Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold76
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: 2182696
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.29
Warning! 286211 characters in sequence are not A, C, G, or T
File 13 of 13
Found at i:2165322 original size:40 final size:40
Alignment explanation
Indices: 2165267--2165348 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
2165257 ATTTGAGAAA
*
2165267 TAAAACGAGCAATGTAATTCAACCTTCCCAAGAAACTTCT
1 TAAAACAAGCAATGTAATTCAACCTTCCCAAGAAACTTCT
*
2165307 TAAAACAAGTAATGTAATTCAACCTTCCCAAGAAACTTCT
1 TAAAACAAGCAATGTAATTCAACCTTCCCAAGAAACTTCT
2165347 TA
1 TA
2165349 CTTCCTTTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (40 bp):
TAAAACAAGCAATGTAATTCAACCTTCCCAAGAAACTTCT
Found at i:2166058 original size:12 final size:13
Alignment explanation
Indices: 2166035--2166064 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2166025 ACTTTTGCTA
2166035 TCTTTCTTCATCT
1 TCTTTCTTCATCT
2166048 TCTTT-TTCATCT
1 TCTTTCTTCATCT
2166060 TCTTT
1 TCTTT
2166065 ATCTTCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (13 bp):
TCTTTCTTCATCT
Found at i:2166060 original size:9 final size:9
Alignment explanation
Indices: 2166015--2166081 Score: 55
Period size: 9 Copynumber: 6.9 Consensus size: 9
2166005 CTCTGGCTTC
2166015 ATCTTCTTT
1 ATCTTCTTT
*
2166024 AACTT-TTGCT
1 ATCTTCTT--T
*
2166034 ATCTTTCTTC
1 ATC-TTCTTT
2166044 ATCTTCTTTTT
1 ATCTTC--TTT
2166055 CATCTTCTTT
1 -ATCTTCTTT
2166065 ATCTTCTTT
1 ATCTTCTTT
2166074 ATCTTCTT
1 ATCTTCTT
2166082 GCTCAACCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
8 2 0.04
9 24 0.51
10 9 0.19
11 4 0.09
12 8 0.17
ACGTcount: A:0.12, C:0.24, G:0.01, T:0.63
Consensus pattern (9 bp):
ATCTTCTTT
Found at i:2166081 original size:21 final size:21
Alignment explanation
Indices: 2166038--2166081 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2166028 TTTGCTATCT
*
2166038 TTCTTCATCTTCTTTTTCATC
1 TTCTTCATCTTCTTTATCATC
* *
2166059 TTCTTTATCTTCTTTATCTTC
1 TTCTTCATCTTCTTTATCATC
2166080 TT
1 TT
2166082 GCTCAACCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.25, G:0.00, T:0.66
Consensus pattern (21 bp):
TTCTTCATCTTCTTTATCATC
Found at i:2166561 original size:130 final size:130
Alignment explanation
Indices: 2166328--2166589 Score: 488
Period size: 130 Copynumber: 2.0 Consensus size: 130
2166318 AGACAAAAGT
2166328 TCGCATCTTATTTCCAAAATGATGGTATGACATGTTCACACCCATTACAAAAAGATCTTCGCATG
1 TCGCATCTTATTTCCAAAATGATGGTATGACATGTTCACACCCATTACAAAAAGATCTTCGCATG
* * * *
2166393 TTTCGGGCTAAAACAAACGAAGTGAGTTCTTGGAATTACTCTGGATTAGTCCTAGACCCTACAAA
66 TTTCGGGCTAAAACAAACGAAGTGAATTCTTAGAATTACTCTAGATTAGTCCTAGACACTACAAA
2166458 TCGCATCTTATTTCCAAAATGATGGTATGACATGTTCACACCCATTACAAAAAGATCTTCGCATG
1 TCGCATCTTATTTCCAAAATGATGGTATGACATGTTCACACCCATTACAAAAAGATCTTCGCATG
2166523 TTTCGGGCTAAAACAAACGAAGTGAATTCTTAGAATTACTCTAGATTAGTCCTAGACACTACAAA
66 TTTCGGGCTAAAACAAACGAAGTGAATTCTTAGAATTACTCTAGATTAGTCCTAGACACTACAAA
2166588 TC
1 TC
2166590 TTTCAATACT
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
130 128 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (130 bp):
TCGCATCTTATTTCCAAAATGATGGTATGACATGTTCACACCCATTACAAAAAGATCTTCGCATG
TTTCGGGCTAAAACAAACGAAGTGAATTCTTAGAATTACTCTAGATTAGTCCTAGACACTACAAA
