Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold945
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: 42549
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:5868 original size:40 final size:40
Alignment explanation
Indices: 5784--5967 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
5774 TTGAATGCTG
* * * *
5784 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
5823 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
5864 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
5904 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
5944 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
5968 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:5921 original size:80 final size:81
Alignment explanation
Indices: 5784--5964 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
5774 TTGAATGCTG
* * *
5784 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
5848 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
5864 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
5925 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
5944 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
5965 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:5988 original size:39 final size:39
Alignment explanation
Indices: 5852--6014 Score: 141
Period size: 40 Copynumber: 4.1 Consensus size: 39
5842 GGTATTTGTG
* * * **
5852 CGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTG
1 CGAGTTATAAAATCCGGGTTAAGTCCCGAAGG-CATTGAA
* * **
5892 CGAGATACT-AATTCCGGGTTAAGTCCCGAAGGCATTCGTG
1 CGAGTTA-TAAAATCCGGGTTAAGTCCCGAAGGCATT-GAA
*
5932 CGAGTTTTAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
1 CGAGTTATAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
* * * *
5971 TGAGTTAATATAA-CCGGGCTATGTCCCGAAGGCACTTGAA
1 CGAGTT-ATAAAATCCGGGTTAAGTCCCGAAGGCA-TTGAA
6011 CGAG
1 CGAG
6015 GAGCTAAATC
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
39 29 0.28
40 75 0.71
41 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (39 bp):
CGAGTTATAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
Found at i:7684 original size:40 final size:40
Alignment explanation
Indices: 7522--7677 Score: 276
Period size: 40 Copynumber: 3.9 Consensus size: 40
7512 TATTCGGATG
7522 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
7562 ATAACCGGGCCAAGTCCCGAAGGCATTTGTGTGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
7602 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
7642 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
7678 AGCTATATCT
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 109 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.23
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:13246 original size:30 final size:30
Alignment explanation
Indices: 13212--13272 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
13202 TCCTTAACTC
13212 AAACTTTTGAAAAATTACAATTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCCT
* * * *
13242 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCCT
13272 A
1 A
13273 GGATCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTTGAAAAATTACAATTTTGCCCCT
Found at i:16024 original size:47 final size:47
Alignment explanation
Indices: 15948--16159 Score: 300
Period size: 47 Copynumber: 4.5 Consensus size: 47
15938 CTTCGGGACT
* * * * * *
15948 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
*
15995 TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-CC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
* *
16041 TCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCT
1 T-ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
*
16089 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
* *
16136 TATCACATATATATACATTCACAT
1 TATCACATATATACACTTTCACAT
16160 CACAATTATC
Statistics
Matches: 150, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
46 3 0.02
47 145 0.97
48 2 0.01
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
Found at i:21351 original size:40 final size:40
Alignment explanation
Indices: 21296--21517 Score: 342
Period size: 40 Copynumber: 5.6 Consensus size: 40
21286 TATTCGGATG
21296 ATAACCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACT
21336 ATAACCGGGCTAAGTC-CTGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCTC-GAAGGCATTTGTGCGAGTTACT
*
21376 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACT
* *
21416 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACT
*
21456 ATAACCGGGCTAAGTCTCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTA-CT
* **
21496 ATATCC-GGCTAAACCTCGAAGG
1 ATAACCGGGCTAAGTCTCGAAGG
21518 TACTTGGTTG
Statistics
Matches: 172, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
39 17 0.10
40 154 0.90
41 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACT
Found at i:24062 original size:92 final size:90
Alignment explanation
Indices: 23907--24074 Score: 275
Period size: 92 Copynumber: 1.8 Consensus size: 90
23897 CGCCCATAAG
*
23907 CGAACTCGGACTCAACCAACGAGCTCGGCGTTCGCATCCATAGTGAACTCGGACTCAACTCAACG
1 CGAACTCGGACTCAACCAACGAGCTCGGCATTCGCATCCATAGTGAACTCGGACTCAACTCAACG
23972 AGTTCGGATGCCTAGTTACATCTCA
66 AGTTCGGATGCCTAGTTACATCTCA
* *
23997 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTC-GACTCAACTCA
1 CGAACTCGGACTCAAC-CAACGAGCTCGG-CATTCGCATCCAT-AGTGAACTCGGACTCAACTCA
24061 ACGAGTTCGGATGC
63 ACGAGTTCGGATGC
24075 TCAACCATCC
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
90 16 0.22
91 11 0.15
92 36 0.50
93 9 0.12
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (90 bp):
CGAACTCGGACTCAACCAACGAGCTCGGCATTCGCATCCATAGTGAACTCGGACTCAACTCAACG
AGTTCGGATGCCTAGTTACATCTCA
Found at i:24090 original size:45 final size:45
Alignment explanation
Indices: 23908--24090 Score: 132
Period size: 47 Copynumber: 4.0 Consensus size: 45
23898 GCCCATAAGC
* * * * *
23908 GAACTCGGACTCAAC-CAACGAGCTCGGCGTTCGCATCCA--TAGT
1 GAACTCGGACTCAACTCAACGAGTTCGG-ATGCTCAACCATCTAGT
*
23951 GAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCTCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT-AGT
* * *
23998 GAACTCGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCAT-AAGT
1 GAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCTAGT
24044 GAACTC-GACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CTAGT
24089 GA
1 GA
24091 CATGTCATTG
Statistics
Matches: 111, Mismatches: 12, Indels: 32
0.72 0.08 0.21
Matches are distributed among these distances:
42 1 0.01
43 26 0.23
44 12 0.11
45 29 0.26
46 6 0.05
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCTAGT
Found at i:24225 original size:20 final size:20
Alignment explanation
Indices: 24200--24243 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
24190 GGTGATAGTT
24200 CATACTCATCAAGTAATTCA
1 CATACTCATCAAGTAATTCA
24220 CATACTCATCAAGTAATTCA
1 CATACTCATCAAGTAATTCA
24240 CATA
1 CATA
24244 ATTACATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.25, G:0.05, T:0.30
Consensus pattern (20 bp):
CATACTCATCAAGTAATTCA
Found at i:26506 original size:15 final size:15
Alignment explanation
Indices: 26474--26523 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
26464 CAAAGATAAC
* *
26474 AAGAAAACC-GAATT
1 AAGAAATCCAGAATA
26488 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
26503 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
26518 AAGAAA
1 AAGAAA
26524 CCCAAGATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 8 0.27
15 22 0.73
ACGTcount: A:0.58, C:0.12, G:0.18, T:0.12
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:29544 original size:92 final size:92
Alignment explanation
Indices: 29387--29555 Score: 295
Period size: 92 Copynumber: 1.8 Consensus size: 92
29377 GCCCATAAGT
* *
29387 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAGTGAACTCGGACTCAACTCAAC
29452 GAGTTCGGATGCCTAGTTACATCTCAC
66 GAGTTCGGATGCCTAGTTACATCTCAC
*
29479 GAACTCGGACTCAACTCAACGAGTTCGGACATT-GCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCAT-AGTGAACTCGGACTCAACTCAA
29543 CGAGTTCGGATGC
65 CGAGTTCGGATGC
29556 TCAACCATCC
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
91 8 0.11
92 65 0.89
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:29552 original size:45 final size:45
Alignment explanation
Indices: 29379--29552 Score: 212
Period size: 45 Copynumber: 3.8 Consensus size: 45
29369 TGTAACCCGC
* * *
29379 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATT-GCAT
*
29425 CCAT-AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTGCAT
* *
29474 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT
29516 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
29553 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 8, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
42 5 0.05
43 2 0.02
44 3 0.03
45 59 0.53
46 4 0.04
47 30 0.27
48 3 0.03
49 3 0.03
50 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT
Done.