Multiple sequence alignment - TraesCS7D01G180100

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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 TraesCS7D01G180100 chr7D 100.000 2957 0 0 1 2957 133321965 133319009 0.000000e+00 5461.0
1 TraesCS7D01G180100 chr7D 80.263 380 57 15 1553 1926 133827807 133828174 1.350000e-68 270.0
2 TraesCS7D01G180100 chr7D 75.862 377 64 18 1553 1926 133665189 133664837 1.820000e-37 167.0
3 TraesCS7D01G180100 chr7D 83.019 106 16 2 2384 2488 15787134 15787238 8.730000e-16 95.3
4 TraesCS7D01G180100 chr7A 93.871 2268 87 15 718 2957 131870368 131868125 0.000000e+00 3371.0
5 TraesCS7D01G180100 chr7A 80.211 379 59 13 1553 1926 132619607 132619974 1.350000e-68 270.0
6 TraesCS7D01G180100 chr7A 79.630 378 63 12 1553 1926 132411074 132410707 2.920000e-65 259.0
7 TraesCS7D01G180100 chr7B 93.898 1737 62 21 449 2178 94608997 94607298 0.000000e+00 2580.0
8 TraesCS7D01G180100 chr7B 86.164 477 50 10 1 465 94609483 94609011 4.400000e-138 501.0
9 TraesCS7D01G180100 chr7B 80.526 380 56 15 1553 1926 95045856 95045489 2.900000e-70 276.0
10 TraesCS7D01G180100 chr7B 83.065 124 16 5 2374 2495 186109993 186110113 1.120000e-19 108.0
11 TraesCS7D01G180100 chr6D 82.787 244 37 3 3 244 460588029 460588269 2.310000e-51 213.0
12 TraesCS7D01G180100 chr4D 83.700 227 35 2 20 246 307276773 307276997 2.310000e-51 213.0
13 TraesCS7D01G180100 chr5B 84.186 215 29 5 3 215 386330518 386330729 1.390000e-48 204.0
14 TraesCS7D01G180100 chr5B 83.721 215 29 5 3 215 383463905 383464115 6.460000e-47 198.0
15 TraesCS7D01G180100 chr5B 81.466 232 38 4 3 232 239432136 239432364 5.030000e-43 185.0
16 TraesCS7D01G180100 chr5B 77.869 122 16 5 2373 2494 255774566 255774676 6.840000e-07 65.8
17 TraesCS7D01G180100 chr5A 81.702 235 39 3 3 235 397510371 397510139 3.010000e-45 193.0
18 TraesCS7D01G180100 chr5A 81.277 235 40 3 3 235 653289851 653289619 1.400000e-43 187.0
19 TraesCS7D01G180100 chr5A 80.132 151 20 7 236 376 426551424 426551274 1.450000e-18 104.0
20 TraesCS7D01G180100 chr5A 90.000 70 7 0 405 474 11277714 11277645 1.130000e-14 91.6
21 TraesCS7D01G180100 chr1D 80.894 246 40 6 8 251 454454976 454454736 1.400000e-43 187.0
22 TraesCS7D01G180100 chr1D 80.488 246 43 4 3 245 96116052 96115809 1.810000e-42 183.0
23 TraesCS7D01G180100 chr3D 83.740 123 19 1 2373 2495 522945280 522945159 6.700000e-22 115.0
24 TraesCS7D01G180100 chr2B 93.506 77 3 2 2415 2490 56531231 56531156 2.410000e-21 113.0
25 TraesCS7D01G180100 chr3A 91.250 80 5 2 2412 2490 728045343 728045421 1.120000e-19 108.0
26 TraesCS7D01G180100 chr3A 81.967 122 20 2 2370 2490 392860684 392860804 5.210000e-18 102.0
27 TraesCS7D01G180100 chr1B 89.610 77 8 0 2415 2491 563051854 563051778 6.740000e-17 99.0
28 TraesCS7D01G180100 chr4A 80.833 120 21 2 2373 2490 253868362 253868481 3.140000e-15 93.5
