Multiple sequence alignment - TraesCS6D01G166800

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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 TraesCS6D01G166800 chr6D 100.000 3605 0 0 1 3605 148796176 148799780 0.000000e+00 6658.0
1 TraesCS6D01G166800 chr6B 92.412 2741 122 30 928 3605 261584095 261586812 0.000000e+00 3831.0
2 TraesCS6D01G166800 chr6A 94.075 1924 62 16 627 2535 198180633 198178747 0.000000e+00 2874.0
3 TraesCS6D01G166800 chr6A 87.500 648 72 7 2921 3567 198168725 198168086 0.000000e+00 739.0
4 TraesCS6D01G166800 chr4B 83.754 634 90 10 8 628 62038926 62038293 4.010000e-164 588.0
5 TraesCS6D01G166800 chr4B 83.646 587 81 9 8 580 535327001 535326416 4.100000e-149 538.0
6 TraesCS6D01G166800 chr1D 83.516 637 89 12 8 628 225407935 225408571 6.710000e-162 580.0
7 TraesCS6D01G166800 chr1D 85.326 552 78 3 80 628 70581025 70581576 5.220000e-158 568.0
8 TraesCS6D01G166800 chr7D 83.307 635 92 10 8 628 249618329 249618963 1.120000e-159 573.0
9 TraesCS6D01G166800 chr7D 83.176 636 91 12 8 628 43372183 43372817 5.220000e-158 568.0
10 TraesCS6D01G166800 chr5D 85.900 539 70 6 80 614 367659676 367660212 1.450000e-158 569.0
11 TraesCS6D01G166800 chr4D 84.497 587 76 9 8 580 435187644 435187059 1.880000e-157 566.0
12 TraesCS6D01G166800 chr2A 85.053 562 75 9 75 628 16179180 16179740 6.760000e-157 564.0
13 TraesCS6D01G166800 chr7A 82.621 351 50 8 8 348 101806235 101805886 2.100000e-77 300.0
14 TraesCS6D01G166800 chr7A 85.121 289 33 8 36 314 108836428 108836716 1.640000e-73 287.0
15 TraesCS6D01G166800 chr4A 75.616 365 75 8 14 365 606196929 606196566 6.190000e-38 169.0
16 TraesCS6D01G166800 chr4A 75.872 344 69 8 35 365 605892416 605892074 2.880000e-36 163.0
17 TraesCS6D01G166800 chr3B 89.474 76 8 0 9 84 630368659 630368734 2.960000e-16 97.1


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 TraesCS6D01G166800 chr6D 148796176 148799780 3604 False 6658 6658 100.000 1 3605 1 chr6D.!!$F1 3604
1 TraesCS6D01G166800 chr6B 261584095 261586812 2717 False 3831 3831 92.412 928 3605 1 chr6B.!!$F1 2677
2 TraesCS6D01G166800 chr6A 198178747 198180633 1886 True 2874 2874 94.075 627 2535 1 chr6A.!!$R2 1908
3 TraesCS6D01G166800 chr6A 198168086 198168725 639 True 739 739 87.500 2921 3567 1 chr6A.!!$R1 646
4 TraesCS6D01G166800 chr4B 62038293 62038926 633 True 588 588 83.754 8 628 1 chr4B.!!$R1 620
