Multiple sequence alignment - TraesCS4A01G152300

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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 TraesCS4A01G152300 chr4A 100.000 2481 0 0 1 2481 309374536 309377016 0.000000e+00 4582
1 TraesCS4A01G152300 chr4A 92.991 642 39 4 1768 2408 205013951 205014587 0.000000e+00 931
2 TraesCS4A01G152300 chr4A 94.915 354 12 5 2076 2428 141127828 141127480 1.300000e-152 549
3 TraesCS4A01G152300 chr4A 91.573 356 11 10 1921 2276 492155055 492155391 8.030000e-130 473
4 TraesCS4A01G152300 chr4A 93.778 225 8 6 2260 2481 141127184 141126963 1.420000e-87 333
5 TraesCS4A01G152300 chr4A 96.053 152 6 0 1 152 97810325 97810174 5.300000e-62 248
6 TraesCS4A01G152300 chr4A 94.375 160 8 1 1 159 115844783 115844624 6.850000e-61 244
7 TraesCS4A01G152300 chr5D 97.322 2278 52 7 145 2413 503330624 503328347 0.000000e+00 3860
8 TraesCS4A01G152300 chr5D 96.809 2288 64 7 145 2426 6236187 6238471 0.000000e+00 3812
9 TraesCS4A01G152300 chr1D 94.854 2293 93 15 145 2428 244768194 244765918 0.000000e+00 3557
10 TraesCS4A01G152300 chr1D 94.549 2293 109 10 145 2428 244201005 244198720 0.000000e+00 3528
11 TraesCS4A01G152300 chr1D 96.916 2075 58 5 145 2214 254476711 254474638 0.000000e+00 3472
12 TraesCS4A01G152300 chr1D 96.171 2037 71 6 145 2176 180356681 180358715 0.000000e+00 3323
13 TraesCS4A01G152300 chr2A 95.134 2096 67 18 419 2481 419795652 419793559 0.000000e+00 3273
14 TraesCS4A01G152300 chr2D 97.519 1693 35 5 145 1831 33929993 33931684 0.000000e+00 2887
15 TraesCS4A01G152300 chr3B 97.460 1693 36 5 145 1831 201492717 201491026 0.000000e+00 2881
16 TraesCS4A01G152300 chr6A 98.611 144 2 0 1 144 414360938 414360795 3.170000e-64 255
17 TraesCS4A01G152300 chr7A 97.917 144 3 0 1 144 431425005 431424862 1.470000e-62 250
18 TraesCS4A01G152300 chr7A 97.279 147 4 0 1 147 484900141 484899995 1.470000e-62 250
19 TraesCS4A01G152300 chr7A 93.252 163 10 1 1 163 555233976 555234137 3.190000e-59 239
20 TraesCS4A01G152300 chr7A 92.727 165 9 3 1 163 41095446 41095283 4.130000e-58 235
21 TraesCS4A01G152300 chr3A 97.917 144 3 0 1 144 718472144 718472287 1.470000e-62 250
22 TraesCS4A01G152300 chr3A 94.839 155 8 0 1 155 71086959 71087113 2.470000e-60 243


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 TraesCS4A01G152300 chr4A 309374536 309377016 2480 False 4582 4582 100.0000 1 2481 1 chr4A.!!$F2 2480
