Multiple sequence alignment - TraesCS5A01G335000

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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 TraesCS5A01G335000 chr5A 100.000 5439 0 0 1 5439 544451905 544457343 0.000000e+00 10045
1 TraesCS5A01G335000 chr5A 84.225 3531 505 30 961 4450 544502313 544505832 0.000000e+00 3387
2 TraesCS5A01G335000 chr5A 86.227 2062 269 12 2400 4450 544246346 544248403 0.000000e+00 2220
3 TraesCS5A01G335000 chr5A 83.905 1721 255 12 1125 2828 544158653 544160368 0.000000e+00 1624
4 TraesCS5A01G335000 chr5A 83.075 1743 269 16 1017 2743 544461637 544463369 0.000000e+00 1561
5 TraesCS5A01G335000 chr5D 94.327 4442 205 13 33 4445 428669663 428674086 0.000000e+00 6763
6 TraesCS5A01G335000 chr5D 84.774 3481 487 31 986 4450 428512205 428515658 0.000000e+00 3452
7 TraesCS5A01G335000 chr5D 85.380 3338 461 20 1134 4450 428593106 428596437 0.000000e+00 3435
8 TraesCS5A01G335000 chr5D 83.945 3326 482 42 1139 4432 428565642 428568947 0.000000e+00 3136
9 TraesCS5A01G335000 chr5D 84.527 782 101 15 4632 5398 24043074 24043850 0.000000e+00 756
10 TraesCS5A01G335000 chr5B 92.662 4347 251 37 154 4450 517796828 517801156 0.000000e+00 6198
11 TraesCS5A01G335000 chr5B 84.695 3489 493 26 984 4450 517774896 517778365 0.000000e+00 3446
12 TraesCS5A01G335000 chr5B 84.928 3324 448 36 1139 4432 517694509 517697809 0.000000e+00 3314
13 TraesCS5A01G335000 chr5B 86.028 866 99 15 3583 4432 517706538 517707397 0.000000e+00 909
14 TraesCS5A01G335000 chr6D 86.567 1005 114 7 4446 5431 19624001 19622999 0.000000e+00 1088
15 TraesCS5A01G335000 chr7B 88.142 818 78 10 4632 5438 63627381 63628190 0.000000e+00 955
16 TraesCS5A01G335000 chr7B 83.376 782 109 15 4632 5398 595572187 595571412 0.000000e+00 704
17 TraesCS5A01G335000 chr7B 81.433 614 114 0 4782 5395 696270441 696269828 2.260000e-138 503
18 TraesCS5A01G335000 chr1D 88.855 664 52 9 4446 5089 484721775 484721114 0.000000e+00 797
19 TraesCS5A01G335000 chr1D 86.068 646 88 2 4754 5398 52114631 52113987 0.000000e+00 693
20 TraesCS5A01G335000 chr7A 87.857 560 52 6 4625 5170 539653828 539654385 1.280000e-180 643
21 TraesCS5A01G335000 chr3A 81.433 684 118 5 4754 5430 518724361 518725042 7.960000e-153 551
22 TraesCS5A01G335000 chr4A 82.439 615 106 2 4782 5395 30361078 30360465 2.230000e-148 536
23 TraesCS5A01G335000 chr6B 88.288 444 37 9 4632 5064 716104724 716104285 8.080000e-143 518
24 TraesCS5A01G335000 chr3B 81.433 614 114 0 4782 5395 572256342 572256955 2.260000e-138 503
25 TraesCS5A01G335000 chr3B 83.193 238 28 10 4446 4679 8580457 8580228 1.990000e-49 207
26 TraesCS5A01G335000 chr1B 86.339 183 16 5 4520 4694 674829493 674829312 2.000000e-44 191


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 TraesCS5A01G335000 chr5A 544451905 544457343 5438 False 10045 10045 100.000 1 5439 1 chr5A.!!$F3 5438
