Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1817
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: 27420
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Found at i:15 original size:8 final size:9
Alignment explanation
Indices: 1--236 Score: 168
Period size: 9 Copynumber: 29.1 Consensus size: 9
1 ACATAACTT
1 ACATAACTT
10 A-ATAACTT
1 ACATAACTT
18 ACATAA--T
1 ACATAACTT
25 ACATAACTT
1 ACATAACTT
*
34 A-ATAACTA
1 ACATAACTT
*
42 ACATTA--T
1 ACATAACTT
*
49 ACACAACTT
1 ACATAACTT
58 ACATAA--T
1 ACATAACTT
65 ACAT-ACTT
1 ACATAACTT
* *
73 ACTTAACAT
1 ACATAACTT
82 ACAT-ACTT
1 ACATAACTT
*
90 ACATAACAT
1 ACATAACTT
99 ACATAA--T
1 ACATAACTT
106 AC--AACTT
1 ACATAACTT
113 ACATAACTT
1 ACATAACTT
122 A-ATAACTT
1 ACATAACTT
130 ACATAA--T
1 ACATAACTT
137 ACATAACTT
1 ACATAACTT
* *
146 ATA-AACTA
1 ACATAACTT
154 ACATTATAC--
1 ACA-TA-ACTT
163 ACA-AACTT
1 ACATAACTT
171 ACATAA--T
1 ACATAACTT
*
178 ACATTACTT
1 ACATAACTT
187 ACATAACTT
1 ACATAACTT
196 ACATAA--T
1 ACATAACTT
203 ACATAACTT
1 ACATAACTT
212 ACATAA--T
1 ACATAACTT
*
219 ACACAACTT
1 ACATAACTT
228 ACAT-ACTT
1 ACATAACTT
236 A
1 A
237 TAATACTTAA
Statistics
Matches: 180, Mismatches: 18, Indels: 59
0.70 0.07 0.23
Matches are distributed among these distances:
5 2 0.01
6 3 0.02
7 49 0.27
8 48 0.27
9 75 0.42
10 1 0.01
11 2 0.01
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (9 bp):
ACATAACTT
Found at i:32 original size:16 final size:16
Alignment explanation
Indices: 1--232 Score: 126
Period size: 16 Copynumber: 15.9 Consensus size: 16
1 ACATAACTTA-ATAACTT
1 ACATAACTTACATAA--T
18 ACATAA--TACATAACTT
1 ACATAACTTACATAA--T
* *
34 A-ATAACTAACATTAT
1 ACATAACTTACATAAT
*
49 ACACAACTTACATAAT
1 ACATAACTTACATAAT
*
65 ACAT-ACTTAC-TTA-
1 ACATAACTTACATAAT
*
78 ACAT-ACATAC-T--T
1 ACATAACTTACATAAT
*
90 ACATAACATACATAAT
1 ACATAACTTACATAAT
106 AC--AACTTACATAACTT
1 ACATAACTTACATAA--T
122 A-ATAACTTACATAAT
1 ACATAACTTACATAAT
137 ACATAACTT--ATAA-
1 ACATAACTTACATAAT
*
150 AC-TAACATT--AT-AC
1 ACATAAC-TTACATAAT
163 ACA-AACTTACATAAT
1 ACATAACTTACATAAT
178 AC---A-TTAC-T--T
1 ACATAACTTACATAAT
187 ACATAACTTACATAAT
1 ACATAACTTACATAAT
203 ACATAACTTACATAAT
1 ACATAACTTACATAAT
*
219 ACACAACTTACATA
1 ACATAACTTACATA
233 CTTATAATAC
Statistics
Matches: 177, Mismatches: 11, Indels: 55
0.73 0.05 0.23
Matches are distributed among these distances:
9 3 0.02
11 1 0.01
12 16 0.09
13 32 0.18
14 20 0.11
15 19 0.11
16 64 0.36
17 22 0.12
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (16 bp):
ACATAACTTACATAAT
Found at i:33 original size:24 final size:24
Alignment explanation
Indices: 1--63 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
*
1 ACATAACTTAATAACTTACATAAT
1 ACATAACTTAATAACTAACATAAT
*
25 ACATAACTTAATAACTAACATTAT
1 ACATAACTTAATAACTAACATAAT
*
49 ACACAACTTACATAA
1 ACATAACTTA-ATAA
64 TACATACTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
24 31 0.89
25 4 0.11
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (24 bp):
ACATAACTTAATAACTAACATAAT
Found at i:83 original size:13 final size:12
Alignment explanation
Indices: 64--117 Score: 58
Period size: 13 Copynumber: 4.5 Consensus size: 12
54 ACTTACATAA
*
64 TACATACTTACT
1 TACATACATACT
76 TAACATACATACT
1 T-ACATACATACT
*
89 TACATAACATACA
1 TACAT-ACATACT
102 TA-ATACA-ACT
1 TACATACATACT
112 TACATA
1 TACATA
118 ACTTAATAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
10 4 0.11
11 6 0.17
12 7 0.19
13 19 0.53
