Multiple sequence alignment - TraesCS4A01G128100

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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 TraesCS4A01G128100 chr4A 100.000 3043 0 0 1 3043 165353816 165356858 0.000000e+00 5620
1 TraesCS4A01G128100 chr4D 95.979 1318 33 5 1134 2434 309704142 309702828 0.000000e+00 2122
2 TraesCS4A01G128100 chr4D 90.220 1135 25 25 5 1087 309705253 309704153 0.000000e+00 1402
3 TraesCS4A01G128100 chr4D 96.245 506 15 2 2541 3043 309702830 309702326 0.000000e+00 826
4 TraesCS4A01G128100 chr4B 93.237 1316 45 22 1134 2434 386750883 386749597 0.000000e+00 1897
5 TraesCS4A01G128100 chr4B 88.703 1133 34 29 14 1087 386751991 386750894 0.000000e+00 1297
6 TraesCS4A01G128100 chr4B 92.669 532 9 8 2541 3043 386749599 386749069 0.000000e+00 739
7 TraesCS4A01G128100 chr7A 82.126 207 26 3 2008 2214 699910980 699910785 1.880000e-37 167
8 TraesCS4A01G128100 chr7A 88.000 100 12 0 2444 2543 337525653 337525752 5.330000e-23 119
9 TraesCS4A01G128100 chr7A 85.714 112 15 1 2435 2546 57873683 57873573 1.920000e-22 117
10 TraesCS4A01G128100 chr7A 84.615 117 14 4 2431 2547 57543856 57543744 2.480000e-21 113
11 TraesCS4A01G128100 chr7A 85.088 114 13 2 2431 2542 608734603 608734492 2.480000e-21 113
12 TraesCS4A01G128100 chr1D 90.741 108 10 0 2434 2541 332596858 332596965 8.790000e-31 145
13 TraesCS4A01G128100 chr7D 88.393 112 10 2 2544 2653 609974186 609974296 6.850000e-27 132
14 TraesCS4A01G128100 chr7D 86.555 119 11 4 2544 2659 607916672 607916556 3.190000e-25 126
15 TraesCS4A01G128100 chr7D 86.555 119 11 4 2544 2659 609746131 609746015 3.190000e-25 126
16 TraesCS4A01G128100 chr6B 88.073 109 13 0 2435 2543 567900901 567900793 2.460000e-26 130
17 TraesCS4A01G128100 chr7B 88.182 110 10 2 2544 2651 694102824 694102716 8.860000e-26 128
18 TraesCS4A01G128100 chr5B 87.156 109 14 0 2435 2543 130153911 130154019 1.150000e-24 124
19 TraesCS4A01G128100 chr5B 87.963 108 9 4 2437 2542 403929309 403929204 1.150000e-24 124
20 TraesCS4A01G128100 chr5B 86.111 108 14 1 2435 2542 349086812 349086918 6.890000e-22 115


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 TraesCS4A01G128100 chr4A 165353816 165356858 3042 False 5620 5620 100.000000 1 3043 1 chr4A.!!$F1 3042
1 TraesCS4A01G128100 chr4D 309702326 309705253 2927 True 1450 2122 94.148000 5 3043 3 chr4D.!!$R1 3038
2 TraesCS4A01G128100 chr4B 386749069 386751991 2922 True 1311 1897 91.536333 14 3043 3 chr4B.!!$R1 3029

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
711 753 0.040514 CGATACGCTCTGCTCCTCTG 60.041 60.0 0.0 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2408 2502 0.531657 TGTTTATGGCCATGCTGCAC 59.468 50.0 29.04 16.25 0.0 4.57 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
154 155 5.585500 GCATTTGCAGCATAACATAATGG 57.415 39.130 14.32 1.06 41.59 3.16
