Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004829.1 Hibiscus syriacus cultivar Beakdansim tig00010877_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: 271781
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
File 2 of 2
Found at i:182422 original size:21 final size:19
Alignment explanation
Indices: 182370--182422 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 19
182360 CCACCCTTCA
*
182370 TCTCTCTTTC-CCCTCCAC
1 TCTCTCTTTCTCCCCCCAC
182388 TCTCTCTGTCTCTCCCCCCAC
1 TCTCTCT-T-TCTCCCCCCAC
182409 TCTTGCTCTTTCTC
1 TC-T-CTCTTTCTC
182423 TCTCTTGCCC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 7 0.24
19 1 0.03
20 2 0.07
21 13 0.45
22 2 0.07
23 4 0.14
ACGTcount: A:0.04, C:0.51, G:0.04, T:0.42
Consensus pattern (19 bp):
TCTCTCTTTCTCCCCCCAC
Found at i:182490 original size:26 final size:26
Alignment explanation
Indices: 182456--182506 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
182446 CTTCCCCATT
182456 ATCTCTTTC-CTACT-ATATCTATCTCC
1 ATCTCTTTCTCT-CTCATA-CTATCTCC
182482 ATCTCTTTCTCTCTCATACTATCTC
1 ATCTCTTTCTCTCTCATACTATCTC
182507 TTTTTATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.18, C:0.35, G:0.00, T:0.47
Consensus pattern (26 bp):
ATCTCTTTCTCTCTCATACTATCTCC
Found at i:182530 original size:24 final size:26
Alignment explanation
Indices: 182491--182539 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
182481 CATCTCTTTC
*
182491 TCTCTCATACTATCTCTTTTTATCTT
1 TCTCTCATACTATCTCTTATTATCTT
182517 TCTCTCATA-T-TCTCTTATTATCT
1 TCTCTCATACTATCTCTTATTATCT
182540 CTCATTATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.55
25 1 0.05
26 9 0.41
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (26 bp):
TCTCTCATACTATCTCTTATTATCTT
Found at i:182621 original size:2 final size:2
Alignment explanation
Indices: 182616--182676 Score: 77
Period size: 2 Copynumber: 30.5 Consensus size: 2
182606 TTCTCTATTA
* * * *
182616 CT CT CT CT CG CC CT CT CT CT AT CT CT CT CT CT CT CT CA CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
182658 CT CT CT CT GT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT C
182677 CCACATACTT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.03, C:0.49, G:0.03, T:0.44
Consensus pattern (2 bp):
CT
Found at i:183093 original size:24 final size:26
Alignment explanation
Indices: 183066--183126 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 26
183056 CTGTATTTCT
183066 TACTCTCTCTCACTCTCCCA-G-ACA
1 TACTCTCTCTCACTCTCCCACGCACA
** *
183090 TACTCTCTCTTTCTCTCTCACGCACA
1 TACTCTCTCTCACTCTCCCACGCACA
*
183116 CACTCTCTCTC
1 TACTCTCTCTC
183127 TTACCCACAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 17 0.57
25 1 0.03
26 12 0.40
ACGTcount: A:0.16, C:0.46, G:0.03, T:0.34
Consensus pattern (26 bp):
TACTCTCTCTCACTCTCCCACGCACA
Found at i:183107 original size:26 final size:26
Alignment explanation
Indices: 183068--183127 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
183058 GTATTTCTTA
* *
183068 CTCTCTCTCACTCTCCCAG-ACATACT
1 CTCTCTCTCACTCTCAC-GCACACACT
* *
183094 CTCTCTTTCTCTCTCACGCACACACT
1 CTCTCTCTCACTCTCACGCACACACT
183120 CTCTCTCT
1 CTCTCTCT
183128 TACCCACACT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 1 0.04
26 27 0.96
ACGTcount: A:0.15, C:0.47, G:0.03, T:0.35
Consensus pattern (26 bp):
CTCTCTCTCACTCTCACGCACACACT
Found at i:183124 original size:18 final size:17
Alignment explanation
Indices: 183101--183145 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
183091 ACTCTCTCTT
183101 TCTCTCTC-ACGCACACAC
1 TCTCTCTCTAC-C-CACAC
183119 TCTCTCTCTTACCCACAC
1 TCTCTCTC-TACCCACAC
183137 TCTCTCTCT
1 TCTCTCTCT
183146 CTCATATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.04
18 21 0.84
19 1 0.04
20 2 0.08
ACGTcount: A:0.16, C:0.49, G:0.02, T:0.33
Consensus pattern (17 bp):
TCTCTCTCTACCCACAC
Found at i:183126 original size:20 final size:20
Alignment explanation
Indices: 183101--183149 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
183091 ACTCTCTCTT
*
183101 TCTCTCTCACGCACACACTC
1 TCTCTCTCACCCACACACTC
* *
183121 TCTCTCTTACCCACACTCTC
1 TCTCTCTCACCCACACACTC
