Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2115
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: 19590
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Found at i:201 original size:12 final size:13
Alignment explanation
Indices: 179--216 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
169 TTCAATATAC
*
179 AAATTAATATAAA
1 AAATTATTATAAA
192 AAA-TATTATAAA
1 AAATTATTATAAA
204 AAATTATTA-AAA
1 AAATTATTATAAA
216 A
1 A
217 TTTTAGATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 15 0.65
13 8 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATTATTATAAA
Found at i:1436 original size:36 final size:36
Alignment explanation
Indices: 1389--1461 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
1379 CCACTGGATA
1389 TGGCTCATCTTCGTCATCACCACAAGGGATTGGAGT
1 TGGCTCATCTTCGTCATCACCACAAGGGATTGGAGT
* *
1425 TGGCTCATCTTCTTCATCATCACAAGGGATTGGAGT
1 TGGCTCATCTTCGTCATCACCACAAGGGATTGGAGT
1461 T
1 T
1462 TCGGGTGAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (36 bp):
TGGCTCATCTTCGTCATCACCACAAGGGATTGGAGT
Found at i:3514 original size:47 final size:48
Alignment explanation
Indices: 3445--3540 Score: 176
Period size: 47 Copynumber: 2.0 Consensus size: 48
3435 TAGATAGACT
3445 TTAAGATGTACATTTGTATTATTAT-CTTAAAATTTTATTCACCCTTA
1 TTAAGATGTACATTTGTATTATTATCCTTAAAATTTTATTCACCCTTA
*
3492 TTAAGATGTACATTTGTATTATTATCCTTAAAGTTTTATTCACCCTTA
1 TTAAGATGTACATTTGTATTATTATCCTTAAAATTTTATTCACCCTTA
3540 T
1 T
3541 CACAAATATG
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 25 0.53
48 22 0.47
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.49
Consensus pattern (48 bp):
TTAAGATGTACATTTGTATTATTATCCTTAAAATTTTATTCACCCTTA
Found at i:3981 original size:5 final size:5
Alignment explanation
Indices: 3963--3999 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
3953 AGTGCTTTTC
3963 ATAAA ATAATA ATAAA AT-AA ATAAA AT-AA ATAAA ATA
1 ATAAA ATAA-A ATAAA ATAAA ATAAA ATAAA ATAAA ATA
4000 TCAATTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 8 0.28
5 16 0.55
6 5 0.17
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
ATAAA
Found at i:3987 original size:9 final size:9
Alignment explanation
Indices: 3963--3999 Score: 56
Period size: 9 Copynumber: 3.9 Consensus size: 9
3953 AGTGCTTTTC
3963 ATAAAATAATA
1 ATAAAAT-A-A
3974 ATAAAATAA
1 ATAAAATAA
3983 ATAAAATAA
1 ATAAAATAA
3992 ATAAAATA
1 ATAAAATA
4000 TCAATTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 18 0.69
10 1 0.04
11 7 0.27
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAAAATAA
Found at i:5475 original size:13 final size:13
Alignment explanation
Indices: 5457--5482 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5447 ATTTTTCTGA
5457 TGTATCGATACAT
1 TGTATCGATACAT
5470 TGTATCGATACAT
1 TGTATCGATACAT
5483 ACTTAGTGTA
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:6169 original size:40 final size:39
Alignment explanation
Indices: 6125--6208 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 39
6115 TTTTCTTTCT
*
6125 CCCTTAATCAAAATAATTTTAACAAATTCGTACATTCTCC
1 CCCTTAAT-AAAATAATTTTAACAAATTCATACATTCTCC
** * *
6165 CCCTTAATAAGGTAATTTTAGCAAATTCATGCATTCTCC
1 CCCTTAATAAAATAATTTTAACAAATTCATACATTCTCC
6204 CCCTT
1 CCCTT
6209 TTATTAAAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (39 bp):
CCCTTAATAAAATAATTTTAACAAATTCATACATTCTCC