5 TraesCS6D01G166800 chr4B 535326416 535327001 585 True 538 538 83.646 8 580 1 chr4B.!!$R2 572
6 TraesCS6D01G166800 chr1D 225407935 225408571 636 False 580 580 83.516 8 628 1 chr1D.!!$F2 620
7 TraesCS6D01G166800 chr1D 70581025 70581576 551 False 568 568 85.326 80 628 1 chr1D.!!$F1 548
8 TraesCS6D01G166800 chr7D 249618329 249618963 634 False 573 573 83.307 8 628 1 chr7D.!!$F2 620
9 TraesCS6D01G166800 chr7D 43372183 43372817 634 False 568 568 83.176 8 628 1 chr7D.!!$F1 620
10 TraesCS6D01G166800 chr5D 367659676 367660212 536 False 569 569 85.900 80 614 1 chr5D.!!$F1 534
11 TraesCS6D01G166800 chr4D 435187059 435187644 585 True 566 566 84.497 8 580 1 chr4D.!!$R1 572
12 TraesCS6D01G166800 chr2A 16179180 16179740 560 False 564 564 85.053 75 628 1 chr2A.!!$F1 553

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
970 994 0.335019 TAGAGCTAGGCCACACTGGA 59.665 55.0 5.01 0.00 40.96 3.86 F
2426 2506 1.260544 TTAGACAGCTGCTCTGCTCA 58.739 50.0 21.70 5.98 46.76 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2485 2571 0.68028 TGGCACCTCTCCGAGACTAC 60.680 60.0 0.00 0.0 0.0 2.73 R
3307 3406 0.52847 CGAACGAGCTCTTCCCTCTT 59.472 55.0 12.85 0.0 0.0 2.85 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
31 32 8.978874 ACCTTTGCATCAATAGATACATACAA 57.021 30.769 0.00 0.00 31.88 2.41
33 34 9.060347 CCTTTGCATCAATAGATACATACAACT 57.940 33.333 0.00 0.00 31.88 3.16
78 79 9.698309 ATAAAGATCTGACAAGAATATACACCG 57.302 33.333 0.00 0.00 35.59 4.94
87 98 4.527509 AGAATATACACCGAGCCATCAG 57.472 45.455 0.00 0.00 0.00 2.90
89 100 4.345257 AGAATATACACCGAGCCATCAGTT 59.655 41.667 0.00 0.00 0.00 3.16
113 125 8.995220 GTTACACCTACAAACTTGATAATGTGA 58.005 33.333 0.00 0.00 0.00 3.58
122 134 7.013655 ACAAACTTGATAATGTGAAGTGCTCTT 59.986 33.333 0.00 0.00 36.51 2.85
170 182 2.035449 TCGTCGATCCATCCACATAACC 59.965 50.000 0.00 0.00 0.00 2.85
234 246 6.378848 ACACCACATGTACACCTTTTAAAAGT 59.621 34.615 23.04 10.92 40.88 2.66
240 252 3.703286 ACACCTTTTAAAAGTCGCCAC 57.297 42.857 23.04 0.00 34.20 5.01
247 259 5.461032 TTTTAAAAGTCGCCACCATCATT 57.539 34.783 0.00 0.00 0.00 2.57
251 263 2.425143 AGTCGCCACCATCATTGAAT 57.575 45.000 0.00 0.00 0.00 2.57
314 327 4.129737 CCAGCCATCCGTCGACGT 62.130 66.667 33.49 16.10 37.74 4.34
315 328 2.126071 CAGCCATCCGTCGACGTT 60.126 61.111 33.49 19.57 37.74 3.99
