Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001194.1 Hibiscus syriacus cultivar Beakdansim tig00002367_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: 109815
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3388 original size:64 final size:64
Alignment explanation
Indices: 3276--3399 Score: 173
Period size: 64 Copynumber: 1.9 Consensus size: 64
3266 AATGCATTTT
*
3276 ATGCATCAATGCACTCAGGTTTTATGAAAAACATCGAATGTGTTTTATGCATCGATGCACAGACC
1 ATGCATCAATGCACTCAGGTTTTATG-AAAACATCGAATGTATTTTATGCATCGATGCACAGACC
*
3341 ATGCATCGATGCACTCAGGCTTGTT-TG-AAACATCGAAT-TCATTTTATGCATCGATGCAC
1 ATGCATCAATGCACTCAGG-TT-TTATGAAAACATCGAATGT-ATTTTATGCATCGATGCAC
3400 TCTTAGTGCA
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
63 1 0.02
64 29 0.54
65 18 0.33
66 4 0.07
67 2 0.04
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (64 bp):
ATGCATCAATGCACTCAGGTTTTATGAAAACATCGAATGTATTTTATGCATCGATGCACAGACC
Found at i:11667 original size:20 final size:20
Alignment explanation
Indices: 11642--11679 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11632 TTTGTGAAGG
11642 GATGCACCGATGCACTCATT
1 GATGCACCGATGCACTCATT
*
11662 GATGCATCGATGCACTCA
1 GATGCACCGATGCACTCA
11680 CCATATCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (20 bp):
GATGCACCGATGCACTCATT
Found at i:11754 original size:64 final size:63
Alignment explanation
Indices: 11684--11832 Score: 187
Period size: 64 Copynumber: 2.3 Consensus size: 63
11674 CACTCACCAT
**
11684 ATCGAATGCATTTTATACATTGATGCACTAT-CATGCAACGATGCACTCAGG-TT-TTATGAAAA
1 ATCGAATGCATTTTATACATCCATGCA-TATACATGCAACGATGCACTCAGGCTTGTT-TG--AA
11746 AC
62 AC
* *
11748 ATCGAATGCATTTTATGCATCCATGCATATACCATGCATCGATGCACTCAGGCTTGTTTGAAAC
1 ATCGAATGCATTTTATACATCCATGCATATA-CATGCAACGATGCACTCAGGCTTGTTTGAAAC
*
11812 ATCGAATGCATTTTATGCATC
1 ATCGAATGCATTTTATACATC
11833 GAAGAGTGCA
Statistics
Matches: 77, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
63 3 0.04
64 49 0.64
65 19 0.25
66 4 0.05
67 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (63 bp):
ATCGAATGCATTTTATACATCCATGCATATACATGCAACGATGCACTCAGGCTTGTTTGAAAC
Found at i:15166 original size:18 final size:18
Alignment explanation
Indices: 15156--15199 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
15146 AATTTATTTT
15156 TAAAATAAAATATTATAA
1 TAAAATAAAATATTATAA
*
15174 TAAAATAAAATA-TAAAGA
1 TAAAATAAAATATTATA-A
15192 TAAAATAA
1 TAAAATAA
15200 TTAATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
TAAAATAAAATATTATAA
Found at i:17113 original size:2 final size:2
Alignment explanation
Indices: 17106--17135 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17096 ATCATTTATC
17106 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
17136 TAGACAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18101 original size:17 final size:17
Alignment explanation
Indices: 18060--18106 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
18050 CATTTTATTT
*
18060 TTAAAA-AATCAGAAAAT
1 TTAAAAGAAT-AGAAAAC
*
18077 TTAAAAGATTAGAAAAC
1 TTAAAAGAATAGAAAAC
*
18094 TTAGAAGAATAGA
1 TTAAAAGAATAGA
18107 GGTTGAGAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 23 0.92
18 2 0.08
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.23
Consensus pattern (17 bp):
TTAAAAGAATAGAAAAC
Found at i:18364 original size:31 final size:31
Alignment explanation
Indices: 18328--18387 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
18318 AACTTAAAAG
18328 AGTTTTACAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
18359 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
18388 CATACAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:19079 original size:28 final size:28
Alignment explanation
Indices: 19048--19163 Score: 149
Period size: 24 Copynumber: 4.4 Consensus size: 28
19038 TATATGATAT
19048 AAAATTAAATATCTATAATATAATATTAA
1 AAAATT-AATATCTATAATATAATATTAA
*
19077 AAAATTAATAT-T-TAAT-TTAT-TTAA
1 AAAATTAATATCTATAATATAATATTAA
19101 AAAATTAATATCTATAATATAATATTAA
1 AAAATTAATATCTATAATATAATATTAA
*
19129 AAAATTAATAT-T-TAAT-TTAT-TTAA
1 AAAATTAATATCTATAATATAATATTAA
19153 AAAATTAATAT
1 AAAATTAATAT
19164 TAAAATTAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 13
0.83 0.03 0.14
Matches are distributed among these distances:
24 30 0.38
25 7 0.09
26 12 0.15
27 5 0.06
28 20 0.25
29 6 0.08
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
AAAATTAATATCTATAATATAATATTAA
Found at i:19111 original size:52 final size:52
Alignment explanation
Indices: 19048--19163 Score: 223
Period size: 52 Copynumber: 2.2 Consensus size: 52
19038 TATATGATAT
19048 AAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
1 AAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
19101 AAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
1 AAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
19153 AAAATTAATAT
1 AAAATTAATAT
19164 TAAAATTAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 57 0.90
53 6 0.10
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (52 bp):
AAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
Found at i:26380 original size:30 final size:30
Alignment explanation
Indices: 26338--26419 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 30
26328 ATTATGAATT
* *
26338 TTAGATTTAATATTAATTTGATCATAAA-C
1 TTAGATTAAATATCAATTTGATCATAAATC
*
26367 TTTAG-TTGAAATATCATTTTGATCATAAATC
1 -TTAGATT-AAATATCAATTTGATCATAAATC
26398 TTAGATTAAATATCAATTTGAT
1 TTAGATTAAATATCAATTTGAT
26420 TTATGAATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 2 0.04
30 40 0.89
31 3 0.07
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (30 bp):
TTAGATTAAATATCAATTTGATCATAAATC
Found at i:32386 original size:42 final size:44
Alignment explanation
Indices: 32339--32433 Score: 160
Period size: 42 Copynumber: 2.2 Consensus size: 44
32329 AAGTTGATGT
32339 TTTTCTATAAAGGATATTTAAAATA-TTTT-TTTACTTCTTTAC
1 TTTTCTATAAAGGATATTTAAAATATTTTTGTTTACTTCTTTAC
*
32381 TTTTCTGTAAAGGATATTTAAAATATTTTTGTTTACTTCTTTAC
1 TTTTCTATAAAGGATATTTAAAATATTTTTGTTTACTTCTTTAC
32425 TTTT-TATAA
1 TTTTCTATAA
32434 TTTAATTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
42 24 0.49
