Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018757.1 Corchorus olitorius cultivar O-4 contig18790, 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: 52410
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1856 original size:7 final size:7
Alignment explanation
Indices: 1846--1872 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1836 TCATTGGTGG
1846 TCTCAAC
1 TCTCAAC
1853 TCTCAAC
1 TCTCAAC
1860 TCTCAAC
1 TCTCAAC
1867 TCTCAA
1 TCTCAA
1873 GTCTGAACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.41, G:0.00, T:0.30
Consensus pattern (7 bp):
TCTCAAC
Found at i:1881 original size:14 final size:14
Alignment explanation
Indices: 1845--1881 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1835 GTCATTGGTG
1845 GTCTCAACTCTCAA
1 GTCTCAACTCTCAA
*
1859 CTCTCAACTCTCAA
1 GTCTCAACTCTCAA
*
1873 GTCTGAACT
1 GTCTCAACT
1882 GAACAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.27, C:0.35, G:0.08, T:0.30
Consensus pattern (14 bp):
GTCTCAACTCTCAA
Found at i:2319 original size:6 final size:6
Alignment explanation
Indices: 2308--2333 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2298 TTCAGGATCT
2308 GAAAGA GAAAGA GAAAGA GAAAGA GA
1 GAAAGA GAAAGA GAAAGA GAAAGA GA
2334 GAGGATGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:7721 original size:7 final size:7
Alignment explanation
Indices: 7709--7746 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
7699 CTCCTCTCTG
7709 TGCAAAA
1 TGCAAAA
7716 TGCAAAA
1 TGCAAAA
7723 TGCAAAA
1 TGCAAAA
7730 TGCAAAA
1 TGCAAAA
7737 TGCAAAA
1 TGCAAAA
7744 TGC
1 TGC
7747 CATTGCCTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (7 bp):
TGCAAAA
Found at i:13379 original size:30 final size:30
Alignment explanation
Indices: 13345--13406 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
13335 ATACCTAGCT
13345 AGCCCTTGAAGATAAGAAAATAAATTAAAG
1 AGCCCTTGAAGATAAGAAAATAAATTAAAG
13375 AGCCCTTGAAGATAAGAAAATAAATTAAAG
1 AGCCCTTGAAGATAAGAAAATAAATTAAAG
13405 AG
1 AG
13407 TAGTGAAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.53, C:0.10, G:0.18, T:0.19
Consensus pattern (30 bp):
AGCCCTTGAAGATAAGAAAATAAATTAAAG
Found at i:18877 original size:57 final size:57
Alignment explanation
Indices: 18789--18904 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
18779 GTTCACAAAG
18789 GTCTTATAAATTATCCAGGTGATAATTGCATGGTCCTGGGAATGATGATGATTGGGT
1 GTCTTATAAATTATCCAGGTGATAATTGCATGGTCCTGGGAATGATGATGATTGGGT
18846 GTCTTATAAATTATCCAGGTGATAATTGCATGGTCCTGGGAATGATGATGATTGGGT
1 GTCTTATAAATTATCCAGGTGATAATTGCATGGTCCTGGGAATGATGATGATTGGGT
18903 GT
1 GT
18905 ACATGAATTC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.35
Consensus pattern (57 bp):
GTCTTATAAATTATCCAGGTGATAATTGCATGGTCCTGGGAATGATGATGATTGGGT
Found at i:24757 original size:13 final size:13
Alignment explanation
Indices: 24739--24765 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24729 AAACGGAAAA
24739 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
24752 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
24765 T
1 T
24766 TCAGTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (13 bp):
TCCAGAAGTGCTT
Found at i:26572 original size:53 final size:53
