Multiple sequence alignment - TraesCS2B01G155600

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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 TraesCS2B01G155600 chr2B 100.000 7810 0 0 1 7810 123378205 123386014 0 14423
1 TraesCS2B01G155600 chr2B 95.943 7838 277 13 1 7810 514557010 514549186 0 12674
2 TraesCS2B01G155600 chr2B 96.019 1457 46 8 6363 7810 88529819 88528366 0 2359
3 TraesCS2B01G155600 chr2B 93.287 1296 52 11 6548 7810 317051959 317050666 0 1879
4 TraesCS2B01G155600 chr3B 95.848 7827 295 19 1 7810 646350869 646358682 0 12626
5 TraesCS2B01G155600 chr3B 95.565 7825 291 31 1 7810 656113166 656105383 0 12477
6 TraesCS2B01G155600 chr3B 94.815 4802 236 11 630 5424 420619167 420623962 0 7476
7 TraesCS2B01G155600 chr3B 95.225 3602 144 9 4219 7810 420625463 420629046 0 5674
8 TraesCS2B01G155600 chr4B 94.877 7827 327 24 1 7810 30497997 30505766 0 12165
9 TraesCS2B01G155600 chr4B 95.942 4239 140 16 3585 7810 89440873 89436654 0 6846
10 TraesCS2B01G155600 chr4B 95.755 4193 156 14 3598 7776 629505874 629510058 0 6737
11 TraesCS2B01G155600 chr4B 95.414 4187 179 13 1 4181 629502195 629506374 0 6656
12 TraesCS2B01G155600 chr4B 95.547 4110 174 9 1 4106 199603023 199607127 0 6567
13 TraesCS2B01G155600 chr4B 96.627 3914 103 12 3907 7810 173393478 173389584 0 6469
14 TraesCS2B01G155600 chr4B 95.467 4015 147 14 3808 7810 199607443 199611434 0 6373
15 TraesCS2B01G155600 chr6B 94.921 6930 331 17 1 6921 9713708 9720625 0 10828
16 TraesCS2B01G155600 chr1B 92.606 5342 358 28 1 5328 256706748 256712066 0 7642
17 TraesCS2B01G155600 chr1B 95.630 4050 151 14 3773 7810 575067193 575063158 0 6475
18 TraesCS2B01G155600 chr1B 94.664 4104 207 11 1 4098 413051777 413055874 0 6355
19 TraesCS2B01G155600 chr1B 94.899 3823 152 14 4004 7810 413055984 413059779 0 5939
20 TraesCS2B01G155600 chr1B 93.713 3913 202 24 3935 7810 84522088 84518183 0 5823
21 TraesCS2B01G155600 chr7B 96.015 3965 150 7 4 3962 192833403 192829441 0 6440
22 TraesCS2B01G155600 chr7B 96.109 3804 123 8 4016 7810 192829159 192825372 0 6181
23 TraesCS2B01G155600 chr5B 95.292 4057 172 12 3766 7810 519961773 519957724 0 6416


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 TraesCS2B01G155600 chr2B 123378205 123386014 7809 False 14423.0 14423 100.0000 1 7810 1 chr2B.!!$F1 7809
1 TraesCS2B01G155600 chr2B 514549186 514557010 7824 True 12674.0 12674 95.9430 1 7810 1 chr2B.!!$R3 7809
2 TraesCS2B01G155600 chr2B 88528366 88529819 1453 True 2359.0 2359 96.0190 6363 7810 1 chr2B.!!$R1 1447