43 8 0.16
44 17 0.35
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.56
Consensus pattern (44 bp):
TTTTCTATAAAGGATATTTAAAATATTTTTGTTTACTTCTTTAC
Found at i:32479 original size:2 final size:2
Alignment explanation
Indices: 32472--32499 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32462 TTAGATCTAA
32472 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
32500 TAGTTTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36605 original size:21 final size:20
Alignment explanation
Indices: 36572--36614 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
36562 ATTATATTCA
**
36572 AAAATAAATATAACTATCAG
1 AAAATAAATATAAAAATCAG
*
36592 AAAATTAATGATAAAAATCAG
1 AAAATAAAT-ATAAAAATCAG
36613 AA
1 AA
36615 GAAAAAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (20 bp):
AAAATAAATATAAAAATCAG
Found at i:38617 original size:31 final size:30
Alignment explanation
Indices: 38539--38623 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 30
38529 TTCGATAATA
* *
38539 TAATAATTATTTTATAGTATTTAGATAAATTT
1 TAATAA-TATTTTATAATTTTTA-ATAAATTT
*
38571 TATTAATAATTTTATAATCTTTTAATAAA-TT
1 TAATAAT-ATTTTATAAT-TTTTAATAAATTT
38602 TAATAAGTATTTTATAATTTTT
1 TAATAA-TATTTTATAATTTTT
38624 TAAACTTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
30 4 0.09
31 18 0.39
32 20 0.43
33 4 0.09
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTAATAAATTT
Found at i:38618 original size:11 final size:10
Alignment explanation
Indices: 38541--38625 Score: 57
Period size: 10 Copynumber: 8.1 Consensus size: 10
38531 CGATAATATA
38541 ATAATTATTTT
1 ATAA-TATTTT
* *
38552 ATAGTATTTAG
1 ATAATATTT-T
38563 ATAA-ATTTT
1 ATAATATTTT
38572 ATTAATAATTTT
1 A-TAAT-ATTTT
*
38584 ATAATCTTTT
1 ATAATATTTT
*
38594 AATAA-ATTTA
1 -ATAATATTTT
38604 ATAAGTATTTT
1 ATAA-TATTTT
*
38615 ATAATTTTTT
1 ATAATATTTT
38625 A
1 A
38626 AACTTTATTG
Statistics
Matches: 58, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
9 5 0.09
10 25 0.43
11 22 0.38
12 6 0.10
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (10 bp):
ATAATATTTT
Found at i:38625 original size:31 final size:31
Alignment explanation
Indices: 38539--38626 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 31
38529 TTCGATAATA
* *
38539 TAATAATTATTTTAT-AGTATTTAGATAAATTT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATTT
* *
38571 TATTAATAATTTTATAATCTTTTAATAAA-TT
1 TAATAAT-ATTTTATAATTTTTTAATAAATTT
38602 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
38627 ACTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
31 24 0.51
32 18 0.38
33 5 0.11
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (31 bp):
TAATAATATTTTATAATTTTTTAATAAATTT
Found at i:39260 original size:31 final size:30
Alignment explanation
Indices: 39225--39311 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
39215 TCAATAAAGT
*
39225 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAACTATAAAATA-TTATTAAATTTA
* *
39256 TTAAAAGACTATAAAATTATTAATAAATTTA
1 TTAAAAAACTATAAAA-TATTATTAAATTTA
*
39287 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAACTATAAAAT-ATTATTA
39312 TATTATCGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (30 bp):
TTAAAAAACTATAAAATATTATTAAATTTA
Found at i:41194 original size:14 final size:14
Alignment explanation
Indices: 41171--41213 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
41161 TATTTTAATA
41171 TCAGCCTTTAAATT
1 TCAGCCTTTAAATT
* *
41185 TCAGCATTTATATT
1 TCAGCCTTTAAATT
41199 TCAGTCCTTTAAATT
1 TCAG-CCTTTAAATT
41214 CTAGCTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.47
Consensus pattern (14 bp):
TCAGCCTTTAAATT
Found at i:41223 original size:29 final size:27
Alignment explanation
Indices: 41163--41227 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 27
41153 ATTTATGTTA
*
41163 TTTTAATATCAGCCTTTAAATTTCAGC
1 TTTTAATTTCAGCCTTTAAATTTCAGC
*
41190 ATTTATATTTCAGTCCTTTAAA-TTCTAGC
1 TTTTA-ATTTCAG-CCTTTAAATTTC-AGC
41219 TTTTAATTT
1 TTTTAATTT
41228 TCTGAATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 4 0.12
28 13 0.41
29 15 0.47
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (27 bp):
TTTTAATTTCAGCCTTTAAATTTCAGC
Found at i:41628 original size:139 final size:139
Alignment explanation
Indices: 41456--41756 Score: 433
Period size: 139 Copynumber: 2.2 Consensus size: 139
41446 CTCTAACTAC
* * ***
41456 TTAATTATTTGAATCAATAGTTGGTTTAAAATTGAATAGATTAATATTTAGCGTCTTCACTTTAG
1 TTAATTATTTGAATCAATAATTGATTTAAAATTGAATAGATTAATATTTAGAACCTTCACTTTAG
* * * *
41521 GTTTAATTTCAAAATTACCCCTTTAATTTAAGGGAATTTTTAATTTGGT-ATTCGCTTTTGCTCG
66 GTTTAATTTCAAAATCACCCCTTTAATTTAAGGGAATTCTTAATTTGGTCA-TCACTTTTGCTCA
**
41585 AGATTTTATT
130 AGATTCCATT
* *
41595 TTAATTATTCGAATCAATAATTGATTTAAAATTGAATAGATTAATATTTAGAACCTTCATTTTAG
1 TTAATTATTTGAATCAATAATTGATTTAAAATTGAATAGATTAATATTTAGAACCTTCACTTTAG
* * *
41660 GTTTAATTTTAAAATCAGCCCTTTAATTTAGGGGAATTCTTAATTTGGTCATCACTTTTGCTCAA
66 GTTTAATTTCAAAATCACCCCTTTAATTTAAGGGAATTCTTAATTTGGTCATCACTTTTGCTCAA
*
41725 GGTTCCATT
131 GATTCCATT
41734 TTAATTATTTGAATCAATAATTG
1 TTAATTATTTGAATCAATAATTG
41757 GTTAACAAAA
Statistics
Matches: 143, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
139 142 0.99
140 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.45
Consensus pattern (139 bp):
TTAATTATTTGAATCAATAATTGATTTAAAATTGAATAGATTAATATTTAGAACCTTCACTTTAG
GTTTAATTTCAAAATCACCCCTTTAATTTAAGGGAATTCTTAATTTGGTCATCACTTTTGCTCAA
GATTCCATT
Found at i:46903 original size:26 final size:24
Alignment explanation
Indices: 46846--46903 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 24
46836 AAGAAGTGAA
* *
46846 AATTTTATAATAATAATATTAATT
1 AATTTTAAAAGAATAATATTAATT
*
46870 ATACTTTAAAAGAATTAATATTTAATT
1 A-ATTTTAAAAGAA-TAATA-TTAATT
46897 AATTTTA
1 AATTTTA
46904 TAACTAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
24 1 0.04
25 9 0.33
26 10 0.37
27 7 0.26
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
AATTTTAAAAGAATAATATTAATT
Found at i:47172 original size:30 final size:31
Alignment explanation
Indices: 47099--47175 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
47089 CAGTTATGTC
47099 AGGGACCATATTGCAAACGGACTAAATGTTG
