Multiple sequence alignment - TraesCS5A01G231800

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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 TraesCS5A01G231800 chr5A 100.000 3545 0 0 1 3545 447364552 447368096 0.000000e+00 6547.0
1 TraesCS5A01G231800 chr5A 93.363 226 10 1 1 221 510287189 510287414 2.640000e-86 329.0
2 TraesCS5A01G231800 chr5A 93.333 225 10 1 1 220 136980981 136980757 9.490000e-86 327.0
3 TraesCS5A01G231800 chr5D 97.196 2960 68 12 590 3545 344696750 344693802 0.000000e+00 4992.0
4 TraesCS5A01G231800 chr5D 91.051 257 18 2 220 471 344696998 344696742 3.390000e-90 342.0
5 TraesCS5A01G231800 chr5B 96.676 2828 74 12 723 3545 407123418 407126230 0.000000e+00 4684.0
6 TraesCS5A01G231800 chr5B 93.496 123 7 1 473 594 419761668 419761546 7.820000e-42 182.0
7 TraesCS5A01G231800 chr5B 91.667 108 8 1 591 697 407123103 407123210 7.930000e-32 148.0
8 TraesCS5A01G231800 chr3A 96.985 199 6 0 1 199 143479932 143479734 5.670000e-88 335.0
9 TraesCS5A01G231800 chr3A 93.304 224 10 1 1 219 171771943 171772166 3.410000e-85 326.0
10 TraesCS5A01G231800 chr2A 94.470 217 12 0 3 219 105626736 105626952 5.670000e-88 335.0
11 TraesCS5A01G231800 chr2A 93.548 124 7 1 469 591 218122246 218122369 2.170000e-42 183.0
12 TraesCS5A01G231800 chr2A 77.311 238 42 8 1697 1927 775615481 775615249 2.870000e-26 130.0
13 TraesCS5A01G231800 chr6A 93.333 225 11 1 1 221 109490956 109491180 2.640000e-86 329.0
14 TraesCS5A01G231800 chr6A 87.778 90 8 3 240 327 97608468 97608380 6.260000e-18 102.0
15 TraesCS5A01G231800 chr4A 92.544 228 13 1 1 224 474966843 474967070 1.230000e-84 324.0
16 TraesCS5A01G231800 chr2D 92.694 219 16 0 1 219 35028069 35028287 2.050000e-82 316.0
17 TraesCS5A01G231800 chr7A 91.818 220 17 1 1 220 705632765 705632983 4.450000e-79 305.0
18 TraesCS5A01G231800 chr7A 95.000 120 5 1 473 591 115736260 115736379 1.680000e-43 187.0
19 TraesCS5A01G231800 chr7A 92.913 127 6 2 469 594 381242901 381242777 7.820000e-42 182.0
20 TraesCS5A01G231800 chr7D 92.969 128 8 1 465 591 194482102 194481975 6.040000e-43 185.0
21 TraesCS5A01G231800 chr7D 92.913 127 8 1 469 594 312470385 312470511 2.170000e-42 183.0
22 TraesCS5A01G231800 chr2B 92.857 126 8 1 473 597 601177698 601177573 7.820000e-42 182.0
23 TraesCS5A01G231800 chr7B 92.126 127 9 1 469 594 303722390 303722516 1.010000e-40 178.0
24 TraesCS5A01G231800 chr1D 89.928 139 11 3 461 597 465126601 465126464 3.640000e-40 176.0
25 TraesCS5A01G231800 chr6D 86.441 59 5 3 443 500 47081143 47081199 1.060000e-05 62.1


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 TraesCS5A01G231800 chr5A 447364552 447368096 3544 False 6547 6547 100.0000 1 3545 1 chr5A.!!$F1 3544
1 TraesCS5A01G231800 chr5D 344693802 344696998 3196 True 2667 4992 94.1235 220 3545 2 chr5D.!!$R1 3325
2 TraesCS5A01G231800 chr5B 407123103 407126230 3127 False 2416 4684 94.1715 591 3545 2 chr5B.!!$F1 2954

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
95 96 0.033366 AACTGCAAAAATGACGGGCC 59.967 50.0 0.00 0.0 0.00 5.80 F
