Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1857
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: 61334
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:7916 original size:46 final size:46
Alignment explanation
Indices: 7849--7977 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
7839 TGTAACCCGC
* * * *
7849 CCATAAGTGAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
7895 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
7941 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
7978 TGCTCAACCA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:7996 original size:46 final size:45
Alignment explanation
Indices: 7854--7996 Score: 137
Period size: 46 Copynumber: 3.1 Consensus size: 45
7844 CCCGCCCATA
* * ** * *
7854 AGTGAACTCGAACTCAACTCAACGAGCTCGGGCGTTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T
*** *
7899 AAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTC-GCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T
7945 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-ACCATCCT
7992 AGTGA
1 AGTGA
7997 CATGTCACTT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
46 81 0.93
47 1 0.01
48 5 0.06
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCCT
Found at i:20045 original size:43 final size:41
Alignment explanation
Indices: 19998--20140 Score: 103
Period size: 43 Copynumber: 3.3 Consensus size: 41
19988 AACATATATA
*
19998 ATGCCAACGTCCCAGGCGCGGTCTTACATGTAATCAAACATCG
1 ATGCCAACGTCCCAGACG-GGTCTTACATGTAATCAAA-ATCG
* * * *
20041 ATGCC-ACTGTCCCAAACAGGGTCTTACACGAAATCAGATAT-G
1 ATGCCAAC-GTCCCAGAC-GGGTCTTACATGTAATCA-AAATCG
* * *
20083 ATG-CAGATGTCCCAGACATGGTCTTACATGTAAAACAAAAGTCG
1 ATGCCA-ACGTCCCAGAC-GGGTCTTACATGT-AATCAAAA-TCG
*
20127 ATGCCATCGTCCCA
1 ATGCCAACGTCCCA
20141 AACATGGTCA
Statistics
Matches: 77, Mismatches: 14, Indels: 17
0.71 0.13 0.16
Matches are distributed among these distances:
41 1 0.01
42 27 0.35
43 35 0.45
44 12 0.16
45 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (41 bp):
ATGCCAACGTCCCAGACGGGTCTTACATGTAATCAAAATCG
Found at i:20106 original size:42 final size:42
Alignment explanation
Indices: 20017--20162 Score: 136
Period size: 43 Copynumber: 3.4 Consensus size: 42
20007 TCCCAGGCGC
* * *
20017 GGTCTTACATGTAATCAAACA-TCGATGCCACTGTCCCAAACAG
1 GGTCTTACACGAAATCAAA-AGTCGATGCCA-TGTCCCAAACAT
* * *
20060 GGTCTTACACGAAATCAGATA-T-GATGCAGATGTCCCAGACAT
1 GGTCTTACACGAAATCA-AAAGTCGATGC-CATGTCCCAAACAT
* *
20102 GGTCTTACATGTAAAACAAAAGTCGATGCCATCGTCCCAAACAT
1 GGTCTTACACG-AAATCAAAAGTCGATGCCAT-GTCCCAAACAT
*
20146 GGTCATACACGAAATCA
1 GGTCTTACACGAAATCA
20163 CAAAACGAAA
Statistics
Matches: 83, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
42 27 0.33
43 31 0.37
44 25 0.30
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (42 bp):
GGTCTTACACGAAATCAAAAGTCGATGCCATGTCCCAAACAT
Found at i:31522 original size:51 final size:50
Alignment explanation
Indices: 31467--31615 Score: 152
Period size: 51 Copynumber: 3.1 Consensus size: 50
31457 CTATCGCATA
* *
31467 ACATGTAACACATCCATAATGAACTCAAACCTCTCAATGAGCTCGGATGTT
1 ACATGTAACGCATCCATAATGAACTCAAACCTCTCAACGAGCTCGGATG-T
* * * *
31518 ACATG-AATTGCATCCATCATGAACTCAAACCACTCAACGAGCTCGAATG-
1 ACATGTAA-CGCATCCATAATGAACTCAAACCTCTCAACGAGCTCGGATGT
*
31567 -C---T--CGCATCCATAATGAACTCGAACCTCTCAACGAGCTCGGATGCT
1 ACATGTAACGCATCCATAATGAACTCAAACCTCTCAACGAGCTCGGATG-T
31612 ACAT
1 ACAT
31616 ACCTCACGAA
Statistics
Matches: 80, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
43 36 0.45
46 1 0.01
48 1 0.01
50 2 0.03
51 40 0.50
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.23
Consensus pattern (50 bp):
ACATGTAACGCATCCATAATGAACTCAAACCTCTCAACGAGCTCGGATGT
Found at i:31575 original size:43 final size:43
Alignment explanation
Indices: 31527--31611 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
31517 TACATGAATT
*
31527 GCATCCATCATGAACTCAAACCACTCAACGAGCTCGAATGCTC
1 GCATCCATAATGAACTCAAACCACTCAACGAGCTCGAATGCTC
* * *
31570 GCATCCATAATGAACTCGAACCTCTCAACGAGCTCGGATGCT
1 GCATCCATAATGAACTCAAACCACTCAACGAGCTCGAATGCT
31612 ACATACCTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.20
Consensus pattern (43 bp):
GCATCCATAATGAACTCAAACCACTCAACGAGCTCGAATGCTC
Found at i:48823 original size:6 final size:6
Alignment explanation
Indices: 48797--48860 Score: 87
Period size: 6 Copynumber: 10.8 Consensus size: 6
