Multiple sequence alignment - TraesCS6A01G156300

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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 TraesCS6A01G156300 chr6A 100.000 6949 0 0 1 6949 145146203 145139255 0.000000e+00 12833
1 TraesCS6A01G156300 chr6A 95.037 403 11 1 404 797 145151478 145151076 5.920000e-175 625
2 TraesCS6A01G156300 chr6B 95.390 5944 190 31 798 6676 207166524 207160600 0.000000e+00 9382
3 TraesCS6A01G156300 chr6B 91.459 281 19 2 6674 6949 207160438 207160158 1.410000e-101 381
4 TraesCS6A01G156300 chr6D 92.753 2732 141 32 2716 5425 116961566 116958870 0.000000e+00 3895
5 TraesCS6A01G156300 chr6D 95.624 1531 56 7 5426 6949 116958832 116957306 0.000000e+00 2446
6 TraesCS6A01G156300 chr6D 90.183 1854 106 27 798 2595 116963513 116961680 0.000000e+00 2346
7 TraesCS6A01G156300 chr2B 87.793 811 63 16 1 797 77285047 77285835 0.000000e+00 917
8 TraesCS6A01G156300 chr7D 84.436 816 96 25 1 797 99025842 99026645 0.000000e+00 774
9 TraesCS6A01G156300 chr7D 81.884 414 47 21 404 798 99002474 99002878 2.420000e-84 324
10 TraesCS6A01G156300 chr7D 80.964 415 64 10 3 406 65812190 65812600 1.450000e-81 315
11 TraesCS6A01G156300 chr5D 82.805 820 98 28 1 797 389504400 389505199 0.000000e+00 693
12 TraesCS6A01G156300 chr1D 82.555 814 105 30 1 797 34634641 34635434 0.000000e+00 682
13 TraesCS6A01G156300 chr1D 82.536 418 51 16 1 404 155887123 155886714 1.430000e-91 348
14 TraesCS6A01G156300 chr1D 79.943 349 56 14 454 797 34629415 34629754 1.940000e-60 244
15 TraesCS6A01G156300 chr7A 85.122 410 50 9 1 406 91668437 91668839 6.490000e-110 409
16 TraesCS6A01G156300 chr1B 77.593 723 109 41 1 697 48137041 48136346 8.450000e-104 388
17 TraesCS6A01G156300 chr1B 83.619 409 55 10 1 406 646267921 646268320 2.370000e-99 374
18 TraesCS6A01G156300 chr3B 79.494 356 49 13 4629 4962 615386020 615385667 1.510000e-56 231
19 TraesCS6A01G156300 chr3B 78.249 354 56 17 4629 4962 616437161 616436809 2.540000e-49 207


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 TraesCS6A01G156300 chr6A 145139255 145146203 6948 True 12833.000000 12833 100.000000 1 6949 1 chr6A.!!$R1 6948
1 TraesCS6A01G156300 chr6B 207160158 207166524 6366 True 4881.500000 9382 93.424500 798 6949 2 chr6B.!!$R1 6151
2 TraesCS6A01G156300 chr6D 116957306 116963513 6207 True 2895.666667 3895 92.853333 798 6949 3 chr6D.!!$R1 6151
3 TraesCS6A01G156300 chr2B 77285047 77285835 788 False 917.000000 917 87.793000 1 797 1 chr2B.!!$F1 796
4 TraesCS6A01G156300 chr7D 99025842 99026645 803 False 774.000000 774 84.436000 1 797 1 chr7D.!!$F3 796
