Multiple sequence alignment - TraesCS7A01G181300

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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 TraesCS7A01G181300 chr7A 100.000 2975 0 0 1 2975 135923314 135920340 0.000000e+00 5494.0
1 TraesCS7A01G181300 chr7A 100.000 84 0 0 55 138 135923140 135923057 3.970000e-34 156.0
2 TraesCS7A01G181300 chr7A 100.000 84 0 0 175 258 135923260 135923177 3.970000e-34 156.0
3 TraesCS7A01G181300 chr7A 85.333 150 19 3 1673 1821 116832840 116832987 5.140000e-33 152.0
4 TraesCS7A01G181300 chr2D 94.950 1307 57 8 1673 2975 9050208 9051509 0.000000e+00 2039.0
5 TraesCS7A01G181300 chr2D 81.034 464 58 13 2538 2975 372589137 372589596 2.840000e-90 342.0
6 TraesCS7A01G181300 chr4B 91.294 1321 61 19 1684 2975 49111529 49112824 0.000000e+00 1753.0
7 TraesCS7A01G181300 chr4B 82.421 347 38 13 2634 2973 39108470 39108140 6.280000e-72 281.0
8 TraesCS7A01G181300 chr4B 90.164 61 3 3 1 59 399269662 399269603 3.180000e-10 76.8
9 TraesCS7A01G181300 chr7D 90.172 1048 70 14 186 1214 136307406 136306373 0.000000e+00 1334.0
10 TraesCS7A01G181300 chr7D 89.509 753 71 6 175 925 136310567 136309821 0.000000e+00 946.0
11 TraesCS7A01G181300 chr7D 90.160 437 34 2 1236 1671 136306103 136305675 7.200000e-156 560.0
12 TraesCS7A01G181300 chr7D 78.571 462 60 16 2538 2973 32448048 32447600 4.890000e-68 268.0
13 TraesCS7A01G181300 chr7D 89.431 123 12 1 38 159 136310584 136310462 1.430000e-33 154.0
14 TraesCS7A01G181300 chr7D 76.437 174 27 12 214 379 269037074 269037241 6.830000e-12 82.4
15 TraesCS7A01G181300 chr7D 95.833 48 1 1 94 140 269037074 269037121 3.180000e-10 76.8
16 TraesCS7A01G181300 chr6A 88.697 1044 72 14 1976 2975 486268747 486269788 0.000000e+00 1232.0
17 TraesCS7A01G181300 chr6A 93.359 783 52 0 1673 2455 213393210 213393992 0.000000e+00 1158.0
18 TraesCS7A01G181300 chr6A 89.593 442 24 7 2555 2975 213393987 213394427 2.610000e-150 542.0
19 TraesCS7A01G181300 chr6A 89.873 237 16 3 1673 1907 486268382 486268612 6.230000e-77 298.0
20 TraesCS7A01G181300 chr6A 79.221 308 48 9 2680 2975 50190786 50191089 1.810000e-47 200.0
21 TraesCS7A01G181300 chr7B 88.538 759 77 7 190 946 99662994 99663744 0.000000e+00 911.0
22 TraesCS7A01G181300 chr7B 90.526 665 50 7 175 837 99680977 99681630 0.000000e+00 867.0
23 TraesCS7A01G181300 chr7B 88.584 438 32 6 1236 1671 99682093 99682514 1.580000e-142 516.0
24 TraesCS7A01G181300 chr7B 85.124 121 16 2 204 322 325991859 325991739 4.030000e-24 122.0
25 TraesCS7A01G181300 chr7B 95.714 70 2 1 70 138 99662994 99663063 8.720000e-21 111.0
26 TraesCS7A01G181300 chr7B 83.471 121 19 1 203 322 325991763 325991643 8.720000e-21 111.0
27 TraesCS7A01G181300 chr7B 96.226 53 0 2 1 51 408044705 408044653 5.280000e-13 86.1
28 TraesCS7A01G181300 chr7B 91.379 58 4 1 1 58 129309944 129310000 8.840000e-11 78.7
