Multiple sequence alignment - TraesCS7B01G195300

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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 TraesCS7B01G195300 chr7B 100.000 4913 0 0 1 4913 335927224 335922312 0.000000e+00 9073
1 TraesCS7B01G195300 chr7B 97.005 935 26 2 3 936 95044021 95044954 0.000000e+00 1570
2 TraesCS7B01G195300 chr7B 98.843 605 7 0 4309 4913 335906070 335905466 0.000000e+00 1079
3 TraesCS7B01G195300 chr7A 91.444 3436 182 48 937 4310 199856800 199853415 0.000000e+00 4614
4 TraesCS7B01G195300 chr7D 91.288 3432 191 34 937 4313 191160560 191157182 0.000000e+00 4582
5 TraesCS7B01G195300 chr4B 98.294 938 14 2 1 936 659571492 659570555 0.000000e+00 1642
6 TraesCS7B01G195300 chrUn 98.190 939 16 1 1 938 17579474 17578536 0.000000e+00 1639
7 TraesCS7B01G195300 chr6B 97.974 938 16 3 1 936 650648807 650649743 0.000000e+00 1624
8 TraesCS7B01G195300 chr6B 97.227 613 9 5 4308 4913 240711049 240710438 0.000000e+00 1031
9 TraesCS7B01G195300 chr6B 96.569 612 13 5 4309 4913 240702889 240702279 0.000000e+00 1007
10 TraesCS7B01G195300 chr6B 93.802 484 25 4 4309 4787 673227773 673227290 0.000000e+00 723
11 TraesCS7B01G195300 chr6B 83.305 587 65 25 4348 4913 516109001 516109575 1.220000e-140 510
12 TraesCS7B01G195300 chr5B 97.974 938 16 3 1 936 658082021 658081085 0.000000e+00 1624
13 TraesCS7B01G195300 chr5B 96.699 939 27 4 1 936 426530682 426529745 0.000000e+00 1559
14 TraesCS7B01G195300 chr5B 88.780 615 42 20 4309 4913 159565603 159566200 0.000000e+00 728
15 TraesCS7B01G195300 chr5B 87.422 644 37 31 4291 4913 216633263 216632643 0.000000e+00 701
16 TraesCS7B01G195300 chr3B 97.759 937 19 2 1 936 393327299 393326364 0.000000e+00 1613
17 TraesCS7B01G195300 chr1B 97.441 938 21 3 1 936 357904273 357905209 0.000000e+00 1596
18 TraesCS7B01G195300 chr1B 97.225 937 23 3 1 936 612405827 612404893 0.000000e+00 1583
19 TraesCS7B01G195300 chr2B 98.841 604 7 0 4310 4913 760201698 760201095 0.000000e+00 1077
20 TraesCS7B01G195300 chr2B 98.512 605 9 0 4309 4913 613395186 613395790 0.000000e+00 1068
21 TraesCS7B01G195300 chr2B 98.347 605 10 0 4309 4913 760193546 760192942 0.000000e+00 1062
22 TraesCS7B01G195300 chr2B 98.179 604 11 0 4310 4913 613387037 613387640 0.000000e+00 1055
23 TraesCS7B01G195300 chr5A 88.889 441 40 8 4297 4732 353253195 353252759 7.240000e-148 534


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 TraesCS7B01G195300 chr7B 335922312 335927224 4912 True 9073 9073 100.000 1 4913 1 chr7B.!!$R2 4912
1 TraesCS7B01G195300 chr7B 95044021 95044954 933 False 1570 1570 97.005 3 936 1 chr7B.!!$F1 933
2 TraesCS7B01G195300 chr7B 335905466 335906070 604 True 1079 1079 98.843 4309 4913 1 chr7B.!!$R1 604
3 TraesCS7B01G195300 chr7A 199853415 199856800 3385 True 4614 4614 91.444 937 4310 1 chr7A.!!$R1 3373
