Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1082
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: 25158
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Found at i:7907 original size:27 final size:27
Alignment explanation
Indices: 7890--8067 Score: 133
Period size: 27 Copynumber: 6.6 Consensus size: 27
7880 ATATTAAGTC
7890 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* *
7917 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * *
7945 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* *** ** *
7972 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTCAGTGCTATATAATCAACT
* * **
7999 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTCAGTGCTAT-ATAATCAACT
* * * * *
8026 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
*
8053 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
8068 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 104 0.79
28 27 0.21
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:8029 original size:54 final size:54
Alignment explanation
Indices: 7890--8066 Score: 214
Period size: 54 Copynumber: 3.3 Consensus size: 54
7880 ATATTAAGTC
* * *
7890 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAA-T
* ** * *
7945 CGCACACTTAGTGC-TACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* **
7999 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
8053 CGCACACTTAGTGC
1 CGCACACTTAGTGC
8067 TGTACAATTT
Statistics
Matches: 105, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
53 1 0.01
54 60 0.57
55 44 0.42
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:8056 original size:81 final size:82
Alignment explanation
Indices: 7911--8066 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
7901 TGCTATATAA
* *
7911 TCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
7976 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * **
7993 TCAATTCGCACACTTAGTGC-ATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
8056 ACACTTAGTGC
65 ACACTTAGTGC
8067 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 42 0.63
82 25 0.37
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Found at i:9176 original size:55 final size:55
Alignment explanation
Indices: 9114--9260 Score: 287
Period size: 54 Copynumber: 2.7 Consensus size: 55
9104 TCTTAGCATT
9114 TTCGGCCAAGGATGATAAAAGATGAACAATTTTTTTTTCTTTCTTCTTTAGAACA
1 TTCGGCCAAGGATGATAAAAGATGAACAATTTTTTTTTCTTTCTTCTTTAGAACA
9169 TTCGGCCAAGGATGATAAAAGATGAAC-ATTTTTTTTTCTTTCTTCTTTAGAACA
1 TTCGGCCAAGGATGATAAAAGATGAACAATTTTTTTTTCTTTCTTCTTTAGAACA
9223 TTCGGCCAAGGATGATAAAAGATGAACAATTTTTTTTT
1 TTCGGCCAAGGATGATAAAAGATGAACAATTTTTTTTT
9261 TCCTTCTTAC
Statistics
Matches: 91, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
54 54 0.59
55 37 0.41
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (55 bp):
TTCGGCCAAGGATGATAAAAGATGAACAATTTTTTTTTCTTTCTTCTTTAGAACA
Found at i:16528 original size:131 final size:132
Alignment explanation
Indices: 16244--16611 Score: 517
Period size: 131 Copynumber: 2.8 Consensus size: 132
16234 GATTACAGAT
* * *
16244 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTATAGACTAGATCTTACCTTCACTG
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACACTAGATCTTATCTTCACTG
* * * *
16309 ACAGGAGTGAAGCAGATCAAATTTTGA-CAAGTCTTATCTCCATGTATCGGAAATGGAGCAGATT
66 ACAGGAGTGAAGCAGATCGAATTTTGATGAA-TCTTATCTCCACGTACCGGAAATGGAGCAGATT
*
16373 TCA
130 CCA
** * * *
16376 GCCACCAGCCTTATCTTCACTGAGTAGGAGTGGAGCAGGCTAAACACCAGATCTTATCTTCACTG
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACACTAGATCTTATCTTCACTG
* * **
16441 ACA-GAGTGGAGCAGATCGAATTTTGATGAATTTTATCTCCACGTACCGGCGATGGAGCAGATTC
66 ACAGGAGTGAAGCAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGAAATGGAGCAGATTC
16505 CA
131 CA
*
16507 ATCATCAGCCATT-TCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCACT
1 ATCATCAGCC-TTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACACTAGATCTTATCTTCACT
*
16571 GAGCAGGAGCGAAGCAGATCGAATTTTGATGAATCTTATCT
65 GA-CAGGAGTGAAGCAGATCGAATTTTGATGAATCTTATCT
16612 TCGCTGGCAG
Statistics
Matches: 206, Mismatches: 26, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
