Multiple sequence alignment - TraesCS2A01G499500

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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 TraesCS2A01G499500 chr2A 100.000 4675 0 0 1 4675 729165773 729170447 0.000000e+00 8634
1 TraesCS2A01G499500 chr2D 92.901 2113 74 19 2619 4675 594545980 594548072 0.000000e+00 3001
2 TraesCS2A01G499500 chr2D 92.385 1090 55 10 816 1898 594544044 594545112 0.000000e+00 1528
3 TraesCS2A01G499500 chr2D 96.761 741 24 0 1882 2622 594545131 594545871 0.000000e+00 1236
4 TraesCS2A01G499500 chr2D 89.727 769 30 20 1 750 594543277 594544015 0.000000e+00 937
5 TraesCS2A01G499500 chr2D 82.155 297 45 3 4148 4444 301752886 301752598 1.000000e-61 248
6 TraesCS2A01G499500 chr2D 82.540 189 27 4 2640 2824 24931797 24931983 1.350000e-35 161
7 TraesCS2A01G499500 chr2B 92.170 2069 81 29 2640 4675 722088132 722090152 0.000000e+00 2848
8 TraesCS2A01G499500 chr2B 89.127 1683 97 28 230 1898 722085651 722087261 0.000000e+00 2015
9 TraesCS2A01G499500 chr2B 94.231 728 36 2 1891 2617 722087289 722088011 0.000000e+00 1107
10 TraesCS2A01G499500 chr3D 85.135 370 49 4 2139 2504 613927472 613927839 1.590000e-99 374
11 TraesCS2A01G499500 chr3D 84.492 187 24 2 2384 2569 614198040 614198222 3.720000e-41 180
12 TraesCS2A01G499500 chr3D 87.943 141 15 1 2639 2779 614198415 614198553 1.040000e-36 165
13 TraesCS2A01G499500 chr3A 83.516 364 44 11 3009 3358 750495940 750496301 4.510000e-85 326
14 TraesCS2A01G499500 chr3A 92.063 126 10 0 2672 2797 750495677 750495802 1.340000e-40 178
15 TraesCS2A01G499500 chr1D 80.000 275 18 17 972 1241 334607813 334608055 8.050000e-38 169
16 TraesCS2A01G499500 chr5A 87.857 140 9 6 1114 1249 329387490 329387625 1.740000e-34 158
17 TraesCS2A01G499500 chr5A 86.331 139 11 5 1114 1248 245501042 245500908 1.360000e-30 145
18 TraesCS2A01G499500 chr7A 91.743 109 5 2 1145 1249 217752827 217752719 1.050000e-31 148
19 TraesCS2A01G499500 chr7A 90.244 82 7 1 2687 2767 43524224 43524143 6.400000e-19 106
20 TraesCS2A01G499500 chr4A 87.879 132 8 6 1114 1241 140710837 140710710 1.050000e-31 148
21 TraesCS2A01G499500 chr4A 90.244 82 7 1 2687 2767 652197360 652197279 6.400000e-19 106
22 TraesCS2A01G499500 chr7D 86.429 140 11 5 1114 1249 366721293 366721428 3.770000e-31 147
23 TraesCS2A01G499500 chr1A 85.612 139 12 6 1114 1248 75388505 75388639 6.310000e-29 139


