Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014355.1 Corchorus olitorius cultivar O-4 contig14388, 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: 49805
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8378 original size:19 final size:20
Alignment explanation
Indices: 8354--8411 Score: 82
Period size: 19 Copynumber: 2.9 Consensus size: 20
8344 CTGTTTGGCA
8354 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTAGC
* *
8373 ACTGTACAGATTAGATTATGT
1 ACTGTACAGATGAGATTA-GC
8394 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
8412 TTAGAGCAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAGC
Found at i:8399 original size:21 final size:20
Alignment explanation
Indices: 8354--8412 Score: 84
Period size: 21 Copynumber: 3.0 Consensus size: 20
8344 CTGTTTGGCA
8354 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTATC
* *
8373 ACTGTACAGATTAGATTATGT
1 ACTGTACAGATGAGATTAT-C
8394 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
8413 TAGAGCAGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 17 0.49
21 18 0.51
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ACTGTACAGATGAGATTATC
Found at i:9942 original size:23 final size:23
Alignment explanation
Indices: 9899--9942 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
9889 TAAATTATTT
*
9899 AATAAAATTAGTAAAATGATAAA
1 AATAAAATTAGTAAAAGGATAAA
*
9922 AATAAAA-TAGGTATAAGGATA
1 AATAAAATTA-GTAAAAGGATA
9943 TTAGATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (23 bp):
AATAAAATTAGTAAAAGGATAAA
Found at i:9991 original size:63 final size:67
Alignment explanation
Indices: 9918--10054 Score: 201
Period size: 69 Copynumber: 2.1 Consensus size: 67
9908 AGTAAAATGA
* *
9918 TAAAAAT-AAA-A-TAG-GTATAAGGATATTAGATTTATTTAAATAAAAATAGAGTTTTTAGTTG
1 TAAAAATAAAATACTAGAGTATAAGGATATTAGATTTAATCAAATAAAAATAGAGTTTTTAGTTG
9979 AG
66 AG
*
9981 TAAAAATAAAATACTAGTACTTATAAGGATATTAGATTTAATCAAATAAAAATAGAGTTTTTAGT
1 TAAAAATAAAATACTAG-A-GTATAAGGATATTAGATTTAATCAAATAAAAATAGAGTTTTTAGT
10046 TGAG
64 TGAG
10050 TAAAA
1 TAAAA
10055 CTATAAAAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
63 7 0.11
64 3 0.05
65 1 0.02
66 3 0.05
69 51 0.78
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.35
Consensus pattern (67 bp):
TAAAAATAAAATACTAGAGTATAAGGATATTAGATTTAATCAAATAAAAATAGAGTTTTTAGTTG
AG
Found at i:15213 original size:135 final size:135
Alignment explanation
Indices: 15009--15268 Score: 520
Period size: 135 Copynumber: 1.9 Consensus size: 135
14999 AATGAGAAGA
15009 ATTGCTTTGCTATTTTGAATGCTCTCCATACTTTTTGTGATAAGTCTGGGCAGAGGGTTAATTTT
1 ATTGCTTTGCTATTTTGAATGCTCTCCATACTTTTTGTGATAAGTCTGGGCAGAGGGTTAATTTT
15074 GACAAATCTAGAGTCTGGTTCTCGCCCAAGGTTGATGTTGACAAGGCCATTGAACTTTCCTGACA
66 GACAAATCTAGAGTCTGGTTCTCGCCCAAGGTTGATGTTGACAAGGCCATTGAACTTTCCTGACA
15139 AGGCC
131 AGGCC
15144 ATTGCTTTGCTATTTTGAATGCTCTCCATACTTTTTGTGATAAGTCTGGGCAGAGGGTTAATTTT
1 ATTGCTTTGCTATTTTGAATGCTCTCCATACTTTTTGTGATAAGTCTGGGCAGAGGGTTAATTTT
15209 GACAAATCTAGAGTCTGGTTCTCGCCCAAGGTTGATGTTGACAAGGCCATTGAACTTTCC
66 GACAAATCTAGAGTCTGGTTCTCGCCCAAGGTTGATGTTGACAAGGCCATTGAACTTTCC
15269 AACTTGCTAG
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
135 125 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.36
Consensus pattern (135 bp):
ATTGCTTTGCTATTTTGAATGCTCTCCATACTTTTTGTGATAAGTCTGGGCAGAGGGTTAATTTT
GACAAATCTAGAGTCTGGTTCTCGCCCAAGGTTGATGTTGACAAGGCCATTGAACTTTCCTGACA
AGGCC
Found at i:23835 original size:217 final size:212
Alignment explanation
Indices: 23553--23989 Score: 678
