Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021251.1 Corchorus olitorius cultivar O-4 contig21284, 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: 44199
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:312 original size:23 final size:23
Alignment explanation
Indices: 266--312 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
256 GCAAATGCTC
* *
266 ATGTACAATGTGATGACAATAAG
1 ATGTAAAATGTGATGACAAGAAG
289 ATGTAAAATGTAGATGA-AAGAAG
1 ATGTAAAATGT-GATGACAAGAAG
312 A
1 A
313 ACCTGTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.49, C:0.04, G:0.23, T:0.23
Consensus pattern (23 bp):
ATGTAAAATGTGATGACAAGAAG
Found at i:5483 original size:12 final size:11
Alignment explanation
Indices: 5468--5497 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5458 GAAAAATATC
5468 AAAAAAATAAA
1 AAAAAAATAAA
*
5479 AAAAAAGTAAA
1 AAAAAAATAAA
5490 AAAAAAAT
1 AAAAAAAT
5498 TCGACCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:6170 original size:2 final size:2
Alignment explanation
Indices: 6163--6190 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6153 CAAGGTATAA
6163 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
6191 TTGTGAGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:9316 original size:41 final size:41
Alignment explanation
Indices: 9217--9316 Score: 112
Period size: 41 Copynumber: 2.4 Consensus size: 41
9207 ATAATTTCTA
* * * *
9217 AAATCAGGGATCAAATTAAATCAAATAGTAACTAATATCCT
1 AAATCAGGGACCAAATTGAATCAAATAGTAAATAATAACCT
* * * *
9258 AAATCAGGGGCTAAATTGCATCAAATAGTAAAT-ATCAACTT
1 AAATCAGGGACCAAATTGAATCAAATAGTAAATAAT-AACCT
9299 AAATCAGGGACCAAATTG
1 AAATCAGGGACCAAATTG
9317 TAAACGGGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
40 2 0.04
41 46 0.96
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (41 bp):
AAATCAGGGACCAAATTGAATCAAATAGTAAATAATAACCT
Found at i:11714 original size:14 final size:15
Alignment explanation
Indices: 11697--11732 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
11687 TCTTTTCCCA
11697 TTTTTTTGTTTTT-G
1 TTTTTTTGTTTTTGG
*
11711 TTTTTTGGTTTTTGG
1 TTTTTTTGTTTTTGG
11726 TTTTTTT
1 TTTTTTT
11733 TTCTTATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (15 bp):
TTTTTTTGTTTTTGG
Found at i:14149 original size:17 final size:17
Alignment explanation
Indices: 14127--14159 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
14117 ATTCACATTA
*
14127 AAAAAACATGAATCATC
1 AAAAAACATAAATCATC
14144 AAAAAACATAAATCAT
1 AAAAAACATAAATCAT
14160 GTGTTTCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.15, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAAACATAAATCATC
Found at i:15065 original size:93 final size:93
Alignment explanation
Indices: 14953--15180 Score: 277
Period size: 93 Copynumber: 2.5 Consensus size: 93
14943 GTTTGTAAAC
*
14953 GCCGCTATATGTAAAATAAATATTTTTATCATATAAAAAATATATCGTTTTGACAAAATAAAATT
1 GCCGCTATATGTAAAATAAATATTTTTATCATATCAAAAATATATCGTTTTGACAAAATAAAATT
15018 TGAAGATC-GCGGCGTTT-ACA-AACCAAAT
66 TGAAGA-CAGCGGCGTTTAACAGAA--AAAT
* * *** *
15046 GCTGCTATATGTAAAATAAATGTTTTTATCATCA-CCGGAA-ATATCGTTTTGACAAAATAGAAT
1 GCCGCTATATGTAAAATAAATATTTTTATCAT-ATCAAAAATATATCGTTTTGACAAAATAAAAT
** *
15109 TTGCCGACAGGGGCGTTTCAACAGAAAAAT
65 TTGAAGACAGCGGCGTTT-AACAGAAAAAT
*
15139 GCCGCTATATGTAAAATAAATATATTTATCATATCAAAAATA
1 GCCGCTATATGTAAAATAAATATTTTTATCATATCAAAAATA
15181 ACATAAGAAT
Statistics
Matches: 112, Mismatches: 16, Indels: 13
0.79 0.11 0.09
Matches are distributed among these distances:
91 1 0.01
92 36 0.32
93 68 0.61
94 5 0.04
95 2 0.02
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (93 bp):
GCCGCTATATGTAAAATAAATATTTTTATCATATCAAAAATATATCGTTTTGACAAAATAAAATT
TGAAGACAGCGGCGTTTAACAGAAAAAT
Found at i:19206 original size:55 final size:55
Alignment explanation
Indices: 19135--19253 Score: 229
Period size: 55 Copynumber: 2.2 Consensus size: 55
19125 ATAGGGTTTT
*
19135 TTTTTTTTTATTTGTTACGTGTAAATTGTATAATGGAAGATAATAGGGATTAGGG
1 TTTTTTTTTATTTGTTACGTGTAAATTGTATAATGGAAGATAATAGGAATTAGGG
19190 TTTTTTTTTATTTGTTACGTGTAAATTGTATAATGGAAGATAATAGGAATTAGGG
1 TTTTTTTTTATTTGTTACGTGTAAATTGTATAATGGAAGATAATAGGAATTAGGG
19245 TTTTTTTTT
1 TTTTTTTTT
19254 TTTTTTGCTG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 63 1.00
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.50
Consensus pattern (55 bp):
TTTTTTTTTATTTGTTACGTGTAAATTGTATAATGGAAGATAATAGGAATTAGGG
Found at i:22214 original size:13 final size:13
Alignment explanation
Indices: 22196--22221 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22186 AAGGTAACAA
22196 CAAAAATCATCAC
