Multiple sequence alignment - TraesCS2A01G378200

Loading Multiple Alignment...

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 TraesCS2A01G378200 chr2A 100.000 3467 0 0 1 3467 621035156 621038622 0.000000e+00 6403.0
1 TraesCS2A01G378200 chr2A 85.366 287 36 5 3182 3465 754213749 754213466 3.380000e-75 292.0
2 TraesCS2A01G378200 chr2B 93.957 2350 109 19 843 3189 560185548 560187867 0.000000e+00 3522.0
3 TraesCS2A01G378200 chr2B 84.760 584 39 20 1 567 560184061 560184611 1.090000e-149 540.0
4 TraesCS2A01G378200 chr2B 91.582 297 22 2 3171 3467 560188083 560188376 1.160000e-109 407.0
5 TraesCS2A01G378200 chr2D 95.227 2221 82 11 866 3080 477992136 477994338 0.000000e+00 3493.0
6 TraesCS2A01G378200 chr2D 91.883 579 38 5 1 570 477989834 477990412 0.000000e+00 800.0
7 TraesCS2A01G378200 chr2D 84.286 280 42 2 3182 3461 594590641 594590364 4.410000e-69 272.0
8 TraesCS2A01G378200 chr2D 95.862 145 6 0 730 874 477990447 477990591 5.780000e-58 235.0
9 TraesCS2A01G378200 chr2D 94.444 108 6 0 572 679 247023680 247023573 2.140000e-37 167.0
10 TraesCS2A01G378200 chr2D 94.393 107 5 1 3077 3183 477994972 477995077 2.770000e-36 163.0
11 TraesCS2A01G378200 chr4D 86.364 286 37 2 3182 3467 416046736 416047019 9.340000e-81 311.0
12 TraesCS2A01G378200 chr4D 83.803 284 44 2 3182 3465 262813489 262813208 5.700000e-68 268.0
13 TraesCS2A01G378200 chr5D 84.507 284 42 2 3182 3465 168403817 168404098 2.630000e-71 279.0
14 TraesCS2A01G378200 chr5D 100.000 29 0 0 1845 1873 544895905 544895877 2.000000e-03 54.7
15 TraesCS2A01G378200 chr5D 100.000 29 0 0 1845 1873 545112053 545112025 2.000000e-03 54.7
16 TraesCS2A01G378200 chr3D 84.507 284 42 2 3182 3465 570402939 570402658 2.630000e-71 279.0
17 TraesCS2A01G378200 chr4A 84.342 281 42 2 3185 3465 594278854 594278576 1.230000e-69 274.0
18 TraesCS2A01G378200 chr4A 100.000 29 0 0 1845 1873 624833773 624833745 2.000000e-03 54.7
19 TraesCS2A01G378200 chr3B 83.803 284 43 3 3182 3465 10718205 10717925 2.050000e-67 267.0
20 TraesCS2A01G378200 chr3B 94.340 106 6 0 572 677 512871763 512871658 2.770000e-36 163.0
21 TraesCS2A01G378200 chr3B 91.379 116 9 1 565 680 750136213 750136327 1.290000e-34 158.0
22 TraesCS2A01G378200 chr5A 94.340 106 6 0 572 677 29712748 29712643 2.770000e-36 163.0
23 TraesCS2A01G378200 chr5A 100.000 29 0 0 1845 1873 624707410 624707382 2.000000e-03 54.7
24 TraesCS2A01G378200 chr1D 93.519 108 7 0 572 679 186442514 186442407 9.960000e-36 161.0
25 TraesCS2A01G378200 chr1D 93.519 108 7 0 572 679 281706742 281706635 9.960000e-36 161.0
26 TraesCS2A01G378200 chr1D 93.519 108 7 0 572 679 335497207 335497314 9.960000e-36 161.0
27 TraesCS2A01G378200 chr6A 91.379 116 10 0 564 679 436115584 436115469 3.580000e-35 159.0
28 TraesCS2A01G378200 chr5B 90.598 117 11 0 568 684 21363005 21363121 4.630000e-34 156.0
29 TraesCS2A01G378200 chr5B 100.000 29 0 0 1845 1873 687695587 687695615 2.000000e-03 54.7
30 TraesCS2A01G378200 chr5B 100.000 28 0 0 1846 1873 687468859 687468832 6.000000e-03 52.8
31 TraesCS2A01G378200 chr1A 100.000 29 0 0 1845 1873 569256540 569256568 2.000000e-03 54.7