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.31
Consensus pattern (12 bp):
TACATACATACT
Found at i:107 original size:24 final size:24
Alignment explanation
Indices: 80--217 Score: 126
Period size: 25 Copynumber: 5.7 Consensus size: 24
70 CTTACTTAAC
*
80 ATACATACTTACATAACATACATA
1 ATACATACTTACATAACTTACATA
104 ATACA-ACTTACATAACTTA-ATA
1 ATACATACTTACATAACTTACATA
* *
126 ACTTACATA-ATACATAACTTATA-A
1 A--TACATACTTACATAACTTACATA
*
150 ACTAACAT--TATACACAAACTTACATA
1 A-T-ACATACT-TACA-TAACTTACATA
176 ATACATTACTTACATAACTTACATA
1 ATACA-TACTTACATAACTTACATA
201 ATACATAACTTACATAA
1 ATACAT-ACTTACATAA
218 TACACAACTT
Statistics
Matches: 95, Mismatches: 7, Indels: 23
0.76 0.06 0.18
Matches are distributed among these distances:
22 4 0.04
23 14 0.15
24 34 0.36
25 36 0.38
26 6 0.06
27 1 0.01
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (24 bp):
ATACATACTTACATAACTTACATA
Found at i:127 original size:31 final size:31
Alignment explanation
Indices: 81--139 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
71 TTACTTAACA
81 TACATACTTACATAACATACATAATACAACT
1 TACATACTTACATAACATACATAATACAACT
*
112 TACATAACTTA-ATAACTTACATAATACA
1 TACAT-ACTTACATAACATACATAATACA
140 TAACTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (31 bp):
TACATACTTACATAACATACATAATACAACT
Found at i:130 original size:40 final size:39
Alignment explanation
Indices: 3--142 Score: 121
Period size: 40 Copynumber: 3.6 Consensus size: 39
1 AC
*
3 ATAACTTA-ATAACTTACATAATACATAACTTA-ATAACTA
1 ATAACTTACATAACATACATAATAC--AACTTACATAACTA
* * * * *
42 A-CATTATACACAACTTACATAATACATACTTACTTAACATA
1 ATAACT-TACATAACATACATAATACA-ACTTACATAAC-TA
83 CAT-ACTTACATAACATACATAATACAACTTACATAACTTA
1 -ATAACTTACATAACATACATAATACAACTTACATAAC-TA
123 ATAACTTACAT-A-ATACATAA
1 ATAACTTACATAACATACATAA
143 CTTATAAACT
Statistics
Matches: 84, Mismatches: 9, Indels: 17
0.76 0.08 0.15
Matches are distributed among these distances:
38 11 0.13
39 11 0.13
40 39 0.46
41 20 0.24
42 3 0.04
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.31
Consensus pattern (39 bp):
ATAACTTACATAACATACATAATACAACTTACATAACTA
Found at i:175 original size:41 final size:41
Alignment explanation
Indices: 125--232 Score: 146
Period size: 41 Copynumber: 2.6 Consensus size: 41
115 ATAACTTAAT
* *
125 AACTTACATAATACATAACTTATA-AACTAACATTATACACA
1 AACTTACATAATACATAACTTACATAACTAACATAATACA-A
* * *
166 AACTTACATAATACATTACTTACATAACTTACATAATACAT
1 AACTTACATAATACATAACTTACATAACTAACATAATACAA
*
207 AACTTACATAATACACAACTTACATA
1 AACTTACATAATACATAACTTACATA
233 CTTATAATAC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 46 0.78
42 13 0.22
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (41 bp):
AACTTACATAATACATAACTTACATAACTAACATAATACAA
Found at i:230 original size:25 final size:23
Alignment explanation
Indices: 80--236 Score: 67
Period size: 25 Copynumber: 6.5 Consensus size: 23
70 CTTACTTAAC
*
80 ATACATACTTACATAACATACATA
1 ATACATACTTACATAAC-TACACA
*
104 ATACA-ACTTACATAACTTA-ATA
1 ATACATACTTACATAAC-TACACA
* *
126 ACTTACATA-ATACATAACTTATA-A
1 A--TACATACTTACATAAC-TACACA
* *
150 ACTAACAT--TATACACAAACTTACATA
1 A-T-ACATACT-TACA-TAAC-TACACA
*
176 ATACATTACTTACATAACTTACATA
1 ATACA-TACTTACATAAC-TACACA
201 ATACATAACTTACATAA-TACACA
1 ATACAT-ACTTACATAACTACACA
224 ACTTACATACTTA
1 A--TACATACTTA
237 TAATACTTAA
Statistics
Matches: 111, Mismatches: 8, Indels: 28
0.76 0.05 0.19
Matches are distributed among these distances:
22 4 0.04
23 20 0.18
24 39 0.35
25 41 0.37
26 6 0.05
27 1 0.01
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (23 bp):
ATACATACTTACATAACTACACA
Found at i:5568 original size:21 final size:21
Alignment explanation
Indices: 5542--5609 Score: 93
Period size: 21 Copynumber: 3.2 Consensus size: 21
5532 CAACTTAAAA
* *
5542 CAGAGGC-GACAGCAAGGGAAG
1 CAGAGGCTG-CAGCGAGAGAAG
*
5563 CAGAGGCTGCAGTGAGAGAAG
1 CAGAGGCTGCAGCGAGAGAAG
5584 CAGAGGCTGCAGCGAGAGAAG
1 CAGAGGCTGCAGCGAGAGAAG
5605 CAGAG
1 CAGAG
5610 AGAGAAGCAG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 41 0.98
22 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.43, T:0.04
Consensus pattern (21 bp):
CAGAGGCTGCAGCGAGAGAAG
Found at i:5612 original size:12 final size:12
Alignment explanation
Indices: 5592--5621 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5582 AGCAGAGGCT
*
5592 GCAGCGAGAGAA
1 GCAGAGAGAGAA
5604 GCAGAGAGAGAA
1 GCAGAGAGAGAA
5616 GCAGAG
1 GCAGAG
5622 GTTCAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.13, G:0.43, T:0.00
Consensus pattern (12 bp):
GCAGAGAGAGAA
Found at i:6084 original size:42 final size:43
Alignment explanation
Indices: 6038--6129 Score: 143
Period size: 43 Copynumber: 2.2 Consensus size: 43
6028 ATCATATAGT
6038 GGCGTTTGT-GAAT-AAGCGCCGCGAAAGAACACTACTTTTAGC
1 GGCGTTTGTAG-ATGAAGCGCCGCGAAAGAACACTACTTTTAGC
* *
6080 GGCGTTTGTAGATGAAGCGCCGCTAAAGAACATTACTTTTAGC
1 GGCGTTTGTAGATGAAGCGCCGCGAAAGAACACTACTTTTAGC
6123 GGCGTTT
1 GGCGTTT
6130 TTTACCAAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
42 11 0.24
43 35 0.76
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (43 bp):
GGCGTTTGTAGATGAAGCGCCGCGAAAGAACACTACTTTTAGC
Found at i:6248 original size:126 final size:125
Alignment explanation
Indices: 6097--6343 Score: 302
Period size: 126 Copynumber: 2.0 Consensus size: 125
6087 GTAGATGAAG
* * * ** * *
6097 CGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACC-AAGTGCCGCTTTAGAACATTA-CTT
1 CGCCGCTAAAGAACATGACTATTAGCGGCGTTTTTTACCTAAGCGCCGCTAAAGAACATGATC-A
* * **
6160 TTAGCGGCATTTTTTTTCCTAAACGCCGCTAAAGATCATGTTCTTTAGCGGCATTTTTCCCAA
65 TTAGCGGC-GTTTTTTTCCTAAACGCCGCTAAA-AACATGACCTTTAGCGGCATTTTTCCCAA
* *
6223 CGCCGCTAAAGAACATGA-TCATTAGCGGCGTTTTTTTCCTAAGCGCTGCTAAAGAACATGATCA
1 CGCCGCTAAAGAACATGACT-ATTAGCGGCGTTTTTTACCTAAGCGCCGCTAAAGAACATGATCA
* *
6287 TTAGCGGCGTTTTTTTCCTAAGCGCCGCTAAAAACATGACCTTTAGCGGCGTTTTTC
65 TTAGCGGCGTTTTTTTCCTAAACGCCGCTAAAAACATGACCTTTAGCGGCATTTTTC
6344 TCTGTAAGCG
Statistics
Matches: 103, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
125 22 0.21
126 56 0.54
127 24 0.23
128 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (125 bp):
CGCCGCTAAAGAACATGACTATTAGCGGCGTTTTTTACCTAAGCGCCGCTAAAGAACATGATCAT
TAGCGGCGTTTTTTTCCTAAACGCCGCTAAAAACATGACCTTTAGCGGCATTTTTCCCAA
Found at i:6294 original size:83 final size:84
Alignment explanation
Indices: 6097--6342 Score: 246
Period size: 85 Copynumber: 2.9 Consensus size: 84
6087 GTAGATGAAG
* * * * * * * * **
6097 CGCCGCTAAAGAACATTA-CTTTTAGCGGCGTTTTTTACCAAGTGCCGCTTTAGAACATTACTTT
1 CGCCGCTAAAGAACATGATC-ATTAGCGGCGATTTTTCCCAAGCGCCGC-TAAAAACATGACCAT
*
6161 TAGCGGCATTTTTTTTCCTAAA
64 TAGCGGC-GTTTTTTTCCTAAA
* * * *
6183 CGCCGCTAAAGATCATGTTCTTTAGCGGC-ATTTTTCCCAA-CGCCGCTAAAGAACATGATCATT
1 CGCCGCTAAAGAACATGATCATTAGCGGCGATTTTTCCCAAGCGCCGCTAAA-AACATGACCATT
*
6246 AGCGGCGTTTTTTTCCTAAG
65 AGCGGCGTTTTTTTCCTAAA
* * * *