29 TraesCS7D01G180100 chr5D 79.508 122 14 5 2373 2494 539320192 539320302 3.160000e-10 76.8
30 TraesCS7D01G180100 chr6B 83.333 78 13 0 405 482 516869021 516869098 4.090000e-09 73.1
31 TraesCS7D01G180100 chr4B 77.869 122 16 5 2373 2494 443719679 443719789 6.840000e-07 65.8


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 TraesCS7D01G180100 chr7D 133319009 133321965 2956 True 5461.0 5461 100.000 1 2957 1 chr7D.!!$R1 2956
1 TraesCS7D01G180100 chr7A 131868125 131870368 2243 True 3371.0 3371 93.871 718 2957 1 chr7A.!!$R1 2239
2 TraesCS7D01G180100 chr7B 94607298 94609483 2185 True 1540.5 2580 90.031 1 2178 2 chr7B.!!$R2 2177

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
541 587 0.175531 AAAACCACTTGTGCACCAGC 59.824 50.0 17.37 0.0 42.57 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2208 2285 0.032678 CAGTGTGTCGAGAAGCACCT 59.967 55.0 1.89 0.0 34.94 4.0 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 3.544698 AGGACTCAAAGAGGTAGACCA 57.455 47.619 0.66 0.00 38.89 4.02
21 22 4.067944 AGGACTCAAAGAGGTAGACCAT 57.932 45.455 0.66 0.00 38.89 3.55
22 23 4.430441 AGGACTCAAAGAGGTAGACCATT 58.570 43.478 0.66 0.00 38.89 3.16
23 24 5.590818 AGGACTCAAAGAGGTAGACCATTA 58.409 41.667 0.66 0.00 38.89 1.90
24 25 6.023603 AGGACTCAAAGAGGTAGACCATTAA 58.976 40.000 0.66 0.00 38.89 1.40
32 35 2.633481 AGGTAGACCATTAATCTCGGCC 59.367 50.000 0.66 0.00 38.89 6.13
33 36 2.609737 GGTAGACCATTAATCTCGGCCG 60.610 54.545 22.12 22.12 35.64 6.13
39 42 2.878406 CCATTAATCTCGGCCGTCAAAT 59.122 45.455 27.15 15.32 0.00 2.32
48 51 1.401552 CGGCCGTCAAATCATGTCAAT 59.598 47.619 19.50 0.00 0.00 2.57
53 56 4.414852 CCGTCAAATCATGTCAATCCAAC 58.585 43.478 0.00 0.00 0.00 3.77
55 58 4.142924 CGTCAAATCATGTCAATCCAACGA 60.143 41.667 0.00 0.00 0.00 3.85
67 70 2.961526 TCCAACGACCTAGATTGCTC 57.038 50.000 0.00 0.00 0.00 4.26
68 71 1.480954 TCCAACGACCTAGATTGCTCC 59.519 52.381 0.00 0.00 0.00 4.70
72 75 3.185246 ACGACCTAGATTGCTCCAATG 57.815 47.619 0.00 0.00 33.90 2.82
95 98 4.082274 TGAGCATTCAACATGTTTAGCG 57.918 40.909 8.77 0.00 0.00 4.26
108 111 9.444534 CAACATGTTTAGCGTGCAATTAATATA 57.555 29.630 8.77 0.00 37.62 0.86
140 143 8.438513 CCAAATATCAACGTCTATGCTAATCAG 58.561 37.037 0.00 0.00 0.00 2.90
143 146 6.650427 ATCAACGTCTATGCTAATCAGGTA 57.350 37.500 0.00 0.00 0.00 3.08
154 157 6.656314 TGCTAATCAGGTAATTAACACGTG 57.344 37.500 15.48 15.48 34.02 4.49
182 185 9.803315 TTGATATCCTATCTAATATCAACGTGC 57.197 33.333 11.72 0.00 44.20 5.34
197 200 6.325919 TCAACGTGCAATTAATTTCCTCTT 57.674 33.333 0.00 0.00 0.00 2.85
218 221 7.039714 CCTCTTTAATATTAAGGTGGATTGGGC 60.040 40.741 23.86 0.00 36.22 5.36
223 226 0.176219 TAAGGTGGATTGGGCGTACG 59.824 55.000 11.84 11.84 0.00 3.67
233 236 0.741574 TGGGCGTACGCATTTACTGG 60.742 55.000 37.99 0.00 44.11 4.00
