Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1366
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: 28975
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Found at i:6685 original size:39 final size:41
Alignment explanation
Indices: 6584--6767 Score: 206
Period size: 39 Copynumber: 4.6 Consensus size: 41
6574 TTGAATGATG
* *
6584 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
6624 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
6664 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
6703 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
6742 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
6768 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
38 1 0.01
39 69 0.55
40 43 0.34
41 12 0.10
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:6720 original size:79 final size:80
Alignment explanation
Indices: 6584--6767 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 80
6574 TTGAATGATG
*
6584 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCA-T
6648 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
6663 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
6725 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
6742 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
6768 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 49 0.54
80 18 0.20
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
GTGCGAGATACTATA
Found at i:6790 original size:78 final size:79
Alignment explanation
Indices: 6637--6800 Score: 201
Period size: 78 Copynumber: 2.1 Consensus size: 79
6627 GGACTAAGAT
* **
6637 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
6702 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
6716 CCGAAGGCA-TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
6778 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
6794 CCGAAGG
1 CCGAAGG
6801 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.03
78 38 0.51
79 34 0.46
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:8213 original size:22 final size:22
Alignment explanation
Indices: 8161--8225 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
8151 GCCAATTATT
*
8161 CTGATTATGGCTTTGCGCCAAC
1 CTGATTATGGCTTTGTGCCAAC
*
8183 CT-ACATATGGCTTTGTGCCAAC
1 CTGA-TTATGGCTTTGTGCCAAC
8205 CTGATTATGG-TTGTGTGCCAA
1 CTGATTATGGCTT-TGTGCCAA
8226 ACATATTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 3 0.08
22 33 0.89
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (22 bp):
CTGATTATGGCTTTGTGCCAAC
Found at i:9518 original size:49 final size:50
Alignment explanation
Indices: 9463--9588 Score: 148
Period size: 50 Copynumber: 2.5 Consensus size: 50
9453 GTTGGCGATT
* * * *
9463 CCATGTCCCAGACATGGTCTTACACTGGCTATCA-TCAT-CGAGGCTGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTATCACACATCCG-GGCCGACG
* * * *
9512 CCATGTCCTAGACATGGTTTTACACTAGCTCTCACACATCCGTGCCGACG
1 CCATGTCCCAGACATGGTCTTACACTAGCTATCACACATCCGGGCCGACG
*
9562 CCATGTCCCAGACACGGTCTTACACTA
1 CCATGTCCCAGACATGGTCTTACACTA
9589 ACACATCTCG
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
49 30 0.47
50 32 0.50
51 2 0.03
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACACTAGCTATCACACATCCGGGCCGACG
Found at i:9617 original size:44 final size:43
Alignment explanation
Indices: 9545--9627 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 43
9535 ACTAGCTCTC
9545 ACACATCCGTGCCGACGCCATGTCCCAGACACGGTCTTACACTA
1 ACACATCCGTGCCGACGCCATGTCCCAGACA-GGTCTTACACTA
* *
9589 ACACATCTCGTAGCCGATG-CATGT-CCAGACATGTCTTAC
1 ACACATC-CGT-GCCGACGCCATGTCCCAGACAGGTCTTAC
9628 GCTAGCTCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
43 7 0.20
44 14 0.40
45 8 0.23
46 6 0.17
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.22
Consensus pattern (43 bp):
ACACATCCGTGCCGACGCCATGTCCCAGACAGGTCTTACACTA
Found at i:17911 original size:40 final size:40
Alignment explanation
Indices: 17810--17994 Score: 246
Period size: 40 Copynumber: 4.6 Consensus size: 40
17800 TATTCGAATG
* *
17810 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GTGACT
* * * * *
17851 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACT
* *
17891 AGATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* *
17931 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
17971 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
17995 CTTGTGGAAG
Statistics
Matches: 123, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 93 0.76
41 29 0.24
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
Found at i:25951 original size:39 final size:40
Alignment explanation
Indices: 25845--26062 Score: 220
Period size: 39 Copynumber: 5.5 Consensus size: 40
25835 TATTCGAATG
*
25845 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGC-AAGTGACT
* * * *
25886 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCAAG-TGACT
* *
25926 ATATCCGGGCTAAGA-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCAAGTGACT
* *
25965 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGAC-
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCAAGTGACT
* * *
26004 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCAAGT-AGTT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCAAGTGA-CT
26043 ATATCC-GGCTAA-ATCCGAAG
1 ATATCCGGGCTAAGATCCGAAG
26063 ATTACTTGAG
Statistics
Matches: 151, Mismatches: 18, Indels: 20
0.80 0.10 0.11
Matches are distributed among these distances:
37 8 0.05
38 15 0.10
39 61 0.40
40 38 0.25
41 28 0.19
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCAAGTGACT
Found at i:25985 original size:79 final size:79
Alignment explanation
Indices: 25845--26027 Score: 228
Period size: 79 Copynumber: 2.3 Consensus size: 79
25835 TATTCGAATG
* * *
25845 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAG-ACCGAAGGCATTTGTGCTAAGCGACTATAACCGGACTAAGATCCGAAGGC
*
25910 ATTCGTGCGAGTTG-C
65 ATTCATGCGAG-TGAC
* *
25925 TATATCCGGGCTAAGACCGAAGGCATTTGTGCT-AGCGACTATATCCGGGCTAAG-TCCCGAAGG
1 -ATATCCGGGCTAAGACCGAAGGCATTTGTGCTAAGCGACTATAACCGGACTAAGAT-CCGAAGG
* *
25988 CATTTATGCTAGTGAC
64 CATTCATGCGAGTGAC
26004 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGA-CCGAAGGC
26028 CTTGTGCAAG
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 18 0.20
79 43 0.47
80 16 0.18
81 14 0.15
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCGAAGGCATTTGTGCTAAGCGACTATAACCGGACTAAGATCCGAAGGCA
TTCATGCGAGTGAC
Done.