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 TraesCS2A01G378200 chr2A 621035156 621038622 3466 False 6403.000000 6403 100.000000 1 3467 1 chr2A.!!$F1 3466
1 TraesCS2A01G378200 chr2B 560184061 560188376 4315 False 1489.666667 3522 90.099667 1 3467 3 chr2B.!!$F1 3466
2 TraesCS2A01G378200 chr2D 477989834 477995077 5243 False 1172.750000 3493 94.341250 1 3183 4 chr2D.!!$F1 3182

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
682 708 0.252197 AAATGGAGGGAGTACACCGC 59.748 55.0 3.06 2.71 0.00 5.68 F
701 727 0.314935 CAGGCCAAGCACGTGAATTT 59.685 50.0 22.23 7.16 0.00 1.82 F
728 754 0.387565 AAAAATTGCGGGTGAAGCGT 59.612 45.0 0.00 0.00 37.44 5.07 F
1988 4417 0.249120 TTGCCCGACGATGTCAAGAT 59.751 50.0 0.00 0.00 32.09 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1625 4054 0.179140 GAGCTCTTGCAGACTCTCCG 60.179 60.000 6.43 0.0 42.74 4.63 R
1988 4417 1.069513 CCGTGTTCTCCTGTAACCACA 59.930 52.381 0.00 0.0 0.00 4.17 R
2319 4748 1.094073 CCATGAGCTTCTCCAAGGCG 61.094 60.000 0.00 0.0 0.00 5.52 R
3266 6571 1.970640 ACCAACAGATTTTCCAAGGGC 59.029 47.619 0.00 0.0 0.00 5.19 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
18 19 3.879912 TGGGAGAGACGTTTCGAAC 57.120 52.632 0.00 0.00 0.00 3.95
28 29 0.794473 CGTTTCGAACAGGGCCTTAC 59.206 55.000 1.32 0.00 0.00 2.34
39 40 6.377429 CGAACAGGGCCTTACTATATCTATGA 59.623 42.308 1.32 0.00 0.00 2.15
135 139 9.729023 TGTTTGTGTACACATTTCTTATTTGAG 57.271 29.630 28.35 0.00 41.52 3.02
170 174 9.308318 GAAAAGAAACTTTAAACTTGTATGGCA 57.692 29.630 0.00 0.00 0.00 4.92
199 203 9.000018 GCGTAATCAAACTCTAACATTTGAATC 58.000 33.333 3.73 0.00 45.34 2.52
229 238 3.895232 AGCACCCTGTACTTACTGATG 57.105 47.619 0.00 0.00 0.00 3.07
236 245 3.439293 CTGTACTTACTGATGCCAGACG 58.561 50.000 0.00 0.00 43.02 4.18
282 291 4.338879 CACACCAGGAAAAAGGATGATCT 58.661 43.478 0.00 0.00 0.00 2.75
288 297 5.591877 CCAGGAAAAAGGATGATCTCGAAAT 59.408 40.000 0.00 0.00 0.00 2.17
359 371 4.139786 CTCTCCTCTCTCTCCATTCTGAG 58.860 52.174 0.00 0.00 0.00 3.35
445 459 6.981559 GGTAGATTAGGAGAGAATTGTCACAC 59.018 42.308 5.28 0.00 0.00 3.82
548 574 4.398044 TGCCGATCTTCTTAAAAATGACCC 59.602 41.667 0.00 0.00 0.00 4.46
549 575 4.398044 GCCGATCTTCTTAAAAATGACCCA 59.602 41.667 0.00 0.00 0.00 4.51
555 581 6.552008 TCTTCTTAAAAATGACCCAGTGGAT 58.448 36.000 11.95 0.00 34.81 3.41
570 596 3.624861 CAGTGGATGATGCACTCTAAACC 59.375 47.826 16.97 0.00 46.32 3.27
573 599 3.264193 TGGATGATGCACTCTAAACCACT 59.736 43.478 0.00 0.00 0.00 4.00
575 601 4.383552 GGATGATGCACTCTAAACCACTCT 60.384 45.833 0.00 0.00 0.00 3.24
576 602 4.193826 TGATGCACTCTAAACCACTCTC 57.806 45.455 0.00 0.00 0.00 3.20
577 603 3.834813 TGATGCACTCTAAACCACTCTCT 59.165 43.478 0.00 0.00 0.00 3.10
578 604 4.284490 TGATGCACTCTAAACCACTCTCTT 59.716 41.667 0.00 0.00 0.00 2.85
579 605 4.258702 TGCACTCTAAACCACTCTCTTC 57.741 45.455 0.00 0.00 0.00 2.87
581 607 3.305471 GCACTCTAAACCACTCTCTTCGT 60.305 47.826 0.00 0.00 0.00 3.85
582 608 4.796618 GCACTCTAAACCACTCTCTTCGTT 60.797 45.833 0.00 0.00 0.00 3.85
583 609 4.918583 CACTCTAAACCACTCTCTTCGTTC 59.081 45.833 0.00 0.00 0.00 3.95
