Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015059.1 Kokia drynarioides strain JFW-HI SEQ_130103, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 126363
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 258 characters in sequence are not A, C, G, or T
Found at i:1222 original size:2 final size:2
Alignment explanation
Indices: 1215--1239 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1205 TTATTAACTA
1215 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1240 AGAAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1329 original size:17 final size:18
Alignment explanation
Indices: 1307--1341 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1297 AACGTAACGG
1307 GGAAAAAG-AAAAGGGAA
1 GGAAAAAGAAAAAGGGAA
1324 GGAAAAAGAAAAAGGGAA
1 GGAAAAAGAAAAAGGGAA
1342 AACTAGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (18 bp):
GGAAAAAGAAAAAGGGAA
Found at i:6189 original size:2 final size:2
Alignment explanation
Indices: 6182--6222 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
6172 AAGAAATCTG
6182 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
6223 TTGGAGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7230 original size:7 final size:7
Alignment explanation
Indices: 7218--7288 Score: 72
Period size: 7 Copynumber: 9.7 Consensus size: 7
7208 TTTGAAGGAA
7218 AAGAAGG
1 AAGAAGG
7225 AAGAAGG
1 AAGAAGG
7232 AAGAAGG
1 AAGAAGG
7239 AAGAAGG
1 AAGAAGG
*
7246 -AGAAGA
1 AAGAAGG
*
7252 AAGAAGA
1 AAGAAGG
7259 AAGAAAGG
1 AAG-AAGG
*
7267 AGAAAGAGG
1 A-AGA-AGG
7276 AAGAAGG
1 AAGAAGG
7283 AGAGAA
1 A-AGAA
7289 AGATAATGTA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
6 5 0.09
7 34 0.62
8 11 0.20
9 5 0.09
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (7 bp):
AAGAAGG
Found at i:7241 original size:27 final size:26
Alignment explanation
Indices: 7211--7288 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 26
7201 CAACGGGTTT
7211 GAAGGAAAAGAAGGAAGAAGGAAGAAG
1 GAAGGAAAAG-AGGAAGAAGGAAGAAG
* *
7238 GAA-G-AAGGA-GAAGAAAGAAGAAAG
1 GAAGGAAAAGAGGAAGAAGGAAG-AAG
*
7262 AAAGGAGAAAGAGGAAGAAGGAGAGAA
1 GAAGGA-AAAGAGGAAGAAGGA-AGAA
7289 AGATAATGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
23 10 0.25
24 6 0.15
25 4 0.10
26 1 0.03
27 7 0.17
28 10 0.25
29 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (26 bp):
GAAGGAAAAGAGGAAGAAGGAAGAAG
Found at i:7326 original size:13 final size:12
Alignment explanation
Indices: 7298--7322 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7288 AAGATAATGT
7298 ATTTATTTTTAA
1 ATTTATTTTTAA
7310 ATTTATTTTTAA
1 ATTTATTTTTAA
7322 A
1 A
7323 ATTTTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTATTTTTAA
Found at i:8000 original size:16 final size:16
Alignment explanation
Indices: 7956--8004 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
7946 AAATATTCTA
*
7956 AATTAATTACCCAAAT
1 AATTAATTACCAAAAT
*
7972 --TTAATATA-AAAAAT
1 AATTAAT-TACCAAAAT
7986 AATTAATTACCAAAAT
1 AATTAATTACCAAAAT
8002 AAT
1 AAT
8005 ATCCCCATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 8
0.70 0.08 0.22
Matches are distributed among these distances:
14 9 0.35
15 4 0.15
16 13 0.50
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTAATTACCAAAAT
Found at i:9393 original size:42 final size:43
Alignment explanation
Indices: 9312--9403 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 43
9302 ATTAACATGT
* * *
9312 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATGACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
9355 TAAA-TATATGACTTTACTCTTATTAATAT-CTTGACATGTTA-
1 TAAATTATATGACTTGACTCGTATTAATATGCTTG-CATGTTAC
*
9396 TTAATTAT
1 TAAATTAT
9404 GCAGTTCATC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
