAATGAATGAGTGACTGC 59.903 50.000 0.00 0.00 0.00 4.40
89 91 3.607741 AGGCTGAATGAATGAGTGACTG 58.392 45.455 0.00 0.00 0.00 3.51
90 92 3.262660 TGAGGCTGAATGAATGAGTGACT 59.737 43.478 0.00 0.00 0.00 3.41
91 93 3.373439 GTGAGGCTGAATGAATGAGTGAC 59.627 47.826 0.00 0.00 0.00 3.67
92 94 3.262660 AGTGAGGCTGAATGAATGAGTGA 59.737 43.478 0.00 0.00 0.00 3.41
99 101 1.980765 AGGTGAGTGAGGCTGAATGAA 59.019 47.619 0.00 0.00 0.00 2.57
140 150 0.560688 TGGGAGGGCTGGTTCTTTTT 59.439 50.000 0.00 0.00 0.00 1.94
141 151 0.178961 GTGGGAGGGCTGGTTCTTTT 60.179 55.000 0.00 0.00 0.00 2.27
142 152 1.460699 GTGGGAGGGCTGGTTCTTT 59.539 57.895 0.00 0.00 0.00 2.52
143 153 2.539081 GGTGGGAGGGCTGGTTCTT 61.539 63.158 0.00 0.00 0.00 2.52
145 155 4.048470 GGGTGGGAGGGCTGGTTC 62.048 72.222 0.00 0.00 0.00 3.62
275 295 7.642186 TGAAATGAAATGAAATCCCTCTCCTA 58.358 34.615 0.00 0.00 0.00 2.94
294 314 4.037684 GGAGGAGGAGCATCAAATGAAATG 59.962 45.833 0.00 0.00 36.25 2.32
295 315 4.079327 AGGAGGAGGAGCATCAAATGAAAT 60.079 41.667 0.00 0.00 36.25 2.17
296 316 3.267812 AGGAGGAGGAGCATCAAATGAAA 59.732 43.478 0.00 0.00 36.25 2.69
297 317 2.848694 AGGAGGAGGAGCATCAAATGAA 59.151 45.455 0.00 0.00 36.25 2.57
298 318 2.485659 AGGAGGAGGAGCATCAAATGA 58.514 47.619 0.00 0.00 36.25 2.57
299 319 3.212685 GAAGGAGGAGGAGCATCAAATG 58.787 50.000 0.00 0.00 36.25 2.32
300 320 2.174424 GGAAGGAGGAGGAGCATCAAAT 59.826 50.000 0.00 0.00 36.25 2.32
301 321 1.561542 GGAAGGAGGAGGAGCATCAAA 59.438 52.381 0.00 0.00 36.25 2.69
302 322 1.207791 GGAAGGAGGAGGAGCATCAA 58.792 55.000 0.00 0.00 36.25 2.57
303 323 0.341258 AGGAAGGAGGAGGAGCATCA 59.659 55.000 0.00 0.00 36.25 3.07
370 394 2.795973 CCGTAGCCGTGTGATCGA 59.204 61.111 0.00 0.00 0.00 3.59
415 440 9.945904 CAACCTCTCTAATTCTTTAGGTAAAGT 57.054 33.333 8.90 0.00 42.43 2.66
608 642 6.024049 CGGAGAAAATGAGCAACTGAATAAC 58.976 40.000 0.00 0.00 0.00 1.89
610 644 5.122239 CACGGAGAAAATGAGCAACTGAATA 59.878 40.000 0.00 0.00 0.00 1.75
612 646 3.250762 CACGGAGAAAATGAGCAACTGAA 59.749 43.478 0.00 0.00 0.00 3.02
614 648 2.807967 TCACGGAGAAAATGAGCAACTG 59.192 45.455 0.00 0.00 0.00 3.16
649 687 1.202651 GGACGGAGAGAGAGAGAGAGG 60.203 61.905 0.00 0.00 0.00 3.69
