Multiple sequence alignment - TraesCS7A01G139200

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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 TraesCS7A01G139200 chr7A 100.000 3742 0 0 1 3742 91381334 91385075 0.000000e+00 6911
1 TraesCS7A01G139200 chr7A 94.771 153 6 1 2 154 135845077 135844927 1.740000e-58 237
2 TraesCS7A01G139200 chr7A 90.805 174 14 2 2 175 416427928 416428099 8.080000e-57 231
3 TraesCS7A01G139200 chr7A 92.568 148 7 3 1 148 649069956 649069813 3.790000e-50 209
4 TraesCS7A01G139200 chr2A 97.019 3590 95 6 162 3742 194522832 194526418 0.000000e+00 6026
5 TraesCS7A01G139200 chr2A 96.461 3645 108 9 107 3742 194872979 194869347 0.000000e+00 5997
6 TraesCS7A01G139200 chr1B 93.976 3569 176 20 193 3742 601409102 601405554 0.000000e+00 5363
7 TraesCS7A01G139200 chr1B 94.264 3347 150 21 169 3498 647521615 647518294 0.000000e+00 5079
8 TraesCS7A01G139200 chr1B 93.924 3226 161 19 175 3386 601364864 601368068 0.000000e+00 4839
9 TraesCS7A01G139200 chr1B 95.706 326 13 1 3418 3742 601368065 601368390 1.190000e-144 523
10 TraesCS7A01G139200 chr2D 96.785 1555 37 4 880 2433 648063580 648062038 0.000000e+00 2582
11 TraesCS7A01G139200 chr2D 94.388 392 15 3 462 847 648063968 648063578 2.490000e-166 595
12 TraesCS7A01G139200 chr2D 85.235 149 18 3 1 149 497857599 497857743 2.330000e-32 150
13 TraesCS7A01G139200 chrUn 94.581 1587 78 6 691 2274 387418188 387419769 0.000000e+00 2447
14 TraesCS7A01G139200 chr5B 92.631 1357 84 9 119 1473 545056196 545054854 0.000000e+00 1938
15 TraesCS7A01G139200 chr5B 89.525 821 63 8 174 983 14669830 14669022 0.000000e+00 1018
16 TraesCS7A01G139200 chr5B 92.958 639 37 2 190 828 398702848 398702218 0.000000e+00 924
17 TraesCS7A01G139200 chr5B 79.724 434 74 12 140 566 542344388 542344814 6.070000e-78 302
18 TraesCS7A01G139200 chr3B 91.768 1312 93 8 164 1473 393302085 393300787 0.000000e+00 1810
19 TraesCS7A01G139200 chr5A 95.489 133 4 1 1 133 151398214 151398344 1.050000e-50 211
20 TraesCS7A01G139200 chr7D 94.444 126 7 0 1 126 102337698 102337573 1.060000e-45 195
21 TraesCS7A01G139200 chr1A 91.096 146 8 5 2 142 226907159 226907304 3.810000e-45 193
22 TraesCS7A01G139200 chr4A 89.855 138 11 2 1 138 14600344 14600478 1.380000e-39 174
23 TraesCS7A01G139200 chr4D 87.500 152 13 5 1 151 406134912 406135058 1.790000e-38 171


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 TraesCS7A01G139200 chr7A 91381334 91385075 3741 False 6911.0 6911 100.0000 1 3742 1 chr7A.!!$F1 3741