3 TraesCS2B01G155600 chr2B 317050666 317051959 1293 True 1879.0 1879 93.2870 6548 7810 1 chr2B.!!$R2 1262
4 TraesCS2B01G155600 chr3B 646350869 646358682 7813 False 12626.0 12626 95.8480 1 7810 1 chr3B.!!$F1 7809
5 TraesCS2B01G155600 chr3B 656105383 656113166 7783 True 12477.0 12477 95.5650 1 7810 1 chr3B.!!$R1 7809
6 TraesCS2B01G155600 chr3B 420619167 420629046 9879 False 6575.0 7476 95.0200 630 7810 2 chr3B.!!$F2 7180
7 TraesCS2B01G155600 chr4B 30497997 30505766 7769 False 12165.0 12165 94.8770 1 7810 1 chr4B.!!$F1 7809
8 TraesCS2B01G155600 chr4B 89436654 89440873 4219 True 6846.0 6846 95.9420 3585 7810 1 chr4B.!!$R1 4225
9 TraesCS2B01G155600 chr4B 629502195 629510058 7863 False 6696.5 6737 95.5845 1 7776 2 chr4B.!!$F3 7775
10 TraesCS2B01G155600 chr4B 199603023 199611434 8411 False 6470.0 6567 95.5070 1 7810 2 chr4B.!!$F2 7809
11 TraesCS2B01G155600 chr4B 173389584 173393478 3894 True 6469.0 6469 96.6270 3907 7810 1 chr4B.!!$R2 3903
12 TraesCS2B01G155600 chr6B 9713708 9720625 6917 False 10828.0 10828 94.9210 1 6921 1 chr6B.!!$F1 6920
13 TraesCS2B01G155600 chr1B 256706748 256712066 5318 False 7642.0 7642 92.6060 1 5328 1 chr1B.!!$F1 5327
14 TraesCS2B01G155600 chr1B 575063158 575067193 4035 True 6475.0 6475 95.6300 3773 7810 1 chr1B.!!$R2 4037
15 TraesCS2B01G155600 chr1B 413051777 413059779 8002 False 6147.0 6355 94.7815 1 7810 2 chr1B.!!$F2 7809
16 TraesCS2B01G155600 chr1B 84518183 84522088 3905 True 5823.0 5823 93.7130 3935 7810 1 chr1B.!!$R1 3875
17 TraesCS2B01G155600 chr7B 192825372 192833403 8031 True 6310.5 6440 96.0620 4 7810 2 chr7B.!!$R1 7806
18 TraesCS2B01G155600 chr5B 519957724 519961773 4049 True 6416.0 6416 95.2920 3766 7810 1 chr5B.!!$R1 4044

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
562 574 0.321653 GTTCAGACCTCCGCCAACAT 60.322 55.0 0.00 0.0 0.00 2.71 F
2279 2307 0.105142 ACACACTGTGGGGGACTAGT 60.105 55.0 15.48 0.0 37.94 2.57 F
3316 3349 0.320421 GACTAAACCCAGAGCGCACA 60.320 55.0 11.47 0.0 0.00 4.57 F
4768 8559 0.238289 GGTTGCCATGACACACTTCG 59.762 55.0 0.00 0.0 0.00 3.79 F
5101 8897 0.249911 GGTTGAGCTCCACGACAAGT 60.250 55.0 12.15 0.0 0.00 3.16 F
5102 8898 1.583054 GTTGAGCTCCACGACAAGTT 58.417 50.0 12.15 0.0 0.00 2.66 F
6457 10294 1.896220 TTCAGCATTGGAGGTGACAC 58.104 50.0 0.00 0.0 44.78 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2325 2353 0.034337 AACCATGACTTGTACGCGGT 59.966 50.000 12.47 0.00 0.0 5.68 R
3387 3420 3.552132 ATTTGGTGGGGTGTTTTGTTC 57.448 42.857 0.00 0.00 0.0 3.18 R
