Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1112
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: 17474
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:134 original size:10 final size:10
Alignment explanation
Indices: 119--183 Score: 57
Period size: 10 Copynumber: 6.5 Consensus size: 10
109 CTTTACACCT
119 AAAAAAAACA
1 AAAAAAAACA
129 AAAAAAAAC-
1 AAAAAAAACA
138 --AAAAAA-A
1 AAAAAAAACA
*
145 AAAACAAACA
1 AAAAAAAACA
155 AAAAAACAACA
1 AAAAAA-AACA
166 AGAAAAAATAGCA
1 A-AAAAAA-A-CA
179 AAAAA
1 AAAAA
184 TAGAAGGGTC
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
7 6 0.13
9 5 0.11
10 15 0.33
11 6 0.13
12 10 0.22
13 3 0.07
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.02
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:136 original size:12 final size:12
Alignment explanation
Indices: 119--183 Score: 71
Period size: 12 Copynumber: 5.2 Consensus size: 12
109 CTTTACACCT
119 AAAAAAAAC--A
1 AAAAAAAACAAA
129 AAAAAAAACAAA
1 AAAAAAAACAAA
141 AAAAAAAACAAA
1 AAAAAAAACAAA
*
153 CAAAAAAACAACA
1 AAAAAAAACAA-A
166 AGAAAAAATAGCAAA
1 A-AAAAAA-A-CAAA
181 AAA
1 AAA
184 TAGAAGGGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
10 9 0.19
12 23 0.49
13 1 0.02
14 8 0.17
15 3 0.06
16 3 0.06
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.02
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:147 original size:16 final size:16
Alignment explanation
Indices: 121--160 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
111 TTACACCTAA
121 AAAAAACAAAAAAAAAC
1 AAAAAA-AAAAAAAAAC
*
138 AAAAAAAAAAACAAAC
1 AAAAAAAAAAAAAAAC
154 AAAAAAA
1 AAAAAAA
161 CAACAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAC
Found at i:1440 original size:28 final size:28
Alignment explanation
Indices: 1399--1783 Score: 339
Period size: 28 Copynumber: 13.1 Consensus size: 28
1389 GTTCAAACCC
*
1399 TTTCAAAGCCCACAAGTCAGTGGCACCCC
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
*
1428 TTTCAAAG-CCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
*
1455 TTTCAAAGCCCACAAGTCAGTGGTACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* *
1483 TTTAAAAGCCCACAAGTCAATGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CT
*
1512 TTTCAAAGCCCACACGAGTCGGTGGCAACTCT
1 TTTCAAAGCCCACA--AGTCAGTGGC-AC-CT
*
1544 TTTCAAAGCCCACAAGTTAGTGGCACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* *
1572 TTTTAAAG-CCACAAGTCAGTGGAACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CT
* *
1600 TTTC-AAGCCTACACGAGTCGGTGGCAACTCT
1 TTTCAAAGCC--CACAAGTCAGTGGC-AC-CT
* *
1631 TTTCAAAGTACACACAAATCAGTGGCAACC-
1 TTTCAAAG--CCCACAAGTCAGTGGC-ACCT
* *
1661 TTCCAAAGCCCACAAGTTAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* * *
1690 TTT-AAAGCCCACAAGCCAATGGTAACTCT
1 TTTCAAAGCCCACAAGTCAGTGG-CAC-CT
*
1719 TTTCAAAGCCCACACGAGTCGGTGGCAACTCT
1 TTTCAAAGCCCACA--AGTCAGTGGC-AC-CT
* *
1751 TTTCAAGGCCCACATAAGTTAGTGGCACCT
1 TTTCAAAGCCCAC--AAGTCAGTGGCACCT
1781 TTT
1 TTT
1784 TTAAAAAAAA
Statistics
Matches: 296, Mismatches: 37, Indels: 45
0.78 0.10 0.12
Matches are distributed among these distances:
27 30 0.10
28 103 0.35
29 33 0.11
30 41 0.14
31 20 0.07
32 67 0.23
34 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCT
Found at i:1567 original size:117 final size:115
Alignment explanation
Indices: 1399--1782 Score: 438
Period size: 117 Copynumber: 3.3 Consensus size: 115
1389 GTTCAAACCC
* * *
1399 TTTCAAAGCCCACA-AGTCAGTGGCACCCCTTTCAAAG-CCACAAGTCAGTGGCACCCTTTCAAA
1 TTTCAAAGCCCACACAGTCAGTGGCA-ACCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTTAAA
**
1462 GCCCACAAGTCAGTGGTAC-CTTTTAAAAGCCCACAAGTCAATGGC-ACTCT
65 GCCCACAAGTCAGTGGTACTCTTTT-AAAGCCCACAAGTCGGTGGCAACTCT
* *
1512 TTTCAAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCACCTTTTTA
1 TTTCAAAGCCCACAC-AGTCAGTGGCAAC-C-TTTCAAAGCCCACAAGTTAGTGGCACCCTTTTA
* * *
1577 AAG-CCACAAGTCAGTGGAACTCTTTTCAAGCCTACACGAGTCGGTGGCAACTCT
63 AAGCCCACAAGTCAGTGGTACTCTTTTAAAGCC--CACAAGTCGGTGGCAACTCT
** * *
1631 TTTCAAAGTACACACAAATCAGTGGCAACCTTCCAAAGCCCACAAGTTAGTGGCACCCTTTTAAA
1 TTTCAAAGCCCACAC-AGTCAGTGGCAACCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTTAAA
* *
