Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022021.1 Corchorus olitorius cultivar O-4 contig22054, 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: 3269
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Found at i:1016 original size:29 final size:27
Alignment explanation
Indices: 948--1022 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
938 AGTTAACCTA
*
948 AAATGACCTAAATGCCCCTGAACATGC
1 AAATGACCAAAATGCCCCTGAACATGC
** *
975 AAATGACCAAAATGCCCCTGAATTTTTGG
1 AAATGACCAAAATGCCCCTGAA--CATGC
1004 AAATGACCAAAATGCCCCT
1 AAATGACCAAAATGCCCCT
1023 AGATGACCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 21 0.50
29 21 0.50
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.21
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAACATGC
Found at i:1508 original size:30 final size:30
Alignment explanation
Indices: 1456--2684 Score: 1465
Period size: 30 Copynumber: 41.1 Consensus size: 30
1446 CAAATAAACC
* * *
1456 AAAGTAATAATCCT-AAATCAGGATAAAAAT
1 AAAGCAATGATCCTCAAA-CAGGATTAAAAT
* * *
1486 ATAGCGATGATCCTCAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * * *
1516 AAAGCAATGGTCTTCAACCATGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
** *
1546 AAAGCAACAATCCTCAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * *
1576 GATGCAAAT-ATCCTCAACCAGGATTAAAAT
1 AAAGC-AATGATCCTCAAACAGGATTAAAAT
** *
1606 GGAGCGAAT-ATCCTCAATCAGGATTAAAAT
1 AAAGC-AATGATCCTCAAACAGGATTAAAAT
* * * *
1636 GAAGCAATGATCCTTAACCAGGATTAAAAC
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
*
1666 AAAGCAATGATCCTCAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* ** *
1696 GAAGTGATGATCCTC-AACTAGGATTAGAAT
1 AAAGCAATGATCCTCAAAC-AGGATTAAAAT
*
1726 AAAGCAATGATCCTCAAACAGGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* *
1756 AAAGCAATGATCCTCAAACGGGATTATAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
1786 AAAGCAATGATCCTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * * *
1816 AAAGTAAGGATCTTCAAACAGGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* *
1846 AAAGCAATGATCCTCAAACAAGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
*
1876 AAAGCAATGATCTTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
*
1906 AAAGCAACGATCCTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
*
1936 AAAGCAATGATCCTCAAACATGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* *
1966 AAAGCATTGTTCCTCAAACAGGATTAAAAAT
1 AAAGCAATGATCCTCAAACAGGATT-AAAAT
* * *
1997 GAAGCAATTATCCTCAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
*
2027 CAAGCAATGATCCTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
*
2057 AAAGCATTGATCCTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * *
2087 AAAGCATTGATCCTCAACCAGGATTTAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* *
2117 GAAGCAATGATCCTCAAACAAGATTAAAAAT
1 AAAGCAATGATCCTCAAACAGGATT-AAAAT
* *
2148 GAAGCAATGATCCTCAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * *
2178 AAAGCATTGATCCTCAACCAGGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
*
2208 AAAACAATGATCCTCAAACAGGATTAAAAAT
1 AAAGCAATGATCCTCAAACAGGATT-AAAAT
* *
2239 GAAGCAATGATCCTCAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * *
2269 AAAGCATTGATCCTCAACCAGGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* *
2299 AAAACAATGATCCTCAAACAGGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* *
2329 AAAGCAATGATCCTTAAAGAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
2359 AAAGCAATGATCCTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * *
2389 AAAACATTGATCCTCAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * * *
2419 GAAGCATTGATCCTCAACCATGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
*
2449 GAAGCAATGATCCTCAAACAGGATTAAAAAT
1 AAAGCAATGATCCTCAAACAGGATT-AAAAT
* * * **
2480 GAAGCGATGATCCTCAAACAGTATTGGAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* *
2510 GAAGCGATGATCCTCAAACAGGA-T----T
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * *
2535 -AAGCAACGATCCTCAACCAGGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * *
2564 AAAGCAATGATCCTCAAACAAGATTAACAC
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* *
2594 AAAGCAGTGCTCCTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
*
2624 AAAGCAATGATCCTCAAGCAGGATT-AAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* *
2653 -AAGGAATGATCCTCAAGCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
2682 AAA
1 AAA
2685 ACTGATAAAG
Statistics
Matches: 1048, Mismatches: 134, Indels: 34
0.86 0.11 0.03
Matches are distributed among these distances:
24 19 0.02
25 2 0.00
28 23 0.02
29 15 0.01
30 876 0.84
31 113 0.11
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.22
Consensus pattern (30 bp):
AAAGCAATGATCCTCAAACAGGATTAAAAT
Found at i:3030 original size:71 final size:71
Alignment explanation
Indices: 2949--3266 Score: 420
Period size: 71 Copynumber: 4.5 Consensus size: 71
2939 ATTTTGCAGT
* * * * * * * **
2949 CAATTGAAATAAACTGCAGAGAAGATCGCCCTGGATCTACTGAAGTAAATTGAGGAAAGATCATC
1 CAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGCC
*
3014 CTGGAC
66 CTAGAC
* * *
3020 CAATTGAAATAAACCGAAGAAAAGATCGCCCTGGATCAAGTGAAATAAACTGAAGAAAGGATCGC
1 CAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAA-GACCGC
*
3085 CCTAGAT
65 CCTAGAC
*
3092 CAATTGAAATAAATTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGCC
1 CAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGCC
* *
3157 CTAAAT
66 CTAGAC
3163 CAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGCC
1 CAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGCC
* *
3228 CTGGGTC
66 CT-AGAC
* * *
3235 AAACTGAAATAAACTGAAGAAAGGATCGCCCT
1 CAATTGAAATAAACTGAAGAAAAGATCGCCCT
3267 AGA
Statistics
Matches: 220, Mismatches: 25, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
71 127 0.58
72 93 0.42
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.18
Consensus pattern (71 bp):
CAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGCC
CTAGAC
Found at i:3045 original size:36 final size:36
Alignment explanation
Indices: 2948--3266 Score: 392
Period size: 36 Copynumber: 8.9 Consensus size: 36
2938 CATTTTGCAG
* *
2948 TCAATTGAAATAAACTGCAGAGAAGATCGCCCTGGA
1 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * * * * **
2984 TCTACTGAAGTAAATTG-AGGAAAGATCATCCTGGA
1 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* *
3019 CCAATTGAAATAAACCGAAGAAAAGATCGCCCTGGA
1 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * *
3055 TCAAGTGAAATAAACTGAAGAAAGGATCGCCCTAGA
1 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGA
*
3091 TCAATTGAAATAAATTGAAGAAAAGATCGCCCTGGA
1 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * **
3127 TCAACTGAAATAAACTGAAG-AAAGACCGCCCTAAA
1 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGA
3162 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGA
1 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * *
3198 TCAACTGAAATAAACTGAAG-AAAGACCGCCCTGGG
1 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* *
3233 TCAAACTGAAATAAACTGAAGAAAGGATCGCCCT
1 TC-AATTGAAATAAACTGAAGAAAAGATCGCCCT
3267 AGA
Statistics
Matches: 239, Mismatches: 40, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
35 71 0.30
36 158 0.66
37 10 0.04
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.18
Consensus pattern (36 bp):
TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGA
Found at i:3207 original size:143 final size:142
Alignment explanation
Indices: 2948--3266 Score: 440
Period size: 143 Copynumber: 2.2 Consensus size: 142
2938 CATTTTGCAG
* * * * * * * *
2948 TCAATTGAAATAAACTGCAGAGAAGATCGCCCTGGATCTACTGAAGTAAATTGAGGAAAGATCAT
1 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCAC
** *
3013 CCTGGACCAATTGAAATAAACCGAAGAAAAGATCGCCCTGGATCAAGTGAAATAAACTGAAGAAA
66 CCTAAACCAATTGAAATAAACCGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAA
*
3078 GGATCGCCCTAGA
131 -GACCGCCCTAGA
* *
3091 TCAATTGAAATAAATTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGC
1 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCAC
* *
3156 CCTAAATCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAA
66 CCTAAACCAATTGAAATAAACCGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAA
* *
3221 GACCGCCCTGGG
131 GACCGCCCTAGA
* *
3233 TCAAACTGAAATAAACTGAAGAAAGGATCGCCCT
1 TC-AATTGAAATAAACTGAAGAAAAGATCGCCCT
3267 AGA
Statistics
Matches: 154, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
142 11 0.07
143 143 0.93
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.18
Consensus pattern (142 bp):
TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCAC
CCTAAACCAATTGAAATAAACCGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAA
GACCGCCCTAGA
Done.