Multiple sequence alignment - TraesCS1A01G251800

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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 TraesCS1A01G251800 chr1A 100.000 3176 0 0 1 3176 443658444 443661619 0.000000e+00 5866.0
1 TraesCS1A01G251800 chr1A 76.506 166 25 11 2377 2529 58202795 58202959 9.450000e-11 78.7
2 TraesCS1A01G251800 chr1A 100.000 36 0 0 3138 3173 443702716 443702751 2.040000e-07 67.6
3 TraesCS1A01G251800 chr1B 91.101 1944 115 25 519 2434 462805579 462803666 0.000000e+00 2579.0
4 TraesCS1A01G251800 chr1B 96.078 1428 44 3 953 2380 462984185 462982770 0.000000e+00 2316.0
5 TraesCS1A01G251800 chr1B 93.750 528 29 4 1 524 462808071 462807544 0.000000e+00 789.0
6 TraesCS1A01G251800 chr1B 93.561 528 23 6 2656 3174 462803619 462803094 0.000000e+00 776.0
7 TraesCS1A01G251800 chr1B 88.356 146 11 1 2384 2529 491543352 491543491 1.510000e-38 171.0
8 TraesCS1A01G251800 chr1B 82.781 151 21 4 2384 2530 675978917 675979066 2.570000e-26 130.0
9 TraesCS1A01G251800 chr1B 82.895 152 11 6 2771 2915 462982296 462982153 4.300000e-24 122.0
10 TraesCS1A01G251800 chr1D 95.543 1436 44 4 953 2380 344136706 344135283 0.000000e+00 2279.0
11 TraesCS1A01G251800 chr1D 94.584 517 28 0 2658 3174 344134176 344133660 0.000000e+00 800.0
12 TraesCS1A01G251800 chr1D 83.871 372 50 5 2805 3174 344134864 344134501 2.350000e-91 346.0
13 TraesCS1A01G251800 chr1D 91.954 87 6 1 2572 2657 344135206 344135120 1.550000e-23 121.0
14 TraesCS1A01G251800 chr1D 80.952 147 18 7 2384 2530 234907464 234907328 1.200000e-19 108.0
15 TraesCS1A01G251800 chr7D 87.333 150 18 1 2384 2532 509926311 509926460 1.510000e-38 171.0
16 TraesCS1A01G251800 chr7D 82.317 164 17 6 2378 2529 537285587 537285750 7.150000e-27 132.0
17 TraesCS1A01G251800 chr3D 87.755 147 17 1 2384 2529 307237210 307237064 1.510000e-38 171.0
18 TraesCS1A01G251800 chr7A 85.616 146 14 4 2385 2529 52313530 52313669 2.550000e-31 147.0
19 TraesCS1A01G251800 chr7A 84.354 147 19 4 2384 2529 6862658 6862515 1.190000e-29 141.0
20 TraesCS1A01G251800 chr2B 85.034 147 16 4 2391 2533 87674872 87674728 9.180000e-31 145.0
21 TraesCS1A01G251800 chr2B 83.544 158 14 5 2384 2529 453265605 453265448 1.540000e-28 137.0
22 TraesCS1A01G251800 chr4B 84.667 150 16 6 2384 2529 191224178 191224032 3.300000e-30 143.0
23 TraesCS1A01G251800 chr4A 83.030 165 16 6 2378 2530 450788270 450788434 4.270000e-29 139.0
24 TraesCS1A01G251800 chr4A 83.221 149 19 4 2385 2529 511022803 511022949 7.150000e-27 132.0
25 TraesCS1A01G251800 chr4D 80.503 159 15 7 2373 2518 9208787 9208942 1.200000e-19 108.0
26 TraesCS1A01G251800 chr2A 79.355 155 18 7 2380 2520 652565090 652564936 2.610000e-16 97.1
27 TraesCS1A01G251800 chr6D 90.741 54 5 0 2370 2423 455971466 455971519 4.390000e-09 73.1
28 TraesCS1A01G251800 chr5D 87.931 58 7 0 2378 2435 216151435 216151492 5.680000e-08 69.4


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 TraesCS1A01G251800 chr1A 443658444 443661619 3175 False 5866.000000 5866 100.0000 1 3176 1 chr1A.!!$F2 3175
