Multiple sequence alignment - TraesCS4B01G042700

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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 TraesCS4B01G042700 chr4B 100.000 3065 0 0 1 3065 30361277 30364341 0.000000e+00 5661
1 TraesCS4B01G042700 chr4A 92.950 2936 134 25 172 3065 582841852 582838948 0.000000e+00 4207
2 TraesCS4B01G042700 chr4A 86.008 243 22 5 54 296 582842107 582841877 1.820000e-62 250
3 TraesCS4B01G042700 chr4D 95.863 1571 51 4 566 2136 18463828 18465384 0.000000e+00 2529
4 TraesCS4B01G042700 chr4D 91.209 910 59 15 2163 3065 18465751 18466646 0.000000e+00 1218
5 TraesCS4B01G042700 chr4D 95.899 317 13 0 173 489 18463340 18463656 5.860000e-142 514
6 TraesCS4B01G042700 chr4D 87.654 243 16 6 54 296 18463087 18463315 1.400000e-68 270
7 TraesCS4B01G042700 chr5A 89.744 156 16 0 1319 1474 1347288 1347133 1.860000e-47 200
8 TraesCS4B01G042700 chr5B 89.404 151 16 0 1324 1474 3475045 3475195 1.120000e-44 191
9 TraesCS4B01G042700 chr5D 86.391 169 23 0 1328 1496 2511786 2511618 5.220000e-43 185
10 TraesCS4B01G042700 chr5D 83.333 150 23 2 1327 1475 322577525 322577673 1.480000e-28 137
11 TraesCS4B01G042700 chr2A 86.111 144 16 3 1334 1475 8543566 8543707 5.290000e-33 152
12 TraesCS4B01G042700 chr2D 85.417 144 17 3 1334 1475 9079999 9080140 2.460000e-31 147
13 TraesCS4B01G042700 chr2B 84.722 144 18 3 1334 1475 11837364 11837223 1.150000e-29 141


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 TraesCS4B01G042700 chr4B 30361277 30364341 3064 False 5661.00 5661 100.00000 1 3065 1 chr4B.!!$F1 3064
1 TraesCS4B01G042700 chr4A 582838948 582842107 3159 True 2228.50 4207 89.47900 54 3065 2 chr4A.!!$R1 3011
2 TraesCS4B01G042700 chr4D 18463087 18466646 3559 False 1132.75 2529 92.65625 54 3065 4 chr4D.!!$F1 3011

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
44 45 0.108329 CAAATACGGGTCGACCTGCT 60.108 55.0 37.81 27.13 46.43 4.24 F
45 46 0.175073 AAATACGGGTCGACCTGCTC 59.825 55.0 37.81 19.44 46.43 4.26 F
166 167 0.321653 CCCAACTCAGAAAGGTCCCG 60.322 60.0 0.00 0.00 0.00 5.14 F
981 1243 0.338814 GGGAGGTCTCAGGGGTCTTA 59.661 60.0 0.14 0.00 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1138 1400 0.178903 AGGTAGCTGTGGTGGAAGGA 60.179 55.0 0.0 0.0 0.00 3.36 R
1874 2136 0.802607 GTTCATGGACGAGGAGCGAC 60.803 60.0 0.0 0.0 44.57 5.19 R
1974 2236 0.822164 AGTTACCGCTGCTTCCGTAT 59.178 50.0 0.0 0.0 0.00 3.06 R
2187 2789 0.107410 AAGGCAAGTTCACCGTCACA 60.107 50.0 0.0 0.0 0.00 3.58 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
20 21 3.434940 AAAGGCTACTACAACCTTGGG 57.565 47.619 0.00 0.00 42.99 4.12
21 22 0.618981 AGGCTACTACAACCTTGGGC 59.381 55.000 0.00 0.00 0.00 5.36
22 23 0.326927 GGCTACTACAACCTTGGGCA 59.673 55.000 0.00 0.00 0.00 5.36
