Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009581.1 Hibiscus syriacus cultivar Beakdansim tig00116958_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: 2551150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 13
Found at i:1862984 original size:22 final size:23
Alignment explanation
Indices: 1862941--1862984 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 23
1862931 ACTCATCAGG
1862941 GTGGTTCTTCATTAATTGCCTTAT
1 GTGGTTC-TCATTAATTGCCTTAT
1862965 GTGGTTC-CATTCAATT-CCTT
1 GTGGTTCTCATT-AATTGCCTT
1862985 CCCCACTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (23 bp):
GTGGTTCTCATTAATTGCCTTAT
Found at i:1863605 original size:4 final size:4
Alignment explanation
Indices: 1863591--1863620 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
1863581 AAAATGTTAG
1863591 TAAA GTAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA -TAAA TAAA TAAA TAAA TAAA TAAA T
1863621 GACGAAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:1864630 original size:26 final size:27
Alignment explanation
Indices: 1864599--1864659 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 27
1864589 AAAACAAACG
1864599 AATAAATAAAAT-AAT-TAAATAAATA
1 AATAAATAAAATGAATGTAAATAAATA
* *
1864624 AAGT-AA-AAAATGTATGTTAATAAATA
1 AA-TAAATAAAATGAATGTAAATAAATA
1864650 AATAAATAAA
1 AATAAATAAA
1864660 TAACAACTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
24 5 0.17
25 7 0.24
26 14 0.48
27 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (27 bp):
AATAAATAAAATGAATGTAAATAAATA
Found at i:1869460 original size:23 final size:21
Alignment explanation
Indices: 1869408--1869469 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
1869398 TTTTGGTGCA
*
1869408 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
1869428 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
1869449 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
1869470 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:1873761 original size:20 final size:20
Alignment explanation
Indices: 1873732--1873770 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1873722 ATTCCACCAC
*
1873732 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
1873752 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
1873771 TATGAGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:1874305 original size:40 final size:40
Alignment explanation
Indices: 1874250--1874330 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
1874240 GTGGTTATTA
* *
1874250 CACTGCTGGAGCTACGGTTAGTACGCAGATGATTTGATTG
1 CACTGCAGGAGCTACGGTTAGTACGCAGATGACTTGATTG
* *
1874290 CACTGCAGGAGCTACGGTTAGTTCGCGGATGACTTGATTG
1 CACTGCAGGAGCTACGGTTAGTACGCAGATGACTTGATTG
1874330 C
1 C
1874331 CCATTCGTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (40 bp):
CACTGCAGGAGCTACGGTTAGTACGCAGATGACTTGATTG
Found at i:1875203 original size:95 final size:94
Alignment explanation
Indices: 1875101--1875317 Score: 335
Period size: 94 Copynumber: 2.3 Consensus size: 94
1875091 AGGAAAATTT
*
1875101 AATTTATTTGAAAATTATTAACCGAATTGAATTAACCAAATTTTTTTCTATAACCATTAATCAAA
1 AATTTATTTGAAAATTATTAACCGAATTAAATTAACCAAATTTTTTTCTATAA-CATTAATCAAA
* *
1875166 CTGAAATTATTTGACCGTTAATCGAACCAA
65 CCGAAATTATTTAACCGTTAATCGAACCAA
