Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007722.1 Corchorus olitorius cultivar O-4 contig07748, 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: 5662
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:437 original size:18 final size:18
Alignment explanation
Indices: 414--450 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
404 ACGCCGCCCT
414 TGGGCGGCATGACCATGG
1 TGGGCGGCATGACCATGG
* *
432 TGGGCGGCGTGGCCATGG
1 TGGGCGGCATGACCATGG
450 T
1 T
451 CATGCCGCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.22, G:0.49, T:0.19
Consensus pattern (18 bp):
TGGGCGGCATGACCATGG
Found at i:1426 original size:53 final size:53
Alignment explanation
Indices: 1341--1453 Score: 190
Period size: 53 Copynumber: 2.1 Consensus size: 53
1331 ATCCCGTGAG
* * *
1341 ATTTAAAACCCAAGATCTCACAATCCAGACACGGTGCAAATACCAGTTGAGCT
1 ATTTCAAACCCAAGACCTCACAATCCAGACACGGTGCAAATACCAATTGAGCT
*
1394 ATTTCAAACCCAAGACCTCACAATCTAGACACGGTGCAAATACCAATTGAGCT
1 ATTTCAAACCCAAGACCTCACAATCCAGACACGGTGCAAATACCAATTGAGCT
1447 ATTTCAA
1 ATTTCAA
1454 GGCCCCCTGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (53 bp):
ATTTCAAACCCAAGACCTCACAATCCAGACACGGTGCAAATACCAATTGAGCT
Found at i:1511 original size:21 final size:22
Alignment explanation
Indices: 1481--1521 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1471 ATTATTATTA
*
1481 TTATTATTAT-TTTTTTAGAAT
1 TTATTATTATATATTTTAGAAT
*
1502 TTATTTTTATATATTTTAGA
1 TTATTATTATATATTTTAGA
1522 GATGTTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (22 bp):
TTATTATTATATATTTTAGAAT
Found at i:2042 original size:31 final size:31
Alignment explanation
Indices: 2001--2066 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
1991 CTCCAACAAG
* * *
2001 TTGAATCATTTTGACATTAACACTAATCAAA
1 TTGAACCATTTTGACATCAAAACTAATCAAA
2032 TTGAACCATTTTGACATCAAAACTAATCAAA
1 TTGAACCATTTTGACATCAAAACTAATCAAA
2063 TTGA
1 TTGA
2067 GCTTGACTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (31 bp):
TTGAACCATTTTGACATCAAAACTAATCAAA
Found at i:2800 original size:30 final size:30
Alignment explanation
Indices: 2739--2802 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
2729 TGGTATCAAA
* * * * *
2739 TTTTTTCAAAGAGATTCATAAGCAAATTTC
1 TTTTTTAAAAAAGAATCATAAACAAAATTC
*
2769 TTTTTTAAAAAAGAATCATAAATAAAATTC
1 TTTTTTAAAAAAGAATCATAAACAAAATTC
2799 TTTT
1 TTTT
2803 GTCAGAATGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (30 bp):
TTTTTTAAAAAAGAATCATAAACAAAATTC
Found at i:3271 original size:24 final size:24
Alignment explanation
Indices: 3244--3290 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
3234 TTAATTTTTT
3244 ATTTTTCTTCCATCTTCTTCCTCG
1 ATTTTTCTTCCATCTTCTTCCTCG
3268 ATTTTTCTTCCATCTTCTTCCTC
1 ATTTTTCTTCCATCTTCTTCCTC
3291 TATGCTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.09, C:0.34, G:0.02, T:0.55
Consensus pattern (24 bp):
ATTTTTCTTCCATCTTCTTCCTCG
Found at i:3299 original size:24 final size:24
Alignment explanation
Indices: 3248--3310 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
3238 TTTTTTATTT
**
3248 TTCTTCCATCTTCTTCCTCGATTT
1 TTCTTCCATCTTCTTCCTCGATGC
*
3272 TTCTTCCATCTTCTTCCTCTATGC
1 TTCTTCCATCTTCTTCCTCGATGC
*
3296 TTC-TCCATCTCCTTC
1 TTCTTCCATCTTCTTC
3311 GATTCTCCCC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
23 11 0.31
24 24 0.69
ACGTcount: A:0.08, C:0.38, G:0.03, T:0.51
Consensus pattern (24 bp):
TTCTTCCATCTTCTTCCTCGATGC
Found at i:3946 original size:34 final size:34
Alignment explanation
Indices: 3908--3973 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 34
3898 AATTTTTGTT
*
3908 TCTGGTGTTGCAATTTTGTTGAATCTGG-GTTGGA
1 TCTGGTGCTG-AATTTTGTTGAATCTGGTGTTGGA
*
3942 TCTGGTGCTGTATTTTGTTGAATCTGGTGTTG
1 TCTGGTGCTGAATTTTGTTGAATCTGGTGTTG
3974 TATTTCGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 16 0.55
34 13 0.45
ACGTcount: A:0.12, C:0.09, G:0.32, T:0.47
Consensus pattern (34 bp):
TCTGGTGCTGAATTTTGTTGAATCTGGTGTTGGA
Found at i:3993 original size:22 final size:22
Alignment explanation
Indices: 3936--3995 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
3926 TTGAATCTGG
* * *
3936 GTTGGATCTGGTGCTGTATTTT
1 GTTGAATCTGGTGTTGTATTTC
3958 GTTGAATCTGGTGTTGTATTTC
1 GTTGAATCTGGTGTTGTATTTC
3980 GTTGAATCTGGTGTTG
1 GTTGAATCTGGTGTTG
3996 CAAATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.12, C:0.08, G:0.32, T:0.48
Consensus pattern (22 bp):
GTTGAATCTGGTGTTGTATTTC
Found at i:5067 original size:66 final size:66
Alignment explanation
Indices: 4961--5094 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
4951 TCATTGAACA
4961 AACAATTAGTCCATTGAATTAACCAAGTAGATACATTATGTATGTTCATTATCATGTATCAATAT
1 AACAATTAGTCCATTGAATTAACCAAGTAGATACATTATGTATGTTCATTATCATGTATCAATAT
5026 T
66 T
5027 AACAATTAGTCCATTGAATTAACCAAGTAGATACATTATGTATGTTCATTATCATGTATCAATAT
1 AACAATTAGTCCATTGAATTAACCAAGTAGATACATTATGTATGTTCATTATCATGTATCAATAT
5092 T
66 T
5093 AA
1 AA
5095 TTAAGATACA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.37
Consensus pattern (66 bp):
AACAATTAGTCCATTGAATTAACCAAGTAGATACATTATGTATGTTCATTATCATGTATCAATAT
T
Done.