Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold703
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: 75967
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Found at i:1906 original size:40 final size:39
Alignment explanation
Indices: 1754--1908 Score: 163
Period size: 39 Copynumber: 4.0 Consensus size: 39
1744 CCTCGTTCAA
* * *
1754 AATGCCTTCGGGACATAGCCCGG--TTAAGTAACTCACAC-
1 AATGCC-TCGGGACTTAACCCGGATTTAA-TAACTCGCACG
* * *
1792 AATGCCTCGGGACATAACCCGGATTTAACAACTCGCAAG
1 AATGCCTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
1831 ACTGCCTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
1870 AATGCTTCGGGACTTAAACCTGGATTTAGTATCTCGCAC
1 AATGCCTCGGGACTT-AACCCGGATTTAATAACTCGCAC
1909 AAAGGCCTTC
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
37 15 0.15
38 13 0.13
39 52 0.52
40 20 0.20
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (39 bp):
AATGCCTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:9870 original size:40 final size:40
Alignment explanation
Indices: 9694--9916 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
9684 TCCTCGTTCA
* * * * *
9694 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
9733 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
9773 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
9813 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
9853 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
9893 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
9917 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 37 0.23
40 113 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:17754 original size:40 final size:40
Alignment explanation
Indices: 17578--17800 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
17568 TCCTCGTTCA
* * * * *
17578 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
17617 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
17657 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
17697 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
17737 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
17777 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
17801 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 37 0.23
40 113 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:21081 original size:14 final size:13
Alignment explanation
Indices: 21050--21087 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
21040 GGGGTGTTAC
21050 AATTAA-AACAAG
1 AATTAAGAACAAG
*
21062 AATTAAGAACATAT
1 AATTAAGAACA-AG
21076 AATTAAGAACAA
1 AATTAAGAACAA
21088 ATCAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 6 0.26
13 5 0.22
14 12 0.52
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.21
Consensus pattern (13 bp):
AATTAAGAACAAG
Found at i:22331 original size:43 final size:43
Alignment explanation
Indices: 22188--22344 Score: 124
Period size: 43 Copynumber: 3.7 Consensus size: 43
22178 TGTGATTTTG
* **
22188 TGTAAGACCACGTCTGGGACGTTGGCATCG--ATTTGATATTTATG
1 TGTAAGACCATGTCTGGGACGTTGGCATCGATATTTG--A-TTACA
* * * * * * * * *
22232 TGTACGATCAGGTTTGGGACATCGGTATC-ATATTTGATTTCG
1 TGTAAGACCATGTCTGGGACGTTGGCATCGATATTTGATTACA
*
22274 TGTAAGACCCTGTCTGGGACAG-TGGCATCGATATTTGATTACA
1 TGTAAGACCATGTCTGGGAC-GTTGGCATCGATATTTGATTACA
*
22317 TGTACGACCATGTCTGGGACGTTGGCAT
1 TGTAAGACCATGTCTGGGACGTTGGCAT
22345 TGTATGAACT
Statistics
Matches: 87, Mismatches: 21, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
42 24 0.28
43 36 0.41
44 22 0.25
45 5 0.06
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.33
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACGTTGGCATCGATATTTGATTACA
Found at i:28498 original size:28 final size:27
Alignment explanation
Indices: 28467--28572 Score: 97
Period size: 28 Copynumber: 3.7 Consensus size: 27
28457 TACATACATG
*
28467 CATATGCCCCACTGGGCCCAATCTC-ATT
1 CATATGGCCCACT-GGCCCAAT-TCAATT
*
28495 CATATGGCCCATCTGGCCCAGTTCAATT
1 CATATGGCCCA-CTGGCCCAATTCAATT
*
28523 CTTATGGCCCACTAGGCCCAATTCACATT
1 CATATGGCCCACT-GGCCCAATTCA-ATT
* * *
28552 AATATAGCCCATTAGGCCCAA
1 CATATGGCCCACT-GGCCCAA
28573 ATCATATTAT
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
27 4 0.06
28 40 0.61
29 22 0.33
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.25
Consensus pattern (27 bp):
CATATGGCCCACTGGCCCAATTCAATT
Found at i:31971 original size:39 final size:40
Alignment explanation
Indices: 31870--32061 Score: 196
Period size: 40 Copynumber: 4.8 Consensus size: 40
31860 TTGAATGATG
* * * *
31870 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTAC-GAGTTACTAAT
* *
31909 ATCCGGACTAAGAT-CCGAAGGCATTTGTACGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTACGAGTTACTAAT
* *
31950 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAT
* *
31989 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAT
* * *
32028 AACCGGGCTATGTCCCGAAGGCATTTGAACGAGT
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGT
32062 AGCTATATCC
Statistics
Matches: 129, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
39 35 0.27
40 85 0.66
41 9 0.07
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAT
Found at i:32006 original size:79 final size:81
Alignment explanation
Indices: 31870--32054 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
31860 TTGAATGATG
*
31870 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