Found at i:2178035 original size:13 final size:13
Alignment explanation
Indices: 2178017--2178041 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2178007 ACAAAACTTA
2178017 TGTATCGATACAT
1 TGTATCGATACAT
2178030 TGTATCGATACA
1 TGTATCGATACA
2178042 ACACTTATGT
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:2178036 original size:32 final size:32
Alignment explanation
Indices: 2177996--2178060 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
2177986 AGTAGCTTAT
2177996 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
*
2178028 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
2178060 A
1 A
2178061 ACACTTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (32 bp):
ATTGTATCGATACAAAACTTATGTATCGATAC
Found at i:2178071 original size:20 final size:19
Alignment explanation
Indices: 2177998--2178081 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
2177988 TAGCTTATAT
*
2177998 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
2178017 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
2178030 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
2178049 TGTATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
2178069 TGTATCGATACAA
1 TGTATCGATACAA
2178082 ATCGTTGAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 13
0.80 0.01 0.18
Matches are distributed among these distances:
13 9 0.16
14 1 0.02
16 5 0.09
18 1 0.02
19 25 0.44
20 16 0.28
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:2179307 original size:13 final size:13
Alignment explanation
Indices: 2179289--2179314 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2179279 CAATTTTTGG
2179289 TGTATCGATACAT
1 TGTATCGATACAT
2179302 TGTATCGATACAT
1 TGTATCGATACAT
2179315 ACTTGGTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2179326 original size:32 final size:33
Alignment explanation
Indices: 2179269--2179332 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2179259 TACAAGCCAA
**
2179269 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
2179302 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
2179333 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:2179339 original size:19 final size:18
Alignment explanation
Indices: 2179269--2179339 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
2179259 TACAAGCCAA
2179269 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
2179289 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
2179302 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
2179321 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
2179340 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:2180032 original size:19 final size:19
Alignment explanation
Indices: 2180008--2180078 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
2179998 TGTGTCGATA
*
2180008 CATTGTATCGGTACATATT
1 CATTGTATCGATACATATT
**
2180027 CATTGTATCGATACATGCT
1 CATTGTATCGATACATATT
*
2180046 CATTATATCGATACATACTT
1 CATTGTATCGATACATA-TT
*
2180066 AATTGTATCGATA
1 CATTGTATCGATA
2180079 TATGAAATTG
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 31 0.72
20 12 0.28
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (19 bp):
CATTGTATCGATACATATT
Found at i:2180965 original size:42 final size:42
Alignment explanation
Indices: 2180906--2180986 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
