Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_069194
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: 420362
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:32074 original size:25 final size:25
Alignment explanation
Indices: 32043--32091 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
32033 CAACTTTAGT
32043 ACTTTAGAGTTGGTTTAACACTAAG
1 ACTTTAGAGTTGGTTTAACACTAAG
32068 ACTTTAGAGTTGGTTTAACACTAA
1 ACTTTAGAGTTGGTTTAACACTAA
32092 TAAGGATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAGAGTTGGTTTAACACTAAG
Left flanking sequence: Indices 31543 -- 32042
CTGAGAGCAGAGGGCTGGTAGCAACGGGAAGGGTGACTGAGAACCTTATTCCCGATGTGCCTTGA
TCATACTACTATACCAGTCCAACTAACCGATAAGCCTTATGAGTGATCGCTCGTGCATTAGTATT
AGTAAGAGTAAGGGGGAAGGCAAGACTGATTTTCTTTAATAGCTATGAGTGGTGGGTTTCTAGTC
CCTCTAACGCTTTCGTTATGGGGTCTATTTTCTCTGACTTGACTCAGCTTGACCTACTTGACTCA
GCGGTTAGAGTCTCGCTTTCATACGGCGAGAGTCATTGGTTCAAATCCAATAGTAGGTAAAAGGC
TCTATGACTTCCTTTTGCTAGCATGACAGCAAGGACTAAGCTAATTAGAAAGACCGGAAAGAGCT
CATCGTAAGGAGGAAACTACGTAACTCCTTCAAGGAAAAGAGCTCAGCTCATCTGTCCTCTACTC
GTACTGCAACAAGGGCAAAGCTACCTTAGAGTGGGCAACTTTAGT
Right flanking sequence: Indices 32092 -- 32591
TAAGGATAAGAGCGCCAAATTTCGAGCCCTTTCTTTTCAATAGGATCAAGGTGCTCTAAGATTGA
AGTTAGCATGCACTAGTATAGTAATCGATTGCTCTTTAGGAAAAAGATTAGAACAAGGCGGTCTC
ATAGCTTTCCTTATCAGCCTTCTTATGTTATGGGAGGCATGCCAACAATCTTTCGTGAAGACCGC
ATATTTAACGGTCGGTGCGAGTTTAGCGAAGCTAGGCTCATTTATGATCCGCTGATCAAATAGCA
TTAGGGGCACTTTCTCACTTTCCCAGAACTGCTACTTTCCTGCTTTTAGTACATTGCTTTTCGTA
TCATCTATGAGAATTCTCGTTTCAGAAACTCCTCAATATAGCCCTTCTTTGATAGGGATTGAGAT
CCAAATAAAGTTGAGGTAGTCCAAAACAAGCTATCGACATTGAGACTGTAACGCTTAACAAAAAC
GGGCATTGTGCGTTGTTTGCATTCGAATCGAAATCGGAGCTACTA
Found at i:97465 original size:20 final size:20
Alignment explanation
Indices: 97440--97479 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
97430 AAGAAAAGCC
97440 CTTTATTGTTCACAAAGAAA
1 CTTTATTGTTCACAAAGAAA
97460 CTTTATTGTTCACAAAGAAA
1 CTTTATTGTTCACAAAGAAA
97480 GAACAAAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (20 bp):
CTTTATTGTTCACAAAGAAA
Left flanking sequence: Indices 96940 -- 97439
ATACTGCTTGTAGCTTTCCTCTCTGATAATATAATAATAGTAGAGAATGATCTTTTTTGAATTTC
ATTATCCGGACAGTAGTTGAATTAGAGTGAAGCGGGTAATAAGACCTCGTGCTTTAGCGCGCTTT
CATGACATGCCATAGACCCGACATCCGCTGTAGATTCTCTCTTTCCGCTAGACTTCCTTGGAACT
ATTCCTCGGTTCATGGGAATTGGGAAAAGTGAGTTGTCAATTTCCCCGCTTCTTCATCTAAATGA
