Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021886.1 Corchorus olitorius cultivar O-4 contig21919, 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: 12705
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1919 original size:7 final size:7
Alignment explanation
Indices: 1907--1931 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1897 CTGTTCCTTT
1907 TTCAGCA
1 TTCAGCA
1914 TTCAGCA
1 TTCAGCA
1921 TTCAGCA
1 TTCAGCA
1928 TTCA
1 TTCA
1932 CGTGCATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (7 bp):
TTCAGCA
Found at i:4532 original size:2 final size:2
Alignment explanation
Indices: 4519--4553 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4509 TGCTTTCCAT
*
4519 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4554 TCTACTGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5005 original size:13 final size:14
Alignment explanation
Indices: 4980--5010 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
4970 TTTTTTTCAA
4980 AAAAATGGTTTTTC
1 AAAAATGGTTTTTC
4994 AAAAATGG-TTTTC
1 AAAAATGGTTTTTC
5007 AAAA
1 AAAA
5011 TTTGTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (14 bp):
AAAAATGGTTTTTC
Found at i:7786 original size:35 final size:35
Alignment explanation
Indices: 7610--8034 Score: 473
Period size: 35 Copynumber: 12.1 Consensus size: 35
7600 TTCATTTTAA
* *
7610 TTGATCCAGGGCGATCTCTAC-TCAA-TTACTTCAG
1 TTGATCCAGGGCGATCT-TTCTTCAATTTATTTCAG
* *
7644 TTGATCCAGGGCGATCTTTATTTCAGTTTATTTCAG
1 TTGATCCAGGGCGATCTTT-CTTCAATTTATTTCAG
* * * * * *
7680 TTGACCCAGGGCGGTCCTTCTTCAATTCATTTTAA
1 TTGATCCAGGGCGATCTTTCTTCAATTTATTTCAG
* * *
7715 TGGATCTAAGGCGATCTTTTCTTCAATTTATTTCAG
1 TTGATCCAGGGCGATC-TTTCTTCAATTTATTTCAG
* *
7751 TTGATCCAGGGTGATCTTTCTTC-ATTATATGTCAG
1 TTGATCCAGGGCGATCTTTCTTCAATT-TATTTCAG
* * *
7786 TTGACCCAGGGCGGTCTCTCTTCAATTTATTTCAG
1 TTGATCCAGGGCGATCTTTCTTCAATTTATTTCAG
* * *
7821 TTGA-CCTAGGGAGGTCTTTCTTCAATTTACTTCAG
1 TTGATCC-AGGGCGATCTTTCTTCAATTTATTTCAG
* * *
7856 TCGATCCAGGGCGATCTTTTCTACAATCTA-TTCAG
1 TTGATCCAGGGCGATC-TTTCTTCAATTTATTTCAG
*
7891 TTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAG
1 TTGATCCAGGGCGATC-TTTCTTCAATTTATTTCAG
*
7927 TTGATCCAGGGCGATCTTTCTTCAATTTATTTCAA
1 TTGATCCAGGGCGATCTTTCTTCAATTTATTTCAG
*
7962 TTGATCCAGGGCGGTCTTTCTTCAATTTATTTCAG
1 TTGATCCAGGGCGATCTTTCTTCAATTTATTTCAG
* * *
7997 TTGATCTAGGGCGATCTTTTCTGCAGTTTATTTCAG
1 TTGATCCAGGGCGATC-TTTCTTCAATTTATTTCAG
8033 TT
1 TT
8035 TACCGCAAAT
Statistics
Matches: 329, Mismatches: 51, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
33 1 0.00
34 22 0.07
35 199 0.60
36 107 0.33
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.41
Consensus pattern (35 bp):
TTGATCCAGGGCGATCTTTCTTCAATTTATTTCAG
Found at i:7842 original size:141 final size:141
Alignment explanation
Indices: 7610--8034 Score: 529
Period size: 141 Copynumber: 3.0 Consensus size: 141