690 754 1.004440 GACAGGAAGAAGGCGCAGT 60.004 57.895 10.83 0.00 0.00 4.40
696 760 0.250295 TGTTGGCGACAGGAAGAAGG 60.250 55.000 2.68 0.00 44.54 3.46
712 776 3.930634 GCAGAAGCTTTCTTGGATGTT 57.069 42.857 0.00 0.00 38.11 2.71
730 794 4.082300 CAGAAGCTTACTGAGAGAAGAGCA 60.082 45.833 16.37 0.00 37.54 4.26
740 804 0.966179 TGTCCGCAGAAGCTTACTGA 59.034 50.000 22.30 6.80 39.10 3.41
789 853 2.796651 CAATCAAGGCTGCGCTCC 59.203 61.111 9.73 10.28 0.00 4.70
795 859 0.529378 GGGTGAAGCAATCAAGGCTG 59.471 55.000 0.00 0.00 41.66 4.85
802 866 0.734889 CGTCCATGGGTGAAGCAATC 59.265 55.000 13.02 0.00 0.00 2.67
831 896 1.668294 CCTCACCTCGAGCTGTTGT 59.332 57.895 6.99 0.00 40.78 3.32
1122 1225 6.414732 TGGAGGAAACTATGTCTGTAATTGG 58.585 40.000 0.00 0.00 44.43 3.16
1135 1250 5.009610 GCAATTGAAGTGTTGGAGGAAACTA 59.990 40.000 10.34 0.00 44.43 2.24
1148 1263 9.361315 TGATGAATGAAAATAGCAATTGAAGTG 57.639 29.630 10.34 0.00 0.00 3.16
1192 1307 7.781324 ACTGAAAATGACCAAACCATAATCT 57.219 32.000 0.00 0.00 0.00 2.40
1195 1310 8.698973 TCTTACTGAAAATGACCAAACCATAA 57.301 30.769 0.00 0.00 0.00 1.90
1255 1373 4.665833 TCACGGACGATAAGGATGATTT 57.334 40.909 0.00 0.00 0.00 2.17
1258 1376 3.284617 TCTTCACGGACGATAAGGATGA 58.715 45.455 0.00 0.00 0.00 2.92
1259 1377 3.710326 TCTTCACGGACGATAAGGATG 57.290 47.619 0.00 0.00 0.00 3.51
1260 1378 4.730949 TTTCTTCACGGACGATAAGGAT 57.269 40.909 0.00 0.00 0.00 3.24
1261 1379 4.524316 TTTTCTTCACGGACGATAAGGA 57.476 40.909 0.00 0.00 0.00 3.36
1262 1380 4.449743 TGTTTTTCTTCACGGACGATAAGG 59.550 41.667 0.00 0.00 0.00 2.69
1264 1382 5.291178 TCTGTTTTTCTTCACGGACGATAA 58.709 37.500 0.00 0.00 0.00 1.75
1266 1384 3.724374 TCTGTTTTTCTTCACGGACGAT 58.276 40.909 0.00 0.00 0.00 3.73
1267 1385 3.120792 CTCTGTTTTTCTTCACGGACGA 58.879 45.455 0.00 0.00 0.00 4.20
1268 1386 2.864343 ACTCTGTTTTTCTTCACGGACG 59.136 45.455 0.00 0.00 0.00 4.79
1269 1387 5.978934 TTACTCTGTTTTTCTTCACGGAC 57.021 39.130 0.00 0.00 0.00 4.79
1270 1388 6.988622 TTTTACTCTGTTTTTCTTCACGGA 57.011 33.333 0.00 0.00 0.00 4.69
1273 1391 9.567848 TCACATTTTTACTCTGTTTTTCTTCAC 57.432 29.630 0.00 0.00 0.00 3.18
1283 1406 8.184192 CAGTGTTTCTTCACATTTTTACTCTGT 58.816 33.333 0.00 0.00 40.37 3.41
1284 1407 7.166473 GCAGTGTTTCTTCACATTTTTACTCTG 59.834 37.037 0.00 0.00 40.37 3.35
