Multiple sequence alignment - TraesCS5A01G213700

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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 TraesCS5A01G213700 chr5A 100.000 2586 0 0 1 2586 429475532 429478117 0.000000e+00 4776.0
1 TraesCS5A01G213700 chr5A 88.136 59 7 0 183 241 528309176 528309118 1.280000e-08 71.3
2 TraesCS5A01G213700 chr5D 91.334 1454 49 32 625 2046 327214697 327213289 0.000000e+00 1916.0
3 TraesCS5A01G213700 chr5D 88.767 365 33 7 93 453 327215323 327214963 8.490000e-120 440.0
4 TraesCS5A01G213700 chr5D 88.618 123 11 2 1961 2083 327209819 327209700 2.070000e-31 147.0
5 TraesCS5A01G213700 chr5B 87.450 1514 99 37 274 1739 379903736 379902266 0.000000e+00 1659.0
6 TraesCS5A01G213700 chr5B 90.104 384 38 0 2203 2586 330740640 330740257 1.380000e-137 499.0
7 TraesCS5A01G213700 chr5B 90.345 290 18 4 1765 2046 379902181 379901894 3.140000e-99 372.0
8 TraesCS5A01G213700 chr2D 90.885 384 35 0 2203 2586 317866438 317866055 1.370000e-142 516.0
9 TraesCS5A01G213700 chr2D 90.501 379 36 0 2208 2586 376695867 376696245 3.840000e-138 501.0
10 TraesCS5A01G213700 chr2D 89.844 384 39 0 2203 2586 441767990 441767607 6.430000e-136 494.0
11 TraesCS5A01G213700 chr2D 89.583 144 15 0 2078 2221 361254349 361254206 1.580000e-42 183.0
12 TraesCS5A01G213700 chr2D 90.511 137 11 2 2087 2221 376694220 376694356 2.040000e-41 180.0
13 TraesCS5A01G213700 chr1D 90.885 384 34 1 2204 2586 98832101 98832484 4.930000e-142 514.0
14 TraesCS5A01G213700 chr3D 90.314 382 37 0 2205 2586 605029770 605030151 3.840000e-138 501.0
15 TraesCS5A01G213700 chr3D 90.237 379 37 0 2208 2586 606871282 606871660 1.790000e-136 496.0
16 TraesCS5A01G213700 chr3D 86.170 94 10 2 182 274 498707830 498707739 5.890000e-17 99.0
17 TraesCS5A01G213700 chr6B 90.104 384 38 0 2203 2586 439355678 439356061 1.380000e-137 499.0
18 TraesCS5A01G213700 chr6B 90.299 134 13 0 2088 2221 439354023 439354156 2.640000e-40 176.0
19 TraesCS5A01G213700 chr6B 87.234 94 9 3 183 275 196915706 196915615 1.270000e-18 104.0
20 TraesCS5A01G213700 chr7D 90.237 379 37 0 2208 2586 595074761 595074383 1.790000e-136 496.0
21 TraesCS5A01G213700 chr6A 92.143 140 9 1 2082 2221 31163623 31163760 2.030000e-46 196.0
22 TraesCS5A01G213700 chr4D 91.045 134 12 0 2088 2221 274462629 274462496 5.680000e-42 182.0
23 TraesCS5A01G213700 chr1B 90.299 134 13 0 2088 2221 41781564 41781431 2.640000e-40 176.0
24 TraesCS5A01G213700 chr1B 93.043 115 8 0 2088 2202 175427026 175427140 4.430000e-38 169.0
25 TraesCS5A01G213700 chr1B 94.595 37 2 0 183 219 612897699 612897663 1.000000e-04 58.4
26 TraesCS5A01G213700 chr6D 88.806 134 10 3 2088 2221 179954143 179954015 2.660000e-35 159.0
27 TraesCS5A01G213700 chr7B 87.143 140 11 6 2088 2221 384200045 384199907 4.460000e-33 152.0
28 TraesCS5A01G213700 chr4B 83.158 95 15 1 183 277 552775511 552775418 4.580000e-13 86.1
29 TraesCS5A01G213700 chr4A 97.297 37 1 0 183 219 645689707 645689743 2.150000e-06 63.9
30 TraesCS5A01G213700 chr3B 91.111 45 4 0 183 227 810620494 810620538 7.730000e-06 62.1
31 TraesCS5A01G213700 chr1A 94.872 39 1 1 182 219 3543737 3543775 2.780000e-05 60.2


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 TraesCS5A01G213700 chr5A 429475532 429478117 2585 False 4776.000000 4776 100.0000 1 2586 1 chr5A.!!$F1 2585
