Multiple sequence alignment - TraesCS2D01G178000

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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 TraesCS2D01G178000 chr2D 100.000 2468 0 0 1 2468 121359469 121361936 0.000000e+00 4558
1 TraesCS2D01G178000 chr2A 86.806 2016 140 53 540 2468 125607475 125609451 0.000000e+00 2134
2 TraesCS2D01G178000 chr2A 84.832 567 41 21 28 556 125606891 125607450 1.680000e-146 529
3 TraesCS2D01G178000 chr2B 88.721 1658 89 42 45 1645 174779875 174781491 0.000000e+00 1936
4 TraesCS2D01G178000 chr2B 85.750 793 44 25 1694 2468 174786784 174787525 0.000000e+00 774
5 TraesCS2D01G178000 chr7A 82.482 137 20 4 1039 1173 118400372 118400238 1.550000e-22 117
6 TraesCS2D01G178000 chr7D 82.353 119 17 4 1057 1173 113348371 113348255 1.560000e-17 100
7 TraesCS2D01G178000 chr7B 82.353 119 17 4 1057 1173 72764667 72764551 1.560000e-17 100


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 TraesCS2D01G178000 chr2D 121359469 121361936 2467 False 4558.0 4558 100.000 1 2468 1 chr2D.!!$F1 2467
1 TraesCS2D01G178000 chr2A 125606891 125609451 2560 False 1331.5 2134 85.819 28 2468 2 chr2A.!!$F1 2440
2 TraesCS2D01G178000 chr2B 174779875 174781491 1616 False 1936.0 1936 88.721 45 1645 1 chr2B.!!$F1 1600
3 TraesCS2D01G178000 chr2B 174786784 174787525 741 False 774.0 774 85.750 1694 2468 1 chr2B.!!$F2 774

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
241 260 0.03563 AAGCATCACTGTCTGCCTCC 60.036 55.0 7.94 0.0 39.22 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 1946 0.036164 TGGTGCTTATGCGTCTGGTT 59.964 50.0 0.0 0.0 43.34 3.67 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
17 18 3.759353 GTTACCCGTCGCTCGAAC 58.241 61.111 0.00 0.00 42.86 3.95
19 20 1.081242 TTACCCGTCGCTCGAACAC 60.081 57.895 0.00 0.00 42.86 3.32
20 21 1.518056 TTACCCGTCGCTCGAACACT 61.518 55.000 0.00 0.00 42.86 3.55
21 22 1.915614 TACCCGTCGCTCGAACACTC 61.916 60.000 0.00 0.00 42.86 3.51
22 23 2.254350 CCGTCGCTCGAACACTCA 59.746 61.111 0.00 0.00 42.86 3.41
24 25 1.406219 CCGTCGCTCGAACACTCATG 61.406 60.000 0.00 0.00 42.86 3.07
25 26 1.406219 CGTCGCTCGAACACTCATGG 61.406 60.000 0.00 0.00 42.86 3.66
26 27 1.446099 TCGCTCGAACACTCATGGC 60.446 57.895 0.00 0.00 0.00 4.40
27 28 1.737735 CGCTCGAACACTCATGGCA 60.738 57.895 0.00 0.00 0.00 4.92
28 29 1.690283 CGCTCGAACACTCATGGCAG 61.690 60.000 0.00 0.00 0.00 4.85
29 30 1.975363 GCTCGAACACTCATGGCAGC 61.975 60.000 0.00 0.00 0.00 5.25
