Multiple sequence alignment - TraesCS7A01G272200

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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 TraesCS7A01G272200 chr7A 100.000 5332 0 0 1 5332 285611141 285605810 0.000000e+00 9847
1 TraesCS7A01G272200 chr7A 98.571 70 1 0 682 751 285616083 285616014 2.020000e-24 124
2 TraesCS7A01G272200 chr7D 95.205 3149 114 13 709 3839 262738289 262735160 0.000000e+00 4944
3 TraesCS7A01G272200 chr7D 91.348 1491 71 20 3818 5257 262735013 262733530 0.000000e+00 1986
4 TraesCS7A01G272200 chr7B 90.415 2702 144 37 709 3349 240964535 240967182 0.000000e+00 3448
5 TraesCS7A01G272200 chr7B 94.966 874 32 6 3880 4747 240967762 240968629 0.000000e+00 1360
6 TraesCS7A01G272200 chr7B 92.130 432 30 1 3360 3787 240967332 240967763 1.640000e-169 606
7 TraesCS7A01G272200 chr7B 95.562 338 12 2 4869 5204 240968820 240969156 6.080000e-149 538
8 TraesCS7A01G272200 chr7B 95.652 161 5 1 4971 5129 240969314 240969154 1.910000e-64 257
9 TraesCS7A01G272200 chr7B 95.283 106 3 1 5227 5332 240969376 240969479 3.300000e-37 167
10 TraesCS7A01G272200 chr5D 92.658 681 50 0 1 681 286311651 286312331 0.000000e+00 981
11 TraesCS7A01G272200 chr3B 91.445 678 58 0 2 679 182217954 182217277 0.000000e+00 931
12 TraesCS7A01G272200 chr6B 85.756 681 97 0 1 681 463255150 463255830 0.000000e+00 721
13 TraesCS7A01G272200 chr2A 73.149 689 166 19 2 681 103809649 103810327 4.150000e-56 230
14 TraesCS7A01G272200 chr2A 85.600 125 13 4 992 1115 31911286 31911406 5.610000e-25 126
15 TraesCS7A01G272200 chr6A 72.308 455 116 10 181 630 38864534 38864983 3.350000e-27 134
16 TraesCS7A01G272200 chr2B 86.916 107 12 2 1010 1115 49384443 49384338 9.380000e-23 119
17 TraesCS7A01G272200 chr3D 89.247 93 9 1 3789 3880 568496482 568496390 1.210000e-21 115
18 TraesCS7A01G272200 chr3D 88.172 93 10 1 3789 3880 80943294 80943202 5.650000e-20 110
19 TraesCS7A01G272200 chr4A 84.545 110 12 5 3782 3887 716980542 716980434 2.630000e-18 104


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 TraesCS7A01G272200 chr7A 285605810 285611141 5331 True 9847.0 9847 100.0000 1 5332 1 chr7A.!!$R1 5331
1 TraesCS7A01G272200 chr7D 262733530 262738289 4759 True 3465.0 4944 93.2765 709 5257 2 chr7D.!!$R1 4548
2 TraesCS7A01G272200 chr7B 240964535 240969479 4944 False 1223.8 3448 93.6712 709 5332 5 chr7B.!!$F1 4623
3 TraesCS7A01G272200 chr5D 286311651 286312331 680 False 981.0 981 92.6580 1 681 1 chr5D.!!$F1 680
4 TraesCS7A01G272200 chr3B 182217277 182217954 677 True 931.0 931 91.4450 2 679 1 chr3B.!!$R1 677
5 TraesCS7A01G272200 chr6B 463255150 463255830 680 False 721.0 721 85.7560 1 681 1 chr6B.!!$F1 680
6 TraesCS7A01G272200 chr2A 103809649 103810327 678 False 230.0 230 73.1490 2 681 1 chr2A.!!$F2 679

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
694 695 0.037877 AGCAGCCACTCTTGATTGCT 59.962 50.000 0.0 0.0 37.38 3.91 F
1271 1283 0.250467 TTCCACTGCTGACTTGAGGC 60.250 55.000 0.0 0.0 0.00 4.70 F
