Multiple sequence alignment - TraesCS1A01G188700

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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 TraesCS1A01G188700 chr1A 100.000 3205 0 0 912 4116 341017660 341014456 0.000000e+00 5919
1 TraesCS1A01G188700 chr1A 100.000 570 0 0 1 570 341018571 341018002 0.000000e+00 1053
2 TraesCS1A01G188700 chr1B 93.018 1948 71 28 2173 4116 353276254 353274368 0.000000e+00 2784
3 TraesCS1A01G188700 chr1B 95.940 468 17 2 916 1381 353277298 353276831 0.000000e+00 758
4 TraesCS1A01G188700 chr1B 89.194 583 40 12 1 570 353278051 353277479 0.000000e+00 706
5 TraesCS1A01G188700 chr1B 87.719 513 33 14 1511 2011 353276744 353276250 4.620000e-159 571
6 TraesCS1A01G188700 chr1D 90.895 1955 68 41 2173 4116 259778676 259780531 0.000000e+00 2523
7 TraesCS1A01G188700 chr1D 89.799 1147 51 21 913 2011 259777552 259778680 0.000000e+00 1410
8 TraesCS1A01G188700 chr1D 89.590 586 35 18 1 569 259776787 259777363 0.000000e+00 721
9 TraesCS1A01G188700 chr1D 94.631 149 7 1 2015 2162 12786496 12786644 3.200000e-56 230
10 TraesCS1A01G188700 chr4A 96.855 159 5 0 2017 2175 38579944 38580102 2.440000e-67 267
11 TraesCS1A01G188700 chr5D 95.031 161 7 1 2015 2175 544141987 544142146 6.830000e-63 252
12 TraesCS1A01G188700 chr7D 94.410 161 8 1 2015 2175 629413234 629413075 3.180000e-61 246
13 TraesCS1A01G188700 chr2D 93.902 164 9 1 2013 2175 107031640 107031477 3.180000e-61 246
14 TraesCS1A01G188700 chr3A 93.252 163 10 1 2014 2175 732967644 732967482 5.320000e-59 239
15 TraesCS1A01G188700 chr5B 93.711 159 8 2 2017 2175 585738353 585738509 1.910000e-58 237
16 TraesCS1A01G188700 chr6B 92.073 164 12 1 2012 2175 636102161 636101999 3.200000e-56 230
17 TraesCS1A01G188700 chr4D 92.025 163 8 3 2018 2175 461841492 461841330 1.490000e-54 224
18 TraesCS1A01G188700 chr4D 78.834 326 49 16 1038 1351 502561188 502560871 6.980000e-48 202
19 TraesCS1A01G188700 chr4B 79.355 310 48 13 1033 1331 646924797 646924493 1.940000e-48 204
20 TraesCS1A01G188700 chr5A 77.676 327 56 14 1034 1351 685963378 685963060 2.530000e-42 183


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 TraesCS1A01G188700 chr1A 341014456 341018571 4115 True 3486.000000 5919 100.000000 1 4116 2 chr1A.!!$R1 4115
1 TraesCS1A01G188700 chr1B 353274368 353278051 3683 True 1204.750000 2784 91.467750 1 4116 4 chr1B.!!$R1 4115
2 TraesCS1A01G188700 chr1D 259776787 259780531 3744 False 1551.333333 2523 90.094667 1 4116 3 chr1D.!!$F2 4115

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
403 420 0.105964 CACAAACAGGTCCACTCGGA 59.894 55.0 0.0 0.0 39.79 4.55 F
408 425 0.113776 ACAGGTCCACTCGGAAGGTA 59.886 55.0 0.0 0.0 45.20 3.08 F
2060 2170 0.178918 CCCCCTGCCCCAACTTTTTA 60.179 55.0 0.0 0.0 0.00 1.52 F
2728 2846 0.107459 AGCTCGATTTCTGCTTCCCC 60.107 55.0 0.0 0.0 32.61 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 2273 0.107456 CAGCTCAGTCTTGTGGGTGT 59.893 55.0 0.0 0.00 0.00 4.16 R
2165 2275 0.839946 AACAGCTCAGTCTTGTGGGT 59.160 50.0 0.0 0.00 0.00 4.51 R
3085 3203 0.039978 ATGACGACGATCGCATCTCC 60.040 55.0 16.6 0.41 45.12 3.71 R
4064 4186 0.374758 CGTCAACCATGCGAGATTGG 59.625 55.0 0.0 0.00 39.02 3.16 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
40 49 2.429571 GCTTGTGTGCATGCGGTG 60.430 61.111 14.09 1.06 36.33 4.94
65 74 4.136796 TGAGCCGGATTTGGATAAGAATG 58.863 43.478 5.05 0.00 0.00 2.67
151 160 2.066999 CCCTCCCTCCAGCTGTACC 61.067 68.421 13.81 0.00 0.00 3.34
198 214 2.766651 TACCCATGGACCGCCCTC 60.767 66.667 15.22 0.00 35.38 4.30
199 215 3.326385 TACCCATGGACCGCCCTCT 62.326 63.158 15.22 0.00 35.38 3.69
200 216 4.181010 CCCATGGACCGCCCTCTG 62.181 72.222 15.22 0.00 35.38 3.35
201 217 4.181010 CCATGGACCGCCCTCTGG 62.181 72.222 5.56 0.00 33.95 3.86
202 218 3.402681 CATGGACCGCCCTCTGGT 61.403 66.667 0.00 0.00 44.10 4.00
203 219 2.063979 CATGGACCGCCCTCTGGTA 61.064 63.158 0.00 0.00 40.63 3.25
206 222 3.468140 GACCGCCCTCTGGTACCC 61.468 72.222 10.07 0.00 40.63 3.69
209 225 3.782443 CGCCCTCTGGTACCCCAC 61.782 72.222 10.07 0.00 35.17 4.61
210 226 2.609610 GCCCTCTGGTACCCCACA 60.610 66.667 10.07 0.00 35.17 4.17
211 227 2.967946 GCCCTCTGGTACCCCACAC 61.968 68.421 10.07 0.00 35.17 3.82
291 307 5.188434 CGGCCATTAATCCACATCATATCT 58.812 41.667 2.24 0.00 0.00 1.98
322 338 9.395898 TGTTTAAACATTAAATCCCGAGTGGGC 62.396 40.741 17.01 0.00 44.25 5.36
347 364 1.538204 CCATGGTCCCGACATTACGAG 60.538 57.143 2.57 0.00 35.09 4.18
376 393 2.279582 CGAGATATTATCGCGGCCTT 57.720 50.000 18.50 0.00 46.53 4.35
403 420 0.105964 CACAAACAGGTCCACTCGGA 59.894 55.000 0.00 0.00 39.79 4.55
408 425 0.113776 ACAGGTCCACTCGGAAGGTA 59.886 55.000 0.00 0.00 45.20 3.08
441 458 0.759060 ACAAACCACTTTCAGGGGGC 60.759 55.000 0.00 0.00 45.32 5.80
457 485 1.464734 GGGCAGAAACTAGAAAGGCC 58.535 55.000 0.00 0.00 39.18 5.19
475 503 2.743752 CGCGTGAACTGCCCATGAG 61.744 63.158 0.00 0.00 0.00 2.90
543 572 2.298163 GCCGTCTATTTATTCCCCTCGA 59.702 50.000 0.00 0.00 0.00 4.04
1030 1062 2.550208 GGGGTCTCGAGCTTTTTCTTCA 60.550 50.000 7.81 0.00 0.00 3.02
1221 1253 1.516423 GGAGAACTACCGCCACCTC 59.484 63.158 0.00 0.00 0.00 3.85
1352 1384 4.878397 CACCAAGGTCAGATATTCTTCCAC 59.122 45.833 0.00 0.00 0.00 4.02
1378 1411 1.946984 ATAGGTCCCTTTCCGTGTGA 58.053 50.000 0.00 0.00 0.00 3.58
