Multiple sequence alignment - TraesCS2D01G153900

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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 TraesCS2D01G153900 chr2D 100.000 2507 0 0 1 2507 96798736 96801242 0.000000e+00 4630.0
1 TraesCS2D01G153900 chr2D 84.181 177 22 6 1957 2131 94386675 94386503 1.540000e-37 167.0
2 TraesCS2D01G153900 chr2D 86.364 110 10 4 505 612 175765287 175765393 5.670000e-22 115.0
3 TraesCS2D01G153900 chr2D 85.981 107 12 2 501 606 67559223 67559327 7.330000e-21 111.0
4 TraesCS2D01G153900 chr2D 97.727 44 1 0 1 44 641606085 641606128 2.670000e-10 76.8
5 TraesCS2D01G153900 chr2D 94.000 50 2 1 1 50 148738068 148738020 9.620000e-10 75.0
6 TraesCS2D01G153900 chr2A 91.197 2522 128 34 35 2507 95824736 95827212 0.000000e+00 3341.0
7 TraesCS2D01G153900 chr2A 87.879 99 9 2 509 606 61487333 61487237 2.040000e-21 113.0
8 TraesCS2D01G153900 chr2A 89.796 49 3 2 894 941 729676737 729676784 7.490000e-06 62.1
9 TraesCS2D01G153900 chr2B 88.957 1947 118 45 605 2507 148143534 148145427 0.000000e+00 2314.0
10 TraesCS2D01G153900 chr2B 87.037 108 10 3 503 609 669438808 669438704 4.380000e-23 119.0
11 TraesCS2D01G153900 chr2B 95.385 65 3 0 261 325 148143015 148143079 1.230000e-18 104.0
12 TraesCS2D01G153900 chr2B 93.182 44 3 0 893 936 649947740 649947697 5.790000e-07 65.8
13 TraesCS2D01G153900 chrUn 92.308 234 12 3 35 267 17372454 17372682 6.690000e-86 327.0
14 TraesCS2D01G153900 chrUn 92.308 234 12 3 35 267 272159171 272158943 6.690000e-86 327.0
15 TraesCS2D01G153900 chrUn 93.182 44 3 0 893 936 278447664 278447621 5.790000e-07 65.8
16 TraesCS2D01G153900 chrUn 93.182 44 3 0 893 936 281845738 281845695 5.790000e-07 65.8
17 TraesCS2D01G153900 chr3A 82.022 178 29 3 1958 2134 595949795 595949620 5.590000e-32 148.0
18 TraesCS2D01G153900 chr3A 84.615 65 9 1 872 936 647710291 647710228 2.080000e-06 63.9
19 TraesCS2D01G153900 chr7B 81.818 176 26 6 1958 2131 72227604 72227775 2.600000e-30 143.0
20 TraesCS2D01G153900 chr6B 80.749 187 27 5 1957 2139 217169260 217169079 1.210000e-28 137.0
21 TraesCS2D01G153900 chr6D 80.541 185 29 4 1957 2139 123159232 123159053 4.350000e-28 135.0
22 TraesCS2D01G153900 chr6A 80.423 189 28 6 1954 2139 157963784 157963966 4.350000e-28 135.0
23 TraesCS2D01G153900 chr6A 100.000 41 0 0 1 41 18536088 18536128 2.670000e-10 76.8
24 TraesCS2D01G153900 chr6A 93.182 44 3 0 893 936 17700359 17700316 5.790000e-07 65.8