279 282 3.052262 TGGATCCAATTAATCCAGGCCAA 60.052 43.478 13.46 0.00 46.05 4.52
306 318 3.450817 TCCAACGATCTAGATTGCTCCAA 59.549 43.478 18.44 0.20 0.00 3.53
307 319 3.557595 CCAACGATCTAGATTGCTCCAAC 59.442 47.826 18.44 0.00 0.00 3.77
308 320 4.183865 CAACGATCTAGATTGCTCCAACA 58.816 43.478 18.44 0.00 0.00 3.33
443 455 7.773149 AGATATCCTACCTAATATCAACGTGC 58.227 38.462 0.00 0.00 37.34 5.34
447 459 6.588204 TCCTACCTAATATCAACGTGCAATT 58.412 36.000 0.00 0.00 0.00 2.32
457 499 9.691362 AATATCAACGTGCAATTAACTTTCTTT 57.309 25.926 0.00 0.00 0.00 2.52
458 500 7.623268 ATCAACGTGCAATTAACTTTCTTTC 57.377 32.000 0.00 0.00 0.00 2.62
460 502 7.030165 TCAACGTGCAATTAACTTTCTTTCAA 58.970 30.769 0.00 0.00 0.00 2.69
474 516 9.522804 AACTTTCTTTCAAATATTAACGTGCAA 57.477 25.926 0.00 0.00 0.00 4.08
532 578 5.066968 ACCAGTAACAACAAAACCACTTG 57.933 39.130 0.00 0.00 0.00 3.16
535 581 4.326009 CAGTAACAACAAAACCACTTGTGC 59.674 41.667 0.00 0.00 39.47 4.57
536 582 3.393089 AACAACAAAACCACTTGTGCA 57.607 38.095 0.00 0.00 39.47 4.57
537 583 2.682836 ACAACAAAACCACTTGTGCAC 58.317 42.857 10.75 10.75 39.47 4.57
538 584 1.999024 CAACAAAACCACTTGTGCACC 59.001 47.619 15.69 0.00 39.47 5.01
539 585 1.261480 ACAAAACCACTTGTGCACCA 58.739 45.000 15.69 1.44 38.12 4.17
540 586 1.204467 ACAAAACCACTTGTGCACCAG 59.796 47.619 15.69 15.85 38.12 4.00
541 587 0.175531 AAAACCACTTGTGCACCAGC 59.824 50.000 17.37 0.00 42.57 4.85
546 592 2.519063 CTTGTGCACCAGCCACCA 60.519 61.111 15.69 0.00 41.13 4.17
570 616 5.468540 TGGTATATCTCAATCCACCTTCG 57.531 43.478 0.00 0.00 0.00 3.79
602 648 7.333423 TGGTAAATCAACTAAGAAATCCAGTCG 59.667 37.037 0.00 0.00 0.00 4.18
638 684 3.181480 CCCGGTCACAACACAAGAAAAAT 60.181 43.478 0.00 0.00 0.00 1.82
642 688 5.448496 CGGTCACAACACAAGAAAAATCTCA 60.448 40.000 0.00 0.00 0.00 3.27
657 703 0.251354 TCTCAGAGCATTCCACAGCC 59.749 55.000 0.00 0.00 0.00 4.85
678 724 1.344114 AGCCATGAAAATTGTTGCGGT 59.656 42.857 0.00 0.00 0.00 5.68
685 731 1.833860 AAATTGTTGCGGTCACGTTG 58.166 45.000 0.00 0.00 43.45 4.10
709 755 1.546323 CCCAAGTGGCACTGACATTCT 60.546 52.381 22.83 0.00 0.00 2.40
710 756 1.808945 CCAAGTGGCACTGACATTCTC 59.191 52.381 22.83 0.00 0.00 2.87
711 757 1.808945 CAAGTGGCACTGACATTCTCC 59.191 52.381 22.83 0.00 0.00 3.71
712 758 1.356124 AGTGGCACTGACATTCTCCT 58.644 50.000 21.37 0.00 0.00 3.69
713 759 1.277557 AGTGGCACTGACATTCTCCTC 59.722 52.381 21.37 0.00 0.00 3.71
714 760 0.247460 TGGCACTGACATTCTCCTCG 59.753 55.000 0.00 0.00 0.00 4.63
715 761 0.247736 GGCACTGACATTCTCCTCGT 59.752 55.000 0.00 0.00 0.00 4.18
716 762 1.634702 GCACTGACATTCTCCTCGTC 58.365 55.000 0.00 0.00 0.00 4.20
717 763 1.737363 GCACTGACATTCTCCTCGTCC 60.737 57.143 0.00 0.00 0.00 4.79
718 764 1.546029 CACTGACATTCTCCTCGTCCA 59.454 52.381 0.00 0.00 0.00 4.02
719 765 2.167281 CACTGACATTCTCCTCGTCCAT 59.833 50.000 0.00 0.00 0.00 3.41