41 6 0.15
42 31 0.76
43 4 0.10
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATGACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:9864 original size:6 final size:6
Alignment explanation
Indices: 9853--9892 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
9843 CTCCTATCCT
* * *
9853 AGAGCC AGAGCC AGAGCC AGAGCC AAAGCA AGAGCA AGAG
1 AGAGCC AGAGCC AGAGCC AGAGCC AGAGCC AGAGCC AGAG
9893 GAAGAGACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.42, C:0.25, G:0.33, T:0.00
Consensus pattern (6 bp):
AGAGCC
Found at i:10035 original size:45 final size:45
Alignment explanation
Indices: 9962--10053 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
9952 GCCTAGCTCA
* * *
9962 TCAAGCTAAAGATATTAGCCTCAATTTGACGAGCCACCGCAATAC
1 TCAAGCCAAAGATATCAGCCTCAATTTGACGAGCCACCACAATAC
* * * * *
10007 TCAAGCCAAGGATATCAGCGTCAGTTTGACGAGTCATCACAATAC
1 TCAAGCCAAAGATATCAGCCTCAATTTGACGAGCCACCACAATAC
10052 TC
1 TC
10054 TACTCCTCCC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (45 bp):
TCAAGCCAAAGATATCAGCCTCAATTTGACGAGCCACCACAATAC
Found at i:10426 original size:14 final size:14
Alignment explanation
Indices: 10403--10442 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
10393 CTTTTCTTTA
*
10403 AAACCTTAAATTTG
1 AAACCCTAAATTTG
10417 AAACCCTAAAATTTG
1 AAACCCT-AAATTTG
*
10432 AAACTCTAAAT
1 AAACCCTAAAT
10443 CATTATACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.30
Consensus pattern (14 bp):
AAACCCTAAATTTG
Found at i:10430 original size:15 final size:15
Alignment explanation
Indices: 10410--10441 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
10400 TTAAAACCTT
10410 AAATTTGAAACCCTA
1 AAATTTGAAACCCTA
*
10425 AAATTTGAAACTCTA
1 AAATTTGAAACCCTA
10440 AA
1 AA
10442 TCATTATACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (15 bp):
AAATTTGAAACCCTA
Found at i:12873 original size:24 final size:24
Alignment explanation
Indices: 12836--12905 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
12826 ACCATACACG
*
12836 GAGTTGGATCTTCATTTTCTGCTA
1 GAGTTGGATCTTCATTTTCTACTA
* * *
12860 GAGTTAGATATTCATTTTCTACTG
1 GAGTTGGATCTTCATTTTCTACTA
*
12884 GATTTGGATCTTCATTTTCTAC
1 GAGTTGGATCTTCATTTTCTAC
12906 AAGTTTCACA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.47
Consensus pattern (24 bp):
GAGTTGGATCTTCATTTTCTACTA
Found at i:13278 original size:20 final size:19
Alignment explanation
Indices: 13253--13295 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
13243 TTATCCATTT
13253 TAAATAAATTTGTTAAA-AAA
1 TAAATAAA-TT-TTAAATAAA
13273 TAAATAAATTTTAAATAAA
1 TAAATAAATTTTAAATAAA
13292 TAAA
1 TAAA
13296 ATACAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.23
19 9 0.41
20 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
TAAATAAATTTTAAATAAA
Found at i:13297 original size:20 final size:18
Alignment explanation
Indices: 13253--13309 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 18
13243 TTATCCATTT
13253 TAAATAAATTTGTTAAAAAA
1 TAAATAAA-TT-TTAAAAAA
13273 TAAATAAATTTTAAATAAA
1 TAAATAAATTTTAAA-AAA
*
13292 TAAAATACAAATTTAAAA
1 T-AAATA-AATTTTAAAA
13310 TTATATAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 5 0.15
19 6 0.18
20 14 0.42
21 8 0.24
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
TAAATAAATTTTAAAAAA
Found at i:18478 original size:13 final size:13
Alignment explanation
Indices: 18456--18489 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
18446 TAAGATGTCA
18456 CTTTTT-TATTTT
1 CTTTTTCTATTTT
18468 CTTTTTCTATTTT
1 CTTTTTCTATTTT
*
18481 TTTTTTCTA
1 CTTTTTCTA
18490 AAATTATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (13 bp):
CTTTTTCTATTTT
Found at i:18996 original size:21 final size:20