584 610 4.583489 ACTCTAAACCACTCTCTTCGTTCA 59.417 41.667 0.00 0.00 0.00 3.18
586 612 4.825634 TCTAAACCACTCTCTTCGTTCAGA 59.174 41.667 0.00 0.00 0.00 3.27
588 614 4.608948 AACCACTCTCTTCGTTCAGAAT 57.391 40.909 0.00 0.00 38.34 2.40
591 617 5.471257 ACCACTCTCTTCGTTCAGAATTAC 58.529 41.667 0.00 0.00 38.34 1.89
592 618 5.244178 ACCACTCTCTTCGTTCAGAATTACT 59.756 40.000 0.00 0.00 38.34 2.24
593 619 6.159988 CCACTCTCTTCGTTCAGAATTACTT 58.840 40.000 0.00 0.00 38.34 2.24
594 620 6.090088 CCACTCTCTTCGTTCAGAATTACTTG 59.910 42.308 0.00 0.00 38.34 3.16
595 621 6.642950 CACTCTCTTCGTTCAGAATTACTTGT 59.357 38.462 0.00 0.00 38.34 3.16
596 622 6.864165 ACTCTCTTCGTTCAGAATTACTTGTC 59.136 38.462 0.00 0.00 38.34 3.18
597 623 5.856986 TCTCTTCGTTCAGAATTACTTGTCG 59.143 40.000 0.00 0.00 38.34 4.35
598 624 4.384846 TCTTCGTTCAGAATTACTTGTCGC 59.615 41.667 0.00 0.00 38.34 5.19
600 626 3.673338 TCGTTCAGAATTACTTGTCGCAG 59.327 43.478 0.00 0.00 0.00 5.18
601 627 3.673338 CGTTCAGAATTACTTGTCGCAGA 59.327 43.478 0.00 0.00 0.00 4.26
602 628 4.149922 CGTTCAGAATTACTTGTCGCAGAA 59.850 41.667 0.00 0.00 39.69 3.02
603 629 5.333035 CGTTCAGAATTACTTGTCGCAGAAA 60.333 40.000 0.00 0.00 39.69 2.52
604 630 6.603095 GTTCAGAATTACTTGTCGCAGAAAT 58.397 36.000 0.00 0.00 39.69 2.17
605 631 6.169419 TCAGAATTACTTGTCGCAGAAATG 57.831 37.500 0.00 0.00 39.69 2.32
606 632 5.122239 TCAGAATTACTTGTCGCAGAAATGG 59.878 40.000 0.00 0.00 39.69 3.16
607 633 5.122239 CAGAATTACTTGTCGCAGAAATGGA 59.878 40.000 0.00 0.00 39.69 3.41
608 634 5.882557 AGAATTACTTGTCGCAGAAATGGAT 59.117 36.000 0.00 0.00 39.69 3.41
609 635 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
610 636 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
611 637 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
612 638 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
613 639 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
614 640 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
615 641 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
616 642 5.532557 TGTCGCAGAAATGGATGTATCTAG 58.467 41.667 0.00 0.00 39.69 2.43
617 643 5.301805 TGTCGCAGAAATGGATGTATCTAGA 59.698 40.000 0.00 0.00 39.69 2.43
618 644 6.015095 TGTCGCAGAAATGGATGTATCTAGAT 60.015 38.462 10.73 10.73 39.69 1.98
619 645 6.309980 GTCGCAGAAATGGATGTATCTAGATG 59.690 42.308 15.79 0.00 39.69 2.90
620 646 6.015095 TCGCAGAAATGGATGTATCTAGATGT 60.015 38.462 15.79 1.25 0.00 3.06
621 647 7.176690 TCGCAGAAATGGATGTATCTAGATGTA 59.823 37.037 15.79 4.44 0.00 2.29
622 648 7.978414 CGCAGAAATGGATGTATCTAGATGTAT 59.022 37.037 15.79 9.11 0.00 2.29
623 649 9.664332 GCAGAAATGGATGTATCTAGATGTATT 57.336 33.333 15.79 4.32 0.00 1.89
671 697 8.792830 TTGAGACAAGTAATTCTAAATGGAGG 57.207 34.615 0.00 0.00 0.00 4.30
672 698 7.338710 TGAGACAAGTAATTCTAAATGGAGGG 58.661 38.462 0.00 0.00 0.00 4.30
673 699 7.182026 TGAGACAAGTAATTCTAAATGGAGGGA 59.818 37.037 0.00 0.00 0.00 4.20
674 700 7.569240 AGACAAGTAATTCTAAATGGAGGGAG 58.431 38.462 0.00 0.00 0.00 4.30
675 701 7.182930 AGACAAGTAATTCTAAATGGAGGGAGT 59.817 37.037 0.00 0.00 0.00 3.85
