Multiple sequence alignment - TraesCS7B01G413900

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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 TraesCS7B01G413900 chr7B 100.000 3769 0 0 1 3769 681858269 681854501 0.000000e+00 6961.0
1 TraesCS7B01G413900 chr7A 91.527 3045 147 49 788 3769 693861205 693858209 0.000000e+00 4091.0
2 TraesCS7B01G413900 chr7D 91.119 3074 145 53 575 3592 602098126 602095125 0.000000e+00 4047.0
3 TraesCS7B01G413900 chr7D 93.039 589 22 5 3 575 602099109 602098524 0.000000e+00 843.0
4 TraesCS7B01G413900 chr7D 96.212 132 3 2 3638 3769 602095132 602095003 8.200000e-52 215.0
5 TraesCS7B01G413900 chr6D 79.097 775 124 30 1924 2688 105558398 105557652 2.020000e-137 499.0
6 TraesCS7B01G413900 chr6D 92.683 82 6 0 1131 1212 105559070 105558989 6.610000e-23 119.0
7 TraesCS7B01G413900 chr6B 78.452 775 129 30 1924 2688 192095985 192096731 4.410000e-129 472.0
8 TraesCS7B01G413900 chr6A 91.463 82 7 0 1131 1212 127612880 127612799 3.080000e-21 113.0
9 TraesCS7B01G413900 chr1B 83.193 119 11 6 1486 1604 452787454 452787563 2.400000e-17 100.0
10 TraesCS7B01G413900 chr3A 84.946 93 13 1 3665 3757 674133543 674133634 4.010000e-15 93.5


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 TraesCS7B01G413900 chr7B 681854501 681858269 3768 True 6961.000000 6961 100.000000 1 3769 1 chr7B.!!$R1 3768
1 TraesCS7B01G413900 chr7A 693858209 693861205 2996 True 4091.000000 4091 91.527000 788 3769 1 chr7A.!!$R1 2981
2 TraesCS7B01G413900 chr7D 602095003 602099109 4106 True 1701.666667 4047 93.456667 3 3769 3 chr7D.!!$R1 3766
3 TraesCS7B01G413900 chr6D 105557652 105559070 1418 True 309.000000 499 85.890000 1131 2688 2 chr6D.!!$R1 1557
4 TraesCS7B01G413900 chr6B 192095985 192096731 746 False 472.000000 472 78.452000 1924 2688 1 chr6B.!!$F1 764

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
489 491 0.320374 TTAGACACAGGTTGAGGCCG 59.680 55.0 0.0 0.0 0.0 6.13 F
1805 2445 0.458543 CGCAGCCTAATCGCCGATAT 60.459 55.0 0.0 0.0 0.0 1.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 2449 0.032952 ACTCGTAAGCAAGCACGGAA 59.967 50.0 5.31 0.0 38.66 4.30 R
3564 4280 0.320374 CGGACTGGTTCTGGTAGCAA 59.680 55.0 0.00 0.0 0.00 3.91 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
22 23 3.134081 AGAAAACTCACTCGGAAGAACCA 59.866 43.478 0.00 0.00 41.32 3.67
32 33 3.138304 TCGGAAGAACCAAACATGAGTG 58.862 45.455 0.00 0.00 38.90 3.51
55 56 5.425217 TGAGTGGTTTCTATAGCATCCTCAA 59.575 40.000 0.00 0.00 30.52 3.02
