Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016738.1 Corchorus olitorius cultivar O-4 contig16771, 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: 17326
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Found at i:2903 original size:24 final size:24
Alignment explanation
Indices: 2876--2921 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
2866 ACAAACAGAT
2876 ATAATTGAACCAATTAATACTAAC
1 ATAATTGAACCAATTAATACTAAC
2900 ATAATTGAACCAATTAATACTA
1 ATAATTGAACCAATTAATACTA
2922 TGGTTCCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.30
Consensus pattern (24 bp):
ATAATTGAACCAATTAATACTAAC
Found at i:4047 original size:11 final size:11
Alignment explanation
Indices: 4031--4056 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4021 TAAAATTGGG
4031 CCTCCCACTTC
1 CCTCCCACTTC
4042 CCTCCCACTTC
1 CCTCCCACTTC
4053 CCTC
1 CCTC
4057 TTAATTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.65, G:0.00, T:0.27
Consensus pattern (11 bp):
CCTCCCACTTC
Found at i:4148 original size:14 final size:14
Alignment explanation
Indices: 4101--4153 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
4091 AACAAAGGAA
*
4101 CCCTTTTCCTTCCTT
1 CCCTTTTCTTTCC-T
*
4116 CCCCTTTCTTTCCT
1 CCCTTTTCTTTCCT
4130 CCCCTTTTCTTTCCT
1 -CCCTTTTCTTTCCT
4145 CCCTATTTC
1 CCCT-TTTC
4154 CTTTGTACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 5 0.15
15 28 0.85
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (14 bp):
CCCTTTTCTTTCCT
Found at i:4153 original size:15 final size:15
Alignment explanation
Indices: 4101--4147 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
4091 AACAAAGGAA
*
4101 CCCTTTTCCTTCCTTC
1 CCCTTTTCTTTCC-TC
4117 CCC-TTTCTTTCCTC
1 CCCTTTTCTTTCCTC
4131 CCCTTTTCTTTCCTC
1 CCCTTTTCTTTCCTC
4146 CC
1 CC
4148 TATTTCCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 5 0.17
15 21 0.72
16 3 0.10
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (15 bp):
CCCTTTTCTTTCCTC
Found at i:10178 original size:26 final size:26
Alignment explanation
Indices: 10153--10201 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
10143 TTAATGTTTA
10153 AATT-TTATTTT-TTATTAAAAAATTT
1 AATTATTATTTTATT-TTAAAAAATTT
10178 AATTATTATTTTATTTTAAAAAAT
1 AATTATTATTTTATTTTAAAAAAT
10202 AAATATGGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.18
26 16 0.73
27 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
AATTATTATTTTATTTTAAAAAATTT
Found at i:11541 original size:19 final size:19
Alignment explanation
Indices: 11517--11553 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
11507 GTAGAATACC
11517 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
11536 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
11554 TGCTAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:11946 original size:2 final size:2
Alignment explanation
Indices: 11939--11972 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
11929 AGAAATTATG
* *
11939 TA TA TA TA TG TG TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11973 ATGTGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11954 original size:12 final size:12
Alignment explanation
Indices: 11935--11972 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
11925 GGAAAGAAAT
11935 TATGTATATATA
1 TATGTATATATA
*
11947 TGTGTATATATA
1 TATGTATATATA
*
11959 TATATATATATA
1 TATGTATATATA
11971 TA
1 TA
11973 ATGTGTTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:12276 original size:22 final size:24
Alignment explanation
Indices: 12223--12280 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
12213 TTATCTGGCA
* *
12223 AGATATTATCAAGTGATAAATGGAG
1 AGATATTATC-AGAGATAAATAGAG
12248 AGA-ATTATCAGAGATAAA-AGAG
1 AGATATTATCAGAGATAAATAGAG
12270 A-ATATTATCAG
1 AGATATTATCAG
12281 TAACATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 1 0.03
22 12 0.40
23 8 0.27
24 6 0.20
25 3 0.10
ACGTcount: A:0.48, C:0.05, G:0.21, T:0.26
Consensus pattern (24 bp):
AGATATTATCAGAGATAAATAGAG
Found at i:13460 original size:30 final size:30
