Multiple sequence alignment - TraesCS3B01G213400

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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 TraesCS3B01G213400 chr3B 100.000 6778 0 0 1 6778 252869236 252862459 0.000000e+00 12517.0
1 TraesCS3B01G213400 chr3B 82.755 864 79 33 5962 6778 807175770 807174930 0.000000e+00 706.0
2 TraesCS3B01G213400 chr3B 87.016 516 38 9 6263 6778 735933298 735933784 7.680000e-154 555.0
3 TraesCS3B01G213400 chr3B 92.806 278 19 1 5962 6239 735932949 735933225 1.060000e-107 401.0
4 TraesCS3B01G213400 chr3B 92.353 170 11 2 6609 6778 26578722 26578889 2.440000e-59 241.0
5 TraesCS3B01G213400 chr3B 90.625 64 5 1 1891 1954 333456655 333456717 4.360000e-12 84.2
6 TraesCS3B01G213400 chr3B 94.340 53 1 1 5910 5962 712812763 712812813 5.630000e-11 80.5
7 TraesCS3B01G213400 chr3B 94.872 39 1 1 5924 5962 764864256 764864293 7.340000e-05 60.2
8 TraesCS3B01G213400 chr3D 95.862 5873 171 32 1 5846 174081785 174075958 0.000000e+00 9433.0
9 TraesCS3B01G213400 chr3D 94.828 58 3 0 1893 1950 360629785 360629842 2.600000e-14 91.6
10 TraesCS3B01G213400 chr3D 100.000 40 0 0 5923 5962 134394486 134394447 2.620000e-09 75.0
11 TraesCS3B01G213400 chr3A 94.032 5898 258 43 1 5861 212774980 212769140 0.000000e+00 8855.0
12 TraesCS3B01G213400 chrUn 96.341 410 10 2 5437 5846 220586394 220585990 0.000000e+00 669.0
13 TraesCS3B01G213400 chrUn 92.063 63 4 1 1892 1954 115103360 115103421 3.370000e-13 87.9
14 TraesCS3B01G213400 chrUn 91.667 60 4 1 1896 1954 122416534 122416593 1.570000e-11 82.4
15 TraesCS3B01G213400 chr2B 81.040 865 79 56 5962 6778 679999127 679998300 1.620000e-170 610.0
16 TraesCS3B01G213400 chr2B 89.394 264 27 1 5956 6218 28472590 28472853 1.410000e-86 331.0
17 TraesCS3B01G213400 chr2B 98.462 65 1 0 5897 5961 703167925 703167989 1.540000e-21 115.0
18 TraesCS3B01G213400 chr1B 87.597 516 29 12 6263 6778 573061605 573061125 3.550000e-157 566.0
19 TraesCS3B01G213400 chr1B 92.832 279 19 1 5961 6239 573061955 573061678 2.940000e-108 403.0
20 TraesCS3B01G213400 chr1B 97.059 34 1 0 5929 5962 191411781 191411748 2.640000e-04 58.4
21 TraesCS3B01G213400 chr1D 90.385 260 21 4 5961 6218 326162045 326162302 8.420000e-89 339.0
22 TraesCS3B01G213400 chr1D 90.000 260 22 4 5961 6218 198905474 198905731 3.920000e-87 333.0
23 TraesCS3B01G213400 chr7A 88.803 259 28 1 5961 6218 178040834 178040576 3.950000e-82 316.0
24 TraesCS3B01G213400 chr7A 94.545 55 1 2 1897 1950 494988726 494988779 4.360000e-12 84.2
25 TraesCS3B01G213400 chr7D 87.209 258 32 1 5962 6218 561113636 561113893 6.650000e-75 292.0
26 TraesCS3B01G213400 chr7D 90.857 175 14 2 6605 6778 632396134 632395961 4.090000e-57 233.0
27 TraesCS3B01G213400 chr7D 92.073 164 8 4 4873 5032 500775618 500775456 6.840000e-55 226.0
