Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 42
Found at i:3175634 original size:36 final size:33
Alignment explanation
Indices: 3175567--3175632 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 33
3175557 ATATTACTTT
*
3175567 TATTATATATATTTTATTTATTTCATTTTTTCC
1 TATTATATATATTTTATTTATCTCATTTTTTCC
3175600 TATTATATATATTATATTATTTA-CTCATTTTTT
1 TATTATATATA-T-T-TTATTTATCTCATTTTTT
3175633 TCTTTTTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 11 0.38
34 1 0.03
35 10 0.34
36 7 0.24
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (33 bp):
TATTATATATATTTTATTTATCTCATTTTTTCC
Found at i:3180161 original size:19 final size:19
Alignment explanation
Indices: 3180137--3180179 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
3180127 TGCGAACAAT
3180137 ATTTTACAGCATTTTTATC
1 ATTTTACAGCATTTTTATC
*
3180156 ATTTTACAGCATTTTTATT
1 ATTTTACAGCATTTTTATC
3180175 ATTTT
1 ATTTT
3180180 CCCTCCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.12, G:0.05, T:0.58
Consensus pattern (19 bp):
ATTTTACAGCATTTTTATC
Found at i:3180991 original size:84 final size:84
Alignment explanation
Indices: 3180815--3181753 Score: 853
Period size: 84 Copynumber: 11.3 Consensus size: 84
3180805 CATTTTTTTA
* * ***
3180815 AAGG-ACATCATTTGCAGCATAGCTCAAGGCCAGAAGGGTTATCTGCC-ACC-AAGACCTTCGAG
1 AAGGCACATCATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
*
3180877 TTCGACTACGCCCAGCTCC
66 TTCGACTACGCTCAGCTCC
* * *
3180896 AAGGCATATCATTTGCAGCATAACTTAATTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAC
1 AAGGCACATCATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
* *
3180961 TTTGACTACGTTCAGCTCC
66 TTCGACTACGCTCAGCTCC
* *
3180980 AAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCT----ACCAAAGACCTTCGAG
1 AAGGCACATCATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
* * *
3181041 TTCGATTACACTCAGCTTCG
66 TTCGACTACGCTCAGC-TCC
* * * * * * ***
3181061 AGGGTACATCATTTACAACATAACTCAAGGCT-AGAAGGGTTATCT-TTGACCAAAAGACCTTCG
1 AAGGCACATCATTTGCAGCATAACTTAA-GTTGAGAAGGGTTATCTGCCAACC-AAAGACCTTCG
*
3181124 AGTTCGACTACGCTCAGCTTC
64 AGTTCGACTACGCTCAGCTCC
* ** * * * * *
3181145 AAGGCACATCATATGCAGCATAGTTTAAGTCGAGAAGGGCTATCTG----CCAAATACCCTCAAG
1 AAGGCACATCATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
* *
3181206 TTCGA-TCACACTCAGCTTCG
66 TTCGACT-ACGCTCAGC-TCC
* ** * * * *
3181226 AGGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGTCAACCGAATACCTTTGAG
1 AAGGCACATCATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
*
3181291 TTTGACTACGCTCAGCTCC
66 TTCGACTACGCTCAGCTCC
* * * * *
3181310 AAGGCACATTATTTGGAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCTTCGAG
1 AAGGCACATCATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
* * *
3181371 TTCGACTACGTTCCGCTTC
66 TTCGACTACGCTCAGCTCC
* * * *
3181390 AAGGCACATCATTTACAGCATAACTCAAGGCT-AGAAGGGTTATCTGCCAA-CAAAGACCTTTGA
1 AAGGCACATCATTTGCAGCATAACTTAA-GTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGA
* * * * *
3181453 GTTTGATTACTCTCAACTCA
65 GTTCGACTACGCTCAGCTCC
* * * * *
3181473 AAGGCATAAT-ATTTGCAGCATAAATTAAGTTGAGAAAGGCTATCTGCCAACCAAAGACCTTCAA
1 AAGGCA-CATCATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGA
* * * **
3181537 GTTTGATTACACTCAGCTTTG
65 GTTCGACTACGCTCAGC-TCC
** * * *
3181558 GGGGCATATCATTTGCAGCATAACTCAAGTTGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAG
1 AAGGCACATCATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
* *
3181623 TTCGACAACGTTCAGCTCC
66 TTCGACTACGCTCAGCTCC
* * * *
3181642 AAGGCACATCATCTACAGCATAACTCAAGGCT-AGAAGGGTTATCTGCCAA-CAAAGACCTTCGA
1 AAGGCACATCATTTGCAGCATAACTTAA-GTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGA
**
3181705 GTTCGACTATTCTCAGCTCC
65 GTTCGACTACGCTCAGCTCC
* * *
3181725 AAGACACATCATTTACATCATAACTTAAG
1 AAGGCACATCATTTGCAGCATAACTTAAG
3181754 GCAATAAGGG
Statistics
Matches: 692, Mismatches: 137, Indels: 57
0.78 0.15 0.06
Matches are distributed among these distances:
79 1 0.00
80 113 0.16
81 85 0.12
82 40 0.06
83 117 0.17
84 218 0.32
85 117 0.17
86 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (84 bp):
AAGGCACATCATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
TTCGACTACGCTCAGCTCC
Found at i:3181119 original size:165 final size:165
Alignment explanation
Indices: 3180815--3181770 Score: 944
Period size: 165 Copynumber: 5.8 Consensus size: 165
3180805 CATTTTTTTA
* * * * *
3180815 AAGG-ACATCATTTGCAGCATAGCTCAAGGCCAGAAGGGTTATCTGCCACCAAGACCTTCGAGTT
1 AAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCA--AAGACCTTCGAGTT
* * * * * * **
3180879 CGACTACGCCCAGC-TCCAAGGCATATCATTTGCAGCATAACTTAA-TTTGAGAAGGGTTATCTG
64 CGACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCT-AGAAGGGTTATCTG
* *
3180942 CCAACCAAAGACCTTCGACTTTGACTACGTTCAGCTCC
128 CCAACCAAAGACCTTTGAGTTTGACTACGTTCAGCTCC
*
3180980 AAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTACCAAAGACCTTCGAGTTCG
1 AAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCTTCGAGTTCG
* * * * ***
3181045 ATTACACTCAGCTTCGAGGGTACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCT-TTG
66 ACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCA
* * * *
3181109 ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTTC
131 ACC-AAAGACCTTTGAGTTTGACTACGTTCAGCTCC
* * * * * *
3181145 AAGGCACATCATATGCAGCATAGTTTAAGTCGAGAAGGGCTATCTGCCAAATACCCTCAAGTTCG
1 AAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCTTCGAGTTCG
* * * * * *
3181210 A-TCACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGTC
66 ACT-ACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCC
* * *
3181274 AACCGAATACCTTTGAGTTTGACTACGCTCAGCTCC
130 AACCAAAGACCTTTGAGTTTGACTACGTTCAGCTCC
* * *
3181310 AAGGCACATTATTTGGAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCG
1 AAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCTTCGAGTTCG
** *
3181375 ACTACGTTCCGCTTC-AAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCA
66 ACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCA
* * *
3181439 A-CAAAGACCTTTGAGTTTGATTAC-TCTCAACTCA
131 ACCAAAGACCTTTGAGTTTGACTACGT-TCAGCTCC
* ** * * *
3181473 AAGGCATAAT-ATTTGCAGCATAAATTAAGTTGAGAAAGGCTATCTGCCAACCAAAGACCTTCAA
1 AAGGCA-CATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT----ACCAAAGACCTTCGA
* * * ** * * *
3181537 GTTTGATTACACTCAGCTTTGGGGGCATATCATTTGCAGCATAACTCAA-GTTGAGAAGGGTTAT
61 GTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCT-AGAAGGGTTAT
* *
3181601 CTGCCAACCAAAGACCTTTGAGTTCGACAACGTTCAGCTCC
125 CTGCCAACCAAAGACCTTTGAGTTTGACTACGTTCAGCTCC
* * * * * * * *
3181642 AAGGCACATCATCTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGT
1 AAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT---ACCAAAGACCTTCGAGT
** * * * * * * *
3181707 TCGACTATTCTCAGC-TCCAAGACACATCATTTACATCATAACTTAAGGCAATAAGGGCTATCTG
63 TCGACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG
3181771 TCAATAAAAT
Statistics
Matches: 652, Mismatches: 120, Indels: 36
0.81 0.15 0.04
Matches are distributed among these distances:
163 62 0.10
164 75 0.12
165 275 0.42
166 46 0.07
167 63 0.10
168 72 0.11
169 58 0.09
170 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.26
Consensus pattern (165 bp):
AAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCTTCGAGTTCG
ACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCA
ACCAAAGACCTTTGAGTTTGACTACGTTCAGCTCC
Found at i:3182403 original size:36 final size:36
Alignment explanation
Indices: 3182341--3182629 Score: 283
Period size: 36 Copynumber: 7.6 Consensus size: 36
3182331 TGAAAATACG
**
3182341 TATATAATATATAGTTTTTTAAAACATTTTTTAAAAT
1 TATATAATATATAG-TTTTTAAAACATTTTAAAAAAT
* *
3182378 TATATAATATATAATTTTTAAAACATTTTAGAAAAT
1 TATATAATATATAGTTTTTAAAACATTTTAAAAAAT
*
3182414 TATATAATATATAGTTTTTGAAAACATTTT-TAAAAT
1 TATATAATATATAGTTTTT-AAAACATTTTAAAAAAT
* * * * *
3182450 ATATATAATATACAATTTTGAAAATATTTTGAAAATATT
1 -TATATAATATATAGTTTTTAAAACATTTT-AAAA-AAT
*
3182489 TATATATTATATAGTTTTTAAAAAAATCATTTTAAAAATAT
1 TATATAATATATAGTTTTT---AAAA-CATTTTAAAAA-AT
* * **
3182530 ATATATAATATATAGTTTTTTAAATCATTTTGAAATTT
1 -TATATAATATATAG-TTTTTAAAACATTTTAAAAAAT
*
3182568 TATATAATATATAGTTTTAAAAACATTTTGAAAATAAT
1 TATATAATATATAGTTTTTAAAACATTTT-AAAA-AAT
*
3182606 TATATATTATATAGTTTTTTAAAA
1 TATATAATATATAG-TTTTTAAAA
3182630 AAAACATGTT
Statistics
Matches: 208, Mismatches: 29, Indels: 28
0.78 0.11 0.11
Matches are distributed among these distances:
36 65 0.31
37 56 0.27
38 32 0.15
39 19 0.09
40 4 0.02
41 9 0.04
42 18 0.09
43 5 0.02
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.47
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTAAAAAAT
Found at i:3182480 original size:11 final size:11
Alignment explanation
Indices: 3182464--3182489 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3182454 ATAATATACA
3182464 ATTTTGAAAAT
1 ATTTTGAAAAT
3182475 ATTTTGAAAAT
1 ATTTTGAAAAT
3182486 ATTT
1 ATTT
3182490 ATATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (11 bp):
ATTTTGAAAAT
Found at i:3182572 original size:117 final size:116
Alignment explanation
Indices: 3182328--3182653 Score: 369
Period size: 117 Copynumber: 2.8 Consensus size: 116
3182318 TGCAAATGAT
* * * ** *
3182328 TTTTGAAAATACGTATATAATATATAGTTTTTTAAAACATTTT-TTAA-AATTATATAATATATA
1 TTTTGAAAATA--TATATAATATACA-ATTTTAAAAACATTTTGAAAATAATTATATATTATATA
* *
3182391 ATTTTT---AAAACATTTTAGAAA-AT-TATATAATATATAGTTTTTGAAAACA
63 GTTTTTAAAAAAACATTTTAAAAATATATATATAATATATAGTTTTTGAAAACA
* * * *
3182440 TTTTTAAAATATATATAATATACAATTTTGAAAATATTTTGAAAATATTTATATATTATATAGTT
1 TTTTGAAAATATATATAATATACAATTTTAAAAACATTTTGAAAATAATTATATATTATATAGTT
* *
3182505 TTTAAAAAAATCATTTTAAAAATATATATATAATATATAGTTTTTTAAATCA
66 TTTAAAAAAA-CATTTTAAAAATATATATATAATATATAGTTTTTGAAAACA
* * * *
3182557 TTTTGAAATTTTATATAATATATAGTTTTAAAAACATTTTGAAAATAATTATATATTATATAGTT
1 TTTTGAAAATATATATAATATACAATTTTAAAAACATTTTGAAAATAATTATATATTATATAG-T
*
3182622 TTTTAAAAAAAACATGTTTGAAAATATATATA
65 TTTT-AAAAAAACAT-TTTAAAAATATATATA
3182654 GTTTTAAAAT
Statistics
Matches: 181, Mismatches: 22, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
109 13 0.07
110 14 0.08
111 19 0.10
112 10 0.06
114 4 0.02
115 10 0.06
116 2 0.01
117 79 0.44
118 8 0.04
119 22 0.12
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (116 bp):
TTTTGAAAATATATATAATATACAATTTTAAAAACATTTTGAAAATAATTATATATTATATAGTT
TTTAAAAAAACATTTTAAAAATATATATATAATATATAGTTTTTGAAAACA