1 TraesCS4A01G152300 chr4A 205013951 205014587 636 False 931 931 92.9910 1768 2408 1 chr4A.!!$F1 640
2 TraesCS4A01G152300 chr4A 141126963 141127828 865 True 441 549 94.3465 2076 2481 2 chr4A.!!$R3 405
3 TraesCS4A01G152300 chr5D 503328347 503330624 2277 True 3860 3860 97.3220 145 2413 1 chr5D.!!$R1 2268
4 TraesCS4A01G152300 chr5D 6236187 6238471 2284 False 3812 3812 96.8090 145 2426 1 chr5D.!!$F1 2281
5 TraesCS4A01G152300 chr1D 244765918 244768194 2276 True 3557 3557 94.8540 145 2428 1 chr1D.!!$R2 2283
6 TraesCS4A01G152300 chr1D 244198720 244201005 2285 True 3528 3528 94.5490 145 2428 1 chr1D.!!$R1 2283
7 TraesCS4A01G152300 chr1D 254474638 254476711 2073 True 3472 3472 96.9160 145 2214 1 chr1D.!!$R3 2069
8 TraesCS4A01G152300 chr1D 180356681 180358715 2034 False 3323 3323 96.1710 145 2176 1 chr1D.!!$F1 2031
9 TraesCS4A01G152300 chr2A 419793559 419795652 2093 True 3273 3273 95.1340 419 2481 1 chr2A.!!$R1 2062
10 TraesCS4A01G152300 chr2D 33929993 33931684 1691 False 2887 2887 97.5190 145 1831 1 chr2D.!!$F1 1686
11 TraesCS4A01G152300 chr3B 201491026 201492717 1691 True 2881 2881 97.4600 145 1831 1 chr3B.!!$R1 1686

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
40 41 0.105039 CGCCAAGTAGAGTCCCATCC 59.895 60.0 0.00 0.0 0.0 3.51 F
41 42 0.105039 GCCAAGTAGAGTCCCATCCG 59.895 60.0 0.00 0.0 0.0 4.18 F
131 132 0.178900 ATCCGGAGACCCCCTAATCC 60.179 60.0 11.34 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1299 1306 2.751806 GCACTTCTCCAAATCCAGAAGG 59.248 50.000 12.18 4.09 46.86 3.46 R
1389 1396 6.266131 TCCAACTTTCAGGCATTAGGATAT 57.734 37.500 0.00 0.00 0.00 1.63 R
2045 2057 3.490348 CAGTTCAAATCTGGTTCCTGGT 58.510 45.455 0.00 0.00 0.00 4.00 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
19 20 2.348411 TATTGCCTAGCTTGCCTTCC 57.652 50.000 0.00 0.00 0.00 3.46
20 21 0.332632 ATTGCCTAGCTTGCCTTCCA 59.667 50.000 0.00 0.00 0.00 3.53
21 22 0.609131 TTGCCTAGCTTGCCTTCCAC 60.609 55.000 0.00 0.00 0.00 4.02
22 23 2.109126 GCCTAGCTTGCCTTCCACG 61.109 63.158 0.00 0.00 0.00 4.94
23 24 2.109126 CCTAGCTTGCCTTCCACGC 61.109 63.158 0.00 0.00 38.87 5.34
24 25 2.046314 TAGCTTGCCTTCCACGCC 60.046 61.111 0.00 0.00 39.36 5.68
25 26 2.803155 CTAGCTTGCCTTCCACGCCA 62.803 60.000 0.00 0.00 39.36 5.69
26 27 2.404566 TAGCTTGCCTTCCACGCCAA 62.405 55.000 0.00 0.00 39.36 4.52
27 28 2.956987 CTTGCCTTCCACGCCAAG 59.043 61.111 0.00 0.00 0.00 3.61
