Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018443.1 Corchorus olitorius cultivar O-4 contig18476, 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: 15887
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--35 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 TA TA TA TA TA 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 TA TA TA TA TA T
36 GGTAATACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1459 original size:178 final size:177
Alignment explanation
Indices: 1177--1620 Score: 530
Period size: 178 Copynumber: 2.5 Consensus size: 177
1167 CAAATCCTTC
* *** * * *
1177 ATGAAAGTTGTAAATCACCAAACAACCTTTTAATAGATACTTGAATCACCTTAATCGGACATCTG
1 ATGAAAGTTGTAGATCATGGAACAACCTTTTAATAGACACTTGAATCA-TTTAATCAGACATCTG
* * * *
1242 GTGCAAAAATTATGTAATATTAAGTGAACGGTCCATTCTCGGTAACCGAAACAACTAATTTTTTG
65 GAGCAAAAATTATATAATATTAAGTGAACCGTCCATTCTCGGTAACCGAAACAACTAATTTTTCG
** * *
1307 GGAGCATATTTTATACTTGAAACATTAAATTTAGCTTTT-GAGTCCTCT
130 AAAACATATTTTATACCTGAAACATTAAATTTAG-TTTTCGAGTCCTCT
* * * * *
1355 ATGAAATTTGTAGATCATGGAACAACCTTTTAAGAGACACTTGAATCATTTCAATTAGATATTTG
1 ATGAAAGTTGTAGATCATGGAACAACCTTTTAATAGACACTTGAATCATTT-AATCAGACATCTG
* * * * * *
1420 GAGCAAAAGTTATATAATATTAAGTGGACCGTTCATTCTCGTTAACCGAAATAGCTAATTTTTCG
65 GAGCAAAAATTATATAATATTAAGTGAACCGTCCATTCTCGGTAACCGAAACAACTAATTTTTCG
* *
1485 AAAACATTTTTTATACCTGAAACATTAAATTTAGTTTTCGAGTCCTTT
130 AAAACATATTTTATACCTGAAACATTAAATTTAGTTTTCGAGTCCTCT
* * * * *
1533 ATGAAAGTTGTAGATCATGGAACAACCTATTAATAGACACTTGAATCATCTTGATCGGATATCCG
1 ATGAAAGTTGTAGATCATGGAACAACCTTTTAATAGACACTTGAATCAT-TTAATCAGACATCTG
* *
1598 GAGCGAAAATTATATAATGTTAA
65 GAGCAAAAATTATATAATATTAA
1621 ATGGATCACT
Statistics
Matches: 224, Mismatches: 39, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
177 6 0.03
178 216 0.96
179 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (177 bp):
ATGAAAGTTGTAGATCATGGAACAACCTTTTAATAGACACTTGAATCATTTAATCAGACATCTGG
AGCAAAAATTATATAATATTAAGTGAACCGTCCATTCTCGGTAACCGAAACAACTAATTTTTCGA
AAACATATTTTATACCTGAAACATTAAATTTAGTTTTCGAGTCCTCT
Found at i:9885 original size:30 final size:30
Alignment explanation
Indices: 9827--9885 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
9817 TTTCTGGTTC
* **
9827 GGTCTAATTTGGGGCAGAAGTTTTCAATTT
1 GGTCTAATTTGGGGCAAAAGTTAGCAATTT
9857 GGTCT-ATTTGGGGCAAAACGTTAGCAATT
1 GGTCTAATTTGGGGCAAAA-GTTAGCAATT
9886 CGTGTCAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.36
Consensus pattern (30 bp):
GGTCTAATTTGGGGCAAAAGTTAGCAATTT
Found at i:10014 original size:16 final size:16
Alignment explanation
Indices: 9993--10027 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
9983 AATTTTGAAA
*
9993 TAAAATTAAATTTATT
1 TAAAATTAAATTCATT
10009 TAAAATTAAATTCATT
1 TAAAATTAAATTCATT
10025 TAA
1 TAA
10028 TTTAACCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAAATTAAATTCATT
Found at i:11249 original size:22 final size:22
Alignment explanation
Indices: 11224--11267 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
11214 TAAAGCCAAT
* *
11224 TTTTCTTTTTTTTACTTTTTAA
1 TTTTCGTTTTTTTAATTTTTAA
11246 TTTTCGTTTTTTTAATTTTTAA
1 TTTTCGTTTTTTTAATTTTTAA
11268 GTAATTCTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTTCGTTTTTTTAATTTTTAA
Found at i:12345 original size:29 final size:28
Alignment explanation
Indices: 12292--12419 Score: 202
Period size: 28 Copynumber: 4.5 Consensus size: 28
12282 CTCTACTTCT
12292 CATTTTGGTCATTTTTCATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
*
12320 CATTTTGGTCATTTTTTCAGGTCCAGGGG
1 CATTTTGGTCA-TTTTTCATGTCCAGGGG
* *
12349 CATTTTGGTCATTTTCCATGTCCATGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
12377 CATTTTGGTCATTTTTCATGTCCAGGGGG
1 CATTTTGGTCATTTTTCATGTCCA-GGGG
*
12406 CTTTTTGGTCATTT
1 CATTTTGGTCATTT
12420 CAAGTGTACT
Statistics
Matches: 91, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
28 48 0.53
29 43 0.47
ACGTcount: A:0.13, C:0.18, G:0.24, T:0.45
Consensus pattern (28 bp):
CATTTTGGTCATTTTTCATGTCCAGGGG
Found at i:12380 original size:57 final size:57
Alignment explanation
Indices: 12292--12419 Score: 204
Period size: 57 Copynumber: 2.2 Consensus size: 57
12282 CTCTACTTCT
*
12292 CATTTTGGTCATTTTTCATGTCCAGGGGCATTTTGGTCATTTTTTCAGGTCCA-GGGG
1 CATTTTGGTCATTTTCCATGTCCAGGGGCATTTTGGTCA-TTTTTCAGGTCCAGGGGG
* *
12349 CATTTTGGTCATTTTCCATGTCCATGGGCATTTTGGTCATTTTTCATGTCCAGGGGG
1 CATTTTGGTCATTTTCCATGTCCAGGGGCATTTTGGTCATTTTTCAGGTCCAGGGGG
*
12406 CTTTTTGGTCATTT
1 CATTTTGGTCATTT
12420 CAAGTGTACT
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
56 12 0.18
57 54 0.82
ACGTcount: A:0.13, C:0.18, G:0.24, T:0.45
Consensus pattern (57 bp):
CATTTTGGTCATTTTCCATGTCCAGGGGCATTTTGGTCATTTTTCAGGTCCAGGGGG
Done.