Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001420.1 Corchorus olitorius cultivar O-4 contig01420, 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: 1693
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:62 original size:22 final size:21
Alignment explanation
Indices: 37--157 Score: 86
Period size: 22 Copynumber: 5.6 Consensus size: 21
27 TCATAGTGTA
*
37 GTTATCAAAATTTTATACAGG
1 GTTATCAAAATTTTATACAAG
* * *
58 CGTTA-CCAAATTTCATAAAAAG
1 -GTTATCAAAATTTTAT-ACAAG
* * *
80 GTTATC-AAATTTTCT-TAGG
1 GTTATCAAAATTTTATACAAG
*
99 CCGTTAACAAAATTTTATACGAAG
1 --GTTATCAAAATTTTATAC-AAG
*
123 GTTAACAAAATTTTATACGAAG
1 GTTATCAAAATTTTATAC-AAG
145 GTTATCAAAATTT
1 GTTATCAAAATTT
158 ATAGTGTGGT
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
19 2 0.03
21 25 0.32
22 50 0.63
24 2 0.03
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (21 bp):
GTTATCAAAATTTTATACAAG
Found at i:84 original size:43 final size:45
Alignment explanation
Indices: 37--140 Score: 117
Period size: 43 Copynumber: 2.4 Consensus size: 45
27 TCATAGTGTA
*
37 GTTATCAAAATTTTATACAGG-CGTT-ACCAAATTTCATAAAAAG
1 GTTATCAAAATTTTATACAGGCCGTTAACAAAATTTCATAAAAAG
* * * **
80 GTTATC-AAATTTTCT-TAGGCCGTTAACAAAATTTTATACGAAG
1 GTTATCAAAATTTTATACAGGCCGTTAACAAAATTTCATAAAAAG
*
123 GTTAACAAAATTTTATAC
1 GTTATCAAAATTTTATAC
141 GAAGGTTATC
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
41 3 0.06
42 12 0.25
43 25 0.52
44 8 0.17
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (45 bp):
GTTATCAAAATTTTATACAGGCCGTTAACAAAATTTCATAAAAAG
Found at i:160 original size:21 final size:22
Alignment explanation
Indices: 101--157 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
91 TTCTTAGGCC
101 GTTAACAAAATTTTATACGAAG
1 GTTAACAAAATTTTATACGAAG
123 GTTAACAAAATTTTATACGAAG
1 GTTAACAAAATTTTATACGAAG
*
145 GTTATCAAAATTT
1 GTTAACAAAATTT
158 ATAGTGTGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (22 bp):
GTTAACAAAATTTTATACGAAG
Found at i:175 original size:65 final size:64
Alignment explanation
Indices: 13--178 Score: 165
Period size: 65 Copynumber: 2.6 Consensus size: 64
3 TTTCATATGG
* * * *
13 AGGTTATCAAAACGTCATAGTGTAGTTATCAAAATTTTATACAGGCGTTACCAAATTTCATAAAA
1 AGGTTATCAAAA-TTTATAGTGTAGTTATCAAAATTTTATACAAGCGTTACAAAATTTCATAAAA
* * ** * * *
78 AGGTTATCAAATTTTCTTAG-GCCGTTAACAAAATTTTATACGAAG-GTTAACAAAATTTTATAC
1 AGGTTATCAAAATTT-ATAGTGTAGTTATCAAAATTTTATAC-AAGCGTT-ACAAAATTTCATAA
*
141 GA
63 AA
*
143 AGGTTATCAAAATTTATAGTGTGGTTATCAAAATTT
1 AGGTTATCAAAATTTATAGTGTAGTTATCAAAATTT
179 CATGGGGGGG
Statistics
Matches: 80, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
64 25 0.31
65 55 0.69
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (64 bp):
AGGTTATCAAAATTTATAGTGTAGTTATCAAAATTTTATACAAGCGTTACAAAATTTCATAAAA
Found at i:236 original size:22 final size:22
Alignment explanation
Indices: 65--243 Score: 98
Period size: 22 Copynumber: 8.1 Consensus size: 22
55 AGGCGTTACC
** *
65 AAATTTCATAAAAAGGTTATCA
1 AAATTTCATAGGAAGGTTAACA
* * **
87 AATTTTCTTAGG-CCGTTAACA
1 AAATTTCATAGGAAGGTTAACA
* *
108 AAATTTTATACGAAGGTTAACA
1 AAATTTCATAGGAAGGTTAACA
* * *
130 AAATTTTATACGAAGGTTATCA
1 AAATTTCATAGGAAGGTTAACA
* *
152 AAATTT-ATAGTG-TGGTTATCA
1 AAATTTCATAG-GAAGGTTAACA
* * *
173 AAATTTCATGGGGGGGAGGTTATCA
1 AAATTTCAT---AGGAAGGTTAACA
* *
198 AAGTTTTC-TAGGGAGGTTAACA
1 AA-ATTTCATAGGAAGGTTAACA
*
220 AAATTTCATTGGAAGGTT-ACA
1 AAATTTCATAGGAAGGTTAACA
