Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008774.1 Hibiscus syriacus cultivar Beakdansim tig00111886_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: 151913
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2960 original size:20 final size:20
Alignment explanation
Indices: 2923--2959 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
2913 AAATTATAAA
2923 TTTAATATTATATATTTTAT
1 TTTAATATTATATATTTTAT
*
2943 TTTAAT-TTATATCTTTT
1 TTTAATATTATATATTTT
2960 TCAGATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTAATATTATATATTTTAT
Found at i:3158 original size:32 final size:32
Alignment explanation
Indices: 3096--3157 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
3086 AAGGGTAAAT
*
3096 TATGTGTTTAGTACCTCAACTATTAGTTTTTG
1 TATGTGTTTAGTACCTAAACTATTAGTTTTTG
* * *
3128 TATGT-TTTAGTATCTAAACTTTTAATTTTT
1 TATGTGTTTAGTACCTAAACTATTAGTTTTT
3158 TTCAAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.24, C:0.10, G:0.11, T:0.55
Consensus pattern (32 bp):
TATGTGTTTAGTACCTAAACTATTAGTTTTTG
Found at i:33828 original size:14 final size:16
Alignment explanation
Indices: 33808--33844 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
33798 GCATTATATA
*
33808 AAATATTATATT-TTT
1 AAATATTAAATTATTT
33823 -AATATTAAATTATTT
1 AAATATTAAATTATTT
33838 AAATATT
1 AAATATT
33845 CATAGGTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.53
15 3 0.16
16 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATATTAAATTATTT
Found at i:35134 original size:3 final size:3
Alignment explanation
Indices: 35128--35152 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35118 ATACTCTTAA
35128 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
35153 TTCTCTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:41953 original size:24 final size:24
Alignment explanation
Indices: 41924--41970 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
41914 CTTGAAAGAG
41924 CTCGACTGAAGCTCAAAACTCGAA
1 CTCGACTGAAGCTCAAAACTCGAA
*
41948 CTCGACTGAAGCTCGAAACTCGA
1 CTCGACTGAAGCTCAAAACTCGA
41971 TTGAAGCTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.30, G:0.19, T:0.17
Consensus pattern (24 bp):
CTCGACTGAAGCTCAAAACTCGAA
Found at i:41969 original size:18 final size:18
Alignment explanation
Indices: 41942--41981 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
41932 AAGCTCAAAA
41942 CTCG-AACTCGACTGAAG
1 CTCGAAACTCGACTGAAG
*
41959 CTCGAAACTCGATTGAAG
1 CTCGAAACTCGACTGAAG
41977 CTCGA
1 CTCGA
41982 TTTTGAGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.20
Consensus pattern (18 bp):
CTCGAAACTCGACTGAAG
Found at i:42236 original size:30 final size:30
Alignment explanation
Indices: 42202--42263 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
42192 CTTCAATGGC
42202 TTCCATCATTATACCAATATTCATCTTCTT
1 TTCCATCATTATACCAATATTCATCTTCTT
42232 TTCCATCATTATACCAATATTCATCTTCTT
1 TTCCATCATTATACCAATATTCATCTTCTT
42262 TT
1 TT
42264 TCTTCTCTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (30 bp):
TTCCATCATTATACCAATATTCATCTTCTT
Found at i:44512 original size:7 final size:7
Alignment explanation
Indices: 44472--44526 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
44462 CATAATCGGA
44472 TTTAGGG
1 TTTAGGG
* *
44479 TTTATGA
1 TTTAGGG
*
44486 TTTAGAG
1 TTTAGGG
*
44493 TTTAAGG
1 TTTAGGG
44500 TTTAGGG
1 TTTAGGG
*
44507 TTTAGGA
1 TTTAGGG
*
44514 TTTAGGT
1 TTTAGGG
44521 TTTAGG
1 TTTAGG
44527 ACTTGGGGTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:44525 original size:14 final size:14
Alignment explanation
Indices: 44469--44527 Score: 75
Period size: 14 Copynumber: 4.2 Consensus size: 14
44459 TCACATAATC
44469 GGATTTAGGGTTTA
1 GGATTTAGGGTTTA
* *
44483 TGATTTAGAGTTTAA
1 GGATTTAGGGTTT-A
44498 GG-TTTAGGGTTTA
1 GGATTTAGGGTTTA
*
44511 GGATTTAGGTTTTA
1 GGATTTAGGGTTTA
44525 GGA
1 GGA
44528 CTTGGGGTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
13 3 0.08
14 33 0.87
15 2 0.05
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (14 bp):
GGATTTAGGGTTTA
Found at i:44535 original size:28 final size:28
Alignment explanation
Indices: 44473--44536 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
44463 ATAATCGGAT
* *
44473 TTAGGGTTTATGATTTAGAGTTTAAGGT
1 TTAGGGTTTAGGATTTAGAGTTTAAGGC
*
44501 TTAGGGTTTAGGATTTAG-GTTTTAGGAC
1 TTAGGGTTTAGGATTTAGAGTTTAAGG-C
*
44529 TTGGGGTT
1 TTAGGGTT
44537 AATTACAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 7 0.23
28 24 0.77
ACGTcount: A:0.20, C:0.02, G:0.33, T:0.45
Consensus pattern (28 bp):
TTAGGGTTTAGGATTTAGAGTTTAAGGC
Found at i:44659 original size:11 final size:11
Alignment explanation
Indices: 44643--44705 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
44633 GTATTATAGA
44643 ATTTTTAATAT
1 ATTTTTAATAT
44654 ATTTTTAA-A-
1 ATTTTTAATAT
44663 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
44674 ATCAATAATGT
1 ATTTTTAATAT
44685 ATTTTTAATAT
1 ATTTTTAATAT
44696 ATTTTTAATA
1 ATTTTTAATA
44706 ATGTAATGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:48492 original size:21 final size:21
Alignment explanation
Indices: 48474--48559 Score: 102
Period size: 21 Copynumber: 4.1 Consensus size: 21
48464 ATGAAGCAAG
*
48474 GGAAACAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
48495 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
48516 GGAAGCAGAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
48537 GGCAGCACAGAGAG-AGGCAGC
1 GGAAGCAGAGAGAGCA-GCAGC
48558 GG
1 GG
48560 CAGAACAGAG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 1 0.02
21 55 0.98
ACGTcount: A:0.37, C:0.20, G:0.42, T:0.01
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:48560 original size:21 final size:21
Alignment explanation
Indices: 48482--48574 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
48472 AGGGAAACAG
* *
48482 AGAGAGCAGCAGCGGAAGCAGC
1 AGAGAGAAGCAGCGGCAGCA-C
* * * *
48504 -TAGAGCAGCAGCGGAAGCAG
1 AGAGAGAAGCAGCGGCAGCAC
48524 AGAGAGAAGCAGCGGCAGCAC
1 AGAGAGAAGCAGCGGCAGCAC
* *
48545 AGAGAGAGGCAGCGGCAGAAC
1 AGAGAGAAGCAGCGGCAGCAC
48566 AGAGAGAAG
1 AGAGAGAAG
48575 TAATGTATCA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.39, C:0.19, G:0.41, T:0.01
Consensus pattern (21 bp):
AGAGAGAAGCAGCGGCAGCAC
Found at i:49111 original size:43 final size:41
Alignment explanation
Indices: 48909--49177 Score: 155
Period size: 43 Copynumber: 6.2 Consensus size: 41
48899 CATACATTTA
* * * * *
48909 GCGGCGTTTTTGATAAAAACGCCGCAAAATCTCAATACATATTCT
1 GCGGCG-TTTT-ATGAAAACGCCGCTAAATATCAAAACCTA-T-T
* * * * ** *
48954 GCGGCGTTTTTAGGAAAACGCCGGTAAAAATAAAAATTTACT
1 GCGGCG-TTTTATGAAAACGCCGCTAAATATCAAAACCTATT
* * *
48996 GCGGCGTTTTGGAAGAAAACGCCGCTAAACATCAACGA-CTATT
1 GCGGCGTTTT--ATGAAAACGCCGCTAAATATCAA-AACCTATT
* * * *
49039 GCGGCGTTTGTCTGCCAAATGCCGTTAAATATCAAAACCTATT
1 GCGGCGTTT-TATG-AAAACGCCGCTAAATATCAAAACCTATT
* *
49082 GCGGCGTTTTAATGATAAACGCCGCTAAATATCAATACCTTTT
1 GCGGCGTTTT-ATGA-AAACGCCGCTAAATATCAAAACCTATT
* * ***
49125 GCGGCGTTTGT-TGAACAATCGCCGCTATATGTTGTAACCTATT
1 GCGGCGTTT-TATGAA-AA-CGCCGCTAAATATCAAAACCTATT