136 137 0.107165 ACCGGGCTCAAAATCTAGGC 60.107 55.0 6.32 0.0 37.55 3.93 F
140 141 0.180406 GGCTCAAAATCTAGGCCCGA 59.820 55.0 0.00 0.0 37.12 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1221 1415 1.615814 CGAAGGGGAGGAGAGGAGA 59.384 63.158 0.00 0.0 0.0 3.71 R
2190 2384 3.430565 CTCCACCAGCTCGCGCATA 62.431 63.158 8.75 0.0 39.1 3.14 R
2723 2918 3.772619 GGCAAGTATAAGCCGTCCA 57.227 52.632 0.00 0.0 41.7 4.02 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
34 35 3.369400 CCGGCCCGAACATGCAAA 61.369 61.111 3.71 0.00 0.00 3.68
35 36 2.647875 CGGCCCGAACATGCAAAA 59.352 55.556 0.00 0.00 0.00 2.44
36 37 1.444212 CGGCCCGAACATGCAAAAG 60.444 57.895 0.00 0.00 0.00 2.27
37 38 1.737735 GGCCCGAACATGCAAAAGC 60.738 57.895 0.00 0.00 0.00 3.51
38 39 1.737735 GCCCGAACATGCAAAAGCC 60.738 57.895 0.00 0.00 0.00 4.35
39 40 1.079888 CCCGAACATGCAAAAGCCC 60.080 57.895 0.00 0.00 0.00 5.19
40 41 1.664873 CCGAACATGCAAAAGCCCA 59.335 52.632 0.00 0.00 0.00 5.36
41 42 0.667184 CCGAACATGCAAAAGCCCAC 60.667 55.000 0.00 0.00 0.00 4.61
42 43 0.667184 CGAACATGCAAAAGCCCACC 60.667 55.000 0.00 0.00 0.00 4.61
43 44 0.667184 GAACATGCAAAAGCCCACCG 60.667 55.000 0.00 0.00 0.00 4.94
44 45 2.098426 AACATGCAAAAGCCCACCGG 62.098 55.000 0.00 0.00 0.00 5.28
75 76 4.360405 GGCCGGGCCCTTTCAGAA 62.360 66.667 28.23 0.00 44.06 3.02
76 77 2.282887 GCCGGGCCCTTTCAGAAA 60.283 61.111 22.43 0.00 0.00 2.52
77 78 1.906333 GCCGGGCCCTTTCAGAAAA 60.906 57.895 22.43 0.00 0.00 2.29
78 79 1.964448 CCGGGCCCTTTCAGAAAAC 59.036 57.895 22.43 0.00 0.00 2.43
79 80 0.539669 CCGGGCCCTTTCAGAAAACT 60.540 55.000 22.43 0.00 0.00 2.66
80 81 0.598065 CGGGCCCTTTCAGAAAACTG 59.402 55.000 22.43 0.00 0.00 3.16
81 82 0.318441 GGGCCCTTTCAGAAAACTGC 59.682 55.000 17.04 0.31 0.00 4.40
82 83 1.039856 GGCCCTTTCAGAAAACTGCA 58.960 50.000 11.16 0.00 0.00 4.41
83 84 1.412343 GGCCCTTTCAGAAAACTGCAA 59.588 47.619 11.16 0.00 0.00 4.08
84 85 2.158971 GGCCCTTTCAGAAAACTGCAAA 60.159 45.455 11.16 0.00 0.00 3.68
85 86 3.530535 GCCCTTTCAGAAAACTGCAAAA 58.469 40.909 0.00 0.00 0.00 2.44
86 87 3.938334 GCCCTTTCAGAAAACTGCAAAAA 59.062 39.130 0.00 0.00 0.00 1.94
87 88 4.576053 GCCCTTTCAGAAAACTGCAAAAAT 59.424 37.500 0.00 0.00 0.00 1.82
88 89 5.504501 GCCCTTTCAGAAAACTGCAAAAATG 60.505 40.000 0.00 0.00 0.00 2.32
89 90 5.816777 CCCTTTCAGAAAACTGCAAAAATGA 59.183 36.000 0.00 0.00 0.00 2.57
90 91 6.238184 CCCTTTCAGAAAACTGCAAAAATGAC 60.238 38.462 0.00 0.00 0.00 3.06
91 92 5.947503 TTCAGAAAACTGCAAAAATGACG 57.052 34.783 0.00 0.00 0.00 4.35
92 93 4.358851 TCAGAAAACTGCAAAAATGACGG 58.641 39.130 0.00 0.00 0.00 4.79
93 94 3.490526 CAGAAAACTGCAAAAATGACGGG 59.509 43.478 0.00 0.00 0.00 5.28
94 95 1.864565 AAACTGCAAAAATGACGGGC 58.135 45.000 0.00 0.00 0.00 6.13
95 96 0.033366 AACTGCAAAAATGACGGGCC 59.967 50.000 0.00 0.00 0.00 5.80
96 97 1.079888 CTGCAAAAATGACGGGCCC 60.080 57.895 13.57 13.57 0.00 5.80
97 98 2.126110 GCAAAAATGACGGGCCCG 60.126 61.111 42.17 42.17 46.03 6.13
98 99 2.571231 CAAAAATGACGGGCCCGG 59.429 61.111 44.99 28.13 44.69 5.73
99 100 2.678580 AAAAATGACGGGCCCGGG 60.679 61.111 44.99 22.37 44.69 5.73
