Multiple sequence alignment - TraesCS7B01G295000

Loading Multiple Alignment...

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 TraesCS7B01G295000 chr7B 100.000 2393 0 0 1 2393 531663913 531666305 0.000000e+00 4420
1 TraesCS7B01G295000 chr7B 90.199 653 56 5 857 1507 531762594 531763240 0.000000e+00 845
2 TraesCS7B01G295000 chr7B 80.870 345 33 15 301 638 531761991 531762309 8.550000e-60 241
3 TraesCS7B01G295000 chr7B 95.495 111 5 0 1 111 458244579 458244689 6.800000e-41 178
4 TraesCS7B01G295000 chr7B 84.118 170 14 6 686 855 531762311 531762467 4.120000e-33 152
5 TraesCS7B01G295000 chr7B 90.566 106 8 2 1522 1626 531776916 531777020 3.210000e-29 139
6 TraesCS7B01G295000 chr7A 92.754 2208 93 24 99 2284 570122493 570124655 0.000000e+00 3129
7 TraesCS7B01G295000 chr7A 90.941 287 14 6 857 1135 570141390 570141672 2.250000e-100 375
8 TraesCS7B01G295000 chr7A 81.361 338 35 11 298 633 570140789 570141100 1.420000e-62 250
9 TraesCS7B01G295000 chr7A 97.143 105 2 1 1 105 39211143 39211040 2.440000e-40 176
10 TraesCS7B01G295000 chr7A 92.562 121 6 1 1126 1243 570143284 570143404 1.140000e-38 171
11 TraesCS7B01G295000 chr7A 84.706 170 14 5 686 855 570141106 570141263 2.460000e-35 159
12 TraesCS7B01G295000 chr7A 86.713 143 17 2 1899 2040 547552356 547552215 8.860000e-35 158
13 TraesCS7B01G295000 chr7A 91.818 110 6 2 2286 2393 570124685 570124793 1.480000e-32 150
14 TraesCS7B01G295000 chr7D 92.440 2209 100 21 100 2284 502998790 503000955 0.000000e+00 3092
15 TraesCS7B01G295000 chr7D 91.564 972 63 8 438 1407 503686493 503687447 0.000000e+00 1323
16 TraesCS7B01G295000 chr7D 88.560 507 52 4 914 1419 503146269 503146770 5.660000e-171 610
17 TraesCS7B01G295000 chr7D 84.615 637 59 9 857 1491 503295998 503296597 4.400000e-167 597
18 TraesCS7B01G295000 chr7D 89.896 386 33 6 1220 1600 503039485 503039869 2.140000e-135 492
19 TraesCS7B01G295000 chr7D 87.413 286 22 8 240 525 503089113 503089384 1.380000e-82 316
20 TraesCS7B01G295000 chr7D 84.926 272 28 2 859 1130 503039007 503039265 1.820000e-66 263
21 TraesCS7B01G295000 chr7D 81.138 334 36 14 301 632 503295401 503295709 2.380000e-60 243
22 TraesCS7B01G295000 chr7D 95.413 109 5 0 2285 2393 503000984 503001092 8.790000e-40 174
23 TraesCS7B01G295000 chr7D 92.920 113 7 1 526 638 503038624 503038735 1.900000e-36 163
24 TraesCS7B01G295000 chr7D 85.294 170 12 5 686 855 503038737 503038893 1.900000e-36 163
25 TraesCS7B01G295000 chr7D 85.294 170 10 6 686 855 503295717 503295871 6.850000e-36 161
26 TraesCS7B01G295000 chr7D 79.498 239 22 10 301 538 503030922 503031134 6.890000e-31 145
27 TraesCS7B01G295000 chr3D 94.669 544 25 2 445 986 141837444 141836903 0.000000e+00 841
28 TraesCS7B01G295000 chr3D 98.095 105 1 1 1 105 147686938 147686835 5.250000e-42 182
29 TraesCS7B01G295000 chr1A 81.172 239 37 7 1904 2138 336216130 336216364 4.060000e-43 185
30 TraesCS7B01G295000 chr5D 98.077 104 2 0 1 104 484573688 484573585 5.250000e-42 182
31 TraesCS7B01G295000 chr5D 97.059 102 3 0 1 102 446762604 446762705 3.160000e-39 172
