Multiple sequence alignment - TraesCS3B01G338800

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 TraesCS3B01G338800 chr3B 100.000 4013 0 0 1 4013 545047601 545051613 0.000000e+00 7411
1 TraesCS3B01G338800 chr3B 96.491 114 4 0 475 588 40198619 40198732 5.290000e-44 189
2 TraesCS3B01G338800 chr3B 95.652 115 5 0 476 590 214547515 214547629 6.850000e-43 185
3 TraesCS3B01G338800 chr3D 97.836 2819 60 1 581 3398 418717591 418720409 0.000000e+00 4867
4 TraesCS3B01G338800 chr3D 97.508 602 13 2 3413 4013 418720389 418720989 0.000000e+00 1027
5 TraesCS3B01G338800 chr3D 90.196 204 12 5 281 478 418717392 418717593 3.980000e-65 259
6 TraesCS3B01G338800 chr3A 96.843 2819 77 7 581 3398 532471093 532468286 0.000000e+00 4702
7 TraesCS3B01G338800 chr3A 96.523 604 18 1 3413 4013 532468306 532467703 0.000000e+00 996
8 TraesCS3B01G338800 chr3A 85.288 469 39 9 18 478 532471537 532471091 1.310000e-124 457
9 TraesCS3B01G338800 chr3A 91.473 129 10 1 475 603 572598404 572598277 4.120000e-40 176
10 TraesCS3B01G338800 chr5D 76.898 922 196 14 1944 2856 515251724 515250811 1.290000e-139 507
11 TraesCS3B01G338800 chr5A 72.281 1811 430 64 1085 2856 643366069 643364292 7.750000e-137 497
12 TraesCS3B01G338800 chr1B 97.248 109 3 0 476 584 624662919 624663027 6.850000e-43 185
13 TraesCS3B01G338800 chr5B 94.915 118 5 1 475 592 90515280 90515396 2.460000e-42 183
14 TraesCS3B01G338800 chr5B 96.396 111 4 0 475 585 679806926 679807036 2.460000e-42 183
15 TraesCS3B01G338800 chr4B 95.575 113 5 0 476 588 449123571 449123683 8.860000e-42 182
16 TraesCS3B01G338800 chr1D 93.443 122 7 1 468 589 85185641 85185521 3.190000e-41 180
17 TraesCS3B01G338800 chr6A 93.162 117 8 0 467 583 484566953 484566837 5.330000e-39 172


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 TraesCS3B01G338800 chr3B 545047601 545051613 4012 False 7411.000000 7411 100.000000 1 4013 1 chr3B.!!$F3 4012
1 TraesCS3B01G338800 chr3D 418717392 418720989 3597 False 2051.000000 4867 95.180000 281 4013 3 chr3D.!!$F1 3732
2 TraesCS3B01G338800 chr3A 532467703 532471537 3834 True 2051.666667 4702 92.884667 18 4013 3 chr3A.!!$R2 3995
3 TraesCS3B01G338800 chr5D 515250811 515251724 913 True 507.000000 507 76.898000 1944 2856 1 chr5D.!!$R1 912
4 TraesCS3B01G338800 chr5A 643364292 643366069 1777 True 497.000000 497 72.281000 1085 2856 1 chr5A.!!$R1 1771

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
836 847 0.037447 AGACTGGGAAGAAGCAAGCC 59.963 55.0 0.0 0.0 0.00 4.35 F
1234 1245 1.982073 GCGCTTCCACAAATCTCCCG 61.982 60.0 0.0 0.0 0.00 5.14 F
1839 1853 0.676151 CCAAACTCTCTGAGCTGCCC 60.676 60.0 0.0 0.0 32.04 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 1671 0.322975 GAAAGCAGTGGCCTCTCAGA 59.677 55.0 3.81 0.0 42.56 3.27 R
2518 2537 0.459489 GTGCCAACAACATGTGTGGT 59.541 50.0 19.36 8.5 40.60 4.16 R
3775 3801 2.170187 ACTCATCTTCACCAGATCAGGC 59.830 50.0 3.64 0.0 40.67 4.85 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
41 42 7.720442 AGTTAATATGGAACGAAGGTAGTACC 58.280 38.462 11.73 11.73 33.35 3.34
72 73 7.805163 TCAGGATAGCTTTCCAAGATTAATCA 58.195 34.615 23.17 0.00 38.32 2.57
73 74 7.935755 TCAGGATAGCTTTCCAAGATTAATCAG 59.064 37.037 23.17 9.21 38.32 2.90