1 TraesCS5A01G335000 chr5A 544502313 544505832 3519 False 3387 3387 84.225 961 4450 1 chr5A.!!$F5 3489
2 TraesCS5A01G335000 chr5A 544246346 544248403 2057 False 2220 2220 86.227 2400 4450 1 chr5A.!!$F2 2050
3 TraesCS5A01G335000 chr5A 544158653 544160368 1715 False 1624 1624 83.905 1125 2828 1 chr5A.!!$F1 1703
4 TraesCS5A01G335000 chr5A 544461637 544463369 1732 False 1561 1561 83.075 1017 2743 1 chr5A.!!$F4 1726
5 TraesCS5A01G335000 chr5D 428669663 428674086 4423 False 6763 6763 94.327 33 4445 1 chr5D.!!$F5 4412
6 TraesCS5A01G335000 chr5D 428512205 428515658 3453 False 3452 3452 84.774 986 4450 1 chr5D.!!$F2 3464
7 TraesCS5A01G335000 chr5D 428593106 428596437 3331 False 3435 3435 85.380 1134 4450 1 chr5D.!!$F4 3316
8 TraesCS5A01G335000 chr5D 428565642 428568947 3305 False 3136 3136 83.945 1139 4432 1 chr5D.!!$F3 3293
9 TraesCS5A01G335000 chr5D 24043074 24043850 776 False 756 756 84.527 4632 5398 1 chr5D.!!$F1 766
10 TraesCS5A01G335000 chr5B 517796828 517801156 4328 False 6198 6198 92.662 154 4450 1 chr5B.!!$F4 4296
11 TraesCS5A01G335000 chr5B 517774896 517778365 3469 False 3446 3446 84.695 984 4450 1 chr5B.!!$F3 3466
12 TraesCS5A01G335000 chr5B 517694509 517697809 3300 False 3314 3314 84.928 1139 4432 1 chr5B.!!$F1 3293
13 TraesCS5A01G335000 chr5B 517706538 517707397 859 False 909 909 86.028 3583 4432 1 chr5B.!!$F2 849
14 TraesCS5A01G335000 chr6D 19622999 19624001 1002 True 1088 1088 86.567 4446 5431 1 chr6D.!!$R1 985
15 TraesCS5A01G335000 chr7B 63627381 63628190 809 False 955 955 88.142 4632 5438 1 chr7B.!!$F1 806
16 TraesCS5A01G335000 chr7B 595571412 595572187 775 True 704 704 83.376 4632 5398 1 chr7B.!!$R1 766
17 TraesCS5A01G335000 chr7B 696269828 696270441 613 True 503 503 81.433 4782 5395 1 chr7B.!!$R2 613
18 TraesCS5A01G335000 chr1D 484721114 484721775 661 True 797 797 88.855 4446 5089 1 chr1D.!!$R2 643
19 TraesCS5A01G335000 chr1D 52113987 52114631 644 True 693 693 86.068 4754 5398 1 chr1D.!!$R1 644
20 TraesCS5A01G335000 chr7A 539653828 539654385 557 False 643 643 87.857 4625 5170 1 chr7A.!!$F1 545
21 TraesCS5A01G335000 chr3A 518724361 518725042 681 False 551 551 81.433 4754 5430 1 chr3A.!!$F1 676
22 TraesCS5A01G335000 chr4A 30360465 30361078 613 True 536 536 82.439 4782 5395 1 chr4A.!!$R1 613
23 TraesCS5A01G335000 chr3B 572256342 572256955 613 False 503 503 81.433 4782 5395 1 chr3B.!!$F1 613

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
301 314 2.421725 TGGAGGACCATATTCCAGCAT 58.578 47.619 0.0 0.0 41.77 3.79 F
1419 1517 0.107654 ACAATTACCAGCTCTCCGGC 60.108 55.000 0.0 0.0 0.00 6.13 F
1716 1814 1.004277 GTCCTTTCTGGCCACATACCA 59.996 52.381 0.0 0.0 35.26 3.25 F
1849 1950 1.895798 TGGCACAAAACAACCTGAACA 59.104 42.857 0.0 0.0 31.92 3.18 F
