Multiple sequence alignment - TraesCS5B01G081600

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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 TraesCS5B01G081600 chr5B 100.000 4445 0 0 1 4445 102255912 102251468 0.000000e+00 8209
1 TraesCS5B01G081600 chr5B 98.649 74 1 0 11 84 454645785 454645712 1.000000e-26 132
2 TraesCS5B01G081600 chr5A 93.457 4463 180 49 4 4445 90222718 90218347 0.000000e+00 6521
3 TraesCS5B01G081600 chr5A 98.649 74 1 0 11 84 672751164 672751091 1.000000e-26 132
4 TraesCS5B01G081600 chr5D 93.840 4042 174 33 4 4023 95294846 95290858 0.000000e+00 6015
5 TraesCS5B01G081600 chr5D 82.932 457 26 15 3992 4445 95290853 95290446 9.090000e-97 364
6 TraesCS5B01G081600 chr7A 100.000 74 0 0 11 84 656722928 656722855 2.160000e-28 137
7 TraesCS5B01G081600 chr7A 89.691 97 10 0 113 209 656722857 656722761 1.680000e-24 124
8 TraesCS5B01G081600 chr7B 94.805 77 4 0 8 84 633826025 633826101 2.170000e-23 121
9 TraesCS5B01G081600 chr2A 93.506 77 5 0 8 84 620986818 620986894 1.010000e-21 115


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 TraesCS5B01G081600 chr5B 102251468 102255912 4444 True 8209.0 8209 100.000 1 4445 1 chr5B.!!$R1 4444
1 TraesCS5B01G081600 chr5A 90218347 90222718 4371 True 6521.0 6521 93.457 4 4445 1 chr5A.!!$R1 4441
2 TraesCS5B01G081600 chr5D 95290446 95294846 4400 True 3189.5 6015 88.386 4 4445 2 chr5D.!!$R1 4441

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
633 643 0.685458 ATGCCCCCTCATTGCAAGTC 60.685 55.0 4.94 0.00 38.69 3.01 F
637 647 0.918983 CCCCTCATTGCAAGTCCCTA 59.081 55.0 4.94 0.00 0.00 3.53 F
1653 1672 0.740149 TGTGTTGCTCAAGCTGTTGG 59.260 50.0 3.32 0.00 42.66 3.77 F
1846 1865 0.316196 GCGACGAGGCATGCAATAAC 60.316 55.0 21.36 6.68 0.00 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 1565 0.179020 CCAAGTGTGTCCTTCCTGCA 60.179 55.000 0.0 0.0 0.00 4.41 R
1702 1721 0.545309 CCTCTCCTTCCTGGACACCA 60.545 60.000 0.0 0.0 40.56 4.17 R
2516 2538 0.784778 GAAACCAGCGAGTTCTGACG 59.215 55.000 0.0 0.0 36.19 4.35 R
3714 3743 1.373497 GGCGGTCCAGATAGCATCG 60.373 63.158 0.0 0.0 0.00 3.84 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
196 198 7.025963 GGCAGAATCTTCAGACTTGTTTATTG 58.974 38.462 0.00 0.00 0.00 1.90
197 199 6.525976 GCAGAATCTTCAGACTTGTTTATTGC 59.474 38.462 0.00 0.00 0.00 3.56
204 206 7.500892 TCTTCAGACTTGTTTATTGCTTTACCA 59.499 33.333 0.00 0.00 0.00 3.25
209 211 5.048013 ACTTGTTTATTGCTTTACCAGGAGC 60.048 40.000 0.00 0.00 39.33 4.70
210 212 3.438781 TGTTTATTGCTTTACCAGGAGCG 59.561 43.478 0.00 0.00 41.75 5.03
291 296 9.624373 ATTCAAATCAATTCTATAGCTGTGAGT 57.376 29.630 0.00 0.00 0.00 3.41
292 297 8.429493 TCAAATCAATTCTATAGCTGTGAGTG 57.571 34.615 0.00 1.94 0.00 3.51
306 311 3.932580 GAGTGATGGTGCGCCGACA 62.933 63.158 12.58 11.36 37.67 4.35
308 313 3.047280 TGATGGTGCGCCGACAAC 61.047 61.111 12.58 0.26 37.67 3.32
359 364 7.039504 AGCATACATGTCTTTCCACTTTTGAAT 60.040 33.333 0.00 0.00 0.00 2.57
509 519 5.345741 CCATGTAGCCGTTCAAGAAATTTTG 59.654 40.000 0.00 0.00 0.00 2.44
