Multiple sequence alignment - TraesCS6B01G203600

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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 TraesCS6B01G203600 chr6B 100.000 2471 0 0 1 2471 250133483 250131013 0.000000e+00 4564
1 TraesCS6B01G203600 chr6B 95.420 524 13 6 1958 2471 252341432 252340910 0.000000e+00 824
2 TraesCS6B01G203600 chr6B 98.276 290 5 0 3 292 252638090 252637801 2.190000e-140 508
3 TraesCS6B01G203600 chr1B 95.468 1677 69 5 293 1964 416803455 416805129 0.000000e+00 2669
4 TraesCS6B01G203600 chr1B 87.302 945 112 6 293 1231 457612712 457611770 0.000000e+00 1074
5 TraesCS6B01G203600 chr1B 98.276 290 5 0 3 292 151922876 151922587 2.190000e-140 508
6 TraesCS6B01G203600 chr1B 97.931 290 6 0 3 292 24398025 24398314 1.020000e-138 503
7 TraesCS6B01G203600 chr1B 97.931 290 6 0 3 292 590136743 590136454 1.020000e-138 503
8 TraesCS6B01G203600 chr3D 96.094 1101 38 5 283 1380 112682818 112683916 0.000000e+00 1790
9 TraesCS6B01G203600 chr3D 86.126 728 90 7 1232 1957 97662326 97661608 0.000000e+00 774
10 TraesCS6B01G203600 chr2D 95.731 1101 43 4 284 1380 308502271 308501171 0.000000e+00 1770
11 TraesCS6B01G203600 chr2D 95.869 1041 39 2 286 1323 363985543 363986582 0.000000e+00 1681
12 TraesCS6B01G203600 chr2D 94.225 1091 59 4 293 1380 603734466 603733377 0.000000e+00 1663
13 TraesCS6B01G203600 chr2D 95.215 627 28 2 1341 1966 603733447 603732822 0.000000e+00 990
14 TraesCS6B01G203600 chr2D 95.674 601 24 2 1367 1966 363986574 363987173 0.000000e+00 965
15 TraesCS6B01G203600 chr2D 94.099 627 32 5 1344 1968 308501238 308500615 0.000000e+00 948
16 TraesCS6B01G203600 chr2D 95.594 522 13 5 1958 2471 110324494 110325013 0.000000e+00 828
17 TraesCS6B01G203600 chr2D 86.420 729 88 7 1232 1957 107538268 107538988 0.000000e+00 787
18 TraesCS6B01G203600 chr1D 95.604 1092 45 3 292 1380 214875631 214874540 0.000000e+00 1748
19 TraesCS6B01G203600 chr1D 96.567 670 20 1 292 958 314483808 314484477 0.000000e+00 1107
20 TraesCS6B01G203600 chr1D 95.631 618 25 2 1341 1957 214874610 214873994 0.000000e+00 990
21 TraesCS6B01G203600 chr1D 94.658 599 30 2 1367 1964 314484753 314485350 0.000000e+00 928
22 TraesCS6B01G203600 chr1D 95.470 287 13 0 1037 1323 314484475 314484761 2.240000e-125 459
23 TraesCS6B01G203600 chr3B 95.154 1073 46 4 891 1957 589505908 589506980 0.000000e+00 1688
24 TraesCS6B01G203600 chr3B 95.969 521 14 2 1958 2471 143334891 143335411 0.000000e+00 839
25 TraesCS6B01G203600 chr3B 97.945 292 6 0 1 292 795698215 795697924 7.890000e-140 507
26 TraesCS6B01G203600 chr3B 88.312 308 30 2 1846 2152 125721617 125721919 5.020000e-97 364
27 TraesCS6B01G203600 chr3B 87.549 257 27 5 152 405 125720737 125720991 2.400000e-75 292
28 TraesCS6B01G203600 chr3A 93.967 1094 59 3 292 1380 158538280 158539371 0.000000e+00 1648
