Multiple sequence alignment - TraesCS3B01G357200

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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 TraesCS3B01G357200 chr3B 100.000 4462 0 0 1 4462 567244316 567248777 0.000000e+00 8240.0
1 TraesCS3B01G357200 chr3B 92.746 965 54 10 1 959 606419166 606420120 0.000000e+00 1380.0
2 TraesCS3B01G357200 chr3B 92.577 970 56 10 1 960 412559016 412558053 0.000000e+00 1378.0
3 TraesCS3B01G357200 chr3D 91.181 1270 77 18 1010 2260 434022708 434023961 0.000000e+00 1692.0
4 TraesCS3B01G357200 chr3D 91.996 987 65 9 1 975 569061926 569062910 0.000000e+00 1373.0
5 TraesCS3B01G357200 chr3D 94.030 804 38 4 2285 3078 434023958 434024761 0.000000e+00 1210.0
6 TraesCS3B01G357200 chr3D 90.137 730 43 16 3152 3865 434025081 434025797 0.000000e+00 922.0
7 TraesCS3B01G357200 chr3D 95.289 467 20 2 3981 4446 434026662 434027127 0.000000e+00 739.0
8 TraesCS3B01G357200 chr3D 92.254 142 6 2 3864 4000 434025879 434026020 3.520000e-46 196.0
9 TraesCS3B01G357200 chr3A 90.584 1285 77 18 1870 3133 572592398 572593659 0.000000e+00 1663.0
10 TraesCS3B01G357200 chr3A 91.629 442 28 3 1438 1871 572591794 572592234 1.780000e-168 603.0
11 TraesCS3B01G357200 chr3A 93.958 331 19 1 4116 4445 572596734 572597064 2.400000e-137 499.0
12 TraesCS3B01G357200 chr3A 92.560 336 22 3 1043 1377 572591186 572591519 3.120000e-131 479.0
13 TraesCS3B01G357200 chr3A 89.815 324 17 5 3670 3986 572594351 572594665 6.950000e-108 401.0
14 TraesCS3B01G357200 chr3A 80.097 618 56 49 3073 3671 572593678 572594247 8.990000e-107 398.0
15 TraesCS3B01G357200 chr3A 94.915 59 1 1 988 1046 572589155 572589211 1.710000e-14 91.6
16 TraesCS3B01G357200 chr7B 92.887 970 55 6 1 960 733421929 733422894 0.000000e+00 1397.0
17 TraesCS3B01G357200 chr7B 92.554 967 59 8 1 960 748034205 748035165 0.000000e+00 1375.0
18 TraesCS3B01G357200 chr1B 92.776 969 57 5 1 960 575893224 575894188 0.000000e+00 1389.0
19 TraesCS3B01G357200 chr1B 92.562 968 61 6 1 960 302037610 302038574 0.000000e+00 1378.0
20 TraesCS3B01G357200 chr5B 92.466 969 62 8 1 960 344934179 344933213 0.000000e+00 1375.0
21 TraesCS3B01G357200 chr6B 91.683 998 61 15 3 989 230769330 230768344 0.000000e+00 1363.0


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 TraesCS3B01G357200 chr3B 567244316 567248777 4461 False 8240.000000 8240 100.000000 1 4462 1 chr3B.!!$F1 4461
1 TraesCS3B01G357200 chr3B 606419166 606420120 954 False 1380.000000 1380 92.746000 1 959 1 chr3B.!!$F2 958
2 TraesCS3B01G357200 chr3B 412558053 412559016 963 True 1378.000000 1378 92.577000 1 960 1 chr3B.!!$R1 959
3 TraesCS3B01G357200 chr3D 569061926 569062910 984 False 1373.000000 1373 91.996000 1 975 1 chr3D.!!$F1 974
4 TraesCS3B01G357200 chr3D 434022708 434027127 4419 False 951.800000 1692 92.578200 1010 4446 5 chr3D.!!$F2 3436
5 TraesCS3B01G357200 chr3A 572589155 572597064 7909 False 590.657143 1663 90.508286 988 4445 7 chr3A.!!$F1 3457
