Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000905.1 Hibiscus syriacus cultivar Beakdansim tig00001787_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: 98744
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:23402 original size:39 final size:39
Alignment explanation
Indices: 23359--23486 Score: 96
Period size: 39 Copynumber: 3.2 Consensus size: 39
23349 AAGAAAGATA
23359 GAGCAAGAGCAGGATCTTGCAGTGGAGAAGACAAACGCC
1 GAGCAAGAGCAGGATCTTGCAGTGGAGAAGACAAACGCC
* ** * ** * ** * * **
23398 GAGCAAGATGGAACAGCCAAGAAGAAAGAGAAAAGAAA-GATA
1 GAGCAAGA-GCAGGA-TCTTGCAG-TGGAGAAGACAAACG-CC
23440 GAGCAAGAGCAGGATCTTGCAGTGGAGAAGACAAACGCC
1 GAGCAAGAGCAGGATCTTGCAGTGGAGAAGACAAACGCC
23479 GAGCAAGA
1 GAGCAAGA
23487 TGGAACAGCC
Statistics
Matches: 58, Mismatches: 26, Indels: 10
0.62 0.28 0.11
Matches are distributed among these distances:
39 25 0.43
40 8 0.14
41 8 0.14
42 17 0.29
ACGTcount: A:0.44, C:0.16, G:0.32, T:0.08
Consensus pattern (39 bp):
GAGCAAGAGCAGGATCTTGCAGTGGAGAAGACAAACGCC
Found at i:23422 original size:81 final size:81
Alignment explanation
Indices: 23335--23513 Score: 344
Period size: 81 Copynumber: 2.2 Consensus size: 81
23325 GGAGAAGAAA
23335 AAGAAGAAAGAGAAAAGAAAGATAGAGCAAGAGCAGGATCTTGCAGTGGAGAAGACAAACGCCGA
1 AAGAAGAAAGAGAAAAGAAAGATAGAGCAAGAGCAGGATCTTGCAGTGGAGAAGACAAACGCCGA
23400 GCAAGATGGAACAGCC
66 GCAAGATGGAACAGCC
23416 AAGAAGAAAGAGAAAAGAAAGATAGAGCAAGAGCAGGATCTTGCAGTGGAGAAGACAAACGCCGA
1 AAGAAGAAAGAGAAAAGAAAGATAGAGCAAGAGCAGGATCTTGCAGTGGAGAAGACAAACGCCGA
23481 GCAAGATGGAACAGCC
66 GCAAGATGGAACAGCC
23497 AAGAAG-AAGA-AAAAGAA
1 AAGAAGAAAGAGAAAAGAA
23514 GAGCAAAGAT
Statistics
Matches: 98, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
79 7 0.07
80 4 0.04
81 87 0.89
ACGTcount: A:0.50, C:0.13, G:0.30, T:0.07
Consensus pattern (81 bp):
AAGAAGAAAGAGAAAAGAAAGATAGAGCAAGAGCAGGATCTTGCAGTGGAGAAGACAAACGCCGA
GCAAGATGGAACAGCC
Found at i:25172 original size:28 final size:26
Alignment explanation
Indices: 25130--25183 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
25120 ACTAAATGTG
25130 TAGTTTACCTAAAATGTAATAGCTCATA
1 TAGTTTACCTAAAATGT--TAGCTCATA
*
25158 TAGTTTACCTCAAATGTTAGCTCATA
1 TAGTTTACCTAAAATGTTAGCTCATA
25184 AAATTATGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 9 0.36
28 16 0.64
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (26 bp):
TAGTTTACCTAAAATGTTAGCTCATA
Found at i:28659 original size:19 final size:19
Alignment explanation
Indices: 28635--28673 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
28625 TACTCAACTT
*
28635 TTTTTCACTCCTATTTTAG
1 TTTTTCACTCATATTTTAG
28654 TTTTTCACTCATATTTTAG
1 TTTTTCACTCATATTTTAG
28673 T
1 T
28674 AATTGAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTTCACTCATATTTTAG
Found at i:30307 original size:17 final size:17
Alignment explanation
Indices: 30287--30325 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
30277 GAAAGTCAAC
30287 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
30304 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
30321 GGTCA
1 GGTCA
30326 GACCGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:30339 original size:9 final size:9
Alignment explanation
Indices: 30321--30390 Score: 68
Period size: 9 Copynumber: 7.3 Consensus size: 9
30311 GGTCGGGTCG
*
30321 GGTCAGACC
1 GGTCAAACC
30330 GGTCAAACC
1 GGTCAAACC
*
30339 GGTTCGAACC
1 GG-TCAAACC
30349 GGTCAAACC
1 GGTCAAACC
30358 GGTCAGAACC
1 GGTCA-AACC
*
30368 GGTTGAAAACC
1 GG-T-CAAACC
*
30379 GGTTAAACC
1 GGTCAAACC
30388 GGT
1 GGT
30391 TTCCAGCAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
9 29 0.56
10 15 0.29
11 7 0.13
12 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.29, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:30349 original size:19 final size:19
Alignment explanation
Indices: 30321--30370 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
30311 GGTCGGGTCG
30321 GGTCAG-ACCGGTCAAACC
1 GGTCAGAACCGGTCAAACC
30339 GGTTC-GAACCGGTCAAACC
1 GG-TCAGAACCGGTCAAACC
30358 GGTCAGAACCGGT
1 GGTCAGAACCGGT
30371 TGAAAACCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.17
19 24 0.83
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.14
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:30389 original size:20 final size:21
Alignment explanation
Indices: 30353--30391 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30343 CGAACCGGTC
30353 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
30374 AAACCGGTTA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
30392 TCCAGCAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:45281 original size:31 final size:31
Alignment explanation
Indices: 45245--45304 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
45235 AACTTAAAAG
* *
45245 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
45276 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
45305 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:45404 original size:22 final size:22
Alignment explanation
Indices: 45332--45405 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
45322 AAATTATTTA
*
45332 AAATAAATCAATCCATACAACTACA
1 AAATAAATCAATCCATACAA--A-T
****
45357 ATAATAAATCAATCCATATTTTT
1 A-AATAAATCAATCCATACAAAT
45380 AAATAAATCAATCCATACAAAT
1 AAATAAATCAATCCATACAAAT
45402 AAAT
1 AAAT
45406 TATTTAAAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
22 21 0.54
23 1 0.03
25 1 0.03
26 16 0.41
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATAAATCAATCCATACAAAT
Found at i:45417 original size:32 final size:32
Alignment explanation
Indices: 45380--45495 Score: 196
Period size: 32 Copynumber: 3.6 Consensus size: 32
45370 CCATATTTTT