1 TraesCS5A01G213700 chr5D 327209700 327215323 5623 True 834.333333 1916 89.5730 93 2083 3 chr5D.!!$R1 1990
2 TraesCS5A01G213700 chr5B 379901894 379903736 1842 True 1015.500000 1659 88.8975 274 2046 2 chr5B.!!$R2 1772
3 TraesCS5A01G213700 chr2D 376694220 376696245 2025 False 340.500000 501 90.5060 2087 2586 2 chr2D.!!$F1 499
4 TraesCS5A01G213700 chr6B 439354023 439356061 2038 False 337.500000 499 90.2015 2088 2586 2 chr6B.!!$F1 498

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
486 503 0.179081 CTTAGGGTGAAGGGCTACGC 60.179 60.0 0.0 0.0 0.0 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 5768 0.246635 GACAAGCAAGGCTCTACCGA 59.753 55.0 0.0 0.0 46.52 4.69 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
23 24 4.946160 AGGATTCCAACCCTACAAATCA 57.054 40.909 5.29 0.00 0.00 2.57
24 25 5.269554 AGGATTCCAACCCTACAAATCAA 57.730 39.130 5.29 0.00 0.00 2.57
25 26 5.650283 AGGATTCCAACCCTACAAATCAAA 58.350 37.500 5.29 0.00 0.00 2.69
26 27 5.480422 AGGATTCCAACCCTACAAATCAAAC 59.520 40.000 5.29 0.00 0.00 2.93
27 28 5.337250 GGATTCCAACCCTACAAATCAAACC 60.337 44.000 0.00 0.00 0.00 3.27
28 29 4.186077 TCCAACCCTACAAATCAAACCA 57.814 40.909 0.00 0.00 0.00 3.67
29 30 4.746466 TCCAACCCTACAAATCAAACCAT 58.254 39.130 0.00 0.00 0.00 3.55
30 31 4.770010 TCCAACCCTACAAATCAAACCATC 59.230 41.667 0.00 0.00 0.00 3.51
31 32 4.526262 CCAACCCTACAAATCAAACCATCA 59.474 41.667 0.00 0.00 0.00 3.07
32 33 5.187576 CCAACCCTACAAATCAAACCATCAT 59.812 40.000 0.00 0.00 0.00 2.45
33 34 6.332630 CAACCCTACAAATCAAACCATCATC 58.667 40.000 0.00 0.00 0.00 2.92
34 35 5.579047 ACCCTACAAATCAAACCATCATCA 58.421 37.500 0.00 0.00 0.00 3.07
35 36 5.418840 ACCCTACAAATCAAACCATCATCAC 59.581 40.000 0.00 0.00 0.00 3.06
36 37 5.418524 CCCTACAAATCAAACCATCATCACA 59.581 40.000 0.00 0.00 0.00 3.58
37 38 6.405065 CCCTACAAATCAAACCATCATCACAG 60.405 42.308 0.00 0.00 0.00 3.66
38 39 6.375174 CCTACAAATCAAACCATCATCACAGA 59.625 38.462 0.00 0.00 0.00 3.41
39 40 6.653526 ACAAATCAAACCATCATCACAGAA 57.346 33.333 0.00 0.00 0.00 3.02
40 41 7.053316 ACAAATCAAACCATCATCACAGAAA 57.947 32.000 0.00 0.00 0.00 2.52
41 42 7.499292 ACAAATCAAACCATCATCACAGAAAA 58.501 30.769 0.00 0.00 0.00 2.29
42 43 7.986320 ACAAATCAAACCATCATCACAGAAAAA 59.014 29.630 0.00 0.00 0.00 1.94
71 72 3.627395 GGATCAAAATCCCCCAAAACC 57.373 47.619 0.00 0.00 45.11 3.27
72 73 2.238646 GGATCAAAATCCCCCAAAACCC 59.761 50.000 0.00 0.00 45.11 4.11
73 74 1.735926 TCAAAATCCCCCAAAACCCC 58.264 50.000 0.00 0.00 0.00 4.95
74 75 1.224381 TCAAAATCCCCCAAAACCCCT 59.776 47.619 0.00 0.00 0.00 4.79
75 76 2.455163 TCAAAATCCCCCAAAACCCCTA 59.545 45.455 0.00 0.00 0.00 3.53
76 77 3.079843 TCAAAATCCCCCAAAACCCCTAT 59.920 43.478 0.00 0.00 0.00 2.57
77 78 2.866923 AATCCCCCAAAACCCCTATG 57.133 50.000 0.00 0.00 0.00 2.23
78 79 2.009186 ATCCCCCAAAACCCCTATGA 57.991 50.000 0.00 0.00 0.00 2.15
79 80 1.774864 TCCCCCAAAACCCCTATGAA 58.225 50.000 0.00 0.00 0.00 2.57
80 81 2.082669 TCCCCCAAAACCCCTATGAAA 58.917 47.619 0.00 0.00 0.00 2.69
81 82 2.662633 TCCCCCAAAACCCCTATGAAAT 59.337 45.455 0.00 0.00 0.00 2.17
82 83 3.079843 TCCCCCAAAACCCCTATGAAATT 59.920 43.478 0.00 0.00 0.00 1.82
83 84 3.849574 CCCCCAAAACCCCTATGAAATTT 59.150 43.478 0.00 0.00 0.00 1.82
84 85 4.080582 CCCCCAAAACCCCTATGAAATTTC 60.081 45.833 11.41 11.41 0.00 2.17