30 31 1.364626 CTCGAACACTCATGGCAGCC 61.365 60.000 3.66 3.66 0.00 4.85
31 32 2.743752 CGAACACTCATGGCAGCCG 61.744 63.158 7.03 0.00 0.00 5.52
32 33 3.044059 GAACACTCATGGCAGCCGC 62.044 63.158 7.03 0.00 37.44 6.53
81 82 1.354337 GCACGAGCAGAAATCGCTGA 61.354 55.000 0.00 0.00 43.91 4.26
100 104 2.307768 GACACGGATAGGAGGATCACA 58.692 52.381 0.00 0.00 36.25 3.58
101 108 2.894126 GACACGGATAGGAGGATCACAT 59.106 50.000 0.00 0.00 36.25 3.21
103 110 2.095008 CACGGATAGGAGGATCACATCG 60.095 54.545 0.00 0.00 36.25 3.84
157 173 2.577593 GACGTAGGCCGGCTTCTT 59.422 61.111 28.56 12.27 43.06 2.52
175 191 1.464997 CTTCCTTGCAAGTTACCGCTC 59.535 52.381 24.35 0.00 0.00 5.03
188 204 2.726691 CCGCTCGCGTGTTCGATTT 61.727 57.895 5.77 0.00 37.87 2.17
206 223 0.539438 TTGCAGGGGCCAGTTGTAAG 60.539 55.000 4.39 0.00 40.13 2.34
207 224 2.343426 GCAGGGGCCAGTTGTAAGC 61.343 63.158 4.39 0.00 0.00 3.09
215 234 3.954258 GGGCCAGTTGTAAGCAAATAGAT 59.046 43.478 4.39 0.00 36.22 1.98
218 237 6.265422 GGGCCAGTTGTAAGCAAATAGATAAT 59.735 38.462 4.39 0.00 36.22 1.28
220 239 7.201821 GGCCAGTTGTAAGCAAATAGATAATGT 60.202 37.037 0.00 0.00 36.22 2.71
238 257 3.238232 TGAAGCATCACTGTCTGCC 57.762 52.632 7.94 0.00 39.22 4.85
239 258 0.689055 TGAAGCATCACTGTCTGCCT 59.311 50.000 7.94 0.00 39.22 4.75
240 259 1.338484 TGAAGCATCACTGTCTGCCTC 60.338 52.381 7.94 6.06 39.22 4.70
241 260 0.035630 AAGCATCACTGTCTGCCTCC 60.036 55.000 7.94 0.00 39.22 4.30
242 261 1.196766 AGCATCACTGTCTGCCTCCA 61.197 55.000 7.94 0.00 39.22 3.86
243 262 0.321919 GCATCACTGTCTGCCTCCAA 60.322 55.000 1.38 0.00 32.15 3.53
265 287 3.070302 ACTCGTTTCTCTTGGCTTCTTCT 59.930 43.478 0.00 0.00 0.00 2.85
308 331 0.165944 CACGAGAATTGTTGCCGTCC 59.834 55.000 0.00 0.00 0.00 4.79
337 360 2.047844 CAGTGAGCCGGACAGGTG 60.048 66.667 5.05 1.33 43.70 4.00
460 499 3.675225 CAGACTGACATAGAAACACCACG 59.325 47.826 0.00 0.00 0.00 4.94
514 553 4.546637 CGCCATCGTATCGTACCC 57.453 61.111 0.00 0.00 0.00 3.69
519 558 2.813061 CCATCGTATCGTACCCGTTTT 58.187 47.619 0.00 0.00 35.01 2.43
530 569 9.195411 GTATCGTACCCGTTTTATTTATCATCA 57.805 33.333 0.00 0.00 35.01 3.07
533 576 7.115236 TCGTACCCGTTTTATTTATCATCATCG 59.885 37.037 0.00 0.00 35.01 3.84
534 577 7.095940 CGTACCCGTTTTATTTATCATCATCGT 60.096 37.037 0.00 0.00 0.00 3.73
535 578 6.954944 ACCCGTTTTATTTATCATCATCGTG 58.045 36.000 0.00 0.00 0.00 4.35
618 707 1.508808 GAAACGGCCGTGGCAAGTTA 61.509 55.000 34.95 0.00 44.11 2.24
915 1035 1.822506 TTCTCTCTGGTCATCGTCGT 58.177 50.000 0.00 0.00 0.00 4.34