45380 AAATAAATCAATCCATACAAATAAATTATTTA
1 AAATAAATCAATCCATACAAATAAATTATTTA
* *
45412 AAATAAATCAATCTATACTAATAAATTATTTA
1 AAATAAATCAATCCATACAAATAAATTATTTA
* *
45444 AAATAAATCAATCAATACTAATAAATTATTTA
1 AAATAAATCAATCCATACAAATAAATTATTTA
45476 AAATAAATCAATCCATACAA
1 AAATAAATCAATCCATACAA
45496 CTACAATAAT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 79 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (32 bp):
AAATAAATCAATCCATACAAATAAATTATTTA
Found at i:45419 original size:54 final size:53
Alignment explanation
Indices: 45359--45724 Score: 164
Period size: 54 Copynumber: 6.6 Consensus size: 53
45349 CAACTACAAT
*
45359 AATAAATCAATCCATATTTTTAAATAAATCAATCCATACAAATAAATTATTTAA
1 AATAAATCAATCCATATTTTTAAATAAATCAATCAATACAAATAAA-TATTTAA
*
45413 AATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCAATACTAATAAATTATTTAA
1 AATAAATCAATC----C--AT--ATT-TTT-AAATAAATCAATCAATACAAATAAA-TATTTAA
**** * *
45477 AATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C---CAAAT-TTTAA
1 AATAAATCAATCCATATTTTTA-AATAAATCAATCAATACAAATAAATATTTAA
* ** * * * * **
45525 AATAAATCAATCCATACTAATAAATTATTTAA--AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTTAAATAAATCAATCAATACA--AATAAATA-TTTAA
* * *
45579 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATACAACTACA-A--T--
1 AATAAATCAAT-C---C--AT--ATT-TTT-AAATAAATCAATCAATACAAATAAATATTTAA
* * * * *
45637 AATAAATCAATCTATATTTTAAAATAAATCAATCCACACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTTAAATAAATCAATCAATACAAATAAA-TATTTAA
*
45691 AATAAATCAATCCATATTTTAAAATAAATCAATC
1 AATAAATCAATCCATATTTTTAAATAAATCAATC
45725 CATATTTTAA
Statistics
Matches: 240, Mismatches: 34, Indels: 76
0.69 0.10 0.22
Matches are distributed among these distances:
46 3 0.01
47 3 0.01
48 49 0.20
49 3 0.01
50 7 0.03
52 5 0.02
53 1 0.00
54 72 0.30
55 5 0.02
56 1 0.00
57 1 0.00
58 15 0.06
60 6 0.03
62 5 0.02
63 5 0.02
64 55 0.23
66 4 0.02
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (53 bp):
AATAAATCAATCCATATTTTTAAATAAATCAATCAATACAAATAAATATTTAA
Found at i:45450 original size:112 final size:109
Alignment explanation
Indices: 45318--45773 Score: 321
Period size: 112 Copynumber: 4.2 Consensus size: 109
45308 ACAACTACAA
* ****
45318 TAATAAATTATTTAAAATAAATCAATCCATAC-AACTACA-A-T-AATAAATCAATCCATATTTT
1 TAATAAATTATTTAAAATAAATCAATCCATACTAA-TAAATATTAAATAAATCAATCCATACAAC
* * * *
45379 TA-AATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCTATAC
65 TACAAT-AATAAATCAAT-C---CAAA-T-TTTAAAATAAATCAATCCATAC
*
45430 TAATAAATTATTTAAAATAAATCAATCAATACTAATAAATTATTTAAAATAAATCAATCCATACA
1 TAATAAATTATTTAAAATAAATCAATCCATACTAATAAA-TA-TT-AAATAAATCAATCCATACA
45495 ACTACAATAATAAATCAATCCAAATTTTAAAATAAATCAATCCATAC
63 ACTACAATAATAAATCAATCCAAATTTTAAAATAAATCAATCCATAC
*
45542 TAATAAATTATTTAAAATAAATCAATCCATA-T--T---T-TAAAATAAATCAATCCATACTAA-
1 TAATAAATTATTTAAAATAAATCAATCCATACTAATAAATATTAAATAAATCAATCCATAC-AAC
* * * * **
45599 TA-AATTATTTAAAATAAAT-C-AATCTATACAACTACAAT-AATAAAT-C
65 TACAA-TA-AT-AAATCAATCCAAAT-TTTA-AAATA-AATCAATCCATAC
** *
45645 -AATCTA-TATTTTAAAATAAATCAATCCACACTAATAAATTATTTAAAATAAATCAATCCAT--
1 TAATAAATTA-TTTAAAATAAATCAATCCATACTAATAAA-TA-TT-AAATAAATCAATCCATAC
* ** * *
45706 -ATTTTAA-AATAAATCAATCCATATTTTAAAATAAAACAATCCATAC
62 AACTACAATAATAAATCAATCCAAATTTTAAAATAAATCAATCCATAC
45752 TAATAAATTATTTAAAATAAAT
1 TAATAAATTATTTAAAATAAAT
45774 TATTTTAAAA
Statistics
Matches: 277, Mismatches: 33, Indels: 72
0.73 0.09 0.19
Matches are distributed among these distances:
101 4 0.01
102 49 0.18
103 10 0.04
104 16 0.06
105 7 0.03
106 16 0.06
107 6 0.02
108 20 0.07
109 5 0.02
110 2 0.01
111 2 0.01
112 101 0.36
113 3 0.01
114 4 0.01
116 1 0.00
117 1 0.00
118 27 0.10
119 3 0.01
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (109 bp):
TAATAAATTATTTAAAATAAATCAATCCATACTAATAAATATTAAATAAATCAATCCATACAACT
ACAATAATAAATCAATCCAAATTTTAAAATAAATCAATCCATAC
Found at i:45549 original size:22 final size:23
Alignment explanation
Indices: 45474--45548 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
45464 ATAAATTATT
45474 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
* **
45496 CTACAATAATAAATCAATCCA-AATTT
1 -T--AA-AATAAATCAATCCATACTAA
45522 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
45545 TAAA
1 TAAA
45549 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
22 14 0.34
23 9 0.22
25 4 0.10
26 14 0.34
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:45556 original size:32 final size:32
Alignment explanation
Indices: 45520--45627 Score: 137
Period size: 32 Copynumber: 3.7 Consensus size: 32
45510 CAATCCAAAT
45520 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
45552 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
45574 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
45606 TTTAAAATAAATCAATCTATAC
1 TTTAAAATAAATCAATCCATAC
45628 AACTACAATA
Statistics
Matches: 65, Mismatches: 1, Indels: 20
0.76 0.01 0.23
Matches are distributed among these distances:
22 16 0.25
23 2 0.03
24 1 0.02
26 3 0.05
28 3 0.05
30 1 0.02
31 2 0.03
32 37 0.57
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:45578 original size:22 final size:22
Alignment explanation
Indices: 45552--45594 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
45542 TAATAAATTA
45552 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
45574 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
45595 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:45596 original size:134 final size:134
Alignment explanation
Indices: 45318--45728 Score: 669
Period size: 134 Copynumber: 3.0 Consensus size: 134
45308 ACAACTACAA
*
45318 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTTAAA
1 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAA
*
45383 TAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTATTTAAAAT
66 TAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC----C--AT--A-T-TTTAAAAT
*
45448 AAATCAATCAATAC
121 AAATCAATCCATAC
*
45462 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCAAATTTTAAAA
1 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAA
45527 TAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCC
66 TAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCC
45592 ATAC
131 ATAC
* *
45596 TAATAAATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCTATATTTTAAAA
1 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAA
*
45661 TAAATCAATCCACACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCC
66 TAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCC
45726 ATA
131 ATA
45729 TTTTAAAATA
Statistics
Matches: 259, Mismatches: 8, Indels: 10
0.94 0.03 0.04
Matches are distributed among these distances:
134 150 0.58
135 1 0.00
136 1 0.00
138 2 0.01
140 1 0.00
144 104 0.40
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (134 bp):
TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAA
TAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCC
ATAC
Found at i:45603 original size:22 final size:22
Alignment explanation
Indices: 45554--45602 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
45544 ATAAATTATT
**
45554 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
45576 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
45599 TAAA
1 TAAA
45603 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:45641 original size:80 final size:76
Alignment explanation
Indices: 45555--45773 Score: 339
Period size: 80 Copynumber: 2.8 Consensus size: 76
45545 TAAATTATTT
45555 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
*
45620 ATCTATACAACTAC
66 ATCCAT---ACTAC
* *
45634 AATAATAAATCAATCTATATTTTAAAATAAATCAATCCACACTAATAAATTATTTAAAATAAATC
1 AA-AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATC
* **
45699 AATCCATATTTT
65 AATCCATACTAC
*
45711 AAAATAAATCAATCCATATTTTAAAATAAAACAATCCATACTAATAAATTATTTAAAATAAAT
1 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
45774 TATTTTAAAA
Statistics
Matches: 130, Mismatches: 9, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
76 58 0.45
77 4 0.03
79 2 0.02
80 66 0.51
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (76 bp):
AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
ATCCATACTAC
Found at i:45712 original size:22 final size:22
Alignment explanation
Indices: 45686--45810 Score: 133
Period size: 22 Copynumber: 5.5 Consensus size: 22
45676 TAATAAATTA
45686 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
45708 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
45730 TTTAAAATAAAACAATCCATACT
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
45753 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCCA-TAT
45777 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
45799 TTTATAATAAAT
1 TTTAAAATAAAT
45811 TATTTTAAAA
Statistics
Matches: 81, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
22 56 0.69
23 11 0.14
24 12 0.15
25 2 0.02
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:45766 original size:54 final size:54
Alignment explanation
Indices: 45503--45773 Score: 249
Period size: 54 Copynumber: 5.1 Consensus size: 54
45493 CAACTACAAT
* *
45503 AATAAATCAATCCAAATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAAACAATCCATACTAATAAATTATTTAA
*
45557 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAAACAATCCATACTAATAAATTATTTAA
* *** * * *
45611 AATAAATCAATCTATACAACTACAATAATA-AATCAAT-CT-AT--A-T-TTTAA
1 AATAAATCAATCCATA-TTTTAAAATAAAACAATCCATACTAATAAATTATTTAA
* ** ** ** **
45659 AATAAATCAATCCACACTAATAAATTATTTAA-AATAAAT-C-AATCCA-TATTTTAA
1 AATAAATCAATCCATA-TTTTAAA--ATAAAACAATCCATACTAATAAATTA-TTTAA
45713 AATAAATCAATCCATATTTTAAAATAAAACAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAAACAATCCATACTAATAAATTATTTAA
45767 AATAAAT
1 AATAAAT
45774 TATTTTAAAA
Statistics
Matches: 178, Mismatches: 27, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
48 24 0.13
49 1 0.01
50 13 0.07
51 4 0.02
52 9 0.05
53 8 0.04
54 110 0.62
55 9 0.05
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAAACAATCCATACTAATAAATTATTTAA
Found at i:45782 original size:15 final size:15
Alignment explanation
Indices: 45753--45870 Score: 157
Period size: 15 Copynumber: 7.5 Consensus size: 15
45743 AATCCATACT
45753 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
45767 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
45782 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
45804 AATAAATTATTTTAA
1 AATAAATTATTTTAA
45819 AATAAATTATTTTAA
1 AATAAATTATTTTAA
45834 AATAAATTATTTTAA
1 AATAAATTATTTTAA
45849 AATAAATTATTTTAA
1 AATAAATTATTTTAA
45864 AATAAAT
1 AATAAAT
45871 AACCTTATTA
Statistics
Matches: 94, Mismatches: 2, Indels: 15
0.85 0.02 0.14
Matches are distributed among these distances:
14 9 0.10
15 67 0.71
17 1 0.01
18 3 0.03
19 3 0.03
20 1 0.01
22 10 0.11
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:45784 original size:47 final size:49
Alignment explanation
Indices: 45727--45839 Score: 167
Period size: 52 Copynumber: 2.3 Consensus size: 49
45717 AATCAATCCA
*
45727 TATTTTAAAATAAAACAATCCATA-CTAATAAATTA-TTTAAAATAAAT
1 TATTTTAAAATAAAACAATCCATATATAATAAATTATTTTAAAATAAAT
*
45774 TATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTAAAATAAAACAATCCATA---TATAATAAATTATTTTAAAATAAAT
45826 TATTTTAAAATAAA
1 TATTTTAAAATAAA
45840 TTATTTTAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
47 23 0.39
51 10 0.17