1404 1449 1.153756 CCAAGCCAAACAGGACCCT 59.846 57.895 0.00 0.00 41.22 4.34
1435 1480 7.665559 TGAGCTTGTCTATGATTTTAACCAGTT 59.334 33.333 0.00 0.00 0.00 3.16
1459 1504 6.882610 AGTCTTGTGCTTGAATCATTGTTA 57.117 33.333 0.00 0.00 0.00 2.41
1480 1525 7.608153 TGTTATTTTCCGAGTCTGATGTCTTA 58.392 34.615 0.00 0.00 0.00 2.10
1481 1526 8.092068 TGTTATTTTCCGAGTCTGATGTCTTAA 58.908 33.333 0.00 0.00 0.00 1.85
1482 1527 9.099454 GTTATTTTCCGAGTCTGATGTCTTAAT 57.901 33.333 0.00 0.00 0.00 1.40
1483 1528 7.778470 ATTTTCCGAGTCTGATGTCTTAATC 57.222 36.000 0.00 0.00 0.00 1.75
1484 1529 4.920640 TCCGAGTCTGATGTCTTAATCC 57.079 45.455 0.00 0.00 0.00 3.01
1485 1530 4.278310 TCCGAGTCTGATGTCTTAATCCA 58.722 43.478 0.00 0.00 0.00 3.41
1486 1531 4.098044 TCCGAGTCTGATGTCTTAATCCAC 59.902 45.833 0.00 0.00 0.00 4.02
1487 1532 4.142160 CCGAGTCTGATGTCTTAATCCACA 60.142 45.833 0.00 0.00 0.00 4.17
1488 1533 5.452496 CCGAGTCTGATGTCTTAATCCACAT 60.452 44.000 0.00 0.00 35.88 3.21
1489 1534 5.689514 CGAGTCTGATGTCTTAATCCACATC 59.310 44.000 12.34 12.34 46.26 3.06
1490 1535 6.460814 CGAGTCTGATGTCTTAATCCACATCT 60.461 42.308 17.03 4.06 46.24 2.90
1491 1536 6.580788 AGTCTGATGTCTTAATCCACATCTG 58.419 40.000 17.03 16.37 46.24 2.90
1492 1537 6.155910 AGTCTGATGTCTTAATCCACATCTGT 59.844 38.462 17.03 5.76 46.24 3.41
1493 1538 6.820656 GTCTGATGTCTTAATCCACATCTGTT 59.179 38.462 17.03 0.00 46.24 3.16
1494 1539 7.335422 GTCTGATGTCTTAATCCACATCTGTTT 59.665 37.037 17.03 0.00 46.24 2.83
1495 1540 8.539544 TCTGATGTCTTAATCCACATCTGTTTA 58.460 33.333 17.03 5.30 46.24 2.01
1496 1541 9.334947 CTGATGTCTTAATCCACATCTGTTTAT 57.665 33.333 17.03 0.00 46.24 1.40
1502 1547 9.982651 TCTTAATCCACATCTGTTTATACTAGC 57.017 33.333 0.00 0.00 0.00 3.42
1503 1548 9.209175 CTTAATCCACATCTGTTTATACTAGCC 57.791 37.037 0.00 0.00 0.00 3.93
1504 1549 6.747414 ATCCACATCTGTTTATACTAGCCA 57.253 37.500 0.00 0.00 0.00 4.75
1505 1550 6.553953 TCCACATCTGTTTATACTAGCCAA 57.446 37.500 0.00 0.00 0.00 4.52
1506 1551 6.953101 TCCACATCTGTTTATACTAGCCAAA 58.047 36.000 0.00 0.00 0.00 3.28
1507 1552 7.573710 TCCACATCTGTTTATACTAGCCAAAT 58.426 34.615 0.00 0.00 0.00 2.32
1508 1553 8.710239 TCCACATCTGTTTATACTAGCCAAATA 58.290 33.333 0.00 0.00 0.00 1.40
1509 1554 9.507329 CCACATCTGTTTATACTAGCCAAATAT 57.493 33.333 0.00 0.00 0.00 1.28
1549 1629 7.801893 TCCAGAGTTAATTAGTGTTAAGGGA 57.198 36.000 0.00 0.00 0.00 4.20
1563 1644 7.970102 AGTGTTAAGGGAAAGAACTATGTACA 58.030 34.615 0.00 0.00 0.00 2.90
1564 1645 8.095169 AGTGTTAAGGGAAAGAACTATGTACAG 58.905 37.037 0.33 0.00 0.00 2.74
1565 1646 7.876582 GTGTTAAGGGAAAGAACTATGTACAGT 59.123 37.037 0.33 0.00 0.00 3.55
1566 1647 9.092338 TGTTAAGGGAAAGAACTATGTACAGTA 57.908 33.333 0.33 0.00 0.00 2.74
1604 1691 7.009540 ACCGTAGCAAATAGTATGTACGTTTTC 59.990 37.037 0.00 0.00 33.17 2.29
1640 1727 5.741011 ACGTCTAAAATTGGAGCCTGAATA 58.259 37.500 0.00 0.00 0.00 1.75
1641 1728 5.817816 ACGTCTAAAATTGGAGCCTGAATAG 59.182 40.000 0.00 0.00 0.00 1.73
1711 1798 7.751768 AACTCTCTTGGTTCCTTTTTATCTG 57.248 36.000 0.00 0.00 0.00 2.90
1872 1981 1.301716 GACACACATGCCGACCACT 60.302 57.895 0.00 0.00 0.00 4.00
1878 1987 0.324614 ACATGCCGACCACTGAATCA 59.675 50.000 0.00 0.00 0.00 2.57
1889 1998 6.294508 CCGACCACTGAATCAAGGTAAAAATT 60.295 38.462 6.97 0.00 33.77 1.82
1891 2000 6.993079 ACCACTGAATCAAGGTAAAAATTCC 58.007 36.000 5.38 0.00 31.32 3.01
1901 2010 3.694566 AGGTAAAAATTCCATCTCGCACC 59.305 43.478 0.00 0.00 0.00 5.01
1905 2014 3.914426 AAATTCCATCTCGCACCTACT 57.086 42.857 0.00 0.00 0.00 2.57
1908 2017 2.730934 TCCATCTCGCACCTACTACT 57.269 50.000 0.00 0.00 0.00 2.57
1909 2018 3.851458 TCCATCTCGCACCTACTACTA 57.149 47.619 0.00 0.00 0.00 1.82
1910 2019 3.474600 TCCATCTCGCACCTACTACTAC 58.525 50.000 0.00 0.00 0.00 2.73
1911 2020 3.136077 TCCATCTCGCACCTACTACTACT 59.864 47.826 0.00 0.00 0.00 2.57
1912 2021 3.499157 CCATCTCGCACCTACTACTACTC 59.501 52.174 0.00 0.00 0.00 2.59
1913 2022 3.191078 TCTCGCACCTACTACTACTCC 57.809 52.381 0.00 0.00 0.00 3.85
1914 2023 1.865970 CTCGCACCTACTACTACTCCG 59.134 57.143 0.00 0.00 0.00 4.63
1915 2024 1.482182 TCGCACCTACTACTACTCCGA 59.518 52.381 0.00 0.00 0.00 4.55
1916 2025 1.596727 CGCACCTACTACTACTCCGAC 59.403 57.143 0.00 0.00 0.00 4.79
1917 2026 1.946081 GCACCTACTACTACTCCGACC 59.054 57.143 0.00 0.00 0.00 4.79
1918 2027 2.681976 GCACCTACTACTACTCCGACCA 60.682 54.545 0.00 0.00 0.00 4.02
1919 2028 2.941720 CACCTACTACTACTCCGACCAC 59.058 54.545 0.00 0.00 0.00 4.16
1920 2029 2.573462 ACCTACTACTACTCCGACCACA 59.427 50.000 0.00 0.00 0.00 4.17
1921 2030 3.204526 CCTACTACTACTCCGACCACAG 58.795 54.545 0.00 0.00 0.00 3.66
1922 2031 2.875094 ACTACTACTCCGACCACAGT 57.125 50.000 0.00 0.00 0.00 3.55
1923 2032 3.988976 ACTACTACTCCGACCACAGTA 57.011 47.619 0.00 0.00 0.00 2.74
1924 2033 4.500499 ACTACTACTCCGACCACAGTAT 57.500 45.455 0.00 0.00 0.00 2.12
1927 2036 5.713861 ACTACTACTCCGACCACAGTATTTT 59.286 40.000 0.00 0.00 0.00 1.82
1986 2096 2.992543 GCAACTTGCAATTAAATGCCGA 59.007 40.909 12.85 1.27 45.83 5.54
2004 2114 4.102649 GCCGAAACAACATACTTATTGGC 58.897 43.478 0.00 0.00 0.00 4.52
2010 2120 7.391148 AAACAACATACTTATTGGCGAGATT 57.609 32.000 0.00 0.00 0.00 2.40
2011 2121 7.391148 AACAACATACTTATTGGCGAGATTT 57.609 32.000 0.00 0.00 0.00 2.17