316 329 2.126071 AGCCATCCGTCGACGTTG 60.126 61.111 33.49 27.93 37.74 4.10
378 391 0.959553 AGACGCGAAGACTCTGGAAA 59.040 50.000 15.93 0.00 0.00 3.13
384 397 2.095053 GCGAAGACTCTGGAAAATCTGC 59.905 50.000 0.00 0.00 0.00 4.26
386 399 3.679389 GAAGACTCTGGAAAATCTGCCA 58.321 45.455 0.00 0.00 0.00 4.92
462 476 2.737252 GACTTGACATCTCCACCGAAAC 59.263 50.000 0.00 0.00 0.00 2.78
463 477 2.368875 ACTTGACATCTCCACCGAAACT 59.631 45.455 0.00 0.00 0.00 2.66
487 502 1.065926 TGCAAGATGAAGTCGCTCCAT 60.066 47.619 0.00 0.00 0.00 3.41
492 507 2.102252 AGATGAAGTCGCTCCATCTTCC 59.898 50.000 3.43 0.00 42.97 3.46
500 515 1.227497 CTCCATCTTCCGCCTCTGC 60.227 63.158 0.00 0.00 0.00 4.26
569 586 1.893808 GTGCCGCCATCATCCGATT 60.894 57.895 0.00 0.00 0.00 3.34
573 590 1.283793 CGCCATCATCCGATTTGGC 59.716 57.895 17.13 17.13 37.36 4.52
593 610 1.985895 CAGACCAGGTCCTAGGGTTTT 59.014 52.381 16.72 0.00 34.39 2.43
600 618 2.712627 AGGTCCTAGGGTTTTTCCGAAA 59.287 45.455 9.46 0.00 37.00 3.46
632 650 6.465084 AGTGGGTTGACAATAGTTACTTCTC 58.535 40.000 0.00 0.00 0.00 2.87
656 674 6.378848 TCTTTTATTTGGCATAGGTAACCACC 59.621 38.462 0.00 0.00 46.19 4.61
670 688 2.507407 ACCACCCTTGTCGCATTATT 57.493 45.000 0.00 0.00 0.00 1.40
707 725 7.324935 TGCATTGATGATTAGTTCTTGCATTT 58.675 30.769 0.00 0.00 33.09 2.32
708 726 7.490079 TGCATTGATGATTAGTTCTTGCATTTC 59.510 33.333 0.00 0.00 33.09 2.17
733 751 9.896263 TCGAAGGTATATTTGTAAAACCAAAAC 57.104 29.630 0.00 0.00 37.81 2.43
734 752 9.902196 CGAAGGTATATTTGTAAAACCAAAACT 57.098 29.630 0.00 0.00 37.81 2.66
769 788 3.863142 TTCTACACTAGCGGAAGAACC 57.137 47.619 0.00 0.00 0.00 3.62
838 861 1.066858 CACTGTACCATGAAGACCGCT 60.067 52.381 0.00 0.00 0.00 5.52
839 862 1.623811 ACTGTACCATGAAGACCGCTT 59.376 47.619 0.00 0.00 36.96 4.68
933 956 2.164219 GCAACCCATTCCTATGTGTGTG 59.836 50.000 0.00 0.00 0.00 3.82
970 994 0.335019 TAGAGCTAGGCCACACTGGA 59.665 55.000 5.01 0.00 40.96 3.86
1165 1207 3.722780 CACTTATCGTTTCTACCGCTACG 59.277 47.826 0.00 0.00 35.46 3.51
1204 1254 2.177734 TCTTGAGCTGAGCTGATGAGT 58.822 47.619 13.71 0.00 39.88 3.41
1378 1428 2.273449 CAGGGGGACATGGTGCTC 59.727 66.667 0.00 0.00 38.79 4.26
1810 1890 4.034858 GTGTAACATCGGTCGTCTGATCTA 59.965 45.833 0.66 0.00 37.56 1.98
2092 2172 3.535629 CTGTCCTTCAGCGTGGGCA 62.536 63.158 0.00 0.00 43.41 5.36
