Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006093.1 Hibiscus syriacus cultivar Beakdansim tig00014444_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: 3172561
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 13
Found at i:1967928 original size:61 final size:61
Alignment explanation
Indices: 1967858--1968037 Score: 261
Period size: 61 Copynumber: 2.9 Consensus size: 61
1967848 ACTGTAGACT
*
1967858 ATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAA
* * *
1967919 ATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACTATAGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAA
** ** * *
1967980 ATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAATTATCGCAACGCGAAATG
1 ATCGCAACGCGAAATGGAA-AATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
1968038 CAACGCGAAT
Statistics
Matches: 106, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
61 72 0.68
62 34 0.32
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (61 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAA
Found at i:1967967 original size:41 final size:41
Alignment explanation
Indices: 1967922--1968012 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
1967912 ATGAAAAATC
1967922 GCAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACTATA
1 GCAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACTATA
* *
1967963 GCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATC
1 GCAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACTATA
1968004 GCAACGCGA
1 GCAACGCGA
1968013 TTTTCAATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.16
Consensus pattern (41 bp):
GCAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACTATA
Found at i:1970479 original size:20 final size:20
Alignment explanation
Indices: 1970427--1970470 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1970417 TATTCATGAG
*
1970427 GTATGGATACC-TGAAGGGCA
1 GTATCGATACCAT-AAGGGCA
*
1970447 GTATCGATACCATAAGGTCA
1 GTATCGATACCATAAGGGCA
1970467 GTAT
1 GTAT
1970471 TGGTACCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (20 bp):
GTATCGATACCATAAGGGCA
Found at i:1971186 original size:22 final size:20
Alignment explanation
Indices: 1971158--1971215 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
1971148 AGTCAAGGGT
*
1971158 TACATAGGTCCTTTGGGATATA
1 TACATAGGTCCTTCGGG--ATA
* *
1971180 TACATAGCTCATTCGGGATA
1 TACATAGGTCCTTCGGGATA
1971200 TACATGAGGTCCTTCG
1 TACAT-AGGTCCTTCG
1971216 AGACAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 8 0.27
21 8 0.27
22 14 0.47
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (20 bp):
TACATAGGTCCTTCGGGATA
Found at i:1976215 original size:21 final size:20
Alignment explanation
Indices: 1976185--1976223 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1976175 TAGAATTCTT
1976185 AATTTCAAGACCAATGATGAA
1 AATTTCAAGA-CAATGATGAA
* *
1976206 AATTTGAAGATAATGATG
1 AATTTCAAGACAATGATG
1976224 GTTTATTTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (20 bp):
AATTTCAAGACAATGATGAA
Found at i:1978753 original size:14 final size:14
Alignment explanation
Indices: 1978712--1978756 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
1978702 GTTCGATTAT
* *
1978712 GTTCGTTTATGTTT
1 GTTCGGTTATGTTC
1978726 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
1978740 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
1978754 GTT
1 GTT
1978757 TATGTTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.07, C:0.11, G:0.27, T:0.56
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:1978773 original size:24 final size:24
Alignment explanation
Indices: 1978702--1978776 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
1978692 GTTCGTGAAC
*
1978702 GTTCGATTATGTTCGTTTATGTT-T
1 GTTCGATTATGTTCGTTCAT-TTAT
* **
1978726 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGATTATGTTCGTTCATTTAT
* *
1978750 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGATTATGTTCGTTCATTTAT
1978774 GTT
1 GTT
1978777 TAACTCAATC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 2 0.05
24 40 0.95
ACGTcount: A:0.12, C:0.11, G:0.21, T:0.56
Consensus pattern (24 bp):
GTTCGATTATGTTCGTTCATTTAT
Found at i:1978774 original size:38 final size:38
Alignment explanation
Indices: 1978701--1978776 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
1978691 CGTTCGTGAA
** *
1978701 CGTTCGATTATGTTCGTTTATGTTTGTTCGGTTATGTT
1 CGTTCGATTATGTTCGTTTATGTTCATTCAGTTATGTT
* *
1978739 CGTTCGGTTATGTTCGTTTATGTTCATTCATTTATGTT
1 CGTTCGATTATGTTCGTTTATGTTCATTCAGTTATGTT
1978777 TAACTCAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (38 bp):
CGTTCGATTATGTTCGTTTATGTTCATTCAGTTATGTT
Found at i:1979872 original size:16 final size:16
Alignment explanation
Indices: 1979848--1979898 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
1979838 GGTCTCCAAC
*
1979848 GTTTATGTTCGTTTAT
1 GTTTGTGTTCGTTTAT
*
1979864 GTTTGTGTTCATTTAT
1 GTTTGTGTTCGTTTAT
*
1979880 GTATGTGTTCGTTTAT
1 GTTTGTGTTCGTTTAT
1979896 GTT
1 GTT
1979899 CATTTATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.12, C:0.06, G:0.22, T:0.61
Consensus pattern (16 bp):
GTTTGTGTTCGTTTAT
Found at i:1981082 original size:30 final size:31
Alignment explanation
Indices: 1981046--1981114 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1981036 TTAACACTAA
*
1981046 ATAAAAT-GTAATTTAAACCC-TACATTTTAG
1 ATAAAATAGTAATTT-AACCCATAAATTTTAG
* *
1981076 ATAAAATATTAATTTGACCCATAAATTTTAG
1 ATAAAATAGTAATTTAACCCATAAATTTTAG
1981107 ATAAAATA
1 ATAAAATA
1981115 TCAATTTGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 11 0.32
31 23 0.68
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (31 bp):
ATAAAATAGTAATTTAACCCATAAATTTTAG
Found at i:1981369 original size:26 final size:24
Alignment explanation
Indices: 1981339--1981390 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 24
1981329 ATAGCATAAT
1981339 ATATATAATAAGTATAGTTTTTGAAA
1 ATATATAAT-A-TATAGTTTTTGAAA
1981365 ATATATAATATATAGTTTTTGAAA
1 ATATATAATATATAGTTTTTGAAA
1981389 AT
1 AT
1981391 GTATTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 16 0.62
25 1 0.04
26 9 0.35
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (24 bp):
ATATATAATATATAGTTTTTGAAA
Found at i:1981464 original size:35 final size:35
Alignment explanation
Indices: 1981352--1981612 Score: 243
Period size: 35 Copynumber: 7.4 Consensus size: 35
1981342 TATAATAAGT
**
1981352 ATAGTTTTTGAAAATATATAATATATAGTTTTTGAAA
1 ATAG-TTTTGAAAACGTATAATATATAGTTTTT-AAA
* *
1981389 AT-GTATTTTTAAAACATAT-ATAATATAGTTTTTTAAA
1 ATAG--TTTTGAAAACGTATAAT-ATATAG-TTTTTAAA
1981426 ATAGTTTTGAAAACGTATAATATATAGTTTTTAAA
1 ATAGTTTTGAAAACGTATAATATATAGTTTTTAAA
*
1981461 ATAGTATTGAAAACGTATAATATATAGTTTTTAAA
1 ATAGTTTTGAAAACGTATAATATATAGTTTTTAAA
* *
1981496 A-GGATTTTGAAAACGTAT-ATAATATAGTTTTTTGAA
1 ATAG-TTTTGAAAACGTATAAT-ATATAG-TTTTTAAA
* *
1981532 ATGGTTTGGAAAACGTATAATATATA--TTTTAAA
1 ATAGTTTTGAAAACGTATAATATATAGTTTTTAAA
* * *
1981565 ACAATTTTTGAAAACATATAATATA-A-TTTTTAAAA
1 A-TAGTTTTGAAAACGTATAATATATAGTTTTT-AAA
1981600 CATA-TTTTGAAAA
1 -ATAGTTTTGAAAA
1981613 TATAGTTTTT
Statistics
Matches: 193, Mismatches: 17, Indels: 31
0.80 0.07 0.13
Matches are distributed among these distances:
33 8 0.04
34 34 0.18
35 66 0.34
36 48 0.25
37 31 0.16
38 6 0.03
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (35 bp):
ATAGTTTTGAAAACGTATAATATATAGTTTTTAAA
Found at i:1981544 original size:71 final size:71
Alignment explanation
Indices: 1981357--1981599 Score: 224
Period size: 71 Copynumber: 3.5 Consensus size: 71
1981347 TAAGTATAGT
* * *
1981357 TTTTGAAAA--TATATAATATATAGTTTTTGAAAAT-GTATTTTTAAAACATAT-ATAATATAGT
1 TTTTGAAAACGTATAT-A-ATATAGTTTTTTAAAATAGTA--TTGAAAACGTATAAT-ATATAG-
*
1981418 TTTTTAAAATAG
60 TTTTTAAAAAAG
1981430 TTTTGAAAACGTATA-ATATATAG-TTTTTAAAATAGTATTGAAAACGTATAATATATAGTTTTT
1 TTTTGAAAACGTATATA-ATATAGTTTTTTAAAATAGTATTGAAAACGTATAATATATAGTTTTT
*
1981493 -AAAAGG
65 AAAAAAG
* *
1981499 ATTTTGAAAACGTATATAATATAGTTTTTTGAAATGGT-TTGGAAAACGTATAATATATA--TTT
1 -TTTTGAAAACGTATATAATATAGTTTTTTAAAATAGTATT-GAAAACGTATAATATATAGTTTT
*
1981561 TAAAACAAT
64 TAAAA-AAG
*
1981570 TTTTGAAAAC--ATATAATATA-ATTTTTAAAA
1 TTTTGAAAACGTATATAATATAGTTTTTTAAAA
1981600 CATATTTTGA
Statistics
Matches: 149, Mismatches: 11, Indels: 26
0.80 0.06 0.14
Matches are distributed among these distances:
67 8 0.05
68 10 0.07
69 8 0.05
70 41 0.28
71 47 0.32
72 11 0.07
73 20 0.13
75 4 0.03
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (71 bp):
TTTTGAAAACGTATATAATATAGTTTTTTAAAATAGTATTGAAAACGTATAATATATAGTTTTTA
AAAAAG
Found at i:1981647 original size:16 final size:15
Alignment explanation
Indices: 1981625--1981685 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 15
1981615 TAGTTTTTAT
1981625 TATTATATATTATTA
1 TATTATATATTATTA
1981640 TATCTATATTCATTA-TA
1 TAT-TATA-T-ATTATTA
1981657 TATTATAT-TTATT-
1 TATTATATATTATTA
* *
1981670 TATTGTTTATTATTA
1 TATTATATATTATTA
1981685 T
1 T
1981686 TTCTTTTGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 9 0.24
14 6 0.16
15 5 0.13
16 8 0.21
17 6 0.16
18 4 0.11
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (15 bp):
TATTATATATTATTA
Found at i:1981680 original size:20 final size:20
Alignment explanation
Indices: 1981634--1981687 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
1981624 TTATTATATA
1981634 TTATTATATCTATATTCATTAT
1 TTATTATAT-T-TATTCATTAT
* * *
1981656 ATATTATATTTATTTATTGT
1 TTATTATATTTATTCATTAT
1981676 TTATTATTATTT
1 TTATTA-TATTT
1981688 CTTTTGTAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 13 0.48
21 6 0.22
22 8 0.30
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (20 bp):
TTATTATATTTATTCATTAT
Found at i:1982249 original size:15 final size:16
Alignment explanation
Indices: 1982229--1982258 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1982219 ATATCCGAGC
1982229 AAGATAC-AACGACAG
1 AAGATACAAACGACAG
1982244 AAGATACAAACGACA
1 AAGATACAAACGACA
1982259 AAAACAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.20, G:0.17, T:0.07
Consensus pattern (16 bp):
AAGATACAAACGACAG
Found at i:1983184 original size:12 final size:12
Alignment explanation
Indices: 1983167--1983195 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1983157 TGTAACATTT
1983167 TTTTATATTTTC
1 TTTTATATTTTC
1983179 TTTTATATTTTC
1 TTTTATATTTTC
1983191 TTTTA
1 TTTTA