2012 2122 7.391148 ACAACATACTTATTGGCGAGATTTT 57.609 32.000 0.00 0.00 0.00 1.82
2013 2123 7.826690 ACAACATACTTATTGGCGAGATTTTT 58.173 30.769 0.00 0.00 0.00 1.94
2040 2150 2.588027 TTTGAAACGAAAGGGGTTGC 57.412 45.000 0.00 0.00 0.00 4.17
2041 2151 0.747852 TTGAAACGAAAGGGGTTGCC 59.252 50.000 0.00 0.00 0.00 4.52
2042 2152 1.110518 TGAAACGAAAGGGGTTGCCC 61.111 55.000 0.00 0.00 44.51 5.36
2058 2168 2.204034 CCCCCTGCCCCAACTTTT 59.796 61.111 0.00 0.00 0.00 2.27
2059 2169 1.461268 CCCCCTGCCCCAACTTTTT 60.461 57.895 0.00 0.00 0.00 1.94
2060 2170 0.178918 CCCCCTGCCCCAACTTTTTA 60.179 55.000 0.00 0.00 0.00 1.52
2061 2171 1.554587 CCCCCTGCCCCAACTTTTTAT 60.555 52.381 0.00 0.00 0.00 1.40
2062 2172 2.265367 CCCCTGCCCCAACTTTTTATT 58.735 47.619 0.00 0.00 0.00 1.40
2063 2173 2.027285 CCCCTGCCCCAACTTTTTATTG 60.027 50.000 0.00 0.00 0.00 1.90
2064 2174 2.903135 CCCTGCCCCAACTTTTTATTGA 59.097 45.455 0.00 0.00 0.00 2.57
2065 2175 3.326297 CCCTGCCCCAACTTTTTATTGAA 59.674 43.478 0.00 0.00 0.00 2.69
2066 2176 4.202409 CCCTGCCCCAACTTTTTATTGAAA 60.202 41.667 0.00 0.00 0.00 2.69
2067 2177 5.372373 CCTGCCCCAACTTTTTATTGAAAA 58.628 37.500 0.00 0.00 35.94 2.29
2068 2178 5.825151 CCTGCCCCAACTTTTTATTGAAAAA 59.175 36.000 0.00 0.00 41.24 1.94
2080 2190 8.626093 TTTTTATTGAAAAAGCAAATGCAACC 57.374 26.923 8.28 0.00 39.16 3.77
2081 2191 6.932356 TTATTGAAAAAGCAAATGCAACCA 57.068 29.167 8.28 0.00 45.16 3.67
2082 2192 5.831702 ATTGAAAAAGCAAATGCAACCAA 57.168 30.435 8.28 4.99 45.16 3.67
2083 2193 5.633830 TTGAAAAAGCAAATGCAACCAAA 57.366 30.435 8.28 0.00 45.16 3.28
2084 2194 5.232610 TGAAAAAGCAAATGCAACCAAAG 57.767 34.783 8.28 0.00 45.16 2.77
2085 2195 3.696281 AAAAGCAAATGCAACCAAAGC 57.304 38.095 8.28 0.00 45.16 3.51
2087 2197 1.585297 AGCAAATGCAACCAAAGCAC 58.415 45.000 8.28 0.00 45.95 4.40
2088 2198 1.134461 AGCAAATGCAACCAAAGCACA 60.134 42.857 8.28 0.00 45.95 4.57
2089 2199 1.003652 GCAAATGCAACCAAAGCACAC 60.004 47.619 0.00 0.00 45.95 3.82
2090 2200 2.553086 CAAATGCAACCAAAGCACACT 58.447 42.857 0.00 0.00 45.95 3.55
2091 2201 2.228138 AATGCAACCAAAGCACACTG 57.772 45.000 0.00 0.00 45.95 3.66
2092 2202 1.113788 ATGCAACCAAAGCACACTGT 58.886 45.000 0.00 0.00 45.95 3.55
2093 2203 0.894141 TGCAACCAAAGCACACTGTT 59.106 45.000 0.00 0.00 37.02 3.16
2094 2204 2.095461 TGCAACCAAAGCACACTGTTA 58.905 42.857 0.00 0.00 37.02 2.41
2095 2205 2.493675 TGCAACCAAAGCACACTGTTAA 59.506 40.909 0.00 0.00 37.02 2.01
2096 2206 2.857748 GCAACCAAAGCACACTGTTAAC 59.142 45.455 0.00 0.00 0.00 2.01
2097 2207 3.674682 GCAACCAAAGCACACTGTTAACA 60.675 43.478 8.28 8.28 0.00 2.41
2098 2208 7.838523 TGCAACCAAAGCACACTGTTAACAG 62.839 44.000 29.76 29.76 42.40 3.16
2122 2232 4.530581 GCTCCAGCCAGAAGTAGC 57.469 61.111 0.00 0.00 34.31 3.58
2123 2233 1.153269 GCTCCAGCCAGAAGTAGCC 60.153 63.158 0.00 0.00 34.31 3.93
2124 2234 1.142748 CTCCAGCCAGAAGTAGCCG 59.857 63.158 0.00 0.00 0.00 5.52
2125 2235 2.512515 CCAGCCAGAAGTAGCCGC 60.513 66.667 0.00 0.00 0.00 6.53
2126 2236 2.265739 CAGCCAGAAGTAGCCGCA 59.734 61.111 0.00 0.00 0.00 5.69
2127 2237 1.812922 CAGCCAGAAGTAGCCGCAG 60.813 63.158 0.00 0.00 0.00 5.18
2128 2238 3.198489 GCCAGAAGTAGCCGCAGC 61.198 66.667 0.00 0.00 40.32 5.25
2129 2239 2.265739 CCAGAAGTAGCCGCAGCA 59.734 61.111 0.00 0.00 43.56 4.41
2130 2240 1.812922 CCAGAAGTAGCCGCAGCAG 60.813 63.158 0.00 0.00 43.56 4.24
2131 2241 1.216444 CAGAAGTAGCCGCAGCAGA 59.784 57.895 0.00 0.00 43.56 4.26
2132 2242 0.390340 CAGAAGTAGCCGCAGCAGAA 60.390 55.000 0.00 0.00 43.56 3.02
2133 2243 0.539051 AGAAGTAGCCGCAGCAGAAT 59.461 50.000 0.00 0.00 43.56 2.40
2134 2244 1.065854 AGAAGTAGCCGCAGCAGAATT 60.066 47.619 0.00 0.00 43.56 2.17
2135 2245 2.168521 AGAAGTAGCCGCAGCAGAATTA 59.831 45.455 0.00 0.00 43.56 1.40
2136 2246 2.918712 AGTAGCCGCAGCAGAATTAT 57.081 45.000 0.00 0.00 43.56 1.28
2137 2247 3.199880 AGTAGCCGCAGCAGAATTATT 57.800 42.857 0.00 0.00 43.56 1.40
2138 2248 4.336889 AGTAGCCGCAGCAGAATTATTA 57.663 40.909 0.00 0.00 43.56 0.98
2139 2249 4.058817 AGTAGCCGCAGCAGAATTATTAC 58.941 43.478 0.00 0.00 43.56 1.89
2140 2250 2.917933 AGCCGCAGCAGAATTATTACA 58.082 42.857 0.00 0.00 43.56 2.41
2141 2251 2.874701 AGCCGCAGCAGAATTATTACAG 59.125 45.455 0.00 0.00 43.56 2.74
2142 2252 2.872245 GCCGCAGCAGAATTATTACAGA 59.128 45.455 0.00 0.00 39.53 3.41
2143 2253 3.303395 GCCGCAGCAGAATTATTACAGAC 60.303 47.826 0.00 0.00 39.53 3.51
2144 2254 3.060272 CCGCAGCAGAATTATTACAGACG 60.060 47.826 0.00 0.00 0.00 4.18
2145 2255 3.796717 CGCAGCAGAATTATTACAGACGA 59.203 43.478 0.00 0.00 0.00 4.20
2146 2256 4.445718 CGCAGCAGAATTATTACAGACGAT 59.554 41.667 0.00 0.00 0.00 3.73
2147 2257 5.611197 CGCAGCAGAATTATTACAGACGATG 60.611 44.000 0.00 0.00 0.00 3.84
2148 2258 5.674008 CAGCAGAATTATTACAGACGATGC 58.326 41.667 0.00 0.00 0.00 3.91
2149 2259 5.234972 CAGCAGAATTATTACAGACGATGCA 59.765 40.000 0.00 0.00 32.53 3.96
2150 2260 5.817296 AGCAGAATTATTACAGACGATGCAA 59.183 36.000 0.00 0.00 32.53 4.08
2151 2261 5.904080 GCAGAATTATTACAGACGATGCAAC 59.096 40.000 0.00 0.00 0.00 4.17
2152 2262 6.238211 GCAGAATTATTACAGACGATGCAACT 60.238 38.462 0.00 0.00 0.00 3.16
2153 2263 7.042725 GCAGAATTATTACAGACGATGCAACTA 60.043 37.037 0.00 0.00 0.00 2.24
2154 2264 8.817100 CAGAATTATTACAGACGATGCAACTAA 58.183 33.333 0.00 0.00 0.00 2.24
