Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5352.1
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: 25681
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.29
Warning! 1985 characters in sequence are not A, C, G, or T
Found at i:604 original size:11 final size:13
Alignment explanation
Indices: 573--605 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
563 ACTGTATGCA
573 ATTTTTTTTCTCG
1 ATTTTTTTTCTCG
586 ATTTTTTTT-T-G
1 ATTTTTTTTCTCG
597 ATTTTTTTT
1 ATTTTTTTT
606 AATCTACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 1 0.05
13 9 0.45
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.79
Consensus pattern (13 bp):
ATTTTTTTTCTCG
Found at i:5062 original size:34 final size:34
Alignment explanation
Indices: 5023--5106 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
5013 TGGGCCATAC
5023 TGTTATCTGAATAAGGGGATAAGGCCTAGTTTAT
1 TGTTATCTGAATAAGGGGATAAGGCCTAGTTTAT
5057 TGTTATCTGAATAAGGGGATAAGGCCTAGTTTAT
1 TGTTATCTGAATAAGGGGATAAGGCCTAGTTTAT
*
5091 TGTAATCTGAA-AAGGG
1 TGTTATCTGAATAAGGG
5107 CTCTGGTCCA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 5 0.10
34 44 0.90
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.33
Consensus pattern (34 bp):
TGTTATCTGAATAAGGGGATAAGGCCTAGTTTAT
Found at i:8384 original size:10 final size:10
Alignment explanation
Indices: 8350--8383 Score: 54
Period size: 9 Copynumber: 3.6 Consensus size: 10
8340 AGTTCATAAG
8350 AAAAAATTCA
1 AAAAAATTCA
8360 AAAAAA-TCA
1 AAAAAATTCA
8369 AAAAAATT-A
1 AAAAAATTCA
8378 AAAAAA
1 AAAAAA
8384 AAGCTTGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 16 0.70
10 7 0.30
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATTCA
Found at i:9314 original size:15 final size:15
Alignment explanation
Indices: 9265--9306 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
9255 ATCTTCTTGT
*
9265 AAAAAGAAAACG-AG
1 AAAAAGAAAAAGAAG
*
9279 -AAAAGCAAAAGAAG
1 AAAAAGAAAAAGAAG
9293 AAAAAGAAAAAGAA
1 AAAAAGAAAAAGAA
9307 ATAAAAGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 9 0.39
14 2 0.09
15 12 0.52
ACGTcount: A:0.76, C:0.05, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAGAAG
Found at i:9432 original size:13 final size:12
Alignment explanation
Indices: 9404--9447 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
9394 GAAAAAGAAC
9404 AAAAAGA-AAGTG
1 AAAAAGAGAA-TG
* *
9416 AAAATGAGATTG
1 AAAAAGAGAATG
9428 AAAAAGAGAATG
1 AAAAAGAGAATG
9440 AAAAAGAG
1 AAAAAGAG
9448 TTTGAGAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 26 0.96
13 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11
Consensus pattern (12 bp):
AAAAAGAGAATG
Found at i:9441 original size:24 final size:24
Alignment explanation
Indices: 9404--9452 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
9394 GAAAAAGAAC
*
9404 AAAAAGAAAGTGAAAATGAGATTG
1 AAAAAGAAAGTGAAAAAGAGATTG
*
9428 AAAAAGAGAA-TGAAAAAGAGTTTG
1 AAAAAGA-AAGTGAAAAAGAGATTG
9452 A
1 A
9453 GAGAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.16
Consensus pattern (24 bp):
AAAAAGAAAGTGAAAAAGAGATTG
Found at i:12504 original size:13 final size:13
Alignment explanation
Indices: 12486--12513 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12476 GTATTGATCA
12486 TGTGTTCACACCT
1 TGTGTTCACACCT
12499 TGTGTTCACACCT
1 TGTGTTCACACCT
12512 TG
1 TG
12514 ATGACCATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.29, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:12973 original size:200 final size:200
Alignment explanation
Indices: 12630--13029 Score: 782
Period size: 200 Copynumber: 2.0 Consensus size: 200
12620 AACAACATGA
12630 ATTAAAGGCTCCATTAAAGGAGTTAGCTGAATCTAGCCATGCATGCATGAAGAACATTTATCCAA
1 ATTAAAGGCTCCATTAAAGGAGTTAGCTGAATCTAGCCATGCATGCATGAAGAACATTTATCCAA
12695 GTACATCAATGCATATTCATGAAGCTAACCACTCACCTCCCATTCGGCTGAACATGGACAAGAAC
66 GTACATCAATGCATATTCATGAAGCTAACCACTCACCTCCCATTCGGCTGAACATGGACAAGAAC
