Multiple sequence alignment - TraesCS6D01G296900

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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 TraesCS6D01G296900 chr6D 100.000 3598 0 0 1 3598 408158081 408154484 0.000000e+00 6645.0
1 TraesCS6D01G296900 chr6D 89.469 2203 158 42 507 2686 59089564 59087413 0.000000e+00 2715.0
2 TraesCS6D01G296900 chr6D 90.627 1707 140 5 993 2686 420559256 420560955 0.000000e+00 2248.0
3 TraesCS6D01G296900 chr6D 90.368 1713 138 11 993 2686 420569161 420567457 0.000000e+00 2224.0
4 TraesCS6D01G296900 chr6D 88.839 224 12 6 1 211 59099248 59099025 2.750000e-66 263.0
5 TraesCS6D01G296900 chr6D 88.517 209 13 3 244 452 59091198 59091001 3.590000e-60 243.0
6 TraesCS6D01G296900 chr6D 75.910 357 18 26 579 891 420558897 420559229 1.750000e-23 121.0
7 TraesCS6D01G296900 chr6A 88.423 2479 175 53 250 2686 553914036 553911628 0.000000e+00 2885.0
8 TraesCS6D01G296900 chr6A 91.713 1786 113 16 868 2641 553767100 553765338 0.000000e+00 2446.0
9 TraesCS6D01G296900 chr6A 90.457 1729 130 12 986 2686 563484752 563486473 0.000000e+00 2246.0
10 TraesCS6D01G296900 chr6A 95.871 775 31 1 2825 3598 553759274 553758500 0.000000e+00 1253.0
11 TraesCS6D01G296900 chr6A 86.934 773 85 3 2841 3598 554104749 554103978 0.000000e+00 854.0
12 TraesCS6D01G296900 chr6A 91.489 141 9 1 109 246 553914217 553914077 1.320000e-44 191.0
13 TraesCS6D01G296900 chr6A 77.561 410 24 28 528 898 563484356 563484736 6.130000e-43 185.0
14 TraesCS6D01G296900 chr6A 78.516 256 22 10 470 703 553767345 553767101 1.740000e-28 137.0
15 TraesCS6D01G296900 chr6A 91.463 82 4 1 2749 2827 553759389 553759308 3.800000e-20 110.0
16 TraesCS6D01G296900 chr6A 85.714 91 7 3 1 88 553914513 553914426 1.380000e-14 91.6
17 TraesCS6D01G296900 chr6B 90.681 1835 120 25 852 2686 612271579 612269796 0.000000e+00 2394.0
18 TraesCS6D01G296900 chr6B 89.988 1708 150 8 993 2686 633730671 633732371 0.000000e+00 2187.0
19 TraesCS6D01G296900 chr6B 91.674 1093 78 6 1607 2686 612744582 612743490 0.000000e+00 1502.0
20 TraesCS6D01G296900 chr6B 90.997 1033 67 21 512 1532 612745634 612744616 0.000000e+00 1369.0
21 TraesCS6D01G296900 chr6B 89.459 740 45 6 2884 3598 612219660 612218929 0.000000e+00 904.0
22 TraesCS6D01G296900 chr6B 80.789 380 25 17 528 891 633730297 633730644 1.660000e-63 254.0
23 TraesCS6D01G296900 chr6B 86.624 157 6 5 1 142 612745828 612745672 3.720000e-35 159.0
24 TraesCS6D01G296900 chr6B 80.303 198 16 11 510 699 612271920 612271738 1.050000e-25 128.0
25 TraesCS6D01G296900 chr4A 76.580 269 57 6 3009 3274 499953395 499953660 3.740000e-30 143.0


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 TraesCS6D01G296900 chr6D 408154484 408158081 3597 True 6645.000000 6645 100.0000 1 3598 1 chr6D.!!$R2 3597