132 133 4.743018 CCACCGGGCTCAAAATCT 57.257 55.556 6.32 0.00 0.00 2.40
133 134 3.873781 CCACCGGGCTCAAAATCTA 57.126 52.632 6.32 0.00 0.00 1.98
134 135 1.668419 CCACCGGGCTCAAAATCTAG 58.332 55.000 6.32 0.00 0.00 2.43
135 136 1.668419 CACCGGGCTCAAAATCTAGG 58.332 55.000 6.32 0.00 0.00 3.02
136 137 0.107165 ACCGGGCTCAAAATCTAGGC 60.107 55.000 6.32 0.00 37.55 3.93
139 140 2.707902 GGCTCAAAATCTAGGCCCG 58.292 57.895 0.00 0.00 37.12 6.13
140 141 0.180406 GGCTCAAAATCTAGGCCCGA 59.820 55.000 0.00 0.00 37.12 5.14
141 142 1.587547 GCTCAAAATCTAGGCCCGAG 58.412 55.000 0.00 0.00 0.00 4.63
142 143 1.587547 CTCAAAATCTAGGCCCGAGC 58.412 55.000 0.00 0.00 38.76 5.03
182 183 3.382832 CCGAGTCGGGTCAGGCTT 61.383 66.667 24.39 0.00 44.15 4.35
183 184 2.657237 CGAGTCGGGTCAGGCTTT 59.343 61.111 4.10 0.00 0.00 3.51
184 185 1.004918 CGAGTCGGGTCAGGCTTTT 60.005 57.895 4.10 0.00 0.00 2.27
185 186 0.602905 CGAGTCGGGTCAGGCTTTTT 60.603 55.000 4.10 0.00 0.00 1.94
186 187 1.157585 GAGTCGGGTCAGGCTTTTTC 58.842 55.000 0.00 0.00 0.00 2.29
187 188 0.602905 AGTCGGGTCAGGCTTTTTCG 60.603 55.000 0.00 0.00 0.00 3.46
188 189 1.302192 TCGGGTCAGGCTTTTTCGG 60.302 57.895 0.00 0.00 0.00 4.30
189 190 2.332654 CGGGTCAGGCTTTTTCGGG 61.333 63.158 0.00 0.00 0.00 5.14
190 191 2.636412 GGGTCAGGCTTTTTCGGGC 61.636 63.158 0.00 0.00 0.00 6.13
247 248 4.535526 GCTTCAAGCCCAATAGGAAAAA 57.464 40.909 0.00 0.00 38.24 1.94
278 279 4.190772 CACAAACAAGGGCAAGTCAAAAT 58.809 39.130 0.00 0.00 0.00 1.82
284 285 6.233905 ACAAGGGCAAGTCAAAATTTTAGT 57.766 33.333 2.44 0.00 0.00 2.24
313 314 7.625469 AGAAAAAGTCAATTTACCCCAAACAA 58.375 30.769 0.00 0.00 0.00 2.83
329 330 5.058490 CCAAACAATGGCAAGTCAAAATCT 58.942 37.500 0.00 0.00 43.80 2.40
332 333 7.095523 CCAAACAATGGCAAGTCAAAATCTAAG 60.096 37.037 0.00 0.00 43.80 2.18
334 335 4.725790 ATGGCAAGTCAAAATCTAAGCC 57.274 40.909 0.00 0.00 37.02 4.35
346 347 9.010366 GTCAAAATCTAAGCCACGAAATAATTC 57.990 33.333 0.00 0.00 0.00 2.17
353 354 5.813080 AGCCACGAAATAATTCACTTACC 57.187 39.130 0.00 0.00 35.15 2.85
361 362 7.177744 ACGAAATAATTCACTTACCCCAAACAT 59.822 33.333 0.00 0.00 35.15 2.71
379 380 7.148373 CCCAAACATGAGCAAATCAAAATTAGG 60.148 37.037 0.00 0.00 42.53 2.69
401 402 4.229876 GCTAAGAAGCCATGAAACAACAC 58.770 43.478 0.00 0.00 43.40 3.32
403 404 3.996150 AGAAGCCATGAAACAACACAG 57.004 42.857 0.00 0.00 0.00 3.66
453 459 7.698836 AAAAACTTGACGATCAGAAAATTGG 57.301 32.000 0.00 0.00 0.00 3.16
511 517 7.579589 CATCTAGATGTGCTCTAAGTATTGC 57.420 40.000 22.42 0.00 36.02 3.56
512 518 6.715347 TCTAGATGTGCTCTAAGTATTGCA 57.285 37.500 0.00 0.00 36.02 4.08
521 527 6.878317 TGCTCTAAGTATTGCACATCTAAGT 58.122 36.000 0.00 0.00 0.00 2.24
522 528 6.980978 TGCTCTAAGTATTGCACATCTAAGTC 59.019 38.462 0.00 0.00 0.00 3.01
523 529 6.422400 GCTCTAAGTATTGCACATCTAAGTCC 59.578 42.308 0.00 0.00 0.00 3.85
524 530 7.661536 TCTAAGTATTGCACATCTAAGTCCT 57.338 36.000 0.00 0.00 0.00 3.85
525 531 8.762481 TCTAAGTATTGCACATCTAAGTCCTA 57.238 34.615 0.00 0.00 0.00 2.94
