Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020574.1 Corchorus olitorius cultivar O-4 contig20607, 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: 36878
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Found at i:417 original size:2 final size:2
Alignment explanation
Indices: 410--460 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
400 AATAATTGAA
410 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
452 AG AG AG AG A
1 AG AG AG AG A
461 AGGAGGGAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:893 original size:3 final size:3
Alignment explanation
Indices: 887--939 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
877 AAAAAAAAAA
887 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
935 ATT AT
1 ATT AT
940 ATATATATAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12263 original size:19 final size:20
Alignment explanation
Indices: 12239--12296 Score: 82
Period size: 19 Copynumber: 2.9 Consensus size: 20
12229 CTGTTTGGTA
12239 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTAGC
* *
12258 ACTGTACAGATTAGATTATGT
1 ACTGTACAGATGAGATTA-GC
12279 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
12297 TTAGAGCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAGC
Found at i:12284 original size:21 final size:20
Alignment explanation
Indices: 12239--12297 Score: 84
Period size: 21 Copynumber: 3.0 Consensus size: 20
12229 CTGTTTGGTA
12239 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTATC
* *
12258 ACTGTACAGATTAGATTATGT
1 ACTGTACAGATGAGATTAT-C
12279 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
12298 TAGAGCAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 17 0.49
21 18 0.51
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ACTGTACAGATGAGATTATC
Found at i:12985 original size:35 final size:35
Alignment explanation
Indices: 12935--13008 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
12925 GGTTCGTTTA
* *
12935 TGTTCATGAATAGGCTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGGCTCGTTTATTGTTCATTTAAG
12970 TGTTCACGAACAGGCTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGGCTCGTTTATTGTTCATTTAAG
13005 TGTT
1 TGTT
13009 TGTTTATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.45
Consensus pattern (35 bp):
TGTTCACGAACAGGCTCGTTTATTGTTCATTTAAG
Found at i:13065 original size:18 final size:19
Alignment explanation
Indices: 13035--13082 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
13025 GAACGTTCGT
*
13035 TTATTATATAATTATTTATA
1 TTATTA-ATAATTATATATA
13055 TT-TTAATAATTATATATA
1 TTATTAATAATTATATATA
13073 TTATTAATAA
1 TTATTAATAA
13083 AAATTATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 14 0.54
19 10 0.38
20 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTAATAATTATATATA
Found at i:13238 original size:18 final size:18
Alignment explanation
Indices: 13211--13245 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13201 AGAGATTACA
13211 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
13229 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
13246 CAGTTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:14257 original size:17 final size:17
Alignment explanation
Indices: 14235--14270 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
14225 AGAAAGACAT
14235 TGACCGTTAATAAATCA
1 TGACCGTTAATAAATCA
14252 TGACCGTTAATAAATCA
1 TGACCGTTAATAAATCA
14269 TG
1 TG
14271 TTTTCCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.31
Consensus pattern (17 bp):
TGACCGTTAATAAATCA
Found at i:14603 original size:103 final size:102
Alignment explanation
Indices: 14424--14628 Score: 374
Period size: 103 Copynumber: 2.0 Consensus size: 102
14414 ACTCAAACAA
14424 CCCATCTATTTATGATGTGGGATGTTTCGCTCACATGTGAATCCCTAACAATCTCCCCAATTCAC
1 CCCATCTATTTATGATGTGGGATGTTTCGCTCACATGTGAATCCCTAACAATCTCCCCAATTCAC
*
14489 TTGTGAGTCCACATCTCTCCCCCGTGCGGCCCAACCCG
66 TTGGGAGTCCACATCTCT-CCCCGTGCGGCCCAACCCG
* *
14527 CCCATTTATTTATGATGTGGGATGTTTCGCTCACATGTGAGTCCCTAACAATCTCCCCAATTCAC
1 CCCATCTATTTATGATGTGGGATGTTTCGCTCACATGTGAATCCCTAACAATCTCCCCAATTCAC
14592 TTGGGAGTCCACATCTCTCCCCGTGCGGCCCAACCCG
66 TTGGGAGTCCACATCTCTCCCCGTGCGGCCCAACCCG
14629 TCAAGTCTTA
Statistics
Matches: 99, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
102 19 0.19
103 80 0.81
ACGTcount: A:0.20, C:0.34, G:0.18, T:0.28
Consensus pattern (102 bp):
CCCATCTATTTATGATGTGGGATGTTTCGCTCACATGTGAATCCCTAACAATCTCCCCAATTCAC
TTGGGAGTCCACATCTCTCCCCGTGCGGCCCAACCCG
Found at i:26576 original size:34 final size:34
Alignment explanation
Indices: 26533--26600 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
26523 CTGTGCATTC
26533 GAATCAAGATATGGAAATGTCCTAATAGCTGAGA
1 GAATCAAGATATGGAAATGTCCTAATAGCTGAGA
26567 GAATCAAGATATGGAAATGTCCTAATAGCTGAGA
1 GAATCAAGATATGGAAATGTCCTAATAGCTGAGA
26601 TACTCCTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (34 bp):
GAATCAAGATATGGAAATGTCCTAATAGCTGAGA
Found at i:30368 original size:56 final size:56
Alignment explanation
Indices: 30282--30395 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
30272 TATCCATTTC
*
30282 CTTTCATACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
30338 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
30394 CT
1 CT
30396 ATAAAATAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.40
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
Found at i:36792 original size:30 final size:27
Alignment explanation
Indices: 36742--36824 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 27
36732 GTTAATTTAG
36742 ACTTATTATTATTATAATAATTATTAA
1 ACTTATTATTATTATAATAATTATTAA
*
36769 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTA-T--TATAATAATTATTAA
* *
36799 ACTTATTCTTATAATAATAATTATTA
1 ACTTATTATTATTATAATAATTATTA
36825 TTAGTGGTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 23 0.47
28 1 0.02
29 1 0.02
30 24 0.49
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.51
Consensus pattern (27 bp):
ACTTATTATTATTATAATAATTATTAA
Done.