1317 1440 5.769162 AGTCTCTAGAGTTTAAGTTCGGTGT 59.231 40.000 19.21 0.00 0.00 4.16
1322 1445 5.415389 ACCGGAGTCTCTAGAGTTTAAGTTC 59.585 44.000 19.21 1.28 0.00 3.01
1345 1469 1.283736 CGCCGTACTTGGTTATGGAC 58.716 55.000 0.00 0.00 0.00 4.02
1458 1582 2.036006 GGATGGTTGGCGCGTACAA 61.036 57.895 8.43 11.27 0.00 2.41
1479 1603 7.714377 GTGTAAAGGAGATGAATGAGATGTGAT 59.286 37.037 0.00 0.00 0.00 3.06
1699 1826 9.517868 AGATTCCATGCCAAAATTTTCAAATAA 57.482 25.926 0.00 0.00 0.00 1.40
1700 1827 8.948145 CAGATTCCATGCCAAAATTTTCAAATA 58.052 29.630 0.00 0.00 0.00 1.40
1701 1828 7.666388 TCAGATTCCATGCCAAAATTTTCAAAT 59.334 29.630 0.00 0.00 0.00 2.32
1702 1829 6.996879 TCAGATTCCATGCCAAAATTTTCAAA 59.003 30.769 0.00 0.00 0.00 2.69
1703 1830 6.531923 TCAGATTCCATGCCAAAATTTTCAA 58.468 32.000 0.00 0.00 0.00 2.69
1704 1831 6.111669 TCAGATTCCATGCCAAAATTTTCA 57.888 33.333 0.00 0.00 0.00 2.69
1705 1832 6.819649 TGATCAGATTCCATGCCAAAATTTTC 59.180 34.615 0.00 0.00 0.00 2.29
1706 1833 6.713276 TGATCAGATTCCATGCCAAAATTTT 58.287 32.000 0.00 0.00 0.00 1.82
1707 1834 6.155565 TCTGATCAGATTCCATGCCAAAATTT 59.844 34.615 21.67 0.00 31.41 1.82
1708 1835 5.659525 TCTGATCAGATTCCATGCCAAAATT 59.340 36.000 21.67 0.00 31.41 1.82
1709 1836 5.068723 GTCTGATCAGATTCCATGCCAAAAT 59.931 40.000 27.51 0.00 39.97 1.82
1804 1932 0.738762 CCTCACGTGTCCTCAGCATG 60.739 60.000 16.51 0.00 37.54 4.06
1886 2014 8.614994 AGAGTAAAAATGTCGAAAAGTTTGTG 57.385 30.769 0.00 0.00 0.00 3.33
1909 2037 5.935206 TGCGTAATGGTGAAAGAAACATAGA 59.065 36.000 0.00 0.00 0.00 1.98
1921 2049 4.378563 CGGTTAAATTGTGCGTAATGGTGA 60.379 41.667 0.00 0.00 0.00 4.02
1994 2157 0.035630 AGTGCCTTCTGTGGAGCATC 60.036 55.000 0.00 0.00 37.60 3.91
2078 2241 2.170397 CCAAACCTTTGAAGTGGCCTTT 59.830 45.455 3.32 0.00 40.55 3.11
2084 2247 4.803613 GCAGTAAACCAAACCTTTGAAGTG 59.196 41.667 0.00 0.00 40.55 3.16
2103 2266 1.636148 AATGTGCCAGGATTTGCAGT 58.364 45.000 0.00 0.00 38.34 4.40
2121 2284 2.776312 TGCGGCGTATTTGAAACAAA 57.224 40.000 9.37 0.00 0.00 2.83
2168 2336 3.839293 ACACGAGTCTCTGCATAGTTTC 58.161 45.455 0.00 0.00 0.00 2.78
2181 2349 8.670135 ACATAGCATAGATATAAGACACGAGTC 58.330 37.037 4.68 4.68 45.31 3.36
