Multiple sequence alignment - TraesCS1B01G222600

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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 TraesCS1B01G222600 chr1B 100.000 5556 0 0 1 5556 400306796 400312351 0.000000e+00 10261.0
1 TraesCS1B01G222600 chr1D 96.788 3487 98 7 1700 5185 297533168 297536641 0.000000e+00 5806.0
2 TraesCS1B01G222600 chr1D 88.883 1745 98 34 1 1704 297531367 297533056 0.000000e+00 2060.0
3 TraesCS1B01G222600 chr1D 96.040 202 7 1 5204 5404 297536632 297536833 1.490000e-85 327.0
4 TraesCS1B01G222600 chr1D 90.083 121 7 1 5435 5555 297536828 297536943 9.640000e-33 152.0
5 TraesCS1B01G222600 chr1A 91.639 3851 217 55 1700 5520 370104777 370108552 0.000000e+00 5230.0
6 TraesCS1B01G222600 chr1A 89.994 1749 110 29 1 1700 370102960 370104692 0.000000e+00 2200.0
7 TraesCS1B01G222600 chr1A 96.875 32 1 0 2339 2370 144554982 144555013 3.000000e-03 54.7
8 TraesCS1B01G222600 chr7A 96.875 32 1 0 2339 2370 126688027 126688058 3.000000e-03 54.7


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 TraesCS1B01G222600 chr1B 400306796 400312351 5555 False 10261.00 10261 100.0000 1 5556 1 chr1B.!!$F1 5555
1 TraesCS1B01G222600 chr1D 297531367 297536943 5576 False 2086.25 5806 92.9485 1 5555 4 chr1D.!!$F1 5554
2 TraesCS1B01G222600 chr1A 370102960 370108552 5592 False 3715.00 5230 90.8165 1 5520 2 chr1A.!!$F2 5519

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
375 405 0.392193 CGATTCTCCAGCTGGCTGTT 60.392 55.0 28.91 12.67 42.15 3.16 F
1197 1277 0.738975 CATCACAGGCTCATTGCTGG 59.261 55.0 0.00 0.00 42.39 4.85 F
3084 3291 0.332972 AGCCCAGGTCTCAAAATCCC 59.667 55.0 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 2021 0.098728 GATTCACACGCCCCAATTCG 59.901 55.000 0.00 0.00 0.00 3.34 R
3173 3380 1.346068 ACAAGGCAAGAGTCTGTCTCC 59.654 52.381 0.00 0.00 43.71 3.71 R
4766 4978 1.158484 CCGCTGTCATGCATCAGAGG 61.158 60.000 19.16 19.16 42.90 3.69 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
71 72 3.145551 CTACCGTGCCGTAGCCCT 61.146 66.667 0.00 0.00 38.69 5.19
104 119 1.757306 CCTCCCTTCCATCCATCCG 59.243 63.158 0.00 0.00 0.00 4.18
161 176 0.467290 AAGGAAGCAACCAAAGCGGA 60.467 50.000 2.26 0.00 38.63 5.54
162 177 0.890996 AGGAAGCAACCAAAGCGGAG 60.891 55.000 2.26 0.00 38.63 4.63
287 311 0.624254 ACCGATTCCTTTCTTCCCCC 59.376 55.000 0.00 0.00 0.00 5.40
367 397 1.410517 TGTGAGGATCGATTCTCCAGC 59.589 52.381 27.37 18.41 38.61 4.85
374 404 1.220206 CGATTCTCCAGCTGGCTGT 59.780 57.895 28.91 13.40 42.15 4.40
375 405 0.392193 CGATTCTCCAGCTGGCTGTT 60.392 55.000 28.91 12.67 42.15 3.16
376 406 1.831580 GATTCTCCAGCTGGCTGTTT 58.168 50.000 28.91 11.16 42.15 2.83
377 407 2.165998 GATTCTCCAGCTGGCTGTTTT 58.834 47.619 28.91 10.04 42.15 2.43
378 408 2.071778 TTCTCCAGCTGGCTGTTTTT 57.928 45.000 28.91 0.00 42.15 1.94
379 409 1.609208 TCTCCAGCTGGCTGTTTTTC 58.391 50.000 28.91 0.00 42.15 2.29
380 410 1.143684 TCTCCAGCTGGCTGTTTTTCT 59.856 47.619 28.91 0.00 42.15 2.52
381 411 1.959282 CTCCAGCTGGCTGTTTTTCTT 59.041 47.619 28.91 0.00 42.15 2.52
