Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000554.1 Hibiscus syriacus cultivar Beakdansim tig00001080_pilon, 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: 74632
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:686 original size:20 final size:21
Alignment explanation
Indices: 663--702 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
653 ATATTACCAT
*
663 CATTTCAT-TTCCACAACATC
1 CATTTCATCTGCCACAACATC
683 CATTTCATCTGCCACAACAT
1 CATTTCATCTGCCACAACAT
703 TCTCATTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.30, C:0.35, G:0.03, T:0.33
Consensus pattern (21 bp):
CATTTCATCTGCCACAACATC
Found at i:1944 original size:20 final size:20
Alignment explanation
Indices: 1919--1970 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1909 ACTAAAGCAA
*
1919 CTATATGCACCTAAAATGAC
1 CTATATGAACCTAAAATGAC
*
1939 CTATATAAACCTAAAATGAC
1 CTATATGAACCTAAAATGAC
1959 CTATATGAACCT
1 CTATATGAACCT
1971 TTAGACAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (20 bp):
CTATATGAACCTAAAATGAC
Found at i:2153 original size:23 final size:22
Alignment explanation
Indices: 2117--2165 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
2107 CAAGGTTAAC
2117 ATTT-TAAGGTTAATGATTACG
1 ATTTATAAGGTTAATGATTACG
*
2138 ATTTATAAGGATTAATGTTTACG
1 ATTTATAAGG-TTAATGATTACG
2161 ATTTA
1 ATTTA
2166 GGTTAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.16
22 5 0.20
23 16 0.64
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTTATAAGGTTAATGATTACG
Found at i:7403 original size:27 final size:27
Alignment explanation
Indices: 7365--7417 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
7355 CGGTTCTCAT
7365 TTGGTTTTCTGGTTCTTGTAAGGGGTG
1 TTGGTTTTCTGGTTCTTGTAAGGGGTG
7392 TTGGTTTTCTGGTTCTTGTAAGGGGT
1 TTGGTTTTCTGGTTCTTGTAAGGGGT
7418 ATTACTGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.08, C:0.08, G:0.36, T:0.49
Consensus pattern (27 bp):
TTGGTTTTCTGGTTCTTGTAAGGGGTG
Found at i:12654 original size:48 final size:49
Alignment explanation
Indices: 12566--12667 Score: 143
Period size: 48 Copynumber: 2.1 Consensus size: 49
12556 ATGCACATCT
* *
12566 CCAACCTAAAAATAAATATATACTTACACCGGTGTAAGTATGTATATATC
1 CCAACCTAAAAATAAACACATAC-TACACCGGTGTAAGTATGTATATATC
* * *
12616 CCAACCTAAAAATAAGCACATAC-ACACCTGTGTAAGTATGTATATCTC
1 CCAACCTAAAAATAAACACATACTACACCGGTGTAAGTATGTATATATC
12664 CCAA
1 CCAA
12668 TATTTTAGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 27 0.57
50 20 0.43
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26
Consensus pattern (49 bp):
CCAACCTAAAAATAAACACATACTACACCGGTGTAAGTATGTATATATC
Found at i:13935 original size:27 final size:29
Alignment explanation
Indices: 13905--13960 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
13895 TACAAAAGAG
*
13905 CATATTAAATTA-TTTAACTACA-TAAAT
1 CATAATAAATTATTTTAACTACATTAAAT
* *
13932 CATAATAACTTATTTTAATTACATTAAAT
1 CATAATAAATTATTTTAACTACATTAAAT
13961 GTTATATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 10 0.42
28 9 0.38
29 5 0.21
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (29 bp):
CATAATAAATTATTTTAACTACATTAAAT
Found at i:14665 original size:19 final size:19
Alignment explanation
Indices: 14619--14665 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
14609 ATTTTATGCA
14619 ATTATTTTATTTTAGTATTT
1 ATTA-TTTATTTTAGTATTT
* *
14639 ATTTTTTATTTT-TTATTT
1 ATTATTTATTTTAGTATTT
14657 GATTATTTA
1 -ATTATTTA
14666 ATTGTAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 5 0.22
19 15 0.65
20 3 0.13
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (19 bp):
ATTATTTATTTTAGTATTT
Found at i:15687 original size:2 final size:2