85 86 4.782691 CCCCAAAACCCCTATGAAATTTCT 59.217 41.667 18.64 7.42 0.00 2.52
86 87 5.250543 CCCCAAAACCCCTATGAAATTTCTT 59.749 40.000 18.64 14.65 0.00 2.52
87 88 6.240147 CCCCAAAACCCCTATGAAATTTCTTT 60.240 38.462 18.64 9.15 0.00 2.52
88 89 6.654582 CCCAAAACCCCTATGAAATTTCTTTG 59.345 38.462 18.64 15.85 0.00 2.77
89 90 7.449247 CCAAAACCCCTATGAAATTTCTTTGA 58.551 34.615 18.64 0.00 0.00 2.69
90 91 7.936301 CCAAAACCCCTATGAAATTTCTTTGAA 59.064 33.333 18.64 0.00 0.00 2.69
91 92 9.506018 CAAAACCCCTATGAAATTTCTTTGAAT 57.494 29.630 18.64 6.48 0.00 2.57
96 97 9.895138 CCCCTATGAAATTTCTTTGAATCAAAT 57.105 29.630 18.64 3.16 32.70 2.32
114 115 7.923414 ATCAAATGAGTCCTTAAAGGTGTAC 57.077 36.000 0.00 0.00 36.53 2.90
116 117 5.479124 AATGAGTCCTTAAAGGTGTACGT 57.521 39.130 0.00 0.00 36.53 3.57
119 120 4.341806 TGAGTCCTTAAAGGTGTACGTGAA 59.658 41.667 0.00 0.00 36.53 3.18
171 173 5.108385 TCCGCTTTCAAAGATTCTTTCAC 57.892 39.130 8.71 0.00 0.00 3.18
174 176 5.280945 CGCTTTCAAAGATTCTTTCACCAA 58.719 37.500 8.71 0.00 0.00 3.67
180 182 7.764141 TCAAAGATTCTTTCACCAATGATCA 57.236 32.000 8.71 0.00 33.85 2.92
185 187 7.544622 AGATTCTTTCACCAATGATCAATGTG 58.455 34.615 9.85 11.95 33.85 3.21
195 197 1.233019 GATCAATGTGATCCTGGCCG 58.767 55.000 6.94 0.00 45.66 6.13
219 221 5.520649 GGTTGACGGCTTTGTTAATTCAAAA 59.479 36.000 0.00 0.00 36.96 2.44
246 248 4.370917 GCTAGATTTGAGCCTTCTCTCAG 58.629 47.826 0.00 0.00 43.23 3.35
267 269 0.790814 CTCGGCCAACGTCTTTTCTC 59.209 55.000 2.24 0.00 44.69 2.87
363 365 0.533755 AGCCATACCGAAGAGCATGC 60.534 55.000 10.51 10.51 0.00 4.06
365 367 1.506493 CCATACCGAAGAGCATGCTC 58.494 55.000 35.57 35.57 43.03 4.26
366 368 1.202568 CCATACCGAAGAGCATGCTCA 60.203 52.381 40.91 24.61 44.99 4.26
372 374 2.031807 CCGAAGAGCATGCTCATGAAAG 59.968 50.000 40.91 26.39 44.99 2.62
374 376 3.242349 CGAAGAGCATGCTCATGAAAGTC 60.242 47.826 40.91 25.27 44.99 3.01
375 377 2.277969 AGAGCATGCTCATGAAAGTCG 58.722 47.619 40.91 0.00 44.99 4.18
417 420 6.511416 CACTAGGTGAGAGATGATAAGGTTG 58.489 44.000 0.00 0.00 35.23 3.77
427 430 5.809001 AGATGATAAGGTTGTTGAGAAGCA 58.191 37.500 0.00 0.00 0.00 3.91
446 449 2.415090 GCATGATTGCTCGTTCAAGCTT 60.415 45.455 0.00 0.00 45.77 3.74
473 490 1.453669 GCCATCTGCTCCCTTAGGG 59.546 63.158 11.94 11.94 46.11 3.53
478 495 1.573108 TCTGCTCCCTTAGGGTGAAG 58.427 55.000 22.19 20.54 44.74 3.02
486 503 0.179081 CTTAGGGTGAAGGGCTACGC 60.179 60.000 0.00 0.00 0.00 4.42
553 595 7.935520 TGCAAAGTCTATTGTGTGTGATTTTA 58.064 30.769 0.00 0.00 32.80 1.52
556 598 6.408858 AGTCTATTGTGTGTGATTTTAGCG 57.591 37.500 0.00 0.00 0.00 4.26
562 604 3.623510 TGTGTGTGATTTTAGCGTGTCAA 59.376 39.130 0.00 0.00 0.00 3.18
579 621 6.534059 CGTGTCAATAAAGTCGTGATGAATT 58.466 36.000 0.00 0.00 36.21 2.17
591 633 7.021196 AGTCGTGATGAATTTGAATTAAACGG 58.979 34.615 0.00 0.00 0.00 4.44
673 780 8.749841 TGAAATTTGAAGAAACGAGACAAAAA 57.250 26.923 0.00 0.00 34.86 1.94
680 787 7.295201 TGAAGAAACGAGACAAAAATTATCGG 58.705 34.615 0.00 0.00 37.69 4.18
729 836 8.208575 AGGATCTCCTGTAAAGAAGTTTTACT 57.791 34.615 0.00 0.00 46.55 2.24
730 837 8.315482 AGGATCTCCTGTAAAGAAGTTTTACTC 58.685 37.037 0.00 0.82 46.55 2.59
731 838 7.549842 GGATCTCCTGTAAAGAAGTTTTACTCC 59.450 40.741 10.17 5.16 36.23 3.85
732 839 7.369551 TCTCCTGTAAAGAAGTTTTACTCCA 57.630 36.000 10.17 0.00 36.23 3.86
