Multiple sequence alignment - TraesCS7D01G401600

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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 TraesCS7D01G401600 chr7D 100.000 2228 0 0 1 2228 518640753 518642980 0.000000e+00 4115
1 TraesCS7D01G401600 chr7B 94.186 1634 54 18 631 2228 551953107 551954735 0.000000e+00 2453
2 TraesCS7D01G401600 chr7B 96.491 513 9 4 1 513 551952617 551953120 0.000000e+00 839
3 TraesCS7D01G401600 chr7A 95.388 1496 53 8 631 2113 593463787 593465279 0.000000e+00 2366
4 TraesCS7D01G401600 chr7A 95.127 513 9 4 1 513 593463304 593463800 0.000000e+00 795
5 TraesCS7D01G401600 chr4D 88.889 252 20 6 1759 2007 15253207 15252961 1.000000e-78 303
6 TraesCS7D01G401600 chr4B 90.351 228 19 2 1771 1998 25784317 25784093 1.670000e-76 296
7 TraesCS7D01G401600 chr4B 90.351 228 19 2 1771 1998 25787769 25787545 1.670000e-76 296
8 TraesCS7D01G401600 chr5B 99.145 117 1 0 513 629 180042788 180042672 6.230000e-51 211
9 TraesCS7D01G401600 chr3D 99.138 116 1 0 513 628 376923754 376923639 2.240000e-50 209
10 TraesCS7D01G401600 chr5A 98.305 118 2 0 513 630 360072576 360072693 8.060000e-50 207
11 TraesCS7D01G401600 chr2D 98.319 119 1 1 513 630 459298816 459298698 8.060000e-50 207
12 TraesCS7D01G401600 chr5D 98.291 117 2 0 513 629 162425185 162425301 2.900000e-49 206
13 TraesCS7D01G401600 chr5D 98.291 117 2 0 513 629 225256310 225256194 2.900000e-49 206
14 TraesCS7D01G401600 chr2B 98.291 117 2 0 513 629 331010334 331010218 2.900000e-49 206
15 TraesCS7D01G401600 chr2B 98.305 118 1 1 513 629 503752673 503752790 2.900000e-49 206
16 TraesCS7D01G401600 chr2A 98.291 117 2 0 513 629 240475356 240475240 2.900000e-49 206


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 TraesCS7D01G401600 chr7D 518640753 518642980 2227 False 4115.0 4115 100.0000 1 2228 1 chr7D.!!$F1 2227
1 TraesCS7D01G401600 chr7B 551952617 551954735 2118 False 1646.0 2453 95.3385 1 2228 2 chr7B.!!$F1 2227
2 TraesCS7D01G401600 chr7A 593463304 593465279 1975 False 1580.5 2366 95.2575 1 2113 2 chr7A.!!$F1 2112
3 TraesCS7D01G401600 chr4B 25784093 25787769 3676 True 296.0 296 90.3510 1771 1998 2 chr4B.!!$R1 227

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
560 561 0.099436 GGAAAGGCTGCGCACAATAG 59.901 55.0 5.66 0.0 0.0 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 1772 0.030638 GCATGACGCCTTGTTTGTGT 59.969 50.0 0.0 0.0 32.94 3.72 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
324 325 7.480810 AGAAAAGTTAGTAGCTGTTTGTTTGG 58.519 34.615 0.00 0.00 0.00 3.28
397 398 8.778358 GGATAATTCACATGAAAGTATCACTCC 58.222 37.037 22.21 11.52 41.93 3.85
487 488 3.314553 GCATATTCACATGCCATTGCTC 58.685 45.455 0.00 0.00 44.55 4.26
