Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold241
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: 33873
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:3609 original size:30 final size:30
Alignment explanation
Indices: 3573--3633 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
3563 CAAACAATAC
3573 TGAAAAATTCATAATATACAAAACATCAAT
1 TGAAAAATTCATAATATACAAAACATCAAT
3603 TGAAAAATTCATAATATACAAAACATCAAT
1 TGAAAAATTCATAATATACAAAACATCAAT
3633 T
1 T
3634 AATAAACACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.13, G:0.03, T:0.28
Consensus pattern (30 bp):
TGAAAAATTCATAATATACAAAACATCAAT
Found at i:3969 original size:40 final size:41
Alignment explanation
Indices: 3918--4012 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 41
3908 CTTGGTATCA
* *
3918 CACACTTAGTGCCT-CATATAGCCGAAGCTAT-TCCAATTCG
1 CACACTAAGTGCCTACATATAGCCGAAGCTATCTCCAA-ACG
* * * *
3958 CACACTAAGTGCTATATATATAGCTGAAGCTATCTCGAAACG
1 CACACTAAGTGC-CTACATATAGCCGAAGCTATCTCCAAACG
4000 CACACTAAGTGCC
1 CACACTAAGTGCC
4013 AAACATAGTA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
40 11 0.24
41 1 0.02
42 29 0.64
43 4 0.09
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (41 bp):
CACACTAAGTGCCTACATATAGCCGAAGCTATCTCCAAACG
Found at i:5599 original size:21 final size:21
Alignment explanation
Indices: 5554--5610 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
5544 ACTATTGTTG
*
5554 AGAAGGAAGTTGCTGCTACAAA
1 AGAA-GAAGTTGTTGCTACAAA
5576 AG-AGAAAGTTGTTGCTA-AAGA
1 AGAAG-AAGTTGTTGCTACAA-A
5597 AGAAGAAGTTGTTG
1 AGAAGAAGTTGTTG
5611 AAAATGAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.10
21 24 0.77
22 4 0.13
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (21 bp):
AGAAGAAGTTGTTGCTACAAA
Found at i:5623 original size:21 final size:21
Alignment explanation
Indices: 5581--5624 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5571 ACAAAAGAGA
* *
5581 AAGTTGTTGCTAAAGAAGAAG
1 AAGTTGTTGCAAAAGAAAAAG
5602 AAGTTGTTG-AAAATGAAAAAG
1 AAGTTGTTGCAAAA-GAAAAAG
5623 AA
1 AA
5625 TAAGAAGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.50, C:0.02, G:0.25, T:0.23
Consensus pattern (21 bp):
AAGTTGTTGCAAAAGAAAAAG
Found at i:16904 original size:39 final size:39
Alignment explanation
Indices: 16850--17033 Score: 264
Period size: 39 Copynumber: 4.7 Consensus size: 39
16840 TCTGTGAGAT
*
16850 TTATATCCGAGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
16889 TTATGTCCGGGCTAAGT-CCGAAGGCATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
16927 TTATGTCCGGGCTAAGTCCCGAAGGCATTCGTGCTAGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
16966 TTGTATCCGAGG-TAAGTCCCGAAGGTATTCGTGCTGGAG
1 TTATATCCG-GGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
17005 TTATATCCGGGCTAAGTTCCGAAGGCATT
1 TTATATCCGGGCTAAGTCCCGAAGGCATT
17034 TATGTTGGAA
Statistics
Matches: 129, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
38 39 0.30
39 88 0.68
40 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:16947 original size:77 final size:78
Alignment explanation
Indices: 16850--17033 Score: 264
Period size: 77 Copynumber: 2.4 Consensus size: 78
16840 TCTGTGAGAT
* * *
16850 TTATATCCGAGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATGTCCG-GGCTAAGT-CCGAAGG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTAGTGTTATATCCGAGG-TAAGTCCCGAAGG
* *
16913 CATTCGTGTTGGTG
65 CATTCGTGCTGGAG
* * *
16927 TTATGTCCGGGCTAAGTCCCGAAGGCATTCGTGCTAGTGTTGTATCCGAGGTAAGTCCCGAAGGT
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTAGTGTTATATCCGAGGTAAGTCCCGAAGGC
16992 ATTCGTGCTGGAG
66 ATTCGTGCTGGAG
*
17005 TTATATCCGGGCTAAGTTCCGAAGGCATT
1 TTATATCCGGGCTAAGTCCCGAAGGCATT
17034 TATGTTGGAA
Statistics
Matches: 95, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
77 48 0.51
78 47 0.49
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (78 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTAGTGTTATATCCGAGGTAAGTCCCGAAGGC
ATTCGTGCTGGAG
Found at i:25130 original size:39 final size:39
Alignment explanation
Indices: 24814--25114 Score: 446
Period size: 39 Copynumber: 7.7 Consensus size: 39
24804 TAATTGAGGA
* * * *
24814 TTATAACCGGGCTAAGACCCGCAGGCCTT-GTG-TGAGAT-
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTG-G-TG
24852 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * * *
24891 TTATATGCGAGCTAAGTCCTGAAAGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
24930 TTATGTCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
24969 TTATATCCGGGCTAATTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
25008 TTATATCCGAGCTAAGTCCCGAAGGTATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
25047 TTATATCCGGGCTAAGTCCCGAAGGTATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
25086 TTATATCCGGGCTAAGTCCCGAAGGCATT
1 TTATATCCGGGCTAAGTCCCGAAGGCATT
25115 TGTGTTGGAA
Statistics
Matches: 240, Mismatches: 20, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
38 26 0.11
39 212 0.88
40 2 0.01
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:30778 original size:31 final size:32
Alignment explanation
Indices: 30720--30779 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
30710 TGGTCAAATA
* *
30720 TAACCGAACATAAGCAAAATGACCAAGCCTTG
1 TAACCGAACATAAGCAAAATAAACAAGCCTTG
*
30752 TAACCGAACTTAA-CAAAATAAACAAGCC
1 TAACCGAACATAAGCAAAATAAACAAGCC
30780 ATCTTCGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 13 0.52
32 12 0.48
ACGTcount: A:0.48, C:0.25, G:0.12, T:0.15
Consensus pattern (32 bp):
TAACCGAACATAAGCAAAATAAACAAGCCTTG
Found at i:31510 original size:56 final size:56
Alignment explanation
Indices: 31439--31671 Score: 378
Period size: 56 Copynumber: 4.2 Consensus size: 56
31429 TCCCAAACAG
*
31439 GGTC-TACTCGCACACATATATCAGAATCACATATCGATGCCAACATATTAAACAT
1 GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACATATTAAACGT
* * *
31494 GGTCTTACTCGCACACATATATCAGAATCACATATCAATGCCAACATTTTAAATGT
1 GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACATATTAAACGT
* * *
31550 GGTCTTACTCGCACACATTTATCAGAATCACATATCGATGCCAACGTACTAAACGT
1 GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACATATTAAACGT
* *
31606 GGTCTTACTCGCACACGTATATCAGAATCACATATCGATGCCAACGTATTAAACGT
1 GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACATATTAAACGT
31662 GGTCTTACTC
1 GGTCTTACTC
31672 ATGATCACAA
Statistics
Matches: 164, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
55 4 0.02
56 160 0.98
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.28
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACATATTAAACGT
Done.