2155 2265 9.378551 AGAATTATTACAGACGATGCAACTAAA 57.621 29.630 0.00 0.00 0.00 1.85
2156 2266 9.982291 GAATTATTACAGACGATGCAACTAAAA 57.018 29.630 0.00 0.00 0.00 1.52
2157 2267 9.988350 AATTATTACAGACGATGCAACTAAAAG 57.012 29.630 0.00 0.00 0.00 2.27
2158 2268 8.542497 TTATTACAGACGATGCAACTAAAAGT 57.458 30.769 0.00 0.00 0.00 2.66
2159 2269 4.992381 ACAGACGATGCAACTAAAAGTC 57.008 40.909 0.00 0.00 0.00 3.01
2160 2270 4.632153 ACAGACGATGCAACTAAAAGTCT 58.368 39.130 0.00 0.00 37.90 3.24
2161 2271 4.950926 CAGACGATGCAACTAAAAGTCTG 58.049 43.478 12.20 12.20 44.93 3.51
2162 2272 4.883083 AGACGATGCAACTAAAAGTCTGA 58.117 39.130 0.00 0.00 36.31 3.27
2163 2273 5.297547 AGACGATGCAACTAAAAGTCTGAA 58.702 37.500 0.00 0.00 36.31 3.02
2164 2274 5.177696 AGACGATGCAACTAAAAGTCTGAAC 59.822 40.000 0.00 0.00 36.31 3.18
2165 2275 4.814234 ACGATGCAACTAAAAGTCTGAACA 59.186 37.500 0.00 0.00 0.00 3.18
2166 2276 5.140177 CGATGCAACTAAAAGTCTGAACAC 58.860 41.667 0.00 0.00 0.00 3.32
2167 2277 4.893424 TGCAACTAAAAGTCTGAACACC 57.107 40.909 0.00 0.00 0.00 4.16
2168 2278 3.630312 TGCAACTAAAAGTCTGAACACCC 59.370 43.478 0.00 0.00 0.00 4.61
2169 2279 3.630312 GCAACTAAAAGTCTGAACACCCA 59.370 43.478 0.00 0.00 0.00 4.51
2170 2280 4.497507 GCAACTAAAAGTCTGAACACCCAC 60.498 45.833 0.00 0.00 0.00 4.61
2171 2281 4.497291 ACTAAAAGTCTGAACACCCACA 57.503 40.909 0.00 0.00 0.00 4.17
2172 2282 4.850680 ACTAAAAGTCTGAACACCCACAA 58.149 39.130 0.00 0.00 0.00 3.33
2173 2283 4.881850 ACTAAAAGTCTGAACACCCACAAG 59.118 41.667 0.00 0.00 0.00 3.16
2174 2284 3.644966 AAAGTCTGAACACCCACAAGA 57.355 42.857 0.00 0.00 0.00 3.02
2175 2285 2.622064 AGTCTGAACACCCACAAGAC 57.378 50.000 0.00 0.00 0.00 3.01
2214 2324 5.036117 TGTGGTAGAAGATGGGAAATAGC 57.964 43.478 0.00 0.00 0.00 2.97
2273 2383 5.655532 ACAAGAGGCATTTGAGAATTATGCT 59.344 36.000 9.40 0.00 43.17 3.79
2320 2430 6.627395 ATTTGTCCGTTGTTCAGAACATAA 57.373 33.333 16.89 0.00 41.79 1.90
2402 2513 6.132056 GCAGACGCATAAATTCAACATAGAG 58.868 40.000 0.00 0.00 38.36 2.43
2511 2629 1.356124 ACTCTGTGCCAGTGGAAGAT 58.644 50.000 15.20 0.58 32.61 2.40
2512 2630 2.540383 ACTCTGTGCCAGTGGAAGATA 58.460 47.619 15.20 0.00 32.61 1.98
2513 2631 2.499289 ACTCTGTGCCAGTGGAAGATAG 59.501 50.000 15.20 5.65 32.61 2.08
2728 2846 0.107459 AGCTCGATTTCTGCTTCCCC 60.107 55.000 0.00 0.00 32.61 4.81
2810 2928 2.243957 CGTGTTTGCAGCACCGAGA 61.244 57.895 14.98 0.00 33.61 4.04
2950 3068 3.365969 GCGATTTTGTTTCCACGAATCCT 60.366 43.478 0.00 0.00 30.07 3.24
3010 3128 3.862063 CTGCACGCACACGAAAGGC 62.862 63.158 0.00 0.00 43.93 4.35
3040 3158 0.885879 TCGACTCGGTGCTTGTGTAT 59.114 50.000 0.00 0.00 0.00 2.29
3085 3203 1.519455 GGTGACCGGCAAGATCTCG 60.519 63.158 0.00 0.00 0.00 4.04
3100 3218 1.439529 CTCGGAGATGCGATCGTCG 60.440 63.158 17.81 11.01 38.57 5.12
3101 3219 2.107151 CTCGGAGATGCGATCGTCGT 62.107 60.000 17.81 10.33 37.98 4.34
3102 3220 1.722852 CGGAGATGCGATCGTCGTC 60.723 63.158 17.81 18.04 42.81 4.20
3103 3221 1.355563 GGAGATGCGATCGTCGTCA 59.644 57.895 23.93 13.10 42.81 4.35
3104 3222 0.039978 GGAGATGCGATCGTCGTCAT 60.040 55.000 23.93 16.48 42.81 3.06
3105 3223 1.322865 GAGATGCGATCGTCGTCATC 58.677 55.000 23.93 21.87 45.06 2.92
3106 3224 0.384849 AGATGCGATCGTCGTCATCG 60.385 55.000 23.93 10.92 46.98 3.84
3107 3225 0.657659 GATGCGATCGTCGTCATCGT 60.658 55.000 17.81 0.00 44.17 3.73
3108 3226 0.657659 ATGCGATCGTCGTCATCGTC 60.658 55.000 17.81 9.62 44.17 4.20
3109 3227 2.340595 GCGATCGTCGTCATCGTCG 61.341 63.158 17.81 7.85 44.17 5.12
3110 3228 1.012562 CGATCGTCGTCATCGTCGT 60.013 57.895 7.03 0.00 45.27 4.34
3111 3229 0.981076 CGATCGTCGTCATCGTCGTC 60.981 60.000 7.03 4.44 45.27 4.20
3152 3270 3.857549 TGCACTGCTAGAGTTGTAGAG 57.142 47.619 1.98 0.00 29.75 2.43
3153 3271 2.493675 TGCACTGCTAGAGTTGTAGAGG 59.506 50.000 1.98 0.00 29.75 3.69
3353 3472 0.810648 TTGATGCTGCGGATGAAACC 59.189 50.000 0.00 0.00 0.00 3.27
3407 3526 8.294954 TGTTTCCATTTTCCTAGTTTGTGTTA 57.705 30.769 0.00 0.00 0.00 2.41
3455 3574 4.808364 GCTCTGCTGTTATCCTAGTTTCTG 59.192 45.833 0.00 0.00 0.00 3.02
3492 3611 8.219546 TCAATTCTGACTTGATTGTGTTGTTA 57.780 30.769 6.37 0.00 0.00 2.41
3553 3672 3.293311 AACTGCAAAATGCTACTGCTG 57.707 42.857 3.78 0.00 45.31 4.41
3592 3711 7.564793 TGATCTATGTACTAAATGTTGTGCCT 58.435 34.615 0.00 0.00 0.00 4.75
3820 3940 8.825667 AACTTTAGAGTTGTTGATTCTCTCTC 57.174 34.615 0.00 0.00 44.27 3.20
3821 3941 8.189119 ACTTTAGAGTTGTTGATTCTCTCTCT 57.811 34.615 0.00 0.00 39.03 3.10
3822 3942 8.303876 ACTTTAGAGTTGTTGATTCTCTCTCTC 58.696 37.037 0.00 0.00 39.03 3.20
3823 3943 8.415950 TTTAGAGTTGTTGATTCTCTCTCTCT 57.584 34.615 0.00 0.00 39.03 3.10
3824 3944 6.515272 AGAGTTGTTGATTCTCTCTCTCTC 57.485 41.667 0.00 0.00 33.98 3.20
3825 3945 6.248433 AGAGTTGTTGATTCTCTCTCTCTCT 58.752 40.000 0.00 0.00 33.98 3.10
3826 3946 6.375455 AGAGTTGTTGATTCTCTCTCTCTCTC 59.625 42.308 0.00 0.00 33.98 3.20
3827 3947 6.248433 AGTTGTTGATTCTCTCTCTCTCTCT 58.752 40.000 0.00 0.00 0.00 3.10
3828 3948 6.375455 AGTTGTTGATTCTCTCTCTCTCTCTC 59.625 42.308 0.00 0.00 0.00 3.20
3829 3949 6.065976 TGTTGATTCTCTCTCTCTCTCTCT 57.934 41.667 0.00 0.00 0.00 3.10
3900 4020 2.673368 GTCATCACCACGACCTTTCATC 59.327 50.000 0.00 0.00 0.00 2.92
3934 4054 3.119708 ACATGAAAGCATCTCCTTTTCGC 60.120 43.478 0.00 0.00 35.31 4.70