49168 GCGGCGTTTT
1 GCGGCGTTTT
49178 TTTGTTGAAA
Statistics
Matches: 175, Mismatches: 38, Indels: 25
0.74 0.16 0.11
Matches are distributed among these distances:
41 5 0.03
42 16 0.09
43 121 0.69
44 22 0.13
45 11 0.06
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTTATGAAAACGCCGCTAAATATCAAAACCTATT
Found at i:69559 original size:201 final size:201
Alignment explanation
Indices: 69214--69615 Score: 804
Period size: 201 Copynumber: 2.0 Consensus size: 201
69204 GTTAGACTCT
69214 GTTCGACTCAACTCATTTAGGTCTCGAGTCAAGTCAACCCGATTCGAACTTTAATCGAATTTTGA
1 GTTCGACTCAACTCATTTAGGTCTCGAGTCAAGTCAACCCGATTCGAACTTTAATCGAATTTTGA
69279 CCGAGTCAAATTCAAACTGCTCACGAGTTGCCCAACTCATTAAACACCCTTAAGTAAGATTAGGG
66 CCGAGTCAAATTCAAACTGCTCACGAGTTGCCCAACTCATTAAACACCCTTAAGTAAGATTAGGG
69344 ATAATTTATAATCTACTCATGTTACACCAAGGTTTCGCATACTCATGATTGTCTACTCAATTTAT
131 ATAATTTATAATCTACTCATGTTACACCAAGGTTTCGCATACTCATGATTGTCTACTCAATTTAT
69409 ACTTGG
196 ACTTGG
69415 GTTCGACTCAACTCATTTAGGTCTCGAGTCAAGTCAACCCGATTCGAACTTTAATCGAATTTTGA
1 GTTCGACTCAACTCATTTAGGTCTCGAGTCAAGTCAACCCGATTCGAACTTTAATCGAATTTTGA
69480 CCGAGTCAAATTCAAACTGCTCACGAGTTGCCCAACTCATTAAACACCCTTAAGTAAGATTAGGG
66 CCGAGTCAAATTCAAACTGCTCACGAGTTGCCCAACTCATTAAACACCCTTAAGTAAGATTAGGG
69545 ATAATTTATAATCTACTCATGTTACACCAAGGTTTCGCATACTCATGATTGTCTACTCAATTTAT
131 ATAATTTATAATCTACTCATGTTACACCAAGGTTTCGCATACTCATGATTGTCTACTCAATTTAT
69610 ACTTGG
196 ACTTGG
69616 TATAATTGTG
Statistics
Matches: 201, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 201 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (201 bp):
GTTCGACTCAACTCATTTAGGTCTCGAGTCAAGTCAACCCGATTCGAACTTTAATCGAATTTTGA
CCGAGTCAAATTCAAACTGCTCACGAGTTGCCCAACTCATTAAACACCCTTAAGTAAGATTAGGG
ATAATTTATAATCTACTCATGTTACACCAAGGTTTCGCATACTCATGATTGTCTACTCAATTTAT
ACTTGG
Found at i:75781 original size:7 final size:6
Alignment explanation
Indices: 75749--75780 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
75739 TTGAATCGGA
75749 TAATTT TAATTT TAATTT TAATTT TCAATTT T
1 TAATTT TAATTT TAATTT TAATTT T-AATTT T
75781 CTCAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (6 bp):
TAATTT
Found at i:78721 original size:16 final size:15
Alignment explanation
Indices: 78687--78743 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
78677 AGATCCAATC
78687 AAGAACAAAAAAGAA
1 AAGAACAAAAAAGAA
78702 AAGAAGCAAAAAA-AA
1 AAGAA-CAAAAAAGAA
*
78717 TAAGAA-AAAAGAGAAA
1 -AAGAACAAAAAAG-AA
78733 CAAGAACAAAA
1 -AAGAACAAAA
78744 GGAAAAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 5 0.14
15 7 0.20
16 19 0.54
17 4 0.11
ACGTcount: A:0.77, C:0.07, G:0.14, T:0.02
Consensus pattern (15 bp):
AAGAACAAAAAAGAA
Found at i:80348 original size:36 final size:36
Alignment explanation
Indices: 80308--80378 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
80298 TTAAAAGAAG
* *
80308 ATTTTGTCTCGCTTGAGATAATTTCCCTTGAAACAA
1 ATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAA
* *
80344 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 ATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACA
80379 TAAACTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (36 bp):
ATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAA
Found at i:81073 original size:206 final size:209
Alignment explanation
Indices: 80714--81129 Score: 633
Period size: 206 Copynumber: 2.0 Consensus size: 209
80704 TCGTGCTATT
* *
80714 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAAATTTCCCAGTT
1 CAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAATTT-CCAG-T
*
80779 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCAC
64 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAGCACAAGCTCAACTTCAC
* * * * *
80844 AGCGAAGGGGCGGCTGACTGTCAACAAACAACTTCCCAATTTCATAGCCAATTTCAACTTCCCAG
129 AGCGAAGGGGCGACTGACTGTCAACAAACAACTTCCCAATTCCAGAACCAATTTCAACTTCACAG
*
80909 CGAAGGATCTTGGACC
194 CGAAGGATATTGGACC
*
80925 CAAGACAACACAAGCTCAACTTCACGACGAATGGG-CGGCTGATTGTCAAC-AAAATTT-CA-TT
1 CAAGACAACACAAGCTCAACTTCACAACGAA-GGGACGGCTGATTGTCAACAAAAATTTCCAGTT
* * *
80986 CAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGATAGCACAAGCTCAACTTCACA
65 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAGCACAAGCTCAACTTCACA
* *
81051 GCGAAGGGGCGACTGACTGTCAACAAACAATTTCCCAGTTCCAGAACCAATTTCAACTTCACAGC
130 GCGAAGGGGCGACTGACTGTCAACAAACAACTTCCCAATTCCAGAACCAATTTCAACTTCACAGC
*
81116 GGAGGATATTGGAC
195 GAAGGATATTGGAC
81130 TCGGAACAAT
Statistics
Matches: 188, Mismatches: 16, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
206 133 0.71
208 2 0.01
210 7 0.04
211 43 0.23
212 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (209 bp):
CAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAATTTCCAGTTC
AGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAGCACAAGCTCAACTTCACAG
CGAAGGGGCGACTGACTGTCAACAAACAACTTCCCAATTCCAGAACCAATTTCAACTTCACAGCG
AAGGATATTGGACC
Found at i:81132 original size:106 final size:105
Alignment explanation
Indices: 80713--81131 Score: 562
Period size: 106 Copynumber: 4.0 Consensus size: 105
80703 ATCGTGCTAT
* * * * **
80713 TCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAAATTTCCCAGT
1 TCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAAAATTTCCCAGT
80778 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* *
80818 TCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTCCCAA
1 TCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAA-AATTTCCCAG
* * *
80883 TTTCATAGCCAATTTCAACTTCCCAGCGAAGGATCTTGGAC
65 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * * *
80924 CCAAGACAACACAAGCTCAACTTCAC-GACGAATGGGCGGCTGATTGTCAAC-AAAATTT--CA-
1 TCAAGACAGCACAAGCTCAACTTCACAG-CGAAGGGGCGGCTGACTGTCAACAAAAATTTCCCAG
* *
80984 -TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGAC
65 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * *
81024 TCGAGATAGCACAAGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAATTTCCCAG
1 TCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAA-AATTTCCCAG
* * *
81089 TTCCAGAACCAATTTCAACTTCACAGCGGAGGATATTGGAC
65 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
81130 TC
1 TC
81132 GGAACAATAC
Statistics
Matches: 272, Mismatches: 33, Indels: 17
0.84 0.10 0.05
Matches are distributed among these distances:
100 77 0.28
101 3 0.01
102 7 0.03
104 6 0.02
105 51 0.19
106 128 0.47
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (105 bp):
TCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAAAATTTCCCAGT
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
Found at i:83973 original size:861 final size:861
Alignment explanation
Indices: 82312--84034 Score: 3419
Period size: 861 Copynumber: 2.0 Consensus size: 861
82302 CGTTTGGATT
82312 CACAATGATCGAAAACTATTCTTGAAAATCTGAAGATTCGAAGCACGCCCAACACGAGGAATGAC
1 CACAATGATCGAAAACTATTCTTGAAAATCTGAAGATTCGAAGCACGCCCAACACGAGGAATGAC
82377 ATACTCCGTCCATAGCTCGATCCAACGGTTCAAACTCACATACTCAAGGTAAAATGACCAAGATT
66 ATACTCCGTCCATAGCTCGATCCAACGGTTCAAACTCACATACTCAAGGTAAAATGACCAAGATT
82442 TTCTTTCTTCTTTCTCGTGTTGAAGTTCGAAATGTGGCTACTGCAGAAAATAATGTTTCTAGGTA
