Multiple sequence alignment - TraesCS5B01G379100

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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 TraesCS5B01G379100 chr5B 100.000 4990 0 0 1 4990 557246854 557251843 0.000000e+00 9215.0
1 TraesCS5B01G379100 chr4A 95.776 4190 140 14 763 4944 695974595 695978755 0.000000e+00 6722.0
2 TraesCS5B01G379100 chr4A 95.178 4189 158 21 763 4937 625833598 625829440 0.000000e+00 6577.0
3 TraesCS5B01G379100 chr4A 85.621 765 58 18 1 764 695973775 695974488 0.000000e+00 756.0
4 TraesCS5B01G379100 chr5D 94.274 4226 172 22 763 4944 543404853 543409052 0.000000e+00 6399.0
5 TraesCS5B01G379100 chr5D 83.938 386 29 3 1 386 543404331 543404683 6.190000e-89 339.0
6 TraesCS5B01G379100 chr5D 80.203 394 63 7 15 406 495895523 495895143 1.060000e-71 281.0
7 TraesCS5B01G379100 chr5D 84.649 228 22 9 2319 2542 542111712 542111494 1.090000e-51 215.0
8 TraesCS5B01G379100 chr5D 87.898 157 18 1 485 641 32247863 32247708 3.070000e-42 183.0
9 TraesCS5B01G379100 chr5D 96.364 55 2 0 709 763 543404682 543404736 1.910000e-14 91.6
10 TraesCS5B01G379100 chr7D 80.848 637 87 24 18 641 5437325 5436711 7.560000e-128 468.0
11 TraesCS5B01G379100 chr7D 82.609 138 22 2 506 643 88716114 88715979 2.440000e-23 121.0
12 TraesCS5B01G379100 chr7D 81.884 138 24 1 505 642 19570893 19570757 1.140000e-21 115.0
13 TraesCS5B01G379100 chr7B 84.310 478 63 10 173 642 646215390 646215863 1.640000e-124 457.0
14 TraesCS5B01G379100 chr2A 82.684 231 37 3 414 643 764782096 764781868 8.470000e-48 202.0
15 TraesCS5B01G379100 chr2A 82.927 123 20 1 414 536 764782219 764782098 5.280000e-20 110.0
16 TraesCS5B01G379100 chr3B 84.699 183 17 2 160 342 618684971 618685142 6.640000e-39 172.0
17 TraesCS5B01G379100 chr6D 82.432 148 24 2 492 639 265898146 265898291 1.460000e-25 128.0
18 TraesCS5B01G379100 chr6D 79.851 134 20 5 506 639 307889732 307889858 1.910000e-14 91.6
19 TraesCS5B01G379100 chr1D 81.208 149 22 5 499 644 372458995 372458850 1.140000e-21 115.0
20 TraesCS5B01G379100 chr4D 82.014 139 20 5 506 642 421971184 421971049 4.080000e-21 113.0
21 TraesCS5B01G379100 chr6B 81.618 136 24 1 506 641 160672199 160672065 1.470000e-20 111.0
22 TraesCS5B01G379100 chr7A 82.308 130 20 3 230 358 78502661 78502534 5.280000e-20 110.0
23 TraesCS5B01G379100 chr2B 82.353 119 17 3 504 619 251783570 251783453 3.180000e-17 100.0
24 TraesCS5B01G379100 chr2D 93.478 46 1 2 16 61 524151036 524150993 3.220000e-07 67.6
25 TraesCS5B01G379100 chr3D 89.583 48 3 2 16 62 338731676 338731630 5.390000e-05 60.2


