Multiple sequence alignment - TraesCS5D01G162700

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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 TraesCS5D01G162700 chr5D 100.000 2603 0 0 1 2603 254430637 254428035 0.000000e+00 4807.0
1 TraesCS5D01G162700 chr5D 86.598 97 13 0 519 615 62133141 62133045 9.850000e-20 108.0
2 TraesCS5D01G162700 chr5D 95.238 42 2 0 478 519 62135277 62135236 1.670000e-07 67.6
3 TraesCS5D01G162700 chr5A 91.803 2562 147 24 1 2520 337634960 337632420 0.000000e+00 3509.0
4 TraesCS5D01G162700 chr5B 92.732 1995 109 17 541 2520 288440010 288441983 0.000000e+00 2848.0
5 TraesCS5D01G162700 chr5B 87.381 420 40 6 140 549 288439573 288439989 1.090000e-128 470.0
6 TraesCS5D01G162700 chr5B 89.583 144 12 2 1 144 288419898 288420038 2.060000e-41 180.0
7 TraesCS5D01G162700 chr5B 79.394 165 24 3 294 450 519154298 519154460 9.850000e-20 108.0
8 TraesCS5D01G162700 chr5B 92.308 52 4 0 468 519 559188672 559188723 9.990000e-10 75.0
9 TraesCS5D01G162700 chr4D 97.727 88 2 0 2516 2603 335282099 335282012 4.490000e-33 152.0
10 TraesCS5D01G162700 chr4D 98.810 84 1 0 2520 2603 133857114 133857197 1.610000e-32 150.0
11 TraesCS5D01G162700 chr3D 98.810 84 1 0 2520 2603 451075345 451075262 1.610000e-32 150.0
12 TraesCS5D01G162700 chr3D 89.815 108 4 5 2494 2600 519613253 519613354 5.850000e-27 132.0
13 TraesCS5D01G162700 chr3D 78.814 118 13 8 404 519 504046365 504046472 4.650000e-08 69.4
14 TraesCS5D01G162700 chr1D 98.810 84 1 0 2520 2603 487795517 487795434 1.610000e-32 150.0
15 TraesCS5D01G162700 chr1D 93.750 96 4 1 2510 2603 116736551 116736646 2.700000e-30 143.0
16 TraesCS5D01G162700 chr1D 91.765 85 7 0 519 603 12310046 12309962 4.550000e-23 119.0
17 TraesCS5D01G162700 chr3B 95.699 93 2 2 2513 2603 451858538 451858446 5.800000e-32 148.0
18 TraesCS5D01G162700 chr3B 100.000 30 0 0 403 432 808854501 808854472 3.620000e-04 56.5
19 TraesCS5D01G162700 chr3A 97.701 87 1 1 2518 2603 146741982 146741896 5.800000e-32 148.0
20 TraesCS5D01G162700 chr3A 83.871 62 8 2 373 433 697513342 697513282 1.010000e-04 58.4
21 TraesCS5D01G162700 chr7D 94.681 94 5 0 2510 2603 35196075 35196168 2.090000e-31 147.0
22 TraesCS5D01G162700 chr7D 90.588 85 8 0 519 603 2015448 2015532 2.120000e-21 113.0
23 TraesCS5D01G162700 chr7D 90.588 85 8 0 519 603 87751962 87752046 2.120000e-21 113.0
24 TraesCS5D01G162700 chr1B 94.186 86 5 0 519 604 605008679 605008764 5.850000e-27 132.0
25 TraesCS5D01G162700 chr1A 91.765 85 7 0 519 603 566063247 566063163 4.550000e-23 119.0