526 532 9.368416 TCTAAGTATTGCACATCTAAGTCCTAT 57.632 33.333 0.00 0.00 0.00 2.57
527 533 9.416794 CTAAGTATTGCACATCTAAGTCCTATG 57.583 37.037 0.00 0.00 0.00 2.23
528 534 7.366847 AGTATTGCACATCTAAGTCCTATGT 57.633 36.000 0.00 0.00 34.22 2.29
529 535 7.437748 AGTATTGCACATCTAAGTCCTATGTC 58.562 38.462 0.00 0.00 31.60 3.06
530 536 5.675684 TTGCACATCTAAGTCCTATGTCA 57.324 39.130 0.00 0.00 31.60 3.58
531 537 5.876651 TGCACATCTAAGTCCTATGTCAT 57.123 39.130 0.00 0.00 31.60 3.06
532 538 6.239217 TGCACATCTAAGTCCTATGTCATT 57.761 37.500 0.00 0.00 31.60 2.57
533 539 6.051074 TGCACATCTAAGTCCTATGTCATTG 58.949 40.000 0.00 0.00 31.60 2.82
534 540 6.127083 TGCACATCTAAGTCCTATGTCATTGA 60.127 38.462 0.00 0.00 31.60 2.57
535 541 6.933521 GCACATCTAAGTCCTATGTCATTGAT 59.066 38.462 0.00 0.00 31.60 2.57
536 542 7.443575 GCACATCTAAGTCCTATGTCATTGATT 59.556 37.037 0.00 0.00 31.60 2.57
537 543 9.334947 CACATCTAAGTCCTATGTCATTGATTT 57.665 33.333 0.00 0.00 31.60 2.17
538 544 9.911788 ACATCTAAGTCCTATGTCATTGATTTT 57.088 29.630 0.00 0.00 0.00 1.82
541 547 9.529325 TCTAAGTCCTATGTCATTGATTTTACG 57.471 33.333 0.00 0.00 0.00 3.18
542 548 9.314321 CTAAGTCCTATGTCATTGATTTTACGT 57.686 33.333 0.00 0.00 0.00 3.57
543 549 8.561738 AAGTCCTATGTCATTGATTTTACGTT 57.438 30.769 0.00 0.00 0.00 3.99
544 550 9.661563 AAGTCCTATGTCATTGATTTTACGTTA 57.338 29.630 0.00 0.00 0.00 3.18
545 551 9.661563 AGTCCTATGTCATTGATTTTACGTTAA 57.338 29.630 0.00 0.00 0.00 2.01
546 552 9.916397 GTCCTATGTCATTGATTTTACGTTAAG 57.084 33.333 0.00 0.00 0.00 1.85
547 553 9.878667 TCCTATGTCATTGATTTTACGTTAAGA 57.121 29.630 0.00 0.00 0.00 2.10
554 560 9.502145 TCATTGATTTTACGTTAAGATTCATGC 57.498 29.630 0.00 0.00 0.00 4.06
555 561 9.288124 CATTGATTTTACGTTAAGATTCATGCA 57.712 29.630 0.00 0.00 0.00 3.96
556 562 9.853555 ATTGATTTTACGTTAAGATTCATGCAA 57.146 25.926 0.00 0.00 0.00 4.08
557 563 8.894409 TGATTTTACGTTAAGATTCATGCAAG 57.106 30.769 0.00 0.00 0.00 4.01
558 564 7.484641 TGATTTTACGTTAAGATTCATGCAAGC 59.515 33.333 0.00 0.00 0.00 4.01
559 565 5.871465 TTACGTTAAGATTCATGCAAGCA 57.129 34.783 0.00 0.00 0.00 3.91
560 566 4.970662 ACGTTAAGATTCATGCAAGCAT 57.029 36.364 0.86 0.86 37.08 3.79
561 567 5.314923 ACGTTAAGATTCATGCAAGCATT 57.685 34.783 4.52 0.00 33.90 3.56
562 568 5.713025 ACGTTAAGATTCATGCAAGCATTT 58.287 33.333 4.52 0.00 33.90 2.32
563 569 6.158598 ACGTTAAGATTCATGCAAGCATTTT 58.841 32.000 4.52 0.00 33.90 1.82
564 570 6.308766 ACGTTAAGATTCATGCAAGCATTTTC 59.691 34.615 4.52 3.08 33.90 2.29
565 571 6.529125 CGTTAAGATTCATGCAAGCATTTTCT 59.471 34.615 4.52 5.25 33.90 2.52
566 572 7.062605 CGTTAAGATTCATGCAAGCATTTTCTT 59.937 33.333 19.26 19.26 33.90 2.52
567 573 8.715088 GTTAAGATTCATGCAAGCATTTTCTTT 58.285 29.630 19.96 10.46 33.90 2.52
568 574 7.739498 AAGATTCATGCAAGCATTTTCTTTT 57.261 28.000 4.52 0.00 33.90 2.27
569 575 8.836268 AAGATTCATGCAAGCATTTTCTTTTA 57.164 26.923 4.52 0.00 33.90 1.52
570 576 9.444600 AAGATTCATGCAAGCATTTTCTTTTAT 57.555 25.926 4.52 0.00 33.90 1.40
571 577 9.095065 AGATTCATGCAAGCATTTTCTTTTATC 57.905 29.630 4.52 0.98 33.90 1.75