1 TraesCS7A01G139200 chr2A 194522832 194526418 3586 False 6026.0 6026 97.0190 162 3742 1 chr2A.!!$F1 3580
2 TraesCS7A01G139200 chr2A 194869347 194872979 3632 True 5997.0 5997 96.4610 107 3742 1 chr2A.!!$R1 3635
3 TraesCS7A01G139200 chr1B 601405554 601409102 3548 True 5363.0 5363 93.9760 193 3742 1 chr1B.!!$R1 3549
4 TraesCS7A01G139200 chr1B 647518294 647521615 3321 True 5079.0 5079 94.2640 169 3498 1 chr1B.!!$R2 3329
5 TraesCS7A01G139200 chr1B 601364864 601368390 3526 False 2681.0 4839 94.8150 175 3742 2 chr1B.!!$F1 3567
6 TraesCS7A01G139200 chr2D 648062038 648063968 1930 True 1588.5 2582 95.5865 462 2433 2 chr2D.!!$R1 1971
7 TraesCS7A01G139200 chrUn 387418188 387419769 1581 False 2447.0 2447 94.5810 691 2274 1 chrUn.!!$F1 1583
8 TraesCS7A01G139200 chr5B 545054854 545056196 1342 True 1938.0 1938 92.6310 119 1473 1 chr5B.!!$R3 1354
9 TraesCS7A01G139200 chr5B 14669022 14669830 808 True 1018.0 1018 89.5250 174 983 1 chr5B.!!$R1 809
10 TraesCS7A01G139200 chr5B 398702218 398702848 630 True 924.0 924 92.9580 190 828 1 chr5B.!!$R2 638
11 TraesCS7A01G139200 chr3B 393300787 393302085 1298 True 1810.0 1810 91.7680 164 1473 1 chr3B.!!$R1 1309

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
440 455 0.592247 GCAACACTTCGTGCAGGTTG 60.592 55.0 6.26 4.47 41.21 3.77 F
2032 2076 0.038801 CGTGCACTCTCTTGCTCTCA 60.039 55.0 16.19 0.00 43.41 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 2223 1.118965 TCCTCGGCCTTCACACTCAA 61.119 55.0 0.0 0.0 0.00 3.02 R
3011 3065 1.153539 TGAAGGACAACCCCATCCAA 58.846 50.0 0.0 0.0 37.47 3.53 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
29 30 8.831000 ATTTACGAAACCTAAAAATACGATGC 57.169 30.769 0.00 0.00 0.00 3.91
30 31 5.866335 ACGAAACCTAAAAATACGATGCA 57.134 34.783 0.00 0.00 0.00 3.96
31 32 6.431198 ACGAAACCTAAAAATACGATGCAT 57.569 33.333 0.00 0.00 0.00 3.96
32 33 6.848451 ACGAAACCTAAAAATACGATGCATT 58.152 32.000 0.00 0.00 0.00 3.56
33 34 6.745450 ACGAAACCTAAAAATACGATGCATTG 59.255 34.615 12.66 12.66 0.00 2.82
34 35 6.964370 CGAAACCTAAAAATACGATGCATTGA 59.036 34.615 21.12 4.83 0.00 2.57
35 36 7.044966 CGAAACCTAAAAATACGATGCATTGAC 60.045 37.037 21.12 0.00 0.00 3.18
36 37 5.806286 ACCTAAAAATACGATGCATTGACG 58.194 37.500 21.12 12.65 0.00 4.35
37 38 5.353123 ACCTAAAAATACGATGCATTGACGT 59.647 36.000 21.12 17.80 42.70 4.34
38 39 6.535865 ACCTAAAAATACGATGCATTGACGTA 59.464 34.615 21.12 19.34 44.32 3.57
39 40 7.064847 ACCTAAAAATACGATGCATTGACGTAA 59.935 33.333 21.12 4.59 43.65 3.18
40 41 7.906010 CCTAAAAATACGATGCATTGACGTAAA 59.094 33.333 21.12 2.80 43.65 2.01