4780 8571 0.248743 CGTGTGTGTAGTGGTCGTGT 60.249 55.000 0.00 0.00 0.0 4.49 R
6465 10302 0.104672 TCCAAACCAGACTCCTCCCA 60.105 55.000 0.00 0.00 0.0 4.37 R
6466 10303 1.064825 TTCCAAACCAGACTCCTCCC 58.935 55.000 0.00 0.00 0.0 4.30 R
6705 10543 1.986378 GTCGATTGTCTTCCACGACTG 59.014 52.381 0.00 0.00 46.0 3.51 R
7368 11254 1.563111 ACCGTGTGTTCAACTGTACG 58.437 50.000 5.25 5.25 0.0 3.67 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
24 25 0.394216 ATATGTGCCCGCTGAAGCAA 60.394 50.000 2.79 0.00 41.48 3.91
79 82 7.984050 TCCTTTTGAATGCAGTCACAAATAAAA 59.016 29.630 17.75 12.20 33.38 1.52
128 131 1.658968 GCAAAACGCTACTGTCAACG 58.341 50.000 0.00 0.00 37.77 4.10
562 574 0.321653 GTTCAGACCTCCGCCAACAT 60.322 55.000 0.00 0.00 0.00 2.71
610 622 7.281100 GGATAAGCAGCTGATAAGTACAACTTT 59.719 37.037 20.43 0.00 39.51 2.66
645 657 1.472082 TGCCACAGTAAAATGCCATCG 59.528 47.619 0.00 0.00 0.00 3.84
709 721 2.917971 CGTACAGCTTGACAAGACTAGC 59.082 50.000 19.51 3.53 38.49 3.42
976 996 1.480137 CTCCAGCGTCTCTCTCCAAAT 59.520 52.381 0.00 0.00 0.00 2.32
987 1007 1.276421 CTCTCCAAATCCCACAGTCGT 59.724 52.381 0.00 0.00 0.00 4.34
1041 1061 1.519234 GCGTCATCATGCCGAGACA 60.519 57.895 0.00 0.00 0.00 3.41
1152 1172 1.468985 AGGAGACACTGGAGATCGTG 58.531 55.000 0.00 0.00 37.18 4.35
1206 1226 0.260230 TCTCGAGGCTCTGGAGGAAT 59.740 55.000 13.56 0.00 37.04 3.01
1336 1356 1.445410 GTGTACCACATCGCAGCGA 60.445 57.895 22.06 22.06 41.13 4.93
1337 1357 1.445410 TGTACCACATCGCAGCGAC 60.445 57.895 22.28 6.62 39.18 5.19
1469 1490 5.197451 AGTGTGGTTTGTGAAAAGTGGATA 58.803 37.500 0.00 0.00 0.00 2.59
1480 1502 7.041721 TGTGAAAAGTGGATATAGTACTGCAG 58.958 38.462 13.48 13.48 0.00 4.41
1496 1518 7.540299 AGTACTGCAGTTTCTCAAGTAGATAC 58.460 38.462 27.06 11.50 36.67 2.24
1528 1551 7.701539 ATGTATTTTTGAACCTGATGCACTA 57.298 32.000 0.00 0.00 0.00 2.74
1598 1621 7.605309 TGATCGACTAGTGTAGTTTCTGAAGTA 59.395 37.037 0.00 0.00 39.59 2.24
2006 2034 4.751767 TTCAAAATGTCTTTGCCCTTGT 57.248 36.364 0.00 0.00 0.00 3.16
2025 2053 2.763988 TAGGCCCAAGCTCCTGACCA 62.764 60.000 0.00 0.00 39.73 4.02
2070 2098 1.003262 CACATTTGCCGGTTTCAGCG 61.003 55.000 1.90 0.00 39.06 5.18
2145 2173 0.314578 GTTCATCGACATTCAGCGCG 60.315 55.000 0.00 0.00 0.00 6.86
2237 2265 5.361857 CCCATTCTACAAAGGCATGAAGAAT 59.638 40.000 0.00 0.00 34.80 2.40
2279 2307 0.105142 ACACACTGTGGGGGACTAGT 60.105 55.000 15.48 0.00 37.94 2.57
2310 2338 1.476891 ACAACCTCATCGAGTACGCAT 59.523 47.619 0.00 0.00 39.58 4.73
2325 2353 4.278419 AGTACGCATGAGTAGATGCATACA 59.722 41.667 9.77 0.00 45.89 2.29
