Multiple sequence alignment - TraesCS2B01G403900

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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 TraesCS2B01G403900 chr2B 100.000 3041 0 0 1 3041 572162745 572165785 0.000000e+00 5616.0
1 TraesCS2B01G403900 chr2B 97.829 1520 21 3 630 2138 184402581 184404099 0.000000e+00 2614.0
2 TraesCS2B01G403900 chr2B 99.505 404 0 1 2525 2928 184404965 184405366 0.000000e+00 734.0
3 TraesCS2B01G403900 chr2B 81.901 547 67 18 1 538 572306360 572306883 1.670000e-117 433.0
4 TraesCS2B01G403900 chr2B 98.930 187 2 0 2112 2298 184404123 184404309 4.860000e-88 335.0
5 TraesCS2B01G403900 chr2B 78.070 456 88 11 955 1403 770435822 770436272 8.300000e-71 278.0
6 TraesCS2B01G403900 chr2B 98.347 121 2 0 2921 3041 184406134 184406254 2.380000e-51 213.0
7 TraesCS2B01G403900 chr2B 94.186 86 5 0 1522 1607 572164180 572164265 6.840000e-27 132.0
8 TraesCS2B01G403900 chr2B 94.186 86 5 0 1436 1521 572164266 572164351 6.840000e-27 132.0
9 TraesCS2B01G403900 chr2B 93.023 86 6 0 1522 1607 184403396 184403481 3.180000e-25 126.0
10 TraesCS2B01G403900 chr2B 93.023 86 6 0 1436 1521 184403482 184403567 3.180000e-25 126.0
11 TraesCS2B01G403900 chr4B 98.677 1512 18 2 629 2138 581079171 581077660 0.000000e+00 2680.0
12 TraesCS2B01G403900 chr4B 99.037 519 1 2 2525 3041 581076871 581076355 0.000000e+00 928.0
13 TraesCS2B01G403900 chr4B 99.272 412 3 0 2112 2523 581077644 581077233 0.000000e+00 745.0
14 TraesCS2B01G403900 chr4B 86.620 284 31 6 2181 2460 270611512 270611232 1.060000e-79 307.0
15 TraesCS2B01G403900 chr4B 85.915 284 32 7 2181 2460 270797536 270797257 2.290000e-76 296.0
16 TraesCS2B01G403900 chr4B 88.827 179 16 3 2283 2460 270796724 270796549 1.840000e-52 217.0
17 TraesCS2B01G403900 chr4B 87.640 178 18 3 2283 2459 270610699 270610525 1.430000e-48 204.0
18 TraesCS2B01G403900 chr4B 94.186 86 5 0 1522 1607 581078364 581078279 6.840000e-27 132.0
19 TraesCS2B01G403900 chr4B 93.023 86 6 0 1436 1521 581078278 581078193 3.180000e-25 126.0
20 TraesCS2B01G403900 chr3B 97.938 1455 19 2 629 2072 785378687 785377233 0.000000e+00 2510.0
21 TraesCS2B01G403900 chr3B 98.459 519 4 2 2525 3041 785376601 785376085 0.000000e+00 911.0
22 TraesCS2B01G403900 chr3B 94.186 86 5 0 1436 1521 785377784 785377699 6.840000e-27 132.0
23 TraesCS2B01G403900 chr3B 94.186 86 5 0 1522 1607 785377870 785377785 6.840000e-27 132.0
24 TraesCS2B01G403900 chr2A 86.392 632 79 7 3 629 632539938 632540567 0.000000e+00 684.0
25 TraesCS2B01G403900 chr2A 78.062 547 76 16 1 538 632581293 632581804 3.810000e-79 305.0
26 TraesCS2B01G403900 chr1A 83.514 461 56 12 2001 2459 568001454 568001896 2.180000e-111 412.0
27 TraesCS2B01G403900 chr6B 88.686 274 29 1 2187 2460 688778693 688778422 1.750000e-87 333.0
28 TraesCS2B01G403900 chr6B 94.828 58 1 2 2549 2604 662141682 662141739 4.180000e-14 89.8
29 TraesCS2B01G403900 chr6D 88.722 266 25 3 2196 2458 453172502 453172765 1.360000e-83 320.0
30 TraesCS2B01G403900 chr6A 87.273 275 29 4 2187 2458 599167763 599168034 2.940000e-80 309.0
31 TraesCS2B01G403900 chr6A 94.828 58 1 2 2549 2604 512818274 512818217 4.180000e-14 89.8
