Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_066984
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: 615370
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:286191 original size:17 final size:17
Alignment explanation
Indices: 286165--286198 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
286155 ACAGTACTGG
286165 AAGGCCAAGAGAAAGAA
1 AAGGCCAAGAGAAAGAA
*
286182 AAGGCTAAGAGAAAGAA
1 AAGGCCAAGAGAAAGAA
286199 GTACCCGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.59, C:0.09, G:0.29, T:0.03
Consensus pattern (17 bp):
AAGGCCAAGAGAAAGAA
Left flanking sequence: Indices 285665 -- 286164
CAAATGGTATTTGCGCCTTCTTTTAAGTGAGGCTATCCAAGTCAATAGCTAGAGTTTGTCTGGGT
GAAGAATTCTTTCGTCCGGATCACGACCCGGCCCCCAATGCAATGGTTAGAAGAAACTTCGTAAA
GAACTGAAGCTAGCAGGGTTTCGGCTTGAGTGTGACATTGATGCTTCAAGTCAAGGTCGATGACA
GAATGGTACAAAGAAAGAAGGAAGACAGCGATCATTAGAAATTCACAAATGCTCAATCTCTGCAC
CTTTCTTTCAAAAGGACAGTTTCTTCTGTAACATTGGTTGTAAGAGCGGATCTTGCCTTAAGTCA
TTCACGTCTAGCTAACATTCCCCTAACGGATCACTTCAACTCACTTAAAAAGCAGGAGATGAGAG
ATCTAACGGGTAACTTCTGCCAATTCAATGCCCAGTAGCAGTGGACTTATTATACTTATACTTAT
GCTCCCATCCAATCCTTCTTTCGTGAAATGCCGGTACAGTACTGG
Right flanking sequence: Indices 286199 -- 286698
GTACCCGAAAGACCTACCTTATTAGAAGATTAACCGGTCTGACCTGCCAAGCTTAGTCATTTCCC
ATCCCGCATCGCTTCCACTTCTAATTCCTTAATGTGCCAAGGGGAAGGGGACTTAAGGTTAAGGA
AGAAGGATCTACTGGTTGAGACTGACGTTCACTAGATAAATTCCCCTTATTCCGTGGCATCATAA
CTGCCCTTCTAGTCTTTCTGCATAACCTAACATGGGTTTACTAGTTGAATTAGGCTAATTCCTAG
GTAAAAAAAGAAAGACTAAAAAGCATACCATTTAGCCTTCGATCCGTGCTATTAACGAATTACCA
CTTTTCGATTCAAAAAAATGGGTTTAGGTTTAGTTTAGATCCTCTCACCTCTGGAGCAGCGGATT
CGCCTAATAGAGGAAGTAACCCCTCTTTCTCTTCCATGCACCGGGCCTCTTGGGCAAGCTTCTGC
TTTGGCTACCTCTTTAAAACTCTACTCTATGAGATTTGCATGGGA
Found at i:301750 original size:12 final size:12
Alignment explanation
Indices: 301733--301758 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
301723 GAAAATGACT
301733 TATATATAGTAA
1 TATATATAGTAA
301745 TATATATAGTAA
1 TATATATAGTAA
301757 TA
1 TA
301759 GTAGCAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (12 bp):
TATATATAGTAA
Left flanking sequence: Indices 301233 -- 301732
GTTGGAAATCCCACATTCTATTCTAATTCTAAGGGTGGTTCACACTTTTGTATGCACTGTTTCCT
GAGAATCAGATTCGAGAATCACTTGATTGTAGCTTAACTACCAAGCCAGCTGCCTTGCTCCTTTA
GATGGAAAAGAATCCTGTCATCACTTCTCTCATGGGTGTTCAAATATTCTAGTATATTAAGGGGC
GTACCGATGTTTGAGTTCATCGATATGAGCTAAGTCCCCGTTGCTAAGGTATTGATGTTGTTCAT
CCCGAGTTTCAGAGTGAAGTAGCCACAGGCTAATTAACATCTCATATTGAAGTTGAGTTGTAGGA
GCAACTGAGCTAAGGCCCAACATCCCTAGTGGGTTTAAGGAACATTTCATCATGGTATAGGCTGC
TTGAGAGGAGGCTCCATATGGAAGGTCGATCACCAACCCAACTCTTCGCCCCAACAGGGAATGGT
AAAGGGCAATTTCTCTTAACTATATGAAAGTGTCAGAAAATGACT
