Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_057654
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: 354155
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:124831 original size:17 final size:19
Alignment explanation
Indices: 124795--124832 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
124785 TTAAAAGCGA
124795 ATCTTTTTATTTATATTAT
1 ATCTTTTTATTTATATTAT
124814 ATCTTTTT-TTTA-ATTAT
1 ATCTTTTTATTTATATTAT
124831 AT
1 AT
124833 TATAGACCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
ATCTTTTTATTTATATTAT
Left flanking sequence: Indices 124295 -- 124794
AATATATTCTCTTTTAATCTTGCTCCAATCTGACCTAGCTGGCGAGCAATCCCAGTTCGCGACAG
AGAACAAGACAGCAAGCGAGCGTACCTTTGTTCGCTTCTTCTCCACCAAGCACGGAAGTTTAAGG
ATAACTGTAGGTCGGTGGTTACCTAAGGAAACTCCGATTCGATCCGCCCCCCGGCCGGGAGGCAT
CTATCTCATCCCGATCACAAGGAGAGGTTCACTATGATGGGGGGTACTTTTTTTTTCCCTTTCGG
AAAAAATGAAATGCATAGGGGACCATCCTTTTGTTGCGGCATGCTCCTCAGATTTACGGATTCGA
AGGGGGCCTCAGGCCCTACTTAGTTGACTGACAATGACAAAGGCTTGCGAAACCTAAGTAGGGCC
TTTTCCTTTTTGTTTGAATAACCCATTCTCATTATCTTTCATAAGTCAAAGTAGGCAAACCTATA
GGTCCTTAGTAGCGTTGACAAAGAAGAAAAGCCGGTTAAAAGCGA
Right flanking sequence: Indices 124833 -- 125332
TATAGACCAGCTTGACAAGCAACCCTTCCTCTTGATCTGAGGTGCGAAGAGAAAGATCTCTTTTT
TATGACTTCCCCGGCCCAGAAAAGTGACCGACCAGGGCCCTATTGATGAATGAAAGAAAGGGTTT
ATGAGCCCTAGCCCTGTAAGCCCACACCTGTGTAGAGTATATCGTTCAACACCTGCGGCACAAAC
CCATTTTGGACCTATTGATCCTAGTATCATAGGCGACCGAACGGCCGCCCCCTAATTACTAGACC
AACCTGCTATAATAATTCCATAAACACCTAGCGAAGATATGGCAAACAAATAAAGTAGCCCTATG
TTCGGATCTGACAATACCATACCATAATCAAAAGGTACAACGGCCCAAGCGACCAGACTTAACAT
AAATGTAGTCACTGGAGCCATTCTAAAAAGGGAGAAATTAGCACTACTTGGTGAAATAGGTTCTT
TTAGAATCAATTTCAAACCATCTGCTAGAGGTTGTAACAATCCAA
Found at i:129199 original size:28 final size:29
Alignment explanation
Indices: 129145--129214 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
129135 GACACGAATG
* * *
129145 ATATACTATATTATTAATTATATAAATTAT
1 ATATA-TATTTTATTAATAATATAAATAAT
*
129175 TTAT-TATTTTATTATATAATA-AAATAAT
1 ATATATATTTTATTA-ATAATATAAATAAT
129203 ATATATATTTTA
1 ATATATATTTTA
129215 ATGCACTAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
28 18 0.55
29 12 0.36
30 3 0.09
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
ATATATATTTTATTAATAATATAAATAAT
Left flanking sequence: Indices 128645 -- 129144
GACTACGAACACAAACAAGAGGTTTGAAGACGCTCGACCAAGGGGAGAGGAAGGGAAGGTTTGTG
TATGTGCTCCCAAGAAACATATGGTACTCTATTCCATGTAATGGATCGGGTCGAAAAACCAGACC
GAGTCTCTCTTGGAATCCTGAATATGGCAATAATTGTACTAATCAACATATGTCTCTCTCCCGGT