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 TraesCS2A01G499500 chr2A 729165773 729170447 4674 False 8634.0 8634 100.000000 1 4675 1 chr2A.!!$F1 4674
1 TraesCS2A01G499500 chr2D 594543277 594548072 4795 False 1675.5 3001 92.943500 1 4675 4 chr2D.!!$F2 4674
2 TraesCS2A01G499500 chr2B 722085651 722090152 4501 False 1990.0 2848 91.842667 230 4675 3 chr2B.!!$F1 4445
3 TraesCS2A01G499500 chr3A 750495677 750496301 624 False 252.0 326 87.789500 2672 3358 2 chr3A.!!$F1 686

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
183 188 0.679505 TCCACCAGAAGACTCGGTTG 59.320 55.000 0.0 0.0 0.00 3.77 F
962 988 0.824759 GCTGTCTGTTACTCCGGGAT 59.175 55.000 0.0 0.0 0.00 3.85 F
1334 1363 1.002544 CTCTGGAAGGACAGGTTGGTC 59.997 57.143 0.0 0.0 38.98 4.02 F
2314 2425 0.165295 GCGTGCTACCGAAAAAGGTC 59.835 55.000 0.0 0.0 44.68 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1633 1666 0.040058 AAGCCATCCCAGAACATGCA 59.960 50.000 0.00 0.0 0.00 3.96 R
1851 1887 0.174845 CTTGCATTGCCACATGGAGG 59.825 55.000 6.12 0.0 37.39 4.30 R
2528 2639 1.133809 TGGCCCACCTGTAAGCTTCT 61.134 55.000 0.00 0.0 36.63 2.85 R
4292 4618 1.209019 GAGAGAGCATTGGGAGAAGCA 59.791 52.381 0.00 0.0 0.00 3.91 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
107 108 4.515944 ACCGAGATCCATAAGAGTACTTCG 59.484 45.833 0.00 0.00 37.53 3.79
128 129 5.297547 TCGAAACTAGCAATCAGAAAGTGT 58.702 37.500 0.00 0.00 0.00 3.55
129 130 5.405571 TCGAAACTAGCAATCAGAAAGTGTC 59.594 40.000 0.00 0.00 0.00 3.67
136 137 3.003275 GCAATCAGAAAGTGTCAAACCGA 59.997 43.478 0.00 0.00 0.00 4.69
173 178 1.676635 GCTGCAGCATCCACCAGAA 60.677 57.895 33.36 0.00 41.59 3.02
183 188 0.679505 TCCACCAGAAGACTCGGTTG 59.320 55.000 0.00 0.00 0.00 3.77
189 194 2.028930 CCAGAAGACTCGGTTGCTAACT 60.029 50.000 0.00 0.00 0.00 2.24
194 199 4.961435 AGACTCGGTTGCTAACTACTAC 57.039 45.455 0.00 0.00 0.00 2.73
195 200 4.587891 AGACTCGGTTGCTAACTACTACT 58.412 43.478 0.00 0.00 0.00 2.57
196 201 5.738909 AGACTCGGTTGCTAACTACTACTA 58.261 41.667 0.00 0.00 0.00 1.82
197 202 5.816777 AGACTCGGTTGCTAACTACTACTAG 59.183 44.000 0.00 0.00 0.00 2.57
198 203 4.335037 ACTCGGTTGCTAACTACTACTAGC 59.665 45.833 0.00 0.00 40.82 3.42
199 204 4.264253 TCGGTTGCTAACTACTACTAGCA 58.736 43.478 0.00 0.00 46.71 3.49
238 243 5.687285 CACATGAGCTGAACCAAAAAGTAAC 59.313 40.000 0.00 0.00 0.00 2.50
266 271 1.200020 CCACGATGCAAAAGGAGAACC 59.800 52.381 0.00 0.00 0.00 3.62