29 TraesCS7A01G181300 chr5B 81.683 606 79 20 1963 2540 302837461 302836860 2.680000e-130 475.0
30 TraesCS7A01G181300 chr5B 86.316 190 21 3 2634 2823 302835789 302835605 5.030000e-48 202.0
31 TraesCS7A01G181300 chr2B 79.004 462 59 17 2538 2973 397052892 397053341 6.280000e-72 281.0
32 TraesCS7A01G181300 chr2B 83.390 295 38 7 2687 2973 221542348 221542057 2.270000e-66 263.0
33 TraesCS7A01G181300 chr2B 84.672 137 16 5 188 322 739635 739768 6.690000e-27 132.0
34 TraesCS7A01G181300 chr2B 94.545 55 2 1 2 56 349930621 349930568 1.900000e-12 84.2
35 TraesCS7A01G181300 chr2B 86.301 73 7 3 68 140 739635 739704 3.180000e-10 76.8
36 TraesCS7A01G181300 chr2B 95.745 47 1 1 1 46 657786373 657786419 1.140000e-09 75.0
37 TraesCS7A01G181300 chr5A 85.593 236 26 4 2652 2880 487739259 487739493 1.070000e-59 241.0
38 TraesCS7A01G181300 chr5A 94.444 54 2 1 1 53 231301823 231301770 6.830000e-12 82.4
39 TraesCS7A01G181300 chr3A 83.041 171 25 4 994 1162 32243753 32243921 5.140000e-33 152.0
40 TraesCS7A01G181300 chr6D 83.537 164 20 7 1663 1822 452956483 452956643 2.390000e-31 147.0
41 TraesCS7A01G181300 chr6B 84.211 152 21 3 1671 1821 274562893 274563042 8.590000e-31 145.0
42 TraesCS7A01G181300 chr1B 84.106 151 21 3 1673 1822 190313662 190313514 3.090000e-30 143.0
43 TraesCS7A01G181300 chr1B 83.660 153 22 3 1673 1824 86948284 86948134 1.110000e-29 141.0
44 TraesCS7A01G181300 chr5D 92.982 57 2 2 1 56 409447997 409447942 6.830000e-12 82.4
45 TraesCS7A01G181300 chr1D 97.826 46 1 0 1 46 178459600 178459645 2.460000e-11 80.5
46 TraesCS7A01G181300 chr3B 91.379 58 4 1 1 58 450140337 450140281 8.840000e-11 78.7
47 TraesCS7A01G181300 chr3B 87.273 55 4 3 176 228 154769138 154769085 3.200000e-05 60.2
48 TraesCS7A01G181300 chr3B 87.273 55 4 3 56 108 154769138 154769085 3.200000e-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 TraesCS7A01G181300 chr7A 135920340 135923314 2974 True 1935.333333 5494 100.0000 1 2975 3 chr7A.!!$R1 2974
1 TraesCS7A01G181300 chr2D 9050208 9051509 1301 False 2039.000000 2039 94.9500 1673 2975 1 chr2D.!!$F1 1302
2 TraesCS7A01G181300 chr4B 49111529 49112824 1295 False 1753.000000 1753 91.2940 1684 2975 1 chr4B.!!$F1 1291
3 TraesCS7A01G181300 chr7D 136305675 136310584 4909 True 748.500000 1334 89.8180 38 1671 4 chr7D.!!$R2 1633
4 TraesCS7A01G181300 chr6A 213393210 213394427 1217 False 850.000000 1158 91.4760 1673 2975 2 chr6A.!!$F2 1302
5 TraesCS7A01G181300 chr6A 486268382 486269788 1406 False 765.000000 1232 89.2850 1673 2975 2 chr6A.!!$F3 1302
6 TraesCS7A01G181300 chr7B 99680977 99682514 1537 False 691.500000 867 89.5550 175 1671 2 chr7B.!!$F3 1496
7 TraesCS7A01G181300 chr7B 99662994 99663744 750 False 511.000000 911 92.1260 70 946 2 chr7B.!!$F2 876
8 TraesCS7A01G181300 chr5B 302835605 302837461 1856 True 338.500000 475 83.9995 1963 2823 2 chr5B.!!$R1 860

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