4 TraesCS7B01G195300 chr7D 191157182 191160560 3378 True 4582 4582 91.288 937 4313 1 chr7D.!!$R1 3376
5 TraesCS7B01G195300 chr4B 659570555 659571492 937 True 1642 1642 98.294 1 936 1 chr4B.!!$R1 935
6 TraesCS7B01G195300 chrUn 17578536 17579474 938 True 1639 1639 98.190 1 938 1 chrUn.!!$R1 937
7 TraesCS7B01G195300 chr6B 650648807 650649743 936 False 1624 1624 97.974 1 936 1 chr6B.!!$F2 935
8 TraesCS7B01G195300 chr6B 240710438 240711049 611 True 1031 1031 97.227 4308 4913 1 chr6B.!!$R2 605
9 TraesCS7B01G195300 chr6B 240702279 240702889 610 True 1007 1007 96.569 4309 4913 1 chr6B.!!$R1 604
10 TraesCS7B01G195300 chr6B 516109001 516109575 574 False 510 510 83.305 4348 4913 1 chr6B.!!$F1 565
11 TraesCS7B01G195300 chr5B 658081085 658082021 936 True 1624 1624 97.974 1 936 1 chr5B.!!$R3 935
12 TraesCS7B01G195300 chr5B 426529745 426530682 937 True 1559 1559 96.699 1 936 1 chr5B.!!$R2 935
13 TraesCS7B01G195300 chr5B 159565603 159566200 597 False 728 728 88.780 4309 4913 1 chr5B.!!$F1 604
14 TraesCS7B01G195300 chr5B 216632643 216633263 620 True 701 701 87.422 4291 4913 1 chr5B.!!$R1 622
15 TraesCS7B01G195300 chr3B 393326364 393327299 935 True 1613 1613 97.759 1 936 1 chr3B.!!$R1 935
16 TraesCS7B01G195300 chr1B 357904273 357905209 936 False 1596 1596 97.441 1 936 1 chr1B.!!$F1 935
17 TraesCS7B01G195300 chr1B 612404893 612405827 934 True 1583 1583 97.225 1 936 1 chr1B.!!$R1 935
18 TraesCS7B01G195300 chr2B 760201095 760201698 603 True 1077 1077 98.841 4310 4913 1 chr2B.!!$R2 603
19 TraesCS7B01G195300 chr2B 613395186 613395790 604 False 1068 1068 98.512 4309 4913 1 chr2B.!!$F2 604
20 TraesCS7B01G195300 chr2B 760192942 760193546 604 True 1062 1062 98.347 4309 4913 1 chr2B.!!$R1 604
21 TraesCS7B01G195300 chr2B 613387037 613387640 603 False 1055 1055 98.179 4310 4913 1 chr2B.!!$F1 603

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
807 811 1.101635 CCAGACGCTAGGATCCGTGA 61.102 60.0 5.98 0.0 37.87 4.35 F
2445 2492 0.319900 CAGTCACGGACAGGAACAGG 60.320 60.0 6.78 0.0 34.60 4.00 F
2702 2767 0.883833 GGTTCAGAACACCATGCCTG 59.116 55.0 15.36 0.0 34.04 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2657 2722 0.325577 TGCTCCCTACATGCTCCTCA 60.326 55.0 0.00 0.0 0.00 3.86 R
3867 3956 0.027716 GAGATGCAATGCACGCTCAG 59.972 55.0 25.34 0.0 43.04 3.35 R
3993 4097 0.109532 TGCCATTGTCGACCAGGAAA 59.890 50.0 14.12 0.0 0.00 3.13 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
807 811 1.101635 CCAGACGCTAGGATCCGTGA 61.102 60.000 5.98 0.00 37.87 4.35
864 868 4.534168 GCGTCTCCTAAAAAGGTCAAAAC 58.466 43.478 0.00 0.00 0.00 2.43
924 929 4.716784 TGTTAGCCAGAGAGGTCATAACAT 59.283 41.667 0.00 0.00 37.68 2.71
939 944 6.750039 GGTCATAACATTAATTTTGTCCACGG 59.250 38.462 0.00 0.00 0.00 4.94
