Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012284.1 Corchorus olitorius cultivar O-4 contig12317, 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: 55362
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:1216 original size:2 final size:2
Alignment explanation
Indices: 1211--1235 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1201 ATCTAGAAGC
1211 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1236 GTTATGTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16357 original size:21 final size:21
Alignment explanation
Indices: 16331--16388 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
16321 ACATATGTAC
*
16331 ACAGTAACAAATTTTATTTGT
1 ACAGTAACAAATTTTATTCGT
* *
16352 ACAGTAACAAATCTAATTCGT
1 ACAGTAACAAATTTTATTCGT
*
16373 ACAGTAACTAATTTTA
1 ACAGTAACAAATTTTA
16389 CTCTCACAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (21 bp):
ACAGTAACAAATTTTATTCGT
Found at i:17416 original size:19 final size:19
Alignment explanation
Indices: 17392--17442 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 19
17382 TACATGTAAC
17392 CGTTTCATCATCGTTTGAT
1 CGTTTCATCATCGTTTGAT
17411 CGTTTCATCA---TTTGAT
1 CGTTTCATCATCGTTTGAT
17427 CGTTTCATCATCGTTT
1 CGTTTCATCATCGTTT
17443 TGGATATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 16 0.55
19 13 0.45
ACGTcount: A:0.16, C:0.22, G:0.14, T:0.49
Consensus pattern (19 bp):
CGTTTCATCATCGTTTGAT
Found at i:25863 original size:27 final size:27
Alignment explanation
Indices: 25833--26263 Score: 273
Period size: 27 Copynumber: 16.0 Consensus size: 27
25823 CAAGTACAGT
* * * *
25833 CTTTGGTCTGGGCACTACAATTCCAAG
1 CTTTGCTCTGGGCACCACAACTACAAG
* *
25860 CTTTTCTTTGGGCACCACAACTACAAG
1 CTTTGCTCTGGGCACCACAACTACAAG
* *
25887 CTTTTCTCCGGGCACCACAAC-AGCAAG
1 CTTTGCTCTGGGCACCACAACTA-CAAG
* *
25914 CTTTTCTCCGGGCACCACAACCT-CAAG
1 CTTTGCTCTGGGCACCACAA-CTACAAG
* * * *
25941 CTTTTCTCTGGGAACCACGACCT-CAAC
1 CTTTGCTCTGGGCACCAC-AACTACAAG
* * * **
25968 CTTTTCTCCGGGCACCACGACCCCAAG
1 CTTTGCTCTGGGCACCACAACTACAAG
* * * *
25995 CTTTTCTCCGGGCACCACGACCT-CGAG
1 CTTTGCTCTGGGCACCAC-AACTACAAG
* **
26022 CTTTTCTCTGGGCACCACAACCCCAAG
1 CTTTGCTCTGGGCACCACAACTACAAG
* * **
26049 CTTTTCTCCGGGCACCACAACCCCAAG
1 CTTTGCTCTGGGCACCACAACTACAAG
* * **
26076 CTTTTCTCCGGGCACCACAACCCCAAG
1 CTTTGCTCTGGGCACCACAACTACAAG
* *
26103 CTTTTCTCTGGGCACCACAACTACAAA
1 CTTTGCTCTGGGCACCACAACTACAAG
*
26130 CTTTTCT-TCGGGCACCACAAC-AGCAAG
1 CTTTGCTCT-GGGCACCACAACTA-CAAG
* *
26157 CTTTTCTCTGGGAACCACAACCT-CAAG
1 CTTTGCTCTGGGCACCACAA-CTACAAG
* * **
26184 CTTTTCTCCGGGCACCACAACCCCAAG
1 CTTTGCTCTGGGCACCACAACTACAAG
* ** * ** *
26211 CTTTTCTCCAGGCGCCACAACCCCTAG
1 CTTTGCTCTGGGCACCACAACTACAAG
* * *
26238 CTTTTCTCTCGGCACTACAACTACAA
1 CTTTGCTCTGGGCACCACAACTACAA
26264 ACCCTACTCC
Statistics
Matches: 345, Mismatches: 46, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
26 7 0.02
27 333 0.97
28 5 0.01
ACGTcount: A:0.23, C:0.38, G:0.16, T:0.23
Consensus pattern (27 bp):
CTTTGCTCTGGGCACCACAACTACAAG
Found at i:25914 original size:54 final size:54
Alignment explanation
Indices: 25856--26258 Score: 522
Period size: 54 Copynumber: 7.5 Consensus size: 54
25846 ACTACAATTC
** ** **
25856 CAAGCTTTTCTTTGGGCACCACAACTACAAGCTTTTCTCCGGGCACCACAACAG
1 CAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCTCCGGGCACCACAACCT
* * * *
