Multiple sequence alignment - TraesCS6D01G285800

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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 TraesCS6D01G285800 chr6D 100.000 5007 0 0 1 5007 394554677 394559683 0.000000e+00 9247.0
1 TraesCS6D01G285800 chr6D 93.060 562 25 3 4 552 436423207 436422647 0.000000e+00 809.0
2 TraesCS6D01G285800 chr6D 88.153 574 40 11 1 552 253673303 253673870 0.000000e+00 658.0
3 TraesCS6D01G285800 chr6D 94.231 52 3 0 615 666 394548117 394548168 4.160000e-11 80.5
4 TraesCS6D01G285800 chr6B 96.526 3569 101 12 987 4542 590444863 590448421 0.000000e+00 5882.0
5 TraesCS6D01G285800 chr6B 89.310 580 40 9 4 563 125077319 125076742 0.000000e+00 708.0
6 TraesCS6D01G285800 chr6B 91.213 478 38 4 1 476 120129332 120129807 0.000000e+00 647.0
7 TraesCS6D01G285800 chr6B 90.192 469 33 9 4536 4998 590448578 590449039 2.580000e-167 599.0
8 TraesCS6D01G285800 chr6B 86.190 210 7 10 615 815 590444084 590444280 1.830000e-49 207.0
9 TraesCS6D01G285800 chr6A 95.292 2889 88 23 1915 4797 540602588 540605434 0.000000e+00 4538.0
10 TraesCS6D01G285800 chr6A 92.157 1224 70 14 678 1880 540601215 540602433 0.000000e+00 1705.0
11 TraesCS6D01G285800 chr3B 89.931 576 38 5 1 558 754854063 754854636 0.000000e+00 725.0
12 TraesCS6D01G285800 chr3B 93.939 66 4 0 4139 4204 130306142 130306077 3.190000e-17 100.0
13 TraesCS6D01G285800 chr3B 82.418 91 11 3 4692 4782 328545478 328545563 1.930000e-09 75.0
14 TraesCS6D01G285800 chr3B 82.895 76 12 1 4707 4782 150098554 150098480 3.230000e-07 67.6
15 TraesCS6D01G285800 chrUn 89.757 576 39 5 1 558 310310284 310310857 0.000000e+00 719.0
16 TraesCS6D01G285800 chrUn 89.878 573 38 5 4 558 315280092 315279522 0.000000e+00 719.0
17 TraesCS6D01G285800 chrUn 88.256 579 42 7 4 556 268822583 268822005 0.000000e+00 669.0
18 TraesCS6D01G285800 chrUn 88.144 582 43 7 1 556 268829105 268829686 0.000000e+00 669.0
19 TraesCS6D01G285800 chr1D 89.929 566 39 4 4 552 209092777 209092213 0.000000e+00 713.0
20 TraesCS6D01G285800 chr2B 88.989 554 47 12 4 548 10216624 10216076 0.000000e+00 673.0
21 TraesCS6D01G285800 chr2B 84.667 150 23 0 1023 1172 746041283 746041134 3.120000e-32 150.0
22 TraesCS6D01G285800 chr2B 95.918 49 2 0 4135 4183 17067097 17067049 4.160000e-11 80.5
23 TraesCS6D01G285800 chr1A 84.229 558 52 19 28 562 355040861 355040317 1.240000e-140 510.0
24 TraesCS6D01G285800 chr1A 83.604 555 53 15 28 562 528797907 528798443 2.100000e-133 486.0
25 TraesCS6D01G285800 chr5B 85.621 459 35 15 121 563 117266241 117265798 2.130000e-123 453.0
26 TraesCS6D01G285800 chr2D 88.755 249 12 4 325 558 649866436 649866683 1.760000e-74 291.0
27 TraesCS6D01G285800 chr2D 84.667 150 23 0 1023 1172 611163931 611163782 3.120000e-32 150.0
28 TraesCS6D01G285800 chr2D 92.308 52 4 0 4132 4183 11181688 11181739 1.930000e-09 75.0