1 TraesCS1A01G251800 chr1B 462803094 462808071 4977 True 1381.333333 2579 92.8040 1 3174 3 chr1B.!!$R1 3173
2 TraesCS1A01G251800 chr1B 462982153 462984185 2032 True 1219.000000 2316 89.4865 953 2915 2 chr1B.!!$R2 1962
3 TraesCS1A01G251800 chr1D 344133660 344136706 3046 True 886.500000 2279 91.4880 953 3174 4 chr1D.!!$R2 2221

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
755 2730 0.030235 GGACGAACAAGCCCAACAAC 59.970 55.000 0.00 0.0 0.00 3.32 F
1404 3415 1.278413 GACTTTTTCGCCTCCCTAGGT 59.722 52.381 8.29 0.0 45.64 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 3734 0.970937 TAGAGGAAGCGTGGGTCCAG 60.971 60.0 0.0 0.0 36.28 3.86 R
2870 5892 0.041090 ACCTTGCCACAAATAGGGGG 59.959 55.0 0.0 0.0 42.99 5.40 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
21 22 2.178890 CCAATGAGGCGAGCAGAGC 61.179 63.158 0.00 0.00 0.00 4.09
53 54 6.230472 AGGCTTCTTCTTCTCTTTCTTCTTC 58.770 40.000 0.00 0.00 0.00 2.87
54 55 5.411361 GGCTTCTTCTTCTCTTTCTTCTTCC 59.589 44.000 0.00 0.00 0.00 3.46
67 68 1.801178 CTTCTTCCACTTCTTCACCGC 59.199 52.381 0.00 0.00 0.00 5.68
130 131 4.302622 GGCTATGCCTCCTCCTCA 57.697 61.111 0.73 0.00 46.69 3.86
143 144 2.846827 TCCTCCTCATTCCCTTTCTTCC 59.153 50.000 0.00 0.00 0.00 3.46
157 158 2.859165 TCTTCCGCTTCTTCACCAAT 57.141 45.000 0.00 0.00 0.00 3.16
158 159 2.426522 TCTTCCGCTTCTTCACCAATG 58.573 47.619 0.00 0.00 0.00 2.82
160 161 0.400213 TCCGCTTCTTCACCAATGGT 59.600 50.000 0.00 0.00 35.62 3.55
162 163 1.068333 CCGCTTCTTCACCAATGGTTG 60.068 52.381 0.16 0.00 31.02 3.77
175 180 4.048470 GGTTGTGCCTCCTCCCCC 62.048 72.222 0.00 0.00 0.00 5.40
193 198 4.508065 CCCCCTCCATCTTCACCT 57.492 61.111 0.00 0.00 0.00 4.00
206 211 0.320374 TTCACCTGGACATCCACGTC 59.680 55.000 0.00 0.00 42.01 4.34
245 250 5.091261 TCAATTAGCTTCTCCTTCACTCC 57.909 43.478 0.00 0.00 0.00 3.85
253 258 1.166129 CTCCTTCACTCCTTCGACGA 58.834 55.000 0.00 0.00 0.00 4.20
323 328 2.036475 CCTCCTCGTCGATGGAAATGAT 59.964 50.000 4.48 0.00 31.23 2.45
326 331 3.255888 TCCTCGTCGATGGAAATGATAGG 59.744 47.826 4.48 1.65 0.00 2.57
371 376 0.324645 GGGACTTGGTACTCGGGGTA 60.325 60.000 0.00 0.00 0.00 3.69
404 409 1.663702 CGACGACCTTGACCACCAC 60.664 63.158 0.00 0.00 0.00 4.16
410 415 3.357079 CTTGACCACCACGCCTGC 61.357 66.667 0.00 0.00 0.00 4.85
428 433 1.290324 CATCCGCTGGATCTACCGG 59.710 63.158 6.49 6.49 40.98 5.28
474 479 1.125093 TGATCCACCGGTTCCACTGT 61.125 55.000 2.97 0.00 0.00 3.55
486 491 2.444624 CCACTGTCGAACATCGCCG 61.445 63.158 0.00 0.00 40.21 6.46
505 510 1.307097 GAAGATGGACTCCAGCATGC 58.693 55.000 15.72 10.51 43.12 4.06
550 2525 4.491675 AGGTGAGATGAGAGAGGCAATAT 58.508 43.478 0.00 0.00 0.00 1.28
555 2530 6.017830 TGAGATGAGAGAGGCAATATGAGAT 58.982 40.000 0.00 0.00 0.00 2.75
579 2554 1.630878 CTGGAGGCTAGGTGGTTTTCT 59.369 52.381 0.00 0.00 0.00 2.52
610 2585 3.499737 GCTCGTGAATGCGGTGGG 61.500 66.667 0.00 0.00 0.00 4.61
618 2593 3.310860 AATGCGGTGGGAGGACGAC 62.311 63.158 0.00 0.00 0.00 4.34