GTCCTTCGAATACGCTCGCTTAGTTGACTTTCCCATGAACCCCAGTATAATGGATTCCACCCAGT
CTTTTTCTTCCGAGTTCAATTCCCGAGGACAGAAGAGTCGTAATAGGAATTAGGTCTTCCCGACC
GAAAGACAGACCTTAGGGGATATACAACAAGAAAGACCACTCCCCTACCCAACACCTTTTTACCG
AATACCCCGCCTAACTCAAACTTGGACTTGGAAGCAAGAAAAGCC
Right flanking sequence: Indices 97480 -- 97979
GAACAAAGCTGCAGCTCTCTCTATTGAAGCTTCTAAATCCATCTCCTCAATTCTGCGCTTAAGTC
GCGATCTCTGAGCACAAGAAAGTATATGGTGCCCGAAATACCTGTTGTTGTTTAGTCAGCTTGAG
AAAAGAAAGTAACTCCAAATTTCTTTGGCTGCTGCTTACTGCTCAAATAAAAACTCACAGTAGGT
GACATAGGGATTCCTTGGTACCTTGGCATCTTCCCACAGGACTTATCCCCTGACAAGTGTCTTAT
CTTCCTGTTTTGATTAGTCATGACTCTGTCCTTGAGTGCTGTCCACATGAATGTTTTAACTCTGG
GTGCAACTTGAAGTTTCCAAAGCTTCGCATCTGTTTCAATAGAGGTACGAGAAAGGGTTGGGGGC
CTCTTCAGACTTAGTTATCAGTTCAAAAGCGGATTTGGTGGAAAACAGGGTATTAGATTTAAAAG
GGGAAAGAAAAGAATGCTAAAGTCAAGACTAGTGAGATTAGCTTG
Found at i:98326 original size:33 final size:33
Alignment explanation
Indices: 98284--98349 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
98274 TCTAATCTAT
98284 TATAACCTCTGTCCTTGCCCGCTATTAGACAGA
1 TATAACCTCTGTCCTTGCCCGCTATTAGACAGA
98317 TATAACCTCTGTCCTTGCCCGCTATTAGACAGA
1 TATAACCTCTGTCCTTGCCCGCTATTAGACAGA
98350 AAAGAAGAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.30
Consensus pattern (33 bp):
TATAACCTCTGTCCTTGCCCGCTATTAGACAGA
Left flanking sequence: Indices 97784 -- 98283
ACATGAATGTTTTAACTCTGGGTGCAACTTGAAGTTTCCAAAGCTTCGCATCTGTTTCAATAGAG
GTACGAGAAAGGGTTGGGGGCCTCTTCAGACTTAGTTATCAGTTCAAAAGCGGATTTGGTGGAAA
ACAGGGTATTAGATTTAAAAGGGGAAAGAAAAGAATGCTAAAGTCAAGACTAGTGAGATTAGCTT
GGTGTGCTGTCCTTCTATCTTCGGATTGATGGACAGATTCCCTTGGAGCAAAGGAGAGATAGTAC
TAGCAACTTCGAAAGAATGGGGAAGGCAAGGGCGGCTGATAGAGAGGGGGATCACGAGCTTGCTA
CGCTATGAGAAGAGAGCCCTAGGAGTTCTTCTCTTTACTGCATCTTTTCTTAAGAATTTATTTGA
TTTTAATACCAGTACTCAGAAGGACATAAACTACAGCAGATAAGCGCATCGGATATATAGGTTGC
AGCTGCCGCTCTTAGTCCTATAGCCTAGCAGAACATCTAATCTAT
Right flanking sequence: Indices 98350 -- 98849
AAAGAAGAGCTATACTATAACTATAATAGTAGCCGCAGAAATCCCAGTGGGCCAGTAACCCGAAT
CCAAAGGAGATAGATAGCTCACAAAGAGAGAAGTTAAAGCATTGCCTACATGAAATCAATTGATT
CGTCATGGTAGACGAGAAGAAAGGTGCAGTTGAGCTCTTTTCCGGCTTAGCGAAAGAAGGAGCTT
TCTTTTTTCCTAGGAGCTGTGAAAGATACTAAACTGGAAATGAAATACCATCAACAGTCTCATTT
ACAGAAAAATGGTACAATTCAACAACTCCATCTTCAATAGTTGCAGTTCTAGCTCTTCTTTCTTT
AGAACAGGTGAATCGTCTCAGCAGTTCGTGTAATAGTAGCAGTTGGAATTTTAGTTGTAGTAGCA