28 29 1.898574 CTTGCCTTCCACGCCAAGT 60.899 57.895 0.00 0.00 0.00 3.16
29 30 0.605319 CTTGCCTTCCACGCCAAGTA 60.605 55.000 0.00 0.00 0.00 2.24
30 31 0.605319 TTGCCTTCCACGCCAAGTAG 60.605 55.000 0.00 0.00 0.00 2.57
31 32 1.295423 GCCTTCCACGCCAAGTAGA 59.705 57.895 0.00 0.00 0.00 2.59
32 33 0.741221 GCCTTCCACGCCAAGTAGAG 60.741 60.000 0.00 0.00 0.00 2.43
33 34 0.608640 CCTTCCACGCCAAGTAGAGT 59.391 55.000 0.00 0.00 0.00 3.24
34 35 1.404315 CCTTCCACGCCAAGTAGAGTC 60.404 57.143 0.00 0.00 0.00 3.36
35 36 0.606604 TTCCACGCCAAGTAGAGTCC 59.393 55.000 0.00 0.00 0.00 3.85
36 37 1.218316 CCACGCCAAGTAGAGTCCC 59.782 63.158 0.00 0.00 0.00 4.46
37 38 1.541310 CCACGCCAAGTAGAGTCCCA 61.541 60.000 0.00 0.00 0.00 4.37
38 39 0.537188 CACGCCAAGTAGAGTCCCAT 59.463 55.000 0.00 0.00 0.00 4.00
39 40 0.824759 ACGCCAAGTAGAGTCCCATC 59.175 55.000 0.00 0.00 0.00 3.51
40 41 0.105039 CGCCAAGTAGAGTCCCATCC 59.895 60.000 0.00 0.00 0.00 3.51
41 42 0.105039 GCCAAGTAGAGTCCCATCCG 59.895 60.000 0.00 0.00 0.00 4.18
42 43 0.753262 CCAAGTAGAGTCCCATCCGG 59.247 60.000 0.00 0.00 0.00 5.14
43 44 1.688311 CCAAGTAGAGTCCCATCCGGA 60.688 57.143 6.61 6.61 38.83 5.14
50 51 2.357446 TCCCATCCGGACACGAGA 59.643 61.111 6.12 0.00 44.60 4.04
51 52 1.076265 TCCCATCCGGACACGAGAT 60.076 57.895 6.12 0.00 44.60 2.75
52 53 1.068083 CCCATCCGGACACGAGATG 59.932 63.158 6.12 0.00 44.60 2.90
53 54 1.391933 CCCATCCGGACACGAGATGA 61.392 60.000 6.12 0.00 43.86 2.92
54 55 0.459899 CCATCCGGACACGAGATGAA 59.540 55.000 6.12 0.00 43.86 2.57
55 56 1.536922 CCATCCGGACACGAGATGAAG 60.537 57.143 6.12 0.00 43.86 3.02
56 57 1.135139 CATCCGGACACGAGATGAAGT 59.865 52.381 6.12 0.00 43.86 3.01
57 58 0.809385 TCCGGACACGAGATGAAGTC 59.191 55.000 0.00 0.00 44.60 3.01
58 59 0.811915 CCGGACACGAGATGAAGTCT 59.188 55.000 0.00 0.00 44.60 3.24
59 60 1.202582 CCGGACACGAGATGAAGTCTT 59.797 52.381 0.00 0.00 44.60 3.01
60 61 2.520979 CGGACACGAGATGAAGTCTTC 58.479 52.381 5.58 5.58 44.60 2.87
61 62 2.095212 CGGACACGAGATGAAGTCTTCA 60.095 50.000 17.46 17.46 44.60 3.02
62 63 3.611766 CGGACACGAGATGAAGTCTTCAA 60.612 47.826 18.93 3.54 42.56 2.69
63 64 4.499183 GGACACGAGATGAAGTCTTCAAT 58.501 43.478 18.93 10.88 43.95 2.57
64 65 4.564769 GGACACGAGATGAAGTCTTCAATC 59.435 45.833 18.93 17.22 43.95 2.67
65 66 5.398603 ACACGAGATGAAGTCTTCAATCT 57.601 39.130 18.93 19.09 43.95 2.40
66 67 5.788450 ACACGAGATGAAGTCTTCAATCTT 58.212 37.500 18.93 10.87 43.95 2.40
