Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: KC784949
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: 104480
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Found at i:18345 original size:19 final size:20
Alignment explanation
Indices: 18303--18345 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
18293 GGATGTTGAT
* *
18303 CATGACTTTCGAAAAGTTCC
1 CATGACTATCGAAAAGTTCA
*
18323 CATGACTAT-GAAAATTTCA
1 CATGACTATCGAAAAGTTCA
18342 CATG
1 CATG
18346 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 17803 -- 18302
CCCCAAAAACTAGAGCTAAAAATGCCTTTTTTTTCTTTTTTCTTTTCAATTTCTCCATTTCCAAA
TTTATGGGAGACTTGTCATATTTAGAATCTTTCTGTGGTGTGCTTTGTTTTTCATTATCTTGTAC
ATTTTTTTTATCATTCAAATATAGGCGCGATACATGGGCGAACGAGGAGCGTAGGCACAGAATAG
GAGGAAAACCGCGTAGGCGGGCACGGAGAGGAAAGCGCCAAGCGCTTTGCTGGCCTAGCGGAAGA
GAGAAACAAAGAAATAAAAATAAAGAAAATTTTTCCTTTTTATTTCTTTCAAATAAATCAAAAAT
ATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAAAAAGCCAAAATTTTGG
CTTTTTATTCTCTGCTTGCTCTTCCGCAAGCTTATTCTCTTGTCCTTGAAAATATTTGGAATAGA
TTCTTCGTTGTTCGCGCCTTGTCAAAAAGACTGATGGATGTTGAT
Right flanking sequence: Indices 18346 -- 18845
GAGGAGTTTGCATCTCTATTATGGGTGTTATTTTGTCGCGCGACCCGGCAGCTTATGCGCGACCA
TCTCGCGTTCAAGCTCACGCCATGTGGGCGTGAACTCTGGTTGAATTCGGGTTATAAATCCCGCC
GCTGAGATGCTCAGTCGACTCTTGAACCTTGATAGGGAGACGGCTTCTTACCAAATTAGTGCAAA
AGGTTCAGGGACTTAGGATGAACTTGATGTGAATGGGTATAAGCTTCGCTGCTCGAAAACACCCA
GTATTGACCACACCAAGAGACTTGCCAATGGCAAAAAAGGTCGCGGGTAACGCTAGTTGGCGAAA
TGGCGTTAAGCATTCCTGGCAATACGGAAAGAGAGGTCATGATGATATCATCTACGTTCGTACTG
TCCCTTGCGGAGTAAATCTCACATCCAGAAATCTAACCAGGGAACGGAATAATTCCCATTAAGTT
CCAGTAAAACTGGTAGGCCAGCCGGGCCGTAAGCTAGTGGGAACA
Found at i:20327 original size:20 final size:20
Alignment explanation
Indices: 20302--20343 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
20292 GATTTACAAA
20302 TTTATGATATAATACTAAAT
1 TTTATGATATAATACTAAAT
20322 TTTATGATATAATACTAAAT
1 TTTATGATATAATACTAAAT
20342 TT
1 TT
20344 CCTAATAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (20 bp):
TTTATGATATAATACTAAAT
Left flanking sequence: Indices 19802 -- 20301
TTTGCCTGTCGGTATCAAAAACCGAAGCCTTTCCACTTGGCTATACTCCAAAAAAAAAATATACC
TACGGCCTTTTTTTCAAAGCCCGTAAAGTGCCATGCACCCACCTGAAACAAAAACGAAATCACTT
CCCACTCTGCCAATGGCTCATGACAGAACAACGTAGGGGCGGTTAATTTGCTTATGTTCTCCTAC
AATATACAATATTTTTTGATAATCGAATTATCCATATCGTGAATGAAGGACCTATAACTTTAAGC
CTGAGCTGTTCTCTTATGCATACATGATAGATAGATAGAGCACATACATAATAGTTTCTAATCTG