3935 4055 2.783135 TGAAAGCATCTCCTTTTCGCT 58.217 42.857 0.00 0.00 35.31 4.93
3939 4059 3.839051 AGCATCTCCTTTTCGCTTTTC 57.161 42.857 0.00 0.00 0.00 2.29
3940 4060 2.489722 AGCATCTCCTTTTCGCTTTTCC 59.510 45.455 0.00 0.00 0.00 3.13
3981 4103 1.003476 GGTCGCTTTCCCGGGTTAA 60.003 57.895 22.86 15.11 0.00 2.01
3993 4115 1.488527 CGGGTTAAGATACGCAGAGC 58.511 55.000 0.00 0.00 0.00 4.09
4006 4128 4.400961 AGAGCGGCAGAGGCAACC 62.401 66.667 1.45 0.00 43.71 3.77
4024 4146 0.037605 CCGGTGGAGACGCTAGTTTT 60.038 55.000 0.00 0.00 41.78 2.43
4025 4147 1.347320 CGGTGGAGACGCTAGTTTTC 58.653 55.000 0.00 0.00 41.78 2.29
4026 4148 1.067776 CGGTGGAGACGCTAGTTTTCT 60.068 52.381 0.00 0.00 41.78 2.52
4027 4149 2.163010 CGGTGGAGACGCTAGTTTTCTA 59.837 50.000 0.00 0.00 41.78 2.10
4061 4183 1.013524 CGGATGCGATCACACACACA 61.014 55.000 0.00 0.00 0.00 3.72
4062 4184 0.443869 GGATGCGATCACACACACAC 59.556 55.000 0.00 0.00 0.00 3.82
4063 4185 1.147473 GATGCGATCACACACACACA 58.853 50.000 0.00 0.00 0.00 3.72
4064 4186 0.867746 ATGCGATCACACACACACAC 59.132 50.000 0.00 0.00 0.00 3.82
4085 4207 1.078709 AATCTCGCATGGTTGACGTG 58.921 50.000 0.00 0.00 39.17 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 0.039346 CAATCACCGCATGCACACAA 60.039 50.000 19.57 0.00 0.00 3.33
28 29 1.925415 GCTCAATCACCGCATGCACA 61.925 55.000 19.57 0.00 0.00 4.57
40 49 4.389374 TCTTATCCAAATCCGGCTCAATC 58.611 43.478 0.00 0.00 0.00 2.67
65 74 3.489513 AGGCTGGCGGGGTTATCC 61.490 66.667 0.00 0.00 0.00 2.59
96 105 3.300013 GGAGACTTCCACGGGAGG 58.700 66.667 0.00 0.00 43.45 4.30
135 144 2.066999 GGGGTACAGCTGGAGGGAG 61.067 68.421 19.93 0.00 0.00 4.30
151 160 4.351054 GTGGGTGCAGGGAGTGGG 62.351 72.222 0.00 0.00 0.00 4.61
201 217 0.916086 TGATGATGGGTGTGGGGTAC 59.084 55.000 0.00 0.00 0.00 3.34
202 218 1.212375 CTGATGATGGGTGTGGGGTA 58.788 55.000 0.00 0.00 0.00 3.69
203 219 2.001803 CTGATGATGGGTGTGGGGT 58.998 57.895 0.00 0.00 0.00 4.95
206 222 1.454479 GGGCTGATGATGGGTGTGG 60.454 63.158 0.00 0.00 0.00 4.17
209 225 2.203252 CGGGGCTGATGATGGGTG 60.203 66.667 0.00 0.00 0.00 4.61
210 226 2.692368 ACGGGGCTGATGATGGGT 60.692 61.111 0.00 0.00 0.00 4.51
211 227 2.203252 CACGGGGCTGATGATGGG 60.203 66.667 0.00 0.00 0.00 4.00
253 269 2.895372 CCGCCATTAGCACGGGAC 60.895 66.667 0.00 0.00 44.04 4.46
254 270 4.849310 GCCGCCATTAGCACGGGA 62.849 66.667 2.57 0.00 46.97 5.14
257 273 2.901840 ATGGCCGCCATTAGCACG 60.902 61.111 19.79 0.00 42.23 5.34
272 288 9.730705 ACAGGTTAGATATGATGTGGATTAATG 57.269 33.333 0.00 0.00 0.00 1.90
291 307 8.632906 TCGGGATTTAATGTTTAAACAGGTTA 57.367 30.769 24.22 16.28 43.04 2.85
328 344 1.852942 CTCGTAATGTCGGGACCATG 58.147 55.000 0.00 0.00 32.52 3.66
347 364 0.601558 TAATATCTCGGAGGGCACGC 59.398 55.000 4.96 0.00 0.00 5.34
371 388 0.317854 GTTTGTGACGCTTCAAGGCC 60.318 55.000 0.00 0.00 31.90 5.19
373 390 1.002468 CCTGTTTGTGACGCTTCAAGG 60.002 52.381 0.00 0.00 31.90 3.61
375 392 1.668751 GACCTGTTTGTGACGCTTCAA 59.331 47.619 0.00 0.00 31.90 2.69
376 393 1.295792 GACCTGTTTGTGACGCTTCA 58.704 50.000 0.00 0.00 0.00 3.02
424 441 0.469892 CTGCCCCCTGAAAGTGGTTT 60.470 55.000 0.00 0.00 0.00 3.27
425 442 1.153756 CTGCCCCCTGAAAGTGGTT 59.846 57.895 0.00 0.00 0.00 3.67
427 444 0.178964 TTTCTGCCCCCTGAAAGTGG 60.179 55.000 0.00 0.00 35.03 4.00
441 458 0.721718 CGCGGCCTTTCTAGTTTCTG 59.278 55.000 0.00 0.00 0.00 3.02
457 485 2.741985 TCATGGGCAGTTCACGCG 60.742 61.111 3.53 3.53 0.00 6.01
475 503 1.705997 AATGGGCCGTGGATAGGGTC 61.706 60.000 0.00 0.00 35.74 4.46
543 572 3.745803 GGACGGAGGAAGCGTCGT 61.746 66.667 0.00 0.00 38.62 4.34
911 940 2.125269 AAACGAATCCCCGCGGAG 60.125 61.111 30.73 15.76 43.12 4.63
912 941 2.125431 GAAACGAATCCCCGCGGA 60.125 61.111 30.73 8.21 44.33 5.54
913 942 3.199891 GGAAACGAATCCCCGCGG 61.200 66.667 21.04 21.04 33.05 6.46
926 955 2.877097 TTGTAGCAGCAGATGGGAAA 57.123 45.000 0.00 0.00 0.00 3.13
1176 1208 2.432628 GCCTCCCACACGAAGTCG 60.433 66.667 0.00 0.00 41.61 4.18
1221 1253 2.719979 CCCTCGACGTACCCGATG 59.280 66.667 5.62 3.77 37.88 3.84
1352 1384 3.646637 ACGGAAAGGGACCTATATTCCTG 59.353 47.826 14.99 11.72 37.89 3.86
1385 1430 1.908299 GGGTCCTGTTTGGCTTGGG 60.908 63.158 0.00 0.00 35.26 4.12
1391 1436 1.630369 TCATGAGAGGGTCCTGTTTGG 59.370 52.381 0.00 0.00 37.10 3.28
1398 1443 0.908198 ACAAGCTCATGAGAGGGTCC 59.092 55.000 27.04 7.27 42.33 4.46
1404 1449 9.102757 GTTAAAATCATAGACAAGCTCATGAGA 57.897 33.333 27.04 3.52 31.35 3.27
1435 1480 6.882610 AACAATGATTCAAGCACAAGACTA 57.117 33.333 0.00 0.00 0.00 2.59
1439 1484 8.437742 GGAAAATAACAATGATTCAAGCACAAG 58.562 33.333 0.00 0.00 0.00 3.16
1459 1504 6.763610 GGATTAAGACATCAGACTCGGAAAAT 59.236 38.462 0.00 0.00 0.00 1.82
1480 1525 7.136822 TGGCTAGTATAAACAGATGTGGATT 57.863 36.000 0.00 0.00 0.00 3.01
1481 1526 6.747414 TGGCTAGTATAAACAGATGTGGAT 57.253 37.500 0.00 0.00 0.00 3.41
1482 1527 6.553953 TTGGCTAGTATAAACAGATGTGGA 57.446 37.500 0.00 0.00 0.00 4.02
1483 1528 7.807977 ATTTGGCTAGTATAAACAGATGTGG 57.192 36.000 0.00 0.00 0.00 4.17
1501 1546 9.774742 GGAACGATTAAGATATCAATATTTGGC 57.225 33.333 5.32 0.00 0.00 4.52
1515 1560 9.582431 CACTAATTAACTCTGGAACGATTAAGA 57.418 33.333 0.00 0.00 0.00 2.10
1516 1561 9.367444 ACACTAATTAACTCTGGAACGATTAAG 57.633 33.333 0.00 0.00 0.00 1.85
