Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013943.1 Corchorus olitorius cultivar O-4 contig13976, 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: 103700
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:89 original size:29 final size:29
Alignment explanation
Indices: 57--112 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
47 TAAAATTTCT
* *
57 TCTACCAATATATGTGCTACATAATTCCA
1 TCTACCAATAAACGTGCTACATAATTCCA
86 TCTACCAATAAACGTGCTACATAATTC
1 TCTACCAATAAACGTGCTACATAATTC
113 TTTAGTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (29 bp):
TCTACCAATAAACGTGCTACATAATTCCA
Found at i:2573 original size:26 final size:26
Alignment explanation
Indices: 2505--2562 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
2495 ATAATGGATA
2505 ATTGTAAGAGATATTATAAGAAAACTT
1 ATTG-AAGAGATATTATAAGAAAACTT
2532 ATTGAAGAGATATTATAAGAAAACTT
1 ATTGAAGAGATATTATAAGAAAACTT
2558 ATTGA
1 ATTGA
2563 GCTCAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 27 0.87
27 4 0.13
ACGTcount: A:0.48, C:0.03, G:0.16, T:0.33
Consensus pattern (26 bp):
ATTGAAGAGATATTATAAGAAAACTT
Found at i:3852 original size:15 final size:15
Alignment explanation
Indices: 3832--3860 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3822 TTACAGCAAA
3832 GTAAGTCTTGATTCG
1 GTAAGTCTTGATTCG
3847 GTAAGTCTTGATTC
1 GTAAGTCTTGATTC
3861 ATGAAATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (15 bp):
GTAAGTCTTGATTCG
Found at i:15616 original size:18 final size:18
Alignment explanation
Indices: 15589--15631 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
15579 CATTCTCTAG
15589 CTTCTCATTCTCG-CTTCT
1 CTTCTCATTCT-GACTTCT
*
15607 CTTCTGATTCTGACTTCT
1 CTTCTCATTCTGACTTCT
15625 CATTCTC
1 C-TTCTC
15632 TCCTCTCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 16 0.76
19 4 0.19
ACGTcount: A:0.09, C:0.35, G:0.07, T:0.49
Consensus pattern (18 bp):
CTTCTCATTCTGACTTCT
Found at i:15709 original size:62 final size:62
Alignment explanation
Indices: 15638--15761 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
15628 TCTCTCCTCT
15638 CCTTTTCTCCTTTTCTCCTCTCTCTCCTCTCTCAATCAGAGCTCTCCCTCCCTCCCAAAAGC
1 CCTTTTCTCCTTTTCTCCTCTCTCTCCTCTCTCAATCAGAGCTCTCCCTCCCTCCCAAAAGC
15700 CCTTTTCTCCTTTTCTCCTCTCTCTCCTCTCTCAATCAGAGCTCTCCCTCCCTCCCAAAAGC
1 CCTTTTCTCCTTTTCTCCTCTCTCTCCTCTCTCAATCAGAGCTCTCCCTCCCTCCCAAAAGC
15762 AAATCTCTTC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.13, C:0.47, G:0.05, T:0.35
Consensus pattern (62 bp):
CCTTTTCTCCTTTTCTCCTCTCTCTCCTCTCTCAATCAGAGCTCTCCCTCCCTCCCAAAAGC
Found at i:27231 original size:13 final size:13
Alignment explanation
Indices: 27213--27240 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
27203 ATTAAATTAC
27213 ATTAAATTGTAGA
1 ATTAAATTGTAGA
27226 ATTAAATTGTAGA
1 ATTAAATTGTAGA
27239 AT
1 AT
27241 GCATATGCAG
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:0.46, C:0.00, G:0.14, T:0.39
