Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023651.1 Corchorus olitorius cultivar O-4 contig23684, 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: 65397
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:98 original size:41 final size:41
Alignment explanation
Indices: 50--250 Score: 266
Period size: 41 Copynumber: 4.9 Consensus size: 41
40 ATCAAGTTTT
* *
50 AGTTTTCAATTTAGGGAAAGATCCCGTCCAGTTTTTTTCAA
1 AGTTTTCAATTTAGGGAAAGATCCCATCAAGTTTTTTTCAA
*
91 AGTTTTCAATTTAGGAAAAGATCCCATCAAGTTTTTTTTTCAA
1 AGTTTTCAATTTAGGGAAAGATCCCATCAAG--TTTTTTTCAA
*
134 AATTTTCAATTTAGGGAAAAGATCCCATCAAG---TTTTCAA
1 AGTTTTCAATTTAGGG-AAAGATCCCATCAAGTTTTTTTCAA
* * *
173 AGTTTTCAATTTAGGAAAAGATCCCATCCAGTCTTTTTCAA
1 AGTTTTCAATTTAGGGAAAGATCCCATCAAGTTTTTTTCAA
214 AGTTTTCAA-TTAGGGGAAAGATCCCATCAAAGTTTTT
1 AGTTTTCAATTTA-GGGAAAGATCCCATC-AAGTTTTT
251 AGAATTGAGT
Statistics
Matches: 141, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
38 14 0.10
39 21 0.15
40 3 0.02
41 58 0.41
42 6 0.04
43 24 0.17
44 15 0.11
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.37
Consensus pattern (41 bp):
AGTTTTCAATTTAGGGAAAGATCCCATCAAGTTTTTTTCAA
Found at i:239 original size:123 final size:121
Alignment explanation
Indices: 31--250 Score: 345
Period size: 123 Copynumber: 1.8 Consensus size: 121
21 TTAGATTGGG
* * * *
31 AAAGTTCCCATCAAGTTTTAGTTTTCAATTTAGGGAAAGATCCCGTCCAGTTTTTTTCAAAGTTT
1 AAAGATCCCATCAAGTTTTAGTTTTCAATTTAGGAAAAGATCCCATCCAGTCTTTTTCAAAGTTT
96 TCAATTTAGGAAAAGATCCCATC-AAGTTTTTTTTTCAAAATTTTCAATTTAGGGA
66 TCAATTTAGGAAAAGATCCCATCAAAGTTTTTTTTTCAAAATTTTCAATTTAGGGA
151 AAAGATCCCATCAAGTTTTCAAAGTTTTCAATTTAGGAAAAGATCCCATCCAGTCTTTTTCAAAG
1 AAAGATCCCATCAAGTTTT---AGTTTTCAATTTAGGAAAAGATCCCATCCAGTCTTTTTCAAAG
*
216 TTTTCAA-TTAGGGGAAAGATCCCATCAAAGTTTTT
63 TTTTCAATTTA-GGAAAAGATCCCATCAAAGTTTTT
251 AGAATTGAGT
Statistics
Matches: 90, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
120 18 0.20
122 3 0.03
123 61 0.68
124 8 0.09
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.37
Consensus pattern (121 bp):
AAAGATCCCATCAAGTTTTAGTTTTCAATTTAGGAAAAGATCCCATCCAGTCTTTTTCAAAGTTT
TCAATTTAGGAAAAGATCCCATCAAAGTTTTTTTTTCAAAATTTTCAATTTAGGGA
Found at i:4072 original size:21 final size:21
Alignment explanation
Indices: 4033--4081 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
4023 TCAATGCTTT
**
4033 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCAATTTCAA
*
4055 AGGAAGCAAGAGCAATTTCCA
1 AGGAAGCAAGAGCAATTTCAA
4076 A-GAAGC
1 AGGAAGC
4082 TACATTTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCAATTTCAA
Found at i:6741 original size:8 final size:8
Alignment explanation
Indices: 6728--6760 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
6718 ATCAAATTCC
6728 TCAAATTT
1 TCAAATTT
6736 TCAAATTT
1 TCAAATTT
6744 TCAAATTT
1 TCAAATTT
*
6752 TCAAGTTT
1 TCAAATTT
6760 T
1 T
6761 GGAGAAGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.52
Consensus pattern (8 bp):
TCAAATTT
Found at i:9080 original size:26 final size:26
Alignment explanation
Indices: 9046--9095 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
9036 TGTCCCTCTG
*
9046 AAAAAAAAAAGAGTGTTAGTAACCTC