382 412 2.363359 CTCCAGCTGGCTGTTTTTCTTT 59.637 45.455 28.91 0.00 42.15 2.52
383 413 2.362077 TCCAGCTGGCTGTTTTTCTTTC 59.638 45.455 28.91 0.00 42.15 2.62
384 414 2.363359 CCAGCTGGCTGTTTTTCTTTCT 59.637 45.455 22.33 0.00 42.15 2.52
385 415 3.181472 CCAGCTGGCTGTTTTTCTTTCTT 60.181 43.478 22.33 0.00 42.15 2.52
386 416 4.436332 CAGCTGGCTGTTTTTCTTTCTTT 58.564 39.130 13.76 0.00 39.10 2.52
387 417 4.872124 CAGCTGGCTGTTTTTCTTTCTTTT 59.128 37.500 13.76 0.00 39.10 2.27
388 418 5.006068 CAGCTGGCTGTTTTTCTTTCTTTTC 59.994 40.000 13.76 0.00 39.10 2.29
408 453 3.375699 TCTTTCTATGTGGGAGGAGACC 58.624 50.000 0.00 0.00 0.00 3.85
461 506 4.093291 CCGGCTGCTGAGGCTTCT 62.093 66.667 10.70 0.00 42.73 2.85
476 521 2.017559 CTTCTCCCCGGTCGTGATCC 62.018 65.000 0.00 0.00 0.00 3.36
555 612 1.375396 CGTTGGTTGGGATCTGCGA 60.375 57.895 0.00 0.00 0.00 5.10
570 627 2.948979 TCTGCGATGTTTTCTGTTGGTT 59.051 40.909 0.00 0.00 0.00 3.67
583 640 3.316868 TCTGTTGGTTGGGATTCGTTTTC 59.683 43.478 0.00 0.00 0.00 2.29
587 644 2.291190 TGGTTGGGATTCGTTTTCGTTC 59.709 45.455 0.00 0.00 44.46 3.95
638 695 5.831997 AGTTTTAACCAATTCACAGTCTGC 58.168 37.500 0.00 0.00 0.00 4.26
643 700 2.105477 ACCAATTCACAGTCTGCTGAGT 59.895 45.455 0.00 0.00 45.28 3.41
644 701 3.324846 ACCAATTCACAGTCTGCTGAGTA 59.675 43.478 0.00 0.00 45.28 2.59
645 702 3.681897 CCAATTCACAGTCTGCTGAGTAC 59.318 47.826 0.00 0.00 45.28 2.73
787 856 8.723942 AAGATTTACTGTACTAGCTTGATTGG 57.276 34.615 1.04 0.00 0.00 3.16
795 864 6.953101 TGTACTAGCTTGATTGGTTATTGGA 58.047 36.000 1.04 0.00 0.00 3.53
818 887 7.181485 TGGATTCATCAGATATCTGCCAATCTA 59.819 37.037 28.21 24.68 43.46 1.98
880 951 6.751514 TGTCTTCAGAGTTCAGAGAGATAC 57.248 41.667 0.00 0.00 0.00 2.24
896 967 5.486332 AGAGATACCATTCCTTCCCCATTA 58.514 41.667 0.00 0.00 0.00 1.90
958 1033 8.478877 AGTGACCCAAGAGATTATTAACTGTAG 58.521 37.037 0.00 0.00 0.00 2.74
962 1037 8.487028 ACCCAAGAGATTATTAACTGTAGGAAG 58.513 37.037 0.00 0.00 0.00 3.46
976 1051 4.149598 TGTAGGAAGCAGTACAAGAGACA 58.850 43.478 0.00 0.00 0.00 3.41
990 1065 6.428385 ACAAGAGACAAAGAAACAACAGAG 57.572 37.500 0.00 0.00 0.00 3.35
1074 1149 2.908015 GTCTGGGGCCTAATGCGA 59.092 61.111 0.84 0.00 42.61 5.10
1163 1238 2.235402 TCCGGGAGATCACAGGTAAAAC 59.765 50.000 0.00 0.00 0.00 2.43
1164 1239 2.027561 CCGGGAGATCACAGGTAAAACA 60.028 50.000 0.00 0.00 0.00 2.83
1166 1241 4.261801 CGGGAGATCACAGGTAAAACAAT 58.738 43.478 0.00 0.00 0.00 2.71
1167 1242 4.332819 CGGGAGATCACAGGTAAAACAATC 59.667 45.833 0.00 0.00 0.00 2.67
1168 1243 5.501156 GGGAGATCACAGGTAAAACAATCT 58.499 41.667 0.00 0.00 0.00 2.40
1169 1244 5.586643 GGGAGATCACAGGTAAAACAATCTC 59.413 44.000 0.00 0.00 37.82 2.75
1170 1245 6.410540 GGAGATCACAGGTAAAACAATCTCT 58.589 40.000 8.78 0.00 38.34 3.10
1171 1246 6.881602 GGAGATCACAGGTAAAACAATCTCTT 59.118 38.462 8.78 0.00 38.34 2.85
1172 1247 8.041323 GGAGATCACAGGTAAAACAATCTCTTA 58.959 37.037 8.78 0.00 38.34 2.10
1197 1277 0.738975 CATCACAGGCTCATTGCTGG 59.261 55.000 0.00 0.00 42.39 4.85
1213 1293 4.032960 TGCTGGTACCAAATTCAGATGT 57.967 40.909 17.11 0.00 0.00 3.06
1218 1298 6.573664 TGGTACCAAATTCAGATGTTTCAG 57.426 37.500 13.60 0.00 0.00 3.02