28 TraesCS3B01G213400 chr5B 94.054 185 11 0 6594 6778 266359900 266359716 1.440000e-71 281.0
29 TraesCS3B01G213400 chr5B 93.678 174 11 0 6605 6778 266357336 266357163 1.870000e-65 261.0
30 TraesCS3B01G213400 chr5B 90.957 188 14 3 6591 6778 19695825 19695641 4.060000e-62 250.0
31 TraesCS3B01G213400 chr5B 76.326 528 79 37 6260 6778 367916743 367917233 2.440000e-59 241.0
32 TraesCS3B01G213400 chr5B 87.113 194 15 9 4872 5061 536228707 536228894 1.920000e-50 211.0
33 TraesCS3B01G213400 chr5B 98.039 51 1 0 1896 1946 184770951 184771001 9.360000e-14 89.8
34 TraesCS3B01G213400 chr4A 90.909 176 16 0 6603 6778 646544631 646544456 3.160000e-58 237.0
35 TraesCS3B01G213400 chr4A 92.025 163 9 2 4873 5031 97530155 97529993 6.840000e-55 226.0
36 TraesCS3B01G213400 chr5A 92.025 163 8 3 4873 5031 320214244 320214405 2.460000e-54 224.0
37 TraesCS3B01G213400 chr5A 91.071 168 9 5 4873 5036 558675658 558675493 8.850000e-54 222.0
38 TraesCS3B01G213400 chr5A 89.714 175 11 5 4861 5031 653299611 653299440 4.120000e-52 217.0
39 TraesCS3B01G213400 chr2A 89.888 178 11 5 4868 5041 184561319 184561145 8.850000e-54 222.0
40 TraesCS3B01G213400 chr1A 88.194 144 17 0 6635 6778 487689010 487688867 9.040000e-39 172.0
41 TraesCS3B01G213400 chr1A 100.000 82 0 0 5881 5962 465273549 465273630 1.180000e-32 152.0
42 TraesCS3B01G213400 chr7B 98.305 59 1 0 5904 5962 54198603 54198545 3.340000e-18 104.0
43 TraesCS3B01G213400 chr7B 90.541 74 3 4 1897 1970 142280367 142280298 2.010000e-15 95.3
44 TraesCS3B01G213400 chr6D 92.857 70 4 1 1896 1964 448432421 448432490 4.330000e-17 100.0
45 TraesCS3B01G213400 chr6D 85.075 67 6 3 1897 1963 168224580 168224518 1.580000e-06 65.8
46 TraesCS3B01G213400 chr2D 100.000 45 0 0 5918 5962 203778759 203778715 4.360000e-12 84.2
47 TraesCS3B01G213400 chr5D 100.000 31 0 0 5932 5962 300319829 300319859 2.640000e-04 58.4


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 TraesCS3B01G213400 chr3B 252862459 252869236 6777 True 12517.0 12517 100.0000 1 6778 1 chr3B.!!$R1 6777
1 TraesCS3B01G213400 chr3B 807174930 807175770 840 True 706.0 706 82.7550 5962 6778 1 chr3B.!!$R2 816
2 TraesCS3B01G213400 chr3B 735932949 735933784 835 False 478.0 555 89.9110 5962 6778 2 chr3B.!!$F5 816
3 TraesCS3B01G213400 chr3D 174075958 174081785 5827 True 9433.0 9433 95.8620 1 5846 1 chr3D.!!$R2 5845
4 TraesCS3B01G213400 chr3A 212769140 212774980 5840 True 8855.0 8855 94.0320 1 5861 1 chr3A.!!$R1 5860
5 TraesCS3B01G213400 chr2B 679998300 679999127 827 True 610.0 610 81.0400 5962 6778 1 chr2B.!!$R1 816
6 TraesCS3B01G213400 chr1B 573061125 573061955 830 True 484.5 566 90.2145 5961 6778 2 chr1B.!!$R2 817
7 TraesCS3B01G213400 chr5B 266357163 266359900 2737 True 271.0 281 93.8660 6594 6778 2 chr5B.!!$R2 184

