Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold669
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: 42679
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:3989 original size:6 final size:6
Alignment explanation
Indices: 3976--4011 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
3966 TCAATTTTTT
* *
3976 TCTCAA TATCAA TATCAA TCTCAA TCTCAA TCTCAA
1 TCTCAA TCTCAA TCTCAA TCTCAA TCTCAA TCTCAA
4012 ATTCTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (6 bp):
TCTCAA
Found at i:4062 original size:20 final size:20
Alignment explanation
Indices: 4019--4062 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
4009 CAAATTCTTT
*
4019 TTTCTTTTTCTCACTCTCAT
1 TTTCTTTTTCTCACTCTCAA
*
4039 TTTCTTTTT-TCTTCTCTCAA
1 TTTCTTTTTCTC-ACTCTCAA
4059 TTTC
1 TTTC
4063 ATTCAAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCTTTTTCTCACTCTCAA
Found at i:4064 original size:26 final size:27
Alignment explanation
Indices: 4000--4065 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
3990 TCAATCTCAA
** *
4000 TCTCAATCTCAAATTCTTTTTTCTTTT
1 TCTCAATCTCATTTTCTTTTTTCTTTC
*
4027 TCTCACTCTCATTTTCTTTTTTC-TTC
1 TCTCAATCTCATTTTCTTTTTTCTTTC
*
4053 TCTCAATTTCATT
1 TCTCAATCTCATT
4066 CAAGATTCGT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 13 0.39
27 20 0.61
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (27 bp):
TCTCAATCTCATTTTCTTTTTTCTTTC
Found at i:4906 original size:14 final size:14
Alignment explanation
Indices: 4889--4942 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
4879 TCAATTTTGA
4889 TTTTTTTCTTCTTT
1 TTTTTTTCTTCTTT
** **
4903 TTTTTTAATTCGAAT
1 TTTTTTTCTTC-TTT
4918 TTTTTTTCTTCTTT
1 TTTTTTTCTTCTTT
4932 TTTTTTTCTTC
1 TTTTTTTCTTC
4943 AATACTAAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
14 21 0.68
15 10 0.32
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTTTTTCTTCTTT
Found at i:4912 original size:28 final size:30
Alignment explanation
Indices: 4871--4937 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
4861 CAATCACTCT
*
4871 TTTTTTTTTCAATTTTG-A-TTTTTTTCTTC
1 TTTTTTTTTCAA-TTCGAATTTTTTTTCTTC
4900 TTTTTTTTT-AATTCGAATTTTTTTTCTTC
1 TTTTTTTTTCAATTCGAATTTTTTTTCTTC
4929 TTTTTTTTT
1 TTTTTTTTT
4938 TCTTCAATAC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 3 0.09
28 3 0.09
29 29 0.83
ACGTcount: A:0.10, C:0.09, G:0.03, T:0.78
Consensus pattern (30 bp):
TTTTTTTTTCAATTCGAATTTTTTTTCTTC
Found at i:5000 original size:11 final size:12
Alignment explanation
Indices: 4984--5037 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
4974 AATACAAACT
* *
4984 TTTTTTTTGAAT
1 TTTTTTTTCAAA
4996 TTTTTTTTCAAA
1 TTTTTTTTCAAA
5008 TTTTTTTTCAAA
1 TTTTTTTTCAAA
*
5020 TTTTTTTT-ATA
1 TTTTTTTTCAAA
5031 TTTTTTT
1 TTTTTTT
5038 ACAATACCGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
11 9 0.23
12 30 0.77
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:5001 original size:13 final size:13
Alignment explanation
Indices: 4978--5027 Score: 68
Period size: 12 Copynumber: 3.9 Consensus size: 13
4968 AAATTGAATA
4978 CAAACTTTTTTTTT
1 CAAA-TTTTTTTTT
*
4992 -GAATTTTTTTTT
1 CAAATTTTTTTTT
5004 CAAA-TTTTTTTT
1 CAAATTTTTTTTT
5016 CAAATTTTTTTT
1 CAAATTTTTTTT
5028 ATATTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 21 0.66
13 11 0.34
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (13 bp):
CAAATTTTTTTTT
Found at i:7143 original size:20 final size:20
Alignment explanation
Indices: 7120--7166 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
7110 GGGTTAAGAT
*
7120 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
7140 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
7160 TGAGCTG
1 TGAGCTG
7167 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:8886 original size:48 final size:48
Alignment explanation
Indices: 8834--8939 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
8824 TTGTCTTTTC
*
8834 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
8882 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
8930 TTTCTTTTTC
1 TTTCTTTTTC
8940 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:11558 original size:20 final size:20
Alignment explanation
Indices: 11535--11581 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
