Multiple sequence alignment - TraesCS3D01G317600

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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 TraesCS3D01G317600 chr3D 100.000 3908 0 0 1 3908 431287748 431283841 0.000000e+00 7217.0
1 TraesCS3D01G317600 chr3D 100.000 43 0 0 4395 4437 431283354 431283312 3.680000e-11 80.5
2 TraesCS3D01G317600 chr3B 94.323 3558 137 30 365 3901 563392733 563396246 0.000000e+00 5391.0
3 TraesCS3D01G317600 chr3B 88.750 160 15 3 166 323 529407948 529407790 4.530000e-45 193.0
4 TraesCS3D01G317600 chr3B 86.207 174 20 4 166 337 125703605 125703776 7.580000e-43 185.0
5 TraesCS3D01G317600 chr3A 93.539 3343 129 35 270 3598 568662990 568666259 0.000000e+00 4896.0
6 TraesCS3D01G317600 chr3A 94.098 305 13 2 3597 3899 568666316 568666617 4.040000e-125 459.0
7 TraesCS3D01G317600 chr3A 93.491 169 7 1 1 165 568662771 568662939 9.530000e-62 248.0
8 TraesCS3D01G317600 chr5B 86.782 174 19 3 166 337 472929642 472929471 1.630000e-44 191.0
9 TraesCS3D01G317600 chr1B 86.782 174 19 4 166 337 555355655 555355826 1.630000e-44 191.0
10 TraesCS3D01G317600 chr1B 86.782 174 19 4 166 337 610318510 610318339 1.630000e-44 191.0
11 TraesCS3D01G317600 chr1B 86.207 174 20 4 166 337 378629700 378629871 7.580000e-43 185.0
12 TraesCS3D01G317600 chr6D 88.199 161 16 3 166 324 431160826 431160667 5.860000e-44 189.0
13 TraesCS3D01G317600 chr5A 86.982 169 19 3 166 332 320214403 320214236 2.110000e-43 187.0
14 TraesCS3D01G317600 chr7B 86.207 174 20 3 166 337 198228846 198229017 7.580000e-43 185.0
15 TraesCS3D01G317600 chrUn 78.723 188 31 7 2863 3046 18059527 18059709 2.800000e-22 117.0


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 TraesCS3D01G317600 chr3D 431283312 431287748 4436 True 3648.750000 7217 100.000000 1 4437 2 chr3D.!!$R1 4436
1 TraesCS3D01G317600 chr3B 563392733 563396246 3513 False 5391.000000 5391 94.323000 365 3901 1 chr3B.!!$F2 3536
2 TraesCS3D01G317600 chr3A 568662771 568666617 3846 False 1867.666667 4896 93.709333 1 3899 3 chr3A.!!$F1 3898

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
165 170 0.104304 ATTGTACCACTCGGATCGGC 59.896 55.000 0.00 0.00 35.59 5.54 F
431 448 0.531974 TGGTGGAAACGTGCAGAGTC 60.532 55.000 0.00 0.00 0.00 3.36 F
1080 1103 1.342496 TCAGCAGAGAGTCACACAAGG 59.658 52.381 0.00 0.00 0.00 3.61 F
1529 1552 0.179121 TCTACCGGCATGCACTAACG 60.179 55.000 21.36 13.09 0.00 3.18 F
3195 3231 0.460284 GACGCCTAGCTTGCTTGCTA 60.460 55.000 0.00 10.02 43.74 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1472 1495 0.036010 GAAGCCTAGAACAGCCAGCA 60.036 55.000 0.00 0.00 0.0 4.41 R
1510 1533 0.179121 CGTTAGTGCATGCCGGTAGA 60.179 55.000 16.68 0.00 0.0 2.59 R
2308 2331 1.226888 GATGAGGGTGTACGCGACC 60.227 63.158 15.93 10.59 0.0 4.79 R
3213 3257 0.119155 AGTCATCCTCCTCCAACCCA 59.881 55.000 0.00 0.00 0.0 4.51 R
4417 4525 0.112412 AGGCCCGTGGAGTTTTGATT 59.888 50.000 0.00 0.00 0.0 2.57 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
153 158 6.103997 TCCGAGTCAATTGTAGAATTGTACC 58.896 40.000 21.00 12.36 45.98 3.34
