Multiple sequence alignment - TraesCS6D01G149700

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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 TraesCS6D01G149700 chr6D 100.000 3788 0 0 1 3788 123165728 123161941 0.000000e+00 6996
1 TraesCS6D01G149700 chr6A 97.746 2928 52 4 871 3788 157958836 157961759 0.000000e+00 5029
2 TraesCS6D01G149700 chr6B 94.150 2513 87 26 830 3316 217174830 217172352 0.000000e+00 3771
3 TraesCS6D01G149700 chr6B 91.018 167 14 1 3470 3636 217172081 217171916 1.370000e-54 224
4 TraesCS6D01G149700 chr6B 98.319 119 2 0 3670 3788 217171916 217171798 3.830000e-50 209
5 TraesCS6D01G149700 chr6B 93.496 123 5 2 3358 3478 217172355 217172234 3.010000e-41 180
6 TraesCS6D01G149700 chr1D 90.226 266 25 1 40 304 33750233 33749968 2.800000e-91 346
7 TraesCS6D01G149700 chr1D 81.017 295 35 10 378 665 33749852 33749572 8.240000e-52 215
8 TraesCS6D01G149700 chr3B 87.500 288 19 11 42 326 224821362 224821635 2.200000e-82 316
9 TraesCS6D01G149700 chr7B 81.846 325 41 13 378 690 552125492 552125174 1.350000e-64 257
10 TraesCS6D01G149700 chr7B 84.932 146 21 1 29 173 552126123 552125978 3.050000e-31 147
11 TraesCS6D01G149700 chr5B 83.513 279 33 6 40 318 116661323 116661588 8.130000e-62 248
12 TraesCS6D01G149700 chr7D 82.414 290 37 9 378 659 518793080 518792797 1.360000e-59 241
13 TraesCS6D01G149700 chr4B 80.916 262 35 9 430 685 634725608 634725860 3.860000e-45 193
14 TraesCS6D01G149700 chr4A 79.736 227 37 6 442 663 109429338 109429116 5.070000e-34 156


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 TraesCS6D01G149700 chr6D 123161941 123165728 3787 True 6996.0 6996 100.00000 1 3788 1 chr6D.!!$R1 3787
1 TraesCS6D01G149700 chr6A 157958836 157961759 2923 False 5029.0 5029 97.74600 871 3788 1 chr6A.!!$F1 2917
2 TraesCS6D01G149700 chr6B 217171798 217174830 3032 True 1096.0 3771 94.24575 830 3788 4 chr6B.!!$R1 2958
3 TraesCS6D01G149700 chr1D 33749572 33750233 661 True 280.5 346 85.62150 40 665 2 chr1D.!!$R1 625
4 TraesCS6D01G149700 chr7B 552125174 552126123 949 True 202.0 257 83.38900 29 690 2 chr7B.!!$R1 661

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
85 86 0.036164 TTACAGCCCGTGCATCAACT 59.964 50.0 0.0 0.0 41.13 3.16 F
125 126 0.606673 GTCCCCTTGAGCCACACTTC 60.607 60.0 0.0 0.0 0.00 3.01 F
1782 2151 0.909623 GCAGTAAGGAGGTTGGGCTA 59.090 55.0 0.0 0.0 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1504 1873 1.272212 GGGATCTGAGCGGAGAATCTC 59.728 57.143 0.71 0.71 33.73 2.75 R
2109 2478 1.610522 ACAGCTTTTCCATGCACAGTC 59.389 47.619 0.00 0.00 0.00 3.51 R
3662 4219 0.329261 CCTGGGCTCAATTGGACAGA 59.671 55.000 5.42 0.00 0.00 3.41 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
17 18 2.111043 TGCCGGGCAATAGCTAGC 59.889 61.111 21.55 6.62 41.70 3.42
24 25 3.669354 GCAATAGCTAGCCACGTCT 57.331 52.632 12.13 0.00 37.91 4.18
25 26 2.795175 GCAATAGCTAGCCACGTCTA 57.205 50.000 12.13 0.00 37.91 2.59
26 27 2.395654 GCAATAGCTAGCCACGTCTAC 58.604 52.381 12.13 0.00 37.91 2.59
27 28 2.034812 GCAATAGCTAGCCACGTCTACT 59.965 50.000 12.13 0.00 37.91 2.57
33 34 4.934515 AGCTAGCCACGTCTACTATTTTC 58.065 43.478 12.13 0.00 0.00 2.29
36 37 5.811100 GCTAGCCACGTCTACTATTTTCTTT 59.189 40.000 2.29 0.00 0.00 2.52