1983196 AAATTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATATTTTC
Found at i:1984342 original size:14 final size:14
Alignment explanation
Indices: 1984304--1984343 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1984294 TGGGGTAGGA
*
1984304 ATTTTTATTTTTTT
1 ATTTTTATTTTATT
* *
1984318 ATTATTCTTTTATT
1 ATTTTTATTTTATT
1984332 ATTTTTATTTTA
1 ATTTTTATTTTA
1984344 CTAACTTGTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (14 bp):
ATTTTTATTTTATT
Found at i:1995388 original size:23 final size:25
Alignment explanation
Indices: 1995357--1995406 Score: 77
Period size: 23 Copynumber: 2.0 Consensus size: 25
1995347 AGCATAATAT
1995357 ATATAATAAATATAT-TTTTTGAAA
1 ATATAATAAATATATATTTTTGAAA
1995381 ATAT-ATAAATATATAGTTTTTGAAA
1 ATATAATAAATATATA-TTTTTGAAA
1995406 A
1 A
1995407 AGTATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 10 0.42
24 4 0.17
25 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (25 bp):
ATATAATAAATATATATTTTTGAAA
Found at i:1995407 original size:26 final size:26
Alignment explanation
Indices: 1995355--1995406 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
1995345 ATAGCATAAT
*
1995355 ATATATAATAAATATATTTTTTGAAA
1 ATATATAATAAATATAGTTTTTGAAA
*
1995381 ATATATAA-ATATATAGTTTTTGAAA
1 ATATATAATAAATATAGTTTTTGAAA
1995406 A
1 A
1995407 AGTATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (26 bp):
ATATATAATAAATATAGTTTTTGAAA
Found at i:1995468 original size:36 final size:36
Alignment explanation
Indices: 1995373--1995804 Score: 340
Period size: 36 Copynumber: 11.8 Consensus size: 36
1995363 TAAATATATT
* *
1995373 TTTTGAAAATATATAAATATATAGTTTTTGAAAA-AG
1 TTTTGAAAACATAT-AATATATAGTTTTTTAAAATAG
*
1995409 TATTTTTAAAACATAT-ATAATATAGTTTTTTAAAATAG
1 --TTTTGAAAACATATAAT-ATATAGTTTTTTAAAATAG
* * *
1995447 TTTTGAAAACGTATAATATATATCTCTTTTTAAAATAA
1 TTTTGAAAACATATAATATATA-GT-TTTTTAAAATAG
1995485 TTTTGAAAACATATAATATATAG-TTTTT-AAATAG
1 TTTTGAAAACATATAATATATAGTTTTTTAAAATAG
* * **
1995519 TTTTGAAAACGTATAATAAATAG-TTTTTAAAACGG
1 TTTTGAAAACATATAATATATAGTTTTTTAAAATAG
* *
1995554 TTTTGAAAACATAT-ATAATATAGTTTTTTGAAATGG
1 TTTTGAAAACATATAAT-ATATAGTTTTTTAAAATAG
* * * *
1995590 TTTTGAAAACGTATAAGATATAGTTTTTAAAAATGG
1 TTTTGAAAACATATAATATATAGTTTTTTAAAATAG
* * * *
1995626 TTTTGAAAACGTATAAGATATAGTTTTTAAAAATGG
1 TTTTGAAAACATATAATATATAGTTTTTTAAAATAG
* * * * *
1995662 TTTTAAAAACAAATAGTATATGATTTTTTTTAAAAATGG
1 TTTTGAAAACATATAATATAT-A-GTTTTTT-AAAATAG
** * * * *
1995701 GCTTGAAAACGTATAATATATATTTTATTTTAAAACAAT
1 TTTTGAAAACATATAATATATA-GTT-TTTTAAAA-TAG
* * *
1995740 TTTTGAAAACGTATAATATA-A-TTTTTGAAAACATAT
1 TTTTGAAAACATATAATATATAGTTTTT-TAAA-ATAG
* *
1995776 TTTTGAAAATATAGTATTATATAGTTTTT
1 TTTTGAAAACATA-TAATATATAGTTTTT
1995805 ATTATTATAT
Statistics
Matches: 330, Mismatches: 45, Indels: 37
0.80 0.11 0.09
Matches are distributed among these distances:
34 33 0.10
35 30 0.09
36 129 0.39
37 27 0.08
38 62 0.19
39 49 0.15
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (36 bp):
TTTTGAAAACATATAATATATAGTTTTTTAAAATAG
Found at i:1995665 original size:143 final size:146
Alignment explanation
Indices: 1995373--1995656 Score: 398
Period size: 143 Copynumber: 2.0 Consensus size: 146
1995363 TAAATATATT
* * *
1995373 TTTTGAAAATATATAAATATATAGTTTTTGAAAAAGTATTTTTAAAACATATATAATATAGTTTT
1 TTTTGAAAACATATAAATAAATAGTTTTTGAAAAAGTATTTTGAAAACATATATAATATAGTTTT
* * *
1995438 TTAAAATAGTTTTGAAAACGTATAATATATATCTCTTTTTAAAATAATTTTGAAAACATATAATA
66 TTAAAATAGTTTTGAAAACGTATAAGATATATCTCTTTTAAAAATAATTTTGAAAACATATAAGA
1995503 TATAGTTTTTAAATAG
131 TATAGTTTTTAAATAG
* * *
1995519 TTTTGAAAACGTAT-AATAAATAGTTTTT-AAAACG-GTTTTGAAAACATATATAATATAGTTTT
1 TTTTGAAAACATATAAATAAATAGTTTTTGAAAAAGTATTTTGAAAACATATATAATATAGTTTT
* * * ** *
1995581 TTGAAATGGTTTTGAAAACGTATAAGATATA-GT-TTTTAAAAATGGTTTTGAAAACGTATAAGA
66 TTAAAATAGTTTTGAAAACGTATAAGATATATCTCTTTTAAAAATAATTTTGAAAACATATAAGA
1995644 TATAGTTTTTAAA
131 TATAGTTTTTAAA
1995657 AATGGTTTTA
Statistics
Matches: 123, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
141 38 0.31
142 1 0.01
143 54 0.44
144 5 0.04
145 13 0.11
146 12 0.10
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (146 bp):
TTTTGAAAACATATAAATAAATAGTTTTTGAAAAAGTATTTTGAAAACATATATAATATAGTTTT
TTAAAATAGTTTTGAAAACGTATAAGATATATCTCTTTTAAAAATAATTTTGAAAACATATAAGA
TATAGTTTTTAAATAG
Found at i:1995692 original size:39 final size:38
Alignment explanation
Indices: 1995649--1995735 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 38
1995639 TAAGATATAG
** *
1995649 TTTTTAAAAATGGTTTTAAAAACAAATAGTATATGATTT
1 TTTTTAAAAATGGGCTTAAAAACAAATAATATAT-ATTT
* **
1995688 TTTTTAAAAATGGGCTTGAAAACGTATAATATATATTT
1 TTTTTAAAAATGGGCTTAAAAACAAATAATATATATTT
1995726 TATTTTAAAA
1 T-TTTTAAAA
1995736 CAATTTTTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 5 0.12
39 36 0.88
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (38 bp):
TTTTTAAAAATGGGCTTAAAAACAAATAATATATATTT
Found at i:1995830 original size:23 final size:25
Alignment explanation
Indices: 1995804--1995857 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
1995794 ATATAGTTTT
*
1995804 TATTATTATAT-T-TATTTATTATA
1 TATTATTATATCTATATTCATTATA
1995827 TATTATTATATCTATATTCATTATA
1 TATTATTATATCTATATTCATTATA
1995852 TATTAT
1 TATTAT
1995858 ATTTATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 11 0.39
24 1 0.04
25 16 0.57
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TATTATTATATCTATATTCATTATA
Found at i:1995875 original size:20 final size:20
Alignment explanation
Indices: 1995800--1995887 Score: 70
Period size: 20 Copynumber: 4.2 Consensus size: 20
1995790 TATTATATAG
1995800 TTTTTA-TTATTATATTTAT
1 TTTTTATTTATTATATTTAT
1995819 TTATTATATATTATTATATCTATAT
1 TT-TT-TAT-TTATTATAT-T-TAT
** *
1995844 TCATTATATATTATATTTAT
1 TTTTTATTTATTATATTTAT
* *
1995864 TTTTTGTTTATTATTATTTCT
1 TTTTTATTTATTA-TATTTAT
1995885 TTT
1 TTT
1995888 ACAGATCGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
19 2 0.04
20 14 0.26
21 12 0.22
22 8 0.15
23 12 0.22
24 2 0.04
25 4 0.07
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.68
Consensus pattern (20 bp):
TTTTTATTTATTATATTTAT
Found at i:1996466 original size:15 final size:16
Alignment explanation
Indices: 1996446--1996475 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1996436 AAATCCGAGC
1996446 AAGATAC-AACGACAG
1 AAGATACGAACGACAG
1996461 AAGATACGAACGACA
1 AAGATACGAACGACA
1996476 AAACACCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.20, G:0.20, T:0.07
Consensus pattern (16 bp):
AAGATACGAACGACAG
Found at i:1997337 original size:14 final size:15
Alignment explanation
Indices: 1997305--1997338 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1997295 TTCTTTATTT
*
1997305 CTTTTATTATTTTTT
1 CTTTTATTATTTTTA
1997320 CTTTTATTA-TTTTA
1 CTTTTATTATTTTTA
1997334 CTTTT
1 CTTTT
1997339 TTAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (15 bp):
CTTTTATTATTTTTA
Found at i:1997374 original size:9 final size:9
Alignment explanation
Indices: 1997356--1997394 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
1997346 AAATTCTACC
*
1997356 ATTTTCTTT
1 ATTTTTTTT
1997365 ATTTTTTTT
1 ATTTTTTTT
*
1997374 ATATTTTTT
1 ATTTTTTTT
*
1997383 ATATTTTTT
1 ATTTTTTTT
1997392 ATT
1 ATT
1997395 ATTCTCTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:1997397 original size:10 final size:9
Alignment explanation
Indices: 1997362--1997430 Score: 59
Period size: 9 Copynumber: 7.2 Consensus size: 9
1997352 TACCATTTTC
*
1997362 TTTATTTTT
1 TTTATATTT
1997371 TTTATATTT
1 TTTATATTT
1997380 TTTATATTT
1 TTTATATTT
1997389 TTTATTATTCT
1 TTTA-TATT-T
*
1997400 CTTGTAACATTT
1 -TT-T-ATATTT
*
1997412 TTT-TATAT
1 TTTATATTT
1997420 TTTATATTT
1 TTTATATTT
1997429 TT
1 TT
1997431 ATTTTGTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
8 6 0.12
9 27 0.55
10 5 0.10
11 3 0.06
12 3 0.06
13 4 0.08
14 1 0.02
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.74
Consensus pattern (9 bp):
TTTATATTT
Found at i:1997509 original size:16 final size:17
Alignment explanation
Indices: 1997480--1997521 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1997470 TATTCTATTT
* *
1997480 TATTTGTCTCTTTTAA-
1 TATTTTTCTATTTTAAC
1997496 TATTTTTCTATTTTAAC
1 TATTTTTCTATTTTAAC
*
1997513 TTTTTTTCT
1 TATTTTTCT
1997522 TCTTAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.17, C:0.12, G:0.02, T:0.69
Consensus pattern (17 bp):
TATTTTTCTATTTTAAC
Found at i:2001712 original size:14 final size:14
Alignment explanation
Indices: 2001693--2001720 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2001683 TGGGTAAGTC
2001693 ACTCATTGTTTTTA
1 ACTCATTGTTTTTA
2001707 ACTCATTGTTTTTA
1 ACTCATTGTTTTTA
2001721 GGATGTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
ACTCATTGTTTTTA
Found at i:2008790 original size:27 final size:28
Alignment explanation
Indices: 2008760--2008822 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
2008750 CCCACAGGGG
*
2008760 AATCGATA-CCCCCTGGGGTTCTGTTAA
1 AATCGACACCCCCCTGGGGTTCTGTTAA
2008787 AATCGACACCCCCCTGGGGTTCTGTTAA
1 AATCGACACCCCCCTGGGGTTCTGTTAA
2008815 AATCGACA
1 AATCGACA
2008823 GAACACCCCC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 7 0.21
28 27 0.79
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (28 bp):
AATCGACACCCCCCTGGGGTTCTGTTAA
Found at i:2012250 original size:2 final size:2
Alignment explanation
Indices: 2012243--2012331 Score: 78
Period size: 2 Copynumber: 46.0 Consensus size: 2
2012233 CACTTATAAG
* *
2012243 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
2012285 T- TA TG CA TA CA T- TA TA -A GTA TA TA TT TA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
2012325 -A TA TA TA
1 TA TA TA TA
2012332 ACTATACATT
Statistics
Matches: 69, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
1 4 0.06
2 64 0.93
3 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2012337 original size:8 final size:7
Alignment explanation
Indices: 2012237--2012337 Score: 53
Period size: 8 Copynumber: 13.3 Consensus size: 7
2012227 ACACTACACT
2012237 TATAAGTA
1 TATAA-TA
2012245 TATATATA
1 TATA-ATA
2012253 TATATATA
1 TATA-ATA
2012261 TATATATA
1 TATA-ATA
2012269 TATATATA
1 TATA-ATA
2012277 TATAA-A
1 TATAATA
* * *
2012283 TGTTATG
1 TATAATA
*
2012290 CATACAT-
1 TATA-ATA
2012297 TATAAGTA
1 TATAA-TA
*
2012305 TATATTTA
1 TATA-ATA
2012313 TATAAATA
1 TAT-AATA
2012321 TATAATA
1 TATAATA
