Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023214.1 Corchorus olitorius cultivar O-4 contig23247, 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: 70981
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:14517 original size:29 final size:27
Alignment explanation
Indices: 14427--14521 Score: 95
Period size: 29 Copynumber: 3.4 Consensus size: 27
14417 TCTGAACATA
*
14427 CAAATGACCAAAATGCCCCTAGGTGTAT
1 CAAATGACCAAAATGCCCCTAGTTGT-T
* *
14455 -AAATGACCAAAATGCCCCTGAATTTTT
1 CAAATGACCAAAATGCCCCT-AGTTGTT
14482 GCAAATGACCAAAATGCCCCCTAGTTGATT
1 -CAAATGACCAAAATG-CCCCTAGTTG-TT
*
14512 CTAATG-CCAA
1 CAAATGACCAA
14522 TTAAGAAATA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
27 20 0.36
28 7 0.12
29 22 0.39
30 7 0.12
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (27 bp):
CAAATGACCAAAATGCCCCTAGTTGTT
Found at i:20179 original size:26 final size:26
Alignment explanation
Indices: 20150--20213 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
20140 AAAATACACA
*
20150 AAAATATATTTTAATAGTG-CATAATT
1 AAAATATATTTTAATAATGACA-AATT
* *
20176 AAAATATTTTTTAATAATGACAATTT
1 AAAATATATTTTAATAATGACAAATT
20202 AGAAATATATTT
1 A-AAATATATTT
20214 GAAAAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 21 0.66
27 11 0.34
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (26 bp):
AAAATATATTTTAATAATGACAAATT
Found at i:21282 original size:13 final size:13
Alignment explanation
Indices: 21264--21288 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21254 TTAGAATTCC
21264 AAATAATATTTAT
1 AAATAATATTTAT
21277 AAATAATATTTA
1 AAATAATATTTA
21289 GAACATTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:21868 original size:12 final size:12
Alignment explanation
Indices: 21851--21875 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21841 TATCGTTTAA
21851 AAAGATCATATT
1 AAAGATCATATT
21863 AAAGATCATATT
1 AAAGATCATATT
21875 A
1 A
21876 GGATTTATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
AAAGATCATATT
Found at i:22238 original size:12 final size:12
Alignment explanation
Indices: 22214--22247 Score: 50
Period size: 12 Copynumber: 2.7 Consensus size: 12
22204 AAAGTTTGGT
22214 TTTGAAGAAGTGC
1 TTTGAA-AAGTGC
22227 TTTGAAAAGTGC
1 TTTGAAAAGTGC
22239 TTTGTAAAA
1 TTTG-AAAA
22248 TTGAGGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (12 bp):
TTTGAAAAGTGC
Found at i:28049 original size:16 final size:15
Alignment explanation
Indices: 28011--28049 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
28001 ACAGAGATTG
*
28011 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
28026 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
28041 ACTAGAAAA
1 AC-AGAAAA
28050 TAAAGCAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.64, C:0.13, G:0.10, T:0.13
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:31440 original size:30 final size:31
Alignment explanation
Indices: 31404--31461 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
31394 GTACACCATC
31404 AACTTCATT-ATCT-AAATTCTCAGCAACATT
1 AACTTCATTCA-CTAAAATTCTCAGCAACATT
*
31434 AACTTCATTCACTAAAATTTTCAGCAAC
1 AACTTCATTCACTAAAATTCTCAGCAAC
31462 TTGAACATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.34
Consensus pattern (31 bp):
AACTTCATTCACTAAAATTCTCAGCAACATT
Found at i:34795 original size:12 final size:13
Alignment explanation
Indices: 34778--34810 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
34768 CAATACCTCA
34778 ATATATCCG-TCG
1 ATATATCCGTTCG
*
34790 ATATATCCGTTCT
1 ATATATCCGTTCG
34803 ATATATCC
1 ATATATCC
34811 ATTGATATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.39
Consensus pattern (13 bp):
ATATATCCGTTCG
Found at i:43013 original size:41 final size:41
Alignment explanation
Indices: 42956--43034 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
42946 GTAAAAACTT
42956 AAATAATGCTGAATTATCTACATAATCCAAAGGGGTACGTG
1 AAATAATGCTGAATTATCTACATAATCCAAAGGGGTACGTG
*
42997 AAATAATGCTGAATTATCTACATAATCCAGAGGGGTAC
1 AAATAATGCTGAATTATCTACATAATCCAAAGGGGTAC
43035 ATGCAAATCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (41 bp):
AAATAATGCTGAATTATCTACATAATCCAAAGGGGTACGTG
Found at i:53315 original size:6 final size:6
Alignment explanation
Indices: 53304--53337 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
53294 AATGGGGGGA
53304 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGA
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGA
53338 ACAAAAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:69627 original size:16 final size:16
Alignment explanation
Indices: 69594--69641 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
69584 TTTGGCATCG
*
69594 TTTTCGTTTTCTTTTT
1 TTTTCGTTTTGTTTTT
69610 TTTTC-TTTTGTTTCTT
1 TTTTCGTTTTGTTT-TT
*
69626 TTGTCGTTTTGTTTTT
1 TTTTCGTTTTGTTTTT
69642 GTTGCGTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 7 0.25
16 13 0.46
17 8 0.29
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.79
Consensus pattern (16 bp):
TTTTCGTTTTGTTTTT
Found at i:70956 original size:2 final size:2
Alignment explanation
Indices: 70951--70979 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
70941 ATTATTGCAT
70951 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
70980 TA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.