1637 1671 3.189287 GTGTTTTACAGAGATGGGTGCTG 59.811 47.826 0.0 0.0 35.81 4.41 F
3163 3233 1.136891 CCGTCTGCTCATGTCCATACA 59.863 52.381 0.0 0.0 40.69 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 2137 1.006813 TACCAGATTGGGCATTGGGT 58.993 50.000 0.00 0.0 43.37 4.51 R
2104 2138 1.063717 ACTACCAGATTGGGCATTGGG 60.064 52.381 0.00 0.0 43.37 4.12 R
3218 3288 1.269413 CCAGAAAACTGCACTGCTTGG 60.269 52.381 1.98 0.0 0.00 3.61 R
4909 5422 0.986527 AGGTGGATGTGTGATCAGCA 59.013 50.000 0.00 0.0 0.00 4.41 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
28 29 9.934784 TTTGGTATAATACTACCTACCACACTA 57.065 33.333 0.00 0.00 42.41 2.74
92 93 3.349927 CACCCATGATTTCTGAGCTTGA 58.650 45.455 0.00 0.00 0.00 3.02
93 94 3.128242 CACCCATGATTTCTGAGCTTGAC 59.872 47.826 0.00 0.00 0.00 3.18
106 107 1.834263 AGCTTGACATACCTGGTCCTC 59.166 52.381 0.63 0.00 34.36 3.71
178 179 5.163513 AGCACTTAAAATCCAATTTGCTCG 58.836 37.500 0.00 0.00 31.77 5.03
226 227 2.670414 GCTGATCTCAAACGAGTGGAAG 59.330 50.000 0.00 0.00 0.00 3.46
331 332 8.832521 TGAAACTACAAAACAAGTACTATGGTG 58.167 33.333 0.00 0.00 0.00 4.17
356 357 7.553760 TGCATTTCTAATTGTGCAGAAGATAGA 59.446 33.333 14.31 14.31 42.13 1.98
369 370 7.226325 GTGCAGAAGATAGACAATTCAGCTTAT 59.774 37.037 0.00 0.00 36.68 1.73
449 450 5.721000 TCAAGAAGCATATTGGTCCCAATTT 59.279 36.000 16.26 6.53 43.32 1.82
492 493 0.539438 TGGTCAACCAAGATGGCACC 60.539 55.000 0.00 1.52 44.35 5.01
508 509 0.251297 CACCATCAAGACTGGCCCAA 60.251 55.000 0.00 0.00 37.27 4.12
517 518 2.240162 GACTGGCCCAACGGAGGTAG 62.240 65.000 0.00 0.00 0.00 3.18
564 565 0.904649 ATCTGCCAGTCGTCCAATGA 59.095 50.000 0.00 0.00 0.00 2.57
589 590 7.961351 ACTGATACAATGGGAAAATTTGTCAA 58.039 30.769 0.00 0.00 35.37 3.18
610 611 3.176924 AGACAGAAGCTACTTGGGAGA 57.823 47.619 0.00 0.00 0.00 3.71
615 616 2.843113 AGAAGCTACTTGGGAGAATGCT 59.157 45.455 0.00 0.00 0.00 3.79
627 628 4.012374 GGGAGAATGCTGACTTCATCAAA 58.988 43.478 0.00 0.00 36.69 2.69
657 658 3.072915 TCCCAGCATTCTTCAAGAAGACA 59.927 43.478 11.80 4.95 46.13 3.41
664 665 6.489361 AGCATTCTTCAAGAAGACAACTCAAT 59.511 34.615 11.80 0.00 46.13 2.57
666 667 7.308469 GCATTCTTCAAGAAGACAACTCAATCT 60.308 37.037 11.80 0.00 46.13 2.40
687 688 4.368391 CGTGAAGCAGCCACTCTT 57.632 55.556 0.00 0.00 32.64 2.85
688 689 1.864862 CGTGAAGCAGCCACTCTTG 59.135 57.895 0.00 0.00 32.64 3.02
689 690 0.601046 CGTGAAGCAGCCACTCTTGA 60.601 55.000 0.00 0.00 32.64 3.02
690 691 1.818642 GTGAAGCAGCCACTCTTGAT 58.181 50.000 0.00 0.00 0.00 2.57
691 692 2.157738 GTGAAGCAGCCACTCTTGATT 58.842 47.619 0.00 0.00 0.00 2.57
692 693 2.095364 GTGAAGCAGCCACTCTTGATTG 60.095 50.000 0.00 0.00 0.00 2.67
693 694 0.886563 AAGCAGCCACTCTTGATTGC 59.113 50.000 0.00 0.00 34.12 3.56
694 695 0.037877 AGCAGCCACTCTTGATTGCT 59.962 50.000 0.00 0.00 37.38 3.91
696 697 1.531423 CAGCCACTCTTGATTGCTGT 58.469 50.000 0.00 0.00 43.32 4.40
697 698 1.884579 CAGCCACTCTTGATTGCTGTT 59.115 47.619 0.00 0.00 43.32 3.16
698 699 1.884579 AGCCACTCTTGATTGCTGTTG 59.115 47.619 0.00 0.00 0.00 3.33
