Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1391
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: 11799
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Found at i:832 original size:111 final size:111
Alignment explanation
Indices: 592--866 Score: 311
Period size: 112 Copynumber: 2.5 Consensus size: 111
582 CCTAGAAAGA
** * * * * *
592 AAAGGTGTAAATATGCTAATTCAAGGCTAGCGATATCGGACCTT-AAGATAAGAAAGTACCAATG
1 AAAGGTGCCAATATGCTGATTCAAGGCTAGCGATAT--TAGCTTGAAGATGACAAAGTACCAATG
* * * * *
656 TGCTGATTCAAGGCCAGCGACATTAGACTTGAAGACGGGAAGAATGAT
64 TGCTGATCCAAGGCAAACGACATTAGACTTAAAGACGAGAAGAATGAT
* * *
704 AAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTAAGCTTGAAGATGACAAGGTGCTAATGT
1 AAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATT-AGCTTGAAGATGACAAAGTACCAATGT
* *
769 GCTGATCCAAGG-AAACGACATTGGACTTAAAGATGAGAAGAATGAT
65 GCTGATCCAAGGCAAACGACATTAGACTTAAAGACGAGAAGAATGAT
* * *
815 AAGGGTGCCAATATGCTGTATTCAAGGCTAACGACATTAGACTTGAAGATGA
1 AAAGGTGCCAATATGCTG-ATTCAAGGCTAGCGATATTAG-CTTGAAGATGA
867 AATGATTAGT
Statistics
Matches: 139, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
111 51 0.37
112 88 0.63
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (111 bp):
AAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTAGCTTGAAGATGACAAAGTACCAATGTG
CTGATCCAAGGCAAACGACATTAGACTTAAAGACGAGAAGAATGAT
Found at i:838 original size:112 final size:112
Alignment explanation
Indices: 652--866 Score: 308
Period size: 111 Copynumber: 1.9 Consensus size: 112
642 AGAAAGTACC
* * * * *
652 AATGTGCTGATTCAAGGCCAGCGACATTAGACTTGAAGACGGGAAGAATGATAAAGGTGCCAATA
1 AATGTGCTGATCCAAGGCAAACGACATTAGACTTAAAGACGAGAAGAATGATAAAGGTGCCAATA
* *
717 TGCTGATTCAAGGCTAGCGATATTA-AGCTTGAAGATGACAAGGTGCT
66 TGCTGATTCAAGGCTAACGACATTAGA-CTTGAAGATGACAAGGTGCT
* * *
764 AATGTGCTGATCCAAGG-AAACGACATTGGACTTAAAGATGAGAAGAATGATAAGGGTGCCAATA
1 AATGTGCTGATCCAAGGCAAACGACATTAGACTTAAAGACGAGAAGAATGATAAAGGTGCCAATA
828 TGCTGTATTCAAGGCTAACGACATTAGACTTGAAGATGA
66 TGCTG-ATTCAAGGCTAACGACATTAGACTTGAAGATGA
867 AATGATTAGT
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
111 45 0.49
112 45 0.49
113 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (112 bp):
AATGTGCTGATCCAAGGCAAACGACATTAGACTTAAAGACGAGAAGAATGATAAAGGTGCCAATA
TGCTGATTCAAGGCTAACGACATTAGACTTGAAGATGACAAGGTGCT
Found at i:890 original size:62 final size:61
Alignment explanation
Indices: 759--935 Score: 155
Period size: 62 Copynumber: 2.9 Consensus size: 61
749 AGATGACAAG
* * * **
759 GTGCTAATGTGCTGATCCAAGG-AAACGACATTGGACTTAAAGATGAGAAGAATGATAAGG
1 GTGCTAATATGCTGATTCAAGGCAAACGACATTAGACTTAAAGATGAGAAGAATGATAAAA
* * * *
819 GTGCCAATATGCTGTATTCAAGGCTAACGACATTAGACTTGAAGATGA-AATG-ATTAGTAAAA
1 GTGCTAATATGCTG-ATTCAAGGCAAACGACATTAGACTTAAAGATGAGAA-GAATGA-TAAAA
* * * * * *
881 GTGCTAATATGTTGATTCAAGGCCAATGACATTGGGCTTAAAAACT-AGAAGAATG
1 GTGCTAATATGCTGATTCAAGGCAAACGACATTAGACTTAAAGA-TGAGAAGAATG
936 CTAATGTGTT
Statistics
Matches: 92, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
60 12 0.13
61 38 0.41
62 42 0.46
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.25
Consensus pattern (61 bp):
GTGCTAATATGCTGATTCAAGGCAAACGACATTAGACTTAAAGATGAGAAGAATGATAAAA
