Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_023209
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: 499236
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:21082 original size:16 final size:16
Alignment explanation
Indices: 21035--21082 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
21025 ACTGTAGTAT
*
21035 GCATTACTGTGGATATA
1 GCATTACTGT-GATAAA
*
21052 GC-TTGACTGTAATAAA
1 GCATT-ACTGTGATAAA
21068 GCATTACTGTGATAA
1 GCATTACTGTGATAA
21083 TGATAATCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (16 bp):
GCATTACTGTGATAAA
Left flanking sequence: Indices 20535 -- 21034
TGCTCTTCCAATGAAGGAAGACCTGTATTGTAGTAAGTAGTCAATTGCCTTGGTTTTTCCAAGCA
AGGAAGGCGACACGACTATCATAATTTGGCTTCGGGCTCCGCTGTTGACTCCATGGACACTCGAC
TTCTTTTCTTTAGAAGGCATAAGCGCTAGGCGTGTGGGCGACAGCGACTCGCTTACGAATGATAG
ACTTTGAAGAATTGCATCTCTCGCGAGATTTCGAGATGATGGTGAATTCTCGTATGAGCTTTAGA
TTGGTGGTAAGAGCTTCCTGACACAGGCAACAGAGGCGAAATCATTCCGGGAAAAGAAAAGCTAT
TACTGAAACCACTCCTGCGTGATATGTTTATCTGCAAAAGCGAAATTCGTAGCATTATTCCATTA
CAAATCTGTATTTAGTTCTTGTATGATATTATACCATGGTTTGAGTTCTTTCTTACCATTGTATC
TTATTTTCTGGGATTCTTAAACTTAAGAATGAAAAACTGTAGTAT
Right flanking sequence: Indices 21083 -- 21582
TGATAATCCATGGATCGCAACAGATTCTATTTGTAGAAAGTGATCGGCTTGAAAGGATACTTTTA
AAGGATTGAGCCGAGTTTAATTGCAATTCAATTAAGAGAACGGAGAGTAATTACTTTTCATTTTC
CTTATTTTTATTTATCCAAAGTATCCACTGCTTTAAACTCAAATTTGATTTCTTTCCATACCTCA
CAAGCGGCAGCTAGTTCAGGACTCCATTTGCAAGCTTCACGGATAATTGCATTACCCTCAGCAGC
AAGATCGCGTCCTTCATTACGAGCTTGTACACACGCTTCTACAGCTACTCGGTTAGCTACAGCAC
CTGGCGCATTACCCCAAGGGTGTCCTAAAGTTCCTCCACCGAACTGTAGTACGGAATCGTCTCCA
AAGATCTCGGTCAGAGCAGGCATATGCCAAACGTGAATACCCCCTGAAGCCACGGGAATAACACC
GGGCAGGGAGACCCAATCTTGAGTGAAATAAATACCGCGACTTCG
Found at i:147810 original size:24 final size:22
Alignment explanation
Indices: 147782--147836 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
147772 ACAAAAAAGA
*
147782 TTTGTCTAAGCCACTTCGTTTCTT
1 TTTGTCCAAGCCACTTC-TTT-TT
*
147806 TTTGTCCAAGTCACTTC-TTTT
1 TTTGTCCAAGCCACTTCTTTTT
147827 TTTGTCCAAG
1 TTTGTCCAAG
147837 TTGCTTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.41
22 2 0.07
24 15 0.52
ACGTcount: A:0.15, C:0.24, G:0.13, T:0.49
Consensus pattern (22 bp):
TTTGTCCAAGCCACTTCTTTTT
Left flanking sequence: Indices 147282 -- 147781