Right flanking sequence: Indices 301759 -- 302258
GTAGCAACCAATCATTCATTGGCTAGCATGGGCTAAACAGTGTGTATCAAATTAAGCTTCCTCGG
GATGTTGGCTCCAAGACTTCGGTCTCGGCCACTTAGCGCAGTGGAATAGGAAAGAGTTCTTTGCA
TCAACAAAGTGTAGTAGTCAAAAACGCTTACTTAATCTCATCGATGTTTACCTCGGCTGTGAAAG
AGAGGTTGCTTCTGAGCTAAATCAATCCCGCACAGGTTCTTACCCGGAACTTTACACTCAATGGA
AAGCAAAAAGGAAGACTAAATCCGCTTTGAAAGCTATTCCAGAGACTATAAGAACAACCAGGTTG
CGGGCGGGAGCAGCAGAAGCATTGAGATTTGCTTGTTCAGAGATGCGTCAAAGTATACCTATGAA
AGTGGATTGCAAGGGTCAGGCACCAATGCATTACTAAAGAATAAGCAACCGGAATAACTTTTCAG
GGAGCGTGGAAAGATTGGTCTTACTATCTATGGGAAGGAAAACTG
Found at i:412210 original size:12 final size:12
Alignment explanation
Indices: 412193--412218 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
412183 GAAAATGACT
412193 TATATATAGTAA
1 TATATATAGTAA
412205 TATATATAGTAA
1 TATATATAGTAA
412217 TA
1 TA
412219 GTAGCAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (12 bp):
TATATATAGTAA
Left flanking sequence: Indices 411693 -- 412192
GTTGGAAATCCCACATTCTATTCTAATTCTAAGGGTGGTTCACACTTTTGTATGCACTGTTTCCT
GAGAATCAGATTCGAGAATCACTTGATTGTAGCTTAACTACCAAGCCAGCTGCCTTGCTCCTTTA
GATGGAAAAGAATCCTGTCATCACTTCTCTCATGGGTGTTCAAATATTCTAGTATATTAAGGGGC
GTACCGATGTTTGAGTTCATCGATATGAGCTAAGTCCCCGTTGCTAAGGTATTGATGTTGTTCAT
CCCGAGTTTCAGAGTGAAGTAGCCACAGGCTAATTAACATCTCATATTGAAGTTGAGTTGTAGGA
GCAACTGAGCTAAGGCCCAACATCCCTAGTGGGTTTAAGGAACATTTCATCATGGTATAGGCTGC
TTGAGAGGAGGCTCCATATGGAAGGTCGATCACCAACCCAACTCTTCGCCCCAACAGGGAATGGT
AAAGGGCAATTTCTCTTAACTATATGAAAGTGTCAGAAAATGACT
Right flanking sequence: Indices 412219 -- 412718
GTAGCAACCAATCATTCATTGGCTAGCATGGGCTAAACAGTGTGTATCAAATTAAGCTTCCTCGG
GATGTTGGCTCCAAGACTTCGGTCTCGGCCACTTAGCGCAGTGGAATAGGAAAGAGTTCTTTGCA
TCAACAAAGTGTAGTAGTCAAAAACGCTTACTTAATCTCATCGATGTTTACCTCGGCTGTGAAAG
AGAGGTTGCTTCTGAGCTAAATCAATCCCGCACAGGTTCTTACCCGGAACTTTACACTCAATGGA
AAGCAAAAAGGAAGACTAAATCCGCTTTGAAAGCTATTCCAGAGACTATAAGAACAACCAGGTTG
CGGGCGGGAGCAGCAGAAGCATTGAGATTTGCTTGTTCAGAGATGCGTCAAAGTATACCTATGAA
AGTGGATTGCAAGGGTCAGGCACCAATGCATTACTAAAGAATAAGCAACCGGAATAACTTTTCAG
GGAGCGTGGAAAGATTGGTCTTACTATCTATGGGAAGGAAAACTG
Found at i:609594 original size:2 final size:2
Alignment explanation
Indices: 609572--609616 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
609562 CCTTCGTCTC
*
609572 AT AT AT -T AT AT -T AT AT TT AT AT AT -T AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
609610 AT AT AT A
1 AT AT AT A
609617 AAAGGAGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 4 0.11
2 33 0.89
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Left flanking sequence: Indices 609072 -- 609571
AAGAGCAAGGGGCGTAGCGACTACTACTCTATAAGTAATATAGAATTACTATGTTCCAAGCTTTG