1 TraesCS6D01G296900 chr6D 420567457 420569161 1704 True 2224.000000 2224 90.3680 993 2686 1 chr6D.!!$R3 1693
2 TraesCS6D01G296900 chr6D 59087413 59091198 3785 True 1479.000000 2715 88.9930 244 2686 2 chr6D.!!$R4 2442
3 TraesCS6D01G296900 chr6D 420558897 420560955 2058 False 1184.500000 2248 83.2685 579 2686 2 chr6D.!!$F1 2107
4 TraesCS6D01G296900 chr6A 553765338 553767345 2007 True 1291.500000 2446 85.1145 470 2641 2 chr6A.!!$R3 2171
5 TraesCS6D01G296900 chr6A 563484356 563486473 2117 False 1215.500000 2246 84.0090 528 2686 2 chr6A.!!$F1 2158
6 TraesCS6D01G296900 chr6A 553911628 553914513 2885 True 1055.866667 2885 88.5420 1 2686 3 chr6A.!!$R4 2685
7 TraesCS6D01G296900 chr6A 554103978 554104749 771 True 854.000000 854 86.9340 2841 3598 1 chr6A.!!$R1 757
8 TraesCS6D01G296900 chr6A 553758500 553759389 889 True 681.500000 1253 93.6670 2749 3598 2 chr6A.!!$R2 849
9 TraesCS6D01G296900 chr6B 612269796 612271920 2124 True 1261.000000 2394 85.4920 510 2686 2 chr6B.!!$R2 2176
10 TraesCS6D01G296900 chr6B 633730297 633732371 2074 False 1220.500000 2187 85.3885 528 2686 2 chr6B.!!$F1 2158
11 TraesCS6D01G296900 chr6B 612743490 612745828 2338 True 1010.000000 1502 89.7650 1 2686 3 chr6B.!!$R3 2685
12 TraesCS6D01G296900 chr6B 612218929 612219660 731 True 904.000000 904 89.4590 2884 3598 1 chr6B.!!$R1 714

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
921 2689 0.251386 ACGAGAGTTCAGCCAGGAGA 60.251 55.0 0.0 0.0 46.4 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2850 4728 0.038166 TGTTAGCTGGGAAGGGCAAG 59.962 55.0 0.0 0.0 0.0 4.01 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 4.456253 CGACACGACGGGACCTCG 62.456 72.222 2.90 0.00 37.17 4.63
65 69 2.932234 CGGGACTTCACGGAGCTGT 61.932 63.158 0.00 0.00 39.49 4.40
142 344 3.338249 CCTTTGACCTGAACGATCACAT 58.662 45.455 0.00 0.00 0.00 3.21
215 417 2.297033 ACATGCACCAGTTCATCCAAAC 59.703 45.455 0.00 0.00 0.00 2.93
219 421 3.181477 TGCACCAGTTCATCCAAACAAAG 60.181 43.478 0.00 0.00 0.00 2.77
227 429 6.088085 CAGTTCATCCAAACAAAGCGAATTAC 59.912 38.462 0.00 0.00 0.00 1.89
241 443 4.989168 AGCGAATTACGTTCAGAGAGTTTT 59.011 37.500 0.00 0.00 44.60 2.43
262 501 2.580815 CAGAGGCCACGCTGATGA 59.419 61.111 5.01 0.00 46.01 2.92
263 502 1.145598 CAGAGGCCACGCTGATGAT 59.854 57.895 5.01 0.00 46.01 2.45
264 503 1.145598 AGAGGCCACGCTGATGATG 59.854 57.895 5.01 0.00 0.00 3.07
282 521 4.341827 GCAACTGCACGCCAAATT 57.658 50.000 0.00 0.00 41.59 1.82
283 522 3.488048 GCAACTGCACGCCAAATTA 57.512 47.368 0.00 0.00 41.59 1.40
284 523 1.777101 GCAACTGCACGCCAAATTAA 58.223 45.000 0.00 0.00 41.59 1.40
314 553 4.383770 CCAATGTTACGGGTCAAGGAGTAT 60.384 45.833 0.00 0.00 0.00 2.12
378 617 2.279851 AGCGTACGCAAGCACACA 60.280 55.556 38.58 0.00 44.88 3.72
436 675 5.046304 AGCAGAACTGAAGCCATAAAGAGTA 60.046 40.000 5.97 0.00 0.00 2.59