733 840 7.442656 TCTCCTGTAAAGAAGTTTTACTCCAG 58.557 38.462 10.17 4.68 36.23 3.86
734 841 7.070821 TCTCCTGTAAAGAAGTTTTACTCCAGT 59.929 37.037 10.17 0.00 36.23 4.00
735 842 8.253867 TCCTGTAAAGAAGTTTTACTCCAGTA 57.746 34.615 10.17 0.00 36.23 2.74
736 843 8.707449 TCCTGTAAAGAAGTTTTACTCCAGTAA 58.293 33.333 10.17 0.00 38.60 2.24
737 844 9.333724 CCTGTAAAGAAGTTTTACTCCAGTAAA 57.666 33.333 7.67 7.67 45.55 2.01
780 895 2.047560 GTAACGTGCCGGGAAGCT 60.048 61.111 9.16 0.00 0.00 3.74
809 924 3.130164 CCGTTACATTCATTCCAATGGCA 59.870 43.478 0.00 0.00 37.98 4.92
994 1109 0.907704 GAAATCCCAAACCCCACCCC 60.908 60.000 0.00 0.00 0.00 4.95
999 1114 3.517497 CAAACCCCACCCCACCCT 61.517 66.667 0.00 0.00 0.00 4.34
1211 1326 4.796495 GCCAAGGCGTACCCCCTG 62.796 72.222 0.00 0.00 36.11 4.45
1561 1686 1.870402 TGATGTTGTACAACGCAGGTG 59.130 47.619 28.58 0.00 43.94 4.00
1562 1687 1.196808 GATGTTGTACAACGCAGGTGG 59.803 52.381 28.58 0.00 43.94 4.61
1615 1740 2.414559 GGATTGCAGATGTTTGGTGTCG 60.415 50.000 0.00 0.00 0.00 4.35
1757 1888 0.247736 AAGGGTTACGAGCTGAGCTG 59.752 55.000 13.71 7.04 39.88 4.24
1760 1891 0.737715 GGTTACGAGCTGAGCTGGTG 60.738 60.000 28.60 13.47 46.30 4.17
1761 1892 0.038159 GTTACGAGCTGAGCTGGTGT 60.038 55.000 28.60 18.13 46.30 4.16
1762 1893 0.243907 TTACGAGCTGAGCTGGTGTC 59.756 55.000 28.60 6.47 46.30 3.67
1763 1894 0.893727 TACGAGCTGAGCTGGTGTCA 60.894 55.000 28.60 9.26 46.30 3.58
1813 2010 3.187227 CGAATCCAAGAGGCGATATTTGG 59.813 47.826 0.00 0.00 41.09 3.28
1863 2067 1.689273 ACCTATCAGGCCAGATTCGAC 59.311 52.381 16.66 0.00 39.63 4.20
1870 2074 1.103398 GGCCAGATTCGACCATTGGG 61.103 60.000 7.78 0.00 41.29 4.12
1875 2079 3.201290 CAGATTCGACCATTGGGAAGAG 58.799 50.000 7.78 0.00 38.05 2.85
1884 2088 5.167303 ACCATTGGGAAGAGAAGTACTTC 57.833 43.478 25.24 25.24 41.79 3.01
1885 2089 4.184629 CCATTGGGAAGAGAAGTACTTCG 58.815 47.826 25.92 10.48 42.96 3.79
1886 2090 4.322801 CCATTGGGAAGAGAAGTACTTCGT 60.323 45.833 25.92 16.64 42.96 3.85
1887 2091 3.936372 TGGGAAGAGAAGTACTTCGTG 57.064 47.619 25.92 0.00 43.97 4.35
1889 2093 2.231721 GGGAAGAGAAGTACTTCGTGCT 59.768 50.000 25.92 21.19 43.97 4.40
1890 2094 3.503891 GGAAGAGAAGTACTTCGTGCTC 58.496 50.000 25.92 18.81 43.97 4.26
1892 2096 2.797786 AGAGAAGTACTTCGTGCTCCT 58.202 47.619 25.92 15.42 43.97 3.69
1894 2098 3.191791 AGAGAAGTACTTCGTGCTCCTTC 59.808 47.826 25.92 16.64 43.97 3.46
1895 2099 2.095161 AGAAGTACTTCGTGCTCCTTCG 60.095 50.000 25.92 0.00 43.97 3.79
1896 2100 0.109226 AGTACTTCGTGCTCCTTCGC 60.109 55.000 0.00 0.00 0.00 4.70
1899 2103 3.589654 CTTCGTGCTCCTTCGCCCA 62.590 63.158 0.00 0.00 0.00 5.36
1924 2128 2.173519 ACGAATGAACGGAAGGTAGGA 58.826 47.619 0.00 0.00 37.61 2.94
1965 2169 4.215109 GCAGGGGAAAAGCCAAAGATATA 58.785 43.478 0.00 0.00 38.95 0.86
2031 5790 1.079127 TAGAGCCTTGCTTGTCCGC 60.079 57.895 0.00 0.00 39.88 5.54
2046 5805 2.279741 GTCCGCTGATCAATGTAAGCA 58.720 47.619 0.00 0.00 35.33 3.91
2047 5806 2.677836 GTCCGCTGATCAATGTAAGCAA 59.322 45.455 0.00 0.00 35.33 3.91
2048 5807 2.938451 TCCGCTGATCAATGTAAGCAAG 59.062 45.455 0.00 0.00 35.33 4.01
2049 5808 2.540361 CCGCTGATCAATGTAAGCAAGC 60.540 50.000 0.00 0.00 35.33 4.01
2050 5809 2.353889 CGCTGATCAATGTAAGCAAGCT 59.646 45.455 0.00 0.00 35.33 3.74
2051 5810 3.545624 CGCTGATCAATGTAAGCAAGCTC 60.546 47.826 0.00 0.00 35.33 4.09