26 TraesCS5D01G162700 chr2A 88.421 95 8 2 512 603 385327425 385327519 7.610000e-21 111.0
27 TraesCS5D01G162700 chr2A 100.000 33 0 0 487 519 603372264 603372232 7.780000e-06 62.1
28 TraesCS5D01G162700 chr6A 88.889 81 8 1 370 450 14387328 14387407 5.930000e-17 99.0
29 TraesCS5D01G162700 chr4B 80.870 115 17 4 406 519 588692026 588691916 4.620000e-13 86.1


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 TraesCS5D01G162700 chr5D 254428035 254430637 2602 True 4807 4807 100.0000 1 2603 1 chr5D.!!$R1 2602
1 TraesCS5D01G162700 chr5A 337632420 337634960 2540 True 3509 3509 91.8030 1 2520 1 chr5A.!!$R1 2519
2 TraesCS5D01G162700 chr5B 288439573 288441983 2410 False 1659 2848 90.0565 140 2520 2 chr5B.!!$F4 2380

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
55 56 0.583917 CGCTCATCTCGTCTCATCGA 59.416 55.000 0.00 0.00 38.19 3.59 F
76 78 1.139095 GACGACCTAGCTTGGACCG 59.861 63.158 21.63 22.34 34.76 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1569 1645 0.391263 GGTTGGAAGGGTCACTAGCG 60.391 60.000 0.00 0.0 0.0 4.26 R
1926 2006 1.065109 GCGCGGACCAAACTTGTTT 59.935 52.632 8.83 0.0 0.0 2.83 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 4.598894 CCCATGCCGCTCCTCTCG 62.599 72.222 0.00 0.00 0.00 4.04
46 47 2.051435 CTCTCGCCGCTCATCTCG 60.051 66.667 0.00 0.00 0.00 4.04
55 56 0.583917 CGCTCATCTCGTCTCATCGA 59.416 55.000 0.00 0.00 38.19 3.59
76 78 1.139095 GACGACCTAGCTTGGACCG 59.861 63.158 21.63 22.34 34.76 4.79
126 128 8.217111 TGTTAACCATTGGATTGATGCTCTATA 58.783 33.333 10.37 0.00 0.00 1.31
159 161 8.683776 TGGAAAGGTAAATAACTAAGGGAGTA 57.316 34.615 0.00 0.00 37.44 2.59
174 176 3.901844 AGGGAGTAGCTACAAAACAGTCA 59.098 43.478 25.28 0.00 0.00 3.41
225 227 2.955660 TGGCTTTCAATCTCAACCGTTT 59.044 40.909 0.00 0.00 0.00 3.60
257 260 2.142356 ACATCCGGGCATCATTTTCA 57.858 45.000 0.00 0.00 0.00 2.69
282 285 1.567357 GGCTCTCTTCTTCCTCACCT 58.433 55.000 0.00 0.00 0.00 4.00
288 291 4.277476 TCTCTTCTTCCTCACCTGATCTC 58.723 47.826 0.00 0.00 0.00 2.75
289 292 3.370104 TCTTCTTCCTCACCTGATCTCC 58.630 50.000 0.00 0.00 0.00 3.71
368 375 4.400961 GCGCTCCTCCACAGCCTT 62.401 66.667 0.00 0.00 32.83 4.35
379 394 4.479993 CAGCCTTGCTCTCCCCGG 62.480 72.222 0.00 0.00 36.40 5.73
555 622 5.529581 TGTTTCTCCCTTCAACCAAAATC 57.470 39.130 0.00 0.00 0.00 2.17
604 671 5.284864 CGACTGACATGTAGCTATTGTGAT 58.715 41.667 14.82 3.08 0.00 3.06
693 760 1.815421 CATACGGGCAGTGCAGTCC 60.815 63.158 18.61 8.18 0.00 3.85
926 993 7.201821 GCAACCTGTTTCCATATATTTGTAGCT 60.202 37.037 0.00 0.00 0.00 3.32