985 993 3.587095 CGACCTACGCTCCACTCA 58.413 61.111 0.00 0.00 34.51 3.41
1092 1101 2.991076 GCGTCGCCTCCACTACACT 61.991 63.158 5.75 0.00 0.00 3.55
1299 1311 2.284921 CAGCTCACTCCCTCCCCA 60.285 66.667 0.00 0.00 0.00 4.96
1807 1819 5.105063 GCAGAAAGAAAAAGAACTGCAGTT 58.895 37.500 31.57 31.57 46.30 3.16
1824 1836 3.834610 CAGTTCTACGTTTCTCGGATGT 58.165 45.455 0.00 0.00 44.69 3.06
1840 1852 2.668550 GTTCCCGTGGTGCAGGTC 60.669 66.667 0.00 0.00 0.00 3.85
1928 1940 9.884465 GAATGCTAATCAAGTAATCATGTTACC 57.116 33.333 11.94 0.48 0.00 2.85
1984 1996 3.056821 TCTGTTTAGATGTCAGGGACACG 60.057 47.826 0.49 0.00 45.65 4.49
1996 2008 3.028850 CAGGGACACGGAGTAGGATAAA 58.971 50.000 0.00 0.00 41.61 1.40
2050 2065 7.720957 AGCATCATGAATAGCATACCTACAAAA 59.279 33.333 17.04 0.00 34.82 2.44
2084 2099 1.949465 CGGAGCAAGGTGGGTTATAC 58.051 55.000 0.00 0.00 0.00 1.47
2085 2100 1.485066 CGGAGCAAGGTGGGTTATACT 59.515 52.381 0.00 0.00 0.00 2.12
2086 2101 2.696707 CGGAGCAAGGTGGGTTATACTA 59.303 50.000 0.00 0.00 0.00 1.82
2103 2118 8.553696 GGTTATACTATTCATTACCAAACACCG 58.446 37.037 0.00 0.00 0.00 4.94
2104 2119 9.316730 GTTATACTATTCATTACCAAACACCGA 57.683 33.333 0.00 0.00 0.00 4.69
2105 2120 9.887629 TTATACTATTCATTACCAAACACCGAA 57.112 29.630 0.00 0.00 0.00 4.30
2106 2121 8.795842 ATACTATTCATTACCAAACACCGAAA 57.204 30.769 0.00 0.00 0.00 3.46
2107 2122 6.905578 ACTATTCATTACCAAACACCGAAAC 58.094 36.000 0.00 0.00 0.00 2.78
2108 2123 5.776173 ATTCATTACCAAACACCGAAACA 57.224 34.783 0.00 0.00 0.00 2.83
2113 2128 7.042335 TCATTACCAAACACCGAAACAAAAAT 58.958 30.769 0.00 0.00 0.00 1.82
2129 2156 5.415221 ACAAAAATCAAAACTTGGCGAGAA 58.585 33.333 9.20 0.00 0.00 2.87
2147 2174 4.260132 CGAGAATGAGTTGAGCTTGCATAC 60.260 45.833 0.00 0.00 0.00 2.39
2163 2190 6.183360 GCTTGCATACATAGGCATCAGAATAG 60.183 42.308 0.00 0.00 42.93 1.73
2345 2379 0.442699 GGAGTCACGGAAAATGTCGC 59.557 55.000 0.00 0.00 0.00 5.19
2363 2397 1.218047 CGCAGAATTCAGGTCCCGA 59.782 57.895 8.44 0.00 0.00 5.14
2413 2460 4.407365 TCTCTGTCATAGGAACAGTGTGA 58.593 43.478 0.00 0.00 33.57 3.58
2425 2472 5.597182 AGGAACAGTGTGAAGTAGTAAGTCA 59.403 40.000 0.00 0.00 0.00 3.41
2440 2487 0.467474 AGTCACAGTCACGGACAGGA 60.467 55.000 6.78 0.00 34.60 3.86
2444 2491 0.389391 ACAGTCACGGACAGGAACAG 59.611 55.000 6.78 0.00 34.60 3.16
2445 2492 0.319900 CAGTCACGGACAGGAACAGG 60.320 60.000 6.78 0.00 34.60 4.00
2446 2493 1.668151 GTCACGGACAGGAACAGGC 60.668 63.158 0.00 0.00 32.09 4.85
2448 2495 1.003355 CACGGACAGGAACAGGCAT 60.003 57.895 0.00 0.00 0.00 4.40
2469 2516 2.368439 TGCATGCCTGAAGTTCCATAC 58.632 47.619 16.68 0.00 0.00 2.39
2626 2683 5.709631 TGGAAGGATTGAACGATGATGAAAA 59.290 36.000 0.00 0.00 0.00 2.29
2638 2703 7.083875 ACGATGATGAAAATATTTCAACCGT 57.916 32.000 9.34 12.07 31.41 4.83
2640 2705 6.075415 CGATGATGAAAATATTTCAACCGTGC 60.075 38.462 9.34 0.00 31.55 5.34