41 42 9.268255 CTAAAAATACGATGCATTGACGTAAAA 57.732 29.630 21.12 2.08 43.65 1.52
42 43 8.508800 AAAAATACGATGCATTGACGTAAAAA 57.491 26.923 21.12 1.73 43.65 1.94
43 44 8.682128 AAAATACGATGCATTGACGTAAAAAT 57.318 26.923 21.12 4.03 43.65 1.82
44 45 9.776158 AAAATACGATGCATTGACGTAAAAATA 57.224 25.926 21.12 0.65 43.65 1.40
45 46 8.987599 AATACGATGCATTGACGTAAAAATAG 57.012 30.769 21.12 0.00 43.65 1.73
46 47 6.656314 ACGATGCATTGACGTAAAAATAGA 57.344 33.333 21.12 0.00 38.47 1.98
47 48 6.705782 ACGATGCATTGACGTAAAAATAGAG 58.294 36.000 21.12 0.00 38.47 2.43
48 49 6.533723 ACGATGCATTGACGTAAAAATAGAGA 59.466 34.615 21.12 0.00 38.47 3.10
49 50 7.059817 CGATGCATTGACGTAAAAATAGAGAG 58.940 38.462 8.37 0.00 0.00 3.20
50 51 7.043391 CGATGCATTGACGTAAAAATAGAGAGA 60.043 37.037 8.37 0.00 0.00 3.10
51 52 7.525688 TGCATTGACGTAAAAATAGAGAGAG 57.474 36.000 0.00 0.00 0.00 3.20
52 53 6.535150 TGCATTGACGTAAAAATAGAGAGAGG 59.465 38.462 0.00 0.00 0.00 3.69
53 54 6.018669 GCATTGACGTAAAAATAGAGAGAGGG 60.019 42.308 0.00 0.00 0.00 4.30
54 55 6.600882 TTGACGTAAAAATAGAGAGAGGGT 57.399 37.500 0.00 0.00 0.00 4.34
55 56 5.962433 TGACGTAAAAATAGAGAGAGGGTG 58.038 41.667 0.00 0.00 0.00 4.61
56 57 5.713389 TGACGTAAAAATAGAGAGAGGGTGA 59.287 40.000 0.00 0.00 0.00 4.02
57 58 6.209986 TGACGTAAAAATAGAGAGAGGGTGAA 59.790 38.462 0.00 0.00 0.00 3.18
58 59 6.631962 ACGTAAAAATAGAGAGAGGGTGAAG 58.368 40.000 0.00 0.00 0.00 3.02
59 60 6.436532 ACGTAAAAATAGAGAGAGGGTGAAGA 59.563 38.462 0.00 0.00 0.00 2.87
60 61 7.039223 ACGTAAAAATAGAGAGAGGGTGAAGAA 60.039 37.037 0.00 0.00 0.00 2.52
61 62 7.982354 CGTAAAAATAGAGAGAGGGTGAAGAAT 59.018 37.037 0.00 0.00 0.00 2.40
64 65 9.674068 AAAAATAGAGAGAGGGTGAAGAATAAC 57.326 33.333 0.00 0.00 0.00 1.89
65 66 8.616799 AAATAGAGAGAGGGTGAAGAATAACT 57.383 34.615 0.00 0.00 0.00 2.24
66 67 9.716556 AAATAGAGAGAGGGTGAAGAATAACTA 57.283 33.333 0.00 0.00 0.00 2.24
67 68 9.890915 AATAGAGAGAGGGTGAAGAATAACTAT 57.109 33.333 0.00 0.00 0.00 2.12
68 69 9.890915 ATAGAGAGAGGGTGAAGAATAACTATT 57.109 33.333 0.00 0.00 0.00 1.73
69 70 8.245195 AGAGAGAGGGTGAAGAATAACTATTC 57.755 38.462 1.83 1.83 41.78 1.75
70 71 7.289084 AGAGAGAGGGTGAAGAATAACTATTCC 59.711 40.741 5.95 0.00 42.29 3.01
71 72 7.136203 AGAGAGGGTGAAGAATAACTATTCCT 58.864 38.462 5.95 0.00 42.29 3.36
72 73 7.289084 AGAGAGGGTGAAGAATAACTATTCCTC 59.711 40.741 5.95 0.00 42.29 3.71
73 74 6.903534 AGAGGGTGAAGAATAACTATTCCTCA 59.096 38.462 0.00 6.65 42.29 3.86
74 75 7.570607 AGAGGGTGAAGAATAACTATTCCTCAT 59.429 37.037 11.92 0.40 42.09 2.90
75 76 7.740805 AGGGTGAAGAATAACTATTCCTCATC 58.259 38.462 11.92 11.37 42.09 2.92
