Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023945.1 Corchorus olitorius cultivar O-4 contig23978, 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: 32121
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:3090 original size:21 final size:21
Alignment explanation
Indices: 3051--3090 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3041 TTGAGTTGCC
*
3051 TAAGATGCCATTTGATCCATT
1 TAAGATGCCATTAGATCCATT
*
3072 TAAGATGCCATTAGGTCCA
1 TAAGATGCCATTAGATCCA
3091 ATGACTAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (21 bp):
TAAGATGCCATTAGATCCATT
Found at i:7296 original size:18 final size:19
Alignment explanation
Indices: 7260--7297 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
7250 CTCCTCTTGC
*
7260 ATGAAAACACTTGTTTTTT
1 ATGAAAACAATTGTTTTTT
7279 ATGAAAACAATT-TTTTTT
1 ATGAAAACAATTGTTTTTT
7297 A
1 A
7298 ACTACCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (19 bp):
ATGAAAACAATTGTTTTTT
Found at i:9019 original size:25 final size:24
Alignment explanation
Indices: 8983--9029 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
8973 TCCTTCTATT
8983 CATCTATCATC-AAGTTTTTCATG
1 CATCTATCATCAAAGTTTTTCATG
9006 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
9030 AATTTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATG
Found at i:15450 original size:28 final size:29
Alignment explanation
Indices: 15374--15450 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
15364 AAACGTTGGA
* *
15374 CCCTGATTTGTGCATTTTTTTTTCTTTAGG
1 CCCTAATTTGAGCA-TTTTTTTTCTTTAGG
* *
15404 CCCTACTTTGAGTATTTTTTTTCTTT-GTG
1 CCCTAATTTGAGCATTTTTTTTCTTTAG-G
*
15433 TCCTAATTTGAGCATTTT
1 CCCTAATTTGAGCATTTT
15451 CATAAACGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 1 0.03
29 28 0.72
30 10 0.26
ACGTcount: A:0.13, C:0.17, G:0.14, T:0.56
Consensus pattern (29 bp):
CCCTAATTTGAGCATTTTTTTTCTTTAGG
Found at i:16664 original size:440 final size:438
Alignment explanation
Indices: 15778--16673 Score: 1236
Period size: 440 Copynumber: 2.0 Consensus size: 438
15768 GAAAAAAATT
* * * *
15778 AAAGCGTTAAATCGAATAAAATAGAATTTGTAAAGGTCTAAGTAGTATAAAATAGAAAAGTATGA
1 AAAGCGTTAAATCGATTAAAATAGAATTAGTAAAGGACTAAGTAGTATAAAATAGAAAAATATGA
* *
15843 GGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATAGAGATCTTCAAACATAAAAAT
66 GGGTCATTTCATAAATAATCCAAATAAAAAAATGTTTGTTAATAGAGATCTTCAAACATAAAAAT
* * * *
15908 TCACTTTTGAACCCTTCATGAAACTTGTATATCAAATTTAACTTTCGGACACTTCATGAAAGTCA
131 TCACTTTTGAACACTTAATGAAACTCGTAAATCAAATTTAACTTTCGGACACTTCATGAAAGTCA
* * *
15973 GAGATCACGCAATAACCTTTTAACCGACACTTAAATTACTTTAACCGGACATGTGGATTTAAAAT
196 GAGATCACGCAATAACCTTCTAACCGACACTTAAA-TACATTAACCGGACATGTGGATTGAAAAT
* * * *
16038 TATATGGTATTAAATAGACTGACAATTAAAACCACCAAATTTGGGAAGCATTTTTCTTTGAATTA
260 TATATGATATTAAATAGACAGACAATTAAAACCACCAAATTTCGAAAGCATTTTTCTTTGAATTA