155 160 6.183360 CCGAGTCAATTGTAGAATTGTACCAC 60.183 42.308 21.00 13.57 45.98 4.16
158 163 6.590292 AGTCAATTGTAGAATTGTACCACTCG 59.410 38.462 21.00 0.00 45.98 4.18
165 170 0.104304 ATTGTACCACTCGGATCGGC 59.896 55.000 0.00 0.00 35.59 5.54
166 171 0.968901 TTGTACCACTCGGATCGGCT 60.969 55.000 0.00 0.00 35.59 5.52
167 172 1.359475 GTACCACTCGGATCGGCTC 59.641 63.158 0.00 0.00 35.59 4.70
168 173 1.826921 TACCACTCGGATCGGCTCC 60.827 63.158 0.00 0.00 41.07 4.70
169 174 3.917760 CCACTCGGATCGGCTCCC 61.918 72.222 0.00 0.00 41.49 4.30
170 175 2.835431 CACTCGGATCGGCTCCCT 60.835 66.667 0.00 0.00 41.49 4.20
171 176 2.519780 ACTCGGATCGGCTCCCTC 60.520 66.667 0.00 0.00 41.49 4.30
172 177 3.299190 CTCGGATCGGCTCCCTCC 61.299 72.222 0.00 0.00 41.49 4.30
187 200 6.293698 GGCTCCCTCCGTTTCTAAATATAAA 58.706 40.000 0.00 0.00 0.00 1.40
255 268 8.804688 AGATGTATTTTAGAGCGTAGATTCAC 57.195 34.615 0.00 0.00 0.00 3.18
256 269 8.634444 AGATGTATTTTAGAGCGTAGATTCACT 58.366 33.333 0.00 0.00 0.00 3.41
257 270 8.804688 ATGTATTTTAGAGCGTAGATTCACTC 57.195 34.615 0.00 0.00 0.00 3.51
258 271 7.768240 TGTATTTTAGAGCGTAGATTCACTCA 58.232 34.615 0.00 0.00 0.00 3.41
259 272 8.414003 TGTATTTTAGAGCGTAGATTCACTCAT 58.586 33.333 0.00 0.00 0.00 2.90
260 273 9.250624 GTATTTTAGAGCGTAGATTCACTCATT 57.749 33.333 0.00 0.00 0.00 2.57
261 274 8.723942 ATTTTAGAGCGTAGATTCACTCATTT 57.276 30.769 0.00 0.00 0.00 2.32
262 275 8.547967 TTTTAGAGCGTAGATTCACTCATTTT 57.452 30.769 0.00 0.00 0.00 1.82
263 276 7.525688 TTAGAGCGTAGATTCACTCATTTTG 57.474 36.000 0.00 0.00 0.00 2.44
264 277 5.482908 AGAGCGTAGATTCACTCATTTTGT 58.517 37.500 0.00 0.00 0.00 2.83
265 278 5.934625 AGAGCGTAGATTCACTCATTTTGTT 59.065 36.000 0.00 0.00 0.00 2.83
266 279 6.428159 AGAGCGTAGATTCACTCATTTTGTTT 59.572 34.615 0.00 0.00 0.00 2.83
267 280 6.970484 AGCGTAGATTCACTCATTTTGTTTT 58.030 32.000 0.00 0.00 0.00 2.43
268 281 8.094798 AGCGTAGATTCACTCATTTTGTTTTA 57.905 30.769 0.00 0.00 0.00 1.52
319 332 8.415392 AAAAGACTTATATTTAGGAAGGGGGA 57.585 34.615 0.00 0.00 0.00 4.81
320 333 7.634526 AAGACTTATATTTAGGAAGGGGGAG 57.365 40.000 0.00 0.00 0.00 4.30
321 334 6.704792 AGACTTATATTTAGGAAGGGGGAGT 58.295 40.000 0.00 0.00 0.00 3.85
322 335 7.844566 AGACTTATATTTAGGAAGGGGGAGTA 58.155 38.462 0.00 0.00 0.00 2.59
324 337 7.612179 ACTTATATTTAGGAAGGGGGAGTACT 58.388 38.462 0.00 0.00 0.00 2.73
325 338 7.513091 ACTTATATTTAGGAAGGGGGAGTACTG 59.487 40.741 0.00 0.00 0.00 2.74
326 339 3.572661 TTTAGGAAGGGGGAGTACTGT 57.427 47.619 0.00 0.00 0.00 3.55
400 417 5.709164 GCAGACTAATGGCCAATCTAATCAT 59.291 40.000 10.96 0.00 0.00 2.45
427 444 2.507339 AAAATGGTGGAAACGTGCAG 57.493 45.000 0.00 0.00 0.00 4.41
431 448 0.531974 TGGTGGAAACGTGCAGAGTC 60.532 55.000 0.00 0.00 0.00 3.36
663 683 3.438360 CAAGCGGACTGGCATTTATTTC 58.562 45.455 0.00 0.00 34.64 2.17
745 765 3.005554 CACAAATGTCAGACCTGGCTAG 58.994 50.000 3.16 0.00 35.92 3.42
856 877 6.101332 GCAGGCAAATGATCATTAGAAACAA 58.899 36.000 21.00 0.00 0.00 2.83
936 959 5.241506 ACACAATTGACAACCCATGAGTAAG 59.758 40.000 13.59 0.00 0.00 2.34