76 77 7.570607 AGGGTGAAGAATAACTATTCCTCATCT 59.429 37.037 15.86 12.23 42.09 2.90
77 78 8.871125 GGGTGAAGAATAACTATTCCTCATCTA 58.129 37.037 15.86 0.00 42.09 1.98
78 79 9.921637 GGTGAAGAATAACTATTCCTCATCTAG 57.078 37.037 11.92 0.00 42.09 2.43
79 80 9.921637 GTGAAGAATAACTATTCCTCATCTAGG 57.078 37.037 11.92 0.00 42.09 3.02
80 81 9.094578 TGAAGAATAACTATTCCTCATCTAGGG 57.905 37.037 6.65 0.00 46.55 3.53
81 82 9.095700 GAAGAATAACTATTCCTCATCTAGGGT 57.904 37.037 5.95 0.00 46.55 4.34
82 83 8.429237 AGAATAACTATTCCTCATCTAGGGTG 57.571 38.462 5.95 0.00 46.55 4.61
83 84 8.235230 AGAATAACTATTCCTCATCTAGGGTGA 58.765 37.037 5.95 0.00 46.55 4.02
84 85 7.784470 ATAACTATTCCTCATCTAGGGTGAC 57.216 40.000 0.00 0.00 46.55 3.67
85 86 4.145807 ACTATTCCTCATCTAGGGTGACG 58.854 47.826 0.00 0.00 46.55 4.35
86 87 2.820728 TTCCTCATCTAGGGTGACGA 57.179 50.000 0.00 0.00 46.55 4.20
87 88 2.820728 TCCTCATCTAGGGTGACGAA 57.179 50.000 0.00 0.00 46.55 3.85
88 89 3.314307 TCCTCATCTAGGGTGACGAAT 57.686 47.619 0.00 0.00 46.55 3.34
89 90 4.448720 TCCTCATCTAGGGTGACGAATA 57.551 45.455 0.00 0.00 46.55 1.75
90 91 4.399219 TCCTCATCTAGGGTGACGAATAG 58.601 47.826 0.00 0.00 46.55 1.73
91 92 3.057174 CCTCATCTAGGGTGACGAATAGC 60.057 52.174 0.00 0.00 42.32 2.97
92 93 6.387972 CCTCATCTAGGGTGACGAATAGCG 62.388 54.167 0.00 0.00 42.32 4.26
93 94 0.666913 TCTAGGGTGACGAATAGCGC 59.333 55.000 0.00 0.00 46.04 5.92
94 95 0.660595 CTAGGGTGACGAATAGCGCG 60.661 60.000 0.00 0.00 46.04 6.86
95 96 1.096967 TAGGGTGACGAATAGCGCGA 61.097 55.000 12.10 0.00 46.04 5.87
96 97 2.228914 GGGTGACGAATAGCGCGAC 61.229 63.158 12.10 0.04 46.04 5.19
97 98 2.228914 GGTGACGAATAGCGCGACC 61.229 63.158 12.10 0.00 46.04 4.79
98 99 2.103538 TGACGAATAGCGCGACCC 59.896 61.111 12.10 0.00 46.04 4.46
99 100 3.022914 GACGAATAGCGCGACCCG 61.023 66.667 12.10 7.82 46.04 5.28
100 101 3.459378 GACGAATAGCGCGACCCGA 62.459 63.158 12.10 0.00 46.04 5.14
101 102 2.050351 CGAATAGCGCGACCCGAT 60.050 61.111 12.10 0.00 40.02 4.18
102 103 1.208358 CGAATAGCGCGACCCGATA 59.792 57.895 12.10 0.00 42.55 2.92
104 105 1.063027 CGAATAGCGCGACCCGATATA 59.937 52.381 12.10 0.00 46.75 0.86
105 106 2.286831 CGAATAGCGCGACCCGATATAT 60.287 50.000 12.10 0.00 46.75 0.86
106 107 3.059393 CGAATAGCGCGACCCGATATATA 60.059 47.826 12.10 0.00 46.75 0.86
107 108 4.378149 CGAATAGCGCGACCCGATATATAT 60.378 45.833 12.10 0.00 46.75 0.86
108 109 5.163923 CGAATAGCGCGACCCGATATATATA 60.164 44.000 12.10 0.00 46.75 0.86
109 110 6.456584 CGAATAGCGCGACCCGATATATATAT 60.457 42.308 12.10 4.86 46.75 0.86