76 77 5.987953 TCAAATGATCGAATAGCTCTTGGAG 59.012 40.000 0.00 0.00 0.00 3.86
77 78 4.533919 ATGATCGAATAGCTCTTGGAGG 57.466 45.455 0.00 0.00 0.00 4.30
78 79 3.300388 TGATCGAATAGCTCTTGGAGGT 58.700 45.455 0.00 4.69 43.16 3.85
79 80 3.706594 TGATCGAATAGCTCTTGGAGGTT 59.293 43.478 4.60 0.00 40.94 3.50
80 81 3.802948 TCGAATAGCTCTTGGAGGTTC 57.197 47.619 4.60 0.00 40.94 3.62
81 82 2.099263 TCGAATAGCTCTTGGAGGTTCG 59.901 50.000 11.92 11.92 40.94 3.95
100 101 4.760530 TCGTGTTAGTAGGCTACCTCTA 57.239 45.455 20.67 4.60 34.61 2.43
151 152 1.343465 GGAGTTGGAGAGTCGGAACAA 59.657 52.381 5.22 0.00 0.00 2.83
161 162 4.899502 AGAGTCGGAACAATTCAAGACAT 58.100 39.130 14.53 4.79 0.00 3.06
172 173 9.322773 GAACAATTCAAGACATGATGAGATAGA 57.677 33.333 0.00 0.00 38.03 1.98
239 240 2.869233 TTTGCAAGAAAAGCTTCGCT 57.131 40.000 0.00 0.00 42.56 4.93
271 272 6.037786 TCGACATCCCCATTTGATAGTATC 57.962 41.667 2.97 2.97 0.00 2.24
348 349 2.211250 AGCATGCCAACACTTGATCT 57.789 45.000 15.66 0.00 0.00 2.75
431 432 8.844244 AGGTTGATCATTATGTAGAGAAAATGC 58.156 33.333 0.00 0.00 30.99 3.56
441 442 6.757897 TGTAGAGAAAATGCTTGTAATGGG 57.242 37.500 0.00 0.00 0.00 4.00
477 479 1.610886 GGGGGTCAAGCAGTTAGACAC 60.611 57.143 0.00 0.00 34.99 3.67
489 491 0.320374 TTAGACACAGGTTGAGGCCG 59.680 55.000 0.00 0.00 0.00 6.13
497 499 1.228154 GGTTGAGGCCGTGAAGGTT 60.228 57.895 0.00 0.00 43.70 3.50
498 500 1.235281 GGTTGAGGCCGTGAAGGTTC 61.235 60.000 0.00 0.00 43.70 3.62
538 555 9.691362 CCTTCTTATATTCTCTCAAAGTCTAGC 57.309 37.037 0.00 0.00 0.00 3.42
634 1049 9.268282 AGTCACTCTGGTTATCTTAGGAAAATA 57.732 33.333 0.00 0.00 0.00 1.40
668 1083 9.909644 TTAGCTAAATTCACTACGGATATCTTC 57.090 33.333 2.97 0.00 0.00 2.87
678 1093 8.582437 TCACTACGGATATCTTCGGAAAATATT 58.418 33.333 2.05 0.00 0.00 1.28
719 1135 4.015872 ACATACACACACGGATTTTCCT 57.984 40.909 0.00 0.00 33.30 3.36
733 1149 4.945543 GGATTTTCCTAACACATTACCGGT 59.054 41.667 13.98 13.98 32.53 5.28
738 1154 3.451540 TCCTAACACATTACCGGTGCATA 59.548 43.478 19.93 0.00 39.87 3.14
751 1167 0.748005 GTGCATAACCGCCAGTGGAT 60.748 55.000 15.20 0.00 0.00 3.41
1030 1471 1.227497 CCCTCATCGGAGCAGAAGC 60.227 63.158 0.00 0.00 39.96 3.86
1031 1472 1.519246 CCTCATCGGAGCAGAAGCA 59.481 57.895 0.00 0.00 45.49 3.91
1032 1473 0.530211 CCTCATCGGAGCAGAAGCAG 60.530 60.000 0.00 0.00 45.49 4.24
1234 1723 1.338200 GCGGCAAGAAGAAGAAGAGGA 60.338 52.381 0.00 0.00 0.00 3.71
1235 1724 2.872038 GCGGCAAGAAGAAGAAGAGGAA 60.872 50.000 0.00 0.00 0.00 3.36
1236 1725 2.999355 CGGCAAGAAGAAGAAGAGGAAG 59.001 50.000 0.00 0.00 0.00 3.46
