Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022692.1 Corchorus olitorius cultivar O-4 contig22725, 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: 21854
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Found at i:1386 original size:29 final size:29
Alignment explanation
Indices: 1344--1404 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
1334 CTTGTTTTGC
*
1344 AGCAACTTGGTGGAGATAATTGGAGCTTG
1 AGCAACTTGGTGGAGATAATTGGAGCCTG
1373 AGCAACTTGGTGGAGATAATTGGAGCCTG
1 AGCAACTTGGTGGAGATAATTGGAGCCTG
1402 AGC
1 AGC
1405 TTTGAGAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.28, C:0.13, G:0.34, T:0.25
Consensus pattern (29 bp):
AGCAACTTGGTGGAGATAATTGGAGCCTG
Found at i:4122 original size:22 final size:21
Alignment explanation
Indices: 4097--4150 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
4087 GAAGTTCGTG
4097 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
4119 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
4138 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
4151 CCCAAGAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:11177 original size:26 final size:26
Alignment explanation
Indices: 11086--11180 Score: 104
Period size: 27 Copynumber: 3.6 Consensus size: 26
11076 TCATATAGGA
* * *
11086 GCATTTTAGTCATTTGCACGTCTAGGG
1 GCATTTTGGTCATTTGTACTTC-AGGG
*
11113 GCATTTCGGTCATTTGCATA-TTCAGGG
1 GCATTTTGGTCATTTG--TACTTCAGGG
11140 GCAGTTTT-GTCATTTGTACTTCAGGG
1 GCA-TTTTGGTCATTTGTACTTCAGGG
11166 GCATTTTGGTCATTT
1 GCATTTTGGTCATTT
11181 TTCTTTCTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
25 6 0.10
26 17 0.29
27 29 0.50
28 5 0.09
29 1 0.02
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.41
Consensus pattern (26 bp):
GCATTTTGGTCATTTGTACTTCAGGG
Found at i:18964 original size:133 final size:133
Alignment explanation
Indices: 18451--19101 Score: 657
Period size: 133 Copynumber: 4.9 Consensus size: 133
18441 TGAAATGCGA
* * * * * *
18451 AAAAGATGAAACTAACCCTTTC-ACCGAAAGGGTATTTCTGGAAAT--CAAA-AGTAAACTTAAA
1 AAAAGACGAAAATGACCC-TTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAA
* * * * ** *
18512 TGCAAGAATGA--AAGAATCGACCCTTTGAGCGAAAGGGCATTTTTGGAGAAAGGTAA-A-CTAA
65 TGCAA-AA-GACGAA-AA-CGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAA
*
18573 CTTAGACATGG
126 CTTA-A-AT-C
** * * * * * * ****
18584 AAAAGTTGAAATTGACTCTTCGACCGAAAGGGCATTTTTTGAAAAAAGAAAGTACTAAACTGGGG
1 AAAAGACGAAAATGACCCTTCGACCGAAAGGGTA-TTTTTGGAAATAGAAAATACTAAACTTAAA
* * * ** *
18649 TACAAAAAGACGAAAACGACCCTTCGACCGGAAGGGCATTTTTGGAAACACTAAACTA--AAAC-
65 TGC-AAAAGACGAAAACGACCCTTCGACCGAAAGGGTATTTTTGGAAA-AAGAAAATACCAAACT
*
18711 -ACA--
128 TAAATC
* * *
18714 AAAAGACGAAAATGACCCTTCGACTGAAAGGGTATTTTTGGAAATAGAAGATACTAAACTTATAT
1 AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAAT
* **
18779 GCAAGAAGACAAAAACGACTGTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAACTTA
66 GCAA-AAGACGAAAACGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAACTTA
18844 AATTC
130 AA-TC
* *
18849 AAAAGACGAAAATGACCCTTCGACCGAAAGGGTA-TTTTGGAAAAAGAAAATACCAAACTTAAAT
1 AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAAT
*
18913 GCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAACTTAA
66 GCAAAAGACGAAAACGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAACTTAA
18978 ATGC
131 AT-C
18982 AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAAT
1 AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAAT
* ** *
19047 GCAAAAGAAGAAAATAACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATA
66 GCAAAAGACGAAAACGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATA
19102 GAGCTTTACT
Statistics
Matches: 433, Mismatches: 65, Indels: 39
0.81 0.12 0.07
Matches are distributed among these distances:
128 8 0.02
129 61 0.14
130 32 0.07
132 6 0.01
133 119 0.27
134 118 0.27
135 34 0.08
136 32 0.07
137 18 0.04
138 5 0.01
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.21
Consensus pattern (133 bp):
AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAAT
GCAAAAGACGAAAACGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAACTTAA
ATC
Found at i:18988 original size:67 final size:67
Alignment explanation
Indices: 18714--19101 Score: 625
Period size: 67 Copynumber: 5.8 Consensus size: 67
18704 CTAAAACACA
* * * * *
18714 AAAAGACGAAAATGACCCTTCGACTGAAAGGGTATTTTTGGAAATAGAAGATACTAAACTTATAT
1 AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAACTTAAAT
18779 GC
66 GC
* * **
18781 AAGAAGACAAAAACGACTGTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAACTTAAA
1 AA-AAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAACTTAAA
*
18846 TTC
65 TGC
18849 AAAAGACGAAAATGACCCTTCGACCGAAAGGGTA-TTTTGGAAAAAGAAAATACCAAACTTAAAT
1 AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAACTTAAAT
18913 GC
66 GC
18915 AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAACTTAAAT
1 AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAACTTAAAT
18980 GC
66 GC
* *
18982 AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAAT
1 AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAACTTAAAT
19047 GC
66 GC
* * *
19049 AAAAGAAGAAAATAACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAATA
1 AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATA
19102 GAGCTTTACT
Statistics
Matches: 300, Mismatches: 19, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
66 65 0.22
67 178 0.59
68 57 0.19
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (67 bp):
AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAACTTAAAT
GC
Found at i:20004 original size:14 final size:14
Alignment explanation
Indices: 19985--20013 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19975 TTCTTGTTTT
19985 GCAGCAACTTGGTG
1 GCAGCAACTTGGTG
19999 GCAGCAACTTGGTG
1 GCAGCAACTTGGTG
20013 G
1 G
20014 AGATAATTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.21
Consensus pattern (14 bp):
GCAGCAACTTGGTG
Found at i:20033 original size:29 final size:29
Alignment explanation
Indices: 20001--20061 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
19991 ACTTGGTGGC
*
20001 AGCAACTTGGTGGAGATAATTGGAGCTTG
1 AGCAACTTGGTGGAGATAATTGGAGCCTG
20030 AGCAACTTGGTGGAGATAATTGGAGCCTG
1 AGCAACTTGGTGGAGATAATTGGAGCCTG
20059 AGC
1 AGC
20062 TTTGAGAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.28, C:0.13, G:0.34, T:0.25
Consensus pattern (29 bp):
AGCAACTTGGTGGAGATAATTGGAGCCTG
Done.