728 3886 0.321564 CACGGCAAACAGGATCTCCA 60.322 55.0 0.0 0.0 38.89 3.86 F
1081 4256 0.319900 GAGCAGCTTTCACGAGGTCA 60.320 55.0 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 5155 0.319211 TTCGGTCGATCGCTGTTGTT 60.319 50.000 14.58 0.0 0.0 2.83 R
2638 7169 1.002430 TGGCTTGAATGACTCTCGCTT 59.998 47.619 0.00 0.0 0.0 4.68 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
25 26 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
26 27 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
27 28 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
28 29 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
29 30 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
30 31 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
31 32 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
32 33 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
33 34 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
34 35 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
35 36 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
36 37 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
46 47 3.268330 GGACGGAGGGAGTACAATTTTC 58.732 50.000 0.00 0.00 0.00 2.29
48 49 3.933332 GACGGAGGGAGTACAATTTTCTG 59.067 47.826 0.00 0.00 0.00 3.02
138 141 8.992835 CCAAATTTGTTTGGGATTTTTGAAAA 57.007 26.923 16.73 0.00 45.86 2.29
139 142 9.597170 CCAAATTTGTTTGGGATTTTTGAAAAT 57.403 25.926 16.73 1.54 45.86 1.82
160 163 9.920826 GAAAATCTTCACACTTTCAAAATTTCC 57.079 29.630 0.00 0.00 0.00 3.13
161 164 8.437360 AAATCTTCACACTTTCAAAATTTCCC 57.563 30.769 0.00 0.00 0.00 3.97
162 165 6.537453 TCTTCACACTTTCAAAATTTCCCA 57.463 33.333 0.00 0.00 0.00 4.37
163 166 6.940739 TCTTCACACTTTCAAAATTTCCCAA 58.059 32.000 0.00 0.00 0.00 4.12
164 167 7.390027 TCTTCACACTTTCAAAATTTCCCAAA 58.610 30.769 0.00 0.00 0.00 3.28
165 168 8.046107 TCTTCACACTTTCAAAATTTCCCAAAT 58.954 29.630 0.00 0.00 0.00 2.32
166 169 7.551035 TCACACTTTCAAAATTTCCCAAATG 57.449 32.000 0.00 0.00 0.00 2.32
167 170 7.108847 TCACACTTTCAAAATTTCCCAAATGT 58.891 30.769 0.00 0.00 0.00 2.71
168 171 7.609532 TCACACTTTCAAAATTTCCCAAATGTT 59.390 29.630 0.00 0.00 0.00 2.71
169 172 7.909641 CACACTTTCAAAATTTCCCAAATGTTC 59.090 33.333 0.00 0.00 0.00 3.18
170 173 7.609532 ACACTTTCAAAATTTCCCAAATGTTCA 59.390 29.630 0.00 0.00 0.00 3.18
171 174 7.909641 CACTTTCAAAATTTCCCAAATGTTCAC 59.090 33.333 0.00 0.00 0.00 3.18
172 175 7.609532 ACTTTCAAAATTTCCCAAATGTTCACA 59.390 29.630 0.00 0.00 0.00 3.58
173 176 6.917217 TCAAAATTTCCCAAATGTTCACAC 57.083 33.333 0.00 0.00 0.00 3.82
174 177 6.648192 TCAAAATTTCCCAAATGTTCACACT 58.352 32.000 0.00 0.00 0.00 3.55
175 178 7.108847 TCAAAATTTCCCAAATGTTCACACTT 58.891 30.769 0.00 0.00 0.00 3.16
176 179 7.609532 TCAAAATTTCCCAAATGTTCACACTTT 59.390 29.630 0.00 0.00 0.00 2.66
177 180 7.552458 AAATTTCCCAAATGTTCACACTTTC 57.448 32.000 0.00 0.00 0.00 2.62