572 578 9.095065 GATTCATGCAAGCATTTTCTTTTATCT 57.905 29.630 4.52 0.00 33.90 1.98
573 579 8.836268 TTCATGCAAGCATTTTCTTTTATCTT 57.164 26.923 4.52 0.00 33.90 2.40
574 580 8.836268 TCATGCAAGCATTTTCTTTTATCTTT 57.164 26.923 4.52 0.00 33.90 2.52
575 581 9.275398 TCATGCAAGCATTTTCTTTTATCTTTT 57.725 25.926 4.52 0.00 33.90 2.27
576 582 9.325150 CATGCAAGCATTTTCTTTTATCTTTTG 57.675 29.630 4.52 0.00 33.90 2.44
577 583 8.436046 TGCAAGCATTTTCTTTTATCTTTTGT 57.564 26.923 0.00 0.00 0.00 2.83
578 584 8.550376 TGCAAGCATTTTCTTTTATCTTTTGTC 58.450 29.630 0.00 0.00 0.00 3.18
579 585 8.768019 GCAAGCATTTTCTTTTATCTTTTGTCT 58.232 29.630 0.00 0.00 0.00 3.41
641 647 8.045176 AGCTAAAGTTTAATTAGACTGCCTTG 57.955 34.615 9.27 1.40 33.16 3.61
724 748 5.648330 AGTTTTCTTACCCCATCCTATCC 57.352 43.478 0.00 0.00 0.00 2.59
870 1064 0.322008 CTCCCTTCACCTGGCTTCAC 60.322 60.000 0.00 0.00 0.00 3.18
914 1108 1.139989 CCAGTGACACTACGCTGTTG 58.860 55.000 8.02 0.00 43.98 3.33
954 1148 0.456312 GCATCAAGCAACTGAGCAGC 60.456 55.000 0.00 0.00 44.79 5.25
1146 1340 1.139095 CTCCTACTTCGACGTGCCC 59.861 63.158 4.57 0.00 0.00 5.36
1209 1403 1.810532 CCACGTCCAGCTCTACCTC 59.189 63.158 0.00 0.00 0.00 3.85
1221 1415 1.686110 CTACCTCCACCGCTCCCTT 60.686 63.158 0.00 0.00 0.00 3.95
2274 2468 2.423446 GAGGGCTGCATACGGGAG 59.577 66.667 0.50 0.00 38.13 4.30
2622 2817 9.522804 TTCACAAGTTTAATGTATTGGTTTGAC 57.477 29.630 0.00 0.00 0.00 3.18
2743 2946 0.179468 GGACGGCTTATACTTGCCCA 59.821 55.000 0.00 0.00 45.90 5.36
2752 2955 2.876368 ATACTTGCCCAGCACGAGCC 62.876 60.000 0.00 0.00 43.56 4.70
2753 2956 4.711949 CTTGCCCAGCACGAGCCT 62.712 66.667 0.00 0.00 43.56 4.58
2754 2957 4.704833 TTGCCCAGCACGAGCCTC 62.705 66.667 0.00 0.00 43.56 4.70
2759 2962 4.154347 CAGCACGAGCCTCCCCTC 62.154 72.222 0.00 0.00 43.56 4.30
2985 3188 0.804989 CAAGAACCTGTGGATTCGGC 59.195 55.000 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.817470 CTTTTGCATGTTCGGGCCGG 62.817 60.000 27.98 10.74 0.00 6.13
18 19 1.444212 CTTTTGCATGTTCGGGCCG 60.444 57.895 22.51 22.51 0.00 6.13
19 20 1.737735 GCTTTTGCATGTTCGGGCC 60.738 57.895 0.00 0.00 46.58 5.80
20 21 3.860717 GCTTTTGCATGTTCGGGC 58.139 55.556 0.00 0.00 46.58 6.13
59 60 1.906333 TTTTCTGAAAGGGCCCGGC 60.906 57.895 18.44 10.57 0.00 6.13
60 61 0.539669 AGTTTTCTGAAAGGGCCCGG 60.540 55.000 18.44 5.76 0.00 5.73
61 62 3.036431 AGTTTTCTGAAAGGGCCCG 57.964 52.632 18.44 0.58 0.00 6.13
72 73 3.716601 CCCGTCATTTTTGCAGTTTTCT 58.283 40.909 0.00 0.00 0.00 2.52
73 74 2.220824 GCCCGTCATTTTTGCAGTTTTC 59.779 45.455 0.00 0.00 0.00 2.29
74 75 2.209273 GCCCGTCATTTTTGCAGTTTT 58.791 42.857 0.00 0.00 0.00 2.43
75 76 1.540146 GGCCCGTCATTTTTGCAGTTT 60.540 47.619 0.00 0.00 0.00 2.66
76 77 0.033366 GGCCCGTCATTTTTGCAGTT 59.967 50.000 0.00 0.00 0.00 3.16
77 78 1.665442 GGCCCGTCATTTTTGCAGT 59.335 52.632 0.00 0.00 0.00 4.40
78 79 1.079888 GGGCCCGTCATTTTTGCAG 60.080 57.895 5.69 0.00 0.00 4.41
79 80 2.925262 CGGGCCCGTCATTTTTGCA 61.925 57.895 36.64 0.00 34.35 4.08
80 81 2.126110 CGGGCCCGTCATTTTTGC 60.126 61.111 36.64 0.00 34.35 3.68