366 371 4.268939 GCAGCTGCGCAACACCAA 62.269 61.111 25.23 0.00 0.00 3.67
371 376 1.298563 CTGCGCAACACCAACACAG 60.299 57.895 13.05 0.00 0.00 3.66
411 416 2.200092 GCCCAAAGAACCCCACCA 59.800 61.111 0.00 0.00 0.00 4.17
476 482 3.695825 GGTGGGGGAGGGGAGAGA 61.696 72.222 0.00 0.00 0.00 3.10
484 495 0.996762 GGAGGGGAGAGAGGAGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
485 496 0.930726 GAGGGGAGAGAGGAGAGGAA 59.069 60.000 0.00 0.00 0.00 3.36
794 814 3.793144 GAAAGCGACGCAGCCCAG 61.793 66.667 23.70 0.00 38.01 4.45
802 822 4.711949 CGCAGCCCAGCAAGTCCT 62.712 66.667 0.00 0.00 0.00 3.85
805 825 1.073722 CAGCCCAGCAAGTCCTCAA 59.926 57.895 0.00 0.00 0.00 3.02
825 845 2.073117 AAAAATAAAACGCGGCCCAG 57.927 45.000 12.47 0.00 0.00 4.45
960 986 1.218316 GGCTGTCTGTTACTCCGGG 59.782 63.158 0.00 0.00 0.00 5.73
961 987 1.255667 GGCTGTCTGTTACTCCGGGA 61.256 60.000 0.00 0.00 0.00 5.14
962 988 0.824759 GCTGTCTGTTACTCCGGGAT 59.175 55.000 0.00 0.00 0.00 3.85
963 989 1.202428 GCTGTCTGTTACTCCGGGATC 60.202 57.143 0.00 0.00 0.00 3.36
964 990 1.065701 CTGTCTGTTACTCCGGGATCG 59.934 57.143 0.00 0.00 0.00 3.69
1119 1145 3.625897 CTCCACTCCCACGCCACA 61.626 66.667 0.00 0.00 0.00 4.17
1183 1212 2.181021 GCATGCTTGCTGCTCACC 59.819 61.111 16.80 0.00 45.77 4.02
1185 1214 3.437795 ATGCTTGCTGCTCACCGC 61.438 61.111 0.00 0.00 43.37 5.68
1334 1363 1.002544 CTCTGGAAGGACAGGTTGGTC 59.997 57.143 0.00 0.00 38.98 4.02
1357 1386 1.272928 TGGAGCTCAGTCCATCACTCT 60.273 52.381 17.19 0.00 41.99 3.24
1374 1407 3.871594 CACTCTGTAATGGGGATTCGTTC 59.128 47.826 0.00 0.00 0.00 3.95
1384 1417 2.167075 GGGGATTCGTTCTTCTTACCGA 59.833 50.000 0.00 0.00 0.00 4.69
1404 1437 6.292150 ACCGAATTCTTCTGACTTCTTTTCT 58.708 36.000 3.52 0.00 32.00 2.52
1434 1467 4.082125 TCTCAAAGCTGAATCCTTTTCCC 58.918 43.478 0.00 0.00 30.52 3.97
1485 1518 7.071572 GGTGGGACAGGTAAAATAATACTCCTA 59.928 40.741 0.00 0.00 41.80 2.94
1486 1519 8.148999 GTGGGACAGGTAAAATAATACTCCTAG 58.851 40.741 0.00 0.00 41.80 3.02
1487 1520 7.847848 TGGGACAGGTAAAATAATACTCCTAGT 59.152 37.037 0.00 0.00 0.00 2.57
1488 1521 8.712103 GGGACAGGTAAAATAATACTCCTAGTT 58.288 37.037 0.00 0.00 0.00 2.24
1565 1598 6.072286 GGGAATCATCAGATTGACGCAATTAT 60.072 38.462 6.54 0.66 44.30 1.28
1577 1610 6.588348 TGACGCAATTATGACAACATAGAG 57.412 37.500 0.00 0.00 39.67 2.43
1617 1650 4.780021 AGTGGAATCAGATGTCTTGGTACT 59.220 41.667 0.00 0.00 0.00 2.73