937 960 4.766891 ACAATTGACAACCCATGAGTAAGG 59.233 41.667 13.59 0.00 0.00 2.69
978 1001 3.759581 TCCGCTCTCTATATAACCCGTT 58.240 45.455 0.00 0.00 0.00 4.44
1019 1042 1.662629 CACAAACCAGCGAGCTGATAG 59.337 52.381 24.93 11.74 46.30 2.08
1060 1083 1.563410 CCTGGGCTCAGAAATCCTCTT 59.437 52.381 17.43 0.00 43.49 2.85
1078 1101 2.695147 TCTTCAGCAGAGAGTCACACAA 59.305 45.455 0.00 0.00 0.00 3.33
1080 1103 1.342496 TCAGCAGAGAGTCACACAAGG 59.658 52.381 0.00 0.00 0.00 3.61
1238 1261 2.023318 CGTACTCGCCGAGATCCTT 58.977 57.895 22.80 0.00 33.32 3.36
1305 1328 4.925861 GCAGCAGCCCCCTCGATC 62.926 72.222 0.00 0.00 33.58 3.69
1458 1481 4.035558 GGTATGCATGACAAGTACACATGG 59.964 45.833 10.16 0.00 40.83 3.66
1475 1498 4.017177 CATGGACTCATGTGGATATGCT 57.983 45.455 0.00 0.00 44.22 3.79
1476 1499 3.480505 TGGACTCATGTGGATATGCTG 57.519 47.619 0.00 0.00 0.00 4.41
1478 1501 2.149578 GACTCATGTGGATATGCTGGC 58.850 52.381 0.00 0.00 0.00 4.85
1479 1502 1.773052 ACTCATGTGGATATGCTGGCT 59.227 47.619 0.00 0.00 0.00 4.75
1480 1503 2.152016 CTCATGTGGATATGCTGGCTG 58.848 52.381 0.00 0.00 0.00 4.85
1481 1504 1.491754 TCATGTGGATATGCTGGCTGT 59.508 47.619 0.00 0.00 0.00 4.40
1483 1506 2.042686 TGTGGATATGCTGGCTGTTC 57.957 50.000 0.00 0.00 0.00 3.18
1484 1507 1.561076 TGTGGATATGCTGGCTGTTCT 59.439 47.619 0.00 0.00 0.00 3.01
1486 1509 3.181462 TGTGGATATGCTGGCTGTTCTAG 60.181 47.826 0.00 0.00 0.00 2.43
1498 1521 4.237349 GCTGTTCTAGGCTTCTAGCTAG 57.763 50.000 15.01 15.01 41.99 3.42
1499 1522 3.634910 GCTGTTCTAGGCTTCTAGCTAGT 59.365 47.826 20.10 3.39 41.99 2.57
1500 1523 4.499019 GCTGTTCTAGGCTTCTAGCTAGTG 60.499 50.000 20.10 14.70 41.99 2.74
1501 1524 4.601084 TGTTCTAGGCTTCTAGCTAGTGT 58.399 43.478 20.10 4.79 41.99 3.55
1502 1525 4.399618 TGTTCTAGGCTTCTAGCTAGTGTG 59.600 45.833 20.10 12.12 41.99 3.82
1503 1526 4.505324 TCTAGGCTTCTAGCTAGTGTGA 57.495 45.455 20.10 7.68 41.99 3.58
1504 1527 4.456535 TCTAGGCTTCTAGCTAGTGTGAG 58.543 47.826 20.10 14.07 41.99 3.51
1505 1528 3.374042 AGGCTTCTAGCTAGTGTGAGA 57.626 47.619 20.10 0.00 41.99 3.27
1506 1529 3.287222 AGGCTTCTAGCTAGTGTGAGAG 58.713 50.000 20.10 10.46 41.99 3.20
1507 1530 3.053991 AGGCTTCTAGCTAGTGTGAGAGA 60.054 47.826 20.10 0.00 41.99 3.10
1508 1531 3.697045 GGCTTCTAGCTAGTGTGAGAGAA 59.303 47.826 20.10 5.93 41.99 2.87
1509 1532 4.158764 GGCTTCTAGCTAGTGTGAGAGAAA 59.841 45.833 20.10 3.39 41.99 2.52
1510 1533 5.163457 GGCTTCTAGCTAGTGTGAGAGAAAT 60.163 44.000 20.10 0.00 41.99 2.17
1511 1534 5.977129 GCTTCTAGCTAGTGTGAGAGAAATC 59.023 44.000 20.10 0.00 38.45 2.17
1512 1535 6.183360 GCTTCTAGCTAGTGTGAGAGAAATCT 60.183 42.308 20.10 0.00 38.45 2.40
1513 1536 7.012894 GCTTCTAGCTAGTGTGAGAGAAATCTA 59.987 40.741 20.10 0.00 38.45 1.98
1514 1537 7.795482 TCTAGCTAGTGTGAGAGAAATCTAC 57.205 40.000 20.10 0.00 0.00 2.59
1515 1538 5.845391 AGCTAGTGTGAGAGAAATCTACC 57.155 43.478 0.00 0.00 0.00 3.18
1516 1539 4.336993 AGCTAGTGTGAGAGAAATCTACCG 59.663 45.833 0.00 0.00 0.00 4.02
1517 1540 4.498345 GCTAGTGTGAGAGAAATCTACCGG 60.498 50.000 0.00 0.00 0.00 5.28
1518 1541 2.166664 AGTGTGAGAGAAATCTACCGGC 59.833 50.000 0.00 0.00 0.00 6.13
