Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016043.1 Corchorus olitorius cultivar O-4 contig16076, 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: 17952
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Found at i:7616 original size:245 final size:241
Alignment explanation
Indices: 7146--7634 Score: 863
Period size: 245 Copynumber: 2.0 Consensus size: 241
7136 GTACAATAAT
*
7146 ATATTAAAATATAATTTTAAATGATATGGTATATGGCAAGGAGACCCTAATAGAAGGATTAGATA
1 ATATAAAAATATAATTTTAAATGATATGGTATATGGCAAGGAGACCCTAATAGAAGGATTAGATA
*
7211 TCTTTAATCAAATAAGCAAGTTCCTATGTTTGAAATAAATTCAATTAGGTGACGATGGTGACCAA
66 ACTTTAATCAAATAAGCAAGTTCCTATGTTTGAAATAAATTCAATTAGGTGACGATGGTGACCAA
*
7276 GAGAAATTAAATCGAAAGTGACGTTCATGAATTTTGTTTGCTAGATTTTATTAGATCTAGTTGAG
131 GAGAAATTAAATCGAAAGTGACGTTCATGAATTTTGTTTGCTAGATTGTATTAGATCTAGTTGAG
*
7341 AAATCACAAAGGAATTAAATGTTGTAATGGAAGCCAAATTGAAACA
196 AAATCACAAAGGAATTAAATGTTGTAATGGAAGCCAAATTAAAACA
7387 ATATAAAAATATAATTTTAAATGATATGGTATATGGCAAGGAGACCCTAATAGAAGGATTAGATA
1 ATATAAAAATATAATTTTAAATGATATGGTATATGGCAAGGAGACCCTAATAGAAGGATTAGATA
*
7452 ACTTTAATCAAATAAGCGAGTTCCTATGTTTGAAATAAATTCAATTAAAGAGGTG-CTGATGGTG
66 ACTTTAATCAAATAAGCAAGTTCCTATGTTTGAAATAAATTCAATT----AGGTGAC-GATGGTG
7516 ACCAAGAGAAATTAAATCGAAAGTGACGTTCATGAATTTTGTTTGCTAGATTGTATTAGATCTAG
126 ACCAAGAGAAATTAAATCGAAAGTGACGTTCATGAATTTTGTTTGCTAGATTGTATTAGATCTAG
* *
7581 TTGAGAAATTACAAAGGATTTAAATGTTGTAATGGAAGCCAAATTAAAACA
191 TTGAGAAATCACAAAGGAATTAAATGTTGTAATGGAAGCCAAATTAAAACA
7632 ATA
1 ATA
7635 GAAGTAGTTA
Statistics
Matches: 236, Mismatches: 7, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
241 108 0.46
244 1 0.00
245 127 0.54
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (241 bp):
ATATAAAAATATAATTTTAAATGATATGGTATATGGCAAGGAGACCCTAATAGAAGGATTAGATA
ACTTTAATCAAATAAGCAAGTTCCTATGTTTGAAATAAATTCAATTAGGTGACGATGGTGACCAA
GAGAAATTAAATCGAAAGTGACGTTCATGAATTTTGTTTGCTAGATTGTATTAGATCTAGTTGAG
AAATCACAAAGGAATTAAATGTTGTAATGGAAGCCAAATTAAAACA
Found at i:13483 original size:33 final size:34
Alignment explanation
Indices: 13413--13552 Score: 112
Period size: 33 Copynumber: 4.2 Consensus size: 34
13403 ATGATCAACC
** *
13413 AAAACAG-ATTT-GTTTTCATCACAATTAGCATCC-
1 AAAACAGAATTTAG-TTTCATCACAAACAACA-CCT
13446 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAGAATTTAGTTTCATCACAAACAACACCT
* *
13479 AAAACA-AATTTAGTGTCATCACAAACAACACTT
1 AAAACAGAATTTAGTTTCATCACAAACAACACCT
** * * * * *
13512 AAATTAG-GTTTGGTATCATCACTAACAACATCT
1 AAAACAGAATTTAGTTTCATCACAAACAACACCT
13545 AAAACAGA
1 AAAACAGA
13553 TTTCATGTCA
Statistics
Matches: 87, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
32 7 0.08
33 75 0.86
34 5 0.06
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.27
Consensus pattern (34 bp):
AAAACAGAATTTAGTTTCATCACAAACAACACCT
Found at i:13533 original size:66 final size:66
Alignment explanation
Indices: 13461--13587 Score: 175
Period size: 66 Copynumber: 1.9 Consensus size: 66
13451 AGAATTTGTT
* *
13461 TCATCACAAACAACACCTAAAACAAATTT-AGTGTCATCACAAACAACACTTAAATTAGGTTTGG
1 TCATCACAAACAACACCTAAAACAAATTTCA-TGTCATCACAAACAACACTCAAATCAGGTTTGG
13525 TA
65 TA
* * * **
13527 TCATCACTAACAACATCTAAAACAGATTTCATGTCATTGCAAACAACACTCAAATCAGGTT
1 TCATCACAAACAACACCTAAAACAAATTTCATGTCATCACAAACAACACTCAAATCAGGTT
13588 CAGAATTACT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
66 52 0.98
67 1 0.02
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (66 bp):
TCATCACAAACAACACCTAAAACAAATTTCATGTCATCACAAACAACACTCAAATCAGGTTTGGT
A
Found at i:15162 original size:25 final size:24
Alignment explanation
Indices: 15125--15171 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
15115 CTAGAAAATT
15125 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
15151 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
15172 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Done.