Multiple sequence alignment - TraesCS2B01G192600

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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 TraesCS2B01G192600 chr2B 100.000 5667 0 0 1 5667 168124159 168118493 0.000000e+00 10466.0
1 TraesCS2B01G192600 chr2B 98.628 5541 27 6 1 5539 168531508 168526015 0.000000e+00 9766.0
2 TraesCS2B01G192600 chr2B 100.000 1362 0 0 6004 7365 168118156 168116795 0.000000e+00 2516.0
3 TraesCS2B01G192600 chr2B 96.908 1035 14 2 6346 7365 168525564 168524533 0.000000e+00 1718.0
4 TraesCS2B01G192600 chr2B 99.077 325 3 0 6024 6348 168526022 168525698 1.060000e-162 584.0
5 TraesCS2B01G192600 chr2D 96.151 2936 104 7 2609 5539 117800015 117797084 0.000000e+00 4787.0
6 TraesCS2B01G192600 chr2D 96.328 1770 59 2 847 2616 117809419 117807656 0.000000e+00 2904.0
7 TraesCS2B01G192600 chr2D 90.116 1032 62 17 6346 7363 117796584 117795579 0.000000e+00 1304.0
8 TraesCS2B01G192600 chr2D 88.856 341 18 6 6024 6348 117797091 117796755 1.150000e-107 401.0
9 TraesCS2B01G192600 chr2D 98.438 128 1 1 5540 5667 492080593 492080467 2.670000e-54 224.0
10 TraesCS2B01G192600 chr2D 87.898 157 9 3 715 862 117810042 117809887 7.590000e-40 176.0
11 TraesCS2B01G192600 chr5D 90.580 552 50 2 6 555 445709564 445709013 0.000000e+00 730.0
12 TraesCS2B01G192600 chr5D 96.000 125 5 0 574 698 445709030 445708906 3.480000e-48 204.0
13 TraesCS2B01G192600 chr3B 85.968 677 76 5 6 679 697707668 697707008 0.000000e+00 706.0
14 TraesCS2B01G192600 chr3B 95.000 60 2 1 5607 5666 30475004 30474946 7.870000e-15 93.5
15 TraesCS2B01G192600 chr4D 89.305 561 53 2 6 559 509079460 509078900 0.000000e+00 697.0
16 TraesCS2B01G192600 chr1A 88.889 549 56 3 6 553 486699992 486699448 0.000000e+00 671.0
17 TraesCS2B01G192600 chr1A 97.458 118 2 1 5540 5657 555529560 555529676 4.510000e-47 200.0
18 TraesCS2B01G192600 chr1A 94.531 128 6 1 576 703 486699463 486699337 5.830000e-46 196.0
19 TraesCS2B01G192600 chr1A 85.034 147 17 5 7221 7363 193516078 193515933 2.140000e-30 145.0
20 TraesCS2B01G192600 chr6B 86.111 576 76 3 6 580 545404997 545404425 1.050000e-172 617.0
21 TraesCS2B01G192600 chr6B 96.094 128 4 1 5540 5667 599887787 599887661 2.690000e-49 207.0
22 TraesCS2B01G192600 chr6A 93.333 135 0 1 5540 5665 574228726 574228860 2.710000e-44 191.0
23 TraesCS2B01G192600 chr6A 92.473 93 3 2 5540 5630 62962786 62962696 6.000000e-26 130.0
24 TraesCS2B01G192600 chr5B 95.041 121 2 2 5542 5660 406529367 406529249 3.510000e-43 187.0