437 676 5.643777 GCAGAACTGAAGCCATAAAGAGTAA 59.356 40.000 5.97 0.00 0.00 2.24
441 680 8.254508 AGAACTGAAGCCATAAAGAGTAACTAG 58.745 37.037 0.00 0.00 0.00 2.57
467 2066 5.810095 AGGAGTCTCCTCTAATTTGGTTTG 58.190 41.667 16.28 0.00 45.66 2.93
475 2074 5.036737 CCTCTAATTTGGTTTGCGCATTAG 58.963 41.667 12.75 14.42 0.00 1.73
710 2450 3.698040 ACCAACACGATCCTAATACGTCT 59.302 43.478 0.00 0.00 38.18 4.18
725 2465 6.476243 AATACGTCTTCACTTGCGTTATTT 57.524 33.333 0.00 0.00 38.56 1.40
761 2507 2.604912 TCTCACTGTCAAGCCTCCTA 57.395 50.000 0.00 0.00 0.00 2.94
765 2511 3.764434 CTCACTGTCAAGCCTCCTACTAA 59.236 47.826 0.00 0.00 0.00 2.24
766 2512 4.353777 TCACTGTCAAGCCTCCTACTAAT 58.646 43.478 0.00 0.00 0.00 1.73
767 2513 5.516044 TCACTGTCAAGCCTCCTACTAATA 58.484 41.667 0.00 0.00 0.00 0.98
768 2514 5.360144 TCACTGTCAAGCCTCCTACTAATAC 59.640 44.000 0.00 0.00 0.00 1.89
770 2516 5.361285 ACTGTCAAGCCTCCTACTAATACAG 59.639 44.000 0.00 0.00 37.29 2.74
801 2548 1.279496 ATGGAGCAGTGCTACCTGAA 58.721 50.000 24.76 6.20 39.07 3.02
802 2549 0.610174 TGGAGCAGTGCTACCTGAAG 59.390 55.000 24.76 0.00 39.07 3.02
803 2550 0.742635 GGAGCAGTGCTACCTGAAGC 60.743 60.000 19.77 2.27 39.88 3.86
921 2689 0.251386 ACGAGAGTTCAGCCAGGAGA 60.251 55.000 0.00 0.00 46.40 3.71
969 2742 1.560860 GGTCAGCTCGAAGCACACAC 61.561 60.000 9.09 1.28 45.56 3.82
973 2746 1.949133 GCTCGAAGCACACACACGA 60.949 57.895 0.00 0.00 41.89 4.35
979 2752 1.933853 GAAGCACACACACGAAGAGTT 59.066 47.619 0.00 0.00 0.00 3.01
990 2763 2.083002 ACGAAGAGTTAGGAGTCGTCC 58.917 52.381 0.00 0.00 40.71 4.79
1470 3254 2.490148 CGCCATCAGCTACCTCGGA 61.490 63.158 0.00 0.00 40.39 4.55
1546 3350 1.335872 ACGTACGGTAGTTTGTTCCCG 60.336 52.381 21.06 0.00 45.72 5.14
1547 3351 1.713597 GTACGGTAGTTTGTTCCCGG 58.286 55.000 0.00 0.00 44.57 5.73
1556 3362 1.990160 TTTGTTCCCGGGTCAGTGCT 61.990 55.000 22.86 0.00 0.00 4.40
1570 3376 0.393944 AGTGCTCCCGTCACTCGATA 60.394 55.000 0.00 0.00 40.47 2.92
1598 3404 1.080772 TTGCGTCTCCAGCACGTAG 60.081 57.895 0.00 0.00 45.10 3.51
1601 3407 4.767633 GTCTCCAGCACGTAGACG 57.232 61.111 0.00 0.00 46.33 4.18
1604 3410 1.213013 CTCCAGCACGTAGACGCTT 59.787 57.895 1.14 0.00 44.43 4.68
1648 3462 9.416794 GATCGAAGCTCTTATCTGAATATTTGA 57.583 33.333 0.00 0.00 0.00 2.69
1667 3487 1.667724 GACTTTATGCGTGCAGATGCT 59.332 47.619 6.35 0.00 42.66 3.79
1694 3514 2.481449 GCTGACGAACGGATACCTTGAT 60.481 50.000 0.00 0.00 0.00 2.57
1697 3517 3.695556 TGACGAACGGATACCTTGATACA 59.304 43.478 0.00 0.00 0.00 2.29
1704 3524 2.433239 GGATACCTTGATACACCGGTGT 59.567 50.000 39.83 39.83 46.87 4.16
1726 3546 2.819984 GATGTGCCGGGCTTGAGGAA 62.820 60.000 21.46 0.00 0.00 3.36
1850 3670 1.813513 CCGTCATCCTCAACAGCTTT 58.186 50.000 0.00 0.00 0.00 3.51
1860 3680 1.138069 TCAACAGCTTTGACGACCTGA 59.862 47.619 7.09 0.00 0.00 3.86