74 75 7.935755 CAGGATAGCTTTCCAAGATTAATCAGA 59.064 37.037 23.17 8.25 38.32 3.27
75 76 8.156165 AGGATAGCTTTCCAAGATTAATCAGAG 58.844 37.037 23.17 6.54 38.32 3.35
76 77 8.153550 GGATAGCTTTCCAAGATTAATCAGAGA 58.846 37.037 17.41 7.58 35.72 3.10
77 78 9.723601 GATAGCTTTCCAAGATTAATCAGAGAT 57.276 33.333 17.56 3.16 0.00 2.75
78 79 9.723601 ATAGCTTTCCAAGATTAATCAGAGATC 57.276 33.333 17.56 3.17 0.00 2.75
79 80 7.571919 AGCTTTCCAAGATTAATCAGAGATCA 58.428 34.615 17.56 1.12 0.00 2.92
80 81 8.219178 AGCTTTCCAAGATTAATCAGAGATCAT 58.781 33.333 17.56 0.00 0.00 2.45
81 82 9.499479 GCTTTCCAAGATTAATCAGAGATCATA 57.501 33.333 17.56 0.00 0.00 2.15
96 97 5.182001 AGAGATCATAACACACAAAACTGCC 59.818 40.000 0.00 0.00 0.00 4.85
102 103 6.488344 TCATAACACACAAAACTGCCAATAGA 59.512 34.615 0.00 0.00 0.00 1.98
112 113 6.530601 AAACTGCCAATAGATACCCCTAAT 57.469 37.500 0.00 0.00 0.00 1.73
113 114 6.530601 AACTGCCAATAGATACCCCTAATT 57.469 37.500 0.00 0.00 0.00 1.40
114 115 6.530601 ACTGCCAATAGATACCCCTAATTT 57.469 37.500 0.00 0.00 0.00 1.82
154 157 4.924305 AATTGGATGATATTTGCGCTGT 57.076 36.364 9.73 0.00 0.00 4.40
156 159 1.948834 TGGATGATATTTGCGCTGTGG 59.051 47.619 9.73 0.00 0.00 4.17
158 161 2.225019 GGATGATATTTGCGCTGTGGAG 59.775 50.000 9.73 0.00 0.00 3.86
166 169 2.248280 TGCGCTGTGGAGAAAACTTA 57.752 45.000 9.73 0.00 0.00 2.24
167 170 2.143122 TGCGCTGTGGAGAAAACTTAG 58.857 47.619 9.73 0.00 0.00 2.18
174 177 6.427974 GCTGTGGAGAAAACTTAGTACAAAC 58.572 40.000 0.00 0.00 0.00 2.93
184 187 6.846325 AACTTAGTACAAACTTCTGCTGAC 57.154 37.500 0.00 0.00 37.15 3.51
193 196 1.151668 CTTCTGCTGACCTGAAACCG 58.848 55.000 0.00 0.00 32.03 4.44
202 205 4.022676 GCTGACCTGAAACCGGAATAAAAA 60.023 41.667 9.46 0.00 0.00 1.94
235 238 3.007506 TCGTTACACTCATGAACCACCAT 59.992 43.478 0.00 0.00 0.00 3.55
243 246 3.605634 TCATGAACCACCATTTCTACCG 58.394 45.455 0.00 0.00 0.00 4.02
250 253 3.945285 ACCACCATTTCTACCGCAATTAG 59.055 43.478 0.00 0.00 0.00 1.73
251 254 3.315191 CCACCATTTCTACCGCAATTAGG 59.685 47.826 0.00 0.00 0.00 2.69
257 260 2.372264 TCTACCGCAATTAGGTCGTCT 58.628 47.619 7.92 0.00 42.81 4.18
269 272 0.526662 GGTCGTCTTCTCGTCACCAT 59.473 55.000 0.00 0.00 31.16 3.55
273 276 1.132453 CGTCTTCTCGTCACCATAGCA 59.868 52.381 0.00 0.00 0.00 3.49
356 359 1.738099 CCAGCTAGCACGCGTTCTT 60.738 57.895 18.16 4.33 34.40 2.52
357 360 1.417592 CAGCTAGCACGCGTTCTTG 59.582 57.895 18.16 16.36 34.40 3.02
393 396 7.466996 GCCATTTCAATTTGTGTTCATTGACAA 60.467 33.333 0.00 0.00 33.37 3.18
475 484 2.040342 AACCCTACCACTAGTTGCCT 57.960 50.000 0.00 0.00 0.00 4.75
476 485 2.934263 ACCCTACCACTAGTTGCCTA 57.066 50.000 0.00 0.00 0.00 3.93
477 486 2.464782 ACCCTACCACTAGTTGCCTAC 58.535 52.381 0.00 0.00 0.00 3.18
478 487 2.044077 ACCCTACCACTAGTTGCCTACT 59.956 50.000 0.00 0.00 41.04 2.57
479 488 2.694109 CCCTACCACTAGTTGCCTACTC 59.306 54.545 0.00 0.00 38.33 2.59
480 489 2.694109 CCTACCACTAGTTGCCTACTCC 59.306 54.545 0.00 0.00 38.33 3.85
481 490 1.569653 ACCACTAGTTGCCTACTCCC 58.430 55.000 0.00 0.00 38.33 4.30
482 491 1.078989 ACCACTAGTTGCCTACTCCCT 59.921 52.381 0.00 0.00 38.33 4.20
483 492 1.757699 CCACTAGTTGCCTACTCCCTC 59.242 57.143 0.00 0.00 38.33 4.30
484 493 1.757699 CACTAGTTGCCTACTCCCTCC 59.242 57.143 0.00 0.00 38.33 4.30