2012328 TATAACTA
1 TATAA-TA
2012336 TA
1 TA
2012338 CATTATACTT
Statistics
Matches: 76, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
6 5 0.07
7 15 0.20
8 54 0.71
9 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (7 bp):
TATAATA
Found at i:2012397 original size:16 final size:16
Alignment explanation
Indices: 2012367--2012408 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2012357 TAATAAAAGT
2012367 ATATATATACT-TATAC
1 ATATATATA-TGTATAC
*
2012383 ATATCTATATGTATAC
1 ATATATATATGTATAC
*
2012399 CTATATATAT
1 ATATATATAT
2012409 AATTACACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.45
Consensus pattern (16 bp):
ATATATATATGTATAC
Found at i:2013329 original size:305 final size:305
Alignment explanation
Indices: 2012778--2013389 Score: 1134
Period size: 305 Copynumber: 2.0 Consensus size: 305
2012768 ACTTCATTCA
*
2012778 TGCATTTATTTCATTTAATAAAGTTAGTTCATTTATTAAACTAACTCTTAATTGTTTCATGCATG
1 TGCATTTATTTCATTTAATAAAGTTAGTTCATTTATTAAACTAAATCTTAATTGTTTCATGCATG
* *
2012843 TTTTCAATTAAAGATTGAATAAAGTTCGCCTTTGTGTCTAGGTGCATGAGAGAAGTTGAACGGTT
66 TTTTCAATTAAAGATTGAATAAAGTTCACCTTTGTGTATAGGTGCATGAGAGAAGTTGAACGGTT
*
2012908 TCATCATATACAAAATATCAGTCAGATTGTCTTCCAATTCTGGATGTGATAAAGACATTTTTGGT
131 TCATCAGATACAAAATATCAGTCAGATTGTCTTCCAATTCTGGATGTGATAAAGACATTTTTGGT
* *
2012973 TCCATAAATCAATTGGGAATTATTCCTCTATCTCTCCAACGCCTTTTGAATCACCTTAATCTGAT
196 TCCATAAATCAATTGGGAATTATTCCTCTATCTCTCCAACGCCTTTTGAATCACCTTAATATGAC
2013038 ATCAAGAGCTTGAGATATGATCGATTTATTGAAGACAGTGCAGGT
261 ATCAAGAGCTTGAGATATGATCGATTTATTGAAGACAGTGCAGGT
2013083 TGCATTTATTTCATTTAATAAAGTTAGTTCATTTATTAAACTAAATCTTAATTGTTTCATGCATG
1 TGCATTTATTTCATTTAATAAAGTTAGTTCATTTATTAAACTAAATCTTAATTGTTTCATGCATG
* *
2013148 TTTTCAATTATAGATTGAATAAAGTTCACCTTTGTGTATAGGTGCATGAGAGAAGTTGAATGGTT
66 TTTTCAATTAAAGATTGAATAAAGTTCACCTTTGTGTATAGGTGCATGAGAGAAGTTGAACGGTT
*
2013213 TCATCAGATGCAAAATATCAGTCAGATTGTCTTCCAATTCTGGATGTGATAAAGACATTTTTGGT
131 TCATCAGATACAAAATATCAGTCAGATTGTCTTCCAATTCTGGATGTGATAAAGACATTTTTGGT
2013278 TCCATAAATCAATTGGGAATTATTCCTCTATCTCTCCAACGCCTTTTGAATCACCTTAATATGAC
196 TCCATAAATCAATTGGGAATTATTCCTCTATCTCTCCAACGCCTTTTGAATCACCTTAATATGAC
*
2013343 ATCAGGAGCTTGAGATATGATCGATTTATTGAAGACAGTGCAGGT
261 ATCAAGAGCTTGAGATATGATCGATTTATTGAAGACAGTGCAGGT
2013388 TG
1 TG
2013390 GAATTTTGTT
Statistics
Matches: 297, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
305 297 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.38
Consensus pattern (305 bp):
TGCATTTATTTCATTTAATAAAGTTAGTTCATTTATTAAACTAAATCTTAATTGTTTCATGCATG
TTTTCAATTAAAGATTGAATAAAGTTCACCTTTGTGTATAGGTGCATGAGAGAAGTTGAACGGTT
TCATCAGATACAAAATATCAGTCAGATTGTCTTCCAATTCTGGATGTGATAAAGACATTTTTGGT
TCCATAAATCAATTGGGAATTATTCCTCTATCTCTCCAACGCCTTTTGAATCACCTTAATATGAC
ATCAAGAGCTTGAGATATGATCGATTTATTGAAGACAGTGCAGGT
Found at i:2020899 original size:40 final size:40
Alignment explanation
Indices: 2020844--2020925 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
2020834 TGCAGTTTTA
2020844 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
* *
2020884 TAATACACTTCGGTGTTTATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
2020924 TA
1 TA
2020926 GCACTACGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
Found at i:2021078 original size:44 final size:46
Alignment explanation
Indices: 2021030--2021139 Score: 125
Period size: 47 Copynumber: 2.4 Consensus size: 46
2021020 GTAACCATGC
*
2021030 AAATAAGCTTATGAGCTTACGGAA-T-AATGACAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTACGGAATTAAATGACAAGTATATAGGAA
* * ** * * *
2021074 AAATAAGCTTGCGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTACGGAA-TTAAATGACAAGTATATAGGAA
2021121 AAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTA
2021140 TGGGATAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
44 21 0.39
46 1 0.02
47 32 0.59
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTACGGAATTAAATGACAAGTATATAGGAA
Found at i:2023347 original size:2 final size:2
Alignment explanation
Indices: 2023336--2023412 Score: 54
Period size: 2 Copynumber: 38.5 Consensus size: 2
2023326 TATCAGTATG
*
2023336 TA TA TA -A TA TA TA TA -A GTA TA AA GTA TA -A TA TA TA -A GTA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA -TA
* * *
2023375 TA TA TA TG TA TA TA TG TA TGA TG TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA T
2023413 CATTAAACAT
Statistics
Matches: 59, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
1 4 0.07
2 50 0.85
3 5 0.08
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2023387 original size:20 final size:20
Alignment explanation
Indices: 2023343--2023389 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2023333 ATGTATATAA
2023343 TATATATAAGTATAAAGTAT
1 TATATATAAGTATAAAGTAT
* *
2023363 AATATATAAGTATATA-TAT
1 TATATATAAGTATAAAGTAT
2023382 GTATATAT
1 -TATATAT
2023390 GTATGATGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (20 bp):
TATATATAAGTATAAAGTAT
Found at i:2023750 original size:42 final size:41
Alignment explanation
Indices: 2023696--2023774 Score: 131
Period size: 42 Copynumber: 1.9 Consensus size: 41
2023686 TAACATTTGT
*
2023696 TAAAAAATAAAATTTCCCTCTTCCCTTTTCTAAATTCAAAA
1 TAAAAAATAAAATTTCCCTCTTCCCTCTTCTAAATTCAAAA
*
2023737 TAAAAAATCAAAATTTCCCTCTTTCCTCTTCTAAATTC
1 TAAAAAAT-AAAATTTCCCTCTTCCCTCTTCTAAATTC
2023775 TCAAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 8 0.23
42 27 0.77
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (41 bp):
TAAAAAATAAAATTTCCCTCTTCCCTCTTCTAAATTCAAAA
Found at i:2023945 original size:21 final size:21
Alignment explanation
Indices: 2023921--2023962 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2023911 AACTCATCAA
2023921 TTTAAAA-TAAGCAATATATAT
1 TTTAAAATTAA-CAATATATAT
2023942 TTTAAAATTAACAATATATAT
1 TTTAAAATTAACAATATATAT
2023963 ATATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (21 bp):
TTTAAAATTAACAATATATAT
Found at i:2037405 original size:2 final size:2
Alignment explanation
Indices: 2037366--2037390 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2037356 GATGTGTAAG
2037366 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2037391 CACAAAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2039645 original size:2 final size:2
Alignment explanation
Indices: 2039606--2039630 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2039596 GATGTGTAAG
2039606 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2039631 CACAAAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2041883 original size:2 final size:2
Alignment explanation
Indices: 2041842--2041868 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2041832 GATGTGTAAG
2041842 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2041869 CACAAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2046372 original size:2 final size:2
Alignment explanation
Indices: 2046321--2046357 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2046311 GATGTGTAAG
2046321 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2046358 AACAAAAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2055799 original size:29 final size:29
Alignment explanation
Indices: 2055765--2055828 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
2055755 GCTTTATCTA
2055765 TACCTTAT-AGCCTTGCAAGTAATCTCTTT
1 TACCTT-TCAGCCTTGCAAGTAATCTCTTT
*
2055794 TACCTTTCAGCCTTGCAAGTAATCTTTTT
1 TACCTTTCAGCCTTGCAAGTAATCTCTTT
*
2055823 TTCCTT
1 TACCTT
2055829 GCATTAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 1 0.03
29 31 0.97
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (29 bp):
TACCTTTCAGCCTTGCAAGTAATCTCTTT
Found at i:2059090 original size:24 final size:24
Alignment explanation
Indices: 2059016--2059099 Score: 105
Period size: 24 Copynumber: 3.5 Consensus size: 24
2059006 TTCGTGAACG
* **
2059016 TTCGATTATGTTCGTTTATGTTTG
1 TTCGGTTATGTTCGTTTATGTTAA
* *
2059040 TTAGGTTATGTTCGTTTATGTTCA
1 TTCGGTTATGTTCGTTTATGTTAA
2059064 TTCGGTTATGTTCGTTTATGTTAA
1 TTCGGTTATGTTCGTTTATGTTAA
**
2059088 TTCATTTATGTT
1 TTCGGTTATGTT
2059100 TAACCCAATC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.15, C:0.08, G:0.19, T:0.57
Consensus pattern (24 bp):
TTCGGTTATGTTCGTTTATGTTAA
Found at i:2061182 original size:20 final size:20
Alignment explanation
Indices: 2061136--2061182 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
2061126 ATTATTTCAA
2061136 ATTTATAATTTTAAGAAAAT
1 ATTTATAATTTTAAGAAAAT
* * *
2061156 ATATTATATTTTTAATAAGAT
1 AT-TTATAATTTTAAGAAAAT
2061177 ATTTAT
1 ATTTAT
2061183 TTATTTAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
ATTTATAATTTTAAGAAAAT
Found at i:2062830 original size:3 final size:3
Alignment explanation
Indices: 2062822--2062884 Score: 72
Period size: 3 Copynumber: 21.0 Consensus size: 3
2062812 TAAAAGTATT
* * * * *
2062822 TAA TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA TTA TTA TAA TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2062870 TAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA
2062885 CCAGGATAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:2063454 original size:33 final size:33
Alignment explanation
Indices: 2063416--2063481 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
2063406 AATTATTAAA
*
2063416 ATTACAAAATGATCATCTGATTACTT-ATATATT
1 ATTACAAAATGATAATCTGATTA-TTCATATATT
2063449 ATTACAAAATGATAATCTGATTATTCATATATT
1 ATTACAAAATGATAATCTGATTATTCATATATT
2063482 CAAAATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.06
33 29 0.94
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (33 bp):
ATTACAAAATGATAATCTGATTATTCATATATT
Found at i:2076175 original size:154 final size:154
Alignment explanation
Indices: 2075895--2076206 Score: 615
Period size: 154 Copynumber: 2.0 Consensus size: 154
2075885 CCGAATATGA
2075895 GGCATTATTTTAGTTTATTCGACAATAAAATTCACATATTCTTTCTTTATTGAATTTTTTTCAAA
1 GGCATTATTTTAGTTTATTCGACAATAAAATTCACATATTCTTTCTTTATTGAATTTTTTTCAAA
2075960 AGAAGAAAAATATTTTCAAATAAGATAATCTCTCTGGAAGTATATCTTGAAATTCAACGAATATC
66 AGAAGAAAAATATTTTCAAATAAGATAATCTCTCTGGAAGTATATCTTGAAATTCAACGAATATC
2076025 TCAGAAGTTTAAGATCGAAGTTGG
131 TCAGAAGTTTAAGATCGAAGTTGG
*
2076049 GGCATTATTTTAGTTTATTCGACAATTAAATTCACATATTCTTTCTTTATTGAATTTTTTTCAAA
1 GGCATTATTTTAGTTTATTCGACAATAAAATTCACATATTCTTTCTTTATTGAATTTTTTTCAAA
2076114 AGAAGAAAAATATTTTCAAATAAGATAATCTCTCTGGAAGTATATCTTGAAATTCAACGAATATC