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 TraesCS5B01G379100 chr5B 557246854 557251843 4989 False 9215.000000 9215 100.000000 1 4990 1 chr5B.!!$F1 4989
1 TraesCS5B01G379100 chr4A 625829440 625833598 4158 True 6577.000000 6577 95.178000 763 4937 1 chr4A.!!$R1 4174
2 TraesCS5B01G379100 chr4A 695973775 695978755 4980 False 3739.000000 6722 90.698500 1 4944 2 chr4A.!!$F1 4943
3 TraesCS5B01G379100 chr5D 543404331 543409052 4721 False 2276.533333 6399 91.525333 1 4944 3 chr5D.!!$F1 4943
4 TraesCS5B01G379100 chr7D 5436711 5437325 614 True 468.000000 468 80.848000 18 641 1 chr7D.!!$R1 623

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
612 651 0.251033 GGGGGTTTAAGGTTCGCAGT 60.251 55.000 0.00 0.00 0.00 4.40 F
1455 1619 0.535780 CTTGGAACCTGCTGCTGTCA 60.536 55.000 0.00 0.00 0.00 3.58 F
2258 2422 0.389948 ACGGTCAAATCTGGACTCGC 60.390 55.000 0.00 0.00 34.50 5.03 F
2981 3153 1.272092 ACCAATGTCCATGGACTGGTG 60.272 52.381 38.85 31.63 46.08 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 1901 0.398696 TCATGGCACCGTAAACCACT 59.601 50.000 0.0 0.0 35.99 4.00 R
3150 3322 1.292242 TGCCAGGAATAGAGGAGACCT 59.708 52.381 0.0 0.0 36.03 3.85 R
3151 3323 1.414550 GTGCCAGGAATAGAGGAGACC 59.585 57.143 0.0 0.0 0.00 3.85 R
4296 4502 0.908198 AGGGAAGCAGCTCTACCTTG 59.092 55.000 0.0 0.0 30.70 3.61 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
89 90 7.234371 TCAGTGGATTTATGGTTTTGGATCAAA 59.766 33.333 0.00 0.00 0.00 2.69
116 117 5.063880 GTGTTCAGAACAGACCCTGTAAAT 58.936 41.667 16.68 0.00 44.62 1.40
123 124 2.038557 ACAGACCCTGTAAATGTTCGCT 59.961 45.455 0.00 0.00 43.46 4.93
136 137 5.351233 AATGTTCGCTGAATCGTAAACAA 57.649 34.783 0.00 0.00 32.57 2.83
164 165 1.164041 CCACCGAAAACGTGAGCCTT 61.164 55.000 0.00 0.00 32.77 4.35
220 222 3.039134 CCACAAACTGGCCGGAAC 58.961 61.111 21.41 0.00 31.36 3.62
221 223 1.528309 CCACAAACTGGCCGGAACT 60.528 57.895 21.41 0.00 31.36 3.01
222 224 1.654220 CACAAACTGGCCGGAACTG 59.346 57.895 21.41 14.18 0.00 3.16
223 225 1.528309 ACAAACTGGCCGGAACTGG 60.528 57.895 21.41 5.26 0.00 4.00
241 243 0.744771 GGCCGAAATTCTCCGCTCTT 60.745 55.000 0.00 0.00 0.00 2.85
275 277 1.987855 CCGTACCAGAGGGCTCCAA 60.988 63.158 0.00 0.00 37.90 3.53
297 299 2.356432 CCATCAATCTCTTGTGGCTCCA 60.356 50.000 0.00 0.00 33.87 3.86
306 308 1.758440 TTGTGGCTCCAGCGAAGTCT 61.758 55.000 0.00 0.00 43.26 3.24
538 577 4.394712 CTCGGGTTTGCGGGCTCT 62.395 66.667 0.00 0.00 0.00 4.09
539 578 4.697756 TCGGGTTTGCGGGCTCTG 62.698 66.667 0.00 0.00 0.00 3.35
541 580 2.597510 GGGTTTGCGGGCTCTGTT 60.598 61.111 0.00 0.00 0.00 3.16
542 581 2.626780 GGGTTTGCGGGCTCTGTTC 61.627 63.158 0.00 0.00 0.00 3.18
