Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_016742
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: 425718
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Found at i:8758 original size:15 final size:15
Alignment explanation
Indices: 8735--8764 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8725 ACTAATTAAT
*
8735 GTATTGTATAGTAGG
1 GTATAGTATAGTAGG
8750 GTATAGTATAGTAGG
1 GTATAGTATAGTAGG
8765 CGAGCGAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (15 bp):
GTATAGTATAGTAGG
Left flanking sequence: Indices 8235 -- 8734
TTTGATTATGGTATGGTATTGTCAGATTCGAACATAGGGCTACTTTATTTGTTTGCCATATCTTC
GTTAGGTGTTTATGGAATTATTACAGCGGGTTGGTCTAGTAATTAGGGGGCGGCCGTTCGGTCGC
CTATGATACTAGGACCAATAGGTCAAAAATGGGTTTGTGCCGCAGGTGTTGAACGATCTACTCTA
CACAGGTGTGGGCTTACAGGGCTAGGGCTCATAAAGCCTTTCTTTCATTCAAAAAGAGGGCCCTG
GTCGGTCACTTTTCCGGGCCGGGATCGATAGATAAGTGGAAGTCATAAAAAAGAGATCTTTCTCT
TCGCACCTAAGATCAAGAGGAAGGGTAGCTTGTCAAGCTGGCCTATATAAAATATCTTTTTCATT
ATTATAGAATCTTTTATAAATATTTATAAAGATTCACTGTCTTTTAACCGGCTGTTCTTCTTTGT
CAACGCTACTAAGGACCTATGGGTTAGCCTACCCTACTAATTAAT
Right flanking sequence: Indices 8765 -- 9264
CGAGCGAGTTAGCGAAGACGCTTAGGCTAATAGATAAGAGAGCGTCAGTGCGTAGCCTTCATTCT
ACTACGCTACGCAAAGGTTACGAAGTCACTTAGCTCGACGTTAGGAGAGTAAAGGGGGAAGGCCA
TACCTACATAGAAGAACCGCTGTTCGCTGACTTTCTAAGGTCTAACCTTTAGCTCCCCTACTGAA
AAGGGGCACAAAGCCGCTTTGCACCACTGATAGACTACTAAAGATTCAATTCATTCAAAAGGCCC
TACTTAGTTTCGCAAGCCTTTGTCATTGTCAGTCAACTAAGTAGGGCCTGAGGCCCCCTGCGAAT
CCGTAAATCTGAGGAGCATGCCGCAACACAACAAAAGGATGGTCCCCTATGCATTTCATTCTTTC
CGGAAGGGAAAAAAAAAAAGTACCCCCATCATGGTGAACCTCTCCTTGTGATCGGGATGAGGTAG
ATGCCTCCCAGCTGGGGGGCGGATCGAATCGGAGTTTCCTTAGGT
Found at i:41352 original size:13 final size:13
Alignment explanation
Indices: 41334--41358 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41324 TGTTTTCATG
41334 TCTTATATATATT
1 TCTTATATATATT
41347 TCTTATATATAT
1 TCTTATATATAT
41359 ATATGTATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
TCTTATATATATT
Left flanking sequence: Indices 40834 -- 41333
AGTGTTCAGAAGCCTTGAAAGACCCAGTCATCATTACCAAACCGCTTCTGGGGCACAGCCAAACT
AAGTAGAACCGCCCAGCCACACTCCGTCTATTCCAAAAAATGAAGTCATTTCTCTGGTCTGCGAT
CCTGGAAAGTCTTCCTTAAGCAGATAATCTAAACTCGAGAGATAAAAATCTTCCTCAAGACCGTC
CATTTTGCCAAATCCCCACTGAAACGGCAAGCCATGTCCTTCTACATTGCCTAAACTTTACTACA
CAGGTTTGGTCCTTGGTTTTTGGTCTTTTTTCTGTTAATTGGTCTCATTCTCATTCTGAATCCAT
TCGCCAGTCATTTTTCTCTTGGGTTAAAATAAGCATTCCATTCCAAACACAAGAGCATATGAATC
TCCGCTTTCCTCATTCCCATCTGGCATATCTGGAAAAAAGCGTAATGAGAGAGTCTTCGACCCCT
CTTCTTCTTCTCCCTTCGGGTCACTTCGTTCACTCTGTTTTCATG
Right flanking sequence: Indices 41359 -- 41858
ATATGTATTCTAGGTGGGTAATTTCTTCTGTTATGAGTGAATCTCTATGGCTTCTTTCTTTTCTT