110 111 7.254218 CGAATAGCGCGACCCGATATATATATA 60.254 40.741 12.10 4.92 46.75 0.86
111 112 8.447924 AATAGCGCGACCCGATATATATATAT 57.552 34.615 12.10 13.97 46.75 0.86
112 113 9.551734 AATAGCGCGACCCGATATATATATATA 57.448 33.333 12.10 13.60 46.75 0.86
113 114 9.722184 ATAGCGCGACCCGATATATATATATAT 57.278 33.333 20.55 20.55 45.73 0.86
115 116 9.722184 AGCGCGACCCGATATATATATATATAT 57.278 33.333 25.54 25.54 41.91 0.86
229 240 3.662247 ATAGCTATCAGTACCGTTGGC 57.338 47.619 0.00 0.00 0.00 4.52
251 262 4.434330 GCTGTGCTTTGTGATTCGTACTAC 60.434 45.833 0.00 0.00 0.00 2.73
424 439 3.244582 TCAGGTTCCAACTACTAGGCAA 58.755 45.455 0.00 0.00 0.00 4.52
440 455 0.592247 GCAACACTTCGTGCAGGTTG 60.592 55.000 6.26 4.47 41.21 3.77
549 564 1.073025 GGTCCATGCATATGCCCGA 59.927 57.895 24.54 13.83 41.18 5.14
581 596 1.593006 GTGAGTGACGTGTTGAACCTG 59.407 52.381 0.00 0.00 0.00 4.00
656 679 3.777925 ACGTCGCTCGCATGTTGC 61.778 61.111 0.00 0.00 44.19 4.17
697 726 5.682212 GCCATCATACGGCTCATGTGATATA 60.682 44.000 0.00 0.00 46.56 0.86
891 930 2.474712 GCACTTAAGACGCGTGCC 59.525 61.111 20.70 2.09 46.09 5.01
983 1024 5.121925 TCGTATAATATGCTCTCACGACCTC 59.878 44.000 0.00 0.00 32.57 3.85
1016 1058 3.134458 GGTGCAGCCATCATACTAGTTC 58.866 50.000 4.03 0.00 37.17 3.01
1118 1160 1.763770 GGCTGAATGGATCCCGGAT 59.236 57.895 9.90 0.00 0.00 4.18
1313 1355 1.654105 GATCATTGACGCGTCGAACTT 59.346 47.619 31.44 18.68 0.00 2.66
1481 1523 3.691342 CTTCACCCTGGCCGACGA 61.691 66.667 0.00 0.00 0.00 4.20
1522 1564 1.336887 GCGTCTGGTGAGTGTGTACAT 60.337 52.381 0.00 0.00 0.00 2.29
1573 1616 1.628340 CACCCAGTTCACCCATGTCTA 59.372 52.381 0.00 0.00 0.00 2.59
1673 1716 2.158871 TCAGGTAACCAAAACAGCGAGT 60.159 45.455 0.00 0.00 37.17 4.18
1929 1973 2.669569 CCCCGCTTCAGTGTGGTG 60.670 66.667 0.00 0.00 35.95 4.17
2032 2076 0.038801 CGTGCACTCTCTTGCTCTCA 60.039 55.000 16.19 0.00 43.41 3.27
2179 2223 1.815421 GATCCATGCCAGCGTCGTT 60.815 57.895 0.00 0.00 0.00 3.85
2537 2583 6.647334 TCTAAAATCACTTGGCAAATGACA 57.353 33.333 14.17 0.00 0.00 3.58
2655 2701 9.836864 AATCTTGTGCTGAATAGTATGTCATTA 57.163 29.630 0.00 0.00 0.00 1.90
2981 3035 8.861086 TCATGAAAAGTACTGAAACTCTACTCT 58.139 33.333 0.00 0.00 0.00 3.24
3038 3092 2.307686 GGGGTTGTCCTTCATACCAAGA 59.692 50.000 0.00 0.00 35.33 3.02
3240 3294 2.526888 ATATCCCGCTCGATTCCCTA 57.473 50.000 0.00 0.00 0.00 3.53
3450 3539 0.883833 CCAAAAGCTCGTCTGCCAAT 59.116 50.000 0.00 0.00 0.00 3.16
3512 3601 0.617935 TTGCTCATCATCGGGTCCAA 59.382 50.000 0.00 0.00 0.00 3.53
3599 3688 3.634910 GGCAGAACAAACTAAAACAGGGA 59.365 43.478 0.00 0.00 0.00 4.20
