Multiple sequence alignment - TraesCS6B01G163900

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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 TraesCS6B01G163900 chr6B 100.000 4922 0 0 1 4922 171181715 171186636 0.000000e+00 9090
1 TraesCS6B01G163900 chr6B 79.726 2703 479 43 992 3671 171029191 171031847 0.000000e+00 1892
2 TraesCS6B01G163900 chr6B 78.703 2653 490 58 908 3521 171699948 171702564 0.000000e+00 1700
3 TraesCS6B01G163900 chr6B 78.244 2096 405 37 1349 3424 171704818 171706882 0.000000e+00 1297
4 TraesCS6B01G163900 chr6B 79.257 1750 323 26 1981 3721 171206041 171207759 0.000000e+00 1184
5 TraesCS6B01G163900 chr6D 95.019 4959 203 21 1 4922 89155257 89160208 0.000000e+00 7749
6 TraesCS6B01G163900 chr6D 79.208 2549 472 36 1215 3745 89166894 89169402 0.000000e+00 1718
7 TraesCS6B01G163900 chr6D 78.715 2396 463 35 996 3370 89068451 89070820 0.000000e+00 1555
8 TraesCS6B01G163900 chr6D 78.794 514 99 10 1040 1548 89299574 89300082 2.190000e-88 337
9 TraesCS6B01G163900 chr6A 95.479 3163 135 5 819 3974 107243201 107246362 0.000000e+00 5042
10 TraesCS6B01G163900 chr6A 79.238 2702 489 46 995 3671 107214452 107217106 0.000000e+00 1816
11 TraesCS6B01G163900 chr6A 78.824 1837 348 27 1981 3802 107270589 107272399 0.000000e+00 1199
12 TraesCS6B01G163900 chr6A 91.385 592 32 14 4340 4922 107246393 107246974 0.000000e+00 793
13 TraesCS6B01G163900 chr6A 83.355 769 68 16 13 724 107242364 107243129 0.000000e+00 656
14 TraesCS6B01G163900 chr6A 94.366 71 4 0 699 769 107243129 107243199 5.210000e-20 110
15 TraesCS6B01G163900 chr7A 77.683 1985 414 21 1676 3642 732158011 732156038 0.000000e+00 1184
16 TraesCS6B01G163900 chrUn 78.426 1868 357 32 908 2754 335904527 335906369 0.000000e+00 1175
17 TraesCS6B01G163900 chrUn 78.426 1868 357 32 908 2754 335907209 335909051 0.000000e+00 1175
18 TraesCS6B01G163900 chrUn 79.428 1677 307 26 1307 2967 325921070 325919416 0.000000e+00 1151
19 TraesCS6B01G163900 chrUn 78.731 1481 280 23 1289 2754 394420116 394421576 0.000000e+00 957
20 TraesCS6B01G163900 chr7D 78.225 1566 301 27 2083 3633 634088400 634089940 0.000000e+00 966
21 TraesCS6B01G163900 chr7B 80.435 414 73 4 959 1371 742417647 742418053 4.780000e-80 309
22 TraesCS6B01G163900 chr1B 77.381 420 93 2 3220 3638 660467247 660467665 1.060000e-61 248


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 TraesCS6B01G163900 chr6B 171181715 171186636 4921 False 9090.00 9090 100.00000 1 4922 1 chr6B.!!$F2 4921
1 TraesCS6B01G163900 chr6B 171029191 171031847 2656 False 1892.00 1892 79.72600 992 3671 1 chr6B.!!$F1 2679
