Multiple sequence alignment - TraesCS6A01G110100

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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 TraesCS6A01G110100 chr6A 100.000 5106 0 0 1 5106 79267257 79272362 0.000000e+00 9430.0
1 TraesCS6A01G110100 chr6A 93.366 1432 58 18 3707 5106 79341052 79342478 0.000000e+00 2084.0
2 TraesCS6A01G110100 chr6A 84.906 106 16 0 4992 5097 79946960 79947065 1.940000e-19 108.0
3 TraesCS6A01G110100 chr6A 93.023 43 2 1 3687 3728 79332422 79332464 1.540000e-05 62.1
4 TraesCS6A01G110100 chr6B 92.575 5199 234 73 1 5106 135858531 135863670 0.000000e+00 7323.0
5 TraesCS6A01G110100 chr6D 91.615 2111 100 37 204 2283 62114074 62116138 0.000000e+00 2846.0
6 TraesCS6A01G110100 chr6D 90.992 1854 72 36 3297 5106 62117242 62119044 0.000000e+00 2410.0
7 TraesCS6A01G110100 chr6D 94.929 986 45 4 2279 3262 62116259 62117241 0.000000e+00 1539.0
8 TraesCS6A01G110100 chr6D 82.108 816 85 34 4314 5106 62192514 62193291 4.310000e-180 641.0
9 TraesCS6A01G110100 chr6D 89.610 154 6 5 1 145 62113535 62113687 2.430000e-43 187.0
10 TraesCS6A01G110100 chr6D 87.755 147 16 2 3840 3986 62138052 62138196 2.440000e-38 171.0
11 TraesCS6A01G110100 chr6D 86.792 106 14 0 4992 5097 62499823 62499928 8.980000e-23 119.0
12 TraesCS6A01G110100 chr6D 97.561 41 1 0 3814 3854 115546343 115546303 2.550000e-08 71.3


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 TraesCS6A01G110100 chr6A 79267257 79272362 5105 False 9430.0 9430 100.0000 1 5106 1 chr6A.!!$F1 5105
1 TraesCS6A01G110100 chr6A 79341052 79342478 1426 False 2084.0 2084 93.3660 3707 5106 1 chr6A.!!$F3 1399
2 TraesCS6A01G110100 chr6B 135858531 135863670 5139 False 7323.0 7323 92.5750 1 5106 1 chr6B.!!$F1 5105
3 TraesCS6A01G110100 chr6D 62113535 62119044 5509 False 1745.5 2846 91.7865 1 5106 4 chr6D.!!$F4 5105
4 TraesCS6A01G110100 chr6D 62192514 62193291 777 False 641.0 641 82.1080 4314 5106 1 chr6D.!!$F2 792

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
225 567 0.179034 AGATCTTGATTGGGGCGAGC 60.179 55.000 0.00 0.0 0.00 5.03 F
978 1366 0.536460 GAGTAGGAGGAGGAGGAGCG 60.536 65.000 0.00 0.0 0.00 5.03 F
1297 1685 0.103208 ATTTGCGCCCGTCAAAAACA 59.897 45.000 4.18 0.0 37.04 2.83 F
1591 1979 1.202463 GCTGCAAAGCCGATCTCTCTA 60.202 52.381 0.00 0.0 0.00 2.43 F
2030 2421 2.158871 TGTCCTTCTAAAACAGCCACGT 60.159 45.455 0.00 0.0 0.00 4.49 F
2751 3268 2.577606 TGGTTTCGATGGGTTCATGT 57.422 45.000 0.00 0.0 32.98 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1253 1641 0.038744 CTCCATGTTGTTCCCAGCCT 59.961 55.000 0.0 0.0 0.0 4.58 R