485 494 1.033574 CTAGTTGCCTACTCCCTCCG 58.966 60.000 0.00 0.00 38.33 4.63
486 495 0.333993 TAGTTGCCTACTCCCTCCGT 59.666 55.000 0.00 0.00 38.33 4.69
487 496 0.544595 AGTTGCCTACTCCCTCCGTT 60.545 55.000 0.00 0.00 28.23 4.44
488 497 0.108281 GTTGCCTACTCCCTCCGTTC 60.108 60.000 0.00 0.00 0.00 3.95
489 498 1.262640 TTGCCTACTCCCTCCGTTCC 61.263 60.000 0.00 0.00 0.00 3.62
490 499 1.684734 GCCTACTCCCTCCGTTCCA 60.685 63.158 0.00 0.00 0.00 3.53
491 500 1.262640 GCCTACTCCCTCCGTTCCAA 61.263 60.000 0.00 0.00 0.00 3.53
492 501 1.272807 CCTACTCCCTCCGTTCCAAA 58.727 55.000 0.00 0.00 0.00 3.28
493 502 1.838077 CCTACTCCCTCCGTTCCAAAT 59.162 52.381 0.00 0.00 0.00 2.32
494 503 2.238898 CCTACTCCCTCCGTTCCAAATT 59.761 50.000 0.00 0.00 0.00 1.82
495 504 3.453353 CCTACTCCCTCCGTTCCAAATTA 59.547 47.826 0.00 0.00 0.00 1.40
496 505 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
497 506 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
498 507 3.329814 ACTCCCTCCGTTCCAAATTACTT 59.670 43.478 0.00 0.00 0.00 2.24
499 508 3.681593 TCCCTCCGTTCCAAATTACTTG 58.318 45.455 0.00 0.00 34.52 3.16
500 509 3.073356 TCCCTCCGTTCCAAATTACTTGT 59.927 43.478 0.00 0.00 32.65 3.16
501 510 3.439129 CCCTCCGTTCCAAATTACTTGTC 59.561 47.826 0.00 0.00 32.65 3.18
502 511 3.124636 CCTCCGTTCCAAATTACTTGTCG 59.875 47.826 0.00 0.00 32.65 4.35
503 512 2.481185 TCCGTTCCAAATTACTTGTCGC 59.519 45.455 0.00 0.00 32.65 5.19
504 513 2.224549 CCGTTCCAAATTACTTGTCGCA 59.775 45.455 0.00 0.00 32.65 5.10
505 514 3.223157 CGTTCCAAATTACTTGTCGCAC 58.777 45.455 0.00 0.00 32.65 5.34
506 515 3.223157 GTTCCAAATTACTTGTCGCACG 58.777 45.455 0.00 0.00 32.65 5.34
507 516 2.485903 TCCAAATTACTTGTCGCACGT 58.514 42.857 0.00 0.00 32.65 4.49
508 517 3.651206 TCCAAATTACTTGTCGCACGTA 58.349 40.909 0.00 0.00 32.65 3.57
509 518 4.247258 TCCAAATTACTTGTCGCACGTAT 58.753 39.130 0.00 0.00 32.65 3.06
510 519 4.092237 TCCAAATTACTTGTCGCACGTATG 59.908 41.667 0.00 0.00 32.65 2.39
511 520 4.331137 CAAATTACTTGTCGCACGTATGG 58.669 43.478 0.00 0.00 0.00 2.74
512 521 3.513680 ATTACTTGTCGCACGTATGGA 57.486 42.857 0.00 0.00 0.00 3.41
513 522 3.513680 TTACTTGTCGCACGTATGGAT 57.486 42.857 0.00 0.00 0.00 3.41
514 523 1.640428 ACTTGTCGCACGTATGGATG 58.360 50.000 0.00 0.00 0.00 3.51
515 524 1.067142 ACTTGTCGCACGTATGGATGT 60.067 47.619 0.00 0.00 0.00 3.06
516 525 2.164827 ACTTGTCGCACGTATGGATGTA 59.835 45.455 0.00 0.00 0.00 2.29
517 526 3.181479 ACTTGTCGCACGTATGGATGTAT 60.181 43.478 0.00 0.00 0.00 2.29
518 527 3.007979 TGTCGCACGTATGGATGTATC 57.992 47.619 0.00 0.00 0.00 2.24
519 528 2.621526 TGTCGCACGTATGGATGTATCT 59.378 45.455 0.00 0.00 0.00 1.98
520 529 3.816523 TGTCGCACGTATGGATGTATCTA 59.183 43.478 0.00 0.00 0.00 1.98
521 530 4.276431 TGTCGCACGTATGGATGTATCTAA 59.724 41.667 0.00 0.00 0.00 2.10
522 531 5.217393 GTCGCACGTATGGATGTATCTAAA 58.783 41.667 0.00 0.00 0.00 1.85
523 532 5.862323 GTCGCACGTATGGATGTATCTAAAT 59.138 40.000 0.00 0.00 0.00 1.40
524 533 5.861787 TCGCACGTATGGATGTATCTAAATG 59.138 40.000 0.00 0.00 0.00 2.32
525 534 5.633601 CGCACGTATGGATGTATCTAAATGT 59.366 40.000 0.00 0.00 0.00 2.71
526 535 6.804783 CGCACGTATGGATGTATCTAAATGTA 59.195 38.462 0.00 0.00 0.00 2.29
527 536 7.488150 CGCACGTATGGATGTATCTAAATGTAT 59.512 37.037 0.00 0.00 0.00 2.29
