Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1158
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: 23069
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Found at i:890 original size:96 final size:93
Alignment explanation
Indices: 725--941 Score: 240
Period size: 96 Copynumber: 2.3 Consensus size: 93
715 TGGTATGTAT
* * *
725 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCCACATTACGAGAGCCAGCGTAAGACTTGTCT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAG-CACATTACGAGAGCCAGCGTAAAACATGTCT
* *
790 GGGACATATGCATCGGCCTCGAGCGATGCAA
65 GGGAC--ATGCATCGGCCTCGAGAGATACAA
* * * * *
821 TCTAGTGTAAGACATGTCTGGGACATGCAT-TG-GCATTGAGACGAGAGCTAGTGTAAAACATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCACATT---ACGAGAGCCAGCGTAAAACATGT
*
884 CTGGGACATGCATCGGCCTCGAGATATACAA
63 CTGGGACATGCATCGGCCTCGAGAGATACAA
* * *
915 GCTACTGTAAGACCTGTTTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
942 GCGTCAGCTT
Statistics
Matches: 103, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
93 4 0.04
94 44 0.43
95 1 0.01
96 54 0.52
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (93 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCACATTACGAGAGCCAGCGTAAAACATGTCTG
GGACATGCATCGGCCTCGAGAGATACAA
Found at i:937 original size:48 final size:47
Alignment explanation
Indices: 725--941 Score: 172
Period size: 46 Copynumber: 4.6 Consensus size: 47
715 TGGTATGTAT
* * * *
725 GCTAGTGTAAGACATGTCTAGGACATGCATCAG-C-C-ACATTACGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGAATAC-A-A
* * * * *
771 GCCAGCGTAAGACTTGTCTGGGACATATGCATCGGCCTCGAGCGATGCAA
1 GCTAGTGTAAGACATGTCTGGGAC--ATGCATCGGCCTCGAG-AATACAA
* * * * ** *
821 TCTAGTGTAAGACATGTCTGGGACATGCATTGGCATTGAGACGA-GA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGAATACAA
*
867 GCTAGTGTAAAACATGTCTGGGACATGCATCGGCCTCGAGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGA-ATACAA
* * *
915 GCTACTGTAAGACCTGTTTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
942 GCGTCAGCTT
Statistics
Matches: 130, Mismatches: 33, Indels: 14
0.73 0.19 0.08
Matches are distributed among these distances:
46 57 0.44
47 1 0.01
48 45 0.35
49 1 0.01
50 22 0.17
51 2 0.02
52 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGAATACAA
Found at i:938 original size:94 final size:95
Alignment explanation
Indices: 765--941 Score: 239
Period size: 94 Copynumber: 1.9 Consensus size: 95
755 CAGCCACATT
* * * * * *
765 ACGAGAGCCAGCGTAAGACTTGTCTGGGACATATGCATCGGCCTCGAGCGATGCAATCTAGTGTA
1 ACGAGAGCCAGCGTAAAACATGTCTGGGACA-ATGCATCGGCCTCGAGAGATACAAGCTACTGTA
830 AGACATGTCTGGGACATGCATTGGCATTGAG
65 AGACATGTCTGGGACATGCATTGGCATTGAG
* * *
861 ACGAGAGCTAGTGTAAAACATGTCTGGGAC-ATGCATCGGCCTCGAGATATACAAGCTACTGTAA
1 ACGAGAGCCAGCGTAAAACATGTCTGGGACAATGCATCGGCCTCGAGAGATACAAGCTACTGTAA
* *
925 GACCTGTTTGGGACATG
66 GACATGTCTGGGACATG
942 GCGTCAGCTT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
94 44 0.63
96 26 0.37
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (95 bp):
ACGAGAGCCAGCGTAAAACATGTCTGGGACAATGCATCGGCCTCGAGAGATACAAGCTACTGTAA
GACATGTCTGGGACATGCATTGGCATTGAG
Found at i:5362 original size:27 final size:27
Alignment explanation
Indices: 5331--5508 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
5321 TAAATTGTAC
5331 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
5358 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
5384 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
5412 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
5440 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
5467 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
5494 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
5509 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:5445 original size:82 final size:81
Alignment explanation
Indices: 5332--5487 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
5322 AAATTGTACA
* *
5332 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
5396 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
5413 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
5478 TGCGAGTTGA
65 TGCGAATTGA
5488 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:5499 original size:82 final size:81
Alignment explanation
Indices: 5328--5508 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
5318 GATTAAATTG
* *
5328 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
5393 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
5409 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
5473 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
5491 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
5509 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:13482 original size:27 final size:27
Alignment explanation
Indices: 13451--13628 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
13441 TAAATTGTAC
13451 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
13478 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
13504 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
13532 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
13560 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
13587 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
13614 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
13629 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:13565 original size:82 final size:81
Alignment explanation
Indices: 13452--13607 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
13442 AAATTGTACA
* *
13452 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
13516 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
13533 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
13598 TGCGAGTTGA
65 TGCGAATTGA
13608 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:13619 original size:82 final size:81
Alignment explanation
Indices: 13448--13628 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
13438 GATTAAATTG
* *
13448 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
13513 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
13529 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
13593 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
13611 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
13629 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:17186 original size:87 final size:86
Alignment explanation
Indices: 17073--17247 Score: 291
Period size: 87 Copynumber: 2.0 Consensus size: 86
17063 CGGATAGAGG
17073 TTTCGCTCGAAACCGAGTTTCTCACCCTGGGGTGCACCAGTA-TGTTCGTGAAAAAGAAGGACGG
1 TTTCGCTCG-AACCGAGTTTCTCACCCTGGGGTGCACCAGTATTG-TCGTG-AAAAGAAGGACGG
17137 AACCATGAGGTTGTTACATTGACTA
63 AACCATGAGGTTG-TACATTGACTA
17162 TTTCGCTCG-ACCGAGTTTCTCACCCTGGGGTGCACCAGTATTGTCGTGAAAAGAAGGACGGAAC
1 TTTCGCTCGAACCGAGTTTCTCACCCTGGGGTGCACCAGTATTGTCGTGAAAAGAAGGACGGAAC
*
17226 CATGAGGTTGTGCATTGACTA
66 CATGAGGTTGTACATTGACTA
17247 T
1 T
17248 CGTCAACTGA
Statistics
Matches: 84, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
85 11 0.13
86 26 0.31
87 36 0.43
88 2 0.02
89 9 0.11
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (86 bp):
TTTCGCTCGAACCGAGTTTCTCACCCTGGGGTGCACCAGTATTGTCGTGAAAAGAAGGACGGAAC
CATGAGGTTGTACATTGACTA
Found at i:21584 original size:27 final size:27
Alignment explanation
Indices: 21553--21730 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
21543 TAAATTGTAC
21553 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
21580 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
21606 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
21634 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
21662 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
21689 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
21716 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
21731 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:21667 original size:82 final size:81
Alignment explanation
Indices: 21554--21709 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
21544 AAATTGTACA
* *
21554 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
21618 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
21635 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
21700 TGCGAGTTGA
65 TGCGAATTGA
21710 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:21721 original size:82 final size:81
Alignment explanation
Indices: 21550--21730 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
21540 GATTAAATTG
* *
21550 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
21615 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
21631 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
21695 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
21713 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
21731 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.