GTAGTAGATGCTGTAGCTGTTCTGTTGGAGTTGCAGAAGAGGTGATGAAATTGACTTTCTTCTTG
CTATAAAATAAAAAATACAATAACATTTTTTGAAAAGATTTTTGC
Found at i:229580 original size:25 final size:24
Alignment explanation
Indices: 229543--229592 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
229533 TTAATTCTTC
*
229543 AGAAAGAGAGAATTTTGTATCTAT
1 AGAAAGAGAGAATTTTATATCTAT
* *
229567 AGAACAGATAGAATTTTATTTCTAT
1 AGAA-AGAGAGAATTTTATATCTAT
229592 A
1 A
229593 AAGTAGATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (24 bp):
AGAAAGAGAGAATTTTATATCTAT
Left flanking sequence: Indices 229043 -- 229542
CTAGACCACGGAGAAAGCAGCGAAATAAAGGAAGTGCCCATATTCTATGGATCGAAGGCGGGTAA
GAAGGAAACATTGATGTATATATTCGCAGACCGATAGCGCCTACTTTGAATACATCCATAGTTGA
ATCCCAAAGAGAAGAAAGAGAAAGAATTGAGTTCCTAAGCTAATAAAGCCCTCTGATTGATCTAA
GGGCGTTAAGGTTCCAAAGTAAACTACAGGCATCGGGATGCTTCAATAGTTCCCTCATCAACGGA
GGCAGCGGATTAGCAGCAGCAGCAAAACAAAAGACGGTTGAATTGGTCTCGGGCTGACAGCCATC
TTAGTGAGGTAGTCTATTTCGTTGAAGTAGCGGGTCTCCCCCATCTGGTACTTCTCGTTCTAGTC
AACGAAGGAACAATCTTTCGAGGAAGAACCTTTTCTGTAGTTGGACTACCAGGATTCTTCAATAG
TAGTAGGTTCAGGTCTTGAAGAGCAAGAATGCATGTTAATTCTTC
Right flanking sequence: Indices 229593 -- 230092
AAGTAGATAAAGTAATTTTCTTTTTACTTCTTATTTGATATACTCTATGTCCTATTACCAAACTT
ATGTTGATCTATTTCTCTAAAGAGTTGATTCTTATACGCCGATAAAGAACGGTATTCTCGGCATA
AAGATGATAGAAAGATCTTTCATTTAGTAGCGATTCATGTAGGTGTTTTATTCGTATTCATAAAG
AGTCTATGAGCTTTGTAGATAAAGATGGGCATTCAAAAAGATATCCTAGGAGCTAATCAAGTGCT
TCTTTTCAGGCTGCGAAACTGGCTGGAGAACGGCCATACTTGACTTCTACTTTTTTTATACTGTC
ACAGGCACCTTAAGTATTTCCTTATTTCATAAAAGATAAAAAAAGAAAATGATCAATCTCCTATG
GTTAGCAAGCAATCTCGATGAATTGAACAAGTAAGAAAGATCTATTTTCACTGACGTGAAGGGAA
GCGCTCAAAGCGGAACCGGTACGACAAGTTCGCTTAGGGTGTTGT
Found at i:252517 original size:19 final size:21
Alignment explanation
Indices: 252493--252532 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
252483 ATATATATGA
252493 GGTTGAC-AT-CCCCCTACAG
1 GGTTGACGATACCCCCTACAG
252512 GGTTGACTGATACCCCCTACA
1 GGTTGAC-GATACCCCCTACA
252533 ATGCCTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.23
Consensus pattern (21 bp):
GGTTGACGATACCCCCTACAG
Left flanking sequence: Indices 251993 -- 252492
GTTGGCACAAGCCCTTGTAGTAGTCTCCTCCGGCCGGATGTTAGAGTCAATTCCATTGTTGGTTT
GACCATTAAGTGAATGCAAATATAGGTAGAATTTGAATCAACGACCTAAGAGTCTTCTTTTGCCT
ATCGTAGTTACCTTGATGTGAGAAATGGTCTCTTTCAAGATCTGATATCGAGAAACTCCTGCTCA