7600 TTCATTTTAA
* * * * *
7610 TTGATCCAGGGCGATCTCTAC-TCA-ATTACT-TCAGTTGATCCAGGGCGATCTTTATTTCAGTT
1 TTGATCCAGGGCGATCTTTTCTTCAGTTTA-TGTCAGTTGATCCAGGGCGATCTTT-CTTCAATT
* * * * * *
7672 TATTTCAGTTGACCCAGGGCGGTCCTTCTTCAATTCATTTTAATGGATCTAAGGCGATCTTTTCT
64 TATTTCAGTTGA-CCAGGGCGGTCTTTCTTCAATTTATTTCAGTCGATCTAGGGCGATCTTTTCT
*
7737 TCAATTTATTTCAG
128 ACAATTTATTTCAG
* * * *
7751 TTGATCCAGGGTGATC-TTTCTTCA-TTATATGTCAGTTGACCCAGGGCGGTCTCTCTTCAATTT
1 TTGATCCAGGGCGATCTTTTCTTCAGTT-TATGTCAGTTGATCCAGGGCGATCTTTCTTCAATTT
* * *
7814 ATTTCAGTTGACCTAGGGAGGTCTTTCTTCAATTTACTTCAGTCGATCCAGGGCGATCTTTTCTA
65 ATTTCAGTTGACC-AGGGCGGTCTTTCTTCAATTTATTTCAGTCGATCTAGGGCGATCTTTTCTA
*
7879 CAATCTA-TTCAG
129 CAATTTATTTCAG
*
7891 TTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAATTTA
1 TTGATCCAGGGCGATCTTTTCTTCAGTTTATGTCAGTTGATCCAGGGCGATCTTTCTTCAATTTA
* * *
7956 TTTCAATTGATCCAGGGCGGTCTTTCTTCAATTTATTTCAGTTGATCTAGGGCGATCTTTTCTGC
66 TTTCAGTTGA-CCAGGGCGGTCTTTCTTCAATTTATTTCAGTCGATCTAGGGCGATCTTTTCTAC
*
8021 AGTTTATTTCAG
130 AATTTATTTCAG
8033 TT
1 TT
8035 TACCGCAAAT
Statistics
Matches: 243, Mismatches: 33, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
140 24 0.10
141 186 0.77
142 33 0.14
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.41
Consensus pattern (141 bp):
TTGATCCAGGGCGATCTTTTCTTCAGTTTATGTCAGTTGATCCAGGGCGATCTTTCTTCAATTTA
TTTCAGTTGACCAGGGCGGTCTTTCTTCAATTTATTTCAGTCGATCTAGGGCGATCTTTTCTACA
ATTTATTTCAG
Found at i:8010 original size:106 final size:105
Alignment explanation
Indices: 7610--8034 Score: 473
Period size: 106 Copynumber: 4.0 Consensus size: 105
7600 TTCATTTTAA
* * *
7610 TTGATCCAGGGCGATCTCTAC-TCAA-TTACTTCAGTTGATCCAGGGCGATCTTTATTTCAGTTT
1 TTGATCCAGGGCGATCT-TTCTTCAATTTACTTCAGTTGATCCAGGGCGATCTTT-CTTCAATTT
* * * * *
7673 ATTTCAGTTGACCCAGGGCGGTCCTTCTTCAATTCATTTTAA
64 ATTTCAGTTGACCCAGGGCGATCTTTCTTCAATTTATTTCAG
* * * * *
7715 TGGATCTAAGGCGATCTTTTCTTCAATTTATTTCAGTTGATCCAGGGTGATCTTTCTTC-ATTAT
1 TTGATCCAGGGCGATC-TTTCTTCAATTTACTTCAGTTGATCCAGGGCGATCTTTCTTCAATT-T
* * *
7779 ATGTCAGTTGACCCAGGGCGGTCTCTCTTCAATTTATTTCAG
64 ATTTCAGTTGACCCAGGGCGATCTTTCTTCAATTTATTTCAG
* * * * *
7821 TTGA-CCTAGGGAGGTCTTTCTTCAATTTACTTCAGTCGATCCAGGGCGATCTTTTCTACAATCT
1 TTGATCC-AGGGCGATCTTTCTTCAATTTACTTCAGTTGATCCAGGGCGATC-TTTCTTCAATTT
* *
7885 A-TTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAG
64 ATTTCAGTTGACCCAGGGCGATC-TTTCTTCAATTTATTTCAG
* * *
7927 TTGATCCAGGGCGATCTTTCTTCAATTTATTTCAATTGATCCAGGGCGGTCTTTCTTCAATTTAT
1 TTGATCCAGGGCGATCTTTCTTCAATTTACTTCAGTTGATCCAGGGCGATCTTTCTTCAATTTAT
* * * *
7992 TTCAGTTGATCTAGGGCGATCTTTTCTGCAGTTTATTTCAG
66 TTCAGTTGACCCAGGGCGATC-TTTCTTCAATTTATTTCAG
8033 TT
1 TT
8035 TACCGCAAAT
Statistics
Matches: 271, Mismatches: 39, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
105 79 0.29
106 162 0.60
107 30 0.11