29 TraesCS6D01G285800 chr1B 88.889 243 13 2 325 553 688545338 688545096 2.280000e-73 287.0
30 TraesCS6D01G285800 chr1B 75.954 262 37 12 4737 4985 486565085 486564837 1.470000e-20 111.0
31 TraesCS6D01G285800 chr2A 84.667 150 23 0 1023 1172 743392016 743391867 3.120000e-32 150.0
32 TraesCS6D01G285800 chr7B 84.615 91 9 3 4692 4782 7207306 7207391 8.930000e-13 86.1


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 TraesCS6D01G285800 chr6D 394554677 394559683 5006 False 9247.000000 9247 100.000000 1 5007 1 chr6D.!!$F3 5006
1 TraesCS6D01G285800 chr6D 436422647 436423207 560 True 809.000000 809 93.060000 4 552 1 chr6D.!!$R1 548
2 TraesCS6D01G285800 chr6D 253673303 253673870 567 False 658.000000 658 88.153000 1 552 1 chr6D.!!$F1 551
3 TraesCS6D01G285800 chr6B 590444084 590449039 4955 False 2229.333333 5882 90.969333 615 4998 3 chr6B.!!$F2 4383
4 TraesCS6D01G285800 chr6B 125076742 125077319 577 True 708.000000 708 89.310000 4 563 1 chr6B.!!$R1 559
5 TraesCS6D01G285800 chr6A 540601215 540605434 4219 False 3121.500000 4538 93.724500 678 4797 2 chr6A.!!$F1 4119
6 TraesCS6D01G285800 chr3B 754854063 754854636 573 False 725.000000 725 89.931000 1 558 1 chr3B.!!$F2 557
7 TraesCS6D01G285800 chrUn 310310284 310310857 573 False 719.000000 719 89.757000 1 558 1 chrUn.!!$F2 557
8 TraesCS6D01G285800 chrUn 315279522 315280092 570 True 719.000000 719 89.878000 4 558 1 chrUn.!!$R2 554
9 TraesCS6D01G285800 chrUn 268822005 268822583 578 True 669.000000 669 88.256000 4 556 1 chrUn.!!$R1 552
10 TraesCS6D01G285800 chrUn 268829105 268829686 581 False 669.000000 669 88.144000 1 556 1 chrUn.!!$F1 555
11 TraesCS6D01G285800 chr1D 209092213 209092777 564 True 713.000000 713 89.929000 4 552 1 chr1D.!!$R1 548
12 TraesCS6D01G285800 chr2B 10216076 10216624 548 True 673.000000 673 88.989000 4 548 1 chr2B.!!$R1 544
13 TraesCS6D01G285800 chr1A 355040317 355040861 544 True 510.000000 510 84.229000 28 562 1 chr1A.!!$R1 534
14 TraesCS6D01G285800 chr1A 528797907 528798443 536 False 486.000000 486 83.604000 28 562 1 chr1A.!!$F1 534

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
260 286 0.446616 TCGTGAGTTCGATCACTCCG 59.553 55.000 15.24 15.59 46.04 4.63 F
700 746 0.768622 TGTCAGGGTTCGGTGGATTT 59.231 50.000 0.00 0.00 0.00 2.17 F
1586 2065 0.251916 CCACTGTTTCGGCTATGGGA 59.748 55.000 0.00 0.00 0.00 4.37 F
3271 3871 1.697432 TCCGAAGAACTTGGTGATGGT 59.303 47.619 0.00 0.00 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1429 1908 1.191535 TCCCGTGACATTGGTAGGAG 58.808 55.000 0.0 0.0 0.00 3.69 R
1955 2555 1.913951 TAGGCACTCCTGCACATGGG 61.914 60.000 0.0 0.0 46.28 4.00 R
3454 4054 2.328319 TGCTTCTGGCTTTTCCCAAAT 58.672 42.857 0.0 0.0 42.39 2.32 R
4489 5107 0.108992 AGAAGCATGCGCACAAATGG 60.109 50.000 14.9 0.0 42.27 3.16 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
91 105 3.617540 TTGTTCACGTTGCCAAGTATG 57.382 42.857 0.00 0.00 0.00 2.39
