Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006744.1 Corchorus olitorius cultivar O-4 contig06769, 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: 1908
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Found at i:422 original size:39 final size:40
Alignment explanation
Indices: 366--445 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
356 TTTAATTCCT
366 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* * *
406 ATGTAATA-CTATAATAACTGAAATACTTATATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
445 A
1 A
446 GTCTTAGGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:436 original size:18 final size:18
Alignment explanation
Indices: 376--436 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 18
366 ATGTAATATA
*
376 TATAATAACTAAAATACT
1 TATAATAACTGAAATACT
* *
394 TACATTAATTAAATGTAATAC-
1 T--A-TAA-TAACTGAAATACT
415 TATAATAACTGAAATACT
1 TATAATAACTGAAATACT
433 TATA
1 TATA
437 TTAATTAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 10 0.30
18 8 0.24
19 1 0.03
20 1 0.03
21 4 0.12
22 9 0.27
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (18 bp):
TATAATAACTGAAATACT
Found at i:477 original size:25 final size:24
Alignment explanation
Indices: 437--483 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
427 AATACTTATA
437 TTAATTAAAGTCTTAGGTATTTTT
1 TTAATTAAAGTCTTAGGTATTTTT
*
461 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAAGTCTTAGGTATTT
484 GTGCAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.53
Consensus pattern (24 bp):
TTAATTAAAGTCTTAGGTATTTTT
Found at i:801 original size:206 final size:204
Alignment explanation
Indices: 557--972 Score: 703
Period size: 206 Copynumber: 2.0 Consensus size: 204
547 TCCTTTAATA
557 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATT-AATCTAATTT
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGAA-CTAATTT
* * *
621 AATTTAATAAATTAGCCACTAATGTTCAACTAA-TTTTTTTT-GGTATAGTTCTATATATATATA
65 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTTGGGTACAGTTC--TATATATATA
*
684 ATAGTAATGTGTAGTATCTTATTCACTACAACTTTGTTTGTAATCTTAGACTTAAAAAATTAATA
128 ATAGTAATGTGTAGTATCTTATTCACTACAACTTTG-TTATAATCTTAGACTTAAAAAATTAATA
749 ACATTCACCATTG
192 ACATTCACCATTG
762 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGAACTAATTT
1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGAACTAATTT
827 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTTTGGGTACAGTTCTATATATATAA
65 AATTTAATAAATCAACCACTAATGTTCAACTAA-TTTTTTTTTGGGTACAGTTCTATATATATAA
* *
892 TAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTATAATTTTAGACTTAAAAAATTAATAAC
129 TAGTAATGTGTAGTATCTTATTCACTACAACTTTGTTATAATCTTAGACTTAAAAAATTAATAAC
957 ATTCACCATTG
194 ATTCACCATTG
968 ATAAA
1 ATAAA
973 GTTATTAAGC
Statistics
Matches: 200, Mismatches: 6, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
205 16 0.08
206 120 0.60
207 47 0.23
208 8 0.04
209 9 0.05
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (204 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGAACTAATTTA
ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTTGGGTACAGTTCTATATATATAATA
GTAATGTGTAGTATCTTATTCACTACAACTTTGTTATAATCTTAGACTTAAAAAATTAATAACAT
TCACCATTG
Found at i:1537 original size:35 final size:36
Alignment explanation
Indices: 1491--1559 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
1481 GAGATTTTGG
* *
1491 AGAAATATGATAATCAAAATTACAAAA-ATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAGATGTAATA
1526 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1560 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 25 0.81
36 6 0.19
ACGTcount: A:0.59, C:0.09, G:0.10, T:0.22
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAGATGTAATA
Found at i:1723 original size:117 final size:116
Alignment explanation
Indices: 1555--1784 Score: 307
Period size: 117 Copynumber: 2.0 Consensus size: 116
1545 TCACAAAAGA
* * * * * **
1555 TGTAAGGTTATTGAATTAGTGGATAGTACTATACCTCTTTTGTGATCATTATAGGTTTTTCAGTA
1 TGTAAGGTCATTAAATTAGTGGATAGTACAATACATCTTTTATGATCATTATACCTTTTTCAGTA
*
1620 ACTTTTGAGAAAACAAAAATGACAAATATTCACCGTTGATGAAAGTTTATTG
66 ACTTTTGAGAAAA-AAAAATGACAAATATTCACCATTGATGAAAGTTTATTG
* * * *
1672 TGTAAGGTCATTAAATTAGTTGATAGTACAATACATTTTTTATGATTATTATACCTTTTTCGGTA
1 TGTAAGGTCATTAAATTAGTGGATAGTACAATACATCTTTTATGATCATTATACCTTTTTCAGTA
* ** *
1737 ACTTTTGAGGAAAAAAAATGGTAAATCTTCACCATTGATGAAAGTTTA
66 ACTTTTGAGAAAAAAAAATGACAAATATTCACCATTGATGAAAGTTTA
1785 CTAATGTTAT
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
116 31 0.32
117 66 0.68
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (116 bp):
TGTAAGGTCATTAAATTAGTGGATAGTACAATACATCTTTTATGATCATTATACCTTTTTCAGTA
ACTTTTGAGAAAAAAAAATGACAAATATTCACCATTGATGAAAGTTTATTG
Done.