5 TraesCS6A01G156300 chr5D 389504400 389505199 799 False 693.000000 693 82.805000 1 797 1 chr5D.!!$F1 796
6 TraesCS6A01G156300 chr1D 34634641 34635434 793 False 682.000000 682 82.555000 1 797 1 chr1D.!!$F2 796
7 TraesCS6A01G156300 chr1B 48136346 48137041 695 True 388.000000 388 77.593000 1 697 1 chr1B.!!$R1 696

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
737 782 0.109458 TTCATCTGGACCGTCGTTCG 60.109 55.000 0.00 0.0 39.52 3.95 F
1727 1815 0.249322 CCCGTTCTGTCTCGTGTTGT 60.249 55.000 0.00 0.0 0.00 3.32 F
2047 2146 1.140816 GTTGACGTCTCACCTTCAGC 58.859 55.000 17.92 0.0 0.00 4.26 F
3253 3404 1.469423 GCAGAGCCTACGTGAACCTAC 60.469 57.143 0.00 0.0 0.00 3.18 F
4816 4972 0.104120 TCGATGGGGTAATCACTGCG 59.896 55.000 0.00 0.0 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2313 0.598419 TTATCTCGGCATGCAGCTCG 60.598 55.000 21.36 13.85 44.79 5.03 R
3134 3274 1.604278 ACTCAAAGTCCAAAGAAGCGC 59.396 47.619 0.00 0.00 0.00 5.92 R
3402 3553 2.361757 TGACCACACAAGATTTTGGCAG 59.638 45.455 0.57 0.00 38.66 4.85 R
5170 5329 1.334869 GTTGGGAGAAAGCTGTGTGTG 59.665 52.381 0.00 0.00 0.00 3.82 R
6537 6745 0.397941 TTTCAGCCTGACCACAGAGG 59.602 55.000 0.00 0.00 46.03 3.69 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
58 59 3.160269 CCTCAAATCTGCCACCTCTTTT 58.840 45.455 0.00 0.00 0.00 2.27
70 71 3.307059 CCACCTCTTTTTCCACTCGATCT 60.307 47.826 0.00 0.00 0.00 2.75
82 83 1.604755 ACTCGATCTACCGTGATCTGC 59.395 52.381 0.00 0.00 40.32 4.26
116 117 0.390340 GTCTGCCATCTGCGACTGAA 60.390 55.000 0.00 0.00 45.60 3.02
122 123 0.997932 CATCTGCGACTGAAGACTGC 59.002 55.000 0.00 0.00 30.55 4.40
365 368 2.279451 TGATTCGCCGCCGATGAG 60.279 61.111 0.00 0.00 43.97 2.90
447 456 4.112634 GGAACTCGATCATCACGATTTCA 58.887 43.478 17.02 0.00 44.79 2.69
450 459 6.088749 GGAACTCGATCATCACGATTTCATAG 59.911 42.308 17.02 0.00 44.79 2.23
452 461 4.809673 TCGATCATCACGATTTCATAGGG 58.190 43.478 0.00 0.00 33.17 3.53
483 505 6.721318 AGCAATTCAGAGGTACAATTTAGGA 58.279 36.000 0.00 0.00 0.00 2.94
484 506 7.349598 AGCAATTCAGAGGTACAATTTAGGAT 58.650 34.615 0.00 0.00 0.00 3.24
516 538 0.406750 TCAGAGACCCCGACTTGGTA 59.593 55.000 0.00 0.00 35.85 3.25
583 623 3.024356 TCCTCTCCTCCCCTCGCT 61.024 66.667 0.00 0.00 0.00 4.93
618 659 3.418068 GACAGCTCACAGCCACGC 61.418 66.667 0.00 0.00 43.77 5.34
623 664 2.433145 CTCACAGCCACGCGTGAT 60.433 61.111 39.10 24.40 39.61 3.06
625 666 0.735978 CTCACAGCCACGCGTGATAA 60.736 55.000 39.10 16.85 39.61 1.75
626 667 1.011968 TCACAGCCACGCGTGATAAC 61.012 55.000 39.10 23.94 37.25 1.89
638 681 3.181534 CGCGTGATAACCACTGTTACAAG 60.182 47.826 0.00 0.00 43.53 3.16
641 684 5.227908 CGTGATAACCACTGTTACAAGTCT 58.772 41.667 0.00 0.00 43.53 3.24