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.41
Consensus pattern (105 bp):
TTGATCCAGGGCGATCTTTCTTCAATTTACTTCAGTTGATCCAGGGCGATCTTTCTTCAATTTAT
TTCAGTTGACCCAGGGCGATCTTTCTTCAATTTATTTCAG
Found at i:8585 original size:30 final size:30
Alignment explanation
Indices: 8543--8997 Score: 642
Period size: 30 Copynumber: 15.0 Consensus size: 30
8533 CTTTATCAGT
*
8543 TTTATTTTAATCCTGGTTGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * * * *
8573 TTTGTCTTAATCCTGTTTGAGGATCGTAGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
8603 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
8633 TTTATGTTAATCCTGGTTGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
8663 TTCATTTTTAATCCTGTTTGAGGATCATTGC
1 TTTA-TTTTAATCCTGGTTGAGGATCATTGC
*
8694 TTTATTTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
8724 TTCATTTTTAATCCTGGTTGAGGATCGTTGC
1 TTTA-TTTTAATCCTGGTTGAGGATCATTGC
*
8755 TTTATTTTAATCCTGGTTGAAGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
8785 TTTATTTTAATCCTGGTTGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
8815 TTTATTTTAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
8845 TTTATTTTAATCCTGGTTGAGGATTA-TGAC
1 TTTATTTTAATCCTGGTTGAGGATCATTG-C
* * *
8875 TTTATTTTATTTCTTGATTGAGGATCATTGC
1 TTTATTTTA-ATCCTGGTTGAGGATCATTGC
8906 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
8936 TTTATTTCAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
8966 TTTATTTTTTAATCCTGGTTTAGGATCATTGC
1 TTTA--TTTTAATCCTGGTTGAGGATCATTGC
8998 CTCTTCAGAT
Statistics
Matches: 380, Mismatches: 38, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
29 2 0.01
30 275 0.72
31 76 0.20
32 27 0.07
ACGTcount: A:0.19, C:0.14, G:0.20, T:0.48
Consensus pattern (30 bp):
TTTATTTTAATCCTGGTTGAGGATCATTGC
Found at i:8703 original size:91 final size:90
Alignment explanation
Indices: 8543--8997 Score: 644
Period size: 91 Copynumber: 5.0 Consensus size: 90
8533 CTTTATCAGT
* * * *
8543 TTTATTTTAATCCTGGTTGAGGATCGTTGCTTTGTCTTAATCCTGTTTGAGGATCGTAGCTTTAT
1 TTTATTTTAATCCTGGTTGAGGATCGTTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTAT
8608 TTTAATCCTGGTTGAGGATCATTGC
66 TTTAATCCTGGTTGAGGATCATTGC
* *
8633 TTTATGTTAATCCTGGTTGAGGATCGTTGCTTCATTTTTAATCCTGTTTGAGGATCATTGCTTTA
1 TTTATTTTAATCCTGGTTGAGGATCGTTGCTTTA-TTTTAATCCTGTTTGAGGATCATTGCTTTA
*
8698 TTTTAATCCTGTTTGAGGATCATTGC
65 TTTTAATCCTGGTTGAGGATCATTGC
* * *
8724 TTCATTTTTAATCCTGGTTGAGGATCGTTGCTTTATTTTAATCCTGGTTGAAGATCATTGCTTTA
1 TTTA-TTTTAATCCTGGTTGAGGATCGTTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTA
*
8789 TTTTAATCCTGGTTGAGGATCGTTGC
65 TTTTAATCCTGGTTGAGGATCATTGC
* * * *
8815 TTTATTTTAATCCTGGTTTAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATTA-TGACTTTA
1 TTTATTTTAATCCTGGTTGAGGATCGTTGCTTTATTTTAATCCTGTTTGAGGATCATTG-CTTTA
* * *
8879 TTTTATTTCTTGATTGAGGATCATTGC
65 TTTTA-ATCCTGGTTGAGGATCATTGC
* *