Found at i:3182669 original size:44 final size:43
Alignment explanation
Indices: 3182586--3182669 Score: 100
Period size: 43 Copynumber: 1.9 Consensus size: 43
3182576 ATATAGTTTT
* *
3182586 AAAAACATTTTGAAAATAATTATATATTATATAGTTTTTTAAA
1 AAAAACATTTTGAAAATAATTATATATTATAAAATTTTTTAAA
*
3182629 AAAAACATGTTTGAAAAT-A-TATATAGTTTTAAAATATTTTT
1 AAAAACAT-TTTGAAAATAATTATATA-TTATAAAAT-TTTTT
3182670 TGAAAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
42 6 0.17
43 15 0.43
44 14 0.40
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (43 bp):
AAAAACATTTTGAAAATAATTATATATTATAAAATTTTTTAAA
Found at i:3182771 original size:21 final size:20
Alignment explanation
Indices: 3182747--3182800 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
3182737 AAAAAAATAT
*
3182747 TTTTTATTTTTTATTAATTTC
1 TTTTTATTTTTTATT-ATTTA
* *
3182768 TTTTTATTATTTGTTATTTA
1 TTTTTATTTTTTATTATTTA
3182788 TTTATTATTTTTT
1 TTT-TTATTTTTT
3182801 CATCTATCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTTATTTTTTATTATTTA
Found at i:3182784 original size:24 final size:23
Alignment explanation
Indices: 3182746--3182799 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
3182736 TAAAAAAATA
*
3182746 TTTTTTATTTTTTATTAATTTCT
1 TTTTTTATTTGTTATTAATTTCT
* *
3182769 TTTTATTATTTGTTATTTATTTAT
1 TTTT-TTATTTGTTATTAATTTCT
3182793 TATTTTT
1 T-TTTTT
3182800 TCATCTATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 19 0.73
25 3 0.12
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (23 bp):
TTTTTTATTTGTTATTAATTTCT
Found at i:3184128 original size:22 final size:22
Alignment explanation
Indices: 3184102--3184144 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3184092 TAATAAATTA
3184102 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
3184124 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
3184145 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:3184153 original size:22 final size:22
Alignment explanation
Indices: 3184104--3184152 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
3184094 ATAAATTATT
**
3184104 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
3184126 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
3184149 TAAA
1 TAAA
3184153 TTATTAAAAT
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:3184282 original size:22 final size:21
Alignment explanation
Indices: 3184234--3184282 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
3184224 AATAATTATT
**
3184234 TAAATAAATCAATCCATATTT
1 TAAATAAATCAATCCATATAA
*
3184255 TAAAATAATTCAATCCATACTAA
1 T-AAATAAATCAATCCATA-TAA
3184278 TAAAT
1 TAAAT
3184283 TATTTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 20 0.87
23 2 0.09
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATAAATCAATCCATATAA
Found at i:3184291 original size:32 final size:32
Alignment explanation
Indices: 3184253--3184788 Score: 247
Period size: 32 Copynumber: 19.4 Consensus size: 32
3184243 CAATCCATAT
*
3184253 TTTAAAATAATTCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3184285 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
3184307 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
3184339 TTTAAAATAAATCAATCTATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* **
3184369 --T--AATAAATTAATCCATA-TTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
3184394 --T-AAATCAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* * *
3184423 TTTAAAATAAATTAGTACATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3184455 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
3184477 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3184509 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
3184531 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
3184563 TTTAAAATAAATCAATTCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
3184593 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3184611 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
3184643 TTTAAAATAAATCAATCTATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
3184673 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
3184691 TTTAAAATAAATCAATCCATATTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
**
3184723 TTTAAAATAAATC-A---AT--GGAT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3184745 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3184777 TTTAAAATAAAT
1 TTTAAAATAAAT
3184789 TATTTTAAAA
Statistics
Matches: 391, Mismatches: 32, Indels: 162
0.67 0.05 0.28
Matches are distributed among these distances:
20 2 0.01
22 89 0.23
23 9 0.02
24 8 0.02
25 7 0.02
26 69 0.18
27 4 0.01
28 16 0.04
29 1 0.00
30 7 0.02
31 14 0.04
32 165 0.42
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:3184311 original size:22 final size:22
Alignment explanation
Indices: 3184285--3184327 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3184275 TAATAAATTA
3184285 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
3184307 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
3184328 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:3184314 original size:54 final size:54
Alignment explanation
Indices: 3184185--3184355 Score: 303
Period size: 54 Copynumber: 3.2 Consensus size: 54
3184175 CAACTACAAT
3184185 AATAAATCAATCCATA-TTTAAAATAAATCAATCCATACTAAT-AATTATTT-A
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
3184236 AATAAATCAATCCATATTTTAAAATAATTCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
3184290 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
3184344 AATAAATCAATC
1 AATAAATCAATC
3184356 TATACAACTA
Statistics
Matches: 114, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
51 16 0.14
52 25 0.22
53 8 0.07
54 65 0.57
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:3184336 original size:22 final size:22
Alignment explanation
Indices: 3184287--3184335 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3184277 ATAAATTATT
**
3184287 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
3184309 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
3184332 TAAA
1 TAAA
3184336 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:3184432 original size:14 final size:14
Alignment explanation
Indices: 3184413--3184466 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
3184403 CAATCCATAC
3184413 AAATAAATTATTTA
1 AAATAAATTATTTA
*
3184427 AAATAAATTAGTACATA
1 AAATAAATTA-T--TTA
*
3184444 CTAATAAATTATTTA
1 -AAATAAATTATTTA
3184459 AAATAAAT
1 AAATAAAT
3184467 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 3 0.09
17 3 0.09
18 9 0.28
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:3184481 original size:54 final size:54
Alignment explanation
Indices: 3184423--3184788 Score: 376
Period size: 54 Copynumber: 6.8 Consensus size: 54
3184413 AAATAAATTA
* * *
3184423 TTTAAAATAAATTAGTACATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
3184477 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* * *
3184531 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATTCATACA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-T
** * * * *
3184586 ACTACAAT-AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-T
** * * * *
3184634 AATAAATTATTTAAAATAAATCAAT-CT-ATACAACTA--CAATAATAAATCAATCCATAT
1 TTTAAA--A--T-AAATCAATCCATACTAATA-AATTATTTAA-AATAAATCAATCCATAT
* **
3184691 TTTAAAATAAATCAATCCATATTAATAAATTATTTAAAATAAATCAATGGATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
3184745 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
3184789 TATTTTAAAA
Statistics
Matches: 264, Mismatches: 30, Indels: 36
0.80 0.09 0.11
Matches are distributed among these distances:
48 25 0.09
49 1 0.00
50 2 0.01
52 13 0.05
53 7 0.03
54 183 0.69
55 8 0.03
57 8 0.03
58 17 0.06
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.35
Consensus pattern (54 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:3184506 original size:22 final size:22
Alignment explanation
Indices: 3184457--3184505 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3184447 ATAAATTATT
**
3184457 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
3184479 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
3184502 TAAA
1 TAAA
3184506 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:3184535 original size:22 final size:22
Alignment explanation
Indices: 3184509--3184551 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3184499 TAATAAATTA
3184509 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
3184531 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
3184552 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:3184557 original size:18 final size:18
Alignment explanation
Indices: 3184535--3184586 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
3184525 CCATATTTTA
3184535 AAATAAATCAATTCATAC
1 AAATAAATCAATTCATAC
* *
3184553 TAATAAAT-TATT--TA-
1 AAATAAATCAATTCATAC
3184567 AAATAAATCAATTCATAC
1 AAATAAATCAATTCATAC
3184585 AA
1 AA
3184587 CTACAATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
14 7 0.27
15 5 0.19
17 5 0.19
18 9 0.35
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAAATCAATTCATAC
Found at i:3184560 original size:22 final size:22
Alignment explanation
Indices: 3184511--3184559 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3184501 ATAAATTATT
**
3184511 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
3184533 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
3184556 TAAA
1 TAAA
3184560 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:3184609 original size:80 final size:81
Alignment explanation
Indices: 3184514--3184738 Score: 418
Period size: 80 Copynumber: 2.8 Consensus size: 81
3184504 AATTATTTAA
*
3184514 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
3184579 TC-ATACAACTACAAT
66 TCTATACAACTACAAT
3184594 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA-
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
3184658 TCTATACAACTACAAT
66 TCTATACAACTACAAT
*
3184674 AATAAATCAATCCATATTTTAAAATAAATCAATCCATATTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
3184739 GGATATTTTA
Statistics
Matches: 141, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
79 2 0.01
80 139 0.99
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (81 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
TCTATACAACTACAAT