Alignment explanation
Indices: 15680--15821 Score: 284
Period size: 2 Copynumber: 71.0 Consensus size: 2
15670 ATAGAATGAC
15680 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
15722 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
15764 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
15806 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
15822 TAAATAGATG
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 140 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16981 original size:24 final size:24
Alignment explanation
Indices: 16954--17014 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
16944 TGAGAGTGAT
16954 GATGACGATGAGAAAAACGACGAC
1 GATGACGATGAGAAAAACGACGAC
* * * ** *
16978 GATGAGGATAAGGATGACGACGTC
1 GATGACGATGAGAAAAACGACGAC
*
17002 GATGATGATGAGA
1 GATGACGATGAGA
17015 GTAAAGAGGA
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.34, T:0.15
Consensus pattern (24 bp):
GATGACGATGAGAAAAACGACGAC
Found at i:16996 original size:18 final size:18
Alignment explanation
Indices: 16954--16997 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
16944 TGAGAGTGAT
16954 GATGACGATGAGAAAAAC
1 GATGACGATGAGAAAAAC
* * * *
16972 GACGACGATGAGGATAAG
1 GATGACGATGAGAAAAAC
16990 GATGACGA
1 GATGACGA
16998 CGTCGATGAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.11, G:0.34, T:0.11
Consensus pattern (18 bp):
GATGACGATGAGAAAAAC
Found at i:17141 original size:26 final size:26
Alignment explanation
Indices: 17105--17157 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
17095 CAAGGAGACA
*
17105 TCGATAGATCTAATAAAATTGTAATC
1 TCGATAAATCTAATAAAATTGTAATC
17131 TCGATAAATCTAATAAAATTGTAATC
1 TCGATAAATCTAATAAAATTGTAATC
17157 T
1 T
17158 TTTTCATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (26 bp):
TCGATAAATCTAATAAAATTGTAATC
Found at i:17541 original size:2 final size:2
Alignment explanation
Indices: 17534--17558 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17524 AAAAAGGTGA
17534 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
17559 ATTTATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24163 original size:38 final size:32
Alignment explanation
Indices: 24091--24151 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
24081 TTGAATTACA
*
24091 TAGTCCAATATCCAAACATAATTAAAAAATGT
1 TAGTCCAACATCCAAACATAATTAAAAAATGT
24123 TAGTCCAACATCCAAACATAATTAAAAAA
1 TAGTCCAACATCCAAACATAATTAAAAAA
24152 ATGTCATGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.25
Consensus pattern (32 bp):
TAGTCCAACATCCAAACATAATTAAAAAATGT
Found at i:24318 original size:37 final size:36
Alignment explanation
Indices: 24277--24459 Score: 111
Period size: 37 Copynumber: 5.3 Consensus size: 36
24267 ATAATATATA
24277 AGTGACCAAATAGCTAGTTTACCCTAAATAATAATCG
1 AGTGACCAAATAG-TAGTTTACCCTAAATAATAATCG
*** * *
24314 AGTGACCAAA-A-TA---TAAATTAGATAATATAT-A
1 AGTGACCAAATAGTAGTTTACCCTAAATAATA-ATCG
24345 AGTGACCAAATAAGTAGTTTACCCTAAATAATAATCG
1 AGTGACCAAAT-AGTAGTTTACCCTAAATAATAATCG
* * * ** *
24382 GGTGACCAAA-ACATAGATTA-GAT-AATATTAA---
1 AGTGACCAAATA-GTAGTTTACCCTAAATAATAATCG
* * *
24413 AGTGACCATATAGGTAGTTTACCCTAAAAAACAATCG
1 AGTGACCAAATA-GTAGTTTACCCTAAATAATAATCG
24450 AGTGACCAAA
1 AGTGACCAAA
24460 ACATAAATTA
Statistics
Matches: 104, Mismatches: 27, Indels: 30
0.65 0.17 0.19
Matches are distributed among these distances:
31 28 0.27
32 9 0.09
33 2 0.02
34 16 0.15
35 2 0.02
36 9 0.09
37 38 0.37
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (36 bp):
AGTGACCAAATAGTAGTTTACCCTAAATAATAATCG
Found at i:24343 original size:68 final size:68
Alignment explanation
Indices: 24234--24508 Score: 444
