Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_016741
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: 510519
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Found at i:5321 original size:17 final size:17
Alignment explanation
Indices: 5295--5330 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5285 AGAAGTTTTT
* *
5295 ATATACGCTTTTCTAAA
1 ATATAAGCTTTTATAAA
5312 ATATAAGCTTTTATAAA
1 ATATAAGCTTTTATAAA
5329 AT
1 AT
5331 CACTCATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.42
Consensus pattern (17 bp):
ATATAAGCTTTTATAAA
Left flanking sequence: Indices 4795 -- 5294
TGTATCCGGTTTGAATAGATAACGAATGGTCTTATATTGTATAAATCATAGGATTTATTTTTGTA
TAAGTTTTTTTTGTTTTTTATTTTATTTTTATTGTTGAATTAAAAAAAGAATGTTTTCGCGGGCG
AATGTTTACTCTTTTATTTCAATTTCAGAATTGTCTAGTGACTTCTGAGAATATATGAATTTATT
TTCGGCTCGTTCCGCCATCCCAACCAGTGAATTATTAAGATTCATTTTTAATAAAAAAAATCTGT
TACATTCACGGCTTACATCGTTCCCATCACTTCTTACTTAATGGTTAGGTTCTAATTTTAGAATG
GAGCTCATAATGAAATTTGTTCTCGAGTCAACTTTCTCAGTCTTTATTGACCCCAAGCTCTTAAT
TTTTTTGTTTTATTCTAGTAATTCTAGTAACGATTAAGAAGGGTCATTTTAGTTTAATTATCGAT
GAATTCGTATTGATGCTTTTATTACACTGCCTTTTAGAAGTTTTT
Right flanking sequence: Indices 5331 -- 5830
CACTCATAAACCCTACTTGAAGTCTATATCATTGATTTTGTATTTTTTTCTCTCTTTCTCTCATC
CTTCCGTTTATCCACATATTTCTTCTCTATTTTGCTTTAGAACTTAAATCCTATTGAGTCTTTTT
TGGCAAAAAAATGCAGTTGCTGATATGACCGATTTCGATTTATCACATCTTGACTGATTCTTTAG
CTTTACATCGAGATAATATGAAGTGATGAATTGGTTATTAGTTCTAGAGTTATTAAGTTCCTATT
ATGTGGCCGATTTATTGAATTCTAACCCTAAAAACCAACGAGTCACACACTAAGCATAGCAATTT
TATCAAACGTTCAATCGAATTTTTATTCAACCTTATAGAATTAAAAATAGAATGAAAATTAGAAT
TGGTAGTTTTGCGAAAAAGACCTAAGGGGTTTAGTTTTCTAGATAGAAGGAAAAGAAAACTTCCA
TTTTATTATTCCCCATCTATAAATATCCATATTTTGATGCCTAAT
Found at i:208565 original size:19 final size:20
Alignment explanation
Indices: 208537--208578 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
208527 CTCACACAGA
208537 AAAAAGGAAGTGAG-TTAGAC
1 AAAAAGGAAGTG-GCTTAGAC
208557 AAAAA-GAAGTGGCTTAGAC
1 AAAAAGGAAGTGGCTTAGAC
208576 AAA
1 AAA
208579 TCTTTTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.05
19 15 0.71
20 5 0.24
ACGTcount: A:0.52, C:0.07, G:0.26, T:0.14
Consensus pattern (20 bp):
AAAAAGGAAGTGGCTTAGAC
Left flanking sequence: Indices 208037 -- 208536
TCCATACGTAAAATCATAATTATTGATACGGGCCTTTTCCACAGAAAAGGGGAATCTTGTGTTAG
AATAGAAGCAGAAGTGATGTGGATTATTCAAGAATCGAAGTCGATTTGCTTTATAAAAAGAAGAT
ATCAATGAACTTCTATGAAATGGTTTCACGGGATTCAGCCAATTGTCTTGATTGTGGAATATCAT
TGAGAAATAGGAATCCGCGTTAGCAAAGGATTTCCTGCGATTATTTCTAGTATGGAATGAGTCAA
TCATCCACTTTGGTATCTTATTGAACAAAAAGGGTGATATTGTTCCTCCATTGATCAAGAATTTC
GATTTTCGGGAAGTATCATGATCATCCAATAAGAAGGGTTTCCATTTTTTCAAATGAACAATTTG