29 TraesCS6B01G203600 chr3A 94.660 618 32 1 1341 1957 158539301 158539918 0.000000e+00 957
30 TraesCS6B01G203600 chr3A 84.392 724 104 7 1241 1958 149435416 149434696 0.000000e+00 702
31 TraesCS6B01G203600 chr4B 95.594 522 15 3 1958 2471 391049106 391048585 0.000000e+00 830
32 TraesCS6B01G203600 chr4B 98.282 291 5 0 1 291 340851644 340851934 6.100000e-141 510
33 TraesCS6B01G203600 chr4B 97.931 290 6 0 3 292 143215946 143216235 1.020000e-138 503
34 TraesCS6B01G203600 chr6D 95.585 521 15 3 1958 2471 47711351 47710832 0.000000e+00 828
35 TraesCS6B01G203600 chr7D 95.577 520 16 2 1958 2471 437142941 437142423 0.000000e+00 826
36 TraesCS6B01G203600 chr7D 85.714 735 99 5 1232 1964 506969918 506969188 0.000000e+00 771
37 TraesCS6B01G203600 chr7D 95.960 99 3 1 204 301 381798995 381799093 2.540000e-35 159
38 TraesCS6B01G203600 chr4D 95.402 522 15 4 1958 2471 7515294 7515814 0.000000e+00 822
39 TraesCS6B01G203600 chr4D 95.393 521 16 3 1958 2471 42675809 42676328 0.000000e+00 822
40 TraesCS6B01G203600 chr4D 95.402 522 15 4 1958 2471 314294313 314293793 0.000000e+00 822
41 TraesCS6B01G203600 chr7B 98.276 290 5 0 3 292 34958153 34957864 2.190000e-140 508
42 TraesCS6B01G203600 chr2B 98.276 290 5 0 3 292 234434784 234435073 2.190000e-140 508


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 TraesCS6B01G203600 chr6B 250131013 250133483 2470 True 4564.000000 4564 100.0000 1 2471 1 chr6B.!!$R1 2470
1 TraesCS6B01G203600 chr6B 252340910 252341432 522 True 824.000000 824 95.4200 1958 2471 1 chr6B.!!$R2 513
2 TraesCS6B01G203600 chr1B 416803455 416805129 1674 False 2669.000000 2669 95.4680 293 1964 1 chr1B.!!$F2 1671
3 TraesCS6B01G203600 chr1B 457611770 457612712 942 True 1074.000000 1074 87.3020 293 1231 1 chr1B.!!$R2 938
4 TraesCS6B01G203600 chr3D 112682818 112683916 1098 False 1790.000000 1790 96.0940 283 1380 1 chr3D.!!$F1 1097
5 TraesCS6B01G203600 chr3D 97661608 97662326 718 True 774.000000 774 86.1260 1232 1957 1 chr3D.!!$R1 725
6 TraesCS6B01G203600 chr2D 308500615 308502271 1656 True 1359.000000 1770 94.9150 284 1968 2 chr2D.!!$R1 1684
7 TraesCS6B01G203600 chr2D 603732822 603734466 1644 True 1326.500000 1663 94.7200 293 1966 2 chr2D.!!$R2 1673
8 TraesCS6B01G203600 chr2D 363985543 363987173 1630 False 1323.000000 1681 95.7715 286 1966 2 chr2D.!!$F3 1680
9 TraesCS6B01G203600 chr2D 110324494 110325013 519 False 828.000000 828 95.5940 1958 2471 1 chr2D.!!$F2 513
10 TraesCS6B01G203600 chr2D 107538268 107538988 720 False 787.000000 787 86.4200 1232 1957 1 chr2D.!!$F1 725
11 TraesCS6B01G203600 chr1D 214873994 214875631 1637 True 1369.000000 1748 95.6175 292 1957 2 chr1D.!!$R1 1665
12 TraesCS6B01G203600 chr1D 314483808 314485350 1542 False 831.333333 1107 95.5650 292 1964 3 chr1D.!!$F1 1672