2 TraesCS6B01G163900 chr6B 171699948 171706882 6934 False 1498.50 1700 78.47350 908 3521 2 chr6B.!!$F4 2613
3 TraesCS6B01G163900 chr6B 171206041 171207759 1718 False 1184.00 1184 79.25700 1981 3721 1 chr6B.!!$F3 1740
4 TraesCS6B01G163900 chr6D 89155257 89160208 4951 False 7749.00 7749 95.01900 1 4922 1 chr6D.!!$F2 4921
5 TraesCS6B01G163900 chr6D 89166894 89169402 2508 False 1718.00 1718 79.20800 1215 3745 1 chr6D.!!$F3 2530
6 TraesCS6B01G163900 chr6D 89068451 89070820 2369 False 1555.00 1555 78.71500 996 3370 1 chr6D.!!$F1 2374
7 TraesCS6B01G163900 chr6D 89299574 89300082 508 False 337.00 337 78.79400 1040 1548 1 chr6D.!!$F4 508
8 TraesCS6B01G163900 chr6A 107214452 107217106 2654 False 1816.00 1816 79.23800 995 3671 1 chr6A.!!$F1 2676
9 TraesCS6B01G163900 chr6A 107242364 107246974 4610 False 1650.25 5042 91.14625 13 4922 4 chr6A.!!$F3 4909
10 TraesCS6B01G163900 chr6A 107270589 107272399 1810 False 1199.00 1199 78.82400 1981 3802 1 chr6A.!!$F2 1821
11 TraesCS6B01G163900 chr7A 732156038 732158011 1973 True 1184.00 1184 77.68300 1676 3642 1 chr7A.!!$R1 1966
12 TraesCS6B01G163900 chrUn 335904527 335909051 4524 False 1175.00 1175 78.42600 908 2754 2 chrUn.!!$F2 1846
13 TraesCS6B01G163900 chrUn 325919416 325921070 1654 True 1151.00 1151 79.42800 1307 2967 1 chrUn.!!$R1 1660
14 TraesCS6B01G163900 chrUn 394420116 394421576 1460 False 957.00 957 78.73100 1289 2754 1 chrUn.!!$F1 1465
15 TraesCS6B01G163900 chr7D 634088400 634089940 1540 False 966.00 966 78.22500 2083 3633 1 chr7D.!!$F1 1550

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
519 579 0.034186 CCATGCCTTCTACCCTGCAA 60.034 55.000 0.00 0.0 37.27 4.08 F
689 751 0.523072 CATTTTGGAGGCACCGTGAG 59.477 55.000 1.65 0.0 42.61 3.51 F
1068 1165 0.901580 CAGCCAAGGCAATCAACCCT 60.902 55.000 14.40 0.0 44.88 4.34 F
2664 2790 1.078159 TCACTAAGGTCCCTGCACCTA 59.922 52.381 0.00 0.0 46.97 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2453 2573 0.111061 TCCCATGAAGCTGCTGTTGT 59.889 50.0 1.35 0.0 0.00 3.32 R
2455 2575 0.694771 TCTCCCATGAAGCTGCTGTT 59.305 50.0 1.35 0.0 0.00 3.16 R
2766 2893 0.036199 TTGCTTTGCCCAATCCATGC 60.036 50.0 0.00 0.0 0.00 4.06 R
4385 10064 0.109365 GCACACGCATGCATACCAAA 60.109 50.0 19.57 0.0 45.39 3.28 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
296 326 3.526534 GGCTTCTCCTGAGTCACATTAC 58.473 50.000 0.00 0.00 0.00 1.89
394 447 1.110442 CTTTGGTTGGTGCCAGTTCA 58.890 50.000 0.00 0.00 40.01 3.18
423 476 1.153349 GGTCGATGGCCAACTCTCC 60.153 63.158 10.96 5.87 0.00 3.71
484 544 3.259876 GGCCGTGTATATCCTAACATCCA 59.740 47.826 0.00 0.00 0.00 3.41
519 579 0.034186 CCATGCCTTCTACCCTGCAA 60.034 55.000 0.00 0.00 37.27 4.08
