Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020021.1 Corchorus olitorius cultivar O-4 contig20054, 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: 23295
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--34 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1 C
2 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
35 GAAAATCTAG
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:8454 original size:20 final size:19
Alignment explanation
Indices: 8417--8457 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
8407 TTGACACTGC
8417 AATAATAATTGTATTATTT
1 AATAATAATTGTATTATTT
8436 AATAA-AATTAGTGATTATTT
1 AATAATAATT-GT-ATTATTT
8456 AA
1 AA
8458 GAGAGAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
20 9 0.45
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (19 bp):
AATAATAATTGTATTATTT
Found at i:11924 original size:45 final size:45
Alignment explanation
Indices: 11860--11985 Score: 234
Period size: 45 Copynumber: 2.8 Consensus size: 45
11850 AGCAACAATT
*
11860 AATATTAGGTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
*
11905 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAT
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
11950 AATATTAGCTTTATTTTGATGAATTACCTAGAGATG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATG
11986 AAGTAGAATT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.38
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
Found at i:13673 original size:2 final size:2
Alignment explanation
Indices: 13668--13694 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13658 ACACACACAG
13668 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 A
13695 GTAAGAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15443 original size:2 final size:2
Alignment explanation
Indices: 15431--15466 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
15421 TGCCTCTATG
15431 TA TA T- TA 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 TA TA TA TA T
15467 TTCAGTTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:15961 original size:109 final size:109
Alignment explanation
Indices: 15763--15967 Score: 367
Period size: 108 Copynumber: 1.9 Consensus size: 109
15753 TGACATCTAC
15763 GGTGAAAACAAAGAGCCATGGAATCTGTTTAAGTTGAACGAAGACTCCCTGAATCTGAATCTTTT
1 GGTGAAAACAAAGAGCCATGGAATCTGTTTAAGTTGAACGAAGACTCCCTGAATCTGAATCTTTT
*
15828 TGGGTATTCACAAGGTTGAGAAAAAAGAGTGATAGATAGGCTAT
66 TAGGTATTCACAAGGTTGAGAAAAAAGAGTGATAGATAGGCTAT
*
15872 GGTGAAAACAAAGAGCCATGGAATTTGTTTAAGTTGAACGAAGACT-CCTGAATCTGAATCTTTT
1 GGTGAAAACAAAGAGCCATGGAATCTGTTTAAGTTGAACGAAGACTCCCTGAATCTGAATCTTTT
* *
15936 TAGGTATTCATAGGGTTGAGAAAAAAGAGTGA
66 TAGGTATTCACAAGGTTGAGAAAAAAGAGTGA
15968 AGGCAAAAAC
Statistics
Matches: 92, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
108 47 0.51
109 45 0.49
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (109 bp):
GGTGAAAACAAAGAGCCATGGAATCTGTTTAAGTTGAACGAAGACTCCCTGAATCTGAATCTTTT
TAGGTATTCACAAGGTTGAGAAAAAAGAGTGATAGATAGGCTAT
Found at i:16491 original size:38 final size:38
Alignment explanation
Indices: 16440--16518 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
16430 GTGTGTCTTC
16440 ATTAGTGTGTTAGGGTTCTTTGTTAGATGTTTTGAGTA
1 ATTAGTGTGTTAGGGTTCTTTGTTAGATGTTTTGAGTA
*
16478 ATTAGTGTGTTAGGGTTCTTTGTTAGATTTTTTGAGTA
1 ATTAGTGTGTTAGGGTTCTTTGTTAGATGTTTTGAGTA
16516 ATT
1 ATT
16519 TAGGTGTATC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.19, C:0.03, G:0.27, T:0.52
Consensus pattern (38 bp):
ATTAGTGTGTTAGGGTTCTTTGTTAGATGTTTTGAGTA
Found at i:19891 original size:14 final size:13
Alignment explanation
Indices: 19848--19894 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
19838 TTTCCTTTAG
19848 TTTTGTTTTTAT-T
1 TTTTGTTTTT-TGT
* *
19861 TTTCGTATTTTGT
1 TTTTGTTTTTTGT
19874 TTTTGTTTTTGTGT
1 TTTTGTTTTT-TGT
19888 TTTTGTT
1 TTTTGTT
19895 AATTTTGCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 1 0.04
13 17 0.61
14 10 0.36
ACGTcount: A:0.04, C:0.02, G:0.15, T:0.79
Consensus pattern (13 bp):
TTTTGTTTTTTGT
Found at i:19894 original size:6 final size:6
Alignment explanation
Indices: 19848--19890 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
19838 TTTCCTTTAG
*
19848 TTTTGT TTTTAT TTTTCGT ATTTTGT TTTTGT TTTTGT GTTTT
1 TTTTGT TTTTGT TTTT-GT -TTTTGT TTTTGT TTTTGT -TTTT
19891 TGTTAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 21 0.66
7 7 0.22
8 4 0.12
ACGTcount: A:0.05, C:0.02, G:0.14, T:0.79
Consensus pattern (6 bp):
TTTTGT
Found at i:22749 original size:16 final size:16
Alignment explanation
Indices: 22730--22836 Score: 180
Period size: 16 Copynumber: 6.7 Consensus size: 16
22720 CTCGGGCGGG
22730 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
22746 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
22762 TTCGGGCTCGGGTATT
1 TTCGGGTTCGGGTATT
22778 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
22794 TTCGGGTTCGGGT-TAT
1 TTCGGGTTCGGGTAT-T
*
22810 GTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
22826 TTCGGGTTCGG
1 TTCGGGTTCGG
22837 TCTCGGGTAG
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
15 1 0.01
16 83 0.98
17 1 0.01
ACGTcount: A:0.06, C:0.14, G:0.39, T:0.41
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:23033 original size:8 final size:8
Alignment explanation
Indices: 23010--23043 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
23000 AAGTTTATTG
23010 ATAATAT-
1 ATAATATA
*
23017 ATGATATA
1 ATAATATA
23025 ATAATATA
1 ATAATATA
23033 ATAATATA
1 ATAATATA
23041 ATA
1 ATA
23044 TAACATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (8 bp):
ATAATATA
Done.