Alignment explanation
Indices: 18961--19005 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 20
18951 AAGCCACAAT
18961 TATTTTTTTAAAAAA-TAAA
1 TATTTTTTTAAAAAAGTAAA
18980 TATTTTATTTCAAAAAAGTAAA
1 TATTTT-TTT-AAAAAAGTAAA
19002 TATT
1 TATT
19006 GAAAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 3 0.13
21 6 0.26
22 8 0.35
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
TATTTTTTTAAAAAAGTAAA
Found at i:30978 original size:18 final size:18
Alignment explanation
Indices: 30957--30999 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
30947 AATAATTTTT
30957 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
30975 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
30993 TTAATTA
1 TTAATTA
31000 TAACTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:31415 original size:22 final size:22
Alignment explanation
Indices: 31349--31404 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 22
31339 AATGAGAGAA
*
31349 AAAAAAATTAAAAATTTGAATTCAC
1 AAAAAAATTAAAAATTTGAA---AG
31374 AAAAAAATTAAAAATTTGAAAG
1 AAAAAAATTAAAAATTTGAAAG
31396 AAAAAAATT
1 AAAAAAATT
31405 CATATTTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 10 0.33
25 20 0.67
ACGTcount: A:0.66, C:0.04, G:0.05, T:0.25
Consensus pattern (22 bp):
AAAAAAATTAAAAATTTGAAAG
Found at i:42676 original size:4 final size:4
Alignment explanation
Indices: 42669--42696 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
42659 CAAATTTATT
42669 TTAG TTAG TTAG TTAG TTAG TTAG TTAG
1 TTAG TTAG TTAG TTAG TTAG TTAG TTAG
42697 ATACGTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TTAG
Found at i:49501 original size:20 final size:17
Alignment explanation
Indices: 49459--49493 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
49449 TCGTATACTC
49459 TCAACAGAAGTAAATTA
1 TCAACAGAAGTAAATTA
49476 TCAACAGAAGTAAATTA
1 TCAACAGAAGTAAATTA
49493 T
1 T
49494 TGTCAACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.26
Consensus pattern (17 bp):
TCAACAGAAGTAAATTA
Found at i:53303 original size:7 final size:7
Alignment explanation
Indices: 53291--53327 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
53281 TTTCGTTTTC
53291 TATTTAA
1 TATTTAA
53298 TATTTAA
1 TATTTAA
53305 TATTTAA
1 TATTTAA
53312 TATTTTAA
1 TA-TTTAA
53320 TATTTAA
1 TATTTAA
53327 T
1 T
53328 CTCAAACCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TATTTAA
Found at i:53320 original size:15 final size:14
Alignment explanation
Indices: 53291--53327 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
53281 TTTCGTTTTC
53291 TATTTAATATTTAA
1 TATTTAATATTTAA
53305 TATTTAATATTTTAA
1 TATTTAATA-TTTAA
53320 TATTTAAT
1 TATTTAAT
53328 CTCAAACCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTAATATTTAA
Found at i:53783 original size:6 final size:6
Alignment explanation
Indices: 53772--53819 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
53762 GTGAGAAACC
53772 TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA
1 TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA
53820 GAATGTAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (6 bp):
TCCAAA
Found at i:55399 original size:40 final size:40
Alignment explanation
Indices: 55345--55437 Score: 168
Period size: 40 Copynumber: 2.3 Consensus size: 40
55335 CGAGGGACCA
*
55345 AACAACAAACTGTAAAGAAACGTGGGAGCCATTGACAAATT
1 AACAA-AAGCTGTAAAGAAACGTGGGAGCCATTGACAAATT
55386 AACAAAAGCTGTAAAGAAACGTGGGAGCCATTGACAAATT
1 AACAAAAGCTGTAAAGAAACGTGGGAGCCATTGACAAATT
55426 AACAAAAGCTGT
1 AACAAAAGCTGT
55438 CCTTTACGGT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 46 0.90
41 5 0.10
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.17
Consensus pattern (40 bp):
AACAAAAGCTGTAAAGAAACGTGGGAGCCATTGACAAATT