1 AGGGACCATATTGCAAACGGACTAAATGTTG
*
47130 AGGGACCATATTGCAAATGGACTAAATGTTG
1 AGGGACCATATTGCAAACGGACTAAATGTTG
**
47161 -GGGACTTTATTGCAA
1 AGGGACCATATTGCAA
47176 GTTTTAAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 13 0.30
31 30 0.70
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (31 bp):
AGGGACCATATTGCAAACGGACTAAATGTTG
Found at i:48595 original size:46 final size:45
Alignment explanation
Indices: 48528--48991 Score: 217
Period size: 46 Copynumber: 10.7 Consensus size: 45
48518 GATCAGGTCA
* *
48528 GGTGATGACATGGTTCCTACGTGATGAGGATGGCATGTCATCTAAG
1 GGTGATGACACGGTTCCTACGTGATGAGGATAGCATGTCATCT-AG
* * *
48574 GGTGATAACACGGTTCCTACGTGATGAGGA-CG-ACTGGTTATCT-G
1 GGTGATGACACGGTTCCTACGTGATGAGGATAGCA-T-GTCATCTAG
** * * *
48618 AGGT--TGACACGACTCCTATGTGATGAGGATATCA-G--GT-T-G
1 -GGTGATGACACGGTTCCTACGTGATGAGGATAGCATGTCATCTAG
* * * * * *
48657 AGTGATGACATGGTTCCTACGTAATGAGGA-CGACAGGCCATCTAAG
1 GGTGATGACACGGTTCCTACGTGATGAGGATAG-CATGTCATCT-AG
* * * *
48703 GGTGATAACACAGTTCTTACGTGATGAGGATAGC-TGGTTATCTAG
1 GGTGATGACACGGTTCCTACGTGATGAGGATAGCAT-GTCATCTAG
* * ** *
48748 GGT--TGACACGGCTCCTACGTGATGA--AGAG-A--TCAGGTCG
1 GGTGATGACACGGTTCCTACGTGATGAGGATAGCATGTCATCTAG
* * * * *
48786 GGAGATGACACGGTTCCTACGTGATAAGGACAGCAGGCCATCTAAG
1 GGTGATGACACGGTTCCTACGTGATGAGGATAGCATGTCATCT-AG
* * * * * *
48832 GGTGATAACATGGCTCCTACATGATGAGGACAGC-TGGTTATCT-G
1 GGTGATGACACGGTTCCTACGTGATGAGGATAGCAT-GTCATCTAG
* * * * ** *
48876 GG-GTTGACATGGCTCCTACATGATGAGG--AG-A--TCAGGTCG
1 GGTGATGACACGGTTCCTACGTGATGAGGATAGCATGTCATCTAG
* * * *
48915 GGTGATGACACGGTTCCTTCGTGGTGAGGATAGAATGCCATCTAAG
1 GGTGATGACACGGTTCCTACGTGATGAGGATAGCATGTCATCT-AG
*
48961 GGTGATAACACGGTTCCTACGTGATGAGGAT
1 GGTGATGACACGGTTCCTACGTGATGAGGAT
48992 GACTGGTTAT
Statistics
Matches: 309, Mismatches: 74, Indels: 70
0.68 0.16 0.15
Matches are distributed among these distances:
38 11 0.04
39 5 0.02
40 63 0.20
41 6 0.02
42 6 0.02
43 66 0.21
44 6 0.02
45 17 0.06
46 128 0.41
47 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (45 bp):
GGTGATGACACGGTTCCTACGTGATGAGGATAGCATGTCATCTAG
Found at i:48724 original size:129 final size:130
Alignment explanation
Indices: 48490--49103 Score: 801
Period size: 129 Copynumber: 4.7 Consensus size: 130
48480 ATCGTCTAAG
* * *
48490 GGTTGACACGGCTCCTACATGATGAGGAGATCAGGTCAGGTGATGACATGGTTCCTACGTGATGA
1 GGTTGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTACGTGATGA
* * * *
48555 GGATGGCATGTCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGA-CTGGTTATCTGA
66 GGACGACAGGCCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGAGCTGGTTATCTGA
* * * * * * *
48619 GGTTGACACGACTCCTATGTGATGAGGATATCAGGTTGAGTGATGACATGGTTCCTACGTAATGA
1 GGTTGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTACGTGATGA
* * *
48684 GGACGACAGGCCATCTAAGGGTGATAACACAGTTCTTACGTGATGAGGA-TAGCTGGTTATCT-A
66 GGACGACAGGCCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGAGCTGGTTATCTGA
* * *
48747 GGGTTGACACGGCTCCTACGTGATGAAGAGATCAGGTCGGGAGATGACACGGTTCCTACGTGATA
1 -GGTTGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTACGTGATG
* * *
48812 AGGAC-AGCAGGCCATCTAAGGGTGATAACATGGCTCCTACATGATGAGGAC-AGCTGGTTATCT
65 AGGACGA-CAGGCCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGAGCTGGTTATCT
*
48875 GG
129 GA
* * * *
48877 GGTTGACATGGCTCCTACATGATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTTCGTGGTGA
1 GGTTGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTACGTGATGA
* * * *
48942 GGATAGA-ATGCCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGATGA-CTGGTTATTTG
66 GGA-CGACAGGCCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGAGCTGGTTATCTG
*
49005 G
130 A
* * *
49006 GGTTGACATGGCTCCTACGTTATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTATGTGATGA
1 GGTTGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTACGTGATGA
*
49071 GGACGACAGGCCATCATTAGGGATGATAACACG
66 GGACGACAGGCCATC-TAAGGG-TGATAACACG
49104 ATTTCAAGAG
Statistics
Matches: 421, Mismatches: 53, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
128 5 0.01
129 399 0.95
130 6 0.01
131 11 0.03
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (130 bp):
GGTTGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTACGTGATGA
GGACGACAGGCCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGAGCTGGTTATCTGA
Found at i:48895 original size:43 final size:44
Alignment explanation
Indices: 48724--48904 Score: 131
Period size: 43 Copynumber: 4.2 Consensus size: 44
48714 AGTTCTTACG
* * * * *
48724 TGATGAGGATAGCTGGTTATCTAGG-GTTGACACGGCTCCTACG
1 TGATGAGGACAGCAGGTTATCTGGGAGATGACACGGCTCCTACA
* * * * *
48767 TGATGAAGAGATCAGG---TC-GGGAGATGACACGGTTCCTACG
1 TGATGAGGACAGCAGGTTATCTGGGAGATGACACGGCTCCTACA
* ** * * *
48807 TGATAAGGACAGCAGGCCATCTAAGGGTGATAACATGGCTCCTACA
1 TGATGAGGACAGCAGGTTATCT--GGGAGATGACACGGCTCCTACA
* * *
48853 TGATGAGGACAGCTGGTTATCTGGG-GTTGACATGGCTCCTACA
1 TGATGAGGACAGCAGGTTATCTGGGAGATGACACGGCTCCTACA
48896 TGATGAGGA
1 TGATGAGGA
48905 GATCAGGTCG
Statistics
Matches: 109, Mismatches: 22, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
39 2 0.02
40 30 0.28
43 39 0.36
44 3 0.03
46 35 0.32
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (44 bp):
TGATGAGGACAGCAGGTTATCTGGGAGATGACACGGCTCCTACA
Found at i:49290 original size:65 final size:65
Alignment explanation
Indices: 49135--49443 Score: 224
Period size: 64 Copynumber: 4.7 Consensus size: 65
49125 CATATGACGC
* ** * * * * * * *
49135 TTCAAGAGAAGCTGTCTCAAAAGAGATAACATCTATTTCAAGGGAAACGA-TCTCAAAG-ATATG
1 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAA-TATTTTCAAAGTTTATG
49198 T
65 T
* *
49199 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATATTTTCAAAGTTTATAT
1 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATATTTTCAAAGTTTATGT
* * *
49264 TTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACT-GTCTCAAGGGAGAC
1 TTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAA-TATTTTCAA---AG--
***
49328 AAAACTTGT
59 TTTA--TGT
* ** *
49337 TTCAAGGGAAACTGAT-TCAA---AG---ATTTTGTGTTTCAAGGGAAACATTTTCAAAGTTTAT
1 TTCAAGAGAAACTG-TCTCAAGGGAGACAAAATT-TGTTTCAAGGGAAATATTTTCAAAGTTTAT
49395 GT
64 GT
* *