1919 3739 4.379243 AAGGTCTGCACGCTCGGG 62.379 66.667 0.00 0.00 0.00 5.14
2081 3901 4.002506 ACCGTCATGACCAGCGCA 62.003 61.111 20.03 0.00 0.00 6.09
2099 3919 0.036952 CACAGATGGTGGAGTTCGCT 60.037 55.000 0.00 0.00 44.04 4.93
2111 3931 3.565214 TTCGCTTGGGGACTGGCA 61.565 61.111 0.00 0.00 0.00 4.92
2193 4013 4.968553 TCCCCGAGGAGTTCTTGT 57.031 55.556 0.00 0.00 37.19 3.16
2264 4084 2.358737 CTGAACCACCCTGCCGTC 60.359 66.667 0.00 0.00 0.00 4.79
2420 4240 0.317160 TGGAGATCGACAGCAACGTT 59.683 50.000 0.00 0.00 0.00 3.99
2516 4336 2.650116 GGAGTGGAAGGAGAGCGCA 61.650 63.158 11.47 0.00 0.00 6.09
2576 4396 4.415332 GACGAGCTGGTCCGCGAA 62.415 66.667 17.35 0.00 34.40 4.70
2598 4418 0.905357 GCTCCTGCCCAAGAACTAGA 59.095 55.000 0.00 0.00 0.00 2.43
2686 4524 1.202582 CGTTCCTTCCGAGAGTGATGT 59.797 52.381 0.00 0.00 0.00 3.06
2687 4525 2.732597 CGTTCCTTCCGAGAGTGATGTC 60.733 54.545 0.00 0.00 0.00 3.06
2688 4526 1.475403 TCCTTCCGAGAGTGATGTCC 58.525 55.000 0.00 0.00 0.00 4.02
2689 4527 0.101399 CCTTCCGAGAGTGATGTCCG 59.899 60.000 0.00 0.00 0.00 4.79
2690 4528 0.811915 CTTCCGAGAGTGATGTCCGT 59.188 55.000 0.00 0.00 0.00 4.69
2691 4529 1.202582 CTTCCGAGAGTGATGTCCGTT 59.797 52.381 0.00 0.00 0.00 4.44
2692 4530 1.254026 TCCGAGAGTGATGTCCGTTT 58.746 50.000 0.00 0.00 0.00 3.60
2693 4531 1.616865 TCCGAGAGTGATGTCCGTTTT 59.383 47.619 0.00 0.00 0.00 2.43
2694 4532 1.726791 CCGAGAGTGATGTCCGTTTTG 59.273 52.381 0.00 0.00 0.00 2.44
2695 4533 2.609491 CCGAGAGTGATGTCCGTTTTGA 60.609 50.000 0.00 0.00 0.00 2.69
2696 4534 3.254060 CGAGAGTGATGTCCGTTTTGAT 58.746 45.455 0.00 0.00 0.00 2.57
2697 4535 3.061295 CGAGAGTGATGTCCGTTTTGATG 59.939 47.826 0.00 0.00 0.00 3.07
2698 4536 3.997021 GAGAGTGATGTCCGTTTTGATGT 59.003 43.478 0.00 0.00 0.00 3.06
2699 4537 5.147330 AGAGTGATGTCCGTTTTGATGTA 57.853 39.130 0.00 0.00 0.00 2.29
2700 4538 4.929808 AGAGTGATGTCCGTTTTGATGTAC 59.070 41.667 0.00 0.00 0.00 2.90
2701 4539 4.637276 AGTGATGTCCGTTTTGATGTACA 58.363 39.130 0.00 0.00 0.00 2.90
2702 4540 5.060506 AGTGATGTCCGTTTTGATGTACAA 58.939 37.500 0.00 0.00 36.65 2.41
2703 4541 5.529430 AGTGATGTCCGTTTTGATGTACAAA 59.471 36.000 0.00 0.00 45.22 2.83
2704 4542 5.851177 GTGATGTCCGTTTTGATGTACAAAG 59.149 40.000 0.00 0.00 46.93 2.77
2705 4543 5.760743 TGATGTCCGTTTTGATGTACAAAGA 59.239 36.000 0.00 0.00 46.93 2.52
2706 4544 6.429692 TGATGTCCGTTTTGATGTACAAAGAT 59.570 34.615 0.00 0.00 46.93 2.40
2707 4545 5.996219 TGTCCGTTTTGATGTACAAAGATG 58.004 37.500 0.00 0.00 46.93 2.90
2708 4546 5.760743 TGTCCGTTTTGATGTACAAAGATGA 59.239 36.000 0.00 0.00 46.93 2.92
2709 4547 6.261158 TGTCCGTTTTGATGTACAAAGATGAA 59.739 34.615 0.00 0.00 46.93 2.57
2710 4548 6.797033 GTCCGTTTTGATGTACAAAGATGAAG 59.203 38.462 0.00 0.00 46.93 3.02
2711 4549 6.485313 TCCGTTTTGATGTACAAAGATGAAGT 59.515 34.615 0.00 0.00 46.93 3.01