2657 2722 1.214305 TGCTGAATGGGTAGGGCCTT 61.214 55.000 13.45 0.00 37.43 4.35
2702 2767 0.883833 GGTTCAGAACACCATGCCTG 59.116 55.000 15.36 0.00 34.04 4.85
2732 2797 4.021719 TCCACTCCTTTACTACCACTTTCG 60.022 45.833 0.00 0.00 0.00 3.46
2802 2867 1.109323 AAGGGTCACAAGCAAGGCAC 61.109 55.000 0.00 0.00 0.00 5.01
2803 2868 2.564721 GGGTCACAAGCAAGGCACC 61.565 63.158 0.00 0.00 0.00 5.01
2804 2869 2.639286 GTCACAAGCAAGGCACCG 59.361 61.111 0.00 0.00 0.00 4.94
2805 2870 3.286751 TCACAAGCAAGGCACCGC 61.287 61.111 0.00 0.00 0.00 5.68
2806 2871 3.289834 CACAAGCAAGGCACCGCT 61.290 61.111 0.00 0.00 39.40 5.52
2807 2872 2.519302 ACAAGCAAGGCACCGCTT 60.519 55.556 2.67 2.67 46.49 4.68
2808 2873 2.256461 CAAGCAAGGCACCGCTTC 59.744 61.111 5.25 0.00 44.24 3.86
2809 2874 2.985847 AAGCAAGGCACCGCTTCC 60.986 61.111 2.67 0.00 42.82 3.46
2812 2877 4.351054 CAAGGCACCGCTTCCCCT 62.351 66.667 0.00 0.00 0.00 4.79
2813 2878 4.035102 AAGGCACCGCTTCCCCTC 62.035 66.667 0.00 0.00 0.00 4.30
2815 2880 4.475135 GGCACCGCTTCCCCTCTC 62.475 72.222 0.00 0.00 0.00 3.20
2816 2881 4.475135 GCACCGCTTCCCCTCTCC 62.475 72.222 0.00 0.00 0.00 3.71
2817 2882 3.787001 CACCGCTTCCCCTCTCCC 61.787 72.222 0.00 0.00 0.00 4.30
2901 2973 8.380743 TGGTTGCTTTACTAGTAATTTTTCGA 57.619 30.769 15.92 0.00 30.90 3.71
2933 3005 5.043356 AGCCCAGTAATTTAGGGGAAAAGAT 60.043 40.000 14.50 0.00 43.57 2.40
3024 3096 3.437867 CCGAGAGATGCGGTAGCT 58.562 61.111 0.00 0.00 43.66 3.32
3056 3128 2.511373 GCATCGTGTCGCATGGGA 60.511 61.111 8.63 8.63 0.00 4.37
3121 3193 2.661718 GGGTTTTGTCCCTTTGTCTGA 58.338 47.619 0.00 0.00 43.85 3.27
3122 3194 3.230976 GGGTTTTGTCCCTTTGTCTGAT 58.769 45.455 0.00 0.00 43.85 2.90
3123 3195 3.641436 GGGTTTTGTCCCTTTGTCTGATT 59.359 43.478 0.00 0.00 43.85 2.57
3124 3196 4.501400 GGGTTTTGTCCCTTTGTCTGATTG 60.501 45.833 0.00 0.00 43.85 2.67
3125 3197 4.099419 GGTTTTGTCCCTTTGTCTGATTGT 59.901 41.667 0.00 0.00 0.00 2.71
3126 3198 5.281727 GTTTTGTCCCTTTGTCTGATTGTC 58.718 41.667 0.00 0.00 0.00 3.18
3127 3199 4.437682 TTGTCCCTTTGTCTGATTGTCT 57.562 40.909 0.00 0.00 0.00 3.41
3136 3208 4.263018 TGTCTGATTGTCTCAACTGGAG 57.737 45.455 0.00 0.00 45.49 3.86
3146 3218 4.017958 TGTCTCAACTGGAGTCTCTATCCT 60.018 45.833 0.00 0.00 44.40 3.24
3147 3219 4.338118 GTCTCAACTGGAGTCTCTATCCTG 59.662 50.000 0.00 0.00 44.40 3.86
3160 3239 2.158460 TCTATCCTGCTCTCCGGATCAA 60.158 50.000 3.57 0.00 40.40 2.57
3165 3244 0.976641 TGCTCTCCGGATCAACAACT 59.023 50.000 3.57 0.00 0.00 3.16
3173 3252 2.742053 CCGGATCAACAACTTGTGGTAG 59.258 50.000 0.00 0.00 0.00 3.18
3190 3276 5.471116 TGTGGTAGCATGCATGATCTATTTC 59.529 40.000 30.64 13.04 0.00 2.17
3214 3300 1.507141 CCACAGTTCCTGGACAACGC 61.507 60.000 0.00 0.00 35.51 4.84
3219 3305 1.134220 AGTTCCTGGACAACGCTGAAA 60.134 47.619 0.00 0.00 0.00 2.69