699 700 1.668047 GCCACTCTTGATTGCTGTTGC 60.668 52.381 0.00 0.00 40.20 4.17
700 701 1.884579 CCACTCTTGATTGCTGTTGCT 59.115 47.619 0.00 0.00 40.48 3.91
701 702 2.295349 CCACTCTTGATTGCTGTTGCTT 59.705 45.455 0.00 0.00 40.48 3.91
702 703 3.503363 CCACTCTTGATTGCTGTTGCTTA 59.497 43.478 0.00 0.00 40.48 3.09
703 704 4.379186 CCACTCTTGATTGCTGTTGCTTAG 60.379 45.833 0.00 0.00 40.48 2.18
704 705 3.190118 ACTCTTGATTGCTGTTGCTTAGC 59.810 43.478 0.00 0.00 41.49 3.09
705 706 3.415212 TCTTGATTGCTGTTGCTTAGCT 58.585 40.909 5.60 0.00 41.66 3.32
706 707 3.189910 TCTTGATTGCTGTTGCTTAGCTG 59.810 43.478 5.60 0.00 41.66 4.24
707 708 1.200716 TGATTGCTGTTGCTTAGCTGC 59.799 47.619 5.60 5.54 41.66 5.25
946 947 2.154462 CTTAGCCCAAACACACCTCAG 58.846 52.381 0.00 0.00 0.00 3.35
947 948 1.429930 TAGCCCAAACACACCTCAGA 58.570 50.000 0.00 0.00 0.00 3.27
990 997 2.030274 GCCGATCTCTTCTCTTCTAGGC 60.030 54.545 0.00 0.00 0.00 3.93
996 1003 2.281517 TCTTCTCTTCTAGGCTCGTCG 58.718 52.381 0.00 0.00 0.00 5.12
1140 1147 2.284921 CCAGCCCCAGTCTCCTGA 60.285 66.667 0.00 0.00 41.50 3.86
1161 1168 3.231207 TCCTCTCCTACTCCATACTGC 57.769 52.381 0.00 0.00 0.00 4.40
1228 1240 2.224314 AGAGCTCGTGTTTTGCTTAAGC 59.776 45.455 20.84 20.84 37.16 3.09
1259 1271 1.289109 CTACCGGCGTTGTTCCACTG 61.289 60.000 6.01 0.00 0.00 3.66
1270 1282 1.202687 TGTTCCACTGCTGACTTGAGG 60.203 52.381 0.00 0.00 0.00 3.86
1271 1283 0.250467 TTCCACTGCTGACTTGAGGC 60.250 55.000 0.00 0.00 0.00 4.70
1296 1308 5.450965 GCATGTCAGATTTGAACTAATGGGG 60.451 44.000 0.00 0.00 34.49 4.96
1394 1416 3.642705 GAGGCAATTTGACAAACACCTC 58.357 45.455 21.06 21.06 36.04 3.85
1417 1439 5.294306 TCACGTGCATGATTTTAGAGATTCC 59.706 40.000 14.17 0.00 0.00 3.01
1426 1448 8.944029 CATGATTTTAGAGATTCCAGCGATTAT 58.056 33.333 0.00 0.00 0.00 1.28
1460 1482 8.425577 GCTGTATGCCACGATTATTATCTAAT 57.574 34.615 0.00 0.00 35.15 1.73
1468 1490 7.268586 CCACGATTATTATCTAATGAGGAGGG 58.731 42.308 0.00 0.00 0.00 4.30
1488 1510 6.710744 GGAGGGTATGGTATTTAGTTCACATG 59.289 42.308 0.00 0.00 0.00 3.21
1512 1536 7.898918 TGGACTATAGTGTTTTACAGTAGCAA 58.101 34.615 10.90 0.00 37.43 3.91
1587 1621 3.469863 TTGCCCGTTCTCGCACCTT 62.470 57.895 0.00 0.00 33.97 3.50
1637 1671 3.189287 GTGTTTTACAGAGATGGGTGCTG 59.811 47.826 0.00 0.00 35.81 4.41
1756 1790 8.445275 TGAAGTTCTGAACATGTAGCTTTTAA 57.555 30.769 21.50 0.00 0.00 1.52
1862 1896 7.686434 AGTAACACCCATAAAACTACATCTGT 58.314 34.615 0.00 0.00 0.00 3.41
1869 1903 6.884295 CCCATAAAACTACATCTGTCTTCCAA 59.116 38.462 0.00 0.00 0.00 3.53
1872 1906 9.778993 CATAAAACTACATCTGTCTTCCAATTG 57.221 33.333 0.00 0.00 0.00 2.32
1902 1936 6.369340 CCTGTATGGTTACGATTTTGTGTGTA 59.631 38.462 0.00 0.00 0.00 2.90
2119 2153 7.722949 ATATATTTACCCAATGCCCAATCTG 57.277 36.000 0.00 0.00 0.00 2.90
2130 2164 3.653164 TGCCCAATCTGGTAGTAGATGA 58.347 45.455 0.00 0.00 37.48 2.92
2171 2231 8.378565 TCATTTTCCTATATGAGGGCTCTTTAG 58.621 37.037 0.00 0.00 46.70 1.85
2172 2232 5.746990 TTCCTATATGAGGGCTCTTTAGC 57.253 43.478 0.00 0.00 46.70 3.09