32 TraesCS7B01G295000 chr4D 98.058 103 2 0 1 103 46587121 46587019 1.890000e-41 180
33 TraesCS7B01G295000 chr5A 98.039 102 2 0 1 102 43664381 43664482 6.800000e-41 178
34 TraesCS7B01G295000 chr5A 98.039 102 2 0 1 102 43704274 43704375 6.800000e-41 178
35 TraesCS7B01G295000 chr2A 98.039 102 2 0 1 102 637229625 637229726 6.800000e-41 178
36 TraesCS7B01G295000 chr1B 79.237 236 43 5 1904 2138 346406839 346407069 2.460000e-35 159


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 TraesCS7B01G295000 chr7B 531663913 531666305 2392 False 4420.000000 4420 100.000000 1 2393 1 chr7B.!!$F2 2392
1 TraesCS7B01G295000 chr7B 531761991 531763240 1249 False 412.666667 845 85.062333 301 1507 3 chr7B.!!$F4 1206
2 TraesCS7B01G295000 chr7A 570122493 570124793 2300 False 1639.500000 3129 92.286000 99 2393 2 chr7A.!!$F1 2294
3 TraesCS7B01G295000 chr7A 570140789 570143404 2615 False 238.750000 375 87.392500 298 1243 4 chr7A.!!$F2 945
4 TraesCS7B01G295000 chr7D 502998790 503001092 2302 False 1633.000000 3092 93.926500 100 2393 2 chr7D.!!$F5 2293
5 TraesCS7B01G295000 chr7D 503686493 503687447 954 False 1323.000000 1323 91.564000 438 1407 1 chr7D.!!$F4 969
6 TraesCS7B01G295000 chr7D 503146269 503146770 501 False 610.000000 610 88.560000 914 1419 1 chr7D.!!$F3 505
7 TraesCS7B01G295000 chr7D 503295401 503296597 1196 False 333.666667 597 83.682333 301 1491 3 chr7D.!!$F7 1190
8 TraesCS7B01G295000 chr7D 503038624 503039869 1245 False 270.250000 492 88.259000 526 1600 4 chr7D.!!$F6 1074
9 TraesCS7B01G295000 chr3D 141836903 141837444 541 True 841.000000 841 94.669000 445 986 1 chr3D.!!$R1 541

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
200 201 0.108138 CTAGCCTTGACCTTCACCGG 60.108 60.0 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 3549 0.10741 ACACGGGAGCACACAGAAAA 60.107 50.0 0.0 0.0 0.0 2.29 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
26 27 8.892723 AGGCTTCTAAAAAGAAAATTTTGGTTG 58.107 29.630 8.47 0.00 33.84 3.77
27 28 8.128582 GGCTTCTAAAAAGAAAATTTTGGTTGG 58.871 33.333 8.47 0.00 33.84 3.77
28 29 8.128582 GCTTCTAAAAAGAAAATTTTGGTTGGG 58.871 33.333 8.47 0.00 33.84 4.12
29 30 7.561021 TCTAAAAAGAAAATTTTGGTTGGGC 57.439 32.000 8.47 0.00 33.84 5.36
30 31 7.342581 TCTAAAAAGAAAATTTTGGTTGGGCT 58.657 30.769 8.47 0.00 33.84 5.19
31 32 6.849085 AAAAAGAAAATTTTGGTTGGGCTT 57.151 29.167 8.47 0.70 31.55 4.35
32 33 6.449635 AAAAGAAAATTTTGGTTGGGCTTC 57.550 33.333 8.47 0.00 0.00 3.86
33 34 5.372343 AAGAAAATTTTGGTTGGGCTTCT 57.628 34.783 8.47 0.00 0.00 2.85
34 35 6.493189 AAGAAAATTTTGGTTGGGCTTCTA 57.507 33.333 8.47 0.00 0.00 2.10
35 36 6.101650 AGAAAATTTTGGTTGGGCTTCTAG 57.898 37.500 8.47 0.00 0.00 2.43
36 37 5.838521 AGAAAATTTTGGTTGGGCTTCTAGA 59.161 36.000 8.47 0.00 0.00 2.43
37 38 6.326323 AGAAAATTTTGGTTGGGCTTCTAGAA 59.674 34.615 8.47 4.81 0.00 2.10
38 39 6.686484 AAATTTTGGTTGGGCTTCTAGAAT 57.314 33.333 5.44 0.00 0.00 2.40
39 40 7.790782 AAATTTTGGTTGGGCTTCTAGAATA 57.209 32.000 5.44 0.00 0.00 1.75
40 41 7.790782 AATTTTGGTTGGGCTTCTAGAATAA 57.209 32.000 5.44 0.00 0.00 1.40