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
424 426 0.031449 TTTTGGCTGTTTGCGTAGGC 59.969 50.000 0.00 0.00 44.05 3.93 F
997 1003 0.176910 TCAGGTTTGAGCACACACGA 59.823 50.000 0.00 0.00 0.00 4.35 F
1500 1506 0.950836 GCACATGCACCAGTTACACA 59.049 50.000 0.00 0.00 41.59 3.72 F
2269 2282 2.893637 CCAAGGTGATCACTCCGTAAG 58.106 52.381 24.50 8.48 35.16 2.34 F
3058 3087 1.074889 ACAGGTACATGGTTGGGGAAC 59.925 52.381 12.79 0.00 0.00 3.62 F
4124 4169 0.681733 CTCCGACATGGACCCTATGG 59.318 60.000 0.00 0.00 43.74 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 2051 0.305922 GTGTCGGCAGCTGCATTATC 59.694 55.000 37.63 20.18 44.36 1.75 R
2513 2527 0.395862 GTCCGATGGAGGTGAGAGGA 60.396 60.000 0.00 0.00 29.39 3.71 R
2514 2528 0.396417 AGTCCGATGGAGGTGAGAGG 60.396 60.000 0.00 0.00 29.39 3.69 R
3339 3368 0.678048 GCTTTCTGCCGACAGGGATT 60.678 55.000 0.00 0.00 44.59 3.01 R
4567 4614 0.387878 GCGACAGTGTCTCTCCTGTG 60.388 60.000 20.64 4.13 41.80 3.66 R
6012 6077 1.541147 CATGTGTGGTAAAGTGCAGGG 59.459 52.381 0.00 0.00 0.00 4.45 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
126 128 0.031994 TTTCTTGCGGCCTTTCAAGC 59.968 50.000 18.69 7.57 39.47 4.01
170 172 2.597217 TTTGGCTGCTGGAACGGG 60.597 61.111 0.00 0.00 33.56 5.28
424 426 0.031449 TTTTGGCTGTTTGCGTAGGC 59.969 50.000 0.00 0.00 44.05 3.93
630 635 8.617290 TTCTTACATCCTGTTCCTTTTACTTC 57.383 34.615 0.00 0.00 0.00 3.01
723 728 6.122277 TGAACTTCCATCATATCTGTTTCCC 58.878 40.000 0.00 0.00 0.00 3.97
777 782 8.579863 CCCCCATATTCTGAGCTAAAATTTAAG 58.420 37.037 0.00 0.00 0.00 1.85
997 1003 0.176910 TCAGGTTTGAGCACACACGA 59.823 50.000 0.00 0.00 0.00 4.35
1359 1365 4.931601 TGTATGTCATTCTTCTGCACTCAC 59.068 41.667 0.00 0.00 0.00 3.51
1470 1476 8.397906 TCAAATTCCATCAGATACGACATTTTC 58.602 33.333 0.00 0.00 0.00 2.29
1500 1506 0.950836 GCACATGCACCAGTTACACA 59.049 50.000 0.00 0.00 41.59 3.72
1722 1734 4.995124 TGAAGCGGAGAGTAACTGAATAC 58.005 43.478 0.00 0.00 0.00 1.89
1791 1803 7.265673 TGGGAGATTTCTTAACAATCTAGACG 58.734 38.462 0.00 0.00 40.43 4.18
1891 1903 7.120579 TGTGTACAACTTCTTCATGTTCAGTTT 59.879 33.333 0.00 0.00 0.00 2.66
2269 2282 2.893637 CCAAGGTGATCACTCCGTAAG 58.106 52.381 24.50 8.48 35.16 2.34
2377 2390 6.711277 AGAGAAGCAACCACTGTATATGAAA 58.289 36.000 0.00 0.00 0.00 2.69
2416 2429 6.892485 TGGATTCATGAACTGATGATGTAGT 58.108 36.000 11.07 0.00 32.35 2.73
2419 2432 7.496920 GGATTCATGAACTGATGATGTAGTTGA 59.503 37.037 11.07 0.00 37.27 3.18
2426 2439 4.646945 ACTGATGATGTAGTTGATCTCGGT 59.353 41.667 0.00 0.00 0.00 4.69
2503 2517 4.351111 ACACCTTTTGACTCCTACCATCTT 59.649 41.667 0.00 0.00 0.00 2.40
2504 2518 4.938226 CACCTTTTGACTCCTACCATCTTC 59.062 45.833 0.00 0.00 0.00 2.87
2505 2519 4.019231 ACCTTTTGACTCCTACCATCTTCC 60.019 45.833 0.00 0.00 0.00 3.46
2506 2520 4.226168 CCTTTTGACTCCTACCATCTTCCT 59.774 45.833 0.00 0.00 0.00 3.36
