Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_060803
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: 279265
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:18228 original size:21 final size:21
Alignment explanation
Indices: 18202--18242 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
18192 TCGGTCCAGC
*
18202 TTGAGCTTGATTGTAAGGAAA
1 TTGAGCTTGATTCTAAGGAAA
18223 TTGAGCTTGATTCTAAGGAA
1 TTGAGCTTGATTCTAAGGAA
18243 TCGAAAGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (21 bp):
TTGAGCTTGATTCTAAGGAAA
Left flanking sequence: Indices 17702 -- 18201
GAGAGGTTTACCACTGGACTCTAACTGCCCGCAAACTCCTGGTATTCATGCTATGCCCCTTAGCC
ACTTATCCTAGTTAGACGAGGCAAAGCACGAAGCACAAGAAGGGATCAGCACTCTGACAGATATT
GGTGAGAAGACTGAGACACTTCGCCCTTCCAAAGAAAAGGCGACTGCTAGCGAGCAGGAGGACGA
AATGAGGGGGCCATCAGAGAAAGAAGTCCCACCGAGATTGGCAGGGACTAAAGAGAATCCCATTT
CTCCGAGGGACAATATCCAATAAATAGAAGAAGAAAGTCTGCCCAAGGCATGTACCAAACAAATC
TTTCACATACCCCCACCAGGTCTCTGGCTCCGCAAAGAAACTAGCTAAAACAGAGCTCGCATGAA
TTGCTCCTAACATAGGGGATTGCCTCATCCGCACCGCCAGCAAGCCTTTCTACCTTTCTACAGCG
AAGATTCAAGGAGAACGTTGATTTCAAAGGAGTCTTCGGTCCAGC
Right flanking sequence: Indices 18243 -- 18742
TCGAAAGCTAAGCGAAGACCATCTATCCCTACCCCTAAGCCACTGTTGTTAAAAAACCAATGCAA
AAGAGAAAAATAAATGAAAGAAAAAATTAATCTAGTTCAAATAAGAAACAAAAAGAATAAATAAA
TAAGGCAGAACGAGAATAAGCCAAATAGTCCCTCATTGAACCAACTTGAATCTGAACTTCTATTT
AGAACGCAAAAGCCCATCTTTTTCTTTATATGTCTAAGGAATTCTGGATTTTTCGATTGCTCCTT
ATAAATGGGTCGTAGCATTGAATGTACTCTCGAGTGATCGAATGACTCTCTATGACACAATTACT
GACCTATGGATGGAGCGATCCCCTCGTAACCAGGATTCTATCACGATCGATTGAACATCTAGTGA
ACGCTTTAGTCTTGTCTCATCCGGATTGATTGACTCCAGAACTAGCTTACTGAGCGAATCCGAAT
TCATTTCGAGACGTGGAGACTGTTCAAACTGAGTATGTTGGAATC
Found at i:19525 original size:24 final size:24
Alignment explanation
Indices: 19493--19538 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
19483 CTAAACTAGA
* *
19493 AGCCGTTGCTTGTTCTTTCGCGTC
1 AGCCCTTGCTTGTTCCTTCGCGTC
19517 AGCCCTTGCTTGTTCCTTCGCG
1 AGCCCTTGCTTGTTCCTTCGCG
19539 CTGGCCGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.04, C:0.33, G:0.24, T:0.39
Consensus pattern (24 bp):
AGCCCTTGCTTGTTCCTTCGCGTC
Left flanking sequence: Indices 18993 -- 19492
CTGCGGTATAGGTAGAAGGAGCTGGTACGGAAAAACCTTCTGTATAAAGTTCGAAATGGTGAATT