Found at i:55798 original size:13 final size:13
Alignment explanation
Indices: 55780--55806 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55770 CGATTGTTTT
55780 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
55793 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
55806 A
1 A
55807 TAATCCCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:57876 original size:22 final size:22
Alignment explanation
Indices: 57851--57894 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
57841 ATCCTAATTC
*
57851 TAAAAAAATTGAAAAAAATATA
1 TAAAAAAATTCAAAAAAATATA
* *
57873 TAAAAAATTTCAGAAAAATATA
1 TAAAAAAATTCAAAAAAATATA
57895 ATAATAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (22 bp):
TAAAAAAATTCAAAAAAATATA
Found at i:57888 original size:24 final size:23
Alignment explanation
Indices: 57861--57905 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
57851 TAAAAAAATT
57861 GAAAAAAATATATAAAAAATTTCA
1 GAAAAAAATA-ATAAAAAATTTCA
* *
57885 GAAAAATATAATAATAAATTT
1 GAAAAAAATAATAAAAAATTT
57906 AAATTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (23 bp):
GAAAAAAATAATAAAAAATTTCA
Found at i:57922 original size:6 final size:6
Alignment explanation
Indices: 57913--57951 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
57903 TTTAAATTTT
*
57913 ATATTA ATATTA ATATTA ATATAA ATATACTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA ATAT--TA ATATTA A
57952 ATAAAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 24 0.83
8 5 0.17
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
ATATTA
Found at i:57959 original size:26 final size:26
Alignment explanation
Indices: 57912--57964 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
57902 ATTTAAATTT
* * *
57912 TATATTAATATTAATATTAATATAAA
1 TATACTAATATTAATATAAATAAAAA
57938 TATACTAATATTAA-ATAAAATAAAAA
1 TATACTAATATTAATAT-AAATAAAAA
57964 T
1 T
57965 TTAAGTTGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
TATACTAATATTAATATAAATAAAAA
Found at i:58557 original size:16 final size:18
Alignment explanation
Indices: 58514--58557 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
58504 TTTATAATTC
58514 TGTTAATTGAATAAATTTAG
1 TGTTAATTG--TAAATTTAG
58534 TGTTAATTGTAAATTT-G
1 TGTTAATTGTAAATTTAG
58551 T-TTAATT
1 TGTTAATT
58558 TATTAAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.25
17 2 0.08
18 7 0.29
20 9 0.38
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (18 bp):
TGTTAATTGTAAATTTAG
Found at i:59471 original size:23 final size:23
Alignment explanation
Indices: 59444--59507 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
59434 TCATTAACAT
*
59444 TGTTCGTGAACGTGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
59467 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
**
59490 -GTTAAATGAACATGTTCG
1 TGTT-CGTGAACATGTTCG
59508 TGAACATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 3 0.08
23 34 0.92
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:59517 original size:23 final size:23
Alignment explanation
Indices: 59473--59518 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
59463 TTAATGTTCG
* *
59473 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
59496 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
59519 CAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:64595 original size:9 final size:9
Alignment explanation
Indices: 64581--64605 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
64571 ATCATAAGCT
64581 AAAAAAAGA
1 AAAAAAAGA
64590 AAAAAAAGA
1 AAAAAAAGA
64599 AAAAAAA
1 AAAAAAA
64606 AAAGAAAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:72556 original size:15 final size:15
Alignment explanation