2507 2521 5.425539 CCTTTTGACTCCTACCATCTTCCTA 59.574 44.000 0.00 0.00 0.00 2.94
2508 2522 6.070194 CCTTTTGACTCCTACCATCTTCCTAA 60.070 42.308 0.00 0.00 0.00 2.69
2509 2523 6.945636 TTTGACTCCTACCATCTTCCTAAA 57.054 37.500 0.00 0.00 0.00 1.85
2510 2524 7.510675 TTTGACTCCTACCATCTTCCTAAAT 57.489 36.000 0.00 0.00 0.00 1.40
2511 2525 7.510675 TTGACTCCTACCATCTTCCTAAATT 57.489 36.000 0.00 0.00 0.00 1.82
2512 2526 8.618240 TTGACTCCTACCATCTTCCTAAATTA 57.382 34.615 0.00 0.00 0.00 1.40
2513 2527 8.798975 TGACTCCTACCATCTTCCTAAATTAT 57.201 34.615 0.00 0.00 0.00 1.28
2514 2528 8.871125 TGACTCCTACCATCTTCCTAAATTATC 58.129 37.037 0.00 0.00 0.00 1.75
2515 2529 8.208575 ACTCCTACCATCTTCCTAAATTATCC 57.791 38.462 0.00 0.00 0.00 2.59
2516 2530 8.019652 ACTCCTACCATCTTCCTAAATTATCCT 58.980 37.037 0.00 0.00 0.00 3.24
2517 2531 8.437274 TCCTACCATCTTCCTAAATTATCCTC 57.563 38.462 0.00 0.00 0.00 3.71
2528 2557 6.498651 TCCTAAATTATCCTCTCACCTCCATC 59.501 42.308 0.00 0.00 0.00 3.51
2881 2910 8.052748 TGTTTGCTCTATTACATGGAATAAGGT 58.947 33.333 11.55 0.00 0.00 3.50
2901 2930 2.191128 AATGGGACTGCACTCTTGAC 57.809 50.000 0.00 0.00 0.00 3.18
3058 3087 1.074889 ACAGGTACATGGTTGGGGAAC 59.925 52.381 12.79 0.00 0.00 3.62
3339 3368 7.014518 CACAGGGATGCTTCCAATGAAATTATA 59.985 37.037 22.36 0.00 44.60 0.98
3533 3562 1.415289 CATCTCTGAGCCATGGCAGTA 59.585 52.381 37.18 21.38 44.88 2.74
3677 3707 4.274950 TCTTGTTGTCACCGGAAATTCTTC 59.725 41.667 9.46 0.00 0.00 2.87
3781 3811 1.327303 AAAAGGCATGGCACTCGAAA 58.673 45.000 22.64 0.00 0.00 3.46
3910 3943 5.827568 TTCTTTAAAACCGTAGTAGTGCG 57.172 39.130 0.49 0.49 0.00 5.34
4017 4061 7.424803 CATCTTCATCTTACTACAGGAGACAG 58.575 42.308 0.00 0.00 0.00 3.51
4089 4133 1.328680 GCGACTGCATGAATGGTGTAG 59.671 52.381 0.00 0.00 42.15 2.74
4093 4137 4.194640 GACTGCATGAATGGTGTAGTGAT 58.805 43.478 0.00 0.00 41.58 3.06
4094 4138 3.943381 ACTGCATGAATGGTGTAGTGATG 59.057 43.478 0.00 0.00 40.32 3.07
4124 4169 0.681733 CTCCGACATGGACCCTATGG 59.318 60.000 0.00 0.00 43.74 2.74
4173 4218 5.780958 AAGAGGAATTAGTAGCCCACTTT 57.219 39.130 0.00 0.00 38.80 2.66
4229 4274 3.792956 GCAATTCACATTGATGCGGTTAG 59.207 43.478 0.00 0.00 42.35 2.34
4234 4279 1.024271 CATTGATGCGGTTAGGTGGG 58.976 55.000 0.00 0.00 0.00 4.61
4439 4485 1.106285 GGTCATCCCACTGCATTTCC 58.894 55.000 0.00 0.00 0.00 3.13
4462 4508 3.616219 TGCGGCACCTCATTATAGTTTT 58.384 40.909 0.00 0.00 0.00 2.43
4567 4614 9.317936 CCATTTTAAGCCCATCTTATTTTTCTC 57.682 33.333 0.00 0.00 37.14 2.87
4605 4652 7.715249 ACTGTCGCATTGTATTTATGTAGGAAT 59.285 33.333 0.00 0.00 0.00 3.01
4606 4653 7.860613 TGTCGCATTGTATTTATGTAGGAATG 58.139 34.615 0.00 0.00 0.00 2.67
4607 4654 7.041440 TGTCGCATTGTATTTATGTAGGAATGG 60.041 37.037 0.00 0.00 0.00 3.16
