Multiple sequence alignment - TraesCS5A01G331700

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 TraesCS5A01G331700 chr5A 100.000 3392 0 0 1 3392 540384196 540387587 0.000000e+00 6264.0
1 TraesCS5A01G331700 chr5A 78.322 286 29 22 1 268 636641784 636641514 1.630000e-33 154.0
2 TraesCS5A01G331700 chr5A 74.503 302 54 12 2709 2991 503643353 503643056 3.580000e-20 110.0
3 TraesCS5A01G331700 chr5D 95.441 1711 61 10 963 2660 426288096 426289802 0.000000e+00 2712.0
4 TraesCS5A01G331700 chr5D 85.573 707 82 8 2706 3392 426290251 426290957 0.000000e+00 723.0
5 TraesCS5A01G331700 chr5D 92.143 280 18 4 488 764 426286716 426286994 3.170000e-105 392.0
6 TraesCS5A01G331700 chr5D 87.550 249 14 4 183 431 426286469 426286700 4.310000e-69 272.0
7 TraesCS5A01G331700 chr5D 94.074 135 5 1 1 132 426286323 426286457 5.740000e-48 202.0
8 TraesCS5A01G331700 chr5D 93.388 121 7 1 767 887 426287107 426287226 9.670000e-41 178.0
9 TraesCS5A01G331700 chr5D 98.684 76 0 1 885 960 426287282 426287356 2.120000e-27 134.0
10 TraesCS5A01G331700 chr5B 95.440 1513 40 8 885 2393 516066272 516067759 0.000000e+00 2385.0
11 TraesCS5A01G331700 chr5B 83.636 715 81 18 2706 3392 516082200 516082906 1.030000e-179 640.0
12 TraesCS5A01G331700 chr5B 89.070 430 18 8 1 427 516065199 516065602 1.090000e-139 507.0
13 TraesCS5A01G331700 chr5B 77.660 282 40 20 1 267 640128819 640128546 2.110000e-32 150.0
14 TraesCS5A01G331700 chr7D 78.947 247 34 12 1 241 588075350 588075116 5.860000e-33 152.0
15 TraesCS5A01G331700 chr7D 72.050 483 96 27 2706 3154 495100568 495100091 1.290000e-19 108.0
16 TraesCS5A01G331700 chr7A 83.436 163 19 6 1 159 724086712 724086870 9.810000e-31 145.0
17 TraesCS5A01G331700 chr4A 84.932 146 15 4 1 142 675802228 675802370 1.270000e-29 141.0
18 TraesCS5A01G331700 chrUn 82.927 164 19 7 1 159 92720927 92721086 4.560000e-29 139.0
19 TraesCS5A01G331700 chr7B 78.761 226 35 9 1 219 730153948 730154167 4.560000e-29 139.0
20 TraesCS5A01G331700 chr7B 76.132 243 37 12 3036 3273 523094218 523093992 1.290000e-19 108.0
21 TraesCS5A01G331700 chr1B 89.474 57 5 1 2938 2994 542585551 542585606 1.690000e-08 71.3
22 TraesCS5A01G331700 chr1D 100.000 29 0 0 2966 2994 403340945 403340973 2.000000e-03 54.7
23 TraesCS5A01G331700 chr1D 100.000 29 0 0 2966 2994 403351163 403351191 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 TraesCS5A01G331700 chr5A 540384196 540387587 3391 False 6264 6264 100.000000 1 3392 1 chr5A.!!$F1 3391
1 TraesCS5A01G331700 chr5D 426286323 426290957 4634 False 659 2712 92.407571 1 3392 7 chr5D.!!$F1 3391
2 TraesCS5A01G331700 chr5B 516065199 516067759 2560 False 1446 2385 92.255000 1 2393 2 chr5B.!!$F2 2392
3 TraesCS5A01G331700 chr5B 516082200 516082906 706 False 640 640 83.636000 2706 3392 1 chr5B.!!$F1 686

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
468 472 0.179200 CACGGCTTTGGCAACGTATC 60.179 55.0 13.02 0.24 40.87 2.24 F