Found at i:7599 original size:21 final size:20
Alignment explanation
Indices: 7570--7612 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
7560 GGTTAGTGTG
*
7570 GGGACTGCCCGGTTACGACCT
1 GGGACTG-CCGGTCACGACCT
* *
7591 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCACGACCT
7611 GG
1 GG
7613 TGGGTGCTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.12, C:0.30, G:0.42, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCACGACCT
Found at i:7911 original size:21 final size:21
Alignment explanation
Indices: 7887--7933 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
7877 TTTGAAGCTG
7887 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
*
7907 AATTTGAAGTGAAAAACAAGT
1 ATTTTGAAGTGAAAAACAAGT
7928 ATTTTG
1 ATTTTG
7934 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:13076 original size:298 final size:296
Alignment explanation
Indices: 12514--13111 Score: 1169
Period size: 298 Copynumber: 2.0 Consensus size: 296
12504 TTGCTCTTGT
12514 CCTTTTTGCTCGATTCTCCTTTGAGCAAACTTTCTTTTGTGGCCTTCTTGATCTCATCTTCAAGA
1 CCTTTTTGCTCGATTCTCCTTTGAGCAAACTTTCTTTTGTGGCCTTCTTGATCTCATCTTCAAGA
12579 ATTTGTTGAATCTTCTGGCCATCGTTGCTATTTCTTCATCTGAGTCACCATCTTCATCAACATCT
66 ATTTGTTGAATCTTCTGGCCATCGTTGCTATTTCTTCATCTGAGTCACCATCTTCATCAACATCT
12644 TCATCATCTTCTTCGTCCTTGATGGTTGACTTGAAAGCAACACTTGCCTTCCTCGGTGGCTCTTG
131 TCATCATCTTCTTCGTCCTTGATGGTTGACTTGAAAGCAACACTTGCCTTCCTCGGTGGCTCTTG
12709 TACGTGAGCATGTTTGATCTTCATTTCATAGGTTAACAACGAACCTATGAGCTCATCCAAGGATA
196 TACGTGAGCATGTTTGATCTTCATTTCATAGGTTAACAACGAACCTATGAGCTCATCCAAGGATA
12774 AGATGTTGGGATCCTTGGACTCTTCGATTTGCGGTCA
261 AGATGTTGGGATCCTTGGACTCTTCGA-TTGCGGTCA
12811 CCTTTTTGCTCGATTCTCCTTTGAGCAAAACTTTCTTTTGTGGCCTTCTTGATCTCATCTTCAAG
1 CCTTTTTGCTCGATTCTCCTTTGAGC-AAACTTTCTTTTGTGGCCTTCTTGATCTCATCTTCAAG
12876 AATTTGTTGAATCTTCTGGCCATCGTTGCTATTTCTTCATCTGAGTCACCATCTTCATCAACATC
65 AATTTGTTGAATCTTCTGGCCATCGTTGCTATTTCTTCATCTGAGTCACCATCTTCATCAACATC
*
12941 TTCATCATCTTCTTTGTCCTTGATGGTTGACTTGAAAGCAACACTTGCCTTCCTCGGTGGCTCTT
130 TTCATCATCTTCTTCGTCCTTGATGGTTGACTTGAAAGCAACACTTGCCTTCCTCGGTGGCTCTT
13006 GTACGTGAGCATGTTTGATCTTCATTTCATAGGTTAACAACGAACCTATGAGCTCATCCAAGGAT
195 GTACGTGAGCATGTTTGATCTTCATTTCATAGGTTAACAACGAACCTATGAGCTCATCCAAGGAT
13071 AAGATGTTGGGATCCTTGGACTCTTCGATTGCGGTCA
260 AAGATGTTGGGATCCTTGGACTCTTCGATTGCGGTCA
13108 CCTT
1 CCTT
13112 AGCTTCCATG
Statistics
Matches: 299, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
297 39 0.13
298 260 0.87
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (296 bp):
CCTTTTTGCTCGATTCTCCTTTGAGCAAACTTTCTTTTGTGGCCTTCTTGATCTCATCTTCAAGA
ATTTGTTGAATCTTCTGGCCATCGTTGCTATTTCTTCATCTGAGTCACCATCTTCATCAACATCT
TCATCATCTTCTTCGTCCTTGATGGTTGACTTGAAAGCAACACTTGCCTTCCTCGGTGGCTCTTG
TACGTGAGCATGTTTGATCTTCATTTCATAGGTTAACAACGAACCTATGAGCTCATCCAAGGATA
AGATGTTGGGATCCTTGGACTCTTCGATTGCGGTCA
Found at i:16177 original size:13 final size:13
Alignment explanation
Indices: 16159--16215 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
16149 ATAATGCACA
16159 GTATCGATACATT
1 GTATCGATACATT
16172 GTATCGATACATAAT
1 GTATCGATACAT--T
16187 GCACGTATCGATACATT
1 ----GTATCGATACATT
16204 GTATCGATACAT
1 GTATCGATACAT
16216 GACCAAATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 24 0.63
15 1 0.03
17 1 0.03
19 12 0.32