928 995 9.561069 AACCTGTTTCCATATATTTGTAGCTAG 57.439 33.333 0.00 0.00 0.00 3.42
931 998 9.277783 CTGTTTCCATATATTTGTAGCTAGCTT 57.722 33.333 24.88 6.85 0.00 3.74
961 1028 7.424167 CGTGTGTATATAAATTGACAAACACCG 59.576 37.037 12.26 11.32 36.12 4.94
980 1047 3.893813 ACCGTAGTTTTGTAGAGACCAGT 59.106 43.478 0.00 0.00 0.00 4.00
1026 1093 3.121030 CGGAGCAACTCGGCCTTG 61.121 66.667 0.00 0.00 0.00 3.61
1090 1157 1.985116 GAGGAGTCAGGAGGCGGTT 60.985 63.158 0.00 0.00 0.00 4.44
1101 1168 4.115199 GGCGGTTGCAGGGGATCT 62.115 66.667 0.00 0.00 45.35 2.75
1368 1435 4.241555 CGGAGGATCAAGGGGCGG 62.242 72.222 0.00 0.00 36.25 6.13
1439 1506 1.202976 AGACCAAGGTTCAAGCAGCAT 60.203 47.619 0.00 0.00 0.00 3.79
1503 1570 2.606587 GCTGGCCAGGAAGGAGGAA 61.607 63.158 33.46 0.00 41.22 3.36
1569 1645 2.109126 CGGCCTAAACCTCTGCTGC 61.109 63.158 0.00 0.00 0.00 5.25
1611 1687 4.649267 TCCATCCACCTGAACAATGTAA 57.351 40.909 0.00 0.00 0.00 2.41
1650 1726 5.814705 GTCTATCCAAGGTCACAAGATTGAG 59.185 44.000 0.00 0.00 0.00 3.02
1703 1779 7.958025 GTCGTATCTTGAGTTCTTCATTTTTCC 59.042 37.037 0.00 0.00 35.27 3.13
1796 1876 3.686016 TGGAAGCTGTAGGAATTGGAAC 58.314 45.455 0.00 0.00 0.00 3.62
1872 1952 7.120579 TGTTGTATCTTTGCGGATTAAGAATGT 59.879 33.333 0.00 0.00 34.35 2.71
1880 1960 8.736751 TTTGCGGATTAAGAATGTTTACTTTC 57.263 30.769 0.00 1.45 0.00 2.62
1882 1962 7.748847 TGCGGATTAAGAATGTTTACTTTCTC 58.251 34.615 10.35 1.21 38.79 2.87
1950 2030 3.203412 TTTGGTCCGCGCGTTGTT 61.203 55.556 29.95 0.00 0.00 2.83
2071 2151 0.036671 CCGGCGAAACCCTAGTCTTT 60.037 55.000 9.30 0.00 33.26 2.52
2083 2163 5.246307 ACCCTAGTCTTTCAGTGTTTATGC 58.754 41.667 0.00 0.00 0.00 3.14
2099 2179 8.107591 GTGTTTATGCAAGCACTACAATAATG 57.892 34.615 0.00 0.00 41.27 1.90
2241 2324 1.836510 CGTGTGTGGCGTTGCATACA 61.837 55.000 0.00 0.00 0.00 2.29
2242 2325 0.521291 GTGTGTGGCGTTGCATACAT 59.479 50.000 0.00 0.00 32.00 2.29
2243 2326 1.735018 GTGTGTGGCGTTGCATACATA 59.265 47.619 0.00 0.00 32.00 2.29
2244 2327 2.006169 TGTGTGGCGTTGCATACATAG 58.994 47.619 0.00 0.00 32.00 2.23
2296 2379 2.785269 AGCCTCCCATCAATTATCCACA 59.215 45.455 0.00 0.00 0.00 4.17
2374 2457 4.154942 AGGGATTTGTGCAGACAGAAAAT 58.845 39.130 0.00 0.00 41.78 1.82
2520 2605 4.400961 GCTTGGTCGGAGCTGGCT 62.401 66.667 8.82 0.00 37.18 4.75
2521 2606 2.435586 CTTGGTCGGAGCTGGCTG 60.436 66.667 8.82 0.00 0.00 4.85
2522 2607 3.241530 TTGGTCGGAGCTGGCTGT 61.242 61.111 8.82 0.00 0.00 4.40
2523 2608 2.738213 CTTGGTCGGAGCTGGCTGTT 62.738 60.000 8.82 0.00 0.00 3.16
