Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015438.1 Corchorus olitorius cultivar O-4 contig15471, 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: 68625
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:280 original size:67 final size:64
Alignment explanation
Indices: 138--258 Score: 158
Period size: 67 Copynumber: 1.9 Consensus size: 64
128 TTTCTATTTA
*
138 AAATTTAGGCACTAATTTAACACCAGGTTTAGCCTCTAATTTCATCTGATGAGATTTATAAGACC
1 AAATTTAGGCACTAATTTAACACCAGGTTTAACCTC--ATTTCATCTGATGAGATTTATAAGACC
203 T
64 T
* *
204 AAATTTTAGGCACTAATTTAGCACCGGGTTTAACC-C-TTTCA-CTAGATGAGATTTA
1 AAA-TTTAGGCACTAATTTAACACCAGGTTTAACCTCATTTCATCT-GATGAGATTTA
259 CAGGTAAGTC
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
62 2 0.04
63 16 0.32
66 4 0.08
67 28 0.56
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (64 bp):
AAATTTAGGCACTAATTTAACACCAGGTTTAACCTCATTTCATCTGATGAGATTTATAAGACCT
Found at i:4675 original size:31 final size:31
Alignment explanation
Indices: 4637--4705 Score: 138
Period size: 31 Copynumber: 2.2 Consensus size: 31
4627 TTACCACTTT
4637 GCACCCTTTTTTTTTTTACTTTGATCTTATC
1 GCACCCTTTTTTTTTTTACTTTGATCTTATC
4668 GCACCCTTTTTTTTTTTACTTTGATCTTATC
1 GCACCCTTTTTTTTTTTACTTTGATCTTATC
4699 GCACCCT
1 GCACCCT
4706 AATGTTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.13, C:0.26, G:0.07, T:0.54
Consensus pattern (31 bp):
GCACCCTTTTTTTTTTTACTTTGATCTTATC
Found at i:17305 original size:23 final size:24
Alignment explanation
Indices: 17275--17320 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
17265 GATTGCTAAT
17275 TATC-AAAATTTTGTTAATGTTTC
1 TATCAAAAATTTTGTTAATGTTTC
17298 TATCAAAAAATTTTGTTAATGTT
1 TATC-AAAAATTTTGTTAATGTT
17321 AGTATAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 4 0.19
25 17 0.81
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.50
Consensus pattern (24 bp):
TATCAAAAATTTTGTTAATGTTTC
Found at i:32779 original size:31 final size:31
Alignment explanation
Indices: 32741--32908 Score: 120
Period size: 31 Copynumber: 5.5 Consensus size: 31
32731 ACTGGCTAAT
32741 TGCTCAAATAAGGGCCTAACGTTTGTTAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGTTAAAA
** * **
32772 TGCTCAAATAAGGATCTGA--TCTT-TTAATT
1 TGCTCAAATAAGGGCCTAACGT-TTGTTAAAA
**
32801 TGAC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 TG-CTCAAATAAGGGCCTAACGTTTGTTAAAA
**
32832 TGCTCAAATAAGGGCC---CGATCTT-TTAATT
1 TGCTCAAATAAGGGCCTAACG-T-TTGTTAAAA
* **
32861 TGGC-CAAATAAGGGCCTAACATTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTTAAAA
32892 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
32909 GGTATCGAAA
Statistics
Matches: 102, Mismatches: 21, Indels: 28
0.68 0.14 0.19
Matches are distributed among these distances:
28 2 0.02
29 35 0.34
30 14 0.14
31 50 0.49
32 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGTTAAAA
Found at i:32905 original size:60 final size:60
Alignment explanation
Indices: 32745--32907 Score: 263
Period size: 60 Copynumber: 2.7 Consensus size: 60
32735 GCTAATTGCT
** ** *
32745 CAAATAAGGGCCTAACGTTTGTTAAAATGCTCAAATAAGGATCTGATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
*
32805 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
*
32865 CAAATAAGGGCCTAACATTTGCCAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
32908 TGGTATCGAA
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 96 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
Found at i:32988 original size:31 final size:31
Alignment explanation
Indices: 32950--33050 Score: 93
Period size: 31 Copynumber: 3.3 Consensus size: 31
32940 TGACGCCAAA
32950 CCCTTATTTGAGCATTTTCGATAACGTTGGG
1 CCCTTATTTGAGCATTTTCGATAACGTTGGG
** * *
32981 CCCTTATTTG-GCCAAATT--A-AAAGATCGGG
1 CCCTTATTTGAG-CATTTTCGATAACG-TTGGG
* *
33010 CCCTTATGTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTGGG
*
33041 CCTTTATTTG
1 CCCTTATTTG
33051 GCCAAATTAA
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
28 3 0.06
29 18 0.35
30 2 0.04
31 26 0.50
32 3 0.06
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTCGATAACGTTGGG
Found at i:33025 original size:60 final size:60
Alignment explanation
Indices: 32949--33110 Score: 227
Period size: 60 Copynumber: 2.7 Consensus size: 60
32939 CTGACGCCAA
* *
32949 ACCCTTATTTGAGCATTTTCGATAACGTTGGGCCCTTATTTGGCCAAATTAAAAGATCGG
1 ACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAG
* * *
33009 GCCCTTATGTGAGCATTTTCGATAACGTTAGGCCTTTATTTGGCCAAATTAAAAGATCAG
1 ACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAG
* * * *
33069 ACTCTTATTTGAGCATTTTGGCA-AACATTATGCCCTTATTTG
1 ACCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
33111 AGCAATTAGC
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 88 0.99
61 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (60 bp):
ACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAG
Found at i:34130 original size:17 final size:15
Alignment explanation
Indices: 34107--34145 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
34097 AATTCATTAA
*
34107 TTTTTTTTGTTCTATT
1 TTTTTTTTCTTC-ATT
34123 TCTTTTTTTCTTCATT
1 T-TTTTTTTCTTCATT
34139 TTTTTTT
1 TTTTTTT
34146 GAAGAGGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 5 0.24
17 10 0.48
ACGTcount: A:0.05, C:0.10, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTTTTTTCTTCATT
Found at i:38295 original size:21 final size:21
Alignment explanation
Indices: 38266--38306 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
38256 TATATATATA
*
38266 TATTTATAGTA-CTTTAACAC
1 TATTTATAGTAGCTTCAACAC
38286 TATTATATAGTAGCTTCAACA
1 TATT-TATAGTAGCTTCAACA
38307 GTGTTAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (21 bp):
TATTTATAGTAGCTTCAACAC
Found at i:38895 original size:81 final size:82
Alignment explanation
Indices: 38724--38914 Score: 280
Period size: 81 Copynumber: 2.3 Consensus size: 82
38714 CAATCTTTAG
*
38724 GTTCAAATAACGTGAATGAAGAAGATAATCATTAAAAGTGTCTTCCAATTTAGAGTTTATCGTAA
1 GTTCAAATAACGTGAATGAAGAAAATAATCATTAAAAGTGTCTTCCAATTTAGAGTTTATCGTAA
38789 CCTGATTCTGATTCTAA
66 CCTGATTCTGATTCTAA
* **
38806 GTTTAAATAACGTGAATGAAGAAAATAATCATTAAAAGTGAT-TT-CGGTTTAG-GATTTATCGT
1 GTTCAAATAACGTGAATGAAGAAAATAATCATTAAAAGTG-TCTTCCAATTTAGAG-TTTATCGT
**
38868 AATTTGATTCTGATTCTAA
64 AACCTGATTCTGATTCTAA
*
38887 GTTCAAATAATGTGAATGAAGAAAATAA
1 GTTCAAATAACGTGAATGAAGAAAATAA
38915 ATTTTTTAAA
Statistics
Matches: 99, Mismatches: 8, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
80 1 0.01
81 57 0.58
82 40 0.40
83 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (82 bp):
GTTCAAATAACGTGAATGAAGAAAATAATCATTAAAAGTGTCTTCCAATTTAGAGTTTATCGTAA
CCTGATTCTGATTCTAA
Found at i:50051 original size:98 final size:99
Alignment explanation
Indices: 49913--50185 Score: 293
Period size: 98 Copynumber: 2.7 Consensus size: 99
49903 GAACGTTAAA
* * * * * *
49913 TCAATTTTGTACCACGTCATATAATTCAAAATCGAGCCGCATCAGACATTAAACAGAAAATATTA
1 TCAATTTCGTACCACCTTATATAATTCAAAGTTGAGCCGCATCAGACATTAAACAGAAAATGTTA
* *
49978 TCTCAACACTCAATT-TTTCTTTTGATC-GAAATG
66 TCTCAACACTCAATTCATTC-TTTGATCAAAAATG
* * *
50011 TCAATTTCGTACCACCTTGTATAATTCAAAGTTGAACCGCATC-GA-ATACTAAACAGAATATGT
1 TCAATTTCGTACCACCTTATATAATTCAAAGTTGAGCCGCATCAGACAT--TAAACAGAAAATGT
*
50074 TATATCAACACTCAATTCATTCTTTGATCAAATTAAAATG
64 TATCTCAACACTCAATTCATTCTTTGATC--A--AAAATG
* *
50114 TCAATTTCGTACCACGTCATATATATAATTCAAAGTTGAGCCCCATCAGACACTAAACAGAAAAT
1 TCAATTTCGTACCAC--C-T-TATATAATTCAAAGTTGAGCCGCATCAGACATTAAACAGAAAAT
50179 GTTATCT
62 GTTATCT
50186 TTATCGAAAT
Statistics
Matches: 143, Mismatches: 18, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
96 2 0.01
97 2 0.01
98 71 0.50
99 3 0.02
103 20 0.14
105 1 0.01
106 1 0.01
107 40 0.28
108 2 0.01
109 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (99 bp):
TCAATTTCGTACCACCTTATATAATTCAAAGTTGAGCCGCATCAGACATTAAACAGAAAATGTTA
TCTCAACACTCAATTCATTCTTTGATCAAAAATG
Found at i:51981 original size:3 final size:3
Alignment explanation
Indices: 51975--52001 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
51965 TTTTTTTAAT
51975 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
52002 CTTTAGGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Done.