659 702 4.183101 AGTCTTAACGGTGTCGACAAAAA 58.817 39.130 21.95 9.17 40.11 1.94
672 717 5.523188 TGTCGACAAAAATAACAGTAACGGT 59.477 36.000 17.62 0.00 0.00 4.83
673 718 6.067039 GTCGACAAAAATAACAGTAACGGTC 58.933 40.000 11.55 0.00 0.00 4.79
691 736 0.397675 TCAGAGATGGCGAGGATGGT 60.398 55.000 0.00 0.00 0.00 3.55
695 740 2.175202 GAGATGGCGAGGATGGTATCT 58.825 52.381 0.00 0.00 0.00 1.98
707 752 0.952280 TGGTATCTGAGCCGTCGATC 59.048 55.000 0.00 0.00 0.00 3.69
736 781 1.336517 TGTTCATCTGGACCGTCGTTC 60.337 52.381 0.00 0.00 0.00 3.95
737 782 0.109458 TTCATCTGGACCGTCGTTCG 60.109 55.000 0.00 0.00 39.52 3.95
739 784 0.388134 CATCTGGACCGTCGTTCGTT 60.388 55.000 0.00 0.00 37.94 3.85
755 800 3.536956 TCGTTTGAACTTCCTGTGAGT 57.463 42.857 0.00 0.00 0.00 3.41
759 804 1.967319 TGAACTTCCTGTGAGTTGCC 58.033 50.000 0.00 0.00 37.46 4.52
767 812 0.601046 CTGTGAGTTGCCTCGCTTCA 60.601 55.000 5.34 0.00 46.31 3.02
808 853 2.049433 CTGACACCGACCGACCAC 60.049 66.667 0.00 0.00 0.00 4.16
1158 1203 1.004080 CCAGCCTCACACTCCACAG 60.004 63.158 0.00 0.00 0.00 3.66
1159 1204 1.750930 CAGCCTCACACTCCACAGT 59.249 57.895 0.00 0.00 0.00 3.55
1174 1219 2.329379 CACAGTTCTCCACTTAGTCGC 58.671 52.381 0.00 0.00 30.92 5.19
1176 1221 0.526662 AGTTCTCCACTTAGTCGCCG 59.473 55.000 0.00 0.00 27.32 6.46
1212 1257 1.883084 GGCGTTCGATCGATTGCCT 60.883 57.895 35.44 0.00 39.87 4.75
1243 1288 2.125106 CCTGCTAAGCCCCGTCAC 60.125 66.667 0.00 0.00 0.00 3.67
1254 1299 2.969950 AGCCCCGTCACATTATAGCTAA 59.030 45.455 0.00 0.00 0.00 3.09
1275 1320 8.150296 AGCTAATTTGTTTGAAATAACTTGCCT 58.850 29.630 1.37 0.00 0.00 4.75
1306 1372 2.017049 GTAGCTGCCCACGATGAATTT 58.983 47.619 0.00 0.00 0.00 1.82
1364 1432 2.857186 TGCTTGTTGGTCTATCAGCA 57.143 45.000 0.00 0.00 0.00 4.41
1365 1433 3.354948 TGCTTGTTGGTCTATCAGCAT 57.645 42.857 0.00 0.00 30.77 3.79
1366 1434 3.273434 TGCTTGTTGGTCTATCAGCATC 58.727 45.455 0.00 0.00 30.77 3.91
1374 1442 2.171448 GGTCTATCAGCATCCTGTTGGT 59.829 50.000 0.00 0.00 40.09 3.67
1392 1460 7.093552 CCTGTTGGTTTGACCCATTAATTGATA 60.094 37.037 0.00 0.00 37.50 2.15
1394 1462 8.310382 TGTTGGTTTGACCCATTAATTGATAAG 58.690 33.333 0.00 0.00 37.50 1.73
1422 1493 2.298729 TGCTTGGTGGTTTCCTTTATGC 59.701 45.455 0.00 0.00 0.00 3.14
1433 1504 1.801771 TCCTTTATGCGAAACGTGGTG 59.198 47.619 0.00 0.00 0.00 4.17
1438 1525 3.276846 GCGAAACGTGGTGGTGCT 61.277 61.111 0.00 0.00 0.00 4.40
1463 1550 3.611530 CGCCTGTCAAATTACCAGGTTTG 60.612 47.826 15.49 0.00 46.09 2.93
1478 1565 4.949856 CCAGGTTTGGTTTATGCAGAGTAT 59.050 41.667 0.00 0.00 39.79 2.12
1496 1584 5.659079 AGAGTATAATATGTGCCTAGCCCTC 59.341 44.000 0.00 0.00 0.00 4.30