4632 4685 5.555966 TGTAGGTTCACATTAACTGCATCA 58.444 37.500 0.00 0.00 0.00 3.07
4653 4706 5.901552 TCAATCTCTGTTGTTTTGGGTTTC 58.098 37.500 0.00 0.00 0.00 2.78
4662 4715 7.440255 TCTGTTGTTTTGGGTTTCGTTTAAAAA 59.560 29.630 0.00 0.00 0.00 1.94
4778 4831 5.713389 CGACATATGTAGGGAGGTAACCATA 59.287 44.000 8.71 0.00 37.17 2.74
4851 4906 9.629878 TTGTTTAGTAAAAGATGTCCTTTGGTA 57.370 29.630 0.00 0.00 43.90 3.25
4882 4937 5.476950 TTCTTAGTATGGTACTCCCTCCA 57.523 43.478 0.00 0.00 40.14 3.86
5198 5261 4.397348 CCAGCTTTAGTTGGCCGT 57.603 55.556 0.00 0.00 39.51 5.68
5485 5548 7.042797 TCATTATTGAATTGCCTTTCTAGCC 57.957 36.000 0.00 0.00 0.00 3.93
5540 5605 9.609950 GAGTAGAAATATTACCACGATGTAGTC 57.390 37.037 0.00 0.00 0.00 2.59
5652 5717 6.904463 ATGCCATATCACAATTCATAGCAA 57.096 33.333 0.00 0.00 0.00 3.91
5686 5751 4.524316 TGTTGCATTGGAAGAATCCTTG 57.476 40.909 0.00 0.00 46.70 3.61
5784 5849 5.991933 TTTGGATAAAGCCTAATGCACAA 57.008 34.783 0.00 0.00 44.83 3.33
5949 6014 3.953542 AGGGAAAATCCATCCTACCAC 57.046 47.619 0.00 0.00 38.64 4.16
5950 6015 3.474920 AGGGAAAATCCATCCTACCACT 58.525 45.455 0.00 0.00 38.64 4.00
5951 6016 3.459969 AGGGAAAATCCATCCTACCACTC 59.540 47.826 0.00 0.00 38.64 3.51
5952 6017 3.467803 GGAAAATCCATCCTACCACTCG 58.532 50.000 0.00 0.00 36.28 4.18
5953 6018 3.467803 GAAAATCCATCCTACCACTCGG 58.532 50.000 0.00 0.00 38.77 4.63
5954 6019 6.206135 GGAAAATCCATCCTACCACTCGGT 62.206 50.000 0.00 0.00 42.28 4.69
5979 6044 8.684520 GTGGTAGTTGTTAGATGTGTATAGTCT 58.315 37.037 0.00 0.00 0.00 3.24
6053 6119 6.920448 ACATGTATATGTATTGGCCTTTGGCT 60.920 38.462 3.32 0.00 46.06 4.75
6054 6120 7.694042 ACATGTATATGTATTGGCCTTTGGCTA 60.694 37.037 3.32 0.00 46.06 3.93
6064 6130 3.699779 GCCTTTGGCTATCAGTAAAGC 57.300 47.619 0.73 0.00 46.69 3.51
6066 6132 3.313803 GCCTTTGGCTATCAGTAAAGCTC 59.686 47.826 0.73 0.00 46.69 4.09
6075 6141 4.550076 ATCAGTAAAGCTCAGTTGCTCT 57.450 40.909 0.00 0.00 43.24 4.09
6239 6311 0.682209 GTCCACGACCCAGCTACCTA 60.682 60.000 0.00 0.00 0.00 3.08
6245 6334 1.508256 GACCCAGCTACCTACCCATT 58.492 55.000 0.00 0.00 0.00 3.16
6250 6339 1.212935 CAGCTACCTACCCATTTGCCT 59.787 52.381 0.00 0.00 0.00 4.75
6383 6503 4.093291 CTCTGCTCGCCTGGCCTT 62.093 66.667 14.12 0.00 0.00 4.35
6385 6505 4.711949 CTGCTCGCCTGGCCTTGT 62.712 66.667 14.12 0.00 0.00 3.16
6387 6507 4.704833 GCTCGCCTGGCCTTGTGA 62.705 66.667 14.12 6.22 0.00 3.58
6388 6508 2.435586 CTCGCCTGGCCTTGTGAG 60.436 66.667 14.12 17.39 33.30 3.51
6389 6509 3.241530 TCGCCTGGCCTTGTGAGT 61.242 61.111 14.12 0.00 0.00 3.41
6493 6617 2.334653 GCTCTCCTCGATCCAGCG 59.665 66.667 0.00 0.00 0.00 5.18
6494 6618 2.190170 GCTCTCCTCGATCCAGCGA 61.190 63.158 0.00 0.00 38.74 4.93
6581 6715 0.958822 GTGCGTGGGATTTCCTGTTT 59.041 50.000 0.00 0.00 36.20 2.83
6586 6720 1.810755 GTGGGATTTCCTGTTTCCGTC 59.189 52.381 0.00 0.00 36.20 4.79
