Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_023103
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: 352069
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Found at i:110727 original size:25 final size:25
Alignment explanation
Indices: 110693--110742 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
110683 CCTTTACTCC
110693 TCCATTGTACCACTCCTATAATTTA
1 TCCATTGTACCACTCCTATAATTTA
110718 TCCATTGTACCACTCCTATAATTTA
1 TCCATTGTACCACTCCTATAATTTA
110743 ATTGGAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (25 bp):
TCCATTGTACCACTCCTATAATTTA
Left flanking sequence: Indices 110193 -- 110692
CCGCAGTTGTATCTGCGCATGCAGAGACAGAGCTTTTTCCTATCCATTGAGGAATCTATCCGGAG
ATGAATAAGACCCATAGCGAGGGAATGCCCTTTCATCGAATGGCTTTCTTCCTTCTGTTTTAGGA
ATAGGAAGAGAAGATATATGAACCACTTTCTTAAAACTTTAGGTGGCCAAAGTTAGTGGATTATC
GAAGAGTGCCATAATAGCATATATAGAACTGATCCGCACACGACCTGGCTAATCCGATTTAGCTT
ACTTTTTTCTAGTGTTAGGCTTGCCCGAACATTGGGCAGCTGTGGTATTTTGGTGCCGTGAGAGG
ATAGTGAAAGTAGTGGATAAAATTCATACAAAGAAGACTAGCTAGGAAGCACCAGCAACCGACAA
GGCTCTTTGTGTTGATATATTTTTTTTTAGTACTCCCGACACCGGGCGTAAGCCCAATCCGAAAT
AGATCTGTTGAAAGAGAAAGATGCTAAGCCTTTCACCTTTACTCC
Right flanking sequence: Indices 110743 -- 111242
ATTGGAAAAGAACTAGTACTAAAACTTTAGCCTCTCCTAAGTCGAGGAATAGCTGAGATAGACCG
CTAAAGCCCTCACTCTCTCCCCTTCTTGCCGCTCTTACCCTCTTCTTTTCTTTCTCGTGGTCAAG
CTCTTGGCGGAGTCGTCGGGCTATATATTATTCGACAAAAATATGGTAATATTTTAAGCTCTTTG
GTACTTGGGATTGATGAGTTTGTGAGGCGCACTTGAAAATTCGATTCTCATGATGGCCTTCTTGA
TCTTATTCGTATTCTAAAGAAATGAACTACGGCGACCTGATTCTCTTGAGAGATACGTAGGCAGC
CCATTCTATGTGGGTGCGGTCCCTTTCTTTTCTAGTCTAGTATTGGAATCAAAGTAGGCAGACGT
AGTAGATCAAAAGTCTTGACGGGCGGACAATGAATGCCCTGTTGTTGCAACACAACAACAAAGGG
ATATTACATGGATGCCCCAGAAGAGGCCGCTAGAGGAACAATAAG
Found at i:208028 original size:21 final size:21
Alignment explanation
Indices: 208003--208043 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
207993 AGAATTTAAT
208003 TTTAATGAGAAGCTTAATAAA
1 TTTAATGAGAAGCTTAATAAA
208024 TTTAATGAGAAGCTTAATAA
1 TTTAATGAGAAGCTTAATAA
208044 GAAGACCCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (21 bp):
TTTAATGAGAAGCTTAATAAA
Left flanking sequence: Indices 207503 -- 208002
CCCTTTATCTTATTTGGCTCTCTTTTATTTCTTTCCTCCACCTAAAATTCCACATTCCCCTTAAG
CCCCTAATAGACGTTTTAATCCTACCTCTTTCGGGGGCAGCGGCCCTCCACTTTTCCTTCTTTGC
TAAGAGCGGCAAGGCCCGGGGCCTCGCCTTTTTGATCTATGCCTTGAACGGGGCAATAATACTTA
TTCTGTCCAAGAAATATCAAGTAGTACTGGCCTTTTTGGCATTTTATGCGATCTTTGCTTTCTTT
ATTGCCACACTAGTCTACTTTATAAGTCTAGTCTTAGGAGTCCCCTTCCTTAGACTTTTGAAGGA
GTACTTATCCGATGAGAAAAATAGGATATTCAAACTCTCGGCCTTATTTTTCTTTGGCCTGTCAG
AATTGCTCTGGCGGAACTTATTTGACGTGCCCGGGTTTGATAAGGCCCCCATACTATTATATTCG
CTGTCTTTACAGCAGGCCCTTTTAATTTTTTGGGAAGAATTTAAT