Found at i:3184633 original size:134 final size:134
Alignment explanation
Indices: 3184092--3184788 Score: 720
Period size: 134 Copynumber: 5.2 Consensus size: 134
3184082 ACAACTACAA
3184092 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA-
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
3184156 TTAAAATAAATC-ATCCATACAACTACAATAATAAATCAATCCATA-TTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATACAACTAAAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
3184219 ATAC
131 ATAC
*
3184223 TAAT-AATTATTT-AAATAAATCAATCCATATTTTAAAATAATTCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*** * *
3184286 TTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATTC-ATACTAATAAATTATTTAAAATAA
66 TTAAAATAAATCAATCCATACAACTAAAAT-AAT-AAATCAAT-C-CAT--A-T-TTTAAAATAA
*
3184349 ATCAATCTATAC
123 ATCAATCCATAC
* * *
3184361 -AACTACA--A--T--AATAAATTAATCCATATTTTAAAATAAATCAATCAATCCATACAAATAA
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAAT--A--AATCAATCCATACTAATAA
* * *
3184419 ATTATTTAAAATAAATTAGTACATACTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAA
61 ATTATTTAAAATAAATCAATCCATAC-AACTAAA--A--T--AATAAATCAATCCATATTTTAAA
*
3184483 ATAAATCAATCTATAC
119 ATAAATCAATCCATAC
*
3184499 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
* *
3184564 TTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATACAACTAAAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
3184629 ATAC
131 ATAC
* *** * * * *
3184633 TAATAAATTATTTAAAATAAATCAATCTATACAACTACAAT-AATAAATCAAT-C-CAT--A-T-
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATACTAATAAATTA
* **
3184691 TTTAAAATAAATCAATCCATATTAA-TAAATTATTTAAAATAAATCAATGGATATTTTAAAATAA
65 TTTAAAATAAATCAATCCATA-CAACTAAA--A--T--AATAAATCAATCCATATTTTAAAATAA
3184755 ATCAATCCATAC
123 ATCAATCCATAC
3184767 TAATAAATTATTTAAAATAAAT
1 TAATAAATTATTTAAAATAAAT
3184789 TATTTTAAAA
Statistics
Matches: 483, Mismatches: 42, Indels: 79
0.80 0.07 0.13
Matches are distributed among these distances:
128 23 0.05
129 52 0.11
130 27 0.06
131 16 0.03
132 8 0.02
133 3 0.01
134 159 0.33
135 7 0.01
136 2 0.00
137 3 0.01
138 87 0.18
139 10 0.02
140 45 0.09
141 1 0.00
142 4 0.01
143 6 0.01
144 30 0.06
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (134 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATCCATACAACTAAAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
ATAC
Found at i:3184640 original size:22 final size:22
Alignment explanation
Indices: 3184565--3184639 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
3184555 ATAAATTATT
* *
3184565 TAAAATAAATCAATTCATACAA
1 TAAAATAAATCAATCCATATAA
**
3184587 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
3184613 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
3184636 TAAA
1 TAAA
3184640 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:3184720 original size:22 final size:22
Alignment explanation
Indices: 3184674--3184719 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
3184664 CAACTACAAT
*
3184674 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTATAA
3184696 AATAAATCAATCCATATTAATAA
1 AATAAATCAATCCATATT-ATAA
3184719 A
1 A
3184720 TTATTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAAATCAATCCATATTATAA
Found at i:3184797 original size:15 final size:15
Alignment explanation
Indices: 3184768--3184869 Score: 109
Period size: 15 Copynumber: 6.5 Consensus size: 15
3184758 AATCCATACT
3184768 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
3184782 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
3184797 AATAAATTAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
3184819 AATAAATTATTTT-A
1 AATAAATTATTTTAA
*
3184833 TATAAATTATTTTAA
1 AATAAATTATTTTAA
3184848 AATAAATTATTTTAA
1 AATAAATTATTTTAA
3184863 AATAAAT
1 AATAAAT
3184870 AACCTTATTA
Statistics
Matches: 75, Mismatches: 4, Indels: 17
0.78 0.04 0.18
Matches are distributed among these distances:
14 21 0.28
15 36 0.48
17 1 0.01
18 3 0.04
19 3 0.04
20 1 0.01
22 10 0.13
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:3184843 original size:51 final size:47
Alignment explanation
Indices: 3184688--3184856 Score: 185
Period size: 54 Copynumber: 3.4 Consensus size: 47
3184678 AATCAATCCA
* *
3184688 TATTTTAAAATAAATCAATCCATATTAATAAATTATTTAAAATAAATCAAT
1 TATTTTAAAATAAATTAATCCATAATAATAAATTATTTAAAAT--A--AAT
* *
3184739 GGATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
1 ---TATTTTAAAATAAATTAATCCATAATAATAAATTATTTAAAATAAAT
* *
3184789 TATTTTAAAATAAATTAATCCATATTTTATAATAAATTATTTTATATAAAT
1 TATTTTAAAATAAATTAATCCATA----ATAATAAATTATTTAAAATAAAT
3184840 TATTTTAAAATAAATTA
1 TATTTTAAAATAAATTA
3184857 TTTTAAAATA
Statistics
Matches: 106, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
47 23 0.22
50 3 0.03
51 37 0.35
52 1 0.01
54 42 0.40
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (47 bp):
TATTTTAAAATAAATTAATCCATAATAATAAATTATTTAAAATAAAT
Found at i:3184905 original size:66 final size:64
Alignment explanation
Indices: 3184714--3184869 Score: 188
Period size: 69 Copynumber: 2.3 Consensus size: 64
3184704 AATCCATATT
* ** * **
3184714 AATAAATTA-TTTAAAATAAATCAATGGATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 AATAAATTATTTTAAAATAAATTAATCCATATTTTATAATAAAT---T--ATTTTAATAAATTAT
3184778 TTAA
61 TTAA
3184782 AATAAATTATTTTAAAATAAATTAATCCATATTTTATAATAAATTATTTTATATAAATTATTTTA
1 AATAAATTATTTTAAAATAAATTAATCCATATTTTATAATAAATTATTTTA-ATAAATTA-TTTA
3184847 A
64 A
3184848 AATAAATTATTTTAAAATAAAT
1 AATAAATTATTTTAAAATAAAT
3184870 AACCTTATTA
Statistics
Matches: 79, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
64 4 0.05
65 8 0.10
66 28 0.35
68 9 0.11
69 30 0.38
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (64 bp):
AATAAATTATTTTAAAATAAATTAATCCATATTTTATAATAAATTATTTTAATAAATTATTTAA
Found at i:3185487 original size:20 final size:21
Alignment explanation
Indices: 3185449--3185489 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3185439 TTACTCATTT
*
3185449 TTTATTTTTATTTCCTTTTTA
1 TTTATTTTTATTTCATTTTTA
*
3185470 TTTA-TTTTATTTTATTTTTA
1 TTTATTTTTATTTCATTTTTA
3185490 AACTAACCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTATTTTTATTTCATTTTTA
Found at i:3185488 original size:11 final size:11
Alignment explanation
Indices: 3185448--3185489 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
3185438 TTTACTCATT
3185448 TTTTATTTTTA
1 TTTTATTTTTA
**
3185459 TTTCCTTTTTA
1 TTTTATTTTTA
3185470 -TTTA-TTTTA
1 TTTTATTTTTA
3185479 TTTTATTTTTA
1 TTTTATTTTTA
3185490 AACTAACCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
9 5 0.20
10 6 0.24
11 14 0.56
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:3189507 original size:16 final size:17
Alignment explanation
Indices: 3189474--3189514 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
3189464 ATGATATTGG
*
3189474 ATAAAA-TATTGAATAA
1 ATAAAATTATTGAAAAA
3189490 ATAAAATTATT-AAAAA
1 ATAAAATTATTGAAAAA
*
3189506 ATTAAATTA
1 ATAAAATTA
3189515 ACATTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
ATAAAATTATTGAAAAA
Found at i:3190483 original size:23 final size:23
Alignment explanation
Indices: 3190448--3190495 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
3190438 ATTAAATAAA
*
3190448 ATAATATATTAGGTAACGCTTAT
1 ATAATATAATAGGTAACGCTTAT
* **
3190471 ATAATGTAATAGGTAGTGCTTAT
1 ATAATATAATAGGTAACGCTTAT
3190494 AT
1 AT
3190496 TGACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:3191240 original size:182 final size:182
Alignment explanation
Indices: 3190928--3191383 Score: 736
Period size: 182 Copynumber: 2.5 Consensus size: 182
3190918 ACCTTTTTAC
*
3190928 TACCAGTTTTGTCATTTCGAGACCGATTATGTT-ATATTTTTACATGTTATATTGTTATGGATCG
1 TACCAGTTTTGTCATTTCGAGACCGATT-TTTTCATATTTTTACATGTTATATTGTTATGGATCG
* * *
3190992 ATACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAATTTCTTTTCTTTTAAATTCCAAAA
65 ATACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTATCTTTTAAATTCCAAAA
* *
3191057 GTGTCGATACTTATAATAAAGTATCGACACTTTCAACATATCCT-GTAGCTATT
130 GTGTCGATACTTATAATAAAGTATCGACACTATCAACATAT-CTGGTAGCGATT
* *
3191110 TACCGGTTTTGTCATTTCGAGACCGATTTTTTCATATTTTTACCTGTTATATTGTTATGGATCGA
1 TACCAGTTTTGTCATTTCGAGACCGATTTTTTCATATTTTTACATGTTATATTGTTATGGATCGA
3191175 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTATCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTATCTTTTAAATTCCAAAAG
* *
3191240 TGTCTATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTT
131 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGATT
* ** * * *
3191292 TACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTACTTGTTATATTGTTATGGATCGA
1 TACCAGTTTTGTCATTTCGAGACCGATTTTTTCATATTTTTACATGTTATATTGTTATGGATCGA
3191357 TACATTTTTATAAAGTATCGACACTTT
66 TACATTTTTATAAAGTATCGACACTTT
3191384 CAATATATCC
Statistics
Matches: 256, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
181 5 0.02
182 251 0.98
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.44
Consensus pattern (182 bp):
TACCAGTTTTGTCATTTCGAGACCGATTTTTTCATATTTTTACATGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTATCTTTTAAATTCCAAAAG
TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGATT
Found at i:3191497 original size:111 final size:112
Alignment explanation
Indices: 3191254--3191613 Score: 587
Period size: 111 Copynumber: 3.2 Consensus size: 112
3191244 TATACTTATA
* * * *
3191254 ATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCACTTTACCTGTTTTGTCATTTATAGACCGAT
3191319 TTTGTCATTTTTTTACTTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACTTGTTATATTGTTATGGATCGATACATTTTT
*
3191366 ATAAAGTATCGACACTTTCAATATATCCGGTAGCACTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCACTTTACCTGTTTTGTCATTTATAGACCGAT
* * *
3191431 TTTGTCA-TTTTTTACCTGTTTTATTGTTATGGATCGATACATTCTT
66 TTTGTCATTTTTTTACTTGTTATATTGTTATGGATCGATACATTTTT
* * *
3191477 ATAAAGTATCGACACTTTCAATATATCCGGTAGAACTTTACCTATTTTGTCATTTATATACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCACTTTACCTGTTTTGTCATTTATAGACCGAT
3191542 TTTGTCATTTTTTTTACTTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCA-TTTTTTTACTTGTTATATTGTTATGGATCGATACATTTTT
* *
3191590 ATAAAATATCGACATTTTCAATAT
1 ATAAAGTATCGACACTTTCAATAT
3191614 CTGTTTTGTC
Statistics
Matches: 229, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
111 104 0.45
112 67 0.29
113 58 0.25
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCACTTTACCTGTTTTGTCATTTATAGACCGAT
