Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021576.1 Corchorus olitorius cultivar O-4 contig21609, 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: 54008
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:499 original size:21 final size:21
Alignment explanation
Indices: 473--585 Score: 158
Period size: 21 Copynumber: 5.4 Consensus size: 21
463 TGCTAGAAGT
473 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
494 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
515 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
536 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
557 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
578 TCATTGGA
1 TCATTGGA
586 AATGCCTAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
20 1 0.01
21 84 0.99
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Found at i:617 original size:21 final size:21
Alignment explanation
Indices: 593--645 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
583 GGAAATGCCT
593 AAGATGCCATTTGATCCATTG
1 AAGATGCCATTTGATCCATTG
614 AAGATGCCATTTGATCCATTG
1 AAGATGCCATTTGATCCATTG
635 AAGATGCCATT
1 AAGATGCCATT
646 AGGCCCAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (21 bp):
AAGATGCCATTTGATCCATTG
Found at i:3747 original size:27 final size:27
Alignment explanation
Indices: 3690--3754 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
3680 AACAGTAAAC
* **
3690 TGCAAATGACCAAAATGCCCCTGGATG
1 TGCAAATGACCAAAATGCCCCTGAACA
*
3717 TGCAAATGACTAAAATGCCCCTGAACA
1 TGCAAATGACCAAAATGCCCCTGAACA
*
3744 TGCAAACGACC
1 TGCAAATGACC
3755 CCAAAATCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.37, C:0.28, G:0.18, T:0.17
Consensus pattern (27 bp):
TGCAAATGACCAAAATGCCCCTGAACA
Found at i:22455 original size:18 final size:18
Alignment explanation
Indices: 22424--22460 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
22414 CATTTGCTTA
*
22424 TATAACTATTATCTTAAT
1 TATAACTATCATCTTAAT
*
22442 TATAATTATCATCTTAAT
1 TATAACTATCATCTTAAT
22460 T
1 T
22461 TTATATTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (18 bp):
TATAACTATCATCTTAAT
Found at i:22631 original size:25 final size:24
Alignment explanation
Indices: 22584--22635 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 24
22574 ATTTCACATA
22584 AAATTTAAATATTTTAATAATGTCT
1 AAATTTAAATATTTTAATAATGT-T
22609 AAATTATAAATA-TTT-ATATATGTT
1 AAATT-TAAATATTTTAATA-ATGTT
22633 AAA
1 AAA
22636 ATAAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 7 0.28
25 12 0.48
26 6 0.24
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
AAATTTAAATATTTTAATAATGTT
Found at i:22803 original size:21 final size:21
Alignment explanation
Indices: 22777--22825 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
22767 CGCTGATTAC
* *
22777 AATCTCATCTGTACAGTATCT
1 AATCTCATCTATACAGTAACT
22798 AATCTCATCTATACAGTAACT
1 AATCTCATCTATACAGTAACT
22819 AATCTCA
1 AATCTCA
22826 CCATTTCAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (21 bp):
AATCTCATCTATACAGTAACT
Found at i:22966 original size:21 final size:21
Alignment explanation
Indices: 22941--22985 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
22931 TTTTAGGGAG
*
22941 TTGCTAAATACCGCCCCCTTT
1 TTGCTAAATACCGCCCCCCTT
** *
22962 TTGCTACTTACCTCCCCCCTT
1 TTGCTAAATACCGCCCCCCTT
22983 TTG
1 TTG
22986 ACACTTTTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.40, G:0.09, T:0.38
