Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021920.1 Corchorus olitorius cultivar O-4 contig21953, 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: 20003
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:5646 original size:53 final size:53
Alignment explanation
Indices: 5587--5691 Score: 174
Period size: 53 Copynumber: 2.0 Consensus size: 53
5577 AACCAAGCAA
* *
5587 ATCCTAAATATTTGAATCTAAATAAAAAGATTGAGCTTTCACCAACAAAATAT
1 ATCCTAAAAATTTGAATCTAAATAAAAAGATTGAACTTTCACCAACAAAATAT
* *
5640 ATCCTAAAAATTTGAATCTTAATAAAAAGATTGAACTTTCACTAACAAAATA
1 ATCCTAAAAATTTGAATCTAAATAAAAAGATTGAACTTTCACCAACAAAATA
5692 CTCCCTCCGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (53 bp):
ATCCTAAAAATTTGAATCTAAATAAAAAGATTGAACTTTCACCAACAAAATAT
Found at i:11927 original size:17 final size:18
Alignment explanation
Indices: 11905--11939 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
11895 TTTTTTTAAT
*
11905 AATTATTTTAA-GAATTA
1 AATTATATTAATGAATTA
11922 AATTATATTAATGAATTA
1 AATTATATTAATGAATTA
11940 TATAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
AATTATATTAATGAATTA
Found at i:15112 original size:132 final size:130
Alignment explanation
Indices: 14936--15187 Score: 398
Period size: 132 Copynumber: 1.9 Consensus size: 130
14926 TTTTATAGTT
* *
14936 CTCAACTACAAACTCTATTTTTATTTAATTCAATCTAATATCCTTATAACTATTTCATTTTTACC
1 CTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTCATTTTTACC
* * *
15001 ATTTTACTATTTTAATT-AAAAACTTATATATATATTAGAATTTTTTAAATATATTTTATAGTTT
66 ATTTTACTAATTTAATTAAAAAAC-T-TAGATATATTAGAATTTTTAAAATATATTTTATAGTTT
15065 TA
129 TA
* * *
15067 CTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATACCTATTTTATTTTTAT
1 CTCAACTAAAAACTCTA-TTTTTATTTAATTAAATCTAATATCCTTATAACTATTTCATTTTTAC
15132 CATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATATATTT
65 CATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATATATTT
15188 CTTAAATGAC
Statistics
Matches: 111, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
131 44 0.40
132 61 0.55
133 6 0.05
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.50
Consensus pattern (130 bp):
CTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTCATTTTTACC
ATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATATATTTTATAGTTTTA
Found at i:16004 original size:13 final size:14
Alignment explanation
Indices: 15986--16014 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
15976 GAAAATACTG
15986 ATTAATTATT-ATT
1 ATTAATTATTCATT
15999 ATTAATTATTCATT
1 ATTAATTATTCATT
16013 AT
1 AT
16015 GTAAAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTAATTATTCATT
Found at i:16929 original size:123 final size:126
Alignment explanation
Indices: 16757--17254 Score: 494
Period size: 123 Copynumber: 3.9 Consensus size: 126
16747 TAGTAAAACA
* * *
16757 AAACAAATTATTAAACC-A-ATAATTGACTATATTA-TT-TA-TAT-TGTCATTATAATACTAAT
1 AAACAAATTATTAAACCAATATAATTGACTATATTATTTATATTATATATAATTATAATAATAAT
* * * *
16816 TAGAAATTTCTTCTATATTTATAATCCCATTTTAATTATCACACTTTAATTGATACATATG
66 AACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATCACACTTTAATTGATACATATG
* *
16877 AAACAAATTATTAAACCAATAATAATTGACTATATTA-TTAT-TTATAT-T-ATTATTATAATAC
1 AAACAAATTATTAAACCAAT-ATAATTGACTATATTATTTATATTATATATAATTATAATAATAA
* *
16938 TAAGAAATTTCTTCTCTATTTATAATTCCATTTTAATTATTACACTTTAATTGATGCATATGTCA
65 TAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATCACACTTTAA-T--TG-ATA---CA
17003 TATG
123 TATG
17007 AAACAAATTATTAAACCAAT-TAATTGACTATATTATTTATATTATTATTGTTATAATTTTATTA
1 AAACAAATTATTAAACCAATATAATTGACTATATTATTTATATTA-TA----TATAA--TTA-TA
* ** * *
17071 TACTAATAATAACAAATTTCTTCTCTATTTAAAATTAAATTTTAATTATCATAC--T--TTGGT-
58 -A-TAATAATAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATCACACTTTAATTGATA
17131 --TATG
121 CATATG
* *
17135 AAACAAATTATTAAACCAATATAATTGACTATATTATTTATGTATATATATATTATTTTTAA-AA
1 AAACAAATTATTAAACCAATATAATTGACTATATTATTTA--TAT-TATATA-TAATTATAATAA
*
