Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012815.1 Corchorus olitorius cultivar O-4 contig12848, 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: 10705
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:1048 original size:3 final size:3
Alignment explanation
Indices: 1024--1070 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
1014 CCAATTTTAA
* * * *
1024 TAT TAT AAT CAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1071 AACACAAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:7156 original size:25 final size:25
Alignment explanation
Indices: 7128--7181 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
7118 ATAATGTGCG
* *
7128 TGCGCTGAGCAAACGCGTCTGTACT
1 TGCGCTGAGCAAACGAGCCTGTACT
* * *
7153 TGCGTTTAGCAAACGAGCCTGTGCT
1 TGCGCTGAGCAAACGAGCCTGTACT
7178 TGCG
1 TGCG
7182 TTTGTAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (25 bp):
TGCGCTGAGCAAACGAGCCTGTACT
Found at i:7182 original size:25 final size:25
Alignment explanation
Indices: 7135--7184 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
7125 GCGTGCGCTG
* *
7135 AGCAAACGCGTCTGTACTTGCGTTT
1 AGCAAACGAGCCTGTACTTGCGTTT
*
7160 AGCAAACGAGCCTGTGCTTGCGTTT
1 AGCAAACGAGCCTGTACTTGCGTTT
7185 GTAAAATGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (25 bp):
AGCAAACGAGCCTGTACTTGCGTTT
Found at i:8591 original size:18 final size:18
Alignment explanation
Indices: 8577--8654 Score: 87
Period size: 15 Copynumber: 4.7 Consensus size: 18
8567 TTTTCTGCAC
8577 CGGATGATGTTTCTGAAA
1 CGGATGATGTTTCTGAAA
*
8595 TGG-T--TGTTTCTGAAA
1 CGGATGATGTTTCTGAAA
* *
8610 CGGATGATGTTTTTGCAA
1 CGGATGATGTTTCTGAAA
8628 CGG-T--TGTTTCTGAAA
1 CGGATGATGTTTCTGAAA
8643 CGGATGATGTTT
1 CGGATGATGTTT
8655 TTGCAACGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
15 25 0.52
16 2 0.04
17 2 0.04
18 19 0.40
ACGTcount: A:0.22, C:0.10, G:0.28, T:0.40
Consensus pattern (18 bp):
CGGATGATGTTTCTGAAA
Found at i:8604 original size:15 final size:15
Alignment explanation
Indices: 8584--8669 Score: 73
Period size: 15 Copynumber: 5.3 Consensus size: 15
8574 CACCGGATGA
*
8584 TGTTTCTGAAATGGT
1 TGTTTCTGAAACGGT
8599 TGTTTCTGAAACGGAT
1 TGTTTCTGAAACGG-T
* *
8615 GATGTTTTTGCAACGGT
1 --TGTTTCTGAAACGGT
8632 TGTTTCTGAAACGGAT
1 TGTTTCTGAAACGG-T
* *
8648 GATGTTTTTGCAACGGT
1 --TGTTTCTGAAACGGT
8665 TGTTT
1 TGTTT
8670 TTGCACCACT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
15 30 0.52
16 2 0.03
17 2 0.03
18 24 0.41
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
TGTTTCTGAAACGGT
Found at i:8614 original size:33 final size:33
Alignment explanation
Indices: 8568--8669 Score: 159
Period size: 33 Copynumber: 3.1 Consensus size: 33
8558 CATTTGCAAT
* * * * *
8568 TTTCTGCACCGGATGATGTTTCTGAAATGGTTG
1 TTTCTGAAACGGATGATGTTTTTGCAACGGTTG
8601 TTTCTGAAACGGATGATGTTTTTGCAACGGTTG
1 TTTCTGAAACGGATGATGTTTTTGCAACGGTTG
8634 TTTCTGAAACGGATGATGTTTTTGCAACGGTTG
1 TTTCTGAAACGGATGATGTTTTTGCAACGGTTG
8667 TTT
1 TTT
8670 TTGCACCACT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.20, C:0.13, G:0.26, T:0.41
Consensus pattern (33 bp):
TTTCTGAAACGGATGATGTTTTTGCAACGGTTG
Found at i:10375 original size:43 final size:42
Alignment explanation
Indices: 10314--10607 Score: 358
Period size: 43 Copynumber: 6.7 Consensus size: 42
10304 CAATAACCAA
*
10314 AAAGTCCCCAAACACATATATAACACAGGGGCAATTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGC-ATTCTATTAC
*
10357 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGGGGCA-TTCTATTAC
* *
10400 AAAAGTCCTCAAACACATATATAACACAGAGGCA-TCTA-TACC
1 -AAAGTCCCCAAACACATATATAACACAGGGGCATTCTATTA-C
*
10442 CAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGC-ATTCTATTAC
*
10485 AAAGTCCCCAAACACATATATAACACAGGGGCATTTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGGGGCA-TTCTATTAC
10528 AAAAGTCCTCACGTCCTCAAACACATATATAACACAGGGGCAATTCTATTAC
1 -AAAG---T--C--CC-CAAACACATATATAACACAGGGGC-ATTCTATTAC
* *
10580 AACGTCCTCAAACACATATATAACACAG
1 AAAGTCCCCAAACACATATATAACACAG
10608 AGACATTTTT
Statistics
Matches: 221, Mismatches: 13, Indels: 34
0.82 0.05 0.13
Matches are distributed among these distances:
41 30 0.14
42 8 0.04
43 103 0.47
44 38 0.17
46 1 0.00
47 1 0.00
48 1 0.00
49 1 0.00
51 5 0.02
52 32 0.14
53 1 0.00
ACGTcount: A:0.40, C:0.27, G:0.11, T:0.22
Consensus pattern (42 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATTCTATTAC
Found at i:10682 original size:2 final size:2
Alignment explanation
Indices: 10670--10705 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
10660 ACCAAATTCC
10670 TA TA T- TA TA TA 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 TA TA TA TA TA TA T
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Done.