3234 3343 2.093235 CCTAGAAGGCTCTGTCCCAAAG 60.093 54.545 0.0 0.0 32.70 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1447 1545 0.482446 TTGAGGGTGGAAAGCATGGT 59.518 50.0 0.00 0.0 0.00 3.55 R
3138 3247 1.308998 GGATGGTACCGCTGAATTGG 58.691 55.0 7.57 0.0 0.00 3.16 R
3708 3821 0.103026 ATAGCTTGACGATGCTGCGA 59.897 50.0 0.00 0.0 40.08 5.10 R
3746 3859 1.340088 TACAAGGAACCTGTACCGCA 58.660 50.0 0.00 0.0 0.00 5.69 R
4935 5084 0.975556 TGCCTGATCCTTGCCGTCTA 60.976 55.0 0.00 0.0 0.00 2.59 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
29 30 7.745620 CCTAATGGGTTGAATTAGTCCATAC 57.254 40.000 0.00 0.00 37.24 2.39
30 31 6.426937 CCTAATGGGTTGAATTAGTCCATACG 59.573 42.308 0.00 0.00 37.24 3.06
31 32 5.623956 ATGGGTTGAATTAGTCCATACGA 57.376 39.130 0.00 0.00 36.55 3.43
99 100 5.551233 TCAGCTAGTTAATGCAAAGACACT 58.449 37.500 0.00 0.00 0.00 3.55
101 102 4.154918 AGCTAGTTAATGCAAAGACACTGC 59.845 41.667 0.00 0.00 40.35 4.40
113 114 7.885297 TGCAAAGACACTGCTAATTTAAATCT 58.115 30.769 0.10 0.00 40.59 2.40
225 238 5.786264 TCCTCCGATCCAAAGTAAGTATC 57.214 43.478 0.00 0.00 0.00 2.24
234 247 4.756135 TCCAAAGTAAGTATCGCGGTTTTT 59.244 37.500 6.13 0.00 0.00 1.94
301 314 2.421725 TGGAGGACCATATTCCAGCAT 58.578 47.619 0.00 0.00 41.77 3.79
335 348 6.037500 TCACAAATATGCATTCACTCTAGCAC 59.962 38.462 3.54 0.00 40.14 4.40
410 429 4.963276 TTTGAACCCTGCTAAATCATCG 57.037 40.909 0.00 0.00 0.00 3.84
606 640 2.997897 ACCTCTGTCTGGTCCCGC 60.998 66.667 0.00 0.00 31.03 6.13
702 736 3.152341 CTGAGGAAAAATGTGAGGCTGT 58.848 45.455 0.00 0.00 0.00 4.40
727 761 5.182190 TGTGCCTGCGAATCTGTTTATAAAA 59.818 36.000 0.00 0.00 0.00 1.52
747 781 3.073735 CTGGACGAGGAGCCAGCT 61.074 66.667 0.00 0.00 44.53 4.24
893 932 4.789784 CGCAGGTACTCTTCTTAGCTATC 58.210 47.826 0.00 0.00 34.60 2.08
894 933 4.611807 CGCAGGTACTCTTCTTAGCTATCG 60.612 50.000 0.00 0.00 34.60 2.92
895 934 4.789784 CAGGTACTCTTCTTAGCTATCGC 58.210 47.826 0.00 0.00 34.60 4.58
897 936 3.057386 GGTACTCTTCTTAGCTATCGCCC 60.057 52.174 0.00 0.00 36.60 6.13
901 940 3.827302 CTCTTCTTAGCTATCGCCCCTTA 59.173 47.826 0.00 0.00 36.60 2.69
981 1031 4.093850 GCGCATGCAGTCATATCATTGATA 59.906 41.667 19.57 8.76 42.15 2.15
1013 1063 1.086634 GAGCTCATGGCGAGTTCCAC 61.087 60.000 9.40 0.00 44.06 4.02
1135 1203 4.562425 CACCACCACCACCACGCT 62.562 66.667 0.00 0.00 0.00 5.07
1293 1383 1.668151 GTCACGCAGAGGAACCACC 60.668 63.158 0.00 0.00 39.35 4.61
1310 1400 3.056628 CCGTGAAGGTCATCAGAGC 57.943 57.895 0.00 0.00 42.53 4.09
1419 1517 0.107654 ACAATTACCAGCTCTCCGGC 60.108 55.000 0.00 0.00 0.00 6.13
1447 1545 1.410517 CTTCTGGCATCGGCTCTCTTA 59.589 52.381 0.00 0.00 40.87 2.10
1667 1765 2.125350 GCTCGGACAGCTTGGGAG 60.125 66.667 0.00 0.00 45.83 4.30
1716 1814 1.004277 GTCCTTTCTGGCCACATACCA 59.996 52.381 0.00 0.00 35.26 3.25
1750 1848 5.472137 GCAAACCTGACAAACCTCAACTATA 59.528 40.000 0.00 0.00 0.00 1.31