2039 2430 1.034838 TTTTGTGCCGCTGAGTTGGT 61.035 50.000 0.0 0.0 0.0 3.67 R
2549 3066 1.207089 TGAACATAAGGAGCCTGACCG 59.793 52.381 0.0 0.0 0.0 4.79 R
2973 3491 2.301346 AGAACAGCCAACAAACAGGAG 58.699 47.619 0.0 0.0 0.0 3.69 R
2974 3492 2.435372 AGAACAGCCAACAAACAGGA 57.565 45.000 0.0 0.0 0.0 3.86 R
4594 5139 1.065998 CCCCCTCGTCCGATTTAAACA 60.066 52.381 0.0 0.0 0.0 2.83 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.508628 GGTATAGGTTCTCCCCCTCCT 59.491 57.143 0.00 0.00 33.35 3.69
87 101 4.864247 GGTTTGATTTGATTTGATCCGTGG 59.136 41.667 0.00 0.00 0.00 4.94
88 102 5.336372 GGTTTGATTTGATTTGATCCGTGGA 60.336 40.000 0.00 0.00 0.00 4.02
185 199 2.730129 TTTTCTCTGGGCTTGGGGGC 62.730 60.000 0.00 0.00 40.05 5.80
225 567 0.179034 AGATCTTGATTGGGGCGAGC 60.179 55.000 0.00 0.00 0.00 5.03
252 594 1.137404 GGTGGTTGTCATGATGCGC 59.863 57.895 0.00 0.00 0.00 6.09
339 682 8.282592 GTGATATACTAGATCTCATCTCATCGC 58.717 40.741 0.00 0.07 40.76 4.58
510 856 3.267860 CGCTGCTGATCGGGCTTC 61.268 66.667 3.14 0.00 0.00 3.86
511 857 2.188994 GCTGCTGATCGGGCTTCT 59.811 61.111 3.14 0.00 0.00 2.85
512 858 2.178890 GCTGCTGATCGGGCTTCTG 61.179 63.158 3.14 0.00 0.00 3.02
517 863 2.037620 CTGATCGGGCTTCTGGGAGG 62.038 65.000 0.00 0.00 0.00 4.30
518 864 1.762460 GATCGGGCTTCTGGGAGGA 60.762 63.158 0.00 0.00 0.00 3.71
519 865 1.753368 GATCGGGCTTCTGGGAGGAG 61.753 65.000 0.00 0.00 0.00 3.69
520 866 3.474570 CGGGCTTCTGGGAGGAGG 61.475 72.222 0.00 0.00 0.00 4.30
521 867 2.041265 GGGCTTCTGGGAGGAGGA 59.959 66.667 0.00 0.00 0.00 3.71
543 897 1.836802 GAGGAGGAGGAATTCTGCTGT 59.163 52.381 5.23 0.00 44.53 4.40
551 905 4.080863 GGAGGAATTCTGCTGTCTTTCCTA 60.081 45.833 17.48 0.00 44.70 2.94
581 943 1.557371 GAGGAGGAAGAAGTGAAGGGG 59.443 57.143 0.00 0.00 0.00 4.79
582 944 0.621082 GGAGGAAGAAGTGAAGGGGG 59.379 60.000 0.00 0.00 0.00 5.40
676 1041 5.607477 CTGGGGAAATGGAATGATGAATTG 58.393 41.667 0.00 0.00 0.00 2.32
682 1047 7.817962 GGGAAATGGAATGATGAATTGATGATC 59.182 37.037 0.00 0.00 0.00 2.92
697 1062 8.985315 AATTGATGATCTTCTTGCCATAACTA 57.015 30.769 9.75 0.00 0.00 2.24
717 1082 2.910688 ACTGACGATTCCACTTGTGT 57.089 45.000 0.00 0.00 0.00 3.72
718 1083 2.483876 ACTGACGATTCCACTTGTGTG 58.516 47.619 0.00 0.00 43.45 3.82
739 1104 4.870991 GTGAAGAAAGGTACTCTGCATACC 59.129 45.833 6.86 6.86 38.49 2.73
778 1146 3.084039 ACACGGCATTCACTCATTCATT 58.916 40.909 0.00 0.00 0.00 2.57
788 1156 8.350722 GCATTCACTCATTCATTTGATGATAGT 58.649 33.333 0.00 0.00 39.39 2.12
791 1159 8.797350 TCACTCATTCATTTGATGATAGTTGT 57.203 30.769 0.00 0.00 39.39 3.32
792 1160 8.671028 TCACTCATTCATTTGATGATAGTTGTG 58.329 33.333 0.00 0.00 39.39 3.33