41 42 6.834168 TTTTGGTTGGGCTTCTAGAATAAG 57.166 37.500 5.44 0.00 0.00 1.73
42 43 3.886123 TGGTTGGGCTTCTAGAATAAGC 58.114 45.455 5.44 5.98 46.90 3.09
43 44 3.523564 TGGTTGGGCTTCTAGAATAAGCT 59.476 43.478 13.28 0.00 46.81 3.74
44 45 3.879892 GGTTGGGCTTCTAGAATAAGCTG 59.120 47.826 13.28 0.00 46.81 4.24
45 46 3.845781 TGGGCTTCTAGAATAAGCTGG 57.154 47.619 13.28 0.00 46.81 4.85
46 47 2.439507 TGGGCTTCTAGAATAAGCTGGG 59.560 50.000 13.28 0.00 46.81 4.45
47 48 2.439880 GGGCTTCTAGAATAAGCTGGGT 59.560 50.000 13.28 0.00 46.81 4.51
48 49 3.646637 GGGCTTCTAGAATAAGCTGGGTA 59.353 47.826 13.28 0.00 46.81 3.69
49 50 4.262678 GGGCTTCTAGAATAAGCTGGGTAG 60.263 50.000 13.28 0.00 46.81 3.18
50 51 4.262678 GGCTTCTAGAATAAGCTGGGTAGG 60.263 50.000 13.28 0.00 46.81 3.18
51 52 4.262678 GCTTCTAGAATAAGCTGGGTAGGG 60.263 50.000 5.44 0.00 44.75 3.53
52 53 3.858135 TCTAGAATAAGCTGGGTAGGGG 58.142 50.000 0.00 0.00 0.00 4.79
53 54 1.821088 AGAATAAGCTGGGTAGGGGG 58.179 55.000 0.00 0.00 0.00 5.40
54 55 0.110678 GAATAAGCTGGGTAGGGGGC 59.889 60.000 0.00 0.00 0.00 5.80
55 56 0.626277 AATAAGCTGGGTAGGGGGCA 60.626 55.000 0.00 0.00 0.00 5.36
56 57 1.062488 ATAAGCTGGGTAGGGGGCAG 61.062 60.000 0.00 0.00 0.00 4.85
59 60 3.017581 CTGGGTAGGGGGCAGCTT 61.018 66.667 0.00 0.00 0.00 3.74
60 61 1.692749 CTGGGTAGGGGGCAGCTTA 60.693 63.158 0.00 0.00 0.00 3.09
61 62 1.005556 TGGGTAGGGGGCAGCTTAT 59.994 57.895 0.00 0.00 0.00 1.73
62 63 0.626277 TGGGTAGGGGGCAGCTTATT 60.626 55.000 0.00 0.00 0.00 1.40
63 64 0.110678 GGGTAGGGGGCAGCTTATTC 59.889 60.000 0.00 0.00 0.00 1.75
64 65 0.843984 GGTAGGGGGCAGCTTATTCA 59.156 55.000 0.00 0.00 0.00 2.57
65 66 1.202818 GGTAGGGGGCAGCTTATTCAG 60.203 57.143 0.00 0.00 0.00 3.02
66 67 1.140312 TAGGGGGCAGCTTATTCAGG 58.860 55.000 0.00 0.00 0.00 3.86
67 68 0.624500 AGGGGGCAGCTTATTCAGGA 60.625 55.000 0.00 0.00 0.00 3.86
68 69 0.258774 GGGGGCAGCTTATTCAGGAA 59.741 55.000 0.00 0.00 0.00 3.36
69 70 1.685148 GGGGCAGCTTATTCAGGAAG 58.315 55.000 0.00 0.00 0.00 3.46
77 78 4.535526 GCTTATTCAGGAAGCCCAAAAA 57.464 40.909 0.00 0.00 42.90 1.94
96 97 3.650070 AAAGCTAGCAAAAGAACTGGC 57.350 42.857 18.83 0.00 40.38 4.85
97 98 1.539157 AGCTAGCAAAAGAACTGGCC 58.461 50.000 18.83 0.00 40.92 5.36
117 118 5.654650 TGGCCCTTAATTTCGTAATGTTCAT 59.345 36.000 0.00 0.00 0.00 2.57
120 121 7.132863 GCCCTTAATTTCGTAATGTTCATCTC 58.867 38.462 0.00 0.00 0.00 2.75
171 172 6.017109 ACCTGTTTGCTTCAAGTTGTATACTG 60.017 38.462 4.17 0.00 37.12 2.74
197 198 0.393132 GGGCTAGCCTTGACCTTCAC 60.393 60.000 32.18 8.62 36.10 3.18
198 199 0.393132 GGCTAGCCTTGACCTTCACC 60.393 60.000 27.17 0.00 0.00 4.02
200 201 0.108138 CTAGCCTTGACCTTCACCGG 60.108 60.000 0.00 0.00 0.00 5.28
228 229 5.105837 GGCGGTACCTTCTCTATATACCAAG 60.106 48.000 10.90 0.00 35.95 3.61
265 266 5.248870 ACTAGTGTCAGCAAAAAGGTTTG 57.751 39.130 0.00 0.00 45.88 2.93
367 368 2.025981 TGCATTGGATTAGCTCCTGTGT 60.026 45.455 0.00 0.00 45.21 3.72
738 761 1.342819 CATAGGCTGACCACCTCTAGC 59.657 57.143 0.00 0.00 38.81 3.42
805 829 5.740513 GCTTACATAGATCCAGTGTTCCCTC 60.741 48.000 1.25 0.00 0.00 4.30
