Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019351.1 Corchorus olitorius cultivar O-4 contig19384, 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: 12153
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:8234 original size:87 final size:85
Alignment explanation
Indices: 7853--8385 Score: 281
Period size: 87 Copynumber: 6.0 Consensus size: 85
7843 ACCATCGGGG
* * * * * *
7853 GGTTACAAAAATTACATAAGGAGGTTACCAAAATTTTATAGGGTGATTACAAAAATTTCAT-AGC
1 GGTTACCAAAATT-CAT-TGGAGGTTACCAAAATTTCATAGCGAGGTTACAAAAA-TTCATAAG-
* * * *
7917 AAGCTTGCCAAAATTTCATAGCGAGGTTA
62 GAGGTTACCAAAATTTCAT----A-GTAA
* * *
7946 GGTTACAAAAATTTCATTGGGTGTGGTTACCAAAATTTCATA-CG-GAGTTACCAAAATTCATAA
1 GGTTACCAAAA-TTCATT--G-GAGGTTACCAAAATTTCATAGCGAG-GTTACAAAAATTCATAA
**
8009 GGAGGTTACCAAAATTTCATAGGGA
61 GGAGGTTACCAAAATTTCATAGTAA
* * * * *
8034 GGTTACCAAAATTTCATAAGGAGGTTACCATAATTTTATAGGGAGGTTACCAAAATTTCATAAGG
1 GGTTACCAAAA-TTCAT-TGGAGGTTACCAAAATTTCATAGCGAGGTTA-CAAAAATTCATAAGG
* *
8099 AGATTACTAAAATTTCATAGTAA
63 AGGTTACCAAAATTTCATAGTAA
** * * *
8122 GGTTACGGAAATT-TTTAAGGAGGTTACCAGAATTTCATAGCGAGGTTACAAGAAATTCATAGGG
1 GGTTACCAAAATTCATT--GGAGGTTACCAAAATTTCATAGCGAGGTTACAA-AAATTCATAAGG
* **
8186 AGGTTACCATAATTTTGTAGTAA
63 AGGTTACCAAAATTTCATAGTAA
* * *
8209 GGGTACCAAAATATCATTGTG-GGTTACCAAAATTTCATAATAGGGAGGTTACTAAAATTTTTCA
1 GGTTACCAAAAT-TCATTG-GAGGTTACCAAAATTTC---ATAGCGAGGTTAC-AAAA--ATTCA
* * * **
8273 T-AGGTAAGTTACCAAAGTTTAATAGGGA
58 TAAGG-AGGTTACCAAAATTTCATAGTAA
* * * * * *
8301 GGTTACCAAAATTTCATAGG-GCAGTTAACAAAATTTCATAAG-AAGGTTATCAAAATTTCTTAG
1 GGTTACCAAAA-TTCATTGGAG--GTTACCAAAATTTCAT-AGCGAGGTTA-CAAAAATTCATAA
** *
8364 GGAGGTTAGTAAAATTTTATAG
61 GGAGGTTACCAAAATTTCATAG
8386 GGTAGTTATC
Statistics
Matches: 348, Mismatches: 63, Indels: 63
0.73 0.13 0.13
Matches are distributed among these distances:
86 21 0.06
87 87 0.25
88 82 0.24
89 5 0.01
90 26 0.07
91 9 0.03
92 36 0.10
93 50 0.14
94 14 0.04
95 18 0.05
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (85 bp):
GGTTACCAAAATTCATTGGAGGTTACCAAAATTTCATAGCGAGGTTACAAAAATTCATAAGGAGG
TTACCAAAATTTCATAGTAA
Found at i:8386 original size:22 final size:22
Alignment explanation
Indices: 7853--8387 Score: 425
Period size: 22 Copynumber: 24.0 Consensus size: 22
7843 ACCATCGGGG
* * *
7853 GGTTACAAAAATTACATAAGGA
1 GGTTACCAAAATTTCATAGGGA
* *
7875 GGTTACCAAAATTTTATAGGGT
1 GGTTACCAAAATTTCATAGGGA
* * **
7897 GATTACAAAAATTTCATAGCAA
1 GGTTACCAAAATTTCATAGGGA
* *
7919 GCTTGCCAAAATTTCATAGCGAGGTTA
1 GGTTACCAAAATTTCATA--G-GG--A
