Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_016122
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: 151983
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:13916 original size:48 final size:50
Alignment explanation
Indices: 13863--14002 Score: 169
Period size: 48 Copynumber: 2.8 Consensus size: 50
13853 TGAAAAGCGA
*
13863 TTATATAAACGAAACTTAAGTTTCTGTATATGTATATGCTA-TTCGAA-G
1 TTATATAAACGAAACTTAAGTTTCTGTATATGTATATGCTATTTCCAATG
* * *
13911 TTATATATACGAAACTTAAGTTTTTGTATATGTATATGCTATTTCCAATTCT
1 TTATATAAACGAAACTTAAGTTTCTGTATATGTATATGCTATTTCCAA-T-G
*
13963 TTATATATACACGAAACTTAAGTTTCGTGTAT-TCTATATG
1 TTATATA-A-ACGAAACTTAAGTTTC-TGTATATGTATATG
14003 ATATAACAAG
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
48 39 0.50
49 5 0.06
52 7 0.09
54 22 0.28
55 5 0.06
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (50 bp):
TTATATAAACGAAACTTAAGTTTCTGTATATGTATATGCTATTTCCAATG
Left flanking sequence: Indices 13363 -- 13862
AGTCGAGTCCTATATCAAATGATACAACACTTAAAGCCGGCGGCACGACATTTGCGGCTGCTGGA
TGATCGCCGATGTGAGCTGTCACATAACCCCGATCTACCAAGTGTTTTACAAATTGCTTTATCAT
TGAAAACCTCTCCCCTATCGGGTCGAGCACTACGTGCCTCGAAAGAACCGCAAAGGCTATAATTA
AGCCTGGAATGTACCAAGGATTGCGCCGACTATCCATAAATAAATGAAAGGCTAAGAACAATCCA
GTACGCGCTGTCGTTCCGCGCACGAAAAGAAAGACATAAACGTGTACAATACGCGGCTTAACTCG
GGCACTCCGAATACATAGAGAACTTTCAAACAAAATTTTGGATTGAGGGTAATAACACAGGCACG
TAGTGCGCGTATTAGCGCATTAAAGCCTCTGACTACTGCAACTAGATAGGAAGCGGCTTCTTTCC
ATAAATTATTTCAACTTACACCTCGGCAATGGATGTGAAAAGCGA
Right flanking sequence: Indices 14003 -- 14502
ATATAACAAGTCGTATATGCCATGCATTATGCCGTACTCTGCGTTACGCCCCGGGCCCGTCTGGG
GCTTCTGAAAACAACACGTAAACCATGTCAAACTGAAGCAAATCAATATCCACAAAACACGAATT
CGAACTTCCTTCAGAATAGTTTTTAATACAAAATTCATTCCATTTCGTGGTGTGTTAAACCTGAT
CGAGACCGGGAACACGCAAAGCGAACAAAAAAAATATCTATTTTTTTTGTTCGTTTTATTCCATT
CGACCTTTTCCTTTTCAGCCTTCTTTCGCGATGCGAAGAAAGCAGGTTCGCATCGCGAAAGAAGC
GTGCTTCTTTCTTCTCGGGACGGGAGTTCACTCTTCCTTTGCGAAGTGGTTAGTAATGTACTGCA
TTCTTAGCTCAGTTGGATAGAGCAACAACCTTCTAAGTTGAAGGTCACAGGTTCAAATCCTGTAG
AATGCGTAAAGTGCACAATGAGTGATATATACCAACGCCCAAAAG
Found at i:50390 original size:47 final size:47
Alignment explanation
Indices: 50321--50412 Score: 175
Period size: 47 Copynumber: 2.0 Consensus size: 47
50311 GTCCGAAGGA
*
50321 CCGAAGGCCGGAAATGGCTTTCCAATTTCCGCACACGATATTGGGGG
1 CCGAAGGCCGGAAATGGCTTTCCAATTTCCACACACGATATTGGGGG
50368 CCGAAGGCCGGAAATGGCTTTCCAATTTCCACACACGATATTGGG
1 CCGAAGGCCGGAAATGGCTTTCCAATTTCCACACACGATATTGGG
50413 AAGAAGGACA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.25, C:0.26, G:0.27, T:0.22
Consensus pattern (47 bp):
CCGAAGGCCGGAAATGGCTTTCCAATTTCCACACACGATATTGGGGG