184 187 7.279758 TCCCAAATGTTCACACTTTCAAAAATC 59.720 33.333 0.00 0.00 0.00 2.17
191 194 6.147864 TCACACTTTCAAAAATCTTCCAGG 57.852 37.500 0.00 0.00 0.00 4.45
199 202 9.112725 CTTTCAAAAATCTTCCAGGTTTCAAAT 57.887 29.630 0.00 0.00 0.00 2.32
244 248 7.920160 AATGTTCACACTTCCAAATTTGTTT 57.080 28.000 16.73 0.00 0.00 2.83
457 3615 6.215845 ACTCAAGATTTGGAAAATTGTTCGG 58.784 36.000 0.00 0.00 0.00 4.30
466 3624 4.101741 TGGAAAATTGTTCGGGATTTGGTT 59.898 37.500 0.00 0.00 0.00 3.67
583 3741 2.371841 TGCACAAGTAGGGAGTGATGTT 59.628 45.455 0.00 0.00 35.33 2.71
604 3762 0.392461 TTCATTCCTAGCCACCGCAC 60.392 55.000 0.00 0.00 37.52 5.34
642 3800 0.527113 TTTCACCCTCGTATTCGCGA 59.473 50.000 3.71 3.71 39.22 5.87
696 3854 2.672651 TGTGCGATGGGGCTTGTG 60.673 61.111 0.00 0.00 0.00 3.33
728 3886 0.321564 CACGGCAAACAGGATCTCCA 60.322 55.000 0.00 0.00 38.89 3.86
742 3900 0.614697 TCTCCAGCAGATCCGGTCAA 60.615 55.000 0.00 0.00 0.00 3.18
840 3998 1.202099 TCCGGCATTTCTACCACCCA 61.202 55.000 0.00 0.00 0.00 4.51
866 4024 0.322456 CCGCAATCCCACCTTCTTCA 60.322 55.000 0.00 0.00 0.00 3.02
872 4030 1.118965 TCCCACCTTCTTCAGCGACA 61.119 55.000 0.00 0.00 0.00 4.35
935 4093 3.458163 GGAGGTCGCCGATGTGGA 61.458 66.667 0.00 0.00 42.00 4.02
938 4096 4.148825 GGTCGCCGATGTGGAGCT 62.149 66.667 0.00 0.00 42.00 4.09
989 4147 4.873129 CACGACATCGAGGCCGGG 62.873 72.222 11.06 1.13 43.02 5.73
1025 4199 1.341606 CTCGAACGAGACCAAAGAGC 58.658 55.000 17.65 0.00 44.53 4.09
1081 4256 0.319900 GAGCAGCTTTCACGAGGTCA 60.320 55.000 0.00 0.00 0.00 4.02
1083 4258 0.601311 GCAGCTTTCACGAGGTCAGT 60.601 55.000 0.00 0.00 0.00 3.41
1088 4263 0.742505 TTTCACGAGGTCAGTGACGT 59.257 50.000 17.97 17.97 46.81 4.34
1142 4317 4.194720 GATCGAGCTCCACGCCGT 62.195 66.667 8.47 0.00 40.39 5.68
1143 4318 2.827190 ATCGAGCTCCACGCCGTA 60.827 61.111 8.47 0.00 40.39 4.02
1147 4322 1.214589 GAGCTCCACGCCGTAAAGA 59.785 57.895 0.87 0.00 40.39 2.52
1160 4335 1.017701 GTAAAGAAGGCGGTGGACGG 61.018 60.000 0.00 0.00 44.51 4.79
1206 4381 2.529389 AAGGCGGACAAGGAGGGT 60.529 61.111 0.00 0.00 0.00 4.34
1247 4671 5.007823 CGAGTTCTACCTCAACAGTATCGAT 59.992 44.000 2.16 2.16 0.00 3.59
1257 4681 1.133884 ACAGTATCGATCTCCCGTCCA 60.134 52.381 0.00 0.00 0.00 4.02
1319 4743 6.103997 TGAGCGAATAGTTCTTTTTACGGAT 58.896 36.000 0.00 0.00 0.00 4.18
1372 4796 1.755380 GTACTCGGCTAGATGTTGGGT 59.245 52.381 0.00 0.00 0.00 4.51
1385 4809 1.896660 TTGGGTTGTCTGAAGCGGC 60.897 57.895 0.00 0.00 0.00 6.53
1406 4830 5.681639 GGCTACATATTGGTCCAGTTTACT 58.318 41.667 0.00 0.00 0.00 2.24
1437 4861 4.265904 TGATTTTTCTCGTGGAGTAGCA 57.734 40.909 0.00 0.00 0.00 3.49
1438 4862 4.637276 TGATTTTTCTCGTGGAGTAGCAA 58.363 39.130 0.00 0.00 0.00 3.91
1447 4871 2.185387 GTGGAGTAGCAACCCCTTAGA 58.815 52.381 0.00 0.00 0.00 2.10
1461 4885 4.785376 ACCCCTTAGAACAGTTGATCTGAT 59.215 41.667 0.00 0.00 46.27 2.90
1495 4919 0.591170 CAAATCAGCCAAACGGACGT 59.409 50.000 0.00 0.00 0.00 4.34