6 TraesCS3B01G357200 chr7B 733421929 733422894 965 False 1397.000000 1397 92.887000 1 960 1 chr7B.!!$F1 959
7 TraesCS3B01G357200 chr7B 748034205 748035165 960 False 1375.000000 1375 92.554000 1 960 1 chr7B.!!$F2 959
8 TraesCS3B01G357200 chr1B 575893224 575894188 964 False 1389.000000 1389 92.776000 1 960 1 chr1B.!!$F2 959
9 TraesCS3B01G357200 chr1B 302037610 302038574 964 False 1378.000000 1378 92.562000 1 960 1 chr1B.!!$F1 959
10 TraesCS3B01G357200 chr5B 344933213 344934179 966 True 1375.000000 1375 92.466000 1 960 1 chr5B.!!$R1 959
11 TraesCS3B01G357200 chr6B 230768344 230769330 986 True 1363.000000 1363 91.683000 3 989 1 chr6B.!!$R1 986

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
179 180 0.253868 TCTCTCCCTCTCTCCTCCCA 60.254 60.000 0.00 0.0 0.00 4.37 F
809 826 1.205417 GACTTAAATCCGGACGGTGGA 59.795 52.381 6.12 0.0 40.46 4.02 F
1441 3694 0.468648 ATTAGGGCTAAGGTGACGCC 59.531 55.000 0.00 0.0 43.03 5.68 F
2826 5266 0.670162 GCACGAATCATCCAATGGGG 59.330 55.000 0.00 0.0 38.37 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1082 3089 0.179200 GCGTATTCTTTGGCGTGGTG 60.179 55.000 0.00 0.00 0.00 4.17 R
1918 4344 0.898326 TACAGGAGCGCCTTGAGACA 60.898 55.000 6.13 0.00 43.90 3.41 R
2946 5386 1.301401 CTTTCCAAGTCGTCCGGCA 60.301 57.895 0.00 0.00 0.00 5.69 R
4253 9888 0.324738 AGAGCAGTACTGGCCAGCTA 60.325 55.000 33.06 20.08 35.36 3.32 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
152 153 8.670135 CGTGTGTTGAATATGGTTAATCCTAAA 58.330 33.333 0.00 0.00 37.07 1.85
179 180 0.253868 TCTCTCCCTCTCTCCTCCCA 60.254 60.000 0.00 0.00 0.00 4.37
321 332 9.840427 CGATGTTTTCTTTTCTGTATATGGTTT 57.160 29.630 0.00 0.00 0.00 3.27
354 365 2.062971 ATTTGCAATCCAGATCGCCT 57.937 45.000 0.00 0.00 0.00 5.52
357 368 1.599240 GCAATCCAGATCGCCTCCC 60.599 63.158 0.00 0.00 0.00 4.30
680 695 7.256756 TCAAATCGGAGTTACGGTTTAAAAA 57.743 32.000 0.00 0.00 44.52 1.94
809 826 1.205417 GACTTAAATCCGGACGGTGGA 59.795 52.381 6.12 0.00 40.46 4.02
824 841 3.506067 ACGGTGGATTGATTTCAGGAAAC 59.494 43.478 0.00 0.00 32.51 2.78
825 842 3.505680 CGGTGGATTGATTTCAGGAAACA 59.494 43.478 0.00 0.00 32.51 2.83
940 966 3.857052 TGCTATGACGGACGAAAGAAAT 58.143 40.909 0.00 0.00 0.00 2.17
1001 1030 7.990886 GGTAAAGAAAAGATTGGGTTTTTCCTT 59.009 33.333 6.18 3.44 41.79 3.36
1081 3088 4.699522 GCCCCACGACCACCAGTC 62.700 72.222 0.00 0.00 42.54 3.51
1082 3089 4.016706 CCCCACGACCACCAGTCC 62.017 72.222 0.00 0.00 43.08 3.85
1083 3090 3.238497 CCCACGACCACCAGTCCA 61.238 66.667 0.00 0.00 43.08 4.02
1084 3091 2.030562 CCACGACCACCAGTCCAC 59.969 66.667 0.00 0.00 43.08 4.02
1085 3092 2.030562 CACGACCACCAGTCCACC 59.969 66.667 0.00 0.00 43.08 4.61
1086 3093 2.445085 ACGACCACCAGTCCACCA 60.445 61.111 0.00 0.00 43.08 4.17
1092 3099 3.484806 ACCAGTCCACCACGCCAA 61.485 61.111 0.00 0.00 0.00 4.52
1106 3120 1.024579 CGCCAAAGAATACGCCCAGT 61.025 55.000 0.00 0.00 0.00 4.00
1136 3150 3.414700 CAGGTGCCGAGAACACGC 61.415 66.667 0.00 0.00 38.98 5.34