Left flanking sequence: Indices 49821 -- 50320
TCGAATATGACCCAAATCGTTCGTCTTGGATTGCTTTAGTACGATGGATCGAAGGGGTTCTACGC
CCTGGAAAGCACTTGGCTTTTTCTAAAGCGAATAGTCGAAGAGAAAAAAAAATGTTCTTTTTCGG
CCTCTTATTTTCGTTCTCTTCGCTGCCTAGACAAGCTCGGGGAGGAAAATACGAAAAAAAAAGGC
CCGTACTACGTACCTGCGGGCAGAGACTTAAAAGTTCCTGGGTCCTAGGGACACAAGACCTTAGG
GCCAAAGAAATGTCCTTAGGACCTTTAGGTAGCTTTCTTGGTTTACCCAGCATAGCGGTAGCTGG
GGCAAAGCCCGCTTTTTTCGCTTTTCGAATGAAAGGCCCTTCCTCCCTAACGGGAAGAGAGCGCC
TGTCGGCCCTCGGAAAAGAAAATACGTTCTCGCAAAGCGAAAGCCCAAGGTGGAGAACGCATAGC
GGGGCGCCGATAAGAAAAAGCCTAGTACTCTCTTGGTCCGAAGGA
Right flanking sequence: Indices 50413 -- 50912
AAGAAGGACACGAGACTCGAGGGAGAGGCACGTAGTGCTCGACCCTTATTTCATAAAGCCCGAAC
ACGCTCCCCGCGCACTACGTGCCGTCGGGCCTTCGGGTTCGGGTCGAGTGCTACGCACCTCCGAG
CCTTTCACTTATATATTAGCCAGTGAAAAATTGGAAGTAGGTAAGACGGTGATTAATTTTCATCG
GTCTAAACTTTCGACCCCGTTAAACAACCATCAACCTTCCCAGAAAGCTAATGACCCTTTGGGCC
TTGGGGTTAAAGAGACCGCGCAGGATAGCCAGGCTTGGCCGCACCCCCGTGGTGACTACGCCTTT
AGTGAGAATAAATACATACTTGATTCATATTATCAAATGGTCGGAAATTGCATACCATTAGCCAA
AATACCTATAGGCACGTGGGTACATAATATAGAAAGGAACCCAGGGCAAGGTGCAAAGTTGACTC
GAGCTGCAGGAACCTTTGCTCAAATAATTAAAAAGGTTGAGAATA
Found at i:52259 original size:59 final size:59
Alignment explanation
Indices: 52163--52276 Score: 192
Period size: 59 Copynumber: 1.9 Consensus size: 59
52153 CCGGCGGGCT
* *
52163 CAAAGGGCCGATAAGGCCGGAAATTGCTTTACCATTTCCGCGCACGAAGACCAACGGCC
1 CAAAGGGCCGAAAAAGCCGGAAATTGCTTTACCATTTCCGCGCACGAAGACCAACGGCC
* *
52222 CAAAGGGCCTAAAAAGCCGGAAATTGCTTTACTATTTCCGCGCACGAAGACCAAC
1 CAAAGGGCCGAAAAAGCCGGAAATTGCTTTACCATTTCCGCGCACGAAGACCAAC
52277 AGGGCAGAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.32, C:0.29, G:0.23, T:0.17
Consensus pattern (59 bp):
CAAAGGGCCGAAAAAGCCGGAAATTGCTTTACCATTTCCGCGCACGAAGACCAACGGCC
Left flanking sequence: Indices 51663 -- 52162
TTCGTCTCGGTAGGTGTATTATTCATCATTTTCCTAAAAGGACATTCATTCATGTATTTTTTCTG
GATCGACTTAGCCAATCAAGACATCAAGGCCTTGGGGCAATACAATCTGTCAAGTTGATTAGGTG
TATTCACGACGATACAGTAAAACAGGGAAATGAAGTCGGGATTTGGCTCAAAAAACGCTATGAAT
ACCACGAACGATCGCCATCAATACAGGAGATTGACCAATTACTTCGAGTCAGCGATTGGATGACC
GACATAAACTCCACTTCGAAAAGTATCTGGCCGAAAGACGAAAATGATGACAGAAGAGCGCCAGA
AGAACGCTATGCGTTCTCTCGCTTCGCGCCTTCCGCCCCGGTAGCTGTGCGTGCTGAAAATAAAC
AATCTATTTTTGGGTCCGAAGGTTCCGAAGGAGGCTTTACGAAAGAAGGACCGATGAGGTCGGAG
ATGGCTTTACAATTTCCGCACACGAACACTCGAACCCGGCGGGCT
Right flanking sequence: Indices 52277 -- 52776
AGGGCAGAAGAGAGGCACGCAGTGCTTCCAGAAATGGCTGAGAAAGAAGAGTCCAATGGAGACTC
CTTTGGTTTTACCGGGCGTGCTTTCCTGGATTATTTTGTCATGCAATACTTCTTTAATCTAAAGA
ACCAAATTCAATTCGATCCTATGGTTAACAGAAGTCCCGTGGCACAAGGCGTAGCTCAAACATCT
