Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017176.1 Corchorus olitorius cultivar O-4 contig17209, 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: 31007
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:817 original size:14 final size:14
Alignment explanation
Indices: 798--828 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
788 GAAACTATTA
798 AACCTGACATAAGT
1 AACCTGACATAAGT
*
812 AACCTGAGATAAGT
1 AACCTGACATAAGT
826 AAC
1 AAC
829 AATCTTCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (14 bp):
AACCTGACATAAGT
Found at i:17228 original size:24 final size:24
Alignment explanation
Indices: 17196--17243 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
17186 CGTTGGCTGG
17196 AGATTTTGGCTTCTTACTATCATC
1 AGATTTTGGCTTCTTACTATCATC
17220 AGATTTTGGCTTCTTACTATCATC
1 AGATTTTGGCTTCTTACTATCATC
17244 GACGCCACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (24 bp):
AGATTTTGGCTTCTTACTATCATC
Found at i:21337 original size:27 final size:28
Alignment explanation
Indices: 21299--21368 Score: 124
Period size: 27 Copynumber: 2.5 Consensus size: 28
21289 AGTAGGTATT
21299 AAGGTGATTATTTATCGTACCAAAA-AA
1 AAGGTGATTATTTATCGTACCAAAATAA
21326 AAGGTGATTATTTATCGTACCAAAATAA
1 AAGGTGATTATTTATCGTACCAAAATAA
*
21354 AAGGTGATTACTTAT
1 AAGGTGATTATTTAT
21369 GTCAATTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 25 0.61
28 16 0.39
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (28 bp):
AAGGTGATTATTTATCGTACCAAAATAA
Found at i:22077 original size:40 final size:40
Alignment explanation
Indices: 22022--22101 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
22012 AGCTCAACTT
22022 TAGCTCCAAATCAGTCGGGACACAATGTAATTATAAGATA
1 TAGCTCCAAATCAGTCGGGACACAATGTAATTATAAGATA
22062 TAGCTCCAAATCAGTCGGGACACAATGTAATTATAAGATA
1 TAGCTCCAAATCAGTCGGGACACAATGTAATTATAAGATA
22102 CAAGGATCGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (40 bp):
TAGCTCCAAATCAGTCGGGACACAATGTAATTATAAGATA
Found at i:27879 original size:316 final size:315
Alignment explanation
Indices: 27302--27925 Score: 1122
Period size: 316 Copynumber: 2.0 Consensus size: 315
27292 TCTTATTCAC
* *
27302 GCTCTATCATTTTCATTTTACCTCTTTCTGTGTCAGTTTTGCTCAGAACTAATCCAGACTCGATC
1 GCTCTATCATTTTCATTTTACCTCTTTCTATGTCAGTTTTGCTCAGAACTAATCCAGACCCGATC
*
27367 CGCATTAGTTTTAATATTTGATATTTTTTTAAATAAAATAATCTTGATAAGTGTCTTACTGTACT
66 CGCATTAGTTTTAATATTTGACATTTTTTTAAATAAAATAATCTTGATAAGTGTCTTACTGTACT
*
27432 GGCTTGAGGCTTACTTCACATTATGTATACTATGAGGAAAGTAATCATTAGACTTAGCAATTCAG
131 GGCTTGAGGCTTACTTCACACTATGTATACTATGAGGAAAGTAATCATTAGACTTAGCAATTCAG
* * *
27497 GTTATGACACGACACGATACGAGAAACGTTTAATTGTGTTTGTGTTTGACTTATCGTGTTTCATG
196 GTTATGACACGACACGACACGAGAAACGTTTAATTGTGTTTGTGTTTGACTTATCATGTCTCATG
27562 TCTGCAGCGTGTCGAACACGATTAGAATAATCATGTTTCGTGTTAAAGTAATCAT
261 TCTGCAGCGTGTCGAACACGATTAGAATAATCATGTTTCGTGTTAAAGTAATCAT
*
27617 GCTCTATCATTTTCATTTTACCTCTTTCTATGTCAGTTTTGCTCTGAACTAATCCAGACCCGATC
1 GCTCTATCATTTTCATTTTACCTCTTTCTATGTCAGTTTTGCTCAGAACTAATCCAGACCCGATC
*
27682 CGCATTAGTTTTAGTATTTGACATTTTTTTTAAATAAAATAATCTTGATAAGTGTCTTACTGTAC
66 CGCATTAGTTTTAATATTTGACA-TTTTTTTAAATAAAATAATCTTGATAAGTGTCTTACTGTAC
* *
27747 TGGCTTGAGGCTTACTTCACACTATGTATATTATGAGGAAAGTAATCATTAGACTTGGCAATTCA
130 TGGCTTGAGGCTTACTTCACACTATGTATACTATGAGGAAAGTAATCATTAGACTTAGCAATTCA
*
27812 GGTTATGACACGACATGACACGAGAAACGTTTAATTGTGTTTGTGTTTGACTTATCATGTCTCAT
195 GGTTATGACACGACACGACACGAGAAACGTTTAATTGTGTTTGTGTTTGACTTATCATGTCTCAT
*
27877 GTCTGCAGCGTGTCGAACACGATTAGGATAATCATGTTTCGTGTTAAAG
260 GTCTGCAGCGTGTCGAACACGATTAGAATAATCATGTTTCGTGTTAAAG
27926 ACATGTTTAA
Statistics
Matches: 295, Mismatches: 13, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
315 83 0.28
316 212 0.72
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (315 bp):
GCTCTATCATTTTCATTTTACCTCTTTCTATGTCAGTTTTGCTCAGAACTAATCCAGACCCGATC
CGCATTAGTTTTAATATTTGACATTTTTTTAAATAAAATAATCTTGATAAGTGTCTTACTGTACT
GGCTTGAGGCTTACTTCACACTATGTATACTATGAGGAAAGTAATCATTAGACTTAGCAATTCAG
GTTATGACACGACACGACACGAGAAACGTTTAATTGTGTTTGTGTTTGACTTATCATGTCTCATG
TCTGCAGCGTGTCGAACACGATTAGAATAATCATGTTTCGTGTTAAAGTAATCAT
Found at i:28747 original size:23 final size:24
Alignment explanation
Indices: 28696--28747 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
28686 GTTGATGATT
*
28696 AAATTGTTATACGAATGGTTTAAAA
1 AAATTGTTATACAAAT-GTTTAAAA
*
28721 AAATTGTTATACAAAT-TTTAAAG
1 AAATTGTTATACAAATGTTTAAAA
28744 AAAT
1 AAAT
28748 AATAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.40
25 15 0.60
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.37
Consensus pattern (24 bp):
AAATTGTTATACAAATGTTTAAAA
Found at i:30845 original size:23 final size:23
Alignment explanation
Indices: 30774--30845 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
30764 TATATATATA
30774 TATTATGTTTA-TTACTAATG-TG
1 TATTATGTTTATTTA-TAATGTTG
* *
30796 ATATTTAT-ATTATTAAT-ATGTAT-
1 -TA-TTATGTTTATTTATAATGT-TG
30819 TATTATGTTTATTTATAATGTTG
1 TATTATGTTTATTTATAATGTTG
30842 TATT
1 TATT
30846 TATTGATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
21 4 0.11
22 13 0.34
23 14 0.37
24 7 0.18
ACGTcount: A:0.31, C:0.01, G:0.10, T:0.58
Consensus pattern (23 bp):
TATTATGTTTATTTATAATGTTG
Done.