Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016734.1 Corchorus olitorius cultivar O-4 contig16767, 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: 26911
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:1077 original size:2 final size:2
Alignment explanation
Indices: 1070--1126 Score: 80
Period size: 2 Copynumber: 28.5 Consensus size: 2
1060 ATTCTTAAAC
* *
1070 AT AT AT AT AT AT AT AT AT AT AT -T AGG GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
1112 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1127 AATTTTGGAC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10050 original size:11 final size:11
Alignment explanation
Indices: 10034--10065 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
10024 ACAGCGCAAT
10034 AAAAACAAAAC
1 AAAAACAAAAC
*
10045 AAAAACGAAAC
1 AAAAACAAAAC
10056 AAAAACAAAA
1 AAAAACAAAA
10066 AACATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.81, C:0.16, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:10082 original size:17 final size:18
Alignment explanation
Indices: 10032--10087 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
10022 TGACAGCGCA
10032 ATAAAAACAAAACAAAAACG
1 ATAAAAAC-AAA-AAAAACG
10052 A-AACAAA-AACAAAAAAC-
1 ATAA-AAACAA-AAAAAACG
10069 ATAAAAACAAAAAAAACG
1 ATAAAAACAAAAAAAACG
10087 A
1 A
10088 AAATGATGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
17 11 0.35
18 13 0.42
19 3 0.10
20 4 0.13
ACGTcount: A:0.79, C:0.14, G:0.04, T:0.04
Consensus pattern (18 bp):
ATAAAAACAAAAAAAACG
Found at i:15697 original size:69 final size:69
Alignment explanation
Indices: 15586--15724 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
15576 CATCTGAACT
15586 TGTACATCCTCTCCTCCTATTGGGCATCTTGCATTATTAGGCATTTCTCTCTCAACTCCTTGTTC
1 TGTACATCCTCTCCTCCTATTGGGCATCTTGCATTATTAGGCATTTCTCTCTCAACTCCTTGTTC
15651 TGCC
66 TGCC
15655 TGTACATCCTCTCCTCCTATTGGGCATCTTGCATTATTAGGCATTTCTCTCTCAACTCCTTGTTC
1 TGTACATCCTCTCCTCCTATTGGGCATCTTGCATTATTAGGCATTTCTCTCTCAACTCCTTGTTC
15720 TGCC
66 TGCC
15724 T
1 T
15725 CCCTTACTTG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.14, C:0.32, G:0.13, T:0.41
Consensus pattern (69 bp):
TGTACATCCTCTCCTCCTATTGGGCATCTTGCATTATTAGGCATTTCTCTCTCAACTCCTTGTTC
TGCC
Found at i:18928 original size:2 final size:2
Alignment explanation
Indices: 18923--18968 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
18913 ACACACACAC
*
18923 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18965 AT AT
1 AT AT
18969 GTGTGTGTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18973 original size:2 final size:2
Alignment explanation
Indices: 18968--18992 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18958 TATATATATA
18968 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
18993 ATTTATTTTT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:22507 original size:50 final size:50
Alignment explanation
Indices: 22448--22542 Score: 181
Period size: 50 Copynumber: 1.9 Consensus size: 50
22438 AATGATGGCT
22448 TTCAAAATTTCCTTCAAACCCTAAGAGATGCAAAGAAAGCCTCATAAGCC
1 TTCAAAATTTCCTTCAAACCCTAAGAGATGCAAAGAAAGCCTCATAAGCC
*
22498 TTCAAAATTTCCTTCAAACCTTAAGAGATGCAAAGAAAGCCTCAT
1 TTCAAAATTTCCTTCAAACCCTAAGAGATGCAAAGAAAGCCTCAT
22543 CAATGTATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (50 bp):
TTCAAAATTTCCTTCAAACCCTAAGAGATGCAAAGAAAGCCTCATAAGCC
Found at i:23841 original size:31 final size:31
Alignment explanation
Indices: 23806--23867 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
23796 CGAGTGGCAA
23806 GCTAGTAGGAATCAAGATTGAGTAGGATGTG
1 GCTAGTAGGAATCAAGATTGAGTAGGATGTG
*
23837 GCTAGTAGGAATCAAGCTTGAGTAGGATGTG
1 GCTAGTAGGAATCAAGATTGAGTAGGATGTG
23868 TTTTTAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.08, G:0.35, T:0.26
Consensus pattern (31 bp):
GCTAGTAGGAATCAAGATTGAGTAGGATGTG
Found at i:23862 original size:17 final size:17
Alignment explanation
Indices: 23809--23863 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
23799 GTGGCAAGCT
*
23809 AGTAGGAATCAAGATTG
1 AGTAGGAATCAAGCTTG
***
23826 AGTAGG-ATGTGGC-T-
1 AGTAGGAATCAAGCTTG
23840 AGTAGGAATCAAGCTTG
1 AGTAGGAATCAAGCTTG
23857 AGTAGGA
1 AGTAGGA
23864 TGTGTTTTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 6
0.68 0.17 0.15
Matches are distributed among these distances:
14 6 0.21
15 5 0.18
16 4 0.14
17 13 0.46
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.24
Consensus pattern (17 bp):
AGTAGGAATCAAGCTTG
Done.