1363 1963 2.149578 GCCTTCCTTGATCATGATCCG 58.850 52.381 28.61 20.09 37.02 4.18
1366 1966 4.564406 GCCTTCCTTGATCATGATCCGTAT 60.564 45.833 28.61 0.00 37.02 3.06
1395 1995 2.050350 CCATGCTTGACCCCTGCTG 61.050 63.158 0.22 0.00 0.00 4.41
1409 2009 1.751351 CCTGCTGTAGCTAGTAGCACA 59.249 52.381 23.77 21.24 45.56 4.57
1411 2011 3.443037 CTGCTGTAGCTAGTAGCACAAG 58.557 50.000 23.77 16.83 45.56 3.16
1412 2012 2.197577 GCTGTAGCTAGTAGCACAAGC 58.802 52.381 23.77 21.74 45.56 4.01
1413 2013 2.159170 GCTGTAGCTAGTAGCACAAGCT 60.159 50.000 23.77 6.50 45.56 3.74
1479 2084 4.558538 TTAAGATCGGTAACTACTCGCC 57.441 45.455 0.00 0.00 0.00 5.54
1534 2143 2.289133 TGTCTTGTGCGTATAGGTTGCA 60.289 45.455 0.00 0.00 36.02 4.08
1618 2239 0.673956 GCACCGGGTCTTCTTCTTCC 60.674 60.000 6.32 0.00 0.00 3.46
1733 2354 3.756963 CAGGTACTTACTTTTGCTTCCCC 59.243 47.826 0.00 0.00 34.60 4.81
1736 2357 1.173913 CTTACTTTTGCTTCCCCCGG 58.826 55.000 0.00 0.00 0.00 5.73
1803 2443 2.356313 CGCAGCCTAATCGCCGAT 60.356 61.111 0.00 0.00 0.00 4.18
1804 2444 1.080772 CGCAGCCTAATCGCCGATA 60.081 57.895 0.00 0.00 0.00 2.92
1805 2445 0.458543 CGCAGCCTAATCGCCGATAT 60.459 55.000 0.00 0.00 0.00 1.63
1806 2446 1.726853 GCAGCCTAATCGCCGATATT 58.273 50.000 0.00 0.00 0.00 1.28
1807 2447 2.076863 GCAGCCTAATCGCCGATATTT 58.923 47.619 0.00 0.00 0.00 1.40
1809 2449 3.058224 GCAGCCTAATCGCCGATATTTTT 60.058 43.478 0.00 0.00 0.00 1.94
1854 2534 0.179084 TCCCTTCTTGCCTAATCGCG 60.179 55.000 0.00 0.00 0.00 5.87
1862 2542 0.101759 TGCCTAATCGCGACTGGTAC 59.898 55.000 12.93 0.00 0.00 3.34
1911 2594 2.429069 CGGCGGCTGTGCTTTTTC 60.429 61.111 7.61 0.00 34.52 2.29
1912 2595 2.049156 GGCGGCTGTGCTTTTTCC 60.049 61.111 0.00 0.00 34.52 3.13
2495 3181 1.170919 GCGCCTACCTCATCTACGGA 61.171 60.000 0.00 0.00 0.00 4.69
2576 3262 4.612279 ATGGCCCGCAACAACCCA 62.612 61.111 0.00 0.00 0.00 4.51
2656 3342 3.019003 GCTGGCACCGCTTCTCCTA 62.019 63.158 0.00 0.00 0.00 2.94
2703 3401 2.125552 TCTCCGACAGCAATGCCG 60.126 61.111 0.00 0.00 0.00 5.69
2795 3493 1.885157 CCGCAATGCCATTGACACT 59.115 52.632 21.24 0.00 42.83 3.55
2796 3494 1.093972 CCGCAATGCCATTGACACTA 58.906 50.000 21.24 0.00 42.83 2.74
2802 3500 4.426416 CAATGCCATTGACACTACCATTG 58.574 43.478 12.09 0.00 42.83 2.82
2806 3504 2.164219 CCATTGACACTACCATTGGCAC 59.836 50.000 1.54 0.00 29.18 5.01
2919 3621 1.076549 GTGGCATCAACTCCCCCAA 59.923 57.895 0.00 0.00 0.00 4.12
2928 3630 2.025321 TCAACTCCCCCAAGGCTTAATC 60.025 50.000 0.00 0.00 34.51 1.75
3025 3727 1.016627 TGAACAATGCATCGCTAGCC 58.983 50.000 9.66 0.00 0.00 3.93