Indices: 72538--72580 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
72528 CACTGTCGAA
72538 TTCATCATCATCTTC
1 TTCATCATCATCTTC
* * *
72553 TTCATCCTCCTCCTC
1 TTCATCATCATCTTC
*
72568 TTCATCAGCATCT
1 TTCATCATCATCT
72581 GAAAGGTAAG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.16, C:0.40, G:0.02, T:0.42
Consensus pattern (15 bp):
TTCATCATCATCTTC
Found at i:74962 original size:31 final size:31
Alignment explanation
Indices: 74890--74964 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
74880 ATATTTTGTT
* * *
74890 TCATTATACTAAATTATTTAAATATTATTTA
1 TCATTATATTTAATTATTTAAATATCATTTA
*
74921 TCATTGTATTTAATTATTTAAATATCATTTA
1 TCATTATATTTAATTATTTAAATATCATTTA
*
74952 TTATTATATTTAA
1 TCATTATATTTAA
74965 AATTTTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.55
Consensus pattern (31 bp):
TCATTATATTTAATTATTTAAATATCATTTA
Found at i:75017 original size:26 final size:26
Alignment explanation
Indices: 74965--75017 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
74955 TTATATTTAA
* *
74965 AATTTTAAAATATTTTATATATCATT
1 AATTTTAAAATAATTTATATATAATT
74991 AATTTTATAAATAATTTATAT-TAATT
1 AATTTTA-AAATAATTTATATATAATT
75017 A
1 A
75018 CTTAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
AATTTTAAAATAATTTATATATAATT
Found at i:75984 original size:12 final size:12
Alignment explanation
Indices: 75967--75998 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
75957 CATATGAACG
75967 AAATTGCTCGCC
1 AAATTGCTCGCC
75979 AAATTGCTCGCC
1 AAATTGCTCGCC
75991 AAATTGCT
1 AAATTGCT
75999 AGTCTAATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (12 bp):
AAATTGCTCGCC
Found at i:80869 original size:29 final size:30
Alignment explanation
Indices: 80835--80912 Score: 97
Period size: 29 Copynumber: 2.6 Consensus size: 30
80825 GGATTCCTGA
* * *
80835 GGTAAAATAGTAATTTTCAGAAAGTTT-TG
1 GGTAAAATGGTAATTTTCAGAAACTTTAGG
*
80864 GGTAAAATGGTAA-TTTCAGATACTTTAGG
1 GGTAAAATGGTAATTTTCAGAAACTTTAGG
80893 GGATAAAATGGTAATTTTCA
1 GG-TAAAATGGTAATTTTCA
80913 AAAAATTTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 11 0.26
29 15 0.36
30 11 0.26
31 5 0.12
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.36
Consensus pattern (30 bp):
GGTAAAATGGTAATTTTCAGAAACTTTAGG
Found at i:80968 original size:29 final size:28
Alignment explanation
Indices: 80936--81300 Score: 265
Period size: 29 Copynumber: 12.5 Consensus size: 28
80926 CAAAAGTGAT
*
80936 ATTTTTGGAAGTTCGAGGGTAAAATGGTG
1 ATTTTTGGAAGTTCGAGGGTAAAAT-GTA
*
80965 ATTTTTGAAAGTTCG-GGGATAAAATGGTA
1 ATTTTTGGAAGTTCGAGGG-TAAAAT-GTA
*
80994 ATTTTTGGAAGTTTGAGGGTAAAAATGTGA
1 ATTTTTGGAAGTTCGAGGGT-AAAATGT-A
**
81024 ATTTTTTAAAGTTC-AGGGGTAAAAATGATA
1 ATTTTTGGAAGTTCGA-GGGT-AAAATG-TA
* * *
81054 TTTTTTGGAAGTTCGAGGGCAAAAATGTG
1 ATTTTTGGAAGTTCGAGGG-TAAAATGTA
* *
81083 ATTTTTTGAAGTTTG-GGGTAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAAT-GTA
* *
81111 ATTTTTGGAAATTCGA-GGTACAAATGCA
1 ATTTTTGGAAGTTCGAGGGTA-AAATGTA
* * * *
81139 ATTTTTGGAAAGTTTGGGGGAAAAATGCA
1 ATTTTTGG-AAGTTCGAGGGTAAAATGTA
*
81168 ATTTTTAGAAAGTTCGAGGGTAAAAAATGTA
1 ATTTTT-GGAAGTTCGAGGGT--AAAATGTA
* * *
81199 ATTTTTGTGAAATTTGGGGGTAAAATGTA
1 ATTTTTG-GAAGTTCGAGGGTAAAATGTA
* *
81228 A-TTTTGGAAAGTT-TAGGGGCAAAAATGTA
1 ATTTTTGG-AAGTTCGA-GGG-TAAAATGTA
* * * *
81257 ATTTTTGAAAAGTTCGAAGGTTAAATATA
1 ATTTTTG-GAAGTTCGAGGGTAAAATGTA
81286 ATTTTTGAGAAGTTC
1 ATTTTTG-GAAGTTC
81301 AAGTGTCAAA
Statistics
Matches: 268, Mismatches: 45, Indels: 46
0.75 0.13 0.13
Matches are distributed among these distances:
27 6 0.02
28 46 0.17
29 122 0.46
30 69 0.26
31 25 0.09
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (28 bp):
ATTTTTGGAAGTTCGAGGGTAAAATGTA
Found at i:81012 original size:58 final size:56
