Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018642.1 Corchorus olitorius cultivar O-4 contig18675, 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: 10180
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:107 original size:15 final size:15
Alignment explanation
Indices: 65--109 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
55 AAAAATAAAA
65 AAAATAAATATTTTTC
1 AAAA-AAATATTTTTC
*
81 AAAAAAACATTTTT-
1 AAAAAAATATTTTTC
95 AAAAAAATTATTTTT
1 AAAAAAA-TATTTTT
110 TAATCAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 7 0.27
15 15 0.58
16 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAAAAATATTTTTC
Found at i:109 original size:16 final size:15
Alignment explanation
Indices: 65--112 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
55 AAAAATAAAA
*
65 AAAATAAATATTTTTC
1 AAAA-AAATATTTTTT
*
81 AAAAAAACA-TTTTT
1 AAAAAAATATTTTTT
95 AAAAAAATTATTTTTT
1 AAAAAAA-TATTTTTT
111 AA
1 AA
113 TCAAAAAAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 11 0.41
15 5 0.19
16 11 0.41
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAAAAATATTTTTT
Found at i:3222 original size:19 final size:19
Alignment explanation
Indices: 3198--3236 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3188 TTTTGTGCTG
3198 AAATCAACTAATCTGACTA
1 AAATCAACTAATCTGACTA
3217 AAATCAACTAATCTGACTA
1 AAATCAACTAATCTGACTA
3236 A
1 A
3237 GTAGTGGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.26
Consensus pattern (19 bp):
AAATCAACTAATCTGACTA
Found at i:5347 original size:19 final size:19
Alignment explanation
Indices: 5325--5375 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
5315 GGGCTGAAAT
5325 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
5344 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
5363 TAATT-ATTATTAA
1 TAATTAATTATTAA
5376 AAATCCCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:6827 original size:51 final size:50
Alignment explanation
Indices: 6726--6827 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
6716 GTTCTTCATA
* **
6726 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
* *
6776 TTTTCTCTTGTTTCA-ATCTTGTCTCGGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGT
6827 T
1 T
6828 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 7 0.16
51 36 0.82
52 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Found at i:7320 original size:46 final size:45
Alignment explanation
Indices: 7254--7353 Score: 150
Period size: 46 Copynumber: 2.2 Consensus size: 45
7244 AGTGCATTAC
*
7254 CTAAAT-TTAACTCCTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAAATATTAACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
* *
7298 CTAAATATTATACTCTTCCATCTCTATATAATTCATCAAAATAAAG
1 CTAAATATTA-ACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
7344 CT-AATATTAA
1 CTAAATATTAA
7354 TTGTTGTTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
44 7 0.14
45 10 0.20
46 34 0.67
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (45 bp):
CTAAATATTAACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:7526 original size:56 final size:56
Alignment explanation
Indices: 7440--7554 Score: 203
Period size: 56 Copynumber: 2.1 Consensus size: 56
7430 GTTAAATTAA
* * *
7440 TAGACTCGGGTAGGTGGAAGAATTTGGCTTCTGCGTAAGGAAGGCCTAATTTTTTG
1 TAGACTCAGGTAGGTGGAAGAATTTGGCTTCTGCATAAGGAAGACCTAATTTTTTG
7496 TAGACTCAGGTAGGTGGAAGAATTTGGCTTCTGCATAAGGAAGACCTAATTTTTTG
1 TAGACTCAGGTAGGTGGAAGAATTTGGCTTCTGCATAAGGAAGACCTAATTTTTTG
7552 TAG
1 TAG
7555 TCAAGGAGCA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.32
Consensus pattern (56 bp):
TAGACTCAGGTAGGTGGAAGAATTTGGCTTCTGCATAAGGAAGACCTAATTTTTTG
Found at i:8928 original size:3 final size:3
Alignment explanation
Indices: 8920--8980 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
8910 GTATATATAT
8920 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
8968 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
8981 CTTGTTATGC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:9647 original size:123 final size:127
Alignment explanation
Indices: 9512--9766 Score: 428
Period size: 131 Copynumber: 2.0 Consensus size: 127
9502 CATTGTTTAA
* *
9512 ACTTTTATAGTTTTACTCAACTAAAATCTCTATTTTTATTTAATTAAATCTAATAT-CTT-TA-T
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACT
9574 A-ATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 ATATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
9635 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATA-C
9700 TATTTTATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
65 TA---TATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
9765 T
127 T
9766 A
1 A
9767 TTTCTTAAAT
Statistics
Matches: 122, Mismatches: 2, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
123 54 0.44
124 3 0.02
125 2 0.02
127 2 0.02
131 61 0.50
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (127 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACT
ATATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:9788 original size:14 final size:13
Alignment explanation
Indices: 9752--9790 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
9742 TATATATTAG
9752 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
9765 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
9779 AATTTTTTAAAT
1 AATTTTTTAAAT
9791 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Done.