3223 3309 3.745799 TCCTGGACAACGCTGAAATTTA 58.254 40.909 0.00 0.00 0.00 1.40
3310 3396 4.770795 CCTGGAAACCTAATCATCTCGTT 58.229 43.478 0.00 0.00 0.00 3.85
3314 3400 5.659525 TGGAAACCTAATCATCTCGTTCCTA 59.340 40.000 0.00 0.00 0.00 2.94
3323 3409 5.147330 TCATCTCGTTCCTATTTGTGTGT 57.853 39.130 0.00 0.00 0.00 3.72
3646 3732 2.341257 CTGCTTCTTCGCTTTCTGCTA 58.659 47.619 0.00 0.00 40.11 3.49
3704 3790 2.159476 GCAAAATCTGATCTTCGCTGCA 60.159 45.455 0.00 0.00 0.00 4.41
3734 3820 8.832521 TCTCTTTGCTATTTCTTCGTTGTTTTA 58.167 29.630 0.00 0.00 0.00 1.52
3737 3823 9.180678 CTTTGCTATTTCTTCGTTGTTTTACAT 57.819 29.630 0.00 0.00 0.00 2.29
3786 3875 8.958043 GTTCAATTTGTTTGTACTTCTGATGTC 58.042 33.333 0.00 0.00 36.65 3.06
3867 3956 1.002087 CGGTGGGGATGCCTAATCTAC 59.998 57.143 2.19 0.00 35.43 2.59
3925 4014 3.157087 ACGTCTTGCATTCCAGGAAAAT 58.843 40.909 5.81 0.00 30.68 1.82
3975 4064 6.477033 AGAACTGTAGAAATGATCACATACGC 59.523 38.462 0.00 0.00 35.50 4.42
3986 4090 0.530650 CACATACGCTACTGGCTGGG 60.531 60.000 0.00 0.00 39.13 4.45
3988 4092 0.178068 CATACGCTACTGGCTGGGTT 59.822 55.000 0.00 0.00 39.13 4.11
3989 4093 0.909623 ATACGCTACTGGCTGGGTTT 59.090 50.000 0.00 0.00 39.13 3.27
3990 4094 0.688487 TACGCTACTGGCTGGGTTTT 59.312 50.000 0.00 0.00 39.13 2.43
3991 4095 0.179001 ACGCTACTGGCTGGGTTTTT 60.179 50.000 0.00 0.00 39.13 1.94
4012 4116 0.109532 TTTCCTGGTCGACAATGGCA 59.890 50.000 18.91 4.53 0.00 4.92
4168 4272 1.967319 TGGACACTTGGTTCAAGAGC 58.033 50.000 13.74 3.71 43.42 4.09
4170 4274 2.703536 TGGACACTTGGTTCAAGAGCTA 59.296 45.455 13.74 0.00 43.42 3.32
4206 4310 7.875041 TCATTTGTGTCTTTCTTTTTGGAAACA 59.125 29.630 0.00 0.00 39.83 2.83
4239 4344 1.277557 AGTGATCCAGCTTCAGGTGTC 59.722 52.381 5.34 0.00 41.60 3.67
4257 4362 0.319040 TCTGCAGCAACGAGACACTC 60.319 55.000 9.47 0.00 0.00 3.51
4288 4393 5.463154 AGCTCTCATTCCTCCTGTACTAAT 58.537 41.667 0.00 0.00 0.00 1.73
4354 4460 7.962373 TGTTTGTAAATAGTTGCATCTTCATCG 59.038 33.333 1.93 0.00 0.00 3.84
4673 4788 8.239681 GGAAAAGTCCATTAAGCAACATAAAC 57.760 34.615 0.00 0.00 44.26 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
729 733 1.002134 CGTGGCAAAGGGACCAGAT 60.002 57.895 0.00 0.00 36.38 2.90
939 944 2.757868 ACGGATAGATAGAGATGCCAGC 59.242 50.000 0.00 0.00 0.00 4.85
1092 1101 2.515854 GCGGAGAGTAGGATGGTGATA 58.484 52.381 0.00 0.00 0.00 2.15
1436 1448 3.291101 TTCGACCACCTGCTACCGC 62.291 63.158 0.00 0.00 0.00 5.68
1440 1452 0.246635 GAAGCTTCGACCACCTGCTA 59.753 55.000 11.40 0.00 33.28 3.49
1680 1692 3.386237 GCGCAGTCCCTCTCCAGT 61.386 66.667 0.30 0.00 0.00 4.00
1807 1819 2.165030 GGGAACATCCGAGAAACGTAGA 59.835 50.000 0.00 0.00 37.43 2.59
1840 1852 1.672030 TTCTGTGAGGCATGCGTGG 60.672 57.895 19.15 5.38 0.00 4.94
1928 1940 7.867909 GGTTGGGTTTTATCTCTTCAAGAAAAG 59.132 37.037 0.00 0.00 37.61 2.27
2043 2058 6.018588 TCCGCGTACATGGAATATTTTTGTAG 60.019 38.462 4.92 4.09 0.00 2.74
