Multiple sequence alignment - TraesCS1D01G215200

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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 TraesCS1D01G215200 chr1D 100.000 3301 0 0 1 3301 300668691 300665391 0.000000e+00 6096
1 TraesCS1D01G215200 chr1A 93.459 2232 92 17 503 2712 374960410 374958211 0.000000e+00 3264
2 TraesCS1D01G215200 chr1A 89.356 404 37 5 1 402 374961227 374960828 1.370000e-138 503
3 TraesCS1D01G215200 chr1A 94.242 330 17 2 2973 3301 554083119 554082791 1.370000e-138 503
4 TraesCS1D01G215200 chr1A 96.047 253 9 1 2711 2962 63008027 63008279 8.530000e-111 411
5 TraesCS1D01G215200 chr1B 93.570 2084 89 24 411 2485 405674455 405672408 0.000000e+00 3064
6 TraesCS1D01G215200 chr1B 85.185 405 43 6 1 404 405674911 405674523 1.850000e-107 399
7 TraesCS1D01G215200 chr1B 89.804 255 18 2 2458 2712 405672403 405672157 1.480000e-83 320
8 TraesCS1D01G215200 chr7A 89.934 606 39 11 2711 3301 734062892 734063490 0.000000e+00 761
9 TraesCS1D01G215200 chr7A 94.848 330 16 1 2973 3301 736318200 736317871 6.320000e-142 514
10 TraesCS1D01G215200 chr7A 96.032 252 9 1 2711 2961 101706532 101706281 3.070000e-110 409
11 TraesCS1D01G215200 chr6D 89.397 547 53 3 1790 2331 15586362 15585816 0.000000e+00 684
12 TraesCS1D01G215200 chr6D 88.991 545 58 2 1768 2310 15551166 15550622 0.000000e+00 673
13 TraesCS1D01G215200 chr6D 85.990 621 74 7 1731 2339 15640466 15641085 0.000000e+00 652
14 TraesCS1D01G215200 chr6D 79.303 918 100 43 709 1593 15552066 15551206 8.000000e-156 560
15 TraesCS1D01G215200 chr6D 93.617 329 15 4 2973 3300 32368685 32369008 1.380000e-133 486
16 TraesCS1D01G215200 chr6D 96.032 252 10 0 2711 2962 322833921 322833670 8.530000e-111 411
17 TraesCS1D01G215200 chr6D 96.047 253 9 1 2711 2962 418462613 418462361 8.530000e-111 411
18 TraesCS1D01G215200 chr6D 82.594 293 29 10 709 985 15599819 15599533 4.260000e-59 239
19 TraesCS1D01G215200 chr6A 89.515 515 54 0 1790 2304 16338192 16338706 0.000000e+00 652
20 TraesCS1D01G215200 chr6A 80.540 889 95 34 709 1536 16337156 16338027 2.180000e-171 612
21 TraesCS1D01G215200 chrUn 88.246 536 63 0 1769 2304 76409293 76409828 2.780000e-180 641
22 TraesCS1D01G215200 chrUn 88.846 520 53 1 1790 2304 319197541 319197022 4.650000e-178 634
23 TraesCS1D01G215200 chrUn 81.862 419 47 12 1125 1532 441169565 441169165 3.180000e-85 326
24 TraesCS1D01G215200 chrUn 80.674 445 56 18 1150 1593 319198036 319197621 5.320000e-83 318
