Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1648
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: 31195
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Found at i:1354 original size:27 final size:27
Alignment explanation
Indices: 1324--1501 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
1314 ATATTAAGTC
* * *
1324 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
1351 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
1379 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
1406 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
1433 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
1460 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
1487 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
1502 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 105 0.80
28 26 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:1408 original size:55 final size:54
Alignment explanation
Indices: 1324--1501 Score: 232
Period size: 54 Copynumber: 3.3 Consensus size: 54
1314 ATATTAAGTC
* * *
1324 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAA-T
* * * *
1379 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* ** *
1433 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
1487 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
1502 GTACAATTTA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:1490 original size:81 final size:82
Alignment explanation
Indices: 1345--1500 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
1335 TGCTATATAA
* *
1345 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
1410 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * **
1427 TCAATTCGCACACTTAGTG-CATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
1490 ACACTTAGTGC
65 ACACTTAGTGC
1501 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 43 0.64
82 24 0.36
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Found at i:9612 original size:27 final size:27
Alignment explanation
Indices: 9582--9759 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
9572 ATATTAAGTC
* * *
9582 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
9609 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
9637 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
9664 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
9691 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
9718 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
9745 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
9760 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 105 0.80
28 26 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:9666 original size:55 final size:54
Alignment explanation
Indices: 9582--9759 Score: 232
Period size: 54 Copynumber: 3.3 Consensus size: 54
9572 ATATTAAGTC
* * *
9582 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAA-T
* * * *
9637 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* ** *
9691 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
9745 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
9760 GTACAATTTA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:9748 original size:81 final size:82
Alignment explanation
Indices: 9603--9758 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
9593 TGCTATATAA
* *
9603 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
9668 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * **
9685 TCAATTCGCACACTTAGTG-CATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
9748 ACACTTAGTGC
65 ACACTTAGTGC
9759 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 43 0.64
82 24 0.36
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Found at i:11916 original size:15 final size:15
Alignment explanation
Indices: 11896--11951 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
11886 GTATCTTGGG
11896 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
11911 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
11926 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
11941 TTTCTTTATTC
1 TTTCTTTATTC
11952 GGTTTCCTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 2 0.05
15 33 0.89
16 2 0.05
ACGTcount: A:0.12, C:0.16, G:0.11, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:14462 original size:93 final size:93
Alignment explanation
Indices: 14347--14517 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
14337 GCCCATAAGT
* *
14347 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
14412 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
14440 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
14505 CGAGTTCGGATGC
66 CGAGTTCGGATGC
14518 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:14514 original size:46 final size:46
Alignment explanation
Indices: 14339--14514 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
14329 TGTAACCCGC
* * *
14339 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
14385 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
14435 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
14478 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
14515 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:21974 original size:93 final size:93
Alignment explanation
Indices: 21861--22032 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
21851 CGCCCATAAG
* *
21861 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
21926 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
21954 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
22019 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
22033 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:22029 original size:46 final size:46
Alignment explanation
Indices: 21854--22029 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
21844 TGTAACCCGC
* * *
21854 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
21900 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
21950 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
21993 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
22030 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:29589 original size:24 final size:24
Alignment explanation
Indices: 29539--29592 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
29529 AATCGAATTT
*
29539 GCACACATAGTGCTCGTCACACTC
1 GCACACATAGTGCTAGTCACACTC
29563 GCACACATAGTGCCATAGT-ACAC-C
1 GCACACATAGTG-C-TAGTCACACTC
29587 GCACAC
1 GCACAC
29593 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 5 0.19
26 3 0.11
ACGTcount: A:0.30, C:0.37, G:0.17, T:0.17
Consensus pattern (24 bp):
GCACACATAGTGCTAGTCACACTC
Done.