Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018993.1 Corchorus olitorius cultivar O-4 contig19026, 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: 31334
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:1155 original size:50 final size:50
Alignment explanation
Indices: 1074--1347 Score: 416
Period size: 50 Copynumber: 5.5 Consensus size: 50
1064 AGATATACAG
* *
1074 AAGAGTGAATTGGAAG---GTTCGAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
*
1121 AAGATTGAATTGGAAGACTGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
* *
1171 -AGAATTGAATTGGAAAACAGTTCAAAGGATAAGCGGAAAACGGTCCTTTT
1 AAG-ATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
*
1221 -AGAATTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTTTT
1 AAG-ATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
1271 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
*
1321 AACATT-AGATTGGAAGACAGTTCAAAG
1 AAGATTGA-ATTGGAAGACAGTTCAAAG
1348 AAGTTGATCG
Statistics
Matches: 211, Mismatches: 10, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
47 15 0.07
49 3 0.01
50 191 0.91
51 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (50 bp):
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
Found at i:1657 original size:29 final size:29
Alignment explanation
Indices: 1591--1716 Score: 191
Period size: 29 Copynumber: 4.4 Consensus size: 29
1581 GGTCACTTAA
*
1591 AGGGGCATTTTGGTCA-TTTTGCATATCC
1 AGGGGCATTTTGGTCATTTTTGCACATCC
* *
1619 AGGGGCATTTTGGTCACTTTCGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCACATCC
*
1648 AGAGGCATTTTGGTCATTTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCACATCC
*
1677 AGGGGCATTTTGGTCATTTTTGCACATAC
1 AGGGGCATTTTGGTCATTTTTGCACATCC
*
1706 AGGGTCATTTT
1 AGGGGCATTTT
1717 TGCACATCTA
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
28 16 0.18
29 73 0.82
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTGCACATCC
Found at i:7041 original size:32 final size:32
Alignment explanation
Indices: 6999--7071 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 32
6989 GCGGGTTGGG
* * * *
6999 TCGGGCTCGGGCTCTGTCGGGTTTGGGTATTT
1 TCGGGTTCGGGCTCTGTCGGATTAGGATATTT
* *
7031 TTGGGTTCGGGCTTTGTCGGATTAGGATATTT
1 TCGGGTTCGGGCTCTGTCGGATTAGGATATTT
7063 TCGGGTTCG
1 TCGGGTTCG
7072 TTCTCGGGTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.07, C:0.15, G:0.38, T:0.40
Consensus pattern (32 bp):
TCGGGTTCGGGCTCTGTCGGATTAGGATATTT
Found at i:8245 original size:45 final size:45
Alignment explanation
Indices: 8195--8289 Score: 181
Period size: 45 Copynumber: 2.1 Consensus size: 45
8185 TTTGATTGCA
*
8195 TTATATTTTTCACCGTTAAATGTATATTGAAAATATTGAAAAATC
1 TTATATTTTTCACCGTTAAATATATATTGAAAATATTGAAAAATC
8240 TTATATTTTTCACCGTTAAATATATATTGAAAATATTGAAAAATC
1 TTATATTTTTCACCGTTAAATATATATTGAAAATATTGAAAAATC
8285 TTATA
1 TTATA
8290 GTCTCGATCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.43
Consensus pattern (45 bp):
TTATATTTTTCACCGTTAAATATATATTGAAAATATTGAAAAATC
Found at i:10888 original size:22 final size:23
Alignment explanation
Indices: 10849--10891 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
10839 AATCCTAATC
10849 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
10872 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
10892 ACTCCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:17118 original size:25 final size:26
Alignment explanation
Indices: 17078--17134 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
17068 GTGGCTTTCA
*
17078 ATTT-TTTT-CTCTTTTTCTTTA-TT
1 ATTTATTTTCCTCTTTTTATTTATTT
17101 ATTATATTTTCCTC-TTTTATTTATTT
1 ATT-TATTTTCCTCTTTTTATTTATTT
17127 ATTTATTT
1 ATTTATTT
17135 GCGAGGCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 3 0.10
24 1 0.03
25 17 0.59
26 8 0.28
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.74
Consensus pattern (26 bp):
ATTTATTTTCCTCTTTTTATTTATTT
Found at i:19555 original size:21 final size:21
Alignment explanation
Indices: 19531--19574 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
19521 TCCAAAGAAC
19531 AATTCATAGTACCATACCAAT
1 AATTCATAGTACCATACCAAT
19552 AATTCATAGTACCATACCAAT
1 AATTCATAGTACCATACCAAT
19573 AA
1 AA
19575 GCAAGTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.27
Consensus pattern (21 bp):
AATTCATAGTACCATACCAAT
Found at i:21256 original size:1 final size:1
Alignment explanation
Indices: 21250--21282 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
21240 GGTCTCAAAG
21250 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
21283 GGGCACAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:26472 original size:20 final size:21
Alignment explanation
Indices: 26440--26493 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
26430 ATAAACTTAC
26440 AAGGTTAAC-AAAAAG-TTTAAT
1 AAGGTT-ACTAAAAAGCTTT-AT
*
26461 AA-GTTACTAAAATGCTTTAT
1 AAGGTTACTAAAAAGCTTTAT
26481 AAGGTTACTAAAA
1 AAGGTTACTAAAA
26494 CCTTAACGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 2 0.07
20 12 0.41
21 15 0.52
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.31
Consensus pattern (21 bp):
AAGGTTACTAAAAAGCTTTAT
Found at i:26599 original size:21 final size:21
Alignment explanation
Indices: 26575--26622 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
26565 TAGTATTCTT
* *
26575 ACTAAAAAACTTTATAAGGTC
1 ACTAAAAAACATAATAAGGTC
26596 ACT-AAAAACATAATAAGGTC
1 ACTAAAAAACATAATAAGGTC
*
26616 ATTAAAA
1 ACTAAAA
26623 GAGGTTGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.25
Consensus pattern (21 bp):
ACTAAAAAACATAATAAGGTC
Done.