131 TTCTTTCTTCTTTCTCGTGTTGAAGTTCGAAATGTGGCTACTGCAGAAAATAATGTTTCTAGGTA
82507 AAAACCCTTTAAATTGCATTTCATGTAAGACCCACGAGCTAATATAGGGGTATTTGAAAAAAACA
196 AAAACCCTTTAAATTGCATTTCATGTAAGACCCACGAGCTAATATAGGGGTATTTGAAAAAAACA
82572 TAAGAAGAGTTGGTCTTCTTTTGTGTTGACCCAGTTTAGCTCAGCACTGAGCAATGAAAATAAGC
261 TAAGAAGAGTTGGTCTTCTTTTGTGTTGACCCAGTTTAGCTCAGCACTGAGCAATGAAAATAAGC
82637 GCCCGATGCAAGTTCCTTGATTGATTTTATAACTCTATCTATTTTAAATATTTATGGTTTAGTTC
326 GCCCGATGCAAGTTCCTTGATTGATTTTATAACTCTATCTATTTTAAATATTTATGGTTTAGTTC
*
82702 AATATTACCTCTGAATGATGCTTATACTATTTTTGTTCTAATGAAAGGATTTTACTTGGATATTC
391 AATATTACCTCTGAATGATGCTTATACTATTTTTGTTCCAATGAAAGGATTTTACTTGGATATTC
82767 GTACCAAACCCATACTAAGAAAAAACAGAATTGGAATTTGCATACCCATCACCCTGTTTTGGATT
456 GTACCAAACCCATACTAAGAAAAAACAGAATTGGAATTTGCATACCCATCACCCTGTTTTGGATT
82832 TTCTAAGGATTAATCCATGATTTAGCCATGTCATCTTTCAATATAATTCATTTTGGTCCTTTTAT
521 TTCTAAGGATTAATCCATGATTTAGCCATGTCATCTTTCAATATAATTCATTTTGGTCCTTTTAT
82897 TTTTTTTATTATTTTACTCTTTTACTAACTTTTATTTTCTTTGGTATCTATTTTATTTTATTTTA
586 TTTTTTTATTATTTTACTCTTTTACTAACTTTTATTTTCTTTGGTATCTATTTTATTTTATTTTA
82962 TTATTATATTAATATTTTTCTCTTTTTATATTTATATTTATTTTACAATCTAATAATATTTTTGA
651 TTATTATATTAATATTTTTCTCTTTTTATATTTATATTTATTTTACAATCTAATAATATTTTTGA
83027 CTTTAGGGATATTTTTTCAACCAATCAAGGGTGAGTAATTTGAATCGGATAATTTGAATTTTAAT
716 CTTTAGGGATATTTTTTCAACCAATCAAGGGTGAGTAATTTGAATCGGATAATTTGAATTTTAAT
83092 TTAAATTTTCAATTTTCGCAAATAAAGACAACAAACAAATTAATTGGTACCGAAAGGGCGGTTCA
781 TTAAATTTTCAATTTTCGCAAATAAAGACAACAAACAAATTAATTGGTACCGAAAGGGCGGTTCA
83157 AGGGTGCTAATCCTTC
846 AGGGTGCTAATCCTTC
83173 CACAATGATCGAAAACTATTCTTGAAAATCTGAAGATTCGAAGCACGCCCAACACGAGGAATGAC
1 CACAATGATCGAAAACTATTCTTGAAAATCTGAAGATTCGAAGCACGCCCAACACGAGGAATGAC
83238 ATACTCCGTCCATAGCTCGATCCAACGGTTCAAACTCACATACTCAAGGTAAAATGACCAAGATT
66 ATACTCCGTCCATAGCTCGATCCAACGGTTCAAACTCACATACTCAAGGTAAAATGACCAAGATT
83303 TTCTTTCTTCTTTCTCGTGTTGAAGTTCGAAATGTGGCTACTGCAGAAAATAATGTTTCTAGGTA
131 TTCTTTCTTCTTTCTCGTGTTGAAGTTCGAAATGTGGCTACTGCAGAAAATAATGTTTCTAGGTA
83368 AAAACCCTTTAAATTGCATTTCATGTAAGACCCACGAGCTAATATAGGGGTATTTGAAAAAAACA
196 AAAACCCTTTAAATTGCATTTCATGTAAGACCCACGAGCTAATATAGGGGTATTTGAAAAAAACA
83433 TAAGAAGAGTTGGTCTTCTTTTGTGTTGACCCAGTTTAGCTCAGCACTGAGCAATGAAAATAAGC
261 TAAGAAGAGTTGGTCTTCTTTTGTGTTGACCCAGTTTAGCTCAGCACTGAGCAATGAAAATAAGC
83498 GCCCGATGCAAGTTCCTTGATTGATTTTATAACTCTATCTATTTTAAATATTTATGGTTTAGTTC
326 GCCCGATGCAAGTTCCTTGATTGATTTTATAACTCTATCTATTTTAAATATTTATGGTTTAGTTC
*
83563 AATATTACCTCTGAATGATGCTTATACTATTTTTGTTCCAATGGAAGGATTTTACTTGGATATTC
391 AATATTACCTCTGAATGATGCTTATACTATTTTTGTTCCAATGAAAGGATTTTACTTGGATATTC
83628 GTACCAAACCCATACTAAGAAAAAACAGAATTGGAATTTGCATACCCATCACCCTGTTTTGGATT
456 GTACCAAACCCATACTAAGAAAAAACAGAATTGGAATTTGCATACCCATCACCCTGTTTTGGATT
83693 TTCTAAGGATTAATCCATGATTTAGCCATGTCATCTTTCAATATAATTCATTTTGGTCCTTTTAT
521 TTCTAAGGATTAATCCATGATTTAGCCATGTCATCTTTCAATATAATTCATTTTGGTCCTTTTAT
83758 TTTTTTTATTATTTTACTCTTTTACTAACTTTTATTTTCTTTGGTATCTATTTTATTTTATTTTA
586 TTTTTTTATTATTTTACTCTTTTACTAACTTTTATTTTCTTTGGTATCTATTTTATTTTATTTTA
*
83823 TTATTATATTAATATTTTTCTCTTTTTATATTTATTTTTATTTTACAATCTAATAATATTTTTGA
651 TTATTATATTAATATTTTTCTCTTTTTATATTTATATTTATTTTACAATCTAATAATATTTTTGA
83888 CTTTAGGGATATTTTTTCAACCAATCAAGGGTGAGTAATTTGAATCGGATAATTTGAATTTTAAT
716 CTTTAGGGATATTTTTTCAACCAATCAAGGGTGAGTAATTTGAATCGGATAATTTGAATTTTAAT
83953 TTAAATTTTCAATTTTCGCAAATAAAGACAACAAACAAATTAATTGGTACCGAAAGGGCGGTTCA
781 TTAAATTTTCAATTTTCGCAAATAAAGACAACAAACAAATTAATTGGTACCGAAAGGGCGGTTCA
84018 AGGGTGCTAATCCTTC
846 AGGGTGCTAATCCTTC
84034 C
1 C
84035 TTGACTATAA
Statistics
Matches: 859, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
861 859 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38
Consensus pattern (861 bp):
CACAATGATCGAAAACTATTCTTGAAAATCTGAAGATTCGAAGCACGCCCAACACGAGGAATGAC
ATACTCCGTCCATAGCTCGATCCAACGGTTCAAACTCACATACTCAAGGTAAAATGACCAAGATT
TTCTTTCTTCTTTCTCGTGTTGAAGTTCGAAATGTGGCTACTGCAGAAAATAATGTTTCTAGGTA
AAAACCCTTTAAATTGCATTTCATGTAAGACCCACGAGCTAATATAGGGGTATTTGAAAAAAACA
TAAGAAGAGTTGGTCTTCTTTTGTGTTGACCCAGTTTAGCTCAGCACTGAGCAATGAAAATAAGC
GCCCGATGCAAGTTCCTTGATTGATTTTATAACTCTATCTATTTTAAATATTTATGGTTTAGTTC
AATATTACCTCTGAATGATGCTTATACTATTTTTGTTCCAATGAAAGGATTTTACTTGGATATTC
GTACCAAACCCATACTAAGAAAAAACAGAATTGGAATTTGCATACCCATCACCCTGTTTTGGATT
TTCTAAGGATTAATCCATGATTTAGCCATGTCATCTTTCAATATAATTCATTTTGGTCCTTTTAT
TTTTTTTATTATTTTACTCTTTTACTAACTTTTATTTTCTTTGGTATCTATTTTATTTTATTTTA
TTATTATATTAATATTTTTCTCTTTTTATATTTATATTTATTTTACAATCTAATAATATTTTTGA
CTTTAGGGATATTTTTTCAACCAATCAAGGGTGAGTAATTTGAATCGGATAATTTGAATTTTAAT
TTAAATTTTCAATTTTCGCAAATAAAGACAACAAACAAATTAATTGGTACCGAAAGGGCGGTTCA
AGGGTGCTAATCCTTC
Found at i:91346 original size:71 final size:72
Alignment explanation
Indices: 91230--91362 Score: 241
Period size: 71 Copynumber: 1.9 Consensus size: 72
91220 TGAAACTTAA
91230 ACTAAATGTCAGACATGATTTTAAAAAAATGAAATTTAGACACTAAAACGAAATAAAAATAATAA
1 ACTAAATGTCAGACATGATTTTAAAAAAATGAAATTTAGACACTAAAACGAAATAAAAATAATAA
91295 TTTAGAT
66 TTTAGAT
* *
91302 ACTAAATGTCATACATGA-TTTAAAAAAATGAAATTTAGATACTAAAACGAAATAAAAATAA
1 ACTAAATGTCAGACATGATTTTAAAAAAATGAAATTTAGACACTAAAACGAAATAAAAATAA
91363 AGTTAGAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
71 42 0.71
72 17 0.29
ACGTcount: A:0.56, C:0.08, G:0.09, T:0.27
Consensus pattern (72 bp):
ACTAAATGTCAGACATGATTTTAAAAAAATGAAATTTAGACACTAAAACGAAATAAAAATAATAA
TTTAGAT
Found at i:96030 original size:149 final size:148
Alignment explanation
Indices: 95758--96063 Score: 477
Period size: 149 Copynumber: 2.1 Consensus size: 148
95748 GAGTCGAGGG
* * * * * *
95758 TCTACGCGGTCATTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCATTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* *
95823 ATTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATAGACATTATTAT
66 ATTGATCCTTAATATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATAGACATTATTAT
*
95888 ATGGCACTACGGTGCAAT
131 AGGGCACTACGGTGCAAT
* * *
95906 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCATTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
* *
95971 ACTTGATCCTTAATATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
65 AATTGATCCTTAATATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATAGACATTATTA
96036 TAGGGCACTACGGTGCAAT
130 TAGGGCACTACGGTGCAAT
96055 TCTACGCGG
1 TCTACGCGG
96064 CACTACGGTG
Statistics
Matches: 143, Mismatches: 14, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
148 47 0.33
149 96 0.67
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (148 bp):
TCTACGCGGTCATTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
ATTGATCCTTAATATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATAGACATTATTAT
AGGGCACTACGGTGCAAT
Found at i:96105 original size:22 final size:23
Alignment explanation
Indices: 96039--96099 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
96029 ATTATTATAG
96039 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
96062 GGCACTACGGTGCAATTCTACG-
1 GGCACTACGGTGCAATTCTACGC
* *
96084 TGCACTTCGGTGCAAT
1 GGCACTACGGTGCAAT