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:16196 original size:19 final size:19
Alignment explanation
Indices: 16139--16202 Score: 68
Period size: 13 Copynumber: 3.6 Consensus size: 19
16129 ACCTTCAACA
*
16139 GTATCGATCCATAATGCAC
1 GTATCGATACATAATGCAC
16158 AGTATCGATACAT--T----
1 -GTATCGATACATAATGCAC
16172 GTATCGATACATAATGCAC
1 GTATCGATACATAATGCAC
16191 GTATCGATACAT
1 GTATCGATACAT
16203 TGTATCGATA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 12 0.32
15 1 0.03
18 1 0.03
19 12 0.32
20 11 0.30
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (19 bp):
GTATCGATACATAATGCAC
Found at i:16200 original size:32 final size:33
Alignment explanation
Indices: 16139--16215 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 33
16129 ACCTTCAACA
*
16139 GTATCGATCCATAATGCACAGTATCGATACATT
1 GTATCGATACATAATGCACAGTATCGATACATT
16172 GTATCGATACATAATGCAC-GTATCGATACATT
1 GTATCGATACATAATGCACAGTATCGATACATT
16204 GTATCGATACAT
1 GTATCGATACAT
16216 GACCAAATGT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 25 0.58
33 18 0.42
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (33 bp):
GTATCGATACATAATGCACAGTATCGATACATT
Found at i:16228 original size:20 final size:21
Alignment explanation
Indices: 16203--16254 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
16193 ATCGATACAT
*
16203 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGACAAGAA
* *
16223 TGTATCGATGC-TTACAAGAA
1 TGTATCGATACATGACAAGAA
16243 TGTATCGATACA
1 TGTATCGATACA
16255 GGTGATTGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (21 bp):
TGTATCGATACATGACAAGAA
Found at i:17101 original size:13 final size:13
Alignment explanation
Indices: 17083--17108 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17073 ATTCCTTGAG
17083 CTTTCTCAATGTA
1 CTTTCTCAATGTA
17096 CTTTCTCAATGTA
1 CTTTCTCAATGTA
17109 ATGTGATTAT
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:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
CTTTCTCAATGTA
Found at i:19006 original size:19 final size:20
Alignment explanation
Indices: 18982--19032 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
18972 TGATACAATA
**
18982 TATCGATACATGTTC-ATCG
1 TATCGATACATGCACAATCG
*
19001 TATCGATACATGCACAATTG
1 TATCGATACATGCACAATCG
19021 TATCGATACATG
1 TATCGATACATG
19033 AAACTGGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (20 bp):
TATCGATACATGCACAATCG
Found at i:19098 original size:33 final size:32
Alignment explanation
Indices: 19061--19129 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
19051 CTACCACTGT
19061 TTGTATCAATACATG-GCACATTATATCGATACA
1 TTGTATCAATACATGAG-A-ATTATATCGATACA
* *
19094 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCAATACATGA-GAATTATATCGATACA
19127 TTG
1 TTG
19130 CCTCAAACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (32 bp):
TTGTATCAATACATGAGAATTATATCGATACA
Found at i:19100 original size:13 final size:13
Alignment explanation
Indices: 19078--19129 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
19068 AATACATGGC
*
19078 ACATTATATCGAT
1 ACATTGTATCGAT
19091 ACATTGTATCGAT
1 ACATTGTATCGAT
19104 ACA-TG-AT-G--
1 ACATTGTATCGAT
19112 A-ATTGTATCGAT
1 ACATTGTATCGAT
19124 ACATTG
1 ACATTG
19130 CCTCAAACGG
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 19 0.59
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Done.