6642 9474 5.422970 AGAGAGAGAGAATCAGCATGTCTTT 59.577 40.000 0.00 0.00 37.82 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 128 2.677971 CGTCTCCGCCATTAACAGG 58.322 57.895 0.00 0.00 0.00 4.00
184 186 4.096833 TCTGAAAATTGCATCGATTCCCTG 59.903 41.667 0.00 0.00 0.00 4.45
249 251 7.700656 AGAAACATAAAACTTGAAAGTGGAACG 59.299 33.333 0.00 0.00 45.86 3.95
315 317 1.122632 TTACTCTCCGCCACCAACCA 61.123 55.000 0.00 0.00 0.00 3.67
424 426 0.528924 TCCTATGTCCACACGAACCG 59.471 55.000 0.00 0.00 0.00 4.44
729 734 4.282496 GAGAGAGAACTGTTCCATCCCTA 58.718 47.826 16.48 0.00 0.00 3.53
730 735 3.103742 GAGAGAGAACTGTTCCATCCCT 58.896 50.000 16.48 5.34 0.00 4.20
777 782 4.083696 CCTGAAGCAAAATTGAATGGTTGC 60.084 41.667 15.27 15.27 45.29 4.17
997 1003 4.700213 CGTTCCACTGAAGATACCCATTTT 59.300 41.667 0.00 0.00 0.00 1.82
1047 1053 2.884997 TAGCCCATTCCGCGCAATGT 62.885 55.000 20.62 5.85 32.61 2.71
1221 1227 4.103153 ACATACCCAACTATCCAGGTCATG 59.897 45.833 0.00 0.00 33.70 3.07
1359 1365 1.892209 AGGTTAAACAAGTCCCTGCG 58.108 50.000 0.00 0.00 0.00 5.18
1470 1476 3.197790 CATGTGCCTCGCGGAAGG 61.198 66.667 6.13 8.08 39.62 3.46
1722 1734 9.256477 TGCTTGGAACTATTATATTAGTGTTCG 57.744 33.333 7.83 0.15 35.88 3.95
1979 1992 6.628919 AGGTAATTATTTAATCCCACGCAC 57.371 37.500 0.00 0.00 0.00 5.34
2038 2051 0.305922 GTGTCGGCAGCTGCATTATC 59.694 55.000 37.63 20.18 44.36 1.75
2117 2130 4.101585 AGTTCTCAGATGACAGAAACCACA 59.898 41.667 0.00 0.00 30.38 4.17
2416 2429 4.819630 ACTACTTTGCAAAACCGAGATCAA 59.180 37.500 13.84 0.00 0.00 2.57
2419 2432 5.767816 AAACTACTTTGCAAAACCGAGAT 57.232 34.783 13.84 0.45 0.00 2.75
2426 2439 8.053026 TGGTAACACTAAACTACTTTGCAAAA 57.947 30.769 13.84 0.00 46.17 2.44
2503 2517 5.788430 TGGAGGTGAGAGGATAATTTAGGA 58.212 41.667 0.00 0.00 0.00 2.94
2504 2518 6.573289 CGATGGAGGTGAGAGGATAATTTAGG 60.573 46.154 0.00 0.00 0.00 2.69
2505 2519 6.393990 CGATGGAGGTGAGAGGATAATTTAG 58.606 44.000 0.00 0.00 0.00 1.85
2506 2520 5.246203 CCGATGGAGGTGAGAGGATAATTTA 59.754 44.000 0.00 0.00 0.00 1.40
2507 2521 4.040952 CCGATGGAGGTGAGAGGATAATTT 59.959 45.833 0.00 0.00 0.00 1.82
2508 2522 3.580458 CCGATGGAGGTGAGAGGATAATT 59.420 47.826 0.00 0.00 0.00 1.40
2509 2523 3.169099 CCGATGGAGGTGAGAGGATAAT 58.831 50.000 0.00 0.00 0.00 1.28
2510 2524 2.177016 TCCGATGGAGGTGAGAGGATAA 59.823 50.000 0.00 0.00 0.00 1.75
2511 2525 1.780919 TCCGATGGAGGTGAGAGGATA 59.219 52.381 0.00 0.00 0.00 2.59
2512 2526 0.558220 TCCGATGGAGGTGAGAGGAT 59.442 55.000 0.00 0.00 0.00 3.24
2513 2527 0.395862 GTCCGATGGAGGTGAGAGGA 60.396 60.000 0.00 0.00 29.39 3.71
2514 2528 0.396417 AGTCCGATGGAGGTGAGAGG 60.396 60.000 0.00 0.00 29.39 3.69
2515 2529 1.950909 GTAGTCCGATGGAGGTGAGAG 59.049 57.143 0.00 0.00 29.39 3.20
2516 2530 1.283905 TGTAGTCCGATGGAGGTGAGA 59.716 52.381 0.00 0.00 29.39 3.27