96100 GATACGAGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:98751 original size:16 final size:18
Alignment explanation
Indices: 98730--98762 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
98720 TTTAAATATT
98730 TTTTAAA-AAAT-TAAAA
1 TTTTAAAGAAATATAAAA
98746 TTTTAAAGAAATATAAA
1 TTTTAAAGAAATATAAA
98763 TGGAACATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TTTTAAAGAAATATAAAA
Found at i:99198 original size:21 final size:21
Alignment explanation
Indices: 99151--99199 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
99141 TGACTATCGT
99151 AATGCGATTTTCCAATTTCGC
1 AATGCGATTTTCCAATTTCGC
**
99172 GTTGCGATTTTCCCAA-TTCGC
1 AATGCGATTTT-CCAATTTCGC
99193 AATGCGA
1 AATGCGA
99200 ATAAGTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.35
Consensus pattern (21 bp):
AATGCGATTTTCCAATTTCGC
Found at i:99232 original size:21 final size:20
Alignment explanation
Indices: 99189--99235 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
99179 TTTTCCCAAT
*
99189 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
99209 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
99230 TCGCAA
1 TCGCAA
99236 CGCGGTACTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:99254 original size:20 final size:20
Alignment explanation
Indices: 99229--99284 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
99219 AATTTGGAAA
*
99229 ATCGCAACGCGGTACTGACT
1 ATCGCAACGCGATACTGACT
99249 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
99269 TTCGCAACTCGATACT
1 ATCGCAACGCGATACT
99285 TAATTTCTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:99276 original size:40 final size:40
Alignment explanation
Indices: 99230--99322 Score: 96
Period size: 40 Copynumber: 2.3 Consensus size: 40
99220 ATTTGGAAAA
* * *
99230 TCGCAACGCGGTACTGACTATCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGAATATCGCAACGCAATACTGACTT
* * * * *
99270 TCGCAACTCGATACTTAATTTCTCAACTCAATACTGACTT
1 TCGCAACGCGATACTGAATATCGCAACGCAATACTGACTT
* *
99310 TCGTAACGAGATA
1 TCGCAACGCGATA
99323 ATACATAATC
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (40 bp):
TCGCAACGCGATACTGAATATCGCAACGCAATACTGACTT
Found at i:99291 original size:20 final size:20
Alignment explanation
Indices: 99230--99312 Score: 76
Period size: 20 Copynumber: 4.2 Consensus size: 20
99220 ATTTGGAAAA
* * * *
99230 TCGCAACGCGGTACTGACTA
1 TCGCAACTCGATACTGAATT
* *
99250 TCGCAACGCGATACTGACTT
1 TCGCAACTCGATACTGAATT
*
99270 TCGCAACTCGATACTTAATT
1 TCGCAACTCGATACTGAATT
* * *
99290 TCTCAACTCAATACTGACTT
1 TCGCAACTCGATACTGAATT
99310 TCG
1 TCG
99313 TAACGAGATA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
TCGCAACTCGATACTGAATT
Found at i:99848 original size:20 final size:20
Alignment explanation
Indices: 99815--99864 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
99805 TTTATTCTCT
* *
99815 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATTGTCAAATTCG
**
99835 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCAAATTCG
*
99855 TGTTGCGATT
1 CGTTGCGATT
99865 TTCATTTTCA
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:0.16, C:0.16, G:0.26, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTGTCAAATTCG
Found at i:99869 original size:20 final size:20
Alignment explanation
Indices: 99831--99873 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
99821 GATAGTCAAA
99831 TTCGCGTTGCGATTGTCATT
1 TTCGCGTTGCGATTGTCATT
* *
99851 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTGTCATT
99871 TTC
1 TTC
99874 AGAAACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.19, G:0.21, T:0.51
Consensus pattern (20 bp):
TTCGCGTTGCGATTGTCATT
Found at i:100064 original size:25 final size:24
Alignment explanation
Indices: 100010--100064 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
100000 TGTTTATTAT
* *
100010 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
100034 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
100060 TGTTT
1 TGTTT
100065 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:101816 original size:19 final size:20
Alignment explanation
Indices: 101762--101828 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
101752 TAGTTTACTT
* *
101762 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
101782 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
101802 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
101821 TCGCAACG
1 TCGCAACG
101829 ACAAAATCGC
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:101836 original size:14 final size:14
Alignment explanation
Indices: 101817--101875 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
101807 ATGCGAAATG
101817 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
101831 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
101850 AAAATCGCAACGAC
1 AAAATCGCAACGAC
101864 AAAATCGCAACG
1 AAAATCGCAACG
101876 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:101843 original size:33 final size:33
Alignment explanation
Indices: 101801--101890 Score: 171
Period size: 33 Copynumber: 2.7 Consensus size: 33
101791 GGAAATGGCT
101801 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
101834 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
101867 ATCGCAACGCGAAATGAAAATCGC
1 ATCGCAATGCGAAATGAAAATCGC
101891 TTTCATTTCG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:101855 original size:19 final size:18
Alignment explanation
Indices: 101801--101890 Score: 79
Period size: 19 Copynumber: 5.3 Consensus size: 18
101791 GGAAATGGCT
101801 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
101820 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
101834 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
101853 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
101867 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
101886 ATCGC
1 ATCGC
101891 TTTCATTTCG
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
14 20 0.35
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 25 0.44
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:101928 original size:20 final size:19
Alignment explanation
Indices: 101894--101966 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
101884 AAATCGCTTT
*
101894 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
101913 CATTTCTGCGTTGCGATAGT
1 CATTTC-GCGTTGCGATAGC
101933 CATTTCCGCGTTGCGATAGTC
1 CATTT-CGCGTTGCGATAG-C
**
101954 GTTTTCGCGTTGC
1 CATTTCGCGTTGC
101967 AAAAGTAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 6 0.13
20 36 0.78
21 4 0.09
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.37
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:101979 original size:20 final size:20
Alignment explanation
Indices: 101956--101994 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
101946 CGATAGTCGT
101956 TTTCGCGTTGCAAAAGTAAG
1 TTTCGCGTTGCAAAAGTAAG
* *
101976 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCAAAAGTAA
101995 ACTATTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (20 bp):
TTTCGCGTTGCAAAAGTAAG
Found at i:103866 original size:14 final size:14