25910 CAAGCTTTTCTCCGGGCACCACAACCTCAAGCTTTTCTCTGGGAACCACGACCT
1 CAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCTCCGGGCACCACAACCT
* * *
25964 CAACCTTTTCTCCGGGCACCACGACCCCAAGCTTTTCTCCGGGCACCACGACCT
1 CAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCTCCGGGCACCACAACCT
* * *
26018 CGAGCTTTTCTCTGGGCACCACAACCCCAAGCTTTTCTCCGGGCACCACAACCC
1 CAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCTCCGGGCACCACAACCT
*
26072 CAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCTCTGGGCACCACAA-CT
1 CAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCTCCGGGCACCACAACCT
* * ** * *
26125 ACAAACTTTTCTTCGGGCACCACAACAGCAAGCTTTTCTCTGGGAACCACAACCT
1 -CAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCTCCGGGCACCACAACCT
* * *
26180 CAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCTCCAGGCGCCACAACCC
1 CAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCTCCGGGCACCACAACCT
* *
26234 CTAGCTTTTCTCTC-GGCACTACAAC
1 CAAGCTTTTCTC-CGGGCACCACAAC
26259 TACAAACCCT
Statistics
Matches: 306, Mismatches: 40, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
53 1 0.00
54 302 0.99
55 3 0.01
ACGTcount: A:0.23, C:0.39, G:0.16, T:0.23
Consensus pattern (54 bp):
CAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCTCCGGGCACCACAACCT
Found at i:25972 original size:81 final size:80
Alignment explanation
Indices: 25856--26258 Score: 529
Period size: 81 Copynumber: 5.0 Consensus size: 80
25846 ACTACAATTC
* * **
25856 CAAGCTTTTCTTTGGGCACCACAACTACAAGCTTTTCTCCGGGCACCACAACAGCAAGCTTTTCT
1 CAAGCTTTTCTCTGGGCACCACACCT-CAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCT
25921 CCGGGCACCACAACCT
65 CCGGGCACCACAACCT
* * *
25937 CAAGCTTTTCTCTGGGAACCACGACCTCAACCTTTTCTCCGGGCACCACGACCCCAAGCTTTTCT
1 CAAGCTTTTCTCTGGGCACCAC-ACCTCAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCT
*
26002 CCGGGCACCACGACCT
65 CCGGGCACCACAACCT
* *
26018 CGAGCTTTTCTCTGGGCACCACAACCCCAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCT
1 CAAGCTTTTCTCTGGGCACCAC-ACCTCAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCT
*
26083 CCGGGCACCACAACCC
65 CCGGGCACCACAACCT
* * * **
26099 CAAGCTTTTCTCTGGGCACCACAACTACAAACTTTTCTTCGGGCACCACAACAGCAAGCTTTTCT
1 CAAGCTTTTCTCTGGGCACCACACCT-CAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCT
* *
26164 CTGGGAACCACAACCT
65 CCGGGCACCACAACCT
* * * * *
26180 CAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCTCCAGGCGCCACAACCCCTAGCTTTTCT
1 CAAGCTTTTCTCTGGGCACCAC-ACCTCAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCT
*
26245 CTC-GGCACTACAAC
65 C-CGGGCACCACAAC
26259 TACAAACCCT
Statistics
Matches: 279, Mismatches: 39, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
80 2 0.01
81 272 0.97
82 5 0.02
ACGTcount: A:0.23, C:0.39, G:0.16, T:0.23
Consensus pattern (80 bp):
CAAGCTTTTCTCTGGGCACCACACCTCAAGCTTTTCTCCGGGCACCACAACCCCAAGCTTTTCTC
CGGGCACCACAACCT
Found at i:26357 original size:27 final size:27
Alignment explanation
Indices: 26342--26511 Score: 259
Period size: 27 Copynumber: 6.3 Consensus size: 27
26332 AGTTCAATGG
* *
26342 CAAGCTTTGCAACAGCTGGTTTGAACC
1 CAAGCTTTGCAACAGCTGGTTCGAACT
**
26369 CAAGCTTTGCTGCAGCTGGTTCGAACT
1 CAAGCTTTGCAACAGCTGGTTCGAACT
26396 CAAGCTTTGCAACAGCTGGTTCGAACT
1 CAAGCTTTGCAACAGCTGGTTCGAACT
26423 CAAGCTTTGCAACAGCTGGTTCGAACT
1 CAAGCTTTGCAACAGCTGGTTCGAACT
26450 CAAGCTTTGCAACAGCTGGTTCGAACT
