Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014054.1 Corchorus olitorius cultivar O-4 contig14087, 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: 45521
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1383 original size:30 final size:31
Alignment explanation
Indices: 1316--1387 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
1306 GTTTATTGTT
* *
1316 CAAAAAAGCCCCTGAACTTACACAAAACGGT
1 CAAATAAGCCCCTGAACTTACACAAAACGGC
* *
1347 CAAATAAGCCCCTGAACTCT-TA-AAAATGGC
1 CAAATAAGCCCCTGAACT-TACACAAAACGGC
1377 CAAATAAGCCC
1 CAAATAAGCCC
1388 TTTTTGTGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 17 0.47
31 18 0.50
32 1 0.03
ACGTcount: A:0.43, C:0.29, G:0.12, T:0.15
Consensus pattern (31 bp):
CAAATAAGCCCCTGAACTTACACAAAACGGC
Found at i:2090 original size:11 final size:11
Alignment explanation
Indices: 2076--2109 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2066 CCCTTCATGT
2076 AAGACAAAAAA
1 AAGACAAAAAA
2087 AAGA-AAAGAAA
1 AAGACAAA-AAA
2098 AAGACAAAAAA
1 AAGACAAAAAA
2109 A
1 A
2110 TAAGGTTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 3 0.14
11 15 0.71
12 3 0.14
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (11 bp):
AAGACAAAAAA
Found at i:8731 original size:101 final size:97
Alignment explanation
Indices: 8539--8732 Score: 316
Period size: 101 Copynumber: 2.0 Consensus size: 97
8529 AAGATGATGA
*
8539 TGTCCCATTTTTTCCTTCCATTGACTTGACTAATTACATTGCATACAATTAAACCATTTCTAATA
1 TGTCCCATTTTTTCCTTCCATTGACTTGACTAATTACATTGCATACAATTAAACCATTTCCAATA
*
8604 AAACTGCCGAGACTACAACAACCATTTTTCAT
66 AAACTGCAGAGACTACAACAACCATTTTTCAT
*
8636 TGTCCCATTTTTTCCTTCCATTTGACTTGATTAATTACATTGCATACAATTAAACAACCATTTCC
1 TGTCCCATTTTTTCCTTCCA-TTGACTTGACTAATTACATTGCATACAATT--A-AACCATTTCC
*
8701 AATAAAACTGCAGAGACTACAATAACCATTTT
62 AATAAAACTGCAGAGACTACAACAACCATTTT
8733 CCAATGAAAC
Statistics
Matches: 89, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
97 20 0.22
98 29 0.33
100 1 0.01
101 39 0.44
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (97 bp):
TGTCCCATTTTTTCCTTCCATTGACTTGACTAATTACATTGCATACAATTAAACCATTTCCAATA
AAACTGCAGAGACTACAACAACCATTTTTCAT
Found at i:10345 original size:25 final size:25
Alignment explanation
Indices: 10311--10361 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
10301 CTCACTCTAA
*
10311 TTTACTTTAGTTGTTTGGATCTTTG
1 TTTACTTTAGTTGCTTGGATCTTTG
*
10336 TTTACTTTAGTTGCTTGGGTCTTTG
1 TTTACTTTAGTTGCTTGGATCTTTG
10361 T
1 T
10362 ATTTGCACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.10, C:0.10, G:0.22, T:0.59
Consensus pattern (25 bp):
TTTACTTTAGTTGCTTGGATCTTTG
Found at i:10828 original size:19 final size:20
Alignment explanation
Indices: 10790--10829 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
10780 CACTTGCTTC
*
10790 TATTGCAGTTTGTATCTTTA
1 TATTGCAGTTAGTATCTTTA
*
10810 TATTGCA-TTAGTGTCTTTA
1 TATTGCAGTTAGTATCTTTA
10829 T
1 T
10830 CTGCATATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.55
Consensus pattern (20 bp):
TATTGCAGTTAGTATCTTTA
Found at i:15611 original size:31 final size:30
Alignment explanation
Indices: 15549--15611 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
15539 CCTTTTCGGG
*
15549 TTTTTTTGGTGTTTTTTTTTTGTATCTTTT
1 TTTTTTTGGTGTTTTTTTTTTCTATCTTTT
*
15579 TTTTCTTTGG-GTATTTTTTTTTCTA-CTGTT
1 TTTT-TTTGGTGT-TTTTTTTTTCTATCTTTT
15609 TTT
1 TTT
15612 CGATGGACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.05, C:0.06, G:0.13, T:0.76
Consensus pattern (30 bp):
TTTTTTTGGTGTTTTTTTTTTCTATCTTTT
Found at i:26431 original size:16 final size:16
Alignment explanation
Indices: 26406--26477 Score: 67
Period size: 16 Copynumber: 4.5 Consensus size: 16
26396 CCTGAATACG
26406 AACCC-AAAAAAGCTCA
1 AACCCGAAAAAA-CTCA
26422 AACCCGAAAAAAC-CA
1 AACCCGAAAAAACTCA
* * *
26437 GAATCCGAAAAATCTGA
1 -AACCCGAAAAAACTCA
* *
26454 AATCCGAAAAAACCCA
1 AACCCGAAAAAACTCA
26470 AACCCGAA
1 AACCCGAA
26478 CATGAAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
15 2 0.04
16 37 0.80
17 7 0.15
ACGTcount: A:0.54, C:0.29, G:0.10, T:0.07
Consensus pattern (16 bp):
AACCCGAAAAAACTCA
Found at i:26477 original size:32 final size:32
Alignment explanation
Indices: 26405--26477 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
26395 GCCTGAATAC
*
26405 GAACCCAAAAAAGCTCAAACCCGAAAAAACCA
1 GAACCCGAAAAAGCTCAAACCCGAAAAAACCA
* * * *
26437 GAATCCGAAAAATCTGAAATCCGAAAAAACCCA
1 GAACCCGAAAAAGCTCAAACCCGAAAAAA-CCA
26470 -AACCCGAA
1 GAACCCGAA
26478 CATGAAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 31 0.91
33 3 0.09
ACGTcount: A:0.53, C:0.29, G:0.11, T:0.07
Consensus pattern (32 bp):
GAACCCGAAAAAGCTCAAACCCGAAAAAACCA
Done.