Consensus pattern (13 bp):
ATTAAATTGTAGA
Found at i:27921 original size:48 final size:48
Alignment explanation
Indices: 27863--28199 Score: 550
Period size: 48 Copynumber: 7.0 Consensus size: 48
27853 AAGCAAGTTC
* *
27863 GGGAACAAGAAGAAGAAAACAGTTGCTGTGACTGATCAGAAAGAAGAA
1 GGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAGAAGAA
* *
27911 AGGAGCAAGAAGAAGAAAACGGTTGATGTGACTGATCAGAAAGAAGAA
1 GGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAGAAGAA
* *
27959 GGGAACAAGAAGAATAAAACGGTTGCTGTGACTGATCAGAAAGAAGAA
1 GGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAGAAGAA
* *
28007 GGGACCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAGAATAA
1 GGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAGAAGAA
28055 GGGAGCAAGAAGAAGAAAACGGTT-CTGGTGACTGATCAGAAAGAAGAA
1 GGGAGCAAGAAGAAGAAAACGGTTGCT-GTGACTGATCAGAAAGAAGAA
* * *
28103 GGGAACAAGAAGAAGAAAACGGTTGTTGTGACTGATCAGAAAGATGAA
1 GGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAGAAGAA
*
28151 GGGAGCAAGAAGAAGAAAACGTTTGCTGTGACTGATCAGAAAGAAGAA
1 GGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAGAAGAA
28199 G
1 G
28200 AACACGGTTG
Statistics
Matches: 267, Mismatches: 20, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
47 2 0.01
48 264 0.99
49 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.31, T:0.14
Consensus pattern (48 bp):
GGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAGAAGAA
Found at i:27987 original size:96 final size:96
Alignment explanation
Indices: 27863--28299 Score: 592
Period size: 96 Copynumber: 4.8 Consensus size: 96
27853 AAGCAAGTTC
* * *
27863 GGGAACAAGAAGAAGAAAACAGTTGCTGTGACTGATCAGAAAGAAGAAAGGAGCAAGAAGAAGAA
1 GGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAGAAGAAGGGAGCAAGAAGAAGAA
*
27928 AACGGTTGATGTGACTGATCAGAAAGAAGAA
66 AACGGTTGTTGTGACTGATCAGAAAGAAGAA
* * *
27959 GGGAACAAGAAGAATAAAACGGTTGCTGTGACTGATCAGAAAGAAGAAGGGACCAAGAAGAAGAA
1 GGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAGAAGAAGGGAGCAAGAAGAAGAA
* *
28024 AACGGTTGCTGTGACTGATCAGAAAGAATAA
66 AACGGTTGTTGTGACTGATCAGAAAGAAGAA
*
28055 GGGAGCAAGAAGAAGAAAACGGTT-CTGGTGACTGATCAGAAAGAAGAAGGGAACAAGAAGAAGA
1 GGGAGCAAGAAGAAGAAAACGGTTGCT-GTGACTGATCAGAAAGAAGAAGGGAGCAAGAAGAAGA
*
28119 AAACGGTTGTTGTGACTGATCAGAAAGATGAA
65 AAACGGTTGTTGTGACTGATCAGAAAGAAGAA
*
28151 GGGAGCAAGAAGAAGAAAACGTTTGCTGTGACTGATC----------A--GA--AAGAAGAAGAA
1 GGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAGAAGAAGGGAGCAAGAAGAAGAA
* *
28202 CACGGTTGTTGTGACTGATGAGAAAGAAGAA
66 AACGGTTGTTGTGACTGATCAGAAAGAAGAA
28233 GGGAGCAAGAAGAAGAAAACGGTTGC--TGA-T--T-AGAAAGAAGAAGGGAGCAAGAAGAAGAA
1 GGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAGAAGAAGGGAGCAAGAAGAAGAA
28292 AACGGTTG
66 AACGGTTG
28300 CTGATGAGAA
Statistics
Matches: 307, Mismatches: 18, Indels: 38
0.85 0.05 0.10
Matches are distributed among these distances:
77 1 0.00
79 1 0.00
80 3 0.01
82 64 0.21