1 AAAAAAAAAAGAGAGTTAGTAACCTC
* *
9072 AAAAGAAAAAGGGAGTTAGTAACC
1 AAAAAAAAAAGAGAGTTAGTAACC
9096 CTTAAATCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.54, C:0.10, G:0.20, T:0.16
Consensus pattern (26 bp):
AAAAAAAAAAGAGAGTTAGTAACCTC
Found at i:12543 original size:50 final size:50
Alignment explanation
Indices: 12379--12618 Score: 282
Period size: 52 Copynumber: 4.8 Consensus size: 50
12369 ATTGAAAACT
* * *
12379 AAAACCTGATGGGAACTTTCACAATTTGAAAACCAAC-TGAATTGAACACTTTG
1 AAAA-CTGATGGGAACTTTCCCAATTTG-AAA--AACTTAAATTGAATACTTTG
*
12432 AAAACTGATGGGAACTTTCCCAATTTGAAAAAGAGC-TAAATAGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAATTTG-AAAA-A-CTTAAATTGAATACTTTG
* *
12484 AAAACTGATGGAAACTTTCCCAATTTGAAACACTTAAATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAACTTAAATTGAATACTTTG
*
12534 AAAATTGATGGGAACTTTCCCAATTTGAAAAACTTAAATTGAATAC-TT-
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAACTTAAATTGAATACTTTG
*
12582 -----TGATGGGAACTTTCCCAATTTGAAAAACTTGAATTGA
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAACTTAAATTGA
12619 TGAAATTCTT
Statistics
Matches: 173, Mismatches: 11, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
43 36 0.21
49 3 0.02
50 60 0.35
51 4 0.02
52 66 0.38
53 4 0.02
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (50 bp):
AAAACTGATGGGAACTTTCCCAATTTGAAAAACTTAAATTGAATACTTTG
Found at i:12543 original size:102 final size:99
Alignment explanation
Indices: 12379--12618 Score: 289
Period size: 102 Copynumber: 2.4 Consensus size: 99
12369 ATTGAAAACT
*
12379 AAAACCTGATGGGAACTTTCACAATTTGAAAACCAAC-TGAATTGAACACTTTGAAAACTGATGG
1 AAAA-CTGAT-GGAACTTTCCCAATTTG-AAA-C-ACTTGAATTGAACACTTTGAAAACTGATGG
12443 GAACTTTCCCAATTTGAAAAAGAGC-TAAATAGAATACTTTG
61 GAACTTTCCCAATTTG-AAAA-A-CTTAAATAGAATACTTTG
* * *
12484 AAAACTGATGGAAACTTTCCCAATTTGAAACACTTAAATTGAATACTTTGAAAATTGATGGGAAC
1 AAAACTGATGG-AACTTTCCCAATTTGAAACACTTGAATTGAACACTTTGAAAACTGATGGGAAC
*
12549 TTTCCCAATTTGAAAAACTTAAATTGAATACTTTG
65 TTTCCCAATTTGAAAAACTTAAATAGAATACTTTG
*
12584 ---A-TG--GGAACTTTCCCAATTTGAAAAACTTGAATTGA
1 AAAACTGATGGAACTTTCCCAATTTGAAACACTTGAATTGA
12619 TGAAATTCTT
Statistics
Matches: 125, Mismatches: 7, Indels: 18
0.83 0.05 0.12
Matches are distributed among these distances:
93 28 0.22
94 2 0.02
96 2 0.02
97 1 0.01
99 1 0.01
100 16 0.13
101 6 0.05
102 41 0.33
103 5 0.04
104 19 0.15
105 4 0.03
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (99 bp):
AAAACTGATGGAACTTTCCCAATTTGAAACACTTGAATTGAACACTTTGAAAACTGATGGGAACT
TTCCCAATTTGAAAAACTTAAATAGAATACTTTG
Found at i:12573 original size:34 final size:36
Alignment explanation
Indices: 12535--12620 Score: 95
Period size: 43 Copynumber: 2.2 Consensus size: 36
12525 AATACTTTGA
12535 AAATTGATGGGAACTTTCCCAATTTGAAAAACTTAAATTG
1 AAATTGATGGGAACTTTCCCAATTTGAAAAAC----ATTG
12575 AATACTTTGATGGGAACTTTCCCAATTTGAAAAAC-TTG
1 AA-A--TTGATGGGAACTTTCCCAATTTGAAAAACATTG
12613 -AATTGATG
1 AAATTGATG
12621 AAATTCTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
34 6 0.14
36 1 0.02
37 1 0.02
38 3 0.07
40 2 0.05
41 1 0.02
43 29 0.67
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (36 bp):
AAATTGATGGGAACTTTCCCAATTTGAAAAACATTG