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCCCTT
Found at i:30653 original size:38 final size:37
Alignment explanation
Indices: 30602--30699 Score: 144
Period size: 38 Copynumber: 2.6 Consensus size: 37
30592 CCACGGGCTG
30602 TGCCGCCCTGTGAGGACGGCACGGCACGACCATGGGCA
1 TGCCGCCCTGTGAGGACGGCACGGCACGACCAT-GGCA
*
30640 TGCCGCCCTGTGAGGACGGCACGGCACGACCATGGCT
1 TGCCGCCCTGTGAGGACGGCACGGCACGACCATGGCA
* *
30677 TGCCGTCCC-CTGAAGACGGCACG
1 TGCCG-CCCTGTGAGGACGGCACG
30700 ACCATGGCTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
37 20 0.36
38 36 0.64
ACGTcount: A:0.17, C:0.36, G:0.35, T:0.12
Consensus pattern (37 bp):
TGCCGCCCTGTGAGGACGGCACGGCACGACCATGGCA
Found at i:30695 original size:37 final size:37
Alignment explanation
Indices: 30612--30726 Score: 143
Period size: 32 Copynumber: 3.2 Consensus size: 37
30602 TGCCGCCCTG
* *
30612 TGAGGACGGCACGGCACGACCATGGGCATGCCG-CCCTG
1 TGAGGACGGCACGGCACGACCAT-GGCTTGCCGTCCC-C
30650 TGAGGACGGCACGGCACGACCATGGCTTGCCGTCCCC
1 TGAGGACGGCACGGCACGACCATGGCTTGCCGTCCCC
*
30687 TGA--A--G-ACGGCACGACCATGGCTTGTCGTCCCC
1 TGAGGACGGCACGGCACGACCATGGCTTGCCGTCCCC
30719 TGAGGACG
1 TGAGGACG
30727 CCTCCGCGTT
Statistics
Matches: 69, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
32 29 0.42
33 1 0.01
34 1 0.01
35 1 0.01
37 11 0.16
38 26 0.38
ACGTcount: A:0.18, C:0.34, G:0.34, T:0.14
Consensus pattern (37 bp):
TGAGGACGGCACGGCACGACCATGGCTTGCCGTCCCC
Found at i:30778 original size:15 final size:15
Alignment explanation
Indices: 30743--30778 Score: 58
Period size: 13 Copynumber: 2.5 Consensus size: 15
30733 CGTTAGGATC
30743 AATTTTTAAAAAAAT
1 AATTTTTAAAAAAAT
30758 AA--TTTAAAAAAAT
1 AATTTTTAAAAAAAT
30771 AATTTTTA
1 AATTTTTA
30779 TATTAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.68
15 6 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTTTTAAAAAAAT
Found at i:32660 original size:41 final size:43
Alignment explanation
Indices: 32609--32688 Score: 137
Period size: 41 Copynumber: 1.9 Consensus size: 43
32599 GACATGTTTG
*
32609 TAATTGTTATTGTATGTAA-TTTTGTAAGTAAT-TTTTTATGT
1 TAATTATTATTGTATGTAATTTTTGTAAGTAATATTTTTATGT
32650 TAATTATTATTGTATGTAATTTTTGTAAGTAATATTTTT
1 TAATTATTATTGTATGTAATTTTTGTAAGTAATATTTTT
32689 TTGTAAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
41 18 0.50
42 13 0.36
43 5 0.14
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (43 bp):
TAATTATTATTGTATGTAATTTTTGTAAGTAATATTTTTATGT
Found at i:32681 original size:13 final size:13
Alignment explanation
Indices: 32618--32687 Score: 63
Period size: 13 Copynumber: 5.2 Consensus size: 13
32608 GTAATTGTTA
32618 TTGTATGTAA-TT
1 TTGTATGTAATTT
*
32630 TTGTAAGTAATTT
1 TTGTATGTAATTT
32643 TT-TATGTTAATTATT
1 TTGTATG-TAA-T-TT
32658 ATTGTATGTAATTT
1 -TTGTATGTAATTT
*
32672 TTGTAAGTAATATT
1 TTGTATGTAAT-TT
32686 TT
1 TT
32688 TTTGTAAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
12 12 0.25
13 17 0.35
14 7 0.15
15 3 0.06
16 5 0.10
17 4 0.08
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.59
Consensus pattern (13 bp):
TTGTATGTAATTT
Found at i:32691 original size:17 final size:17
Alignment explanation
Indices: 32669--32703 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
32659 TTGTATGTAA
*
32669 TTTTTGTAAGTAATATT
1 TTTTTGTAAATAATATT
32686 TTTTTGTAAATAATATT
1 TTTTTGTAAATAATATT
32703 T
1 T
32704 GTCGTTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (17 bp):
TTTTTGTAAATAATATT