260 286 0.446616 TCGTGAGTTCGATCACTCCG 59.553 55.000 15.24 15.59 46.04 4.63
267 293 3.542648 AGTTCGATCACTCCGATACTGA 58.457 45.455 0.00 0.00 35.84 3.41
270 296 1.876799 CGATCACTCCGATACTGAGCT 59.123 52.381 0.00 0.00 33.17 4.09
273 299 2.723273 TCACTCCGATACTGAGCTTGA 58.277 47.619 0.00 0.00 32.98 3.02
281 307 2.988010 TACTGAGCTTGATCCGCATT 57.012 45.000 6.83 0.00 0.00 3.56
357 384 1.667212 CAGTGATAGCTTTCATGCGCA 59.333 47.619 14.96 14.96 38.13 6.09
587 632 6.954616 CACATGTAATTTAGTGTGTACGGA 57.045 37.500 0.00 0.00 37.70 4.69
588 633 6.758149 CACATGTAATTTAGTGTGTACGGAC 58.242 40.000 0.00 0.00 37.70 4.79
589 634 6.588756 CACATGTAATTTAGTGTGTACGGACT 59.411 38.462 0.00 2.48 37.70 3.85
590 635 7.756272 CACATGTAATTTAGTGTGTACGGACTA 59.244 37.037 0.00 0.74 37.70 2.59
591 636 7.756722 ACATGTAATTTAGTGTGTACGGACTAC 59.243 37.037 0.00 0.00 0.00 2.73
592 637 7.452880 TGTAATTTAGTGTGTACGGACTACT 57.547 36.000 11.96 11.96 0.00 2.57
593 638 7.885297 TGTAATTTAGTGTGTACGGACTACTT 58.115 34.615 12.42 0.00 0.00 2.24
594 639 8.359642 TGTAATTTAGTGTGTACGGACTACTTT 58.640 33.333 12.42 5.39 0.00 2.66
595 640 9.840427 GTAATTTAGTGTGTACGGACTACTTTA 57.160 33.333 12.42 4.60 0.00 1.85
596 641 8.976986 AATTTAGTGTGTACGGACTACTTTAG 57.023 34.615 12.42 0.00 0.00 1.85
597 642 7.510549 TTTAGTGTGTACGGACTACTTTAGT 57.489 36.000 12.42 0.00 42.86 2.24
598 643 7.510549 TTAGTGTGTACGGACTACTTTAGTT 57.489 36.000 12.42 0.00 39.59 2.24
599 644 6.396829 AGTGTGTACGGACTACTTTAGTTT 57.603 37.500 0.00 0.00 39.59 2.66
600 645 6.809869 AGTGTGTACGGACTACTTTAGTTTT 58.190 36.000 0.00 0.00 39.59 2.43
601 646 7.940850 AGTGTGTACGGACTACTTTAGTTTTA 58.059 34.615 0.00 0.00 39.59 1.52
602 647 7.862873 AGTGTGTACGGACTACTTTAGTTTTAC 59.137 37.037 0.00 0.00 39.59 2.01
603 648 7.647715 GTGTGTACGGACTACTTTAGTTTTACA 59.352 37.037 0.00 0.00 39.59 2.41
604 649 7.862372 TGTGTACGGACTACTTTAGTTTTACAG 59.138 37.037 0.00 0.00 39.59 2.74
605 650 7.862873 GTGTACGGACTACTTTAGTTTTACAGT 59.137 37.037 0.00 0.00 39.59 3.55
606 651 8.413229 TGTACGGACTACTTTAGTTTTACAGTT 58.587 33.333 0.00 0.00 39.59 3.16
607 652 9.249457 GTACGGACTACTTTAGTTTTACAGTTT 57.751 33.333 0.00 0.00 39.59 2.66
608 653 8.722480 ACGGACTACTTTAGTTTTACAGTTTT 57.278 30.769 0.00 0.00 39.59 2.43
609 654 8.606602 ACGGACTACTTTAGTTTTACAGTTTTG 58.393 33.333 0.00 0.00 39.59 2.44
610 655 8.606602 CGGACTACTTTAGTTTTACAGTTTTGT 58.393 33.333 0.00 0.00 39.59 2.83
624 669 6.403866 ACAGTTTTGTATCAATTTCAGCCA 57.596 33.333 0.00 0.00 35.25 4.75
644 689 4.619973 CCAGAAACAAAATAAGCTGTGCA 58.380 39.130 0.00 0.00 0.00 4.57
665 711 7.066887 TGTGCATCTTTTGAGTTTTTCTCTACA 59.933 33.333 0.00 0.00 43.13 2.74
673 719 5.292765 TGAGTTTTTCTCTACAGCTGTCAG 58.707 41.667 25.56 20.03 43.13 3.51
674 720 4.636249 AGTTTTTCTCTACAGCTGTCAGG 58.364 43.478 25.56 14.81 0.00 3.86
