Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1654
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: 42614
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1607 original size:28 final size:28
Alignment explanation
Indices: 1567--1637 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
1557 AATAAAGCCT
** *
1567 GGGGTTGGAGTATCCCCTCGGAAGTAAC
1 GGGGTTGGAGTATCCCCGAGGAAATAAC
*
1595 GGGGTTGGAGTATCCCCGATGAAATAAC
1 GGGGTTGGAGTATCCCCGAGGAAATAAC
*
1623 GAGGTTGGAGTATCC
1 GGGGTTGGAGTATCC
1638 TCGACTGTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGAGGAAATAAC
Found at i:1724 original size:53 final size:54
Alignment explanation
Indices: 1646--1748 Score: 172
Period size: 53 Copynumber: 1.9 Consensus size: 54
1636 CCTCGACTGT
* * *
1646 GAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAG
1 GAAAAATTGGTAGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTAAAG
1700 GAAAAATTGGT-GTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATT
1 GAAAAATTGGTAGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATT
1749 GTGGAGAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 35 0.76
54 11 0.24
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (54 bp):
GAAAAATTGGTAGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTAAAG
Found at i:4128 original size:13 final size:13
Alignment explanation
Indices: 4110--4135 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4100 ACAAAGATCC
4110 ATGTATCGATACA
1 ATGTATCGATACA
4123 ATGTATCGATACA
1 ATGTATCGATACA
4136 CAAAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4199 original size:19 final size:18
Alignment explanation
Indices: 4175--4274 Score: 94
Period size: 19 Copynumber: 5.9 Consensus size: 18
4165 CAGTAGCTAA
4175 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
4194 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
*
4209 -T-GGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
4226 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
4241 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
4258 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
4275 TTGTTGAATT
Statistics
Matches: 67, Mismatches: 2, Indels: 25
0.71 0.02 0.27
Matches are distributed among these distances:
13 21 0.31
14 2 0.03
16 4 0.06
18 5 0.07
19 35 0.52
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:4220 original size:32 final size:32
Alignment explanation
Indices: 4179--4272 Score: 170
Period size: 32 Copynumber: 2.9 Consensus size: 32
4169 AGCTAATTAT
*
4179 GTATCGATACAATACTTATGTATCGATACATG
1 GTATCGATACAAAACTTATGTATCGATACATG
*
4211 GTATCGATACAAAACTTATGTATCGATACATT
1 GTATCGATACAAAACTTATGTATCGATACATG
4243 GTATCGATACAAAACTTATGTATCGATACA
1 GTATCGATACAAAACTTATGTATCGATACA
4273 AATTGTTGAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (32 bp):
GTATCGATACAAAACTTATGTATCGATACATG
Found at i:4247 original size:13 final size:13
Alignment explanation
Indices: 4229--4253 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4219 ACAAAACTTA
4229 TGTATCGATACAT
1 TGTATCGATACAT
4242 TGTATCGATACA
1 TGTATCGATACA
4254 AAACTTATGT
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:4354 original size:21 final size:21
Alignment explanation
Indices: 4330--4407 Score: 138
Period size: 21 Copynumber: 3.7 Consensus size: 21
4320 CATTTGTAGG
4330 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
4351 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
* *
4372 ATGTATCGATACATTCTAAAA
1 ATGTATCGATACATTCCACAA
4393 ATGTATCGATACATT
1 ATGTATCGATACATT
4408 TGGATAATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:11820 original size:16 final size:16
