Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024521.1 Corchorus olitorius cultivar O-4 contig24554, 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: 10045
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:6139 original size:101 final size:101
Alignment explanation
Indices: 5948--6401 Score: 556
Period size: 101 Copynumber: 4.5 Consensus size: 101
5938 TTAATTACCG
* * * * * *
5948 AATTGACCTTGGATTTCGATCCGGACTCTTCGTGAGAACATTGAAACTAAGTTGTGGCCAAACGT
1 AATTGACCTTAGATTTCGATCCGGACTCCTCGTGAGAACATCGAAACTAAGTTGTAGCCGAATGT
** * *
6013 AAGCCCTAAACTTTTTCTGATAACGGC-AACGTTCGT
66 AAGCCCTGGACTCTTTCTGAGAACGGCTAA-GTTCGT
* * *
6049 AATTGACCTTAGATTTCGATCTGGACTCCTCTTGAGAACATCAAAACTAAGTTGTAGCCGAATGT
1 AATTGACCTTAGATTTCGATCCGGACTCCTCGTGAGAACATCGAAACTAAGTTGTAGCCGAATGT
* *
6114 AAGCCATGGACTCTTTATGAGAACGGCTAAGTTCGT
66 AAGCCCTGGACTCTTTCTGAGAACGGCTAAGTTCGT
* * * * *
6150 ATTTGACATTAGATTTCGATCCGGACTCCTCGTCAGAACATCGAAACTAAGTTGTGGTCGAATGT
1 AATTGACCTTAGATTTCGATCCGGACTCCTCGTGAGAACATCGAAACTAAGTTGTAGCCGAATGT
* * *
6215 AAGCCCTGTACTCTTTCTGAGAATGGC-AACGTCCGT
66 AAGCCCTGGACTCTTTCTGAGAACGGCTAA-GTTCGT
** * * * *
6251 -ATAAACCTTAGATTTTGATCCGGACTCCCCGTGAGAACATCGAAACTAAGTTATAGCCGAAAGT
1 AATTGACCTTAGATTTCGATCCGGACTCCTCGTGAGAACATCGAAACTAAGTTGTAGCCGAATGT
* *
6315 AAGCCCTGGACTCTTTGTGAGAACGACTAAGTTCGT
66 AAGCCCTGGACTCTTTCTGAGAACGGCTAAGTTCGT
* *
6351 ATTTGACCTTAGATTTCGATCCGGACT-CTCTTTGAGAACATCGAAACTAAG
1 AATTGACCTTAGATTTCGATCCGGACTCCTC-GTGAGAACATCGAAACTAAG
6402 CTGAACCAAT
Statistics
Matches: 298, Mismatches: 50, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
100 85 0.29
101 211 0.71
102 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (101 bp):
AATTGACCTTAGATTTCGATCCGGACTCCTCGTGAGAACATCGAAACTAAGTTGTAGCCGAATGT
AAGCCCTGGACTCTTTCTGAGAACGGCTAAGTTCGT
Found at i:6330 original size:201 final size:202
Alignment explanation
Indices: 5950--6401 Score: 638
Period size: 201 Copynumber: 2.2 Consensus size: 202
5940 AATTACCGAA
* * *
5950 TTGACCTTGGATTTCGATCCGGACTCTTCGTGAGAACATTGAAACTAAGTTGTGGCCAAACGTAA
1 TTGACCTTAGATTTCGATCCGGACTCCTCGTGAGAACATCGAAACTAAGTTGTGGCCAAACGTAA
* * * ** * *
6015 GCCCTAAACTTTTTCTGATAACGGCAACGTTCGTAATTGACCTTAGATTTCGATCTGGACTCCTC
66 GCCCTAAACTCTTTCTGAGAACGGCAACGTCCGTAATAAACCTTAGATTTCGATCCGGACTCCCC
* * * *
6080 TTGAGAACATCAAAACTAAGTTGTAGCCGAATGTAAGCCATGGACTCTTTATGAGAACGGCTAAG
131 GTGAGAACATCAAAACTAAGTTATAGCCGAAAGTAAGCCATGGACTCTTTATGAGAACGACTAAG
6145 TTCGTAT
196 TTCGTAT
* * * * *
6152 TTGACATTAGATTTCGATCCGGACTCCTCGTCAGAACATCGAAACTAAGTTGTGGTCGAATGTAA
1 TTGACCTTAGATTTCGATCCGGACTCCTCGTGAGAACATCGAAACTAAGTTGTGGCCAAACGTAA
** * *
6217 GCCCTGTACTCTTTCTGAGAATGGCAACGTCCGT-ATAAACCTTAGATTTTGATCCGGACTCCCC
66 GCCCTAAACTCTTTCTGAGAACGGCAACGTCCGTAATAAACCTTAGATTTCGATCCGGACTCCCC
* * *
6281 GTGAGAACATCGAAACTAAGTTATAGCCGAAAGTAAGCCCTGGACTCTTTGTGAGAACGACTAAG
131 GTGAGAACATCAAAACTAAGTTATAGCCGAAAGTAAGCCATGGACTCTTTATGAGAACGACTAAG
6346 TTCGTAT
196 TTCGTAT
*
6353 TTGACCTTAGATTTCGATCCGGACT-CTCTTTGAGAACATCGAAACTAAG
1 TTGACCTTAGATTTCGATCCGGACTCCTC-GTGAGAACATCGAAACTAAG
6402 CTGAACCAAT
Statistics
Matches: 220, Mismatches: 29, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
200 3 0.01