491 495 0.398318 AGAGTTTCTGCCACCTCACC 59.602 55.0 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1530 2548 1.271127 TGCCATTCCCCATGACGAGA 61.271 55.000 0.0 0.0 34.31 4.04 R
2450 3473 3.012518 ACAGTTGCATGAGTATCTTGGC 58.987 45.455 0.0 0.0 40.31 4.52 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
50 54 2.479837 CTGTTCAAGTAAGGTCGTGCA 58.520 47.619 0.00 0.00 0.00 4.57
92 96 1.614241 ATAAGCTGGTTCCGCTCCGT 61.614 55.000 0.00 0.00 36.56 4.69
93 97 2.221906 TAAGCTGGTTCCGCTCCGTC 62.222 60.000 0.00 0.00 36.56 4.79
181 185 3.090532 ATTGGGAGGGGCCTCGTC 61.091 66.667 0.84 3.93 43.59 4.20
230 234 2.424234 GGCTGGAGAGTAGACAGATCCT 60.424 54.545 0.00 0.00 34.21 3.24
268 272 1.017387 CTGCTCGTATGGCCTTTTCC 58.983 55.000 3.32 0.00 0.00 3.13
427 431 1.591504 ATTAAACAACGCCCGGCCAG 61.592 55.000 2.24 0.00 0.00 4.85
432 436 4.418328 AACGCCCGGCCAGCATTA 62.418 61.111 14.66 0.00 0.00 1.90
433 437 3.714487 AACGCCCGGCCAGCATTAT 62.714 57.895 14.66 0.00 0.00 1.28
434 438 2.031919 CGCCCGGCCAGCATTATA 59.968 61.111 14.66 0.00 0.00 0.98
435 439 1.599518 CGCCCGGCCAGCATTATAA 60.600 57.895 14.66 0.00 0.00 0.98
436 440 1.169661 CGCCCGGCCAGCATTATAAA 61.170 55.000 14.66 0.00 0.00 1.40
437 441 0.313987 GCCCGGCCAGCATTATAAAC 59.686 55.000 9.84 0.00 0.00 2.01
438 442 0.591170 CCCGGCCAGCATTATAAACG 59.409 55.000 2.24 0.00 0.00 3.60
439 443 1.588674 CCGGCCAGCATTATAAACGA 58.411 50.000 2.24 0.00 0.00 3.85
440 444 1.531149 CCGGCCAGCATTATAAACGAG 59.469 52.381 2.24 0.00 0.00 4.18
441 445 1.069906 CGGCCAGCATTATAAACGAGC 60.070 52.381 2.24 0.00 0.00 5.03
442 446 2.222027 GGCCAGCATTATAAACGAGCT 58.778 47.619 0.00 0.00 35.63 4.09
445 449 3.259207 CAGCATTATAAACGAGCTGGC 57.741 47.619 17.68 0.00 46.55 4.85
446 450 2.613595 CAGCATTATAAACGAGCTGGCA 59.386 45.455 17.68 0.00 46.55 4.92
447 451 3.251729 CAGCATTATAAACGAGCTGGCAT 59.748 43.478 17.68 0.00 46.55 4.40
448 452 3.499918 AGCATTATAAACGAGCTGGCATC 59.500 43.478 0.00 0.00 33.67 3.91
449 453 3.365364 GCATTATAAACGAGCTGGCATCC 60.365 47.826 0.00 0.00 0.00 3.51
450 454 3.552132 TTATAAACGAGCTGGCATCCA 57.448 42.857 0.00 0.00 0.00 3.41
451 455 1.668419 ATAAACGAGCTGGCATCCAC 58.332 50.000 0.00 0.00 0.00 4.02
452 456 0.739462 TAAACGAGCTGGCATCCACG 60.739 55.000 0.00 0.00 0.00 4.94
453 457 3.958147 AACGAGCTGGCATCCACGG 62.958 63.158 0.00 0.00 0.00 4.94
457 461 3.064324 GCTGGCATCCACGGCTTT 61.064 61.111 0.00 0.00 37.26 3.51
458 462 2.879907 CTGGCATCCACGGCTTTG 59.120 61.111 0.00 0.00 0.00 2.77
459 463 2.676121 TGGCATCCACGGCTTTGG 60.676 61.111 0.00 0.00 38.10 3.28
460 464 4.133796 GGCATCCACGGCTTTGGC 62.134 66.667 0.00 0.00 36.48 4.52
461 465 3.372730 GCATCCACGGCTTTGGCA 61.373 61.111 0.00 0.00 40.87 4.92
462 466 2.929903 GCATCCACGGCTTTGGCAA 61.930 57.895 0.00 0.00 40.87 4.52
463 467 1.080569 CATCCACGGCTTTGGCAAC 60.081 57.895 0.00 0.00 40.87 4.17
464 468 2.625823 ATCCACGGCTTTGGCAACG 61.626 57.895 0.00 2.89 40.87 4.10