ATTTATGAATTGGGCACACTTCTCATGAATAAACATAGATTCTTTTTTCGCCAATCAAGTCAAGC
AGCATGGCTTCTCTTCCAATTCTTGAGAACAGTTTGATCACGACTCGTGTTCGATCCGCAGGGCA
AGGGTACAAATACTATGCGAGGTGAAAGACCCATTGATTTACAAA
Right flanking sequence: Indices 20344 -- 20843
CCTAATAGTAGTTATACCTTTTTTTTGTCAAATGTCGTTTGTTCTAAAGATGTCTATGAATTTAG
GTGAGAGCCGCAGCCACAAATCTCTAATGAAAAAGTTCAGAACATCATAGAGGGATTTCGCTCGA
TAGATCAAGCAATCTGGTTGCACTCAATCCTGAGGGTCTTGGACCTAACCACTCGAATTACTAAG
CCTGTTTTTTGGGCGTTAGATACACGAAAATAACCGCGGTGATTAGGGGATAGTGCGATCACTGC
GGTCCCTTCCGCACAAATAGGTTGGGATTATAAAATGCATGTCATATTAATATCAAATATATCAC
AATGATATATTTGAGAAAGAATAATGCTAAACAAATAGTTGTTTCTAGAGCCTTGTAACTTCCGC
CGGTAATAATCATAATCTGAGGAAAGATAAGTTTTTGAAAATTATCGTCATAGCCTCATGCTCTG
TGATAAGGGCAGAGTTTAGGGTTAGCTCCAAGCTTCTATTACCTA
Found at i:21598 original size:18 final size:18
Alignment explanation
Indices: 21575--21628 Score: 108
Period size: 18 Copynumber: 3.0 Consensus size: 18
21565 TAATATCCAT
21575 AAGTCATATTGTTTTTTG
1 AAGTCATATTGTTTTTTG
21593 AAGTCATATTGTTTTTTG
1 AAGTCATATTGTTTTTTG
21611 AAGTCATATTGTTTTTTG
1 AAGTCATATTGTTTTTTG
21629 CGTTTGCGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.22, C:0.06, G:0.17, T:0.56
Consensus pattern (18 bp):
AAGTCATATTGTTTTTTG
Left flanking sequence: Indices 21075 -- 21574
TAACTGGGAAACAGTAATTCTATAGTAGGCTAGCCGAACGACCAAAGGCCTAGTGATCGCAGAAC
TTAAAGTTCCGACTTGTACGGATAGAGGGACTCGAACCCCCACAAACATTATGGTTACCAGAACC
TAAACCTGGCATGTCTACCAATTCCATCATATCCGCCAAAACTTTATTCAATATTCAATCTGTGG
AAATTTTTTTTTCTTTTCTTTAGTTATTAGACTCTCTTTCTTAATGGCCTCCATACCATTTCAGA
TGGTAGCTCAAGGGCCCATGGATTGCCAGATTTTTTATCGCCGATCGATAATAACAGTCACATGA
ATGGGTCAAAGGCCATCTCGTCAAACTAGGATTGAACTTACACCATAATATTTGGCCCAACCCTG
TAGGTCAGGTCGTGTTCTATGGTTCCTGAGTCGTGCCTATAGATAAAGTTATTTCTCATGGTTCA
TCACTGTAAAAATAAACTAAACTAGATTTGCTCATTAATATCCAT
Right flanking sequence: Indices 21629 -- 22128
CGTTTGCGGGTATACTATCCAAGCATCGTCTCTTTTTGACTGCGCCGAAAGAAAGAGGGCGAAGC
GGTTCTTTGCTTTCGCGCAGTGAACCACTCTACTAGTGCCGGTAGTTCATCTTGTAGGTCATTTG
ATTGGTATACTGGCGATTTTATTATGTTCTTTTCTATCGTCGCCTCTGTCCCATCGTGGTTCAGC
GCGTGACGTACAAAAACATGCAAAGTTTTGATTCATCCAATACTATACGGATTATGACATCTATA
TATTTCGGTCCAGTGCACCGTGGCGCGTTCCGCGACATGGCTCAGTGTCGCGCCTCAGGCTAAGC
CACGGCACGATACGCGCTGCCCTGCTGAGTAAGAATCTTTTCAAGCTCTTCAGGGTACTGCCCTC
TTCGGCTGCCAAGCACAGAGCCACCAGCTGAAGATCATTCCTTTTTCTTGAATGAATCATCATAA
GTAATGATTATATACTTTTTTTTCATAAAGAGAATATCTTGTTCT
Found at i:25181 original size:12 final size:13
Alignment explanation