676 702 8.388656 ACAAGTAATTCTAAATGGAGGGAGTA 57.611 34.615 0.00 0.00 0.00 2.59
677 703 8.265764 ACAAGTAATTCTAAATGGAGGGAGTAC 58.734 37.037 0.00 0.00 0.00 2.73
678 704 7.989947 AGTAATTCTAAATGGAGGGAGTACA 57.010 36.000 0.00 0.00 0.00 2.90
679 705 7.793036 AGTAATTCTAAATGGAGGGAGTACAC 58.207 38.462 0.00 0.00 0.00 2.90
680 706 5.632034 ATTCTAAATGGAGGGAGTACACC 57.368 43.478 0.00 0.00 0.00 4.16
681 707 3.028850 TCTAAATGGAGGGAGTACACCG 58.971 50.000 3.06 0.00 0.00 4.94
682 708 0.252197 AAATGGAGGGAGTACACCGC 59.748 55.000 3.06 2.71 0.00 5.68
683 709 0.907704 AATGGAGGGAGTACACCGCA 60.908 55.000 11.33 0.74 0.00 5.69
684 710 1.330655 ATGGAGGGAGTACACCGCAG 61.331 60.000 11.33 0.00 0.00 5.18
698 724 3.286751 GCAGGCCAAGCACGTGAA 61.287 61.111 22.23 0.00 0.00 3.18
699 725 2.629656 GCAGGCCAAGCACGTGAAT 61.630 57.895 22.23 3.35 0.00 2.57
700 726 1.959085 CAGGCCAAGCACGTGAATT 59.041 52.632 22.23 10.35 0.00 2.17
701 727 0.314935 CAGGCCAAGCACGTGAATTT 59.685 50.000 22.23 7.16 0.00 1.82
702 728 1.039856 AGGCCAAGCACGTGAATTTT 58.960 45.000 22.23 4.44 0.00 1.82
703 729 1.412343 AGGCCAAGCACGTGAATTTTT 59.588 42.857 22.23 1.78 0.00 1.94
704 730 1.792367 GGCCAAGCACGTGAATTTTTC 59.208 47.619 22.23 0.00 0.00 2.29
705 731 1.792367 GCCAAGCACGTGAATTTTTCC 59.208 47.619 22.23 0.00 0.00 3.13
706 732 2.801342 GCCAAGCACGTGAATTTTTCCA 60.801 45.455 22.23 0.00 0.00 3.53
707 733 3.452474 CCAAGCACGTGAATTTTTCCAA 58.548 40.909 22.23 0.00 0.00 3.53
708 734 3.868077 CCAAGCACGTGAATTTTTCCAAA 59.132 39.130 22.23 0.00 0.00 3.28
709 735 4.331168 CCAAGCACGTGAATTTTTCCAAAA 59.669 37.500 22.23 0.00 0.00 2.44
710 736 5.163814 CCAAGCACGTGAATTTTTCCAAAAA 60.164 36.000 22.23 0.00 41.59 1.94
728 754 0.387565 AAAAATTGCGGGTGAAGCGT 59.612 45.000 0.00 0.00 37.44 5.07
752 1627 4.026310 GTGAAATTTCAAACTGCTGCACAG 60.026 41.667 22.07 12.81 44.95 3.66
770 1645 4.376413 GCACAGATTATTTGATCGCTACCG 60.376 45.833 0.00 0.00 0.00 4.02
773 1648 4.150627 CAGATTATTTGATCGCTACCGGTG 59.849 45.833 19.93 8.61 34.56 4.94
820 1695 6.974622 CACTAATTAATGGCTGGATGTTCAAC 59.025 38.462 0.00 0.00 0.00 3.18
837 1712 2.072298 CAACAGCACAGCTCTAGAACC 58.928 52.381 0.00 0.00 36.40 3.62
850 1725 5.719085 AGCTCTAGAACCTATCCATGGTATG 59.281 44.000 12.58 2.71 36.69 2.39
881 3309 7.429636 TGATTACAGTTTACCAGTAGCAAAC 57.570 36.000 0.00 0.00 33.35 2.93
904 3332 4.363999 CTTCGGCAGGCTATATATACAGC 58.636 47.826 4.32 4.32 37.05 4.40
1023 3452 2.114411 GCGACCCTGTCCCCAAAA 59.886 61.111 0.00 0.00 0.00 2.44
1207 3636 4.271816 CTGCCGGGATCGAGGTCG 62.272 72.222 2.18 0.00 39.00 4.79
1623 4052 0.467474 TACCGTCCTGCTCCATCGAT 60.467 55.000 0.00 0.00 0.00 3.59
1625 4054 1.953138 CGTCCTGCTCCATCGATGC 60.953 63.158 20.25 9.57 0.00 3.91
1698 4127 3.069016 TGGTGAACAGCTTCGAAGAACTA 59.931 43.478 28.95 10.58 45.90 2.24
1854 4283 2.032681 AAGGCCAAGTCCGTGCTC 59.967 61.111 5.01 0.00 0.00 4.26
1988 4417 0.249120 TTGCCCGACGATGTCAAGAT 59.751 50.000 0.00 0.00 32.09 2.40
2013 4442 0.892358 TACAGGAGAACACGGACGCT 60.892 55.000 0.00 0.00 0.00 5.07
2675 5108 1.373570 AAGATAACGAAGCTGGCAGC 58.626 50.000 31.56 31.56 42.84 5.25