25 TraesCS2D01G153900 chr7D 80.682 176 28 6 1958 2131 512733062 512733233 5.630000e-27 132.0
26 TraesCS2D01G153900 chr7D 85.841 113 11 4 505 612 412155302 412155190 5.670000e-22 115.0
27 TraesCS2D01G153900 chr7D 100.000 41 0 0 1 41 98621925 98621885 2.670000e-10 76.8
28 TraesCS2D01G153900 chr7A 83.217 143 16 8 495 635 137142821 137142685 9.420000e-25 124.0
29 TraesCS2D01G153900 chr1D 86.792 106 11 2 502 606 22885701 22885598 5.670000e-22 115.0
30 TraesCS2D01G153900 chr1D 97.727 44 1 0 1 44 351919240 351919197 2.670000e-10 76.8
31 TraesCS2D01G153900 chr1D 89.362 47 5 0 887 933 207658859 207658905 2.690000e-05 60.2
32 TraesCS2D01G153900 chr3D 85.849 106 11 3 503 606 79532656 79532553 2.640000e-20 110.0
33 TraesCS2D01G153900 chr3D 78.395 162 20 11 939 1087 147461876 147461717 9.550000e-15 91.6
34 TraesCS2D01G153900 chr4D 100.000 42 0 0 1 42 484007716 484007675 7.430000e-11 78.7
35 TraesCS2D01G153900 chr1A 94.118 51 1 2 2 52 500979457 500979505 2.670000e-10 76.8
36 TraesCS2D01G153900 chr5B 92.308 52 3 1 1 52 681345045 681344995 3.460000e-09 73.1
37 TraesCS2D01G153900 chr1B 90.741 54 4 1 1 54 356597700 356597648 1.240000e-08 71.3
38 TraesCS2D01G153900 chr4A 100.000 29 0 0 2471 2499 734454908 734454936 1.000000e-03 54.7


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 TraesCS2D01G153900 chr2D 96798736 96801242 2506 False 4630 4630 100.000 1 2507 1 chr2D.!!$F2 2506
1 TraesCS2D01G153900 chr2A 95824736 95827212 2476 False 3341 3341 91.197 35 2507 1 chr2A.!!$F1 2472
2 TraesCS2D01G153900 chr2B 148143015 148145427 2412 False 1209 2314 92.171 261 2507 2 chr2B.!!$F1 2246

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
487 758 0.185901 AGCAATTGTGACCCCACTGT 59.814 50.0 7.4 0.0 43.55 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2359 2703 1.240641 TTCCAATGCGCACGTCCAAT 61.241 50.0 14.9 0.0 0.0 3.16 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
25 26 7.141100 ACTAAAACCATGACGAGTAATTTGG 57.859 36.000 0.00 0.00 0.00 3.28
26 27 6.938030 ACTAAAACCATGACGAGTAATTTGGA 59.062 34.615 0.00 0.00 0.00 3.53
27 28 6.642707 AAAACCATGACGAGTAATTTGGAA 57.357 33.333 0.00 0.00 0.00 3.53
28 29 5.622770 AACCATGACGAGTAATTTGGAAC 57.377 39.130 0.00 0.00 0.00 3.62
29 30 3.682858 ACCATGACGAGTAATTTGGAACG 59.317 43.478 0.00 0.00 0.00 3.95
30 31 3.063452 CCATGACGAGTAATTTGGAACGG 59.937 47.826 0.00 0.00 0.00 4.44
31 32 3.663995 TGACGAGTAATTTGGAACGGA 57.336 42.857 0.00 0.00 0.00 4.69
