Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1172
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: 7483
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Found at i:4713 original size:51 final size:52
Alignment explanation
Indices: 4613--4731 Score: 195
Period size: 51 Copynumber: 2.3 Consensus size: 52
4603 AAAAGTTACT
* * *
4613 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAGATTTGCC
1 TGCATGTATCGATACATTTAATAGAGTATCGATACATCTGGACAAATTTGCC
*
4665 TGCATGTATCGATACATTTTATA-AGTATCGATACATCTGGACAAATTTGCC
1 TGCATGTATCGATACATTTAATAGAGTATCGATACATCTGGACAAATTTGCC
4716 TGCATGTATCGATACA
1 TGCATGTATCGATACA
4732 AAGATCGGTG
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
51 41 0.65
52 22 0.35
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAGAGTATCGATACATCTGGACAAATTTGCC
Found at i:4845 original size:13 final size:13
Alignment explanation
Indices: 4827--4851 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4817 CAAAAAAATA
4827 TGTATCGATACAT
1 TGTATCGATACAT
4840 TGTATCGATACA
1 TGTATCGATACA
4852 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4862 original size:33 final size:33
Alignment explanation
Indices: 4805--4871 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
4795 AGTAGCTTAA
*
4805 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCAATAC
* ***
4838 ATTGTATCGATACAACATTTTATGTATCAATAC
1 ATTGTATCGATACAAAAAAATATGTATCAATAC
4871 A
1 A
4872 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCAATAC
Found at i:5713 original size:67 final size:68
Alignment explanation
Indices: 5587--5713 Score: 159
Period size: 67 Copynumber: 1.9 Consensus size: 68
5577 ATTGGGTTTT
* * * *
5587 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGTAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATGCAAGGCCAATAATATTGGACTTAAAGATGAAGATG
5652 AGA
66 AGA
* * * *
5655 AAAG-TGATAAAGATGCTAATATGTTGATGCACGGCCAATGATATTAGG-CTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATGCAAGGCCAATAATATT-GGACTTAAAGATGA
5714 GAAAAAGGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
67 44 0.88
68 6 0.12
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.25
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATGCAAGGCCAATAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:5934 original size:49 final size:49
Alignment explanation
Indices: 5726--6442 Score: 897
Period size: 49 Copynumber: 14.7 Consensus size: 49
5716 AAAAGGATGT
** *
5726 CAATGTGCTGATTCAAGGCCAGCTCCATTGAAC-TAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
*
5777 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
** *
5820 CAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
5868 CAATGTGCTGATTCAAGGCTAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * * *
5917 CAATGTGCTGAGTCAAGGCCCAGCTACATTGGTCTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGG-CCAGCTATATTGGACTTAAAGATGAAGGTGC
* * * *
5967 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
6016 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
6065 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
6114 CAATGTGCTAAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
* * *
6166 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
6215 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAAGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
*
6267 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
6310 CAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
6358 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
6407 CAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTA
6443 GAAGGGTTGC
Statistics
Matches: 575, Mismatches: 69, Indels: 46
0.83 0.10 0.07
Matches are distributed among these distances:
43 77 0.13
48 91 0.16
49 251 0.44
50 45 0.08
51 30 0.05
52 81 0.14
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
Found at i:6214 original size:101 final size:99
Alignment explanation
Indices: 5726--6442 Score: 1013
Period size: 101 Copynumber: 7.4 Consensus size: 99
5716 AAAAGGATGT
* * *
5726 CAATGTGCTGATTCAAGGCCAGCTCCATTGAAC-TAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G-AAAGGTGCCAATATGCTGATT
5790 CAAGGCCAGCTATATTGGACTT-A-----AAGGTGC
64 CAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
* * * *
5820 CAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGGTG--AGGTGCCAATGTGCTGATTCA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGCCAATATGCTGATTCA
* * *
5883 AGGCTAGCTATATTGGACTTAAAGATGAAGGTGC
66 AGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
*
5917 CAATGTGCTGAGTCAAGGCCCAGCTACATTGGTCTTAAAGAT-AAAGGTGCCAATATGCTGATTC
1 CAATGTGCTGAGTCAAGG-CCAGCTACATTGGACTTAAAGATGAAAGGTGCCAATATGCTGATTC
*
5981 AAGGCCAGCTATATTGGGCTTAATGGTGAAGGTGC
65 AAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
6016 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-AAAGGTGCCAATATGCTGATTCA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGCCAATATGCTGATTCA
6080 AGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
66 AGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
*
6114 CAATGTGCTAAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G-AAAGGTGCCAATATGCTGATT
6179 CAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
64 CAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
*
6215 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAAGTGCCAATATGCTGATT
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G-AAAGGTGCCAATATGCTGATT
6280 CAAGGCCAGCTATATTGGACTT-A-----AAGGTGC
64 CAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
* * * *
6310 CAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGGTG--AGGTGCCAATGTGCTGATTCA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGCCAATATGCTGATTCA
* *
6373 AGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
66 AGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
* * * * *
6407 CAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
6443 GAAGGGTTGC
Statistics
Matches: 574, Mismatches: 30, Indels: 35
0.90 0.05 0.05
Matches are distributed among these distances:
91 78 0.14
92 2 0.00
94 32 0.06
95 51 0.09
97 62 0.11
98 138 0.24
99 68 0.12
100 1 0.00
101 142 0.25
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (99 bp):
CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGCCAATATGCTGATTCA
AGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
Found at i:6486 original size:33 final size:32
Alignment explanation
Indices: 6435--6545 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 32
6425 CCAGCTATAT
*
6435 TGGGC-TTAGA-AGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAAGGTTGCCACCGACTTGTG
*
6465 TGGGCTTTAGAGAATGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAGAA-GGTTGCCACCGACTTGTG
6498 TGGGCTTTAGAGGAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAGA-GAAGGTTGCCACCGACTTGTG
6531 TGGGCTTTAGA-AAGG
1 TGGGCTTTAGAGAAGG
6546 GTGAAAGATG
Statistics
Matches: 74, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
30 5 0.07
31 9 0.12
32 1 0.01
33 56 0.76
34 3 0.04
ACGTcount: A:0.20, C:0.17, G:0.35, T:0.28
Consensus pattern (32 bp):
TGGGCTTTAGAGAAGGTTGCCACCGACTTGTG
Found at i:6653 original size:34 final size:34
Alignment explanation
Indices: 6549--6778 Score: 328
Period size: 34 Copynumber: 6.9 Consensus size: 34
6539 AGAAAGGGTG
* * * *
6549 AAAGA-TGCCACGAAGTTGTGGACTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* *
6582 CAAG-GTGCCACGGAGTTGTGGGCTT-TAA--AA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
6612 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
6646 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
6680 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
6714 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* * * *
6747 AAAGAGTGCCACGTAGTCGTGGACTTAAAAGG
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG
6779 GTGCCACGGA
Statistics
Matches: 182, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
30 5 0.03
31 21 0.12
32 4 0.02
33 50 0.27
34 102 0.56
ACGTcount: A:0.33, C:0.13, G:0.35, T:0.19
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
Found at i:6784 original size:27 final size:27
Alignment explanation
Indices: 6746--6799 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
6736 GCTTAGAAGG
*
6746 AAAAGAGTGCCACGTAGTCGTGGACTT
1 AAAAGAGTGCCACGGAGTCGTGGACTT
*
6773 AAAAGGGTGCCACGGAGTCGTGGACTT
1 AAAAGAGTGCCACGGAGTCGTGGACTT
6800 TGAAAAGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.20
Consensus pattern (27 bp):
AAAAGAGTGCCACGGAGTCGTGGACTT
Done.