2717 5150 6.952935 AGCAAAGTCTAGAGAATGTTTACG 57.047 37.500 0.00 0.00 0.00 3.18
2725 5159 9.339850 AGTCTAGAGAATGTTTACGAATAGCTA 57.660 33.333 0.00 0.00 0.00 3.32
2938 5374 4.008330 GGATGATGCATAGCTAGCAATGT 58.992 43.478 18.83 0.00 46.27 2.71
3064 5500 6.844696 AATGACGCCATATGTAACTAACAG 57.155 37.500 1.24 0.00 34.92 3.16
3159 6232 8.866970 TCCGGTTGTTAAGGAAACTAATTATT 57.133 30.769 0.00 0.00 42.68 1.40
3189 6262 3.309193 GGATTTTTCCCTGCTACTCCCTT 60.309 47.826 0.00 0.00 0.00 3.95
3196 6501 1.275291 CCTGCTACTCCCTTCGTTTCA 59.725 52.381 0.00 0.00 0.00 2.69
3207 6512 4.879545 TCCCTTCGTTTCATTATGTAAGGC 59.120 41.667 0.00 0.00 32.44 4.35
3229 6534 4.784550 GCGTATTATTTTTGACACGGTGAC 59.215 41.667 16.29 9.58 0.00 3.67
3234 6539 1.384525 TTTTGACACGGTGACCAAGG 58.615 50.000 16.29 0.00 0.00 3.61
3244 6549 2.235016 GGTGACCAAGGCACACAATTA 58.765 47.619 15.27 0.00 37.99 1.40
3259 6564 9.277783 GGCACACAATTATAGAGAAGTTATGAT 57.722 33.333 0.00 0.00 0.00 2.45
3285 6590 1.969923 TGCCCTTGGAAAATCTGTTGG 59.030 47.619 0.00 0.00 0.00 3.77
3291 6596 5.048013 CCCTTGGAAAATCTGTTGGTTAGTC 60.048 44.000 0.00 0.00 0.00 2.59
3318 6623 9.877178 ACAAGTACATCAATTAGTCTAGGAAAG 57.123 33.333 0.00 0.00 0.00 2.62
3345 6650 8.458573 AATAGGTACATGTAGTCAAGAGAGAG 57.541 38.462 5.62 0.00 0.00 3.20
3352 6657 8.588290 ACATGTAGTCAAGAGAGAGATACTTT 57.412 34.615 0.00 0.00 0.00 2.66
3353 6658 9.030452 ACATGTAGTCAAGAGAGAGATACTTTT 57.970 33.333 0.00 0.00 0.00 2.27
3357 6662 9.783256 GTAGTCAAGAGAGAGATACTTTTCTTC 57.217 37.037 0.00 0.00 33.63 2.87
3436 6741 8.751215 TTAGAGGGCTAATAAGGGAATTATGA 57.249 34.615 0.00 0.00 34.21 2.15
3443 6748 8.603304 GGCTAATAAGGGAATTATGAGGAGTTA 58.397 37.037 0.00 0.00 34.07 2.24
3450 6755 9.822727 AAGGGAATTATGAGGAGTTAAAAAGAA 57.177 29.630 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 5.067936 CCGTCATAGATATAGTAAGGCCCTG 59.932 48.000 0.00 0.00 0.00 4.45
101 105 9.905713 AGAAATGTGTACACAAACATATAGGAT 57.094 29.630 31.01 8.56 45.41 3.24
102 106 9.733556 AAGAAATGTGTACACAAACATATAGGA 57.266 29.630 31.01 4.75 45.41 2.94
116 120 9.974750 GAGCTTACTCAAATAAGAAATGTGTAC 57.025 33.333 0.00 0.00 42.93 2.90
137 141 9.358872 CAAGTTTAAAGTTTCTTTTCTGAGCTT 57.641 29.630 5.51 0.00 0.00 3.74
170 174 9.378551 TCAAATGTTAGAGTTTGATTACGCTAT 57.621 29.630 0.00 0.00 38.88 2.97
173 177 8.895932 ATTCAAATGTTAGAGTTTGATTACGC 57.104 30.769 1.89 0.00 42.12 4.42
199 203 8.204836 AGTAAGTACAGGGTGCTAATTTCATAG 58.795 37.037 0.00 0.00 0.00 2.23
229 238 1.700955 TAGGGTAGGAATCGTCTGGC 58.299 55.000 0.00 0.00 0.00 4.85
236 245 6.775629 TGGCAAATGTATTTAGGGTAGGAATC 59.224 38.462 0.00 0.00 0.00 2.52
282 291 5.304357 TGAGAGTAGCCCATGATTATTTCGA 59.696 40.000 0.00 0.00 0.00 3.71
288 297 4.546674 TCAGTGAGAGTAGCCCATGATTA 58.453 43.478 0.00 0.00 0.00 1.75
295 304 1.001158 GCGTATCAGTGAGAGTAGCCC 60.001 57.143 0.00 0.00 0.00 5.19
359 371 6.739550 GTCACGTGCCAAAAATTATACTGTAC 59.260 38.462 11.67 0.00 0.00 2.90
548 574 3.624861 GGTTTAGAGTGCATCATCCACTG 59.375 47.826 0.00 0.00 43.17 3.66
549 575 3.264193 TGGTTTAGAGTGCATCATCCACT 59.736 43.478 0.00 0.00 45.61 4.00
