Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016206.1 Corchorus capsularis cultivar CVL-1 contig16227, 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: 28853
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:4881 original size:24 final size:24
Alignment explanation
Indices: 4854--4900 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
4844 ATTCAACTAA
4854 CTGGGGGAGGGGGGATGGGAGAGG
1 CTGGGGGAGGGGGGATGGGAGAGG
4878 CTGGGGGAGGGGGGATGGGAGAG
1 CTGGGGGAGGGGGGATGGGAGAG
4901 CAAGGGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.04, G:0.70, T:0.09
Consensus pattern (24 bp):
CTGGGGGAGGGGGGATGGGAGAGG
Found at i:16978 original size:85 final size:86
Alignment explanation
Indices: 16877--17105 Score: 338
Period size: 85 Copynumber: 2.7 Consensus size: 86
16867 AAATTGTTAA
16877 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGACGATATTTTAAG-A
1 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGA-GATATTTTAAGAA
16941 AATAAATAAATAATAAA-AT-T
65 AATAAATAAATAATAAAGATAT
* * * * * *
16961 GAATAGTAATCAGAATATTTTCTAAATCTTGCCAAATTGTAGAAGGTTTAGGAGATATTTTAGGA
1 -AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTA-GAGATATTTTAAGA
*
17026 AAATAAATAAATTATAAAGATAT
64 AAATAAATAAATAATAAAGATAT
17049 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATAT
1 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAG-AGATAT
17106 AAAAAAGGAA
Statistics
Matches: 127, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
85 54 0.43
86 20 0.16
87 52 0.41
88 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.34
Consensus pattern (86 bp):
AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAGATATTTTAAGAAA
ATAAATAAATAATAAAGATAT
Found at i:19139 original size:13 final size:13
Alignment explanation
Indices: 19121--19146 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19111 GTATATGGGA
19121 GAGGTGAGTCTAC
1 GAGGTGAGTCTAC
19134 GAGGTGAGTCTAC
1 GAGGTGAGTCTAC
19147 CAATATGGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.38, T:0.23
Consensus pattern (13 bp):
GAGGTGAGTCTAC
Found at i:21993 original size:34 final size:34
Alignment explanation
Indices: 21954--22022 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
21944 TTAATTTGTT
21954 TTGGTTGATATCTTTCTGAAATTTGAATTTAATA
1 TTGGTTGATATCTTTCTGAAATTTGAATTTAATA
21988 TTGGTTGATATCTTTCTGAAATTTGAATTTAATA
1 TTGGTTGATATCTTTCTGAAATTTGAATTTAATA
22022 T
1 T
22023 GGAAACTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (34 bp):
TTGGTTGATATCTTTCTGAAATTTGAATTTAATA
Found at i:27221 original size:44 final size:44
Alignment explanation
Indices: 27158--27265 Score: 207
Period size: 44 Copynumber: 2.5 Consensus size: 44
27148 AATAAAAGCT
27158 GGAGATGTTGGTTTTGCTTGAAGGTATTGGATTATTTAGATCTA
1 GGAGATGTTGGTTTTGCTTGAAGGTATTGGATTATTTAGATCTA
*
27202 GGAGATGTTGGGTTTGCTTGAAGGTATTGGATTATTTAGATCTA
1 GGAGATGTTGGTTTTGCTTGAAGGTATTGGATTATTTAGATCTA
27246 GGAGATGTTGGTTTTGCTTG
1 GGAGATGTTGGTTTTGCTTG
27266 GAAAAAATAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 62 1.00
ACGTcount: A:0.20, C:0.05, G:0.32, T:0.43
Consensus pattern (44 bp):
GGAGATGTTGGTTTTGCTTGAAGGTATTGGATTATTTAGATCTA
Found at i:27743 original size:10 final size:10
Alignment explanation
Indices: 27728--27755 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
27718 AACCGTTAGC
27728 CACGTGACGG
1 CACGTGACGG
27738 CACGTGACGG
1 CACGTGACGG
27748 CACGTGAC
1 CACGTGAC
27756 TAACATCCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.32, G:0.36, T:0.11
Consensus pattern (10 bp):
CACGTGACGG
Found at i:28634 original size:33 final size:33
Alignment explanation
Indices: 28589--28683 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 33
28579 AATTGCTCAT
* *
28589 GCCGCCCTAGGGGGGCGGCTGAGCCATGGTAGG
1 GCCGCCCCAGGGGGGCGGCTGAGCCATGGTAAG
* *
28622 GCCGCCCCAGGGGAGCGGCCTG-GCCATGGTAAT
1 GCCGCCCCAGGGGGGCGG-CTGAGCCATGGTAAG
* *
28655 GCCGCACCAGGGGGACGGCTGAGCCATGG
1 GCCGCCCCAGGGGGGCGGCTGAGCCATGG
28684 CCAAGCCGCC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 3 0.06
33 47 0.89
34 3 0.06
ACGTcount: A:0.15, C:0.31, G:0.44, T:0.11
Consensus pattern (33 bp):
GCCGCCCCAGGGGGGCGGCTGAGCCATGGTAAG
Found at i:28692 original size:33 final size:31
Alignment explanation
Indices: 28589--28694 Score: 99
Period size: 33 Copynumber: 3.2 Consensus size: 31
28579 AATTGCTCAT
* *
28589 GCCGCCCTAGGGGGGCGGCTGAGCCATGGTAGG
1 GCCGCCC-AGGGGGACGGCTGAGCCATGGTA-A
28622 GCCGCCCCA-GGGGAGCGGCCTG-GCCATGGTAA
1 GCCG-CCCAGGGGGA-CGG-CTGAGCCATGGTAA
*
28654 TGCCGCACCAGGGGGACGGCTGAGCCATGGCCAA
1 -GCCGC-CCAGGGGGACGGCTGAGCCATGG-TAA
28688 GCCGCCC
1 GCCGCCC
28695 TCCTGGGGCG
Statistics
Matches: 62, Mismatches: 3, Indels: 17
0.76 0.04 0.21
Matches are distributed among these distances:
32 10 0.16
33 39 0.63
34 13 0.21
ACGTcount: A:0.15, C:0.34, G:0.42, T:0.09
Consensus pattern (31 bp):
GCCGCCCAGGGGGACGGCTGAGCCATGGTAA
Found at i:28715 original size:33 final size:33
Alignment explanation
Indices: 28678--28773 Score: 101
Period size: 33 Copynumber: 2.9 Consensus size: 33
28668 GACGGCTGAG
28678 CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA
1 CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA
* * *
28711 CCATGGCCAGGCCG-CCTCCCTGGGGCGGCTCTG
1 CCATGGCCAAGCCGCCCT-CCTGGGGCGGCACTA
*
28744 CCATGG--ATAGACCGCCC-CCTGGGACGGCAC
1 CCATGGCCA-AG-CCGCCCTCCTGGGGCGGCAC
28774 CGGTACTAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
31 1 0.02
32 15 0.28
33 35 0.66
34 2 0.04
ACGTcount: A:0.14, C:0.42, G:0.32, T:0.12
Consensus pattern (33 bp):
CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA
Done.