528 537 9.151471 GCACGTATGGATGTATCTAAATGTATT 57.849 33.333 0.00 0.00 0.00 1.89
556 565 8.354711 AGTTCTAGATATATCCATTTCAGCGA 57.645 34.615 9.18 0.00 0.00 4.93
557 566 8.247562 AGTTCTAGATATATCCATTTCAGCGAC 58.752 37.037 9.18 1.73 0.00 5.19
558 567 6.786207 TCTAGATATATCCATTTCAGCGACG 58.214 40.000 9.18 0.00 0.00 5.12
559 568 5.644977 AGATATATCCATTTCAGCGACGA 57.355 39.130 9.18 0.00 0.00 4.20
560 569 5.645624 AGATATATCCATTTCAGCGACGAG 58.354 41.667 9.18 0.00 0.00 4.18
561 570 3.735237 ATATCCATTTCAGCGACGAGT 57.265 42.857 0.00 0.00 0.00 4.18
562 571 4.848562 ATATCCATTTCAGCGACGAGTA 57.151 40.909 0.00 0.00 0.00 2.59
563 572 3.520290 ATCCATTTCAGCGACGAGTAA 57.480 42.857 0.00 0.00 0.00 2.24
564 573 3.520290 TCCATTTCAGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
565 574 3.857052 TCCATTTCAGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
566 575 4.250464 TCCATTTCAGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
567 576 4.092821 TCCATTTCAGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
568 577 4.334443 CATTTCAGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
569 578 3.306917 TTCAGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
570 579 3.306917 TCAGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
571 580 2.991190 TCAGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
572 581 1.990563 AGCGACGAGTAATTTGGAACG 59.009 47.619 0.00 0.00 0.00 3.95
573 582 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.00 0.00 4.44
574 583 2.598589 CGACGAGTAATTTGGAACGGA 58.401 47.619 0.00 0.00 0.00 4.69
575 584 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
576 585 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
577 586 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
578 587 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
579 588 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
696 707 4.467438 TGTGAGATGTGCTTGGATTCTCTA 59.533 41.667 0.00 0.00 35.09 2.43
704 715 7.435068 TGTGCTTGGATTCTCTAAAACTTAC 57.565 36.000 0.00 0.00 0.00 2.34
706 717 7.387948 TGTGCTTGGATTCTCTAAAACTTACTC 59.612 37.037 0.00 0.00 0.00 2.59
707 718 6.879458 TGCTTGGATTCTCTAAAACTTACTCC 59.121 38.462 0.00 0.00 0.00 3.85
750 761 6.255670 CCTTGGCGGCTTTAATTATTTTCTTC 59.744 38.462 11.43 0.00 0.00 2.87
756 767 7.628580 GCGGCTTTAATTATTTTCTTCCTGACT 60.629 37.037 0.00 0.00 0.00 3.41
775 786 4.696877 TGACTTAGGCAACATGTCTCATTG 59.303 41.667 0.00 0.00 32.64 2.82
779 790 3.079578 AGGCAACATGTCTCATTGTCAG 58.920 45.455 0.00 0.00 41.41 3.51
822 833 4.511527 ACTTGATGCATCCTTACAGACTG 58.488 43.478 23.67 0.00 0.00 3.51
836 847 0.037447 AGACTGGGAAGAAGCAAGCC 59.963 55.000 0.00 0.00 0.00 4.35
865 876 7.231467 AGGAAGGAACTAAGAAAAGTATGCAA 58.769 34.615 0.00 0.00 38.49 4.08
873 884 8.677148 ACTAAGAAAAGTATGCAAAAGACTCA 57.323 30.769 0.00 0.00 0.00 3.41
1167 1178 2.041115 CGGTCTCCTCGAGCTGACA 61.041 63.158 26.08 1.55 37.99 3.58
1234 1245 1.982073 GCGCTTCCACAAATCTCCCG 61.982 60.000 0.00 0.00 0.00 5.14
1660 1671 2.121129 CCCCCATCAATCTGGCAAAAT 58.879 47.619 0.00 0.00 34.77 1.82
1839 1853 0.676151 CCAAACTCTCTGAGCTGCCC 60.676 60.000 0.00 0.00 32.04 5.36
1956 1973 4.470602 TGCTCATACGGAGGAATCTAAGA 58.529 43.478 0.00 0.00 41.45 2.10