TCGTATTCCTCTTTTCTGTAGCAATCAGCCCTCTTCAAGCGATCTTCTATAGGAGAGCCTATATG
AATGAAGCAAGAAATCCAGCCTAGCAGAGTCAGCATTCCCTCTATCAATCTAGCACTCTAGTCTT
TATGGCGCAATCAGTTAATCAATTGGAGAATGGGGGCTGGGGATATGGAATCTTCTTCGTTATTG
CCTGTTACTCCTGTTTGTTTCTTCTGATTCTAAAATGGATCTTTCTATTGCTTTGAGATAAGGGA
AACGTTCTTGTACTATTCATCCCATCACTCCATTTCTTTCCTTTGCTTTGAAGGCCTCTCTCCTT
CCCTTCCTACAGGTCTCTTGCTCTTTCTTCTGCAAAATAGCCTAAAAGTCTACGGGAGGCCCTTG
CTCATCCTGAATGGATAAGGGCTATGGTTGAAGAGAAAGAGGCAC
Found at i:213734 original size:18 final size:18
Alignment explanation
Indices: 213713--213755 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
213703 CAACCTTGTT
213713 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
213731 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
213749 GACTATG
1 GACTATG
213756 GCAGGGCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (18 bp):
GACTATGAAACAGATCGC
Left flanking sequence: Indices 213213 -- 213712
TACCGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGA
GACAGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTAC
CTTAGGACAGTTAGAGTTACTGCCGCCGTTTACCGGGGCTTCCATTCAAAGCTTATAACACTTCT
CCTTCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGT
CCTGTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGA
GAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAG
CGCCCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGAT
CGCCCTCCCAATTCGAAGTTTTTTCCTGGAAGTTTCAACCTTGTT
Right flanking sequence: Indices 213756 -- 214255
GCAGGGCGGTACGCTCTGCTCTCTCGCGACCCCTACTCTAACGAGTAAGCAAGTAAACTACCTTT
TGAAGCGCCAGTCGCGTAGGGCGACCGGGCCAGGCCGAGTCAGAAAGGCTTTGATGACTCAAGCA
AGGTTCATATTAGGGAAAGGAGAGTGAGGGGAAGAGGGGGCAGCCCTCGGCCCGATCATCCAATT
CACTCCAACAGACAGGCATGGTTCTGTAGTCAAAGCAACTTCGTCACTTTCGTGTACCCATCGGA
CGGCAGCCCTTTCGGGGCTTCCTTAGGGACCGATTCACTCTGCGTAGATTGACTGAACGCAGAAA
GCCTTCCACTGGCAGGCGATCGTGTTTTTCACAGGATTTCTCGTTACTCATGTCAGCATTCTCAC
TTCTGATATCTCCAGGTGTTGTCACCAAAAACCTTCCCCGATTGACAGAACGTCCCGCTACTGAC
ACTTGAAAAAGCAACTTTCAAGGTCTCGTCGCTTCGGTGAATCAC
Found at i:219666 original size:22 final size:22
Alignment explanation
Indices: 219612--219667 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
219602 TGCGAAATGA
* * *
219612 AATTAATAGGATATATATGAGT
1 AATTCATAGGATATATATAAAT
*
219634 AATTCAAAGGATATATATAAAT
1 AATTCATAGGATATATATAAAT
* *
219656 ATTTGATAGGAT
1 AATTCATAGGAT
219668 TAAGGTAGCG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.46, C:0.02, G:0.16, T:0.36
Consensus pattern (22 bp):
AATTCATAGGATATATATAAAT
Left flanking sequence: Indices 219112 -- 219611
ATACCGATGGAATGAACGAAATACGAACAGTTAGCATAATATGGTCATAGATCTTAGGTTGTAAC
TTGATCATGAGCGAATTTGTTGATGTTGCACCCACGAAGTATAGAAAGTACCAAACATTGGGAAC
TACCCGGGGAAGAGTTAGGAACAGGAACAAGGAGAAGCGAGAACCACTTAAATAGAGGAATCGAT