851 875 3.270027 CGCAAGTTGGACCATCTTATCA 58.730 45.455 15.88 0.00 0.00 2.15
855 879 5.449588 GCAAGTTGGACCATCTTATCATGTG 60.450 44.000 15.88 5.82 0.00 3.21
875 1027 7.443879 TCATGTGTATTTTGTTTCTGACTGCTA 59.556 33.333 0.00 0.00 0.00 3.49
956 1117 9.433317 GTGTTAAAAATACGATATGTCATGGTG 57.567 33.333 0.00 0.00 0.00 4.17
1095 1257 0.888619 TACTGACAGTTGCTCCTCCG 59.111 55.000 14.50 0.00 0.00 4.63
1585 3555 3.336122 AGCAGTGCTCCCTTTTCTG 57.664 52.632 13.14 0.00 30.62 3.02
1586 3556 0.475906 AGCAGTGCTCCCTTTTCTGT 59.524 50.000 13.14 0.00 30.62 3.41
1587 3557 0.595095 GCAGTGCTCCCTTTTCTGTG 59.405 55.000 8.18 0.00 0.00 3.66
1588 3558 1.972872 CAGTGCTCCCTTTTCTGTGT 58.027 50.000 0.00 0.00 0.00 3.72
1589 3559 1.605710 CAGTGCTCCCTTTTCTGTGTG 59.394 52.381 0.00 0.00 0.00 3.82
1590 3560 0.312102 GTGCTCCCTTTTCTGTGTGC 59.688 55.000 0.00 0.00 0.00 4.57
1591 3561 0.183492 TGCTCCCTTTTCTGTGTGCT 59.817 50.000 0.00 0.00 0.00 4.40
1592 3562 0.877743 GCTCCCTTTTCTGTGTGCTC 59.122 55.000 0.00 0.00 0.00 4.26
1593 3563 1.528129 CTCCCTTTTCTGTGTGCTCC 58.472 55.000 0.00 0.00 0.00 4.70
1594 3564 0.110486 TCCCTTTTCTGTGTGCTCCC 59.890 55.000 0.00 0.00 0.00 4.30
1652 3622 3.003689 AGCTTTGCGGCAATGTATCATAC 59.996 43.478 23.97 10.03 34.17 2.39
1660 3630 4.393062 CGGCAATGTATCATACCCATTCTC 59.607 45.833 0.00 0.00 0.00 2.87
1683 3654 5.012046 TCACTGGTGAGATCTGTGTGTTATT 59.988 40.000 0.00 0.00 36.12 1.40
1684 3655 5.349817 CACTGGTGAGATCTGTGTGTTATTC 59.650 44.000 0.00 0.00 32.04 1.75
1686 3657 6.114187 TGGTGAGATCTGTGTGTTATTCTT 57.886 37.500 0.00 0.00 0.00 2.52
1687 3658 6.533730 TGGTGAGATCTGTGTGTTATTCTTT 58.466 36.000 0.00 0.00 0.00 2.52
1688 3659 6.998074 TGGTGAGATCTGTGTGTTATTCTTTT 59.002 34.615 0.00 0.00 0.00 2.27
1689 3660 7.502226 TGGTGAGATCTGTGTGTTATTCTTTTT 59.498 33.333 0.00 0.00 0.00 1.94
1690 3661 8.999431 GGTGAGATCTGTGTGTTATTCTTTTTA 58.001 33.333 0.00 0.00 0.00 1.52
1718 3710 3.017442 GGAAGGCTGACTAAATGGGTTC 58.983 50.000 0.00 0.00 0.00 3.62
1729 3721 5.623169 ACTAAATGGGTTCACCGACTAAAA 58.377 37.500 0.00 0.00 44.64 1.52
1730 3722 6.063404 ACTAAATGGGTTCACCGACTAAAAA 58.937 36.000 0.00 0.00 44.64 1.94
1768 3760 1.164411 TATCCACAAAAGGCACAGCG 58.836 50.000 0.00 0.00 0.00 5.18
1805 3797 6.957631 TGCTAATGAAATTACAGGGAGAGAA 58.042 36.000 0.00 0.00 37.87 2.87
1831 3823 7.812690 TCAAATGGTATTGGATCAGAATCAG 57.187 36.000 0.00 0.00 33.21 2.90
1847 3839 4.156739 AGAATCAGGCGTTCTTGATTTTCC 59.843 41.667 4.54 0.00 32.17 3.13
1848 3840 3.140325 TCAGGCGTTCTTGATTTTCCT 57.860 42.857 0.00 0.00 0.00 3.36
1851 3843 3.375299 CAGGCGTTCTTGATTTTCCTAGG 59.625 47.826 0.82 0.82 0.00 3.02
1882 3874 7.267128 GCATCAAATGGTATTTGGATCAGAAA 58.733 34.615 12.72 0.00 0.00 2.52
2002 3994 7.174253 TGTTTAGTTTGCATATTCGAGTTCCTT 59.826 33.333 0.00 0.00 0.00 3.36
2003 3995 5.551760 AGTTTGCATATTCGAGTTCCTTG 57.448 39.130 0.00 0.00 0.00 3.61
2101 4095 8.028938 CCTGTTAAAACTTGGTAGGAATGAATG 58.971 37.037 0.00 0.00 0.00 2.67
2155 4149 4.875544 TCAAACTGTCTTTTGAACCTCG 57.124 40.909 0.00 0.00 41.48 4.63
2169 4163 4.255301 TGAACCTCGCCATTAACGTTAAT 58.745 39.130 24.43 24.43 33.82 1.40