2196 2257 4.980339 AAGGAAATCAGTTTGGGCATTT 57.020 36.364 0.00 0.00 0.00 2.32
2199 2260 4.347583 AGGAAATCAGTTTGGGCATTTTCA 59.652 37.500 0.00 0.00 0.00 2.69
2272 2333 4.088634 TGGCTTAAGGACAAGATTGCAAT 58.911 39.130 12.83 12.83 0.00 3.56
2418 2479 9.334693 CATGCACAAGTAAGAGAATTCTTAAAC 57.665 33.333 9.87 7.99 45.08 2.01
2447 2508 9.937876 TTCTATTTTATCTTCTGAGAGGGTCTA 57.062 33.333 0.00 0.00 34.85 2.59
2482 2544 6.543831 GCAATTTGGTCCTAATGATACTCTGT 59.456 38.462 0.00 0.00 0.00 3.41
2491 2553 7.168302 GTCCTAATGATACTCTGTCAAATCACG 59.832 40.741 0.00 0.00 31.56 4.35
2557 2619 3.417185 CTTTCTTCGCTGCGGAAATAAC 58.583 45.455 23.03 0.00 0.00 1.89
3043 3112 7.639113 TTGTTTCTACCTGTCAATGTTTTCT 57.361 32.000 0.00 0.00 0.00 2.52
3163 3233 1.136891 CCGTCTGCTCATGTCCATACA 59.863 52.381 0.00 0.00 40.69 2.29
3164 3234 2.196749 CGTCTGCTCATGTCCATACAC 58.803 52.381 0.00 0.00 38.78 2.90
3168 3238 2.876550 CTGCTCATGTCCATACACCATG 59.123 50.000 0.00 0.00 38.78 3.66
3218 3288 3.317430 GTGAGATGGGATTTCAGGCATTC 59.683 47.826 0.00 0.00 0.00 2.67
3322 3392 5.187381 AGGCTTAACTACTCTTACCTTCACC 59.813 44.000 0.00 0.00 0.00 4.02
3358 3567 3.272581 TGGCCCTTTTACGTGTTATAGC 58.727 45.455 0.00 0.00 0.00 2.97
3371 3580 6.831769 ACGTGTTATAGCTATTATTGCATGC 58.168 36.000 12.39 11.82 0.00 4.06
3499 3712 6.040278 CCAGTGACTGAGACATGTATCTGTAT 59.960 42.308 26.55 15.95 34.04 2.29
3635 3849 3.070018 CTGTGAAGTAGGAGCACCTTTG 58.930 50.000 8.39 0.00 45.36 2.77
3653 3867 4.634004 CCTTTGCATCAGAAACACGGTATA 59.366 41.667 0.00 0.00 0.00 1.47
3787 4053 8.794406 GTTGAATACAAAGCCATAACATTTACG 58.206 33.333 0.00 0.00 37.77 3.18
3863 4298 1.462791 GTTCAAAACCGCGACACTTG 58.537 50.000 8.23 5.74 0.00 3.16
3972 4407 3.846588 AGCTACTGAAAGGGGAATCAGAA 59.153 43.478 9.56 0.00 44.64 3.02
4420 4859 6.909550 ATAAGTGCCAGGTTCAAATAACAA 57.090 33.333 0.00 0.00 0.00 2.83
4596 5035 9.311916 CAAAAGATATTGTTTGTGTCCTGAAAA 57.688 29.630 4.62 0.00 31.46 2.29
4613 5052 8.669243 GTCCTGAAAATATTTCTCAACCTAGTG 58.331 37.037 0.10 0.00 0.00 2.74
4709 5151 1.909781 CTGTTTGCAGCCCCATGGT 60.910 57.895 11.73 0.00 35.77 3.55
4710 5152 1.459158 TGTTTGCAGCCCCATGGTT 60.459 52.632 11.73 0.00 0.00 3.67
4791 5256 4.009675 TGAGTACCAACCTTACGATACGT 58.990 43.478 0.00 0.00 44.35 3.57
4794 5259 5.783111 AGTACCAACCTTACGATACGTTTT 58.217 37.500 0.00 0.00 41.54 2.43
4795 5260 5.863935 AGTACCAACCTTACGATACGTTTTC 59.136 40.000 0.00 0.00 41.54 2.29
4796 5261 4.886579 ACCAACCTTACGATACGTTTTCT 58.113 39.130 0.00 0.00 41.54 2.52
4798 5263 6.454795 ACCAACCTTACGATACGTTTTCTAA 58.545 36.000 0.00 0.00 41.54 2.10
4799 5264 6.928492 ACCAACCTTACGATACGTTTTCTAAA 59.072 34.615 0.00 0.00 41.54 1.85
4800 5265 7.116805 ACCAACCTTACGATACGTTTTCTAAAG 59.883 37.037 0.00 0.00 41.54 1.85
4801 5266 7.329226 CCAACCTTACGATACGTTTTCTAAAGA 59.671 37.037 0.00 0.00 41.54 2.52
4802 5267 8.371053 CAACCTTACGATACGTTTTCTAAAGAG 58.629 37.037 0.00 0.00 41.54 2.85
4805 5270 8.184192 CCTTACGATACGTTTTCTAAAGAGGTA 58.816 37.037 0.00 0.00 41.54 3.08