2517 2531 1.763968 TGTAGTCCGATGGAGGTGAG 58.236 55.000 0.00 0.00 29.39 3.51
2528 2557 8.425577 AGACTGAAATCATAAATTGTAGTCCG 57.574 34.615 0.00 0.00 34.19 4.79
2800 2829 7.035612 GGACACTAATTTGCTTTAAGGAATGG 58.964 38.462 0.00 0.00 0.00 3.16
2881 2910 2.353704 CGTCAAGAGTGCAGTCCCATTA 60.354 50.000 18.04 0.00 0.00 1.90
2901 2930 3.184541 CTGTAACATCCCGAAGTAACCG 58.815 50.000 0.00 0.00 0.00 4.44
3058 3087 3.354089 ACTTTTGTTGTCTGGCGATTG 57.646 42.857 0.00 0.00 0.00 2.67
3339 3368 0.678048 GCTTTCTGCCGACAGGGATT 60.678 55.000 0.00 0.00 44.59 3.01
3533 3562 4.734266 AGAAAGCTTCCAATTCCACTTCT 58.266 39.130 0.00 0.00 0.00 2.85
3677 3707 2.034812 GCACCAGGACTAAGTATCGGAG 59.965 54.545 0.00 0.00 0.00 4.63
4017 4061 6.738114 TGATGACAAATGAGAAAAGTGGAAC 58.262 36.000 0.00 0.00 0.00 3.62
4089 4133 4.101448 AGACAGCGGGGCCATCAC 62.101 66.667 4.39 0.00 0.00 3.06
4146 4191 4.658901 TGGGCTACTAATTCCTCTTAAGGG 59.341 45.833 1.85 0.00 43.56 3.95
4229 4274 8.584063 TTTTATTTTAGTATCCACTTCCCACC 57.416 34.615 0.00 0.00 36.14 4.61
4286 4331 4.594123 TGACAATCAACAACTAGACCGA 57.406 40.909 0.00 0.00 0.00 4.69
4327 4372 3.321111 AGTTCGAGTTACCTCTCTTGCAA 59.679 43.478 0.00 0.00 35.43 4.08
4439 4485 2.838736 ACTATAATGAGGTGCCGCAAG 58.161 47.619 0.00 0.00 0.00 4.01
4462 4508 4.569015 GGAAGGTAGGGGCATCTTTTGTTA 60.569 45.833 0.00 0.00 0.00 2.41
4567 4614 0.387878 GCGACAGTGTCTCTCCTGTG 60.388 60.000 20.64 4.13 41.80 3.66
4582 4629 7.172532 TCCATTCCTACATAAATACAATGCGAC 59.827 37.037 0.00 0.00 0.00 5.19
4605 4652 4.941263 GCAGTTAATGTGAACCTACATCCA 59.059 41.667 0.00 0.00 40.24 3.41
4606 4653 4.941263 TGCAGTTAATGTGAACCTACATCC 59.059 41.667 0.00 0.00 40.24 3.51
4607 4654 6.316140 TGATGCAGTTAATGTGAACCTACATC 59.684 38.462 0.00 0.00 40.24 3.06
4632 4685 4.401202 ACGAAACCCAAAACAACAGAGATT 59.599 37.500 0.00 0.00 0.00 2.40
4662 4715 8.680903 CAGATAAGTTACCAGCATCAGAAATTT 58.319 33.333 0.00 0.00 0.00 1.82
4664 4717 7.497249 GTCAGATAAGTTACCAGCATCAGAAAT 59.503 37.037 0.00 0.00 0.00 2.17
4870 4925 6.954352 ATATTTAGGAATGGAGGGAGTACC 57.046 41.667 0.00 0.00 40.67 3.34
4960 5017 5.221521 TGGACTACGTACGGATGTATAGACT 60.222 44.000 21.06 0.00 32.11 3.24
5003 5066 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
5004 5067 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
5198 5261 9.253832 ACAAATGGATATGAGAACCATAAAACA 57.746 29.630 0.00 0.00 42.59 2.83
5485 5548 3.750130 CCGGAGCCTTATTTGAGATGATG 59.250 47.826 0.00 0.00 0.00 3.07
5652 5717 6.289834 TCCAATGCAACAACTGATTGAAATT 58.710 32.000 0.00 0.00 39.30 1.82
5923 5988 9.004231 GTGGTAGGATGGATTTTCCCTATATAT 57.996 37.037 0.00 0.00 35.03 0.86
5924 5989 8.191110 AGTGGTAGGATGGATTTTCCCTATATA 58.809 37.037 0.00 0.00 35.03 0.86
5925 5990 7.031917 AGTGGTAGGATGGATTTTCCCTATAT 58.968 38.462 0.00 0.00 35.03 0.86