2170 4164 4.696402 TGAACCTCGCCATTAACGTTAATT 59.304 37.500 26.87 13.50 31.28 1.40
2171 4165 5.873712 TGAACCTCGCCATTAACGTTAATTA 59.126 36.000 26.87 13.88 31.28 1.40
2172 4166 6.370994 TGAACCTCGCCATTAACGTTAATTAA 59.629 34.615 26.87 13.58 31.28 1.40
2177 4171 6.047870 TCGCCATTAACGTTAATTAAGGCTA 58.952 36.000 34.50 28.36 36.83 3.93
2184 4178 6.997239 AACGTTAATTAAGGCTAAAGGGAG 57.003 37.500 15.94 0.00 0.00 4.30
2229 4233 3.687321 ATCGCGGTGCAATGCTCCT 62.687 57.895 21.88 2.63 39.70 3.69
2340 4372 4.633565 GCTTTGGTCGATCAATCTCTTCTT 59.366 41.667 12.77 0.00 0.00 2.52
2346 4378 5.163457 GGTCGATCAATCTCTTCTTCCTTCT 60.163 44.000 0.00 0.00 0.00 2.85
2387 4420 3.046390 CGCTGCTATTTTCTAGGACTCG 58.954 50.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.128582 CCCAACCAAAATTTTCTTTTTAGAAGC 58.871 33.333 0.00 0.00 0.00 3.86
3 4 8.128582 GCCCAACCAAAATTTTCTTTTTAGAAG 58.871 33.333 0.00 0.00 0.00 2.85
5 6 7.342581 AGCCCAACCAAAATTTTCTTTTTAGA 58.657 30.769 0.00 0.00 0.00 2.10
6 7 7.566760 AGCCCAACCAAAATTTTCTTTTTAG 57.433 32.000 0.00 0.00 0.00 1.85
7 8 7.831690 AGAAGCCCAACCAAAATTTTCTTTTTA 59.168 29.630 0.00 0.00 0.00 1.52
8 9 6.663093 AGAAGCCCAACCAAAATTTTCTTTTT 59.337 30.769 0.00 0.00 0.00 1.94
9 10 6.186957 AGAAGCCCAACCAAAATTTTCTTTT 58.813 32.000 0.00 0.00 0.00 2.27
10 11 5.754782 AGAAGCCCAACCAAAATTTTCTTT 58.245 33.333 0.00 0.00 0.00 2.52
11 12 5.372343 AGAAGCCCAACCAAAATTTTCTT 57.628 34.783 0.00 0.00 0.00 2.52
12 13 5.838521 TCTAGAAGCCCAACCAAAATTTTCT 59.161 36.000 0.00 0.00 0.00 2.52
13 14 6.096673 TCTAGAAGCCCAACCAAAATTTTC 57.903 37.500 0.00 0.00 0.00 2.29
14 15 6.493189 TTCTAGAAGCCCAACCAAAATTTT 57.507 33.333 0.00 0.00 0.00 1.82
15 16 6.686484 ATTCTAGAAGCCCAACCAAAATTT 57.314 33.333 11.53 0.00 0.00 1.82
16 17 7.579531 GCTTATTCTAGAAGCCCAACCAAAATT 60.580 37.037 11.53 0.00 42.90 1.82
17 18 6.127338 GCTTATTCTAGAAGCCCAACCAAAAT 60.127 38.462 11.53 0.00 42.90 1.82
18 19 5.185056 GCTTATTCTAGAAGCCCAACCAAAA 59.815 40.000 11.53 0.00 42.90 2.44
19 20 4.705023 GCTTATTCTAGAAGCCCAACCAAA 59.295 41.667 11.53 0.00 42.90 3.28
20 21 4.270008 GCTTATTCTAGAAGCCCAACCAA 58.730 43.478 11.53 0.00 42.90 3.67
21 22 3.886123 GCTTATTCTAGAAGCCCAACCA 58.114 45.455 11.53 0.00 42.90 3.67
29 30 4.284746 CCCCTACCCAGCTTATTCTAGAAG 59.715 50.000 11.53 0.00 0.00 2.85
30 31 4.232091 CCCCTACCCAGCTTATTCTAGAA 58.768 47.826 7.82 7.82 0.00 2.10
31 32 3.439558 CCCCCTACCCAGCTTATTCTAGA 60.440 52.174 0.00 0.00 0.00 2.43
32 33 2.907042 CCCCCTACCCAGCTTATTCTAG 59.093 54.545 0.00 0.00 0.00 2.43
33 34 2.986050 CCCCCTACCCAGCTTATTCTA 58.014 52.381 0.00 0.00 0.00 2.10
34 35 1.821088 CCCCCTACCCAGCTTATTCT 58.179 55.000 0.00 0.00 0.00 2.40
35 36 0.110678 GCCCCCTACCCAGCTTATTC 59.889 60.000 0.00 0.00 0.00 1.75
36 37 0.626277 TGCCCCCTACCCAGCTTATT 60.626 55.000 0.00 0.00 0.00 1.40
37 38 1.005556 TGCCCCCTACCCAGCTTAT 59.994 57.895 0.00 0.00 0.00 1.73
38 39 1.692749 CTGCCCCCTACCCAGCTTA 60.693 63.158 0.00 0.00 0.00 3.09
39 40 3.017581 CTGCCCCCTACCCAGCTT 61.018 66.667 0.00 0.00 0.00 3.74
42 43 1.062488 ATAAGCTGCCCCCTACCCAG 61.062 60.000 0.00 0.00 0.00 4.45