2712 4550 7.012894 TCCGTTTTGATGTACAAAGATGAAGTT 59.987 33.333 0.00 0.00 46.93 2.66
2713 4551 7.113404 CCGTTTTGATGTACAAAGATGAAGTTG 59.887 37.037 0.00 0.00 46.93 3.16
2714 4552 7.643764 CGTTTTGATGTACAAAGATGAAGTTGT 59.356 33.333 0.00 0.00 46.93 3.32
2715 4553 8.958043 GTTTTGATGTACAAAGATGAAGTTGTC 58.042 33.333 0.00 0.00 46.93 3.18
2716 4554 8.450578 TTTGATGTACAAAGATGAAGTTGTCT 57.549 30.769 0.00 0.00 42.57 3.41
2717 4555 8.450578 TTGATGTACAAAGATGAAGTTGTCTT 57.549 30.769 0.00 0.00 38.80 3.01
2718 4556 9.554395 TTGATGTACAAAGATGAAGTTGTCTTA 57.446 29.630 0.00 0.00 38.80 2.10
2719 4557 9.554395 TGATGTACAAAGATGAAGTTGTCTTAA 57.446 29.630 0.00 0.00 38.80 1.85
2721 4559 9.778741 ATGTACAAAGATGAAGTTGTCTTAAGA 57.221 29.630 0.00 0.00 38.80 2.10
2722 4560 9.778741 TGTACAAAGATGAAGTTGTCTTAAGAT 57.221 29.630 8.75 0.00 38.80 2.40
2724 4562 7.588512 ACAAAGATGAAGTTGTCTTAAGATGC 58.411 34.615 8.75 2.39 32.52 3.91
2725 4563 7.229306 ACAAAGATGAAGTTGTCTTAAGATGCA 59.771 33.333 8.75 0.00 32.52 3.96
2726 4564 7.750229 AAGATGAAGTTGTCTTAAGATGCAA 57.250 32.000 8.75 6.44 33.15 4.08
2727 4565 7.934855 AGATGAAGTTGTCTTAAGATGCAAT 57.065 32.000 8.75 0.00 33.64 3.56
2728 4566 7.759465 AGATGAAGTTGTCTTAAGATGCAATG 58.241 34.615 8.75 0.00 33.64 2.82
2729 4567 6.258230 TGAAGTTGTCTTAAGATGCAATGG 57.742 37.500 8.75 0.00 33.64 3.16
2730 4568 5.183713 TGAAGTTGTCTTAAGATGCAATGGG 59.816 40.000 8.75 0.00 33.64 4.00
2731 4569 4.666512 AGTTGTCTTAAGATGCAATGGGT 58.333 39.130 8.75 0.00 0.00 4.51
2732 4570 4.702131 AGTTGTCTTAAGATGCAATGGGTC 59.298 41.667 8.75 0.00 0.00 4.46
2733 4571 4.574674 TGTCTTAAGATGCAATGGGTCT 57.425 40.909 8.75 0.00 0.00 3.85
2734 4572 4.517285 TGTCTTAAGATGCAATGGGTCTC 58.483 43.478 8.75 0.00 0.00 3.36
2735 4573 4.225942 TGTCTTAAGATGCAATGGGTCTCT 59.774 41.667 8.75 0.00 0.00 3.10
2736 4574 5.189180 GTCTTAAGATGCAATGGGTCTCTT 58.811 41.667 8.75 0.00 0.00 2.85
2737 4575 6.070251 TGTCTTAAGATGCAATGGGTCTCTTA 60.070 38.462 8.75 0.00 0.00 2.10
2738 4576 6.995091 GTCTTAAGATGCAATGGGTCTCTTAT 59.005 38.462 8.75 0.00 30.78 1.73
2739 4577 8.150945 GTCTTAAGATGCAATGGGTCTCTTATA 58.849 37.037 8.75 0.00 30.78 0.98
2740 4578 8.713971 TCTTAAGATGCAATGGGTCTCTTATAA 58.286 33.333 0.00 0.00 30.78 0.98
2741 4579 9.512588 CTTAAGATGCAATGGGTCTCTTATAAT 57.487 33.333 0.00 0.00 30.78 1.28
2743 4581 8.854614 AAGATGCAATGGGTCTCTTATAATAC 57.145 34.615 0.00 0.00 0.00 1.89
2744 4582 8.212259 AGATGCAATGGGTCTCTTATAATACT 57.788 34.615 0.00 0.00 0.00 2.12
2745 4583 8.317679 AGATGCAATGGGTCTCTTATAATACTC 58.682 37.037 0.00 0.00 0.00 2.59
2746 4584 7.618019 TGCAATGGGTCTCTTATAATACTCT 57.382 36.000 0.00 0.00 0.00 3.24
2747 4585 8.034313 TGCAATGGGTCTCTTATAATACTCTT 57.966 34.615 0.00 0.00 0.00 2.85
2755 4593 6.016108 GTCTCTTATAATACTCTTCCTGCGGT 60.016 42.308 0.00 0.00 0.00 5.68
