Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: KC784959
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: 109586
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:734 original size:22 final size:22
Alignment explanation
Indices: 702--754 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
692 TAGGTTATAA
*
702 ACCTACGCTTTCTACGTAAGTT
1 ACCTACACTTTCTACGTAAGTT
724 ACCTACACTTTCTACGTAAGTT
1 ACCTACACTTTCTACGTAAGTT
746 ACCTACACT
1 ACCTACACT
755 CTGTACTCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.26, C:0.30, G:0.09, T:0.34
Consensus pattern (22 bp):
ACCTACACTTTCTACGTAAGTT
Left flanking sequence: Indices 202 -- 701
GAAATGGATGCGTAACACGTTGCATGTAGGTTCCTGAACAGGAACCTACAATGAGACGCTGCTTA
GGGAAGCCCCGTTCTGTCTCAGGCAGAACTGGGCTGTGTACAAGTAGCACAGGGGGCATTTATTA
GTCGGAATTGACCTTGTGGAGCCCTTGAATTCACCTGGGTCGGTATGAATCTATTTCAGAGATAC
AGTTCCCGCTTTCATGGTAATTAGTATTCCACTTTCTTTCTATTTCGTGCCTACTCTTAGAAAGT
GGAATAGGTACCCTATTTCAGGGTACCCACCAGACATTCGGGGATTGGAGGGATTAGGGAATGAC
TCCACAACCTCCTCAGTGATACTGAGGCCATCTGCGCCTGCTTCTGTAACAAATCGAGGAATTAC
ACACGAGGGGCGAACCCTTAGGAACAAACAAATGGTGTAGGATAGATGTAGGTTGTTGAGTTGCT
GGAGACCCAAAATAGAGAATAGAATGTAGATAGTGTAGGTTATAA
Right flanking sequence: Indices 755 -- 1254
CTGTACTCTCTTTACCTACACTATCTAAGCTATCTCTGCCCTCTTATAGGCTTATCCTGAGTAAG
CCCATTTCCGATTTATTCTGTATGTAATTTGCACTATTCCACTAATTCCCGCCTGTGCCCATAAC
CCCCACATCTATTCTATATATGTACGGGCGTCGCTTTGTTAAGCATTCTTCTGATTTCTTTGAAG
AGGCCCCGGAAGTCATTGTTGTTTTTCATTAATTTATCATCATTAAATTACATAATGATAAAAAA
AAATATATATATATTTTTTTGGGTGTATAGCTTAATTGGTAGAGCATTAGGCTTTTAACTTAATG
GTCGCAGGTTCAAGTCCTGCTATACCCAAATGTTTTTATAGAAGTTCCCCTGGCAGTTCATCTGC
ACATCAAAATCTACGTTGTACCTTGGCTCGTCTAGTACGAGTAATTACGTTAAACTAAAATATAT
ATATATTTTTTTATGTCTTTATGGGCGCTCACGCCCTTCTTTTTC
Found at i:2197 original size:22 final size:22
Alignment explanation
Indices: 2169--2212 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2159 GCTTGTTAAC
*
2169 TTGGTGAAAGTAAGATGAAGAA
1 TTGGTGAAAGTAACATGAAGAA
2191 TTGGTGAAAGTAACATGAAGAA
1 TTGGTGAAAGTAACATGAAGAA
2213 AAGGTAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.30, T:0.23
Consensus pattern (22 bp):
TTGGTGAAAGTAACATGAAGAA
Left flanking sequence: Indices 1669 -- 2168
CCTTATGGCAACATTGGACTAGTATATCATCTGAGGAAAGAACTGCTTGAAACAGATAGCTTATC
AAATTAATAATAGCTATCTGTTAGGAGAGACCAGAAAGCTGTTCGACAGAGTAACTTCTAAGAGT
TCATTCCATTTATTATTGTGATAGTAAGAACTCAATGTTCAAGTTTATTCTAGTCCTTCAGTTTG
TAAGAGAAGCCCAATTGCTAAGCATCTAGTAATTCTGCTTATTCTCGAGATCAACAGTTGTGAAA
GTCTATTGAAAAAATAGATCACTGCTGAGGCTGTTTAATGACCTCAATCGCTGTGACTCTTGCAA
ACTTCGTCGGAAAGATTGTAAACCGATTGGTTTAAAGTCGGTGTGAGTGTCTTCCACACTCATTT
CTGTGCCCCCGGAGAAGTGTGCCTTTGTTTTTTGGCACCCGAAAAAAATATATATATTTTTTTAG
GAGCGTATACGAGCGAAGCCGGGCTAGATTTAGGAGCTTGTTAAC
Right flanking sequence: Indices 2213 -- 2712
AAGGTAAGAATAAAAAAGGCCGCAGGTCTTATGTACTAGCGACACCATAAATACTATTTTAAAAA