Found at i:19378 original size:11 final size:11
Alignment explanation
Indices: 19360--19393 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
19350 CAATAGTCTT
19360 TAAATCTTCAA
1 TAAATCTTCAA
*
19371 TTAATCTTCAA
1 TAAATCTTCAA
19382 TAAATCTTCAA
1 TAAATCTTCAA
19393 T
1 T
19394 CATGAACTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAATCTTCAA
Found at i:21986 original size:36 final size:36
Alignment explanation
Indices: 21939--22012 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
21929 TATAGCTCGT
21939 TTCATATCTCAACTAACTGCAAAATGTGATCCCATC
1 TTCATATCTCAACTAACTGCAAAATGTGATCCCATC
21975 TTCATATCTCAACTAACTGCAAAATGTGATCCCATC
1 TTCATATCTCAACTAACTGCAAAATGTGATCCCATC
22011 TT
1 TT
22013 TAAGTTGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.32
Consensus pattern (36 bp):
TTCATATCTCAACTAACTGCAAAATGTGATCCCATC
Found at i:24390 original size:37 final size:35
Alignment explanation
Indices: 24348--24443 Score: 111
Period size: 36 Copynumber: 2.7 Consensus size: 35
24338 AAAAAGAGAC
24348 TGGACCTAAAATAGAGAGAGGTTGAAAAGGAAAAAAA
1 TGGACCTAAAATAGAGAGAGGTTGAAAA-G-AAAAAA
* * *
24385 TGGACCTAAGATAGAGAGAGGTCAGAAAAGAAAAAC
1 TGGACCTAAAATAGAGAGAGGT-TGAAAAGAAAAAA
* * *
24421 TTGAACTAAAATAGAAAGAGGTT
1 TGGACCTAAAATAGAGAGAGGTT
24444 AGAGAAAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
36 23 0.46
37 22 0.44
38 5 0.10
ACGTcount: A:0.51, C:0.07, G:0.26, T:0.16
Consensus pattern (35 bp):
TGGACCTAAAATAGAGAGAGGTTGAAAAGAAAAAA
Found at i:25385 original size:59 final size:59
Alignment explanation
Indices: 25298--26091 Score: 1161
Period size: 59 Copynumber: 13.5 Consensus size: 59
25288 ATCCCCTTTC
* *
25298 TGTTTTTAAAAATCCT-ATTTGAGGTCTCTGGTAGAGAGTTTTTAATTCAAAATCTTGTCT
1 TGTTTTT-AAAATCCTGA-TCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
*
25358 TGTTTTTAAAATCCTGATCGAGCTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
1 TGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
*
25417 TGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCATGTCT
1 TGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
*
25476 TG-TTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCATGTCT
1 TGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
* * *
25534 TGATTTTGAAATCATGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
1 TGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
* *
25593 TGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAATCTTATCT
1 TGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
25652 TGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
1 TGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
* * * *
25711 TGTTTTTGAAATCGTCATCGAGGTCTCTGGTAGAGAGTTTTGAATTCAAAATCTTGTCT
1 TGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
* *
25770 TGTTTTTAAAATCCTTATC-ATGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTATCT
1 TGTTTTTAAAATCCTGATCGA-GGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
* * * *
25829 TG-TTTTAAAATCCTGTTAGAGGTCTCTAGTAGAGAGTTTTCAATTCAAAATCTTGTAT
1 TGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
* * * * *
25887 TGCTTTTAAAATCCTGATCGAAGTCTCTAGTAGAGAGTTTTCAATTCGAAATATTGTCT