25 TraesCS2B01G192600 chr2A 86.667 135 15 3 5535 5667 134614898 134614765 5.950000e-31 147.0
26 TraesCS2B01G192600 chr1D 84.354 147 18 4 7221 7363 135663521 135663376 9.960000e-29 139.0
27 TraesCS2B01G192600 chr1B 83.673 147 19 4 7221 7363 215515191 215515046 4.640000e-27 134.0
28 TraesCS2B01G192600 chr1B 95.556 45 2 0 6037 6081 508392348 508392304 1.020000e-08 73.1
29 TraesCS2B01G192600 chr1B 91.837 49 4 0 6029 6077 44497715 44497763 1.330000e-07 69.4
30 TraesCS2B01G192600 chr1B 91.667 48 4 0 6034 6081 301273396 301273443 4.770000e-07 67.6
31 TraesCS2B01G192600 chr3D 100.000 43 0 0 5541 5583 164328485 164328527 6.130000e-11 80.5
32 TraesCS2B01G192600 chr7D 95.556 45 2 0 6033 6077 485833352 485833308 1.020000e-08 73.1
33 TraesCS2B01G192600 chr7B 95.556 45 2 0 6037 6081 216938230 216938274 1.020000e-08 73.1
34 TraesCS2B01G192600 chr7B 90.385 52 4 1 6030 6080 740536729 740536678 4.770000e-07 67.6
35 TraesCS2B01G192600 chr4B 95.349 43 0 2 6678 6720 339269331 339269371 4.770000e-07 67.6
36 TraesCS2B01G192600 chr3A 90.566 53 2 2 6033 6084 128524929 128524879 4.770000e-07 67.6
37 TraesCS2B01G192600 chrUn 100.000 34 0 0 5540 5573 30045922 30045955 6.170000e-06 63.9


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 TraesCS2B01G192600 chr2B 168116795 168124159 7364 True 6491.000000 10466 100.000000 1 7365 2 chr2B.!!$R1 7364
1 TraesCS2B01G192600 chr2B 168524533 168531508 6975 True 4022.666667 9766 98.204333 1 7365 3 chr2B.!!$R2 7364
2 TraesCS2B01G192600 chr2D 117795579 117800015 4436 True 2164.000000 4787 91.707667 2609 7363 3 chr2D.!!$R2 4754
3 TraesCS2B01G192600 chr2D 117807656 117810042 2386 True 1540.000000 2904 92.113000 715 2616 2 chr2D.!!$R3 1901
4 TraesCS2B01G192600 chr5D 445708906 445709564 658 True 467.000000 730 93.290000 6 698 2 chr5D.!!$R1 692
5 TraesCS2B01G192600 chr3B 697707008 697707668 660 True 706.000000 706 85.968000 6 679 1 chr3B.!!$R2 673
6 TraesCS2B01G192600 chr4D 509078900 509079460 560 True 697.000000 697 89.305000 6 559 1 chr4D.!!$R1 553
7 TraesCS2B01G192600 chr1A 486699337 486699992 655 True 433.500000 671 91.710000 6 703 2 chr1A.!!$R2 697
8 TraesCS2B01G192600 chr6B 545404425 545404997 572 True 617.000000 617 86.111000 6 580 1 chr6B.!!$R1 574

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
888 1406 0.321564 TTTGTGGCATCTGTCCTCGG 60.322 55.000 0.00 0.0 0.00 4.63 F
991 1509 0.326927 TCCTCACCCCCAATCGAAAC 59.673 55.000 0.00 0.0 0.00 2.78 F
