Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: COLO4_20753
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5871
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Found at i:4601 original size:39 final size:39
Alignment explanation
Indices: 4558--4982 Score: 194
Period size: 39 Copynumber: 10.9 Consensus size: 39
4548 GTTGGTGGAA
4558 CATTCACCA-GTATGGGGCTCCCAACAGAAATCAGCGGAC
1 CATTCACCAGGT-TGGGGCTCCCAACAGAAATCAGCGGAC
* *
4597 CATTCACCAGGTTGGGGCTCCCAACA-AAAGTCTGCTGAC
1 CATTCACCAGGTTGGGGCTCCCAACAGAAA-TCAGCGGAC
* * * **
4636 CATTCACGAGGTTGGGACTCCCAACAGAAGTCAGAAGAC
1 CATTCACCAGGTTGGGGCTCCCAACAGAAATCAGCGGAC
* * * * *
4675 TC-TTCGCCGGGTTGGGGGTCCCAA-AAAAAGTCAGTGGAC
1 -CATTCACCAGGTTGGGGCTCCCAACAGAAA-TCAGCGGAC
** * * * * * * *
4714 CATTCAGAAGGCTGGGACTCACACCA-AAAGTCACCAGAA
1 CATTCACCAGGTTGGGGCTCCCAACAGAAA-TCAGCGGAC
* * * * * * **
4753 CATACACAAGGTTGGGGGTCTCAAAAGAAGTCAATGGAC
1 CATTCACCAGGTTGGGGCTCCCAACAGAAATCAGCGGAC
* * ** * * *
4792 CATTCACAAGGTGGGGGCTTACAAGA-AAAGTCACCTGAAC
1 CATTCACCAGGTTGGGGCTCCCAACAGAAA-TCAGC-GGAC
* * *
4832 C-TTCACCAGGTTGGGGCTCTCAACA-AAAGTCACCTGAAC
1 CATTCACCAGGTTGGGGCTCCCAACAGAAA-TCAGC-GGAC
* * *
4871 C-TTCACCAGGTTGGGGCTCTCAACA-AAAGTCACCTGAAC
1 CATTCACCAGGTTGGGGCTCCCAACAGAAA-TCAGC-GGAC
* * *
4910 C-TTCACCAGGTTGGGGCTCTCAACA-AAAGTCACCTGAAC
1 CATTCACCAGGTTGGGGCTCCCAACAGAAA-TCAGC-GGAC
* * *
4949 C-TTCACAAGGTTGGGGTTCTCAACA-AAATTCAGC
1 CATTCACCAGGTTGGGGCTCCCAACAGAAA-TCAGC
4983 TTGGGGCTCC
Statistics
Matches: 314, Mismatches: 62, Indels: 20
0.79 0.16 0.05
Matches are distributed among these distances:
38 9 0.03
39 293 0.93
40 12 0.04
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.19
Consensus pattern (39 bp):
CATTCACCAGGTTGGGGCTCCCAACAGAAATCAGCGGAC
Found at i:4688 original size:78 final size:78
Alignment explanation
Indices: 4539--4940 Score: 225
Period size: 78 Copynumber: 5.2 Consensus size: 78
4529 GTGGCTGGAA
* * * **
4539 CCAACAAAAGT-TGGTGGAACATTCACCA-GTATGGGGCTCCCAACAGAAATCAGCGGACCATTC
1 CCAACAAAAGTCT-GTGGACCATTCACGAGGT-TGGGACTCCCAACAGAAATCAGAAGACCATTC
4602 ACCAGGTTGGGGCTC
64 ACCAGGTTGGGGCTC
*
4617 CCAACAAAAGTCTGCT-GACCATTCACGAGGTTGGGACTCCCAACAGAAGTCAGAAGACTC-TTC
1 CCAACAAAAGTCTG-TGGACCATTCACGAGGTTGGGACTCCCAACAGAAATCAGAAGAC-CATTC
* * *
4680 GCCGGGTTGGGGGTC
64 ACCAGGTTGGGGCTC
* * * * * ** * *
4695 CCAAAAAAAGTCAGTGGACCATTCA-GAAGGCTGGGACTCACACCA-AAAGTCACCAGAACATAC
1 CCAACAAAAGTCTGTGGACCATTCACG-AGGTTGGGACTCCCAACAGAAA-TCAGAAGACCATTC
* *
4758 ACAAGGTTGGGGGTC
64 ACCAGGTTGGGGCTC
* ** * * * ** * ***
4773 TCAA-AAGAAGTCAATGGACCATTCACAAGGTGGGGGCTTACAAGA-AAAGTCACCTGAACC-TT
1 CCAACAA-AAGTCTGTGGACCATTCACGAGGTTGGGACTCCCAACAGAAA-TCAGAAG-ACCATT
4835 CACCAGGTTGGGGCTC
63 CACCAGGTTGGGGCTC
* ** * * * * ***
4851 TCAACAAAAGTCACCTGAACC-TTCACCAGGTTGGGGCTCTCAACA-AAAGTCACCTGAACC-TT
1 CCAACAAAAGTC-TGTGGACCATTCACGAGGTTGGGACTCCCAACAGAAA-TCAGAAG-ACCATT
4913 CACCAGGTTGGGGCTC
63 CACCAGGTTGGGGCTC
*
4929 TCAACAAAAGTC
1 CCAACAAAAGTC
4941 ACCTGAACCT
Statistics
Matches: 267, Mismatches: 44, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
77 7 0.03
78 246 0.92
79 14 0.05
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.18
