Multiple sequence alignment - TraesCS7D01G339000

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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 TraesCS7D01G339000 chr7D 100.000 2487 0 0 919 3405 433069827 433072313 0.000000e+00 4593.0
1 TraesCS7D01G339000 chr7D 100.000 551 0 0 1 551 433068909 433069459 0.000000e+00 1018.0
2 TraesCS7D01G339000 chr7D 100.000 413 0 0 3635 4047 433072543 433072955 0.000000e+00 763.0
3 TraesCS7D01G339000 chr7A 88.831 958 92 10 1748 2702 483966084 483967029 0.000000e+00 1162.0
4 TraesCS7D01G339000 chr7A 89.233 743 61 12 980 1708 483965360 483966097 0.000000e+00 911.0
5 TraesCS7D01G339000 chr7A 91.866 418 28 3 2785 3202 483970898 483971309 2.710000e-161 579.0
6 TraesCS7D01G339000 chr7A 90.732 205 12 2 342 539 483965040 483965244 2.400000e-67 267.0
7 TraesCS7D01G339000 chr7B 92.968 711 33 4 1748 2448 449547762 449547059 0.000000e+00 1020.0
8 TraesCS7D01G339000 chr7B 93.912 657 31 2 2749 3405 449546755 449546108 0.000000e+00 983.0
9 TraesCS7D01G339000 chr7B 87.995 808 54 21 924 1706 449548539 449547750 0.000000e+00 915.0
10 TraesCS7D01G339000 chr7B 84.545 440 36 16 3637 4047 449546029 449545593 1.350000e-109 407.0
11 TraesCS7D01G339000 chr7B 93.548 186 11 1 2513 2697 449546939 449546754 3.980000e-70 276.0
12 TraesCS7D01G339000 chr7B 82.237 304 18 13 273 550 449548868 449548575 3.150000e-56 230.0
13 TraesCS7D01G339000 chr7B 84.553 123 10 4 7 120 449549087 449548965 3.310000e-21 113.0
14 TraesCS7D01G339000 chr1D 79.000 200 39 3 2085 2283 455766270 455766073 2.540000e-27 134.0
15 TraesCS7D01G339000 chr2B 100.000 37 0 0 1708 1744 541946677 541946713 7.260000e-08 69.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G339000 chr7D 433068909 433072955 4046 False 2124.666667 4593 100.000000 1 4047 3 chr7D.!!$F1 4046
1 TraesCS7D01G339000 chr7A 483965040 483971309 6269 False 729.750000 1162 90.165500 342 3202 4 chr7A.!!$F1 2860
2 TraesCS7D01G339000 chr7B 449545593 449549087 3494 True 563.428571 1020 88.536857 7 4047 7 chr7B.!!$R1 4040

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
164 187 0.109319 CATTACGTTTGGCCTGCACC 60.109 55.0 3.32 0.0 0.0 5.01 F
1332 1414 0.250295 CTGCAGTTTCGGGGAGTGAA 60.250 55.0 5.25 0.0 0.0 3.18 F
2119 2232 0.249120 TTCTGTCATGGTACCTGGCG 59.751 55.0 14.36 7.3 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1593 0.032952 GCTAAGACCACACACGGACA 59.967 55.0 0.0 0.0 0.0 4.02 R
2502 2671 0.108472 GGGCGGTAGTAAGTGGACAC 60.108 60.0 0.0 0.0 0.0 3.67 R
3659 7647 0.034477 AGCCCAATCCAGTAAACCGG 60.034 55.0 0.0 0.0 0.0 5.28 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 1.946768 TCAGAAACCGCCACTTTTCAG 59.053 47.619 0.00 0.00 34.68 3.02
37 38 2.553079 TTCAGGCACGTGACAAAAAC 57.447 45.000 26.11 0.73 0.00 2.43
41 42 2.032030 CAGGCACGTGACAAAAACCTAG 60.032 50.000 26.11 7.51 0.00 3.02
42 43 1.944709 GGCACGTGACAAAAACCTAGT 59.055 47.619 22.23 0.00 0.00 2.57
43 44 2.286772 GGCACGTGACAAAAACCTAGTG 60.287 50.000 22.23 0.00 0.00 2.74
44 45 2.353579 GCACGTGACAAAAACCTAGTGT 59.646 45.455 22.23 0.00 0.00 3.55
56 66 7.760340 ACAAAAACCTAGTGTAATTTTTCGCAA 59.240 29.630 0.00 0.00 33.18 4.85
72 82 1.439679 GCAAAGACCTACCACCTTCG 58.560 55.000 0.00 0.00 0.00 3.79
103 113 8.447833 GTGATCGGTTCAGACAATTTAAACATA 58.552 33.333 0.00 0.00 34.17 2.29
122 145 0.395312 ATTTACGATAGGGGTGGGCG 59.605 55.000 0.00 0.00 43.77 6.13
125 148 3.925090 CGATAGGGGTGGGCGGAC 61.925 72.222 0.00 0.00 0.00 4.79
143 166 0.750850 ACGTGGCACAGTAGTCAACT 59.249 50.000 19.09 0.00 41.80 3.16
146 169 1.070134 GTGGCACAGTAGTCAACTCCA 59.930 52.381 13.86 0.00 41.80 3.86
150 173 3.933332 GGCACAGTAGTCAACTCCATTAC 59.067 47.826 0.00 0.00 35.76 1.89
156 179 5.120208 CAGTAGTCAACTCCATTACGTTTGG 59.880 44.000 10.21 10.21 35.76 3.28
159 182 2.159382 CAACTCCATTACGTTTGGCCT 58.841 47.619 3.32 0.00 34.06 5.19
164 187 0.109319 CATTACGTTTGGCCTGCACC 60.109 55.000 3.32 0.00 0.00 5.01
167 190 1.169661 TACGTTTGGCCTGCACCTTG 61.170 55.000 3.32 0.00 0.00 3.61
168 191 2.736531 GTTTGGCCTGCACCTTGG 59.263 61.111 3.32 0.00 0.00 3.61
172 195 4.329545 GGCCTGCACCTTGGACGA 62.330 66.667 0.00 0.00 0.00 4.20
189 212 1.416401 ACGATATGACATGTGGGACCC 59.584 52.381 1.15 2.45 0.00 4.46
190 213 1.605457 CGATATGACATGTGGGACCCG 60.605 57.143 1.15 0.00 0.00 5.28
197 220 3.245346 TGTGGGACCCGCATGTCA 61.245 61.111 23.34 0.00 39.28 3.58