17199 TACTAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATCACACTTTAATTG
62 TAATAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATCACACTTTAATTG
17255 GTTGATGCTG
Statistics
Matches: 319, Mismatches: 23, Indels: 66
0.78 0.06 0.16
Matches are distributed among these distances:
120 17 0.05
121 1 0.00
122 45 0.14
123 74 0.23
124 8 0.03
125 3 0.01
126 7 0.02
127 5 0.02
128 41 0.13
129 23 0.07
130 29 0.09
131 7 0.02
132 2 0.01
134 1 0.00
135 3 0.01
136 1 0.00
137 2 0.01
139 3 0.01
140 2 0.01
141 1 0.00
142 44 0.14
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.46
Consensus pattern (126 bp):
AAACAAATTATTAAACCAATATAATTGACTATATTATTTATATTATATATAATTATAATAATAAT
AACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATCACACTTTAATTGATACATATG
Found at i:17097 original size:142 final size:130
Alignment explanation
Indices: 16921--17254 Score: 373
Period size: 142 Copynumber: 2.5 Consensus size: 130
16911 TTATTATTTA
*
16921 TATTATTATTATAATACTAAGAAATTTCTTCTCTATTTATAATTCCATTTTAATTATTACACTTT
1 TATTATTA-TATAATACTAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATTACACTTT
*
16986 AATTGATGCATATGTCATATGAAACAAATTATTAAACCAAT-TAATTGACTATATTATTTATATT
65 AATTG-TG-----GT--TATGAAACAAATTATTAAACCAATATAATTGACTATATTATTTAT-GT
*
17050 ATTATTGTTATAAT
121 A-TA-T-ATAT-AT
* * **
17064 T-TTATTATACTAATAATAACAAATTTCTTCTCTATTTAAAATTAAATTTTAATTA-T-CA---T
1 TATTATTATA-TAATACTAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATTACACTTT
*
17123 ACTT-TGGTTATGAAACAAATTATTAAACCAATATAATTGACTATATTATTTATGTATATATATA
65 AATTGTGGTTATGAAACAAATTATTAAACCAATATAATTGACTATATTATTTATGTATATATATA
17187 T
130 T
* *
17188 TATT-TT-TAAAATACTAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATCACACTTTA
1 TATTATTATATAATACTAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATTACACTTTA
17251 ATTG
66 ATTG
17255 GTTGATGCTG
Statistics
Matches: 167, Mismatches: 15, Indels: 33
0.78 0.07 0.15
Matches are distributed among these distances:
122 40 0.24
123 2 0.01
124 7 0.04
125 5 0.03
126 1 0.01
127 6 0.04
128 26 0.16
129 20 0.12
130 2 0.01
135 2 0.01
137 4 0.02
140 2 0.01
141 3 0.02
142 46 0.28
143 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.47
Consensus pattern (130 bp):
TATTATTATATAATACTAACAAATTTCTTCTCTATTTATAATTCCATTTTAATTATTACACTTTA
ATTGTGGTTATGAAACAAATTATTAAACCAATATAATTGACTATATTATTTATGTATATATATAT
Found at i:18906 original size:6 final size:6
Alignment explanation
Indices: 18895--18961 Score: 66
Period size: 6 Copynumber: 11.3 Consensus size: 6
18885 AAAAGAGAGG
* * *
18895 AAAGAA AAAGAA AAAGGAA AAGGAA AAAGAA AAGGAA AAGGAA AAA-AA
1 AAAGAA AAAGAA AAA-GAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* *
18943 AGAGGA AAAGAA AAA-AA AA
1 AAAGAA AAAGAA AAAGAA AA
18962 TATTAATAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
5 8 0.16
6 38 0.75
7 5 0.10
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:18915 original size:12 final size:12
Alignment explanation
Indices: 18895--18957 Score: 76
Period size: 12 Copynumber: 5.2 Consensus size: 12
18885 AAAAGAGAGG
*
18895 AAAGAAAAAGAA
1 AAAGGAAAAGAA
18907 AAAGGAAAAGGAA
1 AAAGGAAAA-GAA
*
18920 AAA-GAAAAGGA
1 AAAGGAAAAGAA
18931 AAAGGAAAA-AA
1 AAAGGAAAAGAA
18942 AAGAGGAAAAGAA
1 AA-AGGAAAAGAA
18955 AAA
1 AAA
18958 AAAATATTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
11 8 0.18
12 26 0.59
13 10 0.23
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAGGAAAAGAA
Found at i:18921 original size:18 final size:17
Alignment explanation
Indices: 18895--18961 Score: 91
Period size: 18 Copynumber: 3.8 Consensus size: 17
18885 AAAAGAGAGG
*
18895 AAAGAAAAAGAAAAAGGA
1 AAAGGAAAA-AAAAAGGA
18913 AAAGGAAAAAGAAAAGGA
1 AAAGGAAAAA-AAAAGGA
18931 AAAGGAAAAAAAAGAGGA
1 AAAGGAAAAAAAA-AGGA
18949 AAA-GAAAAAAAAA
1 AAAGGAAAAAAAAA
18962 TATTAATAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
16 1 0.02
17 13 0.28
18 32 0.70
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAAGGAAAAAAAAAGGA
Done.