1504 4928 2.211806 CCAAACGGACGTTTAGGAACA 58.788 47.619 20.60 0.00 45.32 3.18
1535 4960 1.305213 GGGCTGGGATTTGGCTCAA 60.305 57.895 0.00 0.00 0.00 3.02
1547 4972 6.551227 GGGATTTGGCTCAATTTTACTATCCT 59.449 38.462 0.00 0.00 0.00 3.24
1548 4973 7.724061 GGGATTTGGCTCAATTTTACTATCCTA 59.276 37.037 0.00 0.00 0.00 2.94
1549 4974 9.131791 GGATTTGGCTCAATTTTACTATCCTAA 57.868 33.333 0.00 0.00 0.00 2.69
1589 5014 7.868415 CACTATTTCCAGTCTACCTACTATTGC 59.132 40.741 0.00 0.00 0.00 3.56
1601 5026 8.537016 TCTACCTACTATTGCTGTTTACAACAT 58.463 33.333 0.00 0.00 41.26 2.71
1642 5067 1.068121 CCTCCCAACTCTCCCAACTT 58.932 55.000 0.00 0.00 0.00 2.66
1648 5074 3.319122 CCCAACTCTCCCAACTTCAAAAG 59.681 47.826 0.00 0.00 0.00 2.27
1671 5097 1.153745 GCTTCTCGCTCCACGTGAT 60.154 57.895 19.30 0.00 43.19 3.06
1756 5182 3.675225 CAGCGATCGACCGAATTAATGAT 59.325 43.478 21.57 0.00 0.00 2.45
1768 5194 7.001674 ACCGAATTAATGATGGGCTAAATACA 58.998 34.615 6.01 0.00 0.00 2.29
1787 5214 4.467198 ACATACCGTAGCTTGCTTTACT 57.533 40.909 0.00 0.00 0.00 2.24
1823 5252 6.670695 AATTTAGGCCTTTGTTTCTCACAT 57.329 33.333 12.58 0.00 34.43 3.21
2123 5618 4.644103 TCCGGTAGGAAACTAAGAATCG 57.356 45.455 0.00 0.00 46.54 3.34
2508 6045 9.118300 CTGCTGGTAAAGAGAGAATTATTTCAT 57.882 33.333 0.56 0.00 34.08 2.57
2510 6047 9.727627 GCTGGTAAAGAGAGAATTATTTCATTG 57.272 33.333 0.56 0.00 34.08 2.82
2552 7064 5.331902 CAAACTAAATATTGCCGGTGTCAG 58.668 41.667 1.90 0.00 0.00 3.51
2582 7095 3.490933 GGTGGGAGAGCTTTTTCAACAAC 60.491 47.826 0.00 0.00 0.00 3.32
2629 7142 7.655490 ACTTAGCAAGATCAATAATGAATGGC 58.345 34.615 0.00 0.00 39.49 4.40
2638 7169 5.015515 TCAATAATGAATGGCTCAACACCA 58.984 37.500 0.00 0.00 42.61 4.17
2643 7174 0.537143 AATGGCTCAACACCAAGCGA 60.537 50.000 0.00 0.00 41.49 4.93
2798 7329 9.577110 TCTTGCAAGCTTTCTATTTTGAATATG 57.423 29.630 21.99 0.00 0.00 1.78
2890 7424 1.295792 GTCAACACGAGTTTGCCTCA 58.704 50.000 0.00 0.00 40.48 3.86
2894 7428 1.967319 ACACGAGTTTGCCTCAATGT 58.033 45.000 0.00 0.00 40.48 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
2 3 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
3 4 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
4 5 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
5 6 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
6 7 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
7 8 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
8 9 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
9 10 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
10 11 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
11 12 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
12 13 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
13 14 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
14 15 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
15 16 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