1219 1299 5.048083 TGGTACCAAATTCAGATGTTTCAGC 60.048 40.000 13.60 0.00 0.00 4.26
1264 1344 2.171659 TCACCTGTCCAGCAAAGTTACA 59.828 45.455 0.00 0.00 0.00 2.41
1269 1349 4.498009 CCTGTCCAGCAAAGTTACAAGTTG 60.498 45.833 0.00 0.00 0.00 3.16
1294 1374 2.159626 ACGAAAACCACACAACGAGTTG 60.160 45.455 13.76 13.76 45.58 3.16
1324 1414 8.571461 AGAAATCAAAAGAGATGTTGATGCTA 57.429 30.769 0.00 0.00 42.30 3.49
1328 1418 7.312657 TCAAAAGAGATGTTGATGCTATCAC 57.687 36.000 0.00 0.00 39.39 3.06
1368 1458 1.269257 GGTTGCTTTCACTGGCTTGTC 60.269 52.381 0.00 0.00 0.00 3.18
1386 1476 6.261826 GGCTTGTCTCACAGAATTATGCTTAT 59.738 38.462 0.00 0.00 0.00 1.73
1389 1479 7.953158 TGTCTCACAGAATTATGCTTATAGC 57.047 36.000 0.00 0.00 42.82 2.97
1400 1490 7.588143 ATTATGCTTATAGCTTAGAAGTGCG 57.412 36.000 0.00 0.00 42.97 5.34
1401 1491 3.717707 TGCTTATAGCTTAGAAGTGCGG 58.282 45.455 0.00 0.00 42.97 5.69
1511 1601 8.734386 GCCCAATCTAGAAATAGTAAATGATGG 58.266 37.037 0.00 0.00 0.00 3.51
1642 1733 1.604915 GACTTGGGGAAGAGGCCTC 59.395 63.158 26.22 26.22 0.00 4.70
1729 1936 9.410556 CATACAGAAACATTGGTTTTCCTAAAG 57.589 33.333 0.00 0.00 46.84 1.85
1756 1963 9.595357 CGGTTCTATTTTACTTTCTCTGTTTTC 57.405 33.333 0.00 0.00 0.00 2.29
1856 2063 5.656416 TCTTTTGAGGACAGTTCCAAACAAT 59.344 36.000 0.00 0.00 45.72 2.71
1874 2081 6.814506 AACAATGAGGTTCAGAGAAGATTG 57.185 37.500 0.00 0.00 0.00 2.67
1878 2085 3.055530 TGAGGTTCAGAGAAGATTGGCTC 60.056 47.826 0.00 0.00 0.00 4.70
1892 2099 3.675348 TTGGCTCATCTGGGAAATGAT 57.325 42.857 0.00 0.00 32.91 2.45
1935 2142 6.898041 TCAGAGCATACAAATAACACAACAC 58.102 36.000 0.00 0.00 0.00 3.32
2303 2510 1.471676 GCACTGGAGATACTGGGTTCG 60.472 57.143 0.00 0.00 0.00 3.95
2915 3122 0.670546 ACATCGCCAGACCTTCAACG 60.671 55.000 0.00 0.00 0.00 4.10
3084 3291 0.332972 AGCCCAGGTCTCAAAATCCC 59.667 55.000 0.00 0.00 0.00 3.85
3173 3380 2.166050 CCACACTGATCTCTCACCTGAG 59.834 54.545 0.00 0.00 43.36 3.35
3231 3438 3.118261 TGAAGAAACCACACAAGAGAGCT 60.118 43.478 0.00 0.00 0.00 4.09
3388 3595 4.074259 TCATCAGGTTGAATTGAGTGGTG 58.926 43.478 0.00 0.00 0.00 4.17
3392 3599 3.006110 CAGGTTGAATTGAGTGGTGCATT 59.994 43.478 0.00 0.00 0.00 3.56
3575 3782 2.592308 CAGCCAGTAAGCTCCCCC 59.408 66.667 0.00 0.00 42.61 5.40
3580 3787 1.825641 GCCAGTAAGCTCCCCCAAAAA 60.826 52.381 0.00 0.00 0.00 1.94
3632 3839 9.852481 GTTGCGATATTATTTATGTTAACGTCA 57.148 29.630 2.93 0.00 0.00 4.35
3913 4124 7.675062 ACAATGTGAGCCCAATTTACATAAAA 58.325 30.769 0.00 0.00 32.18 1.52
3914 4125 8.320617 ACAATGTGAGCCCAATTTACATAAAAT 58.679 29.630 0.00 0.00 39.56 1.82
4081 4293 4.910458 TCTAAAGGTCTTTTGGGAGGAG 57.090 45.455 1.04 0.00 34.23 3.69
4088 4300 2.039084 GTCTTTTGGGAGGAGAAGAGCA 59.961 50.000 0.00 0.00 0.00 4.26
4099 4311 2.223852 GGAGAAGAGCATCCGGTTAGAC 60.224 54.545 0.00 0.00 33.66 2.59
4294 4506 7.454380 ACAGAGATCCAGGAGAGATATTTTAGG 59.546 40.741 0.00 0.00 0.00 2.69
4597 4809 2.203480 TGGTGCTTTGTGAGGGGC 60.203 61.111 0.00 0.00 0.00 5.80
4605 4817 2.880890 GCTTTGTGAGGGGCATATACAG 59.119 50.000 0.00 0.00 0.00 2.74