AAGACCTATTGATTCTAACAACTGATTGTAGAGTTGATCATTCGGACCTTTCAATTCATAGATGT
AGATCTCGGACCTATGAATGGGGATCTTCCCCAAACTCACACAGA
Right flanking sequence: Indices 208579 -- 209078
TCTTTTTTGTCGATAACCTCAGACCAATCAATCGAATATTGATTAATACGTAATCGATCGAACAC
TATTTGAAAACGGCTCTTCTGCTCAGAAACGAAATGTTCCATATCTTCCTGGAAATTCTTGCTCC
CATTGGACCATTTGTATCTATATGCATCAGGATCCCCGGATCTCTCGGTTCGAGAAATCAAGATA
AGAGGATCGAACCATTTCTTCTGACTCTTTTTCAAATTCGATAAAGGTTGGTTGATCGTATATTT
CATTATAGTTCTATGATTCAGAGGATCCTTTCCTATTTGATCCCTTTGAATTCCATATTCGAAGT
TGCGATCGGATCTATTCATTAAAAAGACTCGATTCAATACATTTCTTATGTACCCATAGGTACTA
TATGGGATTTGAATCAGATTTCGGATCAATCTATATTGATTGACTGCCTCCATTATGTTGTTGCT
AGCAAATACCACCATTTTTGGTTTTGGATCTTTCAAATCATTCCC
Found at i:237505 original size:21 final size:21
Alignment explanation
Indices: 237481--237523 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
237471 TACGAAAAGA
237481 TCGCTTGGACTTAAGAAAGGG
1 TCGCTTGGACTTAAGAAAGGG
*
237502 TCGCTTGGATTTAAGAAAGGG
1 TCGCTTGGACTTAAGAAAGGG
237523 T
1 T
237524 TTGTTTAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.12, G:0.33, T:0.28
Consensus pattern (21 bp):
TCGCTTGGACTTAAGAAAGGG
Left flanking sequence: Indices 236981 -- 237480
GAATGAACTCCGGGAAGGGGAAGGGATGAAGTCGAAATTACTATGAGAAAATATTTTTCTTAAAG
TAGTCAAAACGAATGAACACGTTCAACAAAAAAAGATTTTTTTTCCGATTCGGTTTTTTTCTTAC
AACACGCGATAATAAAATATGGATTCTCGTATTTGTCGAACAAAACACCAATCCGGGTTTGAGTT
CGGATTGGAATTCTGATTCAAGTGAACAAAGAATAAGCCTATTTCTTTCTGATTCTAAGACTAGT
AGTTCTAGCGGTCGACTCGGTTCTTTCAAACTTTTTCTCATTATTGAGAAAGGGTAACAAAGATA
AAATACGAGCTTGTTTTATAGCAATAGTAATTAATCGTTGTTGTTTCAAGGTCAATCTATTCACT
CGCCTAGATAATATTTTTCCTTGTTCACTAATAAATCGACTAATTAAACTCATGTTTCTATAATC
AATTTGATCCCCCGATTCCATCGGGGGCAAACGCCTACGAAAAGA
Right flanking sequence: Indices 237524 -- 238023
TTGTTTAGTTTATTTCTGATTTTCTTATTCCGAAAATCCTATTTCTGAATTGTCATTTTAACCCA
AAATAGAATTATTTAAATATGAATATGTTCTATGATTTTTCCCCTTTCCTTGAAAGGCTTGGTTC
GATCTATTTCTTTATTTCCCCATGAATCATATGTTTGTAACAATAGGGGCAGAATTTTATCAATT
CTAATCGATTAGGGGTATTGTGCCGGTTCTTTTGAGTAATATATCTGGAAATGCCCGTTGATGCC
TTCTTAACATTAACACCATTTCGAATACAACCGGTACATTCCAAAATCACCGTTCCTCGTGCATC
TTTCCTCTTGGCCATGAACCTCTCCTCTATTAATTCATTTAATTCGAACCTGAATCCGAGTCTCG
CAGACGTTGAATACACATTTATTCTTTCTCTTTCGTCCCTTATTCTTATTCTAAAAATAAGAAAA
AAGGGGGAAGGATTAGTCACAGATATTTGATTGTATCTCTAATCT
Found at i:283977 original size:16 final size:16
Alignment explanation
Indices: 283955--283988 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
283945 CACACAATAG
283955 TATATATAATAATATAAA
1 TATATAT-AT-ATATAAA
283973 TATATATATATATAAA
1 TATATATATATATAAA
283989 GAATCGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATATATATATAAA
Left flanking sequence: Indices 283455 -- 283954