720 766 2.167281 ACTGACATTCTCCTCGTCCATG 59.833 50.000 0.00 0.00 0.00 3.66
721 767 2.167281 CTGACATTCTCCTCGTCCATGT 59.833 50.000 0.00 0.00 0.00 3.21
722 768 2.166459 TGACATTCTCCTCGTCCATGTC 59.834 50.000 4.04 4.04 42.72 3.06
944 1000 1.335810 CACACAAGTCAGCAAGCACAT 59.664 47.619 0.00 0.00 0.00 3.21
948 1004 1.878088 CAAGTCAGCAAGCACATCACT 59.122 47.619 0.00 0.00 0.00 3.41
951 1007 2.301296 AGTCAGCAAGCACATCACTAGT 59.699 45.455 0.00 0.00 0.00 2.57
952 1008 2.670414 GTCAGCAAGCACATCACTAGTC 59.330 50.000 0.00 0.00 0.00 2.59
953 1009 2.299867 TCAGCAAGCACATCACTAGTCA 59.700 45.455 0.00 0.00 0.00 3.41
954 1010 2.671888 CAGCAAGCACATCACTAGTCAG 59.328 50.000 0.00 0.00 0.00 3.51
955 1011 2.301296 AGCAAGCACATCACTAGTCAGT 59.699 45.455 0.00 0.00 34.42 3.41
956 1012 3.511540 AGCAAGCACATCACTAGTCAGTA 59.488 43.478 0.00 0.00 32.21 2.74
957 1013 3.614616 GCAAGCACATCACTAGTCAGTAC 59.385 47.826 0.00 0.00 32.21 2.73
970 1040 3.169099 AGTCAGTACTCACAGCCAGAAT 58.831 45.455 0.00 0.00 0.00 2.40
988 1058 2.430546 ATCAGCTCGATCGTTGATCC 57.569 50.000 15.94 0.00 35.83 3.36
989 1059 1.393603 TCAGCTCGATCGTTGATCCT 58.606 50.000 15.94 1.01 35.83 3.24
990 1060 1.335182 TCAGCTCGATCGTTGATCCTC 59.665 52.381 15.94 0.00 35.83 3.71
1031 1101 3.121030 GATGGCGTCGTTGCTGCT 61.121 61.111 0.00 0.00 34.52 4.24
1057 1127 0.032217 CTGCCTCTTCTCCCTCCTCT 60.032 60.000 0.00 0.00 0.00 3.69
1206 1279 4.197498 TACTACGGCCGCTTCGCC 62.197 66.667 28.58 0.00 46.13 5.54
1996 2069 2.073252 ATGGATGGTCTCGCACTCTA 57.927 50.000 0.00 0.00 0.00 2.43
2208 2285 5.651387 TTCCATGCATGTTTATTTTCGGA 57.349 34.783 24.58 8.36 0.00 4.55
2211 2288 4.142182 CCATGCATGTTTATTTTCGGAGGT 60.142 41.667 24.58 0.00 0.00 3.85
2218 2295 4.454504 TGTTTATTTTCGGAGGTGCTTCTC 59.545 41.667 0.00 0.00 0.00 2.87
2235 2312 1.686587 TCTCGACACACTGGATGTTGT 59.313 47.619 0.00 0.00 40.64 3.32
2250 2327 2.305928 TGTTGTTGCTGGTGCTATTGT 58.694 42.857 0.00 0.00 40.48 2.71
2251 2328 2.293122 TGTTGTTGCTGGTGCTATTGTC 59.707 45.455 0.00 0.00 40.48 3.18
2252 2329 2.554032 GTTGTTGCTGGTGCTATTGTCT 59.446 45.455 0.00 0.00 40.48 3.41
2253 2330 2.862541 TGTTGCTGGTGCTATTGTCTT 58.137 42.857 0.00 0.00 40.48 3.01
2254 2331 3.221771 TGTTGCTGGTGCTATTGTCTTT 58.778 40.909 0.00 0.00 40.48 2.52
2255 2332 3.004629 TGTTGCTGGTGCTATTGTCTTTG 59.995 43.478 0.00 0.00 40.48 2.77
2256 2333 3.138884 TGCTGGTGCTATTGTCTTTGA 57.861 42.857 0.00 0.00 40.48 2.69
2257 2334 3.689347 TGCTGGTGCTATTGTCTTTGAT 58.311 40.909 0.00 0.00 40.48 2.57
2258 2335 4.842574 TGCTGGTGCTATTGTCTTTGATA 58.157 39.130 0.00 0.00 40.48 2.15
2259 2336 4.877823 TGCTGGTGCTATTGTCTTTGATAG 59.122 41.667 0.00 0.00 40.48 2.08
2260 2337 5.118990 GCTGGTGCTATTGTCTTTGATAGA 58.881 41.667 0.00 0.00 36.03 1.98
2261 2338 5.236047 GCTGGTGCTATTGTCTTTGATAGAG 59.764 44.000 0.00 0.00 32.66 2.43
2262 2339 6.544928 TGGTGCTATTGTCTTTGATAGAGA 57.455 37.500 0.00 0.00 32.23 3.10