2365 2393 5.295292 GGTTCATGATTGACTACATCACAGG 59.705 44.000 0.00 0.00 36.92 4.00
2395 2423 1.860641 TATGCGAAACAGAGGGAGGA 58.139 50.000 0.00 0.00 0.00 3.71
2555 2583 5.130975 ACCAGTATGATTATGTCCTGCTTGA 59.869 40.000 0.00 0.00 39.69 3.02
2999 3028 8.739972 ACAAAACTGACAAGAACTAGAACAAAT 58.260 29.630 0.00 0.00 0.00 2.32
3213 3246 3.700961 CGCCGTGTATAAGCGCTT 58.299 55.556 27.97 27.97 43.72 4.68
3238 3271 3.651803 AAGTGTTCAGAGGAGTTCGAG 57.348 47.619 0.00 0.00 0.00 4.04
3316 3349 0.320421 GACTAAACCCAGAGCGCACA 60.320 55.000 11.47 0.00 0.00 4.57
3387 3420 1.512926 GCCCAATAGCCTACATCGTG 58.487 55.000 0.00 0.00 0.00 4.35
3442 3475 2.359975 CCAGAGGGCGGGACAAAC 60.360 66.667 0.00 0.00 0.00 2.93
3866 3997 6.846325 ACTGACAAGTTCAACTACTAAAGC 57.154 37.500 0.00 0.00 32.21 3.51
3867 3998 6.583562 ACTGACAAGTTCAACTACTAAAGCT 58.416 36.000 0.00 0.00 32.21 3.74
3868 3999 6.702282 ACTGACAAGTTCAACTACTAAAGCTC 59.298 38.462 0.00 0.00 32.21 4.09
3869 4000 6.578944 TGACAAGTTCAACTACTAAAGCTCA 58.421 36.000 0.00 0.00 0.00 4.26
3874 4005 9.226345 CAAGTTCAACTACTAAAGCTCAAAAAG 57.774 33.333 0.00 0.00 0.00 2.27
3875 4006 8.507524 AGTTCAACTACTAAAGCTCAAAAAGT 57.492 30.769 0.00 0.00 0.00 2.66
3877 4008 9.222916 GTTCAACTACTAAAGCTCAAAAAGTTC 57.777 33.333 0.00 0.00 0.00 3.01
3878 4009 8.500753 TCAACTACTAAAGCTCAAAAAGTTCA 57.499 30.769 0.00 0.00 0.00 3.18
3882 4013 9.569167 ACTACTAAAGCTCAAAAAGTTCAAAAC 57.431 29.630 0.00 0.00 0.00 2.43
4309 5374 1.222936 CAGGATCAGTCAGGCCACC 59.777 63.158 5.01 0.00 0.00 4.61
4326 5391 1.003355 CCCGCACCACTCTGACATT 60.003 57.895 0.00 0.00 0.00 2.71
4413 5479 9.066892 AGTGCACTAGAAATGAGAATACAAAAA 57.933 29.630 20.16 0.00 0.00 1.94
4613 8403 3.688694 ACAGTGCAAAATGCCATCATT 57.311 38.095 0.00 0.00 44.23 2.57
4684 8474 5.698545 GCTTGACAAGACTAGTCAGTTCAAT 59.301 40.000 24.44 0.00 45.72 2.57
4766 8556 1.795170 GCGGTTGCCATGACACACTT 61.795 55.000 0.00 0.00 33.98 3.16
4768 8559 0.238289 GGTTGCCATGACACACTTCG 59.762 55.000 0.00 0.00 0.00 3.79
4771 8562 2.183478 TGCCATGACACACTTCGAAT 57.817 45.000 0.00 0.00 0.00 3.34
4774 8565 2.426522 CCATGACACACTTCGAATGGT 58.573 47.619 0.00 0.00 31.80 3.55
4955 8751 2.594303 CAAAGCCCACAGTCGCCA 60.594 61.111 0.00 0.00 0.00 5.69
4971 8767 2.679092 CAGAGGAAGGCCATGGCA 59.321 61.111 36.56 0.00 44.11 4.92
5002 8798 2.409055 GCCAAGCGTCATCATGCCA 61.409 57.895 0.00 0.00 34.73 4.92
5101 8897 0.249911 GGTTGAGCTCCACGACAAGT 60.250 55.000 12.15 0.00 0.00 3.16
5102 8898 1.583054 GTTGAGCTCCACGACAAGTT 58.417 50.000 12.15 0.00 0.00 2.66
5182 8978 4.570874 GGATGAAGGGAGGCGGCC 62.571 72.222 12.11 12.11 0.00 6.13