Alignment explanation
Indices: 103832--103870 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
103822 TTGATTGTTT
103832 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
103846 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
103860 TGTTGATTTGT
1 AATTGATTTGT
103871 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:104031 original size:19 final size:19
Alignment explanation
Indices: 104007--104074 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
103997 ATCGCAACGA
104007 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
* *
104026 GAAAATCACAATGTGAAAT
1 GAAAATCGCAATGCGAAAT
104045 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
104059 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
104075 TTTTCATTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 1 0.02
19 27 0.64
ACGTcount: A:0.49, C:0.16, G:0.21, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:104118 original size:20 final size:20
Alignment explanation
Indices: 104093--104179 Score: 79
Period size: 20 Copynumber: 4.3 Consensus size: 20
104083 TCGCATTGCG
*
104093 ATTTTCTAATTGCGATAGCC
1 ATTTTCGAATTGCGATAGCC
** *
104113 ATTTTCGCGTTGCGATTTA-TC
1 ATTTTCGAATTGCGA--TAGCC
*
104134 A-TTTCGAATTGCGATGGCC
1 ATTTTCGAATTGCGATAGCC
**
104153 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGAATTGCGATAGCC
104173 ATTTTCG
1 ATTTTCG
104180 CGTTGCGATT
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
18 1 0.02
19 2 0.04
20 45 0.87
21 2 0.04
22 2 0.04
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTTTCGAATTGCGATAGCC
Found at i:104180 original size:20 final size:20
Alignment explanation
Indices: 104102--104188 Score: 106
Period size: 20 Copynumber: 4.3 Consensus size: 20
104092 GATTTTCTAA
104102 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
* **
104122 TTGCGATTTA-TCA-TTTCGAA
1 TTGCGA--TAGCCATTTTCGCG
*
104142 TTGCGATGGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
104162 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
104182 TTGCGAT
1 TTGCGAT
104189 TTCCCCGTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
18 1 0.02
19 2 0.04
20 48 0.87
21 2 0.04
22 2 0.04
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCG
Found at i:104427 original size:20 final size:20
Alignment explanation
Indices: 104402--104469 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
104392 TTGAAGATGA
104402 TTGCGATTTTTAGAATCTCG
1 TTGCGATTTTTAGAATCTCG
*** * *
104422 TTGCGAAAGTCAGAATCTCA
1 TTGCGATTTTTAGAATCTCG
**
104442 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-TAGAATCTCG
104463 TTGCGAT
1 TTGCGAT
104470 AGTCAGTATC
Statistics
Matches: 35, Mismatches: 12, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCGATTTTTAGAATCTCG
Found at i:104467 original size:41 final size:40
Alignment explanation
Indices: 104401--104492 Score: 130
Period size: 41 Copynumber: 2.3 Consensus size: 40
104391 TTTGAAGATG
*
104401 ATTGCGATTTTTAGAATCTCGTTGCGAAAGTCAGAATCTC
1 ATTGCGATTTTTAGAATCTCGTTGCGAAAGTCAGAATCGC
** * *
104441 ATTGCGATTTTGTATTATCTCGTTGCGATAGTCAGTATCGC
1 ATTGCGATTTT-TAGAATCTCGTTGCGAAAGTCAGAATCGC
104482 ATTGCGATTTT
1 ATTGCGATTTT
104493 CCAAATTCGC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 11 0.24
41 35 0.76
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (40 bp):
ATTGCGATTTTTAGAATCTCGTTGCGAAAGTCAGAATCGC
Found at i:104522 original size:20 final size:21
Alignment explanation
Indices: 104478--104529 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
104468 ATAGTCAGTA
*
104478 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
104499 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
104519 TCGCATTGCGA
1 TCGCATTGCGA
104530 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:105329 original size:24 final size:24
Alignment explanation
Indices: 105302--105355 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
105292 GTATTCAAAA
*
105302 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
105326 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
105350 TTTGAT
1 TTTGAT
105356 GATGTTTCAG
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:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:105548 original size:12 final size:12
Alignment explanation
Indices: 105530--105562 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
105520 ATATAATCCT
105530 GAAGAAGAAAATA
1 GAAGAAGAAAA-A
105543 -AAGAAGAAAAA
1 GAAGAAGAAAAA
105554 GAAGAAGAA
1 GAAGAAGAA
105563 CAAGTCCCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.05
12 18 0.95
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:106246 original size:19 final size:19
Alignment explanation
Indices: 106222--106289 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
106212 ATCGCAACGA
106222 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
106241 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
106260 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
106274 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
106290 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:106341 original size:34 final size:36
Alignment explanation
Indices: 106296--106383 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 36
106286 GCGATTTTCA
* *
106296 TTTCGCATTGCGATTTTC-T-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
106330 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC--TTC-AATTGCGATAGCCAT
106370 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
106384 AGCCATTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
34 12 0.26
35 5 0.11
38 1 0.02
39 1 0.02
40 27 0.59
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
Found at i:106395 original size:20 final size:20
Alignment explanation
Indices: 106316--106403 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
106306 CGATTTTCTA
106316 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
106336 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
*
106356 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
106376 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*
106396 GATGCGAT
1 GTTGCGAT
106404 TTCCCCGTTG
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
19 3 0.05
20 49 0.89
21 3 0.05
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:106642 original size:20 final size:20
Alignment explanation
Indices: 106617--106684 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
106607 TTGAAGATGA
106617 TTGCGATTTTTAGAATCTCG
1 TTGCGATTTTTAGAATCTCG
*** *
106637 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTTAGAATCTCG
**
106657 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-TAGAATCTCG
106678 TTGCGAT
1 TTGCGAT
106685 AGTCAGTATC
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 23 0.62
21 14 0.38
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGCGATTTTTAGAATCTCG
Found at i:106681 original size:41 final size:40
Alignment explanation
Indices: 106616--106707 Score: 121
Period size: 41 Copynumber: 2.3 Consensus size: 40
106606 TTTGAAGATG
*