2524 2609 2.743928 GGTCGGAGCTGGCTGTTG 60.744 66.667 0.00 0.00 0.00 3.33
2525 2610 2.743928 GTCGGAGCTGGCTGTTGG 60.744 66.667 0.00 0.00 0.00 3.77
2526 2611 4.020617 TCGGAGCTGGCTGTTGGG 62.021 66.667 0.00 0.00 0.00 4.12
2528 2613 3.650950 GGAGCTGGCTGTTGGGGA 61.651 66.667 0.00 0.00 0.00 4.81
2529 2614 2.436109 GAGCTGGCTGTTGGGGAA 59.564 61.111 0.00 0.00 0.00 3.97
2530 2615 1.973812 GAGCTGGCTGTTGGGGAAC 60.974 63.158 0.00 0.00 0.00 3.62
2531 2616 3.365265 GCTGGCTGTTGGGGAACG 61.365 66.667 0.00 0.00 0.00 3.95
2532 2617 2.113139 CTGGCTGTTGGGGAACGT 59.887 61.111 0.00 0.00 0.00 3.99
2533 2618 1.373435 CTGGCTGTTGGGGAACGTA 59.627 57.895 0.00 0.00 0.00 3.57
2534 2619 0.673644 CTGGCTGTTGGGGAACGTAG 60.674 60.000 0.00 0.00 0.00 3.51
2536 2621 0.609662 GGCTGTTGGGGAACGTAGTA 59.390 55.000 0.00 0.00 45.00 1.82
2537 2622 1.002315 GGCTGTTGGGGAACGTAGTAA 59.998 52.381 0.00 0.00 45.00 2.24
2538 2623 2.355412 GGCTGTTGGGGAACGTAGTAAT 60.355 50.000 0.00 0.00 45.00 1.89
2539 2624 3.118665 GGCTGTTGGGGAACGTAGTAATA 60.119 47.826 0.00 0.00 45.00 0.98
2540 2625 4.506758 GCTGTTGGGGAACGTAGTAATAA 58.493 43.478 0.00 0.00 45.00 1.40
2541 2626 5.121105 GCTGTTGGGGAACGTAGTAATAAT 58.879 41.667 0.00 0.00 45.00 1.28
2542 2627 5.587443 GCTGTTGGGGAACGTAGTAATAATT 59.413 40.000 0.00 0.00 45.00 1.40
2543 2628 6.238293 GCTGTTGGGGAACGTAGTAATAATTC 60.238 42.308 0.00 0.00 45.00 2.17
2544 2629 6.709281 TGTTGGGGAACGTAGTAATAATTCA 58.291 36.000 0.00 0.00 45.00 2.57
2545 2630 7.166851 TGTTGGGGAACGTAGTAATAATTCAA 58.833 34.615 0.00 0.00 45.00 2.69
2546 2631 7.664731 TGTTGGGGAACGTAGTAATAATTCAAA 59.335 33.333 0.00 0.00 45.00 2.69
2547 2632 8.513774 GTTGGGGAACGTAGTAATAATTCAAAA 58.486 33.333 0.00 0.00 45.00 2.44
2548 2633 8.810990 TGGGGAACGTAGTAATAATTCAAAAT 57.189 30.769 0.00 0.00 45.00 1.82
2549 2634 9.245481 TGGGGAACGTAGTAATAATTCAAAATT 57.755 29.630 0.00 0.00 45.00 1.82
2563 2648 7.924103 AATTCAAAATTTTCCTACGTGTCAC 57.076 32.000 0.00 0.00 0.00 3.67
2564 2649 5.427036 TCAAAATTTTCCTACGTGTCACC 57.573 39.130 0.00 0.00 0.00 4.02
2565 2650 4.882427 TCAAAATTTTCCTACGTGTCACCA 59.118 37.500 0.00 0.00 0.00 4.17
2566 2651 5.357314 TCAAAATTTTCCTACGTGTCACCAA 59.643 36.000 0.00 0.00 0.00 3.67
2567 2652 5.432885 AAATTTTCCTACGTGTCACCAAG 57.567 39.130 0.00 0.00 0.00 3.61
2568 2653 3.823281 TTTTCCTACGTGTCACCAAGA 57.177 42.857 0.00 0.00 0.00 3.02
2569 2654 4.345859 TTTTCCTACGTGTCACCAAGAT 57.654 40.909 0.00 0.00 0.00 2.40
2570 2655 3.587797 TTCCTACGTGTCACCAAGATC 57.412 47.619 0.00 0.00 0.00 2.75