635 697 2.094675 CATCCACAGGGGCAAACTAAG 58.905 52.381 0.00 0.00 36.21 2.18
689 751 0.523072 CATTTTGGAGGCACCGTGAG 59.477 55.000 1.65 0.00 42.61 3.51
928 1015 5.103000 GCATTCGTTCTGTGTGTACTCTAT 58.897 41.667 0.00 0.00 0.00 1.98
1048 1145 3.521560 TCAGTTTTCCTGCTAGTATGCG 58.478 45.455 0.00 0.00 41.25 4.73
1068 1165 0.901580 CAGCCAAGGCAATCAACCCT 60.902 55.000 14.40 0.00 44.88 4.34
1412 1509 4.096984 ACTCAGCAAGCTACCAATAATTGC 59.903 41.667 0.00 0.11 45.05 3.56
1480 1577 1.134670 AGTTCTCGCCTATGTTCAGCC 60.135 52.381 0.00 0.00 0.00 4.85
1895 1992 3.186613 GCTGGTTTGGTTTCTACTCTTCG 59.813 47.826 0.00 0.00 0.00 3.79
2047 2145 2.109181 GTACCATCCCGGCAGAGC 59.891 66.667 0.00 0.00 39.03 4.09
2400 2499 4.877251 GGCAACAAGTTTACGGGTATCATA 59.123 41.667 0.00 0.00 0.00 2.15
2445 2565 1.896660 GTCTGTCAAGGCGGCCAAA 60.897 57.895 23.09 2.50 0.00 3.28
2450 2570 1.964223 TGTCAAGGCGGCCAAAAATAA 59.036 42.857 23.09 0.00 0.00 1.40
2451 2571 2.365617 TGTCAAGGCGGCCAAAAATAAA 59.634 40.909 23.09 0.00 0.00 1.40
2452 2572 3.181465 TGTCAAGGCGGCCAAAAATAAAA 60.181 39.130 23.09 0.00 0.00 1.52
2453 2573 3.810386 GTCAAGGCGGCCAAAAATAAAAA 59.190 39.130 23.09 0.00 0.00 1.94
2454 2574 3.810386 TCAAGGCGGCCAAAAATAAAAAC 59.190 39.130 23.09 0.00 0.00 2.43
2455 2575 3.477210 AGGCGGCCAAAAATAAAAACA 57.523 38.095 23.09 0.00 0.00 2.83
2456 2576 3.809905 AGGCGGCCAAAAATAAAAACAA 58.190 36.364 23.09 0.00 0.00 2.83
2457 2577 3.562141 AGGCGGCCAAAAATAAAAACAAC 59.438 39.130 23.09 0.00 0.00 3.32
2458 2578 3.312697 GGCGGCCAAAAATAAAAACAACA 59.687 39.130 15.62 0.00 0.00 3.33
2625 2745 3.391506 GCTTTTGCTGGTGAAATTCCT 57.608 42.857 0.00 0.00 43.35 3.36
2664 2790 1.078159 TCACTAAGGTCCCTGCACCTA 59.922 52.381 0.00 0.00 46.97 3.08
2740 2867 4.576463 CCTTGTTATTTTGGATCTCGGGAG 59.424 45.833 0.00 0.00 0.00 4.30
2750 2877 5.344743 TGGATCTCGGGAGCAATAATATC 57.655 43.478 1.57 0.00 0.00 1.63
2766 2893 8.725148 GCAATAATATCTCTGGTGTAATTCCTG 58.275 37.037 0.00 0.00 0.00 3.86
2774 2901 3.956199 CTGGTGTAATTCCTGCATGGATT 59.044 43.478 0.87 0.87 45.68 3.01
2810 3781 4.457257 CCTTTGTTGAGGATTCTTGGACTC 59.543 45.833 0.00 0.00 39.25 3.36
3112 4583 3.960102 TCTGCCAATTCTCTTTTTGGTGT 59.040 39.130 3.85 0.00 43.54 4.16
3114 4585 4.692228 TGCCAATTCTCTTTTTGGTGTTC 58.308 39.130 3.85 0.00 43.54 3.18
3264 5242 7.202139 GGAACAAGATATCAGGTCCTATTCCTT 60.202 40.741 19.59 0.00 32.37 3.36
3323 5301 9.112789 CTTAATCTCTCGAACAATCTTCTATCG 57.887 37.037 0.00 0.00 34.98 2.92
3327 5305 4.036498 TCTCGAACAATCTTCTATCGGGAC 59.964 45.833 0.00 0.00 38.03 4.46
3722 9397 8.670804 AGATGTAAGCGTCGTGATAATTATAC 57.329 34.615 0.00 0.00 35.84 1.47
