Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017106.1 Corchorus olitorius cultivar O-4 contig17139, 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: 30689
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:2809 original size:10 final size:10
Alignment explanation
Indices: 2794--2818 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2784 GATTGTCTCG
2794 TTTTTTTATT
1 TTTTTTTATT
2804 TTTTTTTATT
1 TTTTTTTATT
2814 TTTTT
1 TTTTT
2819 ATTTGAGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:21990 original size:19 final size:19
Alignment explanation
Indices: 21969--22008 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21959 ATTTATAATT
*
21969 AAATATATATTTTACATATA
1 AAATA-ATATTATACATATA
*
21989 AAATAATATTATATATATA
1 AAATAATATTATACATATA
22008 A
1 A
22009 TTACATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATAATATTATACATATA
Found at i:22016 original size:12 final size:12
Alignment explanation
Indices: 21996--22036 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
21986 ATAAAATAAT
21996 ATTATATATATA
1 ATTATATATATA
*
22008 ATTACATATATA
1 ATTATATATATA
*
22020 ATAATATATATA
1 ATTATATATATA
22032 ATTAT
1 ATTAT
22037 TTAACGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
ATTATATATATA
Found at i:22954 original size:29 final size:30
Alignment explanation
Indices: 22921--22996 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 30
22911 TTTAAACTTT
22921 AAAGTTTCGATATTCTTTATTC-AAAAAAA
1 AAAGTTTCGATATTCTTTATTCAAAAAAAA
22950 AAAGTTTCGATATTCTTTATTCAAAAAAAAA
1 AAAGTTTCGATATTCTTTATTC-AAAAAAAA
22981 AAAGTTTCGATATTCT
1 AAAGTTTCGATATTCT
22997 CAATGAGAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
29 22 0.49
31 23 0.51
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (30 bp):
AAAGTTTCGATATTCTTTATTCAAAAAAAA
Found at i:23868 original size:123 final size:124
Alignment explanation
Indices: 23668--23923 Score: 343
Period size: 123 Copynumber: 2.0 Consensus size: 124
23658 TATTGTTTAA
* * *
23668 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATGTCATTTAATTAAATCTATTATCTTTATAAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATGTCATTTAATTAAATCTAATATCCTTATAAT
**
23733 TTTTACCATTTTACTATTTTAATT-AAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TTTTATAATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
* * *
23791 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATGTCATTTAATTAAATCTAATATCCTTATA--
* *
23856 TATTTTATTTTTACCATTTTACTATTTTATTTAAAAAAACTTATATATATTAGAATTTTTTAAAT
64 -A--TT-TTTATA--ATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAAT
23921 AT
123 AT
23923 A
1 A
23924 TTTCTTAAAT
Statistics
Matches: 114, Mismatches: 10, Indels: 9
0.86 0.08 0.07
Matches are distributed among these distances:
123 57 0.50
126 1 0.01
128 2 0.02
129 3 0.03
131 16 0.14
132 35 0.31
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (124 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATGTCATTTAATTAAATCTAATATCCTTATAAT
TTTTATAATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:23945 original size:14 final size:13
Alignment explanation
Indices: 23909--23947 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
23899 TATATATTAG
23909 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
23922 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
23936 AATTTTTTAAAT
1 AATTTTTTAAAT
23948 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:29070 original size:16 final size:17
Alignment explanation
Indices: 29051--29085 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29041 AAAAATCTAC
29051 AACCCG-AAAAAACTCG
1 AACCCGAAAAAAACTCG
*
29067 AACCTGAAAAAAACTCG
1 AACCCGAAAAAAACTCG
29084 AA
1 AA
29086 TTCAATACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.54, C:0.26, G:0.11, T:0.09
Consensus pattern (17 bp):
AACCCGAAAAAAACTCG
Found at i:29381 original size:32 final size:32
Alignment explanation
Indices: 29304--29393 Score: 117
Period size: 32 Copynumber: 2.8 Consensus size: 32
29294 GAACTTGAAG
* * * *
29304 CCGAATTAACATGACCCAAAATTGACCCGAAC
1 CCGAATCAACCTGACCCAAATTTAACCCGAAC
29336 CCGAATCAACCTGACCCAAATTTAACCCGAAC
1 CCGAATCAACCTGACCCAAATTTAACCCGAAC
* * *
29368 CCGAATCAGCCTGACACAATTTTAAC
1 CCGAATCAACCTGACCCAAATTTAAC
29394 TCGACCTTAC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.38, C:0.33, G:0.11, T:0.18
Consensus pattern (32 bp):
CCGAATCAACCTGACCCAAATTTAACCCGAAC
Found at i:30521 original size:20 final size:20
Alignment explanation
Indices: 30496--30533 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30486 ATAATATAAA
30496 TTACTAAATACCGCCCCCTT
1 TTACTAAATACCGCCCCCTT
**
30516 TTACTAGTTACCGCCCCC
1 TTACTAAATACCGCCCCC
30534 CTTTGGACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.42, G:0.08, T:0.29
Consensus pattern (20 bp):
TTACTAAATACCGCCCCCTT
Found at i:30543 original size:22 final size:20
Alignment explanation
Indices: 30504--30543 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
30494 AATTACTAAA
*
30504 TACCGCCCCCTTTTACTAGT
1 TACCGCCCCCTTTGACTAGT
30524 TACCGCCCCCCTTTGGACTA
1 TACCG-CCCCCTTT-GACTA
30544 TTTTGCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.42, G:0.12, T:0.30
Consensus pattern (20 bp):
TACCGCCCCCTTTGACTAGT
Done.