2177 2714 1.071699 TCAAGCGCCTGTAGGTTCTTT 59.928 47.619 2.29 0.0 37.57 2.52 F
3179 3716 6.491062 TCAAGTGATCACAACCAGAAAATGAT 59.509 34.615 27.02 0.0 32.74 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2177 2714 4.362677 ACCTCCAAGACTTATGCTCCTTA 58.637 43.478 0.00 0.00 0.0 2.69 R
4756 5296 6.166279 GGTTGTACTCAAATGTCATCAGAGA 58.834 40.000 16.96 0.67 35.2 3.10 R
5539 6081 3.052082 CACCAAGCTCCGCCACTG 61.052 66.667 0.00 0.00 0.0 3.66 R
6513 7260 0.745845 CAGGGAAATGAGTGGCCGAG 60.746 60.000 0.00 0.00 0.0 4.63 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
36 37 1.697754 ACTCCCCCATCATCCACCC 60.698 63.158 0.00 0.00 0.00 4.61
53 54 1.212195 ACCCGGCTCCCTTTAATTCTC 59.788 52.381 0.00 0.00 0.00 2.87
144 151 4.096003 CGCAATCCTGGGTCGGGT 62.096 66.667 0.00 0.00 0.00 5.28
145 152 2.727392 CGCAATCCTGGGTCGGGTA 61.727 63.158 0.00 0.00 0.00 3.69
313 320 6.039829 CCCTTAACTGCCTCTAAATTTGATCC 59.960 42.308 0.00 0.00 0.00 3.36
504 512 2.932736 CCCTAGCGGGTCCTCCTA 59.067 66.667 0.00 0.00 46.12 2.94
545 573 2.393646 GGGATGTAGGCACTCTCTCTT 58.606 52.381 0.00 0.00 41.75 2.85
546 574 2.769095 GGGATGTAGGCACTCTCTCTTT 59.231 50.000 0.00 0.00 41.75 2.52
547 575 3.181470 GGGATGTAGGCACTCTCTCTTTC 60.181 52.174 0.00 0.00 41.75 2.62
548 576 3.704061 GGATGTAGGCACTCTCTCTTTCT 59.296 47.826 0.00 0.00 41.75 2.52
549 577 4.202111 GGATGTAGGCACTCTCTCTTTCTC 60.202 50.000 0.00 0.00 41.75 2.87
550 578 4.040936 TGTAGGCACTCTCTCTTTCTCT 57.959 45.455 0.00 0.00 41.75 3.10
551 579 4.013728 TGTAGGCACTCTCTCTTTCTCTC 58.986 47.826 0.00 0.00 41.75 3.20
552 580 3.456380 AGGCACTCTCTCTTTCTCTCT 57.544 47.619 0.00 0.00 0.00 3.10
553 581 3.356290 AGGCACTCTCTCTTTCTCTCTC 58.644 50.000 0.00 0.00 0.00 3.20
554 582 3.010584 AGGCACTCTCTCTTTCTCTCTCT 59.989 47.826 0.00 0.00 0.00 3.10
555 583 3.378427 GGCACTCTCTCTTTCTCTCTCTC 59.622 52.174 0.00 0.00 0.00 3.20
556 584 4.265073 GCACTCTCTCTTTCTCTCTCTCT 58.735 47.826 0.00 0.00 0.00 3.10
557 585 4.333926 GCACTCTCTCTTTCTCTCTCTCTC 59.666 50.000 0.00 0.00 0.00 3.20
558 586 5.738909 CACTCTCTCTTTCTCTCTCTCTCT 58.261 45.833 0.00 0.00 0.00 3.10
559 587 5.814705 CACTCTCTCTTTCTCTCTCTCTCTC 59.185 48.000 0.00 0.00 0.00 3.20
560 588 5.723887 ACTCTCTCTTTCTCTCTCTCTCTCT 59.276 44.000 0.00 0.00 0.00 3.10
561 589 6.127196 ACTCTCTCTTTCTCTCTCTCTCTCTC 60.127 46.154 0.00 0.00 0.00 3.20
562 590 5.960811 TCTCTCTTTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
