Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_069573
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: 494599
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:27935 original size:21 final size:22
Alignment explanation
Indices: 27886--27937 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
27876 CGCTCTTAGC
**
27886 TGCCTCTTAGCGGATAGGTGGG
1 TGCCTCTTAGCGGATAGGTACG
27908 TGCCTCTTAGCGGATAGGTACG
1 TGCCTCTTAGCGGATAGGTACG
27930 -GCCTCTTA
1 TGCCTCTTA
27938 AGTAACTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.29
Consensus pattern (22 bp):
TGCCTCTTAGCGGATAGGTACG
Left flanking sequence: Indices 27386 -- 27885
ACGTGCTGCTATCTAGACCGTACACGATAATTTTATCACAACTCCGCCTTATGTAAAAGTAGTCC
CTGATATATATACCAAGGCCTTTATTAATATGGGTCATCCACTTCAAATAATTAATGATTTTATT
AAGAGAAATCTGATTCTTCCATACTCCCATACTCAAGATATTAATAACATATCACTCGTATACAA
TCACAAGGATAATGATCCTATTCCATCTGATTATCTTACAGATTTCTTGAATTCATTTTCACCAA
CTAAAGATAAAAAGAAATGGCGTAAAATGGTATCAGACTTTCTTAAGTATTACAACAACTATGTA
GATGCTGTGTGCGGTAATCAAGTGATTGATTCTGAGGAACCTTCTAATGAAGTGAAGTGGAATAA
ATTTAAGCAACTTCTAGAGAACAGAAGTCATAATTACAGCGTGCATTACTAATTAGAATAGACGC
TAGGGAAATAGGGAGTTATAGCAGCGGCCTCAACGCGCTCTTAGC
Right flanking sequence: Indices 27938 -- 28437
AGTAACTTAGTTCAACGTGTCTGTATTGGAAAATGAAAAATAAATGGATGAAAAAACGACTTATG
ACTACCTGTCCTATGAGTGAATTGGCCTTTTTTTTTGCGTGTTTGGAACATAACTATCAATTGAA
TTCTAGTGAGTATCCTTTGATTTCTAGTATAGATAGAAACAATTTGTTGGATCGAATTTCAGTAA
CAATGGGATGGGATTGGAGGAGGTATTGGATGTGATATGCTATATGATCCTATAATGGAACCATT
GGTTCAATCGTCGTTGGCGCACTTCCTTTACATGAAGAAGAATCGTATTGATTTCAAAGGGTACG
AAAATGGAGAAAAATGACCTGATAGAATGCCATTCCATCCTAATTCTATTTTTAGATTTATGGAT
AGCTTAATAGCTAATAAAGCATCGGTCACGCTGGGTTCTTTTAAACTTTATGACTTTTCACCAAG
TACTACAACGGATAAGCTTATGCTAAAGGTTAATGAGTTGTTACA
Found at i:31326 original size:20 final size:20
Alignment explanation
Indices: 31301--31338 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31291 GTCAACAAAA
*
31301 AGAATCGACCAAAAAACCGC
1 AGAATCGACAAAAAAACCGC
31321 AGAATCGACAAAAAAACC
1 AGAATCGACAAAAAAACC
31339 TATATGCCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.26, G:0.13, T:0.05
Consensus pattern (20 bp):
AGAATCGACAAAAAAACCGC
Left flanking sequence: Indices 30801 -- 31300
CGTCTCTTTGACGATATAGCCTTTCTAGGGATTCTTCTCCCGTGCGAGTTCGGGAGTTTTCCAGC
