Multiple sequence alignment - TraesCS1B01G212000

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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 TraesCS1B01G212000 chr1B 100.000 3124 0 0 1 3124 385295093 385298216 0.000000e+00 5770.0
1 TraesCS1B01G212000 chr1D 91.252 3098 166 48 82 3124 283616224 283619271 0.000000e+00 4122.0
2 TraesCS1B01G212000 chr1A 90.581 3047 146 51 139 3124 355342187 355345153 0.000000e+00 3906.0
3 TraesCS1B01G212000 chr2D 87.582 153 18 1 1704 1856 553729964 553729813 3.200000e-40 176.0
4 TraesCS1B01G212000 chr2D 100.000 28 0 0 2421 2448 160195552 160195525 6.000000e-03 52.8
5 TraesCS1B01G212000 chr2B 87.582 153 18 1 1704 1856 659533300 659533149 3.200000e-40 176.0
6 TraesCS1B01G212000 chr3D 91.870 123 10 0 1702 1824 399380486 399380364 4.140000e-39 172.0
7 TraesCS1B01G212000 chr3D 85.075 67 10 0 1638 1704 390041932 390041998 5.590000e-08 69.4
8 TraesCS1B01G212000 chr3A 91.870 123 10 0 1702 1824 518642730 518642608 4.140000e-39 172.0
9 TraesCS1B01G212000 chr7D 81.731 208 31 6 1645 1847 428952600 428952805 1.930000e-37 167.0
10 TraesCS1B01G212000 chr7B 81.731 208 31 6 1645 1847 446665453 446665658 1.930000e-37 167.0
11 TraesCS1B01G212000 chr7A 81.731 208 31 6 1645 1847 503052300 503052095 1.930000e-37 167.0
12 TraesCS1B01G212000 chr5D 80.769 104 16 3 67 169 238903717 238903617 9.290000e-11 78.7
13 TraesCS1B01G212000 chr6B 100.000 28 0 0 2415 2442 11317259 11317286 6.000000e-03 52.8


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 TraesCS1B01G212000 chr1B 385295093 385298216 3123 False 5770 5770 100.000 1 3124 1 chr1B.!!$F1 3123
1 TraesCS1B01G212000 chr1D 283616224 283619271 3047 False 4122 4122 91.252 82 3124 1 chr1D.!!$F1 3042
2 TraesCS1B01G212000 chr1A 355342187 355345153 2966 False 3906 3906 90.581 139 3124 1 chr1A.!!$F1 2985

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
241 248 0.037512 CTGCTGCCCAGGATAGATCG 60.038 60.0 0.0 0.0 37.93 3.69 F
1197 1227 0.179037 GGCATGGTGATGAGCAGCTA 60.179 55.0 0.5 0.0 45.14 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1279 1315 0.316442 CGTGTATATGTCGTCGCCGT 60.316 55.0 0.00 0.0 35.01 5.68 R
2375 2428 0.038744 AACTGCAGGCATTGGTAGCT 59.961 50.0 19.93 0.0 0.00 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
20 21 3.931907 AGTATATGTGGTGTGTGCCAT 57.068 42.857 0.00 0.00 41.08 4.40
22 23 5.366482 AGTATATGTGGTGTGTGCCATAA 57.634 39.130 0.00 0.00 41.08 1.90
23 24 5.750524 AGTATATGTGGTGTGTGCCATAAA 58.249 37.500 0.00 0.00 41.08 1.40
24 25 6.184068 AGTATATGTGGTGTGTGCCATAAAA 58.816 36.000 0.00 0.00 41.08 1.52
25 26 3.940209 ATGTGGTGTGTGCCATAAAAG 57.060 42.857 0.00 0.00 41.08 2.27
26 27 2.660572 TGTGGTGTGTGCCATAAAAGT 58.339 42.857 0.00 0.00 41.08 2.66
27 28 3.027412 TGTGGTGTGTGCCATAAAAGTT 58.973 40.909 0.00 0.00 41.08 2.66
28 29 4.207955 TGTGGTGTGTGCCATAAAAGTTA 58.792 39.130 0.00 0.00 41.08 2.24
29 30 4.036971 TGTGGTGTGTGCCATAAAAGTTAC 59.963 41.667 0.00 0.00 41.08 2.50
30 31 3.251245 TGGTGTGTGCCATAAAAGTTACG 59.749 43.478 0.00 0.00 32.81 3.18
31 32 3.365565 GGTGTGTGCCATAAAAGTTACGG 60.366 47.826 0.00 0.00 0.00 4.02
32 33 3.499157 GTGTGTGCCATAAAAGTTACGGA 59.501 43.478 0.00 0.00 0.00 4.69