675 721 4.101741 AGTTTTTCTCTACAGCTGTCAGGT 59.898 41.667 25.56 0.00 0.00 4.00
676 722 5.304614 AGTTTTTCTCTACAGCTGTCAGGTA 59.695 40.000 25.56 4.02 0.00 3.08
700 746 0.768622 TGTCAGGGTTCGGTGGATTT 59.231 50.000 0.00 0.00 0.00 2.17
739 785 5.425217 TCATCATGGGTGCGTATAGGATTAT 59.575 40.000 0.00 0.00 0.00 1.28
823 887 1.235724 CGTCCTTCCCTGGAAACAAC 58.764 55.000 0.00 0.00 42.06 3.32
861 926 4.711949 CAGGCAGGCAGGAACGCT 62.712 66.667 0.00 0.00 0.00 5.07
879 944 1.544759 GCTCTCGTTTTCCTTTCCCCA 60.545 52.381 0.00 0.00 0.00 4.96
890 955 1.550179 CCTTTCCCCACTTTTCCTCCC 60.550 57.143 0.00 0.00 0.00 4.30
1288 1765 1.424493 GCCTGCGTGAATTCCGAGAG 61.424 60.000 17.10 11.97 0.00 3.20
1309 1786 2.044946 GCGGTTCCAGGGCAGATT 60.045 61.111 0.00 0.00 0.00 2.40
1336 1813 2.677003 AATTCGAACTGGCGCGTGG 61.677 57.895 8.43 0.23 0.00 4.94
1353 1830 3.181537 GCGTGGTAGTATCGTGTGAAAAC 60.182 47.826 0.00 0.00 0.00 2.43
1357 1834 6.509837 CGTGGTAGTATCGTGTGAAAACAAAA 60.510 38.462 0.00 0.00 0.00 2.44
1417 1896 5.521735 CGATCAATCAGAGAGGATTTCGTTT 59.478 40.000 0.00 0.00 35.37 3.60
1429 1908 5.578776 AGGATTTCGTTTCAGTGTTTGTTC 58.421 37.500 0.00 0.00 0.00 3.18
1442 1921 5.049405 CAGTGTTTGTTCTCCTACCAATGTC 60.049 44.000 0.00 0.00 0.00 3.06
1555 2034 7.066404 GCTCTTCTTAACTAGGAATTTCAAGGG 59.934 40.741 0.00 0.00 0.00 3.95
1586 2065 0.251916 CCACTGTTTCGGCTATGGGA 59.748 55.000 0.00 0.00 0.00 4.37
1590 2069 2.835764 ACTGTTTCGGCTATGGGAGTTA 59.164 45.455 0.00 0.00 0.00 2.24
1855 2335 8.899771 CCGAATTTGGATAGTTGGTAGTAAATT 58.100 33.333 5.72 0.00 31.45 1.82
1945 2545 7.156673 GTGGTGTCACCTTACTCTAATTTGTA 58.843 38.462 22.56 0.00 39.58 2.41
3271 3871 1.697432 TCCGAAGAACTTGGTGATGGT 59.303 47.619 0.00 0.00 0.00 3.55
3454 4054 3.931907 ACAGCTGATATAAAGGCCACA 57.068 42.857 23.35 0.00 0.00 4.17
3952 4552 3.365868 GCATAGAATCTCTGATCGAGCGT 60.366 47.826 0.00 1.41 39.70 5.07
4097 4697 1.605710 CCCTTGTGCTTGAGTTCAGTG 59.394 52.381 0.00 0.00 0.00 3.66
4154 4754 7.186021 AGCAGTTATTAAATTCGGTTATCGG 57.814 36.000 0.00 0.00 39.77 4.18
4333 4942 9.618890 TCCTATAGAAGTCATTTGAATCAAAGG 57.381 33.333 13.48 13.48 36.76 3.11
4441 5059 4.829064 ATTGTACATGCAACTTTGACGT 57.171 36.364 0.00 0.00 0.00 4.34
4448 5066 0.040958 GCAACTTTGACGTGCCTGAG 60.041 55.000 0.00 0.00 0.00 3.35
4502 5120 1.289694 CACACCCATTTGTGCGCAT 59.710 52.632 15.91 0.00 40.51 4.73
4543 5337 5.136105 GTCAAGATTCATCCCCAGCTTAAT 58.864 41.667 0.00 0.00 0.00 1.40
4544 5338 6.126507 TGTCAAGATTCATCCCCAGCTTAATA 60.127 38.462 0.00 0.00 0.00 0.98
4545 5339 6.772716 GTCAAGATTCATCCCCAGCTTAATAA 59.227 38.462 0.00 0.00 0.00 1.40
4546 5340 7.449704 GTCAAGATTCATCCCCAGCTTAATAAT 59.550 37.037 0.00 0.00 0.00 1.28
4547 5341 7.449395 TCAAGATTCATCCCCAGCTTAATAATG 59.551 37.037 0.00 0.00 0.00 1.90
4548 5342 6.856757 AGATTCATCCCCAGCTTAATAATGT 58.143 36.000 0.00 0.00 0.00 2.71
4549 5343 6.944862 AGATTCATCCCCAGCTTAATAATGTC 59.055 38.462 0.00 0.00 0.00 3.06