3779 9456 4.782019 TGTTCCAGTGGACATATTTTGC 57.218 40.909 12.69 0.00 0.00 3.68
3844 9522 0.166814 GGTTTGTGTCTCGCTCATGC 59.833 55.000 0.00 0.00 0.00 4.06
3924 9602 8.697507 ATTTTTCCTGTTGTTCAGAGTAGAAT 57.302 30.769 0.00 0.00 46.27 2.40
3933 9611 7.715249 TGTTGTTCAGAGTAGAATAGCAGTTTT 59.285 33.333 0.00 0.00 29.44 2.43
3936 9614 8.585881 TGTTCAGAGTAGAATAGCAGTTTTAGT 58.414 33.333 0.00 0.00 0.00 2.24
3959 9637 2.756760 AGCATACATTGGAACTGCCTTG 59.243 45.455 0.00 0.00 37.63 3.61
3960 9638 2.754552 GCATACATTGGAACTGCCTTGA 59.245 45.455 0.00 0.00 37.63 3.02
3970 9648 0.615850 ACTGCCTTGAAGCCTACCTC 59.384 55.000 0.00 0.00 0.00 3.85
4004 9683 0.111061 AAACCTCCAGCATGCACTGA 59.889 50.000 21.98 11.78 40.25 3.41
4020 9699 7.707893 GCATGCACTGAAATTTTACTCCATATT 59.292 33.333 14.21 0.00 0.00 1.28
4037 9716 6.791371 TCCATATTCTAGTACTTCTCCCGAT 58.209 40.000 0.00 0.00 0.00 4.18
4038 9717 7.925622 TCCATATTCTAGTACTTCTCCCGATA 58.074 38.462 0.00 0.00 0.00 2.92
4040 9719 7.610692 CCATATTCTAGTACTTCTCCCGATACA 59.389 40.741 0.00 0.00 0.00 2.29
4067 9746 7.227512 GCATCTGTATCAAGGCTTTAACTACAT 59.772 37.037 0.00 0.00 0.00 2.29
4071 9750 9.378551 CTGTATCAAGGCTTTAACTACATGTAA 57.621 33.333 7.06 0.00 0.00 2.41
4072 9751 9.158233 TGTATCAAGGCTTTAACTACATGTAAC 57.842 33.333 7.06 0.00 0.00 2.50
4074 9753 5.640357 TCAAGGCTTTAACTACATGTAACGG 59.360 40.000 7.06 0.00 0.00 4.44
4087 9766 2.262637 TGTAACGGTCTTCAAGGGGAT 58.737 47.619 0.00 0.00 0.00 3.85
4093 9772 1.676014 GGTCTTCAAGGGGATCACACG 60.676 57.143 0.00 0.00 0.00 4.49
4096 9775 0.036388 TTCAAGGGGATCACACGCTC 60.036 55.000 0.00 0.00 0.00 5.03
4097 9776 0.904865 TCAAGGGGATCACACGCTCT 60.905 55.000 0.00 0.00 0.00 4.09
4098 9777 0.824109 CAAGGGGATCACACGCTCTA 59.176 55.000 0.00 0.00 0.00 2.43
4099 9778 0.824759 AAGGGGATCACACGCTCTAC 59.175 55.000 0.00 0.00 0.00 2.59
4100 9779 0.033011 AGGGGATCACACGCTCTACT 60.033 55.000 0.00 0.00 0.00 2.57
4102 9781 1.202428 GGGGATCACACGCTCTACTTC 60.202 57.143 0.00 0.00 0.00 3.01
4103 9782 1.751924 GGGATCACACGCTCTACTTCT 59.248 52.381 0.00 0.00 0.00 2.85
4107 9786 3.833545 TCACACGCTCTACTTCTCTTC 57.166 47.619 0.00 0.00 0.00 2.87
4109 9788 4.576879 TCACACGCTCTACTTCTCTTCTA 58.423 43.478 0.00 0.00 0.00 2.10
4136 9815 0.039618 TCCCTGGAGAAAATGGTGCC 59.960 55.000 0.00 0.00 0.00 5.01
4137 9816 0.251742 CCCTGGAGAAAATGGTGCCA 60.252 55.000 0.00 0.00 0.00 4.92
4161 9840 1.978617 CTGGCAATGACACCCCCAC 60.979 63.158 0.00 0.00 0.00 4.61
4165 9844 2.032634 CAATGACACCCCCACGACG 61.033 63.158 0.00 0.00 0.00 5.12
4166 9845 3.248446 AATGACACCCCCACGACGG 62.248 63.158 0.00 0.00 0.00 4.79