4806 5271 9.559958 CTTACGATACGTTTTCTAAAGAGGTAA 57.440 33.333 0.00 0.00 41.54 2.85
4810 5275 9.079833 CGATACGTTTTCTAAAGAGGTAATCAA 57.920 33.333 0.00 0.00 0.00 2.57
4812 5277 9.939802 ATACGTTTTCTAAAGAGGTAATCAAGT 57.060 29.630 0.00 0.00 0.00 3.16
4814 5279 9.201127 ACGTTTTCTAAAGAGGTAATCAAGTAC 57.799 33.333 0.00 0.00 0.00 2.73
4825 5290 8.529476 AGAGGTAATCAAGTACATACGTTTTCT 58.471 33.333 0.00 0.00 0.00 2.52
4867 5332 3.830178 TCCTCGACAAGTAATTCTGGACA 59.170 43.478 0.00 0.00 0.00 4.02
4909 5422 2.800985 CGTGAACTCGCTGATGATCCAT 60.801 50.000 0.00 0.00 0.00 3.41
4929 5442 1.352017 TGCTGATCACACATCCACCTT 59.648 47.619 0.00 0.00 0.00 3.50
4932 5445 1.066215 TGATCACACATCCACCTTCGG 60.066 52.381 0.00 0.00 0.00 4.30
4974 5487 8.635124 CCTTGTGTTTTAATACTAACAATTGCG 58.365 33.333 5.05 0.00 36.15 4.85
4989 5502 2.489938 TTGCGATTCTAAGCAAGGGT 57.510 45.000 0.00 0.00 46.83 4.34
5077 5591 2.734606 TGCGTGCACAACATAGTTAGTC 59.265 45.455 18.64 0.00 0.00 2.59
5160 5676 4.524316 TTCAAGGTCAGCAATTGGAATG 57.476 40.909 7.72 0.00 0.00 2.67
5202 5718 1.795768 TTGAAACAGTAGCAGCCGAG 58.204 50.000 0.00 0.00 0.00 4.63
5296 6011 3.507622 AGCCTGCAGTAACTTTGGAATTC 59.492 43.478 13.81 0.00 0.00 2.17
5321 6036 1.530293 GAGAACAGACAAGTGCAGCAG 59.470 52.381 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.049344 GGAAGGGGGACATCTTGATAGT 58.951 50.000 0.00 0.00 0.00 2.12
106 107 0.906756 TTCTGTGCCTCCTCCTCCTG 60.907 60.000 0.00 0.00 0.00 3.86
178 179 2.489722 GTTTCATTCTGTTCTGGGCCTC 59.510 50.000 4.53 0.00 0.00 4.70
226 227 2.891191 TCACCCACTTCAAATACCCC 57.109 50.000 0.00 0.00 0.00 4.95
331 332 7.854916 GTCTATCTTCTGCACAATTAGAAATGC 59.145 37.037 0.00 0.00 38.59 3.56
356 357 9.143631 GAAATTGCAGTTTATAAGCTGAATTGT 57.856 29.630 27.59 12.63 39.29 2.71
369 370 4.523943 ACATGCTCTGGAAATTGCAGTTTA 59.476 37.500 14.00 2.69 37.12 2.01
449 450 1.306654 AGGTTCGGGCTGGGTATGA 60.307 57.895 0.00 0.00 0.00 2.15
492 493 1.308069 CCGTTGGGCCAGTCTTGATG 61.308 60.000 6.23 0.00 0.00 3.07
508 509 0.038526 CGAACTTGCACTACCTCCGT 60.039 55.000 0.00 0.00 0.00 4.69
517 518 1.658409 GCACTTGCCGAACTTGCAC 60.658 57.895 0.00 0.00 38.72 4.57
564 565 7.537596 TGACAAATTTTCCCATTGTATCAGT 57.462 32.000 0.00 0.00 37.41 3.41
589 590 3.511477 TCTCCCAAGTAGCTTCTGTCTT 58.489 45.455 0.00 0.00 0.00 3.01
610 611 5.877012 ACGAGTATTTGATGAAGTCAGCATT 59.123 36.000 0.00 0.00 42.26 3.56
615 616 5.175859 GGGAACGAGTATTTGATGAAGTCA 58.824 41.667 0.00 0.00 34.25 3.41
627 628 3.197766 TGAAGAATGCTGGGAACGAGTAT 59.802 43.478 0.00 0.00 0.00 2.12
657 658 1.537202 GCTTCACGCCAAGATTGAGTT 59.463 47.619 0.00 0.00 0.00 3.01
664 665 2.669569 GGCTGCTTCACGCCAAGA 60.670 61.111 0.00 0.00 45.59 3.02
681 682 3.637998 AAGCAACAGCAATCAAGAGTG 57.362 42.857 0.00 0.00 0.00 3.51
682 683 3.190118 GCTAAGCAACAGCAATCAAGAGT 59.810 43.478 0.00 0.00 38.93 3.24
683 684 3.439476 AGCTAAGCAACAGCAATCAAGAG 59.561 43.478 6.93 0.00 41.66 2.85
684 685 3.189910 CAGCTAAGCAACAGCAATCAAGA 59.810 43.478 6.93 0.00 41.66 3.02