4550 5344 5.645056 TCATCCCCAGCTTAATAATGTCA 57.355 39.130 0.00 0.00 0.00 3.58
4551 5345 5.376625 TCATCCCCAGCTTAATAATGTCAC 58.623 41.667 0.00 0.00 0.00 3.67
4552 5346 5.132648 TCATCCCCAGCTTAATAATGTCACT 59.867 40.000 0.00 0.00 0.00 3.41
4553 5347 5.450818 TCCCCAGCTTAATAATGTCACTT 57.549 39.130 0.00 0.00 0.00 3.16
4554 5348 6.569127 TCCCCAGCTTAATAATGTCACTTA 57.431 37.500 0.00 0.00 0.00 2.24
4563 5357 7.805071 GCTTAATAATGTCACTTATGATGTGGC 59.195 37.037 0.00 0.00 40.12 5.01
4574 5368 2.502142 TGATGTGGCATCTTTCTGCT 57.498 45.000 10.02 0.00 41.95 4.24
4582 5376 4.860907 GTGGCATCTTTCTGCTAATTTGTG 59.139 41.667 0.00 0.00 41.95 3.33
4599 5397 4.829064 TTGTGGAAGATAAACAGTGTGC 57.171 40.909 0.00 0.00 0.00 4.57
4613 5411 1.280421 AGTGTGCCTGGATTCTTCTCC 59.720 52.381 0.00 0.00 35.74 3.71
4631 5429 5.055265 TCTCCAAACATTTCCCAGTTGTA 57.945 39.130 0.00 0.00 0.00 2.41
4633 5431 5.894393 TCTCCAAACATTTCCCAGTTGTAAA 59.106 36.000 0.00 0.00 0.00 2.01
4663 5461 4.383850 TTGTGCTTGTGTTGCTGTTATT 57.616 36.364 0.00 0.00 0.00 1.40
4701 5499 3.146618 CTGCATCAGGCTGTGATTTTC 57.853 47.619 15.27 0.49 44.05 2.29
4704 5502 3.282021 GCATCAGGCTGTGATTTTCCTA 58.718 45.455 15.27 0.00 44.05 2.94
4705 5503 3.696051 GCATCAGGCTGTGATTTTCCTAA 59.304 43.478 15.27 0.00 44.05 2.69
4879 5677 5.202765 TGGATACTGCATGATTGGTTGATT 58.797 37.500 0.00 0.00 37.61 2.57
4890 5688 6.964807 TGATTGGTTGATTATGGGATCTTG 57.035 37.500 0.00 0.00 0.00 3.02
4892 5690 4.879295 TGGTTGATTATGGGATCTTGGT 57.121 40.909 0.00 0.00 0.00 3.67
4893 5691 5.985175 TGGTTGATTATGGGATCTTGGTA 57.015 39.130 0.00 0.00 0.00 3.25
4898 5697 8.793592 GGTTGATTATGGGATCTTGGTAAATAC 58.206 37.037 0.00 0.00 0.00 1.89
4967 5766 3.971245 AACAGATCAGGACTTCAGGAC 57.029 47.619 0.00 0.00 0.00 3.85
4998 5797 7.106439 AGTCCAAACAACATCAAAATGTACA 57.894 32.000 0.00 0.00 45.48 2.90
4999 5798 7.551585 AGTCCAAACAACATCAAAATGTACAA 58.448 30.769 0.00 0.00 45.48 2.41
5000 5799 7.491048 AGTCCAAACAACATCAAAATGTACAAC 59.509 33.333 0.00 0.00 45.48 3.32
5001 5800 6.758886 TCCAAACAACATCAAAATGTACAACC 59.241 34.615 0.00 0.00 45.48 3.77
5002 5801 6.292061 CCAAACAACATCAAAATGTACAACCG 60.292 38.462 0.00 0.00 45.48 4.44
5003 5802 5.759506 ACAACATCAAAATGTACAACCGA 57.240 34.783 0.00 0.00 45.48 4.69
5004 5803 5.516090 ACAACATCAAAATGTACAACCGAC 58.484 37.500 0.00 0.00 45.48 4.79
5005 5804 5.066634 ACAACATCAAAATGTACAACCGACA 59.933 36.000 0.00 0.00 45.48 4.35
5006 5805 5.957842 ACATCAAAATGTACAACCGACAT 57.042 34.783 0.00 0.00 44.38 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
184 201 1.539827 ACAAATGCGTTCTGCTAACCC 59.460 47.619 0.00 0.00 46.63 4.11
260 286 2.515926 TGCGGATCAAGCTCAGTATC 57.484 50.000 12.59 0.00 35.28 2.24
349 376 6.638063 GCATATTCTCTTTTATTTGCGCATGA 59.362 34.615 12.75 3.07 0.00 3.07
564 609 6.588756 AGTCCGTACACACTAAATTACATGTG 59.411 38.462 9.11 12.10 46.32 3.21