555 581 3.834813 AGAGAGTGGTTTAGAGTGCATCA 59.165 43.478 0.00 0.00 0.00 3.07
570 596 6.642950 ACAAGTAATTCTGAACGAAGAGAGTG 59.357 38.462 0.00 0.00 34.56 3.51
573 599 5.856986 CGACAAGTAATTCTGAACGAAGAGA 59.143 40.000 0.00 0.00 34.56 3.10
575 601 4.384846 GCGACAAGTAATTCTGAACGAAGA 59.615 41.667 0.00 0.00 34.56 2.87
576 602 4.149922 TGCGACAAGTAATTCTGAACGAAG 59.850 41.667 0.00 0.00 34.56 3.79
577 603 4.052608 TGCGACAAGTAATTCTGAACGAA 58.947 39.130 0.00 0.00 35.78 3.85
578 604 3.644823 TGCGACAAGTAATTCTGAACGA 58.355 40.909 0.00 0.00 0.00 3.85
579 605 3.673338 TCTGCGACAAGTAATTCTGAACG 59.327 43.478 0.00 0.00 0.00 3.95
581 607 6.348458 CCATTTCTGCGACAAGTAATTCTGAA 60.348 38.462 0.00 0.00 0.00 3.02
582 608 5.122239 CCATTTCTGCGACAAGTAATTCTGA 59.878 40.000 0.00 0.00 0.00 3.27
583 609 5.122239 TCCATTTCTGCGACAAGTAATTCTG 59.878 40.000 0.00 0.00 0.00 3.02
584 610 5.245531 TCCATTTCTGCGACAAGTAATTCT 58.754 37.500 0.00 0.00 0.00 2.40
586 612 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
588 614 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
591 617 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
592 618 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
593 619 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
594 620 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
595 621 6.015095 ACATCTAGATACATCCATTTCTGCGA 60.015 38.462 4.54 0.00 0.00 5.10
596 622 6.162079 ACATCTAGATACATCCATTTCTGCG 58.838 40.000 4.54 0.00 0.00 5.18
597 623 9.664332 AATACATCTAGATACATCCATTTCTGC 57.336 33.333 4.54 0.00 0.00 4.26
645 671 9.231297 CCTCCATTTAGAATTACTTGTCTCAAA 57.769 33.333 0.00 0.00 0.00 2.69
646 672 7.829211 CCCTCCATTTAGAATTACTTGTCTCAA 59.171 37.037 0.00 0.00 0.00 3.02
647 673 7.182026 TCCCTCCATTTAGAATTACTTGTCTCA 59.818 37.037 0.00 0.00 0.00 3.27
648 674 7.565680 TCCCTCCATTTAGAATTACTTGTCTC 58.434 38.462 0.00 0.00 0.00 3.36
649 675 7.182930 ACTCCCTCCATTTAGAATTACTTGTCT 59.817 37.037 0.00 0.00 0.00 3.41
650 676 7.339482 ACTCCCTCCATTTAGAATTACTTGTC 58.661 38.462 0.00 0.00 0.00 3.18
651 677 7.272144 ACTCCCTCCATTTAGAATTACTTGT 57.728 36.000 0.00 0.00 0.00 3.16
652 678 8.265055 TGTACTCCCTCCATTTAGAATTACTTG 58.735 37.037 0.00 0.00 0.00 3.16
653 679 8.265764 GTGTACTCCCTCCATTTAGAATTACTT 58.734 37.037 0.00 0.00 0.00 2.24
654 680 7.147532 GGTGTACTCCCTCCATTTAGAATTACT 60.148 40.741 2.33 0.00 0.00 2.24
655 681 6.990939 GGTGTACTCCCTCCATTTAGAATTAC 59.009 42.308 2.33 0.00 0.00 1.89
656 682 6.183360 CGGTGTACTCCCTCCATTTAGAATTA 60.183 42.308 8.36 0.00 0.00 1.40
657 683 5.396436 CGGTGTACTCCCTCCATTTAGAATT 60.396 44.000 8.36 0.00 0.00 2.17
658 684 4.101119 CGGTGTACTCCCTCCATTTAGAAT 59.899 45.833 8.36 0.00 0.00 2.40
659 685 3.449737 CGGTGTACTCCCTCCATTTAGAA 59.550 47.826 8.36 0.00 0.00 2.10
660 686 3.028850 CGGTGTACTCCCTCCATTTAGA 58.971 50.000 8.36 0.00 0.00 2.10
661 687 2.483188 GCGGTGTACTCCCTCCATTTAG 60.483 54.545 8.36 0.00 0.00 1.85
662 688 1.483415 GCGGTGTACTCCCTCCATTTA 59.517 52.381 8.36 0.00 0.00 1.40
663 689 0.252197 GCGGTGTACTCCCTCCATTT 59.748 55.000 8.36 0.00 0.00 2.32