13 TraesCS6B01G203600 chr3B 589505908 589506980 1072 False 1688.000000 1688 95.1540 891 1957 1 chr3B.!!$F2 1066
14 TraesCS6B01G203600 chr3B 143334891 143335411 520 False 839.000000 839 95.9690 1958 2471 1 chr3B.!!$F1 513
15 TraesCS6B01G203600 chr3B 125720737 125721919 1182 False 328.000000 364 87.9305 152 2152 2 chr3B.!!$F3 2000
16 TraesCS6B01G203600 chr3A 158538280 158539918 1638 False 1302.500000 1648 94.3135 292 1957 2 chr3A.!!$F1 1665
17 TraesCS6B01G203600 chr3A 149434696 149435416 720 True 702.000000 702 84.3920 1241 1958 1 chr3A.!!$R1 717
18 TraesCS6B01G203600 chr4B 391048585 391049106 521 True 830.000000 830 95.5940 1958 2471 1 chr4B.!!$R1 513
19 TraesCS6B01G203600 chr6D 47710832 47711351 519 True 828.000000 828 95.5850 1958 2471 1 chr6D.!!$R1 513
20 TraesCS6B01G203600 chr7D 437142423 437142941 518 True 826.000000 826 95.5770 1958 2471 1 chr7D.!!$R1 513
21 TraesCS6B01G203600 chr7D 506969188 506969918 730 True 771.000000 771 85.7140 1232 1964 1 chr7D.!!$R2 732
22 TraesCS6B01G203600 chr4D 7515294 7515814 520 False 822.000000 822 95.4020 1958 2471 1 chr4D.!!$F1 513
23 TraesCS6B01G203600 chr4D 42675809 42676328 519 False 822.000000 822 95.3930 1958 2471 1 chr4D.!!$F2 513
24 TraesCS6B01G203600 chr4D 314293793 314294313 520 True 822.000000 822 95.4020 1958 2471 1 chr4D.!!$R1 513

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
958 1208 0.103026 CTCTCGATCCATTCACCGCA 59.897 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 2574 0.901124 GGTTGCCCCAACATGCATTA 59.099 50.0 0.0 0.0 45.11 1.9 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
39 40 8.964476 AAGTCTTTTTAGAGATTTCACTGTGA 57.036 30.769 6.36 6.36 0.00 3.58
40 41 8.964476 AGTCTTTTTAGAGATTTCACTGTGAA 57.036 30.769 18.69 18.69 34.03 3.18
41 42 8.831550 AGTCTTTTTAGAGATTTCACTGTGAAC 58.168 33.333 21.95 12.17 35.89 3.18
42 43 8.831550 GTCTTTTTAGAGATTTCACTGTGAACT 58.168 33.333 21.95 17.09 35.89 3.01
45 46 9.607988 TTTTTAGAGATTTCACTGTGAACTACA 57.392 29.630 21.95 8.78 35.89 2.74
46 47 9.778741 TTTTAGAGATTTCACTGTGAACTACAT 57.221 29.630 21.95 13.11 38.92 2.29
48 49 9.856488 TTAGAGATTTCACTGTGAACTACATAC 57.144 33.333 21.95 10.66 38.92 2.39
49 50 7.030165 AGAGATTTCACTGTGAACTACATACG 58.970 38.462 21.95 0.00 38.92 3.06
50 51 6.920817 AGATTTCACTGTGAACTACATACGA 58.079 36.000 21.95 5.56 38.92 3.43
51 52 7.375834 AGATTTCACTGTGAACTACATACGAA 58.624 34.615 21.95 4.85 38.92 3.85
52 53 7.870954 AGATTTCACTGTGAACTACATACGAAA 59.129 33.333 21.95 4.35 38.92 3.46
53 54 6.758593 TTCACTGTGAACTACATACGAAAC 57.241 37.500 18.69 0.00 38.92 2.78
54 55 5.834169 TCACTGTGAACTACATACGAAACA 58.166 37.500 8.27 0.00 38.92 2.83
55 56 6.274579 TCACTGTGAACTACATACGAAACAA 58.725 36.000 8.27 0.00 38.92 2.83
56 57 6.757478 TCACTGTGAACTACATACGAAACAAA 59.243 34.615 8.27 0.00 38.92 2.83
57 58 7.278203 TCACTGTGAACTACATACGAAACAAAA 59.722 33.333 8.27 0.00 38.92 2.44