52 26 0.44
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (49 bp):
TATTTTAAAATAAAACAATCCATATATAATAAATTATTTTAAAATAAAT
Found at i:48369 original size:2 final size:2
Alignment explanation
Indices: 48362--48400 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
48352 TAAAAAGTAA
48362 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48401 AGTAGGGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50413 original size:123 final size:123
Alignment explanation
Indices: 50242--50813 Score: 934
Period size: 123 Copynumber: 4.7 Consensus size: 123
50232 TAGAGTAAAA
* *
50242 TGAATAAGTTCTTCAGATTATGAACTTATTCTTCCTCTTCAAATGAGTTCTTCTTATTACGAACT
1 TGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACT
*
50307 CCTTCTGGAAATGTTAATGTTGCTCTATCTTC-TTCTG-TAATAGAGTCGAGCAAAAGGT
66 CCTTCTGGAAATGTTAATGATGCTCTATC-TCATTCTGCT-ATAGAGTCGAGCAAAAGGT
*
50365 TGAATAAGTTCTTCATATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACT
1 TGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACT
* * * *
50430 CCTTCTGGAAATATTGATGCTGCTCTATCTCATTCTGTTATAGAGTCGAGCAAAAGGT
66 CCTTCTGGAAATGTTAATGATGCTCTATCTCATTCTGCTATAGAGTCGAGCAAAAGGT
50488 TGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACT
1 TGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACT
* * * *
50553 ACTTCTGGAAATGTTGATGATGCTCTATCTTC-TTTTGCTATTGAGTCGAGCAAAAGGT
66 CCTTCTGGAAATGTTAATGATGCTCTATC-TCATTCTGCTATAGAGTCGAGCAAAAGGT
* * * *
50611 TGAATAAGTTCTTCAGATTATGAACTTATTCTTCATCTTCAAATGAGTTATTCTTATTACGAACT
1 TGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACT
*
50676 CCTTCTGGAAATGTTAATGATGCTCTATCTCTTTCTGCTATAGAGTCGAGCAAAAGGT
66 CCTTCTGGAAATGTTAATGATGCTCTATCTCATTCTGCTATAGAGTCGAGCAAAAGGT
*
50734 TGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTTAGATGAGTTCTTCTTATTACGAACT
1 TGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACT
50799 CCTTCTGGAAATGTT
66 CCTTCTGGAAATGTT
50814 TTAAGAAAAA
Statistics
Matches: 419, Mismatches: 26, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
122 4 0.01
123 412 0.98
124 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (123 bp):
TGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACT
CCTTCTGGAAATGTTAATGATGCTCTATCTCATTCTGCTATAGAGTCGAGCAAAAGGT
Found at i:50906 original size:36 final size:35
Alignment explanation
Indices: 50810--51094 Score: 133
Period size: 37 Copynumber: 7.8 Consensus size: 35
50800 CTTCTGGAAA
* *
50810 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAA-T
1 TGTTTTAAGAAAAACAATCTCAAGCGAGAAAAATT
* ** ***
50844 TGTTATTTCGAGTTAAATTTTCTCAAGCGAGAAACAATT
1 TG-T-TTT-AAGAAAAACAATCTCAAGCGAGAAA-AATT
* *
50883 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAA-T
1 TGTTTTAAGAAAAACAATCTCAAGCGAGAAAAATT
** *** *
50917 TGTTATTTCAAGTGAAATTTTCTCTAGCGAGAAATAATT
1 TG-T-TTT-AAGAAAAACAATCTCAAGCGAGAAA-AATT
* * *
50956 TGTTTTAAGAAAAACAATATCAAGTGAGATAAATT
1 TGTTTTAAGAAAAACAATCTCAAGCGAGAAAAATT
* * ** ** *
50991 GCTATTTTGAGTGAAACTTTCTTAAGCGAGAAACAATT
1 --TGTTTTAAGAAAAACAATCTCAAGCGAGAAA-AATT
* * *
51029 TGTTTTAAGAAAAACAATCTGAAGTGAGATAAATCTT
1 TGTTTTAAGAAAAACAATCTCAAGCGAGA-AAA-ATT
* * ** *
51066 TGCTTTGAGAAAAATTATCTCAAGTGAGA
1 TGTTTTAAGAAAAACAATCTCAAGCGAGA
51095 TAATTTTTTT
Statistics
Matches: 179, Mismatches: 57, Indels: 27
0.68 0.22 0.10
Matches are distributed among these distances:
34 5 0.03
35 8 0.04
36 61 0.34
37 89 0.50
38 10 0.06
39 6 0.03
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (35 bp):
TGTTTTAAGAAAAACAATCTCAAGCGAGAAAAATT
Found at i:50935 original size:73 final size:73
Alignment explanation
Indices: 50810--51062 Score: 416
Period size: 73 Copynumber: 3.5 Consensus size: 73
50800 CTTCTGGAAA
*
50810 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCGAGTTAAATTTTCTCAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCGAGTGAAATTTTCTCAAGCGAG
50875 AAACAATT
66 AAACAATT
* *
50883 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCAAGTGAAATTTTCTCTAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCGAGTGAAATTTTCTCAAGCGAG
*
50948 AAATAATT
66 AAACAATT
* * * * *
50956 TGTTTTAAGAAAAACAATATCAAGTGAGATAAATTGCTATTTTGAGTGAAACTTTCTTAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCGAGTGAAATTTTCTCAAGCGAG
51021 AAACAATT
66 AAACAATT
*
51029 TGTTTTAAGAAAAACAATCTGAAGTGAGATAAAT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAAT
51063 CTTTGCTTTG
Statistics
Matches: 166, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 166 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (73 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCGAGTGAAATTTTCTCAAGCGAG
AAACAATT
Found at i:55679 original size:16 final size:16
Alignment explanation
Indices: 55658--55688 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55648 TCGAAATCCT
55658 TATTTTAATGAATGAA
1 TATTTTAATGAATGAA
*
55674 TATTTTAATGCATGA
1 TATTTTAATGAATGA
55689 TTTGGAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (16 bp):
TATTTTAATGAATGAA
Found at i:57487 original size:25 final size:26
Alignment explanation
Indices: 57436--57497 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 26
57426 AATTGAAATT
*
57436 AAAT-AAATAAAAAGTAAATGGAATA
1 AAATAAAATATAAAGTAAATGGAATA
* *
57461 AATTAAAATATAAAGTAAAT-GACTA
1 AAATAAAATATAAAGTAAATGGAATA
57486 AAATAAAATATA
1 AAATAAAATATA
57498 TCATAAGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 18 0.56
26 14 0.44
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.24
Consensus pattern (26 bp):
AAATAAAATATAAAGTAAATGGAATA
Found at i:58987 original size:18 final size:19
Alignment explanation
Indices: 58952--58987 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
58942 GATACACTTT
58952 GATTTAATTTTATTTAAAA
