Multiple sequence alignment - TraesCS7D01G160200

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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 TraesCS7D01G160200 chr7D 100.000 2616 0 0 393 3008 110565702 110568317 0.000000e+00 4831.0
1 TraesCS7D01G160200 chr7D 100.000 156 0 0 1 156 110565310 110565465 3.790000e-74 289.0
2 TraesCS7D01G160200 chr7A 95.862 1450 46 9 814 2253 115818393 115816948 0.000000e+00 2333.0
3 TraesCS7D01G160200 chr7A 92.143 700 39 8 2318 3004 115816541 115815845 0.000000e+00 974.0
4 TraesCS7D01G160200 chr7A 91.429 70 5 1 698 766 115820211 115820142 8.880000e-16 95.3
5 TraesCS7D01G160200 chr7B 93.798 1564 52 12 696 2253 69581924 69583448 0.000000e+00 2309.0
6 TraesCS7D01G160200 chr7B 93.786 692 41 2 2318 3008 69583819 69584509 0.000000e+00 1038.0
7 TraesCS7D01G160200 chr7B 93.277 119 8 0 27 145 69571064 69571182 3.080000e-40 176.0
8 TraesCS7D01G160200 chr7B 93.043 115 8 0 27 141 69579361 69579475 5.160000e-38 169.0
9 TraesCS7D01G160200 chr7B 100.000 36 0 0 2 37 69571016 69571051 1.940000e-07 67.6
10 TraesCS7D01G160200 chr7B 100.000 36 0 0 2 37 69579313 69579348 1.940000e-07 67.6
11 TraesCS7D01G160200 chr3D 83.069 189 30 2 393 580 515194551 515194738 1.430000e-38 171.0
12 TraesCS7D01G160200 chr6B 80.769 208 37 3 395 600 590019516 590019722 3.100000e-35 159.0
13 TraesCS7D01G160200 chr4B 80.193 207 39 2 393 599 432254347 432254143 1.440000e-33 154.0
14 TraesCS7D01G160200 chr1D 82.659 173 30 0 393 565 267343021 267343193 1.440000e-33 154.0
15 TraesCS7D01G160200 chr1D 79.808 208 41 1 393 600 454199547 454199341 1.870000e-32 150.0
16 TraesCS7D01G160200 chr3A 81.218 197 29 8 408 599 426867840 426868033 5.190000e-33 152.0
17 TraesCS7D01G160200 chr6D 80.905 199 31 7 406 600 394212211 394212406 1.870000e-32 150.0
18 TraesCS7D01G160200 chr5B 80.526 190 35 2 395 582 548317261 548317072 8.690000e-31 145.0
19 TraesCS7D01G160200 chr5A 79.426 209 40 3 393 600 649254583 649254377 8.690000e-31 145.0


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 TraesCS7D01G160200 chr7D 110565310 110568317 3007 False 2560.0 4831 100.000000 1 3008 2 chr7D.!!$F1 3007
1 TraesCS7D01G160200 chr7A 115815845 115820211 4366 True 1134.1 2333 93.144667 698 3004 3 chr7A.!!$R1 2306
2 TraesCS7D01G160200 chr7B 69579313 69584509 5196 False 895.9 2309 95.156750 2 3008 4 chr7B.!!$F2 3006

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
873 2791 0.038159 CCTCTTAGCGGGCCTATTCG 60.038 60.000 0.84 0.0 0.0 3.34 F