58 59 8.067784 CACTGTGAACTACATACGAAACAAAAT 58.932 33.333 0.32 0.00 38.92 1.82
59 60 8.067784 ACTGTGAACTACATACGAAACAAAATG 58.932 33.333 0.00 0.00 38.92 2.32
60 61 8.144155 TGTGAACTACATACGAAACAAAATGA 57.856 30.769 0.00 0.00 33.42 2.57
61 62 8.279800 TGTGAACTACATACGAAACAAAATGAG 58.720 33.333 0.00 0.00 33.42 2.90
62 63 8.280497 GTGAACTACATACGAAACAAAATGAGT 58.720 33.333 0.00 0.00 0.00 3.41
63 64 8.279800 TGAACTACATACGAAACAAAATGAGTG 58.720 33.333 0.00 0.00 0.00 3.51
64 65 7.956420 ACTACATACGAAACAAAATGAGTGA 57.044 32.000 0.00 0.00 0.00 3.41
65 66 8.373048 ACTACATACGAAACAAAATGAGTGAA 57.627 30.769 0.00 0.00 0.00 3.18
66 67 8.999431 ACTACATACGAAACAAAATGAGTGAAT 58.001 29.630 0.00 0.00 0.00 2.57
67 68 9.478019 CTACATACGAAACAAAATGAGTGAATC 57.522 33.333 0.00 0.00 0.00 2.52
68 69 8.099364 ACATACGAAACAAAATGAGTGAATCT 57.901 30.769 0.00 0.00 0.00 2.40
69 70 9.214957 ACATACGAAACAAAATGAGTGAATCTA 57.785 29.630 0.00 0.00 0.00 1.98
70 71 9.478019 CATACGAAACAAAATGAGTGAATCTAC 57.522 33.333 0.00 0.00 0.00 2.59
71 72 7.490962 ACGAAACAAAATGAGTGAATCTACA 57.509 32.000 0.00 0.00 0.00 2.74
72 73 7.352739 ACGAAACAAAATGAGTGAATCTACAC 58.647 34.615 0.00 0.00 40.60 2.90
84 85 7.113658 AGTGAATCTACACTCCGAAATATGT 57.886 36.000 0.00 0.00 46.36 2.29
85 86 7.203910 AGTGAATCTACACTCCGAAATATGTC 58.796 38.462 0.00 0.00 46.36 3.06
86 87 7.068839 AGTGAATCTACACTCCGAAATATGTCT 59.931 37.037 0.00 0.00 46.36 3.41
87 88 8.350722 GTGAATCTACACTCCGAAATATGTCTA 58.649 37.037 0.00 0.00 37.73 2.59
88 89 9.078990 TGAATCTACACTCCGAAATATGTCTAT 57.921 33.333 0.00 0.00 0.00 1.98
96 97 9.737427 CACTCCGAAATATGTCTATATACATCC 57.263 37.037 7.00 0.00 40.52 3.51
97 98 9.475620 ACTCCGAAATATGTCTATATACATCCA 57.524 33.333 7.00 0.00 40.52 3.41
115 116 7.432148 ACATCCATATGTAGTTTGTAGTGGA 57.568 36.000 1.24 0.00 44.66 4.02
116 117 7.857456 ACATCCATATGTAGTTTGTAGTGGAA 58.143 34.615 1.24 0.00 44.66 3.53
117 118 8.494433 ACATCCATATGTAGTTTGTAGTGGAAT 58.506 33.333 1.24 0.00 44.66 3.01
118 119 8.993121 CATCCATATGTAGTTTGTAGTGGAATC 58.007 37.037 1.24 0.00 37.96 2.52
119 120 7.506114 TCCATATGTAGTTTGTAGTGGAATCC 58.494 38.462 1.24 0.00 32.02 3.01
120 121 6.710744 CCATATGTAGTTTGTAGTGGAATCCC 59.289 42.308 1.24 0.00 0.00 3.85
121 122 7.420214 CCATATGTAGTTTGTAGTGGAATCCCT 60.420 40.741 1.24 0.00 0.00 4.20
122 123 8.647796 CATATGTAGTTTGTAGTGGAATCCCTA 58.352 37.037 0.00 0.00 0.00 3.53
123 124 6.938698 TGTAGTTTGTAGTGGAATCCCTAA 57.061 37.500 0.00 0.00 0.00 2.69
124 125 7.319052 TGTAGTTTGTAGTGGAATCCCTAAA 57.681 36.000 0.00 0.00 0.00 1.85
125 126 7.747690 TGTAGTTTGTAGTGGAATCCCTAAAA 58.252 34.615 0.00 0.00 0.00 1.52
126 127 8.219178 TGTAGTTTGTAGTGGAATCCCTAAAAA 58.781 33.333 0.00 3.26 0.00 1.94
127 128 7.761038 AGTTTGTAGTGGAATCCCTAAAAAG 57.239 36.000 11.14 0.00 0.00 2.27