2417 2497 4.260375 GCATCCGTGTTAATTAGACAGCTG 60.260 45.833 13.48 13.48 0.00 4.24
2418 2498 3.259064 TCCGTGTTAATTAGACAGCTGC 58.741 45.455 15.27 6.85 0.00 5.25
2419 2499 3.056107 TCCGTGTTAATTAGACAGCTGCT 60.056 43.478 15.27 14.40 0.00 4.24
2420 2500 3.307242 CCGTGTTAATTAGACAGCTGCTC 59.693 47.826 15.27 10.79 0.00 4.26
2421 2501 4.177026 CGTGTTAATTAGACAGCTGCTCT 58.823 43.478 15.27 17.39 0.00 4.09
2426 2506 1.260544 TTAGACAGCTGCTCTGCTCA 58.739 50.000 21.70 5.98 46.76 4.26
2427 2507 1.482954 TAGACAGCTGCTCTGCTCAT 58.517 50.000 21.70 0.00 46.76 2.90
2449 2529 2.032030 TGCTTAAGCGCTCAACTCAAAC 60.032 45.455 21.97 0.00 45.83 2.93
2473 2559 3.848726 CTTATTGGGTTGAATGTGCACC 58.151 45.455 15.69 0.00 0.00 5.01
2485 2571 0.950836 TGTGCACCAAGGAATTCGTG 59.049 50.000 15.69 4.27 0.00 4.35
2486 2572 0.951558 GTGCACCAAGGAATTCGTGT 59.048 50.000 5.22 0.00 0.00 4.49
2487 2573 2.147958 GTGCACCAAGGAATTCGTGTA 58.852 47.619 5.22 0.00 0.00 2.90
2488 2574 2.159627 GTGCACCAAGGAATTCGTGTAG 59.840 50.000 5.22 0.00 0.00 2.74
2489 2575 2.224426 TGCACCAAGGAATTCGTGTAGT 60.224 45.455 0.58 0.00 0.00 2.73
2490 2576 2.415512 GCACCAAGGAATTCGTGTAGTC 59.584 50.000 0.58 0.00 0.00 2.59
2491 2577 3.864921 GCACCAAGGAATTCGTGTAGTCT 60.865 47.826 0.58 0.00 0.00 3.24
2560 2652 4.048970 ACTGTACCTCTGCCTTCTCTTA 57.951 45.455 0.00 0.00 0.00 2.10
2564 2656 5.577100 TGTACCTCTGCCTTCTCTTAACTA 58.423 41.667 0.00 0.00 0.00 2.24
2594 2687 9.197694 GATGATATTCTCTTAGCAACGTATGTT 57.802 33.333 0.00 0.00 39.43 2.71
2597 2690 5.756950 TTCTCTTAGCAACGTATGTTTCG 57.243 39.130 0.00 0.00 35.72 3.46
2598 2691 4.801891 TCTCTTAGCAACGTATGTTTCGT 58.198 39.130 0.00 0.00 43.45 3.85
2734 2833 3.533913 GCGCAAAATGCCTACTAGC 57.466 52.632 0.30 0.00 41.12 3.42
2736 2835 1.286501 CGCAAAATGCCTACTAGCGA 58.713 50.000 0.00 0.00 45.78 4.93
2756 2855 4.785453 GGCAAGGCACCCTCTCCG 62.785 72.222 0.00 0.00 30.89 4.63
2828 2927 7.202972 TGCCCACCACTAGTAACTAAAATAT 57.797 36.000 0.00 0.00 0.00 1.28
2831 2930 9.049523 GCCCACCACTAGTAACTAAAATATAAC 57.950 37.037 0.00 0.00 0.00 1.89
2847 2946 7.696992 AAATATAACAGTGACGAACCCAAAT 57.303 32.000 0.00 0.00 0.00 2.32
2872 2971 8.138365 TCATTTCACGCCACTAGTATATTTTC 57.862 34.615 0.00 0.00 0.00 2.29
2873 2972 7.985184 TCATTTCACGCCACTAGTATATTTTCT 59.015 33.333 0.00 0.00 0.00 2.52
2875 2974 9.826574 ATTTCACGCCACTAGTATATTTTCTTA 57.173 29.630 0.00 0.00 0.00 2.10