2263 2340 6.577103 TGGTGCTATTGTCTTTGATAGAGAG 58.423 40.000 0.00 0.00 32.23 3.20
2264 2341 5.988561 GGTGCTATTGTCTTTGATAGAGAGG 59.011 44.000 0.00 0.00 32.23 3.69
2265 2342 5.465056 GTGCTATTGTCTTTGATAGAGAGGC 59.535 44.000 0.00 0.00 32.23 4.70
2266 2343 4.683781 GCTATTGTCTTTGATAGAGAGGCG 59.316 45.833 0.00 0.00 32.23 5.52
2267 2344 5.508153 GCTATTGTCTTTGATAGAGAGGCGA 60.508 44.000 0.00 0.00 32.23 5.54
2268 2345 5.543507 ATTGTCTTTGATAGAGAGGCGAT 57.456 39.130 0.00 0.00 32.23 4.58
2345 2422 7.437748 AGGAAGAAGACGATCGATATGATTTT 58.562 34.615 24.34 0.00 37.47 1.82
2465 2542 9.632807 AAGTCTAGATATATTCATTTCTGCGAC 57.367 33.333 0.00 0.00 31.66 5.19
2468 2545 9.631452 TCTAGATATATTCATTTCTGCGACAAG 57.369 33.333 0.00 0.00 0.00 3.16
2476 2553 6.552859 TCATTTCTGCGACAAGTAATTTGA 57.447 33.333 0.00 0.00 39.21 2.69
2477 2554 6.602179 TCATTTCTGCGACAAGTAATTTGAG 58.398 36.000 0.00 0.00 39.21 3.02
2480 2557 4.627058 TCTGCGACAAGTAATTTGAGACA 58.373 39.130 0.00 0.00 39.21 3.41
2481 2558 4.686091 TCTGCGACAAGTAATTTGAGACAG 59.314 41.667 0.00 0.00 39.21 3.51
2530 2607 7.361542 CCTCTGTGTTGTCTATGATTTTCCTTG 60.362 40.741 0.00 0.00 0.00 3.61
2564 2643 8.651588 CAGATATAAGATAGAAACGCATTGGAC 58.348 37.037 0.00 0.00 0.00 4.02
2575 2654 1.134995 CGCATTGGACTCAGCTGACTA 60.135 52.381 13.74 0.00 0.00 2.59
2593 2672 6.647067 GCTGACTAATCCTTAGTTAATCGCAT 59.353 38.462 1.40 0.00 46.01 4.73
2598 2677 6.712241 AATCCTTAGTTAATCGCATGATCG 57.288 37.500 0.00 0.00 32.24 3.69
2601 2680 5.690409 TCCTTAGTTAATCGCATGATCGTTC 59.310 40.000 0.00 0.00 32.24 3.95
2625 2704 8.172159 TCGTCATGCAATTATGAACATTTTTC 57.828 30.769 0.00 0.00 38.69 2.29
2711 2790 5.776173 TCAACATAATTTTGAACACGGGT 57.224 34.783 2.69 0.00 29.89 5.28
2712 2791 6.150396 TCAACATAATTTTGAACACGGGTT 57.850 33.333 0.56 0.56 40.76 4.11
2750 2829 9.844257 TCAGAACAATGTTTAAAATTCCCAAAT 57.156 25.926 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.574826 GCCGAGATTAATGGTCTACCTCT 59.425 47.826 0.00 0.00 36.82 3.69
11 12 2.633481 GGCCGAGATTAATGGTCTACCT 59.367 50.000 0.00 0.00 36.82 3.08
14 15 2.295349 GACGGCCGAGATTAATGGTCTA 59.705 50.000 35.90 0.00 0.00 2.59
16 17 1.202486 TGACGGCCGAGATTAATGGTC 60.202 52.381 35.90 15.39 0.00 4.02
18 19 1.948104 TTGACGGCCGAGATTAATGG 58.052 50.000 35.90 0.00 0.00 3.16
20 21 3.804036 TGATTTGACGGCCGAGATTAAT 58.196 40.909 35.90 21.47 0.00 1.40
21 22 3.254470 TGATTTGACGGCCGAGATTAA 57.746 42.857 35.90 17.74 0.00 1.40
22 23 2.971660 TGATTTGACGGCCGAGATTA 57.028 45.000 35.90 13.22 0.00 1.75
23 24 1.942657 CATGATTTGACGGCCGAGATT 59.057 47.619 35.90 9.58 0.00 2.40
24 25 1.134401 ACATGATTTGACGGCCGAGAT 60.134 47.619 35.90 18.87 0.00 2.75
32 35 4.090729 CGTTGGATTGACATGATTTGACG 58.909 43.478 0.00 0.00 0.00 4.35
33 36 5.088739 GTCGTTGGATTGACATGATTTGAC 58.911 41.667 0.00 0.00 35.20 3.18
