Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015574.1 Corchorus olitorius cultivar O-4 contig15607, 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: 39126
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:261 original size:51 final size:52
Alignment explanation
Indices: 160--261 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 52
150 GTTCATCAAA
* **
160 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGTTT
1 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
* *
212 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TTCTCCTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGTT
262 CTTCATTCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 2 0.05
51 36 0.84
52 5 0.12
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (52 bp):
TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
Found at i:6734 original size:20 final size:19
Alignment explanation
Indices: 6700--6737 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
6690 ATATTTACTA
*
6700 AAAACAATTAGAGGTTATC
1 AAAACAATTAAAGGTTATC
6719 AAAACAATTATAAGGTTAT
1 AAAACAATTA-AAGGTTAT
6738 TAATAAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAACAATTAAAGGTTATC
Found at i:7727 original size:43 final size:43
Alignment explanation
Indices: 7674--7761 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
7664 TAGCTCCTCT
7674 TTTTTTATAGGTTATTCCTAACTACCAACTTCTTCCCTCTGTG
1 TTTTTTATAGGTTATTCCTAACTACCAACTTCTTCCCTCTGTG
*
7717 TTTTTTATAGGTTATTTCTAACTACCAACTTCTTCCCTCTGTG
1 TTTTTTATAGGTTATTCCTAACTACCAACTTCTTCCCTCTGTG
7760 TT
1 TT
7762 CATAGAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.18, C:0.24, G:0.09, T:0.49
Consensus pattern (43 bp):
TTTTTTATAGGTTATTCCTAACTACCAACTTCTTCCCTCTGTG
Found at i:7917 original size:48 final size:48
Alignment explanation
Indices: 7865--7962 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
7855 ACGTTAATTT
* * *
7865 AATACCAAAATATTATGAGATTAGAGCAAATCATAACACTTATGAATC
1 AATACAAAAATATCATGAGATTAGAGCAAATCATAACACTCATGAATC
7913 AATACAAAAATATCATGAGATTAGAGCAAATCATAACACTCATGAATC
1 AATACAAAAATATCATGAGATTAGAGCAAATCATAACACTCATGAATC
7961 AA
1 AA
7963 AATAGATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.24
Consensus pattern (48 bp):
AATACAAAAATATCATGAGATTAGAGCAAATCATAACACTCATGAATC
Found at i:8423 original size:2 final size:2
Alignment explanation
Indices: 8416--8448 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
8406 GAAATGGCCA
8416 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8449 ATTGGTACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8843 original size:15 final size:15
Alignment explanation
Indices: 8823--8866 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
8813 GGCTTACTCA
8823 AGCTTTGTCTCTCTT
1 AGCTTTGTCTCTCTT
8838 AGCTTTGTCTCTCTT
1 AGCTTTGTCTCTCTT
* *
8853 AGCTCTCTCTCTCT
1 AGCTTTGTCTCTCT
8867 CTCTACAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.07, C:0.32, G:0.11, T:0.50
Consensus pattern (15 bp):
AGCTTTGTCTCTCTT
Found at i:34437 original size:22 final size:21
Alignment explanation
Indices: 34412--34465 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
34402 GAAGTTCGTG
34412 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
34434 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
34453 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
34466 TCAAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:36984 original size:17 final size:18
Alignment explanation
Indices: 36957--36995 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
36947 TGTCTTTAAC
36957 ATATGTATATAATTAT-TT
1 ATATGTATAT-ATTATATT
36975 ATAT-TATATATTATATT
1 ATATGTATATATTATATT
36992 ATAT
1 ATAT
36996 ATAATATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 5 0.25
17 11 0.55
18 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
ATATGTATATATTATATT
Found at i:36988 original size:12 final size:12
Alignment explanation
Indices: 36973--37002 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
36963 ATATAATTAT
36973 TTATATTATATA
1 TTATATTATATA
36985 TTATATTATATA
1 TTATATTATATA
*
36997 TAATAT
1 TTATAT
37003 AGTGTATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTATATTATATA
Found at i:37317 original size:23 final size:23
Alignment explanation
Indices: 37284--37337 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
37274 CAATAAATAT
*
37284 TATATTTAATTCTTAACGTTATA
1 TATATTTAATTCTTAACGTTACA
*
37307 TATTTTTAATTCTTAACGTTACA
1 TATATTTAATTCTTAACGTTACA
37330 TATATTTA
1 TATATTTA
37338 CGTTATTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (23 bp):
TATATTTAATTCTTAACGTTACA
Found at i:37648 original size:16 final size:17
Alignment explanation
Indices: 37627--37666 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
37617 TATAAATTAT
*
37627 TTTGTTGGTCTA-ATCC
1 TTTGTTGCTCTATATCC
37643 TTTGTTGCTCTATTATCC
1 TTTGTTGCTCTA-TATCC
37661 TTTGTT
1 TTTGTT
37667 TCTCAACTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
18 10 0.48
ACGTcount: A:0.10, C:0.17, G:0.15, T:0.57
Consensus pattern (17 bp):
TTTGTTGCTCTATATCC
Done.