49397 TTCAAGAGAAATTGTCTCAAGGAAGACAAAATTTGTTTCAAGGGAAA
1 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAA
49444 CTATCTCAAG
Statistics
Matches: 192, Mismatches: 32, Indels: 41
0.72 0.12 0.15
Matches are distributed among these distances:
59 1 0.01
60 19 0.10
62 1 0.01
63 3 0.02
64 50 0.26
65 47 0.24
66 26 0.14
67 21 0.11
69 2 0.01
70 2 0.01
71 1 0.01
73 18 0.09
74 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (65 bp):
TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATATTTTCAAAGTTTATGT
Found at i:49344 original size:36 final size:35
Alignment explanation
Indices: 49196--49724 Score: 304
Period size: 36 Copynumber: 15.4 Consensus size: 35
49186 CTCAAAGATA
* *
49196 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-T
* ***
49232 TGTTTCAAGGGAAA-TATTTTC-A-A-AG--TTTA-
1 TGTTTCAAGGGAAACTA-TCTCAAGAGAGACAAAAT
* * * * *
49261 TATTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA--T
* *
49298 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAACT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-T
***
49334 TGTTTCAAGGGAAACTGAT-TC-A-A-AG--ATTTT
1 TGTTTCAAGGGAAACT-ATCTCAAGAGAGACAAAAT
* ***
49364 GTGTTTCAAGGGAAAC-ATTTTC-A-A-AG--TTTA-
1 -TGTTTCAAGGGAAACTA-TCTCAAGAGAGACAAAAT
* * *
49394 TGTTTCAAGAGAAATTGTCTCAAG-GAAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAG-AGACAAAA-T
*
49430 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-T
*
49466 TGTTTCAAGGGAAACTATCTCAAAAGAGACAAAAT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
* * *
49501 TCGTTCCAAGTGAAACTATCTCAAAAGAGACAAAAAT
1 T-GTTTCAAGGGAAACTATCTCAAGAGAGAC-AAAAT
** * ***
49538 CATTTCAAGGGAAACGT-TTTC-A-A-AG--TTTA-
1 TGTTTCAAGGGAAAC-TATCTCAAGAGAGACAAAAT
* *
49567 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-T
* *
49603 TGTTTCAAGGGAAACTATCTCGAGAGAAACAAAAT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
* *
49638 TCGTTTCAAGAGAAACTATCTCGAGAGAGACAAAAT
1 T-GTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
* *
49674 TCGTTTCAAGAGAAACTATTTCAAGAGAGACAAAAT
1 T-GTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
* *
49710 TCATTTTAAGGGAAA
1 T-GTTTCAAGGGAAA
49725 TGTTTTCAAA
Statistics
Matches: 391, Mismatches: 66, Indels: 72
0.74 0.12 0.14
Matches are distributed among these distances:
28 1 0.00
29 47 0.12
30 7 0.02
31 25 0.06
32 6 0.02
33 6 0.02
34 5 0.01
35 8 0.02
36 247 0.63
37 39 0.10
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (35 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
Found at i:49407 original size:29 final size:30
Alignment explanation
Indices: 49334--49407 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 30
49324 AGACAAAACT
*
49334 TGTTTCAAGGGAAACTGATTCAAAGATTTTG
1 TGTTTCAAGGGAAACTGATTCAAAGA-TTTA
*
49365 TGTTTCAAGGGAAACAT-TTTCAAAG-TTTA
1 TGTTTCAAGGGAAAC-TGATTCAAAGATTTA
*
49394 TGTTTCAAGAGAAA
1 TGTTTCAAGGGAAA
49408 TTGTCTCAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 16 0.41
31 22 0.56
32 1 0.03
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.35
Consensus pattern (30 bp):
TGTTTCAAGGGAAACTGATTCAAAGATTTA
Found at i:49492 original size:133 final size:133
Alignment explanation
Indices: 49232--49489 Score: 448
Period size: 133 Copynumber: 1.9 Consensus size: 133
49222 AGACAAAATT
* *
49232 TGTTTCAAGGGAAATATTTTCAAAGTTTATATTTCAAGAGAAATTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACATTTTCAAAGTTTATATTTCAAGAGAAATTGTCTCAAGGAAGACAAAATT
*
49297 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAACTGATTCAAAGATT
66 TTGTTTCAAGGGAAACTATCTCAAGGGAGACAAAACTTGTTTCAAGGGAAACTGATTCAAAGATT
49362 TTG
131 TTG
*
49365 TGTTTCAAGGGAAACATTTTCAAAGTTTATGTTTCAAGAGAAATTGTCTCAAGGAAGACAAAA-T
1 TGTTTCAAGGGAAACATTTTCAAAGTTTATATTTCAAGAGAAATTGTCTCAAGGAAGACAAAATT
*
49429 TTGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACT-ATCTCAAA
66 TTGTTTCAAGGGAAACTATCTCAAGGGAGACAAAACTTGTTTCAAGGGAAACTGAT-TCAAA
49490 AGAGACAAAA
Statistics
Matches: 119, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
131 2 0.02
132 57 0.48
133 60 0.50
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (133 bp):
TGTTTCAAGGGAAACATTTTCAAAGTTTATATTTCAAGAGAAATTGTCTCAAGGAAGACAAAATT
TTGTTTCAAGGGAAACTATCTCAAGGGAGACAAAACTTGTTTCAAGGGAAACTGATTCAAAGATT
TTG
Found at i:49567 original size:173 final size:172
Alignment explanation
Indices: 49263--49776 Score: 657
Period size: 173 Copynumber: 3.0 Consensus size: 172
49253 AAAGTTTATA
* * * * *
49263 TTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTGTCTCAAGGGAGAC
1 TTTCAAGGGAAACTATCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
* ***** * *
49328 AAAACTT-GTTTCAAGGGAAACTGATTC--AA-AGA-TTTTGT-GTTTCAAGGGAAACATTTTCA
65 AAAA-TTCGTTTCAAGAGAAACT-ATTCAAAAGAGACAAAAATCATTTCAAGGGAAACGTTTTCA
* *
49387 AAGTTTATGTTTCAAGAGAAATTGTCTCAAGGAAGACAAAATTTG
128 AAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTG
*
49432 TTTCAAGGGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAAAGAGACA
1 TTTCAAGGGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACA
* *
49497 AAATTCGTTCCAAGTGAAACTATCTCAAAAGAGACAAAAATCATTTCAAGGGAAACGTTTTCAAA
66 AAATTCGTTTCAAGAGAAACTAT-TCAAAAGAGACAAAAATCATTTCAAGGGAAACGTTTTCAAA
*
49562 GTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTG
130 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTG
* * * * * *
49605 TTTCAAGGGAAACTATCTCGAGAGAAACAAAATTCGTTTCAAGAGAAACTATCTCGAGAGAGACA
1 TTTCAAGGGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACA
* * * *
49670 AAATTCGTTTCAAGAGAAACTATTTCAAGAGAGACAAAATTCATTTTAAGGGAAATGTTTTCAAA
66 AAATTCGTTTCAAGAGAAACTA-TTCAAAAGAGACAAAAATCATTTCAAGGGAAACGTTTTCAAA
49735 G-TTATGTTTCAAGAGAAACTGTCTCAAGGGAGA-AAATATTTG
130 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAA-ATTTG
49777 AAATCATTGA
Statistics
Matches: 304, Mismatches: 32, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
167 4 0.01
168 48 0.16
169 29 0.10
170 2 0.01
171 6 0.02
172 37 0.12
173 177 0.58
174 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (172 bp):
TTTCAAGGGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACA
AAATTCGTTTCAAGAGAAACTATTCAAAAGAGACAAAAATCATTTCAAGGGAAACGTTTTCAAAG
TTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTG
Found at i:49573 original size:101 final size:101
Alignment explanation
Indices: 49466--49653 Score: 268
Period size: 101 Copynumber: 1.9 Consensus size: 101
49456 AGACAAAATT
* * *
49466 TGTTTCAAGGGAAACTATCTCAAAAGAGACAAAATTCGTTCCAAGTGAAACTATCTCAAAAGAGA
1 TGTTTCAAGAGAAACTATCTCAAAAGAGACAAAATTCGTTCCAAGGGAAACTATCTCAAAAGAAA
*
49531 CAAAAATCATTTCAAGGGAAACGTTTTCAAAGTTTA
66 CAAAAATCATTTCAAGAGAAACGTTTTCAAAGTTTA
** * * * *
49567 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCGAGAGAAA
1 TGTTTCAAGAGAAACTATCTCAAAAGAGACAAAATTCGTTCCAAGGGAAACTATCTCAAAAGAAA
* *
49632 CAAAATTCGTTTCAAGAGAAAC
66 CAAAAATCATTTCAAGAGAAAC
49654 TATCTCGAGA
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
101 75 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (101 bp):
TGTTTCAAGAGAAACTATCTCAAAAGAGACAAAATTCGTTCCAAGGGAAACTATCTCAAAAGAAA
CAAAAATCATTTCAAGAGAAACGTTTTCAAAGTTTA
Found at i:49595 original size:137 final size:137
Alignment explanation
Indices: 49430--49697 Score: 421
Period size: 137 Copynumber: 2.0 Consensus size: 137
49420 AGACAAAATT
* *
49430 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAAAGAGA
1 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAAAGAAA
* *
49495 CAAAATTCGTTCCAAGTGAAACTATCTCAAAAGAGACAAAAATCATTTCAAGGGAAACGT-TTTC
66 CAAAATTCGTTCCAAGAGAAACTATCTCAAAAGAGACAAAAATCATTTCAAGAGAAAC-TATTTC
49559 AAAGTTTA
130 AAAGTTTA
* *
49567 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCGAGAGAAA
1 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAAAGAAA
* * * * *
49632 CAAAATTCGTTTCAAGAGAAACTATCTCGAGAGAGACAAAATTCGTTTCAAGAGAAACTATTTCA
66 CAAAATTCGTTCCAAGAGAAACTATCTCAAAAGAGACAAAAATCATTTCAAGAGAAACTATTTCA
49697 A
131 A
49698 GAGAGACAAA
Statistics
Matches: 119, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
136 1 0.01
137 118 0.99
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.25
Consensus pattern (137 bp):
TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAAAGAAA
CAAAATTCGTTCCAAGAGAAACTATCTCAAAAGAGACAAAAATCATTTCAAGAGAAACTATTTCA
AAGTTTA
Found at i:49651 original size:21 final size:21
Alignment explanation
Indices: 49625--49689 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
49615 AACTATCTCG
49625 AGAGAAACAAAATTCGTTTCA
1 AGAGAAACAAAATTCGTTTCA
* *
49646 AGAGAAAC--TA-TC---TCG
1 AGAGAAACAAAATTCGTTTCA
*
49661 AGAGAGACAAAATTCGTTTCA
1 AGAGAAACAAAATTCGTTTCA
49682 AGAGAAAC
1 AGAGAAAC
49690 TATTTCAAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 9 0.28
17 1 0.03
18 4 0.12
19 1 0.03
21 17 0.53
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.20
Consensus pattern (21 bp):
AGAGAAACAAAATTCGTTTCA
Found at i:50768 original size:15 final size:15
Alignment explanation
Indices: 50748--50781 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
50738 AATCCCCAAA
*
50748 GATGCCCCAATATTT
1 GATGCCCCAACATTT
50763 GATGCCCCAACATTT
1 GATGCCCCAACATTT
50778 GATG
1 GATG
50782 TTGAATCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (15 bp):
GATGCCCCAACATTT
Found at i:52007 original size:2 final size:2
Alignment explanation
Indices: 52000--52047 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
51990 ACAACAAGGG
* *
52000 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52042 AT AT AT
1 AT AT AT
52048 GGATAAATGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:55661 original size:146 final size:147
Alignment explanation
Indices: 55305--55692 Score: 426
Period size: 146 Copynumber: 2.7 Consensus size: 147
55295 GATCTGCTGT
* *
55305 CATCCACCGT-TCGATCGTCCTGATTTTTCAATATGTTGTTCGTGTTGACAT-AGCGCAACTTTT
1 CATCCACCGTCT-GATCGTCTTGATTTTTCAGTATGTTGTTCGTGTTGACATCA-CGCAACTTTT
* * * * *** **
55368 CATTGTTCGGAATGTTGATCGG-GGATCATGATCGTTGGCAAGAGGCCTAAAATTGTCTGGATTT
64 GATCGTTCGGAATGTTGATCGGAGGATCATGATCGCTGGCAAGAGGCCAAAAACCATCCAGATTT
*
55432 GTTTTCTCCGATCCTCCAC
129 GTTTTCTCCGATCCGCCAC
** ** * * * * ** *
55451 TTTCCACTTTCCGATCGTCTTGATTTTTCAGCATGTTGTTCGAGTTGACATCTCAAAAGTTTTGA
1 CATCCACCGTCTGATCGTCTTGATTTTTCAGTATGTTGTTCGTGTTGACATCACGCAACTTTTGA
* * *
55516 TCGTTCGGAATGTTGACCGGAGG-TCTTGATCGCTGGCCAGAGGCCAAAAACCATCCAGATTTGT
66 TCGTTCGGAATGTTGATCGGAGGATCATGATCGCTGGCAAGAGGCCAAAAACCATCCAGATTTGT
* *
55580 TTTTTTCGATCCGCCAC
131 TTTCTCCGATCCGCCAC
*
55597 CATCCACCGTCTGATCGTCTTGATTTTTCAGTATGTTGTTCGTGTTGACATCACGCAACCTTTGA
1 CATCCACCGTCTGATCGTCTTGATTTTTCAGTATGTTGTTCGTGTTGACATCACGCAACTTTTGA
* * * *
55662 CCATTCGAAATGTTGATCGGAGGCTCA-GATC
66 TCGTTCGGAATGTTGATCGGAGGATCATGATC
55693 ACCGGAAAGA
Statistics
Matches: 193, Mismatches: 45, Indels: 8
0.78 0.18 0.03
Matches are distributed among these distances:
146 189 0.98
147 4 0.02
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.35
Consensus pattern (147 bp):
CATCCACCGTCTGATCGTCTTGATTTTTCAGTATGTTGTTCGTGTTGACATCACGCAACTTTTGA
TCGTTCGGAATGTTGATCGGAGGATCATGATCGCTGGCAAGAGGCCAAAAACCATCCAGATTTGT
TTTCTCCGATCCGCCAC
Found at i:55994 original size:3 final size:3
Alignment explanation
Indices: 55986--56044 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
55976 AATGGTTTTA
* * *
55986 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AGT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
56034 ATTT AAT AAT A
1 A-AT AAT AAT A
56045 TTTTTTTGAC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
3 45 0.96
4 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:56009 original size:15 final size:15
Alignment explanation
Indices: 55986--56044 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
55976 AATGGTTTTA
*
55986 AATAATAATAATAAT
1 AATAGTAATAATAAT
56001 AATAGTAATAATAAT
1 AATAGTAATAATAAT
*
56016 AATAGTAATGATAAT
1 AATAGTAATAATAAT
*
56031 AATATTTAATAATA
1 AATA-GTAATAATA
56045 TTTTTTTGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
15 32 0.82
16 7 0.18
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (15 bp):
AATAGTAATAATAAT
Found at i:58125 original size:30 final size:30
Alignment explanation
Indices: 58091--58153 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
58081 GTTATATGAG
*
58091 CTATGTGATAAAGGTATGGAAATGATATGT
1 CTATGTGATAAAGGTATGGAAATAATATGT
*
58121 CTATGTGATAAATGTATGGAAATAATATGT