563 591 6.097554 TCTCTCTTTCTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
564 592 5.721480 TCTCTTTCTCTCTCTCTCTCTCTCA 59.279 44.000 0.00 0.00 0.00 3.27
565 593 5.734720 TCTTTCTCTCTCTCTCTCTCTCAC 58.265 45.833 0.00 0.00 0.00 3.51
566 594 5.485353 TCTTTCTCTCTCTCTCTCTCTCACT 59.515 44.000 0.00 0.00 0.00 3.41
887 1405 1.667724 GATTTGTGGCATCTGTCCTCG 59.332 52.381 0.00 0.00 0.00 4.63
888 1406 0.321564 TTTGTGGCATCTGTCCTCGG 60.322 55.000 0.00 0.00 0.00 4.63
889 1407 2.512515 GTGGCATCTGTCCTCGGC 60.513 66.667 0.00 0.00 0.00 5.54
890 1408 3.002583 TGGCATCTGTCCTCGGCA 61.003 61.111 0.00 0.00 0.00 5.69
891 1409 2.512515 GGCATCTGTCCTCGGCAC 60.513 66.667 0.00 0.00 0.00 5.01
973 1491 1.305930 AAACCTCCCAAATCGCGCTC 61.306 55.000 5.56 0.00 0.00 5.03
974 1492 2.897350 CCTCCCAAATCGCGCTCC 60.897 66.667 5.56 0.00 0.00 4.70
975 1493 2.187946 CTCCCAAATCGCGCTCCT 59.812 61.111 5.56 0.00 0.00 3.69
976 1494 1.884926 CTCCCAAATCGCGCTCCTC 60.885 63.158 5.56 0.00 0.00 3.71
977 1495 2.125147 CCCAAATCGCGCTCCTCA 60.125 61.111 5.56 0.00 0.00 3.86
978 1496 2.464459 CCCAAATCGCGCTCCTCAC 61.464 63.158 5.56 0.00 0.00 3.51
979 1497 2.464459 CCAAATCGCGCTCCTCACC 61.464 63.158 5.56 0.00 0.00 4.02
980 1498 2.125106 AAATCGCGCTCCTCACCC 60.125 61.111 5.56 0.00 0.00 4.61
981 1499 3.682292 AAATCGCGCTCCTCACCCC 62.682 63.158 5.56 0.00 0.00 4.95
985 1503 4.115199 GCGCTCCTCACCCCCAAT 62.115 66.667 0.00 0.00 0.00 3.16
986 1504 2.190578 CGCTCCTCACCCCCAATC 59.809 66.667 0.00 0.00 0.00 2.67
987 1505 2.190578 GCTCCTCACCCCCAATCG 59.809 66.667 0.00 0.00 0.00 3.34
988 1506 2.367202 GCTCCTCACCCCCAATCGA 61.367 63.158 0.00 0.00 0.00 3.59
989 1507 1.910580 GCTCCTCACCCCCAATCGAA 61.911 60.000 0.00 0.00 0.00 3.71
990 1508 0.618458 CTCCTCACCCCCAATCGAAA 59.382 55.000 0.00 0.00 0.00 3.46
991 1509 0.326927 TCCTCACCCCCAATCGAAAC 59.673 55.000 0.00 0.00 0.00 2.78
2177 2714 1.071699 TCAAGCGCCTGTAGGTTCTTT 59.928 47.619 2.29 0.00 37.57 2.52
3179 3716 6.491062 TCAAGTGATCACAACCAGAAAATGAT 59.509 34.615 27.02 0.00 32.74 2.45
4756 5296 7.826252 CGGAAATATGGGATGATACTCTTCAAT 59.174 37.037 0.00 0.00 0.00 2.57
5539 6081 3.788937 ACCGTGTGCTACATAATGTACC 58.211 45.455 0.00 0.00 0.00 3.34
5540 6082 3.196039 ACCGTGTGCTACATAATGTACCA 59.804 43.478 0.00 0.00 0.00 3.25
5541 6083 3.802139 CCGTGTGCTACATAATGTACCAG 59.198 47.826 0.00 0.00 0.00 4.00
5542 6084 4.430007 CGTGTGCTACATAATGTACCAGT 58.570 43.478 0.00 0.00 0.00 4.00
5543 6085 4.267690 CGTGTGCTACATAATGTACCAGTG 59.732 45.833 0.00 0.00 0.00 3.66