GCCCTTGCGCCCCGATTCTCCCAATCCCCCTCCGGATGAAGGATGGCCATCCGGTTGATGATTTC
GGCCTTGACCTGGAAGAGATCTTCGGCTTGAATCTCGGCCAGATGGATATCCATGGCCGACGGAT
TGTCGAATTTCGACAAAAGTCGGCGTGCTACATCCTCTACGCGTTCCCCCCCAACTACCTCATGA
TTGTTGGGCCCTGCAGCGAGGTGATTCTGCTGTTGAGCTGCTGTGGCAGCGGCGGGTTGGGGTGG
AACATGAGCGGGCTGGGGGGCGGGTACGGCATTGGAAGGCCCAGCTTGTTCCCTCGGAATCGGTT
GATTGACCGATGAGGTACTTCCACTACGCCCGGAACTGGCCGAATCTTCTTCCAAATCGGAAGTA
TATGTAAACCACCCAGAAGAGGCGTCGCCCGGGTTGTCAACAAAA
Right flanking sequence: Indices 31339 -- 31838
TATATGCCGTGTTACATAGATACGGAAACAATAACAAAACAATAGGGTGAAGCAAAGAAGGCATA
TATGACTAAAATTGACTATATGTTTGCCATATCTTCTATTTAAAGAAGACAAAGAAAGACGAAAC
AGAAGGCTAAAGGCAAAAATAAAAATTCCAAAAAGAACCAGATTGATACCACTGGTCATTATAGC
GCCTCCTTTTACTGATAGATCGGACCTCCTGCAATAGAGACCAGGGAAAGTAGTCTCAGTTGCAC
TCACTCAAAGCGGTCAATGAAGAAGTTTCCCTAGTCTATTTAGTAATGGTGCTATAGATATCATG
AGCTGACCATGCCATAGCGTAGTAAGCCTACCTATCATCTATTCCACGTAGCGACCAAGGATGGG
ACTTTCCCTATTCTAACTGGTCGGAAGGGAATCGGTAGCATGAGCTCCCATCGAGCTGGAAACCG
GCTTTCATTAGCTTCCTCGGTCTGATGGAGGGTACGATATTTATT
Found at i:181639 original size:22 final size:22
Alignment explanation
Indices: 181596--181640 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
181586 CTCTAGTCTA
* *
181596 TTCCTTCTTCTATGACGCAATG
1 TTCCTTCTTATATGAAGCAATG
* *
181618 TTCCTTCTTATCTGAAGGAATG
1 TTCCTTCTTATATGAAGCAATG
181640 T
1 T
181641 ATCCGTACGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (22 bp):
TTCCTTCTTATATGAAGCAATG
Left flanking sequence: Indices 181096 -- 181595
AGGGAAAAACTTTTGTTTCACATTTCCAGAAAGACCACCTATTTGTTCGTTTACCAGGTTCGGCA
CAAAATCATAAATAAGCTCTACCAGGGATTGCCAAGCATTTGGTACTGACTTTCCTCCTCCCTTT
TTAGTAACTAAATGAAAAAAAAATAGGACAAAACTGAGAGTGAGTAGCAGAAAGAAAGATGGATT
TGTGAATGAGAAATATAACTTTCCAATTTGAAGAGGAAGAAATGGGACAATGGAAAATTGATCAA
GGGGGCTCTGCTGTAACATGGATTTCTTTTTTTTCATTGACTGCTCCGCTCTACCCTAACATGAA
GGGAGAAACTTAGATATATGTAGTTGCTTGGTTGTTGACCAAGGAAAAACATGGGAATAATTGGA
CGTAACATTCTTTTTCTTCTCTTACGATACGAGATTTCGAAATAAGGCAAAAGATTGGTCGGAAC
TCTTTCTTTTTCCTCCAATGCTGCGTTGGGTGTTCCTCTAGTCTA
Right flanking sequence: Indices 181641 -- 182140
ATCCGTACGTGGATATGGATAGAGCCGCGGCAGACTTCATGGTCTAATACGGATGAGAGGGGCTT
CCTTTTGTTTGACCCTGAGACGGGAATGATGGGAATGTACTCCCGTAAATGTACATGAATAGATC
AAAGGAAGACTTCATGTTAGAAGACGAGGTAGCACGATCAAGGTAGGTATGGAAGATTTGCAATA