198 221 2.272146 GTGGGACCCGCATGTCAT 59.728 61.111 19.72 0.00 36.97 3.06
199 222 2.114670 GTGGGACCCGCATGTCATG 61.115 63.158 19.72 8.56 36.97 3.07
200 223 2.272146 GGGACCCGCATGTCATGT 59.728 61.111 14.26 0.00 36.97 3.21
201 224 2.114670 GGGACCCGCATGTCATGTG 61.115 63.158 17.81 17.81 40.37 3.21
206 229 3.501396 CGCATGTCATGTGGGACC 58.499 61.111 17.11 0.00 36.97 4.46
207 230 2.114670 CGCATGTCATGTGGGACCC 61.115 63.158 17.11 2.45 36.97 4.46
208 231 1.001020 GCATGTCATGTGGGACCCA 60.001 57.895 9.95 9.95 36.97 4.51
217 240 4.330056 TGGGACCCACATGTCAGT 57.670 55.556 9.95 0.00 36.97 3.41
218 241 1.760527 TGGGACCCACATGTCAGTG 59.239 57.895 9.95 0.00 36.97 3.66
219 242 1.059584 TGGGACCCACATGTCAGTGT 61.060 55.000 9.95 0.00 37.82 3.55
220 243 0.321653 GGGACCCACATGTCAGTGTC 60.322 60.000 5.33 0.12 37.82 3.67
221 244 0.670546 GGACCCACATGTCAGTGTCG 60.671 60.000 0.00 0.00 37.82 4.35
222 245 0.317160 GACCCACATGTCAGTGTCGA 59.683 55.000 0.00 0.00 37.82 4.20
223 246 0.976641 ACCCACATGTCAGTGTCGAT 59.023 50.000 0.00 0.00 37.82 3.59
224 247 2.165641 GACCCACATGTCAGTGTCGATA 59.834 50.000 0.00 0.00 37.82 2.92
225 248 2.565391 ACCCACATGTCAGTGTCGATAA 59.435 45.455 0.00 0.00 37.82 1.75
226 249 3.197766 ACCCACATGTCAGTGTCGATAAT 59.802 43.478 0.00 0.00 37.82 1.28
227 250 4.404394 ACCCACATGTCAGTGTCGATAATA 59.596 41.667 0.00 0.00 37.82 0.98
228 251 5.105106 ACCCACATGTCAGTGTCGATAATAA 60.105 40.000 0.00 0.00 37.82 1.40
229 252 5.991606 CCCACATGTCAGTGTCGATAATAAT 59.008 40.000 0.00 0.00 37.82 1.28
230 253 7.151976 CCCACATGTCAGTGTCGATAATAATA 58.848 38.462 0.00 0.00 37.82 0.98
231 254 7.329471 CCCACATGTCAGTGTCGATAATAATAG 59.671 40.741 0.00 0.00 37.82 1.73
232 255 7.867909 CCACATGTCAGTGTCGATAATAATAGT 59.132 37.037 0.00 0.00 37.82 2.12
233 256 9.893305 CACATGTCAGTGTCGATAATAATAGTA 57.107 33.333 0.00 0.00 34.83 1.82
314 340 0.254747 AGTCTCACTCTCCCTCCTCG 59.745 60.000 0.00 0.00 0.00 4.63
335 361 0.976073 TCCTCACGAACCATCTCCCC 60.976 60.000 0.00 0.00 0.00 4.81
336 362 1.522569 CTCACGAACCATCTCCCCC 59.477 63.158 0.00 0.00 0.00 5.40
338 364 1.221840 CACGAACCATCTCCCCCTG 59.778 63.158 0.00 0.00 0.00 4.45
339 365 1.229529 ACGAACCATCTCCCCCTGT 60.230 57.895 0.00 0.00 0.00 4.00
340 366 1.221840 CGAACCATCTCCCCCTGTG 59.778 63.158 0.00 0.00 0.00 3.66
415 462 4.537015 GCTACTGAAATTGTTTGTTCGCT 58.463 39.130 0.00 0.00 0.00 4.93
462 516 2.117156 CCCCATGCAGCTTCTTCGG 61.117 63.158 0.00 0.00 0.00 4.30
480 534 2.911926 GCCCTGCCTTCCTTCCAGT 61.912 63.158 0.00 0.00 0.00 4.00
514 570 1.004560 CAGGAAGCGTCTCCAGCAA 60.005 57.895 0.00 0.00 38.02 3.91
544 600 4.563184 CCAGCGAGTCAACAACTTATCTAC 59.437 45.833 0.00 0.00 38.74 2.59
547 603 4.496183 GCGAGTCAACAACTTATCTACGAG 59.504 45.833 0.00 0.00 38.74 4.18
550 606 6.402334 CGAGTCAACAACTTATCTACGAGACT 60.402 42.308 0.00 0.00 38.74 3.24
1068 1150 1.005394 GAGGACGCACGGAAAGGAA 60.005 57.895 0.00 0.00 0.00 3.36
1074 1156 2.677979 GCACGGAAAGGAAGTCGCC 61.678 63.158 0.00 0.00 0.00 5.54
1323 1405 2.031769 TGAAATCACAGCTGCAGTTTCG 60.032 45.455 15.27 2.44 0.00 3.46
1324 1406 0.877071 AATCACAGCTGCAGTTTCGG 59.123 50.000 15.27 1.84 0.00 4.30
1329 1411 2.032681 GCTGCAGTTTCGGGGAGT 59.967 61.111 16.64 0.00 0.00 3.85
1330 1412 2.328099 GCTGCAGTTTCGGGGAGTG 61.328 63.158 16.64 0.00 0.00 3.51
1331 1413 1.371183 CTGCAGTTTCGGGGAGTGA 59.629 57.895 5.25 0.00 0.00 3.41
1332 1414 0.250295 CTGCAGTTTCGGGGAGTGAA 60.250 55.000 5.25 0.00 0.00 3.18
1333 1415 0.534203 TGCAGTTTCGGGGAGTGAAC 60.534 55.000 0.00 0.00 0.00 3.18
1334 1416 0.250338 GCAGTTTCGGGGAGTGAACT 60.250 55.000 0.00 0.00 0.00 3.01
1335 1417 1.797025 CAGTTTCGGGGAGTGAACTC 58.203 55.000 1.63 1.63 42.14 3.01
1336 1418 0.317479 AGTTTCGGGGAGTGAACTCG 59.683 55.000 4.44 0.00 43.76 4.18
1337 1419 0.316204 GTTTCGGGGAGTGAACTCGA 59.684 55.000 4.44 0.00 43.76 4.04
1338 1420 0.601558 TTTCGGGGAGTGAACTCGAG 59.398 55.000 11.84 11.84 43.76 4.04
1339 1421 0.538977 TTCGGGGAGTGAACTCGAGT 60.539 55.000 13.58 13.58 43.76 4.18
1340 1422 1.213013 CGGGGAGTGAACTCGAGTG 59.787 63.158 20.85 0.00 43.76 3.51
1344 1426 2.484947 GGGGAGTGAACTCGAGTGTTTT 60.485 50.000 20.85 2.28 43.76 2.43
1345 1427 2.801111 GGGAGTGAACTCGAGTGTTTTC 59.199 50.000 20.85 13.39 43.76 2.29
1346 1428 3.454375 GGAGTGAACTCGAGTGTTTTCA 58.546 45.455 20.85 16.04 43.76 2.69
1348 1430 4.331717 GGAGTGAACTCGAGTGTTTTCAAA 59.668 41.667 20.85 0.00 43.76 2.69
