Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_069572
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: 212159
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Found at i:40940 original size:18 final size:18
Alignment explanation
Indices: 40914--40949 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40904 CCTTATCCAA
*
40914 GAGTGGGTTATAATCTTG
1 GAGTAGGTTATAATCTTG
*
40932 GAGTAGGTTATCATCTTG
1 GAGTAGGTTATAATCTTG
40950 ATTCCCTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.08, G:0.31, T:0.39
Consensus pattern (18 bp):
GAGTAGGTTATAATCTTG
Left flanking sequence: Indices 40414 -- 40913
CTAAGATCATTTATCATGGTGATAATCGTCTTACCATATATCAAGGGCATGAAGAGTCTTTTCAC
TAGTTTTCTAGAAAGCTTTGATTCTATAATTGGCATTTTAGAGTGATCCTCGAAATGCATATTTA
AATAGTCCAAAAGCTCCTTATGCATGTGCATGTATACGTCTTGTATTTGCCCATCCGGGTGAGGA
AGCAGATTCGTTTTCACTGCCATATCAATGTTTAGCAATAAATAACTCATGATCTGATAAGCACT
GGAGGAAGCATCTTGAGATATAGCTTCTTCCTTATATTCTTCCATTATCTCGTTCGAGGCACACT
GAGACTTCGAAATGAACTGAAAAGGATCACTGGCCCCTTTAACAAAACGAATTAAGGATTCCTCT
GAAGAATGGATCAAACTCTTCTTTGACTTAACCCATTCAAGTGCTTTCTCGTAGTTTTTGAATTT
TTGATATTTAAAGGCAGCTGATACTTCAAGTATGTCCTTATCCAA
Right flanking sequence: Indices 40950 -- 41449
ATTCCCTTTCTCAAAGACTATGAGGCTTCTAGCTAAATCCCGCTCATGAAAATGAAAGATTCCTG
ATCGATAGATTCTTCCCCTAAAATCCATAAATGCAGGGAGATAAAATACATAACCCTCATATGCG
GAGGCTAAACTAATAATGGATTCTTCAAACATAGCCACTTGCATCTCATTAGATAATTGTTGAAA
GAGAGAACCTAAGGATGTGACTTTCTTTATTTCATCATTATTGAAATAAGCTAGCCTCAGATGAT
CATAAGCATCTTTCATATTCACGTATGCTAGTTTTCTTGGCATAAGAATCCCCTCTCTTTCTAAT
GTGTTCCTATTTCTTTTAATGAACTCCAACATTCTTTTATTAATCTGAAACCCTTGTTTCTGAAG
ACCATTTAATATAAAGCACATATCTCGTATCTTATTTTCATTTAATTCTATATTGAAATTATTAA
GATTATGGGAAGAAATGACCTTAAATCTATTATATAAATCAGCTG
Found at i:41835 original size:28 final size:28
Alignment explanation
Indices: 41795--41851 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
41785 CTAATTGAAA
* *
41795 ATCATGATATTATTATTCTGATTATTCT
1 ATCATGAGATTATTATTATGATTATTCT
*
41823 ATCATGAGATTATTATTATGATTCTTCT
1 ATCATGAGATTATTATTATGATTATTCT
41851 A
1 A
41852 AGCGAGTGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (28 bp):
ATCATGAGATTATTATTATGATTATTCT
Left flanking sequence: Indices 41295 -- 41794
GAACTCCAACATTCTTTTATTAATCTGAAACCCTTGTTTCTGAAGACCATTTAATATAAAGCACA
TATCTCGTATCTTATTTTCATTTAATTCTATATTGAAATTATTAAGATTATGGGAAGAAATGACC
TTAAATCTATTATATAAATCAGCTGTCGGCTCACTTAAGTAACCTCCACACATATCCGATAACAT