TTTGTCATTTTTTTACTTGTTATATTGTTATGGATCGATACATTTTT
Found at i:3191663 original size:96 final size:96
Alignment explanation
Indices: 3191521--3191699 Score: 297
Period size: 96 Copynumber: 1.9 Consensus size: 96
3191511 ACTTTACCTA
* * *
3191521 TTTTGTCATTTATATACCGATTTTGTCATTTTTTTTACTTGTTATATTGTTATGGATCGATACAT
1 TTTTGTCATTTATAGACCGATTTTATCATTTTTTTTACTTGTTATATTGTTATGGATCAATACAT
3191586 TTTTATAAAATATCGACATTTTCAATATCTG
66 TTTTATAAAATATCGACATTTTCAATATCTG
* *
3191617 TTTTGTCATTTATAGACCGGTTTTATCATTTTTTTTA-TCTGTTATATTGTTATGGATCAATATA
1 TTTTGTCATTTATAGACCGATTTTATCATTTTTTTTACT-TGTTATATTGTTATGGATCAATACA
3191681 TTTTTATAAAATATCGACA
65 TTTTTATAAAATATCGACA
3191700 CAAACCGGCA
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
95 1 0.01
96 76 0.99
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.52
Consensus pattern (96 bp):
TTTTGTCATTTATAGACCGATTTTATCATTTTTTTTACTTGTTATATTGTTATGGATCAATACAT
TTTTATAAAATATCGACATTTTCAATATCTG
Found at i:3194777 original size:18 final size:18
Alignment explanation
Indices: 3194728--3194778 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
3194718 TCGCATTATC
*
3194728 TATTTATAATT-TTAATTA
1 TATTT-TAATTATTTATTA
*
3194746 TATATT-ATTCATTTATTA
1 TATTTTAATT-ATTTATTA
3194764 TATTTTAATTATTTA
1 TATTTTAATTATTTA
3194779 CCTCATTAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 1 0.04
18 20 0.74
19 3 0.11
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTTAATTATTTATTA
Found at i:3195636 original size:2 final size:2
Alignment explanation
Indices: 3195629--3195664 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3195619 ATTGATTTAA
*
3195629 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3195665 GTGTGTGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3195706 original size:169 final size:163
Alignment explanation
Indices: 3195421--3195753 Score: 578
Period size: 169 Copynumber: 2.0 Consensus size: 163
3195411 CATAAAGCAC
*
3195421 AGTCCATTTGTTTGATTTTTTAAAAGAAACATCGATTTATTTAAATATATATATATATATATATA
1 AGTCCATTTGTTTGATTTTTTAAAAGAAACATCGATTGATTTAAATATATATATATATATATATA
3195486 TGATGTATATGTGTGTGCATTTTTTATGTATAAATTAAATAAAAATATTAAAATTACCAATTTCT
66 TGATGTATATGTGTGTGCATTTTTTATGTATAAATTAAATAAAAATATTAAAATTACCAATTTCT
3195551 -AAAAGAAGTAAAACATTCTGAATACGAGTTGGG
131 AAAAAG-AGTAAAACATTCTGAATACGAGTTGGG
3195584 AGTCCATTTGTTTGATTTTTTTAAAAGAAACATCGATTGATTTAAATATATATATATATATATAT
1 AGTCCATTTGTTTGA-TTTTTTAAAAGAAACATCGATTGATTT--A-A-ATATATATATATATAT
*
3195649 ATATATATATGTATATGTGTGTGCATTTTTTATGTATAAATTAAATAAAAATATTAAAATTACCA
61 ATATAT-GATGTATATGTGTGTGCATTTTTTATGTATAAATTAAATAAAAATATTAAAATTACCA
3195714 ATTTCTAAAAAGAGTAAAACATTCTGAATACGAGTTGGG
125 ATTTCTAAAAAGAGTAAAACATTCTGAATACGAGTTGGG
3195753 A
1 A
3195754 TTTAGGTGTG
Statistics
Matches: 161, Mismatches: 2, Indels: 8
0.94 0.01 0.05
Matches are distributed among these distances:
163 15 0.09
164 26 0.16
166 1 0.01
167 1 0.01
168 22 0.14
169 91 0.57
170 5 0.03
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.41
Consensus pattern (163 bp):
AGTCCATTTGTTTGATTTTTTAAAAGAAACATCGATTGATTTAAATATATATATATATATATATA
TGATGTATATGTGTGTGCATTTTTTATGTATAAATTAAATAAAAATATTAAAATTACCAATTTCT
AAAAAGAGTAAAACATTCTGAATACGAGTTGGG
Found at i:3196141 original size:20 final size:20
Alignment explanation
Indices: 3196089--3196130 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3196079 GAATATGTAA
3196089 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
3196109 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
3196129 AT
1 AT
3196131 TGCGTTGCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:3196333 original size:22 final size:22
Alignment explanation
Indices: 3196303--3196366 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
3196293 ACTCTCTATG
*
3196303 GCGACATCCGTTCCTATCTCC-
1 GCGAAATCCGTTCCTATCTCCA
3196324 GACGAAATCCGTCTCC-ATCTCCA
1 G-CGAAATCCGT-TCCTATCTCCA
3196347 GCGAAATCCG-T-CTATCTCCA
1 GCGAAATCCGTTCCTATCTCCA
3196367 TCTCTCAGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 1 0.03
20 8 0.21
21 1 0.03
22 24 0.63
23 4 0.11
ACGTcount: A:0.22, C:0.39, G:0.14, T:0.25
Consensus pattern (22 bp):
GCGAAATCCGTTCCTATCTCCA
Found at i:3196864 original size:20 final size:19
Alignment explanation
Indices: 3196759--3196888 Score: 163
Period size: 19 Copynumber: 6.7 Consensus size: 19
3196749 GCGATTTTAG
* *
3196759 TTTCGCGTTGCGAT-TTTA
1 TTTCGCGTTGCGATAGTCA
*
3196777 GTTTCGCATTGCGATAGTCA
1 -TTTCGCGTTGCGATAGTCA
3196797 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGTCA
3196816 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGTCA
3196835 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGTCA
* **
3196854 TTTTCGTGTTGCGATTTTCA
1 -TTTCGCGTTGCGATAGTCA
*
3196874 TTTTCGTGTTGCGAT
1 -TTTCGCGTTGCGAT
3196889 TTTAAGTTCC
Statistics
Matches: 102, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
19 69 0.68
20 33 0.32
ACGTcount: A:0.14, C:0.18, G:0.25, T:0.43
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:3198116 original size:20 final size:20
Alignment explanation
Indices: 3198091--3198168 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
3198081 AGGTACACTT
*
3198091 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACTCAAAA
* *
3198111 TCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAACTCAAAA
*
3198131 TCGCAATGCGAAAGC-CAAAA
1 TCGCAACGCGAAA-CTCAAAA
*
3198151 TCGCAACGCGAAAGTCAA
1 TCGCAACGCGAAACTCAA
3198169 TTCGCGTTGC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.44, C:0.26, G:0.18, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:3198135 original size:40 final size:40
Alignment explanation
Indices: 3198091--3198168 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
3198081 AGGTACACTT
* *
3198091 TCGCAACGCTAAA-CTCAAAATCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAAGC-CAAAATCGCAACGCGAAAGTCAAAA
*
3198131 TCGCAATGCGAAAGCCAAAATCGCAACGCGAAAGTCAA
1 TCGCAACGCGAAAGCCAAAATCGCAACGCGAAAGTCAA
3198169 TTCGCGTTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.44, C:0.26, G:0.18, T:0.13
Consensus pattern (40 bp):
TCGCAACGCGAAAGCCAAAATCGCAACGCGAAAGTCAAAA
Found at i:3198249 original size:20 final size:20
Alignment explanation
Indices: 3198220--3198297 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 20
3198210 TGTGATTTTT
* *
3198220 GCGTTCCGATAGTCATATTC
1 GCGTTGCGATAGTCAAATTC
3198240 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
3198260 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
* *
3198280 GCTTTGCGATATTCAAAT
1 GCGTTGCGATAGTCAAAT
3198298 GAATGTGTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:3198520 original size:140 final size:140
Alignment explanation
Indices: 3198268--3198550 Score: 550
Period size: 140 Copynumber: 2.0 Consensus size: 140
3198258 TCGCGTTGCG
3198268 ATAGTCAAATTCGCTTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCTTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
3198333 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
3198398 AATATACATA
131 AATATACATA
3198408 ATAGTCAAATTCG-TGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATC
1 ATAGTCAAATTCGCT-TTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATC
3198472 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
65 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
3198537 AAATATACATA
130 AAATATACATA
3198548 ATA
1 ATA
3198551 CAACGTTTGC
Statistics
Matches: 142, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
139 1 0.01
140 141 0.99
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCTTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATATACATA
Found at i:3200924 original size:24 final size:24
Alignment explanation
Indices: 3200890--3200943 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
3200880 CTGAAACATC
3200890 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
3200914 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
3200938 ATCAAA
1 ATCAAA
3200944 TTTCGAATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3200957 original size:24 final size:24
Alignment explanation
Indices: 3200890--3200957 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
3200880 CTGAAACATC
* * *
3200890 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
3200914 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
3200938 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
3200958 TAGTACTCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:3201790 original size:20 final size:20
Alignment explanation
Indices: 3201765--3201803 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3201755 AAAATCAATG
3201765 TTGCGACAGTCAGAATCGCT
1 TTGCGACAGTCAGAATCGCT
*
3201785 TTGCGATAGTCAGAATCGC
1 TTGCGACAGTCAGAATCGC
3201804 GTTACGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (20 bp):
TTGCGACAGTCAGAATCGCT
Found at i:3201811 original size:20 final size:20
Alignment explanation
Indices: 3201772--3201811 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3201762 ATGTTGCGAC
* *
3201772 AGTCAGAATCGCTTTGCGAT
1 AGTCAGAATCGCGTTACGAT
3201792 AGTCAGAATCGCGTTACGAT
1 AGTCAGAATCGCGTTACGAT
3201812 TTACATATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (20 bp):
AGTCAGAATCGCGTTACGAT
Found at i:3201851 original size:21 final size:21
Alignment explanation
Indices: 3201827--3201867 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3201817 TATTCGCATT
*
3201827 GCGATTTTAGAAAATCGCAAC
1 GCGAATTTAGAAAATCGCAAC
* *
3201848 GCGAATTTGGAAATTCGCAA
1 GCGAATTTAGAAAATCGCAA
3201868 TGAGATTATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (21 bp):
GCGAATTTAGAAAATCGCAAC
Found at i:3203875 original size:17 final size:17
Alignment explanation
Indices: 3203852--3203891 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3203842 TTTATAATAA
*
3203852 AAATTAAAATGAAGTTT
1 AAATTAAAATCAAGTTT
* *
3203869 TAATTAATATCAAGTTT
1 AAATTAAAATCAAGTTT
3203886 AAATTA
1 AAATTA
3203892 TACGGATAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (17 bp):
AAATTAAAATCAAGTTT
Found at i:3204289 original size:2 final size:2
Alignment explanation
Indices: 3204282--3204319 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3204272 AAATAAGCTT
3204282 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3204320 GAAATTACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3204551 original size:2 final size:2
Alignment explanation