623 2598 3.052082 GTGGGAGGACGACGACGA 61.052 66.667 15.32 0.00 42.66 4.20
632 2607 0.039708 GACGACGACGAGGGTTTTCT 60.040 55.000 15.32 0.00 42.66 2.52
700 2675 2.434884 ACAACCAGCGGCGATCTG 60.435 61.111 12.98 9.57 0.00 2.90
719 2694 0.864797 GCTACTTAGCGAACGACCCG 60.865 60.000 0.00 0.00 39.82 5.28
737 2712 0.249322 CGGTAGGACAATGCTACGGG 60.249 60.000 7.04 0.00 41.48 5.28
755 2730 0.030235 GGACGAACAAGCCCAACAAC 59.970 55.000 0.00 0.00 0.00 3.32
766 2741 2.010043 GCCCAACAACGTATGTCCGAT 61.010 52.381 0.00 0.00 42.99 4.18
768 2743 1.931172 CCAACAACGTATGTCCGATCC 59.069 52.381 0.00 0.00 42.99 3.36
788 2790 3.414700 GTCGCTGTTGTCGGCCTG 61.415 66.667 0.00 0.00 42.47 4.85
857 2859 3.366476 CCGGTGTTTTTGTCACTGTCAAA 60.366 43.478 0.00 0.00 39.64 2.69
858 2860 4.420168 CGGTGTTTTTGTCACTGTCAAAT 58.580 39.130 2.83 0.00 37.40 2.32
880 2882 8.533153 CAAATTTTTGGTTCAATGCAAAATGTC 58.467 29.630 0.00 0.00 34.59 3.06
884 2886 4.619973 TGGTTCAATGCAAAATGTCACTC 58.380 39.130 0.00 0.00 0.00 3.51
891 2893 6.581919 TCAATGCAAAATGTCACTCGTAAATG 59.418 34.615 0.00 0.00 0.00 2.32
896 2898 3.695830 ATGTCACTCGTAAATGGTGGT 57.304 42.857 0.00 0.00 0.00 4.16
932 2934 2.487762 CGTGGTGGCTGTGTGATTTTAT 59.512 45.455 0.00 0.00 0.00 1.40
933 2935 3.426159 CGTGGTGGCTGTGTGATTTTATC 60.426 47.826 0.00 0.00 0.00 1.75
934 2936 2.746904 TGGTGGCTGTGTGATTTTATCG 59.253 45.455 0.00 0.00 0.00 2.92
935 2937 2.747446 GGTGGCTGTGTGATTTTATCGT 59.253 45.455 0.00 0.00 0.00 3.73
936 2938 3.426159 GGTGGCTGTGTGATTTTATCGTG 60.426 47.826 0.00 0.00 0.00 4.35
937 2939 3.435327 GTGGCTGTGTGATTTTATCGTGA 59.565 43.478 0.00 0.00 0.00 4.35
938 2940 3.435327 TGGCTGTGTGATTTTATCGTGAC 59.565 43.478 0.00 0.00 0.00 3.67
939 2941 3.435327 GGCTGTGTGATTTTATCGTGACA 59.565 43.478 0.00 0.00 0.00 3.58
940 2942 4.394795 GCTGTGTGATTTTATCGTGACAC 58.605 43.478 0.00 0.00 35.48 3.67
941 2943 4.084066 GCTGTGTGATTTTATCGTGACACA 60.084 41.667 6.37 0.00 39.72 3.72
942 2944 5.559991 GCTGTGTGATTTTATCGTGACACAA 60.560 40.000 6.37 0.00 40.72 3.33
943 2945 6.552859 TGTGTGATTTTATCGTGACACAAT 57.447 33.333 6.37 0.00 39.34 2.71
944 2946 6.369799 TGTGTGATTTTATCGTGACACAATG 58.630 36.000 6.37 0.00 39.34 2.82
945 2947 6.017523 TGTGTGATTTTATCGTGACACAATGT 60.018 34.615 6.37 0.00 39.34 2.71
1120 3131 2.055042 CCTCTCGCCCACTGCTACT 61.055 63.158 0.00 0.00 38.05 2.57
1404 3415 1.278413 GACTTTTTCGCCTCCCTAGGT 59.722 52.381 8.29 0.00 45.64 3.08
1670 3681 3.138375 CGTGCTCTTGTCGTCACG 58.862 61.111 0.00 0.00 44.62 4.35
1723 3734 2.588877 CGATGGGCATGTCCGTCC 60.589 66.667 28.71 13.88 39.14 4.79
1873 3884 2.287915 CAGCCCACGATATTCCTTTTCG 59.712 50.000 0.00 0.00 38.76 3.46
1998 4009 3.321648 TGCATCCTGCCGAGGTGT 61.322 61.111 0.00 0.00 44.23 4.16
2244 4261 7.168219 TCTAGTGCCAATGTTAAAGATCAAGT 58.832 34.615 0.00 0.00 0.00 3.16
2245 4262 6.259550 AGTGCCAATGTTAAAGATCAAGTC 57.740 37.500 0.00 0.00 0.00 3.01
2246 4263 5.769662 AGTGCCAATGTTAAAGATCAAGTCA 59.230 36.000 0.00 0.00 0.00 3.41
2247 4264 6.435277 AGTGCCAATGTTAAAGATCAAGTCAT 59.565 34.615 0.00 0.00 0.00 3.06