2571 2656 2.521126 TCCTACGTGTCACCAAGATCA 58.479 47.619 0.00 0.00 0.00 2.92
2572 2657 2.894765 TCCTACGTGTCACCAAGATCAA 59.105 45.455 0.00 0.00 0.00 2.57
2573 2658 3.513912 TCCTACGTGTCACCAAGATCAAT 59.486 43.478 0.00 0.00 0.00 2.57
2574 2659 3.865745 CCTACGTGTCACCAAGATCAATC 59.134 47.826 0.00 0.00 0.00 2.67
2575 2660 3.685139 ACGTGTCACCAAGATCAATCT 57.315 42.857 0.00 0.00 39.22 2.40
2576 2661 4.801330 ACGTGTCACCAAGATCAATCTA 57.199 40.909 0.00 0.00 35.76 1.98
2577 2662 4.748892 ACGTGTCACCAAGATCAATCTAG 58.251 43.478 0.00 0.00 35.76 2.43
2578 2663 4.115516 CGTGTCACCAAGATCAATCTAGG 58.884 47.826 0.00 0.00 35.76 3.02
2579 2664 4.142160 CGTGTCACCAAGATCAATCTAGGA 60.142 45.833 0.00 0.00 35.76 2.94
2580 2665 5.355596 GTGTCACCAAGATCAATCTAGGAG 58.644 45.833 0.00 0.00 35.76 3.69
2581 2666 5.127845 GTGTCACCAAGATCAATCTAGGAGA 59.872 44.000 0.00 0.00 35.76 3.71
2582 2667 5.901853 TGTCACCAAGATCAATCTAGGAGAT 59.098 40.000 0.00 0.00 36.28 2.75
2583 2668 7.014711 GTGTCACCAAGATCAATCTAGGAGATA 59.985 40.741 0.00 0.00 32.89 1.98
2584 2669 7.014711 TGTCACCAAGATCAATCTAGGAGATAC 59.985 40.741 0.00 0.00 32.89 2.24
2585 2670 7.232534 GTCACCAAGATCAATCTAGGAGATACT 59.767 40.741 0.00 0.00 32.89 2.12
2586 2671 8.448816 TCACCAAGATCAATCTAGGAGATACTA 58.551 37.037 0.00 0.00 32.89 1.82
2587 2672 8.739039 CACCAAGATCAATCTAGGAGATACTAG 58.261 40.741 0.00 0.00 41.41 2.57
2588 2673 7.396055 ACCAAGATCAATCTAGGAGATACTAGC 59.604 40.741 0.00 0.00 40.18 3.42
2589 2674 7.395772 CCAAGATCAATCTAGGAGATACTAGCA 59.604 40.741 0.00 0.00 40.18 3.49
2590 2675 8.801299 CAAGATCAATCTAGGAGATACTAGCAA 58.199 37.037 0.00 0.00 40.18 3.91
2591 2676 9.545928 AAGATCAATCTAGGAGATACTAGCAAT 57.454 33.333 0.00 0.00 40.18 3.56
2592 2677 8.970020 AGATCAATCTAGGAGATACTAGCAATG 58.030 37.037 0.00 0.00 40.18 2.82
2593 2678 8.891985 ATCAATCTAGGAGATACTAGCAATGA 57.108 34.615 0.00 0.33 40.18 2.57
2594 2679 8.347004 TCAATCTAGGAGATACTAGCAATGAG 57.653 38.462 0.00 0.00 40.18 2.90
2595 2680 8.166726 TCAATCTAGGAGATACTAGCAATGAGA 58.833 37.037 0.00 0.00 40.18 3.27
2596 2681 8.801299 CAATCTAGGAGATACTAGCAATGAGAA 58.199 37.037 0.00 0.00 40.18 2.87
2597 2682 8.948401 ATCTAGGAGATACTAGCAATGAGAAA 57.052 34.615 0.00 0.00 40.18 2.52
2598 2683 8.402798 TCTAGGAGATACTAGCAATGAGAAAG 57.597 38.462 0.00 0.00 40.18 2.62
2599 2684 8.221251 TCTAGGAGATACTAGCAATGAGAAAGA 58.779 37.037 0.00 0.00 40.18 2.52
2600 2685 7.288810 AGGAGATACTAGCAATGAGAAAGAG 57.711 40.000 0.00 0.00 0.00 2.85
2601 2686 6.267471 AGGAGATACTAGCAATGAGAAAGAGG 59.733 42.308 0.00 0.00 0.00 3.69