106616 ATTGCGATTTTTAGAATCTCGTTGCGAAAGTCAGAATCTC
1 ATTGCGATTTTTAGAATCTCGTTGCGAAAGTCAGAATCGC
* ** * *
106656 GTTGCGATTTTGTATTATCTCGTTGCGATAGTCAGTATCGC
1 ATTGCGATTTT-TAGAATCTCGTTGCGAAAGTCAGAATCGC
106697 ATTGCGATTTT
1 ATTGCGATTTT
106708 CCAAATTCGC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 10 0.23
41 34 0.77
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (40 bp):
ATTGCGATTTTTAGAATCTCGTTGCGAAAGTCAGAATCGC
Found at i:106737 original size:20 final size:21
Alignment explanation
Indices: 106693--106744 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
106683 ATAGTCAGTA
*
106693 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
106714 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
106734 TCGCATTGCGA
1 TCGCATTGCGA
106745 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:106960 original size:12 final size:12
Alignment explanation
Indices: 106941--106974 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
106931 CTCTCCGGCG
106941 ACATCCGTTCCT
1 ACATCCGTTCCT
*
106953 ATATCCGTTCCT
1 ACATCCGTTCCT
106965 ACATCC-TTCC
1 ACATCCGTTCC
106975 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:107555 original size:24 final size:24
Alignment explanation
Indices: 107528--107581 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
107518 GTATTCGAAA
*
107528 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
107552 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
107576 TTTGAT
1 TTTGAT
107582 GATGTTTCAG
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:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:107773 original size:12 final size:12
Alignment explanation
Indices: 107756--107788 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
107746 ATATAATCCT
*
107756 GAAGAAGAAAAC
1 GAAGAAGAAAAA
107768 GAAGAAGAAAAA
1 GAAGAAGAAAAA
107780 GAAGAAGAA
1 GAAGAAGAA
107789 CAAGTCCCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.70, C:0.03, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:110107 original size:19 final size:19
Alignment explanation
Indices: 110085--110248 Score: 98
Period size: 19 Copynumber: 9.7 Consensus size: 19
110075 GGAAATTACT
*
110085 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
110104 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
110118 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
110137 ATCGCAACGCG-AAT----
1 ATCGCAATGCGAAATGAAA
*
110151 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
110170 ATCGCAACGC-AAAT----
1 ATCGCAATGCGAAATGAAA
* *
110184 TTTGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
110203 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
110217 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
110236 ATCGCAACGCGAA
1 ATCGCAATGCGAA
110249 TTTAGTTTCG
Statistics
Matches: 107, Mismatches: 18, Indels: 40
0.65 0.11 0.24
Matches are distributed among these distances:
14 34 0.32
15 9 0.08
16 4 0.04
17 4 0.04
18 9 0.08
19 47 0.44
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:110127 original size:33 final size:33
Alignment explanation
Indices: 110084--110249 Score: 221
Period size: 33 Copynumber: 5.0 Consensus size: 33
110074 GGGAAATTAC
*
110084 TATCGCAATGCGAAATAAAAATCGCAACGAGAGA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGA-A
*
110118 -ATCGCAATGCGAAATGAAAATCGCAACGCGAA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGAA
*
110150 TTTCGCAATGCGAAATGAAAATCGCAACGCA-AA
1 TATCGCAATGCGAAATGAAAATCGCAACG-AGAA
* * *
110183 TTTTGCAATGCGAAATGAAAATCGCAACGAGGGA
1 TATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
110217 -ATCGCAATGCGAAATGAAAATCGCAACGCGAA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGAA
110249 T
1 T
110250 TTAGTTTCGC
Statistics
Matches: 117, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
32 4 0.03
33 112 0.96
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (33 bp):
TATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:110302 original size:33 final size:33
Alignment explanation
Indices: 110255--110351 Score: 142
Period size: 33 Copynumber: 2.9 Consensus size: 33
110245 CGAATTTAGT
110255 TTCGCGTTGCGATTTTCATTTCGCATTGCGAAA
1 TTCGCGTTGCGATTTTCATTTCGCATTGCGAAA
* * *
110288 TTCGCGTTGTGATTTTCATTTCGCATTGTG-AT
1 TTCGCGTTGCGATTTTCATTTCGCATTGCGAAA
*
110320 TCTCTCGTTGCGATTTTCATTTCGCATTGCGA
1 T-TCGCGTTGCGATTTTCATTTCGCATTGCGA
110352 TAGTACTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.44
Consensus pattern (33 bp):
TTCGCGTTGCGATTTTCATTTCGCATTGCGAAA
Found at i:110352 original size:19 final size:19
Alignment explanation
Indices: 110254--110352 Score: 74
Period size: 19 Copynumber: 5.7 Consensus size: 19
110244 GCGAATTTAG
*
110254 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
110273 TTTCGCATTGCGA-----A
1 TTTCGCATTGCGATTTTCA
* * *
110287 ATTCGCGTTGTGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
110306 TTTCGCATTGTGA--TTC-
1 TTTCGCATTGCGATTTTCA
*
110322 TCTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
110339 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
110353 AGTACTTTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
14 16 0.26
16 7 0.11
17 7 0.11
19 31 0.51
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.45
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:112344 original size:91 final size:90
Alignment explanation
Indices: 112166--112350 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
112156 ATTTCAAACT
*
112166 TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
112231 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
112259 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGAC-AAA-AAAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
112323 GTATTGGCAGCAACCTAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
112350 T
1 T
112351 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.47
93 14 0.16
94 3 0.03
95 29 0.33
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:113991 original size:20 final size:19
Alignment explanation
Indices: 113960--114048 Score: 73
Period size: 20 Copynumber: 4.8 Consensus size: 19
113950 TCTTTTGGTT
113960 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
113979 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
114000 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
114019 G--A-G--AATCGCAAC-A
1 GAAATGAAAATCGCAACGA
114032 CGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
114049 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
13 1 0.02
14 9 0.16
16 2 0.04
17 2 0.04
19 11 0.20
20 29 0.52
21 2 0.04
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:114046 original size:33 final size:34
Alignment explanation
Indices: 113985--114048 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
113975 ACGAGATAAT
* **
113985 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACACGGAAATGAAAATCGCAACGA
114019 GAGAATCGCAACAC-GAAATGAAAATCGCAA
1 GAGAATCGCAACACGGAAATGAAAATCGCAA
114049 TGCGATTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 14 0.52
34 13 0.48