1139 3153 2.970324 GTGCCGAGAACACGCCAA 60.970 61.111 0.00 0.00 0.00 4.52
1423 3453 4.489771 CTCCCCCGCCTCGCAAAT 62.490 66.667 0.00 0.00 0.00 2.32
1424 3454 3.995506 CTCCCCCGCCTCGCAAATT 62.996 63.158 0.00 0.00 0.00 1.82
1425 3455 2.124487 CCCCCGCCTCGCAAATTA 60.124 61.111 0.00 0.00 0.00 1.40
1426 3456 2.186826 CCCCCGCCTCGCAAATTAG 61.187 63.158 0.00 0.00 0.00 1.73
1427 3457 2.186826 CCCCGCCTCGCAAATTAGG 61.187 63.158 0.00 0.00 35.86 2.69
1428 3458 2.186826 CCCGCCTCGCAAATTAGGG 61.187 63.158 0.00 0.00 33.17 3.53
1429 3459 2.715624 CGCCTCGCAAATTAGGGC 59.284 61.111 0.00 0.00 39.43 5.19
1430 3460 1.819632 CGCCTCGCAAATTAGGGCT 60.820 57.895 0.00 0.00 40.52 5.19
1431 3461 0.531974 CGCCTCGCAAATTAGGGCTA 60.532 55.000 0.00 0.00 40.52 3.93
1432 3462 1.675552 GCCTCGCAAATTAGGGCTAA 58.324 50.000 0.00 0.00 39.68 3.09
1433 3463 1.604278 GCCTCGCAAATTAGGGCTAAG 59.396 52.381 0.00 0.00 39.68 2.18
1441 3694 0.468648 ATTAGGGCTAAGGTGACGCC 59.531 55.000 0.00 0.00 43.03 5.68
1637 3890 0.883833 AACCTTCTGCCATTCTTGCG 59.116 50.000 0.00 0.00 0.00 4.85
1670 3923 3.665190 CTCCATTTCTATAACCCGGCTC 58.335 50.000 0.00 0.00 0.00 4.70
1676 3929 1.456145 TATAACCCGGCTCGCCTCA 60.456 57.895 6.35 0.00 0.00 3.86
1682 3935 3.522731 CGGCTCGCCTCAGCTACT 61.523 66.667 6.35 0.00 39.58 2.57
1787 4048 4.118410 GACAGTGATGCAGACCTTATCAG 58.882 47.826 0.00 0.00 32.00 2.90
1794 4055 3.485394 TGCAGACCTTATCAGTTGCAAA 58.515 40.909 0.00 0.00 38.47 3.68
1820 4081 4.202111 GGGCGGCAGTTTGTGAATTATAAT 60.202 41.667 12.47 0.00 0.00 1.28
1827 4088 6.127479 GCAGTTTGTGAATTATAATGACCCCA 60.127 38.462 0.00 0.00 0.00 4.96
1847 4108 4.082787 CCCATTTATTATGTTGGCGGCTAG 60.083 45.833 11.43 0.00 0.00 3.42
1861 4122 1.162800 GGCTAGATTTGCCTCTGCCG 61.163 60.000 0.00 0.00 46.38 5.69
1911 4337 6.821388 ACTCTACAACTTCAGAACATGTCTT 58.179 36.000 0.00 0.00 32.70 3.01
1918 4344 5.300752 ACTTCAGAACATGTCTTCGAACAT 58.699 37.500 0.00 0.00 40.49 2.71
1929 4355 1.391485 CTTCGAACATGTCTCAAGGCG 59.609 52.381 0.00 0.00 0.00 5.52
1943 4369 0.685097 AAGGCGCTCCTGTAGTTTCA 59.315 50.000 7.64 0.00 43.40 2.69
2110 4536 4.792521 AATACGAGGAGCTGATACATCC 57.207 45.455 0.00 0.00 0.00 3.51
2140 4566 9.885934 GAGGTTTTCTCTCAAGTTAAATCTTTC 57.114 33.333 0.00 0.00 39.38 2.62
2180 4607 3.073503 AGCATCATATTGCCTGCCTAAGA 59.926 43.478 0.00 0.00 43.83 2.10
2194 4621 6.017852 GCCTGCCTAAGATCACTTTAACATAC 60.018 42.308 0.00 0.00 37.53 2.39
2196 4623 7.195374 TGCCTAAGATCACTTTAACATACCT 57.805 36.000 0.00 0.00 37.53 3.08
2217 4645 7.823745 ACCTTTAATGTGATCTTGTTTCTGT 57.176 32.000 0.00 0.00 0.00 3.41
2219 4647 7.502226 ACCTTTAATGTGATCTTGTTTCTGTGA 59.498 33.333 0.00 0.00 0.00 3.58
2266 4694 7.312415 AGAACCTACTTATGTAACTGGTTGT 57.688 36.000 12.79 8.21 35.90 3.32
2314 4743 5.243426 ACAAGCGTTCTGTAAACACAAAT 57.757 34.783 0.00 0.00 0.00 2.32
2359 4788 5.106118 TGGATTCGTTGAGAACACAACAAAA 60.106 36.000 13.40 8.36 46.96 2.44
2401 4831 6.059484 TCAGGTAAACTTTAGGTCCAAGTTG 58.941 40.000 7.84 0.00 42.47 3.16