1 TGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
** * * * **
25946 TGTTTTTTTAATCCTGATCGATGTC-CTTGGTAGAAAGTTTTTCAATTCAAAGTCTTACCT
1 TGTTTTTAAAATCCTGATCGAGGTCTC-TGGTAGAGAG-TTTTCAATTCAAAATCTTGTCT
* * *
26006 TG-TTTTAAAATCTTGTTCGAGGTCTCTGGTATAGAGTTTTCAATTCAAAATCTTGTCT
1 TGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
* *
26064 TG-TTTTAAAGTCCTGATCGAGGTTTCTG
1 TGTTTTTAAAATCCTGATCGAGGTCTCTG
26092 ATTGAAAGTC
Statistics
Matches: 665, Mismatches: 61, Indels: 18
0.89 0.08 0.02
Matches are distributed among these distances:
58 153 0.23
59 484 0.73
60 28 0.04
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (59 bp):
TGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
Found at i:25837 original size:235 final size:236
Alignment explanation
Indices: 25298--26091 Score: 1154
Period size: 235 Copynumber: 3.4 Consensus size: 236
25288 ATCCCCTTTC
* *
25298 TGTTTTTAAAAATCC-TATTTGAGGTCTCTGGTAGAGAGTTTTTAATTCAAAATCTTGTCTTGTT
1 TGTTTTT-AAAATCCTTA-TCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTT
*
25362 TTTAAAATCCTGATCGAGCTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAA
64 TTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAA
*
25427 ATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCATGTCTTG-TTTTAAAATCCTG
129 ATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTG
*
25491 ATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCATGTCT
194 ATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
* * * *
25534 TGATTTTGAAATCATGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTT
1 TGTTTTTAAAATCCTTATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTT
* *
25599 TAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAATCTTATCTTGTTTTTAAAAT
66 TAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAAT
* * *
25664 CCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTGAAATCGTCAT
131 CCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGAT
*
25729 CGAGGTCTCTGGTAGAGAGTTTTGAATTCAAAATCTTGTCT
196 CGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
*
25770 TGTTTTTAAAATCCTTATC-ATGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTATCTTG-TT
1 TGTTTTTAAAATCCTTATCGA-GGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTT
* * * * *
25833 TTAAAATCCTGTTAGAGGTCTCTAGTAGAGAGTTTTCAATTCAAAATCTTGTATTGCTTTTAAAA
65 TTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAA
* * * * **
25898 TCCTGATCGAAGTCTCTAGTAGAGAGTTTTCAATTCGAAATATTGTCTTGTTTTTTTAATCCTGA
130 TCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGA
* * * **
25963 TCGATGTC-CTTGGTAGAAAGTTTTTCAATTCAAAGTCTTACCT
195 TCGAGGTCTC-TGGTAGAGAG-TTTTCAATTCAAAATCTTGTCT
* *
26006 TG-TTTTAAAAT-CTTGTTCGAGGTCTCTGGTATAGAGTTTTCAATTCAAAATCTTGTCTTG-TT
1 TGTTTTTAAAATCCTT-ATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTT
* *
26068 TTAAAGTCCTGATCGAGGTTTCTG
65 TTAAAATCCTGATCGAGGTCTCTG
26092 ATTGAAAGTC
Statistics
Matches: 502, Mismatches: 49, Indels: 15
0.89 0.09 0.03
Matches are distributed among these distances:
234 4 0.01
235 365 0.73
236 133 0.26
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (236 bp):
TGTTTTTAAAATCCTTATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTT
TAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAAT
CCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGAT
CGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCT
Found at i:26380 original size:27 final size:27
Alignment explanation
Indices: 26342--26439 Score: 144
Period size: 27 Copynumber: 3.6 Consensus size: 27
26332 TAATCAGTCA
26342 TTTTGCACACTCAGGGGCATTTTGGTC
1 TTTTGCACACTCAGGGGCATTTTGGTC
26369 TTTTGCACACTCAGGGGCATTTTGGTC
1 TTTTGCACACTCAGGGGCATTTTGGTC
* * *
26396 ATTTG-ACACTCCGAGAGCATTTTGGTC
1 TTTTGCACACTCAG-GGGCATTTTGGTC
26423 ATTTTGCACACTCAGGG
1 -TTTTGCACACTCAGGG
26440 TTTTTCTTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
26 7 0.11
27 43 0.69
28 5 0.08
29 7 0.11
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.35
Consensus pattern (27 bp):
TTTTGCACACTCAGGGGCATTTTGGTC
Found at i:33443 original size:18 final size:18
Alignment explanation
Indices: 33403--33444 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
33393 CCTTAGGATG
33403 TTTGGGCTTTAAGTTTTA
1 TTTGGGCTTTAAGTTTTA
* *
33421 ATTGGGCTTT-AGATTTTT
1 TTTGGGCTTTAAG-TTTTA
33439 TTTGGG
1 TTTGGG
33445 GACCTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.14, C:0.05, G:0.26, T:0.55
Consensus pattern (18 bp):
TTTGGGCTTTAAGTTTTA
Found at i:33681 original size:13 final size:13
Alignment explanation
Indices: 33663--33690 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
33653 AATTTGGGTC
33663 TTGATTGTTTTAT
1 TTGATTGTTTTAT
33676 TTGATTGTTTTAT
1 TTGATTGTTTTAT
33689 TT
1 TT
33691 TTTGGGGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (13 bp):
TTGATTGTTTTAT
Found at i:34530 original size:41 final size:41
Alignment explanation
Indices: 34482--34674 Score: 223
Period size: 41 Copynumber: 4.7 Consensus size: 41
34472 ACCGAGTTTT
*
34482 AGTTTTCAATTTAGGGAAAGATCCCGTCCATTTTTTTTCAA
1 AGTTTTCAATTTAGGGAAAGATCCCATCCATTTTTTTTCAA
*
34523 AGTTTTCAATTTAGGGAAAGATCCCATCAAGATTTTTTTTTCAA
1 AGTTTTCAATTTAGGGAAAGATCCCATC--CA-TTTTTTTTCAA
* **
34567 AATTTTCAATTTAGGGAAAAGATCCCAT-CA--AGTTTTCAA
1 AGTTTTCAATTTAGGG-AAAGATCCCATCCATTTTTTTTCAA
* * * * *
34606 AGTTTTCAATTTAGGGAATGATTCCATACAGTCTTTTTCAA
1 AGTTTTCAATTTAGGGAAAGATCCCATCCATTTTTTTTCAA
34647 AGTTTTCAA-TTAGGGGAAAGATCCCATC
1 AGTTTTCAATTTA-GGGAAAGATCCCATC
34675 AAAGTTTTTA
Statistics
Matches: 130, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
38 9 0.07
39 24 0.18
40 3 0.02
41 55 0.42
42 1 0.01
43 1 0.01
44 26 0.20
45 11 0.08
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (41 bp):
AGTTTTCAATTTAGGGAAAGATCCCATCCATTTTTTTTCAA
Found at i:37109 original size:17 final size:17
Alignment explanation
Indices: 37087--37119 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
37077 GTTTGGGCGT
37087 CCATGCTAAGTCGGGGA
1 CCATGCTAAGTCGGGGA
37104 CCATGCTAAGTCGGGG
1 CCATGCTAAGTCGGGG
37120 TTGGATCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.36, T:0.18
Consensus pattern (17 bp):
CCATGCTAAGTCGGGGA
Found at i:44252 original size:2 final size:2
Alignment explanation
Indices: 44245--44273 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44235 AACTATCCTC
44245 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
