Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold57
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: 6742
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Found at i:2268 original size:22 final size:22
Alignment explanation
Indices: 2238--2281 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2228 GAGCTCGGCA
2238 TGCTGGTGCCGGTGGTGGTGAT
1 TGCTGGTGCCGGTGGTGGTGAT
* *
2260 TGCTTGTGCGGGTGGTGGTGAT
1 TGCTGGTGCCGGTGGTGGTGAT
2282 GCCGAGGACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.05, C:0.11, G:0.50, T:0.34
Consensus pattern (22 bp):
TGCTGGTGCCGGTGGTGGTGAT
Left flanking sequence: Indices 1738 -- 2237
CCATACTTTTCGAAGGTCGTCGAGTGCGGTGTCGGTGTGATGTTGCCGCTGGTGTTTGTCACCTG
TACGCTGGACGACACTGTGGGCGCGATCATGATTGAGGACAAGCTGGGCCGCGTCATGTACGGCT
ACGAGGTGTTGGGCGCAGAGCAGTTGGTGACTGGGTGCACTGTCGCTGTGCATGGAGTAGCGGGG
AAGTGGGGTTTTGAGGTGTTGGAAATGGTCCATCCACAGCCTATAGCGCTGAGGACCTGGAAGGC
GATTGCCGACGGCGATACCGCCAGCATTCTCCGCCTCGAAGTCTTGAAACAGTACGTGTTGGGTG
AGACCGGCGACCCGCACCGGACATGGCTTATCGCCGAAGTGGTGGTGGGCGACCTGATCGCCGCC
AAACACGAAGTGGTTACCGACTCATTCCTGTCTTCCAACAACAACGGTCTGAAAATACCCTGAAG
TTCTCGCCCGCATCACTGGCCAAGTTCGACGCCTGGAGCTCGGCA
Right flanking sequence: Indices 2282 -- 2781
GCCGAGGACCCTTGATCCTGCAGTAATCTGCTGGCCCCAGGCGCTGTTGCACCGGTCAGTGATGT
CCCGTGCCGCCGGGCTGCAGGGATTCACCCGGTTGACCAACCCCCAGTATTTGCATGTGTCCACT
AACATCTCTCCTCAGCGGGTGTTGCTCAGTTCTGGGCATAACATGGCGGACATGTAGATTCATAG
TTTCTAGGCTTTTATAAGGATAATATACATACTCCATTACACGAAGACGATGGCGGAGAGTACTG
TGATGGCCACGGAGTGCGTGGCCCAGTTCAGAGGCAACCGACCGGTTGGTGGGTACATGTGTCGG
CCGCCGCCTTAGCGCCCAGCGTTAGGAGGGGCAGTGCACAACGCCCTCAAGCCCCAGCTGTAGTG
GCTGGTCTACGACGCTGGCGCCGGCGATAGCGCCCAGGAACCGGGCAGGCACGCTGACAGTGTCG
TCCTTGACATGCCAAAACAAGGAAATGTAGTCGGAGAAGGGTGAC
Found at i:3938 original size:30 final size:30
Alignment explanation
Indices: 3904--3973 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
3894 TATGGATCGC
*
3904 TTGGACCGAATTGATGCTAAGATAGAGAAA
1 TTGGACCGAATCGATGCTAAGATAGAGAAA
* *
3934 TTGGACCGAATCGATGCTAGGTTAGAGAAA
1 TTGGACCGAATCGATGCTAAGATAGAGAAA
*
3964 TTGGAACGAA
1 TTGGACCGAA
3974 ATTACGCGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.23
Consensus pattern (30 bp):
TTGGACCGAATCGATGCTAAGATAGAGAAA
Left flanking sequence: Indices 3404 -- 3903