66 AGAAGAAAAATATTTTCAAATAAGATAATCTCTCTGGAAGTATATCTTGAAATTCAACGAATATC
2076179 TCAGAAGTTTAAGATCGAAGTTGG
131 TCAGAAGTTTAAGATCGAAGTTGG
2076203 GGCA
1 GGCA
2076207 AGGAAAGTCA
Statistics
Matches: 157, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 157 1.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (154 bp):
GGCATTATTTTAGTTTATTCGACAATAAAATTCACATATTCTTTCTTTATTGAATTTTTTTCAAA
AGAAGAAAAATATTTTCAAATAAGATAATCTCTCTGGAAGTATATCTTGAAATTCAACGAATATC
TCAGAAGTTTAAGATCGAAGTTGG
Found at i:2077241 original size:99 final size:98
Alignment explanation
Indices: 2077052--2077389 Score: 291
Period size: 99 Copynumber: 3.3 Consensus size: 98
2077042 ATTTTTCTTA
* * * * * * * *
2077052 AAAATAAAATTCGTCTCACTTGAGAGAGTTTCCCCTAGAAATACAAATTTTGAAACTGTTTCACG
1 AAAACAAATTTCGTCTCACTTGAGACAGTTTCCCCTCGAAATA-AAAATTTGAAATTATTTCACT
**
2077117 TGAAACAAAATTTATTTCACTTGAGATTG-TTCTC
65 TGAAACAAAATTTATAACA-TTGAGATTGTTTCTC
* ** * *
2077151 AAAACAAATTTCGTCTCACTTGAGATAGTTTTTCTTCGAAATAAAAATTCTAAAATTATTTCACT
1 AAAACAAATTTCGTCTCACTTGAGACAGTTTCCCCTCGAAATAAAAATT-TGAAATTATTTCACT
* *
2077216 TGAAACAAAATTGATAACATGTGAGATTGTTTTTCTTA
65 TGAAACAAAATTTATAACAT-TGAGATTG--TTTC-TC
* * * * * * *
2077254 AAAACAAATTTCGTTTCGCTTAAGACAATTTTCCCTCAAAACATAAAATTTGGAAATTATTTCAC
1 AAAACAAATTTCGTCTCACTTGAGACAGTTTCCCCTCGAAATA-AAAATTT-GAAATTATTTCAC
* *
2077319 TTGAAATAAAATTTATAAACCTTTGAGATTGTTTCTC
64 TTGAAACAAAATTTAT-AA-CATTGAGATTGTTTCTC
* * *
2077356 TTGAAACAAATTTTGTCTCGCTTGAGACAGTTTC
1 --AAAACAAATTTCGTCTCACTTGAGACAGTTTC
2077390 TCTTGAATCA
Statistics
Matches: 191, Mismatches: 36, Indels: 19
0.78 0.15 0.08
Matches are distributed among these distances:
98 6 0.03
99 71 0.37
102 4 0.02
103 40 0.21
104 58 0.30
105 10 0.05
106 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (98 bp):
AAAACAAATTTCGTCTCACTTGAGACAGTTTCCCCTCGAAATAAAAATTTGAAATTATTTCACTT
GAAACAAAATTTATAACATTGAGATTGTTTCTC
Found at i:2077381 original size:36 final size:36
Alignment explanation
Indices: 2077341--2077500 Score: 199
Period size: 36 Copynumber: 4.6 Consensus size: 36
2077331 TTATAAACCT
*
2077341 TTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGC
1 TTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCGC
* *
2077377 TTGAGACAGTTTCTCTTGAATCAAATTTTGTCTCGC
1 TTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCGC
* * *
2077413 TTGAGACAGTTTCTCTTGAAACATAA-----AC-C-T
1 TTGAGATAGTTTCTCTTGAAACA-AATTTTGTCTCGC
*
2077443 TTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGC
1 TTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCGC
2077479 TTGAGATAGTTTCTCTTGAAAC
1 TTGAGATAGTTTCTCTTGAAAC
2077501 GTAAACCTTT
Statistics
Matches: 105, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
29 2 0.02
30 21 0.20
31 1 0.01
32 1 0.01
34 1 0.01
35 1 0.01
36 76 0.72
37 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.41
Consensus pattern (36 bp):
TTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCGC
Found at i:2077455 original size:30 final size:30
Alignment explanation
Indices: 2077421--2077531 Score: 116
Period size: 30 Copynumber: 3.5 Consensus size: 30
2077411 GCTTGAGACA
2077421 GTTTCTCTTGAAACATAAACCTTTGAGATT
1 GTTTCTCTTGAAACATAAACCTTTGAGATT
* * *
2077451 GTTTCTCTTGAAACA-AATTTTGTCTCGCTTGAGATA
1 GTTTCTCTTGAAACATAA-----AC-C-TTTGAGATT
*
2077487 GTTTCTCTTGAAACGTAAACCTTTGAGATT
1 GTTTCTCTTGAAACATAAACCTTTGAGATT
2077517 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
2077532 AATTGTTGAG
Statistics
Matches: 65, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
29 2 0.03
30 36 0.55
31 1 0.02
32 1 0.02
34 1 0.02
35 1 0.02
36 21 0.32
37 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (30 bp):
GTTTCTCTTGAAACATAAACCTTTGAGATT
Found at i:2077483 original size:66 final size:66
Alignment explanation
Indices: 2077385--2077535 Score: 275
Period size: 66 Copynumber: 2.3 Consensus size: 66
2077375 GCTTGAGACA
*
2077385 GTTTCTCTTGAATCAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGAT
1 GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGAT
2077450 T
66 T
* *
2077451 GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTCTCTTGAAACGTAAACCTTTGAGAT
1 GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGAT
2077516 T
66 T
2077517 GTTTCTCTTGAAACAAATT
1 GTTTCTCTTGAAACAAATT
2077536 GTTGAGTTAA
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 82 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (66 bp):
GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGAT
T
Found at i:2078770 original size:13 final size:13
Alignment explanation
Indices: 2078752--2078785 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
2078742 TAATATTTTC
*
2078752 TTTGAAAATCATT
1 TTTGAAAATCAAT
2078765 TTTG-AAATCAAT
1 TTTGAAAATCAAT
2078777 TTTGAAAAT
1 TTTGAAAAT
2078786 TACTCCTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:2087299 original size:139 final size:138
Alignment explanation
Indices: 2087068--2087606 Score: 576
Period size: 139 Copynumber: 3.9 Consensus size: 138
2087058 AAGGCTAGAT
* * * *
2087068 ATCCTCGTCACGTAGAAACAATGTCGTCCATCGACCAGATCTCCTCAACACGTAGGAGCAGTGTC
1 ATCCTCATCATGTAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACACGTAGGAGCAGTGTC
* * * * * * * *
2087133 ATCATTAGATAACCAAATTTCCACATCACGTAGGAACTGTGTTATATCCAAATTATCCCTAAATA
66 ATCCTCAGATAACCAGACTTCCTCATCACGTAGGAACCGTGTTGTCTCCAAATTATCCCTAAATA
*
2087198 TGGTTTGAC
131 CGG-TTGAC
* * * * * *
2087207 ATCCTTATCATGTAGGAACAATGTCATTCACCGACCAGATCTCCTCAACACGCAGGAGTAGCGTC
1 ATCCTCATCATGTAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACACGTAGGAGCAGTGTC
2087272 ATCCTCAGATAACCAGACTTCCTCATCACGTAGGAACCGTGTTGTCTCCAAATTATCCCTAAATA
66 ATCCTCAGATAACCAGACTTCCTCATCACGTAGGAACCGTGTTGTCTCCAAATTATCCCTAAATA
* * *
2087337 CGGCTAAA
131 CGGTTGAC
** * * * * *
2087345 AGTCCTCATCACATAGGAACATTATCGTCCACCGACCAGATCTCCTCAACGCGTGGGAGTAG-GA
1 A-TCCTCATCATGTAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACACGTAGGAGCAGTG-
* * ** *
2087409 TCATCCTCAGACAATCAGACTTCCTCATCACGTAGGAACCGTGTTGTCTTGAAAGTATCCCTAAA
64 TCATCCTCAGATAACCAGACTTCCTCATCACGTAGGAACCGTGTTGTCTCCAAATTATCCCTAAA
** * *
2087474 GGCAGCTAGAC
129 TAC-GGTTGAC
* * *** * * *
2087485 GTCCTCATCATGTAGGAACAATGTTGTCCGTTGACCAGATCTCTTCAACGCATAGGAGCAGTGTC
1 ATCCTCATCATGTAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACACGTAGGAGCAGTGTC
* * * **
2087550 ATTCTCAGATAACCAGACTTTCTCATCACGTAGAAACAATGTTGTCTCCAAATTATC
66 ATCCTCAGATAACCAGACTTCCTCATCACGTAGGAACCGTGTTGTCTCCAAATTATC
2087607 TCCAGATTGA
Statistics
Matches: 329, Mismatches: 67, Indels: 8
0.81 0.17 0.02
Matches are distributed among these distances:
138 4 0.01
139 322 0.98
140 3 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (138 bp):
ATCCTCATCATGTAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACACGTAGGAGCAGTGTC
ATCCTCAGATAACCAGACTTCCTCATCACGTAGGAACCGTGTTGTCTCCAAATTATCCCTAAATA
CGGTTGAC
Found at i:2087559 original size:278 final size:278
Alignment explanation
Indices: 2087033--2087606 Score: 639
Period size: 278 Copynumber: 2.1 Consensus size: 278
2087023 CATTTGAAAT
* * * * * * *
2087033 TGTTGTCTTCAAATTATCTCTAAGGAAGGCTAGATATCCTCGTCACGTAGAAACAATGTCGTCCA
1 TGTTGTCTCCAAATTATCCCTAAAGAAGGCTAGAAATCCTCATCACATAGAAACAATATCGTCCA
* * * *
2087098 TCGACCAGATCTCCTCAACACGTAGGAGCAGTGTCATCATTAGATAACCAAATTTCCACATCACG
66 CCGACCAGATCTCCTCAACACGTAGGAGCAGTGTCATCATCAGACAACCAAACTTCCACATCACG
* * * ** * * *
2087163 TAGGAACTGTGTTATATCCAAATTATCCCTAAATATGGTTTGACATCCTTATCATGTAGGAACAA
131 TAGGAACCGTGTTATATCCAAAGTATCCCTAAAGACAGCTAGACATCCTCATCATGTAGGAACAA
* * *
2087228 TGTCATTCACCGACCAGATCTCCTCAACACGCAGGAGTAGCGTCATCCTCAGATAACCAGACTTC
196 TGTCATCCACCGACCAGATCTCCTCAACACACAGGAGCAGCGTCATCCTCAGATAACCAGACTTC
* **
2087293 CTCATCACGTAGGAACCG
261 CTCATCACGTAGAAACAA
* * * *
2087311 TGTTGTCTCCAAATTATCCCTAAATACGGCTA-AAAGTCCTCATCACATAGGAACATTATCGTCC
1 TGTTGTCTCCAAATTATCCCTAAAGAAGGCTAGAAA-TCCTCATCACATAGAAACAATATCGTCC
* * * * * * *
2087375 ACCGACCAGATCTCCTCAACGCGTGGGAGTAG-GATCATCCTCAGACAATCAGACTTCCTCATCA
65 ACCGACCAGATCTCCTCAACACGTAGGAGCAGTG-TCATCATCAGACAACCAAACTTCCACATCA
* * ** * *
2087439 CGTAGGAACCGTGTTGTCTTGAAAGTATCCCTAAAGGCAGCTAGACGTCCTCATCATGTAGGAAC
129 CGTAGGAACCGTGTTATATCCAAAGTATCCCTAAAGACAGCTAGACATCCTCATCATGTAGGAAC
** *** * * * * *
2087504 AATGTTGTCCGTTGACCAGATCTCTTCAACGCATAGGAGCAGTGTCATTCTCAGATAACCAGACT
194 AATGTCATCCACCGACCAGATCTCCTCAACACACAGGAGCAGCGTCATCCTCAGATAACCAGACT
*
2087569 TTCTCATCACGTAGAAACAA
259 TCCTCATCACGTAGAAACAA
2087589 TGTTGTCTCCAAATTATC
1 TGTTGTCTCCAAATTATC
2087607 TCCAGATTGA
Statistics
Matches: 241, Mismatches: 53, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
277 3 0.01
278 238 0.99
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (278 bp):
TGTTGTCTCCAAATTATCCCTAAAGAAGGCTAGAAATCCTCATCACATAGAAACAATATCGTCCA
CCGACCAGATCTCCTCAACACGTAGGAGCAGTGTCATCATCAGACAACCAAACTTCCACATCACG
TAGGAACCGTGTTATATCCAAAGTATCCCTAAAGACAGCTAGACATCCTCATCATGTAGGAACAA
TGTCATCCACCGACCAGATCTCCTCAACACACAGGAGCAGCGTCATCCTCAGATAACCAGACTTC
CTCATCACGTAGAAACAA
Found at i:2087856 original size:6 final size:6
Alignment explanation
Indices: 2087847--2087886 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
2087837 TTAGGTTTTA
* * *
2087847 ATTAAT ATTATT ACTATT ATTAAT ATTAAT ATTAAT ATTA
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTA
2087887 TTTTATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (6 bp):
ATTAAT
Found at i:2087918 original size:29 final size:29
Alignment explanation
Indices: 2087886--2087951 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
2087876 TATTAATATT
2087886 ATTTTATTTTATTAAATAATTACTATTAC
1 ATTTTATTTTATTAAATAATTACTATTAC
2087915 ATTTTATTTTATTAAATAATTACTATTAC
1 ATTTTATTTTATTAAATAATTACTATTAC
2087944 A-TTTATTT
1 ATTTTATTT
2087952 GTAGGCCCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 7 0.19
29 30 0.81
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (29 bp):
ATTTTATTTTATTAAATAATTACTATTAC
Found at i:2090112 original size:22 final size:23
Alignment explanation
Indices: 2090068--2090127 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
2090058 AAAATTGCCA
*
2090068 ATTTTTCAAATAAATTCATAATT
1 ATTTTTTAAATAAATTCATAATT
*
2090091 GTTTTTTAAATAATATT-A-AATT
1 ATTTTTTAAATAA-ATTCATAATT
2090113 ATTTTTCTAAA-AAAT
1 ATTTTT-TAAATAAAT
2090128 GGTTATGACA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.06
22 11 0.34
23 16 0.50
24 3 0.09