** * ** * *
16103 AAATGTAAAAATTGGCTTTTGAGTTTTTCATGAAAGTTGGAGATCATGAAATTACCTTTTAATTG
325 AAACATAAAAATTGGCTTTTAAGTCCTTCATGAAAGTTGGAAATCATGAAATTACCTTTTAATAG
*
16168 ACACCTGAATCACCTTAATCGGACAAATAGAAAAAAAAAAGATAAAACT
390 ACACCTGAATCACCTTAATCGGACAAATAGAAAAAAAAAAGATAAAACA
* *
16217 TAAGCGTTAAATCGATTAAAATAGAATTAGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGA
1 AAAGCGTTAAATCGATTAAAATAGAATTAGTAAAGGACTAAGTAGTATAAAATAGAAAAATATGA
* *
16282 GGGTCATTTCATAAATAATCCAAATAAAAAAAATGTTTGTTGAT-GTAGATCTTGAAACATAAAA
66 GGGTCATTTCATAAATAATCCAAAT-AAAAAAATGTTTGTTAATAG-AGATCTTCAAACATAAAA
* * *
16346 ATTCCCTTTTGAACACTTAATGAAACTCGTAAATCAAATTTAGCTTTCGGGTC-CTTCATGAAAG
129 ATTCACTTTTGAACACTTAATGAAACTCGTAAATCAAATTTAACTTTC-GGACACTTCATGAAAG
* * *
16410 TC-GTAGATCATGCAATAACCTTCTAACCGACACTTGAGAA-ACATTAATCGGACATGTTGATTG
193 TCAG-AGATCACGCAATAACCTTCTAACCGACACTT-A-AATACATTAACCGGACATGTGGATTG
*
16473 AAAATTATATGATATTAAATAGATCAG-CAATTAAAATCACCAAATTTCGAAAGCA-TTTT-TTT
255 AAAATTATATGATATTAAATAGA-CAGACAATTAAAACCACCAAATTTCGAAAGCATTTTTCTTT
* * *
16535 GAATTGAAACATAAAAATTGGCTTTTAAGTCCTTCATGAAAGTTGTAAATCATGAAATTACTTTT
319 GAATTAAAACATAAAAATTGGCTTTTAAGTCCTTCATGAAAGTTGGAAATCATGAAATTACCTTT
* *
16600 TAATAGACACCTGAATCACCTTAATTGGACTAATA-AAAAAATTTTAAAA-A-AAAACCA
384 TAATAGACACCTGAATCACCTTAATCGGACAAATAGAAAAAA----AAAAGATAAAA-CA
16657 AAAGCGTTAAATCGATT
1 AAAGCGTTAAATCGATT
16674 TGTAAAGGAC
Statistics
Matches: 403, Mismatches: 42, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
437 6 0.01
438 91 0.23
439 93 0.23
440 201 0.50
441 10 0.02
442 2 0.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (438 bp):
AAAGCGTTAAATCGATTAAAATAGAATTAGTAAAGGACTAAGTAGTATAAAATAGAAAAATATGA
GGGTCATTTCATAAATAATCCAAATAAAAAAATGTTTGTTAATAGAGATCTTCAAACATAAAAAT
TCACTTTTGAACACTTAATGAAACTCGTAAATCAAATTTAACTTTCGGACACTTCATGAAAGTCA
GAGATCACGCAATAACCTTCTAACCGACACTTAAATACATTAACCGGACATGTGGATTGAAAATT
ATATGATATTAAATAGACAGACAATTAAAACCACCAAATTTCGAAAGCATTTTTCTTTGAATTAA
AACATAAAAATTGGCTTTTAAGTCCTTCATGAAAGTTGGAAATCATGAAATTACCTTTTAATAGA
CACCTGAATCACCTTAATCGGACAAATAGAAAAAAAAAAGATAAAACA
Found at i:19694 original size:65 final size:65
Alignment explanation
Indices: 19582--19704 Score: 201
Period size: 65 Copynumber: 1.9 Consensus size: 65
19572 TAGGAAAAAC
* **
19582 TGGTCCTACCCATGCATAGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTTGAA
1 TGGTCCAACCCATGCATAGGGTACCCTTGGCCTACCCACGCAAGGGCTAGTGCAGAAAGTTTGAA
* *
19647 TGGTCCAACCCATGCATGGGGTACCCTTGGCCTACCCATGCAAGGGCTAGTGCAGAAA
1 TGGTCCAACCCATGCATAGGGTACCCTTGGCCTACCCACGCAAGGGCTAGTGCAGAAA
19705 ATTGGAATCA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 53 1.00
ACGTcount: A:0.23, C:0.29, G:0.27, T:0.21
Consensus pattern (65 bp):
TGGTCCAACCCATGCATAGGGTACCCTTGGCCTACCCACGCAAGGGCTAGTGCAGAAAGTTTGAA
