Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015467.1 Corchorus olitorius cultivar O-4 contig15500, 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: 64028
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7195 original size:10 final size:10
Alignment explanation
Indices: 7180--7204 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
7170 TTGGGGTTAC
7180 TTTGGAATGG
1 TTTGGAATGG
7190 TTTGGAATGG
1 TTTGGAATGG
7200 TTTGG
1 TTTGG
7205 GTTAGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.40, T:0.44
Consensus pattern (10 bp):
TTTGGAATGG
Found at i:21811 original size:29 final size:29
Alignment explanation
Indices: 21778--21836 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
21768 ATTAAAACGT
21778 CGCCATAATCATAAAACATTACAATCCAG
1 CGCCATAATCATAAAACATTACAATCCAG
21807 CGCCATAATCATAAAACATTACAATCCAG
1 CGCCATAATCATAAAACATTACAATCCAG
21836 C
1 C
21837 AATTTTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.29, G:0.07, T:0.20
Consensus pattern (29 bp):
CGCCATAATCATAAAACATTACAATCCAG
Found at i:25335 original size:30 final size:28
Alignment explanation
Indices: 25274--25344 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 28
25264 CATAATGGTG
* **
25274 AGTCCATTAATATTTTTTCTGTAGGGTAA
1 AGTCCATTAAT-TTTTTTCTGAACAGTAA
25303 AGTCCATTAATTTTTTTCTGAAAACAGTAA
1 AGTCCATTAATTTTTTTCTG--AACAGTAA
25333 AGTCCATTAATT
1 AGTCCATTAATT
25345 AATAGTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.24
29 11 0.30
30 17 0.46
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (28 bp):
AGTCCATTAATTTTTTTCTGAACAGTAA
Found at i:28199 original size:71 final size:71
Alignment explanation
Indices: 28083--28224 Score: 223
Period size: 71 Copynumber: 2.0 Consensus size: 71
28073 GAGTTTTATG
* *
28083 GTAAGAGTATAACACTACAAAGAAAAGATGGTTTGGATTGGAATTCATTCAGCTT-TGTGTGTGC
1 GTAAGAGTATAACACTACAAAGAAAAGATGGTTTGGATTGGAATTCATTCA-ATTCTGTATGTGC
28147 CTAGCCT
65 CTAGCCT
* * *
28154 GTAAGATTATAATACTACAAAGAACAGATGGTTTGGATTGGAATTCATTCAATTCTGTATGTGCC
1 GTAAGAGTATAACACTACAAAGAAAAGATGGTTTGGATTGGAATTCATTCAATTCTGTATGTGCC
28219 TAGCCT
66 TAGCCT
28225 CTCATATATT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
70 2 0.03
71 63 0.97
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (71 bp):
GTAAGAGTATAACACTACAAAGAAAAGATGGTTTGGATTGGAATTCATTCAATTCTGTATGTGCC
TAGCCT
Found at i:28821 original size:2 final size:2
Alignment explanation
Indices: 28814--28838 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28804 AGGGTCTGTT
28814 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
28839 GCCATGTGAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:30297 original size:23 final size:23
Alignment explanation
Indices: 30267--30311 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
30257 GTTTACTTAG
*
30267 ACTCCAATTCATAATCACGCCTA
1 ACTCCAATCCATAATCACGCCTA
30290 ACTCCAATCCATAATCACGCCT
1 ACTCCAATCCATAATCACGCCT
30312 GCAAATAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.38, G:0.04, T:0.24
Consensus pattern (23 bp):
ACTCCAATCCATAATCACGCCTA
Found at i:34112 original size:22 final size:21
Alignment explanation
Indices: 34089--34127 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34079 TTTTGTTACT
*
34089 CTCTCTTT-TTTTATCTTTCC
1 CTCTCTTTCTTTTAACTTTCC
34109 CTCTCTTTCTTTTAACTTT
1 CTCTCTTTCTTTTAACTTT
34128 TTCTACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (21 bp):
CTCTCTTTCTTTTAACTTTCC
Found at i:44421 original size:96 final size:96
Alignment explanation
Indices: 44255--44436 Score: 240
Period size: 96 Copynumber: 1.9 Consensus size: 96
44245 TCGGGTATTG
* * ** * *
44255 TGAATGGATAAAATCATAGGCGAAGTGTCGAACCATCCGATTAAATAAGTATCGAGTTCAAGTTT
1 TGAATAGATAAAACCATAAACGAAGTGTAGAACCATCCGATTAAATAAGTATCAAGTTCAAGTTT
*
44320 AATGAATAGAGAAAACCATAATCGAGTCTTT
66 AATGAATAGAAAAAACCATAATCGAGTCTTT
* * **
44351 TGAATAGATAAAACCATAAACGAAGTGTAGAACCA-CTTGATTAAATAAGTTTCAAGTTCGGGTT
1 TGAATAGATAAAACCATAAACGAAGTGTAGAACCATC-CGATTAAATAAGTATCAAGTTCAAGTT
*
44415 TTATGAATAGAAAAAACCATAA
65 TAATGAATAGAAAAAACCATAA
44437 CTGAGAGAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
95 1 0.01
96 72 0.99
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (96 bp):
TGAATAGATAAAACCATAAACGAAGTGTAGAACCATCCGATTAAATAAGTATCAAGTTCAAGTTT
AATGAATAGAAAAAACCATAATCGAGTCTTT
Found at i:52381 original size:20 final size:21
Alignment explanation
Indices: 52356--52413 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
52346 CTGTTTAGTA
52356 ACTGTACAGATGAGATTT-AC
1 ACTGTACAGATGAGATTTGAC
* **
52376 ACTGTACAGATTAGATTTGGT
1 ACTGTACAGATGAGATTTGAC
*
52397 GCTGTACAGATGAGATT
1 ACTGTACAGATGAGATT
52414 ATTAGAGCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (21 bp):
ACTGTACAGATGAGATTTGAC
Done.