Multiple sequence alignment - TraesCS2D01G571100

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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 TraesCS2D01G571100 chr2D 100.000 5364 0 0 1 5364 637641854 637636491 0.000000e+00 9906
1 TraesCS2D01G571100 chr2B 93.768 4220 245 9 166 4384 795055815 795051613 0.000000e+00 6320
2 TraesCS2D01G571100 chr2B 90.238 799 51 13 4421 5210 795051615 795050835 0.000000e+00 1018
3 TraesCS2D01G571100 chr2B 90.278 144 9 1 5219 5362 795050734 795050596 3.300000e-42 183
4 TraesCS2D01G571100 chr2A 89.844 4480 377 30 895 5361 762309002 762313416 0.000000e+00 5681
5 TraesCS2D01G571100 chr2A 93.289 149 9 1 14 162 762306214 762306361 9.050000e-53 219
6 TraesCS2D01G571100 chr7D 83.199 3357 465 61 1078 4392 575928466 575925167 0.000000e+00 2983
7 TraesCS2D01G571100 chr7D 83.243 2781 396 41 1079 3838 5657067 5654336 0.000000e+00 2490
8 TraesCS2D01G571100 chr7D 89.627 241 18 4 4464 4697 592269577 592269337 3.140000e-77 300
9 TraesCS2D01G571100 chr4A 82.052 3382 509 66 1078 4414 736140658 736143986 0.000000e+00 2793
10 TraesCS2D01G571100 chr4A 80.455 3341 534 78 1078 4384 736802974 736806229 0.000000e+00 2442
11 TraesCS2D01G571100 chr4A 83.229 2546 397 18 1305 3838 734576762 734579289 0.000000e+00 2309
12 TraesCS2D01G571100 chr4A 81.500 2627 409 50 1580 4186 736459168 736456599 0.000000e+00 2087
13 TraesCS2D01G571100 chr4A 83.462 1421 214 15 2067 3477 736790563 736791972 0.000000e+00 1303
14 TraesCS2D01G571100 chr4A 81.497 481 81 6 3939 4416 734579446 734579921 6.510000e-104 388
15 TraesCS2D01G571100 chr4A 81.420 479 84 4 3939 4416 735762056 735762530 2.340000e-103 387
16 TraesCS2D01G571100 chr4A 79.661 354 68 3 4065 4416 736049497 736049848 8.920000e-63 252
17 TraesCS2D01G571100 chr4A 82.209 163 24 4 258 419 736139976 736140134 9.370000e-28 135
18 TraesCS2D01G571100 chr7A 82.949 3120 449 47 1305 4394 666797662 666794596 0.000000e+00 2737
19 TraesCS2D01G571100 chr5B 82.579 2784 401 47 1078 3836 98510979 98513703 0.000000e+00 2377
20 TraesCS2D01G571100 chr5B 85.584 437 61 1 3971 4407 98513802 98514236 1.760000e-124 457


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 TraesCS2D01G571100 chr2D 637636491 637641854 5363 True 9906.0 9906 100.0000 1 5364 1 chr2D.!!$R1 5363
1 TraesCS2D01G571100 chr2B 795050596 795055815 5219 True 2507.0 6320 91.4280 166 5362 3 chr2B.!!$R1 5196
2 TraesCS2D01G571100 chr2A 762306214 762313416 7202 False 2950.0 5681 91.5665 14 5361 2 chr2A.!!$F1 5347
3 TraesCS2D01G571100 chr7D 575925167 575928466 3299 True 2983.0 2983 83.1990 1078 4392 1 chr7D.!!$R2 3314
4 TraesCS2D01G571100 chr7D 5654336 5657067 2731 True 2490.0 2490 83.2430 1079 3838 1 chr7D.!!$R1 2759
5 TraesCS2D01G571100 chr4A 736802974 736806229 3255 False 2442.0 2442 80.4550 1078 4384 1 chr4A.!!$F4 3306
6 TraesCS2D01G571100 chr4A 736456599 736459168 2569 True 2087.0 2087 81.5000 1580 4186 1 chr4A.!!$R1 2606
7 TraesCS2D01G571100 chr4A 736139976 736143986 4010 False 1464.0 2793 82.1305 258 4414 2 chr4A.!!$F6 4156
8 TraesCS2D01G571100 chr4A 734576762 734579921 3159 False 1348.5 2309 82.3630 1305 4416 2 chr4A.!!$F5 3111