16 17 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
17 18 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
18 19 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
19 20 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
20 21 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
21 22 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
22 23 0.251297 TTGTACTCCCTCCGTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
23 24 0.033796 ATTGTACTCCCTCCGTCCGA 60.034 55.000 0.00 0.00 0.00 4.55
24 25 0.822164 AATTGTACTCCCTCCGTCCG 59.178 55.000 0.00 0.00 0.00 4.79
25 26 3.055312 AGAAAATTGTACTCCCTCCGTCC 60.055 47.826 0.00 0.00 0.00 4.79
26 27 3.933332 CAGAAAATTGTACTCCCTCCGTC 59.067 47.826 0.00 0.00 0.00 4.79
27 28 3.581332 TCAGAAAATTGTACTCCCTCCGT 59.419 43.478 0.00 0.00 0.00 4.69
28 29 4.202245 TCAGAAAATTGTACTCCCTCCG 57.798 45.455 0.00 0.00 0.00 4.63
29 30 6.238648 TCTTTCAGAAAATTGTACTCCCTCC 58.761 40.000 0.00 0.00 0.00 4.30
30 31 7.929941 ATCTTTCAGAAAATTGTACTCCCTC 57.070 36.000 0.00 0.00 0.00 4.30
31 32 8.712228 AAATCTTTCAGAAAATTGTACTCCCT 57.288 30.769 0.00 0.00 0.00 4.20
32 33 8.576442 TGAAATCTTTCAGAAAATTGTACTCCC 58.424 33.333 1.28 0.00 41.88 4.30
33 34 9.965824 TTGAAATCTTTCAGAAAATTGTACTCC 57.034 29.630 5.58 0.00 46.68 3.85
48 49 8.893219 AACCTGGAAGATTTTTGAAATCTTTC 57.107 30.769 22.43 21.28 44.45 2.62
138 141 7.123355 TGGGAAATTTTGAAAGTGTGAAGAT 57.877 32.000 0.00 0.00 0.00 2.40
139 142 6.537453 TGGGAAATTTTGAAAGTGTGAAGA 57.463 33.333 0.00 0.00 0.00 2.87
140 143 7.608308 TTTGGGAAATTTTGAAAGTGTGAAG 57.392 32.000 0.00 0.00 0.00 3.02
141 144 7.609532 ACATTTGGGAAATTTTGAAAGTGTGAA 59.390 29.630 0.00 0.00 0.00 3.18
142 145 7.108847 ACATTTGGGAAATTTTGAAAGTGTGA 58.891 30.769 0.00 0.00 0.00 3.58
143 146 7.319142 ACATTTGGGAAATTTTGAAAGTGTG 57.681 32.000 0.00 0.00 0.00 3.82
144 147 7.609532 TGAACATTTGGGAAATTTTGAAAGTGT 59.390 29.630 0.00 0.00 0.00 3.55
145 148 7.909641 GTGAACATTTGGGAAATTTTGAAAGTG 59.090 33.333 0.00 0.00 0.00 3.16
146 149 7.609532 TGTGAACATTTGGGAAATTTTGAAAGT 59.390 29.630 0.00 0.00 0.00 2.66
147 150 7.909641 GTGTGAACATTTGGGAAATTTTGAAAG 59.090 33.333 0.00 0.00 0.00 2.62
148 151 7.609532 AGTGTGAACATTTGGGAAATTTTGAAA 59.390 29.630 0.00 0.00 0.00 2.69
149 152 7.108847 AGTGTGAACATTTGGGAAATTTTGAA 58.891 30.769 0.00 0.00 0.00 2.69
150 153 6.648192 AGTGTGAACATTTGGGAAATTTTGA 58.352 32.000 0.00 0.00 0.00 2.69
151 154 6.923928 AGTGTGAACATTTGGGAAATTTTG 57.076 33.333 0.00 0.00 0.00 2.44
152 155 7.609532 TGAAAGTGTGAACATTTGGGAAATTTT 59.390 29.630 0.00 0.00 0.00 1.82
153 156 7.108847 TGAAAGTGTGAACATTTGGGAAATTT 58.891 30.769 0.00 0.00 0.00 1.82
154 157 6.648192 TGAAAGTGTGAACATTTGGGAAATT 58.352 32.000 0.00 0.00 0.00 1.82
155 158 6.232581 TGAAAGTGTGAACATTTGGGAAAT 57.767 33.333 0.00 0.00 0.00 2.17
156 159 5.667539 TGAAAGTGTGAACATTTGGGAAA 57.332 34.783 0.00 0.00 0.00 3.13