2248 4265 6.529125 GTGCCAATGTTAAAGATCAAGTCATG 59.471 38.462 0.00 0.00 0.00 3.07
2249 4266 6.433716 TGCCAATGTTAAAGATCAAGTCATGA 59.566 34.615 0.00 0.00 43.67 3.07
2317 4334 2.799126 TTGGTAGCCCATGTTACTGG 57.201 50.000 0.00 0.00 41.49 4.00
2334 4351 6.373216 TGTTACTGGGTATCAACTACATTTGC 59.627 38.462 0.00 0.00 31.44 3.68
2340 4357 6.266558 TGGGTATCAACTACATTTGCAGTTTT 59.733 34.615 0.00 0.00 32.72 2.43
2380 4397 3.251004 GTCCTGCGGCCTATTAAAATCTG 59.749 47.826 0.00 0.00 0.00 2.90
2381 4398 2.030805 CCTGCGGCCTATTAAAATCTGC 60.031 50.000 0.00 0.00 0.00 4.26
2389 4417 3.140144 CCTATTAAAATCTGCCCCCTCCA 59.860 47.826 0.00 0.00 0.00 3.86
2406 4434 5.952347 CCCCTCCATTTCTAAATATAAGCCC 59.048 44.000 0.00 0.00 0.00 5.19
2469 4497 7.986085 AGTGTGTAGATTCACTTATTTTGCT 57.014 32.000 0.00 0.00 41.33 3.91
2472 4500 6.092122 TGTGTAGATTCACTTATTTTGCTCCG 59.908 38.462 0.00 0.00 38.90 4.63
2475 4503 7.985184 TGTAGATTCACTTATTTTGCTCCGTAT 59.015 33.333 0.00 0.00 0.00 3.06
2476 4504 7.251704 AGATTCACTTATTTTGCTCCGTATG 57.748 36.000 0.00 0.00 0.00 2.39
2479 4507 7.534085 TTCACTTATTTTGCTCCGTATGTAG 57.466 36.000 0.00 0.00 0.00 2.74
2481 4509 6.755141 TCACTTATTTTGCTCCGTATGTAGTC 59.245 38.462 0.00 0.00 0.00 2.59
2484 4512 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
2490 4518 5.303333 TGCTCCGTATGTAGTCCATATTTGA 59.697 40.000 0.00 0.00 38.29 2.69
2492 4520 6.874134 GCTCCGTATGTAGTCCATATTTGAAT 59.126 38.462 0.00 0.00 38.29 2.57
2493 4521 7.063544 GCTCCGTATGTAGTCCATATTTGAATC 59.936 40.741 0.00 0.00 38.29 2.52
2494 4522 8.190326 TCCGTATGTAGTCCATATTTGAATCT 57.810 34.615 0.00 0.00 38.29 2.40
2495 4523 8.304596 TCCGTATGTAGTCCATATTTGAATCTC 58.695 37.037 0.00 0.00 38.29 2.75
2496 4524 8.307483 CCGTATGTAGTCCATATTTGAATCTCT 58.693 37.037 0.00 0.00 38.29 3.10
2504 4532 9.692325 AGTCCATATTTGAATCTCTAAAAAGCT 57.308 29.630 0.00 0.00 0.00 3.74
2534 4562 6.945636 TTAGAAATGGAGGGAGTAGAAACA 57.054 37.500 0.00 0.00 0.00 2.83
2535 4563 7.510675 TTAGAAATGGAGGGAGTAGAAACAT 57.489 36.000 0.00 0.00 0.00 2.71
2536 4564 8.618240 TTAGAAATGGAGGGAGTAGAAACATA 57.382 34.615 0.00 0.00 0.00 2.29
2537 4565 7.130681 AGAAATGGAGGGAGTAGAAACATAG 57.869 40.000 0.00 0.00 0.00 2.23
2550 4578 5.391312 AGAAACATAGGATGGTTTGTTGC 57.609 39.130 0.00 0.00 41.00 4.17
2552 4580 6.245408 AGAAACATAGGATGGTTTGTTGCTA 58.755 36.000 0.00 0.00 41.00 3.49
2554 4582 6.699575 AACATAGGATGGTTTGTTGCTATC 57.300 37.500 0.00 0.00 31.45 2.08
2555 4583 5.133221 ACATAGGATGGTTTGTTGCTATCC 58.867 41.667 0.00 0.00 42.21 2.59
2556 4584 2.643551 AGGATGGTTTGTTGCTATCCG 58.356 47.619 0.00 0.00 45.18 4.18
2557 4585 2.238646 AGGATGGTTTGTTGCTATCCGA 59.761 45.455 0.00 0.00 45.18 4.55
2558 4586 2.614057 GGATGGTTTGTTGCTATCCGAG 59.386 50.000 0.00 0.00 34.98 4.63
2559 4587 2.851263 TGGTTTGTTGCTATCCGAGT 57.149 45.000 0.00 0.00 0.00 4.18
2560 4588 3.134574 TGGTTTGTTGCTATCCGAGTT 57.865 42.857 0.00 0.00 0.00 3.01
2561 4589 3.482436 TGGTTTGTTGCTATCCGAGTTT 58.518 40.909 0.00 0.00 0.00 2.66