1 CTATGTGATAAAGGTATGGAAATAATATGT
58151 CTA
1 CTA
58154 CGCGATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGGAAATAATATGT
Found at i:58429 original size:23 final size:23
Alignment explanation
Indices: 58397--58479 Score: 89
Period size: 23 Copynumber: 3.6 Consensus size: 23
58387 ATCATATATA
*
58397 GCACTACGGTGCATTTCTACGTG
1 GCACTTCGGTGCATTTCTACGTG
* *
58420 GCACTTCGGTGCATTTCTAAGCG
1 GCACTTCGGTGCATTTCTACGTG
*
58443 GTC-CTTCGG-GACAAATTCTACGTG
1 G-CACTTCGGTG-C-ATTTCTACGTG
58467 GCACTTCGGTGCA
1 GCACTTCGGTGCA
58480 AATTTATACG
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
22 1 0.02
23 30 0.61
24 17 0.35
25 1 0.02
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGTG
Found at i:60567 original size:31 final size:31
Alignment explanation
Indices: 60529--60596 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
60519 TAGTTACGTC
**
60529 AGGGACCATATTGCAAACGGACTAAATGTTG
1 AGGGACCATATTGCAAACAAACTAAATGTTG
*
60560 AGGGACCATATTGTAAACAAACTAAATGTTG
1 AGGGACCATATTGCAAACAAACTAAATGTTG
*
60591 GGGGAC
1 AGGGAC
60597 TGTATTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (31 bp):
AGGGACCATATTGCAAACAAACTAAATGTTG
Found at i:62758 original size:41 final size:42
Alignment explanation
Indices: 62713--62808 Score: 178
Period size: 41 Copynumber: 2.3 Consensus size: 42
62703 CGATTTTCCC
62713 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATT-GGAA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
62754 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
62796 AA-TCGCAATGCGA
1 AATTCGCAATGCGA
62809 TACTGACTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 48 0.89
42 6 0.11
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (42 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
Found at i:62762 original size:21 final size:20
Alignment explanation
Indices: 62716--62844 Score: 100
Period size: 20 Copynumber: 6.3 Consensus size: 20
62706 TTTTCCCAAT
*
62716 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
62736 TCGCAACGCGAATTGGAAAA
1 TCGCAATGCGAATAAGAAAA
*
62756 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGAAAA
* **
62777 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
* **
62798 TCGCAATGCG-ATACTGACTA
1 TCGCAATGCGAATA-AGAAAA
62818 TCGCAATGCGATAATAA-AAAA
1 TCGCAATGCG--AATAAGAAAA
62839 TCGCAA
1 TCGCAA
62845 CGAGATACTT
Statistics
Matches: 83, Mismatches: 20, Indels: 11
0.73 0.18 0.10
Matches are distributed among these distances:
19 1 0.01
20 41 0.49
21 38 0.46
23 3 0.04
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:62821 original size:41 final size:40
Alignment explanation
Indices: 62735--62869 Score: 121
Period size: 41 Copynumber: 3.3 Consensus size: 40
62725 GAATAAGTAA
* *
62735 ATCGCAACGCGAATTGGAAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGAAAA-TCGCAATGCG-ATACTG-ACT
62776 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATT-GGAAAATCGCAATGCGATACTGACT
* * ** * * *
62817 ATCGCAATGCGATAATAAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGAAAATCGCAATGCGATACTGACT
*
62858 TTCGCAACGCGA
1 ATCGCAACGCGA
62870 TACTGACTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
40 4 0.05
41 67 0.85
42 8 0.10
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (40 bp):
ATCGCAACGCGAATTGGAAAATCGCAATGCGATACTGACT
Found at i:62887 original size:20 final size:20
Alignment explanation
Indices: 62797--62890 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
62787 AATTGGGAAA
*
62797 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
62817 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
62838 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
62858 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
62878 TTCGCAACGCGAT
1 ATCGCAACGCGAT
62891 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:63468 original size:19 final size:19
Alignment explanation
Indices: 63444--63488 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
63434 GGAACGAGAG
**
63444 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
63463 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
63482 AATCGCA
1 AATCGCA
63489 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:63506 original size:19 final size:19
Alignment explanation
Indices: 63484--63648 Score: 152
Period size: 19 Copynumber: 9.1 Consensus size: 19
63474 GAAACCAAAA
*
63484 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
63503 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
63522 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
63541 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
63555 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
63574 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
63588 TCTCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
63608 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
63627 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
63647 TC
1 TC
63649 AACCAAAAGA
Statistics
Matches: 120, Mismatches: 14, Indels: 24
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.16
16 4 0.03
17 5 0.04
19 61 0.51
20 31 0.26
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:63540 original size:38 final size:33
Alignment explanation
Indices: 63489--63623 Score: 162
Period size: 33 Copynumber: 3.9 Consensus size: 33
63479 CAAAATCGCA
*
63489 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TTC---TCTCG
63527 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* **
63560 TCGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
63593 TTGCGATAGTCATTTTCGCGTTGCGATTCTC
1 TTGCGATTTTCA-TTTCGCGTTGCGATTCTC
63624 ATTATCTCGT
Statistics
Matches: 91, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
33 45 0.49
34 18 0.20
36 3 0.03
38 25 0.27
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:63640 original size:20 final size:20
Alignment explanation
Indices: 63588--63646 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
63578 GTTGCGATTC
** *
63588 TCTCGTTGCGATAGTCATTT
1 TCTCGTTGCGATTCTCATTA
*
63608 TCGCGTTGCGATTCTCATTA
1 TCTCGTTGCGATTCTCATTA
*
63628 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTCTCATT
63647 TCAACCAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (20 bp):
TCTCGTTGCGATTCTCATTA
Found at i:65730 original size:42 final size:42
Alignment explanation
Indices: 65650--65733 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
65640 GCCCGACTCG
* * * *
65650 CCTATCATCCCTCAAGATTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
65692 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
65734 ATTGTCATCG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.21, C:0.39, G:0.15, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:67149 original size:14 final size:14
Alignment explanation
Indices: 67130--67165 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
67120 ATTGTTTAAT
67130 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
67144 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
67158 TGATTTGT
1 TGATTTGT
67166 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:67384 original size:33 final size:33
Alignment explanation
Indices: 67348--67507 Score: 277
Period size: 33 Copynumber: 4.8 Consensus size: 33
67338 ATTAAATTCG
* **
67348 CGTTGCGATTTTCATTTCGCATTGCGAAAT-TAG
1 CGTTGCGATTTTCATTTCGCATTGCG-ATTCTCT
67381 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
67414 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
67447 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
67480 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
67508 AGTAATTTCC
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
32 2 0.02
33 121 0.98
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:67421 original size:14 final size:14
Alignment explanation
Indices: 67402--67489 Score: 68
Period size: 14 Copynumber: 5.6 Consensus size: 14
67392 TCATTTCGCA
67402 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
67416 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
67433 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
67449 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
67466 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
67482 TTGCGATT
1 TTGCGATT
67490 TTCATTTCGC
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 20 0.33
16 14 0.23
17 14 0.23
19 12 0.20
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:69817 original size:12 final size:12
Alignment explanation
Indices: 69800--69824 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
69790 TCTTCGGGGA
69800 CTTTTTCTTCTT
1 CTTTTTCTTCTT
69812 CTTTTTCTTCTT
1 CTTTTTCTTCTT
69824 C
1 C
69825 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:70033 original size:24 final size:24
Alignment explanation
Indices: 69999--70052 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
69989 CTGAAACATC
* *
69999 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
70023 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
70047 ATCAAA
1 ATCAAA
70053 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:72646 original size:19 final size:20
Alignment explanation
Indices: 72592--72658 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
72582 TAGTTTACTT
* *
72592 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
72612 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
72632 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
72651 TCGCAACG
1 TCGCAACG
72659 AAAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:72666 original size:14 final size:14
Alignment explanation
Indices: 72647--72704 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
72637 ATGCGAAATG
72647 AAAATCGCAACGAA
1 AAAATCGCAACGAA
72661 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAA
*
72677 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAA
72693 AAAATCGCAACG
1 AAAATCGCAACG
72705 CGAAACACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 21 0.54
16 9 0.23
18 9 0.23
ACGTcount: A:0.50, C:0.24, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:72689 original size:32 final size:33
Alignment explanation
Indices: 72631--72709 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
72621 GGAAATGGCT
*
72631 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
*
72664 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
72696 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
72710 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
Found at i:72738 original size:19 final size:17
Alignment explanation
Indices: 72716--72811 Score: 60
Period size: 19 Copynumber: 5.6 Consensus size: 17
72706 GAAACACAAA
72716 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
72735 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
*
72751 TCG-TTACGATTTCATT
1 TCGCTTGCGATTTCATT
* *
72767 TCGTGTTGCGATTT--TG
1 TCG-CTTGCGATTTCATT
72783 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
72800 TCGCATTGCGAT
1 TCGC-TTGCGAT
72812 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
14 14 0.23
15 3 0.05
16 12 0.20
17 4 0.07
18 12 0.20
19 16 0.26
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:72760 original size:14 final size:14
Alignment explanation
Indices: 72738--72795 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
72728 TTTCATTTCG
72738 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
72752 CGTTACGATTTCATTT
1 CGTTGCGATTT--TGT
72768 CGTGTTGCGATTTTGT
1 C--GTTGCGATTTTGT
72784 CGTTGCGATTTT
1 CGTTGCGATTTT
72796 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 21 0.58
16 6 0.17
18 9 0.25
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:72802 original size:33 final size:33
Alignment explanation
Indices: 72721--72811 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
72711 ACAAATCGCA
72721 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
72754 TTACGA-TTTCATTTCGTGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
72786 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
72812 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
32 30 0.58
33 22 0.42
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:72848 original size:20 final size:20
Alignment explanation
Indices: 72796--72839 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
72786 TTGCGATTTT
*