84 2 0.01
86 2 0.01
88 2 0.01
90 18 0.06
95 2 0.01
96 210 0.68
97 2 0.01
ACGTcount: A:0.45, C:0.10, G:0.32, T:0.14
Consensus pattern (96 bp):
GGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAGAAGAAGGGAGCAAGAAGAAGAA
AACGGTTGTTGTGACTGATCAGAAAGAAGAA
Found at i:28086 original size:144 final size:141
Alignment explanation
Indices: 27863--28302 Score: 583
Period size: 144 Copynumber: 3.2 Consensus size: 141
27853 AAGCAAGTTC
* *
27863 GGGAACAAGAAGAAGAAAACAGTTGCTGTGACTGATCAGAAAGAAGAAAGGAGCAAGAAGAAGAA
1 GGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAG-A-AAAGGAGCAAGAAGAAGAA
*
27928 AACGGTTGATGTGACTGATCAGAAAGAAGAAGGGAACAAGAAGAATAAAACGGTTGCTGTGACTG
64 AACGGTT-ATGTGACTGATCAGAAAGAAGAAGGGAACAAGAAGAAGAAAACGGTTGCTGTGACTG
27993 ATCAGAAAGAAGAA
128 ATCAGAAAGAAGAA
*
28007 GGGACCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAGAATAAGGGAGCAAGAAGAAGAA
1 GGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAGAA-AA-GGAGCAAGAAGAAGAA
* *
28072 AACGGTTCTGGTGACTGATCAGAAAGAAGAAGGGAACAAGAAGAAGAAAACGGTTGTTGTGACTG
64 AACGGTTAT-GTGACTGATCAGAAAGAAGAAGGGAACAAGAAGAAGAAAACGGTTGCTGTGACTG
*
28137 ATCAGAAAGATGAA
128 ATCAGAAAGAAGAA
* *
28151 GGGAGCAAGAAGAAGAAAACGTTTGCTGTGACTGATC---------A-GA--AAGAAGAAGAACA
1 GGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAGAAAAGGAGCAAGAAGAAGAAAA
* * *
28204 CGGTTGTTGTGACTGATGAGAAAGAAGAAGGGAGCAAGAAGAAGAAAACGGTTGC--TGA-T--T
66 CGGTT-ATGTGACTGATCAGAAAGAAGAAGGGAACAAGAAGAAGAAAACGGTTGCTGTGACTGAT
28264 -AGAAAGAAGAA
130 CAGAAAGAAGAA
28275 GGGAGCAAGAAGAAGAAAACGGTTGCTG
1 GGGAGCAAGAAGAAGAAAACGGTTGCTG
28303 ATGAGAAAGA
Statistics
Matches: 277, Mismatches: 15, Indels: 28
0.87 0.05 0.09
Matches are distributed among these distances:
124 37 0.13
125 1 0.00
127 1 0.00
128 3 0.01
130 61 0.22
131 1 0.00
132 2 0.01
134 1 0.00
142 1 0.00
143 4 0.01
144 165 0.60
ACGTcount: A:0.45, C:0.10, G:0.32, T:0.14
Consensus pattern (141 bp):
GGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGAAAGAAAAGGAGCAAGAAGAAGAAAA
CGGTTATGTGACTGATCAGAAAGAAGAAGGGAACAAGAAGAAGAAAACGGTTGCTGTGACTGATC
AGAAAGAAGAA
Found at i:28216 original size:130 final size:124
Alignment explanation
Indices: 28061--28302 Score: 358
Period size: 130 Copynumber: 1.9 Consensus size: 124
28051 ATAAGGGAGC
28061 AAGAAGAAGAAAACGGTTCTGGTGACTGATCAGAAAGAAGAAGGGAACAAGAAGAAGAAAACGGT
1 AAGAAGAAGAAAACGGTTCTGGTGACTGATCAGAAAGAAGAAGGGAACAAGAAGAAGAAAAC-G-
* *
28126 TGTTGTGACTGATCAGAAAGATGAAGGGAGCAAGAAGAAGAAAACGTTTGCTGTGACTGATCAGA
64 -G-T-TG-CTGATCAGAAAGAAGAAGGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGA
* * * * *
28191 AAGAAGAAGAACACGGTTGTTGTGACTGATGAGAAAGAAGAAGGGAGCAAGAAGAAGAAAACGGT
1 AAGAAGAAGAAAACGGTTCTGGTGACTGATCAGAAAGAAGAAGGGAACAAGAAGAAGAAAACGGT
*
28256 TGCTGATTAGAAAGAAGAAGGGAGCAAGAAGAAGAAAACGGTTGCTG
66 TGCTGATCAGAAAGAAGAAGGGAGCAAGAAGAAGAAAACGGTTGCTG
28303 ATGAGAAAGA
Statistics
Matches: 104, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