Period size: 217 Copynumber: 2.0 Consensus size: 212
23543 CCTTCCATTA
23553 GACTATTACAAGACACAGGACACTCACTACGTGAGTAATTTTTTGTATTTTTTTTAAATGGGTAG
1 GACT-TTACAAGACACAGGACACTCACTACGTGAGTAATTTTTTGTATTTTTTTTAAATGGGTAG
* * *
23618 TTTTTTTAAAATGATATAAATAAAATTTGAATACTTATATTTATCATGTAATGGGTAGTTTTATT
65 TTTTTTAAAAATGATATAAATAAAATTTAAATACTTATATTTATCATGTAATGGGTAATTTTATT
* * *
23683 TAAAATGGGTAGTTTTTATTTTGTTTTAAATTTTTAAAAACTGAGTTTGTGTCCGAGTTAACTCG
130 TAAAATGGGTAGTTTTTATTTAGTTTTAAATTTTT-AAAACTGAGTTTGAGTCCGAGTCAACTCG
23748 TGACACAAACTCAGGATTT
194 TGACACAAACTCAGGATTT
* *
23767 GACTTTACAAGACACAGG-CACTCACTACGTGAGTAGTTTTTGGTAGTTTTTATTTTTTAAATGG
1 GACTTTACAAGACACAGGACACTCACTACGTGAGTAATTTTT--T-G-TATT-TTTTTTAAATGG
** * *
23831 GTAGTTTTTTAAAAATGATATAAATAAAATTTAAATGTTTATATTTATCCTTTAATGGGTAATTT
61 GTAGTTTTTTAAAAATGATATAAATAAAATTTAAATACTTATATTTATCATGTAATGGGTAATTT
* *
23896 TATTTAAAATGGGTAGTTTTTATTTAGTTTTGAATTTTTAAAACTGAGTTTGAGTCTGAGTCAAC
126 TATTTAAAATGGGTAGTTTTTATTTAGTTTTAAATTTTTAAAACTGAGTTTGAGTCCGAGTCAAC
23961 TCGTGACACAAACTCAGGATTT
191 TCGTGACACAAACTCAGGATTT
23983 GACTTTA
1 GACTTTA
23990 TAATTAGTAT
Statistics
Matches: 204, Mismatches: 14, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
212 22 0.11
213 14 0.07
214 5 0.02
215 1 0.00
216 55 0.27
217 107 0.52
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (212 bp):
GACTTTACAAGACACAGGACACTCACTACGTGAGTAATTTTTTGTATTTTTTTTAAATGGGTAGT
TTTTTAAAAATGATATAAATAAAATTTAAATACTTATATTTATCATGTAATGGGTAATTTTATTT
AAAATGGGTAGTTTTTATTTAGTTTTAAATTTTTAAAACTGAGTTTGAGTCCGAGTCAACTCGTG
ACACAAACTCAGGATTT
Found at i:23906 original size:19 final size:20
Alignment explanation
Indices: 23884--23921 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23874 TTTATCCTTT
23884 AATGGGTA-ATTTTATTTAA
1 AATGGGTAGATTTTATTTAA
*
23903 AATGGGTAGTTTTTATTTA
1 AATGGGTAGATTTTATTTA
23922 GTTTTGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (20 bp):
AATGGGTAGATTTTATTTAA
Found at i:24029 original size:19 final size:20
Alignment explanation
Indices: 24005--24042 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23995 AGTATAGATT
24005 AATGGGTA-ATTTTATTTAA
1 AATGGGTAGATTTTATTTAA
*
24024 AATGGGTAGTTTTTATTTA
1 AATGGGTAGATTTTATTTA
24043 GTTTTGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (20 bp):
AATGGGTAGATTTTATTTAA
Found at i:24111 original size:121 final size:121
Alignment explanation
Indices: 23882--24124 Score: 407
Period size: 121 Copynumber: 2.0 Consensus size: 121
23872 TATTTATCCT
23882 TTAATGGGTAATTTTATTTAAAATGGGTAGTTTTTATTTAGTTTTGAATTTTTAAAACTGAGTTT
1 TTAATGGGTAATTTTATTTAAAATGGGTAGTTTTTATTTAGTTTTGAATTTTTAAAACTGAGTTT
* ** *
23947 GAGTCTGAGTCAACTCGTGACACAAACTCAGGATTTGACTTTATAATTAGTATAGA
66 GAGTCCGAGTCAACTCGTGACACAAACTCAAAATTAGACTTTATAATTAGTATAGA
*
24003 TTAATGGGTAATTTTATTTAAAATGGGTAGTTTTTATTTAGTTTTGAATTTTTAAAATTGAGTTT
1 TTAATGGGTAATTTTATTTAAAATGGGTAGTTTTTATTTAGTTTTGAATTTTTAAAACTGAGTTT
* *
24068 GAGTCCGAGTCAACTCGTGACACAAACTTAAAACTTAG-TTTTATAATTAGTATAGA
66 GAGTCCGAGTCAACTCGTGACACAAACTCAAAA-TTAGACTTTATAATTAGTATAGA
24124 T
1 T
24125 AATTAGTATA
Statistics
Matches: 114, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
121 111 0.97
122 3 0.03
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (121 bp):
TTAATGGGTAATTTTATTTAAAATGGGTAGTTTTTATTTAGTTTTGAATTTTTAAAACTGAGTTT
GAGTCCGAGTCAACTCGTGACACAAACTCAAAATTAGACTTTATAATTAGTATAGA
Found at i:24128 original size:13 final size:13
Alignment explanation
Indices: 24110--24135 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24100 ACTTAGTTTT
24110 ATAATTAGTATAG