85 86 0.036164 TTACAGCCCGTGCATCAACT 59.964 50.000 0.00 0.00 41.13 3.16
123 124 1.136329 ATGTCCCCTTGAGCCACACT 61.136 55.000 0.00 0.00 0.00 3.55
125 126 0.606673 GTCCCCTTGAGCCACACTTC 60.607 60.000 0.00 0.00 0.00 3.01
162 262 1.227089 CCCTCACGCCTTCATCTCG 60.227 63.158 0.00 0.00 0.00 4.04
170 270 2.093447 ACGCCTTCATCTCGAGGAAATT 60.093 45.455 13.56 0.00 30.25 1.82
240 340 3.447025 AACTCCCATCTAGCGCCGC 62.447 63.158 2.29 0.00 0.00 6.53
282 382 2.556766 CCTTTCTCCTTTCCTCCTCCT 58.443 52.381 0.00 0.00 0.00 3.69
283 383 2.503765 CCTTTCTCCTTTCCTCCTCCTC 59.496 54.545 0.00 0.00 0.00 3.71
293 393 3.673543 TCCTCCTCCTCTCTCCTTAAC 57.326 52.381 0.00 0.00 0.00 2.01
294 394 2.927007 TCCTCCTCCTCTCTCCTTAACA 59.073 50.000 0.00 0.00 0.00 2.41
295 395 3.028130 CCTCCTCCTCTCTCCTTAACAC 58.972 54.545 0.00 0.00 0.00 3.32
296 396 3.309556 CCTCCTCCTCTCTCCTTAACACT 60.310 52.174 0.00 0.00 0.00 3.55
297 397 3.951680 CTCCTCCTCTCTCCTTAACACTC 59.048 52.174 0.00 0.00 0.00 3.51
298 398 3.594232 TCCTCCTCTCTCCTTAACACTCT 59.406 47.826 0.00 0.00 0.00 3.24
299 399 3.951680 CCTCCTCTCTCCTTAACACTCTC 59.048 52.174 0.00 0.00 0.00 3.20
300 400 4.325030 CCTCCTCTCTCCTTAACACTCTCT 60.325 50.000 0.00 0.00 0.00 3.10
301 401 4.850680 TCCTCTCTCCTTAACACTCTCTC 58.149 47.826 0.00 0.00 0.00 3.20
302 402 4.538490 TCCTCTCTCCTTAACACTCTCTCT 59.462 45.833 0.00 0.00 0.00 3.10
303 403 4.881850 CCTCTCTCCTTAACACTCTCTCTC 59.118 50.000 0.00 0.00 0.00 3.20
304 404 5.339200 CCTCTCTCCTTAACACTCTCTCTCT 60.339 48.000 0.00 0.00 0.00 3.10
305 405 5.741011 TCTCTCCTTAACACTCTCTCTCTC 58.259 45.833 0.00 0.00 0.00 3.20
306 406 5.487488 TCTCTCCTTAACACTCTCTCTCTCT 59.513 44.000 0.00 0.00 0.00 3.10
307 407 5.741011 TCTCCTTAACACTCTCTCTCTCTC 58.259 45.833 0.00 0.00 0.00 3.20
308 408 5.487488 TCTCCTTAACACTCTCTCTCTCTCT 59.513 44.000 0.00 0.00 0.00 3.10
309 409 5.741011 TCCTTAACACTCTCTCTCTCTCTC 58.259 45.833 0.00 0.00 0.00 3.20
310 410 5.487488 TCCTTAACACTCTCTCTCTCTCTCT 59.513 44.000 0.00 0.00 0.00 3.10
311 411 5.817816 CCTTAACACTCTCTCTCTCTCTCTC 59.182 48.000 0.00 0.00 0.00 3.20
312 412 6.352222 CCTTAACACTCTCTCTCTCTCTCTCT 60.352 46.154 0.00 0.00 0.00 3.10
320 420 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
327 427 1.143684 CTCTCTCTCTCTCCCTCCCAG 59.856 61.905 0.00 0.00 0.00 4.45
352 706 2.806945 CTCCCATGGGTGCTTTTCTA 57.193 50.000 30.28 6.77 36.47 2.10
393 749 7.656412 TGTAAAATATTTCTGCAACAAGAGCA 58.344 30.769 0.10 0.00 40.19 4.26
465 821 8.600449 TTTGTAAAATAATTCTGCAACAAGGG 57.400 30.769 0.00 0.00 0.00 3.95
503 863 7.759489 AAAATACAATAAGACCTCTGTTGCA 57.241 32.000 0.00 0.00 0.00 4.08
508 868 6.507023 ACAATAAGACCTCTGTTGCAAAAAG 58.493 36.000 0.00 1.90 30.26 2.27
510 870 7.014615 ACAATAAGACCTCTGTTGCAAAAAGAT 59.985 33.333 12.23 1.00 39.99 2.40
511 871 5.859205 AAGACCTCTGTTGCAAAAAGATT 57.141 34.783 12.23 4.57 39.99 2.40
512 872 5.859205 AGACCTCTGTTGCAAAAAGATTT 57.141 34.783 12.23 4.28 39.99 2.17
513 873 5.594926 AGACCTCTGTTGCAAAAAGATTTG 58.405 37.500 12.23 7.84 39.99 2.32
603 966 1.913778 TGTGTTGCAATGATGGAGCT 58.086 45.000 0.59 0.00 0.00 4.09
604 967 1.542472 TGTGTTGCAATGATGGAGCTG 59.458 47.619 0.59 0.00 0.00 4.24
660 1023 1.713830 CGACCCGGCGAATCTTTTC 59.286 57.895 9.30 0.00 0.00 2.29