32 33 3.581755 TGACGAGTAATTTGGAACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
33 34 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
34 35 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
35 36 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
36 37 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
37 38 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
38 39 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
51 52 3.385433 GGAGGGAGTAGAAGGCTAAGAAC 59.615 52.174 0.00 0.00 0.00 3.01
80 81 2.428544 TGTATAACTGGCGGCCATTT 57.571 45.000 25.11 25.11 30.82 2.32
83 84 1.102978 ATAACTGGCGGCCATTTGTC 58.897 50.000 28.58 0.00 30.82 3.18
89 90 1.031571 GGCGGCCATTTGTCAGATCA 61.032 55.000 15.62 0.00 0.00 2.92
95 96 3.304257 GGCCATTTGTCAGATCAATAGCG 60.304 47.826 0.00 0.00 0.00 4.26
96 97 3.851105 GCCATTTGTCAGATCAATAGCGC 60.851 47.826 0.00 0.00 0.00 5.92
115 116 1.404583 GCCAACAGCAATGGATTCACC 60.405 52.381 6.62 0.00 40.56 4.02
141 142 7.909121 CACGTACTCCAGTCTACTATACAAAAG 59.091 40.741 0.00 0.00 0.00 2.27
142 143 7.609532 ACGTACTCCAGTCTACTATACAAAAGT 59.390 37.037 0.00 0.00 0.00 2.66
192 193 4.359971 TTTTCAAGTGATCATGATGGCG 57.640 40.909 14.30 0.00 0.00 5.69
235 236 2.157834 TGAACACACGTCCGCTAATT 57.842 45.000 0.00 0.00 0.00 1.40
242 243 3.430895 CACACGTCCGCTAATTAACTTGT 59.569 43.478 0.00 0.00 0.00 3.16
243 244 4.622313 CACACGTCCGCTAATTAACTTGTA 59.378 41.667 0.00 0.00 0.00 2.41
383 653 4.487714 AATCATGGCTAGTTCCGAAGAA 57.512 40.909 0.00 0.00 0.00 2.52
404 674 9.651913 GAAGAATGGAAGTTTGGCATTTTTATA 57.348 29.630 0.00 0.00 0.00 0.98
451 721 6.959639 TTTTAGTGGAAAGACAATGCTCTT 57.040 33.333 0.00 0.00 31.41 2.85
462 732 5.241662 AGACAATGCTCTTGTAGTTTCTCC 58.758 41.667 5.40 0.00 31.96 3.71
463 733 4.973168 ACAATGCTCTTGTAGTTTCTCCA 58.027 39.130 3.78 0.00 0.00 3.86
480 751 5.643379 TCTCCAAAATAGCAATTGTGACC 57.357 39.130 7.40 0.00 32.75 4.02
487 758 0.185901 AGCAATTGTGACCCCACTGT 59.814 50.000 7.40 0.00 43.55 3.55
498 769 5.072600 TGTGACCCCACTGTTAAAATAGAGT 59.927 40.000 0.00 0.00 43.55 3.24
518 789 7.439108 AGAGTGCTAATTATTACTCCCTTGT 57.561 36.000 18.41 4.83 40.21 3.16
522 793 8.107095 AGTGCTAATTATTACTCCCTTGTTTCA 58.893 33.333 0.00 0.00 0.00 2.69
524 795 9.303116 TGCTAATTATTACTCCCTTGTTTCAAA 57.697 29.630 0.00 0.00 0.00 2.69
532 803 8.754991 TTACTCCCTTGTTTCAAAATAAGTGA 57.245 30.769 10.00 4.74 35.95 3.41
535 806 7.013369 ACTCCCTTGTTTCAAAATAAGTGACTC 59.987 37.037 10.00 0.00 35.95 3.36