520 530 8.629986 CGTTCAAGAAATTTTGCTAGTGTTATG 58.370 33.333 0.00 0.00 0.00 1.90
557 567 3.512329 TGCCTTCTATTGTCACGGTAAGA 59.488 43.478 0.00 0.00 0.00 2.10
560 570 5.475719 CCTTCTATTGTCACGGTAAGAACA 58.524 41.667 0.00 0.00 0.00 3.18
572 582 4.153475 ACGGTAAGAACATTCATGGTTTCG 59.847 41.667 0.00 0.00 0.00 3.46
584 594 3.380004 TCATGGTTTCGTTGTCTGCTTTT 59.620 39.130 0.00 0.00 0.00 2.27
589 599 4.412207 GTTTCGTTGTCTGCTTTTGTTCT 58.588 39.130 0.00 0.00 0.00 3.01
603 613 6.183360 TGCTTTTGTTCTTGCATCTTGTTCTA 60.183 34.615 0.00 0.00 0.00 2.10
633 643 0.685458 ATGCCCCCTCATTGCAAGTC 60.685 55.000 4.94 0.00 38.69 3.01
636 646 1.693640 CCCCTCATTGCAAGTCCCT 59.306 57.895 4.94 0.00 0.00 4.20
637 647 0.918983 CCCCTCATTGCAAGTCCCTA 59.081 55.000 4.94 0.00 0.00 3.53
638 648 1.496429 CCCCTCATTGCAAGTCCCTAT 59.504 52.381 4.94 0.00 0.00 2.57
639 649 2.579873 CCCTCATTGCAAGTCCCTATG 58.420 52.381 4.94 0.00 0.00 2.23
640 650 2.092212 CCCTCATTGCAAGTCCCTATGT 60.092 50.000 4.94 0.00 0.00 2.29
641 651 3.136443 CCCTCATTGCAAGTCCCTATGTA 59.864 47.826 4.94 0.00 0.00 2.29
642 652 4.384056 CCTCATTGCAAGTCCCTATGTAG 58.616 47.826 4.94 0.00 0.00 2.74
729 741 5.272167 TCCGTTTTACTTTTACTGCATCG 57.728 39.130 0.00 0.00 0.00 3.84
731 743 5.236911 TCCGTTTTACTTTTACTGCATCGTT 59.763 36.000 0.00 0.00 0.00 3.85
732 744 5.338559 CCGTTTTACTTTTACTGCATCGTTG 59.661 40.000 0.00 0.00 0.00 4.10
740 752 6.857964 ACTTTTACTGCATCGTTGAAGATTTG 59.142 34.615 8.52 0.00 32.21 2.32
741 753 6.552859 TTTACTGCATCGTTGAAGATTTGA 57.447 33.333 8.52 0.00 32.21 2.69
745 757 5.239306 ACTGCATCGTTGAAGATTTGAAGAA 59.761 36.000 8.52 0.00 32.21 2.52
746 758 5.692814 TGCATCGTTGAAGATTTGAAGAAG 58.307 37.500 0.00 0.00 0.00 2.85
749 761 5.095691 TCGTTGAAGATTTGAAGAAGCAC 57.904 39.130 0.00 0.00 0.00 4.40
761 773 6.647334 TTGAAGAAGCACAAAATGGATGTA 57.353 33.333 0.00 0.00 0.00 2.29
763 775 7.230849 TGAAGAAGCACAAAATGGATGTATT 57.769 32.000 0.00 0.00 0.00 1.89
778 790 7.953005 TGGATGTATTTTGGCATCTTCTTTA 57.047 32.000 0.00 0.00 40.76 1.85
823 839 6.573664 AGTTGTTTTTCATACAGCTGCATA 57.426 33.333 15.27 0.00 36.01 3.14
832 848 4.452114 TCATACAGCTGCATAAATTAGGCG 59.548 41.667 15.27 1.80 38.52 5.52
838 854 3.181491 GCTGCATAAATTAGGCGACCAAA 60.181 43.478 5.17 0.00 38.52 3.28
866 882 6.833933 TCAGATGTACTACAAGCAATCTAGGA 59.166 38.462 0.00 0.00 0.00 2.94
888 904 3.788227 AGGCACACAAGTAATCTCCAA 57.212 42.857 0.00 0.00 0.00 3.53
902 920 7.283329 AGTAATCTCCAAACTGAAGAACAAGT 58.717 34.615 0.00 0.00 0.00 3.16
969 987 4.003648 GTCTACATTTTGGTCAGACCCTG 58.996 47.826 17.59 11.28 37.50 4.45
977 995 2.123589 TGGTCAGACCCTGTGAAGAAA 58.876 47.619 17.59 0.00 37.50 2.52
1098 1116 1.547372 AGAAACACGCCTACCATACGT 59.453 47.619 0.00 0.00 41.45 3.57
1146 1164 5.152623 CTTCTGGAGAAGTTGTCCATGTA 57.847 43.478 21.17 8.24 43.33 2.29
1188 1206 2.611292 CAGGAAATCTGATGGCTCGAAC 59.389 50.000 0.00 0.00 46.18 3.95
1251 1269 6.396209 GAGCTAGACTCGGAAAACGGAAGT 62.396 50.000 0.00 0.00 44.45 3.01
1445 1464 1.732259 CAGTGTCAACGGAGGTATTGC 59.268 52.381 0.00 0.00 0.00 3.56