25 TraesCS1D01G215200 chrUn 80.674 445 56 18 1150 1593 347746837 347746422 5.320000e-83 318
26 TraesCS1D01G215200 chrUn 86.301 219 18 10 826 1036 76417722 76417508 9.220000e-56 228
27 TraesCS1D01G215200 chrUn 86.301 219 18 10 826 1036 311042719 311042505 9.220000e-56 228
28 TraesCS1D01G215200 chrUn 81.304 230 24 9 790 1002 319199735 319199508 5.660000e-38 169
29 TraesCS1D01G215200 chrUn 81.304 230 24 9 790 1002 347748536 347748309 5.660000e-38 169
30 TraesCS1D01G215200 chrUn 86.301 146 20 0 1391 1536 76409062 76409207 3.410000e-35 159
31 TraesCS1D01G215200 chr6B 87.523 553 66 2 1790 2339 27669222 27669774 1.290000e-178 636
32 TraesCS1D01G215200 chr6B 82.100 419 46 12 1125 1532 27456173 27455773 6.830000e-87 331
33 TraesCS1D01G215200 chr6B 81.862 419 47 12 1125 1532 27420105 27419705 3.180000e-85 326
34 TraesCS1D01G215200 chr6B 81.862 419 47 12 1125 1532 27486305 27485905 3.180000e-85 326
35 TraesCS1D01G215200 chr6B 81.862 419 47 12 1125 1532 27532895 27532495 3.180000e-85 326
36 TraesCS1D01G215200 chr6B 79.439 214 32 7 1384 1593 27668907 27669112 1.230000e-29 141
37 TraesCS1D01G215200 chr4D 95.166 331 13 3 2973 3301 92198792 92199121 1.360000e-143 520
38 TraesCS1D01G215200 chr4D 93.030 330 21 2 2973 3301 494043166 494043494 6.410000e-132 481
39 TraesCS1D01G215200 chr7D 94.495 327 17 1 2976 3301 614243857 614244183 1.370000e-138 503
40 TraesCS1D01G215200 chr7D 96.838 253 7 1 2711 2962 208557858 208558110 3.940000e-114 422
41 TraesCS1D01G215200 chr4A 94.154 325 16 3 2979 3301 593294950 593294627 2.960000e-135 492
42 TraesCS1D01G215200 chr4B 93.598 328 19 2 2975 3301 69123897 69124223 3.830000e-134 488
43 TraesCS1D01G215200 chr5D 96.047 253 9 1 2711 2962 70887095 70886843 8.530000e-111 411
44 TraesCS1D01G215200 chr2D 96.047 253 9 1 2711 2962 591105847 591105595 8.530000e-111 411
45 TraesCS1D01G215200 chr2A 95.669 254 9 2 2711 2962 185357781 185358034 1.100000e-109 407
46 TraesCS1D01G215200 chr2A 94.361 266 11 4 2711 2974 507566431 507566168 3.970000e-109 405


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 TraesCS1D01G215200 chr1D 300665391 300668691 3300 True 6096.000000 6096 100.000000 1 3301 1 chr1D.!!$R1 3300
1 TraesCS1D01G215200 chr1A 374958211 374961227 3016 True 1883.500000 3264 91.407500 1 2712 2 chr1A.!!$R2 2711
2 TraesCS1D01G215200 chr1B 405672157 405674911 2754 True 1261.000000 3064 89.519667 1 2712 3 chr1B.!!$R1 2711
3 TraesCS1D01G215200 chr7A 734062892 734063490 598 False 761.000000 761 89.934000 2711 3301 1 chr7A.!!$F1 590