ACGATTGGGGAAGCAATTTCGGCCAAGACCGAGCAAGGAACACAAAGCGGGGAGTCAATTCGTCA
ACCCAGGTCCACATTCTATTTCGATGCTATCATATTTTTGAGGTATGCCCGATTTAGGTTTGTTG
GTACAACAACCAGTCGTTATTATTATTTTAAAAAAATGCAATCTTTATTTTCTAAGAAAACGAAA
ACTAATACCTTAATTCAGCCAGTCAAAATAGCTTCTGTTTATCAAAGTGCCTCTCTAATTGCTCA
AGAAATATCTTGGAAACTGGAACAAAAAAAATCATTTCGACAAAT
Found at i:58665 original size:27 final size:27
Alignment explanation
Indices: 58635--58690 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
58625 ATACAAACTC
*
58635 ATGCAAAAAAAGCACGGCATTACTAAT
1 ATGCAAAAAAAACACGGCATTACTAAT
* * *
58662 ATGCAAAAAAAACACTGTATTACTTAT
1 ATGCAAAAAAAACACGGCATTACTAAT
58689 AT
1 AT
58691 TCAATCAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (27 bp):
ATGCAAAAAAAACACGGCATTACTAAT
Left flanking sequence: Indices 58135 -- 58634
AAAATAAATCATGTCATATATTTTAGGAACTAATTTCAATTCCAATAAACAAGTAAAAATTGCCT
TAACTCGAATCTTTGGAATTGGCCCTAAAAAGGCCATTCAAGTTTGTGATCAATTGGGCCTCAGC
GAGAATATTAAGGTTAATAAGTTAACTAAGTATCAATTTGACCAAATTCTAAAAATAATAAGTCA
AAATTATTTAGTTGATTCAGAATTGAAGAGAGTCATTCAGAGAGACATCAAACGATTAATTGGTA
TTGGTTGTTATCGCGGGTTTCGCCATAATGCAGGATTGCCCTTACGCGGCCAACGAACTCATACT
AATGCTAAGACTTGTCGCAAATTAAGATACGTTTTGATCAAAAGTTGATCAAAAATTTTTTTGTT
TTTTTTCAGTTCGTACAAAATATCTCTGTAATTAGTAAACGGATTAGATGGATCGTAAAAAAACA
AAATCGATGATATCGAACAACACCAAAAACATTCGATACAAACTC
Right flanking sequence: Indices 58691 -- 59190
TCAATCAACTTTTGGTAATACAATTATTACTTTAACAGATTATAACGGAAATACAAAAACTTGGT
CCTCCTCAGGTTCAGTGGGGTTTAAGGGATCTCGTCGCTCAACCAATTATGCTGCTCAAGCAACT
GCAGAAAATGCCGCGCGAGCTGCCATTCAACTGGGATTTAAGTTTGTTGAAGTAAGAATAAAAGG
ATTAGGTTATGGAAAGGAATCTTCGCTACGTGGTTTAAAACTAGGGGGTCTTATTATTACTAAAA
TTCGCGATGTAACCCCAACGCCACATAATGGATGCCGACCCCCAAAAAAACGTCGTGTTTAAATA
TCATTGTAAAGTCCTATGTCATTATAAAATGGTAAATTGAGGTTTGGGAGTAAACAAACTTTTTT
TAGGGTTCGAAGCGAAGGAGGCTTTACGAAAAAAGAGTAGGGTTCGGGCTTTGGCCAATACCAAA
GAGCGCCTTCAGTCGTGCCGGGAAAGAGTCGGATAAAAAAAAATT
Found at i:126922 original size:24 final size:21
Alignment explanation
Indices: 126864--126926 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
126854 TTAAATATCC
**
126864 TTCATATATGATTCCTCATCT
1 TTCATATATGATTTTTCATCT
*
126885 TTCATATATAATTTTTCATCT
1 TTCATATATGATTTTTCATCT
126906 TTCTATCTATATGATTTTTCA
1 TTC-A--TATATGATTTTTCA
126927 GAAAACTCCG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 21 0.60
22 1 0.03
24 13 0.37
ACGTcount: A:0.25, C:0.17, G:0.03, T:0.54
Consensus pattern (21 bp):
TTCATATATGATTTTTCATCT
Left flanking sequence: Indices 126364 -- 126863
TAAAAACCCCGCTCCGAGTAATACTTTCCATCCATTTCTTCTAAACTAAGCCCAAATCAAACAAA
CAGTTGAAACATATCCGATTTGGATACAGAAAACAAGGCCGCGTCAGTATTAAGCCATCTCTTCC