4183 9862 2.793946 GCAGCTTGCCGTACATGG 59.206 61.111 0.00 0.00 37.42 3.66
4212 9891 3.251004 ACGACTTTCTTCCAGTCATTTGC 59.749 43.478 0.00 0.00 40.78 3.68
4267 9946 4.100035 TCTCAGTGCTACATGTTCCTATGG 59.900 45.833 2.30 0.00 32.32 2.74
4273 9952 1.737838 ACATGTTCCTATGGTGTGCG 58.262 50.000 0.00 0.00 32.32 5.34
4304 9983 4.721132 TCCTCGAAACCCAACATTAAGTT 58.279 39.130 0.00 0.00 42.42 2.66
4320 9999 6.369065 ACATTAAGTTGAGAACCTTAAGAGCG 59.631 38.462 3.36 0.00 0.00 5.03
4325 10004 4.330944 TGAGAACCTTAAGAGCGTTCAA 57.669 40.909 19.07 8.92 36.42 2.69
4326 10005 4.056050 TGAGAACCTTAAGAGCGTTCAAC 58.944 43.478 19.07 14.33 36.42 3.18
4336 10015 2.058798 GAGCGTTCAACGATGTCTCAA 58.941 47.619 15.79 0.00 41.80 3.02
4337 10016 2.668457 GAGCGTTCAACGATGTCTCAAT 59.332 45.455 15.79 0.00 41.80 2.57
4360 10039 1.071605 GAAGTGTGCGACCAGATGAC 58.928 55.000 0.00 0.00 0.00 3.06
4384 10063 1.933181 CGAGTGAATGTGTGTGTGTGT 59.067 47.619 0.00 0.00 0.00 3.72
4385 10064 2.351418 CGAGTGAATGTGTGTGTGTGTT 59.649 45.455 0.00 0.00 0.00 3.32
4386 10065 3.181511 CGAGTGAATGTGTGTGTGTGTTT 60.182 43.478 0.00 0.00 0.00 2.83
4422 10101 0.178068 GCATCTTGGCGTCTTCCCTA 59.822 55.000 0.00 0.00 0.00 3.53
4562 10245 6.973642 TGAATGGTGAATAGATTTTCTCCCT 58.026 36.000 3.61 0.00 38.10 4.20
4610 10302 4.166144 GTCATATGGAGGGAGAGGGAAAAA 59.834 45.833 2.13 0.00 0.00 1.94
4868 10567 6.229733 CACTCTTTCCAGTCATCTTCTTCTT 58.770 40.000 0.00 0.00 0.00 2.52
4870 10569 7.228308 CACTCTTTCCAGTCATCTTCTTCTTTT 59.772 37.037 0.00 0.00 0.00 2.27
4871 10570 7.443879 ACTCTTTCCAGTCATCTTCTTCTTTTC 59.556 37.037 0.00 0.00 0.00 2.29
4872 10571 6.712547 TCTTTCCAGTCATCTTCTTCTTTTCC 59.287 38.462 0.00 0.00 0.00 3.13
4874 10573 4.283467 TCCAGTCATCTTCTTCTTTTCCGA 59.717 41.667 0.00 0.00 0.00 4.55
4875 10574 4.997395 CCAGTCATCTTCTTCTTTTCCGAA 59.003 41.667 0.00 0.00 0.00 4.30
4877 10576 5.698545 CAGTCATCTTCTTCTTTTCCGAAGT 59.301 40.000 0.00 0.00 40.89 3.01
4878 10577 5.929415 AGTCATCTTCTTCTTTTCCGAAGTC 59.071 40.000 0.00 0.00 40.89 3.01
4879 10578 5.696724 GTCATCTTCTTCTTTTCCGAAGTCA 59.303 40.000 0.00 0.00 40.89 3.41
4880 10579 5.696724 TCATCTTCTTCTTTTCCGAAGTCAC 59.303 40.000 0.00 0.00 40.89 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.028926 TCACTTTCGTAGTTGCCAAATTAAA 57.971 32.000 0.00 0.00 33.85 1.52
296 326 2.289002 GGAAGAATGCCGCATCTAACAG 59.711 50.000 6.27 0.00 0.00 3.16
423 476 1.970917 GCCGCTGAACCATGAAGACG 61.971 60.000 0.00 0.00 0.00 4.18
465 518 5.243060 TGAGGTGGATGTTAGGATATACACG 59.757 44.000 0.00 0.00 38.67 4.49
519 579 4.546674 AGGTTGATGAGGTTTTGGAAAGT 58.453 39.130 0.00 0.00 0.00 2.66
560 620 6.128117 GCAAATAAGTTTTCAGGGACGATACA 60.128 38.462 0.00 0.00 0.00 2.29