4658 4870 3.750639 ATAACACCATTTTACGTGGCG 57.249 42.857 0.00 0.00 40.49 5.69
4668 4880 2.747396 TTACGTGGCGGAATAACACT 57.253 45.000 0.00 0.00 33.13 3.55
4689 4901 1.151172 GCTGTTTTGTTTGGCCCGTG 61.151 55.000 0.00 0.00 0.00 4.94
4766 4978 1.230324 AACTGCAGCGGAAGAAACTC 58.770 50.000 15.27 0.00 0.00 3.01
4793 5005 0.874390 GCATGACAGCGGAAGTTTCA 59.126 50.000 0.00 0.00 0.00 2.69
5064 5285 1.689984 TGCCACTGCATGTTCTTCAA 58.310 45.000 0.00 0.00 44.23 2.69
5076 5297 6.089283 TGCATGTTCTTCAATTTGCGAAATAC 59.911 34.615 0.00 0.00 32.90 1.89
5079 5300 5.151389 GTTCTTCAATTTGCGAAATACCGT 58.849 37.500 0.00 0.00 0.00 4.83
5107 5328 1.139256 TCAGTTAAGTTGGACCACGCA 59.861 47.619 0.00 0.00 0.00 5.24
5115 5336 1.336755 GTTGGACCACGCATTGTTTCT 59.663 47.619 0.00 0.00 0.00 2.52
5124 5345 4.858692 CCACGCATTGTTTCTTTGGATAAG 59.141 41.667 0.00 0.00 0.00 1.73
5125 5346 5.335583 CCACGCATTGTTTCTTTGGATAAGA 60.336 40.000 0.00 0.00 0.00 2.10
5127 5348 6.640499 CACGCATTGTTTCTTTGGATAAGAAA 59.360 34.615 8.23 8.23 42.15 2.52
5128 5349 7.329226 CACGCATTGTTTCTTTGGATAAGAAAT 59.671 33.333 13.80 0.00 44.87 2.17
5129 5350 7.329226 ACGCATTGTTTCTTTGGATAAGAAATG 59.671 33.333 13.80 10.25 44.87 2.32
5130 5351 7.329226 CGCATTGTTTCTTTGGATAAGAAATGT 59.671 33.333 13.80 3.64 44.87 2.71
5131 5352 8.437742 GCATTGTTTCTTTGGATAAGAAATGTG 58.562 33.333 13.80 13.09 44.87 3.21
5132 5353 7.945033 TTGTTTCTTTGGATAAGAAATGTGC 57.055 32.000 13.80 4.46 44.87 4.57
5133 5354 6.148948 TGTTTCTTTGGATAAGAAATGTGCG 58.851 36.000 13.80 0.00 44.87 5.34
5137 5358 5.822519 TCTTTGGATAAGAAATGTGCGCTAT 59.177 36.000 9.73 0.00 0.00 2.97
5163 5384 4.853924 ATTTGCTGTTACTCAAAGTGGG 57.146 40.909 8.61 0.00 35.89 4.61
5174 5395 2.800544 CTCAAAGTGGGTGTCAACTACG 59.199 50.000 0.00 0.00 0.00 3.51
5176 5397 2.234300 AAGTGGGTGTCAACTACGTG 57.766 50.000 0.00 0.00 0.00 4.49
5178 5399 1.300311 TGGGTGTCAACTACGTGCG 60.300 57.895 0.00 0.00 0.00 5.34
5179 5400 1.300388 GGGTGTCAACTACGTGCGT 60.300 57.895 0.00 2.05 0.00 5.24
5180 5401 1.554042 GGGTGTCAACTACGTGCGTG 61.554 60.000 7.55 0.00 0.00 5.34
5181 5402 1.200839 GTGTCAACTACGTGCGTGC 59.799 57.895 7.55 0.00 0.00 5.34
5182 5403 2.297195 TGTCAACTACGTGCGTGCG 61.297 57.895 7.55 1.32 37.94 5.34
5184 5405 2.167684 CAACTACGTGCGTGCGTG 59.832 61.111 14.68 8.48 45.33 5.34
5200 5421 3.858989 TGCGTGCGTGTGTGTGTG 61.859 61.111 0.00 0.00 0.00 3.82
5201 5422 3.860125 GCGTGCGTGTGTGTGTGT 61.860 61.111 0.00 0.00 0.00 3.72
5202 5423 2.021243 CGTGCGTGTGTGTGTGTG 59.979 61.111 0.00 0.00 0.00 3.82
5216 5437 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
5278 5501 8.995220 TGTTATCGCAGTAAATTCAACTAAACT 58.005 29.630 0.00 0.00 0.00 2.66
5396 5621 6.942532 AACAAGCTTTTTGACAGTCATAGA 57.057 33.333 3.45 0.00 0.00 1.98
5402 5627 7.168219 AGCTTTTTGACAGTCATAGATACCAA 58.832 34.615 3.45 0.00 0.00 3.67
5406 5631 5.268118 TGACAGTCATAGATACCAAGCAG 57.732 43.478 0.00 0.00 0.00 4.24
5408 5633 3.452264 ACAGTCATAGATACCAAGCAGCA 59.548 43.478 0.00 0.00 0.00 4.41
5409 5634 4.080919 ACAGTCATAGATACCAAGCAGCAA 60.081 41.667 0.00 0.00 0.00 3.91
5410 5635 4.510711 CAGTCATAGATACCAAGCAGCAAG 59.489 45.833 0.00 0.00 0.00 4.01