32 TraesCS2B01G403900 chr6A 93.103 58 2 2 2549 2604 183265098 183265155 1.940000e-12 84.2
33 TraesCS2B01G403900 chr7D 91.071 112 8 1 2353 2462 543211765 543211876 1.890000e-32 150.0
34 TraesCS2B01G403900 chr1D 90.323 93 8 1 2030 2122 439144497 439144406 1.480000e-23 121.0
35 TraesCS2B01G403900 chr7A 94.828 58 1 2 2549 2604 603086972 603087029 4.180000e-14 89.8
36 TraesCS2B01G403900 chr3A 94.828 58 1 2 2549 2604 483240656 483240713 4.180000e-14 89.8
37 TraesCS2B01G403900 chr1B 94.828 58 1 2 2549 2604 549693824 549693767 4.180000e-14 89.8


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 TraesCS2B01G403900 chr2B 572162745 572165785 3040 False 1960.000000 5616 96.124000 1 3041 3 chr2B.!!$F4 3040
1 TraesCS2B01G403900 chr2B 184402581 184406254 3673 False 691.333333 2614 96.776167 630 3041 6 chr2B.!!$F3 2411
2 TraesCS2B01G403900 chr2B 572306360 572306883 523 False 433.000000 433 81.901000 1 538 1 chr2B.!!$F1 537
3 TraesCS2B01G403900 chr4B 581076355 581079171 2816 True 922.200000 2680 96.839000 629 3041 5 chr4B.!!$R3 2412
4 TraesCS2B01G403900 chr4B 270796549 270797536 987 True 256.500000 296 87.371000 2181 2460 2 chr4B.!!$R2 279
5 TraesCS2B01G403900 chr4B 270610525 270611512 987 True 255.500000 307 87.130000 2181 2460 2 chr4B.!!$R1 279
6 TraesCS2B01G403900 chr3B 785376085 785378687 2602 True 921.250000 2510 96.192250 629 3041 4 chr3B.!!$R1 2412
7 TraesCS2B01G403900 chr2A 632539938 632540567 629 False 684.000000 684 86.392000 3 629 1 chr2A.!!$F1 626
8 TraesCS2B01G403900 chr2A 632581293 632581804 511 False 305.000000 305 78.062000 1 538 1 chr2A.!!$F2 537

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
290 297 0.248784 GCGTGGGCGTACCTTAGTAG 60.249 60.0 0.15 0.0 41.11 2.57 F
494 527 0.532862 AAGTGTGCGAGTTGAGGGTG 60.533 55.0 0.00 0.0 0.00 4.61 F
1353 1396 0.534203 GCCGTCAACAGGGAAAGACA 60.534 55.0 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1353 1396 1.000396 GCCAGGTGCCTTGAGGATT 60.000 57.895 0.06 0.0 37.39 3.01 R
1864 1944 3.518705 TGAGCCATGCATAACCCATTTTT 59.481 39.130 0.00 0.0 0.00 1.94 R
2966 4517 5.805728 AGGCCCTAATAAACATATCTTCCG 58.194 41.667 0.00 0.0 0.00 4.30 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
20 21 1.065401 CCTCTTCAAAACGCACTTGCA 59.935 47.619 1.48 0.00 42.21 4.08
24 31 2.686558 TCAAAACGCACTTGCATCTC 57.313 45.000 1.48 0.00 42.21 2.75
25 32 1.266718 TCAAAACGCACTTGCATCTCC 59.733 47.619 1.48 0.00 42.21 3.71
30 37 1.271054 ACGCACTTGCATCTCCTTTCT 60.271 47.619 1.48 0.00 42.21 2.52
31 38 1.808945 CGCACTTGCATCTCCTTTCTT 59.191 47.619 1.48 0.00 42.21 2.52
32 39 2.159599 CGCACTTGCATCTCCTTTCTTC 60.160 50.000 1.48 0.00 42.21 2.87
33 40 2.163211 GCACTTGCATCTCCTTTCTTCC 59.837 50.000 0.00 0.00 41.59 3.46
45 52 5.551977 TCTCCTTTCTTCCCTAGTCCATTTT 59.448 40.000 0.00 0.00 0.00 1.82
46 53 5.570320 TCCTTTCTTCCCTAGTCCATTTTG 58.430 41.667 0.00 0.00 0.00 2.44
54 61 0.391927 TAGTCCATTTTGTCGCCGGG 60.392 55.000 2.18 0.00 0.00 5.73
59 66 2.902457 ATTTTGTCGCCGGGTCCCT 61.902 57.895 6.29 0.00 0.00 4.20
68 75 2.421739 CGGGTCCCTAATCCGCTG 59.578 66.667 6.29 0.00 37.25 5.18
119 126 2.826979 TTGAGCGACTACTCACGATC 57.173 50.000 0.00 0.00 46.13 3.69