9 TraesCS2D01G571100 chr4A 736790563 736791972 1409 False 1303.0 1303 83.4620 2067 3477 1 chr4A.!!$F3 1410
10 TraesCS2D01G571100 chr7A 666794596 666797662 3066 True 2737.0 2737 82.9490 1305 4394 1 chr7A.!!$R1 3089
11 TraesCS2D01G571100 chr5B 98510979 98514236 3257 False 1417.0 2377 84.0815 1078 4407 2 chr5B.!!$F1 3329

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
685 2525 0.249031 GCCCAGTTCTGCAACAACAC 60.249 55.000 10.12 0.0 34.60 3.32 F
1534 3865 0.108138 CGTGGACCTGATGGAGAACC 60.108 60.000 0.00 0.0 37.04 3.62 F
1555 3886 0.622665 CCTCTCTGGTTCCATGCCTT 59.377 55.000 0.00 0.0 0.00 4.35 F
1701 4032 0.709397 TCCATGGCCAAATCCCAAGA 59.291 50.000 10.96 0.0 35.67 3.02 F
2347 4686 0.913451 AATCCTCTCCCTGCAGCAGT 60.913 55.000 21.26 0.0 0.00 4.40 F
2675 5014 1.000163 CATCCCAACTCGGATAGGACG 60.000 57.143 0.00 0.0 40.88 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2587 4926 0.033642 GGGATGCTAAGTACCTCCGC 59.966 60.0 0.0 0.0 0.00 5.54 R
2684 5023 0.177141 TAGGTCGATTTTGCCGAGGG 59.823 55.0 0.0 0.0 36.66 4.30 R
2733 5072 1.633852 CGCAACTGCTGAGAGCTTCC 61.634 60.0 0.0 0.0 42.97 3.46 R
3645 6016 0.537188 AGTGAACTATGGGTGGCTCG 59.463 55.0 0.0 0.0 0.00 5.03 R
3776 6147 0.940126 AAGTGTGCTGCTTTCAGTCG 59.060 50.0 0.0 0.0 42.29 4.18 R
4419 6874 0.442310 CTTGTAACCACATCGCCACG 59.558 55.0 0.0 0.0 33.76 4.94 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
78 79 2.766313 TGTCGGTTGGTCATCAAGAAG 58.234 47.619 0.00 0.00 35.80 2.85
79 80 2.104111 TGTCGGTTGGTCATCAAGAAGT 59.896 45.455 0.00 0.00 35.80 3.01
83 84 3.222603 GGTTGGTCATCAAGAAGTGGTT 58.777 45.455 0.00 0.00 35.80 3.67
86 87 5.476945 GGTTGGTCATCAAGAAGTGGTTATT 59.523 40.000 0.00 0.00 35.80 1.40
106 107 9.050601 GGTTATTGAAAACAAAAACATGGATCA 57.949 29.630 0.00 0.00 0.00 2.92
217 2030 9.342308 TGATTTCATTGACTTTTCTGACTAAGT 57.658 29.630 4.53 4.53 37.31 2.24
232 2045 7.741785 TCTGACTAAGTGGGTTTTCAATCTTA 58.258 34.615 0.00 0.00 0.00 2.10
234 2047 7.514721 TGACTAAGTGGGTTTTCAATCTTAGT 58.485 34.615 12.94 12.94 45.26 2.24
244 2057 8.624776 GGGTTTTCAATCTTAGTCCATATCAAG 58.375 37.037 0.00 0.00 0.00 3.02
413 2239 6.625960 GCATCAGGATATCGCACTAGTCAATA 60.626 42.308 0.00 0.00 0.00 1.90
420 2246 7.598869 GGATATCGCACTAGTCAATATCACAAA 59.401 37.037 20.07 0.00 33.11 2.83
432 2258 8.689972 AGTCAATATCACAAATCATTTTCTCCC 58.310 33.333 0.00 0.00 0.00 4.30
493 2325 6.563398 AAAAGTTTGTTTTACTTAGCACGC 57.437 33.333 0.00 0.00 34.88 5.34
503 2335 0.800012 CTTAGCACGCGCCCTTTTTA 59.200 50.000 5.73 0.00 39.83 1.52
508 2340 0.872388 CACGCGCCCTTTTTAGAAGT 59.128 50.000 5.73 0.00 0.00 3.01
509 2341 1.265905 CACGCGCCCTTTTTAGAAGTT 59.734 47.619 5.73 0.00 0.00 2.66
511 2343 3.058777 CACGCGCCCTTTTTAGAAGTTAA 60.059 43.478 5.73 0.00 0.00 2.01
515 2347 5.963586 CGCGCCCTTTTTAGAAGTTAATTAG 59.036 40.000 0.00 0.00 0.00 1.73
596 2431 5.333299 TGAAATCATGATCAGCCTTTTGG 57.667 39.130 9.06 0.00 44.18 3.28
671 2511 0.457035 AAAATACAGCATGCGCCCAG 59.543 50.000 13.01 3.89 42.53 4.45
684 2524 1.723608 CGCCCAGTTCTGCAACAACA 61.724 55.000 10.12 0.00 34.60 3.33
685 2525 0.249031 GCCCAGTTCTGCAACAACAC 60.249 55.000 10.12 0.00 34.60 3.32