1696 GCCCACAAGCCAATGGTAACTCTTTTCAAAGCCCACACGAGTCGGTGGCAACTCT
65 GCCCACAAGTCAGTGGT-ACTCTTTT-AAAGCCCACA--AGTCGGTGGCAACTCT
* * *
1751 TTTCAAGGCCCACATAAGTTAGTGGC-ACCTTT
1 TTTCAAAGCCCACA-CAGTCAGTGGCAACCTTT
1783 TTTAAAAAAA
Statistics
Matches: 227, Mismatches: 29, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
113 14 0.06
114 1 0.00
115 11 0.05
116 29 0.13
117 63 0.28
118 27 0.12
119 42 0.19
120 40 0.18
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.23
Consensus pattern (115 bp):
TTTCAAAGCCCACACAGTCAGTGGCAACCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTTAAAG
CCCACAAGTCAGTGGTACTCTTTTAAAGCCCACAAGTCGGTGGCAACTCT
Found at i:2365 original size:20 final size:20
Alignment explanation
Indices: 2336--2410 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
2326 TTTTTACCCA
2336 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * * *
2356 AATATATCGATACATGTATG
1 AATGTATCGATACATTTTTC
* * *
2376 AATGTATTGATATATTCTTC
1 AATGTATCGATACATTTTTC
2396 AATGTATCGATACAT
1 AATGTATCGATACAT
2411 CTAGTTAAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:8984 original size:27 final size:27
Alignment explanation
Indices: 8946--9014 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
8936 TTGAAAACGA
*
8946 GGTTGGAGTGTCCCCTCGGAAGAATGG
1 GGTTGGAGTGTCCCCTCAGAAGAATGG
8973 GGTTGGAGTGTCCCCTCAGAAGAATGG
1 GGTTGGAGTGTCCCCTCAGAAGAATGG
9000 GGTTGGAGTGTCCCC
1 GGTTGGAGTGTCCCC
9015 GATGAATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.17, C:0.20, G:0.39, T:0.23
Consensus pattern (27 bp):
GGTTGGAGTGTCCCCTCAGAAGAATGG
Found at i:11202 original size:52 final size:52
Alignment explanation
Indices: 11124--11254 Score: 208
Period size: 52 Copynumber: 2.5 Consensus size: 52
11114 CCCAAAATAT
* *
11124 GAAAATTTACCTGCATGTATCGATACATGTAATAGTGTATCGATAAATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATGTAATAATGTATCGATAAATCTGG
* * *
11176 GAAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATGTAATAATGTATCGATAAATCTGG
*
11228 GCAAATTTGCCTGCATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
11255 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATGTAATAATGTATCGATAAATCTGG
Found at i:11267 original size:52 final size:51
Alignment explanation
Indices: 11124--11274 Score: 196
Period size: 52 Copynumber: 2.9 Consensus size: 51
11114 CCCAAAATAT
* *
11124 GAAAATTTACCTGCATGTATCGATAC-ATGTAATAGTGTATCGATAAATCTGG
1 GAAAATTTGCCTGCATGTATCGATACAATG--ATAGTGTATCGATACATCTGG
* * *
11176 GAAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACA-ATGATAGTGTATCGATACATCTGG
* *
11228 GCAAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACAATGAT-AGTGTATCGATACA
11275 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
51 2 0.02
52 83 0.97
54 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (51 bp):
GAAAATTTGCCTGCATGTATCGATACAATGATAGTGTATCGATACATCTGG
Found at i:11281 original size:13 final size:13
Alignment explanation
Indices: 11263--11287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11253 CAAAGATCAG
11263 TGTATCGATACAA
1 TGTATCGATACAA
11276 TGTATCGATACA
1 TGTATCGATACA
11288 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:11365 original size:33 final size:33
Alignment explanation
Indices: 11328--11394 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
11318 AGTAGCTTAA
11328 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
11361 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
11394 A
1 A
11395 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:11368 original size:13 final size:13
Alignment explanation
Indices: 11350--11374 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11340 CAAAAAAATA
11350 TGTATCGATACAT
1 TGTATCGATACAT
11363 TGTATCGATACA
1 TGTATCGATACA
11375 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:14187 original size:13 final size:13
Alignment explanation
Indices: 14169--14208 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
14159 ACAATTAAGT
*
14169 ATGTATTGATACA
1 ATGTATCGATACA
14182 ATGTATCGATACA
1 ATGTATCGATACA
14195 ATGTATCGATACA
1 ATGTATCGATACA
14208 A
1 A
14209 AGCATAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Done.