GAGGTAGAGTAGACTGATGATCCTGTAGTCATTTGGCCGGCTATTGAAAGAAAAAGCTTGCATCT
GCTTCCCCTATTATATAACCGGTCCCATCTCTCTCCAAACCTAACGTGGTAGTTTCCCATCATAG
GGCTTTCTATCTATAGATTAAGCCATTACCAAGGAGCTAATTCGTTCAGAACTAAGTTGACTGCT
TCTATAGATAAGGCGGAGCGTCCTTGGCTCAGCATTATAGCACGCACATAGGGCTTCGGCGCTAC
TACAGCGCTTCGCTAACTCGAAGCGCCTCGCTATGAGAATATAGCTTCGCGGACCAAGAAAACGG
ATGCGCGTTAGCTAAACGAACAAGGAAGACGCGTAGCGTCACTTTACTCACGCACAACGGCTTCT
TAAATAACTATATGAATAGCGTCTGTAGCGCTAGTCTAAACTAGA
Right flanking sequence: Indices 19539 -- 20038
CTGGCCGTTCGCTTTCTCAGTAGCAAAAGCGCTTCTCTTTGCCCCTATTAGATTAGAACAACCCA
TAAATTATTTAGAAAGAGTTTCTTTGTTGGTGTTAAGTTTAAAGGACAAGAAAGATATTATTTTT
TTCTTGCTCCCGCTTCCTCATCTGTGCTCATCAAGCCAACTTTGCTCTTTGGGGGGTGAAACAGC
GGTTGAAGCGGACATTTCGAAATGACAGCATCGAAGATATATTTATATATATACACGGTTACGGT
TATCTCGGACTGCGTTCTGGAAAAAGCAGCCTACTTGTGGGGCACTGTGTACTTACAGCCTATAC
GATAAGCAAGTGAATGGGGCCGGTGCGTGGCGAATGGAACGGTTCATCAAACCATTTTTCGCCTC
AACTCCCTAAATAGGGGTAATTTGTTCGCACCTGACTGTGATAGCCCTCTCGATACCTTATTGGA
GCTTTGTAACTAGTGGCCGGTTTCCCGTCGCTAGAGCGTTTTCCC
Found at i:41859 original size:24 final size:24
Alignment explanation
Indices: 41827--41873 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
41817 CCATTTCTTC
* *
41827 GGAATTGTCCGCTCATAGCACGAT
1 GGAAGTGTCCGATCATAGCACGAT
*
41851 GGAAGTGTCCGATTATAGCACGA
1 GGAAGTGTCCGATCATAGCACGA
41874 CGCGCTGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (24 bp):
GGAAGTGTCCGATCATAGCACGAT
Left flanking sequence: Indices 41327 -- 41826
AGCCCACTTACTTTAGTTTGACTGAAACAACTTCCTTTCCTGAATCTTAGCTCTTCTCTTTCTTA
TTTATTCTTACTACTAGAACTTTATAAACCGGTCCGGAAGAAAGAAACCTTAACGTATCCGGGTC
GTACGCCTGGAACAGTCGTACAATTTCGGCGATTCTAAAAAGGAGTATATCCCTCTCCCTTAGTG
TCTTTCCACTTCCCTCGTTCAGGAACAAACACTTCGCCTAATTCTTTTGAATTTCCCCACTAACT
AATTAGCTTACGACCACTGAACAAACTTGGTTGACGAACATAGTTTATGCGCCGCTAATCTAGCG
GCTTGTCGAGCATTTGACAAACTCACACCATCCATTTCAAATAGGATTTGTCCCGTGGACACACG
AGCAATCCAACCCGTAGGATTTCCTTTTCCTCTTCCCATTCTTACTTCTGTAGGTTTCCCGGTAA
TAGGGATATCTGCGAAAACTCTTACCCATATCTTACCATTTCTTC
Right flanking sequence: Indices 41874 -- 42373
CGCGCTGCTTCAATGGCTCGATATGAAAGACGACCAGCTCTACAACTTTTAGTGCCATATCTTCC
AAAACCAAGTTGTGTACCGTCCGGTTTGCAACCCCTACTACATCTGCCTTTACGATATTTACTAT