CAAAGGCATTGGCAAGAGACATGGGAATACGACGCATGGGATTTATGCTATTCATGGAAGCCCGC
ATGTATGAAGCAAGAGGGCAGGCCCGAGATAGAAGTCGGAATCCACGATCCAATCCGGAATGGAA
TCATTGAGCCCATTTAGTCCATCTTCTCTTTTTTAGCTCTCTATCAAGCATCTCATGAGAGGCAT
ACTGAGTCCACTTTCCAACCCCCTTCAGGTCGTATCGGCCTTTCTAACTTCGAACTTCGGATTCC
GCGTCGCACACTGCCGCGTAGGGCGTCCTAGTCAAACTACTGCAA
Found at i:255960 original size:21 final size:22
Alignment explanation
Indices: 255911--255962 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
255901 CGCTCTTAGC
**
255911 TGCCTCTTAGCGGATAGGTGGG
1 TGCCTCTTAGCGGATAGGTACG
255933 TGCCTCTTAGCGGATAGGTACG
1 TGCCTCTTAGCGGATAGGTACG
255955 -GCCTCTTA
1 TGCCTCTTA
255963 AGTAACTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.29
Consensus pattern (22 bp):
TGCCTCTTAGCGGATAGGTACG
Left flanking sequence: Indices 255411 -- 255910
ACGTGCTGCTATCTAGACCGTACACGATAATTTTATCACAACTCCGCCTTATGTAAAAGTAGTCC
CTGATATATATACCAAGGCCTTTATTAATATGGGTCATCCACTTCAAATAATTAATGATTTTATT
AAGAGAAATCTGATTCTTCCATACTCCCATACTCAAGATATTAATAACATATCACTCGTATACAA
TCACAAGGATAATGATCCTATTCCATCTGATTATCTTACAGATTTCTTGAATTCATTTTCACCAA
CTAAAGATAAAAAGAAATGGCGTAAAATGGTATCAGACTTTCTTAAGTATTACAACAACTATGTA
GATGCTGTGTGCGGTAATCAAGTGATTGATTCTGAGGAACCTTCTAATGAAGTGAAGTGGAATAA
ATTTAAGCAACTTCTAGAGAACAGAAGTCATAATTACAGCGTGCATTACTAATTAGAATAGACGC
TAGGGAAATAGGGAGTTATAGCAGCGGCCTCAACGCGCTCTTAGC
Right flanking sequence: Indices 255963 -- 256462
AGTAACTTAGTTCAACGTGTCTGTATTGGAAAATGAAAAATAAATGGATGAAAAAACGACTTATG
ACTACCTGTCCTATGAGTGAATTGGCCTTTTTTTTTGCGTGTTTGGAACATAACTATCAATTGAA
TTCTAGTGAGTATCCTTTGATTTCTAGTATAGATAGAAACAATTTGTTGGATCGAATTTCAGTAA
CAATGGGATGGGATTGGAGGAGGTATTGGATGTGATATGCTATATGATCCTATAATGGAACCATT
GGTTCAATCGTCGTTGGCGCACTTCCTTTACATGAAGAAGAATCGTATTGATTTCAAAGGGTACG
AAAATGGAGAAAAATGACCTGATAGAATGCCATTCCATCCTAATTCTATTTTTAGATTTATGGAT
AGCTTAATAGCTAATAAAGCATCGGTCACGCTGGGTTCTTTTAAACTTTATGACTTTTCACCAAG
TACTACAACGGATAAGCTTATGCTAAAGGTTAATGAGTTGTTACA
Found at i:259351 original size:20 final size:20
Alignment explanation
Indices: 259326--259363 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
259316 GTCAACAAAA
*
259326 AGAATCGACCAAAAAACCGC
1 AGAATCGACAAAAAAACCGC
259346 AGAATCGACAAAAAAACC
1 AGAATCGACAAAAAAACC
259364 TATATGCCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.26, G:0.13, T:0.05