Found at i:32805 original size:28 final size:28
Alignment explanation
Indices: 32763--32818 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
32753 GACACGACCA
*
32763 TGGTGAGATGCCCTCAGGAGGCGGCACG
1 TGGTGAGATGCCCTCAGGAGGCGACACG
*
32791 TGGTGAGATGTCCTCAGGAGGCGACACG
1 TGGTGAGATGCCCTCAGGAGGCGACACG
32819 GGTCATCAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.23, G:0.41, T:0.16
Consensus pattern (28 bp):
TGGTGAGATGCCCTCAGGAGGCGACACG
Found at i:34357 original size:65 final size:64
Alignment explanation
Indices: 34253--34376 Score: 176
Period size: 65 Copynumber: 1.9 Consensus size: 64
34243 GCATGCTATT
* * ** *
34253 GATTCCAATTTTCTGCACTAGCCCTTGCATGGGTTGGCCAAGGGTACCCCATGCATGGGTTGGAC
1 GATTCAAACTTTCTGCACTAGCCCAGGCATGGGTTGGCC-AGAGTACCCCATGCATGGGTTGGAC
* *
34318 GATTCAAACTTTCTGCACTAGCTCAGGCGTGGGTTGGCCAGAGTACCCCATGCATGGGT
1 GATTCAAACTTTCTGCACTAGCCCAGGCATGGGTTGGCCAGAGTACCCCATGCATGGGT
34377 AGGAACAGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
64 19 0.37
65 33 0.63
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.27
Consensus pattern (64 bp):
GATTCAAACTTTCTGCACTAGCCCAGGCATGGGTTGGCCAGAGTACCCCATGCATGGGTTGGAC
Found at i:34597 original size:24 final size:24
Alignment explanation
Indices: 34564--34611 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
34554 AAGGAGTAGG
*
34564 ATCTTTCCTTGCTCATTCCTTTAA
1 ATCTTGCCTTGCTCATTCCTTTAA
*
34588 ATCTTGCCTTGCTCCTTCCTTTAA
1 ATCTTGCCTTGCTCATTCCTTTAA
34612 GCTTAGCCGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.15, C:0.31, G:0.06, T:0.48
Consensus pattern (24 bp):
ATCTTGCCTTGCTCATTCCTTTAA
Found at i:36149 original size:14 final size:14
Alignment explanation
Indices: 36130--36168 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 14
36120 TATGATAATT
36130 ATATTTTAGCATAC
1 ATATTTTAGCATAC
36144 ATATTTTTTTAGCATAC
1 ATA---TTTTAGCATAC
36161 ATATTTTA
1 ATATTTTA
36169 TTTTATGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 8 0.36
17 14 0.64
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.51
Consensus pattern (14 bp):
ATATTTTAGCATAC
Found at i:36155 original size:17 final size:17
Alignment explanation
Indices: 36133--36167 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
36123 GATAATTATA
36133 TTTTAGCATACATATTT
1 TTTTAGCATACATATTT
36150 TTTTAGCATACATATTT
1 TTTTAGCATACATATTT
36167 T
1 T
36168 ATTTTATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTTAGCATACATATTT
Found at i:40015 original size:35 final size:35
Alignment explanation
Indices: 39975--40069 Score: 109
Period size: 35 Copynumber: 2.7 Consensus size: 35
39965 CTCTACCGTT
*
39975 CGTGTGCATCTCCCGCACACCATAACAATAATAAT
1 CGTGTGCATCTCCCGCACACCATAACAATAATAAC
* * * * **
40010 TGTGTGCACCTCCCGCACACTATCATGATAATAAC
1 CGTGTGCATCTCCCGCACACCATAACAATAATAAC
* *
40045 CATGTGCATCTCCCGCACAACATAA
1 CGTGTGCATCTCCCGCACACCATAA
40070 TGTCTGTGTA
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.32, C:0.33, G:0.13, T:0.23
Consensus pattern (35 bp):
CGTGTGCATCTCCCGCACACCATAACAATAATAAC
Found at i:40126 original size:29 final size:29
Alignment explanation
Indices: 40046--40192 Score: 125
Period size: 29 Copynumber: 5.1 Consensus size: 29
40036 GATAATAACC
* *
40046 ATGTGCATCTCCCGCACAAC-ATAATGTCT
1 ATGTGCATCTCCCGCACACCAAT-ATGTAT
* * * * * * **
40075 GTGTACTTCTCCAGAACATCAATACATAT
1 ATGTGCATCTCCCGCACACCAATATGTAT
* *
40104 ATGCGCATCTCCCGCCCACCAATATGTAT
1 ATGTGCATCTCCCGCACACCAATATGTAT