1770 3692 1.135333 CTCGTCTTCTTCTACCAGGGC 59.865 57.143 0.00 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 3728 0.389426 CGAGGGTGTACAGGAAACCG 60.389 60.0 0.0 0.0 34.62 4.44 R
2605 4881 0.912487 TGGGGGAGGACACATGGTAC 60.912 60.0 0.0 0.0 0.00 3.34 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
59 83 5.584649 TGCAATCTTTAGGGTATCTTCAACG 59.415 40.000 0.00 0.00 0.00 4.10
60 84 5.504173 GCAATCTTTAGGGTATCTTCAACGC 60.504 44.000 0.00 0.00 0.00 4.84
71 95 3.126001 TCTTCAACGCTGACCTCAAAT 57.874 42.857 0.00 0.00 0.00 2.32
77 101 1.291184 CGCTGACCTCAAATCGCACA 61.291 55.000 0.00 0.00 0.00 4.57
86 110 3.483574 CCTCAAATCGCACACATACGTTC 60.484 47.826 0.00 0.00 0.00 3.95
142 166 4.148825 GTCCGCTCCCAGACGCAT 62.149 66.667 0.00 0.00 0.00 4.73
143 167 3.390521 TCCGCTCCCAGACGCATT 61.391 61.111 0.00 0.00 0.00 3.56
144 168 2.436646 CCGCTCCCAGACGCATTT 60.437 61.111 0.00 0.00 0.00 2.32
145 169 2.040544 CCGCTCCCAGACGCATTTT 61.041 57.895 0.00 0.00 0.00 1.82
146 170 1.586154 CCGCTCCCAGACGCATTTTT 61.586 55.000 0.00 0.00 0.00 1.94
147 171 0.179189 CGCTCCCAGACGCATTTTTC 60.179 55.000 0.00 0.00 0.00 2.29
149 173 1.826385 CTCCCAGACGCATTTTTCCT 58.174 50.000 0.00 0.00 0.00 3.36
151 175 0.109132 CCCAGACGCATTTTTCCTGC 60.109 55.000 0.00 0.00 36.26 4.85
152 176 0.597568 CCAGACGCATTTTTCCTGCA 59.402 50.000 0.00 0.00 39.64 4.41
153 177 1.000385 CCAGACGCATTTTTCCTGCAA 60.000 47.619 0.00 0.00 39.64 4.08
154 178 2.545532 CCAGACGCATTTTTCCTGCAAA 60.546 45.455 0.00 0.00 39.64 3.68
155 179 2.472488 CAGACGCATTTTTCCTGCAAAC 59.528 45.455 0.00 0.00 39.64 2.93
410 434 1.365633 CGCTCCTGACTATCCTGGC 59.634 63.158 0.00 0.00 0.00 4.85
411 435 1.751563 GCTCCTGACTATCCTGGCC 59.248 63.158 0.00 0.00 0.00 5.36
412 436 1.763546 GCTCCTGACTATCCTGGCCC 61.764 65.000 0.00 0.00 0.00 5.80
413 437 0.399091 CTCCTGACTATCCTGGCCCA 60.399 60.000 0.00 0.00 0.00 5.36
414 438 0.691078 TCCTGACTATCCTGGCCCAC 60.691 60.000 0.00 0.00 0.00 4.61
415 439 0.982852 CCTGACTATCCTGGCCCACA 60.983 60.000 0.00 0.00 0.00 4.17
416 440 0.911769 CTGACTATCCTGGCCCACAA 59.088 55.000 0.00 0.00 0.00 3.33
417 441 1.281867 CTGACTATCCTGGCCCACAAA 59.718 52.381 0.00 0.00 0.00 2.83
418 442 1.707989 TGACTATCCTGGCCCACAAAA 59.292 47.619 0.00 0.00 0.00 2.44
434 458 3.341263 AAAAACCCTCCTCCTTCGC 57.659 52.632 0.00 0.00 0.00 4.70
435 459 0.251209 AAAAACCCTCCTCCTTCGCC 60.251 55.000 0.00 0.00 0.00 5.54
436 460 2.138453 AAAACCCTCCTCCTTCGCCC 62.138 60.000 0.00 0.00 0.00 6.13
474 498 1.895707 GCTAGCTGCCCGCATTCAT 60.896 57.895 7.70 0.00 42.61 2.57
