Multiple sequence alignment - TraesCS1D01G145300

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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 TraesCS1D01G145300 chr1D 100.000 6708 0 0 1 6708 200710508 200717215 0.000000e+00 12388.0
1 TraesCS1D01G145300 chr1B 93.871 6265 292 45 460 6708 288644053 288650241 0.000000e+00 9358.0
2 TraesCS1D01G145300 chr1B 91.294 402 34 1 32 432 288642394 288642795 1.270000e-151 547.0
3 TraesCS1D01G145300 chr1A 93.450 2733 140 20 2359 5078 254185249 254187955 0.000000e+00 4019.0
4 TraesCS1D01G145300 chr1A 94.569 2357 78 14 32 2362 254182520 254184852 0.000000e+00 3598.0
5 TraesCS1D01G145300 chr1A 92.748 1572 92 15 5142 6708 254187955 254189509 0.000000e+00 2252.0
6 TraesCS1D01G145300 chr4A 79.924 264 47 6 871 1131 330084988 330085248 8.880000e-44 189.0
7 TraesCS1D01G145300 chr5B 82.412 199 22 9 2158 2346 55187025 55186830 1.940000e-35 161.0
8 TraesCS1D01G145300 chr2B 80.087 231 33 10 2150 2370 56626984 56626757 6.960000e-35 159.0
9 TraesCS1D01G145300 chr6B 82.967 182 21 7 2173 2346 516082798 516082977 9.010000e-34 156.0
10 TraesCS1D01G145300 chr6B 78.261 138 22 7 4287 4422 135949091 135949222 1.550000e-11 82.4
11 TraesCS1D01G145300 chrUn 79.221 231 35 10 2150 2370 348911431 348911204 1.510000e-31 148.0
12 TraesCS1D01G145300 chrUn 78.788 231 36 10 2150 2370 217886493 217886266 7.010000e-30 143.0
13 TraesCS1D01G145300 chrUn 78.788 231 36 10 2150 2370 338142295 338142522 7.010000e-30 143.0
14 TraesCS1D01G145300 chrUn 77.489 231 36 14 4199 4422 29748480 29748701 2.540000e-24 124.0
15 TraesCS1D01G145300 chr7D 84.247 146 15 7 2230 2370 614354606 614354748 1.170000e-27 135.0
16 TraesCS1D01G145300 chr3B 76.623 231 40 11 4199 4422 452458797 452458574 1.530000e-21 115.0
17 TraesCS1D01G145300 chr5D 73.810 294 57 17 4145 4428 412463647 412463364 1.540000e-16 99.0
18 TraesCS1D01G145300 chr5D 79.021 143 22 6 4203 4341 344541761 344541623 2.580000e-14 91.6
19 TraesCS1D01G145300 chr6A 87.805 82 6 4 1 79 540152802 540152882 7.160000e-15 93.5
20 TraesCS1D01G145300 chr6A 81.707 82 10 4 1 80 88608335 88608257 5.620000e-06 63.9
21 TraesCS1D01G145300 chr2A 77.596 183 21 11 4278 4453 1319364 1319195 7.160000e-15 93.5
22 TraesCS1D01G145300 chr2A 83.333 90 11 3 12 99 468599305 468599218 5.580000e-11 80.5
23 TraesCS1D01G145300 chr3D 75.107 233 38 18 4199 4422 543916838 543917059 2.580000e-14 91.6


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 TraesCS1D01G145300 chr1D 200710508 200717215 6707 False 12388.000000 12388 100.0000 1 6708 1 chr1D.!!$F1 6707
1 TraesCS1D01G145300 chr1B 288642394 288650241 7847 False 4952.500000 9358 92.5825 32 6708 2 chr1B.!!$F1 6676
2 TraesCS1D01G145300 chr1A 254182520 254189509 6989 False 3289.666667 4019 93.5890 32 6708 3 chr1A.!!$F1 6676