157 160 5.667539 TTGAAAGTGTGAACATTTGGGAA 57.332 34.783 0.00 0.00 0.00 3.97
158 161 5.667539 TTTGAAAGTGTGAACATTTGGGA 57.332 34.783 0.00 0.00 0.00 4.37
159 162 6.734104 TTTTTGAAAGTGTGAACATTTGGG 57.266 33.333 0.00 0.00 0.00 4.12
160 163 8.200364 AGATTTTTGAAAGTGTGAACATTTGG 57.800 30.769 0.00 0.00 0.00 3.28
161 164 9.693157 GAAGATTTTTGAAAGTGTGAACATTTG 57.307 29.630 0.00 0.00 0.00 2.32
162 165 8.882736 GGAAGATTTTTGAAAGTGTGAACATTT 58.117 29.630 0.00 0.00 0.00 2.32
163 166 8.040132 TGGAAGATTTTTGAAAGTGTGAACATT 58.960 29.630 0.00 0.00 0.00 2.71
164 167 7.555087 TGGAAGATTTTTGAAAGTGTGAACAT 58.445 30.769 0.00 0.00 0.00 2.71
165 168 6.929625 TGGAAGATTTTTGAAAGTGTGAACA 58.070 32.000 0.00 0.00 0.00 3.18
166 169 6.476706 CCTGGAAGATTTTTGAAAGTGTGAAC 59.523 38.462 0.00 0.00 34.07 3.18
167 170 6.154363 ACCTGGAAGATTTTTGAAAGTGTGAA 59.846 34.615 0.00 0.00 34.07 3.18
168 171 5.656416 ACCTGGAAGATTTTTGAAAGTGTGA 59.344 36.000 0.00 0.00 34.07 3.58
169 172 5.906073 ACCTGGAAGATTTTTGAAAGTGTG 58.094 37.500 0.00 0.00 34.07 3.82
170 173 6.544928 AACCTGGAAGATTTTTGAAAGTGT 57.455 33.333 0.00 0.00 34.07 3.55
171 174 7.041107 TGAAACCTGGAAGATTTTTGAAAGTG 58.959 34.615 0.00 0.00 21.56 3.16
172 175 7.181569 TGAAACCTGGAAGATTTTTGAAAGT 57.818 32.000 0.00 0.00 21.56 2.66
173 176 8.491331 TTTGAAACCTGGAAGATTTTTGAAAG 57.509 30.769 0.00 0.00 21.56 2.62
174 177 9.460019 AATTTGAAACCTGGAAGATTTTTGAAA 57.540 25.926 0.00 0.00 21.56 2.69
175 178 9.460019 AAATTTGAAACCTGGAAGATTTTTGAA 57.540 25.926 0.00 0.00 21.56 2.69
184 187 8.928733 CATGAACATAAATTTGAAACCTGGAAG 58.071 33.333 0.00 0.00 0.00 3.46
457 3615 7.434013 CACACTTAACACTGTTTAACCAAATCC 59.566 37.037 0.00 0.00 0.00 3.01
466 3624 7.380333 CGACAGTATCACACTTAACACTGTTTA 59.620 37.037 6.63 0.00 44.79 2.01
583 3741 1.271652 TGCGGTGGCTAGGAATGAAAA 60.272 47.619 0.00 0.00 40.82 2.29
604 3762 4.333926 TGAAAAATGGCAAAAAGGGTTTCG 59.666 37.500 0.00 0.00 0.00 3.46
642 3800 3.497942 GGTCGGCCCATTATTTAGTCCAT 60.498 47.826 0.00 0.00 0.00 3.41
696 3854 3.304613 CCGTGTTTTGCGGCAAAC 58.695 55.556 26.39 20.31 42.82 2.93
872 4030 4.228097 GCATGCGCACGCGAATCT 62.228 61.111 14.53 0.00 45.51 2.40
927 4085 3.190849 CACCGCAGCTCCACATCG 61.191 66.667 0.00 0.00 0.00 3.84
964 4122 2.576053 CGATGTCGTGTCGGGACG 60.576 66.667 1.23 1.23 44.44 4.79
966 4124 2.404186 CCTCGATGTCGTGTCGGGA 61.404 63.158 7.98 0.00 42.00 5.14
1081 4256 2.594592 GGGCCAAAGCACGTCACT 60.595 61.111 4.39 0.00 42.56 3.41
1142 4317 1.294138 CCGTCCACCGCCTTCTTTA 59.706 57.895 0.00 0.00 34.38 1.85
1143 4318 2.032071 CCGTCCACCGCCTTCTTT 59.968 61.111 0.00 0.00 34.38 2.52
1160 4335 4.005472 CGGCGCCATCTTCATCGC 62.005 66.667 28.98 0.00 45.99 4.58
1189 4364 0.838987 TAACCCTCCTTGTCCGCCTT 60.839 55.000 0.00 0.00 0.00 4.35
1196 4371 1.183676 ACGCTCGTAACCCTCCTTGT 61.184 55.000 0.00 0.00 0.00 3.16
1206 4381 1.440850 CGGTCGTGAACGCTCGTAA 60.441 57.895 0.00 0.00 39.60 3.18
