Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_016743
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: 380861
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:139547 original size:13 final size:13
Alignment explanation
Indices: 139529--139554 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
139519 GGGGTATCAC
139529 CATATTAAGTAAG
1 CATATTAAGTAAG
139542 CATATTAAGTAAG
1 CATATTAAGTAAG
139555 GATTCAATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
CATATTAAGTAAG
Left flanking sequence: Indices 139029 -- 139528
CTTCCACGATTTCATCTATATCGAATCTGAATATCAGAATAGCTTATATAGTCATGATTCAATTC
AGGTCTTTTTTTTTTTTCTCTTCGGATCTGATTGGAACATTGGAGAAGTAGGAAGACTTTGGCGG
GCGATTCATAATGGGTATCTAGAATATCTATGTCCTAGGACATAAAATATGAATAATTAAGATAA
AGATATATCTAATCTAAGAATTTATAGGCTGTATACCTAATTTTTTTCCTGGGATTGTAGTTCAA
TCGGTCAGAGCACCGCCCTGTCAAGGCGGAAGCTGCGGGTTCGAGCCCCGTCAGTCCCGACCTAG
GATCCGATGAATCGATCAATTCATCTCTGTAGGGGGGGCGTCAGGATCTAATTCCCAGCTGGAGG
ATCCTTCTTTCGCATTTCTCATCGGACAAATCAAGGAATCAAAATGACAATAACTAGTACCGATT
GATGGAGGAGAGACATATGTAGGTTGGTACAATCGGGGGTATCAC
Right flanking sequence: Indices 139555 -- 140054
GATTCAATCTTATCGTATCAGCCTGGCTGGCTTTTTTTTTTTGCCTGTTTTGAAATCAATTGGAT
GTTCTTACCTTCTGGTCTCTTTGAGGCTAAAAGGGGCTGGCTACAGGCGGTATTCGTCTTCGTCT
TCTATTACCTTCAAAAGAACAAAGGCAACTGAGAATCCAGATTTACGCGCGGAGTACCTCTACTC
TAGCAGGGATCCCTTCGCTCATAAGGAGGGTCTAGAGGTAAAGATATTCTGCATGCCCCTTATCC
CGAACTGATCGATAGAATCCATTCTAATAGAGCCTAGTTAGAAACCTCACCTCAGTATTCCATTC
AAGAACCGACGCCTTGTTTGTCACATCTAGCTACTCGGATACGAAGGAAAGAGCGGATCGGATAG
TAGCATCGGGTGTAAACTCCTATCTATCGGTTGCATCCTTAGGAACTACCAACGGAAAGAGGAGA
GCAAAGACAGAACAGAACTAATTAGATCTAGCCATGGTAGCTAGT
Found at i:162900 original size:14 final size:16
Alignment explanation
Indices: 162881--162917 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
162871 ACAGCTCTCG
162881 GAAAGCCGTG-GTGC-
1 GAAAGCCGTGCGTGCA
*
162895 GAAAGCAGTGCGTGCA
1 GAAAGCCGTGCGTGCA
162911 GAAAGCC
1 GAAAGCC
162918 ATGGGAGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 9 0.47
15 4 0.21
16 6 0.32
ACGTcount: A:0.30, C:0.22, G:0.38, T:0.11
Consensus pattern (16 bp):
GAAAGCCGTGCGTGCA
Left flanking sequence: Indices 162381 -- 162880
CTATAATATGAATATGCATTGCTTGTAAGGATAAGGAGCGCATTCACGAGCACTAGCTTTCCAGG
CTTTGGGGTAAGCTATCCCACTAATGCAATTCGATGCTTCCTGCGTCGAAGGAAAGTATGGTCAA
TCAGTCAAAGACTTCCTCCTCCATAATAAATGGATCCTAAGCATCTGAGTCAGCAAGCGCGAGCC
TAGATCCTACTCTTTTCTTTTATCCCAGTATCGATCCCTGCATACACAATAGATCATCATCCTTC