TGTATTTCCTCCTTTGTTCCCCATAGCAACTGGGGATCAAAAAGCACCAAATTTGATGACTTATT
AAGGGAAAGACGAAGTAAGAACATGCTATTGAAGACGTTGCAACATATGTCGGGGAGGCCTCCGT
TGATTGTGTACAAACAAAATACGAGTCCAAAGACAGGGTAAGAAAGGGTTTAGCTAATGGAGATA
TTAACTCTTCCGGGAACCAGTAACGCGTAAACCATGTCAAACCAAGACCGATCAATATCCGAACG
GAACGGATTCGAACTTCTCCTAGAATAGTTTCCGGTGCGAAATGA
Right flanking sequence: Indices 219668 -- 220167
TAAGGTAGCGGTAGTATATTGGAAGAGGAACTAGCTTTTACTTTCGCTATCTGATTTGAAGTGCG
AAAGCTCTTTCAAAGTTAGAGAAGAGATAATAGATCTTACGTAAGCCAAAGGCTATTTAAAGAGC
TTCTATTTCACCAACTGCGTCTACGCATTCACCAATAAGAACTGGCAGCGGGTAGACATGAAGTA
AAGTAATAGCTCCCAGGACAAAAATCTTTGCCTTCACCACCAACTACTCGTACTCCCATACCGGT
AACACCAGTCAAGAAGGTAAGGCAGATTCTATAGCTGCTGATTCTAGCACACCGGAAACCCTCAC
AGTAAGAGTGGATAGGCTTACACCGGTTAATTGAACACTTTACCATTCTCGATGCAGCGGGAACG
CTCACTCGCGCCAACGGATACTGTCACAGCTAATTGAAGTGCTAGTCCAGCAACTGCAGTTGTCT
TTCTGTTTGCAATTGAATCACTAAAGTAGGAGGGTGCTATTGACT
Found at i:248464 original size:5 final size:5
Alignment explanation
Indices: 248456--248482 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
248446 GTAATTCAAT
248456 TATTA TATTA TATTA TATTA TATTA TA
1 TATTA TATTA TATTA TATTA TATTA TA
248483 ATAGGGTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Left flanking sequence: Indices 247956 -- 248455
GCGAAGGGAGCCCACTTCCCACTCTCCCTTCCCCACCCCAGTAGGGGTGGCCTCGTCCTCTTCCT
CAGGGACTACACCTTTCAAAAGGAGAAAGTTAGAAAACAAATAGAATCAAAAAGGCCATCATTAA
TGCGAACAAGGCAATAGCCTCGGTTAGAGCAAAGCCCAGGATTGCATATCCGAATAACTGTTTTG
CCAATGATGGATTTCTTGCCACGGAATGAATTAATGAACTGAATACGTTTCCAATACCTACAGCA
GCTCCCGCTGAAGCAATTGTAGCAGCTCCGGCACCCATTGATTTTGCACCTTCTAACATCTCGAA
TGGAGAAAGAATCGTCACGCTCTTTCATTCACGATTTTATGTTCTCGTCGCTTCTTCCCCTCGTT
CCTTTTCTCTTGGACATCTCACTGGAAATGCAATCATTCTTTTCGATCTATTTAGTAAAAGAAAG
TCTCTCACGGATATCCTATTTGTAGATATGGGTCCGTAATTCAAT
Right flanking sequence: Indices 248483 -- 248982
ATAGGGTGGTAATAGTTCCTATATTTGCCTATCGAACAACAAGTCTTAATGTATCGTCGACTTGA
TACTACCAGCTTAGATACATGTACCGGATGAGGCGGAAACCCATACTAAAAATAAGAAAGGAAGA
CCCATGCATCAATCAAGATCTCTATCTATAATATAACATACCTCAGGTTGGATTCAACCACTTAG
GATGATGATCTGCAAAACCAAACCCCATGACTTTATGCTCTGCCAGTCTTCCCCTCTTCTAGCTA
TTCGCATGCGTCGATCAATCATCTTCGGCAAAATGACCAGATAAAGTATGCACCAAGGATCCATT
AGATTAAACTAAGTGCATGATAGACCGATTCTTATATCCTTTGAATGTGACCACTGCTTAGATTA
TGATTATGTAAATGGATCCCCATTAAGTCGGGCCTGTGGACAATGTTTTAATGGATCACCCGCCT
GATGGGCAAAAGAAAAACATGAGCCCAATACGGTACCTCATAGGG
Found at i:280839 original size:15 final size:15
Alignment explanation
Indices: 280819--280849 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
280809 AAGAGCAATC
*
280819 AATTAATATTACTAT
1 AATTAAGATTACTAT
280834 AATTAAGATTACTAT
1 AATTAAGATTACTAT
280849 A
1 A
280850 TATATAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (15 bp):