1 GATTTAATTTTATTTAAAA
*
58971 GATTTTATTTT-TTTAAA
1 GATTTAATTTTATTTAAA
58988 TATGATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
GATTTAATTTTATTTAAAA
Found at i:59231 original size:6 final size:7
Alignment explanation
Indices: 59214--59239 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
59204 TTCTCCTTTC
59214 TTTTTAA
1 TTTTTAA
59221 TTTTTAA
1 TTTTTAA
59228 TTTTTAA
1 TTTTTAA
59235 TTTTT
1 TTTTT
59240 CCTAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:59925 original size:16 final size:15
Alignment explanation
Indices: 59906--59947 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
59896 TGTTAGTATT
59906 TTATTTAATTATTGTA
1 TTATTTAATT-TTGTA
*
59922 TTATTTAATTTTTTA
1 TTATTTAATTTTGTA
*
59937 TTATTTTATTT
1 TTATTTAATTT
59948 AATTATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTATTTAATTTTGTA
Found at i:59937 original size:20 final size:21
Alignment explanation
Indices: 59914--59959 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
59904 TTTTATTTAA
*
59914 TTATTGTATTATTTAATT-TT
1 TTATTATATTATTTAATTATT
*
59934 TTATTATTTTATTTAATTATT
1 TTATTATATTATTTAATTATT
59955 TTATT
1 TTATT
59960 TTTTTGCAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (21 bp):
TTATTATATTATTTAATTATT
Found at i:59963 original size:20 final size:20
Alignment explanation
Indices: 59922--59963 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
59912 AATTATTGTA
59922 TTATTTAATTTTTTATTATT
1 TTATTTAATTTTTTATTATT
59942 TTATTTAATTATTTTATT-TT
1 TTATTTAATT-TTTTATTATT
59962 TT
1 TT
59964 TGCAGTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
TTATTTAATTTTTTATTATT
Found at i:60233 original size:15 final size:15
Alignment explanation
Indices: 60213--60242 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
60203 TTATAACTGC
60213 AAAAAATAAAATAAT
1 AAAAAATAAAATAAT
60228 AAAAAATAAAATAAT
1 AAAAAATAAAATAAT
60243 TAATACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAAAATAAAATAAT
Found at i:61336 original size:21 final size:22
Alignment explanation
Indices: 61312--61352 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
61302 TTACCAATCA
*
61312 TATAAT-TTTTAAATTAAAAAT
1 TATAATATCTTAAATTAAAAAT
*
61333 TATAATATCTTAACTTAAAA
1 TATAATATCTTAAATTAAAA
61353 TTTACTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (22 bp):
TATAATATCTTAAATTAAAAAT
Found at i:61695 original size:20 final size:19
Alignment explanation
Indices: 61670--61734 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
61660 GATCGATAAT
61670 TCGCAACGCGATCTCCGATA
1 TCGCAACGCGAT-TCCGATA
** *
61690 TCGCAAATCAATTTCCAGAT-
1 TCGCAACGCGA-TTCC-GATA
*
61710 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCCGA-TA
61730 TCGCA
1 TCGCA
61735 TTGCGATTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
18 2 0.06
19 4 0.12
20 24 0.71
21 4 0.12
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.25
Consensus pattern (19 bp):
TCGCAACGCGATTCCGATA
Found at i:61764 original size:21 final size:21
Alignment explanation
Indices: 61735--61774 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
61725 GACTATCGCA
*
61735 TTGCGATTTCCCAAATTCGTG
1 TTGCAATTTCCCAAATTCGTG
* *
61756 TTGCAATTTTCCTAATTCG
1 TTGCAATTTCCCAAATTCG
61775 CAACGCGAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (21 bp):
TTGCAATTTCCCAAATTCGTG
Found at i:61797 original size:20 final size:20
Alignment explanation
Indices: 61772--61865 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
61762 TTTTCCTAAT
*
61772 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
61792 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
61812 TCGCAATGCGAATTA-GAAAAA
1 TCGCAATGCGAA-TACG-TAAA
*
61833 TCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
61853 TCGCAATGCGAAT
1 TCGCAATGCGAAT
61866 CTGACTATCG
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
20 49 0.74
21 17 0.26
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:62440 original size:20 final size:19
Alignment explanation
Indices: 62415--62519 Score: 85
Period size: 20 Copynumber: 5.6 Consensus size: 19
62405 TTCTAAACTT
62415 AAAATCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
62435 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
**
62455 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
*
62476 AAAATCACAAC-G---A-G
1 AAAATCGCAACAGAAAATG
* * *
62490 AGAATCGCAACGGGAAATG
1 AAAATCGCAACAGAAAATG
62509 AAAATCGCAAC
1 AAAATCGCAAC
62520 GCGAAACCAA
Statistics
Matches: 69, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
14 10 0.14
15 2 0.03
18 1 0.01
19 12 0.17
20 30 0.43
21 14 0.20
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:62516 original size:19 final size:19
Alignment explanation
Indices: 62415--62536 Score: 74
Period size: 20 Copynumber: 6.5 Consensus size: 19
62405 TTCTAAACTT
* *
62415 AAAATCGCAACATGAAAATG
1 AAAATCGCAAC-GGGAAATG
* *
62435 AAAATCGCAACACGAAAATG
1 AAAATCGCAAC-GGGAAATG
**
62455 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACG-G-GAAATG
*
62476 AAAATCACAAC--G--A-G
1 AAAATCGCAACGGGAAATG
*
62490 AGAATCGCAACGGGAAATG
1 AAAATCGCAACGGGAAATG
* **
62509 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGGGAAATG
62528 AAAATCGCA
1 AAAATCGCA
62537 TTGCGATTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 15
0.74 0.13 0.14
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 25 0.31
20 29 0.36
21 13 0.16
ACGTcount: A:0.50, C:0.20, G:0.19, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGGGAAATG
Found at i:62554 original size:19 final size:19
Alignment explanation
Indices: 62532--62649 Score: 137
Period size: 19 Copynumber: 6.1 Consensus size: 19
62522 GAAACCAAAA
*
62532 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