2073 5832 4.475527 AAGGGTCCTTGAACACGC 57.524 55.556 0.81 0.00 34.60 5.34
2074 5833 1.529796 AAGGGTCCTTGAACACGCA 59.470 52.632 0.81 0.00 34.60 5.24
2076 5835 0.981183 AGGGTCCTTGAACACGCATA 59.019 50.000 0.00 0.00 0.00 3.14
2083 5842 2.643551 CTTGAACACGCATAATCCCCT 58.356 47.619 0.00 0.00 0.00 4.79
2084 5843 2.799126 TGAACACGCATAATCCCCTT 57.201 45.000 0.00 0.00 0.00 3.95
2085 5844 3.080300 TGAACACGCATAATCCCCTTT 57.920 42.857 0.00 0.00 0.00 3.11
2150 5909 2.003548 GGTGGAAGGAGGGATGGCT 61.004 63.158 0.00 0.00 0.00 4.75
2234 7549 1.977009 GGCTAAAGGCAAAGGCGGT 60.977 57.895 0.00 0.00 44.01 5.68
2272 7587 0.179134 GCGAGGAACGTGTAGATGCT 60.179 55.000 0.00 0.00 44.60 3.79
2317 7632 1.630126 ATGGCAGCCGTCATCTCCTT 61.630 55.000 7.03 0.00 28.90 3.36
2355 7670 2.070654 GACGGGCACAACAAAGGTGG 62.071 60.000 0.00 0.00 36.76 4.61
2478 7793 2.922758 GCACCGAAGCTATCTGATACCG 60.923 54.545 0.00 0.00 0.00 4.02
2506 7821 0.398098 GGAACCGGATCCCTACCAGA 60.398 60.000 19.83 0.00 33.05 3.86
2526 7841 3.322828 AGAGCGTGGTTTTAGGTTGTAGA 59.677 43.478 0.00 0.00 0.00 2.59
2531 7846 4.501915 CGTGGTTTTAGGTTGTAGAGGTGA 60.502 45.833 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.395780 TGATTTGTAGGGTTGGAATCCTTA 57.604 37.500 0.00 0.00 34.75 2.69
1 2 5.269554 TGATTTGTAGGGTTGGAATCCTT 57.730 39.130 0.00 0.00 34.75 3.36
2 3 4.946160 TGATTTGTAGGGTTGGAATCCT 57.054 40.909 0.00 0.00 37.18 3.24
3 4 5.337250 GGTTTGATTTGTAGGGTTGGAATCC 60.337 44.000 0.00 0.00 0.00 3.01
4 5 5.245075 TGGTTTGATTTGTAGGGTTGGAATC 59.755 40.000 0.00 0.00 0.00 2.52
5 6 5.151454 TGGTTTGATTTGTAGGGTTGGAAT 58.849 37.500 0.00 0.00 0.00 3.01
6 7 4.547671 TGGTTTGATTTGTAGGGTTGGAA 58.452 39.130 0.00 0.00 0.00 3.53
7 8 4.186077 TGGTTTGATTTGTAGGGTTGGA 57.814 40.909 0.00 0.00 0.00 3.53
8 9 4.526262 TGATGGTTTGATTTGTAGGGTTGG 59.474 41.667 0.00 0.00 0.00 3.77
9 10 5.720371 TGATGGTTTGATTTGTAGGGTTG 57.280 39.130 0.00 0.00 0.00 3.77
10 11 6.015918 TGATGATGGTTTGATTTGTAGGGTT 58.984 36.000 0.00 0.00 0.00 4.11
11 12 5.418840 GTGATGATGGTTTGATTTGTAGGGT 59.581 40.000 0.00 0.00 0.00 4.34
12 13 5.418524 TGTGATGATGGTTTGATTTGTAGGG 59.581 40.000 0.00 0.00 0.00 3.53
13 14 6.375174 TCTGTGATGATGGTTTGATTTGTAGG 59.625 38.462 0.00 0.00 0.00 3.18
14 15 7.381766 TCTGTGATGATGGTTTGATTTGTAG 57.618 36.000 0.00 0.00 0.00 2.74
15 16 7.757941 TTCTGTGATGATGGTTTGATTTGTA 57.242 32.000 0.00 0.00 0.00 2.41
16 17 6.653526 TTCTGTGATGATGGTTTGATTTGT 57.346 33.333 0.00 0.00 0.00 2.83
17 18 7.949903 TTTTCTGTGATGATGGTTTGATTTG 57.050 32.000 0.00 0.00 0.00 2.32
39 40 7.092444 GGGGGATTTTGATCCTTAGGAATTTTT 60.092 37.037 4.56 0.00 40.54 1.94
40 41 6.386927 GGGGGATTTTGATCCTTAGGAATTTT 59.613 38.462 4.56 0.00 40.54 1.82
41 42 5.905331 GGGGGATTTTGATCCTTAGGAATTT 59.095 40.000 4.56 0.00 40.54 1.82
42 43 5.042676 TGGGGGATTTTGATCCTTAGGAATT 60.043 40.000 4.56 0.00 40.54 2.17
43 44 4.485775 TGGGGGATTTTGATCCTTAGGAAT 59.514 41.667 4.56 0.00 40.54 3.01
44 45 3.861695 TGGGGGATTTTGATCCTTAGGAA 59.138 43.478 4.56 0.00 40.54 3.36
45 46 3.480012 TGGGGGATTTTGATCCTTAGGA 58.520 45.455 2.37 2.37 40.54 2.94
46 47 3.971468 TGGGGGATTTTGATCCTTAGG 57.029 47.619 5.50 0.00 40.54 2.69
47 48 5.104941 GGTTTTGGGGGATTTTGATCCTTAG 60.105 44.000 5.50 0.00 40.54 2.18
48 49 4.780554 GGTTTTGGGGGATTTTGATCCTTA 59.219 41.667 5.50 0.00 40.54 2.69