23 24 1.271707 GGCTACTACAACCTTGGGCAA 60.272 52.381 0.00 0.00 0.00 4.52
24 25 1.810755 GCTACTACAACCTTGGGCAAC 59.189 52.381 0.00 0.00 0.00 4.17
37 38 1.798087 GGCAACCAAATACGGGTCG 59.202 57.895 0.00 0.00 37.77 4.79
38 39 0.674269 GGCAACCAAATACGGGTCGA 60.674 55.000 0.00 0.00 37.77 4.20
39 40 0.445043 GCAACCAAATACGGGTCGAC 59.555 55.000 7.13 7.13 37.77 4.20
40 41 1.081094 CAACCAAATACGGGTCGACC 58.919 55.000 27.04 27.04 37.77 4.79
41 42 0.978907 AACCAAATACGGGTCGACCT 59.021 50.000 32.52 17.66 37.77 3.85
43 44 1.087771 CCAAATACGGGTCGACCTGC 61.088 60.000 37.81 20.52 46.43 4.85
44 45 0.108329 CAAATACGGGTCGACCTGCT 60.108 55.000 37.81 27.13 46.43 4.24
45 46 0.175073 AAATACGGGTCGACCTGCTC 59.825 55.000 37.81 19.44 46.43 4.26
46 47 2.001361 AATACGGGTCGACCTGCTCG 62.001 60.000 37.81 30.33 46.43 5.03
47 48 3.907260 TACGGGTCGACCTGCTCGT 62.907 63.158 37.81 33.55 46.43 4.18
48 49 4.052229 CGGGTCGACCTGCTCGTT 62.052 66.667 32.52 0.00 43.45 3.85
49 50 2.126031 GGGTCGACCTGCTCGTTC 60.126 66.667 32.52 10.90 43.45 3.95
50 51 2.637383 GGGTCGACCTGCTCGTTCT 61.637 63.158 32.52 0.00 43.45 3.01
51 52 1.444553 GGTCGACCTGCTCGTTCTG 60.445 63.158 27.64 0.00 43.45 3.02
52 53 1.444553 GTCGACCTGCTCGTTCTGG 60.445 63.158 3.51 2.28 43.45 3.86
66 67 4.660168 TCGTTCTGGTCCTAGTAACTTCT 58.340 43.478 0.00 0.00 0.00 2.85
103 104 8.664211 ATCGAAAGGTAGAGATTAATTTGGTC 57.336 34.615 0.00 0.00 0.00 4.02
110 111 7.039882 GGTAGAGATTAATTTGGTCAAGTCGA 58.960 38.462 0.00 0.00 0.00 4.20
111 112 7.548075 GGTAGAGATTAATTTGGTCAAGTCGAA 59.452 37.037 0.00 0.00 0.00 3.71
112 113 7.365840 AGAGATTAATTTGGTCAAGTCGAAC 57.634 36.000 0.00 0.00 0.00 3.95
113 114 6.090898 AGAGATTAATTTGGTCAAGTCGAACG 59.909 38.462 0.00 0.00 32.01 3.95
114 115 4.735662 TTAATTTGGTCAAGTCGAACGG 57.264 40.909 0.00 0.00 32.01 4.44
116 117 2.886862 TTTGGTCAAGTCGAACGGTA 57.113 45.000 0.00 0.00 32.01 4.02
118 119 2.357327 TGGTCAAGTCGAACGGTATG 57.643 50.000 0.00 0.00 32.01 2.39
119 120 1.614903 TGGTCAAGTCGAACGGTATGT 59.385 47.619 0.00 0.00 32.01 2.29
120 121 2.036217 TGGTCAAGTCGAACGGTATGTT 59.964 45.455 0.00 0.00 45.61 2.71
121 122 3.062042 GGTCAAGTCGAACGGTATGTTT 58.938 45.455 0.00 0.00 42.09 2.83
123 124 4.376717 GGTCAAGTCGAACGGTATGTTTTC 60.377 45.833 0.00 0.00 42.09 2.29
124 125 4.209703 GTCAAGTCGAACGGTATGTTTTCA 59.790 41.667 0.00 0.00 42.09 2.69
125 126 4.809958 TCAAGTCGAACGGTATGTTTTCAA 59.190 37.500 0.00 0.00 42.09 2.69
126 127 5.293814 TCAAGTCGAACGGTATGTTTTCAAA 59.706 36.000 0.00 0.00 42.09 2.69
127 128 5.738118 AGTCGAACGGTATGTTTTCAAAA 57.262 34.783 0.00 0.00 42.09 2.44
128 129 6.121613 AGTCGAACGGTATGTTTTCAAAAA 57.878 33.333 0.00 0.00 42.09 1.94
129 130 5.967088 AGTCGAACGGTATGTTTTCAAAAAC 59.033 36.000 10.67 10.67 46.40 2.43