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
321 322 0.039617 TGAAAATGTCCCTTTGCGCG 60.040 50.000 0.00 0.00 0.00 6.86 F
356 358 0.043485 TAGCTGGGTATGGGGTGTCA 59.957 55.000 0.00 0.00 0.00 3.58 F
433 435 1.064685 GGAATTTGGATGTCCGGACCT 60.065 52.381 31.19 22.52 39.43 3.85 F
839 2070 2.496817 GCCGACGCTGAAGAGGAT 59.503 61.111 0.00 0.00 0.00 3.24 F
2229 3460 2.604969 TGACAAATTTAGTTCGCGGC 57.395 45.000 6.13 0.00 0.00 6.53 F
3405 5046 0.605319 GAACAACATCGCCACCTGGA 60.605 55.000 0.00 0.00 37.39 3.86 F
4095 5737 0.540365 AGGTGAACAAGGGTGCATGG 60.540 55.000 0.00 0.00 34.29 3.66 F
5309 6956 1.029681 GCATGAGCATCTTGGATGCA 58.970 50.000 27.00 13.12 46.77 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2224 3455 1.016130 ACTGAGACAGATTTGCCGCG 61.016 55.000 0.00 0.0 35.18 6.46 R
2256 3487 2.836262 TGCAAGCCCAACAATTTTCTG 58.164 42.857 0.00 0.0 0.00 3.02 R
2346 3578 8.708742 TCAGAAACACTTAAACATCTAACATCG 58.291 33.333 0.00 0.0 0.00 3.84 R
2679 4318 1.067565 CGGGTATAGATGTGCGAGCAT 60.068 52.381 0.00 0.0 0.00 3.79 R
3556 5197 2.241176 ACCCCTGACTTCAACTTTGACA 59.759 45.455 0.00 0.0 36.83 3.58 R
5034 6679 1.475280 CCAAGTGCAGATGAACATGGG 59.525 52.381 7.24 0.0 38.48 4.00 R
5365 7013 2.700897 CCCAGACTCAATTACTCCCGAT 59.299 50.000 0.00 0.0 0.00 4.18 R
6376 8025 1.626825 CCTTCGACCTTGACCCCTAAA 59.373 52.381 0.00 0.0 0.00 1.85 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 2.692368 ACGAGGCATCCCCACCAT 60.692 61.111 0.00 0.00 35.39 3.55
18 19 2.203252 CGAGGCATCCCCACCATG 60.203 66.667 0.00 0.00 35.39 3.66
19 20 2.745308 CGAGGCATCCCCACCATGA 61.745 63.158 0.00 0.00 35.39 3.07
20 21 1.614711 GAGGCATCCCCACCATGAA 59.385 57.895 0.00 0.00 35.39 2.57
21 22 0.186873 GAGGCATCCCCACCATGAAT 59.813 55.000 0.00 0.00 35.39 2.57
22 23 1.425066 GAGGCATCCCCACCATGAATA 59.575 52.381 0.00 0.00 35.39 1.75
23 24 1.858910 AGGCATCCCCACCATGAATAA 59.141 47.619 0.00 0.00 35.39 1.40
24 25 1.963515 GGCATCCCCACCATGAATAAC 59.036 52.381 0.00 0.00 0.00 1.89
25 26 2.665165 GCATCCCCACCATGAATAACA 58.335 47.619 0.00 0.00 0.00 2.41
26 27 3.030291 GCATCCCCACCATGAATAACAA 58.970 45.455 0.00 0.00 0.00 2.83
27 28 3.181476 GCATCCCCACCATGAATAACAAC 60.181 47.826 0.00 0.00 0.00 3.32
28 29 2.717390 TCCCCACCATGAATAACAACG 58.283 47.619 0.00 0.00 0.00 4.10
29 30 2.306219 TCCCCACCATGAATAACAACGA 59.694 45.455 0.00 0.00 0.00 3.85
30 31 3.053991 TCCCCACCATGAATAACAACGAT 60.054 43.478 0.00 0.00 0.00 3.73
94 95 1.838073 AAATTCCCCGTGCGACCTCT 61.838 55.000 0.00 0.00 0.00 3.69
131 132 2.700897 ACTATGCAAGGCACCCTACTAG 59.299 50.000 0.00 0.00 43.04 2.57
148 149 3.447950 ACTAGGGGTACTGACGGAAATT 58.552 45.455 0.00 0.00 0.00 1.82
180 181 0.243907 CTCCAACTCCGACGTGACAT 59.756 55.000 0.00 0.00 0.00 3.06
184 185 0.809385 AACTCCGACGTGACATCGAT 59.191 50.000 1.41 0.00 42.25 3.59
268 269 4.504916 CGGTCAGGGCAGAGAGCG 62.505 72.222 9.52 9.52 46.96 5.03