488 516 3.518590 GGTCCGGCCGAATACAATATAG 58.481 50.000 30.73 4.77 0.00 1.31
489 517 3.518590 GTCCGGCCGAATACAATATAGG 58.481 50.000 30.73 4.53 0.00 2.57
623 665 2.171635 GCCACTTGTAGGGCTTTCG 58.828 57.895 0.00 0.00 46.74 3.46
709 751 4.933483 CGATACGCTCTGCTCCTC 57.067 61.111 0.00 0.00 0.00 3.71
710 752 2.326222 CGATACGCTCTGCTCCTCT 58.674 57.895 0.00 0.00 0.00 3.69
711 753 0.040514 CGATACGCTCTGCTCCTCTG 60.041 60.000 0.00 0.00 0.00 3.35
712 754 0.318614 GATACGCTCTGCTCCTCTGC 60.319 60.000 0.00 0.00 0.00 4.26
730 772 3.086600 CCTCTGGGACTGGGAGCC 61.087 72.222 0.00 0.00 33.58 4.70
734 776 4.974438 TGGGACTGGGAGCCGGTT 62.974 66.667 1.90 0.00 44.10 4.44
735 777 2.686106 GGGACTGGGAGCCGGTTA 60.686 66.667 1.90 0.00 44.10 2.85
736 778 2.732619 GGGACTGGGAGCCGGTTAG 61.733 68.421 1.90 0.00 44.10 2.34
737 779 2.732619 GGACTGGGAGCCGGTTAGG 61.733 68.421 1.90 0.00 44.10 2.69
782 827 5.757320 ACAAGATTATCTTTGCATCTCTCCG 59.243 40.000 4.51 0.00 33.78 4.63
783 828 5.543507 AGATTATCTTTGCATCTCTCCGT 57.456 39.130 0.00 0.00 0.00 4.69
784 829 5.537188 AGATTATCTTTGCATCTCTCCGTC 58.463 41.667 0.00 0.00 0.00 4.79
785 830 2.611225 ATCTTTGCATCTCTCCGTCC 57.389 50.000 0.00 0.00 0.00 4.79
786 831 1.561643 TCTTTGCATCTCTCCGTCCT 58.438 50.000 0.00 0.00 0.00 3.85
787 832 1.478510 TCTTTGCATCTCTCCGTCCTC 59.521 52.381 0.00 0.00 0.00 3.71
788 833 0.537188 TTTGCATCTCTCCGTCCTCC 59.463 55.000 0.00 0.00 0.00 4.30
791 836 1.045911 GCATCTCTCCGTCCTCCCTT 61.046 60.000 0.00 0.00 0.00 3.95
966 1033 2.243736 TCTTCTTCCTCTCCTCTCCTCC 59.756 54.545 0.00 0.00 0.00 4.30
995 1062 0.473694 TTCTTGCTCTGGGACTGGGA 60.474 55.000 0.00 0.00 0.00 4.37
1072 1139 4.907879 AGGTCAGTTTTCTGCTTCTTTG 57.092 40.909 0.00 0.00 46.59 2.77
1087 1154 6.211515 TGCTTCTTTGCATCTTTCTTTTCTC 58.788 36.000 0.00 0.00 38.12 2.87
1088 1155 6.040166 TGCTTCTTTGCATCTTTCTTTTCTCT 59.960 34.615 0.00 0.00 38.12 3.10
1089 1156 6.581919 GCTTCTTTGCATCTTTCTTTTCTCTC 59.418 38.462 0.00 0.00 0.00 3.20
1090 1157 7.521910 GCTTCTTTGCATCTTTCTTTTCTCTCT 60.522 37.037 0.00 0.00 0.00 3.10
1091 1158 7.432350 TCTTTGCATCTTTCTTTTCTCTCTC 57.568 36.000 0.00 0.00 0.00 3.20
1092 1159 7.222872 TCTTTGCATCTTTCTTTTCTCTCTCT 58.777 34.615 0.00 0.00 0.00 3.10
1093 1160 7.387397 TCTTTGCATCTTTCTTTTCTCTCTCTC 59.613 37.037 0.00 0.00 0.00 3.20
1094 1161 6.357579 TGCATCTTTCTTTTCTCTCTCTCT 57.642 37.500 0.00 0.00 0.00 3.10
1095 1162 6.397272 TGCATCTTTCTTTTCTCTCTCTCTC 58.603 40.000 0.00 0.00 0.00 3.20
1096 1163 6.211184 TGCATCTTTCTTTTCTCTCTCTCTCT 59.789 38.462 0.00 0.00 0.00 3.10
1097 1164 6.753744 GCATCTTTCTTTTCTCTCTCTCTCTC 59.246 42.308 0.00 0.00 0.00 3.20
1098 1165 7.363268 GCATCTTTCTTTTCTCTCTCTCTCTCT 60.363 40.741 0.00 0.00 0.00 3.10
1099 1166 9.177608 CATCTTTCTTTTCTCTCTCTCTCTCTA 57.822 37.037 0.00 0.00 0.00 2.43
1100 1167 9.927081 ATCTTTCTTTTCTCTCTCTCTCTCTAT 57.073 33.333 0.00 0.00 0.00 1.98