974 1101 3.666253 CGGCGGCGGGTTTTCTTT 61.666 61.111 25.36 0.00 0.00 2.52
975 1102 2.257371 GGCGGCGGGTTTTCTTTC 59.743 61.111 9.78 0.00 0.00 2.62
977 1104 1.209383 GCGGCGGGTTTTCTTTCTC 59.791 57.895 9.78 0.00 0.00 2.87
978 1105 1.495951 CGGCGGGTTTTCTTTCTCG 59.504 57.895 0.00 0.00 0.00 4.04
981 1108 1.495951 CGGGTTTTCTTTCTCGGCG 59.504 57.895 0.00 0.00 0.00 6.46
983 1110 1.583495 GGGTTTTCTTTCTCGGCGGG 61.583 60.000 7.21 2.41 0.00 6.13
984 1111 1.583495 GGTTTTCTTTCTCGGCGGGG 61.583 60.000 7.05 0.00 0.00 5.73
985 1112 0.604511 GTTTTCTTTCTCGGCGGGGA 60.605 55.000 7.05 0.00 0.00 4.81
986 1113 0.326927 TTTTCTTTCTCGGCGGGGAT 59.673 50.000 7.05 0.00 0.00 3.85
987 1114 1.196911 TTTCTTTCTCGGCGGGGATA 58.803 50.000 7.05 0.42 0.00 2.59
999 1126 0.669077 CGGGGATAGAGGTCTTGACG 59.331 60.000 0.00 0.00 0.00 4.35
1473 1606 1.079819 GCTCGTGGAGTAGCAAGCA 60.080 57.895 0.00 0.00 38.63 3.91
1481 1614 2.305635 TGGAGTAGCAAGCATCCAAGAA 59.694 45.455 10.11 0.00 38.86 2.52
1482 1615 2.680339 GGAGTAGCAAGCATCCAAGAAC 59.320 50.000 0.00 0.00 0.00 3.01
1485 1618 1.999648 AGCAAGCATCCAAGAACCAA 58.000 45.000 0.00 0.00 0.00 3.67
1486 1619 2.532843 AGCAAGCATCCAAGAACCAAT 58.467 42.857 0.00 0.00 0.00 3.16
1487 1620 2.232941 AGCAAGCATCCAAGAACCAATG 59.767 45.455 0.00 0.00 0.00 2.82
1489 1622 3.306225 GCAAGCATCCAAGAACCAATGAA 60.306 43.478 0.00 0.00 0.00 2.57
1490 1623 4.800249 GCAAGCATCCAAGAACCAATGAAA 60.800 41.667 0.00 0.00 0.00 2.69
1491 1624 4.525912 AGCATCCAAGAACCAATGAAAC 57.474 40.909 0.00 0.00 0.00 2.78
1492 1625 3.259123 AGCATCCAAGAACCAATGAAACC 59.741 43.478 0.00 0.00 0.00 3.27
1528 1680 6.322456 TGATGGTAGTCTCATCTAGTTTCCTG 59.678 42.308 0.00 0.00 41.01 3.86
1530 1682 4.202172 GGTAGTCTCATCTAGTTTCCTGCC 60.202 50.000 0.00 0.00 0.00 4.85
1531 1683 3.718723 AGTCTCATCTAGTTTCCTGCCT 58.281 45.455 0.00 0.00 0.00 4.75
1650 1809 9.803315 CAATGTGTACAGAGTACATACAGTAAT 57.197 33.333 12.53 0.00 34.18 1.89
1682 1841 7.277174 ACAAAAAGAGTAAATGGAAGTGGAG 57.723 36.000 0.00 0.00 0.00 3.86
1729 1889 6.231211 TCCAAGTGGTTTCTATTTCTCTGTC 58.769 40.000 0.00 0.00 36.34 3.51
1741 1901 0.322975 TCTCTGTCTTGCTCCTTGCC 59.677 55.000 0.00 0.00 42.00 4.52
1760 1920 1.467734 CCTCTGCTCAAGTTCATGCAC 59.532 52.381 0.00 0.00 0.00 4.57
1785 1945 4.816385 CACCTGTTCTTCAAACAGCTTCTA 59.184 41.667 11.50 0.00 44.62 2.10
1786 1946 5.296780 CACCTGTTCTTCAAACAGCTTCTAA 59.703 40.000 11.50 0.00 44.62 2.10
1788 1948 6.183360 ACCTGTTCTTCAAACAGCTTCTAAAC 60.183 38.462 11.50 0.00 44.62 2.01