5544 6086 4.570772 GTGTGCTACATAATGTACCAGTGG 59.429 45.833 7.91 7.91 0.00 4.00
5545 6087 3.560068 GTGCTACATAATGTACCAGTGGC 59.440 47.826 9.78 0.00 37.23 5.01
5546 6088 2.800544 GCTACATAATGTACCAGTGGCG 59.199 50.000 9.78 0.00 0.00 5.69
5547 6089 2.325583 ACATAATGTACCAGTGGCGG 57.674 50.000 9.78 0.00 0.00 6.13
5548 6090 1.834896 ACATAATGTACCAGTGGCGGA 59.165 47.619 9.78 0.00 0.00 5.54
5549 6091 2.158957 ACATAATGTACCAGTGGCGGAG 60.159 50.000 9.78 0.00 0.00 4.63
5564 6106 4.299796 GAGCTTGGTGGGGGCCAA 62.300 66.667 4.39 0.00 45.37 4.52
5565 6107 4.621087 AGCTTGGTGGGGGCCAAC 62.621 66.667 4.39 2.38 42.98 3.77
5567 6109 3.914713 CTTGGTGGGGGCCAACCT 61.915 66.667 23.54 0.00 41.25 3.50
5568 6110 4.232061 TTGGTGGGGGCCAACCTG 62.232 66.667 23.54 0.00 41.25 4.00
5636 6178 9.614792 CCTTAGTATTAGGCATATTTATCCACC 57.385 37.037 0.00 0.00 0.00 4.61
5640 6182 9.875708 AGTATTAGGCATATTTATCCACCAAAA 57.124 29.630 0.00 0.00 0.00 2.44
5644 6186 7.673641 AGGCATATTTATCCACCAAAAATCA 57.326 32.000 0.00 0.00 0.00 2.57
5645 6187 8.266363 AGGCATATTTATCCACCAAAAATCAT 57.734 30.769 0.00 0.00 0.00 2.45
5646 6188 8.716779 AGGCATATTTATCCACCAAAAATCATT 58.283 29.630 0.00 0.00 0.00 2.57
5647 6189 8.992073 GGCATATTTATCCACCAAAAATCATTC 58.008 33.333 0.00 0.00 0.00 2.67
5648 6190 9.545105 GCATATTTATCCACCAAAAATCATTCA 57.455 29.630 0.00 0.00 0.00 2.57
5655 6197 8.977267 ATCCACCAAAAATCATTCAAAAGAAA 57.023 26.923 0.00 0.00 0.00 2.52
5656 6198 8.977267 TCCACCAAAAATCATTCAAAAGAAAT 57.023 26.923 0.00 0.00 0.00 2.17
5657 6199 9.406113 TCCACCAAAAATCATTCAAAAGAAATT 57.594 25.926 0.00 0.00 0.00 1.82
6022 6564 3.123620 GCTCAAGCTCCGCCACTG 61.124 66.667 0.00 0.00 38.21 3.66
6023 6565 2.345244 CTCAAGCTCCGCCACTGT 59.655 61.111 0.00 0.00 0.00 3.55
6024 6566 1.591703 CTCAAGCTCCGCCACTGTA 59.408 57.895 0.00 0.00 0.00 2.74
6025 6567 0.037326 CTCAAGCTCCGCCACTGTAA 60.037 55.000 0.00 0.00 0.00 2.41
6026 6568 0.613260 TCAAGCTCCGCCACTGTAAT 59.387 50.000 0.00 0.00 0.00 1.89
6027 6569 0.729116 CAAGCTCCGCCACTGTAATG 59.271 55.000 0.00 0.00 0.00 1.90
6028 6570 0.324943 AAGCTCCGCCACTGTAATGT 59.675 50.000 0.00 0.00 0.00 2.71
6029 6571 1.191535 AGCTCCGCCACTGTAATGTA 58.808 50.000 0.00 0.00 0.00 2.29
6030 6572 1.134788 AGCTCCGCCACTGTAATGTAC 60.135 52.381 0.00 0.00 0.00 2.90
6164 6710 9.927081 ATATCACATCTCCTTTTCTAATTTGGT 57.073 29.630 0.00 0.00 0.00 3.67
6210 6756 6.237901 TGTAACATCATCTTTGCAGGTAGTT 58.762 36.000 0.00 0.00 0.00 2.24