516 540 4.477975 GTCGACGTCGGCCCAGAG 62.478 72.222 35.05 7.30 38.15 3.35
519 543 4.803426 GACGTCGGCCCAGAGCAG 62.803 72.222 0.00 0.00 46.50 4.24
527 551 4.803426 CCCAGAGCAGACGCGACC 62.803 72.222 15.93 3.72 45.49 4.79
528 552 3.753434 CCAGAGCAGACGCGACCT 61.753 66.667 15.93 6.53 45.49 3.85
531 555 2.101380 GAGCAGACGCGACCTCTC 59.899 66.667 15.93 12.42 45.49 3.20
533 557 2.505118 GCAGACGCGACCTCTCAC 60.505 66.667 15.93 0.00 0.00 3.51
534 558 2.983930 GCAGACGCGACCTCTCACT 61.984 63.158 15.93 0.00 0.00 3.41
535 559 1.135731 CAGACGCGACCTCTCACTC 59.864 63.158 15.93 0.00 0.00 3.51
536 560 2.098680 GACGCGACCTCTCACTCG 59.901 66.667 15.93 0.00 0.00 4.18
540 564 3.268986 CGACCTCTCACTCGCACT 58.731 61.111 0.00 0.00 0.00 4.40
542 566 1.214062 GACCTCTCACTCGCACTGG 59.786 63.158 0.00 0.00 0.00 4.00
543 567 2.125753 CCTCTCACTCGCACTGGC 60.126 66.667 0.00 0.00 0.00 4.85
544 568 2.653115 CTCTCACTCGCACTGGCA 59.347 61.111 0.00 0.00 41.24 4.92
545 569 1.217511 CTCTCACTCGCACTGGCAT 59.782 57.895 0.00 0.00 41.24 4.40
546 570 0.390866 CTCTCACTCGCACTGGCATT 60.391 55.000 0.00 0.00 41.24 3.56
547 571 0.671472 TCTCACTCGCACTGGCATTG 60.671 55.000 0.00 0.00 41.24 2.82
548 572 0.671472 CTCACTCGCACTGGCATTGA 60.671 55.000 9.24 0.00 41.24 2.57
549 573 0.250252 TCACTCGCACTGGCATTGAA 60.250 50.000 9.24 0.00 41.24 2.69
551 575 1.136147 CTCGCACTGGCATTGAAGC 59.864 57.895 9.24 0.00 41.24 3.86
554 578 2.180017 CACTGGCATTGAAGCGGC 59.820 61.111 0.00 0.00 34.64 6.53
555 579 3.434319 ACTGGCATTGAAGCGGCG 61.434 61.111 0.51 0.51 34.64 6.46
596 620 2.109181 GCCGCATCCCTAGTGTCC 59.891 66.667 0.00 0.00 0.00 4.02
597 621 2.417516 CCGCATCCCTAGTGTCCG 59.582 66.667 0.00 0.00 0.00 4.79
598 622 2.279517 CGCATCCCTAGTGTCCGC 60.280 66.667 0.00 0.00 0.00 5.54
599 623 2.279517 GCATCCCTAGTGTCCGCG 60.280 66.667 0.00 0.00 0.00 6.46
600 624 3.077519 GCATCCCTAGTGTCCGCGT 62.078 63.158 4.92 0.00 0.00 6.01
602 626 1.379443 ATCCCTAGTGTCCGCGTGA 60.379 57.895 4.92 0.00 0.00 4.35
603 627 0.755698 ATCCCTAGTGTCCGCGTGAT 60.756 55.000 4.92 0.00 0.00 3.06
604 628 0.968901 TCCCTAGTGTCCGCGTGATT 60.969 55.000 4.92 0.00 0.00 2.57
606 630 1.674817 CCCTAGTGTCCGCGTGATTTT 60.675 52.381 4.92 0.00 0.00 1.82
607 631 1.659098 CCTAGTGTCCGCGTGATTTTC 59.341 52.381 4.92 0.00 0.00 2.29
608 632 1.320555 CTAGTGTCCGCGTGATTTTCG 59.679 52.381 4.92 0.00 0.00 3.46
638 662 9.500785 TTTTTGTTTCTGTTTTCTCATTTCCTT 57.499 25.926 0.00 0.00 0.00 3.36
639 663 9.500785 TTTTGTTTCTGTTTTCTCATTTCCTTT 57.499 25.926 0.00 0.00 0.00 3.11