702 1065 4.813296 CGTAGCACACCTCTTTCTTTTT 57.187 40.909 0.00 0.00 0.00 1.94
703 1066 4.773510 CGTAGCACACCTCTTTCTTTTTC 58.226 43.478 0.00 0.00 0.00 2.29
704 1067 4.319549 CGTAGCACACCTCTTTCTTTTTCC 60.320 45.833 0.00 0.00 0.00 3.13
705 1068 3.903467 AGCACACCTCTTTCTTTTTCCT 58.097 40.909 0.00 0.00 0.00 3.36
706 1069 4.281657 AGCACACCTCTTTCTTTTTCCTT 58.718 39.130 0.00 0.00 0.00 3.36
707 1070 5.445964 AGCACACCTCTTTCTTTTTCCTTA 58.554 37.500 0.00 0.00 0.00 2.69
708 1071 6.071320 AGCACACCTCTTTCTTTTTCCTTAT 58.929 36.000 0.00 0.00 0.00 1.73
709 1072 6.551227 AGCACACCTCTTTCTTTTTCCTTATT 59.449 34.615 0.00 0.00 0.00 1.40
710 1073 7.069950 AGCACACCTCTTTCTTTTTCCTTATTT 59.930 33.333 0.00 0.00 0.00 1.40
711 1074 7.710907 GCACACCTCTTTCTTTTTCCTTATTTT 59.289 33.333 0.00 0.00 0.00 1.82
712 1075 9.599866 CACACCTCTTTCTTTTTCCTTATTTTT 57.400 29.630 0.00 0.00 0.00 1.94
713 1076 9.599866 ACACCTCTTTCTTTTTCCTTATTTTTG 57.400 29.630 0.00 0.00 0.00 2.44
714 1077 9.816354 CACCTCTTTCTTTTTCCTTATTTTTGA 57.184 29.630 0.00 0.00 0.00 2.69
721 1084 9.750125 TTCTTTTTCCTTATTTTTGAGAGAAGC 57.250 29.630 0.00 0.00 0.00 3.86
722 1085 8.360390 TCTTTTTCCTTATTTTTGAGAGAAGCC 58.640 33.333 0.00 0.00 0.00 4.35
723 1086 7.595819 TTTTCCTTATTTTTGAGAGAAGCCA 57.404 32.000 0.00 0.00 0.00 4.75
724 1087 6.575162 TTCCTTATTTTTGAGAGAAGCCAC 57.425 37.500 0.00 0.00 0.00 5.01
725 1088 4.695455 TCCTTATTTTTGAGAGAAGCCACG 59.305 41.667 0.00 0.00 0.00 4.94
726 1089 4.455877 CCTTATTTTTGAGAGAAGCCACGT 59.544 41.667 0.00 0.00 0.00 4.49
727 1090 5.390991 CCTTATTTTTGAGAGAAGCCACGTC 60.391 44.000 0.00 0.00 0.00 4.34
728 1091 2.910688 TTTTGAGAGAAGCCACGTCT 57.089 45.000 0.00 0.00 0.00 4.18
729 1092 4.330944 TTTTTGAGAGAAGCCACGTCTA 57.669 40.909 0.00 0.00 0.00 2.59
730 1093 3.299340 TTTGAGAGAAGCCACGTCTAC 57.701 47.619 0.00 0.00 0.00 2.59
731 1094 2.201921 TGAGAGAAGCCACGTCTACT 57.798 50.000 0.00 0.00 0.00 2.57
732 1095 2.515854 TGAGAGAAGCCACGTCTACTT 58.484 47.619 0.00 0.00 0.00 2.24
733 1096 2.891580 TGAGAGAAGCCACGTCTACTTT 59.108 45.455 0.00 0.00 0.00 2.66
734 1097 3.057456 TGAGAGAAGCCACGTCTACTTTC 60.057 47.826 0.00 0.00 0.00 2.62
735 1098 3.158676 AGAGAAGCCACGTCTACTTTCT 58.841 45.455 0.00 0.00 0.00 2.52
736 1099 3.574826 AGAGAAGCCACGTCTACTTTCTT 59.425 43.478 0.00 0.00 0.00 2.52
737 1100 3.654414 AGAAGCCACGTCTACTTTCTTG 58.346 45.455 0.00 0.00 0.00 3.02
738 1101 3.321111 AGAAGCCACGTCTACTTTCTTGA 59.679 43.478 0.00 0.00 0.00 3.02
739 1102 3.305398 AGCCACGTCTACTTTCTTGAG 57.695 47.619 0.00 0.00 0.00 3.02
740 1103 2.891580 AGCCACGTCTACTTTCTTGAGA 59.108 45.455 0.00 0.00 0.00 3.27
741 1104 3.057174 AGCCACGTCTACTTTCTTGAGAG 60.057 47.826 0.00 0.00 0.00 3.20
742 1105 3.246619 CCACGTCTACTTTCTTGAGAGC 58.753 50.000 0.00 0.00 0.00 4.09
743 1106 3.305403 CCACGTCTACTTTCTTGAGAGCA 60.305 47.826 0.00 0.00 0.00 4.26
744 1107 4.299155 CACGTCTACTTTCTTGAGAGCAA 58.701 43.478 0.00 0.00 0.00 3.91
745 1108 4.926238 CACGTCTACTTTCTTGAGAGCAAT 59.074 41.667 0.00 0.00 32.68 3.56
746 1109 6.093404 CACGTCTACTTTCTTGAGAGCAATA 58.907 40.000 0.00 0.00 32.68 1.90
747 1110 6.754209 CACGTCTACTTTCTTGAGAGCAATAT 59.246 38.462 0.00 0.00 32.68 1.28
748 1111 7.915923 CACGTCTACTTTCTTGAGAGCAATATA 59.084 37.037 0.00 0.00 32.68 0.86
