Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012098.1 Kokia drynarioides strain JFW-HI SEQ_127097, 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: 57337
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Found at i:1051 original size:23 final size:22
Alignment explanation
Indices: 1001--1144 Score: 128
Period size: 23 Copynumber: 6.2 Consensus size: 22
991 ACACTAGCAC
* * *
1001 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCACTTGT-GT
*
1024 ACTCTCTGTTATTAGCAC-TGTGT
1 GCTCTCTG--ATTAGCACTTGTGT
*
1047 GCTCTCTGATTAGCACTTTGTAT
1 GCTCTCTGATTAGCAC-TTGTGT
*
1070 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCAC-TTGTGT
* *
1093 ACTCTCTATTATTAGCACTGTGTGT
1 GCTCTC--TGATTAGCACT-TGTGT
1118 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCAC-TTGTGT
1141 GCTC
1 GCTC
1145 AGTACTTTGT
Statistics
Matches: 101, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
21 8 0.08
23 64 0.63
24 4 0.04
25 25 0.25
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (22 bp):
GCTCTCTGATTAGCACTTGTGT
Found at i:3258 original size:21 final size:23
Alignment explanation
Indices: 3219--3261 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
3209 GAGTTGTAAA
3219 TGTTATATCTTATCAATTCTTAC
1 TGTTATATCTTATCAATTCTTAC
*
3242 TGTTA-ATC-TATCGATTCTTA
1 TGTTATATCTTATCAATTCTTA
3262 AATTGATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 3 0.16
23 5 0.26
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (23 bp):
TGTTATATCTTATCAATTCTTAC
Found at i:4026 original size:22 final size:22
Alignment explanation
Indices: 3998--4042 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
3988 GGATGGTAGG
3998 TTACGATGC-AGTGCGTTTAGCT
1 TTACGATGCGA-TGCGTTTAGCT
4020 TTACGATGCGATGCGTTTAGCT
1 TTACGATGCGATGCGTTTAGCT
4042 T
1 T
4043 ACTTTTAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.38
Consensus pattern (22 bp):
TTACGATGCGATGCGTTTAGCT
Found at i:8831 original size:91 final size:87
Alignment explanation
Indices: 8675--8882 Score: 258
Period size: 89 Copynumber: 2.3 Consensus size: 87
8665 GTAAAAAGCT
* *
8675 CTCAAACTTTTTAAAAAAAAGTAATTAAGCTCCTCTTTTTTTTGCACTCAATTGAGCACTTGAAC
1 CTCAAACTTTTT-CAAAAAAGCAATTAAGCTCCTCTTTTTTTTGCACTCAATTGAGCACTTGAAC
8740 TTTCAAAATGCAT-AAAAAGAAAGTC
65 TTTCAAAATGCATAAAAAAG-AA--C
* * * * *
8765 CTCAAACTTCTTCAAAAAAGCAATTAAGCTTCTGCTTTTCTTTTTCACTTAATTG-GTTACTTGA
1 CTCAAACTTTTTCAAAAAAGCAATTAAGCTCCT-CTTTT-TTTTGCACTCAATTGAG-CACTTGA
8829 ACTTTCAAAATGCATAAAAAAGAAC
63 ACTTTCAAAATGCATAAAAAAGAAC
**
8854 CTCAATTTTTTTCAAAAAAGCAATTAAGC
1 CTCAAACTTTTTCAAAAAAGCAATTAAGC
8883 CCTTGCTCTT
Statistics
Matches: 104, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
89 45 0.43
90 17 0.16
91 36 0.35
92 6 0.06
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (87 bp):
CTCAAACTTTTTCAAAAAAGCAATTAAGCTCCTCTTTTTTTTGCACTCAATTGAGCACTTGAACT
TTCAAAATGCATAAAAAAGAAC
Found at i:9047 original size:19 final size:19
Alignment explanation
Indices: 9000--9047 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