Indices: 3204544--3204597 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
3204534 TTACATAATC
3204544 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
3204586 AT AT AT AT AT AT
1 AT AT AT AT AT AT
3204598 GTAGAAATAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3207936 original size:23 final size:23
Alignment explanation
Indices: 3207910--3207978 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
3207900 CACCACTGCT
*
3207910 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
3207933 CGTAGAATTGCACCGGAGTGCCGA
1 CGTAGAATTGCACCGAAGTGCC-A
* *
3207957 -GTAGAATTGCATCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
3207979 TATAATAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
22 1 0.02
23 39 0.95
24 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:3208606 original size:19 final size:20
Alignment explanation
Indices: 3208569--3208606 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3208559 CTTTTTTTTA
*
3208569 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
3208589 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
3208607 TCTAGCATTC
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:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:3209148 original size:20 final size:20
Alignment explanation
Indices: 3209123--3209162 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3209113 TAGCTTGGGT
*
3209123 CTCACGTATGAAGAATAAGA
1 CTCACGTATGAAGAAGAAGA
3209143 CTCACGTATGAAGAAGAAGA
1 CTCACGTATGAAGAAGAAGA
3209163 AAGAAGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.15, G:0.23, T:0.17
Consensus pattern (20 bp):
CTCACGTATGAAGAAGAAGA
Found at i:3216908 original size:23 final size:23
Alignment explanation
Indices: 3216855--3216915 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
3216845 CAATTTTATA
* *
3216855 TGGCACTACGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
3216878 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
3216901 TGGCACTTTGGTGCA
1 TGGCACTTCGGTGCA
3216916 TTTATAAGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:3223172 original size:64 final size:64
Alignment explanation
Indices: 3223057--3223196 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 64
3223047 CATGAAGTAT
** * *
3223057 ATCGATGCAATCCTTTAAAATAAAAACATCGAATACGATTAGTATATCGATGCACAAG-TAGTGC
1 ATCGATGCACCCCCTTAAAATAAAAACATCGAATACGATTAGTATACCGATGCA-AAGATAGTGC
* * *
3223121 ATCGATGCACCCCCTTAAAATACAAACATCGAATGA-GATTTA-TGTACCGATGCATAGATAGTG
1 ATCGATGCACCCCCTTAAAATAAAAACATCGAAT-ACGA-TTAGTATACCGATGCAAAGATAGTG
*
3223184 T
64 C
3223185 ATCGATGCACCC
1 ATCGATGCACCC
3223197 GTTAAGGGAT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
63 2 0.03
64 59 0.91
65 4 0.06
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (64 bp):
ATCGATGCACCCCCTTAAAATAAAAACATCGAATACGATTAGTATACCGATGCAAAGATAGTGC
Found at i:3223793 original size:23 final size:23
Alignment explanation
Indices: 3223767--3223849 Score: 139
Period size: 23 Copynumber: 3.6 Consensus size: 23
3223757 AATCTTATAT
*
3223767 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
3223790 GGCATTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
3223813 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
3223836 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
3223850 TTTATAAGAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:3227447 original size:24 final size:24
Alignment explanation
Indices: 3227415--3227464 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
3227405 AGGGGTGGGG
*
3227415 GATTAGGTTAAATTTGTTGTATTA
1 GATTAGGTTAAATTTGTTGGATTA
3227439 GATTAGGTTAAATTTGTTGGATTA
1 GATTAGGTTAAATTTGTTGGATTA
3227463 GA
1 GA
3227465 AAACGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (24 bp):
GATTAGGTTAAATTTGTTGGATTA
Found at i:3229605 original size:20 final size:20
Alignment explanation
Indices: 3229572--3229616 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3229562 TTAAATTTTC
*
3229572 AAAAGTTATAAAATGATTAT
1 AAAATTTATAAAATGATTAT
* * *
3229592 TAAATTTATCAAATTATTAT
1 AAAATTTATAAAATGATTAT
3229612 AAAAT
1 AAAAT
3229617 AATCATTAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (20 bp):
AAAATTTATAAAATGATTAT
Found at i:3229615 original size:31 final size:30
Alignment explanation
Indices: 3229559--3229635 Score: 104
Period size: 31 Copynumber: 2.6 Consensus size: 30
3229549 ATTATTTTAG
*
3229559 TCATTAAATTT-TCAAAAGTTATAAAATGA
1 TCATTAAATTTATCAAAAGTTATAAAATAA
*
3229588 TTATTAAATTTATCAAATTA-TTATAAAATAA
1 TCATTAAATTTATCAAA--AGTTATAAAATAA
3229619 TCATTAAATTTATCAAA
1 TCATTAAATTTATCAAA
3229636 CCTTTTCATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 10 0.24
30 5 0.12
31 26 0.62
32 1 0.02
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (30 bp):
TCATTAAATTTATCAAAAGTTATAAAATAA
Found at i:3239400 original size:18 final size:18
Alignment explanation
Indices: 3239377--3239459 Score: 84
Period size: 18 Copynumber: 4.7 Consensus size: 18
3239367 TAATTTTTAA
3239377 AAAATAATTAAAATATTC
1 AAAATAATTAAAATATTC
*
3239395 AAAATAATT-AAATA-AC
1 AAAATAATTAAAATATTC
**
3239411 TAAAATAAAAATAAATAATT-
1 -AAAATAATTA-AAAT-ATTC
3239431 -AAATAATTAAAATATTC
1 AAAATAATTAAAATATTC
3239448 AAAATAATTAAA
1 AAAATAATTAAA
3239460 TAACTAAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
16 4 0.08
17 16 0.31
18 27 0.52
19 4 0.08
20 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATAATTAAAATATTC
Found at i:3239409 original size:8 final size:8
Alignment explanation
Indices: 3239378--3239467 Score: 59
Period size: 8 Copynumber: 11.4 Consensus size: 8
3239368 AATTTTTAAA
3239378 AAATAATT
1 AAATAATT
3239386 AAA-ATATT
1 AAATA-ATT
3239394 CAAAATAATT
1 --AAATAATT
*
3239404 AAATAACT
1 AAATAATT
3239412 -AA-AA-T
1 AAATAATT
3239417 AAA-AA-T
1 AAATAATT
3239423 AAATAATT
1 AAATAATT
3239431 AAATAATT
1 AAATAATT
3239439 AAA-ATATT
1 AAATA-ATT
3239447 CAAAATAATT
1 --AAATAATT
*
3239457 AAATAACT
1 AAATAATT
3239465 AAA
1 AAA
3239468 ATAAAATAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 22
0.74 0.02 0.24
Matches are distributed among these distances:
5 1 0.01
6 10 0.14
7 6 0.09
8 38 0.55
10 12 0.17
11 2 0.03
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (8 bp):
AAATAATT
Found at i:3239409 original size:26 final size:26
Alignment explanation
Indices: 3239378--3239470 Score: 132
Period size: 26 Copynumber: 3.5 Consensus size: 26
3239368 AATTTTTAAA
*
3239378 AAATAATTAAAATATTCAAAATAATT
1 AAATAACTAAAATATTCAAAATAATT
***
3239404 AAATAACTAAAATAAAAATAAATAATT
1 AAATAACTAAAATATTCA-AAATAATT
*
3239431 AAATAATTAAAATATTCAAAATAATT
1 AAATAACTAAAATATTCAAAATAATT
3239457 AAATAACTAAAATA
1 AAATAACTAAAATA
3239471 AAATAAAAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
26 35 0.61
27 22 0.39
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (26 bp):
AAATAACTAAAATATTCAAAATAATT
Found at i:3239440 original size:53 final size:52
Alignment explanation
Indices: 3239378--3239477 Score: 191
Period size: 53 Copynumber: 1.9 Consensus size: 52
3239368 AATTTTTAAA
3239378 AAATAATTAAAATATTCAAAATAATTAAATAACTAAAATAAAAATAAATAATT
1 AAATAATTAAAATATTCAAAATAATTAAATAACTAAAAT-AAAATAAATAATT
3239431 AAATAATTAAAATATTCAAAATAATTAAATAACTAAAATAAAATAAA
1 AAATAATTAAAATATTCAAAATAATTAAATAACTAAAATAAAATAAA
3239478 AATAGTAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 8 0.17
53 39 0.83
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (52 bp):
AAATAATTAAAATATTCAAAATAATTAAATAACTAAAATAAAATAAATAATT
Found at i:3240744 original size:30 final size:30
Alignment explanation
Indices: 3240687--3240760 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 30
3240677 GTTGATTTAT
** *
3240687 GTTAAGGATTTATTTAGGACTACATT-AAG
1 GTTAAGGGCTTATTTAGGACTAAATTAAAG
3240716 AGTT-AGGAGCTTATTTAGGTA-TAAATTAAAG
1 -GTTAAGG-GCTTATTTAGG-ACTAAATTAAAG
3240747 GTTAAGGGCTTATT
1 GTTAAGGGCTTATT
3240761 AGAATACAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
29 3 0.08
30 27 0.73
31 7 0.19
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (30 bp):
GTTAAGGGCTTATTTAGGACTAAATTAAAG
Found at i:3252159 original size:38 final size:38
Alignment explanation
Indices: 3252107--3252298 Score: 244
Period size: 38 Copynumber: 5.1 Consensus size: 38
3252097 GTTTTTTGTA
*
3252107 TGGATGATACTGTGTCATGAACATACCATGCTCGGATT
1 TGGATGATATTGTGTCATGAACATACCATGCTCGGATT
**
3252145 TGGATGATATTGTGTCATGTGCATACCATGCTCGGATT
1 TGGATGATATTGTGTCATGAACATACCATGCTCGGATT
* * *
3252183 TGAATGATATTGTGTCATGCGA-ATACCATGCTTGGATT
1 TGGATGATATTGTGTCATG-AACATACCATGCTCGGATT
* ** * *
3252221 TGGATGATATTATGTCATGCGCATATCATTCTCGGATT
1 TGGATGATATTGTGTCATGAACATACCATGCTCGGATT
*
3252259 TGGATGATATTGTGTCAT-ACACATACCATGCTTGGATT
1 TGGATGATATTGTGTCATGA-ACATACCATGCTCGGATT
3252297 TG
1 TG
3252299 TTCTAGAACC
Statistics
Matches: 131, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
38 131 1.00
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.36
Consensus pattern (38 bp):
TGGATGATATTGTGTCATGAACATACCATGCTCGGATT
Found at i:3252198 original size:76 final size:76
Alignment explanation
Indices: 3252110--3252298 Score: 274
Period size: 76 Copynumber: 2.5 Consensus size: 76
3252100 TTTTGTATGG
* * * *
3252110 ATGATACTGTGTCATGAACATACCATGCTCGGATTTGGATGATATTGTGTCATGTGCATACCATG
1 ATGATATTGTGTCATGAACATACCATGCTTGGATTTGGATGATATTATGTCATGCGCATACCATG
3252175 CTCGGATTTGA
66 CTCGGATTTGA
* *
3252186 ATGATATTGTGTCATGCGA-ATACCATGCTTGGATTTGGATGATATTATGTCATGCGCATATCAT
1 ATGATATTGTGTCATG-AACATACCATGCTTGGATTTGGATGATATTATGTCATGCGCATACCAT
* *
3252250 TCTCGGATTTGG
65 GCTCGGATTTGA
3252262 ATGATATTGTGTCAT-ACACATACCATGCTTGGATTTG
1 ATGATATTGTGTCATGA-ACATACCATGCTTGGATTTG
3252299 TTCTAGAACC
Statistics
Matches: 101, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
75 1 0.01
76 99 0.98
77 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.37
Consensus pattern (76 bp):
ATGATATTGTGTCATGAACATACCATGCTTGGATTTGGATGATATTATGTCATGCGCATACCATG
CTCGGATTTGA
Found at i:3257008 original size:257 final size:258
Alignment explanation
Indices: 3256552--3257065 Score: 994
Period size: 257 Copynumber: 2.0 Consensus size: 258
3256542 ATTTATTATA
3256552 TCAAATAAATATAATTATTTATTTTTATATTTGATAAATATAATTATTCTGTGTACACAATATTA
1 TCAAATAAATATAATTATTTATTTTTATATTTGATAAATATAATTATTCTGTGTACACAATATTA
3256617 AAATGTGAAATAATACTATTTCGATTTTGTAAAAATTAAATCAAATTAAAATTTGATGTATAGAA
66 AAATGTGAAATAATACTATTTCGATTTTGTAAAAATTAAATCAAATTAAAATTTGATGTATAGAA