81 82 2.571231 CCGGGCCCGTCATTTTTG 59.429 61.111 40.52 20.46 37.81 2.44
82 83 2.678580 CCCGGGCCCGTCATTTTT 60.679 61.111 40.52 0.00 37.81 1.94
115 116 1.668419 CTAGATTTTGAGCCCGGTGG 58.332 55.000 0.00 0.00 0.00 4.61
116 117 1.668419 CCTAGATTTTGAGCCCGGTG 58.332 55.000 0.00 0.00 0.00 4.94
117 118 0.107165 GCCTAGATTTTGAGCCCGGT 60.107 55.000 0.00 0.00 0.00 5.28
118 119 0.819666 GGCCTAGATTTTGAGCCCGG 60.820 60.000 0.00 0.00 37.66 5.73
119 120 2.707902 GGCCTAGATTTTGAGCCCG 58.292 57.895 0.00 0.00 37.66 6.13
121 122 0.180406 TCGGGCCTAGATTTTGAGCC 59.820 55.000 0.84 0.00 43.09 4.70
122 123 1.587547 CTCGGGCCTAGATTTTGAGC 58.412 55.000 0.84 0.00 0.00 4.26
123 124 1.587547 GCTCGGGCCTAGATTTTGAG 58.412 55.000 9.63 2.79 0.00 3.02
124 125 3.780624 GCTCGGGCCTAGATTTTGA 57.219 52.632 9.63 0.00 0.00 2.69
166 167 0.602905 AAAAAGCCTGACCCGACTCG 60.603 55.000 0.00 0.00 0.00 4.18
167 168 1.157585 GAAAAAGCCTGACCCGACTC 58.842 55.000 0.00 0.00 0.00 3.36
168 169 0.602905 CGAAAAAGCCTGACCCGACT 60.603 55.000 0.00 0.00 0.00 4.18
169 170 1.574702 CCGAAAAAGCCTGACCCGAC 61.575 60.000 0.00 0.00 0.00 4.79
170 171 1.302192 CCGAAAAAGCCTGACCCGA 60.302 57.895 0.00 0.00 0.00 5.14
171 172 2.332654 CCCGAAAAAGCCTGACCCG 61.333 63.158 0.00 0.00 0.00 5.28
172 173 2.636412 GCCCGAAAAAGCCTGACCC 61.636 63.158 0.00 0.00 0.00 4.46
173 174 2.636412 GGCCCGAAAAAGCCTGACC 61.636 63.158 0.00 0.00 46.14 4.02
174 175 2.962569 GGCCCGAAAAAGCCTGAC 59.037 61.111 0.00 0.00 46.14 3.51
203 204 1.141053 GTTACTAGACCTGGCCATGGG 59.859 57.143 20.97 16.10 0.00 4.00
204 205 1.202533 CGTTACTAGACCTGGCCATGG 60.203 57.143 5.51 13.05 0.00 3.66
205 206 1.202533 CCGTTACTAGACCTGGCCATG 60.203 57.143 5.51 6.06 0.00 3.66
206 207 1.120530 CCGTTACTAGACCTGGCCAT 58.879 55.000 5.51 0.00 0.00 4.40
207 208 0.974010 CCCGTTACTAGACCTGGCCA 60.974 60.000 4.71 4.71 0.00 5.36
208 209 1.821258 CCCGTTACTAGACCTGGCC 59.179 63.158 0.00 0.00 0.00 5.36
209 210 1.143401 GCCCGTTACTAGACCTGGC 59.857 63.158 0.00 0.00 0.00 4.85
210 211 1.136500 GAAGCCCGTTACTAGACCTGG 59.864 57.143 0.00 0.00 0.00 4.45
211 212 1.822990 TGAAGCCCGTTACTAGACCTG 59.177 52.381 0.00 0.00 0.00 4.00
212 213 2.226962 TGAAGCCCGTTACTAGACCT 57.773 50.000 0.00 0.00 0.00 3.85
213 214 2.889852 CTTGAAGCCCGTTACTAGACC 58.110 52.381 0.00 0.00 0.00 3.85
214 215 2.269172 GCTTGAAGCCCGTTACTAGAC 58.731 52.381 5.74 0.00 34.48 2.59
215 216 2.667473 GCTTGAAGCCCGTTACTAGA 57.333 50.000 5.74 0.00 34.48 2.43
242 243 5.513849 CCTTGTTTGTGGTAAGTCGTTTTTC 59.486 40.000 0.00 0.00 0.00 2.29
247 248 2.567985 CCCTTGTTTGTGGTAAGTCGT 58.432 47.619 0.00 0.00 0.00 4.34
284 285 8.770010 TTGGGGTAAATTGACTTTTTCTTAGA 57.230 30.769 0.00 0.00 0.00 2.10
313 314 4.082026 GTGGCTTAGATTTTGACTTGCCAT 60.082 41.667 6.64 0.00 42.52 4.40
317 318 5.356882 TTCGTGGCTTAGATTTTGACTTG 57.643 39.130 0.00 0.00 0.00 3.16
329 330 6.316890 GGGTAAGTGAATTATTTCGTGGCTTA 59.683 38.462 0.00 0.00 34.39 3.09
332 333 4.201980 GGGGTAAGTGAATTATTTCGTGGC 60.202 45.833 0.00 0.00 34.39 5.01
334 335 6.503589 TTGGGGTAAGTGAATTATTTCGTG 57.496 37.500 0.00 0.00 34.39 4.35
