Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold65
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: 7174
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Found at i:232 original size:129 final size:129
Alignment explanation
Indices: 1--516 Score: 768
Period size: 129 Copynumber: 4.0 Consensus size: 129
*
1 GTACACCACTACTTGGACGACCACCGCT-GGCGACGGTAAAGCGAGCACTGGTACGGGTATTGTT
1 GTACACCACTACTTGGACGACCACCG-TAGGCGACGGTAAAGTGAGCACTGGTACGGGTATTGTT
*
65 GATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTACGAATGGCTGTCTCGAGTGCACTCA
65 GATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTACGAATGACTGTCTCGAGTGCACTCA
* * * * * * * * ** * **
130 ATACACCACTACGTGGACCACGACTGATAAG-AATGGCCAGGCCAGCACTGGTACGGGTATTGTT
1 GTACACCACTACTTGGACGACCACCG-TAGGCGACGGTAAAGTGAGCACTGGTACGGGTATTGTT
194 GATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTACGAATGACTGTCTCGAGTGCACTCA
65 GATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTACGAATGACTGTCTCGAGTGCACTCA
259 GTACACCACTACTTGGACGACCACCGCT-GGCGACGGTAAAGTGAGCACTGGTACGGGTATTGTT
1 GTACACCACTACTTGGACGACCACCG-TAGGCGACGGTAAAGTGAGCACTGGTACGGGTATTGTT
* *
323 GATGTGACCACCGACTCCAACGGGTCGTTGTACACAACTACGAATGACTGTCTCGAGTGTACTCA
65 GATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTACGAATGACTGTCTCGAGTGCACTCA
* *
388 GTACACCACTACTTGGACGACCACCGCAGGTGACGGTAAAGTGAGCACTGGTACGGGTATTGTTG
1 GTACACCACTACTTGGACGACCACCGTAGGCGACGGTAAAGTGAGCACTGGTACGGGTATTGTTG
* * * * *
453 ATGTGACCACTGACTCTAACGGGTCGTTGTACACATCTACGAATGATTGTTTCGAATGCACTCA
66 ATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTACGAATGACTGTCTCGAGTGCACTCA
517 CTATCCCGAT
Statistics
Matches: 345, Mismatches: 39, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
128 1 0.00
129 343 0.99
130 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.23
Consensus pattern (129 bp):
GTACACCACTACTTGGACGACCACCGTAGGCGACGGTAAAGTGAGCACTGGTACGGGTATTGTTG
ATGTGACCACCGACTCTAACGGGTCGTTGTACACAACTACGAATGACTGTCTCGAGTGCACTCA
Left flanking sequence: None
Right flanking sequence: Indices 517 -- 1016
CTATCCCGATCGTGTGACGACTGTATTGGATGATGGCGATATCTATGAGCTCATTGCTATTGTTG
AGTCCACTTCCCAGTTGGAAGGAGATATTCATACTACAGTCTACGACAACCTGGACAACACCCTG
TGTACTATCACGCTGGCCACTTCGAATATCCAAGTATTCAATTCTGTTGGCATCGACTTGACTGG
AAGTTTGGCGACCTTGTCGGGAAATCTCAATATTTCTGAATGTTCAGATTGTTTGGAGCAAGAAA
TGATTTCGACAATCGTCAATGAACAAGGTGTATCTGCAACTGCTTTAGATTCAGTGACAAAAGAT
GCGGAAGGATCTCCAACCACTTTGCAGCCAACTCTCGGTGGTGACGATTGTGCGGGCTGTACCAT
TTATACCACAACATGGACATCCACGGATTCAGAAGGGGAGGAATTCACTATTGCTGGTGTTGTAA
ATGTCACCACTGACACCGACGGATCGCTAGCCACGTCTACACGTA
Found at i:4967 original size:18 final size:18
Alignment explanation
Indices: 4944--4994 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
4934 AAATTCCAGG