1469 1488 9.017509 TGCATTTTCTCTAGACAGATTTCATTT 57.982 29.630 0.00 0.00 0.00 2.32
1543 1562 2.189594 CAGACTTTCCTGCCATGTCA 57.810 50.000 0.00 0.00 0.00 3.58
1546 1565 2.107204 AGACTTTCCTGCCATGTCAAGT 59.893 45.455 0.00 0.00 0.00 3.16
1564 1583 0.947244 GTGCAGGAAGGACACACTTG 59.053 55.000 0.00 0.00 38.62 3.16
1628 1647 4.206609 AGAAGTTCGAGAAGTTTTTCGACG 59.793 41.667 11.50 0.00 44.58 5.12
1653 1672 0.740149 TGTGTTGCTCAAGCTGTTGG 59.260 50.000 3.32 0.00 42.66 3.77
1689 1708 6.765036 ACAAGAGATGCAAACTGTATGGATAG 59.235 38.462 0.00 0.00 0.00 2.08
1702 1721 6.271857 ACTGTATGGATAGATCAAGCCAATCT 59.728 38.462 0.00 0.00 37.29 2.40
1708 1727 2.996631 AGATCAAGCCAATCTGGTGTC 58.003 47.619 0.00 0.00 40.46 3.67
1732 1751 2.614520 GGAAGGAGAGGCGCTTAAAATC 59.385 50.000 7.64 0.00 0.00 2.17
1746 1765 4.662145 CTTAAAATCGCAAGCTCGGAAAT 58.338 39.130 0.00 0.00 37.18 2.17
1750 1769 1.865865 TCGCAAGCTCGGAAATATCC 58.134 50.000 0.00 0.00 38.99 2.59
1765 1784 2.073252 TATCCGATGTCTCTGGTGCT 57.927 50.000 0.00 0.00 0.00 4.40
1791 1810 4.112634 GTGGAGGAAGCAAAGACAAAAAC 58.887 43.478 0.00 0.00 0.00 2.43
1795 1814 5.254339 AGGAAGCAAAGACAAAAACTGAG 57.746 39.130 0.00 0.00 0.00 3.35
1823 1842 5.949233 AAAAATGCTGACAAAACTTCGAC 57.051 34.783 0.00 0.00 0.00 4.20
1828 1847 1.192534 CTGACAAAACTTCGACGAGGC 59.807 52.381 6.92 0.00 0.00 4.70
1846 1865 0.316196 GCGACGAGGCATGCAATAAC 60.316 55.000 21.36 6.68 0.00 1.89
1874 1893 8.190784 TGAAGTCTTTCAAAGATGGAGAAAAAC 58.809 33.333 2.39 0.00 40.26 2.43
1981 2000 0.881796 GGGGCCAAAAGAAGAAGTCG 59.118 55.000 4.39 0.00 0.00 4.18
2005 2024 2.435805 AGTTGTCAGGCTCTCTTTCACA 59.564 45.455 0.00 0.00 0.00 3.58
2065 2084 3.748568 GTGAGTTTTCCTCTGATGTGTCC 59.251 47.826 0.00 0.00 41.11 4.02
2070 2089 1.763968 TCCTCTGATGTGTCCTACCG 58.236 55.000 0.00 0.00 0.00 4.02
2077 2096 5.416083 TCTGATGTGTCCTACCGTATTTTG 58.584 41.667 0.00 0.00 0.00 2.44
2273 2295 4.261614 GCTTTTTCAGGTAAGAGTTGGTGG 60.262 45.833 0.00 0.00 0.00 4.61
2397 2419 5.148502 AGTTCTCCATATACTCCAATCGGT 58.851 41.667 0.00 0.00 0.00 4.69
2488 2510 2.808543 CCAAGTGAGAAAGTTCCTTCGG 59.191 50.000 0.00 0.00 0.00 4.30
2536 2558 1.603172 CGTCAGAACTCGCTGGTTTCT 60.603 52.381 0.00 0.00 36.55 2.52
2547 2569 3.813166 TCGCTGGTTTCTCCTAAACTTTG 59.187 43.478 0.00 0.00 37.07 2.77
2601 2623 4.513692 GCGTATGTATTTTGCACCCAGATA 59.486 41.667 0.00 0.00 0.00 1.98
2662 2684 1.685180 GGGAAGGGATTAACCTGGTGC 60.685 57.143 0.00 0.00 40.87 5.01
2682 2704 5.504994 GGTGCTGTATTTCAAACTGAACGAA 60.505 40.000 0.00 0.00 35.89 3.85
2859 2881 2.163211 CAGAGACTTGTGAGCGATGAGA 59.837 50.000 0.00 0.00 0.00 3.27
2996 3018 5.824904 AACTTGTGCAGGCTTATAATGAG 57.175 39.130 0.00 0.00 0.00 2.90
3238 3263 4.480115 TGGTGTAATCGATCTGGGTCTAT 58.520 43.478 0.00 0.00 0.00 1.98
3265 3290 3.053395 ACAGGTAGCATGATGACCCATTT 60.053 43.478 0.00 0.00 33.40 2.32
3480 3509 5.298527 GGTGTGCTAAGTTAAACCTGAAGTT 59.701 40.000 0.00 0.00 41.81 2.66
3540 3569 3.008485 AGTTCTGACCCTTGAGGATTGAC 59.992 47.826 0.00 0.00 39.89 3.18
3569 3598 2.163010 CCTTTGCTATGTGTGCTTGGAG 59.837 50.000 0.00 0.00 0.00 3.86