504 505 7.035612 CCATTGCTCTTTTTAATAACCCTCAC 58.964 38.462 0.00 0.00 0.00 3.51
505 506 7.093771 CCATTGCTCTTTTTAATAACCCTCACT 60.094 37.037 0.00 0.00 0.00 3.41
506 507 7.833285 TTGCTCTTTTTAATAACCCTCACTT 57.167 32.000 0.00 0.00 0.00 3.16
507 508 7.448748 TGCTCTTTTTAATAACCCTCACTTC 57.551 36.000 0.00 0.00 0.00 3.01
508 509 7.001674 TGCTCTTTTTAATAACCCTCACTTCA 58.998 34.615 0.00 0.00 0.00 3.02
509 510 7.040686 TGCTCTTTTTAATAACCCTCACTTCAC 60.041 37.037 0.00 0.00 0.00 3.18
510 511 7.175119 GCTCTTTTTAATAACCCTCACTTCACT 59.825 37.037 0.00 0.00 0.00 3.41
511 512 9.720769 CTCTTTTTAATAACCCTCACTTCACTA 57.279 33.333 0.00 0.00 0.00 2.74
512 513 9.498176 TCTTTTTAATAACCCTCACTTCACTAC 57.502 33.333 0.00 0.00 0.00 2.73
513 514 8.625786 TTTTTAATAACCCTCACTTCACTACC 57.374 34.615 0.00 0.00 0.00 3.18
514 515 7.563724 TTTAATAACCCTCACTTCACTACCT 57.436 36.000 0.00 0.00 0.00 3.08
515 516 5.422214 AATAACCCTCACTTCACTACCTG 57.578 43.478 0.00 0.00 0.00 4.00
516 517 1.645710 ACCCTCACTTCACTACCTGG 58.354 55.000 0.00 0.00 0.00 4.45
517 518 1.149288 ACCCTCACTTCACTACCTGGA 59.851 52.381 0.00 0.00 0.00 3.86
518 519 2.257207 CCCTCACTTCACTACCTGGAA 58.743 52.381 0.00 0.00 0.00 3.53
519 520 2.637872 CCCTCACTTCACTACCTGGAAA 59.362 50.000 0.00 0.00 0.00 3.13
520 521 3.557264 CCCTCACTTCACTACCTGGAAAC 60.557 52.174 0.00 0.00 0.00 2.78
521 522 3.071023 CCTCACTTCACTACCTGGAAACA 59.929 47.826 0.00 0.00 39.59 2.83
532 533 3.025924 TGGAAACAGCCTCTTGCAG 57.974 52.632 0.00 0.00 44.83 4.41
533 534 0.473755 TGGAAACAGCCTCTTGCAGA 59.526 50.000 0.00 0.00 44.83 4.26
534 535 1.133823 TGGAAACAGCCTCTTGCAGAA 60.134 47.619 0.00 0.00 44.83 3.02
535 536 1.956477 GGAAACAGCCTCTTGCAGAAA 59.044 47.619 0.00 0.00 44.83 2.52
536 537 2.560105 GGAAACAGCCTCTTGCAGAAAT 59.440 45.455 0.00 0.00 44.83 2.17
537 538 3.572584 GAAACAGCCTCTTGCAGAAATG 58.427 45.455 0.00 0.00 44.83 2.32
538 539 2.283145 ACAGCCTCTTGCAGAAATGT 57.717 45.000 0.00 0.00 44.83 2.71
539 540 3.423539 ACAGCCTCTTGCAGAAATGTA 57.576 42.857 0.00 0.00 44.83 2.29
540 541 3.341823 ACAGCCTCTTGCAGAAATGTAG 58.658 45.455 0.00 0.00 44.83 2.74
541 542 2.681848 CAGCCTCTTGCAGAAATGTAGG 59.318 50.000 0.00 0.00 44.83 3.18
542 543 2.019984 GCCTCTTGCAGAAATGTAGGG 58.980 52.381 0.00 0.00 40.77 3.53
543 544 2.356125 GCCTCTTGCAGAAATGTAGGGA 60.356 50.000 0.00 0.00 40.77 4.20
544 545 3.873801 GCCTCTTGCAGAAATGTAGGGAA 60.874 47.826 0.00 0.00 40.77 3.97
545 546 4.335416 CCTCTTGCAGAAATGTAGGGAAA 58.665 43.478 0.00 0.00 0.00 3.13
546 547 4.397417 CCTCTTGCAGAAATGTAGGGAAAG 59.603 45.833 0.00 0.00 0.00 2.62
547 548 4.335416 TCTTGCAGAAATGTAGGGAAAGG 58.665 43.478 0.00 0.00 0.00 3.11
548 549 2.446435 TGCAGAAATGTAGGGAAAGGC 58.554 47.619 0.00 0.00 0.00 4.35