1350 1432 6.436843 AGTGAACTCGAGTGTTTTCAAATT 57.563 33.333 20.85 5.59 30.00 1.82
1351 1433 6.852664 AGTGAACTCGAGTGTTTTCAAATTT 58.147 32.000 20.85 0.00 30.00 1.82
1353 1435 7.812669 AGTGAACTCGAGTGTTTTCAAATTTTT 59.187 29.630 20.85 0.00 30.00 1.94
1380 1476 1.201181 GTTATTGCCATCGTTGTGCCA 59.799 47.619 5.02 0.00 0.00 4.92
1394 1490 1.336702 TGTGCCAATGGTTTTCATCGC 60.337 47.619 0.00 0.00 34.44 4.58
1454 1550 1.828595 TCACGCTATCCTTGGCAAGTA 59.171 47.619 24.57 10.98 0.00 2.24
1474 1570 7.589954 GCAAGTAAATTTCTCTTCTTACGCAAA 59.410 33.333 0.00 0.00 31.07 3.68
1483 1579 8.542497 TTCTCTTCTTACGCAAAGCTAATTTA 57.458 30.769 0.00 0.00 34.97 1.40
1484 1580 8.186178 TCTCTTCTTACGCAAAGCTAATTTAG 57.814 34.615 0.00 0.00 34.97 1.85
1486 1582 8.991243 TCTTCTTACGCAAAGCTAATTTAGTA 57.009 30.769 5.38 0.00 34.97 1.82
1495 1591 7.530863 GCAAAGCTAATTTAGTATATCTGGGC 58.469 38.462 5.38 0.00 0.00 5.36
1496 1592 7.624344 GCAAAGCTAATTTAGTATATCTGGGCG 60.624 40.741 5.38 0.00 0.00 6.13
1497 1593 6.607004 AGCTAATTTAGTATATCTGGGCGT 57.393 37.500 5.38 0.00 0.00 5.68
1501 1604 4.595762 TTTAGTATATCTGGGCGTGTCC 57.404 45.455 0.00 0.00 0.00 4.02
1507 1610 4.602259 CTGGGCGTGTCCGTGTGT 62.602 66.667 0.00 0.00 36.15 3.72
1508 1611 4.901123 TGGGCGTGTCCGTGTGTG 62.901 66.667 0.00 0.00 36.15 3.82
1510 1613 4.903010 GGCGTGTCCGTGTGTGGT 62.903 66.667 0.00 0.00 36.15 4.16
1513 1616 1.227147 CGTGTCCGTGTGTGGTCTT 60.227 57.895 0.00 0.00 0.00 3.01
1525 1628 6.097356 CGTGTGTGGTCTTAGCTTATTTCTA 58.903 40.000 0.00 0.00 0.00 2.10
1529 1632 7.386848 TGTGTGGTCTTAGCTTATTTCTAACAC 59.613 37.037 0.00 0.00 0.00 3.32
1544 1647 2.380084 AACACGCACACGATATTCCT 57.620 45.000 0.00 0.00 43.93 3.36
1657 1760 1.831580 GCTGCTTTCCTGATGGAGTT 58.168 50.000 0.00 0.00 44.24 3.01
1696 1799 1.190643 GCTTCCTCAGAGCTACCAGT 58.809 55.000 0.00 0.00 37.18 4.00
1697 1800 2.379972 GCTTCCTCAGAGCTACCAGTA 58.620 52.381 0.00 0.00 37.18 2.74
1698 1801 2.360801 GCTTCCTCAGAGCTACCAGTAG 59.639 54.545 0.23 0.23 37.18 2.57
1719 1822 3.752339 GCTTTTGCAGAGGCCGGG 61.752 66.667 2.18 0.00 46.58 5.73
1720 1823 3.064324 CTTTTGCAGAGGCCGGGG 61.064 66.667 2.18 0.00 40.13 5.73
1721 1824 3.567579 CTTTTGCAGAGGCCGGGGA 62.568 63.158 2.18 0.00 40.13 4.81
1722 1825 3.567579 TTTTGCAGAGGCCGGGGAG 62.568 63.158 2.18 0.00 40.13 4.30
1738 1841 2.474410 GGAGCTCCCTCTTTTCGAAA 57.526 50.000 23.19 6.47 38.21 3.46
1739 1842 2.779506 GGAGCTCCCTCTTTTCGAAAA 58.220 47.619 23.19 21.35 38.21 2.29
1740 1843 3.146847 GGAGCTCCCTCTTTTCGAAAAA 58.853 45.455 23.19 13.22 38.21 1.94
1794 1897 5.445845 GTCACCACTGTAAAATTTACACGG 58.554 41.667 19.94 19.94 0.00 4.94
1821 1931 7.357429 TCTAGCTTGGGTAATAAGTAGAACC 57.643 40.000 0.00 0.00 0.00 3.62
1829 1939 5.069516 GGGTAATAAGTAGAACCGTGATGGA 59.930 44.000 0.00 0.00 42.00 3.41
2011 2124 3.842007 AGCCATTCTCTGAATCTCTGG 57.158 47.619 0.00 0.00 0.00 3.86
2074 2187 2.037772 TGGCTGTCTTTCTTGTCCTCTC 59.962 50.000 0.00 0.00 0.00 3.20
2119 2232 0.249120 TTCTGTCATGGTACCTGGCG 59.751 55.000 14.36 7.30 0.00 5.69
2170 2283 1.519234 CGTCGCCAAGCTCTGCATA 60.519 57.895 8.02 0.00 0.00 3.14
2182 2295 2.200067 CTCTGCATAGTTCTTCTGCCG 58.800 52.381 0.00 0.00 35.02 5.69
2189 2302 0.952984 AGTTCTTCTGCCGCTGCTTC 60.953 55.000 0.70 0.00 38.71 3.86
2301 2414 6.238648 CCAATTCAGTTCAGTTACTTTCCGTT 60.239 38.462 0.00 0.00 0.00 4.44
2316 2429 9.846248 TTACTTTCCGTTTACTATAACTCTGAC 57.154 33.333 0.00 0.00 0.00 3.51
2342 2455 4.183865 TCCTGAATTAAGATCACACAGCG 58.816 43.478 0.00 0.00 0.00 5.18
2349 2462 2.046892 ATCACACAGCGGCTGACC 60.047 61.111 34.70 0.00 35.18 4.02
2360 2473 3.386543 GGCTGACCGTGCTTGATAT 57.613 52.632 0.00 0.00 0.00 1.63
2414 2527 0.602905 ACCTTCAGTTCTTTCCGCCG 60.603 55.000 0.00 0.00 0.00 6.46
2429 2542 2.033194 GCCGCCCTACAGTGAACAC 61.033 63.158 0.00 0.00 0.00 3.32
2448 2561 4.127171 ACACGGTATGATGCATAGTTTCC 58.873 43.478 0.00 0.00 0.00 3.13
2449 2562 3.184379 CACGGTATGATGCATAGTTTCCG 59.816 47.826 20.29 20.29 37.86 4.30
2450 2563 3.181469 ACGGTATGATGCATAGTTTCCGT 60.181 43.478 21.23 21.23 39.17 4.69
2452 2565 4.084537 CGGTATGATGCATAGTTTCCGTTC 60.085 45.833 16.32 0.00 31.84 3.95
2453 2566 4.084537 GGTATGATGCATAGTTTCCGTTCG 60.085 45.833 0.00 0.00 0.00 3.95
2454 2567 2.276201 TGATGCATAGTTTCCGTTCGG 58.724 47.619 0.00 4.74 0.00 4.30
2458 2571 4.652421 TGCATAGTTTCCGTTCGGTATA 57.348 40.909 11.04 1.56 0.00 1.47