1124 1191 4.990543 ATATATATGTGTGTGTGTGCGC 57.009 40.909 0.00 0.00 0.00 6.09
1125 1192 0.995728 TATATGTGTGTGTGTGCGCG 59.004 50.000 0.00 0.00 0.00 6.86
1126 1193 2.239341 ATATGTGTGTGTGTGCGCGC 62.239 55.000 27.26 27.26 36.27 6.86
1306 1392 1.247567 CAACTTTCCCAGGTTCGCAT 58.752 50.000 0.00 0.00 0.00 4.73
1325 1411 2.125512 CCGCCTTTGGTCTCCTCG 60.126 66.667 0.00 0.00 0.00 4.63
1359 1445 8.865793 CTCATTTGGTGATCTGCATCTGCATG 62.866 46.154 5.16 0.78 42.64 4.06
1398 1491 2.835580 AGTATCTAGCGCCTCGTCTA 57.164 50.000 2.29 0.00 0.00 2.59
1422 1516 3.364964 GCACATCACAAGTCTTTTACCGG 60.365 47.826 0.00 0.00 0.00 5.28
1432 1526 2.100989 TCTTTTACCGGCCTCTCTCTC 58.899 52.381 0.00 0.00 0.00 3.20
1481 1575 8.553085 TTCTTCTCATCCAAATCTACCATAGA 57.447 34.615 0.00 0.00 39.50 1.98
1529 1623 7.147408 ACCAATATATGAGAAGAAGCCTCAGTT 60.147 37.037 0.00 0.00 43.07 3.16
1532 1626 4.906747 ATGAGAAGAAGCCTCAGTTCTT 57.093 40.909 0.00 0.00 45.05 2.52
1557 1651 5.052960 CGATTTACTCACAGAAGATTCGTCG 60.053 44.000 0.00 0.00 0.00 5.12
1694 1788 3.834610 AGTCACATACTACAACGAGCAC 58.165 45.455 0.00 0.00 36.36 4.40
1724 1818 2.759795 GCCTTCCTTGCCCTCACT 59.240 61.111 0.00 0.00 0.00 3.41
2434 2528 4.158394 CAGCATGGCCATAAACAAGTTACT 59.842 41.667 20.30 0.40 0.00 2.24
2435 2529 5.356751 CAGCATGGCCATAAACAAGTTACTA 59.643 40.000 20.30 0.00 0.00 1.82
2436 2530 5.357032 AGCATGGCCATAAACAAGTTACTAC 59.643 40.000 20.30 0.00 0.00 2.73
2437 2531 5.357032 GCATGGCCATAAACAAGTTACTACT 59.643 40.000 20.30 0.00 35.68 2.57
2438 2532 6.458342 GCATGGCCATAAACAAGTTACTACTC 60.458 42.308 20.30 0.00 31.99 2.59
2439 2533 5.493809 TGGCCATAAACAAGTTACTACTCC 58.506 41.667 0.00 0.00 31.99 3.85
2440 2534 4.880120 GGCCATAAACAAGTTACTACTCCC 59.120 45.833 0.00 0.00 31.99 4.30
2441 2535 5.338953 GGCCATAAACAAGTTACTACTCCCT 60.339 44.000 0.00 0.00 31.99 4.20
2442 2536 5.816258 GCCATAAACAAGTTACTACTCCCTC 59.184 44.000 0.00 0.00 31.99 4.30
2443 2537 6.346896 CCATAAACAAGTTACTACTCCCTCC 58.653 44.000 0.00 0.00 31.99 4.30
2444 2538 4.532314 AAACAAGTTACTACTCCCTCCG 57.468 45.455 0.00 0.00 31.99 4.63
2445 2539 3.166560 ACAAGTTACTACTCCCTCCGT 57.833 47.619 0.00 0.00 31.99 4.69
2446 2540 3.087781 ACAAGTTACTACTCCCTCCGTC 58.912 50.000 0.00 0.00 31.99 4.79
2447 2541 2.426381 CAAGTTACTACTCCCTCCGTCC 59.574 54.545 0.00 0.00 31.99 4.79
2448 2542 1.637553 AGTTACTACTCCCTCCGTCCA 59.362 52.381 0.00 0.00 0.00 4.02
2449 2543 1.747924 GTTACTACTCCCTCCGTCCAC 59.252 57.143 0.00 0.00 0.00 4.02
2450 2544 1.293062 TACTACTCCCTCCGTCCACT 58.707 55.000 0.00 0.00 0.00 4.00
2451 2545 0.408700 ACTACTCCCTCCGTCCACTT 59.591 55.000 0.00 0.00 0.00 3.16
2452 2546 1.203149 ACTACTCCCTCCGTCCACTTT 60.203 52.381 0.00 0.00 0.00 2.66
2453 2547 1.900486 CTACTCCCTCCGTCCACTTTT 59.100 52.381 0.00 0.00 0.00 2.27
2454 2548 2.019807 ACTCCCTCCGTCCACTTTTA 57.980 50.000 0.00 0.00 0.00 1.52