1678 1713 8.324163 ACCTTACACAAACTTCATACTGATTC 57.676 34.615 0.00 0.00 0.00 2.52
1792 1827 4.111198 CTCCTCGTTCATTCTCTGTCATG 58.889 47.826 0.00 0.00 0.00 3.07
1851 1887 8.056407 AGTATTTAAATTTCTGTTCTGCCTCC 57.944 34.615 5.91 0.00 0.00 4.30
1852 1888 5.722021 TTTAAATTTCTGTTCTGCCTCCC 57.278 39.130 0.00 0.00 0.00 4.30
1862 1902 3.711059 CTGCCTCCCTCCATGTGGC 62.711 68.421 0.00 0.00 43.49 5.01
1982 2092 6.484643 TCATAGCCTTGTTCTAGATTGATTGC 59.515 38.462 0.00 0.00 0.00 3.56
2091 2202 5.456548 TCTGCACCAATATATTGCCAATG 57.543 39.130 18.40 13.78 36.48 2.82
2283 2394 9.797642 TGTGACATTAATCCAAATATGCTAGAT 57.202 29.630 0.00 0.00 0.00 1.98
2302 2413 2.248280 TGTTGGAAAGAAGCGTGCTA 57.752 45.000 0.00 0.00 0.00 3.49
2304 2415 1.197036 GTTGGAAAGAAGCGTGCTACC 59.803 52.381 0.00 0.00 0.00 3.18
2314 2425 0.165295 GCGTGCTACCGAAAAAGGTC 59.835 55.000 0.00 0.00 44.68 3.85
2373 2484 9.868277 TTAATTTCAAATGTTGTTCTGTTGTCT 57.132 25.926 0.00 0.00 0.00 3.41
2379 2490 3.270027 TGTTGTTCTGTTGTCTGACAGG 58.730 45.455 10.77 5.97 45.54 4.00
2528 2639 5.798132 ACACACATTGAGAAAGCTCTATCA 58.202 37.500 0.00 0.00 41.84 2.15
2550 2661 1.000896 GCTTACAGGTGGGCCACAT 60.001 57.895 35.69 28.70 35.86 3.21
2573 2684 8.576442 ACATAAAAATCCTGAACCAACTAACAG 58.424 33.333 0.00 0.00 0.00 3.16
2577 2688 5.762179 ATCCTGAACCAACTAACAGATCA 57.238 39.130 0.00 0.00 32.90 2.92
2591 2702 3.303938 ACAGATCATACCCCAGTCTCAG 58.696 50.000 0.00 0.00 0.00 3.35
2596 2707 4.286297 TCATACCCCAGTCTCAGTTTTG 57.714 45.455 0.00 0.00 0.00 2.44
2631 2854 7.852263 AGTTTCTACTATGCTGTAGGATTTGT 58.148 34.615 10.53 0.00 40.05 2.83
2639 2862 2.665519 GCTGTAGGATTTGTTGCGTGTG 60.666 50.000 0.00 0.00 0.00 3.82
2640 2863 2.805671 CTGTAGGATTTGTTGCGTGTGA 59.194 45.455 0.00 0.00 0.00 3.58
2641 2864 3.206964 TGTAGGATTTGTTGCGTGTGAA 58.793 40.909 0.00 0.00 0.00 3.18
2644 2867 3.900941 AGGATTTGTTGCGTGTGAAATC 58.099 40.909 0.00 0.00 35.13 2.17
2645 2868 3.569701 AGGATTTGTTGCGTGTGAAATCT 59.430 39.130 0.00 0.00 35.84 2.40
2646 2869 3.670055 GGATTTGTTGCGTGTGAAATCTG 59.330 43.478 0.00 0.00 35.84 2.90
2647 2870 2.118228 TTGTTGCGTGTGAAATCTGC 57.882 45.000 0.00 0.00 0.00 4.26
2648 2871 0.310543 TGTTGCGTGTGAAATCTGCC 59.689 50.000 0.00 0.00 0.00 4.85
2649 2872 0.593128 GTTGCGTGTGAAATCTGCCT 59.407 50.000 0.00 0.00 0.00 4.75
2650 2873 1.804151 GTTGCGTGTGAAATCTGCCTA 59.196 47.619 0.00 0.00 0.00 3.93