1523 1546 1.486310 AGAGAAATCTACCGGCATGCA 59.514 47.619 21.36 0.00 0.00 3.96
1529 1552 0.179121 TCTACCGGCATGCACTAACG 60.179 55.000 21.36 13.09 0.00 3.18
1530 1553 1.762222 CTACCGGCATGCACTAACGC 61.762 60.000 21.36 0.00 0.00 4.84
1558 1581 3.664014 GCGCAATGGTTTGTTTTATGTGC 60.664 43.478 0.30 0.00 35.17 4.57
1625 1648 2.962569 CCGACGAGCTTGACAGGA 59.037 61.111 8.31 0.00 0.00 3.86
1768 1791 2.590575 CGGCCGGTGTTGACAAGT 60.591 61.111 20.10 0.00 0.00 3.16
1796 1819 4.373116 GCCGGCAGTTCCTCGACA 62.373 66.667 24.80 0.00 0.00 4.35
1844 1867 4.115199 GCCCCAACGAGGCCATCT 62.115 66.667 5.01 0.00 45.16 2.90
2206 2229 1.585521 GTCGCAGTACATCCCGACG 60.586 63.158 10.33 0.00 40.27 5.12
2224 2247 3.048941 GCTCGAGTTCTACGGCGGT 62.049 63.158 15.13 1.39 0.00 5.68
2788 2824 1.299926 CACCAGCTACGCCGATACC 60.300 63.158 0.00 0.00 0.00 2.73
2959 2995 3.967335 CCCCTCGAGATCCGCGTC 61.967 72.222 15.71 0.00 38.37 5.19
3194 3230 1.743252 GACGCCTAGCTTGCTTGCT 60.743 57.895 0.00 8.85 46.11 3.91
3195 3231 0.460284 GACGCCTAGCTTGCTTGCTA 60.460 55.000 0.00 10.02 43.74 3.49
3427 3471 9.577110 TTTATGTAGAACTACCTGTCAATTACG 57.423 33.333 9.11 0.00 35.26 3.18
3466 3510 0.108520 CCGCAAGCTGCATTCCAAAT 60.109 50.000 1.02 0.00 45.36 2.32
3507 3551 8.053355 TGTTGTATGGACTTCTAGTCTCTATGA 58.947 37.037 6.77 0.00 44.46 2.15
3516 3560 6.831868 ACTTCTAGTCTCTATGAGAAAGGACC 59.168 42.308 0.00 0.00 40.59 4.46
3519 3563 4.689062 AGTCTCTATGAGAAAGGACCCAA 58.311 43.478 0.00 0.00 40.59 4.12
3535 3579 4.887071 GGACCCAATTATCTACACAATGCA 59.113 41.667 0.00 0.00 0.00 3.96
3536 3580 5.536161 GGACCCAATTATCTACACAATGCAT 59.464 40.000 0.00 0.00 0.00 3.96
3543 3587 9.983804 CAATTATCTACACAATGCATATGCTAG 57.016 33.333 27.13 18.40 42.66 3.42
3570 3614 6.925718 GCTAGCAAAGAATGGAAGAAAAACTT 59.074 34.615 10.63 0.00 42.03 2.66
3699 3805 6.420008 CCTTCAGTTCAAGCTTTTGAATCAAG 59.580 38.462 4.22 6.83 42.20 3.02
3703 3809 7.915397 TCAGTTCAAGCTTTTGAATCAAGTAAC 59.085 33.333 4.22 0.00 42.20 2.50
3874 3982 4.758674 AGATTGGACGGCAATATCAATCTG 59.241 41.667 16.08 0.00 46.78 2.90
3882 3990 3.802139 GGCAATATCAATCTGACGTTCGA 59.198 43.478 0.00 0.00 0.00 3.71
3884 3992 4.504461 GCAATATCAATCTGACGTTCGACT 59.496 41.667 0.00 0.00 0.00 4.18
3891 3999 0.927537 CTGACGTTCGACTTGTTGCA 59.072 50.000 0.00 0.00 0.00 4.08
3899 4007 0.680921 CGACTTGTTGCATCCCCCAT 60.681 55.000 0.00 0.00 0.00 4.00
3900 4008 0.819582 GACTTGTTGCATCCCCCATG 59.180 55.000 0.00 0.00 35.29 3.66
3902 4010 1.963464 CTTGTTGCATCCCCCATGGC 61.963 60.000 6.09 0.00 32.37 4.40
3903 4011 3.530260 GTTGCATCCCCCATGGCG 61.530 66.667 6.09 0.00 32.37 5.69
3907 4015 4.528039 CATCCCCCATGGCGCCTT 62.528 66.667 29.70 19.97 0.00 4.35
4415 4523 2.699321 ACCCCTTCTAGAACCTTATCGC 59.301 50.000 0.00 0.00 0.00 4.58
4416 4524 2.966516 CCCCTTCTAGAACCTTATCGCT 59.033 50.000 0.00 0.00 0.00 4.93
4417 4525 4.150359 CCCCTTCTAGAACCTTATCGCTA 58.850 47.826 0.00 0.00 0.00 4.26
4418 4526 4.587684 CCCCTTCTAGAACCTTATCGCTAA 59.412 45.833 0.00 0.00 0.00 3.09
4419 4527 5.246429 CCCCTTCTAGAACCTTATCGCTAAT 59.754 44.000 0.00 0.00 0.00 1.73