549 550 2.041620 TGCAGAAATGTAGGGAAAGGCT 59.958 45.455 0.00 0.00 0.00 4.58
550 551 2.424956 GCAGAAATGTAGGGAAAGGCTG 59.575 50.000 0.00 0.00 0.00 4.85
551 552 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
552 553 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
553 554 1.032114 AATGTAGGGAAAGGCTGCGC 61.032 55.000 0.00 0.00 0.00 6.09
554 555 2.046314 GTAGGGAAAGGCTGCGCA 60.046 61.111 10.98 10.98 0.00 6.09
555 556 2.046314 TAGGGAAAGGCTGCGCAC 60.046 61.111 5.66 3.30 0.00 5.34
556 557 2.889606 TAGGGAAAGGCTGCGCACA 61.890 57.895 5.66 0.00 0.00 4.57
557 558 2.404566 TAGGGAAAGGCTGCGCACAA 62.405 55.000 5.66 0.00 0.00 3.33
558 559 2.639327 GGGAAAGGCTGCGCACAAT 61.639 57.895 5.66 0.00 0.00 2.71
559 560 1.312371 GGGAAAGGCTGCGCACAATA 61.312 55.000 5.66 0.00 0.00 1.90
560 561 0.099436 GGAAAGGCTGCGCACAATAG 59.901 55.000 5.66 0.00 0.00 1.73
561 562 1.086696 GAAAGGCTGCGCACAATAGA 58.913 50.000 5.66 0.00 0.00 1.98
562 563 0.804989 AAAGGCTGCGCACAATAGAC 59.195 50.000 5.66 0.00 0.00 2.59
563 564 1.026718 AAGGCTGCGCACAATAGACC 61.027 55.000 5.66 2.41 0.00 3.85
564 565 2.472909 GGCTGCGCACAATAGACCC 61.473 63.158 5.66 0.00 0.00 4.46
565 566 1.745115 GCTGCGCACAATAGACCCA 60.745 57.895 5.66 0.00 0.00 4.51
566 567 1.305219 GCTGCGCACAATAGACCCAA 61.305 55.000 5.66 0.00 0.00 4.12
567 568 1.164411 CTGCGCACAATAGACCCAAA 58.836 50.000 5.66 0.00 0.00 3.28
568 569 1.131126 CTGCGCACAATAGACCCAAAG 59.869 52.381 5.66 0.00 0.00 2.77
569 570 1.165270 GCGCACAATAGACCCAAAGT 58.835 50.000 0.30 0.00 0.00 2.66
570 571 1.135689 GCGCACAATAGACCCAAAGTG 60.136 52.381 0.30 0.00 0.00 3.16
571 572 1.468520 CGCACAATAGACCCAAAGTGG 59.531 52.381 0.00 0.00 37.25 4.00
572 573 2.514803 GCACAATAGACCCAAAGTGGT 58.485 47.619 0.00 0.00 42.79 4.16
577 578 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
578 579 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
579 580 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
580 581 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
581 582 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
582 583 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
583 584 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
584 585 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
585 586 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
592 593 4.735599 GACCCTTCCCCGGACCCT 62.736 72.222 0.73 0.00 0.00 4.34
619 620 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
620 621 2.897350 GAGCTACATGCACCGGGC 60.897 66.667 6.32 7.25 45.94 6.13
621 622 3.391665 GAGCTACATGCACCGGGCT 62.392 63.158 6.32 0.81 45.94 5.19
622 623 3.204827 GCTACATGCACCGGGCTG 61.205 66.667 6.32 9.21 45.15 4.85
623 624 3.204827 CTACATGCACCGGGCTGC 61.205 66.667 6.32 8.50 45.15 5.25