2876 2975 9.826574 TTTCACGCCACTAGTATATTTTCTTAT 57.173 29.630 0.00 0.00 0.00 1.73
2877 2976 8.812147 TCACGCCACTAGTATATTTTCTTATG 57.188 34.615 0.00 0.00 0.00 1.90
2879 2978 7.170828 CACGCCACTAGTATATTTTCTTATGCA 59.829 37.037 0.00 0.00 0.00 3.96
2880 2979 7.170998 ACGCCACTAGTATATTTTCTTATGCAC 59.829 37.037 0.00 0.00 0.00 4.57
2881 2980 7.385205 CGCCACTAGTATATTTTCTTATGCACT 59.615 37.037 0.00 0.00 0.00 4.40
2918 3017 2.260434 GTTGCTCACTACCGGCGA 59.740 61.111 9.30 0.00 0.00 5.54
2953 3052 1.432270 CCTCGATGGAGAAAAGGCGC 61.432 60.000 6.27 0.00 43.27 6.53
2979 3078 1.433053 CGGCAACCAACTCGTGACAA 61.433 55.000 0.00 0.00 0.00 3.18
2984 3083 3.862845 GCAACCAACTCGTGACAATTTTT 59.137 39.130 0.00 0.00 0.00 1.94
3079 3178 0.960364 GACGACATTGGCCACCACAT 60.960 55.000 3.88 0.00 30.78 3.21
3164 3263 2.683867 GCATATATAGTCGCCCTCGAGT 59.316 50.000 12.31 0.67 46.46 4.18
3168 3267 2.061182 ATAGTCGCCCTCGAGTTCGC 62.061 60.000 12.31 8.88 45.30 4.70
3213 3312 3.681835 GTGTCGTCGGACCCTGCT 61.682 66.667 1.91 0.00 42.73 4.24
3243 3342 1.153229 TCTAGCTCGAGCAGGCGTA 60.153 57.895 36.87 19.88 45.16 4.42
3277 3376 5.567037 AGTAGTAGGGCATGCATAAATCA 57.433 39.130 21.36 0.00 0.00 2.57
3307 3406 2.027285 TCAAGCAGATTGACCGGATGAA 60.027 45.455 9.46 0.00 43.09 2.57
3310 3409 2.237143 AGCAGATTGACCGGATGAAAGA 59.763 45.455 9.46 0.00 0.00 2.52
3342 3441 1.790623 GTTCGCGACAATAGTGTGTGT 59.209 47.619 9.15 0.00 38.41 3.72
3362 3461 4.023707 GTGTGTGTCATTGGGAGAAAGAAG 60.024 45.833 0.00 0.00 0.00 2.85
3429 3528 0.611618 TTGGGTGTGCATGGTGGATC 60.612 55.000 0.00 0.00 0.00 3.36
3484 3584 2.932614 CGTCCAATCAGAAGTCACCATC 59.067 50.000 0.00 0.00 0.00 3.51
3519 3619 4.425180 TTGCCCAAGTACTAGTGTCAAA 57.575 40.909 5.39 0.00 0.00 2.69
3596 3696 0.743345 GATGGGTGTAACGTGGAGCC 60.743 60.000 0.00 0.00 38.12 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.994911 TGTATCTATTGATGCAAAGGTTGAGAT 59.005 33.333 5.53 0.00 41.20 2.75
1 2 7.337938 TGTATCTATTGATGCAAAGGTTGAGA 58.662 34.615 5.53 0.00 41.20 3.27
3 4 9.056005 GTATGTATCTATTGATGCAAAGGTTGA 57.944 33.333 11.40 0.00 45.65 3.18
4 5 8.839343 TGTATGTATCTATTGATGCAAAGGTTG 58.161 33.333 11.40 0.00 45.65 3.77
5 6 8.978874 TGTATGTATCTATTGATGCAAAGGTT 57.021 30.769 11.40 0.00 45.65 3.50
6 7 8.840321 GTTGTATGTATCTATTGATGCAAAGGT 58.160 33.333 11.40 0.00 45.65 3.50