CTAACAATATCATAAATACTACTCGAAGCTTCGCCCTTTACTCCAGTTCATCAGGAGTCCACTTT
AATCCTCGCGCCGAAGGCGGATTCCCGGTATTTTAAAGCTCTTAAGTAATCTACGTCACCGTCTT
AATTAATTCAAGAGACGGGTATCTCATGAATTAATTATCTAAATTATGCCAACCTATCTTATGAA
ACCCAGCCCGGCAGTATAATCAATACTGGCGACACGATTGAGAAGCAGTGCTTCGGTTGGCAGGA
ACGGCTTGCAGTCGTGCTACCGGCGGTGTTTGCCTTCCGCTGCCGCTGCCACGTTATTGAAATGC
CAGACCTAGAGTAGGTGCGCATATATAGCGCCACCTAATGTGGGCCGAAGGCAAGCCTTCTCCTT
GGGCCTTCAATTAATAAATTTATATAAATAAACATATAAATATTG
Found at i:19121 original size:19 final size:20
Alignment explanation
Indices: 19079--19121 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
19069 GGATGTTGGT
* *
19079 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
19099 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
19118 CATG
1 CATG
19122 GAGGAGTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
CATGACTATCGAAAAGTTCA
Left flanking sequence: Indices 18579 -- 19078
CTAGAGCTAAAAATGCATTTTTTTTATTTTTTATTTTCATTTTCAATTTTTTTATTTTCAAATTT
ATGGGAGACTTGTCATATTTAGAATCTTTCTGTGGTGTGCTTTGTTTTTTATTATTTTGTACCTT
TTTCTTATCATCTAAATATAGGCGCGATACGTGGGCAAACAAGGAGCCTAGGCTTGGAATAGAAA
AAAAAAGAAAAGCGCCTAAGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTAACGAA
AAAAAGAAACAAAGAAATAAGAAGAAAGAAAATGCATTTTTATTTCTTTCAAATAAATCAAAAAT
ATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAAAAAGCCAAAATTTTGG
CTTTTTATTCTCTGCTTGCTTTTTCGCAAGCTTATTCTTCCGTCCCTGAAAATAGTTGGAATAGA
TTTTTTCTTGTTCGCGCCTTACCAAAAAGACTGATGGATGTTGGT
Right flanking sequence: Indices 19122 -- 19621
GAGGAGTTTGCATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGCAGCTTATGCGCGACCA
TCTCGTGTTTAAGCTCACGCCATGTGGGCGTGAACTCTGGTTGAATTCGGGTTCTAAATCCCGCC
GCTGAGATGCTCAGTCGACTCTTGAACCTTGATAGGAAGACGGCTTCTTCCCAAATTAGTGCAAA
AGGTTCCAGGACTTAGGATGAACTTAATGTGAATGAGTATAAGCTTCGCCGCTCAAAAACACCCA
GTATTGACCACACTGAGAGACTTGCCAATGGCAAGAAAGGCCGCGGGTAACGCTAGTTGGCGAAA
TGGCGTTAAGCATTCCTAGCGATACGGAAAGAGAGGTCGTGATGGATGATATCATCTACGTTCGT
ACTGTTCCTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGGATAATTCCCATTA
AGTTCCAGTCAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGG
Found at i:38034 original size:12 final size:12
Alignment explanation
Indices: 38017--38041 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38007 ACGTGACTTT
38017 ATAATAGTAATG
1 ATAATAGTAATG
38029 ATAATAGTAATG
1 ATAATAGTAATG
38041 A
1 A
38042 GGTGATGACA
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:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
ATAATAGTAATG
Left flanking sequence: Indices 37517 -- 38016
CTGCGAGAAGCCAACCCTAGTACGAGAGGACTGGGTTGGGTCAACCTATGGTGTACCGGTTGTTA
TGCCAATAGCAGCGCCGGGTAGCTAAGTTGGTATAGAAGAACTGCTGAAAGCATCTAAGCGGGAA
ATCCTTCTCTATACAAGTTCTCATAAAAGGTGAAAGACCATCACTTTGATAGGCGAGAGGTATAA
ACACCGTGAGGTGTGAAACAAGGCTTACGGCTCTTGTTGAGCTTACTCGTACTAATTATCTACTT