304 305 1.370609 TTCGCACGAAAAAGTGGTGA 58.629 45.000 2.45 0.00 42.09 4.02
321 322 0.039617 TGAAAATGTCCCTTTGCGCG 60.040 50.000 0.00 0.00 0.00 6.86
329 330 2.978010 CCTTTGCGCGGGTTCTGT 60.978 61.111 8.83 0.00 0.00 3.41
346 348 2.042569 TCTGTCTGGTTCTAGCTGGGTA 59.957 50.000 0.00 0.00 0.00 3.69
356 358 0.043485 TAGCTGGGTATGGGGTGTCA 59.957 55.000 0.00 0.00 0.00 3.58
366 368 4.367023 GGGTGTCACGCGCCTACA 62.367 66.667 5.73 5.17 46.69 2.74
370 372 2.125673 GTCACGCGCCTACATGGT 60.126 61.111 5.73 0.00 38.35 3.55
389 391 1.404035 GTTGGACGCTCACAAACCTTT 59.596 47.619 0.00 0.00 0.00 3.11
395 397 2.224670 ACGCTCACAAACCTTTCCCATA 60.225 45.455 0.00 0.00 0.00 2.74
419 421 2.699846 TGCTTCTGGCTTGTTGGAATTT 59.300 40.909 0.00 0.00 42.39 1.82
432 434 1.340600 TGGAATTTGGATGTCCGGACC 60.341 52.381 31.19 17.25 39.43 4.46
433 435 1.064685 GGAATTTGGATGTCCGGACCT 60.065 52.381 31.19 22.52 39.43 3.85
437 489 5.455612 GGAATTTGGATGTCCGGACCTATAA 60.456 44.000 31.19 17.90 39.43 0.98
472 524 4.403137 GCTGTTTGATGCGCGGCA 62.403 61.111 8.83 7.01 44.86 5.69
839 2070 2.496817 GCCGACGCTGAAGAGGAT 59.503 61.111 0.00 0.00 0.00 3.24
1035 2266 4.399395 CTGCAGCGGGAGAAGGCA 62.399 66.667 0.00 0.00 33.71 4.75
2166 3397 9.095700 GATAGGAAAGGACTCCACTATAAATCT 57.904 37.037 0.00 0.00 38.02 2.40
2174 3405 7.345653 AGGACTCCACTATAAATCTGATGTCAA 59.654 37.037 0.00 0.00 0.00 3.18
2212 3443 5.296780 GGCAAATTATGTTCTCCGAGAATGA 59.703 40.000 13.92 4.90 36.50 2.57
2224 3455 7.596749 TCTCCGAGAATGACAAATTTAGTTC 57.403 36.000 0.00 0.00 0.00 3.01
2229 3460 2.604969 TGACAAATTTAGTTCGCGGC 57.395 45.000 6.13 0.00 0.00 6.53
2235 3466 4.165779 CAAATTTAGTTCGCGGCAAATCT 58.834 39.130 6.13 0.00 0.00 2.40
2335 3567 6.319658 GCCATGAAAAGATCAGATTTGTCCTA 59.680 38.462 0.00 0.00 42.53 2.94
2349 3581 9.277783 CAGATTTGTCCTATCTAAAAATCCGAT 57.722 33.333 0.00 0.00 37.76 4.18
2355 3587 8.920174 TGTCCTATCTAAAAATCCGATGTTAGA 58.080 33.333 13.41 13.41 37.09 2.10
2357 3589 9.929180 TCCTATCTAAAAATCCGATGTTAGATG 57.071 33.333 23.24 17.08 41.28 2.90
2370 4001 7.876068 TCCGATGTTAGATGTTTAAGTGTTTCT 59.124 33.333 0.00 0.00 0.00 2.52
2382 4013 9.349713 TGTTTAAGTGTTTCTGATAGGAAATGT 57.650 29.630 0.00 0.00 37.50 2.71
2679 4318 5.534654 AGCTTGCTGGTTGTGAAATACTTAA 59.465 36.000 0.00 0.00 0.00 1.85
3021 4662 7.406031 TCATTAAACAACAAGGGTTACACAA 57.594 32.000 0.00 0.00 34.87 3.33
3151 4792 3.709653 TCTTGGAGAACCTTGTACACTGT 59.290 43.478 0.00 0.00 37.04 3.55
3156 4797 5.063880 GGAGAACCTTGTACACTGTCAAAT 58.936 41.667 0.00 0.00 0.00 2.32
3209 4850 2.029623 GGCACGACCAGATAAGTAGGA 58.970 52.381 0.00 0.00 38.86 2.94
3240 4881 6.544928 TGCCACAACAAGATCTATAAGAGA 57.455 37.500 0.00 0.00 39.01 3.10
3405 5046 0.605319 GAACAACATCGCCACCTGGA 60.605 55.000 0.00 0.00 37.39 3.86
3454 5095 3.069300 AGAGATGGACGAGATGAATGTGG 59.931 47.826 0.00 0.00 0.00 4.17