536 807 6.017440 TCCCTTGTTTCAAAATAAGTGACTCG 60.017 38.462 10.00 0.00 35.95 4.18
542 813 7.908082 TGTTTCAAAATAAGTGACTCGACTTTG 59.092 33.333 0.00 0.00 37.38 2.77
549 820 8.739649 AATAAGTGACTCGACTTTGTACTAAC 57.260 34.615 0.00 0.00 37.38 2.34
597 875 9.768662 AAAGTTAAGTCACTTATTTTAGGACGA 57.231 29.630 0.00 0.00 35.87 4.20
599 877 9.939802 AGTTAAGTCACTTATTTTAGGACGAAT 57.060 29.630 0.00 0.00 33.84 3.34
729 1016 1.407618 TGTCCGTCGGGATATGTCAAG 59.592 52.381 12.29 0.00 46.14 3.02
749 1036 1.062587 GCTCCGAATTTGACGTCATGG 59.937 52.381 20.80 15.59 0.00 3.66
768 1055 1.586422 GGTGTGTGCATGCGATAGAT 58.414 50.000 14.09 0.00 39.76 1.98
769 1056 2.547855 GGGTGTGTGCATGCGATAGATA 60.548 50.000 14.09 0.00 39.76 1.98
770 1057 2.733552 GGTGTGTGCATGCGATAGATAG 59.266 50.000 14.09 0.00 39.76 2.08
771 1058 3.552890 GGTGTGTGCATGCGATAGATAGA 60.553 47.826 14.09 0.00 39.76 1.98
772 1059 4.051237 GTGTGTGCATGCGATAGATAGAA 58.949 43.478 14.09 0.00 39.76 2.10
798 1085 8.270744 AGTCTCTATCAACATGGAAAAGCTTAT 58.729 33.333 0.00 0.00 0.00 1.73
811 1099 5.638234 GGAAAAGCTTATGTACGTGTCTCTT 59.362 40.000 0.00 0.00 0.00 2.85
824 1112 9.964303 TGTACGTGTCTCTTATTTAGTTTGTAA 57.036 29.630 0.00 0.00 0.00 2.41
831 1119 8.870879 GTCTCTTATTTAGTTTGTAATGAGCGT 58.129 33.333 0.00 0.00 0.00 5.07
880 1168 1.200948 GTACAAGCGTCGTACTCCCTT 59.799 52.381 0.00 0.00 36.98 3.95
885 1173 1.201880 AGCGTCGTACTCCCTTCTTTC 59.798 52.381 0.00 0.00 0.00 2.62
886 1174 1.068055 GCGTCGTACTCCCTTCTTTCA 60.068 52.381 0.00 0.00 0.00 2.69
953 1261 9.749340 TCGGAGTGATATATCCTATGTTTAGAA 57.251 33.333 10.25 0.00 33.12 2.10
1032 1340 2.594303 CGCCAGGACCACAAAGCA 60.594 61.111 0.00 0.00 0.00 3.91
1115 1446 3.406361 GGCACACACTGCTCGTCG 61.406 66.667 0.00 0.00 46.25 5.12
1117 1448 1.949133 GCACACACTGCTCGTCGAA 60.949 57.895 0.00 0.00 43.33 3.71
1173 1505 0.852777 CGACGGCGAATAAGATGGTG 59.147 55.000 16.62 0.00 40.82 4.17
1749 2082 3.343617 TCATCCCACCGACTTTCATTTC 58.656 45.455 0.00 0.00 0.00 2.17
1750 2083 2.940994 TCCCACCGACTTTCATTTCA 57.059 45.000 0.00 0.00 0.00 2.69
1751 2084 3.433306 TCCCACCGACTTTCATTTCAT 57.567 42.857 0.00 0.00 0.00 2.57
1752 2085 3.761897 TCCCACCGACTTTCATTTCATT 58.238 40.909 0.00 0.00 0.00 2.57
1753 2086 4.148838 TCCCACCGACTTTCATTTCATTT 58.851 39.130 0.00 0.00 0.00 2.32
1754 2087 4.217550 TCCCACCGACTTTCATTTCATTTC 59.782 41.667 0.00 0.00 0.00 2.17
1755 2088 4.022416 CCCACCGACTTTCATTTCATTTCA 60.022 41.667 0.00 0.00 0.00 2.69
