Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024253.1 Corchorus olitorius cultivar O-4 contig24286, whole genome shotgun sequence
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: 12343
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:5987 original size:21 final size:22
Alignment explanation
Indices: 5963--6003 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5953 TTGCCTCATA
*
5963 CATTCATTCAT-CATGCCATGG
1 CATTCATTCATGCATCCCATGG
5984 CATTCATTCATGCATCCCAT
1 CATTCATTCATGCATCCCAT
6004 TAAACTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.32, G:0.10, T:0.34
Consensus pattern (22 bp):
CATTCATTCATGCATCCCATGG
Found at i:8235 original size:5 final size:5
Alignment explanation
Indices: 8227--8306 Score: 55
Period size: 5 Copynumber: 16.6 Consensus size: 5
8217 AAATTAAAAA
* **
8227 AAATC AAATC AAA-- AAATA AAATC AAAGTC -AAT- AAAAA AAATC AAATC
1 AAATC AAATC AAATC AAATC AAATC AAA-TC AAATC AAATC AAATC AAATC
*
8274 AAAAT- AAA-A AAATC AAATC AAATC AAAATC AAA
1 -AAATC AAATC AAATC AAATC AAATC -AAATC AAA
8307 AGAGAATCGA
Statistics
Matches: 61, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
3 3 0.05
4 9 0.15
5 38 0.62
6 11 0.18
ACGTcount: A:0.70, C:0.12, G:0.01, T:0.16
Consensus pattern (5 bp):
AAATC
Found at i:8257 original size:19 final size:17
Alignment explanation
Indices: 8222--8295 Score: 103
Period size: 19 Copynumber: 4.1 Consensus size: 17
8212 AAAAAAAATT
8222 AAAAAAAATCAAATCAA
1 AAAAAAAATCAAATCAA
8239 AAAATAAAATCAAAGTCAA
1 AAAA-AAAATCAAA-TCAA
8258 TAAAAAAAATCAAATCAAA
1 -AAAAAAAATCAAATC-AA
8277 ATAAAAAAATCAAATCAA
1 A-AAAAAAATCAAATCAA
8295 A
1 A
8296 TCAAAATCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.08
18 15 0.29
19 29 0.56
20 4 0.08
ACGTcount: A:0.73, C:0.11, G:0.01, T:0.15
Consensus pattern (17 bp):
AAAAAAAATCAAATCAA
Found at i:8257 original size:24 final size:24
Alignment explanation
Indices: 8214--8307 Score: 87
Period size: 24 Copynumber: 4.2 Consensus size: 24
8204 AAATTCAAAA
*
8214 AAAAAATTAAAA-AAAATC-AAATC
1 AAAAAA-TAAAATCAAATCAAAATC
8237 AAAAAATAAAATCAAAGTC--AAT-
1 AAAAAATAAAATCAAA-TCAAAATC
*
8259 --AAAA-AAAATCAAATCAAAATA
1 AAAAAATAAAATCAAATCAAAATC
*
8280 AAAAAATCAAATCAAATCAAAATC
1 AAAAAATAAAATCAAATCAAAATC
8304 AAAA
1 AAAA
8308 GAGAATCGAT
Statistics
Matches: 60, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
18 2 0.03
19 9 0.15
20 7 0.12
22 5 0.08
23 16 0.27
24 21 0.35
ACGTcount: A:0.72, C:0.11, G:0.01, T:0.16
Consensus pattern (24 bp):
AAAAAATAAAATCAAATCAAAATC
Found at i:8262 original size:37 final size:37
Alignment explanation
Indices: 8221--8294 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
8211 AAAAAAAAAT
*
8221 TAAAAAAAATCAAATCAAAA-AATAAAATCAAAGTCAA
1 TAAAAAAAATCAAATCAAAATAAAAAAATCAAA-TCAA
8258 TAAAAAAAATCAAATCAAAATAAAAAAATCAAATCAA
1 TAAAAAAAATCAAATCAAAATAAAAAAATCAAATCAA
8295 ATCAAAATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 24 0.69
38 11 0.31
ACGTcount: A:0.72, C:0.11, G:0.01, T:0.16
Consensus pattern (37 bp):
TAAAAAAAATCAAATCAAAATAAAAAAATCAAATCAA
Found at i:8972 original size:50 final size:50
Alignment explanation
Indices: 8887--9035 Score: 190
Period size: 50 Copynumber: 3.0 Consensus size: 50
8877 AATTTTACAA
* * * * *
8887 TAAAATTTCATTCCATTTGTGAGCCCAAGAGCAAAATTCGCTTTTCAAAG
1 TAAAATTACATTCCATTTGTAAGTCCAAAATCAAAATTCGCTTTTCAAAG
* * *
8937 TAAAATTGCTTTCCATTTGTAAGTTCAAAATCAAAATTCGCTTTTCAAAG
1 TAAAATTACATTCCATTTGTAAGTCCAAAATCAAAATTCGCTTTTCAAAG
** * *
8987 TAGGATTACATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAA
1 TAAAATTACATTCCATTTGTAAGTCCAAAATCAAAATTCGCTTTTCAAA
9036 AGGCATTTAA
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 85 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (50 bp):
TAAAATTACATTCCATTTGTAAGTCCAAAATCAAAATTCGCTTTTCAAAG
Found at i:9708 original size:50 final size:50
Alignment explanation
Indices: 9649--9929 Score: 449
Period size: 50 Copynumber: 5.6 Consensus size: 50
9639 TGAATGCTTT
* * * *
9649 GGCTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACATA
* *
9699 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAATATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACATA
9749 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACATA
9799 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACATA
*
9849 GGCTTTTCCACAAGCCAAATTCG-TTCTCATACGAGTCAGTTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTC-CATACGAGTCAGTTATCAACATA
* *
9899 AGCTTTTCCACAAGCCACA-TCCGTTTCCATA
1 GGCTTTTCCACAAGCCAAACT-CGTTTCCATA
9930 AGGTGCATTA
Statistics
Matches: 219, Mismatches: 9, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
49 4 0.02
50 212 0.97
51 3 0.01
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAACATA
Found at i:10123 original size:50 final size:50
Alignment explanation
Indices: 9943--10096 Score: 290
Period size: 50 Copynumber: 3.1 Consensus size: 50
9933 TGCATTACCT
9943 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
9993 TTTTAAGATTGAATTGGTAGACAGTTCAGAGGATAAGCGGAAGACGATCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
10043 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
10093 TTTT
1 TTTT
10097 GATATTAGTT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 100 1.00
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:10428 original size:28 final size:28
Alignment explanation
Indices: 10397--10468 Score: 119
Period size: 27 Copynumber: 2.6 Consensus size: 28
10387 AAAATCCAGT
* *
10397 GGCATTTTGGTCATTTTTTATATTCAGG
1 GGCATTTTGGTCATTTTGTACATTCAGG
10425 GGCATTTTGGTCA-TTTGTACATTCAGG
1 GGCATTTTGGTCATTTTGTACATTCAGG
10452 GGCATTTTGGTCATTTT
1 GGCATTTTGGTCATTTT
10469 AAGTTCACTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 25 0.61
28 16 0.39
ACGTcount: A:0.17, C:0.12, G:0.24, T:0.47
Consensus pattern (28 bp):
GGCATTTTGGTCATTTTGTACATTCAGG
Done.