749 1112 8.467598 ACGTCTACTTTCTTGAGAGCAATATAA 58.532 33.333 0.00 0.00 32.68 0.98
750 1113 8.963130 CGTCTACTTTCTTGAGAGCAATATAAG 58.037 37.037 0.00 0.00 32.68 1.73
751 1114 9.255304 GTCTACTTTCTTGAGAGCAATATAAGG 57.745 37.037 0.00 0.00 32.68 2.69
752 1115 9.201989 TCTACTTTCTTGAGAGCAATATAAGGA 57.798 33.333 0.00 0.00 32.68 3.36
753 1116 9.995003 CTACTTTCTTGAGAGCAATATAAGGAT 57.005 33.333 0.00 0.00 32.68 3.24
754 1117 8.674263 ACTTTCTTGAGAGCAATATAAGGATG 57.326 34.615 0.00 0.00 32.68 3.51
755 1118 7.718753 ACTTTCTTGAGAGCAATATAAGGATGG 59.281 37.037 0.00 0.00 32.68 3.51
756 1119 6.753913 TCTTGAGAGCAATATAAGGATGGT 57.246 37.500 0.00 0.00 32.68 3.55
757 1120 7.855784 TCTTGAGAGCAATATAAGGATGGTA 57.144 36.000 0.00 0.00 32.68 3.25
758 1121 7.671302 TCTTGAGAGCAATATAAGGATGGTAC 58.329 38.462 0.00 0.00 32.68 3.34
759 1122 7.510685 TCTTGAGAGCAATATAAGGATGGTACT 59.489 37.037 0.00 0.00 32.68 2.73
760 1123 7.618019 TGAGAGCAATATAAGGATGGTACTT 57.382 36.000 0.00 0.00 0.00 2.24
761 1124 8.034313 TGAGAGCAATATAAGGATGGTACTTT 57.966 34.615 0.00 0.00 0.00 2.66
762 1125 8.494433 TGAGAGCAATATAAGGATGGTACTTTT 58.506 33.333 0.00 0.00 0.00 2.27
763 1126 9.343539 GAGAGCAATATAAGGATGGTACTTTTT 57.656 33.333 0.00 0.00 0.00 1.94
788 1151 8.934023 TTTTTGGAGACATAGTAAGGATGTTT 57.066 30.769 0.00 0.00 42.32 2.83
789 1152 8.934023 TTTTGGAGACATAGTAAGGATGTTTT 57.066 30.769 0.00 0.00 42.32 2.43
790 1153 8.934023 TTTGGAGACATAGTAAGGATGTTTTT 57.066 30.769 0.00 0.00 42.32 1.94
844 1207 7.110155 ACAAACATAGTAAGGATGGTACTTGG 58.890 38.462 0.00 0.00 33.80 3.61
1522 1891 1.665735 GCGAGATTCTCCGCTCAGATC 60.666 57.143 17.51 0.00 46.96 2.75
1525 1894 1.043816 GATTCTCCGCTCAGATCCCA 58.956 55.000 0.00 0.00 0.00 4.37
1533 1902 1.938577 CGCTCAGATCCCAATGAGTTG 59.061 52.381 10.42 2.15 43.94 3.16
1782 2151 0.909623 GCAGTAAGGAGGTTGGGCTA 59.090 55.000 0.00 0.00 0.00 3.93
1799 2168 2.030096 GGCTAGATAAGGAGGTGTACGC 60.030 54.545 0.00 0.00 0.00 4.42
2224 2593 3.004752 AGTTGGATCCACTTGTATGGC 57.995 47.619 15.91 0.00 39.85 4.40
2336 2705 1.079127 TTGGTAGCGCTCTTGAGGC 60.079 57.895 16.34 0.00 0.00 4.70
2856 3237 3.106827 CATTTTGTATTCCCCCTTGGCT 58.893 45.455 0.00 0.00 0.00 4.75
2857 3238 3.268034 TTTTGTATTCCCCCTTGGCTT 57.732 42.857 0.00 0.00 0.00 4.35
2858 3239 3.268034 TTTGTATTCCCCCTTGGCTTT 57.732 42.857 0.00 0.00 0.00 3.51
2859 3240 2.230130 TGTATTCCCCCTTGGCTTTG 57.770 50.000 0.00 0.00 0.00 2.77
3033 3415 4.153835 GCTTCATGTAGCAATAGCCATCTC 59.846 45.833 18.39 0.00 43.56 2.75
3088 3470 5.365895 AGTGTACCAGTTTCCTGTAGTTCTT 59.634 40.000 0.00 0.00 36.95 2.52
3139 3521 3.646611 TGATGGTCGTACGAACTTGAA 57.353 42.857 31.45 13.93 32.08 2.69
3347 3741 4.705023 TGTATACACAGCTCTGCTTGAGTA 59.295 41.667 0.08 4.33 44.41 2.59
3383 3777 1.118033 CAGATTGATCAAATGCGCGC 58.882 50.000 27.26 27.26 0.00 6.86
3552 4109 8.035394 TCTTTTAATCTTAGTTGAGCGACAGAT 58.965 33.333 0.00 0.00 0.00 2.90
3564 4121 4.756642 TGAGCGACAGATTCAAACAATCTT 59.243 37.500 0.00 0.00 34.96 2.40
3568 4125 5.560760 GCGACAGATTCAAACAATCTTGTCA 60.561 40.000 17.47 0.00 41.31 3.58
3619 4176 4.203226 TGGAACAACATTGCAGAAGTACA 58.797 39.130 0.00 0.00 31.92 2.90
3660 4217 2.124277 TTTCATCAGAGCAGCAGCAT 57.876 45.000 3.17 0.00 45.49 3.79