724 2642 1.378646 GCAACCTCTTACCTGGCCC 60.379 63.158 0.00 0.00 0.00 5.80
802 2720 7.222031 ACACGCTTTAAGAAAAGGAAATGTTTC 59.778 33.333 0.00 0.00 42.07 2.78
803 2721 7.221838 CACGCTTTAAGAAAAGGAAATGTTTCA 59.778 33.333 7.69 0.00 42.07 2.69
804 2722 7.222031 ACGCTTTAAGAAAAGGAAATGTTTCAC 59.778 33.333 7.69 0.00 42.07 3.18
805 2723 7.306574 CGCTTTAAGAAAAGGAAATGTTTCACC 60.307 37.037 7.69 0.00 42.07 4.02
806 2724 7.042051 GCTTTAAGAAAAGGAAATGTTTCACCC 60.042 37.037 7.69 0.00 42.07 4.61
807 2725 4.584327 AGAAAAGGAAATGTTTCACCCG 57.416 40.909 7.69 0.00 38.92 5.28
808 2726 2.812358 AAAGGAAATGTTTCACCCGC 57.188 45.000 7.69 0.00 38.92 6.13
809 2727 1.698506 AAGGAAATGTTTCACCCGCA 58.301 45.000 7.69 0.00 38.92 5.69
810 2728 1.698506 AGGAAATGTTTCACCCGCAA 58.301 45.000 7.69 0.00 38.92 4.85
811 2729 2.035632 AGGAAATGTTTCACCCGCAAA 58.964 42.857 7.69 0.00 38.92 3.68
812 2730 2.432510 AGGAAATGTTTCACCCGCAAAA 59.567 40.909 7.69 0.00 38.92 2.44
813 2731 3.118592 AGGAAATGTTTCACCCGCAAAAA 60.119 39.130 7.69 0.00 38.92 1.94
838 2756 4.126520 AGGAAATGTTTAAGGCCCAGAA 57.873 40.909 0.00 0.00 0.00 3.02
872 2790 1.049402 ACCTCTTAGCGGGCCTATTC 58.951 55.000 0.84 0.00 0.00 1.75
873 2791 0.038159 CCTCTTAGCGGGCCTATTCG 60.038 60.000 0.84 0.00 0.00 3.34
892 2810 3.601277 CAGTGCTTGCACTCTCTCA 57.399 52.632 23.37 0.00 32.26 3.27
897 2815 1.739562 CTTGCACTCTCTCACGGGC 60.740 63.158 0.00 0.00 0.00 6.13
902 2820 4.135153 CTCTCTCACGGGCCCACG 62.135 72.222 24.92 12.42 40.31 4.94
1567 3489 1.459158 ATGATCCTGCTCGGCCTCT 60.459 57.895 0.00 0.00 0.00 3.69
1728 3650 1.603802 CATACGCCCATGTTCATCACC 59.396 52.381 0.00 0.00 0.00 4.02
1770 3692 1.135333 CTCGTCTTCTTCTACCAGGGC 59.865 57.143 0.00 0.00 0.00 5.19
1806 3728 2.328099 CGCAGAGGGGTTTGCTGTC 61.328 63.158 0.00 0.00 38.16 3.51
1992 3914 0.947244 GCATTCATACCTTCTGGCCG 59.053 55.000 0.00 0.00 36.63 6.13
2100 4028 5.480642 TTGTACATGGCATTTTGGTTCAT 57.519 34.783 0.00 0.00 0.00 2.57
2103 4031 7.180322 TGTACATGGCATTTTGGTTCATATT 57.820 32.000 0.00 0.00 0.00 1.28
2168 4098 3.785505 GCAATTCACGCAATCTCGTTAGG 60.786 47.826 0.00 0.00 41.21 2.69
2178 4108 4.440802 GCAATCTCGTTAGGTGAGTCAGAT 60.441 45.833 0.00 0.00 34.99 2.90
2245 4175 5.406477 CACACCGACTCATAATGTCATATGG 59.594 44.000 2.13 0.00 34.66 2.74
2301 4491 8.862325 AGATTCACTGTAAAATTACACCATCA 57.138 30.769 1.96 0.00 38.64 3.07
2304 4494 9.912634 ATTCACTGTAAAATTACACCATCAAAG 57.087 29.630 1.96 0.00 38.64 2.77
2305 4495 8.458573 TCACTGTAAAATTACACCATCAAAGT 57.541 30.769 1.96 0.00 38.64 2.66