2433 4863 5.163519 CCTGGTAACCTAGCATTTTCATTGG 60.164 44.000 0.00 0.00 35.39 3.16
2479 4909 2.949447 AGACATCAGTTGGCCTGTTTT 58.051 42.857 3.32 0.00 42.19 2.43
2504 4934 9.831737 TTGTTTTTGGTGTGAACAATATTTTTG 57.168 25.926 0.00 0.00 38.09 2.44
2510 4943 3.648067 TGTGAACAATATTTTTGGCCCCA 59.352 39.130 0.00 0.00 0.00 4.96
2517 4950 4.824479 ATATTTTTGGCCCCAAGAACTG 57.176 40.909 0.00 0.00 37.24 3.16
2559 4992 6.041523 ACCACTTAAAATTTGTGCCACATACT 59.958 34.615 0.00 0.00 0.00 2.12
2560 4993 6.365789 CCACTTAAAATTTGTGCCACATACTG 59.634 38.462 0.00 0.00 0.00 2.74
2655 5095 9.643693 ACCATGAAATTGTCTAATGATTTTGAC 57.356 29.630 0.00 4.72 37.87 3.18
2826 5266 0.670162 GCACGAATCATCCAATGGGG 59.330 55.000 0.00 0.00 38.37 4.96
2928 5368 0.842467 AGTACAGCCCTTGCCCTCTT 60.842 55.000 0.00 0.00 38.69 2.85
2946 5386 5.453903 CCCTCTTCTTGTCCAATATGTCGAT 60.454 44.000 0.00 0.00 0.00 3.59
2982 5422 0.679002 AGAAGCGCGGACTAGGTGTA 60.679 55.000 8.83 0.00 0.00 2.90
2992 5432 4.818546 GCGGACTAGGTGTATACTCTTACA 59.181 45.833 4.17 0.00 0.00 2.41
2999 5439 8.334734 ACTAGGTGTATACTCTTACAGGAGAAA 58.665 37.037 4.17 0.00 37.13 2.52
3021 5461 4.721132 ACTCTTCATCCGTTAAACCCAAA 58.279 39.130 0.00 0.00 0.00 3.28
3032 5479 5.878116 CCGTTAAACCCAAATCATCTCTGTA 59.122 40.000 0.00 0.00 0.00 2.74
3035 5482 8.293867 CGTTAAACCCAAATCATCTCTGTAAAA 58.706 33.333 0.00 0.00 0.00 1.52
3041 5488 9.699410 ACCCAAATCATCTCTGTAAAAATATCA 57.301 29.630 0.00 0.00 0.00 2.15
3043 5490 9.674824 CCAAATCATCTCTGTAAAAATATCAGC 57.325 33.333 0.00 0.00 0.00 4.26
3084 5531 8.539770 AGAAATGAAGTTGTGTATGTACTCTG 57.460 34.615 0.00 0.00 0.00 3.35
3086 5533 9.419297 GAAATGAAGTTGTGTATGTACTCTGTA 57.581 33.333 0.00 0.00 0.00 2.74
3087 5534 9.944376 AAATGAAGTTGTGTATGTACTCTGTAT 57.056 29.630 0.00 0.00 0.00 2.29
3105 5631 9.403583 ACTCTGTATAGTGGAAGAAAACAAAAA 57.596 29.630 0.00 0.00 0.00 1.94
3178 5983 3.554129 GCGGGCTTGGTTTTGTAGAATTT 60.554 43.478 0.00 0.00 0.00 1.82
3214 6019 6.428083 TTCTGAGACAATGGGTGTTTACTA 57.572 37.500 0.00 0.00 41.96 1.82
3239 6044 3.068024 TCAAGGTGCCATGTGAAACTTTC 59.932 43.478 0.00 0.00 38.04 2.62
3295 6100 4.202567 GGATACCTGAAAATCCATGCCCTA 60.203 45.833 0.00 0.00 41.21 3.53
3332 6137 2.967599 TGCTGACTGTGGCATAGTAG 57.032 50.000 17.28 14.54 33.23 2.57
3333 6138 1.134699 TGCTGACTGTGGCATAGTAGC 60.135 52.381 24.65 24.65 33.23 3.58
3453 6267 0.740149 TGTTCAAGCACAACAGCAGG 59.260 50.000 0.00 0.00 36.85 4.85
3456 6297 0.107263 TCAAGCACAACAGCAGGTCA 60.107 50.000 0.00 0.00 36.85 4.02
3461 6302 0.740149 CACAACAGCAGGTCAGCAAA 59.260 50.000 0.00 0.00 36.85 3.68
3549 6390 5.721510 GCTGAACACGAACGATATCAAGTTC 60.722 44.000 11.44 11.44 42.23 3.01
3555 6396 8.301730 ACACGAACGATATCAAGTTCTTTTTA 57.698 30.769 16.56 0.00 43.15 1.52
3556 6397 8.219105 ACACGAACGATATCAAGTTCTTTTTAC 58.781 33.333 16.56 0.00 43.15 2.01
3557 6398 7.418801 CACGAACGATATCAAGTTCTTTTTACG 59.581 37.037 16.56 8.44 43.15 3.18