163 164 5.167303 ACTTATCCCAACTCAGAAAGGTC 57.833 43.478 0.00 0.00 0.00 3.85
166 167 0.321653 CCCAACTCAGAAAGGTCCCG 60.322 60.000 0.00 0.00 0.00 5.14
168 169 1.608283 CCAACTCAGAAAGGTCCCGTC 60.608 57.143 0.00 0.00 0.00 4.79
169 170 1.344763 CAACTCAGAAAGGTCCCGTCT 59.655 52.381 0.00 0.00 0.00 4.18
170 171 1.258676 ACTCAGAAAGGTCCCGTCTC 58.741 55.000 0.00 0.00 0.00 3.36
198 341 1.076632 CTCGGTCCCCAGAGTAGCT 60.077 63.158 0.00 0.00 0.00 3.32
209 352 4.409247 CCCCAGAGTAGCTACCAAATAGTT 59.591 45.833 20.31 0.00 32.90 2.24
283 426 0.449388 GGCGAATTCCTGTGCAGAAG 59.551 55.000 0.00 0.00 0.00 2.85
317 460 4.316205 AAAACAAGGTCATTCGTTTCCC 57.684 40.909 0.00 0.00 31.45 3.97
318 461 2.649531 ACAAGGTCATTCGTTTCCCA 57.350 45.000 0.00 0.00 0.00 4.37
350 493 1.028905 CAAGGAACAAAGGCGTCCAA 58.971 50.000 0.00 0.00 0.00 3.53
453 602 3.776158 GCACACATGCCCTTTCCA 58.224 55.556 0.00 0.00 46.97 3.53
454 603 1.290009 GCACACATGCCCTTTCCAC 59.710 57.895 0.00 0.00 46.97 4.02
457 606 0.827507 ACACATGCCCTTTCCACCAC 60.828 55.000 0.00 0.00 0.00 4.16
458 607 0.540365 CACATGCCCTTTCCACCACT 60.540 55.000 0.00 0.00 0.00 4.00
495 644 4.968719 TGCCTTGTATTCTCTCCCTATCAA 59.031 41.667 0.00 0.00 0.00 2.57
501 650 7.531857 TGTATTCTCTCCCTATCAACTCATC 57.468 40.000 0.00 0.00 0.00 2.92
532 693 2.024846 CACTCAGACCCTCCCTCTCTAA 60.025 54.545 0.00 0.00 0.00 2.10
586 830 5.721225 AGTAGGGAGAGTATCACATCCAAT 58.279 41.667 0.00 0.00 37.82 3.16
655 899 2.790433 CTAGCTAGCCCTCCTACAGAG 58.210 57.143 12.13 0.00 42.83 3.35
703 965 1.060553 GTGTGTGTGTGTGTGAACTCG 59.939 52.381 0.00 0.00 0.00 4.18
759 1021 1.565390 CCCCTCTGCAACTCCCATGA 61.565 60.000 0.00 0.00 0.00 3.07
793 1055 4.166531 TCCTCCTAGTCCTAGACCTCTTTC 59.833 50.000 2.86 0.00 35.21 2.62
796 1058 3.955551 CCTAGTCCTAGACCTCTTTCACC 59.044 52.174 2.86 0.00 35.21 4.02
803 1065 4.340950 CCTAGACCTCTTTCACCATCTCTC 59.659 50.000 0.00 0.00 0.00 3.20
816 1078 5.418524 TCACCATCTCTCTCTTTCTCTCTTG 59.581 44.000 0.00 0.00 0.00 3.02
820 1082 4.148079 TCTCTCTCTTTCTCTCTTGCACA 58.852 43.478 0.00 0.00 0.00 4.57
822 1084 3.638627 TCTCTCTTTCTCTCTTGCACACA 59.361 43.478 0.00 0.00 0.00 3.72
823 1085 3.987547 TCTCTTTCTCTCTTGCACACAG 58.012 45.455 0.00 0.00 0.00 3.66
862 1124 2.203337 GGCTTATGCATGGCCGGA 60.203 61.111 23.20 0.00 41.91 5.14
867 1129 0.747644 TTATGCATGGCCGGACACAG 60.748 55.000 15.41 10.38 0.00 3.66
873 1135 1.337384 ATGGCCGGACACAGCTGATA 61.337 55.000 23.35 0.00 0.00 2.15
958 1220 0.397254 TCTTCTTCCGAGGGCCTAGG 60.397 60.000 25.41 25.41 0.00 3.02
981 1243 0.338814 GGGAGGTCTCAGGGGTCTTA 59.661 60.000 0.14 0.00 0.00 2.10
1128 1390 0.712380 ACCATTCCTCCCCTGCATTT 59.288 50.000 0.00 0.00 0.00 2.32
1138 1400 3.434319 CTGCATTTGCCGCCGACT 61.434 61.111 0.00 0.00 41.18 4.18