124 131 2.102757 AGCGACTACTCACGATCTCCTA 59.897 50.000 0.00 0.00 0.00 2.94
132 139 3.024547 CTCACGATCTCCTAAGTGGGAA 58.975 50.000 0.00 0.00 37.26 3.97
133 140 2.758979 TCACGATCTCCTAAGTGGGAAC 59.241 50.000 0.00 0.00 34.66 3.62
173 180 3.439857 TCTGATTTGACCAAAGGGAGG 57.560 47.619 1.57 0.00 38.05 4.30
181 188 4.115199 CAAAGGGAGGGGAGGCGG 62.115 72.222 0.00 0.00 0.00 6.13
202 209 2.010145 GTGCACACGGTATGTCAGAT 57.990 50.000 13.17 0.00 40.64 2.90
210 217 1.002430 CGGTATGTCAGATGATGGGGG 59.998 57.143 0.00 0.00 0.00 5.40
215 222 0.251077 GTCAGATGATGGGGGATGCC 60.251 60.000 0.00 0.00 0.00 4.40
218 225 1.002868 GATGATGGGGGATGCCTCG 60.003 63.158 2.19 0.00 0.00 4.63
234 241 0.320073 CTCGGCGGTAACAAGTGGAA 60.320 55.000 7.21 0.00 0.00 3.53
261 268 4.268359 CCAAGAATGGGAGAGAAAAGAGG 58.732 47.826 0.00 0.00 43.51 3.69
262 269 4.018960 CCAAGAATGGGAGAGAAAAGAGGA 60.019 45.833 0.00 0.00 43.51 3.71
263 270 5.339861 CCAAGAATGGGAGAGAAAAGAGGAT 60.340 44.000 0.00 0.00 43.51 3.24
264 271 6.126652 CCAAGAATGGGAGAGAAAAGAGGATA 60.127 42.308 0.00 0.00 43.51 2.59
265 272 6.745794 AGAATGGGAGAGAAAAGAGGATAG 57.254 41.667 0.00 0.00 0.00 2.08
266 273 5.606329 AGAATGGGAGAGAAAAGAGGATAGG 59.394 44.000 0.00 0.00 0.00 2.57
267 274 3.658725 TGGGAGAGAAAAGAGGATAGGG 58.341 50.000 0.00 0.00 0.00 3.53
268 275 3.274959 TGGGAGAGAAAAGAGGATAGGGA 59.725 47.826 0.00 0.00 0.00 4.20
269 276 3.901222 GGGAGAGAAAAGAGGATAGGGAG 59.099 52.174 0.00 0.00 0.00 4.30
270 277 3.901222 GGAGAGAAAAGAGGATAGGGAGG 59.099 52.174 0.00 0.00 0.00 4.30
271 278 3.901222 GAGAGAAAAGAGGATAGGGAGGG 59.099 52.174 0.00 0.00 0.00 4.30
278 285 3.942439 GATAGGGAGGGCGTGGGC 61.942 72.222 0.00 0.00 38.90 5.36
289 296 1.666209 GGCGTGGGCGTACCTTAGTA 61.666 60.000 0.15 0.00 41.24 1.82
290 297 0.248784 GCGTGGGCGTACCTTAGTAG 60.249 60.000 0.15 0.00 41.11 2.57
316 323 4.156556 CCATCATGCATTATTCCTAACGGG 59.843 45.833 0.00 0.00 0.00 5.28
319 326 2.128535 TGCATTATTCCTAACGGGGGA 58.871 47.619 0.00 0.00 35.33 4.81
320 327 2.158726 TGCATTATTCCTAACGGGGGAC 60.159 50.000 0.00 0.00 35.33 4.46
333 342 1.221021 GGGGACGCCAACTTAGGAG 59.779 63.158 3.14 0.00 34.32 3.69
353 362 0.839946 AAATCGGGATGGGAGGACTG 59.160 55.000 0.00 0.00 0.00 3.51
367 376 2.366469 GACTGAAGGAGGCCAGACA 58.634 57.895 5.01 0.00 34.65 3.41
369 378 1.280421 GACTGAAGGAGGCCAGACAAT 59.720 52.381 5.01 0.00 34.65 2.71
373 382 1.556911 GAAGGAGGCCAGACAATGAGA 59.443 52.381 5.01 0.00 0.00 3.27
389 398 5.297776 ACAATGAGAAATCAATAGGGAAGCG 59.702 40.000 0.00 0.00 0.00 4.68
392 401 3.545703 AGAAATCAATAGGGAAGCGTGG 58.454 45.455 0.00 0.00 0.00 4.94
400 409 1.377987 GGGAAGCGTGGCAATGGTA 60.378 57.895 0.00 0.00 0.00 3.25
411 420 1.532868 GGCAATGGTAGCATTAGAGCG 59.467 52.381 19.18 8.45 40.15 5.03
434 448 1.368268 AAAGGGGAGGGGCTTTGACA 61.368 55.000 0.00 0.00 0.00 3.58
446 460 3.320826 GGGCTTTGACATGTTTTAGTGGT 59.679 43.478 0.00 0.00 0.00 4.16
448 462 4.298332 GCTTTGACATGTTTTAGTGGTGG 58.702 43.478 0.00 0.00 0.00 4.61
460 474 2.586648 AGTGGTGGTGAGAATTTCCC 57.413 50.000 0.00 0.00 0.00 3.97
461 475 1.780309 AGTGGTGGTGAGAATTTCCCA 59.220 47.619 0.00 0.00 0.00 4.37
462 476 2.176798 AGTGGTGGTGAGAATTTCCCAA 59.823 45.455 0.00 0.00 30.88 4.12
