Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold296
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: 679504
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.24
Warning! 166439 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:656458 original size:41 final size:41
Alignment explanation
Indices: 656413--656490 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
656403 CAAGACCTCA
*
656413 TCCATTTTCACTACTACATATAATGCCTTTTAAGAGGCTCG
1 TCCATTTTCACTACTACATATAACGCCTTTTAAGAGGCTCG
656454 TCCATTTTCACTACTACATATAACGCCTTTTAAGAGG
1 TCCATTTTCACTACTACATATAACGCCTTTTAAGAGG
656491 ATAGCCTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (41 bp):
TCCATTTTCACTACTACATATAACGCCTTTTAAGAGGCTCG
Found at i:657529 original size:13 final size:13
Alignment explanation
Indices: 657511--657536 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
657501 TACACCAAGT
657511 ATGTATCGATACA
1 ATGTATCGATACA
657524 ATGTATCGATACA
1 ATGTATCGATACA
657537 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:657534 original size:32 final size:33
Alignment explanation
Indices: 657493--657556 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
657483 TAGCCAAACT
* **
657493 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
657525 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
657557 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:661611 original size:16 final size:16
Alignment explanation
Indices: 661575--661611 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
661565 GATAAAAATG
661575 TCCAAAATGAGAAAGC
1 TCCAAAATGAGAAAGC
661591 T-CAAAATGA-AGAAGC
1 TCCAAAATGAGA-AAGC
661606 TCCAAA
1 TCCAAA
661612 CGAAATTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.05
15 13 0.68
16 5 0.26
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (16 bp):
TCCAAAATGAGAAAGC
Found at i:663696 original size:13 final size:13
Alignment explanation
Indices: 663678--663716 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
663668 ACATTTTTCT
663678 TTGTATCGATACA
1 TTGTATCGATACA
*
663691 TTGTATCGATAGA
1 TTGTATCGATACA
663704 TTGTATCGATACA
1 TTGTATCGATACA
663717 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:663880 original size:20 final size:20
Alignment explanation
Indices: 663837--663882 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
663827 AAATCTTTTG
663837 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
663858 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
663878 CAAAA
1 CAAAA
663883 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:666583 original size:13 final size:13
Alignment explanation
Indices: 666565--666590 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
666555 CAATTTTTTG
666565 TGTATCGATACAT
1 TGTATCGATACAT
666578 TGTATCGATACAT
1 TGTATCGATACAT
666591 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:666605 original size:32 final size:33
Alignment explanation
Indices: 666545--666608 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
666535 TACAAGCCAA
** *
666545 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
666578 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
666609 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:667339 original size:21 final size:21
Alignment explanation
Indices: 667298--667341 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
667288 CTCCCCTTTA
* *
667298 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
667319 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
667340 TC
1 TC
667342 ATATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:667361 original size:25 final size:25
Alignment explanation
Indices: 667333--667382 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
667323 CCCCTTAATC
667333 AAGTAATTCATATAAAAAATTTATT
1 AAGTAATTCATATAAAAAATTTATT
*
667358 AAGTAATTCATATCAAAAATTTATT
1 AAGTAATTCATATAAAAAATTTATT
667383 TGCACATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (25 bp):
AAGTAATTCATATAAAAAATTTATT
Found at i:669189 original size:13 final size:13
Alignment explanation
Indices: 669171--669208 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
669161 ATAATCACCC
669171 TGTATCGATACAA
1 TGTATCGATACAA
669184 TGTATCGATACAA
1 TGTATCGATACAA
669197 TGTATCGATACA
1 TGTATCGATACA
669209 TTGAATTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:671288 original size:15 final size:15
Alignment explanation
Indices: 671268--671298 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
671258 ATTTCGTTTG
*
671268 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
671283 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
671298 G
1 G
671299 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:673131 original size:21 final size:21
Alignment explanation
Indices: 673102--673146 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
673092 AAGTTTTCAT
*
673102 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
673122 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
673144 TTT
1 TTT
673147 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:673753 original size:12 final size:12
Alignment explanation
Indices: 673738--673762 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
673728 TCTGAGTCAC
673738 CATCTTCATCAA
1 CATCTTCATCAA
673750 CATCTTCATCAA
1 CATCTTCATCAA
673762 C
1 C
673763 TTCATCGTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (12 bp):
CATCTTCATCAA
Found at i:675379 original size:13 final size:13
Alignment explanation
Indices: 675361--675386 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
675351 CAATTTTTTG
675361 TGTATCGATACAT
1 TGTATCGATACAT
675374 TGTATCGATACAT
1 TGTATCGATACAT
675387 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Done.