2909 3161 4.104776 CACTGTTCGTTTTCAGCATTTGT 58.895 39.130 0.00 0.00 35.37 2.83
2911 3163 5.396362 CACTGTTCGTTTTCAGCATTTGTAG 59.604 40.000 0.00 0.00 35.37 2.74
3072 3327 4.926860 TGCTTCAATCATAGTGTTGTCG 57.073 40.909 0.00 0.00 0.00 4.35
3087 3342 1.988293 TGTCGCATCCTTCCCAAAAA 58.012 45.000 0.00 0.00 0.00 1.94
3314 3583 4.340950 GGTTTCCAAAACAGGTGAAGATCA 59.659 41.667 0.00 0.00 0.00 2.92
3327 3596 6.596888 CAGGTGAAGATCAGCATTTCTAAAGA 59.403 38.462 11.61 0.00 46.52 2.52
3407 3694 8.783660 TTCTACCATATGTCAAACCTCTAGAT 57.216 34.615 1.24 0.00 0.00 1.98
3731 4018 0.541863 GTGGGTAGTGGTGGATCTGG 59.458 60.000 0.00 0.00 0.00 3.86
3844 4133 1.552337 ACGATGATCTGCTCAGTGGTT 59.448 47.619 0.00 0.00 37.28 3.67
3918 4225 4.760530 TTGTGCTATACCTTGCATCTCT 57.239 40.909 0.00 0.00 41.45 3.10
3931 4238 6.995091 ACCTTGCATCTCTATATCTTTGAACC 59.005 38.462 0.00 0.00 0.00 3.62
4005 4312 6.011981 ACCAAAATGTAGGGAGGAAATCACTA 60.012 38.462 0.00 0.00 41.08 2.74
4063 4381 8.735692 AAAAACAATGTGTCTTTCCATTGATT 57.264 26.923 16.66 9.80 46.93 2.57
4064 4382 7.718272 AAACAATGTGTCTTTCCATTGATTG 57.282 32.000 16.66 0.00 46.93 2.67
4074 4392 4.524802 TTCCATTGATTGCAGATACCCT 57.475 40.909 0.00 0.00 0.00 4.34
4117 4442 6.938596 TGATTCAATCATACATAGCTTGGAGG 59.061 38.462 0.00 0.00 33.59 4.30
4216 4542 2.523168 TCCAGACGCACCACCTCA 60.523 61.111 0.00 0.00 0.00 3.86
4232 4558 2.765807 CACCCCGATGCTCCCTCT 60.766 66.667 0.00 0.00 0.00 3.69
4257 4583 6.382869 CCATCTTTGTAATCCTGATGGTTC 57.617 41.667 11.00 0.00 45.28 3.62
4268 4594 3.071023 TCCTGATGGTTCGAGTTTTCTGT 59.929 43.478 0.00 0.00 34.23 3.41
4292 4618 2.029288 CATCGGTCGTTGCTGTGCT 61.029 57.895 0.00 0.00 0.00 4.40
4299 4625 1.206072 CGTTGCTGTGCTGCTTCTC 59.794 57.895 0.00 0.00 0.00 2.87
4314 4640 2.742530 GCTTCTCCCAATGCTCTCTCTG 60.743 54.545 0.00 0.00 0.00 3.35
4467 4793 2.500910 CTGAAGAGGAGCAGAGGAACAT 59.499 50.000 0.00 0.00 34.06 2.71
4641 4967 4.410448 CATGTATACACGCAAAATGCACA 58.590 39.130 7.96 0.00 45.36 4.57
4649 4975 1.187704 CGCAAAATGCACAGTGAAACG 59.812 47.619 4.15 0.00 45.36 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.194861 GGTTTGCCAGGTGAAGAAAAAC 58.805 45.455 0.00 0.00 34.09 2.43
11 12 2.834549 TGGTTTGCCAGGTGAAGAAAAA 59.165 40.909 0.00 0.00 40.46 1.94
12 13 2.461695 TGGTTTGCCAGGTGAAGAAAA 58.538 42.857 0.00 0.00 40.46 2.29
107 108 6.545504 TGACACTTTCTGATTGCTAGTTTC 57.454 37.500 0.00 0.00 0.00 2.78