39 42 3.767131 TCTAGGTCGTTGGATTGACATGA 59.233 43.478 0.00 0.00 36.83 3.07
48 51 1.480954 GGAGCAATCTAGGTCGTTGGA 59.519 52.381 0.00 0.00 36.90 3.53
53 56 3.459232 TCATTGGAGCAATCTAGGTCG 57.541 47.619 0.00 0.00 36.90 4.79
55 58 4.970711 CTCATCATTGGAGCAATCTAGGT 58.029 43.478 0.00 0.00 31.05 3.08
67 70 5.006153 ACATGTTGAATGCTCATCATTGG 57.994 39.130 0.00 0.00 44.95 3.16
68 71 6.961359 AAACATGTTGAATGCTCATCATTG 57.039 33.333 12.82 0.00 44.95 2.82
72 75 4.731961 CGCTAAACATGTTGAATGCTCATC 59.268 41.667 12.82 0.00 0.00 2.92
78 81 3.563508 TGCACGCTAAACATGTTGAATG 58.436 40.909 12.82 7.87 0.00 2.67
79 82 3.913548 TGCACGCTAAACATGTTGAAT 57.086 38.095 12.82 0.00 0.00 2.57
80 83 3.699779 TTGCACGCTAAACATGTTGAA 57.300 38.095 12.82 2.69 0.00 2.69
108 111 6.293626 GCATAGACGTTGATATTTGGCAAGAT 60.294 38.462 0.00 0.00 0.00 2.40
109 112 5.007626 GCATAGACGTTGATATTTGGCAAGA 59.992 40.000 0.00 0.00 0.00 3.02
125 128 8.700644 GTGTTAATTACCTGATTAGCATAGACG 58.299 37.037 0.00 0.00 35.90 4.18
140 143 8.603242 AGGATATCAATCACGTGTTAATTACC 57.397 34.615 16.51 11.26 33.41 2.85
167 170 9.944663 GGAAATTAATTGCACGTTGATATTAGA 57.055 29.630 8.47 0.00 0.00 2.10
170 173 8.686334 AGAGGAAATTAATTGCACGTTGATATT 58.314 29.630 8.47 0.00 0.00 1.28
197 200 5.697067 ACGCCCAATCCACCTTAATATTAA 58.303 37.500 7.66 7.66 0.00 1.40
207 210 3.199891 GCGTACGCCCAATCCACC 61.200 66.667 29.51 0.00 34.56 4.61
208 211 1.373590 AATGCGTACGCCCAATCCAC 61.374 55.000 35.11 7.28 41.09 4.02
218 221 5.900339 ATATTGACCAGTAAATGCGTACG 57.100 39.130 11.84 11.84 0.00 3.67
223 226 9.516314 GGTCTTTTTATATTGACCAGTAAATGC 57.484 33.333 6.18 0.00 45.87 3.56
279 282 6.038714 GGAGCAATCTAGATCGTTGGATTTTT 59.961 38.462 5.51 0.00 31.51 1.94
295 307 3.759581 ACACTCATTGTTGGAGCAATCT 58.240 40.909 0.00 0.00 37.00 2.40
306 318 8.109705 TGCTAAATATGTTGAACACTCATTGT 57.890 30.769 0.00 0.00 41.74 2.71
307 319 9.016623 CATGCTAAATATGTTGAACACTCATTG 57.983 33.333 0.00 0.00 0.00 2.82
308 320 7.703621 GCATGCTAAATATGTTGAACACTCATT 59.296 33.333 11.37 0.00 0.00 2.57
418 430 7.396339 TGCACGTTGATATTAGGTAGGATATCT 59.604 37.037 2.05 0.00 36.60 1.98
424 436 6.861065 AATTGCACGTTGATATTAGGTAGG 57.139 37.500 0.00 0.00 0.00 3.18
474 516 5.750067 ACGTTTTCTTCAACACTACGTGTAT 59.250 36.000 0.00 0.00 46.79 2.29
480 522 4.267357 TGCACGTTTTCTTCAACACTAC 57.733 40.909 0.00 0.00 0.00 2.73
485 527 2.857152 TGCAATGCACGTTTTCTTCAAC 59.143 40.909 2.72 0.00 31.71 3.18
488 530 3.693300 CATGCAATGCACGTTTTCTTC 57.307 42.857 11.23 0.00 43.04 2.87
512 558 4.326009 GCACAAGTGGTTTTGTTGTTACTG 59.674 41.667 2.00 0.00 39.17 2.74
532 578 2.652530 CATTGGTGGCTGGTGCAC 59.347 61.111 8.80 8.80 41.91 4.57
546 592 6.270000 TCGAAGGTGGATTGAGATATACCATT 59.730 38.462 0.00 0.00 33.19 3.16
570 616 9.561270 GATTTCTTAGTTGATTTACCAGCTTTC 57.439 33.333 0.00 0.00 0.00 2.62
638 684 0.251354 GGCTGTGGAATGCTCTGAGA 59.749 55.000 9.28 0.00 0.00 3.27
