Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023591.1 Corchorus olitorius cultivar O-4 contig23624, 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: 26417
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:109 original size:40 final size:40
Alignment explanation
Indices: 1--155 Score: 247
Period size: 40 Copynumber: 3.9 Consensus size: 40
1 AGGAATTTAAACAACACCTTCCGGTGGGGAAGGGTAAAAC
1 AGGAATTTAAACAACACCTTCCGGTGGGGAAGGGTAAAAC
41 AGGAATTTAAAACAACACCTTCCGGTGGGGAAGGGTAAAAC
1 AGGAATTT-AAACAACACCTTCCGGTGGGGAAGGGTAAAAC
* * *
82 AGGAATTTAAACAGCACCTTCCTGTGGGGAAGGGTAAACC
1 AGGAATTTAAACAACACCTTCCGGTGGGGAAGGGTAAAAC
* * *
122 AAGAATTTAAACAACACCTTCTGGTTGGGAAGGG
1 AGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
156 CAAATTGGGA
Statistics
Matches: 106, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 66 0.62
41 40 0.38
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.19
Consensus pattern (40 bp):
AGGAATTTAAACAACACCTTCCGGTGGGGAAGGGTAAAAC
Found at i:184 original size:48 final size:47
Alignment explanation
Indices: 128--308 Score: 224
Period size: 47 Copynumber: 3.9 Consensus size: 47
118 AACCAAGAAT
* *
128 TTAAACAACACCTTCTGGTTG-GGAAGGGCAAAT-TGGGAAAAAGCAGAC
1 TTAAACAACACCTTC-CGATGAGGAAGGGC-AATCTGGG-AAAAGCAGAC
* *
176 TTAAACAACACCTTCCGATGAGGAAGGACAATCTAGGAAAAGCAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAATCTGGGAAAAGCAGAC
* * *
223 TTAAACAACACCTTCCAATGAGGAAGGGCAATCTGGG-TAAGCATAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAATCTGGGAAAAGCAGAC
* * *
269 TTAAACAACACCTTCCGATGAGAAAGGGCAAGCTGAGAAA
1 TTAAACAACACCTTCCGATGAGGAAGGGCAATCTGGGAAA
309 GGACAACAAA
Statistics
Matches: 116, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
46 40 0.34
47 51 0.44
48 25 0.22
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (47 bp):
TTAAACAACACCTTCCGATGAGGAAGGGCAATCTGGGAAAAGCAGAC
Found at i:398 original size:41 final size:41
Alignment explanation
Indices: 341--486 Score: 178
Period size: 40 Copynumber: 3.6 Consensus size: 41
331 GGGGAAAGGC
341 AAGTAAACAACACCTTCCGGTGGGGGAAAGGC-AAACTGGGA
1 AAGTAAACAACACCTTCCGGT-GGGGAAAGGCAAAACTGGGA
382 AAGTAAACAACACCTTCCGGT-GGGAAAGGGCAAAAC-GGG-
1 AAGTAAACAACACCTTCCGGTGGGGAAA-GGCAAAACTGGGA
* * *
421 AATTGAAACCACACCTTCCGGTGGGAAAAGGCAAAACAT--GA
1 AAGT-AAACAACACCTTCCGGTGGGGAAAGGCAAAAC-TGGGA
*
462 AAGTAAGCAACACCTTCCGGTGGGG
1 AAGTAAACAACACCTTCCGGTGGGG
487 GAGGAACTTT
Statistics
Matches: 91, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
39 9 0.10
40 49 0.54
41 33 0.36
ACGTcount: A:0.37, C:0.21, G:0.29, T:0.13
Consensus pattern (41 bp):
AAGTAAACAACACCTTCCGGTGGGGAAAGGCAAAACTGGGA
Found at i:7909 original size:25 final size:25
Alignment explanation
Indices: 7875--7923 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
7865 CCAAACAATC
*
7875 TTGAACACTCTCGCTCGGTCTCTAT
1 TTGAACACTCTCACTCGGTCTCTAT
*
7900 TTGAGCACTCTCACTCGGTCTCTA
1 TTGAACACTCTCACTCGGTCTCTA
7924 CAAACCAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.16, C:0.33, G:0.16, T:0.35
Consensus pattern (25 bp):
TTGAACACTCTCACTCGGTCTCTAT
Found at i:7949 original size:21 final size:21
