Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold661
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: 31478
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Found at i:6738 original size:40 final size:40
Alignment explanation
Indices: 6683--6867 Score: 334
Period size: 40 Copynumber: 4.6 Consensus size: 40
6673 CGGATGATAA
* * *
6683 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
6723 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
6763 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
6803 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
6843 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
6868 AGCAAGTAGT
Statistics
Matches: 141, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 141 1.00
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:6882 original size:80 final size:80
Alignment explanation
Indices: 6679--6899 Score: 331
Period size: 80 Copynumber: 2.8 Consensus size: 80
6669 TATTCGGATG
* *
6679 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGT-GACTATTTCCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTAG-CTATATCCGGGCTAAGTCCCGAAGGC
6743 ATTTGTGCGAGTTACT
65 ATTTGTGCGAGTTACT
* *
6759 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TAGCTATATCCGGGCTAAGTCCCGAAGGC
6823 ATTTGTGCGAGTTACT
65 ATTTGTGCGAGTTACT
* * * *
6839 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTAGTTATATTC-GGCTAAATCCCGAAG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTAGCTATATCCGGGCTAAGTCCCGAAG
6900 ATGCTTGGGT
Statistics
Matches: 129, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
79 16 0.12
80 112 0.87
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTAGCTATATCCGGGCTAAGTCCCGAAGGCA
TTTGTGCGAGTTACT
Found at i:7167 original size:22 final size:21
Alignment explanation
Indices: 7126--7169 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
7116 GAATGTGCAT
7126 ATATGAAGTTATCCAGTTAGCC
1 ATATGAAGTTATCCA-TTAGCC
7148 ATATGAATGTTATACC-TTAGCC
1 ATATGAA-GTTAT-CCATTAGCC
7170 GAAACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 5 0.25
24 2 0.10
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (21 bp):
ATATGAAGTTATCCATTAGCC
Found at i:8326 original size:48 final size:48
Alignment explanation
Indices: 8255--8486 Score: 383
Period size: 48 Copynumber: 4.8 Consensus size: 48
8245 GGGTGTTACA
*
8255 GTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATAT
1 GTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATAT
* *
8303 GTGGTAGAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATAT
1 GTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATAT
* * *
8351 GTGGTAGAGCCGAATGACTAGTGTGAAATATATATGAGATATGTATAT
1 GTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATAT
*
8399 GTGGTAAAGCCGAATGGCTAGTGTGAAATATGAATGAGATATGTATAT
1 GTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATAT
* *
8447 GCGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
1 GTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
8487 GTGTGTATAT
Statistics
Matches: 173, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 173 1.00
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.29
Consensus pattern (48 bp):
GTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATAT
Found at i:8677 original size:37 final size:37
Alignment explanation
Indices: 8627--8729 Score: 170
Period size: 37 Copynumber: 2.8 Consensus size: 37
8617 GGAAATATAT
8627 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
8664 TCCGGGTAAGACCCGATGATTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
8701 TCCGGGTAAGACCCAATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
8730 GGACTATTCG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:22189 original size:40 final size:40
Alignment explanation
Indices: 22134--22430 Score: 429
Period size: 40 Copynumber: 7.5 Consensus size: 40
22124 GAATGATAAT
* * *
22134 CGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-TC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATC
22174 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
*
22214 CGGGCTAAGTCCCGAAGGTATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* *
22254 CAGGCTATGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
22294 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* *
22334 CGGGCTAAGTCCCGAAGGCATTGGTGTGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* * * *
22374 CGGGCTATGTCCCGAAGGCATTCGAGCAAG-TAGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATC
* *
22414 C-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
22431 TACTTGGCTT
Statistics
Matches: 236, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
39 16 0.07
40 220 0.93
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:30405 original size:40 final size:39
Alignment explanation
Indices: 30280--30422 Score: 213
Period size: 40 Copynumber: 3.7 Consensus size: 39
30270 TGGATGATAA
* * *
30280 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGATAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATA-TAT
30319 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAG-T-TATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATATAT
30355 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-TATAT
30395 CCGGGCTAAGTCCCGAAGGCATTTGTGC
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC
30423 TATAGAAGTC
Statistics
Matches: 96, Mismatches: 3, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
35 1 0.01
36 14 0.15
37 19 0.20
38 18 0.19
39 11 0.11
40 33 0.34
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATATAT
Done.