686 2526 0.385390 CCCAGTTCTGCAACAACACC 59.615 55.000 10.12 0.00 34.60 4.16
793 2633 1.673337 GGGACCCCGTTTTTCTCCG 60.673 63.158 0.00 0.00 0.00 4.63
979 2913 4.566907 GGACCACCTCCAGCTTATTTAACA 60.567 45.833 0.00 0.00 39.21 2.41
1141 3467 0.737367 CGTCGCATCCAGCTCTCAAA 60.737 55.000 0.00 0.00 42.61 2.69
1296 3625 0.673644 ATGGTACCAGCAGCACGAAC 60.674 55.000 21.41 0.00 0.00 3.95
1434 3765 2.643232 GCTCGGTAACCTGACCCGT 61.643 63.158 0.00 0.00 42.30 5.28
1443 3774 1.676635 CCTGACCCGTCTCCGTGTA 60.677 63.158 0.00 0.00 0.00 2.90
1456 3787 3.385433 TCTCCGTGTACTCAACCTTTCAA 59.615 43.478 0.00 0.00 0.00 2.69
1458 3789 3.118702 TCCGTGTACTCAACCTTTCAACA 60.119 43.478 0.00 0.00 0.00 3.33
1514 3845 2.620112 GCTGTGCATCACTTGGCGT 61.620 57.895 0.00 0.00 35.11 5.68
1526 3857 2.507110 CTTGGCGTCGTGGACCTGAT 62.507 60.000 0.00 0.00 0.00 2.90
1534 3865 0.108138 CGTGGACCTGATGGAGAACC 60.108 60.000 0.00 0.00 37.04 3.62
1555 3886 0.622665 CCTCTCTGGTTCCATGCCTT 59.377 55.000 0.00 0.00 0.00 4.35
1663 3994 1.071471 ACGTCCCTCACAAGCCTTG 59.929 57.895 2.11 2.11 0.00 3.61
1664 3995 1.371183 CGTCCCTCACAAGCCTTGA 59.629 57.895 12.25 0.00 0.00 3.02
1673 4004 4.008330 CTCACAAGCCTTGACATGAAGAT 58.992 43.478 12.25 0.00 0.00 2.40
1701 4032 0.709397 TCCATGGCCAAATCCCAAGA 59.291 50.000 10.96 0.00 35.67 3.02
1741 4072 8.154203 TGACTTCATTGACACACTTAGGATTAA 58.846 33.333 0.00 0.00 0.00 1.40
1827 4158 8.587608 ACATTTGATGTCATGGATAACAAACTT 58.412 29.630 0.00 0.00 39.92 2.66
1876 4207 8.637099 TGTTCAATATTTCTTCCATCACAAACA 58.363 29.630 0.00 0.00 0.00 2.83
1882 4213 9.787532 ATATTTCTTCCATCACAAACATAAACG 57.212 29.630 0.00 0.00 0.00 3.60
2032 4370 5.239744 TCCGCACTTAAATGTTTGCTTCTTA 59.760 36.000 0.00 0.00 32.56 2.10
2040 4378 8.865590 TTAAATGTTTGCTTCTTAGTGGAAAC 57.134 30.769 13.79 13.79 0.00 2.78
2041 4379 6.715347 AATGTTTGCTTCTTAGTGGAAACT 57.285 33.333 18.16 7.97 0.00 2.66
2042 4380 6.715347 ATGTTTGCTTCTTAGTGGAAACTT 57.285 33.333 18.16 12.82 0.00 2.66
2107 4445 5.393678 CGTTTGATGGTATTTTTGGTAGGGG 60.394 44.000 0.00 0.00 0.00 4.79
2205 4543 3.568007 TGCTAAGCCTTGACGAAAACAAT 59.432 39.130 0.00 0.00 0.00 2.71
2327 4666 6.592220 GGTTTAAGCAAGTTTCAAAACCTTGA 59.408 34.615 12.25 0.00 41.56 3.02
2347 4686 0.913451 AATCCTCTCCCTGCAGCAGT 60.913 55.000 21.26 0.00 0.00 4.40
2397 4736 2.621556 TTGGCCAAATTCCTAGCCTT 57.378 45.000 17.98 0.00 45.94 4.35
2537 4876 3.679389 CAAGCCTTGGTAATCTCACAGT 58.321 45.455 0.00 0.00 0.00 3.55
2648 4987 2.575279 ACCTCTCCAACAATGCTCTGAT 59.425 45.455 0.00 0.00 0.00 2.90
2658 4997 2.273538 ATGCTCTGATTGGCTCCATC 57.726 50.000 0.00 0.00 0.00 3.51
2664 5003 1.002069 TGATTGGCTCCATCCCAACT 58.998 50.000 0.00 0.00 44.48 3.16
2675 5014 1.000163 CATCCCAACTCGGATAGGACG 60.000 57.143 0.00 0.00 40.88 4.79
2681 5020 3.551046 CCAACTCGGATAGGACGATTGAG 60.551 52.174 0.00 0.00 39.89 3.02
2684 5023 1.337071 TCGGATAGGACGATTGAGCAC 59.663 52.381 0.00 0.00 35.12 4.40
2693 5032 1.377202 GATTGAGCACCCTCGGCAA 60.377 57.895 0.00 0.00 41.13 4.52
2733 5072 2.874701 CAAGCTATCTGGTGAAATCCCG 59.125 50.000 0.00 0.00 0.00 5.14
2826 5165 5.351458 CCAAAAGGTTTGTCTTCTTTGAGG 58.649 41.667 0.47 0.00 31.93 3.86
3097 5453 3.678806 GCATCGTCTTTGGGTCATACTCA 60.679 47.826 0.00 0.00 0.00 3.41