* *
40133 ATGTGCATCTCTCGCACACTAATATGTAT
1 ATGTGCATCTCCCGCACACCAATATGTAT
* * *
40162 GTGTGCATCTCCCGCACACTAATATGCAT
1 ATGTGCATCTCCCGCACACCAATATGTAT
40191 AT
1 AT
40193 CTTTGTTCTT
Statistics
Matches: 90, Mismatches: 27, Indels: 2
0.76 0.23 0.02
Matches are distributed among these distances:
29 88 0.98
30 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (29 bp):
ATGTGCATCTCCCGCACACCAATATGTAT
Found at i:41874 original size:37 final size:37
Alignment explanation
Indices: 41827--41900 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
41817 TCAGAACAAG
41827 CTCTCGGGGGATATGGCGTTGGGGTAGCAGTGGGGCT
1 CTCTCGGGGGATATGGCGTTGGGGTAGCAGTGGGGCT
41864 CTCTCGGGGGATATGGCGTTGGGGTAGCAGTGGGGCT
1 CTCTCGGGGGATATGGCGTTGGGGTAGCAGTGGGGCT
41901 GATTCTTGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.11, C:0.16, G:0.49, T:0.24
Consensus pattern (37 bp):
CTCTCGGGGGATATGGCGTTGGGGTAGCAGTGGGGCT
Found at i:45200 original size:11 final size:11
Alignment explanation
Indices: 45184--45222 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
45174 AATTAGCATG
45184 AAAAAAAGGTT
1 AAAAAAAGGTT
45195 AAAAAAAGG--
1 AAAAAAAGGTT
45204 --AAAAAGGTT
1 AAAAAAAGGTT
45213 AAAAAAAGGT
1 AAAAAAAGGT
45223 GCCCCATGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
7 7 0.29
11 17 0.71
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.13
Consensus pattern (11 bp):
AAAAAAAGGTT
Found at i:45209 original size:18 final size:18
Alignment explanation
Indices: 45186--45221 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
45176 TTAGCATGAA
45186 AAAAAGGTTAAAAAAAGG
1 AAAAAGGTTAAAAAAAGG
45204 AAAAAGGTTAAAAAAAGG
1 AAAAAGGTTAAAAAAAGG
45222 TGCCCCATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.11
Consensus pattern (18 bp):
AAAAAGGTTAAAAAAAGG
Found at i:48147 original size:20 final size:19
Alignment explanation
Indices: 48109--48147 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
48099 GCCTCTTCTC
*
48109 CTCTTCTCTCGATACCCCA
1 CTCTTCTCTCGATAACCCA
*
48128 CTCTCTCTCTCGTTAACCCA
1 CTCT-TCTCTCGATAACCCA
48148 TAATTTTGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.15, C:0.46, G:0.05, T:0.33
Consensus pattern (19 bp):
CTCTTCTCTCGATAACCCA
Found at i:49124 original size:19 final size:19
Alignment explanation
Indices: 49089--49147 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
49079 CGTTTGATTA
49089 ATATTAT-TATTACTTATATT
1 ATATTATAT-TTA-TTATATT
49109 ATATTATATTTATTAT-TT
1 ATATTATATTTATTATATT
49127 ATAATTATATTTATTA-ATT
1 AT-ATTATATTTATTATATT
49146 AT
1 AT
49148 TCGTCTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
18 4 0.11
19 21 0.58
20 10 0.28
21 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATTATATTTATTATATT
Found at i:49128 original size:23 final size:23
Alignment explanation
Indices: 49095--49148 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
49085 ATTAATATTA
*
49095 TTATTACTTAT-ATTATATTATAT
1 TTATTATTTATAATTATATT-TAT
49118 TTATTATTTATAATTATATTTAT
1 TTATTATTTATAATTATATTTAT
*
49141 TAATTATT
1 TTATTATT
49149 CGTCTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
TTATTATTTATAATTATATTTAT
Found at i:50261 original size:21 final size:21
Alignment explanation
Indices: 50187--50263 Score: 91
Period size: 22 Copynumber: 3.6 Consensus size: 21
50177 TATTTTTATG
*
50187 AAATTTTGATAATTATCCTATT
1 AAATTTTGATAATTA-CCTATA
** *
50209 AAATTTTGATAACCACCATATG
1 AAATTTTGATAATTACC-TATA