* ** * *
1875196 AATTTATTTGAAAATTATTAACTGAACCAAATTAACCAAATTTTTTTCTTTAACATTAATCTAAC
1 AATTTATTTGAAAATTATTAACCGAATTAAATTAACCAAATTTTTTTCTATAACATTAATCAAAC
*
1875261 CGAAATTATTTAACCGTTAATCGAACCGA
66 CGAAATTATTTAACCGTTAATCGAACCAA
*
1875290 AATTTATTTGAAAATTATTAACCAAATT
1 AATTTATTTGAAAATTATTAACCGAATT
1875318 TTTTTCTTTA
Statistics
Matches: 109, Mismatches: 13, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
94 61 0.56
95 48 0.44
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.38
Consensus pattern (94 bp):
AATTTATTTGAAAATTATTAACCGAATTAAATTAACCAAATTTTTTTCTATAACATTAATCAAAC
CGAAATTATTTAACCGTTAATCGAACCAA
Found at i:1875293 original size:94 final size:92
Alignment explanation
Indices: 1875101--1875460 Score: 397
Period size: 81 Copynumber: 4.1 Consensus size: 92
1875091 AGGAAAATTT
* *
1875101 AATTTATTTGAAAATTATTAACCGAATTGAATTAACCAAATTTTTTTCTATAACCATTAATCAAA
1 AATTTATTTGAAAATTATTAACTGAA---AATTAACCAAATTTTTTTCTTTAACCATTAATCAAA
* *
1875166 CTGAAATTATTTGACCGTTAATCGAACCAA
63 CCGAAATTATTTGACCGTTAATCGAACCGA
*
1875196 AATTTATTTGAAAATTATTAACTGAACCAAATTAACCAAATTTTTTTCTTTAA-CATTAATCTAA
1 AATTTATTTGAAAATTATTAACTG-A--AAATTAACCAAATTTTTTTCTTTAACCATTAATCAAA
*
1875260 CCGAAATTATTTAACCGTTAATCGAACCGA
63 CCGAAATTATTTGACCGTTAATCGAACCGA
*
1875290 AATTTATTTG-AAA--A-T---T----ATTAACCAAATTTTTTTCTTTAACCATTAATCAAAACG
1 AATTTATTTGAAAATTATTAACTGAAAATTAACCAAATTTTTTTCTTTAACCATTAATCAAACCG
*
1875344 AAATTATTTGACCGTTAATTGAACCGA
66 AAATTATTTGACCGTTAATCGAACCGA
* *
1875371 AATTTATTTGAAAATTATTAACTG-----------AATTTTTTTCTTTAACCATTAATCGAACCA
1 AATTTATTTGAAAATTATTAACTGAAAATTAACCAAATTTTTTTCTTTAACCATTAATCAAACCG
* *
1875425 AAATTATTTGACAGTTAATCGAACCCA
66 AAATTATTTGACCGTTAATCGAACCGA
1875452 AATTTATTT
1 AATTTATTT
1875461 TATTCAGTTA
Statistics
Matches: 237, Mismatches: 16, Indels: 38
0.81 0.05 0.13
Matches are distributed among these distances:
80 23 0.10
81 107 0.45
82 3 0.01
84 1 0.00
85 1 0.00
87 1 0.00
88 1 0.00
90 1 0.00
91 1 0.00
93 3 0.01
94 47 0.20
95 46 0.19
96 1 0.00
98 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (92 bp):
AATTTATTTGAAAATTATTAACTGAAAATTAACCAAATTTTTTTCTTTAACCATTAATCAAACCG
AAATTATTTGACCGTTAATCGAACCGA
Found at i:1875779 original size:93 final size:94
Alignment explanation
Indices: 1875615--1875824 Score: 350
Period size: 93 Copynumber: 2.2 Consensus size: 94
1875605 AAAAAATCGT
*
1875615 TTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGTT-
1 TTAATAATTTTCAAATAAATTTCAGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGTTA
* * * *
1875679 AAGGAAAAAATTTGGTTAATTTGGTTCAG
66 AAGAAAAAAATTCGATTAACTTGGTTCAG
*
1875708 TTAATAATTTTCAAATAAATTTCAGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAATGTTA
1 TTAATAATTTTCAAATAAATTTCAGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGTTA
*
1875773 AAGAAAAAAATTCGATTAACTTGGTTCGG
66 AAGAAAAAAATTCGATTAACTTGGTTCAG
1875802 TTAATAATTTTCAAATAAATTTC
1 TTAATAATTTTCAAATAAATTTC
1875825 GGTTAACGGT
Statistics
Matches: 109, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
93 62 0.57
94 47 0.43
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (94 bp):
TTAATAATTTTCAAATAAATTTCAGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGTTA
AAGAAAAAAATTCGATTAACTTGGTTCAG