5736 9535 9.945904 AACTTAATTAAAACTTGTTTCCCAACA 57.054 25.926 0.00 0.00 41.39 3.33
5839 9653 6.318648 GTGGATTGTTTCACCAGATTAGCATA 59.681 38.462 0.00 0.00 34.21 3.14
5920 9735 6.094193 TGTACTGGCATAGATTCTGATCTG 57.906 41.667 0.00 0.00 42.55 2.90
6128 9947 6.716898 TCAAGAAGCGCATATATCATTGAG 57.283 37.500 11.47 0.00 0.00 3.02
6457 10294 1.896220 TTCAGCATTGGAGGTGACAC 58.104 50.000 0.00 0.00 44.78 3.67
6465 10302 2.261671 GAGGTGACACGCGGATGT 59.738 61.111 12.47 6.55 34.78 3.06
6466 10303 2.048222 AGGTGACACGCGGATGTG 60.048 61.111 12.47 1.02 45.41 3.21
6560 10398 4.708421 ACCAGCAAATACTACGACTCCTTA 59.292 41.667 0.00 0.00 0.00 2.69
6638 10476 3.288092 GAACAGGGAAGACCACAAACTT 58.712 45.455 0.00 0.00 43.89 2.66
6710 10548 0.911856 CATACGCAACGTACCAGTCG 59.088 55.000 1.43 0.00 45.07 4.18
6924 10780 2.472029 ACCAGCTACCTTATGCTCAGT 58.528 47.619 0.00 0.00 37.44 3.41
7618 11518 9.884465 ATAAGTTCGACAAAAGAGAAAAATCAG 57.116 29.630 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
203 208 9.509956 TTGTTATTACTATGCCTTTTGTACTGT 57.490 29.630 0.00 0.00 0.00 3.55
283 294 0.962356 AATTTGGACTGGCAGGAGCG 60.962 55.000 20.34 0.00 43.41 5.03
298 309 9.739276 TTATGTACTGATGGTCTTTCTGAATTT 57.261 29.630 0.00 0.00 0.00 1.82
555 567 2.027073 TGTCAGCGTCGATGTTGGC 61.027 57.895 17.96 17.96 0.00 4.52
562 574 3.759766 TTGCACGTGTCAGCGTCGA 62.760 57.895 18.38 0.00 43.83 4.20
610 622 2.950975 TGTGGCACCGATTCGTATAGTA 59.049 45.455 16.26 0.00 0.00 1.82
645 657 2.430921 CGTCTCTGCGGTGGTGAC 60.431 66.667 0.00 0.00 0.00 3.67
709 721 8.813282 GTTAAATGGTTTTTACTGTTGAACTGG 58.187 33.333 7.13 0.00 0.00 4.00
803 815 4.832608 GTCATGGGGGTCGCCGTC 62.833 72.222 0.00 0.00 0.00 4.79
817 829 1.068417 GGCGTGTGTGTAGTGGTCA 59.932 57.895 0.00 0.00 0.00 4.02
869 889 1.709578 TGGGGTATTTTTGCAGTGCA 58.290 45.000 15.37 15.37 36.47 4.57
987 1007 3.797353 GCCATGGCCTTCCTCCGA 61.797 66.667 27.24 0.00 34.56 4.55
1041 1061 0.321653 GGTTGCTCCTGTTGTCCGAT 60.322 55.000 0.00 0.00 0.00 4.18
1152 1172 2.280797 TCTGGTTCGCTGGTGCAC 60.281 61.111 8.80 8.80 39.64 4.57
1206 1226 0.326595 TATGAAACCTGCCGCCAAGA 59.673 50.000 0.00 0.00 0.00 3.02
1303 1323 3.133362 TGGTACACCAAGAAGAGTTCGTT 59.867 43.478 0.00 0.00 44.35 3.85
1469 1490 7.704578 TCTACTTGAGAAACTGCAGTACTAT 57.295 36.000 22.01 7.82 0.00 2.12
1528 1551 7.556275 TCCGCAAGATTTTCCAAATAGTAATCT 59.444 33.333 0.00 0.00 37.20 2.40
1696 1720 8.442374 ACCAAGTCCTTAGTTTATTTCCTTACA 58.558 33.333 0.00 0.00 0.00 2.41
1702 1727 7.040686 TGCTTCACCAAGTCCTTAGTTTATTTC 60.041 37.037 0.00 0.00 31.45 2.17