4420 4528 6.391537 CCCTTCTAGAACCTTATCGCTAATC 58.608 44.000 0.00 0.00 0.00 1.75
4421 4529 6.015350 CCCTTCTAGAACCTTATCGCTAATCA 60.015 42.308 0.00 0.00 0.00 2.57
4422 4530 7.434492 CCTTCTAGAACCTTATCGCTAATCAA 58.566 38.462 0.00 0.00 0.00 2.57
4423 4531 7.926555 CCTTCTAGAACCTTATCGCTAATCAAA 59.073 37.037 0.00 0.00 0.00 2.69
4424 4532 9.314321 CTTCTAGAACCTTATCGCTAATCAAAA 57.686 33.333 0.00 0.00 0.00 2.44
4425 4533 8.644318 TCTAGAACCTTATCGCTAATCAAAAC 57.356 34.615 0.00 0.00 0.00 2.43
4426 4534 8.475639 TCTAGAACCTTATCGCTAATCAAAACT 58.524 33.333 0.00 0.00 0.00 2.66
4427 4535 7.541122 AGAACCTTATCGCTAATCAAAACTC 57.459 36.000 0.00 0.00 0.00 3.01
4428 4536 6.539103 AGAACCTTATCGCTAATCAAAACTCC 59.461 38.462 0.00 0.00 0.00 3.85
4429 4537 5.741011 ACCTTATCGCTAATCAAAACTCCA 58.259 37.500 0.00 0.00 0.00 3.86
4430 4538 5.585047 ACCTTATCGCTAATCAAAACTCCAC 59.415 40.000 0.00 0.00 0.00 4.02
4431 4539 5.276868 CCTTATCGCTAATCAAAACTCCACG 60.277 44.000 0.00 0.00 0.00 4.94
4432 4540 2.343101 TCGCTAATCAAAACTCCACGG 58.657 47.619 0.00 0.00 0.00 4.94
4433 4541 1.396996 CGCTAATCAAAACTCCACGGG 59.603 52.381 0.00 0.00 0.00 5.28
4434 4542 1.132453 GCTAATCAAAACTCCACGGGC 59.868 52.381 0.00 0.00 0.00 6.13
4435 4543 1.743394 CTAATCAAAACTCCACGGGCC 59.257 52.381 0.00 0.00 0.00 5.80
4436 4544 0.112412 AATCAAAACTCCACGGGCCT 59.888 50.000 0.84 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.251354 GAGGCTTGCCTGATCAGACA 59.749 55.000 24.62 16.55 0.00 3.41
13 14 0.391661 TTCTTAGCGAGGCTTGCCTG 60.392 55.000 22.99 13.10 40.44 4.85
120 125 4.310769 ACAATTGACTCGGAGCATATAGC 58.689 43.478 13.59 0.00 46.19 2.97
135 140 6.295405 TCCGAGTGGTACAATTCTACAATTGA 60.295 38.462 13.59 0.00 44.16 2.57
165 170 9.780186 AAGATTTATATTTAGAAACGGAGGGAG 57.220 33.333 0.00 0.00 0.00 4.30
229 242 9.894783 GTGAATCTACGCTCTAAAATACATCTA 57.105 33.333 0.00 0.00 0.00 1.98
230 243 8.634444 AGTGAATCTACGCTCTAAAATACATCT 58.366 33.333 0.00 0.00 0.00 2.90
231 244 8.804688 AGTGAATCTACGCTCTAAAATACATC 57.195 34.615 0.00 0.00 0.00 3.06
232 245 8.414003 TGAGTGAATCTACGCTCTAAAATACAT 58.586 33.333 0.00 0.00 44.58 2.29
233 246 7.768240 TGAGTGAATCTACGCTCTAAAATACA 58.232 34.615 0.00 0.00 44.58 2.29
234 247 8.804688 ATGAGTGAATCTACGCTCTAAAATAC 57.195 34.615 0.00 0.00 44.58 1.89
235 248 9.817809 AAATGAGTGAATCTACGCTCTAAAATA 57.182 29.630 0.00 0.00 44.58 1.40
236 249 8.723942 AAATGAGTGAATCTACGCTCTAAAAT 57.276 30.769 0.00 0.00 44.58 1.82
237 250 8.443160 CAAAATGAGTGAATCTACGCTCTAAAA 58.557 33.333 0.00 0.00 44.58 1.52
238 251 7.602644 ACAAAATGAGTGAATCTACGCTCTAAA 59.397 33.333 0.00 0.00 44.58 1.85
239 252 7.097192 ACAAAATGAGTGAATCTACGCTCTAA 58.903 34.615 0.00 0.00 44.58 2.10
240 253 6.631016 ACAAAATGAGTGAATCTACGCTCTA 58.369 36.000 0.00 0.00 44.58 2.43
241 254 5.482908 ACAAAATGAGTGAATCTACGCTCT 58.517 37.500 0.00 0.00 44.58 4.09
242 255 5.786401 ACAAAATGAGTGAATCTACGCTC 57.214 39.130 0.00 0.00 44.55 5.03
243 256 6.560253 AAACAAAATGAGTGAATCTACGCT 57.440 33.333 0.00 0.00 0.00 5.07