72796 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
72815 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
72835 CATTT
1 CATTT
72840 TCGTGTTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:73349 original size:18 final size:18
Alignment explanation
Indices: 73323--73367 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
73313 GTCGATCAGA
*
73323 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
73341 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
73359 TGATGGCTC
1 TGATGGCTC
73368 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:75011 original size:22 final size:22
Alignment explanation
Indices: 74986--75029 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
74976 AGATTTAGAT
74986 AGACGGATTTCGCCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
*
75008 AGACGGATTTCGTCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
75030 GTGAGAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.16, G:0.41, T:0.20
Consensus pattern (22 bp):
AGACGGATTTCGCCGGAGATGG
Found at i:75243 original size:20 final size:20
Alignment explanation
Indices: 75218--75311 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
75208 GATTATGTAT
75218 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
75238 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
75258 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
75279 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
75299 TATCGCATTGCGA
1 TATCGCGTTGCGA
75312 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:75283 original size:41 final size:41
Alignment explanation
Indices: 75238--75315 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
75228 CGAAAGTCAG
* * *
75238 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
75279 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
75316 CCCAATTCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:75312 original size:20 final size:20
Alignment explanation
Indices: 75198--75312 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
75188 CGCTTTGAAA
*
75198 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
75219 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
75239 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
75259 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
75280 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
75300 ATCGCATTGCGAT
1 ATCGCATTGCGAT
75313 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:75331 original size:41 final size:41
Alignment explanation
Indices: 75301--75396 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
75291 ATAGTCAGTA
* * *
75301 TCGCATTGCGATTTTCCCAATTCACGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCACGTTGCGATTCACGTAT
* * *
75342 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCACGTTGCGATTCACGTAT
75383 TCGCATTGCGAATT
1 TCGCATTGCGAATT
75397 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCACGTTGCGATTCACGTAT
Found at i:75332 original size:21 final size:21
Alignment explanation
Indices: 75301--75376 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
75291 ATAGTCAGTA
*
75301 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* * **
75322 TCACGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
* *
75342 TCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
75363 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
75377 ACTTATTCGC
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 15 0.36
21 27 0.64
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:75350 original size:20 final size:20
Alignment explanation
Indices: 75327--75393 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
75317 CCAATTCACG
75327 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
* ** *
75347 TTGCGAATTTCCCAATTCGCG
1 TTGCG-ATTTACTTATTCGCA
75368 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
75388 TTGCGA
1 TTGCGA
75394 ATTGGGAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACTTATTCGCA
Found at i:80056 original size:33 final size:33
Alignment explanation
Indices: 80019--80083 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
80009 GTTGATCAAG
* * * *
80019 TCGAATTCGAGTTAATGGGTCTTGTTTGTTAAC
1 TCGAATTCAAGTTAACGAGTCTTGTTTATTAAC
80052 TCGAATTCAAGTTAACGAGTCTTGTTTATTAA
1 TCGAATTCAAGTTAACGAGTCTTGTTTATTAA
80084 ATTTGATTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (33 bp):
TCGAATTCAAGTTAACGAGTCTTGTTTATTAAC
Found at i:89456 original size:20 final size:22
Alignment explanation
Indices: 89428--89467 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
89418 CAATAAAATT
*
89428 ATGTTTTTAT-TTTG-TTTTAA
1 ATGTATTTATGTTTGATTTTAA
89448 ATGTATTTATGTTTGATTTT
1 ATGTATTTATGTTTGATTTT
89468 TGTTGGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 4 0.24
22 4 0.24
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (22 bp):
ATGTATTTATGTTTGATTTTAA
Found at i:97532 original size:9 final size:10
Alignment explanation
Indices: 97509--97533 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
97499 AGCTGTGCTA
97509 AAAAATGAAG
1 AAAAATGAAG
97519 AAAAATGAAG
1 AAAAATGAAG
97529 AAAAA
1 AAAAA
97534 AAGAGAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (10 bp):
AAAAATGAAG
Found at i:99680 original size:27 final size:27
Alignment explanation
Indices: 99649--99716 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
99639 TCTATTTACA
99649 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
*
99676 AAATCATATCTCTATTGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
99703 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
99717 ATTCCTACAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 8 0.21
27 31 0.79
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:103415 original size:27 final size:27
Alignment explanation
Indices: 103384--103451 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
103374 TCTATTTACA
103384 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
103411 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
103438 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
103452 ATTCCTATAC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Done.