183141 TCTCTCTCA
1 TCTCTCTCA
183150 TATACTCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.16, C:0.49, G:0.02, T:0.33
Consensus pattern (20 bp):
TCTCTCTCACCCACACACTC
Found at i:183569 original size:2 final size:2
Alignment explanation
Indices: 183562--183596 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
183552 CTCTTCCCTA
* *
183562 CT CT CT CT AT CT CT CT CT CT CT CC CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
183597 CCCTTACTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.51, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:183724 original size:35 final size:35
Alignment explanation
Indices: 183650--183726 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
183640 TCCCCCATTG
*
183650 TCTCTCTATCCTACTATATCTCTTTCTCCCCCCTT
1 TCTCTCTATCCTACTATATCTCTTTCTCCCCCCTA
* * * * * *
183685 TCTCTCTATCCTACTTTCTTTCTTTCTCTCTCGTA
1 TCTCTCTATCCTACTATATCTCTTTCTCCCCCCTA
183720 TCTCTCT
1 TCTCTCT
183727 CTCCCCTTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.09, C:0.39, G:0.01, T:0.51
Consensus pattern (35 bp):
TCTCTCTATCCTACTATATCTCTTTCTCCCCCCTA
Found at i:183882 original size:38 final size:38
Alignment explanation
Indices: 183838--183922 Score: 113
Period size: 38 Copynumber: 2.2 Consensus size: 38
183828 AACCACATAC
183838 TTTCTCTCTCCCTTCCTC-AGTCTC-TCTCTTGCTCACAA
1 TTTCTCTCTCCCTTCCTCTA-TCTCATCTCTTGCTCAC-A
*
183876 TTTCTCTCTCCTTTCCTCTATCTCTATCTCTTGCTCACA
1 TTTCTCTCTCCCTTCCTCTATCTC-ATCTCTTGCTCACA
183915 -TTCTCTCT
1 TTTCTCTCT
183923 ATATATCTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
38 29 0.67
39 2 0.05
40 12 0.28
ACGTcount: A:0.09, C:0.40, G:0.04, T:0.47
Consensus pattern (38 bp):
TTTCTCTCTCCCTTCCTCTATCTCATCTCTTGCTCACA
Found at i:184238 original size:2 final size:2
Alignment explanation
Indices: 184225--184340 Score: 60
Period size: 2 Copynumber: 57.5 Consensus size: 2
184215 TCTTACTCAT
* * * * *
184225 TC TC TT TC TC TC TC TC TC GC CC TC TC TC -C CC TC TC TG TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
184266 TA TC TC ATAC TC TC TC TC GC CC TA TC TG TC TC TT TC TC TC TC TC
1 TC TC TC -T-C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
184310 TC AT- TC TC TC TC T- TGC TC TC -C TAC TC TC TC T
1 TC -TC TC TC TC TC TC T-C TC TC TC T-C TC TC TC T
184341 GTTGGCCAAT
Statistics
Matches: 86, Mismatches: 19, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
1 4 0.05
2 75 0.87
3 6 0.07
4 1 0.01
ACGTcount: A:0.05, C:0.45, G:0.04, T:0.46
Consensus pattern (2 bp):
TC
Found at i:184963 original size:20 final size:20
Alignment explanation
Indices: 184918--184967 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
184908 CTCACCCACT
* *
184918 ATCTCTCTCTTGTCCACTCA
1 ATCTCTCTCTTGCCCACCCA
*
184938 ACCTCTCTCTTGCCCACCCA
1 ATCTCTCTCTTGCCCACCCA
*
184958 TTCTCTCTCT
1 ATCTCTCTCT
184968 CTCTCTCTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.12, C:0.46, G:0.04, T:0.38
Consensus pattern (20 bp):
ATCTCTCTCTTGCCCACCCA
Found at i:185164 original size:22 final size:23
Alignment explanation
Indices: 185139--185199 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
185129 TTTTTTTCTG
185139 TCTATCTCACTCTCTCTCAACT-
1 TCTATCTCACTCTCTCTCAACTA
* *
185161 TCTATCTCTCTCTCAC-CAACTA
1 TCTATCTCACTCTCTCTCAACTA
* *
185183 TCTTTCTGACTCTCTCT
1 TCTATCTCACTCTCTCT
185200 TACCCTCTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 5 0.16
22 26 0.84
ACGTcount: A:0.16, C:0.39, G:0.02, T:0.43
Consensus pattern (23 bp):
TCTATCTCACTCTCTCTCAACTA
Found at i:185209 original size:26 final size:26
Alignment explanation
Indices: 185166--185224 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
185156 CAACTTCTAT
* *
185166 CTCTCTCTCACCAACTATCTTTCTGA
1 CTCTCTCTCACCAACTATATCTCTGA
* ** *
185192 CTCTCTCTTACCCTCTATATCTCTGT
1 CTCTCTCTCACCAACTATATCTCTGA
185218 CTCTCTC
1 CTCTCTC
185225 CCTCACTCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.14, C:0.41, G:0.03, T:0.42
Consensus pattern (26 bp):
CTCTCTCTCACCAACTATATCTCTGA
Found at i:185754 original size:26 final size:27
Alignment explanation
Indices: 185715--185767 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