8990 ATTAGAATTT
9000 TTTTATAAAAATAGTAAAA
1 TTTTATAAAAATAGTAAAA
*** * *
9019 AAATAAAAAAATTGTAAAA
1 TTTTATAAAAATAGTAAAA
9038 TTTTATAAAA
1 TTTTATAAAA
9048 TCATAAAAAA
Statistics
Matches: 20, Mismatches: 9, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (19 bp):
TTTTATAAAAATAGTAAAA
Found at i:9277 original size:10 final size:9
Alignment explanation
Indices: 9264--9383 Score: 61
Period size: 10 Copynumber: 12.9 Consensus size: 9
9254 TATAAAATAT
9264 TATATTTCTA
1 TATATTT-TA
9274 TATATTTTA
1 TATATTTTA
*
9283 TA-ATTTTT
1 TATATTTTA
9291 TATGACTTTTA
1 TAT-A-TTTTA
*
9302 TAAAATTTTA
1 T-ATATTTTA
*
9312 CAT-TTTT-
1 TATATTTTA
*
9319 TATATTTTT
1 TATATTTTA
9328 TCATGATTTATA
1 T-AT-ATTT-TA
*
9340 TATATATATA
1 TATAT-TTTA
*
9350 TATATATATA
1 TATAT-TTTA
9360 TATATTTTA
1 TATATTTTA
*
9369 -ATTTTTTA
1 TATATTTTA
9377 TA-ATTTT
1 TATATTTT
9384 TTCTAATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 24
0.72 0.09 0.20
Matches are distributed among these distances:
7 2 0.02
8 26 0.30
9 10 0.11
10 34 0.39
11 13 0.15
12 3 0.03
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (9 bp):
TATATTTTA
Found at i:9302 original size:46 final size:46
Alignment explanation
Indices: 9204--9326 Score: 144
Period size: 46 Copynumber: 2.7 Consensus size: 46
9194 TTTTATAAAT
* *
9204 TTTTATGAAATTTATATTTCTTTACATTTTGTATAATTTTCTTAAGAC
1 TTTTATAAAATTTATATTTCTTTATA-TTT-TATAATTTTCTTAAGAC
* *
9252 -TTTATAAAATATTATATTTCTATATATTTTATAATTTT-TTATGAC
1 TTTTATAAAAT-TTATATTTCTTTATATTTTATAATTTTCTTAAGAC
*
9297 TTTTATAAAATTTTACATTT-TTTATATTTT
1 TTTTATAAAA-TTTATATTTCTTTATATTTT
9327 TTCATGATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
45 15 0.23
46 25 0.38
47 13 0.20
48 13 0.20
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (46 bp):
TTTTATAAAATTTATATTTCTTTATATTTTATAATTTTCTTAAGAC
Found at i:9341 original size:2 final size:2
Alignment explanation
Indices: 9336--9364 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9326 TTTCATGATT
9336 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9365 TTTAATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9395 original size:84 final size:84
Alignment explanation
Indices: 9194--9383 Score: 203
Period size: 84 Copynumber: 2.3 Consensus size: 84
9184 GTACAATAAT
* * **
9194 TTTTATAAATTTTTATGAAATTTAT-ATTTCTTTACATTTTGTATAATTTTCTTAAGACTTTATA
1 TTTTATAATTTTTTATGAATTTTATAAAAT-TTTACATTTTGTATAATTTTCTTAAGACTTTATA
* *
9258 AAATATTATATTTCTATATA
65 AAATATTATATATATATATA
* * *
9278 TTTTATAATTTTTTATGACTTTTATAAAATTTTACATTTTTTAT-ATTTT-TTCATGA-TTTATA
1 TTTTATAATTTTTTATGAATTTTATAAAATTTTACATTTTGTATAATTTTCTT-AAGACTTTATA
*
9340 TATATATATATATATATATATA
65 -AAATAT-TATATATATATATA
9362 TATTT-TAATTTTTTAT-AATTTT
1 T-TTTATAATTTTTTATGAATTTT
9384 TTCTAATTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
82 8 0.09
83 18 0.20
84 59 0.66
85 5 0.06
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (84 bp):
TTTTATAATTTTTTATGAATTTTATAAAATTTTACATTTTGTATAATTTTCTTAAGACTTTATAA
AATATTATATATATATATA