6552 7299 1.952296 GCAGGCATACTTCCTTCCATG 59.048 52.381 0.00 0.00 0.00 3.66
6567 7314 1.702401 TCCATGAGGCCAACACTAACA 59.298 47.619 5.01 0.00 33.74 2.41
6782 7539 0.692419 TTGGCCTCCTGATCCTCCTC 60.692 60.000 3.32 0.00 0.00 3.71
7232 7992 2.632996 CCATGGACGTGATGTAGGGTAT 59.367 50.000 5.56 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 1.477014 GGGGAGAATTAAAGGGAGCCG 60.477 57.143 0.00 0.00 0.00 5.52
53 54 0.912486 AGGATTTTGAGTCCGAGGGG 59.088 55.000 0.00 0.00 40.76 4.79
144 151 3.712016 TTGTGGTGCTATGCTTCCTTA 57.288 42.857 0.00 0.00 0.00 2.69
145 152 2.584835 TTGTGGTGCTATGCTTCCTT 57.415 45.000 0.00 0.00 0.00 3.36
313 320 1.453155 CAGGACCATGGAAGGAAACG 58.547 55.000 21.47 0.00 0.00 3.60
504 512 2.419198 GGCACCGCGATCTCATCT 59.581 61.111 8.23 0.00 0.00 2.90
545 573 5.026121 AGAGTGAGAGAGAGAGAGAGAGAA 58.974 45.833 0.00 0.00 0.00 2.87
546 574 4.614475 AGAGTGAGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
547 575 4.648762 AGAGAGTGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
548 576 4.614475 AGAGAGTGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
549 577 4.648762 AGAGAGAGTGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
550 578 4.614475 AGAGAGAGTGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
551 579 4.648762 AGAGAGAGAGTGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
552 580 4.614475 AGAGAGAGAGTGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
553 581 4.648762 AGAGAGAGAGAGTGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
554 582 4.614475 AGAGAGAGAGAGTGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
555 583 4.648762 AGAGAGAGAGAGAGTGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
556 584 4.614475 AGAGAGAGAGAGAGTGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
557 585 4.648762 AGAGAGAGAGAGAGAGTGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
558 586 4.614475 AGAGAGAGAGAGAGAGTGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
559 587 4.648762 AGAGAGAGAGAGAGAGAGTGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
560 588 4.614475 AGAGAGAGAGAGAGAGAGTGAGA 58.386 47.826 0.00 0.00 0.00 3.27
561 589 4.648762 AGAGAGAGAGAGAGAGAGAGTGAG 59.351 50.000 0.00 0.00 0.00 3.51
562 590 4.614475 AGAGAGAGAGAGAGAGAGAGTGA 58.386 47.826 0.00 0.00 0.00 3.41
563 591 4.648762 AGAGAGAGAGAGAGAGAGAGAGTG 59.351 50.000 0.00 0.00 0.00 3.51
564 592 4.877773 AGAGAGAGAGAGAGAGAGAGAGT 58.122 47.826 0.00 0.00 0.00 3.24
565 593 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