43 44 0.626277 AATAAGCTGCCCCCTACCCA 60.626 55.000 0.00 0.00 0.00 4.51
44 45 0.110678 GAATAAGCTGCCCCCTACCC 59.889 60.000 0.00 0.00 0.00 3.69
45 46 0.843984 TGAATAAGCTGCCCCCTACC 59.156 55.000 0.00 0.00 0.00 3.18
46 47 1.202818 CCTGAATAAGCTGCCCCCTAC 60.203 57.143 0.00 0.00 0.00 3.18
47 48 1.140312 CCTGAATAAGCTGCCCCCTA 58.860 55.000 0.00 0.00 0.00 3.53
48 49 0.624500 TCCTGAATAAGCTGCCCCCT 60.625 55.000 0.00 0.00 0.00 4.79
49 50 0.258774 TTCCTGAATAAGCTGCCCCC 59.741 55.000 0.00 0.00 0.00 5.40
50 51 1.685148 CTTCCTGAATAAGCTGCCCC 58.315 55.000 0.00 0.00 0.00 5.80
51 52 1.028130 GCTTCCTGAATAAGCTGCCC 58.972 55.000 0.00 0.00 44.75 5.36
52 53 1.028130 GGCTTCCTGAATAAGCTGCC 58.972 55.000 7.65 0.00 46.81 4.85
53 54 1.028130 GGGCTTCCTGAATAAGCTGC 58.972 55.000 7.65 0.00 46.81 5.25
54 55 2.425143 TGGGCTTCCTGAATAAGCTG 57.575 50.000 7.65 0.00 46.81 4.24
55 56 3.456380 TTTGGGCTTCCTGAATAAGCT 57.544 42.857 7.65 0.00 46.81 3.74
56 57 4.535526 TTTTTGGGCTTCCTGAATAAGC 57.464 40.909 0.00 0.00 46.90 3.09
74 75 4.371786 GCCAGTTCTTTTGCTAGCTTTTT 58.628 39.130 17.23 0.00 0.00 1.94
75 76 3.243873 GGCCAGTTCTTTTGCTAGCTTTT 60.244 43.478 17.23 0.00 0.00 2.27
76 77 2.297315 GGCCAGTTCTTTTGCTAGCTTT 59.703 45.455 17.23 0.00 0.00 3.51
77 78 1.889170 GGCCAGTTCTTTTGCTAGCTT 59.111 47.619 17.23 0.00 0.00 3.74
78 79 1.539157 GGCCAGTTCTTTTGCTAGCT 58.461 50.000 17.23 0.00 0.00 3.32
79 80 0.528017 GGGCCAGTTCTTTTGCTAGC 59.472 55.000 8.10 8.10 0.00 3.42
80 81 2.206576 AGGGCCAGTTCTTTTGCTAG 57.793 50.000 6.18 0.00 0.00 3.42
81 82 2.675658 AAGGGCCAGTTCTTTTGCTA 57.324 45.000 6.18 0.00 0.00 3.49
82 83 2.675658 TAAGGGCCAGTTCTTTTGCT 57.324 45.000 6.18 0.00 0.00 3.91
83 84 3.961480 ATTAAGGGCCAGTTCTTTTGC 57.039 42.857 6.18 0.00 0.00 3.68
84 85 4.923281 CGAAATTAAGGGCCAGTTCTTTTG 59.077 41.667 6.18 0.00 0.00 2.44
85 86 4.587262 ACGAAATTAAGGGCCAGTTCTTTT 59.413 37.500 6.18 1.23 0.00 2.27
86 87 4.149598 ACGAAATTAAGGGCCAGTTCTTT 58.850 39.130 6.18 0.00 0.00 2.52
87 88 3.763057 ACGAAATTAAGGGCCAGTTCTT 58.237 40.909 6.18 0.29 0.00 2.52
88 89 3.434940 ACGAAATTAAGGGCCAGTTCT 57.565 42.857 6.18 0.00 0.00 3.01
89 90 5.124936 ACATTACGAAATTAAGGGCCAGTTC 59.875 40.000 6.18 0.00 0.00 3.01
90 91 5.014202 ACATTACGAAATTAAGGGCCAGTT 58.986 37.500 6.18 0.00 0.00 3.16
91 92 4.595986 ACATTACGAAATTAAGGGCCAGT 58.404 39.130 6.18 0.00 0.00 4.00
92 93 5.124776 TGAACATTACGAAATTAAGGGCCAG 59.875 40.000 6.18 0.00 0.00 4.85
93 94 5.010933 TGAACATTACGAAATTAAGGGCCA 58.989 37.500 6.18 0.00 0.00 5.36
94 95 5.570234 TGAACATTACGAAATTAAGGGCC 57.430 39.130 0.00 0.00 0.00 5.80
95 96 7.027778 AGATGAACATTACGAAATTAAGGGC 57.972 36.000 0.00 0.00 0.00 5.19
96 97 7.345192 CGAGATGAACATTACGAAATTAAGGG 58.655 38.462 0.00 0.00 0.00 3.95
97 98 7.345192 CCGAGATGAACATTACGAAATTAAGG 58.655 38.462 12.76 0.00 0.00 2.69
117 118 1.048601 ACTGAGGTTTCTTGCCGAGA 58.951 50.000 0.00 0.00 0.00 4.04
120 121 1.308998 AACACTGAGGTTTCTTGCCG 58.691 50.000 0.00 0.00 0.00 5.69
171 172 1.077429 CAAGGCTAGCCCCCAACTC 60.077 63.158 30.42 2.38 36.58 3.01
200 201 1.660560 TAGAGAAGGTACCGCCGTGC 61.661 60.000 6.18 0.00 43.70 5.34