44274 CTTATTATCT
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:46188 original size:22 final size:22
Alignment explanation
Indices: 46162--46444 Score: 102
Period size: 22 Copynumber: 12.6 Consensus size: 22
46152 TTACAAAGGA
*
46162 AGGTTATCAAATTTTCAT-TGTG
1 AGGTTATCAAAATTTCATATG-G
*
46184 TGGTTA-CTAAAATTTCATATGG
1 AGGTTATC-AAAATTTCATATGG
** *
46206 AGGTTATCAAAACGTCATAGTGT
1 AGGTTATCAAAATTTCATA-TGG
* **
46229 A-GTTATCAAAATTCCATACAG
1 AGGTTATCAAAATTTCATATGG
* * ***
46250 ACGTTA-CTAAAATTTTATAAAA
1 AGGTTATC-AAAATTTCATATGG
*
46272 AGGTTATCAAAATTTCTTA-GAG
1 AGGTTATCAAAATTTCATATG-G
* * * * *
46294 TGTCGTTAACAAAATTTTATACGA
1 AG--GTTATCAAAATTTCATATGG
*
46318 AGGTTATCAAAGTTT-ATA-GTG
1 AGGTTATCAAAATTTCATATG-G
* * *
46339 TGGTTATCAAAATTTTATAGGG
1 AGGTTATCAAAATTTCATATGG
* * *
46361 AGGGAGTTTATCAAAGTTTCCTAGGG
1 A--G-G-TTATCAAAATTTCATATGG
*
46387 AGGTTAACAAAATTTCATA-GG
1 AGGTTATCAAAATTTCATATGG
46408 AAGGTTA-CAAAAATTT--TATGG
1 -AGGTTATC-AAAATTTCATATGG
46429 AGATGTTATCAAAATT
1 AG--GTTATCAAAATT
46445 AAATAAAGAG
Statistics
Matches: 198, Mismatches: 39, Indels: 48
0.69 0.14 0.17
Matches are distributed among these distances:
20 5 0.03
21 24 0.12
22 123 0.62
23 10 0.05
24 17 0.09
25 2 0.01
26 17 0.09
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGG
Found at i:46310 original size:46 final size:43
Alignment explanation
Indices: 46258--46357 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
46248 AGACGTTACT
*
46258 AAAATTTTATAAAAAGGTTATCAAAATTTCTTAGAGTGTCGTTAAC
1 AAAATTTTATAAAAAGGTTATC-AAA-GT-TTAGAGTGTCGTTAAC
** * * *
46304 AAAATTTTATACGAAGGTTATCAAAGTTTATAGTGTGGTTATC
1 AAAATTTTATAAAAAGGTTATCAAAGTTTAGAGTGTCGTTAAC
46347 AAAATTTTATA
1 AAAATTTTATA
46358 GGGAGGGAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
43 24 0.50
44 1 0.02
45 3 0.06
46 20 0.42
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (43 bp):
AAAATTTTATAAAAAGGTTATCAAAGTTTAGAGTGTCGTTAAC
Found at i:46400 original size:48 final size:44
Alignment explanation
Indices: 46298--46418 Score: 122
Period size: 43 Copynumber: 2.7 Consensus size: 44
46288 TTAGAGTGTC
* * *
46298 GTTAACAAAATTTTATA-CGAAGGTTATCAAAGTTTATAGTGTG
1 GTTAACAAAATTTTATAGGGAAGGTTATCAAAGTTTATAGGGAG
* * *
46341 GTTATCAAAATTTTATAGGGAGGGAGTTTATCAAAGTTTCCTAGGGAG
1 GTTAACAAAATTTTATAGGGA---AGGTTATCAAAGTTT-ATAGGGAG
*
46389 GTTAACAAAATTTCATA-GGAAGGTTA-CAAA
1 GTTAACAAAATTTTATAGGGAAGGTTATCAAA
46419 AATTTTATGG
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
43 20 0.31
44 7 0.11
47 17 0.27
48 20 0.31
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.33
Consensus pattern (44 bp):
GTTAACAAAATTTTATAGGGAAGGTTATCAAAGTTTATAGGGAG
Found at i:46573 original size:66 final size:66
Alignment explanation
Indices: 46501--46663 Score: 165
Period size: 66 Copynumber: 2.5 Consensus size: 66
46491 CATGTTGTGG
* * * * *
46501 TTATCAAAATTTTCATAATGCGGTTA-CCAATTTTTATAGTGTGATTATCAAAATTTCATAGGGA
1 TTATCAAAA-TTTCATAATGCGGTTATCAAAATTTCACAGTGCGATTATCAAAATTTCATAGGGA
46565 GA
65 GA
* * * *
46567 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAGTGCGTTTATCAAATTTTCATA--G-G