Alignment explanation
Indices: 13406--13546 Score: 264
Period size: 30 Copynumber: 4.7 Consensus size: 30
13396 TAATATATAT
13406 TGACACCAGAAGTTGTCAATGGCCTTGCAAA
1 TGACACCAGAAGTTGTC-ATGGCCTTGCAAA
13437 TGACACCAGAAGTTGTCATGGCCTTGCAAA
1 TGACACCAGAAGTTGTCATGGCCTTGCAAA
*
13467 TGACACCAGAAGTTGTCATAGCCTTGCAAA
1 TGACACCAGAAGTTGTCATGGCCTTGCAAA
13497 TGACACCAGAAGTTGTCATGGCCTTGCAAA
1 TGACACCAGAAGTTGTCATGGCCTTGCAAA
13527 TGACACCAGAAGTTGTCATG
1 TGACACCAGAAGTTGTCATG
13547 AAAATTTTTG
Statistics
Matches: 108, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
30 91 0.84
31 17 0.16
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGGCCTTGCAAA
Found at i:13607 original size:62 final size:62
Alignment explanation
Indices: 13527--13980 Score: 473
Period size: 62 Copynumber: 7.3 Consensus size: 62
13517 GCCTTGCAAA
13527 TGACACCAGAAGTTGTCATGAAA-ATT-T-TTGACACCAGAAGTTGTCATATCAAATTATTATCT
1 TGACACCAGAAGTTGTCATGAAATATTATCTTGACACCAGAAGTTGTCATATCAAA--ATTAT-T
*
13589 TGACACCAGAAGTTGTCATGAAA-ATTA--TTGACACCAGAAGTTGTCATAGCAAATTATTATCT
1 TGACACCAGAAGTTGTCATGAAATATTATCTTGACACCAGAAGTTGTCATATCAAA--ATTAT-T
13651 TGACACCAGAAGTTGTCATGAAA-ATT-T-TTGACACCTAGAAGTTGTCATATCAAATTATTATC
1 TGACACCAGAAGTTGTCATGAAATATTATCTTGACACC-AGAAGTTGTCATATCAAA--ATTAT-
13713 T
62 T
*
13714 TGACACCAGAAGTTGTCATAGCAAATTATTATCTTGACACCAGAAGTTGTC--ATGAAAATT-TT
1 TGACACCAGAAGTTGTCAT-G-AAA-TATTATCTTGACACCAGAAGTTGTCATATCAAAATTATT
* * * *
13776 TGACACCAGAGGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTATC--ATGAAAATT-TT
1 TGACACCAGAAGTTGTC--ATGAAA-TATTATCTTGACACCAGAAGTTGTCATATCAAAATTATT
* *
13838 TGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTC--ATGAAAATTA-T
1 TGACACCAGAAGTTGTC--ATGAAA-TATTATCTTGACACCAGAAGTTGTCATATCAAAATTATT
*
13900 TGACACCAGAAGTTGTCATAGCAAATTATTATCTTGACACCAGAAGTTGTC--ATGAAAATT-TT
1 TGACACCAGAAGTTGTCAT-G-AAA-TATTATCTTGACACCAGAAGTTGTCATATCAAAATTATT
*
13962 TGACACTAGAAGTTGTCAT
1 TGACACCAGAAGTTGTCAT
13981 CCTAAGATTG
Statistics
Matches: 367, Mismatches: 10, Indels: 30
0.90 0.02 0.07
Matches are distributed among these distances:
60 2 0.01
62 283 0.77
63 46 0.13
64 6 0.02
65 3 0.01
66 5 0.01
67 3 0.01
68 11 0.03
69 8 0.02
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (62 bp):
TGACACCAGAAGTTGTCATGAAATATTATCTTGACACCAGAAGTTGTCATATCAAAATTATT
Found at i:13953 original size:124 final size:122
Alignment explanation
Indices: 13527--13980 Score: 522
Period size: 124 Copynumber: 3.6 Consensus size: 122
13517 GCCTTGCAAA
13527 TGACACCAGAAGTTGTCATGAAAATTTTTGACACCAGAAGTTGTCATATCAAATTATTATCTTGA
1 TGACACCAGAAGTTGTCATGAAAATTTTTGACACCAGAAGTTGTCA-ATCAAA-TATTATCTTGA
*
13592 CACCAGAAGTTGTC--ATGAAA--ATTA--TTGACACCAGAAGTTGTCATAGCAAATTATTATCT
64 CACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCAT-G-AAA--ATTA--T
13651 TGACACCAGAAGTTGTCATGAAAATTTTTGACACCTAGAAGTTGTCATATCAAATTATTATCTTG
1 TGACACCAGAAGTTGTCATGAAAATTTTTGACACC-AGAAGTTGTCA-ATCAAA-TATTATCTTG
* *
13716 ACACCAGAAGTTGTCATAGCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTTT
63 ACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTAT
* * * *
13776 TGACACCAGAGGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTATC-ATGAAA-ATT-T-
1 TGACACCAGAAGTTGTC--ATGAAA--ATT-T-TTGACACCAGAAGTTGTCAATCAAATATTATC
13837 TTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTAT
60 TTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTAT
*
13900 TGACACCAGAAGTTGTCATAGCAAATTATTATCTTGACACCAGAAGTTGTC-ATGAAA-ATT-T-
1 TGACACCAGAAGTTGTCAT-G-AAA--ATT-T-TTGACACCAGAAGTTGTCAATCAAATATTATC
*
13961 TTGACACTAGAAGTTGTCAT
60 TTGACACCAGAAGTTGTCAT
13981 CCTAAGATTG
Statistics
Matches: 302, Mismatches: 13, Indels: 30
0.88 0.04 0.09
Matches are distributed among these distances:
122 2 0.01
124 169 0.56
125 62 0.21
126 3 0.01
127 12 0.04
128 5 0.02
129 10 0.03
130 11 0.04
131 28 0.09
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (122 bp):
TGACACCAGAAGTTGTCATGAAAATTTTTGACACCAGAAGTTGTCAATCAAATATTATCTTGACA
CCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTAT
Done.