2455 2549 2.547990 ACTCCCTCCGTCCACTTTTAT 58.452 47.619 0.00 0.00 0.00 1.40
2456 2550 3.716431 ACTCCCTCCGTCCACTTTTATA 58.284 45.455 0.00 0.00 0.00 0.98
2457 2551 4.098894 ACTCCCTCCGTCCACTTTTATAA 58.901 43.478 0.00 0.00 0.00 0.98
2458 2552 4.161754 ACTCCCTCCGTCCACTTTTATAAG 59.838 45.833 0.00 0.00 37.40 1.73
2459 2553 4.098894 TCCCTCCGTCCACTTTTATAAGT 58.901 43.478 0.00 0.00 45.40 2.24
2460 2554 4.161001 TCCCTCCGTCCACTTTTATAAGTC 59.839 45.833 0.00 0.00 42.67 3.01
2461 2555 4.110482 CCTCCGTCCACTTTTATAAGTCG 58.890 47.826 0.00 0.00 42.67 4.18
2462 2556 4.381292 CCTCCGTCCACTTTTATAAGTCGT 60.381 45.833 0.00 0.00 42.67 4.34
2463 2557 5.138125 TCCGTCCACTTTTATAAGTCGTT 57.862 39.130 0.00 0.00 42.67 3.85
2464 2558 5.540911 TCCGTCCACTTTTATAAGTCGTTT 58.459 37.500 0.00 0.00 42.67 3.60
2465 2559 5.634859 TCCGTCCACTTTTATAAGTCGTTTC 59.365 40.000 0.00 0.00 42.67 2.78
2466 2560 5.406175 CCGTCCACTTTTATAAGTCGTTTCA 59.594 40.000 0.00 0.00 42.67 2.69
2467 2561 6.400727 CCGTCCACTTTTATAAGTCGTTTCAG 60.401 42.308 0.00 0.00 42.67 3.02
2468 2562 6.364165 CGTCCACTTTTATAAGTCGTTTCAGA 59.636 38.462 0.00 0.00 42.67 3.27
2469 2563 7.508134 GTCCACTTTTATAAGTCGTTTCAGAC 58.492 38.462 0.00 0.00 42.67 3.51
2470 2564 7.170320 GTCCACTTTTATAAGTCGTTTCAGACA 59.830 37.037 0.00 0.00 42.67 3.41
2471 2565 7.711772 TCCACTTTTATAAGTCGTTTCAGACAA 59.288 33.333 0.00 0.00 42.67 3.18
2472 2566 7.797123 CCACTTTTATAAGTCGTTTCAGACAAC 59.203 37.037 0.00 0.00 42.67 3.32
2473 2567 8.548721 CACTTTTATAAGTCGTTTCAGACAACT 58.451 33.333 0.00 0.00 42.67 3.16
2474 2568 9.754382 ACTTTTATAAGTCGTTTCAGACAACTA 57.246 29.630 0.00 0.00 40.60 2.24
2480 2574 9.878599 ATAAGTCGTTTCAGACAACTAAAAATG 57.121 29.630 0.00 0.00 43.24 2.32
2481 2575 7.548196 AGTCGTTTCAGACAACTAAAAATGA 57.452 32.000 0.00 0.00 43.24 2.57
2482 2576 7.981142 AGTCGTTTCAGACAACTAAAAATGAA 58.019 30.769 0.00 0.00 43.24 2.57
2483 2577 7.908601 AGTCGTTTCAGACAACTAAAAATGAAC 59.091 33.333 0.00 0.00 43.24 3.18
2484 2578 7.908601 GTCGTTTCAGACAACTAAAAATGAACT 59.091 33.333 0.00 0.00 40.65 3.01
2485 2579 9.100554 TCGTTTCAGACAACTAAAAATGAACTA 57.899 29.630 0.00 0.00 30.36 2.24
2486 2580 9.155053 CGTTTCAGACAACTAAAAATGAACTAC 57.845 33.333 0.00 0.00 0.00 2.73
2490 2584 9.607988 TCAGACAACTAAAAATGAACTACTTCA 57.392 29.630 0.00 0.00 40.77 3.02
2500 2594 9.574516 AAAAATGAACTACTTCATACCTTGTCT 57.425 29.630 0.00 0.00 44.93 3.41
2501 2595 8.553459 AAATGAACTACTTCATACCTTGTCTG 57.447 34.615 0.00 0.00 44.93 3.51
2502 2596 6.911250 TGAACTACTTCATACCTTGTCTGA 57.089 37.500 0.00 0.00 31.00 3.27
2503 2597 7.297936 TGAACTACTTCATACCTTGTCTGAA 57.702 36.000 0.00 0.00 31.00 3.02
2504 2598 7.732025 TGAACTACTTCATACCTTGTCTGAAA 58.268 34.615 0.00 0.00 30.48 2.69
2505 2599 8.375506 TGAACTACTTCATACCTTGTCTGAAAT 58.624 33.333 0.00 0.00 30.48 2.17