2183 2351 9.847706 AAACATAGCATAGATATAAGACACGAG 57.152 33.333 0.00 0.00 0.00 4.18
2250 2427 9.454585 GTGTTTTTCTAAAAGTGTGTATTACCC 57.545 33.333 0.00 0.00 0.00 3.69
2256 2433 6.740411 ACCGTGTTTTTCTAAAAGTGTGTA 57.260 33.333 0.00 0.00 0.00 2.90
2263 2440 4.639310 TGGTGCTACCGTGTTTTTCTAAAA 59.361 37.500 0.00 0.00 42.58 1.52
2264 2441 4.035441 GTGGTGCTACCGTGTTTTTCTAAA 59.965 41.667 0.00 0.00 42.58 1.85
2265 2442 3.560896 GTGGTGCTACCGTGTTTTTCTAA 59.439 43.478 0.00 0.00 42.58 2.10
2267 2444 1.944709 GTGGTGCTACCGTGTTTTTCT 59.055 47.619 0.00 0.00 42.58 2.52
2268 2445 1.944709 AGTGGTGCTACCGTGTTTTTC 59.055 47.619 0.00 0.00 42.58 2.29
2274 2451 1.206132 TGGATTAGTGGTGCTACCGTG 59.794 52.381 0.00 0.00 42.58 4.94
2275 2452 1.563924 TGGATTAGTGGTGCTACCGT 58.436 50.000 0.00 0.00 42.58 4.83
2276 2453 2.102420 TCATGGATTAGTGGTGCTACCG 59.898 50.000 0.00 0.00 42.58 4.02
2277 2454 3.838244 TCATGGATTAGTGGTGCTACC 57.162 47.619 0.00 0.00 39.22 3.18
2301 2481 7.390162 CCAAATTGTTTGTGTTTGGGCTATTAT 59.610 33.333 7.95 0.00 45.05 1.28
2327 2507 6.060028 TCACTTTTCAGTTGAGTATGCAAC 57.940 37.500 0.00 0.00 46.47 4.17
2404 2584 2.803030 ATTGAAGGTGCAGATGAGCT 57.197 45.000 0.00 0.00 34.99 4.09
2587 2767 2.287069 CCTGAGTTATGTACCTCGCTCG 60.287 54.545 0.00 0.00 0.00 5.03
2616 2798 7.130917 GTCATGAATCAAATGTACTCATCTGC 58.869 38.462 0.00 0.00 32.56 4.26
2628 2813 9.017509 ACTTCATACTGTTGTCATGAATCAAAT 57.982 29.630 0.00 0.00 37.86 2.32
2632 2817 6.595326 TGGACTTCATACTGTTGTCATGAATC 59.405 38.462 0.00 5.26 37.86 2.52
2634 2819 5.863965 TGGACTTCATACTGTTGTCATGAA 58.136 37.500 0.00 4.25 36.57 2.57
2679 2864 3.228188 TCTTGATCCACCTGCTGTTTT 57.772 42.857 0.00 0.00 0.00 2.43
2730 2915 7.042456 GCAGATTGCTTGATATCTCTTAAACGA 60.042 37.037 3.98 0.00 40.96 3.85
2734 2919 6.204301 GCTGCAGATTGCTTGATATCTCTTAA 59.796 38.462 20.43 0.00 45.31 1.85
2806 2991 8.419442 GCTGAAAATAATCAATCAAGGGAGATT 58.581 33.333 0.00 0.00 38.72 2.40
2867 3052 4.225942 AGTTGAGTCAGGCATATTTCCAGA 59.774 41.667 0.00 0.00 0.00 3.86
2912 3097 0.319555 CTTCGAAGCCGGTCTTGACA 60.320 55.000 13.09 0.00 34.56 3.58
2937 3122 5.046304 AGCATTCAAGAAGTTGACTAGGCTA 60.046 40.000 0.00 0.00 42.60 3.93