1247 4671 0.924090 TAGAGGATGTGGACGGGAGA 59.076 55.000 0.00 0.00 0.00 3.71
1257 4681 3.627747 GGGGCGGTCTATATAGAGGATGT 60.628 52.174 12.87 0.00 32.01 3.06
1372 4796 3.819564 ATATGTAGCCGCTTCAGACAA 57.180 42.857 0.00 0.00 0.00 3.18
1385 4809 9.132923 TCTCTAGTAAACTGGACCAATATGTAG 57.867 37.037 0.00 0.00 30.10 2.74
1406 4830 5.639506 CCACGAGAAAAATCAAAGCTCTCTA 59.360 40.000 0.00 0.00 32.13 2.43
1437 4861 4.597507 TCAGATCAACTGTTCTAAGGGGTT 59.402 41.667 0.00 0.00 45.86 4.11
1438 4862 4.168101 TCAGATCAACTGTTCTAAGGGGT 58.832 43.478 0.00 0.00 45.86 4.95
1447 4871 1.355381 TGGCCCATCAGATCAACTGTT 59.645 47.619 0.00 0.00 45.86 3.16
1461 4885 3.237746 TGATTTGATTGTTTCTGGCCCA 58.762 40.909 0.00 0.00 0.00 5.36
1504 4928 4.400251 AGCCCTCCCACGCCTAGT 62.400 66.667 0.00 0.00 0.00 2.57
1551 4976 9.461312 AGACTGGAAATAGTGTGCATTTATTTA 57.539 29.630 10.92 0.87 29.67 1.40
1552 4977 8.353423 AGACTGGAAATAGTGTGCATTTATTT 57.647 30.769 10.80 10.80 31.58 1.40
1553 4978 7.944729 AGACTGGAAATAGTGTGCATTTATT 57.055 32.000 0.00 0.00 0.00 1.40
1554 4979 7.499232 GGTAGACTGGAAATAGTGTGCATTTAT 59.501 37.037 0.00 0.00 30.03 1.40
1566 4991 7.563924 ACAGCAATAGTAGGTAGACTGGAAATA 59.436 37.037 0.00 0.00 0.00 1.40
1601 5026 4.282703 GGACTTCCGAACAAGCCCTATATA 59.717 45.833 0.00 0.00 0.00 0.86
1729 5155 0.319211 TTCGGTCGATCGCTGTTGTT 60.319 50.000 14.58 0.00 0.00 2.83
1756 5182 3.899360 AGCTACGGTATGTATTTAGCCCA 59.101 43.478 0.00 0.00 36.60 5.36
1768 5194 3.490419 CCGAGTAAAGCAAGCTACGGTAT 60.490 47.826 0.00 0.00 35.40 2.73
1800 5229 6.041979 ACATGTGAGAAACAAAGGCCTAAATT 59.958 34.615 5.16 0.00 43.61 1.82
1801 5230 5.539955 ACATGTGAGAAACAAAGGCCTAAAT 59.460 36.000 5.16 0.00 43.61 1.40
1805 5234 2.624838 CACATGTGAGAAACAAAGGCCT 59.375 45.455 21.64 0.00 43.61 5.19
1812 5241 1.569003 CGCGCACATGTGAGAAACA 59.431 52.632 30.52 0.00 44.79 2.83
2009 5504 2.665000 CCTGGCGTGATGGTGTCT 59.335 61.111 0.00 0.00 0.00 3.41
2033 5528 3.391382 GTAGACTGCCTGGCCGGT 61.391 66.667 17.53 14.92 34.25 5.28
2335 5863 9.965824 ATTAATCGGCCTGAAAATAAATACTTG 57.034 29.630 0.00 0.00 0.00 3.16
2459 5988 2.653726 AGACCACAAACTGCACATGAA 58.346 42.857 0.00 0.00 0.00 2.57
2461 5990 3.067180 AGAAAGACCACAAACTGCACATG 59.933 43.478 0.00 0.00 0.00 3.21
2508 6045 4.312443 TGCGGTTAACCAAACAAAAACAA 58.688 34.783 24.14 0.00 40.08 2.83
2510 6047 4.923264 TTGCGGTTAACCAAACAAAAAC 57.077 36.364 24.14 2.72 40.08 2.43
2552 7064 3.056313 GCTCTCCCACCAAATGCGC 62.056 63.158 0.00 0.00 0.00 6.09
2629 7142 1.269778 TGACTCTCGCTTGGTGTTGAG 60.270 52.381 0.00 0.00 0.00 3.02
2638 7169 1.002430 TGGCTTGAATGACTCTCGCTT 59.998 47.619 0.00 0.00 0.00 4.68
2643 7174 3.777106 TCAACTGGCTTGAATGACTCT 57.223 42.857 0.00 0.00 35.84 3.24
2890 7424 8.409358 AAAGAAAGACACATAAGCCTTACATT 57.591 30.769 0.00 0.00 0.00 2.71
2894 7428 6.294508 GCCAAAAGAAAGACACATAAGCCTTA 60.295 38.462 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.