Found at i:14003 original size:6 final size:6
Alignment explanation
Indices: 13987--14021 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
13977 ATTTTCTTGT
*
13987 GGAAT- GGAATA GGAATA GGAATA GGAATA GAAATA
1 GGAATA GGAATA GGAATA GGAATA GGAATA GGAATA
14022 CCGCCATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.51, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
GGAATA
Found at i:15370 original size:12 final size:12
Alignment explanation
Indices: 15353--15392 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
15343 AAAGATTTAA
15353 TAAACTAAAAAT
1 TAAACTAAAAAT
*
15365 TAAACTAACAAT
1 TAAACTAAAAAT
* *
15377 TTAACTAAAAAA
1 TAAACTAAAAAT
15389 TAAA
1 TAAA
15393 AATTCCAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (12 bp):
TAAACTAAAAAT
Found at i:17179 original size:4 final size:4
Alignment explanation
Indices: 17172--17198 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
17162 GAAGGAAAAA
17172 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
17199 AAGCCTCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:19049 original size:29 final size:29
Alignment explanation
Indices: 19016--19079 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
19006 TTATGTGCTT
* *
19016 AATTTTGCCATTAAATTTTAATTTT-ATTG
1 AATTTT-CCACTAAATTTTAATTTTAATTA
* *
19045 AATTTTCCACTAATTTTTATTTTTAATTA
1 AATTTTCCACTAAATTTTAATTTTAATTA
19074 AATTTT
1 AATTTT
19080 ACTATGATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (29 bp):
AATTTTCCACTAAATTTTAATTTTAATTA
Found at i:22735 original size:33 final size:34
Alignment explanation
Indices: 22673--22736 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
22663 GGACTCCACT
*
22673 ATTAACTTAATTTAATTGAGCATATTATATAATA
1 ATTAACTTAATTTAATTGACCATATTATATAATA
*
22707 ATTAATTTAATTTAATT-ACCATATTATATA
1 ATTAACTTAATTTAATTGACCATATTATATA
22737 TATCACTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 12 0.43
34 16 0.57
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (34 bp):
ATTAACTTAATTTAATTGACCATATTATATAATA
Found at i:33931 original size:42 final size:42
Alignment explanation
Indices: 33884--33967 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
33874 AAAAAGAGTT
** *
33884 GTTTATGAGTATTATTT-AGGAATAAAATTATATTTGGGTTTA
1 GTTTATGAGTATT-TTTGAAAAATAAAATTATATTTAGGTTTA
*
33926 GTTTATGAGTGTTTTTGAAAAATAAAATTATATTTAGGTTTA
1 GTTTATGAGTATTTTTGAAAAATAAAATTATATTTAGGTTTA
33968 AAAATATTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 3 0.08
42 34 0.92
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.48
Consensus pattern (42 bp):
GTTTATGAGTATTTTTGAAAAATAAAATTATATTTAGGTTTA
Found at i:36985 original size:15 final size:14
Alignment explanation
Indices: 36949--37000 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
36939 ATTATATTAC
36949 TAAAATTTTCATTT
1 TAAAATTTTCATTT
*
36963 TAAAATTTTTATTT
1 TAAAATTTTCATTT
*
36977 ATAATATTTATCATATT
1 -TAAAATTT-TCAT-TT
36994 TATAAAT
1 TA-AAAT
37001 AAAAATTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 13 0.43
15 7 0.23
16 5 0.17