33 34 3.749088 TGTGTGCCATAAAAGTTACGGAG 59.251 43.478 0.00 0.00 0.00 4.63
35 36 4.931002 GTGTGCCATAAAAGTTACGGAGTA 59.069 41.667 0.00 0.00 45.11 2.59
36 37 5.583457 GTGTGCCATAAAAGTTACGGAGTAT 59.417 40.000 0.00 0.00 45.21 2.12
37 38 6.757947 GTGTGCCATAAAAGTTACGGAGTATA 59.242 38.462 0.00 0.00 45.21 1.47
38 39 7.440255 GTGTGCCATAAAAGTTACGGAGTATAT 59.560 37.037 0.00 0.00 45.21 0.86
39 40 7.654520 TGTGCCATAAAAGTTACGGAGTATATC 59.345 37.037 0.00 0.00 45.21 1.63
40 41 7.654520 GTGCCATAAAAGTTACGGAGTATATCA 59.345 37.037 0.00 0.00 45.21 2.15
41 42 7.654520 TGCCATAAAAGTTACGGAGTATATCAC 59.345 37.037 0.00 0.00 45.21 3.06
42 43 7.871463 GCCATAAAAGTTACGGAGTATATCACT 59.129 37.037 0.00 0.00 45.21 3.41
43 44 9.193133 CCATAAAAGTTACGGAGTATATCACTG 57.807 37.037 0.00 0.00 45.21 3.66
44 45 9.193133 CATAAAAGTTACGGAGTATATCACTGG 57.807 37.037 0.00 0.00 45.21 4.00
45 46 7.414222 AAAAGTTACGGAGTATATCACTGGA 57.586 36.000 0.00 0.00 45.21 3.86
46 47 7.414222 AAAGTTACGGAGTATATCACTGGAA 57.586 36.000 0.00 0.00 45.21 3.53
47 48 7.414222 AAGTTACGGAGTATATCACTGGAAA 57.586 36.000 0.00 0.00 45.21 3.13
48 49 6.803642 AGTTACGGAGTATATCACTGGAAAC 58.196 40.000 0.00 0.00 45.21 2.78
49 50 6.606395 AGTTACGGAGTATATCACTGGAAACT 59.394 38.462 0.00 0.00 45.21 2.66
50 51 5.934402 ACGGAGTATATCACTGGAAACTT 57.066 39.130 0.00 0.00 41.94 2.66
51 52 5.903810 ACGGAGTATATCACTGGAAACTTC 58.096 41.667 0.00 0.00 41.94 3.01
52 53 5.657302 ACGGAGTATATCACTGGAAACTTCT 59.343 40.000 0.00 0.00 41.94 2.85
53 54 6.154706 ACGGAGTATATCACTGGAAACTTCTT 59.845 38.462 0.00 0.00 41.94 2.52
54 55 7.042335 CGGAGTATATCACTGGAAACTTCTTT 58.958 38.462 0.00 0.00 37.72 2.52
55 56 7.222999 CGGAGTATATCACTGGAAACTTCTTTC 59.777 40.741 0.00 0.00 37.72 2.62
56 57 8.041323 GGAGTATATCACTGGAAACTTCTTTCA 58.959 37.037 0.00 0.00 37.72 2.69
57 58 9.436957 GAGTATATCACTGGAAACTTCTTTCAA 57.563 33.333 0.00 0.00 37.72 2.69
58 59 9.793259 AGTATATCACTGGAAACTTCTTTCAAA 57.207 29.630 0.00 0.00 38.04 2.69
62 63 7.873719 TCACTGGAAACTTCTTTCAAATACA 57.126 32.000 0.00 0.00 38.04 2.29
63 64 8.287439 TCACTGGAAACTTCTTTCAAATACAA 57.713 30.769 0.00 0.00 38.04 2.41
64 65 8.912988 TCACTGGAAACTTCTTTCAAATACAAT 58.087 29.630 0.00 0.00 38.04 2.71
65 66 9.533253 CACTGGAAACTTCTTTCAAATACAATT 57.467 29.630 0.00 0.00 38.04 2.32
66 67 9.750125 ACTGGAAACTTCTTTCAAATACAATTC 57.250 29.630 0.00 0.00 38.04 2.17
67 68 9.971922 CTGGAAACTTCTTTCAAATACAATTCT 57.028 29.630 0.00 0.00 38.04 2.40
75 76 9.748708 TTCTTTCAAATACAATTCTTCTTGTGG 57.251 29.630 0.00 0.00 39.60 4.17
76 77 7.867403 TCTTTCAAATACAATTCTTCTTGTGGC 59.133 33.333 0.00 0.00 39.60 5.01
77 78 6.647334 TCAAATACAATTCTTCTTGTGGCA 57.353 33.333 0.00 0.00 39.60 4.92
78 79 7.230849 TCAAATACAATTCTTCTTGTGGCAT 57.769 32.000 0.00 0.00 39.60 4.40
79 80 8.347004 TCAAATACAATTCTTCTTGTGGCATA 57.653 30.769 0.00 0.00 39.60 3.14
80 81 8.243426 TCAAATACAATTCTTCTTGTGGCATAC 58.757 33.333 0.00 0.00 39.60 2.39
130 131 8.742777 TCTGATGGTCAAAATAAATCTTGAAGG 58.257 33.333 0.00 0.00 33.52 3.46
132 133 9.258629 TGATGGTCAAAATAAATCTTGAAGGAT 57.741 29.630 0.00 0.00 33.52 3.24
161 163 3.036091 CCCTTATAACCCTGTCGGAGAA 58.964 50.000 0.00 0.00 39.69 2.87
182 184 4.589216 AAATACCACATATGCCATGTGC 57.411 40.909 18.49 0.00 45.81 4.57