664 690 0.907704 TGCGGTGTACTCCCTCCATT 60.908 55.000 8.36 0.00 0.00 3.16
665 691 1.305802 TGCGGTGTACTCCCTCCAT 60.306 57.895 8.36 0.00 0.00 3.41
666 692 1.982395 CTGCGGTGTACTCCCTCCA 60.982 63.158 8.36 3.07 0.00 3.86
667 693 2.722201 CCTGCGGTGTACTCCCTCC 61.722 68.421 8.36 0.00 0.00 4.30
668 694 2.893398 CCTGCGGTGTACTCCCTC 59.107 66.667 8.36 1.74 0.00 4.30
669 695 3.391382 GCCTGCGGTGTACTCCCT 61.391 66.667 8.36 0.00 0.00 4.20
670 696 4.468689 GGCCTGCGGTGTACTCCC 62.469 72.222 8.36 0.44 0.00 4.30
671 697 3.248446 TTGGCCTGCGGTGTACTCC 62.248 63.158 3.32 3.76 0.00 3.85
672 698 1.741770 CTTGGCCTGCGGTGTACTC 60.742 63.158 3.32 0.00 0.00 2.59
673 699 2.347490 CTTGGCCTGCGGTGTACT 59.653 61.111 3.32 0.00 0.00 2.73
674 700 3.431725 GCTTGGCCTGCGGTGTAC 61.432 66.667 3.32 0.00 0.00 2.90
675 701 3.947459 TGCTTGGCCTGCGGTGTA 61.947 61.111 3.32 0.00 0.00 2.90
681 707 2.146073 AATTCACGTGCTTGGCCTGC 62.146 55.000 11.67 9.51 0.00 4.85
682 708 0.314935 AAATTCACGTGCTTGGCCTG 59.685 50.000 11.67 0.00 0.00 4.85
683 709 1.039856 AAAATTCACGTGCTTGGCCT 58.960 45.000 11.67 0.00 0.00 5.19
684 710 1.792367 GAAAAATTCACGTGCTTGGCC 59.208 47.619 11.67 0.00 0.00 5.36
685 711 1.792367 GGAAAAATTCACGTGCTTGGC 59.208 47.619 11.67 0.00 0.00 4.52
686 712 3.090952 TGGAAAAATTCACGTGCTTGG 57.909 42.857 11.67 0.00 0.00 3.61
687 713 5.462034 TTTTGGAAAAATTCACGTGCTTG 57.538 34.783 11.67 0.00 0.00 4.01
709 735 0.387565 ACGCTTCACCCGCAATTTTT 59.612 45.000 0.00 0.00 0.00 1.94
710 736 0.318614 CACGCTTCACCCGCAATTTT 60.319 50.000 0.00 0.00 0.00 1.82
711 737 1.285641 CACGCTTCACCCGCAATTT 59.714 52.632 0.00 0.00 0.00 1.82
712 738 1.896660 ACACGCTTCACCCGCAATT 60.897 52.632 0.00 0.00 0.00 2.32
713 739 2.281484 ACACGCTTCACCCGCAAT 60.281 55.556 0.00 0.00 0.00 3.56
714 740 3.276091 CACACGCTTCACCCGCAA 61.276 61.111 0.00 0.00 0.00 4.85
715 741 3.741830 TTCACACGCTTCACCCGCA 62.742 57.895 0.00 0.00 0.00 5.69
716 742 1.852067 ATTTCACACGCTTCACCCGC 61.852 55.000 0.00 0.00 0.00 6.13
717 743 0.591170 AATTTCACACGCTTCACCCG 59.409 50.000 0.00 0.00 0.00 5.28
718 744 2.034053 TGAAATTTCACACGCTTCACCC 59.966 45.455 16.91 0.00 31.01 4.61
719 745 3.347958 TGAAATTTCACACGCTTCACC 57.652 42.857 16.91 0.00 31.01 4.02
720 746 4.798387 AGTTTGAAATTTCACACGCTTCAC 59.202 37.500 24.47 11.15 41.46 3.18
721 747 4.797868 CAGTTTGAAATTTCACACGCTTCA 59.202 37.500 24.47 6.38 41.46 3.02
722 748 4.317348 GCAGTTTGAAATTTCACACGCTTC 60.317 41.667 27.63 17.70 41.46 3.86
723 749 3.551485 GCAGTTTGAAATTTCACACGCTT 59.449 39.130 27.63 14.81 41.46 4.68
728 754 3.864583 GTGCAGCAGTTTGAAATTTCACA 59.135 39.130 20.35 11.69 36.83 3.58
752 1627 3.120649 GCACCGGTAGCGATCAAATAATC 60.121 47.826 17.33 0.00 0.00 1.75
770 1645 2.988010 TCAGATCTACCATGTGCACC 57.012 50.000 15.69 0.00 0.00 5.01
773 1648 6.094603 AGTGATTTTTCAGATCTACCATGTGC 59.905 38.462 0.00 0.00 0.00 4.57
820 1695 3.243704 GGATAGGTTCTAGAGCTGTGCTG 60.244 52.174 6.54 0.00 39.88 4.41
837 1712 5.672421 TCATCTCAGCATACCATGGATAG 57.328 43.478 21.47 8.24 0.00 2.08
850 1725 6.109359 ACTGGTAAACTGTAATCATCTCAGC 58.891 40.000 0.00 0.00 33.12 4.26
1113 3542 1.883732 CGTCGTGAGGATGGTGACT 59.116 57.895 0.00 0.00 0.00 3.41