17 5 0.17
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (14 bp):
TAAAATTTTCATTT
Found at i:37213 original size:17 final size:18
Alignment explanation
Indices: 37191--37242 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 18
37181 ATTTTAATTA
37191 TTTATATAATA-ATTAAC
1 TTTATATAATATATTAAC
* *
37208 TTTATATTATATATAAAC
1 TTTATATAATATATTAAC
*
37226 TCTAATATAATATATTA
1 T-TTATATAATATATTA
37243 TATATGTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
17 10 0.36
18 6 0.21
19 12 0.43
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTATATAATATATTAAC
Found at i:40969 original size:234 final size:234
Alignment explanation
Indices: 40535--41253 Score: 859
Period size: 234 Copynumber: 3.0 Consensus size: 234
40525 ATTTGGAAGG
* *
40535 TTGTTAGAGGATCATATCTCCTTTGAAAATGTGTTGGATAATGGTACTTAAAAGGAAAAAAAATG
1 TTGTTAGAGGATCATATCTCCTTTGAAAATGTGTTGGAT-AGGGTACTT--AA--AAAGAAAATG
* * * * *
40600 TATAGTTGGAACAACATAGGAAAAATATTTACATCTTCTCATTTATTTGATTGTGAAAGTTAATG
61 AATAGTCGGAACAACATAGGAAAAA-ATTTACATCTTCCCATTTATTTGATTGTGAAAGTAAAGG
** * * *
40665 AACAAT-GGATATGATTTATTAAGACGTTGAAGTTACTGAATGTCTTTCTGGATATTCGAT-GTT
125 AACAATGGGATATGATTTATTAAGGTGTTGAAGTTACTGAATGTCTTTCTGAATATTTGATGGCT
* ** *
40728 CGGTAATAAGTTTTTTATTTATTTATGATCTACCGATTGGTGCCCT
190 -GGTAATAAGTTATTCGTTTATTTATGATCTACCGATTGGTGCCAT
* * *
40774 TTGTTAGAGGATCATATCTCCTTTGGAAATGTGTTGGATAGGATACTTAAAAAGAAAACGAATAG
1 TTGTTAGAGGATCATATCTCCTTTGAAAATGTGTTGGATAGGGTACTTAAAAAGAAAATGAATAG
* * *
40839 TCGAAACAACACAGGAAAAAAGTTACATCTTCCCATTTATTTGATTGTGAAAGTAAAGGAACAAT
66 TCGGAACAACATAGGAAAAAATTTACATCTTCCCATTTATTTGATTGTGAAAGTAAAGGAACAAT
* * *
40904 GGGATATGATCTATTAAGGTGTTGAAGTTATTGAATGTCTTTCTGAATATTTAATGGCTGGTAAT
131 GGGATATGATTTATTAAGGTGTTGAAGTTACTGAATGTCTTTCTGAATATTTGATGGCTGGTAAT
* * * * *
40969 AAGCTATTCGTTTATCTATGATCTACCGGTCGGTGCTAT
196 AAGTTATTCGTTTATTTATGATCTACCGATTGGTGCCAT
*
41008 TTGTTAGAGGATCATATCTCCTTAGAAAATGTGTTGGATAGGGTTACTTAAAAAGAAAAATGAAT
1 TTGTTAGAGGATCATATCTCCTTTGAAAATGTGTTGGATAGGG-TACTTAAAAAG-AAAATGAAT
* ** * *
41073 AGTCGGAGCAACATAGGAAAATTTTTTACATGTTTCCCATTTATTTGATTGTAAAAGTGAATGAA
64 AGTCGGAACAACATAGGAAAA-AATTTACAT-CTTCCCATTTATTTGATTGTGAAAGT--A--AA
** **
41138 GTTGAACAATGAAATATGATTTATTAAGGTGTCAAAGTTACTGAATGTCTTTCTGCAA-ATTTGA
123 G--GAACAATGGGATATGATTTATTAAGGTGTTGAAGTTACTGAATGTCTTTCTG-AATATTTGA
* * *
41202 TGTCTGGTAATTAAGTTATTGGTTTATTTATGATCTACCAATTGGTGCCAT
185 TGGCTGGTAA-TAAGTTATTCGTTTATTTATGATCTACCGATTGGTGCCAT
41253 T
1 T
41254 GTATGAGAAT
Statistics
Matches: 409, Mismatches: 57, Indels: 22
0.84 0.12 0.05
Matches are distributed among these distances:
233 41 0.10
234 152 0.37
235 13 0.03
236 28 0.07
237 6 0.01
238 31 0.08
239 38 0.09
240 1 0.00
242 3 0.01
244 60 0.15
245 36 0.09
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.37
Consensus pattern (234 bp):
TTGTTAGAGGATCATATCTCCTTTGAAAATGTGTTGGATAGGGTACTTAAAAAGAAAATGAATAG
TCGGAACAACATAGGAAAAAATTTACATCTTCCCATTTATTTGATTGTGAAAGTAAAGGAACAAT
GGGATATGATTTATTAAGGTGTTGAAGTTACTGAATGTCTTTCTGAATATTTGATGGCTGGTAAT