1498 1586 5.966935 AGTATAATATGTGCCTAGCCCTCAT 59.033 40.000 0.00 0.00 0.00 2.90
1500 1588 4.459852 AATATGTGCCTAGCCCTCATTT 57.540 40.909 2.81 0.00 0.00 2.32
1546 1634 1.675552 CCGGAGTTGACAAAACCACT 58.324 50.000 0.00 0.00 0.00 4.00
1567 1655 5.639931 CACTAAGCCTAAGAGGAACTTGTTC 59.360 44.000 5.03 5.03 41.55 3.18
1727 1815 0.249322 CCCGTTCTGTCTCGTGTTGT 60.249 55.000 0.00 0.00 0.00 3.32
1747 1835 9.083080 GTGTTGTTTACTCTTTTTATTGCAGTT 57.917 29.630 0.00 0.00 0.00 3.16
1779 1867 3.748568 GCCTACTGGAAGCATGTATTAGC 59.251 47.826 0.00 0.00 37.60 3.09
1783 1871 2.212652 TGGAAGCATGTATTAGCTGCG 58.787 47.619 0.00 0.00 41.70 5.18
1787 1875 1.202568 AGCATGTATTAGCTGCGCTCA 60.203 47.619 9.73 0.00 40.44 4.26
2047 2146 1.140816 GTTGACGTCTCACCTTCAGC 58.859 55.000 17.92 0.00 0.00 4.26
2079 2178 5.680619 TCGCATAACATCATTTAAGAGGGT 58.319 37.500 0.00 0.00 0.00 4.34
2080 2179 5.527214 TCGCATAACATCATTTAAGAGGGTG 59.473 40.000 0.00 0.00 0.00 4.61
2114 2213 7.542130 ACATTAAAATGAACTTCTCGATTTGGC 59.458 33.333 9.60 0.00 39.67 4.52
2245 2344 2.846550 GCCGAGATAAAAAGAAAAGCGC 59.153 45.455 0.00 0.00 0.00 5.92
2266 2365 3.679917 GCTAGTAGCAGGAGCATCACAAA 60.680 47.826 17.47 0.00 45.49 2.83
2324 2423 2.353889 GAGTTGTGCTGCTGTCATATGG 59.646 50.000 2.13 0.00 0.00 2.74
2339 2439 8.623903 GCTGTCATATGGTAGAATTTCATTTGA 58.376 33.333 2.13 0.00 30.50 2.69
2611 2747 5.194432 TGAAACTCTAGATAAGCTCGGACT 58.806 41.667 0.00 0.00 0.00 3.85
2705 2841 7.660030 AAATACATGTAAGGAAAATCCCTGG 57.340 36.000 10.14 0.00 37.19 4.45
2743 2879 6.319658 ACATGTAAGGAATAACTGCTGGATTG 59.680 38.462 0.00 0.00 0.00 2.67
2965 3105 5.080969 TGTACACCAGTATAAGTTCCTGC 57.919 43.478 0.00 0.00 31.84 4.85
2980 3120 4.714308 AGTTCCTGCTAGTCAATAGAAGCT 59.286 41.667 0.00 0.00 35.95 3.74
3011 3151 6.319658 ACTGTTGTCCATTGATATGAATCCAC 59.680 38.462 0.00 0.00 33.37 4.02
3126 3266 3.199946 CCAGTCCTGCTAATTGGTCCTAA 59.800 47.826 0.00 0.00 0.00 2.69
3134 3274 4.345257 TGCTAATTGGTCCTAAGCTCCTAG 59.655 45.833 0.00 0.00 34.28 3.02
3154 3295 1.604278 GCGCTTCTTTGGACTTTGAGT 59.396 47.619 0.00 0.00 0.00 3.41
3166 3307 3.686726 GGACTTTGAGTCAACTAGCATGG 59.313 47.826 4.68 0.00 46.79 3.66
3253 3404 1.469423 GCAGAGCCTACGTGAACCTAC 60.469 57.143 0.00 0.00 0.00 3.18
3338 3489 9.559958 GGTGTCAATTTAAACTTGTGATATCAG 57.440 33.333 5.42 0.00 0.00 2.90
3452 3603 0.107831 ACAAGCTTGACCGTGGCTTA 59.892 50.000 32.50 0.00 43.28 3.09
3823 3977 7.610865 TCTGTTCTGGTTTTCAAAATTGAGTT 58.389 30.769 0.00 0.00 38.61 3.01
4041 4196 0.250295 CCAAGACAGCGGAAGTTCCA 60.250 55.000 21.76 0.00 35.91 3.53
4045 4200 1.569479 GACAGCGGAAGTTCCACAGC 61.569 60.000 21.76 16.14 35.91 4.40