8906 TTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTCAATCCTGGTTT-AGGATCATTGCTTTA
1 TTTATTTTAATCCTGGTTGAGGATCGTTGCTTTATTTTAATCCT-GTTTGAGGATCATTGCTTTA
*
8970 TTTTTTAATCCTGGTTTAGGATCATTGC
65 --TTTTAATCCTGGTTGAGGATCATTGC
8998 CTCTTCAGAT
Statistics
Matches: 326, Mismatches: 31, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
89 2 0.01
90 89 0.27
91 180 0.55
92 50 0.15
93 5 0.02
ACGTcount: A:0.19, C:0.14, G:0.20, T:0.48
Consensus pattern (90 bp):
TTTATTTTAATCCTGGTTGAGGATCGTTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTAT
TTTAATCCTGGTTGAGGATCATTGC
Found at i:8793 original size:121 final size:120
Alignment explanation
Indices: 8543--8997 Score: 646
Period size: 121 Copynumber: 3.8 Consensus size: 120
8533 CTTTATCAGT
* * * * *
8543 TTTATTTTAATCCTGGTTGAGGATCGTTGCTTTGTCTTAATCCT-GTTTGAGGATCGTAGCTTTA
1 TTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTT-AGGATCATTGCTTTA
* *
8607 TTTTAATCCTGGTTGAGGATCATTGCTTTATGTTAATCCTGGTTGAGGATCGTTGC
65 TTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
8663 TTCATTTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCT-GTTTGAGGATCATTGCTTC
1 TTTA-TTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTT-AGGATCATTGCTTT
* *
8727 ATTTTTAATCCTGGTTGAGGATCGTTGCTTTATTTTAATCCTGGTTGAAGATCATTGC
64 A-TTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCATTGC
*
8785 TTTATTTTAATCCTGGTTGAGGATCGTTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTTTAT
1 TTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTTTAT
* * * *
8850 TTTAATCCTGGTTGAGGATTA-TGACTTTATTTTATTTCTTGATTGAGGATCATTGC
66 TTTAATCCTGGTTGAGGATCATTG-CTTTATTTTA-ATCCTGGTTGAGGATCATTGC
*
8906 TTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTCAATCCTGGTTTAGGATCATTGCTTTAT
1 TTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTTTA-
*
8971 TTTTTAATCCTGGTTTAGGATCATTGC
65 -TTTTAATCCTGGTTGAGGATCATTGC
8998 CTCTTCAGAT
Statistics
Matches: 301, Mismatches: 26, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
119 2 0.01
120 33 0.11
121 184 0.61
122 59 0.20
123 21 0.07
124 2 0.01
ACGTcount: A:0.19, C:0.14, G:0.20, T:0.48
Consensus pattern (120 bp):
TTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTTTAT
TTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCATTGC
Found at i:9531 original size:28 final size:28
Alignment explanation
Indices: 9495--9576 Score: 105
Period size: 28 Copynumber: 3.0 Consensus size: 28
9485 GCACTTAGGT
*
9495 CATTTAGGGGGCATTTTGGTCATTTTTA
1 CATTCAGGGGGCATTTTGGTCATTTTTA
*
9523 CATTCAGGGGGCATTTTGGTCATTTTTG
1 CATTCAGGGGGCATTTTGGTCATTTTTA
* *
9551 CATTCCA--GGGCATTTTGATCCTTTTT
1 CATT-CAGGGGGCATTTTGGTCATTTTT
9577 TAACTAATTC
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 17 0.35
28 30 0.61
29 2 0.04
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (28 bp):
CATTCAGGGGGCATTTTGGTCATTTTTA
Done.