2850 4728 1.384222 CCGTTTATCTGCCCTTGCCC 61.384 60.000 0.00 0.00 36.33 5.36
2961 4839 6.627087 ATCTGAGTTTCAAGGAACCTGATA 57.373 37.500 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.269309 CCTACTGGCTAGACATGCGTC 60.269 57.143 3.17 0.00 42.95 5.19
65 69 0.824109 CCTGGATAGAGTTGCGGACA 59.176 55.000 0.00 0.00 0.00 4.02
70 74 0.872021 CGTCGCCTGGATAGAGTTGC 60.872 60.000 0.00 0.00 0.00 4.17
97 108 6.460676 GGGAGCAAATTATTGATGACTTCAGG 60.461 42.308 0.00 0.00 38.94 3.86
98 109 6.320672 AGGGAGCAAATTATTGATGACTTCAG 59.679 38.462 0.00 0.00 38.94 3.02
157 359 0.320073 GATTGGGTCCACAACGACGA 60.320 55.000 0.00 0.00 33.30 4.20
180 382 1.811195 CATGTGGCATGCAACGGAT 59.189 52.632 20.19 6.47 0.00 4.18
215 417 4.386049 ACTCTCTGAACGTAATTCGCTTTG 59.614 41.667 0.00 0.00 44.19 2.77
219 421 4.905412 AAACTCTCTGAACGTAATTCGC 57.095 40.909 0.00 0.00 44.19 4.70
227 429 2.872245 TCTGGCAAAAACTCTCTGAACG 59.128 45.455 0.00 0.00 0.00 3.95
279 518 5.105513 CCCGTAACATTGGCCTCTTTTAATT 60.106 40.000 3.32 0.00 0.00 1.40
280 519 4.401202 CCCGTAACATTGGCCTCTTTTAAT 59.599 41.667 3.32 0.00 0.00 1.40
281 520 3.759618 CCCGTAACATTGGCCTCTTTTAA 59.240 43.478 3.32 0.00 0.00 1.52
282 521 3.244981 ACCCGTAACATTGGCCTCTTTTA 60.245 43.478 3.32 0.00 0.00 1.52
283 522 2.167662 CCCGTAACATTGGCCTCTTTT 58.832 47.619 3.32 0.00 0.00 2.27
284 523 1.074889 ACCCGTAACATTGGCCTCTTT 59.925 47.619 3.32 0.00 0.00 2.52
314 553 7.464844 CGTCGATGGTTAGCAAATTTGTACATA 60.465 37.037 19.03 5.47 0.00 2.29
378 617 1.209019 GATCAGACATCCACAGTGGCT 59.791 52.381 15.64 1.48 37.47 4.75
452 2051 3.508744 ATGCGCAAACCAAATTAGAGG 57.491 42.857 17.11 0.00 0.00 3.69
454 2053 5.182190 TCACTAATGCGCAAACCAAATTAGA 59.818 36.000 24.06 6.98 35.39 2.10
458 2057 3.574614 GTCACTAATGCGCAAACCAAAT 58.425 40.909 17.11 0.00 0.00 2.32
459 2058 2.603412 CGTCACTAATGCGCAAACCAAA 60.603 45.455 17.11 0.00 0.00 3.28
467 2066 2.847254 GCTGAAATCGTCACTAATGCGC 60.847 50.000 0.00 0.00 31.13 6.09
475 2074 2.276058 GCGCGCTGAAATCGTCAC 60.276 61.111 26.67 0.00 31.13 3.67
765 2511 8.213679 ACTGCTCCATTTTGTATCATACTGTAT 58.786 33.333 0.00 0.00 0.00 2.29
766 2512 7.495606 CACTGCTCCATTTTGTATCATACTGTA 59.504 37.037 0.00 0.00 0.00 2.74
767 2513 6.317140 CACTGCTCCATTTTGTATCATACTGT 59.683 38.462 0.00 0.00 0.00 3.55
768 2514 6.722301 CACTGCTCCATTTTGTATCATACTG 58.278 40.000 0.00 0.00 0.00 2.74
770 2516 5.297776 AGCACTGCTCCATTTTGTATCATAC 59.702 40.000 0.00 0.00 30.62 2.39
841 2595 2.746142 GCTGGGGATCGATGTGAATTGA 60.746 50.000 0.54 0.00 0.00 2.57
969 2742 2.159544 GGACGACTCCTAACTCTTCGTG 60.160 54.545 0.00 0.00 42.69 4.35
973 2746 0.810016 GCGGACGACTCCTAACTCTT 59.190 55.000 0.00 0.00 33.79 2.85
979 2752 2.513204 CTCCGCGGACGACTCCTA 60.513 66.667 27.28 0.00 43.93 2.94
990 2763 4.292178 GAGCCCATCTCCTCCGCG 62.292 72.222 0.00 0.00 35.77 6.46