4112 4267 4.743493 TGCAAAAGAAACAAGACAGGTTC 58.257 39.130 0.00 0.00 0.00 3.62
4122 4277 0.107410 AGACAGGTTCGTGCCAACAA 60.107 50.000 1.38 0.00 0.00 2.83
4163 4318 4.499188 GGTGCCTTTTTCTGGAACTTGTAC 60.499 45.833 0.00 0.00 33.62 2.90
4251 4406 6.184789 TCATTGAAGGTTGGTTCCTATTACC 58.815 40.000 0.00 0.00 36.74 2.85
4437 4592 7.068839 TCGCCCATGTAATGTTTAATTTGGTAT 59.931 33.333 0.00 0.00 44.81 2.73
4505 4660 2.288395 GCACAGGGAGTTTCCAATGTTG 60.288 50.000 0.00 0.00 38.64 3.33
4589 4744 3.334691 TCTTGGTTTGTGATAGCTTCGG 58.665 45.455 0.00 0.00 0.00 4.30
4685 4840 2.494471 GGCCCAGGTACACATTTTAACC 59.506 50.000 0.00 0.00 0.00 2.85
4706 4861 6.032956 ACCGACATGAACAGATAACTAACA 57.967 37.500 0.00 0.00 0.00 2.41
4816 4972 0.104120 TCGATGGGGTAATCACTGCG 59.896 55.000 0.00 0.00 0.00 5.18
4831 4987 2.227388 CACTGCGGAAAAGCTCAAGAAT 59.773 45.455 0.00 0.00 38.13 2.40
4832 4988 2.485814 ACTGCGGAAAAGCTCAAGAATC 59.514 45.455 0.00 0.00 38.13 2.52
4969 5128 1.879380 TGCTTGCAAAATCACTAGCGT 59.121 42.857 0.00 0.00 37.45 5.07
5126 5285 1.202290 CCACCATTGTTAATCAGGCGC 60.202 52.381 0.00 0.00 0.00 6.53
5135 5294 0.465642 TAATCAGGCGCTCTCTCCGA 60.466 55.000 7.64 0.00 0.00 4.55
5170 5329 4.396478 GCCAGGTTCCATCTTCTCTTTAAC 59.604 45.833 0.00 0.00 0.00 2.01
5244 5403 3.461061 CATGCGATGTGATACCTGACTT 58.539 45.455 0.00 0.00 0.00 3.01
5644 5840 3.192001 GCGATGTATCCCAACGAGGTATA 59.808 47.826 0.00 0.00 41.41 1.47
5998 6194 6.396829 AGCTTTGCTTATTGTTGACTTCTT 57.603 33.333 0.00 0.00 33.89 2.52
6110 6306 4.795469 ACCATCATCTGAAACATATGGCA 58.205 39.130 7.80 0.00 37.91 4.92
6154 6350 3.965379 TGCATGCATCCAAACAGAATT 57.035 38.095 18.46 0.00 0.00 2.17
6328 6534 2.606961 ATCGCTGTTGTGCCGTGTG 61.607 57.895 0.00 0.00 0.00 3.82
6384 6590 8.377799 AGAAGCCCACAGAATTAAATTCAAAAT 58.622 29.630 0.00 0.00 41.71 1.82
6430 6638 4.081031 GGGCAAGTAAGCTACTCCTACTTT 60.081 45.833 5.24 0.00 38.26 2.66
6537 6745 4.803613 GTGGTTCTTGTGATGGTGAAAAAC 59.196 41.667 0.00 0.00 0.00 2.43
6554 6762 3.797331 CCTCTGTGGTCAGGCTGA 58.203 61.111 14.43 14.43 41.59 4.26
6638 6847 1.082756 GCACGTTTCAGCGACCTTG 60.083 57.895 0.00 0.00 35.59 3.61
6639 6848 1.082756 CACGTTTCAGCGACCTTGC 60.083 57.895 0.00 0.00 35.59 4.01
6722 7095 3.181474 ACGAAAGCCTAATCTACCTCTGC 60.181 47.826 0.00 0.00 0.00 4.26
6768 7142 4.275196 CCTCCAGTCGACTTGATACGATTA 59.725 45.833 17.26 0.00 40.50 1.75
6940 7319 4.219070 TGCAGATTTCAGTTTGAGGATTGG 59.781 41.667 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 2.118313 TCACGGTAGATCGAGTGGAA 57.882 50.000 11.07 0.00 35.50 3.53
70 71 0.249120 CCAAGGTGCAGATCACGGTA 59.751 55.000 0.00 0.00 46.56 4.02