GGGAATGATTTGGAAGATCCAAAACCAAAAATAGTGGTATTTGCTAGCAACAACATAATGGAGGC
AGTCAATCAATATAGATTGATCCGAAATCTGATTCAAATCCAATATAGTACCTATGGGTACATAA
GAAATGTATTGAATCAATTCTTTTTAATGAATCGATCCGATCGCAACTTCGAATATGGAATTCAA
AGGGATCAAATAGGAAAGGATACTCTGAATCATAGAACTATAATGAAATATATGATCAACCAACA
TTTATCAAATTTGAAAAAGAGTCAGAAGAAACGGTTCGATCCTCTTATCTTGATTTCTCGAACCG
ACGAGAGATTCATGAATCGGGATCCTGATGCATATAGATACAAATGGTCCAATGGGAGCAAGAAT
TTCCAGGAACATTTCGTTTCTGAGCAGAAGAGCCATTTTCAAATAGTGTTCGATCAATTATGTAT
TAATCAATATTCGATTGATTGGTCTGAGGTTATCGACAAAAAAGA
Right flanking sequence: Indices 147837 -- 148336
TTGCTTTTCTTTTTGTCGAACTCACTTCCTTTTTTCTGTGTGAGTTTCGGGAATATCCCCATTCA
TGGGTCCGAGATCTACATCTATGAATTGAAAGGTCCGAATGATCAACTCTGCAATCAGTTGTTAG
AATCAATAGGTCTTCAAATTGTTCATTTGAAAAAATGGAAACCCTTCTTATTGGATGATCATGAT
ACTTCCCAAAAATGGAAATTCTTGATCAATGGAGGAACGCCCTTTTTGTTCAATAAGATACCAAA
GTGGATGATTGACTCATTCCATACTAGAAATAATCGCAGGAAATCCTTTGATAACGCGGATTCCT
ATTTCTCAATGATATTCCACAATCAAGACAATTGGCTGAATCCCGTGAAACCATTCCATAGAAGT
TCATTGATATCTTCTTTTTATAAAGCAAATCGACTTCGATTCTTGAATAATCCACATCACTTCTG
CTTCTACTGTAACACAAGATTCCCCTTTTCTGTGGAAAAGGCCCG
Found at i:147850 original size:23 final size:21
Alignment explanation
Indices: 147804--147871 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
147794 ACTTCGTTTC
147804 TTTTTGTCCAAGTCACTTCTT
1 TTTTTGTCCAAGTCACTTCTT
**
147825 TTTTTGTCCAAGTTGCTT-TT
1 TTTTTGTCCAAGTCACTTCTT
* * *
147845 CTTTTTGTCGAACTCACTTCCT
1 -TTTTTGTCCAAGTCACTTCTT
147867 TTTTT
1 TTTTT
147872 CTGTGTGAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.05
21 35 0.92
22 1 0.03
ACGTcount: A:0.12, C:0.22, G:0.10, T:0.56
Consensus pattern (21 bp):
TTTTTGTCCAAGTCACTTCTT
Left flanking sequence: Indices 147304 -- 147803
AACCAAAAATAGTGGTATTTGCTAGCAACAACATAATGGAGGCAGTCAATCAATATAGATTGATC
CGAAATCTGATTCAAATCCAATATAGTACCTATGGGTACATAAGAAATGTATTGAATCAATTCTT
TTTAATGAATCGATCCGATCGCAACTTCGAATATGGAATTCAAAGGGATCAAATAGGAAAGGATA
CTCTGAATCATAGAACTATAATGAAATATATGATCAACCAACATTTATCAAATTTGAAAAAGAGT
CAGAAGAAACGGTTCGATCCTCTTATCTTGATTTCTCGAACCGACGAGAGATTCATGAATCGGGA
TCCTGATGCATATAGATACAAATGGTCCAATGGGAGCAAGAATTTCCAGGAACATTTCGTTTCTG
AGCAGAAGAGCCATTTTCAAATAGTGTTCGATCAATTATGTATTAATCAATATTCGATTGATTGG
TCTGAGGTTATCGACAAAAAAGATTTGTCTAAGCCACTTCGTTTC
Right flanking sequence: Indices 147872 -- 148371
CTGTGTGAGTTTCGGGAATATCCCCATTCATGGGTCCGAGATCTACATCTATGAATTGAAAGGTC