3664 3754 7.661437 TCAAGTAGAATGCTTATAATCGCCAAT 59.339 33.333 0.00 0.00 39.72 3.16
3689 3779 6.947733 TGGAAAATCTGAAGACATGTACCATT 59.052 34.615 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.804712 TGCATCGTATTTTTAGGTTTCGTAAA 58.195 30.769 0.00 0.00 0.00 2.01
6 7 7.361889 TGCATCGTATTTTTAGGTTTCGTAA 57.638 32.000 0.00 0.00 0.00 3.18
7 8 6.964741 TGCATCGTATTTTTAGGTTTCGTA 57.035 33.333 0.00 0.00 0.00 3.43
8 9 5.866335 TGCATCGTATTTTTAGGTTTCGT 57.134 34.783 0.00 0.00 0.00 3.85
9 10 6.964370 TCAATGCATCGTATTTTTAGGTTTCG 59.036 34.615 0.00 0.00 0.00 3.46
10 11 7.044966 CGTCAATGCATCGTATTTTTAGGTTTC 60.045 37.037 0.00 0.00 0.00 2.78
11 12 6.745450 CGTCAATGCATCGTATTTTTAGGTTT 59.255 34.615 0.00 0.00 0.00 3.27
12 13 6.128117 ACGTCAATGCATCGTATTTTTAGGTT 60.128 34.615 9.89 0.00 36.05 3.50
13 14 5.353123 ACGTCAATGCATCGTATTTTTAGGT 59.647 36.000 9.89 0.00 36.05 3.08
14 15 5.806286 ACGTCAATGCATCGTATTTTTAGG 58.194 37.500 9.89 0.00 36.05 2.69
15 16 8.814733 TTTACGTCAATGCATCGTATTTTTAG 57.185 30.769 16.83 0.00 39.24 1.85
16 17 9.608617 TTTTTACGTCAATGCATCGTATTTTTA 57.391 25.926 16.83 2.83 39.24 1.52
17 18 8.508800 TTTTTACGTCAATGCATCGTATTTTT 57.491 26.923 16.83 0.00 39.24 1.94
18 19 8.682128 ATTTTTACGTCAATGCATCGTATTTT 57.318 26.923 16.83 3.97 39.24 1.82
19 20 9.433317 CTATTTTTACGTCAATGCATCGTATTT 57.567 29.630 16.83 7.59 39.24 1.40
20 21 8.822855 TCTATTTTTACGTCAATGCATCGTATT 58.177 29.630 16.83 7.84 39.24 1.89
21 22 8.360325 TCTATTTTTACGTCAATGCATCGTAT 57.640 30.769 16.83 8.23 39.24 3.06
22 23 7.703197 TCTCTATTTTTACGTCAATGCATCGTA 59.297 33.333 13.34 13.34 38.69 3.43
23 24 6.533723 TCTCTATTTTTACGTCAATGCATCGT 59.466 34.615 15.15 15.15 40.78 3.73
24 25 6.933130 TCTCTATTTTTACGTCAATGCATCG 58.067 36.000 0.00 1.52 0.00 3.84
25 26 8.131455 TCTCTCTATTTTTACGTCAATGCATC 57.869 34.615 0.00 0.00 0.00 3.91
26 27 7.225538 CCTCTCTCTATTTTTACGTCAATGCAT 59.774 37.037 0.00 0.00 0.00 3.96
27 28 6.535150 CCTCTCTCTATTTTTACGTCAATGCA 59.465 38.462 0.00 0.00 0.00 3.96
28 29 6.018669 CCCTCTCTCTATTTTTACGTCAATGC 60.019 42.308 0.00 0.00 0.00 3.56
29 30 7.010552 CACCCTCTCTCTATTTTTACGTCAATG 59.989 40.741 0.00 0.00 0.00 2.82
30 31 7.042335 CACCCTCTCTCTATTTTTACGTCAAT 58.958 38.462 0.00 0.00 0.00 2.57
31 32 6.209986 TCACCCTCTCTCTATTTTTACGTCAA 59.790 38.462 0.00 0.00 0.00 3.18
32 33 5.713389 TCACCCTCTCTCTATTTTTACGTCA 59.287 40.000 0.00 0.00 0.00 4.35
33 34 6.205101 TCACCCTCTCTCTATTTTTACGTC 57.795 41.667 0.00 0.00 0.00 4.34
34 35 6.436532 TCTTCACCCTCTCTCTATTTTTACGT 59.563 38.462 0.00 0.00 0.00 3.57
35 36 6.864342 TCTTCACCCTCTCTCTATTTTTACG 58.136 40.000 0.00 0.00 0.00 3.18