49 50 3.587061 GGTTTTGGGGGATTTTGATCCTT 59.413 43.478 5.50 0.00 40.54 3.36
50 51 3.181329 GGTTTTGGGGGATTTTGATCCT 58.819 45.455 5.50 0.00 40.54 3.24
51 52 2.238646 GGGTTTTGGGGGATTTTGATCC 59.761 50.000 0.00 0.00 39.99 3.36
52 53 2.238646 GGGGTTTTGGGGGATTTTGATC 59.761 50.000 0.00 0.00 0.00 2.92
53 54 2.157864 AGGGGTTTTGGGGGATTTTGAT 60.158 45.455 0.00 0.00 0.00 2.57
54 55 1.224381 AGGGGTTTTGGGGGATTTTGA 59.776 47.619 0.00 0.00 0.00 2.69
55 56 1.741028 AGGGGTTTTGGGGGATTTTG 58.259 50.000 0.00 0.00 0.00 2.44
56 57 3.079843 TCATAGGGGTTTTGGGGGATTTT 59.920 43.478 0.00 0.00 0.00 1.82
57 58 2.662633 TCATAGGGGTTTTGGGGGATTT 59.337 45.455 0.00 0.00 0.00 2.17
58 59 2.302779 TCATAGGGGTTTTGGGGGATT 58.697 47.619 0.00 0.00 0.00 3.01
59 60 2.009186 TCATAGGGGTTTTGGGGGAT 57.991 50.000 0.00 0.00 0.00 3.85
60 61 1.774864 TTCATAGGGGTTTTGGGGGA 58.225 50.000 0.00 0.00 0.00 4.81
61 62 2.632763 TTTCATAGGGGTTTTGGGGG 57.367 50.000 0.00 0.00 0.00 5.40
62 63 4.782691 AGAAATTTCATAGGGGTTTTGGGG 59.217 41.667 19.99 0.00 0.00 4.96
63 64 6.373005 AAGAAATTTCATAGGGGTTTTGGG 57.627 37.500 19.99 0.00 0.00 4.12
64 65 7.449247 TCAAAGAAATTTCATAGGGGTTTTGG 58.551 34.615 19.99 0.69 0.00 3.28
65 66 8.900983 TTCAAAGAAATTTCATAGGGGTTTTG 57.099 30.769 19.99 16.67 0.00 2.44
66 67 9.725019 GATTCAAAGAAATTTCATAGGGGTTTT 57.275 29.630 19.99 6.48 0.00 2.43
67 68 8.879227 TGATTCAAAGAAATTTCATAGGGGTTT 58.121 29.630 19.99 7.15 0.00 3.27
68 69 8.434589 TGATTCAAAGAAATTTCATAGGGGTT 57.565 30.769 19.99 1.14 0.00 4.11
69 70 8.434589 TTGATTCAAAGAAATTTCATAGGGGT 57.565 30.769 19.99 0.87 0.00 4.95
70 71 9.895138 ATTTGATTCAAAGAAATTTCATAGGGG 57.105 29.630 19.99 3.93 36.76 4.79
76 77 9.480053 GGACTCATTTGATTCAAAGAAATTTCA 57.520 29.630 19.99 0.00 36.76 2.69
77 78 9.702494 AGGACTCATTTGATTCAAAGAAATTTC 57.298 29.630 16.34 10.33 36.76 2.17
83 84 8.796475 CCTTTAAGGACTCATTTGATTCAAAGA 58.204 33.333 16.34 12.37 37.67 2.52
84 85 8.579863 ACCTTTAAGGACTCATTTGATTCAAAG 58.420 33.333 18.97 6.52 37.67 2.77
85 86 8.359642 CACCTTTAAGGACTCATTTGATTCAAA 58.640 33.333 18.97 13.88 37.67 2.69
86 87 7.505585 ACACCTTTAAGGACTCATTTGATTCAA 59.494 33.333 18.97 0.00 37.67 2.69
87 88 7.004086 ACACCTTTAAGGACTCATTTGATTCA 58.996 34.615 18.97 0.00 37.67 2.57
88 89 7.454260 ACACCTTTAAGGACTCATTTGATTC 57.546 36.000 18.97 0.00 37.67 2.52
89 90 7.119262 CGTACACCTTTAAGGACTCATTTGATT 59.881 37.037 18.97 0.00 37.67 2.57
90 91 6.594159 CGTACACCTTTAAGGACTCATTTGAT 59.406 38.462 18.97 0.00 37.67 2.57
91 92 5.929992 CGTACACCTTTAAGGACTCATTTGA 59.070 40.000 18.97 0.00 37.67 2.69
96 97 3.890756 TCACGTACACCTTTAAGGACTCA 59.109 43.478 18.97 0.00 37.67 3.41
100 101 7.444299 AGTATTTTCACGTACACCTTTAAGGA 58.556 34.615 18.97 0.00 37.67 3.36
114 115 5.931532 ACAATGAGCTTGAGTATTTTCACG 58.068 37.500 0.00 0.00 38.29 4.35
116 117 7.877612 TGTCTACAATGAGCTTGAGTATTTTCA 59.122 33.333 0.00 0.00 38.29 2.69
119 120 7.161404 TGTGTCTACAATGAGCTTGAGTATTT 58.839 34.615 0.00 0.00 38.29 1.40
180 182 0.680921 CAACCGGCCAGGATCACATT 60.681 55.000 18.74 0.76 45.00 2.71
185 187 2.511600 CGTCAACCGGCCAGGATC 60.512 66.667 18.74 6.41 45.00 3.36
195 197 4.231718 TGAATTAACAAAGCCGTCAACC 57.768 40.909 0.00 0.00 0.00 3.77
237 239 2.498726 GGCCGAGCCTGAGAGAAG 59.501 66.667 7.58 0.00 46.69 2.85