2307 4497 9.180678 CACTGTAAAATTACACCATCAAAGTTC 57.819 33.333 1.96 0.00 38.64 3.01
2308 4498 8.908903 ACTGTAAAATTACACCATCAAAGTTCA 58.091 29.630 1.96 0.00 38.64 3.18
2309 4499 9.912634 CTGTAAAATTACACCATCAAAGTTCAT 57.087 29.630 1.96 0.00 38.64 2.57
2314 4504 9.829507 AAATTACACCATCAAAGTTCATTTCAA 57.170 25.926 0.00 0.00 0.00 2.69
2315 4505 8.816640 ATTACACCATCAAAGTTCATTTCAAC 57.183 30.769 0.00 0.00 0.00 3.18
2316 4506 6.219417 ACACCATCAAAGTTCATTTCAACA 57.781 33.333 0.00 0.00 0.00 3.33
2325 4598 8.690884 TCAAAGTTCATTTCAACATGTCCTTTA 58.309 29.630 0.00 0.00 30.73 1.85
2330 4603 9.643693 GTTCATTTCAACATGTCCTTTATTGAT 57.356 29.630 0.00 0.00 0.00 2.57
2353 4626 6.951062 TTGTGATGACTTTGATGGTGTAAA 57.049 33.333 0.00 0.00 0.00 2.01
2528 4804 9.277565 CAACAAGATTGTATTTATTTCGGTCAG 57.722 33.333 0.00 0.00 41.31 3.51
2559 4835 8.212259 AGTATATTGCCTTCACCTAGATTCAT 57.788 34.615 0.00 0.00 0.00 2.57
2588 4864 2.034558 ACAATTGACCTTTTGTCCTGCG 59.965 45.455 13.59 0.00 43.78 5.18
2605 4881 8.652810 TGTCCTGCGATATGATTATATGAATG 57.347 34.615 0.00 0.00 29.67 2.67
2657 4933 8.749841 AAAAGATGTATGTATCGTCTAGATGC 57.250 34.615 7.11 0.00 40.40 3.91
2697 4973 9.194271 GAGTTCGTTAACTAGAAGTTCTTGAAT 57.806 33.333 19.28 10.72 46.09 2.57
2724 5000 6.985188 TTGGAGTTTGATGCTGTTAGTATC 57.015 37.500 0.71 0.71 37.76 2.24
2914 5201 4.275689 TCACTGTTGATTAGTTTGGCTGTG 59.724 41.667 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 83 0.166814 GTGTGCGATTTGAGGTCAGC 59.833 55.000 0.00 0.00 0.00 4.26
60 84 1.511850 TGTGTGCGATTTGAGGTCAG 58.488 50.000 0.00 0.00 0.00 3.51
71 95 0.730155 GTCCGAACGTATGTGTGCGA 60.730 55.000 1.41 0.00 43.81 5.10
77 101 1.444895 GCACGGTCCGAACGTATGT 60.445 57.895 20.51 0.00 43.58 2.29
392 416 1.365633 GCCAGGATAGTCAGGAGCG 59.634 63.158 0.00 0.00 0.00 5.03
393 417 1.751563 GGCCAGGATAGTCAGGAGC 59.248 63.158 0.00 0.00 0.00 4.70
394 418 0.399091 TGGGCCAGGATAGTCAGGAG 60.399 60.000 0.00 0.00 0.00 3.69
395 419 0.691078 GTGGGCCAGGATAGTCAGGA 60.691 60.000 6.40 0.00 0.00 3.86
396 420 0.982852 TGTGGGCCAGGATAGTCAGG 60.983 60.000 6.40 0.00 0.00 3.86
397 421 0.911769 TTGTGGGCCAGGATAGTCAG 59.088 55.000 6.40 0.00 0.00 3.51
399 423 2.507407 TTTTGTGGGCCAGGATAGTC 57.493 50.000 6.40 0.00 0.00 2.59
400 424 2.990740 TTTTTGTGGGCCAGGATAGT 57.009 45.000 6.40 0.00 0.00 2.12
416 440 0.251209 GGCGAAGGAGGAGGGTTTTT 60.251 55.000 0.00 0.00 0.00 1.94
417 441 1.379146 GGCGAAGGAGGAGGGTTTT 59.621 57.895 0.00 0.00 0.00 2.43
418 442 2.603652 GGGCGAAGGAGGAGGGTTT 61.604 63.158 0.00 0.00 0.00 3.27