190 192 0.109153 TATGCCATGTGCTAGCTGGG 59.891 55.000 19.86 14.49 42.00 4.45
191 193 1.638679 ATGCCATGTGCTAGCTGGGA 61.639 55.000 19.86 18.17 42.00 4.37
194 196 1.147824 CATGTGCTAGCTGGGAGGG 59.852 63.158 17.23 0.00 0.00 4.30
195 197 2.750657 ATGTGCTAGCTGGGAGGGC 61.751 63.158 17.23 0.00 0.00 5.19
197 199 2.285668 TGCTAGCTGGGAGGGCTT 60.286 61.111 17.23 0.00 40.74 4.35
198 200 2.191641 GCTAGCTGGGAGGGCTTG 59.808 66.667 7.70 0.00 40.74 4.01
199 201 2.191641 CTAGCTGGGAGGGCTTGC 59.808 66.667 0.00 0.00 40.74 4.01
200 202 2.610546 TAGCTGGGAGGGCTTGCA 60.611 61.111 0.00 0.00 40.74 4.08
201 203 2.883267 CTAGCTGGGAGGGCTTGCAC 62.883 65.000 0.00 0.00 40.74 4.57
203 205 4.020617 CTGGGAGGGCTTGCACGA 62.021 66.667 0.00 0.00 0.00 4.35
204 206 4.329545 TGGGAGGGCTTGCACGAC 62.330 66.667 0.00 0.00 0.00 4.34
241 248 0.037512 CTGCTGCCCAGGATAGATCG 60.038 60.000 0.00 0.00 37.93 3.69
244 251 1.277557 GCTGCCCAGGATAGATCGATT 59.722 52.381 0.00 0.00 0.00 3.34
249 256 3.431486 GCCCAGGATAGATCGATTCATCC 60.431 52.174 22.56 22.56 37.76 3.51
260 267 5.545723 AGATCGATTCATCCCATTTCTACCT 59.454 40.000 0.00 0.00 0.00 3.08
339 346 0.620556 AAGATGTGGCTGGAATCGGT 59.379 50.000 0.00 0.00 0.00 4.69
347 354 0.468226 GCTGGAATCGGTGGGATACA 59.532 55.000 0.00 0.00 34.08 2.29
427 434 6.426937 CGAGAGGTCCTTTTTGACAGAAAATA 59.573 38.462 0.00 0.00 36.97 1.40
529 542 0.813610 CGTGCAAGACAAGACCACCA 60.814 55.000 0.00 0.00 0.00 4.17
594 607 5.959527 CCGTTCGTTCAAATATTGTGATCAG 59.040 40.000 0.00 0.00 0.00 2.90
621 634 8.138928 TGATTAGATATAGTTACCTGCATGCT 57.861 34.615 20.33 0.40 0.00 3.79
622 635 8.253810 TGATTAGATATAGTTACCTGCATGCTC 58.746 37.037 20.33 3.05 0.00 4.26
623 636 5.413309 AGATATAGTTACCTGCATGCTCC 57.587 43.478 20.33 0.18 0.00 4.70
626 639 0.254178 AGTTACCTGCATGCTCCCTG 59.746 55.000 20.33 5.18 0.00 4.45
627 640 1.077501 TTACCTGCATGCTCCCTGC 60.078 57.895 20.33 0.00 43.25 4.85
656 669 5.735892 GGCGAATTAGTTACCGTGAATTTTC 59.264 40.000 0.00 0.00 0.00 2.29
659 672 7.536281 GCGAATTAGTTACCGTGAATTTTCTTT 59.464 33.333 0.00 0.00 0.00 2.52
746 765 2.359975 CCGCCGCTTTTCCTTCCT 60.360 61.111 0.00 0.00 0.00 3.36
767 786 1.418637 AGTGTTAAAAGTCAGCCCCGA 59.581 47.619 0.00 0.00 0.00 5.14
869 889 1.593196 CTCGGCTGACTCCTCTCTAG 58.407 60.000 0.00 0.00 0.00 2.43
887 907 8.893563 CTCTCTAGGAGGGAGTAAATATTGAT 57.106 38.462 0.00 0.00 38.35 2.57
888 908 8.657387 TCTCTAGGAGGGAGTAAATATTGATG 57.343 38.462 0.00 0.00 33.06 3.07
889 909 8.456940 TCTCTAGGAGGGAGTAAATATTGATGA 58.543 37.037 0.00 0.00 33.06 2.92
890 910 9.265862 CTCTAGGAGGGAGTAAATATTGATGAT 57.734 37.037 0.00 0.00 0.00 2.45
917 937 3.077519 ATGGTAGGTCACGGCGCTC 62.078 63.158 6.90 0.00 0.00 5.03
965 989 1.877637 CACCAGTGAATCAACACCGA 58.122 50.000 0.00 0.00 41.12 4.69
967 991 1.140052 ACCAGTGAATCAACACCGACA 59.860 47.619 0.00 0.00 41.12 4.35
1047 1071 1.754226 GGCGAACAAGGAGATCTCTCT 59.246 52.381 21.81 14.15 42.48 3.10
1158 1188 3.003763 GGAGGAAGCGGTGGAGGT 61.004 66.667 0.00 0.00 0.00 3.85
1167 1197 3.580319 GGTGGAGGTGGCCTGGTT 61.580 66.667 3.32 0.00 31.76 3.67
1179 1209 2.751436 CTGGTTGTCGGCCATGGG 60.751 66.667 15.13 0.00 35.19 4.00
1197 1227 0.179037 GGCATGGTGATGAGCAGCTA 60.179 55.000 0.50 0.00 45.14 3.32
1207 1237 1.571955 TGAGCAGCTAGGAATGGTGA 58.428 50.000 0.00 0.00 35.20 4.02