Found at i:990 original size:52 final size:52
Alignment explanation
Indices: 876--1116 Score: 202
Period size: 52 Copynumber: 4.7 Consensus size: 52
866 AAATGATTAG
* * ** **
876 TAAAAGTGCTAATATGTTGATTCAAGGCCAATGACATTGGGCTTAAAAACTAGA
1 TAAATGTGCTAATATGTTAATTCAAGGCCAGCGACATTGGGCTTAGGAA-T-GA
* * * * * *
930 -AGAA--TGCTAATGTGTTGATTTAGGGCCAGCGACATTGGGCCTAGGAATGG
1 TA-AATGTGCTAATATGTTAATTCAAGGCCAGCGACATTGGGCTTAGGAATGA
* ** * *
980 TAAATGTGCTAATATGTTAATTCAAGGCCAGCGATATCAGACTTAAG-ATGA
1 TAAATGTGCTAATATGTTAATTCAAGGCCAGCGACATTGGGCTTAGGAATGA
* * * *** * *
1031 CAAATATGCTAATGTGCCGATTCAAGGCTAGCAACATTGGGCTTAGGAATGA
1 TAAATGTGCTAATATGTTAATTCAAGGCCAGCGACATTGGGCTTAGGAATGA
1083 TAAATGTGCTAATATGTTAATTCAAGGCCAGCGA
1 TAAATGTGCTAATATGTTAATTCAAGGCCAGCGA
1117 TATCATACTT
Statistics
Matches: 141, Mismatches: 41, Indels: 12
0.73 0.21 0.06
Matches are distributed among these distances:
50 3 0.02
51 39 0.28
52 96 0.68
53 1 0.01
54 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (52 bp):
TAAATGTGCTAATATGTTAATTCAAGGCCAGCGACATTGGGCTTAGGAATGA
Found at i:1054 original size:51 final size:51
Alignment explanation
Indices: 981--1151 Score: 171
Period size: 51 Copynumber: 3.3 Consensus size: 51
971 TAGGAATGGT
* **
981 AAATGTGCTAATATGTTAATTCAAGGCCAGCGATATCAGACTTAAGATGAC
1 AAATGTGCTAATGTGCCAATTCAAGGCCAGCGATATCAGACTTAAGATGAC
* * * * * ** * * *
1032 AAATATGCTAATGTGCCGATTCAAGGCTAGCAACATTGGGCTTAGGAATGAT
1 AAATGTGCTAATGTGCCAATTCAAGGCCAGCGATATCAGACTTAAG-ATGAC
* ** *
1084 AAATGTGCTAATATGTTAATTCAAGGCCAGCGATATCATACTTAAGATGAC
1 AAATGTGCTAATGTGCCAATTCAAGGCCAGCGATATCAGACTTAAGATGAC
*
1135 AAAGGTGCTAATGTGCC
1 AAATGTGCTAATGTGCC
1152 TGTAGACACC
Statistics
Matches: 88, Mismatches: 31, Indels: 2
0.73 0.26 0.02
Matches are distributed among these distances:
51 51 0.58
52 37 0.42
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (51 bp):
AAATGTGCTAATGTGCCAATTCAAGGCCAGCGATATCAGACTTAAGATGAC
Found at i:1087 original size:103 final size:103
Alignment explanation
Indices: 933--1151 Score: 339
Period size: 103 Copynumber: 2.1 Consensus size: 103
923 AACTAGAAGA
** * * * *
933 ATGCTAATGTGTTGATTTAGGGCCAGCGACATTGGGCCTAGGAATGGTAAATGTGCTAATATGTT
1 ATGCTAATGTGCCGATTCAAGGCCAGCAACATTGGGCCTAGGAATGATAAATGTGCTAATATGTT
*
998 AATTCAAGGCCAGCGATATCAGACTTAAGATGACAAAT
66 AATTCAAGGCCAGCGATATCAGACTTAAGATGACAAAG
* *
1036 ATGCTAATGTGCCGATTCAAGGCTAGCAACATTGGGCTTAGGAATGATAAATGTGCTAATATGTT
1 ATGCTAATGTGCCGATTCAAGGCCAGCAACATTGGGCCTAGGAATGATAAATGTGCTAATATGTT
*
1101 AATTCAAGGCCAGCGATATCATACTTAAGATGACAAAG
66 AATTCAAGGCCAGCGATATCAGACTTAAGATGACAAAG
*
1139 GTGCTAATGTGCC
1 ATGCTAATGTGCC
1152 TGTAGACACC
Statistics
Matches: 105, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (103 bp):
ATGCTAATGTGCCGATTCAAGGCCAGCAACATTGGGCCTAGGAATGATAAATGTGCTAATATGTT
AATTCAAGGCCAGCGATATCAGACTTAAGATGACAAAG
Found at i:1506 original size:20 final size:21
Alignment explanation
Indices: 1481--1531 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1471 CAAGGAAATA
1481 TATCGATACATT-ATTCAATG
1 TATCGATACATTGATTCAATG
**
1501 TATCGATACATTGA-TCTTTG
1 TATCGATACATTGATTCAATG
1521 TATCGATACAT
1 TATCGATACAT
1532 CTGGAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (21 bp):
TATCGATACATTGATTCAATG
Done.