624 625 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
649 650 1.676014 GCCCTCGCTTCATACAGTGTT 60.676 52.381 0.00 0.00 0.00 3.32
671 672 7.492994 GTGTTTATCCAGGTAGAAGAAGCTTAG 59.507 40.741 0.00 0.00 0.00 2.18
734 735 8.378172 TCCCTTTAGCATATAATTCGTGAAAG 57.622 34.615 0.00 0.00 0.00 2.62
737 738 9.869844 CCTTTAGCATATAATTCGTGAAAGAAG 57.130 33.333 0.00 0.00 33.19 2.85
759 760 9.300681 AGAAGAAAATATGTTGAGACATCCAAA 57.699 29.630 0.00 0.00 42.83 3.28
823 824 1.479709 CTCCCATCACTCGACTCCTT 58.520 55.000 0.00 0.00 0.00 3.36
824 825 1.407258 CTCCCATCACTCGACTCCTTC 59.593 57.143 0.00 0.00 0.00 3.46
832 833 4.868067 TCACTCGACTCCTTCAAAAGTAC 58.132 43.478 0.00 0.00 0.00 2.73
941 942 6.217294 AGTAACTTGTGTCTTCAGCTCTTAC 58.783 40.000 0.00 0.00 0.00 2.34
950 951 1.944177 TCAGCTCTTACTCTTGCCCT 58.056 50.000 0.00 0.00 0.00 5.19
952 953 1.552337 CAGCTCTTACTCTTGCCCTCA 59.448 52.381 0.00 0.00 0.00 3.86
1111 1112 0.103208 AGAAGTGAAGGCGCCTATCG 59.897 55.000 33.07 0.00 42.12 2.92
1151 1152 1.197430 ACTGGAAGGAGCACTCTGGG 61.197 60.000 0.00 0.00 39.30 4.45
1235 1236 0.251297 CCACCAAACTGAGATGGCCA 60.251 55.000 8.56 8.56 40.51 5.36
1237 1238 0.610232 ACCAAACTGAGATGGCCAGC 60.610 55.000 14.72 14.72 40.51 4.85
1288 1289 5.307976 TGCAGCTTGGTATATGATACTCCTT 59.692 40.000 0.00 0.00 0.00 3.36
1355 1356 2.658285 TCGACGCTAGGGGAGATTTTA 58.342 47.619 11.95 0.00 0.00 1.52
1419 1420 5.985781 TGCATTTTCTTTCACTCTTACGTC 58.014 37.500 0.00 0.00 0.00 4.34
1782 1791 3.364964 GGAACAGATACACAAACAAGGCG 60.365 47.826 0.00 0.00 0.00 5.52
1817 5278 5.278463 CCTTTGTTGTTGGTGGTCTTATCAG 60.278 44.000 0.00 0.00 0.00 2.90
1848 5309 0.249447 TGATCCGGCTGAATGTAGCG 60.249 55.000 0.00 0.00 44.60 4.26
2113 5579 1.382522 ATGGCTGTATTCCTGTTGCG 58.617 50.000 0.00 0.00 0.00 4.85
2114 5580 0.323302 TGGCTGTATTCCTGTTGCGA 59.677 50.000 0.00 0.00 0.00 5.10
2116 5582 1.398390 GGCTGTATTCCTGTTGCGAAG 59.602 52.381 0.00 0.00 0.00 3.79
2117 5583 2.076863 GCTGTATTCCTGTTGCGAAGT 58.923 47.619 0.00 0.00 0.00 3.01
2118 5584 2.159653 GCTGTATTCCTGTTGCGAAGTG 60.160 50.000 0.00 0.00 0.00 3.16
2119 5585 3.325870 CTGTATTCCTGTTGCGAAGTGA 58.674 45.455 0.00 0.00 0.00 3.41
2120 5586 3.325870 TGTATTCCTGTTGCGAAGTGAG 58.674 45.455 0.00 0.00 0.00 3.51
2121 5587 1.160137 ATTCCTGTTGCGAAGTGAGC 58.840 50.000 0.00 0.00 0.00 4.26
2122 5588 0.106708 TTCCTGTTGCGAAGTGAGCT 59.893 50.000 0.00 0.00 35.28 4.09
2123 5589 0.601046 TCCTGTTGCGAAGTGAGCTG 60.601 55.000 0.00 0.00 35.28 4.24
2124 5590 0.601046 CCTGTTGCGAAGTGAGCTGA 60.601 55.000 0.00 0.00 35.28 4.26
2127 5617 1.001293 TGTTGCGAAGTGAGCTGATCT 59.999 47.619 0.00 0.00 35.28 2.75
2130 5620 2.341257 TGCGAAGTGAGCTGATCTTTC 58.659 47.619 0.00 0.00 35.28 2.62