793 1161 8.456471 CACTCATTCATTTGATGATAGTTGTGT 58.544 33.333 0.00 0.00 39.39 3.72
794 1162 9.671279 ACTCATTCATTTGATGATAGTTGTGTA 57.329 29.630 0.00 0.00 39.39 2.90
795 1163 9.926751 CTCATTCATTTGATGATAGTTGTGTAC 57.073 33.333 0.00 0.00 39.39 2.90
796 1164 9.671279 TCATTCATTTGATGATAGTTGTGTACT 57.329 29.630 0.00 0.00 39.39 2.73
799 1167 8.492673 TCATTTGATGATAGTTGTGTACTTCC 57.507 34.615 0.00 0.00 34.74 3.46
813 1193 1.567357 ACTTCCTCTCTCTTGCCCTC 58.433 55.000 0.00 0.00 0.00 4.30
870 1250 5.534207 TCATTGACTTTTCCAAGTGCAAT 57.466 34.783 0.00 0.00 43.79 3.56
871 1251 5.916318 TCATTGACTTTTCCAAGTGCAATT 58.084 33.333 0.00 0.00 43.79 2.32
872 1252 6.347696 TCATTGACTTTTCCAAGTGCAATTT 58.652 32.000 0.00 0.00 43.79 1.82
873 1253 6.822676 TCATTGACTTTTCCAAGTGCAATTTT 59.177 30.769 0.00 0.00 43.79 1.82
874 1254 7.336427 TCATTGACTTTTCCAAGTGCAATTTTT 59.664 29.630 0.00 0.00 43.79 1.94
913 1300 1.210478 TGCTAATTCTGCTCCTCACCC 59.790 52.381 5.21 0.00 0.00 4.61
974 1362 1.104577 GTGCGAGTAGGAGGAGGAGG 61.105 65.000 0.00 0.00 0.00 4.30
975 1363 1.279749 TGCGAGTAGGAGGAGGAGGA 61.280 60.000 0.00 0.00 0.00 3.71
978 1366 0.536460 GAGTAGGAGGAGGAGGAGCG 60.536 65.000 0.00 0.00 0.00 5.03
1008 1396 3.806667 GGCTCTGGCATGGGCTCT 61.807 66.667 8.37 0.00 40.87 4.09
1089 1477 1.580059 TAGGCGAGAACCCCAAGAAT 58.420 50.000 0.00 0.00 0.00 2.40
1140 1528 2.516225 GCGGCTACCATGGGGAAC 60.516 66.667 18.09 2.02 38.05 3.62
1160 1548 1.373570 GAACCGCTCCATTCTTCTGG 58.626 55.000 0.00 0.00 37.66 3.86
1161 1549 0.678048 AACCGCTCCATTCTTCTGGC 60.678 55.000 0.00 0.00 36.16 4.85
1162 1550 2.176273 CCGCTCCATTCTTCTGGCG 61.176 63.158 0.00 0.00 41.84 5.69
1163 1551 2.176273 CGCTCCATTCTTCTGGCGG 61.176 63.158 0.00 0.00 39.12 6.13
1164 1552 2.476320 GCTCCATTCTTCTGGCGGC 61.476 63.158 0.00 0.00 36.16 6.53
1165 1553 1.078214 CTCCATTCTTCTGGCGGCA 60.078 57.895 12.58 12.58 36.16 5.69
1253 1641 2.790123 CGTCGATCGATTCTTCGTCCAA 60.790 50.000 22.50 0.00 45.65 3.53
1287 1675 0.960364 TGGAGTTCAGATTTGCGCCC 60.960 55.000 4.18 0.00 0.00 6.13
1297 1685 0.103208 ATTTGCGCCCGTCAAAAACA 59.897 45.000 4.18 0.00 37.04 2.83
1310 1698 5.181245 CCGTCAAAAACACTGATAGGAACAT 59.819 40.000 0.00 0.00 0.00 2.71
1320 1708 5.821470 CACTGATAGGAACATGAGCAAGAAT 59.179 40.000 0.00 0.00 0.00 2.40
1416 1804 1.522580 GGTGATCGGCCTGAAGCTC 60.523 63.158 0.00 0.00 43.05 4.09
1484 1872 4.457496 CTCGCCATCGGGTGCTGT 62.457 66.667 0.00 0.00 44.64 4.40
1510 1898 1.401931 CGCCAAACAAATCTCCTGCTG 60.402 52.381 0.00 0.00 0.00 4.41
1591 1979 1.202463 GCTGCAAAGCCGATCTCTCTA 60.202 52.381 0.00 0.00 0.00 2.43