4 TraesCS1D01G215200 chr6D 15585816 15586362 546 True 684.000000 684 89.397000 1790 2331 1 chr6D.!!$R1 541
5 TraesCS1D01G215200 chr6D 15640466 15641085 619 False 652.000000 652 85.990000 1731 2339 1 chr6D.!!$F1 608
6 TraesCS1D01G215200 chr6D 15550622 15552066 1444 True 616.500000 673 84.147000 709 2310 2 chr6D.!!$R5 1601
7 TraesCS1D01G215200 chr6A 16337156 16338706 1550 False 632.000000 652 85.027500 709 2304 2 chr6A.!!$F1 1595
8 TraesCS1D01G215200 chrUn 76409062 76409828 766 False 400.000000 641 87.273500 1391 2304 2 chrUn.!!$F1 913
9 TraesCS1D01G215200 chrUn 319197022 319199735 2713 True 373.666667 634 83.608000 790 2304 3 chrUn.!!$R4 1514
10 TraesCS1D01G215200 chrUn 347746422 347748536 2114 True 243.500000 318 80.989000 790 1593 2 chrUn.!!$R5 803
11 TraesCS1D01G215200 chr6B 27668907 27669774 867 False 388.500000 636 83.481000 1384 2339 2 chr6B.!!$F1 955

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
250 256 0.103937 CCGCCCAGTTTCTTTGCAAA 59.896 50.0 12.14 12.14 0.00 3.68 F
1081 1444 0.861837 CGGTCTTCAGCGATATTGGC 59.138 55.0 0.00 0.00 46.86 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 3546 0.395312 AAAGGTCAACGTCCCGATGT 59.605 50.0 0.00 0.0 31.79 3.06 R
2677 4563 0.028770 CGTGGAACAAGAAAGCGCAA 59.971 50.0 11.47 0.0 44.16 4.85 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
50 51 6.238374 GGACATGTTGGTTGTGCTATGTATAC 60.238 42.308 0.00 0.00 33.20 1.47
63 64 9.705290 TGTGCTATGTATACATTGTTGTATAGG 57.295 33.333 22.90 3.64 46.76 2.57
64 65 9.923143 GTGCTATGTATACATTGTTGTATAGGA 57.077 33.333 22.90 10.33 46.76 2.94
87 92 6.863126 GGAGTACACATTTTTGTCTGAATTGG 59.137 38.462 0.00 0.00 0.00 3.16
147 152 1.461127 GCTCTTTGCCGAGTGTTACAG 59.539 52.381 0.00 0.00 35.15 2.74
247 253 1.007387 CACCGCCCAGTTTCTTTGC 60.007 57.895 0.00 0.00 0.00 3.68
250 256 0.103937 CCGCCCAGTTTCTTTGCAAA 59.896 50.000 12.14 12.14 0.00 3.68
288 294 9.350357 TCTAAAAGCACTCTACTTACATTTACG 57.650 33.333 0.00 0.00 0.00 3.18
312 318 5.488645 TGTGTATTAAGCGTAGACATCGA 57.511 39.130 0.00 0.00 0.00 3.59
313 319 5.882553 TGTGTATTAAGCGTAGACATCGAA 58.117 37.500 0.00 0.00 0.00 3.71
343 349 5.651576 TGTACACCATGAACATGCAACATAT 59.348 36.000 9.03 0.00 37.49 1.78
345 351 6.381481 ACACCATGAACATGCAACATATAG 57.619 37.500 9.03 0.00 37.49 1.31
355 361 4.394439 TGCAACATATAGTCGGCTTACA 57.606 40.909 0.00 0.00 33.17 2.41
404 410 2.223711 CCGGGATGAAAAATTAAGCCGG 60.224 50.000 0.00 0.00 0.00 6.13
405 411 2.798145 CGGGATGAAAAATTAAGCCGGC 60.798 50.000 21.89 21.89 0.00 6.13