1517 1562 9.715121 AACACTAATTAACTCTGGAACGATTAA 57.285 29.630 0.00 0.00 0.00 1.40
1575 1656 8.322906 ACGTACATACTATTTGCTACGGTATA 57.677 34.615 0.00 0.00 32.98 1.47
1576 1657 7.206981 ACGTACATACTATTTGCTACGGTAT 57.793 36.000 0.00 0.00 32.98 2.73
1616 1703 3.596214 TCAGGCTCCAATTTTAGACGTC 58.404 45.455 7.70 7.70 0.00 4.34
1622 1709 5.754782 TCAGCTATTCAGGCTCCAATTTTA 58.245 37.500 0.00 0.00 38.03 1.52
1623 1710 4.603131 TCAGCTATTCAGGCTCCAATTTT 58.397 39.130 0.00 0.00 38.03 1.82
1676 1763 2.224314 CCAAGAGAGTTTTCGGTTCTGC 59.776 50.000 0.00 0.00 0.00 4.26
1680 1767 3.118000 AGGAACCAAGAGAGTTTTCGGTT 60.118 43.478 0.00 0.00 39.38 4.44
1872 1981 7.628366 GCGAGATGGAATTTTTACCTTGATTCA 60.628 37.037 0.00 0.00 31.72 2.57
1878 1987 4.157840 GGTGCGAGATGGAATTTTTACCTT 59.842 41.667 0.00 0.00 0.00 3.50
1889 1998 2.730934 AGTAGTAGGTGCGAGATGGA 57.269 50.000 0.00 0.00 0.00 3.41
1891 2000 3.499157 GGAGTAGTAGTAGGTGCGAGATG 59.501 52.174 0.00 0.00 0.00 2.90
1901 2010 3.871485 ACTGTGGTCGGAGTAGTAGTAG 58.129 50.000 0.00 0.00 0.00 2.57
1905 2014 6.594788 AAAAATACTGTGGTCGGAGTAGTA 57.405 37.500 0.00 0.00 0.00 1.82
1927 2036 7.541783 CACATCTTTCTCACACAAACTGAAAAA 59.458 33.333 0.00 0.00 0.00 1.94
1942 2051 5.855395 GCAACTCAAACATCACATCTTTCTC 59.145 40.000 0.00 0.00 0.00 2.87
1986 2096 7.391148 AATCTCGCCAATAAGTATGTTGTTT 57.609 32.000 0.00 0.00 0.00 2.83
2019 2129 3.263261 GCAACCCCTTTCGTTTCAAAAA 58.737 40.909 0.00 0.00 0.00 1.94
2020 2130 2.418884 GGCAACCCCTTTCGTTTCAAAA 60.419 45.455 0.00 0.00 0.00 2.44
2021 2131 1.137282 GGCAACCCCTTTCGTTTCAAA 59.863 47.619 0.00 0.00 0.00 2.69
2022 2132 0.747852 GGCAACCCCTTTCGTTTCAA 59.252 50.000 0.00 0.00 0.00 2.69
2023 2133 2.421220 GGCAACCCCTTTCGTTTCA 58.579 52.632 0.00 0.00 0.00 2.69
2041 2151 0.178918 TAAAAAGTTGGGGCAGGGGG 60.179 55.000 0.00 0.00 0.00 5.40
2042 2152 1.951209 ATAAAAAGTTGGGGCAGGGG 58.049 50.000 0.00 0.00 0.00 4.79
2043 2153 2.903135 TCAATAAAAAGTTGGGGCAGGG 59.097 45.455 0.00 0.00 0.00 4.45
2044 2154 4.615588 TTCAATAAAAAGTTGGGGCAGG 57.384 40.909 0.00 0.00 0.00 4.85
2045 2155 6.934048 TTTTTCAATAAAAAGTTGGGGCAG 57.066 33.333 0.00 0.00 39.16 4.85
2055 2165 8.246180 TGGTTGCATTTGCTTTTTCAATAAAAA 58.754 25.926 3.94 0.00 41.32 1.94
2056 2166 7.765307 TGGTTGCATTTGCTTTTTCAATAAAA 58.235 26.923 3.94 0.00 42.66 1.52
2057 2167 7.325660 TGGTTGCATTTGCTTTTTCAATAAA 57.674 28.000 3.94 0.00 42.66 1.40
2058 2168 6.932356 TGGTTGCATTTGCTTTTTCAATAA 57.068 29.167 3.94 0.00 42.66 1.40
2059 2169 6.932356 TTGGTTGCATTTGCTTTTTCAATA 57.068 29.167 3.94 0.00 42.66 1.90
2060 2170 5.831702 TTGGTTGCATTTGCTTTTTCAAT 57.168 30.435 3.94 0.00 42.66 2.57
2061 2171 5.633830 TTTGGTTGCATTTGCTTTTTCAA 57.366 30.435 3.94 0.00 42.66 2.69
2062 2172 4.438472 GCTTTGGTTGCATTTGCTTTTTCA 60.438 37.500 3.94 0.00 42.66 2.69
2063 2173 4.037021 GCTTTGGTTGCATTTGCTTTTTC 58.963 39.130 3.94 0.00 42.66 2.29
2064 2174 3.442977 TGCTTTGGTTGCATTTGCTTTTT 59.557 34.783 3.94 0.00 42.66 1.94
2065 2175 3.015327 TGCTTTGGTTGCATTTGCTTTT 58.985 36.364 3.94 0.00 42.66 2.27
2066 2176 2.355444 GTGCTTTGGTTGCATTTGCTTT 59.645 40.909 3.94 0.00 42.69 3.51
2067 2177 1.941975 GTGCTTTGGTTGCATTTGCTT 59.058 42.857 3.94 0.00 42.69 3.91
2068 2178 1.134461 TGTGCTTTGGTTGCATTTGCT 60.134 42.857 3.94 0.00 42.69 3.91
2069 2179 1.003652 GTGTGCTTTGGTTGCATTTGC 60.004 47.619 0.00 0.00 42.69 3.68
2070 2180 2.285756 CAGTGTGCTTTGGTTGCATTTG 59.714 45.455 0.00 0.00 42.69 2.32
2071 2181 2.093553 ACAGTGTGCTTTGGTTGCATTT 60.094 40.909 0.00 0.00 42.69 2.32
2072 2182 1.481772 ACAGTGTGCTTTGGTTGCATT 59.518 42.857 0.00 0.00 42.69 3.56
2073 2183 1.113788 ACAGTGTGCTTTGGTTGCAT 58.886 45.000 0.00 0.00 42.69 3.96
2074 2184 0.894141 AACAGTGTGCTTTGGTTGCA 59.106 45.000 0.00 0.00 38.19 4.08
2075 2185 2.857748 GTTAACAGTGTGCTTTGGTTGC 59.142 45.455 0.00 0.00 0.00 4.17
2076 2186 4.103365 TGTTAACAGTGTGCTTTGGTTG 57.897 40.909 3.59 0.00 0.00 3.77
2077 2187 3.428862 GCTGTTAACAGTGTGCTTTGGTT 60.429 43.478 30.90 0.00 45.45 3.67
2078 2188 2.099098 GCTGTTAACAGTGTGCTTTGGT 59.901 45.455 30.90 0.00 45.45 3.67
2079 2189 2.358898 AGCTGTTAACAGTGTGCTTTGG 59.641 45.455 30.90 8.36 45.45 3.28
2080 2190 3.313526 AGAGCTGTTAACAGTGTGCTTTG 59.686 43.478 30.90 9.03 45.45 2.77
2081 2191 3.545703 AGAGCTGTTAACAGTGTGCTTT 58.454 40.909 30.90 18.03 45.45 3.51
2082 2192 3.134458 GAGAGCTGTTAACAGTGTGCTT 58.866 45.455 30.90 15.92 45.45 3.91
2083 2193 2.760374 GAGAGCTGTTAACAGTGTGCT 58.240 47.619 30.90 24.13 45.45 4.40
2084 2194 1.457303 CGAGAGCTGTTAACAGTGTGC 59.543 52.381 30.90 20.31 45.45 4.57
2085 2195 2.061773 CCGAGAGCTGTTAACAGTGTG 58.938 52.381 30.90 18.37 45.45 3.82
2086 2196 1.605712 GCCGAGAGCTGTTAACAGTGT 60.606 52.381 30.90 21.11 45.45 3.55
2087 2197 1.071605 GCCGAGAGCTGTTAACAGTG 58.928 55.000 30.90 17.80 45.45 3.66
2088 2198 3.516578 GCCGAGAGCTGTTAACAGT 57.483 52.632 30.90 20.09 45.45 3.55
2105 2215 1.153269 GGCTACTTCTGGCTGGAGC 60.153 63.158 0.00 0.00 41.14 4.70
2106 2216 1.142748 CGGCTACTTCTGGCTGGAG 59.857 63.158 0.00 0.00 0.00 3.86
2107 2217 3.019003 GCGGCTACTTCTGGCTGGA 62.019 63.158 0.00 0.00 35.57 3.86
2108 2218 2.512515 GCGGCTACTTCTGGCTGG 60.513 66.667 0.00 0.00 35.57 4.85
2109 2219 1.812922 CTGCGGCTACTTCTGGCTG 60.813 63.158 0.00 0.00 37.83 4.85