1231 1267 0.537143 GATGATGGGCGGCAATACCA 60.537 55.000 12.47 0.00 39.03 3.25
1245 1281 1.049289 ATACCAGGCCTCCTTCGTCC 61.049 60.000 0.00 0.00 0.00 4.79
1254 1290 1.000827 CCTCCTTCGTCCGATCATCAG 60.001 57.143 0.00 0.00 0.00 2.90
1279 1315 0.745486 CTCCATGCTGCATTCACCGA 60.745 55.000 13.38 3.05 0.00 4.69
1340 1376 4.508128 GATGCTTCGTCGGCCGGA 62.508 66.667 27.83 13.34 37.11 5.14
1416 1455 0.458543 AGCACATGTCGATCGTCCAC 60.459 55.000 15.94 6.75 0.00 4.02
1437 1476 2.507102 CCTCGTGTACCTGCTGCG 60.507 66.667 0.00 0.00 0.00 5.18
1451 1490 1.986575 GCTGCGATGAAGCCAAGGTC 61.987 60.000 0.00 0.00 34.45 3.85
1454 1493 1.098050 GCGATGAAGCCAAGGTCAAT 58.902 50.000 0.00 0.00 0.00 2.57
1483 1528 7.938686 TCCTCATCTATCTAATCTAGCTTCCT 58.061 38.462 0.00 0.00 0.00 3.36
1485 1530 7.012327 CCTCATCTATCTAATCTAGCTTCCTCG 59.988 44.444 0.00 0.00 0.00 4.63
1503 1548 2.016704 GCGGATCGATGGCACTACG 61.017 63.158 0.54 0.00 0.00 3.51
1504 1549 1.359117 CGGATCGATGGCACTACGT 59.641 57.895 0.54 0.00 0.00 3.57
1505 1550 0.934901 CGGATCGATGGCACTACGTG 60.935 60.000 0.54 0.00 36.51 4.49
1506 1551 0.102481 GGATCGATGGCACTACGTGT 59.898 55.000 0.54 0.00 35.75 4.49
1507 1552 1.470979 GGATCGATGGCACTACGTGTT 60.471 52.381 0.54 0.00 35.75 3.32
1508 1553 2.223641 GGATCGATGGCACTACGTGTTA 60.224 50.000 0.54 0.00 35.75 2.41
1559 1611 1.372683 GTGCAGGAAGAGCCAGTCA 59.627 57.895 0.00 0.00 40.02 3.41
1583 1635 2.983030 GTGGTGTGCATTCCGGCA 60.983 61.111 0.00 0.00 42.53 5.69
1968 2020 2.554775 TCGACGTCGACTGTGCTC 59.445 61.111 34.97 0.00 44.22 4.26
2042 2094 1.801913 CGCCCTCAACGTCTTCTCG 60.802 63.158 0.00 0.00 0.00 4.04
2064 2116 2.837591 TCCATCGACAAGATCCAGGAAA 59.162 45.455 0.00 0.00 37.52 3.13
2078 2130 2.608752 CCAGGAAAATGACAGCAAGCAC 60.609 50.000 0.00 0.00 0.00 4.40
2122 2174 1.565305 GGCTTCTGCGACTACATCTG 58.435 55.000 0.00 0.00 40.82 2.90
2141 2193 7.519057 ACATCTGATCCAGAATTCATCATCTT 58.481 34.615 8.44 0.00 44.04 2.40
2300 2353 7.008447 GTCACTATAGTTAGCAACAAGAGAACG 59.992 40.741 1.56 0.00 0.00 3.95
2368 2421 6.824958 ATTATACTGAACCCAGCTTAAGGA 57.175 37.500 4.29 0.00 44.16 3.36
2374 2427 7.394144 ACTGAACCCAGCTTAAGGAATATAT 57.606 36.000 4.29 0.00 44.16 0.86
2375 2428 8.506196 ACTGAACCCAGCTTAAGGAATATATA 57.494 34.615 4.29 0.00 44.16 0.86
2376 2429 8.598041 ACTGAACCCAGCTTAAGGAATATATAG 58.402 37.037 4.29 0.00 44.16 1.31
2377 2430 7.394816 TGAACCCAGCTTAAGGAATATATAGC 58.605 38.462 4.29 0.00 0.00 2.97
2387 2440 9.331282 CTTAAGGAATATATAGCTACCAATGCC 57.669 37.037 0.00 0.00 0.00 4.40
2414 2467 2.533266 TTCACTCGCTTCTTGAAGCT 57.467 45.000 26.25 10.73 43.38 3.74
2441 2494 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2443 2496 2.238898 ACTCCCTCCGTCCCAAAATTAG 59.761 50.000 0.00 0.00 0.00 1.73
2448 2501 2.671396 CTCCGTCCCAAAATTAGTGTCG 59.329 50.000 0.00 0.00 0.00 4.35
2450 2503 2.073816 CGTCCCAAAATTAGTGTCGCT 58.926 47.619 0.00 0.00 0.00 4.93
2503 2556 6.237901 TGGAGTAGTAGTTTACTAACACGGA 58.762 40.000 0.00 0.00 42.45 4.69
2584 2637 3.553904 TGATGATTGATGGCGAAATCCA 58.446 40.909 0.00 0.00 40.97 3.41
2761 2814 3.340928 TGATGAGACTGGACAATGCAAG 58.659 45.455 0.00 0.00 0.00 4.01
2836 2889 7.631717 AAAGAGAACTTTCTATATGGCCAAC 57.368 36.000 10.96 0.00 41.80 3.77