2602 2687 6.418057 AGATACTAGCAATGAGAAAGAGGG 57.582 41.667 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.257409 GAGGAGCGGCATGGGAGAAA 62.257 60.000 1.45 0.00 0.00 2.52
34 35 0.662970 GATGAGACGAGATGAGCGGC 60.663 60.000 0.00 0.00 36.94 6.53
55 56 1.303888 TCCAAGCTAGGTCGTCGGT 60.304 57.895 0.00 0.00 0.00 4.69
62 64 1.066143 CACATTCGGTCCAAGCTAGGT 60.066 52.381 0.00 0.00 0.00 3.08
76 78 7.012421 ACAGGAGAAACTAGAAACAACACATTC 59.988 37.037 0.00 0.00 0.00 2.67
174 176 8.842358 TCGACTGATAACTTTAAATTTCAGGT 57.158 30.769 15.41 0.00 35.93 4.00
205 207 3.004315 TCAAACGGTTGAGATTGAAAGCC 59.996 43.478 12.93 0.00 38.88 4.35
225 227 2.158769 CCCGGATGTTGGATCTTGATCA 60.159 50.000 0.73 0.00 0.00 2.92
257 260 0.899019 GGAAGAAGAGAGCCGAGGTT 59.101 55.000 0.00 0.00 0.00 3.50
358 365 2.596851 GGGAGAGCAAGGCTGTGGA 61.597 63.158 0.00 0.00 39.88 4.02
368 375 2.683933 GAGGTTCCGGGGAGAGCA 60.684 66.667 0.00 0.00 0.00 4.26
379 394 2.671682 GGCAGTGGGAGGAGGTTC 59.328 66.667 0.00 0.00 0.00 3.62
555 622 2.806244 ACTTTCGAATTTGGGTCAGTCG 59.194 45.455 0.00 0.00 0.00 4.18
716 783 3.064408 AGCTGTAATTCATGTCATGCGTG 59.936 43.478 8.03 0.00 35.47 5.34
926 993 8.361889 TCAATTTATATACACACGGCTAAGCTA 58.638 33.333 0.00 0.00 0.00 3.32
928 995 7.042321 TGTCAATTTATATACACACGGCTAAGC 60.042 37.037 0.00 0.00 0.00 3.09
931 998 8.605746 GTTTGTCAATTTATATACACACGGCTA 58.394 33.333 0.00 0.00 0.00 3.93
932 999 7.119992 TGTTTGTCAATTTATATACACACGGCT 59.880 33.333 0.00 0.00 0.00 5.52
933 1000 7.217447 GTGTTTGTCAATTTATATACACACGGC 59.783 37.037 8.78 0.00 35.82 5.68
934 1001 7.694784 GGTGTTTGTCAATTTATATACACACGG 59.305 37.037 13.60 0.00 37.08 4.94
935 1002 7.424167 CGGTGTTTGTCAATTTATATACACACG 59.576 37.037 13.60 11.14 37.08 4.49
936 1003 8.231837 ACGGTGTTTGTCAATTTATATACACAC 58.768 33.333 13.60 8.91 37.08 3.82
961 1028 6.100668 GGATGACTGGTCTCTACAAAACTAC 58.899 44.000 2.38 0.00 0.00 2.73
980 1047 1.680522 GCCCTCGCTCTTCTGGATGA 61.681 60.000 0.00 0.00 0.00 2.92
1231 1298 4.191544 CAGGAGATCGGAAAGCAAATACA 58.808 43.478 0.00 0.00 0.00 2.29
1439 1506 2.740826 GCACCGCACTTCCGCTAA 60.741 61.111 0.00 0.00 0.00 3.09
1503 1570 1.153289 GCGAGTGATGCCATCCACT 60.153 57.895 1.49 5.92 45.37 4.00
1547 1623 1.614241 GCAGAGGTTTAGGCCGAGGA 61.614 60.000 0.00 0.00 0.00 3.71
1569 1645 0.391263 GGTTGGAAGGGTCACTAGCG 60.391 60.000 0.00 0.00 0.00 4.26
1611 1687 1.732941 TAGACGGCGTTTGATTGCAT 58.267 45.000 16.19 0.00 0.00 3.96
1684 1760 7.927629 TGGAAATGGAAAAATGAAGAACTCAAG 59.072 33.333 0.00 0.00 37.67 3.02
