Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6453.1
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: 11622
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:4226 original size:9 final size:9
Alignment explanation
Indices: 4212--4265 Score: 81
Period size: 9 Copynumber: 6.0 Consensus size: 9
4202 GGGAGCAGGC
*
4212 CTTACATAG
1 CTTACATAA
4221 CTTACATAA
1 CTTACATAA
4230 CTTACATAA
1 CTTACATAA
*
4239 CTTACATAG
1 CTTACATAA
*
4248 TTTACATAA
1 CTTACATAA
4257 CTTACATAA
1 CTTACATAA
4266 ATATACATCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (9 bp):
CTTACATAA
Found at i:4252 original size:27 final size:27
Alignment explanation
Indices: 4212--4265 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
4202 GGGAGCAGGC
4212 CTTACATAGCTTACATAACTTACATAA
1 CTTACATAGCTTACATAACTTACATAA
*
4239 CTTACATAGTTTACATAACTTACATAA
1 CTTACATAGCTTACATAACTTACATAA
4266 ATATACATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (27 bp):
CTTACATAGCTTACATAACTTACATAA
Found at i:7642 original size:14 final size:14
Alignment explanation
Indices: 7616--7658 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
7606 TTTTAAATAT
7616 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
7629 TTATAATGGTTTAA
1 TTATAATGGTTTAA
*
7643 TTATATTGGTTTAA
1 TTATAATGGTTTAA
7657 TT
1 TT
7659 CGTCGTTAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 7 0.25
14 21 0.75
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:8507 original size:42 final size:42
Alignment explanation
Indices: 8461--8593 Score: 203
Period size: 43 Copynumber: 3.1 Consensus size: 42
8451 GAACATGACT
* * *
8461 TTTAGTGGCGTTTTTGTAAAAGCGTCGCTAAAGGTCATGTTC
1 TTTAGCGGAGTTTGTGTAAAAGCGTCGCTAAAGGTCATGTTC
8503 TTTAGCGGAGTTTGTGTTAAAAGCGTCGCTAAAGGTCATGTTC
1 TTTAGCGGAGTTTGTG-TAAAAGCGTCGCTAAAGGTCATGTTC
* *
8546 TTTAGCGGAGTTTGTGTGAAAAGCGCCGCTAAAGGTCACGTTC
1 TTTAGCGGAGTTTGTGT-AAAAGCGTCGCTAAAGGTCATGTTC
8589 TTTAG
1 TTTAG
8594 TGGCGCTTTT
Statistics
Matches: 84, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
42 14 0.17
43 70 0.83
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.35
Consensus pattern (42 bp):
TTTAGCGGAGTTTGTGTAAAAGCGTCGCTAAAGGTCATGTTC
Found at i:8524 original size:43 final size:43
Alignment explanation
Indices: 8477--8593 Score: 207
Period size: 43 Copynumber: 2.7 Consensus size: 43
8467 GGCGTTTTTG
8477 TAAAAGCGTCGCTAAAGGTCATGTTCTTTAGCGGAGTTTGTGT
1 TAAAAGCGTCGCTAAAGGTCATGTTCTTTAGCGGAGTTTGTGT
8520 TAAAAGCGTCGCTAAAGGTCATGTTCTTTAGCGGAGTTTGTGT
1 TAAAAGCGTCGCTAAAGGTCATGTTCTTTAGCGGAGTTTGTGT
* * *
8563 GAAAAGCGCCGCTAAAGGTCACGTTCTTTAG
1 TAAAAGCGTCGCTAAAGGTCATGTTCTTTAG
8594 TGGCGCTTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 71 1.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (43 bp):
TAAAAGCGTCGCTAAAGGTCATGTTCTTTAGCGGAGTTTGTGT
Found at i:10056 original size:59 final size:59
Alignment explanation
Indices: 9983--10102 Score: 213
Period size: 59 Copynumber: 2.0 Consensus size: 59
9973 TACGCAATTT
*
9983 ACCGATATCAAACTTGCTTCACAACATTAACAACCCTTATGTACATACACAATAAACTA
1 ACCGATATCAAACTTGCTTCACAACATTAACAACCCTTATGTACATACAAAATAAACTA
* *
10042 ACCGATATCGAACTTGCTTCACAACATTTACAACCCTTATGTACATACAAAATAAACTA
1 ACCGATATCAAACTTGCTTCACAACATTAACAACCCTTATGTACATACAAAATAAACTA
10101 AC
1 AC
10103 TTGGCCGAAG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.42, C:0.27, G:0.06, T:0.26
Consensus pattern (59 bp):
ACCGATATCAAACTTGCTTCACAACATTAACAACCCTTATGTACATACAAAATAAACTA
Found at i:10173 original size:20 final size:20
Alignment explanation
Indices: 10148--10187 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
10138 CGAACATTTA
10148 TTTGTAAGGGCTCGATTAAT
1 TTTGTAAGGGCTCGATTAAT
10168 TTTGTAAGGGCTCGATTAAT
1 TTTGTAAGGGCTCGATTAAT
10188 ATTCAACACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (20 bp):
TTTGTAAGGGCTCGATTAAT
Found at i:10407 original size:40 final size:40
Alignment explanation
Indices: 10316--10694 Score: 466
Period size: 40 Copynumber: 9.6 Consensus size: 40
10306 TCCTCGTTCA
* * * * *
10316 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
