Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold637
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: 41449
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:5088 original size:17 final size:17
Alignment explanation
Indices: 5039--5088 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
5029 TATATATATG
5039 TATAAGTAAT-TAT-AAA
1 TATAA-TAATATATAAAA
*
5055 TATAAT-ATATGTGAAAA
1 TATAATAATATAT-AAAA
5072 TATAATAATATATAAAA
1 TATAATAATATATAAAA
5089 AGATGTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 2 0.07
15 3 0.11
16 5 0.18
17 13 0.46
18 5 0.18
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
TATAATAATATATAAAA
Found at i:5155 original size:20 final size:20
Alignment explanation
Indices: 5119--5156 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5109 GGAAAATAAT
*
5119 ATATATAATAAGTAATAACA
1 ATATATAATAAGAAATAACA
5139 ATATATAATTAA-AAATAA
1 ATATATAA-TAAGAAATAA
5157 TACTCATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (20 bp):
ATATATAATAAGAAATAACA
Found at i:8254 original size:30 final size:30
Alignment explanation
Indices: 8220--8316 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
8210 AGCTCACTCC
8220 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
8250 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * * *
8280 CAACTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
8310 TAGCTCA
1 TAGCTCA
8317 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:10053 original size:13 final size:12
Alignment explanation
Indices: 10033--10067 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
10023 GTTATACAAG
10033 TCAAAAAAAAATT
1 TCAAAAAAAAA-T
*
10046 TGAAAAAAAAAT
1 TCAAAAAAAAAT
10058 TCAAAAAAAA
1 TCAAAAAAAA
10068 TCGAAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (12 bp):
TCAAAAAAAAAT
Found at i:10079 original size:16 final size:16
Alignment explanation
Indices: 10060--10094 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
10050 AAAAAAATTC
10060 AAAAAAAATC-GAAAA
1 AAAAAAAATCTGAAAA
*
10075 GAAAAAAATCTGAAAA
1 AAAAAAAATCTGAAAA
10091 AAAA
1 AAAA
10095 GTGTTTAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.77, C:0.06, G:0.09, T:0.09
Consensus pattern (16 bp):
AAAAAAAATCTGAAAA
Found at i:10092 original size:13 final size:13
Alignment explanation
Indices: 10035--10094 Score: 54
Period size: 13 Copynumber: 4.6 Consensus size: 13
10025 TATACAAGTC
*
10035 AAAAAAAAATTTG
1 AAAAAAAAATCTG
10048 AAAAAAAAAT-T-
1 AAAAAAAAATCTG
*
10059 CAAAAAAAATC-G
1 AAAAAAAAATCTG
10071 AAAAGAAAAAAATCTG
1 --AA-AAAAAAATCTG
10087 AAAAAAAA
1 AAAAAAAA
10095 GTGTTTAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
11 9 0.23
12 1 0.03
13 16 0.41
14 3 0.08
15 9 0.23
16 1 0.03
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAAAAAAATCTG
Found at i:11016 original size:9 final size:10
Alignment explanation
Indices: 11009--11065 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
10999 AAGAGAAAAC
11009 AAAGAAAAGA
1 AAAGAAAAGA
11019 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
11031 AAAGAAGA-A
1 AAAGAAAAGA
11040 AAAGAAAATGA
1 AAAGAAAA-GA
11051 AATA-AAAAGA
1 AA-AGAAAAGA
11061 AAAGA
1 AAAGA
11066 GATGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:11032 original size:21 final size:20
Alignment explanation
Indices: 10998--11065 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
10988 ACATTCTTGT
10998 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
11019 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
11040 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
11061 AAAGA
1 AAAGA
11066 GATGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:11033 original size:6 final size:5
Alignment explanation
Indices: 11009--11065 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
10999 AAGAGAAAAC
*
11009 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
11056 AAAGA AAAGA
1 AAAGA AAAGA
11066 GATGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:11040 original size:15 final size:14
Alignment explanation
Indices: 11009--11065 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
10999 AAGAGAAAAC
11009 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
11025 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
11040 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
11056 AAAGAAAAGA
1 AAAGAAAAGA
11066 GATGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:11130 original size:12 final size:12
Alignment explanation
Indices: 11113--11144 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
11103 TTGAGAGAAC
11113 TTGAAAAGGCCT
1 TTGAAAAGGCCT
*
11125 TTGAAAAAGCCT
1 TTGAAAAGGCCT
11137 TTGAAAAG
1 TTGAAAAG
11145 CAAAATGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (12 bp):
TTGAAAAGGCCT
Found at i:11191 original size:30 final size:31
Alignment explanation
Indices: 11157--11227 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
11147 AAATGAAAAA
*
11157 GAAAAAGAAA-ATGAGATTGAAAAAG-AGAAC
1 GAAAAAGAAATATGAGAGTGAAAAAGAAG-AC
* *
11187 G-AAAAGAAATTTGAGAGTGAAAAAGAAGAT
1 GAAAAAGAAATATGAGAGTGAAAAAGAAGAC
11217 GAAAAAGAAAT
1 GAAAAAGAAAT
11228 TGAAACAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 8 0.23
30 16 0.46
31 11 0.31
ACGTcount: A:0.62, C:0.01, G:0.24, T:0.13
Consensus pattern (31 bp):
GAAAAAGAAATATGAGAGTGAAAAAGAAGAC
Found at i:11200 original size:24 final size:24
Alignment explanation
Indices: 11150--11220 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 24
11140 AAAAGCAAAA
*
11150 TGAAAAAGAAAAAGAAAATGAGAT
1 TGAAAAAGAAAAAGAAAATGAAAT
* *
11174 TGAAAAAGAGAACGAAAA-GAAATT
1 TGAAAAAGAAAAAGAAAATGAAA-T
* ** *
11198 TGAGAGTGAAAAAGAAGATGAAA
1 TGAAAAAGAAAAAGAAAATGAAA