67 68 5.636965 ACACGAGATGAAGTCTTCAATCTTG 59.363 40.000 18.93 22.15 43.95 3.02
68 69 5.636965 CACGAGATGAAGTCTTCAATCTTGT 59.363 40.000 24.60 24.60 43.95 3.16
69 70 6.808704 CACGAGATGAAGTCTTCAATCTTGTA 59.191 38.462 26.88 7.24 43.95 2.41
70 71 7.490725 CACGAGATGAAGTCTTCAATCTTGTAT 59.509 37.037 26.88 15.48 43.95 2.29
71 72 7.704472 ACGAGATGAAGTCTTCAATCTTGTATC 59.296 37.037 26.58 16.80 43.95 2.24
72 73 7.920151 CGAGATGAAGTCTTCAATCTTGTATCT 59.080 37.037 18.93 13.71 43.95 1.98
73 74 9.598517 GAGATGAAGTCTTCAATCTTGTATCTT 57.401 33.333 18.93 0.00 43.95 2.40
74 75 9.598517 AGATGAAGTCTTCAATCTTGTATCTTC 57.401 33.333 18.93 7.66 43.95 2.87
75 76 9.376075 GATGAAGTCTTCAATCTTGTATCTTCA 57.624 33.333 18.93 16.08 43.95 3.02
76 77 9.902684 ATGAAGTCTTCAATCTTGTATCTTCAT 57.097 29.630 18.93 17.75 43.95 2.57
81 82 9.809096 GTCTTCAATCTTGTATCTTCATAGTCA 57.191 33.333 0.00 0.00 0.00 3.41
90 91 9.186323 CTTGTATCTTCATAGTCAAATAGTCCG 57.814 37.037 0.00 0.00 0.00 4.79
91 92 8.459911 TGTATCTTCATAGTCAAATAGTCCGA 57.540 34.615 0.00 0.00 0.00 4.55
92 93 8.350722 TGTATCTTCATAGTCAAATAGTCCGAC 58.649 37.037 0.00 0.00 0.00 4.79
93 94 6.145338 TCTTCATAGTCAAATAGTCCGACC 57.855 41.667 0.00 0.00 0.00 4.79
94 95 5.655090 TCTTCATAGTCAAATAGTCCGACCA 59.345 40.000 0.00 0.00 0.00 4.02
95 96 5.925506 TCATAGTCAAATAGTCCGACCAA 57.074 39.130 0.00 0.00 0.00 3.67
96 97 6.288941 TCATAGTCAAATAGTCCGACCAAA 57.711 37.500 0.00 0.00 0.00 3.28
97 98 6.338146 TCATAGTCAAATAGTCCGACCAAAG 58.662 40.000 0.00 0.00 0.00 2.77
98 99 3.939066 AGTCAAATAGTCCGACCAAAGG 58.061 45.455 0.00 0.00 0.00 3.11
99 100 3.581332 AGTCAAATAGTCCGACCAAAGGA 59.419 43.478 0.00 0.00 34.99 3.36
100 101 4.225267 AGTCAAATAGTCCGACCAAAGGAT 59.775 41.667 0.00 0.00 40.30 3.24
101 102 5.424252 AGTCAAATAGTCCGACCAAAGGATA 59.576 40.000 0.00 0.00 40.30 2.59
102 103 6.099845 AGTCAAATAGTCCGACCAAAGGATAT 59.900 38.462 0.00 0.00 40.30 1.63
103 104 7.289317 AGTCAAATAGTCCGACCAAAGGATATA 59.711 37.037 0.00 0.00 40.30 0.86
104 105 7.929785 GTCAAATAGTCCGACCAAAGGATATAA 59.070 37.037 0.00 0.00 40.30 0.98
105 106 8.656806 TCAAATAGTCCGACCAAAGGATATAAT 58.343 33.333 0.00 0.00 40.30 1.28
106 107 8.936864 CAAATAGTCCGACCAAAGGATATAATC 58.063 37.037 0.00 0.00 40.30 1.75
125 126 2.923568 GGCTATCCGGAGACCCCC 60.924 72.222 11.34 1.76 0.00 5.40
126 127 2.201771 GCTATCCGGAGACCCCCT 59.798 66.667 11.34 0.00 0.00 4.79
127 128 1.463824 GCTATCCGGAGACCCCCTA 59.536 63.158 11.34 0.00 0.00 3.53
