Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012718.1 Corchorus olitorius cultivar O-4 contig12751, 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: 23072
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7123 original size:32 final size:32
Alignment explanation
Indices: 7051--7124 Score: 89
Period size: 34 Copynumber: 2.3 Consensus size: 32
7041 CCAATTTCAT
*
7051 AAGC-AAAACAGAGACATTTCGAAAGCTATTTTG
1 AAGCAAAAACAGAGACATTTCGAAACCTA--TTG
*
7084 AAGCAAAAACAGAGGCATTTCGAAACCCTA-TG
1 AAGCAAAAACAGAGACATTTCGAAA-CCTATTG
7116 AAGCAAAAA
1 AAGCAAAAA
7125 AGATTCATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
32 11 0.30
33 4 0.11
34 19 0.51
35 3 0.08
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (32 bp):
AAGCAAAAACAGAGACATTTCGAAACCTATTG
Found at i:8155 original size:17 final size:18
Alignment explanation
Indices: 8130--8170 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
8120 GGTGTCCTTG
*
8130 TTTTGCCATT-TTCTTTA
1 TTTTTCCATTATTCTTTA
*
8147 TTTTTCCATTATTCTTTG
1 TTTTTCCATTATTCTTTA
8165 TTTTTC
1 TTTTTC
8171 AACATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.10, C:0.17, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTTCCATTATTCTTTA
Found at i:9634 original size:2 final size:2
Alignment explanation
Indices: 9601--9626 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9591 TCAGATAAAC
9601 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
9627 TGTATATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10803 original size:26 final size:26
Alignment explanation
Indices: 10767--10819 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
10757 ATTGGTACTG
10767 TAAAAATTGAATTATTCTAAACAAAA
1 TAAAAATTGAATTATTCTAAACAAAA
* *
10793 TAAAAATTGAATTTTTCTAAATAAAA
1 TAAAAATTGAATTATTCTAAACAAAA
10819 T
1 T
10820 TTTTTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.36
Consensus pattern (26 bp):
TAAAAATTGAATTATTCTAAACAAAA
Found at i:15719 original size:29 final size:29
Alignment explanation
Indices: 15687--15744 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
15677 TAATCTTGAG
15687 ACGAAAATTTTGGCTAATTAAAGTTGGAT
1 ACGAAAATTTTGGCTAATTAAAGTTGGAT
15716 ACGAAAATTTTGGCTAATTAAAGTTGGAT
1 ACGAAAATTTTGGCTAATTAAAGTTGGAT
15745 CAGCAACGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (29 bp):
ACGAAAATTTTGGCTAATTAAAGTTGGAT
Found at i:17823 original size:75 final size:75
Alignment explanation
Indices: 17654--17823 Score: 164
Period size: 75 Copynumber: 2.3 Consensus size: 75
17644 ATTCTCCTTC
* * * *
17654 TCAGGTTGCTAATTCGAATTCAAATAATGAGTTTGCTGATGGTGTTAGGCAAAATCTTGAAGTTG
1 TCAGGTTCCTAATTCGAATTCAAATAATAAGTTTGCTGATGATGTTAGGCAAAATCTTGAAGCTG
17719 ATTCACCTGA
66 ATTCACCTGA
* * ** * * * *
17729 CCAGATTCCTCTTTTGAATTCAAATACTAAGTTTTCTGATGATGATT-TGCAACAA-CTTGAAGC
1 TCAGGTTCCTAATTCGAATTCAAATAATAAGTTTGCTGATGATG-TTAGGCAA-AATCTTGAAGC
* *
17792 TGATTCACTTTA
64 TGATTCACCTGA
* *
17804 TCAGGTTTCTGATTCGAATT
1 TCAGGTTCCTAATTCGAATT
17824 TAAAATTTGA
Statistics
Matches: 73, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
75 69 0.95
76 4 0.05
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (75 bp):
TCAGGTTCCTAATTCGAATTCAAATAATAAGTTTGCTGATGATGTTAGGCAAAATCTTGAAGCTG
ATTCACCTGA
Found at i:18461 original size:23 final size:23
Alignment explanation
Indices: 18431--18474 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
18421 TGGAGGAAGA
18431 GGGTTAGTGGTGACTGTTTTGAT
1 GGGTTAGTGGTGACTGTTTTGAT
18454 GGGTTAGTGGTGACTGTTTTG
1 GGGTTAGTGGTGACTGTTTTG
18475 GTGCATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.05, G:0.41, T:0.43
Consensus pattern (23 bp):
GGGTTAGTGGTGACTGTTTTGAT
Found at i:22074 original size:22 final size:22
Alignment explanation
Indices: 22048--22089 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
22038 AACAGTCTGC
*
22048 ATATAAGATCATCTAAACAAGA
1 ATATAAGATAATCTAAACAAGA
22070 ATATAAGATAATCTAAACAA
1 ATATAAGATAATCTAAACAA
22090 AAAAATAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.24
Consensus pattern (22 bp):
ATATAAGATAATCTAAACAAGA
Done.