642 688 1.378250 GCTGGCTGTGGAATGCTCT 60.378 57.895 0.00 0.00 0.00 4.09
657 703 1.727880 CCGCAACAATTTTCATGGCTG 59.272 47.619 0.00 0.00 0.00 4.85
678 724 1.821759 CACTTGGGTGCCAACGTGA 60.822 57.895 1.14 0.00 41.03 4.35
685 731 3.297620 CAGTGCCACTTGGGTGCC 61.298 66.667 0.00 0.00 41.75 5.01
701 747 2.166459 GACATGGACGAGGAGAATGTCA 59.834 50.000 8.75 0.00 44.15 3.58
709 755 2.758327 CGGGGACATGGACGAGGA 60.758 66.667 0.00 0.00 0.00 3.71
710 756 2.355986 TTCGGGGACATGGACGAGG 61.356 63.158 0.00 0.00 36.65 4.63
711 757 1.153628 GTTCGGGGACATGGACGAG 60.154 63.158 0.00 0.00 36.65 4.18
712 758 1.473497 TTGTTCGGGGACATGGACGA 61.473 55.000 0.00 0.00 0.00 4.20
713 759 1.004320 TTGTTCGGGGACATGGACG 60.004 57.895 0.00 0.00 0.00 4.79
714 760 1.296056 CGTTGTTCGGGGACATGGAC 61.296 60.000 0.00 0.00 35.71 4.02
715 761 1.004320 CGTTGTTCGGGGACATGGA 60.004 57.895 0.00 0.00 35.71 3.41
716 762 0.604243 TTCGTTGTTCGGGGACATGG 60.604 55.000 0.00 0.00 40.32 3.66
717 763 0.515564 GTTCGTTGTTCGGGGACATG 59.484 55.000 0.00 0.00 40.32 3.21
718 764 0.395312 AGTTCGTTGTTCGGGGACAT 59.605 50.000 0.00 0.00 40.32 3.06
719 765 0.249573 GAGTTCGTTGTTCGGGGACA 60.250 55.000 0.00 0.00 40.32 4.02
720 766 0.249573 TGAGTTCGTTGTTCGGGGAC 60.250 55.000 0.00 0.00 40.32 4.46
721 767 0.464870 TTGAGTTCGTTGTTCGGGGA 59.535 50.000 0.00 0.00 40.32 4.81
722 768 1.003223 GTTTGAGTTCGTTGTTCGGGG 60.003 52.381 0.00 0.00 40.32 5.73
817 864 0.981183 ATACGTGATGGGGTGTGTGT 59.019 50.000 0.00 0.00 0.00 3.72
897 945 2.060326 TGAGTTTGTCGATCGACCAC 57.940 50.000 37.58 32.28 43.97 4.16
900 948 3.241804 GCTTGATGAGTTTGTCGATCGAC 60.242 47.826 35.46 35.46 44.77 4.20
902 950 2.667969 TGCTTGATGAGTTTGTCGATCG 59.332 45.455 9.36 9.36 0.00 3.69
944 1000 3.082548 GGCTGTGAGTACTGACTAGTGA 58.917 50.000 13.79 0.00 37.78 3.41
948 1004 3.434940 TCTGGCTGTGAGTACTGACTA 57.565 47.619 13.79 0.00 35.45 2.59
951 1007 3.165071 TGATTCTGGCTGTGAGTACTGA 58.835 45.455 0.00 0.00 0.00 3.41
952 1008 3.519579 CTGATTCTGGCTGTGAGTACTG 58.480 50.000 0.00 0.00 0.00 2.74
953 1009 2.093764 GCTGATTCTGGCTGTGAGTACT 60.094 50.000 0.00 0.00 0.00 2.73
954 1010 2.093764 AGCTGATTCTGGCTGTGAGTAC 60.094 50.000 0.00 0.00 37.41 2.73
955 1011 2.167281 GAGCTGATTCTGGCTGTGAGTA 59.833 50.000 0.00 0.00 39.05 2.59
956 1012 0.982704 AGCTGATTCTGGCTGTGAGT 59.017 50.000 0.00 0.00 37.41 3.41
957 1013 1.654317 GAGCTGATTCTGGCTGTGAG 58.346 55.000 0.00 0.00 39.05 3.51
970 1040 1.335182 GAGGATCAACGATCGAGCTGA 59.665 52.381 24.34 19.87 39.72 4.26
1031 1101 1.479709 GGAGAAGAGGCAGAGCAGTA 58.520 55.000 0.00 0.00 0.00 2.74
1996 2069 1.747145 CTCCGGATCTCATGCAGCT 59.253 57.895 3.57 0.00 0.00 4.24
2208 2285 0.032678 CAGTGTGTCGAGAAGCACCT 59.967 55.000 1.89 0.00 34.94 4.00
2211 2288 0.969149 ATCCAGTGTGTCGAGAAGCA 59.031 50.000 0.00 0.00 0.00 3.91