2006 2034 1.995626 GGTCAGGAGCTTGGGCCTA 60.996 63.158 4.53 0.00 39.73 3.93
2070 2098 3.002759 AGCTTCTCTTTGTCGCTTTCAAC 59.997 43.478 0.00 0.00 0.00 3.18
2210 2238 3.010027 TCATGCCTTTGTAGAATGGGTGA 59.990 43.478 6.66 0.00 0.00 4.02
2237 2265 3.258372 AGTCTTCCTGCGTGTTGATCTTA 59.742 43.478 0.00 0.00 0.00 2.10
2279 2307 1.372683 GAGGTTGTCTGGCAGCTCA 59.627 57.895 10.34 8.83 37.46 4.26
2310 2338 1.269051 CGCGGTGTATGCATCTACTCA 60.269 52.381 0.19 0.00 0.00 3.41
2325 2353 0.034337 AACCATGACTTGTACGCGGT 59.966 50.000 12.47 0.00 0.00 5.68
2365 2393 2.417239 TGTTTCGCATATTCCGAACCAC 59.583 45.455 7.31 5.68 43.48 4.16
2388 2416 4.081586 GTCGTAGAAGTTTTCATCCTCCCT 60.082 45.833 0.00 0.00 39.69 4.20
2395 2423 2.735134 GCGTGGTCGTAGAAGTTTTCAT 59.265 45.455 0.00 0.00 39.69 2.57
2555 2583 8.232913 ACATAACTAAACTTGTTCAACCATGT 57.767 30.769 0.00 0.00 0.00 3.21
2613 2641 4.274214 ACGAAGCTACCAAACCAAACTTAC 59.726 41.667 0.00 0.00 0.00 2.34
2948 2977 8.725148 GTGTGAGTGTAATCTTTTTCATCTGAT 58.275 33.333 0.00 0.00 0.00 2.90
2952 2981 9.515020 TTTTGTGTGAGTGTAATCTTTTTCATC 57.485 29.630 0.00 0.00 0.00 2.92
2999 3028 5.892119 CCTCCAGTAACTTGGACTGATACTA 59.108 44.000 4.38 0.00 46.01 1.82
3128 3159 4.497291 TTGTGCGGATTACTAGGGATTT 57.503 40.909 0.00 0.00 0.00 2.17
3213 3246 4.458295 CGAACTCCTCTGAACACTTACCTA 59.542 45.833 0.00 0.00 0.00 3.08
3387 3420 3.552132 ATTTGGTGGGGTGTTTTGTTC 57.448 42.857 0.00 0.00 0.00 3.18
3752 3883 9.561069 AGTAGTTGAACTTGTCAGATTTTGTAT 57.439 29.630 1.97 0.00 37.61 2.29
3753 3884 8.958119 AGTAGTTGAACTTGTCAGATTTTGTA 57.042 30.769 1.97 0.00 37.61 2.41
3754 3885 7.865706 AGTAGTTGAACTTGTCAGATTTTGT 57.134 32.000 1.97 0.00 37.61 2.83
3835 3966 9.614792 AGTAGTTGAACTTGTCAGTTTTTCTAT 57.385 29.630 1.97 0.00 43.79 1.98
3837 3968 7.923414 AGTAGTTGAACTTGTCAGTTTTTCT 57.077 32.000 1.97 0.00 43.79 2.52
3844 3975 6.701841 TGAGCTTTAGTAGTTGAACTTGTCAG 59.298 38.462 1.97 0.00 37.61 3.51
3845 3976 6.578944 TGAGCTTTAGTAGTTGAACTTGTCA 58.421 36.000 1.97 0.00 0.00 3.58
3846 3977 7.478520 TTGAGCTTTAGTAGTTGAACTTGTC 57.521 36.000 1.97 0.00 0.00 3.18
3848 3979 9.226345 CTTTTTGAGCTTTAGTAGTTGAACTTG 57.774 33.333 1.97 0.00 0.00 3.16
3849 3980 8.957466 ACTTTTTGAGCTTTAGTAGTTGAACTT 58.043 29.630 1.97 0.00 0.00 2.66
3851 3982 9.222916 GAACTTTTTGAGCTTTAGTAGTTGAAC 57.777 33.333 8.57 0.00 0.00 3.18
3852 3983 8.952278 TGAACTTTTTGAGCTTTAGTAGTTGAA 58.048 29.630 8.57 0.00 0.00 2.69
3854 3985 9.567848 TTTGAACTTTTTGAGCTTTAGTAGTTG 57.432 29.630 8.57 0.00 0.00 3.16