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (34 bp):
GAGAATCGCAACACGGAAATGAAAATCGCAACGA
Found at i:114071 original size:19 final size:19
Alignment explanation
Indices: 114049--114096 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
114039 AAAATCGCAA
*
114049 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTT-ATTTCCGCGT
*
114068 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTTCCGCGT
114088 TGCGATTTT
1 TGCGATTTT
114097 CATTCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTATTTCCGCGT
Found at i:114638 original size:20 final size:20
Alignment explanation
Indices: 114613--114724 Score: 82
Period size: 20 Copynumber: 5.5 Consensus size: 20
114603 GCTATGTAAA
114613 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* *
114633 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
* ***
114653 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATGTAAGT-AT
* ** *
114674 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATGTAAGTAT
* * *
114694 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
114714 TCGCATTGCGA
1 TCGCATTGCGA
114725 ATTATGAAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.04
20 58 0.73
21 18 0.23
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:114683 original size:41 final size:40
Alignment explanation
Indices: 114631--114724 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 40
114621 CGATAGTAAG
* *
114631 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
114671 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
114712 ATTCGCATTGCGA
1 ATTCGCATTGCGA
114725 ATTATGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 13 0.27
41 35 0.73
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:114868 original size:20 final size:22
Alignment explanation
Indices: 114821--114868 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
114811 CCAAATTTGT
114821 ATTGCG-AATTGGGAAAATCGC
1 ATTGCGAAATTGGGAAAATCGC
**
114842 AACGCGAAATT-GG-AAATCGC
1 ATTGCGAAATTGGGAAAATCGC
114862 ATTGCGA
1 ATTGCGA
114869 TAGTCATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 12 0.55
21 6 0.27
22 4 0.18
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (22 bp):
ATTGCGAAATTGGGAAAATCGC
Found at i:117779 original size:19 final size:19
Alignment explanation
Indices: 117755--117792 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
117745 TATTATTAAA
117755 AATTATAAAATAATATTTT
1 AATTATAAAATAATATTTT
* *
117774 AATTATAAAGTGATATTTT
1 AATTATAAAATAATATTTT
117793 GTTAAGTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
AATTATAAAATAATATTTT
Found at i:118140 original size:28 final size:28
Alignment explanation
Indices: 118108--118178 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
118098 CATTTATTAC
118108 TTTCAAACACT-AGCTCAACAATATAATA
1 TTTCAAACACTGA-CTCAACAATATAATA
* * * *
118136 TTTCAAATACTGACTCGACGATATAATG
1 TTTCAAACACTGACTCAACAATATAATA
*
118164 TTTCAAACATTGACT
1 TTTCAAACACTGACT
118179 TGATGACATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 35 0.97
29 1 0.03
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.32
Consensus pattern (28 bp):
TTTCAAACACTGACTCAACAATATAATA
Found at i:118189 original size:28 final size:28
Alignment explanation
Indices: 118108--118192 Score: 73
Period size: 28 Copynumber: 3.0 Consensus size: 28
118098 CATTTATTAC
* * *
118108 TTTCAAACACT-AGCTCAACAATATAATA
1 TTTCAAACACTGA-CTCGACGACATAATA
* * *
118136 TTTCAAATACTGACTCGACGATATAATG
1 TTTCAAACACTGACTCGACGACATAATA
* * *
118164 TTTCAAACATTGACTTGATGACATAATA
1 TTTCAAACACTGACTCGACGACATAATA
118192 T
1 T
118193 AAACAGATAT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
28 45 0.98
29 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (28 bp):
TTTCAAACACTGACTCGACGACATAATA
Found at i:121518 original size:16 final size:17
Alignment explanation
Indices: 121497--121531 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
121487 TATTAGTTGA
*
121497 TAATTATTAT-TTTTAT
1 TAATTAGTATATTTTAT
121513 TAATTAGTATATTTTAT
1 TAATTAGTATATTTTAT
121530 TA
1 TA
121532 TAAAAAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TAATTAGTATATTTTAT
Found at i:121637 original size:17 final size:16
Alignment explanation
Indices: 121615--121676 Score: 74
Period size: 17 Copynumber: 3.9 Consensus size: 16
121605 ATAATTTTTT
121615 TATTATATTTTAGTTAA
1 TATTATATTTTA-TTAA
121632 TATTATATTTTATTAA
1 TATTATATTTTATTAA
*
121648 -A-AATATTTTATTAA
1 TATTATATTTTATTAA
*
121662 TTATTATACTTTATT
1 -TATTATATTTTATT
121677 TTATTTTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
14 12 0.31
15 1 0.03
16 5 0.13
17 21 0.54
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (16 bp):
TATTATATTTTATTAA
Found at i:121702 original size:26 final size:24
Alignment explanation
Indices: 121641--121711 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 24
121631 ATATTATATT
*
121641 TTATTA-AAAATATTTTA--TTAA
1 TTATTATAATATATTTTATTTTAA
* *
121662 TTATTATACTTTATTTTATTTTAA
1 TTATTATAATATATTTTATTTTAA
121686 TATGATTATAATATATTTTTATTTTA
1 T-T-ATTATAATATA-TTTTATTTTA
121712 TTTTATTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 6 0.15
22 8 0.21
24 5 0.13
25 1 0.03
26 9 0.23
27 10 0.26
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (24 bp):
TTATTATAATATATTTTATTTTAA
Found at i:121716 original size:37 final size:34
Alignment explanation
Indices: 121671--121766 Score: 111
Period size: 37 Copynumber: 2.6 Consensus size: 34
121661 ATTATTATAC
* *
121671 TTTATTTTATTTTAATATGATTATAATATATTTTTAT
1 TTTATTTTA-TTT-ATATAATTATAATATA-TTTAAT
121708 TTTATTTTATTTATATAATTATAATATATTTAAT
1 TTTATTTTATTTATATAATTATAATATATTTAAT
*
121742 TTTATTAATTATTTGTGATAATTAT
1 TTTATT--TTATTTAT-ATAATTAT
121767 TTTTTCTACA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
34 11 0.21
35 15 0.28
36 10 0.19
37 17 0.32
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (34 bp):
TTTATTTTATTTATATAATTATAATATATTTAAT
Found at i:128927 original size:110 final size:109
Alignment explanation
Indices: 128696--128929 Score: 267
Period size: 109 Copynumber: 2.1 Consensus size: 109
128686 ACAAAAATCC
*
128696 AAAAACACGCTAAACTTAGAGGGACTAAACAGTGAATAACCCAATAATTACATAACATACAAAGA
1 AAAAACACGCTAAACTTAGAAGGACTAAACAGTGAATAACCCAATAATTACATAACATACAAAGA
** * * **
128761 AAAGGGAAAATAATGATTTTAGTCCTCACAGATGACCTGAATAT
66 AAAGGGAAAATAACAAATTCAGTCCTCACAGATGACCAAAATAT
* * * * *
128805 AAAAACACGCTAAATTTATAAGGACTAAACAGTGAATAGA-CCAATAATTATATAACTTGCACGA
1 AAAAACACGCTAAACTTAGAAGGACTAAACAGTGAATA-ACCCAATAATTACATAACAT--ACAA
* * *
128869 A-AAAAGGGGAAATAACAAATTCAGTCCTTACATG-TGACCAAAATGT
63 AGAAAAGGGAAAATAACAAATTCAGTCCTCACA-GATGACCAAAATAT
*
128915 AAAAACGCGCTAAAC
1 AAAAACACGCTAAAC
128930 CTAGGGGATC
Statistics
Matches: 104, Mismatches: 17, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
109 51 0.49
110 48 0.46
111 5 0.05
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (109 bp):
AAAAACACGCTAAACTTAGAAGGACTAAACAGTGAATAACCCAATAATTACATAACATACAAAGA
AAAGGGAAAATAACAAATTCAGTCCTCACAGATGACCAAAATAT