AAGTTATTCGTTTATTTATGATCTACCGATTGGTGCCAT
Found at i:42820 original size:96 final size:96
Alignment explanation
Indices: 42653--42893 Score: 288
Period size: 96 Copynumber: 2.5 Consensus size: 96
42643 TTCTGATAGC
* * * *
42653 TCCGTGAACAATACCGGGAATCGTCCTGCATCCCTACCAAACAGCCAACCAAACTCCTTTGCCAG
1 TCCGTGAACAATACTGGGAACCCTCCTGCATCCCTACCGAACAGCCAACCAAACTCCTTTGCCAG
* ** *
42718 CTTTAACAGCCTGAGTGCA-ATCACTTCTAAT
66 CTTTAACAGCCCGA-CCCAGATCACTACTAAT
* *
42749 TCTGTGAACAATTCTGGGAACCCTCCTGCATCCCTACCGAACAGCCAACCAAACTCCTCTT-CCA
1 TCCGTGAACAATACTGGGAACCCTCCTGCATCCCTACCGAACAGCCAACCAAACTCCT-TTGCCA
* * * *
42813 GTTTTAACAGCCCGACCCAGTTCAGTACTAGT
65 GCTTTAACAGCCCGACCCAGATCACTACTAAT
* * * *
42845 TCCGTGAACAATACTGGGAACACTCCGGCATCCCTACTGAACAACCAAC
1 TCCGTGAACAATACTGGGAACCCTCCTGCATCCCTACCGAACAGCCAAC
42894 TGAACTCTGC
Statistics
Matches: 123, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
95 2 0.02
96 119 0.97
97 2 0.02
ACGTcount: A:0.29, C:0.34, G:0.15, T:0.22
Consensus pattern (96 bp):
TCCGTGAACAATACTGGGAACCCTCCTGCATCCCTACCGAACAGCCAACCAAACTCCTTTGCCAG
CTTTAACAGCCCGACCCAGATCACTACTAAT
Found at i:46639 original size:30 final size:31
Alignment explanation
Indices: 46582--46641 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
46572 AGAAAAACTG
*
46582 AACAGTTCAATGACTTAAATCAAAAATTTTA
1 AACAATTCAATGACTTAAATCAAAAATTTTA
*
46613 AACAATTCAATGATTTAAAT-AAAAATTTT
1 AACAATTCAATGACTTAAATCAAAAATTTT
46642 CGAATAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (31 bp):
AACAATTCAATGACTTAAATCAAAAATTTTA
Found at i:49213 original size:63 final size:63
Alignment explanation
Indices: 49088--49209 Score: 149
Period size: 63 Copynumber: 2.0 Consensus size: 63
49078 TATACATTTT
* ** **
49088 GGTACCTGAACTTGGTTTCAAGGTTCAAATTGGTACCTAGGGTGTTGTTTTTTTGTCCAATTA
1 GGTACCTGAACTTGATTTCAAGGTTCAAATTGGTACCTAGAATGTTGGCTTTTTGTCCAATTA
* **
49151 GGTACTTGAACTTGATTTCTTGGTTCAAATTGGTACCT-GAAT-TTGGCTTTTTGATCCAA
1 GGTACCTGAACTTGATTTCAAGGTTCAAATTGGTACCTAGAATGTTGGCTTTTTG-TCCAA
49210 ATTAATATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
61 9 0.18
62 7 0.14
63 34 0.68
ACGTcount: A:0.21, C:0.15, G:0.22, T:0.42
Consensus pattern (63 bp):
GGTACCTGAACTTGATTTCAAGGTTCAAATTGGTACCTAGAATGTTGGCTTTTTGTCCAATTA
Found at i:50463 original size:16 final size:16
Alignment explanation
Indices: 50437--50492 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
50427 CCCCATCCAG
50437 CCCCA-CCCCGCCCTA
1 CCCCATCCCCGCCCTA
50452 CCCCATCCCCGCCCTA
1 CCCCATCCCCGCCCTA
* **
50468 CCCCATCCTCGCCCCG
1 CCCCATCCCCGCCCTA
50484 CCCCATCCC
1 CCCCATCCC
50493 ATCCCCGTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
15 5 0.14
16 31 0.86
ACGTcount: A:0.11, C:0.71, G:0.07, T:0.11
Consensus pattern (16 bp):
CCCCATCCCCGCCCTA
Found at i:51120 original size:32 final size:32
Alignment explanation
Indices: 51079--51168 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 32
51069 AGACCTACGT
*
51079 GAGTGGTGGGGTGGTGATGGTTTTAGTCTTGC
1 GAGTTGTGGGGTGGTGATGGTTTTAGTCTTGC
