Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024438.1 Corchorus olitorius cultivar O-4 contig24471, 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: 16628
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1506 original size:33 final size:32
Alignment explanation
Indices: 1488--1656 Score: 180
Period size: 33 Copynumber: 5.1 Consensus size: 32
1478 ATTAGCATCC
1488 AAAACAGAATTTAGTTCATCACAAACAACACCT
1 AAAACAG-ATTTAGTTCATCACAAACAACACCT
1521 AAAACAGATTTAGTGTCATCACAAACAACA-CT
1 AAAACAGATTTAGT-TCATCACAAACAACACCT
** * *
1553 CAAATTAGGTTTAGTATCATCGCAAACAACACCT
1 -AAAACAGATTTAGT-TCATCACAAACAACACCT
1587 AAAACAGATTTAGTGTCATCACAAACAACA-CT
1 AAAACAGATTTAGT-TCATCACAAACAACACCT
** * * *
1619 CAAATTAGGTTTAGTATCATCGCAAACAACATCT
1 -AAAACAGATTTAGT-TCATCACAAACAACACCT
1653 AAAA
1 AAAA
1657 TACTATTTGC
Statistics
Matches: 115, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
32 11 0.10
33 100 0.87
34 4 0.03
ACGTcount: A:0.45, C:0.22, G:0.09, T:0.24
Consensus pattern (32 bp):
AAAACAGATTTAGTTCATCACAAACAACACCT
Found at i:1540 original size:66 final size:66
Alignment explanation
Indices: 1487--1656 Score: 243
Period size: 66 Copynumber: 2.6 Consensus size: 66
1477 AATTAGCATC
1487 CAAAACAGAATTTAGT-TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACA
1 CAAAACAG-ATTTAGTATCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACA
1551 CT
65 CT
** * *
1553 CAAATTAGGTTTAGTATCATCGCAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACAC
1 CAAAACAGATTTAGTATCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACAC
1618 T
66 T
** * * *
1619 CAAATTAGGTTTAGTATCATCGCAAACAACATCTAAAA
1 CAAAACAGATTTAGTATCATCACAAACAACACCTAAAA
1657 TACTATTTGC
Statistics
Matches: 98, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
65 6 0.06
66 92 0.94
ACGTcount: A:0.45, C:0.22, G:0.09, T:0.24
Consensus pattern (66 bp):
CAAAACAGATTTAGTATCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACAC
T
Found at i:3242 original size:25 final size:24
Alignment explanation
Indices: 3205--3251 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
3195 CTAGAAAATT
3205 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
3231 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
3252 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
Found at i:6274 original size:21 final size:21
Alignment explanation
Indices: 6241--6289 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
6231 AAGAATTGTA
**
6241 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
6261 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
6282 GCATTCCT
1 GC-TTCCT
6290 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:7053 original size:19 final size:18
Alignment explanation
Indices: 7029--7064 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7019 TGAACACTCA
7029 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
7048 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
7065 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:13891 original size:85 final size:85
Alignment explanation
Indices: 13797--13967 Score: 254
Period size: 85 Copynumber: 2.0 Consensus size: 85
13787 TTGTTTAAAT
* *
13797 TTTTATAGTTTTAGTCAACTAAAAGCTCTATTATTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTATTATTTAATTAAATCTAATATCCTTATAACTA
*
13862 -TATTATTTTTACCATTTTAC
66 CT-TTATTTTTACCATATTAC
* ** *
13882 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATTTTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTATTATTTAATTAAATCTAATATCCTTATAACTA
*
13947 CTTTATTTTTACGATATTAC
66 CTTTATTTTTACCATATTAC
13967 T
1 T
13968 AATCTATACT
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
85 76 0.99
86 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.03, T:0.51
Consensus pattern (85 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTATTATTTAATTAAATCTAATATCCTTATAACTA
CTTTATTTTTACCATATTAC
Found at i:15715 original size:24 final size:26
Alignment explanation
Indices: 15686--15748 Score: 82
Period size: 24 Copynumber: 2.6 Consensus size: 26
15676 CCATTTAGTA
15686 ATTAAATATATATTATTTATTT-TTT
1 ATTAAATATATATTATTTATTTATTT
*
15711 -TTAAATACAT-TTA-TTATTTATTT
1 ATTAAATATATATTATTTATTTATTT
15734 ATT-AATATATATTAT
1 ATTAAATATATATTAT
15749 ATCTAAGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
22 6 0.19
23 12 0.38
24 14 0.44
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTAAATATATATTATTTATTTATTT
Done.