565 610 6.694447 AGTCCGTACACACTAAATTACATGT 58.306 36.000 2.69 2.69 0.00 3.21
566 611 7.972277 AGTAGTCCGTACACACTAAATTACATG 59.028 37.037 3.10 0.00 33.55 3.21
567 612 8.059798 AGTAGTCCGTACACACTAAATTACAT 57.940 34.615 3.10 0.00 33.55 2.29
568 613 7.452880 AGTAGTCCGTACACACTAAATTACA 57.547 36.000 3.10 0.00 33.55 2.41
569 614 8.748380 AAAGTAGTCCGTACACACTAAATTAC 57.252 34.615 3.10 0.00 33.55 1.89
571 616 8.579863 ACTAAAGTAGTCCGTACACACTAAATT 58.420 33.333 3.10 4.61 32.47 1.82
572 617 8.115490 ACTAAAGTAGTCCGTACACACTAAAT 57.885 34.615 3.10 0.00 32.47 1.40
573 618 7.510549 ACTAAAGTAGTCCGTACACACTAAA 57.489 36.000 3.10 0.00 32.47 1.85
574 619 7.510549 AACTAAAGTAGTCCGTACACACTAA 57.489 36.000 3.10 0.00 38.26 2.24
575 620 7.510549 AAACTAAAGTAGTCCGTACACACTA 57.489 36.000 0.00 0.00 38.26 2.74
576 621 6.396829 AAACTAAAGTAGTCCGTACACACT 57.603 37.500 0.00 0.00 38.26 3.55
577 622 7.647715 TGTAAAACTAAAGTAGTCCGTACACAC 59.352 37.037 0.00 0.00 38.26 3.82
578 623 7.711846 TGTAAAACTAAAGTAGTCCGTACACA 58.288 34.615 0.00 0.00 38.26 3.72
579 624 7.862873 ACTGTAAAACTAAAGTAGTCCGTACAC 59.137 37.037 0.00 0.00 38.26 2.90
580 625 7.940850 ACTGTAAAACTAAAGTAGTCCGTACA 58.059 34.615 0.00 0.00 38.26 2.90
581 626 8.803201 AACTGTAAAACTAAAGTAGTCCGTAC 57.197 34.615 0.00 0.00 38.26 3.67
582 627 9.816354 AAAACTGTAAAACTAAAGTAGTCCGTA 57.184 29.630 0.00 0.00 38.26 4.02
583 628 8.606602 CAAAACTGTAAAACTAAAGTAGTCCGT 58.393 33.333 0.00 0.00 38.26 4.69
584 629 8.606602 ACAAAACTGTAAAACTAAAGTAGTCCG 58.393 33.333 0.00 0.00 38.26 4.79
597 642 9.255304 GGCTGAAATTGATACAAAACTGTAAAA 57.745 29.630 0.00 0.00 0.00 1.52
598 643 8.417106 TGGCTGAAATTGATACAAAACTGTAAA 58.583 29.630 0.00 0.00 0.00 2.01
599 644 7.946207 TGGCTGAAATTGATACAAAACTGTAA 58.054 30.769 0.00 0.00 0.00 2.41
600 645 7.446931 TCTGGCTGAAATTGATACAAAACTGTA 59.553 33.333 0.00 0.00 0.00 2.74
601 646 6.265196 TCTGGCTGAAATTGATACAAAACTGT 59.735 34.615 0.00 0.00 0.00 3.55
602 647 6.680810 TCTGGCTGAAATTGATACAAAACTG 58.319 36.000 0.00 0.00 0.00 3.16
603 648 6.899393 TCTGGCTGAAATTGATACAAAACT 57.101 33.333 0.00 0.00 0.00 2.66
604 649 7.437862 TGTTTCTGGCTGAAATTGATACAAAAC 59.562 33.333 20.24 6.54 45.19 2.43
605 650 7.495901 TGTTTCTGGCTGAAATTGATACAAAA 58.504 30.769 20.24 0.00 45.19 2.44
606 651 7.048629 TGTTTCTGGCTGAAATTGATACAAA 57.951 32.000 20.24 0.00 45.19 2.83
607 652 6.647334 TGTTTCTGGCTGAAATTGATACAA 57.353 33.333 20.24 0.00 45.19 2.41
608 653 6.647334 TTGTTTCTGGCTGAAATTGATACA 57.353 33.333 20.24 11.67 45.19 2.29
609 654 7.945033 TTTTGTTTCTGGCTGAAATTGATAC 57.055 32.000 20.24 9.47 45.19 2.24
611 656 9.211485 CTTATTTTGTTTCTGGCTGAAATTGAT 57.789 29.630 20.24 14.34 45.19 2.57
612 657 7.171337 GCTTATTTTGTTTCTGGCTGAAATTGA 59.829 33.333 20.24 8.65 45.19 2.57
613 658 7.172019 AGCTTATTTTGTTTCTGGCTGAAATTG 59.828 33.333 20.24 7.86 45.19 2.32