2218 2295 1.334059 GCAACAACATCCAGTGTGTCG 60.334 52.381 0.00 0.00 41.14 4.35
2235 2312 3.485394 TCAAAGACAATAGCACCAGCAA 58.515 40.909 0.00 0.00 45.49 3.91
2250 2327 8.964476 ATTTTTAATCGCCTCTCTATCAAAGA 57.036 30.769 0.00 0.00 0.00 2.52
2251 2328 8.286097 GGATTTTTAATCGCCTCTCTATCAAAG 58.714 37.037 0.00 0.00 0.00 2.77
2252 2329 7.773224 TGGATTTTTAATCGCCTCTCTATCAAA 59.227 33.333 0.00 0.00 0.00 2.69
2253 2330 7.279615 TGGATTTTTAATCGCCTCTCTATCAA 58.720 34.615 0.00 0.00 0.00 2.57
2254 2331 6.826668 TGGATTTTTAATCGCCTCTCTATCA 58.173 36.000 0.00 0.00 0.00 2.15
2255 2332 7.730364 TTGGATTTTTAATCGCCTCTCTATC 57.270 36.000 0.00 0.00 0.00 2.08
2256 2333 7.775561 AGTTTGGATTTTTAATCGCCTCTCTAT 59.224 33.333 0.00 0.00 0.00 1.98
2257 2334 7.110155 AGTTTGGATTTTTAATCGCCTCTCTA 58.890 34.615 0.00 0.00 0.00 2.43
2258 2335 5.946377 AGTTTGGATTTTTAATCGCCTCTCT 59.054 36.000 0.00 0.00 0.00 3.10
2259 2336 6.196079 AGTTTGGATTTTTAATCGCCTCTC 57.804 37.500 0.00 0.00 0.00 3.20
2260 2337 6.208599 TGAAGTTTGGATTTTTAATCGCCTCT 59.791 34.615 0.00 0.00 0.00 3.69
2261 2338 6.308041 GTGAAGTTTGGATTTTTAATCGCCTC 59.692 38.462 0.00 0.00 0.00 4.70
2262 2339 6.156519 GTGAAGTTTGGATTTTTAATCGCCT 58.843 36.000 0.00 0.00 0.00 5.52
2263 2340 5.923684 TGTGAAGTTTGGATTTTTAATCGCC 59.076 36.000 0.00 0.00 0.00 5.54
2264 2341 7.169140 ACTTGTGAAGTTTGGATTTTTAATCGC 59.831 33.333 0.00 0.00 39.04 4.58
2265 2342 8.574196 ACTTGTGAAGTTTGGATTTTTAATCG 57.426 30.769 0.00 0.00 39.04 3.34
2366 2443 3.493699 CCAGACGAAGGGAGTACAAAACA 60.494 47.826 0.00 0.00 0.00 2.83
2440 2517 8.797438 TGTCGCAGAAATGAATATATCTAGACT 58.203 33.333 0.00 0.00 39.69 3.24
2450 2527 8.726068 TCAAATTACTTGTCGCAGAAATGAATA 58.274 29.630 0.00 0.00 39.69 1.75
2458 2535 4.627058 TGTCTCAAATTACTTGTCGCAGA 58.373 39.130 0.00 0.00 36.34 4.26
2465 2542 5.799213 ACTCCCTCTGTCTCAAATTACTTG 58.201 41.667 0.00 0.00 36.25 3.16
2468 2545 7.113658 TGATACTCCCTCTGTCTCAAATTAC 57.886 40.000 0.00 0.00 0.00 1.89
2476 2553 4.027437 GGACTTTGATACTCCCTCTGTCT 58.973 47.826 0.00 0.00 0.00 3.41
2477 2554 4.027437 AGGACTTTGATACTCCCTCTGTC 58.973 47.826 0.00 0.00 0.00 3.51
2480 2557 3.648739 GGAGGACTTTGATACTCCCTCT 58.351 50.000 0.00 0.00 42.87 3.69
2555 2634 0.390866 AGTCAGCTGAGTCCAATGCG 60.391 55.000 18.89 0.00 0.00 4.73
2575 2654 6.223852 ACGATCATGCGATTAACTAAGGATT 58.776 36.000 0.00 0.00 34.83 3.01
2593 2672 4.808364 TCATAATTGCATGACGAACGATCA 59.192 37.500 0.00 2.02 29.93 2.92
2598 2677 7.510428 AAATGTTCATAATTGCATGACGAAC 57.490 32.000 0.00 8.68 34.69 3.95
2601 2680 7.951287 TGAAAAATGTTCATAATTGCATGACG 58.049 30.769 0.00 0.00 34.69 4.35
2909 2992 6.208007 CCTAACCCGGTTTTTCTCTTTATGTT 59.792 38.462 8.44 0.00 0.00 2.71
2925 3008 3.132467 CCTCTAGAAGTTTCCTAACCCGG 59.868 52.174 0.00 0.00 34.71 5.73


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

AutoCloner maintained by Alex Coulton.