463 477 2.962421 GTGGTGGTGAGAATTTCCCAAA 59.038 45.455 0.00 0.00 30.88 3.28
464 478 3.386402 GTGGTGGTGAGAATTTCCCAAAA 59.614 43.478 0.00 0.00 30.88 2.44
465 479 4.033709 TGGTGGTGAGAATTTCCCAAAAA 58.966 39.130 0.00 0.00 30.88 1.94
494 527 0.532862 AAGTGTGCGAGTTGAGGGTG 60.533 55.000 0.00 0.00 0.00 4.61
538 571 2.345244 AGCTCTGCTGAACCACCG 59.655 61.111 0.00 0.00 37.57 4.94
539 572 2.031163 GCTCTGCTGAACCACCGT 59.969 61.111 0.00 0.00 0.00 4.83
540 573 1.598130 GCTCTGCTGAACCACCGTT 60.598 57.895 0.00 0.00 33.88 4.44
557 590 8.617290 ACCACCGTTCAAGAAAATATATATCC 57.383 34.615 0.00 0.00 0.00 2.59
558 591 8.215050 ACCACCGTTCAAGAAAATATATATCCA 58.785 33.333 0.00 0.00 0.00 3.41
559 592 9.231297 CCACCGTTCAAGAAAATATATATCCAT 57.769 33.333 0.00 0.00 0.00 3.41
576 609 7.821134 ATATCCATATTGGCTATCCCTATCC 57.179 40.000 0.00 0.00 37.47 2.59
577 610 5.240702 TCCATATTGGCTATCCCTATCCT 57.759 43.478 0.00 0.00 37.47 3.24
578 611 5.613826 TCCATATTGGCTATCCCTATCCTT 58.386 41.667 0.00 0.00 37.47 3.36
579 612 5.667626 TCCATATTGGCTATCCCTATCCTTC 59.332 44.000 0.00 0.00 37.47 3.46
580 613 5.669447 CCATATTGGCTATCCCTATCCTTCT 59.331 44.000 0.00 0.00 31.31 2.85
581 614 6.409005 CCATATTGGCTATCCCTATCCTTCTG 60.409 46.154 0.00 0.00 31.31 3.02
582 615 2.260822 TGGCTATCCCTATCCTTCTGC 58.739 52.381 0.00 0.00 0.00 4.26
583 616 2.260822 GGCTATCCCTATCCTTCTGCA 58.739 52.381 0.00 0.00 0.00 4.41
584 617 2.843113 GGCTATCCCTATCCTTCTGCAT 59.157 50.000 0.00 0.00 0.00 3.96
585 618 3.118445 GGCTATCCCTATCCTTCTGCATC 60.118 52.174 0.00 0.00 0.00 3.91
586 619 3.118445 GCTATCCCTATCCTTCTGCATCC 60.118 52.174 0.00 0.00 0.00 3.51
587 620 1.734655 TCCCTATCCTTCTGCATCCC 58.265 55.000 0.00 0.00 0.00 3.85
588 621 1.224120 TCCCTATCCTTCTGCATCCCT 59.776 52.381 0.00 0.00 0.00 4.20
589 622 1.627834 CCCTATCCTTCTGCATCCCTC 59.372 57.143 0.00 0.00 0.00 4.30
590 623 2.618794 CCTATCCTTCTGCATCCCTCT 58.381 52.381 0.00 0.00 0.00 3.69
591 624 2.978278 CCTATCCTTCTGCATCCCTCTT 59.022 50.000 0.00 0.00 0.00 2.85
592 625 4.163427 CCTATCCTTCTGCATCCCTCTTA 58.837 47.826 0.00 0.00 0.00 2.10
593 626 4.782156 CCTATCCTTCTGCATCCCTCTTAT 59.218 45.833 0.00 0.00 0.00 1.73
594 627 4.906747 ATCCTTCTGCATCCCTCTTATC 57.093 45.455 0.00 0.00 0.00 1.75
595 628 2.975489 TCCTTCTGCATCCCTCTTATCC 59.025 50.000 0.00 0.00 0.00 2.59
596 629 2.978278 CCTTCTGCATCCCTCTTATCCT 59.022 50.000 0.00 0.00 0.00 3.24
597 630 3.007831 CCTTCTGCATCCCTCTTATCCTC 59.992 52.174 0.00 0.00 0.00 3.71
598 631 3.334910 TCTGCATCCCTCTTATCCTCA 57.665 47.619 0.00 0.00 0.00 3.86
599 632 3.657610 TCTGCATCCCTCTTATCCTCAA 58.342 45.455 0.00 0.00 0.00 3.02
600 633 4.040047 TCTGCATCCCTCTTATCCTCAAA 58.960 43.478 0.00 0.00 0.00 2.69
601 634 4.133078 CTGCATCCCTCTTATCCTCAAAC 58.867 47.826 0.00 0.00 0.00 2.93
602 635 3.117888 TGCATCCCTCTTATCCTCAAACC 60.118 47.826 0.00 0.00 0.00 3.27
603 636 3.117888 GCATCCCTCTTATCCTCAAACCA 60.118 47.826 0.00 0.00 0.00 3.67
604 637 4.628715 GCATCCCTCTTATCCTCAAACCAA 60.629 45.833 0.00 0.00 0.00 3.67
605 638 5.509498 CATCCCTCTTATCCTCAAACCAAA 58.491 41.667 0.00 0.00 0.00 3.28
606 639 5.796502 TCCCTCTTATCCTCAAACCAAAT 57.203 39.130 0.00 0.00 0.00 2.32