Period size: 68 Copynumber: 4.0 Consensus size: 68
24224 ATTTTGAAAA
* *
24234 AAATAATAATCGAGTGAACAAAACATAAATTAGATAATATATAAGTGACCAAATAGCTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
24299 CCT
66 CCT
* *
24302 AAATAATAATCGAGTGACCAAAATATAAATTAGATAATATATAAGTGACCAAATAAGTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
24367 CCT
66 CCT
* * *
24370 AAATAATAATCGGGTGACCAAAACATAGATTAGATAATAT-TAAAGTGACCATATAGGTAGTTTA
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATAT-AAGTGACCAAATAGGTAGTTTA
24434 CCCT
65 CCCT
* * *
24438 AAAAAACAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCCAATAGGTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
24503 CCT
66 CCT
24506 AAA
1 AAA
24509 AAAATCCCTA
Statistics
Matches: 190, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
67 1 0.01
68 188 0.99
69 1 0.01
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (68 bp):
AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
CCT
Found at i:24349 original size:31 final size:31
Alignment explanation
Indices: 24246--24354 Score: 85
Period size: 31 Copynumber: 3.3 Consensus size: 31
24236 ATAATAATCG
* *
24246 AGTGAACAAAACATAAATTAGATAATATATA
1 AGTGACCAAAATATAAATTAGATAATATATA
** ** *
24277 AGTGACC-AAATAGCTAGTTTACCCTAAATAATAATCG
1 AGTGACCAAAATA--TAAATTA-GAT-AAT-AT-AT-A
24314 AGTGACCAAAATATAAATTAGATAATATATA
1 AGTGACCAAAATATAAATTAGATAATATATA
24345 AGTGACCAAA
1 AGTGACCAAA
24355 TAAGTAGTTT
Statistics
Matches: 58, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
30 4 0.07
31 16 0.28
32 7 0.12
33 3 0.05
34 6 0.10
35 3 0.05
36 7 0.12
37 7 0.12
38 5 0.09
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (31 bp):
AGTGACCAAAATATAAATTAGATAATATATA
Found at i:26691 original size:46 final size:46
Alignment explanation
Indices: 26627--26915 Score: 481
Period size: 46 Copynumber: 6.3 Consensus size: 46
26617 ATGCCTTAAT
*
26627 GCATCCTTTTATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
* * * *
26673 GAATCCTTTCATGTCTTAATGCACCCTTTCATGCATTTTAGTTGTG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
*
26719 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
**
26765 GCATCCTTTCATGCCTTAATGCATATTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
*
26811 GCATCCTTTTATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
*
26857 ACATCCTTTCATGCCTTAATGCATCCTTTCATGCA-TTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
26902 GCATCCTTTCATGC
1 GCATCCTTTCATGC
26916 ATTTAGTTAT
Statistics
Matches: 225, Mismatches: 18, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
45 23 0.10
46 202 0.90
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.44
Consensus pattern (46 bp):
GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
Found at i:26911 original size:25 final size:25
Alignment explanation
Indices: 26831--26940 Score: 158
Period size: 25 Copynumber: 4.6 Consensus size: 25
26821 ATGCCTTAAT
26831 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCA-TTTAGTTATG
* *
26857 ACATCCTTTCATGC-CTTA---AT-
1 GCATCCTTTCATGCATTTAGTTATG
26877 GCATCCTTTCATGCATTTAGTTATG
1 GCATCCTTTCATGCATTTAGTTATG
26902 GCATCCTTTCATGCATTTAGTTATG
1 GCATCCTTTCATGCATTTAGTTATG
26927 GCATCCTTTCATGC
1 GCATCCTTTCATGC
26941 CTTAATGATA
Statistics
Matches: 75, Mismatches: 4, Indels: 11
0.83 0.04 0.12
Matches are distributed among these distances:
20 13 0.17
21 5 0.07
24 5 0.07
25 39 0.52
26 13 0.17
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.43
Consensus pattern (25 bp):
GCATCCTTTCATGCATTTAGTTATG
Found at i:27422 original size:54 final size:52
Alignment explanation
Indices: 27318--27441 Score: 153