TCTAAACCATGCATGTGACCTACGAGATAGGTCTTTTTGATCTGTTTGTAGCGGCTCGACCCGAT
CTCTTTCGCCTCCGGTTCGACTAACTCCAAGGGTAAGCAATGTGACTTGCCTACATTGCTTCTAG
CTGGGCGGGTGGGTTGCGTGCGCGAAACTTCACACCGGTTGAAACCTGCGGTAATTGGACACTTG
TTGTCTGGAACCTCGAACATATAGACATTAGAGCTACAGCTCTCG
Right flanking sequence: Indices 162918 -- 163417
ATGGGAGGGAGCAGGCGAAAGGGAATTTCTTGTTGATGGAGTTCCCGTAGAAAGGGCTCTTACTG
ATTCAAGTATTGTAGGAAGGGTGGATACTCTATCTTTTTGAGATTGTCAGGGCCAGGAGTTGAAG
AAGAGCTAACCGTAGGCAGTCCTTATGCCGACAAGAAAGAGGAAGACTGGAATAGCAGACAAAGT
GGAATATGACTCACTAGGATCAGCGCTTTGGTTAACAGTGGGAATTCTCCCTCGTAAGGCAGGCT
CTAGTTCGACTAGCTTTTAGCTGGAACGTGGCTAATTTAACCGGAGATCGTAGTCTCAATCCTAA
CCGCAGTGAACAGAGGATTTGGCCCAGCTTCTCTGATCTTTCTTGGCTCTTGAATAGGATTTTCT
ACCTAACGGGAACCAATCAGTCCCAGATCCAACAGAGGACAATTGGGACGAAAGCAGCAGGAACC
TAATCTGACTGAGCAGGCAAGGTAAGCATCCACAAGCAAGATGGG
Found at i:244125 original size:24 final size:21
Alignment explanation
Indices: 244098--244141 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
244088 TATGAAAGCT
244098 TTCCTATTCAAGACCTACTACCAA
1 TTCCT-TTCAAG--CTACTACCAA
*
244122 TTCCTTTGAAGCTACTACCA
1 TTCCTTTCAAGCTACTACCA
244142 CTACCGAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
23 5 0.26
24 5 0.26
ACGTcount: A:0.30, C:0.32, G:0.07, T:0.32
Consensus pattern (21 bp):
TTCCTTTCAAGCTACTACCAA
Left flanking sequence: Indices 243598 -- 244097
CTGGTCCCTGTGAAAGGTCCAGTCGATGGGAAAGAATCCAAGTTTTAGTCTTATTACCGAGTGCG
AGCTGCTTTCTGTGGAAGGTTCGATTACGGGAAGGAAATAGAGGTCACAAGGTAAGGGACCGCTT
TCCTTTTATGCGTGGAAAATGAATCAAAGCAGTTCTCCCTCGACCTGCAGGTCTTCTAAATAAAT
GGTTCTTGTTTATGCTCGTATAGCATAAAAAGGATTCATTGGGAGGGCCATGAGAAATCCACTTT
GTACCTTCGTTTCGATAATCTAAACACTTCTCACCCCTGTGCCTTCTGTACTTCCCGGCTCAAGC
AAGAGCCACAGTGACTGCAACAAGAGGAAAGCCACCTTAATCAGTAATTTGAATAGGGATTATGA
ACAGGCCCTTACCTTGGCCTTAGCCGTTCGATTGATTGTTCTAAGGTCAAGCCTTTCACTTCATT
GTTCAAGCTCTTCAACATGGGTTGAGTTCATACATTATGAAAGCT
Right flanking sequence: Indices 244142 -- 244641
CTACCGAAGCCGGCTTGCTTCTTTTGGTTACCGGTTGGGGGTTTGAAACCAGAGAAAGAAGATCC
GGTTGGGTATACCATACCATCTCGATACAGAGTGAAATTCATTACCAGCTTTCATACCAAGGAGT
CTTTTCCCGTATAACTTCCTTACTCTTTCAGTATTCATACGCACCTGCATCCGCAGCTAATTCTT
AAAAGTAGTTGCTGAGTTATTTTATACGCACGAGGCTCGAGGTTGAGTTCTACACCGATCCCTTC
ACATTTGAATGAGCGGCTCTTTATGCTTTAGTAAGAAGGATTAGTCTCGCCCTGAGGCGTACCCC
GCTTGAAGAATGCTCTTTGAGGGTTTTAAGAATAGCAATTCTAGGGGAAACTAATTCATTGATGG
AGCCGAAGCCCTAGTTTCTTGATGATAGGAATTGCCGTTTTCTTCTTTCAATCCCACCGTATCTG
