Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020986.1 Corchorus olitorius cultivar O-4 contig21019, 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: 15666
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Found at i:11914 original size:2 final size:2
Alignment explanation
Indices: 11907--11944 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11897 CGCTGGCACC
11907 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11945 GTTAAATTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12691 original size:50 final size:50
Alignment explanation
Indices: 12616--12836 Score: 356
Period size: 50 Copynumber: 4.4 Consensus size: 50
12606 TATCAGGAGC
* *
12616 GAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGATCCTTTTAAGATT
1 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT
* *
12666 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGATGGTCCTCTT-AGAATT
1 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAG-ATT
*
12716 GAATTGGAAGACAGTTCAAAGGATAAGTGGAAGACGGTCCTTTTAAGATT
1 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT
*
12766 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAACATT
1 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT
12816 -AGATTGGAAGACAGTTCAAAG
1 GA-ATTGGAAGACAGTTCAAAG
12837 AAGTTGATCG
Statistics
Matches: 159, Mismatches: 9, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
49 3 0.02
50 154 0.97
51 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.28, T:0.24
Consensus pattern (50 bp):
GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT
Found at i:12750 original size:23 final size:23
Alignment explanation
Indices: 12670--12800 Score: 66
Period size: 23 Copynumber: 5.3 Consensus size: 23
12660 AAGATTGAAT
12670 TGGAAGACAGTTCAAAGGATAAG
1 TGGAAGACAGTTCAAAGGATAAG
* ** ** * *
12693 CGGAAGATGGTCCTCTTAGAATTGAAT
1 TGGAAGACAGT--TCAAAGGA-T-AAG
12720 TGGAAGACAGTTCAAAGGATAAG
1 TGGAAGACAGTTCAAAGGATAAG
* ** *
12743 TGGAAGACGGTCCTTTTAA-GATTGAAT
1 TGGAAGACAG---TTCAAAGGA-T-AAG
12770 TGGAAGACAGTTCAAAGGATAAG
1 TGGAAGACAGTTCAAAGGATAAG
*
12793 CGGAAGAC
1 TGGAAGAC
12801 GGTCCTTTTA
Statistics
Matches: 75, Mismatches: 23, Indels: 20
0.64 0.19 0.17
Matches are distributed among these distances:
23 28 0.37
24 6 0.08
25 14 0.19
26 6 0.08
27 21 0.28
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.22
Consensus pattern (23 bp):
TGGAAGACAGTTCAAAGGATAAG
Found at i:13100 original size:28 final size:28
Alignment explanation
Indices: 13057--13211 Score: 247
Period size: 28 Copynumber: 5.5 Consensus size: 28
13047 CTTTACTTCC
*
13057 CATTTTGGTCACTTTTCATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
*
13085 CGTTTTGGTCATTTTTCATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
* *
13113 CATTTTGGTCATTTTTCATATCCAGTGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
*
13141 CATTTTGGTCATTTTTTTATGTCCAGGGG
1 CATTTTGGTCA-TTTTTCATGTCCAGGGG
*
13170 CATTTTGGTCACTTTTCATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
13198 CATTTTGGTCATTT
1 CATTTTGGTCATTT
13212 CAAGTGTACT
Statistics
Matches: 115, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
28 90 0.78
29 25 0.22
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (28 bp):
CATTTTGGTCATTTTTCATGTCCAGGGG
Found at i:13179 original size:57 final size:57
Alignment explanation
Indices: 13057--13211 Score: 258
Period size: 57 Copynumber: 2.7 Consensus size: 57
13047 CTTTACTTCC
*
13057 CATTTTGGTCACTTTTCATGTCCAGGGGCGTTTTGGTCA-TTTTTCATGTCCAGGGG
1 CATTTTGGTCACTTTTCATGTCCAGGGGCATTTTGGTCATTTTTTCATGTCCAGGGG
* * * *
13113 CATTTTGGTCATTTTTCATATCCAGTGGCATTTTGGTCATTTTTTTATGTCCAGGGG
1 CATTTTGGTCACTTTTCATGTCCAGGGGCATTTTGGTCATTTTTTCATGTCCAGGGG
13170 CATTTTGGTCACTTTTCATGTCCAGGGGCATTTTGGTCATTT
1 CATTTTGGTCACTTTTCATGTCCAGGGGCATTTTGGTCATTT
13212 CAAGTGTACT
Statistics
Matches: 90, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
56 35 0.39
57 55 0.61
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (57 bp):
CATTTTGGTCACTTTTCATGTCCAGGGGCATTTTGGTCATTTTTTCATGTCCAGGGG
Found at i:13199 original size:85 final size:84
Alignment explanation
Indices: 13057--13211 Score: 265
Period size: 85 Copynumber: 1.8 Consensus size: 84
13047 CTTTACTTCC
* *
13057 CATTTTGGTCACTTTTCATGTCCAGGGGCGTTTTGGTCATTTTTCATGTCCAGGGGCATTTTGGT
1 CATTTTGGTCACTTTTCATGTCCAGGGGCATTTTGGTCACTTTTCATGTCCAGGGGCATTTTGGT
13122 CATTTTTCATATCCAGTGG
66 CATTTTTCATATCCAGTGG
* *
13141 CATTTTGGTCATTTTTTTATGTCCAGGGGCATTTTGGTCACTTTTCATGTCCAGGGGCATTTTGG
1 CATTTTGGTCA-CTTTTCATGTCCAGGGGCATTTTGGTCACTTTTCATGTCCAGGGGCATTTTGG
13206 TCATTT
65 TCATTT
13212 CAAGTGTACT
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
84 11 0.17
85 55 0.83
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (84 bp):
CATTTTGGTCACTTTTCATGTCCAGGGGCATTTTGGTCACTTTTCATGTCCAGGGGCATTTTGGT
CATTTTTCATATCCAGTGG
Found at i:13686 original size:21 final size:21
Alignment explanation
Indices: 13648--13687 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13638 TTGATTGCAC
* *
13648 CAAAAAAGAAATACAAAAATT
1 CAAAAAAGAAAGAAAAAAATT
*
13669 CAAAAAAGGAAGAAAAAAA
1 CAAAAAAGAAAGAAAAAAA
13688 AGAGGGTTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.75, C:0.07, G:0.10, T:0.07
Consensus pattern (21 bp):
CAAAAAAGAAAGAAAAAAATT
Found at i:15309 original size:18 final size:19
Alignment explanation
Indices: 15274--15309 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
15264 TCACCAAAAG
*
15274 AAAACAGAAAATCTTTCTC
1 AAAAAAGAAAATCTTTCTC
15293 AAAAAAGAAAA-CTTTCT
1 AAAAAAGAAAATCTTTCT
15310 GATTTACCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.53, C:0.17, G:0.06, T:0.25
Consensus pattern (19 bp):
AAAAAAGAAAATCTTTCTC
Done.