Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011115.1 Corchorus olitorius cultivar O-4 contig11148, 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: 41061
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:6530 original size:29 final size:30
Alignment explanation
Indices: 6484--6542 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
6474 ACAATTTTTA
*
6484 CGTATTTAAAAGGCAACTAGGACATGGCTT
1 CGTATTTAAAAGGCAACTAGGACAGGGCTT
6514 CGTATTT-AAAGGCAACTAGGACAGGGCTT
1 CGTATTTAAAAGGCAACTAGGACAGGGCTT
6543 TTACGAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (30 bp):
CGTATTTAAAAGGCAACTAGGACAGGGCTT
Found at i:9194 original size:15 final size:15
Alignment explanation
Indices: 9174--9204 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
9164 ACAATACATT
9174 AACTATCAAATAGAA
1 AACTATCAAATAGAA
9189 AACTATCAAATAGAA
1 AACTATCAAATAGAA
9204 A
1 A
9205 CATGTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (15 bp):
AACTATCAAATAGAA
Found at i:9251 original size:14 final size:14
Alignment explanation
Indices: 9232--9266 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
9222 CCTTTTAAAT
9232 TAAAATAGTAAAAA
1 TAAAATAGTAAAAA
*
9246 TAAAATGGTAAAAA
1 TAAAATAGTAAAAA
9260 TAAAATA
1 TAAAATA
9267 ATTATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (14 bp):
TAAAATAGTAAAAA
Found at i:25075 original size:14 final size:15
Alignment explanation
Indices: 25056--25113 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
25046 TCATTATTCA
25056 TAAAATA-AATTTAT
1 TAAAATATAATTTAT
* *
25070 TAAAATATATTTTCCT
1 TAAAATATAATTT-AT
25086 TCAAAA-A-AATTTAT
1 T-AAAATATAATTTAT
25100 TAAAATATAATTTA
1 TAAAATATAATTTA
25114 CTTGACAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
13 4 0.11
14 10 0.29
15 14 0.40
16 3 0.09
17 4 0.11
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAAATATAATTTAT
Found at i:25124 original size:30 final size:30
Alignment explanation
Indices: 25057--25125 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
25047 CATTATTCAT
* *
25057 AAAATAAATTTATTAAAATATATTTTCCTTC
1 AAAA-AAATTTATTAAAATATAATTTACTTC
*
25088 AAAAAAATTTATTAAAATATAATTTACTTG
1 AAAAAAATTTATTAAAATATAATTTACTTC
*
25118 ACAAAAAT
1 AAAAAAAT
25126 AATTGAGGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.39
Consensus pattern (30 bp):
AAAAAAATTTATTAAAATATAATTTACTTC
Found at i:27440 original size:2 final size:2
Alignment explanation
Indices: 27433--27457 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27423 ATTACGTGTC
27433 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 T
27458 TTCTATGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28234 original size:140 final size:142
Alignment explanation
Indices: 27991--28276 Score: 443
Period size: 140 Copynumber: 2.0 Consensus size: 142
27981 AATAATAAGT
*
27991 TTTTTTTTTGTGAAAATAGTTTGAACCTATTCTCTTCATCAAATGGAAAAAAGGAATAATCTAAA
1 TTTTTTTTTGTGAAAATAGTTTGAACATATTCTCTTCATCAAATGGAAAAAAGGAATAATCTAAA
* * * * *
28056 AAGCTATATATTTGATATTTTAAACTAAATATTAATTAATTGCATGTACATAA-T-TAAGATCCT
66 AAACTATATATTTGACATTTCAAACTAAATATTAATTAATTGCATGTACAAAATTATAAGATCCA
28119 TTAATAATGTGA
131 TTAATAATGTGA
*
28131 TTTTTTTTTGTGAAAATAGTTTGAATATATTCTCTTCATCAAATGGAAAAAAGGAATAATATTCT
1 TTTTTTTTTGTGAAAATAGTTTGAACATATTCTCTTCATCAAATGGAAAAAAGGAAT-A-A-TCT
28196 AAAAAA-TACATATATTTGACATTTCAAACTAAATATTAATTAATTGCATGTACAAAATTATAAG
63 AAAAAACT--ATATATTTGACATTTCAAACTAAATATTAATTAATTGCATGTACAAAATTATAAG
28260 ATCCATTAATAATGTGA
126 ATCCATTAATAATGTGA
28277 AATGTGATTA
Statistics
Matches: 132, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
140 55 0.42
141 1 0.01
142 2 0.02
143 8 0.06
144 45 0.34
145 1 0.01
146 20 0.15
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (142 bp):
TTTTTTTTTGTGAAAATAGTTTGAACATATTCTCTTCATCAAATGGAAAAAAGGAATAATCTAAA
AAACTATATATTTGACATTTCAAACTAAATATTAATTAATTGCATGTACAAAATTATAAGATCCA
TTAATAATGTGA
Found at i:30005 original size:30 final size:28
Alignment explanation
Indices: 29943--30005 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 28
29933 AGAAAAGATT
** **
29943 TTTTGAAACAGTAAATCATAGTTTTTTT
1 TTTTGAAACAGTAAATCATAGTTGGTAG
29971 TTTTGAAAGTCAGTAAATCATAGTTGGTAG
1 TTTTGAAA--CAGTAAATCATAGTTGGTAG
30001 TTTTG
1 TTTTG
30006 CATTTGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 8 0.28
30 21 0.72
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.46
Consensus pattern (28 bp):
TTTTGAAACAGTAAATCATAGTTGGTAG
Found at i:37266 original size:16 final size:17
Alignment explanation
Indices: 37242--37274 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
37232 ATGGTGTACG
37242 TATAAATTATAT-TTAA
1 TATAAATTATATATTAA
*
37258 TATATATTATATATTAA
1 TATAAATTATATATTAA
37275 CAAATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATAAATTATATATTAA
Found at i:41034 original size:2 final size:2
Alignment explanation
Indices: 41027--41061 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
41017 CGTTTCCTAC
41027 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 A
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.