1 CAAAAATCATCAC
22209 CAAAAATCATCAC
1 CAAAAATCATCAC
22222 TCATGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:23776 original size:19 final size:21
Alignment explanation
Indices: 23735--23776 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
23725 AAATATTACC
*
23735 ATAATTATTTTTGACAGCCATA
1 ATAATTATTTTTGACA-CAATA
23757 ATAATTATTTTTG-C-CAATA
1 ATAATTATTTTTGACACAATA
23776 A
1 A
23777 ATAAAATTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 5 0.26
21 1 0.05
22 13 0.68
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (21 bp):
ATAATTATTTTTGACACAATA
Found at i:36125 original size:30 final size:30
Alignment explanation
Indices: 36089--36150 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
36079 CTTCCAGTTT
36089 TGCATTTTCTTCCCATCAATGACTCCCTGA
1 TGCATTTTCTTCCCATCAATGACTCCCTGA
*
36119 TGCATTTTCTTCCCATCAATGATTCCCTGA
1 TGCATTTTCTTCCCATCAATGACTCCCTGA
36149 TG
1 TG
36151 TTATGGTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.19, C:0.31, G:0.11, T:0.39
Consensus pattern (30 bp):
TGCATTTTCTTCCCATCAATGACTCCCTGA
Found at i:36539 original size:3 final size:3
Alignment explanation
Indices: 36531--36615 Score: 86
Period size: 3 Copynumber: 27.0 Consensus size: 3
36521 CATGGGATGG
36531 GAA GAA GAA -ATA GAA GAA GAA GAA GAA GAAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GA-A GAA GAA GAA GAA GAA G-AA GAA GAA GAA GAA GAA
36577 GAAA GAAA GAAA GAAA GAAA GAA -AA G-A GAA GAA GAA GAA
1 G-AA G-AA G-AA G-AA G-AA GAA GAA GAA GAA GAA GAA GAA
36616 TGTATAATTA
Statistics
Matches: 76, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
2 5 0.07
3 48 0.63
4 23 0.30
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:36582 original size:4 final size:4
Alignment explanation
Indices: 36556--36600 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
36546 GAAGAAGAAG
36556 AAGA AAG- AAG- AAG- AAG- AAG- AAGA AAGA AAGA AAGA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
36599 AA
1 AA
36601 AGAGAAGAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 15 0.38
4 25 0.62
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:37836 original size:2 final size:2
Alignment explanation
Indices: 37829--37859 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
37819 CCAACCCACT
37829 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
37860 ACCAGAAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39061 original size:29 final size:30
Alignment explanation
Indices: 39028--39097 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 30
39018 TGATTGTTGA
39028 AGGCAAAATGTCCAAAAT-TA-AAGTTCAAGG
1 AGGCAAAATGTCC-AAATGTACAAGTTC-AGG
**
39058 -GGCAAAGCGTCCAAATGGTACAAGTTCAGG
1 AGGCAAAATGTCCAAAT-GTACAAGTTCAGG
39088 AGGCAAAATG
1 AGGCAAAATG
39098 GTTCTTTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
28 4 0.12
29 10 0.31
30 5 0.16
31 13 0.41
ACGTcount: A:0.41, C:0.16, G:0.26, T:0.17
Consensus pattern (30 bp):
AGGCAAAATGTCCAAATGTACAAGTTCAGG
Found at i:40498 original size:14 final size:14
Alignment explanation
Indices: 40479--40506 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40469 TTTGAGTTTT
40479 TCCTTATAACTTGC
1 TCCTTATAACTTGC
40493 TCCTTATAACTTGC
1 TCCTTATAACTTGC
40507 AGTCATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.07, T:0.43
Consensus pattern (14 bp):
TCCTTATAACTTGC
Found at i:40856 original size:54 final size:54
Alignment explanation
Indices: 40797--40967 Score: 299
Period size: 54 Copynumber: 3.1 Consensus size: 54
40787 TTGTGCATTA
40797 ATAGCTCAATTGCTTCAATTACAGAACCTTTTACAAGCAATTATATCTGCATCT
1 ATAGCTCAATTGCTTCAATTACAGAACCTTTTACAAGCAATTATATCTGCATCT
40851 ATAGCTCAATTGCTTCAATTACAGAACCTTTTACAAGCAATTATATCTGCATCT
1 ATAGCTCAATTGCTTCAATTACAGAACCTTTTACAAGCAATTATATCTGCATCT
* *
40905 ATAGCTCAATTGCTTCAATTACAGAACCCTTTTACAAGCAAATATATTTGCAT-T
1 ATAGCTCAATTGCTTCAATTACAGAA-CCTTTTACAAGCAATTATATCTGCATCT
40959 CATAGCTCA
1 -ATAGCTCA
40968 CATGTGCATA
Statistics
Matches: 113, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
54 81 0.72
55 32 0.28
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.35
Consensus pattern (54 bp):
ATAGCTCAATTGCTTCAATTACAGAACCTTTTACAAGCAATTATATCTGCATCT
Found at i:43982 original size:8 final size:8
Alignment explanation
Indices: 43969--43998 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
43959 TAGTAGTCAG
43969 AACATACA
1 AACATACA
43977 AACATACA
1 AACATACA
43985 AACATACA
1 AACATACA
43993 AACATA
1 AACATA
43999 GATAACATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.63, C:0.23, G:0.00, T:0.13
Consensus pattern (8 bp):
AACATACA
Done.