2499 2516 3.826524 TGGTCTTGCAAGGTTGTATGAA 58.173 40.909 25.73 0.31 31.08 2.57
2518 2537 0.981183 ACATGGTAGCGACCCAGAAA 59.019 50.000 13.95 0.00 46.32 2.52
2589 2608 1.891722 CTGGCAAGGCAACCCCATTC 61.892 60.000 0.00 0.00 35.39 2.67
2708 2730 1.080569 GGGTGCTTGAACATTGGCG 60.081 57.895 0.00 0.00 0.00 5.69
3287 3309 5.996219 TCACAACAAAATTACATGGAGACG 58.004 37.500 0.00 0.00 0.00 4.18
3383 3405 7.432350 ACAAGAAAGAGCTAGAGTGAAATTG 57.568 36.000 0.00 0.00 0.00 2.32
3384 3406 6.995091 ACAAGAAAGAGCTAGAGTGAAATTGT 59.005 34.615 0.00 0.00 0.00 2.71
3385 3407 8.150945 ACAAGAAAGAGCTAGAGTGAAATTGTA 58.849 33.333 0.00 0.00 0.00 2.41
3386 3408 8.993121 CAAGAAAGAGCTAGAGTGAAATTGTAA 58.007 33.333 0.00 0.00 0.00 2.41
3387 3409 9.732130 AAGAAAGAGCTAGAGTGAAATTGTAAT 57.268 29.630 0.00 0.00 0.00 1.89
3388 3410 9.732130 AGAAAGAGCTAGAGTGAAATTGTAATT 57.268 29.630 0.00 0.00 0.00 1.40
3392 3414 9.289782 AGAGCTAGAGTGAAATTGTAATTTTGT 57.710 29.630 4.27 0.00 38.64 2.83
3393 3415 9.899226 GAGCTAGAGTGAAATTGTAATTTTGTT 57.101 29.630 4.27 0.00 38.64 2.83
3775 3801 3.212377 CCTGGGGATGGGAAATGTG 57.788 57.895 0.00 0.00 0.00 3.21
3915 3941 1.180456 TCGTCGGGTTACTTGGCTCA 61.180 55.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.511272 ACTACCTTCGTTCCATATTAACTTTTT 57.489 29.630 0.00 0.00 0.00 1.94
14 15 9.591792 GTACTACCTTCGTTCCATATTAACTTT 57.408 33.333 0.00 0.00 0.00 2.66
15 16 8.200120 GGTACTACCTTCGTTCCATATTAACTT 58.800 37.037 0.00 0.00 34.73 2.66
16 17 7.720442 GGTACTACCTTCGTTCCATATTAACT 58.280 38.462 0.00 0.00 34.73 2.24
41 42 4.412796 TGGAAAGCTATCCTGATGTCAG 57.587 45.455 3.01 3.01 43.40 3.51
72 73 5.182001 GGCAGTTTTGTGTGTTATGATCTCT 59.818 40.000 0.00 0.00 0.00 3.10
73 74 5.048782 TGGCAGTTTTGTGTGTTATGATCTC 60.049 40.000 0.00 0.00 0.00 2.75
74 75 4.826733 TGGCAGTTTTGTGTGTTATGATCT 59.173 37.500 0.00 0.00 0.00 2.75
75 76 5.119931 TGGCAGTTTTGTGTGTTATGATC 57.880 39.130 0.00 0.00 0.00 2.92
76 77 5.528043 TTGGCAGTTTTGTGTGTTATGAT 57.472 34.783 0.00 0.00 0.00 2.45
77 78 4.991153 TTGGCAGTTTTGTGTGTTATGA 57.009 36.364 0.00 0.00 0.00 2.15
78 79 6.676950 TCTATTGGCAGTTTTGTGTGTTATG 58.323 36.000 0.00 0.00 0.00 1.90
79 80 6.892658 TCTATTGGCAGTTTTGTGTGTTAT 57.107 33.333 0.00 0.00 0.00 1.89
80 81 6.892658 ATCTATTGGCAGTTTTGTGTGTTA 57.107 33.333 0.00 0.00 0.00 2.41
81 82 5.789643 ATCTATTGGCAGTTTTGTGTGTT 57.210 34.783 0.00 0.00 0.00 3.32
82 83 5.183140 GGTATCTATTGGCAGTTTTGTGTGT 59.817 40.000 0.00 0.00 0.00 3.72
83 84 5.393027 GGGTATCTATTGGCAGTTTTGTGTG 60.393 44.000 0.00 0.00 0.00 3.82
126 129 6.611381 CGCAAATATCATCCAATTAATCGGT 58.389 36.000 0.00 0.00 0.00 4.69
128 131 6.249893 CAGCGCAAATATCATCCAATTAATCG 59.750 38.462 11.47 0.00 0.00 3.34
131 134 6.207928 CACAGCGCAAATATCATCCAATTAA 58.792 36.000 11.47 0.00 0.00 1.40
135 138 2.358582 CCACAGCGCAAATATCATCCAA 59.641 45.455 11.47 0.00 0.00 3.53
154 157 7.012044 GCAGAAGTTTGTACTAAGTTTTCTCCA 59.988 37.037 10.76 0.00 33.17 3.86
156 159 8.064814 CAGCAGAAGTTTGTACTAAGTTTTCTC 58.935 37.037 10.76 0.25 33.17 2.87
158 161 7.851472 GTCAGCAGAAGTTTGTACTAAGTTTTC 59.149 37.037 10.76 6.28 33.17 2.29
166 169 3.388024 TCAGGTCAGCAGAAGTTTGTACT 59.612 43.478 0.00 0.00 35.68 2.73