607 640 6.901615 TCCCTCTTATCCTCAAACCAAATA 57.098 37.500 0.00 0.00 0.00 1.40
608 641 7.278724 TCCCTCTTATCCTCAAACCAAATAA 57.721 36.000 0.00 0.00 0.00 1.40
609 642 7.704727 TCCCTCTTATCCTCAAACCAAATAAA 58.295 34.615 0.00 0.00 0.00 1.40
610 643 8.343787 TCCCTCTTATCCTCAAACCAAATAAAT 58.656 33.333 0.00 0.00 0.00 1.40
611 644 8.416329 CCCTCTTATCCTCAAACCAAATAAATG 58.584 37.037 0.00 0.00 0.00 2.32
612 645 9.189156 CCTCTTATCCTCAAACCAAATAAATGA 57.811 33.333 0.00 0.00 0.00 2.57
614 647 9.527157 TCTTATCCTCAAACCAAATAAATGACA 57.473 29.630 0.00 0.00 0.00 3.58
616 649 9.921637 TTATCCTCAAACCAAATAAATGACAAC 57.078 29.630 0.00 0.00 0.00 3.32
617 650 7.595819 TCCTCAAACCAAATAAATGACAACT 57.404 32.000 0.00 0.00 0.00 3.16
618 651 8.698973 TCCTCAAACCAAATAAATGACAACTA 57.301 30.769 0.00 0.00 0.00 2.24
619 652 8.573035 TCCTCAAACCAAATAAATGACAACTAC 58.427 33.333 0.00 0.00 0.00 2.73
620 653 8.576442 CCTCAAACCAAATAAATGACAACTACT 58.424 33.333 0.00 0.00 0.00 2.57
638 671 4.772624 ACTACTAGAAAGATGAGTGTGGCA 59.227 41.667 0.00 0.00 0.00 4.92
738 771 3.070159 AGCGGTAATGCTCACTGTATCAT 59.930 43.478 0.00 0.00 42.95 2.45
857 900 5.108517 TCAACACGGTACTTCTAAAACGTT 58.891 37.500 0.00 0.00 31.61 3.99
869 912 6.092259 ACTTCTAAAACGTTGTCTCATATGGC 59.908 38.462 0.00 0.00 0.00 4.40
1077 1120 2.233922 CAGGTATCTTCCCTTCACGTGT 59.766 50.000 16.51 0.00 0.00 4.49
1353 1396 0.534203 GCCGTCAACAGGGAAAGACA 60.534 55.000 0.00 0.00 0.00 3.41
2523 2655 0.543883 TTGACCTCTGCTCCAGCTCT 60.544 55.000 0.00 0.00 42.66 4.09
2966 4517 6.255215 TCGATTTTGTGTGAAGAAACTTCAC 58.745 36.000 27.16 27.16 46.57 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.646798 AGGGAAGAAAGGAGATGCAAGT 59.353 45.455 0.00 0.00 0.00 3.16
20 21 4.354208 TGGACTAGGGAAGAAAGGAGAT 57.646 45.455 0.00 0.00 0.00 2.75
24 31 5.325239 ACAAAATGGACTAGGGAAGAAAGG 58.675 41.667 0.00 0.00 0.00 3.11
25 32 5.122396 CGACAAAATGGACTAGGGAAGAAAG 59.878 44.000 0.00 0.00 0.00 2.62
30 37 2.617021 GGCGACAAAATGGACTAGGGAA 60.617 50.000 0.00 0.00 0.00 3.97
31 38 1.065709 GGCGACAAAATGGACTAGGGA 60.066 52.381 0.00 0.00 0.00 4.20
32 39 1.379527 GGCGACAAAATGGACTAGGG 58.620 55.000 0.00 0.00 0.00 3.53
33 40 1.006832 CGGCGACAAAATGGACTAGG 58.993 55.000 0.00 0.00 0.00 3.02
45 52 2.364579 ATTAGGGACCCGGCGACA 60.365 61.111 9.30 0.00 0.00 4.35
46 53 2.420466 GATTAGGGACCCGGCGAC 59.580 66.667 9.30 0.00 0.00 5.19
54 61 2.111251 GGGCAGCGGATTAGGGAC 59.889 66.667 0.00 0.00 0.00 4.46
59 66 1.379309 GGGTTTGGGCAGCGGATTA 60.379 57.895 0.00 0.00 0.00 1.75
68 75 1.751351 GAAGAATGCTAGGGTTTGGGC 59.249 52.381 0.00 0.00 0.00 5.36
119 126 3.367087 CGTAGTGTGTTCCCACTTAGGAG 60.367 52.174 0.00 0.00 42.99 3.69
124 131 0.250166 GGCGTAGTGTGTTCCCACTT 60.250 55.000 0.00 0.00 42.99 3.16
132 139 1.848652 ATAGTCCAGGCGTAGTGTGT 58.151 50.000 0.00 0.00 0.00 3.72
133 140 3.821600 AGATATAGTCCAGGCGTAGTGTG 59.178 47.826 0.00 0.00 0.00 3.82
136 143 4.368565 TCAGATATAGTCCAGGCGTAGT 57.631 45.455 0.00 0.00 0.00 2.73
142 149 6.425210 TGGTCAAATCAGATATAGTCCAGG 57.575 41.667 0.00 0.00 0.00 4.45
191 198 2.338809 TCCCCCATCATCTGACATACC 58.661 52.381 0.00 0.00 0.00 2.73
202 209 3.170672 CCGAGGCATCCCCCATCA 61.171 66.667 0.00 0.00 0.00 3.07