5926 5991 6.399013 AGTGGTAGGATGGATTTTCCCTATA 58.601 40.000 0.00 0.00 35.03 1.31
5927 5992 5.235534 AGTGGTAGGATGGATTTTCCCTAT 58.764 41.667 0.00 0.00 35.03 2.57
5928 5993 4.641868 AGTGGTAGGATGGATTTTCCCTA 58.358 43.478 0.00 0.00 35.03 3.53
5929 5994 3.459969 GAGTGGTAGGATGGATTTTCCCT 59.540 47.826 0.00 0.00 35.03 4.20
5930 5995 3.744530 CGAGTGGTAGGATGGATTTTCCC 60.745 52.174 0.00 0.00 35.03 3.97
5931 5996 3.467803 CGAGTGGTAGGATGGATTTTCC 58.532 50.000 0.00 0.00 36.96 3.13
5932 5997 3.467803 CCGAGTGGTAGGATGGATTTTC 58.532 50.000 0.00 0.00 0.00 2.29
5933 5998 3.560636 CCGAGTGGTAGGATGGATTTT 57.439 47.619 0.00 0.00 0.00 1.82
5947 6012 3.928727 TCTAACAACTACCACCGAGTG 57.071 47.619 0.00 0.00 0.00 3.51
5948 6013 3.830755 ACATCTAACAACTACCACCGAGT 59.169 43.478 0.00 0.00 0.00 4.18
5949 6014 4.174009 CACATCTAACAACTACCACCGAG 58.826 47.826 0.00 0.00 0.00 4.63
5950 6015 3.575256 ACACATCTAACAACTACCACCGA 59.425 43.478 0.00 0.00 0.00 4.69
5951 6016 3.921677 ACACATCTAACAACTACCACCG 58.078 45.455 0.00 0.00 0.00 4.94
5952 6017 7.779073 ACTATACACATCTAACAACTACCACC 58.221 38.462 0.00 0.00 0.00 4.61
5953 6018 8.684520 AGACTATACACATCTAACAACTACCAC 58.315 37.037 0.00 0.00 0.00 4.16
5954 6019 8.818622 AGACTATACACATCTAACAACTACCA 57.181 34.615 0.00 0.00 0.00 3.25
5955 6020 9.122779 AGAGACTATACACATCTAACAACTACC 57.877 37.037 0.00 0.00 0.00 3.18
5979 6044 5.640158 ACAATGGGGATATACCGAAAAGA 57.360 39.130 0.00 0.00 40.11 2.52
6012 6077 1.541147 CATGTGTGGTAAAGTGCAGGG 59.459 52.381 0.00 0.00 0.00 4.45
6023 6089 5.070001 GGCCAATACATATACATGTGTGGT 58.930 41.667 9.11 7.72 45.12 4.16
6053 6119 5.667539 AGAGCAACTGAGCTTTACTGATA 57.332 39.130 0.00 0.00 46.75 2.15
6054 6120 4.550076 AGAGCAACTGAGCTTTACTGAT 57.450 40.909 0.00 0.00 46.75 2.90
6059 6125 5.804639 TGGATAAAGAGCAACTGAGCTTTA 58.195 37.500 0.00 0.00 46.75 1.85
6064 6130 5.163683 CCATGTTGGATAAAGAGCAACTGAG 60.164 44.000 0.00 0.00 40.96 3.35
6066 6132 4.460382 ACCATGTTGGATAAAGAGCAACTG 59.540 41.667 0.00 0.00 40.96 3.16
6075 6141 9.559732 CTAACATCTGATACCATGTTGGATAAA 57.440 33.333 7.41 0.00 41.57 1.40
6338 6458 3.198489 GGCGGCAACAGCTAGAGC 61.198 66.667 3.07 0.00 42.49 4.09
6339 6459 2.887568 CGGCGGCAACAGCTAGAG 60.888 66.667 10.53 0.00 36.55 2.43
6340 6460 4.451150 CCGGCGGCAACAGCTAGA 62.451 66.667 15.42 0.00 36.55 2.43
6382 6502 2.661537 CCGCACGCTCACTCACAA 60.662 61.111 0.00 0.00 0.00 3.33
6383 6503 4.662961 CCCGCACGCTCACTCACA 62.663 66.667 0.00 0.00 0.00 3.58
6472 6596 2.069465 CTGGATCGAGGAGAGCGTGG 62.069 65.000 0.00 0.00 35.79 4.94
6581 6715 1.540267 CTCTCTTTTGGAGTCGACGGA 59.460 52.381 10.46 0.00 42.40 4.69
6586 6720 4.006989 TCTCTCTCTCTCTTTTGGAGTCG 58.993 47.826 0.00 0.00 42.40 4.18


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

AutoCloner maintained by Alex Coulton.