2459 2572 5.204409 TGCATAGTTTCCGTTCGGTATAT 57.796 39.130 11.04 3.58 0.00 0.86
2460 2573 5.603596 TGCATAGTTTCCGTTCGGTATATT 58.396 37.500 11.04 0.00 0.00 1.28
2462 2575 7.380536 TGCATAGTTTCCGTTCGGTATATTAT 58.619 34.615 11.04 2.80 0.00 1.28
2464 2577 9.525409 GCATAGTTTCCGTTCGGTATATTATAT 57.475 33.333 11.04 0.00 0.00 0.86
2472 2585 9.797556 TCCGTTCGGTATATTATATCAGAATTG 57.202 33.333 11.04 0.00 0.00 2.32
2547 2716 1.905922 GCTTGAAGACGTCTGCAGCC 61.906 60.000 24.98 16.31 32.06 4.85
2625 2795 2.043526 AGGGATGGCATTCAGAAAACCT 59.956 45.455 8.30 0.83 0.00 3.50
2635 2805 7.450014 TGGCATTCAGAAAACCTATAGTCAAAA 59.550 33.333 0.00 0.00 0.00 2.44
2697 2867 5.063180 TGTTCTTGAATCACCAATGCATC 57.937 39.130 0.00 0.00 0.00 3.91
2698 2868 4.768448 TGTTCTTGAATCACCAATGCATCT 59.232 37.500 0.00 0.00 0.00 2.90
2699 2869 5.106038 TGTTCTTGAATCACCAATGCATCTC 60.106 40.000 0.00 0.00 0.00 2.75
2700 2870 3.624410 TCTTGAATCACCAATGCATCTCG 59.376 43.478 0.00 0.00 0.00 4.04
2701 2871 2.989909 TGAATCACCAATGCATCTCGT 58.010 42.857 0.00 0.00 0.00 4.18
2702 2872 2.938451 TGAATCACCAATGCATCTCGTC 59.062 45.455 0.00 0.00 0.00 4.20
2703 2873 2.996249 ATCACCAATGCATCTCGTCT 57.004 45.000 0.00 0.00 0.00 4.18
2704 2874 2.768253 TCACCAATGCATCTCGTCTT 57.232 45.000 0.00 0.00 0.00 3.01
2705 2875 3.057969 TCACCAATGCATCTCGTCTTT 57.942 42.857 0.00 0.00 0.00 2.52
2706 2876 3.411446 TCACCAATGCATCTCGTCTTTT 58.589 40.909 0.00 0.00 0.00 2.27
2707 2877 3.820467 TCACCAATGCATCTCGTCTTTTT 59.180 39.130 0.00 0.00 0.00 1.94
2708 2878 4.083324 TCACCAATGCATCTCGTCTTTTTC 60.083 41.667 0.00 0.00 0.00 2.29
2709 2879 4.074970 ACCAATGCATCTCGTCTTTTTCT 58.925 39.130 0.00 0.00 0.00 2.52
2710 2880 4.520492 ACCAATGCATCTCGTCTTTTTCTT 59.480 37.500 0.00 0.00 0.00 2.52
2711 2881 5.010012 ACCAATGCATCTCGTCTTTTTCTTT 59.990 36.000 0.00 0.00 0.00 2.52
2712 2882 5.922544 CCAATGCATCTCGTCTTTTTCTTTT 59.077 36.000 0.00 0.00 0.00 2.27
2713 2883 6.129009 CCAATGCATCTCGTCTTTTTCTTTTG 60.129 38.462 0.00 0.00 0.00 2.44
2714 2884 4.290155 TGCATCTCGTCTTTTTCTTTTGC 58.710 39.130 0.00 0.00 0.00 3.68
2715 2885 3.358993 GCATCTCGTCTTTTTCTTTTGCG 59.641 43.478 0.00 0.00 0.00 4.85
2716 2886 4.772434 CATCTCGTCTTTTTCTTTTGCGA 58.228 39.130 0.00 0.00 0.00 5.10
2717 2887 4.452890 TCTCGTCTTTTTCTTTTGCGAG 57.547 40.909 0.00 0.00 43.60 5.03
2718 2888 3.869246 TCTCGTCTTTTTCTTTTGCGAGT 59.131 39.130 10.16 0.00 43.02 4.18
2719 2889 5.045215 TCTCGTCTTTTTCTTTTGCGAGTA 58.955 37.500 10.16 0.00 43.02 2.59
2720 2890 5.521010 TCTCGTCTTTTTCTTTTGCGAGTAA 59.479 36.000 10.16 0.00 43.02 2.24
2721 2891 5.495502 TCGTCTTTTTCTTTTGCGAGTAAC 58.504 37.500 0.00 0.00 0.00 2.50
2722 2892 5.063691 TCGTCTTTTTCTTTTGCGAGTAACA 59.936 36.000 0.00 0.00 0.00 2.41
2723 2893 5.169032 CGTCTTTTTCTTTTGCGAGTAACAC 59.831 40.000 0.00 0.00 0.00 3.32
2724 2894 5.454554 GTCTTTTTCTTTTGCGAGTAACACC 59.545 40.000 0.00 0.00 0.00 4.16
2725 2895 4.966965 TTTTCTTTTGCGAGTAACACCA 57.033 36.364 0.00 0.00 0.00 4.17
2726 2896 4.966965 TTTCTTTTGCGAGTAACACCAA 57.033 36.364 0.00 0.00 0.00 3.67
2727 2897 5.508200 TTTCTTTTGCGAGTAACACCAAT 57.492 34.783 0.00 0.00 0.00 3.16
2728 2898 4.481930 TCTTTTGCGAGTAACACCAATG 57.518 40.909 0.00 0.00 0.00 2.82
2729 2899 2.697431 TTTGCGAGTAACACCAATGC 57.303 45.000 0.00 0.00 0.00 3.56
2730 2900 1.598882 TTGCGAGTAACACCAATGCA 58.401 45.000 0.00 0.00 0.00 3.96
2731 2901 1.819928 TGCGAGTAACACCAATGCAT 58.180 45.000 0.00 0.00 0.00 3.96
2740 2910 3.673746 ACACCAATGCATATCGTTTCG 57.326 42.857 0.00 0.00 0.00 3.46
2754 2924 7.253983 GCATATCGTTTCGAACAAAGATAGTCA 60.254 37.037 0.00 0.00 39.99 3.41
2900 6888 1.390123 CGTACTTGGAGCACATTCGTG 59.610 52.381 0.00 0.00 46.56 4.35
2922 6910 2.544726 CGGAGGGTGAACTGAAAGC 58.455 57.895 0.00 0.00 37.60 3.51
3067 7055 2.424601 ACAGATGAATGCATGGTTTCCG 59.575 45.455 0.00 0.00 34.11 4.30
3079 7067 8.785329 ATGCATGGTTTCCGTTTATTTATTTT 57.215 26.923 0.00 0.00 0.00 1.82
3180 7168 7.391148 AACCGCCAATAGCATAATTATAAGG 57.609 36.000 0.00 0.00 44.04 2.69
3206 7194 5.032863 GGAATTTCATGAATGCAGAAGTCG 58.967 41.667 9.40 0.00 0.00 4.18
3215 7203 7.928167 TCATGAATGCAGAAGTCGTTTATAGAT 59.072 33.333 0.00 0.00 0.00 1.98
3216 7204 8.554528 CATGAATGCAGAAGTCGTTTATAGATT 58.445 33.333 0.00 0.00 0.00 2.40
3217 7205 8.492673 TGAATGCAGAAGTCGTTTATAGATTT 57.507 30.769 0.00 0.00 0.00 2.17
3218 7206 8.946085 TGAATGCAGAAGTCGTTTATAGATTTT 58.054 29.630 0.00 0.00 0.00 1.82
