Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019803.1 Corchorus olitorius cultivar O-4 contig19836, 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: 29723
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2916 original size:22 final size:23
Alignment explanation
Indices: 2891--2933 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2881 CCACGTTTCA
*
2891 AATGAAGATTTATTAT-AAATGG
1 AATGAAGATTTAGTATCAAATGG
*
2913 AATGAATATTTAGTATCAAAT
1 AATGAAGATTTAGTATCAAAT
2934 AAGTTAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (23 bp):
AATGAAGATTTAGTATCAAATGG
Found at i:5953 original size:20 final size:20
Alignment explanation
Indices: 5928--5968 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5918 AGAGAGATTA
*
5928 TCAAAAATCATAGGAAGGTT
1 TCAAAAATCATAGGAAAGTT
*
5948 TCAAAATTCATAGGAAAGTT
1 TCAAAAATCATAGGAAAGTT
5968 T
1 T
5969 ATTAAAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (20 bp):
TCAAAAATCATAGGAAAGTT
Found at i:6035 original size:21 final size:22
Alignment explanation
Indices: 6011--6067 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
6001 CTTATGGAGT
* *
6011 TTATCACAATTTTATA-GGTAA
1 TTATCAAAATTTCATATGGTAA
6032 TTATCAAAATTTCATATGGT-A
1 TTATCAAAATTTCATATGGTAA
*
6053 GT-TCAAAATTTCATA
1 TTATCAAAATTTCATA
6068 AAATATTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.41
21 16 0.50
22 3 0.09
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTCATATGGTAA
Found at i:7721 original size:48 final size:48
Alignment explanation
Indices: 7665--7784 Score: 213
Period size: 48 Copynumber: 2.5 Consensus size: 48
7655 ATCGTATTCA
*
7665 ATGCGTGTGGGTTTTGTGCAGTTTTATGTTATAGTTTGTTTATTGGTC
1 ATGCGTGTGGGTTTTGTGCAGCTTTATGTTATAGTTTGTTTATTGGTC
* *
7713 ATGTGTGTGGGTTTTGTGCAACTTTATGTTATAGTTTGTTTATTGGTC
1 ATGCGTGTGGGTTTTGTGCAGCTTTATGTTATAGTTTGTTTATTGGTC
7761 ATGCGTGTGGGTTTTGTGCAGCTT
1 ATGCGTGTGGGTTTTGTGCAGCTT
7785 GATGGGAGTC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 67 1.00
ACGTcount: A:0.12, C:0.07, G:0.30, T:0.50
Consensus pattern (48 bp):
ATGCGTGTGGGTTTTGTGCAGCTTTATGTTATAGTTTGTTTATTGGTC
Found at i:20163 original size:42 final size:43
Alignment explanation
Indices: 20112--20205 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
20102 AGTACGTTAC
*
20112 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
20153 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
20198 CTAATATT
1 CTAATATT
20206 AATTGTTGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
45 38 0.79
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:25067 original size:38 final size:38
Alignment explanation
Indices: 25016--25091 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
25006 AAGGCCCAAG
* * *
25016 TCAAGAAACAAACCGTA-CTCAATTCATGAAATAAACCA
1 TCAAGAAACAAACC-AAGCCCAAGTCATGAAATAAACCA
*
25054 TCAAGAAATAAACCAAGCCCAAGTCATGAAATAAACCA
1 TCAAGAAACAAACCAAGCCCAAGTCATGAAATAAACCA
25092 AGCCCATGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.51, C:0.24, G:0.09, T:0.16
Consensus pattern (38 bp):
TCAAGAAACAAACCAAGCCCAAGTCATGAAATAAACCA
Found at i:25828 original size:20 final size:19
Alignment explanation
Indices: 25803--25847 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
25793 ACTGACAGGC
*
25803 ACCTAATTGACCAAATTTAA
1 ACCTAATGGACCAAA-TTAA
*
25823 ACCTAAGGGACCAAATTAA
1 ACCTAATGGACCAAATTAA
25842 A-CTAAT
1 ACCTAAT
25848 CCAGGGGCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 4 0.18
19 5 0.23
20 13 0.59
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (19 bp):
ACCTAATGGACCAAATTAA
Found at i:28236 original size:6 final size:6
Alignment explanation
Indices: 28212--28248 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
28202 ATGAACCTGA
28212 AACCCG AAACCCG --CCCG AACCCG AACCCG AACCCG AA
1 AACCCG -AACCCG AACCCG AACCCG AACCCG AACCCG AA
28249 ATTACCCGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