685 686 3.499048 CAGCTAAGCAACAGCAATCAAG 58.501 45.455 6.93 0.00 41.66 3.02
686 687 2.352030 GCAGCTAAGCAACAGCAATCAA 60.352 45.455 6.93 0.00 41.66 2.57
687 688 1.200716 GCAGCTAAGCAACAGCAATCA 59.799 47.619 6.93 0.00 41.66 2.57
688 689 1.468736 GGCAGCTAAGCAACAGCAATC 60.469 52.381 6.93 0.00 41.66 2.67
689 690 0.529378 GGCAGCTAAGCAACAGCAAT 59.471 50.000 6.93 0.00 41.66 3.56
690 691 0.822944 TGGCAGCTAAGCAACAGCAA 60.823 50.000 6.93 0.00 41.66 3.91
691 692 1.228215 TGGCAGCTAAGCAACAGCA 60.228 52.632 6.93 0.00 41.66 4.41
692 693 1.505353 CTGGCAGCTAAGCAACAGC 59.495 57.895 0.00 0.00 39.41 4.40
693 694 1.239296 TGCTGGCAGCTAAGCAACAG 61.239 55.000 36.50 6.68 46.06 3.16
694 695 1.228215 TGCTGGCAGCTAAGCAACA 60.228 52.632 36.50 14.20 46.06 3.33
695 696 3.672293 TGCTGGCAGCTAAGCAAC 58.328 55.556 36.50 9.19 46.06 4.17
697 698 1.228215 TTGTGCTGGCAGCTAAGCA 60.228 52.632 36.50 25.84 46.84 3.91
698 699 1.211190 GTTGTGCTGGCAGCTAAGC 59.789 57.895 36.50 23.25 42.97 3.09
699 700 1.499056 CGTTGTGCTGGCAGCTAAG 59.501 57.895 36.50 20.88 42.97 2.18
700 701 1.965930 CCGTTGTGCTGGCAGCTAA 60.966 57.895 36.50 27.76 42.97 3.09
701 702 2.358615 CCGTTGTGCTGGCAGCTA 60.359 61.111 36.50 24.06 42.97 3.32
702 703 3.772853 TTCCGTTGTGCTGGCAGCT 62.773 57.895 36.50 0.00 42.97 4.24
703 704 3.286751 TTCCGTTGTGCTGGCAGC 61.287 61.111 31.91 31.91 42.82 5.25
704 705 2.639286 GTTCCGTTGTGCTGGCAG 59.361 61.111 10.94 10.94 0.00 4.85
705 706 3.276091 CGTTCCGTTGTGCTGGCA 61.276 61.111 0.00 0.00 0.00 4.92
706 707 2.054140 TTTCGTTCCGTTGTGCTGGC 62.054 55.000 0.00 0.00 0.00 4.85
707 708 0.378962 TTTTCGTTCCGTTGTGCTGG 59.621 50.000 0.00 0.00 0.00 4.85
758 759 4.408821 TCCTGATGTGGTGCGGGC 62.409 66.667 0.00 0.00 0.00 6.13
905 906 3.429080 GAGAGAGGAGCAGCGGCAG 62.429 68.421 12.44 0.00 44.61 4.85
906 907 3.456365 GAGAGAGGAGCAGCGGCA 61.456 66.667 12.44 0.00 44.61 5.69
907 908 4.219999 GGAGAGAGGAGCAGCGGC 62.220 72.222 0.00 0.00 41.61 6.53
908 909 2.441901 AGGAGAGAGGAGCAGCGG 60.442 66.667 0.00 0.00 0.00 5.52
909 910 1.037030 AAGAGGAGAGAGGAGCAGCG 61.037 60.000 0.00 0.00 0.00 5.18
946 947 3.462678 GGGGAGCGAGGTGAGGTC 61.463 72.222 0.00 0.00 35.57 3.85
1140 1147 3.401002 AGCAGTATGGAGTAGGAGAGGAT 59.599 47.826 0.00 0.00 35.86 3.24
1161 1168 1.194098 CAGACGAGCAAACAGAAGCAG 59.806 52.381 0.00 0.00 0.00 4.24
1228 1240 1.366366 CCGGTAGGTAATCGCAGGG 59.634 63.158 0.00 0.00 0.00 4.45
1259 1271 1.975363 GACATGCGCCTCAAGTCAGC 61.975 60.000 4.18 0.00 41.61 4.26
1270 1282 2.907910 AGTTCAAATCTGACATGCGC 57.092 45.000 0.00 0.00 0.00 6.09
1271 1283 5.268544 CCATTAGTTCAAATCTGACATGCG 58.731 41.667 0.00 0.00 0.00 4.73
1296 1308 0.659123 CGCGGCAGTAACAAACCAAC 60.659 55.000 0.00 0.00 0.00 3.77
1320 1332 4.166888 GCGAGGCCTGGCATCTGA 62.167 66.667 32.34 0.00 37.20 3.27
1394 1416 5.065090 TGGAATCTCTAAAATCATGCACGTG 59.935 40.000 12.28 12.28 0.00 4.49
1417 1439 3.002656 ACAGCCGAAATTCATAATCGCTG 59.997 43.478 14.04 14.04 41.72 5.18
1460 1482 6.099269 GTGAACTAAATACCATACCCTCCTCA 59.901 42.308 0.00 0.00 0.00 3.86