3641 6482 9.745018 TCAGATAAAAGAATCCAATGAGTTCTT 57.255 29.630 6.90 6.90 42.30 2.52
3648 6489 4.543590 ATCCAATGAGTTCTTCAGACGT 57.456 40.909 0.00 0.00 39.68 4.34
3663 6504 2.212869 GACGTGTGTCAGTTGGTACA 57.787 50.000 0.00 0.00 44.82 2.90
3665 6506 2.283351 GACGTGTGTCAGTTGGTACAAC 59.717 50.000 0.00 4.04 44.61 3.32
3669 6513 7.500883 GACGTGTGTCAGTTGGTACAACATAT 61.501 42.308 13.83 0.00 44.61 1.78
3703 6647 0.409876 TGCTCTAGGTGAGACTGGGT 59.590 55.000 0.00 0.00 45.39 4.51
3711 6655 1.625818 GGTGAGACTGGGTCTTCACAT 59.374 52.381 20.29 0.00 43.53 3.21
3919 6952 1.208293 GCTGTTAAGGGACAGGAGAGG 59.792 57.143 7.10 0.00 45.59 3.69
3942 6976 5.594317 GGATAAAAGATTACATGGGCTGTGT 59.406 40.000 0.00 1.38 38.92 3.72
3943 6977 6.770785 GGATAAAAGATTACATGGGCTGTGTA 59.229 38.462 0.00 0.00 38.92 2.90
3946 6980 9.860650 ATAAAAGATTACATGGGCTGTGTATTA 57.139 29.630 0.00 1.46 38.92 0.98
3950 6984 5.950544 TTACATGGGCTGTGTATTACTCT 57.049 39.130 0.00 0.00 38.92 3.24
4140 9774 5.393461 GGTCATTCCAGAAACATCCATGAAC 60.393 44.000 0.00 0.00 35.97 3.18
4247 9882 1.291033 ACCTAGAGGACCCACTATGCA 59.709 52.381 1.60 0.00 38.94 3.96
4253 9888 2.105477 GAGGACCCACTATGCATGTCAT 59.895 50.000 10.16 5.14 39.17 3.06
4279 9914 2.012673 GCCAGTACTGCTCTCCAAATG 58.987 52.381 17.86 0.84 0.00 2.32
4346 9981 2.334946 GCTGGAGGCGCACAAATCA 61.335 57.895 10.83 0.00 0.00 2.57
4402 10037 2.418368 GGTGTTGGACCATCATGCTA 57.582 50.000 8.48 0.00 45.34 3.49
4403 10038 2.936202 GGTGTTGGACCATCATGCTAT 58.064 47.619 8.48 0.00 45.34 2.97
4454 10089 2.496070 TGTGAAGAACATACTCCCTCCG 59.504 50.000 0.00 0.00 32.36 4.63
4455 10090 2.496470 GTGAAGAACATACTCCCTCCGT 59.504 50.000 0.00 0.00 0.00 4.69
4456 10091 2.758979 TGAAGAACATACTCCCTCCGTC 59.241 50.000 0.00 0.00 0.00 4.79
4457 10092 1.777941 AGAACATACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
4458 10093 1.288335 AGAACATACTCCCTCCGTCCT 59.712 52.381 0.00 0.00 0.00 3.85
4459 10094 2.108970 GAACATACTCCCTCCGTCCTT 58.891 52.381 0.00 0.00 0.00 3.36
4460 10095 1.777941 ACATACTCCCTCCGTCCTTC 58.222 55.000 0.00 0.00 0.00 3.46
4461 10096 1.006758 ACATACTCCCTCCGTCCTTCA 59.993 52.381 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 153 0.180406 GAGAGGGAGAGAGAGACGCT 59.820 60.000 0.00 0.00 0.00 5.07
179 180 1.293683 GGGGGAGAGAGAGAGGGAGT 61.294 65.000 0.00 0.00 0.00 3.85
201 212 2.542907 GCGAGCGAGAGAGAGAGGG 61.543 68.421 0.00 0.00 0.00 4.30
202 213 1.095228 AAGCGAGCGAGAGAGAGAGG 61.095 60.000 0.00 0.00 0.00 3.69
321 332 6.897966 TGGATTGCAAATAAATACCCCACTAA 59.102 34.615 1.71 0.00 0.00 2.24
443 454 9.956720 GAAAAATGTGTGGGATCTAAATATGAG 57.043 33.333 0.00 0.00 0.00 2.90
759 776 6.032670 CCGAACCGTTATTTTACATTTTTCGG 59.967 38.462 0.00 0.00 43.92 4.30
809 826 5.011023 GTCCCTGTTGTTTCCTGAAATCAAT 59.989 40.000 0.00 0.00 32.36 2.57
824 841 7.484975 TGTATTTTACACAAAAGTCCCTGTTG 58.515 34.615 0.00 0.00 37.08 3.33
825 842 7.648039 TGTATTTTACACAAAAGTCCCTGTT 57.352 32.000 0.00 0.00 37.08 3.16
975 1004 7.506114 AGGAAAAACCCAATCTTTTCTTTACC 58.494 34.615 7.10 0.00 40.08 2.85