124 42 0.40
125 2 0.02
126 1 0.01
127 1 0.01
129 1 0.01
130 57 0.55
ACGTcount: A:0.44, C:0.09, G:0.32, T:0.15
Consensus pattern (124 bp):
AAGAAGAAGAAAACGGTTCTGGTGACTGATCAGAAAGAAGAAGGGAACAAGAAGAAGAAAACGGT
TGCTGATCAGAAAGAAGAAGGGAGCAAGAAGAAGAAAACGGTTGCTGTGACTGATCAGA
Found at i:28232 original size:37 final size:34
Alignment explanation
Indices: 28157--28233 Score: 118
Period size: 34 Copynumber: 2.3 Consensus size: 34
28147 TGAAGGGAGC
*
28157 AAGAAGAAGAAAACGTTTGCTGTGACTGATCAGA
1 AAGAAGAAGAAAACGGTTGCTGTGACTGATCAGA
* * *
28191 AAGAAGAAGAACACGGTTGTTGTGACTGATGAGA
1 AAGAAGAAGAAAACGGTTGCTGTGACTGATCAGA
28225 AAGAAGAAG
1 AAGAAGAAG
28234 GGAGCAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.43, C:0.09, G:0.30, T:0.18
Consensus pattern (34 bp):
AAGAAGAAGAAAACGGTTGCTGTGACTGATCAGA
Found at i:28246 original size:82 final size:82
Alignment explanation
Indices: 28109--28260 Score: 268
Period size: 82 Copynumber: 1.9 Consensus size: 82
28099 AGAAGGGAAC
* *
28109 AAGAAGAAGAAAACGGTTGTTGTGACTGATCAGAAAGATGAAGGGAGCAAGAAGAAGAAAACGTT
1 AAGAAGAAGAAAACGGTTGTTGTGACTGATCAGAAAGAAGAAGGGAGCAAGAAGAAGAAAACGGT
28174 TGCTGTGACTGATCAGA
66 TGCTGTGACTGATCAGA
* *
28191 AAGAAGAAGAACACGGTTGTTGTGACTGATGAGAAAGAAGAAGGGAGCAAGAAGAAGAAAACGGT
1 AAGAAGAAGAAAACGGTTGTTGTGACTGATCAGAAAGAAGAAGGGAGCAAGAAGAAGAAAACGGT
28256 TGCTG
66 TGCTG
28261 ATTAGAAAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 66 1.00
ACGTcount: A:0.42, C:0.09, G:0.32, T:0.16
Consensus pattern (82 bp):
AAGAAGAAGAAAACGGTTGTTGTGACTGATCAGAAAGAAGAAGGGAGCAAGAAGAAGAAAACGGT
TGCTGTGACTGATCAGA
Found at i:28268 original size:42 final size:42
Alignment explanation
Indices: 28216--28312 Score: 185
Period size: 42 Copynumber: 2.3 Consensus size: 42
28206 GTTGTTGTGA
28216 CTGATGAGAAAGAAGAAGGGAGCAAGAAGAAGAAAACGGTTG
1 CTGATGAGAAAGAAGAAGGGAGCAAGAAGAAGAAAACGGTTG
*
28258 CTGATTAGAAAGAAGAAGGGAGCAAGAAGAAGAAAACGGTTG
1 CTGATGAGAAAGAAGAAGGGAGCAAGAAGAAGAAAACGGTTG
28300 CTGATGAGAAAGA
1 CTGATGAGAAAGA
28313 GAAAGCCCCT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.47, C:0.07, G:0.34, T:0.11
Consensus pattern (42 bp):
CTGATGAGAAAGAAGAAGGGAGCAAGAAGAAGAAAACGGTTG
Found at i:28285 original size:39 final size:40
Alignment explanation
Indices: 27894--28312 Score: 157
Period size: 48 Copynumber: 9.3 Consensus size: 40
27884 GTTGCTGTGA
* *
27894 CTGATCAGAAAGAAGAAAGGAGCAAGAAGAAGAAAACGGTTGATGTG
1 CTGATGAGAAAGAAGAAGGGAGC-A-AAGAAGAAAAC-G--G-T-TG
* * *
27941 ACTGATCAGAAAGAAGAAGGGAACAAGAAGAATAAAACGGTTG
1 -CTGATGAGAAAGAAGAAGGGAGC-A-AAGAAGAAAACGGTTG
*
27984 CTGTGACTGATCAGAAAGAAGAAGGGACCAAGAAGAAGAAAACGGTTG
1 C--TGA-TG---AGAAAGAAGAAGGGAGC-A-AAGAAGAAAACGGTTG
*
28032 CTGTGACTGATCAGAAAGAATAAGGGAGCAAGAAGAAGAAAACGGTTCTGGTG
1 C--TGA-TG---AGAAAGAAGAAGGGAGC-A-AAGAAGAAAACGG---T--TG
* *
28085 ACTGATCAGAAAGAAGAAGGGAACAAGAAGAAGAAAACGGTTGTTGTG
1 -CTGATGAGAAAGAAGAAGGGAGC-A-AAGAAGAAAAC-G--G-T-TG