1 TTATCAAAATTTCATAATGCGGTTATCAAAATTTCACAGTGCGATTATCAAAATTTCATAGGGAG
46629 -
66 A
* ** *
46629 TTATCGAAATTTCATAATGATGTTATCAAATTTTC
1 TTATCAAAATTTCATAATGCGGTTATCAAAATTTC
46664 GCATCATTAT
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
62 30 0.37
63 1 0.01
64 1 0.01
65 14 0.17
66 36 0.44
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (66 bp):
TTATCAAAATTTCATAATGCGGTTATCAAAATTTCACAGTGCGATTATCAAAATTTCATAGGGAG
A
Found at i:46584 original size:44 final size:44
Alignment explanation
Indices: 46536--46627 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
46526 ACCAATTTTT
*
46536 ATAGTGTGATTATCAAAATTTCATAGGGAGATTATCAAAATTTC
1 ATAGTGTGATTATCAAAATTTCACAGGGAGATTATCAAAATTTC
* * * * *
46580 ATAGTGTGGTTATCAAAATTTCACAGTGCGTTTATCAAATTTTC
1 ATAGTGTGATTATCAAAATTTCACAGGGAGATTATCAAAATTTC
46624 ATAG
1 ATAG
46628 GTTATCGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (44 bp):
ATAGTGTGATTATCAAAATTTCACAGGGAGATTATCAAAATTTC
Found at i:46663 original size:22 final size:21
Alignment explanation
Indices: 46500--46663 Score: 113
Period size: 22 Copynumber: 7.7 Consensus size: 21
46490 TCATGTTGTG
* *
46500 GTTATCAAAATTTTCATAATGCG
1 GTTATC-AAATTTTCATAGTG-T
* *
46523 GTTA-CCAATTTTTATAGTGT
1 GTTATCAAATTTTCATAGTGT
* * *
46543 GATTATCAAAATTTCATAGGGA
1 G-TTATCAAATTTTCATAGTGT
*
46565 GATTATCAAAATTTCATAGTGT
1 G-TTATCAAATTTTCATAGTGT
* * *
46587 GGTTATCAAAATTTCACAGTGC
1 -GTTATCAAATTTTCATAGTGT
46609 GTTTATCAAATTTTCATA--G-
1 G-TTATCAAATTTTCATAGTGT
*
46628 GTTATCGAAA-TTTCATAATGAT
1 GTTATC-AAATTTTCATAGTG-T
46650 GTTATCAAATTTTC
1 GTTATCAAATTTTC
46664 GCATCATTAT
Statistics
Matches: 116, Mismatches: 15, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
18 12 0.10
19 4 0.03
20 3 0.03
21 18 0.16
22 74 0.64
23 5 0.04
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41
Consensus pattern (21 bp):
GTTATCAAATTTTCATAGTGT
Found at i:47117 original size:70 final size:70
Alignment explanation
Indices: 47043--47257 Score: 412
Period size: 70 Copynumber: 3.1 Consensus size: 70
47033 TGCATGTTTG
*
47043 TGTGTAGAATGTTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTGTGTAATCAATGCTCA
1 TGTGTAGAACGTTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTGTGTAATCAATGCTCA
47108 TATGT
66 TATGT
*
47113 TGTGTAGAACGTTGTTTTGGAGAAAATATTTATTTCGAATGTGTTATTTGTGTAATCAATGCTCA
1 TGTGTAGAACGTTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTGTGTAATCAATGCTCA
47178 TATGT
66 TATGT
47183 TGTGTAGAACGTTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTGTGTAATCAATGCTCA
1 TGTGTAGAACGTTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTGTGTAATCAATGCTCA
47248 TATGT
66 TATGT
47253 TGTGT
1 TGTGT
47258 TTCGAAGTTA
Statistics
Matches: 142, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 142 1.00
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.45
Consensus pattern (70 bp):
TGTGTAGAACGTTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTGTGTAATCAATGCTCA
TATGT
Found at i:47796 original size:38 final size:38
Alignment explanation
Indices: 47748--47820 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
47738 ATATATAACC
* * *
47748 TTTTTCATAACTGTTATGGCTTTTTGAGTTATTAACTT
1 TTTTTCATAACCGTTATAGCTTTTTGAGTAATTAACTT