2506 2600 8.553459 AACTACTTCATACCTTGTCTGAAATG 57.447 34.615 0.00 0.00 30.48 2.32
2507 2601 7.680730 ACTACTTCATACCTTGTCTGAAATGT 58.319 34.615 0.00 0.00 30.48 2.71
2508 2602 8.157476 ACTACTTCATACCTTGTCTGAAATGTT 58.843 33.333 0.00 0.00 30.48 2.71
2509 2603 7.823745 ACTTCATACCTTGTCTGAAATGTTT 57.176 32.000 0.00 0.00 30.48 2.83
2510 2604 8.237811 ACTTCATACCTTGTCTGAAATGTTTT 57.762 30.769 0.00 0.00 30.48 2.43
2511 2605 8.352942 ACTTCATACCTTGTCTGAAATGTTTTC 58.647 33.333 0.00 0.00 30.48 2.29
2512 2606 7.815840 TCATACCTTGTCTGAAATGTTTTCA 57.184 32.000 2.96 2.96 0.00 2.69
2513 2607 8.231692 TCATACCTTGTCTGAAATGTTTTCAA 57.768 30.769 4.43 0.00 0.00 2.69
2514 2608 8.352201 TCATACCTTGTCTGAAATGTTTTCAAG 58.648 33.333 4.43 0.00 0.00 3.02
2516 2610 4.746611 CCTTGTCTGAAATGTTTTCAAGGC 59.253 41.667 7.86 2.07 42.07 4.35
2517 2611 4.320608 TGTCTGAAATGTTTTCAAGGCC 57.679 40.909 0.00 0.00 0.00 5.19
2518 2612 3.960102 TGTCTGAAATGTTTTCAAGGCCT 59.040 39.130 0.00 0.00 0.00 5.19
2519 2613 4.405358 TGTCTGAAATGTTTTCAAGGCCTT 59.595 37.500 13.78 13.78 0.00 4.35
2520 2614 5.596361 TGTCTGAAATGTTTTCAAGGCCTTA 59.404 36.000 20.00 0.00 0.00 2.69
2521 2615 6.097554 TGTCTGAAATGTTTTCAAGGCCTTAA 59.902 34.615 20.00 7.21 0.00 1.85
2522 2616 6.983890 GTCTGAAATGTTTTCAAGGCCTTAAA 59.016 34.615 20.00 13.65 0.00 1.52
2523 2617 7.494298 GTCTGAAATGTTTTCAAGGCCTTAAAA 59.506 33.333 20.00 14.67 0.00 1.52
2524 2618 8.043710 TCTGAAATGTTTTCAAGGCCTTAAAAA 58.956 29.630 20.69 20.69 0.00 1.94
2585 2679 4.718961 AGCACAACATAGAAAAGACCACT 58.281 39.130 0.00 0.00 0.00 4.00
2692 2786 4.725790 ATAAGCAAAATCCAGTTCAGGC 57.274 40.909 0.00 0.00 0.00 4.85
2728 2843 5.339177 TCATTTTATTTGTGCATGGCGTAG 58.661 37.500 0.00 0.00 0.00 3.51
2961 3084 4.884164 AGAGAGAACAAAACAAGGACAAGG 59.116 41.667 0.00 0.00 0.00 3.61
2970 3093 6.183360 ACAAAACAAGGACAAGGCATCAAATA 60.183 34.615 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 2.352001 CGATGCGTCGGGTACTCG 60.352 66.667 20.66 9.43 44.00 4.18
107 108 1.153208 CCCTCTGCTCTGCATCACC 60.153 63.158 0.00 0.00 38.13 4.02
154 155 3.645268 GATGCCTGGTCACCCCCAC 62.645 68.421 0.00 0.00 0.00 4.61
208 209 2.590821 CCCCAAACATGAGATCATCCC 58.409 52.381 0.00 0.00 33.61 3.85
319 323 1.371635 GCACATCCACGGTTTGCAC 60.372 57.895 0.00 0.00 33.24 4.57
320 324 2.902419 CGCACATCCACGGTTTGCA 61.902 57.895 0.00 0.00 32.51 4.08
325 329 1.079405 CCTAACGCACATCCACGGT 60.079 57.895 0.00 0.00 0.00 4.83
525 567 6.314400 TCGCAACTGGGTCTAACAATAATAAC 59.686 38.462 0.00 0.00 0.00 1.89
623 665 2.747855 CTCCGCACCTTCTTGGGC 60.748 66.667 0.00 0.00 41.11 5.36
625 667 1.826385 ATTTCTCCGCACCTTCTTGG 58.174 50.000 0.00 0.00 42.93 3.61
626 668 3.503748 AGAAATTTCTCCGCACCTTCTTG 59.496 43.478 15.11 0.00 29.94 3.02
706 748 2.040278 AGTCCCAGAGGGCAGAGG 59.960 66.667 0.00 0.00 43.94 3.69
707 749 2.365586 CCAGTCCCAGAGGGCAGAG 61.366 68.421 0.00 0.00 43.94 3.35