185705 GGCCCTTCCT
*
185715 CTCTATCCCTCACTC-TCTCTTTCTCC
1 CTCTATCCCCCACTCTTCTCTTTCTCC
*
185741 CTCTGTCCCCCACTCTTTCTCTTTCTC
1 CTCTATCCCCCACTC-TTCTCTTTCTC
185768 TATCTTATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 13 0.57
28 10 0.43
ACGTcount: A:0.06, C:0.49, G:0.02, T:0.43
Consensus pattern (27 bp):
CTCTATCCCCCACTCTTCTCTTTCTCC
Found at i:185835 original size:12 final size:12
Alignment explanation
Indices: 185820--185972 Score: 79
Period size: 12 Copynumber: 12.8 Consensus size: 12
185810 TCCTATTATC
185820 TCTCTCTCTCAT
1 TCTCTCTCTCAT
185832 TCTCACTCTCTCAT
1 TCT--CTCTCTCAT
* *
185846 CCCCTCTCTC--
1 TCTCTCTCTCAT
* * * * *
185856 TCACACACACAC
1 TCTCTCTCTCAT
185868 TCTCTCTCTCATAT
1 TCTCTCTCTC--AT
* *
185882 TCTCTTTATCTAT
1 TCTCTCTCTC-AT
*
185895 TTTCTTCTCTC-T
1 TCTC-TCTCTCAT
185907 -CTCTCTCTCAT
1 TCTCTCTCTCAT
*
185918 TTTCTCTCTCAT
1 TCTCTCTCTCAT
*
185930 TTTCTCTCTC-T
1 TCTCTCTCTCAT
185941 T-TCATCTCT--T
1 TCTC-TCTCTCAT
185951 TCTCTCTCTCAT
1 TCTCTCTCTCAT
185963 TCTCTCTCTC
1 TCTCTCTCTC
185973 TTGTATCTCT
Statistics
Matches: 109, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
10 20 0.18
11 12 0.11
12 48 0.44
13 6 0.06
14 23 0.21
ACGTcount: A:0.10, C:0.41, G:0.00, T:0.49
Consensus pattern (12 bp):
TCTCTCTCTCAT
Found at i:185962 original size:33 final size:33
Alignment explanation
Indices: 185899--185989 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
185889 ATCTATTTTC
*
185899 TTCTCTCTCTCTC-TCTCATTT-TCTCTCTCATT
1 TTCTCTCTCTTTCATCTC-TTTCTCTCTCTCATT
185931 TTCTCTCTCTTTCATCTCTTTCTCTCTCTCATT
1 TTCTCTCTCTTTCATCTCTTTCTCTCTCTCATT
*
185964 CTCTCTCTCTTGT-ATCTCTTTCTCTC
1 TTCTCTCTCTT-TCATCTCTTTCTCTC
185990 CCCATCTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
32 15 0.28
33 38 0.70
34 1 0.02
ACGTcount: A:0.05, C:0.37, G:0.01, T:0.56
Consensus pattern (33 bp):
TTCTCTCTCTTTCATCTCTTTCTCTCTCTCATT
Found at i:185989 original size:2 final size:2
Alignment explanation
Indices: 185900--185973 Score: 55
Period size: 2 Copynumber: 36.5 Consensus size: 2
185890 TCTATTTTCT
* * *
185900 TC TC TC TC TC TC TC TC AT- TT TC TC TC TC AT- TT TC TC TC TC TT
1 TC TC TC TC TC TC TC TC -TC TC TC TC TC TC -TC TC TC TC TC TC TC
*
185942 TC ATC TC TT TC TC TC TC TC AT- TC TC TC TC TC T
1 TC -TC TC TC TC TC TC TC TC -TC TC TC TC TC TC T
185974 TGTATCTCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
1 3 0.05
2 51 0.86
3 5 0.08
ACGTcount: A:0.05, C:0.39, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:186590 original size:34 final size:33
Alignment explanation
Indices: 186550--186624 Score: 116
Period size: 34 Copynumber: 2.2 Consensus size: 33
186540 CTCACTCAAA
186550 TCTCTCTCGCTTCTCTTTATCTATCTCTTACCC-C
1 TCTCTCTCGCTTCTCTTTATC--TCTCTTACCCAC
186584 TCTCTCTCGCTTCTCTTTATCTCTCTTACCCAC
1 TCTCTCTCGCTTCTCTTTATCTCTCTTACCCAC
*
186617 ACTCTCTC
1 TCTCTCTC
186625 TAACTCACTC
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
32 10 0.26
33 8 0.21
34 21 0.54
ACGTcount: A:0.09, C:0.43, G:0.03, T:0.45
Consensus pattern (33 bp):
TCTCTCTCGCTTCTCTTTATCTCTCTTACCCAC
Found at i:186608 original size:17 final size:17
Alignment explanation
Indices: 186552--186608 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
186542 CACTCAAATC
186552 TCTCTCGCTTCTCTTTA
1 TCTCTCGCTTCTCTTTA
* * ** *
186569 TCTATCTCTTAC-CCCTC
1 TCTCTCGCTT-CTCTTTA
186586 TCTCTCGCTTCTCTTTA
1 TCTCTCGCTTCTCTTTA
186603 TCTCTC
1 TCTCTC
186609 TTACCCACAC
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
16 1 0.04
17 26 0.93
18 1 0.04
ACGTcount: A:0.07, C:0.40, G:0.04, T:0.49
Consensus pattern (17 bp):
TCTCTCGCTTCTCTTTA
Found at i:186853 original size:18 final size:17
Alignment explanation
Indices: 186832--186872 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
186822 TCTCTATATG
186832 TCTCTCTATCTCTCGCC-C
1 TCTCTCTATC-CTC-CCGC
186850 TCTCTC-ATCCTCCCGC
1 TCTCTCTATCCTCCCGC
186866 TCTCTCT
1 TCTCTCT
186873 CACTCATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.10
16 10 0.48
17 3 0.14
18 6 0.29
ACGTcount: A:0.05, C:0.51, G:0.05, T:0.39
Consensus pattern (17 bp):