2050 2065 2.224185 TGCTCCGCGTACATGGAATATT 60.224 45.455 4.92 0.00 32.89 1.28
2084 2099 6.904498 TGTTTCGGTGTTTGGTAATGAATAG 58.096 36.000 0.00 0.00 0.00 1.73
2085 2100 6.879276 TGTTTCGGTGTTTGGTAATGAATA 57.121 33.333 0.00 0.00 0.00 1.75
2086 2101 5.776173 TGTTTCGGTGTTTGGTAATGAAT 57.224 34.783 0.00 0.00 0.00 2.57
2103 2118 6.035542 TCTCGCCAAGTTTTGATTTTTGTTTC 59.964 34.615 0.00 0.00 0.00 2.78
2104 2119 5.872070 TCTCGCCAAGTTTTGATTTTTGTTT 59.128 32.000 0.00 0.00 0.00 2.83
2105 2120 5.415221 TCTCGCCAAGTTTTGATTTTTGTT 58.585 33.333 0.00 0.00 0.00 2.83
2106 2121 5.004922 TCTCGCCAAGTTTTGATTTTTGT 57.995 34.783 0.00 0.00 0.00 2.83
2107 2122 5.964887 TTCTCGCCAAGTTTTGATTTTTG 57.035 34.783 0.00 0.00 0.00 2.44
2108 2123 6.279882 TCATTCTCGCCAAGTTTTGATTTTT 58.720 32.000 0.00 0.00 0.00 1.94
2113 2128 3.476552 ACTCATTCTCGCCAAGTTTTGA 58.523 40.909 0.00 0.00 0.00 2.69
2129 2156 5.061853 CCTATGTATGCAAGCTCAACTCAT 58.938 41.667 0.00 0.00 0.00 2.90
2147 2174 7.412346 GCGTATTTGTCTATTCTGATGCCTATG 60.412 40.741 0.00 0.00 0.00 2.23
2163 2190 2.095213 TCATTTGCCTCGCGTATTTGTC 59.905 45.455 5.77 0.00 0.00 3.18
2288 2322 4.675063 AATACTGGGACCTGGATTTTGT 57.325 40.909 0.00 0.00 0.00 2.83
2289 2323 6.017109 CGATAAATACTGGGACCTGGATTTTG 60.017 42.308 19.44 9.57 38.66 2.44
2293 2327 3.583086 CCGATAAATACTGGGACCTGGAT 59.417 47.826 0.00 0.00 0.00 3.41
2294 2328 2.969950 CCGATAAATACTGGGACCTGGA 59.030 50.000 0.00 0.00 0.00 3.86
2297 2331 3.577415 GCTACCGATAAATACTGGGACCT 59.423 47.826 0.00 0.00 0.00 3.85
2345 2379 0.807667 CTCGGGACCTGAATTCTGCG 60.808 60.000 4.14 5.51 0.00 5.18
2413 2460 4.023365 GTCCGTGACTGTGACTTACTACTT 60.023 45.833 0.00 0.00 0.00 2.24
2425 2472 0.389391 CTGTTCCTGTCCGTGACTGT 59.611 55.000 5.77 0.00 33.15 3.55
2446 2493 6.896819 AGTATGGAACTTCAGGCATGCAATG 61.897 44.000 21.36 17.33 41.27 2.82
2448 2495 1.927487 ATGGAACTTCAGGCATGCAA 58.073 45.000 21.36 4.23 0.00 4.08
2461 2508 3.615224 TTTACCCGGACAGTATGGAAC 57.385 47.619 0.73 0.00 43.62 3.62
2464 2511 3.622166 AGTTTTACCCGGACAGTATGG 57.378 47.619 0.73 0.00 43.62 2.74
2469 2516 4.634199 TCAGTTAAGTTTTACCCGGACAG 58.366 43.478 0.73 0.00 0.00 3.51
2534 2584 6.915843 ACTACAATCAGCTTTTAACGGTTTTG 59.084 34.615 0.00 0.00 0.00 2.44
2615 2672 6.075415 GCACGGTTGAAATATTTTCATCATCG 60.075 38.462 1.43 5.03 0.00 3.84
2626 2683 3.381272 CCCATTCAGCACGGTTGAAATAT 59.619 43.478 7.12 0.00 38.01 1.28
2638 2703 1.214305 AAGGCCCTACCCATTCAGCA 61.214 55.000 0.00 0.00 40.58 4.41
2640 2705 0.918983 TCAAGGCCCTACCCATTCAG 59.081 55.000 0.00 0.00 40.58 3.02
2657 2722 0.325577 TGCTCCCTACATGCTCCTCA 60.326 55.000 0.00 0.00 0.00 3.86
2702 2767 1.903183 AGTAAAGGAGTGGAGTGGAGC 59.097 52.381 0.00 0.00 0.00 4.70
2802 2867 3.157949 GAGGGAGAGGGGAAGCGG 61.158 72.222 0.00 0.00 0.00 5.52