Right flanking sequence: Indices 208044 -- 208543
GAAGACCCCAGGAGGAGGGCCGTCTGGGGGGGGTGAGAGCTTATACTCTGGAAAGGCTAAGGAGA
GCAAAAAAGAAGAGAATGCTGCCCAGAAAGGTAAGGACGAGGAGAGCAGAAGCCCGCTGGATCAA
TTCTCTATTCTCCCATTGATGGATATTCAAATCGGAAAGCTCTACTTCTCATTCACAAATCCATC
CCTCTTCATGCTACTCACTCTCAGTTTTGTCCTACTTTTCTTTTCTTTTGTGACTAAAAAGGGCG
GAGGAAAGTCAGTACCAAATGCCTGGCAATCCCTGGTAGAGCTTCTTTATTCAAAAGAGAGAGAT
GATAACTATGTTCGACTTGATCCCCGTTCAAGGGTACATAGGCAACTTGGGGCAGCCAAGTCCAG
TCATCTTTTGAAAGTGTTTACCGATAAGTCACATCATGCTGGAGTAGGTCCGCTAAGTCCGGTGG
ATCGAACCAGGATAAAAAAAGTCACTCTTGAATAAGAGGAAATTC
Found at i:246857 original size:16 final size:17
Alignment explanation
Indices: 246827--246860 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
246817 TTGAATATAT
*
246827 ATATAATACATTAATTG
1 ATATAATACACTAATTG
246844 ATAT-ATACACTAATTG
1 ATATAATACACTAATTG
246860 A
1 A
246861 ATTGGGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (17 bp):
ATATAATACACTAATTG
Left flanking sequence: Indices 246327 -- 246826
TTGGCATCAATCCATCCAAAACAAAATGAGAGCCAGCTACCCGCATGCAGAGGATTTTCCATTTG
GTTCCCCGTTCTCTCACCAATGAGTACCTACTTAATACCACCCCCGCCTTTTGAACACTTGTTGG
GAATATCAACTAGTGAATACTTGGGAATACCACTCCCTACTTGGTGCTTACCCATGTACGGACTG
TACACACCGATTTCCATATTCCGATGGATTAGATATTCACACTGATAGATTCTATTCATACTAAC
TGGGGGTATATTCATATAACTACTGACTACCTACCCACCATTGAACACTTGTTTGGAATACCCGC
CAGTGCTGCACTTCAATTCCTACTCTTTCTCACTCCCCTGTGAATGGGGTGAATACTCACTACCA
CCCACTCAATACCCTACCCCTAGGAATACCGTTTGCTAACCACAGTTTGTTTGGTTTGCTTACCA
CCGTTCTCTTCGCACTGATTGATTGTATACACTGTTTGAATATAT
Right flanking sequence: Indices 246861 -- 247360
ATTGGGAAATTCATTCACATTGATACTAGTTTCTGCTCTAGTTCGGCTTTCTGCTCGTTGATTTG
GTCTATTCGATCCAGCTTCTTCTTTTTCCGTGGAGAAGTCAGAAGCTCATTTTGGTTGAAGCTGG
TGCAACGACTCGGGGAGAGCGGAGGAGTGGGCGGTCGTCATCAGTCCTTAAGACAAGTCTTGACC
AGGGAAGAGAGGTGTTTCATCCGAGTTCAATTCTTCATTGTCATAAGACAAGGTACACCATGTTC
GAAGACAGGATATGGAGAACGGAGATTTGAGATAGGCTTACACTTCTTTTTCTATTGGTATAACC
AACTACTAAGTTTTGCCCGCTTGAGTCTTCCAATTGGTATAACCTAAATGAGCATTCTTGCTGAG
ATCAAACGGACACTTATAACCAGAGTCAAGAAGCCCTATTCGTTTCACTAAAAATCTATTTTTGG
GGCTTGGGATACCATAAAATCTTTTAGTGATATTCTTTATCCGCG
Found at i:246863 original size:21 final size:21
Alignment explanation
Indices: 246807--246864 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 21
246797 TGATTGATTG
**
246807 TATACACTGTTTGAATAT-ATA
1 TATACACTAATTGAAT-TGATA
246828 TATA-A-TACATT-AATTGATA
1 TATACACTA-ATTGAATTGATA
246847 TATACACTAATTGAATTG
1 TATACACTAATTGAATTG
246865 GGAAATTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
18 1 0.03
19 11 0.37
20 7 0.23
21 11 0.37
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (21 bp):
TATACACTAATTGAATTGATA