3219 7207 9.427127 GAATGCAGAAGTCGTTTATAGATTTTC 57.573 33.333 0.00 0.00 0.00 2.29
3220 7208 7.303634 TGCAGAAGTCGTTTATAGATTTTCC 57.696 36.000 0.00 0.00 0.00 3.13
3221 7209 7.103641 TGCAGAAGTCGTTTATAGATTTTCCT 58.896 34.615 0.00 0.00 0.00 3.36
3222 7210 7.606456 TGCAGAAGTCGTTTATAGATTTTCCTT 59.394 33.333 0.00 0.00 0.00 3.36
3288 7276 1.997874 GGAGTGATGGGCCCTGTCT 60.998 63.158 25.70 15.70 0.00 3.41
3294 7282 0.257039 GATGGGCCCTGTCTTCACAT 59.743 55.000 25.70 3.84 0.00 3.21
3312 7300 5.693961 TCACATACAATCCTAATGCCACAT 58.306 37.500 0.00 0.00 0.00 3.21
3322 7310 3.316308 CCTAATGCCACATAACTTGGAGC 59.684 47.826 0.00 0.00 36.02 4.70
3354 7342 2.787723 CAATTGTGCTTCGGTAGTCG 57.212 50.000 0.00 0.00 40.90 4.18
3367 7355 2.573369 GGTAGTCGGTCTCATCTGCTA 58.427 52.381 0.00 0.00 0.00 3.49
3672 7660 1.003928 GTTCCCACCGGTTTACTGGAT 59.996 52.381 2.97 0.00 45.36 3.41
3677 7665 0.323087 ACCGGTTTACTGGATTGGGC 60.323 55.000 14.55 0.00 45.36 5.36
3682 7670 3.366985 CGGTTTACTGGATTGGGCTTTTC 60.367 47.826 0.00 0.00 0.00 2.29
3684 7672 3.426787 TTACTGGATTGGGCTTTTCGA 57.573 42.857 0.00 0.00 0.00 3.71
3687 7675 1.406539 CTGGATTGGGCTTTTCGATGG 59.593 52.381 0.00 0.00 0.00 3.51
3862 7856 8.594881 TTTGTGCTTTTTCTGTAGTTTGAAAA 57.405 26.923 0.00 0.00 39.47 2.29
3863 7857 7.575332 TGTGCTTTTTCTGTAGTTTGAAAAC 57.425 32.000 0.00 0.00 40.46 2.43
3868 7862 9.741168 GCTTTTTCTGTAGTTTGAAAACTTTTC 57.259 29.630 13.30 7.24 46.52 2.29
4038 8053 9.244799 GTGAACTTTCCTTAAATTCGTGATTTT 57.755 29.630 5.19 0.00 38.80 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.755655 TGAAAAGTGGCGGTTTCTGAAA 59.244 40.909 0.00 0.00 35.26 2.69
1 2 2.357637 CTGAAAAGTGGCGGTTTCTGAA 59.642 45.455 8.28 0.00 35.74 3.02
2 3 1.946768 CTGAAAAGTGGCGGTTTCTGA 59.053 47.619 8.28 0.00 35.74 3.27
3 4 1.001378 CCTGAAAAGTGGCGGTTTCTG 60.001 52.381 8.28 7.63 35.26 3.02
4 5 1.318576 CCTGAAAAGTGGCGGTTTCT 58.681 50.000 8.28 0.00 35.26 2.52
5 6 0.318699 GCCTGAAAAGTGGCGGTTTC 60.319 55.000 0.00 1.64 39.71 2.78
18 19 1.133407 GGTTTTTGTCACGTGCCTGAA 59.867 47.619 11.67 0.29 0.00 3.02
22 23 1.944709 ACTAGGTTTTTGTCACGTGCC 59.055 47.619 11.67 0.00 0.00 5.01
37 38 6.072673 AGGTCTTTGCGAAAAATTACACTAGG 60.073 38.462 0.00 0.00 0.00 3.02
41 42 5.854866 GGTAGGTCTTTGCGAAAAATTACAC 59.145 40.000 0.00 0.00 0.00 2.90
42 43 5.531659 TGGTAGGTCTTTGCGAAAAATTACA 59.468 36.000 0.00 0.00 0.00 2.41
43 44 5.854866 GTGGTAGGTCTTTGCGAAAAATTAC 59.145 40.000 0.00 0.00 0.00 1.89
44 45 5.048573 GGTGGTAGGTCTTTGCGAAAAATTA 60.049 40.000 0.00 0.00 0.00 1.40
72 82 3.587797 TGTCTGAACCGATCACTAACC 57.412 47.619 0.00 0.00 33.47 2.85
103 113 0.395312 CGCCCACCCCTATCGTAAAT 59.605 55.000 0.00 0.00 0.00 1.40
108 118 3.925090 GTCCGCCCACCCCTATCG 61.925 72.222 0.00 0.00 0.00 2.92
122 145 0.032952 TTGACTACTGTGCCACGTCC 59.967 55.000 0.00 0.00 0.00 4.79
125 148 1.419374 GAGTTGACTACTGTGCCACG 58.581 55.000 0.00 0.00 37.17 4.94
129 152 3.612860 CGTAATGGAGTTGACTACTGTGC 59.387 47.826 0.00 0.00 37.17 4.57
132 155 5.120208 CCAAACGTAATGGAGTTGACTACTG 59.880 44.000 13.64 0.00 40.56 2.74
134 157 4.142966 GCCAAACGTAATGGAGTTGACTAC 60.143 45.833 21.08 0.16 40.56 2.73
143 166 0.250945 TGCAGGCCAAACGTAATGGA 60.251 50.000 21.08 0.44 40.56 3.41
146 169 0.251165 AGGTGCAGGCCAAACGTAAT 60.251 50.000 5.01 0.00 0.00 1.89
150 173 2.336088 CAAGGTGCAGGCCAAACG 59.664 61.111 5.01 0.00 0.00 3.60
156 179 0.179045 ATATCGTCCAAGGTGCAGGC 60.179 55.000 0.00 0.00 0.00 4.85
159 182 1.552792 TGTCATATCGTCCAAGGTGCA 59.447 47.619 0.00 0.00 0.00 4.57
164 187 3.133691 CCCACATGTCATATCGTCCAAG 58.866 50.000 0.00 0.00 0.00 3.61
167 190 2.548067 GGTCCCACATGTCATATCGTCC 60.548 54.545 0.00 0.00 0.00 4.79
168 191 2.548067 GGGTCCCACATGTCATATCGTC 60.548 54.545 1.78 0.00 0.00 4.20
172 195 0.108585 GCGGGTCCCACATGTCATAT 59.891 55.000 9.12 0.00 0.00 1.78
189 212 2.114670 GGGTCCCACATGACATGCG 61.115 63.158 15.49 5.88 36.97 4.73
190 213 1.001020 TGGGTCCCACATGACATGC 60.001 57.895 15.49 0.00 36.97 4.06
200 223 1.059584 ACACTGACATGTGGGTCCCA 61.060 55.000 6.47 6.47 41.84 4.37
201 224 0.321653 GACACTGACATGTGGGTCCC 60.322 60.000 1.15 0.00 41.84 4.46
202 225 0.670546 CGACACTGACATGTGGGTCC 60.671 60.000 1.15 0.00 41.84 4.46
203 226 0.317160 TCGACACTGACATGTGGGTC 59.683 55.000 1.15 5.71 41.84 4.46
204 227 0.976641 ATCGACACTGACATGTGGGT 59.023 50.000 1.15 0.00 41.84 4.51