167 170 3.728845 TCAGGTCAGCAGAAGTTTGTAC 58.271 45.455 0.00 0.00 0.00 2.90
174 177 1.151668 CGGTTTCAGGTCAGCAGAAG 58.848 55.000 0.00 0.00 0.00 2.85
204 207 8.232513 GGTTCATGAGTGTAACGACGATATATA 58.767 37.037 0.00 0.00 45.86 0.86
206 209 6.038492 TGGTTCATGAGTGTAACGACGATATA 59.962 38.462 0.00 0.00 45.86 0.86
207 210 5.163591 TGGTTCATGAGTGTAACGACGATAT 60.164 40.000 0.00 0.00 45.86 1.63
208 211 4.156373 TGGTTCATGAGTGTAACGACGATA 59.844 41.667 0.00 0.00 45.86 2.92
209 212 3.057104 TGGTTCATGAGTGTAACGACGAT 60.057 43.478 0.00 0.00 45.86 3.73
210 213 2.293955 TGGTTCATGAGTGTAACGACGA 59.706 45.455 0.00 0.00 45.86 4.20
211 214 2.407361 GTGGTTCATGAGTGTAACGACG 59.593 50.000 0.00 0.00 45.86 5.12
212 215 2.735134 GGTGGTTCATGAGTGTAACGAC 59.265 50.000 0.00 0.00 45.86 4.34
215 218 5.473504 AGAAATGGTGGTTCATGAGTGTAAC 59.526 40.000 0.00 0.00 0.00 2.50
235 238 3.194116 AGACGACCTAATTGCGGTAGAAA 59.806 43.478 13.22 0.00 34.19 2.52
243 246 2.853003 GACGAGAAGACGACCTAATTGC 59.147 50.000 0.00 0.00 37.03 3.56
250 253 0.526662 ATGGTGACGAGAAGACGACC 59.473 55.000 0.00 0.00 37.03 4.79
251 254 2.791849 GCTATGGTGACGAGAAGACGAC 60.792 54.545 0.00 0.00 37.03 4.34
257 260 3.562182 TCCTATGCTATGGTGACGAGAA 58.438 45.455 0.00 0.00 0.00 2.87
269 272 3.557054 GCAACGATGGGAATCCTATGCTA 60.557 47.826 1.85 0.00 0.00 3.49
273 276 3.646162 TGTAGCAACGATGGGAATCCTAT 59.354 43.478 0.00 0.00 0.00 2.57
356 359 5.534207 AATTGAAATGGCTGTTGACTTCA 57.466 34.783 0.00 0.00 0.00 3.02
357 360 5.754890 ACAAATTGAAATGGCTGTTGACTTC 59.245 36.000 0.00 0.00 0.00 3.01
393 396 4.643387 GTCCTTGCCGCCACAGGT 62.643 66.667 0.00 0.00 0.00 4.00
475 484 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
476 485 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
477 486 3.629142 AGTAATTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
478 487 3.073356 ACAAGTAATTTGGAACGGAGGGA 59.927 43.478 0.00 0.00 41.25 4.20
479 488 3.418047 ACAAGTAATTTGGAACGGAGGG 58.582 45.455 0.00 0.00 41.25 4.30
480 489 3.124636 CGACAAGTAATTTGGAACGGAGG 59.875 47.826 0.00 0.00 41.25 4.30
481 490 3.424433 GCGACAAGTAATTTGGAACGGAG 60.424 47.826 0.00 0.00 41.25 4.63
482 491 2.481185 GCGACAAGTAATTTGGAACGGA 59.519 45.455 0.00 0.00 41.25 4.69
483 492 2.224549 TGCGACAAGTAATTTGGAACGG 59.775 45.455 0.00 0.00 41.25 4.44
484 493 3.223157 GTGCGACAAGTAATTTGGAACG 58.777 45.455 0.00 0.00 41.25 3.95
485 494 3.223157 CGTGCGACAAGTAATTTGGAAC 58.777 45.455 0.00 0.00 41.25 3.62
486 495 2.873472 ACGTGCGACAAGTAATTTGGAA 59.127 40.909 0.00 0.00 41.25 3.53
487 496 2.485903 ACGTGCGACAAGTAATTTGGA 58.514 42.857 0.00 0.00 41.25 3.53
488 497 2.961522 ACGTGCGACAAGTAATTTGG 57.038 45.000 0.00 0.00 41.25 3.28
489 498 4.092237 TCCATACGTGCGACAAGTAATTTG 59.908 41.667 0.00 4.77 42.68 2.32
490 499 4.247258 TCCATACGTGCGACAAGTAATTT 58.753 39.130 0.00 0.00 32.82 1.82
491 500 3.852286 TCCATACGTGCGACAAGTAATT 58.148 40.909 0.00 0.00 32.82 1.40
492 501 3.513680 TCCATACGTGCGACAAGTAAT 57.486 42.857 0.00 0.00 32.82 1.89
493 502 3.183754 CATCCATACGTGCGACAAGTAA 58.816 45.455 0.00 0.00 32.82 2.24
494 503 2.164827 ACATCCATACGTGCGACAAGTA 59.835 45.455 0.00 7.72 33.49 2.24
495 504 1.067142 ACATCCATACGTGCGACAAGT 60.067 47.619 0.00 0.00 0.00 3.16
496 505 1.640428 ACATCCATACGTGCGACAAG 58.360 50.000 0.00 0.00 0.00 3.16