1752 1850 7.626452 GCAAACCTGACAAACCTCAACTATATC 60.626 40.741 0.00 0.00 0.00 1.63
1849 1950 1.895798 TGGCACAAAACAACCTGAACA 59.104 42.857 0.00 0.00 31.92 3.18
1911 2012 8.427902 TCAGCTTCCTGTACATATATCAGAAT 57.572 34.615 0.00 0.00 40.09 2.40
1977 2078 6.749923 AGCTTGATTGAGTTAGATTTGTCC 57.250 37.500 0.00 0.00 0.00 4.02
1980 2081 6.128282 GCTTGATTGAGTTAGATTTGTCCGAA 60.128 38.462 0.00 0.00 0.00 4.30
2031 2132 3.004419 GTGTTGCTGGAAACCTTACTTCC 59.996 47.826 0.00 0.00 42.41 3.46
2053 2154 6.848069 TCCTTGACCTATTTTTCTCTTTGGA 58.152 36.000 0.00 0.00 0.00 3.53
2116 2217 1.895798 TCGTGAATCTGGAAGCACTCT 59.104 47.619 0.00 0.00 0.00 3.24
2133 2234 7.497925 AGCACTCTTACTCTCGAAAAATTTT 57.502 32.000 0.00 0.00 0.00 1.82
2459 2560 4.082026 GCCAGATTTGTGCCAGAGTAAAAT 60.082 41.667 0.00 0.00 0.00 1.82
2514 2615 2.783510 GGATGGTCCTATCCCAAAAGGA 59.216 50.000 8.45 0.00 40.81 3.36
2676 2777 4.566070 CCAAATTGGGGCTCATGTCAAAAT 60.566 41.667 3.60 0.00 32.67 1.82
2769 2870 4.593864 GGATGGCTCGACCTCGGC 62.594 72.222 5.77 0.00 40.22 5.54
2796 2897 7.963532 TCAATAGGTTGAATAGTGAGATACCC 58.036 38.462 0.00 0.00 41.22 3.69
2797 2898 7.567250 TCAATAGGTTGAATAGTGAGATACCCA 59.433 37.037 0.00 0.00 41.22 4.51
2838 2939 2.947652 CAGCCTGTATTGGATGGACTTG 59.052 50.000 0.00 0.00 39.61 3.16
2881 2982 3.055240 CCAAATCCCTAAGCAAATTGGCA 60.055 43.478 7.75 0.00 35.83 4.92
3234 3343 2.093235 CCTAGAAGGCTCTGTCCCAAAG 60.093 54.545 0.00 0.00 32.70 2.77
3486 3598 4.946157 AGCAAAAGGGATGTATTCTCTGTG 59.054 41.667 0.00 0.00 34.48 3.66
3604 3716 7.113544 GCAGTGTTTATAAAGCAGAACTTCAAC 59.886 37.037 0.00 0.00 37.75 3.18
3615 3727 5.822519 AGCAGAACTTCAACATGAACAAGTA 59.177 36.000 0.00 0.00 32.21 2.24
3630 3742 7.246674 TGAACAAGTAGTTGCAGTAAAGAAG 57.753 36.000 10.30 0.00 41.51 2.85
3684 3797 5.821470 TGAAGAAAGATTCCAGCATGAGATC 59.179 40.000 0.00 0.00 39.69 2.75
3708 3821 6.642950 TCGAAATGTTAACAAAAATTCGCCAT 59.357 30.769 26.81 4.82 38.35 4.40
3746 3859 7.805083 AGCTATATGGGTATTGTTCTCATCT 57.195 36.000 0.00 0.00 0.00 2.90
3882 3995 0.111061 ATGTTGCTCAAGCCCTCACA 59.889 50.000 0.00 0.00 41.18 3.58
4019 4132 9.563748 AATGTTGAAACCTGATTCATCAAATTT 57.436 25.926 2.77 0.00 40.47 1.82
4061 4174 1.003812 TGGGTACATTGCACCTGGTAC 59.996 52.381 0.00 0.00 36.25 3.34
4142 4267 9.507329 TGCATAATCCTAATTCTTATGTTCCTC 57.493 33.333 0.00 0.00 35.97 3.71
4236 4361 0.742281 CTCGAGGTGTTGATGGGCAG 60.742 60.000 3.91 0.00 0.00 4.85
4275 4400 5.825507 ACAAGCTTTTCATTCTTCACTCAC 58.174 37.500 0.00 0.00 0.00 3.51
4329 4454 1.007336 CGACTTCCACGACCCGAAAG 61.007 60.000 0.00 0.00 0.00 2.62
4404 4532 2.397044 TCACCCAAAGAAAGGCCAAT 57.603 45.000 5.01 0.00 0.00 3.16
4432 4560 9.606631 ATGCTAAAAGTTTATCGAGATCTTTCT 57.393 29.630 0.00 5.42 33.88 2.52
4433 4561 8.873830 TGCTAAAAGTTTATCGAGATCTTTCTG 58.126 33.333 0.00 7.85 30.30 3.02