TCTCTCTATCCTCCCGC
Found at i:186873 original size:18 final size:17
Alignment explanation
Indices: 186832--186874 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
186822 TCTCTATATG
*
186832 TCTCTCT-ATCTCTCGC
1 TCTCTCTCATCTCCCGC
*
186848 CCTCTCTCATCCTCCCGC
1 TCTCTCTCAT-CTCCCGC
186866 TCTCTCTCA
1 TCTCTCTCA
186875 CTCATTCTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 6 0.27
17 2 0.09
18 14 0.64
ACGTcount: A:0.07, C:0.51, G:0.05, T:0.37
Consensus pattern (17 bp):
TCTCTCTCATCTCCCGC
Found at i:187002 original size:30 final size:30
Alignment explanation
Indices: 186968--187024 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
186958 TATCACCCTA
* *
186968 TTTATCTATATGTTTGTTTCTCTCTCTCTC
1 TTTATCTATATCTTTGTTTCTCCCTCTCTC
* *
186998 TTTATCTATCTCTTTTTTTCTCCCTCT
1 TTTATCTATATCTTTGTTTCTCCCTCT
187025 TTCATCTATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.09, C:0.26, G:0.04, T:0.61
Consensus pattern (30 bp):
TTTATCTATATCTTTGTTTCTCCCTCTCTC
Found at i:187045 original size:27 final size:26
Alignment explanation
Indices: 186990--187046 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
186980 TTTGTTTCTC
* ** *
186990 TCTCTCTCTTTATCTATCTCTTTTTT
1 TCTCCCTCTTTATCTATCTCTCATAT
187016 TCTCCCTCTTTCATCTATCTCTCATAT
1 TCTCCCTCTTT-ATCTATCTCTCATAT
187043 TCTC
1 TCTC
187047 TTGCTCTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.11, C:0.33, G:0.00, T:0.56
Consensus pattern (26 bp):
TCTCCCTCTTTATCTATCTCTCATAT
Found at i:187316 original size:22 final size:22
Alignment explanation
Indices: 187278--187327 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
187268 CACTCACTCC
*
187278 CTCTCTTACCCAATCTCCCTAT
1 CTCTCTTACCCAATCTCCCAAT
** *
187300 CTCTCTTACCCCCTCTCTCAAT
1 CTCTCTTACCCAATCTCCCAAT
187322 CTCTCT
1 CTCTCT
187328 ATGCCCACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.14, C:0.48, G:0.00, T:0.38
Consensus pattern (22 bp):
CTCTCTTACCCAATCTCCCAAT
Found at i:187545 original size:26 final size:26
Alignment explanation
Indices: 187516--187581 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
187506 ATTATCTTTA
* *
187516 TCTCTCTCATTCTCTCATTCACTATC
1 TCTCTCTCTTTCTCTCACTCACTATC
* * *
187542 TCTCTGTCTTTCTCTCCCTCTCTATC
1 TCTCTCTCTTTCTCTCACTCACTATC
*
187568 TTTCTCTCTTTCTC
1 TCTCTCTCTTTCTC
187582 ACACCATTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.08, C:0.39, G:0.02, T:0.52
Consensus pattern (26 bp):
TCTCTCTCTTTCTCTCACTCACTATC
Found at i:187581 original size:18 final size:18
Alignment explanation
Indices: 187541--187575 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
187531 CATTCACTAT
*
187541 CTCTCTGTCTTTCTCTCC
1 CTCTCTATCTTTCTCTCC
187559 CTCTCTATCTTTCTCTC
1 CTCTCTATCTTTCTCTC
187576 TTTCTCACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.43, G:0.03, T:0.51
Consensus pattern (18 bp):
CTCTCTATCTTTCTCTCC
Found at i:187638 original size:14 final size:13
Alignment explanation
Indices: 187600--187638 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
187590 TCTCTTCTGA
187600 CTATCTCTCTCGC
1 CTATCTCTCTCGC
187613 CTACTCTCTCTCGCC
1 CTA-TCTCTCTCG-C
*
187628 CTATCTGTCTC
1 CTATCTCTCTC
187639 TTTTCCCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 16 0.70
15 4 0.17
ACGTcount: A:0.08, C:0.46, G:0.08, T:0.38
Consensus pattern (13 bp):
CTATCTCTCTCGC
Found at i:187748 original size:22 final size:22
Alignment explanation
Indices: 187706--187750 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
187696 ATTTGCTCGA
* *
187706 TTTCTCTCTCGCTCTCTCTTTC
1 TTTCTCTCTCACTATCTCTTTC
187728 TTTCTCTCTCACTAT-TGCTTTC
1 TTTCTCTCTCACTATCT-CTTTC
187750 T
1 T
187751 CTGTCGCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.04, C:0.36, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTCTCTCTCACTATCTCTTTC
Found at i:187875 original size:2 final size:2
Alignment explanation
Indices: 187868--188275 Score: 141
Period size: 2 Copynumber: 205.0 Consensus size: 2
187858 TCATTCGTTT
* * * *
187868 TC TC TC TC TC GC TA TC TC TT TC TC TA TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
187910 TC TC TC TC TC TC TC TC TT TC GT- TC TC TC TC TC AC TC TC AC TC