1815 2206 5.590259 TGATTCTAGGTTTCATGCTTTAGCC 59.410 40.000 0.00 0.00 41.18 3.93
1926 2317 6.358974 TTCAGTTCATCAAGGATGTCTACA 57.641 37.500 6.15 0.00 40.55 2.74
1942 2333 7.228706 GGATGTCTACAATGTTTTATGGTAGGG 59.771 40.741 0.00 0.00 33.86 3.53
1994 2385 7.197071 TGTGAAATTCATGCGTTAAGTAAGT 57.803 32.000 0.00 0.00 0.00 2.24
1995 2386 8.312896 TGTGAAATTCATGCGTTAAGTAAGTA 57.687 30.769 0.00 0.00 0.00 2.24
1996 2387 8.775527 TGTGAAATTCATGCGTTAAGTAAGTAA 58.224 29.630 0.00 0.00 0.00 2.24
1997 2388 9.047871 GTGAAATTCATGCGTTAAGTAAGTAAC 57.952 33.333 0.00 0.00 0.00 2.50
2030 2421 2.158871 TGTCCTTCTAAAACAGCCACGT 60.159 45.455 0.00 0.00 0.00 4.49
2033 2424 4.092968 GTCCTTCTAAAACAGCCACGTATG 59.907 45.833 0.00 0.00 0.00 2.39
2126 2517 8.661352 TTTCTTTGTTGATTCAAATTTCCTCC 57.339 30.769 0.00 0.00 36.83 4.30
2329 2845 6.318648 TGCCCAATGTACTATTCATTTCACTC 59.681 38.462 0.00 0.00 33.92 3.51
2344 2860 9.745018 TTCATTTCACTCTAGATTCCTCAAAAT 57.255 29.630 0.00 0.00 0.00 1.82
2502 3019 9.463443 ACTTATGAACATTTTGTGCTAAAACTC 57.537 29.630 2.33 1.99 0.00 3.01
2512 3029 8.850454 TTTTGTGCTAAAACTCTTGTAATGAC 57.150 30.769 0.00 0.00 0.00 3.06
2751 3268 2.577606 TGGTTTCGATGGGTTCATGT 57.422 45.000 0.00 0.00 32.98 3.21
2797 3314 5.736616 AGTTCCCTAATCAAGGTATTTCCCT 59.263 40.000 0.00 0.00 44.90 4.20
2872 3389 6.128902 GGTCGTCACTTACATGTAAACTCTTG 60.129 42.308 18.55 8.87 0.00 3.02
2945 3463 3.773418 TTTTCCACGGACCACTTCATA 57.227 42.857 0.00 0.00 0.00 2.15
2946 3464 3.328382 TTTCCACGGACCACTTCATAG 57.672 47.619 0.00 0.00 0.00 2.23
2953 3471 5.395324 CCACGGACCACTTCATAGAATTAGT 60.395 44.000 0.00 0.00 0.00 2.24
2987 3505 5.897377 AATATGTACTCCTGTTTGTTGGC 57.103 39.130 0.00 0.00 0.00 4.52
3009 3527 6.483974 TGGCTGTTCTTTCGAGTTAACATAAA 59.516 34.615 8.61 4.39 31.88 1.40
3101 3620 4.919677 TTGCAACATGTGACTATACACG 57.080 40.909 0.00 0.00 42.86 4.49
3137 3656 0.250081 GATCCGAGGACCTGATTGCC 60.250 60.000 0.00 0.00 0.00 4.52
3204 3723 6.970191 AGTCACCTACCCTTATTTTAGCAAT 58.030 36.000 0.00 0.00 0.00 3.56
3245 3764 5.593909 TCTTTTCACTGAATTTGCTTCCTCA 59.406 36.000 0.00 0.00 32.49 3.86
3263 3782 7.472663 GCTTCCTCATAGATGATTGTACTTCCT 60.473 40.741 0.00 0.00 36.02 3.36
3326 3845 2.235898 CCTTAAGAAGAGCTGTCAGCCT 59.764 50.000 21.32 14.62 43.77 4.58
3327 3846 3.260740 CTTAAGAAGAGCTGTCAGCCTG 58.739 50.000 21.32 2.21 43.77 4.85
3328 3847 1.055040 AAGAAGAGCTGTCAGCCTGT 58.945 50.000 21.32 6.33 43.77 4.00
3329 3848 0.607620 AGAAGAGCTGTCAGCCTGTC 59.392 55.000 21.32 14.82 43.77 3.51
3330 3849 0.390998 GAAGAGCTGTCAGCCTGTCC 60.391 60.000 21.32 6.01 43.77 4.02