708 750 2.284921 CCAGTCCCAGAGGGCAGA 60.285 66.667 0.00 0.00 43.94 4.26
709 751 3.406200 CCCAGTCCCAGAGGGCAG 61.406 72.222 0.00 0.00 43.94 4.85
710 752 3.931631 CTCCCAGTCCCAGAGGGCA 62.932 68.421 0.00 0.00 43.94 5.36
711 753 3.086600 CTCCCAGTCCCAGAGGGC 61.087 72.222 0.00 0.00 43.94 5.19
712 754 3.086600 GCTCCCAGTCCCAGAGGG 61.087 72.222 0.00 0.00 46.11 4.30
728 770 3.162154 CCTCCCTCCCTAACCGGC 61.162 72.222 0.00 0.00 0.00 6.13
729 771 2.446036 CCCTCCCTCCCTAACCGG 60.446 72.222 0.00 0.00 0.00 5.28
730 772 1.457831 CTCCCTCCCTCCCTAACCG 60.458 68.421 0.00 0.00 0.00 4.44
733 775 1.231197 TCCCTCCCTCCCTCCCTAA 60.231 63.158 0.00 0.00 0.00 2.69
734 776 1.705450 CTCCCTCCCTCCCTCCCTA 60.705 68.421 0.00 0.00 0.00 3.53
735 777 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
736 778 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
737 779 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
782 827 3.003763 AGACCGGCAAGGGAGGAC 61.004 66.667 0.00 0.00 46.96 3.85
783 828 2.683933 GAGACCGGCAAGGGAGGA 60.684 66.667 0.00 0.00 46.96 3.71
784 829 3.003173 TGAGACCGGCAAGGGAGG 61.003 66.667 0.00 0.00 46.96 4.30
785 830 1.831652 AACTGAGACCGGCAAGGGAG 61.832 60.000 0.00 0.00 46.96 4.30
786 831 1.415672 AAACTGAGACCGGCAAGGGA 61.416 55.000 0.00 0.00 46.96 4.20
787 832 0.323629 TAAACTGAGACCGGCAAGGG 59.676 55.000 0.00 0.00 46.96 3.95
814 860 4.767409 GCATGGATTATAAAACTCCCCCTC 59.233 45.833 0.00 0.00 0.00 4.30
895 941 5.009210 AGCCTTAATCAGAAGCGTACTAGAG 59.991 44.000 0.00 0.00 0.00 2.43
966 1033 1.133458 GAGCAAGAAAGGAAGCGCG 59.867 57.895 0.00 0.00 0.00 6.86
995 1062 2.641197 GGCACGGGAGACATTGTTT 58.359 52.632 0.00 0.00 0.00 2.83
1072 1139 6.633856 AGAGAGAGAGAGAAAAGAAAGATGC 58.366 40.000 0.00 0.00 0.00 3.91
1098 1165 9.458374 GCGCACACACACACATATATATATATA 57.542 33.333 13.72 13.60 0.00 0.86
1099 1166 7.167468 CGCGCACACACACACATATATATATAT 59.833 37.037 8.75 9.12 0.00 0.86
1100 1167 6.470877 CGCGCACACACACACATATATATATA 59.529 38.462 8.75 4.92 0.00 0.86
1101 1168 5.288472 CGCGCACACACACACATATATATAT 59.712 40.000 8.75 0.00 0.00 0.86
1102 1169 4.619336 CGCGCACACACACACATATATATA 59.381 41.667 8.75 0.00 0.00 0.86
1103 1170 3.428534 CGCGCACACACACACATATATAT 59.571 43.478 8.75 0.00 0.00 0.86
1104 1171 2.792116 CGCGCACACACACACATATATA 59.208 45.455 8.75 0.00 0.00 0.86
1129 1196 3.702334 GATTGAACTGACCGCGCGC 62.702 63.158 27.36 23.91 0.00 6.86
1130 1197 2.395690 GATTGAACTGACCGCGCG 59.604 61.111 25.67 25.67 0.00 6.86
1131 1198 2.395690 CGATTGAACTGACCGCGC 59.604 61.111 0.00 0.00 0.00 6.86
1132 1199 1.413767 CTCCGATTGAACTGACCGCG 61.414 60.000 0.00 0.00 0.00 6.46
1306 1392 2.203938 AGGAGACCAAAGGCGGGA 60.204 61.111 0.00 0.00 0.00 5.14
1325 1411 3.634397 TCACCAAATGAGGATGAGGAC 57.366 47.619 0.00 0.00 31.91 3.85
1372 1458 3.057456 CGAGGCGCTAGATACTAATGGTT 60.057 47.826 7.64 0.00 0.00 3.67