3714 3743 1.084370 CCCGCGAATCAGGAGTTGAC 61.084 60.000 8.23 0.00 38.99 3.18
3729 3758 2.101582 AGTTGACGATGCTATCTGGACC 59.898 50.000 0.00 0.00 0.00 4.46
3874 3905 4.036852 TGTTCTGGACGTAGCTATCATCAG 59.963 45.833 0.00 3.95 0.00 2.90
4082 4147 0.395586 GCACCAGAATATGCCCCACA 60.396 55.000 0.00 0.00 35.73 4.17
4101 4166 2.838813 ACAAGACCTAGTAAAGCCCTCC 59.161 50.000 0.00 0.00 0.00 4.30
4105 4170 1.344189 ACCTAGTAAAGCCCTCCCCTC 60.344 57.143 0.00 0.00 0.00 4.30
4106 4171 1.425694 CTAGTAAAGCCCTCCCCTCC 58.574 60.000 0.00 0.00 0.00 4.30
4107 4172 0.030399 TAGTAAAGCCCTCCCCTCCC 60.030 60.000 0.00 0.00 0.00 4.30
4108 4173 2.043941 TAAAGCCCTCCCCTCCCC 59.956 66.667 0.00 0.00 0.00 4.81
4109 4174 3.670620 TAAAGCCCTCCCCTCCCCC 62.671 68.421 0.00 0.00 0.00 5.40
4118 4183 3.672503 CCCTCCCCCAACCCCAAG 61.673 72.222 0.00 0.00 0.00 3.61
4119 4184 3.672503 CCTCCCCCAACCCCAAGG 61.673 72.222 0.00 0.00 40.04 3.61
4120 4185 4.382541 CTCCCCCAACCCCAAGGC 62.383 72.222 0.00 0.00 36.11 4.35
4124 4189 4.010018 CCCAACCCCAAGGCCCAT 62.010 66.667 0.00 0.00 36.11 4.00
4125 4190 2.684655 CCAACCCCAAGGCCCATG 60.685 66.667 0.00 0.00 36.11 3.66
4126 4191 2.444696 CAACCCCAAGGCCCATGA 59.555 61.111 0.00 0.00 36.11 3.07
4127 4192 1.002017 CAACCCCAAGGCCCATGAT 59.998 57.895 0.00 0.00 36.11 2.45
4128 4193 0.261402 CAACCCCAAGGCCCATGATA 59.739 55.000 0.00 0.00 36.11 2.15
4152 4222 1.214305 ATGCCTTCTACCCAGCCCAA 61.214 55.000 0.00 0.00 0.00 4.12
4185 4255 1.226407 GAAGAATTCGGCTTGCCGC 60.226 57.895 26.94 14.16 34.17 6.53
4210 4280 1.251527 ACACGCCGAACCAGAGATCT 61.252 55.000 0.00 0.00 0.00 2.75
4212 4282 1.025812 ACGCCGAACCAGAGATCTAG 58.974 55.000 0.00 0.00 0.00 2.43
4213 4283 0.312416 CGCCGAACCAGAGATCTAGG 59.688 60.000 11.24 11.24 0.00 3.02
4214 4284 1.693627 GCCGAACCAGAGATCTAGGA 58.306 55.000 18.08 0.00 0.00 2.94
4215 4285 1.611491 GCCGAACCAGAGATCTAGGAG 59.389 57.143 18.08 9.82 0.00 3.69
4234 4304 1.275573 AGGACTCTTCAACCGCCTTAC 59.724 52.381 0.00 0.00 0.00 2.34
4236 4306 0.037605 ACTCTTCAACCGCCTTACCG 60.038 55.000 0.00 0.00 0.00 4.02
4256 4326 3.593096 CGGACTAGGAAACTTGTAACCC 58.407 50.000 0.00 0.00 46.54 4.11
4257 4327 3.260128 CGGACTAGGAAACTTGTAACCCT 59.740 47.826 0.00 0.00 46.54 4.34
4258 4328 4.463891 CGGACTAGGAAACTTGTAACCCTA 59.536 45.833 0.00 0.00 46.54 3.53
4259 4329 5.393896 CGGACTAGGAAACTTGTAACCCTAG 60.394 48.000 11.08 11.08 46.54 3.02
4260 4330 5.105023 GGACTAGGAAACTTGTAACCCTAGG 60.105 48.000 15.59 0.06 46.54 3.02
4261 4331 5.409712 ACTAGGAAACTTGTAACCCTAGGT 58.590 41.667 8.29 0.00 46.59 3.08
4262 4332 4.904895 AGGAAACTTGTAACCCTAGGTC 57.095 45.455 8.29 0.00 37.44 3.85
4263 4333 4.500452 AGGAAACTTGTAACCCTAGGTCT 58.500 43.478 8.29 0.00 37.44 3.85
4264 4334 4.531339 AGGAAACTTGTAACCCTAGGTCTC 59.469 45.833 8.29 0.00 37.44 3.36
4265 4335 4.492611 GAAACTTGTAACCCTAGGTCTCG 58.507 47.826 8.29 0.00 33.12 4.04
4266 4336 3.166560 ACTTGTAACCCTAGGTCTCGT 57.833 47.619 8.29 0.00 33.12 4.18
4267 4337 3.504375 ACTTGTAACCCTAGGTCTCGTT 58.496 45.455 8.29 7.18 33.12 3.85