3552 4071 2.203684 CAGGCAAGCCTTGGGGTT 60.204 61.111 11.67 0.00 45.70 4.11
3754 4274 6.763303 GGTGATGAACATTAACACCAAAAC 57.237 37.500 14.85 0.00 46.75 2.43
3963 4484 4.592192 CGCGCTGGGATCATCGGT 62.592 66.667 5.56 0.00 33.63 4.69
4029 4550 2.492449 TTCCAGGTCTTCGAGCGCTG 62.492 60.000 18.48 7.71 35.00 5.18
4311 4846 3.057596 TCGTGTTGCCATGGAAAAAGATC 60.058 43.478 18.40 0.00 0.00 2.75
4465 5001 1.368209 CAGTGCCAGCCATTGCAAA 59.632 52.632 1.71 0.00 39.57 3.68
4493 5030 2.224719 GGCAATGGCTGGACATAGATCT 60.225 50.000 0.00 0.00 40.87 2.75
4522 5059 1.737816 GCATAACATGGCCAGGCAG 59.262 57.895 19.26 6.52 0.00 4.85
4594 5139 0.811915 CAGTTCCTGTCGATCCGTCT 59.188 55.000 0.00 0.00 0.00 4.18
4679 5238 5.113502 AGTTCTAAAAACATGAGCACAGC 57.886 39.130 0.00 0.00 0.00 4.40
4803 5368 7.834068 TCATCTTTTCAGACTTCTTATTCCG 57.166 36.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.543637 AGGGAGGGAGGGAGGGAA 60.544 66.667 0.00 0.00 0.00 3.97
87 101 2.716017 CCTCTGCGTCACCCTCCTC 61.716 68.421 0.00 0.00 0.00 3.71
88 102 2.681778 CCTCTGCGTCACCCTCCT 60.682 66.667 0.00 0.00 0.00 3.69
97 111 3.865929 CTCCACGTTGCCTCTGCGT 62.866 63.158 0.00 0.00 41.78 5.24
128 142 1.358103 ACTGGTACTGCTACCTCAGGA 59.642 52.381 0.00 0.00 42.94 3.86
187 201 3.778097 TTCACCAGCAGCAGCAGCA 62.778 57.895 12.92 0.00 45.49 4.41
189 203 0.887836 TCTTTCACCAGCAGCAGCAG 60.888 55.000 3.17 0.00 45.49 4.24
190 204 0.251033 ATCTTTCACCAGCAGCAGCA 60.251 50.000 3.17 0.00 45.49 4.41
192 206 2.110901 AGATCTTTCACCAGCAGCAG 57.889 50.000 0.00 0.00 0.00 4.24
193 207 2.156917 CAAGATCTTTCACCAGCAGCA 58.843 47.619 4.86 0.00 0.00 4.41
195 209 4.142447 CCAATCAAGATCTTTCACCAGCAG 60.142 45.833 4.86 0.00 0.00 4.24
196 210 3.760151 CCAATCAAGATCTTTCACCAGCA 59.240 43.478 4.86 0.00 0.00 4.41
198 212 3.698040 CCCCAATCAAGATCTTTCACCAG 59.302 47.826 4.86 0.00 0.00 4.00
296 638 6.840780 ATATCACCTTGAAAGAAACCCAAG 57.159 37.500 0.00 0.00 37.58 3.61
339 682 1.144503 CCCTCAAATCTCATCCCTGGG 59.855 57.143 6.33 6.33 0.00 4.45
460 803 3.471806 GAGCTCCCCCTCGAACCC 61.472 72.222 0.87 0.00 0.00 4.11
463 806 4.377760 ACGGAGCTCCCCCTCGAA 62.378 66.667 27.20 0.00 32.57 3.71
508 854 0.855855 TCCTCCTCCTCCTCCCAGAA 60.856 60.000 0.00 0.00 0.00 3.02
509 855 1.230650 TCCTCCTCCTCCTCCCAGA 60.231 63.158 0.00 0.00 0.00 3.86
510 856 1.232792 CTCCTCCTCCTCCTCCCAG 59.767 68.421 0.00 0.00 0.00 4.45
511 857 2.328589 CCTCCTCCTCCTCCTCCCA 61.329 68.421 0.00 0.00 0.00 4.37
512 858 2.015726 TCCTCCTCCTCCTCCTCCC 61.016 68.421 0.00 0.00 0.00 4.30
517 863 2.090775 AGAATTCCTCCTCCTCCTCCTC 60.091 54.545 0.65 0.00 0.00 3.71
518 864 1.943860 AGAATTCCTCCTCCTCCTCCT 59.056 52.381 0.65 0.00 0.00 3.69
