Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016268.1 Corchorus olitorius cultivar O-4 contig16301, 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: 27267
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:889 original size:178 final size:178
Alignment explanation
Indices: 599--928 Score: 443
Period size: 178 Copynumber: 1.9 Consensus size: 178
589 CCGATTAAAC
* *
599 TGATTTAAGTGTCTATTAAAAAATTGTTCCATCATCTACAGCTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAAATTGTTCCATCATCTACAACTTTCATGAAGGACTCGAAAACTA
* * * *
664 AATTTAATGTTTCAAGTATCAAAAATGCTTCTGAAAAATTTGTTGTTTCGGTTAACGGGAATAAA
66 AATTTAATGTTTCAAGTATCAAAAATGCTTCTCAAAAATTAGTTGTTTCGGTTAAAGGAAATAAA
* *
729 CAGTCCAGTTAATATTATATAACTTTTGCTCCAGATGTGTAATTGAGA
131 CAGTCCACTTAATATTACATAACTTTTGCTCCAGATGTGTAATTGAGA
* * ** *
777 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGAACGG-CTCGAAAACT
1 TGATTCAAGTGTCTATTAAAAAATTGTTCCATCATCTACAACTTTCATGAA-GGACTCGAAAACT
*
841 AAATTTAATG-TTCGAGGTAT-AAAAATTGCTTC-CAAAGAATTAGTTGTTTCGGTTAAAGGAAA
65 AAATTTAATGTTTC-AAGTATCAAAAA-TGCTTCTCAAA-AATTAGTTGTTTCGGTTAAAGGAAA
* * *
903 TAGACGGTCTACTTAATATTACATAA
127 TAAACAGTCCACTTAATATTACATAA
929 TTTGTGTTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
177 11 0.08
178 118 0.90
179 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAAATTGTTCCATCATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATCAAAAATGCTTCTCAAAAATTAGTTGTTTCGGTTAAAGGAAATAAA
CAGTCCACTTAATATTACATAACTTTTGCTCCAGATGTGTAATTGAGA
Found at i:2594 original size:31 final size:31
Alignment explanation
Indices: 2559--2651 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
2549 TTTTTCTGTT
2559 TTTAGACTCAAATTGAGTAATTTTTAAAATG
1 TTTAGACTCAAATTGAGTAATTTTTAAAATG
* ** * * *
2590 TTTAGACTCCAATTGAACAACTTTTGAAAGG
1 TTTAGACTCAAATTGAGTAATTTTTAAAATG
** *
2621 TTTAGGTTCAAATTG-GTAATTTGATAAAATG
1 TTTAGACTCAAATTGAGTAATTT-TTAAAATG
2652 GAAATGTAAG
Statistics
Matches: 46, Mismatches: 15, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
30 4 0.09
31 42 0.91
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTAGACTCAAATTGAGTAATTTTTAAAATG
Found at i:10426 original size:6 final size:6
Alignment explanation
Indices: 10417--10449 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
10407 AATGTGGAAA
10417 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTT
10450 TTATTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTAAT
Found at i:10832 original size:14 final size:15
Alignment explanation
Indices: 10813--10875 Score: 62
Period size: 14 Copynumber: 4.5 Consensus size: 15
10803 ATGGTTCAGA
10813 TTCAATTGTG-ACGG
1 TTCAATTGTGAACGG
* *
10827 TTCAATT-TGAATGA
1 TTCAATTGTGAACGG
*
10841 TTCAATTGTG-ACCG
1 TTCAATTGTGAACGG
*
10855 TTCAATTG-GAATGG
1 TTCAATTGTGAACGG
10869 TTCAATT
1 TTCAATT