3661 4218 2.124277 TTCATCAGAGCAGCAGCATT 57.876 45.000 3.17 0.00 45.49 3.56
3662 4219 2.124277 TCATCAGAGCAGCAGCATTT 57.876 45.000 3.17 0.00 45.49 2.32
3663 4220 2.014857 TCATCAGAGCAGCAGCATTTC 58.985 47.619 3.17 0.00 45.49 2.17
3665 4222 1.450025 TCAGAGCAGCAGCATTTCTG 58.550 50.000 11.24 11.24 45.49 3.02
3666 4223 1.166129 CAGAGCAGCAGCATTTCTGT 58.834 50.000 3.17 0.00 44.66 3.41
3667 4224 1.130749 CAGAGCAGCAGCATTTCTGTC 59.869 52.381 3.17 0.00 44.66 3.51
3668 4225 0.450983 GAGCAGCAGCATTTCTGTCC 59.549 55.000 3.17 0.00 44.66 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.111043 GCTAGCTATTGCCCGGCA 59.889 61.111 8.43 8.43 40.80 5.69
1 2 2.669910 GGCTAGCTATTGCCCGGC 60.670 66.667 15.72 1.04 43.11 6.13
6 7 2.034812 AGTAGACGTGGCTAGCTATTGC 59.965 50.000 15.72 1.86 40.05 3.56
7 8 3.992260 AGTAGACGTGGCTAGCTATTG 57.008 47.619 15.72 8.18 0.00 1.90
8 9 6.651975 AAATAGTAGACGTGGCTAGCTATT 57.348 37.500 15.72 4.58 32.46 1.73
9 10 6.490721 AGAAAATAGTAGACGTGGCTAGCTAT 59.509 38.462 15.72 0.00 0.00 2.97
10 11 5.826737 AGAAAATAGTAGACGTGGCTAGCTA 59.173 40.000 15.72 5.44 0.00 3.32
11 12 4.645588 AGAAAATAGTAGACGTGGCTAGCT 59.354 41.667 15.72 0.00 0.00 3.32
12 13 4.934515 AGAAAATAGTAGACGTGGCTAGC 58.065 43.478 6.04 6.04 0.00 3.42
13 14 7.829378 AAAAGAAAATAGTAGACGTGGCTAG 57.171 36.000 0.00 0.00 0.00 3.42
14 15 7.118680 CCAAAAAGAAAATAGTAGACGTGGCTA 59.881 37.037 0.00 0.00 0.00 3.93
15 16 6.072673 CCAAAAAGAAAATAGTAGACGTGGCT 60.073 38.462 0.00 0.00 0.00 4.75
16 17 6.072893 TCCAAAAAGAAAATAGTAGACGTGGC 60.073 38.462 0.00 0.00 0.00 5.01
17 18 7.429636 TCCAAAAAGAAAATAGTAGACGTGG 57.570 36.000 0.00 0.00 0.00 4.94
18 19 9.724839 TTTTCCAAAAAGAAAATAGTAGACGTG 57.275 29.630 0.00 0.00 40.04 4.49
36 37 3.039252 TGAGGGGAAGCTTTTTCCAAA 57.961 42.857 0.00 0.00 40.32 3.28
104 105 1.136329 AGTGTGGCTCAAGGGGACAT 61.136 55.000 0.00 0.00 0.00 3.06
162 262 5.695851 TTGCTGTTGAGAGAAATTTCCTC 57.304 39.130 20.83 20.83 0.00 3.71
170 270 1.230635 GGCGCTTGCTGTTGAGAGAA 61.231 55.000 7.64 0.00 39.13 2.87
252 352 4.035102 GAGAAAGGGGCTGGCGGT 62.035 66.667 0.00 0.00 0.00 5.68
282 382 5.487488 AGAGAGAGAGAGTGTTAAGGAGAGA 59.513 44.000 0.00 0.00 0.00 3.10
283 383 5.745227 AGAGAGAGAGAGTGTTAAGGAGAG 58.255 45.833 0.00 0.00 0.00 3.20
293 393 4.648762 AGAGAGAGAGAGAGAGAGAGAGTG 59.351 50.000 0.00 0.00 0.00 3.51
294 394 4.877773 AGAGAGAGAGAGAGAGAGAGAGT 58.122 47.826 0.00 0.00 0.00 3.24
295 395 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
296 396 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
297 397 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
298 398 4.219115 GGAGAGAGAGAGAGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
299 399 3.323403 GGGAGAGAGAGAGAGAGAGAGAG 59.677 56.522 0.00 0.00 0.00 3.20
300 400 3.051803 AGGGAGAGAGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
301 401 3.312890 AGGGAGAGAGAGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
302 402 3.309296 GAGGGAGAGAGAGAGAGAGAGA 58.691 54.545 0.00 0.00 0.00 3.10
303 403 2.370189 GGAGGGAGAGAGAGAGAGAGAG 59.630 59.091 0.00 0.00 0.00 3.20
304 404 2.408565 GGAGGGAGAGAGAGAGAGAGA 58.591 57.143 0.00 0.00 0.00 3.10
305 405 1.421646 GGGAGGGAGAGAGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