1793 1955 5.527582 TCTTCAAACAGCTTCTAAACCAGAC 59.472 40.000 0.00 0.00 31.12 3.51
1823 1992 2.154462 CCAGAATGCACCTTTTCGTCT 58.846 47.619 0.00 0.00 31.97 4.18
1838 2008 6.239036 CCTTTTCGTCTCAAAGAGGGAAAAAT 60.239 38.462 18.30 0.00 37.21 1.82
1840 2010 3.502211 TCGTCTCAAAGAGGGAAAAATGC 59.498 43.478 0.00 0.00 31.47 3.56
1845 2015 6.707608 GTCTCAAAGAGGGAAAAATGCAAAAT 59.292 34.615 0.00 0.00 0.00 1.82
1912 2087 3.326006 ACCAGATCAATCATCTATGCCGT 59.674 43.478 0.00 0.00 40.20 5.68
1946 2127 5.333952 GGTGATGAGATTGATTCTGATTCGC 60.334 44.000 0.00 0.00 33.74 4.70
1947 2128 5.235831 GTGATGAGATTGATTCTGATTCGCA 59.764 40.000 0.00 0.00 33.74 5.10
1948 2129 5.465724 TGATGAGATTGATTCTGATTCGCAG 59.534 40.000 0.00 0.00 46.31 5.18
1949 2130 3.558829 TGAGATTGATTCTGATTCGCAGC 59.441 43.478 0.00 0.00 44.52 5.25
1950 2131 3.538591 AGATTGATTCTGATTCGCAGCA 58.461 40.909 0.00 0.00 44.52 4.41
1952 2133 2.678471 TGATTCTGATTCGCAGCAGA 57.322 45.000 0.00 0.00 44.52 4.26
1953 2134 2.547826 TGATTCTGATTCGCAGCAGAG 58.452 47.619 2.80 0.00 44.52 3.35
1954 2135 1.865970 GATTCTGATTCGCAGCAGAGG 59.134 52.381 2.80 0.00 44.52 3.69
1955 2136 0.742281 TTCTGATTCGCAGCAGAGGC 60.742 55.000 2.80 0.00 44.52 4.70
1982 2163 7.392953 TCTCGATATGAGCATAGATCACTTTCT 59.607 37.037 0.00 0.00 44.86 2.52
1985 2166 5.627182 ATGAGCATAGATCACTTTCTGGT 57.373 39.130 0.00 0.00 28.34 4.00
1990 2171 4.937620 GCATAGATCACTTTCTGGTTCACA 59.062 41.667 0.00 0.00 0.00 3.58
2008 2202 6.147985 GGTTCACAGATAAACTTCTCCTTGTC 59.852 42.308 0.00 0.00 0.00 3.18
2081 2278 2.137523 ACCGCGGTACTGTAGTTTTTG 58.862 47.619 33.34 0.00 0.00 2.44
2176 2378 1.135859 CAAAGCCTCGCAATCAGACAC 60.136 52.381 0.00 0.00 0.00 3.67
2182 2384 1.723542 CTCGCAATCAGACACACAGAC 59.276 52.381 0.00 0.00 0.00 3.51
2188 2394 3.584406 ATCAGACACACAGACTAGCAC 57.416 47.619 0.00 0.00 0.00 4.40
2193 2399 1.615883 ACACACAGACTAGCACAGAGG 59.384 52.381 0.00 0.00 0.00 3.69
2227 2433 0.525668 GTGCCATCTCGATCGTTCGT 60.526 55.000 15.94 0.00 45.65 3.85
2232 2438 0.029035 ATCTCGATCGTTCGTTCCCG 59.971 55.000 15.94 1.88 45.65 5.14
2365 2572 7.870954 TCGCGAGATCAACCATATAATTAAAGT 59.129 33.333 3.71 0.00 33.31 2.66
2366 2573 7.952101 CGCGAGATCAACCATATAATTAAAGTG 59.048 37.037 0.00 0.00 0.00 3.16
2367 2574 7.746475 GCGAGATCAACCATATAATTAAAGTGC 59.254 37.037 0.00 0.00 0.00 4.40
2368 2575 8.773645 CGAGATCAACCATATAATTAAAGTGCA 58.226 33.333 0.00 0.00 0.00 4.57
2372 2579 8.759481 TCAACCATATAATTAAAGTGCATCCA 57.241 30.769 0.00 0.00 0.00 3.41
2373 2580 9.365906 TCAACCATATAATTAAAGTGCATCCAT 57.634 29.630 0.00 0.00 0.00 3.41