3087 3272 7.432350 ACTTGAAGATGAAACAGAATGACTC 57.568 36.000 0.00 0.00 39.69 3.36
3120 3305 2.103538 TCATTACGACGCCTCGGC 59.896 61.111 9.87 0.00 44.80 5.54
3377 3562 8.786898 TGGATGCAGTAGAAATATTTTATCAGC 58.213 33.333 1.43 5.69 0.00 4.26
3379 3564 9.288576 CCTGGATGCAGTAGAAATATTTTATCA 57.711 33.333 13.65 0.00 0.00 2.15
3380 3565 9.289782 ACCTGGATGCAGTAGAAATATTTTATC 57.710 33.333 13.65 0.00 0.00 1.75
3489 3837 5.408204 TCAATACATGCATGACTAAAGCG 57.592 39.130 32.75 11.94 0.00 4.68
3511 3859 6.546034 GGTTGCTAATGTATTTGGGTGTAGAT 59.454 38.462 0.00 0.00 0.00 1.98
3532 3880 2.481795 CCCTTCACACAGCAAAAGGTTG 60.482 50.000 0.00 0.00 37.22 3.77
3533 3881 1.756538 CCCTTCACACAGCAAAAGGTT 59.243 47.619 0.00 0.00 37.22 3.50
3549 3906 3.846588 TCTGATTTCTGAGGCTAACCCTT 59.153 43.478 0.00 0.00 46.60 3.95
3551 3908 3.914426 TCTGATTTCTGAGGCTAACCC 57.086 47.619 0.00 0.00 36.11 4.11
3590 3947 2.874701 GCCTGTATATCACAAGGCAGTG 59.125 50.000 7.65 3.98 44.40 3.66
3633 3990 4.218635 TCAGTGCTCTTCAGTCGTTTATCT 59.781 41.667 0.00 0.00 0.00 1.98
3642 3999 3.977134 ATCATGTCAGTGCTCTTCAGT 57.023 42.857 0.00 0.00 0.00 3.41
3715 4073 9.574458 CAGATATGAGTAGAGTTCTTTTCGAAA 57.426 33.333 6.47 6.47 32.41 3.46
3716 4074 8.957466 TCAGATATGAGTAGAGTTCTTTTCGAA 58.043 33.333 0.00 0.00 0.00 3.71
3717 4075 8.507524 TCAGATATGAGTAGAGTTCTTTTCGA 57.492 34.615 0.00 0.00 0.00 3.71
3718 4076 9.574458 TTTCAGATATGAGTAGAGTTCTTTTCG 57.426 33.333 0.00 0.00 0.00 3.46
3721 4079 9.868277 CACTTTCAGATATGAGTAGAGTTCTTT 57.132 33.333 8.12 0.00 0.00 2.52
3722 4080 7.978975 GCACTTTCAGATATGAGTAGAGTTCTT 59.021 37.037 8.12 0.00 0.00 2.52
3723 4081 7.417342 GGCACTTTCAGATATGAGTAGAGTTCT 60.417 40.741 8.12 0.00 0.00 3.01
3724 4082 6.699642 GGCACTTTCAGATATGAGTAGAGTTC 59.300 42.308 8.12 0.00 0.00 3.01
3725 4083 6.382570 AGGCACTTTCAGATATGAGTAGAGTT 59.617 38.462 8.12 0.00 27.25 3.01
3726 4084 5.896678 AGGCACTTTCAGATATGAGTAGAGT 59.103 40.000 8.12 1.68 27.25 3.24
3727 4085 6.040278 TCAGGCACTTTCAGATATGAGTAGAG 59.960 42.308 8.12 2.81 34.60 2.43
3728 4086 5.893824 TCAGGCACTTTCAGATATGAGTAGA 59.106 40.000 8.12 0.00 34.60 2.59
3729 4087 6.154203 TCAGGCACTTTCAGATATGAGTAG 57.846 41.667 0.00 0.00 34.60 2.57