* * *
28133 ACTGATCAGAAAGATGAAGGGAGCAAGAAGAAGAAAACGTTTG
1 -CTGATGAGAAAGAAGAAGGGAGC-A-AAGAAGAAAACGGTTG
*** ** *
28176 CTG-TGACTGATCAGAA---AG--AAGAAGAACACGGTTGTTGTG
1 CTGATGAGAAAGAAGAAGGGAGCAAAGAAGAAAAC-G--G-T-TG
28215 ACTGATGAGAAAGAAGAAGGGAGCAAGAAGAAGAAAACGGTTG
1 -CTGATGAGAAAGAAGAAGGGAGC-A-AAGAAGAAAACGGTTG
*
28258 CTGATTAGAAAGAAGAAGGGAGCAAGAAGAAGAAAACGGTTG
1 CTGATGAGAAAGAAGAAGGGAGC-A-AAGAAGAAAACGGTTG
28300 CTGATGAGAAAGA
1 CTGATGAGAAAGA
28313 GAAAGCCCCT
Statistics
Matches: 310, Mismatches: 32, Indels: 64
0.76 0.08 0.16
Matches are distributed among these distances:
34 10 0.03
35 1 0.00
38 3 0.01
39 2 0.01
40 3 0.01
41 14 0.05
42 57 0.18
43 6 0.02
44 8 0.03
45 3 0.01
47 3 0.01
48 189 0.61
49 2 0.01
51 3 0.01
52 3 0.01
53 2 0.01
54 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.32, T:0.14
Consensus pattern (40 bp):
CTGATGAGAAAGAAGAAGGGAGCAAAGAAGAAAACGGTTG
Found at i:28316 original size:48 final size:46
Alignment explanation
Indices: 28191--28317 Score: 147
Period size: 42 Copynumber: 2.8 Consensus size: 46
28181 ACTGATCAGA
* *
28191 AAGAAGAAGAACACGGTTGTTG-TGACTGATGAGAAAGAAGAAGGGAGC
1 AAGAAGAAGAAAACGGTTGCTGATGA--GA-GAGAAAGAAGAAGGGAGC
*
28239 AAGAAGAAGAAAACGGTTGCTGAT----TAGAAAGAAGAAGGGAGC
1 AAGAAGAAGAAAACGGTTGCTGATGAGAGAGAAAGAAGAAGGGAGC
28281 AAGAAGAAGAAAACGGTTGCTGATGAGAAAGAGAAAG
1 AAGAAGAAGAAAACGGTTGCTGATGAG--AGAGAAAG
28318 CCCCTTCTGA
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
42 41 0.60
48 26 0.38
49 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.34, T:0.13
Consensus pattern (46 bp):
AAGAAGAAGAAAACGGTTGCTGATGAGAGAGAAAGAAGAAGGGAGC
Found at i:30892 original size:21 final size:22
Alignment explanation
Indices: 30856--30897 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
30846 TTCTCCTGTT
30856 TCGACCTTCATCAGGGTCGAAC
1 TCGACCTTCATCAGGGTCGAAC
30878 TCGACCTTC-TCAGGGTCGAA
1 TCGACCTTCATCAGGGTCGAA
30898 ACAGGGCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.24
Consensus pattern (22 bp):
TCGACCTTCATCAGGGTCGAAC
Found at i:32204 original size:33 final size:32
Alignment explanation
Indices: 32140--32213 Score: 103
Period size: 33 Copynumber: 2.3 Consensus size: 32
32130 AACGTTCAGT
* * *
32140 AAAGACAAGTAAGAGATTTTTTTCGTCAAAAAA
1 AAAGACAAGTAAGAGATTTTGTGCG-AAAAAAA
*
32173 AATGACAAGTAAGAGATTTTGTGCGAAAAAAA
1 AAAGACAAGTAAGAGATTTTGTGCGAAAAAAA
32205 AAAGACAAG
1 AAAGACAAG
32214 AGGTTTTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 14 0.39
33 22 0.61
ACGTcount: A:0.51, C:0.08, G:0.19, T:0.22
Consensus pattern (32 bp):
AAAGACAAGTAAGAGATTTTGTGCGAAAAAAA
Found at i:32342 original size:22 final size:22
Alignment explanation
Indices: 32300--32342 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
32290 TTTTTCTGTT
*
32300 TTTTGTTTTTGTTTCGTTTTCG
1 TTTTGTTTTTGTTTCGCTTTCG
32322 TTTTGTTTTTGTTGT-GCTTTC
1 TTTTGTTTTTGTT-TCGCTTTC