5411 5636 3.249559 GTCATAGATACCAAGCAGCAAGC 59.750 47.826 0.00 0.00 46.19 4.01
5429 5654 3.902881 AGCATCTCACTTGGTCCTTAG 57.097 47.619 0.00 0.00 0.00 2.18
5433 5658 3.963428 TCTCACTTGGTCCTTAGCTTC 57.037 47.619 0.00 0.00 0.00 3.86
5490 5720 1.299541 CACACTGTTGGTCAGACACC 58.700 55.000 2.17 0.00 46.27 4.16
5512 5743 4.082571 CCGCCTGAAATCAGATGAAAAAGT 60.083 41.667 11.94 0.00 46.59 2.66
5549 5780 6.867662 AAAATCTTACAGGACTCACAGTTG 57.132 37.500 0.00 0.00 0.00 3.16
5555 5786 1.051812 AGGACTCACAGTTGGTCAGG 58.948 55.000 5.37 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 105 1.889105 CGGTGCGGATGGATGGAAG 60.889 63.158 0.00 0.00 0.00 3.46
120 135 2.826128 GGTGGAAAGGAAAGGAATGGAC 59.174 50.000 0.00 0.00 0.00 4.02
367 397 7.547019 AGAAAGAAAAGAAAGAAAAACAGCCAG 59.453 33.333 0.00 0.00 0.00 4.85
374 404 9.816354 CCCACATAGAAAGAAAAGAAAGAAAAA 57.184 29.630 0.00 0.00 0.00 1.94
375 405 9.196139 TCCCACATAGAAAGAAAAGAAAGAAAA 57.804 29.630 0.00 0.00 0.00 2.29
376 406 8.760980 TCCCACATAGAAAGAAAAGAAAGAAA 57.239 30.769 0.00 0.00 0.00 2.52
377 407 7.448469 CCTCCCACATAGAAAGAAAAGAAAGAA 59.552 37.037 0.00 0.00 0.00 2.52
378 408 6.942576 CCTCCCACATAGAAAGAAAAGAAAGA 59.057 38.462 0.00 0.00 0.00 2.52
379 409 6.942576 TCCTCCCACATAGAAAGAAAAGAAAG 59.057 38.462 0.00 0.00 0.00 2.62
380 410 6.848069 TCCTCCCACATAGAAAGAAAAGAAA 58.152 36.000 0.00 0.00 0.00 2.52
381 411 6.272324 TCTCCTCCCACATAGAAAGAAAAGAA 59.728 38.462 0.00 0.00 0.00 2.52
382 412 5.785423 TCTCCTCCCACATAGAAAGAAAAGA 59.215 40.000 0.00 0.00 0.00 2.52
383 413 5.877564 GTCTCCTCCCACATAGAAAGAAAAG 59.122 44.000 0.00 0.00 0.00 2.27
384 414 5.280521 GGTCTCCTCCCACATAGAAAGAAAA 60.281 44.000 0.00 0.00 0.00 2.29
385 415 4.225267 GGTCTCCTCCCACATAGAAAGAAA 59.775 45.833 0.00 0.00 0.00 2.52
386 416 3.775316 GGTCTCCTCCCACATAGAAAGAA 59.225 47.826 0.00 0.00 0.00 2.52
387 417 3.375699 GGTCTCCTCCCACATAGAAAGA 58.624 50.000 0.00 0.00 0.00 2.52
388 418 2.101582 CGGTCTCCTCCCACATAGAAAG 59.898 54.545 0.00 0.00 0.00 2.62
408 453 2.440430 TCCGGCCTCTTCTCTCCG 60.440 66.667 0.00 0.00 41.41 4.63
427 472 2.438614 GCCGCTTTCCCCTTCTCC 60.439 66.667 0.00 0.00 0.00 3.71
476 521 3.116300 CCTACCTGACGAATGAATCACG 58.884 50.000 0.00 0.00 0.00 4.35
555 612 4.261994 CGAATCCCAACCAACAGAAAACAT 60.262 41.667 0.00 0.00 0.00 2.71
570 627 3.003897 CCAAAGAACGAAAACGAATCCCA 59.996 43.478 0.00 0.00 0.00 4.37
583 640 3.297830 GGGAAATGAACCCAAAGAACG 57.702 47.619 0.00 0.00 46.05 3.95
643 700 4.388485 TCTTGTTGCAAGCATGAGAAGTA 58.612 39.130 0.00 0.00 0.00 2.24
644 701 3.216800 TCTTGTTGCAAGCATGAGAAGT 58.783 40.909 0.00 0.00 0.00 3.01
645 702 3.909776 TCTTGTTGCAAGCATGAGAAG 57.090 42.857 0.00 0.00 0.00 2.85
779 848 8.229253 TCTGATGAATCCAATAACCAATCAAG 57.771 34.615 0.00 0.00 0.00 3.02
787 856 7.609146 TGGCAGATATCTGATGAATCCAATAAC 59.391 37.037 32.38 11.71 46.59 1.89
795 864 7.182387 AGGTAGATTGGCAGATATCTGATGAAT 59.818 37.037 32.38 23.84 46.59 2.57
818 887 2.122167 TTCGGCCGCAAAACAAGGT 61.122 52.632 23.51 0.00 0.00 3.50
880 951 5.453198 CGGATTTTTAATGGGGAAGGAATGG 60.453 44.000 0.00 0.00 0.00 3.16