465 469 3.591835 CCACGGCTTTGGCAACGT 61.592 61.111 8.35 8.35 40.87 3.99
466 470 2.255172 CCACGGCTTTGGCAACGTA 61.255 57.895 13.02 0.00 40.87 3.57
467 471 1.582610 CCACGGCTTTGGCAACGTAT 61.583 55.000 13.02 0.00 40.87 3.06
468 472 0.179200 CACGGCTTTGGCAACGTATC 60.179 55.000 13.02 0.24 40.87 2.24
469 473 1.060308 CGGCTTTGGCAACGTATCG 59.940 57.895 0.00 0.79 40.87 2.92
470 474 1.226295 GGCTTTGGCAACGTATCGC 60.226 57.895 0.00 0.00 40.87 4.58
476 480 4.496670 GCAACGTATCGCCAGAGT 57.503 55.556 0.00 0.00 0.00 3.24
479 483 1.060698 GCAACGTATCGCCAGAGTTTC 59.939 52.381 0.00 0.00 0.00 2.78
484 488 0.901827 TATCGCCAGAGTTTCTGCCA 59.098 50.000 0.54 0.00 42.98 4.92
485 489 0.674895 ATCGCCAGAGTTTCTGCCAC 60.675 55.000 0.54 0.00 42.98 5.01
491 495 0.398318 AGAGTTTCTGCCACCTCACC 59.602 55.000 0.00 0.00 0.00 4.02
544 548 3.501445 AGAAAGTCTACGACGTAACTGCT 59.499 43.478 17.55 15.37 37.67 4.24
547 551 2.351111 AGTCTACGACGTAACTGCTAGC 59.649 50.000 8.10 8.10 37.67 3.42
583 587 0.911769 TCCTGCATTGTACTCCCCAG 59.088 55.000 0.00 0.00 0.00 4.45
613 617 1.404986 CCAGATTCGCCGTCAAGGTTA 60.405 52.381 0.00 0.00 43.70 2.85
614 618 2.343101 CAGATTCGCCGTCAAGGTTAA 58.657 47.619 0.00 0.00 43.70 2.01
729 763 2.781595 GAAGCCGCGGAGAAAGTGGA 62.782 60.000 33.48 0.00 41.54 4.02
778 991 1.448717 GCTCGCAGGGAGGAAGAAC 60.449 63.158 15.92 0.00 43.36 3.01
782 995 0.895530 CGCAGGGAGGAAGAACACTA 59.104 55.000 0.00 0.00 0.00 2.74
786 999 1.900486 AGGGAGGAAGAACACTAACCG 59.100 52.381 0.00 0.00 0.00 4.44
954 1231 6.854381 CAGATCAACGCGTATTACTGTACATA 59.146 38.462 14.46 0.00 0.00 2.29
979 1997 5.241403 TCATCACCTTAACCACACAGAAT 57.759 39.130 0.00 0.00 0.00 2.40
1129 2147 1.522569 GTCCGGGAGATGAACAGGG 59.477 63.158 0.00 0.00 0.00 4.45
1530 2548 0.615331 TCCTCGCCAAGCTCTTCAAT 59.385 50.000 0.00 0.00 0.00 2.57
1554 2572 3.140141 ATGGGGAATGGCAACGCG 61.140 61.111 3.53 3.53 42.51 6.01
1587 2605 1.306997 CCAGGGGCTCCTTCACCTA 60.307 63.158 0.00 0.00 42.67 3.08
1968 2986 3.799755 GTCATCAACGGCGGCACC 61.800 66.667 13.24 0.00 0.00 5.01
2420 3439 9.939802 AAATAAGTTACTGTATTTCTTCGGAGT 57.060 29.630 0.00 0.00 0.00 3.85
2421 3440 9.939802 AATAAGTTACTGTATTTCTTCGGAGTT 57.060 29.630 0.00 0.00 0.00 3.01
2422 3441 7.886405 AAGTTACTGTATTTCTTCGGAGTTC 57.114 36.000 0.00 0.00 0.00 3.01
2423 3442 6.091437 AGTTACTGTATTTCTTCGGAGTTCG 58.909 40.000 0.00 0.00 40.90 3.95
2424 3443 3.846360 ACTGTATTTCTTCGGAGTTCGG 58.154 45.455 0.00 0.00 39.77 4.30
2425 3444 3.508793 ACTGTATTTCTTCGGAGTTCGGA 59.491 43.478 0.00 0.00 39.77 4.55
2448 3471 3.658725 ACTCAATATGGACCTGGTAGCT 58.341 45.455 0.00 0.00 0.00 3.32
2449 3472 4.816126 ACTCAATATGGACCTGGTAGCTA 58.184 43.478 0.00 0.00 0.00 3.32
2450 3473 4.835615 ACTCAATATGGACCTGGTAGCTAG 59.164 45.833 0.00 0.00 0.00 3.42
2451 3474 3.578716 TCAATATGGACCTGGTAGCTAGC 59.421 47.826 16.08 16.08 0.00 3.42