3461 5102 1.411977 CGAGATGAATGTGGCTCCTCT 59.588 52.381 0.00 0.00 0.00 3.69
3477 5118 4.109050 CTCCTCTTGTTGTCGATTAGAGC 58.891 47.826 0.00 0.00 32.83 4.09
3482 5123 5.641709 TCTTGTTGTCGATTAGAGCACTAG 58.358 41.667 0.00 0.00 0.00 2.57
3499 5140 3.997021 CACTAGCAAATTGGACGAGAAGT 59.003 43.478 0.00 0.00 0.00 3.01
3525 5166 6.777580 AGAGACAATTTATTTGAGGTGGTGTT 59.222 34.615 0.00 0.00 38.76 3.32
3550 5191 1.327690 TGCCCTCGATGTGACCCTAC 61.328 60.000 0.00 0.00 0.00 3.18
3556 5197 3.223435 CTCGATGTGACCCTACCTACAT 58.777 50.000 0.00 0.00 36.54 2.29
3702 5343 2.976903 GGCAGCGGAGATCATGGC 60.977 66.667 0.00 0.00 0.00 4.40
3821 5462 4.112634 TGCACCCTAGATTTGAAGGTTT 57.887 40.909 0.00 0.00 0.00 3.27
3842 5483 4.314522 TGTATTCCCTGAGAATTGCCAA 57.685 40.909 0.00 0.00 42.86 4.52
3851 5492 4.943705 CCTGAGAATTGCCAAGCTACTTTA 59.056 41.667 0.00 0.00 0.00 1.85
3893 5534 0.958822 AGGTTGGATTGGCAACGTTC 59.041 50.000 0.00 0.00 42.51 3.95
4035 5677 2.162408 GCTACTTTGACCTTGCATCCAC 59.838 50.000 0.00 0.00 0.00 4.02
4085 5727 5.935945 TCTGGAGAATACAAAGGTGAACAA 58.064 37.500 0.00 0.00 0.00 2.83
4095 5737 0.540365 AGGTGAACAAGGGTGCATGG 60.540 55.000 0.00 0.00 34.29 3.66
4180 5822 3.057456 GTCGACTAGTCCACTGACATGTT 60.057 47.826 17.23 0.00 44.33 2.71
4182 5824 4.395231 TCGACTAGTCCACTGACATGTTAG 59.605 45.833 17.23 15.61 44.33 2.34
4274 5916 8.801715 TCAAACATTGTCTTTTTATTGCTCTC 57.198 30.769 0.00 0.00 0.00 3.20
4462 6106 5.220378 CCAAAAATCCGTGTCTGTTTTGTTG 60.220 40.000 0.00 0.00 37.43 3.33
4528 6172 5.621193 ACTAGAATTAGGGCGTGCATTTAT 58.379 37.500 0.00 0.00 0.00 1.40
4537 6181 2.293122 GGCGTGCATTTATATTGGCTCA 59.707 45.455 0.00 0.00 0.00 4.26
4832 6477 3.451894 GCTCACCAAATGCCCCCG 61.452 66.667 0.00 0.00 0.00 5.73
4834 6479 1.076777 CTCACCAAATGCCCCCGAT 60.077 57.895 0.00 0.00 0.00 4.18
4872 6517 9.717892 GTTAAGAATACAAGGTTTGCTATAAGC 57.282 33.333 0.00 0.00 42.82 3.09
4986 6631 4.702131 AGTATAGCAGCCCTTTTGTCAAAG 59.298 41.667 0.00 0.00 39.45 2.77
5034 6679 4.385358 ACCCGATAATTCAAAATGGTGC 57.615 40.909 0.00 0.00 0.00 5.01
5168 6813 6.900568 TTTCATTGTGTTTGGACATTTGAC 57.099 33.333 0.00 0.00 38.23 3.18
5175 6820 2.542020 TTGGACATTTGACGAGCTCA 57.458 45.000 15.40 0.00 0.00 4.26
5178 6823 3.521560 TGGACATTTGACGAGCTCATAC 58.478 45.455 15.40 4.73 0.00 2.39
5218 6864 9.284594 CGAATAGTGTTCTTTTTCAAAGTTTCA 57.715 29.630 0.00 0.00 0.00 2.69
5289 6936 4.202202 TGAAAATTTGCACGAACCTTCCAT 60.202 37.500 0.00 0.00 0.00 3.41
5309 6956 1.029681 GCATGAGCATCTTGGATGCA 58.970 50.000 27.00 13.12 46.77 3.96
5314 6961 4.906065 TGAGCATCTTGGATGCATAAAC 57.094 40.909 27.00 15.76 46.77 2.01
5429 7077 7.833682 TCATAATTACCTTGCTTTTGATCTCCA 59.166 33.333 0.00 0.00 0.00 3.86
5510 7158 4.575645 TGAAACCCTTGTTACCTTGTTACG 59.424 41.667 0.00 0.00 33.30 3.18