2148 5638 6.662865 TCTTTCCACAATTATTTTGCCTCA 57.337 33.333 0.00 0.00 0.00 3.86
2150 5640 4.799564 TCCACAATTATTTTGCCTCACC 57.200 40.909 0.00 0.00 0.00 4.02
2177 5667 5.988561 GTGTTTTCATTTGCAATTACCCTGA 59.011 36.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 151 3.297134 AGTATGGCATACTTGGGGTTG 57.703 47.619 29.77 0.00 43.27 3.77
151 152 4.045022 ACTAGTATGGCATACTTGGGGTT 58.955 43.478 37.01 20.27 43.27 4.11
152 153 3.665443 ACTAGTATGGCATACTTGGGGT 58.335 45.455 37.01 26.87 43.27 4.95
153 154 4.591498 TGTACTAGTATGGCATACTTGGGG 59.409 45.833 37.01 26.37 43.27 4.96
154 155 5.801531 TGTACTAGTATGGCATACTTGGG 57.198 43.478 37.01 28.26 43.27 4.12
155 156 6.701841 CAGTTGTACTAGTATGGCATACTTGG 59.298 42.308 37.01 30.17 43.27 3.61
306 307 6.734137 CATCAACCAAACAAACAGCTACTAA 58.266 36.000 0.00 0.00 0.00 2.24
397 398 4.875536 TGATATTGTTTCCATGACCAGTCG 59.124 41.667 0.00 0.00 0.00 4.18
487 488 8.727910 GGTAGTGAAGTGAGGGTTATTAAAAAG 58.272 37.037 0.00 0.00 0.00 2.27
504 505 2.039084 AGGCTGTTTCCAGGTAGTGAAG 59.961 50.000 0.00 0.00 39.22 3.02
505 506 2.038557 GAGGCTGTTTCCAGGTAGTGAA 59.961 50.000 0.00 0.00 39.22 3.18
506 507 1.623811 GAGGCTGTTTCCAGGTAGTGA 59.376 52.381 0.00 0.00 39.22 3.41
507 508 1.625818 AGAGGCTGTTTCCAGGTAGTG 59.374 52.381 0.00 0.00 39.22 2.74
508 509 2.031495 AGAGGCTGTTTCCAGGTAGT 57.969 50.000 0.00 0.00 39.22 2.73
509 510 2.704572 CAAGAGGCTGTTTCCAGGTAG 58.295 52.381 0.00 0.00 39.22 3.18
510 511 1.271379 GCAAGAGGCTGTTTCCAGGTA 60.271 52.381 0.00 0.00 39.22 3.08
511 512 0.538287 GCAAGAGGCTGTTTCCAGGT 60.538 55.000 0.00 0.00 39.22 4.00
512 513 0.538057 TGCAAGAGGCTGTTTCCAGG 60.538 55.000 0.00 0.00 45.15 4.45
513 514 0.879765 CTGCAAGAGGCTGTTTCCAG 59.120 55.000 0.00 0.00 45.15 3.86
514 515 0.473755 TCTGCAAGAGGCTGTTTCCA 59.526 50.000 0.00 0.00 38.67 3.53
515 516 3.329300 TCTGCAAGAGGCTGTTTCC 57.671 52.632 0.00 0.00 38.67 3.13
525 526 4.335416 CCTTTCCCTACATTTCTGCAAGA 58.665 43.478 0.00 0.00 44.68 3.02
526 527 3.119352 GCCTTTCCCTACATTTCTGCAAG 60.119 47.826 0.00 0.00 0.00 4.01
527 528 2.825532 GCCTTTCCCTACATTTCTGCAA 59.174 45.455 0.00 0.00 0.00 4.08
528 529 2.041620 AGCCTTTCCCTACATTTCTGCA 59.958 45.455 0.00 0.00 0.00 4.41
529 530 2.424956 CAGCCTTTCCCTACATTTCTGC 59.575 50.000 0.00 0.00 0.00 4.26
530 531 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
531 532 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
532 533 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
533 534 1.463674 CGCAGCCTTTCCCTACATTT 58.536 50.000 0.00 0.00 0.00 2.32
534 535 3.175133 CGCAGCCTTTCCCTACATT 57.825 52.632 0.00 0.00 0.00 2.71
535 536 4.963878 CGCAGCCTTTCCCTACAT 57.036 55.556 0.00 0.00 0.00 2.29