3264 5629 1.070758 GCAACAGAGTCCTTCTCACCA 59.929 52.381 0.00 0.00 44.98 4.17
3447 5812 2.884639 CCGGAAACTTGTCAAGGTGATT 59.115 45.455 16.85 6.27 0.00 2.57
3645 6016 5.888161 ACTGGAATATCTTCACCACCAAATC 59.112 40.000 0.00 0.00 32.70 2.17
3763 6134 2.486951 GCATACTGAAGCATGCAAGG 57.513 50.000 21.98 9.29 45.51 3.61
3776 6147 2.644992 CAAGGAAAGTGGCGGTGC 59.355 61.111 0.00 0.00 0.00 5.01
3790 6161 3.333414 GTGCGACTGAAAGCAGCA 58.667 55.556 0.00 0.00 46.26 4.41
3929 6372 5.460091 GCCAATTCAAACTGAAGAGTGAAAC 59.540 40.000 5.11 0.00 40.05 2.78
3932 6375 6.757897 ATTCAAACTGAAGAGTGAAACACA 57.242 33.333 4.75 0.00 40.05 3.72
3965 6409 7.987268 ATGTGTACTCATTACGTAGTCAATG 57.013 36.000 4.59 2.91 43.93 2.82
3994 6442 8.364142 CCCTTGGTTTATATGTTTGTTTCAGAA 58.636 33.333 0.00 0.00 0.00 3.02
4048 6496 5.195940 GGTGATGTATATAGCTACGGGGTA 58.804 45.833 0.00 0.00 0.00 3.69
4088 6536 1.072965 CTGGAAGAAGGCCAACTGACT 59.927 52.381 5.01 0.00 34.07 3.41
4186 6634 0.460284 CTAGTGCAACCTACAGCGGG 60.460 60.000 0.00 0.00 37.80 6.13
4317 6770 3.950395 GAGCTGAATGCCATAAAGAAGGT 59.050 43.478 0.00 0.00 44.23 3.50
4394 6849 3.653344 GCAATGGAGTGCTACGATCATA 58.347 45.455 0.00 0.00 41.51 2.15
4419 6874 2.564721 GCTCTGTTGTTGCCACCCC 61.565 63.158 0.00 0.00 0.00 4.95
4446 6901 2.949177 TGTGGTTACAAGCATGTCCT 57.051 45.000 0.00 0.00 41.05 3.85
4591 7052 4.758773 TCATGGCATCAAGACTGTATCA 57.241 40.909 0.00 0.00 0.00 2.15
4631 7092 3.505293 GCAGATTTTCAGTTCTCCTTGCT 59.495 43.478 0.00 0.00 0.00 3.91
4675 7137 2.677836 TGAATTGCTACATCGGTTCAGC 59.322 45.455 0.00 0.00 34.56 4.26
4703 7165 7.391554 AGCTAAAGTTCAAGATAATGCTTGTCA 59.608 33.333 0.00 0.00 44.30 3.58
4768 7233 3.314357 GTGCTTCGAGTTTTTGGGTACTT 59.686 43.478 0.00 0.00 0.00 2.24
4769 7234 3.562557 TGCTTCGAGTTTTTGGGTACTTC 59.437 43.478 0.00 0.00 0.00 3.01
4770 7235 3.813724 GCTTCGAGTTTTTGGGTACTTCT 59.186 43.478 0.00 0.00 0.00 2.85
4776 7241 6.070424 TCGAGTTTTTGGGTACTTCTGGATAT 60.070 38.462 0.00 0.00 0.00 1.63
4780 7245 9.239551 AGTTTTTGGGTACTTCTGGATATAAAC 57.760 33.333 0.00 0.00 0.00 2.01
4838 7303 4.240096 GCAATCTTGGTCATTGGTTCTTG 58.760 43.478 0.00 0.00 32.66 3.02
4848 7313 3.335183 TCATTGGTTCTTGGGGGTATGAA 59.665 43.478 0.00 0.00 0.00 2.57
4870 7335 5.401531 ACTTTTTAGTCATCCAGCGACTA 57.598 39.130 0.00 0.00 41.91 2.59
4871 7336 5.411781 ACTTTTTAGTCATCCAGCGACTAG 58.588 41.667 0.00 0.00 44.53 2.57
4883 7348 2.480419 CAGCGACTAGTTGAACCCAAAG 59.520 50.000 14.70 0.00 33.49 2.77
4933 7416 1.284785 CCCCTCCCTTTGCTGATACAA 59.715 52.381 0.00 0.00 0.00 2.41
4934 7417 2.369394 CCCTCCCTTTGCTGATACAAC 58.631 52.381 0.00 0.00 0.00 3.32
4935 7418 2.290896 CCCTCCCTTTGCTGATACAACA 60.291 50.000 0.00 0.00 0.00 3.33
4936 7419 3.624777 CCTCCCTTTGCTGATACAACAT 58.375 45.455 0.00 0.00 0.00 2.71
4937 7420 3.379372 CCTCCCTTTGCTGATACAACATG 59.621 47.826 0.00 0.00 0.00 3.21
4938 7421 2.754552 TCCCTTTGCTGATACAACATGC 59.245 45.455 0.00 0.00 0.00 4.06
4939 7422 2.492881 CCCTTTGCTGATACAACATGCA 59.507 45.455 0.00 0.00 0.00 3.96
4940 7423 3.131577 CCCTTTGCTGATACAACATGCAT 59.868 43.478 0.00 0.00 33.50 3.96
4941 7424 4.338964 CCCTTTGCTGATACAACATGCATA 59.661 41.667 0.00 0.00 33.50 3.14