32343 AATTTTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.00, C:0.09, G:0.19, T:0.72
Consensus pattern (22 bp):
TTTTGTTTTTGTTTCGCTTTCG
Found at i:33130 original size:51 final size:49
Alignment explanation
Indices: 33056--33156 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 49
33046 TCTACCCAAT
33056 AAATATTGATGTTCGTTTTATTTATTATTTTTAACAAGAATTCCTATGA
1 AAATATTGATGTTCGTTTTATTTATTATTTTTAACAAGAATTCCTATGA
33105 AAATATTGATGAATTCGTTTTATTTATTATTTTTAACAAGAATTCCTATGA
1 AAATATTGATG--TTCGTTTTATTTATTATTTTTAACAAGAATTCCTATGA
33156 A
1 A
33157 GTTCTTGTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 11 0.22
51 39 0.78
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.48
Consensus pattern (49 bp):
AAATATTGATGTTCGTTTTATTTATTATTTTTAACAAGAATTCCTATGA
Found at i:35483 original size:113 final size:111
Alignment explanation
Indices: 35287--35513 Score: 391
Period size: 113 Copynumber: 2.0 Consensus size: 111
35277 ATCCTTTGGG
* **
35287 CAAATTCCCAAGCCTCTCACACAACCTTTCAACACAGTTTTTTTGAGTTTCACCTAAAACCCTAG
1 CAAATTCCCAAGCCTCTCACACAACCTTTCAACACAGCTTTTTTGAGCCTCACCTAAAACCCTAG
* *
35352 ATATAACTCTTTATTTATACTAAAAAATACTAAAACCCTAATTGAC
66 ATATAACTCTCTATTTATACTAAAAAATACTAAAACCCTAATGGAC
35398 CAAATTCCCAAGCCTCTCACACAACCTTTCAACACATAGCTTTTTTGAGCCTCACCTAAAACCCT
1 CAAATTCCCAAGCCTCTCACACAACCTTTCAACAC--AGCTTTTTTGAGCCTCACCTAAAACCCT
35463 AGATATAACTCTCTATTTATACTAAAAAATACTAAAACCCTAATGGAC
64 AGATATAACTCTCTATTTATACTAAAAAATACTAAAACCCTAATGGAC
35511 CAA
1 CAA
35514 CTAAATAAAA
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
111 35 0.32
113 74 0.68
ACGTcount: A:0.37, C:0.28, G:0.06, T:0.29
Consensus pattern (111 bp):
CAAATTCCCAAGCCTCTCACACAACCTTTCAACACAGCTTTTTTGAGCCTCACCTAAAACCCTAG
ATATAACTCTCTATTTATACTAAAAAATACTAAAACCCTAATGGAC
Found at i:41183 original size:15 final size:14
Alignment explanation
Indices: 41160--41189 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
41150 ATAAAAATTA
41160 AATATTTTTATTTT
1 AATATTTTTATTTT
41174 AATATATTTTATTTT
1 AATAT-TTTTATTTT
41189 A
1 A
41190 TTGAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATATTTTTATTTT
Found at i:42922 original size:26 final size:26
Alignment explanation
Indices: 42886--43051 Score: 269
Period size: 26 Copynumber: 6.4 Consensus size: 26
42876 GCGCAGTGCC
*
42886 TGATAAAAGAAAGCAAGCACGGAGCT
1 TGATAAAAGAAAACAAGCACGGAGCT
*
42912 TGATAAAAGAAAGCAAGCACGGAGCT
1 TGATAAAAGAAAACAAGCACGGAGCT
42938 TGATAAAAGAAAACAAGCACGGAGCT
1 TGATAAAAGAAAACAAGCACGGAGCT
* *
42964 TGATAAAAGAAAGCAAGCAAGGAGCT
1 TGATAAAAGAAAACAAGCACGGAGCT
42990 TGATAAAAGAAAACAAGCACGGAGCT
1 TGATAAAAGAAAACAAGCACGGAGCT
**
43016 TGATAAAAGAAAACAAGCACATAGCT
1 TGATAAAAGAAAACAAGCACGGAGCT
*
43042 TGATTAAAGA
1 TGATAAAAGA
43052 GAGTGGCGCA
Statistics
Matches: 132, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 132 1.00
ACGTcount: A:0.49, C:0.14, G:0.23, T:0.13
Consensus pattern (26 bp):
TGATAAAAGAAAACAAGCACGGAGCT