AAAGATACAACTCTAAGGGGAACTATTATATTCTCTATAGTCTATGTGCCCGCCGGGACTGGGGT
TGGTTCTGACCTCGTCATGGAAGATTCATACTTAATCTATGAATGCAAGCTGAGAGGGAGGACAA
ATCCTCAATCAACTTGAATTCGAGACAGCTATTCGAAAAGAGTTCTTTTACGGTCAAAAGCTGTA
TGGGGATTCCATTCTTTTTGAGTTGGATAAGCCAGCAAAGGACTCGTCTTACTTTATTCTTTATT
TACTTACTGGTGAGGTAGCTGAGCTGTGACGATAGAAATCGGACTTGAAGGCTTAGCTCGTCTGT
GTACCCGGATAAAGGAGAAGATCTAATTAGCTCTGCTTCGAGGAGGTCGTGGCTATCTCAGATCA
GGAAGAGCGGGATGCTAAAGAAAAAAAGATTATGCCCTTCGTCTC
Right flanking sequence: Indices 609617 -- 610116
AAAGGAGATTGTGAATCAGTTGAATTAGGTTTGGTAAAGTAAAGATTGACCTTATTTTTGATACA
GAAGAAGCTGTTAAACCTATACGACATTTTGGTTCTAGACCAATAGAATAAACTATTTCACGAGT
CAGCTGCTACTTCGCAGCTAATTCCATTCATTCACATCTATCTGTATCGCCTGCGAATCCTTTTT
CCTGCAAAGAAAAAAACTTCTCGGCATCAATGCACTAACTCCTGCCAAGATCCGTTTGATTGACT
CATTCTAACAGAATGCTTTTTGGCATATCGCTCTTCTTCCTCAGATCAGGAGCTCTTTACAATCG
ACTCGTTTTTCACTATATTAAGCTATAAATACGGTATGCTGGCGAGCTTAAGCTTAAGGAATGGG
AATAGTAGTTGGTTTTTTACGAGAATGTAAAGAAAGCTACAGTCATCCTTTAGTCAGGAGGCACT
CAACGTTTTCCTTAGTTTTGCAATTGGAATACAGAGAAGATAGGG
Found at i:609596 original size:13 final size:13
Alignment explanation
Indices: 609572--609616 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
609562 CCTTCGTCTC
609572 ATATAT-TATATT
1 ATATATATATATT
*
609584 ATATTTATATATT
1 ATATATATATATT
*
609597 ATATATATATATA
1 ATATATATATATT
609610 ATATATA
1 ATATATA
609617 AAAGGAGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 5 0.17
13 24 0.83
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATATATATATATT
Left flanking sequence: Indices 609072 -- 609571
AAGAGCAAGGGGCGTAGCGACTACTACTCTATAAGTAATATAGAATTACTATGTTCCAAGCTTTG
AAAGATACAACTCTAAGGGGAACTATTATATTCTCTATAGTCTATGTGCCCGCCGGGACTGGGGT
TGGTTCTGACCTCGTCATGGAAGATTCATACTTAATCTATGAATGCAAGCTGAGAGGGAGGACAA
ATCCTCAATCAACTTGAATTCGAGACAGCTATTCGAAAAGAGTTCTTTTACGGTCAAAAGCTGTA
TGGGGATTCCATTCTTTTTGAGTTGGATAAGCCAGCAAAGGACTCGTCTTACTTTATTCTTTATT
TACTTACTGGTGAGGTAGCTGAGCTGTGACGATAGAAATCGGACTTGAAGGCTTAGCTCGTCTGT
GTACCCGGATAAAGGAGAAGATCTAATTAGCTCTGCTTCGAGGAGGTCGTGGCTATCTCAGATCA
GGAAGAGCGGGATGCTAAAGAAAAAAAGATTATGCCCTTCGTCTC
Right flanking sequence: Indices 609617 -- 610116
AAAGGAGATTGTGAATCAGTTGAATTAGGTTTGGTAAAGTAAAGATTGACCTTATTTTTGATACA
GAAGAAGCTGTTAAACCTATACGACATTTTGGTTCTAGACCAATAGAATAAACTATTTCACGAGT
CAGCTGCTACTTCGCAGCTAATTCCATTCATTCACATCTATCTGTATCGCCTGCGAATCCTTTTT
CCTGCAAAGAAAAAAACTTCTCGGCATCAATGCACTAACTCCTGCCAAGATCCGTTTGATTGACT
CATTCTAACAGAATGCTTTTTGGCATATCGCTCTTCTTCCTCAGATCAGGAGCTCTTTACAATCG
ACTCGTTTTTCACTATATTAAGCTATAAATACGGTATGCTGGCGAGCTTAAGCTTAAGGAATGGG
AATAGTAGTTGGTTTTTTACGAGAATGTAAAGAAAGCTACAGTCATCCTTTAGTCAGGAGGCACT
CAACGTTTTCCTTAGTTTTGCAATTGGAATACAGAGAAGATAGGG
Done.