1398 1491 3.821033 GGTAAAAGACTTGTGATGTGCCT 59.179 43.478 0.00 0.00 0.00 4.75
1422 1516 2.037511 CCAGGAATCATGAGAGAGAGGC 59.962 54.545 0.09 0.00 0.00 4.70
1432 1526 2.814805 AAGACCACCCAGGAATCATG 57.185 50.000 0.00 0.00 41.22 3.07
1481 1575 5.238650 GGTAAGTTTGTTACACTGTGCATCT 59.761 40.000 7.90 0.00 0.00 2.90
1515 1609 3.305398 TCGAAGAACTGAGGCTTCTTC 57.695 47.619 14.07 14.07 45.49 2.87
1516 1610 3.971245 ATCGAAGAACTGAGGCTTCTT 57.029 42.857 13.04 6.74 43.58 2.52
1529 1623 6.747739 CGAATCTTCTGTGAGTAAATCGAAGA 59.252 38.462 0.00 0.00 40.48 2.87
1532 1626 5.950883 ACGAATCTTCTGTGAGTAAATCGA 58.049 37.500 0.00 0.00 0.00 3.59
1557 1651 4.187694 CTGTGGCAGGATAGAAAGAAGAC 58.812 47.826 0.00 0.00 0.00 3.01
1694 1788 1.136147 GAAGGCGCTGTTGCATGAG 59.864 57.895 7.64 0.00 39.64 2.90
1724 1818 2.061220 CAGCTGGAACTCTGTGGGA 58.939 57.895 5.57 0.00 0.00 4.37
1802 1896 2.899339 GAGCTCGCATTGGCTCCC 60.899 66.667 0.00 0.00 46.32 4.30
1856 1950 0.962855 GGGGCTTGTTCTTGCTCTCC 60.963 60.000 0.00 0.00 0.00 3.71
2408 2502 0.531657 TGTTTATGGCCATGCTGCAC 59.468 50.000 29.04 16.25 0.00 4.57
2434 2528 2.019807 AAAAGTGGACGGAGGGAGTA 57.980 50.000 0.00 0.00 0.00 2.59
2435 2529 2.019807 TAAAAGTGGACGGAGGGAGT 57.980 50.000 0.00 0.00 0.00 3.85
2436 2530 4.161754 ACTTATAAAAGTGGACGGAGGGAG 59.838 45.833 0.00 0.00 44.40 4.30
2437 2531 4.098894 ACTTATAAAAGTGGACGGAGGGA 58.901 43.478 0.00 0.00 44.40 4.20
2438 2532 4.439968 GACTTATAAAAGTGGACGGAGGG 58.560 47.826 0.00 0.00 46.09 4.30
2439 2533 4.110482 CGACTTATAAAAGTGGACGGAGG 58.890 47.826 0.00 0.00 46.09 4.30
2440 2534 4.741342 ACGACTTATAAAAGTGGACGGAG 58.259 43.478 7.19 0.00 46.09 4.63
2441 2535 4.789012 ACGACTTATAAAAGTGGACGGA 57.211 40.909 7.19 0.00 46.09 4.69
2442 2536 5.406175 TGAAACGACTTATAAAAGTGGACGG 59.594 40.000 7.19 0.00 46.09 4.79
2443 2537 6.364165 TCTGAAACGACTTATAAAAGTGGACG 59.636 38.462 7.19 2.66 46.09 4.79
2444 2538 7.170320 TGTCTGAAACGACTTATAAAAGTGGAC 59.830 37.037 7.19 0.00 46.09 4.02
2445 2539 7.211573 TGTCTGAAACGACTTATAAAAGTGGA 58.788 34.615 7.19 0.00 46.09 4.02
2446 2540 7.416154 TGTCTGAAACGACTTATAAAAGTGG 57.584 36.000 0.00 0.00 46.09 4.00
2447 2541 8.695355 GTTGTCTGAAACGACTTATAAAAGTG 57.305 34.615 0.00 0.00 46.09 3.16
2458 2552 7.908601 AGTTCATTTTTAGTTGTCTGAAACGAC 59.091 33.333 0.00 0.00 41.93 4.34
2459 2553 7.981142 AGTTCATTTTTAGTTGTCTGAAACGA 58.019 30.769 0.00 0.00 35.13 3.85
2460 2554 9.155053 GTAGTTCATTTTTAGTTGTCTGAAACG 57.845 33.333 0.00 0.00 35.13 3.60
2464 2558 9.607988 TGAAGTAGTTCATTTTTAGTTGTCTGA 57.392 29.630 8.98 0.00 37.79 3.27
2479 2573 6.911250 TCAGACAAGGTATGAAGTAGTTCA 57.089 37.500 15.21 15.21 46.81 3.18
2480 2574 8.660373 CATTTCAGACAAGGTATGAAGTAGTTC 58.340 37.037 3.15 3.15 43.10 3.01
2481 2575 8.157476 ACATTTCAGACAAGGTATGAAGTAGTT 58.843 33.333 6.54 0.00 43.10 2.24