Period size: 54 Copynumber: 2.3 Consensus size: 52
27308 CAATACTTCT
*
27318 ATACTATGGTAAT-GATACCCCCTTTCAGTATCGATACCATTTATATATTCTGTG
1 ATAC-ATGGT-ATCGATACCCCCTTTCAGTATCGATACCATTTATACATTCTG-G
* * *
27372 TTTGCATGGTATCGATACCCTCTTTCAGTATCGATACCATTT-TGACATTCTGG
1 -ATACATGGTATCGATACCCCCTTTCAGTATCGATACCATTTAT-ACATTCTGG
27425 ATACATGGTATCGATAC
1 ATACATGGTATCGATAC
27442 TTCCCTTTGT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
52 15 0.25
53 4 0.07
54 40 0.66
55 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (52 bp):
ATACATGGTATCGATACCCCCTTTCAGTATCGATACCATTTATACATTCTGG
Found at i:28690 original size:23 final size:23
Alignment explanation
Indices: 28664--28712 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
28654 TAATTCTACA
28664 TTTGTGACACATTTTTC-TTTATC
1 TTTGTGACACATTTTTCATTT-TC
* *
28687 TTTGTGGCATATTTTTCATTTTC
1 TTTGTGACACATTTTTCATTTTC
28710 TTT
1 TTT
28713 CTCGGTCGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.14, C:0.14, G:0.10, T:0.61
Consensus pattern (23 bp):
TTTGTGACACATTTTTCATTTTC
Found at i:33572 original size:2 final size:2
Alignment explanation
Indices: 33567--33614 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
33557 ATAAATTATG
*
33567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
33607 AT TT AT AT
1 AT AT AT AT
33615 GTACTTATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:34030 original size:74 final size:74
Alignment explanation
Indices: 33965--34118 Score: 200
Period size: 74 Copynumber: 2.1 Consensus size: 74
33955 CATCTGTCCT
* *
33965 GAGACAGTTTCTCTCGAAATAAAAATTTTATTTCACTTGAGAAAAATTCCCTCGAAACAAATTTC
1 GAGACAGTTTCTCTCGAAACAAAAATTTTATCTCACTTGAGAAAAATTCCCTCGAAACAAATTTC
34030 ATCTTAATC
66 ATCTTAATC
* * * ** * * *
34039 GAGACAGTTTCTTTTGAAACAAAATTTTTATCTCACTTGAGAAAGTTTTCCTTGAAACATATTTC
1 GAGACAGTTTCTCTCGAAACAAAAATTTTATCTCACTTGAGAAAAATTCCCTCGAAACAAATTTC
* *
34104 ATCTCACTC
66 ATCTTAATC
34113 GAGACA
1 GAGACA
34119 ATTTTTTTTA
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (74 bp):
GAGACAGTTTCTCTCGAAACAAAAATTTTATCTCACTTGAGAAAAATTCCCTCGAAACAAATTTC
ATCTTAATC
Found at i:35758 original size:24 final size:24
Alignment explanation
Indices: 35712--35774 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
35702 CACATGTAAT
* * *
35712 ATTTATATTTATATTTGATATATC
1 ATTTATATTTATATTTAACATATA
35736 ATTTATATTTAT-TATTAACATATA
1 ATTTATATTTATAT-TTAACATATA
*
35760 ATTTTTATTATATAT
1 ATTTATATT-TATAT
35775 CATATTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 1 0.03
24 27 0.84
25 3 0.09
26 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.59
Consensus pattern (24 bp):
ATTTATATTTATATTTAACATATA
Found at i:35795 original size:24 final size:22
Alignment explanation
Indices: 35714--35788 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 22
35704 CATGTAATAT
35714 TTATATTTATATTTGATATATCAT-
1 TTATATTT-TA-TT-ATATATCATA
*
35738 TTATA-TTTATTAT-TAACATA
1 TTATATTTTATTATATATCATA
*
35758 TAAT-TTTTATTATATATCATA
1 TTATATTTTATTATATATCATA
35779 TTATATTTTA
1 TTATATTTTA
35789 CATTATACTA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 5 0.12
20 13 0.30
21 11 0.26
22 7 0.16
23 2 0.05
24 5 0.12
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (22 bp):
TTATATTTTATTATATATCATA
Found at i:35844 original size:25 final size:23
Alignment explanation
Indices: 35805--35851 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
35795 ACTATATACA
35805 TATTTTTACATATTTTATTTACCTC
1 TATTTTTACATA-TTTA-TTACCTC
35830 TATTTTT-CATAATTTATTACCT
1 TATTTTTACAT-ATTTATTACCT
35852 TCCTTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTTTTACATATTTATTACCTC
Found at i:35868 original size:8 final size:8
Alignment explanation
Indices: 35855--35889 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
35845 ATTACCTTCC
35855 TTTTATAT
1 TTTTATAT
35863 TTTTATAT
1 TTTTATAT
35871 TTTTA-AT
1 TTTTATAT
35878 TTTTATTAT
1 TTTTA-TAT
35887 TTT
1 TTT
35890 CTTCATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 7 0.28
8 13 0.52
9 5 0.20
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTATAT
Found at i:35939 original size:41 final size:39
Alignment explanation
Indices: 35856--35947 Score: 105
Period size: 41 Copynumber: 2.3 Consensus size: 39
35846 TTACCTTCCT
* *
35856 TTTATATTTTTATATTTTTAATTTTTATTATTTTCTTCA
1 TTTATATATTTATATTTTTAATTTTTATTATTTTCGTCA
* *
35895 TTTATATATTTACTATTTTATTATTTTTATTAATTTTGGT-A
1 TTTATATATTTA-TATTTT-TAATTTTTATT-ATTTTCGTCA
35936 TTTATATCATTT
1 TTTATAT-ATTT
35948 TGCATTTACT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
39 11 0.24
40 6 0.13
41 18 0.40
42 10 0.22
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.68
Consensus pattern (39 bp):
TTTATATATTTATATTTTTAATTTTTATTATTTTCGTCA
Found at i:35977 original size:23 final size:23
Alignment explanation
Indices: 35934--35988 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
35924 TTAATTTTGG
35934 TATTTATATCATTTTGCATTTAC
1 TATTTATATCATTTTGCATTTAC
* *
35957 TTTTTCATAT-ATTTTGGATTTAC
1 TATTT-ATATCATTTTGCATTTAC
35980 TATTTATAT
1 TATTTATAT
35989 TGTAATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.14
23 20 0.71
24 4 0.14
ACGTcount: A:0.25, C:0.09, G:0.05, T:0.60
Consensus pattern (23 bp):
TATTTATATCATTTTGCATTTAC
Found at i:40368 original size:30 final size:30
Alignment explanation
Indices: 40323--40398 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 30
40313 AAAACAATAC
*
40323 ATAAATATTAAATAAATC-AAA-GA-AAAAA
1 ATAAA-ATAAAATAAATCAAAAGGAGAAAAA
40351 CATAAAAATAAAAATAAATCAAAAGGAGAAAAA
1 -AT-AAAAT-AAAATAAATCAAAAGGAGAAAAA
40384 ATAAAATAAAATAAA
1 ATAAAATAAAATAAA
40399 AAATAAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
29 4 0.10
30 20 0.49
31 8 0.20
32 4 0.10
33 5 0.12
ACGTcount: A:0.74, C:0.04, G:0.05, T:0.17
Consensus pattern (30 bp):
ATAAAATAAAATAAATCAAAAGGAGAAAAA
Found at i:40391 original size:5 final size:5
Alignment explanation
Indices: 40381--40438 Score: 55
Period size: 5 Copynumber: 11.2 Consensus size: 5
40371 AAAAGGAGAA
** *
40381 AAAAT AAAAT AAAAT AAAAAAT AAAA- AAAAT CAAAGG AAACT AAAAT
1 AAAAT AAAAT AAAAT --AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT
40428 AAAAT AAAAT A
1 AAAAT AAAAT A
40439 TATATCAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
4 4 0.09
5 32 0.73
6 3 0.07
7 5 0.11
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:40398 original size:42 final size:42
Alignment explanation
Indices: 40352--40455 Score: 126
Period size: 42 Copynumber: 2.5 Consensus size: 42
40342 AAGAAAAAAC
40352 ATAAAAATAAAAATAAATCAAAAGGAGAA-AAAATAAAATAAA
1 ATAAAAATAAAAATAAATCAAAAGGA-AACAAAATAAAATAAA
40394 ATAAAAAATAAAAA-AAATC-AAAGGAAACTAAAATAAAATAAA
1 AT-AAAAATAAAAATAAATCAAAAGGAAAC-AAAATAAAATAAA
* * *
40436 ATATATAT-CAAATAAATCAA
1 ATAAAAATAAAAATAAATCAA
40456 TGGGAAAATG
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
40 5 0.09
41 15 0.28
42 23 0.43
43 11 0.20
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (42 bp):
ATAAAAATAAAAATAAATCAAAAGGAAACAAAATAAAATAAA
Found at i:40462 original size:42 final size:42
Alignment explanation
Indices: 40354--40438 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 42
40344 GAAAAAACAT
40354 AAAAATAAAAATAAATCAAAAGGAGAA--AAAATAAAATAAAATA
1 AAAAATAAAAA-AAATC-AAAGGA-AACTAAAATAAAATAAAATA
