Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3380
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: 29013
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.33
Found at i:2001 original size:17 final size:19
Alignment explanation
Indices: 1979--2015 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1969 AGCTTTCACT
1979 TATTC-ATCACA-TAGTCA
1 TATTCAATCACACTAGTCA
*
1996 TATTCAATTACACTAGTCA
1 TATTCAATCACACTAGTCA
2015 T
1 T
2016 TTCCCATGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (19 bp):
TATTCAATCACACTAGTCA
Found at i:2659 original size:16 final size:17
Alignment explanation
Indices: 2626--2659 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2616 AATTAGCCTG
2626 AATTCACATTTTTGCAA
1 AATTCACATTTTTGCAA
*
2643 AATTTACATTTTT-CAA
1 AATTCACATTTTTGCAA
2659 A
1 A
2660 CTTTGTCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (17 bp):
AATTCACATTTTTGCAA
Found at i:12030 original size:40 final size:40
Alignment explanation
Indices: 11951--12127 Score: 216
Period size: 40 Copynumber: 4.5 Consensus size: 40
11941 CGGATGATAA
* * * *
11951 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * * *
11991 CCGGGCTATGTCTCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
* *
12031 CCGGGCTAAGACCCAAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
12071 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
12111 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
12128 ATACTTGGGT
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.01
39 15 0.13
40 98 0.84
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:12395 original size:22 final size:22
Alignment explanation
Indices: 12355--12396 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12345 GAATGTGCAT
*
12355 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
12377 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
12397 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:19118 original size:40 final size:40
Alignment explanation
Indices: 19039--19215 Score: 227
Period size: 40 Copynumber: 4.5 Consensus size: 40
19029 CAGATGATAA
* * * *
19039 CCGGACTAAGATCCGAAGGCATTAGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * *
19079 CCGGGCTATGTCCCGAAGGCATTTATGCTG-G-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGC-GAGTTG-TTATAT
*
19119 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
19159 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
19199 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
19216 ATACTTGGGT
Statistics
Matches: 120, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
38 1 0.01
39 16 0.13
40 100 0.83
41 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:19483 original size:22 final size:22
Alignment explanation
Indices: 19443--19484 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
19433 GAATGTGAAT
*
19443 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
19465 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
19485 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:21712 original size:48 final size:47
Alignment explanation
Indices: 21601--21890 Score: 303
Period size: 48 Copynumber: 5.9 Consensus size: 47
21591 ATGAGATCCT
* * * *
21601 GTGTAAGACCATGACTAGGACATGGCATCGGCATTCGAGATGAGAGCCA
1 GTGTAAGACCATGTCT-GGACATGGCATCGGCATT-GATATGTGTGCCA
*
21650 GTGTAAGACCATGTCTGCGACATGGCATCGGCGTTGATATGTGTGCCA
1 GTGTAAGACCATGTCTG-GACATGGCATCGGCATTGATATGTGTGCCA
* * *
21698 ATGTAAGACCATGTCTAGGACATGACATCGACATTGATATGTGTGCCA
1 GTGTAAGACCATGTCT-GGACATGGCATCGGCATTGATATGTGTGCCA
* **
21746 ATGTAAGACCATGTGACCATGTCTAGGACATGGCATCGGGGTTGATATGTGTGCCA
1 GTGT---A--A---GACCATGTCT-GGACATGGCATCGGCATTGATATGTGTGCCA
* *
21802 GTGTAAGACCATGTCTGGGACATGGCATCGGGGA-TGATATGTGTGCTA
1 GTGTAAGACCATGTCT-GGACATGGCATC-GGCATTGATATGTGTGCCA
*
21850 GTGTAAGACCATGTCTGGGACATGGCATCGGCACTGATATG
1 GTGTAAGACCATGTCT-GGACATGGCATCGGCATTGATATG
21891 AGACTTCGTG
Statistics
Matches: 211, Mismatches: 18, Indels: 25
0.83 0.07 0.10
Matches are distributed among these distances:
47 3 0.01
48 128 0.61
49 35 0.17