62551 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
62570 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
62589 TCGCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
62608 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
* *
62628 CTCTCGTTGCGATTTTTATT
1 -TCGCGTTGCGATTTTCATT
62648 TC
1 TC
62650 AACCAAAAGA
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
19 54 0.63
20 31 0.36
21 1 0.01
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:63637 original size:96 final size:96
Alignment explanation
Indices: 63473--63669 Score: 394
Period size: 96 Copynumber: 2.1 Consensus size: 96
63463 TCAGGCTTTG
63473 TTTGGGCCTTTAAGGTAAGAATTTCTATATAATGTTTTCAAAATTATAATTAATTATTTAACAAT
1 TTTGGGCCTTTAAGGTAAGAATTTCTATATAATGTTTTCAAAATTATAATTAATTATTTAACAAT
63538 TACTAATTTTTGTTATTATATTGTTTGTAGA
66 TACTAATTTTTGTTATTATATTGTTTGTAGA
63569 TTTGGGCCTTTAAGGTAAGAATTTCTATATAATGTTTTCAAAATTATAATTAATTATTTAACAAT
1 TTTGGGCCTTTAAGGTAAGAATTTCTATATAATGTTTTCAAAATTATAATTAATTATTTAACAAT
63634 TACTAATTTTTGTTATTATATTGTTTGTAGA
66 TACTAATTTTTGTTATTATATTGTTTGTAGA
63665 TTTGG
1 TTTGG
63670 ATATTTGAGG
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 101 1.00
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.49
Consensus pattern (96 bp):
TTTGGGCCTTTAAGGTAAGAATTTCTATATAATGTTTTCAAAATTATAATTAATTATTTAACAAT
TACTAATTTTTGTTATTATATTGTTTGTAGA
Found at i:64658 original size:94 final size:94
Alignment explanation
Indices: 64445--64818 Score: 573
Period size: 94 Copynumber: 4.1 Consensus size: 94
64435 TAGATTGCTT
* *
64445 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* **
64506 ATTTGTCTTT-TGTTAACTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
64533 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
64598 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
64627 AATAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
64692 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * * * *
64721 AGTAAATTTGTTCGTTTGCTGTCAATTCTGCTAAACTGTGTGTTATTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
64786 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
64814 AGTAA
1 AGTAA
64819 TGCAATCCAT
Statistics
Matches: 266, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
88 35 0.13
90 3 0.01
91 2 0.01
92 29 0.11
93 19 0.07
94 178 0.67
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:64936 original size:20 final size:20
Alignment explanation
Indices: 64911--64972 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
64901 TTTTGGTTGA
*
64911 AATGAAAATCGAAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
64931 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
64950 AACGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
64970 AAT
1 AAT
64973 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
19 17 0.47
20 19 0.53
ACGTcount: A:0.52, C:0.16, G:0.23, T:0.10
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:64974 original size:33 final size:33
Alignment explanation
Indices: 64935--65072 Score: 141
Period size: 33 Copynumber: 3.9 Consensus size: 33
64925 CGAGAGAATG
*
64935 AAAATCGCAACGCGAAACGAAAATCGCAACGAG
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
* * *
64968 AGAATCGCAACGCGAAATGAAAATCGTAACGAC
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
* *
65001 AAAATCGCAACGCGAAACCAAAAAGCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-CGAAAATCGCAA--CG--A-C
*
65040 AAAAATCGCAACGCGAAACCAAAAATCGCAACG
1 -AAAATCGCAACGCGAAA-CGAAAATCGCAACG
65073 CGAAACTATA
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
33 45 0.51
34 8 0.09
36 2 0.02
38 3 0.03
39 1 0.01
40 29 0.33
ACGTcount: A:0.49, C:0.26, G:0.19, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACGAAAATCGCAACGAC
Found at i:65024 original size:20 final size:20
Alignment explanation
Indices: 65001--65078 Score: 147
Period size: 20 Copynumber: 3.9 Consensus size: 20
64991 TCGTAACGAC
65001 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
*
65021 AAAAGCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
65041 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
65061 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
65079 TATAATCGCG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.50, C:0.29, G:0.17, T:0.04
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:65628 original size:21 final size:21
Alignment explanation
Indices: 65604--65670 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
65594 TCATTCCTCG
65604 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
65625 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
65646 AGATGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
65667 AGAG
1 AGAG
65671 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:67029 original size:14 final size:14
Alignment explanation
Indices: 67010--67045 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
67000 ATTGTTTAAT
67010 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
67024 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
67038 TGATTTGT
1 TGATTTGT
67046 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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:67168 original size:19 final size:19
Alignment explanation
Indices: 67152--67198 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
67142 AAAAATGACT
67152 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
67171 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
67190 ATCGCAATG
1 ATCGCAATG
67199 ACAAAATCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:67251 original size:19 final size:18
Alignment explanation
Indices: 67229--67320 Score: 74