40397 AAAAATAAAAAAAATCAAAGGAAACTAAAATAAAATAAAATA
1 AAAAATAAAAAAAATCAAAGGAAACTAAAATAAAATAAAATA
40439 TATATCAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
40 2 0.05
41 6 0.15
42 21 0.52
43 11 0.28
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (42 bp):
AAAAATAAAAAAAATCAAAGGAAACTAAAATAAAATAAAATA
Found at i:40484 original size:4 final size:4
Alignment explanation
Indices: 40475--40559 Score: 52
Period size: 4 Copynumber: 21.0 Consensus size: 4
40465 GTAAAAATAA
* * * * *
40475 AAAT AAAT AAAT AAAT AAAT AAAGGA AAAG AAAT CAAAG AGA- AAAG AAAT
1 AAAT AAAT AAAT AAAT AAAT AAA--T AAAT AAAT -AAAT AAAT AAAT AAAT
40525 GAAAT AAA- ATAAT AAAT AAAT AAA- AAAT -AAT AAAT
1 -AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT
40560 GAATCAAAGG
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
3 9 0.14
4 45 0.69
5 8 0.12
6 3 0.05
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:40565 original size:55 final size:55
Alignment explanation
Indices: 40469--40580 Score: 142
Period size: 59 Copynumber: 2.0 Consensus size: 55
40459 GAAAATGTAA
40469 AAATAAAAATAAATAAATAAATAAATAAAGGAAAAGAAATCAAAGAGAAAAGAAATG
1 AAATAAAAATAAATAAATAAATAAATAAAGGAAAAGAAATCAAAG-GAAAA-AAATG
* *
40526 AAATAAAATAATAAATAAATAAA-AAAT-AA-TAAATG-AATCAAAGGAAAAAAATG
1 AAAT-AAA-AATAAATAAATAAATAAATAAAGGAAAAGAAATCAAAGGAAAAAAATG
40579 AA
1 AA
40581 TAGTTAGAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
53 7 0.14
54 5 0.10
55 8 0.16
56 4 0.08
57 6 0.12
58 7 0.14
59 14 0.27
ACGTcount: A:0.72, C:0.02, G:0.10, T:0.16
Consensus pattern (55 bp):
AAATAAAAATAAATAAATAAATAAATAAAGGAAAAGAAATCAAAGGAAAAAAATG
Found at i:42247 original size:164 final size:165
Alignment explanation
Indices: 42048--42347 Score: 440
Period size: 164 Copynumber: 1.8 Consensus size: 165
42038 AGTTAAATGC
* * * * * * *
42048 AATCGAACTAGAAGGTCTTTGGCATATATCCCTTCTCGACTTAAGCTATGTTGCAAATGATGTGC
1 AATCGAACTAGAAGGACTTTGACAGATAGCCCTTCTCGACTTAAGCTATATTGCAAATAATATGC
* * * * *
42113 CTTAGAGTTGAGCGTAGTCGAACTCGCAGGTCTTT-GTTGATAGATAACCCTTCTAGCCTTGAGT
66 CTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGT
42177 TATGCTGTAAATGATGTGCCCTCAAAGATAAGTGT
131 TATGCTGTAAATGATGTGCCCTCAAAGATAAGTGT
* *
42212 AATCGAACTCGAGGGACTTTGACAGATAGCCCTTCTCGACTTAAGCTATATTGCAAATAATATGC
1 AATCGAACTAGAAGGACTTTGACAGATAGCCCTTCTCGACTTAAGCTATATTGCAAATAATATGC
* * *
42277 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGT
66 CTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGT
42342 TATGCT
131 TATGCT
42348 ACAAATGACA
Statistics
Matches: 118, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
164 88 0.75
165 30 0.25
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (165 bp):
AATCGAACTAGAAGGACTTTGACAGATAGCCCTTCTCGACTTAAGCTATATTGCAAATAATATGC
CTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGT
TATGCTGTAAATGATGTGCCCTCAAAGATAAGTGT
Found at i:42378 original size:84 final size:83
Alignment explanation
Indices: 42050--42396 Score: 319
Period size: 84 Copynumber: 4.2 Consensus size: 83
42040 TTAAATGCAA
* * * * *
42050 TCGAACTAGAAGGTCTTTG--G-CATATATCCCTTCTCGACTTAAGCTATGTTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATG
*
42112 CCTTAGAGTTGAGCGTAG
66 CCTTAGAGCTGAGCGTAG
* * * * * * * *
42130 TCGAACTCGCAGGTCTTTGTTGATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATG
* * * * * *
42195 CCCTCAAAGATAAGTGTAA
66 -CCTTAGAGCTGAGCGTAG
* * * ** *
42214 TCGAACTCGAGGGAC--T-TTGACAGATAGCCCTTCTCGACTTAAGCTATATTGCAAATAATATG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATG
*
42276 CCTTGGAGCTGAGCGTAG
66 CCTTAGAGCTGAGCGTAG
* * * *
42294 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGACAT
1 TCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATAT
* * *
42359 GTCTTGGAGCTGAGGGTAG
65 GCCTTAGAGCTGAGCGTAG
*
42378 TCGAACTCGAAGGTTTTTG
1 TCGAACTCGAAGGTCTTTG
42397 GTGGGAACGA
Statistics
Matches: 208, Mismatches: 51, Indels: 13
0.76 0.19 0.05
Matches are distributed among these distances:
80 41 0.20
81 35 0.17
82 3 0.01
83 34 0.16
84 95 0.46
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (83 bp):
TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATG
CCTTAGAGCTGAGCGTAG
Found at i:42725 original size:110 final size:110
Alignment explanation
Indices: 42515--42941 Score: 666
Period size: 110 Copynumber: 3.9 Consensus size: 110
42505 TTATGCTGTT
* *
42515 TCGAGGCCAATATCCTTCGCCGTGAAGTTGAAATTGACTC----TGAAACTCG-AAAGTTGTTTG
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACT-GAAAAGTTGTTTG
* * *
42575 TTGACAGCCAGCCGCCCCTTCGCTGTGAAGTTGAGTTTGTGTTGTC
65 TTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * *
42621 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTTACTCTGAATGAAATTGAAATGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
42686 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* *
42731 TCGAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* *
42796 TGACACTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTATC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
*
42841 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* **
42906 TTACAGTCAGTCGCCCCTTCTATGTGAAGTTGAGCT
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCT
42942 GAACTGGAAT
Statistics
Matches: 294, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
106 37 0.13
109 1 0.00
110 256 0.87
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (110 bp):
TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
Found at i:43416 original size:32 final size:32
Alignment explanation
Indices: 43366--43442 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
43356 CATCATAATT
* * * *
43366 TTGAATCCCCGAAGATGCCCCAATATTCGATG
1 TTGAATCTCCAAAAATGCCCCAACATTCGATG
*
43398 TTGAATCTCCAAAAATGCCCCAACATTTGATG
1 TTGAATCTCCAAAAATGCCCCAACATTCGATG
* *
43430 TTAAATCTTCAAA
1 TTGAATCTCCAAA
43443 GGTACCCCCA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.29
Consensus pattern (32 bp):
TTGAATCTCCAAAAATGCCCCAACATTCGATG
Found at i:44550 original size:15 final size:16
Alignment explanation
Indices: 44522--44567 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
44512 TTTCTTCACT
44522 TTTTC-CTTTGTTTT-
1 TTTTCTCTTTGTTTTA
44536 TGTTTCTCTTT-TTTTA
1 T-TTTCTCTTTGTTTTA
44552 TTTTCTCTTTGCTTTT
1 TTTTCTCTTTG-TTTT
44568 TTCTTTGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.04
15 17 0.63
16 5 0.19
17 4 0.15
ACGTcount: A:0.02, C:0.15, G:0.07, T:0.76
Consensus pattern (16 bp):
TTTTCTCTTTGTTTTA
Found at i:44567 original size:12 final size:12
Alignment explanation
Indices: 44552--44595 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
44542 TCTTTTTTTA
*
44552 TTTTCTCTTTGC
1 TTTTTTCTTTGC
44564 TTTTTTCTTTGC
1 TTTTTTCTTTGC
44576 TTTTTTCTTT--
1 TTTTTTCTTTGC
44586 TTTTTTCTTT
1 TTTTTTCTTT
44596 TTATTCTGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 10 0.32
12 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.80
Consensus pattern (12 bp):
TTTTTTCTTTGC
Found at i:44567 original size:19 final size:19
Alignment explanation
Indices: 44545--44588 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
44535 TTGTTTCTCT
*
44545 TTTTTTATTTTCTCTTTGC
1 TTTTTTATTTGCTCTTTGC
* * *
44564 TTTTTTCTTTGCTTTTTTC
1 TTTTTTATTTGCTCTTTGC
44583 TTTTTT
1 TTTTTT
44589 TTTCTTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.80