CGAATGATCAACTCTGCAATCAGTTGTTAGAATCAATAGGTCTTCAAATTGTTCATTTGAAAAAA
TGGAAACCCTTCTTATTGGATGATCATGATACTTCCCAAAAATGGAAATTCTTGATCAATGGAGG
AACGCCCTTTTTGTTCAATAAGATACCAAAGTGGATGATTGACTCATTCCATACTAGAAATAATC
GCAGGAAATCCTTTGATAACGCGGATTCCTATTTCTCAATGATATTCCACAATCAAGACAATTGG
CTGAATCCCGTGAAACCATTCCATAGAAGTTCATTGATATCTTCTTTTTATAAAGCAAATCGACT
TCGATTCTTGAATAATCCACATCACTTCTGCTTCTACTGTAACACAAGATTCCCCTTTTCTGTGG
AAAAGGCCCGTATCAATAATTATGATTTTACGTATGGACAATTCC
Found at i:150240 original size:18 final size:18
Alignment explanation
Indices: 150188--150242 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
150178 AAGGTTTTCT
* * *
150188 TATTGATGATTGTGACAA
1 TATTGATGCTAGTGACGA
150206 TATTGATGCTAGTGACGA
1 TATTGATGCTAGTGACGA
150224 TATTGATGCTAGTGACGA
1 TATTGATGCTAGTGACGA
150242 T
1 T
150243 GTCGATCGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.29, C:0.09, G:0.25, T:0.36
Consensus pattern (18 bp):
TATTGATGCTAGTGACGA
Left flanking sequence: Indices 149688 -- 150187
GTCGCGAACAGTGATTCGATTGATGATGAAGAAAGAGAATTCTTGGTTCAGTTCTCCGCCTTAAC
GACAGAAAAAAGGATTGATCAAATTCTATTGAGTCTGACTCATAGTGATCATTTATCAAAGAATG
ACTCTGGTTATCAAATGATTGAACAACCGGGAGCAATTTACTTACGATACTTAGTTGACATTCAT
AAAAAGTATCTATTGAATTATGAGTTCAATACATCCTCTTTAGCAGAAAGACGGGTATTCCTTGC
TCATTATCAGACAATCACTTATTCACAAACTTCGTGTGGGACTAATACTTTGCATTTCCCATCTC
ATGGAAAACCCTTTTCGCTCCGCTTAGCCTTATCCCCCTCTAAGGGGATTTTAGTGATAGGTTCT
ATAGGAACTGGACGATCCTATTTGGTCAAATACCTAGCGACAAACTCCTATGTTCCTTTCATTAC
GGTATTTTTGAACAAGTTCCTGGATAACAAGCCTAAAGGTTTTCT
Right flanking sequence: Indices 150243 -- 150742
GTCGATCGTGACCTTGATACGGAGCTGGAACTGCTAACTATGATGAATGCGCTAACTATGGATAT
GATGCCGGAAATAGACCGATTTTATATCATCCTTCAATTCGAATTGGCAAAAGCAATGTCTCCCT
GCATAATATGGATTCCAAACATTCATGATCTGGATGTGAATGAGTCGAATTACTTATCCCTCGGT
CTATTAGCGAACCATCTCTCTGAAAGATGTTCCACTAGAAATATTCTTGTTATTGCTTCGACTCA
TATTCCCCAAAAAGTGGATCCCGCTCTAATAGCTCCGAATAAATTAAATACGTGCATTAAGATAC
GAAGGCTTCTTATTCCACAACAACGAAAGCACTTTTTCACTCTTTCATATACTAGGGGATTTCAC
TTGGAAAAGAAAATGTTCCATACTAACGGATTCGGGTCCATAACCATGGGTTCCAATGCAAGAGA
TCTTGTAGCACTTACCAATGAGGCCCTATCGATTAGTATTACACA
Found at i:172627 original size:15 final size:17
Alignment explanation
Indices: 172593--172632 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
172583 GAGTAGGTAG