4268 4338 3.257624 ACTTGTAACCCTAGGTCTCGTTG 59.742 47.826 8.29 0.00 33.12 4.10
4269 4339 2.880443 TGTAACCCTAGGTCTCGTTGT 58.120 47.619 8.29 0.00 33.12 3.32
4270 4340 4.032960 TGTAACCCTAGGTCTCGTTGTA 57.967 45.455 8.29 0.00 33.12 2.41
4271 4341 4.406456 TGTAACCCTAGGTCTCGTTGTAA 58.594 43.478 8.29 0.00 33.12 2.41
4272 4342 3.949842 AACCCTAGGTCTCGTTGTAAC 57.050 47.619 8.29 0.00 33.12 2.50
4273 4343 2.174360 ACCCTAGGTCTCGTTGTAACC 58.826 52.381 8.29 0.00 0.00 2.85
4360 4430 5.067936 AGTTTCACTCCCTCGATACACATAG 59.932 44.000 0.00 0.00 0.00 2.23
4367 4439 5.386060 TCCCTCGATACACATAGACATCTT 58.614 41.667 0.00 0.00 0.00 2.40
4408 4480 5.415701 GCACCCTATGAACAAATCAGAAAGA 59.584 40.000 0.00 0.00 42.53 2.52
4434 4506 1.367346 TTACCTTCACCATGAGGGCA 58.633 50.000 6.88 0.00 46.46 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.020437 GCTGGATCTTGCTACTTGGC 58.980 55.000 0.00 0.00 0.00 4.52
1 2 2.559440 GAGCTGGATCTTGCTACTTGG 58.441 52.381 11.73 0.00 39.91 3.61
2 3 2.559440 GGAGCTGGATCTTGCTACTTG 58.441 52.381 13.11 0.00 39.91 3.16
196 198 1.815840 GGAGCGCTCCTGGTAAAGC 60.816 63.158 42.50 17.91 46.16 3.51
197 199 4.522971 GGAGCGCTCCTGGTAAAG 57.477 61.111 42.50 0.00 46.16 1.85
209 211 2.457366 ACTGGAAACAACTAGGAGCG 57.543 50.000 0.00 0.00 42.06 5.03
210 212 4.267349 TGTACTGGAAACAACTAGGAGC 57.733 45.455 0.00 0.00 42.06 4.70
291 296 3.047280 GTTGTCGGCGCACCATCA 61.047 61.111 10.83 0.00 34.57 3.07
292 297 3.799755 GGTTGTCGGCGCACCATC 61.800 66.667 10.83 1.16 34.57 3.51
306 311 3.535280 AAAACCGCAAATCAACAGGTT 57.465 38.095 0.00 0.00 45.99 3.50
308 313 7.032580 TCATAATAAAACCGCAAATCAACAGG 58.967 34.615 0.00 0.00 0.00 4.00
359 364 4.742417 CGCACAAATCCATTTATTGACCA 58.258 39.130 0.00 0.00 0.00 4.02
408 413 2.604855 CCTACTAGTAATCACCAGCGCG 60.605 54.545 0.00 0.00 0.00 6.86
509 519 7.925483 AGAGAGATCAATCAACATAACACTAGC 59.075 37.037 0.00 0.00 0.00 3.42
520 530 4.768583 AGAAGGCAGAGAGATCAATCAAC 58.231 43.478 0.00 0.00 0.00 3.18
557 567 4.792704 GCAGACAACGAAACCATGAATGTT 60.793 41.667 0.00 0.00 0.00 2.71
560 570 3.149196 AGCAGACAACGAAACCATGAAT 58.851 40.909 0.00 0.00 0.00 2.57
572 582 3.510719 TGCAAGAACAAAAGCAGACAAC 58.489 40.909 0.00 0.00 32.48 3.32
584 594 6.936335 TGATCTTAGAACAAGATGCAAGAACA 59.064 34.615 4.31 0.00 37.14 3.18
589 599 6.151480 TGCATTGATCTTAGAACAAGATGCAA 59.849 34.615 22.24 12.72 37.38 4.08
603 613 0.263765 AGGGGGCATGCATTGATCTT 59.736 50.000 21.36 0.00 0.00 2.40
671 681 3.053359 CCCCCTCCTACTGAAGATCTT 57.947 52.381 7.95 7.95 0.00 2.40
709 721 6.130723 TCAACGATGCAGTAAAAGTAAAACG 58.869 36.000 0.00 0.00 0.00 3.60
710 722 7.853929 TCTTCAACGATGCAGTAAAAGTAAAAC 59.146 33.333 0.00 0.00 0.00 2.43
711 723 7.921787 TCTTCAACGATGCAGTAAAAGTAAAA 58.078 30.769 0.00 0.00 0.00 1.52
712 724 7.485418 TCTTCAACGATGCAGTAAAAGTAAA 57.515 32.000 0.00 0.00 0.00 2.01
713 725 7.667043 ATCTTCAACGATGCAGTAAAAGTAA 57.333 32.000 0.00 0.00 0.00 2.24
714 726 7.667043 AATCTTCAACGATGCAGTAAAAGTA 57.333 32.000 0.00 0.00 0.00 2.24
715 727 6.560253 AATCTTCAACGATGCAGTAAAAGT 57.440 33.333 0.00 0.00 0.00 2.66