2110 2220 2.581354 CTGCGGCTACTTCTGGCT 59.419 61.111 0.00 0.00 0.00 4.75
2111 2221 3.198489 GCTGCGGCTACTTCTGGC 61.198 66.667 11.21 0.00 35.22 4.85
2112 2222 1.812922 CTGCTGCGGCTACTTCTGG 60.813 63.158 20.27 0.00 39.59 3.86
2113 2223 0.390340 TTCTGCTGCGGCTACTTCTG 60.390 55.000 20.27 0.51 39.59 3.02
2114 2224 0.539051 ATTCTGCTGCGGCTACTTCT 59.461 50.000 20.27 0.00 39.59 2.85
2115 2225 1.373570 AATTCTGCTGCGGCTACTTC 58.626 50.000 20.27 0.00 39.59 3.01
2116 2226 2.691409 TAATTCTGCTGCGGCTACTT 57.309 45.000 20.27 9.79 39.59 2.24
2117 2227 2.918712 ATAATTCTGCTGCGGCTACT 57.081 45.000 20.27 0.00 39.59 2.57
2118 2228 3.807622 TGTAATAATTCTGCTGCGGCTAC 59.192 43.478 20.27 10.46 39.59 3.58
2119 2229 4.058124 CTGTAATAATTCTGCTGCGGCTA 58.942 43.478 20.27 3.81 39.59 3.93
2120 2230 2.874701 CTGTAATAATTCTGCTGCGGCT 59.125 45.455 20.27 0.00 39.59 5.52
2121 2231 2.872245 TCTGTAATAATTCTGCTGCGGC 59.128 45.455 11.65 11.65 39.26 6.53
2122 2232 3.060272 CGTCTGTAATAATTCTGCTGCGG 60.060 47.826 0.95 0.95 0.00 5.69
2123 2233 3.796717 TCGTCTGTAATAATTCTGCTGCG 59.203 43.478 0.00 0.00 0.00 5.18
2124 2234 5.674008 CATCGTCTGTAATAATTCTGCTGC 58.326 41.667 0.00 0.00 0.00 5.25
2125 2235 5.234972 TGCATCGTCTGTAATAATTCTGCTG 59.765 40.000 0.00 0.00 0.00 4.41
2126 2236 5.359756 TGCATCGTCTGTAATAATTCTGCT 58.640 37.500 0.00 0.00 0.00 4.24
2127 2237 5.657470 TGCATCGTCTGTAATAATTCTGC 57.343 39.130 0.00 0.00 0.00 4.26
2128 2238 7.239166 AGTTGCATCGTCTGTAATAATTCTG 57.761 36.000 0.00 0.00 31.82 3.02
2129 2239 8.942338 TTAGTTGCATCGTCTGTAATAATTCT 57.058 30.769 0.00 0.00 31.82 2.40
2130 2240 9.982291 TTTTAGTTGCATCGTCTGTAATAATTC 57.018 29.630 0.00 0.00 31.82 2.17
2131 2241 9.988350 CTTTTAGTTGCATCGTCTGTAATAATT 57.012 29.630 0.00 0.00 31.82 1.40
2132 2242 9.162764 ACTTTTAGTTGCATCGTCTGTAATAAT 57.837 29.630 0.00 0.00 31.82 1.28
2133 2243 8.542497 ACTTTTAGTTGCATCGTCTGTAATAA 57.458 30.769 0.00 0.00 31.82 1.40
2134 2244 8.033038 AGACTTTTAGTTGCATCGTCTGTAATA 58.967 33.333 0.00 0.00 31.82 0.98
2135 2245 6.874134 AGACTTTTAGTTGCATCGTCTGTAAT 59.126 34.615 0.00 0.00 31.82 1.89
2136 2246 6.145534 CAGACTTTTAGTTGCATCGTCTGTAA 59.854 38.462 15.82 0.00 40.96 2.41
2137 2247 5.633601 CAGACTTTTAGTTGCATCGTCTGTA 59.366 40.000 15.82 0.00 40.96 2.74
2138 2248 4.449068 CAGACTTTTAGTTGCATCGTCTGT 59.551 41.667 15.82 3.65 40.96 3.41
2139 2249 4.686091 TCAGACTTTTAGTTGCATCGTCTG 59.314 41.667 17.06 17.06 44.86 3.51
2140 2250 4.883083 TCAGACTTTTAGTTGCATCGTCT 58.117 39.130 0.00 0.00 0.00 4.18
2141 2251 5.050363 TGTTCAGACTTTTAGTTGCATCGTC 60.050 40.000 0.00 0.00 0.00 4.20
2142 2252 4.814234 TGTTCAGACTTTTAGTTGCATCGT 59.186 37.500 0.00 0.00 0.00 3.73
2143 2253 5.140177 GTGTTCAGACTTTTAGTTGCATCG 58.860 41.667 0.00 0.00 0.00 3.84
2144 2254 5.452777 GGTGTTCAGACTTTTAGTTGCATC 58.547 41.667 0.00 0.00 0.00 3.91
2145 2255 4.278419 GGGTGTTCAGACTTTTAGTTGCAT 59.722 41.667 0.00 0.00 0.00 3.96
2146 2256 3.630312 GGGTGTTCAGACTTTTAGTTGCA 59.370 43.478 0.00 0.00 0.00 4.08
2147 2257 3.630312 TGGGTGTTCAGACTTTTAGTTGC 59.370 43.478 0.00 0.00 0.00 4.17
2148 2258 4.638421 TGTGGGTGTTCAGACTTTTAGTTG 59.362 41.667 0.00 0.00 0.00 3.16
2149 2259 4.850680 TGTGGGTGTTCAGACTTTTAGTT 58.149 39.130 0.00 0.00 0.00 2.24
2150 2260 4.497291 TGTGGGTGTTCAGACTTTTAGT 57.503 40.909 0.00 0.00 0.00 2.24
2151 2261 5.007724 GTCTTGTGGGTGTTCAGACTTTTAG 59.992 44.000 0.00 0.00 0.00 1.85
2152 2262 4.879545 GTCTTGTGGGTGTTCAGACTTTTA 59.120 41.667 0.00 0.00 0.00 1.52
2153 2263 3.694566 GTCTTGTGGGTGTTCAGACTTTT 59.305 43.478 0.00 0.00 0.00 2.27
2154 2264 3.054361 AGTCTTGTGGGTGTTCAGACTTT 60.054 43.478 0.00 0.00 32.05 2.66
2155 2265 2.505819 AGTCTTGTGGGTGTTCAGACTT 59.494 45.455 0.00 0.00 32.05 3.01
2156 2266 2.119495 AGTCTTGTGGGTGTTCAGACT 58.881 47.619 0.00 0.00 0.00 3.24
2157 2267 2.158957 TCAGTCTTGTGGGTGTTCAGAC 60.159 50.000 0.00 0.00 0.00 3.51
2158 2268 2.103094 CTCAGTCTTGTGGGTGTTCAGA 59.897 50.000 0.00 0.00 0.00 3.27
2159 2269 2.487934 CTCAGTCTTGTGGGTGTTCAG 58.512 52.381 0.00 0.00 0.00 3.02
2160 2270 1.475034 GCTCAGTCTTGTGGGTGTTCA 60.475 52.381 0.00 0.00 0.00 3.18
2161 2271 1.202698 AGCTCAGTCTTGTGGGTGTTC 60.203 52.381 0.00 0.00 0.00 3.18
2162 2272 0.839946 AGCTCAGTCTTGTGGGTGTT 59.160 50.000 0.00 0.00 0.00 3.32
2163 2273 0.107456 CAGCTCAGTCTTGTGGGTGT 59.893 55.000 0.00 0.00 0.00 4.16
2164 2274 0.107456 ACAGCTCAGTCTTGTGGGTG 59.893 55.000 0.00 0.00 35.01 4.61
2165 2275 0.839946 AACAGCTCAGTCTTGTGGGT 59.160 50.000 0.00 0.00 0.00 4.51
2166 2276 1.517242 GAACAGCTCAGTCTTGTGGG 58.483 55.000 0.00 0.00 0.00 4.61
2167 2277 1.143305 CGAACAGCTCAGTCTTGTGG 58.857 55.000 0.00 0.00 0.00 4.17
2168 2278 1.858091 ACGAACAGCTCAGTCTTGTG 58.142 50.000 0.00 0.00 0.00 3.33
2169 2279 2.205074 CAACGAACAGCTCAGTCTTGT 58.795 47.619 0.00 0.00 0.00 3.16
2170 2280 2.205074 ACAACGAACAGCTCAGTCTTG 58.795 47.619 0.00 0.00 0.00 3.02
2171 2281 2.604046 ACAACGAACAGCTCAGTCTT 57.396 45.000 0.00 0.00 0.00 3.01
2172 2282 2.604046 AACAACGAACAGCTCAGTCT 57.396 45.000 0.00 0.00 0.00 3.24
2173 2283 2.351726 ACAAACAACGAACAGCTCAGTC 59.648 45.455 0.00 0.00 0.00 3.51
2174 2284 2.095853 CACAAACAACGAACAGCTCAGT 59.904 45.455 0.00 0.00 0.00 3.41
2175 2285 2.539547 CCACAAACAACGAACAGCTCAG 60.540 50.000 0.00 0.00 0.00 3.35
2214 2324 2.224079 AGCATGCAAAAGTAGACGTGTG 59.776 45.455 21.98 0.00 0.00 3.82