128 129 0.178941 GCTATCCGGAGACCCCCTAA 60.179 60.000 11.34 0.00 0.00 2.69
129 130 1.552719 GCTATCCGGAGACCCCCTAAT 60.553 57.143 11.34 0.00 0.00 1.73
130 131 2.458620 CTATCCGGAGACCCCCTAATC 58.541 57.143 11.34 0.00 0.00 1.75
131 132 0.178900 ATCCGGAGACCCCCTAATCC 60.179 60.000 11.34 0.00 0.00 3.01
132 133 1.074775 CCGGAGACCCCCTAATCCA 60.075 63.158 0.00 0.00 0.00 3.41
133 134 1.122019 CCGGAGACCCCCTAATCCAG 61.122 65.000 0.00 0.00 0.00 3.86
134 135 1.122019 CGGAGACCCCCTAATCCAGG 61.122 65.000 0.00 0.00 45.07 4.45
302 305 6.368791 TCAACTACACCAAATGATCTTTCGAG 59.631 38.462 0.00 0.00 0.00 4.04
339 342 5.520748 CCAGTTTATGGCCCCTTCTATAT 57.479 43.478 0.00 0.00 43.83 0.86
353 356 6.353602 CCCCTTCTATATGGTACCAGTTGTTT 60.354 42.308 21.41 4.59 0.00 2.83
354 357 7.147444 CCCCTTCTATATGGTACCAGTTGTTTA 60.147 40.741 21.41 6.93 0.00 2.01
400 403 2.673368 GGCTCACGATTCGACTTTGATT 59.327 45.455 13.95 0.00 0.00 2.57
438 442 4.323792 CCAAGATCAAGTCCTAGGAAGCAA 60.324 45.833 14.65 0.00 0.00 3.91
500 504 7.019388 TGGCTCCCTCTTTAGTGAGATTATAT 58.981 38.462 0.00 0.00 36.23 0.86
931 936 8.978539 GGGCTCTTTTGTGTAGAAAAATAAAAG 58.021 33.333 0.00 0.00 36.80 2.27
1019 1024 3.023119 CAATGCAGCAGGGTTGGTTATA 58.977 45.455 0.00 0.00 31.36 0.98
1062 1067 4.111577 AGGTGGTTCATAGATCTTTGGGA 58.888 43.478 12.51 0.73 0.00 4.37
1299 1306 5.172205 GGATAATCCTAGAATTCCGTCTGC 58.828 45.833 0.65 0.00 32.53 4.26
1346 1353 6.682863 CGATTTTCAAGAACGCGAATCTTATT 59.317 34.615 23.96 6.44 35.43 1.40
1389 1396 1.745232 AATCATCCGCGCCTTAAACA 58.255 45.000 0.00 0.00 0.00 2.83
1422 1429 1.635487 TGAAAGTTGGATAGGCTGGCT 59.365 47.619 9.28 9.28 0.00 4.75
1427 1434 3.321950 AGTTGGATAGGCTGGCTCTTAT 58.678 45.455 7.13 0.00 0.00 1.73
1454 1461 7.432148 AAGGATTACATAACCCCCAATTTTC 57.568 36.000 0.00 0.00 0.00 2.29
1572 1580 6.985188 TCTTTTCCTAGATGAAACGGAATG 57.015 37.500 0.00 0.00 35.63 2.67
2385 2424 8.840321 CCTTTGTGAAAGAGTAGAATGAGAAAA 58.160 33.333 0.00 0.00 41.02 2.29
2420 2459 9.956640 TCTTAAACCCATTGCATTGATAAAAAT 57.043 25.926 10.14 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.563879 TGGAAGGCAAGCTAGGCAATA 59.436 47.619 11.85 0.00 36.37 1.90
1 2 0.332632 TGGAAGGCAAGCTAGGCAAT 59.667 50.000 11.85 0.52 36.37 3.56
2 3 0.609131 GTGGAAGGCAAGCTAGGCAA 60.609 55.000 11.85 0.00 36.37 4.52
3 4 1.002134 GTGGAAGGCAAGCTAGGCA 60.002 57.895 11.85 0.00 36.37 4.75
4 5 2.109126 CGTGGAAGGCAAGCTAGGC 61.109 63.158 1.78 1.78 0.00 3.93