3039 3741 2.351726 CGCTAGCCACCTTGTTTATGTC 59.648 50.000 9.66 0.00 0.00 3.06
3066 3768 0.107263 TCACGGTGCATACATGGCAT 60.107 50.000 2.51 0.00 44.11 4.40
3115 3817 2.427410 CCGCGCTGTTGCACTTTC 60.427 61.111 5.56 0.00 39.64 2.62
3116 3818 2.427410 CGCGCTGTTGCACTTTCC 60.427 61.111 5.56 0.00 39.64 3.13
3235 3937 3.266772 TCCTGCAATCACCTCCAAACTAT 59.733 43.478 0.00 0.00 0.00 2.12
3236 3938 4.473196 TCCTGCAATCACCTCCAAACTATA 59.527 41.667 0.00 0.00 0.00 1.31
3237 3939 5.132648 TCCTGCAATCACCTCCAAACTATAT 59.867 40.000 0.00 0.00 0.00 0.86
3238 3940 6.328934 TCCTGCAATCACCTCCAAACTATATA 59.671 38.462 0.00 0.00 0.00 0.86
3265 3967 4.171754 GCTGGCTCATTTTTCATCTCAAC 58.828 43.478 0.00 0.00 0.00 3.18
3266 3968 4.082354 GCTGGCTCATTTTTCATCTCAACT 60.082 41.667 0.00 0.00 0.00 3.16
3268 3970 6.017400 TGGCTCATTTTTCATCTCAACTTC 57.983 37.500 0.00 0.00 0.00 3.01
3309 4011 3.568853 CCCTAGACTACCGTATCCACAAG 59.431 52.174 0.00 0.00 0.00 3.16
3322 4024 5.354234 CGTATCCACAAGCACTTATTTCCTT 59.646 40.000 0.00 0.00 0.00 3.36
3326 4028 4.466828 CACAAGCACTTATTTCCTTGACG 58.533 43.478 6.27 0.00 38.37 4.35
3348 4050 5.958428 CGATTTCATTATCGCGTAAACAGA 58.042 37.500 5.77 1.38 40.66 3.41
3409 4111 6.198778 CACGTATGCATGGTTCAAAAATATGG 59.801 38.462 10.16 0.00 0.00 2.74
3418 4120 7.782897 TGGTTCAAAAATATGGATTGGTACA 57.217 32.000 0.00 0.00 0.00 2.90
3464 4166 1.746470 AACCTATTTACCGCACCAGC 58.254 50.000 0.00 0.00 37.42 4.85
3476 4178 1.693083 GCACCAGCGCGTAAAGGTAG 61.693 60.000 8.43 7.12 32.01 3.18
3485 4187 3.803778 GCGCGTAAAGGTAGCCTATTTAA 59.196 43.478 8.43 0.00 31.13 1.52
3500 4216 8.838649 AGCCTATTTAATTACCTTGAAACCAT 57.161 30.769 0.00 0.00 0.00 3.55
3568 4284 7.981225 ACATTTGAACTTCATTTTGTACTTGCT 59.019 29.630 0.00 0.00 0.00 3.91
3569 4285 9.462174 CATTTGAACTTCATTTTGTACTTGCTA 57.538 29.630 0.00 0.00 0.00 3.49
3570 4286 8.850454 TTTGAACTTCATTTTGTACTTGCTAC 57.150 30.769 0.00 0.00 0.00 3.58
3571 4287 6.966021 TGAACTTCATTTTGTACTTGCTACC 58.034 36.000 0.00 0.00 0.00 3.18
3572 4288 6.544197 TGAACTTCATTTTGTACTTGCTACCA 59.456 34.615 0.00 0.00 0.00 3.25
3577 4293 5.472137 TCATTTTGTACTTGCTACCAGAACC 59.528 40.000 0.00 0.00 0.00 3.62
3633 4349 3.965379 TGACAGTTTAGGCCGTGATTA 57.035 42.857 0.00 0.00 0.00 1.75
3662 4378 7.410942 CGAGTCCAACGAATTTGAAAACAAAAA 60.411 33.333 0.00 0.00 37.39 1.94
3721 4437 5.769662 TCTGCATAAGAACAACACAGGATTT 59.230 36.000 0.00 0.00 29.54 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.134081 TGGTTCTTCCGAGTGAGTTTTCT 59.866 43.478 0.00 0.00 39.52 2.52