306 406 1.274708 TGGGAGGGAGAGAGAGAGAGA 60.275 57.143 0.00 0.00 0.00 3.10
307 407 1.143684 CTGGGAGGGAGAGAGAGAGAG 59.856 61.905 0.00 0.00 0.00 3.20
308 408 1.221635 CTGGGAGGGAGAGAGAGAGA 58.778 60.000 0.00 0.00 0.00 3.10
309 409 0.468029 GCTGGGAGGGAGAGAGAGAG 60.468 65.000 0.00 0.00 0.00 3.20
310 410 0.923729 AGCTGGGAGGGAGAGAGAGA 60.924 60.000 0.00 0.00 0.00 3.10
311 411 0.756442 CAGCTGGGAGGGAGAGAGAG 60.756 65.000 5.57 0.00 0.00 3.20
312 412 1.217747 TCAGCTGGGAGGGAGAGAGA 61.218 60.000 15.13 0.00 0.00 3.10
320 420 3.478274 GGGAGCTCAGCTGGGAGG 61.478 72.222 20.53 5.17 39.88 4.30
327 427 2.124403 CACCCATGGGAGCTCAGC 60.124 66.667 38.07 0.00 38.96 4.26
370 726 9.142515 CATTGCTCTTGTTGCAGAAATATTTTA 57.857 29.630 1.43 0.00 41.71 1.52
439 795 9.218440 CCCTTGTTGCAGAATTATTTTACAAAT 57.782 29.630 0.00 0.00 0.00 2.32
447 803 4.159135 CAGAGCCCTTGTTGCAGAATTATT 59.841 41.667 0.00 0.00 0.00 1.40
448 804 3.698040 CAGAGCCCTTGTTGCAGAATTAT 59.302 43.478 0.00 0.00 0.00 1.28
449 805 3.084039 CAGAGCCCTTGTTGCAGAATTA 58.916 45.455 0.00 0.00 0.00 1.40
450 806 1.891150 CAGAGCCCTTGTTGCAGAATT 59.109 47.619 0.00 0.00 0.00 2.17
451 807 1.202976 ACAGAGCCCTTGTTGCAGAAT 60.203 47.619 0.00 0.00 0.00 2.40
452 808 0.183492 ACAGAGCCCTTGTTGCAGAA 59.817 50.000 0.00 0.00 0.00 3.02
453 809 0.183492 AACAGAGCCCTTGTTGCAGA 59.817 50.000 0.00 0.00 0.00 4.26
454 810 0.313043 CAACAGAGCCCTTGTTGCAG 59.687 55.000 11.19 0.00 36.86 4.41
455 811 2.417978 CAACAGAGCCCTTGTTGCA 58.582 52.632 11.19 0.00 36.86 4.08
488 848 6.959639 AATCTTTTTGCAACAGAGGTCTTA 57.040 33.333 12.06 0.00 0.00 2.10
502 862 6.365247 CAGAGATCCTGTTGCAAATCTTTTTG 59.635 38.462 11.64 8.04 40.29 2.44
503 863 6.453092 CAGAGATCCTGTTGCAAATCTTTTT 58.547 36.000 11.64 1.05 38.10 1.94
518 878 5.595952 AGAAAAGTTTTGCAACAGAGATCCT 59.404 36.000 5.36 0.00 35.05 3.24
519 879 5.689068 CAGAAAAGTTTTGCAACAGAGATCC 59.311 40.000 5.36 0.00 35.05 3.36
520 880 5.174579 GCAGAAAAGTTTTGCAACAGAGATC 59.825 40.000 5.36 0.00 37.75 2.75
580 943 3.553508 GCTCCATCATTGCAACACAAGTT 60.554 43.478 0.00 0.00 42.87 2.66
604 967 4.654412 ATCGAGCGGATGAGCGGC 62.654 66.667 0.00 0.00 43.00 6.53
652 1015 3.375299 CCGGCTGATCTTTCGAAAAGATT 59.625 43.478 12.41 0.00 37.14 2.40
660 1023 3.264897 CCGCCGGCTGATCTTTCG 61.265 66.667 26.68 4.88 0.00 3.46
695 1058 9.750125 GCTTCTCTCAAAAATAAGGAAAAAGAA 57.250 29.630 0.00 0.00 0.00 2.52
696 1059 8.360390 GGCTTCTCTCAAAAATAAGGAAAAAGA 58.640 33.333 0.00 0.00 0.00 2.52
697 1060 8.143835 TGGCTTCTCTCAAAAATAAGGAAAAAG 58.856 33.333 0.00 0.00 0.00 2.27
698 1061 7.926018 GTGGCTTCTCTCAAAAATAAGGAAAAA 59.074 33.333 0.00 0.00 0.00 1.94
699 1062 7.433680 GTGGCTTCTCTCAAAAATAAGGAAAA 58.566 34.615 0.00 0.00 0.00 2.29
700 1063 6.293955 CGTGGCTTCTCTCAAAAATAAGGAAA 60.294 38.462 0.00 0.00 0.00 3.13
701 1064 5.181245 CGTGGCTTCTCTCAAAAATAAGGAA 59.819 40.000 0.00 0.00 0.00 3.36
702 1065 4.695455 CGTGGCTTCTCTCAAAAATAAGGA 59.305 41.667 0.00 0.00 0.00 3.36
703 1066 4.455877 ACGTGGCTTCTCTCAAAAATAAGG 59.544 41.667 0.00 0.00 0.00 2.69
704 1067 5.409826 AGACGTGGCTTCTCTCAAAAATAAG 59.590 40.000 0.00 0.00 0.00 1.73
705 1068 5.305585 AGACGTGGCTTCTCTCAAAAATAA 58.694 37.500 0.00 0.00 0.00 1.40
706 1069 4.894784 AGACGTGGCTTCTCTCAAAAATA 58.105 39.130 0.00 0.00 0.00 1.40
