Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017718.1 Corchorus olitorius cultivar O-4 contig17751, 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: 20295
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:278 original size:22 final size:22
Alignment explanation
Indices: 175--278 Score: 79
Period size: 22 Copynumber: 4.8 Consensus size: 22
165 ATAGGAAAAT
*
175 TTATTAAAATTTCAT-AGTTAGA
1 TTATCAAAATTTCATAAG-TAGA
* * * * *
197 TTATCAAAGTTTCTTATGGAGT
1 TTATCAAAATTTCATAAGTAGA
* * *
219 TTATCACAATTTTATAGGTA-A
1 TTATCAAAATTTCATAAGTAGA
*
240 TTATCAAAATTTAATAAGATAG-
1 TTATCAAAATTTCATAAG-TAGA
262 TTATCAAAATTTCATAA
1 TTATCAAAATTTCATAA
279 AAATATTTAA
Statistics
Matches: 62, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
21 15 0.24
22 46 0.74
23 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGTAGA
Found at i:343 original size:2 final size:2
Alignment explanation
Indices: 336--374 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
326 ATAAAACTAG
336 TA TA TA TA 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 TA T
375 TCGATAACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1543 original size:26 final size:26
Alignment explanation
Indices: 1511--1563 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1501 AGTGGAAGTA
1511 AGAATTTTGTGTTTTTATGTTTTTCC
1 AGAATTTTGTGTTTTTATGTTTTTCC
1537 AGAATTTTGTGTTTTTATGTTTTTCC
1 AGAATTTTGTGTTTTTATGTTTTTCC
1563 A
1 A
1564 AAACACTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.17, C:0.08, G:0.15, T:0.60
Consensus pattern (26 bp):
AGAATTTTGTGTTTTTATGTTTTTCC
Found at i:6888 original size:49 final size:49
Alignment explanation
Indices: 6823--6933 Score: 136
Period size: 49 Copynumber: 2.3 Consensus size: 49
6813 GATAATTACA
* * *
6823 TTACATTAAATTTCGACTTATTCGAAGCCAAGTTAGGTC-TAT-CTGATAG
1 TTACATTGAATTTCGACTAATTCGAAGCCAAGTTAGGTCGGATGC--ATAG
* * *
6872 TTACATTGAATTTCGACTAATTTGAAGCCGAGTTGGGTCGGATGCATAG
1 TTACATTGAATTTCGACTAATTCGAAGCCAAGTTAGGTCGGATGCATAG
6921 TTACATTGAATTT
1 TTACATTGAATTT
6934 GATGCATAGT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
49 51 0.94
50 2 0.04
51 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (49 bp):
TTACATTGAATTTCGACTAATTCGAAGCCAAGTTAGGTCGGATGCATAG
Found at i:6940 original size:22 final size:22
Alignment explanation
Indices: 6912--6999 Score: 94
Period size: 22 Copynumber: 4.0 Consensus size: 22
6902 AGTTGGGTCG
6912 GATGCATAGTTACATTGAATTT
1 GATGCATAGTTACATTGAATTT
6934 GATGCATAGTTACATTGAATTT
1 GATGCATAGTTACATTGAATTT
*
6956 CGA--C-TAATTTGA-AGTTGAATTT
1 -GATGCAT-AGTT-ACA-TTGAATTT
*
6978 TATGCATAGTTACATTGAATTT
1 GATGCATAGTTACATTGAATTT
7000 CGACTAATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
20 1 0.02
21 6 0.11
22 40 0.73
23 7 0.13
24 1 0.02
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (22 bp):
GATGCATAGTTACATTGAATTT
Found at i:6989 original size:44 final size:44
Alignment explanation
Indices: 6926--7013 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
6916 CATAGTTACA
6926 TTGAATTTGATGCATAGTTACATTGAATTTCGACTAATTTGAAG
1 TTGAATTTGATGCATAGTTACATTGAATTTCGACTAATTTGAAG
*
6970 TTGAATTTTATGCATAGTTACATTGAATTTCGACTAATTTGAAG
1 TTGAATTTGATGCATAGTTACATTGAATTTCGACTAATTTGAAG
7014 CCGAATTGGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (44 bp):
TTGAATTTGATGCATAGTTACATTGAATTTCGACTAATTTGAAG
Found at i:13238 original size:9 final size:9
Alignment explanation
Indices: 13224--13270 Score: 51
Period size: 9 Copynumber: 4.9 Consensus size: 9
13214 GACTTCAGTG
13224 ATGATGATT
1 ATGATGATT
13233 ATGATGATTT
1 ATGATGA-TT
13243 GGATGATGATT
1 --ATGATGATT
13254 ATGATGACTT
1 ATGATGA-TT
13264 A-GATGAT
1 ATGATGAT
13271 GACTTTGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 1 0.03
9 19 0.56
10 5 0.15
11 2 0.06
12 7 0.21
ACGTcount: A:0.32, C:0.02, G:0.26, T:0.40
Consensus pattern (9 bp):
ATGATGATT
Found at i:13247 original size:21 final size:21
Alignment explanation
Indices: 13223--13294 Score: 99
Period size: 21 Copynumber: 3.3 Consensus size: 21
13213 TGACTTCAGT
13223 GATGATGATTATGATGATTTG
1 GATGATGATTATGATGATTTG
* *
13244 GATGATGATTATGATGACTTA
1 GATGATGATTATGATGATTTG
13265 GATGATGACTTTGATGATGATTTG
1 GATGATGA--TT-ATGATGATTTG
13289 GATGAT
1 GATGAT
13295 CATGATCCTC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 27 0.61
23 2 0.05
24 15 0.34
ACGTcount: A:0.29, C:0.03, G:0.28, T:0.40
Consensus pattern (21 bp):
GATGATGATTATGATGATTTG
Found at i:13292 original size:12 final size:11
Alignment explanation
Indices: 13222--13294 Score: 73
Period size: 12 Copynumber: 6.6 Consensus size: 11
13212 ATGACTTCAG
13222 TGATGATGA-T
1 TGATGATGATT
13232 T-ATGATGATT
1 TGATGATGATT
13242 TGGATGATGA-T
1 T-GATGATGATT
13253 T-ATGATGACTT
1 TGATGATGA-TT
*
13264 AGATGATGACTT
1 TGATGATGA-TT
13276 TGATGATGATT
1 TGATGATGATT
13287 TGGATGAT
1 T-GATGAT
13295 CATGATCCTC
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
9 14 0.26
10 3 0.06
11 6 0.11
12 31 0.57
ACGTcount: A:0.29, C:0.03, G:0.27, T:0.41
Consensus pattern (11 bp):
TGATGATGATT
Done.