241 AAA
1 AAA
244 ATTTTGTGGA
Statistics
Matches: 124, Mismatches: 24, Indels: 19
0.74 0.14 0.11
Matches are distributed among these distances:
21 41 0.33
22 66 0.53
24 1 0.01
25 12 0.10
26 4 0.03
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (22 bp):
AAATTTCATAGGAAGGTTAACA
Found at i:386 original size:22 final size:22
Alignment explanation
Indices: 358--520 Score: 154
Period size: 22 Copynumber: 7.5 Consensus size: 22
348 TGCGCTTACC
*
358 AATTTCATAGTGTGATTATCAA
1 AATTTCATAGAGTGATTATCAA
**
380 AATTTCATAGAAAGATTATCAA
1 AATTTCATAGAGTGATTATCAA
* *
402 AATTTCACAGAGTGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* * *
424 AATTTTCATA-ATGCGCTTA-C-C
1 AA-TTTCATAGA-GTGATTATCAA
*
445 AATTTCATAGTGTGATTATCAA
1 AATTTCATAGAGTGATTATCAA
*
467 AATTTCATAG-GAAGATTATCAA
1 AATTTCATAGAG-TGATTATCAA
* *
489 AATTTCACAGAGTGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
*
511 ATTTTCATAG
1 AATTTCATAG
521 GTTATCGAAA
Statistics
Matches: 113, Mismatches: 21, Indels: 14
0.76 0.14 0.09
Matches are distributed among these distances:
20 12 0.11
21 4 0.04
22 85 0.75
23 12 0.11
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (22 bp):
AATTTCATAGAGTGATTATCAA
Found at i:433 original size:87 final size:87
Alignment explanation
Indices: 327--519 Score: 370
Period size: 87 Copynumber: 2.2 Consensus size: 87
317 CTTAATGGTA
327 TGGTTATCAAAATTTTCATAATGCGCTTACCAATTTCATAGTGTGATTATCAAAATTTCATAGAA
1 TGGTTATCAAAATTTTCATAATGCGCTTACCAATTTCATAGTGTGATTATCAAAATTTCATAGAA
392 AGATTATCAAAATTTCACAGAG
66 AGATTATCAAAATTTCACAGAG
*
414 TGGTTATCAAAATTTTCATAATGCGCTTACCAATTTCATAGTGTGATTATCAAAATTTCATAGGA
1 TGGTTATCAAAATTTTCATAATGCGCTTACCAATTTCATAGTGTGATTATCAAAATTTCATAGAA
479 AGATTATCAAAATTTCACAGAG
66 AGATTATCAAAATTTCACAGAG
501 TGGTTATC-AAATTTTCATA
1 TGGTTATCAAAATTTTCATA
520 GGTTATCGAA
Statistics
Matches: 105, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
86 11 0.10
87 94 0.90
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (87 bp):
TGGTTATCAAAATTTTCATAATGCGCTTACCAATTTCATAGTGTGATTATCAAAATTTCATAGAA
AGATTATCAAAATTTCACAGAG
Found at i:521 original size:44 final size:44
Alignment explanation
Indices: 358--521 Score: 181
Period size: 44 Copynumber: 3.8 Consensus size: 44
348 TGCGCTTACC
* * *
358 AATTTCATAGTGTGATTATCAAAATTTCATAGAAAGATTATCAA
1 AATTTCACAGAGTGATTATCAAAATTTCATAGGAAGATTATCAA
* * * * *
402 AATTTCACAGAGTGGTTATCAAAATTTTCATAATG-CGCTTA-C-C
1 AATTTCACAGAGTGATTATCAAAA-TTTCAT-AGGAAGATTATCAA
* *
445 AATTTCATAGTGTGATTATCAAAATTTCATAGGAAGATTATCAA
1 AATTTCACAGAGTGATTATCAAAATTTCATAGGAAGATTATCAA
* *
489 AATTTCACAGAGTGGTTATCAAATTTTCATAGG
1 AATTTCACAGAGTGATTATCAAAATTTCATAGG
522 TTATCGAAAT
Statistics
Matches: 96, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
41 2 0.02
42 10 0.10
43 22 0.23
44 51 0.53
45 10 0.10
46 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (44 bp):
AATTTCACAGAGTGATTATCAAAATTTCATAGGAAGATTATCAA
Found at i:525 original size:18 final size:19
Alignment explanation
Indices: 502--557 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
492 TTCACAGAGT
502 GGTTATCAAATTTTCAT-A
1 GGTTATCAAATTTTCATGA
*
520 GGTTATCGAAATTTCGTAATGA
1 GGTTATC-AAATTT--TCATGA
*
542 TGTTATCAAATTTTCA
1 GGTTATCAAATTTTCA
558 CATCATTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 7 0.23
19 8 0.26
21 9 0.29
22 7 0.23
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (19 bp):
GGTTATCAAATTTTCATGA
Done.