2803 2868 3.157949 GGAGGGAGAGGGGAAGCG 61.158 72.222 0.00 0.00 0.00 4.68
2804 2869 2.770475 GGGAGGGAGAGGGGAAGC 60.770 72.222 0.00 0.00 0.00 3.86
2805 2870 1.690985 GTGGGAGGGAGAGGGGAAG 60.691 68.421 0.00 0.00 0.00 3.46
2806 2871 2.454941 GTGGGAGGGAGAGGGGAA 59.545 66.667 0.00 0.00 0.00 3.97
2807 2872 3.695825 GGTGGGAGGGAGAGGGGA 61.696 72.222 0.00 0.00 0.00 4.81
2808 2873 4.825679 GGGTGGGAGGGAGAGGGG 62.826 77.778 0.00 0.00 0.00 4.79
2809 2874 3.579451 TTGGGTGGGAGGGAGAGGG 62.579 68.421 0.00 0.00 0.00 4.30
2810 2875 1.997874 CTTGGGTGGGAGGGAGAGG 60.998 68.421 0.00 0.00 0.00 3.69
2811 2876 2.674220 GCTTGGGTGGGAGGGAGAG 61.674 68.421 0.00 0.00 0.00 3.20
2812 2877 2.610859 GCTTGGGTGGGAGGGAGA 60.611 66.667 0.00 0.00 0.00 3.71
2813 2878 3.732849 GGCTTGGGTGGGAGGGAG 61.733 72.222 0.00 0.00 0.00 4.30
2816 2881 2.893682 GATTCGGCTTGGGTGGGAGG 62.894 65.000 0.00 0.00 0.00 4.30
2817 2882 1.452108 GATTCGGCTTGGGTGGGAG 60.452 63.158 0.00 0.00 0.00 4.30
2901 2973 2.292828 AATTACTGGGCTTGCTGTGT 57.707 45.000 0.00 0.00 0.00 3.72
2933 3005 1.697432 ACGGAGACATTTCCCTTGACA 59.303 47.619 0.00 0.00 33.46 3.58
3024 3096 1.468127 CGATGCCACAGTGTAATTGCA 59.532 47.619 10.22 10.22 0.00 4.08
3027 3099 2.778299 ACACGATGCCACAGTGTAATT 58.222 42.857 5.37 0.00 45.92 1.40
3028 3100 2.472695 ACACGATGCCACAGTGTAAT 57.527 45.000 5.37 0.00 45.92 1.89
3079 3151 1.301244 CTCTCACACAAGCTGGCGT 60.301 57.895 0.00 0.00 0.00 5.68
3120 3192 4.799564 AGAGACTCCAGTTGAGACAATC 57.200 45.455 0.00 0.00 44.42 2.67
3121 3193 5.362430 GGATAGAGACTCCAGTTGAGACAAT 59.638 44.000 0.00 0.00 44.42 2.71
3122 3194 4.707448 GGATAGAGACTCCAGTTGAGACAA 59.293 45.833 0.00 0.00 44.42 3.18
3123 3195 4.017958 AGGATAGAGACTCCAGTTGAGACA 60.018 45.833 0.00 0.00 44.42 3.41
3124 3196 4.338118 CAGGATAGAGACTCCAGTTGAGAC 59.662 50.000 0.00 0.00 44.42 3.36
3125 3197 4.531854 CAGGATAGAGACTCCAGTTGAGA 58.468 47.826 0.00 0.00 44.42 3.27
3127 3199 3.027412 GCAGGATAGAGACTCCAGTTGA 58.973 50.000 0.00 0.00 35.08 3.18
3136 3208 1.202830 TCCGGAGAGCAGGATAGAGAC 60.203 57.143 0.00 0.00 33.20 3.36
3146 3218 0.976641 AGTTGTTGATCCGGAGAGCA 59.023 50.000 11.34 5.22 36.39 4.26
3147 3219 1.734465 CAAGTTGTTGATCCGGAGAGC 59.266 52.381 11.34 2.16 35.46 4.09
3160 3239 1.979855 TGCATGCTACCACAAGTTGT 58.020 45.000 20.33 1.64 0.00 3.32
3165 3244 3.286329 AGATCATGCATGCTACCACAA 57.714 42.857 22.25 2.12 0.00 3.33
3173 3252 4.082895 GGAGGTGAAATAGATCATGCATGC 60.083 45.833 22.25 11.82 0.00 4.06
3223 3309 6.691388 GCGACAGTAATTTTGAAAGAAACTGT 59.309 34.615 16.07 16.07 38.42 3.55
3310 3396 3.631686 GCATGGCATACACACAAATAGGA 59.368 43.478 0.00 0.00 0.00 2.94
3378 3464 2.124570 CCCCATGACTGGCCTTCG 60.125 66.667 3.32 0.00 41.64 3.79
3577 3663 1.212616 CGTTGATCTCCGAAGATGCC 58.787 55.000 0.00 0.00 42.46 4.40
3583 3669 2.508439 GCGCCGTTGATCTCCGAA 60.508 61.111 0.00 0.00 0.00 4.30