562 622 5.941058 TGCAAATAAGTTTTCAGGGACGATA 59.059 36.000 0.00 0.00 0.00 2.92
563 623 4.764823 TGCAAATAAGTTTTCAGGGACGAT 59.235 37.500 0.00 0.00 0.00 3.73
635 697 5.469084 AGAAAAACGAGTACAACCCTTCATC 59.531 40.000 0.00 0.00 0.00 2.92
880 967 8.124586 CACAATTGCACAAAAGTACAAATACA 57.875 30.769 5.05 0.00 33.30 2.29
903 990 2.800544 AGTACACACAGAACGAATGCAC 59.199 45.455 0.00 0.00 0.00 4.57
906 993 6.556212 AGATAGAGTACACACAGAACGAATG 58.444 40.000 0.00 0.00 0.00 2.67
1048 1145 1.079612 GGTTGATTGCCTTGGCTGC 60.080 57.895 13.18 0.00 0.00 5.25
1068 1165 1.067565 CGGAGTAGTGCTTCAGCTTCA 60.068 52.381 0.00 0.00 42.66 3.02
1331 1428 0.240945 GTCCAAAATGGTGAGCGTGG 59.759 55.000 0.00 0.00 39.03 4.94
1412 1509 6.423182 TGGTTATTTCCCAGATTAACCTCAG 58.577 40.000 10.93 0.00 38.15 3.35
1533 1630 5.104941 CCTCACATTGGTGTAGTTGAGGATA 60.105 44.000 9.42 0.00 42.86 2.59
1826 1923 1.002868 TGAAGCTGCCCAAGAGAGC 60.003 57.895 0.00 0.00 0.00 4.09
1830 1927 1.699634 AGTAACTGAAGCTGCCCAAGA 59.300 47.619 0.00 0.00 0.00 3.02
2041 2139 3.793492 GTCAAGTTTGAAAACAGCTCTGC 59.207 43.478 8.53 0.00 41.30 4.26
2047 2145 5.072040 AGGTTGGTCAAGTTTGAAAACAG 57.928 39.130 16.86 1.24 41.30 3.16
2400 2499 5.179452 ACTGCCTGTTGTCAATATTAGGT 57.821 39.130 2.45 0.00 0.00 3.08
2438 2537 4.034510 TGCTGTTGTTTTTATTTTTGGCCG 59.965 37.500 0.00 0.00 0.00 6.13
2445 2565 6.203338 CCATGAAGCTGCTGTTGTTTTTATTT 59.797 34.615 1.35 0.00 0.00 1.40
2450 2570 2.224113 CCCATGAAGCTGCTGTTGTTTT 60.224 45.455 1.35 0.00 0.00 2.43
2451 2571 1.342174 CCCATGAAGCTGCTGTTGTTT 59.658 47.619 1.35 0.00 0.00 2.83
2452 2572 0.963962 CCCATGAAGCTGCTGTTGTT 59.036 50.000 1.35 0.00 0.00 2.83
2453 2573 0.111061 TCCCATGAAGCTGCTGTTGT 59.889 50.000 1.35 0.00 0.00 3.32
2454 2574 0.809385 CTCCCATGAAGCTGCTGTTG 59.191 55.000 1.35 1.19 0.00 3.33
2455 2575 0.694771 TCTCCCATGAAGCTGCTGTT 59.305 50.000 1.35 0.00 0.00 3.16
2456 2576 0.694771 TTCTCCCATGAAGCTGCTGT 59.305 50.000 1.35 0.00 0.00 4.40
2457 2577 2.054232 ATTCTCCCATGAAGCTGCTG 57.946 50.000 1.35 0.00 0.00 4.41
2458 2578 2.376109 CAATTCTCCCATGAAGCTGCT 58.624 47.619 0.00 0.00 0.00 4.24
2625 2745 9.706691 CTTAGTGAAGAATTACAACTTGAGGTA 57.293 33.333 0.00 0.00 34.25 3.08
2664 2790 5.221048 GCAACCTGTAAAGTTGTTGTCTGAT 60.221 40.000 5.62 0.00 45.14 2.90
2740 2867 8.725148 CAGGAATTACACCAGAGATATTATTGC 58.275 37.037 0.00 0.00 0.00 3.56
2750 2877 2.947652 CCATGCAGGAATTACACCAGAG 59.052 50.000 0.00 0.00 41.22 3.35
2766 2893 0.036199 TTGCTTTGCCCAATCCATGC 60.036 50.000 0.00 0.00 0.00 4.06
2774 2901 1.422531 ACAAAGGATTGCTTTGCCCA 58.577 45.000 25.10 0.00 43.37 5.36