* *
12760 ATCATTGGACATTTTTCTAGAAGTTTCATGTTTTAATTAGGTACATTACTTAATTGTTAAGTTCA
131 ATCATTGGACATTTTTCTAGAAGTTTAATGTTTTAATTAGGTACATTACTTAATTGGTAAGTTCA
12825 TGAAT
196 TGAAT
12830 ATTAAAGGCTCCATTAAAGGAGTTAGCTGAATCTAGCCATGCATGCATGAAGAACATTTATCCAA
1 ATTAAAGGCTCCATTAAAGGAGTTAGCTGAATCTAGCCATGCATGCATGAAGAACATTTATCCAA
12895 GTACATCAATGCATATTCATGAAGCTAACCACTCACCTCCCATTCGGCTGAACATGGACAAGAAC
66 GTACATCAATGCATATTCATGAAGCTAACCACTCACCTCCCATTCGGCTGAACATGGACAAGAAC
12960 ATCATTGGACATTTTTCTAGAAGTTTAATGTTTTAATTAGGTACATTACTTAATTGGTAAGTTCA
131 ATCATTGGACATTTTTCTAGAAGTTTAATGTTTTAATTAGGTACATTACTTAATTGGTAAGTTCA
13025 TGAAT
196 TGAAT
13030 GGACTATTCG
Statistics
Matches: 198, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 198 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (200 bp):
ATTAAAGGCTCCATTAAAGGAGTTAGCTGAATCTAGCCATGCATGCATGAAGAACATTTATCCAA
GTACATCAATGCATATTCATGAAGCTAACCACTCACCTCCCATTCGGCTGAACATGGACAAGAAC
ATCATTGGACATTTTTCTAGAAGTTTAATGTTTTAATTAGGTACATTACTTAATTGGTAAGTTCA
TGAAT
Found at i:14420 original size:10 final size:10
Alignment explanation
Indices: 14405--14469 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
14395 AGTTTTTCCC
14405 AGCTCAATTT
1 AGCTCAATTT
*
14415 AGCTCACA-TG
1 AGCTCA-ATTT
*
14425 AGCTTAATTT
1 AGCTCAATTT
*
14435 AGCTC-GTTT
1 AGCTCAATTT
14444 GAGCTCAATTT
1 -AGCTCAATTT
* *
14455 AGCTTACTTT
1 AGCTCAATTT
14465 AGCTC
1 AGCTC
14470 GTTTGAGCTT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
9 4 0.10
10 34 0.81
11 4 0.10
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (10 bp):
AGCTCAATTT
Found at i:14428 original size:20 final size:20
Alignment explanation
Indices: 14405--14458 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
14395 AGTTTTTCCC
14405 AGCTCAATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
14425 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
14445 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
14459 TACTTTAGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:14439 original size:30 final size:30
Alignment explanation
Indices: 14405--14478 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
14395 AGTTTTTCCC
14405 AGCTCAATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTC-ATTTGAGCTCA-ATTGAGCTTAATTT
* * *
14435 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCATTTGAGCTCAATTGAGCTTAATTT
*
14465 AGCTCGTTTGAGCT
1 AGCTCATTTGAGCT
14479 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 4 0.10
30 35 0.90
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (30 bp):
AGCTCATTTGAGCTCAATTGAGCTTAATTT
Found at i:14468 original size:20 final size:20
Alignment explanation
Indices: 14405--14469 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
14395 AGTTTTTCCC
* * *
14405 AGCTCAATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
14425 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
14444 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
14465 AGCTC
1 AGCTC
14470 GTTTGAGCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 29 0.81
21 4 0.11
22 1 0.03
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:16902 original size:71 final size:71
Alignment explanation
Indices: 16786--16927 Score: 241
Period size: 71 Copynumber: 2.0 Consensus size: 71
16776 AACGGGTAAG
16786 GAAATTTTAGAAACCGAGTCCAGTGCAGATTTGAAAATTATTGATAAAACTTTTGGTGACTTAGA
1 GAAATTTTAGAAACCGAGTCCAGTGCAGATTTGAAAATTATTGATAAAACTTTTGGTGACTTA-A
16851 -TCTTAA
65 TTCTTAA
** *
16857 GAAATTTTATCAACCGAGTCCTGTGCAGATTTGAAAATTATTGATAAAACTTTTGGTGACTTAAT
1 GAAATTTTAGAAACCGAGTCCAGTGCAGATTTGAAAATTATTGATAAAACTTTTGGTGACTTAAT
16922 TCTTAA
66 TCTTAA
16928 AAGATCCATT
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
70 1 0.01
71 66 0.99
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (71 bp):
GAAATTTTAGAAACCGAGTCCAGTGCAGATTTGAAAATTATTGATAAAACTTTTGGTGACTTAAT
TCTTAA
Done.