128 129 2.859165 ATTTGCTCTCCTCGGTTTGA 57.141 45.000 0.00 0.00 0.00 2.69
129 130 4.201950 CCATAATTTGCTCTCCTCGGTTTG 60.202 45.833 0.00 0.00 0.00 2.93
136 137 1.972872 CCGCCATAATTTGCTCTCCT 58.027 50.000 0.00 0.00 0.00 3.69
173 178 4.587891 AGTAGTAGTTAGCAACCGAGTCT 58.412 43.478 0.00 0.00 0.00 3.24
238 243 0.030504 TTTGCATCGTGGTGCTTGTG 59.969 50.000 6.66 0.00 45.27 3.33
362 367 1.185618 TAGCTCGCTCCTGTGTTGGT 61.186 55.000 0.00 0.00 0.00 3.67
363 368 0.459237 CTAGCTCGCTCCTGTGTTGG 60.459 60.000 0.00 0.00 0.00 3.77
364 369 0.244994 ACTAGCTCGCTCCTGTGTTG 59.755 55.000 0.00 0.00 0.00 3.33
365 370 0.528470 GACTAGCTCGCTCCTGTGTT 59.472 55.000 0.00 0.00 0.00 3.32
366 371 0.609406 TGACTAGCTCGCTCCTGTGT 60.609 55.000 0.00 0.00 0.00 3.72
461 467 3.368501 CCTCTCTCCCCTCCCCCA 61.369 72.222 0.00 0.00 0.00 4.96
476 482 1.261238 CGCCAAGGTCTTCCTCTCCT 61.261 60.000 0.00 0.00 44.35 3.69
700 720 2.034879 CCCAAGCGGTGTAGCACAG 61.035 63.158 1.61 0.00 40.15 3.66
750 770 3.113514 TTTGTCGGCCCTGCAGTCA 62.114 57.895 13.81 0.00 0.00 3.41
783 803 3.426568 GACTTGCTGGGCTGCGTC 61.427 66.667 0.00 0.00 35.36 5.19
811 831 2.594882 TTGCTGGGCCGCGTTTTA 60.595 55.556 4.92 0.00 0.00 1.52
825 845 1.669115 TGCTGTTCTCTCGGCTTGC 60.669 57.895 0.00 0.00 40.06 4.01
914 940 3.408853 GGAACGGGGGAGAAGGGG 61.409 72.222 0.00 0.00 0.00 4.79
940 966 1.805945 CGGAGTAACAGACAGCCGC 60.806 63.158 0.00 0.00 40.08 6.53
960 986 2.340443 GAGATGGCCGGTCCGATC 59.660 66.667 14.39 8.13 37.80 3.69
961 987 3.606662 CGAGATGGCCGGTCCGAT 61.607 66.667 14.39 0.00 37.80 4.18
980 1006 4.840005 CCTTCCTTCCTCGGCGGC 62.840 72.222 7.21 0.00 0.00 6.53
1092 1118 2.066999 GGAGTGGAGGAAGGCCGAT 61.067 63.158 0.00 0.00 39.96 4.18
1093 1119 2.683933 GGAGTGGAGGAAGGCCGA 60.684 66.667 0.00 0.00 39.96 5.54
1119 1145 3.315949 TGGGGCGTACCGAAGCTT 61.316 61.111 0.00 0.00 41.60 3.74
1136 1162 3.069318 GGCGACGAGGGAGGAAGT 61.069 66.667 0.00 0.00 0.00 3.01
1183 1212 2.202492 CTGACGAGGAACGAGGCG 60.202 66.667 0.00 0.00 45.77 5.52
1185 1214 3.998156 TCCTGACGAGGAACGAGG 58.002 61.111 0.00 0.00 46.19 4.63
1250 1279 2.510238 GAGGCGACGCTGCTGAAT 60.510 61.111 20.77 0.00 34.52 2.57
1334 1363 0.900421 TGATGGACTGAGCTCCACTG 59.100 55.000 12.15 1.41 43.38 3.66
1352 1381 3.543680 ACGAATCCCCATTACAGAGTG 57.456 47.619 0.00 0.00 0.00 3.51
1357 1386 4.837093 AGAAGAACGAATCCCCATTACA 57.163 40.909 0.00 0.00 0.00 2.41