4942 7425 5.163530 CCCTTTGCTGATACAACATGCATAA 60.164 40.000 0.00 0.00 33.50 1.90
4943 7426 5.745294 CCTTTGCTGATACAACATGCATAAC 59.255 40.000 0.00 0.00 33.50 1.89
4944 7427 5.893897 TTGCTGATACAACATGCATAACA 57.106 34.783 0.00 0.00 33.50 2.41
4945 7428 5.893897 TGCTGATACAACATGCATAACAA 57.106 34.783 0.00 0.00 0.00 2.83
4946 7429 6.264841 TGCTGATACAACATGCATAACAAA 57.735 33.333 0.00 0.00 0.00 2.83
4947 7430 6.865411 TGCTGATACAACATGCATAACAAAT 58.135 32.000 0.00 0.00 0.00 2.32
4948 7431 7.994194 TGCTGATACAACATGCATAACAAATA 58.006 30.769 0.00 0.00 0.00 1.40
5057 7541 2.621055 CCAAAACGATCCACACCAAAGA 59.379 45.455 0.00 0.00 0.00 2.52
5058 7542 3.255642 CCAAAACGATCCACACCAAAGAT 59.744 43.478 0.00 0.00 0.00 2.40
5084 7569 5.854010 AACTTGCCTATATCTCGTCTTCA 57.146 39.130 0.00 0.00 0.00 3.02
5102 7590 4.017222 TCTTCATCATCAAATGGGTCCCTT 60.017 41.667 10.00 0.00 0.00 3.95
5176 7664 5.888724 TCCTGAATTTTTAACCGGATGCATA 59.111 36.000 9.46 0.00 0.00 3.14
5180 7668 7.831753 TGAATTTTTAACCGGATGCATAAAGA 58.168 30.769 9.46 1.68 0.00 2.52
5182 7670 5.570234 TTTTAACCGGATGCATAAAGACC 57.430 39.130 9.46 0.00 0.00 3.85
5199 7687 5.968387 AAGACCGAATGTTATAAGAAGCG 57.032 39.130 0.00 0.00 0.00 4.68
5236 7819 5.317600 AGTACTAGGTAAGGTAGGTAGGC 57.682 47.826 0.00 0.00 0.00 3.93
5300 7883 2.214181 GAGGGCACTCGAAGAAGCGA 62.214 60.000 0.00 0.00 38.32 4.93
5362 7945 5.759763 ACAAAATGAATTGTTTCTCCAAGGC 59.240 36.000 0.00 0.00 40.52 4.35
5363 7946 5.813513 AAATGAATTGTTTCTCCAAGGCT 57.186 34.783 0.00 0.00 32.78 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.652095 TTAAGTAGCGCGGGCCACT 61.652 57.895 19.21 19.21 43.16 4.00
2 3 2.125431 TTAAGTAGCGCGGGCCAC 60.125 61.111 22.01 18.32 41.24 5.01
5 6 0.096454 CTTTGTTAAGTAGCGCGGGC 59.904 55.000 17.92 17.92 40.37 6.13
6 7 0.096454 GCTTTGTTAAGTAGCGCGGG 59.904 55.000 8.83 0.00 33.74 6.13
7 8 1.076332 AGCTTTGTTAAGTAGCGCGG 58.924 50.000 8.83 0.00 39.82 6.46
8 9 3.367025 ACTTAGCTTTGTTAAGTAGCGCG 59.633 43.478 0.00 0.00 37.69 6.86
9 10 4.923264 ACTTAGCTTTGTTAAGTAGCGC 57.077 40.909 0.00 0.00 37.69 5.92
10 11 6.790825 GTGAAACTTAGCTTTGTTAAGTAGCG 59.209 38.462 0.00 0.00 38.30 4.26
11 12 7.076362 GGTGAAACTTAGCTTTGTTAAGTAGC 58.924 38.462 0.00 0.00 38.30 3.58
12 13 8.149973 TGGTGAAACTTAGCTTTGTTAAGTAG 57.850 34.615 0.00 0.00 38.30 2.57
47 48 2.093447 ACCAACCGACAAAATTGGCAAA 60.093 40.909 3.01 0.00 45.73 3.68
78 79 8.202745 TCCATGTTTTTGTTTTCAATAACCAC 57.797 30.769 10.09 0.00 44.83 4.16
79 80 8.970859 ATCCATGTTTTTGTTTTCAATAACCA 57.029 26.923 10.09 2.60 44.83 3.67
86 87 8.256605 TCTTTCTGATCCATGTTTTTGTTTTCA 58.743 29.630 0.00 0.00 0.00 2.69
162 163 6.603201 GGATCTCAGGAAACATGATGGTTTAA 59.397 38.462 0.00 0.00 40.85 1.52
163 164 6.122277 GGATCTCAGGAAACATGATGGTTTA 58.878 40.000 0.00 0.00 40.85 2.01
217 2030 7.638444 TGATATGGACTAAGATTGAAAACCCA 58.362 34.615 0.00 0.00 0.00 4.51
232 2045 7.335422 CAGCTCTACAAAAACTTGATATGGACT 59.665 37.037 0.00 0.00 0.00 3.85
234 2047 7.394016 TCAGCTCTACAAAAACTTGATATGGA 58.606 34.615 0.00 0.00 0.00 3.41
244 2057 2.911102 GCGCAATCAGCTCTACAAAAAC 59.089 45.455 0.30 0.00 42.61 2.43