1210 1472 1.215647 GCCGAGATCGACAACCAGT 59.784 57.895 3.31 0.00 43.02 4.00
1628 1890 4.082523 CGGCGAGGGGAAGAAGCA 62.083 66.667 0.00 0.00 0.00 3.91
1874 2136 2.223112 CGAGGCCGAACAATTTGATCAG 60.223 50.000 2.79 0.00 38.22 2.90
1974 2236 2.272146 GGCTTCGGCAATGGAGGA 59.728 61.111 0.00 0.00 43.96 3.71
1989 2251 2.017559 GAGGATACGGAAGCAGCGGT 62.018 60.000 0.00 0.00 46.39 5.68
2052 2314 1.605753 GAGTGGTGTTTCCCAACTCC 58.394 55.000 0.19 0.19 44.01 3.85
2138 2400 6.140896 GCACGTGCACTTATATACATACTG 57.859 41.667 34.52 0.00 41.59 2.74
2236 2842 5.739752 GCATGATGCAGTATTGTAGTTGA 57.260 39.130 13.36 0.00 44.26 3.18
2295 2901 5.824429 CATGTAATTCATGCGTGGATTCTT 58.176 37.500 15.93 4.33 45.69 2.52
2338 2944 4.766404 AATTGTCAAACTGGAATCCGAC 57.234 40.909 0.00 0.00 0.00 4.79
2504 3111 9.135843 GCGCTTCAATGTTACATACATATACTA 57.864 33.333 0.00 0.00 46.75 1.82
2725 3334 9.612066 TTTATGCATATACTCACAAATCACTCA 57.388 29.630 7.36 0.00 0.00 3.41
2769 3378 9.750125 GGTAAAAGAAAGTCTTCATGTTTGAAT 57.250 29.630 0.00 0.00 40.95 2.57
2808 3417 9.897744 TTTATTCAGCTGACAAATTTTAGAGTG 57.102 29.630 18.03 0.00 0.00 3.51
2828 3437 4.690748 AGTGTCAATCTTGTAACATCACCG 59.309 41.667 0.00 0.00 0.00 4.94
2831 3440 4.092968 GTCAATCTTGTAACATCACCGTCC 59.907 45.833 0.00 0.00 0.00 4.79
2841 3450 2.498481 ACATCACCGTCCGATTAAAGGA 59.502 45.455 0.00 0.00 34.99 3.36
2883 3492 6.698329 TGTCAACAAATTCTGCTTTCTTGATG 59.302 34.615 0.00 0.00 29.68 3.07
2884 3493 6.919662 GTCAACAAATTCTGCTTTCTTGATGA 59.080 34.615 0.00 0.00 29.68 2.92
2885 3494 7.597743 GTCAACAAATTCTGCTTTCTTGATGAT 59.402 33.333 0.00 0.00 33.31 2.45
2886 3495 8.795513 TCAACAAATTCTGCTTTCTTGATGATA 58.204 29.630 0.00 0.00 0.00 2.15
2887 3496 9.414295 CAACAAATTCTGCTTTCTTGATGATAA 57.586 29.630 0.00 0.00 0.00 1.75
2888 3497 8.976986 ACAAATTCTGCTTTCTTGATGATAAC 57.023 30.769 0.00 0.00 0.00 1.89
2897 3506 7.172532 TGCTTTCTTGATGATAACGTTAACACT 59.827 33.333 18.98 9.57 0.00 3.55
2902 3511 7.654116 TCTTGATGATAACGTTAACACTGTTGA 59.346 33.333 18.98 11.47 0.00 3.18
2918 3527 6.127842 ACACTGTTGAAGTTAAAACACCGATT 60.128 34.615 0.56 0.00 36.83 3.34
2925 3534 3.823873 AGTTAAAACACCGATTGCCATCA 59.176 39.130 0.00 0.00 0.00 3.07
2971 3580 1.737838 TAGGAAAACCTGCATCTGCG 58.262 50.000 0.00 0.00 45.83 5.18
3009 3618 7.326968 TGCATGATTTTACGACCATAATTGA 57.673 32.000 0.00 0.00 0.00 2.57
3011 3620 8.412456 TGCATGATTTTACGACCATAATTGATT 58.588 29.630 0.00 0.00 0.00 2.57
3014 3623 8.627487 TGATTTTACGACCATAATTGATTTGC 57.373 30.769 0.00 0.00 0.00 3.68
3023 3632 9.256477 CGACCATAATTGATTTGCTAGTTAGTA 57.744 33.333 0.00 0.00 0.00 1.82
3060 3669 1.737838 ACGCAGTCATACATGTTGGG 58.262 50.000 2.30 6.83 29.74 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.554564 GCCCAAGGTTGTAGTAGCCTTT 60.555 50.000 0.00 0.00 46.59 3.11