1384 1417 7.390162 CAGCCTAGAAAAGAAGTCAGAAGAATT 59.610 37.037 0.00 0.00 34.26 2.17
1404 1437 4.444022 GGATTCAGCTTTGAGATCAGCCTA 60.444 45.833 0.00 0.00 36.62 3.93
1434 1467 1.519455 GTCGAGGTGCTTCATCCCG 60.519 63.158 0.00 0.00 0.00 5.14
1485 1518 3.595021 AGGACACCCCTGTTAACTAACT 58.405 45.455 7.22 0.00 45.61 2.24
1565 1598 4.982295 CGTTTGTGACTCTCTATGTTGTCA 59.018 41.667 0.00 0.00 37.14 3.58
1577 1610 5.917541 TCCACTAAATTCGTTTGTGACTC 57.082 39.130 2.84 0.00 43.23 3.36
1617 1650 0.178967 TGCAATTTGGGAGAGCCACA 60.179 50.000 0.00 0.00 35.15 4.17
1633 1666 0.040058 AAGCCATCCCAGAACATGCA 59.960 50.000 0.00 0.00 0.00 3.96
1849 1885 1.380246 GCATTGCCACATGGAGGGA 60.380 57.895 0.87 2.80 37.39 4.20
1850 1886 1.259142 TTGCATTGCCACATGGAGGG 61.259 55.000 6.12 2.66 37.39 4.30
1851 1887 0.174845 CTTGCATTGCCACATGGAGG 59.825 55.000 6.12 0.00 37.39 4.30
1852 1888 1.179152 TCTTGCATTGCCACATGGAG 58.821 50.000 6.12 0.00 37.39 3.86
1893 1933 7.309194 GGTCCTTACTTAAATGCATCACTTTGT 60.309 37.037 0.00 0.00 0.00 2.83
1982 2092 3.131396 GGAAGACAAGGTGTACACTGTG 58.869 50.000 24.55 22.37 0.00 3.66
2091 2202 5.591643 TTTCATAACGAGTGTTCAAGAGC 57.408 39.130 0.00 0.00 39.54 4.09
2283 2394 1.871039 GTAGCACGCTTCTTTCCAACA 59.129 47.619 0.00 0.00 0.00 3.33
2302 2413 1.302366 GAACCACGACCTTTTTCGGT 58.698 50.000 0.00 0.00 43.58 4.69
2304 2415 2.546368 TCATGAACCACGACCTTTTTCG 59.454 45.455 0.00 0.00 44.87 3.46
2314 2425 5.107109 TGAAATGAGTTTCATGAACCACG 57.893 39.130 7.89 0.00 46.49 4.94
2373 2484 6.721318 AGCCTGAAATAAGAATAACCTGTCA 58.279 36.000 0.00 0.00 0.00 3.58
2528 2639 1.133809 TGGCCCACCTGTAAGCTTCT 61.134 55.000 0.00 0.00 36.63 2.85
2550 2661 8.934023 ATCTGTTAGTTGGTTCAGGATTTTTA 57.066 30.769 0.00 0.00 0.00 1.52
2573 2684 4.762289 AAACTGAGACTGGGGTATGATC 57.238 45.455 0.00 0.00 0.00 2.92
2577 2688 4.785376 AGATCAAAACTGAGACTGGGGTAT 59.215 41.667 0.00 0.00 0.00 2.73
2591 2702 7.971183 AGTAGAAACTTCAGGAGATCAAAAC 57.029 36.000 0.00 0.00 29.00 2.43
2596 2707 6.922957 CAGCATAGTAGAAACTTCAGGAGATC 59.077 42.308 0.00 0.00 37.15 2.75
2631 2854 2.076100 CTAGGCAGATTTCACACGCAA 58.924 47.619 0.00 0.00 0.00 4.85
2639 2862 3.956744 ACAGAAACCCTAGGCAGATTTC 58.043 45.455 2.05 10.09 0.00 2.17
2640 2863 4.043435 AGAACAGAAACCCTAGGCAGATTT 59.957 41.667 2.05 0.66 0.00 2.17
2641 2864 3.589288 AGAACAGAAACCCTAGGCAGATT 59.411 43.478 2.05 0.00 0.00 2.40