AAATCGGCTCATCAAACAGCCCGGGATCCATTGCCCTCGCAATGACGTAGGCGTACCTAGGCGTA
CCCGTCCGCTTACGGATTTTTGTGCCCGCAACATCAGGGAGAAAACGCAGGTACAGCCGGGGGAA
TCCGGCGCATATGATAATAGCGTCCACCACGTCTGGGAAAAGAACGAGCGATTTAGGGTTTCGTT
CGCTCCAATATATCTGGTTATACTTCTAACCAAGTACGGTAACCATCTAACCACGAGGTAGTTAT
AGACATCAGACCACAATAGGTTATACAAAACCACATTCCTGCATATTTTTGGAGTATATCACCCA
ATTCCATAACCGTATTCCGTACTTTCGAACTGAAAAAACATATTCCATGGCTGAGAACGACAAGA
AATTCACCAACGGTGCCGTTGCCCCCTTGGCTACTGACCCTGAAGTCGGGTCGCGACATGATGAG
GCGGAAATTTCTCTCAACTCCTTTATGGTCAAGATTATGGATCGC
Right flanking sequence: Indices 3974 -- 4473
ATTACGCGTGCTTGGGTAACCTTGAGCAGCACTTCGCCAACTTTTTCACTTATAGTAGTACCCCA
ATATTCCTGGACTATACCCCTTCCGAGGATTCTTCCGACGGCTCTGATTTGCCCACACCAGTATT
CCTGGACTACACCCCCTCCGAGGATTCTGTCGACGACTCTTGTTTGTCCACACCTTCTTCTGCCA
ATGCCTCGGCTCTGCATGTGCCGACGGACACTGCACCTGACACGACTGGCCCCAAACGATCCAAA
GAAGACTTTGGTCACAATGAGAACCCTTTTGCTGGTAGGCTCCCCGATGATCTCATCGACCGCTC
TGTTCCTGAATTGATCGACTGGATTGATTCCTGTACTGACCTTGTTCGTGAAGCTGAGATCAACA
ATACCGAGGCGAAACTCAAGTACCAACTTAACGCGTCTTTTGCCCCGTACGTGAGACGCCACAAC
CCCCACGTGAAATTTGACCCCAACCTTCGTGTGAGTGAATATTTT
Found at i:4138 original size:60 final size:60
Alignment explanation
Indices: 4040--4157 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 60
4030 AGTACCCCAA
* * *
4040 TATTCCTGGACTATACCCCTTCCGAGGATTCTTCCGACGGCTC-TGATTTGCCCACACCAG
1 TATTCCTGGACTACACCCCCTCCGAGGATTCTTCCGACGACTCTTG-TTTGCCCACACCAG
*
4100 TATTCCTGGACTACACCCCCTCCGAGGATTCTGT-CGACGACTCTTGTTTGTCCACACC
1 TATTCCTGGACTACACCCCCTCCGAGGATTCT-TCCGACGACTCTTGTTTGCCCACACC
4158 TTCTTCTGCC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
60 49 0.94
61 3 0.06
ACGTcount: A:0.18, C:0.36, G:0.18, T:0.29
Consensus pattern (60 bp):
TATTCCTGGACTACACCCCCTCCGAGGATTCTTCCGACGACTCTTGTTTGCCCACACCAG
Left flanking sequence: Indices 3540 -- 4039
GCATATGATAATAGCGTCCACCACGTCTGGGAAAAGAACGAGCGATTTAGGGTTTCGTTCGCTCC
AATATATCTGGTTATACTTCTAACCAAGTACGGTAACCATCTAACCACGAGGTAGTTATAGACAT
CAGACCACAATAGGTTATACAAAACCACATTCCTGCATATTTTTGGAGTATATCACCCAATTCCA
TAACCGTATTCCGTACTTTCGAACTGAAAAAACATATTCCATGGCTGAGAACGACAAGAAATTCA
CCAACGGTGCCGTTGCCCCCTTGGCTACTGACCCTGAAGTCGGGTCGCGACATGATGAGGCGGAA
ATTTCTCTCAACTCCTTTATGGTCAAGATTATGGATCGCTTGGACCGAATTGATGCTAAGATAGA