1 TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC TC TC TC
* * * * * * *
187952 TC AC TC TC AC TC TC TC TC T- TGC TC TC TA TC AC GC TA TC GC TC
1 TC TC TC TC TC TC TC TC TC TC T-C TC TC TC TC TC TC TC TC TC TC
* * * * * *
187994 TC AC AC TC TC TC TC TC TC TC TC TC TC AC TA TT TC TC TC TC TG
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
** * * * *
188036 GA TC -C GC TC -C TGC TC TC TC TC TC TC TC GC TC CC GC TC -C TGC
1 TC TC TC TC TC TC T-C TC TC TC TC TC TC TC TC TC TC TC TC TC T-C
* * * * * * * *
188077 TC TC TC TC TC TC GC TC -C AGC TC TT TA TC TC TC GC CC GC TC CC
1 TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * * * * * *
188119 GC TC TT TA TC TC TC GC TC TC TC CC AC AC AC TC TC TC TC GC TT
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * * * * * * *
188161 TA TC CC TC TC TC AC TA TA TC GC TC TC TC TC TC AC AC AC AC TT
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
188203 TC GC TC TC AC TC TC TC AT- TC TC TG TC -C TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
188244 TC TC TC TT TT TC T- TAC TC GC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC T-C TC TC TC TC TC TC TC TC
188276 ACACACACAC
Statistics
Matches: 297, Mismatches: 93, Indels: 32
0.70 0.22 0.08
Matches are distributed among these distances:
1 9 0.03
2 279 0.94
3 9 0.03
ACGTcount: A:0.08, C:0.45, G:0.06, T:0.42
Consensus pattern (2 bp):
TC
Found at i:196479 original size:36 final size:36
Alignment explanation
Indices: 196378--196480 Score: 88
Period size: 35 Copynumber: 2.9 Consensus size: 36
196368 ACCTTAGATA
* * *
196378 CGTAATGAATTACCAGTTCGATCAGTCTGAACCTAT
1 CGTAAGGAATTACCAGTTCTATCGGTCTGAACCTAT
* * * *
196414 -ATAAGAAATTA-CTGATT-TGATCGAG-CTGAACCTGT
1 CGTAAGGAATTACCAG-TTCT-ATCG-GTCTGAACCTAT
196449 CGTAAGGAATTACCAGTTCTATCGGTCTGAAC
1 CGTAAGGAATTACCAGTTCTATCGGTCTGAAC
196481 TTATATAAGG
Statistics
Matches: 50, Mismatches: 10, Indels: 14
0.68 0.14 0.19
Matches are distributed among these distances:
34 2 0.04
35 23 0.46
36 22 0.44
37 3 0.06
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (36 bp):
CGTAAGGAATTACCAGTTCTATCGGTCTGAACCTAT
Found at i:196508 original size:71 final size:71
Alignment explanation
Indices: 196378--196518 Score: 185
Period size: 71 Copynumber: 2.0 Consensus size: 71
196368 ACCTTAGATA
* * *
196378 CGTAATGAATTACCAGTTCGATCAGTCTGAACCTATATAAGAAATTACTGATTTGATCGAGCTGA
1 CGTAAGGAATTACCAGTTCGATCAGTCTGAACCTATATAAGAAATTACAGATTTAATCGAGCTGA
196443 ACCTGT
66 ACCTGT
* * * * * *
196449 CGTAAGGAATTACCAGTTCTATCGGTCTGAACTTATATAAGGAGTTATCAG-TTTAATCGAGTTG
1 CGTAAGGAATTACCAGTTCGATCAGTCTGAACCTATATAAGAAATTA-CAGATTTAATCGAGCTG
196513 AACCTG
65 AACCTG
196519 CAGAGACTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
71 58 0.97
72 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (71 bp):
CGTAAGGAATTACCAGTTCGATCAGTCTGAACCTATATAAGAAATTACAGATTTAATCGAGCTGA
ACCTGT
Found at i:199789 original size:5 final size:5
Alignment explanation
Indices: 199779--199808 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
199769 TAAGCTCGTC
199779 CCCCT CCCCT CCCCT CCCCT CCCCT CCCCT
1 CCCCT CCCCT CCCCT CCCCT CCCCT CCCCT
199809 TAACTTGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
CCCCT
Found at i:203314 original size:136 final size:141
Alignment explanation
Indices: 203065--203328 Score: 340
Period size: 136 Copynumber: 1.9 Consensus size: 141
203055 GTGTTTGGGA
* * ***
203065 CATGGGTATTTTAAGAAATATGATGAGTTTGAGCAACATTAGCTCAAGATACATCACCTATGTAT
1 CATGGGTATTTTAAGAAAAATGAAGAGTTTGAGCAACATTAGAAAAAGATACATCACCTA-GTAT
* * * * *
203130 ATGTAAATGTTTAACTTGCTTGGCTTCTCGTGAAGATAATTGAGTA-GGGTCTGATGAAAAATAA
65 ATGTAAATGTTTAACTTGCCTGGCTTCTCATGAAGAGAATGGAGTAGGGGCCTGATGAAAAATAA
203194 ACGAGTTTCGGT
130 ACGAGTTTCGGT
* * * *
203206 CATGGGTATTTTAAGAAAAATGAAGAGTTTGAGCAACA-TGGAAAAATATACAT-GCC-A-TCTA
1 CATGGGTATTTTAAGAAAAATGAAGAGTTTGAGCAACATTAGAAAAAGATACATCACCTAGTATA
* *
203267 TGTAAATGTTTAACTTGCCTGGCTTCTCATGAATAGAATGGAGTAGGGGCCTGTTGAAAAAT
66 TGTAAATGTTTAACTTGCCTGGCTTCTCATGAAGAGAATGGAGTAGGGGCCTGATGAAAAAT
203329 GAAGTGATAG