707 1070 3.744660 AGACGTGGCTTCTCTCAAAAAT 58.255 40.909 0.00 0.00 0.00 1.82
708 1071 3.194005 AGACGTGGCTTCTCTCAAAAA 57.806 42.857 0.00 0.00 0.00 1.94
709 1072 2.910688 AGACGTGGCTTCTCTCAAAA 57.089 45.000 0.00 0.00 0.00 2.44
710 1073 2.891580 AGTAGACGTGGCTTCTCTCAAA 59.108 45.455 0.00 0.00 0.00 2.69
711 1074 2.515854 AGTAGACGTGGCTTCTCTCAA 58.484 47.619 0.00 0.00 0.00 3.02
712 1075 2.201921 AGTAGACGTGGCTTCTCTCA 57.798 50.000 0.00 0.00 0.00 3.27
713 1076 3.191791 AGAAAGTAGACGTGGCTTCTCTC 59.808 47.826 0.00 0.00 0.00 3.20
714 1077 3.158676 AGAAAGTAGACGTGGCTTCTCT 58.841 45.455 0.00 0.00 0.00 3.10
715 1078 3.579335 AGAAAGTAGACGTGGCTTCTC 57.421 47.619 0.00 0.00 0.00 2.87
716 1079 3.321111 TCAAGAAAGTAGACGTGGCTTCT 59.679 43.478 0.00 0.00 0.00 2.85
717 1080 3.650139 TCAAGAAAGTAGACGTGGCTTC 58.350 45.455 0.00 0.00 0.00 3.86
718 1081 3.321111 TCTCAAGAAAGTAGACGTGGCTT 59.679 43.478 0.00 0.00 0.00 4.35
719 1082 2.891580 TCTCAAGAAAGTAGACGTGGCT 59.108 45.455 0.00 0.00 0.00 4.75
720 1083 3.246619 CTCTCAAGAAAGTAGACGTGGC 58.753 50.000 0.00 0.00 0.00 5.01
721 1084 3.246619 GCTCTCAAGAAAGTAGACGTGG 58.753 50.000 0.00 0.00 0.00 4.94
722 1085 3.902150 TGCTCTCAAGAAAGTAGACGTG 58.098 45.455 0.00 0.00 0.00 4.49
723 1086 4.585955 TTGCTCTCAAGAAAGTAGACGT 57.414 40.909 0.00 0.00 0.00 4.34
724 1087 8.858003 TTATATTGCTCTCAAGAAAGTAGACG 57.142 34.615 0.00 0.00 35.37 4.18
725 1088 9.255304 CCTTATATTGCTCTCAAGAAAGTAGAC 57.745 37.037 0.00 0.00 35.37 2.59
726 1089 9.201989 TCCTTATATTGCTCTCAAGAAAGTAGA 57.798 33.333 0.00 0.00 35.37 2.59
727 1090 9.995003 ATCCTTATATTGCTCTCAAGAAAGTAG 57.005 33.333 0.00 0.00 35.37 2.57
728 1091 9.770097 CATCCTTATATTGCTCTCAAGAAAGTA 57.230 33.333 0.00 0.00 35.37 2.24
729 1092 7.718753 CCATCCTTATATTGCTCTCAAGAAAGT 59.281 37.037 0.00 0.00 35.37 2.66
730 1093 7.718753 ACCATCCTTATATTGCTCTCAAGAAAG 59.281 37.037 0.00 0.00 35.37 2.62
731 1094 7.577303 ACCATCCTTATATTGCTCTCAAGAAA 58.423 34.615 0.00 0.00 35.37 2.52
732 1095 7.141758 ACCATCCTTATATTGCTCTCAAGAA 57.858 36.000 0.00 0.00 35.37 2.52
733 1096 6.753913 ACCATCCTTATATTGCTCTCAAGA 57.246 37.500 0.00 0.00 35.37 3.02
734 1097 7.675062 AGTACCATCCTTATATTGCTCTCAAG 58.325 38.462 0.00 0.00 35.37 3.02
735 1098 7.618019 AGTACCATCCTTATATTGCTCTCAA 57.382 36.000 0.00 0.00 36.51 3.02
736 1099 7.618019 AAGTACCATCCTTATATTGCTCTCA 57.382 36.000 0.00 0.00 0.00 3.27
737 1100 8.910351 AAAAGTACCATCCTTATATTGCTCTC 57.090 34.615 0.00 0.00 0.00 3.20
763 1126 8.934023 AAACATCCTTACTATGTCTCCAAAAA 57.066 30.769 0.00 0.00 36.56 1.94
764 1127 8.934023 AAAACATCCTTACTATGTCTCCAAAA 57.066 30.769 0.00 0.00 36.56 2.44
765 1128 8.934023 AAAAACATCCTTACTATGTCTCCAAA 57.066 30.769 0.00 0.00 36.56 3.28
812 1175 9.802039 ACCATCCTTACTATGTTTGTCTAAAAA 57.198 29.630 0.00 0.00 0.00 1.94
814 1177 9.880157 GTACCATCCTTACTATGTTTGTCTAAA 57.120 33.333 0.00 0.00 0.00 1.85
815 1178 9.263446 AGTACCATCCTTACTATGTTTGTCTAA 57.737 33.333 0.00 0.00 0.00 2.10
816 1179 8.834004 AGTACCATCCTTACTATGTTTGTCTA 57.166 34.615 0.00 0.00 0.00 2.59
817 1180 7.735326 AGTACCATCCTTACTATGTTTGTCT 57.265 36.000 0.00 0.00 0.00 3.41
818 1181 7.280205 CCAAGTACCATCCTTACTATGTTTGTC 59.720 40.741 0.00 0.00 0.00 3.18