Alignment explanation
Indices: 11798--11859 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
11788 ATCACTTCCT
11798 AATTTATTCAGATTTA
1 AATTTATTCAGATTTA
* * *
11814 TATTTATTTAGGTTTA
1 AATTTATTCAGATTTA
* *
11830 AATTTTTTTA-AGTTTA
1 AATTTATTCAGA-TTTA
11846 AATTTATTCAGATT
1 AATTTATTCAGATT
11860 CGAATTTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
16 35 0.97
17 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.56
Consensus pattern (16 bp):
AATTTATTCAGATTTA
Found at i:12112 original size:18 final size:18
Alignment explanation
Indices: 12073--12112 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12063 ATATTTATAT
*
12073 ATAAAATTAATTTGTTAT
1 ATAAAATTAATTTGTTAA
*
12091 ATAAAATTAATTTTTTAA
1 ATAAAATTAATTTGTTAA
12109 ATAA
1 ATAA
12113 TTTATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATAAAATTAATTTGTTAA
Found at i:13062 original size:13 final size:13
Alignment explanation
Indices: 13044--13069 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13034 ACATTTTGTC
13044 ATGTATCGATACA
1 ATGTATCGATACA
13057 ATGTATCGATACA
1 ATGTATCGATACA
13070 TCTTGTATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:13064 original size:33 final size:32
Alignment explanation
Indices: 13022--13089 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 32
13012 CGTTACAAGC
*
13022 CAATGTATCGATACATTTTGTCATGTATCGATA
1 CAATGTATCGATACATCTTGT-ATGTATCGATA
13055 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
13087 CAA
1 CAA
13090 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 14 0.41
33 20 0.59
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:13187 original size:13 final size:13
Alignment explanation
Indices: 13169--13193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13159 TACAGTGGTC
13169 ATGTATCGATACA
1 ATGTATCGATACA
13182 ATGTATCGATAC
1 ATGTATCGATAC
13194 TGTGCATTAT
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):
ATGTATCGATACA
Found at i:13226 original size:20 final size:20
Alignment explanation
Indices: 13203--13243 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
13193 CTGTGCATTA
13203 TGTATCGATACATCTGAAGG
1 TGTATCGATACATCTGAAGG
*
13223 TGTATCGATACATTTGAAGG
1 TGTATCGATACATCTGAAGG
13243 T
1 T
13244 TTTGACCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATCTGAAGG
Found at i:15688 original size:13 final size:13
Alignment explanation
Indices: 15670--15694 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15660 ATAAACCCCT
15670 TGTATCGATACAC
1 TGTATCGATACAC
15683 TGTATCGATACA
1 TGTATCGATACA
15695 GAGAATGCTG
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:21912 original size:19 final size:20
Alignment explanation
Indices: 21868--21919 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
21858 TTACAAACCA
21868 ATGTATCGATACATTTGGTC
1 ATGTATCGATACATTTGGTC
21888 ATGTATCGATACATCTT-GT-
1 ATGTATCGATACAT-TTGGTC
21907 ATGTATCGATACA
1 ATGTATCGATACA
21920 AACAGTTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 13 0.42
20 16 0.52
21 2 0.06
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTTGGTC
Found at i:22018 original size:13 final size:13
Alignment explanation
Indices: 22000--22024 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21990 TACAGTGGTC
22000 ATGTATCGATACA
1 ATGTATCGATACA
22013 ATGTATCGATAC
1 ATGTATCGATAC
22025 TGTGCATTAT
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):
ATGTATCGATACA
Found at i:22042 original size:33 final size:32
Alignment explanation
Indices: 21983--22045 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
21973 TTCTTTGCAA
*
21983 GTATCGATACAGTGGTCATGTATCGATACAAT
1 GTATCGATACAGTGATCATGTATCGATACAAT
* *