2452 3475 2.011122 TATGGACCTGGTAGCTAGCC 57.989 55.000 19.78 12.11 0.00 3.93
2453 3476 0.031111 ATGGACCTGGTAGCTAGCCA 60.031 55.000 19.78 15.70 34.42 4.75
2467 3490 3.135348 AGCTAGCCAAGATACTCATGCAA 59.865 43.478 12.13 0.00 0.00 4.08
2496 3519 8.251721 GTCTCTGTAAATAACCTGTGACATACT 58.748 37.037 0.00 0.00 30.85 2.12
2500 3523 7.681679 TGTAAATAACCTGTGACATACTCCAA 58.318 34.615 0.00 0.00 0.00 3.53
2502 3525 9.826574 GTAAATAACCTGTGACATACTCCAATA 57.173 33.333 0.00 0.00 0.00 1.90
2507 3537 7.432148 ACCTGTGACATACTCCAATAACATA 57.568 36.000 0.00 0.00 0.00 2.29
2534 3564 9.603921 ATCAATCATGTTCAAGTTGAAACTTTT 57.396 25.926 19.63 7.80 46.52 2.27
2545 3575 5.442391 AGTTGAAACTTTTAGTGGCCACTA 58.558 37.500 36.63 36.63 38.24 2.74
2575 3605 8.853847 AAAAATGTTTTTCTTTCGAAACGAAC 57.146 26.923 6.47 9.59 39.52 3.95
2583 3613 1.942677 TTCGAAACGAACTTGCCTCA 58.057 45.000 0.00 0.00 41.05 3.86
2594 3624 5.418840 ACGAACTTGCCTCATCCATTAATTT 59.581 36.000 0.00 0.00 0.00 1.82
2597 3627 6.396829 ACTTGCCTCATCCATTAATTTAGC 57.603 37.500 0.00 0.00 0.00 3.09
2604 3634 6.263842 CCTCATCCATTAATTTAGCAGCAGAA 59.736 38.462 0.00 0.00 0.00 3.02
2624 3654 8.150296 AGCAGAAAATTGCCAAGTTAATTAGTT 58.850 29.630 0.00 0.00 45.18 2.24
2625 3655 8.223100 GCAGAAAATTGCCAAGTTAATTAGTTG 58.777 33.333 0.00 3.66 38.13 3.16
2653 3683 3.559238 AGCGAAAACCATCAACATCAC 57.441 42.857 0.00 0.00 0.00 3.06
2655 3685 4.323417 AGCGAAAACCATCAACATCACTA 58.677 39.130 0.00 0.00 0.00 2.74
2660 3690 3.610040 ACCATCAACATCACTAAGCGA 57.390 42.857 0.00 0.00 0.00 4.93
2661 3691 4.142609 ACCATCAACATCACTAAGCGAT 57.857 40.909 0.00 0.00 0.00 4.58
2663 3693 5.050490 ACCATCAACATCACTAAGCGATAC 58.950 41.667 0.00 0.00 0.00 2.24
2672 4088 2.029623 ACTAAGCGATACACATCCCGT 58.970 47.619 0.00 0.00 0.00 5.28
2675 4091 1.977056 AGCGATACACATCCCGTAGA 58.023 50.000 0.00 0.00 0.00 2.59
2679 4095 2.356695 CGATACACATCCCGTAGACACA 59.643 50.000 0.00 0.00 0.00 3.72
2680 4096 3.004419 CGATACACATCCCGTAGACACAT 59.996 47.826 0.00 0.00 0.00 3.21
2688 4104 1.065701 CCCGTAGACACATCGGAGAAG 59.934 57.143 4.38 0.00 46.05 2.85
2690 4106 1.828832 GTAGACACATCGGAGAAGCG 58.171 55.000 0.00 0.00 43.58 4.68
2727 4161 1.526887 GCTCCCCCATCATCGTTGA 59.473 57.895 0.00 0.00 36.00 3.18
2739 4173 4.471904 TCATCGTTGACATAGAAGCCTT 57.528 40.909 0.00 0.00 0.00 4.35
2754 4188 0.953727 GCCTTGATGCCAATATCGCA 59.046 50.000 0.33 0.33 41.28 5.10
2763 4197 1.224069 CCAATATCGCAGCCGTCCAG 61.224 60.000 0.00 0.00 35.54 3.86
2786 4220 2.514592 CCGCTTGTCGATGCCCAT 60.515 61.111 0.00 0.00 41.67 4.00
2788 4222 1.815003 CGCTTGTCGATGCCCATCA 60.815 57.895 8.79 0.00 41.67 3.07
2790 4224 0.745845 GCTTGTCGATGCCCATCACT 60.746 55.000 8.79 0.00 37.69 3.41
2828 4263 2.232941 GAGGGAATACGACACCAAGACA 59.767 50.000 0.00 0.00 0.00 3.41
2849 4284 2.230940 GCCATCGTCCGATCACACG 61.231 63.158 7.03 7.03 37.36 4.49
2854 4289 1.092348 TCGTCCGATCACACGAGATT 58.908 50.000 11.16 0.00 40.05 2.40