* * *
7946 GGTTACAAAAATTTCATTGGGTGT
1 GGTTACCAAAATTTCA-TAGG-GA
*
7970 GGTTACCAAAATTTCATACGGA
1 GGTTACCAAAATTTCATAGGGA
*
7992 -GTTACCAAAA-TTCATAAGGA
1 GGTTACCAAAATTTCATAGGGA
8012 GGTTACCAAAATTTCATAGGGA
1 GGTTACCAAAATTTCATAGGGA
*
8034 GGTTACCAAAATTTCATAAGGA
1 GGTTACCAAAATTTCATAGGGA
* *
8056 GGTTACCATAATTTTATAGGGA
1 GGTTACCAAAATTTCATAGGGA
*
8078 GGTTACCAAAATTTCATAAGGA
1 GGTTACCAAAATTTCATAGGGA
* * **
8100 GATTACTAAAATTTCATAGTAA
1 GGTTACCAAAATTTCATAGGGA
** * *
8122 GGTTACGGAAATTT-TTAAGGA
1 GGTTACCAAAATTTCATAGGGA
* *
8143 GGTTACCAGAATTTCATAGCGA
1 GGTTACCAAAATTTCATAGGGA
*
8165 GGTTA-CAAGAAATTCATAGGGA
1 GGTTACCAA-AATTTCATAGGGA
* ** **
8187 GGTTACCATAATTTTGTAGTAA
1 GGTTACCAAAATTTCATAGGGA
* * * *
8209 GGGTACCAAAATATCATTGTG-
1 GGTTACCAAAATTTCATAGGGA
8230 GGTTACCAAAATTTCATAATAGGGA
1 GGTTACCAAAATTTC---ATAGGGA
* *
8255 GGTTACTAAAATTTTTCATAGGTA
1 GGTTACCAAAA--TTTCATAGGGA
* * *
8279 AGTTACCAAAGTTTAATAGGGA
1 GGTTACCAAAATTTCATAGGGA
8301 GGTTACCAAAATTTCATAGGGCA
1 GGTTACCAAAATTTCATAGGG-A
* * *
8324 -GTTAACAAAATTTCATAAGAA
1 GGTTACCAAAATTTCATAGGGA
* *
8345 GGTTATCAAAATTTCTTAGGGA
1 GGTTACCAAAATTTCATAGGGA
** *
8367 GGTTAGTAAAATTTTATAGGG
1 GGTTACCAAAATTTCATAGGG
8388 TAGTTATCCA
Statistics
Matches: 400, Mismatches: 93, Indels: 40
0.75 0.17 0.08
Matches are distributed among these distances:
20 9 0.02
21 50 0.12
22 270 0.68
23 5 0.01
24 34 0.09
25 11 0.03
26 2 0.00
27 18 0.05
28 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (22 bp):
GGTTACCAAAATTTCATAGGGA
Found at i:10633 original size:1 final size:1
Alignment explanation
Indices: 10627--10652 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
10617 TTACAGAGAA
10627 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
10653 CCATGTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:11756 original size:12 final size:13
Alignment explanation
Indices: 11739--11767 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
11729 ATGCTGGCCA
11739 ATATCTATAT-CT
1 ATATCTATATACT
11751 ATATCTATATACT
1 ATATCTATATACT
11764 ATAT
1 ATAT
11768 AAGTCTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATCTATATACT
Found at i:12062 original size:16 final size:16
Alignment explanation
Indices: 12041--12080 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12031 TGGATACATG
12041 ATCATCATTATCATTC
1 ATCATCATTATCATTC
* *
12057 ATCATCATTTTCCTTC
1 ATCATCATTATCATTC
12073 ATCATCAT
1 ATCATCAT
12081 CAGCATACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.45
Consensus pattern (16 bp):
ATCATCATTATCATTC
Done.