58 59 5.509840 GGCTCGGTGTATATTCTTGTCAGAT 60.510 44.000 0.00 0.00 0.00 2.90
76 77 0.537188 AGGTGTAACTGATGGCTCGG 59.463 55.000 0.00 0.00 36.74 4.63
78 79 3.887621 TGTAGGTGTAACTGATGGCTC 57.112 47.619 0.00 0.00 36.74 4.70
87 98 8.995220 TCACATTATCAAGTTTGTAGGTGTAAC 58.005 33.333 0.00 0.00 0.00 2.50
89 100 9.214957 CTTCACATTATCAAGTTTGTAGGTGTA 57.785 33.333 0.00 0.00 0.00 2.90
113 125 8.540507 TTTAGATATGAGGAGTAAGAGCACTT 57.459 34.615 1.05 1.05 39.81 3.16
122 134 5.895534 ACACCGGTTTTAGATATGAGGAGTA 59.104 40.000 2.97 0.00 0.00 2.59
170 182 0.174845 TCGGCTGTTGGTTCCGATAG 59.825 55.000 0.00 0.00 46.12 2.08
189 201 0.036010 ACGCTTTAGGTCTGCTGCAT 60.036 50.000 1.31 0.00 0.00 3.96
224 236 4.497473 TGATGGTGGCGACTTTTAAAAG 57.503 40.909 23.38 23.38 41.73 2.27
230 242 2.198827 TCAATGATGGTGGCGACTTT 57.801 45.000 0.00 0.00 0.00 2.66
234 246 1.298602 CGATTCAATGATGGTGGCGA 58.701 50.000 0.00 0.00 0.00 5.54
240 252 1.605710 GGGTCAGCGATTCAATGATGG 59.394 52.381 0.00 0.00 0.00 3.51
247 259 1.554617 TGAAGATGGGTCAGCGATTCA 59.445 47.619 0.00 0.00 0.00 2.57
251 263 0.614697 TCCTGAAGATGGGTCAGCGA 60.615 55.000 0.00 0.00 41.04 4.93
280 292 1.211212 CTGGACTGGCAAGGATGATGA 59.789 52.381 0.00 0.00 0.00 2.92
378 391 0.392863 TGTGCTACGCATGGCAGATT 60.393 50.000 0.00 0.00 43.89 2.40
386 399 1.939974 ATTCGACATGTGCTACGCAT 58.060 45.000 1.15 0.00 41.91 4.73
397 410 3.541996 TGTGTCATGCCTATTCGACAT 57.458 42.857 0.00 0.00 40.27 3.06
463 477 2.674852 GAGCGACTTCATCTTGCATGAA 59.325 45.455 6.36 3.74 36.67 2.57
479 494 2.759973 AGGCGGAAGATGGAGCGA 60.760 61.111 0.00 0.00 0.00 4.93
487 502 0.537188 CTAAAGGCAGAGGCGGAAGA 59.463 55.000 0.00 0.00 42.47 2.87
500 515 0.955428 TTGTGGAGCAGCGCTAAAGG 60.955 55.000 10.99 0.00 39.88 3.11
569 586 0.909610 CCTAGGACCTGGTCTGCCAA 60.910 60.000 25.01 6.83 45.51 4.52
573 590 1.657804 AAACCCTAGGACCTGGTCTG 58.342 55.000 25.01 15.25 32.47 3.51
581 598 3.479489 TGTTTCGGAAAAACCCTAGGAC 58.521 45.455 11.48 0.00 34.64 3.85
593 610 1.021202 CCACTTGTGCTGTTTCGGAA 58.979 50.000 0.00 0.00 0.00 4.30
600 618 0.034574 TGTCAACCCACTTGTGCTGT 60.035 50.000 0.00 0.00 0.00 4.40
632 650 6.406512 GGGTGGTTACCTATGCCAAATAAAAG 60.407 42.308 2.07 0.00 46.66 2.27
642 660 2.640184 GACAAGGGTGGTTACCTATGC 58.360 52.381 2.07 0.00 46.66 3.14
656 674 4.790766 GCAAGGATGAATAATGCGACAAGG 60.791 45.833 0.00 0.00 0.00 3.61