497 506 2.943449 TACATCCATACGTGCGACAA 57.057 45.000 0.00 0.00 0.00 3.18
498 507 2.621526 AGATACATCCATACGTGCGACA 59.378 45.455 0.00 0.00 0.00 4.35
499 508 3.284323 AGATACATCCATACGTGCGAC 57.716 47.619 0.00 0.00 0.00 5.19
500 509 5.441709 TTTAGATACATCCATACGTGCGA 57.558 39.130 0.00 0.00 0.00 5.10
501 510 5.633601 ACATTTAGATACATCCATACGTGCG 59.366 40.000 0.00 0.00 0.00 5.34
502 511 8.703604 ATACATTTAGATACATCCATACGTGC 57.296 34.615 0.00 0.00 0.00 5.34
530 539 9.462606 TCGCTGAAATGGATATATCTAGAACTA 57.537 33.333 12.42 0.00 0.00 2.24
531 540 8.247562 GTCGCTGAAATGGATATATCTAGAACT 58.752 37.037 12.42 0.00 0.00 3.01
532 541 7.219154 CGTCGCTGAAATGGATATATCTAGAAC 59.781 40.741 12.42 3.21 0.00 3.01
533 542 7.120726 TCGTCGCTGAAATGGATATATCTAGAA 59.879 37.037 12.42 0.00 0.00 2.10
534 543 6.598064 TCGTCGCTGAAATGGATATATCTAGA 59.402 38.462 12.42 0.00 0.00 2.43
535 544 6.786207 TCGTCGCTGAAATGGATATATCTAG 58.214 40.000 12.42 3.81 0.00 2.43
536 545 6.374613 ACTCGTCGCTGAAATGGATATATCTA 59.625 38.462 12.42 6.97 0.00 1.98
537 546 5.184096 ACTCGTCGCTGAAATGGATATATCT 59.816 40.000 12.42 0.00 0.00 1.98
538 547 5.403246 ACTCGTCGCTGAAATGGATATATC 58.597 41.667 3.96 3.96 0.00 1.63
539 548 5.392767 ACTCGTCGCTGAAATGGATATAT 57.607 39.130 0.00 0.00 0.00 0.86
540 549 4.848562 ACTCGTCGCTGAAATGGATATA 57.151 40.909 0.00 0.00 0.00 0.86
541 550 3.735237 ACTCGTCGCTGAAATGGATAT 57.265 42.857 0.00 0.00 0.00 1.63
542 551 4.642445 TTACTCGTCGCTGAAATGGATA 57.358 40.909 0.00 0.00 0.00 2.59
543 552 3.520290 TTACTCGTCGCTGAAATGGAT 57.480 42.857 0.00 0.00 0.00 3.41
544 553 3.520290 ATTACTCGTCGCTGAAATGGA 57.480 42.857 0.00 0.00 0.00 3.41
545 554 4.334443 CAAATTACTCGTCGCTGAAATGG 58.666 43.478 0.00 0.00 0.00 3.16
546 555 4.092821 TCCAAATTACTCGTCGCTGAAATG 59.907 41.667 0.00 0.00 0.00 2.32
547 556 4.250464 TCCAAATTACTCGTCGCTGAAAT 58.750 39.130 0.00 0.00 0.00 2.17
548 557 3.655486 TCCAAATTACTCGTCGCTGAAA 58.345 40.909 0.00 0.00 0.00 2.69
549 558 3.306917 TCCAAATTACTCGTCGCTGAA 57.693 42.857 0.00 0.00 0.00 3.02
550 559 2.991190 GTTCCAAATTACTCGTCGCTGA 59.009 45.455 0.00 0.00 0.00 4.26
551 560 2.222508 CGTTCCAAATTACTCGTCGCTG 60.223 50.000 0.00 0.00 0.00 5.18
552 561 1.990563 CGTTCCAAATTACTCGTCGCT 59.009 47.619 0.00 0.00 0.00 4.93
553 562 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.00 0.00 0.00 5.19
554 563 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
555 564 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
556 565 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
557 566 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
558 567 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
559 568 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
560 569 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
561 570 3.839490 TGTACTCCCTCCGTTCCAAATTA 59.161 43.478 0.00 0.00 0.00 1.40
562 571 2.640826 TGTACTCCCTCCGTTCCAAATT 59.359 45.455 0.00 0.00 0.00 1.82
563 572 2.262637 TGTACTCCCTCCGTTCCAAAT 58.737 47.619 0.00 0.00 0.00 2.32
564 573 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
565 574 1.621814 CTTGTACTCCCTCCGTTCCAA 59.378 52.381 0.00 0.00 0.00 3.53
566 575 1.203087 TCTTGTACTCCCTCCGTTCCA 60.203 52.381 0.00 0.00 0.00 3.53