2 3 0.618981 GCCCAAGGTTGTAGTAGCCT 59.381 55.000 0.00 0.00 42.54 4.58
3 4 0.326927 TGCCCAAGGTTGTAGTAGCC 59.673 55.000 0.00 0.00 0.00 3.93
4 5 1.810755 GTTGCCCAAGGTTGTAGTAGC 59.189 52.381 0.00 0.00 0.00 3.58
5 6 2.224670 TGGTTGCCCAAGGTTGTAGTAG 60.225 50.000 0.00 0.00 37.98 2.57
6 7 1.775459 TGGTTGCCCAAGGTTGTAGTA 59.225 47.619 0.00 0.00 37.98 1.82
7 8 0.553819 TGGTTGCCCAAGGTTGTAGT 59.446 50.000 0.00 0.00 37.98 2.73
8 9 1.698506 TTGGTTGCCCAAGGTTGTAG 58.301 50.000 0.00 0.00 45.93 2.74
9 10 3.926729 TTGGTTGCCCAAGGTTGTA 57.073 47.368 0.00 0.00 45.93 2.41
10 11 4.796408 TTGGTTGCCCAAGGTTGT 57.204 50.000 0.00 0.00 45.93 3.32
17 18 0.609681 GACCCGTATTTGGTTGCCCA 60.610 55.000 0.00 0.00 39.65 5.36
18 19 1.650314 CGACCCGTATTTGGTTGCCC 61.650 60.000 0.00 0.00 35.85 5.36
19 20 0.674269 TCGACCCGTATTTGGTTGCC 60.674 55.000 0.00 0.00 37.22 4.52
20 21 0.445043 GTCGACCCGTATTTGGTTGC 59.555 55.000 3.51 0.00 37.22 4.17
21 22 1.081094 GGTCGACCCGTATTTGGTTG 58.919 55.000 24.75 0.00 38.44 3.77
22 23 0.978907 AGGTCGACCCGTATTTGGTT 59.021 50.000 30.82 5.32 35.85 3.67
23 24 0.248289 CAGGTCGACCCGTATTTGGT 59.752 55.000 30.82 6.14 39.32 3.67
24 25 1.087771 GCAGGTCGACCCGTATTTGG 61.088 60.000 30.82 11.15 38.74 3.28
25 26 0.108329 AGCAGGTCGACCCGTATTTG 60.108 55.000 30.82 21.29 38.74 2.32
26 27 0.175073 GAGCAGGTCGACCCGTATTT 59.825 55.000 30.82 8.61 38.74 1.40
27 28 1.814527 GAGCAGGTCGACCCGTATT 59.185 57.895 30.82 9.44 38.74 1.89
28 29 3.522808 GAGCAGGTCGACCCGTAT 58.477 61.111 30.82 14.70 38.74 3.06
37 38 4.580835 GACCAGAACGAGCAGGTC 57.419 61.111 7.73 7.73 43.18 3.85
38 39 0.251653 TAGGACCAGAACGAGCAGGT 60.252 55.000 0.00 0.00 37.00 4.00
39 40 0.457851 CTAGGACCAGAACGAGCAGG 59.542 60.000 0.00 0.00 0.00 4.85
40 41 1.178276 ACTAGGACCAGAACGAGCAG 58.822 55.000 0.00 0.00 0.00 4.24
41 42 2.490903 GTTACTAGGACCAGAACGAGCA 59.509 50.000 0.00 0.00 0.00 4.26
42 43 2.754002 AGTTACTAGGACCAGAACGAGC 59.246 50.000 0.00 0.00 0.00 5.03
43 44 4.701171 AGAAGTTACTAGGACCAGAACGAG 59.299 45.833 0.00 0.00 0.00 4.18
44 45 4.660168 AGAAGTTACTAGGACCAGAACGA 58.340 43.478 0.00 0.00 0.00 3.85
45 46 5.388408 AAGAAGTTACTAGGACCAGAACG 57.612 43.478 0.00 0.00 0.00 3.95
46 47 7.331440 GCTAAAAGAAGTTACTAGGACCAGAAC 59.669 40.741 0.00 0.00 0.00 3.01
47 48 7.384477 GCTAAAAGAAGTTACTAGGACCAGAA 58.616 38.462 0.00 0.00 0.00 3.02
48 49 6.070938 GGCTAAAAGAAGTTACTAGGACCAGA 60.071 42.308 0.00 0.00 0.00 3.86
49 50 6.107343 GGCTAAAAGAAGTTACTAGGACCAG 58.893 44.000 0.00 0.00 0.00 4.00
50 51 5.337009 CGGCTAAAAGAAGTTACTAGGACCA 60.337 44.000 0.00 0.00 0.00 4.02
51 52 5.107824 CGGCTAAAAGAAGTTACTAGGACC 58.892 45.833 0.00 0.00 0.00 4.46