38 39 9.674068 GTTATTCTTCACCCTCTCTCTATTTTT 57.326 33.333 0.00 0.00 0.00 1.94
39 40 9.052365 AGTTATTCTTCACCCTCTCTCTATTTT 57.948 33.333 0.00 0.00 0.00 1.82
40 41 8.616799 AGTTATTCTTCACCCTCTCTCTATTT 57.383 34.615 0.00 0.00 0.00 1.40
41 42 9.890915 ATAGTTATTCTTCACCCTCTCTCTATT 57.109 33.333 0.00 0.00 0.00 1.73
42 43 9.890915 AATAGTTATTCTTCACCCTCTCTCTAT 57.109 33.333 0.00 0.00 0.00 1.98
43 44 9.357161 GAATAGTTATTCTTCACCCTCTCTCTA 57.643 37.037 4.93 0.00 39.13 2.43
44 45 7.289084 GGAATAGTTATTCTTCACCCTCTCTCT 59.711 40.741 10.71 0.00 41.33 3.10
45 46 7.289084 AGGAATAGTTATTCTTCACCCTCTCTC 59.711 40.741 10.71 0.00 41.33 3.20
46 47 7.136203 AGGAATAGTTATTCTTCACCCTCTCT 58.864 38.462 10.71 0.00 41.33 3.10
47 48 7.070074 TGAGGAATAGTTATTCTTCACCCTCTC 59.930 40.741 17.60 10.76 46.85 3.20
48 49 6.903534 TGAGGAATAGTTATTCTTCACCCTCT 59.096 38.462 17.60 3.75 46.85 3.69
49 50 7.125792 TGAGGAATAGTTATTCTTCACCCTC 57.874 40.000 17.60 12.38 46.85 4.30
69 70 3.057174 GCTATTCGTCACCCTAGATGAGG 60.057 52.174 9.25 9.25 46.25 3.86
70 71 3.365465 CGCTATTCGTCACCCTAGATGAG 60.365 52.174 0.00 0.00 35.17 2.90
71 72 2.552743 CGCTATTCGTCACCCTAGATGA 59.447 50.000 0.00 0.00 0.00 2.92
72 73 2.922758 GCGCTATTCGTCACCCTAGATG 60.923 54.545 0.00 0.00 41.07 2.90
73 74 1.269998 GCGCTATTCGTCACCCTAGAT 59.730 52.381 0.00 0.00 41.07 1.98
74 75 0.666913 GCGCTATTCGTCACCCTAGA 59.333 55.000 0.00 0.00 41.07 2.43
75 76 0.660595 CGCGCTATTCGTCACCCTAG 60.661 60.000 5.56 0.00 41.07 3.02
76 77 1.096967 TCGCGCTATTCGTCACCCTA 61.097 55.000 5.56 0.00 41.07 3.53
77 78 2.104331 CGCGCTATTCGTCACCCT 59.896 61.111 5.56 0.00 41.07 4.34
78 79 2.103538 TCGCGCTATTCGTCACCC 59.896 61.111 5.56 0.00 41.07 4.61
79 80 2.228914 GGTCGCGCTATTCGTCACC 61.229 63.158 5.56 0.00 41.07 4.02
80 81 2.228914 GGGTCGCGCTATTCGTCAC 61.229 63.158 5.56 0.00 41.07 3.67
81 82 2.103538 GGGTCGCGCTATTCGTCA 59.896 61.111 5.56 0.00 41.07 4.35
82 83 2.728427 ATCGGGTCGCGCTATTCGTC 62.728 60.000 5.56 0.00 41.07 4.20
83 84 1.509644 TATCGGGTCGCGCTATTCGT 61.510 55.000 5.56 0.00 41.07 3.85
84 85 0.179171 ATATCGGGTCGCGCTATTCG 60.179 55.000 5.56 4.72 42.12 3.34
85 86 2.838386 TATATCGGGTCGCGCTATTC 57.162 50.000 5.56 0.00 0.00 1.75
86 87 6.754702 ATATATATATCGGGTCGCGCTATT 57.245 37.500 5.56 3.22 0.00 1.73
87 88 9.722184 ATATATATATATATCGGGTCGCGCTAT 57.278 33.333 16.85 10.05 31.98 2.97
89 90 9.722184 ATATATATATATATATCGGGTCGCGCT 57.278 33.333 22.90 0.00 37.30 5.92
229 240 4.091509 GGTAGTACGAATCACAAAGCACAG 59.908 45.833 0.00 0.00 0.00 3.66