976 1005 8.958119 AAGGAAAAACCCAATCTTTTCTTTAC 57.042 30.769 7.10 0.00 38.38 2.01
1001 1030 8.173542 TGACGTTAGAGCAACTTCCATATATA 57.826 34.615 0.00 0.00 35.15 0.86
1002 1031 7.050970 TGACGTTAGAGCAACTTCCATATAT 57.949 36.000 0.00 0.00 35.15 0.86
1079 3086 1.467342 GTATTCTTTGGCGTGGTGGAC 59.533 52.381 0.00 0.00 0.00 4.02
1080 3087 1.816074 GTATTCTTTGGCGTGGTGGA 58.184 50.000 0.00 0.00 0.00 4.02
1081 3088 0.446222 CGTATTCTTTGGCGTGGTGG 59.554 55.000 0.00 0.00 0.00 4.61
1082 3089 0.179200 GCGTATTCTTTGGCGTGGTG 60.179 55.000 0.00 0.00 0.00 4.17
1083 3090 1.303091 GGCGTATTCTTTGGCGTGGT 61.303 55.000 0.00 0.00 0.00 4.16
1084 3091 1.427819 GGCGTATTCTTTGGCGTGG 59.572 57.895 0.00 0.00 0.00 4.94
1085 3092 1.302383 TGGGCGTATTCTTTGGCGTG 61.302 55.000 0.00 0.00 0.00 5.34
1086 3093 1.003112 TGGGCGTATTCTTTGGCGT 60.003 52.632 0.00 0.00 0.00 5.68
1106 3120 1.374631 CACCTGCTACGCTTCAGCA 60.375 57.895 0.00 4.07 46.47 4.41
1126 3140 1.291877 CCTTCCTTGGCGTGTTCTCG 61.292 60.000 0.00 0.00 0.00 4.04
1136 3150 2.422093 GGGTTATCTCTGCCTTCCTTGG 60.422 54.545 0.00 0.00 0.00 3.61
1139 3153 1.274416 TGGGGTTATCTCTGCCTTCCT 60.274 52.381 0.00 0.00 0.00 3.36
1173 3196 2.892425 CGTCCCCATGCTTCGCTC 60.892 66.667 0.00 0.00 0.00 5.03
1331 3354 3.838271 GAGATGGAGGCGACGGCA 61.838 66.667 24.23 2.93 42.47 5.69
1413 3443 1.604278 CTTAGCCCTAATTTGCGAGGC 59.396 52.381 0.00 0.00 44.20 4.70
1423 3453 1.902556 GGCGTCACCTTAGCCCTAA 59.097 57.895 0.00 0.00 44.80 2.69
1424 3454 3.625099 GGCGTCACCTTAGCCCTA 58.375 61.111 0.00 0.00 44.80 3.53
1427 3457 2.047560 AACGGCGTCACCTTAGCC 60.048 61.111 15.17 0.00 46.88 3.93
1428 3458 2.442188 CGAACGGCGTCACCTTAGC 61.442 63.158 15.17 0.00 35.61 3.09
1429 3459 3.763319 CGAACGGCGTCACCTTAG 58.237 61.111 15.17 0.00 35.61 2.18
1441 3694 4.029198 CGAGACTAGAAATGTCAACGAACG 59.971 45.833 0.00 0.00 38.05 3.95
1637 3890 1.541588 GAAATGGAGCTGGTGTTGGAC 59.458 52.381 0.00 0.00 0.00 4.02
1676 3929 2.522193 GAGGGGCGGCTAGTAGCT 60.522 66.667 21.20 0.26 41.99 3.32
1682 3935 4.075793 ACCTGAGAGGGGCGGCTA 62.076 66.667 9.56 0.00 40.58 3.93
1728 3989 1.949525 CAAGCAAGCAACTGGTGTAGT 59.050 47.619 0.00 0.00 42.89 2.73
1787 4048 3.938019 CTGCCGCCCCATTTGCAAC 62.938 63.158 0.00 0.00 32.58 4.17
1794 4055 2.990967 CACAAACTGCCGCCCCAT 60.991 61.111 0.00 0.00 0.00 4.00
1820 4081 3.634448 CGCCAACATAATAAATGGGGTCA 59.366 43.478 0.00 0.00 40.06 4.02
1827 4088 7.370383 CAAATCTAGCCGCCAACATAATAAAT 58.630 34.615 0.00 0.00 0.00 1.40
1831 4092 3.004734 GCAAATCTAGCCGCCAACATAAT 59.995 43.478 0.00 0.00 0.00 1.28
1847 4108 1.660560 ATGCACGGCAGAGGCAAATC 61.661 55.000 11.07 0.00 43.65 2.17
1859 4120 3.925379 TCCTATGTAATAGCATGCACGG 58.075 45.455 21.98 6.24 45.64 4.94
1861 4122 5.181811 TGCAATCCTATGTAATAGCATGCAC 59.818 40.000 21.98 9.82 45.01 4.57
1911 4337 1.014044 GCGCCTTGAGACATGTTCGA 61.014 55.000 0.00 0.00 0.00 3.71
1918 4344 0.898326 TACAGGAGCGCCTTGAGACA 60.898 55.000 6.13 0.00 43.90 3.41