467 491 3.315635 GCTCTACAGCGGCATGAATGC 62.316 57.143 6.73 6.73 43.87 3.56
468 492 0.585357 GCTCTACAGCGGCATGAATG 59.415 55.000 1.45 0.00 35.39 2.67
499 523 4.477975 CTCTGGGCCGACGTCGAC 62.478 72.222 37.65 27.72 43.02 4.20
504 528 4.803426 GTCTGCTCTGGGCCGACG 62.803 72.222 8.33 0.00 43.15 5.12
505 529 4.803426 CGTCTGCTCTGGGCCGAC 62.803 72.222 13.35 13.35 46.79 4.79
511 535 3.691744 GAGGTCGCGTCTGCTCTGG 62.692 68.421 5.77 0.00 39.65 3.86
512 536 2.202544 GAGGTCGCGTCTGCTCTG 60.203 66.667 5.77 0.00 39.65 3.35
513 537 2.360600 AGAGGTCGCGTCTGCTCT 60.361 61.111 5.77 6.15 39.65 4.09
515 539 2.673341 TGAGAGGTCGCGTCTGCT 60.673 61.111 5.77 1.84 39.65 4.24
516 540 2.505118 GTGAGAGGTCGCGTCTGC 60.505 66.667 5.77 0.00 37.91 4.26
517 541 1.135731 GAGTGAGAGGTCGCGTCTG 59.864 63.158 5.77 0.00 38.32 3.51
518 542 2.392181 CGAGTGAGAGGTCGCGTCT 61.392 63.158 5.77 0.52 38.32 4.18
519 543 2.098680 CGAGTGAGAGGTCGCGTC 59.901 66.667 5.77 0.00 38.32 5.19
523 547 1.154131 CAGTGCGAGTGAGAGGTCG 60.154 63.158 0.00 0.00 39.25 4.79
524 548 1.214062 CCAGTGCGAGTGAGAGGTC 59.786 63.158 0.00 0.00 0.00 3.85
525 549 2.936912 GCCAGTGCGAGTGAGAGGT 61.937 63.158 0.00 0.00 0.00 3.85
526 550 2.125753 GCCAGTGCGAGTGAGAGG 60.126 66.667 0.00 0.00 0.00 3.69
527 551 0.390866 AATGCCAGTGCGAGTGAGAG 60.391 55.000 0.00 0.00 41.78 3.20
528 552 0.671472 CAATGCCAGTGCGAGTGAGA 60.671 55.000 0.00 0.00 41.78 3.27
531 555 0.167470 CTTCAATGCCAGTGCGAGTG 59.833 55.000 0.00 0.00 41.78 3.51
533 557 1.136147 GCTTCAATGCCAGTGCGAG 59.864 57.895 0.00 0.00 41.78 5.03
534 558 2.679934 CGCTTCAATGCCAGTGCGA 61.680 57.895 0.00 0.00 45.15 5.10
535 559 2.202388 CGCTTCAATGCCAGTGCG 60.202 61.111 0.00 0.00 41.78 5.34
536 560 2.180017 CCGCTTCAATGCCAGTGC 59.820 61.111 0.00 0.00 38.26 4.40
537 561 2.180017 GCCGCTTCAATGCCAGTG 59.820 61.111 0.00 0.00 0.00 3.66
538 562 3.434319 CGCCGCTTCAATGCCAGT 61.434 61.111 0.00 0.00 0.00 4.00
539 563 4.842091 GCGCCGCTTCAATGCCAG 62.842 66.667 0.00 0.00 0.00 4.85
543 567 4.851114 CGTCGCGCCGCTTCAATG 62.851 66.667 7.78 0.00 0.00 2.82
577 601 4.530857 ACACTAGGGATGCGGCGC 62.531 66.667 27.44 27.44 0.00 6.53
580 604 2.417516 CGGACACTAGGGATGCGG 59.582 66.667 0.00 0.00 0.00 5.69
582 606 2.279517 CGCGGACACTAGGGATGC 60.280 66.667 0.00 0.00 0.00 3.91
583 607 1.226974 CACGCGGACACTAGGGATG 60.227 63.158 12.47 0.00 0.00 3.51
586 610 0.108329 AAATCACGCGGACACTAGGG 60.108 55.000 12.47 0.00 0.00 3.53
589 613 1.342555 CGAAAATCACGCGGACACTA 58.657 50.000 12.47 0.00 0.00 2.74