4 4 0.14
6 18 0.64
7 6 0.21
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
AACCCG
Found at i:28313 original size:16 final size:16
Alignment explanation
Indices: 28294--28337 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
28284 ACCCGTCCGA
*
28294 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAAAT
*
28310 ACCCGAGCCCGAAAAT
1 ACCCGAACCCGAAAAT
28326 ACCCGAACCCGA
1 ACCCGAACCCGA
28338 CCCGAGACCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.36, C:0.41, G:0.16, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:28342 original size:11 final size:12
Alignment explanation
Indices: 28327--28371 Score: 60
Period size: 11 Copynumber: 3.9 Consensus size: 12
28317 CCCGAAAATA
28327 CCCGAACCCGA-
1 CCCGAACCCGAG
28338 CCCGAGA-CCGAG
1 CCCGA-ACCCGAG
28350 CCCG-ACCCGAG
1 CCCGAACCCGAG
28361 CCCGAACCCGA
1 CCCGAACCCGA
28372 AATAATTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 18 0.60
12 11 0.37
ACGTcount: A:0.24, C:0.51, G:0.24, T:0.00
Consensus pattern (12 bp):
CCCGAACCCGAG
Found at i:28353 original size:17 final size:17
Alignment explanation
Indices: 28328--28371 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
28318 CCGAAAATAC
28328 CCGAACCCGACCCGAGA
1 CCGAACCCGACCCGAGA
* *
28345 CCGAGCCCGACCCGAGC
1 CCGAACCCGACCCGAGA
28362 CCGAACCCGA
1 CCGAACCCGA
28372 AATAATTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.25, C:0.50, G:0.25, T:0.00
Consensus pattern (17 bp):
CCGAACCCGACCCGAGA
Found at i:29182 original size:12 final size:11
Alignment explanation
Indices: 29165--29204 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
29155 ATCAAAATCA
29165 AACCCGAGCCCG
1 AACCCGA-CCCG
29177 AACCCGACCCG
1 AACCCGACCCG
*
29188 AGCCCGAACCCG
1 AACCCG-ACCCG
29200 AACCC
1 AACCC
29205 TACTCGAGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.28, C:0.53, G:0.20, T:0.00
Consensus pattern (11 bp):
AACCCGACCCG
Found at i:29188 original size:17 final size:17
Alignment explanation
Indices: 29166--29200 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
29156 TCAAAATCAA
29166 ACCCGAGCCCGAACCCG
1 ACCCGAGCCCGAACCCG
29183 ACCCGAGCCCGAACCCG
1 ACCCGAGCCCGAACCCG
29200 A
1 A
29201 ACCCTACTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.26, C:0.51, G:0.23, T:0.00
Consensus pattern (17 bp):
ACCCGAGCCCGAACCCG
Found at i:29193 original size:23 final size:23
Alignment explanation
Indices: 29167--29223 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
29157 CAAAATCAAA
29167 CCCGAGCCCGAACCCGACCCGAG
1 CCCGAGCCCGAACCCGACCCGAG
* * *
29190 CCCGAACCCGAACCCTACTCGAG
1 CCCGAGCCCGAACCCGACCCGAG
*
29213 CCCGAGTCCGA
1 CCCGAGCCCGA
29224 CATAACCCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.23, C:0.49, G:0.23, T:0.05
Consensus pattern (23 bp):
CCCGAGCCCGAACCCGACCCGAG
Found at i:29254 original size:16 final size:16
Alignment explanation
Indices: 29228--29288 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
29218 GTCCGACATA
*
29228 ACCCGAGCCCGAAAAT
1 ACCCGAACCCGAAAAT
* **
29244 ACCTGAACCCG-ACTT
1 ACCCGAACCCGAAAAT
*
29259 AACCCGAACCCAAAAAT
1 -ACCCGAACCCGAAAAT
29276 ACCCGAACCCGAA
1 ACCCGAACCCGAA
29289 CCCGTCCAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
15 2 0.06
16 30 0.88
17 2 0.06
ACGTcount: A:0.39, C:0.39, G:0.13, T:0.08
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:29262 original size:32 final size:32
Alignment explanation
Indices: 29220--29287 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
29210 GAGCCCGAGT
* * *
29220 CCGACATAACCCGAGCCCGAAAATACCTGAAC
1 CCGACATAACCCGAACCCAAAAATACCCGAAC
*
29252 CCGACTTAACCCGAACCCAAAAATACCCGAAC
1 CCGACATAACCCGAACCCAAAAATACCCGAAC
29284 CCGA
1 CCGA
29288 ACCCGTCCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.40, G:0.13, T:0.09
Consensus pattern (32 bp):
CCGACATAACCCGAACCCAAAAATACCCGAAC
Done.