128 129 7.523415 AGTTTGTAGTGGAATCCCTAAAAAGA 58.477 34.615 11.14 0.00 0.00 2.52
129 130 7.447545 AGTTTGTAGTGGAATCCCTAAAAAGAC 59.552 37.037 11.14 4.86 0.00 3.01
130 131 6.697641 TGTAGTGGAATCCCTAAAAAGACT 57.302 37.500 0.00 0.00 0.00 3.24
131 132 7.086685 TGTAGTGGAATCCCTAAAAAGACTT 57.913 36.000 0.00 0.00 0.00 3.01
132 133 8.209802 TGTAGTGGAATCCCTAAAAAGACTTA 57.790 34.615 0.00 0.00 0.00 2.24
133 134 8.098912 TGTAGTGGAATCCCTAAAAAGACTTAC 58.901 37.037 0.00 0.00 0.00 2.34
134 135 7.086685 AGTGGAATCCCTAAAAAGACTTACA 57.913 36.000 0.00 0.00 0.00 2.41
135 136 7.699878 AGTGGAATCCCTAAAAAGACTTACAT 58.300 34.615 0.00 0.00 0.00 2.29
136 137 8.170730 AGTGGAATCCCTAAAAAGACTTACATT 58.829 33.333 0.00 0.00 0.00 2.71
137 138 8.803235 GTGGAATCCCTAAAAAGACTTACATTT 58.197 33.333 0.00 0.00 0.00 2.32
146 147 9.211485 CTAAAAAGACTTACATTTAGGAACGGA 57.789 33.333 8.91 0.00 33.69 4.69
147 148 7.668525 AAAAGACTTACATTTAGGAACGGAG 57.331 36.000 0.00 0.00 0.00 4.63
148 149 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
149 150 4.161754 AGACTTACATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
150 151 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
178 179 7.420800 AGTCACTTGTTGCAATCTCTAAAAAG 58.579 34.615 0.59 0.00 0.00 2.27
390 392 3.674997 CCCAACTCAGTTAGCTTGCTTA 58.325 45.455 0.00 0.00 0.00 3.09
632 795 3.080641 CTGGAGCCACACATCCCA 58.919 61.111 0.00 0.00 34.47 4.37
958 1208 0.103026 CTCTCGATCCATTCACCGCA 59.897 55.000 0.00 0.00 0.00 5.69
980 1230 1.413767 CGCGAACCCTGTTCGATCTG 61.414 60.000 27.68 12.97 43.97 2.90
982 1232 0.246635 CGAACCCTGTTCGATCTGGT 59.753 55.000 21.19 9.64 43.97 4.00
1030 1280 2.332654 GCATGTGTCCCCGTTGACC 61.333 63.158 0.00 0.00 34.25 4.02
1113 1368 1.198713 GAGGGAGGCACAGATCTCAA 58.801 55.000 0.00 0.00 0.00 3.02
1116 1371 0.532573 GGAGGCACAGATCTCAACGA 59.467 55.000 0.00 0.00 0.00 3.85
1849 2177 0.682852 ATGGAAACGTGACGGAAGGA 59.317 50.000 10.66 0.00 0.00 3.36
1917 2245 6.696441 TTTCGAAAACTAAGGGCAAAACTA 57.304 33.333 8.44 0.00 0.00 2.24
2125 2455 4.524328 CACTTTGACTTGCCTAAGGGAATT 59.476 41.667 0.00 0.00 38.26 2.17
2242 2574 5.666265 AGGAACGGAGGGAGTAGAAAATATT 59.334 40.000 0.00 0.00 0.00 1.28
2304 2642 2.794350 CGTGGGCTTGTTCACAATTTTC 59.206 45.455 0.00 0.00 35.02 2.29
2307 2645 3.196469 TGGGCTTGTTCACAATTTTCACA 59.804 39.130 0.00 0.00 35.02 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 8.964476 TCACAGTGAAATCTCTAAAAAGACTT 57.036 30.769 0.00 0.00 0.00 3.01
15 16 8.831550 GTTCACAGTGAAATCTCTAAAAAGACT 58.168 33.333 17.83 0.00 38.22 3.24
16 17 8.831550 AGTTCACAGTGAAATCTCTAAAAAGAC 58.168 33.333 17.83 1.05 38.22 3.01
17 18 8.964476 AGTTCACAGTGAAATCTCTAAAAAGA 57.036 30.769 17.83 0.00 38.22 2.52
19 20 9.607988 TGTAGTTCACAGTGAAATCTCTAAAAA 57.392 29.630 19.19 0.00 38.22 1.94
20 21 9.778741 ATGTAGTTCACAGTGAAATCTCTAAAA 57.221 29.630 19.19 8.16 41.51 1.52