Indices: 25157--25185 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
25147 CATTAAAGGT
25157 TACATACCATACA
1 TACATACCATACA
25170 TACATA-CATACA
1 TACATACCATACA
25182 TACA
1 TACA
25186 CGCGCGGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (13 bp):
TACATACCATACA
Left flanking sequence: Indices 24657 -- 25156
AAGTGTGCAATCAATCGTAAGGCCCTACCAAGATTTTATTTCTATTTCATTAGTAGTTAAGGGTT
CGCCTCTAGAATTTTACTACATTTACGGGTACTCATTCACCATAATGCAATTACTATGTACTAAA
ACCGTATTACAGCCGAGCATTTTTATTTCATTGAGTAAAGGGCATGGCATGGGGCGCATATAGCC
ACGAGAATCTATGGCTAAATCATATTTTTCTCGCTCCACGTATGACCTTCATTCCTGGTGCTATT
CTCACGCTGCGCGCCCTTTGTTCGTCACACGAAGACAGCTTTTTTCTCTGTAGTTCGCGAATGAA
TGCAGGTTAGTATTGTACTGCATTCTTAGCTCAGTTGGATAGAGCAACAACCTTCTAAGTTGAAG
GTCACAGGTTCAAATCCTGTAGGATGCTCGAGGAAAATGCATAATGAATGAATCGATAATATATA
TCAACGGTACATGCATCTATCGATTGGGTCAAACCCATTAAAGGT
Right flanking sequence: Indices 25186 -- 25685
CGCGCGGATTGACCAATTTATAAATAAATAATTTTCTTTATTTTGGGGGAGAGTGGCCGAGTGGT
TAAAAGCGACAGACTGTAAATCTGTTGAAGGTTTTCTACGTAGGTTCGAATCCTGCCTCTCCCAT
ATACTTCGCATTTGAGGAATAGAGACGAAGCACTTGTTTTTGTGCCTATCCTTTCATGCAATTAA
ATAGAGTGGAACTTTCTCAGAAACATATTGAATGCTTTGGTATTCGAGCCCTCTCCGAACCGTAC
GAGATAGTCGCCCATCATACGGCTCTCTAATTCAACCTCTATTCGGATTTGCCTCTGTCGTTAGA
TCCTGGCCCGTCCTTCCAATGACCAATCCTCAAGTGGCTTAAGTACCATAAAGAAAGCAACTTAC
TTTTTCGTTATAACGATCATGAGGAATTGTAGCGAGAGATAATAACATAAAAAAAATGCAGTTTC
ATTATCTCCTCTGAGCTCGTTCCTAATGCCCTGAACATGGTGCAT
Found at i:41059 original size:81 final size:81
Alignment explanation
Indices: 40924--41073 Score: 248
Period size: 81 Copynumber: 1.9 Consensus size: 81
40914 AAAATACTCG
*
40924 CTATCGGATTCGAACCGATAACCCATAAGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAAGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
40989 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* * *
41005 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAAGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
41069 CCAAG
65 CCAAG
41074 TGAGCTTAGG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
81 62 0.97
82 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (81 bp):
CTATCGGATTCGAACCGATAACCCATAAGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
CAAGCGAGTATGCTCA
Left flanking sequence: Indices 40424 -- 40923
CAACCTCAATCTACTTTAGTCAATCATATGGATATAGAAAAAGCGGCTAATTTAGAAATAACATC
AGTATTTCAACAACTTTCTGAGCTCATTTTTTACCCATATAATTCTCTATGTTTTCGTTTGAACA
AGCCAATTCATGCTCTACCCACTATACAAGAAAAGATGCAAGGAGGATTGCTTAGTCACCAGGGG