3730 4088 5.452496 GCTCAGGCACTTTCAGATATGAGTA 60.452 44.000 0.00 0.00 34.60 2.59
3731 4089 4.682859 GCTCAGGCACTTTCAGATATGAGT 60.683 45.833 0.00 0.00 34.60 3.41
3732 4090 3.808726 GCTCAGGCACTTTCAGATATGAG 59.191 47.826 0.00 0.00 34.60 2.90
3733 4091 3.198417 TGCTCAGGCACTTTCAGATATGA 59.802 43.478 0.00 0.00 44.28 2.15
3734 4092 3.538591 TGCTCAGGCACTTTCAGATATG 58.461 45.455 0.00 0.00 44.28 1.78
3735 4093 3.920231 TGCTCAGGCACTTTCAGATAT 57.080 42.857 0.00 0.00 44.28 1.63
3757 4115 2.230992 CCTGGCAATTCATTCGGTTCAA 59.769 45.455 0.00 0.00 0.00 2.69
3764 4122 0.526954 CGCAGCCTGGCAATTCATTC 60.527 55.000 22.65 0.00 0.00 2.67
3773 4131 2.040544 ACATTGTACGCAGCCTGGC 61.041 57.895 11.65 11.65 0.00 4.85
3774 4132 1.647545 CCACATTGTACGCAGCCTGG 61.648 60.000 0.00 0.00 0.00 4.45
3813 4171 5.665459 AGGATCGAGTTCTGAATAGTTTGG 58.335 41.667 0.00 0.00 0.00 3.28
3904 4262 9.344772 TGTTAGTGTGTTGGTTCTTGTTAATAT 57.655 29.630 0.00 0.00 0.00 1.28
3918 4276 5.689383 AGGTAATGCTTGTTAGTGTGTTG 57.311 39.130 0.00 0.00 0.00 3.33
4010 4368 0.391927 CGGAATGGTGAAGGGCGTAA 60.392 55.000 0.00 0.00 0.00 3.18
4128 4486 1.691976 ACGGTGAGATTTGACACAGGA 59.308 47.619 0.00 0.00 38.57 3.86
4147 4507 2.353011 CCTGCCACATGGTGAATTTCAC 60.353 50.000 19.17 19.17 46.23 3.18
4211 4571 2.240162 GATGAACTCGGTCCGGGCTT 62.240 60.000 12.23 4.77 0.00 4.35
4243 4603 2.032681 GGCCTGCTTCTTCACCGT 59.967 61.111 0.00 0.00 0.00 4.83
4498 4863 2.404923 AAACCCAAAACCCAAAACCG 57.595 45.000 0.00 0.00 0.00 4.44
4499 4864 3.422796 ACAAAACCCAAAACCCAAAACC 58.577 40.909 0.00 0.00 0.00 3.27
4500 4865 5.455056 AAACAAAACCCAAAACCCAAAAC 57.545 34.783 0.00 0.00 0.00 2.43
4501 4866 6.479972 AAAAACAAAACCCAAAACCCAAAA 57.520 29.167 0.00 0.00 0.00 2.44
4502 4867 7.309805 CCATAAAAACAAAACCCAAAACCCAAA 60.310 33.333 0.00 0.00 0.00 3.28
4503 4868 6.152831 CCATAAAAACAAAACCCAAAACCCAA 59.847 34.615 0.00 0.00 0.00 4.12
4504 4869 5.652452 CCATAAAAACAAAACCCAAAACCCA 59.348 36.000 0.00 0.00 0.00 4.51
4505 4870 5.652891 ACCATAAAAACAAAACCCAAAACCC 59.347 36.000 0.00 0.00 0.00 4.11
4522 4887 5.483583 ACCCGGTAACTACTTACACCATAAA 59.516 40.000 0.00 0.00 34.88 1.40
4632 5004 0.883833 CCACAATTCAGACCACCAGC 59.116 55.000 0.00 0.00 0.00 4.85