3256682 TTGCACTTAATCAAAGCTTATATATAACACGTTACATATTCGATCGAACTTGGTGTAATCTTAAT
131 TTGCACTTAATCAAAGCTTATATATAACACGTTACATATTCGATCGAACTTGGTGTAATCTTAAT
3256747 ATTTATCACTCTAAATATACCGCAGAATGAA-AAAAAAAAAACCGATAGCTGAAATGGAACTT
196 ATTTATCACTCTAAATATACCGCAGAATGAAGAAAAAAAAAACCGATAGCTGAAATGGAACTT
*
3256809 TCAAATAAATATAATTATTTATTTTTATATTTGATAAATATAATTATTCTGTGTACTCAATATTA
1 TCAAATAAATATAATTATTTATTTTTATATTTGATAAATATAATTATTCTGTGTACACAATATTA
3256874 AAATGTGAAATAATACTATTTCGATTTTGTAAAAATTAAATCAAATTAAAATTTGATGTATAGAA
66 AAATGTGAAATAATACTATTTCGATTTTGTAAAAATTAAATCAAATTAAAATTTGATGTATAGAA
*
3256939 TTGCACTTAATCAAAGCTTATATATGACACGTTACATATTCGATCGAACTTGGTGTAATCTTAAT
131 TTGCACTTAATCAAAGCTTATATATAACACGTTACATATTCGATCGAACTTGGTGTAATCTTAAT
*
3257004 ATTTATCACTCTAAATATACCGCAGAATGAAGAAAAAAAATACCGATAGCTGAAATGGAACT
196 ATTTATCACTCTAAATATACCGCAGAATGAAGAAAAAAAAAACCGATAGCTGAAATGGAACT
3257066 GCAAACAAGG
Statistics
Matches: 253, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
257 224 0.89
258 29 0.11
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (258 bp):
TCAAATAAATATAATTATTTATTTTTATATTTGATAAATATAATTATTCTGTGTACACAATATTA
AAATGTGAAATAATACTATTTCGATTTTGTAAAAATTAAATCAAATTAAAATTTGATGTATAGAA
TTGCACTTAATCAAAGCTTATATATAACACGTTACATATTCGATCGAACTTGGTGTAATCTTAAT
ATTTATCACTCTAAATATACCGCAGAATGAAGAAAAAAAAAACCGATAGCTGAAATGGAACTT
Found at i:3266374 original size:57 final size:57
Alignment explanation
Indices: 3266227--3266390 Score: 166
Period size: 60 Copynumber: 2.8 Consensus size: 57
3266217 ATGAATTTTG
* * ** *
3266227 GGATAAAATTAGAATATTCAAAAGTTTGGGGACTAATTTAGAAAGAGGGTCAAAGTTTAA
1 GGATGAAACTAGAAT-TTCAAAAGTTTAAGGACTAATTTAGAATGA--GTCAAAGTTTAA
* * * * * *
3266287 GGATGAAATTAGAACGTTCAAAATTTTAAGGAATAATTTAGAATGAGTCATAGTTTTA
1 GGATGAAACTAGAA-TTTCAAAAGTTTAAGGACTAATTTAGAATGAGTCAAAGTTTAA
* * *
3266345 GGATGAAACTGGAATTTCAAAAGTTTAAGGACCAATTTAAAATGAG
1 GGATGAAACTAGAATTTCAAAAGTTTAAGGACTAATTTAGAATGAG
3266391 AGTTATAGTT
Statistics
Matches: 87, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
57 27 0.31
58 22 0.25
60 38 0.44
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30
Consensus pattern (57 bp):
GGATGAAACTAGAATTTCAAAAGTTTAAGGACTAATTTAGAATGAGTCAAAGTTTAA
Found at i:3273797 original size:22 final size:23
Alignment explanation
Indices: 3273747--3273797 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
3273737 TATTTATTTT
*
3273747 TTAAATGTATAATTGAATCAAAA
1 TTAAATGTATAATTGAAACAAAA
* * *
3273770 TCAAATGTAT-ATTTAAACTAAA
1 TTAAATGTATAATTGAAACAAAA
3273792 TTAAAT
1 TTAAAT
3273798 ATTTACGCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (23 bp):
TTAAATGTATAATTGAAACAAAA
Found at i:3274824 original size:44 final size:44
Alignment explanation
Indices: 3274745--3274832 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
3274735 CTAACCCAAA
*
3274745 ATCACTTAAAAACAAAAATCGAACTTCCTACTATTCGACTCAAC
1 ATCACTTAAAAACAAAAATCGAACTCCCTACTATTCGACTCAAC
*
3274789 ATCACTTAAAAAGCGAAAATCGAACTCCCTA-TATTCGACTCAAC
1 ATCACTTAAAAA-CAAAAATCGAACTCCCTACTATTCGACTCAAC
3274833 GTTGGTACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 25 0.61
45 16 0.39
ACGTcount: A:0.42, C:0.27, G:0.07, T:0.24
Consensus pattern (44 bp):
ATCACTTAAAAACAAAAATCGAACTCCCTACTATTCGACTCAAC
Found at i:3277726 original size:46 final size:46
Alignment explanation
Indices: 3277659--3277750 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
3277649 AGATAAAATC
3277659 ATGTGTACATCTATCAGTATAGGGATGAAAAAGATGAAAAGAACAT
1 ATGTGTACATCTATCAGTATAGGGATGAAAAAGATGAAAAGAACAT
* * * *
3277705 ATGTGTACGTCTATGAGTATAGTGATGAAAAAGATTAAAAGAACAT
1 ATGTGTACATCTATCAGTATAGGGATGAAAAAGATGAAAAGAACAT
3277751 TAGTGACAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.26
Consensus pattern (46 bp):
ATGTGTACATCTATCAGTATAGGGATGAAAAAGATGAAAAGAACAT
Found at i:3278887 original size:17 final size:17
Alignment explanation
Indices: 3278865--3278900 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3278855 ATTATTAACG
* *
3278865 TTTTATTTTATGTGATA
1 TTTTATTTGATGTAATA
3278882 TTTTATTTGATGTAATA
1 TTTTATTTGATGTAATA
3278899 TT
1 TT
3278901 ATTTTATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (17 bp):
TTTTATTTGATGTAATA
Found at i:3281255 original size:28 final size:28
Alignment explanation
Indices: 3281215--3281293 Score: 149
Period size: 28 Copynumber: 2.8 Consensus size: 28
3281205 GTACCCGATA
3281215 GCCACATCTAAGACCTATAACTCTGATT
1 GCCACATCTAAGACCTATAACTCTGATT
*
3281243 GCCACAGCTAAGACCTATAACTCTGATT
1 GCCACATCTAAGACCTATAACTCTGATT
3281271 GCCACATCTAAGACCTATAACTC
1 GCCACATCTAAGACCTATAACTC
3281294 GAAGAGAGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.33, C:0.30, G:0.11, T:0.25
Consensus pattern (28 bp):
GCCACATCTAAGACCTATAACTCTGATT
Found at i:3304608 original size:8 final size:8
Alignment explanation
Indices: 3304595--3304644 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 8
3304585 ATATAGATTT
3304595 TAATTTTA
1 TAATTTTA
3304603 TAATTTT-
1 TAATTTTA
*
3304610 TAAATTTA
1 TAATTTTA
3304618 T-ATTTTA
1 TAATTTTA
3304625 TAAGATTTTA
1 T-A-ATTTTA
3304635 TAATATTTA
1 TAAT-TTTA
3304644 T
1 T
3304645 TTAATTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
7 12 0.34
8 10 0.29
9 6 0.17
10 7 0.20
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (8 bp):
TAATTTTA
Found at i:3304610 original size:15 final size:15
Alignment explanation
Indices: 3304592--3304643 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
3304582 TATATATAGA
3304592 TTTTAATTTTATAAT
1 TTTTAATTTTATAAT
*
3304607 TTTTAAATTTAT-AT
1 TTTTAATTTTATAAT
3304621 TTTATAAGATTTTATAAT
1 TTT-T-A-ATTTTATAAT
*
3304639 ATTTA
1 TTTTA
3304644 TTTAATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
14 5 0.17
15 12 0.40
16 2 0.07
17 7 0.23
18 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (15 bp):
TTTTAATTTTATAAT
Found at i:3304872 original size:18 final size:17
Alignment explanation
Indices: 3304835--3304887 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
3304825 AATTTTCATT
3304835 TTTTTTATATTTTGAAAT-
1 TTTTTTAT-TTTT-AAATA
*
3304853 TTATTTATTTTTAAATA
1 TTTTTTATTTTTAAATA
3304870 TTTTTGTA-TTTTAAATA
1 TTTTT-TATTTTTAAATA
3304887 T
1 T
3304888 AAATTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 4 0.13
17 18 0.58
18 9 0.29
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (17 bp):
TTTTTTATTTTTAAATA
Found at i:3305369 original size:29 final size:29
Alignment explanation
Indices: 3305337--3305396 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
3305327 ATGTCTAATT
*
3305337 TTTTTTTATCAAAATAGATACATAAAGTA
1 TTTTTTGATCAAAATAGATACATAAAGTA
* * * *
3305366 TTTTTTGGTCGAAATAGGTACCTAAAGTA
1 TTTTTTGATCAAAATAGATACATAAAGTA
3305395 TT
1 TT
3305397 CGATTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (29 bp):
TTTTTTGATCAAAATAGATACATAAAGTA
Found at i:3305520 original size:29 final size:29
Alignment explanation
Indices: 3305478--3305537 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
3305468 AAAAAGATTG
* *
3305478 AATACTTTATGTACTTATTTTGATAAAAA
1 AATACTATAAGTACTTATTTTGATAAAAA
3305507 AATACTATAAGTACTTATTTTGATAAAAA
1 AATACTATAAGTACTTATTTTGATAAAAA
3305536 AA
1 AA
3305538 AGAGAAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (29 bp):
AATACTATAAGTACTTATTTTGATAAAAA
Found at i:3305757 original size:21 final size:20
Alignment explanation
Indices: 3305730--3305827 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
3305720 AATCAGTGTC
3305730 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
3305751 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
3305771 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3305791 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
3305812 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3305828 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3305780 original size:41 final size:41
Alignment explanation
Indices: 3305671--3305827 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
3305661 AAATGACCAA
* **
3305671 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
3305710 CAGAATCGCAAATC-AGTGTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
3305751 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
3305792 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
3305828 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:3305837 original size:20 final size:20
Alignment explanation
Indices: 3305814--3305984 Score: 107
Period size: 20 Copynumber: 8.6 Consensus size: 20
3305804 GCGAATATGA
3305814 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
3305834 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
3305854 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
** *
3305874 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGTAACCAT
* * *
3305894 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* *
3305914 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
* **
3305934 AAATCGCAACGAG-AATCTGT
1 AAATCGCAACGCGTAA-CCAT
* *
3305954 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
3305974 AAATCGCAACG
1 AAATCGCAACG
3305985 AGAATCTGTA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.02
20 127 0.97
21 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:3305879 original size:60 final size:58
Alignment explanation
Indices: 3305794--3306003 Score: 208
Period size: 60 Copynumber: 3.5 Consensus size: 58
3305784 CGATTTTCCA
* ** * *
3305794 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCGAAC-CGTAAATCGCAA-GCGTATCCGT
* ** *
3305854 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTTTCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCG-AACCGTAAATCGCAA-GCGTATCCGT
* *
3305914 AAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCTGTAAATCGCAA-CGATAATCCGT
1 AAATCGCAACG-TGAATCCGTAAATCGCAACGCGAA-CCGTAAATCGCAAGCG-T-ATCCGT
* * *
3305974 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGTGAATCCGTAAATCGCAAC
3306004 ACTGAAATTT
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
58 2 0.02
59 1 0.01
60 120 0.96
61 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (58 bp):
AAATCGCAACGTGAATCCGTAAATCGCAACGCGAACCGTAAATCGCAAGCGTATCCGT
Found at i:3305985 original size:20 final size:20
Alignment explanation
Indices: 3305848--3306003 Score: 174
Period size: 20 Copynumber: 7.8 Consensus size: 20
3305838 CGCAATGCGT
*
3305848 ATCCGTAAATCGCAACG-TGT