52 53 4.565962 GCGGCTAAAAGAAGTTACTAGGAC 59.434 45.833 0.00 0.00 0.00 3.85
66 67 2.006888 CCTTTCGATCTGCGGCTAAAA 58.993 47.619 0.00 0.00 41.33 1.52
103 104 4.718858 TGAAAACATACCGTTCGACTTG 57.281 40.909 0.00 0.00 36.59 3.16
110 111 6.121613 TCTCGTTTTTGAAAACATACCGTT 57.878 33.333 16.79 0.00 46.52 4.44
111 112 5.295045 ACTCTCGTTTTTGAAAACATACCGT 59.705 36.000 16.79 6.40 46.52 4.83
112 113 5.619607 CACTCTCGTTTTTGAAAACATACCG 59.380 40.000 16.79 5.36 46.52 4.02
113 114 6.492254 ACACTCTCGTTTTTGAAAACATACC 58.508 36.000 16.79 0.00 46.52 2.73
114 115 8.333186 ACTACACTCTCGTTTTTGAAAACATAC 58.667 33.333 16.79 0.00 46.52 2.39
116 117 7.316544 ACTACACTCTCGTTTTTGAAAACAT 57.683 32.000 16.79 0.00 46.52 2.71
118 119 7.903062 AGTACTACACTCTCGTTTTTGAAAAC 58.097 34.615 8.85 8.85 38.00 2.43
119 120 8.483307 AAGTACTACACTCTCGTTTTTGAAAA 57.517 30.769 0.00 0.00 36.04 2.29
120 121 9.754382 ATAAGTACTACACTCTCGTTTTTGAAA 57.246 29.630 0.00 0.00 36.04 2.69
121 122 9.403110 GATAAGTACTACACTCTCGTTTTTGAA 57.597 33.333 0.00 0.00 36.04 2.69
123 124 7.275123 GGGATAAGTACTACACTCTCGTTTTTG 59.725 40.741 0.00 0.00 36.04 2.44
124 125 7.039504 TGGGATAAGTACTACACTCTCGTTTTT 60.040 37.037 0.00 0.00 36.04 1.94
125 126 6.435277 TGGGATAAGTACTACACTCTCGTTTT 59.565 38.462 0.00 0.00 36.04 2.43
126 127 5.948162 TGGGATAAGTACTACACTCTCGTTT 59.052 40.000 0.00 0.00 36.04 3.60
127 128 5.503927 TGGGATAAGTACTACACTCTCGTT 58.496 41.667 0.00 0.00 36.04 3.85
128 129 5.108187 TGGGATAAGTACTACACTCTCGT 57.892 43.478 0.00 0.00 36.04 4.18
129 130 5.589452 AGTTGGGATAAGTACTACACTCTCG 59.411 44.000 0.00 0.00 36.04 4.04
163 164 0.969894 GAGGTCATATGGGAGACGGG 59.030 60.000 2.13 0.00 35.63 5.28
166 167 1.614413 GACCGAGGTCATATGGGAGAC 59.386 57.143 16.75 0.00 44.02 3.36
168 169 0.969894 GGACCGAGGTCATATGGGAG 59.030 60.000 22.17 0.00 46.20 4.30
169 170 0.471211 GGGACCGAGGTCATATGGGA 60.471 60.000 22.17 0.00 46.20 4.37
170 171 1.481056 GGGGACCGAGGTCATATGGG 61.481 65.000 22.17 0.00 46.20 4.00
209 352 2.992124 TCAGACAACGGAACCAAAGA 57.008 45.000 0.00 0.00 0.00 2.52
220 363 3.279434 GTTGGGGTATGGATCAGACAAC 58.721 50.000 0.00 0.00 0.00 3.32
317 460 0.405585 TCCTTGGAGCCCCTTCTTTG 59.594 55.000 0.00 0.00 0.00 2.77
318 461 1.158007 TTCCTTGGAGCCCCTTCTTT 58.842 50.000 0.00 0.00 0.00 2.52
350 493 3.009115 AGCCATGGCCGTGTAGGT 61.009 61.111 33.14 9.27 43.70 3.08
453 602 2.300437 GCAGAAGAAGGACACTAGTGGT 59.700 50.000 26.12 12.20 34.19 4.16
454 603 2.354203 GGCAGAAGAAGGACACTAGTGG 60.354 54.545 26.12 9.07 34.19 4.00
457 606 3.007398 ACAAGGCAGAAGAAGGACACTAG 59.993 47.826 0.00 0.00 0.00 2.57
458 607 2.972713 ACAAGGCAGAAGAAGGACACTA 59.027 45.455 0.00 0.00 0.00 2.74
495 644 1.070758 GAGTGTGGTGTGTGGATGAGT 59.929 52.381 0.00 0.00 0.00 3.41