335 337 5.784177 CTCTTCGGTATGGCTATGTACATT 58.216 41.667 14.77 0.00 0.00 2.71
340 342 2.039418 TGCTCTTCGGTATGGCTATGT 58.961 47.619 0.00 0.00 0.00 2.29
348 350 2.366590 TCATGAGCATGCTCTTCGGTAT 59.633 45.455 39.46 24.97 43.12 2.73
363 365 4.002982 TCAATTGACCCGACTTTCATGAG 58.997 43.478 3.38 0.00 0.00 2.90
365 367 4.395854 TCATCAATTGACCCGACTTTCATG 59.604 41.667 11.07 0.54 0.00 3.07
366 368 4.588899 TCATCAATTGACCCGACTTTCAT 58.411 39.130 11.07 0.00 0.00 2.57
404 407 5.809001 TGCTTCTCAACAACCTTATCATCT 58.191 37.500 0.00 0.00 0.00 2.90
427 430 3.076621 TCAAGCTTGAACGAGCAATCAT 58.923 40.909 26.61 0.00 45.12 2.45
446 449 1.676678 GAGCAGATGGCCGGTAGTCA 61.677 60.000 1.90 0.00 46.50 3.41
486 503 2.899256 AGTTCCATGGTGGTGAAAATGG 59.101 45.455 12.58 0.00 40.85 3.16
490 507 1.993956 CCAGTTCCATGGTGGTGAAA 58.006 50.000 12.58 0.00 39.03 2.69
553 595 3.021269 TCACGACTTTATTGACACGCT 57.979 42.857 0.00 0.00 0.00 5.07
556 598 8.015087 TCAAATTCATCACGACTTTATTGACAC 58.985 33.333 0.00 0.00 0.00 3.67
645 752 5.963004 TGTCTCGTTTCTTCAAATTTCAACG 59.037 36.000 0.00 0.00 38.64 4.10
653 760 9.165014 CGATAATTTTTGTCTCGTTTCTTCAAA 57.835 29.630 0.00 0.00 0.00 2.69
659 766 5.726679 CGACCGATAATTTTTGTCTCGTTTC 59.273 40.000 0.00 0.00 0.00 2.78
673 780 2.806244 GCAATGCCTAACGACCGATAAT 59.194 45.455 0.00 0.00 0.00 1.28
677 784 0.036765 AAGCAATGCCTAACGACCGA 60.037 50.000 0.00 0.00 0.00 4.69
700 807 6.228616 ACTTCTTTACAGGAGATCCTTAGC 57.771 41.667 0.00 0.00 46.09 3.09
725 832 7.352738 TGGGGTTTTACTTTTTACTGGAGTAA 58.647 34.615 0.00 0.00 38.60 2.24
726 833 6.909076 TGGGGTTTTACTTTTTACTGGAGTA 58.091 36.000 0.00 0.00 0.00 2.59
727 834 5.768752 TGGGGTTTTACTTTTTACTGGAGT 58.231 37.500 0.00 0.00 0.00 3.85
729 836 4.585581 GCTGGGGTTTTACTTTTTACTGGA 59.414 41.667 0.00 0.00 0.00 3.86
730 837 4.557895 CGCTGGGGTTTTACTTTTTACTGG 60.558 45.833 0.00 0.00 0.00 4.00
731 838 4.276431 TCGCTGGGGTTTTACTTTTTACTG 59.724 41.667 0.00 0.00 0.00 2.74
732 839 4.463070 TCGCTGGGGTTTTACTTTTTACT 58.537 39.130 0.00 0.00 0.00 2.24
733 840 4.516321 TCTCGCTGGGGTTTTACTTTTTAC 59.484 41.667 0.00 0.00 0.00 2.01
734 841 4.516321 GTCTCGCTGGGGTTTTACTTTTTA 59.484 41.667 0.00 0.00 0.00 1.52
735 842 3.317149 GTCTCGCTGGGGTTTTACTTTTT 59.683 43.478 0.00 0.00 0.00 1.94
736 843 2.882761 GTCTCGCTGGGGTTTTACTTTT 59.117 45.455 0.00 0.00 0.00 2.27
737 844 2.158726 TGTCTCGCTGGGGTTTTACTTT 60.159 45.455 0.00 0.00 0.00 2.66
738 845 1.418637 TGTCTCGCTGGGGTTTTACTT 59.581 47.619 0.00 0.00 0.00 2.24
780 895 3.429822 GGAATGAATGTAACGGAGGTCGA 60.430 47.826 0.00 0.00 42.43 4.20
782 897 3.869065 TGGAATGAATGTAACGGAGGTC 58.131 45.455 0.00 0.00 0.00 3.85
809 924 4.327087 GGTTTCGATGTATTTACGTTCCGT 59.673 41.667 0.00 0.00 44.35 4.69
1488 1603 3.528370 CGCCCCTCGTCCGATTCT 61.528 66.667 0.00 0.00 0.00 2.40
1561 1686 7.558444 TCAATTTGTACACCATCTTATTACCCC 59.442 37.037 0.00 0.00 0.00 4.95
1562 1687 8.514330 TCAATTTGTACACCATCTTATTACCC 57.486 34.615 0.00 0.00 0.00 3.69
1615 1740 3.622166 TTCTACAATTTCCTCCCGGAC 57.378 47.619 0.73 0.00 39.60 4.79
1757 1888 2.488545 ACAGAGTACGATGTCTGACACC 59.511 50.000 13.50 1.43 42.49 4.16
1759 1890 3.146847 ACACAGAGTACGATGTCTGACA 58.853 45.455 13.60 13.60 42.49 3.58
1760 1891 3.833545 ACACAGAGTACGATGTCTGAC 57.166 47.619 14.78 0.00 42.49 3.51
1761 1892 4.612939 CGAAACACAGAGTACGATGTCTGA 60.613 45.833 14.78 0.00 42.49 3.27