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTTTTTAAATAAATTCATAATT
Found at i:2090242 original size:2 final size:2
Alignment explanation
Indices: 2090235--2090272 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2090225 TTATCCTTAT
2090235 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2090273 TTTTAACAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2090467 original size:17 final size:17
Alignment explanation
Indices: 2090447--2090479 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2090437 ATATTTATTT
2090447 ATAT-AAAATATAATATA
1 ATATGAAAA-ATAATATA
2090464 ATATGAAAAATAATAT
1 ATATGAAAAATAATAT
2090480 TGTGATATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATGAAAAATAATATA
Found at i:2091355 original size:29 final size:28
Alignment explanation
Indices: 2091322--2091394 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
2091312 AATTGAATTA
* *
2091322 AAATTAATATTTTAATACTTGAAAATGTT
1 AAATTAATATTTTAA-ACATGAAAATGCT
* * *
2091351 AAATTATTTTTTTGAAAGATGAAAATGCT
1 AAATTAATATTTT-AAACATGAAAATGCT
2091380 AAATTAATATTTTAA
1 AAATTAATATTTTAA
2091395 CTTTGGGGTG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 2 0.06
29 32 0.89
30 2 0.06
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (28 bp):
AAATTAATATTTTAAACATGAAAATGCT
Found at i:2091591 original size:24 final size:24
Alignment explanation
Indices: 2091564--2091636 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
2091554 CGTTCATTAA
2091564 CGTTCG-TGAACGTTCGGTTATGTT
1 CGTTCGAT-AACGTTCGGTTATGTT
* * *
2091588 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGATAACGTTCGGTTATGTT
* * * *
2091612 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGATAACGTTCGGTTATGTT
2091636 C
1 C
2091637 ATTCATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 43 0.98
25 1 0.02
ACGTcount: A:0.11, C:0.15, G:0.25, T:0.49
Consensus pattern (24 bp):
CGTTCGATAACGTTCGGTTATGTT
Found at i:2091593 original size:14 final size:14
Alignment explanation
Indices: 2091574--2091629 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
2091564 CGTTCGTGAA
2091574 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
2091588 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
2091602 CG-T---TTATGTT
1 CGTTCGGTTATGTT
2091612 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
2091626 CGTT
1 CGTT
2091630 TATGTTCATT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:2091646 original size:24 final size:23
Alignment explanation
Indices: 2091575--2091649 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
2091565 GTTCGTGAAC
*
2091575 GTTCGGTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
2091599 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
2091623 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
2091647 GTT
1 GTT
2091650 TAACCCAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:2091764 original size:7 final size:7
Alignment explanation
Indices: 2091752--2091799 Score: 71
Period size: 7 Copynumber: 7.0 Consensus size: 7
2091742 AATATATTAA
2091752 AAACCCT
1 AAACCCT
2091759 AAACCCT
1 AAACCCT
2091766 AAACCCT
1 AAACCCT
2091773 AAACCC-
1 AAACCCT
*
2091779 AAACTCT
1 AAACCCT
*
2091786 AAACCAT
1 AAACCCT
2091793 AAACCCT
1 AAACCCT
2091800 TAATCTAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
6 5 0.14
7 31 0.86
ACGTcount: A:0.46, C:0.40, G:0.00, T:0.15
Consensus pattern (7 bp):
AAACCCT
Found at i:2091787 original size:20 final size:21
Alignment explanation
Indices: 2091752--2091799 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
2091742 AATATATTAA
*
2091752 AAACCCTAAACCCTAAACCCT
1 AAACCCTAAACCCTAAACCAT
*
2091773 AAACCC-AAACTCTAAACCAT
1 AAACCCTAAACCCTAAACCAT
2091793 AAACCCT
1 AAACCCT
2091800 TAATCTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.46, C:0.40, G:0.00, T:0.15
Consensus pattern (21 bp):
AAACCCTAAACCCTAAACCAT
Found at i:2093355 original size:16 final size:16
Alignment explanation
Indices: 2093334--2093390 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
2093324 CCAACTTTTA
2093334 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
2093350 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
2093366 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
2093382 T-TT-ATTTAT
1 TGTTCATTTAT
2093391 TAAATGAACG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.13
15 2 0.05
16 32 0.82
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:2093662 original size:28 final size:28
Alignment explanation
Indices: 2093622--2093692 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 28
2093612 ATTAAAATTT
** * *
2093622 GATATGGCCATTAGTGGGCGTAGACCAG
1 GATATGGGAATTAGTGGGAGCAGACCAG
*
2093650 GATATGGGAATTAAGTGGGAGCAGACCAT
1 GATATGGGAATT-AGTGGGAGCAGACCAG
*
2093679 GATATGGGTATTAG
1 GATATGGGAATTAG
2093693 GTGTGCTAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 12 0.33
29 24 0.67
ACGTcount: A:0.30, C:0.11, G:0.35, T:0.24
Consensus pattern (28 bp):
GATATGGGAATTAGTGGGAGCAGACCAG
Found at i:2093676 original size:29 final size:29
Alignment explanation
Indices: 2093634--2093691 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
2093624 TATGGCCATT
* *
2093634 AGTGGGCGTAGACCAGGATATGGGAATTA
1 AGTGGGAGCAGACCAGGATATGGGAATTA
* *
2093663 AGTGGGAGCAGACCATGATATGGGTATTA
1 AGTGGGAGCAGACCAGGATATGGGAATTA
2093692 GGTGTGCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.31, C:0.10, G:0.36, T:0.22
Consensus pattern (29 bp):
AGTGGGAGCAGACCAGGATATGGGAATTA
Found at i:2097590 original size:20 final size:20
Alignment explanation
Indices: 2097565--2097605 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2097555 GGGTAATTAA
*
2097565 TTATGCTTGCAATAATAAAT
1 TTATGCTTGCAACAATAAAT
2097585 TTATGCTTGCAACAATAAAT
1 TTATGCTTGCAACAATAAAT
2097605 T
1 T
2097606 ATACTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (20 bp):
TTATGCTTGCAACAATAAAT
Found at i:2099870 original size:55 final size:55
Alignment explanation
Indices: 2099793--2100194 Score: 621
Period size: 55 Copynumber: 7.3 Consensus size: 55
2099783 CATTAAGCTA
* * *
2099793 CACATATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTTCGTGGGTTTG
1 CACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTG
* * * * *
2099848 CACACATAGTGCCTTTATGGTTATTCATTAAGTCATGATGAATTTCGTGGATTTT
1 CACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTG
2099903 CACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTAT-GTGGATTTG
1 CACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATT-TCGTGGATTTG
*
2099958 CACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAA-TTCTGTGGATTTG
1 CACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTC-GTGGATTTG
*
2100013 CACACATAGTACCTGTACGGTTATTCATCAACTCATGATGAA-TTCTGTGGATTTG
1 CACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTC-GTGGATTTG
* * *
2100068 CACACATAGTGCATGTACGGTTATTCATCAACTAATGATGAATTTTGTGGATTTG
1 CACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTG
* *
2100123 CACACATAGTTCCTGTACGGTTATTCATCAACTCATGATGAATTTCATGGATTTG
1 CACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTG
2100178 CACACATAGTGCCTGTA
1 CACACATAGTGCCTGTA
2100195 GTACACATAG
Statistics
Matches: 318, Mismatches: 25, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
53 1 0.00
54 1 0.00
55 313 0.98
56 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (55 bp):
CACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTG
Found at i:2107340 original size:27 final size:28
Alignment explanation
Indices: 2107276--2107340 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
2107266 TTAGATCTCC
*
2107276 CATATTTCATCATTCTCTTAGTTTTGAT
1 CATATTTAATCATTCTCTTAGTTTTGAT
*
2107304 CACATTTAATCATTCT-TTAAGTTTT-AT
1 CATATTTAATCATTCTCTT-AGTTTTGAT
2107331 CATATTTAAT
1 CATATTTAAT
2107341 GCTTCAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 13 0.39
28 20 0.61
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.52
Consensus pattern (28 bp):
CATATTTAATCATTCTCTTAGTTTTGAT
Found at i:2113030 original size:20 final size:22
Alignment explanation
Indices: 2113005--2113044 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2112995 GTATAAGACC
2113005 TATGAGCT-A-AAATGAATGCA
1 TATGAGCTAACAAATGAATGCA
2113025 TATGAGCTAACAAATGAATG
1 TATGAGCTAACAAATGAATG
2113045 ATTAAGCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (22 bp):
TATGAGCTAACAAATGAATGCA
Found at i:2121607 original size:124 final size:124
Alignment explanation
Indices: 2121309--2121654 Score: 344
Period size: 124 Copynumber: 2.8 Consensus size: 124
2121299 CTATTAATCC
* * * * *
2121309 GGTGATGATCTCACTCTTTCTCC-TGAAAGACGTTGAGTCGTGGAATGATCTTGCTCCTTCTTTT
1 GGTGATGATCTCACTATTT-TCCTTGAAAGACGTAGAGTCGTGGAATGATCTTACTCCTTCATCT
* * * * *
2121373 GAAGGA-CTCTAAGTCATAATTTGGGGTGAT-CACTCCTTTTGTTGAAGGATGCTGAATCT
65 GAAGGATC-CTAAGTCGTAATTCGAGGTGATCCACTCCTTTTGCTGAAGGATGCTGAATAT
* * * * * ** * *
2121432 AGTGACGATCTTACTATTTT-ATCTAAAAGACACAGAGTTGTGGAACGATCTTACTCCTTCATCT
1 GGTGATGATCTCACTATTTTCCT-TGAAAGACGTAGAGTCGTGGAATGATCTTACTCCTTCATCT
* * *
2121496 GAAGGATCCTAAGTCGTAATTCGAGGTGATCCAGTCTTTTTGCT-ATAGGATGTTGAATAT
65 GAAGGATCCTAAGTCGTAATTCGAGGTGATCCACTCCTTTTGCTGA-AGGATGCTGAATAT
* * * *
2121556 GGTGATGATCTCACT-TTTTCCTTTGAAAGACGTGGAGTCATGGAATGATCTTACTCTTTCCTCT
1 GGTGATGATCTCACTATTTTCC-TTGAAAGACGTAGAGTCGTGGAATGATCTTACTCCTTCATCT
* * *
2121620 GAAGGATGCTAAGTCGTGATTCTAGGTGATCCACT
65 GAAGGATCCTAAGTCGTAATTCGAGGTGATCCACT
2121655 ATTGAGATGG
Statistics
Matches: 177, Mismatches: 39, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
122 1 0.01
123 77 0.44
124 98 0.55
125 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (124 bp):
GGTGATGATCTCACTATTTTCCTTGAAAGACGTAGAGTCGTGGAATGATCTTACTCCTTCATCTG
AAGGATCCTAAGTCGTAATTCGAGGTGATCCACTCCTTTTGCTGAAGGATGCTGAATAT
Found at i:2122689 original size:19 final size:18
Alignment explanation
Indices: 2122665--2122718 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
2122655 TGAACCCTCC
2122665 TCATTTTTTTCTTCTTTTT
1 TCATTTTTTT-TTCTTTTT
*
2122684 TCATTTTTATTATCTTTTT
1 TCATTTTT-TTTTCTTTTT
*
2122703 TCTTTCTTTTTTTCTT
1 TCATT-TTTTTTTCTT
2122719 CATGTGTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 25 0.83
20 5 0.17
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (18 bp):
TCATTTTTTTTTCTTTTT
Found at i:2130264 original size:15 final size:15
Alignment explanation