Period size: 19 Copynumber: 5.4 Consensus size: 18
67219 TAAATTCACA
67229 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
**
67247 TTTGCGA--TTC-CCTCG-
1 -TTGCGATTTTCATTTCGC
67262 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
*
67280 ATTGCGA--TTC-TCTCG-
1 -TTGCGATTTTCATTTCGC
67295 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
67313 ATTGCGAT
1 -TTGCGAT
67321 AGTTATTTCC
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 12 0.21
16 13 0.23
17 13 0.23
19 19 0.33
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGC
Found at i:67271 original size:33 final size:33
Alignment explanation
Indices: 67229--67320 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
67219 TAAATTCACA
*
67229 TTGCGATTTTCATTTCGCTTTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
*
67262 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
67295 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
67321 AGTTATTTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
Found at i:67339 original size:20 final size:20
Alignment explanation
Indices: 67293--67342 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
67283 GCGATTCTCT
*
67293 CGTTGCGAT-TTTCATTTCG
1 CGTTGCGATAGTTCATTTCG
*
67312 CATTGCGATAGTT-ATTTCCG
1 CGTTGCGATAGTTCATTT-CG
67332 CGTTGCGATAG
1 CGTTGCGATAG
67343 ACATTAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTTCATTTCG
Found at i:70716 original size:20 final size:20
Alignment explanation
Indices: 70689--70768 Score: 119
Period size: 20 Copynumber: 4.1 Consensus size: 20
70679 TCGTTGCAAT
70689 TTAC-TAAATCGCAATGCGA
1 TTACGTAAATCGCAATGCGA
*
70708 TTACGTAAATCGCAATGAGA
1 TTACGTAAATCGCAATGCGA
70728 TTACGTAAATCGCAATGCGA
1 TTACGTAAATCGCAATGCGA
* *
70748 ATACGT-AATCGCATTGCGA
1 TTACGTAAATCGCAATGCGA
70767 TT
1 TT
70769 TTCCTAATTC
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 17 0.31
20 38 0.69
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (20 bp):
TTACGTAAATCGCAATGCGA
Found at i:70786 original size:21 final size:21
Alignment explanation
Indices: 70761--70811 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
70751 CGTAATCGCA
70761 TTGCGATTTTCCTAATTCGTT
1 TTGCGATTTTCCTAATTCGTT
70782 TTGCGATTTTCCTAATTCGTT
1 TTGCGATTTTCCTAATTCGTT
70803 TTGCGATTT
1 TTGCGATTT
70812 ACGTATTCGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.14, C:0.18, G:0.16, T:0.53
Consensus pattern (21 bp):
TTGCGATTTTCCTAATTCGTT
Found at i:70826 original size:20 final size:21
Alignment explanation
Indices: 70682--70843 Score: 111
Period size: 20 Copynumber: 8.0 Consensus size: 21
70672 CAGAATCTCG
*
70682 TTGCAATTTAC-TAAATCGCA
1 TTGCGATTTACGTAAATCGCA
*
70702 ATGCGA-TTACGTAAATCGCA
1 TTGCGATTTACGTAAATCGCA
* *
70722 ATGAGA-TTACGTAAATCGCA
1 TTGCGATTTACGTAAATCGCA
* *
70742 ATGCGA-ATACGT-AATCGCA
1 TTGCGATTTACGTAAATCGCA
* * * **
70761 TTGCGATTTTCCTAATTCGTT
1 TTGCGATTTACGTAAATCGCA
* * * **
70782 TTGCGATTTTCCTAATTCGTT
1 TTGCGATTTACGTAAATCGCA
*
70803 TTGCGATTTACGT-ATTCGCA
1 TTGCGATTTACGTAAATCGCA
* *
70823 TTGCGATTTAGGAAAATCGCA
1 TTGCGATTTACGTAAATCGCA
70844 ACGCGAATTT
Statistics
Matches: 119, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.13
20 61 0.51
21 42 0.35
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (21 bp):
TTGCGATTTACGTAAATCGCA
Found at i:70858 original size:22 final size:21
Alignment explanation
Indices: 70828--70870 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
70818 TCGCATTGCG
70828 ATTTAGGAAAATCGCAACGCGA
1 ATTTAGG-AAATCGCAACGCGA
* *
70850 ATTTGGGAAATCGCAATGCGA
1 ATTTAGGAAATCGCAACGCGA
70871 TAGTCAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (21 bp):
ATTTAGGAAATCGCAACGCGA
Found at i:73109 original size:14 final size:15
Alignment explanation
Indices: 73089--73127 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
73079 TCGTGTTCTT
73089 ATATTTAAAA-AAAA
1 ATATTTAAAATAAAA
*
73103 TTATTTAAAATAAAA
1 ATATTTAAAATAAAA
73118 AT-TTTAAAAT
1 ATATTTAAAAT
73128 TATATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATTTAAAATAAAA
Found at i:74523 original size:21 final size:23
Alignment explanation
Indices: 74497--74543 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
74487 GTACATTATC
*
74497 TTTTATT-AA-AATTATAATATA
1 TTTTATTGAAGAATAATAATATA
*
74518 TTTTATTGAAGAATAATAATTTA
1 TTTTATTGAAGAATAATAATATA
74541 TTT
1 TTT
74544 AAACAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 2 0.09
23 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
TTTTATTGAAGAATAATAATATA
Found at i:75387 original size:19 final size:20
Alignment explanation
Indices: 75344--75388 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
75334 TTTAAAGTTT
*
75344 TATTGTATTTAATTTTATAAA
1 TATT-TATTTAATTTGATAAA
75365 -ATTTATTTAA-TTGATAAA
1 TATTTATTTAATTTGATAAA
75383 TATTTA
1 TATTTA
75389 ATATAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 7 0.32
19 12 0.55
20 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTATTTAATTTGATAAA
Found at i:76218 original size:16 final size:17
Alignment explanation
Indices: 76197--76231 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
76187 GAATACTACA
*
76197 TTCAATTTTATA-AAAT
1 TTCAATTTCATACAAAT
76213 TTCAATTTCATACAAAT
1 TTCAATTTCATACAAAT
76230 TT
1 TT
76232 TAACTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (17 bp):
TTCAATTTCATACAAAT
Found at i:78071 original size:157 final size:153
Alignment explanation
Indices: 77797--78220 Score: 510
Period size: 157 Copynumber: 2.7 Consensus size: 153
77787 TATATGTTCA
** * * * *
77797 TATTTGAAATTTACATGGGAATCCGAATAATATAATCTTTTCACATGATGAACTTTTCCTGCCTT
1 TATTTGAAATTTACATTCGAATTCGAATAATATAATCTTTTAACATGATGAACTTTTCTTGGCTT
* *