10876 CAATTGTGAC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
13 3 0.08
14 34 0.87
15 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.40
Consensus pattern (15 bp):
TTCAATTGTGAACGG
Found at i:10843 original size:28 final size:28
Alignment explanation
Indices: 10811--10875 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
10801 GAATGGTTCA
* *
10811 GATTCAATTGTGACGGTTCAATTTGAAT
1 GATTCAATTGTGACCGTTCAATTGGAAT
10839 GATTCAATTGTGACCGTTCAATTGGAAT
1 GATTCAATTGTGACCGTTCAATTGGAAT
*
10867 GGTTCAATT
1 GATTCAATT
10876 CAATTGTGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (28 bp):
GATTCAATTGTGACCGTTCAATTGGAAT
Found at i:12119 original size:15 final size:15
Alignment explanation
Indices: 12099--12145 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
12089 GTAGTCACAT
12099 TGAGTCAACTAATCC
1 TGAGTCAACTAATCC
*
12114 TGAGTCCAC--AT--
1 TGAGTCAACTAATCC
12125 TGAGTCAACTAATCC
1 TGAGTCAACTAATCC
12140 TGAGTC
1 TGAGTC
12146 CAGCCGTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
11 8 0.31
13 4 0.15
15 14 0.54
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (15 bp):
TGAGTCAACTAATCC
Found at i:12123 original size:26 final size:26
Alignment explanation
Indices: 12094--12147 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
12084 ATCCAGTAGT
12094 CACATTGAGTCAACTAATCCTGAGTC
1 CACATTGAGTCAACTAATCCTGAGTC
12120 CACATTGAGTCAACTAATCCTGAGTC
1 CACATTGAGTCAACTAATCCTGAGTC
12146 CA
1 CA
12148 GCCGTATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (26 bp):
CACATTGAGTCAACTAATCCTGAGTC
Found at i:26015 original size:163 final size:164
Alignment explanation
Indices: 25743--26054 Score: 475
Period size: 163 Copynumber: 1.9 Consensus size: 164
25733 TTCCATTGAT
* **
25743 CTCCAAAACTCTTACTCTTTATCTTGCTTCTCAGTATTCTATCTCAGGTTGAAGCTTCTGATTAG
1 CTCCAAAACTCTTACTCATTATCTTGCTTCTCAGTATTCTATCTCAGGTTGAAGCTTCTGAACAG
* * **
25808 GTTTTGTCTTTATCCTTAGAAGCTACATTTTGTTTACCCCTGTTTTGTTTGTGAACCATTTAAAT
66 GTTTTCTCTTTATCCTTAGAAGCTACATTTTGTTTACCCCTGTTTTGTCTACGAACCATTTAAAT
*
25873 GCTTTGTGCTTTGGAAATCTATGTTTTTTTGTAC
131 GCTATGTGCTTTGGAAATCTATGTTTTTTTGTAC
*
25907 CTCCAAAACTCTTACTCATTATCTTGCTTCTCAG-ATTCTGTCTC-GGTTTGAAGCTTCTGAACA
1 CTCCAAAACTCTTACTCATTATCTTGCTTCTCAGTATTCTATCTCAGG-TTGAAGCTTCTGAACA
* * * *
25970 GGTTTTCTCTTTGTCTTTAGAAGCTATATTTTGTTTACTCCTGTTTTGTCTACGAACCATTTAAA
65 GGTTTTCTCTTTATCCTTAGAAGCTACATTTTGTTTACCCCTGTTTTGTCTACGAACCATTTAAA
*
26035 TGGTATGTGCTTTGGAAATC
130 TGCTATGTGCTTTGGAAATC
26055 CATGCTTCTG
Statistics
Matches: 133, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
162 2 0.02
163 98 0.74
164 33 0.25
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (164 bp):
CTCCAAAACTCTTACTCATTATCTTGCTTCTCAGTATTCTATCTCAGGTTGAAGCTTCTGAACAG
GTTTTCTCTTTATCCTTAGAAGCTACATTTTGTTTACCCCTGTTTTGTCTACGAACCATTTAAAT
GCTATGTGCTTTGGAAATCTATGTTTTTTTGTAC
Done.