Consensus pattern (20 bp):
AGAATCGACAAAAAAACCGC
Left flanking sequence: Indices 258826 -- 259325
CGTCTCTTTGACGATATAGCCTTTCTAGGGATTCTTCTCCCGTGCGAGTTCGGGAGTTTTCCAGC
GCCCTTGCGCCCCGATTCTCCCAATCCCCCTCCGGATGAAGGATGGCCATCCGGTTGATGATTTC
GGCCTTGACCTGGAAGAGATCTTCGGCTTGAATCTCGGCCAGATGGATATCCATGGCCGACGGAT
TGTCGAATTTCGACAAAAGTCGGCGTGCTACATCCTCTACGCGTTCCCCCCCAACTACCTCATGA
TTGTTGGGCCCTGCAGCGAGGTGATTCTGCTGTTGAGCTGCTGTGGCAGCGGCGGGTTGGGGTGG
AACATGAGCGGGCTGGGGGGCGGGTACGGCATTGGAAGGCCCAGCTTGTTCCCTCGGAATCGGTT
GATTGACCGATGAGGTACTTCCACTACGCCCGGAACTGGCCGAATCTTCTTCCAAATCGGAAGTA
TATGTAAACCACCCAGAAGAGGCGTCGCCCGGGTTGTCAACAAAA
Right flanking sequence: Indices 259364 -- 259863
TATATGCCGTGTTACATAGATACGGAAACAATAACAAAACAATAGGGTGAAGCAAAGAAGGCATA
TATGACTAAAATTGACTATATGTTTGCCATATCTTCTATTTAAAGAAGACAAAGAAAGACGAAAC
AGAAGGCTAAAGGCAAAAATAAAAATTCCAAAAAGAACCAGATTGATACCACTGGTCATTATAGC
GCCTCCTTTTACTGATAGATCGGACCTCCTGCAATAGAGACCAGGGAAAGTAGTCTCAGTTGCAC
TCACTCAAAGCGGTCAATGAAGAAGTTTCCCTAGTCTATTTAGTAATGGTGCTATAGATATCATG
AGCTGACCATGCCATAGCGTAGTAAGCCTACCTATCATCTATTCCACGTAGCGACCAAGGATGGG
ACTTTCCCTATTCTAACTGGTCGGAAGGGAATCGGTAGCATGAGCTCCCATCGAGCTGGAAACCG
GCTTTCATTAGCTTCCTCGGTCTGATGGAGGGTACGATATTTATT
Found at i:326720 original size:27 final size:27
Alignment explanation
Indices: 326686--326784 Score: 198
Period size: 27 Copynumber: 3.7 Consensus size: 27
326676 GCTTTAGCAA
326686 CTCGACTTACAGGAGAGGTTTAAATAG
1 CTCGACTTACAGGAGAGGTTTAAATAG
326713 CTCGACTTACAGGAGAGGTTTAAATAG
1 CTCGACTTACAGGAGAGGTTTAAATAG
326740 CTCGACTTACAGGAGAGGTTTAAATAG
1 CTCGACTTACAGGAGAGGTTTAAATAG
326767 CTCGACTTACAGGAGAGG
1 CTCGACTTACAGGAGAGG
326785 GAGCTCTTTC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 72 1.00
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (27 bp):
CTCGACTTACAGGAGAGGTTTAAATAG
Left flanking sequence: Indices 326186 -- 326685
GACACTCGAATCAGACGCAGTGGCAATCTATTAATTCAATTCGGAAGAGACCCCACACACGAGAG
CGAGATTGCGCTCAGGTGCGCCTACAGTCTTATAGATGATGGACGAGGGACAGGCAGAACTAGAA
GTACCCCCTAGAAGGGCGAAGTAACCAGGTTTTGGATAAATCCTGCCTGCCCGTTTTGAAGAAAG
CTTCTTCTATGTAACAAAGTCGCTTGTGGCCACCAGTCTTGACCACAAATCTAGCCCGAACTGAG
GACCTTGGAGCCCGAGCGGGATGGTCCCGTCTTCGTTATTGACTTCATGAAAAAAAGTGTACACC
CTTACCAAGGCCAAGGATGAAATGCCAGATTGAACTGATACTGTTGGCCAATCAAGGCAATCATC