48787 TGAATCCTCC
*
48797 TATTTT T-TTATT TATTCT TATTTT TA-TTT TATTTT TATTTT TATTTT
1 TATTTT TATT-TT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
*
48844 TATTTT TATTTT CATTT
1 TATTTT TATTTT TATTT
48861 CAATTTTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
5 7 0.13
6 43 0.83
7 2 0.04
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
TATTTT
Found at i:48827 original size:17 final size:17
Alignment explanation
Indices: 48801--48880 Score: 90
Period size: 17 Copynumber: 4.6 Consensus size: 17
48791 TCCTCCTATT
*
48801 TTTTTA-TTTATTCTTA
1 TTTTTATTTTATTTTTA
48817 TTTTTATTTTATTTTTA
1 TTTTTATTTTATTTTTA
48834 TTTTTATTTTTATTTTTA
1 TTTTTA-TTTTATTTTTA
* * *
48852 TTTTCATTTCAATTTTA
1 TTTTTATTTTATTTTTA
48869 TTATTTTATTTT
1 -T-TTTTATTTT
48881 GAAAGACATA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
16 6 0.11
17 24 0.44
18 17 0.31
19 7 0.13
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTATTTTATTTTTA
Found at i:48839 original size:29 final size:29
Alignment explanation
Indices: 48797--48860 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
48787 TGAATCCTCC
48797 TATTTTTTTATTTATTCTTATTTTTATTT
1 TATTTTTTTATTTATTCTTATTTTTATTT
*
48826 TATTTTTATT-TTTATTTTTATTTTTATTT
1 TATTTTT-TTATTTATTCTTATTTTTATTT
48855 TCATTT
1 T-ATTT
48861 CAATTTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 26 0.81
30 6 0.19
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (29 bp):
TATTTTTTTATTTATTCTTATTTTTATTT
Found at i:48867 original size:29 final size:29
Alignment explanation
Indices: 48807--48880 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
48797 TATTTTTTTA
* * *
48807 TTTATTCTTATTTTTATTTTATTTTTATT
1 TTTATTTTTATTTTTATTTTATTTTCAAT
48836 TTTATTTTTATTTTTATTTTCA-TTTCAAT
1 TTTATTTTTATTTTTATTTT-ATTTTCAAT
48865 TTTATTATTTTATTTT
1 TTTA-T-TTTTATTTT
48881 GAAAGACATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 28 0.72
30 2 0.05
31 9 0.23
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (29 bp):
TTTATTTTTATTTTTATTTTATTTTCAAT
Found at i:51641 original size:27 final size:28
Alignment explanation
Indices: 51557--51654 Score: 119
Period size: 27 Copynumber: 3.5 Consensus size: 28
51547 CATGAGATTG
* * *
51557 GCACTAAGTGTGCGGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGAGTTT-GATTATAT-A
51586 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
51614 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
51641 GCAGTGAGTGTGCG
1 GCACTAAGTGTGCG
51655 GACTTAATAT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
27 23 0.37
28 21 0.33
29 19 0.30
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:51668 original size:29 final size:27
Alignment explanation
Indices: 51585--51668 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 27
51575 TAAATTGTTC
* *
51585 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTAATTATAT
* *
51613 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTAATTATAT
* *
51640 AGCAGTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGC-GACTTAAT-TATAT
51669 TTTTGAATCA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
27 22 0.45
28 22 0.45
29 5 0.10
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTAATTATAT
Found at i:59860 original size:27 final size:28
Alignment explanation
Indices: 59776--59873 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
59766 CATGAGATTG
* * *
59776 GCACTAAGTGTGCGGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGAGTTT-GATTATAT-A
59805 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
59833 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
59860 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
59874 GACTTAATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 24 0.38
28 21 0.33
29 19 0.30
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:59887 original size:29 final size:27
Alignment explanation
Indices: 59804--59887 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
59794 TAAATTGTTC
* *
59804 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTAATTATAT
* *
59832 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTAATTATAT
*
59859 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGC-GACTTAAT-TATAT
59888 TTTTGAATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.46
28 22 0.44
29 5 0.10
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTAATTATAT
Done.