2893 4328 0.176680 GTCGTGATGGCTGGATCTGT 59.823 55.000 0.00 0.00 0.00 3.41
2904 4339 2.191641 GATCTGTGCAGGAGGGGC 59.808 66.667 0.00 0.00 0.00 5.80
2905 4340 2.611800 ATCTGTGCAGGAGGGGCA 60.612 61.111 0.00 0.00 39.32 5.36
2929 4381 0.806868 AGCAATGCAGTCAACGATGG 59.193 50.000 8.35 0.00 0.00 3.51
2935 4387 2.031919 AGTCAACGATGGCCGCAA 59.968 55.556 0.00 0.00 43.32 4.85
2957 4413 1.146930 CCGCCATAGCTGGTCATGT 59.853 57.895 0.00 0.00 45.10 3.21
2973 4429 2.479566 ATGTCACAAAGCCGAGACAT 57.520 45.000 0.00 0.00 44.41 3.06
3008 4464 3.049674 CCACGCCGCACATCAACT 61.050 61.111 0.00 0.00 0.00 3.16
3011 4467 1.375908 ACGCCGCACATCAACTGAT 60.376 52.632 0.00 0.00 34.56 2.90
3074 4535 2.148768 ACCCATCGACGAAAAAGAACC 58.851 47.619 0.00 0.00 0.00 3.62
3075 4536 1.127951 CCCATCGACGAAAAAGAACCG 59.872 52.381 0.00 0.00 0.00 4.44
3154 4615 2.180769 CGCCAGATCCGTCAACGA 59.819 61.111 3.71 0.00 43.02 3.85
3156 4617 1.080093 GCCAGATCCGTCAACGACA 60.080 57.895 3.71 0.00 43.02 4.35
3179 4640 1.523154 GGAACGCAGGCCATCAAACA 61.523 55.000 5.01 0.00 0.00 2.83
3182 4643 1.106351 ACGCAGGCCATCAAACACAA 61.106 50.000 5.01 0.00 0.00 3.33
3184 4645 0.664166 GCAGGCCATCAAACACAACG 60.664 55.000 5.01 0.00 0.00 4.10
3189 4650 2.288152 GGCCATCAAACACAACGTGAAT 60.288 45.455 0.00 0.00 36.96 2.57
3227 4688 2.217750 CACCATGTCGACAAGGAACAA 58.782 47.619 38.48 8.61 38.06 2.83
3237 4698 1.071699 ACAAGGAACAAAGGAGCGCTA 59.928 47.619 11.50 0.00 0.00 4.26
3267 4728 0.392998 AGAACCACCATGATGCCGAC 60.393 55.000 0.00 0.00 0.00 4.79
3285 4746 2.103094 CGACCCACATCCATACATCAGT 59.897 50.000 0.00 0.00 0.00 3.41
3290 4751 2.938451 CACATCCATACATCAGTTGCGT 59.062 45.455 0.00 0.00 0.00 5.24
3330 4791 2.438392 TCACCGGAGACTAGATCTGCTA 59.562 50.000 9.46 0.00 43.46 3.49
3336 4797 3.954904 GGAGACTAGATCTGCTACACCAA 59.045 47.826 5.18 0.00 42.38 3.67
3366 4827 1.305213 GCCCTTCTTTGCCATCCCA 60.305 57.895 0.00 0.00 0.00 4.37
3379 4840 3.924013 ATCCCAGGACACCGAGCCA 62.924 63.158 0.00 0.00 0.00 4.75
3382 4843 2.659063 CCAGGACACCGAGCCATGA 61.659 63.158 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 96 2.097825 GTCCCACCTCGCTAGTTTAGA 58.902 52.381 0.00 0.00 0.00 2.10
93 97 2.100989 AGTCCCACCTCGCTAGTTTAG 58.899 52.381 0.00 0.00 0.00 1.85
230 234 1.421268 AGATATTTCGCAGATGGGCCA 59.579 47.619 9.61 9.61 35.04 5.36
268 272 3.188048 AGCTGATGCAACGAAAAAGAGAG 59.812 43.478 0.00 0.00 42.74 3.20
339 343 9.440761 ACAGTAATTTATCAGATACTCCTTCCT 57.559 33.333 0.00 0.00 0.00 3.36
355 359 8.876275 AACACGAGTACTGAAACAGTAATTTA 57.124 30.769 12.22 0.00 46.55 1.40
362 366 5.174035 CAGAAGAACACGAGTACTGAAACAG 59.826 44.000 0.00 0.00 37.52 3.16
427 431 3.365364 GGATGCCAGCTCGTTTATAATGC 60.365 47.826 0.00 0.00 0.00 3.56
431 435 2.801699 CGTGGATGCCAGCTCGTTTATA 60.802 50.000 0.00 0.00 32.34 0.98
432 436 1.668419 GTGGATGCCAGCTCGTTTAT 58.332 50.000 0.00 0.00 32.34 1.40
433 437 0.739462 CGTGGATGCCAGCTCGTTTA 60.739 55.000 0.00 0.00 32.34 2.01