468 535 2.154567 AGGTAAGTCGAGTGCCCATA 57.845 50.000 10.23 0.00 0.00 2.74
469 536 2.032620 AGGTAAGTCGAGTGCCCATAG 58.967 52.381 10.23 0.00 0.00 2.23
472 539 2.898729 AAGTCGAGTGCCCATAGATG 57.101 50.000 0.00 0.00 0.00 2.90
486 553 5.432680 CCATAGATGGGATCTGTGCTTAT 57.567 43.478 0.10 0.00 44.30 1.73
502 569 8.297426 TCTGTGCTTATATCTTATAAGTCGGTG 58.703 37.037 12.19 2.10 34.86 4.94
518 840 4.023365 AGTCGGTGTAATATAAGTCGAGCC 60.023 45.833 0.00 0.00 0.00 4.70
550 873 2.603560 GGTGCAACACTCGACTTATAGC 59.396 50.000 0.00 0.00 39.98 2.97
605 928 9.992910 GTATTTTTAGTACTCGGGTTTATTTGG 57.007 33.333 0.00 0.00 0.00 3.28
615 938 4.038162 TCGGGTTTATTTGGTTTTCCTGTG 59.962 41.667 0.00 0.00 41.38 3.66
760 1087 6.680625 GCATAACGATGGTCTGACTTTCTCTA 60.681 42.308 7.85 0.92 33.26 2.43
816 1144 4.148825 GCGGGTGCTCGGTGATCT 62.149 66.667 0.00 0.00 38.39 2.75
820 1149 1.142748 GGTGCTCGGTGATCTCCTG 59.857 63.158 11.86 5.91 0.00 3.86
964 1311 4.719369 ACTTGCGCCGACTCGTCC 62.719 66.667 4.18 0.00 0.00 4.79
1050 1410 4.024048 CCATCACAACACAAACAGGAGTAC 60.024 45.833 0.00 0.00 0.00 2.73
1068 1431 5.163353 GGAGTACTACTACTACTCCGGTCTT 60.163 48.000 0.00 0.00 46.58 3.01
1075 1438 1.025812 CTACTCCGGTCTTCAGCGAT 58.974 55.000 0.00 0.00 46.86 4.58
1076 1439 2.219458 CTACTCCGGTCTTCAGCGATA 58.781 52.381 0.00 0.00 46.86 2.92
1077 1440 1.693627 ACTCCGGTCTTCAGCGATAT 58.306 50.000 0.00 0.00 46.86 1.63
1078 1441 2.032620 ACTCCGGTCTTCAGCGATATT 58.967 47.619 0.00 0.00 46.86 1.28
1079 1442 2.223829 ACTCCGGTCTTCAGCGATATTG 60.224 50.000 0.00 0.00 46.86 1.90
1080 1443 1.068588 TCCGGTCTTCAGCGATATTGG 59.931 52.381 0.00 0.00 46.86 3.16
1081 1444 0.861837 CGGTCTTCAGCGATATTGGC 59.138 55.000 0.00 0.00 46.86 4.52
1082 1445 0.861837 GGTCTTCAGCGATATTGGCG 59.138 55.000 0.00 0.00 35.00 5.69
1358 3155 1.017177 TTTCATGCCGTCGCTGTACC 61.017 55.000 0.00 0.00 35.36 3.34
1369 3166 4.384846 CCGTCGCTGTACCAAATCATATAC 59.615 45.833 0.00 0.00 0.00 1.47
1461 3274 2.233922 CGTGAACCAGTACCCAATCTCT 59.766 50.000 0.00 0.00 0.00 3.10
1718 3535 3.504863 CAAAGCACAATGTACTCCATGC 58.495 45.455 0.00 0.00 32.82 4.06
1727 3544 1.206132 TGTACTCCATGCCCAAGTACG 59.794 52.381 15.24 0.00 45.32 3.67
1729 3546 1.563924 ACTCCATGCCCAAGTACGTA 58.436 50.000 0.00 0.00 0.00 3.57
2129 3966 2.017559 CTACGGGCTACTGGCAGGAC 62.018 65.000 20.34 3.43 44.01 3.85
2176 4013 3.124921 GATGGACACCAACCGCCG 61.125 66.667 0.00 0.00 36.95 6.46
2470 4322 2.551721 CCTGAAGATGTGTGGCTGTCTT 60.552 50.000 0.00 0.00 33.87 3.01
