Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1900
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: 28563
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Found at i:102 original size:27 final size:27
Alignment explanation
Indices: 1--103 Score: 82
Period size: 27 Copynumber: 3.7 Consensus size: 27
** *
1 TCAAACTCGCACACCTTAGTGCCGCATGG
1 TCAAA-TCGCACA-CTTAGTGCAACATAG
* * *
30 TC-ATTCGCACACTTAGTGCTCATCATTAT
1 TCAAATCGCACACTTAGTG--CAACA-TAG
**
59 TCATTTCGCACACTTAGTGCAACATAG
1 TCAAATCGCACACTTAGTGCAACATAG
86 TCAAATCGCACACTTAGT
1 TCAAATCGCACACTTAGT
104 ACTGCTACAA
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
26 7 0.12
27 25 0.42
28 8 0.13
29 5 0.08
30 15 0.25
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (27 bp):
TCAAATCGCACACTTAGTGCAACATAG
Found at i:655 original size:27 final size:27
Alignment explanation
Indices: 614--695 Score: 110
Period size: 27 Copynumber: 3.0 Consensus size: 27
604 ATCTCTCTCT
* *
614 GAGTTGACTATGTAGCACTAAGTGTGC
1 GAGTTGATTACGTAGCACTAAGTGTGC
*
641 GATTTGATTACGTAGCACTAAGTGTGC
1 GAGTTGATTACGTAGCACTAAGTGTGC
** *
668 GAGTTGATTATATAGCACTGAGTGTGC
1 GAGTTGATTACGTAGCACTAAGTGTGC
695 G
1 G
696 GACTCAATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (27 bp):
GAGTTGATTACGTAGCACTAAGTGTGC
Found at i:8705 original size:27 final size:27
Alignment explanation
Indices: 8674--8851 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
8664 TAAATTGTAC
8674 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
8701 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
8727 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
8755 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
8783 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
8810 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
8837 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
8852 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:8788 original size:82 final size:81
Alignment explanation
Indices: 8675--8830 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
8665 AAATTGTACA
* *
8675 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
8739 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
8756 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
8821 TGCGAGTTGA
65 TGCGAATTGA
8831 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:8842 original size:82 final size:81
Alignment explanation
Indices: 8671--8851 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
8661 GATTAAATTG
* *
8671 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
8736 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
8752 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
8816 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
8834 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
8852 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:13925 original size:41 final size:42
Alignment explanation
Indices: 13845--13936 Score: 109
Period size: 41 Copynumber: 2.2 Consensus size: 42
13835 TCTGTTACGC
* *
13845 TGGCATCG-ATCTGTGATTACGTGTAAGACCATGTTTGGGACA-
1 TGGCATCGTAT-T-TGATTACGTATAAGACCATGTCTGGGACAG
*
13887 TCGGCATCGTATTTGATT-CGTATAAGACCCTGTCTGGGACAG
1 T-GGCATCGTATTTGATTACGTATAAGACCATGTCTGGGACAG
13929 TGGCATCG
1 TGGCATCG
13937 ATATGAGATA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
41 27 0.61
42 7 0.16
43 8 0.18
44 2 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (42 bp):
TGGCATCGTATTTGATTACGTATAAGACCATGTCTGGGACAG
Found at i:17433 original size:110 final size:110
Alignment explanation
Indices: 17240--17459 Score: 431
Period size: 110 Copynumber: 2.0 Consensus size: 110
17230 TGTGACTATT
17240 ATAGAATTAAACTTGAGTAAGTAATTAAACAAATTCATTTGTTTAAATTTAAAGCTCAAGAGCAA
1 ATAGAATTAAACTTGAGTAAGTAATTAAACAAATTCATTTGTTTAAATTTAAAGCTCAAGAGCAA
17305 AGAGGAACTAAATCAGATAGGGGAAAGGAGAAAGCAATCGAGTAG
66 AGAGGAACTAAATCAGATAGGGGAAAGGAGAAAGCAATCGAGTAG
*
17350 ATAGAATTAAAGTTGAGTAAGTAATTAAACAAATTCATTTGTTTAAATTTAAAGCTCAAGAGCAA