51111 GAGTTGTGGGGTGGAT-ATGGTTTTAGTCTTGC
1 GAGTTGTGGGGTGG-TGATGGTTTTAGTCTTGC
* * * *
51143 -AGGTTGTAGGGCGGGGATGATTTTAG
1 GA-GTTGTGGGGTGGTGATGGTTTTAG
51169 GTTTTGTACC
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
31 1 0.02
32 48 0.96
33 1 0.02
ACGTcount: A:0.13, C:0.06, G:0.44, T:0.37
Consensus pattern (32 bp):
GAGTTGTGGGGTGGTGATGGTTTTAGTCTTGC
Found at i:51564 original size:16 final size:18
Alignment explanation
Indices: 51525--51566 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
51515 TAAGTTTGTA
51525 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
51542 ATTTTTATATATTAT-TT
1 ATATTTATATATTATGTT
51559 A-ATTTATA
1 ATATTTATA
51567 ACACATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 8 0.36
18 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:53967 original size:12 final size:12
Alignment explanation
Indices: 53950--53984 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
53940 TCAAAATTGA
53950 AAGTGAAAGTGG
1 AAGTGAAAGTGG
*
53962 AAGTGAAATTGG
1 AAGTGAAAGTGG
*
53974 AATTGAAAGTG
1 AAGTGAAAGTG
53985 ATATGAATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.34, T:0.23
Consensus pattern (12 bp):
AAGTGAAAGTGG
Found at i:54182 original size:37 final size:38
Alignment explanation
Indices: 54113--54191 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 38
54103 GTGTCATTAT
**
54113 TTTACTTCGGATAGATACGATGAGGTACTGGGTACCAC
1 TTTACTTCGGATAGATACGATGAGACACTGGGTACCAC
* * * **
54151 TTTACTTCGGCTAGGT-CGATGAGACATTGGGTGTCAC
1 TTTACTTCGGATAGATACGATGAGACACTGGGTACCAC
54188 TTTA
1 TTTA
54192 TTGCTTTGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
37 20 0.59
38 14 0.41
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.33
Consensus pattern (38 bp):
TTTACTTCGGATAGATACGATGAGACACTGGGTACCAC
Found at i:55826 original size:12 final size:12
Alignment explanation
Indices: 55806--55846 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
55796 AATCAAAAGG
55806 GAAGAAGATGAA
1 GAAGAAGATGAA
*
55818 GATGAAGATGAA
1 GAAGAAGATGAA
*
55830 GAAGAAGAAGAA
1 GAAGAAGATGAA
55842 GAAGA
1 GAAGA
55847 GAGGTGCGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.07
Consensus pattern (12 bp):
GAAGAAGATGAA
Found at i:55835 original size:3 final size:3
Alignment explanation
Indices: 55806--55846 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
55796 AATCAAAAGG
* * *
55806 GAA GAA GAT GAA GAT GAA GAT GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
55847 GAGGTGCGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.07
Consensus pattern (3 bp):
GAA
Found at i:55935 original size:16 final size:16
Alignment explanation
Indices: 55898--55938 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
55888 TTAGGGTTTA
* *
55898 AAATTTTTAATTAATT
1 AAATATTTATTTAATT
55914 -AA-ATTTATTTAATT
1 AAATATTTATTTAATT
55928 AAATATTTATT
1 AAATATTTATT
55939 CTCATTCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 10 0.48
15 4 0.19
16 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AAATATTTATTTAATT
Done.