Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2681
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: 21244
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Found at i:1452 original size:47 final size:47
Alignment explanation
Indices: 1276--1818 Score: 984
Period size: 47 Copynumber: 11.6 Consensus size: 47
1266 CCCTTCGGGA
* * * * * *
1276 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1323 C-TATCAC-TATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1368 CTTATCACATATATA-ACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1414 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1461 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1508 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1555 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1604 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1651 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1698 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1745 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1792 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
1819 TATTCAAATA
Statistics
Matches: 483, Mismatches: 8, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
45 33 0.07
46 58 0.12
47 345 0.71
49 47 0.10
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:1625 original size:190 final size:188
Alignment explanation
Indices: 1276--1818 Score: 984
Period size: 190 Copynumber: 2.9 Consensus size: 188
1266 CCCTTCGGGA
* * * * * *
1276 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCC-TATCAC-TATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1339 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA-ACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
1403 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1461 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1526 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACA
1591 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
129 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1651 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1716 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
1781 GGCCATTAGGCCTTATCACATATATACACTTTCACATT
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATT
1819 TATTCAAATA
Statistics
Matches: 345, Mismatches: 8, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
185 41 0.12
186 6 0.02
187 46 0.13
188 66 0.19
189 7 0.02
190 179 0.52
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (188 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:5876 original size:40 final size:40
Alignment explanation
Indices: 5844--6034 Score: 269
Period size: 40 Copynumber: 4.8 Consensus size: 40
5834 CCAGCATGAT
* * * *
5844 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
5884 TGCT-TTCAGGG-TTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTC-GGGACTTAGCCCGGATACATCACTAGCACGAA
* *
5923 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
5963 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
6003 TGCTCTTCGGGACTTAGCCCGGATACATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
6035 CTCAATTCTC
Statistics
Matches: 134, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
39 32 0.24
40 102 0.76
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:7519 original size:47 final size:47
Alignment explanation
Indices: 7448--8042 Score: 1019
Period size: 47 Copynumber: 12.6 Consensus size: 47
7438 CCCTTCGGGA
* * * * * *
7448 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7495 CCTATCACTTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7542 CTTATCACATATATACACTTTAACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7589 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7636 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7683 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7730 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7779 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7826 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7873 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7920 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7969 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8016 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
8043 TATTCAAATA
Statistics
Matches: 520, Mismatches: 24, Indels: 8
0.94 0.04 0.01
Matches are distributed among these distances:
47 430 0.83
49 90 0.17
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:7820 original size:190 final size:190
Alignment explanation
Indices: 7448--8042 Score: 1068
Period size: 190 Copynumber: 3.1 Consensus size: 190
7438 CCCTTCGGGA
* * * * * * * * *
7448 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTATCACTTATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
*
7513 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTAACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
* *
7576 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 TTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7636 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
7701 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
7766 TTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 TTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7826 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
7891 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
7956 TTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 TTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8016 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
8043 TATTCAAATA
Statistics
Matches: 393, Mismatches: 12, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
188 93 0.24
190 300 0.76
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (190 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
TTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:11941 original size:40 final size:40
Alignment explanation
Indices: 11740--11941 Score: 218
Period size: 40 Copynumber: 5.1 Consensus size: 40
11730 CGGAATTTAA
** *
11740 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
11780 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
11820 CC-GATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
11858 CCGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
11897 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
11937 CCGGA
1 CCGGA
11942 CATCATTCAA
Statistics
Matches: 136, Mismatches: 19, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
37 2 0.01
38 29 0.21
39 40 0.29
40 54 0.40
41 11 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:19008 original size:38 final size:39
Alignment explanation
Indices: 18956--19136 Score: 199
Period size: 39 Copynumber: 4.6 Consensus size: 39
18946 GCTACTCGTT
*
18956 CAAATGCCTTCGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGTTATAGTAACTCGCA
*
18995 C-AATGCCTTCGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGG-TTATAGTAACTCGCA
* * *
19033 CAAATGCCTTCGGGCTTAGCCCGG-AATTAGTATCTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGTTA-TAGTAACTCGCA
* * * * *
19072 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
19113 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTC-GGACTTAGCCCGG
19137 ACATCATTCA
Statistics
Matches: 120, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
38 33 0.28
39 47 0.39
40 28 0.23
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:19053 original size:77 final size:80
Alignment explanation
Indices: 18956--19137 Score: 221
Period size: 77 Copynumber: 2.3 Consensus size: 80
18946 GCTACTCGTT
* * *
18956 CAAATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCAC-AATGCCTTCGGA-CTTAACCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
19018 ATTTAGTAAC-TCGCA
65 ATATAGTAACTTAGCA
* **
19033 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
19098 TATGGTCACTTAGCA
66 TATAGTAACTTAGCA
19113 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
19138 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
77 34 0.38
78 13 0.14
79 24 0.27
80 19 0.21
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCA
Done.