2867 2921 5.652452 GCTCTTTATCCTTGGGTACACATTT 59.348 40.000 0.00 0.00 0.00 2.32
2868 2922 6.404734 GCTCTTTATCCTTGGGTACACATTTG 60.405 42.308 0.00 0.00 0.00 2.32
2942 2996 7.315142 CAGTTACCAGCAAATACAACATTCAT 58.685 34.615 0.00 0.00 0.00 2.57
2957 3011 1.825090 TTCATCATGCAGCCGAAAGT 58.175 45.000 0.00 0.00 0.00 2.66
2993 3047 3.907474 TGGTTTCACCAGTAAGATCTCCA 59.093 43.478 0.00 0.00 44.79 3.86
3011 3081 3.625853 TCCAAATCACAACCACAGAACA 58.374 40.909 0.00 0.00 0.00 3.18
3043 3120 4.096732 AGAAAACACAGCACAGAACAAC 57.903 40.909 0.00 0.00 0.00 3.32
3045 3122 0.732571 AACACAGCACAGAACAACGG 59.267 50.000 0.00 0.00 0.00 4.44
3086 3163 4.531854 TGAACTCCAGGTCAAAACATTGA 58.468 39.130 0.00 0.00 0.00 2.57
3100 3177 5.717078 AAACATTGACATGTGAAGCTCAT 57.283 34.783 1.15 0.00 43.34 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.654520 TGATATACTCCGTAACTTTTATGGCAC 59.345 37.037 0.00 0.00 0.00 5.01
15 16 7.654520 GTGATATACTCCGTAACTTTTATGGCA 59.345 37.037 0.00 0.00 0.00 4.92
16 17 7.871463 AGTGATATACTCCGTAACTTTTATGGC 59.129 37.037 0.00 0.00 33.17 4.40
17 18 9.193133 CAGTGATATACTCCGTAACTTTTATGG 57.807 37.037 0.00 0.00 37.60 2.74
18 19 9.193133 CCAGTGATATACTCCGTAACTTTTATG 57.807 37.037 0.00 0.00 37.60 1.90
19 20 9.139734 TCCAGTGATATACTCCGTAACTTTTAT 57.860 33.333 0.00 0.00 37.60 1.40
20 21 8.523915 TCCAGTGATATACTCCGTAACTTTTA 57.476 34.615 0.00 0.00 37.60 1.52
21 22 7.414222 TCCAGTGATATACTCCGTAACTTTT 57.586 36.000 0.00 0.00 37.60 2.27
22 23 7.414222 TTCCAGTGATATACTCCGTAACTTT 57.586 36.000 0.00 0.00 37.60 2.66
23 24 7.123847 AGTTTCCAGTGATATACTCCGTAACTT 59.876 37.037 0.00 0.00 37.60 2.66
24 25 6.606395 AGTTTCCAGTGATATACTCCGTAACT 59.394 38.462 0.00 0.00 37.60 2.24
25 26 6.803642 AGTTTCCAGTGATATACTCCGTAAC 58.196 40.000 0.00 0.00 37.60 2.50
26 27 7.341256 AGAAGTTTCCAGTGATATACTCCGTAA 59.659 37.037 0.00 0.00 37.60 3.18
27 28 6.832384 AGAAGTTTCCAGTGATATACTCCGTA 59.168 38.462 0.00 0.00 37.60 4.02
28 29 5.657302 AGAAGTTTCCAGTGATATACTCCGT 59.343 40.000 0.00 0.00 37.60 4.69
29 30 6.150396 AGAAGTTTCCAGTGATATACTCCG 57.850 41.667 0.00 0.00 37.60 4.63
30 31 8.041323 TGAAAGAAGTTTCCAGTGATATACTCC 58.959 37.037 0.00 0.00 41.37 3.85
31 32 9.436957 TTGAAAGAAGTTTCCAGTGATATACTC 57.563 33.333 0.00 0.00 41.37 2.59
32 33 9.793259 TTTGAAAGAAGTTTCCAGTGATATACT 57.207 29.630 0.00 0.00 41.37 2.12
36 37 9.567776 TGTATTTGAAAGAAGTTTCCAGTGATA 57.432 29.630 0.00 0.00 41.37 2.15
37 38 8.463930 TGTATTTGAAAGAAGTTTCCAGTGAT 57.536 30.769 0.00 0.00 41.37 3.06
38 39 7.873719 TGTATTTGAAAGAAGTTTCCAGTGA 57.126 32.000 0.00 0.00 41.37 3.41
39 40 9.533253 AATTGTATTTGAAAGAAGTTTCCAGTG 57.467 29.630 0.00 0.00 41.37 3.66
40 41 9.750125 GAATTGTATTTGAAAGAAGTTTCCAGT 57.250 29.630 0.00 0.00 41.37 4.00
41 42 9.971922 AGAATTGTATTTGAAAGAAGTTTCCAG 57.028 29.630 0.00 0.00 41.37 3.86
49 50 9.748708 CCACAAGAAGAATTGTATTTGAAAGAA 57.251 29.630 6.14 0.00 41.41 2.52
50 51 7.867403 GCCACAAGAAGAATTGTATTTGAAAGA 59.133 33.333 6.14 0.00 41.41 2.52
51 52 7.652909 TGCCACAAGAAGAATTGTATTTGAAAG 59.347 33.333 6.14 0.00 41.41 2.62
52 53 7.495901 TGCCACAAGAAGAATTGTATTTGAAA 58.504 30.769 6.14 0.00 41.41 2.69
53 54 7.048629 TGCCACAAGAAGAATTGTATTTGAA 57.951 32.000 6.14 0.00 41.41 2.69