1 ATCCGTAAATCGCAACGAT-A
*
3305868 ATCCGTAAATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
* * *
3305888 TTCCGTATATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
3305908 ATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
3305928 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
*
3305948 ATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
3305968 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
* *
3305988 ATCTGTAAATCACAAC
1 ATCCGTAAATCGCAAC
3306004 ACTGAAATTT
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 119 0.98
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGATA
Found at i:3305985 original size:40 final size:40
Alignment explanation
Indices: 3305814--3306003 Score: 208
Period size: 40 Copynumber: 4.8 Consensus size: 40
3305804 GCGAATATGA
* *
3305814 AAATCGCAACGCGAA-CACATAAATCGCAATGCG-T-ATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAA--CGATAATCCGT
* * * *
3305854 AAATCGCAACGTGTATCCGTAAATCGCAACGCGT-TTCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACG-ATAATCCGT
* * *
3305894 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
*
3305934 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
3305974 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
3306004 ACTGAAATTT
Statistics
Matches: 133, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 129 0.97
41 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
Found at i:3306725 original size:24 final size:24
Alignment explanation
Indices: 3306686--3306732 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3306676 AAATTTGGTC
3306686 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
3306710 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
3306733 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:3306923 original size:12 final size:12
Alignment explanation
Indices: 3306906--3306930 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3306896 ATATAATCCT
3306906 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3306918 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3306930 G
1 G
3306931 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3309236 original size:19 final size:19
Alignment explanation
Indices: 3309214--3309487 Score: 363
Period size: 19 Copynumber: 15.4 Consensus size: 19
3309204 CGGAAATTAC
*
3309214 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3309233 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
3309247 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
3309267 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3309281 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3309300 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3309319 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3309333 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3309352 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3309371 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3309390 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3309409 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3309428 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3309447 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
3309461 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3309480 AATCGCAA
1 AATCGCAA
3309488 CGAGAGAATC
Statistics
Matches: 228, Mismatches: 6, Indels: 42
0.83 0.02 0.15
Matches are distributed among these distances:
14 40 0.18
15 2 0.01
16 11 0.05
17 10 0.04
18 3 0.01
19 149 0.65
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3309301 original size:33 final size:34
Alignment explanation
Indices: 3309214--3309509 Score: 315
Period size: 33 Copynumber: 8.5 Consensus size: 34
3309204 CGGAAATTAC
* *
3309214 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
3309247 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
3309281 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
3309319 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
3309352 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
3309390 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
3309428 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
3309460 GAATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 -AATCGCAATGCGAAATGAAAATCGCAACGATGAA
3309494 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
3309510 TATAAACGCA
Statistics
Matches: 242, Mismatches: 7, Indels: 28
0.87 0.03 0.10
Matches are distributed among these distances:
32 2 0.01
33 101 0.42
34 32 0.13
35 5 0.02
36 4 0.02
37 2 0.01
38 96 0.40
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:3309466 original size:14 final size:14
Alignment explanation
Indices: 3309447--3309501 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3309437 GCGAAATGAA
3309447 AATCGCAACGAAAG
1 AATCGCAACGAAAG
3309461 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
3309478 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
3309494 AATCGCAA
1 AATCGCAA
3309502 TGCGAAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 5 0.14
19 8 0.23
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3309525 original size:52 final size:52
Alignment explanation
Indices: 3309242--3309509 Score: 384
Period size: 52 Copynumber: 5.0 Consensus size: 52
3309232 AAATCCCAAC
3309242 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
3309295 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
3309347 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
3309404 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
3309459 A-G--AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
3309508 AT
1 AT
3309510 TATAAACGCA
Statistics
Matches: 205, Mismatches: 2, Indels: 19
0.91 0.01 0.08
Matches are distributed among these distances:
47 10 0.05
48 1 0.00
49 5 0.02
50 2 0.01
52 95 0.46
53 16 0.08
54 3 0.01
55 5 0.02
56 1 0.00
57 67 0.33
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:3309625 original size:19 final size:19
Alignment explanation
Indices: 3309516--3309617 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
3309506 AAATTATAAA
3309516 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3309535 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
3309555 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
3309571 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3309588 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3309607 CGCATTGCGAT
1 CGCATTGCGAT
3309618 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:3309743 original size:14 final size:14
Alignment explanation
Indices: 3309724--3309760 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3309714 CATCAATTAC
3309724 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3309738 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3309752 ACAAATCAA
1 ACAAATCAA
3309761 TTAAATAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3310876 original size:14 final size:14
Alignment explanation
Indices: 3310857--3310946 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
3310847 TTGAAATGAA
3310857 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3310871 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
3310890 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3310904 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3310923 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3310937 AATCGCAACG
1 AATCGCAACG
3310947 CGAAATAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3310894 original size:33 final size:33
Alignment explanation
Indices: 3310849--3310963 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
3310839 TCTTTTGGTT
3310849 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
3310882 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3310915 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
3310948 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
3310964 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.47, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3310895 original size:19 final size:19
Alignment explanation
Indices: 3310871--3310968 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
3310861 GCAACGAGAG
*
3310871 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
3310890 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
3310904 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
3310923 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
3310937 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
*
3310956 AATCGCAATGCGA
1 AATCGCAACGCGA
3310969 TTTTGGTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:3310999 original size:14 final size:14
Alignment explanation
Indices: 3310980--3311036 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3310970 TTTGGTTTCG
3310980 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3310994 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3311013 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3311027 CGTTGCGATT
1 CGTTGCGATT
3311037 GTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3311018 original size:19 final size:19
Alignment explanation
Indices: 3310994--3311082 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
3310984 GCGATTCTCT
3310994 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3311013 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
3311027 CGTTGCGATTGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*** *
3311046 CGTTGCGACAGTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
3311066 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
3311083 ATCTCGTTGC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 25 0.45
20 15 0.27
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:3311074 original size:39 final size:33
Alignment explanation
Indices: 3310964--3311082 Score: 157
Period size: 33 Copynumber: 3.4 Consensus size: 33
3310954 AAAATCGCAA
**
3310964 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3310997 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
3311030 TGCGATTGTCATTTCGCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCGT
3311069 TGCGATTTTCATTT
1 TGCGATTTTCATTT
3311083 ATCTCGTTGC
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
33 50 0.66
35 1 0.01
36 1 0.01
37 1 0.01
39 23 0.30