2474 4360 3.769739 AGATGTGTGGCTGTCTTTGTA 57.230 42.857 0.00 0.00 0.00 2.41
2539 4425 3.078836 TGCTACCCCGGCCACTAC 61.079 66.667 2.24 0.00 0.00 2.73
2642 4528 7.071069 ACAGTGTGGACATATATCATCATGT 57.929 36.000 0.00 0.00 38.08 3.21
2677 4563 2.304092 TCGAGTATATGCCACGGTTCT 58.696 47.619 7.77 0.00 0.00 3.01
2719 4605 2.428171 CCCATACCAAAATGGCTCAGTG 59.572 50.000 0.00 0.00 44.40 3.66
2749 4635 1.019278 CGGTTGTGCAGCCTAACGAT 61.019 55.000 3.70 0.00 0.00 3.73
2773 4659 6.106673 TCCGAGTTCAATTCCTAGAATTGAC 58.893 40.000 24.95 20.09 43.81 3.18
2788 4674 0.250858 TTGACAGGTGATGCACAGGG 60.251 55.000 0.00 0.00 35.86 4.45
2794 4680 0.603065 GGTGATGCACAGGGGTTTTC 59.397 55.000 0.00 0.00 35.86 2.29
2795 4681 0.603065 GTGATGCACAGGGGTTTTCC 59.397 55.000 0.00 0.00 35.19 3.13
2919 4805 8.139989 GGTACTCATACTAAAATGGTCGTATGT 58.860 37.037 0.00 0.00 39.87 2.29
2935 4821 3.069016 CGTATGTATCCCTAGTTGGTGCA 59.931 47.826 0.00 0.00 0.00 4.57
2936 4822 3.845781 ATGTATCCCTAGTTGGTGCAG 57.154 47.619 0.00 0.00 0.00 4.41
2937 4823 2.827755 TGTATCCCTAGTTGGTGCAGA 58.172 47.619 0.00 0.00 0.00 4.26
2938 4824 2.766263 TGTATCCCTAGTTGGTGCAGAG 59.234 50.000 0.00 0.00 0.00 3.35
2939 4825 1.207791 ATCCCTAGTTGGTGCAGAGG 58.792 55.000 0.00 0.00 0.00 3.69
2940 4826 1.078143 CCCTAGTTGGTGCAGAGGC 60.078 63.158 0.00 0.00 41.68 4.70
2941 4827 1.078143 CCTAGTTGGTGCAGAGGCC 60.078 63.158 0.00 0.00 40.13 5.19
2962 4859 1.641192 GGGAAGTGAAATTCTCCCCCT 59.359 52.381 7.38 0.00 0.00 4.79
2964 4861 3.268595 GGGAAGTGAAATTCTCCCCCTTA 59.731 47.826 7.38 0.00 0.00 2.69
2965 4862 4.079154 GGGAAGTGAAATTCTCCCCCTTAT 60.079 45.833 7.38 0.00 0.00 1.73
2966 4863 5.133830 GGGAAGTGAAATTCTCCCCCTTATA 59.866 44.000 7.38 0.00 0.00 0.98
2967 4864 6.062749 GGAAGTGAAATTCTCCCCCTTATAC 58.937 44.000 0.00 0.00 0.00 1.47
2968 4865 6.126449 GGAAGTGAAATTCTCCCCCTTATACT 60.126 42.308 0.00 0.00 0.00 2.12
2969 4866 6.910259 AGTGAAATTCTCCCCCTTATACTT 57.090 37.500 0.00 0.00 0.00 2.24
2970 4867 8.401955 AAGTGAAATTCTCCCCCTTATACTTA 57.598 34.615 0.00 0.00 0.00 2.24
2971 4868 8.035448 AGTGAAATTCTCCCCCTTATACTTAG 57.965 38.462 0.00 0.00 0.00 2.18
2985 4882 0.544595 ACTTAGCCCGTGACCTCCTT 60.545 55.000 0.00 0.00 0.00 3.36
2991 4888 3.771160 CGTGACCTCCTTCCCCCG 61.771 72.222 0.00 0.00 0.00 5.73
3179 5077 1.081376 CGACATACTCCGGCCGATC 60.081 63.158 30.73 10.83 0.00 3.69
3226 5124 4.320456 CAGGGCTGTCGTGCTGGT 62.320 66.667 0.00 0.00 0.00 4.00
