Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1210
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: 31427
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:1403 original size:39 final size:39
Alignment explanation
Indices: 1360--1579 Score: 203
Period size: 40 Copynumber: 5.6 Consensus size: 39
1350 TCCTCGTTCA
* * *
1360 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC
* *
1399 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC
* *
1438 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCGCACA-
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC
* * * * *
1477 AAGGCCTTCGGGGCTTAACCCGGAATT-GTATCTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC
** * * * *
1515 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCA-CAC
* *
1556 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
1580 CAGCATTCAA
Statistics
Matches: 147, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
37 8 0.05
38 26 0.18
39 52 0.35
40 55 0.37
41 6 0.04
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC
Found at i:1451 original size:40 final size:39
Alignment explanation
Indices: 1360--1579 Score: 214
Period size: 39 Copynumber: 5.6 Consensus size: 39
1350 TCCTCGTTCA
* * * *
1360 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
1399 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
1438 GAATGCCTTCGGGACTTAACCCGGATTTAGT-A-TCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * * *
1476 AAAGGCCTTCGGGGCTTAACCCGGAATT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
** * * * *
1515 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
1556 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
1580 CAGCATTCAA
Statistics
Matches: 151, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
37 2 0.01
38 32 0.21
39 60 0.40
40 49 0.32
41 8 0.05
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:1588 original size:41 final size:41
Alignment explanation
Indices: 1511--1588 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
1501 ATTGTATCTC
* * *
1511 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
1552 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
1589 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:8921 original size:39 final size:40
Alignment explanation
Indices: 8876--9100 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
8866 GCTCCTCGTT
* * * *
8876 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
8916 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
8955 CGAATGCCTTCGGGACTTAACCCGGATTTAGTACCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
8995 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
9035 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
9076 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
9101 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.24
40 104 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:9109 original size:41 final size:41
Alignment explanation
Indices: 9032--9109 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
9022 CTTGTATCTC
* * *
9032 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
9073 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
9110 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:13569 original size:43 final size:42
Alignment explanation
Indices: 13480--13636 Score: 120
Period size: 43 Copynumber: 3.7 Consensus size: 42
13470 TGTGATGACA
* * * **
13480 TGTAAGACCATATCTAGGACATTGGCATTGTATTAAGATTATG
1 TGTAAGACCATATCTGGGACATTGGCATCGTTTTGTGATT-TG
*
13523 TGTAAGACCATATCTGGGATATTGGCATCGTTTTGTGATTTCG
1 TGTAAGACCATATCTGGGACATTGGCATCGTTTTGTGATTT-G
* * * * * * * *
13566 TGTAAGACCCTGTCAGAGACAGTGGCATCGAATATGT-ATTTATA
1 TGTAAGACCATATCTGGGACATTGGCATCG-TTTTGTGA-TT-TG
*
13610 TGTAAGACCATATCTGGGATA-TGGCAT
1 TGTAAGACCATATCTGGGACATTGGCAT
13637 TGTACGAGCT
Statistics
Matches: 90, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
42 1 0.01
43 66 0.73
44 22 0.24
45 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.34
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGACATTGGCATCGTTTTGTGATTTG
Found at i:18809 original size:34 final size:33
Alignment explanation
Indices: 18739--18814 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 33
18729 AGTACAGTCC
* * * *
18739 AGTATTAGTTGGGCCTTAGCCTATTATAGTACT
1 AGTATCAGTTGGGCCTTAGCCAATTACAGTAAT
18772 AGTATCAGTGTGGGCCTTAGCCCAATT-CAGTAAT
1 AGTATCAGT-TGGGCCTTAG-CCAATTACAGTAAT
18806 AGTATCAGT
1 AGTATCAGT
18815 ATCAATACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 8 0.22
34 24 0.65
35 5 0.14
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (33 bp):
AGTATCAGTTGGGCCTTAGCCAATTACAGTAAT
Found at i:21199 original size:14 final size:14
Alignment explanation
Indices: 21180--21214 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
21170 CCTCTTAATG
21180 TCACACATGGCATA
1 TCACACATGGCATA
* *
21194 TCACACATGGCCTG
1 TCACACATGGCATA
21208 TCACACA
1 TCACACA
21215 ATCTAGTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.34, G:0.14, T:0.20
Consensus pattern (14 bp):
TCACACATGGCATA
Found at i:26437 original size:46 final size:46
Alignment explanation
Indices: 26385--26555 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
26375 GGTTGAGCAT
26385 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
* * * *
26431 CAAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TC
* * *
26478 CGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-C
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
*
26523 CTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 C-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
26556 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 56 0.54
47 26 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
Done.