Indices: 2130244--2130275 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2130234 TAATTTGGTG
2130244 ATTAAATGAAATAAA
1 ATTAAATGAAATAAA
2130259 ATTAAATGAAATAAA
1 ATTAAATGAAATAAA
2130274 AT
1 AT
2130276 CAGCCTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (15 bp):
ATTAAATGAAATAAA
Found at i:2131063 original size:26 final size:27
Alignment explanation
Indices: 2131015--2131065 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2131005 CAATTTAATG
2131015 TCATGCAACTAATAAACTCATGCAAAT
1 TCATGCAACTAATAAACTCATGCAAAT
*
2131042 TCATGCTAAGTAA-AAA-TCATGCAA
1 TCATGC-AACTAATAAACTCATGCAA
2131066 GGAATGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 9 0.41
28 5 0.23
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (27 bp):
TCATGCAACTAATAAACTCATGCAAAT
Found at i:2135387 original size:92 final size:92
Alignment explanation
Indices: 2135277--2135469 Score: 359
Period size: 92 Copynumber: 2.1 Consensus size: 92
2135267 CGAATAAATT
2135277 AAAAAGTTATCGTAAAAAAATTACAATAACATAAACTAAAATAAAATTTTAATATAATAAATAAA
1 AAAAA-TTATCGTAAAAAAATTACAATAACATAAACTAAAATAAAATTTTAATATAATAAATAAA
2135342 TAACCTAAAATAAATAAACATAGATTTC
65 TAACCTAAAATAAATAAACATAGATTTC
* *
2135370 AAAAATTATCGTAAAAAAATTACAATAACATAAACTAAACTAAAGTTTTAATATAATAAATAAAT
1 AAAAATTATCGTAAAAAAATTACAATAACATAAACTAAAATAAAATTTTAATATAATAAATAAAT
2135435 AACCTAAAATAAATAAACATAGATTTC
66 AACCTAAAATAAATAAACATAGATTTC
2135462 AAAAATTA
1 AAAAATTA
2135470 CATGTTTAAT
Statistics
Matches: 98, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
92 93 0.95
93 5 0.05
ACGTcount: A:0.60, C:0.09, G:0.03, T:0.28
Consensus pattern (92 bp):
AAAAATTATCGTAAAAAAATTACAATAACATAAACTAAAATAAAATTTTAATATAATAAATAAAT
AACCTAAAATAAATAAACATAGATTTC
Found at i:2135914 original size:18 final size:17
Alignment explanation
Indices: 2135888--2135959 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 17
2135878 TTCGTACCGC
2135888 TTCAAATAAATAAATTA
1 TTCAAATAAATAAATTA
2135905 TTCGAAATAAATAAATAAATTA
1 TTC-----AAATAAATAAATTA
*
2135927 TTCTAAATAAATAAATAA
1 TTC-AAATAAATAAATTA
2135945 TTCAAAGTAAA-AAAT
1 TTCAAA-TAAATAAAT
2135960 AGAAAAAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
17 10 0.21
18 21 0.44
22 17 0.35
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.32
Consensus pattern (17 bp):
TTCAAATAAATAAATTA
Found at i:2135919 original size:22 final size:22
Alignment explanation
Indices: 2135891--2135944 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
2135881 GTACCGCTTC
2135891 AAATAAATAAATTATTCGAAAT
1 AAATAAATAAATTATTCGAAAT
*
2135913 AAATAAATAAATTATTCTAAAT
1 AAATAAATAAATTATTCGAAAT
2135935 AAATAAATAA
1 AAATAAATAA
2135945 TTCAAAGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATAAATAAATTATTCGAAAT
Found at i:2140170 original size:3 final size:3
Alignment explanation
Indices: 2140162--2140191 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2140152 CCAGATGTCC
*
2140162 TCT TCT TCT TCT TCT TCT TAT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2140192 ATTAAAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:2141373 original size:122 final size:123
Alignment explanation
Indices: 2141170--2141394 Score: 407
Period size: 122 Copynumber: 1.8 Consensus size: 123
2141160 GAAGTTGCTT
* *
2141170 AAGTGTTTTCTATTTTGTATTTATACACGTAGAGGGTCTGCAAACTGATGCATATTAGATTAAAT
1 AAGTCTTTTCTATTTTGTATTTATACACGTAGAGGGTCTGCAAACTGAAGCATATTAGATTAAAT
**
2141235 ATTCAAAAAATTGTCTAAAGCTTTAAGCAGCAAACTTAAAGAAGAAGTTGCTTTAATA
66 ATTCAAAAAAAGGTCTAAAGCTTTAAGCAGCAAACTTAAAGAAGAAGTTGCTTTAATA
2141293 AAGTCTTTTCTATTTTGTATTTATACACGTAGA-GGTCTGCAAACTGAAGCATATTAGATTAAAT
1 AAGTCTTTTCTATTTTGTATTTATACACGTAGAGGGTCTGCAAACTGAAGCATATTAGATTAAAT
2141357 ATTCAAAAAAAGGTCTAAAGCTTTAAGCAGCAAACTTA
66 ATTCAAAAAAAGGTCTAAAGCTTTAAGCAGCAAACTTA
2141395 TCTCAAGGGC
Statistics
Matches: 98, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
122 66 0.67
123 32 0.33
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (123 bp):
AAGTCTTTTCTATTTTGTATTTATACACGTAGAGGGTCTGCAAACTGAAGCATATTAGATTAAAT
ATTCAAAAAAAGGTCTAAAGCTTTAAGCAGCAAACTTAAAGAAGAAGTTGCTTTAATA
Found at i:2143602 original size:43 final size:42
Alignment explanation
Indices: 2143554--2143663 Score: 112
Period size: 44 Copynumber: 2.5 Consensus size: 42
2143544 TGCTCCAATA
* * *
2143554 ATATAAAGAAATAGTTAAAATAAAAATATAAATCGGATTCAGG
1 ATATAAA-AAATAGTTAAAATAAAAAGATAAATCAGATTCAAG
*** * *
2143597 ATATAAATTTTTTTGTTAAAATAACAAGATAAATCAGATTCAAG
1 ATATAAA--AAATAGTTAAAATAAAAAGATAAATCAGATTCAAG
2143641 ATATGAAAAAATAGTTAAAATAA
1 ATAT-AAAAAATAGTTAAAATAA
2143664 CAATTCAAAG
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
43 18 0.35
44 31 0.60
45 3 0.06
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.30
Consensus pattern (42 bp):
ATATAAAAAATAGTTAAAATAAAAAGATAAATCAGATTCAAG
Found at i:2144268 original size:31 final size:31
Alignment explanation
Indices: 2144197--2144260 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
2144187 AAAAACATAA
2144197 ATATAATCACTTTCATTTTTATTTAATTAAG
1 ATATAATCACTTTCATTTTTATTTAATTAAG
*
2144228 ATATAATCACTTTCGTTTTTATTTAATTAAG
1 ATATAATCACTTTCATTTTTATTTAATTAAG
2144259 AT
1 AT
2144261 TTGATCACCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (31 bp):
ATATAATCACTTTCATTTTTATTTAATTAAG
Found at i:2145236 original size:31 final size:31
Alignment explanation
Indices: 2145193--2145267 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
2145183 TTAACTCGAG
* *
2145193 GTGACTACATCTTAATTAAATAAAAACGAAA
1 GTGACTATATCTTAATTAAATAAAAACAAAA
*
2145224 GTGACTATATCTTTATTAAATAAAAACAAAA
1 GTGACTATATCTTAATTAAATAAAAACAAAA
* *
2145255 ATGACCATATCTT
1 GTGACTATATCTT
2145268 CTTCTTCTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.31
Consensus pattern (31 bp):
GTGACTATATCTTAATTAAATAAAAACAAAA
Found at i:2146468 original size:14 final size:14
Alignment explanation
Indices: 2146425--2146483 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 14
2146415 TAAATAAAAT
2146425 TAAACATAAAAACTA
1 TAAACATAAAAAC-A
* *
2146440 GATAACAT-TAAACA
1 TA-AACATAAAAACA
*
2146454 TAAATATAAAAACA
1 TAAACATAAAAACA
*
2146468 T-AACATGAAAACA
1 TAAACATAAAAACA
2146481 TAA
1 TAA
2146484 TATTCAAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
13 15 0.44
14 9 0.26
15 5 0.15
16 5 0.15
ACGTcount: A:0.64, C:0.12, G:0.03, T:0.20
Consensus pattern (14 bp):
TAAACATAAAAACA
Found at i:2146499 original size:27 final size:26
Alignment explanation
Indices: 2146469--2146570 Score: 80
Period size: 27 Copynumber: 3.9 Consensus size: 26
2146459 ATAAAAACAT
*
2146469 AACATGAAAACATAATATTCAAATAAA
1 AACATAAAAACATAATATT-AAATAAA
** * ***
2146496 AACATAAAATTA-AACATTAAAGCTA
1 AACATAAAAACATAATATTAAATAAA
* * *
2146521 AATATAAAAATATAATATTTAATTAAA
1 AACATAAAAACATAATA-TTAAATAAA
*
2146548 AACATAAAAACATAATATAAAAT
1 AACATAAAAACATAATATTAAAT
2146571 CTAACTATTT
Statistics
Matches: 55, Mismatches: 18, Indels: 5
0.71 0.23 0.06
Matches are distributed among these distances:
25 14 0.25
26 12 0.22
27 29 0.53
ACGTcount: A:0.64, C:0.08, G:0.02, T:0.26
Consensus pattern (26 bp):
AACATAAAAACATAATATTAAATAAA
Found at i:2153035 original size:79 final size:79
Alignment explanation
Indices: 2152901--2153153 Score: 371
Period size: 79 Copynumber: 3.2 Consensus size: 79
2152891 CTTTTATATT
* * * * ** *
2152901 GATAATGCACCCATATGCATTTCAACTTTGGCATCCTTTCATGCCAATAATGCACCCATATGCAT
1 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
*
2152966 TATTCTGATATGCC
66 TATTCTGTTATGCC
* * *
2152980 GATAATGTACCCATATACATATCAGCTAAGGAATCCTTTCATGCCGCTAAAGCACCCATATGCAT
1 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
*
2153045 TATTCTGTTATGCT
66 TATTCTGTTATGCC
2153059 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
1 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
* *
2153124 TATTCTTTTATGTC
66 TATTCTGTTATGCC
*
2153138 GATAATATACCCATAT
1 GATAATGTACCCATAT
2153154 GCATTATTCT
Statistics
Matches: 155, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 155 1.00
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (79 bp):
GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
TATTCTGTTATGCC
Found at i:2153155 original size:34 final size:34
Alignment explanation
Indices: 2153112--2153187 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 34
2153102 CCACTAATGC
*
2153112 ACCCATATGCATTATTCTTTTATGTCGATAATAT
1 ACCCATATGCATTATTCTTTTATGCCGATAATAT
*
2153146 ACCCATATGCATTATTCTTTTATGCCGATAATGT
1 ACCCATATGCATTATTCTTTTATGCCGATAATAT
2153180 ACCCATAT
1 ACCCATAT
2153188 ACATGTCAGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (34 bp):
ACCCATATGCATTATTCTTTTATGCCGATAATAT
Found at i:2153169 original size:113 final size:113
Alignment explanation
Indices: 2153033--2153266 Score: 423
Period size: 113 Copynumber: 2.1 Consensus size: 113
2153023 CCGCTAAAGC
*
2153033 ACCCATATGCATTATTCTGTTATGCTGATAATGTACCCATATACATATCAGCTAAGGCATCCTTT
1 ACCCATATGCATTATTCTGTTATGCCGATAATGTACCCATATACATATCAGCTAAGGCATCCTTT
*
2153098 CATGCCACTAATGCACCCATATGCATTATTCTTTTATGTCGATAATAT
66 CATGCCACTAATGCACCCATATGCATTATTCTTTTATGCCGATAATAT
* *
2153146 ACCCATATGCATTATTCTTTTATGCCGATAATGTACCCATATACATGTCAGCTAAGGCATCCTTT
1 ACCCATATGCATTATTCTGTTATGCCGATAATGTACCCATATACATATCAGCTAAGGCATCCTTT
*
2153211 CATGCCACTAATGCACCCATATGCATTATTCTTTTATGCCGATAATGT
66 CATGCCACTAATGCACCCATATGCATTATTCTTTTATGCCGATAATAT
2153259 ACCCATAT
1 ACCCATAT
2153267 ACATATCAGC
Statistics
Matches: 116, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 116 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (113 bp):
ACCCATATGCATTATTCTGTTATGCCGATAATGTACCCATATACATATCAGCTAAGGCATCCTTT
CATGCCACTAATGCACCCATATGCATTATTCTTTTATGCCGATAATAT
Found at i:2153223 original size:45 final size:44
Alignment explanation
Indices: 2153174--2153316 Score: 146
Period size: 45 Copynumber: 3.4 Consensus size: 44
2153164 TTTATGCCGA
2153174 TAATGTACCCATATACATGTCAGCTAAGGCATCCTTTCATGCCAC
1 TAATGTACCCATATACAT-TCAGCTAAGGCATCCTTTCATGCCAC
* * *
2153219 TAATGCACCCATATGCATT-A--T------T-CTTTTATGCCGA-
1 TAATGTACCCATATACATTCAGCTAAGGCATCCTTTCATGCC-AC
2153253 TAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCAC
1 TAATGTACCCATATACAT-TCAGCTAAGGCATCCTTTCATGCCAC
*
2153298 TAATGTACCCATATGCATT
1 TAATGTACCCATATACATT
2153317 ATTCTTTTAT
Statistics
Matches: 78, Mismatches: 7, Indels: 27
0.70 0.06 0.24
Matches are distributed among these distances:
34 25 0.32
35 3 0.04
36 1 0.01
38 1 0.01
41 1 0.01