2810 3781 5.586243 ACTTCCATAGAACATGTTTGATCGG 59.414 40.000 13.36 10.11 30.44 4.18
3112 4583 5.544176 AGATTTGTCAACTCCAGAGGTAGAA 59.456 40.000 0.00 0.00 0.00 2.10
3114 4585 5.413309 AGATTTGTCAACTCCAGAGGTAG 57.587 43.478 0.00 0.00 0.00 3.18
3293 5271 6.546428 AGATTGTTCGAGAGATTAAGGGAA 57.454 37.500 0.00 0.00 41.60 3.97
3323 5301 0.186873 TCCCTGTAGGTATCCGTCCC 59.813 60.000 0.00 0.00 36.75 4.46
3327 5305 3.641906 AGTTGATTCCCTGTAGGTATCCG 59.358 47.826 0.00 0.00 40.78 4.18
3779 9456 6.316390 ACAACAAACTTGTCTAGAACCTTGAG 59.684 38.462 0.00 0.00 41.31 3.02
3880 9558 7.712205 GGAAAAATCATGCACAATAGGCTTTAT 59.288 33.333 0.00 0.00 0.00 1.40
3924 9602 8.044309 TCCAATGTATGCTAACTAAAACTGCTA 58.956 33.333 0.00 0.00 0.00 3.49
3933 9611 5.104527 AGGCAGTTCCAATGTATGCTAACTA 60.105 40.000 0.00 0.00 34.09 2.24
3936 9614 4.235079 AGGCAGTTCCAATGTATGCTAA 57.765 40.909 0.00 0.00 37.08 3.09
3959 9637 1.286248 TTGAAGGGGAGGTAGGCTTC 58.714 55.000 0.00 0.00 0.00 3.86
3960 9638 1.755200 TTTGAAGGGGAGGTAGGCTT 58.245 50.000 0.00 0.00 0.00 4.35
3970 9648 4.017126 GGAGGTTTCACTATTTGAAGGGG 58.983 47.826 0.00 0.00 45.22 4.79
4020 9699 4.141551 TGCTGTATCGGGAGAAGTACTAGA 60.142 45.833 0.00 0.00 45.37 2.43
4040 9719 5.749462 AGTTAAAGCCTTGATACAGATGCT 58.251 37.500 0.00 0.00 0.00 3.79
4055 9734 6.366877 TGAAGACCGTTACATGTAGTTAAAGC 59.633 38.462 5.56 0.00 0.00 3.51
4067 9746 1.719529 TCCCCTTGAAGACCGTTACA 58.280 50.000 0.00 0.00 0.00 2.41
4071 9750 0.613777 GTGATCCCCTTGAAGACCGT 59.386 55.000 0.00 0.00 0.00 4.83
4072 9751 0.613260 TGTGATCCCCTTGAAGACCG 59.387 55.000 0.00 0.00 0.00 4.79
4074 9753 1.726853 CGTGTGATCCCCTTGAAGAC 58.273 55.000 0.00 0.00 0.00 3.01
4087 9766 3.413327 AGAAGAGAAGTAGAGCGTGTGA 58.587 45.455 0.00 0.00 0.00 3.58
4093 9772 8.661257 GGAACAATTTTAGAAGAGAAGTAGAGC 58.339 37.037 0.00 0.00 0.00 4.09
4096 9775 8.940952 CAGGGAACAATTTTAGAAGAGAAGTAG 58.059 37.037 0.00 0.00 0.00 2.57
4097 9776 7.883311 CCAGGGAACAATTTTAGAAGAGAAGTA 59.117 37.037 0.00 0.00 0.00 2.24
4098 9777 6.717084 CCAGGGAACAATTTTAGAAGAGAAGT 59.283 38.462 0.00 0.00 0.00 3.01
4099 9778 6.942576 TCCAGGGAACAATTTTAGAAGAGAAG 59.057 38.462 0.00 0.00 0.00 2.85
4100 9779 6.848069 TCCAGGGAACAATTTTAGAAGAGAA 58.152 36.000 0.00 0.00 0.00 2.87
4102 9781 6.476378 TCTCCAGGGAACAATTTTAGAAGAG 58.524 40.000 0.00 0.00 0.00 2.85
4103 9782 6.448369 TCTCCAGGGAACAATTTTAGAAGA 57.552 37.500 0.00 0.00 0.00 2.87
4107 9786 7.099120 CCATTTTCTCCAGGGAACAATTTTAG 58.901 38.462 0.00 0.00 0.00 1.85
4109 9788 5.369404 ACCATTTTCTCCAGGGAACAATTTT 59.631 36.000 0.00 0.00 0.00 1.82
4136 9815 1.200716 GGTGTCATTGCCAGTGATGTG 59.799 52.381 0.00 0.00 0.00 3.21