22 23 9.856488 GTATGTAGTTCACAGTGAAATCTCTAA 57.144 33.333 19.19 0.00 41.51 2.10
23 24 8.182227 CGTATGTAGTTCACAGTGAAATCTCTA 58.818 37.037 19.19 12.33 41.51 2.43
24 25 7.030165 CGTATGTAGTTCACAGTGAAATCTCT 58.970 38.462 19.19 13.27 41.51 3.10
25 26 7.027760 TCGTATGTAGTTCACAGTGAAATCTC 58.972 38.462 19.19 13.84 41.51 2.75
26 27 6.920817 TCGTATGTAGTTCACAGTGAAATCT 58.079 36.000 19.19 14.27 41.51 2.40
27 28 7.576750 TTCGTATGTAGTTCACAGTGAAATC 57.423 36.000 19.19 11.65 41.51 2.17
28 29 7.439955 TGTTTCGTATGTAGTTCACAGTGAAAT 59.560 33.333 19.51 19.51 41.51 2.17
29 30 6.757478 TGTTTCGTATGTAGTTCACAGTGAAA 59.243 34.615 17.83 2.62 41.51 2.69
30 31 6.274579 TGTTTCGTATGTAGTTCACAGTGAA 58.725 36.000 12.24 12.24 41.51 3.18
31 32 5.834169 TGTTTCGTATGTAGTTCACAGTGA 58.166 37.500 0.00 0.00 41.51 3.41
32 33 6.519353 TTGTTTCGTATGTAGTTCACAGTG 57.481 37.500 0.00 0.00 41.51 3.66
33 34 7.542534 TTTTGTTTCGTATGTAGTTCACAGT 57.457 32.000 0.00 0.00 41.51 3.55
34 35 8.279800 TCATTTTGTTTCGTATGTAGTTCACAG 58.720 33.333 0.00 0.00 41.51 3.66
35 36 8.144155 TCATTTTGTTTCGTATGTAGTTCACA 57.856 30.769 0.00 0.00 42.69 3.58
36 37 8.280497 ACTCATTTTGTTTCGTATGTAGTTCAC 58.720 33.333 0.00 0.00 0.00 3.18
37 38 8.279800 CACTCATTTTGTTTCGTATGTAGTTCA 58.720 33.333 0.00 0.00 0.00 3.18
38 39 8.492748 TCACTCATTTTGTTTCGTATGTAGTTC 58.507 33.333 0.00 0.00 0.00 3.01
39 40 8.373048 TCACTCATTTTGTTTCGTATGTAGTT 57.627 30.769 0.00 0.00 0.00 2.24
40 41 7.956420 TCACTCATTTTGTTTCGTATGTAGT 57.044 32.000 0.00 0.00 0.00 2.73
41 42 9.478019 GATTCACTCATTTTGTTTCGTATGTAG 57.522 33.333 0.00 0.00 0.00 2.74
42 43 9.214957 AGATTCACTCATTTTGTTTCGTATGTA 57.785 29.630 0.00 0.00 0.00 2.29
43 44 8.099364 AGATTCACTCATTTTGTTTCGTATGT 57.901 30.769 0.00 0.00 0.00 2.29
44 45 9.478019 GTAGATTCACTCATTTTGTTTCGTATG 57.522 33.333 0.00 0.00 0.00 2.39
45 46 9.214957 TGTAGATTCACTCATTTTGTTTCGTAT 57.785 29.630 0.00 0.00 0.00 3.06
46 47 8.492748 GTGTAGATTCACTCATTTTGTTTCGTA 58.507 33.333 0.00 0.00 35.68 3.43
47 48 7.226720 AGTGTAGATTCACTCATTTTGTTTCGT 59.773 33.333 0.00 0.00 44.07 3.85
48 49 7.576236 AGTGTAGATTCACTCATTTTGTTTCG 58.424 34.615 0.00 0.00 44.07 3.46
61 62 7.203910 AGACATATTTCGGAGTGTAGATTCAC 58.796 38.462 0.00 0.00 38.46 3.18
62 63 7.348080 AGACATATTTCGGAGTGTAGATTCA 57.652 36.000 0.00 0.00 0.00 2.57
70 71 9.737427 GGATGTATATAGACATATTTCGGAGTG 57.263 37.037 12.82 0.00 40.18 3.51
71 72 9.475620 TGGATGTATATAGACATATTTCGGAGT 57.524 33.333 12.82 0.00 40.18 3.85
89 90 9.154632 TCCACTACAAACTACATATGGATGTAT 57.845 33.333 7.80 0.00 45.42 2.29
90 91 8.541899 TCCACTACAAACTACATATGGATGTA 57.458 34.615 7.80 3.84 44.77 2.29
92 93 8.908786 ATTCCACTACAAACTACATATGGATG 57.091 34.615 7.80 0.00 35.03 3.51
93 94 8.157476 GGATTCCACTACAAACTACATATGGAT 58.843 37.037 7.80 0.00 35.03 3.41
94 95 7.419750 GGGATTCCACTACAAACTACATATGGA 60.420 40.741 7.80 0.00 33.21 3.41