31934 TGTACGAGATACTA-A
66 TGTACGAGATACTATA
* * * **
31949 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
* *
32011 TTTGTGCGAGTTACTATA
64 TTTGTACGAGATACTATA
* *
32029 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
32055 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTACGAGATACTATA
Found at i:32076 original size:79 final size:79
Alignment explanation
Indices: 31923--32087 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
31913 GGACTAAGAT
* **
31923 CCGAAGGCATTTGTACGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTACGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
31988 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
32002 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTACGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
32065 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
32081 CCGAAGG
1 CCGAAGG
32088 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTACGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:39784 original size:40 final size:39
Alignment explanation
Indices: 39701--39884 Score: 219
Period size: 40 Copynumber: 4.6 Consensus size: 39
39691 TTGAATGATG
* * * *
39701 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
39740 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
39780 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
39819 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
39860 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
39885 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
39 45 0.36
40 72 0.57
41 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:39836 original size:79 final size:80
Alignment explanation
Indices: 39701--39884 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 80
39691 TTGAATGATG
* *
39701 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
39765 GTGCGAGATACTA-A
66 GTGCGAGATACTATA
* * * **
39779 TTCCGGGCTAAGCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 -TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
*
39842 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
39859 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAG-CCCGAAGGCATTTG
39885 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
78 1 0.01
79 68 0.75
80 22 0.24
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTATA
Found at i:39906 original size:79 final size:79
Alignment explanation
Indices: 39753--39917 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
39743 GGACTAAGAT
* **
39753 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
39818 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
39832 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
39895 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
39911 CCGAAGG
1 CCGAAGG
39918 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:40814 original size:17 final size:18
Alignment explanation
Indices: 40792--40826 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40782 TCACATTGAA
40792 GTGTTTT-AGTGAAAACT
1 GTGTTTTCAGTGAAAACT
*
40809 GTGTTTTCATTGAAAACT
1 GTGTTTTCAGTGAAAACT
40827 CTTCTTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.43
Consensus pattern (18 bp):
GTGTTTTCAGTGAAAACT
Found at i:42824 original size:14 final size:14
Alignment explanation
Indices: 42805--42841 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
42795 GTACAGATTA
42805 AAGAAGAAAAGGAG
1 AAGAAGAAAAGGAG
*
42819 AAGAAGAAAAGTAG
1 AAGAAGAAAAGGAG
42833 AAGAAGAAA
1 AAGAAGAAA
42842 TCGACTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03
Consensus pattern (14 bp):
AAGAAGAAAAGGAG
Found at i:47833 original size:22 final size:22
Alignment explanation
Indices: 47807--47850 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
47797 TATATACTAA
47807 TTTATTACTAATTTACCTAACT
1 TTTATTACTAATTTACCTAACT
*
47829 TTTATTAGTAATTTACCTAACT
1 TTTATTACTAATTTACCTAACT
47851 AACCTTAATG
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:0.32, C:0.16, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTATTACTAATTTACCTAACT
Found at i:67872 original size:40 final size:40
Alignment explanation
Indices: 67790--68007 Score: 257
Period size: 40 Copynumber: 5.5 Consensus size: 40
67780 AAGCCAAGTA
* * *
67790 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
67828 CCTTCGGGACATAGCCCGGATATAGTAACTTGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
67868 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
67908 CCTTCAGGACTTAGCCCGGATATAATAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
67948 CCTTTGGGACTTAGCCTGGA-ACTAGTCACTAGCGCA-AAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACT--CGCACAAATG
67989 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
68008 TTATCATCCA
Statistics
Matches: 155, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
38 12 0.08
39 17 0.11
40 100 0.65
41 22 0.14
42 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:74988 original size:20 final size:20
Alignment explanation
Indices: 74965--75005 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
74955 ATATATGATG
74965 ACTTCTAATTATCTCTGGTT
1 ACTTCTAATTATCTCTGGTT
74985 ACTTCTAATTATCTCTGGTT
1 ACTTCTAATTATCTCTGGTT
75005 A
1 A
75006 ATTTATAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (20 bp):
ACTTCTAATTATCTCTGGTT
Done.