51 2 0.01
53 2 0.01
56 41 0.19
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (47 bp):
GTGTAAGACCATGTCTGGACATGGCATCGGCATTGATATGTGTGCCA
Found at i:21770 original size:56 final size:56
Alignment explanation
Indices: 21704--21815 Score: 179
Period size: 56 Copynumber: 2.0 Consensus size: 56
21694 GCCAATGTAA
21704 GACCATGTCTAGGACATGACATCGACATTGATATGTGTGCCAATGTAAGACCATGT
1 GACCATGTCTAGGACATGACATCGACATTGATATGTGTGCCAATGTAAGACCATGT
* *** *
21760 GACCATGTCTAGGACATGGCATCGGGGTTGATATGTGTGCCAGTGTAAGACCATGT
1 GACCATGTCTAGGACATGACATCGACATTGATATGTGTGCCAATGTAAGACCATGT
21816 CTGGGACATG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.27
Consensus pattern (56 bp):
GACCATGTCTAGGACATGACATCGACATTGATATGTGTGCCAATGTAAGACCATGT
Found at i:21790 original size:104 final size:104
Alignment explanation
Indices: 21656--21863 Score: 312
Period size: 104 Copynumber: 2.0 Consensus size: 104
21646 GCCAGTGTAA
21656 GACCATGTCTGCGACATGGCATCGGCGTTGATATGTGTGCCAATGTAAGACCATGTCTAGGACAT
1 GACCATGTCTGCGACATGGCATCGGCGTTGATATGTGTGCCAATGTAAGACCATGTCTAGGACAT
21721 GACATC-GACATTGATATGTGTGCCAATGTAAGACCATGT
66 GACATCGGACA-TGATATGTGTGCCAATGTAAGACCATGT
* * *
21760 GACCATGTCTAG-GACATGGCATCGGGGTTGATATGTGTGCCAGTGTAAGACCATGTCTGGGACA
1 GACCATGTCT-GCGACATGGCATCGGCGTTGATATGTGTGCCAATGTAAGACCATGTCTAGGACA
* ** * *
21824 TGGCATCGGGGATGATATGTGTGCTAGTGTAAGACCATGT
65 TGACATCGGACATGATATGTGTGCCAATGTAAGACCATGT
21864 CTGGGACATG
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
104 91 0.97
105 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (104 bp):
GACCATGTCTGCGACATGGCATCGGCGTTGATATGTGTGCCAATGTAAGACCATGTCTAGGACAT
GACATCGGACATGATATGTGTGCCAATGTAAGACCATGT
Found at i:21840 original size:152 final size:153
Alignment explanation
Indices: 21607--21890 Score: 426
Period size: 152 Copynumber: 1.9 Consensus size: 153
21597 TCCTGTGTAA
21607 GACCATGACTAGGACATGGCATCGGCATTCGAGATGAGAGCCAGTGTAAGACCATGTCTGCGACA
1 GACCATGACTAGGACATGGCATCGGCATTCGAGATGAGAGCCAGTGTAAGACCATGTCTGCGACA
* *
21672 TGGCATCGGCGTTGATATGTGTGCCAATGTAAGACCATGTCTAGGACATGACATCGACATTGATA
66 TGGCATCGGCGATGATATGTGTGCCAATGTAAGACCATGTCTAGGACATGACATCGACACTGATA
21737 TGTGTGCCAATGTAAGACCATGT
131 TGTGTGCCAATGTAAGACCATGT
* ** * * * *
21760 GACCATGTCTAGGACATGGCATCGGGGTT-GATATGTGTGCCAGTGTAAGACCATGTCTGGGACA
1 GACCATGACTAGGACATGGCATCGGCATTCGAGATGAGAGCCAGTGTAAGACCATGTCTGCGACA
* * * * * *
21824 TGGCATCGGGGATGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTGATA
66 TGGCATCGGCGATGATATGTGTGCCAATGTAAGACCATGTCTAGGACATGACATCGACACTGATA
21889 TG
131 TG
21891 AGACTTCGTG
Statistics
Matches: 116, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
152 90 0.78
153 26 0.22
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (153 bp):
GACCATGACTAGGACATGGCATCGGCATTCGAGATGAGAGCCAGTGTAAGACCATGTCTGCGACA
TGGCATCGGCGATGATATGTGTGCCAATGTAAGACCATGTCTAGGACATGACATCGACACTGATA
TGTGTGCCAATGTAAGACCATGT
Found at i:21902 original size:48 final size:48
Alignment explanation
Indices: 21760--21906 Score: 172
Period size: 48 Copynumber: 3.1 Consensus size: 48
21750 AAGACCATGT
* ** * * *
21760 GACCATGTCTAGGACATGGCATCGGGGTTGATATGTGTGCCAGTGTAA
1 GACCATGTCTGGGACATGGCATCGGGCATGATATGAGTACTAGTGTAA
* * *
21808 GACCATGTCTGGGACATGGCATCGGGGATGATATGTGTGCTAGTGTAA
1 GACCATGTCTGGGACATGGCATCGGGCATGATATGAGTACTAGTGTAA
*
21856 GACCATGTCTGGGACATGGCATC-GGCACTGATATGAG-ACTTCGTGTAA
1 GACCATGTCTGGGACATGGCATCGGGCA-TGATATGAGTAC-TAGTGTAA
21904 GAC
1 GAC
21907 GATATCTAGG
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
47 4 0.04
48 86 0.96
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.26
Consensus pattern (48 bp):
GACCATGTCTGGGACATGGCATCGGGCATGATATGAGTACTAGTGTAA
Found at i:23506 original size:21 final size:21
Alignment explanation
Indices: 23482--23523 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
23472 GACATGACTA
*
23482 TGAATGCTAGATGACTAAGTT
1 TGAATGCTAAATGACTAAGTT
23503 TGAATGCTAAATGACTAAGTT
1 TGAATGCTAAATGACTAAGTT
23524 GAGAATATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (21 bp):
TGAATGCTAAATGACTAAGTT
Done.