566 594 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
887 1405 2.654912 CGAACGTTGAGTCGGTGCC 61.655 63.158 5.00 0.00 34.94 5.01
888 1406 2.654912 CCGAACGTTGAGTCGGTGC 61.655 63.158 16.45 0.00 38.13 5.01
889 1407 1.299620 ACCGAACGTTGAGTCGGTG 60.300 57.895 26.51 6.66 46.78 4.94
890 1408 3.122850 ACCGAACGTTGAGTCGGT 58.877 55.556 22.85 22.85 45.20 4.69
891 1409 0.239347 AGTACCGAACGTTGAGTCGG 59.761 55.000 21.62 21.62 43.88 4.79
973 1491 0.679960 GGTTTCGATTGGGGGTGAGG 60.680 60.000 0.00 0.00 0.00 3.86
974 1492 0.679960 GGGTTTCGATTGGGGGTGAG 60.680 60.000 0.00 0.00 0.00 3.51
975 1493 1.381076 GGGTTTCGATTGGGGGTGA 59.619 57.895 0.00 0.00 0.00 4.02
976 1494 0.540830 TTGGGTTTCGATTGGGGGTG 60.541 55.000 0.00 0.00 0.00 4.61
977 1495 0.541063 GTTGGGTTTCGATTGGGGGT 60.541 55.000 0.00 0.00 0.00 4.95
978 1496 1.254975 GGTTGGGTTTCGATTGGGGG 61.255 60.000 0.00 0.00 0.00 5.40
979 1497 0.540830 TGGTTGGGTTTCGATTGGGG 60.541 55.000 0.00 0.00 0.00 4.96
980 1498 1.000394 GTTGGTTGGGTTTCGATTGGG 60.000 52.381 0.00 0.00 0.00 4.12
981 1499 1.335506 CGTTGGTTGGGTTTCGATTGG 60.336 52.381 0.00 0.00 0.00 3.16
982 1500 1.928595 GCGTTGGTTGGGTTTCGATTG 60.929 52.381 0.00 0.00 0.00 2.67
983 1501 0.312729 GCGTTGGTTGGGTTTCGATT 59.687 50.000 0.00 0.00 0.00 3.34
984 1502 0.820074 TGCGTTGGTTGGGTTTCGAT 60.820 50.000 0.00 0.00 0.00 3.59
985 1503 1.451567 TGCGTTGGTTGGGTTTCGA 60.452 52.632 0.00 0.00 0.00 3.71
986 1504 1.298788 GTGCGTTGGTTGGGTTTCG 60.299 57.895 0.00 0.00 0.00 3.46
987 1505 1.066752 GGTGCGTTGGTTGGGTTTC 59.933 57.895 0.00 0.00 0.00 2.78
988 1506 2.776913 CGGTGCGTTGGTTGGGTTT 61.777 57.895 0.00 0.00 0.00 3.27
989 1507 3.213402 CGGTGCGTTGGTTGGGTT 61.213 61.111 0.00 0.00 0.00 4.11
990 1508 4.493049 ACGGTGCGTTGGTTGGGT 62.493 61.111 0.00 0.00 36.35 4.51
991 1509 3.656045 GACGGTGCGTTGGTTGGG 61.656 66.667 0.00 0.00 41.37 4.12
2177 2714 4.362677 ACCTCCAAGACTTATGCTCCTTA 58.637 43.478 0.00 0.00 0.00 2.69
4756 5296 6.166279 GGTTGTACTCAAATGTCATCAGAGA 58.834 40.000 16.96 0.67 35.20 3.10
5539 6081 3.052082 CACCAAGCTCCGCCACTG 61.052 66.667 0.00 0.00 0.00 3.66
5540 6082 4.335647 CCACCAAGCTCCGCCACT 62.336 66.667 0.00 0.00 0.00 4.00
5547 6089 4.299796 TTGGCCCCCACCAAGCTC 62.300 66.667 0.00 0.00 44.80 4.09
5610 6152 9.614792 GGTGGATAAATATGCCTAATACTAAGG 57.385 37.037 0.00 0.00 37.17 2.69
5614 6156 9.875708 TTTTGGTGGATAAATATGCCTAATACT 57.124 29.630 0.00 0.00 0.00 2.12
5618 6160 9.206690 TGATTTTTGGTGGATAAATATGCCTAA 57.793 29.630 0.00 0.00 0.00 2.69