5569 7217 5.467063 GTGTTCCCCGCAAAATGAAAATTAA 59.533 36.000 0.00 0.00 0.00 1.40
5715 7363 5.279685 TCCCAAAAGGATTTAGATGCCATT 58.720 37.500 0.00 0.00 40.93 3.16
5854 7502 3.826157 TGGAAGCCATCAATTTTTCTCGT 59.174 39.130 0.00 0.00 0.00 4.18
5860 7508 5.691754 AGCCATCAATTTTTCTCGTTGTTTC 59.308 36.000 0.00 0.00 0.00 2.78
5861 7509 5.461737 GCCATCAATTTTTCTCGTTGTTTCA 59.538 36.000 0.00 0.00 0.00 2.69
5863 7511 7.307337 GCCATCAATTTTTCTCGTTGTTTCAAT 60.307 33.333 0.00 0.00 0.00 2.57
5892 7540 1.388431 AGCGTTGTTGTTTTTGTTGCG 59.612 42.857 0.00 0.00 0.00 4.85
5976 7624 1.202211 TGCGTAGTACACAGTATGCCG 60.202 52.381 0.38 0.00 42.53 5.69
6014 7662 6.773200 TGTACATGGTGTTTGTTAAGAATGGA 59.227 34.615 0.00 0.00 0.00 3.41
6028 7676 1.936547 GAATGGACAAGAGCTAAGGCG 59.063 52.381 0.00 0.00 44.37 5.52
6040 7688 2.632996 AGCTAAGGCGCTTCACCATATA 59.367 45.455 7.64 0.00 44.37 0.86
6093 7741 7.043961 TGTGTGCAACTATTGGTTCATTTTA 57.956 32.000 0.00 0.00 38.04 1.52
6094 7742 7.665690 TGTGTGCAACTATTGGTTCATTTTAT 58.334 30.769 0.00 0.00 38.04 1.40
6108 7756 9.267084 TGGTTCATTTTATTTTCTTTTAGGCAC 57.733 29.630 0.00 0.00 0.00 5.01
6123 7771 0.953960 GGCACTTAACTGGACCACCG 60.954 60.000 0.00 0.00 39.42 4.94
6126 7774 0.034896 ACTTAACTGGACCACCGCAG 59.965 55.000 0.00 0.00 39.42 5.18
6140 7788 3.072211 CACCGCAGAGATGCATATCATT 58.928 45.455 22.54 0.49 35.05 2.57
6173 7821 7.886338 TGCAACAAATACCACATATTGTACAA 58.114 30.769 11.41 11.41 33.53 2.41
6223 7871 9.710900 AAGGATGTCTCAACCAAATTAATTTTC 57.289 29.630 10.77 2.64 0.00 2.29
6297 7946 5.786401 AAAATGTAGCTCATGTCGAGAAC 57.214 39.130 0.00 0.00 45.45 3.01
6386 8035 3.053077 CCATCCTATGGTTTAGGGGTCA 58.947 50.000 0.00 0.00 45.54 4.02
6560 8212 6.314784 CAAAAACATGGAGAATACGAAGGTC 58.685 40.000 0.00 0.00 0.00 3.85
6564 8216 2.719739 TGGAGAATACGAAGGTCGACT 58.280 47.619 16.46 0.00 43.74 4.18
6588 8240 9.933723 ACTACCAAATCGTATTACTTGTACTTT 57.066 29.630 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.692368 ATGGTGGGGATGCCTCGT 60.692 61.111 2.19 0.00 0.00 4.18
1 2 2.203252 CATGGTGGGGATGCCTCG 60.203 66.667 2.19 0.00 0.00 4.63
2 3 0.186873 ATTCATGGTGGGGATGCCTC 59.813 55.000 2.19 0.00 0.00 4.70
3 4 1.533187 TATTCATGGTGGGGATGCCT 58.467 50.000 2.19 0.00 0.00 4.75
4 5 1.963515 GTTATTCATGGTGGGGATGCC 59.036 52.381 0.00 0.00 0.00 4.40
5 6 2.665165 TGTTATTCATGGTGGGGATGC 58.335 47.619 0.00 0.00 0.00 3.91
6 7 3.066621 CGTTGTTATTCATGGTGGGGATG 59.933 47.826 0.00 0.00 0.00 3.51
7 8 3.053991 TCGTTGTTATTCATGGTGGGGAT 60.054 43.478 0.00 0.00 0.00 3.85
8 9 2.306219 TCGTTGTTATTCATGGTGGGGA 59.694 45.455 0.00 0.00 0.00 4.81
9 10 2.717390 TCGTTGTTATTCATGGTGGGG 58.283 47.619 0.00 0.00 0.00 4.96
10 11 3.944650 TCATCGTTGTTATTCATGGTGGG 59.055 43.478 0.00 0.00 0.00 4.61
11 12 4.496341 GCTCATCGTTGTTATTCATGGTGG 60.496 45.833 0.00 0.00 0.00 4.61