Alignment explanation
Indices: 7920--7961 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
7910 TCACTCGGTC
*
7920 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
7940 TCTACCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
7962 CACACACACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:11277 original size:175 final size:173
Alignment explanation
Indices: 10980--11294 Score: 400
Period size: 175 Copynumber: 1.8 Consensus size: 173
10970 ACTTTCGAAT
* * * * * * *
10980 CCTTCATGAAAGTTATAGATCATGCAATAATCTTTTAACCGGCACTTCAATAACTTTAATCGAAC
1 CCTTCATAAAAGTCATAGATCACGCAATAACCTTTTAACCGACACTTCAACAACTTCAATCGAAC
* * ** * * *
11045 ATGTGTATCAAAAATTATATGGTATCAAATAGACCGCCATTGAAACGACTCAAATTTCGGAAAGC
66 ACGTGGATCAAAAATTATATACTATCAAATAGACCGCAATCGAAACCACTCAAATTTCGGAAA-C
11110 ACTTTTTTAGAATTGAGGCATAAAAATTGCCTTTCGAGTCCTTCG
130 A-TTTTTTAGAATTGAGGCATAAAAATTGCCTTTCGAGTCCTTCG
* *
11155 CCTTCATAAAAGTCATAGA-CTACGCAATAACCTTTTAACCGACACTTGAACAACTTCAATCGGA
1 CCTTCATAAAAGTCATAGATC-ACGCAATAACCTTTTAACCGACACTTCAACAACTTCAATCGAA
* * * *
11219 CACGTGGATCAAAAATTATATACTATTAGATAGACCATCAATCGAGACCACT-AAATTTCGGAAA
65 CACGTGGATCAAAAATTATATACTATCAAATAGACC-GCAATCGAAACCACTCAAATTTCGGAAA
11283 CATTTTTTAGAA
129 CATTTTTTAGAA
11295 CCGAAACCTC
Statistics
Matches: 118, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
173 10 0.08
174 3 0.03
175 95 0.81
176 10 0.08
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.30
Consensus pattern (173 bp):
CCTTCATAAAAGTCATAGATCACGCAATAACCTTTTAACCGACACTTCAACAACTTCAATCGAAC
ACGTGGATCAAAAATTATATACTATCAAATAGACCGCAATCGAAACCACTCAAATTTCGGAAACA
TTTTTTAGAATTGAGGCATAAAAATTGCCTTTCGAGTCCTTCG
Found at i:12610 original size:30 final size:31
Alignment explanation
Indices: 12562--12622 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
12552 TTATAAGTTC
12562 TAGTTCCATGACATTTGCATATAATTTGTAA
1 TAGTTCCATGACATTTGCATATAATTTGTAA
12593 TAGTTCCATGACA-TTGCATATAATTTGTAA
1 TAGTTCCATGACATTTGCATATAATTTGTAA
12623 CAGGCAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (31 bp):
TAGTTCCATGACATTTGCATATAATTTGTAA
Found at i:13645 original size:17 final size:17
Alignment explanation
Indices: 13623--13664 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
13613 CTAAACGCTA
*
13623 GATGCATGAGTGCAAAT
1 GATGCATGAATGCAAAT
13640 GATGCATGAATGCAAAT
1 GATGCATGAATGCAAAT
13657 GATGCATG
1 GATGCATG
13665 TTTTCCGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.24
Consensus pattern (17 bp):
GATGCATGAATGCAAAT
Found at i:14045 original size:28 final size:28
Alignment explanation
Indices: 13992--14048 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
13982 GTACATGGTG
** *
13992 AAAGCCCAACATAAGTGATAACAAAAAC
1 AAAGCCCAACATAAGCAACAACAAAAAC
14020 AAAGCCCAA-ATAAGCAACAACAAAAAC
1 AAAGCCCAACATAAGCAACAACAAAAAC
14047 AA
1 AA
14049 GAAATGTGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.61, C:0.23, G:0.09, T:0.07
Consensus pattern (28 bp):
AAAGCCCAACATAAGCAACAACAAAAAC
Found at i:18707 original size:15 final size:16
Alignment explanation
Indices: 18686--18724 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