2562 4590 3.500680 TGGTTTGTTGCTATCCGAGTTTC 59.499 43.478 0.00 0.00 0.00 2.78
2563 4591 3.751698 GGTTTGTTGCTATCCGAGTTTCT 59.248 43.478 0.00 0.00 0.00 2.52
2564 4592 4.215613 GGTTTGTTGCTATCCGAGTTTCTT 59.784 41.667 0.00 0.00 0.00 2.52
2566 4594 4.265904 TGTTGCTATCCGAGTTTCTTGA 57.734 40.909 0.00 0.00 0.00 3.02
2567 4595 4.832248 TGTTGCTATCCGAGTTTCTTGAT 58.168 39.130 0.00 0.00 0.00 2.57
2568 4596 4.870426 TGTTGCTATCCGAGTTTCTTGATC 59.130 41.667 0.00 0.00 0.00 2.92
2570 4598 4.686972 TGCTATCCGAGTTTCTTGATCAG 58.313 43.478 0.00 0.00 0.00 2.90
2592 4651 7.676004 TCAGTTGATCTAGTATGTTGAACCAA 58.324 34.615 0.00 0.00 0.00 3.67
2607 4666 6.752815 TGTTGAACCAATTCTTTTAACCGTTC 59.247 34.615 0.00 0.00 35.69 3.95
2608 4667 6.452494 TGAACCAATTCTTTTAACCGTTCA 57.548 33.333 0.00 0.00 36.83 3.18
2627 4687 8.686334 ACCGTTCATGCTTTTAGATTGATTATT 58.314 29.630 0.00 0.00 0.00 1.40
2671 4790 5.735285 AACATCACTCATCTGAAGTCTCA 57.265 39.130 0.00 0.00 0.00 3.27
2731 5753 4.815269 AGTAGAGAACTTGCACTTGCTAG 58.185 43.478 10.59 10.59 46.63 3.42
2870 5892 5.007682 GTCTATCCTAGAGAGACATGGACC 58.992 50.000 13.10 0.00 46.33 4.46
2906 5933 5.221165 GGCAAGGTCTATTCTAGAGAGACAC 60.221 48.000 26.16 19.07 41.18 3.67
2942 5969 4.154942 ACAATGATCTTTGCCCTTGAAGT 58.845 39.130 18.52 0.00 0.00 3.01
2951 5978 2.517959 TGCCCTTGAAGTTTGATGGAG 58.482 47.619 0.00 0.00 0.00 3.86
2957 5984 4.457257 CCTTGAAGTTTGATGGAGTTCCTC 59.543 45.833 0.00 0.00 36.82 3.71
2970 5997 3.823304 GGAGTTCCTCTCAGTTTGCATTT 59.177 43.478 0.00 0.00 44.40 2.32
2977 6007 7.149569 TCCTCTCAGTTTGCATTTTATCAAG 57.850 36.000 0.00 0.00 0.00 3.02
2993 6023 2.487934 TCAAGTGCTTCAGACTTCAGC 58.512 47.619 0.00 0.00 31.05 4.26
3034 6064 6.837471 AATATAGAAGGGTAAGCTAGTCCG 57.163 41.667 0.00 0.00 0.00 4.79
3035 6065 2.822707 AGAAGGGTAAGCTAGTCCGA 57.177 50.000 0.00 0.00 0.00 4.55
3055 6085 0.968405 AACCGGAATTGTTGCATGCT 59.032 45.000 20.33 0.00 0.00 3.79
3095 6126 0.895530 TTCTCTTGTTCCGGATCGCT 59.104 50.000 4.15 0.00 0.00 4.93
3136 6167 9.162764 GTCTGTATGTTAATGTTGTACCTGATT 57.837 33.333 0.00 0.00 0.00 2.57
3174 6205 6.763355 AGCAAGAATCAGAGAGTTTTGAGTA 58.237 36.000 2.55 0.00 0.00 2.59
3175 6206 7.393216 AGCAAGAATCAGAGAGTTTTGAGTAT 58.607 34.615 2.55 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.945398 GAAGCCTCTACGCCGCTCTG 62.945 65.000 0.00 0.00 30.92 3.35
21 22 0.173708 AAGAAGAAGCCTCTACGCCG 59.826 55.000 0.00 0.00 0.00 6.46
26 27 6.723977 AGAAGAAAGAGAAGAAGAAGCCTCTA 59.276 38.462 0.00 0.00 35.16 2.43
53 54 2.027625 GTCGGCGGTGAAGAAGTGG 61.028 63.158 7.21 0.00 0.00 4.00
54 55 0.242825 TAGTCGGCGGTGAAGAAGTG 59.757 55.000 7.21 0.00 0.00 3.16
67 68 0.676736 GAAGGAGGAGGCATAGTCGG 59.323 60.000 0.00 0.00 0.00 4.79
130 131 3.244911 TGAAGAAGCGGAAGAAAGGGAAT 60.245 43.478 0.00 0.00 0.00 3.01
143 144 1.608590 ACAACCATTGGTGAAGAAGCG 59.391 47.619 9.62 0.00 35.34 4.68
157 158 3.256960 GGGGAGGAGGCACAACCA 61.257 66.667 0.00 0.00 43.14 3.67
158 159 4.048470 GGGGGAGGAGGCACAACC 62.048 72.222 0.00 0.00 39.61 3.77