4456 4584 7.985184 TCTGTTTGAACTTACTGTTAGACATGT 59.015 33.333 0.00 0.00 39.30 3.21
4475 4603 6.052360 ACATGTAATATGCGGTATTGTGTGA 58.948 36.000 0.00 0.00 34.82 3.58
4557 4685 5.310409 AGGAGTCCTCTCTTATCTCTCTG 57.690 47.826 5.62 0.00 40.29 3.35
4560 4695 5.163195 GGAGTCCTCTCTTATCTCTCTGTCT 60.163 48.000 0.41 0.00 40.29 3.41
4572 4707 2.420722 CTCTCTGTCTCACGTAACCTCC 59.579 54.545 0.00 0.00 0.00 4.30
4574 4709 1.202964 TCTGTCTCACGTAACCTCCCA 60.203 52.381 0.00 0.00 0.00 4.37
4579 4714 3.194116 GTCTCACGTAACCTCCCATGTAA 59.806 47.826 0.00 0.00 0.00 2.41
4580 4715 4.028131 TCTCACGTAACCTCCCATGTAAT 58.972 43.478 0.00 0.00 0.00 1.89
4581 4716 4.098960 TCTCACGTAACCTCCCATGTAATC 59.901 45.833 0.00 0.00 0.00 1.75
4582 4717 3.770388 TCACGTAACCTCCCATGTAATCA 59.230 43.478 0.00 0.00 0.00 2.57
4620 4756 1.157870 GGCTGCCGCATATTGTACGT 61.158 55.000 1.35 0.00 38.10 3.57
4630 4766 4.920927 CGCATATTGTACGTACCATCATCA 59.079 41.667 22.43 3.07 0.00 3.07
4652 4788 7.102847 TCAATCAATATATACATCGCGGGTA 57.897 36.000 6.13 10.27 0.00 3.69
4690 4827 8.816894 AGATTGAGACACTTCCATAACTCTTTA 58.183 33.333 0.00 0.00 0.00 1.85
4701 4838 9.193133 CTTCCATAACTCTTTACATGGTATACG 57.807 37.037 0.00 0.00 39.21 3.06
4705 4842 5.786264 ACTCTTTACATGGTATACGGAGG 57.214 43.478 0.00 0.00 0.00 4.30
4750 4899 4.797912 AGTTCTTCTTCAACCCTTCCTT 57.202 40.909 0.00 0.00 0.00 3.36
4855 5004 1.203038 TGGAAAGCCCAAGCAAGATCA 60.203 47.619 0.00 0.00 43.29 2.92
4935 5084 4.581309 AGATCATCACCACCAAAGACAT 57.419 40.909 0.00 0.00 0.00 3.06
4953 5102 0.394565 ATAGACGGCAAGGATCAGGC 59.605 55.000 0.00 0.00 0.00 4.85
4954 5103 0.975556 TAGACGGCAAGGATCAGGCA 60.976 55.000 0.00 0.00 0.00 4.75
4967 5117 0.551377 TCAGGCAATCCCCAACCCTA 60.551 55.000 0.00 0.00 0.00 3.53
5024 5174 1.002366 CGCTTATCTCTTGCGCAACT 58.998 50.000 21.02 6.86 43.08 3.16
5035 5185 1.282875 GCGCAACTTGTCCAAGGAC 59.717 57.895 12.30 12.30 42.53 3.85
5072 5222 2.039418 CGTCCCTTGAGATGTCCCATA 58.961 52.381 0.00 0.00 0.00 2.74
5119 5269 1.775385 TCTCTGTGGTGTCACTGTCA 58.225 50.000 2.35 0.00 43.94 3.58
5220 5370 1.826054 CCCTCTCCGATGAGCTCGT 60.826 63.158 8.55 8.55 46.18 4.18
5304 5454 5.133322 ACATGGACTATCAACCCATCATCTT 59.867 40.000 0.00 0.00 38.53 2.40
5307 5457 4.202264 GGACTATCAACCCATCATCTTCGT 60.202 45.833 0.00 0.00 0.00 3.85
5336 5487 4.408821 GCACCGAGCCCATCACCA 62.409 66.667 0.00 0.00 37.23 4.17
5431 5588 4.010224 TCCGCCAACGCTGCCTTA 62.010 61.111 0.00 0.00 38.22 2.69
5432 5589 3.799755 CCGCCAACGCTGCCTTAC 61.800 66.667 0.00 0.00 38.22 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.987992 GTCGTATGGACTAATTCAACCCATTA 59.012 38.462 0.00 0.00 42.62 1.90
8 9 5.820947 GTCGTATGGACTAATTCAACCCATT 59.179 40.000 0.00 0.00 42.62 3.16
9 10 5.365619 GTCGTATGGACTAATTCAACCCAT 58.634 41.667 0.00 0.00 42.62 4.00