5619 6161 8.774546 TGATTTTTGGTGGATAAATATGCCTA 57.225 30.769 0.00 0.00 0.00 3.93
5620 6162 7.673641 TGATTTTTGGTGGATAAATATGCCT 57.326 32.000 0.00 0.00 0.00 4.75
5621 6163 8.907222 AATGATTTTTGGTGGATAAATATGCC 57.093 30.769 0.00 0.00 0.00 4.40
5622 6164 9.545105 TGAATGATTTTTGGTGGATAAATATGC 57.455 29.630 0.00 0.00 0.00 3.14
5630 6172 8.977267 TTTCTTTTGAATGATTTTTGGTGGAT 57.023 26.923 0.00 0.00 38.37 3.41
5631 6173 8.977267 ATTTCTTTTGAATGATTTTTGGTGGA 57.023 26.923 0.00 0.00 38.37 4.02
6012 6554 2.961526 AGTACATTACAGTGGCGGAG 57.038 50.000 0.00 0.00 0.00 4.63
6013 6555 5.135383 ACTATAGTACATTACAGTGGCGGA 58.865 41.667 2.75 0.00 0.00 5.54
6014 6556 5.449107 ACTATAGTACATTACAGTGGCGG 57.551 43.478 2.75 0.00 0.00 6.13
6015 6557 5.919141 GGAACTATAGTACATTACAGTGGCG 59.081 44.000 5.65 0.00 0.00 5.69
6016 6558 7.052142 AGGAACTATAGTACATTACAGTGGC 57.948 40.000 5.65 0.00 36.02 5.01
6017 6559 7.861372 CGAAGGAACTATAGTACATTACAGTGG 59.139 40.741 5.65 0.00 38.49 4.00
6018 6560 8.404000 ACGAAGGAACTATAGTACATTACAGTG 58.596 37.037 5.65 0.00 38.49 3.66
6019 6561 8.517062 ACGAAGGAACTATAGTACATTACAGT 57.483 34.615 5.65 0.00 38.49 3.55
6020 6562 8.074972 GGACGAAGGAACTATAGTACATTACAG 58.925 40.741 5.65 0.00 38.49 2.74
6021 6563 7.254898 CGGACGAAGGAACTATAGTACATTACA 60.255 40.741 5.65 0.00 38.49 2.41
6022 6564 7.074502 CGGACGAAGGAACTATAGTACATTAC 58.925 42.308 5.65 0.00 38.49 1.89
6023 6565 6.205464 CCGGACGAAGGAACTATAGTACATTA 59.795 42.308 5.65 0.00 38.49 1.90
6024 6566 5.009410 CCGGACGAAGGAACTATAGTACATT 59.991 44.000 5.65 1.05 38.49 2.71
6025 6567 4.518211 CCGGACGAAGGAACTATAGTACAT 59.482 45.833 5.65 0.00 38.49 2.29
6026 6568 3.879295 CCGGACGAAGGAACTATAGTACA 59.121 47.826 5.65 0.00 38.49 2.90
6027 6569 4.130118 TCCGGACGAAGGAACTATAGTAC 58.870 47.826 5.65 2.59 38.49 2.73
6028 6570 4.422073 TCCGGACGAAGGAACTATAGTA 57.578 45.455 5.65 0.00 38.49 1.82
6029 6571 3.287867 TCCGGACGAAGGAACTATAGT 57.712 47.619 0.00 0.00 38.49 2.12
6164 6710 3.820467 AGATCAAAACTTGAATGCCGTCA 59.180 39.130 0.00 0.00 43.95 4.35
6513 7260 0.745845 CAGGGAAATGAGTGGCCGAG 60.746 60.000 0.00 0.00 0.00 4.63
6552 7299 1.200020 GCACATGTTAGTGTTGGCCTC 59.800 52.381 3.32 0.00 41.52 4.70
6567 7314 2.030007 CCAATCCAAACAGAACGCACAT 60.030 45.455 0.00 0.00 0.00 3.21
7115 7874 1.978617 CCACGAGGGCAAAAGCCAT 60.979 57.895 8.94 0.05 0.00 4.40


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

AutoCloner maintained by Alex Coulton.