Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold307
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: 27634
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:5460 original size:46 final size:49
Alignment explanation
Indices: 5409--5547 Score: 184
Period size: 46 Copynumber: 2.9 Consensus size: 49
5399 ATGATTGAGC
5409 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T-G
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACTAG
* * *
5456 -TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACTA-G
5501 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
5548 GCCTGAGCTG
Statistics
Matches: 77, Mismatches: 6, Indels: 14
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.03
43 5 0.06
45 3 0.04
46 29 0.38
47 29 0.38
48 2 0.03
50 4 0.05
51 3 0.04
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (49 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACTAG
Found at i:5591 original size:29 final size:30
Alignment explanation
Indices: 5539--5598 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
5529 TTCACTTATG
5539 GATGCGAACGCCTGAGCTGTTGAGCTGAGTC
1 GATGCGAACG-CTGAGCTGTTGAGCTGAGTC
*
5570 GATGCGAACG-TGAGCTCG-TGAGTTGAGTC
1 GATGCGAACGCTGAGCT-GTTGAGCTGAGTC
5599 CGAGTTCGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 16 0.59
30 1 0.04
31 10 0.37
ACGTcount: A:0.20, C:0.20, G:0.37, T:0.23
Consensus pattern (30 bp):
GATGCGAACGCTGAGCTGTTGAGCTGAGTC
Found at i:7447 original size:30 final size:30
Alignment explanation
Indices: 7403--7491 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 30
7393 CAAAGATAAC
*
7403 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAACCCGGAATAAAGAAATCCAAGATA
* *
7432 GAGAAACCCGGAATAAATAAATCC-AGAATA
1 AAGAAACCCGGAATAAAGAAATCCAAG-ATA
* * *
7462 AAGAGATCCAGG-ATAAAGAAACCCAAGATA
1 AAGA-AACCCGGAATAAAGAAATCCAAGATA
7492 CGATACTATG
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
29 9 0.19
30 32 0.67
31 7 0.15
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.11
Consensus pattern (30 bp):
AAGAAACCCGGAATAAAGAAATCCAAGATA
Found at i:7462 original size:15 final size:15
Alignment explanation
Indices: 7403--7482 Score: 74
Period size: 15 Copynumber: 5.4 Consensus size: 15
7393 CAAAGATAAC
*
7403 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
7417 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* * *
7432 GAGAAACCCGGAATA
1 AAGAAATCCAGAATA
*
7447 AATAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
7462 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
7477 AAGAAA
1 AAGAAA
7483 CCCAAGATAC
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
14 9 0.18
15 41 0.80
16 1 0.02
ACGTcount: A:0.57, C:0.14, G:0.17, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:7491 original size:15 final size:15
Alignment explanation
Indices: 7414--7491 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
7404 AGAAAACCGA
7414 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* **
7429 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
*
7443 AATAAATAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
7458 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
7474 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
7489 ATA
1 ATA
7492 CGATACTATG
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
14 3 0.06
15 42 0.88
16 3 0.06
ACGTcount: A:0.55, C:0.15, G:0.17, T:0.13
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:10482 original size:46 final size:46
Alignment explanation
Indices: 10415--10584 Score: 195
Period size: 46 Copynumber: 3.7 Consensus size: 46
10405 TGTAACCCGC
10415 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCAT
* * * *
10461 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G-C-ATTTGCAT
* * *
10511 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 C-CATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCAT
*
10554 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGCGAACTCGGACTCAACTCAACGAG
10585 TTTGGATGCC
Statistics
Matches: 103, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
42 1 0.01
43 7 0.07
44 1 0.01
46 57 0.55
47 26 0.25
48 1 0.01
49 1 0.01
50 8 0.08
51 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCAT
Found at i:10529 original size:93 final size:93
Alignment explanation
Indices: 10422--10594 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
10412 CGCCCATAAG
* *
10422 CGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
10487 ACGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
* *
10515 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
* *
10580 ACGAGTTTGGATGCC
66 ACGAGCTCGGATGCC
10595 CAAACATCCT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:10609 original size:46 final size:46
Alignment explanation
Indices: 10423--10609 Score: 134
Period size: 46 Copynumber: 4.0 Consensus size: 46
10413 GCCCATAAGC
* *** *
10423 GAACTCGGACTCAACTCAACGAGCTCGG--GCATTTGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCC-T-AGT
* * * *
10469 GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT--C
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TACATC-CTAGT
* * * *
10516 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--AAGT
1 GAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCATACATCCTAGT
* *
10562 GAACTCGGACTCAACTCAACGAGTTTGGATGCCCAAACATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCTAGT
10608 GA
1 GA
10610 CATGTCACTT
Statistics
Matches: 111, Mismatches: 19, Indels: 22
0.73 0.12 0.14
Matches are distributed among these distances:
44 8 0.07
46 59 0.53
47 30 0.27
48 3 0.03
49 4 0.04
50 6 0.05
51 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCTAGT
Found at i:13139 original size:27 final size:26
Alignment explanation
Indices: 13095--13145 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
13085 CTCGCTGCAA
*
13095 TCTGGTGGCCTCGCCACATATATCTAT
1 TCTGGTGACCTCGCCACA-ATATCTAT
* *
13122 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACCTCGCCACAATATCT
13146 GGCAGCCTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTAT
Found at i:14970 original size:28 final size:28
Alignment explanation
Indices: 14907--15004 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
14897 ATATTAAGTC
*
14907 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
14934 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
14962 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
14991 CGCACACTTAGTGC
1 CGCACACTTAGTGC
15005 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:15468 original size:12 final size:12
Alignment explanation
Indices: 15451--15476 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15441 TGGGCATACT
15451 TATGTATATATA
1 TATGTATATATA
15463 TATGTATATATA
1 TATGTATATATA
15475 TA
1 TA
15477 CTTCGGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:24260 original size:23 final size:23
Alignment explanation
Indices: 24217--24261 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
24207 CTAATAACTC
**
24217 TAATAATTATTAAGTTTTCTTTA
1 TAATAATTATTAAGTCATCTTTA
24240 TAATAATTATTAAGTCATCTTT
1 TAATAATTATTAAGTCATCTTT
24262 TAAAAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (23 bp):
TAATAATTATTAAGTCATCTTTA
Done.