201 132 0.60
202 85 0.39
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (202 bp):
TTGACCTTAGATTTCGATCCGGACTCCTCGTGAGAACATCGAAACTAAGTTGTGGCCAAACGTAA
GCCCTAAACTCTTTCTGAGAACGGCAACGTCCGTAATAAACCTTAGATTTCGATCCGGACTCCCC
GTGAGAACATCAAAACTAAGTTATAGCCGAAAGTAAGCCATGGACTCTTTATGAGAACGACTAAG
TTCGTAT
Found at i:7949 original size:224 final size:224
Alignment explanation
Indices: 7559--8008 Score: 767
Period size: 224 Copynumber: 2.0 Consensus size: 224
7549 TTCAATATAT
*
7559 TCTACATATTATTTTTGTAACCAGATGAAATTACTAAATGCTCCTTCTAACTTTTAACCTAGGAC
1 TCTACATATTATTTTTGTAACCAGATGAAATTACTAAATGCTCCTTCTAACTTTTAACCCAGGAC
*
7624 GACCTTATCGCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAATCGATTCGTATTCCATC
66 GACCTTATCGCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAACCGATTCGTATTCCATC
7689 ACAGTATAACCTCATAAATCATATTTATTATATTTAAACCCACAGAAAACACATTCACATTTACA
131 ACAGTATAACCTCATAAATCATATTTATTATATTTAAACCCACAGAAAACACATTCACATTTACA
* *
7754 GAGCAGAAAAACATTCTATAAAAATGGAC
196 GAGCAAAAAAACAATCTATAAAAATGGAC
* *
7783 TCTACATATTATTTTTGTAACCA-AGTGAAATTACTAAATGCTTCTTCTAACTTTTAACCCGGGA
1 TCTACATATTATTTTTGTAACCAGA-TGAAATTACTAAATGCTCCTTCTAACTTTTAACCCAGGA
* *
7847 GGACCTTATCGCCCCGTTTTAGTCATTTCTCACATGCGGTTATACTGAACCGATTCGTATTCCAT
65 CGACCTTATCGCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAACCGATTCGTATTCCAT
** *
7912 CACTTTATAACCTCATAAATCATATTTATTATATTTAAACCCACAGAAAACACGTTCACATTTAC
130 CACAGTATAACCTCATAAATCATATTTATTATATTTAAACCCACAGAAAACACATTCACATTTAC
* *
7977 AGAGTAAAAAAACAATCTATAAAAATTGAC
195 AGAGCAAAAAAACAATCTATAAAAATGGAC
8007 TC
1 TC
8009 ATATGATAAT
Statistics
Matches: 212, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
223 1 0.00
224 211 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.33
Consensus pattern (224 bp):
TCTACATATTATTTTTGTAACCAGATGAAATTACTAAATGCTCCTTCTAACTTTTAACCCAGGAC
GACCTTATCGCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAACCGATTCGTATTCCATC
ACAGTATAACCTCATAAATCATATTTATTATATTTAAACCCACAGAAAACACATTCACATTTACA
GAGCAAAAAAACAATCTATAAAAATGGAC
Found at i:9404 original size:132 final size:132
Alignment explanation
Indices: 9167--9440 Score: 521
Period size: 132 Copynumber: 2.1 Consensus size: 132
9157 AATCTTATGC
**
9167 CAACATAAAACAACATATGATAATTTGTTACTGAACTTTATCCTAATGGCAACACAGACTTTATA
1 CAACATATGACAACATATGATAATTTGTTACTGAACTTTATCCTAATGGCAACACAGACTTTATA
9232 GGTTATAACTTAATAACAATGAAAGCTAAATAGAGCAAGAAGTTGAAAAAAATCAGCAACCTTAA
66 GGTTATAACTTAATAACAATGAAAGCTAAATAGAGCAAGAAGTTGAAAAAAATCAGCAACCTTAA
9297 AA
131 AA
*
9299 CAACATATGACAACATATGATAATTTGTTACTGAACTTTATCCTAATGGCAACACAGATTTTATA
1 CAACATATGACAACATATGATAATTTGTTACTGAACTTTATCCTAATGGCAACACAGACTTTATA
9364 GGTTATAACTTAATAACAATGAAAGCTAAATAGAGCAAGAAGTTGAAAAAAATCAGCAACCTTAA
66 GGTTATAACTTAATAACAATGAAAGCTAAATAGAGCAAGAAGTTGAAAAAAATCAGCAACCTTAA
9429 AA
131 AA
9431 CAACATATGA
1 CAACATATGA
9441 TAAATTTTGC
Statistics
Matches: 139, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 139 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.26
Consensus pattern (132 bp):
CAACATATGACAACATATGATAATTTGTTACTGAACTTTATCCTAATGGCAACACAGACTTTATA
GGTTATAACTTAATAACAATGAAAGCTAAATAGAGCAAGAAGTTGAAAAAAATCAGCAACCTTAA
AA
Done.