11525 GGGTTAAGAT
*
11535 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
11555 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
11575 TGAGCTG
1 TGAGCTG
11582 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:12267 original size:11 final size:12
Alignment explanation
Indices: 12248--12280 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12238 CATTCTAATA
12248 AATTAAGTTT-T
1 AATTAAGTTTAT
*
12259 AATTCAGTTTAT
1 AATTAAGTTTAT
12271 AATTAAGTTT
1 AATTAAGTTT
12281 GCTACAGCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (12 bp):
AATTAAGTTTAT
Found at i:14087 original size:11 final size:11
Alignment explanation
Indices: 14071--14095 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
14061 TGTGGTGAGG
14071 ATTTGAAAATT
1 ATTTGAAAATT
14082 ATTTGAAAATT
1 ATTTGAAAATT
14093 ATT
1 ATT
14096 ATGGAACGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (11 bp):
ATTTGAAAATT
Found at i:17165 original size:56 final size:56
Alignment explanation
Indices: 17079--17198 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
17069 ACAAGGGATG
17079 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
17135 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
17191 ATGGGCAA
1 ATGGGCAA
17199 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:37937 original size:40 final size:40
Alignment explanation
Indices: 37882--38129 Score: 337
Period size: 40 Copynumber: 6.3 Consensus size: 40
37872 TAGTAAAATA
37882 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
1 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
*
37922 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCAGAAG
1 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
37962 AGCATTCATGCTA-TGATGTATCCGGGGCTAAGT-CCGAAG
1 AGCATTCATGCTAGTGATGTATCC-GGGCTAAGTCCCGAAG
38001 AGCATTCATGCTAGTGATGTATCCGGGCTAAGT-CCGAAG
1 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
* * * * **
38040 AGCATTCGTGCTAGTGATATATCTGTGCTAAACCCCGAAG
1 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
* * *
38080 AGCATTC-TGCTGGTG-T-TAATCCGGGCTAGGCCCCGAAG
1 AGCATTCATGCTAGTGATGT-ATCCGGGCTAAGTCCCGAAG
*
38118 AGCAATCATGCT
1 AGCATTCATGCT
38130 GATCGACGTG
Statistics
Matches: 189, Mismatches: 14, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
37 1 0.01
38 23 0.12
39 81 0.43
40 84 0.44
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
Found at i:38014 original size:79 final size:78
Alignment explanation
Indices: 37882--38129 Score: 324
Period size: 79 Copynumber: 3.2 Consensus size: 78
37872 TAGTAAAATA
37882 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCG
1 AGCATTCATGCTAGTGATGTATCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGTGATGTATCCG
37947 GGCTAAGTCCAGAAG
65 GGCTAAGTCC-GAAG
37962 AGCATTCATGCTA-TGATGTATCCGGGGCTAAGTCCGAAGAGCATTCATGCTAGTGATGTATCCG
1 AGCATTCATGCTAGTGATGTATCC-GGGCTAAGTCCGAAGAGCATTCATGCTAGTGATGTATCCG
38026 GGCTAAGTCCGAAG
65 GGCTAAGTCCGAAG
* * * * ** *
38040 AGCATTCGTGCTAGTGATATATCTGTGCTAAACCCCGAAGAGCATTC-TGCTGGTG-T-TAATCC
1 AGCATTCATGCTAGTGATGTATCCGGGCT-AAGTCCGAAGAGCATTCATGCTAGTGATGT-ATCC
* *
38102 GGGCTAGGCCCCGAAG
64 GGGCTAAG-TCCGAAG
*
38118 AGCAATCATGCT
1 AGCATTCATGCT
38130 GATCGACGTG
Statistics
Matches: 152, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
76 1 0.01
77 12 0.08
78 43 0.28
79 74 0.49
80 22 0.14
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (78 bp):
AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTGATGTATCCGG
GCTAAGTCCGAAG
Found at i:41595 original size:48 final size:53
Alignment explanation
Indices: 41531--41656 Score: 158
Period size: 48 Copynumber: 2.5 Consensus size: 53
41521 GGGCCTTGAA
*
41531 GGCCAA-TGTGATGAATGTTAAC-TGGTGTAA-GTGT-GATAA-GG-CCGAAAT
1 GGCCAAGTGTGATGAATGTGAACAT-GTGTAATGTGTGGATAAGGGCCCGAAAT
* *
41579 GG-CGAGTGTGATGAATGTGAACATGTGTAATGTGTGGATAAGGGCCCGAATT
1 GGCCAAGTGTGATGAATGTGAACATGTGTAATGTGTGGATAAGGGCCCGAAAT
*
41631 GGCCAAGTGTGATGCATGTGAACATG
1 GGCCAAGTGTGATGAATGTGAACATG
41657 CAATATACGT
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
47 2 0.03
48 23 0.35
49 5 0.08
50 5 0.08
51 2 0.03
52 8 0.12
53 21 0.32
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (53 bp):
GGCCAAGTGTGATGAATGTGAACATGTGTAATGTGTGGATAAGGGCCCGAAAT
Done.