346 347 2.513753 TGCTCATGTTTGGGGTAAGTG 58.486 47.619 0.00 0.00 0.00 3.16
353 354 6.563222 AATTTTGATTTGCTCATGTTTGGG 57.437 33.333 0.00 0.00 32.72 4.12
361 362 7.701539 TCTTAGCCTAATTTTGATTTGCTCA 57.298 32.000 0.00 0.00 0.00 4.26
436 442 5.296780 GGATAAGCCAATTTTCTGATCGTCA 59.703 40.000 0.00 0.00 36.34 4.35
487 493 7.150640 TGCAATACTTAGAGCACATCTAGATG 58.849 38.462 27.63 27.63 41.57 2.90
488 494 7.295322 TGCAATACTTAGAGCACATCTAGAT 57.705 36.000 0.00 0.00 41.57 1.98
489 495 6.715347 TGCAATACTTAGAGCACATCTAGA 57.285 37.500 0.00 0.00 41.57 2.43
497 503 6.878317 ACTTAGATGTGCAATACTTAGAGCA 58.122 36.000 0.00 0.00 34.10 4.26
498 504 6.422400 GGACTTAGATGTGCAATACTTAGAGC 59.578 42.308 0.00 0.00 0.00 4.09
499 505 7.721402 AGGACTTAGATGTGCAATACTTAGAG 58.279 38.462 0.00 0.00 0.00 2.43
500 506 7.661536 AGGACTTAGATGTGCAATACTTAGA 57.338 36.000 0.00 0.00 0.00 2.10
501 507 9.416794 CATAGGACTTAGATGTGCAATACTTAG 57.583 37.037 0.00 0.00 0.00 2.18
502 508 8.924303 ACATAGGACTTAGATGTGCAATACTTA 58.076 33.333 0.00 0.00 32.62 2.24
503 509 7.796054 ACATAGGACTTAGATGTGCAATACTT 58.204 34.615 0.00 0.00 32.62 2.24
504 510 7.069950 TGACATAGGACTTAGATGTGCAATACT 59.930 37.037 0.00 0.00 33.99 2.12
505 511 7.210174 TGACATAGGACTTAGATGTGCAATAC 58.790 38.462 0.00 0.00 33.99 1.89
506 512 7.360113 TGACATAGGACTTAGATGTGCAATA 57.640 36.000 0.00 0.00 33.99 1.90
507 513 6.239217 TGACATAGGACTTAGATGTGCAAT 57.761 37.500 0.00 0.00 33.99 3.56
508 514 5.675684 TGACATAGGACTTAGATGTGCAA 57.324 39.130 0.00 0.00 33.99 4.08
509 515 5.876651 ATGACATAGGACTTAGATGTGCA 57.123 39.130 0.00 0.00 33.99 4.57
510 516 6.283694 TCAATGACATAGGACTTAGATGTGC 58.716 40.000 0.00 0.00 33.99 4.57
511 517 8.899427 AATCAATGACATAGGACTTAGATGTG 57.101 34.615 0.00 0.00 33.99 3.21
512 518 9.911788 AAAATCAATGACATAGGACTTAGATGT 57.088 29.630 0.00 0.00 36.52 3.06
515 521 9.529325 CGTAAAATCAATGACATAGGACTTAGA 57.471 33.333 0.00 0.00 0.00 2.10
516 522 9.314321 ACGTAAAATCAATGACATAGGACTTAG 57.686 33.333 0.00 0.00 0.00 2.18
517 523 9.661563 AACGTAAAATCAATGACATAGGACTTA 57.338 29.630 0.00 0.00 0.00 2.24
518 524 8.561738 AACGTAAAATCAATGACATAGGACTT 57.438 30.769 0.00 0.00 0.00 3.01
519 525 9.661563 TTAACGTAAAATCAATGACATAGGACT 57.338 29.630 0.00 0.00 0.00 3.85
520 526 9.916397 CTTAACGTAAAATCAATGACATAGGAC 57.084 33.333 0.00 0.00 0.00 3.85
521 527 9.878667 TCTTAACGTAAAATCAATGACATAGGA 57.121 29.630 0.00 0.00 0.00 2.94
528 534 9.502145 GCATGAATCTTAACGTAAAATCAATGA 57.498 29.630 0.00 0.00 0.00 2.57
529 535 9.288124 TGCATGAATCTTAACGTAAAATCAATG 57.712 29.630 0.00 0.00 0.00 2.82
530 536 9.853555 TTGCATGAATCTTAACGTAAAATCAAT 57.146 25.926 0.00 0.00 0.00 2.57
531 537 9.340695 CTTGCATGAATCTTAACGTAAAATCAA 57.659 29.630 0.00 0.00 0.00 2.57
532 538 7.484641 GCTTGCATGAATCTTAACGTAAAATCA 59.515 33.333 3.33 0.00 0.00 2.57
533 539 7.484641 TGCTTGCATGAATCTTAACGTAAAATC 59.515 33.333 3.33 0.00 0.00 2.17
534 540 7.312154 TGCTTGCATGAATCTTAACGTAAAAT 58.688 30.769 3.33 0.00 0.00 1.82
535 541 6.673106 TGCTTGCATGAATCTTAACGTAAAA 58.327 32.000 3.33 0.00 0.00 1.52