210 217 1.429148 CTTGTTACCGCCGAGGCATC 61.429 60.000 15.03 0.00 46.52 3.91
215 222 0.320073 TTCCACTTGTTACCGCCGAG 60.320 55.000 0.00 0.00 0.00 4.63
218 225 1.154197 GAGTTCCACTTGTTACCGCC 58.846 55.000 0.00 0.00 0.00 6.13
234 241 0.539051 CTCTCCCATTCTTGGCGAGT 59.461 55.000 0.77 0.00 42.15 4.18
238 245 3.690460 TCTTTTCTCTCCCATTCTTGGC 58.310 45.455 0.00 0.00 42.15 4.52
241 248 6.101005 CCTATCCTCTTTTCTCTCCCATTCTT 59.899 42.308 0.00 0.00 0.00 2.52
242 249 5.606329 CCTATCCTCTTTTCTCTCCCATTCT 59.394 44.000 0.00 0.00 0.00 2.40
246 253 3.274959 TCCCTATCCTCTTTTCTCTCCCA 59.725 47.826 0.00 0.00 0.00 4.37
247 254 3.901222 CTCCCTATCCTCTTTTCTCTCCC 59.099 52.174 0.00 0.00 0.00 4.30
250 257 3.935172 CCCTCCCTATCCTCTTTTCTCT 58.065 50.000 0.00 0.00 0.00 3.10
251 258 2.370519 GCCCTCCCTATCCTCTTTTCTC 59.629 54.545 0.00 0.00 0.00 2.87
252 259 2.413601 GCCCTCCCTATCCTCTTTTCT 58.586 52.381 0.00 0.00 0.00 2.52
253 260 1.070914 CGCCCTCCCTATCCTCTTTTC 59.929 57.143 0.00 0.00 0.00 2.29
254 261 1.132500 CGCCCTCCCTATCCTCTTTT 58.868 55.000 0.00 0.00 0.00 2.27
255 262 0.031010 ACGCCCTCCCTATCCTCTTT 60.031 55.000 0.00 0.00 0.00 2.52
256 263 0.760945 CACGCCCTCCCTATCCTCTT 60.761 60.000 0.00 0.00 0.00 2.85
257 264 1.152440 CACGCCCTCCCTATCCTCT 60.152 63.158 0.00 0.00 0.00 3.69
258 265 2.210711 CCACGCCCTCCCTATCCTC 61.211 68.421 0.00 0.00 0.00 3.71
259 266 2.122813 CCACGCCCTCCCTATCCT 60.123 66.667 0.00 0.00 0.00 3.24
260 267 3.242291 CCCACGCCCTCCCTATCC 61.242 72.222 0.00 0.00 0.00 2.59
261 268 3.942439 GCCCACGCCCTCCCTATC 61.942 72.222 0.00 0.00 0.00 2.08
269 276 3.728279 CTAAGGTACGCCCACGCCC 62.728 68.421 0.00 0.00 45.53 6.13
270 277 1.666209 TACTAAGGTACGCCCACGCC 61.666 60.000 0.00 0.00 45.53 5.68
271 278 0.248784 CTACTAAGGTACGCCCACGC 60.249 60.000 0.00 0.00 45.53 5.34
278 285 4.799678 CATGATGGCTCTACTAAGGTACG 58.200 47.826 0.00 0.00 0.00 3.67
289 296 4.383931 AGGAATAATGCATGATGGCTCT 57.616 40.909 0.00 0.00 34.04 4.09
290 297 5.391310 CGTTAGGAATAATGCATGATGGCTC 60.391 44.000 0.00 0.00 34.04 4.70
316 323 0.611714 TTCTCCTAAGTTGGCGTCCC 59.388 55.000 0.00 0.00 0.00 4.46
319 326 2.618053 CGATTTCTCCTAAGTTGGCGT 58.382 47.619 0.00 0.00 0.00 5.68
320 327 1.933853 CCGATTTCTCCTAAGTTGGCG 59.066 52.381 0.00 0.00 0.00 5.69
324 331 3.136626 CCCATCCCGATTTCTCCTAAGTT 59.863 47.826 0.00 0.00 0.00 2.66
328 335 2.609747 CTCCCATCCCGATTTCTCCTA 58.390 52.381 0.00 0.00 0.00 2.94
333 342 1.132500 AGTCCTCCCATCCCGATTTC 58.868 55.000 0.00 0.00 0.00 2.17
353 362 1.556911 TCTCATTGTCTGGCCTCCTTC 59.443 52.381 3.32 0.00 0.00 3.46
366 375 5.297776 ACGCTTCCCTATTGATTTCTCATTG 59.702 40.000 0.00 0.00 0.00 2.82
367 376 5.297776 CACGCTTCCCTATTGATTTCTCATT 59.702 40.000 0.00 0.00 0.00 2.57
369 378 4.191544 CACGCTTCCCTATTGATTTCTCA 58.808 43.478 0.00 0.00 0.00 3.27
373 382 2.024414 GCCACGCTTCCCTATTGATTT 58.976 47.619 0.00 0.00 0.00 2.17
389 398 2.291741 GCTCTAATGCTACCATTGCCAC 59.708 50.000 0.00 0.00 41.58 5.01
392 401 2.478134 CTCGCTCTAATGCTACCATTGC 59.522 50.000 0.00 0.00 41.58 3.56
400 409 2.420687 CCCCTTTTCTCGCTCTAATGCT 60.421 50.000 0.00 0.00 0.00 3.79
411 420 0.409876 AAAGCCCCTCCCCTTTTCTC 59.590 55.000 0.00 0.00 0.00 2.87