Found at i:24654 original size:12 final size:12
Alignment explanation
Indices: 24637--24661 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24627 GTGTAATGTG
24637 TGTATATATATA
1 TGTATATATATA
24649 TGTATATATATA
1 TGTATATATATA
24661 T
1 T
24662 ATATGGTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TGTATATATATA
Found at i:26474 original size:2 final size:2
Alignment explanation
Indices: 26467--26492 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26457 ATTCATTGAC
26467 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
26493 TACCAGACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27554 original size:33 final size:33
Alignment explanation
Indices: 27514--27652 Score: 143
Period size: 33 Copynumber: 4.2 Consensus size: 33
27504 AATCAAAAGT
*
27514 TTATTTAGTGGCGTTTACAAAATCGAAACGTCA
1 TTATTTAGTGGCGTTTACAAAATCGAAACGCCA
*
27547 TTATTTAGTGGTGTTTACAAAATCGAAACGCCA
1 TTATTTAGTGGCGTTTACAAAATCGAAACGCCA
* ** * * *
27580 CTAAATAGTGGCGTTTACAACATCAAAACCCCA
1 TTATTTAGTGGCGTTTACAAAATCGAAACGCCA
* ** * * *
27613 CTAAATAATGGCGTTTACAACATCAAAACGCCA
1 TTATTTAGTGGCGTTTACAAAATCGAAACGCCA
*
27646 CTATTTA
1 TTATTTA
27653 TAATTTGAGA
Statistics
Matches: 93, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 93 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (33 bp):
TTATTTAGTGGCGTTTACAAAATCGAAACGCCA
Found at i:27739 original size:64 final size:64
Alignment explanation
Indices: 27638--27786 Score: 183
Period size: 64 Copynumber: 2.3 Consensus size: 64
27628 TACAACATCA
* * * * * *
27638 AAACGCCACTATTTATAATTTGAGATCTATTTTTTAAAAAAAATCCTTAAATATAACGGTGTTT
1 AAACGCCACTATATATAATTTGAGATATATTTTTTAAAAAAAACCCATAAATATAACGGCGTCT
* *
27702 AAACGCCCCTATATATAATTTGAGATA-ATTTTTTTAAAAAAAACCCATAAATGTAACGGCGTCT
1 AAACGCCACTATATATAATTTGAGATATA-TTTTTTAAAAAAAACCCATAAATATAACGGCGTCT
* * *
27766 AAGCGCCGCTATATACAATTT
1 AAACGCCACTATATATAATTT
27787 AAAAAAACTT
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
63 1 0.01
64 72 0.99
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (64 bp):
AAACGCCACTATATATAATTTGAGATATATTTTTTAAAAAAAACCCATAAATATAACGGCGTCT
Found at i:31121 original size:65 final size:65
Alignment explanation
Indices: 31004--31133 Score: 188
Period size: 65 Copynumber: 2.0 Consensus size: 65
30994 GGAAAAATTG
* * ** * * *
31004 GTCCTACCTATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTTGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCAAGGGCTAATGCAGAAAATTGGAATC
*
31069 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCATGCAAGGGCTAATGCAGAAAATTGGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCAAGGGCTAATGCAGAAAATTGGAATC
31134 AACGCAAGCA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.22
Consensus pattern (65 bp):
GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCAAGGGCTAATGCAGAAAATTGGAATC
Done.