5 6 4.208632 CGTGGAAGGCAAGCTAGG 57.791 61.111 0.00 0.00 0.00 3.02
14 15 0.608640 ACTCTACTTGGCGTGGAAGG 59.391 55.000 0.00 0.00 32.33 3.46
15 16 1.404315 GGACTCTACTTGGCGTGGAAG 60.404 57.143 0.00 0.00 32.33 3.46
16 17 0.606604 GGACTCTACTTGGCGTGGAA 59.393 55.000 0.00 0.00 32.33 3.53
17 18 1.255667 GGGACTCTACTTGGCGTGGA 61.256 60.000 0.00 0.00 0.00 4.02
18 19 1.218316 GGGACTCTACTTGGCGTGG 59.782 63.158 0.00 0.00 0.00 4.94
19 20 0.537188 ATGGGACTCTACTTGGCGTG 59.463 55.000 0.00 0.00 0.00 5.34
20 21 0.824759 GATGGGACTCTACTTGGCGT 59.175 55.000 0.00 0.00 0.00 5.68
21 22 0.105039 GGATGGGACTCTACTTGGCG 59.895 60.000 0.00 0.00 0.00 5.69
22 23 0.105039 CGGATGGGACTCTACTTGGC 59.895 60.000 0.00 0.00 0.00 4.52
23 24 0.753262 CCGGATGGGACTCTACTTGG 59.247 60.000 0.00 0.00 38.47 3.61
24 25 1.776662 TCCGGATGGGACTCTACTTG 58.223 55.000 0.00 0.00 40.94 3.16
33 34 1.076265 ATCTCGTGTCCGGATGGGA 60.076 57.895 7.81 6.91 44.68 4.37
34 35 1.068083 CATCTCGTGTCCGGATGGG 59.932 63.158 7.81 0.18 37.74 4.00
35 36 0.459899 TTCATCTCGTGTCCGGATGG 59.540 55.000 7.81 0.00 39.81 3.51
36 37 1.135139 ACTTCATCTCGTGTCCGGATG 59.865 52.381 7.81 0.00 40.27 3.51
37 38 1.405821 GACTTCATCTCGTGTCCGGAT 59.594 52.381 7.81 0.00 33.95 4.18
38 39 0.809385 GACTTCATCTCGTGTCCGGA 59.191 55.000 0.00 0.00 33.95 5.14
39 40 0.811915 AGACTTCATCTCGTGTCCGG 59.188 55.000 0.00 0.00 28.16 5.14
40 41 2.095212 TGAAGACTTCATCTCGTGTCCG 60.095 50.000 13.99 0.00 36.27 4.79
41 42 3.577649 TGAAGACTTCATCTCGTGTCC 57.422 47.619 13.99 0.00 36.27 4.02
42 43 5.406649 AGATTGAAGACTTCATCTCGTGTC 58.593 41.667 18.38 8.42 39.84 3.67
43 44 5.398603 AGATTGAAGACTTCATCTCGTGT 57.601 39.130 18.38 1.77 39.84 4.49
44 45 5.636965 ACAAGATTGAAGACTTCATCTCGTG 59.363 40.000 25.43 25.43 39.84 4.35
45 46 5.788450 ACAAGATTGAAGACTTCATCTCGT 58.212 37.500 18.38 14.45 39.84 4.18
46 47 7.920151 AGATACAAGATTGAAGACTTCATCTCG 59.080 37.037 18.38 13.92 39.84 4.04
47 48 9.598517 AAGATACAAGATTGAAGACTTCATCTC 57.401 33.333 18.38 16.68 39.84 2.75
48 49 9.598517 GAAGATACAAGATTGAAGACTTCATCT 57.401 33.333 18.38 17.79 39.84 2.90
49 50 9.376075 TGAAGATACAAGATTGAAGACTTCATC 57.624 33.333 18.38 16.14 39.84 2.92
50 51 9.902684 ATGAAGATACAAGATTGAAGACTTCAT 57.097 29.630 18.38 20.84 39.84 2.57
55 56 9.809096 TGACTATGAAGATACAAGATTGAAGAC 57.191 33.333 0.00 0.00 0.00 3.01
64 65 9.186323 CGGACTATTTGACTATGAAGATACAAG 57.814 37.037 0.00 0.00 0.00 3.16