ATTTCGTACGTTTCGGATATAGCACGTCCCTTTTTTTTTTTACTATATGAAATCCACACTTTGAC
ACCTGAGATTCCGTAACGAGTAGATACTTCCGCAGGAGCATAATCTATTTTCTGGTTAAATACAT
TACGAGATGTTTTTCCATACTTTCCGCATTCAGTTCTAGCTATTTCTGCACCTTTTAATCGACCT
GAACAACATATACGGATCCCCTCCACCCCCTTTTTCATTACTAATGGAATATCCTTCACTATTTT
ACTAAAAATGGAACGAAATGATCTTGTTTTGTTCCTCGGTTGAAAAGAGATGTCTTGAGCAATCG
GAGAAGCACTTTGATAAACAGATTTGATCTTGACTGATTCAATTA
Found at i:119751 original size:62 final size:60
Alignment explanation
Indices: 119661--119781 Score: 197
Period size: 62 Copynumber: 2.0 Consensus size: 60
119651 CGCTAGGCGA
* *
119661 ACCAAGGAAGACGCTTCGCGTCACATTACTCACGCACAACGGCTTCATATTCACTATATAT
1 ACCAAGGAAGACGCATCGCGTCACATTACTCACGCACAACGGCTTCATATTAAC-ATATAT
*
119722 ACCAAGGAAGACGCAATCGCGTCACATTACTCACGCACAACGGCTTCTTATTAACATATA
1 ACCAAGGAAGACGC-ATCGCGTCACATTACTCACGCACAACGGCTTCATATTAACATATA
119782 GCGTCTGTAG
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 19 0.34
62 37 0.66
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.23
Consensus pattern (60 bp):
ACCAAGGAAGACGCATCGCGTCACATTACTCACGCACAACGGCTTCATATTAACATATAT
Left flanking sequence: Indices 119161 -- 119660
ATTGCGCTCCCTAGACCACTACCATGTAGTTAGGTAGGGACAATCAATCCGTAGTGACGGGAATC
TAGGAATGAATGGGGATCCCTATCAATATAAAAAGAATATCTAATTAGAGGTTTCTCCCTTTCTC
TCACTCAATAGATCTATCTGGTCTGATACGGCACAGTACAATACGAGACGATGGAATGAAATGGG
ATAGAAGGTAGAGGGCTGCCTGCGACGCCCAAAAGCGATGATTCACTTGTCCCCTTGTCCATAGG
GACCTCGTGGCATACAACCGAAACGACTCCCGCTAGATAGCCGCCCCTTTCTCTCTTTTTACAGC
CTCGTGGACGGACGAAAGAAGGGAAGTTACAGAACGGGGCAGTCAAGGCTCGCGCAGTAGACAGC
AAGCAGCAAGCAACAGCTTCTCAGCCCCCTCACCTTTCTATTAGTCAAGTTTATAAGCGGTTAAC
AAATAAAAAAGGCAAGCAACGCTTTATAATAGAGGCGCTAGGCGA
Right flanking sequence: Indices 119782 -- 120281
GCGTCTGTAGCGTTAGAAGCCGTTGCTTGTTCACCCCTTTTCATAATAATAAGGTAAGCTTTGAA
GCTGGCTGCTCTGCTATACTATACTAGTTGTAGGGCGCTAGCGCTTGACTAATATAATAGAAAGT
AAAGGGACTCTATTATGATCTTACGAATCTAAAGATCTAAAAATTGAAGAACGAGCTCTTTTGCT
CGCCCCTATCTCTAATGGGGCGTAAGCATTTCACTCGCTAGGGGATGGGATTCATTCACTTGCAT
TTCTGCTAGCACTACAAAAAGCTCCGGTCTTAACGCCCTTACTACTGCTGTGCAGCCTTTCCTCG
GGTTCGTAGAGTCGGGTTTCCCGTTTACCCACAACGGAGGAGCCGCCCCCACCAGGCAGGCGGCC
ACGGGTCATAACGCATTCTTCGCACAACAAATCCACTTTGAAGTTGACTTATTCGCTCGGCCAAT
CGTCGGAATGTGTACGAGATACCATAAGGGCCCAATATCTCAATA
Done.