1765 1845 3.513515 CCTACAGCTTCCATAGGATCTCC 59.486 52.174 4.70 0.00 38.20 3.71
1796 1876 1.318158 GCCCATGAGTTGGCCAGAAG 61.318 60.000 5.11 0.00 44.97 2.85
1926 2006 1.065109 GCGCGGACCAAACTTGTTT 59.935 52.632 8.83 0.00 0.00 2.83
1950 2030 1.341089 ACTCCACTCTACTCCATCGCA 60.341 52.381 0.00 0.00 0.00 5.10
2071 2151 4.384940 TGTAGTGCTTGCATAAACACTGA 58.615 39.130 16.95 5.53 43.00 3.41
2083 2163 6.500684 AAGACCACATTATTGTAGTGCTTG 57.499 37.500 0.00 0.00 33.76 4.01
2090 2170 5.872617 CCTCACGAAAGACCACATTATTGTA 59.127 40.000 0.00 0.00 33.76 2.41
2098 2178 1.116308 TCACCTCACGAAAGACCACA 58.884 50.000 0.00 0.00 0.00 4.17
2099 2179 2.457366 ATCACCTCACGAAAGACCAC 57.543 50.000 0.00 0.00 0.00 4.16
2210 2293 3.422303 CACACGACACCATGCCCG 61.422 66.667 0.00 0.00 0.00 6.13
2241 2324 1.134491 GGCAAGGTACCAAGCGACTAT 60.134 52.381 15.94 0.00 0.00 2.12
2242 2325 0.248289 GGCAAGGTACCAAGCGACTA 59.752 55.000 15.94 0.00 0.00 2.59
2243 2326 1.003718 GGCAAGGTACCAAGCGACT 60.004 57.895 15.94 0.00 0.00 4.18
2244 2327 2.038837 GGGCAAGGTACCAAGCGAC 61.039 63.158 15.94 9.95 0.00 5.19
2374 2457 0.475044 AGCGGTTGGGTGGTTTTCTA 59.525 50.000 0.00 0.00 0.00 2.10
2446 2531 2.761465 GGATGGAGGAGCTTGGGGG 61.761 68.421 0.00 0.00 0.00 5.40
2516 2601 1.373435 CTACGTTCCCCAACAGCCA 59.627 57.895 0.00 0.00 32.14 4.75
2520 2605 6.709281 TGAATTATTACTACGTTCCCCAACA 58.291 36.000 0.00 0.00 32.14 3.33
2521 2606 7.614124 TTGAATTATTACTACGTTCCCCAAC 57.386 36.000 0.00 0.00 0.00 3.77
2522 2607 8.632906 TTTTGAATTATTACTACGTTCCCCAA 57.367 30.769 0.00 0.00 0.00 4.12
2523 2608 8.810990 ATTTTGAATTATTACTACGTTCCCCA 57.189 30.769 0.00 0.00 0.00 4.96
2537 2622 9.620660 GTGACACGTAGGAAAATTTTGAATTAT 57.379 29.630 8.47 0.00 0.00 1.28
2538 2623 8.077386 GGTGACACGTAGGAAAATTTTGAATTA 58.923 33.333 8.47 0.00 0.00 1.40
2539 2624 6.921307 GGTGACACGTAGGAAAATTTTGAATT 59.079 34.615 8.47 0.00 0.00 2.17
2540 2625 6.039941 TGGTGACACGTAGGAAAATTTTGAAT 59.960 34.615 8.47 0.00 33.40 2.57
2541 2626 5.357314 TGGTGACACGTAGGAAAATTTTGAA 59.643 36.000 8.47 0.00 33.40 2.69
2542 2627 4.882427 TGGTGACACGTAGGAAAATTTTGA 59.118 37.500 8.47 0.00 33.40 2.69
2543 2628 5.176407 TGGTGACACGTAGGAAAATTTTG 57.824 39.130 8.47 0.00 33.40 2.44
2544 2629 5.591067 TCTTGGTGACACGTAGGAAAATTTT 59.409 36.000 2.28 2.28 42.67 1.82
2545 2630 5.127491 TCTTGGTGACACGTAGGAAAATTT 58.873 37.500 0.00 0.00 42.67 1.82
2546 2631 4.710324 TCTTGGTGACACGTAGGAAAATT 58.290 39.130 0.00 0.00 42.67 1.82
2547 2632 4.345859 TCTTGGTGACACGTAGGAAAAT 57.654 40.909 0.00 0.00 42.67 1.82