2384 2495 7.792374 TCACTCCTCTATGTTGAATTTATGC 57.208 36.000 0.00 0.00 0.00 3.14
2402 2513 7.712639 TGATAAGATAAAAGCAGTCATCACTCC 59.287 37.037 0.00 0.00 0.00 3.85
2578 2696 6.675026 CATCATGCATCCTATTTGTGTTAGG 58.325 40.000 0.00 0.00 38.06 2.69
2728 2846 5.334724 AGTATAAACTGTAGGTTCCCACG 57.665 43.478 0.00 0.00 37.12 4.94
2950 3068 3.573229 AGCTTCAGTGCCTGGCCA 61.573 61.111 17.53 4.71 31.51 5.36
3085 3203 0.039978 ATGACGACGATCGCATCTCC 60.040 55.000 16.60 0.41 45.12 3.71
3100 3218 2.238245 ACAACTACGACGACGATGAC 57.762 50.000 15.32 0.00 42.66 3.06
3101 3219 2.995939 ACTACAACTACGACGACGATGA 59.004 45.455 15.32 0.00 42.66 2.92
3102 3220 3.089267 CACTACAACTACGACGACGATG 58.911 50.000 15.32 8.37 42.66 3.84
3103 3221 2.094894 CCACTACAACTACGACGACGAT 59.905 50.000 15.32 0.95 42.66 3.73
3104 3222 1.460743 CCACTACAACTACGACGACGA 59.539 52.381 15.32 0.00 42.66 4.20
3105 3223 1.195448 ACCACTACAACTACGACGACG 59.805 52.381 5.58 5.58 45.75 5.12
3106 3224 2.578495 CACCACTACAACTACGACGAC 58.422 52.381 0.00 0.00 0.00 4.34
3107 3225 1.536766 CCACCACTACAACTACGACGA 59.463 52.381 0.00 0.00 0.00 4.20
3108 3226 1.267806 ACCACCACTACAACTACGACG 59.732 52.381 0.00 0.00 0.00 5.12
3109 3227 2.669364 CACCACCACTACAACTACGAC 58.331 52.381 0.00 0.00 0.00 4.34
3110 3228 1.000060 GCACCACCACTACAACTACGA 60.000 52.381 0.00 0.00 0.00 3.43
3111 3229 1.000506 AGCACCACCACTACAACTACG 59.999 52.381 0.00 0.00 0.00 3.51
3353 3472 2.743664 TGATCTCATTTCAGCACAACCG 59.256 45.455 0.00 0.00 0.00 4.44
3361 3480 6.814506 ACAAAACCTCTGATCTCATTTCAG 57.185 37.500 0.00 0.00 41.61 3.02
3455 3574 6.518208 AGTCAGAATTGAGAGTAGTACCAC 57.482 41.667 0.00 0.00 32.98 4.16
3492 3611 1.145738 ACCAAGAAACATGGCCAGTCT 59.854 47.619 13.05 8.42 41.89 3.24
3553 3672 6.798315 ACATAGATCAGTCATGCAATTAGC 57.202 37.500 0.00 0.00 45.96 3.09
3575 3694 4.082949 GGGAACAGGCACAACATTTAGTAC 60.083 45.833 0.00 0.00 0.00 2.73
3580 3699 1.786937 TGGGAACAGGCACAACATTT 58.213 45.000 0.00 0.00 35.01 2.32
3581 3700 3.529948 TGGGAACAGGCACAACATT 57.470 47.368 0.00 0.00 35.01 2.71
3684 3803 1.956802 GTTGGCGAAACCTTCCAGG 59.043 57.895 0.00 0.00 42.49 4.45
3697 3816 8.785329 TTATTTATTCATTTGGAAAGGTTGGC 57.215 30.769 0.00 0.00 39.39 4.52
3816 3936 5.598005 AGAGAGAAGAGAGAGAGAGAGAGAG 59.402 48.000 0.00 0.00 0.00 3.20
3817 3937 5.523588 AGAGAGAAGAGAGAGAGAGAGAGA 58.476 45.833 0.00 0.00 0.00 3.10
3818 3938 5.867903 AGAGAGAAGAGAGAGAGAGAGAG 57.132 47.826 0.00 0.00 0.00 3.20
3819 3939 6.213397 TGAAAGAGAGAAGAGAGAGAGAGAGA 59.787 42.308 0.00 0.00 0.00 3.10
3820 3940 6.409704 TGAAAGAGAGAAGAGAGAGAGAGAG 58.590 44.000 0.00 0.00 0.00 3.20
3821 3941 6.373005 TGAAAGAGAGAAGAGAGAGAGAGA 57.627 41.667 0.00 0.00 0.00 3.10
3822 3942 6.018425 CGATGAAAGAGAGAAGAGAGAGAGAG 60.018 46.154 0.00 0.00 0.00 3.20
3823 3943 5.817296 CGATGAAAGAGAGAAGAGAGAGAGA 59.183 44.000 0.00 0.00 0.00 3.10
3824 3944 5.586243 ACGATGAAAGAGAGAAGAGAGAGAG 59.414 44.000 0.00 0.00 0.00 3.20
3825 3945 5.496556 ACGATGAAAGAGAGAAGAGAGAGA 58.503 41.667 0.00 0.00 0.00 3.10
3826 3946 5.353956 TGACGATGAAAGAGAGAAGAGAGAG 59.646 44.000 0.00 0.00 0.00 3.20
3827 3947 5.123186 GTGACGATGAAAGAGAGAAGAGAGA 59.877 44.000 0.00 0.00 0.00 3.10
3828 3948 5.331902 GTGACGATGAAAGAGAGAAGAGAG 58.668 45.833 0.00 0.00 0.00 3.20
3829 3949 4.156922 GGTGACGATGAAAGAGAGAAGAGA 59.843 45.833 0.00 0.00 0.00 3.10
3870 3990 1.148310 GTGGTGATGACCGTGAACAG 58.852 55.000 0.00 0.00 46.62 3.16
3909 4029 6.017934 GCGAAAAGGAGATGCTTTCATGTATA 60.018 38.462 0.00 0.00 31.96 1.47
3910 4030 5.220931 GCGAAAAGGAGATGCTTTCATGTAT 60.221 40.000 0.00 0.00 31.96 2.29
3911 4031 4.094887 GCGAAAAGGAGATGCTTTCATGTA 59.905 41.667 0.00 0.00 31.96 2.29
3912 4032 3.119708 GCGAAAAGGAGATGCTTTCATGT 60.120 43.478 0.00 0.00 31.96 3.21
3913 4033 3.128242 AGCGAAAAGGAGATGCTTTCATG 59.872 43.478 0.00 0.00 31.96 3.07
3914 4034 3.350833 AGCGAAAAGGAGATGCTTTCAT 58.649 40.909 0.00 0.00 35.17 2.57
3915 4035 2.783135 AGCGAAAAGGAGATGCTTTCA 58.217 42.857 0.00 0.00 30.27 2.69
3916 4036 3.839051 AAGCGAAAAGGAGATGCTTTC 57.161 42.857 0.00 0.00 42.83 2.62
3940 4060 2.189521 CCGTTGATTCCTCGGGGG 59.810 66.667 0.00 0.00 40.49 5.40
3944 4066 1.449601 CCCCACCGTTGATTCCTCG 60.450 63.158 0.00 0.00 0.00 4.63
3995 4117 4.329545 TCCACCGGTTGCCTCTGC 62.330 66.667 2.97 0.00 38.26 4.26
3996 4118 2.046892 CTCCACCGGTTGCCTCTG 60.047 66.667 2.97 0.00 0.00 3.35
3997 4119 2.203788 TCTCCACCGGTTGCCTCT 60.204 61.111 2.97 0.00 0.00 3.69
3998 4120 2.047179 GTCTCCACCGGTTGCCTC 60.047 66.667 2.97 0.00 0.00 4.70
3999 4121 4.003788 CGTCTCCACCGGTTGCCT 62.004 66.667 2.97 0.00 0.00 4.75
4001 4123 3.291101 TAGCGTCTCCACCGGTTGC 62.291 63.158 2.97 2.11 37.26 4.17
4002 4124 1.153823 CTAGCGTCTCCACCGGTTG 60.154 63.158 2.97 0.00 37.26 3.77
4003 4125 1.183676 AACTAGCGTCTCCACCGGTT 61.184 55.000 2.97 0.00 37.26 4.44
4006 4128 1.067776 AGAAAACTAGCGTCTCCACCG 60.068 52.381 0.00 0.00 0.00 4.94
4061 4183 1.167851 CAACCATGCGAGATTGGTGT 58.832 50.000 0.00 0.00 45.44 4.16
4062 4184 1.131126 GTCAACCATGCGAGATTGGTG 59.869 52.381 0.00 0.00 45.44 4.17
4064 4186 0.374758 CGTCAACCATGCGAGATTGG 59.625 55.000 0.00 0.00 39.02 3.16
4085 4207 4.878971 GGGTGAAAGAGAGAAGAATTAGCC 59.121 45.833 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.