Alignment explanation
Indices: 80936--81300 Score: 294
Period size: 58 Copynumber: 6.2 Consensus size: 56
80926 CAAAAGTGAT
*
80936 ATTTTTGGAAGTTCGAGGGTAAAATGGTGATTTTTGAAAGTTCGGGGATAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAAT-GTAATTTTTGAAAGTTCGGGG-TAAAATGGTA
* * *
80994 ATTTTTGGAAGTTTGAGGGTAAAAATGTGAATTTTTTAAAGTTCAGGGGTAAAAATGATA
1 ATTTTTGGAAGTTCGAGGGT-AAAATGT-AATTTTTGAAAGTTC-GGGGT-AAAATGGTA
* * * *
81054 TTTTTTGGAAGTTCGAGGGCAAAAATGTGATTTTTTG-AAGTTTGGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGAGGG-TAAAATGT-AATTTTTGAAAGTTCGGGGTAAAATGGTA
* * * * *
81111 ATTTTTGGAAATTCGA-GGTACAAATGCAATTTTTGGAAAGTTTGGGGGAAAAAT-GCA
1 ATTTTTGGAAGTTCGAGGGTA-AAATGTAATTTTT-GAAAG-TTCGGGGTAAAATGGTA
* * *
81168 ATTTTTAGAAAGTTCGAGGGTAAAAAATGTAATTTTTGTGAAATTTGGGGGTAAAAT-GTA
1 ATTTTT-GGAAGTTCGAGGGT--AAAATGTAA-TTTT-TGAAAGTTCGGGGTAAAATGGTA
* * * * *
81228 A-TTTTGGAAAGTT-TAGGGGCAAAAATGTAATTTTTGAAAAGTTCGAAGGTTAAAT-ATA
1 ATTTTTGG-AAGTTCGA-GGG-TAAAATGTAATTTTTG-AAAGTTCG-GGGTAAAATGGTA
81286 ATTTTTGAGAAGTTC
1 ATTTTTG-GAAGTTC
81301 AAGTGTCAAA
Statistics
Matches: 251, Mismatches: 33, Indels: 44
0.77 0.10 0.13
Matches are distributed among these distances:
55 7 0.03
56 10 0.04
57 43 0.17
58 66 0.26
59 49 0.20
60 66 0.26
61 9 0.04
62 1 0.00
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (56 bp):
ATTTTTGGAAGTTCGAGGGTAAAATGTAATTTTTGAAAGTTCGGGGTAAAATGGTA
Found at i:81028 original size:88 final size:85
Alignment explanation
Indices: 80863--81266 Score: 297
Period size: 89 Copynumber: 4.6 Consensus size: 85
80853 AGAAAGTTTT
** * * * ** * * *
80863 GGGTAAAATGGTAATTTCAGATACTTTAGGGGATAAAATGGTAATTTTCAAAAAATTTGGTGTCA
1 GGGTAAAAT-GTAATTTTTGAAAGTTTCGGGGA-AAAAT-GTAATTTT-TGAAAGTTTGGGGTAA
*
80928 AAA-GTGATATTTTTGGAAGTTCGA
62 AAATGTGA-ATTTTTGGAAATTCGA
* *
80952 GGGTAAAATGGTGATTTTTGAAAG-TTCGGGGATAAAATGGTAATTTTTGGAAGTTTGAGGGTAA
1 GGGTAAAAT-GTAATTTTTGAAAGTTTCGGGGA-AAAAT-GTAATTTTTGAAAGTTTG-GGGTAA
*
81016 AAATGTGAATTTTT-TAAAGTTC-A
62 AAATGTGAATTTTTGGAAA-TTCGA
* * *
81039 GGGGTAAAAATGATATTTTTTGGAAG-TTCGAGGGCAAAAATGTGATTTTTTG-AAGTTTGGGGT
1 -GGGT-AAAATG-TAATTTTTGAAAGTTTCG-GGG-AAAAATGT-AATTTTTGAAAGTTTGGGGT
81102 -AAAATG-GTAATTTTTGGAAATTCGA
60 AAAAATGTG-AATTTTTGGAAATTCGA
* * * *
81127 -GGTACAAATGCAATTTTTGGAAAGTTTGGGGGAAAAATGCAATTTTTAGAAAGTTCGAGGGTAA
1 GGGTA-AAATGTAATTTTT-GAAAGTTTCGGGGAAAAATGTAATTTTT-GAAAGTTTG-GGGT-A
* *
81191 AAAATGT-AATTTTTGTGAAATTTGG
61 AAAATGTGAATTTTTG-GAAATTCGA
* *
81216 GGGTAAAATGTAATTTTGGAAAGTTTAGGGGCAAAAATGTAATTTTTGAAA
1 GGGTAAAATGTAATTTTTGAAAGTTTCGGGG-AAAAATGTAATTTTTGAAA
81267 AGTTCGAAGG
Statistics
Matches: 259, Mismatches: 32, Indels: 49
0.76 0.09 0.14
Matches are distributed among these distances:
84 6 0.02
85 15 0.06
86 22 0.08
87 32 0.12
88 75 0.29
89 89 0.34
90 19 0.07
91 1 0.00
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (85 bp):
GGGTAAAATGTAATTTTTGAAAGTTTCGGGGAAAAATGTAATTTTTGAAAGTTTGGGGTAAAAAT
GTGAATTTTTGGAAATTCGA
Found at i:83149 original size:17 final size:17
Alignment explanation
Indices: 83127--83160 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
83117 TTTGATTAAG
83127 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
83144 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
83161 ATAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:88507 original size:6 final size:6
Alignment explanation
Indices: 88496--88523 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
88486 TTGCCAAGCT
88496 TTTTGC TTTTGC TTTTGC TTTTGC TTTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTT
88524 CTATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.14, T:0.71
Consensus pattern (6 bp):
TTTTGC
Found at i:100487 original size:28 final size:27