50231 AAATTTTGATAATTACCTATA
1 AAATTTTGATAATTACCTATA
*
50252 AAATTGTGATAA
1 AAATTTTGATAA
50264 ACTCCATAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
21 16 0.34
22 31 0.66
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (21 bp):
AAATTTTGATAATTACCTATA
Found at i:50271 original size:43 final size:44
Alignment explanation
Indices: 50183--50285 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 44
50173 TGAATATTTT
* * *
50183 TATGAAATTTTGATAATTATCCTATTAAATTTTGATAACCACCA
1 TATGAAATTTTGATAATTATCCTATAAAATTGTGATAAACACCA
*
50227 TATGAAATTTTGATAATTA-CCTATAAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAATTATCCTATAAAATTGTGATAAACACCA
* *
50270 TAAGAAACTTTGATAA
1 TATGAAATTTTGATAA
50286 CCTAACTATG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 34 0.64
44 19 0.36
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAATTATCCTATAAAATTGTGATAAACACCA
Found at i:50336 original size:20 final size:21
Alignment explanation
Indices: 50183--50379 Score: 89
Period size: 22 Copynumber: 9.1 Consensus size: 21
50173 TGAATATTTT
50183 TATGAAATTTTGATAAT-TATCC
1 TATG-AATTTTGATAATCT-TCC
* **
50205 TATTAAATTTTGATAA-CCACC
1 TA-TGAATTTTGATAATCTTCC
*
50226 ATATGAAATTTTGATAAT-TACC
1 -TATG-AATTTTGATAATCTTCC
* * *
50248 TATAAAATTGTGATAAAC-TCC
1 TAT-GAATTTTGATAATCTTCC
* * * **
50269 ATAAGAAACTTTGATAACCTAAC
1 -TATG-AATTTTGATAATCTTCC
* *
50292 TATGAAATTTTAATAAACTTTCC
1 TATG-AATTTTGATAATC-TTCC
50315 TATGAATTTTG-TAATCTTCC
1 TATGAATTTTGATAATCTTCC
* **
50335 TATGATTTTTGATAATCTTTG
1 TATGAATTTTGATAATCTTCC
* *
50356 TATGAGATTTTGTTAATCTCCC
1 TATGA-ATTTTGATAATCTTCC
50378 TA
1 TA
50380 CAATTTTTTT
Statistics
Matches: 130, Mismatches: 32, Indels: 26
0.69 0.17 0.14
Matches are distributed among these distances:
20 14 0.11
21 34 0.26
22 74 0.57
23 8 0.06
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (21 bp):
TATGAATTTTGATAATCTTCC
Found at i:50372 original size:22 final size:20
Alignment explanation
Indices: 50311--50379 Score: 75
Period size: 20 Copynumber: 3.3 Consensus size: 20
50301 TTAATAAACT
50311 TTCCTATGAATTTTGTAATC
1 TTCCTATGAATTTTGTAATC
*
50331 TTCCTATGATTTTTGATAATC
1 TTCCTATGAATTTTG-TAATC
**
50352 TTTGTATGAGATTTTGTTAATC
1 TTCCTATGA-ATTTTG-TAATC
*
50374 TCCCTA
1 TTCCTA
50380 CAATTTTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 14 0.36
21 12 0.31
22 13 0.33
ACGTcount: A:0.23, C:0.14, G:0.12, T:0.51
Consensus pattern (20 bp):
TTCCTATGAATTTTGTAATC
Found at i:51094 original size:32 final size:33
Alignment explanation
Indices: 51027--51094 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
51017 GTCATAATGT
*
51027 AAAGGTTTTAACATCGACATTTACTAGTTGTTA
1 AAAGGTTTTAACAACGACATTTACTAGTTGTTA
* * *
51060 AAAGGTTTTAGCAACGCCATTT-CTCGTTGTTA
1 AAAGGTTTTAACAACGACATTTACTAGTTGTTA
51092 AAA
1 AAA
51095 TATATAGACA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 12 0.39
33 19 0.61
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (33 bp):
AAAGGTTTTAACAACGACATTTACTAGTTGTTA
Found at i:51190 original size:20 final size:20
Alignment explanation
Indices: 51165--51209 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
51155 GCAGCGGATG
51165 CTTAAGTCGTTG-TGTTAGAT
1 CTTAAGTCGTTGCT-TTAGAT
51185 CTTAAGTCGTTGCTTTAGAT
1 CTTAAGTCGTTGCTTTAGAT
*
51205 ATTAA
1 CTTAA
51210 ACAACAGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.44
Consensus pattern (20 bp):
CTTAAGTCGTTGCTTTAGAT
Done.