1756 2089 5.336690 CCCACCGACTTTCATTTCATTTCAT 60.337 40.000 0.00 0.00 0.00 2.57
1757 2090 6.158598 CCACCGACTTTCATTTCATTTCATT 58.841 36.000 0.00 0.00 0.00 2.57
1758 2091 6.646240 CCACCGACTTTCATTTCATTTCATTT 59.354 34.615 0.00 0.00 0.00 2.32
1759 2092 7.148755 CCACCGACTTTCATTTCATTTCATTTC 60.149 37.037 0.00 0.00 0.00 2.17
1760 2093 7.381948 CACCGACTTTCATTTCATTTCATTTCA 59.618 33.333 0.00 0.00 0.00 2.69
1761 2094 8.090214 ACCGACTTTCATTTCATTTCATTTCAT 58.910 29.630 0.00 0.00 0.00 2.57
1762 2095 8.928733 CCGACTTTCATTTCATTTCATTTCATT 58.071 29.630 0.00 0.00 0.00 2.57
1857 2194 6.934645 TCGAGGAAGTCATGAATTTTGTAAGT 59.065 34.615 10.13 0.00 0.00 2.24
1926 2263 1.351017 GGAGGTTGGTTGAGGTCATGA 59.649 52.381 0.00 0.00 0.00 3.07
2177 2521 8.496534 TGATTTCAGACAGATCTTATATGGGA 57.503 34.615 0.00 0.00 30.42 4.37
2194 2538 7.738437 ATATGGGAAACAAAAATGACTGGAT 57.262 32.000 0.00 0.00 0.00 3.41
2280 2624 9.768662 AGACAATAGTTACGGAAAAGTCTTTTA 57.231 29.630 10.56 0.00 31.94 1.52
2300 2644 7.588488 TCTTTTATCAACCGACGAAACATTTTC 59.412 33.333 0.00 0.00 0.00 2.29
2359 2703 2.569059 ACGTCGGCTATTAGTGCTAGA 58.431 47.619 0.00 0.00 0.00 2.43
2387 2734 3.685058 GTGCGCATTGGAATAAGTCTTC 58.315 45.455 15.91 0.00 0.00 2.87
2419 2766 1.459450 GTCAGCCCGCAAAAAGGATA 58.541 50.000 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.446013 TCCAAATTACTCGTCATGGTTTTAGTT 59.554 33.333 0.00 0.00 0.00 2.24
2 3 7.372451 TCCAAATTACTCGTCATGGTTTTAG 57.628 36.000 0.00 0.00 0.00 1.85
3 4 7.571613 CGTTCCAAATTACTCGTCATGGTTTTA 60.572 37.037 0.00 0.00 0.00 1.52
4 5 6.443792 GTTCCAAATTACTCGTCATGGTTTT 58.556 36.000 0.00 0.00 0.00 2.43
6 7 4.153475 CGTTCCAAATTACTCGTCATGGTT 59.847 41.667 0.00 0.00 0.00 3.67
7 8 3.682858 CGTTCCAAATTACTCGTCATGGT 59.317 43.478 0.00 0.00 0.00 3.55
8 9 3.063452 CCGTTCCAAATTACTCGTCATGG 59.937 47.826 0.00 0.00 0.00 3.66
9 10 3.930229 TCCGTTCCAAATTACTCGTCATG 59.070 43.478 0.00 0.00 0.00 3.07
10 11 4.181578 CTCCGTTCCAAATTACTCGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
11 12 3.581755 CTCCGTTCCAAATTACTCGTCA 58.418 45.455 0.00 0.00 0.00 4.35
12 13 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
13 14 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
14 15 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
15 16 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
16 17 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