Found at i:1879225 original size:16 final size:16
Alignment explanation
Indices: 1879201--1879231 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1879191 TATATATAAA
1879201 ATATAATGAATTATTT
1 ATATAATGAATTATTT
*
1879217 ATATTATGAATTATT
1 ATATAATGAATTATT
1879232 AGATTTTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
ATATAATGAATTATTT
Found at i:1883529 original size:23 final size:23
Alignment explanation
Indices: 1883503--1883549 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1883493 CATCCCCTAC
*
1883503 AGAAAATTTGAGCAATTGAATAT
1 AGAAAATTTGAGAAATTGAATAT
1883526 AGAAAATTTGAGAAATTGAATAT
1 AGAAAATTTGAGAAATTGAATAT
1883549 A
1 A
1883550 TATATATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.51, C:0.02, G:0.17, T:0.30
Consensus pattern (23 bp):
AGAAAATTTGAGAAATTGAATAT
Found at i:1883783 original size:2 final size:2
Alignment explanation
Indices: 1883776--1883821 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1883766 GATATTAACC
1883776 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
1883818 AT AT
1 AT AT
1883822 CCTTCAATTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1885054 original size:21 final size:21
Alignment explanation
Indices: 1885029--1885069 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1885019 AAAGAAATTA
*
1885029 GGTAAAAAAATTAACATTTTC
1 GGTAAAAAAAATAACATTTTC
*
1885050 GGTAAAAAAAATAATATTTT
1 GGTAAAAAAAATAACATTTT
1885070 ATTAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (21 bp):
GGTAAAAAAAATAACATTTTC
Found at i:1885623 original size:38 final size:36
Alignment explanation
Indices: 1885547--1885624 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 36
1885537 TTTTTATATT
*
1885547 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
1885583 TTTAATTTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAA-TTTTGTAAA-AAAATTATATAAATATTAT-CAA
1885621 TTTA
1 TTTA
1885625 TAATATTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 5 0.14
37 21 0.58
38 10 0.28
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:1885644 original size:18 final size:18
Alignment explanation
Indices: 1885600--1885647 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1885590 TTTTTAAAGA
*
1885600 AAATATATAAATATTTTAC
1 AAATATAT-AATATTATAC
*
1885619 -AATTTATAATATTATAC
1 AAATATATAATATTATAC
1885636 AAATATATAATA
1 AAATATATAATA
1885648 AGGACAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:1890376 original size:22 final size:22
Alignment explanation
Indices: 1890350--1890394 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1890340 CAATTTTTAC
1890350 TAAGGGTCTCTTTATAAGAATT
1 TAAGGGTCTCTTTATAAGAATT
*
1890372 TAAGGGTCTCTTTTTAAGAATT
1 TAAGGGTCTCTTTATAAGAATT
1890394 T
1 T
1890395 GCACAGGGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (22 bp):
TAAGGGTCTCTTTATAAGAATT
Found at i:1891163 original size:24 final size:24
Alignment explanation
Indices: 1891131--1891257 Score: 114
Period size: 24 Copynumber: 5.4 Consensus size: 24
1891121 CATTTAAATG
* *
1891131 ATAAACGAACACAAATGAACAAAC
1 ATAAACGAACACAAATAAACGAAC
** ** *
1891155 ATAAACGAACGGATGTAAACGAAT
1 ATAAACGAACACAAATAAACGAAC
*
1891179 ATAAACGAACAC-AATAAAGGAAC
1 ATAAACGAACACAAATAAACGAAC
* * **
1891202 GTAAGCGAACACAAACGAACGAAC
