Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023830.1 Corchorus olitorius cultivar O-4 contig23863, 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: 15196
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:3351 original size:15 final size:16
Alignment explanation
Indices: 3322--3351 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3312 GTGTGAATTC
3322 AAATTGATCTTTTGAA
1 AAATTGATCTTTTGAA
3338 AAATTGAT-TTTTGA
1 AAATTGATCTTTTGA
3352 TAAACTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (16 bp):
AAATTGATCTTTTGAA
Found at i:8021 original size:15 final size:15
Alignment explanation
Indices: 8001--8050 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
7991 CAAGAGACGT
*
8001 TTTTCAAGAAAATTG
1 TTTTCAAGAAAATGG
8016 TTTTCAAAGAAAA-GG
1 TTTTC-AAGAAAATGG
8031 TTTTC-A-AAAATGG
1 TTTTCAAGAAAATGG
8044 TTTTCAA
1 TTTTCAA
8051 AAGGTTTTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 4 0.13
13 8 0.26
14 1 0.03
15 11 0.35
16 7 0.23
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (15 bp):
TTTTCAAGAAAATGG
Found at i:8047 original size:13 final size:13
Alignment explanation
Indices: 8009--8052 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
7999 GTTTTTCAAG
*
8009 AAAATTGTTTTCAA
1 AAAATGGTTTTC-A
*
8023 AGAAAAGGTTTTCA
1 A-AAATGGTTTTCA
8037 AAAATGGTTTTCA
1 AAAATGGTTTTCA
8050 AAA
1 AAA
8053 GGTTTTGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 14 0.54
14 3 0.12
15 9 0.35
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (13 bp):
AAAATGGTTTTCA
Found at i:8056 original size:11 final size:12
Alignment explanation
Indices: 8025--8058 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
8015 GTTTTCAAAG
8025 AAAAGGTTTTCA
1 AAAAGGTTTTCA
8037 AAAATGGTTTTC-
1 AAAA-GGTTTTCA
8049 AAAAGGTTTT
1 AAAAGGTTTT
8059 GGGTTTTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.29
12 8 0.38
13 7 0.33
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (12 bp):
AAAAGGTTTTCA
Found at i:10419 original size:64 final size:64
Alignment explanation
Indices: 10244--10764 Score: 722
Period size: 64 Copynumber: 8.0 Consensus size: 64
10234 AGAGGATTTT
* * * * * * *
10244 AGAAGTACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAGATGTTGTTCGGAAGATGATCTTGT
1 AGAAGTACACCAGAAGATGGTTT-CT--CAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTGT
10309 CA
63 CA
*
10311 AGAAGTACACACCAGAAGATGGTTTCTCAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTATC
1 AGAAGT--ACACCAGAAGATGGTTTCTCAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTGTC
10376 A
64 A
*
10377 AGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTCAAAAGTTGATCGGAAGACGATCTTGTCA
1 AGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTGTCA
* *
10441 AAAAGTACACCAGAAGATGGTTTCTGAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTGTCA
1 AGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTGTCA
* *
10505 AGAAGTACACCAAAAGATGGTTTCTCAAGAGTTTTCAGAAGATGATCGGAAGACGATCTTGTCA
1 AGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTGTCA
10569 AGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTGTCA
1 AGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTGTCA
* * ** * * * * *
10633 AGAAGTATACCAGAGGATGGAATCTAAAAAATTTTCAGAAGTTGATCGGAAGATGATCTTGTTA
1 AGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTGTCA
* * *
10697 AAAAGTACACCAGAAGGTGGTTTCTCGGAA-A-TGTTTCAGAGGTTGATCGGAAGACGATCTTGT
1 AGAAGTACACCAGAAGATGGTTTCTC--AAGAGT-TTTCAGAAGTTGATCGGAAGACGATCTTGT
*
10760 TA
63 CA
10762 AGA
1 AGA
10765 GATGCACCGG
Statistics
Matches: 411, Mismatches: 38, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
64 314 0.76
65 33 0.08
66 41 0.10
67 6 0.01
68 2 0.00
69 15 0.04
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (64 bp):
AGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTGTCA
Found at i:11052 original size:50 final size:49
Alignment explanation
Indices: 10992--11110 Score: 141
Period size: 50 Copynumber: 2.4 Consensus size: 49
10982 TGATTTTCTC
10992 AAGATTGAATTGGAAGACAGTCCAAAGGATAAGCGGGAGACGG-TCCTTTT
1 AAGA-TGAATTGGAAGACAGTCCAAAGGATAAGCGGGAGACGGCT-CTTTT
* * * *
11042 AAGATCGAATTGGAAGACAGTTCGAGGGATGAGCGGGAGACGGCTCTTTT
1 AAGAT-GAATTGGAAGACAGTCCAAAGGATAAGCGGGAGACGGCTCTTTT
* *
11092 AATATTAGATTGGAAGACA
1 AAGATGA-ATTGGAAGACA
11111 ATCCTTTTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