591 615 1.509162 GCGAAAATCACGCGGACAC 60.509 57.895 12.47 0.00 46.05 3.67
592 616 2.857448 GCGAAAATCACGCGGACA 59.143 55.556 12.47 0.00 46.05 4.02
613 637 9.500785 AAAGGAAATGAGAAAACAGAAACAAAA 57.499 25.926 0.00 0.00 0.00 2.44
697 2615 7.147549 GGCCAGGTAAGAGGTTGCATATATATA 60.148 40.741 0.00 0.00 0.00 0.86
719 2637 2.476852 TTAGCACTGCGAATGGGCCA 62.477 55.000 9.61 9.61 0.00 5.36
724 2642 0.029834 GCCCATTAGCACTGCGAATG 59.970 55.000 23.04 23.04 46.09 2.67
763 2681 3.014085 GCGTGTCCTCCAATCGGGA 62.014 63.158 0.00 0.00 45.89 5.14
764 2682 2.511600 GCGTGTCCTCCAATCGGG 60.512 66.667 0.00 0.00 38.37 5.14
813 2731 5.368230 TCTGGGCCTTAAACATTTCCTTTTT 59.632 36.000 4.53 0.00 0.00 1.94
814 2732 4.904853 TCTGGGCCTTAAACATTTCCTTTT 59.095 37.500 4.53 0.00 0.00 2.27
815 2733 4.488770 TCTGGGCCTTAAACATTTCCTTT 58.511 39.130 4.53 0.00 0.00 3.11
816 2734 4.126520 TCTGGGCCTTAAACATTTCCTT 57.873 40.909 4.53 0.00 0.00 3.36
817 2735 3.825908 TCTGGGCCTTAAACATTTCCT 57.174 42.857 4.53 0.00 0.00 3.36
818 2736 5.420725 AATTCTGGGCCTTAAACATTTCC 57.579 39.130 4.53 0.00 0.00 3.13
819 2737 5.643348 CCAAATTCTGGGCCTTAAACATTTC 59.357 40.000 4.53 0.00 42.17 2.17
820 2738 5.559770 CCAAATTCTGGGCCTTAAACATTT 58.440 37.500 4.53 0.00 42.17 2.32
821 2739 4.565444 GCCAAATTCTGGGCCTTAAACATT 60.565 41.667 4.53 0.00 46.54 2.71
822 2740 3.055167 GCCAAATTCTGGGCCTTAAACAT 60.055 43.478 4.53 0.00 46.54 2.71
823 2741 2.301583 GCCAAATTCTGGGCCTTAAACA 59.698 45.455 4.53 0.00 46.54 2.83
824 2742 2.972625 GCCAAATTCTGGGCCTTAAAC 58.027 47.619 4.53 0.00 46.54 2.01
838 2756 0.614812 GAGGTTGCAATGGGCCAAAT 59.385 50.000 11.89 0.00 43.89 2.32
897 2815 2.358737 GGAGACCTGTTGCGTGGG 60.359 66.667 0.00 0.00 0.00 4.61
902 2820 2.763448 AGTATGAGAGGAGACCTGTTGC 59.237 50.000 0.00 0.00 31.76 4.17
975 2897 1.281199 TGGGTGGATGTGGATCTGGG 61.281 60.000 0.00 0.00 0.00 4.45
1567 3489 1.486310 CGGGATGGAGATCAGGAACAA 59.514 52.381 0.00 0.00 0.00 2.83
1728 3650 1.153429 GTTTGGATCCTCCCGGTCG 60.153 63.158 14.23 0.00 35.03 4.79
1770 3692 2.108566 CCGAGCTGCATCCCTGAG 59.891 66.667 1.02 0.00 0.00 3.35
1803 3725 0.393820 GGGTGTACAGGAAACCGACA 59.606 55.000 0.00 0.00 34.62 4.35
1806 3728 0.389426 CGAGGGTGTACAGGAAACCG 60.389 60.000 0.00 0.00 34.62 4.44
1992 3914 4.833390 ACAACATTTACCTCCAGCTACTC 58.167 43.478 0.00 0.00 0.00 2.59
2080 4002 9.762933 AATAATATGAACCAAAATGCCATGTAC 57.237 29.630 0.00 0.00 0.00 2.90
2082 4004 9.328845 GAAATAATATGAACCAAAATGCCATGT 57.671 29.630 0.00 0.00 0.00 3.21