17 18 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
18 19 4.355549 TCTACTCCCTCCGTTCCAAATTA 58.644 43.478 0.00 0.00 0.00 1.40
19 20 3.178865 TCTACTCCCTCCGTTCCAAATT 58.821 45.455 0.00 0.00 0.00 1.82
20 21 2.829023 TCTACTCCCTCCGTTCCAAAT 58.171 47.619 0.00 0.00 0.00 2.32
21 22 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
22 23 2.176889 CTTCTACTCCCTCCGTTCCAA 58.823 52.381 0.00 0.00 0.00 3.53
23 24 1.618888 CCTTCTACTCCCTCCGTTCCA 60.619 57.143 0.00 0.00 0.00 3.53
24 25 1.112950 CCTTCTACTCCCTCCGTTCC 58.887 60.000 0.00 0.00 0.00 3.62
25 26 0.460722 GCCTTCTACTCCCTCCGTTC 59.539 60.000 0.00 0.00 0.00 3.95
26 27 0.041386 AGCCTTCTACTCCCTCCGTT 59.959 55.000 0.00 0.00 0.00 4.44
27 28 0.924823 TAGCCTTCTACTCCCTCCGT 59.075 55.000 0.00 0.00 0.00 4.69
28 29 1.957877 CTTAGCCTTCTACTCCCTCCG 59.042 57.143 0.00 0.00 0.00 4.63
29 30 3.315880 TCTTAGCCTTCTACTCCCTCC 57.684 52.381 0.00 0.00 0.00 4.30
30 31 4.283337 AGTTCTTAGCCTTCTACTCCCTC 58.717 47.826 0.00 0.00 0.00 4.30
31 32 4.283337 GAGTTCTTAGCCTTCTACTCCCT 58.717 47.826 0.00 0.00 0.00 4.20
32 33 3.067040 CGAGTTCTTAGCCTTCTACTCCC 59.933 52.174 0.00 0.00 0.00 4.30
33 34 3.695556 ACGAGTTCTTAGCCTTCTACTCC 59.304 47.826 0.00 0.00 0.00 3.85
34 35 4.968812 ACGAGTTCTTAGCCTTCTACTC 57.031 45.455 0.00 0.00 0.00 2.59
35 36 5.477637 AGAAACGAGTTCTTAGCCTTCTACT 59.522 40.000 0.00 0.00 44.64 2.57
36 37 5.712004 AGAAACGAGTTCTTAGCCTTCTAC 58.288 41.667 0.00 0.00 44.64 2.59
37 38 5.979288 AGAAACGAGTTCTTAGCCTTCTA 57.021 39.130 0.00 0.00 44.64 2.10
38 39 4.875561 AGAAACGAGTTCTTAGCCTTCT 57.124 40.909 0.00 0.00 44.64 2.85
51 52 4.201685 CCGCCAGTTATACAAAGAAACGAG 60.202 45.833 0.00 0.00 0.00 4.18
70 71 1.031571 TGATCTGACAAATGGCCGCC 61.032 55.000 1.04 1.04 0.00 6.13
80 81 2.279741 GTTGGCGCTATTGATCTGACA 58.720 47.619 7.64 0.00 0.00 3.58
83 84 1.003116 GCTGTTGGCGCTATTGATCTG 60.003 52.381 7.64 0.00 0.00 2.90
89 90 0.457035 CCATTGCTGTTGGCGCTATT 59.543 50.000 7.64 0.00 45.43 1.73
95 96 1.404583 GGTGAATCCATTGCTGTTGGC 60.405 52.381 0.00 0.00 37.55 4.52
96 97 1.894466 TGGTGAATCCATTGCTGTTGG 59.106 47.619 0.00 0.00 41.93 3.77
115 116 6.915544 TTGTATAGTAGACTGGAGTACGTG 57.084 41.667 0.00 0.00 0.00 4.49
141 142 0.441145 GCCGTTTACATCACGTCCAC 59.559 55.000 0.00 0.00 35.81 4.02
142 143 1.009903 CGCCGTTTACATCACGTCCA 61.010 55.000 0.00 0.00 35.81 4.02
217 218 3.676646 AGTTAATTAGCGGACGTGTGTTC 59.323 43.478 0.00 0.00 0.00 3.18
372 642 3.821033 CCAAACTTCCATTCTTCGGAACT 59.179 43.478 0.00 0.00 37.62 3.01