Left flanking sequence: Indices 246307 -- 246806
GAGGTCACGGCATCGCGAACTTGGCATCAATCCATCCAAAACAAAATGAGAGCCAGCTACCCGCA
TGCAGAGGATTTTCCATTTGGTTCCCCGTTCTCTCACCAATGAGTACCTACTTAATACCACCCCC
GCCTTTTGAACACTTGTTGGGAATATCAACTAGTGAATACTTGGGAATACCACTCCCTACTTGGT
GCTTACCCATGTACGGACTGTACACACCGATTTCCATATTCCGATGGATTAGATATTCACACTGA
TAGATTCTATTCATACTAACTGGGGGTATATTCATATAACTACTGACTACCTACCCACCATTGAA
CACTTGTTTGGAATACCCGCCAGTGCTGCACTTCAATTCCTACTCTTTCTCACTCCCCTGTGAAT
GGGGTGAATACTCACTACCACCCACTCAATACCCTACCCCTAGGAATACCGTTTGCTAACCACAG
TTTGTTTGGTTTGCTTACCACCGTTCTCTTCGCACTGATTGATTG
Right flanking sequence: Indices 246865 -- 247364
GGAAATTCATTCACATTGATACTAGTTTCTGCTCTAGTTCGGCTTTCTGCTCGTTGATTTGGTCT
ATTCGATCCAGCTTCTTCTTTTTCCGTGGAGAAGTCAGAAGCTCATTTTGGTTGAAGCTGGTGCA
ACGACTCGGGGAGAGCGGAGGAGTGGGCGGTCGTCATCAGTCCTTAAGACAAGTCTTGACCAGGG
AAGAGAGGTGTTTCATCCGAGTTCAATTCTTCATTGTCATAAGACAAGGTACACCATGTTCGAAG
ACAGGATATGGAGAACGGAGATTTGAGATAGGCTTACACTTCTTTTTCTATTGGTATAACCAACT
ACTAAGTTTTGCCCGCTTGAGTCTTCCAATTGGTATAACCTAAATGAGCATTCTTGCTGAGATCA
AACGGACACTTATAACCAGAGTCAAGAAGCCCTATTCGTTTCACTAAAAATCTATTTTTGGGGCT
TGGGATACCATAAAATCTTTTAGTGATATTCTTTATCCGCGTTCT
Found at i:342417 original size:14 final size:14
Alignment explanation
Indices: 342398--342426 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
342388 CACACCGGAA
342398 TTTAGGAATACTTT
1 TTTAGGAATACTTT
342412 TTTAGGAATACTTT
1 TTTAGGAATACTTT
342426 T
1 T
342427 CATTGTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.52
Consensus pattern (14 bp):
TTTAGGAATACTTT
Left flanking sequence: Indices 341898 -- 342397
AAACTAGAATTGGCACAATATCGAGAAGTAGCCGCCTTTGCTCAATTTGGCTCAGACCTTGATGC
TGCCACTCAGGCCTTACTCAATAGAGGAGCAAGGCTAACAGAAATACTCAAACAGCCACAATATA
CACCATTGCCAATTGAAAAGCAGATTCTAGTCATTTACGCGGCGGTCAATGGATTCTGCGATCGA
ATGCCATTAGACAAGATTGCTCAATATGAAAAAAGACTTCTATCTACTGTCAAAGCAGACTTACT
AGAAGACTTAAAAGAGCCCTTAACAAAAGAAAAAAAAAGAGAATTAGATACATTCTTAAAAGAAG
CAGAGAAAGGAATATGAATATGAAAAAACTTTCTCCTTCTTATAAGGAACAGGCTTCCAAGTGGG
GGGCCCGAGTGCAACCTCACTCTACTGTCTCTCGCATTGTTTTGGCTTTTACCTCCCTATATCTA
CTTGCATATCTACGATCTACAACCACTCTCCTTTCCACACCGGAA
Right flanking sequence: Indices 342427 -- 342926
CATTGTTATTTTCATTTTGATTTTTGTTTATCGAATTCGACTTTCGAAAGGAAAAAAGAACAAAT
TTCTGATCATGCTCATTCTTCTTCTCATTTTCTTAGAATGTTCACTCTTTCGCACCTTCCTTTTT
GAAAGTCTTTTCGCTTTCTTAGGAGTGCCCTTATCCACTTTCATTTTGAAGGTTTCTTCCGGATC
GAATGAAAGTGGAAATTCCGGCGGGGAAAGAAGTGTGCCGGCTTTGGAGTCTTCCTCAAGCAGTG
AATCACTGGCTACGTTTAGAGGAGTCATAGCTGCCGGGAACGAGGCGGAGATTTATGAAAGGATC
AGAAATCTAGAAACCCGAGATTTCTACAACCTTCCACCCCAAAATCAGCCGGGAGAGTACGAAGG
AATTGTTCGAGAACACTTCGATAAAGCTCTCAATGTTCCGCATTTTAGATATATCATGGATACGG
AATATTTTGAGCTCACGGTATTGGAACGAAAGGGTGTTTTACAGG
Done.