Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023024.1 Corchorus olitorius cultivar O-4 contig23057, 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: 22877
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:685 original size:43 final size:43
Alignment explanation
Indices: 578--705 Score: 214
Period size: 38 Copynumber: 3.1 Consensus size: 43
568 ATCGTTGTTG
578 CTTTCGCCTTTCAGGACTGGAAAACTAGGGTTTTCTTTTTTCT
1 CTTTCGCCTTTCAGGACTGGAAAACTAGGGTTTTCTTTTTTCT
621 CTTTCGCCTTT-----CTGGAAAACTAGGGTTTTCTTTTTTCT
1 CTTTCGCCTTTCAGGACTGGAAAACTAGGGTTTTCTTTTTTCT
659 CTTTCGCCTTTCAGGACTGGAAAACTAGGGTTTTCTTTTTTCT
1 CTTTCGCCTTTCAGGACTGGAAAACTAGGGTTTTCTTTTTTCT
702 -TTTC
1 CTTTC
706 TTCTTCGGTA
Statistics
Matches: 80, Mismatches: 0, Indels: 11
0.88 0.00 0.12
Matches are distributed among these distances:
38 38 0.47
42 4 0.05
43 38 0.47
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (43 bp):
CTTTCGCCTTTCAGGACTGGAAAACTAGGGTTTTCTTTTTTCT
Found at i:13274 original size:19 final size:19
Alignment explanation
Indices: 13221--13263 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
13211 CTAACCTAAT
13221 AAATCCAAAAACACCATCA
1 AAATCCAAAAACACCATCA
*
13240 AAATCCAAAACCACCATCA
1 AAATCCAAAAACACCATCA
13259 AAATC
1 AAATC
13264 AAGAAAGACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.56, C:0.33, G:0.00, T:0.12
Consensus pattern (19 bp):
AAATCCAAAAACACCATCA
Found at i:14491 original size:13 final size:14
Alignment explanation
Indices: 14469--14501 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
14459 TAGAAATACG
14469 TAAAAATAAAAA-C
1 TAAAAATAAAAAGC
*
14482 TAAAATTAAAAAGC
1 TAAAAATAAAAAGC
14496 TAAAAA
1 TAAAAA
14502 AAGAAAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (14 bp):
TAAAAATAAAAAGC
Found at i:16519 original size:28 final size:28
Alignment explanation
Indices: 16479--16535 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
16469 TTAGCTTAGC
16479 ATGTTGAATGCTAATTTAAGTTATTTAT
1 ATGTTGAATGCTAATTTAAGTTATTTAT
*
16507 ATGTTGACTGCTAATTTAAGTTATTTAT
1 ATGTTGAATGCTAATTTAAGTTATTTAT
16535 A
1 A
16536 GCATTGCCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (28 bp):
ATGTTGAATGCTAATTTAAGTTATTTAT
Found at i:16975 original size:3 final size:3
Alignment explanation
Indices: 16969--17027 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
16959 ATTATTATAT
16969 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17017 ATA ATA ATA AT
1 ATA ATA ATA AT
17028 GATATATATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:17229 original size:11 final size:12
Alignment explanation
Indices: 17209--17244 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
17199 CAACAATATA
17209 AATAAAAAAATT
1 AATAAAAAAATT
17221 AATAAAAAAA-T
1 AATAAAAAAATT
17232 -ATAAAAAAATT
1 AATAAAAAAATT
17243 AA
1 AA
17245 AGAAAAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 9 0.41
11 2 0.09
12 11 0.50
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AATAAAAAAATT
Found at i:17236 original size:22 final size:21
Alignment explanation
Indices: 17210--17252 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
17200 AACAATATAA
17210 ATAAAAAAATTAATAAAAAAAT
1 ATAAAAAAATTAA-AAAAAAAT
*
17232 ATAAAAAAATTAAAGAAAAAT
1 ATAAAAAAATTAAAAAAAAAT
17253 GATGTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (21 bp):
ATAAAAAAATTAAAAAAAAAT
Found at i:17240 original size:13 final size:13
Alignment explanation
Indices: 17203--17240 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
17193 ATGTAACAAC
17203 AATATAAATAAAAA
1 AATATAAA-AAAAA
*
17217 AAT-TAATAAAAA
1 AATATAAAAAAAA
17229 AATATAAAAAAA
1 AATATAAAAAAA
17241 TTAAAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 8 0.38
13 10 0.48
14 3 0.14
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AATATAAAAAAAA
Found at i:18693 original size:66 final size:66
Alignment explanation
Indices: 18583--18714 Score: 194
Period size: 66 Copynumber: 2.0 Consensus size: 66
18573 GGGTAACTTT
* * * * *
18583 GCTCTGATTAATTCGGATCCGATCCGTGTCGCGCATCTGGTTTTGATAGG-TGAGTCTCCCAACG
1 GCTCTGATTAATCCGGATCCGAGCCGTGTCGCGCACCTGATTTTGAT-GGATGAGCCTCCCAACG
18647 GG
65 GG
*
18649 GCTCTGATTAATCCGGATCCGAGCCGTGTCGCGCACCTGATTTTGATGGATGAGCCTCGCAACGG
1 GCTCTGATTAATCCGGATCCGAGCCGTGTCGCGCACCTGATTTTGATGGATGAGCCTCCCAACGG
18714 G
66 G
18715 AACAGCTGCG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 2 0.03
66 57 0.97
ACGTcount: A:0.17, C:0.26, G:0.30, T:0.27
Consensus pattern (66 bp):
GCTCTGATTAATCCGGATCCGAGCCGTGTCGCGCACCTGATTTTGATGGATGAGCCTCCCAACGG
G
Found at i:19813 original size:24 final size:24
Alignment explanation
Indices: 19769--19819 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
19759 TTATTAATAA
*
19769 ATACCCAAATTTCATCACAATTAT
1 ATACCCAAATTTCATCACAATCAT
**
19793 ATACCCAAATTTCATTGCAATCAT
1 ATACCCAAATTTCATCACAATCAT
19817 ATA
1 ATA
19820 AATTTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.24, G:0.02, T:0.33
Consensus pattern (24 bp):
ATACCCAAATTTCATCACAATCAT
Found at i:20303 original size:13 final size:13
Alignment explanation
Indices: 20285--20310 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20275 TTAAAATGTC
20285 ATAATAGAAAGAG
1 ATAATAGAAAGAG
20298 ATAATAGAAAGAG
1 ATAATAGAAAGAG
20311 TGTCTACTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (13 bp):
ATAATAGAAAGAG
Found at i:21505 original size:30 final size:31
Alignment explanation
Indices: 21471--21529 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 31
21461 TATACTTCGG
21471 TTTGG-ATTGTAAATTTACAT-AC-AAAATTTC
1 TTTGGAATTG-AAATTT-CATAACTAAAATTTC
21501 TTTGGAATTGAAATTTCATAACTAAAATT
1 TTTGGAATTGAAATTTCATAACTAAAATT
21530 ATATTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 3 0.12
30 13 0.50
31 10 0.38
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42
Consensus pattern (31 bp):
TTTGGAATTGAAATTTCATAACTAAAATTTC
Found at i:21678 original size:2 final size:2
Alignment explanation
Indices: 21671--21715 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
21661 ATTCATGCAG
21671 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21713 TA T
1 TA T
21716 GGGGGTAAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22795 original size:2 final size:2
Alignment explanation
Indices: 22788--22824 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
22778 CCTCCTCATA
22788 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22825 CTAGTTTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.