12 13 4.094739 TGCTCATCGTTGTTATTCATGGTG 59.905 41.667 0.00 0.00 0.00 4.17
13 14 4.260985 TGCTCATCGTTGTTATTCATGGT 58.739 39.130 0.00 0.00 0.00 3.55
14 15 4.880886 TGCTCATCGTTGTTATTCATGG 57.119 40.909 0.00 0.00 0.00 3.66
15 16 6.051646 TCATGCTCATCGTTGTTATTCATG 57.948 37.500 0.00 0.00 0.00 3.07
16 17 6.261603 ACATCATGCTCATCGTTGTTATTCAT 59.738 34.615 0.00 0.00 0.00 2.57
17 18 5.585844 ACATCATGCTCATCGTTGTTATTCA 59.414 36.000 0.00 0.00 0.00 2.57
18 19 6.052840 ACATCATGCTCATCGTTGTTATTC 57.947 37.500 0.00 0.00 0.00 1.75
19 20 6.203530 CCTACATCATGCTCATCGTTGTTATT 59.796 38.462 0.00 0.00 0.00 1.40
20 21 5.698089 CCTACATCATGCTCATCGTTGTTAT 59.302 40.000 0.00 0.00 0.00 1.89
21 22 5.049828 CCTACATCATGCTCATCGTTGTTA 58.950 41.667 0.00 0.00 0.00 2.41
22 23 3.873361 CCTACATCATGCTCATCGTTGTT 59.127 43.478 0.00 0.00 0.00 2.83
23 24 3.461061 CCTACATCATGCTCATCGTTGT 58.539 45.455 0.00 0.00 0.00 3.32
24 25 2.804527 CCCTACATCATGCTCATCGTTG 59.195 50.000 0.00 0.00 0.00 4.10
25 26 2.435805 ACCCTACATCATGCTCATCGTT 59.564 45.455 0.00 0.00 0.00 3.85
26 27 2.042464 ACCCTACATCATGCTCATCGT 58.958 47.619 0.00 0.00 0.00 3.73
27 28 2.827800 ACCCTACATCATGCTCATCG 57.172 50.000 0.00 0.00 0.00 3.84
28 29 6.940739 AGTAATACCCTACATCATGCTCATC 58.059 40.000 0.00 0.00 0.00 2.92
29 30 6.728164 AGAGTAATACCCTACATCATGCTCAT 59.272 38.462 0.00 0.00 0.00 2.90
30 31 6.077993 AGAGTAATACCCTACATCATGCTCA 58.922 40.000 0.00 0.00 0.00 4.26
94 95 4.956075 TGCATAGTAGGAAGTCACAGATCA 59.044 41.667 0.00 0.00 0.00 2.92
131 132 1.471287 GCAAATTTCCGTCAGTACCCC 59.529 52.381 0.00 0.00 0.00 4.95
148 149 0.605319 GTTGGAGGATGACGGTGCAA 60.605 55.000 0.00 0.00 0.00 4.08
180 181 0.661552 GAACCGATGGAGACGATCGA 59.338 55.000 24.34 0.00 41.04 3.59
184 185 0.744874 GATGGAACCGATGGAGACGA 59.255 55.000 0.00 0.00 0.00 4.20
218 219 0.605589 CCCAGTTCCCACTCGTTTCC 60.606 60.000 0.00 0.00 0.00 3.13
268 269 1.228459 AAAGTCCGCCCTTTCCCAC 60.228 57.895 0.00 0.00 28.57 4.61
281 282 2.223180 ACCACTTTTTCGTGCGAAAGTC 60.223 45.455 17.30 0.00 42.47 3.01
304 305 1.288752 CCGCGCAAAGGGACATTTT 59.711 52.632 8.75 0.00 34.27 1.82
321 322 1.903183 AGCTAGAACCAGACAGAACCC 59.097 52.381 0.00 0.00 0.00 4.11
329 330 2.398588 CCATACCCAGCTAGAACCAGA 58.601 52.381 0.00 0.00 0.00 3.86
356 358 2.435938 CCAACCATGTAGGCGCGT 60.436 61.111 8.43 8.08 43.14 6.01
366 368 0.951558 GTTTGTGAGCGTCCAACCAT 59.048 50.000 0.00 0.00 0.00 3.55
370 372 1.673920 GAAAGGTTTGTGAGCGTCCAA 59.326 47.619 0.00 0.00 0.00 3.53
419 421 3.576982 GACATTATAGGTCCGGACATCCA 59.423 47.826 34.40 15.70 35.14 3.41
432 434 4.675565 CGTGTAAGCGTCTGGACATTATAG 59.324 45.833 1.63 0.00 0.00 1.31
433 435 4.603985 CGTGTAAGCGTCTGGACATTATA 58.396 43.478 1.63 0.00 0.00 0.98
437 489 0.736325 GCGTGTAAGCGTCTGGACAT 60.736 55.000 1.63 0.00 0.00 3.06
472 524 5.643421 AGACAGATAAGGGCATCTTCAAT 57.357 39.130 0.00 0.00 36.93 2.57