95 96 6.710744 GGGATTCCACTACAAACTACATATGG 59.289 42.308 7.80 0.00 0.00 2.74
96 97 7.509546 AGGGATTCCACTACAAACTACATATG 58.490 38.462 4.80 0.00 34.83 1.78
97 98 7.691993 AGGGATTCCACTACAAACTACATAT 57.308 36.000 4.80 0.00 34.83 1.78
98 99 8.612486 TTAGGGATTCCACTACAAACTACATA 57.388 34.615 4.80 0.00 34.83 2.29
99 100 7.504926 TTAGGGATTCCACTACAAACTACAT 57.495 36.000 4.80 0.00 34.83 2.29
100 101 6.938698 TTAGGGATTCCACTACAAACTACA 57.061 37.500 4.80 0.00 34.83 2.74
101 102 8.625786 TTTTTAGGGATTCCACTACAAACTAC 57.374 34.615 4.80 0.00 34.83 2.73
102 103 8.662255 TCTTTTTAGGGATTCCACTACAAACTA 58.338 33.333 4.80 0.00 34.83 2.24
103 104 7.447545 GTCTTTTTAGGGATTCCACTACAAACT 59.552 37.037 4.80 0.00 34.83 2.66
104 105 7.447545 AGTCTTTTTAGGGATTCCACTACAAAC 59.552 37.037 4.80 1.09 34.83 2.93
105 106 7.523415 AGTCTTTTTAGGGATTCCACTACAAA 58.477 34.615 4.80 8.22 34.83 2.83
106 107 7.086685 AGTCTTTTTAGGGATTCCACTACAA 57.913 36.000 4.80 1.18 34.83 2.41
107 108 6.697641 AGTCTTTTTAGGGATTCCACTACA 57.302 37.500 4.80 0.00 34.83 2.74
108 109 8.098912 TGTAAGTCTTTTTAGGGATTCCACTAC 58.901 37.037 4.80 0.00 34.83 2.73
109 110 8.209802 TGTAAGTCTTTTTAGGGATTCCACTA 57.790 34.615 4.80 1.21 34.83 2.74
110 111 7.086685 TGTAAGTCTTTTTAGGGATTCCACT 57.913 36.000 4.80 2.18 34.83 4.00
111 112 7.939784 ATGTAAGTCTTTTTAGGGATTCCAC 57.060 36.000 4.80 0.00 34.83 4.02
112 113 8.950007 AAATGTAAGTCTTTTTAGGGATTCCA 57.050 30.769 4.80 0.00 34.83 3.53
117 118 9.511272 GTTCCTAAATGTAAGTCTTTTTAGGGA 57.489 33.333 22.79 16.88 0.00 4.20
118 119 8.448615 CGTTCCTAAATGTAAGTCTTTTTAGGG 58.551 37.037 22.79 11.36 0.00 3.53
119 120 8.448615 CCGTTCCTAAATGTAAGTCTTTTTAGG 58.551 37.037 19.74 19.74 0.00 2.69
120 121 9.211485 TCCGTTCCTAAATGTAAGTCTTTTTAG 57.789 33.333 7.75 7.75 0.00 1.85
121 122 9.211485 CTCCGTTCCTAAATGTAAGTCTTTTTA 57.789 33.333 0.00 0.00 0.00 1.52
122 123 7.174426 CCTCCGTTCCTAAATGTAAGTCTTTTT 59.826 37.037 0.00 0.00 0.00 1.94
123 124 6.653740 CCTCCGTTCCTAAATGTAAGTCTTTT 59.346 38.462 0.00 0.00 0.00 2.27
124 125 6.171213 CCTCCGTTCCTAAATGTAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
125 126 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
126 127 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
127 128 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
128 129 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
129 130 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
130 131 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
131 132 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
132 133 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
133 134 3.705072 ACTACTCCCTCCGTTCCTAAATG 59.295 47.826 0.00 0.00 0.00 2.32
134 135 3.959449 GACTACTCCCTCCGTTCCTAAAT 59.041 47.826 0.00 0.00 0.00 1.40