43 1 0.01
44 4 0.05
45 42 0.54
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (44 bp):
TAATGTACCCATATACATTCAGCTAAGGCATCCTTTCATGCCAC
Found at i:2153277 original size:79 final size:79
Alignment explanation
Indices: 2153146--2153326 Score: 344
Period size: 79 Copynumber: 2.3 Consensus size: 79
2153136 TCGATAATAT
*
2153146 ACCCATATGCATTATTCTTTTATGCCGATAATGTACCCATATACATGTCAGCTAAGGCATCCTTT
1 ACCCATATGCATTATTCTTTTATGCCGATAATGTACCCATATACATATCAGCTAAGGCATCCTTT
2153211 CATGCCACTAATGC
66 CATGCCACTAATGC
2153225 ACCCATATGCATTATTCTTTTATGCCGATAATGTACCCATATACATATCAGCTAAGGCATCCTTT
1 ACCCATATGCATTATTCTTTTATGCCGATAATGTACCCATATACATATCAGCTAAGGCATCCTTT
*
2153290 CATGCCACTAATGT
66 CATGCCACTAATGC
2153304 ACCCATATGCATTATTCTTTTAT
1 ACCCATATGCATTATTCTTTTAT
2153327 TCATTAGTTT
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 100 1.00
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.35
Consensus pattern (79 bp):
ACCCATATGCATTATTCTTTTATGCCGATAATGTACCCATATACATATCAGCTAAGGCATCCTTT
CATGCCACTAATGC
Found at i:2153281 original size:192 final size:192
Alignment explanation
Indices: 2152954--2153326 Score: 665
Period size: 192 Copynumber: 1.9 Consensus size: 192
2152944 CCAATAATGC
2152954 ACCCATATGCATTATTCTGATATGCCGATAATGTACCCATATACATATCAGCTAAGGAATCCTTT
1 ACCCATATGCATTATTCTGATATGCCGATAATGTACCCATATACATATCAGCTAAGGAATCCTTT
* *
2153019 CATGCCGCTAAAGCACCCATATGCATTATTCTGTTATGCTGATAATGTACCCATATACATATCAG
66 CATGCCACTAAAGCACCCATATGCATTATTCTGTTATGCCGATAATGTACCCATATACATATCAG
2153084 CTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCATTATTCTTTTATGTCGATAATAT
131 CTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCATTATTCTTTTATGTCGATAATAT
** * *
2153146 ACCCATATGCATTATTCTTTTATGCCGATAATGTACCCATATACATGTCAGCTAAGGCATCCTTT
1 ACCCATATGCATTATTCTGATATGCCGATAATGTACCCATATACATATCAGCTAAGGAATCCTTT
* *
2153211 CATGCCACTAATGCACCCATATGCATTATTCTTTTATGCCGATAATGTACCCATATACATATCAG
66 CATGCCACTAAAGCACCCATATGCATTATTCTGTTATGCCGATAATGTACCCATATACATATCAG
*
2153276 CTAAGGCATCCTTTCATGCCACTAATGTACCCATATGCATTATTCTTTTAT
131 CTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCATTATTCTTTTAT
2153327 TCATTAGTTT
Statistics
Matches: 172, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
192 172 1.00
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (192 bp):
ACCCATATGCATTATTCTGATATGCCGATAATGTACCCATATACATATCAGCTAAGGAATCCTTT
CATGCCACTAAAGCACCCATATGCATTATTCTGTTATGCCGATAATGTACCCATATACATATCAG
CTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCATTATTCTTTTATGTCGATAATAT
Found at i:2153991 original size:31 final size:31
Alignment explanation
Indices: 2153950--2154008 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2153940 TGACTTAAGG
* * **
2153950 AAGATGATAAGGTTGAGGTTTCTTGGTTGAA
1 AAGATAATAAGGATGAGGTGGCTTGGTTGAA
2153981 AAGATAATAAGGATGAGGTGGCTTGGTT
1 AAGATAATAAGGATGAGGTGGCTTGGTT
2154009 TAATGGTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.32
Consensus pattern (31 bp):
AAGATAATAAGGATGAGGTGGCTTGGTTGAA
Found at i:2154926 original size:28 final size:29
Alignment explanation
Indices: 2154804--2154934 Score: 174
Period size: 29 Copynumber: 4.6 Consensus size: 29
2154794 ACCCGACCCA
*
2154804 GTGATATTTTAGTAATTATTTTGAAATCG
1 GTGATATTTTAGTAATTATTTTGAAATAG
* *
2154833 ATGATATTTTAGTAATTATTTTGAAATCG
1 GTGATATTTTAGTAATTATTTTGAAATAG
* *
2154862 GTGATATTTTGGTAATTATTTTGAAAAAG
1 GTGATATTTTAGTAATTATTTTGAAATAG
* *
2154891 GTGATATTTTGGTAATTATTTTTAAA-AG
1 GTGATATTTTAGTAATTATTTTGAAATAG
* *
2154919 GTTATATTTTCGTAAT
1 GTGATATTTTAGTAAT
2154935 AGTTGACTGT
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
28 16 0.17
29 78 0.83
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (29 bp):
GTGATATTTTAGTAATTATTTTGAAATAG
Found at i:2159889 original size:14 final size:14
Alignment explanation
Indices: 2159870--2159896 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2159860 CTTCTAAAGG
2159870 ATTATGATTGTGTC
1 ATTATGATTGTGTC
2159884 ATTATGATTGTGT
1 ATTATGATTGTGT
2159897 GATTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.22, T:0.52
Consensus pattern (14 bp):
ATTATGATTGTGTC
Found at i:2162354 original size:29 final size:29
Alignment explanation
Indices: 2162316--2162503 Score: 252
Period size: 29 Copynumber: 6.5 Consensus size: 29
2162306 CCCGACCCGA
* * *
2162316 TGATATTTTAGTAATTATTTTGAAACCGA
1 TGATATTTTGGTAATTATTTTGAAAACGG
* * *
2162345 TGATAGTTTAGTAATTATTTTGAAACCGG
1 TGATATTTTGGTAATTATTTTGAAAACGG
*
2162374 TGATATTTTGGTAATTATTTTGAAAAAGG
1 TGATATTTTGGTAATTATTTTGAAAACGG
**
2162403 TGATATTTTGGTAATTATTTTGAAAAATG
1 TGATATTTTGGTAATTATTTTGAAAACGG
*
2162432 TGATATTTTGGTAATTATTTTGAAAAAGG
1 TGATATTTTGGTAATTATTTTGAAAACGG
* *
2162461 TGATATTTTTGTAATTATTTTGAAAA-AG
1 TGATATTTTGGTAATTATTTTGAAAACGG
*
2162489 TGATATTTTCGTAAT
1 TGATATTTTGGTAAT
2162504 AGTTGACTGT
Statistics
Matches: 148, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
28 15 0.10
29 133 0.90
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.46
Consensus pattern (29 bp):
TGATATTTTGGTAATTATTTTGAAAACGG
Found at i:2171756 original size:482 final size:482
Alignment explanation
Indices: 2170851--2171821 Score: 1942
Period size: 482 Copynumber: 2.0 Consensus size: 482
2170841 TGCTCAATTA
2170851 TGAATGTTCAATACTGTAAATTAATGTTTAAATTTTAAATTTGAAGTTAGAATATTTTTTGGATC
1 TGAATGTTCAATACTGTAAATTAATGTTTAAATTTTAAATTTGAAGTTAGAATATTTTTTGGATC
2170916 AAAATGCAAGTGTTGGTGTTAATTCAAATGGATTAGGAAATTAGGGATTGGAATGCAAGTTTTCA
66 AAAATGCAAGTGTTGGTGTTAATTCAAATGGATTAGGAAATTAGGGATTGGAATGCAAGTTTTCA
2170981 AATGTGAATTTACTTGATTGAATATATTATTACAATGCTAGAAATTTTGGTATTGGGTTTAAATT
131 AATGTGAATTTACTTGATTGAATATATTATTACAATGCTAGAAATTTTGGTATTGGGTTTAAATT
2171046 GAGTAAAAATGGTGAAGGACCATTTTGAATAGATTTGAAACGTTGGTATGAATTCTAAAAGAATT
196 GAGTAAAAATGGTGAAGGACCATTTTGAATAGATTTGAAACGTTGGTATGAATTCTAAAAGAATT
2171111 CATAAATAGTGACTAAATTGTAAAGTTTATGAAATTGAGTGGCTTGGTGAGAAATTTGAATATTT
261 CATAAATAGTGACTAAATTGTAAAGTTTATGAAATTGAGTGGCTTGGTGAGAAATTTGAATATTT
2171176 ATGGGATTGAAGTTTTATTTTGGAAATGTTGAAGTTATTATGGAATAGTGAAGTGACTTTATCTC
326 ATGGGATTGAAGTTTTATTTTGGAAATGTTGAAGTTATTATGGAATAGTGAAGTGACTTTATCTC
2171241 GAATTATTATTGAATTATAGTTTATGGATTTTATCGTTAGATTTTGATTATGTTAGTATAATACT
391 GAATTATTATTGAATTATAGTTTATGGATTTTATCGTTAGATTTTGATTATGTTAGTATAATACT
2171306 AACATATGCTTTGAAACGTATGTGTTG
456 AACATATGCTTTGAAACGTATGTGTTG
2171333 TGAATGTTCAATACTGTAAATTAATGTTTAAATTTTAAATTTGAAGTTAGAATATTTTTTGGATC
1 TGAATGTTCAATACTGTAAATTAATGTTTAAATTTTAAATTTGAAGTTAGAATATTTTTTGGATC
2171398 AAAATGCAAGTGTTGGTGTTAATTCAAATGGATTAGGAAATTAGGGATTGGAATGCAAGTTTTCA
66 AAAATGCAAGTGTTGGTGTTAATTCAAATGGATTAGGAAATTAGGGATTGGAATGCAAGTTTTCA
2171463 AATGTGAATTTACTTGATTGAATATATTATTACAATGCTAGAAATTTTGGTATTGGGTTTAAATT
131 AATGTGAATTTACTTGATTGAATATATTATTACAATGCTAGAAATTTTGGTATTGGGTTTAAATT
2171528 GAGTAAAAATGGTGAAGGACCATTTTGAATAGATTTGAAACGTTGGTATGAATTCTAAAAGAATT
196 GAGTAAAAATGGTGAAGGACCATTTTGAATAGATTTGAAACGTTGGTATGAATTCTAAAAGAATT
2171593 CATAAATAGTGACTAAATTGTAAAGTTTATGAAATTGAGTGGCTTGGTGAGAAATTTGAATATTT
261 CATAAATAGTGACTAAATTGTAAAGTTTATGAAATTGAGTGGCTTGGTGAGAAATTTGAATATTT
2171658 ATGGGATTGAAGTTTTATTTTGGAAATGTTGAAGTTATTATGGAATAGTGAAGTGACTTTATCTC
326 ATGGGATTGAAGTTTTATTTTGGAAATGTTGAAGTTATTATGGAATAGTGAAGTGACTTTATCTC
2171723 GAATTATTATTGAATTATAGTTTATGGATTTTATCGTTAGATTTTGATTATGTTAGTATAATACT
391 GAATTATTATTGAATTATAGTTTATGGATTTTATCGTTAGATTTTGATTATGTTAGTATAATACT
2171788 AACATATGCTTTGAAACGTATGTGTTG
456 AACATATGCTTTGAAACGTATGTGTTG
2171815 TGAATGT
1 TGAATGT
2171822 GATTTCTATT
Statistics
Matches: 489, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
482 489 1.00
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.40
Consensus pattern (482 bp):
TGAATGTTCAATACTGTAAATTAATGTTTAAATTTTAAATTTGAAGTTAGAATATTTTTTGGATC
AAAATGCAAGTGTTGGTGTTAATTCAAATGGATTAGGAAATTAGGGATTGGAATGCAAGTTTTCA
AATGTGAATTTACTTGATTGAATATATTATTACAATGCTAGAAATTTTGGTATTGGGTTTAAATT
GAGTAAAAATGGTGAAGGACCATTTTGAATAGATTTGAAACGTTGGTATGAATTCTAAAAGAATT
CATAAATAGTGACTAAATTGTAAAGTTTATGAAATTGAGTGGCTTGGTGAGAAATTTGAATATTT
ATGGGATTGAAGTTTTATTTTGGAAATGTTGAAGTTATTATGGAATAGTGAAGTGACTTTATCTC
GAATTATTATTGAATTATAGTTTATGGATTTTATCGTTAGATTTTGATTATGTTAGTATAATACT
AACATATGCTTTGAAACGTATGTGTTG
Found at i:2178709 original size:45 final size:45
Alignment explanation
Indices: 2178645--2178734 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
2178635 GAAGAAAAAA
*
2178645 TTCTTGAAATTTTTAATAAAAATCTCTTAACACTTGGCTTATAAT
1 TTCTTGAAATTTCTAATAAAAATCTCTTAACACTTGGCTTATAAT
* *
2178690 TTCTTGAAATTTCTAATAAAAATCTCTTAACTCTTGGTTTATAAT
1 TTCTTGAAATTTCTAATAAAAATCTCTTAACACTTGGCTTATAAT
2178735 CTATAATTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.34, C:0.13, G:0.07, T:0.46
Consensus pattern (45 bp):
TTCTTGAAATTTCTAATAAAAATCTCTTAACACTTGGCTTATAAT
Found at i:2178717 original size:23 final size:23
Alignment explanation
Indices: 2178640--2178717 Score: 58
Period size: 22 Copynumber: 3.5 Consensus size: 23
2178630 AAGATGAAGA
*
2178640 AAAAAT-TCTTGAAATTTTTAAT
1 AAAAATCTCTTGAAATTTCTAAT
*
2178662 AAAAATCTCTT-AACACTTGGCT--T
1 AAAAATCTCTTGAA-A-TT-TCTAAT
* *
2178685 -ATAATTTCTTGAAATTTCTAAT
1 AAAAATCTCTTGAAATTTCTAAT
2178707 AAAAATCTCTT
1 AAAAATCTCTT
2178718 AACTCTTGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 15
0.65 0.11 0.24
Matches are distributed among these distances:
20 2 0.05
21 2 0.05
22 18 0.44
23 16 0.39
24 2 0.05
25 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.42
Consensus pattern (23 bp):
AAAAATCTCTTGAAATTTCTAAT
Found at i:2179275 original size:29 final size:31
Alignment explanation
Indices: 2179216--2179277 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 31
2179206 TTTAGATCCA
* *
2179216 AAACTTTTGCAAAGTTTATACTTTGGCCACT
1 AAACTTTTGCAAAATTTATACTTTGACCACT
* *
2179247 AAAC-TTT-CAAAATTTATATTTTGATCACT
1 AAACTTTTGCAAAATTTATACTTTGACCACT
2179276 AA
1 AA
2179278 CCAAAATTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 20 0.74
30 3 0.11
31 4 0.15
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.40
Consensus pattern (31 bp):
AAACTTTTGCAAAATTTATACTTTGACCACT
Found at i:2181416 original size:4 final size:4
Alignment explanation
Indices: 2181407--2181598 Score: 109
Period size: 4 Copynumber: 44.8 Consensus size: 4
2181397 ATACCCCTTC
**
2181407 AAAT AAAT AAAT AAAAT AAAAT AAAT AACCG AACA- AAAT AAAT AAAT
1 AAAT AAAT AAAT -AAAT -AAAT AAAT AA-AT AA-AT AAAT AAAT AAAT