1 CAAGCTTTGCAACAGCTGGTTCGAACT
* ** *
26477 CAAGCTTTCCGGCAGCTGGTTTGAACT
1 CAAGCTTTGCAACAGCTGGTTCGAACT
*
26504 CAGGCTTT
1 CAAGCTTT
26512 ATATTTGGCA
Statistics
Matches: 132, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 132 1.00
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.28
Consensus pattern (27 bp):
CAAGCTTTGCAACAGCTGGTTCGAACT
Found at i:33369 original size:6 final size:6
Alignment explanation
Indices: 33358--33392 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
33348 AAAGAATACA
33358 AGAATT AGAATT AGAATT AGAATT AGAATT AGAAT
1 AGAATT AGAATT AGAATT AGAATT AGAATT AGAAT
33393 AATTTTAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.31
Consensus pattern (6 bp):
AGAATT
Found at i:40373 original size:245 final size:245
Alignment explanation
Indices: 39825--40523 Score: 1057
Period size: 245 Copynumber: 2.9 Consensus size: 245
39815 GAAGTGGACT
* * * * * * **
39825 TTGTTGGCCGGTTATAACTTCTCTTAATGGCAGTTTGTAATTCTTATTGGTGATTCATTCCAAAA
1 TTGTTGGCTGGTTATAACTGCTCTTTATGGTAGTTTTTCATTCTTATTGGCCATTCATTCCAAAA
* *
39890 TATTAGTTCATTAACTCCGTGTGTTTGTTCGTTATATTAGTTAAGTCAACAAGACTTGAATAGGA
66 TATCAGTTCATTAACTCCGTGTGTTTGTTCGTTATATTAGTTAAGTAAACAAGACTTGAATAGGA
* * * *
39955 AATGTAGCTCTTATGTGCTTAGAGG-CTAATGAGTGTTTATGACGTAATA-AGGCTTTGTTGCTT
131 AATGTAGCTTTTATGTGCTTAGAGGTCTAACGAGTGTTTATGACGTAATACAAGCTTTGCTGCTT
* * *
40018 GGCACGTGTACTTGCTAAAATTCGATCGATAGTGAAGTGGTCTTGTTTAA
196 GGCACGTGTACTTGCTAAAATTCAATCGATAATGAAGTGGACTTGTTTAA
*
40068 TTGTTGG-TCGGTTATAACTGCTGTTTATGGTAGTTTTTCATTCTTATTGGCCATTCATTCCAAA
1 TTGTTGGCT-GGTTATAACTGCTCTTTATGGTAGTTTTTCATTCTTATTGGCCATTCATTCCAAA
40132 ATATCAGTTCATTAACTCCGTGTGTTTGTTCGTTATATTAGTTAAGTAAACAAGACTTGAATAGG
65 ATATCAGTTCATTAACTCCGTGTGTTTGTTCGTTATATTAGTTAAGTAAACAAGACTTGAATAGG
* *
40197 AAATGCAGCTTTTATGTGCTTAGAGGTTTAACGAGTGTTTATGACGTAATACAAGCTTTGCTGCT
130 AAATGTAGCTTTTATGTGCTTAGAGGTCTAACGAGTGTTTATGACGTAATACAAGCTTTGCTGCT
* *
40262 TGGCACGTGTGCTTGCTAAATTTCAATC-AGTAATGAAGTGGACTTGTTTAA
195 TGGCACGTGTACTTGCTAAAATTCAATCGA-TAATGAAGTGGACTTGTTTAA
* *
40313 TTGTTGGCTGGTTATAACTGCTCTTTATGGTAGTTTTTCATTCTTGTCGGCCATTCATTCCAAAA
1 TTGTTGGCTGGTTATAACTGCTCTTTATGGTAGTTTTTCATTCTTATTGGCCATTCATTCCAAAA
* * *
40378 TAACAGTTCATTAACTCCGTGTATTTGTTCGTTATATTAGTTAAGTAAACAAGACTTGAATATGA
66 TATCAGTTCATTAACTCCGTGTGTTTGTTCGTTATATTAGTTAAGTAAACAAGACTTGAATAGGA
* * * *
40443 AATGTAGCTTTTATGTGCTTAGAGGTGTAACGAGTATTTCTGACGTAATACATA-CTTTGCCGCT
131 AATGTAGCTTTTATGTGCTTAGAGGTCTAACGAGTGTTTATGACGTAATACA-AGCTTTGCTGCT
40507 TGGCACGTGTACTTGCT
195 TGGCACGTGTACTTGCT
40524 TTACTTGAAA
Statistics
Matches: 416, Mismatches: 34, Indels: 10
0.90 0.07 0.02
Matches are distributed among these distances:
243 141 0.34
244 23 0.06
245 250 0.60
246 2 0.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (245 bp):
TTGTTGGCTGGTTATAACTGCTCTTTATGGTAGTTTTTCATTCTTATTGGCCATTCATTCCAAAA
TATCAGTTCATTAACTCCGTGTGTTTGTTCGTTATATTAGTTAAGTAAACAAGACTTGAATAGGA
AATGTAGCTTTTATGTGCTTAGAGGTCTAACGAGTGTTTATGACGTAATACAAGCTTTGCTGCTT
GGCACGTGTACTTGCTAAAATTCAATCGATAATGAAGTGGACTTGTTTAA
Found at i:55280 original size:3 final size:3
Alignment explanation
Indices: 55272--55298 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
55262 ATATATATAT
55272 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
55299 CATCTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.