Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1676
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: 22870
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Found at i:9273 original size:17 final size:16
Alignment explanation
Indices: 9251--9293 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
9241 CTTTACACCC
9251 AAAAAAAAACAAAACAA
1 AAAAAAAAACAAAA-AA
9268 AAAAAAAAACAAAAAA
1 AAAAAAAAACAAAAAA
9284 AAAGAAAAAA
1 AAA-AAAAAA
9294 ATAGCAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.91, C:0.07, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAAAAAAACAAAAAA
Found at i:9275 original size:11 final size:11
Alignment explanation
Indices: 9254--9305 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
9244 TACACCCAAA
9254 AAAAAACAAAAC
1 AAAAAA-AAAAC
9266 AAAAAAAAAA-
1 AAAAAAAAAAC
*
9276 ACAAAAAAAAAG
1 A-AAAAAAAAAC
* *
9288 AAAAAAATAGC
1 AAAAAAAAAAC
9299 AAAAAAA
1 AAAAAAA
9306 TAGAAGGGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 1 0.03
11 27 0.77
12 7 0.20
ACGTcount: A:0.87, C:0.08, G:0.04, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:9294 original size:12 final size:12
Alignment explanation
Indices: 9253--9286 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
9243 TTACACCCAA
9253 AAAAAAACAAAAC
1 AAAAAAA-AAAAC
9266 AAAAAAAAAAAC
1 AAAAAAAAAAAC
9278 AAAAAAAAA
1 AAAAAAAAA
9287 GAAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:9305 original size:1 final size:1
Alignment explanation
Indices: 9251--9294 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
9241 CTTTACACCC
* * * *
9251 AAAAAAAAACAAAACAAAAAAAAAAACAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9295 TAGCAAAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.07, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:9308 original size:11 final size:11
Alignment explanation
Indices: 9267--9305 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
9257 AAACAAAACA
*
9267 AAAAAAAAAAC
1 AAAAAAAAAGC
9278 AAAAAAAAAG-
1 AAAAAAAAAGC
*
9288 AAAAAAATAGC
1 AAAAAAAAAGC
9299 AAAAAAA
1 AAAAAAA
9306 TAGAAGGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.87, C:0.05, G:0.05, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAGC
Found at i:9310 original size:21 final size:21
Alignment explanation
Indices: 9251--9310 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
9241 CTTTACACCC
* *
9251 AAAAAAA-AACAAAACA-AAA
1 AAAAAAACAAAAAAAAAGAAA
9270 AAAAAAACAAAAAAAAAGAAA
1 AAAAAAACAAAAAAAAAGAAA
* * *
9291 AAAATAGCAAAAAAATAGAA
1 AAAAAAACAAAAAAAAAGAA
9311 GGGTCTAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 7 0.21
20 7 0.21
21 20 0.59
ACGTcount: A:0.85, C:0.07, G:0.05, T:0.03
Consensus pattern (21 bp):
AAAAAAACAAAAAAAAAGAAA
Found at i:10566 original size:29 final size:29
Alignment explanation
Indices: 10524--11468 Score: 1323
Period size: 28 Copynumber: 32.9 Consensus size: 29
10514 AATGTTCATC
*
10524 CCTTTCAAAGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
10553 CCTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
10582 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
10610 CCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
10638 CCTTTCAAAGCCCACAAATCAGTGGCATT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
10667 CTTTTCAAAGCCCACAAGTCAATGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
10695 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
10724 CCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
10752 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
10781 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
10810 CCTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
10839 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
10867 CCTTTCAAAGCCCACAACTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
10895 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
10924 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
10953 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
10982 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
11010 CCTTTCAAAGCCCACAAGTCAGTGGCATT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
11039 CCTTTCAAAGCCCACAAGTTAGTGGCATT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
11068 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
11097 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
11125 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
11153 CCTTTCAGAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
11181 CCTTTCGAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
11209 CATTGCGAAGCCCACAATTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
11238 -CTTTTAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
11265 CCTTTTAAAGCCCACACAAGTCAGTGGCACT
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCACT
* * *
11296 CCTTTTAAAGCTCATGCAAGTCAGTGGTAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
*
11326 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
11355 -CTTTCAAAGCCCACAAGTAAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
11382 CCTTTCAAAGCCCACGAGTTAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
11410 TCTTTCAAAGCCCACGCAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* * *
11440 CCTTTTAAATCCCATGCAAGTCAATGGCA
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCA
11469 ACCCTTTTCA
Statistics
Matches: 833, Mismatches: 66, Indels: 33
0.89 0.07 0.04
Matches are distributed among these distances:
27 1 0.00
28 393 0.47
29 353 0.42
30 63 0.08
31 23 0.03
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (29 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:10635 original size:57 final size:56
Alignment explanation
Indices: 10523--11480 Score: 1295
Period size: 57 Copynumber: 16.7 Consensus size: 56
10513 GAATGTTCAT
* *
10523 CCCTTTCAAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
10580 CTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
10637 CCCTTTCAAAGCCCACAAATCAGTGGCATTCTTTTCAAAGCCCACAAGTCAATGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCA
10694 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCA
10751 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
10808 CTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
10866 CCCTTTCAAAGCCCACAACTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
10922 CTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
10980 CTCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * *
11037 TTCCTTTCAAAGCCCACAAGTTAGTGGCATTCTTTTCAAAGCCCACAAATCAGTGGCA
1 -CCCTTTCAAAGCCCACAAGTCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
11095 CTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
11152 CCCTTTCAGAGCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * * *
11208 CCATTGCGAAGCCCACAATTCAGTGGCACTCTTTTAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
11264 CCCTTTTAAAGCCCACACAAGTCAGTGGCACTCCTTTTAAAGCTCATGCAAGTCAGTGGTA
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCAC-CCTTTCAAAGCCCA--CAAGTCAGTGGCA
* * *
11325 CCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTAAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * **
11381 TCCTTTCAAAGCCCACGAGTTAGTGGCATTCTTTCAAAGCCCACGCAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGGCA
* * *
11439 CCCTTTTAAATCCCATGCAAGTCAATGGCAACCCTTTTCAAA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGC-ACCC-TTTCAAA
11481 TCACCACTGT
Statistics
Matches: 803, Mismatches: 78, Indels: 35
0.88 0.09 0.04
Matches are distributed among these distances:
56 206 0.26
57 295 0.37
58 233 0.29
59 28 0.03
60 11 0.01
61 23 0.03
62 7 0.01
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (56 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:12022 original size:20 final size:20
Alignment explanation
Indices: 11994--12068 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
11984 TCATACCCTG
11994 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
12014 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
12034 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
12054 ATGTATCGATACATT
1 ATGTATCGATACATT
12069 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:12061 original size:40 final size:39
Alignment explanation
Indices: 11994--12071 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
11984 TCATACCCTG
* *
11994 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
12034 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
12072 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:18421 original size:2 final size:2
Alignment explanation
Indices: 18414--18451 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
18404 ATGGACAAAA
18414 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18452 TGCAATCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.