3251 5149 3.221834 GACGAAGAGATCACGTCGG 57.778 57.895 25.89 12.54 44.55 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.888512 GCACAACCAACATGTCCAGAT 59.111 47.619 0.00 0.00 0.00 2.90
62 63 6.863126 CCAATTCAGACAAAAATGTGTACTCC 59.137 38.462 0.00 0.00 0.00 3.85
63 64 7.648142 TCCAATTCAGACAAAAATGTGTACTC 58.352 34.615 0.00 0.00 0.00 2.59
64 65 7.255590 CCTCCAATTCAGACAAAAATGTGTACT 60.256 37.037 0.00 0.00 0.00 2.73
65 66 6.863126 CCTCCAATTCAGACAAAAATGTGTAC 59.137 38.462 0.00 0.00 0.00 2.90
66 67 6.015519 CCCTCCAATTCAGACAAAAATGTGTA 60.016 38.462 0.00 0.00 0.00 2.90
67 68 5.221501 CCCTCCAATTCAGACAAAAATGTGT 60.222 40.000 0.00 0.00 0.00 3.72
68 69 5.232463 CCCTCCAATTCAGACAAAAATGTG 58.768 41.667 0.00 0.00 0.00 3.21
69 70 4.262592 GCCCTCCAATTCAGACAAAAATGT 60.263 41.667 0.00 0.00 0.00 2.71
70 71 4.020839 AGCCCTCCAATTCAGACAAAAATG 60.021 41.667 0.00 0.00 0.00 2.32
147 152 1.197721 GGCATATGCATGTAAGCCGAC 59.802 52.381 28.07 3.35 44.36 4.79
247 253 4.382754 GCTTTTAGAAATGCACTCGGTTTG 59.617 41.667 7.73 0.00 38.50 2.93
250 256 3.146066 TGCTTTTAGAAATGCACTCGGT 58.854 40.909 10.53 0.00 42.03 4.69
276 282 8.164153 CGCTTAATACACAACGTAAATGTAAGT 58.836 33.333 9.67 0.34 32.80 2.24
287 293 5.330571 CGATGTCTACGCTTAATACACAACG 60.331 44.000 0.00 0.00 0.00 4.10
288 294 5.740569 TCGATGTCTACGCTTAATACACAAC 59.259 40.000 0.00 0.00 0.00 3.32
343 349 1.542915 GTGTCTGGTGTAAGCCGACTA 59.457 52.381 3.34 0.00 35.06 2.59
345 351 1.007336 CGTGTCTGGTGTAAGCCGAC 61.007 60.000 0.00 0.00 34.80 4.79
404 410 1.730064 TCTCGGCAACATAAACGAAGC 59.270 47.619 0.00 0.00 34.70 3.86
405 411 3.424433 GGTTCTCGGCAACATAAACGAAG 60.424 47.826 0.00 0.00 34.70 3.79
468 535 6.949117 AAGATATAAGCACAGATCCCATCT 57.051 37.500 0.00 0.00 41.15 2.90
472 539 9.810545 GACTTATAAGATATAAGCACAGATCCC 57.189 37.037 19.38 0.00 35.57 3.85
502 569 6.796072 CACTTACTCGGCTCGACTTATATTAC 59.204 42.308 0.00 0.00 0.00 1.89
512 579 2.050350 CCCCACTTACTCGGCTCGA 61.050 63.158 0.00 0.00 0.00 4.04
518 840 0.250124 TGTTGCACCCCACTTACTCG 60.250 55.000 0.00 0.00 0.00 4.18
550 873 2.298163 AGGCCAATTTCAACTCTGCTTG 59.702 45.455 5.01 0.00 0.00 4.01
615 938 4.518970 TGATGCTAAAGAGGTTTTCACACC 59.481 41.667 0.00 0.00 37.04 4.16
656 979 4.201783 GGTTCGCTTATCTTAACGCATTGT 60.202 41.667 0.00 0.00 0.00 2.71
760 1087 5.291614 GTGCACAAGTCAAATTGTTGATTGT 59.708 36.000 13.17 3.61 45.38 2.71
816 1144 7.611467 ACAACTATAAAATCACATCTTGCAGGA 59.389 33.333 0.00 0.00 0.00 3.86
820 1149 6.195244 CGCACAACTATAAAATCACATCTTGC 59.805 38.462 0.00 0.00 0.00 4.01
964 1311 5.163581 CCAATAGGCAAAATGAGGTGAGAAG 60.164 44.000 0.00 0.00 0.00 2.85