**
2181454 AGAA- AAAT AAAT AAAAT AAATT ACCAAT AAAAT AAAAT AAAT AAAT AACC
1 A-AAT AAAT AAAT -AAAT AAA-T A--AAT -AAAT -AAAT AAAT AAAT AAAT
* * * ** * *
2181504 AACT AAAT AAAAT TAAT AAAAT AAAT TACC AAAT AAAT AACT GAAT AAAT
1 AAAT AAAT -AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * *
2181554 AAAAT AAAT AAAC AATT GAAT AAAAT AAAT AAAT AAAT AAAT AAA
1 -AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAA
2181599 ATACCTCCAG
Statistics
Matches: 149, Mismatches: 25, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
3 3 0.02
4 100 0.67
5 42 0.28
6 1 0.01
7 3 0.02
ACGTcount: A:0.70, C:0.06, G:0.02, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:2181470 original size:21 final size:20
Alignment explanation
Indices: 2181407--2181601 Score: 119
Period size: 21 Copynumber: 9.1 Consensus size: 20
2181397 ATACCCCTTC
2181407 AAATAAATAAATAAAATAAAAT
1 AAATAAA-AAAT-AAATAAAAT
*
2181429 AAATAACCGAACA-AAAT-AAAT
1 AAATAA---AAAATAAATAAAAT
2181450 AAATAGAAAAATAAATAAAAT
1 AAATA-AAAAATAAATAAAAT
* **
2181471 AAATTACCAATAAAATAAAAT
1 AAATAAAAAAT-AAATAAAAT
2181492 AAATAAATAACCAACTAAATAAAAT
1 AAAT-AA-AA--AA-TAAATAAAAT
*
2181517 TAAT--AAAATAAATTACCAAAT
1 AAATAAAAAATAAA-TA--AAAT
**
2181538 AAATAACTGAATAAATAAAAT
1 AAATAA-AAAATAAATAAAAT
* *
2181559 AAATAAACAATTGAATAAAAT
1 AAATAAA-AAATAAATAAAAT
2181580 AAATAAATAAATAAATAAAAT
1 AAATAAA-AAATAAATAAAAT
2181601 A
1 A
2181602 CCTCCAGATT
Statistics
Matches: 135, Mismatches: 19, Indels: 39
0.70 0.10 0.20
Matches are distributed among these distances:
18 4 0.03
19 7 0.05
20 8 0.06
21 78 0.58
22 12 0.09
23 2 0.01
24 8 0.06
25 15 0.11
26 1 0.01
ACGTcount: A:0.70, C:0.06, G:0.02, T:0.22
Consensus pattern (20 bp):
AAATAAAAAATAAATAAAAT
Found at i:2181485 original size:25 final size:26
Alignment explanation
Indices: 2181457--2181540 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 26
2181447 AATAAATAGA
2181457 AAAATAAATAAAATAAATTACC-AAT
1 AAAATAAATAAAATAAATTACCAAAT
*
2181482 AAAATAAA-ATAAATAAATAACCAACTAAAT
1 AAAATAAATA-AAATAAATTA-C--C-AAAT
*
2181512 AAAATTAATAAAATAAATTACCAAAT
1 AAAATAAATAAAATAAATTACCAAAT
2181538 AAA
1 AAA
2181541 TAACTGAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
24 1 0.02
25 17 0.35
26 8 0.16
27 1 0.02
28 1 0.02
29 1 0.02
30 19 0.39
31 1 0.02
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (26 bp):
AAAATAAATAAAATAAATTACCAAAT
Found at i:2181492 original size:42 final size:41
Alignment explanation
Indices: 2181407--2181601 Score: 171
Period size: 42 Copynumber: 4.5 Consensus size: 41
2181397 ATACCCCTTC
*
2181407 AAATAAATAAATAAAATAAAATAAATAACCGAACAAAAT-AAAT
1 AAATAAA-AAAT-AAATAAAATAAATAACC-AATAAAATAAAAT
*
2181450 AAATAGAAAAATAAATAAAATAAATTACCAATAAAATAAAAT
1 AAATA-AAAAATAAATAAAATAAATAACCAATAAAATAAAAT
* *
2181492 AAATAAATAACCAACTAAATAAAATTAATAA--AATAAATTACCAAAT
1 AAAT-AA-AA--AA-TAAATAAAATAAATAACCAATAAAATA--AAAT
** * **
2181538 AAATAACTGAATAAATAAAATAAATAAACAATTGAATAAAAT
1 AAATAA-AAAATAAATAAAATAAATAACCAATAAAATAAAAT
2181580 AAATAAATAAATAAATAAAATA
1 AAATAAA-AAATAAATAAAATA
2181602 CCTCCAGATT
Statistics
Matches: 126, Mismatches: 14, Indels: 25
0.76 0.08 0.15
Matches are distributed among these distances:
41 7 0.06
42 63 0.50
43 14 0.11
44 16 0.13
45 4 0.03
46 22 0.17
ACGTcount: A:0.70, C:0.06, G:0.02, T:0.22
Consensus pattern (41 bp):
AAATAAAAAATAAATAAAATAAATAACCAATAAAATAAAAT
Found at i:2181541 original size:25 final size:25
Alignment explanation
Indices: 2181458--2181541 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 25
2181448 ATAAATAGAA
*
2181458 AAATAAATAAAATAAATTACC-AAT
1 AAATTAATAAAATAAATTACCAAAT
* * *
2181482 AAAATAAAATAAATAAATAACCAACTAAAT
1 AAATTAATA-AAATAAATTA-C--C-AAAT
2181512 AAAATTAATAAAATAAATTACCAAAT
1 -AAATTAATAAAATAAATTACCAAAT
2181538 AAAT
1 AAAT
2181542 AACTGAATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
24 6 0.13
25 13 0.28
26 5 0.11
27 1 0.02
28 1 0.02
29 1 0.02
30 12 0.26
31 7 0.15
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (25 bp):
AAATTAATAAAATAAATTACCAAAT
Found at i:2181565 original size:25 final size:25
Alignment explanation
Indices: 2181415--2181555 Score: 60
Period size: 25 Copynumber: 5.7 Consensus size: 25
2181405 TCAAATAAAT
* *
2181415 AAATAAAATAAAATAAATAACCGAACA
1 AAAT-AAAT-AAATAAATAACTGAATA
* *
2181442 AAATAAATAAATAGAA-AAATAAATA
1 AAATAAATAAATA-AATAACTGAATA
* **
2181467 AAATAAAT-TACCAATAA---AATA
1 AAATAAATAAATAAATAACTGAATA
** *
2181488 AAATAAATAAATAACCAACTAAATA
1 AAATAAATAAATAAATAACTGAATA
* * **
2181513 AAATTAATAAAATAAATTACCAAAT-
1 AAATAAAT-AAATAAATAACTGAATA
* *
2181538 AAATAACTGAATAAATAA
1 AAATAAATAAATAAATAA
2181556 AATAAATAAA
Statistics
Matches: 86, Mismatches: 21, Indels: 17
0.69 0.17 0.14
Matches are distributed among these distances:
21 12 0.14
22 4 0.05
23 2 0.02
24 11 0.13
25 35 0.41
26 18 0.21
27 4 0.05
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.21
Consensus pattern (25 bp):
AAATAAATAAATAAATAACTGAATA
Found at i:2181573 original size:25 final size:25
Alignment explanation
Indices: 2181534--2181590 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
2181524 ATAAATTACC
*
2181534 AAATAAATAACTGAAT-AAATAAAAT
1 AAATAAACAACTGAATAAAAT-AAAT
*
2181559 AAATAAACAATTGAATAAAATAAAT
1 AAATAAACAACTGAATAAAATAAAT
2181584 AAATAAA
1 AAATAAA
2181591 TAAATAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (25 bp):
AAATAAACAACTGAATAAAATAAAT
Found at i:2184982 original size:14 final size:14
Alignment explanation
Indices: 2184963--2184990 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2184953 TCTTGATGGC
2184963 TTCCACCTAAAGAA
1 TTCCACCTAAAGAA
2184977 TTCCACCTAAAGAA
1 TTCCACCTAAAGAA
2184991 ACAGTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.07, T:0.21
Consensus pattern (14 bp):
TTCCACCTAAAGAA
Found at i:2194540 original size:160 final size:161
Alignment explanation
Indices: 2194271--2194592 Score: 587
Period size: 160 Copynumber: 2.0 Consensus size: 161
2194261 TACCGTCTGA
2194271 ACATCAAGTGGCAGATGTGATGACAAAACCGTTGGCTAAGTCTGCACATGTAATGTTTACTCAGA
1 ACATCAAGTGGCAGATGTGATGACAAAACCGTTGGCTAAGTCTGCACATGTAATGTTTACTCAGA
*
2194336 AAGTGCAGGTAGCAGAGAGAGAACAACTGAGAGGAGGGGGGGAGAATGTTGAAGCATGA-TACAT
66 AAGTGCAGGTAGCAGAGAGAGAACAACTGAGAGGA-GCGGGGAGAATGTTGAAGCATGACTACAT
2194400 GCGTACGTGC-TGCTGCTAATAGTTTGTGTGT
130 GCGTACGTGCATGCTGCTAATAGTTTGTGTGT
2194431 ACATCAAGTGGCAGATGTGATGACAAAACCGTTGGCTAAGTCTGCACATGTAATGTTTACTCAGA
1 ACATCAAGTGGCAGATGTGATGACAAAACCGTTGGCTAAGTCTGCACATGTAATGTTTACTCAGA
2194496 AAGTGCAGGTAGCAGAGAAGAGAACAACTGAGAAGGA-CGGGGAGAATGTTGAAGCATGACTACA
66 AAGTGCAGGTAGCAGAG-AGAGAACAACTGAG-AGGAGCGGGGAGAATGTTGAAGCATGACTACA
2194560 TGCGTACGTGCATGCTGCTAATAGTTTGTGTGT
129 TGCGTACGTGCATGCTGCTAATAGTTTGTGTGT
2194593 GTGTGCAGTT
Statistics
Matches: 157, Mismatches: 1, Indels: 6
0.96 0.01 0.04
Matches are distributed among these distances:
160 103 0.66
161 29 0.18
162 25 0.16
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (161 bp):
ACATCAAGTGGCAGATGTGATGACAAAACCGTTGGCTAAGTCTGCACATGTAATGTTTACTCAGA
AAGTGCAGGTAGCAGAGAGAGAACAACTGAGAGGAGCGGGGAGAATGTTGAAGCATGACTACATG
CGTACGTGCATGCTGCTAATAGTTTGTGTGT
Found at i:2195196 original size:34 final size:34
Alignment explanation
Indices: 2195152--2195218 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
2195142 TCAATCAGTC
* * *
2195152 AAACTGAAGGACAACTGGCACAAGAAATTAGCAA
1 AAACTAAAGGACAACTGACACAAGAAACTAGCAA
*
2195186 AAACTAAAGGACATCTGACACAAGAAACTAGCA
1 AAACTAAAGGACAACTGACACAAGAAACTAGCA
2195219 GTGCTAACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.51, C:0.19, G:0.18, T:0.12
Consensus pattern (34 bp):
AAACTAAAGGACAACTGACACAAGAAACTAGCAA
Found at i:2197252 original size:55 final size:54
Alignment explanation
Indices: 2197182--2197423 Score: 335
Period size: 55 Copynumber: 4.4 Consensus size: 54
2197172 TCATTTATTA
* * *
2197182 ATTTGCACACGTAGTGCCTATACAG-TAGTTCATCAACTCATGATGAATTCCG-CG
1 ATTTGCACACATAGTGCCTGTAC-GTTA-TTCATCAACTCATGATGAATTCCGTGG
*
2197236 ATTCTGCACACATAGTGCCTGTACGTTTATTCATCAACTCATGATGAATTCCATGG
1 ATT-TGCACACATAGTGCCTGTACG-TTATTCATCAACTCATGATGAATTCCGTGG
* * *
2197292 ATCTGTACACATAGTGCCTGTACGTTTATTCATCAACTCATGATGAATTCTGTGG
1 ATTTGCACACATAGTGCCTGTACG-TTATTCATCAACTCATGATGAATTCCGTGG
*
2197347 ATTTGCACACATAGTTCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGG
1 ATTTGCACACATAGTGCCTGTAC-GTTATTCATCAACTCATGATGAATTCCGTGG
*
2197402 ATTTGCACACATAGTGTCTGTA
1 ATTTGCACACATAGTGCCTGTA
2197424 GTACACATAG
Statistics
Matches: 169, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
54 4 0.02
55 159 0.94
56 6 0.04
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (54 bp):
ATTTGCACACATAGTGCCTGTACGTTATTCATCAACTCATGATGAATTCCGTGG
Found at i:2201908 original size:14 final size:14
Alignment explanation
Indices: 2201889--2201921 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
2201879 CAAATCCTGC
2201889 ACACCATCAAACAA
1 ACACCATCAAACAA
2201903 ACACCATCAAACAA
1 ACACCATCAAACAA
2201917 ACACC
1 ACACC
2201922 TTCCCCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.55, C:0.39, G:0.00, T:0.06
Consensus pattern (14 bp):
ACACCATCAAACAA
Found at i:2219223 original size:18 final size:19
Alignment explanation
Indices: 2219196--2219245 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
2219186 GTTAAATTTG
* *
2219196 GTATCAATACTCATGG-AA
1 GTATCGATACTCAAGGAAA
*
2219214 GTATCGATACTTAAGGTAAA
1 GTATCGATACTCAAGG-AAA
2219234 GTATCGATACTC
1 GTATCGATACTC
2219246 CCTATGGGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 13 0.50
20 13 0.50
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (19 bp):
GTATCGATACTCAAGGAAA
Found at i:2220574 original size:13 final size:13
Alignment explanation
Indices: 2220556--2220580 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2220546 TTACCATTGA
2220556 GAAATACAATTTT
1 GAAATACAATTTT
2220569 GAAATACAATTT
1 GAAATACAATTT
2220581 ATGTAACTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (13 bp):
GAAATACAATTTT
Found at i:2223717 original size:16 final size:16
Alignment explanation
Indices: 2223679--2223720 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2223669 AAAAATGAAG
*
2223679 AATAAA-AATAAGTAAA
1 AATAAATAA-AAGGAAA
*
2223695 AAAAAATAAAAGGAAA
1 AATAAATAAAAGGAAA
2223711 AATAAATAAA
1 AATAAATAAA
2223721 TAAATAAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (16 bp):
AATAAATAAAAGGAAA
Done.