1 ATAGAATTAAACTTGAGTAAGTAATTAAACAAATTCATTTGTTTAAATTTAAAGCTCAAGAGCAA
17415 AGAGGAACTAAATCAGATAGGGGAAAGGAGAAAGCAATCGAGTAG
66 AGAGGAACTAAATCAGATAGGGGAAAGGAGAAAGCAATCGAGTAG
17460 CCTATCCACA
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 109 1.00
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.24
Consensus pattern (110 bp):
ATAGAATTAAACTTGAGTAAGTAATTAAACAAATTCATTTGTTTAAATTTAAAGCTCAAGAGCAA
AGAGGAACTAAATCAGATAGGGGAAAGGAGAAAGCAATCGAGTAG
Found at i:17852 original size:22 final size:22
Alignment explanation
Indices: 17824--17867 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
17814 GAAGGCATTC
*
17824 GTGCTGGTGTTATATCTGGGCT
1 GTGCTGGTGTTATATCCGGGCT
17846 GTGCTGGTGTTATATCCGGGCT
1 GTGCTGGTGTTATATCCGGGCT
17868 AAGTCCCGAA
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:0.09, C:0.16, G:0.36, T:0.39
Consensus pattern (22 bp):
GTGCTGGTGTTATATCCGGGCT
Found at i:17900 original size:39 final size:39
Alignment explanation
Indices: 17846--17991 Score: 195
Period size: 39 Copynumber: 3.7 Consensus size: 39
17836 TATCTGGGCT
17846 GTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTC
1 GTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTC
* *
17885 GTGCTGGTGTTATATCCGGGTTAAGCCCCGAAGGCATTC
1 GTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTC
* * * *
17924 TTGATGGTGTTATATCCGGGCTAAAGTCCCGCAGGC-TTT
1 GTGCTGGTGTTATATCCGGGCT-AAGTCCCGAAGGCATTC
* *
17963 GTGCTGGTATTATATACGGGCTTAAGTCC
1 GTGCTGGTGTTATATCCGGGC-TAAGTCC
17992 AGCATGCTTT
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 81 0.87
40 12 0.13
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.31
Consensus pattern (39 bp):
GTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTC
Found at i:21907 original size:31 final size:31
Alignment explanation
Indices: 21866--21929 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
21856 CCTTTTCATA
* *
21866 TTTCATATTTCATAACACTGGGCCGAATCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
21897 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
21928 TT
1 TT
21930 ACTGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:22195 original size:23 final size:23
Alignment explanation
Indices: 22144--22216 Score: 110
Period size: 23 Copynumber: 3.1 Consensus size: 23
22134 CCTAGCCTCT
*
22144 TTTAATAACTGGGGAAAAAGCCCC
1 TTTAATAACTGGGGCAAAAG-CCC
*
22168 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCAAAAGCCC
*
22191 TTTAATAACTGGGGCACAAGCCC
1 TTTAATAACTGGGGCAAAAGCCC
22214 TTT
1 TTT
22217 TTCACTTCCT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
23 28 0.61
24 18 0.39
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (23 bp):
TTTAATAACTGGGGCAAAAGCCC
Found at i:22295 original size:20 final size:20
Alignment explanation
Indices: 22267--22333 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
22257 TTATGATTAC
*
22267 ATCACGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
22287 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
22307 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
22327 ACCATGT
1 ATCATGT
22334 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:22402 original size:25 final size:25
Alignment explanation
Indices: 22370--22417 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
22360 ATACATAAAC
* * *
22370 CCTAGGGGTATAATAGTCATTTTTA
1 CCTAGGGGCAAAACAGTCATTTTTA
22395 CCTAGGGGCAAAACAGTCATTTT
1 CCTAGGGGCAAAACAGTCATTTT
22418 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACAGTCATTTTTA
Found at i:27037 original size:24 final size:26
Alignment explanation
Indices: 26998--27047 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
26988 GAAATGTGAA
*
26998 AGGGGTTGCTATGTGCTGA-TCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
27023 AGGGG-TGCTAAGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
27048 TTCATGGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.14, C:0.24, G:0.36, T:0.26
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCTGATTCCCCG
Done.