Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015578.1 Corchorus olitorius cultivar O-4 contig15611, 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: 31636
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:16604 original size:53 final size:53
Alignment explanation
Indices: 16541--16646 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
16531 ACAACCAACA
* *
16541 TATATGTTTGAGTATATCTTTCTAATATATGTTTATCATGTTTGTTAAAGTTT
1 TATATGTTTGAGTATATCTTTCTAATATATATTTATCATGTTTGTCAAAGTTT
16594 TATATGTTTGAGTATATCTTTCTAATATATATTTATCATGTTTGTCAAAGTTT
1 TATATGTTTGAGTATATCTTTCTAATATATATTTATCATGTTTGTCAAAGTTT
16647 ATGAATTACA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.27, C:0.07, G:0.12, T:0.54
Consensus pattern (53 bp):
TATATGTTTGAGTATATCTTTCTAATATATATTTATCATGTTTGTCAAAGTTT
Found at i:21351 original size:60 final size:60
Alignment explanation
Indices: 21258--21385 Score: 238
Period size: 60 Copynumber: 2.1 Consensus size: 60
21248 ATCATACCGA
* *
21258 GAGATCATATCTTGTCCCTTAAACATCGGGGAGGATTCCCTTCAAGACAACCTGAAACGG
1 GAGATCATATCTTGTCCCTTAAACATCGGGGAGGATTCCCTTCAAGACAACCCGAAACAG
21318 GAGATCATATCTTGTCCCTTAAACATCGGGGAGGATTCCCTTCAAGACAACCCGAAACAG
1 GAGATCATATCTTGTCCCTTAAACATCGGGGAGGATTCCCTTCAAGACAACCCGAAACAG
21378 GAGATCAT
1 GAGATCAT
21386 TCTATCACAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (60 bp):
GAGATCATATCTTGTCCCTTAAACATCGGGGAGGATTCCCTTCAAGACAACCCGAAACAG
Found at i:24090 original size:21 final size:19
Alignment explanation
Indices: 24064--24121 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
24054 GCTGCTTTAA
*
24064 TAATCTCATTTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
24085 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
24104 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
24122 TGCTAAACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:24708 original size:13 final size:13
Alignment explanation
Indices: 24687--24749 Score: 85
Period size: 12 Copynumber: 5.0 Consensus size: 13
24677 ACAGATATTC
24687 ATGGATATATCGA
1 ATGGATATATCGA
*
24700 ATAGATATATCGA
1 ATGGATATATCGA
*
24713 ACGGATATATCG-
1 ATGGATATATCGA
24725 ATGGATATATCG-
1 ATGGATATATCGA
*
24737 ACGGATATATCGA
1 ATGGATATATCGA
24750 GGTATTGATG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
12 22 0.50
13 22 0.50
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (13 bp):
ATGGATATATCGA
Found at i:24740 original size:24 final size:25
Alignment explanation
Indices: 24689--24749 Score: 97
Period size: 24 Copynumber: 2.4 Consensus size: 25
24679 AGATATTCAT
24689 GGATATATCGAATAGATATATCGAAC
1 GGATATATCG-ATAGATATATCGAAC
*
24715 GGATATATCGATGGATATATCG-AC
1 GGATATATCGATAGATATATCGAAC
24739 GGATATATCGA
1 GGATATATCGA
24750 GGTATTGATG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
24 13 0.38
25 11 0.32
26 10 0.29
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (25 bp):
GGATATATCGATAGATATATCGAAC
Found at i:25631 original size:10 final size:10
Alignment explanation
Indices: 25616--25641 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
25606 AATCTAATAT
25616 GGATATTTAC
1 GGATATTTAC
25626 GGATATTTAC
1 GGATATTTAC
25636 GGATAT
1 GGATAT
25642 ATTGAGATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Found at i:25661 original size:10 final size:10
Alignment explanation
Indices: 25648--25674 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
25638 ATATATTGAG
25648 ATATCGATAA
1 ATATCGATAA
25658 ATATCGATAA
1 ATATCGATAA
25668 ATATCGA
1 ATATCGA
25675 CGGATATACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (10 bp):
ATATCGATAA
Found at i:25699 original size:10 final size:8
Alignment explanation
Indices: 25674--25698 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
25664 ATAAATATCG
25674 ACGGATAT
1 ACGGATAT
25682 ACGGATAT
1 ACGGATAT
25690 ACGGATAT
1 ACGGATAT
25698 A
1 A
25699 TCGACAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (8 bp):
ACGGATAT
Found at i:26061 original size:69 final size:70
Alignment explanation
Indices: 25927--26061 Score: 218
Period size: 69 Copynumber: 1.9 Consensus size: 70
25917 CGAGTTGATC
* *
25927 AGACTTTCTACTTCATAAATTCTACCTCTAGTTTTATATGGTTAGAGTAAAGGTTAGAATTCATT
1 AGACTTTCTACTTCATAAATTCTACCTCTAGTTTTATATGATTAGAGCAAAGGTTAGAATTCATT