434 448 6.015434 GGAAATTCTCACCACCACTAAAACAT 60.015 38.462 0.00 0.00 0.00 2.71
463 477 2.494073 TCGCACACTTTGAACCCTTTTT 59.506 40.909 0.00 0.00 0.00 1.94
464 478 2.096248 TCGCACACTTTGAACCCTTTT 58.904 42.857 0.00 0.00 0.00 2.27
465 479 1.676006 CTCGCACACTTTGAACCCTTT 59.324 47.619 0.00 0.00 0.00 3.11
466 480 1.308998 CTCGCACACTTTGAACCCTT 58.691 50.000 0.00 0.00 0.00 3.95
467 481 0.180406 ACTCGCACACTTTGAACCCT 59.820 50.000 0.00 0.00 0.00 4.34
468 482 1.021968 AACTCGCACACTTTGAACCC 58.978 50.000 0.00 0.00 0.00 4.11
469 483 1.668751 TCAACTCGCACACTTTGAACC 59.331 47.619 0.00 0.00 0.00 3.62
470 484 2.286418 CCTCAACTCGCACACTTTGAAC 60.286 50.000 0.00 0.00 0.00 3.18
471 485 1.939934 CCTCAACTCGCACACTTTGAA 59.060 47.619 0.00 0.00 0.00 2.69
472 486 1.581934 CCTCAACTCGCACACTTTGA 58.418 50.000 0.00 0.00 0.00 2.69
480 513 1.227823 CAACCACCCTCAACTCGCA 60.228 57.895 0.00 0.00 0.00 5.10
494 527 0.605319 TGTGACGGATGAAGCCAACC 60.605 55.000 0.00 0.00 32.43 3.77
553 586 6.949997 AGGATAGGGATAGCCAATATGGATA 58.050 40.000 0.00 0.00 43.23 2.59
554 587 5.808510 AGGATAGGGATAGCCAATATGGAT 58.191 41.667 0.00 0.00 40.96 3.41
555 588 5.240702 AGGATAGGGATAGCCAATATGGA 57.759 43.478 0.00 0.00 40.96 3.41
556 589 5.669447 AGAAGGATAGGGATAGCCAATATGG 59.331 44.000 0.00 0.00 41.55 2.74
557 590 6.590068 CAGAAGGATAGGGATAGCCAATATG 58.410 44.000 0.00 0.00 35.15 1.78
558 591 5.131809 GCAGAAGGATAGGGATAGCCAATAT 59.868 44.000 0.00 0.00 35.15 1.28
559 592 4.471386 GCAGAAGGATAGGGATAGCCAATA 59.529 45.833 0.00 0.00 35.15 1.90
560 593 3.265479 GCAGAAGGATAGGGATAGCCAAT 59.735 47.826 0.00 0.00 35.15 3.16
561 594 2.639839 GCAGAAGGATAGGGATAGCCAA 59.360 50.000 0.00 0.00 35.15 4.52
562 595 2.260822 GCAGAAGGATAGGGATAGCCA 58.739 52.381 0.00 0.00 35.15 4.75
563 596 2.260822 TGCAGAAGGATAGGGATAGCC 58.739 52.381 0.00 0.00 0.00 3.93
564 597 3.118445 GGATGCAGAAGGATAGGGATAGC 60.118 52.174 0.00 0.00 0.00 2.97
565 598 3.454082 GGGATGCAGAAGGATAGGGATAG 59.546 52.174 0.00 0.00 0.00 2.08
566 599 3.079689 AGGGATGCAGAAGGATAGGGATA 59.920 47.826 0.00 0.00 0.00 2.59
567 600 2.157880 AGGGATGCAGAAGGATAGGGAT 60.158 50.000 0.00 0.00 0.00 3.85
568 601 1.224120 AGGGATGCAGAAGGATAGGGA 59.776 52.381 0.00 0.00 0.00 4.20
569 602 1.627834 GAGGGATGCAGAAGGATAGGG 59.372 57.143 0.00 0.00 0.00 3.53
570 603 2.618794 AGAGGGATGCAGAAGGATAGG 58.381 52.381 0.00 0.00 0.00 2.57
571 604 5.104982 GGATAAGAGGGATGCAGAAGGATAG 60.105 48.000 0.00 0.00 0.00 2.08
572 605 4.780021 GGATAAGAGGGATGCAGAAGGATA 59.220 45.833 0.00 0.00 0.00 2.59
573 606 3.586618 GGATAAGAGGGATGCAGAAGGAT 59.413 47.826 0.00 0.00 0.00 3.24
574 607 2.975489 GGATAAGAGGGATGCAGAAGGA 59.025 50.000 0.00 0.00 0.00 3.36
575 608 2.978278 AGGATAAGAGGGATGCAGAAGG 59.022 50.000 0.00 0.00 0.00 3.46
576 609 3.645212 TGAGGATAAGAGGGATGCAGAAG 59.355 47.826 0.00 0.00 0.00 2.85
577 610 3.657610 TGAGGATAAGAGGGATGCAGAA 58.342 45.455 0.00 0.00 0.00 3.02
578 611 3.334910 TGAGGATAAGAGGGATGCAGA 57.665 47.619 0.00 0.00 0.00 4.26
579 612 4.133078 GTTTGAGGATAAGAGGGATGCAG 58.867 47.826 0.00 0.00 0.00 4.41
580 613 3.117888 GGTTTGAGGATAAGAGGGATGCA 60.118 47.826 0.00 0.00 0.00 3.96