Alignment explanation
Indices: 26509--26618 Score: 184
Period size: 53 Copynumber: 2.1 Consensus size: 53
26499 TGTTTATTCA
26509 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
* * * *
26562 ATTGAACCTATTTAATAAGCACGCATATCAAATAATACAAAATGCAATGAATT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
26615 ATTG
1 ATTG
26619 GATTTAAAGA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.26
Consensus pattern (53 bp):
ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
Found at i:32936 original size:129 final size:129
Alignment explanation
Indices: 32706--32964 Score: 482
Period size: 129 Copynumber: 2.0 Consensus size: 129
32696 TACAAGATAA
32706 CGCCATATGCCATAGCCATGATTCCCGCTACAAGCTCCACCAACTCTGCCATAGCATCTTCCGAA
1 CGCCATATGCCATAGCCATGATTCCCGCTACAAGCTCCACCAACTCTGCCATAGCATCTTCCGAA
32771 TCGAGCATATGAACAAGCTTGCTTTTCATAATTTTGAATTTCCGTTGCTTTAGGGGTGATGAGT
66 TCGAGCATATGAACAAGCTTGCTTTTCATAATTTTGAATTTCCGTTGCTTTAGGGGTGATGAGT
*
32835 CGCCATATGCCATAGCCATGATTCCCGCTGCAAGCTCCACCAACTCTGCCATAGCATCTTCCGAA
1 CGCCATATGCCATAGCCATGATTCCCGCTACAAGCTCCACCAACTCTGCCATAGCATCTTCCGAA
* * *
32900 TCGGGCATATGAACAAGCTTGCTTTTGATAATTTTGAATTTTCGTTGCTTTAGGGGTGATGAGT
66 TCGAGCATATGAACAAGCTTGCTTTTCATAATTTTGAATTTCCGTTGCTTTAGGGGTGATGAGT
32964 C
1 C
32965 CACTTCATTG
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 126 1.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.31
Consensus pattern (129 bp):
CGCCATATGCCATAGCCATGATTCCCGCTACAAGCTCCACCAACTCTGCCATAGCATCTTCCGAA
TCGAGCATATGAACAAGCTTGCTTTTCATAATTTTGAATTTCCGTTGCTTTAGGGGTGATGAGT
Found at i:33462 original size:50 final size:50
Alignment explanation
Indices: 33415--33550 Score: 227
Period size: 50 Copynumber: 2.7 Consensus size: 50
33405 AGTTCGTGAT
* *
33415 GCGGTAGATCTTTATGCCATGCTATGTGATATGGCATATGGCCTCGTGGC
1 GCGGTAGATCCTTATGCCATGTTATGTGATATGGCATATGGCCTCGTGGC
* *
33465 GCGGTAGATCCTTATGCCATGTTATGTGATACGACATATGGCCTCGTGGC
1 GCGGTAGATCCTTATGCCATGTTATGTGATATGGCATATGGCCTCGTGGC
*
33515 GTGGTAGATCCTTATGCCATGTTATGTGATATGGCA
1 GCGGTAGATCCTTATGCCATGTTATGTGATATGGCA
33551 CCATACTATG
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 79 1.00
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (50 bp):
GCGGTAGATCCTTATGCCATGTTATGTGATATGGCATATGGCCTCGTGGC
Found at i:33631 original size:20 final size:20
Alignment explanation
Indices: 33602--33641 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
33592 AGATCTTTAG
*
33602 GCCATGCTATGTGATATGGC
1 GCCATACTATGTGATATGGC
33622 GCCATACTATGTGATATGGC
1 GCCATACTATGTGATATGGC
33642 ATATGGCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (20 bp):
GCCATACTATGTGATATGGC
Found at i:33680 original size:70 final size:70
Alignment explanation
Indices: 33487--33828 Score: 479
Period size: 72 Copynumber: 4.8 Consensus size: 70
33477 TATGCCATGT
* * * *
33487 TATGTGATACGACATATGGCCTCGTGGCGTGGTAGATCCTTATGCCATGTTATGTGATATGGCAC
1 TATGTGATACGACATATGGCCTCGTGGCGTGGTAGATCTTTATGCCATGCTATGTGATATAGCGC
33552 CATAC
66 CATAC
* * * *
33557 TATGTGATACGACATATATGGCCTCGTGGCGCGGCAGATCTTTAGGCCATGCTATGTGATATGGC
1 TATGTGATACGAC--ATATGGCCTCGTGGCGTGGTAGATCTTTATGCCATGCTATGTGATATAGC
33622 GCCATAC
64 GCCATAC
* * * ** * * *