519 865 2.046292 CAGAATTCCTCCTCCTCCTCC 58.954 57.143 0.65 0.00 0.00 4.30
520 866 1.416030 GCAGAATTCCTCCTCCTCCTC 59.584 57.143 0.65 0.00 0.00 3.71
521 867 1.009429 AGCAGAATTCCTCCTCCTCCT 59.991 52.381 0.65 0.00 0.00 3.69
543 897 5.488341 CTCCTCCGAAAACAATAGGAAAGA 58.512 41.667 0.00 0.00 35.97 2.52
551 905 4.202472 ACTTCTTCCTCCTCCGAAAACAAT 60.202 41.667 0.00 0.00 0.00 2.71
581 943 4.399303 CCAAAGATCAAGTTGTGGTATCCC 59.601 45.833 2.11 0.00 0.00 3.85
582 944 5.010282 ACCAAAGATCAAGTTGTGGTATCC 58.990 41.667 12.17 0.00 37.60 2.59
676 1041 7.712639 TCAGTTAGTTATGGCAAGAAGATCATC 59.287 37.037 0.00 0.00 0.00 2.92
682 1047 5.168569 TCGTCAGTTAGTTATGGCAAGAAG 58.831 41.667 0.00 0.00 0.00 2.85
697 1062 2.872245 CACACAAGTGGAATCGTCAGTT 59.128 45.455 5.08 0.00 42.13 3.16
717 1082 4.081087 GGGTATGCAGAGTACCTTTCTTCA 60.081 45.833 13.39 0.00 41.11 3.02
718 1083 4.162509 AGGGTATGCAGAGTACCTTTCTTC 59.837 45.833 13.39 0.00 41.11 2.87
778 1146 7.397476 AGAGAGGAAGTACACAACTATCATCAA 59.603 37.037 0.00 0.00 37.50 2.57
788 1156 3.006967 GGCAAGAGAGAGGAAGTACACAA 59.993 47.826 0.00 0.00 0.00 3.33
790 1158 2.093921 GGGCAAGAGAGAGGAAGTACAC 60.094 54.545 0.00 0.00 0.00 2.90
791 1159 2.180276 GGGCAAGAGAGAGGAAGTACA 58.820 52.381 0.00 0.00 0.00 2.90
792 1160 2.429250 GAGGGCAAGAGAGAGGAAGTAC 59.571 54.545 0.00 0.00 0.00 2.73
793 1161 2.043115 TGAGGGCAAGAGAGAGGAAGTA 59.957 50.000 0.00 0.00 0.00 2.24
794 1162 1.203237 TGAGGGCAAGAGAGAGGAAGT 60.203 52.381 0.00 0.00 0.00 3.01
795 1163 1.481772 CTGAGGGCAAGAGAGAGGAAG 59.518 57.143 0.00 0.00 0.00 3.46
796 1164 1.203237 ACTGAGGGCAAGAGAGAGGAA 60.203 52.381 0.00 0.00 0.00 3.36
797 1165 0.411452 ACTGAGGGCAAGAGAGAGGA 59.589 55.000 0.00 0.00 0.00 3.71
799 1167 0.536260 CCACTGAGGGCAAGAGAGAG 59.464 60.000 0.00 0.00 0.00 3.20
813 1193 3.603532 AGAACACATATGAGCACCACTG 58.396 45.455 10.38 0.00 0.00 3.66
873 1253 4.101430 AGCAAGCTTGGAAATCAGGAAAAA 59.899 37.500 27.10 0.00 0.00 1.94
874 1254 3.642848 AGCAAGCTTGGAAATCAGGAAAA 59.357 39.130 27.10 0.00 0.00 2.29
886 1273 2.098770 GGAGCAGAATTAGCAAGCTTGG 59.901 50.000 27.10 9.42 35.36 3.61
913 1300 2.168313 AGCAACAAAAGGGAACACAAGG 59.832 45.455 0.00 0.00 0.00 3.61
974 1362 2.354072 CGAAGATCTCCGGCGCTC 60.354 66.667 7.64 0.00 0.00 5.03
975 1363 3.905678 CCGAAGATCTCCGGCGCT 61.906 66.667 7.71 0.00 39.22 5.92
1008 1396 1.501170 TGGTTCCACTCCATCCCAAAA 59.499 47.619 0.00 0.00 0.00 2.44
1089 1477 4.916293 GGATCGGCCTGCATCGCA 62.916 66.667 0.00 0.00 36.92 5.10
1140 1528 1.002366 CAGAAGAATGGAGCGGTTCG 58.998 55.000 0.00 0.00 0.00 3.95
