Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold60
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 5478
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Found at i:3477 original size:5 final size:5
Alignment explanation
Indices: 3464--3521 Score: 73
Period size: 5 Copynumber: 11.6 Consensus size: 5
3454 ACTCAACTTC
* * *
3464 CTCCA CTCCC CTCCC CTCCA CTCCA CTCCC CTCCA CTCCA CTCCA CTACC-
1 CTCCA CTCCA CTCCA CTCCA CTCCA CTCCA CTCCA CTCCA CTCCA CT-CCA
3514 CTCCA CTC
1 CTCCA CTC
3522 TCCTTCTCCT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
4 2 0.04
5 43 0.91
6 2 0.04
ACGTcount: A:0.14, C:0.66, G:0.00, T:0.21
Consensus pattern (5 bp):
CTCCA
Left flanking sequence: Indices 2964 -- 3463
TGGGGAGAAACGTAAACCCCAGCTGCATGTCAAGCATTATCGAGACCGTTTTGGGGCTTTTGGCG
GTGCTGATTAACCCGAGCTTAGCCCCGGTCATTTTGTTGTGGACTATGGTATCGTCAAGCACCAC
GATGGGGAAACTAAGGTTGCCCACTAACGAGTTACCTTCGCTGTCGTCAACGGGACACCGGTAGC
CCTTATAGTTCACCATGTGAAAACCGAAAAGGGCTCTTCAAACAGCCTGAATCCAATGAGGTAGC
CGTGCTTGTCGCCGGTTACGTTATTTCGTGCCCGCTACGTCAGCGAGAACCAACGCAGGTACAGC
AGAGGATCTGGCGCATACGATGATAGCAACCGTCCACCATGTCTGGGAAGAGAACGAGCAGTTTA
GGGTTTTGTCAGCTTCCATATACCACCAAAATCAAAGCCATATTTTTACGAGTAGATACGATGCC
ATCTTTTTGTAGATACGAATGCTTTCCACATTAGGACTCAACTTC
Right flanking sequence: Indices 3522 -- 4021
TCCTTCTCCTCCGTTCCATATTCCCCTAACTACACACCACCTCTCCGCCGCTCAAATCAAATGAG
ATGCTCGGGCCATGGCCCAATCCCCTTCTTCTCCATATTAGTAATAAACCAGTCGTTTACGAACG
ACACCAACAGAAGCACAAACATGTTGCGCTCGTTGATCCGGTTGTAATCGTGCTGGGTGACAATC
CCCTCCTCCTTGGCCGCCTTGGGCGTCTGGTGCCGTGGCCAAACTCCGCGTACACCAAATCCTCA
ATCCCGTGCATCAGGTCGTAGCGAATGTCCTCCCGCTCAATGCCAAGGAACCGGTTGCCAATCAG
CCGCTAGTACTTGAAGTAGCGGTAGATCCACACGCTAAGGATGGTGGTCTTTTTGTTGAACGACG
CCGTCAGCGCCTTGGAGGAGGTGCCCACCTCCTCGAAACGTTTCTCGTGCTCTGCACCAACTCGT
GGTGCTGGCGGTTGGTGCGGAGGTGGTCTGGGTAGATGTGCTCGA
Found at i:3483 original size:15 final size:15
Alignment explanation
Indices: 3463--3521 Score: 84
Period size: 15 Copynumber: 3.9 Consensus size: 15
3453 GACTCAACTT
*
3463 CCTCCACTCCCCTCC
1 CCTCCACTCCACTCC
3478 CCTCCACTCCACTCC
1 CCTCCACTCCACTCC
3493 CCTCCACTCCACTCC
1 CCTCCACTCCACTCC
*
3508 ACTACC-CTCCACTC
1 CCT-CCACTCCACTC
3522 TCCTTCTCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
15 39 0.95
16 2 0.05
ACGTcount: A:0.14, C:0.66, G:0.00, T:0.20
Consensus pattern (15 bp):
CCTCCACTCCACTCC
Left flanking sequence: Indices 2963 -- 3462
GTGGGGAGAAACGTAAACCCCAGCTGCATGTCAAGCATTATCGAGACCGTTTTGGGGCTTTTGGC
GGTGCTGATTAACCCGAGCTTAGCCCCGGTCATTTTGTTGTGGACTATGGTATCGTCAAGCACCA