543 582 2.626780 GGTTTGCGGGCTCTGTTCC 61.627 63.158 0.00 0.00 0.00 3.62
544 583 1.896660 GTTTGCGGGCTCTGTTCCA 60.897 57.895 0.00 0.00 0.00 3.53
583 622 4.442018 AAACCGCGGTTTTCTCGA 57.558 50.000 42.58 0.00 44.84 4.04
584 623 2.922779 AAACCGCGGTTTTCTCGAT 58.077 47.368 42.58 24.76 44.84 3.59
591 630 2.471743 CGCGGTTTTCTCGATCCTTATC 59.528 50.000 0.00 0.00 0.00 1.75
593 632 3.050619 CGGTTTTCTCGATCCTTATCCG 58.949 50.000 0.00 0.00 0.00 4.18
606 645 2.242965 CCTTATCCGGGGGTTTAAGGTT 59.757 50.000 0.00 0.00 36.20 3.50
607 646 3.548770 CTTATCCGGGGGTTTAAGGTTC 58.451 50.000 0.00 0.00 0.00 3.62
608 647 0.253894 ATCCGGGGGTTTAAGGTTCG 59.746 55.000 0.00 0.00 0.00 3.95
609 648 2.042259 CCGGGGGTTTAAGGTTCGC 61.042 63.158 0.00 0.00 0.00 4.70
610 649 1.302671 CGGGGGTTTAAGGTTCGCA 60.303 57.895 0.00 0.00 0.00 5.10
611 650 1.303091 CGGGGGTTTAAGGTTCGCAG 61.303 60.000 0.00 0.00 0.00 5.18
612 651 0.251033 GGGGGTTTAAGGTTCGCAGT 60.251 55.000 0.00 0.00 0.00 4.40
613 652 0.879090 GGGGTTTAAGGTTCGCAGTG 59.121 55.000 0.00 0.00 0.00 3.66
639 678 1.036707 GGTCCGCTAGAGATGCTCTT 58.963 55.000 1.88 0.00 41.50 2.85
640 679 2.158593 AGGTCCGCTAGAGATGCTCTTA 60.159 50.000 1.88 0.00 41.50 2.10
641 680 2.227865 GGTCCGCTAGAGATGCTCTTAG 59.772 54.545 1.88 0.64 41.50 2.18
642 681 1.883275 TCCGCTAGAGATGCTCTTAGC 59.117 52.381 1.88 8.49 41.50 3.09
643 682 1.885887 CCGCTAGAGATGCTCTTAGCT 59.114 52.381 16.38 0.00 42.97 3.32
644 683 2.095263 CCGCTAGAGATGCTCTTAGCTC 60.095 54.545 16.38 0.00 42.97 4.09
645 684 2.412716 CGCTAGAGATGCTCTTAGCTCG 60.413 54.545 16.38 0.00 42.97 5.03
646 685 2.552315 GCTAGAGATGCTCTTAGCTCGT 59.448 50.000 1.88 0.00 42.97 4.18
689 728 3.816523 TCGTTTTAACCCTGGTGTGATTC 59.183 43.478 0.00 0.00 0.00 2.52
1251 1415 4.424566 TTCACCTACGCCGCGGTC 62.425 66.667 28.70 18.03 0.00 4.79
1389 1553 1.683943 CCAAGTGCGGGATGATTGAT 58.316 50.000 0.00 0.00 0.00 2.57
1392 1556 1.959042 AGTGCGGGATGATTGATGAC 58.041 50.000 0.00 0.00 0.00 3.06
1455 1619 0.535780 CTTGGAACCTGCTGCTGTCA 60.536 55.000 0.00 0.00 0.00 3.58
1465 1629 1.371758 CTGCTGTCAGCGTACGTGT 60.372 57.895 19.68 1.34 46.26 4.49
1737 1901 1.031571 GCACCCCGAATCAGAATGCA 61.032 55.000 0.00 0.00 34.76 3.96
1853 2017 1.339727 GCTCCGGATGGGTGTAAAACT 60.340 52.381 3.57 0.00 37.00 2.66
1962 2126 3.433306 TTCAATGGGTTTCAGGACGAT 57.567 42.857 0.00 0.00 0.00 3.73
2090 2254 4.454678 ACATCCATGATTACAGCATTCGT 58.545 39.130 0.00 0.00 0.00 3.85
2190 2354 4.141846 ACCTTATCGAGTGTGATGAATGCT 60.142 41.667 0.00 0.00 0.00 3.79
2258 2422 0.389948 ACGGTCAAATCTGGACTCGC 60.390 55.000 0.00 0.00 34.50 5.03