Consensus pattern (78 bp):
CCAACAAAAGTCTGTGGACCATTCACGAGGTTGGGACTCCCAACAGAAATCAGAAGACCATTCAC
CAGGTTGGGGCTC
Found at i:4941 original size:78 final size:78
Alignment explanation
Indices: 4599--4976 Score: 372
Period size: 78 Copynumber: 4.8 Consensus size: 78
4589 CAGCGGACCA
* * * * * *
4599 TTCACCAGGTTGGGGCTCCCAACAAAAGTCTGCTG-ACCATTCACGAGGTTGGGACTCCCAACAG
1 TTCACCAGGTTGGGGCTCTCAACAAAAGTC-ACTGAACCATTCACAAGGTTGGGGCTCTCAACAA
**
4663 AAGTCAGAAG-ACTC
65 AAGTCACCAGAAC-C
* * * * * * * * * * * *
4677 TTCGCCGGGTTGGGGGTCCCAAAAAAAGTCAGTGGACCATTCAGAAGGCTGGGACTCACACCAAA
1 TTCACCAGGTTGGGGCTCTCAACAAAAGTCACTGAACCATTCACAAGGTTGGGGCTCTCAACAAA
*
4742 AGTCACCAGAACA
66 AGTCACCAGAACC
* * * * * * *
4755 TACACAAGGTTGGGGGTCTCAA-AAGAAGTCAATGGACCATTCACAAGGTGGGGGCT-TACAAGA
1 TTCACCAGGTTGGGGCTCTCAACAA-AAGTCACTGAACCATTCACAAGGTTGGGGCTCT-CAACA
*
4818 AAAGTCACCTGAACC
64 AAAGTCACCAGAACC
*
4833 TTCACCAGGTTGGGGCTCTCAACAAAAGTCACCTGAACC-TTCACCAGGTTGGGGCTCTCAACAA
1 TTCACCAGGTTGGGGCTCTCAACAAAAGTCA-CTGAACCATTCACAAGGTTGGGGCTCTCAACAA
*
4897 AAGTCACCTGAACC
65 AAGTCACCAGAACC
*
4911 TTCACCAGGTTGGGGCTCTCAACAAAAGTCACCTGAACC-TTCACAAGGTTGGGGTTCTCAACAA
1 TTCACCAGGTTGGGGCTCTCAACAAAAGTCA-CTGAACCATTCACAAGGTTGGGGCTCTCAACAA
4975 AA
65 AA
4977 TTCAGCTTGG
Statistics
Matches: 253, Mismatches: 40, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
77 4 0.02
78 239 0.94
79 10 0.04
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.19
Consensus pattern (78 bp):
TTCACCAGGTTGGGGCTCTCAACAAAAGTCACTGAACCATTCACAAGGTTGGGGCTCTCAACAAA
AGTCACCAGAACC
Found at i:4964 original size:117 final size:117
Alignment explanation
Indices: 4555--4976 Score: 367
Period size: 117 Copynumber: 3.6 Consensus size: 117
4545 AAAGTTGGTG
* * * *
4555 GAACATTCACCA-GTATGGGGCTCCCAACAGAAA-TCAGC-GGACCATTCACCAGGTTGGGGCTC
1 GAACCTTCACCAGGT-TGGGGCTCCCAACA-AAAGTCACCTGAACCATTCACAAGGTTGGGGCTC
* ** * * * * *
4617 CCAACAAAAGTCTGCTG-ACCATTCACGAGGTTGGGACTCCCAACAGAAGTCAGAA
64 TCAACAAAAGTCACCTGAACC-TTCACAAGGTTGGGGCTCTCAACAAAAGTCA-AT
* * * * * * * * * *
4672 G-ACTCTTCGCCGGGTTGGGGGTCCCAAAAAAAGTCA-GTGGACCATTCAGAAGGCTGGGACTCA
1 GAAC-CTTCACCAGGTTGGGGCTCCCAACAAAAGTCACCTGAACCATTCACAAGGTTGGGGCTCT
* * * * *
4735 CACCAAAAGTCACCAGAACATACACAAGGTTGGGGGTCTCAA-AAGAAGTCAAT
65 CAACAAAAGTCACCTGAACCTTCACAAGGTTGGGGCTCTCAACAA-AAGTCAAT
* * * ** * *
4788 GGACCATTCACAAGGTGGGGGCTTACAAGAAAAGTCACCTGAACC-TTCACCAGGTTGGGGCTCT
1 GAACC-TTCACCAGGTTGGGGCTCCCAACAAAAGTCACCTGAACCATTCACAAGGTTGGGGCTCT
* *
4852 CAACAAAAGTCACCTGAACCTTCACCAGGTTGGGGCTCTCAACAAAAGTCACCT
65 CAACAAAAGTCACCTGAACCTTCACAAGGTTGGGGCTCTCAACAAAAGTCA-AT
* *
4906 GAACCTTCACCAGGTTGGGGCTCTCAACAAAAGTCACCTGAACC-TTCACAAGGTTGGGGTTCTC
1 GAACCTTCACCAGGTTGGGGCTCCCAACAAAAGTCACCTGAACCATTCACAAGGTTGGGGCTCTC
4970 AACAAAA
66 AACAAAA
4977 TTCAGCTTGG
Statistics
Matches: 241, Mismatches: 53, Indels: 22
0.76 0.17 0.07
Matches are distributed among these distances:
116 9 0.04
117 216 0.90
118 16 0.07
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (117 bp):
GAACCTTCACCAGGTTGGGGCTCCCAACAAAAGTCACCTGAACCATTCACAAGGTTGGGGCTCTC
AACAAAAGTCACCTGAACCTTCACAAGGTTGGGGCTCTCAACAAAAGTCAAT
Done.