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
136 43 0.41
137 14 0.13
138 1 0.01
139 2 0.02
140 10 0.09
141 36 0.34
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (141 bp):
CATGGGTATTTTAAGAAAAATGAAGAGTTTGAGCAACATTAGAAAAAGATACATCACCTAGTATA
TGTAAATGTTTAACTTGCCTGGCTTCTCATGAAGAGAATGGAGTAGGGGCCTGATGAAAAATAAA
CGAGTTTCGGT
Found at i:206420 original size:32 final size:32
Alignment explanation
Indices: 206379--206444 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
206369 TAGATTTCAA
* * *
206379 ATCGGGTCAATATCGGATCGGTTGATTTTTCG
1 ATCGAGTCAATATCGAATCGATTGATTTTTCG
*
206411 ATCGAGTCAATATCTAATCGATTGATTTTTCG
1 ATCGAGTCAATATCGAATCGATTGATTTTTCG
206443 AT
1 AT
206445 TTGGATCAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.39
Consensus pattern (32 bp):
ATCGAGTCAATATCGAATCGATTGATTTTTCG
Found at i:212549 original size:16 final size:16
Alignment explanation
Indices: 212525--212558 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
212515 TCTCGCCGAC
*
212525 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
212541 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
212557 CG
1 CG
212559 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:216098 original size:2 final size:2
Alignment explanation
Indices: 216093--216127 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
216083 TATATATATA
*
216093 TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
216128 ATGTATTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (2 bp):
TG
Found at i:218919 original size:50 final size:50
Alignment explanation
Indices: 218850--218963 Score: 201
Period size: 50 Copynumber: 2.3 Consensus size: 50
218840 TTTATTGATG
*
218850 AACCTCTTGTTTTAGATCTCTTACCGTTTTATGATGGAAGAGGGTGAACC
1 AACCTCTTGTTTTAGATCTCTTACCATTTTATGATGGAAGAGGGTGAACC
218900 AACCTCTTGTTTTAGATCTCTTACCATTTTATGATGGAAGAGGGTGAACC
1 AACCTCTTGTTTTAGATCTCTTACCATTTTATGATGGAAGAGGGTGAACC
* *
218950 AATCTCATGTTTTA
1 AACCTCTTGTTTTA
218964 ATTTTGGGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (50 bp):
AACCTCTTGTTTTAGATCTCTTACCATTTTATGATGGAAGAGGGTGAACC
Found at i:241626 original size:16 final size:16
Alignment explanation
Indices: 241601--241674 Score: 139
Period size: 16 Copynumber: 4.6 Consensus size: 16
241591 TGAAAAATTA
241601 GCAAAGTTGAAAGTTG
1 GCAAAGTTGAAAGTTG
*
241617 GCAAAATTGAAAGTTG
1 GCAAAGTTGAAAGTTG
241633 GCAAAGTTGAAAGTTG
1 GCAAAGTTGAAAGTTG
241649 GCAAAGTTGAAAGTTG
1 GCAAAGTTGAAAGTTG
241665 GCAAAGTTGA
1 GCAAAGTTGA
241675 CATCTTTGGT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 56 1.00
ACGTcount: A:0.39, C:0.07, G:0.30, T:0.24
Consensus pattern (16 bp):
GCAAAGTTGAAAGTTG
Found at i:251550 original size:23 final size:23
Alignment explanation
Indices: 251515--251570 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
251505 CATATTTAAT
* * *
251515 ATATTTGTGAATACTAAATGAAC
1 ATATTTATAAATACTAAACGAAC
* *
251538 ATATTTATAAATATTAAACGAAT
1 ATATTTATAAATACTAAACGAAC
*
251561 ATAATTATAA
1 ATATTTATAA
251571 TTATGTTCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (23 bp):
ATATTTATAAATACTAAACGAAC
Found at i:255828 original size:2 final size:2
Alignment explanation
Indices: 255821--255853 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
255811 CCTTCAAATA
255821 AT AT AT AT 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 AT AT AT AT A
255854 AGCCCTTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:258612 original size:18 final size:19
Alignment explanation
Indices: 258564--258615 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 19
258554 TCTTTAATTT
* *
258564 TTTAATATTCTAATTATATT
1 TTTAATA-TCTAATTTTATA
258584 TTTAA-AT-TAATTTTA-A
1 TTTAATATCTAATTTTATA
258600 TTTAATATCTAATTTT
1 TTTAATATCTAATTTT
258616 TGGTAAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 5 0.18
17 9 0.32
18 8 0.29
19 1 0.04
20 5 0.18
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAATATCTAATTTTATA
Found at i:264704 original size:41 final size:41
Alignment explanation
Indices: 264659--264833 Score: 131
Period size: 41 Copynumber: 4.3 Consensus size: 41
264649 TTTTCTAATT
* **