172593 TTCTATTCTTTTGATTT
1 TTCTATTCTTTTGATTT
*
172610 TTCTATTC-TTT-CTTT
1 TTCTATTCTTTTGATTT
172625 TTCTATTC
1 TTCTATTC
172633 ATAGTAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.50
16 3 0.14
17 8 0.36
ACGTcount: A:0.10, C:0.17, G:0.03, T:0.70
Consensus pattern (17 bp):
TTCTATTCTTTTGATTT
Left flanking sequence: Indices 172093 -- 172592
TCCCGAGAGAGGCCGCCTTCTCTCAGGCCAGCAGTCTTCGACTTCTAGTCGACTGCTTTATGACG
GGCTTCCCTGTTTCCTGGGCTCTGCTCGCTTCGTCTACGCTCCGACCCTAATATAATAATTGAAA
AACGAGATTTCCTTGCCCTGCATTAAGATTTAAAACTTGTGGTCAAAAACAAAAAAAGGCAATCA
ATCGAAAAAAAATGGAAATAGTGATTCAAGGTCTAGATGGATCCCTATCTTTATCTCTATCCACG
AAGATACCTGGATAGAGATCTATCTATGAATAGATCTAGACTATCCTCTATCCGGATAGATATGT
CCCTTATGAGCGACTACGCCGATCTTTATATGTTTTGGCCACGTTCGTTTCCGCTCCGAAGAAGA
AGGTTTGGATCTTTCAATCTTATGTCATGAGGGATGTGACCTATGTTAGGTCCATAAGATACCAC
AGCTTTTGGTGTTCTATGATTCACCTCCGAATAATGAGTAGGTAG
Right flanking sequence: Indices 172633 -- 173132
ATAGTAAACTGATGGGGGGATGCGGAGCAATAGGTCGAATTACTATATAAAGAAGAGTTGTAAAC
TATAGGATTTCTTGTTTGAGTAGGAATATTCATATTTCGGTTTTTCTCGTTCCTTCTCTTCGATA
AGAATAGGGATTTGAAATGATACAAATTCCTCTTCATTCTGTTGTGCTCATCGAAATAACTGCCT
AAGCATACTTTTTTGGATCCAAACTTCTTTGTGTCTTCTTCTTGCATAGAAGAACGCAACTGTTG
CAAAAACTTGGATTTTAGTAGTAGGCGGCATTCCTTCTTAGTTTTGAGTTTTCGGAACCATTTTG
TTTTGGTTCTTCTCCACATTCTGACCGGGCGATCCAGAAATTTTCCTATGAATTTTTCAACTGAT
ATTTCGATATAGAAAGATCTCCTTATTTCTTCACCGCGGGTTCTCGCATCATTTTCTTGAAAAGA
TATTATATCACCGTGGGACACTTTAAAATGAATAATGTTTACCAT
Found at i:295056 original size:21 final size:22
Alignment explanation
Indices: 295019--295071 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
295009 GCCGCTTGCT
295019 TAAAT-TATATTATTATTATATA
1 TAAATATA-ATTATTATTATATA
295041 TAAATATAATTA-TATTATATA
1 TAAATATAATTATTATTATATA
*
295062 TATATATAAT
1 TAAATATAAT
295072 AATAGACATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 18 0.62
22 9 0.31
23 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAAATATAATTATTATTATATA
Left flanking sequence: Indices 294519 -- 295018
GTCTGCCACCAAAACTTGGCTGAACTATCAAGAAACATGGCAGCCGTATTCACCGACGCCTCCTC
GGACGTAGTCCGACAAGCCGCTCCATATCCCAAAAGTGAGTTTTCGACCCTTAGCATCTCGGGTG
CCAACGAATGCCTTTGGTTTCGCTTGATTCGAACCTCCGTCGAGCCTCTTCGATGGCACTAGCCT
ACGGGTTCTTTCCACTAGCCATGGCTTGGCCCAACCTTTGGCTCTGATACCACTTGTCACGGCGC
TAAGTCCTTTGTGGGCTTCTATGTTTTTCTTTCGAACTCCTTATTTATATGTACTTTTTCTGACT