205 228 2.959507 TATCGACACTGACATGTGGG 57.040 50.000 1.15 0.00 41.84 4.61
206 229 7.867909 ACTATTATTATCGACACTGACATGTGG 59.132 37.037 1.15 0.00 41.84 4.17
207 230 8.803201 ACTATTATTATCGACACTGACATGTG 57.197 34.615 1.15 0.00 43.07 3.21
296 319 0.750182 CCGAGGAGGGAGAGTGAGAC 60.750 65.000 0.00 0.00 35.97 3.36
297 320 1.208844 ACCGAGGAGGGAGAGTGAGA 61.209 60.000 0.00 0.00 46.96 3.27
298 321 0.750182 GACCGAGGAGGGAGAGTGAG 60.750 65.000 0.00 0.00 46.96 3.51
299 322 1.303615 GACCGAGGAGGGAGAGTGA 59.696 63.158 0.00 0.00 46.96 3.41
300 323 1.755008 GGACCGAGGAGGGAGAGTG 60.755 68.421 0.00 0.00 46.96 3.51
301 324 1.928714 GAGGACCGAGGAGGGAGAGT 61.929 65.000 0.00 0.00 46.96 3.24
335 361 2.320587 GCGAACACAGGAGCACAGG 61.321 63.158 0.00 0.00 0.00 4.00
336 362 2.320587 GGCGAACACAGGAGCACAG 61.321 63.158 0.00 0.00 0.00 3.66
338 364 3.050275 GGGCGAACACAGGAGCAC 61.050 66.667 0.00 0.00 0.00 4.40
339 365 3.555324 TGGGCGAACACAGGAGCA 61.555 61.111 0.00 0.00 0.00 4.26
340 366 3.050275 GTGGGCGAACACAGGAGC 61.050 66.667 5.21 0.00 40.99 4.70
462 516 2.044551 CTGGAAGGAAGGCAGGGC 60.045 66.667 0.00 0.00 0.00 5.19
480 534 0.378962 CCTGCGTTTGTTCGTGGAAA 59.621 50.000 0.00 0.00 0.00 3.13
514 570 0.814010 GTTGACTCGCTGGTTGGTGT 60.814 55.000 0.00 0.00 0.00 4.16
929 985 1.725164 CGAGTTGAGGGCGTTTTCTAC 59.275 52.381 0.00 0.00 0.00 2.59
1283 1365 8.048514 TGATTTCATCAGTGATGTATGGAAGAA 58.951 33.333 28.03 12.86 40.55 2.52
1284 1366 7.496920 GTGATTTCATCAGTGATGTATGGAAGA 59.503 37.037 28.03 7.75 40.53 2.87
1285 1367 7.281549 TGTGATTTCATCAGTGATGTATGGAAG 59.718 37.037 28.03 4.92 40.53 3.46
1323 1405 0.680061 AACACTCGAGTTCACTCCCC 59.320 55.000 17.26 0.00 39.79 4.81
1324 1406 2.528041 AAACACTCGAGTTCACTCCC 57.472 50.000 17.26 0.00 39.79 4.30
1329 1411 9.796120 ATAAAAATTTGAAAACACTCGAGTTCA 57.204 25.926 17.26 14.47 0.00 3.18
1331 1413 8.539674 GCATAAAAATTTGAAAACACTCGAGTT 58.460 29.630 17.26 0.01 0.00 3.01
1332 1414 7.704472 TGCATAAAAATTTGAAAACACTCGAGT 59.296 29.630 13.58 13.58 0.00 4.18
1333 1415 8.060020 TGCATAAAAATTTGAAAACACTCGAG 57.940 30.769 11.84 11.84 0.00 4.04
1334 1416 7.168972 CCTGCATAAAAATTTGAAAACACTCGA 59.831 33.333 0.00 0.00 0.00 4.04
1335 1417 7.042791 ACCTGCATAAAAATTTGAAAACACTCG 60.043 33.333 0.00 0.00 0.00 4.18
1336 1418 8.141835 ACCTGCATAAAAATTTGAAAACACTC 57.858 30.769 0.00 0.00 0.00 3.51
1337 1419 8.504812 AACCTGCATAAAAATTTGAAAACACT 57.495 26.923 0.00 0.00 0.00 3.55
1344 1426 7.164122 TGGCAATAACCTGCATAAAAATTTGA 58.836 30.769 0.00 0.00 44.52 2.69
1345 1427 7.375106 TGGCAATAACCTGCATAAAAATTTG 57.625 32.000 0.00 0.00 44.52 2.32
1346 1428 7.011295 CGATGGCAATAACCTGCATAAAAATTT 59.989 33.333 0.00 0.00 44.52 1.82
1348 1430 5.984926 CGATGGCAATAACCTGCATAAAAAT 59.015 36.000 0.00 0.00 44.52 1.82
1350 1432 4.400884 ACGATGGCAATAACCTGCATAAAA 59.599 37.500 0.00 0.00 44.52 1.52
1351 1433 3.951037 ACGATGGCAATAACCTGCATAAA 59.049 39.130 0.00 0.00 44.52 1.40
1353 1435 3.207265 ACGATGGCAATAACCTGCATA 57.793 42.857 0.00 0.00 44.52 3.14
1380 1476 6.545666 TGTATATTCCAGCGATGAAAACCATT 59.454 34.615 0.06 0.00 35.17 3.16
1394 1490 6.924913 TCCTCCTCTTGATGTATATTCCAG 57.075 41.667 0.00 0.00 0.00 3.86
1454 1550 6.319141 AGCTTTGCGTAAGAAGAGAAATTT 57.681 33.333 2.82 0.00 43.02 1.82
1474 1570 6.014499 ACACGCCCAGATATACTAAATTAGCT 60.014 38.462 0.00 0.00 0.00 3.32
1483 1579 0.959553 CGGACACGCCCAGATATACT 59.040 55.000 0.00 0.00 0.00 2.12
1484 1580 0.672342 ACGGACACGCCCAGATATAC 59.328 55.000 0.00 0.00 46.04 1.47
1486 1582 1.327690 ACACGGACACGCCCAGATAT 61.328 55.000 0.00 0.00 46.04 1.63
1488 1584 3.311110 ACACGGACACGCCCAGAT 61.311 61.111 0.00 0.00 46.04 2.90
1496 1592 1.779569 CTAAGACCACACACGGACAC 58.220 55.000 0.00 0.00 0.00 3.67
1497 1593 0.032952 GCTAAGACCACACACGGACA 59.967 55.000 0.00 0.00 0.00 4.02
1501 1604 4.929808 AGAAATAAGCTAAGACCACACACG 59.070 41.667 0.00 0.00 0.00 4.49
1507 1610 5.579511 GCGTGTTAGAAATAAGCTAAGACCA 59.420 40.000 0.00 0.00 38.29 4.02
1508 1611 5.579511 TGCGTGTTAGAAATAAGCTAAGACC 59.420 40.000 0.00 0.00 38.29 3.85
1509 1612 6.090358 TGTGCGTGTTAGAAATAAGCTAAGAC 59.910 38.462 0.00 0.00 38.21 3.01
1510 1613 6.090358 GTGTGCGTGTTAGAAATAAGCTAAGA 59.910 38.462 0.00 0.00 0.00 2.10
1513 1616 4.325204 CGTGTGCGTGTTAGAAATAAGCTA 59.675 41.667 0.00 0.00 0.00 3.32
1525 1628 2.380084 AGGAATATCGTGTGCGTGTT 57.620 45.000 0.00 0.00 39.49 3.32
1529 1632 2.469826 TGCTTAGGAATATCGTGTGCG 58.530 47.619 0.00 0.00 39.92 5.34