264659 TCGCATTGCGATTTTCCCAATTCGCAATGCGAATAAGTAAA
1 TCGCAATGCGATTTTCATAATTCGCAATGCGAATAAGTAAA
* * * * * *
264700 TCGCAATGCGAATTTGAAAAATCGCAATGCG-AT-ACTGACTA
1 TCGCAATGCGATTTTCATAATTCGCAATGCGAATAAGT-A-AA
* * * * * *
264741 TCGCAATGCAATTTTCCTAATTCGCATTGCGATTTATGT-AT
1 TCGCAATGCGATTTTCATAATTCGCAATGCGA-ATAAGTAAA
** * *
264782 TCGCGTTGCGATTTTCATAATTCGCAATGCAAATACGTAAA
1 TCGCAATGCGATTTTCATAATTCGCAATGCGAATAAGTAAA
264823 TCGCAATGCGA
1 TCGCAATGCGA
264834 ATCTTACTAT
Statistics
Matches: 97, Mismatches: 31, Indels: 12
0.69 0.22 0.09
Matches are distributed among these distances:
39 2 0.02
40 7 0.07
41 86 0.89
43 1 0.01
44 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (41 bp):
TCGCAATGCGATTTTCATAATTCGCAATGCGAATAAGTAAA
Found at i:264705 original size:20 final size:21
Alignment explanation
Indices: 264680--264731 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
264670 TTTTCCCAAT
*
264680 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
**
264700 TCGCAATGCGAATTTGAAAAA
1 TCGCAATGCGAATAAGAAAAA
264721 TCGCAATGCGA
1 TCGCAATGCGA
264732 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:264775 original size:21 final size:21
Alignment explanation
Indices: 264741--264807 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
264731 ATACTGACTA
* * *
264741 TCGCAATGCAATTTTCCTAAT
1 TCGCATTGCGATTTTCATAAT
*
264762 TCGCATTGCGA-TTT-ATGTAT
1 TCGCATTGCGATTTTCAT-AAT
*
264782 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCATAAT
264803 TCGCA
1 TCGCA
264808 ATGCAAATAC
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
19 1 0.03
20 15 0.42
21 18 0.50
22 2 0.06
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCATAAT
Found at i:265407 original size:19 final size:19
Alignment explanation
Indices: 265368--265434 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
265358 TTCGAGAATG
265368 AAAATCGCAACGCGAAAATA
1 AAAATCGCAACGCG-AAATA
**
265388 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
265407 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
265426 AAAATCGCA
1 AAAATCGCA
265435 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.49, C:0.25, G:0.15, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:265452 original size:19 final size:19
Alignment explanation
Indices: 265430--265575 Score: 107
Period size: 19 Copynumber: 8.1 Consensus size: 19
265420 GAAACCAAAA
*
265430 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
265449 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
265463 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
265482 TCGCGTTGCGATAGTT-ATT
1 TCGCGTTGCGAT-TTTCATT
*
265501 TCGCGTTGTGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
265515 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
265534 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
265554 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
265574 TC
1 TC
265576 AACCAAAAGA
Statistics
Matches: 100, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
14 19 0.19
16 7 0.07
17 3 0.03
19 37 0.37
20 33 0.33
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:265514 original size:52 final size:53
Alignment explanation
Indices: 265446--265546 Score: 168
Period size: 52 Copynumber: 1.9 Consensus size: 53
265436 TGCGATTTTC
**
265446 ATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTT-CGCGTTGCGATAGTT
1 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATAGTT
*
265498 ATTTCGCGTTGTGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGAT
1 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGAT
265547 TCTCATTATC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 34 0.76
53 11 0.24
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.43
Consensus pattern (53 bp):
ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATAGTT
Found at i:265522 original size:33 final size:34
Alignment explanation
Indices: 265485--265550 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
265475 TTTCATTTCG
* *
265485 CGTTGCGATAGTTATTT-CGCGTTGTGATTCTCT
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
265518 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