1245 3029 3.281395 TCCTGCGTGACGTCGTCA 61.281 61.111 23.70 23.70 40.50 4.35
1470 3254 2.443390 AGGCGGTAGTGGCGGTAT 60.443 61.111 0.00 0.00 39.82 2.73
1533 3329 1.071228 ACTGACCCGGGAACAAACTAC 59.929 52.381 32.02 6.95 0.00 2.73
1546 3350 3.311110 TGACGGGAGCACTGACCC 61.311 66.667 0.00 0.00 42.43 4.46
1547 3351 2.048127 GTGACGGGAGCACTGACC 60.048 66.667 0.00 0.00 35.17 4.02
1556 3362 1.712018 CGCTGTATCGAGTGACGGGA 61.712 60.000 0.00 0.00 42.82 5.14
1598 3404 1.672881 AGCTGATAATGGCAAAGCGTC 59.327 47.619 0.00 0.00 38.90 5.19
1601 3407 1.407979 AGCAGCTGATAATGGCAAAGC 59.592 47.619 20.43 0.00 0.00 3.51
1604 3410 2.423446 TCAGCAGCTGATAATGGCAA 57.577 45.000 21.85 0.00 35.39 4.52
1648 3462 1.399440 CAGCATCTGCACGCATAAAGT 59.601 47.619 4.79 0.00 45.16 2.66
1667 3487 1.877576 ATCCGTTCGTCAGCTGCTCA 61.878 55.000 9.47 0.00 0.00 4.26
1694 3514 1.066716 GGCACATCTTACACCGGTGTA 60.067 52.381 37.58 37.58 44.42 2.90
1697 3517 1.079405 CGGCACATCTTACACCGGT 60.079 57.895 0.00 0.00 40.18 5.28
1704 3524 0.107703 CTCAAGCCCGGCACATCTTA 60.108 55.000 13.15 0.00 0.00 2.10
1726 3546 0.908198 GAAGTCCCTGAGCCTCATGT 59.092 55.000 0.00 0.00 0.00 3.21
1850 3670 2.599281 TCGCCCTTCAGGTCGTCA 60.599 61.111 0.00 0.00 38.26 4.35
1963 3783 3.512516 GGCTGAGGTTGATGGCGC 61.513 66.667 0.00 0.00 0.00 6.53
2081 3901 0.687354 AAGCGAACTCCACCATCTGT 59.313 50.000 0.00 0.00 0.00 3.41
2099 3919 3.160585 CTCTGTGCCAGTCCCCAA 58.839 61.111 2.68 0.00 32.61 4.12
2111 3931 1.004440 GAACTGCTTCCCGCTCTGT 60.004 57.895 0.00 0.00 40.11 3.41
2660 4498 2.030096 ACTCTCGGAAGGAACGAACTTC 60.030 50.000 9.06 9.06 42.73 3.01
2686 4524 6.485313 ACTTCATCTTTGTACATCAAAACGGA 59.515 34.615 0.00 0.00 44.08 4.69
2687 4525 6.668323 ACTTCATCTTTGTACATCAAAACGG 58.332 36.000 0.00 0.00 44.08 4.44
2688 4526 7.643764 ACAACTTCATCTTTGTACATCAAAACG 59.356 33.333 0.00 0.00 44.08 3.60
2689 4527 8.856490 ACAACTTCATCTTTGTACATCAAAAC 57.144 30.769 0.00 0.00 44.08 2.43
2690 4528 8.902806 AGACAACTTCATCTTTGTACATCAAAA 58.097 29.630 0.00 0.00 44.08 2.44
2691 4529 8.450578 AGACAACTTCATCTTTGTACATCAAA 57.549 30.769 0.00 0.00 42.79 2.69
2692 4530 8.450578 AAGACAACTTCATCTTTGTACATCAA 57.549 30.769 0.00 0.00 36.06 2.57
2693 4531 9.554395 TTAAGACAACTTCATCTTTGTACATCA 57.446 29.630 0.00 0.00 36.06 3.07
2695 4533 9.778741 TCTTAAGACAACTTCATCTTTGTACAT 57.221 29.630 0.00 0.00 36.06 2.29
2696 4534 9.778741 ATCTTAAGACAACTTCATCTTTGTACA 57.221 29.630 7.48 0.00 36.06 2.90
2698 4536 8.721478 GCATCTTAAGACAACTTCATCTTTGTA 58.279 33.333 7.48 0.00 36.06 2.41
2699 4537 7.229306 TGCATCTTAAGACAACTTCATCTTTGT 59.771 33.333 7.48 0.00 38.67 2.83
2700 4538 7.587629 TGCATCTTAAGACAACTTCATCTTTG 58.412 34.615 7.48 0.00 36.56 2.77
2701 4539 7.750229 TGCATCTTAAGACAACTTCATCTTT 57.250 32.000 7.48 0.00 36.56 2.52
2702 4540 7.750229 TTGCATCTTAAGACAACTTCATCTT 57.250 32.000 7.48 0.00 38.67 2.40