624 669 6.336842 AGATGCACAGCTTATTTTGTTTCT 57.663 33.333 0.00 0.00 0.00 2.52
673 719 0.389948 CGAACCCTGACAGCTGTACC 60.390 60.000 21.73 9.17 0.00 3.34
674 720 0.389948 CCGAACCCTGACAGCTGTAC 60.390 60.000 21.73 13.90 0.00 2.90
675 721 0.830444 ACCGAACCCTGACAGCTGTA 60.830 55.000 21.73 7.57 0.00 2.74
676 722 2.140792 ACCGAACCCTGACAGCTGT 61.141 57.895 21.88 21.88 0.00 4.40
700 746 5.887598 CCCATGATGAGAACTGATTTTACCA 59.112 40.000 0.00 0.00 0.00 3.25
711 757 2.309528 TACGCACCCATGATGAGAAC 57.690 50.000 7.48 0.00 0.00 3.01
739 785 6.423905 GCAGTCAGTTATTACAGACAGTTTGA 59.576 38.462 9.61 0.00 41.69 2.69
764 818 2.621668 GGAAGGAGGGGGATTTTCACTG 60.622 54.545 0.00 0.00 0.00 3.66
809 873 1.151908 CGGGGTTGTTTCCAGGGAA 59.848 57.895 0.00 0.00 0.00 3.97
847 912 2.817396 GAGAGCGTTCCTGCCTGC 60.817 66.667 0.00 0.00 34.65 4.85
848 913 2.507992 CGAGAGCGTTCCTGCCTG 60.508 66.667 0.00 0.00 34.65 4.85
858 923 0.796927 GGGAAAGGAAAACGAGAGCG 59.203 55.000 0.00 0.00 44.79 5.03
861 926 1.772453 AGTGGGGAAAGGAAAACGAGA 59.228 47.619 0.00 0.00 0.00 4.04
871 936 1.429299 AGGGAGGAAAAGTGGGGAAAG 59.571 52.381 0.00 0.00 0.00 2.62
879 944 0.253327 GCGATGGAGGGAGGAAAAGT 59.747 55.000 0.00 0.00 0.00 2.66
1195 1672 5.609423 CAAGATCAATCAGGCTAGCTTAGT 58.391 41.667 15.72 0.00 0.00 2.24
1288 1765 2.361104 TGCCCTGGAACCGCATTC 60.361 61.111 0.00 0.00 36.48 2.67
1309 1786 1.333308 CCAGTTCGAATTGCACACACA 59.667 47.619 14.68 0.00 0.00 3.72
1336 1813 6.573725 CAGCTTTTGTTTTCACACGATACTAC 59.426 38.462 0.00 0.00 30.32 2.73
1353 1830 3.941483 AGGATACGAACATCCAGCTTTTG 59.059 43.478 14.75 0.00 46.04 2.44
1357 1834 2.111384 ACAGGATACGAACATCCAGCT 58.889 47.619 14.75 0.00 46.04 4.24
1398 1877 5.641209 CACTGAAACGAAATCCTCTCTGATT 59.359 40.000 0.00 0.00 36.53 2.57
1417 1896 4.764050 TTGGTAGGAGAACAAACACTGA 57.236 40.909 0.00 0.00 0.00 3.41
1429 1908 1.191535 TCCCGTGACATTGGTAGGAG 58.808 55.000 0.00 0.00 0.00 3.69
1442 1921 6.747280 CACAAAAGAAGCTAATTATTCCCGTG 59.253 38.462 0.00 0.00 0.00 4.94
1555 2034 5.234543 GCCGAAACAGTGGAGAGTATATTTC 59.765 44.000 0.00 0.00 0.00 2.17
1617 2096 4.335400 TTCTGGGGAAGAACAAAAATGC 57.665 40.909 0.00 0.00 40.09 3.56
1666 2146 4.624882 CAGAGACAGCAAAGACTGATACAC 59.375 45.833 0.00 0.00 40.25 2.90
1906 2386 4.081309 GTGACACCACAATAGCCCTTAGTA 60.081 45.833 0.00 0.00 42.72 1.82
1945 2545 3.094572 CCTGCACATGGGAAGAGAATTT 58.905 45.455 3.78 0.00 0.00 1.82
1955 2555 1.913951 TAGGCACTCCTGCACATGGG 61.914 60.000 0.00 0.00 46.28 4.00
3454 4054 2.328319 TGCTTCTGGCTTTTCCCAAAT 58.672 42.857 0.00 0.00 42.39 2.32
3952 4552 5.013079 TGCTTTGTCCCTCTCTAAGAATTCA 59.987 40.000 8.44 0.00 0.00 2.57
4097 4697 2.625790 TGGACAGTGCCCAACAAATAAC 59.374 45.455 0.00 0.00 0.00 1.89
4154 4754 4.201920 GGTAAAGCCTCCATTTCAATCGAC 60.202 45.833 0.00 0.00 0.00 4.20
4333 4942 1.745890 GGAACAAAACACAGGGCCC 59.254 57.895 16.46 16.46 0.00 5.80