Consensus pattern (19 bp):
TTTTTTATTTGCTCTTTGC
Found at i:44602 original size:19 final size:19
Alignment explanation
Indices: 44563--44597 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
44553 TTTCTCTTTG
44563 CTTTTTTCTTTGCTTTTTT
1 CTTTTTTCTTTGCTTTTTT
44582 CTTTTTT-TTT-CTTTTT
1 CTTTTTTCTTTGCTTTTT
44598 ATTCTGATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (19 bp):
CTTTTTTCTTTGCTTTTTT
Found at i:47359 original size:6 final size:6
Alignment explanation
Indices: 47348--47374 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
47338 TTAATTGTAG
47348 AAATTT AAATTT AAATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAA
47375 AAACTCGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
AAATTT
Found at i:47483 original size:3 final size:3
Alignment explanation
Indices: 47477--47504 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
47467 AGAAAAAAAC
47477 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
47505 ATCAAAAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:47530 original size:32 final size:31
Alignment explanation
Indices: 47482--47574 Score: 98
Period size: 32 Copynumber: 2.8 Consensus size: 31
47472 AAAACATAAT
47482 AATAATAATAATAATAATAATAAATCAAAAGGAGA
1 AATAA-AATAA-AATAA-AATAAATCAAAAGGA-A
**
47517 AA-AAAATAAAATAAAATAAAAAATAAAGGAA
1 AATAAAATAAAATAAAATAAATCA-AAAGGAA
*
47548 AATAAAATAAAATAAAAATATATCAAA
1 AATAAAATAAAAT-AAAATAAATCAAA
47575 TAAATCAATG
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
31 10 0.20
32 23 0.46
33 13 0.26
34 2 0.04
35 2 0.04
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.19
Consensus pattern (31 bp):
AATAAAATAAAATAAAATAAATCAAAAGGAA
Found at i:47533 original size:27 final size:26
Alignment explanation
Indices: 47514--47565 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
47504 AATCAAAAGG
47514 AGAAA-AAAATAAAATAAAATAAAAA
1 AGAAAGAAAATAAAATAAAATAAAAA
*
47539 ATAAAGGAAAATAAAATAAAATAAAAA
1 AGAAA-GAAAATAAAATAAAATAAAAA
47566 TATATCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 4 0.17
27 20 0.83
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (26 bp):
AGAAAGAAAATAAAATAAAATAAAAA
Found at i:47633 original size:14 final size:16
Alignment explanation
Indices: 47614--47645 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
47604 ATAAATATAT
47614 AAATAAAT-AAAG-GA
1 AAATAAATCAAAGAGA
47628 AAATAAATCAAAGAGA
1 AAATAAATCAAAGAGA
47644 AA
1 AA
47646 TGAAATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.72, C:0.03, G:0.12, T:0.12
Consensus pattern (16 bp):
AAATAAATCAAAGAGA
Found at i:63840 original size:18 final size:18
Alignment explanation
Indices: 63817--63882 Score: 105
Period size: 18 Copynumber: 3.7 Consensus size: 18
63807 CAACGGTCAA
*
63817 TGGTCAATGGGTTGGGTC
1 TGGTCAACGGGTTGGGTC
63835 TGGTCAACGGGTTGGGTC
1 TGGTCAACGGGTTGGGTC
*
63853 TGGTCAACGGGTCGGGTC
1 TGGTCAACGGGTTGGGTC
*
63871 GGGTCAACGGGT
1 TGGTCAACGGGT
63883 CAAAACCGGG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.45, T:0.26
Consensus pattern (18 bp):
TGGTCAACGGGTTGGGTC
Found at i:74148 original size:39 final size:41
Alignment explanation
Indices: 74104--74183 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
74094 GTTTTCATCA
74104 ATAATATAATTTAAAT-A-AATGAATCAAAGTTAAAAAATC
1 ATAATATAATTTAAATAATAATGAATCAAAGTTAAAAAATC
*
74143 ATAATATAATTTAAATAATAATGAGTCAAAGTTAAAAAATC
1 ATAATATAATTTAAATAATAATGAATCAAAGTTAAAAAATC
74184 TGAAAAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 16 0.42
40 1 0.03
41 21 0.55
ACGTcount: A:0.57, C:0.05, G:0.06, T:0.31
Consensus pattern (41 bp):
ATAATATAATTTAAATAATAATGAATCAAAGTTAAAAAATC
Done.