413 2239 6.097839 CAGGATGGGAGAAAATGATTTGTGAT 59.902 38.462 0.00 0.00 0.00 3.06
420 2246 4.868172 TGTCAGGATGGGAGAAAATGAT 57.132 40.909 0.00 0.00 36.16 2.45
493 2325 8.943002 TCTTCTAATTAACTTCTAAAAAGGGCG 58.057 33.333 0.00 0.00 0.00 6.13
567 2399 8.473358 AAGGCTGATCATGATTTCATATTTGA 57.527 30.769 10.14 0.00 34.26 2.69
568 2400 9.542462 AAAAGGCTGATCATGATTTCATATTTG 57.458 29.630 10.14 0.00 34.26 2.32
671 2511 2.159435 ACGAAAGGTGTTGTTGCAGAAC 60.159 45.455 0.00 4.18 0.00 3.01
684 2524 1.597027 CAGTTCCGCCACGAAAGGT 60.597 57.895 0.00 0.00 0.00 3.50
685 2525 2.325082 CCAGTTCCGCCACGAAAGG 61.325 63.158 0.00 0.00 0.00 3.11
686 2526 1.291877 CTCCAGTTCCGCCACGAAAG 61.292 60.000 0.00 0.00 0.00 2.62
793 2633 5.463061 ACAGCGCAATGGCAATAATTATTTC 59.537 36.000 11.47 3.68 41.24 2.17
945 2786 0.909623 AGGTGGTCCTATGGGTTTCG 59.090 55.000 0.00 0.00 43.12 3.46
979 2913 5.241506 CCATCTGTTTGTGTATGTCCAAGTT 59.758 40.000 0.00 0.00 0.00 2.66
1141 3467 3.561143 TGGCAGTTTCATTGTTGGTAGT 58.439 40.909 0.00 0.00 0.00 2.73
1296 3625 0.535102 AGAAACCAGGCACCTTCGTG 60.535 55.000 0.00 0.00 43.35 4.35
1434 3765 2.960384 TGAAAGGTTGAGTACACGGAGA 59.040 45.455 0.00 0.00 0.00 3.71
1443 3774 3.119137 GGCTGTTTGTTGAAAGGTTGAGT 60.119 43.478 0.00 0.00 0.00 3.41
1456 3787 1.151450 CACCTCCCAGGCTGTTTGT 59.849 57.895 14.43 2.11 39.63 2.83
1458 3789 0.768221 TCTCACCTCCCAGGCTGTTT 60.768 55.000 14.43 0.00 39.63 2.83
1514 3845 0.895530 GTTCTCCATCAGGTCCACGA 59.104 55.000 0.00 0.00 35.89 4.35
1526 3857 3.073228 CCAGAGAGGTGGTTCTCCA 57.927 57.895 0.00 0.00 43.74 3.86
1555 3886 3.260269 TGAAAGGAGACCCAGAGAAGA 57.740 47.619 0.00 0.00 33.88 2.87
1663 3994 6.259608 CCATGGAAGTAGTTGATCTTCATGTC 59.740 42.308 5.56 0.00 40.98 3.06
1664 3995 6.118170 CCATGGAAGTAGTTGATCTTCATGT 58.882 40.000 5.56 0.00 40.98 3.21
1673 4004 3.517296 TTTGGCCATGGAAGTAGTTGA 57.483 42.857 18.40 0.00 0.00 3.18
1701 4032 2.036256 GTCAGGTTGCCCAGCCAT 59.964 61.111 3.98 0.00 33.73 4.40
1827 4158 1.005924 GATGGAGGAAAAGGGCCTTCA 59.994 52.381 21.20 12.46 44.89 3.02
1876 4207 2.073816 CTGGTTGAAGCCGACGTTTAT 58.926 47.619 0.00 0.00 0.00 1.40
1878 4209 1.782028 GCTGGTTGAAGCCGACGTTT 61.782 55.000 0.00 0.00 37.20 3.60
1882 4213 0.796927 GTTAGCTGGTTGAAGCCGAC 59.203 55.000 0.00 0.00 44.68 4.79
2021 4359 5.891451 ACAAGTTTCCACTAAGAAGCAAAC 58.109 37.500 0.00 0.00 30.68 2.93
2032 4370 4.589908 GGACCATGATACAAGTTTCCACT 58.410 43.478 0.00 0.00 33.11 4.00
2040 4378 3.809832 GTGGAATCGGACCATGATACAAG 59.190 47.826 0.00 0.00 39.69 3.16
2041 4379 3.739830 CGTGGAATCGGACCATGATACAA 60.740 47.826 0.00 0.00 44.44 2.41
2042 4380 2.223947 CGTGGAATCGGACCATGATACA 60.224 50.000 0.00 0.00 44.44 2.29
2107 4445 4.681744 TCTGTGGTTTGAAGCAAATTGTC 58.318 39.130 0.00 0.00 38.25 3.18
2189 4527 4.223320 TCAAGATTGTTTTCGTCAAGGC 57.777 40.909 0.00 0.00 0.00 4.35
2205 4543 1.992557 ACTGGCATAACCCCTTCAAGA 59.007 47.619 0.00 0.00 37.83 3.02
2327 4666 0.255318 CTGCTGCAGGGAGAGGATTT 59.745 55.000 21.71 0.00 35.24 2.17
2397 4736 5.717178 GCTATGGGATAGGTCAAGATACTGA 59.283 44.000 0.00 0.00 33.43 3.41
2537 4876 5.396101 CCAGAAAGATCCAGAGATGTAAGCA 60.396 44.000 0.00 0.00 30.90 3.91
2587 4926 0.033642 GGGATGCTAAGTACCTCCGC 59.966 60.000 0.00 0.00 0.00 5.54