251 262 3.386768 AACAGTACTACAGCACACAGG 57.613 47.619 0.00 0.00 0.00 4.00
287 298 4.022068 CCTGCCAACAAAGCTAAATCTCAA 60.022 41.667 0.00 0.00 0.00 3.02
393 405 8.090788 AGTAGTTGGAACCTGATATACACAAT 57.909 34.615 0.00 0.00 0.00 2.71
440 455 2.318696 GCGCGCCGTACACATAAC 59.681 61.111 23.24 0.00 0.00 1.89
549 564 3.323979 ACGTCACTCACATAGGTTCCTTT 59.676 43.478 0.00 0.00 0.00 3.11
566 581 1.872237 GCTAGCAGGTTCAACACGTCA 60.872 52.381 10.63 0.00 0.00 4.35
567 582 0.790814 GCTAGCAGGTTCAACACGTC 59.209 55.000 10.63 0.00 0.00 4.34
581 596 5.106634 ACGTATACATAGTGTAGCAGCTAGC 60.107 44.000 6.62 6.62 46.19 3.42
635 657 2.583319 CATGCGAGCGACGTGGAT 60.583 61.111 0.11 0.00 44.60 3.41
656 679 1.081906 GCAGACCACATGTGTTGCG 60.082 57.895 23.79 11.29 0.00 4.85
697 726 5.048294 ACGACTTTTTCAAACCAACAAGACT 60.048 36.000 0.00 0.00 0.00 3.24
891 930 1.446792 CACTCGCACAGGCCTGTAG 60.447 63.158 37.27 30.93 42.83 2.74
1080 1122 0.978146 CGGAGGAGGGGATCAACACT 60.978 60.000 0.00 0.00 0.00 3.55
1313 1355 2.664851 CGCCCGTTGCAGTGAGAA 60.665 61.111 0.00 0.00 41.33 2.87
1573 1616 1.142870 TGGTCAGGCTAACAAAGTGCT 59.857 47.619 0.00 0.00 0.00 4.40
1673 1716 6.828273 CCATAGAGAATTAACCCACAATCACA 59.172 38.462 0.00 0.00 0.00 3.58
1773 1816 3.726607 ACCGGTTAATTTGACGTACACA 58.273 40.909 0.00 0.00 0.00 3.72
1929 1973 8.390354 TGATGAGTGATATCGTTGAAATTTGTC 58.610 33.333 0.00 0.00 0.00 3.18
2032 2076 2.195567 CGGATGCGGCAAATGGGAT 61.196 57.895 6.82 0.00 0.00 3.85
2055 2099 2.047844 CGTGCAGTGCTAGCCAGT 60.048 61.111 17.60 0.24 0.00 4.00
2179 2223 1.118965 TCCTCGGCCTTCACACTCAA 61.119 55.000 0.00 0.00 0.00 3.02
2248 2292 5.339990 CCGTTTTGTGATGATTTCATACCC 58.660 41.667 0.00 0.00 36.54 3.69
2392 2436 6.100279 TGCTTCTGATTCTGGTATACCAAGAT 59.900 38.462 24.59 19.73 46.97 2.40
2537 2583 3.331150 TCGATAAGAATGCACGGTTGTT 58.669 40.909 0.00 0.00 0.00 2.83
2655 2701 5.764686 TCAGAATGACAGCATTGTACAACTT 59.235 36.000 11.22 0.00 42.56 2.66
2981 3035 1.268352 CCTTTCGATCGGTGCCAAAAA 59.732 47.619 16.41 5.53 0.00 1.94
3011 3065 1.153539 TGAAGGACAACCCCATCCAA 58.846 50.000 0.00 0.00 37.47 3.53
3038 3092 3.760684 GGATGATCCTGCTGTTTGAAGTT 59.239 43.478 3.71 0.00 32.53 2.66
3450 3539 4.113815 CAAGGGGAGCATGGCCGA 62.114 66.667 0.00 0.00 0.00 5.54
3512 3601 4.649674 TCCAGAGAAGGCGAACTACAATAT 59.350 41.667 0.00 0.00 0.00 1.28
3664 3754 5.875224 TGGTACATGTCTTCAGATTTTCCA 58.125 37.500 0.00 0.00 0.00 3.53
3689 3779 2.001872 CACGCTGTTCATCTATGCACA 58.998 47.619 0.00 0.00 33.15 4.57


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

AutoCloner maintained by Alex Coulton.