3857 3988 9.567848 TGTTTTGAACTTTTTGAGCTTTAGTAG 57.432 29.630 0.00 0.00 0.00 2.57
4309 5374 2.093306 TTAATGTCAGAGTGGTGCGG 57.907 50.000 0.00 0.00 0.00 5.69
4326 5391 3.006323 ACAGCGCATGGGTTTGAAATTTA 59.994 39.130 11.47 0.00 0.00 1.40
4413 5479 6.436218 CCAACCAAAGTTAGGCCTTTATAGTT 59.564 38.462 12.58 3.92 33.00 2.24
4557 8330 3.119849 GGATCTGTGATGTTTTTCCGTGG 60.120 47.826 0.00 0.00 0.00 4.94
4613 8403 1.289066 GCACGTCTCTGCAGTGGTA 59.711 57.895 14.67 0.00 37.11 3.25
4684 8474 7.501892 ACCGTCCAAGTTAAATGGTTTTTACTA 59.498 33.333 8.08 0.00 34.52 1.82
4761 8551 0.762418 TGGGTCACCATTCGAAGTGT 59.238 50.000 14.90 6.92 43.37 3.55
4771 8562 2.764547 TGGTCGTGTGGGTCACCA 60.765 61.111 0.00 0.00 46.94 4.17
4774 8565 0.756070 TGTAGTGGTCGTGTGGGTCA 60.756 55.000 0.00 0.00 0.00 4.02
4780 8571 0.248743 CGTGTGTGTAGTGGTCGTGT 60.249 55.000 0.00 0.00 0.00 4.49
4955 8751 1.617536 TCTGCCATGGCCTTCCTCT 60.618 57.895 33.44 0.00 41.09 3.69
4971 8767 2.920912 TTGGCGGACGGTTCCTCT 60.921 61.111 0.00 0.00 40.23 3.69
5002 8798 1.271102 GCTCCTCTTGTCTGACGTCTT 59.729 52.381 17.92 0.00 0.00 3.01
5059 8855 2.902705 TTGAGCGTTCTGGTGTACTT 57.097 45.000 0.00 0.00 0.00 2.24
5538 9335 8.896744 AGTAATGATGTATGTTCTTCATTGGTG 58.103 33.333 13.92 0.00 40.16 4.17
5903 9718 3.940221 GCATCCAGATCAGAATCTATGCC 59.060 47.826 10.18 0.00 42.79 4.40
6050 9869 7.380423 AAAGACCTATACCAGTGCTTGATAT 57.620 36.000 0.00 0.00 0.00 1.63
6457 10294 3.432051 GACTCCTCCCACATCCGCG 62.432 68.421 0.00 0.00 0.00 6.46
6465 10302 0.104672 TCCAAACCAGACTCCTCCCA 60.105 55.000 0.00 0.00 0.00 4.37
6466 10303 1.064825 TTCCAAACCAGACTCCTCCC 58.935 55.000 0.00 0.00 0.00 4.30
6705 10543 1.986378 GTCGATTGTCTTCCACGACTG 59.014 52.381 0.00 0.00 46.00 3.51
6710 10548 4.327854 GATGTTGTCGATTGTCTTCCAC 57.672 45.455 0.00 0.00 0.00 4.02
6924 10780 5.359576 AGACATAGGCAAACTTGTTCAAACA 59.640 36.000 0.00 0.00 37.08 2.83
7220 11105 3.159472 TGTCCTCGGCTGAAACTTAGTA 58.841 45.455 0.00 0.00 0.00 1.82
7368 11254 1.563111 ACCGTGTGTTCAACTGTACG 58.437 50.000 5.25 5.25 0.00 3.67
7467 11353 3.641437 TTTCAGTTGTATTGCCACTGC 57.359 42.857 1.72 0.00 38.26 4.40
7563 11463 8.800370 TTTTTGATTTAGTTTTTGGCCTTCTT 57.200 26.923 3.32 0.00 0.00 2.52
7564 11464 8.264347 TCTTTTTGATTTAGTTTTTGGCCTTCT 58.736 29.630 3.32 0.00 0.00 2.85
7618 11518 4.859629 ACGTCTTCTGTTGTGTTTCTTC 57.140 40.909 0.00 0.00 0.00 2.87
7676 11576 9.384764 GAGATTCCAATAGTGCTAGTACTTTTT 57.615 33.333 19.04 10.35 32.19 1.94


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

AutoCloner maintained by Alex Coulton.