1962 4388 7.275999 TCCAAAAACAATAAAGACACGAAAACC 59.724 33.333 0.00 0.00 0.00 3.27
1969 4395 5.278604 ACGCTCCAAAAACAATAAAGACAC 58.721 37.500 0.00 0.00 0.00 3.67
2056 4482 5.544176 CAGCTTCATTATAGGAGGAGGGTTA 59.456 44.000 0.00 0.00 0.00 2.85
2140 4566 5.702670 TGATGCTTTCACTTACCTTTCAGAG 59.297 40.000 0.00 0.00 0.00 3.35
2194 4621 7.874940 TCACAGAAACAAGATCACATTAAAGG 58.125 34.615 0.00 0.00 0.00 3.11
2229 4657 6.980416 AAGTAGGTTCTACTTCAGAGTTGT 57.020 37.500 12.89 0.00 37.33 3.32
2242 4670 7.312415 ACAACCAGTTACATAAGTAGGTTCT 57.688 36.000 0.00 0.00 32.65 3.01
2314 4743 7.260387 TCCATTAACAATAGGAAGTGGTACA 57.740 36.000 0.00 0.00 0.00 2.90
2359 4788 4.965532 ACCTGAACTCCAGAGTATAGCAAT 59.034 41.667 0.00 0.00 45.78 3.56
2401 4831 4.654915 TGCTAGGTTACCAGGTAAAAACC 58.345 43.478 14.03 13.61 41.41 3.27
2451 4881 3.319122 GGCCAACTGATGTCTTTCAAAGT 59.681 43.478 0.00 0.00 0.00 2.66
2467 4897 3.078097 ACCAAAAACAAAACAGGCCAAC 58.922 40.909 5.01 0.00 0.00 3.77
2479 4909 8.454106 CCAAAAATATTGTTCACACCAAAAACA 58.546 29.630 0.00 0.00 0.00 2.83
2504 4934 2.037847 ATGGCAGTTCTTGGGGCC 59.962 61.111 0.00 0.00 46.58 5.80
2510 4943 2.840651 AGTAGGTAGCATGGCAGTTCTT 59.159 45.455 0.00 0.00 0.00 2.52
2517 4950 3.118371 AGTGGTTTAGTAGGTAGCATGGC 60.118 47.826 0.00 0.00 0.00 4.40
2559 4992 4.099113 CAGTCTCAGATCTGTGCTAATCCA 59.901 45.833 21.92 0.00 0.00 3.41
2560 4993 4.340666 TCAGTCTCAGATCTGTGCTAATCC 59.659 45.833 21.92 4.91 33.89 3.01
2655 5095 1.821136 GTCTTCCCAATCCTGCAAAGG 59.179 52.381 0.00 0.00 0.00 3.11
2928 5368 3.466836 GGCATCGACATATTGGACAAGA 58.533 45.455 0.00 0.00 0.00 3.02
2946 5386 1.301401 CTTTCCAAGTCGTCCGGCA 60.301 57.895 0.00 0.00 0.00 5.69
2970 5410 5.469421 CCTGTAAGAGTATACACCTAGTCCG 59.531 48.000 5.50 0.00 34.07 4.79
2982 5422 8.602472 ATGAAGAGTTTCTCCTGTAAGAGTAT 57.398 34.615 0.00 0.00 35.28 2.12
2992 5432 5.740290 TTAACGGATGAAGAGTTTCTCCT 57.260 39.130 0.00 0.00 32.75 3.69
2999 5439 4.360951 TTGGGTTTAACGGATGAAGAGT 57.639 40.909 0.00 0.00 0.00 3.24
3021 5461 6.128715 CGCGCTGATATTTTTACAGAGATGAT 60.129 38.462 5.56 0.00 34.40 2.45
3042 5489 4.326766 TTTGCTCAACAGCCGCGC 62.327 61.111 0.00 0.00 46.26 6.86
3043 5490 2.116736 TTCTTTGCTCAACAGCCGCG 62.117 55.000 0.00 0.00 46.26 6.46
3105 5631 3.463944 CACAAGTACCACCTTTCGTCTT 58.536 45.455 0.00 0.00 0.00 3.01
3106 5632 2.224209 CCACAAGTACCACCTTTCGTCT 60.224 50.000 0.00 0.00 0.00 4.18
3107 5633 2.140717 CCACAAGTACCACCTTTCGTC 58.859 52.381 0.00 0.00 0.00 4.20
3178 5983 8.084073 CCATTGTCTCAGAAAAGCTTATTTGAA 58.916 33.333 0.00 0.00 0.00 2.69
3191 5996 5.304686 AGTAAACACCCATTGTCTCAGAA 57.695 39.130 0.00 0.00 37.51 3.02
3195 6000 6.228258 TGAACTAGTAAACACCCATTGTCTC 58.772 40.000 0.00 0.00 37.51 3.36
3197 6002 6.072673 CCTTGAACTAGTAAACACCCATTGTC 60.073 42.308 0.00 0.00 37.51 3.18
3214 6019 2.362077 GTTTCACATGGCACCTTGAACT 59.638 45.455 9.37 0.00 0.00 3.01
3295 6100 1.484240 GCATAGAGTCCAGAACAGCCT 59.516 52.381 0.00 0.00 0.00 4.58