717 729 6.964908 TCAAATCTTCAACGATGCAGTAAAA 58.035 32.000 0.00 0.00 0.00 1.52
722 734 5.287170 TCTTCAAATCTTCAACGATGCAG 57.713 39.130 0.00 0.00 0.00 4.41
724 736 4.556523 GCTTCTTCAAATCTTCAACGATGC 59.443 41.667 0.00 0.00 0.00 3.91
725 737 5.566774 GTGCTTCTTCAAATCTTCAACGATG 59.433 40.000 0.00 0.00 0.00 3.84
729 741 7.524294 TTTTGTGCTTCTTCAAATCTTCAAC 57.476 32.000 0.00 0.00 34.30 3.18
731 743 6.702723 CCATTTTGTGCTTCTTCAAATCTTCA 59.297 34.615 0.00 0.00 34.30 3.02
732 744 6.925165 TCCATTTTGTGCTTCTTCAAATCTTC 59.075 34.615 0.00 0.00 34.30 2.87
740 752 8.437742 CAAAATACATCCATTTTGTGCTTCTTC 58.562 33.333 11.38 0.00 44.96 2.87
741 753 8.314143 CAAAATACATCCATTTTGTGCTTCTT 57.686 30.769 11.38 0.00 44.96 2.52
823 839 5.975693 TCTGAAATTTGGTCGCCTAATTT 57.024 34.783 21.16 21.16 45.93 1.82
832 848 7.094805 TGCTTGTAGTACATCTGAAATTTGGTC 60.095 37.037 3.28 0.00 0.00 4.02
838 854 9.539825 CTAGATTGCTTGTAGTACATCTGAAAT 57.460 33.333 3.28 4.40 0.00 2.17
866 882 5.435686 TTGGAGATTACTTGTGTGCCTAT 57.564 39.130 0.00 0.00 0.00 2.57
888 904 6.529220 AGATCAGCTAACTTGTTCTTCAGTT 58.471 36.000 0.00 0.00 0.00 3.16
902 920 3.102972 AGGCTCAACAGAGATCAGCTAA 58.897 45.455 0.00 0.00 0.00 3.09
977 995 6.681729 TGGTAGTAGTTGTGAGAGGATTTT 57.318 37.500 0.00 0.00 0.00 1.82
1098 1116 2.756400 GTCCCCACATCACTGGCA 59.244 61.111 0.00 0.00 0.00 4.92
1146 1164 4.070552 GTGGCCGCGGAAGTCTCT 62.071 66.667 33.48 0.00 0.00 3.10
1188 1206 2.736721 CTGTGTGAGGTGGAATGTTACG 59.263 50.000 0.00 0.00 0.00 3.18
1245 1263 4.393680 TGAAAATTCCGATTACCACTTCCG 59.606 41.667 0.00 0.00 0.00 4.30
1251 1269 7.931578 AGTAACATGAAAATTCCGATTACCA 57.068 32.000 0.00 0.00 0.00 3.25
1325 1343 7.004691 ACCAATAGGGCAAAATATAAGGACTC 58.995 38.462 0.00 0.00 42.05 3.36
1445 1464 9.286946 GCAAATGAAATCTGTCTAGAGAAAATG 57.713 33.333 0.00 0.00 36.14 2.32
1543 1562 0.839946 AGTGTGTCCTTCCTGCACTT 59.160 50.000 0.00 0.00 37.12 3.16
1546 1565 0.179020 CCAAGTGTGTCCTTCCTGCA 60.179 55.000 0.00 0.00 0.00 4.41
1564 1583 1.580845 AAGCATCTTCGCACTGCACC 61.581 55.000 1.11 0.00 38.37 5.01
1573 1592 4.271776 TCAGCAATACATGAAGCATCTTCG 59.728 41.667 0.00 0.00 0.00 3.79
1628 1647 1.610522 AGCTTGAGCAACACATGAACC 59.389 47.619 0.00 0.00 45.16 3.62
1653 1672 5.073311 TGCATCTCTTGTTAGGTACTGTC 57.927 43.478 0.00 0.00 41.52 3.51
1689 1708 2.019984 GGACACCAGATTGGCTTGATC 58.980 52.381 0.00 0.00 42.67 2.92
1702 1721 0.545309 CCTCTCCTTCCTGGACACCA 60.545 60.000 0.00 0.00 40.56 4.17
1708 1727 1.330655 TAAGCGCCTCTCCTTCCTGG 61.331 60.000 2.29 0.00 37.10 4.45
1746 1765 2.073252 AGCACCAGAGACATCGGATA 57.927 50.000 0.00 0.00 0.00 2.59
1750 1769 1.478510 ACCTTAGCACCAGAGACATCG 59.521 52.381 0.00 0.00 0.00 3.84
1754 1773 1.205893 CTCCACCTTAGCACCAGAGAC 59.794 57.143 0.00 0.00 0.00 3.36
1765 1784 2.708861 TGTCTTTGCTTCCTCCACCTTA 59.291 45.455 0.00 0.00 0.00 2.69
1791 1810 2.083774 TCAGCATTTTTACGCCCTCAG 58.916 47.619 0.00 0.00 0.00 3.35
1795 1814 2.715737 TTGTCAGCATTTTTACGCCC 57.284 45.000 0.00 0.00 0.00 6.13