2342 2506 3.434984 GCTTCAAAGAAGACATTCGAGCT 59.565 43.478 10.72 0.00 40.58 4.09
2771 2940 1.994779 GTTGTGCAATGCAACATAGCC 59.005 47.619 10.44 0.00 43.91 3.93
2776 2945 2.094597 TGCAATGCAACATAGCCAAGTC 60.095 45.455 5.01 0.00 34.76 3.01
2818 2987 3.070115 AATGCCCCACATTCTTGCA 57.930 47.368 0.00 0.00 46.28 4.08
2972 3144 6.741724 ACCTTTCCTAATTACCAATGTCCAT 58.258 36.000 0.00 0.00 0.00 3.41
2981 3153 1.272092 ACCAATGTCCATGGACTGGTG 60.272 52.381 38.85 31.63 46.08 4.17
3071 3243 3.073274 AGTTTGACATACCCTTCCTGC 57.927 47.619 0.00 0.00 0.00 4.85
3096 3268 7.756722 GCACAAAATTATGTATGCTCAGAACTT 59.243 33.333 0.00 0.00 30.84 2.66
3127 3299 9.903682 GTATGATGCTAATTGAATAATGTGCTT 57.096 29.630 0.00 0.00 0.00 3.91
3150 3322 7.335171 GCTTTAAAGGAACGTTAGAAATAGGGA 59.665 37.037 16.78 0.00 33.29 4.20
3151 3323 8.782339 TTTAAAGGAACGTTAGAAATAGGGAG 57.218 34.615 0.00 0.00 33.29 4.30
3511 3683 2.236146 TGCTGTACAACCTCTACATGGG 59.764 50.000 0.00 0.00 0.00 4.00
3843 4015 2.616256 CCATCTGCTGCTCCTGTAACAA 60.616 50.000 0.00 0.00 0.00 2.83
4192 4398 5.462068 GCTGTGAACATGTAGCATACGATTA 59.538 40.000 12.46 0.00 46.99 1.75
4261 4467 1.004277 CACACGTCTCGAGCTGTTCC 61.004 60.000 7.81 0.00 0.00 3.62
4296 4502 1.673168 GTGGGATTGCTGGAGATGTC 58.327 55.000 0.00 0.00 0.00 3.06
4301 4507 2.356535 GGATTGCTGGAGATGTCAAGGT 60.357 50.000 0.00 0.00 0.00 3.50
4391 4597 4.044336 CAAAATGTGCTGACCTGAACAA 57.956 40.909 0.00 0.00 0.00 2.83
4449 4656 2.167219 CCCATCTGCAGCACGTACG 61.167 63.158 15.01 15.01 0.00 3.67
4513 4720 6.581388 AATATTGAGAAGTTCCTGATGGGA 57.419 37.500 0.00 0.00 43.41 4.37
4762 4975 7.153315 TGGTGTACATTCGTGTTTTAGATACA 58.847 34.615 0.00 0.00 0.00 2.29
4763 4976 7.656542 TGGTGTACATTCGTGTTTTAGATACAA 59.343 33.333 0.00 0.00 0.00 2.41
4775 4988 7.542130 GTGTTTTAGATACAAAAATGCAGGAGG 59.458 37.037 0.00 0.00 0.00 4.30
4778 4991 5.649782 AGATACAAAAATGCAGGAGGTTG 57.350 39.130 0.00 0.00 0.00 3.77
4815 5030 9.512588 AAACACATCATTCTCTTCAGACTTAAT 57.487 29.630 0.00 0.00 0.00 1.40
4917 5132 2.879026 GGTGAAGGAGGTGTTTCTTGAC 59.121 50.000 0.00 0.00 0.00 3.18
4929 5144 1.865865 TTCTTGACTCTGCCGACAAC 58.134 50.000 0.00 0.00 0.00 3.32
4940 5155 2.616842 CTGCCGACAACTGTTAAAACCT 59.383 45.455 0.00 0.00 0.00 3.50
4944 5159 4.865925 GCCGACAACTGTTAAAACCTTTTT 59.134 37.500 0.00 0.00 0.00 1.94
4966 5181 4.695217 TTTTTGCGAGAAGACAACTGTT 57.305 36.364 0.00 0.00 0.00 3.16
4967 5182 5.804692 TTTTTGCGAGAAGACAACTGTTA 57.195 34.783 0.00 0.00 0.00 2.41
4968 5183 5.804692 TTTTGCGAGAAGACAACTGTTAA 57.195 34.783 0.00 0.00 0.00 2.01
4969 5184 5.804692 TTTGCGAGAAGACAACTGTTAAA 57.195 34.783 0.00 0.00 0.00 1.52