CTCGGGAGCCCAGGGCTCCCGGAGAGAACCTCTTAATTAAGCAGAGATTGCTGCGGTCTGTACGG
AAAGTAAAAAAAAATTTATCATAGAAGATTGTTAGTTCTTCACATTTCTGTGGATTTTCTAGTAG
AGTACCTAAAAATATAGTAAGCTACTGAATCTTTTTGCTTCTTTTTGTTATCTTCAAAATTACTG
TAAGACTAGTTATTCTACATAAATATAATGTCATCACGTGACTTT
Right flanking sequence: Indices 38042 -- 38541
GGTGATGACAAAAAAAAAGGATTTGATTCGTGCTGGTCAAAAAAAGGAAAATGAATAATGAATAA
AATCAATATTAATAATAAATGTCTATTTATTTATTTATAACCCCTTTTTAATACCTCTCCTTAAT
AAGCCTCCGCCGGAGGCGCTTGTCGTCGCGTGCTTTCTATTATAAGATAACACGATGACATTATT
ATACCCGTTAATTAATACGTTCCCGCCGGGGGCGTTGGCCAACAAGCCTCTATACCATATTCTAA
TAAAGCCCGCTATTATTTAACACGTACGCAACTGTGTTATTTCTTTCTGGAACATTTTTGATTTC
AAAATGATTATTCTGACATAAAAGTCCATAATGAAATTACGGCATTTCCGAGATGTTTTCTTATT
TAAGTATCATGGTTTTTAGATTTACTATTGTGTCTATCTTGCCGGGTTGTTATGAGGTTTCGCAA
AAAAATGAACCGAACTTAGATTTAATCGAAGTAGCGGGAACCTAG
Found at i:39341 original size:9 final size:9
Alignment explanation
Indices: 39327--39356 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
39317 CAATCTTCGC
39327 GGAAATGTA
1 GGAAATGTA
39336 GGAAATGTA
1 GGAAATGTA
39345 GGAAATGTA
1 GGAAATGTA
39354 GGA
1 GGA
39357 TTTTATGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (9 bp):
GGAAATGTA
Left flanking sequence: Indices 38827 -- 39326
TTTTAGACTTAGCTGAACTATAATCAGTTCTGGAGAACGGAGGAGGCTGCCGTCTTTGGAAAAAC
GAAGGATGTCGCAGAGAGATGGCACCCTTCCCTGGTTCAATTTGATTGGCAATTATTTTATGTGA
AGGAAGTACATTGTTTACAGGCCATAAATAATGTTTTATTTACTTAAGTTATTTCAATGAAGTAT
AAATCATTGTAGATAAATTACCATAGATGATCTAAATACATGTAAAACACGACAGAGATTAATGA
TCATAAAGGATCAAATACATTTACCTCATCATCACCCAAAAACAAAAAATATTTATTATATTCGA
TATATTGCTATTTTCCTGCTAATTCTTTTTGTACGTGGTTTTGTGGAGGAGCCTATAAGCATTCT
TTAGCGTATGACTATGTGGATATCTTATAATGAAAATAAATCATTATATATGAAGGTTTATATGT
AAGATAAATGTACACTATCCTAAGAAATGATACTTCAATCTTCGC
Right flanking sequence: Indices 39357 -- 39856
TTTTATGTAGATTATATATGATATTACATGGAATTGAATATTCATGGGGATGAGCATTAATGTAG
AATTAATGTAGGTTATATATGAGATTACATCATTATTTAGATTCATTAAATAATGAATATGAAGG
TCTATGAAGGTCTATATGTAAGTTGGATGTAAACGTATTATAGGATACGACGGTTAAATCCTCGC
GGAAATGTAGGTATGTAGGTTATGTAGGTTCTTTTTGAATTAGCTGGGCCATTGATTTTTTACCT
CGAGTGTCTGTCTATATGATAAGCCCAAAGAGTATCCGAGTTTCGTTAATATATCCTCAAGATTA
GTCATACTTTCTTGTAAATCGCCCTCCGGGATAATCAACACATTGCCATCATGAAAATGGCCTAT
GACTTCTATCTTTGGGTTTTTCTTAATTACCCGGAGAGTTGTCTCAGCAAGTAAAGCGAATTCAA
AGGATTGTAGATAACTAGAATAAGCCGATCGGAAAGAATCGTCGG
Found at i:44231 original size:81 final size:81
Alignment explanation
Indices: 44096--44245 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 81
44086 AAAATACTCG
*
44096 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
44161 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
44177 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
44241 CCAAG
65 CCAAG
44246 TGAGCTTAGG
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
81 63 0.97
82 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (81 bp):
CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
CAAGCGAGTATGCTCA
Left flanking sequence: Indices 43596 -- 44095
CTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTAGAAATAACATCAGT
ATTTCAACAACTTTTTGAGCTCATTTTTTACCCATATAATTCTTTATGTTTTTGTTTGAACAAGC
CAATTGATGCTTCACCCACTATACAAGAAAAGACGCAAGGAGGGTTACTTAGTCCCCAGAGGATA
CCCACTTAGTAACTTGGGCCCCCACTTTGCCAATATTAAGGCCGCAGGCTTTATTGACAGAACTG
GGGCGTGTAGTTTATAGCGAAGCTTTCTTTTTTTTTCAATATTTGGGAAATCCCCAAAAAATCTT
TTTTGCTGCGAAAAGCAGCGCCCTCGAAGATTGTAAAGATTTAATTTAATGGATGATTTGTTTTT
TTGGCGAATAACGGGAATCGAACCCGTGTTTTCAAATTCACAATCTGACACTTTAACCTATTAAG
TTATACTCGCCCTTTTTTCCAATTTAGACGACATTAAAATACTCG
Right flanking sequence: Indices 44246 -- 44745
TGAGCTTAGGGAAGCGAAGCGCAGAGCGGAAACACAATCTTTTTGTTTTGTTTTATTTTCGCCAT
TTCATTTTATAGACACCCCCGGCTTATTCCGGCTCGGCTGGACCCGCGGCATTTTTTCAAATATT
TGAAAAATCTATAGTCCTCTGTCTTAAGGCGTGTAGAGACTCCTTTTTTCTTGATTTATACTAGT
CTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTAATCTAACCATGGTTGCCTTGGC
AATGGCAATGACTTTTATACGATATGCATAATATCCCAAAACCTCTATTTATTCTATTTAGAACT
AAAAGAAGATAACGCTTTTTTAGAAAAAAATCATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGT
TTTACGTAGTTTTGCCATCTATATAATAGAATATAGTAAGAAATAATAAGTTGCCGAGGAAGTAA
AAATATATATATATTATATATATTTTTTTTCATTCTGTTGTTAAG
Found at i:88899 original size:22 final size:22
Alignment explanation
Indices: 88871--88914 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
88861 GGCGCTTAGA
88871 GGCTGCAAGTGATGCATGTGTG
1 GGCTGCAAGTGATGCATGTGTG
*
88893 GGCTGCAAGTTATGCATGTGTG
1 GGCTGCAAGTGATGCATGTGTG
88915 AGCGTTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.14, G:0.39, T:0.30
Consensus pattern (22 bp):
GGCTGCAAGTGATGCATGTGTG
Left flanking sequence: Indices 88371 -- 88870
TTGTCAAAAATTTACACAGAGCTTCTTAGCGACTCATTCAGTTTAAAAAGATTCAACTAAAAAAA
AATTTTCAGGCCGCGGGTTTTGTTTCCGTGCTTCCGGGTGGAGGGTGAAAGCGGCCAGGGCGCAG
CCAATTTTTTTTCTTCCGCCCTCTGGCTACGCCCCTAGTAAGGCTTCGTCATACGAGCGGAGCTC
GAAAACCCTCCATCCCCACATTAACAACGTGTAGATTTGTAGAAAACAGGAAGGCAACAAAACAT
TAACAAAATCGGGCCAGGAACGCTTATTTGTAAAATGTACTATTTGTAGGTTCTGTAGGTTTTTA
CTGCGTATTTGTACTATTAGATATTATTTACGTATGCAATAAGGGCGTTCTAATGCCGGCAAAGA
TAACTGGATGACCCAGATTGACTATGTATTGCCGTAATGCATCTGGCCGCAGGCTCGCGCTTAGA
TAGAGTAATGCATCAGTCTTTTCTGGAAACTTTCTGGCGCTTAGA
Right flanking sequence: Indices 88915 -- 89414
AGCGTTAACAAAAACAATATATATTACATGGCTCCAGCAAATCAAGTCTATCGCTCCGCAACAAT
TTCTAAAATGAATCAATCATCAAAATGATTGATAGCTACCTCCACCAAATTCTGGCTGGTGTAAT
CAGGAGAAAAGGGATTCGAACCCTTAACCTGTGGTTTTGGAGACCATTGTTCTACCATTGGAACT
ATTCTCCTAAAAAAAAAAGTGGTTCTTGGTTTATGGAATTTGCACCTATTTGTGTCTATTTAGTA
ATAAGTTTGCTACTTTCTTTGATCTTAATCGGTGTTTCCTTTCTATTTGCTTCTTCTTCTAATTC
GGCTTATCCAGAGAAATTGTCAGCTTACGAATGCGGGTTTGATCCTTTTGATGATGCCAGAAGTC
GTTTTGATATACGATTTTATCTCGTTTCTATTTTATTTATTATATTTGATTTGGAAGTCACCTTT
TTATTTCCTTGGGCAGTTTCTCTTAACAAGATTGGTTTGTTTGGA
Done.