Alignment explanation
Indices: 100455--100509 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
100445 AAAATATTTA
* *
100455 AAATATTTTTTATAATTTATATATTTTT
1 AAATAATTTTAATAATTTATA-ATTTTT
* *
100483 AAATAATTTTAATGATTTTTAATTTTT
1 AAATAATTTTAATAATTTATAATTTTT
100510 TTTTTTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
AAATAATTTTAATAATTTATAATTTTT
Found at i:100488 original size:19 final size:19
Alignment explanation
Indices: 100431--100504 Score: 59
Period size: 20 Copynumber: 3.9 Consensus size: 19
100421 ATTTAATTAA
100431 AATTTTAA-A-TTTTAAA-
1 AATTTTAATATTTTTAAAT
*
100447 AATATTTAAAATATTTTT-TAT
1 AAT-TTT--AATATTTTTAAAT
100468 AA-TTTATATATTTTTAAAT
1 AATTTTA-ATATTTTTAAAT
100487 AATTTTAATGATTTTTAA
1 AATTTTAAT-ATTTTTAA
100505 TTTTTTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
16 3 0.07
17 4 0.09
18 8 0.17
19 11 0.24
20 14 0.30
21 6 0.13
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (19 bp):
AATTTTAATATTTTTAAAT
Found at i:100742 original size:14 final size:14
Alignment explanation
Indices: 100723--100751 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
100713 TATAACTTGT
100723 TGCAACCATGGTTG
1 TGCAACCATGGTTG
100737 TGCAACCATGGTTG
1 TGCAACCATGGTTG
100751 T
1 T
100752 AAACTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (14 bp):
TGCAACCATGGTTG
Found at i:101757 original size:45 final size:45
Alignment explanation
Indices: 101693--101783 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
101683 TATAGAACAC
101693 AATAGAATATACGAAAATGTCAGTAAGATGCACCAAAGTTCTACT
1 AATAGAATATACGAAAATGTCAGTAAGATGCACCAAAGTTCTACT
* *
101738 AATAGGATATACGAAAATGTCAGTGAGATGCACCAAAGTTCTACT
1 AATAGAATATACGAAAATGTCAGTAAGATGCACCAAAGTTCTACT
101783 A
1 A
101784 TTCTTTGCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (45 bp):
AATAGAATATACGAAAATGTCAGTAAGATGCACCAAAGTTCTACT
Found at i:101894 original size:17 final size:17
Alignment explanation
Indices: 101845--101883 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
101835 TTGCACCGTA
*
101845 GTGCCACTCTCACTAGC
1 GTGCTACTCTCACTAGC
101862 GTGCTACTCTCACTAGC
1 GTGCTACTCTCACTAGC
101879 GTGCT
1 GTGCT
101884 TACTTTCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.36, G:0.21, T:0.28
Consensus pattern (17 bp):
GTGCTACTCTCACTAGC
Found at i:109148 original size:28 final size:28
Alignment explanation
Indices: 109116--109172 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
109106 AAGCTGAGTA
109116 CATGCGATTACCGAGGCTTGTAAAGAAG
1 CATGCGATTACCGAGGCTTGTAAAGAAG
109144 CATGCGATTACCGAGGCTTGTAAAGAAG
1 CATGCGATTACCGAGGCTTGTAAAGAAG
109172 C
1 C
109173 TATTTGGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (28 bp):
CATGCGATTACCGAGGCTTGTAAAGAAG
Found at i:109517 original size:17 final size:17
Alignment explanation
Indices: 109495--109533 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
109485 AGGTGGAGAA
* * *
109495 CTTGTTCGTTGAGATTT
1 CTTGTTAGTAGAGAATT
109512 CTTGTTAGTAGAGAATT
1 CTTGTTAGTAGAGAATT
109529 CTTGT
1 CTTGT
109534 AAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.10, G:0.23, T:0.49
Consensus pattern (17 bp):
CTTGTTAGTAGAGAATT
Found at i:112028 original size:16 final size:17
Alignment explanation
Indices: 111907--112029 Score: 89
Period size: 16 Copynumber: 7.6 Consensus size: 17
111897 TTGGTTAGTT
111907 GGGTTGACTTTGA-CTA
1 GGGTTGACTTTGATCTA
** *
111923 AAGTTGACATTGAT-TA
1 GGGTTGACTTTGATCTA
*
111939 GGGTCGACTTTGATC-A
1 GGGTTGACTTTGATCTA
* *
111955 AGGTTGACTTT-TTCTA
1 GGGTTGACTTTGATCTA
* ** *
111971 GAGTCAACTTTGA-CAA
1 GGGTTGACTTTGATCTA
111987 GGGTTGACTTTGA-CTA
1 GGGTTGACTTTGATCTA
*
112003 GGATTGACTTTGATC-A
1 GGGTTGACTTTGATCTA
*
112019 GGGTTAACTTT
1 GGGTTGACTTT