82 83 1.233019 CAGACACAAGAGCCAAGGTG 58.767 55.000 0.00 0.00 37.29 4.00
122 123 1.820056 TGGAGCGAGTCTAGCGGAG 60.820 63.158 0.00 0.00 40.04 4.63
365 368 2.657620 GTAATCCTCGGCGGCGAC 60.658 66.667 31.46 16.51 0.00 5.19
379 388 2.159338 GGTATCAGAGCGTCGGTTGTAA 60.159 50.000 0.00 0.00 0.00 2.41
419 428 3.181496 CGTGATGATCGAGTTCCTCTGAA 60.181 47.826 0.00 0.00 0.00 3.02
447 456 5.163258 CCTCTGAATTGCTACAGTTCCCTAT 60.163 44.000 0.00 0.00 35.84 2.57
450 459 3.274288 CCTCTGAATTGCTACAGTTCCC 58.726 50.000 0.00 0.00 35.84 3.97
452 461 5.479306 TGTACCTCTGAATTGCTACAGTTC 58.521 41.667 0.00 0.00 35.84 3.01
483 505 3.006323 GGTCTCTGATCTCGCACCATTAT 59.994 47.826 0.00 0.00 0.00 1.28
484 506 2.362397 GGTCTCTGATCTCGCACCATTA 59.638 50.000 0.00 0.00 0.00 1.90
488 510 1.439644 GGGTCTCTGATCTCGCACC 59.560 63.158 0.00 0.00 0.00 5.01
516 538 6.077202 AGTAGTTAGAACCCTAGCTAGTGT 57.923 41.667 19.31 11.63 39.41 3.55
619 660 8.493547 GTTAAGACTTGTAACAGTGGTTATCAC 58.506 37.037 0.00 0.00 46.39 3.06
620 661 7.383029 CGTTAAGACTTGTAACAGTGGTTATCA 59.617 37.037 0.00 0.00 41.28 2.15
621 662 7.148689 CCGTTAAGACTTGTAACAGTGGTTATC 60.149 40.741 0.00 0.00 41.28 1.75
623 664 5.984926 CCGTTAAGACTTGTAACAGTGGTTA 59.015 40.000 0.00 0.00 38.45 2.85
625 666 4.141869 ACCGTTAAGACTTGTAACAGTGGT 60.142 41.667 0.00 0.00 32.07 4.16
626 667 4.210537 CACCGTTAAGACTTGTAACAGTGG 59.789 45.833 8.45 2.36 36.70 4.00
638 681 4.519191 TTTTTGTCGACACCGTTAAGAC 57.481 40.909 19.90 0.00 37.05 3.01
641 684 6.036953 ACTGTTATTTTTGTCGACACCGTTAA 59.963 34.615 19.90 6.64 37.05 2.01
659 702 4.441634 GCCATCTCTGACCGTTACTGTTAT 60.442 45.833 0.00 0.00 0.00 1.89
672 717 0.397675 ACCATCCTCGCCATCTCTGA 60.398 55.000 0.00 0.00 0.00 3.27
673 718 1.332195 TACCATCCTCGCCATCTCTG 58.668 55.000 0.00 0.00 0.00 3.35
691 736 2.552599 AGAGATCGACGGCTCAGATA 57.447 50.000 16.96 0.00 33.62 1.98
695 740 0.735471 CAGAAGAGATCGACGGCTCA 59.265 55.000 16.96 0.00 33.62 4.26
707 752 3.594134 GTCCAGATGAACACCAGAAGAG 58.406 50.000 0.00 0.00 0.00 2.85
736 781 3.788797 GCAACTCACAGGAAGTTCAAACG 60.789 47.826 5.01 0.00 0.00 3.60
737 782 3.489229 GGCAACTCACAGGAAGTTCAAAC 60.489 47.826 5.01 0.00 0.00 2.93
739 784 2.297701 GGCAACTCACAGGAAGTTCAA 58.702 47.619 5.01 0.00 0.00 2.69
754 799 2.010145 TACTGATGAAGCGAGGCAAC 57.990 50.000 0.00 0.00 0.00 4.17
755 800 2.621338 CTTACTGATGAAGCGAGGCAA 58.379 47.619 0.00 0.00 0.00 4.52
961 1006 1.376037 CGCAGTGGGAGAAGGTTCC 60.376 63.158 0.00 0.00 36.46 3.62
1158 1203 0.458025 CCGGCGACTAAGTGGAGAAC 60.458 60.000 9.30 0.00 0.00 3.01
1159 1204 0.896940 ACCGGCGACTAAGTGGAGAA 60.897 55.000 9.30 0.00 0.00 2.87