179 184 1.279496 TGTCCAGGTGAAGATGGAGG 58.721 55.000 0.00 0.00 46.09 4.30
193 198 4.077184 GGCCGACGTGGATGTCCA 62.077 66.667 0.00 0.00 45.30 4.02
206 211 0.597568 TGATGTTGAGCTTTTGGCCG 59.402 50.000 0.00 0.00 43.05 6.13
245 250 2.805353 CACGGGCTGTCGTCGAAG 60.805 66.667 0.00 0.00 41.86 3.79
275 280 1.001641 GAGGTGCAGGTCATGGCTT 60.002 57.895 0.00 0.00 0.00 4.35
323 328 0.987613 TCCCCATGCTGATGTGCCTA 60.988 55.000 0.00 0.00 0.00 3.93
326 331 1.610522 GTAATCCCCATGCTGATGTGC 59.389 52.381 0.00 0.00 0.00 4.57
371 376 2.910479 TCGTGCCAGACCGTGTCT 60.910 61.111 1.23 1.23 44.44 3.41
404 409 4.923942 ATCCAGCGGATGCAGGCG 62.924 66.667 8.94 0.00 46.71 5.52
410 415 4.974792 CGGTAGATCCAGCGGATG 57.025 61.111 13.68 0.00 43.27 3.51
416 421 1.473434 GCAGGTTTCCGGTAGATCCAG 60.473 57.143 0.00 0.00 35.57 3.86
424 429 1.698506 TTGAAATGCAGGTTTCCGGT 58.301 45.000 0.00 0.00 37.31 5.28
428 433 2.416747 GCCCTTTGAAATGCAGGTTTC 58.583 47.619 5.94 5.94 38.32 2.78
474 479 0.527600 CCATCTTCGGCGATGTTCGA 60.528 55.000 20.25 8.78 43.74 3.71
486 491 1.307097 GCATGCTGGAGTCCATCTTC 58.693 55.000 13.56 3.24 30.82 2.87
505 510 1.871676 CATTGCCATCATCGTCTCCTG 59.128 52.381 0.00 0.00 0.00 3.86
550 2525 1.203112 CCTAGCCTCCAGCCTATCTCA 60.203 57.143 0.00 0.00 45.47 3.27
555 2530 1.075226 CCACCTAGCCTCCAGCCTA 60.075 63.158 0.00 0.00 45.47 3.93
567 2542 1.870580 CGTCGCACAGAAAACCACCTA 60.871 52.381 0.00 0.00 0.00 3.08
568 2543 1.157870 CGTCGCACAGAAAACCACCT 61.158 55.000 0.00 0.00 0.00 4.00
610 2585 1.860484 AAACCCTCGTCGTCGTCCTC 61.860 60.000 1.33 0.00 38.33 3.71
618 2593 2.486982 TGTCTCTAGAAAACCCTCGTCG 59.513 50.000 0.00 0.00 0.00 5.12
623 2598 3.803340 TCCCATGTCTCTAGAAAACCCT 58.197 45.455 0.00 0.00 0.00 4.34
632 2607 2.094390 CGTTCGGTTTCCCATGTCTCTA 60.094 50.000 0.00 0.00 0.00 2.43
662 2637 2.104451 TGGTGGCCGTTCACTACTTAAA 59.896 45.455 0.00 0.00 37.75 1.52
700 2675 0.864797 CGGGTCGTTCGCTAAGTAGC 60.865 60.000 0.00 0.00 45.62 3.58
709 2684 1.865788 TTGTCCTACCGGGTCGTTCG 61.866 60.000 6.32 0.00 36.25 3.95
719 2694 1.117150 TCCCGTAGCATTGTCCTACC 58.883 55.000 0.00 0.00 33.30 3.18
737 2712 0.316689 CGTTGTTGGGCTTGTTCGTC 60.317 55.000 0.00 0.00 0.00 4.20
755 2730 1.285023 GACGGGGATCGGACATACG 59.715 63.158 0.00 0.00 44.45 3.06
766 2741 4.351938 CGACAACAGCGACGGGGA 62.352 66.667 0.00 0.00 0.00 4.81
786 2788 2.279120 GATCCCTCGCAGTCGCAG 60.279 66.667 0.00 0.00 38.40 5.18
787 2789 3.068064 TGATCCCTCGCAGTCGCA 61.068 61.111 0.00 0.00 38.40 5.10
788 2790 2.279120 CTGATCCCTCGCAGTCGC 60.279 66.667 0.00 0.00 35.26 5.19
789 2791 3.201494 ACTGATCCCTCGCAGTCG 58.799 61.111 0.00 0.00 41.21 4.18
832 2834 1.474879 CAGTGACAAAAACACCGGGTT 59.525 47.619 6.32 4.20 42.98 4.11
857 2859 7.067251 AGTGACATTTTGCATTGAACCAAAAAT 59.933 29.630 8.86 0.54 42.22 1.82
858 2860 6.373774 AGTGACATTTTGCATTGAACCAAAAA 59.626 30.769 8.86 0.00 42.22 1.94
880 2882 4.628333 ACGATAAACCACCATTTACGAGTG 59.372 41.667 0.00 0.00 0.00 3.51
884 2886 4.389382 TGTCACGATAAACCACCATTTACG 59.611 41.667 0.00 0.00 0.00 3.18
