Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024116.1 Corchorus olitorius cultivar O-4 contig24149, 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: 26161
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Found at i:2973 original size:17 final size:18
Alignment explanation
Indices: 2948--2981 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2938 ATTTTATTAG
2948 TTTTGTTTTGGT-TTTTT
1 TTTTGTTTTGGTATTTTT
*
2965 TTTTTTTTTGGTATTTT
1 TTTTGTTTTGGTATTTT
2982 AAACCATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (18 bp):
TTTTGTTTTGGTATTTTT
Found at i:11810 original size:183 final size:183
Alignment explanation
Indices: 11502--11868 Score: 716
Period size: 183 Copynumber: 2.0 Consensus size: 183
11492 AAATCCTTGC
11502 TATTCGGTTTGGCCTACTTCGCACGTGATCTAGGATAGTTTTACTCTTTAGGGAGAGGGAGTTTG
1 TATTCGGTTTGGCCTACTTCGCACGTGATCTAGGATAGTTTTACTCTTTAGGGAGAGGGAGTTTG
11567 TTTGATGAGATAGGGGTTTGTTGGCTCATATGTTAGCTCGGTACGTTTTGGTACTGAAGCTAATA
66 TTTGATGAGATAGGGGTTTGTTGGCTCATATGTTAGCTCGGTACGTTTTGGTACTGAAGCTAATA
11632 ATGTGTGGTACAAGGTCTTCTCTATGCGTTTATAATCCCAAATTCCCAATCCA
131 ATGTGTGGTACAAGGTCTTCTCTATGCGTTTATAATCCCAAATTCCCAATCCA
*
11685 TATTCGGTTTGGCCTACTTCGCACGTGATCTAGGATAGTTTTACTTTTTAGGGAGAGGGAGTTTG
1 TATTCGGTTTGGCCTACTTCGCACGTGATCTAGGATAGTTTTACTCTTTAGGGAGAGGGAGTTTG
*
11750 TTTGATGAGATAGGGGTTTGTTGGCTCATATGTTAGCTCGGTACGTTTTGGTACTGAAGCTAGTA
66 TTTGATGAGATAGGGGTTTGTTGGCTCATATGTTAGCTCGGTACGTTTTGGTACTGAAGCTAATA
11815 ATGTGTGGTACAAGGTCTTCTCTATGCGTTTATAATCCCAAATTCCCAATCCA
131 ATGTGTGGTACAAGGTCTTCTCTATGCGTTTATAATCCCAAATTCCCAATCCA
11868 T
1 T
11869 TTTAGATTTT
Statistics
Matches: 182, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 182 1.00
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (183 bp):
TATTCGGTTTGGCCTACTTCGCACGTGATCTAGGATAGTTTTACTCTTTAGGGAGAGGGAGTTTG
TTTGATGAGATAGGGGTTTGTTGGCTCATATGTTAGCTCGGTACGTTTTGGTACTGAAGCTAATA
ATGTGTGGTACAAGGTCTTCTCTATGCGTTTATAATCCCAAATTCCCAATCCA
Found at i:12665 original size:28 final size:28
Alignment explanation
Indices: 12628--12714 Score: 165
Period size: 28 Copynumber: 3.1 Consensus size: 28
12618 ATGTATACTT
12628 AAATAGAACTTAACAAAGATTGGAATTA
1 AAATAGAACTTAACAAAGATTGGAATTA
12656 AAATAGAACTTAACAAAGATTGGAATTA
1 AAATAGAACTTAACAAAGATTGGAATTA
*
12684 AAAAAGAACTTAACAAAGATTGGAATTA
1 AAATAGAACTTAACAAAGATTGGAATTA
12712 AAA
1 AAA
12715 AAAAACGATG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.56, C:0.07, G:0.14, T:0.23
Consensus pattern (28 bp):
AAATAGAACTTAACAAAGATTGGAATTA
Found at i:12689 original size:16 final size:16
Alignment explanation
Indices: 12637--12716 Score: 50
Period size: 16 Copynumber: 5.5 Consensus size: 16
12627 TAAATAGAAC
*
12637 TTAACAAAGATTGGAA
1 TTAAAAAAGATTGGAA
* *
12653 TTAAAATAGA----AC
1 TTAAAAAAGATTGGAA
*
12665 TTAACAAAGATTGGAA
1 TTAAAAAAGATTGGAA
*
12681 TTAAAAAAGA----AC
1 TTAAAAAAGATTGGAA
*
12693 TTAACAAAGATTGGAA
1 TTAAAAAAGATTGGAA
12709 TTAAAAAA
1 TTAAAAAA
12717 AAACGATGTG
Statistics
Matches: 45, Mismatches: 11, Indels: 16
0.62 0.15 0.22
Matches are distributed among these distances:
12 19 0.42
16 26 0.58
ACGTcount: A:0.56, C:0.06, G:0.14, T:0.24
Consensus pattern (16 bp):
TTAAAAAAGATTGGAA
Found at i:13053 original size:14 final size:14
Alignment explanation
Indices: 13034--13061 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13024 ATATATATAT
13034 ACTAGTAAATGCAC
1 ACTAGTAAATGCAC
13048 ACTAGTAAATGCAC
1 ACTAGTAAATGCAC
13062 GTGTGTTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
ACTAGTAAATGCAC
Found at i:13089 original size:13 final size:11
Alignment explanation
Indices: 13057--13098 Score: 84
Period size: 11 Copynumber: 3.8 Consensus size: 11
13047 CACTAGTAAA
13057 TGCACGTGTGT
1 TGCACGTGTGT
13068 TGCACGTGTGT
1 TGCACGTGTGT
13079 TGCACGTGTGT
1 TGCACGTGTGT
13090 TGCACGTGT
1 TGCACGTGT
13099 ATGTTAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.10, C:0.19, G:0.36, T:0.36
Consensus pattern (11 bp):
TGCACGTGTGT
Found at i:13215 original size:16 final size:16
Alignment explanation
Indices: 13194--13225 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
13184 TAAATCATAT
13194 ATATATAATAAAAATC
1 ATATATAATAAAAATC
13210 ATATATAATAAAAATC
1 ATATATAATAAAAATC
13226 TAAATTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (16 bp):
ATATATAATAAAAATC
Found at i:15276 original size:12 final size:12
Alignment explanation
Indices: 15261--15297 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
15251 TCAATTCAAA
15261 CAATCAGTCACC
1 CAATCAGTCACC
15273 CAATCAGTCACC
1 CAATCAGTCACC
15285 CAATCAGTCACC
1 CAATCAGTCACC
15297 C
1 C
15298 GAAGCTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.32, C:0.43, G:0.08, T:0.16
Consensus pattern (12 bp):
CAATCAGTCACC
Found at i:16447 original size:26 final size:27
Alignment explanation
Indices: 16396--16450 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
16386 CTTAATAAGT
* *
16396 GCCTTATATCCTTTTATAATTTTAGTA
1 GCCTTATAACCTTTAATAATTTTAGTA
16423 GCCTTATAACC-TTAATAATTTTAGTA
1 GCCTTATAACCTTTAATAATTTTAGTA
16449 GC
1 GC
16451 TTTCTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.45
Consensus pattern (27 bp):
GCCTTATAACCTTTAATAATTTTAGTA
Done.