4639 5011 4.389374 TGAGAAGGTTCCACAATTCAGAC 58.611 43.478 0.00 0.00 0.00 3.51
4651 5023 2.746362 CACAGGCAGAATGAGAAGGTTC 59.254 50.000 0.00 0.00 39.69 3.62
4664 5036 3.933879 TGGTACACATCACAGGCAG 57.066 52.632 0.00 0.00 0.00 4.85
4681 5055 3.511182 CAGCTGACTGGAGTGAGTG 57.489 57.895 8.42 0.00 40.48 3.51
4696 5070 1.202110 CGTCAATTCTGGATGCACAGC 60.202 52.381 0.00 0.00 38.36 4.40
4716 5090 3.538591 TCTCTGATGCCATTGTCATCAC 58.461 45.455 6.29 0.00 43.63 3.06
4722 5096 5.302568 TGAAAGTTTTCTCTGATGCCATTGT 59.697 36.000 6.21 0.00 38.02 2.71
4725 5099 5.640189 CTGAAAGTTTTCTCTGATGCCAT 57.360 39.130 6.21 0.00 38.02 4.40
4741 5115 2.166270 GCGAAGGCCAGACTGAAAG 58.834 57.895 5.01 0.00 42.29 2.62
4753 5127 1.156736 ATTTCGAAGTGTGGCGAAGG 58.843 50.000 0.00 0.00 45.71 3.46
4757 5131 4.092821 TCATCTTAATTTCGAAGTGTGGCG 59.907 41.667 0.00 0.00 0.00 5.69
4758 5132 5.545658 TCATCTTAATTTCGAAGTGTGGC 57.454 39.130 0.00 0.00 0.00 5.01
4760 5134 9.611284 TGAATTTCATCTTAATTTCGAAGTGTG 57.389 29.630 0.00 0.00 0.00 3.82
4798 5173 9.077885 TGAAAAGCCAAATTACTAGACAAATCT 57.922 29.630 0.00 0.00 39.15 2.40
4822 5197 1.065199 GCCAGATCACTCCCACAATGA 60.065 52.381 0.00 0.00 0.00 2.57
4831 5206 4.197750 ACTTCATCATTGCCAGATCACTC 58.802 43.478 0.00 0.00 0.00 3.51
4832 5207 4.232188 ACTTCATCATTGCCAGATCACT 57.768 40.909 0.00 0.00 0.00 3.41
4834 5209 5.587443 CACTTACTTCATCATTGCCAGATCA 59.413 40.000 0.00 0.00 0.00 2.92
4840 5215 2.754552 TGCCACTTACTTCATCATTGCC 59.245 45.455 0.00 0.00 0.00 4.52
4841 5216 3.181493 CCTGCCACTTACTTCATCATTGC 60.181 47.826 0.00 0.00 0.00 3.56
4845 5220 2.906389 ACTCCTGCCACTTACTTCATCA 59.094 45.455 0.00 0.00 0.00 3.07
4847 5222 2.616510 GCACTCCTGCCACTTACTTCAT 60.617 50.000 0.00 0.00 37.45 2.57
4853 5228 1.888436 CTCCGCACTCCTGCCACTTA 61.888 60.000 0.00 0.00 40.73 2.24
4862 5237 4.965119 ATTTATTTCAACTCCGCACTCC 57.035 40.909 0.00 0.00 0.00 3.85
4863 5238 9.997482 TTATTTATTTATTTCAACTCCGCACTC 57.003 29.630 0.00 0.00 0.00 3.51
4939 5314 1.077140 TGCCTGGTGTTGCTGACAA 60.077 52.632 0.00 0.00 40.65 3.18
4940 5315 1.526686 CTGCCTGGTGTTGCTGACA 60.527 57.895 0.00 0.00 35.42 3.58
4941 5316 1.510480 GACTGCCTGGTGTTGCTGAC 61.510 60.000 0.00 0.00 0.00 3.51
4942 5317 1.227943 GACTGCCTGGTGTTGCTGA 60.228 57.895 0.00 0.00 0.00 4.26