CTGAGCCTATCGGAGTTGCCTATGTGAGGCATATAAATTTCCTTC
Found at i:247350 original size:18 final size:18
Alignment explanation
Indices: 247327--247363 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
247317 ATCTGTCCAG
247327 GATGCACTATCCATAAGT
1 GATGCACTATCCATAAGT
247345 GATGCACTATCCATAAGT
1 GATGCACTATCCATAAGT
247363 G
1 G
247364 GAGACCACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (18 bp):
GATGCACTATCCATAAGT
Left flanking sequence: Indices 246827 -- 247326
CCTGCGAATAAGGAATGAGATGAGGAAGAAAGGAGAGTCTATGCCACCCCGGCTTCACACTTACC
GTACTTCCGGCAAACATAACTAGTTATAGAGGAAGATTGGTTGAAAGCTGCAGGAGATGTCTTAG
CTAAGGCTGATTGAATTGCTAACTGAACTAGTCGAATTCCCTTATTCTTACCCTGCCGGGACTGG
GTTCAACTCCCTTTCTTAATCTTGATGGCGGCTTGGTGGAAGCAAAATGACCGATCCTGTATTTG
TAGCAGAACCGGTAGAATCTCGAAACTAAGGTTATAATGCATGAACCCTTTCTTCCTCGAGTCAA
TATATGGTTTGTCTGCCGAATCAGCATACGTAGATCGAAGGCAGAAGAATGAAACCCTTTCTATG
GCATGCGCTGTTGGGGCACGTAGAATACAAGAAGTTGCGAATCTTGATGAATCGCAGCATGGTGA
GAAGTCTTCCACAATTAGAGCTTCGAGAAAAGACAATCTGTCCAG
Right flanking sequence: Indices 247364 -- 247863
GAGACCACAGATCCATATCCAACAGATACGAGGGTGACAGTCTGAGTACCTACAGTAGCATATCC
AAGTACAGATCCTATAGAAGCTAAGGTATAAGCATAGCCAAGACCGGTAAAGCCACACCAGCAGT
CGATGACGCTTTCTTCCTTAGTTACATATCCAGTTCCGGCTCCAGGAGGTGAAGATCCAGCACTT
CGAGATATTGTTGCGTGCCTATAACAGCTGGGGAACTCCCGCCACCAACGGGGTTCACTTTAGGA
AACAAACGAAAGAGCATCTCCCGTCCTTTCTCACAAAGCTACATGCCCTGTTTCTCCAGAACCAG
AGGGCCGTTTCATCCGCAGAATCCGAATCATTTGTCGAATCTCAAGATAGAGATGAAGCGAAGCC
GCTAACTCACCCGAAAAGAGGAACTTGAATCTCGATCGAACAAGGCTCGAAGGAAGCTATTAGAT
ACGAATAAGTGTTGGAACACGGGGCATAAAGCAAAGGTGTAAGAA
Found at i:293523 original size:21 final size:22
Alignment explanation
Indices: 293485--293529 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
293475 TGCAGCTATT
* *
293485 TTTTTAACTAATATAGAAT-TC
1 TTTTTAAATAATAAAGAATCTC
*
293506 TTTTTAAATTATAAAGAATCTC
1 TTTTTAAATAATAAAGAATCTC
293528 TT
1 TT
293530 ATTATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (22 bp):
TTTTTAAATAATAAAGAATCTC
Left flanking sequence: Indices 292985 -- 293484
ATCCTACTTCTACAATTGGTAGGTCACCGGGTTATTCAAATAAGTTGTGTTTTATGTGGTTTTCC
CATGTTACAACTTCCGTACCAATTCGGTCGATCCGGAATGGATCGGTTAAACATTCCATTAGGGA
GCCTGGTCTTTACTCTTCTGTGTGGTATTCATTCTCGTTTAGCTCTTGGAATCACATCCAGCAGT
GGTTGGAACAGCTCGCAAAATCCAACCACTTCACCTACTTCATTGCCCCCAACCGTTTCTCGTAC
CTCTATTGAAACAGAATGGTTTCATGTTCTTTCATCGATTGGTTATTCCTCTCCGTTCGTATCTC
TTTTTCCAATTGCGGTCTCAATGAGTTTACAAGATTGAATGGCCAATTATCTTCCGGACCCTCGA
