Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2940
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: 25321
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Found at i:5158 original size:40 final size:40
Alignment explanation
Indices: 5100--5355 Score: 358
Period size: 40 Copynumber: 6.4 Consensus size: 40
5090 AAACCAAGTA
* * *
5100 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* **
5139 CCTTCAGGACTTAGCCCGGATATAGTAGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5179 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
5219 CCTTCGGGACTTAGCCCGAAAATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5259 CCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
* *
5299 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
5339 CCTTTGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
5356 CGTTATCATC
Statistics
Matches: 199, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
39 13 0.07
40 186 0.93
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:9994 original size:30 final size:29
Alignment explanation
Indices: 9953--10010 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
9943 CACGACCGAC
*
9953 CACATGCCAATATG-CCAGCCCGTGTGTCA
1 CACATGCCAATA-GACAAGCCCGTGTGTCA
9982 CACATGACCAATAGACAAGCCCGTGTGTC
1 CACATG-CCAATAGACAAGCCCGTGTGTC
10011 TAAGTCGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.28, C:0.33, G:0.21, T:0.19
Consensus pattern (29 bp):
CACATGCCAATAGACAAGCCCGTGTGTCA
Found at i:10502 original size:91 final size:91
Alignment explanation
Indices: 10385--10583 Score: 353
Period size: 91 Copynumber: 2.2 Consensus size: 91
10375 AACCTTTTTC
* *
10385 CATCACATAGTCTATACTAAAACCAATTCCATAGTCTCAATCATATTCATACCATATAACATGGC
1 CATCAC-TAGCCTATACCAAAACCAATTCCATAGTCTCAATCATATTCATACCATATAACATGGC
10450 AAGAAATTCACATAACACATATCATAA
65 AAGAAATTCACATAACACATATCATAA
*
10477 CATCACTAGCCTATACCAAAACCAATTCCATAGTCTCAATCATATTCATATCATATAACATGGCA
1 CATCACTAGCCTATACCAAAACCAATTCCATAGTCTCAATCATATTCATACCATATAACATGGCA
10542 AGAAATTCACATAACACATATCATAA
66 AGAAATTCACATAACACATATCATAA
*
10568 TATCACTAGCCTATAC
1 CATCACTAGCCTATAC
10584 ATGCCAGATA
Statistics
Matches: 103, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
91 97 0.94
92 6 0.06
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (91 bp):
CATCACTAGCCTATACCAAAACCAATTCCATAGTCTCAATCATATTCATACCATATAACATGGCA
AGAAATTCACATAACACATATCATAA
Found at i:13243 original size:48 final size:48
Alignment explanation
Indices: 13180--13421 Score: 387
Period size: 48 Copynumber: 5.0 Consensus size: 48
13170 TACAAGATAA
* *
13180 ATATATATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
* *
13228 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
* *
13276 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATTTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
*
13324 ACATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
* *
13372 ATATGTATATGTGGTAAAGCCGAATGGCTAATGA-GCAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAAT-ATGAAATATGTATGAG
13420 AT
1 AT
13422 GTGTGTATAT
Statistics
Matches: 183, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
48 182 0.99
49 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.30
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
Found at i:13612 original size:37 final size:37
Alignment explanation
Indices: 13562--13632 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
13552 GGAAATATAT
* *
13562 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCAATAACTACGTGTGGAGATTTTG
*
13599 TCCGGGTAAGACCCAATAACTACGTGTGGGGATT
1 TCCGGGTAAGACCCAATAACTACGTGTGGAGATT
13633 ATTCGAGCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCAATAACTACGTGTGGAGATTTTG
Found at i:14863 original size:42 final size:43
Alignment explanation
Indices: 14805--14928 Score: 119
Period size: 42 Copynumber: 2.9 Consensus size: 43
14795 TTATCAAATG
* * *
14805 TCGATGCCACTATCCTAGACAGGGTCTTACATGAAATCGT-ATA
1 TCGATGCCAATGTCCTAGACAGGGTCTTACATGAAATC-TCAAA
* *
14848 -CGATGCCAATGTCCTAGACATGTTCTTACATGTAAATCTCAAA
1 TCGATGCCAATGTCCTAGACAGGGTCTTACATG-AAATCTCAAA
* * * *
14891 TCGTTGCCAACGTCCCAGAC-GTGGTCTTACACGAAATC
1 TCGATGCCAATGTCCTAGACAG-GGTCTTACATGAAATC
14929 ACATACCTCA
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
42 29 0.44
43 12 0.18
44 25 0.38
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (43 bp):
TCGATGCCAATGTCCTAGACAGGGTCTTACATGAAATCTCAAA
Found at i:16819 original size:40 final size:40
Alignment explanation
Indices: 16764--16950 Score: 313
Period size: 40 Copynumber: 4.7 Consensus size: 40
16754 ATTTGAATGA
16764 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
16804 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
16844 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
* * * *
16884 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTT
*
16924 TATCCGGGCTAAGACCCGAAGGCATTT
1 TATCCGGGCTAAGTCCCGAAGGCATTT
16951 GTGCGAGTTG
Statistics
Matches: 142, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
40 139 0.98
41 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (40 bp):
TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
Found at i:16951 original size:40 final size:40
Alignment explanation
Indices: 16763--17007 Score: 305
Period size: 40 Copynumber: 6.1 Consensus size: 40
16753 CATTTGAATG
*
16763 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
* *
16803 TTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
* *
16843 TTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
* * *
16883 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATT
* * *
16923 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATT
* * * * * *
16963 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
17003 ATATC
1 ATATC
17008 TGGCTAAATT
Statistics
Matches: 190, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
39 2 0.01
40 185 0.97
41 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
Done.