135 136 3.245371 TGACTACTCCCTCCGTTCCTAAA 60.245 47.826 0.00 0.00 0.00 1.85
136 137 2.309755 TGACTACTCCCTCCGTTCCTAA 59.690 50.000 0.00 0.00 0.00 2.69
137 138 1.918262 TGACTACTCCCTCCGTTCCTA 59.082 52.381 0.00 0.00 0.00 2.94
138 139 0.702902 TGACTACTCCCTCCGTTCCT 59.297 55.000 0.00 0.00 0.00 3.36
139 140 0.816373 GTGACTACTCCCTCCGTTCC 59.184 60.000 0.00 0.00 0.00 3.62
140 141 1.836802 AGTGACTACTCCCTCCGTTC 58.163 55.000 0.00 0.00 28.79 3.95
141 142 1.893801 CAAGTGACTACTCCCTCCGTT 59.106 52.381 0.00 0.00 35.69 4.44
142 143 1.203025 ACAAGTGACTACTCCCTCCGT 60.203 52.381 0.00 0.00 35.69 4.69
143 144 1.546961 ACAAGTGACTACTCCCTCCG 58.453 55.000 0.00 0.00 35.69 4.63
144 145 2.613223 GCAACAAGTGACTACTCCCTCC 60.613 54.545 0.00 0.00 35.69 4.30
145 146 2.037251 TGCAACAAGTGACTACTCCCTC 59.963 50.000 0.00 0.00 35.69 4.30
146 147 2.047061 TGCAACAAGTGACTACTCCCT 58.953 47.619 0.00 0.00 35.69 4.20
147 148 2.543777 TGCAACAAGTGACTACTCCC 57.456 50.000 0.00 0.00 35.69 4.30
148 149 4.319177 AGATTGCAACAAGTGACTACTCC 58.681 43.478 0.00 0.00 35.69 3.85
149 150 5.233988 AGAGATTGCAACAAGTGACTACTC 58.766 41.667 0.00 0.00 35.69 2.59
150 151 5.220710 AGAGATTGCAACAAGTGACTACT 57.779 39.130 0.00 0.00 39.32 2.57
178 179 7.290813 ACTCCCTCCATTTCCAAATATAAGTC 58.709 38.462 0.00 0.00 0.00 3.01
184 185 6.184789 GTTGTACTCCCTCCATTTCCAAATA 58.815 40.000 0.00 0.00 0.00 1.40
194 195 0.249120 CATGCGTTGTACTCCCTCCA 59.751 55.000 0.00 0.00 0.00 3.86
224 225 6.072112 TGCAAGTATCAAAAGGAAAGTCAC 57.928 37.500 0.00 0.00 0.00 3.67
390 392 1.029681 GACGGAAGGGCAAAAACACT 58.970 50.000 0.00 0.00 0.00 3.55
632 795 1.925285 TTCCTTCGCTGGCCATGGAT 61.925 55.000 18.40 0.00 0.00 3.41
966 1216 1.194781 AGCACCAGATCGAACAGGGT 61.195 55.000 8.94 6.19 0.00 4.34
980 1230 1.589716 GCCTCACACATTCCAGCACC 61.590 60.000 0.00 0.00 0.00 5.01
982 1232 0.038599 ATGCCTCACACATTCCAGCA 59.961 50.000 0.00 0.00 0.00 4.41
1014 1264 1.838073 GAGGGTCAACGGGGACACAT 61.838 60.000 12.61 0.30 43.76 3.21
1113 1368 1.165907 CCGCATACATTGGCCATCGT 61.166 55.000 6.09 9.81 0.00 3.73
1116 1371 2.554636 CGCCGCATACATTGGCCAT 61.555 57.895 6.09 0.00 46.12 4.40
1198 1455 1.132721 TCCTCCACCATCTATCCCCAG 60.133 57.143 0.00 0.00 0.00 4.45
1381 1701 4.829518 GCCAAACGAATCGGCGCC 62.830 66.667 19.07 19.07 35.79 6.53
1648 1974 6.126883 ACGGACCAAATATCTCTAATGGACAA 60.127 38.462 0.00 0.00 35.16 3.18
1849 2177 3.507622 GCTTGCTCCTCTTATGGTTTTGT 59.492 43.478 0.00 0.00 0.00 2.83
1917 2245 1.825474 CCTAGTTGTGTCCCACTCGAT 59.175 52.381 0.00 0.00 35.11 3.59
2109 2439 2.567169 GGCAAAATTCCCTTAGGCAAGT 59.433 45.455 0.00 0.00 0.00 3.16
2242 2574 0.901124 GGTTGCCCCAACATGCATTA 59.099 50.000 0.00 0.00 45.11 1.90
2304 2642 2.051334 TGAACAACCACTCCCTTGTG 57.949 50.000 0.00 0.00 37.66 3.33
2307 2645 5.245977 CCATTAAATGAACAACCACTCCCTT 59.754 40.000 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.