TTCGATTGTTTTCCAAGAATGTTGAGCCGGGTATGTAAGCCATGTATCTGGGAGGAACTTAAAAG
AAGGGCTCTCGGTTTTTTGCACCCTGTTTTGGTCTTGCAGCTATT
Right flanking sequence: Indices 293530 -- 294029
ATTATATATATGTCCAATCTCTAGTGGTGGTGGAACCAACCAAGATGTATGTCGTCCGACCCGAC
CTCAGACTCTTTCTTCCCTACCTATTTGACTCTCTGGCAGCAGTTATTTAGGTGGTATCCCGAGA
TTGAAGAGATCGAATTCATCCCGGGAACACACGAAACAAAGATATGAACTAGGTAAATAAAAATG
GAAAAGAGATGTTTCCAAATCAGAAGCTTTTTCTACATCCATATGATCTACTAAAGTAGATCGAT
ATTGCCCATATAATGAAAGCAGATCTTGGTCCATGGAGTCCCATGAAGGTAAGAACTCCAACCTG
TCCGATGCTTCTTCGGCCAAATACAATATACAAGTGGGACCTGCACTATGAGCAAGCTGTGCGAA
AAACCGCTTCTTTTTTCCGGTTTCGCAACAACTTGGGCGAAATGGGGTTCTACCGGGAAACCATT
GATTTTAGAGTTTTCGCCATTGGTTACTGGTCGAGCCACTGGAAT
Found at i:333736 original size:28 final size:28
Alignment explanation
Indices: 333704--333795 Score: 184
Period size: 28 Copynumber: 3.3 Consensus size: 28
333694 TTTCTCGGTC
333704 AGGAGAGGTACGAAGTCACTCGACTGAA
1 AGGAGAGGTACGAAGTCACTCGACTGAA
333732 AGGAGAGGTACGAAGTCACTCGACTGAA
1 AGGAGAGGTACGAAGTCACTCGACTGAA
333760 AGGAGAGGTACGAAGTCACTCGACTGAA
1 AGGAGAGGTACGAAGTCACTCGACTGAA
333788 AGGAGAGG
1 AGGAGAGG
333796 GAACAACCAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 64 1.00
ACGTcount: A:0.36, C:0.16, G:0.35, T:0.13
Consensus pattern (28 bp):
AGGAGAGGTACGAAGTCACTCGACTGAA
Left flanking sequence: Indices 333204 -- 333703
CTCTATGAATGGAAAAGGGGTGCTTCGGATCGGGAGTAATCACTAGTGATAGGGCAAAAATAGGG
AGGAAGGACAAAGGAAAGAGCGATGCCTACATTAAATCAATTGATTCGTCATGGTAGAGAAGAAA
AACGGCGCACGGACCGTACTCGAGCTTCGGATCAATGTCCCCAGAAGCAAGGAGTACGCCCGCGT
GTTTCAACGAGAACGCCGAAAAAACCAAATTCAGCTCCACGTAAGATAGCCAAAGTACGATTGAG
CAATCGACATGATATATTTGCTCACATTCCGGGCGAAGGTCATAATTCGCAGGAACATTCTATGG
TGTTAATAAGAGGAGGTAGAGTGAAAGATTTGCCAGGTGTGAAATCCCATTGTATTCGAGGAGTC
AAGGATTTGTTGGGAATTCCGGATCGAAGAAGAGGCAGATCAAAATATGGTGCAGAAAAACCCAA
ATCGATATGAATGGAGGATGCCTCTGGAACTTCTTTTTCTCGGTC
Right flanking sequence: Indices 333796 -- 334295
GAACAACCACAACGTTATGCCCTAAAATAGAAACGGAGCCCTTCCGAATTACCTATAATGGAGTC
TAATACACTAGACGACGAAAGGGAGAAACCGGGCCGACGAAAGAATACCGCCCGTCCGATTTCTT
CGTCCGGTTTTTTTTTTCACTTTTTTACAGATATTTCGTTTCTAAGTTTCCGGACTTGCCCTTCG
CACGATTCTATCATAAAATGCTTGTTCCAATCGGAACTGCATGCAAAGTAAAAAAATAGGTTCTC
TTATTTCTAGAGAATTCCTGTATGGATGAAGGAGTTCAATTTGAAATTCTGAAGCCCGGAGATGG
ATAGGTGGTTTCTTGTAATTTTTGGAATATTTTCGTTAACAAATATGGATTCCCCATAGTCTCGG
TGTCTGAGGATCCTAAAATATAAGCACGATATGATTTCTTCATTATAGATTTATCAATTTTTAGA
GAAAAAGATGGATAGGATTTATGACTTCCACTTCCTATAGGACAT
Done.