Found at i:44692 original size:14 final size:15
Alignment explanation
Indices: 44659--44692 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
44649 AAATTTCAAG
44659 AAAATAAAATATATT
1 AAAATAAAATATATT
44674 AAAATAAAA-ATATT
1 AAAATAAAATATATT
*
44688 TAAAT
1 AAAAT
44693 TTTATTCCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATAAAATATATT
Found at i:45882 original size:72 final size:72
Alignment explanation
Indices: 45795--45940 Score: 238
Period size: 72 Copynumber: 2.0 Consensus size: 72
45785 TCAATTAAGC
** *
45795 TTGTGCCTTGGAAATTTTTTAATGAGTATACTACCAGGGGTAAATGAGTAATGTAGACATTTTGC
1 TTGTGCCTTAAAAATTTTTTAATGAGTATACTACCAGGGGTAAATCAGTAATGTAGACATTTTGC
45860 ATGCATT
66 ATGCATT
* * *
45867 TTGTGCCTTAAAAATTTTTTAATGAGTATACTACCATGGGTAAATCCGTAATGTAGGCATTTTGC
1 TTGTGCCTTAAAAATTTTTTAATGAGTATACTACCAGGGGTAAATCAGTAATGTAGACATTTTGC
45932 ATGCATT
66 ATGCATT
45939 TT
1 TT
45941 ATTACCCCAA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (72 bp):
TTGTGCCTTAAAAATTTTTTAATGAGTATACTACCAGGGGTAAATCAGTAATGTAGACATTTTGC
ATGCATT
Found at i:46743 original size:30 final size:30
Alignment explanation
Indices: 46707--46796 Score: 180
Period size: 30 Copynumber: 3.0 Consensus size: 30
46697 GTTGGAGCAG
46707 TAGGTCAACAATCCCATTGAAAGCAGAACA
1 TAGGTCAACAATCCCATTGAAAGCAGAACA
46737 TAGGTCAACAATCCCATTGAAAGCAGAACA
1 TAGGTCAACAATCCCATTGAAAGCAGAACA
46767 TAGGTCAACAATCCCATTGAAAGCAGAACA
1 TAGGTCAACAATCCCATTGAAAGCAGAACA
46797 ACACGACAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (30 bp):
TAGGTCAACAATCCCATTGAAAGCAGAACA
Found at i:52531 original size:12 final size:12
Alignment explanation
Indices: 52514--52548 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
52504 CTCCTCGTCT
52514 TCCTCTTCTTCC
1 TCCTCTTCTTCC
*
52526 TCCTCTTCTTTC
1 TCCTCTTCTTCC
52538 TCCTCTTCTTC
1 TCCTCTTCTTC
52549 GGTTTTTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (12 bp):
TCCTCTTCTTCC
Found at i:71744 original size:37 final size:37
Alignment explanation
Indices: 71694--71795 Score: 125
Period size: 37 Copynumber: 3.0 Consensus size: 37
71684 ATTTAAGGAC
71694 TGAACAAATGTCCGATTCATAATAGATTATTATGAAT
1 TGAACAAATGTCCGATTCATAATAGATTATTATGAAT
71731 TGAACAAATGTCCGA-TC---------TATTATGAAT
1 TGAACAAATGTCCGATTCATAATAGATTATTATGAAT
*
71758 CGAACAAATGTCCGATTCATAATAGATTATTATGAAT
1 TGAACAAATGTCCGATTCATAATAGATTATTATGAAT
71795 T
1 T
71796 CAGTTTATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 20
0.71 0.03 0.27
Matches are distributed among these distances:
27 24 0.45
28 2 0.04
36 2 0.04
37 25 0.47
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (37 bp):
TGAACAAATGTCCGATTCATAATAGATTATTATGAAT
Found at i:71762 original size:27 final size:27
Alignment explanation
Indices: 71721--71773 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
71711 CATAATAGAT
*
71721 TATTATGAATTGAACAAATGTCCGATC
1 TATTATGAATCGAACAAATGTCCGATC
71748 TATTATGAATCGAACAAATGTCCGAT