ACTAGTTGAAGTAATGAAAATTCCCCTATTTGTTTGATGAGAAATGCGAGGATAGAAAAAAAAGA
TCCCCCGTTGGGAATGAAATTCTGCTTTCTGTCCCCCTTTTCACAGAAAATGGAGAGATGAATTG
ATGTATTTATTGAATCCGTCGGGACTGACGGGGCTCGAACCCGCAGCTTCCGCCTTGACAGGGCG
GTGCTCTGACCGATTGAACTACAATCCCAGGTATACAGCCTAAAAATTCTTCTTTTTTTCTATTC
ATTCGAACCATTTAGTTTCGCCGTGTTGTAACAGAGACACGAATG
Right flanking sequence: Indices 129215 -- 129714
ATGCACTAGACTCATAGTGGGCTAATTCATGAATTGAATCATGACTATATAAGCTATTCTGATAT
TAAGAGATTCAATATAGATGAGTGGAAGCGGACCTTTGATTTCCTTGGACCACGCAAGAATTCGT
CGTCCGATTGAATCTGCTTGTTCCTTGTTCCTGGATGCTCTATAGGAATCCATGGTTATTCCTTT
CCAAAGGTTCATTCCGAGTCACAAGAGCAATCTCTTTTTTTTTAATGATTTTTTTTCTTTTTGTT
ATGGTAATGCAATGCAAGAGGTCGGAAATCAGGTTCTTTCTGATGATGAAAAGAGCTTTTATCTT
ATTATGAAAACCCGAAATGTCGGTAATGTTAGAAGACGACTGTCGGTATCTGATGGTCAGATACC
TATGGTCGGTATATCTTTGAAAGCTCAGACGGAGAGAATAAACGGACTCCTCGAGGGCTACTTAA
GCCACTTTAGTGCAAACCAGAAGGACTGGAGTTGTTGGATGTTGC
Found at i:265585 original size:24 final size:24
Alignment explanation
Indices: 265553--265599 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
265543 CCATTTCTTC
* *
265553 GGAATTGTCCGCTCATAGCACGAT
1 GGAAGTGTCCGATCATAGCACGAT
*
265577 GGAAGTGTCCGATTATAGCACGA
1 GGAAGTGTCCGATCATAGCACGA
265600 CGCGCTGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (24 bp):
GGAAGTGTCCGATCATAGCACGAT
Left flanking sequence: Indices 265053 -- 265552
GTGCGGTTAAGGTTGTTGTACACGACCTCATAAGAAAATAATGAAAAAAAGGGCAAAAAAAATAA
AAAATCAAACTCCTATCACGGGTTTTCTCAAATTCCTTGAGAAACTTATTGAATTTCTGAAACAG
TTTTAATAATGCTATACTTCAATTAAAGATCGAGTCAAGGGTCGATGGTTTTGAGCTCGACCAAC
GGGAGAGGAAGGGGGTTAGCACTTGGATTTCATCTTTCATAAATCCCCTATCCTTCTTTTTATCC
ACTTAGGTTATGACCATTGAACAAACTTGGTTGACGAAGATGGTTTATGCGCCGCTAATGTAGCT
GCTTGTCGAGCATTTGACAAAGTCACACCATCCATTTCAAATAGGATTTGTCCCGTGGACACACA
AGCAACCCAACCCGTAGGATTTCCTTTTCCTCTTCCCATTCTTACTTCTGTAGGTTTCCCGGTAA
TAGGGAGATCTGCGAGAACTCTTACCCATATCTTACCATTTCTTC
Right flanking sequence: Indices 265600 -- 266099
CGCGCTGCTTCAATGGCTCGATATGAAAGACGACCAGCTCTACAACTTTTAGTGCCATATCTTCC
AAAACCAAGTTGTGTACCGTCCGGTTTGCAACGCCTACTACATCTGCCTTTACGATATTTACTAT
ATTTCGTACGTTTCGGATATAGCACGCCCCCCTTTTTTTTTACTATATGAAATCCACACTTTGAC
ACCTGAGATTCCGTAACGAGTAGATACTTCCGCAGGAGCATAATCGATTTTCTGGTTAAATACAT
TACGAGATGTTTTTCCATACTTTCCGCATTCAGTTCTAGCTATTTCTGCACCTTCTAATCGACCT
GAACAACATATACGGACCCCCTCCACCCCCTTTTTCATTACTAATGGAATATCCTTCACTATTTT
ACTAAAAATGGAACGAAATGATCTTGTTTTGTTCTTCGGTTGAAAAGAGATGTCTTGAGCAATCG
GAGAAGCACTTTGATAAACAGATTTGATCTTGACCGATTCAATTA
Done.