54 55 6.647334 TGCCACAAGAAGAATTGTATTTGA 57.353 33.333 6.14 0.00 41.41 2.69
55 56 8.028354 TGTATGCCACAAGAAGAATTGTATTTG 58.972 33.333 0.00 0.00 41.41 2.32
56 57 8.121305 TGTATGCCACAAGAAGAATTGTATTT 57.879 30.769 0.00 0.00 41.41 1.40
57 58 7.701539 TGTATGCCACAAGAAGAATTGTATT 57.298 32.000 0.00 0.00 41.41 1.89
58 59 7.886629 ATGTATGCCACAAGAAGAATTGTAT 57.113 32.000 0.00 0.00 41.41 2.29
59 60 8.978874 ATATGTATGCCACAAGAAGAATTGTA 57.021 30.769 0.00 0.00 41.41 2.41
60 61 7.557358 TGATATGTATGCCACAAGAAGAATTGT 59.443 33.333 0.00 0.00 44.12 2.71
61 62 7.933396 TGATATGTATGCCACAAGAAGAATTG 58.067 34.615 0.00 0.00 41.55 2.32
62 63 8.701908 ATGATATGTATGCCACAAGAAGAATT 57.298 30.769 0.00 0.00 41.55 2.17
63 64 9.970553 ATATGATATGTATGCCACAAGAAGAAT 57.029 29.630 0.00 0.00 41.55 2.40
129 130 8.333226 ACAGGGTTATAAGGGCTAATATATCC 57.667 38.462 0.00 0.00 0.00 2.59
130 131 8.142551 CGACAGGGTTATAAGGGCTAATATATC 58.857 40.741 0.00 0.00 0.00 1.63
132 133 6.381994 CCGACAGGGTTATAAGGGCTAATATA 59.618 42.308 0.00 0.00 0.00 0.86
135 136 3.326880 CCGACAGGGTTATAAGGGCTAAT 59.673 47.826 0.00 0.00 0.00 1.73
161 163 4.589216 GCACATGGCATATGTGGTATTT 57.411 40.909 25.36 0.00 46.85 1.40
182 184 2.191641 GCAAGCCCTCCCAGCTAG 59.808 66.667 0.00 0.00 40.49 3.42
194 196 2.235536 ATTTACCGCGTCGTGCAAGC 62.236 55.000 4.92 0.00 46.97 4.01
195 197 0.165079 AATTTACCGCGTCGTGCAAG 59.835 50.000 4.92 0.00 46.97 4.01
197 199 0.944788 TGAATTTACCGCGTCGTGCA 60.945 50.000 4.92 0.00 46.97 4.57
198 200 0.247145 CTGAATTTACCGCGTCGTGC 60.247 55.000 4.92 0.00 41.47 5.34
199 201 1.342555 TCTGAATTTACCGCGTCGTG 58.657 50.000 4.92 0.00 0.00 4.35
200 202 2.068837 TTCTGAATTTACCGCGTCGT 57.931 45.000 4.92 0.00 0.00 4.34
201 203 2.783316 GCTTTCTGAATTTACCGCGTCG 60.783 50.000 4.92 0.00 0.00 5.12
202 204 2.415512 AGCTTTCTGAATTTACCGCGTC 59.584 45.455 4.92 0.00 0.00 5.19
203 205 2.159627 CAGCTTTCTGAATTTACCGCGT 59.840 45.455 4.92 0.00 42.95 6.01
204 206 2.774007 CAGCTTTCTGAATTTACCGCG 58.226 47.619 0.00 0.00 42.95 6.46
206 208 3.751621 CAGCAGCTTTCTGAATTTACCG 58.248 45.455 6.87 0.00 42.95 4.02
207 209 3.505836 GCAGCAGCTTTCTGAATTTACC 58.494 45.455 15.02 0.00 42.95 2.85
241 248 5.574970 AGGAGGTAGAAATGGGATGAATC 57.425 43.478 0.00 0.00 0.00 2.52
244 251 4.635473 AGAAGGAGGTAGAAATGGGATGA 58.365 43.478 0.00 0.00 0.00 2.92
249 256 3.282885 GGCAAGAAGGAGGTAGAAATGG 58.717 50.000 0.00 0.00 0.00 3.16
260 267 2.351924 AAACTGGCCGGCAAGAAGGA 62.352 55.000 37.65 5.69 0.00 3.36
356 363 8.888716 CCTCCTCTAGCTTTTATCTTTTCTTTC 58.111 37.037 0.00 0.00 0.00 2.62
427 434 4.778213 TCGATCCATCCATCTCCTTTTT 57.222 40.909 0.00 0.00 0.00 1.94
529 542 2.104451 CACTGATAGAGCCAGCCATTCT 59.896 50.000 0.00 0.00 35.14 2.40
626 639 1.306148 GTAACTAATTCGCCAGGGGC 58.694 55.000 0.00 0.00 46.75 5.80
627 640 1.808891 CGGTAACTAATTCGCCAGGGG 60.809 57.143 0.00 0.00 0.00 4.79
638 651 9.280174 AGATCAAAGAAAATTCACGGTAACTAA 57.720 29.630 0.00 0.00 0.00 2.24
683 702 3.493699 GGTGCTACCATTATACAGGCGAA 60.494 47.826 0.00 0.00 38.42 4.70
746 765 2.633967 TCGGGGCTGACTTTTAACACTA 59.366 45.455 0.00 0.00 0.00 2.74
767 786 4.956075 ACAAATGAGTGGAAACTGGAAACT 59.044 37.500 0.00 0.00 0.00 2.66
869 889 8.049117 TGCATATCATCAATATTTACTCCCTCC 58.951 37.037 0.00 0.00 0.00 4.30