896 967 2.890945 ACAAGTTAGCAGCCGGATTTTT 59.109 40.909 5.05 0.00 0.00 1.94
958 1033 4.632153 TCTTTGTCTCTTGTACTGCTTCC 58.368 43.478 0.00 0.00 0.00 3.46
962 1037 5.734855 TGTTTCTTTGTCTCTTGTACTGC 57.265 39.130 0.00 0.00 0.00 4.40
990 1065 1.200020 CGCTTCCCCATTTCAGAACAC 59.800 52.381 0.00 0.00 0.00 3.32
1074 1149 1.157870 CGCGGCGGAAATAGACCATT 61.158 55.000 15.84 0.00 0.00 3.16
1163 1238 7.215789 AGCCTGTGATGAGTAATAAGAGATTG 58.784 38.462 0.00 0.00 0.00 2.67
1164 1239 7.070447 TGAGCCTGTGATGAGTAATAAGAGATT 59.930 37.037 0.00 0.00 0.00 2.40
1166 1241 5.893824 TGAGCCTGTGATGAGTAATAAGAGA 59.106 40.000 0.00 0.00 0.00 3.10
1167 1242 6.154203 TGAGCCTGTGATGAGTAATAAGAG 57.846 41.667 0.00 0.00 0.00 2.85
1168 1243 6.737720 ATGAGCCTGTGATGAGTAATAAGA 57.262 37.500 0.00 0.00 0.00 2.10
1169 1244 6.293298 GCAATGAGCCTGTGATGAGTAATAAG 60.293 42.308 0.00 0.00 37.23 1.73
1170 1245 5.528690 GCAATGAGCCTGTGATGAGTAATAA 59.471 40.000 0.00 0.00 37.23 1.40
1171 1246 5.059161 GCAATGAGCCTGTGATGAGTAATA 58.941 41.667 0.00 0.00 37.23 0.98
1172 1247 3.881688 GCAATGAGCCTGTGATGAGTAAT 59.118 43.478 0.00 0.00 37.23 1.89
1197 1277 6.259550 AGCTGAAACATCTGAATTTGGTAC 57.740 37.500 0.00 0.00 0.00 3.34
1213 1293 6.339730 TCTGAAATTCAAAAGCAAGCTGAAA 58.660 32.000 0.00 0.00 33.08 2.69
1218 1298 4.689345 AGCATCTGAAATTCAAAAGCAAGC 59.311 37.500 13.12 4.76 0.00 4.01
1219 1299 5.694910 ACAGCATCTGAAATTCAAAAGCAAG 59.305 36.000 13.12 8.84 35.18 4.01
1255 1335 9.161684 GGTTTTCGTATACAACTTGTAACTTTG 57.838 33.333 5.73 0.00 36.31 2.77
1264 1344 6.488817 GTTGTGTGGTTTTCGTATACAACTT 58.511 36.000 3.32 0.00 41.67 2.66
1269 1349 4.445385 ACTCGTTGTGTGGTTTTCGTATAC 59.555 41.667 0.00 0.00 0.00 1.47
1296 1376 9.798994 GCATCAACATCTCTTTTGATTTCTTAT 57.201 29.630 0.00 0.00 39.86 1.73
1297 1377 9.017509 AGCATCAACATCTCTTTTGATTTCTTA 57.982 29.630 0.00 0.00 39.86 2.10
1298 1378 7.893658 AGCATCAACATCTCTTTTGATTTCTT 58.106 30.769 0.00 0.00 39.86 2.52
1316 1406 5.418676 TGATCAACGAAGTGATAGCATCAA 58.581 37.500 0.00 0.00 45.00 2.57
1321 1411 5.453587 GCAAAATGATCAACGAAGTGATAGC 59.546 40.000 0.00 0.00 45.00 2.97
1324 1414 5.633830 AGCAAAATGATCAACGAAGTGAT 57.366 34.783 0.00 0.00 45.00 3.06
1328 1418 3.120199 ACCGAGCAAAATGATCAACGAAG 60.120 43.478 0.00 0.00 31.10 3.79
1368 1458 9.920133 TCTAAGCTATAAGCATAATTCTGTGAG 57.080 33.333 1.22 0.00 45.56 3.51
1386 1476 0.175760 CAGGCCGCACTTCTAAGCTA 59.824 55.000 0.00 0.00 0.00 3.32
1389 1479 0.320771 ACACAGGCCGCACTTCTAAG 60.321 55.000 0.00 0.00 0.00 2.18
1511 1601 5.877012 TCCTTTGCTGAACTATCTGAACATC 59.123 40.000 0.00 0.00 0.00 3.06
1517 1608 5.675575 GCACATTCCTTTGCTGAACTATCTG 60.676 44.000 0.00 0.00 35.74 2.90
1611 1702 0.685097 CCAAGTCCCTTCCGTCTGAA 59.315 55.000 0.00 0.00 0.00 3.02
1642 1733 7.826690 TCTTTTTCTATTTCCTCAAAATCCCG 58.173 34.615 0.00 0.00 38.53 5.14
1729 1936 6.723131 ACAGAGAAAGTAAAATAGAACCGC 57.277 37.500 0.00 0.00 0.00 5.68
1756 1963 2.678336 GGGCCGTTTTCTATGTTCTGAG 59.322 50.000 0.00 0.00 0.00 3.35
1814 2021 0.098728 GATTCACACGCCCCAATTCG 59.901 55.000 0.00 0.00 0.00 3.34