662 680 3.427528 GCAATGCAAGGATGAATAATGCG 59.572 43.478 0.00 0.00 39.81 4.73
670 688 4.053469 CATCAATGCAATGCAAGGATGA 57.947 40.909 31.18 23.62 46.33 2.92
707 725 9.896263 GTTTTGGTTTTACAAATATACCTTCGA 57.104 29.630 0.00 0.00 39.80 3.71
708 726 9.902196 AGTTTTGGTTTTACAAATATACCTTCG 57.098 29.630 0.00 0.00 39.80 3.79
739 757 6.040247 TCCGCTAGTGTAGAATTGTGTAATG 58.960 40.000 1.99 0.00 0.00 1.90
781 804 4.899502 TGAGTCCATGTTCTTCTTTCTCC 58.100 43.478 0.00 0.00 0.00 3.71
782 805 6.419980 CATGAGTCCATGTTCTTCTTTCTC 57.580 41.667 0.00 0.00 43.90 2.87
855 878 2.674420 ACCGGCTAGCTAGGATGTTTA 58.326 47.619 28.02 0.00 0.00 2.01
858 881 2.364647 GTTAACCGGCTAGCTAGGATGT 59.635 50.000 28.02 17.63 0.00 3.06
933 956 3.332034 TCTAGCCCTTTTAAACGCAGAC 58.668 45.455 0.00 0.00 0.00 3.51
970 994 3.834813 TGGTAGTTCTGAGCTTCTGATGT 59.165 43.478 0.00 0.00 0.00 3.06
1165 1207 4.510038 AGAAACATCCATCAACACAAGC 57.490 40.909 0.00 0.00 0.00 4.01
1204 1254 1.373435 GACCACCCACACCATCGAA 59.627 57.895 0.00 0.00 0.00 3.71
1237 1287 2.470286 CGCTCGAAGTTGCCGTTC 59.530 61.111 0.00 0.00 0.00 3.95
1679 1729 3.148279 ACGGAGTCGATGAGGGGC 61.148 66.667 0.00 0.00 29.74 5.80
1770 1820 0.529992 CACGGCGTAGGGAAGGAATC 60.530 60.000 14.22 0.00 0.00 2.52
1810 1890 4.785376 ACCATTCTTCACCAGGTTCTCTAT 59.215 41.667 0.00 0.00 0.00 1.98
1926 2006 1.153549 GAGCGACTCCACCATCCAC 60.154 63.158 0.00 0.00 0.00 4.02
2063 2143 3.934391 AAGGACAGCGCGTACTGCC 62.934 63.158 16.04 12.59 38.09 4.85
2426 2506 2.426522 TGAGTTGAGCGCTTAAGCAAT 58.573 42.857 26.29 14.23 42.21 3.56
2427 2507 1.877637 TGAGTTGAGCGCTTAAGCAA 58.122 45.000 26.29 10.07 42.21 3.91
2449 2529 3.056678 TGCACATTCAACCCAATAAGCAG 60.057 43.478 0.00 0.00 0.00 4.24
2473 2559 3.119602 TCCGAGACTACACGAATTCCTTG 60.120 47.826 0.00 0.00 32.29 3.61
2485 2571 0.680280 TGGCACCTCTCCGAGACTAC 60.680 60.000 0.00 0.00 0.00 2.73
2486 2572 0.680280 GTGGCACCTCTCCGAGACTA 60.680 60.000 6.29 0.00 0.00 2.59
2487 2573 1.979693 GTGGCACCTCTCCGAGACT 60.980 63.158 6.29 0.00 0.00 3.24
2488 2574 2.574399 GTGGCACCTCTCCGAGAC 59.426 66.667 6.29 0.00 0.00 3.36
2489 2575 2.680352 GGTGGCACCTCTCCGAGA 60.680 66.667 29.22 0.00 34.73 4.04
2490 2576 3.775654 GGGTGGCACCTCTCCGAG 61.776 72.222 33.87 0.00 38.64 4.63
2491 2577 4.316823 AGGGTGGCACCTCTCCGA 62.317 66.667 33.87 0.00 38.64 4.55
2571 2663 8.208560 CGAAACATACGTTGCTAAGAGAATATC 58.791 37.037 0.00 0.00 34.86 1.63