3304 6109 1.827344 CCACAGTCAGCATAGAGTCCA 59.173 52.381 0.00 0.00 0.00 4.02
3330 6135 3.520290 ACGCTTGTAACTGCATAGCTA 57.480 42.857 0.00 0.00 0.00 3.32
3331 6136 2.386661 ACGCTTGTAACTGCATAGCT 57.613 45.000 0.00 0.00 0.00 3.32
3332 6137 3.369756 TGTAACGCTTGTAACTGCATAGC 59.630 43.478 0.00 0.00 0.00 2.97
3333 6138 4.625742 ACTGTAACGCTTGTAACTGCATAG 59.374 41.667 0.00 0.00 0.00 2.23
3343 6148 4.690122 ACTTGTAAGACTGTAACGCTTGT 58.310 39.130 0.00 0.00 0.00 3.16
3388 6195 2.681344 CAACAGCGTAGGGGTAATTTCC 59.319 50.000 0.00 0.00 0.00 3.13
3453 6267 5.922544 ACAGAAGTGCATTTATTTTGCTGAC 59.077 36.000 11.42 0.00 40.77 3.51
3456 6297 6.514947 TCAACAGAAGTGCATTTATTTTGCT 58.485 32.000 9.75 0.00 40.77 3.91
3461 6302 6.149308 TGACGATCAACAGAAGTGCATTTATT 59.851 34.615 0.00 0.00 0.00 1.40
3549 6390 5.971202 GGGAATATGATGTGTGCGTAAAAAG 59.029 40.000 0.00 0.00 0.00 2.27
3555 6396 1.490490 AGGGGAATATGATGTGTGCGT 59.510 47.619 0.00 0.00 0.00 5.24
3556 6397 2.146342 GAGGGGAATATGATGTGTGCG 58.854 52.381 0.00 0.00 0.00 5.34
3557 6398 2.158623 TGGAGGGGAATATGATGTGTGC 60.159 50.000 0.00 0.00 0.00 4.57
3641 6482 0.821517 ACCAACTGACACACGTCTGA 59.178 50.000 0.00 0.00 42.13 3.27
3648 6489 9.758651 GATATATATGTTGTACCAACTGACACA 57.241 33.333 0.00 0.00 0.00 3.72
3662 6503 8.713737 AGCATAGCACAGTGATATATATGTTG 57.286 34.615 11.01 0.40 26.54 3.33
3663 6504 8.756927 AGAGCATAGCACAGTGATATATATGTT 58.243 33.333 11.01 0.00 26.54 2.71
3665 6506 9.896263 CTAGAGCATAGCACAGTGATATATATG 57.104 37.037 11.01 3.16 26.54 1.78
3669 6513 6.151817 CACCTAGAGCATAGCACAGTGATATA 59.848 42.308 11.01 0.00 26.54 0.86
3703 6647 5.375773 TGTGAAGTTTGATCCATGTGAAGA 58.624 37.500 0.00 0.00 0.00 2.87
3711 6655 5.063204 AGAACGATTGTGAAGTTTGATCCA 58.937 37.500 0.00 0.00 0.00 3.41
3861 6807 7.010183 TGCTTGTGCTAGTTTTTCGTAGATATC 59.990 37.037 0.00 0.00 40.48 1.63
3919 6952 6.699575 ACACAGCCCATGTAATCTTTTATC 57.300 37.500 0.00 0.00 41.41 1.75
3943 6977 9.784376 TTATATAGGCCCATTGTCTAGAGTAAT 57.216 33.333 0.00 0.00 0.00 1.89
3946 6980 7.479579 TCTTATATAGGCCCATTGTCTAGAGT 58.520 38.462 0.00 0.00 0.00 3.24
3950 6984 8.783660 CCTATCTTATATAGGCCCATTGTCTA 57.216 38.462 0.00 0.00 35.26 2.59
4017 8113 4.746729 CATTCCGATGCTTGGATTCAAAA 58.253 39.130 0.00 0.00 34.91 2.44
4140 9774 1.025113 TCGGTGACTCGGTGCTCTAG 61.025 60.000 0.00 0.00 0.00 2.43
4247 9882 2.103771 CAGTACTGGCCAGCTATGACAT 59.896 50.000 33.06 13.10 0.00 3.06
4253 9888 0.324738 AGAGCAGTACTGGCCAGCTA 60.325 55.000 33.06 20.08 35.36 3.32
4335 9970 2.049077 TTGTGATGTGATTTGTGCGC 57.951 45.000 0.00 0.00 0.00 6.09
4346 9981 0.534877 TGGCGTCTGCTTTGTGATGT 60.535 50.000 0.00 0.00 42.25 3.06
4394 10029 3.301794 TGGAGCCAACAATAGCATGAT 57.698 42.857 0.00 0.00 0.00 2.45
4402 10037 3.956199 CCAACATCTATGGAGCCAACAAT 59.044 43.478 0.00 0.00 40.56 2.71
4403 10038 3.010027 TCCAACATCTATGGAGCCAACAA 59.990 43.478 0.00 0.00 41.98 2.83


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

AutoCloner maintained by Alex Coulton.