204 205 4.338879 TGGTATATAGAGAAGGTACCGCC 58.661 47.826 6.18 2.12 38.07 6.13
205 206 5.105837 CCTTGGTATATAGAGAAGGTACCGC 60.106 48.000 6.18 2.72 38.07 5.68
206 207 5.418209 CCCTTGGTATATAGAGAAGGTACCG 59.582 48.000 6.18 0.00 38.07 4.02
207 208 6.559429 TCCCTTGGTATATAGAGAAGGTACC 58.441 44.000 2.73 2.73 36.26 3.34
208 209 7.240167 ACTCCCTTGGTATATAGAGAAGGTAC 58.760 42.308 11.07 0.00 32.72 3.34
209 210 7.417811 ACTCCCTTGGTATATAGAGAAGGTA 57.582 40.000 11.07 0.00 32.72 3.08
228 229 5.221581 TGACACTAGTTTCTGGTTTACTCCC 60.222 44.000 10.27 0.00 0.00 4.30
265 266 5.296780 TGTTTGAGGACAGAAACATGACTTC 59.703 40.000 0.00 1.72 31.06 3.01
400 401 8.709386 AGTAAGAGTACAAATATGCAACTCTG 57.291 34.615 14.10 2.31 45.41 3.35
638 648 0.833287 AGGCTGGTGCTCATTATCGT 59.167 50.000 0.00 0.00 39.59 3.73
738 761 2.159310 CCAGAGCTTCTCTAAGTGGTCG 60.159 54.545 0.00 0.00 38.99 4.79
762 786 3.825328 AGCATGATACATGGGGTCTTTC 58.175 45.455 12.56 0.00 0.00 2.62
829 853 1.448985 TAAGATGGTCCAACTTGCGC 58.551 50.000 21.43 0.00 29.69 6.09
851 875 6.639632 AGCAGTCAGAAACAAAATACACAT 57.360 33.333 0.00 0.00 0.00 3.21
875 1027 5.743636 ACAACCAAAATGTGCCAGATTAT 57.256 34.783 0.00 0.00 0.00 1.28
932 1085 9.864034 CTCACCATGACATATCGTATTTTTAAC 57.136 33.333 0.00 0.00 0.00 2.01
933 1086 9.051679 CCTCACCATGACATATCGTATTTTTAA 57.948 33.333 0.00 0.00 0.00 1.52
939 1092 4.160329 ACCCTCACCATGACATATCGTAT 58.840 43.478 0.00 0.00 0.00 3.06
956 1117 3.314541 TCAGCGTTAAAAGAGACCCTC 57.685 47.619 0.00 0.00 0.00 4.30
1579 3549 0.107410 ACACGGGAGCACACAGAAAA 60.107 50.000 0.00 0.00 0.00 2.29
1580 3550 0.531974 GACACGGGAGCACACAGAAA 60.532 55.000 0.00 0.00 0.00 2.52
1581 3551 1.069090 GACACGGGAGCACACAGAA 59.931 57.895 0.00 0.00 0.00 3.02
1582 3552 2.734591 GACACGGGAGCACACAGA 59.265 61.111 0.00 0.00 0.00 3.41
1583 3553 2.357517 GGACACGGGAGCACACAG 60.358 66.667 0.00 0.00 0.00 3.66
1584 3554 2.449031 GATGGACACGGGAGCACACA 62.449 60.000 0.00 0.00 0.00 3.72
1585 3555 1.741770 GATGGACACGGGAGCACAC 60.742 63.158 0.00 0.00 0.00 3.82
1586 3556 1.480212 AAGATGGACACGGGAGCACA 61.480 55.000 0.00 0.00 0.00 4.57
1587 3557 0.741221 GAAGATGGACACGGGAGCAC 60.741 60.000 0.00 0.00 0.00 4.40
1588 3558 1.596934 GAAGATGGACACGGGAGCA 59.403 57.895 0.00 0.00 0.00 4.26
1589 3559 1.519455 CGAAGATGGACACGGGAGC 60.519 63.158 0.00 0.00 0.00 4.70
1590 3560 1.141881 CCGAAGATGGACACGGGAG 59.858 63.158 0.00 0.00 41.41 4.30
1591 3561 3.014085 GCCGAAGATGGACACGGGA 62.014 63.158 0.00 0.00 44.61 5.14
1592 3562 1.672854 TAGCCGAAGATGGACACGGG 61.673 60.000 0.00 0.00 44.61 5.28
1593 3563 0.389391 ATAGCCGAAGATGGACACGG 59.611 55.000 0.00 0.00 46.74 4.94
1594 3564 1.067060 TCATAGCCGAAGATGGACACG 59.933 52.381 0.00 0.00 0.00 4.49
1660 3630 2.827800 ACACACAGATCTCACCAGTG 57.172 50.000 8.23 8.23 36.34 3.66
1683 3654 4.039973 TCAGCCTTCCGAGACTTAAAAAGA 59.960 41.667 0.00 0.00 0.00 2.52
1684 3655 4.152580 GTCAGCCTTCCGAGACTTAAAAAG 59.847 45.833 0.00 0.00 0.00 2.27
1686 3657 3.323979 AGTCAGCCTTCCGAGACTTAAAA 59.676 43.478 0.00 0.00 38.08 1.52
