Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1037
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: 3210
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Found at i:350 original size:30 final size:31
Alignment explanation
Indices: 314--374 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
304 TATCAGTACA
*
314 GTGTGGGCCTTAGCCCATTACAGTAA-CAGT
1 GTGTGGGCCTTAGCCCAATACAGTAATCAGT
344 GTGTGGGCCTTAGCCCAATACAGTAATCAGT
1 GTGTGGGCCTTAGCCCAATACAGTAATCAGT
375 ACAATGCAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (31 bp):
GTGTGGGCCTTAGCCCAATACAGTAATCAGT
Found at i:504 original size:26 final size:26
Alignment explanation
Indices: 475--525 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
465 CCAACACACC
* * * *
475 AATATCGCAGCAAAGCTGTCAGTAAT
1 AATAACGCAACAAAGATGCCAGTAAT
501 AATAACGCAACAAAGATGCCAGTAA
1 AATAACGCAACAAAGATGCCAGTAA
526 CAGTAATGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.18
Consensus pattern (26 bp):
AATAACGCAACAAAGATGCCAGTAAT
Found at i:540 original size:26 final size:26
Alignment explanation
Indices: 481--568 Score: 86
Period size: 26 Copynumber: 3.3 Consensus size: 26
471 CACCAATATC
* * * * *
481 GCAGCAAAGCTGTCAGTAATAATAAC
1 GCAGCAAAGATGCCAGTAACAGTAAT
*
507 GCAACAAAGATGCCAGTAACAGTAAT
1 GCAGCAAAGATGCCAGTAACAGTAAT
* *
533 GCAGCAAAGTTGCCAATAACAGTATAT
1 GCAGCAAAGATGCCAGTAACAGTA-AT
*
560 GTAGCAAAG
1 GCAGCAAAG
569 CCACTAGTAC
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 41 0.80
27 10 0.20
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.18
Consensus pattern (26 bp):
GCAGCAAAGATGCCAGTAACAGTAAT
Found at i:761 original size:27 final size:26
Alignment explanation
Indices: 731--978 Score: 266
Period size: 27 Copynumber: 9.2 Consensus size: 26
721 GAGTATAAAA
*
731 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCT-TGAGGGTATTTCG
*
758 GTCATTTTACCCTTCGAGGGTATTTCA
1 GTCATTTTACCCTT-GAGGGTATTTCG
785 GTCA-TTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTT-GAGGGTATTTCG
*
811 GTTATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTT-GAGGGTATTTCG
* * *
838 ATCATTTTACCCTTTAGGGGGTATTTTG
1 GTCATTTTACCC-TT-GAGGGTATTTCG
*
866 GTTATTTTACCCTTCG-GGGTATTTCG
1 GTCATTTTACCCTT-GAGGGTATTTCG
* *
892 ATCATTTTACCCTTTGAGGGTATTTCA
1 GTCATTTTACCC-TTGAGGGTATTTCG
* * *
919 GTTATTTTACCCTTTGGGGGTATTTCA
1 GTCATTTTACCC-TTGAGGGTATTTCG
* *
946 GTCATTTTACCTTTTGAGGGTATTTCA
1 GTCATTTTACC-CTTGAGGGTATTTCG
973 GTCATT
1 GTCATT
979 GTACTATTCG
Statistics
Matches: 193, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
26 45 0.23
27 126 0.65
28 22 0.11
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.44
Consensus pattern (26 bp):
GTCATTTTACCCTTGAGGGTATTTCG
Found at i:903 original size:81 final size:81
Alignment explanation
Indices: 732--1007 Score: 310
Period size: 81 Copynumber: 3.4 Consensus size: 81
722 AGTATAAAAG
* * * *
732 TCATTTTACCCTAT-GGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCA-TTTACC
1 TCATTTTACCCT-TCGAGGGTATTTCGATCATTTTACCCTTTGGGGGTATTTCAGTCATTTTACC
*
795 CTTCGAGGGTATTTCGG
65 CTTCGAGGGTATTTCGA
* ** *
