Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016018.1 Corchorus capsularis cultivar CVL-1 contig16039, 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: 49392
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:170 original size:72 final size:68
Alignment explanation
Indices: 84--238 Score: 186
Period size: 72 Copynumber: 2.2 Consensus size: 68
74 TTGTTTAGGT
* * * *
84 TTTTA-TAGTTTTACTTAACTAAAAACTTTATTTTTATTTTTAATTAAATATAATATCTTTATAA
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTA--TATAATTAAATATAATATCCTTATAA
*
148 CTATTTTA
63 C--TTATA
* *
156 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATTACTT
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTT
221 ATA
66 ATA
*
224 TTTTACCATTTTACT
1 TTTTACTATTTTACT
239 ATTTTAATTA
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
68 18 0.24
70 23 0.31
72 31 0.42
73 2 0.03
ACGTcount: A:0.35, C:0.12, G:0.01, T:0.53
Consensus pattern (68 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTT
ATA
Found at i:2760 original size:135 final size:135
Alignment explanation
Indices: 2492--2756 Score: 369
Period size: 135 Copynumber: 2.0 Consensus size: 135
2482 AATATCTAAC
* * * *
2492 CCTAACAGAGATAGTATTTTCACGTTGGTCGATATAACCTATTTTGATGTTGCTAGATTACGATG
1 CCTAACAAAGATAGTATTTTCACGTCGGTCAATATAACCTATTTTGATGTTGCTAGATTACAATG
* *
2557 TAAATTTTGTTGTTGTACTATAATACTATCAAATTAAATTAGGTTTATTTTTTCACTTCTGACAT
66 TAAATTTTGTTGTTGTACTATAATACTATC-AATCAAATTAGGTTCATTTTTTCACTTCTGACAT
2622 TTATAT
130 TTATAT
* * *
2628 CCTAACAAATATAGTA-TTTCACGTCGGTTAATATAATCTATTTTGATGTTGCTAGATTACAATG
1 CCTAACAAAGATAGTATTTTCACGTCGGTCAATATAACCTATTTTGATGTTGCTAGATTACAATG
* * *
2692 TCAATTTTGTTGTTTGTACTAT-A-A-TATC-ATCAAATTGGGTTCATTTTTTCACTTCTGATAT
66 TAAATTTTGTTG-TTGTACTATAATACTATCAATCAAATTAGGTTCATTTTTTCACTTCTGACAT
2753 TTAT
130 TTAT
2757 TTATTGTCTT
Statistics
Matches: 116, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
131 33 0.28
133 4 0.03
134 1 0.01
135 55 0.47
136 23 0.20
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (135 bp):
CCTAACAAAGATAGTATTTTCACGTCGGTCAATATAACCTATTTTGATGTTGCTAGATTACAATG
TAAATTTTGTTGTTGTACTATAATACTATCAATCAAATTAGGTTCATTTTTTCACTTCTGACATT
TATAT
Found at i:4142 original size:20 final size:20
Alignment explanation
Indices: 4107--4156 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
4097 GTGGGGTAAA
* *
4107 ATTAACGGTGTTAAGTGATTT
1 ATTAACGG-ATTAAGTAATTT
*
4128 GTTAACGGATTAAGTAATTT
1 ATTAACGGATTAAGTAATTT
4148 ATTAACGGA
1 ATTAACGGA
4157 AAATAAACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTAACGGATTAAGTAATTT
Found at i:7958 original size:21 final size:21
Alignment explanation
Indices: 7933--7973 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
7923 TAACTTTTAA
* *
7933 AAAAATTAAATTAAATAAAAC
1 AAAAATAAAATAAAATAAAAC
7954 AAAAATAAAATAAAATAAAA
1 AAAAATAAAATAAAATAAAA
7974 TAACCCACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAAATAAAATAAAATAAAAC
Found at i:7959 original size:16 final size:16
Alignment explanation
Indices: 7940--7973 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
7930 TAAAAAAATT
*
7940 AAATTAAATAAAACAA
1 AAATAAAATAAAACAA
*
7956 AAATAAAATAAAATAA
1 AAATAAAATAAAACAA
7972 AA
1 AA
7974 TAACCCACCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (16 bp):
AAATAAAATAAAACAA
Found at i:7963 original size:5 final size:5
Alignment explanation
Indices: 7934--7976 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
7924 AACTTTTAAA
* * *
7934 AAAAT TAAAT TAAAT AAAACA AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AA
7977 CCCACCCTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 29 0.88
6 4 0.12
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:11567 original size:11 final size:11
Alignment explanation
Indices: 11551--11575 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11541 CACGTAATTG
11551 CTTAATCATCC
1 CTTAATCATCC
11562 CTTAATCATCC
1 CTTAATCATCC
11573 CTT
1 CTT
11576 TGTGAATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.36, G:0.00, T:0.40
Consensus pattern (11 bp):
CTTAATCATCC
Found at i:17601 original size:29 final size:29
Alignment explanation
Indices: 17567--17625 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
17557 CACCAAGAAA
17567 CAGCCATAGTCATACTAGGCTAAGAGCAC
1 CAGCCATAGTCATACTAGGCTAAGAGCAC
17596 CAGCCATAGTCATACTAGGCTAAGAGCAC
1 CAGCCATAGTCATACTAGGCTAAGAGCAC
17625 C
1 C
17626 GCAAACTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.29, G:0.20, T:0.17
Consensus pattern (29 bp):
CAGCCATAGTCATACTAGGCTAAGAGCAC
Found at i:24686 original size:3 final size:3
Alignment explanation
Indices: 24678--24716 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
24668 CTATTTAAAA
24678 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
24717 TTAGCAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:27468 original size:5 final size:5
Alignment explanation
Indices: 27458--27488 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
27448 ATGATGTAAT
27458 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA T
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA T
27489 AGGAATCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TTAAA
Found at i:39355 original size:23 final size:22
Alignment explanation
Indices: 39310--39377 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
39300 AGCAACCGAA
39310 TTGCTAAAT-ACCGCCCCCCTTT
1 TTGCT-AATCACCGCCCCCCTTT
*
39332 TTGCTATTCACCGCCCCCCTTT
1 TTGCTAATCACCGCCCCCCTTT
* *
39354 TTGCTAATCACCGTCCCACTTT
1 TTGCTAATCACCGCCCCCCTTT
39376 TT
1 TT
39378 ACACTTTTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 2 0.05
22 39 0.95
ACGTcount: A:0.15, C:0.40, G:0.09, T:0.37
Consensus pattern (22 bp):
TTGCTAATCACCGCCCCCCTTT
Done.