2573 2665 7.031372 ACGAAACATACGTTGCTAAGAGAATA 58.969 34.615 0.00 0.00 41.18 1.75
2574 2666 5.867716 ACGAAACATACGTTGCTAAGAGAAT 59.132 36.000 0.00 0.00 41.18 2.40
2594 2687 9.078990 ACTAGATATCCTCAAATATGTGACGAA 57.921 33.333 0.00 0.00 0.00 3.85
2669 2768 5.402568 CAGTAGTGCACGCAATATAGGTAAG 59.597 44.000 12.01 0.00 0.00 2.34
2717 2816 1.286501 TCGCTAGTAGGCATTTTGCG 58.713 50.000 0.00 0.00 46.21 4.85
2828 2927 4.074627 TGATTTGGGTTCGTCACTGTTA 57.925 40.909 0.00 0.00 0.00 2.41
2831 2930 4.023279 TGAAATGATTTGGGTTCGTCACTG 60.023 41.667 0.00 0.00 0.00 3.66
2840 2939 1.272212 GTGGCGTGAAATGATTTGGGT 59.728 47.619 0.00 0.00 0.00 4.51
2841 2940 1.545582 AGTGGCGTGAAATGATTTGGG 59.454 47.619 0.00 0.00 0.00 4.12
2847 2946 7.985184 AGAAAATATACTAGTGGCGTGAAATGA 59.015 33.333 5.39 0.00 0.00 2.57
2886 2985 3.821600 TGAGCAACACCGCCTTTATTAAA 59.178 39.130 0.00 0.00 0.00 1.52
2901 3000 0.739813 AATCGCCGGTAGTGAGCAAC 60.740 55.000 1.90 0.00 38.70 4.17
2918 3017 4.252570 TCGAGGAGGAAACTAGAGGAAT 57.747 45.455 0.00 0.00 44.43 3.01
2953 3052 4.114997 GTTGGTTGCCGCATCCCG 62.115 66.667 16.33 0.00 0.00 5.14
2979 3078 9.860898 CTCCCTTCTTTTCGAATTATCAAAAAT 57.139 29.630 0.00 0.00 0.00 1.82
2984 3083 6.308015 TCCTCCCTTCTTTTCGAATTATCA 57.692 37.500 0.00 0.00 0.00 2.15
3136 3235 3.978687 GGCGACTATATATGCCGCTATT 58.021 45.455 19.85 0.00 44.56 1.73
3164 3263 2.582436 GTTCTCCCCATCCGCGAA 59.418 61.111 8.23 0.00 0.00 4.70
3168 3267 3.231298 GGAGGTTCTCCCCATCCG 58.769 66.667 2.65 0.00 44.36 4.18
3243 3342 2.289945 CCCTACTACTATACTCCCGCGT 60.290 54.545 4.92 0.00 0.00 6.01
3277 3376 5.056894 GTCAATCTGCTTGAGCTCAAAAT 57.943 39.130 28.16 16.48 44.44 1.82
3307 3406 0.528470 CGAACGAGCTCTTCCCTCTT 59.472 55.000 12.85 0.00 0.00 2.85
3310 3409 2.574399 GCGAACGAGCTCTTCCCT 59.426 61.111 12.85 0.00 0.00 4.20
3342 3441 4.347876 TCTCTTCTTTCTCCCAATGACACA 59.652 41.667 0.00 0.00 0.00 3.72
3362 3461 5.212745 TCCCTTATCTTTCTCTCCCTTCTC 58.787 45.833 0.00 0.00 0.00 2.87
3429 3528 5.738909 ACCTTAATTGATGAGGTGTCTCTG 58.261 41.667 4.48 0.00 42.04 3.35
3484 3584 2.180017 GCAATCCAGCGTGCCAAG 59.820 61.111 0.00 0.00 34.58 3.61
3519 3619 6.435277 TGGGAAAGTCGTAGAGTACAAGTTAT 59.565 38.462 0.00 0.00 40.67 1.89
3577 3677 0.743345 GGCTCCACGTTACACCCATC 60.743 60.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.