244 257 8.895932 ATAAAACAAAATGAGTGAATCTACGC 57.104 30.769 0.00 0.00 0.00 4.42
300 313 7.513091 ACAGTACTCCCCCTTCCTAAATATAAG 59.487 40.741 0.00 0.00 0.00 1.73
311 324 7.852550 AAGTATAATACAGTACTCCCCCTTC 57.147 40.000 0.00 0.00 31.10 3.46
314 327 7.607615 TCAAAGTATAATACAGTACTCCCCC 57.392 40.000 0.00 0.00 31.10 5.40
322 335 9.368416 TGAGGATAGCTCAAAGTATAATACAGT 57.632 33.333 0.00 0.00 0.00 3.55
324 337 9.982651 GTTGAGGATAGCTCAAAGTATAATACA 57.017 33.333 0.00 0.00 41.70 2.29
358 371 3.055385 TCTGCTTTATTTCCGTGCCTACT 60.055 43.478 0.00 0.00 0.00 2.57
360 373 3.055385 AGTCTGCTTTATTTCCGTGCCTA 60.055 43.478 0.00 0.00 0.00 3.93
400 417 6.809196 GCACGTTTCCACCATTTTTATTCATA 59.191 34.615 0.00 0.00 0.00 2.15
427 444 3.482436 ACGATGGATCTCTACCAGACTC 58.518 50.000 0.00 0.00 40.89 3.36
431 448 4.557695 GCACTTACGATGGATCTCTACCAG 60.558 50.000 0.00 0.00 40.89 4.00
663 683 2.584608 CTGTTAGCTGGACCCGGG 59.415 66.667 22.25 22.25 0.00 5.73
828 848 4.823442 TCTAATGATCATTTGCCTGCGATT 59.177 37.500 25.26 0.71 32.50 3.34
829 849 4.392047 TCTAATGATCATTTGCCTGCGAT 58.608 39.130 25.26 0.37 32.50 4.58
869 890 5.664006 TGGGCCTACTACTAACATTACACAT 59.336 40.000 4.53 0.00 0.00 3.21
936 959 1.076995 GGTGGTAATGGGGAGTGCC 60.077 63.158 0.00 0.00 0.00 5.01
937 960 1.076995 GGGTGGTAATGGGGAGTGC 60.077 63.158 0.00 0.00 0.00 4.40
978 1001 1.085091 GAGCGAGAAGTACGAGTGGA 58.915 55.000 0.00 0.00 0.00 4.02
1019 1042 1.019673 TCGTCAGGATGCCGTAGTAC 58.980 55.000 0.00 0.00 34.76 2.73
1060 1083 1.342496 CCTTGTGTGACTCTCTGCTGA 59.658 52.381 0.00 0.00 0.00 4.26
1078 1101 4.335647 CGCACTGTGAAGGGGCCT 62.336 66.667 12.86 0.00 0.00 5.19
1080 1103 4.643387 ACCGCACTGTGAAGGGGC 62.643 66.667 21.17 2.26 41.17 5.80
1223 1246 2.496817 GCAAGGATCTCGGCGAGT 59.503 61.111 33.31 21.83 0.00 4.18
1235 1258 2.720758 CGTCTCGTTCTGCGCAAGG 61.721 63.158 13.05 3.05 41.07 3.61
1249 1272 3.450115 GCAGGTACTCGGCCGTCT 61.450 66.667 27.15 13.83 34.60 4.18
1305 1328 4.867599 GCGGAAGGCGTCTACGGG 62.868 72.222 14.57 0.00 40.23 5.28
1458 1481 2.149578 GCCAGCATATCCACATGAGTC 58.850 52.381 0.00 0.00 0.00 3.36
1468 1491 2.038295 AGCCTAGAACAGCCAGCATATC 59.962 50.000 0.00 0.00 0.00 1.63
1472 1495 0.036010 GAAGCCTAGAACAGCCAGCA 60.036 55.000 0.00 0.00 0.00 4.41
1473 1496 0.251634 AGAAGCCTAGAACAGCCAGC 59.748 55.000 0.00 0.00 0.00 4.85
1475 1498 1.482593 GCTAGAAGCCTAGAACAGCCA 59.517 52.381 0.00 0.00 44.00 4.75
1476 1499 1.760029 AGCTAGAAGCCTAGAACAGCC 59.240 52.381 0.00 0.00 43.77 4.85
1478 1501 4.642885 ACACTAGCTAGAAGCCTAGAACAG 59.357 45.833 27.45 0.00 43.77 3.16
1479 1502 4.399618 CACACTAGCTAGAAGCCTAGAACA 59.600 45.833 27.45 0.00 43.77 3.18
1480 1503 4.641094 TCACACTAGCTAGAAGCCTAGAAC 59.359 45.833 27.45 0.00 43.77 3.01
1481 1504 4.856509 TCACACTAGCTAGAAGCCTAGAA 58.143 43.478 27.45 0.19 43.77 2.10
1483 1506 4.456535 TCTCACACTAGCTAGAAGCCTAG 58.543 47.826 27.45 14.84 43.77 3.02
1484 1507 4.164413 TCTCTCACACTAGCTAGAAGCCTA 59.836 45.833 27.45 7.45 43.77 3.93
1486 1509 3.283751 TCTCTCACACTAGCTAGAAGCC 58.716 50.000 27.45 0.00 43.77 4.35
1488 1511 7.333528 AGATTTCTCTCACACTAGCTAGAAG 57.666 40.000 27.45 19.62 0.00 2.85