891 2893 2.096614 CGTTGTGTCACGATAAACCACC 60.097 50.000 0.00 0.00 43.15 4.61
896 2898 2.540516 CACCACGTTGTGTCACGATAAA 59.459 45.455 11.45 0.00 43.15 1.40
919 2921 5.590104 TGTGTCACGATAAAATCACACAG 57.410 39.130 7.30 0.00 39.28 3.66
937 2939 0.034896 GGGGACGAGTGACATTGTGT 59.965 55.000 0.00 0.00 0.00 3.72
938 2940 0.673644 GGGGGACGAGTGACATTGTG 60.674 60.000 0.00 0.00 0.00 3.33
939 2941 1.677552 GGGGGACGAGTGACATTGT 59.322 57.895 0.00 0.00 0.00 2.71
940 2942 4.617875 GGGGGACGAGTGACATTG 57.382 61.111 0.00 0.00 0.00 2.82
1226 3237 0.247736 GATGCGGAGGTGTTGAGAGT 59.752 55.000 0.00 0.00 0.00 3.24
1404 3415 3.606886 GAGCTTGTGGGTCTCGAAA 57.393 52.632 0.00 0.00 39.18 3.46
1723 3734 0.970937 TAGAGGAAGCGTGGGTCCAG 60.971 60.000 0.00 0.00 36.28 3.86
1873 3884 3.198068 TCTTGTTTATGCTCTCATCGGC 58.802 45.455 0.00 0.00 34.22 5.54
1998 4009 2.179547 CAACACACTCAGCACGGCA 61.180 57.895 0.00 0.00 0.00 5.69
2340 4357 5.049954 GCAGGACGTAAAAATGACAGTTGTA 60.050 40.000 0.00 0.00 0.00 2.41
2380 4397 5.419155 GCTTATATTTAGAAATGGAGGGGGC 59.581 44.000 0.00 0.00 0.00 5.80
2381 4398 5.952347 GGCTTATATTTAGAAATGGAGGGGG 59.048 44.000 0.00 0.00 0.00 5.40
2443 4471 9.502091 AGCAAAATAAGTGAATCTACACACTAA 57.498 29.630 0.00 0.00 44.94 2.24
2444 4472 9.151471 GAGCAAAATAAGTGAATCTACACACTA 57.849 33.333 0.00 0.00 44.94 2.74
2446 4474 7.244192 GGAGCAAAATAAGTGAATCTACACAC 58.756 38.462 0.00 0.00 42.45 3.82
2447 4475 6.092122 CGGAGCAAAATAAGTGAATCTACACA 59.908 38.462 0.00 0.00 42.45 3.72
2448 4476 6.092259 ACGGAGCAAAATAAGTGAATCTACAC 59.908 38.462 0.00 0.00 40.60 2.90
2449 4477 6.170506 ACGGAGCAAAATAAGTGAATCTACA 58.829 36.000 0.00 0.00 0.00 2.74
2450 4478 6.663944 ACGGAGCAAAATAAGTGAATCTAC 57.336 37.500 0.00 0.00 0.00 2.59
2451 4479 7.985184 ACATACGGAGCAAAATAAGTGAATCTA 59.015 33.333 0.00 0.00 0.00 1.98
2452 4480 6.823689 ACATACGGAGCAAAATAAGTGAATCT 59.176 34.615 0.00 0.00 0.00 2.40
2453 4481 7.016361 ACATACGGAGCAAAATAAGTGAATC 57.984 36.000 0.00 0.00 0.00 2.52
2454 4482 7.769044 ACTACATACGGAGCAAAATAAGTGAAT 59.231 33.333 0.00 0.00 0.00 2.57
2455 4483 7.101054 ACTACATACGGAGCAAAATAAGTGAA 58.899 34.615 0.00 0.00 0.00 3.18
2456 4484 6.636705 ACTACATACGGAGCAAAATAAGTGA 58.363 36.000 0.00 0.00 0.00 3.41
2457 4485 6.018994 GGACTACATACGGAGCAAAATAAGTG 60.019 42.308 0.00 0.00 0.00 3.16
2458 4486 6.047231 GGACTACATACGGAGCAAAATAAGT 58.953 40.000 0.00 0.00 0.00 2.24
2459 4487 6.046593 TGGACTACATACGGAGCAAAATAAG 58.953 40.000 0.00 0.00 0.00 1.73
2460 4488 5.979993 TGGACTACATACGGAGCAAAATAA 58.020 37.500 0.00 0.00 0.00 1.40
2461 4489 5.601583 TGGACTACATACGGAGCAAAATA 57.398 39.130 0.00 0.00 0.00 1.40
2463 4491 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
2468 4496 8.307483 AGATTCAAATATGGACTACATACGGAG 58.693 37.037 0.00 0.00 44.41 4.63
2469 4497 8.190326 AGATTCAAATATGGACTACATACGGA 57.810 34.615 0.00 0.00 44.41 4.69
2499 4527 9.936329 TCCCTCCATTTCTAAATATAAAGCTTT 57.064 29.630 17.30 17.30 0.00 3.51
2500 4528 9.579932 CTCCCTCCATTTCTAAATATAAAGCTT 57.420 33.333 0.00 0.00 0.00 3.74
