Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold861
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: 143541
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:118965 original size:147 final size:147
Alignment explanation
Indices: 118697--119092 Score: 490
Period size: 147 Copynumber: 2.6 Consensus size: 147
118687 CACAAGTCCG
118697 TGGCACCCTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTAACACCCTCATCTTT
1 TGGCACCCTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTAACACCCTCATCTTT
* * *
118762 AAGTCCAATGTAGCTGGCCTTGAATCAGTACATTAGCACCTTCATCTTTATGTCCAATATAGCTG
66 AAGTCCAATGTAGCTGGCCTTGAATCAGCACATTAGCACCTTCATCTTTATGTCCAATAGACCTG
118827 GCCTTGAATCAGCATAT
131 GCCTTGAATCAGCATAT
** *
118844 TGGCACCCTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTTATCTTT
1 TGGCACCCTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTAACACCCTCATCTTT
* * * *
118909 AAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGTACCTTCATCTTTATTTCCAATAGCCCTG
66 AAGTCCAATGTAGCTGGCCTTGAATCAGCACATTAGCACCTTCATCTTTATGTCCAATAGACCTG
*
118974 TCCTTGAATCAGCATAT
131 GCCTTGAATCAGCATAT
* * * * * * *
118991 GGGTA-CCTTTTCTGTCTTGAGTCCAATGCCGCT-GACTGTGAATCAGCACATTAACATCTTTTT
1 TGGCACCCTTATC--T-TTAAGACCAATGTCGCTGGCCT-TGAATCAGCACATTAACA-C-----
* * * *
119054 TCTCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGC
56 CCTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGC
119093 GTATTGGCAT
Statistics
Matches: 214, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
146 6 0.03
147 139 0.65
148 4 0.02
149 30 0.14
150 1 0.00
155 34 0.16
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.33
Consensus pattern (147 bp):
TGGCACCCTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTAACACCCTCATCTTT
AAGTCCAATGTAGCTGGCCTTGAATCAGCACATTAGCACCTTCATCTTTATGTCCAATAGACCTG
GCCTTGAATCAGCATAT
Found at i:119089 original size:55 final size:52
Alignment explanation
Indices: 119029--119268 Score: 159
Period size: 52 Copynumber: 4.6 Consensus size: 52
119019 CCGCTGACTG
* *
119029 TGAATCAGCACATTAACATCTTTTTTCTCATCTTTAAGTCCAATATCGTTGGCCT
1 TGAATCAGCACATTGACATC---TTTCTCATCTTTAAGCCCAATATCGTTGGCCT
** * ** ** *
119084 TGAATCAGCGTATTGGCATCTTTAACATCCCTAAGCCCAATGTCGTTGGCCT
1 TGAATCAGCACATTGACATCTTTCTCATCTTTAAGCCCAATATCGTTGGCCT
** * * * * * * *
119136 TGTCTCAGCACATTGACATCCTTCTC--C---AAGTCTAATACCGCTGACCA
1 TGAATCAGCACATTGACATCTTTCTCATCTTTAAGCCCAATATCGTTGGCCT
* * *
119183 TGAATCAGCACATTGACATCTTTTTTCCCATCTTTAAGCCCAATATCGTTGGTCG
1 TGAATCAGCACATTGACATC---TTTCTCATCTTTAAGCCCAATATCGTTGGCCT
* **
119238 TGAATCAGCATATTGGTATCTTTCTCA-CTTT
1 TGAATCAGCACATTGACATCTTTCTCATCTTT
119269 TCTCATCCTC
Statistics
Matches: 137, Mismatches: 40, Indels: 20
0.70 0.20 0.10
Matches are distributed among these distances:
47 31 0.23
50 5 0.04
51 4 0.03
52 51 0.37
55 46 0.34
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.35
Consensus pattern (52 bp):
TGAATCAGCACATTGACATCTTTCTCATCTTTAAGCCCAATATCGTTGGCCT
Found at i:119897 original size:20 final size:19
Alignment explanation
Indices: 119872--119955 Score: 90
Period size: 19 Copynumber: 4.7 Consensus size: 19
119862 ATTCAACGAT
119872 TTGTATCGATACATAAAGTA
1 TTGTATCGATACAT-AAGTA
*
119892 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTA
119911 TTGTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
*
119925 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTA
*
119943 TTGTATTGATACA
1 TTGTATCGATACA
119956 ATTTAAGATA
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
13 11 0.20
16 2 0.04
19 27 0.50
20 14 0.26
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:119930 original size:13 final size:13
Alignment explanation
Indices: 119912--119936 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
119902 ACATAAGTGT
119912 TGTATCGATACAA
1 TGTATCGATACAA
119925 TGTATCGATACA
1 TGTATCGATACA
119937 TAAGTTTTGT
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):