501 650 0.532862 GGTCTGAGTGTGGTGTGTGG 60.533 60.000 0.00 0.00 0.00 4.17
532 693 2.706190 GAGGGGTGTGCCATCTTATAGT 59.294 50.000 0.00 0.00 36.17 2.12
548 709 2.703007 CCCTACTTGAGATTGAGAGGGG 59.297 54.545 0.00 0.00 38.83 4.79
586 830 3.782523 GGGATGGATGGATGCCTAGAATA 59.217 47.826 0.00 0.00 31.24 1.75
655 899 0.322816 ACACACACATCATGGGCTCC 60.323 55.000 0.00 0.00 33.53 4.70
703 965 1.689273 CACTGGTACCTAGCTCATCCC 59.311 57.143 14.36 0.00 0.00 3.85
759 1021 7.742213 TCTAGGACTAGGAGGAGATAAATCTCT 59.258 40.741 17.25 5.96 41.63 3.10
793 1055 5.653507 CAAGAGAGAAAGAGAGAGATGGTG 58.346 45.833 0.00 0.00 0.00 4.17
796 1058 5.104374 GTGCAAGAGAGAAAGAGAGAGATG 58.896 45.833 0.00 0.00 0.00 2.90
803 1065 3.987547 TCTGTGTGCAAGAGAGAAAGAG 58.012 45.455 0.00 0.00 0.00 2.85
816 1078 0.305922 GCTTGTGTGTCTCTGTGTGC 59.694 55.000 0.00 0.00 0.00 4.57
820 1082 0.459899 TCACGCTTGTGTGTCTCTGT 59.540 50.000 13.06 0.00 44.22 3.41
822 1084 1.409064 TCTTCACGCTTGTGTGTCTCT 59.591 47.619 13.06 0.00 44.22 3.10
823 1085 1.789464 CTCTTCACGCTTGTGTGTCTC 59.211 52.381 13.06 0.00 44.22 3.36
867 1129 2.834549 TGGCCTAGGAGCTATTATCAGC 59.165 50.000 14.75 0.00 42.12 4.26
873 1135 0.761802 GCTGTGGCCTAGGAGCTATT 59.238 55.000 14.75 0.00 0.00 1.73
898 1160 2.163509 TCTACTGTGTGTGAGAGAGGC 58.836 52.381 0.00 0.00 0.00 4.70
958 1220 2.760385 CCCTGAGACCTCCCGTCC 60.760 72.222 0.00 0.00 43.08 4.79
981 1243 3.521126 ACATGCTTTAGTGATGGGACTCT 59.479 43.478 0.00 0.00 0.00 3.24
1138 1400 0.178903 AGGTAGCTGTGGTGGAAGGA 60.179 55.000 0.00 0.00 0.00 3.36
1598 1860 2.047274 CGCCGTGATCACCACCTT 60.047 61.111 20.03 0.00 42.76 3.50
1662 1924 1.047801 ATTTCCTTTGCGGCTTTGGT 58.952 45.000 0.00 0.00 0.00 3.67
1752 2014 1.406341 CGCATCCGGTTCTTTTCCCTA 60.406 52.381 0.00 0.00 0.00 3.53
1848 2110 1.289109 AATTGTTCGGCCTCGTGACG 61.289 55.000 0.00 0.00 37.69 4.35
1874 2136 0.802607 GTTCATGGACGAGGAGCGAC 60.803 60.000 0.00 0.00 44.57 5.19
1974 2236 0.822164 AGTTACCGCTGCTTCCGTAT 59.178 50.000 0.00 0.00 0.00 3.06
2052 2314 1.142748 CGCTTCTCAGTAGGGCTGG 59.857 63.158 0.00 0.00 45.08 4.85
2132 2394 9.590451 AAATAATCCATTGAACAAAGCAGTATG 57.410 29.630 0.00 0.00 40.87 2.39
2138 2400 7.656707 ACACAAATAATCCATTGAACAAAGC 57.343 32.000 0.00 0.00 0.00 3.51
2187 2789 0.107410 AAGGCAAGTTCACCGTCACA 60.107 50.000 0.00 0.00 0.00 3.58
2236 2842 4.951094 CAGGTTCTGGACTAGTAGTAGCTT 59.049 45.833 1.88 0.00 0.00 3.74
2504 3111 7.820648 AGAATTTAACTCGATCAATGCTTGTT 58.179 30.769 0.00 0.00 0.00 2.83
2598 3205 2.084546 GTACCACCATGCTTTGAGGTC 58.915 52.381 0.00 0.00 35.80 3.85
2699 3308 9.612066 TGAGTGATTTGTGAGTATATGCATAAA 57.388 29.630 11.13 0.00 31.36 1.40
2701 3310 9.264719 CTTGAGTGATTTGTGAGTATATGCATA 57.735 33.333 9.27 9.27 0.00 3.14
2702 3311 7.255035 GCTTGAGTGATTTGTGAGTATATGCAT 60.255 37.037 3.79 3.79 0.00 3.96