49 2 0.03
50 57 0.95
51 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.31, T:0.23
Consensus pattern (49 bp):
AAGATGAATTGGAAGACAGTCCAAAGGATAAGCGGGAGACGGCTCTTTT
Found at i:11185 original size:127 final size:127
Alignment explanation
Indices: 10992--11366 Score: 687
Period size: 127 Copynumber: 3.0 Consensus size: 127
10982 TGATTTTCTC
*
10992 AAGATTGAATTGGAAGACAGTCCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATCGAATTGGAA
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATCGAATTGGAA
11057 GACAGTTCGAGGGATGAGCGGGAGACGGCTCTTTTAATATTAGATTGGAAGACAATCCTTTT
66 GACAGTTCGAGGGATGAGCGGGAGACGGCTCTTTTAATATTAGATTGGAAGACAATCCTTTT
* *
11119 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGTTCCTTTTAAGATCGAATTTGAA
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATCGAATTGGAA
* * *
11184 GATAGTTCGAGGGATGAGCGGGAGACGACTCTTTTAATATTAGATTGGAAAACAATCCTTTT
66 GACAGTTCGAGGGATGAGCGGGAGACGGCTCTTTTAATATTAGATTGGAAGACAATCCTTTT
*
11246 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATCAAATTGGAA
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATCGAATTGGAA
11311 GACAGTTCGAGGGATGAGCGGGAGACGGCTCTTTTAATATTAGATTGGAAGACAAT
66 GACAGTTCGAGGGATGAGCGGGAGACGGCTCTTTTAATATTAGATTGGAAGACAAT
11367 TAGAAAGAGT
Statistics
Matches: 236, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 236 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (127 bp):
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATCGAATTGGAA
GACAGTTCGAGGGATGAGCGGGAGACGGCTCTTTTAATATTAGATTGGAAGACAATCCTTTT
Found at i:11191 original size:50 final size:50
Alignment explanation
Indices: 11112--11210 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
11102 TGGAAGACAA
*
11112 TCCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGT
1 TCCTTTTAAGATCGAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGT
* * * * *
11162 TCCTTTTAAGATCGAATTTGAAGATAGTTCGAGGGATGAGCGGGAGACG
1 TCCTTTTAAGATCGAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACG
11211 ACTCTTTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.26
Consensus pattern (50 bp):
TCCTTTTAAGATCGAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGT
Found at i:11308 original size:77 final size:77
Alignment explanation
Indices: 11162--11310 Score: 192
Period size: 77 Copynumber: 1.9 Consensus size: 77
11152 CGGGAGACGT
* * * * * * * *
11162 TCCTTTTAAGATCGAATTTGAAGATAGTTCGAGGGATGAGCGGGAGACGACTCTTTTAATATTAG
1 TCCTTTTAAGATCGAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGACTCTTTTAAGATCAA
11227 ATTGGAAAACAA
66 ATTGGAAAACAA
* *
11239 TCCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACG-GTCCTTTTAAGATCA
1 TCCTTTTAAGATCGAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGACT-CTTTTAAGATCA
11303 AATTGGAA
65 AATTGGAA
11311 GACAGTTCGA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
76 1 0.02
77 60 0.98
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (77 bp):
TCCTTTTAAGATCGAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGACTCTTTTAAGATCAA
ATTGGAAAACAA
Found at i:11314 original size:50 final size:50
Alignment explanation
Indices: 11239--11364 Score: 173
Period size: 50 Copynumber: 2.5 Consensus size: 50
11229 TGGAAAACAA
*
11239 TCCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGG
1 TCCTTTTAAGATTAAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGG
* * * *
11289 TCCTTTTAAGATCAAATTGGAAGACAGTTCGAGGGATGAGCGGGAGACGG
1 TCCTTTTAAGATTAAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGG
* *
11339 -CTCTTTTAATATTAGATTGGAAGACA
1 TC-CTTTTAAGATTAAATTGGAAGACA
11365 ATTAGAAAGA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
49 1 0.01
50 66 0.99
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.26
Consensus pattern (50 bp):
TCCTTTTAAGATTAAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGG
Found at i:11676 original size:26 final size:27
Alignment explanation
Indices: 11647--11715 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
11637 TTTCTTATTT
* *
11647 GGCATTCTAGTCATTTGCACA-TCAGG
1 GGCATTTTGGTCATTTGCACATTCAGG
*
11673 GGCATTTTGGTCATTTGCATATTCAGG
1 GGCATTTTGGTCATTTGCACATTCAGG
11700 GGCATTTTGGTCATTT
1 GGCATTTTGGTCATTT
11716 TAAGTTCACT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 18 0.46
27 21 0.54
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (27 bp):
GGCATTTTGGTCATTTGCACATTCAGG
Done.