434 438 2.034879 CGTGGATGCCAGCTCGTTT 61.035 57.895 0.00 0.00 32.34 3.60
435 439 2.434884 CGTGGATGCCAGCTCGTT 60.435 61.111 0.00 0.00 32.34 3.85
436 440 4.457496 CCGTGGATGCCAGCTCGT 62.457 66.667 0.00 0.00 32.34 4.18
438 442 3.984193 AAGCCGTGGATGCCAGCTC 62.984 63.158 0.00 0.00 34.60 4.09
439 443 3.574074 AAAGCCGTGGATGCCAGCT 62.574 57.895 0.00 0.00 36.75 4.24
440 444 3.064324 AAAGCCGTGGATGCCAGC 61.064 61.111 0.00 0.00 32.34 4.85
441 445 2.703798 CCAAAGCCGTGGATGCCAG 61.704 63.158 0.00 0.00 41.65 4.85
442 446 2.676121 CCAAAGCCGTGGATGCCA 60.676 61.111 0.00 0.00 41.65 4.92
443 447 4.133796 GCCAAAGCCGTGGATGCC 62.134 66.667 7.45 0.00 41.65 4.40
444 448 2.929903 TTGCCAAAGCCGTGGATGC 61.930 57.895 7.45 0.00 41.65 3.91
445 449 1.080569 GTTGCCAAAGCCGTGGATG 60.081 57.895 7.45 0.00 41.65 3.51
446 450 2.625823 CGTTGCCAAAGCCGTGGAT 61.626 57.895 7.45 0.00 41.65 3.41
447 451 2.661840 TACGTTGCCAAAGCCGTGGA 62.662 55.000 7.45 0.00 41.65 4.02
448 452 1.582610 ATACGTTGCCAAAGCCGTGG 61.583 55.000 0.00 0.00 37.44 4.94
449 453 0.179200 GATACGTTGCCAAAGCCGTG 60.179 55.000 0.00 0.00 37.44 4.94
450 454 1.632046 CGATACGTTGCCAAAGCCGT 61.632 55.000 0.00 0.00 39.66 5.68
451 455 1.060308 CGATACGTTGCCAAAGCCG 59.940 57.895 0.00 0.00 38.69 5.52
452 456 1.226295 GCGATACGTTGCCAAAGCC 60.226 57.895 0.00 0.00 38.69 4.35
453 457 4.360101 GCGATACGTTGCCAAAGC 57.640 55.556 0.00 0.00 40.48 3.51
459 463 1.060698 GAAACTCTGGCGATACGTTGC 59.939 52.381 0.00 0.00 0.00 4.17
460 464 2.345641 CAGAAACTCTGGCGATACGTTG 59.654 50.000 0.00 0.00 40.71 4.10
461 465 2.607187 CAGAAACTCTGGCGATACGTT 58.393 47.619 0.00 0.00 40.71 3.99
462 466 1.736032 GCAGAAACTCTGGCGATACGT 60.736 52.381 5.84 0.00 44.43 3.57
463 467 0.924090 GCAGAAACTCTGGCGATACG 59.076 55.000 5.84 0.00 44.43 3.06
470 474 0.397941 TGAGGTGGCAGAAACTCTGG 59.602 55.000 5.84 0.00 44.43 3.86
471 475 1.517242 GTGAGGTGGCAGAAACTCTG 58.483 55.000 0.00 0.00 46.90 3.35
472 476 0.398318 GGTGAGGTGGCAGAAACTCT 59.602 55.000 0.00 0.00 0.00 3.24
476 480 1.761174 GGAGGTGAGGTGGCAGAAA 59.239 57.895 0.00 0.00 0.00 2.52
479 483 3.314331 ACGGAGGTGAGGTGGCAG 61.314 66.667 0.00 0.00 0.00 4.85
491 495 5.541845 ACATCCATATGTTATGACACGGAG 58.458 41.667 17.64 6.18 44.07 4.63
547 551 2.663852 AACGGCGGTTGAAGGACG 60.664 61.111 13.24 0.00 34.37 4.79
583 587 4.117685 ACGGCGAATCTGGATTACTAAAC 58.882 43.478 16.62 0.00 0.00 2.01
631 636 6.701145 TGCAAGTCGAATCTCTAATCTAGT 57.299 37.500 0.00 0.00 0.00 2.57
639 644 4.404073 ACTTAGGATGCAAGTCGAATCTCT 59.596 41.667 0.00 0.00 30.36 3.10
729 763 0.663568 CTTTGTCGTCGTCTCCGCTT 60.664 55.000 0.00 0.00 0.00 4.68
742 776 2.585888 GCTCTTTGCTCGACTTTGTC 57.414 50.000 0.00 0.00 38.95 3.18
764 798 2.615747 GGTTAGTGTTCTTCCTCCCTGC 60.616 54.545 0.00 0.00 0.00 4.85
765 799 2.353803 CGGTTAGTGTTCTTCCTCCCTG 60.354 54.545 0.00 0.00 0.00 4.45
954 1231 4.041567 TCTGTGTGGTTAAGGTGATGATGT 59.958 41.667 0.00 0.00 0.00 3.06