1017 1364 3.266686 TTGTGATGGCTGGACGGGG 62.267 63.158 0.00 0.00 0.00 5.73
1050 1410 3.560896 GCTGAAGACCGGAGTAGTAGTAG 59.439 52.174 9.46 0.00 0.00 2.57
1063 1423 0.861837 CGCCAATATCGCTGAAGACC 59.138 55.000 0.00 0.00 0.00 3.85
1075 1438 4.994907 TCTTAGACTTGTAGCGCCAATA 57.005 40.909 2.29 0.00 0.00 1.90
1076 1439 3.887621 TCTTAGACTTGTAGCGCCAAT 57.112 42.857 2.29 0.00 0.00 3.16
1077 1440 3.585862 CTTCTTAGACTTGTAGCGCCAA 58.414 45.455 2.29 0.39 0.00 4.52
1078 1441 2.094182 CCTTCTTAGACTTGTAGCGCCA 60.094 50.000 2.29 0.00 0.00 5.69
1079 1442 2.094130 ACCTTCTTAGACTTGTAGCGCC 60.094 50.000 2.29 0.00 0.00 6.53
1080 1443 3.233684 ACCTTCTTAGACTTGTAGCGC 57.766 47.619 0.00 0.00 0.00 5.92
1081 1444 4.806330 TGAACCTTCTTAGACTTGTAGCG 58.194 43.478 0.00 0.00 0.00 4.26
1082 1445 7.773149 TCTATGAACCTTCTTAGACTTGTAGC 58.227 38.462 6.57 0.00 38.35 3.58
1110 1477 1.391577 TATTGGCGCTACAGGTCGTA 58.608 50.000 7.64 0.00 0.00 3.43
1138 1505 0.458669 GCAATGGCATTGGTGGAGAG 59.541 55.000 34.19 12.85 40.57 3.20
1207 2987 2.202401 GACGGCGGTGTCGTAGTC 60.202 66.667 13.24 0.00 46.30 2.59
1305 3085 4.019950 TCATCGGATCCTATAGACGTACCA 60.020 45.833 10.75 0.00 0.00 3.25
1358 3155 5.991328 AGTTGGCACGAGTATATGATTTG 57.009 39.130 0.00 0.00 0.00 2.32
1369 3166 7.705325 ACATTATTAGTACTAAGTTGGCACGAG 59.295 37.037 19.58 5.22 0.00 4.18
1718 3535 1.105457 TCCCGATGTACGTACTTGGG 58.895 55.000 29.28 29.28 40.78 4.12
1727 3544 0.529378 AGGTCAACGTCCCGATGTAC 59.471 55.000 0.00 0.00 31.79 2.90
1729 3546 0.395312 AAAGGTCAACGTCCCGATGT 59.605 50.000 0.00 0.00 31.79 3.06
2048 3885 1.134907 GTCCCGTCCACATTCACGTAT 60.135 52.381 0.00 0.00 34.06 3.06
2111 3948 2.056223 GTCCTGCCAGTAGCCCGTA 61.056 63.158 0.00 0.00 42.71 4.02
2470 4322 6.768381 TCCTTACATTTCACACACACATACAA 59.232 34.615 0.00 0.00 0.00 2.41
2474 4360 4.216257 GCTCCTTACATTTCACACACACAT 59.784 41.667 0.00 0.00 0.00 3.21
2539 4425 2.658679 TATCAGGCATGGAACCGCGG 62.659 60.000 26.86 26.86 0.00 6.46
2543 4429 2.171448 ACACTCTATCAGGCATGGAACC 59.829 50.000 0.00 0.00 0.00 3.62
2623 4509 6.997239 ATGCACATGATGATATATGTCCAC 57.003 37.500 0.00 0.00 35.46 4.02
2642 4528 7.436376 GCATATACTCGATGATAAGCTAATGCA 59.564 37.037 0.00 0.00 42.74 3.96
2677 4563 0.028770 CGTGGAACAAGAAAGCGCAA 59.971 50.000 11.47 0.00 44.16 4.85
2719 4605 3.302344 ACAACCGCATGCCCAACC 61.302 61.111 13.15 0.00 0.00 3.77
2749 4635 6.106673 GTCAATTCTAGGAATTGAACTCGGA 58.893 40.000 26.66 9.48 45.06 4.55
2773 4659 0.540365 AAACCCCTGTGCATCACCTG 60.540 55.000 0.00 0.00 32.73 4.00