GAAATTGGACCGAATCGATGCTAGGTTAGAGAAATTGGAACGAAATTACGCGTGCTTGGGTAACC
TTGAGCAGCACTTCGCCAACTTTTTCACTTATAGTAGTACCCCAA
Right flanking sequence: Indices 4158 -- 4657
TTCTTCTGCCAATGCCTCGGCTCTGCATGTGCCGACGGACACTGCACCTGACACGACTGGCCCCA
AACGATCCAAAGAAGACTTTGGTCACAATGAGAACCCTTTTGCTGGTAGGCTCCCCGATGATCTC
ATCGACCGCTCTGTTCCTGAATTGATCGACTGGATTGATTCCTGTACTGACCTTGTTCGTGAAGC
TGAGATCAACAATACCGAGGCGAAACTCAAGTACCAACTTAACGCGTCTTTTGCCCCGTACGTGA
GACGCCACAACCCCCACGTGAAATTTGACCCCAACCTTCGTGTGAGTGAATATTTTGCTCAAGCC
CGGCTTGCCTTGATGGATTCCCCCAAAATGTTCAACCACTACATTACCGCGATTGGAGTGAGACC
TCTCCAGCAGGCCATGCTTTACAACCATACTTGGTTCAACGACTTCTCAATCACTCTCACCAAGC
TTCTGGACGACATTCGTTACATGAGCCCCACAAAGGTCCATGCCA
Found at i:4861 original size:15 final size:15
Alignment explanation
Indices: 4841--4894 Score: 90
Period size: 15 Copynumber: 3.6 Consensus size: 15
4831 AATCTCCCGC
4841 TATAGCAACAACTCG
1 TATAGCAACAACTCG
4856 TATAGCAACAACTCG
1 TATAGCAACAACTCG
*
4871 TATGGCAACAACTCG
1 TATAGCAACAACTCG
*
4886 TATGGCAAC
1 TATAGCAAC
4895 TGGCAATGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (15 bp):
TATAGCAACAACTCG
Left flanking sequence: Indices 4341 -- 4840
TGTTCGTGAAGCTGAGATCAACAATACCGAGGCGAAACTCAAGTACCAACTTAACGCGTCTTTTG
CCCCGTACGTGAGACGCCACAACCCCCACGTGAAATTTGACCCCAACCTTCGTGTGAGTGAATAT
TTTGCTCAAGCCCGGCTTGCCTTGATGGATTCCCCCAAAATGTTCAACCACTACATTACCGCGAT
TGGAGTGAGACCTCTCCAGCAGGCCATGCTTTACAACCATACTTGGTTCAACGACTTCTCAATCA
CTCTCACCAAGCTTCTGGACGACATTCGTTACATGAGCCCCACAAAGGTCCATGCCATTGGTACT
ACTCTCTTTGCTTACCGACTTTCACTTTCCATGGATCTTAAGCTTGAACTTTACCCGGCTATTTC
CTTCTTCAGTGACTGTAACATGCAAACACAAGAGACCGTCAGTGCTCGCGCCCCGAACATGATCA
TGTCAGTTGTTAACGCCGTATCCACTATCCGGAACAATCTCCCGC
Right flanking sequence: Indices 4895 -- 5394
TGGCAATGAATTCTCTGGCACCCGGAATTGTTCTCACAATTGTGGCTCCAGACCACCCACAAGTC
CGAATAAGCGTGGAGGATTCAACTAACTGAGCGAAACACGAACCTACCCTTAGAAAATATGCAGA
ACAACGCCTTTTAATGACAAGACACAGCGCGCAATACCTAGCTACAGGTAAGTTTAGCGACGAAC
TTTTCGCTCTAGACCTATTTGCCTACTCTAATATTGCTGCTGATTTCTAATTGCCCTGACAGATA
CTATTTTGACTTTTACCCCGGAACCACAGCACTATGATGCCACCAACGGCACACCAATACTCGTG
ACGGGCTAAAGCACTTTTACCATCTGTGACACTAAGGGCCACAAGGCTCATTTCGAGACTGCTCT
AGTTTCCCACACACCTGGATATTTGAGTGCTATATACCCCGCTGATTGAGGCATGTTTGCTTCAC
CAAGGCAATGTAACCAAGGCAGAATCGACTCCACCACATGCCCCG
Done.