581 614 3.117888 TGGTTTGAGGATAAGAGGGATGC 60.118 47.826 0.00 0.00 0.00 3.91
582 615 4.778213 TGGTTTGAGGATAAGAGGGATG 57.222 45.455 0.00 0.00 0.00 3.51
583 616 5.796502 TTTGGTTTGAGGATAAGAGGGAT 57.203 39.130 0.00 0.00 0.00 3.85
584 617 5.796502 ATTTGGTTTGAGGATAAGAGGGA 57.203 39.130 0.00 0.00 0.00 4.20
585 618 7.954666 TTTATTTGGTTTGAGGATAAGAGGG 57.045 36.000 0.00 0.00 0.00 4.30
586 619 9.189156 TCATTTATTTGGTTTGAGGATAAGAGG 57.811 33.333 0.00 0.00 0.00 3.69
588 621 9.527157 TGTCATTTATTTGGTTTGAGGATAAGA 57.473 29.630 0.00 0.00 0.00 2.10
590 623 9.921637 GTTGTCATTTATTTGGTTTGAGGATAA 57.078 29.630 0.00 0.00 0.00 1.75
591 624 9.308000 AGTTGTCATTTATTTGGTTTGAGGATA 57.692 29.630 0.00 0.00 0.00 2.59
592 625 8.193953 AGTTGTCATTTATTTGGTTTGAGGAT 57.806 30.769 0.00 0.00 0.00 3.24
593 626 7.595819 AGTTGTCATTTATTTGGTTTGAGGA 57.404 32.000 0.00 0.00 0.00 3.71
594 627 8.576442 AGTAGTTGTCATTTATTTGGTTTGAGG 58.424 33.333 0.00 0.00 0.00 3.86
607 640 9.429359 CACTCATCTTTCTAGTAGTTGTCATTT 57.571 33.333 0.00 0.00 0.00 2.32
608 641 8.589338 ACACTCATCTTTCTAGTAGTTGTCATT 58.411 33.333 0.00 0.00 0.00 2.57
609 642 8.031864 CACACTCATCTTTCTAGTAGTTGTCAT 58.968 37.037 0.00 0.00 0.00 3.06
610 643 7.371159 CACACTCATCTTTCTAGTAGTTGTCA 58.629 38.462 0.00 0.00 0.00 3.58
611 644 6.809196 CCACACTCATCTTTCTAGTAGTTGTC 59.191 42.308 0.00 0.00 0.00 3.18
612 645 6.692486 CCACACTCATCTTTCTAGTAGTTGT 58.308 40.000 0.00 0.00 0.00 3.32
613 646 5.578727 GCCACACTCATCTTTCTAGTAGTTG 59.421 44.000 0.00 0.00 0.00 3.16
614 647 5.246203 TGCCACACTCATCTTTCTAGTAGTT 59.754 40.000 0.00 0.00 0.00 2.24
615 648 4.772624 TGCCACACTCATCTTTCTAGTAGT 59.227 41.667 0.00 0.00 0.00 2.73
616 649 5.330455 TGCCACACTCATCTTTCTAGTAG 57.670 43.478 0.00 0.00 0.00 2.57
617 650 5.738619 TTGCCACACTCATCTTTCTAGTA 57.261 39.130 0.00 0.00 0.00 1.82
618 651 4.623932 TTGCCACACTCATCTTTCTAGT 57.376 40.909 0.00 0.00 0.00 2.57
619 652 6.577103 TCTATTGCCACACTCATCTTTCTAG 58.423 40.000 0.00 0.00 0.00 2.43
620 653 6.544928 TCTATTGCCACACTCATCTTTCTA 57.455 37.500 0.00 0.00 0.00 2.10
621 654 5.426504 CTCTATTGCCACACTCATCTTTCT 58.573 41.667 0.00 0.00 0.00 2.52
622 655 4.034975 GCTCTATTGCCACACTCATCTTTC 59.965 45.833 0.00 0.00 0.00 2.62
623 656 3.944015 GCTCTATTGCCACACTCATCTTT 59.056 43.478 0.00 0.00 0.00 2.52
624 657 3.054875 TGCTCTATTGCCACACTCATCTT 60.055 43.478 0.00 0.00 0.00 2.40
625 658 2.502947 TGCTCTATTGCCACACTCATCT 59.497 45.455 0.00 0.00 0.00 2.90
626 659 2.611292 GTGCTCTATTGCCACACTCATC 59.389 50.000 0.00 0.00 0.00 2.92
627 660 2.026915 TGTGCTCTATTGCCACACTCAT 60.027 45.455 0.00 0.00 32.49 2.90
664 697 1.000607 CCTATTCGCTAGCGCTACCAA 60.001 52.381 31.82 20.37 39.59 3.67
738 771 0.165295 CTCACTGTTCGCTCGTACGA 59.835 55.000 18.41 18.41 41.04 3.43
857 900 0.102300 CGTCACGGCCATATGAGACA 59.898 55.000 2.24 0.00 0.00 3.41
1077 1120 2.711009 ACTGTGATGGAGAGGGAAAACA 59.289 45.455 0.00 0.00 0.00 2.83
1353 1396 1.000396 GCCAGGTGCCTTGAGGATT 60.000 57.895 0.06 0.00 37.39 3.01
1864 1944 3.518705 TGAGCCATGCATAACCCATTTTT 59.481 39.130 0.00 0.00 0.00 1.94
2966 4517 5.805728 AGGCCCTAATAAACATATCTTCCG 58.194 41.667 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.