TCATCCATACTTTTTTACTTTCTTTTAAATAAAATTGTGTTCAAAAACAAAAAACCCTCTACTTC
TAACTAAATAACTAAAGGCGAACAGCCGTCATTGCAAGCAAATAGAGAGCCCCCGCCCGTTTGAG
CCGTTGCGAGCCGGAAAGCGGTGAGTCGCGAAAGGGCCGCTTGCT
Right flanking sequence: Indices 295072 -- 295571
AATAGACATATAATATTCTATATATATCTATAAACAATAATAAAATAGAGAAATCATTTTTTTAT
CCAATTGTTCATTCCTGAGAAGAGAAAGAAGCAGATAAAGCAAAGGCCTCCTCTTTCCATCCGCT
CTTCCCTAAGTGAGCGAATTGCATGTAGAGATCCGTAAGGGCTTATAGTTTAATTGGTTGAAACG
TACCGCTCATAACGGTGATATTGTAGGTTCGAGCCCTACTAAGCCTACCACCCCCCTCTCTTCAC
CTGATACAAGGCAGTCAAAGTACCCGCCGCCCTTTCGATCTAGTCCCACCAAGTCGAAGCTAAAA
AGCAAGTCTTATTAAAGAAAGATCTGGGGCCGTTGGTACGTACGGATAGTGGTCACTACTACGAT
GGATCAAGCAGACCGGACCCGCGGAGGTGACTCGGTGAAGTTTTGAAAAAGATATGACAACGTCC
CGTGGCGATAATCTTATTTATGCCAACCGCCCTTAGTGGGTTAGT
Found at i:371167 original size:16 final size:16
Alignment explanation
Indices: 371146--371177 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
371136 AAACAAGTAG
371146 TTAGCTTATCCGAATC
1 TTAGCTTATCCGAATC
*
371162 TTAGCTTATCGGAATC
1 TTAGCTTATCCGAATC
371178 AAAGTCACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (16 bp):
TTAGCTTATCCGAATC
Left flanking sequence: Indices 370646 -- 371145
AAAAAAGCGGGATGCTATATTTCCAAGATTGGATTTCATATTCGAATAAACCTCGTAATCGCAAG
AAAGTAGGTTTTTTCGTTATGGGCCTAGCAAAAGAAAAATTAGGATAGGATCTCCCCCTTTCAAA
ATCGGACGTGAAAGTTTCCTTTCATCCGGCTCAAGTAGATACACCAACTAAATAAAGGAGTTCTC
GCTTTCAAATTCTAGAAAACCCCAAAACAAAAAGATCTACTCCTTACTCAAGTTCCCAGTGAAGA
CCAAGCAAGATTTCATCGATTCCGCCTTCTTTTTATTTATTAATATTATTAAGATTTTCTTAATT
CTCAATTACGACATAAATGAAATGTGAAATTCTTGAGTAGTCTACTTCCCTTCGAATGAGAAATC
CCTTAATTCTTAATTAGAATTAAAAAATGAAATTAAAGAATACCTTTGAATTCCAATTCAATCAA
GTAGAGTGCACTAAGTTCCATTTTTTATTTGTAGCAAACAAGTAG
Right flanking sequence: Indices 371178 -- 371677
AAAGTCACTAAAAAGGGAGTTTTCTTTGGCGACCTAAGATTAAGATCTAATTGTAGAAAAAATCA
AAAGTTGCGGATAACGCTTTCTTTATTAAAATCGAAGACAAGAACAAAACACAAAGAAACGAAGA
AAAATCAAATGGATTATCATATGTATCTTTCATGTAGACAGATGAATAAGTCCATTTATTTAGTT
CTACATTCCTTGGACTTTTTACTTATTCTATATACTCACTTAGATACTAATATCTCTAATGAAAA
ATTTTCAAATTAATTCAATTTGAATCAAACTTTCCTTCCAAGTTCTTATCAAAAATTTACGAAAT
CAAATGAAAGGGATTCAATTCCACGTCTTAACTTAAATGAAATGAGCGCACGATAATTATAATCG
GAAATTTTCTAAGAGATAGATAGTATGGTAGAAAAAAAAAGAATTAAGAAAAACTCATGGTAACT
ATTTAAGCCGACTCATAGCATTACATTAAAGTAGTCAACATTTTT
Done.