Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1563
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: 35152
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Found at i:5548 original size:46 final size:46
Alignment explanation
Indices: 5498--5670 Score: 163
Period size: 46 Copynumber: 3.7 Consensus size: 46
5488 TGGTTGAGCA
*
5498 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
** * * * *
5544 TCCGAGGTCGTTGAGTTGAGTCCGAGTT--CGTGT-GATGTAACGAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * * *
5591 TCCGAACTCATTGAGTTGAGTTCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
5637 CCCGAGCTCTTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
5671 GGGGCGGGTT
Statistics
Matches: 98, Mismatches: 22, Indels: 14
0.73 0.16 0.10
Matches are distributed among these distances:
43 6 0.06
44 3 0.03
45 1 0.01
46 56 0.57
47 24 0.24
48 1 0.01
49 2 0.02
50 5 0.05
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:5654 original size:93 final size:93
Alignment explanation
Indices: 5495--5665 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
5485 GGATGGTTGA
* * * *
5495 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAGGTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAGCTCGTTGAGT
5560 TGAGTCCGAGTTCGTGTGATGTAACGAG
66 TGAGTCCGAGTTCGTGTGATGTAACGAG
* * * *
5588 GCATCCGAACTCATTGAGTTGAGTTCGAGTTCATTTATGGATGCGAACGCCCGAGCTCTTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAGCTCGTTGAGT
5653 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
5666 ACTTAGGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAGCTCGTTGAGT
TGAGTCCGAGTTCGTGTGATGTAACGAG
Found at i:8476 original size:22 final size:23
Alignment explanation
Indices: 8433--8480 Score: 55
Period size: 25 Copynumber: 2.1 Consensus size: 23
8423 TTTTCTTTTT
8433 ATGTTTTATTATATTATAACTTATA
1 ATGTTTTATTATA-TATAACTT-TA
*
8458 ATGTTTTATTA-A-ATGACTTTA
1 ATGTTTTATTATATATAACTTTA
8479 AT
1 AT
8481 AACCTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 4 0.18
22 6 0.27
24 1 0.05
25 11 0.50
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.54
Consensus pattern (23 bp):
ATGTTTTATTATATATAACTTTA
Found at i:9842 original size:42 final size:43
Alignment explanation
Indices: 9732--9845 Score: 140
Period size: 43 Copynumber: 2.7 Consensus size: 43
9722 AATCTCGTAC
* **
9732 AATGCCAATGTCCTAGACGTGGTCTTACATGTAATCAAATATT
1 AATGCCAATGTCCTAGACATGGTCTTACATCAAATCAAATATT
* * * *
9775 GACGCCACTGTCCTAGACAGGGTCTTACATCAAATCAAATA-T
1 AATGCCAATGTCCTAGACATGGTCTTACATCAAATCAAATATT
* *
9817 AATGCCAATGTCCCAAACATGGTCTTACA
1 AATGCCAATGTCCTAGACATGGTCTTACA
9846 CGTAAATCTC
Statistics
Matches: 58, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
42 24 0.41
43 34 0.59
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (43 bp):
AATGCCAATGTCCTAGACATGGTCTTACATCAAATCAAATATT
Found at i:21884 original size:40 final size:40
Alignment explanation
Indices: 21829--22074 Score: 359
Period size: 40 Copynumber: 6.2 Consensus size: 40
21819 GGACTAAGAT
* * * *
21829 CCGAAGGCATTTGTGCTAGTGACTATATCCGAGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
* *
21869 CCGAAGGCATTTGTGCGAGTTACTATATCCGAGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
21909 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
* *
21949 CCGAAGGCATTTGTCCGAATTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
**
21989 CCGAAGGCATTTGTGCGAGTTACTATATTTGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
** * *
22029 CCGAAGGCATTTGTGCGAGTTGTTGTATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
22068 CCGAAGG
1 CCGAAGG
22075 TTCTTGGGTT
Statistics
Matches: 190, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
39 15 0.08
40 175 0.92
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
Found at i:24243 original size:37 final size:37
Alignment explanation
Indices: 24185--24292 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
24175 GCTCAGATGA
* *
24185 AATCTCCACACGAAGTTATCGGGTCTTACCCGGACA-
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
24221 AATTCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AA-TCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
24259 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
24293 ATATATTTCC
Statistics
Matches: 68, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
36 2 0.03
37 64 0.94
38 2 0.03
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
Found at i:24494 original size:48 final size:48
Alignment explanation
Indices: 24439--24923 Score: 844
Period size: 48 Copynumber: 10.1 Consensus size: 48
24429 ACACATCGCC
*
24439 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
24487 TACATATTTCACATTAGCCATTCGGTTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
24535 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* * *
24583 TACATATTTCACATTAGCCATTCGGCTTTACCTCCTGTACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
24631 TACATATTTCACATTAGCCATTCGGCTTCACCACCTATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
24679 TACATATTTCACATTAGCCATTCGGCTTCACCACGTATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
24727 TACATATTTCACATTAGCCATTCGGCTTCACCACATGTACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
24775 TACATATTTCACATTAGCCATTCGGCTTTACCACATGTACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
24823 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
24871 TACATATTTCACATTAGCCATTCGACTTTACCACATATACATATCTTA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
24919 TACAT
1 TACAT
24924 CAATTTCAGC
Statistics
Matches: 421, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 421 1.00
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:33992 original size:39 final size:39
Alignment explanation
Indices: 33901--34137 Score: 372
Period size: 39 Copynumber: 6.1 Consensus size: 39
33891 CTAAGATCCA
* * *
33901 AAGGCATTTGTGCTAGTGACTATATCGGGTTAAGT-CCG
1 AAGGCATTTGTGCGAGTTACTATATCGGGCTAAGTCCCG
*
33939 AAGGCATTTGTGCGAGTTACTATATCCGGGCTCAGTCCCG
1 AAGGCATTTGTGCGAGTTACTATAT-CGGGCTAAGTCCCG
33979 AAGGCATTT-TGCGAGTTACTATATCGGGCTAAGTCCCG
1 AAGGCATTTGTGCGAGTTACTATATCGGGCTAAGTCCCG
34017 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
1 AAGGCATTTGTGCGAGTTACTATAT-CGGGCTAAGTCCCG
34057 AAGGCATTTGTGCGAGTTACTATATCGGGCTAAGTCCCG
1 AAGGCATTTGTGCGAGTTACTATATCGGGCTAAGTCCCG
* * *
34096 AAGGCATTTGTGCGAGTT-TTATATCCGGCTAAATCCCG
1 AAGGCATTTGTGCGAGTTACTATATCGGGCTAAGTCCCG
34134 AAGG
1 AAGG
34138 TACTTGGGTT
Statistics
Matches: 187, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
38 66 0.35
39 70 0.37
40 51 0.27
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (39 bp):
AAGGCATTTGTGCGAGTTACTATATCGGGCTAAGTCCCG
Done.