65 66 8.909923 TCGGACTATTTGACTATGAAGATACAA 58.090 33.333 0.00 0.00 0.00 2.41
66 67 8.350722 GTCGGACTATTTGACTATGAAGATACA 58.649 37.037 0.00 0.00 0.00 2.29
67 68 7.808856 GGTCGGACTATTTGACTATGAAGATAC 59.191 40.741 8.23 0.00 33.21 2.24
68 69 7.504574 TGGTCGGACTATTTGACTATGAAGATA 59.495 37.037 8.23 0.00 33.21 1.98
69 70 6.323996 TGGTCGGACTATTTGACTATGAAGAT 59.676 38.462 8.23 0.00 33.21 2.40
70 71 5.655090 TGGTCGGACTATTTGACTATGAAGA 59.345 40.000 8.23 0.00 33.21 2.87
71 72 5.902681 TGGTCGGACTATTTGACTATGAAG 58.097 41.667 8.23 0.00 33.21 3.02
72 73 5.925506 TGGTCGGACTATTTGACTATGAA 57.074 39.130 8.23 0.00 33.21 2.57
73 74 5.925506 TTGGTCGGACTATTTGACTATGA 57.074 39.130 8.23 0.00 33.21 2.15
74 75 5.523916 CCTTTGGTCGGACTATTTGACTATG 59.476 44.000 8.23 0.00 33.21 2.23
75 76 5.424252 TCCTTTGGTCGGACTATTTGACTAT 59.576 40.000 8.23 0.00 33.21 2.12
76 77 4.773674 TCCTTTGGTCGGACTATTTGACTA 59.226 41.667 8.23 0.00 33.21 2.59
77 78 3.581332 TCCTTTGGTCGGACTATTTGACT 59.419 43.478 8.23 0.00 33.21 3.41
78 79 3.934068 TCCTTTGGTCGGACTATTTGAC 58.066 45.455 8.23 0.00 0.00 3.18
79 80 4.837093 ATCCTTTGGTCGGACTATTTGA 57.163 40.909 8.23 0.91 32.41 2.69
80 81 8.848474 ATTATATCCTTTGGTCGGACTATTTG 57.152 34.615 8.23 0.00 32.41 2.32
81 82 8.101419 GGATTATATCCTTTGGTCGGACTATTT 58.899 37.037 8.23 0.00 46.19 1.40
82 83 7.621796 GGATTATATCCTTTGGTCGGACTATT 58.378 38.462 8.23 0.00 46.19 1.73
83 84 7.184067 GGATTATATCCTTTGGTCGGACTAT 57.816 40.000 8.23 0.00 46.19 2.12
84 85 6.600882 GGATTATATCCTTTGGTCGGACTA 57.399 41.667 8.23 0.00 46.19 2.59
85 86 5.485209 GGATTATATCCTTTGGTCGGACT 57.515 43.478 8.23 0.00 46.19 3.85
108 109 2.090377 TAGGGGGTCTCCGGATAGCC 62.090 65.000 25.67 25.67 36.01 3.93
109 110 0.178941 TTAGGGGGTCTCCGGATAGC 60.179 60.000 3.57 7.72 36.01 2.97
110 111 2.458620 GATTAGGGGGTCTCCGGATAG 58.541 57.143 3.57 0.00 36.01 2.08
111 112 1.078324 GGATTAGGGGGTCTCCGGATA 59.922 57.143 3.57 0.00 36.01 2.59
112 113 0.178900 GGATTAGGGGGTCTCCGGAT 60.179 60.000 3.57 0.00 36.01 4.18
113 114 1.235112 GGATTAGGGGGTCTCCGGA 59.765 63.158 2.93 2.93 36.01 5.14
114 115 1.074775 TGGATTAGGGGGTCTCCGG 60.075 63.158 0.00 0.00 36.01 5.14
115 116 1.122019 CCTGGATTAGGGGGTCTCCG 61.122 65.000 0.00 0.00 43.33 4.63
116 117 2.855669 CCTGGATTAGGGGGTCTCC 58.144 63.158 0.00 0.00 43.33 3.71
124 125 2.478872 TGAGGGAGTCCTGGATTAGG 57.521 55.000 9.58 0.00 45.05 2.69