1828 1847 1.290203 AGTTATTGCATGCCTCGTCG 58.710 50.000 16.68 0.00 0.00 5.12
1874 1893 9.403110 CAAACTTTTGAAGATACTTTCATGAGG 57.597 33.333 0.00 0.00 40.55 3.86
1981 2000 0.980423 AAGAGAGCCTGACAACTCCC 59.020 55.000 0.00 0.00 33.18 4.30
2005 2024 3.879321 GCTCCCCATCAAAAGATGTCCTT 60.879 47.826 4.93 0.00 36.47 3.36
2273 2295 3.801114 AAACAAGACAAGCAAAGGGTC 57.199 42.857 0.00 0.00 0.00 4.46
2359 2381 2.129555 GAACTTCCTGGGGCAGCTGA 62.130 60.000 20.43 0.00 0.00 4.26
2516 2538 0.784778 GAAACCAGCGAGTTCTGACG 59.215 55.000 0.00 0.00 36.19 4.35
2536 2558 6.173339 CAACTAGCATCCTCAAAGTTTAGGA 58.827 40.000 13.05 13.05 45.76 2.94
2547 2569 3.691118 TCATTGCAACAACTAGCATCCTC 59.309 43.478 0.00 0.00 40.94 3.71
2601 2623 4.924625 AGATAGCAGTCGGATATGTAGGT 58.075 43.478 0.00 0.00 0.00 3.08
2662 2684 8.614994 AAGTTTTCGTTCAGTTTGAAATACAG 57.385 30.769 0.00 0.00 38.22 2.74
2743 2765 2.664851 CAAAGACGGCGCCTGACA 60.665 61.111 26.68 0.00 0.00 3.58
2849 2871 4.938080 TGACCTTTTCTATCTCATCGCTC 58.062 43.478 0.00 0.00 0.00 5.03
2859 2881 5.711698 TGGAAACCCTTTGACCTTTTCTAT 58.288 37.500 0.00 0.00 0.00 1.98
2996 3018 1.569479 GCCGTGACAGAACTGGCTTC 61.569 60.000 9.14 2.07 42.44 3.86
3238 3263 3.324846 GGTCATCATGCTACCTGTATGGA 59.675 47.826 4.28 0.00 38.93 3.41
3265 3290 5.487488 TCCCTCCTAGCAACTTATCAAGAAA 59.513 40.000 0.00 0.00 0.00 2.52
3480 3509 2.507886 TGGTTTTGAGGTCCTGACTGAA 59.492 45.455 0.00 0.00 0.00 3.02
3540 3569 2.009774 CACATAGCAAAGGGAAGGTCG 58.990 52.381 0.00 0.00 0.00 4.79
3569 3598 4.043200 GCAGAGCAACGCAACCCC 62.043 66.667 0.00 0.00 0.00 4.95
3652 3681 8.040002 TGACCCACATATCCAGATTGTTAATA 57.960 34.615 0.00 0.00 0.00 0.98
3714 3743 1.373497 GGCGGTCCAGATAGCATCG 60.373 63.158 0.00 0.00 0.00 3.84
4017 4082 3.815809 TCGTCAGTTTTGGTGGAAAGAT 58.184 40.909 0.00 0.00 0.00 2.40
4072 4137 2.263895 ACTAGGTCTTGTGGGGCATA 57.736 50.000 0.00 0.00 0.00 3.14
4073 4138 2.263895 TACTAGGTCTTGTGGGGCAT 57.736 50.000 0.00 0.00 0.00 4.40
4074 4139 2.032965 TTACTAGGTCTTGTGGGGCA 57.967 50.000 0.00 0.00 0.00 5.36
4076 4141 2.355818 GGCTTTACTAGGTCTTGTGGGG 60.356 54.545 0.00 0.00 0.00 4.96
4082 4147 2.479340 GGGAGGGCTTTACTAGGTCTT 58.521 52.381 0.00 0.00 0.00 3.01
4101 4166 3.672503 CTTGGGGTTGGGGGAGGG 61.673 72.222 0.00 0.00 0.00 4.30
4107 4172 4.010018 ATGGGCCTTGGGGTTGGG 62.010 66.667 4.53 0.00 34.45 4.12
4108 4173 2.534594 ATCATGGGCCTTGGGGTTGG 62.535 60.000 18.35 0.00 34.45 3.77
4109 4174 0.261402 TATCATGGGCCTTGGGGTTG 59.739 55.000 18.35 0.00 34.45 3.77
4110 4175 0.557729 CTATCATGGGCCTTGGGGTT 59.442 55.000 18.35 5.26 34.45 4.11
4111 4176 2.011617 GCTATCATGGGCCTTGGGGT 62.012 60.000 18.35 8.42 34.45 4.95
4112 4177 1.228675 GCTATCATGGGCCTTGGGG 60.229 63.158 18.35 10.20 0.00 4.96
4113 4178 1.228675 GGCTATCATGGGCCTTGGG 60.229 63.158 18.35 10.51 44.48 4.12
4114 4179 1.228675 GGGCTATCATGGGCCTTGG 60.229 63.158 18.35 4.88 46.80 3.61
4115 4180 4.507969 GGGCTATCATGGGCCTTG 57.492 61.111 13.02 13.02 46.80 3.61
4119 4184 1.980772 GGCATGGGCTATCATGGGC 60.981 63.158 13.85 0.00 43.34 5.36