2374 2581 9.630098 CAACCATATAATTAAAGTGCATCCATC 57.370 33.333 0.00 0.00 0.00 3.51
2375 2582 8.353423 ACCATATAATTAAAGTGCATCCATCC 57.647 34.615 0.00 0.00 0.00 3.51
2376 2583 7.949565 ACCATATAATTAAAGTGCATCCATCCA 59.050 33.333 0.00 0.00 0.00 3.41
2377 2584 8.974238 CCATATAATTAAAGTGCATCCATCCAT 58.026 33.333 0.00 0.00 0.00 3.41
2410 2617 1.071542 TCGTCTTCACCCAATTGCTGA 59.928 47.619 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.081242 TGTTCGAGCGACGGGTAAC 60.081 57.895 0.00 4.98 42.82 2.50
1 2 1.081242 GTGTTCGAGCGACGGGTAA 60.081 57.895 0.00 0.00 42.82 2.85
2 3 1.915614 GAGTGTTCGAGCGACGGGTA 61.916 60.000 0.00 0.00 42.82 3.69
4 5 2.504244 GAGTGTTCGAGCGACGGG 60.504 66.667 0.00 0.00 42.82 5.28
8 9 1.446099 GCCATGAGTGTTCGAGCGA 60.446 57.895 0.00 0.00 0.00 4.93
12 13 1.375908 GGCTGCCATGAGTGTTCGA 60.376 57.895 15.17 0.00 0.00 3.71
14 15 3.044059 GCGGCTGCCATGAGTGTTC 62.044 63.158 20.29 0.00 33.98 3.18
15 16 3.058160 GCGGCTGCCATGAGTGTT 61.058 61.111 20.29 0.00 33.98 3.32
44 45 2.280797 AACACGATGGCACTGCGT 60.281 55.556 6.12 6.12 39.04 5.24
45 46 2.174107 CAACACGATGGCACTGCG 59.826 61.111 0.00 0.00 0.00 5.18
46 47 2.126734 GCAACACGATGGCACTGC 60.127 61.111 0.00 0.00 0.00 4.40
47 48 3.342909 TGCAACACGATGGCACTG 58.657 55.556 0.00 0.00 31.58 3.66
81 82 2.454336 TGTGATCCTCCTATCCGTGT 57.546 50.000 0.00 0.00 0.00 4.49
157 173 0.669318 CGAGCGGTAACTTGCAAGGA 60.669 55.000 29.18 14.76 0.00 3.36
175 191 1.509787 CCTGCAAATCGAACACGCG 60.510 57.895 3.53 3.53 0.00 6.01
188 204 1.074775 CTTACAACTGGCCCCTGCA 59.925 57.895 0.00 0.00 40.13 4.41
220 239 0.689055 AGGCAGACAGTGATGCTTCA 59.311 50.000 19.50 0.00 42.19 3.02
235 254 1.048601 AGAGAAACGAGTTGGAGGCA 58.951 50.000 0.00 0.00 0.00 4.75
236 255 1.801178 CAAGAGAAACGAGTTGGAGGC 59.199 52.381 0.00 0.00 0.00 4.70
237 256 2.417719 CCAAGAGAAACGAGTTGGAGG 58.582 52.381 0.00 0.00 41.82 4.30
238 257 1.801178 GCCAAGAGAAACGAGTTGGAG 59.199 52.381 4.13 0.00 41.82 3.86
239 258 1.416401 AGCCAAGAGAAACGAGTTGGA 59.584 47.619 4.13 0.00 41.82 3.53
240 259 1.884235 AGCCAAGAGAAACGAGTTGG 58.116 50.000 0.00 0.00 42.11 3.77
241 260 3.134458 AGAAGCCAAGAGAAACGAGTTG 58.866 45.455 0.00 0.00 0.00 3.16
242 261 3.477210 AGAAGCCAAGAGAAACGAGTT 57.523 42.857 0.00 0.00 0.00 3.01
243 262 3.070302 AGAAGAAGCCAAGAGAAACGAGT 59.930 43.478 0.00 0.00 0.00 4.18
265 287 0.322456 ATGTAGGGCGCTTGCTGAAA 60.322 50.000 9.23 0.00 39.13 2.69
440 471 2.412089 GCGTGGTGTTTCTATGTCAGTC 59.588 50.000 0.00 0.00 0.00 3.51