2548 2633 3.823281 TCTTGGTGACACGTAGGAAAA 57.177 42.857 0.00 0.00 42.67 2.29
2549 2634 3.322541 TGATCTTGGTGACACGTAGGAAA 59.677 43.478 0.00 0.00 42.67 3.13
2550 2635 2.894765 TGATCTTGGTGACACGTAGGAA 59.105 45.455 0.00 0.00 42.67 3.36
2551 2636 2.521126 TGATCTTGGTGACACGTAGGA 58.479 47.619 0.00 0.00 42.67 2.94
2552 2637 3.313012 TTGATCTTGGTGACACGTAGG 57.687 47.619 0.00 0.00 42.67 3.18
2553 2638 4.748892 AGATTGATCTTGGTGACACGTAG 58.251 43.478 0.00 0.00 42.67 3.51
2554 2639 4.801330 AGATTGATCTTGGTGACACGTA 57.199 40.909 0.00 0.00 42.67 3.57
2555 2640 3.685139 AGATTGATCTTGGTGACACGT 57.315 42.857 0.00 0.00 42.67 4.49
2556 2641 4.115516 CCTAGATTGATCTTGGTGACACG 58.884 47.826 11.74 0.00 42.44 4.49
2557 2642 5.127845 TCTCCTAGATTGATCTTGGTGACAC 59.872 44.000 17.17 0.00 45.88 3.67
2558 2643 5.272402 TCTCCTAGATTGATCTTGGTGACA 58.728 41.667 17.17 2.34 45.88 3.58
2559 2644 5.860941 TCTCCTAGATTGATCTTGGTGAC 57.139 43.478 17.17 0.00 45.88 3.67
2561 2646 7.537596 AGTATCTCCTAGATTGATCTTGGTG 57.462 40.000 17.17 15.36 45.88 4.17
2562 2647 7.396055 GCTAGTATCTCCTAGATTGATCTTGGT 59.604 40.741 17.17 5.32 45.88 3.67
2563 2648 7.395772 TGCTAGTATCTCCTAGATTGATCTTGG 59.604 40.741 13.24 13.24 46.71 3.61
2564 2649 8.347004 TGCTAGTATCTCCTAGATTGATCTTG 57.653 38.462 0.00 0.00 37.24 3.02
2565 2650 8.948401 TTGCTAGTATCTCCTAGATTGATCTT 57.052 34.615 0.00 0.00 37.24 2.40
2566 2651 8.970020 CATTGCTAGTATCTCCTAGATTGATCT 58.030 37.037 0.00 0.00 37.24 2.75
2567 2652 8.965819 TCATTGCTAGTATCTCCTAGATTGATC 58.034 37.037 0.00 0.00 37.24 2.92
2568 2653 8.891985 TCATTGCTAGTATCTCCTAGATTGAT 57.108 34.615 0.00 0.00 37.24 2.57
2569 2654 8.166726 TCTCATTGCTAGTATCTCCTAGATTGA 58.833 37.037 0.00 0.00 37.24 2.57
2570 2655 8.347004 TCTCATTGCTAGTATCTCCTAGATTG 57.653 38.462 0.00 0.00 37.24 2.67
2571 2656 8.948401 TTCTCATTGCTAGTATCTCCTAGATT 57.052 34.615 0.00 0.00 37.24 2.40
2572 2657 8.948401 TTTCTCATTGCTAGTATCTCCTAGAT 57.052 34.615 0.00 0.00 37.24 1.98
2573 2658 8.221251 TCTTTCTCATTGCTAGTATCTCCTAGA 58.779 37.037 0.00 0.00 37.24 2.43
2574 2659 8.402798 TCTTTCTCATTGCTAGTATCTCCTAG 57.597 38.462 0.00 0.00 37.96 3.02
2575 2660 7.450014 CCTCTTTCTCATTGCTAGTATCTCCTA 59.550 40.741 0.00 0.00 0.00 2.94
2576 2661 6.267471 CCTCTTTCTCATTGCTAGTATCTCCT 59.733 42.308 0.00 0.00 0.00 3.69
2577 2662 6.454795 CCTCTTTCTCATTGCTAGTATCTCC 58.545 44.000 0.00 0.00 0.00 3.71
2578 2663 6.454795 CCCTCTTTCTCATTGCTAGTATCTC 58.545 44.000 0.00 0.00 0.00 2.75
2579 2664 6.418057 CCCTCTTTCTCATTGCTAGTATCT 57.582 41.667 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.