1536 1639 2.909662 AGGAGGCCTGCTTAGGAATATC 59.090 50.000 23.00 0.00 29.57 1.63
1564 1667 6.270815 GGTCACGATAGCAGTTATAAGAACA 58.729 40.000 0.00 0.00 42.67 3.18
1657 1760 1.980052 GTGGGATGAACTCACCGGA 59.020 57.895 9.46 0.00 43.61 5.14
1692 1795 1.881973 TCTGCAAAAGCAAGCTACTGG 59.118 47.619 0.00 0.00 0.00 4.00
1693 1796 2.095364 CCTCTGCAAAAGCAAGCTACTG 60.095 50.000 0.00 0.00 0.00 2.74
1694 1797 2.157738 CCTCTGCAAAAGCAAGCTACT 58.842 47.619 0.00 0.00 0.00 2.57
1695 1798 1.402062 GCCTCTGCAAAAGCAAGCTAC 60.402 52.381 0.00 0.00 37.47 3.58
1696 1799 0.883833 GCCTCTGCAAAAGCAAGCTA 59.116 50.000 0.00 0.00 37.47 3.32
1697 1800 1.664306 GCCTCTGCAAAAGCAAGCT 59.336 52.632 0.00 0.00 37.47 3.74
1698 1801 1.373873 GGCCTCTGCAAAAGCAAGC 60.374 57.895 0.00 0.00 40.13 4.01
1699 1802 1.080974 CGGCCTCTGCAAAAGCAAG 60.081 57.895 0.00 0.00 40.13 4.01
1700 1803 2.563798 CCGGCCTCTGCAAAAGCAA 61.564 57.895 0.00 0.00 40.13 3.91
1701 1804 2.985282 CCGGCCTCTGCAAAAGCA 60.985 61.111 0.00 0.00 40.13 3.91
1702 1805 3.752339 CCCGGCCTCTGCAAAAGC 61.752 66.667 0.00 0.00 40.13 3.51
1703 1806 3.064324 CCCCGGCCTCTGCAAAAG 61.064 66.667 0.00 0.00 40.13 2.27
1704 1807 3.567579 CTCCCCGGCCTCTGCAAAA 62.568 63.158 0.00 0.00 40.13 2.44
1705 1808 4.033776 CTCCCCGGCCTCTGCAAA 62.034 66.667 0.00 0.00 40.13 3.68
1719 1822 2.474410 TTTCGAAAAGAGGGAGCTCC 57.526 50.000 25.59 25.59 0.00 4.70
1740 1843 3.031013 ACAAGCAAGCTACTGGGTTTTT 58.969 40.909 0.00 0.00 32.86 1.94
1741 1844 2.666317 ACAAGCAAGCTACTGGGTTTT 58.334 42.857 0.00 0.00 32.86 2.43
1742 1845 2.364972 ACAAGCAAGCTACTGGGTTT 57.635 45.000 0.00 0.00 32.86 3.27
1743 1846 2.364972 AACAAGCAAGCTACTGGGTT 57.635 45.000 0.00 0.00 35.89 4.11
1744 1847 2.158608 AGAAACAAGCAAGCTACTGGGT 60.159 45.455 0.00 0.00 0.00 4.51
1745 1848 2.485814 GAGAAACAAGCAAGCTACTGGG 59.514 50.000 0.00 0.00 0.00 4.45
1746 1849 2.485814 GGAGAAACAAGCAAGCTACTGG 59.514 50.000 0.00 0.00 0.00 4.00
1794 1897 9.096160 GTTCTACTTATTACCCAAGCTAGAAAC 57.904 37.037 0.00 0.00 33.08 2.78
1829 1939 4.959210 AGCTCAGTGTTACAGATGGATAGT 59.041 41.667 0.00 0.00 0.00 2.12
1845 1958 6.546403 TGAGGTAGATAAATCGTTAGCTCAGT 59.454 38.462 13.11 0.00 42.42 3.41
2026 2139 7.108847 CCATTACAAGAGTGAGAAGAGGATTT 58.891 38.462 0.00 0.00 0.00 2.17
2027 2140 6.648192 CCATTACAAGAGTGAGAAGAGGATT 58.352 40.000 0.00 0.00 0.00 3.01
2028 2141 5.396213 GCCATTACAAGAGTGAGAAGAGGAT 60.396 44.000 0.00 0.00 0.00 3.24
2029 2142 4.081420 GCCATTACAAGAGTGAGAAGAGGA 60.081 45.833 0.00 0.00 0.00 3.71
2030 2143 4.081198 AGCCATTACAAGAGTGAGAAGAGG 60.081 45.833 0.00 0.00 0.00 3.69
2031 2144 4.869297 CAGCCATTACAAGAGTGAGAAGAG 59.131 45.833 0.00 0.00 0.00 2.85
2032 2145 4.323028 CCAGCCATTACAAGAGTGAGAAGA 60.323 45.833 0.00 0.00 0.00 2.87
2033 2146 3.937706 CCAGCCATTACAAGAGTGAGAAG 59.062 47.826 0.00 0.00 0.00 2.85
2034 2147 3.869912 GCCAGCCATTACAAGAGTGAGAA 60.870 47.826 0.00 0.00 0.00 2.87
2046 2159 3.084039 CAAGAAAGACAGCCAGCCATTA 58.916 45.455 0.00 0.00 0.00 1.90
2074 2187 1.368579 CCCAGCAAAAGCACCTTGG 59.631 57.895 0.00 0.00 0.00 3.61
2119 2232 1.866853 CGAAGGCCTTCAGTTTGCCC 61.867 60.000 37.88 14.58 46.55 5.36
2170 2283 0.952984 GAAGCAGCGGCAGAAGAACT 60.953 55.000 12.44 0.00 44.61 3.01
2301 2414 8.515695 TTCAGGAATCGTCAGAGTTATAGTAA 57.484 34.615 0.00 0.00 0.00 2.24
2316 2429 6.510799 GCTGTGTGATCTTAATTCAGGAATCG 60.511 42.308 0.00 0.00 0.00 3.34
2342 2455 2.526304 TATATCAAGCACGGTCAGCC 57.474 50.000 0.00 0.00 0.00 4.85
2349 2462 2.469826 TGCGGAGTTATATCAAGCACG 58.530 47.619 0.00 0.00 32.10 5.34
2360 2473 0.174845 CGACCAATCCTGCGGAGTTA 59.825 55.000 2.36 0.00 34.05 2.24
2378 2491 1.263217 AGGTAGCAAAACGAAGCAACG 59.737 47.619 0.00 1.28 39.31 4.10
2414 2527 0.604578 TACCGTGTTCACTGTAGGGC 59.395 55.000 3.76 0.00 0.00 5.19
2429 2542 3.390135 ACGGAAACTATGCATCATACCG 58.610 45.455 21.60 21.60 37.86 4.02
2493 2638 7.115947 GCGGTAGTAAGTGGACACATATATTTC 59.884 40.741 5.14 0.00 0.00 2.17
2502 2671 0.108472 GGGCGGTAGTAAGTGGACAC 60.108 60.000 0.00 0.00 0.00 3.67
2503 2672 0.542467 TGGGCGGTAGTAAGTGGACA 60.542 55.000 0.00 0.00 0.00 4.02
2504 2673 0.609662 TTGGGCGGTAGTAAGTGGAC 59.390 55.000 0.00 0.00 0.00 4.02
2505 2674 0.899720 CTTGGGCGGTAGTAAGTGGA 59.100 55.000 0.00 0.00 0.00 4.02
2506 2675 0.611714 ACTTGGGCGGTAGTAAGTGG 59.388 55.000 0.00 0.00 32.56 4.00