TCATTCTTGATTTTATTAAAGAGTAGCTTCCTACTCAGAAGCAGTGGGAAGCAGAATACATGAGG
CCAAGGCGCTTTTAAGCCCTCTAGTTCAGAATAATTTGAACGTGTATTCGATTCGAGAGGTTTGA
AGAAAAATCAAAAGCCATCATCGAAGACACTGAAGATGTCAACTTGGGTACCCATCCCATCAAGG
AGAAAAAGACTAGCTGACCCACCCTACCTTATGGAAGGAATAGACCCGACCTGTCCAGCTCTATC
ATAGATTAGGCTCGTAGCTTCATTCCTTCGCCAGCCGCATCCGGTTACGGGCATAGACACTGAAA
GAAGAAACTTAATAACTTATCTTTGATGTAGCAGGCTAAGCTGGTCTTCCCCCAATATCTGGAAG
AAGAACCAGAAATCGGACTGGGTAGTTGGTCATCACCAAGCGGATCGAGGAATGAAAGGAGAGGT
CTCTCGAGCCTGCCTATAAGTTGTCTTCGAGAACACACACAATAG
Right flanking sequence: Indices 283989 -- 284488
GAATCGGAAATTAATATAGAATGTATATGAGCCCTATGACCTTTCACTACCGGAATGTGCTTTAA
TCCAAGGAAGCACTTCCCTTACATCTATATCTAGGGCTTTTGAAACCGGAGATCCTTCTTTTTTC
AATTCGGGAACTGAAGGTGGCTAAGTCAAGGCGCCTTATCTTTCTAATCAGGTAGATTTGAGAAA
AGGCCATAGCTATTAGTTTCATTGCAAGAAACACAACATTTGAAAAATCCGCCTTAACCTCAGGT
AGTTGATACTATACTTTCAGGGGGAGCAGGCTCATCATTTCCACAAAAGTCGTGTAACTCTTAGT
AATGGCTTCCATCTCAAAAAAAGATTTTGAATTTTCTTTTGATTTTTTATATAAATTGAGAATGA
TCCTTTGGCAGAAGGCCTTTCAACCGGCTCTCCACCTGCGACCTGGAAAGAAGATCCACCTATTG
AGCTTTCTTTCAGGGCAATGAGGTTGCTTTAGTGTACCTTGTACT
Found at i:364294 original size:18 final size:17
Alignment explanation
Indices: 364263--364297 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
364253 TTGTTTCATC
364263 TTTCTGTTCATGTTTTT
1 TTTCTGTTCATGTTTTT
*
364280 TTTCATGTTCTTGTTTTT
1 TTTC-TGTTCATGTTTTT
364298 ATTTTTCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.06, C:0.11, G:0.11, T:0.71
Consensus pattern (17 bp):
TTTCTGTTCATGTTTTT
Left flanking sequence: Indices 363763 -- 364262
GATTTCTTCGATTCTTTTTAGAATAGCTATATTATTGATTTCCACGTTTGCCTCTTTGTGTTGTT
CATTCGCCCATGCTATTGCTTTTATTTGTTCTAGATTGAATTCCCCCCAAACTTCTGGTTCTTTA
TCCTCTTTAAGTAAGTACTTACAGATGGATCTCCGTCCCTTATGTAAACTCATCTCCCTTTCCAC
TCTGGAAAAGCCTTTCTTTTTTTAGTTCGTACTGTGTTTTTGGATGCGTCGTTATATGCCAACGT
GGTAGTGATTGCCTTCATTTTCCTCATGTTTTTCCGTTGCCAAAACAAAGAATTGATTTACATTC
AAAAAGTTGTATTATTCTATTTATGACCATTTTATTCTCAATCTTTTCTCTTAATTCTGCGTGTA
TGAGAGTAAGCATAATAAATTTTCTTAAAGTACTTCCAGTTATTTCATAATTATTTCTTGCTTCC
ATAAGTTCCTCCATTGTTTTTATTTCGCTATCTTGTTGTTTCATC
Right flanking sequence: Indices 364298 -- 364797
ATTTTTCGTTGTTTTTTTCTTTTCTTTGCTGTCCCCTCTTCTATTTTCCTTGTTGCACTAAGATA
CATACGTAGTTATTTCTGAACTGGAAAGCAAGCGTAGGACCTATGATTATATCTATTGTTCTTTC
CGTTGAGCACCACTACTAGAGCTAAGTGGGTATTTTCGGAGAATCGTCTTCTCTTATGGTTTTAT
TCTTTTTAACATTATAGATTCCATGGTTGTTTCTCTCCATTCCTCGATATAGAGACTTCACATTT
GATAGATTCGATCTTTTTTATCTCTAATGTTTCCGAATTCTCATCTTATTGTATTCCTGTTTTCT
TCTTTGTTCTTCTTCTCCTCCTTCACTTATATTTTAAATGATAGCAGGAAATACTTTTGTTATTT
TCTCATTTTCGTAAAACTGAATTTCAAGTGGCCACATTGCATAATCATTCTCATGTTCCTTCTTA
CTTCTCTGTACGCTGATTACGTTCCAAACTTCGTCATTATTAGGT
Done.