TATCTACCAAATCGAAAAGTATATACGTAATGCGGGAACCAACGCCACCCGTAGAGTTGGCAAAC
AATCGCGATTTAACACCTTTTACATCAATCATCAGGGCCGGAGGCGACCTCGTGAAAAGGTTTAG
AGTTCTGTAATAAATATTCCCAATTCGCTTTTATTGAAGCGGAATTCAAAAGTCTTTATTTCTAC
AAGACGCAATCTTTTGTACCAAATTTGGGTCTAATCGTATTTCCAATGCCTGATTCATGAATTGA
ACAATTTTATCCCAATCTTCAGGCCCGTAGGGCTCACCCGTAAATCCATTGCCTGCGATGGAAAA
ATTTTTTGTACGCAGACCTAACCTATTTCTCATATTTAAATATCC
Right flanking sequence: Indices 126927 -- 127426
GAAAACTCCGTTTCCTCATCACATGGTCTAACGTATCTCTCTGAACTTGGTACTCAATTTCTCTC
GGGTATCCACTCTTTAACACATCACGATTAAGTGTCGGGTGAAGTGGACATAACCTTTTAATCAA
ACACTAAAGCCAAACGTTTACTATTTCAAAACTCTTTATAGTTCAAGGCCCGGAGGGCTTGCATT
CGATTTTTTGACGACTTCGATTTCCCATTTTGTATGTATCAATTTAACTCCCTGCCCCATCTTAT
ACTCTTTAAACCCGTGCTAGGCCCCTCGGAGACAGACGTTCAACTTGTCAAAGTTTTTGTTACAT
TGAAAGTTTGACAACTGGAACACATTACCTTACTTTTAAACCAATCAAATAATTGACTTATATCA
ACGGTCTCGGTTTCTGGAGACCCGCCACGGCTGATATTTGACCTCGAAACAAGTCCAATTGTCTT
CGAGTTTTCCAGGAATATAACTTGGAAATACTACCTGTCTCTTCC
Found at i:143681 original size:16 final size:17
Alignment explanation
Indices: 143653--143693 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
143643 GATCTAGAGA
* *
143653 GAGGG-CCGTAGGCTCG
1 GAGGGCCCGGAGGCCCG
143669 GA-GGCCCGGAGGCCCG
1 GAGGGCCCGGAGGCCCG
143685 GAGGGCCCG
1 GAGGGCCCG
143694 ACCCGACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 2 0.10
16 13 0.62
17 6 0.29
ACGTcount: A:0.12, C:0.32, G:0.51, T:0.05
Consensus pattern (17 bp):
GAGGGCCCGGAGGCCCG
Left flanking sequence: Indices 143153 -- 143652
TCGTATATGGAGATTCGGAAAATAAACAAAATATGCTCTGGCCCTCCGGGCCTCCGGTCTTCGCA
CCCCTCGGGCCTTTGTTCGTCAGTTTATTGTTCTTCTCTCGTCTGACAGTCCCCCCTGGGCCCTT
TTTTTTCAGTTTCTGTTTCCCTTTCCCGTCCGACAGTCCCGGGCCCTTTCTTTCGTCGGACAGTC
TTTTGGTTTTGTGGTGTCCGACAATAGAAAGTATGGGGCCCTGTCTGACGAAGCAAAGTGCTTAC
GCACCTTCGGACCCATAGGCACGTCATGCGCGGGGAGGGCTTTGGGAAATAAAAGGTAAAAATAT
TTTTTTTTTATTCCACGTTTCGTTCGGGTCGGAGACGCTCGACCCGACGCGTAAGCAAGTGTTAC
CCCGCTTGAATCCAAAGCCGGGGAAGATTATAGGGCCGTAGGCCAAAGGGCCGTAGGCGGAGGCC
CGGAGGGCTCTGTTGGGGGACGGGAATAATGCCATGATCTAGAGA
Right flanking sequence: Indices 143694 -- 144193
ACCCGACTTTCGGGTCAGGTACGAGAAGGCCGTCTATGTAGTGCGTAGCTCACAGCAGACGAACA
TGCCCCCGGGGGCCTGCCGACATAGTGTACACCATGTACAAAGACCAACTGGGTGCAACGGGCCA
TACGTACCAGATCACAAATAGCACGAAATAGGTTCTTCCTGGTGAGAGACAGGTATTATACAATA
ACTTCATTGTATAATAAAGGTCCAAACTTCGAAGTATTGTATAATACAGGGAAGGATTTCGTTCA
TCGCCGGCCGTGGGTGAAGGAAGAACTAAATCTCACGGGCCAGGCCCCCGGGCCCCAGAGCCAGG
TTAACCTTGTACCCAGCGTATGAGCGTTCATGTCTGAGGCTTAAAGCCTACCTATTTCGGTGAAG
CGTTTTGTAAACAACCTCATATACCGGGACCGAGGGAATGAAGTTTCCAAGGTTCGGCGAACCGA
AGGGGCTTTTGTTACAGGGGAGGGGTATAGTCGAACCCCAAGGCG
Done.