1 2 3.463944 TGGTTCTTCCGAGTGAGTTTTC 58.536 45.455 0.00 0.00 39.52 2.29
22 23 6.595716 GCTATAGAAACCACTCACTCATGTTT 59.404 38.462 3.21 0.00 32.23 2.83
32 33 5.537300 TGAGGATGCTATAGAAACCACTC 57.463 43.478 9.62 6.31 0.00 3.51
55 56 4.346418 ACCTCCAAGAGCTATTCGATCATT 59.654 41.667 0.00 0.00 0.00 2.57
76 77 2.757314 AGGTAGCCTACTAACACGAACC 59.243 50.000 1.24 0.00 38.67 3.62
77 78 3.693578 AGAGGTAGCCTACTAACACGAAC 59.306 47.826 1.24 0.00 38.67 3.95
78 79 3.960571 AGAGGTAGCCTACTAACACGAA 58.039 45.455 1.24 0.00 38.67 3.85
79 80 3.641434 AGAGGTAGCCTACTAACACGA 57.359 47.619 1.24 0.00 38.67 4.35
80 81 7.502120 TTAATAGAGGTAGCCTACTAACACG 57.498 40.000 1.24 0.00 38.67 4.49
81 82 8.358895 CCTTTAATAGAGGTAGCCTACTAACAC 58.641 40.741 1.24 0.00 38.67 3.32
100 101 3.844211 TGGAGCCACTGACTACCTTTAAT 59.156 43.478 0.00 0.00 0.00 1.40
151 152 8.805175 CCTAGTCTATCTCATCATGTCTTGAAT 58.195 37.037 0.00 0.00 38.03 2.57
161 162 8.443979 TCTCATTCTTCCTAGTCTATCTCATCA 58.556 37.037 0.00 0.00 0.00 3.07
172 173 4.230455 CCCTCCATCTCATTCTTCCTAGT 58.770 47.826 0.00 0.00 0.00 2.57
239 240 1.905894 TGGGGATGTCGAGATTGTGAA 59.094 47.619 0.00 0.00 0.00 3.18
271 272 7.504238 AGATCACTTGAGTCCTTAGGTATACTG 59.496 40.741 2.25 0.00 0.00 2.74
315 316 3.119531 TGGCATGCTTAAGGACAATTTCG 60.120 43.478 18.92 0.00 0.00 3.46
330 331 3.308438 AAAGATCAAGTGTTGGCATGC 57.692 42.857 9.90 9.90 0.00 4.06
348 349 6.014925 GGTTTTTGAGCCCCTCAGTATTAAAA 60.015 38.462 0.00 0.00 41.75 1.52
406 407 8.844244 AGCATTTTCTCTACATAATGATCAACC 58.156 33.333 0.00 0.00 31.29 3.77
416 417 8.052748 ACCCATTACAAGCATTTTCTCTACATA 58.947 33.333 0.00 0.00 0.00 2.29
460 462 2.224305 ACCTGTGTCTAACTGCTTGACC 60.224 50.000 0.00 0.00 0.00 4.02
468 470 1.348036 GGCCTCAACCTGTGTCTAACT 59.652 52.381 0.00 0.00 0.00 2.24
477 479 1.672356 CCTTCACGGCCTCAACCTG 60.672 63.158 0.00 0.00 0.00 4.00
489 491 3.561725 CCAGAACACAAGAGAACCTTCAC 59.438 47.826 0.00 0.00 31.42 3.18
497 499 2.050144 AGAAGGCCAGAACACAAGAGA 58.950 47.619 5.01 0.00 0.00 3.10
498 500 2.557920 AGAAGGCCAGAACACAAGAG 57.442 50.000 5.01 0.00 0.00 2.85
538 555 7.653713 ACTCACTGATATTAGTTTAGCCATTCG 59.346 37.037 0.00 0.00 0.00 3.34
598 1013 8.594550 AGATAACCAGAGTGACTTTAGCTAAAA 58.405 33.333 19.10 2.79 0.00 1.52
700 1115 5.410439 GTGTTAGGAAAATCCGTGTGTGTAT 59.590 40.000 0.00 0.00 42.75 2.29
701 1116 4.751098 GTGTTAGGAAAATCCGTGTGTGTA 59.249 41.667 0.00 0.00 42.75 2.90
702 1117 3.562557 GTGTTAGGAAAATCCGTGTGTGT 59.437 43.478 0.00 0.00 42.75 3.72
703 1118 3.562141 TGTGTTAGGAAAATCCGTGTGTG 59.438 43.478 0.00 0.00 42.75 3.82