476 1707 3.950395 GCAAAGACAGATAAGGGCATCTT 59.050 43.478 0.00 0.00 39.40 2.40
839 2070 2.281484 GCGCCTCTGGTGGTGAAA 60.281 61.111 0.00 0.00 39.82 2.69
939 2170 2.042259 CAGCTCGGCCTGCAAATCA 61.042 57.895 17.81 0.00 0.00 2.57
1035 2266 2.815945 CGCCTCCATCATGGCCTCT 61.816 63.158 3.32 0.00 45.90 3.69
1725 2956 2.105128 CGCATGGTCTCTCGGTCC 59.895 66.667 0.00 0.00 0.00 4.46
2166 3397 6.014755 TGCCATGGTAAAAGAATTTGACATCA 60.015 34.615 14.67 0.00 41.41 3.07
2174 3405 9.737844 AACATAATTTGCCATGGTAAAAGAATT 57.262 25.926 28.47 20.46 33.78 2.17
2178 3409 7.492344 GGAGAACATAATTTGCCATGGTAAAAG 59.508 37.037 28.47 20.30 33.78 2.27
2212 3443 3.357166 TTTGCCGCGAACTAAATTTGT 57.643 38.095 8.23 0.00 0.00 2.83
2224 3455 1.016130 ACTGAGACAGATTTGCCGCG 61.016 55.000 0.00 0.00 35.18 6.46
2256 3487 2.836262 TGCAAGCCCAACAATTTTCTG 58.164 42.857 0.00 0.00 0.00 3.02
2325 3557 9.057089 ACATCGGATTTTTAGATAGGACAAATC 57.943 33.333 0.00 0.00 34.44 2.17
2346 3578 8.708742 TCAGAAACACTTAAACATCTAACATCG 58.291 33.333 0.00 0.00 0.00 3.84
2382 4013 8.774890 TCTAGTACGGCAAACAATATTACAAA 57.225 30.769 0.00 0.00 0.00 2.83
2383 4014 8.951787 ATCTAGTACGGCAAACAATATTACAA 57.048 30.769 0.00 0.00 0.00 2.41
2679 4318 1.067565 CGGGTATAGATGTGCGAGCAT 60.068 52.381 0.00 0.00 0.00 3.79
2710 4349 4.270834 TGATACTACTCGCTCTGAAGGTT 58.729 43.478 0.00 0.00 0.00 3.50
3021 4662 2.548067 GGGAGAGTGATCGTGTGTGTTT 60.548 50.000 0.00 0.00 0.00 2.83
3087 4728 3.526931 TCTTCCAGAGTCCTTTATGCG 57.473 47.619 0.00 0.00 0.00 4.73
3127 4768 4.039245 CAGTGTACAAGGTTCTCCAAGAGA 59.961 45.833 0.00 0.00 36.86 3.10
3151 4792 3.709141 TCCTATGGTGGATGACGATTTGA 59.291 43.478 0.00 0.00 0.00 2.69
3156 4797 2.454336 AGTCCTATGGTGGATGACGA 57.546 50.000 0.00 0.00 38.52 4.20
3209 4850 5.014858 AGATCTTGTTGTGGCAATGATTCT 58.985 37.500 0.00 0.00 0.00 2.40
3240 4881 3.891366 AGCAGCATTCACTACAAAAGGTT 59.109 39.130 0.00 0.00 0.00 3.50
3405 5046 3.754965 GTGGTGGCATATGACATACCAT 58.245 45.455 20.64 0.00 40.01 3.55
3416 5057 3.232720 TCTCTATACCGTGGTGGCATA 57.767 47.619 0.72 0.00 43.94 3.14
3454 5095 4.109050 CTCTAATCGACAACAAGAGGAGC 58.891 47.826 0.00 0.00 31.94 4.70
3461 5102 4.174009 GCTAGTGCTCTAATCGACAACAA 58.826 43.478 0.00 0.00 36.03 2.83
3477 5118 3.997021 ACTTCTCGTCCAATTTGCTAGTG 59.003 43.478 0.00 0.00 0.00 2.74
3482 5123 4.327627 GTCTCTACTTCTCGTCCAATTTGC 59.672 45.833 0.00 0.00 0.00 3.68
3499 5140 7.458397 ACACCACCTCAAATAAATTGTCTCTA 58.542 34.615 0.00 0.00 40.11 2.43
3525 5166 2.284625 ACATCGAGGGCAGGGACA 60.285 61.111 0.69 0.00 0.00 4.02
3550 5191 5.180117 CCTGACTTCAACTTTGACATGTAGG 59.820 44.000 0.00 0.00 36.83 3.18
3556 5197 2.241176 ACCCCTGACTTCAACTTTGACA 59.759 45.455 0.00 0.00 36.83 3.58
3740 5381 5.278604 TGGATGATCGTATTACTTGTCACG 58.721 41.667 0.00 0.00 35.78 4.35
