Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008232.1 Corchorus olitorius cultivar O-4 contig08259, 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, 643
Length: 1072
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Found at i:363 original size:116 final size:116
Alignment explanation
Indices: 9--380 Score: 480
Period size: 116 Copynumber: 3.2 Consensus size: 116
1 GTTTTTAA
*
9 AAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTTAAAAAA
1 AAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTCATCTTG--TTT--AAAA
* * * * *
74 TCCTGTTCGAGGTCTCTGTTAGGGAGTTTTCAATTCAAAA-TCTAACCTGACTTCT
62 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTTATCTTGA-TTTT
**
129 AAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAAAACAAAATCTCAT-TTCGTTTAAAATCC
1 AAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTCATCTT-GTTTAAAATCC
* *
193 TGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTT
65 TGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTTATCTTGATTTT
* * * * *
245 AAAATCCTATTAGAGATCTCTGTTACAGAGTTTTCAATTCAAAATCTCATCTTGTCCTAAAATCC
1 AAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTCATCTTGT-TTAAAATCC
**
310 TGTTCGAGAACTCTGTTAGAGAGTTTTCAATTCAAAATTTTATCTTG-TTTT
65 TGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTTATCTTGATTTT
* * *
361 AAACTCCTGGTCGAGATCTC
1 AAAATCCTGTTCGAGGTCTC
381 CATTTGAGAG
Statistics
Matches: 224, Mismatches: 24, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
116 112 0.50
117 59 0.26
118 3 0.01
119 2 0.01
120 48 0.21
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (116 bp):
AAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTCATCTTGTTTAAAATCCT
GTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTTATCTTGATTTT
Found at i:391 original size:58 final size:59
Alignment explanation
Indices: 9--380 Score: 468
Period size: 59 Copynumber: 6.3 Consensus size: 59
1 GTTTTTAA
*
9 AAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTT
1 AAAATCCTGTTCGAGATCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTT
* * * * * *
68 AAAAAATCCTGTTCGAGGTCTCTGTTAGGGAGTTTTCAATTCAAAATC-TAACCTGACTTCT
1 --AAAATCCTGTTCGAGATCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTG-TTTTT
* ** *
129 AAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAAAACAAAATCTCAT-TTCG--TTT
1 AAAATCCTGTTCGAGATCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTT-GTTTTT
*
186 AAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTT
1 AAAATCCTGTTCGAGATCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTT
* * * * **
245 AAAATCCTATTAGAGATCTCTGTTACAGAGTTTTCAATTCAAAATCTCATCTTG-TCCT
1 AAAATCCTGTTCGAGATCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTT
* *
303 AAAATCCTGTTCGAGAACTCTGTTAGAGAGTTTTCAATTCAAAATTTTATCTTG-TTTT
1 AAAATCCTGTTCGAGATCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTT
* *
361 AAACTCCTGGTCGAGATCTC
1 AAAATCCTGTTCGAGATCTC
381 CATTTGAGAG
Statistics
Matches: 272, Mismatches: 33, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
57 50 0.18
58 71 0.26
59 96 0.35
60 7 0.03
61 48 0.18
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (59 bp):
AAAATCCTGTTCGAGATCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTT
Found at i:669 original size:29 final size:29
Alignment explanation
Indices: 636--873 Score: 228
Period size: 29 Copynumber: 8.1 Consensus size: 29
626 TCGCACGCTC
* *
636 AGGGGAATTTTGGTCATTTTTGCATATAT
1 AGGGGCATTTTGGTCATTTTTGCATATCT
* * *
665 GGGGGCATTTTGGTCATTTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCATATCT
* * ***
694 GGAGGGCATTTTGGTTATTTCCACATATCT
1 AG-GGGCATTTTGGTCATTTTTGCATATCT
*
724 AGGGGCATTCTGGTCATTTTTGCATA-CT
1 AGGGGCATTTTGGTCATTTTTGCATATCT
*
752 CAGGGGCATTTTGGTCATTTTTGCACATCT
1 -AGGGGCATTTTGGTCATTTTTGCATATCT
* * *
782 AGGAGCATTTTGGTCATTCTTGCATATCC
1 AGGGGCATTTTGGTCATTTTTGCATATCT
* * * *
811 AGGGGCATTTCGGTCATCTTTACACATTCT
1 AGGGGCATTTTGGTCATTTTTGCATA-TCT
* *
841 -GGGGCAGTTTGGTTATTTTTTGCATACTCT
1 AGGGGCATTTTGGTCA-TTTTTGCATA-TCT
871 AGG
1 AGG
874 TTCTCTTTGG
Statistics
Matches: 166, Mismatches: 37, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
28 2 0.01
29 126 0.76
30 36 0.22
31 2 0.01
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.40
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTGCATATCT
Found at i:861 original size:117 final size:117
Alignment explanation
Indices: 633--869 Score: 302
Period size: 117 Copynumber: 2.0 Consensus size: 117
623 CATTCGCACG
* * * * *
633 CTCAGGGGAATTTTGGTCATTTTTGCATATATGGGGGCATTTTGGTCATTTTTGCACATCCGGAG
1 CTCAGGGGAATTTTGGTCATTTTTGCACATATAGGAGCATTTTGGTCATTCTTGCACATCCAGAG
* *
698 GGCATTTTGGTTATTTCCACATATCTAGGGGCATTCTGGTCATTTTTGCATA
66 GGCATTTCGGTTATTTACACATATCTAGGGGCATTCTGGTCATTTTTGCATA
* * *
750 CTCAGGGGCATTTTGGTCATTTTTGCACATCTAGGAGCATTTTGGTCATTCTTGCATATCCAG-G
1 CTCAGGGGAATTTTGGTCATTTTTGCACATATAGGAGCATTTTGGTCATTCTTGCACATCCAGAG
* *
814 GGCATTTCGGTCATCTTTACACAT-TCT-GGGGCAGTT-TGGTTATTTTTTGCATA
66 GGCATTTCGGT--TATTTACACATATCTAGGGGCA-TTCTGGTCA-TTTTTGCATA
867 CTC
1 CTC
870 TAGGTTCTCT
Statistics
Matches: 104, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
116 22 0.21
117 73 0.70
118 9 0.09
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (117 bp):
CTCAGGGGAATTTTGGTCATTTTTGCACATATAGGAGCATTTTGGTCATTCTTGCACATCCAGAG
GGCATTTCGGTTATTTACACATATCTAGGGGCATTCTGGTCATTTTTGCATA
Done.