1207 3636 4.580551 CGGGTACGGGATCACGGC 62.581 72.222 23.42 13.78 38.39 5.68
1378 3807 1.643868 TTGCACATTCCGGCGATGAC 61.644 55.000 20.24 13.39 0.00 3.06
1623 4052 1.588597 CTCTTGCAGACTCTCCGCA 59.411 57.895 0.00 0.00 0.00 5.69
1625 4054 0.179140 GAGCTCTTGCAGACTCTCCG 60.179 60.000 6.43 0.00 42.74 4.63
1698 4127 4.427661 GCAGCGGAGTCGTGCTCT 62.428 66.667 5.60 0.00 43.62 4.09
1854 4283 4.079090 CTGCCGAAGCTGACGTAG 57.921 61.111 11.53 6.71 40.18 3.51
1988 4417 1.069513 CCGTGTTCTCCTGTAACCACA 59.930 52.381 0.00 0.00 0.00 4.17
2291 4720 1.229368 TGTTCCATCCCGACCTCCA 60.229 57.895 0.00 0.00 0.00 3.86
2318 4747 1.451028 ATGAGCTTCTCCAAGGCGC 60.451 57.895 0.00 0.00 0.00 6.53
2319 4748 1.094073 CCATGAGCTTCTCCAAGGCG 61.094 60.000 0.00 0.00 0.00 5.52
2675 5108 6.441093 TTGCTTATTCAAATGGTAGAGCAG 57.559 37.500 0.00 0.00 39.68 4.24
2717 5150 4.548991 TCGGTTCTCGAAGTAGCTATTC 57.451 45.455 0.00 1.54 45.86 1.75
2763 5198 0.105964 CCAACGAGGTCACCAGTGAA 59.894 55.000 1.23 0.00 41.85 3.18
2764 5199 1.745890 CCAACGAGGTCACCAGTGA 59.254 57.895 0.00 0.00 37.24 3.41
2862 5297 5.717119 ACACGAGTATTTTGTCGGTTCTAT 58.283 37.500 0.00 0.00 40.59 1.98
2962 5398 2.500098 AGCTCATTTCAAGCCATGCAAT 59.500 40.909 0.00 0.00 40.75 3.56
3027 5463 4.812091 TGGCGTCATTTATTTATAGCACGT 59.188 37.500 0.00 0.00 0.00 4.49
3028 5464 5.337219 TGGCGTCATTTATTTATAGCACG 57.663 39.130 0.00 0.00 0.00 5.34
3029 5465 8.450964 ACATATGGCGTCATTTATTTATAGCAC 58.549 33.333 8.30 0.00 34.96 4.40
3040 5476 7.045416 TCTGTTAGTTACATATGGCGTCATTT 58.955 34.615 8.30 0.00 35.85 2.32
3060 5496 8.599624 ATGAATCCCAAAACATAATCTCTGTT 57.400 30.769 0.00 0.00 38.44 3.16
3159 6232 5.628797 AGCAGGGAAAAATCCTTTTGAAA 57.371 34.783 0.00 0.00 34.83 2.69
3189 6262 8.821147 ATAATACGCCTTACATAATGAAACGA 57.179 30.769 0.00 0.00 0.00 3.85
3207 6512 5.107026 TGGTCACCGTGTCAAAAATAATACG 60.107 40.000 0.00 0.00 0.00 3.06
3229 6534 5.882557 ACTTCTCTATAATTGTGTGCCTTGG 59.117 40.000 0.00 0.00 0.00 3.61
3244 6549 8.223330 AGGGCAATTTCATCATAACTTCTCTAT 58.777 33.333 0.00 0.00 0.00 1.98
3259 6564 4.347583 ACAGATTTTCCAAGGGCAATTTCA 59.652 37.500 0.00 0.00 0.00 2.69
3266 6571 1.970640 ACCAACAGATTTTCCAAGGGC 59.029 47.619 0.00 0.00 0.00 5.19
3285 6590 9.640963 AGACTAATTGATGTACTTGTGACTAAC 57.359 33.333 0.00 0.00 0.00 2.34
3291 6596 9.653287 TTTCCTAGACTAATTGATGTACTTGTG 57.347 33.333 0.00 0.00 0.00 3.33
3318 6623 9.339850 TCTCTCTTGACTACATGTACCTATTAC 57.660 37.037 0.08 0.00 0.00 1.89
3322 6627 7.196637 TCTCTCTCTTGACTACATGTACCTA 57.803 40.000 0.08 0.00 0.00 3.08
3332 6637 9.747898 AGAAGAAAAGTATCTCTCTCTTGACTA 57.252 33.333 0.00 0.00 0.00 2.59
3352 6657 9.778741 TTATCTCTCTTTGTAGCAAAAGAAGAA 57.221 29.630 16.05 5.16 43.67 2.52
3353 6658 9.778741 TTTATCTCTCTTTGTAGCAAAAGAAGA 57.221 29.630 9.60 12.97 43.67 2.87
3357 6662 8.993121 TGTCTTTATCTCTCTTTGTAGCAAAAG 58.007 33.333 0.00 0.00 38.31 2.27
3369 6674 8.821686 TCTCTCTTGATTGTCTTTATCTCTCT 57.178 34.615 0.00 0.00 0.00 3.10
3436 6741 6.731292 AAGGTGCATTTCTTTTTAACTCCT 57.269 33.333 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.