1468 1490 9.998106 ATAGTCCATGTGAACTAAATACCATAC 57.002 33.333 4.54 0.00 0.00 2.39
1488 1510 8.248945 TCTTGCTACTGTAAAACACTATAGTCC 58.751 37.037 1.26 0.00 0.00 3.85
1512 1536 1.349357 GGGGCAGTTCTCAACTTCTCT 59.651 52.381 0.00 0.00 40.46 3.10
1587 1621 5.197451 TGTAAAGAAAAGTTCAAGAGGCCA 58.803 37.500 5.01 0.00 0.00 5.36
1637 1671 8.850156 ACATATTTCTTCCCAAGTGCATATAAC 58.150 33.333 0.00 0.00 0.00 1.89
1697 1731 6.432403 AAGTTTTTATCCCTTTCATTGCCA 57.568 33.333 0.00 0.00 0.00 4.92
1862 1896 4.220382 CCATACAGGCAAACAATTGGAAGA 59.780 41.667 10.83 0.00 37.02 2.87
1869 1903 4.328536 TCGTAACCATACAGGCAAACAAT 58.671 39.130 0.00 0.00 43.14 2.71
1872 1906 4.957759 AATCGTAACCATACAGGCAAAC 57.042 40.909 0.00 0.00 43.14 2.93
1902 1936 3.425659 GAAAAGCAAGGAAGTCCAGGAT 58.574 45.455 0.00 0.00 38.89 3.24
2098 2132 4.222336 CCAGATTGGGCATTGGGTAAATA 58.778 43.478 0.00 0.00 32.67 1.40
2099 2133 3.040477 CCAGATTGGGCATTGGGTAAAT 58.960 45.455 0.00 0.00 32.67 1.40
2101 2135 1.360852 ACCAGATTGGGCATTGGGTAA 59.639 47.619 0.00 0.00 43.37 2.85
2103 2137 1.006813 TACCAGATTGGGCATTGGGT 58.993 50.000 0.00 0.00 43.37 4.51
2104 2138 1.063717 ACTACCAGATTGGGCATTGGG 60.064 52.381 0.00 0.00 43.37 4.12
2110 2144 3.643792 AGTCATCTACTACCAGATTGGGC 59.356 47.826 0.00 0.00 43.37 5.36
2171 2231 2.166459 GCCCAAACTGATTTCCTTAGGC 59.834 50.000 0.00 0.00 0.00 3.93
2172 2232 3.430453 TGCCCAAACTGATTTCCTTAGG 58.570 45.455 0.00 0.00 0.00 2.69
2221 2282 4.017380 ACGTACAGCGATAGAAACAGAG 57.983 45.455 0.00 0.00 44.77 3.35
2233 2294 3.812256 GCCATTGCATGACGTACAGCG 62.812 57.143 0.00 0.00 41.45 5.18
2296 2357 5.416083 TCCGTGTGTAATCATCCTAAACTG 58.584 41.667 0.00 0.00 0.00 3.16
2396 2457 7.797819 AGCGTTTAAGAATTCTCTTACTTGTG 58.202 34.615 8.78 0.00 42.61 3.33
2418 2479 6.644592 CCCTCTCAGAAGATAAAATAGAAGCG 59.355 42.308 0.00 0.00 0.00 4.68
2447 2508 4.154942 AGGACCAAATTGCAATTCTGTCT 58.845 39.130 31.71 22.69 33.19 3.41
2482 2544 6.366604 TGAAATTAGTTAGTCGCGTGATTTGA 59.633 34.615 5.77 0.00 0.00 2.69
2491 2553 7.481798 CCAACAAATCTGAAATTAGTTAGTCGC 59.518 37.037 0.00 0.00 0.00 5.19
2723 2785 2.410939 CATCGGCTCACATATGTGGAG 58.589 52.381 30.56 25.31 45.65 3.86
3103 3172 4.276642 TGCAACTACATTTGATATGCCCA 58.723 39.130 0.00 0.00 0.00 5.36
3168 3238 6.531594 GGTAAAAAGTATCAAATGCCAAGAGC 59.468 38.462 0.00 0.00 44.14 4.09
3218 3288 1.269413 CCAGAAAACTGCACTGCTTGG 60.269 52.381 1.98 0.00 0.00 3.61
3247 3317 3.133721 AGCTGTACATGAGGAGATTGGTC 59.866 47.826 0.00 0.00 0.00 4.02
3322 3392 1.549170 GGGCCAGTATACGGGTGATAG 59.451 57.143 21.16 0.00 33.54 2.08
3358 3567 9.770503 GAAACATAGATCAGCATGCAATAATAG 57.229 33.333 21.98 5.76 34.76 1.73
3499 3712 2.355756 GCGCCTGCTCATGAAGAAATAA 59.644 45.455 0.00 0.00 38.39 1.40
3635 3849 8.648097 CATTACTATATACCGTGTTTCTGATGC 58.352 37.037 0.00 0.00 0.00 3.91
3653 3867 9.280456 TCCCTAAGAGAAAAAGTCCATTACTAT 57.720 33.333 0.00 0.00 37.50 2.12
3787 4053 1.710816 ATTCTGGATCGGAGGGAGTC 58.289 55.000 0.00 0.00 0.00 3.36