4970 5185 5.804692 TTGCGAGAAGACAACTGTTAAAA 57.195 34.783 0.00 0.00 0.00 1.52
4971 5186 5.151632 TGCGAGAAGACAACTGTTAAAAC 57.848 39.130 0.00 0.00 0.00 2.43
4972 5187 4.034742 TGCGAGAAGACAACTGTTAAAACC 59.965 41.667 0.00 0.00 0.00 3.27
4973 5188 4.554134 GCGAGAAGACAACTGTTAAAACCC 60.554 45.833 0.00 0.00 0.00 4.11
4974 5189 4.814771 CGAGAAGACAACTGTTAAAACCCT 59.185 41.667 0.00 0.00 0.00 4.34
4975 5190 5.277345 CGAGAAGACAACTGTTAAAACCCTG 60.277 44.000 0.00 0.00 0.00 4.45
4976 5191 4.887655 AGAAGACAACTGTTAAAACCCTGG 59.112 41.667 0.00 0.00 0.00 4.45
4977 5192 4.513406 AGACAACTGTTAAAACCCTGGA 57.487 40.909 0.00 0.00 0.00 3.86
4978 5193 4.862371 AGACAACTGTTAAAACCCTGGAA 58.138 39.130 0.00 0.00 0.00 3.53
4979 5194 5.454966 AGACAACTGTTAAAACCCTGGAAT 58.545 37.500 0.00 0.00 0.00 3.01
4980 5195 5.897250 AGACAACTGTTAAAACCCTGGAATT 59.103 36.000 0.00 0.00 0.00 2.17
4981 5196 6.382859 AGACAACTGTTAAAACCCTGGAATTT 59.617 34.615 0.00 0.00 0.00 1.82
4982 5197 7.562088 AGACAACTGTTAAAACCCTGGAATTTA 59.438 33.333 0.00 0.00 0.00 1.40
4983 5198 8.257602 ACAACTGTTAAAACCCTGGAATTTAT 57.742 30.769 0.00 0.00 0.00 1.40
4984 5199 9.369672 ACAACTGTTAAAACCCTGGAATTTATA 57.630 29.630 0.00 0.00 0.00 0.98
4987 5202 9.369672 ACTGTTAAAACCCTGGAATTTATAACA 57.630 29.630 17.43 17.43 0.00 2.41
4988 5203 9.634163 CTGTTAAAACCCTGGAATTTATAACAC 57.366 33.333 0.00 0.00 0.00 3.32
4989 5204 9.144298 TGTTAAAACCCTGGAATTTATAACACA 57.856 29.630 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.036616 GGTTTGGCGTTTTTAAGGTGTCTA 59.963 41.667 0.00 0.00 0.00 2.59
35 36 2.761767 ACAGGTTTGGCGTTTTTAAGGT 59.238 40.909 0.00 0.00 0.00 3.50
89 90 3.885297 CAGGGTCTGTTCTGAACACAAAT 59.115 43.478 18.69 2.48 36.25 2.32
116 117 5.351233 AATTGTTTACGATTCAGCGAACA 57.649 34.783 0.00 0.00 34.83 3.18
123 124 5.473846 TGGCCTGTAAATTGTTTACGATTCA 59.526 36.000 3.32 2.88 46.53 2.57
136 137 1.538075 CGTTTTCGGTGGCCTGTAAAT 59.462 47.619 3.32 0.00 39.94 1.40
220 222 3.102097 GCGGAGAATTTCGGCCAG 58.898 61.111 2.24 0.00 44.02 4.85
224 226 1.661112 GTGAAGAGCGGAGAATTTCGG 59.339 52.381 0.00 0.00 0.00 4.30
225 227 1.321743 CGTGAAGAGCGGAGAATTTCG 59.678 52.381 0.00 0.00 0.00 3.46
226 228 1.061276 GCGTGAAGAGCGGAGAATTTC 59.939 52.381 0.00 0.00 0.00 2.17
227 229 1.079503 GCGTGAAGAGCGGAGAATTT 58.920 50.000 0.00 0.00 0.00 1.82
228 230 2.755929 GCGTGAAGAGCGGAGAATT 58.244 52.632 0.00 0.00 0.00 2.17
229 231 4.504132 GCGTGAAGAGCGGAGAAT 57.496 55.556 0.00 0.00 0.00 2.40
275 277 2.356535 GGAGCCACAAGAGATTGATGGT 60.357 50.000 0.00 0.00 32.71 3.55
306 308 2.370849 AGGAAACGTAAAGAGAAGGCCA 59.629 45.455 5.01 0.00 0.00 5.36