567 576 1.553706 TCTTGTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 0.00 3.62
568 577 3.889520 AATCTTGTACTCCCTCCGTTC 57.110 47.619 0.00 0.00 0.00 3.95
569 578 4.091549 TGTAATCTTGTACTCCCTCCGTT 58.908 43.478 0.00 0.00 0.00 4.44
570 579 3.705051 TGTAATCTTGTACTCCCTCCGT 58.295 45.455 0.00 0.00 0.00 4.69
571 580 4.081862 TGTTGTAATCTTGTACTCCCTCCG 60.082 45.833 0.00 0.00 0.00 4.63
572 581 5.416271 TGTTGTAATCTTGTACTCCCTCC 57.584 43.478 0.00 0.00 0.00 4.30
573 582 5.347907 CGTTGTTGTAATCTTGTACTCCCTC 59.652 44.000 0.00 0.00 0.00 4.30
574 583 5.011329 TCGTTGTTGTAATCTTGTACTCCCT 59.989 40.000 0.00 0.00 0.00 4.20
575 584 5.232463 TCGTTGTTGTAATCTTGTACTCCC 58.768 41.667 0.00 0.00 0.00 4.30
576 585 6.774354 TTCGTTGTTGTAATCTTGTACTCC 57.226 37.500 0.00 0.00 0.00 3.85
577 586 9.659830 ATTTTTCGTTGTTGTAATCTTGTACTC 57.340 29.630 0.00 0.00 0.00 2.59
677 688 6.479884 AGTTTTAGAGAATCCAAGCACATCT 58.520 36.000 0.00 0.00 33.66 2.90
681 692 7.148390 GGAGTAAGTTTTAGAGAATCCAAGCAC 60.148 40.741 0.00 0.00 33.66 4.40
696 707 2.922740 TCGGCACAGGAGTAAGTTTT 57.077 45.000 0.00 0.00 0.00 2.43
704 715 1.959985 ACTCATAGATCGGCACAGGAG 59.040 52.381 0.00 0.00 0.00 3.69
706 717 1.000283 GGACTCATAGATCGGCACAGG 60.000 57.143 0.00 0.00 0.00 4.00
707 718 1.959985 AGGACTCATAGATCGGCACAG 59.040 52.381 0.00 0.00 0.00 3.66
756 767 4.650734 TGACAATGAGACATGTTGCCTAA 58.349 39.130 0.00 0.00 0.00 2.69
758 769 3.079578 CTGACAATGAGACATGTTGCCT 58.920 45.455 0.00 0.00 0.00 4.75
803 814 2.171237 CCCAGTCTGTAAGGATGCATCA 59.829 50.000 27.25 6.93 0.00 3.07
816 827 1.163554 GCTTGCTTCTTCCCAGTCTG 58.836 55.000 0.00 0.00 0.00 3.51
822 833 1.303317 TTCGGGCTTGCTTCTTCCC 60.303 57.895 0.00 0.00 35.42 3.97
836 847 5.306394 ACTTTTCTTAGTTCCTTCCTTCGG 58.694 41.667 0.00 0.00 0.00 4.30
865 876 3.941483 CACCACTTGTTGTCTGAGTCTTT 59.059 43.478 0.00 0.00 0.00 2.52
873 884 2.172717 ACTTAGGCACCACTTGTTGTCT 59.827 45.455 0.00 0.00 0.00 3.41
956 967 1.443194 CTGCGATGTGGTTTGCAGC 60.443 57.895 0.00 0.00 46.97 5.25
1167 1178 3.706600 TTAACCCGAGCTGTACCATTT 57.293 42.857 0.00 0.00 0.00 2.32
1234 1245 1.237285 AAAGACTGCACCGTGCCATC 61.237 55.000 20.67 16.72 44.23 3.51
1660 1671 0.322975 GAAAGCAGTGGCCTCTCAGA 59.677 55.000 3.81 0.00 42.56 3.27
1839 1853 0.390472 GAGCCTTCTGACCAAGACGG 60.390 60.000 0.00 0.00 45.27 4.79
1956 1973 5.938710 CCAATCTTCACATAGCTCAGCATAT 59.061 40.000 0.00 0.00 0.00 1.78
2405 2422 5.804473 GCCTTGATGTCTCGATGTATGATAG 59.196 44.000 0.00 0.00 0.00 2.08
2518 2537 0.459489 GTGCCAACAACATGTGTGGT 59.541 50.000 19.36 8.50 40.60 4.16
2708 2730 5.182001 ACTGCATCATTGAGTGAACCTTTAC 59.818 40.000 0.00 0.00 40.97 2.01
3287 3309 8.343366 GCAACAAGAACTATAATAAACTAGCCC 58.657 37.037 0.00 0.00 0.00 5.19
3441 3463 2.976099 GGGGGTGGGAATGAAACAG 58.024 57.895 0.00 0.00 0.00 3.16
3547 3572 9.383519 TCTTTGGACAATGTGTCTTAAGATATC 57.616 33.333 8.75 0.04 46.19 1.63
3775 3801 2.170187 ACTCATCTTCACCAGATCAGGC 59.830 50.000 3.64 0.00 40.67 4.85
3842 3868 0.535102 GTCCACAGGTGACCACTTGG 60.535 60.000 15.14 7.13 41.98 3.61
3915 3941 2.031163 AAGCAGAGCGGCGAAACT 59.969 55.556 12.98 2.67 39.27 2.66


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

AutoCloner maintained by Alex Coulton.