Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024308.1 Corchorus olitorius cultivar O-4 contig24341, 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: 12233
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Found at i:5979 original size:145 final size:145
Alignment explanation
Indices: 5504--6735 Score: 1578
Period size: 145 Copynumber: 8.5 Consensus size: 145
5494 TCTCTACTCA
*
5504 GAGTTTGCATTTATAAGACCTCCGGGCACAATTTCAGAAACCTCC-GGTATTAATTCTGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
* * * * *
5568 CCTCTGGGTATCATCACATTTCATCAAGTTT--AATCAAAGATGCGTTTCAGTTTCAAAATCAAA
66 CCTCCGGGTATCATCTCATTTCATCAAGTTTCAAATCAAAGTTGCGTTTAAATTTCAAAATCAAA
5631 ACCTTGCCTCAAGGTC
131 ACCTTG-CTCAAGGTC
* * * *
5647 GAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAGACCTCTGGGTATTACTTCCGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
* * * * **
5712 CCTCAGGGTATCATTTCATTTCCTCAAGTTGT-TAATCAAAGTTGCGTTTAAATTT-AAAAAAAA
66 CCTCCGGGTATCATCTCATTTCATCAAGTT-TCAAATCAAAGTTGCGTTTAAATTTCAAAATCAA
* *
5775 AACCTTGCTTAAGGTT
130 AACCTTGCTCAAGGTC
* * *
5791 GAGTTTGCATTTGTAAGACCTCCAGGCACAATTTCAGAGACCTCCGGGTATTGATTCTGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
* * * * * *
5856 CCTCCGGGTATTC-CCTCCTTTTATCAAATTTCAAATCAAAGTTGCATTTAAGTTTCAAAATCAA
66 CCTCCGGGTA-TCATCTCATTTCATCAAGTTTCAAATCAAAGTTGCGTTTAAATTTCAAAATCAA
*
5920 AACCTTGCTTAAGGTC
130 AACCTTGCTCAAGGTC
* * *
5936 GAGTTTGCATTTGTAAGACCTCTGGGCACGATTGCAGAAACCTCCGGGTATTAATTCTGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
** * *
6001 CCTCCGGGTATCATCTCATTTCATCAAGTTTTTTAATCAAGGTTGCGTTTAAATTTTAAAA--AA
66 CCTCCGGGTATCATCTCATTTCATCAAG-TTTCAAATCAAAGTTGCGTTTAAATTTCAAAATCAA
* *
6064 GAGCCTTGCTCAAGGTT
130 -AACCTTGCTCAAGGTC
* *
6081 GAGTTTGCATTTGTAAGACCTCCGGGAACAATTTCAGAAACCTCCGGGTATTAGTTCTGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
* * * * * *
6146 CCTCCGGGTATTC-CCTAATTTCATTAAATTTCAAATCAAAGTTGCATTTAAGTTTCAAAATCAA
66 CCTCCGGGTA-TCATCTCATTTCATCAAGTTTCAAATCAAAGTTGCGTTTAAATTTCAAAATCAA
*
6210 AACCTTGGTCAAGGTC
130 AACCTTGCTCAAGGTC
* * * *
6226 GAGTTTGCATTTGTAAGACCTCCGGGAACGATTCCAGAAACCTCCGGGTATTAATTATGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
6291 CCTCCGGGTATCATCTCATTTCATCAAGTTTTC-AATCAAAGTTGCGTTTAAATTTCAAAA--AA
66 CCTCCGGGTATCATCTCATTTCATCAAG-TTTCAAATCAAAGTTGCGTTTAAATTTCAAAATCAA
*
6353 AACCTTGCTCAAGGTT
130 AACCTTGCTCAAGGTC
* * *
6369 GAGTTTGCATTTGTAAGACCTCCGAGCACCATTTCAGAAACCTCCAGGTATTAATTCTGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
* * * * *
6434 CCTCCGAGTATCATCTCATTTCATCAAGTTTTAAATCAAAATTGCGCTTAAATTTCAAAACCAAA
66 CCTCCGGGTATCATCTCATTTCATCAAGTTTCAAATCAAAGTTGCGTTTAAATTTCAAAATCAAA
*
6499 ACCTTGCCCAAGGTC
131 ACCTTGCTCAAGGTC
* * * *
6514 GAGTTTGCATTTGTAAGACCTCCGGACACCATTTCATAAACCTCCGGGTATTAGTTCTGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
** *
6579 CCTCCGGGTATCATCTCATTTCATCAAGTTTTTAATCAAATTTGCGTTTAAATTTC--AAT--AA
66 CCTCCGGGTATCATCTCATTTCATCAAGTTTCAAATCAAAGTTGCGTTTAAATTTCAAAATCAAA
*
6640 ACTTTGCTCAAGGTCTTTAC
131 ACCTTGCTCAAGG----T-C
* *
6660 TTAGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTAAGAAACCTCCGGGTATTAATTCTGACA
1 ---GAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATA
*
6725 AGTCCTCCGGG
63 AATCCTCCGGG
6736 CATTCCATAT
Statistics
Matches: 950, Mismatches: 114, Indels: 44
0.86 0.10 0.04
Matches are distributed among these distances:
141 13 0.01
142 3 0.00
143 172 0.18
144 182 0.19
145 460 0.48
146 54 0.06
149 66 0.07
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (145 bp):
GAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
CCTCCGGGTATCATCTCATTTCATCAAGTTTCAAATCAAAGTTGCGTTTAAATTTCAAAATCAAA
ACCTTGCTCAAGGTC
Found at i:6886 original size:39 final size:37
Alignment explanation
Indices: 6823--6919 Score: 104
Period size: 39 Copynumber: 2.6 Consensus size: 37
6813 AGTCAATTTT
* * * * * *
6823 AATCCTATTCATGATCGTTGCTTTAATAGTCGATTTCAG
1 AATCCTACTCAGGATCATTGCTTTAACAGTC-A-GTCAC
* *
6862 AATCCTACTCAGGATCATTTCTTTACCAGTCAGTCAC
1 AATCCTACTCAGGATCATTGCTTTAACAGTCAGTCAC
6899 AATCCTACTCAGGATCATTGC
1 AATCCTACTCAGGATCATTGC
6920 ATCATCAGTC
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 23 0.47
38 1 0.02
39 25 0.51
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (37 bp):
AATCCTACTCAGGATCATTGCTTTAACAGTCAGTCAC
Found at i:7007 original size:39 final size:38
Alignment explanation
Indices: 6964--7065 Score: 107
Period size: 41 Copynumber: 2.6 Consensus size: 38
6954 ATTTATATAC
6964 CAGTTAATTTCGAAATCCTATTCAGGATCATTGCTCTT-T
1 CAGTTAATTTC-AAATCCTATTCAGGATCATTGCT-TTGT
* *
7003 CAGTTAATTTTAGAATCCTATACTTAGGATCATTGCTTTGT
1 CAGTTAATTTCA-AATCCTAT--TCAGGATCATTGCTTTGT
* *
7044 GAGTCAATTTCAAAGTCCTATT
1 CAGTTAATTTCAAA-TCCTATT
7066 TTAGGATCTC
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
38 1 0.02
39 19 0.36
40 4 0.08
41 29 0.55
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (38 bp):
CAGTTAATTTCAAATCCTATTCAGGATCATTGCTTTGT
Found at i:7063 original size:41 final size:40
Alignment explanation
Indices: 6850--7073 Score: 105
Period size: 39 Copynumber: 5.7 Consensus size: 40
6840 TTGCTTTAAT
* *
6850 AGTCGATTTCAGAATCCTA-CTCAGGATCATT--TCTTTACC
1 AGTCAATTTCAGAATCCTATCTTAGGATCATTGCTCTTT--C
* * * *
6889 AGTC-A-GTCACAATCCTA-CTCAGGATCATTGCATC-ATC
1 AGTCAATTTCAGAATCCTATCTTAGGATCATTGC-TCTTTC
* * * ** * **
6926 AGTCAATTT-GGAAGTCTTAT-TTAGGATTATTTATATACC
1 AGTCAATTTCAGAA-TCCTATCTTAGGATCATTGCTCTTTC
* *
6965 AGTTAATTTC-GAAATCCTAT-TCAGGATCATTGCTCTTTC
1 AGTCAATTTCAG-AATCCTATCTTAGGATCATTGCTCTTTC
* * *
7004 AGTTAATTTTAGAATCCTATACTTAGGATCATTGCT-TTGTG
1 AGTCAATTTCAGAATCCTAT-CTTAGGATCATTGCTCTT-TC
*
7045 AGTCAATTTCA-AAGTCCTATTTTAGGATC
1 AGTCAATTTCAGAA-TCCTATCTTAGGATC
7074 TCTTCTAGAA
Statistics
Matches: 142, Mismatches: 28, Indels: 29
0.71 0.14 0.15
Matches are distributed among these distances:
37 27 0.19
38 5 0.04
39 64 0.45
40 17 0.12
41 29 0.20
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (40 bp):
AGTCAATTTCAGAATCCTATCTTAGGATCATTGCTCTTTC
Found at i:7850 original size:31 final size:31
Alignment explanation
Indices: 7805--7865 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
7795 CGATGAGAAA
*
7805 ATGGAAGTTCAAAATACAAAATCAGAATAAC
1 ATGGAAGTTCAAAATACAAAAACAGAATAAC
* *
7836 ATGGATGTTGAAAATACAAAAACAGAATAA
1 ATGGAAGTTCAAAATACAAAAACAGAATAA
7866 TCCAAGTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (31 bp):
ATGGAAGTTCAAAATACAAAAACAGAATAAC
Done.