125 126 3.072184 CCATTGAGGGAGTCCTGGATTAG 59.928 52.174 9.58 0.00 45.05 1.73
126 127 3.048600 CCATTGAGGGAGTCCTGGATTA 58.951 50.000 9.58 0.00 45.05 1.75
127 128 1.849039 CCATTGAGGGAGTCCTGGATT 59.151 52.381 9.58 0.00 45.05 3.01
128 129 1.516110 CCATTGAGGGAGTCCTGGAT 58.484 55.000 9.58 0.00 45.05 3.41
129 130 1.274703 GCCATTGAGGGAGTCCTGGA 61.275 60.000 16.67 0.00 45.05 3.86
130 131 1.225704 GCCATTGAGGGAGTCCTGG 59.774 63.158 9.58 9.57 45.05 4.45
131 132 1.153289 CGCCATTGAGGGAGTCCTG 60.153 63.158 9.58 0.00 45.05 3.86
133 134 0.035439 TTTCGCCATTGAGGGAGTCC 60.035 55.000 0.00 0.00 38.09 3.85
134 135 1.740025 CTTTTCGCCATTGAGGGAGTC 59.260 52.381 0.00 0.00 38.09 3.36
135 136 1.073923 ACTTTTCGCCATTGAGGGAGT 59.926 47.619 0.00 0.00 38.09 3.85
136 137 1.826385 ACTTTTCGCCATTGAGGGAG 58.174 50.000 0.00 0.00 38.09 4.30
137 138 2.939640 GCTACTTTTCGCCATTGAGGGA 60.940 50.000 0.00 0.00 38.09 4.20
138 139 1.401905 GCTACTTTTCGCCATTGAGGG 59.598 52.381 0.00 0.00 38.09 4.30
139 140 1.401905 GGCTACTTTTCGCCATTGAGG 59.598 52.381 0.00 0.00 45.59 3.86
140 141 2.832672 GGCTACTTTTCGCCATTGAG 57.167 50.000 0.00 0.00 45.59 3.02
302 305 3.477210 AACTGGAGAGTCTTGACCAAC 57.523 47.619 0.00 0.00 31.85 3.77
339 342 7.825331 TTCAATGAATAAACAACTGGTACCA 57.175 32.000 15.39 15.39 0.00 3.25
400 403 6.320434 TGATCTTGGTACCAATCCATAACA 57.680 37.500 27.24 16.27 35.20 2.41
438 442 4.392754 CGTACCGGCTGTTAAAATTAGGTT 59.607 41.667 0.00 0.00 32.47 3.50
464 468 4.591321 AGAGGGAGCCATTTTCATTGTA 57.409 40.909 0.00 0.00 0.00 2.41
500 504 1.702182 TTGGTTCAGGCATTTGCTCA 58.298 45.000 2.12 0.00 41.70 4.26
567 571 7.308469 CCGAACAGTACTATAGGAATCTGTACC 60.308 44.444 8.31 4.25 35.53 3.34
931 936 1.620323 AGTTTGAAAGATTGCCCTGCC 59.380 47.619 0.00 0.00 0.00 4.85
1019 1024 6.319658 CACCTCATGTTTGACTAGCCAATTAT 59.680 38.462 0.00 0.00 0.00 1.28
1062 1067 5.600484 AGTCTCTATTCCTCGGTGATCAAAT 59.400 40.000 0.00 0.00 0.00 2.32
1299 1306 2.751806 GCACTTCTCCAAATCCAGAAGG 59.248 50.000 12.18 4.09 46.86 3.46
1389 1396 6.266131 TCCAACTTTCAGGCATTAGGATAT 57.734 37.500 0.00 0.00 0.00 1.63
1438 1445 7.846066 TGTATTTCAGAAAATTGGGGGTTATG 58.154 34.615 0.00 0.00 36.49 1.90
1454 1461 8.403236 TCATTCAATGAGCATCTTGTATTTCAG 58.597 33.333 0.00 0.00 33.59 3.02
2045 2057 3.490348 CAGTTCAAATCTGGTTCCTGGT 58.510 45.455 0.00 0.00 0.00 4.00
2385 2424 7.716799 TGCAATGGGTTTAAGATTCATTAGT 57.283 32.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.