3646 3732 0.616111 AGATGAAGGCAGACGTCCCT 60.616 55.000 13.01 9.91 0.00 4.20
3704 3790 3.927142 CGAAGAAATAGCAAAGAGACCGT 59.073 43.478 0.00 0.00 0.00 4.83
3786 3875 4.468153 AGTCCCTAGCCTTTCAAGAACTAG 59.532 45.833 8.54 8.54 34.80 2.57
3867 3956 0.027716 GAGATGCAATGCACGCTCAG 59.972 55.000 25.34 0.00 43.04 3.35
3925 4014 1.164411 GACCATGTCCGTGAAATGCA 58.836 50.000 0.00 0.00 0.00 3.96
3949 4038 7.648112 GCGTATGTGATCATTTCTACAGTTCTA 59.352 37.037 0.00 0.00 35.70 2.10
3991 4095 1.611491 GCCATTGTCGACCAGGAAAAA 59.389 47.619 14.12 0.00 0.00 1.94
3992 4096 1.243902 GCCATTGTCGACCAGGAAAA 58.756 50.000 14.12 0.00 0.00 2.29
3993 4097 0.109532 TGCCATTGTCGACCAGGAAA 59.890 50.000 14.12 0.00 0.00 3.13
3994 4098 0.605319 GTGCCATTGTCGACCAGGAA 60.605 55.000 14.12 3.70 0.00 3.36
3995 4099 1.003839 GTGCCATTGTCGACCAGGA 60.004 57.895 14.12 0.00 0.00 3.86
3996 4100 0.677731 ATGTGCCATTGTCGACCAGG 60.678 55.000 14.12 12.99 0.00 4.45
3997 4101 1.131126 GAATGTGCCATTGTCGACCAG 59.869 52.381 14.12 2.42 0.00 4.00
3998 4102 1.164411 GAATGTGCCATTGTCGACCA 58.836 50.000 14.12 1.38 0.00 4.02
3999 4103 1.453155 AGAATGTGCCATTGTCGACC 58.547 50.000 14.12 0.00 0.00 4.79
4000 4104 2.029244 CGTAGAATGTGCCATTGTCGAC 59.971 50.000 9.11 9.11 0.00 4.20
4001 4105 2.267426 CGTAGAATGTGCCATTGTCGA 58.733 47.619 5.31 0.00 0.00 4.20
4002 4106 1.327460 CCGTAGAATGTGCCATTGTCG 59.673 52.381 5.31 7.23 0.00 4.35
4003 4107 2.627945 TCCGTAGAATGTGCCATTGTC 58.372 47.619 5.31 0.00 0.00 3.18
4004 4108 2.779755 TCCGTAGAATGTGCCATTGT 57.220 45.000 5.31 4.44 0.00 2.71
4005 4109 5.389830 CGATTATCCGTAGAATGTGCCATTG 60.390 44.000 5.31 0.00 0.00 2.82
4006 4110 4.690748 CGATTATCCGTAGAATGTGCCATT 59.309 41.667 0.67 0.67 0.00 3.16
4012 4116 4.617959 CACCACGATTATCCGTAGAATGT 58.382 43.478 0.00 0.00 41.29 2.71
4143 4247 5.502079 TCTTGAACCAAGTGTCCAAACTAA 58.498 37.500 6.59 0.00 41.66 2.24
4146 4250 3.489229 GCTCTTGAACCAAGTGTCCAAAC 60.489 47.826 6.59 0.00 41.66 2.93
4181 4285 8.027440 TGTTTCCAAAAAGAAAGACACAAATG 57.973 30.769 0.00 0.00 36.45 2.32
4186 4290 6.262601 TCGATGTTTCCAAAAAGAAAGACAC 58.737 36.000 0.00 0.00 36.45 3.67
4215 4320 3.055530 CACCTGAAGCTGGATCACTAGTT 60.056 47.826 0.00 0.00 0.00 2.24
4239 4344 1.287730 GGAGTGTCTCGTTGCTGCAG 61.288 60.000 10.11 10.11 0.00 4.41
4257 4362 3.401182 GAGGAATGAGAGCTTAGCATGG 58.599 50.000 7.07 0.00 0.00 3.66
4288 4393 6.421501 TGACAAAAAGTTACTCTTCGCGAATA 59.578 34.615 23.67 14.73 35.02 1.75
4500 4607 8.689972 TCATTATTTTTGGTTTGGTGCAAAAAT 58.310 25.926 8.26 8.26 44.38 1.82
4501 4608 8.055279 TCATTATTTTTGGTTTGGTGCAAAAA 57.945 26.923 0.00 0.00 39.69 1.94
4673 4788 7.121759 ACCAGTGTCAAAATTCCTCTGAATATG 59.878 37.037 0.00 0.00 40.34 1.78


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

AutoCloner maintained by Alex Coulton.