444 475 1.463444 GTGGCGTGGTGTTTCTATGTC 59.537 52.381 0.00 0.00 0.00 3.06
447 486 1.519408 GTGTGGCGTGGTGTTTCTAT 58.481 50.000 0.00 0.00 0.00 1.98
514 553 6.083649 CGTGCACGATGATGATAAATAAAACG 59.916 38.462 34.93 0.00 43.02 3.60
533 576 1.472276 CGCCTCGTTATCTCGTGCAC 61.472 60.000 6.82 6.82 33.08 4.57
534 577 1.226575 CGCCTCGTTATCTCGTGCA 60.227 57.895 0.00 0.00 33.08 4.57
535 578 2.577785 GCGCCTCGTTATCTCGTGC 61.578 63.158 0.00 0.00 0.00 5.34
881 997 2.480802 GAGAGAAAGAAAAGTCCCGTGC 59.519 50.000 0.00 0.00 0.00 5.34
888 1008 5.221541 ACGATGACCAGAGAGAAAGAAAAGT 60.222 40.000 0.00 0.00 0.00 2.66
963 1090 1.495951 CGCCGAGAAAGAAAACCCG 59.504 57.895 0.00 0.00 0.00 5.28
965 1092 1.583495 CCCCGCCGAGAAAGAAAACC 61.583 60.000 0.00 0.00 0.00 3.27
966 1093 0.604511 TCCCCGCCGAGAAAGAAAAC 60.605 55.000 0.00 0.00 0.00 2.43
967 1094 0.326927 ATCCCCGCCGAGAAAGAAAA 59.673 50.000 0.00 0.00 0.00 2.29
968 1095 1.138266 CTATCCCCGCCGAGAAAGAAA 59.862 52.381 0.00 0.00 0.00 2.52
969 1096 0.750850 CTATCCCCGCCGAGAAAGAA 59.249 55.000 0.00 0.00 0.00 2.52
970 1097 0.106369 TCTATCCCCGCCGAGAAAGA 60.106 55.000 0.00 0.00 0.00 2.52
971 1098 0.315568 CTCTATCCCCGCCGAGAAAG 59.684 60.000 0.00 0.00 0.00 2.62
973 1100 1.530891 CCTCTATCCCCGCCGAGAA 60.531 63.158 0.00 0.00 0.00 2.87
974 1101 2.115480 CCTCTATCCCCGCCGAGA 59.885 66.667 0.00 0.00 0.00 4.04
975 1102 2.203509 ACCTCTATCCCCGCCGAG 60.204 66.667 0.00 0.00 0.00 4.63
977 1104 1.833049 AAGACCTCTATCCCCGCCG 60.833 63.158 0.00 0.00 0.00 6.46
978 1105 0.759436 TCAAGACCTCTATCCCCGCC 60.759 60.000 0.00 0.00 0.00 6.13
981 1108 2.068834 TCGTCAAGACCTCTATCCCC 57.931 55.000 0.00 0.00 0.00 4.81
983 1110 3.223435 TCCATCGTCAAGACCTCTATCC 58.777 50.000 0.00 0.00 0.00 2.59
984 1111 3.254657 CCTCCATCGTCAAGACCTCTATC 59.745 52.174 0.00 0.00 0.00 2.08
985 1112 3.226777 CCTCCATCGTCAAGACCTCTAT 58.773 50.000 0.00 0.00 0.00 1.98
986 1113 2.656002 CCTCCATCGTCAAGACCTCTA 58.344 52.381 0.00 0.00 0.00 2.43
987 1114 1.479709 CCTCCATCGTCAAGACCTCT 58.520 55.000 0.00 0.00 0.00 3.69
999 1126 3.329542 TTGCACCTCCGCCTCCATC 62.330 63.158 0.00 0.00 0.00 3.51
1071 1198 1.734477 CGTGCACTCCTCCGTGAAG 60.734 63.158 16.19 0.00 37.06 3.02
1131 1258 2.827423 CAGAGCCCGCAGATCCAT 59.173 61.111 0.00 0.00 0.00 3.41
1473 1606 5.885449 TTTGGTTTCATTGGTTCTTGGAT 57.115 34.783 0.00 0.00 0.00 3.41
1481 1614 5.188751 TCAGGTTCTTTTTGGTTTCATTGGT 59.811 36.000 0.00 0.00 0.00 3.67
1482 1615 5.669477 TCAGGTTCTTTTTGGTTTCATTGG 58.331 37.500 0.00 0.00 0.00 3.16