548 549 1.131126 CTTTGGGTCTATTGTGCGCAG 59.869 52.381 12.22 0.00 0.00 5.18
549 550 1.164411 CTTTGGGTCTATTGTGCGCA 58.836 50.000 5.66 5.66 0.00 6.09
550 551 1.135689 CACTTTGGGTCTATTGTGCGC 60.136 52.381 0.00 0.00 0.00 6.09
551 552 1.468520 CCACTTTGGGTCTATTGTGCG 59.531 52.381 0.00 0.00 32.67 5.34
552 553 2.514803 ACCACTTTGGGTCTATTGTGC 58.485 47.619 0.00 0.00 43.37 4.57
561 562 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
562 563 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
563 564 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
564 565 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
565 566 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
566 567 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
567 568 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
568 569 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
575 576 4.735599 AGGGTCCGGGGAAGGGTC 62.736 72.222 0.00 0.00 0.00 4.46
591 592 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
594 595 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
595 596 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
596 597 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
597 598 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
603 604 2.897350 GCCCGGTGCATGTAGCTC 60.897 66.667 11.25 0.00 45.94 4.09
604 605 3.402681 AGCCCGGTGCATGTAGCT 61.403 61.111 15.92 4.82 45.94 3.32
605 606 3.204827 CAGCCCGGTGCATGTAGC 61.205 66.667 15.92 2.56 44.83 3.58
606 607 3.204827 GCAGCCCGGTGCATGTAG 61.205 66.667 13.70 0.91 43.41 2.74
607 608 4.794648 GGCAGCCCGGTGCATGTA 62.795 66.667 19.47 0.00 45.93 2.29
622 623 3.443925 GAAGCGAGGGCAAAGGGC 61.444 66.667 0.00 0.00 43.41 5.19
623 624 0.107214 TATGAAGCGAGGGCAAAGGG 60.107 55.000 0.00 0.00 43.41 3.95
624 625 1.017387 GTATGAAGCGAGGGCAAAGG 58.983 55.000 0.00 0.00 43.41 3.11
625 626 1.667724 CTGTATGAAGCGAGGGCAAAG 59.332 52.381 0.00 0.00 43.41 2.77
626 627 1.003118 ACTGTATGAAGCGAGGGCAAA 59.997 47.619 0.00 0.00 43.41 3.68
627 628 0.613260 ACTGTATGAAGCGAGGGCAA 59.387 50.000 0.00 0.00 43.41 4.52
628 629 0.108186 CACTGTATGAAGCGAGGGCA 60.108 55.000 0.00 0.00 43.41 5.36
629 630 0.108138 ACACTGTATGAAGCGAGGGC 60.108 55.000 0.00 0.00 40.37 5.19
630 631 2.386661 AACACTGTATGAAGCGAGGG 57.613 50.000 0.00 0.00 0.00 4.30
631 632 4.508124 GGATAAACACTGTATGAAGCGAGG 59.492 45.833 0.00 0.00 0.00 4.63
632 633 5.109210 TGGATAAACACTGTATGAAGCGAG 58.891 41.667 0.00 0.00 0.00 5.03
633 634 5.079689 TGGATAAACACTGTATGAAGCGA 57.920 39.130 0.00 0.00 0.00 4.93
634 635 4.271049 CCTGGATAAACACTGTATGAAGCG 59.729 45.833 0.00 0.00 0.00 4.68
635 636 5.186198 ACCTGGATAAACACTGTATGAAGC 58.814 41.667 0.00 0.00 0.00 3.86
