Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4084.1
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: 82032
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.32
Warning! 1624 characters in sequence are not A, C, G, or T
Found at i:6115 original size:16 final size:15
Alignment explanation
Indices: 6085--6119 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6075 TTCTATTGTC
6085 TATATTTTTTATAGA
1 TATATTTTTTATAGA
*
6100 TATATTTTTATCTAGA
1 TATATTTTT-TATAGA
6116 TATA
1 TATA
6120 CAAGATCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (15 bp):
TATATTTTTTATAGA
Found at i:6456 original size:20 final size:21
Alignment explanation
Indices: 6431--6474 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
6421 TTACACGAGG
*
6431 AAATTGTTATTTCTAATT-AA
1 AAATTGGTATTTCTAATTCAA
6451 AAATTGGTATTTCTAATTCAA
1 AAATTGGTATTTCTAATTCAA
6472 AAA
1 AAA
6475 AAAAATAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (21 bp):
AAATTGGTATTTCTAATTCAA
Found at i:14426 original size:7 final size:8
Alignment explanation
Indices: 14406--14430 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
14396 ATCATTAAAT
14406 ATTTTTAA
1 ATTTTTAA
14414 ATTTTTAA
1 ATTTTTAA
14422 ATTTTTAA
1 ATTTTTAA
14430 A
1 A
14431 AATTATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTTTAA
Found at i:15748 original size:24 final size:24
Alignment explanation
Indices: 15697--15748 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
15687 CACATAGTTG
* *
15697 TGTGGTAGGCCGTGTGCCATGCCG
1 TGTGGTAGGCCGTGTGCCAGGCCC
* **
15721 TGTGGTAGGCTGTGTGTGAGGCCC
1 TGTGGTAGGCCGTGTGCCAGGCCC
15745 TGTG
1 TGTG
15749 TGACACACGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.08, C:0.19, G:0.44, T:0.29
Consensus pattern (24 bp):
TGTGGTAGGCCGTGTGCCAGGCCC
Found at i:23994 original size:19 final size:20
Alignment explanation
Indices: 23970--24007 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23960 CAAATCTGCA
*
23970 CAAAAC-ATTAAATTTAAGG
1 CAAAACTATAAAATTTAAGG
23989 CAAAACTATAAAATTTAAG
1 CAAAACTATAAAATTTAAG
24008 AAATAGGGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.26
Consensus pattern (20 bp):
CAAAACTATAAAATTTAAGG
Found at i:26252 original size:35 final size:35
Alignment explanation
Indices: 26206--26275 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
26196 AGTTTAGCAG
26206 CAAAATCACAAATTTCAACAACAATAACATGCATA
1 CAAAATCACAAATTTCAACAACAATAACATGCATA
26241 CAAAATCACAAATTTCAACAACAATAACATGCATA
1 CAAAATCACAAATTTCAACAACAATAACATGCATA
26276 GACTAGATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (35 bp):
CAAAATCACAAATTTCAACAACAATAACATGCATA
Found at i:38200 original size:39 final size:39
Alignment explanation
Indices: 37793--38203 Score: 459
Period size: 39 Copynumber: 10.5 Consensus size: 39
37783 TATAATCAAT
* * * *
37793 GGCACGTAAGTGCAAATCACGGGTACCAAAGTACAACAGG
1 GGCACGTATGTGC-ATTCAGGGGTACCGAAGTACAACAGG
* * *
37833 GGCATGT-TGGTGCAGTT-AGGGGTATCGAAGTACAATAGG
1 GGCACGTAT-GTGCA-TTCAGGGGTACCGAAGTACAACAGG
* * * * *
37872 GGCGCGTAGGTGCATTCAGGGGTACCAAAATACAACATG
1 GGCACGTATGTGCATTCAGGGGTACCGAAGTACAACAGG
* * *
37911 GGCACGTATGTGTATTTAGGGGTATCGAAGTACAACAGG
1 GGCACGTATGTGCATTCAGGGGTACCGAAGTACAACAGG
* *
37950 GGCACATATGTGCATTTAGGGGTACCGAAGTACAACAGG
1 GGCACGTATGTGCATTCAGGGGTACCGAAGTACAACAGG
* **
37989 GGCATGTGGGTGCATTCAGGGGTACCGAAGTACAACAGG
1 GGCACGTATGTGCATTCAGGGGTACCGAAGTACAACAGG
