Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2177
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: 37653
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.33
Found at i:2608 original size:15 final size:15
Alignment explanation
Indices: 2588--2643 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
2578 GTATCTTGGG
2588 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
2603 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
2618 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
2633 TTTCTTTATTC
1 TTTCTTTATTC
2644 GGTTTCCTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 2 0.05
15 33 0.89
16 2 0.05
ACGTcount: A:0.12, C:0.16, G:0.11, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:8075 original size:15 final size:15
Alignment explanation
Indices: 8055--8110 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
8045 GTATCTTGGG
8055 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
8070 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
8085 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
8100 TTTCTTTATTC
1 TTTCTTTATTC
8111 GGTTTCCTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 2 0.05
15 33 0.89
16 2 0.05
ACGTcount: A:0.12, C:0.16, G:0.11, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:10559 original size:46 final size:46
Alignment explanation
Indices: 10509--10681 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
10499 TGGTTGAGCA
10509 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
10555 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
10600 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
10648 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
10682 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:10665 original size:93 final size:93
Alignment explanation
Indices: 10506--10676 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
10496 GGATGGTTGA
* *
10506 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
10571 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
10599 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
10664 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
10677 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:14172 original size:68 final size:67
Alignment explanation
Indices: 14026--14179 Score: 150
Period size: 68 Copynumber: 2.2 Consensus size: 67
14016 AGCCGATTTG
* * * * *
14026 TCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATT
1 TCTCGTAGCTCTCTTGTCTACATGGTGTACATCACAT-G-ATCACACATGCGACCTAGCTACACT
*
14091 TATC
64 TATA
* *
14095 TCTCACGTAGCTCTCTTGTCTACAT-GTGATACATCCCAT-ATCACACATGTGACCTAGCTACTA
1 TCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACATGATCACACATGCGACCTAGCTAC-A
14158 CTTAGTA
62 CTTA-TA
*
14165 TCTCGTAGCTTTCTT
1 TCTCGTAGCTCTCTT
14180 TTACACATGA
Statistics
Matches: 71, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
68 31 0.44
69 7 0.10
70 7 0.10
71 26 0.37
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.36
Consensus pattern (67 bp):
TCTCGTAGCTCTCTTGTCTACATGGTGTACATCACATGATCACACATGCGACCTAGCTACACTTA
TA
Found at i:20396 original size:41 final size:41
Alignment explanation
Indices: 20339--20509 Score: 198
Period size: 41 Copynumber: 4.2 Consensus size: 41
20329 ATCTGAGTGT
* * *
20339 AAACAGGGGCACATATATGCAATTCAGAGGTATCGAAGTAC
1 AAACAGGGGCACATATATGCAATTCAGGGGTACCAAAGTAC
* * * *
20380 AAACAGGGGTACATATATGCAATTTAGGGATACCGAAGTAC
1 AAACAGGGGCACATATATGCAATTCAGGGGTACCAAAGTAC
* * * * *
20421 AAACAAGGGCACGTATGTGTAATTCAGGGGTACTAAAGTAC
1 AAACAGGGGCACATATATGCAATTCAGGGGTACCAAAGTAC
** * *
20462 AAACAGGGGCATGTATGTGCGATTCAGGGGTACCAAAGTAC
1 AAACAGGGGCACATATATGCAATTCAGGGGTACCAAAGTAC
20503 AAACAGG
1 AAACAGG
20510 TAATCACAAA
Statistics
Matches: 111, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 111 1.00
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (41 bp):
AAACAGGGGCACATATATGCAATTCAGGGGTACCAAAGTAC
Found at i:28382 original size:25 final size:25
Alignment explanation
Indices: 28353--28400 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28343 TTATAACATG
* * *
28353 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
28378 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
28401 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:28592 original size:24 final size:23
Alignment explanation
Indices: 28514--28630 Score: 164
Period size: 23 Copynumber: 5.0 Consensus size: 23
28504 AAGAAGTGAA
28514 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
28537 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
28560 AAAGGGCTTATGCCCGAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
28583 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
*
28607 CAAAGAGGC-TAGGCCTCCAGTTAT
1 -AAAG-GGCTTATGCC-CCAGTTAT
28631 ATGATAAAGT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 45 0.53
24 29 0.34
25 11 0.13
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.29
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:28859 original size:31 final size:31
Alignment explanation
Indices: 28824--28887 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
28814 TGTTTACAGT
28824 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
28855 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
28886 AA
1 AA
28888 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:36521 original size:11 final size:11
Alignment explanation
Indices: 36485--36540 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
36475 CATGGTATGT
36485 ATGATATGCAC
1 ATGATATGCAC
* *
36496 ATGACATG--T
1 ATGATATGCAC
36505 ATGATATGCAC
1 ATGATATGCAC
*
36516 ATGATATG--T
1 ATGATATGCAC
36525 ATGATATGCAC
1 ATGATATGCAC
36536 ATGAT
1 ATGAT
36541 GTAATCAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:36540 original size:20 final size:20
Alignment explanation
Indices: 36474--36540 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
36464 ATTTTGATAA
*
36474 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
36494 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
36514 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
36534 ACATGAT
1 ACATGAT
36541 GTAATCAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:36658 original size:25 final size:24
Alignment explanation
Indices: 36590--36664 Score: 125
Period size: 23 Copynumber: 3.1 Consensus size: 24
36580 GAGGAAGTGA
36590 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
36614 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
36637 AAAAGGGCTTTTTGCCCCAGTTATT
1 AAAAGGGC-TTATGCCCCAGTTATT
36662 AAA
1 AAA
36665 GAGGCTAGGC
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
23 23 0.48
24 7 0.15
25 18 0.38
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:36912 original size:31 final size:31
Alignment explanation
Indices: 36877--36940 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
36867 CGTTTACAGT
36877 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
36908 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
36939 AA
1 AA
36941 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Done.