383 653 9.737844 AAACATATAAAAATGCCAAACTTCCAT 57.262 25.926 0.00 0.00 0.00 3.41
404 674 6.966534 AAGAAACATCTGTCCAAGAAACAT 57.033 33.333 0.00 0.00 38.79 2.71
451 721 8.081633 CACAATTGCTATTTTGGAGAAACTACA 58.918 33.333 5.05 0.00 0.00 2.74
462 732 4.021192 AGTGGGGTCACAATTGCTATTTTG 60.021 41.667 5.05 1.21 45.91 2.44
463 733 4.021192 CAGTGGGGTCACAATTGCTATTTT 60.021 41.667 5.05 0.00 45.91 1.82
480 751 7.865706 ATTAGCACTCTATTTTAACAGTGGG 57.134 36.000 0.00 0.00 37.36 4.61
498 769 8.871629 TTGAAACAAGGGAGTAATAATTAGCA 57.128 30.769 0.00 0.00 0.00 3.49
516 787 7.548196 AAGTCGAGTCACTTATTTTGAAACA 57.452 32.000 0.00 0.00 34.70 2.83
517 788 7.908601 ACAAAGTCGAGTCACTTATTTTGAAAC 59.091 33.333 12.97 0.00 35.45 2.78
518 789 7.981142 ACAAAGTCGAGTCACTTATTTTGAAA 58.019 30.769 12.97 0.00 35.45 2.69
522 793 9.754382 TTAGTACAAAGTCGAGTCACTTATTTT 57.246 29.630 0.00 0.00 35.45 1.82
524 795 8.574737 AGTTAGTACAAAGTCGAGTCACTTATT 58.425 33.333 0.00 2.93 35.45 1.40
525 796 8.108551 AGTTAGTACAAAGTCGAGTCACTTAT 57.891 34.615 0.00 4.10 35.45 1.73
526 797 7.502120 AGTTAGTACAAAGTCGAGTCACTTA 57.498 36.000 0.00 0.00 35.45 2.24
529 800 8.739649 ATAAAGTTAGTACAAAGTCGAGTCAC 57.260 34.615 0.00 0.00 0.00 3.67
557 828 8.886719 GTGACTTAACTTTGTACCAACTTTAGT 58.113 33.333 0.00 0.00 0.00 2.24
558 829 9.106070 AGTGACTTAACTTTGTACCAACTTTAG 57.894 33.333 0.00 0.00 0.00 1.85
577 855 7.391620 TCCATTCGTCCTAAAATAAGTGACTT 58.608 34.615 2.37 2.37 0.00 3.01
580 858 6.942976 ACTCCATTCGTCCTAAAATAAGTGA 58.057 36.000 0.00 0.00 0.00 3.41
609 890 7.373617 TGTGGCTAATAGTCATCCATCTAAA 57.626 36.000 0.00 0.00 29.73 1.85
611 892 6.994421 TTGTGGCTAATAGTCATCCATCTA 57.006 37.500 0.00 0.00 29.73 1.98
627 908 4.649218 ACTTAGTTTTCACCATTTGTGGCT 59.351 37.500 0.00 0.00 45.48 4.75
680 961 1.895020 TACCACCATGCCCACTCGTC 61.895 60.000 0.00 0.00 0.00 4.20
717 1000 2.910688 TTCGGAGCTTGACATATCCC 57.089 50.000 0.00 0.00 0.00 3.85
729 1016 1.062587 CCATGACGTCAAATTCGGAGC 59.937 52.381 24.13 0.00 0.00 4.70
749 1036 1.586422 ATCTATCGCATGCACACACC 58.414 50.000 19.57 0.00 0.00 4.16
768 1055 7.766278 GCTTTTCCATGTTGATAGAGACTTCTA 59.234 37.037 0.00 0.00 40.10 2.10
769 1056 6.597280 GCTTTTCCATGTTGATAGAGACTTCT 59.403 38.462 0.00 0.00 37.46 2.85
770 1057 6.597280 AGCTTTTCCATGTTGATAGAGACTTC 59.403 38.462 0.00 0.00 0.00 3.01
771 1058 6.479884 AGCTTTTCCATGTTGATAGAGACTT 58.520 36.000 0.00 0.00 0.00 3.01