1191 1236 1.145759 GCAATCGATCGAACGCCTGA 61.146 55.000 23.50 0.00 0.00 3.86
1265 1310 8.487028 AGCTACAGAGTTAAATAGGCAAGTTAT 58.513 33.333 0.00 0.00 0.00 1.89
1270 1315 4.876107 GCAGCTACAGAGTTAAATAGGCAA 59.124 41.667 0.00 0.00 0.00 4.52
1275 1320 4.679639 CGTGGGCAGCTACAGAGTTAAATA 60.680 45.833 0.00 0.00 0.00 1.40
1306 1372 9.393512 GTACTCTGTACTAAGTGAAGAAGGATA 57.606 37.037 9.99 0.00 0.00 2.59
1351 1419 3.370846 CCAACAGGATGCTGATAGACCAA 60.371 47.826 22.24 0.00 42.53 3.67
1364 1432 2.999185 ATGGGTCAAACCAACAGGAT 57.001 45.000 0.00 0.00 45.13 3.24
1365 1433 2.765689 AATGGGTCAAACCAACAGGA 57.234 45.000 0.00 0.00 45.13 3.86
1366 1434 5.011533 TCAATTAATGGGTCAAACCAACAGG 59.988 40.000 0.00 0.00 45.13 4.00
1392 1460 6.435164 AGGAAACCACCAAGCATTATATCTT 58.565 36.000 0.00 0.00 0.00 2.40
1394 1462 6.715347 AAGGAAACCACCAAGCATTATATC 57.285 37.500 0.00 0.00 0.00 1.63
1422 1493 2.631428 CAGCACCACCACGTTTCG 59.369 61.111 0.00 0.00 0.00 3.46
1438 1525 0.250945 TGGTAATTTGACAGGCGCCA 60.251 50.000 31.54 6.82 0.00 5.69
1463 1550 7.607991 AGGCACATATTATACTCTGCATAAACC 59.392 37.037 0.00 0.00 0.00 3.27
1468 1555 6.344500 GCTAGGCACATATTATACTCTGCAT 58.656 40.000 0.00 0.00 0.00 3.96
1478 1565 5.582950 AAATGAGGGCTAGGCACATATTA 57.417 39.130 19.14 0.00 32.33 0.98
1496 1584 5.163834 GGCATCTGCATAAACACCAAAAATG 60.164 40.000 4.33 0.00 44.36 2.32
1498 1586 4.202295 TGGCATCTGCATAAACACCAAAAA 60.202 37.500 4.33 0.00 44.36 1.94
1500 1588 2.896044 TGGCATCTGCATAAACACCAAA 59.104 40.909 4.33 0.00 44.36 3.28
1546 1634 4.525487 TCGAACAAGTTCCTCTTAGGCTTA 59.475 41.667 7.32 0.00 36.27 3.09
1567 1655 2.443957 GAAGGTTGCTGGCGTTGTCG 62.444 60.000 0.00 0.00 40.37 4.35
1747 1835 3.807209 GCTTCCAGTAGGCAGAACAAAGA 60.807 47.826 0.00 0.00 28.40 2.52
1759 1847 4.450419 GCAGCTAATACATGCTTCCAGTAG 59.550 45.833 0.00 0.00 37.44 2.57
1783 1871 4.152526 CGTGTATCTACTATTCGCTGAGC 58.847 47.826 0.00 0.00 0.00 4.26
1787 1875 4.318618 CGTCACGTGTATCTACTATTCGCT 60.319 45.833 16.51 0.00 0.00 4.93
1906 2002 5.643379 TGAACATGGAGTTAGAAAATGGC 57.357 39.130 0.00 0.00 41.51 4.40
2027 2126 1.409412 CTGAAGGTGAGACGTCAACG 58.591 55.000 19.50 0.12 46.04 4.10
2214 2313 0.598419 TTATCTCGGCATGCAGCTCG 60.598 55.000 21.36 13.85 44.79 5.03
2245 2344 3.808466 TTGTGATGCTCCTGCTACTAG 57.192 47.619 0.00 0.00 40.48 2.57
2611 2747 8.410141 GCTACAAATAAGTTGCCAACCATTATA 58.590 33.333 3.45 1.46 41.31 0.98
2713 2849 7.716998 CCAGCAGTTATTCCTTACATGTATTCT 59.283 37.037 6.36 0.00 0.00 2.40
2714 2850 7.715249 TCCAGCAGTTATTCCTTACATGTATTC 59.285 37.037 6.36 0.00 0.00 1.75
2980 3120 7.111466 TCATATCAATGGACAACAGTCAATCA 58.889 34.615 0.00 0.00 33.90 2.57