3808 5449 6.552008 TCAGGGAATACAAACCTTCAAATCT 58.448 36.000 0.00 0.00 30.66 2.40
3821 5462 4.272489 CTTGGCAATTCTCAGGGAATACA 58.728 43.478 0.00 0.00 43.17 2.29
4002 5644 3.123621 GTCAAAGTAGCAATGTCCTCACG 59.876 47.826 0.00 0.00 0.00 4.35
4035 5677 4.657075 ATAGGTAAACGAACAAGCAACG 57.343 40.909 0.00 0.00 0.00 4.10
4173 5815 4.846779 TCTTGGCAAAACCTAACATGTC 57.153 40.909 0.00 0.00 40.22 3.06
4180 5822 4.525100 GGGTGTATTTCTTGGCAAAACCTA 59.475 41.667 0.00 0.00 40.22 3.08
4182 5824 3.070302 TGGGTGTATTTCTTGGCAAAACC 59.930 43.478 0.00 0.00 39.84 3.27
4475 6119 7.496346 TGAAGATGTACTTTTATCTCTGGGT 57.504 36.000 0.00 0.00 39.13 4.51
4992 6637 9.706691 TCGGGTAATTATGTTTTATTTGCAAAA 57.293 25.926 17.19 2.96 0.00 2.44
5034 6679 1.475280 CCAAGTGCAGATGAACATGGG 59.525 52.381 7.24 0.00 38.48 4.00
5088 6733 8.466798 GGATGCCTAAAAATTCTAGCTGTTTTA 58.533 33.333 0.00 0.00 0.00 1.52
5093 6738 6.319658 TCTTGGATGCCTAAAAATTCTAGCTG 59.680 38.462 0.00 0.00 0.00 4.24
5190 6836 9.503427 AAACTTTGAAAAAGAACACTATTCGAG 57.497 29.630 6.73 0.00 0.00 4.04
5191 6837 9.498307 GAAACTTTGAAAAAGAACACTATTCGA 57.502 29.630 6.73 0.00 0.00 3.71
5356 7004 5.309638 TCAATTACTCCCGATTGTGAACAA 58.690 37.500 0.00 0.00 40.51 2.83
5365 7013 2.700897 CCCAGACTCAATTACTCCCGAT 59.299 50.000 0.00 0.00 0.00 4.18
5510 7158 4.595762 AGATGCCAAATATGCAATGACC 57.404 40.909 0.00 0.00 42.92 4.02
5569 7217 5.415701 ACATTGATGAAAGCACGAAGGTAAT 59.584 36.000 0.00 0.00 0.00 1.89
5892 7540 8.916654 CAGTATAACATATGAAGAATCGTCACC 58.083 37.037 10.38 0.00 0.00 4.02
5976 7624 6.106673 ACACCATGTACATTACTCAACTAGC 58.893 40.000 5.37 0.00 0.00 3.42
6028 7676 7.880195 ACTATGATTGTTCCTATATGGTGAAGC 59.120 37.037 0.00 0.00 37.07 3.86
6040 7688 7.121315 GCTAACTTGGAAACTATGATTGTTCCT 59.879 37.037 3.20 0.00 0.00 3.36
6093 7741 7.255836 GGTCCAGTTAAGTGCCTAAAAGAAAAT 60.256 37.037 4.65 0.00 0.00 1.82
6094 7742 6.040054 GGTCCAGTTAAGTGCCTAAAAGAAAA 59.960 38.462 4.65 0.00 0.00 2.29
6108 7756 0.320374 TCTGCGGTGGTCCAGTTAAG 59.680 55.000 0.00 0.00 0.00 1.85
6126 7774 7.300320 TGCATTTTACGAATGATATGCATCTC 58.700 34.615 0.19 3.24 42.21 2.75
6140 7788 6.073327 TGTGGTATTTGTTGCATTTTACGA 57.927 33.333 0.00 0.00 0.00 3.43
6185 7833 6.861065 TGAGACATCCTTGTTAGAAACAAC 57.139 37.500 1.21 0.00 45.79 3.32
6273 7922 6.244275 GTTCTCGACATGAGCTACATTTTTC 58.756 40.000 0.00 0.00 44.86 2.29
6297 7946 5.718724 AAAGGAAATCTGAAAGCTTCTGG 57.281 39.130 0.00 0.00 0.00 3.86
6330 7979 6.718454 AGATATGAAAGGCATCCGAAATGATT 59.282 34.615 2.37 0.00 38.44 2.57
6376 8025 1.626825 CCTTCGACCTTGACCCCTAAA 59.373 52.381 0.00 0.00 0.00 1.85
6542 8191 3.066900 AGTCGACCTTCGTATTCTCCATG 59.933 47.826 13.01 0.00 41.35 3.66
6560 8212 7.912250 AGTACAAGTAATACGATTTGGTAGTCG 59.088 37.037 0.00 0.00 43.13 4.18
6607 8259 2.039418 TGGGAGGACTATCGGATGTTG 58.961 52.381 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.