18676 ATTGTGGCAG
18686 TAGAAAAAAT-ACAAAA
1 TAGAAAAAATGA-AAAA
18702 -AGAAAAAATGAAAAA
1 TAGAAAAAATGAAAAA
18717 TAGAAAAA
1 TAGAAAAA
18725 GATGCAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (16 bp):
TAGAAAAAATGAAAAA
Found at i:20331 original size:20 final size:20
Alignment explanation
Indices: 20286--20331 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
20276 TGGTATTTGG
*
20286 TTGT-TTGTTTCTTGTTTAT
1 TTGTGTTGTTTCGTGTTTAT
**
20305 TCATGTTGTTTCGTGTTTAT
1 TTGTGTTGTTTCGTGTTTAT
20325 TTGTGTT
1 TTGTGTT
20332 TACATGCTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.07, C:0.07, G:0.20, T:0.67
Consensus pattern (20 bp):
TTGTGTTGTTTCGTGTTTAT
Found at i:24264 original size:84 final size:84
Alignment explanation
Indices: 24106--24393 Score: 445
Period size: 84 Copynumber: 3.4 Consensus size: 84
24096 ATAAAGAGAA
* * ** *
24106 ATGCCTCTGTGTTATATATGTTTTTGAAGACTTTGGAATAGAGATGCC-CTTGTGTTATATATGT
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT-G-ATATAGATGCCTC-TGTGTTATATATGT
*
24170 GTTTGGGGACTTTGATATAGAG
63 GTTTGAGGACTTTGATATAGAG
* *
24192 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAGATGCCTCTATGTTATATCTGTGTT
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTT
24257 TGAGGACTTTGATATAGAG
66 TGAGGACTTTGATATAGAG
*
24276 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAGATGCCTATGTGTTATATATGTGTT
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTT
24341 TGAGGACTTTTGA-ATAGAG
66 TGAGGAC-TTTGATATAGAG
24360 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
24394 TGGTCATTGG
Statistics
Matches: 189, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
84 152 0.80
85 7 0.04
86 30 0.16
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.42
Consensus pattern (84 bp):
ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTT
TGAGGACTTTGATATAGAG
Found at i:24391 original size:127 final size:126
Alignment explanation
Indices: 24106--24393 Score: 427
Period size: 127 Copynumber: 2.3 Consensus size: 126
24096 ATAAAGAGAA
* * *
24106 ATGCCTCTGTGTTATATATGTTTTTGAAGACTTTGGAATAGAGATGCCCTTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAGATGCCCCTGTGTTATATATGTG
* * *
24171 TTTGGGGACTTTGATATAGAGATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAG
66 TTTGGGGACTTTGATATA-AGATGCCCATGTGTTATATATGTGTTTGAGGACTTTGATAGAG
* *
24233 ATGCCTCTATGTTATATCTGTGTTTGAGGACTTT-GATATAGAGATGCCCCTGTGTTATATATGT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGA-ATAGAGATGCCCCTGTGTTATATATGT
*
24297 GTTTGGGGACTTTGATAT-AGATGCCTATGTGTTATATATGTGTTTGAGGACTTTTGAATAGAG
65 GTTTGGGGACTTTGATATAAGATGCCCATGTGTTATATATGTGTTTGAGGAC-TTTG-ATAGAG
* *
24360 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTT
24394 TGGTCATTGG
Statistics
Matches: 145, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
125 30 0.21
126 6 0.04
127 109 0.75
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.42
Consensus pattern (126 bp):
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAGATGCCCCTGTGTTATATATGTG
TTTGGGGACTTTGATATAAGATGCCCATGTGTTATATATGTGTTTGAGGACTTTGATAGAG
Found at i:24395 original size:43 final size:42
