Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3035
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: 39827
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Found at i:1461 original size:27 final size:27
Alignment explanation
Indices: 1431--1632 Score: 244
Period size: 27 Copynumber: 7.4 Consensus size: 27
1421 TGAGTCCGCT
* * * *
1431 CACTCAGTGCTATATAATCAACTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* *
1458 CACTTAGTGCTACGTAATCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
1485 CACTTAGTGCTACATAGTCAAACTCGCA
1 CACTTAGTGCTACATAGTCAAA-TCGCA
** * *
1513 CACTTAGTGCCGCATGGTCAATTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* **
1540 CACTTAGTGC-ATCATATTCATTTCGCA
1 CACTTAGTGCTA-CATAGTCAAATCGCA
*
1567 CACTTAGTGCAACATAGTCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
1594 CACTTAGTGCTAACATAGTCAAATCGCA
1 CACTTAGTGCT-ACATAGTCAAATCGCA
1622 CACTTAGTGCT
1 CACTTAGTGCT
1633 GTACAATTTA
Statistics
Matches: 153, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
27 102 0.67
28 51 0.33
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (27 bp):
CACTTAGTGCTACATAGTCAAATCGCA
Found at i:1573 original size:82 final size:82
Alignment explanation
Indices: 1431--1632 Score: 248
Period size: 82 Copynumber: 2.5 Consensus size: 82
1421 TGAGTCCGCT
* * * * *
1431 CACTCAGTGCT-ATATAATCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGC
1 CACTTAGTGCTAACATAGTCAAATCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGC
*
1495 TACATAGTCAAACTCGCA
66 AACATAGTCAAA-TCGCA
** * * * **
1513 CACTTAGTGC-CGCATGGTCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTG
1 CACTTAGTGCTAACATAGTCAAATCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTG
1576 CAACATAGTCAAATCGCA
65 CAACATAGTCAAATCGCA
1594 CACTTAGTGCTAACATAGTCAAATCGCACACTTAGTGCT
1 CACTTAGTGCTAACATAGTCAAATCGCACACTTAGTGCT
1633 GTACAATTTA
Statistics
Matches: 101, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
81 16 0.16
82 85 0.84
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (82 bp):
CACTTAGTGCTAACATAGTCAAATCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGC
AACATAGTCAAATCGCA
Found at i:2179 original size:22 final size:21
Alignment explanation
Indices: 2146--2189 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
2136 GTTCCACATA
*
2146 TAATGACATACATTTTACTAAC
1 TAATGACATACATATTA-TAAC
2168 TAATG-CATTACATATTATAAC
1 TAATGACA-TACATATTATAAC
2189 T
1 T
2190 CAATATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.39
Consensus pattern (21 bp):
TAATGACATACATATTATAAC
Found at i:7371 original size:31 final size:31
Alignment explanation
Indices: 7336--7399 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
7326 CCTTTTCATA
7336 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
7367 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
7398 TT
1 TT
7400 ACTGTAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:7674 original size:23 final size:23
Alignment explanation
Indices: 7614--7732 Score: 186
Period size: 23 Copynumber: 5.1 Consensus size: 23
7604 CCTAGCCTCT
7614 TTTAATAACTGGGGCCA-AAGCCC
1 TTTAATAACTGGGG-CATAAGCCC
*
7637 TTTTAATAGCTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
*
7661 TTTAATAACCGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
7684 TTCAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
7707 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
7730 TTT
1 TTT
7733 TGCACTTCCT
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
23 69 0.78
24 19 0.22
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.26
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:7808 original size:20 final size:20
Alignment explanation
Indices: 7783--7847 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
7773 ATGAATACAC
*
7783 CATGTGCATATGATACATAT
1 CATGTGCATATCATACATAT
*
7803 CATGTGCATATCATACATGT
1 CATGTGCATATCATACATAT
*
7823 CATGTGCATATCATACATAC
1 CATGTGCATATCATACATAT
7843 CATGT
1 CATGT
7848 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (20 bp):
CATGTGCATATCATACATAT
Found at i:10011 original size:19 final size:18
Alignment explanation
Indices: 9974--10017 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
9964 ATACTTACAG
9974 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
9991 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
10010 TACTAATT
1 TAATAATT
10018 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:12276 original size:29 final size:29
Alignment explanation
Indices: 12234--12341 Score: 155
Period size: 29 Copynumber: 3.8 Consensus size: 29
12224 GCGAGCATGA
*
12234 ATATGAATGTGATTTGGGCCTGATGGGCC
1 ATATAAATGTGATTTGGGCCTGATGGGCC
12263 ATATAAATGTGATTTGGGCCTGATGGGCC
1 ATATAAATGTGATTTGGGCCTGATGGGCC
** * *
12292 ATATAAATGCAAATTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTGATGGGCC
*
12321 ATACAAATGTGA-TTGGGCCTG
1 ATATAAATGTGATTTGGGCCTG
12342 GTGGACCAGA
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
28 8 0.11
29 62 0.89
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.29
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCCTGATGGGCC
Found at i:22401 original size:29 final size:29
Alignment explanation
Indices: 22336--22422 Score: 97
Period size: 29 Copynumber: 3.1 Consensus size: 29
22326 GTGAGCATGA
* *
22336 ATAT-AATGTGATTTGGGCCTAAAGGGCC
1 ATATAAATATGATTTGGGCCTAATGGGCC
22364 ATATAAATATGATTTGGGCCTAATGGGCC
1 ATATAAATATGATTTGGGCCTAATGGGCC
* * * * *
22393 ATGTGAATAT-AATTGGGTCTAGTGGGCC
1 ATATAAATATGATTTGGGCCTAATGGGCC
22421 AT
1 AT
22423 TTACAGGTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
28 21 0.41
29 30 0.59
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.31
Consensus pattern (29 bp):
ATATAAATATGATTTGGGCCTAATGGGCC
Done.