536 542 6.247727 TGCTTGCATGAATCTTAACGTAAA 57.752 33.333 3.33 0.00 0.00 2.01
537 543 5.871465 TGCTTGCATGAATCTTAACGTAA 57.129 34.783 3.33 0.00 0.00 3.18
538 544 6.435430 AATGCTTGCATGAATCTTAACGTA 57.565 33.333 8.98 0.00 0.00 3.57
539 545 4.970662 ATGCTTGCATGAATCTTAACGT 57.029 36.364 7.35 0.00 0.00 3.99
540 546 6.529125 AGAAAATGCTTGCATGAATCTTAACG 59.471 34.615 8.98 0.00 0.00 3.18
541 547 7.823149 AGAAAATGCTTGCATGAATCTTAAC 57.177 32.000 8.98 0.00 0.00 2.01
542 548 8.836268 AAAGAAAATGCTTGCATGAATCTTAA 57.164 26.923 20.54 0.00 0.00 1.85
543 549 8.836268 AAAAGAAAATGCTTGCATGAATCTTA 57.164 26.923 20.54 0.00 0.00 2.10
544 550 7.739498 AAAAGAAAATGCTTGCATGAATCTT 57.261 28.000 8.98 14.34 0.00 2.40
545 551 9.095065 GATAAAAGAAAATGCTTGCATGAATCT 57.905 29.630 8.98 9.80 0.00 2.40
546 552 9.095065 AGATAAAAGAAAATGCTTGCATGAATC 57.905 29.630 8.98 7.87 0.00 2.52
547 553 9.444600 AAGATAAAAGAAAATGCTTGCATGAAT 57.555 25.926 8.98 0.00 0.00 2.57
548 554 8.836268 AAGATAAAAGAAAATGCTTGCATGAA 57.164 26.923 8.98 0.00 0.00 2.57
549 555 8.836268 AAAGATAAAAGAAAATGCTTGCATGA 57.164 26.923 8.98 0.00 0.00 3.07
550 556 9.325150 CAAAAGATAAAAGAAAATGCTTGCATG 57.675 29.630 8.98 0.00 0.00 4.06
551 557 9.059260 ACAAAAGATAAAAGAAAATGCTTGCAT 57.941 25.926 1.81 1.81 0.00 3.96
552 558 8.436046 ACAAAAGATAAAAGAAAATGCTTGCA 57.564 26.923 0.00 0.00 0.00 4.08
553 559 8.768019 AGACAAAAGATAAAAGAAAATGCTTGC 58.232 29.630 0.00 0.00 0.00 4.01
641 647 9.691362 TGAAATGTGCTTTATAAAGGTCTTTTC 57.309 29.630 23.37 16.62 36.53 2.29
724 748 2.029200 TGTATGCATGCACCAAAAGGTG 60.029 45.455 25.37 10.21 42.22 4.00
781 974 1.211703 TCAAAAGGAGGTGTGCACTGA 59.788 47.619 19.41 6.97 0.00 3.41
870 1064 5.634859 GGTTTTGGATTATCTTGCAGTTGTG 59.365 40.000 0.00 0.00 0.00 3.33
914 1108 1.908299 CCACCTTGGGCTTTGGGAC 60.908 63.158 0.00 0.00 32.67 4.46
954 1148 2.430921 GCTTTGCTGCTGCTGCTG 60.431 61.111 27.67 16.73 40.48 4.41
1209 1403 2.685380 AGGAGAAGGGAGCGGTGG 60.685 66.667 0.00 0.00 0.00 4.61
1221 1415 1.615814 CGAAGGGGAGGAGAGGAGA 59.384 63.158 0.00 0.00 0.00 3.71
2190 2384 3.430565 CTCCACCAGCTCGCGCATA 62.431 63.158 8.75 0.00 39.10 3.14
2723 2918 3.772619 GGCAAGTATAAGCCGTCCA 57.227 52.632 0.00 0.00 41.70 4.02
2752 2955 4.179599 GAGGGGAGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
2756 2959 3.795924 ATGGGAGGGGAGGGGAGG 61.796 72.222 0.00 0.00 0.00 4.30
2757 2960 2.122189 GATGGGAGGGGAGGGGAG 60.122 72.222 0.00 0.00 0.00 4.30
2758 2961 3.791076 GGATGGGAGGGGAGGGGA 61.791 72.222 0.00 0.00 0.00 4.81
2759 2962 4.928520 GGGATGGGAGGGGAGGGG 62.929 77.778 0.00 0.00 0.00 4.79
2760 2963 4.122670 TGGGATGGGAGGGGAGGG 62.123 72.222 0.00 0.00 0.00 4.30
2761 2964 2.774351 GTGGGATGGGAGGGGAGG 60.774 72.222 0.00 0.00 0.00 4.30
2985 3188 0.602638 TGTGCTTCTGCCAACCGTAG 60.603 55.000 0.00 0.00 38.71 3.51
3038 3241 2.813908 GTCATGGTCGTCGTGCCC 60.814 66.667 0.00 0.09 32.54 5.36
3192 3395 1.379176 GCCTTCTCCCTTTCTGGCC 60.379 63.158 0.00 0.00 34.81 5.36
3383 3586 2.964310 GCAGGCCTCCTTGAGCAGA 61.964 63.158 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.