1856 2063 2.909006 AGCCAATCTTCTCTGAACCTCA 59.091 45.455 0.00 0.00 0.00 3.86
1874 2081 3.505480 AGATCATTTCCCAGATGAGCC 57.495 47.619 0.00 0.00 39.96 4.70
1878 2085 7.677892 TCAAGAGATAGATCATTTCCCAGATG 58.322 38.462 0.00 0.00 0.00 2.90
1935 2142 3.185594 TCCGTGCTGTCATTTAAAGTTCG 59.814 43.478 0.00 0.00 0.00 3.95
3173 3380 1.346068 ACAAGGCAAGAGTCTGTCTCC 59.654 52.381 0.00 0.00 43.71 3.71
3231 3438 1.899142 TGAGTCGTCCCATGATTGACA 59.101 47.619 0.00 0.00 33.54 3.58
3467 3674 7.887996 TTTGCCAATTTCTTCAATACATGTC 57.112 32.000 0.00 0.00 0.00 3.06
3512 3719 3.423749 TGAGATGGATTGTGTGTTGCAT 58.576 40.909 0.00 0.00 0.00 3.96
3661 3868 3.068732 GGTTCTTTTCCTTGCTCTGCTTT 59.931 43.478 0.00 0.00 0.00 3.51
3914 4125 9.816787 GGGGAAAAGGGTTACATATATTTATGA 57.183 33.333 9.80 0.00 37.94 2.15
4081 4293 4.857509 ATAGTCTAACCGGATGCTCTTC 57.142 45.455 9.46 0.00 0.00 2.87
4088 4300 8.488308 ACCAACTTTATATAGTCTAACCGGAT 57.512 34.615 9.46 0.00 0.00 4.18
4099 4311 8.738645 AGAGCTCCAAAACCAACTTTATATAG 57.261 34.615 10.93 0.00 0.00 1.31
4294 4506 2.156343 ACGACAACCAAGAAGAGAGC 57.844 50.000 0.00 0.00 0.00 4.09
4381 4593 4.768130 ACTATGTCGGAGGTAATCATCG 57.232 45.455 0.00 0.00 0.00 3.84
4384 4596 5.188163 TGGAAAACTATGTCGGAGGTAATCA 59.812 40.000 0.00 0.00 0.00 2.57
4668 4880 1.524482 GGGCCAAACAAAACAGCCA 59.476 52.632 4.39 0.00 45.72 4.75
4689 4901 5.399858 TCACACTCTCATTACTTTACTCGC 58.600 41.667 0.00 0.00 0.00 5.03
4766 4978 1.158484 CCGCTGTCATGCATCAGAGG 61.158 60.000 19.16 19.16 42.90 3.69
4793 5005 1.531602 GCTGGGAGGTTTGCAGGTT 60.532 57.895 0.00 0.00 0.00 3.50
4958 5171 4.201773 ACATGTACACACAAACACAACGAG 60.202 41.667 0.00 0.00 38.42 4.18
4960 5173 3.783418 CACATGTACACACAAACACAACG 59.217 43.478 0.00 0.00 38.42 4.10
4961 5174 4.728534 ACACATGTACACACAAACACAAC 58.271 39.130 0.00 0.00 38.42 3.32
5048 5269 3.120616 CGCAAATTGAAGAACATGCAGTG 59.879 43.478 0.00 0.00 33.55 3.66
5057 5278 5.365403 ACGGTATTTCGCAAATTGAAGAA 57.635 34.783 0.00 0.00 32.38 2.52
5064 5285 4.759516 AAGACAACGGTATTTCGCAAAT 57.240 36.364 0.00 0.00 34.90 2.32
5076 5297 5.065474 TCCAACTTAACTGAAAAGACAACGG 59.935 40.000 0.00 0.00 0.00 4.44
5079 5300 5.946972 TGGTCCAACTTAACTGAAAAGACAA 59.053 36.000 0.00 0.00 0.00 3.18
5107 5328 7.329226 CGCACATTTCTTATCCAAAGAAACAAT 59.671 33.333 13.47 2.31 45.58 2.71
5115 5336 5.822519 AGATAGCGCACATTTCTTATCCAAA 59.177 36.000 11.47 0.00 0.00 3.28
5124 5345 4.672413 GCAAATACAGATAGCGCACATTTC 59.328 41.667 11.47 0.00 0.00 2.17
5125 5346 4.336433 AGCAAATACAGATAGCGCACATTT 59.664 37.500 11.47 1.27 0.00 2.32
5127 5348 3.249320 CAGCAAATACAGATAGCGCACAT 59.751 43.478 11.47 1.15 0.00 3.21
5128 5349 2.609002 CAGCAAATACAGATAGCGCACA 59.391 45.455 11.47 0.00 0.00 4.57
5129 5350 2.609459 ACAGCAAATACAGATAGCGCAC 59.391 45.455 11.47 0.00 0.00 5.34
5130 5351 2.905075 ACAGCAAATACAGATAGCGCA 58.095 42.857 11.47 0.00 0.00 6.09
5131 5352 3.951979 AACAGCAAATACAGATAGCGC 57.048 42.857 0.00 0.00 0.00 5.92
5132 5353 5.748630 TGAGTAACAGCAAATACAGATAGCG 59.251 40.000 0.00 0.00 0.00 4.26
5133 5354 7.539712 TTGAGTAACAGCAAATACAGATAGC 57.460 36.000 0.00 0.00 0.00 2.97