AATATGCCCACTTGTCATCTGTTTCTCTTTGAGTTTCCAATTGACAGGCATACATACCATTGGCA
GATTGAGTTTTAATGGAAGATGTGAATATACATCCTTCATAAAATCCTCAATAAGAACATGTGAC
ACTGTCGAATAACACTTATTAGACCCCTTTAACACTCTAACTATACTATCTTCTGAGAAATACCT
GTTAATCATTTGGGTTTATCTCTTTTAAAAGTAATTCTAATGGTAAAACGAAAACGAACTCGAAA
GCGAAGCCCTTTAAATGGTGCAGGCGAACCGTTTACTAATTGAAA
Right flanking sequence: Indices 41852 -- 42351
AGCGAGTGGATTATGTGGTTTTACGGATCTTATCTCTAAAGGCTGCCATGTATGTTATGGGTATT
TTTTTTTGTATTCATATCATTTATGGATATTAACAACTTGGAACTATTTTGCGTTCTAATACGAG
AAGAGTTTTCTACGAGTACTTATAAATATCCTTCACTAAGGGAAATCGACGTGGATACGTATTTA
AAGCACCTTCATGACTGTCAGTTCAGGGATAAGGATATAGAAGTAGTTTCAGATATGGGGGAAAA
CTCTAATTCTTTTATAGAGGACCACGTGGGTCCGACTGCTCCTAAATGAAGTTTTCCTATTGAGA
TGGTCCCATTACTCCGTGTATCATTATCCACTCTTATCTATAGATTGCAGAGTGGCATTTCCAAT
GATATAGCTGCCAATGTTCATGCATTTCTACCAAATCGCATACGAGTCCATAAATTAAGTAAAAC
GATGGATTCAATACATGAAAATAATGAACGTTTCTATTCATTCCA
Found at i:97922 original size:19 final size:18
Alignment explanation
Indices: 97898--97933 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
97888 ACCTATCCAG
97898 AATATAATAAACATAATAT
1 AATATAATAAA-ATAATAT
97917 AATATAATAAAATAATA
1 AATATAATAAAATAATA
97934 ATACGAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AATATAATAAAATAATAT
Left flanking sequence: Indices 97398 -- 97897
ATTTTTTTTATTGACATAGCCTCAAGTCATACCGTAAAATTAGACTGATACGGAAAGGATGGTCG
GGATAGCTCAGCTGGTAGAGCAGAGGACTGAAAATCCTCGTGTCACCAGTTCAAATCTGGTTCCT
GGCATATGATTTTTTTTTTAATTTAAAGTAGTTAAAAGAATATTATTTTTTTTCATACCTTCTCT
GTTCTCGTTCAAAAAAAAACTATTAATACTTCATACGTATTTGAAAGGTTAGTTGGTTAAAAGAT
CCAAAGGCCTACTCTATAGAAATTGCAGGATAGGACTAGAAAAAAAAGAATTTCAGATACAATAC
AAATATAATAAATTATAGTCTACTCTTTTTGATTTCTTGGTCGCTTTTTCCGCGTATTATGAATC
GATCTAAGTCGTGTGCGCAGTACAAAGTTCATGTTCCTGATGGAGAGCTCTTTTAGTTCATGCTA
TTGGTTAGGCTTATCCGAACTCAAAAGAATTTTTAACCTATCCAG
Right flanking sequence: Indices 97934 -- 98433
ATACGAATGACGCTTGCATTACTCTGTTTGATCTAGCACAGAACGTACAAATCAAATATTCCTTT
AATATCTGGAGTTGTAAAAGTGAGGATTAGTTTCTTATCATTCAATGAGCATCTTGGATTTCATA
AAAATTGGGAGCAATATAATCCTTACGTAAAGGCCATCCTATCCAACTTTCAGGCATTAAGATAC
GTTTCAAGCGGGGATGATTATCATAATATATTCCTAACATATCATAAGATTCCCGCTCTTGAAAA
TCTGCACTTTTCCAAACCCAGAAAACCGAGGGAATTCTAGGACTCTTCCTCGGAACAAATACTTT
TATGCATACCTCTTCGGGTTGATCTACACCATACTATATTCTCGTAAGATGATATACGCTAGCTA
ACATCCCGCCTGGTGCTACATCATAGGCACATTGGGAACGTAGATAATTGTAACCGTATACGTAT
AAAATGACAGCAATAGAATGCCAATCCTCGGACTTTATTTGTAAA
Done.