265551 ATTATCTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 16 0.53
34 14 0.47
ACGTcount: A:0.12, C:0.23, G:0.24, T:0.41
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:267720 original size:21 final size:21
Alignment explanation
Indices: 267696--267762 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
267686 TCATTCCTCG
267696 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
267717 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
267738 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
267759 AGAG
1 AGAG
267763 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:267720 original size:42 final size:42
Alignment explanation
Indices: 267644--267762 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
267634 GACTCGCCTG
* * * * * * *
267644 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
267686 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
267728 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
267763 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:269132 original size:14 final size:14
Alignment explanation
Indices: 269113--269148 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
269103 ATTGTTTAAT
269113 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
269127 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
269141 TGATTTGT
1 TGATTTGT
269149 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:269277 original size:19 final size:19
Alignment explanation
Indices: 269255--269334 Score: 107
Period size: 19 Copynumber: 4.5 Consensus size: 19
269245 AAAAATTACT
*
269255 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
269274 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
269293 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
269307 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
269326 ATCGCAACG
1 ATCGCAACG
269335 ACAAAATCGC
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 37 0.70
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:269315 original size:33 final size:33
Alignment explanation
Indices: 269271--269353 Score: 148
Period size: 33 Copynumber: 2.5 Consensus size: 33
269261 ATGCGAAATG
*
269271 AAAATCGCAACGCGAAATGAAAATCGCAACGAG
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
*
269304 AGAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
269337 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
269354 CTAAATTCGC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.48, C:0.23, G:0.20, T:0.08
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGAC
Found at i:269402 original size:33 final size:33
Alignment explanation
Indices: 269359--269437 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
269349 CGAAACTAAA
*
269359 TTCGCGTTGCGATTCCCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
*
269392 TTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
269425 TTCGCATTGCGAT
1 TTCGCATTGCGAT
269438 AGTAATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.43
Consensus pattern (33 bp):
TTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
Found at i:269403 original size:19 final size:19
Alignment explanation
Indices: 269379--269437 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
269369 GATTCCCTCG
269379 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
269398 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
269412 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
269431 TTGCGAT
1 TTGCGAT
269438 AGTAATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:269417 original size:14 final size:14
Alignment explanation
Indices: 269363--269419 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
269353 ACTAAATTCG
*
269363 CGTTGCGATTCCCT
1 CGTTGCGATTCTCT
*
269377 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
269394 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
269410 CGTTGCGATT
1 CGTTGCGATT
269420 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 16 0.46
16 7 0.20
17 6 0.17
19 6 0.17
ACGTcount: A:0.11, C:0.26, G:0.21, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Done.