3033 3173 6.704289 AAGTTAACCTTTGGTTGTTAGGTC 57.296 37.500 11.78 0.00 46.35 3.85
3038 3178 8.973182 TGAAAGATAAGTTAACCTTTGGTTGTT 58.027 29.630 11.78 5.76 46.35 2.83
3134 3274 1.604278 ACTCAAAGTCCAAAGAAGCGC 59.396 47.619 0.00 0.00 0.00 5.92
3193 3344 4.461081 TGAAAAGTTGCGCCATAAGGTAAT 59.539 37.500 4.18 0.00 37.19 1.89
3253 3404 2.772568 TTGTGAATGCAAACACGAGG 57.227 45.000 17.39 0.00 39.52 4.63
3388 3539 4.657814 TTTGGCAGAACCCTTAGATTCT 57.342 40.909 0.00 0.00 37.83 2.40
3402 3553 2.361757 TGACCACACAAGATTTTGGCAG 59.638 45.455 0.57 0.00 38.66 4.85
3452 3603 4.630111 CACCATTACAAAATGCAGTGGTT 58.370 39.130 0.00 0.00 41.06 3.67
3837 3991 6.763135 TCATCCTAAACATGCAAGATGAGTAC 59.237 38.462 0.00 0.00 36.20 2.73
4251 4406 2.354003 GCATGACCCAACAAAATCAGGG 60.354 50.000 0.00 0.00 46.96 4.45
4505 4660 8.777413 ACAAAGTAAAACTTCGAAGGGTATTAC 58.223 33.333 27.86 24.80 37.47 1.89
4589 4744 7.682824 CGATAAGCATTGTCATAAGATCATCC 58.317 38.462 0.00 0.00 35.80 3.51
4816 4972 3.339141 ACTCCGATTCTTGAGCTTTTCC 58.661 45.455 0.00 0.00 31.65 3.13
4831 4987 7.643569 TGGTAACATAAGTAACATACTCCGA 57.356 36.000 0.00 0.00 46.17 4.55
5126 5285 4.054671 GCAATTTATCAGGTCGGAGAGAG 58.945 47.826 0.00 0.00 36.95 3.20
5170 5329 1.334869 GTTGGGAGAAAGCTGTGTGTG 59.665 52.381 0.00 0.00 0.00 3.82
5262 5421 4.380843 ACCCACCTATGAATTTGTGTGA 57.619 40.909 0.00 0.00 0.00 3.58
5644 5840 1.691976 TGACGAGACCAATGTTCAGGT 59.308 47.619 0.00 0.00 41.83 4.00
5798 5994 2.343758 GTTGACTCCAGGAGCGCA 59.656 61.111 17.31 12.24 32.04 6.09
5871 6067 3.133003 CCCGTCACCATCTCTACTTCATT 59.867 47.826 0.00 0.00 0.00 2.57
5900 6096 3.445805 ACAACCCGTTCTTTGTGTGAATT 59.554 39.130 0.00 0.00 34.61 2.17
5998 6194 0.669012 TAAAGCATGCAGACGACGCA 60.669 50.000 21.98 6.82 44.94 5.24
6154 6350 3.703921 TGGCATGGAGTGTACTACTGTA 58.296 45.455 0.00 0.00 40.53 2.74
6384 6590 4.255126 GCTATCGGCGGCGATTTA 57.745 55.556 44.59 29.82 0.00 1.40
6537 6745 0.397941 TTTCAGCCTGACCACAGAGG 59.602 55.000 0.00 0.00 46.03 3.69
6578 6787 5.117584 TGCAACATCAACAGCAAAAATTCT 58.882 33.333 0.00 0.00 33.48 2.40
6579 6788 5.406767 TGCAACATCAACAGCAAAAATTC 57.593 34.783 0.00 0.00 33.48 2.17
6722 7095 6.016443 AGGTGATTCAAGAAAAGAAGCAAGAG 60.016 38.462 0.00 0.00 42.24 2.85
6796 7173 7.956420 ATTCCATACATATAAAAAGACGCGA 57.044 32.000 15.93 0.00 0.00 5.87
6823 7202 6.456853 GCTGTTGCTACATTCATCACGAAATA 60.457 38.462 0.34 0.00 34.99 1.40
6895 7274 2.234661 ACATCTGGAAATCGCAGACTGA 59.765 45.455 6.65 0.00 42.51 3.41
6896 7275 2.625737 ACATCTGGAAATCGCAGACTG 58.374 47.619 0.00 0.00 42.51 3.51


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

AutoCloner maintained by Alex Coulton.