2513 4541 6.100424 CCTATGTTTCTACTCCCTCCATTTCT 59.900 42.308 0.00 0.00 0.00 2.52
2515 4543 5.970640 TCCTATGTTTCTACTCCCTCCATTT 59.029 40.000 0.00 0.00 0.00 2.32
2516 4544 5.538877 TCCTATGTTTCTACTCCCTCCATT 58.461 41.667 0.00 0.00 0.00 3.16
2518 4546 4.620086 TCCTATGTTTCTACTCCCTCCA 57.380 45.455 0.00 0.00 0.00 3.86
2529 4557 5.391312 AGCAACAAACCATCCTATGTTTC 57.609 39.130 0.00 0.00 33.97 2.78
2530 4558 6.096846 GGATAGCAACAAACCATCCTATGTTT 59.903 38.462 0.00 0.00 33.97 2.83
2531 4559 5.594317 GGATAGCAACAAACCATCCTATGTT 59.406 40.000 0.00 0.00 36.49 2.71
2532 4560 5.133221 GGATAGCAACAAACCATCCTATGT 58.867 41.667 0.00 0.00 33.74 2.29
2533 4561 4.214119 CGGATAGCAACAAACCATCCTATG 59.786 45.833 0.00 0.00 34.26 2.23
2534 4562 4.102524 TCGGATAGCAACAAACCATCCTAT 59.897 41.667 0.00 0.00 34.26 2.57
2535 4563 3.452990 TCGGATAGCAACAAACCATCCTA 59.547 43.478 0.00 0.00 34.26 2.94
2536 4564 2.238646 TCGGATAGCAACAAACCATCCT 59.761 45.455 0.00 0.00 34.26 3.24
2537 4565 2.614057 CTCGGATAGCAACAAACCATCC 59.386 50.000 0.00 0.00 33.28 3.51
2550 4578 6.333416 TCAACTGATCAAGAAACTCGGATAG 58.667 40.000 0.00 0.00 0.00 2.08
2552 4580 5.152623 TCAACTGATCAAGAAACTCGGAT 57.847 39.130 0.00 0.00 0.00 4.18
2566 4594 7.851228 TGGTTCAACATACTAGATCAACTGAT 58.149 34.615 0.00 0.00 37.51 2.90
2567 4595 7.239763 TGGTTCAACATACTAGATCAACTGA 57.760 36.000 0.00 0.00 0.00 3.41
2568 4596 7.905604 TTGGTTCAACATACTAGATCAACTG 57.094 36.000 0.00 0.00 0.00 3.16
2570 4598 9.167311 AGAATTGGTTCAACATACTAGATCAAC 57.833 33.333 0.00 0.00 36.79 3.18
2578 4637 8.079809 CGGTTAAAAGAATTGGTTCAACATACT 58.920 33.333 0.00 0.00 36.79 2.12
2586 4645 6.128929 GCATGAACGGTTAAAAGAATTGGTTC 60.129 38.462 0.00 0.00 34.62 3.62
2592 4651 8.573035 TCTAAAAGCATGAACGGTTAAAAGAAT 58.427 29.630 0.00 0.00 0.00 2.40
2627 4687 2.495669 TGTCATGCACAGAGTTATCGGA 59.504 45.455 0.00 0.00 0.00 4.55
2671 4790 9.860898 GACAGCATTATTTATTTGAAAGAACCT 57.139 29.630 0.00 0.00 0.00 3.50
2731 5753 3.319689 GCACTACATCTAGGGAGAGGAAC 59.680 52.174 0.00 0.00 36.95 3.62
2870 5892 0.041090 ACCTTGCCACAAATAGGGGG 59.959 55.000 0.00 0.00 42.99 5.40
2906 5933 5.699143 AGATCATTGTTTCAGGAATAGGGG 58.301 41.667 0.00 0.00 0.00 4.79
2951 5978 6.913170 TGATAAAATGCAAACTGAGAGGAAC 58.087 36.000 0.00 0.00 0.00 3.62
2957 5984 6.154445 AGCACTTGATAAAATGCAAACTGAG 58.846 36.000 0.00 0.00 40.63 3.35
2970 5997 4.692625 GCTGAAGTCTGAAGCACTTGATAA 59.307 41.667 2.81 0.00 34.10 1.75
2977 6007 1.889545 AAGGCTGAAGTCTGAAGCAC 58.110 50.000 8.78 0.44 38.73 4.40
3034 6064 1.726248 GCATGCAACAATTCCGGTTTC 59.274 47.619 14.21 0.00 0.00 2.78
3035 6065 1.344114 AGCATGCAACAATTCCGGTTT 59.656 42.857 21.98 0.00 0.00 3.27
3095 6126 1.206132 ACAGACCAACACACTCGTTCA 59.794 47.619 0.00 0.00 0.00 3.18
3104 6135 6.966021 ACAACATTAACATACAGACCAACAC 58.034 36.000 0.00 0.00 0.00 3.32
3106 6137 7.389607 AGGTACAACATTAACATACAGACCAAC 59.610 37.037 0.00 0.00 0.00 3.77
3136 6167 3.388552 TCTTGCTCTATCCTGTCCTCA 57.611 47.619 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.