4944 AGAATCGTCCATTTCAAA
1 AGAATCGTCCATTTCAAA
* *
4962 AGAATCGTCCTTTTCAAG
1 AGAATCGTCCATTTCAAA
*
4980 AGAATCGTCCCTTTC
1 AGAATCGTCCATTTC
4995 GCTTGACGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.31
Consensus pattern (18 bp):
AGAATCGTCCATTTCAAA
Left flanking sequence: Indices 4444 -- 4943
TCCGAGATTGAGCACGTTAAGCACCCGAATCCCACACAAGCAACTCAATTTCCTACAATTGACCC
AGAACTTGAATGTGAAGATGAGGAGGTTGCTTCAACCGTCCATGGGGATTCAAGCCCAAATACGG
AGCAGATAGCGGTGCCCACCAAAGACGCTAATGAGAGTGGATTTTTAGCTGCTACGTCTTCCGTC
GAGCTGCCCGTATTCAGCGACAGCTCGGCTTCTACTCCGGCTGAATACGACGAGTTGGAGTGTTC
GGACGATGGGGAGAAACAGGAGGCGTTTACCGGGTTTGCTCCAACCACCGACAATATTTTTCCCG
TTCCCACCTCAAAGTCTTCAAGTCCGATTTCCATTGAGTCTATCTCATGGCTCGACGACCTCGAC
TGCTCCGAGGAAGACATTCACCCCACTCTTTTACCGGAAAACCCCGTGGTGACCACGACATATGC
TACTAACGGATGGCCCGAGACAGCGAGTGCCCATGAAATTCCAGG
Right flanking sequence: Indices 4995 -- 5494
GCTTGACGCTGACGAATGGGAGTGTGACGAGTACGACACCTGGACGACCACGGGAGCCACTGCCC
AGCCAACCATCAACCCAGGGGCTGTGGACCTGAACACCCCAGACAAACAGTGGCAAGCCACCTCG
TCTATTGTTCCGTCGTGGGCTCCAGTGCCCTCAGAGCTTCCGGATTGCCCTGACGAGTACGACAC
CTGGACGACCACGGGGGCTGACGGCCAGCCAACGGTCAACTCGGGCGTGGTGGATGTCACCACCG
GGCCGGGCGGGGAGCTCTTGACCACCTCGTCTGCTGTTCCGTCACGGCTCCCCTCGCCAACGGAG
CTTCCCGACTGTCCAGACGACTACGACACCTGGACGGTCGTCGGATCCGACGGTACGCCCACCAC
GCTAGCTGGCATTGTAGACGTCACTACCGGGGCTGACGGGATGTTGGCCACCACCTCTTCAGCTC
TCCCCATTGCTCCCCAGGGTACTGACGAGCTCGACTGCGACGACG
Found at i:6871 original size:20 final size:20
Alignment explanation
Indices: 6846--6903 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
6836 TCGCTCGTCG
6846 CCATGTCCTCCTCTCTCCTC
1 CCATGTCCTCCTCTCTCCTC
*
6866 CCATGTCCTCCTCTCTTCTC
1 CCATGTCCTCCTCTCTCCTC
* *
6886 CCATATCCTCCCCTCTCC
1 CCATGTCCTCCTCTCTCC
6904 ACTCTTTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.07, C:0.55, G:0.03, T:0.34
Consensus pattern (20 bp):
CCATGTCCTCCTCTCTCCTC
Left flanking sequence: Indices 6346 -- 6845
TGATCTTGTGCTAACACGACCGGTAGGGTATGAATGTCGGATCCATGGGTTCAGCCAGTACTGAA
TGATCCGTTAGGTTTATACGATAAATAAGGCGTTTTGGTATACAAATCCACCATGGTTAAGAACG
ACAAAAAATCACCAACGGGGCCTTTGGCCTTTGGCTTCTGACCCGAAGTCGAGTCGCAACAGGTT
ATATAGTCAATGCCCTTGTGACATTTCTCTTAGTGCAAGCGGGTATAGTTAACTGAATATCACAT
GTGGCGTCGCTAACAGTGAAAAGCTACCGCACTGTCATCGTATTCCAACAAAAGTATCAGTCCTT
TCGACTGGTGTCTTCAATAACTGTAGGTCTAATTAGCCCTTGTCTAGCACCACGCTAATGCTTAC
CAATCATCTACCTACAACCAACCCCATTCCCACGACTTCCACCATAACAGCTGCCTCACCCTATC
CTCCTCTTTCCTCCACTGTCCCCTTCCCCACTCATTCGCTCGTCG
Right flanking sequence: Indices 6904 -- 7174
ACTCTTTCTCCCCTCTATCCCCACTCCACCCTTCCCCCACTCCAATACGTCGCCATATCCTCCTC
TCCCACCTCTCACCTCATCCCCTCTACCCTCTCCCCTCCTTCTTCTCTACCCTCTCCCCTTCCCC
CACTCATTCGCGTCCCCCCTCCCCTCCACCCCTCTTCCCCTGCACACAACCCCAAACCAAAACAA
CGCGTGTGTCCCACCCCCCCATGTCCCGCTCGGAGTTCGACGAGATCGTCGCCCAGGCGGCGCTC
CCGCCCCCCAG
Done.