Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010936.1 Corchorus olitorius cultivar O-4 contig10968, 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: 4054
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Found at i:694 original size:19 final size:17
Alignment explanation
Indices: 656--689 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
646 AGTGCCACCT
656 ATTGACAGAAATATATA
1 ATTGACAGAAATATATA
673 ATTGACAGAAATATATA
1 ATTGACAGAAATATATA
690 TAATTTCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (17 bp):
ATTGACAGAAATATATA
Found at i:2218 original size:18 final size:18
Alignment explanation
Indices: 2197--2238 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2187 ATGACACTTG
* *
2197 AAAGAAACTCTAGGGAGT
1 AAAGAAACTCAAGAGAGT
*
2215 AAAGAAACTGAAGAGAGT
1 AAAGAAACTCAAGAGAGT
2233 AAAGAA
1 AAAGAA
2239 GAAGACTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.55, C:0.07, G:0.26, T:0.12
Consensus pattern (18 bp):
AAAGAAACTCAAGAGAGT
Found at i:2907 original size:29 final size:31
Alignment explanation
Indices: 2875--2941 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
2865 ATGCAATTTG
*
2875 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAACCAATTAA
*
2904 GGATATAACGTTACGAAAAGCGACCAATTAA
1 GGATATAACGTTACGAAAAGCAACCAATTAA
2935 GGATATA
1 GGATATA
2942 GTCTGTTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
30 4 0.12
31 16 0.47
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAACCAATTAA
Found at i:3023 original size:11 final size:11
Alignment explanation
Indices: 3009--3045 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
2999 CGTGTCATCT
*
3009 ACGTGGATACC
1 ACGTGGATGCC
3020 ACGTGGATGCC
1 ACGTGGATGCC
*
3031 ACGCGGATGCC
1 ACGTGGATGCC
3042 ACGT
1 ACGT
3046 CATCAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.22, C:0.30, G:0.32, T:0.16
Consensus pattern (11 bp):
ACGTGGATGCC
Found at i:3108 original size:31 final size:31
Alignment explanation
Indices: 3073--3151 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
3063 TTAACTGATT
**
3073 ATATCCTTAATTGCTTGAAATCGAAAACGTC
1 ATATCCTTAATTGCTTGAAATAAAAAACGTC
*
3104 ATATCCTTAATTGCTTGAAATAAAAAACGTT
1 ATATCCTTAATTGCTTGAAATAAAAAACGTC
3135 ATATCCTTAATTGCTTG
1 ATATCCTTAATTGCTTG
3152 TTTTGTAACG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (31 bp):
ATATCCTTAATTGCTTGAAATAAAAAACGTC
Found at i:3177 original size:60 final size:62
Alignment explanation
Indices: 3071--3207 Score: 161
Period size: 60 Copynumber: 2.2 Consensus size: 62
3061 CCTTAACTGA
*
3071 TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCTTAATTGCTTGAAATAAAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCTTAATTGCTTGAAACAAAAAACG
** * * * *** *
3133 TTATATCCTTAATTGCTTG-TTTTG-TAACGTTATATCCTTAATTGCTTGTGGCAACAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCTTAATTGCTTGAAACAAAAAACG
*
3193 TTATATCCTAAATTG
1 TTATATCCTTAATTG
3208 ATTATTTGAC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 43 0.67
61 2 0.03
62 19 0.30
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (62 bp):
TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCTTAATTGCTTGAAACAAAAAACG
Found at i:3196 original size:31 final size:29
Alignment explanation
Indices: 3071--3207 Score: 112
Period size: 31 Copynumber: 4.5 Consensus size: 29
3061 CCTTAACTGA
*
3071 TTATATCCTTAATTGCTTGAAATCGAAAACG
1 TTATATCCTTAATTGCTTG-AA-CAAAAACG
* *
3102 TCATATCCTTAATTGCTTGAAATAAAAAACG
1 TTATATCCTTAATTGCTTG-AA-CAAAAACG
******
3133 TTATATCCTTAATTGCTTGTTTTGTAACG
1 TTATATCCTTAATTGCTTGAACAAAAACG
**
3162 TTATATCCTTAATTGCTTGTGGCAACAAACG
1 TTATATCCTTAATTGCTTG-AACAA-AAACG
*
3193 TTATATCCTAAATTG
1 TTATATCCTTAATTG
3208 ATTATTTGAC
Statistics
Matches: 87, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
29 23 0.26
31 64 0.74
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (29 bp):
TTATATCCTTAATTGCTTGAACAAAAACG
Done.