10 11 4.383335 GGTCGTATGGACTAATTCAACCCA 60.383 45.833 0.00 0.00 45.35 4.51
11 12 4.124970 GGTCGTATGGACTAATTCAACCC 58.875 47.826 0.00 0.00 45.35 4.11
12 13 4.761975 TGGTCGTATGGACTAATTCAACC 58.238 43.478 0.00 0.00 45.35 3.77
13 14 7.208080 AGTATGGTCGTATGGACTAATTCAAC 58.792 38.462 0.00 0.00 45.35 3.18
14 15 7.356089 AGTATGGTCGTATGGACTAATTCAA 57.644 36.000 0.00 0.00 45.35 2.69
15 16 6.971726 AGTATGGTCGTATGGACTAATTCA 57.028 37.500 0.00 0.00 45.35 2.57
16 17 9.355215 CATTAGTATGGTCGTATGGACTAATTC 57.645 37.037 10.14 0.00 45.35 2.17
17 18 7.817962 GCATTAGTATGGTCGTATGGACTAATT 59.182 37.037 10.14 0.00 45.35 1.40
18 19 7.039293 TGCATTAGTATGGTCGTATGGACTAAT 60.039 37.037 0.00 0.00 45.35 1.73
19 20 6.265876 TGCATTAGTATGGTCGTATGGACTAA 59.734 38.462 0.00 0.00 45.35 2.24
20 21 5.771165 TGCATTAGTATGGTCGTATGGACTA 59.229 40.000 0.00 0.00 45.35 2.59
21 22 4.587262 TGCATTAGTATGGTCGTATGGACT 59.413 41.667 0.00 0.00 45.35 3.85
22 23 4.684703 GTGCATTAGTATGGTCGTATGGAC 59.315 45.833 0.00 0.00 45.31 4.02
23 24 4.342665 TGTGCATTAGTATGGTCGTATGGA 59.657 41.667 0.00 0.00 32.15 3.41
24 25 4.627058 TGTGCATTAGTATGGTCGTATGG 58.373 43.478 0.00 0.00 32.15 2.74
25 26 6.785488 ATTGTGCATTAGTATGGTCGTATG 57.215 37.500 0.00 0.00 32.15 2.39
26 27 9.502091 AATAATTGTGCATTAGTATGGTCGTAT 57.498 29.630 0.00 0.00 30.48 3.06
27 28 8.896320 AATAATTGTGCATTAGTATGGTCGTA 57.104 30.769 0.00 0.00 30.48 3.43
28 29 7.801716 AATAATTGTGCATTAGTATGGTCGT 57.198 32.000 0.00 0.00 30.48 4.34
79 80 4.154918 AGCAGTGTCTTTGCATTAACTAGC 59.845 41.667 0.00 0.00 43.92 3.42
225 238 6.912051 ACTAAGGTTAAACTTTAAAAACCGCG 59.088 34.615 11.79 0.00 44.90 6.46
253 266 9.480053 CTGATCCAAAATAAATGTCACAGTTTT 57.520 29.630 0.00 0.00 0.00 2.43
257 270 7.919091 CCATCTGATCCAAAATAAATGTCACAG 59.081 37.037 0.00 0.00 0.00 3.66
258 271 7.614974 TCCATCTGATCCAAAATAAATGTCACA 59.385 33.333 0.00 0.00 0.00 3.58
259 272 7.999679 TCCATCTGATCCAAAATAAATGTCAC 58.000 34.615 0.00 0.00 0.00 3.67
260 273 7.286087 CCTCCATCTGATCCAAAATAAATGTCA 59.714 37.037 0.00 0.00 0.00 3.58
261 274 7.503566 TCCTCCATCTGATCCAAAATAAATGTC 59.496 37.037 0.00 0.00 0.00 3.06
262 275 7.286316 GTCCTCCATCTGATCCAAAATAAATGT 59.714 37.037 0.00 0.00 0.00 2.71
264 277 6.779539 GGTCCTCCATCTGATCCAAAATAAAT 59.220 38.462 0.00 0.00 0.00 1.40
301 314 6.370166 TGAATGCATATTTGTGAAGTGACGTA 59.630 34.615 0.00 0.00 0.00 3.57
335 348 5.858049 CACTAATAATGTTTGTGTGTGCAGG 59.142 40.000 0.00 0.00 0.00 4.85
410 429 3.632145 TCTTTGTTTTGGCCTCTCTTGAC 59.368 43.478 3.32 0.00 0.00 3.18
446 466 3.688694 ACAAAGATACGGTGCTTACCA 57.311 42.857 0.00 0.00 0.00 3.25
606 640 3.270877 GCTATATGCCTTTCATACGGGG 58.729 50.000 0.00 0.00 40.22 5.73
685 719 3.383761 CACAACAGCCTCACATTTTTCC 58.616 45.455 0.00 0.00 0.00 3.13
702 736 1.317613 AAACAGATTCGCAGGCACAA 58.682 45.000 0.00 0.00 0.00 3.33