TGTATCGATACAA
Found at i:119934 original size:32 final size:32
Alignment explanation
Indices: 119893--119957 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
119883 CATAAAGTAT
119893 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
119925 TGTATCGATACATAAGTTTTGTATTGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
119957 T
1 T
119958 TTAAGATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:120016 original size:13 final size:13
Alignment explanation
Indices: 119998--120022 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
119988 ATTACTCAAA
119998 TGTATCGATACAT
1 TGTATCGATACAT
120011 TGTATCGATACA
1 TGTATCGATACA
120023 CTAATCTTTG
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:123540 original size:13 final size:13
Alignment explanation
Indices: 123522--123547 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
123512 CAATTTTTTG
123522 TGTATCGATACAT
1 TGTATCGATACAT
123535 TGTATCGATACAT
1 TGTATCGATACAT
123548 ACTTGCTGTA
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:123631 original size:20 final size:20
Alignment explanation
Indices: 123586--123661 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
123576 CTGCCAAGAA
***
123586 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGAATC
123607 ATGTATCGATACATTGCAA-C
1 ATGTATCGATACATTG-AATC
* *
123627 ATGTATCGATACTTTGAATT
1 ATGTATCGATACATTGAATC
*
123647 GTGTATCGATACATT
1 ATGTATCGATACATT
123662 TAAGGGTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.04
20 30 0.65
21 14 0.30
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTGAATC
Found at i:125952 original size:21 final size:21
Alignment explanation
Indices: 125928--125974 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
125918 TTTGATGCTG
125928 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
125948 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
125969 ATTTTG
1 ATTTTG
125975 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:126113 original size:13 final size:13
Alignment explanation
Indices: 126095--126120 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
126085 ATAATCACCC
126095 TGTATCGATACAA
1 TGTATCGATACAA
126108 TGTATCGATACAA
1 TGTATCGATACAA
126121 AGAAAAATGT
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):
TGTATCGATACAA
Found at i:128211 original size:15 final size:15
Alignment explanation
Indices: 128191--128221 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
128181 ATTTCGTTTG
*
128191 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
128206 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
128221 G
1 G
128222 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:130054 original size:21 final size:21
Alignment explanation
Indices: 130025--130069 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
130015 AAGTTTTCAT
*
130025 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
130045 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
130067 TTT
1 TTT
130070 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:132316 original size:13 final size:13
Alignment explanation
Indices: 132298--132323 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
132288 CAATTTTTTG
132298 TGTATCGATACAT
1 TGTATCGATACAT
132311 TGTATCGATACAT
1 TGTATCGATACAT
132324 ACTTGCTGTA
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:132407 original size:20 final size:20
Alignment explanation
Indices: 132362--132437 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
132352 CTGCCAAGAA
***
132362 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGAATC
132383 ATGTATCGATACATTGCAA-C
1 ATGTATCGATACATTG-AATC
* *
132403 ATGTATCGATACTTTGAATT
1 ATGTATCGATACATTGAATC
*
132423 GTGTATCGATACATT
1 ATGTATCGATACATT
132438 TAAGGGTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.04
20 30 0.65
21 14 0.30
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTGAATC
Done.