879 899 7.418337 ACCATGCATGCATATCATCAATATT 57.582 32.000 31.73 4.16 34.91 1.28
880 900 7.230712 CCTACCATGCATGCATATCATCAATAT 59.769 37.037 31.73 4.38 34.91 1.28
881 901 6.544564 CCTACCATGCATGCATATCATCAATA 59.455 38.462 31.73 13.84 34.91 1.90
882 902 5.359860 CCTACCATGCATGCATATCATCAAT 59.640 40.000 31.73 13.48 34.91 2.57
883 903 4.703093 CCTACCATGCATGCATATCATCAA 59.297 41.667 31.73 12.59 34.91 2.57
884 904 4.263594 ACCTACCATGCATGCATATCATCA 60.264 41.667 31.73 13.26 34.91 3.07
885 905 4.267536 ACCTACCATGCATGCATATCATC 58.732 43.478 31.73 0.00 34.91 2.92
886 906 4.263594 TGACCTACCATGCATGCATATCAT 60.264 41.667 31.73 18.95 34.91 2.45
887 907 3.072768 TGACCTACCATGCATGCATATCA 59.927 43.478 31.73 22.42 34.91 2.15
888 908 3.438087 GTGACCTACCATGCATGCATATC 59.562 47.826 31.73 20.47 34.91 1.63
889 909 3.415212 GTGACCTACCATGCATGCATAT 58.585 45.455 31.73 23.95 34.91 1.78
890 910 2.806382 CGTGACCTACCATGCATGCATA 60.806 50.000 31.73 16.54 34.91 3.14
891 911 1.683943 GTGACCTACCATGCATGCAT 58.316 50.000 27.46 27.46 37.08 3.96
917 937 2.374830 ATCGATCAGCCCTCAAGCGG 62.375 60.000 0.00 0.00 38.01 5.52
924 944 2.301296 CAGGTTATGATCGATCAGCCCT 59.699 50.000 30.11 27.70 40.64 5.19
982 1006 1.685355 ATGATCGACCGATGGTGGCA 61.685 55.000 9.83 1.75 35.25 4.92
984 1008 0.104855 ACATGATCGACCGATGGTGG 59.895 55.000 9.83 0.00 35.25 4.61
986 1010 0.824109 ACACATGATCGACCGATGGT 59.176 50.000 9.83 2.87 39.44 3.55
987 1011 1.202405 TCACACATGATCGACCGATGG 60.202 52.381 9.83 2.28 34.60 3.51
988 1012 1.854743 GTCACACATGATCGACCGATG 59.145 52.381 9.83 0.00 37.14 3.84
989 1013 1.202417 GGTCACACATGATCGACCGAT 60.202 52.381 13.65 4.42 38.68 4.18
990 1014 0.172578 GGTCACACATGATCGACCGA 59.827 55.000 13.65 0.00 38.68 4.69
991 1015 2.665777 GGTCACACATGATCGACCG 58.334 57.895 13.65 0.00 38.68 4.79
1032 1056 3.631686 CGACATCAGAGAGATCTCCTTGT 59.368 47.826 19.30 15.87 43.88 3.16
1047 1071 1.375908 GCTTGCCCTGACGACATCA 60.376 57.895 0.00 0.00 35.45 3.07
1099 1123 2.272797 CTCCTCCTCCTCGTCGGT 59.727 66.667 0.00 0.00 0.00 4.69
1179 1209 1.227639 CTAGCTGCTCATCACCATGC 58.772 55.000 4.91 0.00 0.00 4.06
1180 1210 1.415289 TCCTAGCTGCTCATCACCATG 59.585 52.381 4.91 0.00 0.00 3.66
1181 1211 1.798626 TCCTAGCTGCTCATCACCAT 58.201 50.000 4.91 0.00 0.00 3.55
1182 1212 1.571955 TTCCTAGCTGCTCATCACCA 58.428 50.000 4.91 0.00 0.00 4.17
1183 1213 2.492012 CATTCCTAGCTGCTCATCACC 58.508 52.381 4.91 0.00 0.00 4.02
1184 1214 2.158842 ACCATTCCTAGCTGCTCATCAC 60.159 50.000 4.91 0.00 0.00 3.06
1185 1215 2.121948 ACCATTCCTAGCTGCTCATCA 58.878 47.619 4.91 0.00 0.00 3.07
1197 1227 3.436035 CCATCATCATGGTCACCATTCCT 60.436 47.826 6.58 0.00 42.23 3.36
1231 1267 2.042843 ATCGGACGAAGGAGGCCT 60.043 61.111 3.86 3.86 33.87 5.19
1254 1290 1.607628 GAATGCAGCATGGAGATCACC 59.392 52.381 9.18 1.62 42.42 4.02
1263 1299 1.061411 CGTCGGTGAATGCAGCATG 59.939 57.895 9.18 0.00 42.53 4.06
1264 1300 2.108514 CCGTCGGTGAATGCAGCAT 61.109 57.895 0.52 0.52 42.53 3.79
1265 1301 2.741985 CCGTCGGTGAATGCAGCA 60.742 61.111 2.08 0.00 42.53 4.41
1279 1315 0.316442 CGTGTATATGTCGTCGCCGT 60.316 55.000 0.00 0.00 35.01 5.68
1314 1350 2.270205 CGAAGCATCCCAGCCAGT 59.730 61.111 0.00 0.00 34.23 4.00
1320 1356 4.467084 GGCCGACGAAGCATCCCA 62.467 66.667 0.00 0.00 0.00 4.37
