Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010038.1 Corchorus capsularis cultivar CVL-1 contig10059, 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: 23539
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:1602 original size:16 final size:16
Alignment explanation
Indices: 1581--1631 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
1571 ATCTGAAATA
1581 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
1597 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
*
1613 CTTCAGAGCCTTTCTG
1 CTTCAGAGCTTTTCTG
1629 CTT
1 CTT
1632 TCTAATTTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.12, C:0.27, G:0.18, T:0.43
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:4999 original size:48 final size:49
Alignment explanation
Indices: 4906--5005 Score: 148
Period size: 54 Copynumber: 2.0 Consensus size: 49
4896 ACTCTCTCAA
4906 ATCCTGAATCTGACGAAATCTTGGATGAAATCAAGAAAAAGAAAAAAGTATCAG
1 ATCCTGAATCTGACGAAATCTTGGATGAAATC-----AAAGAAAAAAGTATCAG
4960 ATCCTGAATCTGACGAAATCTTGGATGAAATC-AAGAAAAAAGTATC
1 ATCCTGAATCTGACGAAATCTTGGATGAAATCAAAGAAAAAAGTATC
5006 CGATTTTTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
48 14 0.30
54 32 0.70
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.22
Consensus pattern (49 bp):
ATCCTGAATCTGACGAAATCTTGGATGAAATCAAAGAAAAAAGTATCAG
Found at i:11430 original size:11 final size:11
Alignment explanation
Indices: 11414--11449 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
11404 TCATTATAAT
11414 ATATCTAATTA
1 ATATCTAATTA
11425 ATATCTAATTA
1 ATATCTAATTA
11436 ATAGT-TAATTA
1 ATA-TCTAATTA
11447 ATA
1 ATA
11450 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 23 0.96
12 1 0.04
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (11 bp):
ATATCTAATTA
Found at i:12284 original size:12 final size:12
Alignment explanation
Indices: 12252--12290 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
12242 ATGGAATTAA
12252 ATATCCGTCG--
1 ATATCCGTCGAT
12262 ATA-CC-TCGAT
1 ATATCCGTCGAT
12272 ATATCCGTCGAT
1 ATATCCGTCGAT
12284 ATATCCG
1 ATATCCG
12291 ATATCTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.12
9 2 0.08
10 6 0.24
11 2 0.08
12 12 0.48
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (12 bp):
ATATCCGTCGAT
Found at i:12399 original size:18 final size:18
Alignment explanation
Indices: 12378--12412 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12368 TCGATATTTA
* *
12378 TCGATATCTCGATAAATC
1 TCGATATATCCATAAATC
12396 TCGATATATCCATAAAT
1 TCGATATATCCATAAAT
12413 ATCCGTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (18 bp):
TCGATATATCCATAAATC
Found at i:13273 original size:13 final size:13
Alignment explanation
Indices: 13255--13283 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
13245 TTCGCAGTAC
13255 AAAAAATTAAAAA
1 AAAAAATTAAAAA
13268 AAAAAATTAAAAA
1 AAAAAATTAAAAA
13281 AAA
1 AAA
13284 TGTCTACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAAATTAAAAA
Found at i:13452 original size:10 final size:11
Alignment explanation
Indices: 13439--13486 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 11
13429 AATTTCATTG
13439 ATATC-TCGAT
1 ATATCGTCGAT
13449 ATATCCGTCGAT
1 ATAT-CGTCGAT
13461 ATATCCGTTCGAT
1 ATAT-CG-TCGAT
13474 ATATCCGTCGAT
1 ATAT-CGTCGAT
13486 A
1 A
13487 CCTGTATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
10 4 0.11
11 1 0.03
12 18 0.51
13 12 0.34
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (11 bp):
ATATCGTCGAT
Found at i:13474 original size:13 final size:12
Alignment explanation
Indices: 13444--13486 Score: 77
Period size: 12 Copynumber: 3.5 Consensus size: 12
13434 CATTGATATC
13444 TCGATATATCCG
1 TCGATATATCCG
13456 TCGATATATCCG
1 TCGATATATCCG
13468 TTCGATATATCCG
1 -TCGATATATCCG
13481 TCGATA
1 TCGATA
13487 CCTGTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:15265 original size:19 final size:18
Alignment explanation
Indices: 15237--15278 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
15227 CTCAGACTCA
*
15237 AACTAACTCAGAAAACTG
1 AACTAACTCAAAAAACTG
15255 AACTGAACTCAAAAAACTG
1 AACT-AACTCAAAAAACTG
15274 -ACTAA
1 AACTAA
15279 ACCCAACAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 7 0.32
19 13 0.59
ACGTcount: A:0.52, C:0.21, G:0.10, T:0.17
Consensus pattern (18 bp):
AACTAACTCAAAAAACTG
Done.