360 362 1.376609 GGCGCCGTGAGAAATTGGAT 61.377 55.000 12.58 0.00 0.00 3.41
397 399 4.738998 CTGACCCATGCCCGCCAA 62.739 66.667 0.00 0.00 0.00 4.52
406 408 0.463295 CGCTCAGATTGCTGACCCAT 60.463 55.000 0.00 0.00 45.88 4.00
407 409 1.078918 CGCTCAGATTGCTGACCCA 60.079 57.895 0.00 0.00 45.88 4.51
412 451 2.816958 ACGCCGCTCAGATTGCTG 60.817 61.111 0.00 0.00 43.67 4.41
489 528 4.438200 GAGAATATTCTCCGAGATCCTCGC 60.438 50.000 28.23 5.42 46.20 5.03
502 541 5.290386 CCGAGCGGTAAAAGAGAATATTCT 58.710 41.667 17.96 17.96 41.00 2.40
503 542 4.448060 CCCGAGCGGTAAAAGAGAATATTC 59.552 45.833 7.41 7.41 0.00 1.75
529 568 4.329545 GGTGGAACAGAGCCCGCA 62.330 66.667 0.00 0.00 41.80 5.69
532 571 4.329545 TGCGGTGGAACAGAGCCC 62.330 66.667 0.00 0.00 41.80 5.19
533 572 2.743928 CTGCGGTGGAACAGAGCC 60.744 66.667 0.00 0.00 41.80 4.70
534 573 3.426568 GCTGCGGTGGAACAGAGC 61.427 66.667 0.00 0.00 41.80 4.09
536 575 4.680237 CGGCTGCGGTGGAACAGA 62.680 66.667 0.00 0.00 41.80 3.41
537 576 3.958147 ATCGGCTGCGGTGGAACAG 62.958 63.158 7.10 0.00 41.80 3.16
538 577 3.545124 AATCGGCTGCGGTGGAACA 62.545 57.895 7.10 0.00 39.98 3.18
539 578 2.253414 GAAATCGGCTGCGGTGGAAC 62.253 60.000 7.10 0.00 0.00 3.62
540 579 2.033448 AAATCGGCTGCGGTGGAA 59.967 55.556 7.10 0.00 0.00 3.53
541 580 2.435938 GAAATCGGCTGCGGTGGA 60.436 61.111 7.10 0.00 0.00 4.02
542 581 3.864686 CGAAATCGGCTGCGGTGG 61.865 66.667 7.10 0.00 35.37 4.61
561 600 2.221517 CGAGAAAACCGCGGTTTAAAGA 59.778 45.455 45.99 0.00 46.22 2.52
583 622 2.714793 CCTTAAACCCCCGGATAAGGAT 59.285 50.000 17.68 1.76 42.51 3.24
584 623 2.129363 CCTTAAACCCCCGGATAAGGA 58.871 52.381 17.68 0.00 42.51 3.36
591 630 2.042259 GCGAACCTTAAACCCCCGG 61.042 63.158 0.00 0.00 0.00 5.73
593 632 0.251033 ACTGCGAACCTTAAACCCCC 60.251 55.000 0.00 0.00 0.00 5.40
606 645 1.582968 GGACCTCGTAACACTGCGA 59.417 57.895 0.00 0.00 37.34 5.10
607 646 1.800315 CGGACCTCGTAACACTGCG 60.800 63.158 0.00 0.00 0.00 5.18
608 647 2.092882 GCGGACCTCGTAACACTGC 61.093 63.158 0.00 0.00 41.72 4.40
609 648 0.806868 TAGCGGACCTCGTAACACTG 59.193 55.000 0.00 0.00 41.72 3.66
610 649 1.093159 CTAGCGGACCTCGTAACACT 58.907 55.000 0.00 0.00 41.72 3.55
611 650 1.063764 CTCTAGCGGACCTCGTAACAC 59.936 57.143 0.00 0.00 41.72 3.32
612 651 1.065926 TCTCTAGCGGACCTCGTAACA 60.066 52.381 0.00 0.00 41.72 2.41
613 652 1.661341 TCTCTAGCGGACCTCGTAAC 58.339 55.000 0.00 0.00 41.72 2.50
659 698 6.265876 ACACCAGGGTTAAAACGATTTACATT 59.734 34.615 0.00 0.00 30.86 2.71
668 707 3.057806 GGAATCACACCAGGGTTAAAACG 60.058 47.826 0.00 0.00 0.00 3.60
689 728 1.072331 ACAGCCTCCAAACTACTGTGG 59.928 52.381 0.00 0.00 39.97 4.17