AATTAAGATTACTAT
Left flanking sequence: Indices 280319 -- 280818
TGCAACGGAAAAAAACGGAGCTGATTTGACTCGGCACAACCTAACGATGCATCCAATACCAATGA
TATTACCCCATGTGAAAGTGCACCAACACTTCCAAGGGAGCAATTTGAATAATTCCCTTAGGTCG
TCCACATGATTACCATAGTCAAATAGGGAGACCTCAGTCCAGCTCCCCACCTATGAATGTTGGTG
ACTTCTGTTCCAACTGAACTGGGGACAGTCAGGTGCACCCATTGGACCCGAGGGACCAGGGTATA
GTCCGGTCTTTTTTTCCCGGTCCAATGTTCTACACAAAAGAAGGACTGCACTAAAACTAAAAAAA
AAGAAACCATGAAAAAAAATTTATGCTAAATTATATCCTTCGCAGTAGTTTATGTTTGACGGCTG
TCTATCTCGTACAGTGTCTCCGATCACAAACCGCTATTCTTTCCACCCCAGAGTCATAAATCAGG
TTTTTTTTTTAATTGTTGTTTATCCGGAAAGAAAAAAGAGCAATC
Right flanking sequence: Indices 280850 -- 281349
TATATAATTTTGCTTCGATGTTCTCGTTCTTGTCCTTTCCTCATCCTTGCTGCTTTGTGCCTCTT
GTGCTTTTATCAGCGCGTGGCACCCTGTAACAATGAATTGAGCTTGGCTCTGTCTGTCCTTCAGT
TTGTCTTGCTTCATTTCTTTGCCTTTCTCCGGAGAGGAAGAAGAGAGTGTCTTGACTCGCTCTCC
TAGTCTTTGACCAAGTCCCGTAGTCTTATAAAATAAAAAGTCCCCTTTCGCTTCAACTGTCCTGT
CTATAGGTTCGATAGTGGGTTGCTCTGTTTCTGTATCTCGACCGTTGACTGTGACCTGGAGACTC
TGGTCTCGCTTCGATGGTTACTGGTTGTTTGAATCTCTCCTCTTCTTTTATTTCGAGTGTTAGAG
TCAACCATTTACTCTAAAGAGAGTGAGCGACCTACTAGTAGCGGAATGAGGAATATAAGACTTCT
GTCTTACCGCTACGCCCCTTTTTTACTCTTTTCGAATCCCCTCTT
Found at i:367300 original size:12 final size:12
Alignment explanation
Indices: 367283--367307 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
367273 TTCTTCTTTG
367283 TTTGTATATATA
1 TTTGTATATATA
367295 TTTGTATATATA
1 TTTGTATATATA
367307 T
1 T
367308 AAATAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (12 bp):
TTTGTATATATA
Left flanking sequence: Indices 366783 -- 367282
AATAAGACAACACAGGGGGTGGAGTGAGCCTAGAGTAGAATAAGACTCCCTCTTAAACTCTCAAC
TCATACCAGGGCAGGCAGGGAAAGACTGAGACTACCGATACCGAGCCGGGGTTGATGAAAGATCA
CAGGATAGATACCCTATGGTTTGGTTGGTCTCTATGCCTGCTTCACTTCGTAGCATTAAGGGGAC
AGTGCAATGAGGGAAATCGACTAGGAACGCGATGTCTTCCCATAAAATGAAGAGTGGAGGGGACT
TCGACTGCCTTCTTGTATCGGGTGAAGAGAAGGGGGTGGTAGGCTTAGTAGGGCTCGAACCTACA
ATATTACCGTTATGAGCGGTACGTTTCAACCAATTAAACTATAAGCCCCTACGGATCTCTACATG
CAATTCGCTCACTTCGGGAAGAGTGGACGGAAAGAGGAGGCCTTTGCTCTATCTGCTTCTTCCTC
TTCCCAGGAATGAACAATTGGATAAAAAAATGATTTTCTTCTTTG
Right flanking sequence: Indices 367308 -- 367807
AAATAATAAAATAAAGATTAAGCAAGCGGCCCTTTCGTGACTCAAACTGCCGGTACGCTTTCCGG
CTCGCAACGACTCAAACGGGCGGGGGCTATCTATTTGCTTGCAATGCGGGCTGTTCGCCTTTCGG
ATTCGGAAAGGGTTCGCCTATTTGATTTTTATTCAAAAGGCGCTACTAAACTACTCTAGTACAGC
TAGTGTTAGTAGTACAACAGAATGCCGTTCACCCCGCAATCCCTTCTTCTTCAAGAGCTCCCTAT
TCTCTAGCAGCCCCTTCTTTCACAGCTCCTTCTCAAGCACTTGCCATTGTCTGGAAATTTGCCTT
GCCCCATTCTTCGATTATTGGCGCATCAATTCCTTGCCTTTGCTCTCATTGCTGCTTGAAGTCCA
GTCTTTTAAGTCCCAAAAAGAAAAAAGGAAAGTCAGTAGTAATTGTCGGGATGGAAAGCTACTCT
TCAACCACTTATTTAAGCGCTATGCACCTAAGCTCAGTCTTTCTG
Done.