1485 1618 5.857268 CCATCAGGTTCTTTTTGGTTTCAT 58.143 37.500 0.00 0.00 0.00 2.57
1486 1619 5.275067 CCATCAGGTTCTTTTTGGTTTCA 57.725 39.130 0.00 0.00 0.00 2.69
1653 1812 8.594687 CACTTCCATTTACTCTTTTTGTTGTTG 58.405 33.333 0.00 0.00 0.00 3.33
1656 1815 7.488322 TCCACTTCCATTTACTCTTTTTGTTG 58.512 34.615 0.00 0.00 0.00 3.33
1657 1816 7.201911 CCTCCACTTCCATTTACTCTTTTTGTT 60.202 37.037 0.00 0.00 0.00 2.83
1659 1818 6.265422 ACCTCCACTTCCATTTACTCTTTTTG 59.735 38.462 0.00 0.00 0.00 2.44
1660 1819 6.373759 ACCTCCACTTCCATTTACTCTTTTT 58.626 36.000 0.00 0.00 0.00 1.94
1662 1821 5.584551 ACCTCCACTTCCATTTACTCTTT 57.415 39.130 0.00 0.00 0.00 2.52
1663 1822 6.697641 TTACCTCCACTTCCATTTACTCTT 57.302 37.500 0.00 0.00 0.00 2.85
1664 1823 6.893020 ATTACCTCCACTTCCATTTACTCT 57.107 37.500 0.00 0.00 0.00 3.24
1665 1824 6.542735 GGAATTACCTCCACTTCCATTTACTC 59.457 42.308 0.00 0.00 37.65 2.59
1666 1825 6.011981 TGGAATTACCTCCACTTCCATTTACT 60.012 38.462 0.00 0.00 41.60 2.24
1667 1826 6.184789 TGGAATTACCTCCACTTCCATTTAC 58.815 40.000 0.00 0.00 41.60 2.01
1668 1827 6.395780 TGGAATTACCTCCACTTCCATTTA 57.604 37.500 0.00 0.00 41.60 1.40
1682 1841 8.859090 TGGATGATGATAAAACATGGAATTACC 58.141 33.333 0.00 0.00 39.54 2.85
1741 1901 2.415857 GAGTGCATGAACTTGAGCAGAG 59.584 50.000 8.06 0.00 37.72 3.35
1760 1920 3.615849 GCTGTTTGAAGAACAGGTGAG 57.384 47.619 17.59 0.00 45.72 3.51
1785 1945 1.165270 GGTGCTTATGCGTCTGGTTT 58.835 50.000 0.00 0.00 43.34 3.27
1786 1946 0.036164 TGGTGCTTATGCGTCTGGTT 59.964 50.000 0.00 0.00 43.34 3.67
1788 1948 0.108186 TCTGGTGCTTATGCGTCTGG 60.108 55.000 0.00 0.00 43.34 3.86
1793 1955 0.734309 TGCATTCTGGTGCTTATGCG 59.266 50.000 0.00 0.00 44.77 4.73
1799 1961 1.615392 GAAAAGGTGCATTCTGGTGCT 59.385 47.619 0.00 0.00 45.27 4.40
1814 1983 5.751243 TTTTCCCTCTTTGAGACGAAAAG 57.249 39.130 13.41 0.00 35.23 2.27
1823 1992 7.734942 AGTATTTTGCATTTTTCCCTCTTTGA 58.265 30.769 0.00 0.00 0.00 2.69
1933 2114 2.547826 CTCTGCTGCGAATCAGAATCA 58.452 47.619 0.00 0.00 45.72 2.57
1948 2129 2.634982 CTCATATCGAGAGCCTCTGC 57.365 55.000 0.00 0.00 45.45 4.26
1955 2136 6.682423 AGTGATCTATGCTCATATCGAGAG 57.318 41.667 0.00 0.00 45.45 3.20
1956 2137 7.392953 AGAAAGTGATCTATGCTCATATCGAGA 59.607 37.037 0.00 0.00 45.45 4.04
1957 2138 7.485595 CAGAAAGTGATCTATGCTCATATCGAG 59.514 40.741 0.00 0.00 45.37 4.04
1958 2139 7.311408 CAGAAAGTGATCTATGCTCATATCGA 58.689 38.462 0.00 0.00 0.00 3.59
1959 2140 6.530887 CCAGAAAGTGATCTATGCTCATATCG 59.469 42.308 0.00 0.00 0.00 2.92