727 761 4.316823 TGGCTCCTCGTCCAGGGT 62.317 66.667 0.00 0.00 43.67 4.34
747 781 1.209261 TGAAGTGTGAGTTGGTGCTCA 59.791 47.619 0.00 0.00 42.56 4.26
817 854 0.104120 GCTTGGTTTTGGTTTCGCCT 59.896 50.000 0.00 0.00 38.35 5.52
893 932 3.947834 AGAAAAGACATGATTAAGGGGCG 59.052 43.478 0.00 0.00 0.00 6.13
894 933 5.921962 AAGAAAAGACATGATTAAGGGGC 57.078 39.130 0.00 0.00 0.00 5.80
895 934 6.555315 CGAAAGAAAAGACATGATTAAGGGG 58.445 40.000 0.00 0.00 0.00 4.79
897 936 6.611381 TGCGAAAGAAAAGACATGATTAAGG 58.389 36.000 0.00 0.00 0.00 2.69
901 940 6.694411 GCATATGCGAAAGAAAAGACATGATT 59.306 34.615 12.82 0.00 0.00 2.57
981 1031 6.792311 GCCATGAGCTCACGACGTAGTATT 62.792 50.000 20.97 0.00 39.29 1.89
1293 1383 2.084610 TTGCTCTGATGACCTTCACG 57.915 50.000 0.00 0.00 0.00 4.35
1310 1400 2.202932 CACCGCCGAGGGAGATTG 60.203 66.667 0.00 0.00 46.96 2.67
1447 1545 0.482446 TTGAGGGTGGAAAGCATGGT 59.518 50.000 0.00 0.00 0.00 3.55
1667 1765 4.958509 TCTCAGATCCATCTTTCTCATGC 58.041 43.478 0.00 0.00 34.22 4.06
1716 1814 2.158475 TGTCAGGTTTGCAAAGGAGGAT 60.158 45.455 13.26 0.00 0.00 3.24
1953 2054 6.535150 CGGACAAATCTAACTCAATCAAGCTA 59.465 38.462 0.00 0.00 0.00 3.32
1968 2069 5.508994 GGTCAAATGGTTTTCGGACAAATCT 60.509 40.000 0.00 0.00 0.00 2.40
1977 2078 0.596082 AGCCGGTCAAATGGTTTTCG 59.404 50.000 1.90 0.00 0.00 3.46
1980 2081 2.871096 TAGAGCCGGTCAAATGGTTT 57.129 45.000 1.90 0.00 0.00 3.27
2031 2132 7.751768 ACTCCAAAGAGAAAAATAGGTCAAG 57.248 36.000 0.00 0.00 43.39 3.02
2133 2234 7.818997 ACTTGACTGTATCGATCCAACTATA 57.181 36.000 0.00 0.00 0.00 1.31
2150 2251 5.505181 AGACATGTTCCCAATACTTGACT 57.495 39.130 0.00 0.00 0.00 3.41
2199 2300 5.583932 GGCAATCCCCCAGAGATATTATTT 58.416 41.667 0.00 0.00 0.00 1.40
2459 2560 5.669164 AAAAACTTGGAAAACCTGTAGCA 57.331 34.783 0.00 0.00 0.00 3.49
2514 2615 3.446442 AGTGAACTGCAATCCCTCAAT 57.554 42.857 0.00 0.00 0.00 2.57
2676 2777 8.858003 TGTTTGCAAAATAAATACTCGTCAAA 57.142 26.923 14.67 0.00 0.00 2.69
2796 2897 5.517770 GCTGCTTAACTTGCCAATTTCTATG 59.482 40.000 0.00 0.00 0.00 2.23
2797 2898 5.394553 GGCTGCTTAACTTGCCAATTTCTAT 60.395 40.000 0.00 0.00 44.34 1.98
2838 2939 4.943705 TGGCCAGATAGTTGATTGTTTCTC 59.056 41.667 0.00 0.00 0.00 2.87
2881 2982 7.158021 CCAAGAACTTCAAGATTACTCAGTCT 58.842 38.462 0.00 0.00 0.00 3.24
3138 3247 1.308998 GGATGGTACCGCTGAATTGG 58.691 55.000 7.57 0.00 0.00 3.16
3234 3343 1.325355 CTGATGCATTGTGGATCCCC 58.675 55.000 9.90 0.00 43.46 4.81
3417 3529 5.747951 TTTTCTTGCGGCAAATCAAAAAT 57.252 30.435 17.13 0.00 0.00 1.82
3453 3565 1.021390 CCCTTTTGCTCGCGTCATCT 61.021 55.000 5.77 0.00 0.00 2.90
3486 3598 1.538047 TTCTGCCATCAAAGCTCCAC 58.462 50.000 0.00 0.00 0.00 4.02
3604 3716 7.189693 TCTTTACTGCAACTACTTGTTCATG 57.810 36.000 0.00 0.00 36.63 3.07
3615 3727 6.889198 TGGATATAGCTTCTTTACTGCAACT 58.111 36.000 0.00 0.00 0.00 3.16
