Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012989.1 Corchorus olitorius cultivar O-4 contig13022, 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: 28906
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:437 original size:16 final size:15
Alignment explanation
Indices: 399--440 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
389 ACAGAGGTTG
*
399 ACAGAAAATAATTAA
1 ACAGAAAACAATTAA
414 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
429 ACTAGAAAACAA
1 AC-AGAAAACAA
441 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.67, C:0.12, G:0.07, T:0.14
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:4276 original size:55 final size:55
Alignment explanation
Indices: 4216--4326 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
4206 TTGTGTGGAA
4216 ATGCAATGTTGTGAATTTTGGGGTTAAGAAGTACTAGAAATTGTTAATTTTATAT
1 ATGCAATGTTGTGAATTTTGGGGTTAAGAAGTACTAGAAATTGTTAATTTTATAT
4271 ATGCAATGTTGTGAATTTTGGGGTTAAGAAGTACTAGAAATTGTTAATTTTATAT
1 ATGCAATGTTGTGAATTTTGGGGTTAAGAAGTACTAGAAATTGTTAATTTTATAT
4326 A
1 A
4327 ATATATATAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.41
Consensus pattern (55 bp):
ATGCAATGTTGTGAATTTTGGGGTTAAGAAGTACTAGAAATTGTTAATTTTATAT
Found at i:4332 original size:2 final size:2
Alignment explanation
Indices: 4321--4350 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4311 TTGTTAATTT
4321 TA TA TA -A 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 TA T
4351 TTAAGGGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24293 original size:276 final size:275
Alignment explanation
Indices: 23800--24350 Score: 960
Period size: 276 Copynumber: 2.0 Consensus size: 275
23790 AAGCTATTTT
* *
23800 AAAGTGATTGCACAAACGGTTATGAAACTGAGCGTCAGGTGGGCGGGTTGGGAGGATCTGGGCTA
1 AAAGTGATTGCACAAAAGGCTATGAAACTGAGCGTCAGGTGGGCGGGTTGGGAGGATCTGGGCTA
*
23865 AATAGGTTTACCGATCGCTAGACTAGATAATGCCGGACATAAAGGTATACGATCTCGATGTATAC
66 AATAGGTTTACCGATCGCAAGACTAGATAATGCCGGACATAAAGGTATACGATCTCGATGTATAC
* *
23930 TCCATGTGGAGAGTGTTGAATCGTAGAATGCTCAATTTGGTAGTGTGCCCCTCTGTCGAACTATG
131 TCCATGTGGAGAGTGTTGAATCGTAGAACGCTCAATTTGGTAGTGCGCCCCTCTGTCGAACTATG
* * * *
23995 GTGCTCTGTGAGACGAATGAGAGATATTCCATGAATGCCAAAAAGGGGAGCACTGAATTTGATGA
196 ATGCTCTGTAAGACGAATGAGAGATATTCCATGAATACCAAAAAGGGGAGCACTGAA-TTGAGGA
24060 TCGAGTAGGAGAGTGC
260 TCGAGTAGGAGAGTGC
*
24076 AAAGTGATTGCACAAAAGGCTATGAAACTGAGTGTCAGGTGGGCGGGTTGGGAGGATCTGGGCTA
1 AAAGTGATTGCACAAAAGGCTATGAAACTGAGCGTCAGGTGGGCGGGTTGGGAGGATCTGGGCTA
**
24141 AATAGGTTTATTGATCGCAAGACTAGATAATGCCGGACAT-AAGAGTATACGATCTCGATGTATA
66 AATAGGTTTACCGATCGCAAGACTAGATAATGCCGGACATAAAG-GTATACGATCTCGATGTATA
24205 CTCCATGTGGAGAGTGTTGAATCGTAGAACGCTCAATTTGGTAGTGCGCCCCTCTGTCGAACTAT
130 CTCCATGTGGAGAGTGTTGAATCGTAGAACGCTCAATTTGGTAGTGCGCCCCTCTGTCGAACTAT
24270 GATGCTCTGTAAGACGAATGAGAGATATTCCATGAATACCAAAAAGGGGAGCACTGAATTGAGGA
195 GATGCTCTGTAAGACGAATGAGAGATATTCCATGAATACCAAAAAGGGGAGCACTGAATTGAGGA
*
24335 TTGAGTAGGAGAGTGC
260 TCGAGTAGGAGAGTGC
24351 GCTCTAGGAA
Statistics
Matches: 261, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
275 24 0.09
276 237 0.91
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (275 bp):
AAAGTGATTGCACAAAAGGCTATGAAACTGAGCGTCAGGTGGGCGGGTTGGGAGGATCTGGGCTA
AATAGGTTTACCGATCGCAAGACTAGATAATGCCGGACATAAAGGTATACGATCTCGATGTATAC
TCCATGTGGAGAGTGTTGAATCGTAGAACGCTCAATTTGGTAGTGCGCCCCTCTGTCGAACTATG
ATGCTCTGTAAGACGAATGAGAGATATTCCATGAATACCAAAAAGGGGAGCACTGAATTGAGGAT
CGAGTAGGAGAGTGC
Found at i:26200 original size:53 final size:53
Alignment explanation
Indices: 26141--26241 Score: 166
Period size: 53 Copynumber: 1.9 Consensus size: 53
26131 CAAATCCTTA
** *
26141 TAAATATTTGAATCTTAATAAAAAGATTGAGTTTTCACCAACAAAATATATCC
1 TAAATATTTGAATCTTAATAAAAAGATTGAACTATCACCAACAAAATATATCC
*
26194 TAAATATTTGAATCTTAATAAAAAGATTGAACTATCACTAACAAAATA
1 TAAATATTTGAATCTTAATAAAAAGATTGAACTATCACCAACAAAATA
26242 AGTATACTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.33
Consensus pattern (53 bp):
TAAATATTTGAATCTTAATAAAAAGATTGAACTATCACCAACAAAATATATCC
Found at i:27426 original size:67 final size:67
Alignment explanation
Indices: 27343--27479 Score: 274
Period size: 67 Copynumber: 2.0 Consensus size: 67
27333 CTTACGCTGC
27343 TCCTCCAACAAAATCTAAGAATTTTGAAGCAAGTCCAGATTGCATCAGAGTATGGAAAATATATA
1 TCCTCCAACAAAATCTAAGAATTTTGAAGCAAGTCCAGATTGCATCAGAGTATGGAAAATATATA
27408 AA
66 AA
27410 TCCTCCAACAAAATCTAAGAATTTTGAAGCAAGTCCAGATTGCATCAGAGTATGGAAAATATATA
1 TCCTCCAACAAAATCTAAGAATTTTGAAGCAAGTCCAGATTGCATCAGAGTATGGAAAATATATA
27475 AA
66 AA
27477 TCC
1 TCC
27480 AGTACTATTG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.26
Consensus pattern (67 bp):
TCCTCCAACAAAATCTAAGAATTTTGAAGCAAGTCCAGATTGCATCAGAGTATGGAAAATATATA
AA
Done.