1489 1512 7.283580 GGTAGATTTCTCTCACACTAGCTAGAA 59.716 40.741 27.45 7.49 32.66 2.10
1491 1514 6.293190 CGGTAGATTTCTCTCACACTAGCTAG 60.293 46.154 19.44 19.44 32.66 3.42
1493 1516 4.336993 CGGTAGATTTCTCTCACACTAGCT 59.663 45.833 0.00 0.00 32.66 3.32
1494 1517 4.498345 CCGGTAGATTTCTCTCACACTAGC 60.498 50.000 0.00 0.00 32.66 3.42
1495 1518 4.498345 GCCGGTAGATTTCTCTCACACTAG 60.498 50.000 1.90 0.00 32.66 2.57
1496 1519 3.380637 GCCGGTAGATTTCTCTCACACTA 59.619 47.826 1.90 0.00 32.66 2.74
1497 1520 2.166664 GCCGGTAGATTTCTCTCACACT 59.833 50.000 1.90 0.00 32.66 3.55
1498 1521 2.094182 TGCCGGTAGATTTCTCTCACAC 60.094 50.000 1.90 0.00 32.66 3.82
1499 1522 2.176045 TGCCGGTAGATTTCTCTCACA 58.824 47.619 1.90 0.00 32.66 3.58
1500 1523 2.961526 TGCCGGTAGATTTCTCTCAC 57.038 50.000 1.90 0.00 32.66 3.51
1501 1524 2.483714 GCATGCCGGTAGATTTCTCTCA 60.484 50.000 6.36 0.00 32.66 3.27
1502 1525 2.139118 GCATGCCGGTAGATTTCTCTC 58.861 52.381 6.36 0.00 32.66 3.20
1503 1526 1.486310 TGCATGCCGGTAGATTTCTCT 59.514 47.619 16.68 0.00 35.39 3.10
1504 1527 1.599542 GTGCATGCCGGTAGATTTCTC 59.400 52.381 16.68 0.00 0.00 2.87
1505 1528 1.210478 AGTGCATGCCGGTAGATTTCT 59.790 47.619 16.68 0.00 0.00 2.52
1506 1529 1.668419 AGTGCATGCCGGTAGATTTC 58.332 50.000 16.68 0.00 0.00 2.17
1507 1530 2.943033 GTTAGTGCATGCCGGTAGATTT 59.057 45.455 16.68 0.00 0.00 2.17
1508 1531 2.561569 GTTAGTGCATGCCGGTAGATT 58.438 47.619 16.68 0.00 0.00 2.40
1509 1532 1.538204 CGTTAGTGCATGCCGGTAGAT 60.538 52.381 16.68 0.00 0.00 1.98
1510 1533 0.179121 CGTTAGTGCATGCCGGTAGA 60.179 55.000 16.68 0.00 0.00 2.59
1511 1534 1.762222 GCGTTAGTGCATGCCGGTAG 61.762 60.000 16.68 3.52 34.15 3.18
1512 1535 1.812093 GCGTTAGTGCATGCCGGTA 60.812 57.895 16.68 0.00 34.15 4.02
1513 1536 3.124921 GCGTTAGTGCATGCCGGT 61.125 61.111 16.68 1.64 34.15 5.28
1514 1537 4.222589 CGCGTTAGTGCATGCCGG 62.223 66.667 16.68 0.00 34.15 6.13
1558 1581 2.743928 GAAGTGCCGGAGCTGGTG 60.744 66.667 5.05 0.00 40.80 4.17
1585 1608 1.078143 GGTCGGCATGAGCTTCCTT 60.078 57.895 0.00 0.00 41.93 3.36
1618 1641 2.601666 AGCAGCGACCTCCTGTCA 60.602 61.111 0.00 0.00 44.71 3.58
1762 1785 1.468736 CGGCTCCGGTAGTAACTTGTC 60.469 57.143 0.00 0.00 35.56 3.18
1843 1866 0.389948 GGTAGGAGTCCACGCACAAG 60.390 60.000 12.86 0.00 0.00 3.16
1844 1867 1.116536 TGGTAGGAGTCCACGCACAA 61.117 55.000 12.86 0.00 0.00 3.33
1966 1989 2.659016 CGAGGCCAGTGCTTCTCA 59.341 61.111 5.01 0.00 41.19 3.27
2206 2229 2.278013 CCGCCGTAGAACTCGAGC 60.278 66.667 13.61 0.00 0.00 5.03
2224 2247 4.478371 CAGATGAGCGGCAGGCCA 62.478 66.667 5.01 0.00 45.17 5.36
2308 2331 1.226888 GATGAGGGTGTACGCGACC 60.227 63.158 15.93 10.59 0.00 4.79
2410 2433 2.504244 CCGAGCTTCACGTCGACC 60.504 66.667 10.58 0.00 38.50 4.79
2959 2995 3.934391 GAAGGTGCCCTCGGACACG 62.934 68.421 0.00 0.00 37.68 4.49
3149 3185 1.229304 TCAGCAGCTCCTTGGAGGA 60.229 57.895 17.33 4.32 43.43 3.71
3213 3257 0.119155 AGTCATCCTCCTCCAACCCA 59.881 55.000 0.00 0.00 0.00 4.51
3263 3307 3.619242 CGAGATATCGTAGCCCCTACAGA 60.619 52.174 0.53 2.49 36.83 3.41