2648 4987 1.299648 CGAGTTGGGATGGAGCCAA 59.700 57.895 0.00 0.00 0.00 4.52
2658 4997 1.329256 ATCGTCCTATCCGAGTTGGG 58.671 55.000 0.00 0.00 37.81 4.12
2664 5003 1.337071 GTGCTCAATCGTCCTATCCGA 59.663 52.381 0.00 0.00 38.89 4.55
2675 5014 0.960364 TTTGCCGAGGGTGCTCAATC 60.960 55.000 0.00 0.00 0.00 2.67
2681 5020 2.038269 TCGATTTTGCCGAGGGTGC 61.038 57.895 0.00 0.00 0.00 5.01
2684 5023 0.177141 TAGGTCGATTTTGCCGAGGG 59.823 55.000 0.00 0.00 36.66 4.30
2693 5032 4.576463 GCTTGTTCATGGATAGGTCGATTT 59.424 41.667 0.00 0.00 0.00 2.17
2733 5072 1.633852 CGCAACTGCTGAGAGCTTCC 61.634 60.000 0.00 0.00 42.97 3.46
2765 5104 6.456795 AAAGATTTCCTTGCAAGTATAGGC 57.543 37.500 24.35 9.54 34.79 3.93
2826 5165 2.529632 AGATCCAACTTTTCAAGGCCC 58.470 47.619 0.00 0.00 0.00 5.80
3097 5453 4.686191 TCAAAGTTCCAACCATGCAAAT 57.314 36.364 0.00 0.00 0.00 2.32
3231 5596 5.275067 ACTCTGTTGCTTCATCTATCTCC 57.725 43.478 0.00 0.00 0.00 3.71
3264 5629 2.612721 GCCGGAACCAATCAAATTTGCT 60.613 45.455 13.54 0.29 0.00 3.91
3645 6016 0.537188 AGTGAACTATGGGTGGCTCG 59.463 55.000 0.00 0.00 0.00 5.03
3763 6134 2.665185 AGTCGCACCGCCACTTTC 60.665 61.111 0.00 0.00 0.00 2.62
3776 6147 0.940126 AAGTGTGCTGCTTTCAGTCG 59.060 50.000 0.00 0.00 42.29 4.18
3861 6258 9.158364 CGACATAAAATGTATACTGAACAATGC 57.842 33.333 4.17 0.00 45.03 3.56
3896 6293 4.159321 TCAGTTTGAATTGGCAAGTGAACA 59.841 37.500 19.14 5.22 0.00 3.18
3929 6372 9.973246 GTAATGAGTACACATAAATTCAGTGTG 57.027 33.333 16.29 14.76 45.27 3.82
3932 6375 8.997621 ACGTAATGAGTACACATAAATTCAGT 57.002 30.769 6.20 0.00 32.45 3.41
3945 6388 6.474751 GGGTTCATTGACTACGTAATGAGTAC 59.525 42.308 10.46 7.84 42.35 2.73
3965 6409 8.145122 TGAAACAAACATATAAACCAAGGGTTC 58.855 33.333 0.40 0.00 46.20 3.62
3994 6442 2.305343 GGCTTCAGATCCTGAGCCATAT 59.695 50.000 20.14 0.00 45.28 1.78
4048 6496 7.716799 TCCAGTAAACATTTCCAATAGCAAT 57.283 32.000 0.00 0.00 0.00 3.56
4088 6536 1.014044 GTCGCGCCATCTCTGAAACA 61.014 55.000 0.00 0.00 0.00 2.83
4186 6634 2.793232 GTCTATGATACGTTGCGGGTTC 59.207 50.000 0.00 0.00 0.00 3.62
4317 6770 3.271586 GCATATGAGCGGCGCACA 61.272 61.111 32.15 32.15 33.26 4.57
4379 6834 5.123186 AGCTGTAGATATGATCGTAGCACTC 59.877 44.000 12.50 0.00 37.07 3.51
4394 6849 2.704572 GGCAACAACAGAGCTGTAGAT 58.295 47.619 3.21 0.00 44.13 1.98
4419 6874 0.442310 CTTGTAACCACATCGCCACG 59.558 55.000 0.00 0.00 33.76 4.94
4446 6901 5.013704 ACAGGAATGGTCACCAAACATACTA 59.986 40.000 0.00 0.00 36.95 1.82
4499 6954 9.224267 CTACTTATGCTTCTAATACAATGCCAT 57.776 33.333 0.00 0.00 0.00 4.40
4532 6993 6.910536 ACTTATTTTCTACGAGGATTGCAG 57.089 37.500 0.00 0.00 0.00 4.41
4591 7052 1.007238 TGCTAGGAGTAGGAGCCACTT 59.993 52.381 0.00 0.00 35.24 3.16
4667 7129 3.585862 TGAACTTTAGCTAGCTGAACCG 58.414 45.455 27.68 15.95 0.00 4.44
4675 7137 8.887717 ACAAGCATTATCTTGAACTTTAGCTAG 58.112 33.333 10.10 0.00 44.61 3.42
4703 7165 5.183904 GGAATCAAAGCAGTAACCTGATTGT 59.816 40.000 0.61 0.00 46.14 2.71
4760 7222 5.899631 GGGTTTATATCCAGAAGTACCCA 57.100 43.478 0.00 0.00 42.78 4.51
4780 7245 9.020731 GGGTATATAAACTTGATAACCATTGGG 57.979 37.037 7.78 0.00 33.73 4.12