704 1119 3.811083 TGTGTTAGGAAAATCCGTGTGT 58.189 40.909 0.00 0.00 42.75 3.72
719 1135 3.940221 GGTTATGCACCGGTAATGTGTTA 59.060 43.478 6.87 0.00 35.12 2.41
733 1149 0.034574 AATCCACTGGCGGTTATGCA 60.035 50.000 0.00 0.00 36.28 3.96
738 1154 0.966179 GGAAAAATCCACTGGCGGTT 59.034 50.000 0.00 0.00 0.00 4.44
778 1194 3.973425 ACAATTTCATAGAGCTGCCCTT 58.027 40.909 0.00 0.00 0.00 3.95
942 1383 2.024941 GGATGACCCTTGGGTTCAATCT 60.025 50.000 13.18 0.00 31.75 2.40
1030 1471 2.871099 CTGCTGCTGCTGCTTCTG 59.129 61.111 27.67 13.98 40.48 3.02
1102 1543 4.087892 CTCCACCGCCACCCTCTG 62.088 72.222 0.00 0.00 0.00 3.35
1409 2009 4.003648 GCCAATTATATACGCAGGAGCTT 58.996 43.478 0.00 0.00 39.10 3.74
1411 2011 3.600388 AGCCAATTATATACGCAGGAGC 58.400 45.455 0.00 0.00 37.42 4.70
1412 2012 3.859961 CGAGCCAATTATATACGCAGGAG 59.140 47.826 0.00 0.00 0.00 3.69
1413 2013 3.257375 ACGAGCCAATTATATACGCAGGA 59.743 43.478 0.00 0.00 0.00 3.86
1416 2016 4.245845 TCACGAGCCAATTATATACGCA 57.754 40.909 0.00 0.00 0.00 5.24
1479 2084 7.027760 TCGATCACAAGTTAGTTAGCTACTTG 58.972 38.462 19.95 19.95 39.45 3.16
1485 2090 5.348986 TGGATCGATCACAAGTTAGTTAGC 58.651 41.667 25.93 4.84 0.00 3.09
1534 2143 1.760086 CATCTCCTCCCCGCACTCT 60.760 63.158 0.00 0.00 0.00 3.24
1602 2223 0.537653 GGAGGAAGAAGAAGACCCGG 59.462 60.000 0.00 0.00 0.00 5.73
1733 2354 2.613506 GGCCGTGTGAAAAGACCGG 61.614 63.158 0.00 0.00 41.50 5.28
1736 2357 0.240945 CCATGGCCGTGTGAAAAGAC 59.759 55.000 23.39 0.00 0.00 3.01
1806 2446 1.941294 TCGTAAGCAAGCACGGAAAAA 59.059 42.857 5.31 0.00 38.66 1.94
1807 2447 1.529438 CTCGTAAGCAAGCACGGAAAA 59.471 47.619 5.31 0.00 38.66 2.29
1809 2449 0.032952 ACTCGTAAGCAAGCACGGAA 59.967 50.000 5.31 0.00 38.66 4.30
1811 2491 1.781555 CACTCGTAAGCAAGCACGG 59.218 57.895 5.31 0.34 38.66 4.94
1854 2534 7.316544 TCAAAAGAAGAAACTTGTACCAGTC 57.683 36.000 0.00 0.00 0.00 3.51
1862 2542 5.050567 GCCATTGCTCAAAAGAAGAAACTTG 60.051 40.000 0.00 0.00 33.53 3.16
1905 2585 4.399978 CGCCTATAACACAACGGAAAAAG 58.600 43.478 0.00 0.00 0.00 2.27
1911 2594 0.461339 AGCCGCCTATAACACAACGG 60.461 55.000 0.00 0.00 43.37 4.44
1912 2595 0.650512 CAGCCGCCTATAACACAACG 59.349 55.000 0.00 0.00 0.00 4.10
2644 3330 1.367599 CTCGTCGTAGGAGAAGCGGT 61.368 60.000 0.00 0.00 32.18 5.68
2795 3493 2.744318 CCGTGCGTGCCAATGGTA 60.744 61.111 0.00 0.00 0.00 3.25
2919 3621 0.905357 AGCACGACTGGATTAAGCCT 59.095 50.000 11.74 0.00 0.00 4.58
2928 3630 2.747989 TCTACTTGAGTAGCACGACTGG 59.252 50.000 12.30 0.00 45.69 4.00