1960 2141 7.385267 ACCAGAAAGTGATCTATGCTCATATC 58.615 38.462 0.00 0.00 0.00 1.63
1961 2142 7.313740 ACCAGAAAGTGATCTATGCTCATAT 57.686 36.000 0.00 0.00 0.00 1.78
1962 2143 6.737720 ACCAGAAAGTGATCTATGCTCATA 57.262 37.500 0.00 0.00 0.00 2.15
1968 2149 6.659361 CTGTGAACCAGAAAGTGATCTATG 57.341 41.667 0.00 0.00 44.49 2.23
1982 2163 5.825593 AGGAGAAGTTTATCTGTGAACCA 57.174 39.130 0.00 0.00 0.00 3.67
1985 2166 6.183361 TGGACAAGGAGAAGTTTATCTGTGAA 60.183 38.462 0.00 0.00 0.00 3.18
1990 2171 6.013379 TGTCATGGACAAGGAGAAGTTTATCT 60.013 38.462 0.00 0.00 39.78 1.98
1999 2180 4.916041 ATTTCTGTCATGGACAAGGAGA 57.084 40.909 0.33 0.00 42.26 3.71
2002 2196 7.452880 TCTTTTATTTCTGTCATGGACAAGG 57.547 36.000 0.33 0.00 42.26 3.61
2030 2224 2.436646 GGCTGCTTCCTGCGCTAA 60.437 61.111 9.73 0.00 46.63 3.09
2081 2278 4.573201 TGCGCTGTAATAAAGATGGTAACC 59.427 41.667 9.73 0.00 0.00 2.85
2176 2378 2.166829 AGACCTCTGTGCTAGTCTGTG 58.833 52.381 0.00 0.00 38.15 3.66
2193 2399 0.179108 GGCACTGGACGGATACAGAC 60.179 60.000 0.00 0.00 39.47 3.51
2227 2433 1.595929 GGTTCGCTGTTGACGGGAA 60.596 57.895 0.00 0.00 0.00 3.97
2232 2438 6.905609 GCTAAATTAATAGGTTCGCTGTTGAC 59.094 38.462 0.00 0.00 0.00 3.18
2350 2557 7.949565 TGGATGGATGCACTTTAATTATATGGT 59.050 33.333 0.00 0.00 0.00 3.55
2363 2570 1.064240 TCTGCAATGGATGGATGCACT 60.064 47.619 0.00 0.00 44.52 4.40
2365 2572 1.341187 TGTCTGCAATGGATGGATGCA 60.341 47.619 0.00 0.00 46.97 3.96
2366 2573 1.337071 CTGTCTGCAATGGATGGATGC 59.663 52.381 0.00 0.00 40.45 3.91
2367 2574 2.927028 TCTGTCTGCAATGGATGGATG 58.073 47.619 0.00 0.00 0.00 3.51
2368 2575 3.878237 ATCTGTCTGCAATGGATGGAT 57.122 42.857 0.00 0.00 0.00 3.41
2370 2577 3.683340 CGATATCTGTCTGCAATGGATGG 59.317 47.826 0.34 0.00 0.00 3.51
2372 2579 4.282957 AGACGATATCTGTCTGCAATGGAT 59.717 41.667 21.49 0.00 44.69 3.41
2373 2580 3.638627 AGACGATATCTGTCTGCAATGGA 59.361 43.478 21.49 0.00 44.69 3.41
2374 2581 3.987547 AGACGATATCTGTCTGCAATGG 58.012 45.455 21.49 0.00 44.69 3.16
2375 2582 5.045872 TGAAGACGATATCTGTCTGCAATG 58.954 41.667 24.25 1.97 46.56 2.82
2376 2583 5.268118 TGAAGACGATATCTGTCTGCAAT 57.732 39.130 24.25 13.60 46.56 3.56
2377 2584 4.718940 TGAAGACGATATCTGTCTGCAA 57.281 40.909 24.25 14.33 46.56 4.08
2379 2586 3.376540 GGTGAAGACGATATCTGTCTGC 58.623 50.000 22.32 21.23 45.62 4.26
2410 2617 0.389426 GTCCTGATTGCGTGTACCGT 60.389 55.000 5.79 0.00 39.32 4.83


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

AutoCloner maintained by Alex Coulton.