976 1140 4.284550 GTGGGTCAGCCTGGCCAA 62.285 66.667 18.72 1.81 45.98 4.52
1337 1501 1.366366 ACGGAGTTGGTCAGGAACG 59.634 57.895 0.00 0.00 37.78 3.95
1389 1553 1.069090 GAACACCAGCCTCACGTCA 59.931 57.895 0.00 0.00 0.00 4.35
1392 1556 2.022129 GTCGAACACCAGCCTCACG 61.022 63.158 0.00 0.00 0.00 4.35
1437 1601 0.535780 CTGACAGCAGCAGGTTCCAA 60.536 55.000 0.00 0.00 34.95 3.53
1455 1619 2.434185 CCCATGCACACGTACGCT 60.434 61.111 16.72 0.00 0.00 5.07
1721 1885 1.019673 CACTGCATTCTGATTCGGGG 58.980 55.000 0.00 0.00 0.00 5.73
1737 1901 0.398696 TCATGGCACCGTAAACCACT 59.601 50.000 0.00 0.00 35.99 4.00
1853 2017 5.123227 CACTCTTGAAAGTAAACCTGGACA 58.877 41.667 0.00 0.00 0.00 4.02
1962 2126 2.096335 CAGCGCATTTGCTATGAACTCA 59.904 45.455 11.47 0.00 45.23 3.41
2090 2254 5.393787 GCCTTCTCAAAATTCTCATCATGCA 60.394 40.000 0.00 0.00 0.00 3.96
2190 2354 1.273606 GGTAGACTCAGAGCAGCACAA 59.726 52.381 0.00 0.00 0.00 3.33
2258 2422 1.835483 GCCGCACACAGTGAACTGAG 61.835 60.000 17.11 11.51 46.59 3.35
2677 2846 5.741388 AGGATGAGTTGAATATTGAACGC 57.259 39.130 13.14 13.14 29.32 4.84
2771 2940 6.428385 AATCGATTTTTGGAGCTAGACTTG 57.572 37.500 4.39 0.00 0.00 3.16
2776 2945 4.142403 TGGCAAATCGATTTTTGGAGCTAG 60.142 41.667 20.56 7.56 37.13 3.42
2886 3058 3.042059 TCCAATCTGGAGGGTAGGTAC 57.958 52.381 0.00 0.00 42.67 3.34
2972 3144 2.234661 GTCTGATGATCACACCAGTCCA 59.765 50.000 16.44 1.47 0.00 4.02
2981 3153 6.036517 GGTGTTACTTCATGTCTGATGATCAC 59.963 42.308 0.00 0.00 32.37 3.06
3118 3290 7.966246 TCTAACGTTCCTTTAAAGCACATTA 57.034 32.000 2.82 6.85 0.00 1.90
3127 3299 7.038088 ACCTCCCTATTTCTAACGTTCCTTTAA 60.038 37.037 2.82 0.00 0.00 1.52
3150 3322 1.292242 TGCCAGGAATAGAGGAGACCT 59.708 52.381 0.00 0.00 36.03 3.85
3151 3323 1.414550 GTGCCAGGAATAGAGGAGACC 59.585 57.143 0.00 0.00 0.00 3.85
3164 3336 4.530875 AGAAATTGGATAGAAGTGCCAGG 58.469 43.478 0.00 0.00 32.47 4.45
3511 3683 1.632422 CAATGAGATTTTGCCGGCAC 58.368 50.000 32.95 18.64 0.00 5.01
3843 4015 7.037730 CCAGGATATCCTCTGGTTCTTCATAAT 60.038 40.741 22.02 0.00 46.65 1.28
4192 4398 3.285484 GGAGTTGGACATCATCAAGCAT 58.715 45.455 0.00 0.00 0.00 3.79
4261 4467 1.081892 CCACGGTTTCAGCAGAGATG 58.918 55.000 0.00 0.00 0.00 2.90
4296 4502 0.908198 AGGGAAGCAGCTCTACCTTG 59.092 55.000 0.00 0.00 30.70 3.61
4301 4507 4.135293 TGCAGGGAAGCAGCTCTA 57.865 55.556 0.00 0.00 40.11 2.43
4391 4597 2.127232 AAAAACAGCAGCTGCCGGT 61.127 52.632 34.39 28.46 43.38 5.28
4513 4720 3.003275 TCGTTTCGCAATGAGCTTTTCTT 59.997 39.130 0.00 0.00 42.61 2.52
4587 4800 3.188159 ACCTACGTCAGACTGCAAAAA 57.812 42.857 0.00 0.00 0.00 1.94
4588 4801 2.902705 ACCTACGTCAGACTGCAAAA 57.097 45.000 0.00 0.00 0.00 2.44