819 1182 7.110155 CCAAGTACCATCCTTACTATGTTTGT 58.890 38.462 0.00 0.00 0.00 2.83
820 1183 6.038271 GCCAAGTACCATCCTTACTATGTTTG 59.962 42.308 0.00 0.00 0.00 2.93
821 1184 6.120220 GCCAAGTACCATCCTTACTATGTTT 58.880 40.000 0.00 0.00 0.00 2.83
822 1185 5.190925 TGCCAAGTACCATCCTTACTATGTT 59.809 40.000 0.00 0.00 0.00 2.71
823 1186 4.719773 TGCCAAGTACCATCCTTACTATGT 59.280 41.667 0.00 0.00 0.00 2.29
824 1187 5.290493 TGCCAAGTACCATCCTTACTATG 57.710 43.478 0.00 0.00 0.00 2.23
825 1188 5.968676 TTGCCAAGTACCATCCTTACTAT 57.031 39.130 0.00 0.00 0.00 2.12
826 1189 5.765576 TTTGCCAAGTACCATCCTTACTA 57.234 39.130 0.00 0.00 0.00 1.82
827 1190 4.650972 TTTGCCAAGTACCATCCTTACT 57.349 40.909 0.00 0.00 0.00 2.24
828 1191 4.157840 CCTTTTGCCAAGTACCATCCTTAC 59.842 45.833 0.00 0.00 0.00 2.34
835 1198 6.926630 ATATTTTCCTTTTGCCAAGTACCA 57.073 33.333 0.00 0.00 0.00 3.25
844 1207 7.007117 CGTTTTCGGAAATATTTTCCTTTTGC 58.993 34.615 15.09 4.44 39.94 3.68
1504 1873 1.272212 GGGATCTGAGCGGAGAATCTC 59.728 57.143 0.71 0.71 33.73 2.75
1522 1891 3.012518 CCAGCTTAGACAACTCATTGGG 58.987 50.000 0.00 0.00 40.42 4.12
1525 1894 4.623932 TGTCCAGCTTAGACAACTCATT 57.376 40.909 12.83 0.00 41.17 2.57
1533 1902 4.997395 TCATTCAACTTGTCCAGCTTAGAC 59.003 41.667 6.69 6.69 34.72 2.59
1782 2151 5.386924 AGAATAGCGTACACCTCCTTATCT 58.613 41.667 0.00 0.00 0.00 1.98
1799 2168 8.572185 TCTTGAGAAACCTATCGATGAGAATAG 58.428 37.037 8.54 0.00 0.00 1.73
2109 2478 1.610522 ACAGCTTTTCCATGCACAGTC 59.389 47.619 0.00 0.00 0.00 3.51
2224 2593 4.156739 GGAATACTTCTGAACCAAAGCAGG 59.843 45.833 0.00 0.00 33.05 4.85
2281 2650 1.098050 CTTTCCAGCATTTCGGGGAG 58.902 55.000 0.00 0.00 0.00 4.30
2336 2705 1.796151 CACAGCCCATACACAAGCG 59.204 57.895 0.00 0.00 0.00 4.68
2523 2892 6.828273 TGATAAATGGATTGATATAAGGCGGG 59.172 38.462 0.00 0.00 0.00 6.13
2856 3237 4.679372 GCTCAAAGGCCAGTTACAAACAAA 60.679 41.667 5.01 0.00 0.00 2.83
2857 3238 3.181480 GCTCAAAGGCCAGTTACAAACAA 60.181 43.478 5.01 0.00 0.00 2.83
2858 3239 2.360801 GCTCAAAGGCCAGTTACAAACA 59.639 45.455 5.01 0.00 0.00 2.83
2859 3240 3.013276 GCTCAAAGGCCAGTTACAAAC 57.987 47.619 5.01 0.00 0.00 2.93
3088 3470 4.081406 ACCAAATGAGCAGTGCATTAAGA 58.919 39.130 19.20 0.00 35.06 2.10
3139 3521 8.928448 ACACATATAGTACCAGAATGACAGAAT 58.072 33.333 0.00 0.00 39.69 2.40
3347 3741 8.038862 ATCAATCTGATGTTACCTTGATAGGT 57.961 34.615 2.01 2.01 45.50 3.08
3383 3777 5.118990 ACATGGATATGTTTTCTCCTCACG 58.881 41.667 0.00 0.00 45.01 4.35
3539 4096 3.878086 TGTTTGAATCTGTCGCTCAAC 57.122 42.857 0.00 0.00 0.00 3.18
3552 4109 6.554419 CAGAACAGTGACAAGATTGTTTGAA 58.446 36.000 0.00 0.00 42.43 2.69
3564 4121 1.227527 CCGGTGCAGAACAGTGACA 60.228 57.895 0.00 0.00 0.00 3.58
3568 4125 2.372040 TAACGCCGGTGCAGAACAGT 62.372 55.000 16.69 0.00 37.32 3.55
3660 4217 2.517959 CTGGGCTCAATTGGACAGAAA 58.482 47.619 5.42 0.00 0.00 2.52
3661 4218 1.272092 CCTGGGCTCAATTGGACAGAA 60.272 52.381 5.42 0.00 0.00 3.02
3662 4219 0.329261 CCTGGGCTCAATTGGACAGA 59.671 55.000 5.42 0.00 0.00 3.41
3663 4220 1.318158 GCCTGGGCTCAATTGGACAG 61.318 60.000 5.42 8.72 38.26 3.51
3665 4222 3.608432 GCCTGGGCTCAATTGGAC 58.392 61.111 5.42 0.00 38.26 4.02


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

AutoCloner maintained by Alex Coulton.