4410 5019 9.624697 AAAGTTGCATGTACAATACAAATACTG 57.375 29.630 0.00 0.00 42.76 2.74
4441 5059 1.401761 ACACAATTTGCACTCAGGCA 58.598 45.000 0.00 0.00 43.19 4.75
4448 5066 3.504863 CAGGAGCATACACAATTTGCAC 58.495 45.455 2.16 0.00 38.84 4.57
4489 5107 0.108992 AGAAGCATGCGCACAAATGG 60.109 50.000 14.90 0.00 42.27 3.16
4502 5120 0.181114 ACACAGGCAGAACAGAAGCA 59.819 50.000 0.00 0.00 0.00 3.91
4543 5337 6.594744 AGATGCCACATCATAAGTGACATTA 58.405 36.000 10.02 0.00 39.64 1.90
4544 5338 5.443283 AGATGCCACATCATAAGTGACATT 58.557 37.500 10.02 0.00 39.64 2.71
4545 5339 5.045012 AGATGCCACATCATAAGTGACAT 57.955 39.130 10.02 0.00 41.73 3.06
4546 5340 4.492494 AGATGCCACATCATAAGTGACA 57.508 40.909 10.02 0.00 39.30 3.58
4547 5341 5.587844 AGAAAGATGCCACATCATAAGTGAC 59.412 40.000 10.02 0.00 39.30 3.67
4548 5342 5.587443 CAGAAAGATGCCACATCATAAGTGA 59.413 40.000 10.02 0.00 39.30 3.41
4549 5343 5.732528 GCAGAAAGATGCCACATCATAAGTG 60.733 44.000 10.02 0.00 40.43 3.16
4550 5344 4.337555 GCAGAAAGATGCCACATCATAAGT 59.662 41.667 10.02 0.00 40.43 2.24
4551 5345 4.856664 GCAGAAAGATGCCACATCATAAG 58.143 43.478 10.02 0.00 40.43 1.73
4552 5346 4.906065 GCAGAAAGATGCCACATCATAA 57.094 40.909 10.02 0.00 40.43 1.90
4563 5357 7.149569 TCTTCCACAAATTAGCAGAAAGATG 57.850 36.000 0.00 0.00 0.00 2.90
4574 5368 7.367285 GCACACTGTTTATCTTCCACAAATTA 58.633 34.615 0.00 0.00 0.00 1.40
4582 5376 2.749621 CCAGGCACACTGTTTATCTTCC 59.250 50.000 0.00 0.00 46.06 3.46
4613 5411 4.208253 GCGTTTACAACTGGGAAATGTTTG 59.792 41.667 0.00 0.00 0.00 2.93
4631 5429 0.887933 CAAGCACAATAGGGGCGTTT 59.112 50.000 0.00 0.00 0.00 3.60
4633 5431 0.960364 CACAAGCACAATAGGGGCGT 60.960 55.000 0.00 0.00 0.00 5.68
4643 5441 4.383850 AAATAACAGCAACACAAGCACA 57.616 36.364 0.00 0.00 0.00 4.57
4663 5461 6.489700 TGATGCAGTTCTTTATGGTTCAGAAA 59.510 34.615 0.00 0.00 0.00 2.52
4725 5523 3.486383 TGAATCCTGAACTTCGCCTTTT 58.514 40.909 0.00 0.00 0.00 2.27
4726 5524 3.077359 CTGAATCCTGAACTTCGCCTTT 58.923 45.455 0.00 0.00 0.00 3.11
4727 5525 2.039084 ACTGAATCCTGAACTTCGCCTT 59.961 45.455 0.00 0.00 0.00 4.35
4728 5526 1.625818 ACTGAATCCTGAACTTCGCCT 59.374 47.619 0.00 0.00 0.00 5.52
4729 5527 2.100605 ACTGAATCCTGAACTTCGCC 57.899 50.000 0.00 0.00 0.00 5.54
4730 5528 3.498397 TGAAACTGAATCCTGAACTTCGC 59.502 43.478 0.00 0.00 0.00 4.70
4731 5529 5.869753 ATGAAACTGAATCCTGAACTTCG 57.130 39.130 0.00 0.00 0.00 3.79
4732 5530 8.950210 TGAATATGAAACTGAATCCTGAACTTC 58.050 33.333 0.00 0.00 0.00 3.01
4739 5537 7.417116 GGCATTGTGAATATGAAACTGAATCCT 60.417 37.037 0.00 0.00 0.00 3.24
4780 5578 1.003233 CCACTTCCTGTTCCTGTACCC 59.997 57.143 0.00 0.00 0.00 3.69
4944 5743 3.903714 TCCTGAAGTCCTGATCTGTTTGA 59.096 43.478 0.00 0.00 0.00 2.69
4949 5748 4.142049 GGTAAGTCCTGAAGTCCTGATCTG 60.142 50.000 0.00 0.00 0.00 2.90
4967 5766 5.766150 TGATGTTGTTTGGACTTGGTAAG 57.234 39.130 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.