979 1997 1.372838 CTCCTCGCTCTCGCTCTCAA 61.373 60.000 0.00 0.00 35.26 3.02
1207 2225 3.479203 CCGGAGCATGGGCCACTA 61.479 66.667 9.28 0.00 42.56 2.74
1530 2548 1.271127 TGCCATTCCCCATGACGAGA 61.271 55.000 0.00 0.00 34.31 4.04
1554 2572 4.077184 TGGTCCGCATCGTCCACC 62.077 66.667 0.00 0.00 0.00 4.61
1556 2574 3.770040 CCTGGTCCGCATCGTCCA 61.770 66.667 0.00 0.00 0.00 4.02
1836 2854 4.980805 ACGGTCACGCACGGCATT 62.981 61.111 0.00 0.00 46.04 3.56
2420 3439 4.513442 CAGGTCCATATTGAGTTTCCGAA 58.487 43.478 0.00 0.00 0.00 4.30
2421 3440 3.118408 CCAGGTCCATATTGAGTTTCCGA 60.118 47.826 0.00 0.00 0.00 4.55
2422 3441 3.206150 CCAGGTCCATATTGAGTTTCCG 58.794 50.000 0.00 0.00 0.00 4.30
2423 3442 4.236527 ACCAGGTCCATATTGAGTTTCC 57.763 45.455 0.00 0.00 0.00 3.13
2424 3443 4.816925 GCTACCAGGTCCATATTGAGTTTC 59.183 45.833 0.00 0.00 0.00 2.78
2425 3444 4.475016 AGCTACCAGGTCCATATTGAGTTT 59.525 41.667 0.00 0.00 0.00 2.66
2448 3471 4.080919 ACAGTTGCATGAGTATCTTGGCTA 60.081 41.667 0.00 0.00 40.31 3.93
2449 3472 3.276857 CAGTTGCATGAGTATCTTGGCT 58.723 45.455 0.00 0.00 40.31 4.75
2450 3473 3.012518 ACAGTTGCATGAGTATCTTGGC 58.987 45.455 0.00 0.00 40.31 4.52
2451 3474 4.511527 AGACAGTTGCATGAGTATCTTGG 58.488 43.478 0.00 0.00 40.31 3.61
2452 3475 5.291371 CAGAGACAGTTGCATGAGTATCTTG 59.709 44.000 0.00 2.11 42.60 3.02
2453 3476 5.046735 ACAGAGACAGTTGCATGAGTATCTT 60.047 40.000 0.00 0.00 30.87 2.40
2467 3490 6.041637 TGTCACAGGTTATTTACAGAGACAGT 59.958 38.462 0.00 0.00 32.95 3.55
2520 3550 5.394115 AGTGGCCACTAAAAGTTTCAACTTG 60.394 40.000 37.12 0.00 43.16 3.16
2567 3597 2.151202 TGGATGAGGCAAGTTCGTTTC 58.849 47.619 0.00 0.00 0.00 2.78
2573 3603 6.380846 TGCTAAATTAATGGATGAGGCAAGTT 59.619 34.615 0.00 0.00 0.00 2.66
2575 3605 6.395426 TGCTAAATTAATGGATGAGGCAAG 57.605 37.500 0.00 0.00 0.00 4.01
2583 3613 9.321562 CAATTTTCTGCTGCTAAATTAATGGAT 57.678 29.630 15.12 0.00 32.04 3.41
2594 3624 2.892852 ACTTGGCAATTTTCTGCTGCTA 59.107 40.909 0.00 0.00 42.25 3.49
2597 3627 6.790285 AATTAACTTGGCAATTTTCTGCTG 57.210 33.333 8.17 0.00 42.25 4.41
2624 3654 3.131223 TGATGGTTTTCGCTTGGTTTTCA 59.869 39.130 0.00 0.00 0.00 2.69
2625 3655 3.712187 TGATGGTTTTCGCTTGGTTTTC 58.288 40.909 0.00 0.00 0.00 2.29
2633 3663 3.149196 AGTGATGTTGATGGTTTTCGCT 58.851 40.909 0.00 0.00 0.00 4.93
2635 3665 5.088739 GCTTAGTGATGTTGATGGTTTTCG 58.911 41.667 0.00 0.00 0.00 3.46
2653 3683 2.795175 ACGGGATGTGTATCGCTTAG 57.205 50.000 0.00 0.00 42.37 2.18
2655 3685 2.034305 GTCTACGGGATGTGTATCGCTT 59.966 50.000 0.00 0.00 42.37 4.68
2660 3690 3.004419 CGATGTGTCTACGGGATGTGTAT 59.996 47.826 0.00 0.00 0.00 2.29
2661 3691 2.356695 CGATGTGTCTACGGGATGTGTA 59.643 50.000 0.00 0.00 0.00 2.90
2663 3693 1.536072 CCGATGTGTCTACGGGATGTG 60.536 57.143 0.00 0.00 42.48 3.21
2672 4088 0.100682 GCGCTTCTCCGATGTGTCTA 59.899 55.000 0.00 0.00 0.00 2.59