649 650 7.565398 ACATCTAAGCTTCTTCTACCTGGATAA 59.435 37.037 0.00 0.00 0.00 1.75
737 738 9.643693 ACAATTTGGATGTCTCAACATATTTTC 57.356 29.630 0.78 0.00 46.20 2.29
759 760 4.046286 TCTCCAGCCCATTGTTTACAAT 57.954 40.909 2.33 2.33 46.62 2.71
832 833 8.836413 TGTGTCACTATTTTAGTTCAAGAAAGG 58.164 33.333 4.27 0.00 36.76 3.11
941 942 2.431954 ACAATGGATGAGGGCAAGAG 57.568 50.000 0.00 0.00 0.00 2.85
950 951 4.226427 AGCTAGCTTGAACAATGGATGA 57.774 40.909 12.68 0.00 0.00 2.92
952 953 4.080356 TGGTAGCTAGCTTGAACAATGGAT 60.080 41.667 24.88 0.00 0.00 3.41
1237 1238 1.009829 GGTATGGAACGAAGCAGCAG 58.990 55.000 0.00 0.00 0.00 4.24
1288 1289 5.189928 ACAAACACACAGAGAATACACCAA 58.810 37.500 0.00 0.00 0.00 3.67
1355 1356 8.875168 TGGTGACAAAACAAATATAAGGGAAAT 58.125 29.630 0.00 0.00 37.44 2.17
1769 1772 0.030638 GCATGACGCCTTGTTTGTGT 59.969 50.000 0.00 0.00 32.94 3.72
1782 1791 0.037975 CAACAAAGGCTGGGCATGAC 60.038 55.000 0.00 0.00 0.00 3.06
1796 5257 4.578516 CACTGATAAGACCACCAACAACAA 59.421 41.667 0.00 0.00 0.00 2.83
1817 5278 0.879400 CCGGATCAGCTGCAGATCAC 60.879 60.000 28.56 19.33 42.84 3.06
1848 5309 4.641989 ACATGGATGTTCAGCTAATGTTCC 59.358 41.667 0.00 0.00 37.90 3.62
2010 5472 6.370166 ACCAAACAATTTACAAACCTGTGTTG 59.630 34.615 0.00 0.00 36.96 3.33
2017 5479 9.373603 AGTAAGAAACCAAACAATTTACAAACC 57.626 29.630 0.00 0.00 0.00 3.27
2113 5579 3.668447 TGTGGAAAGATCAGCTCACTTC 58.332 45.455 0.00 0.00 0.00 3.01
2114 5580 3.777106 TGTGGAAAGATCAGCTCACTT 57.223 42.857 0.00 0.00 0.00 3.16
2116 5582 6.690194 ATAATTGTGGAAAGATCAGCTCAC 57.310 37.500 0.00 0.00 0.00 3.51
2117 5583 7.707624 AAATAATTGTGGAAAGATCAGCTCA 57.292 32.000 0.00 0.00 0.00 4.26
2118 5584 7.009907 GCAAAATAATTGTGGAAAGATCAGCTC 59.990 37.037 0.00 0.00 0.00 4.09
2119 5585 6.815142 GCAAAATAATTGTGGAAAGATCAGCT 59.185 34.615 0.00 0.00 0.00 4.24
2120 5586 6.036408 GGCAAAATAATTGTGGAAAGATCAGC 59.964 38.462 0.00 0.00 0.00 4.26
2121 5587 7.325694 AGGCAAAATAATTGTGGAAAGATCAG 58.674 34.615 0.00 0.00 0.00 2.90
2122 5588 7.039152 TGAGGCAAAATAATTGTGGAAAGATCA 60.039 33.333 0.00 0.00 0.00 2.92
2123 5589 7.276438 GTGAGGCAAAATAATTGTGGAAAGATC 59.724 37.037 0.00 0.00 0.00 2.75
2124 5590 7.099120 GTGAGGCAAAATAATTGTGGAAAGAT 58.901 34.615 0.00 0.00 0.00 2.40
2127 5617 5.546526 GGTGAGGCAAAATAATTGTGGAAA 58.453 37.500 0.00 0.00 0.00 3.13
2130 5620 3.192422 TCGGTGAGGCAAAATAATTGTGG 59.808 43.478 0.00 0.00 0.00 4.17
2148 5638 3.791973 TTGCAAATGAAAACACTCGGT 57.208 38.095 0.00 0.00 0.00 4.69
2150 5640 5.118510 GGGTAATTGCAAATGAAAACACTCG 59.881 40.000 1.71 0.00 0.00 4.18
2177 5667 8.688747 TTTAAATCCTTTGTGGCATGAATTTT 57.311 26.923 0.00 0.00 35.26 1.82


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

AutoCloner maintained by Alex Coulton.