ATAACCACTTAGTGACTAACTTGAGCCCCCACTTTGCCAAGTAAGGCCGCAGGCTTTATTGACAG
AACTGGGGCGCGTAGTTCATAGCGAAGCTCTTTTCTTTCAATATTTTGGGAAATCCCCCGAAAAT
ATTTTTTGTTGCGAAAAGCAGCGCCCTCGAAGATTGTAAAGATTTAAGCTAATGGATGATTTGTT
TTTTTGGCGAATAACGGGATTTGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTATT
AAGTTATACTCGCCCTTTCTTCTAATTCAGACATTAAAATACTCG
Right flanking sequence: Indices 41074 -- 41573
TGAGCTTAGGGAAGCGAAGCGCAGAATGGAAACACAATCTTTTTGTTTCGTTTTCTTTTTGCCAT
TTCATTTTATAGACATCTCCGGCTCATCCCGACTCGGCCGAATCTGCGGCATCTTCTCAAATATT
TGAAAAATATAATGCTTTTTTATAAGAAAATAATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGT
TTTACGTAGTTTCGCCATCTATATAATAGAATATGGTAGAGGATAATAAGTTGGCGAGGAAGTAA
AAATATATATATATATCTATATATATATATATATATTTTTTATTCTGTGGTCTTGCAATTGTGCT
TGAAGCTAAGGGCCCAGCCCCCTATCTCTTAACGTTTTCGTCAATCAAATAAAGGCTTCGTTTAG
CCAGGGTTATTCTCCTCCCCTGTCGAATCGCCCCGCGAACAAAGTAGGCGAAAAAAATAAAGATT
TTTTTTGTCCGCCTTACTCTCTTCCATCACTCAAATGGCCCTATG
Found at i:41343 original size:2 final size:2
Alignment explanation
Indices: 41336--41369 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
41326 GGAAGTAAAA
*
41336 AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41370 TTTTTATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Left flanking sequence: Indices 40836 -- 41335
GAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTATTAAGTTATACTCGCCCTTTCTTC
TAATTCAGACATTAAAATACTCGCTATCGGATTCGAACCGATAACCCATAAGAACAGATTTTGAG
ACTGCCGTGTTTACCATTTTCACCAAGCGAGTATGCTCACTATCGGACTTGAACCGATAACCCAT
AGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCACCAAGTGAGCTTAGGGAAGCGAAGCGC
AGAATGGAAACACAATCTTTTTGTTTCGTTTTCTTTTTGCCATTTCATTTTATAGACATCTCCGG
CTCATCCCGACTCGGCCGAATCTGCGGCATCTTCTCAAATATTTGAAAAATATAATGCTTTTTTA
TAAGAAAATAATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGTTTTACGTAGTTTCGCCATCTAT
ATAATAGAATATGGTAGAGGATAATAAGTTGGCGAGGAAGTAAAA
Right flanking sequence: Indices 41370 -- 41869
TTTTTATTCTGTGGTCTTGCAATTGTGCTTGAAGCTAAGGGCCCAGCCCCCTATCTCTTAACGTT
TTCGTCAATCAAATAAAGGCTTCGTTTAGCCAGGGTTATTCTCCTCCCCTGTCGAATCGCCCCGC
GAACAAAGTAGGCGAAAAAAATAAAGATTTTTTTTGTCCGCCTTACTCTCTTCCATCACTCAAAT
GGCCCTATGAGCTTTTGCCAAGCAAAATATTGATTGCATAAGCCATCGACTTTCACAAAGACCAA
TAAAGTGATAACAGCAGCGTAGCCAGGCTTGTTCCGCCCGCTGTGCGCAAAAAAAGAGTTTTTTC
CGGCACTTAGTAAAACAAAATTTTGACACTCCTTGCGTTGCGGATGGTGAGTGGATTACTAATAA
CATGGAGTGATCCAAGATGACCTCTCTTTCAATTTCAATTATGTTCTTATATAGTAGTAATGGCA
TGCGGCGAACTCTATTGGATGCGCCAAAAACGTGATTTGTTGGGC
Done.