TATACATACTAATATGATTGCTACCAGGTCATCCCACTACACACCATCAAGCAACTACTACTGGA
AGCTATCAACATAGGATCTAGTAAGTAAGATATGCAAGAAATACGATTACACTGCTTTGATAGAA
CCATGAACAATAAGTTCAGACGTCGTTACAGTTTTATCCGTTTGCTACTTTTCGAGCAACTATTG
GGATGGAACTCTTCTTCATAAACTCATCCGCATCCGCTAATTCTTCCTTATTGACTCGTAAGGTT
CTATGCCTGGTCCGCTATTTCACTGGTAAAGCCATATATATATGA
Right flanking sequence: Indices 252533 -- 253032
ATGCCTCTAAGGCTGTTTTCCCTTCCTCATTCGAAGCATCATGAGCCAGTGAACTCCCTGAGGAT
GGAGTGGTTGAACCTCTAGTTGAGTTTCCTTCGGAATCTACTATTAGCTTCTCTTCTTGAGTGAT
CTTCCTGCCTAACTGTAAGCGGAGGCCCTTCCCTCTTAGCCCTCAAGGCAGGTTGCTTTCCCTCT
GGACGTTCATACCTAGCTAATAGAATGTATTTCCTTCTTGTGAGGACTGCCCTTTCCCTTCCTTA
AGTCACTGTTAGTTGCATAAGGACTGTAAGCTTCTTCTTTGTGATTGCCTTTAGTTTAGTAAGTA
CTAGAGTGATTTTTTCCATCTTTCTCGATAGGTAAAGGCTCCGAAGGAGGGCTATTAACATAGCG
CCTTTCAATAAACCTTGCCGAGAGAAGAGATAGGGTATTAGACGGCTTCTTTATTGCTCTTGTTC
CTTGTAGCTAGATGTTACCTACGTTTGTTTCTCTCGCGTTTCCAC
Found at i:294322 original size:12 final size:12
Alignment explanation
Indices: 294305--294329 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
294295 CTGGTTGCCC
294305 TTTTCTTCTTAT
1 TTTTCTTCTTAT
294317 TTTTCTTCTTAT
1 TTTTCTTCTTAT
294329 T
1 T
294330 AGTAAGCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTCTTAT
Left flanking sequence: Indices 293805 -- 294304
TCTCAACAATAAAGAAAGCTCGTTCCCAAGCTTTCTTATATTATTATGCCGCACAAAGTCAGGCA
TGTTCCATTGCGGAGGTAATTGCCTGCCGGAAATAAGCATCCACTCCGGCAATAAAAAGCTCACA
GACGCCCGAAAAGAGCCCTCCTATATCCGAGGGGGCGCTCTGGGCAGTCGATGTGATACTTACTA
TCGGATGAAGCTGTCGTGGATAAATCGATGTTACTAAAGTGGAAGTTTCATTTACATTTAGACTG
AGTCTCACTAGTTGTAGTTGTCCACCTTGTAACAGGATAAGTCCCATTATTTAGAATAGTGGTTT
AGTCTATTTACGATAATATAGTGGGAGTAGCATTAGCAGAAGAAAAAAAGTAAGAGAAGGGATGC
AAGGGTATCCCGATTAATCGAACTATCCGCTTATTTATATTATAGGAAAGTCCGCATTTCTATTT
AGTTTCTTAGTAAAGGGAAAGAAAAATGCTGATCGCTGGTTGCCC
Right flanking sequence: Indices 294330 -- 294829
AGTAAGCTCTTCGGAACTTTCTTTTGGGGTGGTGACGTCTGAATAGGACTTCGGCAATGCGTCGA
TCTTGTCATGGGAGGAAAGGAGAGAAAGGTCGCTGTAAGGGCTTGATAAAAAGACGGGCGGCGGC
TCTACCTAGACTAGACCCCTTCACTAATGGGTCTGCTCATCGAGCTTTCATCCTAATCCTAAAAA
AGGAACCGGTTAAGTAGCAACCTTGGGAACTGGAGATCGAGAGAAAGGGTTGCTACAAGCTCCCT
GTCCCACGCATCTAACCAACGCTCGTGCCAGTTCTAAGTTGAACAGGGGGTGAAAACGGAGTTTA
GACGTCAATAGAGTAGTAGGCCTCGTTGTAGAGTTACATACGTATGGTCTTCACTATTTCTTTGT
GGACTATAGAAGGAGCCCTGCTAGAATTCTAATAAAGAATACCCGGCAAAGTCATTCAATCTCCA
ATTCTTCCTCCTTTTACGTAGAATGAAAAAAATCAAGCCCAAGGC
Done.