33629 TATGTGATATGGCATATGGCCTCGTGGCGCGGTAGATCCGTATGCCATGCTATGTGATACAGTGA
1 TATGTGATACGACATATGGCCTCGTGGCGTGGTAGATCTTTATGCCATGCTATGTGATATAGCGC
33694 CATAC
66 CATAC
33699 TATGTGATACGACATGTATGGCCTCGTGGCGTGGTAGATCTTTATGCCATGCTATGTGATATAGC
1 TATGTGATACGACA--TATGGCCTCGTGGCGTGGTAGATCTTTATGCCATGCTATGTGATATAGC
33764 GCCATAC
64 GCCATAC
* *
33771 -ATGTGATACGGCATATGGCCTCGTGGCATGGTAGATCTTTATGCCATGCTATGTGATA
1 TATGTGATACGACATATGGCCTCGTGGCGTGGTAGATCTTTATGCCATGCTATGTGATA
33829 CGACATATGG
Statistics
Matches: 242, Mismatches: 26, Indels: 9
0.87 0.09 0.03
Matches are distributed among these distances:
69 44 0.18
70 74 0.31
71 12 0.05
72 112 0.46
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (70 bp):
TATGTGATACGACATATGGCCTCGTGGCGTGGTAGATCTTTATGCCATGCTATGTGATATAGCGC
CATAC
Found at i:33738 original size:142 final size:143
Alignment explanation
Indices: 33487--33829 Score: 532
Period size: 142 Copynumber: 2.4 Consensus size: 143
33477 TATGCCATGT
* * *
33487 TATGTGATACGACATATGGCCTCGTGGCGTGGTAGATCCTTATGCCATGTTATGTGATA-TGGCA
1 TATGTGATACGGCATATGGCCTCGTGGCGTGGTAGATCCTTATGCCATGCTATGTGATACAGGCA
33551 CCATACTATGTGATACGACATATATGGCCTCGTGGCGCGGCAGATCTTTAGGCCATGCTATGTGA
66 CCATACTATGTGATACGACATATATGGCCTCGTGGCGCGGCAGATCTTTAGGCCATGCTATGTGA
*
33616 TATGGCGCCATAC
131 TATAGCGCCATAC
* * *
33629 TATGTGATATGGCATATGGCCTCGTGGCGCGGTAGATCCGTATGCCATGCTATGTGATACAGTG-
1 TATGTGATACGGCATATGGCCTCGTGGCGTGGTAGATCCTTATGCCATGCTATGTGATACAG-GC
* * * *
33693 A-CATACTATGTGATACGACATGTATGGCCTCGTGGCGTGGTAGATCTTTATGCCATGCTATGTG
65 ACCATACTATGTGATACGACATATATGGCCTCGTGGCGCGGCAGATCTTTAGGCCATGCTATGTG
33757 ATATAGCGCCATAC
130 ATATAGCGCCATAC
* *
33771 -ATGTGATACGGCATATGGCCTCGTGGCATGGTAGATCTTTATGCCATGCTATGTGATAC
1 TATGTGATACGGCATATGGCCTCGTGGCGTGGTAGATCCTTATGCCATGCTATGTGATAC
33830 GACATATGGC
Statistics
Matches: 183, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
141 54 0.30
142 126 0.69
143 2 0.01
144 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.30
Consensus pattern (143 bp):
TATGTGATACGGCATATGGCCTCGTGGCGTGGTAGATCCTTATGCCATGCTATGTGATACAGGCA
CCATACTATGTGATACGACATATATGGCCTCGTGGCGCGGCAGATCTTTAGGCCATGCTATGTGA
TATAGCGCCATAC
Found at i:34578 original size:32 final size:32
Alignment explanation
Indices: 34542--34603 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
34532 CTTGTATATC
*
34542 TGTTGCTAAGATTTGTTTGTTTCTT-TGTAACA
1 TGTTGCTAAGACTTGTTTG-TTCTTCTGTAACA
**
34574 TGTTGCTATTACTTGTTTGTTCTTCTGTAA
1 TGTTGCTAAGACTTGTTTGTTCTTCTGTAA
34604 AAGCACAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 5 0.19
32 21 0.81
ACGTcount: A:0.16, C:0.11, G:0.18, T:0.55
Consensus pattern (32 bp):
TGTTGCTAAGACTTGTTTGTTCTTCTGTAACA
Found at i:49999 original size:26 final size:28
Alignment explanation
Indices: 49970--50021 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
49960 GTCTTTCAGT
*
49970 CGTCTTTTCCTATGTTT-TT-TTTGGCA
1 CGTCGTTTCCTATGTTTATTGTTTGGCA
49996 CGTCGTTTCCTATGTTTATTGTTTGG
1 CGTCGTTTCCTATGTTTATTGTTTGG
50022 TGTTAGAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 16 0.70
27 2 0.09
28 5 0.22
ACGTcount: A:0.08, C:0.17, G:0.19, T:0.56
Consensus pattern (28 bp):
CGTCGTTTCCTATGTTTATTGTTTGGCA
Done.