2703 4541 7.148120 CCATTGCATCTTAAGACAACTTCATCT 60.148 37.037 7.48 0.00 37.53 2.90
2704 4542 6.971184 CCATTGCATCTTAAGACAACTTCATC 59.029 38.462 7.48 0.00 37.53 2.92
2705 4543 6.127535 CCCATTGCATCTTAAGACAACTTCAT 60.128 38.462 7.48 0.00 37.53 2.57
2706 4544 5.183713 CCCATTGCATCTTAAGACAACTTCA 59.816 40.000 7.48 0.00 37.53 3.02
2707 4545 5.183904 ACCCATTGCATCTTAAGACAACTTC 59.816 40.000 7.48 0.00 37.53 3.01
2708 4546 5.079643 ACCCATTGCATCTTAAGACAACTT 58.920 37.500 7.48 0.00 39.81 2.66
2709 4547 4.666512 ACCCATTGCATCTTAAGACAACT 58.333 39.130 7.48 0.00 0.00 3.16
2710 4548 4.702131 AGACCCATTGCATCTTAAGACAAC 59.298 41.667 7.48 0.76 0.00 3.32
2711 4549 4.922206 AGACCCATTGCATCTTAAGACAA 58.078 39.130 7.48 9.05 0.00 3.18
2712 4550 4.225942 AGAGACCCATTGCATCTTAAGACA 59.774 41.667 7.48 0.00 0.00 3.41
2713 4551 4.775236 AGAGACCCATTGCATCTTAAGAC 58.225 43.478 7.48 0.00 0.00 3.01
2714 4552 5.441718 AAGAGACCCATTGCATCTTAAGA 57.558 39.130 7.82 7.82 0.00 2.10
2715 4553 8.908786 TTATAAGAGACCCATTGCATCTTAAG 57.091 34.615 7.55 0.00 36.40 1.85
2717 4555 9.944376 GTATTATAAGAGACCCATTGCATCTTA 57.056 33.333 6.23 6.23 37.01 2.10
2718 4556 8.664079 AGTATTATAAGAGACCCATTGCATCTT 58.336 33.333 2.36 2.36 34.71 2.40
2719 4557 8.212259 AGTATTATAAGAGACCCATTGCATCT 57.788 34.615 0.00 0.00 0.00 2.90
2720 4558 8.317679 AGAGTATTATAAGAGACCCATTGCATC 58.682 37.037 0.00 0.00 0.00 3.91
2721 4559 8.212259 AGAGTATTATAAGAGACCCATTGCAT 57.788 34.615 0.00 0.00 0.00 3.96
2722 4560 7.618019 AGAGTATTATAAGAGACCCATTGCA 57.382 36.000 0.00 0.00 0.00 4.08
2723 4561 7.604545 GGAAGAGTATTATAAGAGACCCATTGC 59.395 40.741 0.00 0.00 0.00 3.56
2724 4562 8.875168 AGGAAGAGTATTATAAGAGACCCATTG 58.125 37.037 0.00 0.00 0.00 2.82
2725 4563 8.875168 CAGGAAGAGTATTATAAGAGACCCATT 58.125 37.037 0.00 0.00 0.00 3.16
2726 4564 7.038658 GCAGGAAGAGTATTATAAGAGACCCAT 60.039 40.741 0.00 0.00 0.00 4.00
2727 4565 6.267928 GCAGGAAGAGTATTATAAGAGACCCA 59.732 42.308 0.00 0.00 0.00 4.51
2728 4566 6.570764 CGCAGGAAGAGTATTATAAGAGACCC 60.571 46.154 0.00 0.00 0.00 4.46
2729 4567 6.383415 CGCAGGAAGAGTATTATAAGAGACC 58.617 44.000 0.00 0.00 0.00 3.85
2770 4608 5.834742 ACTCTGAAGTCTCTATGCATCATCT 59.165 40.000 0.19 0.00 0.00 2.90
2850 4728 0.038166 TGTTAGCTGGGAAGGGCAAG 59.962 55.000 0.00 0.00 0.00 4.01
3023 4926 2.096248 GATTTGGGCGGACAATTACCA 58.904 47.619 0.00 0.00 0.00 3.25
3067 4970 1.754226 GATCTCTCACCTGTCCTCACC 59.246 57.143 0.00 0.00 0.00 4.02
3126 5029 1.275291 CCGAGCTCAACCTCTGGTTTA 59.725 52.381 15.40 0.00 44.33 2.01
3322 5239 1.004440 GACCTGGCAGTGTGAGGAC 60.004 63.158 14.43 6.47 0.00 3.85
3355 5272 0.676466 CCGGCCAGCACTACAATGAA 60.676 55.000 2.24 0.00 0.00 2.57
3458 5375 3.998672 GGCCGTCTCCGTTCCACA 61.999 66.667 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.