10355 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
10395 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
10435 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
10475 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
10515 AAGGCCTTC--G--TTAACCCGGATTTAACAACTCACACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
10551 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
10591 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
10631 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
10671 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
10695 CAGCATTCAA
Statistics
Matches: 296, Mismatches: 36, Indels: 15
0.85 0.10 0.04
Matches are distributed among these distances:
36 29 0.10
38 2 0.01
39 36 0.12
40 221 0.75
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:10567 original size:156 final size:157
Alignment explanation
Indices: 10314--10655 Score: 501
Period size: 156 Copynumber: 2.2 Consensus size: 157
10304 GCTCCTCGTT
* * * *
10314 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACACAAGGCCTTC-GGA-TTAACCCGGA
* *
10379 TTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTC
64 TTTAACAACTCACACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCCTC
10444 GGGACTTAACCCGGATTTAATAACTCGCA
129 GGGACTTAACCCGGATTTAATAACTCGCA
* * *
10473 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-G-TTAACCCGGAT
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGATTAACCCGGAT
*
10536 TTAACAACTCACACGAATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACGAATGCCCTCG
65 TTAACAACTCACACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCCTCG
* *
10601 GGACTTAACCCGGATTTAGTATCTCGCA
130 GGACTTAACCCGGATTTAATAACTCGCA
* *
10629 CAAAGGCCTTC-GGATCTTAATCCGGAT
1 CAAATGCCTTCGGGA-CTTAACCCGGAT
10656 ATATTCACTT
Statistics
Matches: 166, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
155 3 0.02
156 119 0.72
158 1 0.01
159 35 0.21
160 8 0.05
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (157 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACACAAGGCCTTCGGATTAACCCGGATT
TAACAACTCACACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCCTCGG
GACTTAACCCGGATTTAATAACTCGCA
Found at i:10568 original size:116 final size:117
Alignment explanation
Indices: 10316--10640 Score: 483
Period size: 116 Copynumber: 2.8 Consensus size: 117
10306 TCCTCGTTCA
* * * * *
10316 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
** * * * * *
10380 TTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
66 TTAGTATCTCGCACAAAGGCCTTC--GA-TTAACCCGGATTTAACAACTCACACG
10435 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
10500 TTAGTATCTCGCACAAAGGCCTTCG-TTAACCCGGATTTAACAACTCACACG
66 TTAGTATCTCGCACAAAGGCCTTCGATTAACCCGGATTTAACAACTCACACG
* *
10551 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACGAATGCCCTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
10616 TTAGTATCTCGCACAAAGGCCTTCG
66 TTAGTATCTCGCACAAAGGCCTTCG
10641 GATCTTAATC
Statistics
Matches: 191, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
116 112 0.59
118 1 0.01
119 34 0.18
120 44 0.23
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (117 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
TTAGTATCTCGCACAAAGGCCTTCGATTAACCCGGATTTAACAACTCACACG
Found at i:10873 original size:83 final size:83
Alignment explanation
Indices: 10734--10900 Score: 316
Period size: 83 Copynumber: 2.0 Consensus size: 83
10724 AATAATTCAT
10734 AGCACATTCATATTTCATTTTCGTTTACGAAACTCAAACACAAGGCACATATTGTCCTTGCACAT
1 AGCACATTCATATTTCATTTTCGTTTACGAAACTCAAACACAAGGCACATATTGTCCTTGCACAT
10799 TCGGCTCAATAGCCACAC
66 TCGGCTCAATAGCCACAC
**
10817 AGCACATTCATATTTCATTTTCGTTTATTAAACTCAAACACAAGGCACATATTGTCCTTGCACAT
1 AGCACATTCATATTTCATTTTCGTTTACGAAACTCAAACACAAGGCACATATTGTCCTTGCACAT
10882 TCGGCTCAATAGCCACAC
66 TCGGCTCAATAGCCACAC
10900 A
1 A
10901 TAGAGCATGA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (83 bp):
AGCACATTCATATTTCATTTTCGTTTACGAAACTCAAACACAAGGCACATATTGTCCTTGCACAT
TCGGCTCAATAGCCACAC
Done.