Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011118.1 Corchorus capsularis cultivar CVL-1 contig11139, 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: 8768
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1066 original size:31 final size:30
Alignment explanation
Indices: 1028--1131 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 30
1018 AACGGCTAAT
1028 TGCTCAAATAAGGGCATACTGTCTGCCAAAA
1 TGCTCAAATAAGGGCATA-TGTCTGCCAAAA
*** **
1059 TGCTCAAATAAGGG--TATGATCTTTTAATT
1 TGCTCAAATAAGGGCATATG-TCTGCCAAAA
*
1088 TGGC-CAAATAAGGGCATAATGTTTGCCAAAA
1 T-GCTCAAATAAGGGCAT-ATGTCTGCCAAAA
1119 TGCTCAAATAAGG
1 TGCTCAAATAAGG
1132 ACCCATCTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 2 0.04
29 18 0.32
30 4 0.07
31 29 0.52
32 3 0.05
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (30 bp):
TGCTCAAATAAGGGCATATGTCTGCCAAAA
Found at i:1125 original size:60 final size:61
Alignment explanation
Indices: 1032--1192 Score: 238
Period size: 59 Copynumber: 2.7 Consensus size: 61
1022 GCTAATTGCT
* * ** *
1032 CAAATAAGGGCATACTGTCTGCCAAAATGCTCAAATAAGGGTA-TGATCTTTTAATTTGGC
1 CAAATAAGGGCATAATGTTTGCCAAAATGCTCAAATAAGGGTACCCATCTTTGAATTTGGC
1092 CAAATAAGGGCATAATGTTTGCCAAAATGCTCAAATAA-GG-ACCCATCTTTGAATTTGGC
1 CAAATAAGGGCATAATGTTTGCCAAAATGCTCAAATAAGGGTACCCATCTTTGAATTTGGC
* *
1151 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGT
1 CAAATAAGGGCATAATGTTTGCCAAAATGCTCAAATAAGGGT
1193 TTGTCTCATG
Statistics
Matches: 91, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
58 1 0.01
59 52 0.57
60 38 0.42
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (61 bp):
CAAATAAGGGCATAATGTTTGCCAAAATGCTCAAATAAGGGTACCCATCTTTGAATTTGGC
Found at i:1187 original size:31 final size:31
Alignment explanation
Indices: 1092--1191 Score: 100
Period size: 31 Copynumber: 3.3 Consensus size: 31
1082 TTAATTTGGC
* *
1092 CAAATAAGGGCATAATGTTTGCCAAAATGCT
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCT
* * * **
1123 CAAATAAGGACCCATC-TTTG--AATTTGGC-
1 CAAATAAGGGCCTAACGTTTGCCAAAAT-GCT
1151 CAAATAAGGGCCTAACGTTTGCCAAAATGCT
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCT
1182 CAAATAAGGG
1 CAAATAAGGG
1192 TTTGTCTCAT
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
28 16 0.31
29 6 0.12
30 6 0.12
31 24 0.46
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCT
Found at i:1265 original size:31 final size:31
Alignment explanation
Indices: 1222--1417 Score: 129
Period size: 31 Copynumber: 6.5 Consensus size: 31
1212 AACTGACACC
* *
1222 AGACCCTTATTTGAGTATTTTTGATAACGTT
1 AGACCCTTATTTGAGCATTTTCGATAACGTT
*
1253 AGACTCTTATTTGAGCATTTTCGATAACGTT
1 AGACCCTTATTTGAGCATTTTCGATAACGTT
** * *
1284 AGACCCTTATTTG-GCCAAATT--A-AAAGATC
1 AGACCCTTATTTGAG-CATTTTCGATAACG-TT
* *
1313 GGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGACCCTTATTTGAGCATTTTCGATAACGTT
* * ** * ** *
1344 AGGCTCTTATTTG-GCCAAATT--AAAAAATC
1 AGACCCTTATTTGAG-CATTTTCGATAACGTT
*
1373 AGACCCTTATTTGAGCATTTTGGCA-AACGTT
1 AGACCCTTATTTGAGCATTTTCG-ATAACGTT
*
1404 AGGCCCTTATTTGA
1 AGACCCTTATTTGA
1418 ACAATTAGCC
Statistics
Matches: 124, Mismatches: 30, Indels: 22
0.70 0.17 0.12
Matches are distributed among these distances:
28 3 0.02
29 36 0.29
30 4 0.03
31 77 0.62
32 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (31 bp):
AGACCCTTATTTGAGCATTTTCGATAACGTT
Found at i:1330 original size:60 final size:60
Alignment explanation
Indices: 1253--1416 Score: 249
Period size: 60 Copynumber: 2.7 Consensus size: 60
1243 TGATAACGTT
* * *
1253 AGACTCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATC
1 AGACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATC
* * *
1313 GGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCTCTTATTTGGCCAAATTAAAAAATC
1 AGACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATC
*
1373 AGACCCTTATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTTG
1 AGACCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
1417 AACAATTAGC
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
60 92 0.99
61 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (60 bp):
AGACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATC
Found at i:6467 original size:10 final size:10
Alignment explanation
Indices: 6454--6489 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
6444 AAATCTCGGT
6454 ATATCCGTAA
1 ATATCCGTAA
6464 ATATCCGTAA
1 ATATCCGTAA
**
6474 ATATTTGTAA
1 ATATCCGTAA
6484 ATATCC
1 ATATCC
6490 ATATTAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:7783 original size:13 final size:12
Alignment explanation
Indices: 7765--7795 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
7755 CATCGATACC
7765 TCGATATATCCG
1 TCGATATATCCG
7777 TTCGATATATCCG
1 -TCGATATATCCG
7790 TCGATA
1 TCGATA
7796 CCTGTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Done.