1687 3658 2.897969 AGTCAGCCTTCCGAGACTTAAA 59.102 45.455 0.00 0.00 38.08 1.52
1688 3659 2.526432 AGTCAGCCTTCCGAGACTTAA 58.474 47.619 0.00 0.00 38.08 1.85
1689 3660 2.217510 AGTCAGCCTTCCGAGACTTA 57.782 50.000 0.00 0.00 38.08 2.24
1690 3661 2.217510 TAGTCAGCCTTCCGAGACTT 57.782 50.000 0.00 0.00 41.27 3.01
1691 3662 2.217510 TTAGTCAGCCTTCCGAGACT 57.782 50.000 0.00 0.00 43.25 3.24
1737 3729 8.664992 TGCCTTTTGTGGATAACTGGATATATA 58.335 33.333 0.00 0.00 0.00 0.86
1738 3730 7.448469 GTGCCTTTTGTGGATAACTGGATATAT 59.552 37.037 0.00 0.00 0.00 0.86
1739 3731 6.770785 GTGCCTTTTGTGGATAACTGGATATA 59.229 38.462 0.00 0.00 0.00 0.86
1741 3733 4.947388 GTGCCTTTTGTGGATAACTGGATA 59.053 41.667 0.00 0.00 0.00 2.59
1742 3734 3.763897 GTGCCTTTTGTGGATAACTGGAT 59.236 43.478 0.00 0.00 0.00 3.41
1743 3735 3.153919 GTGCCTTTTGTGGATAACTGGA 58.846 45.455 0.00 0.00 0.00 3.86
1744 3736 2.890311 TGTGCCTTTTGTGGATAACTGG 59.110 45.455 0.00 0.00 0.00 4.00
1745 3737 3.612479 GCTGTGCCTTTTGTGGATAACTG 60.612 47.826 0.00 0.00 0.00 3.16
1746 3738 2.558359 GCTGTGCCTTTTGTGGATAACT 59.442 45.455 0.00 0.00 0.00 2.24
1747 3739 2.668279 CGCTGTGCCTTTTGTGGATAAC 60.668 50.000 0.00 0.00 0.00 1.89
1748 3740 1.539388 CGCTGTGCCTTTTGTGGATAA 59.461 47.619 0.00 0.00 0.00 1.75
1749 3741 1.164411 CGCTGTGCCTTTTGTGGATA 58.836 50.000 0.00 0.00 0.00 2.59
1750 3742 0.823356 ACGCTGTGCCTTTTGTGGAT 60.823 50.000 0.00 0.00 0.00 3.41
1805 3797 8.771521 TGATTCTGATCCAATACCATTTGATT 57.228 30.769 0.00 0.00 0.00 2.57
1831 3823 2.683362 CCCTAGGAAAATCAAGAACGCC 59.317 50.000 11.48 0.00 0.00 5.68
1847 3839 2.092212 ACCATTTGATGCCTGTCCCTAG 60.092 50.000 0.00 0.00 0.00 3.02
1848 3840 1.922447 ACCATTTGATGCCTGTCCCTA 59.078 47.619 0.00 0.00 0.00 3.53
1851 3843 4.441913 CCAAATACCATTTGATGCCTGTCC 60.442 45.833 12.13 0.00 0.00 4.02
1882 3874 0.250513 GTCACAAATCGCCTCCCTCT 59.749 55.000 0.00 0.00 0.00 3.69
1995 3987 1.705873 AGACCTCGTCACAAGGAACT 58.294 50.000 0.00 0.00 37.35 3.01
2002 3994 5.849510 TCTTATTTCAAAGACCTCGTCACA 58.150 37.500 0.00 0.00 34.60 3.58
2003 3995 6.590292 TGATCTTATTTCAAAGACCTCGTCAC 59.410 38.462 0.00 0.00 38.28 3.67
2061 4055 7.312899 AGTTTTAACAGGTCAAACTTTGTGAG 58.687 34.615 1.44 0.00 37.44 3.51
2155 4149 7.646526 CCTTTAGCCTTAATTAACGTTAATGGC 59.353 37.037 33.04 33.04 37.70 4.40
2169 4163 3.799432 TGCAACTCCCTTTAGCCTTAA 57.201 42.857 0.00 0.00 0.00 1.85
2170 4164 3.561313 CCTTGCAACTCCCTTTAGCCTTA 60.561 47.826 0.00 0.00 0.00 2.69
2171 4165 2.519013 CTTGCAACTCCCTTTAGCCTT 58.481 47.619 0.00 0.00 0.00 4.35
2172 4166 1.272147 CCTTGCAACTCCCTTTAGCCT 60.272 52.381 0.00 0.00 0.00 4.58
2177 4171 3.243359 TGATTCCTTGCAACTCCCTTT 57.757 42.857 0.00 0.00 0.00 3.11
2215 4219 3.818787 GCCAGGAGCATTGCACCG 61.819 66.667 17.76 12.88 43.81 4.94
2263 4267 0.033109 ATTCCCAAGGGCTTACAGGC 60.033 55.000 0.00 0.00 40.51 4.85
2340 4372 5.527385 AGAAGAGATGGATCTTGAGAAGGA 58.473 41.667 0.00 0.00 39.63 3.36
2346 4378 2.961741 CGGGAGAAGAGATGGATCTTGA 59.038 50.000 0.00 0.00 39.63 3.02


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

AutoCloner maintained by Alex Coulton.