* * * * *
38028 GGCACATATCTACA-TCTAGAGGTATCGAAGTACAACAGG
1 GGCACGTATGTGCATTC-AGGGGTACCGAAGTACAACAGG
* * *
38067 GGCACATATGTGCATTCAAGGGTACCAAAGTACAACAGG
1 GGCACGTATGTGCATTCAGGGGTACCGAAGTACAACAGG
* *
38106 GGCACGTATGTGCATTTAGGGGTACCGAAGTACAATAGG
1 GGCACGTATGTGCATTCAGGGGTACCGAAGTACAACAGG
* ** *
38145 GGAAAATATGTGCATTCAGGGGTACCGAACTACAACAGG
1 GGCACGTATGTGCATTCAGGGGTACCGAAGTACAACAGG
38184 GGCACGTATGTGCATTCAGG
1 GGCACGTATGTGCATTCAGG
38204 TTTAATTACA
Statistics
Matches: 306, Mismatches: 59, Indels: 13
0.81 0.16 0.03
Matches are distributed among these distances:
38 4 0.01
39 289 0.94
40 13 0.04
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.20
Consensus pattern (39 bp):
GGCACGTATGTGCATTCAGGGGTACCGAAGTACAACAGG
Found at i:60667 original size:18 final size:19
Alignment explanation
Indices: 60648--60691 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
60638 CAAATGACAG
*
60648 AATGAAATGAGAAATGAGA
1 AATGAAATAAGAAATGAGA
60667 AAT-AAATAAGAAATGAGA
1 AATGAAATAAGAAATGAGA
60685 AATGAAA
1 AATGAAA
60692 AAATGATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (19 bp):
AATGAAATAAGAAATGAGA
Found at i:63089 original size:104 final size:104
Alignment explanation
Indices: 62909--63116 Score: 407
Period size: 104 Copynumber: 2.0 Consensus size: 104
62899 TTAGCCCCTA
62909 AGCTATTACCCATTTCTTAGTTATTTTCTACCATATTTATTTTCTATACTAACTTGGTTTTCATC
1 AGCTATTACCCATTTCTTAGTTATTTTCTACCATATTTATTTTCTATACTAACTTGGTTTTCATC
*
62974 CTCAATTGCTAAAAAATAAGTAGGAAAAATTCAAAAAGT
66 CTCAATTGCTAAAAAATAAATAGGAAAAATTCAAAAAGT
63013 AGCTATTACCCATTTCTTAGTTATTTTCTACCATATTTATTTTCTATACTAACTTGGTTTTCATC
1 AGCTATTACCCATTTCTTAGTTATTTTCTACCATATTTATTTTCTATACTAACTTGGTTTTCATC
63078 CTCAATTGCTAAAAAATAAATAGGAAAAATTCAAAAAGT
66 CTCAATTGCTAAAAAATAAATAGGAAAAATTCAAAAAGT
63117 GAGAGTTGAA
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 103 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.40
Consensus pattern (104 bp):
AGCTATTACCCATTTCTTAGTTATTTTCTACCATATTTATTTTCTATACTAACTTGGTTTTCATC
CTCAATTGCTAAAAAATAAATAGGAAAAATTCAAAAAGT
Found at i:66153 original size:22 final size:24
Alignment explanation
Indices: 66125--66169 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
66115 TTTCCACAAG
66125 ATCTTGC-ACCA-TATCCCCATAC
1 ATCTTGCTACCATTATCCCCATAC
*
66147 ATCTTGCTACCATTTTCCCCATA
1 ATCTTGCTACCATTATCCCCATA
66170 AATTTACAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 9 0.45
ACGTcount: A:0.24, C:0.38, G:0.04, T:0.33
Consensus pattern (24 bp):
ATCTTGCTACCATTATCCCCATAC
Found at i:73566 original size:22 final size:22
Alignment explanation
Indices: 73538--73583 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
73528 TGAACATTGG
73538 TTCTCTAGAGTTTTTGCTAAGC
1 TTCTCTAGAGTTTTTGCTAAGC
73560 TTCTCTAGAGTTTTTGCTAAGC
1 TTCTCTAGAGTTTTTGCTAAGC
73582 TT
1 TT
73584 TTAGACATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (22 bp):
TTCTCTAGAGTTTTTGCTAAGC
Found at i:76986 original size:26 final size:26
Alignment explanation
Indices: 76950--77011 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
76940 CTCGTAAGTG
76950 TTCTGAAACTGATACATGCTATGATA
1 TTCTGAAACTGATACATGCTATGATA
* *
76976 TTCTGAAACTGATATATGTTATGATA
1 TTCTGAAACTGATACATGCTATGATA
*
77002 TTTTGAAACT
1 TTCTGAAACT
77012 ACTGTGGGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (26 bp):
TTCTGAAACTGATACATGCTATGATA
Done.