4120 4185 0.113776 AAGGCATGGGCTATCATGGG 59.886 55.000 13.85 0.00 43.34 4.00
4121 4186 1.075050 AGAAGGCATGGGCTATCATGG 59.925 52.381 13.85 0.00 43.34 3.66
4122 4187 2.581216 AGAAGGCATGGGCTATCATG 57.419 50.000 0.00 9.67 45.26 3.07
4123 4188 2.307098 GGTAGAAGGCATGGGCTATCAT 59.693 50.000 0.00 0.00 37.50 2.45
4124 4189 1.699634 GGTAGAAGGCATGGGCTATCA 59.300 52.381 0.00 0.00 37.50 2.15
4125 4190 1.003696 GGGTAGAAGGCATGGGCTATC 59.996 57.143 0.00 0.00 37.50 2.08
4126 4191 1.068121 GGGTAGAAGGCATGGGCTAT 58.932 55.000 0.00 0.00 37.50 2.97
4127 4192 0.327095 TGGGTAGAAGGCATGGGCTA 60.327 55.000 0.00 0.00 37.50 3.93
4128 4193 1.619363 TGGGTAGAAGGCATGGGCT 60.619 57.895 0.00 0.00 41.24 5.19
4152 4222 0.772124 TCTTCCTTTGGTGGAGGCCT 60.772 55.000 3.86 3.86 37.43 5.19
4185 4255 3.047877 GGTTCGGCGTGTCTTGGG 61.048 66.667 6.85 0.00 0.00 4.12
4210 4280 1.183549 GCGGTTGAAGAGTCCTCCTA 58.816 55.000 0.00 0.00 0.00 2.94
4212 4282 1.079057 GGCGGTTGAAGAGTCCTCC 60.079 63.158 0.00 0.00 0.00 4.30
4213 4283 0.321996 AAGGCGGTTGAAGAGTCCTC 59.678 55.000 0.00 0.00 0.00 3.71
4214 4284 1.275573 GTAAGGCGGTTGAAGAGTCCT 59.724 52.381 0.00 0.00 0.00 3.85
4215 4285 1.675116 GGTAAGGCGGTTGAAGAGTCC 60.675 57.143 0.00 0.00 0.00 3.85
4234 4304 3.593096 GGTTACAAGTTTCCTAGTCCGG 58.407 50.000 0.00 0.00 0.00 5.14
4236 4306 4.904895 AGGGTTACAAGTTTCCTAGTCC 57.095 45.455 0.00 0.00 0.00 3.85
4256 4326 3.631227 CCTAGGGTTACAACGAGACCTAG 59.369 52.174 0.00 8.26 44.44 3.02
4257 4327 3.010584 ACCTAGGGTTACAACGAGACCTA 59.989 47.826 14.81 0.00 33.90 3.08
4258 4328 2.225217 ACCTAGGGTTACAACGAGACCT 60.225 50.000 14.81 0.00 33.90 3.85
4259 4329 2.165234 GACCTAGGGTTACAACGAGACC 59.835 54.545 14.81 0.00 35.25 3.85
4260 4330 3.087781 AGACCTAGGGTTACAACGAGAC 58.912 50.000 14.81 0.00 35.25 3.36
4261 4331 3.350833 GAGACCTAGGGTTACAACGAGA 58.649 50.000 14.81 0.00 35.25 4.04
4262 4332 2.097142 CGAGACCTAGGGTTACAACGAG 59.903 54.545 14.81 0.00 35.25 4.18
4263 4333 2.086869 CGAGACCTAGGGTTACAACGA 58.913 52.381 14.81 0.00 35.25 3.85
4264 4334 1.815003 ACGAGACCTAGGGTTACAACG 59.185 52.381 14.81 10.77 35.25 4.10
4265 4335 2.165234 GGACGAGACCTAGGGTTACAAC 59.835 54.545 14.81 0.00 35.25 3.32
4266 4336 2.042162 AGGACGAGACCTAGGGTTACAA 59.958 50.000 14.81 0.00 38.65 2.41
4267 4337 1.637553 AGGACGAGACCTAGGGTTACA 59.362 52.381 14.81 0.00 38.65 2.41
4268 4338 2.296792 GAGGACGAGACCTAGGGTTAC 58.703 57.143 14.81 1.59 40.73 2.50
4269 4339 1.213926 GGAGGACGAGACCTAGGGTTA 59.786 57.143 14.81 0.00 40.73 2.85
4270 4340 0.033306 GGAGGACGAGACCTAGGGTT 60.033 60.000 14.81 0.00 40.73 4.11
4271 4341 0.920271 AGGAGGACGAGACCTAGGGT 60.920 60.000 14.81 0.07 40.73 4.34
4272 4342 0.259356 AAGGAGGACGAGACCTAGGG 59.741 60.000 14.81 0.00 40.73 3.53
4273 4343 2.146920 AAAGGAGGACGAGACCTAGG 57.853 55.000 7.41 7.41 40.73 3.02
4305 4375 3.589951 AGATACCTAACGACTAGCCCA 57.410 47.619 0.00 0.00 0.00 5.36
4360 4430 6.470235 GCACAAGCATAATGTACAAAGATGTC 59.530 38.462 0.00 1.41 39.83 3.06


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

AutoCloner maintained by Alex Coulton.