6266 CGCTGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCTAAGCGCCGCTAAAAACATGACCTTT
1 CGCCGCTAAAGAACATGATCATTAGCGGCG-ATTTTTCCCAAGCGCCGCTAAAAACATGACCATT
6331 AGCGGCGTTTTT
65 AGCGGCGTTTTT
6343 CTCTGTAAGC
Statistics
Matches: 133, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
83 39 0.29
84 19 0.14
85 40 0.30
86 34 0.26
87 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (84 bp):
CGCCGCTAAAGAACATGATCATTAGCGGCGATTTTTCCCAAGCGCCGCTAAAAACATGACCATTA
GCGGCGTTTTTTTCCTAAA
Found at i:6352 original size:43 final size:42
Alignment explanation
Indices: 6050--6362 Score: 267
Period size: 43 Copynumber: 7.4 Consensus size: 42
6040 CGTTTGTGAA
* * * ***
6050 TAAGCGCCGCGAAAGAACACT-ACTTTTAGCGGCGTTTGTAGA
1 TAAGCGCCGCTAAAGAACA-TGACCTTTAGCGGCGTTTTTTCC
* *
6092 TGAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACC
1 T-AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTT-CC
* ** * * *
6136 -AAGTGCCGCTTTAGAACATTACTTTTAGCGGCATTTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGACCTTTAGCGGC--GTTTTTTCC
* * ** *
6179 TAAACGCCGCTAAAGATCATGTTCTTTAGCGGC-ATTTTTCC
1 TAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTCC
* * *
6220 CAA-CGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGACCTTTAGCGGCG-TTTTTTCC
* * *
6262 TAAGCGCTGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGACCTTTAGCGGCG-TTTTTTCC
*
6305 TAAGCGCCGCTAAA-AACATGACCTTTAGCGGCGTTTTTCTCTG
1 TAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTT-TC-C
*
6348 TAAGCGCCGCAAAAG
1 TAAGCGCCGCTAAAG
6363 TTAGCGACGT
Statistics
Matches: 228, Mismatches: 31, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
40 26 0.11
41 14 0.06
42 59 0.26
43 100 0.44
44 29 0.13
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTCC
Found at i:6465 original size:22 final size:22
Alignment explanation
Indices: 6434--6493 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
6424 TAGTGGCGTT
* *
6434 AAAAAGCGCCGCTAAAGGCTTA
1 AAAAAACGCCGCTAAAGGCCTA
6456 AAAAAACGCCGCTAAAGGCCTA
1 AAAAAACGCCGCTAAAGGCCTA
* *
6478 AAAAAATGCTGCTAAA
1 AAAAAACGCCGCTAAA
6494 AACCTATTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.13
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAGGCCTA
Found at i:19740 original size:18 final size:17
Alignment explanation
Indices: 19719--19761 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
19709 AAAAAAACGT
19719 TTTGAAATTGAATAATGA
1 TTTGAAA-TGAATAATGA
*
19737 TTTGGAAATGAATAATGT
1 TTT-GAAATGAATAATGA
19755 TTTGAAA
1 TTTGAAA
19762 ACGAGCGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 15 0.65
19 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (17 bp):
TTTGAAATGAATAATGA
Found at i:20118 original size:25 final size:25
Alignment explanation
Indices: 20090--20144 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
20080 AATTATGTTT
* *
20090 GATAGTATATCCTGAAACTGCTATA
1 GATAGTATATACTGAAACTACTATA
* *
20115 GATAATATATACTGAGACTACTATA
1 GATAGTATATACTGAAACTACTATA
20140 GATAG
1 GATAG
20145 GCTATACTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (25 bp):
GATAGTATATACTGAAACTACTATA
Found at i:22537 original size:21 final size:21
Alignment explanation
Indices: 22513--22554 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
22503 CTTTGTTTCC
*
22513 ATGAGAGAATCTCTGTTCCGA
1 ATGAGAGAATCTCTGTACCGA
*
22534 ATGATAGAATCTCTGTACCGA
1 ATGAGAGAATCTCTGTACCGA
22555 GACCTCCGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (21 bp):
ATGAGAGAATCTCTGTACCGA
Done.