3863 4298 5.485209 AATAAGTCCCTCCGATCCATAAC 57.515 43.478 0.00 0.00 0.00 1.89
3972 4407 2.043801 AGTAGGGAGCTTCAGAAGACCT 59.956 50.000 14.86 17.73 34.49 3.85
4211 4648 8.025445 GCAGTTGAAACATCTGATTTTGTAGAT 58.975 33.333 12.17 0.00 34.27 1.98
4262 4699 4.715523 GCCGCAACTGCTACCCCA 62.716 66.667 0.00 0.00 39.32 4.96
4407 4846 9.612620 CATCACTAGAGTTTTGTTATTTGAACC 57.387 33.333 0.00 0.00 0.00 3.62
4420 4859 6.119536 TGTTGGTTGTTCATCACTAGAGTTT 58.880 36.000 0.00 0.00 0.00 2.66
4476 4915 9.935241 GTATGATGTATACATGAAGGAGATGTT 57.065 33.333 22.93 0.00 41.11 2.71
4578 5017 9.696917 GAGAAATATTTTCAGGACACAAACAAT 57.303 29.630 1.43 0.00 0.00 2.71
4613 5052 7.161404 TGGTCTCTATTGGTCAATATATGCAC 58.839 38.462 4.15 0.00 33.29 4.57
4723 5165 2.029073 ACGGTTGGCACTCGTCAG 59.971 61.111 8.25 0.00 30.89 3.51
4784 5249 8.624701 TGATTACCTCTTTAGAAAACGTATCG 57.375 34.615 0.00 0.00 0.00 2.92
4794 5259 9.182214 ACGTATGTACTTGATTACCTCTTTAGA 57.818 33.333 0.00 0.00 0.00 2.10
4795 5260 9.798994 AACGTATGTACTTGATTACCTCTTTAG 57.201 33.333 0.00 0.00 0.00 1.85
4798 5263 9.148104 GAAAACGTATGTACTTGATTACCTCTT 57.852 33.333 0.00 0.00 0.00 2.85
4799 5264 8.529476 AGAAAACGTATGTACTTGATTACCTCT 58.471 33.333 0.00 0.00 0.00 3.69
4800 5265 8.699283 AGAAAACGTATGTACTTGATTACCTC 57.301 34.615 0.00 0.00 0.00 3.85
4806 5271 9.367444 CCTCTTTAGAAAACGTATGTACTTGAT 57.633 33.333 0.00 0.00 0.00 2.57
4813 5278 9.715121 TTGATTACCTCTTTAGAAAACGTATGT 57.285 29.630 0.00 0.00 0.00 2.29
4817 5282 9.201127 GTACTTGATTACCTCTTTAGAAAACGT 57.799 33.333 0.00 0.00 0.00 3.99
4818 5283 9.199982 TGTACTTGATTACCTCTTTAGAAAACG 57.800 33.333 0.00 0.00 0.00 3.60
4825 5290 7.558807 TCGAGGATGTACTTGATTACCTCTTTA 59.441 37.037 0.00 0.00 39.85 1.85
4846 5311 4.188247 TGTCCAGAATTACTTGTCGAGG 57.812 45.455 0.00 0.00 0.00 4.63
4867 5332 1.134037 TGTCGGTTGCCCTTGTAACTT 60.134 47.619 0.00 0.00 37.27 2.66
4909 5422 0.986527 AGGTGGATGTGTGATCAGCA 59.013 50.000 0.00 0.00 0.00 4.41
4929 5442 7.670140 ACACAAGGATATCATAGACTATTCCGA 59.330 37.037 4.83 0.00 0.00 4.55
4968 5481 3.356290 ACCCTTGCTTAGAATCGCAATT 58.644 40.909 0.00 0.00 44.22 2.32
4974 5487 5.297029 GTCCATGTTACCCTTGCTTAGAATC 59.703 44.000 0.00 0.00 0.00 2.52
4989 5502 7.851228 AGAAGAACATCACTATGTCCATGTTA 58.149 34.615 0.00 0.00 45.79 2.41
5077 5591 6.238320 GCTATTCCAAAGTTGATGAGCTAGTG 60.238 42.308 0.00 0.00 0.00 2.74
5202 5718 0.254178 TCCCAAATCCAGCTCAGCTC 59.746 55.000 0.00 0.00 36.40 4.09
5209 5725 0.243636 CGTTTGGTCCCAAATCCAGC 59.756 55.000 14.19 1.25 45.90 4.85
5210 5726 1.904287 TCGTTTGGTCCCAAATCCAG 58.096 50.000 14.19 7.29 45.90 3.86
5211 5727 1.957877 GTTCGTTTGGTCCCAAATCCA 59.042 47.619 14.19 0.00 45.90 3.41
5259 5974 7.938140 ACTGCAGGCTATTTACTTTCATTTA 57.062 32.000 19.93 0.00 0.00 1.40
5260 5975 6.840780 ACTGCAGGCTATTTACTTTCATTT 57.159 33.333 19.93 0.00 0.00 2.32
5272 5987 4.301072 TTCCAAAGTTACTGCAGGCTAT 57.699 40.909 19.93 0.00 0.00 2.97


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

AutoCloner maintained by Alex Coulton.