47786 TTTTTCATAACCGTTATAGCTTTTTGAGTAATTAA
1 TTTTTCATAACCGTTATAGCTTTTTGAGTAATTAA
47821 GTATTGTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.25, C:0.11, G:0.12, T:0.52
Consensus pattern (38 bp):
TTTTTCATAACCGTTATAGCTTTTTGAGTAATTAACTT
Found at i:51214 original size:8 final size:7
Alignment explanation
Indices: 51197--51230 Score: 50
Period size: 8 Copynumber: 4.6 Consensus size: 7
51187 TAAAAGCTTT
51197 AGAGTTG
1 AGAGTTG
51204 AGAGTTTG
1 AGAG-TTG
51212 AGAGTTG
1 AGAGTTG
51219 AAGAGTTG
1 -AGAGTTG
51227 AGAG
1 AGAG
51231 ATAAAGCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 11 0.44
8 14 0.56
ACGTcount: A:0.32, C:0.00, G:0.41, T:0.26
Consensus pattern (7 bp):
AGAGTTG
Found at i:51217 original size:15 final size:15
Alignment explanation
Indices: 51197--51230 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
51187 TAAAAGCTTT
51197 AGAGTTG-AGAGTTTG
1 AGAGTTGAAGAG-TTG
51212 AGAGTTGAAGAGTTG
1 AGAGTTGAAGAGTTG
51227 AGAG
1 AGAG
51231 ATAAAGCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.32, C:0.00, G:0.41, T:0.26
Consensus pattern (15 bp):
AGAGTTGAAGAGTTG
Found at i:60165 original size:6 final size:6
Alignment explanation
Indices: 60146--60184 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
60136 CTAATACTAG
* *
60146 TGGCGG TGGAGA TGGCGA TGGCGA TGGCGA TGGCGA TGG
1 TGGCGA TGGCGA TGGCGA TGGCGA TGGCGA TGGCGA TGG
60185 TGGTAACCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.15, C:0.13, G:0.54, T:0.18
Consensus pattern (6 bp):
TGGCGA
Found at i:60588 original size:32 final size:32
Alignment explanation
Indices: 60552--60638 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 32
60542 GCGCGAAAAG
** *
60552 AAAACGCCAATATTTAGCGGCGTCTATAGAAT
1 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
60584 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
*
60616 AAAACACCCTTATTTAGCGGCGT
1 AAAACGCCCTTATTTAGCGGCGT
60639 TGATCGGTCG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (32 bp):
AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
Found at i:60838 original size:12 final size:13
Alignment explanation
Indices: 60816--60845 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
60806 ACTAACAACT
60816 AAAATCAATCAAG
1 AAAATCAATCAAG
60829 AAAA-CAATCAAG
1 AAAATCAATCAAG
60841 AAAAT
1 AAAAT
60846 TAAAGAAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAATCAATCAAG
Found at i:63441 original size:11 final size:11
Alignment explanation
Indices: 63425--63449 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
63415 GGGGAATAAT
63425 CAATCCAAAAA
1 CAATCCAAAAA
63436 CAATCCAAAAA
1 CAATCCAAAAA
63447 CAA
1 CAA
63450 ACAATTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.28, G:0.00, T:0.08
Consensus pattern (11 bp):
CAATCCAAAAA
Found at i:63837 original size:21 final size:22
Alignment explanation
Indices: 63802--63844 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
63792 TAAGATGCAT
*
63802 AAAAATAAATCTTAAATCTAAA
1 AAAAAGAAATCTTAAATCTAAA
63824 AAAAAGAAAT-TTAAATCTAAA
1 AAAAAGAAATCTTAAATCTAAA
63845 CCTAAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAAAGAAATCTTAAATCTAAA
Done.