11221 AAGAAATTGA
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
23 3 0.08
24 29 0.81
25 4 0.11
ACGTcount: A:0.62, C:0.01, G:0.24, T:0.13
Consensus pattern (24 bp):
TGAAAAAGAAAAAGAAAATGAAAT
Found at i:13364 original size:30 final size:30
Alignment explanation
Indices: 13330--13426 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
13320 AGCTCACTCC
13330 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
13360 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * * *
13390 CAACTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
13420 TAGCTCA
1 TAGCTCA
13427 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:16769 original size:40 final size:40
Alignment explanation
Indices: 16712--16976 Score: 335
Period size: 40 Copynumber: 6.7 Consensus size: 40
16702 TTGAATGATG
* * * * *
16712 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTAAA
*
16752 TCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
16792 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
16832 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
**
16872 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
**
16912 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AA
* *
16953 -CCGGGCTATG-TCCGAAGGCATTTG
1 TCCGGACTAAGATCCGAAGGCATTTG
16977 AACGAGTAGC
Statistics
Matches: 210, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
39 14 0.07
40 187 0.89
41 9 0.04
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:16845 original size:80 final size:80
Alignment explanation
Indices: 16712--16976 Score: 369
Period size: 80 Copynumber: 3.3 Consensus size: 80
16702 TTGAATGATG
* * * *
16712 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGACTAAGATCCGAAGGCATT
*
16776 TGTACGAGTTACTAAA
65 TGTGCGAGTTACTAAA
*
16792 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATT
16856 TGTGCGAGTTACTAAA
65 TGTGCGAGTTACTAAA
* **
16872 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT-CCGAAGGCATT
16936 TGTGCGAGTTACTATAA
65 TGTGCGAGTTACTA-AA
*
16953 -CCGGGCTATGT-CCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
16977 AACGAGTAGC
Statistics
Matches: 168, Mismatches: 12, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
79 15 0.09
80 143 0.85
81 10 0.06
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGTTACTAAA
Found at i:20178 original size:27 final size:28
Alignment explanation
Indices: 20094--20191 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
20084 CATGAGATTG
* * * *
20094 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
20123 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
20151 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
20178 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
20192 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:20202 original size:27 final size:27
Alignment explanation
Indices: 20122--20204 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
20112 TAAATTGTAC
* *
20122 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
20150 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
20177 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
20204 A
1 A
20205 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:20205 original size:29 final size:27
Alignment explanation
Indices: 20094--20205 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
20084 CATGAGATTG
** * *
20094 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
20123 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
20151 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
20178 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
20206 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:35083 original size:41 final size:40
Alignment explanation
Indices: 34990--35118 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
34980 CGATGACAAA
* *
34990 TCAGCTATATGTGGCACTTAGTGTACGA-TTCGACATAGCT
1 TCAGCTATATATGGCACTTAGTGTACGAGTT-GAGATAGCT
* *
35030 TCAACTACATATGGCACTTAGTGTACGAGGTTGAGATAGCT
1 TCAGCTATATATGGCACTTAGTGTACGA-GTTGAGATAGCT
* * *
35071 TCGGCTATATATGGCACTCAGTGTGC-AGTTTGAGATAGCT
1 TCAGCTATATATGGCACTTAGTGTACGAG-TTGAGATAGCT
35111 TCAGCTAT
1 TCAGCTAT
35119 GTACAACACT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
39 1 0.01
40 44 0.58
41 29 0.38
42 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (40 bp):
TCAGCTATATATGGCACTTAGTGTACGAGTTGAGATAGCT
Found at i:35134 original size:40 final size:41
Alignment explanation
Indices: 35044--35135 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 41
35034 CTACATATGG
* * ***
35044 CACTTAGTGTACGAGGTTGAGATAGCTTCGGCTATATATGG
1 CACTTAGTGTGCGAGGTTGAGATAGCTTCAGCTATATACAA
* * *
35085 CACTCAGTGTGC-AGTTTGAGATAGCTTCAGCTATGTACAA
1 CACTTAGTGTGCGAGGTTGAGATAGCTTCAGCTATATACAA
35125 CACTTAGTGTG
1 CACTTAGTGTG
35136 TGAGATATCG
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
40 32 0.76
41 10 0.24
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (41 bp):
CACTTAGTGTGCGAGGTTGAGATAGCTTCAGCTATATACAA
Found at i:38543 original size:28 final size:28
Alignment explanation
Indices: 38479--38601 Score: 158
Period size: 28 Copynumber: 4.4 Consensus size: 28
38469 ATATTAAGTC
* *
38479 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATACAATCAAACT
* *
38506 CGCACTCTTAGTGTTATACAATCAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
*
38534 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
* * *
38562 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATACAA-TCAAACT
38591 CGCACACTTAG
1 CGCACACTTAG
38602 CGCCAATCTC
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
27 19 0.23
28 48 0.58
29 16 0.19
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATCAAACT
Done.