2180896 AAGAAAAATC
*
2180906 GGATATTTGCACTTTGGTCTTTAACCACTTAAACTACACTTT
1 GGATATTTGCACTTTGGTCCTTAACCACTTAAACTACACTTT
2180948 GGATATTTGCACTTTGGTCCTTAACCACTTAAACTACAC
1 GGATATTTGCACTTTGGTCCTTAACCACTTAAACTACAC
2180987 AAAAACACTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.37
Consensus pattern (42 bp):
GGATATTTGCACTTTGGTCCTTAACCACTTAAACTACACTTT
Found at i:2181507 original size:10 final size:10
Alignment explanation
Indices: 2181479--2181513 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
2181469 TTTCTACCTA
*
2181479 TTTTCTCCTAT
1 TTTTCT-CTTT
2181490 TTTTCTCTTT
1 TTTTCTCTTT
2181500 TTTTCTCTTT
1 TTTTCTCTTT
2181510 TTTT
1 TTTT
2181514 TTCTCTCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 17 0.74
11 6 0.26
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTCTCTTT
Found at i:2181828 original size:13 final size:14
Alignment explanation
Indices: 2181810--2181838 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2181800 GTGAATGACT
2181810 AATAAAAT-AATAA
1 AATAAAATAAATAA
2181823 AATAAAATAAATAA
1 AATAAAATAAATAA
2181837 AA
1 AA
2181839 GGCTGAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AATAAAATAAATAA
Found at i:2182205 original size:160 final size:158
Alignment explanation
Indices: 2182017--2182550 Score: 540
Period size: 163 Copynumber: 3.4 Consensus size: 158
2182007 ATATTAGATT
** * * *
2182017 AATTTTAAAAATTTTAAATCAAGAAAAATCT-ACGAAAAAATTTATGGAGTAGAAAATTCGGT-T
1 AATTTTAAAAA-TCAAAACCAAGAAAAATCTCCCGAAAAAATTTACGGAGTAGAAAATTC--TAT
* *
2182080 TTTGGAGAAAGGGGATTTCAAGGAAAAAATTTAAAATTCATGGAAATGAATGAATTTTCGAAAA-
63 TTTGGA-AAAGGGGATTTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAATTTT-GAAAAC
2182144 TGGAATTAATATGAAATAAATAATAATTTGATG
126 TGGAATTAATATGAAATAAATAATAATTTGATG
*
2182177 AATTTTAAAAATCAAAAACCAAGAAAAATCTCCCGAAAAAATTTACGGAGTAGAAAACTCCATAT
1 AATTTTAAAAATC-AAAACCAAGAAAAATCTCCCGAAAAAATTTACGGAGTAGAAAA-TTC-TAT
* * ** *
2182242 TTCGGAAAAAAAGAAATTTCAAGGAAAAAATTCAAAATTTATGGAGATGAATGAATTTTTGAAAA
63 TTTGG--AAAAGGGGATTTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAA-TTTTGAAAA
* *
2182307 CTGAAATTAATATAAAATAAATAAT-ATTTGATG
125 CTGGAATTAATATGAAATAAATAATAATTTGATG
* * *
2182340 AA-TTTGAAAATCAAAACCAAGAAAAATTTCCCAAAAAAAATTTACGGAGTAGAAAACTT-TATT
1 AATTTTAAAAATCAAAACCAAGAAAAATCTCCC-GAAAAAATTTACGGAGTAGAAAA-TTCTATT
* * * *
2182403 TTAGAAAAGGGAGAATTTCAAAG-AAAAATTCAAAATTTATAGAAATTAATGAACTTTTGAAAAC
64 TTGGAAAAGGG-G-ATTTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAA-TTTTGAAAAC
*
2182467 T-GAATT-ATATGAAAT-AATAATAATATTTGTTG
126 TGGAATTAATATGAAATAAATAAT-A-ATTTGATG
* * * * * *
2182499 AATTTTTAAAAT----ACCTAG-AAATTCTCTCGAAAAAATTTACGAAGAAGAAAAT
1 AATTTTAAAAATCAAAACCAAGAAAAATCTCCCGAAAAAATTTACGGAGTAGAAAAT
2182551 ATCGTAATTT
Statistics
Matches: 318, Mismatches: 41, Indels: 37
0.80 0.10 0.09
Matches are distributed among these distances:
153 1 0.00
154 20 0.06
155 7 0.02
156 11 0.03
157 8 0.03
158 9 0.03
159 48 0.15
160 48 0.15
161 43 0.14
162 40 0.13
163 56 0.18
164 27 0.08
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.29
Consensus pattern (158 bp):
AATTTTAAAAATCAAAACCAAGAAAAATCTCCCGAAAAAATTTACGGAGTAGAAAATTCTATTTT
GGAAAAGGGGATTTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAATTTTGAAAACTGGAA
TTAATATGAAATAAATAATAATTTGATG
Done.