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:3311216 original size:33 final size:33
Alignment explanation
Indices: 3311174--3311244 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3311164 AATACTAACT
3311174 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
3311207 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
3311240 TGAAA
1 TGAAA
3311245 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:3311478 original size:22 final size:22
Alignment explanation
Indices: 3311426--3311480 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3311416 TGGTTGTGAG
**
3311426 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
3311448 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
3311470 GGATTTCTTCG
1 GGATTTCTTCG
3311481 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3311652 original size:20 final size:20
Alignment explanation
Indices: 3311627--3311820 Score: 194
Period size: 20 Copynumber: 9.7 Consensus size: 20
3311617 CTTTAAATAT
3311627 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3311647 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
3311669 -TCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
*
3311688 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* * **
3311708 CACATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3311728 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3311748 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
3311768 CGCATTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3311788 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3311808 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3311821 TAGAAAATCG
Statistics
Matches: 141, Mismatches: 28, Indels: 10
0.79 0.16 0.06
Matches are distributed among these distances:
19 2 0.01
20 122 0.87
21 15 0.11
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3311814 original size:60 final size:60
Alignment explanation
Indices: 3311627--3311820 Score: 235
Period size: 60 Copynumber: 3.2 Consensus size: 60
3311617 CTTTAAATAT
* ** *
3311627 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACAGATA
* * *** * *
3311688 CGCGTTGCGATATACGGATACACATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
* * * * *
3311748 CACGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
3311808 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3311821 TAGAAAATCG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 83 0.75
61 27 0.25
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
Found at i:3311837 original size:21 final size:21
Alignment explanation
Indices: 3311807--3311888 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
3311797 ATTTTCATAT
*
3311807 TCGCGTTGCGATTTTAGAAAA
1 TCGCATTGCGATTTTAGAAAA
* * **
3311828 TCGCAATGCGAATTT-GACTA
1 TCGCATTGCGATTTTAGAAAA
*
3311848 TCGCATTGCGATTTTCA-AGAA
1 TCGCATTGCGATTTT-AGAAAA
*
3311869 TCGCATTGCGATTTTGGAAA
1 TCGCATTGCGATTTTAGAAA
3311889 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
20 16 0.34
21 31 0.66
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATTTTAGAAAA
Found at i:3311857 original size:41 final size:41
Alignment explanation
Indices: 3311807--3311884 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
3311797 ATTTTCATAT
*
3311807 TCGCGTTGCGATTTT-AGAAAATCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTCA-AAAATCGCAATGCGAATTTGACTA
* * *
3311848 TCGCATTGCGATTTTCAAGAATCGCATTGCGATTTTG
1 TCGCATTGCGATTTTCAAAAATCGCAATGCGAATTTG
3311885 GAAACTGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 31 0.97
42 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (41 bp):
TCGCATTGCGATTTTCAAAAATCGCAATGCGAATTTGACTA
Found at i:3325546 original size:16 final size:16
Alignment explanation
Indices: 3325525--3325557 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3325515 TATTGGGAAC
3325525 AGTAATCCTTTCAGAT
1 AGTAATCCTTTCAGAT
3325541 AGTAATCCTTTCAGAT
1 AGTAATCCTTTCAGAT
3325557 A
1 A
3325558 TAGAGGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (16 bp):
AGTAATCCTTTCAGAT
Found at i:3333127 original size:16 final size:17
Alignment explanation
Indices: 3333106--3333137 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3333096 CAATTTATCT
3333106 CATAAATAAGG-AACAA
1 CATAAATAAGGCAACAA
3333122 CATAAATAAGGCAACA
1 CATAAATAAGGCAACA
3333138 TCAAGACATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.12
Consensus pattern (17 bp):
CATAAATAAGGCAACAA
Found at i:3343839 original size:82 final size:84
Alignment explanation
Indices: 3343728--3343883 Score: 253
Period size: 82 Copynumber: 1.9 Consensus size: 84
3343718 AGAGGTCAAT
* *
3343728 CAATGCATAATTTAAACAACTTTTTAGAAAACGGGTGAAATAGTGGT-AT-ATTATCATCTTCTA
1 CAATGCATAATTTAAACAACTTTTCAGAAAACGGGTGAAATAGTGGTGATCATTATCATCTTCAA
3343791 CAACTTTTTAAAGGTTATC
66 CAACTTTTTAAAGGTTATC
* *
3343810 CAATGCATAATTTAAACAACTTTTCAGAAAATGGGTGAAATAGTGGTGGTGCATTATCATCTTCA
1 CAATGCATAATTTAAACAACTTTTCAGAAAACGGGTGAAATAGTGGTGAT-CATTATCATCTTCA
3343875 ACAACTTTT
65 ACAACTTTT
3343884 CAATGATGTA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
82 45 0.67
83 1 0.01
85 21 0.31
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (84 bp):
CAATGCATAATTTAAACAACTTTTCAGAAAACGGGTGAAATAGTGGTGATCATTATCATCTTCAA
CAACTTTTTAAAGGTTATC
Found at i:3345280 original size:16 final size:18
Alignment explanation
Indices: 3345251--3345291 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
3345241 CACCAAACAC
*
3345251 TCTTTCTATTTTC-T-TA
1 TCTTTCTATCTTCTTCTA
*
3345267 TCTTTCTCTCTTCTTCTA
1 TCTTTCTATCTTCTTCTA
3345285 TCTTTCT
1 TCTTTCT
3345292 TTAAGTAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 11 0.52
17 1 0.05
18 9 0.43
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (18 bp):
TCTTTCTATCTTCTTCTA
Found at i:3346006 original size:189 final size:189
Alignment explanation
Indices: 3345666--3346013 Score: 608
Period size: 189 Copynumber: 1.8 Consensus size: 189
3345656 TAGTGAGTCA
* *
3345666 TTAGAAGTTCAAAATAGTTTAACTGGTTGAGTTGAGCATGATAAGCATTTTCATAGTACAATTAT
1 TTAGAAGTTCAAAATAGTTTAAATGGTTGAGTTGAGCATGATAAGCATTTTCATAGTACAAATAT
3345731 TGTTTTAGAGTTATAAATGTGTTTAAAGCATCTATTATGACCCTTATTGATCAAATAAAACTTCA
66 TGTTTTAGAGTTATAAATGTGTTTAAAGCATCTATTATGACCCTTATTGATCAAATAAAACTTCA
*
3345796 AGCATATTTAGGGACCTCACTAAGGTCTTTGGGATTGAATTATAGCATTTTAGTATGTT
131 AACATATTTAGGGACCTCACTAAGGTCTTTGGGATTGAATTATAGCATTTTAGTATGTT
*
3345855 TTAGAAGTTCAAAATAGTTTAAATGGTTGAGTTGAGCATGATAAGCATTTTCATAGTACAAATCT
1 TTAGAAGTTCAAAATAGTTTAAATGGTTGAGTTGAGCATGATAAGCATTTTCATAGTACAAATAT
*
3345920 TGTTTTAGAGTTATAAATGTGTTTAAAGCATCTATTATGACCCTTGTTGATCAAATAAAACTTCA
66 TGTTTTAGAGTTATAAATGTGTTTAAAGCATCTATTATGACCCTTATTGATCAAATAAAACTTCA
* * *
3345985 AACATGTTT-GGGAATCTCACTAAGTTCTT
131 AACATATTTAGGG-ACCTCACTAAGGTCTT
3346014 CATTTTGGGG
Statistics
Matches: 150, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
188 3 0.02
189 147 0.98
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.38
Consensus pattern (189 bp):
TTAGAAGTTCAAAATAGTTTAAATGGTTGAGTTGAGCATGATAAGCATTTTCATAGTACAAATAT
TGTTTTAGAGTTATAAATGTGTTTAAAGCATCTATTATGACCCTTATTGATCAAATAAAACTTCA
AACATATTTAGGGACCTCACTAAGGTCTTTGGGATTGAATTATAGCATTTTAGTATGTT
Found at i:3350038 original size:17 final size:18
Alignment explanation
Indices: 3350013--3350046 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3350003 TCATTTTAAT
*
3350013 TTCTACATCAATTATCTA
1 TTCTACATCAAGTATCTA
3350031 TTCT-CATCAAGTATCT
1 TTCTACATCAAGTATCT
3350047 GACCTCTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.24, G:0.03, T:0.44
Consensus pattern (18 bp):
TTCTACATCAAGTATCTA
Found at i:3350859 original size:51 final size:51
Alignment explanation
Indices: 3350800--3350914 Score: 158
Period size: 51 Copynumber: 2.3 Consensus size: 51
3350790 GTAACTACTG
* * *
3350800 AATAAAATAATAATAAACTAAAGATAATATTTTGACTTTACCCTAATTCTT
1 AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTACCCTAATTCCT
* * ***
3350851 AATAAAATAATAATAAATTAAAGATAATGTTTTAACTCTATTTTAATTCCT
1 AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTACCCTAATTCCT
3350902 AATAAAATAATAA
1 AATAAAATAATAA
3350915 ATCTAATCCT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.37
Consensus pattern (51 bp):
AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTACCCTAATTCCT
Found at i:3356491 original size:32 final size:31
Alignment explanation
Indices: 3356455--3356536 Score: 76
Period size: 36 Copynumber: 2.4 Consensus size: 31
3356445 AACCTTTTTT
3356455 ATATTTTTAATTTTGTTAAA-AAAATTACATAA
1 ATATTTTTAATTTT-TTAAAGAAAA-TACATAA
*
3356487 ATATTATGAATTTAATTTTTTAAAGAAAATATATAA
1 ATA-T-T---TTTAATTTTTTAAAGAAAATACATAA
3356523 ATATTTTATAATTT
1 ATATTTT-TAATTT
3356537 GTAATATTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
31 2 0.05
32 9 0.21
33 1 0.02
34 2 0.05
35 1 0.02
36 14 0.33
37 13 0.31
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (31 bp):
ATATTTTTAATTTTTTAAAGAAAATACATAA
Found at i:3356536 original size:37 final size:38
Alignment explanation
Indices: 3356451--3356536 Score: 99
Period size: 37 Copynumber: 2.3 Consensus size: 38
3356441 ATTAAACCTT
*
3356451 TTTTATATTTTTAATTTTGTTAAAAAAATTACATAAATA
1 TTTTATA-ATTTAATTTTGTTAAAAAAATTACATAAATA
*
3356490 --TTATGAATTTAATTTT-TTAAAGAAAA-TATATAAATA
1 TTTTAT-AATTTAATTTTGTTAAA-AAAATTACATAAATA
3356526 TTTTATAATTT
1 TTTTATAATTT
3356537 GTAATATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
36 14 0.34
37 22 0.54
38 5 0.12
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (38 bp):
TTTTATAATTTAATTTTGTTAAAAAAATTACATAAATA
Found at i:3357544 original size:5 final size:5
Alignment explanation
Indices: 3357534--3357559 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3357524 AAATTATGAG
3357534 TTAAA TTAAA TTAAA TTAAA TTAAA T
1 TTAAA TTAAA TTAAA TTAAA TTAAA T
3357560 AGTTTATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TTAAA
Found at i:3370429 original size:21 final size:21
Alignment explanation
Indices: 3370395--3370455 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
3370385 GTTTGAAAAA
*
3370395 TTAACTAA-GTATTGATACCT
1 TTAATTAAGGTATTGATACCT
3370415 TTAATTAAGGTATTGATACCT
1 TTAATTAAGGTATTGATACCT
3370436 TTAATTAAGGTATTGATACC
1 TTAATTAAGGTATTGATACC
3370456 CTTACCCCAG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
20 7 0.18
21 32 0.82
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.41
Consensus pattern (21 bp):
TTAATTAAGGTATTGATACCT
Done.