2140 4070 4.260656 CGAGATTGCGTGAATTGCTAAAAC 59.739 41.667 0.00 0.00 0.00 2.43
2168 4098 7.224753 TCCGAAATGCTAAATTATCTGACTCAC 59.775 37.037 0.00 0.00 0.00 3.51
2178 4108 7.607250 ACAACCATTTCCGAAATGCTAAATTA 58.393 30.769 23.23 0.00 45.36 1.40
2206 4136 1.408422 GTGTGCATTTCGTTTCAGCC 58.592 50.000 0.00 0.00 0.00 4.85
2287 4477 9.829507 TGAAATGAACTTTGATGGTGTAATTTT 57.170 25.926 0.00 0.00 0.00 1.82
2292 4482 7.340122 TGTTGAAATGAACTTTGATGGTGTA 57.660 32.000 0.00 0.00 0.00 2.90
2293 4483 6.219417 TGTTGAAATGAACTTTGATGGTGT 57.781 33.333 0.00 0.00 0.00 4.16
2294 4484 6.702723 ACATGTTGAAATGAACTTTGATGGTG 59.297 34.615 0.00 0.00 0.00 4.17
2295 4485 6.819284 ACATGTTGAAATGAACTTTGATGGT 58.181 32.000 0.00 0.00 0.00 3.55
2296 4486 6.366877 GGACATGTTGAAATGAACTTTGATGG 59.633 38.462 0.00 0.00 0.00 3.51
2297 4487 7.149973 AGGACATGTTGAAATGAACTTTGATG 58.850 34.615 0.00 0.00 0.00 3.07
2298 4488 7.294017 AGGACATGTTGAAATGAACTTTGAT 57.706 32.000 0.00 0.00 0.00 2.57
2300 4490 7.775397 AAAGGACATGTTGAAATGAACTTTG 57.225 32.000 0.00 0.00 36.57 2.77
2304 4494 9.643693 ATCAATAAAGGACATGTTGAAATGAAC 57.356 29.630 0.00 0.00 33.12 3.18
2307 4497 9.426837 ACAATCAATAAAGGACATGTTGAAATG 57.573 29.630 0.00 4.71 33.12 2.32
2308 4498 9.426837 CACAATCAATAAAGGACATGTTGAAAT 57.573 29.630 0.00 0.00 33.12 2.17
2309 4499 8.637099 TCACAATCAATAAAGGACATGTTGAAA 58.363 29.630 0.00 0.00 33.12 2.69
2311 4501 7.757941 TCACAATCAATAAAGGACATGTTGA 57.242 32.000 0.00 0.00 33.82 3.18
2314 4504 7.613022 AGTCATCACAATCAATAAAGGACATGT 59.387 33.333 0.00 0.00 0.00 3.21
2315 4505 7.993101 AGTCATCACAATCAATAAAGGACATG 58.007 34.615 0.00 0.00 0.00 3.21
2316 4506 8.585471 AAGTCATCACAATCAATAAAGGACAT 57.415 30.769 0.00 0.00 0.00 3.06
2325 4598 6.209986 ACACCATCAAAGTCATCACAATCAAT 59.790 34.615 0.00 0.00 0.00 2.57
2327 4600 5.072055 ACACCATCAAAGTCATCACAATCA 58.928 37.500 0.00 0.00 0.00 2.57
2330 4603 6.951062 TTTACACCATCAAAGTCATCACAA 57.049 33.333 0.00 0.00 0.00 3.33
2559 4835 5.197451 ACAAAAGGTCAATTGTACAGGACA 58.803 37.500 19.50 0.00 37.96 4.02
2605 4881 0.912487 TGGGGGAGGACACATGGTAC 60.912 60.000 0.00 0.00 0.00 3.34
2657 4933 4.506886 ACGAACTCTTACTCTGACAAGG 57.493 45.455 0.00 0.00 0.00 3.61
2697 4973 2.665165 ACAGCATCAAACTCCAAACCA 58.335 42.857 0.00 0.00 0.00 3.67
2724 5000 4.011698 TGGATGTCATTTCCATGTCACTG 58.988 43.478 0.00 0.00 38.35 3.66
2939 5226 5.065988 AGTCCCAACGTGCATTAATATGTTC 59.934 40.000 0.00 0.00 34.12 3.18


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

AutoCloner maintained by Alex Coulton.