131 108 0.52
132 66 0.32
133 32 0.16
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (132 bp):
ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACACTAGATCTTATCTTCACTG
ACAGGAGTGAAGCAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGAAATGGAGCAGATTC
CA
Found at i:16632 original size:45 final size:47
Alignment explanation
Indices: 16557--16644 Score: 144
Period size: 46 Copynumber: 1.9 Consensus size: 47
16547 TAAATACTAG
16557 ATCTTATCTTCACTGAGCAGGAGCGAAGCAGA-TCGAATTTTGATGA
1 ATCTTATCTTCACTGAGCAGGAGCGAAGCAGATTCGAATTTTGATGA
* *
16603 ATCTTATCTTCGCTG-GCAGGAGCGGAGCAGATTCGAATTTTG
1 ATCTTATCTTCACTGAGCAGGAGCGAAGCAGATTCGAATTTTG
16645 GTCTCCTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 15 0.38
46 24 0.62
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (47 bp):
ATCTTATCTTCACTGAGCAGGAGCGAAGCAGATTCGAATTTTGATGA
Found at i:24949 original size:27 final size:27
Alignment explanation
Indices: 24918--25084 Score: 205
Period size: 27 Copynumber: 6.2 Consensus size: 27
24908 GTCACACACC
* *
24918 AGTGCTATATAATCAACTCGCACACTT
1 AGTGCTACATAGTCAACTCGCACACTT
*
24945 AGTGCTACATAATCAAACTCGCACACTT
1 AGTGCTACATAGTC-AACTCGCACACTT
24973 AGTGCTACATAGTCAACTCGCACACTT
1 AGTGCTACATAGTCAACTCGCACACTT
* * *
25000 AGTGC-GCATGGTCAATTCGCACACTT
1 AGTGCTACATAGTCAACTCGCACACTT
* *
25026 AGTGC-ATCATATTC-ATTCGCACACTT
1 AGTGCTA-CATAGTCAACTCGCACACTT
* *
25052 AGTGCAACATAGTCAAATCGCACACTT
1 AGTGCTACATAGTCAACTCGCACACTT
25079 AGTGCT
1 AGTGCT
25085 GTACAATTTA
Statistics
Matches: 125, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
26 46 0.37
27 53 0.42
28 26 0.21
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (27 bp):
AGTGCTACATAGTCAACTCGCACACTT
Found at i:25020 original size:26 final size:27
Alignment explanation
Indices: 24930--25083 Score: 195
Period size: 26 Copynumber: 5.7 Consensus size: 27
24920 TGCTATATAA
* *
24930 TCAACTCGCACACTTAGTGCTACATAA
1 TCAACTCGCACACTTAGTGCAACATAG
*
24957 TCAAACTCGCACACTTAGTGCTACATAG
1 TC-AACTCGCACACTTAGTGCAACATAG
* *
24985 TCAACTCGCACACTTAGTGC-GCATGG
1 TCAACTCGCACACTTAGTGCAACATAG
* * *
25011 TCAATTCGCACACTTAGTGCATCATAT
1 TCAACTCGCACACTTAGTGCAACATAG
*
25038 TC-ATTCGCACACTTAGTGCAACATAG
1 TCAACTCGCACACTTAGTGCAACATAG
*
25064 TCAAATCGCACACTTAGTGC
1 TCAACTCGCACACTTAGTGC
25084 TGTACAATTT
Statistics
Matches: 114, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
26 47 0.41
27 41 0.36
28 26 0.23
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
TCAACTCGCACACTTAGTGCAACATAG
Found at i:25062 original size:79 final size:80
Alignment explanation
Indices: 24930--25083 Score: 231
Period size: 79 Copynumber: 1.9 Consensus size: 80
24920 TGCTATATAA
* *
24930 TCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCAACATAGTCAAATCGCA
24995 CACTTAGTGCGCATGG
65 CACTTAGTGCGCATGG
* * *
25011 TCAATTCGCACACTTAGTGC-ATCATATTC-ATTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
25074 CACTTAGTGC
65 CACTTAGTGC
25084 TGTACAATTT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
79 41 0.61
80 1 0.01
81 25 0.37
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (80 bp):
TCAACTCGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCGCATGG
Found at i:25067 original size:53 final size:53
Alignment explanation
Indices: 24918--25084 Score: 212
Period size: 53 Copynumber: 3.1 Consensus size: 53
24908 GTCACACACC
* * *
24918 AGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTT
1 AGTGCTACATAGTCAACTCGCACACTTAGTGC-ACATAGTCAAA-TCGCACACTT
* * *
24973 AGTGCTACATAGTCAACTCGCACACTTAGTGCGCATGGTCAATTCGCACACTT
1 AGTGCTACATAGTCAACTCGCACACTTAGTGCACATAGTCAAATCGCACACTT
* *
25026 AGTGC-ATCATATTC-ATTCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
1 AGTGCTA-CATAGTCAACTCGCACACTTAGTGC-ACATAGTCAAATCGCACACTT
25079 AGTGCT
1 AGTGCT
25085 GTACAATTTA
Statistics
Matches: 98, Mismatches: 11, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
52 17 0.17
53 44 0.45
54 7 0.07
55 30 0.31
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (53 bp):
AGTGCTACATAGTCAACTCGCACACTTAGTGCACATAGTCAAATCGCACACTT
Done.