2507 2676 1.674817 CCACTTGGGCGGTAGTAAGTG 60.675 57.143 0.00 0.00 45.82 3.16
2508 2677 0.611714 CCACTTGGGCGGTAGTAAGT 59.388 55.000 0.00 0.00 33.94 2.24
2547 2716 6.699895 TGCTTAGTCGTGTGTTTTATAGTG 57.300 37.500 0.00 0.00 0.00 2.74
2645 2815 5.186256 TGCCTTTTCATATGTCCACCTAA 57.814 39.130 1.90 0.00 0.00 2.69
2698 2868 5.063691 TGTTACTCGCAAAAGAAAAAGACGA 59.936 36.000 0.00 0.00 0.00 4.20
2699 2869 5.169032 GTGTTACTCGCAAAAGAAAAAGACG 59.831 40.000 0.00 0.00 0.00 4.18
2700 2870 5.454554 GGTGTTACTCGCAAAAGAAAAAGAC 59.545 40.000 0.00 0.00 0.00 3.01
2701 2871 5.124138 TGGTGTTACTCGCAAAAGAAAAAGA 59.876 36.000 0.00 0.00 0.00 2.52
2702 2872 5.336744 TGGTGTTACTCGCAAAAGAAAAAG 58.663 37.500 0.00 0.00 0.00 2.27
2703 2873 5.312120 TGGTGTTACTCGCAAAAGAAAAA 57.688 34.783 0.00 0.00 0.00 1.94
2704 2874 4.966965 TGGTGTTACTCGCAAAAGAAAA 57.033 36.364 0.00 0.00 0.00 2.29
2705 2875 4.966965 TTGGTGTTACTCGCAAAAGAAA 57.033 36.364 0.00 0.00 0.00 2.52
2706 2876 4.791411 GCATTGGTGTTACTCGCAAAAGAA 60.791 41.667 0.00 0.00 0.00 2.52
2707 2877 3.304391 GCATTGGTGTTACTCGCAAAAGA 60.304 43.478 0.00 0.00 0.00 2.52
2708 2878 2.979813 GCATTGGTGTTACTCGCAAAAG 59.020 45.455 0.00 0.00 0.00 2.27
2709 2879 2.359214 TGCATTGGTGTTACTCGCAAAA 59.641 40.909 0.00 0.00 0.00 2.44
2710 2880 1.950216 TGCATTGGTGTTACTCGCAAA 59.050 42.857 0.00 0.00 0.00 3.68
2711 2881 1.598882 TGCATTGGTGTTACTCGCAA 58.401 45.000 0.00 0.00 0.00 4.85
2712 2882 1.819928 ATGCATTGGTGTTACTCGCA 58.180 45.000 0.00 0.00 0.00 5.10
2713 2883 3.362986 CGATATGCATTGGTGTTACTCGC 60.363 47.826 3.54 0.00 0.00 5.03
2714 2884 3.802139 ACGATATGCATTGGTGTTACTCG 59.198 43.478 3.54 3.09 0.00 4.18
2715 2885 5.734855 AACGATATGCATTGGTGTTACTC 57.265 39.130 3.54 0.00 0.00 2.59
2716 2886 5.220586 CGAAACGATATGCATTGGTGTTACT 60.221 40.000 3.54 0.00 0.00 2.24
2717 2887 4.961551 CGAAACGATATGCATTGGTGTTAC 59.038 41.667 3.54 0.00 0.00 2.50
2718 2888 4.870991 TCGAAACGATATGCATTGGTGTTA 59.129 37.500 3.54 0.00 0.00 2.41
2719 2889 3.687212 TCGAAACGATATGCATTGGTGTT 59.313 39.130 3.54 2.42 0.00 3.32
2720 2890 3.266636 TCGAAACGATATGCATTGGTGT 58.733 40.909 3.54 0.00 0.00 4.16
2721 2891 3.942539 TCGAAACGATATGCATTGGTG 57.057 42.857 3.54 0.00 0.00 4.17
2722 2892 3.687212 TGTTCGAAACGATATGCATTGGT 59.313 39.130 3.54 0.00 35.23 3.67
2723 2893 4.271590 TGTTCGAAACGATATGCATTGG 57.728 40.909 3.54 0.00 35.23 3.16
2724 2894 6.020984 TCTTTGTTCGAAACGATATGCATTG 58.979 36.000 3.54 0.00 35.23 2.82
2725 2895 6.176975 TCTTTGTTCGAAACGATATGCATT 57.823 33.333 3.54 0.00 35.23 3.56
2726 2896 5.794687 TCTTTGTTCGAAACGATATGCAT 57.205 34.783 3.79 3.79 35.23 3.96
2727 2897 5.794687 ATCTTTGTTCGAAACGATATGCA 57.205 34.783 0.00 0.00 35.23 3.96
2728 2898 6.934210 ACTATCTTTGTTCGAAACGATATGC 58.066 36.000 0.00 0.00 35.23 3.14
2729 2899 8.115491 TGACTATCTTTGTTCGAAACGATATG 57.885 34.615 0.00 2.15 35.23 1.78
2730 2900 8.697846 TTGACTATCTTTGTTCGAAACGATAT 57.302 30.769 0.00 0.00 35.23 1.63
2731 2901 8.697846 ATTGACTATCTTTGTTCGAAACGATA 57.302 30.769 0.00 3.46 35.23 2.92
2900 6888 1.477685 TTCAGTTCACCCTCCGGACC 61.478 60.000 0.00 0.00 0.00 4.46
2915 6903 2.730069 TGTTGTTGATTGCGCTTTCAG 58.270 42.857 9.73 0.00 0.00 3.02
2918 6906 3.520569 AGTTTGTTGTTGATTGCGCTTT 58.479 36.364 9.73 0.00 0.00 3.51
2922 6910 2.980586 TCGAGTTTGTTGTTGATTGCG 58.019 42.857 0.00 0.00 0.00 4.85
3022 7010 3.033184 CTGATCTCTGCTCCCTTCTTCT 58.967 50.000 0.00 0.00 0.00 2.85
3180 7168 5.126707 ACTTCTGCATTCATGAAATTCCTCC 59.873 40.000 13.09 0.00 0.00 4.30
3288 7276 5.504853 TGTGGCATTAGGATTGTATGTGAA 58.495 37.500 0.00 0.00 0.00 3.18
3294 7282 6.545666 CCAAGTTATGTGGCATTAGGATTGTA 59.454 38.462 0.00 0.00 0.00 2.41
3312 7300 0.323629 CCCAACTCCGCTCCAAGTTA 59.676 55.000 0.00 0.00 34.05 2.24
3322 7310 0.673437 ACAATTGCAACCCAACTCCG 59.327 50.000 0.00 0.00 35.99 4.63
3343 7331 2.032302 CAGATGAGACCGACTACCGAAG 59.968 54.545 0.00 0.00 41.76 3.79
3354 7342 3.376540 GTCGAACATAGCAGATGAGACC 58.623 50.000 5.69 0.00 0.00 3.85
3659 7647 0.034477 AGCCCAATCCAGTAAACCGG 60.034 55.000 0.00 0.00 0.00 5.28
3668 7656 1.272425 ACCATCGAAAAGCCCAATCCA 60.272 47.619 0.00 0.00 0.00 3.41
3672 7660 3.828875 AAAAACCATCGAAAAGCCCAA 57.171 38.095 0.00 0.00 0.00 4.12
3835 7829 8.770438 TTCAAACTACAGAAAAAGCACAAAAT 57.230 26.923 0.00 0.00 0.00 1.82
4010 8024 7.323049 TCACGAATTTAAGGAAAGTTCACAA 57.677 32.000 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.