22015 GTATCGATACTGTGCATTATGTATCGATACA
1 GTATCGATACAGTG-ATCATGTATCGATACA
22046 TCTGAAGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (32 bp):
GTATCGATACAGTGATCATGTATCGATACAAT
Found at i:26026 original size:26 final size:26
Alignment explanation
Indices: 25995--26044 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
25985 TTACTTATAC
* * *
25995 TATTTTTTATAATTTAATTTTTAATA
1 TATTTTTAAAAATTTAATCTTTAATA
26021 TATTTTTAAAAATTTAATCTTTAA
1 TATTTTTAAAAATTTAATCTTTAA
26045 AAATTTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TATTTTTAAAAATTTAATCTTTAATA
Found at i:26045 original size:15 final size:15
Alignment explanation
Indices: 26025--26053 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
26015 TTAATATATT
26025 TTTAAAAATTTAATC
1 TTTAAAAATTTAATC
26040 TTTAAAAATTTAAT
1 TTTAAAAATTTAAT
26054 ATTTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTAAAAATTTAATC
Found at i:26066 original size:36 final size:36
Alignment explanation
Indices: 26014--26099 Score: 97
Period size: 35 Copynumber: 2.4 Consensus size: 36
26004 TAATTTAATT
**
26014 TTTAATATATTTTTA--AAAATTTAATCTTTAAA-AA
1 TTTAATAT-TTTTTATTAAAATTTAAAATTTAAACAA
*
26048 TTTAATATTTTTTATTAAATTTTAAAATTTAAACAA
1 TTTAATATTTTTTATTAAAATTTAAAATTTAAACAA
26084 TTTAACATATTTTTTA
1 TTT-A-ATATTTTTTA
26100 ATGTTTATAC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
33 6 0.14
34 8 0.18
35 14 0.32
36 5 0.11
37 1 0.02
38 10 0.23
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (36 bp):
TTTAATATTTTTTATTAAAATTTAAAATTTAAACAA
Found at i:29626 original size:22 final size:21
Alignment explanation
Indices: 29576--29627 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
29566 GATTTTCAAC
29576 ATAAAAAAATAATAATATAAA
1 ATAAAAAAATAATAATATAAA
* *
29597 AAATAAAAAATAATAATATATTA
1 ATA-AAAAAATAATAATATA-AA
29620 ATAAAAAA
1 ATAAAAAA
29628 TCAAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 2 0.08
22 21 0.81
23 3 0.12
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
ATAAAAAAATAATAATATAAA
Found at i:30007 original size:28 final size:28
Alignment explanation
Indices: 29967--30034 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
29957 ATGAAATCTA
* *
29967 AAGCAGCCACATGGACACGTGAAGAAAC
1 AAGCAGCTACATGGACACATGAAGAAAC
*
29995 AAGTAGCTACATGGACACATGAAGAAAC
1 AAGCAGCTACATGGACACATGAAGAAAC
30023 AAGCAGCTACAT
1 AAGCAGCTACAT
30035 CGAAACAGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (28 bp):
AAGCAGCTACATGGACACATGAAGAAAC
Found at i:30888 original size:12 final size:13
Alignment explanation
Indices: 30867--30937 Score: 69
Period size: 15 Copynumber: 5.4 Consensus size: 13
30857 AGTGCAAAGC
30867 AAAA-AAAATAA-
1 AAAATAAAATAAT
30878 AAAATAAAATAAT
1 AAAATAAAATAAT
30891 AATAATAATAATAAT
1 AA-AATAA-AATAAT
30906 AATAATAATAATAAT
1 AA-AATAA-AATAAT
30921 AAAA-ATAAATAA-
1 AAAATA-AAATAAT
30933 AAAAT
1 AAAAT
30938 GAAACGAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
11 4 0.07
12 11 0.20
13 8 0.15
14 8 0.15
15 23 0.43
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:30891 original size:3 final size:3
Alignment explanation
Indices: 30880--30928 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
30870 AAAAATAAAA
*
30880 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
30927 AA
1 AA
30929 ATAAAAAATG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:31631 original size:13 final size:14
Alignment explanation
Indices: 31610--31638 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
31600 AAATTTTCGT
31610 AAATAAAAATAATA
1 AAATAAAAATAATA
31624 AAAT-AAAATAATA
1 AAATAAAAATAATA
31637 AA
1 AA
31639 TAGATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAAATAATA
Done.