1340 1376 0.463204 CATGCCACCTCTCTCGATGT 59.537 55.000 0.00 0.00 0.00 3.06
1350 1386 4.722700 GCGACCACCATGCCACCT 62.723 66.667 0.00 0.00 0.00 4.00
1437 1476 6.479884 AGGATATATTGACCTTGGCTTCATC 58.520 40.000 0.00 0.00 0.00 2.92
1485 1530 2.016704 CGTAGTGCCATCGATCCGC 61.017 63.158 0.00 0.27 0.00 5.54
1503 1548 8.794406 CGATTATGGCATGTTTTAAGTTAACAC 58.206 33.333 10.98 5.18 38.23 3.32
1504 1549 8.731605 TCGATTATGGCATGTTTTAAGTTAACA 58.268 29.630 10.98 0.00 39.58 2.41
1505 1550 9.730420 ATCGATTATGGCATGTTTTAAGTTAAC 57.270 29.630 10.98 0.00 0.00 2.01
1506 1551 9.729023 CATCGATTATGGCATGTTTTAAGTTAA 57.271 29.630 10.98 0.00 31.38 2.01
1507 1552 7.860373 GCATCGATTATGGCATGTTTTAAGTTA 59.140 33.333 10.98 0.00 35.99 2.24
1508 1553 6.697019 GCATCGATTATGGCATGTTTTAAGTT 59.303 34.615 10.98 0.00 35.99 2.66
1559 1611 1.963515 GGAATGCACACCACCTTCTTT 59.036 47.619 6.18 0.00 0.00 2.52
1643 1695 3.314331 CTCCACGCCCACAGGTCT 61.314 66.667 0.00 0.00 34.57 3.85
1934 1986 1.608109 TCGACGTTGGTGTTGCTACTA 59.392 47.619 2.20 0.00 0.00 1.82
1968 2020 1.079612 TCAGCTGATGGTGAGCACG 60.080 57.895 13.74 0.00 44.58 5.34
2042 2094 1.757118 TCCTGGATCTTGTCGATGGAC 59.243 52.381 0.12 0.12 43.71 4.02
2064 2116 1.962144 GCTGGTGCTTGCTGTCATT 59.038 52.632 0.00 0.00 36.03 2.57
2078 2130 2.094854 GCTGAAAGGATCAAACAGCTGG 60.095 50.000 19.93 0.00 46.66 4.85
2122 2174 6.771573 AGAGGAAGATGATGAATTCTGGATC 58.228 40.000 7.05 2.31 0.00 3.36
2141 2193 2.058595 GGCCTTCAGCGGTAGAGGA 61.059 63.158 16.93 0.00 45.17 3.71
2300 2353 1.098050 ATTCGAATCTGGCCTTGCAC 58.902 50.000 4.39 0.00 0.00 4.57
2368 2421 6.065976 TGCAGGCATTGGTAGCTATATATT 57.934 37.500 0.00 0.00 0.00 1.28
2374 2427 0.911769 ACTGCAGGCATTGGTAGCTA 59.088 50.000 19.93 0.00 0.00 3.32
2375 2428 0.038744 AACTGCAGGCATTGGTAGCT 59.961 50.000 19.93 0.00 0.00 3.32
2376 2429 0.890683 AAACTGCAGGCATTGGTAGC 59.109 50.000 19.93 0.00 0.00 3.58
2377 2430 2.557924 TGAAAACTGCAGGCATTGGTAG 59.442 45.455 19.93 0.00 0.00 3.18
2387 2440 1.869767 AGAAGCGAGTGAAAACTGCAG 59.130 47.619 13.48 13.48 0.00 4.41
2414 2467 3.659195 TGGGACGGAGGGAGTATTAGATA 59.341 47.826 0.00 0.00 0.00 1.98
2443 2496 6.523201 CCAAAATAAGTGTAAATCAGCGACAC 59.477 38.462 0.00 0.00 43.08 3.67
2448 2501 6.027749 CGTCCCAAAATAAGTGTAAATCAGC 58.972 40.000 0.00 0.00 0.00 4.26
2450 2503 6.239396 TCCGTCCCAAAATAAGTGTAAATCA 58.761 36.000 0.00 0.00 0.00 2.57
2503 2556 9.956640 ATAGATCAAGAGATTCAGAAACAGTTT 57.043 29.630 0.00 0.00 33.72 2.66
2584 2637 3.818121 TTAACAGTGCGGCGTGGCT 62.818 57.895 9.37 1.06 0.00 4.75
2630 2683 2.751806 CCTTTCAGCATGTTCCTCCTTC 59.248 50.000 0.00 0.00 37.40 3.46
2942 2996 1.810151 GGTAAACTTTCGGCTGCATGA 59.190 47.619 0.50 0.00 0.00 3.07
2993 3047 5.126869 TCACATTGTTCTGTGGTTGTGATTT 59.873 36.000 4.54 0.00 45.29 2.17
3011 3081 4.275689 TGCTGTGTTTTCTCGAATCACATT 59.724 37.500 14.00 0.00 36.12 2.71
3043 3120 4.635765 TCAATTGTAGAAATTCAGAGGCCG 59.364 41.667 5.13 0.00 0.00 6.13
3045 3122 7.150783 AGTTCAATTGTAGAAATTCAGAGGC 57.849 36.000 5.13 0.00 0.00 4.70
3086 3163 5.250982 TCAGATTCAATGAGCTTCACATGT 58.749 37.500 0.00 0.00 0.00 3.21
3100 3177 6.179906 CCCTTATCCTAGCTTCAGATTCAA 57.820 41.667 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.