3630 3742 3.516615 GTCTTCATCGCCTGGATATAGC 58.483 50.000 0.00 0.00 32.85 2.97
3684 3797 6.204075 TGGCGAATTTTTGTTAACATTTCG 57.796 33.333 24.19 24.19 0.00 3.46
3708 3821 0.103026 ATAGCTTGACGATGCTGCGA 59.897 50.000 0.00 0.00 40.08 5.10
3746 3859 1.340088 TACAAGGAACCTGTACCGCA 58.660 50.000 0.00 0.00 0.00 5.69
3882 3995 4.506271 GGCTGAACATCATGATGGAGGTAT 60.506 45.833 33.31 13.52 42.91 2.73
3972 4085 3.601435 TCTTGCAATACCGAAATCCGAA 58.399 40.909 0.00 0.00 41.76 4.30
4019 4132 2.283604 TCCCCGCTAGTGCACTCA 60.284 61.111 25.56 9.17 39.64 3.41
4142 4267 4.796038 AGGAACATTCTGCATCCAAAAG 57.204 40.909 4.66 0.00 31.30 2.27
4236 4361 3.133721 AGCTTGTATGTCTCCTGGATGTC 59.866 47.826 0.00 0.00 0.00 3.06
4432 4560 9.602568 TTACATGTCTAACAGTAAGTTCAAACA 57.397 29.630 0.00 0.00 41.64 2.83
4456 4584 6.201997 GTGACATCACACAATACCGCATATTA 59.798 38.462 7.15 0.00 45.75 0.98
4475 4603 7.432059 CATGACTCTCATGTATACTGTGACAT 58.568 38.462 4.17 4.80 46.80 3.06
4517 4645 6.662663 GGACTCCTAACAACTCTAACTTCCTA 59.337 42.308 0.00 0.00 0.00 2.94
4522 4650 5.894653 AGAGGACTCCTAACAACTCTAACT 58.105 41.667 0.00 0.00 33.87 2.24
4557 4685 1.549170 ACATGGGAGGTTACGTGAGAC 59.451 52.381 0.00 0.00 0.00 3.36
4560 4695 3.770388 TGATTACATGGGAGGTTACGTGA 59.230 43.478 0.00 0.00 0.00 4.35
4572 4707 5.349817 GCTAACCATCGAGATGATTACATGG 59.650 44.000 14.12 0.00 41.20 3.66
4574 4709 5.012046 TGGCTAACCATCGAGATGATTACAT 59.988 40.000 14.12 0.00 42.67 2.29
4630 4766 7.152645 GGATACCCGCGATGTATATATTGATT 58.847 38.462 8.23 0.00 0.00 2.57
4652 4788 3.960755 TGTCTCAATCTCCATACACGGAT 59.039 43.478 0.00 0.00 33.56 4.18
4690 4827 1.133136 AGCCTCCTCCGTATACCATGT 60.133 52.381 0.00 0.00 0.00 3.21
4701 4838 1.047801 GAGATGGAAGAGCCTCCTCC 58.952 60.000 2.14 2.14 38.96 4.30
4705 4842 3.056607 GCTAGATGAGATGGAAGAGCCTC 60.057 52.174 0.00 0.00 37.63 4.70
4750 4899 1.119684 CGGTGGAGGTGGACATGATA 58.880 55.000 0.00 0.00 0.00 2.15
4855 5004 2.781158 GCCGGCGCCCATTATTTGT 61.781 57.895 23.46 0.00 0.00 2.83
4935 5084 0.975556 TGCCTGATCCTTGCCGTCTA 60.976 55.000 0.00 0.00 0.00 2.59
4953 5102 2.489073 GCATAGGTAGGGTTGGGGATTG 60.489 54.545 0.00 0.00 0.00 2.67
4954 5103 1.780919 GCATAGGTAGGGTTGGGGATT 59.219 52.381 0.00 0.00 0.00 3.01
5024 5174 3.580904 CGAGAACGTCCTTGGACAA 57.419 52.632 18.51 0.00 34.56 3.18
5035 5185 2.426183 CGCGACTTGGACGAGAACG 61.426 63.158 0.00 0.00 45.75 3.95
5072 5222 1.599047 CCAAGGCTGTCCAGATCGT 59.401 57.895 0.00 0.00 33.74 3.73
5119 5269 1.574428 GCGAAGATTGTTGGCGTGT 59.426 52.632 0.00 0.00 0.00 4.49
5307 5457 4.662961 CGGTGCAGACGTCCAGCA 62.663 66.667 24.26 24.26 35.63 4.41
5336 5487 1.135333 GAGAGAGAAAAGGCCGTCGAT 59.865 52.381 0.00 0.00 0.00 3.59
5381 5532 1.336755 GGTGTTGCCGTGAAACATCTT 59.663 47.619 1.44 0.00 39.57 2.40


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

AutoCloner maintained by Alex Coulton.