812 TTATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTTAGGGGGTATTTTGGTTATTTTACC
1 TCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTT-GGGGGTATTTCAGTCATTTTACC
877 CTTCG-GGGTATTTCGA
65 CTTCGAGGGTATTTCGA
* *
893 TCATTTTACCCTTTGAGGGTATTTC-AGTTATTTTACCCTTTGGGGGTATTTCAGTCATTTTACC
1 TCATTTTACCCTTCGAGGGTATTTCGA-TCATTTTACCCTTTGGGGGTATTTCAGTCATTTTACC
* *
957 TTTTGAGGGTATTTC-A
65 CTTCGAGGGTATTTCGA
* ** * * *
973 GTCATTGTACTATTCGAGTGTATTACGATTATTTT
1 -TCATTTTACCCTTCGAGGGTATTTCGATCATTTT
1008 GCCCACGAAT
Statistics
Matches: 166, Mismatches: 23, Indels: 13
0.82 0.11 0.06
Matches are distributed among these distances:
79 1 0.01
80 60 0.36
81 93 0.56
82 12 0.07
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.45
Consensus pattern (81 bp):
TCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTTGGGGGTATTTCAGTCATTTTACCC
TTCGAGGGTATTTCGA
Found at i:996 original size:54 final size:54
Alignment explanation
Indices: 730--971 Score: 339
Period size: 54 Copynumber: 4.5 Consensus size: 54
720 GGAGTATAAA
* * *
730 AGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTC
1 AGTCATTTTACCCTTTGAGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTTC
*
784 AGTCA-TTTACCCTTCGAGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTTC
1 AGTCATTTTACCCTTTGAGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTTC
* *
837 -GATCATTTTACCCTTTAGGGGGTATTTTGGTTATTTTACCCTTCG-GGGTATTTC
1 AG-TCATTTTACCCTTT-GAGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTTC
* * *
891 -GATCATTTTACCCTTTGAGGGTATTTCAGTTATTTTACCCTTTGGGGGTATTTC
1 AG-TCATTTTACCCTTTGAGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTTC
*
945 AGTCATTTTACCTTTTGAGGGTATTTC
1 AGTCATTTTACCCTTTGAGGGTATTTC
972 AGTCATTGTA
Statistics
Matches: 171, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
52 1 0.01
53 71 0.42
54 72 0.42
55 27 0.16
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.44
Consensus pattern (54 bp):
AGTCATTTTACCCTTTGAGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTTC
Found at i:1007 original size:54 final size:54
Alignment explanation
Indices: 732--1007 Score: 326
Period size: 54 Copynumber: 5.1 Consensus size: 54
722 AGTATAAAAG
* * * *
732 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTC-A
1 TCATTTTACCCTTTGAGGGTATTTCAGTTATTTTACCCTTCGAGGGTATTTCGA
* *
785 GTCA-TTTACCCTTCGAGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTTCGA
1 -TCATTTTACCCTTTGAGGGTATTTCAGTTATTTTACCCTTCGAGGGTATTTCGA
* **
839 TCATTTTACCCTTTAGGGGGTATTTTGGTTATTTTACCCTTCG-GGGTATTTCGA
1 TCATTTTACCCTTT-GAGGGTATTTCAGTTATTTTACCCTTCGAGGGTATTTCGA
* *
893 TCATTTTACCCTTTGAGGGTATTTCAGTTATTTTACCCTTTGGGGGTATTTC-A
1 TCATTTTACCCTTTGAGGGTATTTCAGTTATTTTACCCTTCGAGGGTATTTCGA
* * * ** * *
946 GTCATTTTACCTTTTGAGGGTATTTCAGTCATTGTACTATTCGAGTGTATTACGA
1 -TCATTTTACCCTTTGAGGGTATTTCAGTTATTTTACCCTTCGAGGGTATTTCGA
*
1001 TTATTTT
1 TCATTTT
1008 GCCCACGAAT
Statistics
Matches: 195, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
53 72 0.37
54 96 0.49
55 27 0.14
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.45
Consensus pattern (54 bp):
TCATTTTACCCTTTGAGGGTATTTCAGTTATTTTACCCTTCGAGGGTATTTCGA
Done.