3025 3727 7.305935 CGTGAACAATTTGACATAAACAAGGTG 60.306 37.037 2.79 0.00 0.00 4.00
3039 3741 3.894920 TGTATGCACCGTGAACAATTTG 58.105 40.909 1.65 0.00 0.00 2.32
3116 3818 3.758023 GCCTTTTCATTTTTCATTGGGGG 59.242 43.478 0.00 0.00 0.00 5.40
3235 3937 5.207354 TGAAAAATGAGCCAGCCCAATATA 58.793 37.500 0.00 0.00 0.00 0.86
3236 3938 4.032310 TGAAAAATGAGCCAGCCCAATAT 58.968 39.130 0.00 0.00 0.00 1.28
3237 3939 3.439154 TGAAAAATGAGCCAGCCCAATA 58.561 40.909 0.00 0.00 0.00 1.90
3238 3940 2.259012 TGAAAAATGAGCCAGCCCAAT 58.741 42.857 0.00 0.00 0.00 3.16
3281 3983 4.764308 GGATACGGTAGTCTAGGGGTTTAG 59.236 50.000 0.00 0.00 0.00 1.85
3292 3994 2.165845 AGTGCTTGTGGATACGGTAGTC 59.834 50.000 0.00 0.00 42.51 2.59
3309 4011 5.938322 TGAAATCGTCAAGGAAATAAGTGC 58.062 37.500 0.00 0.00 31.51 4.40
3326 4028 8.276325 AGAATCTGTTTACGCGATAATGAAATC 58.724 33.333 15.93 10.84 0.00 2.17
3348 4050 9.883142 TTGTTACAAAGTTTTGAATTCCAGAAT 57.117 25.926 11.29 0.00 40.55 2.40
3378 4080 3.126686 TGAACCATGCATACGTGACAATG 59.873 43.478 0.00 0.00 34.49 2.82
3385 4087 6.096141 TCCATATTTTTGAACCATGCATACGT 59.904 34.615 0.00 0.00 0.00 3.57
3409 4111 3.623060 ACACGCTGATCATTGTACCAATC 59.377 43.478 0.00 0.00 0.00 2.67
3418 4120 7.391148 AGGTTATTTTTACACGCTGATCATT 57.609 32.000 0.00 0.00 0.00 2.57
3464 4166 6.535274 AATTAAATAGGCTACCTTTACGCG 57.465 37.500 3.53 3.53 34.61 6.01
3544 4260 9.463443 GTAGCAAGTACAAAATGAAGTTCAAAT 57.537 29.630 10.14 0.00 0.00 2.32
3546 4262 7.067615 TGGTAGCAAGTACAAAATGAAGTTCAA 59.932 33.333 10.14 0.00 32.62 2.69
3548 4264 6.966021 TGGTAGCAAGTACAAAATGAAGTTC 58.034 36.000 0.00 0.00 32.62 3.01
3554 4270 5.240623 TGGTTCTGGTAGCAAGTACAAAATG 59.759 40.000 0.00 0.00 32.62 2.32
3561 4277 2.565834 GGACTGGTTCTGGTAGCAAGTA 59.434 50.000 0.00 0.00 0.00 2.24
3562 4278 1.348036 GGACTGGTTCTGGTAGCAAGT 59.652 52.381 0.00 0.00 0.00 3.16
3563 4279 1.673033 CGGACTGGTTCTGGTAGCAAG 60.673 57.143 0.00 0.00 0.00 4.01
3564 4280 0.320374 CGGACTGGTTCTGGTAGCAA 59.680 55.000 0.00 0.00 0.00 3.91
3566 4282 1.218316 CCGGACTGGTTCTGGTAGC 59.782 63.158 0.00 0.00 45.10 3.58
3571 4287 2.266055 GCCTCCGGACTGGTTCTG 59.734 66.667 11.18 0.00 39.52 3.02
3572 4288 3.003763 GGCCTCCGGACTGGTTCT 61.004 66.667 11.18 0.00 39.52 3.01
3577 4293 1.937546 GCATTTTGGCCTCCGGACTG 61.938 60.000 0.00 0.00 0.00 3.51
3588 4304 9.419297 CATATTCATATCTTGGAAGCATTTTGG 57.581 33.333 0.00 0.00 0.00 3.28
3633 4349 1.156736 CAAATTCGTTGGACTCGGCT 58.843 50.000 0.00 0.00 33.18 5.52


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

AutoCloner maintained by Alex Coulton.