AGCCTACGAGGTCTAGGGAATGAAAGTCTTATAGAGGAGACTGGCTTCGTAAGTAAAGTAAATGA
ATTTGAGATAGATAGCTCGGAGAAGCTGGAGAGGTGCTTTAGCAA
Right flanking sequence: Indices 326785 -- 327284
GAGCTCTTTCTTGATGGCAACAAACCGGTGTACCTACTCGCTTGCTAATGGACTATAGCCGGAAC
GAAGGGACTGTTTCCAATTAAACAAAGAAGAATGCCCACCCCTCTCTGTTTGATAACAGTTTCCC
CCTAGTTTGCTTGAAACAGATAAGCTTGCCCGTGCTCGCATTTTGAAATACCTCTTGTAATCGAA
TGAATCCCCCTGCTAGTATTCTTTCTTTTCCCTTCACTACCGTAACTTACTCGCACCCCGAAAGA
AAGGAAGCTTTTAGCGCTCGATTGACGCGCGGGCTACTGATTAGATTAAAGCTCGTAAACTCGCT
CTCTGTCTTGATCAGATGCTGACTAAGCAATAGAAACTGGAACTGTTGCTACTAGGTCAACTGAG
TCAATCCATTCAGTCAACTAAAGAAAATGCAATTGCTCCAGTTCCCTCCTGGTCAATTCGTTGAT
CGCTAAATCTCTATAATTACCAGCTCTCGTCTCTGCTGACGAAGC
Found at i:334181 original size:24 final size:24
Alignment explanation
Indices: 334154--334205 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
334144 GGGGGAGCTA
*
334154 CAGGCAGAGCCTGAGGGGGAGTGC
1 CAGGCAGAACCTGAGGGGGAGTGC
334178 CAGGCAGAACCTGAGGGGGAGTGC
1 CAGGCAGAACCTGAGGGGGAGTGC
334202 CAGG
1 CAGG
334206 TTGTTCCGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.48, T:0.08
Consensus pattern (24 bp):
CAGGCAGAACCTGAGGGGGAGTGC
Left flanking sequence: Indices 333654 -- 334153
ACACTCTCGCGTCATACGGCTTCGTCCCGGAATCAGGACCTTCCCTTTTCTTTGACCAACCTGTC
CTCCCCAAACATGACGTTTGCCCCGGTAAGTGCGCCCCATCCCCGATCATCGTTCTAAAAGGAGA
TCATGGTTCCGGATTGCTCGCATAATGCGGCGATACGGAACGCTTTCGCGTGTTCCATACTGCTC
AATTTGAGCGAGGTACCTGGAATAGGTACGGGGCTGTAAAAGCTCCCCTTGCGGGGAATGGAGCA
AGCCCCGAATCTGGGGGCGCTTGGATAGAATGGAATGACGGCTATACCCATCATCCACCAAGGCT
GCTTCCACATACCGTTCCACTCTCACTTGTGAATCAATAATGGATACCATGCGCCCAAGATTGTC
ATTCCCCCCTATATTGAGGAGCGAGTACCTGTGATAAAGCTCGCTCCGTCTTGCTTCCTCCGAGA
GAAGGGGTTGGAGCAGTTCGGGGATCACAACGGGCGGGGGAGCTA
Right flanking sequence: Indices 334206 -- 334705
TTGTTCCGCCGGCGGACTAGGCGGGGGGGAGAAGGCATTCCTCTCCTCGCAATAGGCGATAGGAA
GATTCGTTTTCAAAAATAAGTATATATATAGTAAAGAAAAAAAGGCAATCAATCGAAAAAAAATG
GAAATAGTGATTCAAGGTCTAGATGGATCCCTATCTTTATCTCTATCCACGAAGATACAACTCTA
TATGGATAGAGATCTATCTATGAATAGATCTAGACTATCCTCTATCCGGATAGATATGTCCCTTA
TGAGCGAGCCGATCTTTATATGTTTTGGCCACGTTCGTTTCCGCTCCGAAGAAGAAGGTTTGGAT
CTTTCAATCTTATGTCGTGAGGGATGTGACCTATGTTAGGTCCATAAGATACCACAGCTTTTGGT
GTTCTATGATTCACCTCCGAATAATGAGTAGGTAGTTCGATTCTTTTTCTATTCATAGTAAACTG
ATGGGGGGATGCGGAGCAATAGGTCGAATTACTATATAAAGAAGA
Done.