3388 3432 2.671130 ACATAAAATGCGGCCCAAAG 57.329 45.000 0.00 0.00 0.00 2.77
3466 3510 9.787435 GTCCATACAACATTGGGATAAACTATA 57.213 33.333 0.00 0.00 33.62 1.31
3507 3551 6.636454 TGTGTAGATAATTGGGTCCTTTCT 57.364 37.500 0.00 0.00 0.00 2.52
3516 3560 7.823665 AGCATATGCATTGTGTAGATAATTGG 58.176 34.615 28.62 0.00 45.16 3.16
3519 3563 9.597170 CTCTAGCATATGCATTGTGTAGATAAT 57.403 33.333 28.62 6.05 45.16 1.28
3543 3587 5.886960 TTTCTTCCATTCTTTGCTAGCTC 57.113 39.130 17.23 0.00 0.00 4.09
3699 3805 8.824159 ATATGATAGATGCAGACAACAGTTAC 57.176 34.615 0.00 0.00 0.00 2.50
3703 3809 7.376615 TCTGATATGATAGATGCAGACAACAG 58.623 38.462 0.00 0.00 0.00 3.16
3861 3969 4.504461 AGTCGAACGTCAGATTGATATTGC 59.496 41.667 0.00 0.00 0.00 3.56
3874 3982 1.136336 GGATGCAACAAGTCGAACGTC 60.136 52.381 0.00 0.00 0.00 4.34
3882 3990 0.615544 CCATGGGGGATGCAACAAGT 60.616 55.000 2.85 0.00 40.01 3.16
3884 3992 1.988956 GCCATGGGGGATGCAACAA 60.989 57.895 15.13 0.00 40.01 2.83
4394 4502 2.699321 GCGATAAGGTTCTAGAAGGGGT 59.301 50.000 5.12 0.00 0.00 4.95
4395 4503 2.966516 AGCGATAAGGTTCTAGAAGGGG 59.033 50.000 5.12 0.00 0.00 4.79
4396 4504 5.786264 TTAGCGATAAGGTTCTAGAAGGG 57.214 43.478 5.12 0.00 0.00 3.95
4397 4505 6.982852 TGATTAGCGATAAGGTTCTAGAAGG 58.017 40.000 5.12 0.00 0.00 3.46
4398 4506 8.873215 TTTGATTAGCGATAAGGTTCTAGAAG 57.127 34.615 5.12 0.00 0.00 2.85
4399 4507 9.095065 GTTTTGATTAGCGATAAGGTTCTAGAA 57.905 33.333 0.00 0.00 0.00 2.10
4400 4508 8.475639 AGTTTTGATTAGCGATAAGGTTCTAGA 58.524 33.333 0.00 0.00 0.00 2.43
4401 4509 8.649973 AGTTTTGATTAGCGATAAGGTTCTAG 57.350 34.615 0.00 0.00 0.00 2.43
4402 4510 7.709613 GGAGTTTTGATTAGCGATAAGGTTCTA 59.290 37.037 0.00 0.00 0.00 2.10
4403 4511 6.539103 GGAGTTTTGATTAGCGATAAGGTTCT 59.461 38.462 0.00 0.00 0.00 3.01
4404 4512 6.315393 TGGAGTTTTGATTAGCGATAAGGTTC 59.685 38.462 0.00 0.00 0.00 3.62
4405 4513 6.093633 GTGGAGTTTTGATTAGCGATAAGGTT 59.906 38.462 0.00 0.00 0.00 3.50
4406 4514 5.585047 GTGGAGTTTTGATTAGCGATAAGGT 59.415 40.000 0.00 0.00 0.00 3.50
4407 4515 5.276868 CGTGGAGTTTTGATTAGCGATAAGG 60.277 44.000 0.00 0.00 0.00 2.69
4408 4516 5.276868 CCGTGGAGTTTTGATTAGCGATAAG 60.277 44.000 0.00 0.00 0.00 1.73
4409 4517 4.569162 CCGTGGAGTTTTGATTAGCGATAA 59.431 41.667 0.00 0.00 0.00 1.75
4410 4518 4.116961 CCGTGGAGTTTTGATTAGCGATA 58.883 43.478 0.00 0.00 0.00 2.92
4411 4519 2.936498 CCGTGGAGTTTTGATTAGCGAT 59.064 45.455 0.00 0.00 0.00 4.58
4412 4520 2.343101 CCGTGGAGTTTTGATTAGCGA 58.657 47.619 0.00 0.00 0.00 4.93
4413 4521 1.396996 CCCGTGGAGTTTTGATTAGCG 59.603 52.381 0.00 0.00 0.00 4.26
4414 4522 1.132453 GCCCGTGGAGTTTTGATTAGC 59.868 52.381 0.00 0.00 0.00 3.09
4415 4523 1.743394 GGCCCGTGGAGTTTTGATTAG 59.257 52.381 0.00 0.00 0.00 1.73
4416 4524 1.353022 AGGCCCGTGGAGTTTTGATTA 59.647 47.619 0.00 0.00 0.00 1.75
4417 4525 0.112412 AGGCCCGTGGAGTTTTGATT 59.888 50.000 0.00 0.00 0.00 2.57
4418 4526 1.767692 AGGCCCGTGGAGTTTTGAT 59.232 52.632 0.00 0.00 0.00 2.57
4419 4527 3.246687 AGGCCCGTGGAGTTTTGA 58.753 55.556 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.