Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6578.1
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: 10994
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Found at i:191 original size:12 final size:13
Alignment explanation
Indices: 174--233 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
164 TTGGAGTAAC
174 AAAAAAAA-TCAA
1 AAAAAAAATTCAA
*
186 AAAAAAAATTCGA
1 AAAAAAAATTCAA
* *
199 AAAAAAATTTGATTGA
1 AAAAAAAATTCA---A
215 AAAAAAAATTCAA
1 AAAAAAAATTCAA
228 AAAAAA
1 AAAAAA
234 GTGAAAAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
12 8 0.21
13 19 0.50
16 11 0.29
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:1324 original size:12 final size:12
Alignment explanation
Indices: 1312--1429 Score: 50
Period size: 12 Copynumber: 9.8 Consensus size: 12
1302 GAAAGAGATT
*
1312 GAAAAAGAAATT
1 GAAAAAGAAATA
1324 G--AAAGAAA-A
1 GAAAAAGAAATA
*
1333 CAAAAAGAAA-A
1 GAAAAAGAAATA
*
1344 CGAAAAAGAAAAA
1 -GAAAAAGAAATA
**
1357 GAAATTGCAAA-A
1 GAAAAAG-AAATA
*
1369 GAAAAAGAAATC
1 GAAAAAGAAATA
** *
1381 GAAAAAGTGAGA
1 GAAAAAGAAATA
1393 GAAAAAGAAA-A
1 GAAAAAGAAATA
*
1404 TGAAGAAAAGAAAATT
1 -G-A-AAAAG-AAATA
1420 GAAAAAGAAA
1 GAAAAAGAAA
1430 AAGCGAAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
10 7 0.09
11 12 0.15
12 41 0.51
13 10 0.12
14 6 0.08
15 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
GAAAAAGAAATA
Found at i:1355 original size:18 final size:18
Alignment explanation
Indices: 1329--1432 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
1319 AAATTGAAAG
*
1329 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
1347 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
1365 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
1383 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
1401 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
1422 AAAAGAAAAAG
1 AAAAGAAAAAG
1433 CGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 47 0.71
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:1357 original size:6 final size:6
Alignment explanation
Indices: 1325--1432 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
1315 AAAGAAATTG
* * ** *
1325 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
1372 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
1423 AAAGAA AAAG
1 AAAGAA AAAG
1433 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 61 0.81
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:1414 original size:14 final size:13
Alignment explanation
Indices: 1393--1430 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
1383 AAAAGTGAGA
1393 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
1405 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
1420 GAAAAAGAAAA
1 GAAAAAGAAAA
1431 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:1444 original size:21 final size:21
Alignment explanation
Indices: 1394--1444 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
1384 AAAGTGAGAG
*
1394 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
1415 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
1436 AAAAAGAAA
1 AAAAAGAAA
1445 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:1484 original size:33 final size:33
Alignment explanation
Indices: 1447--1509 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1437 AAAAGAAATT
1447 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
1480 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
1510 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:5412 original size:40 final size:40
Alignment explanation
Indices: 5328--5471 Score: 161
Period size: 40 Copynumber: 3.6 Consensus size: 40
5318 TTGAATGCTG
* *
5328 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACTACA-
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTA-AT
** * *
5368 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
*
5408 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
5448 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
5472 GTATGAGTTA
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
39 2 0.02
40 77 0.87
41 10 0.11
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:8916 original size:28 final size:28
Alignment explanation
Indices: 8875--8930 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
8865 ACGCTGATTT
*
8875 CGATAGCTCCGTATCGAATGGCACCAAC
1 CGATAGCTCAGTATCGAATGGCACCAAC
*
8903 CGATAGCTCAGTATCGTATGGCACCAAC
1 CGATAGCTCAGTATCGAATGGCACCAAC
8931 TGAGTTAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (28 bp):
CGATAGCTCAGTATCGAATGGCACCAAC
Found at i:9799 original size:35 final size:35
Alignment explanation
Indices: 9753--9821 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
9743 CTGAAGCTCC
9753 AATTTTGGTGCAACCCGAATCAGGTAAAGAGTTTT
1 AATTTTGGTGCAACCCGAATCAGGTAAAGAGTTTT
*
9788 AATTTTGGTGCAACCCGAATCGGGTAAAGAGTTT
1 AATTTTGGTGCAACCCGAATCAGGTAAAGAGTTT
9822 GTCATTTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (35 bp):
AATTTTGGTGCAACCCGAATCAGGTAAAGAGTTTT
Done.