77862 GTTAGGTGATGGTCCTATGCACTAATCTATGCATACTTATCCCTAGTTTTTTTTCCCATATGTAT
66 GTTAGGTGATGGTCCTATGCACTAATCTATGC-TACTTATCCCTAGTATTTTTT---ATATGAAT
77927 ATAAAACTAAAT-TTGAATACATAATCG
127 ATAAAACTAAATCTT-AATACATAATCG
* * * *
77954 TATTTAAAATTTACATTCAAATTCGAATGATATAATCTTTTGACATGATGAACTTTTCTTGGCTT
1 TATTTGAAATTTACATTCGAATTCGAATAATATAATCTTTTAACATGATGAACTTTTCTTGGCTT
* * * *
78019 GTTAGGTTATGATCCTATGCAGTAATCTATGCTACTAATCCCTAGTAATTTTTTATATGAATATA
66 GTTAGGTGATGGTCCTATGCACTAATCTATGCTACTTATCCCTAGT-ATTTTTTATATGAATATA
* * * **
78084 AAATTACATCTTAATACATATTTT
130 AAACTAAATCTTAATACATAATCG
* ** *
78108 TATTTGAATTTTATGTTCGAA-TCTGAATAATATAATCTTTTTAACATGATGAATTTTTCTTGGC
1 TATTTGAAATTTACATTCGAATTC-GAATAATATAATC-TTTTAACATGATGAACTTTTCTTGGC
* *
78172 TTGTTAAGTGATGGTCCTAATGCACTGATCTATGCTACTTATCCCTAGT
64 TTGTTAGGTGATGGTCCT-ATGCACTAATCTATGCTACTTATCCCTAGT
78221 TTAGGTGAAT
Statistics
Matches: 228, Mismatches: 34, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
153 2 0.01
154 54 0.24
155 41 0.18
156 40 0.18
157 91 0.40
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (153 bp):
TATTTGAAATTTACATTCGAATTCGAATAATATAATCTTTTAACATGATGAACTTTTCTTGGCTT
GTTAGGTGATGGTCCTATGCACTAATCTATGCTACTTATCCCTAGTATTTTTTATATGAATATAA
AACTAAATCTTAATACATAATCG
Found at i:79795 original size:2 final size:2
Alignment explanation
Indices: 79788--79836 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
79778 AAACTATAGA
79788 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
79830 AT AT AT A
1 AT AT AT A
79837 CCAAATTGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:80244 original size:16 final size:16
Alignment explanation
Indices: 80223--80269 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
80213 TCCTTAAACT
80223 ATGATTTTATTTTCAA
1 ATGATTTTATTTTCAA
80239 ATGATTTGTAATTTT-AA
1 ATGATTT-T-ATTTTCAA
*
80256 AT-ATTTTAGTTTCA
1 ATGATTTTATTTTCA
80270 TCCCTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 4 0.15
15 2 0.07
16 11 0.41
17 5 0.19
18 5 0.19
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.55
Consensus pattern (16 bp):
ATGATTTTATTTTCAA
Found at i:80582 original size:60 final size:58
Alignment explanation
Indices: 80494--80673 Score: 175
Period size: 60 Copynumber: 3.1 Consensus size: 58
80484 GCATATATTG
* ** * * ** *
80494 ATAGTTTGGGATGAAATTGAAACGTTCAAAAGTTTGGGGATCAATTTAGAATTAGGGTT
1 ATAGTTTGAGATGAAATT-AAATTTTCAAAAGTTTGAGGATCAATTTAGAATGAGAATC
*
80553 ATAGTTTTGAGATGAAATTAAAATTTTCAAAAGGTTGAGGA-C-ATTTAGAATGAGAATC
1 ATAG-TTTGAGATGAAATT-AAATTTTCAAAAGTTTGAGGATCAATTTAGAATGAGAATC
* * * * *
80611 ATAGTTTGAGGATGAAACTAAATTGTTCAAAAGTTTAAGGATCAATTTAAAATAAAAATC
1 ATAGTTTGA-GATGAAATTAAATT-TTCAAAAGTTTGAGGATCAATTTAGAATGAGAATC
80671 ATA
1 ATA
80674 ATTTATGTAA
Statistics
Matches: 100, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
57 10 0.10
58 38 0.38
59 6 0.06
60 46 0.46
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.33
Consensus pattern (58 bp):
ATAGTTTGAGATGAAATTAAATTTTCAAAAGTTTGAGGATCAATTTAGAATGAGAATC
Found at i:80905 original size:12 final size:12
Alignment explanation
Indices: 80888--80917 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
80878 GAACAAACTC
80888 GTTTATAAGCTT
1 GTTTATAAGCTT
*
80900 GTTTATGAGCTT
1 GTTTATAAGCTT
80912 GTTTAT
1 GTTTAT
80918 CGACTCGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (12 bp):
GTTTATAAGCTT
Found at i:82428 original size:29 final size:29
Alignment explanation
Indices: 82386--82455 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
82376 GGAACATATG
82386 AATAGTCGGGTAACCATTGTGTAACTTCT
1 AATAGTCGGGTAACCATTGTGTAACTTCT
82415 AATAGTCGGGTAACCATTGTGTAACTTCT
1 AATAGTCGGGTAACCATTGTGTAACTTCT
82444 AATAGTCGGGTA
1 AATAGTCGGGTA
82456 CTTAACAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (29 bp):
AATAGTCGGGTAACCATTGTGTAACTTCT
Found at i:83880 original size:19 final size:19
Alignment explanation
Indices: 83845--83883 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
83835 CCATTCAAAA
*
83845 TAAAAAATAATTATAATAT
1 TAAAAAATAATCATAATAT
83864 TAAAAAAT-ATCATTAATAT
1 TAAAAAATAATCA-TAATAT
83883 T
1 T
83884 TGATTAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAAATAATCATAATAT
Found at i:88914 original size:15 final size:15
Alignment explanation
Indices: 88894--88924 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
88884 TAACAGATAG
88894 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
88909 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
88924 A
1 A
88925 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:89138 original size:19 final size:20
Alignment explanation
Indices: 89067--89132 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
89057 TAGTCCCTGG
*
89067 TAATATTTTATTCCCACTGA
1 TAATCTTTTATTCCCACTGA
*
89087 TAATCTTTTATTCTCACTGA
1 TAATCTTTTATTCCCACTGA
89107 TAATCTTTTATTCCCACT-A
1 TAATCTTTTATTCCCACTGA
89126 TAATCTT
1 TAATCTT
89133 ACATTCAGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
19 8 0.19
20 35 0.81
ACGTcount: A:0.27, C:0.21, G:0.03, T:0.48
Consensus pattern (20 bp):
TAATCTTTTATTCCCACTGA
Found at i:90985 original size:18 final size:19
Alignment explanation
Indices: 90950--90986 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
90940 CACGGAATGT
90950 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
90970 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
90987 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:91697 original size:2 final size:2
Alignment explanation
Indices: 91690--91724 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
91680 ATTAAAACTT
91690 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
91725 GGAAGGAGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.