2644 2867 3.425162 AAGAACAGAAACCCTAGGCAG 57.575 47.619 2.05 0.00 0.00 4.85
2645 2868 3.486383 CAAAGAACAGAAACCCTAGGCA 58.514 45.455 2.05 0.00 0.00 4.75
2646 2869 2.229062 GCAAAGAACAGAAACCCTAGGC 59.771 50.000 2.05 0.00 0.00 3.93
2647 2870 3.486383 TGCAAAGAACAGAAACCCTAGG 58.514 45.455 0.06 0.06 0.00 3.02
2648 2871 5.006386 AGATGCAAAGAACAGAAACCCTAG 58.994 41.667 0.00 0.00 0.00 3.02
2649 2872 4.985538 AGATGCAAAGAACAGAAACCCTA 58.014 39.130 0.00 0.00 0.00 3.53
2650 2873 3.837355 AGATGCAAAGAACAGAAACCCT 58.163 40.909 0.00 0.00 0.00 4.34
2909 3161 3.485463 ACTTTGTTGCAGTGCCTACTA 57.515 42.857 13.72 5.13 34.74 1.82
2911 3163 4.766404 ATAACTTTGTTGCAGTGCCTAC 57.234 40.909 13.72 11.40 0.00 3.18
2951 3203 3.127895 GCCGATGTTTAACACATAGCCAA 59.872 43.478 0.00 0.00 46.96 4.52
3060 3315 2.609459 GGAAGGATGCGACAACACTATG 59.391 50.000 0.00 0.00 0.00 2.23
3087 3342 4.038402 CACAAAAGCACTGGGAAGATCTTT 59.962 41.667 9.87 0.00 0.00 2.52
3090 3348 2.229784 CCACAAAAGCACTGGGAAGATC 59.770 50.000 0.00 0.00 0.00 2.75
3187 3446 5.655090 TGAATAGATGTCGTAACTGGAGGAA 59.345 40.000 0.00 0.00 0.00 3.36
3314 3583 9.301897 AGTAACAGGAAATTCTTTAGAAATGCT 57.698 29.630 0.00 0.00 37.61 3.79
3327 3596 4.999950 CAGTCAGCTCAGTAACAGGAAATT 59.000 41.667 0.00 0.00 0.00 1.82
3611 3898 3.809832 CCAGATTTTCATATTCGACCGCT 59.190 43.478 0.00 0.00 0.00 5.52
3731 4018 1.683385 GTTAGCCCCAAATGCCTGATC 59.317 52.381 0.00 0.00 0.00 2.92
3918 4225 7.526142 ACTCGATAGCAGGTTCAAAGATATA 57.474 36.000 0.00 0.00 0.00 0.86
3931 4238 7.307042 CCAGATGACAAATTTACTCGATAGCAG 60.307 40.741 0.00 0.00 0.00 4.24
4063 4381 7.067008 GCTATTTTGTTTTCTAGGGTATCTGCA 59.933 37.037 0.00 0.00 0.00 4.41
4064 4382 7.283354 AGCTATTTTGTTTTCTAGGGTATCTGC 59.717 37.037 0.00 0.00 0.00 4.26
4216 4542 2.765807 CAGAGGGAGCATCGGGGT 60.766 66.667 0.00 0.00 34.37 4.95
4232 4558 4.209538 CCATCAGGATTACAAAGATGGCA 58.790 43.478 6.80 0.00 46.28 4.92
4257 4583 4.211389 CCGATGAAACAACAGAAAACTCG 58.789 43.478 0.00 0.00 0.00 4.18
4268 4594 1.262950 CAGCAACGACCGATGAAACAA 59.737 47.619 3.88 0.00 0.00 2.83
4292 4618 1.209019 GAGAGAGCATTGGGAGAAGCA 59.791 52.381 0.00 0.00 0.00 3.91
4314 4640 0.813821 GCTTCCTGCATCAGAAACCC 59.186 55.000 0.00 0.00 42.31 4.11
4467 4793 5.474532 AGCAAGCTCATGTAATCTTTGTTGA 59.525 36.000 0.00 0.00 0.00 3.18
4641 4967 8.658499 AACTAACATTTTCTCTACGTTTCACT 57.342 30.769 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.