4589 4802 2.902705 AACCTACGTCAGACTGCAAA 57.097 45.000 0.00 0.00 0.00 3.68
4590 4803 2.624364 TGTAACCTACGTCAGACTGCAA 59.376 45.455 0.00 0.00 0.00 4.08
4591 4804 2.228103 CTGTAACCTACGTCAGACTGCA 59.772 50.000 0.00 0.00 0.00 4.41
4593 4806 2.818432 ACCTGTAACCTACGTCAGACTG 59.182 50.000 0.00 0.00 0.00 3.51
4594 4807 3.151912 ACCTGTAACCTACGTCAGACT 57.848 47.619 0.00 0.00 0.00 3.24
4595 4808 5.819901 ACTATACCTGTAACCTACGTCAGAC 59.180 44.000 0.00 0.00 0.00 3.51
4596 4809 5.994250 ACTATACCTGTAACCTACGTCAGA 58.006 41.667 0.00 0.00 0.00 3.27
4661 4874 9.017669 GCAATTTCAGATCAAAAGCTATGTAAG 57.982 33.333 0.00 0.00 0.00 2.34
4677 4890 9.420118 ACAAGGGTATATAAATGCAATTTCAGA 57.580 29.630 0.00 0.00 44.81 3.27
4736 4949 7.820386 TGTATCTAAAACACGAATGTACACCAT 59.180 33.333 0.00 0.00 38.45 3.55
4775 4988 5.042593 TGATGTGTTTTGAATCAGTGCAAC 58.957 37.500 0.00 0.00 0.00 4.17
4778 4991 6.154445 AGAATGATGTGTTTTGAATCAGTGC 58.846 36.000 0.00 0.00 34.02 4.40
4879 5094 0.992695 ACCCTAAAAGGTGAGAGGCC 59.007 55.000 0.00 0.00 39.24 5.19
4917 5132 3.303791 GGTTTTAACAGTTGTCGGCAGAG 60.304 47.826 0.00 0.00 0.00 3.35
4945 5160 4.695217 AACAGTTGTCTTCTCGCAAAAA 57.305 36.364 0.00 0.00 0.00 1.94
4946 5161 5.804692 TTAACAGTTGTCTTCTCGCAAAA 57.195 34.783 0.00 0.00 0.00 2.44
4947 5162 5.804692 TTTAACAGTTGTCTTCTCGCAAA 57.195 34.783 0.00 0.00 0.00 3.68
4948 5163 5.448089 GGTTTTAACAGTTGTCTTCTCGCAA 60.448 40.000 0.00 0.00 0.00 4.85
4949 5164 4.034742 GGTTTTAACAGTTGTCTTCTCGCA 59.965 41.667 0.00 0.00 0.00 5.10
4950 5165 4.524749 GGTTTTAACAGTTGTCTTCTCGC 58.475 43.478 0.00 0.00 0.00 5.03
4951 5166 4.814771 AGGGTTTTAACAGTTGTCTTCTCG 59.185 41.667 0.00 0.00 0.00 4.04
4952 5167 5.008712 CCAGGGTTTTAACAGTTGTCTTCTC 59.991 44.000 0.00 0.00 0.00 2.87
4953 5168 4.887655 CCAGGGTTTTAACAGTTGTCTTCT 59.112 41.667 0.00 0.00 0.00 2.85
4954 5169 4.885325 TCCAGGGTTTTAACAGTTGTCTTC 59.115 41.667 0.00 0.00 0.00 2.87
4955 5170 4.862371 TCCAGGGTTTTAACAGTTGTCTT 58.138 39.130 0.00 0.00 0.00 3.01
4956 5171 4.513406 TCCAGGGTTTTAACAGTTGTCT 57.487 40.909 0.00 0.00 0.00 3.41
4957 5172 5.784578 ATTCCAGGGTTTTAACAGTTGTC 57.215 39.130 0.00 0.00 0.00 3.18
4958 5173 6.553953 AAATTCCAGGGTTTTAACAGTTGT 57.446 33.333 0.00 0.00 0.00 3.32
4961 5176 9.369672 TGTTATAAATTCCAGGGTTTTAACAGT 57.630 29.630 13.86 0.00 0.00 3.55
4962 5177 9.634163 GTGTTATAAATTCCAGGGTTTTAACAG 57.366 33.333 15.84 0.00 30.71 3.16
4963 5178 9.144298 TGTGTTATAAATTCCAGGGTTTTAACA 57.856 29.630 13.86 13.86 0.00 2.41


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

AutoCloner maintained by Alex Coulton.