2482 2576 7.680730 ACATTTCAGACAAGGTATGAAGTAGT 58.319 34.615 6.54 4.88 43.10 2.73
2483 2577 8.553459 AACATTTCAGACAAGGTATGAAGTAG 57.447 34.615 6.54 4.38 43.10 2.57
2484 2578 8.918202 AAACATTTCAGACAAGGTATGAAGTA 57.082 30.769 6.54 0.00 43.10 2.24
2485 2579 7.823745 AAACATTTCAGACAAGGTATGAAGT 57.176 32.000 6.54 1.95 43.10 3.01
2486 2580 8.352201 TGAAAACATTTCAGACAAGGTATGAAG 58.648 33.333 6.54 0.44 43.10 3.02
2487 2581 8.231692 TGAAAACATTTCAGACAAGGTATGAA 57.768 30.769 2.59 2.59 41.12 2.57
2488 2582 7.815840 TGAAAACATTTCAGACAAGGTATGA 57.184 32.000 1.57 0.00 31.69 2.15
2489 2583 7.596248 CCTTGAAAACATTTCAGACAAGGTATG 59.404 37.037 0.00 0.00 44.15 2.39
2490 2584 7.661040 CCTTGAAAACATTTCAGACAAGGTAT 58.339 34.615 0.00 0.00 44.15 2.73
2491 2585 7.038154 CCTTGAAAACATTTCAGACAAGGTA 57.962 36.000 0.00 0.00 44.15 3.08
2492 2586 5.906073 CCTTGAAAACATTTCAGACAAGGT 58.094 37.500 0.00 0.00 44.15 3.50
2494 2588 4.746611 GGCCTTGAAAACATTTCAGACAAG 59.253 41.667 0.00 0.00 34.85 3.16
2495 2589 4.405358 AGGCCTTGAAAACATTTCAGACAA 59.595 37.500 0.00 0.00 0.00 3.18
2496 2590 3.960102 AGGCCTTGAAAACATTTCAGACA 59.040 39.130 0.00 0.00 0.00 3.41
2497 2591 4.590850 AGGCCTTGAAAACATTTCAGAC 57.409 40.909 0.00 0.00 0.00 3.51
2498 2592 6.723298 TTAAGGCCTTGAAAACATTTCAGA 57.277 33.333 28.77 0.00 0.00 3.27
2499 2593 7.784633 TTTTAAGGCCTTGAAAACATTTCAG 57.215 32.000 27.89 0.00 0.00 3.02
2521 2615 6.697641 TGGTACTCCCTCTATTCACTTTTT 57.302 37.500 0.00 0.00 0.00 1.94
2522 2616 6.697641 TTGGTACTCCCTCTATTCACTTTT 57.302 37.500 0.00 0.00 0.00 2.27
2523 2617 6.043938 TGTTTGGTACTCCCTCTATTCACTTT 59.956 38.462 0.00 0.00 0.00 2.66
2524 2618 5.546499 TGTTTGGTACTCCCTCTATTCACTT 59.454 40.000 0.00 0.00 0.00 3.16
2525 2619 5.091552 TGTTTGGTACTCCCTCTATTCACT 58.908 41.667 0.00 0.00 0.00 3.41
2526 2620 5.416271 TGTTTGGTACTCCCTCTATTCAC 57.584 43.478 0.00 0.00 0.00 3.18
2527 2621 5.964477 AGATGTTTGGTACTCCCTCTATTCA 59.036 40.000 0.00 0.00 0.00 2.57
2528 2622 6.487299 AGATGTTTGGTACTCCCTCTATTC 57.513 41.667 0.00 0.00 0.00 1.75
2529 2623 6.353082 CCAAGATGTTTGGTACTCCCTCTATT 60.353 42.308 0.00 0.00 34.92 1.73
2530 2624 5.131142 CCAAGATGTTTGGTACTCCCTCTAT 59.869 44.000 0.00 0.00 34.92 1.98
2531 2625 4.469945 CCAAGATGTTTGGTACTCCCTCTA 59.530 45.833 0.00 0.00 34.92 2.43
2532 2626 3.264450 CCAAGATGTTTGGTACTCCCTCT 59.736 47.826 0.00 0.00 34.92 3.69
2533 2627 3.610911 CCAAGATGTTTGGTACTCCCTC 58.389 50.000 0.00 0.00 34.92 4.30
2534 2628 3.721087 CCAAGATGTTTGGTACTCCCT 57.279 47.619 0.00 0.00 34.92 4.20
2542 2636 5.125900 TGCTTCATATCACCAAGATGTTTGG 59.874 40.000 4.45 4.45 44.91 3.28
2585 2679 5.882000 CCCATCTTTCATGTTCATGTACTCA 59.118 40.000 11.73 0.00 0.00 3.41
2728 2843 3.947834 AGATGGTAAAGCTGGTATGTTGC 59.052 43.478 0.00 0.00 0.00 4.17
2936 3059 5.818136 TGTCCTTGTTTTGTTCTCTCTTG 57.182 39.130 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.