1178 1566 3.365536 TCCGAGCTGGAAGAGAAGT 57.634 52.632 0.00 0.00 46.38 3.01
1253 1641 0.038744 CTCCATGTTGTTCCCAGCCT 59.961 55.000 0.00 0.00 0.00 4.58
1287 1675 5.666969 TGTTCCTATCAGTGTTTTTGACG 57.333 39.130 0.00 0.00 0.00 4.35
1297 1685 5.426689 TTCTTGCTCATGTTCCTATCAGT 57.573 39.130 0.00 0.00 0.00 3.41
1310 1698 1.134699 CCAGCTCGGTATTCTTGCTCA 60.135 52.381 0.00 0.00 0.00 4.26
1320 1708 2.250031 TCAACTTTACCCAGCTCGGTA 58.750 47.619 6.07 6.07 37.34 4.02
1416 1804 1.201647 TCGAAGTAGGTTCTCTTGCCG 59.798 52.381 0.00 0.00 32.33 5.69
1428 1816 3.017442 TCCACAGACATCCTCGAAGTAG 58.983 50.000 0.00 0.00 0.00 2.57
1484 1872 1.081509 GATTTGTTTGGCGCGCTCA 60.082 52.632 32.29 23.70 0.00 4.26
1510 1898 1.667722 CCTTTGCCTTCTTGCCCAC 59.332 57.895 0.00 0.00 0.00 4.61
1591 1979 5.585047 GCTTCCGATGGTAATCTTTAACAGT 59.415 40.000 0.00 0.00 0.00 3.55
1636 2024 1.911057 ACAACTTTGGGAGCCTTAGC 58.089 50.000 0.00 0.00 40.32 3.09
1815 2206 2.286833 TCGCTTTTTCTGGTCAAACTCG 59.713 45.455 0.00 0.00 0.00 4.18
1926 2317 6.388983 AGCCTAGTACCCTACCATAAAACATT 59.611 38.462 0.00 0.00 0.00 2.71
1968 2359 7.803189 ACTTACTTAACGCATGAATTTCACAAG 59.197 33.333 0.15 0.00 0.00 3.16
1995 2386 9.461312 TTTTAGAAGGACATATGTAAGCATGTT 57.539 29.630 8.71 0.00 35.55 2.71
1996 2387 8.893727 GTTTTAGAAGGACATATGTAAGCATGT 58.106 33.333 8.71 0.00 38.08 3.21
1997 2388 8.892723 TGTTTTAGAAGGACATATGTAAGCATG 58.107 33.333 8.71 0.00 36.58 4.06
2033 2424 1.961277 CCGCTGAGTTGGTGTGACC 60.961 63.158 0.00 0.00 39.22 4.02
2039 2430 1.034838 TTTTGTGCCGCTGAGTTGGT 61.035 50.000 0.00 0.00 0.00 3.67
2502 3019 6.245115 TGCATCTGTTCAAGTCATTACAAG 57.755 37.500 0.00 0.00 0.00 3.16
2512 3029 2.034939 TGTTGCCTTGCATCTGTTCAAG 59.965 45.455 0.00 0.00 38.76 3.02
2549 3066 1.207089 TGAACATAAGGAGCCTGACCG 59.793 52.381 0.00 0.00 0.00 4.79
2797 3314 6.918626 TCGTTTGGAAATTCATTCATAAGCA 58.081 32.000 0.00 0.00 39.98 3.91
2851 3368 7.441458 AGGAACAAGAGTTTACATGTAAGTGAC 59.559 37.037 17.36 13.30 38.30 3.67
2933 3450 9.614792 AAACATACTAATTCTATGAAGTGGTCC 57.385 33.333 9.15 0.00 0.00 4.46
2968 3486 3.149196 CAGCCAACAAACAGGAGTACAT 58.851 45.455 0.00 0.00 0.00 2.29
2973 3491 2.301346 AGAACAGCCAACAAACAGGAG 58.699 47.619 0.00 0.00 0.00 3.69
2974 3492 2.435372 AGAACAGCCAACAAACAGGA 57.565 45.000 0.00 0.00 0.00 3.86
2975 3493 3.447742 GAAAGAACAGCCAACAAACAGG 58.552 45.455 0.00 0.00 0.00 4.00
2987 3505 9.530129 GTCATTTATGTTAACTCGAAAGAACAG 57.470 33.333 7.22 0.00 41.32 3.16
3009 3527 4.595762 AAGTGCAAAAGCTTCATGTCAT 57.404 36.364 0.00 0.00 0.00 3.06
3077 3596 5.333721 CGTGTATAGTCACATGTTGCAAACA 60.334 40.000 0.00 2.08 45.39 2.83