1762 1893 3.604198 CGAAACACAGAGTACGATGTCTG 59.396 47.826 8.00 8.00 44.92 3.51
1763 1894 3.822996 CGAAACACAGAGTACGATGTCT 58.177 45.455 3.35 0.00 33.91 3.41
1813 2010 2.093447 TCCGATTTCTTCTCTTCCCTGC 60.093 50.000 0.00 0.00 0.00 4.85
1863 2067 4.184629 CGAAGTACTTCTCTTCCCAATGG 58.815 47.826 28.30 8.74 38.31 3.16
1870 2074 3.191791 AGGAGCACGAAGTACTTCTCTTC 59.808 47.826 28.30 20.75 33.69 2.87
1875 2079 2.251893 CGAAGGAGCACGAAGTACTTC 58.748 52.381 23.25 23.25 41.61 3.01
1886 2090 3.916438 TAGGGTGGGCGAAGGAGCA 62.916 63.158 0.00 0.00 39.27 4.26
1887 2091 3.081409 TAGGGTGGGCGAAGGAGC 61.081 66.667 0.00 0.00 0.00 4.70
1889 2093 3.072468 CGTAGGGTGGGCGAAGGA 61.072 66.667 0.00 0.00 0.00 3.36
1890 2094 1.968050 ATTCGTAGGGTGGGCGAAGG 61.968 60.000 0.00 0.00 45.66 3.46
1892 2096 1.219664 CATTCGTAGGGTGGGCGAA 59.780 57.895 0.00 0.00 46.33 4.70
1894 2098 1.087771 GTTCATTCGTAGGGTGGGCG 61.088 60.000 0.00 0.00 0.00 6.13
1895 2099 1.087771 CGTTCATTCGTAGGGTGGGC 61.088 60.000 0.00 0.00 0.00 5.36
1896 2100 0.461339 CCGTTCATTCGTAGGGTGGG 60.461 60.000 0.00 0.00 0.00 4.61
1899 2103 1.206371 CCTTCCGTTCATTCGTAGGGT 59.794 52.381 0.00 0.00 31.65 4.34
1924 2128 1.342374 GCATTCCAAGGGACAAGGGAT 60.342 52.381 0.00 0.00 0.00 3.85
1965 2169 3.181448 ACAGAACTGGGAACAATACGGTT 60.181 43.478 6.76 0.00 42.06 4.44
2009 5768 0.246635 GACAAGCAAGGCTCTACCGA 59.753 55.000 0.00 0.00 46.52 4.69
2010 5769 0.741221 GGACAAGCAAGGCTCTACCG 60.741 60.000 0.00 0.00 46.52 4.02
2031 5790 4.634883 AGTGAGCTTGCTTACATTGATCAG 59.365 41.667 17.53 0.00 29.74 2.90
2046 5805 1.439543 AAGGACCCTTGAGTGAGCTT 58.560 50.000 0.00 0.00 34.60 3.74
2047 5806 3.172208 AAGGACCCTTGAGTGAGCT 57.828 52.632 0.00 0.00 34.60 4.09
2073 5832 5.377478 GTTCCTACCAGAAAGGGGATTATG 58.623 45.833 0.00 0.00 43.89 1.90
2074 5833 4.415846 GGTTCCTACCAGAAAGGGGATTAT 59.584 45.833 0.00 0.00 44.36 1.28
2076 5835 2.581246 GGTTCCTACCAGAAAGGGGATT 59.419 50.000 0.00 0.00 44.36 3.01
2083 5842 2.237893 GGGATTCGGTTCCTACCAGAAA 59.762 50.000 4.83 0.00 45.31 2.52
2084 5843 1.835531 GGGATTCGGTTCCTACCAGAA 59.164 52.381 4.83 0.00 45.31 3.02
2085 5844 1.007963 AGGGATTCGGTTCCTACCAGA 59.992 52.381 4.83 0.00 45.31 3.86
2107 5866 2.997315 CCTGAGACCACGCCCTGA 60.997 66.667 0.00 0.00 0.00 3.86
2150 5909 4.939368 CCCAACACCGGCGACCAA 62.939 66.667 9.30 0.00 0.00 3.67
2215 7530 2.485122 CGCCTTTGCCTTTAGCCG 59.515 61.111 0.00 0.00 42.71 5.52
2219 7534 1.663173 GCAACCGCCTTTGCCTTTA 59.337 52.632 5.76 0.00 45.22 1.85
2234 7549 1.754745 GAGATCCTATGGGCCGCAA 59.245 57.895 0.00 0.00 0.00 4.85
2343 7658 3.223589 GCCGGCCACCTTTGTTGT 61.224 61.111 18.11 0.00 0.00 3.32
2392 7707 3.822192 CGACGACCGCCCTGATGA 61.822 66.667 0.00 0.00 0.00 2.92
2444 7759 1.141665 CGGTGCGATCATGTCCTCA 59.858 57.895 0.00 0.00 0.00 3.86
2478 7793 2.486727 GGGATCCGGTTCCTACCAATTC 60.487 54.545 26.93 7.77 45.31 2.17
2506 7821 3.556423 CCTCTACAACCTAAAACCACGCT 60.556 47.826 0.00 0.00 0.00 5.07
2514 7829 5.012768 CCTCCTTTCACCTCTACAACCTAAA 59.987 44.000 0.00 0.00 0.00 1.85
2516 7831 4.094476 CCTCCTTTCACCTCTACAACCTA 58.906 47.826 0.00 0.00 0.00 3.08
2526 7841 1.915078 CGCCATCCCTCCTTTCACCT 61.915 60.000 0.00 0.00 0.00 4.00
2531 7846 1.915078 CTCCACGCCATCCCTCCTTT 61.915 60.000 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.