2788 4674 6.156083 TGATTCTCAATAAATGGGGGAAAACC 59.844 38.462 0.00 0.00 39.11 3.27
2794 4680 6.796785 AACTTGATTCTCAATAAATGGGGG 57.203 37.500 0.00 0.00 35.59 5.40
2795 4681 7.839907 TCAAACTTGATTCTCAATAAATGGGG 58.160 34.615 0.00 0.00 35.59 4.96
2809 4695 4.214310 TCCACCACACATCAAACTTGATT 58.786 39.130 2.11 0.00 45.13 2.57
2874 4760 4.236527 ACCAAGATAAACATGGTCCTCC 57.763 45.455 0.00 0.00 45.86 4.30
2912 4798 3.319972 GCACCAACTAGGGATACATACGA 59.680 47.826 0.00 0.00 43.89 3.43
2919 4805 2.398588 CCTCTGCACCAACTAGGGATA 58.601 52.381 0.00 0.00 43.89 2.59
2935 4821 0.698818 AATTTCACTTCCCGGCCTCT 59.301 50.000 0.00 0.00 0.00 3.69
2936 4822 1.095600 GAATTTCACTTCCCGGCCTC 58.904 55.000 0.00 0.00 0.00 4.70
2937 4823 0.698818 AGAATTTCACTTCCCGGCCT 59.301 50.000 0.00 0.00 0.00 5.19
2938 4824 1.095600 GAGAATTTCACTTCCCGGCC 58.904 55.000 0.00 0.00 0.00 6.13
2939 4825 1.095600 GGAGAATTTCACTTCCCGGC 58.904 55.000 0.00 0.00 0.00 6.13
2940 4826 1.682087 GGGGAGAATTTCACTTCCCGG 60.682 57.143 13.34 0.00 42.52 5.73
2941 4827 1.751437 GGGGAGAATTTCACTTCCCG 58.249 55.000 13.34 0.00 42.52 5.14
2962 4859 2.961062 GGAGGTCACGGGCTAAGTATAA 59.039 50.000 0.00 0.00 0.00 0.98
2964 4861 1.063114 AGGAGGTCACGGGCTAAGTAT 60.063 52.381 0.00 0.00 0.00 2.12
2965 4862 0.333993 AGGAGGTCACGGGCTAAGTA 59.666 55.000 0.00 0.00 0.00 2.24
2966 4863 0.544595 AAGGAGGTCACGGGCTAAGT 60.545 55.000 0.00 0.00 0.00 2.24
2967 4864 0.175989 GAAGGAGGTCACGGGCTAAG 59.824 60.000 0.00 0.00 0.00 2.18
2968 4865 1.262640 GGAAGGAGGTCACGGGCTAA 61.263 60.000 0.00 0.00 0.00 3.09
2969 4866 1.684734 GGAAGGAGGTCACGGGCTA 60.685 63.158 0.00 0.00 0.00 3.93
2970 4867 3.003763 GGAAGGAGGTCACGGGCT 61.004 66.667 0.00 0.00 0.00 5.19
2971 4868 4.097361 GGGAAGGAGGTCACGGGC 62.097 72.222 0.00 0.00 0.00 6.13
3117 5015 3.577313 GAGGAAGATTGCCGCCGC 61.577 66.667 0.00 0.00 0.00 6.53
3165 5063 1.472662 CCTTGGATCGGCCGGAGTAT 61.473 60.000 27.83 11.69 40.66 2.12
3166 5064 2.131709 CCTTGGATCGGCCGGAGTA 61.132 63.158 27.83 5.87 40.66 2.59
3226 5124 3.411418 GATCTCTTCGTCGCCGGCA 62.411 63.158 28.98 11.20 33.95 5.69
3228 5126 1.586564 GTGATCTCTTCGTCGCCGG 60.587 63.158 0.00 0.00 33.95 6.13
3239 5137 2.718993 CTAGCCGCCGACGTGATCTC 62.719 65.000 0.00 0.00 37.70 2.75
3251 5149 3.501458 GATCGGACACCCTAGCCGC 62.501 68.421 0.00 0.00 44.45 6.53
3265 5163 0.969149 TCCGAATGGGATCCAGATCG 59.031 55.000 15.23 17.94 40.94 3.69


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

AutoCloner maintained by Alex Coulton.