2703 3312 6.037500 GCTTGAGTGATTTGTGAGTATATGCA 59.962 38.462 0.00 0.00 0.00 3.96
2704 3313 6.259608 AGCTTGAGTGATTTGTGAGTATATGC 59.740 38.462 0.00 0.00 0.00 3.14
2705 3314 7.254692 CCAGCTTGAGTGATTTGTGAGTATATG 60.255 40.741 0.00 0.00 0.00 1.78
2706 3315 6.765036 CCAGCTTGAGTGATTTGTGAGTATAT 59.235 38.462 0.00 0.00 0.00 0.86
2707 3316 6.108687 CCAGCTTGAGTGATTTGTGAGTATA 58.891 40.000 0.00 0.00 0.00 1.47
2708 3317 4.940046 CCAGCTTGAGTGATTTGTGAGTAT 59.060 41.667 0.00 0.00 0.00 2.12
2709 3318 4.202357 ACCAGCTTGAGTGATTTGTGAGTA 60.202 41.667 0.00 0.00 0.00 2.59
2710 3319 3.144506 CCAGCTTGAGTGATTTGTGAGT 58.855 45.455 0.00 0.00 0.00 3.41
2711 3320 3.144506 ACCAGCTTGAGTGATTTGTGAG 58.855 45.455 0.00 0.00 0.00 3.51
2713 3322 3.189287 GGTACCAGCTTGAGTGATTTGTG 59.811 47.826 7.15 0.00 0.00 3.33
2714 3323 3.412386 GGTACCAGCTTGAGTGATTTGT 58.588 45.455 7.15 0.00 0.00 2.83
2715 3324 2.416547 CGGTACCAGCTTGAGTGATTTG 59.583 50.000 13.54 0.00 0.00 2.32
2716 3325 2.699954 CGGTACCAGCTTGAGTGATTT 58.300 47.619 13.54 0.00 0.00 2.17
2717 3326 1.676014 GCGGTACCAGCTTGAGTGATT 60.676 52.381 13.54 0.00 0.00 2.57
2725 3334 0.392998 CCAATCAGCGGTACCAGCTT 60.393 55.000 23.04 11.34 44.06 3.74
2783 3392 9.066892 ACACTCTAAAATTTGTCAGCTGAATAA 57.933 29.630 20.19 15.60 0.00 1.40
2784 3393 8.621532 ACACTCTAAAATTTGTCAGCTGAATA 57.378 30.769 20.19 8.00 0.00 1.75
2785 3394 7.229306 TGACACTCTAAAATTTGTCAGCTGAAT 59.771 33.333 20.19 5.68 42.61 2.57
2790 3399 7.588512 AGATTGACACTCTAAAATTTGTCAGC 58.411 34.615 8.07 5.84 46.69 4.26
2791 3400 9.390795 CAAGATTGACACTCTAAAATTTGTCAG 57.609 33.333 8.07 0.19 46.69 3.51
2792 3401 8.902806 ACAAGATTGACACTCTAAAATTTGTCA 58.097 29.630 4.63 4.63 45.08 3.58
2808 3417 4.092968 GGACGGTGATGTTACAAGATTGAC 59.907 45.833 0.00 0.00 0.00 3.18
2883 3492 9.919348 TTTAACTTCAACAGTGTTAACGTTATC 57.081 29.630 8.49 9.11 36.35 1.75
2885 3494 9.540431 GTTTTAACTTCAACAGTGTTAACGTTA 57.460 29.630 8.49 6.17 36.35 3.18
2886 3495 8.074972 TGTTTTAACTTCAACAGTGTTAACGTT 58.925 29.630 8.49 7.22 36.35 3.99
2887 3496 7.534918 GTGTTTTAACTTCAACAGTGTTAACGT 59.465 33.333 8.49 0.00 36.35 3.99
2888 3497 7.007636 GGTGTTTTAACTTCAACAGTGTTAACG 59.992 37.037 8.49 0.00 36.35 3.18
2897 3506 5.038033 GCAATCGGTGTTTTAACTTCAACA 58.962 37.500 0.00 0.00 0.00 3.33
2902 3511 4.279671 TGATGGCAATCGGTGTTTTAACTT 59.720 37.500 0.00 0.00 35.37 2.66
3011 3620 8.437742 GCTTTTACAAACGATACTAACTAGCAA 58.562 33.333 0.00 0.00 0.00 3.91
3014 3623 9.350357 TCAGCTTTTACAAACGATACTAACTAG 57.650 33.333 0.00 0.00 0.00 2.57
3023 3632 3.551551 GCGTTCAGCTTTTACAAACGAT 58.448 40.909 9.81 0.00 43.89 3.73


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

AutoCloner maintained by Alex Coulton.