CGATGGGGAAACTAAGGTTGCCCACTAACGAGTTACCTTCGCTGTCGTCAACGGGACACCGGTAG
CCCTTATAGTTCACCATGTGAAAACCGAAAAGGGCTCTTCAAACAGCCTGAATCCAATGAGGTAG
CCGTGCTTGTCGCCGGTTACGTTATTTCGTGCCCGCTACGTCAGCGAGAACCAACGCAGGTACAG
CAGAGGATCTGGCGCATACGATGATAGCAACCGTCCACCATGTCTGGGAAGAGAACGAGCAGTTT
AGGGTTTTGTCAGCTTCCATATACCACCAAAATCAAAGCCATATTTTTACGAGTAGATACGATGC
CATCTTTTTGTAGATACGAATGCTTTCCACATTAGGACTCAACTT
Right flanking sequence: Indices 3522 -- 4021
TCCTTCTCCTCCGTTCCATATTCCCCTAACTACACACCACCTCTCCGCCGCTCAAATCAAATGAG
ATGCTCGGGCCATGGCCCAATCCCCTTCTTCTCCATATTAGTAATAAACCAGTCGTTTACGAACG
ACACCAACAGAAGCACAAACATGTTGCGCTCGTTGATCCGGTTGTAATCGTGCTGGGTGACAATC
CCCTCCTCCTTGGCCGCCTTGGGCGTCTGGTGCCGTGGCCAAACTCCGCGTACACCAAATCCTCA
ATCCCGTGCATCAGGTCGTAGCGAATGTCCTCCCGCTCAATGCCAAGGAACCGGTTGCCAATCAG
CCGCTAGTACTTGAAGTAGCGGTAGATCCACACGCTAAGGATGGTGGTCTTTTTGTTGAACGACG
CCGTCAGCGCCTTGGAGGAGGTGCCCACCTCCTCGAAACGTTTCTCGTGCTCTGCACCAACTCGT
GGTGCTGGCGGTTGGTGCGGAGGTGGTCTGGGTAGATGTGCTCGA
Found at i:3489 original size:20 final size:20
Alignment explanation
Indices: 3464--3521 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
3454 ACTCAACTTC
*
3464 CTCCACTCCCCTCCCCTCCA
1 CTCCACTCCCCTCCACTCCA
3484 CTCCACTCCCCTCCACTCCA
1 CTCCACTCCCCTCCACTCCA
*
3504 CTCCACTACCCTCCACTC
1 CTCCACTCCCCTCCACTC
3522 TCCTTCTCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.14, C:0.66, G:0.00, T:0.21
Consensus pattern (20 bp):
CTCCACTCCCCTCCACTCCA
Left flanking sequence: Indices 2964 -- 3463
TGGGGAGAAACGTAAACCCCAGCTGCATGTCAAGCATTATCGAGACCGTTTTGGGGCTTTTGGCG
GTGCTGATTAACCCGAGCTTAGCCCCGGTCATTTTGTTGTGGACTATGGTATCGTCAAGCACCAC
GATGGGGAAACTAAGGTTGCCCACTAACGAGTTACCTTCGCTGTCGTCAACGGGACACCGGTAGC
CCTTATAGTTCACCATGTGAAAACCGAAAAGGGCTCTTCAAACAGCCTGAATCCAATGAGGTAGC
CGTGCTTGTCGCCGGTTACGTTATTTCGTGCCCGCTACGTCAGCGAGAACCAACGCAGGTACAGC
AGAGGATCTGGCGCATACGATGATAGCAACCGTCCACCATGTCTGGGAAGAGAACGAGCAGTTTA
GGGTTTTGTCAGCTTCCATATACCACCAAAATCAAAGCCATATTTTTACGAGTAGATACGATGCC
ATCTTTTTGTAGATACGAATGCTTTCCACATTAGGACTCAACTTC
Right flanking sequence: Indices 3522 -- 4021
TCCTTCTCCTCCGTTCCATATTCCCCTAACTACACACCACCTCTCCGCCGCTCAAATCAAATGAG
ATGCTCGGGCCATGGCCCAATCCCCTTCTTCTCCATATTAGTAATAAACCAGTCGTTTACGAACG
ACACCAACAGAAGCACAAACATGTTGCGCTCGTTGATCCGGTTGTAATCGTGCTGGGTGACAATC
CCCTCCTCCTTGGCCGCCTTGGGCGTCTGGTGCCGTGGCCAAACTCCGCGTACACCAAATCCTCA
ATCCCGTGCATCAGGTCGTAGCGAATGTCCTCCCGCTCAATGCCAAGGAACCGGTTGCCAATCAG
CCGCTAGTACTTGAAGTAGCGGTAGATCCACACGCTAAGGATGGTGGTCTTTTTGTTGAACGACG
CCGTCAGCGCCTTGGAGGAGGTGCCCACCTCCTCGAAACGTTTCTCGTGCTCTGCACCAACTCGT
GGTGCTGGCGGTTGGTGCGGAGGTGGTCTGGGTAGATGTGCTCGA
Done.