5137 5358 6.204688 CCACTTTGAGTAACAGCAAATACAGA 59.795 38.462 0.00 0.00 33.94 3.41
5163 5384 1.200839 GCACGCACGTAGTTGACAC 59.799 57.895 0.00 0.00 41.61 3.67
5181 5402 4.918060 CACACACACGCACGCACG 62.918 66.667 0.00 0.00 39.50 5.34
5182 5403 3.860125 ACACACACACGCACGCAC 61.860 61.111 0.00 0.00 0.00 5.34
5183 5404 3.858989 CACACACACACGCACGCA 61.859 61.111 0.00 0.00 0.00 5.24
5184 5405 3.860125 ACACACACACACGCACGC 61.860 61.111 0.00 0.00 0.00 5.34
5186 5407 1.225991 CACACACACACACACGCAC 60.226 57.895 0.00 0.00 0.00 5.34
5187 5408 1.669437 ACACACACACACACACGCA 60.669 52.632 0.00 0.00 0.00 5.24
5188 5409 1.225991 CACACACACACACACACGC 60.226 57.895 0.00 0.00 0.00 5.34
5189 5410 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
5190 5411 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5191 5412 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5192 5413 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5193 5414 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5194 5415 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5195 5416 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5196 5417 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5197 5418 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5200 5421 1.152510 TCACACACACACACACACAC 58.847 50.000 0.00 0.00 0.00 3.82
5201 5422 1.803555 CTTCACACACACACACACACA 59.196 47.619 0.00 0.00 0.00 3.72
5202 5423 1.804151 ACTTCACACACACACACACAC 59.196 47.619 0.00 0.00 0.00 3.82
5216 5437 2.780065 TCAAATGCACTGCACTTCAC 57.220 45.000 5.67 0.00 43.04 3.18
5278 5501 2.613026 TGACTCGCTGAAAACCTCAA 57.387 45.000 0.00 0.00 32.17 3.02
5396 5621 2.295885 GAGATGCTTGCTGCTTGGTAT 58.704 47.619 0.00 0.00 43.37 2.73
5402 5627 1.166129 CAAGTGAGATGCTTGCTGCT 58.834 50.000 0.00 0.00 43.37 4.24
5406 5631 0.807496 GGACCAAGTGAGATGCTTGC 59.193 55.000 0.00 0.00 41.27 4.01
5408 5633 3.620966 GCTAAGGACCAAGTGAGATGCTT 60.621 47.826 0.00 0.00 0.00 3.91
5409 5634 2.093235 GCTAAGGACCAAGTGAGATGCT 60.093 50.000 0.00 0.00 0.00 3.79
5410 5635 2.093235 AGCTAAGGACCAAGTGAGATGC 60.093 50.000 0.00 0.00 0.00 3.91
5411 5636 3.902881 AGCTAAGGACCAAGTGAGATG 57.097 47.619 0.00 0.00 0.00 2.90
5412 5637 3.840666 TGAAGCTAAGGACCAAGTGAGAT 59.159 43.478 0.00 0.00 0.00 2.75
5413 5638 3.006967 GTGAAGCTAAGGACCAAGTGAGA 59.993 47.826 0.00 0.00 0.00 3.27
5414 5639 3.330267 GTGAAGCTAAGGACCAAGTGAG 58.670 50.000 0.00 0.00 0.00 3.51
5415 5640 2.038557 GGTGAAGCTAAGGACCAAGTGA 59.961 50.000 0.00 0.00 0.00 3.41
5429 5654 1.596727 GCTCATCGATCTTGGTGAAGC 59.403 52.381 0.00 0.00 0.00 3.86
5433 5658 2.897436 TCTTGCTCATCGATCTTGGTG 58.103 47.619 0.00 0.00 0.00 4.17
5490 5720 5.051891 ACTTTTTCATCTGATTTCAGGCG 57.948 39.130 7.68 0.20 43.91 5.52
5491 5721 6.017400 TGACTTTTTCATCTGATTTCAGGC 57.983 37.500 7.68 0.00 43.91 4.85
5525 5756 6.263168 CCAACTGTGAGTCCTGTAAGATTTTT 59.737 38.462 0.00 0.00 34.07 1.94
5528 5759 4.348168 ACCAACTGTGAGTCCTGTAAGATT 59.652 41.667 0.00 0.00 34.07 2.40


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

AutoCloner maintained by Alex Coulton.