Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold571
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: 37045
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:3359 original size:10 final size:10
Alignment explanation
Indices: 3335--3383 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
3325 AGCTCGTTTC
*
3335 CAGCTCACTT
1 CAGCTCAATT
* *
3345 GAGCTCAAGT
1 CAGCTCAATT
3355 CAGCTC-ATT
1 CAGCTCAATT
3364 CGAGCTCAATT
1 C-AGCTCAATT
3375 CAGCTCAAT
1 CAGCTCAAT
3384 CTTAACCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 25 0.78
11 4 0.12
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:3360 original size:20 final size:20
Alignment explanation
Indices: 3335--3381 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
3325 AGCTCGTTTC
3335 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
*
3355 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
3375 CAGCTCA
1 CAGCTCA
3382 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Found at i:5956 original size:10 final size:10
Alignment explanation
Indices: 5928--5958 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5918 TTTTCAAAAT
*
5928 ATTTTTTTCG
1 ATTTTTTTTG
5938 ATTTTTTTTG
1 ATTTTTTTTG
5948 ATTTTTTTTG
1 ATTTTTTTTG
5958 A
1 A
5959 ATCTACAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.13, C:0.03, G:0.10, T:0.74
Consensus pattern (10 bp):
ATTTTTTTTG
Found at i:8310 original size:102 final size:101
Alignment explanation
Indices: 8135--8356 Score: 408
Period size: 102 Copynumber: 2.2 Consensus size: 101
8125 TGTAGTGTCA
*
8135 TCATCGATGGAGGAAGCTGTAGAACGTAGCGAGCACTCTCATGGTGGAAAAATTAAATCTACCAA
1 TCATCGATGGAGGAAGTTGTAGAACGTAGCGAGCACTCTCATGGTGGAAAAATTAAATCTACCAA
8200 CCACCAAGCATCCAACTCCGTACAAACTTCAATGGC
66 CCACCAAGCATCCAACTCCGTACAAACTTCAATGGC
8236 TCATCGATGGAGGAAGTTGTACGAACGTAGCGAGCACTCTCATGGTGGAAAAATTAAATCTACCA
1 TCATCGATGGAGGAAGTTGTA-GAACGTAGCGAGCACTCTCATGGTGGAAAAATTAAATCTACCA
8301 ACCACCAAGCATCCAACTCCGTACAAACTTCAATGGC
65 ACCACCAAGCATCCAACTCCGTACAAACTTCAATGGC
*
8338 TCAACGATGGAGGAGAGTT
1 TCATCGATGGAGGA-AGTT
8357 AAAGGTGACA
Statistics
Matches: 117, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
101 20 0.17
102 93 0.79
103 4 0.03
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.20
Consensus pattern (101 bp):
TCATCGATGGAGGAAGTTGTAGAACGTAGCGAGCACTCTCATGGTGGAAAAATTAAATCTACCAA
CCACCAAGCATCCAACTCCGTACAAACTTCAATGGC
Found at i:10988 original size:22 final size:22
Alignment explanation
Indices: 10960--11003 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
10950 TTTTGAACCA
10960 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
10982 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
11004 AAATACCAAA
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:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:11661 original size:20 final size:20
Alignment explanation
Indices: 11636--11680 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
11626 GCAAAAATAC
*
11636 AAAAGAAAAGAAAAATGAAA
1 AAAAGAAAAGAAAAATCAAA
*
11656 AAAAG-AAAGAAAATTCAAA
1 AAAAGAAAAGAAAAATCAAA
11675 AAAAGA
1 AAAAGA
11681 GAATGAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATCAAA
Found at i:12978 original size:22 final size:22
Alignment explanation
Indices: 12948--12991 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
12938 TTTGGTATTT
12948 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
12970 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
12992 TGGTTCAAAA
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:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:17283 original size:19 final size:19
Alignment explanation
Indices: 17259--17300 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
17249 TTCATTCTCT
*
17259 TTTTTTGAATTTTCTTTTC
1 TTTTTTCAATTTTCTTTTC
*
17278 TTTTTTCATTTTTCTTTTC
1 TTTTTTCAATTTTCTTTTC
17297 TTTT
1 TTTT
17301 GTATTTTCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTTCAATTTTCTTTTC
Found at i:19873 original size:22 final size:22
Alignment explanation
Indices: 19843--19886 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
19833 TTTGGTATTT
19843 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
19865 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
19887 TGGTTCAAAA
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:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:23886 original size:45 final size:45
Alignment explanation
Indices: 23822--24057 Score: 427
Period size: 45 Copynumber: 5.2 Consensus size: 45
23812 CATGAAATTA
*
23822 AGGAAGCATTTGACCAACATCATGCATAATTCATGGGAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
23867 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* *
23912 AGGAAGCATTTGACCAACATCATGCATAATTCATGGGAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
23957 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
24002 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
24047 AGGAAGAATTT
1 AGGAAGCATTT
24058 AAGGAAGCAT
Statistics
Matches: 184, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 184 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:24051 original size:12 final size:12
Alignment explanation
Indices: 24036--24069 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
24026 CATAATTCAT
24036 GGAAGAATTTAA
1 GGAAGAATTTAA
24048 GGAAGAATTTAA
1 GGAAGAATTTAA
*
24060 GGAAGCATTT
1 GGAAGAATTT
24070 GGCCAACATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.44, C:0.03, G:0.26, T:0.26
Consensus pattern (12 bp):
GGAAGAATTTAA
Found at i:24108 original size:57 final size:57
Alignment explanation
Indices: 23991--24109 Score: 184
Period size: 57 Copynumber: 2.1 Consensus size: 57
23981 CATAATTCAT
* * *
23991 GGAAGAATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTAA
1 GGAAGAATTTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAACAAATTAA
* * *
24048 GGAAGAATTTAAGGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTGA
1 GGAAGAATTTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAACAAATTAA
24105 GGAAG
1 GGAAG
24110 CACCATGGCC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (57 bp):
GGAAGAATTTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAACAAATTAA
Found at i:28978 original size:40 final size:40
Alignment explanation
Indices: 28926--29109 Score: 178
Period size: 40 Copynumber: 4.6 Consensus size: 40
28916 TAACTCATTC
* *
28926 AATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAGAAACTCGCACA
* *
28966 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGAAACTCGCACA
* * *
29006 AAGGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGAAACTCGCACA
* ** ** *
29046 AAGGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAGAAAC-TCGCACA
*
29087 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
29110 CAGCATTCAA
Statistics
Matches: 127, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
39 8 0.06
40 108 0.85
41 11 0.09
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAGAAACTCGCACA
Found at i:29042 original size:80 final size:80
Alignment explanation
Indices: 28929--29109 Score: 201
Period size: 80 Copynumber: 2.3 Consensus size: 80
28919 CTCATTCAAT
* * *
28929 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAAGGCCTTC-GGATCTTAACCCGGATA-
*
28992 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
* * **
29008 GGCCTTCGGGACTTAACCCGGA-ATTAGTATCTCGCACAAAGGCCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTA-AAACTCGCACAAAGGCCTTCGGATCTTAACCCGGATA
29072 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
29089 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
29110 CAGCATTCAA
Statistics
Matches: 87, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
79 6 0.07
80 70 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAAGGCCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:33374 original size:23 final size:22
Alignment explanation
Indices: 33322--33374 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
33312 TCCACGTCTT
*
33322 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
33344 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
33367 TTTCTTTT
1 TTTCTTTT
33375 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Done.