1 TATTATGAATCGAACAAATGTCCGAT
71774 TCATAATAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (27 bp):
TATTATGAATCGAACAAATGTCCGATC
Found at i:82078 original size:12 final size:13
Alignment explanation
Indices: 82049--82089 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 13
82039 TTTATAACCT
82049 TTTTATATAAATG
1 TTTTATATAAATG
*
82062 CTTTATA-AAATG
1 TTTTATATAAATG
82074 TTTTA-ATAAATG
1 TTTTATATAAATG
82086 TTTT
1 TTTT
82090 GGGTGCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 1 0.04
12 18 0.72
13 6 0.24
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (13 bp):
TTTTATATAAATG
Found at i:89328 original size:24 final size:24
Alignment explanation
Indices: 89275--89333 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
89265 AATCAAGTAG
* *
89275 AGGATTCCAACCTCAGTCAAATCC
1 AGGATTGCAACCTCAATCAAATCC
* *
89299 AAGATTGCAACCTCAATCAAATCT
1 AGGATTGCAACCTCAATCAAATCC
89323 AGGATTGCAAC
1 AGGATTGCAAC
89334 GACAGCCAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (24 bp):
AGGATTGCAACCTCAATCAAATCC
Found at i:92785 original size:15 final size:15
Alignment explanation
Indices: 92765--92793 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
92755 TAATAAGAAC
92765 ATAATAATGTAATTA
1 ATAATAATGTAATTA
92780 ATAATAATGTAATT
1 ATAATAATGTAATT
92794 TTCTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (15 bp):
ATAATAATGTAATTA
Found at i:92953 original size:18 final size:17
Alignment explanation
Indices: 92929--92982 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
92919 ACAAAAAAAT
92929 AAAAACATTATAAAAGA
1 AAAAACATTATAAAAGA
* * *
92946 AAACAACACTCTAACA-A
1 AAA-AACATTATAAAAGA
*
92963 AAAAATATTATAAAAGA
1 AAAAACATTATAAAAGA
92980 AAA
1 AAA
92983 GAAAAATACA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
16 8 0.29
17 11 0.39
18 9 0.32
ACGTcount: A:0.69, C:0.11, G:0.04, T:0.17
Consensus pattern (17 bp):
AAAAACATTATAAAAGA
Found at i:98718 original size:31 final size:31
Alignment explanation
Indices: 98682--98778 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 31
98672 ATATATAATC
98682 AATTGACAGATTTTGTTAAGTAGAGGGACTC-
1 AATTGACAGATTTTGTTAAGTAGAGGGAC-CA
* * **
98713 AATTGATACCAAATTG-TAAGTAGAGGGACCA
1 AATTGACA-GATTTTGTTAAGTAGAGGGACCA
* *
98744 AATTGACAG-TTTT-TAAAATAGAGGGACCA
1 AATTGACAGATTTTGTTAAGTAGAGGGACCA
98773 AATTGA
1 AATTGA
98779 TCCTTTTTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
29 21 0.40
30 1 0.02
31 27 0.51
32 4 0.08
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.28
Consensus pattern (31 bp):
AATTGACAGATTTTGTTAAGTAGAGGGACCA
Found at i:103099 original size:13 final size:13
Alignment explanation
Indices: 103083--103108 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
103073 GAACTCCAAA
103083 AACAGTTTTTAGT
1 AACAGTTTTTAGT
103096 AACAGTTTTTAGT
1 AACAGTTTTTAGT
103109 GGGAATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
AACAGTTTTTAGT
Done.