772 1059 6.059787 AGCTTTTCCATGTTGATAGAGACT 57.940 37.500 0.00 0.00 0.00 3.24
786 1073 4.890088 AGACACGTACATAAGCTTTTCCA 58.110 39.130 3.20 0.00 0.00 3.53
798 1085 9.964303 TTACAAACTAAATAAGAGACACGTACA 57.036 29.630 0.00 0.00 0.00 2.90
811 1099 9.589111 TCATACACGCTCATTACAAACTAAATA 57.411 29.630 0.00 0.00 0.00 1.40
824 1112 2.493675 ACTGTCACTCATACACGCTCAT 59.506 45.455 0.00 0.00 0.00 2.90
831 1119 5.408299 GCAAATACACACTGTCACTCATACA 59.592 40.000 0.00 0.00 0.00 2.29
1027 1335 2.711542 CCGGAACATTAGGTCTGCTTT 58.288 47.619 0.00 0.00 0.00 3.51
1032 1340 1.867363 AGAGCCGGAACATTAGGTCT 58.133 50.000 5.05 0.00 0.00 3.85
1115 1446 1.154836 CGTTCGTGCGCTTGAGTTC 60.155 57.895 9.73 0.85 0.00 3.01
1621 1954 4.779489 ACTAGATGGAGTATATGGCATGCA 59.221 41.667 21.36 6.13 0.00 3.96
1757 2090 9.015577 CGCCTCGCTAAAATAAAATAAAATGAA 57.984 29.630 0.00 0.00 0.00 2.57
1758 2091 7.646130 CCGCCTCGCTAAAATAAAATAAAATGA 59.354 33.333 0.00 0.00 0.00 2.57
1759 2092 7.566868 GCCGCCTCGCTAAAATAAAATAAAATG 60.567 37.037 0.00 0.00 0.00 2.32
1760 2093 6.419710 GCCGCCTCGCTAAAATAAAATAAAAT 59.580 34.615 0.00 0.00 0.00 1.82
1761 2094 5.744819 GCCGCCTCGCTAAAATAAAATAAAA 59.255 36.000 0.00 0.00 0.00 1.52
1762 2095 5.066764 AGCCGCCTCGCTAAAATAAAATAAA 59.933 36.000 0.00 0.00 37.32 1.40
1763 2096 4.577283 AGCCGCCTCGCTAAAATAAAATAA 59.423 37.500 0.00 0.00 37.32 1.40
1803 2140 4.274147 TCAACAACCTGAAAGCCTTTGTA 58.726 39.130 0.00 0.00 32.02 2.41
1857 2194 4.458989 ACACAAGTCAGCAAAAGTTGAGAA 59.541 37.500 7.35 0.00 32.53 2.87
1899 2236 3.178865 CCTCAACCAACCTCCTAACCTA 58.821 50.000 0.00 0.00 0.00 3.08
1900 2237 1.985895 CCTCAACCAACCTCCTAACCT 59.014 52.381 0.00 0.00 0.00 3.50
1903 2240 2.696775 TGACCTCAACCAACCTCCTAA 58.303 47.619 0.00 0.00 0.00 2.69
1926 2263 4.866508 TTAGTCTTGTTCGATCCACACT 57.133 40.909 0.00 0.00 0.00 3.55
2177 2521 5.147032 TCCTCCATCCAGTCATTTTTGTTT 58.853 37.500 0.00 0.00 0.00 2.83
2190 2534 6.437162 CCTTCTTTGTTTTATTCCTCCATCCA 59.563 38.462 0.00 0.00 0.00 3.41
2194 2538 7.066781 AGTTCCTTCTTTGTTTTATTCCTCCA 58.933 34.615 0.00 0.00 0.00 3.86
2280 2624 3.495377 TCGAAAATGTTTCGTCGGTTGAT 59.505 39.130 19.25 0.00 42.09 2.57
2300 2644 3.257127 ACTCCTGAACTCTCTTCCTTTCG 59.743 47.826 0.00 0.00 0.00 3.46
2359 2703 1.240641 TTCCAATGCGCACGTCCAAT 61.241 50.000 14.90 0.00 0.00 3.16
2387 2734 1.347320 GGCTGACGTCGGTCTTTTAG 58.653 55.000 24.68 8.46 43.79 1.85


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

AutoCloner maintained by Alex Coulton.