Alignment explanation
Indices: 24106--24393 Score: 400
Period size: 43 Copynumber: 6.8 Consensus size: 42
24096 ATAAAGAGAA
* * **
24106 ATGCCTCTGTGTTATATATGTTTTTGAAGACTTTGGAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT-GAATAGAG
*
24149 ATGCCCTTGTGTTATATATGTGTTTGGGGACTTTGATATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGA-ATAGAG
*
24192 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATAG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGAATAGAG
* * * *
24233 ATGCCTCTATGTTATATCTGTGTTTGAGGACTTTGATATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGA-ATAGAG
*
24276 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATAG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGAATAGAG
** *
24317 ATGCCTATGTGTTATATATGTGTTTGAGGACTTTTGAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGAC-TTTGAATAGAG
24360 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
24394 TGGTCATTGG
Statistics
Matches: 216, Mismatches: 24, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
41 69 0.32
42 9 0.04
43 138 0.64
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.42
Consensus pattern (42 bp):
ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGAATAGAG
Found at i:26054 original size:276 final size:276
Alignment explanation
Indices: 25561--26110 Score: 1064
Period size: 276 Copynumber: 2.0 Consensus size: 276
25551 GGAAAATGAT
25561 AAAGGACAGAGAAAGAGGAAAGGAAGCGAAATGGGTGAGCATAGCTATATTGGGTTTATAGATCG
1 AAAGGACAGAGAAAGAGGAAAGGAAGCGAAATGGGTGAGCATAGCTATATTGGGTTTATAGATCG
* *
25626 AAATGTGAAGCATGACAAGTTCATACCTCGAAAGAAGGCCTGAGCTGCAAATCAATCTGAGATTG
66 AAATGTGAAGCATGACAAGTTCATACCTCGAAAGAAGGCCCGAGCTGCAAATCAATCCGAGATTG
25691 ATCAATTGTCGATCCCAGTTGCTGATCTCCTACCACTACTGGTCCCAAATCAACTTATCTCTCCA
131 ATCAATTGTCGATCCCAGTTGCTGATCTCCTACCACTACTGGTCCCAAATCAACTTATCTCTCCA
25756 ATAGCCATGAAAACAGTTCCTAACCCATCAGCCAGAAGCTATGACTCGGACAGTAAATGTGATTA
196 ATAGCCATGAAAACAGTTCCTAACCCATCAGCCAGAAGCTATGACTCGGACAGTAAATGTGATTA
25821 TCATATGGGTGTTGAC
261 TCATATGGGTGTTGAC
*
25837 AAAGGACAGAGAAAGAGGAAAGGAAGCGAAATGGGTGAGCATAGCTATATTGGGTTTATAGATCT
1 AAAGGACAGAGAAAGAGGAAAGGAAGCGAAATGGGTGAGCATAGCTATATTGGGTTTATAGATCG
25902 AAATGTGAAGCATGACAAGTTCATACCTCGAAAGAAGGCCCGAGCTGCAAATCAATCCGAGATTG
66 AAATGTGAAGCATGACAAGTTCATACCTCGAAAGAAGGCCCGAGCTGCAAATCAATCCGAGATTG
*
25967 ATCAATTGTCGATCCCAGTTGCTGATCTCCTACCACTGCTGGTCCCAAATCAACTTATCTCTCCA
131 ATCAATTGTCGATCCCAGTTGCTGATCTCCTACCACTACTGGTCCCAAATCAACTTATCTCTCCA
26032 ATAGCCATGAAAACAGTTCCTAACCCATCAGCCAGAAGCTATGACTCGGACAGTAAATGTGATTA
196 ATAGCCATGAAAACAGTTCCTAACCCATCAGCCAGAAGCTATGACTCGGACAGTAAATGTGATTA
26097 TCATATGGGTGTTG
261 TCATATGGGTGTTG
26111 TTGGGCATTC
Statistics
Matches: 270, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
276 270 1.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (276 bp):
AAAGGACAGAGAAAGAGGAAAGGAAGCGAAATGGGTGAGCATAGCTATATTGGGTTTATAGATCG
AAATGTGAAGCATGACAAGTTCATACCTCGAAAGAAGGCCCGAGCTGCAAATCAATCCGAGATTG
ATCAATTGTCGATCCCAGTTGCTGATCTCCTACCACTACTGGTCCCAAATCAACTTATCTCTCCA
ATAGCCATGAAAACAGTTCCTAACCCATCAGCCAGAAGCTATGACTCGGACAGTAAATGTGATTA
TCATATGGGTGTTGAC
Done.