112030 TTTAAGTAAA
Statistics
Matches: 79, Mismatches: 23, Indels: 10
0.71 0.21 0.09
Matches are distributed among these distances:
15 2 0.03
16 76 0.96
17 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.37
Consensus pattern (17 bp):
GGGTTGACTTTGATCTA
Found at i:115083 original size:16 final size:16
Alignment explanation
Indices: 115062--115113 Score: 72
Period size: 16 Copynumber: 3.2 Consensus size: 16
115052 GTTGATTTTA
115062 TTGACTTTGACATGAG
1 TTGACTTTGACATGAG
115078 TTGACTTTGACCATG-G
1 TTGACTTTGA-CATGAG
115094 TTGACTTTGAC-TAGAG
1 TTGACTTTGACAT-GAG
115110 TTGA
1 TTGA
115114 GTTTTTTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.03
15 2 0.06
16 26 0.79
17 4 0.12
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.38
Consensus pattern (16 bp):
TTGACTTTGACATGAG
Found at i:121315 original size:30 final size:29
Alignment explanation
Indices: 121274--121516 Score: 276
Period size: 30 Copynumber: 8.2 Consensus size: 29
121264 AATCCATAAC
* *
121274 CTTCCAAAAATTACATTTTGACCCCTAAA
1 CTTCTAAAAATTACATTTTGACCCTTAAA
*
121303 CTTTCTAAAAATTACATTTTAACCCTTAAA
1 C-TTCTAAAAATTACATTTTGACCCTTAAA
*
121333 CTTCTTAAAAATTACATTTTAACCCTTAAA
1 CTTC-TAAAAATTACATTTTGACCCTTAAA
* *
121363 CTTCTCAAAGATTACATTTTAAGCCCTTAAA
1 CTTCT-AAAAATTACATTTTGA-CCCTTAAA
* *
121394 CTTCTTAAAAATTACATTTTGACCCCTAAG
1 CTTC-TAAAAATTACATTTTGACCCTTAAA
121424 CTTCTCAAAAATTACA-TTTGACCCTTAAA
1 CTTCT-AAAAATTACATTTTGACCCTTAAA
121453 CTT-TGCAAAAATTACATTTTGACCCTTAAA
1 CTTCT--AAAAATTACATTTTGACCCTTAAA
** * *
121483 CCTTCCCAAAATCACATTTTGA-CCTCAAA
1 -CTTCTAAAAATTACATTTTGACCCTTAAA
121512 CTTCT
1 CTTCT
121517 CCAAAATCCC
Statistics
Matches: 189, Mismatches: 15, Indels: 21
0.84 0.07 0.09
Matches are distributed among these distances:
28 5 0.03
29 37 0.20
30 117 0.62
31 29 0.15
32 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (29 bp):
CTTCTAAAAATTACATTTTGACCCTTAAA
Found at i:121323 original size:59 final size:60
Alignment explanation
Indices: 121259--121523 Score: 308
Period size: 59 Copynumber: 4.5 Consensus size: 60
121249 TTAAAGTTAT
* * *
121259 ATTTTAATCCATAACCTTC-CAAAAATTACATTTTGACCCCTAAACTT-TCTAAAAATTAC
1 ATTTTAACCCTTAAACTTCTCAAAAATTACATTTTGACCCCTAAACTTCTC-AAAAATTAC
* * * *
121318 ATTTTAACCCTTAAACTTCTTAAAAATTACATTTTAACCCTTAAACTTCTCAAAGATTAC
1 ATTTTAACCCTTAAACTTCTCAAAAATTACATTTTGACCCCTAAACTTCTCAAAAATTAC
* *
121378 ATTTTAAGCCCTTAAACTTCTTAAAAATTACATTTTGACCCCTAAGCTTCTCAAAAATTAC
1 ATTTTAA-CCCTTAAACTTCTCAAAAATTACATTTTGACCCCTAAACTTCTCAAAAATTAC
* * * *
121439 A-TTTGACCCTTAAACTT-TGCAAAAATTACATTTTGACCCTTAAACCTTC-CCAAAATCAC
1 ATTTTAACCCTTAAACTTCT-CAAAAATTACATTTTGACCCCTAAA-CTTCTCAAAAATTAC
* * *
121498 ATTTTGA-CCTCAAACTTCTCCAAAAT
1 ATTTTAACCCTTAAACTTCTCAAAAAT
121524 CCCATTTTCC
Statistics
Matches: 180, Mismatches: 19, Indels: 14
0.85 0.09 0.07
Matches are distributed among these distances:
58 1 0.01
59 73 0.41
60 54 0.30
61 52 0.29
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.35
Consensus pattern (60 bp):
ATTTTAACCCTTAAACTTCTCAAAAATTACATTTTGACCCCTAAACTTCTCAAAAATTAC
Found at i:121540 original size:29 final size:28
Alignment explanation
Indices: 121460--121559 Score: 83
Period size: 29 Copynumber: 3.5 Consensus size: 28
121450 AAACTTTGCA
* * *
121460 AAAATTACATTTTGACCCTTAAACCTTCCC
1 AAAATCACATTTTCACCC-CAAA-CTTCCC
* *
121490 AAAATCACATTTTGACCTCAAACTTCTCC
1 AAAATCACATTTTCACCCCAAACTTC-CC
* * * **
121519 AAAATCCCATTTTCCCCCCAAATTTCAA
1 AAAATCACATTTTCACCCCAAACTTCCC
121547 AAAATCACATTTT
1 AAAATCACATTTT
121560 TCAACCTCAA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
28 16 0.28
29 26 0.45
30 16 0.28
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (28 bp):
AAAATCACATTTTCACCCCAAACTTCCC
Done.