3101 3620 4.698304 TCGGATCACAAAAATAAGGACCAC 59.302 41.667 0.00 0.00 0.00 4.16
3137 3656 3.947868 ACATGGAGAAGAATGTGACCTG 58.052 45.455 0.00 0.00 35.71 4.00
3204 3723 4.537135 AAAGAGCGTGATTAACCAGAGA 57.463 40.909 0.00 0.00 0.00 3.10
3245 3764 6.463614 GCAGGTCAGGAAGTACAATCATCTAT 60.464 42.308 0.00 0.00 0.00 1.98
3263 3782 3.264193 AGATTGTGGATAACTGCAGGTCA 59.736 43.478 19.93 2.57 0.00 4.02
3326 3845 4.652679 TCAGTACTAAGAGGACAGGACA 57.347 45.455 0.00 0.00 0.00 4.02
3327 3846 6.153000 TCAAATCAGTACTAAGAGGACAGGAC 59.847 42.308 0.00 0.00 0.00 3.85
3328 3847 6.253758 TCAAATCAGTACTAAGAGGACAGGA 58.746 40.000 0.00 0.00 0.00 3.86
3329 3848 6.531503 TCAAATCAGTACTAAGAGGACAGG 57.468 41.667 0.00 0.00 0.00 4.00
3330 3849 8.474025 AGAATCAAATCAGTACTAAGAGGACAG 58.526 37.037 0.00 0.00 0.00 3.51
3383 3902 6.201044 CCAAAGCTATAGTCTCAAATGGTACG 59.799 42.308 0.84 0.00 0.00 3.67
3496 4015 7.429636 TCAACAACTTTCCGGTATAGAAAAG 57.570 36.000 0.00 5.37 33.06 2.27
3501 4020 8.657074 TCATTATCAACAACTTTCCGGTATAG 57.343 34.615 0.00 0.00 0.00 1.31
3749 4269 7.768240 AGGGTAAACAAGTAGAACAAGTTTTG 58.232 34.615 0.00 0.00 32.43 2.44
3754 4274 6.059484 TGGAAGGGTAAACAAGTAGAACAAG 58.941 40.000 0.00 0.00 0.00 3.16
3963 4484 2.759973 CGTCTAGCCAGAGCCCCA 60.760 66.667 0.00 0.00 41.25 4.96
4217 4752 2.106844 GCCAAAACCATAGGCCTCG 58.893 57.895 9.68 0.55 42.58 4.63
4311 4846 6.812998 ACAAATGGCTAAATGATGGATCAAG 58.187 36.000 0.00 0.00 40.69 3.02
4465 5001 2.361610 CAGCCATTGCCGGTCCTT 60.362 61.111 1.90 0.00 38.69 3.36
4484 5020 3.641436 TGCCGTGGTCATTAGATCTATGT 59.359 43.478 2.58 0.00 0.00 2.29
4487 5024 5.303333 TGTTATGCCGTGGTCATTAGATCTA 59.697 40.000 0.00 0.00 0.00 1.98
4493 5030 3.210227 CCATGTTATGCCGTGGTCATTA 58.790 45.455 0.00 0.00 36.85 1.90
4522 5059 1.518572 CTACGGGGTCGATGCACAC 60.519 63.158 0.00 0.00 40.11 3.82
4594 5139 1.065998 CCCCCTCGTCCGATTTAAACA 60.066 52.381 0.00 0.00 0.00 2.83
4616 5167 4.434354 TAACGGTGGCATGCCCCC 62.434 66.667 33.44 30.20 34.56 5.40
4617 5168 3.138128 GTAACGGTGGCATGCCCC 61.138 66.667 33.44 29.24 34.56 5.80
4619 5170 1.644786 GACAGTAACGGTGGCATGCC 61.645 60.000 30.54 30.54 0.00 4.40
4620 5171 1.644786 GGACAGTAACGGTGGCATGC 61.645 60.000 9.90 9.90 0.00 4.06
4630 5181 4.767478 CCTTAGGCTTTAGGGACAGTAAC 58.233 47.826 0.00 0.00 0.00 2.50
4679 5238 4.547859 GCCATACCTGCCAGTCTG 57.452 61.111 0.00 0.00 0.00 3.51
4755 5314 7.501892 TGATACCAAGATGCTTAATTATGTGCA 59.498 33.333 9.63 9.63 39.83 4.57
4756 5315 7.874940 TGATACCAAGATGCTTAATTATGTGC 58.125 34.615 0.84 0.65 0.00 4.57


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

AutoCloner maintained by Alex Coulton.