2675 4091 2.125512 GGCGCTTCTCCGATGTGT 60.126 61.111 7.64 0.00 0.00 3.72
2688 4104 2.508663 GGTTGAGGTAGTCGGCGC 60.509 66.667 0.00 0.00 0.00 6.53
2690 4106 0.527817 CGATGGTTGAGGTAGTCGGC 60.528 60.000 0.00 0.00 0.00 5.54
2695 4111 0.105039 GGGAGCGATGGTTGAGGTAG 59.895 60.000 0.00 0.00 0.00 3.18
2727 4161 3.370840 TTGGCATCAAGGCTTCTATGT 57.629 42.857 16.42 0.00 44.55 2.29
2739 4173 1.229975 CGGCTGCGATATTGGCATCA 61.230 55.000 3.25 0.00 40.09 3.07
2763 4197 2.100631 CATCGACAAGCGGGACCAC 61.101 63.158 0.00 0.00 41.33 4.16
2786 4220 1.719529 TGGGGGTTCGTCTTTAGTGA 58.280 50.000 0.00 0.00 0.00 3.41
2788 4222 2.302157 CTCTTGGGGGTTCGTCTTTAGT 59.698 50.000 0.00 0.00 0.00 2.24
2790 4224 1.626825 CCTCTTGGGGGTTCGTCTTTA 59.373 52.381 0.00 0.00 0.00 1.85
2817 4252 1.298859 GATGGCGGTGTCTTGGTGTC 61.299 60.000 0.00 0.00 0.00 3.67
2828 4263 3.144871 TGATCGGACGATGGCGGT 61.145 61.111 12.40 0.00 43.17 5.68
2893 4328 3.496309 CTGTTGTGCCCCTCCTGCA 62.496 63.158 0.00 0.00 36.12 4.41
2904 4339 2.121786 GTTGACTGCATTGCTGTTGTG 58.878 47.619 20.23 2.63 40.59 3.33
2905 4340 1.268692 CGTTGACTGCATTGCTGTTGT 60.269 47.619 20.23 9.19 40.59 3.32
2907 4342 1.308047 TCGTTGACTGCATTGCTGTT 58.692 45.000 20.23 6.50 40.59 3.16
2908 4343 1.198408 CATCGTTGACTGCATTGCTGT 59.802 47.619 19.51 19.51 43.03 4.40
2957 4413 0.396435 ACCATGTCTCGGCTTTGTGA 59.604 50.000 0.00 0.00 0.00 3.58
2973 4429 1.761174 GGAGCTTGGGTGAAGACCA 59.239 57.895 0.00 0.00 45.25 4.02
3008 4464 3.657448 ATTGCCGACGCCGACATCA 62.657 57.895 0.00 0.00 38.22 3.07
3026 4486 2.527123 TGGTGGTGGTTAGCGGGA 60.527 61.111 0.00 0.00 0.00 5.14
3075 4536 4.838152 TTGGCTGCGGCGGATCTC 62.838 66.667 14.15 0.00 39.81 2.75
3154 4615 4.681978 GGCCTGCGTTCCGACTGT 62.682 66.667 0.00 0.00 0.00 3.55
3156 4617 3.665675 GATGGCCTGCGTTCCGACT 62.666 63.158 3.32 0.00 0.00 4.18
3175 4636 3.795150 GCATGGTGATTCACGTTGTGTTT 60.795 43.478 10.56 0.00 34.83 2.83
3176 4637 2.287547 GCATGGTGATTCACGTTGTGTT 60.288 45.455 10.56 0.00 34.83 3.32
3179 4640 0.881118 GGCATGGTGATTCACGTTGT 59.119 50.000 10.56 0.00 34.83 3.32
3182 4643 0.908910 TAGGGCATGGTGATTCACGT 59.091 50.000 10.56 0.00 34.83 4.49
3184 4645 1.680338 GGTAGGGCATGGTGATTCAC 58.320 55.000 8.34 8.34 0.00 3.18
3189 4650 2.731571 GCTCGGTAGGGCATGGTGA 61.732 63.158 0.00 0.00 45.11 4.02
3227 4688 3.148279 CCTCGGGTAGCGCTCCTT 61.148 66.667 16.34 0.00 0.00 3.36
3237 4698 1.551019 GGTGGTTCTTAGCCTCGGGT 61.551 60.000 0.00 0.00 0.00 5.28
3267 4728 2.620115 GCAACTGATGTATGGATGTGGG 59.380 50.000 0.00 0.00 0.00 4.61
3311 4772 2.172930 TGTAGCAGATCTAGTCTCCGGT 59.827 50.000 0.00 0.00 34.00 5.28
3320 4781 2.831526 TGCTGTTGGTGTAGCAGATCTA 59.168 45.455 0.00 0.00 44.36 1.98
3330 4791 3.100545 CACCTCTTGCTGTTGGTGT 57.899 52.632 0.00 0.00 43.41 4.16
3366 4827 3.023949 GCTCATGGCTCGGTGTCCT 62.024 63.158 0.00 0.00 38.06 3.85


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

AutoCloner maintained by Alex Coulton.