4137 9816 1.538047 GGTGTCATTGCCAGTGATGT 58.462 50.000 0.00 0.00 0.00 3.06
4166 9845 1.305219 TTCCATGTACGGCAAGCTGC 61.305 55.000 0.00 0.00 44.08 5.25
4173 9852 1.082117 CGTCAGGTTCCATGTACGGC 61.082 60.000 0.00 0.00 0.00 5.68
4175 9854 1.201647 AGTCGTCAGGTTCCATGTACG 59.798 52.381 0.00 0.00 0.00 3.67
4182 9861 2.224209 TGGAAGAAAGTCGTCAGGTTCC 60.224 50.000 0.00 0.00 33.89 3.62
4183 9862 3.060602 CTGGAAGAAAGTCGTCAGGTTC 58.939 50.000 0.00 0.00 34.07 3.62
4267 9946 1.145803 GAGGAACCTTGTACGCACAC 58.854 55.000 0.00 0.00 33.30 3.82
4273 9952 2.224354 TGGGTTTCGAGGAACCTTGTAC 60.224 50.000 16.58 2.98 46.63 2.90
4304 9983 4.056050 GTTGAACGCTCTTAAGGTTCTCA 58.944 43.478 18.14 7.49 40.44 3.27
4320 9999 3.745975 TCACCATTGAGACATCGTTGAAC 59.254 43.478 0.00 0.00 0.00 3.18
4325 10004 3.244215 ACACTTCACCATTGAGACATCGT 60.244 43.478 0.00 0.00 31.71 3.73
4326 10005 3.124128 CACACTTCACCATTGAGACATCG 59.876 47.826 0.00 0.00 31.71 3.84
4336 10015 0.603707 CTGGTCGCACACTTCACCAT 60.604 55.000 0.00 0.00 38.26 3.55
4337 10016 1.227527 CTGGTCGCACACTTCACCA 60.228 57.895 0.00 0.00 37.37 4.17
4360 10039 2.091122 CACACACACATTCACTCGATCG 59.909 50.000 9.36 9.36 0.00 3.69
4384 10063 1.668337 GCACACGCATGCATACCAAAA 60.668 47.619 19.57 0.00 45.39 2.44
4385 10064 0.109365 GCACACGCATGCATACCAAA 60.109 50.000 19.57 0.00 45.39 3.28
4386 10065 1.505807 GCACACGCATGCATACCAA 59.494 52.632 19.57 0.00 45.39 3.67
4511 10194 5.336770 GGGGAAAGAGCCAACTTAATTTCTG 60.337 44.000 0.00 0.00 0.00 3.02
4562 10245 2.076100 CAAGCACGTAATCTCCTTGCA 58.924 47.619 0.00 0.00 35.57 4.08
4610 10302 9.311916 CTACTACGACTAGTACAGAACTGTAAT 57.688 37.037 16.74 16.74 46.33 1.89
4706 10405 6.477253 ACCATACACCATACACAAACACATA 58.523 36.000 0.00 0.00 0.00 2.29
4868 10567 3.120338 GCAATCGATTGTGACTTCGGAAA 60.120 43.478 32.52 0.00 39.88 3.13
4870 10569 1.999735 GCAATCGATTGTGACTTCGGA 59.000 47.619 32.52 0.00 39.88 4.55
4871 10570 2.002586 AGCAATCGATTGTGACTTCGG 58.997 47.619 32.52 10.37 39.88 4.30
4872 10571 2.284684 CGAGCAATCGATTGTGACTTCG 60.285 50.000 32.52 26.80 39.88 3.79
4874 10573 2.959516 TCGAGCAATCGATTGTGACTT 58.040 42.857 32.52 16.99 39.88 3.01
4875 10574 2.654749 TCGAGCAATCGATTGTGACT 57.345 45.000 32.52 23.39 39.88 3.41
4877 10576 2.667969 CTGTTCGAGCAATCGATTGTGA 59.332 45.455 32.52 25.27 42.02 3.58
4878 10577 2.413112 ACTGTTCGAGCAATCGATTGTG 59.587 45.455 32.52 23.78 42.02 3.33
4879 10578 2.688507 ACTGTTCGAGCAATCGATTGT 58.311 42.857 32.52 21.84 42.02 2.71
4880 10579 3.369147 AGAACTGTTCGAGCAATCGATTG 59.631 43.478 29.67 29.67 42.02 2.67


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

AutoCloner maintained by Alex Coulton.