1 ATAATTAGTATAG
24123 ATAATTAGTATAG
1 ATAATTAGTATAG
24136 TGATGCCAAA
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:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
ATAATTAGTATAG
Found at i:45498 original size:21 final size:21
Alignment explanation
Indices: 45458--45498 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
45448 AAAGAAAAAT
**
45458 TATTATTAAAAAATGTATAAA
1 TATTATTAAAAAATAAATAAA
*
45479 TATTATTAAGAAATAAATAA
1 TATTATTAAAAAATAAATAA
45499 CACACACTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (21 bp):
TATTATTAAAAAATAAATAAA
Found at i:46208 original size:43 final size:41
Alignment explanation
Indices: 46160--46488 Score: 441
Period size: 43 Copynumber: 7.8 Consensus size: 41
46150 CCAATAACTA
* *
46160 AAAGTCCCCAAACACATATATAACACATGGACATCTCTATTCC
1 AAAGTCCTCAAACACATATATAACACA-GGGCATCTCTATT-C
*
46203 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATT-
1 AAAGTCCTCAAACACATATATAACACAG-GGCATCTCTATTC
*
46244 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACA-GGGCATCTCTATT-C
*
46287 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATTC
1 AAAGTCCTCAAACACATATATAACACAG-GGCATCTCTATTC
46329 -AAGT-CTCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCT-CAAACACATATATAACACA-GGGCATCTCTATT-C
* *
46371 AAAGTCCTCAAACACATATATAACACAGAGGCATCT-AAATC
1 AAAGTCCTCAAACACATATATAACACAG-GGCATCTCTATTC
*
46412 AAAGTCCCCAAACACATATATAACACATGGGCATCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACA-GGGCATCTCTATT-C
46455 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCTCAAACACATATATAACACAG-GGCAT
46489 TTCTCCTTAT
Statistics
Matches: 257, Mismatches: 14, Indels: 30
0.85 0.05 0.10
Matches are distributed among these distances:
40 2 0.01
41 105 0.41
42 13 0.05
43 135 0.53
44 2 0.01
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (41 bp):
AAAGTCCTCAAACACATATATAACACAGGGCATCTCTATTC
Found at i:46256 original size:84 final size:84
Alignment explanation
Indices: 46160--46488 Score: 568
Period size: 84 Copynumber: 3.9 Consensus size: 84
46150 CCAATAACTA
* * *
46160 AAAGTCCCCAAACACATATATAACACATGGACATCTCTATTCCAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
46225 ACACAGAGGCATCTATATT
66 ACACAGAGGCATCTATATT
* *
46244 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
46309 ACACAGAGGCATCTATATT
66 ACACAGAGGCATCTATATT
* *
46328 CAAGTCTCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
* *
46393 ACACAGAGGCATCTAAATC
66 ACACAGAGGCATCTATATT
*
46412 AAAGTCCCCAAACACATATATAACACATGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
46477 ACACAGAGGCAT
66 ACACAGAGGCAT
46489 TTCTCCTTAT
Statistics
Matches: 231, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 231 1.00
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATT
Found at i:48087 original size:20 final size:19
Alignment explanation
Indices: 48046--48090 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
48036 AATCAACCTC
* * *
48046 TTTTAATGACCTTAATATG
1 TTTTTATGACCTTAAAAGG
48065 TTTTTATGACCTTATAAAGG
1 TTTTTATGACCTTA-AAAGG
48085 TTTTTA
1 TTTTTA
48091 GTAAGCTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (19 bp):
TTTTTATGACCTTAAAAGG
Found at i:48655 original size:20 final size:21
Alignment explanation
Indices: 48627--48665 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
48617 AAACTTCTAG
* *
48627 TAACTTTA-TAAAGTTTTTAA
1 TAACCTTATTAAACTTTTTAA
48647 TAACCTTATTAAACTTTTT
1 TAACCTTATTAAACTTTTT
48666 TATACTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (21 bp):
TAACCTTATTAAACTTTTTAA
Done.