Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023980.1 Corchorus olitorius cultivar O-4 contig24013, 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: 12509
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:4699 original size:162 final size:164
Alignment explanation
Indices: 4473--4767 Score: 558
Period size: 162 Copynumber: 1.8 Consensus size: 164
4463 CGCCGCCATA
4473 TTAATATATGGAGGGAGAGATTTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCCCCACTAA
1 TTAATATATGGAGGGAGAGATTTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCCCCACTAA
*
4538 AACAAAGAAATTTTCCAACTCTACACCTATAATATATAGCGGCGTTTGGACATCAAACGCCGCTA
66 AACAAAGAAATTTTACAACTCTACACCTATAATATATAGCGGCGTTTGGACATCAAACGCCGCTA
4603 ATTAGTGGCGTCTAGAAAAGGAAACACCGCTATT
131 ATTAGTGGCGTCTAGAAAAGGAAACACCGCTATT
4637 TTAATATATGGAGGGAGAGA-TTTTTTTC-CCTTTTTTTGGAGGGAAAAATTCCCTCCCCACTAA
1 TTAATATATGGAGGGAGAGATTTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCCCCACTAA
*
4700 AACAAAGAAATTTTACAACTCTACACCTGTAATATATAGCGGCGTTTGGACATCAAACGCCGCTA
66 AACAAAGAAATTTTACAACTCTACACCTATAATATATAGCGGCGTTTGGACATCAAACGCCGCTA
4765 ATT
131 ATT
4768 TAATATATGG
Statistics
Matches: 129, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
162 101 0.78
163 8 0.06
164 20 0.16
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (164 bp):
TTAATATATGGAGGGAGAGATTTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCCCCACTAA
AACAAAGAAATTTTACAACTCTACACCTATAATATATAGCGGCGTTTGGACATCAAACGCCGCTA
ATTAGTGGCGTCTAGAAAAGGAAACACCGCTATT
Found at i:4862 original size:130 final size:130
Alignment explanation
Indices: 4624--4876 Score: 470
Period size: 130 Copynumber: 1.9 Consensus size: 130
4614 CTAGAAAAGG
*
4624 AAACACCGCTATTTTAATATATGGAGGGAGAGATTTTTTTCCCTTTTTTTGGAGGGAAAAATTCC
1 AAACACCGCTAATTTAATATATGGAGGGAGAGATTTTTTTCCCTTTTTTTGGAGGGAAAAATTCC
4689 CTCCCCACTAAAACAAAGAAATTTTACAACTCTACACCTGTAATATATAGCGGCGTTTGGACATC
66 CTCCCCACTAAAACAAAGAAATTTTACAACTCTACACCTGTAATATATAGCGGCGTTTGGACATC
* *
4754 AAACGCCGCTAATTTAATATATGGAGGGATAGATTTTTTTCCCTTTTTTTGGAGGGAAAAATTCC
1 AAACACCGCTAATTTAATATATGGAGGGAGAGATTTTTTTCCCTTTTTTTGGAGGGAAAAATTCC
*
4819 CTCCCCACTAAAACAAAGAAATTTTACAACTCTTCACCTGTAATATATAGCGGCGTTT
66 CTCCCCACTAAAACAAAGAAATTTTACAACTCTACACCTGTAATATATAGCGGCGTTT
4877 TCCCACAAGA
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
130 119 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (130 bp):
AAACACCGCTAATTTAATATATGGAGGGAGAGATTTTTTTCCCTTTTTTTGGAGGGAAAAATTCC
CTCCCCACTAAAACAAAGAAATTTTACAACTCTACACCTGTAATATATAGCGGCGTTTGGACATC
Found at i:4904 original size:31 final size:31
Alignment explanation
Indices: 4866--4930 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
4856 CTGTAATATA
4866 TAGCGGCGTTTTCCCA-CAAGACGCCGCTATT
1 TAGCGGCGTTTT-CCAGCAAGACGCCGCTATT
* *
4897 TAGCGGCGTTTTCTAGCTAGACGCCGCTATT
1 TAGCGGCGTTTTCCAGCAAGACGCCGCTATT
4928 TAG
1 TAG
4931 TGGCATCTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.18, C:0.28, G:0.25, T:0.29
Consensus pattern (31 bp):
TAGCGGCGTTTTCCAGCAAGACGCCGCTATT
Found at i:9937 original size:32 final size:33
Alignment explanation
Indices: 9901--9974 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 33
9891 TGCTGGCAAA
*
9901 TAGCGGCGTCT-ATCGAA-ACAAACGCC-CTTATT
1 TAGCGGCGTCTAAT-GAAGA-AAACGCCGCTAATT
9933 TAGCGGCGTCTAATGAAGAAAACGCCGCTAATT
1 TAGCGGCGTCTAATGAAGAAAACGCCGCTAATT
*
9966 TAGTGGCGT
1 TAGCGGCGT
9975 TTAAGGCCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
32 21 0.57
33 16 0.43
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.24
Consensus pattern (33 bp):
TAGCGGCGTCTAATGAAGAAAACGCCGCTAATT
Found at i:10495 original size:17 final size:17
Alignment explanation
Indices: 10473--10507 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
10463 GAAAAAGTGC
10473 ATTCTTGTGGGTACATT
1 ATTCTTGTGGGTACATT
* *
10490 ATTCTTGTTGGTATATT
1 ATTCTTGTGGGTACATT
10507 A
1 A
10508 ACATTATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.51
Consensus pattern (17 bp):
ATTCTTGTGGGTACATT
Found at i:12078 original size:32 final size:32
Alignment explanation
Indices: 12042--12187 Score: 229
Period size: 32 Copynumber: 4.5 Consensus size: 32
12032 GTGTGAAAAG
* *
12042 AAAACGCCCTTATTTAGCTGCGTCTATAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
*
12074 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
12106 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
**
12138 AAAACGCCCTTATTTAGCGGCGTCTACATTAC
1 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
12170 AAAACGCCGCTATATTTA
1 AAAACGCC-CT-TATTTA
12188 ATTGCTTTTA
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
32 100 0.93
33 2 0.02
34 6 0.06
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (32 bp):
AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
Done.