4943 5318 1.512996 CTGACTGCCTGGTGTTGCTG 61.513 60.000 0.00 0.00 0.00 4.41
4944 5319 1.228063 CTGACTGCCTGGTGTTGCT 60.228 57.895 0.00 0.00 0.00 3.91
4945 5320 2.263741 CCTGACTGCCTGGTGTTGC 61.264 63.158 0.00 0.00 0.00 4.17
4946 5321 2.263741 GCCTGACTGCCTGGTGTTG 61.264 63.158 0.00 0.00 36.37 3.33
4952 5327 2.746671 CTGCTGCCTGACTGCCTG 60.747 66.667 0.00 0.00 42.24 4.85
4960 5335 0.391130 ATGCATTTTGCTGCTGCCTG 60.391 50.000 13.47 6.64 45.31 4.85
4965 5340 5.484715 ACTTTTATCATGCATTTTGCTGCT 58.515 33.333 0.00 0.00 45.31 4.24
4966 5341 5.789710 ACTTTTATCATGCATTTTGCTGC 57.210 34.783 0.00 0.00 45.31 5.25
5055 5430 3.991605 ATGCGACTACACGAAATGTTC 57.008 42.857 0.00 0.00 43.19 3.18
5113 5488 9.967346 CTCTTCAAATAATTCCTATGTCGTCTA 57.033 33.333 0.00 0.00 0.00 2.59
5203 5578 6.846283 GTGAAAATAGAGACAACACGAACAAG 59.154 38.462 0.00 0.00 0.00 3.16
5204 5579 6.314152 TGTGAAAATAGAGACAACACGAACAA 59.686 34.615 0.00 0.00 0.00 2.83
5206 5581 6.281848 TGTGAAAATAGAGACAACACGAAC 57.718 37.500 0.00 0.00 0.00 3.95
5208 5583 5.051307 CGTTGTGAAAATAGAGACAACACGA 60.051 40.000 12.77 0.00 45.52 4.35
5209 5584 5.130519 CGTTGTGAAAATAGAGACAACACG 58.869 41.667 12.77 0.00 45.52 4.49
5339 5714 1.202533 GGAAAGCAGGCGTATCAGCTA 60.203 52.381 0.00 0.00 36.07 3.32
5360 5735 0.960861 GCAGGCTCAACAACCCCTAC 60.961 60.000 0.00 0.00 0.00 3.18
5369 5744 0.886563 AATTGCTCTGCAGGCTCAAC 59.113 50.000 22.36 5.48 40.61 3.18
5370 5745 1.542915 GAAATTGCTCTGCAGGCTCAA 59.457 47.619 22.36 18.65 40.61 3.02
5385 5760 5.184864 TGATCCAAATGCGTACCTTGAAATT 59.815 36.000 0.00 0.00 0.00 1.82
5404 5779 3.194116 TCTTGAAGCCAGCATTTTGATCC 59.806 43.478 0.00 0.00 0.00 3.36
5405 5780 4.157289 TCTCTTGAAGCCAGCATTTTGATC 59.843 41.667 0.00 0.00 0.00 2.92
5406 5781 4.084287 TCTCTTGAAGCCAGCATTTTGAT 58.916 39.130 0.00 0.00 0.00 2.57
5414 5789 2.345124 ATCCATCTCTTGAAGCCAGC 57.655 50.000 0.00 0.00 0.00 4.85
5416 5791 4.267536 CTTCAATCCATCTCTTGAAGCCA 58.732 43.478 10.92 0.00 46.52 4.75
5433 5808 9.624697 GCTGTGAACATACATATTTTTCTTCAA 57.375 29.630 0.00 0.00 0.00 2.69
5434 5809 8.791675 TGCTGTGAACATACATATTTTTCTTCA 58.208 29.630 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.