4788 7253 9.439500 GGCGTTATGGGTATATAAACTTGATAA 57.561 33.333 0.00 0.00 0.00 1.75
4789 7254 8.042515 GGGCGTTATGGGTATATAAACTTGATA 58.957 37.037 0.00 0.00 0.00 2.15
4809 7274 2.282180 ACCAAGATTGCGGGCGTT 60.282 55.556 0.00 0.00 0.00 4.84
4838 7303 5.593095 GGATGACTAAAAAGTTCATACCCCC 59.407 44.000 0.00 0.00 0.00 5.40
4848 7313 4.273148 AGTCGCTGGATGACTAAAAAGT 57.727 40.909 0.00 0.00 44.57 2.66
4870 7335 5.319043 TGGAGATTACTTTGGGTTCAACT 57.681 39.130 0.00 0.00 31.78 3.16
4871 7336 7.696992 TTATGGAGATTACTTTGGGTTCAAC 57.303 36.000 0.00 0.00 31.78 3.18
4918 7383 2.492881 TGCATGTTGTATCAGCAAAGGG 59.507 45.455 0.00 0.00 31.42 3.95
4933 7416 6.122277 ACTGGCTAGTATTTGTTATGCATGT 58.878 36.000 10.16 0.00 34.74 3.21
4934 7417 6.624352 ACTGGCTAGTATTTGTTATGCATG 57.376 37.500 10.16 0.00 34.74 4.06
4935 7418 7.279615 TGTACTGGCTAGTATTTGTTATGCAT 58.720 34.615 13.51 3.79 41.22 3.96
4936 7419 6.645306 TGTACTGGCTAGTATTTGTTATGCA 58.355 36.000 13.51 0.54 41.22 3.96
4937 7420 7.576236 CATGTACTGGCTAGTATTTGTTATGC 58.424 38.462 13.51 0.00 41.22 3.14
4938 7421 7.226523 TGCATGTACTGGCTAGTATTTGTTATG 59.773 37.037 13.51 11.44 41.22 1.90
4939 7422 7.279615 TGCATGTACTGGCTAGTATTTGTTAT 58.720 34.615 13.51 0.00 41.22 1.89
4940 7423 6.645306 TGCATGTACTGGCTAGTATTTGTTA 58.355 36.000 13.51 5.60 41.22 2.41
4941 7424 5.496556 TGCATGTACTGGCTAGTATTTGTT 58.503 37.500 13.51 0.00 41.22 2.83
4942 7425 5.097742 TGCATGTACTGGCTAGTATTTGT 57.902 39.130 13.51 0.00 41.22 2.83
4943 7426 5.528690 ACATGCATGTACTGGCTAGTATTTG 59.471 40.000 30.50 13.96 41.22 2.32
4944 7427 5.684704 ACATGCATGTACTGGCTAGTATTT 58.315 37.500 30.50 0.00 41.22 1.40
4945 7428 5.296151 ACATGCATGTACTGGCTAGTATT 57.704 39.130 30.50 0.30 41.22 1.89
4946 7429 4.963318 ACATGCATGTACTGGCTAGTAT 57.037 40.909 30.50 0.79 41.22 2.12
4947 7430 4.161377 TGAACATGCATGTACTGGCTAGTA 59.839 41.667 31.55 5.74 40.80 1.82
4948 7431 3.055167 TGAACATGCATGTACTGGCTAGT 60.055 43.478 31.55 13.47 40.80 2.57
5058 7542 9.074576 TGAAGACGAGATATAGGCAAGTTTATA 57.925 33.333 0.00 0.00 0.00 0.98
5078 7563 3.633986 GGGACCCATTTGATGATGAAGAC 59.366 47.826 5.33 0.00 0.00 3.01
5084 7569 3.646534 GGAAAGGGACCCATTTGATGAT 58.353 45.455 14.60 0.00 0.00 2.45
5102 7590 1.529713 GGTTGGCAACTTCCCGGAA 60.530 57.895 27.77 0.00 37.61 4.30
5113 7601 0.179124 GTTTCGTTTGCAGGTTGGCA 60.179 50.000 0.00 0.00 43.19 4.92
5127 7615 4.213270 TGGAAGTGTTATTGAGCAGTTTCG 59.787 41.667 0.00 0.00 0.00 3.46
5176 7664 6.103997 TCGCTTCTTATAACATTCGGTCTTT 58.896 36.000 0.00 0.00 0.00 2.52
5180 7668 5.597806 TCATCGCTTCTTATAACATTCGGT 58.402 37.500 0.00 0.00 0.00 4.69
5182 7670 8.820628 TTTTTCATCGCTTCTTATAACATTCG 57.179 30.769 0.00 0.00 0.00 3.34
5215 7798 5.053978 TGCCTACCTACCTTACCTAGTAC 57.946 47.826 0.00 0.00 0.00 2.73
5216 7799 5.614402 AGATGCCTACCTACCTTACCTAGTA 59.386 44.000 0.00 0.00 0.00 1.82
5217 7800 4.419537 AGATGCCTACCTACCTTACCTAGT 59.580 45.833 0.00 0.00 0.00 2.57
5234 7817 4.187694 CAGAGAAAGTGAAGGTAGATGCC 58.812 47.826 0.00 0.00 0.00 4.40
5236 7819 4.187694 GCCAGAGAAAGTGAAGGTAGATG 58.812 47.826 0.00 0.00 0.00 2.90
5300 7883 0.538287 GCTGCAGGGTGAAAGGAGTT 60.538 55.000 17.12 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.