25992 CTTTG
66 CTTTG
* * *
25997 AGACTTTCTACTTCATAAATTTTCCCTCTAG-TTTATATTATTAGAGCAAAGGTTAGAATTCATT
1 AGACTTTCTACTTCATAAATTCTACCTCTAGTTTTATATGATTAGAGCAAAGGTTAGAATTCATT
26061 C
66 C
26062 ATCATCATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
69 31 0.52
70 29 0.48
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.42
Consensus pattern (70 bp):
AGACTTTCTACTTCATAAATTCTACCTCTAGTTTTATATGATTAGAGCAAAGGTTAGAATTCATT
CTTTG
Found at i:27174 original size:16 final size:16
Alignment explanation
Indices: 27152--27183 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
27142 GTATGGCAAA
27152 AAAAAAAAACTCTCATT
1 AAAAAAAAA-TCTCATT
27169 AAAAAAAAATCTCAT
1 AAAAAAAAATCTCAT
27184 AAATTCATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAAAAAATCTCATT
Found at i:27418 original size:13 final size:14
Alignment explanation
Indices: 27395--27430 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
27385 TGTTATTGGG
27395 CTTTCTTTTTTTTT
1 CTTTCTTTTTTTTT
27409 CTTT-TTTTTTTTT
1 CTTTCTTTTTTTTT
*
27422 CTCTCTTTT
1 CTTTCTTTT
27431 CTACCTGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
CTTTCTTTTTTTTT
Found at i:30704 original size:124 final size:124
Alignment explanation
Indices: 30574--30914 Score: 369
Period size: 139 Copynumber: 2.6 Consensus size: 124
30564 CCTTTTAAAT
* *
30574 TAAAATGGTTAAAATAAAATAATTATAAAAATATTGAATTTGATTAAATGAAAATAGAGTTTTTA
1 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTA
* *
30639 GTATAATAAAACTGTGTATTAAAAAATTTTAATATATCCAAGTTTTTAATGAAAAATAC
66 GTAGAATAAAACTGTATATTAAAAAATTTTAATATATCCAAGTTTTTAATGAAAAATAC
30698 TAAAATGGTAAAAATAAAGTTTAAATTAAAATGGTAAAAATAAAAATATTGAATTTAATTAAATG
1 TAAAATGGTAAAAAT--A----AAA-T--AAT--T----ATAAAAATATTGAATTTAATTAAATG
* ** *** *
30763 AAAATAAAACTTTTAGTAGAATAAAACTGTATATTAAATTTTTTTAATATATCCTAGTTTTTAAT
51 AAAATAGAGTTTTTAGTAGAATAAAACTGTATATTAAAAAATTTTAATATATCCAAGTTTTTAAT
*
30828 GAAAAATAG
116 GAAAAATAC
** * * *
30837 TAAAATGGTAAAAATAAGGTAATTATAAAGATATT-ACATTTAACTAAATAAAAATAGAGTTTTT
1 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGA-ATTTAATTAAATGAAAATAGAGTTTTT
*
30901 AATAGAATAAAACT
65 AGTAGAATAAAACT
30915 ATAATAGTTT
Statistics
Matches: 180, Mismatches: 21, Indels: 32
0.77 0.09 0.14
Matches are distributed among these distances:
123 1 0.01
124 59 0.33
126 1 0.01
128 1 0.01
130 6 0.03
131 1 0.01
132 1 0.01
133 4 0.02
135 1 0.01
137 1 0.01
139 104 0.58
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (124 bp):
TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTA
GTAGAATAAAACTGTATATTAAAAAATTTTAATATATCCAAGTTTTTAATGAAAAATAC
Found at i:30752 original size:139 final size:139
Alignment explanation
Indices: 30598--30853 Score: 413
Period size: 139 Copynumber: 1.8 Consensus size: 139
30588 TAAAATAATT
* * ** * *
30598 ATAAAAATATTGAATTTGATTAAATGAAAATAGAGTTTTTAGTATAATAAAACTGTGTATTAAAA
1 ATAAAAATATTGAATTTAATTAAATGAAAATAAAACTTTTAGTAGAATAAAACTGTATATTAAAA
30663 AATTTTAATATATCCAAGTTTTTAATGAAAAATACTAAAATGGTAAAAATAAAGTTTAAATTAAA
66 AATTTTAATATATCCAAGTTTTTAATGAAAAATACTAAAATGGTAAAAATAAAGTTTAAATTAAA
30728 ATGGTAAAA
131 ATGGTAAAA
*
30737 ATAAAAATATTGAATTTAATTAAATGAAAATAAAACTTTTAGTAGAATAAAACTGTATATTAAAT
1 ATAAAAATATTGAATTTAATTAAATGAAAATAAAACTTTTAGTAGAATAAAACTGTATATTAAAA
** * *
30802 TTTTTTAATATATCCTAGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAA
66 AATTTTAATATATCCAAGTTTTTAATGAAAAATACTAAAATGGTAAAAATAA
30854 GGTAATTATA
Statistics
Matches: 106, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
139 106 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (139 bp):
ATAAAAATATTGAATTTAATTAAATGAAAATAAAACTTTTAGTAGAATAAAACTGTATATTAAAA
AATTTTAATATATCCAAGTTTTTAATGAAAAATACTAAAATGGTAAAAATAAAGTTTAAATTAAA
ATGGTAAAA
Found at i:31487 original size:31 final size:31
Alignment explanation
Indices: 31442--31513 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
31432 CCAGACATGC
* *
31442 ATGACCCTAAATCCAGCA-GACCCGAGACCCGA
1 ATGA-CCTGAATCCAG-ATGACCCGAAACCCGA
*
31474 ATGACCTGAATCCAGATGAGCCGAAACCCGA
1 ATGACCTGAATCCAGATGACCCGAAACCCGA
*
31505 ATGATCTGA
1 ATGACCTGA
31514 GAAAATTTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.03
31 30 0.86
32 4 0.11
ACGTcount: A:0.35, C:0.31, G:0.21, T:0.14
Consensus pattern (31 bp):
ATGACCTGAATCCAGATGACCCGAAACCCGA
Done.