Found at i:129801 original size:12 final size:12
Alignment explanation
Indices: 129784--129823 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
129774 TTGGGGCATG
129784 GTTTAGGGTTTA
1 GTTTAGGGTTTA
**
129796 GTTTAGGGCCTA
1 GTTTAGGGTTTA
129808 GTTTAGGGTTTA
1 GTTTAGGGTTTA
129820 GTTT
1 GTTT
129824 GGACTCAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.15, C:0.05, G:0.33, T:0.47
Consensus pattern (12 bp):
GTTTAGGGTTTA
Found at i:129804 original size:24 final size:24
Alignment explanation
Indices: 129758--129823 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
129748 GGGTCGGGTT
* *
129758 TGGTTT-GGGTTTTGATTTGGGGCA
1 TGGTTTAGGGTTTAG-TTTAGGGCA
*
129782 TGGTTTAGGGTTTAGTTTAGGGCC
1 TGGTTTAGGGTTTAGTTTAGGGCA
*
129806 TAGTTTAGGGTTTAGTTT
1 TGGTTTAGGGTTTAGTTT
129824 GGACTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 30 0.81
25 7 0.19
ACGTcount: A:0.12, C:0.05, G:0.36, T:0.47
Consensus pattern (24 bp):
TGGTTTAGGGTTTAGTTTAGGGCA
Found at i:134584 original size:12 final size:12
Alignment explanation
Indices: 134567--134593 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
134557 CAAATATAAA
134567 ATAAGAAAATTC
1 ATAAGAAAATTC
134579 ATAAGAAAATTC
1 ATAAGAAAATTC
134591 ATA
1 ATA
134594 GCACAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.26
Consensus pattern (12 bp):
ATAAGAAAATTC
Found at i:137148 original size:14 final size:14
Alignment explanation
Indices: 137126--137155 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
137116 TCTATACCCC
137126 CCATAGTATCGATA
1 CCATAGTATCGATA
*
137140 CCATGGTATCGATA
1 CCATAGTATCGATA
137154 CC
1 CC
137156 CCCCAGGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (14 bp):
CCATAGTATCGATA
Found at i:137155 original size:32 final size:33
Alignment explanation
Indices: 137110--137175 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
137100 GATTGCTCGG
* *
137110 ATGGTATCTATACCCCCCA-TAGTATCGATACC
1 ATGGTATCGATACCCCCCAGGAGTATCGATACC
*
137142 ATGGTATCGATACCCCCCAGGGGTATCGATACC
1 ATGGTATCGATACCCCCCAGGAGTATCGATACC
137175 A
1 A
137176 CCTGGATGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.24
Consensus pattern (33 bp):
ATGGTATCGATACCCCCCAGGAGTATCGATACC
Found at i:137316 original size:20 final size:22
Alignment explanation
Indices: 137278--137317 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
137268 TTTGAGCAGA
137278 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
137300 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
137318 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:138486 original size:19 final size:20
Alignment explanation
Indices: 138462--138509 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
138452 AGTGGTTTTC
* *
138462 TTTTGAAAGCAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
*
138481 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
138501 TTTTGAAAA
1 TTTTGAAAA
138510 ATGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:139309 original size:20 final size:20
Alignment explanation
Indices: 139286--139323 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
139276 ATATGCTTTT
*
139286 AATTTTAACAATTAGTATCA
1 AATTTCAACAATTAGTATCA
*
139306 AATTTCAACAATTGGTAT
1 AATTTCAACAATTAGTAT
139324 TGCATAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (20 bp):
AATTTCAACAATTAGTATCA
Found at i:139673 original size:21 final size:21
Alignment explanation
Indices: 139647--139686 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
139637 CACCAATTGG
139647 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
139668 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCATTTT
139687 CATTAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:139821 original size:29 final size:30
Alignment explanation
Indices: 139789--139855 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
139779 TTGATATAAC
* *
139789 AATTTAAGGCA-AAAATGTTTTTGGACTTG
1 AATTGAAGGCACAAAATGTTTTTGGACTTA
***
139818 AATTGAATTTACAAAATGTTTTTGGACTTA
1 AATTGAAGGCACAAAATGTTTTTGGACTTA
139848 AATTGAAG
1 AATTGAAG
139856 TTTTAAAAGG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.39
Consensus pattern (30 bp):
AATTGAAGGCACAAAATGTTTTTGGACTTA
Found at i:140007 original size:18 final size:18
Alignment explanation
Indices: 139984--140035 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
139974 TATTGCTCGG
139984 ATGGTATCTATACCCCCC
1 ATGGTATCTATACCCCCC
*
140002 ATGGTATCGATA--CCCC
1 ATGGTATCTATACCCCCC
*
140018 AGGGGTATCTATACCCCC
1 A-TGGTATCTATACCCCC
140036 TGGATGCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 5 0.18
17 9 0.32
18 11 0.39
19 3 0.11
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (18 bp):
ATGGTATCTATACCCCCC
Found at i:142026 original size:2 final size:2
Alignment explanation
Indices: 142019--142048 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
142009 TGTAACAATG
142019 TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
142049 GTTTGTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:147633 original size:228 final size:227
Alignment explanation
Indices: 147237--147692 Score: 858
Period size: 228 Copynumber: 2.0 Consensus size: 227
147227 AGTCCTATGT
* *
147237 TCAAAATCAATGAAATAGAGAGTTTAGAAAAATTTACCTTGAAAGATGAGATTGAGTGGATTTTG
1 TCAAAATCAATGAAATACAGAGTTTAGAAAAAATTACCTTGAAAGATGAGATTGAGTGGATTTTG
*
147302 ATTTTTTTGCACGATTTTAATGATGCTAGCAAGTTTAGAAGATGATATTTGAAGAGAATTCCGAT
66 ATTTTTTTGCACGATTTTAATGATGCTAGCAAGTTTAGAAGATGATAATTGAAGAGAATTCCGAT
147367 TAAAAACGTTGTTTTGAGGCAAGAATGAAGATAGGGAGATTAGAGAGGGGAAACGGCGGAAGAGA
131 TAAAAACGTTGTTTTGAGGCAAGAATGAAGATAGGGAGATTAGAGAGGGGAAACGGCGGAAGAGA
147432 AGAGAAGAGAGGTTTTGAGCCAAAACCAAGGG
196 AGAGAAGAGAGGTTTTGAGCCAAAACCAAGGG
147464 TCAAAATCAATGAAATACAGAGTTTAGAAAAAATTACCTTGAAAGATGAGATTGAGTGGATTTTG
1 TCAAAATCAATGAAATACAGAGTTTAGAAAAAATTACCTTGAAAGATGAGATTGAGTGGATTTTG
147529 ATGTTTTTTGCACGATTTTAATGATGCTAGCAAGTTTAGAAGATGATAATTGAAGAGAATTCCGA
66 AT-TTTTTTGCACGATTTTAATGATGCTAGCAAGTTTAGAAGATGATAATTGAAGAGAATTCCGA
* *
147594 TTAAAAACGTTGTTTTGAGGCAAGAATGGAGATAGGGAGATTAGATAGGGGAAACGGCGGAAGAG
130 TTAAAAACGTTGTTTTGAGGCAAGAATGAAGATAGGGAGATTAGAGAGGGGAAACGGCGGAAGAG
147659 AAGAGAAGAGAGGTTTTGAGCCAAAACCAAGGG
195 AAGAGAAGAGAGGTTTTGAGCCAAAACCAAGGG
147692 T
1 T
147693 TCTGCCCGAT
Statistics
Matches: 223, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
227 65 0.29
228 158 0.71
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.26
Consensus pattern (227 bp):
TCAAAATCAATGAAATACAGAGTTTAGAAAAAATTACCTTGAAAGATGAGATTGAGTGGATTTTG
ATTTTTTTGCACGATTTTAATGATGCTAGCAAGTTTAGAAGATGATAATTGAAGAGAATTCCGAT
TAAAAACGTTGTTTTGAGGCAAGAATGAAGATAGGGAGATTAGAGAGGGGAAACGGCGGAAGAGA
AGAGAAGAGAGGTTTTGAGCCAAAACCAAGGG
Found at i:147744 original size:21 final size:21
Alignment explanation
Indices: 147718--147757 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
147708 CAGAACCCCA
*
147718 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
147739 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
147758 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Done.