Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020643.1 Corchorus olitorius cultivar O-4 contig20676, 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: 15203
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:2170 original size:29 final size:28
Alignment explanation
Indices: 2138--2213 Score: 134
Period size: 29 Copynumber: 2.7 Consensus size: 28
2128 TTAATTAAAT
2138 AAAAATAGAGTTCTTAGTTTTTTTTTCC
1 AAAAATAGAGTTCTTAGTTTTTTTTTCC
2166 AAAAATAGAGTTCTTAGTTTTTTTTTTCC
1 AAAAATAGAGTTCTTAG-TTTTTTTTTCC
*
2195 AAAAATAGAGTTTTTAGTT
1 AAAAATAGAGTTCTTAGTT
2214 GAGTAAAACT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 19 0.41
29 27 0.59
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.49
Consensus pattern (28 bp):
AAAAATAGAGTTCTTAGTTTTTTTTTCC
Found at i:3139 original size:16 final size:16
Alignment explanation
Indices: 3118--3151 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3108 TCAATCACAT
3118 GGTTGCCACCATCTGA
1 GGTTGCCACCATCTGA
3134 GGTTGCCACCATCTGA
1 GGTTGCCACCATCTGA
3150 GG
1 GG
3152 GTCAAGTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.29, G:0.29, T:0.24
Consensus pattern (16 bp):
GGTTGCCACCATCTGA
Found at i:3188 original size:22 final size:22
Alignment explanation
Indices: 3157--3198 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3147 TGAGGGTCAA
**
3157 GTGCTAGACTTGTAATTCCACT
1 GTGCTAGACTCATAATTCCACT
*
3179 GTGCTGGACTCATAATTCCA
1 GTGCTAGACTCATAATTCCA
3199 TTATCTACAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (22 bp):
GTGCTAGACTCATAATTCCACT
Found at i:3288 original size:22 final size:22
Alignment explanation
Indices: 3260--3303 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3250 GGGAGCTGGA
3260 CTTATAATTCCATTGACTGATG
1 CTTATAATTCCATTGACTGATG
3282 CTTATAATTCCATTGACTGATG
1 CTTATAATTCCATTGACTGATG
3304 GTTAAGTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (22 bp):
CTTATAATTCCATTGACTGATG
Found at i:11951 original size:30 final size:30
Alignment explanation
Indices: 11911--12008 Score: 89
Period size: 30 Copynumber: 3.4 Consensus size: 30
11901 TTAATGTCAA
11911 TTCCCTTTTGGGGACTAACTACGATTCGCT
1 TTCCCTTTTGGGGACTAACTACGATTCGCT
* *** **
11941 TT-CCTTTTTGGG-CTCGTTA--ATGTC-AA
1 TTCCCTTTTGGGGACTAACTACGAT-TCGCT
11967 TTCCCTTTTGGGGACTAACTACGATTCGCT
1 TTCCCTTTTGGGGACTAACTACGATTCGCT
*
11997 TTCCTTTTTGGG
1 TTCCCTTTTGGG
12009 CTCGTTACTA
Statistics
Matches: 49, Mismatches: 13, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
26 4 0.08
27 11 0.22
28 8 0.16
29 11 0.22
30 15 0.31
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.42
Consensus pattern (30 bp):
TTCCCTTTTGGGGACTAACTACGATTCGCT
Found at i:11977 original size:56 final size:56
Alignment explanation
Indices: 11901--12015 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
11891 AAATTTGGCC
11901 TTAATGTCAATTCCCTTTTGGGGACTAACTACGATTCGCTTTCCTTTTTGGGCTCG
1 TTAATGTCAATTCCCTTTTGGGGACTAACTACGATTCGCTTTCCTTTTTGGGCTCG
11957 TTAATGTCAATTCCCTTTTGGGGACTAACTACGATTCGCTTTCCTTTTTGGGCTCG
1 TTAATGTCAATTCCCTTTTGGGGACTAACTACGATTCGCTTTCCTTTTTGGGCTCG
12013 TTA
1 TTA
12016 CTACCCTTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.42
Consensus pattern (56 bp):
TTAATGTCAATTCCCTTTTGGGGACTAACTACGATTCGCTTTCCTTTTTGGGCTCG
Found at i:13195 original size:2 final size:2
Alignment explanation
Indices: 13190--13383 Score: 388
Period size: 2 Copynumber: 97.0 Consensus size: 2
13180 ATATATATAC
13190 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
13232 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
13274 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
13316 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
13358 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
13384 ACATGTACTA
Statistics
Matches: 192, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 192 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Done.