1 ATAAACGAACACAAATAAACGAAC
* *
1891226 GTAAACGAACAC-AATAAATGAAC
1 ATAAACGAACACAAATAAACGAAC
1891249 ATAAACGAA
1 ATAAACGAA
1891258 TGTAACCAAA
Statistics
Matches: 79, Mismatches: 23, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
23 33 0.42
24 46 0.58
ACGTcount: A:0.57, C:0.18, G:0.15, T:0.10
Consensus pattern (24 bp):
ATAAACGAACACAAATAAACGAAC
Found at i:1891477 original size:14 final size:14
Alignment explanation
Indices: 1891459--1891498 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1891449 GAATGAATAC
1891459 ACATAAACGAACGA
1 ACATAAACGAACGA
* * *
1891473 TCATAAATGAATGA
1 ACATAAACGAACGA
1891487 ACATAAACGAAC
1 ACATAAACGAAC
1891499 ATATTACTGA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.55, C:0.17, G:0.12, T:0.15
Consensus pattern (14 bp):
ACATAAACGAACGA
Found at i:1893544 original size:19 final size:19
Alignment explanation
Indices: 1893517--1893554 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1893507 TACAGTTACC
*
1893517 TCATTGGTCGCCAAGTGCT
1 TCATAGGTCGCCAAGTGCT
1893536 TCATAGGTCGCCAAGTGCT
1 TCATAGGTCGCCAAGTGCT
1893555 CCTTGCGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (19 bp):
TCATAGGTCGCCAAGTGCT
Found at i:1893674 original size:30 final size:30
Alignment explanation
Indices: 1893638--1893702 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
1893628 AGTCCTCCAT
* *
1893638 AGGTCGCCGTGTGCTCCTGGAGAGCTATGG
1 AGGTCGCCATGTGCTCCTGGAGACCTATGG
1893668 AGGTCGCCATGTGCTCCTGGAGACCTATGG
1 AGGTCGCCATGTGCTCCTGGAGACCTATGG
*
1893698 TGGTC
1 AGGTC
1893703 ACTGTAGCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.14, C:0.25, G:0.37, T:0.25
Consensus pattern (30 bp):
AGGTCGCCATGTGCTCCTGGAGACCTATGG
Found at i:1895216 original size:29 final size:29
Alignment explanation
Indices: 1895145--1895278 Score: 118
Period size: 29 Copynumber: 4.7 Consensus size: 29
1895135 CTTATATTAT
1895145 AAATAAGTA-CTTAAAGTATTTTTT--TC-
1 AAATAAGTATC-TAAAGTATTTTTTGGTCA
** * ** *
1895171 ATCTAAGTATTTAAAGTATTTTTTAATTA
1 AAATAAGTATCTAAAGTATTTTTTGGTCA
1895200 AAATAAGTATCTAAAGTTATTTTTTGGTCA
1 AAATAAGTATCTAAAG-TATTTTTTGGTCA
* *
1895230 AAATAGGTA-CTTAAAATATTTTTTGGTCA
1 AAATAAGTATC-TAAAGTATTTTTTGGTCA
1895259 AAATATA-TATCTAAAGTATT
1 AAATA-AGTATCTAAAGTATT
1895279 CAAGTTTTTT
Statistics
Matches: 86, Mismatches: 14, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
26 20 0.23
28 1 0.01
29 42 0.49
30 23 0.27
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.45
Consensus pattern (29 bp):
AAATAAGTATCTAAAGTATTTTTTGGTCA
Found at i:1895410 original size:31 final size:30
Alignment explanation
Indices: 1895366--1895438 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
1895356 AATTGAATGT
* *
1895366 TTTAGTACCTATTTTGACCAAAAAGATAAG
1 TTTAGTACTTATTTTGACCAAAAAAATAAG
* *
1895396 TTTATGTACTTATTTTGACCAAAAAAATTAT
1 TTTA-GTACTTATTTTGACCAAAAAAATAAG
1895427 TTTAGGTACTTA
1 TTTA-GTACTTA
1895439 AATGAAAAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 4 0.11
31 33 0.89
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (30 bp):
TTTAGTACTTATTTTGACCAAAAAAATAAG
Found at i:1896506 original size:2 final size:2
Alignment explanation
Indices: 1896499--1896525 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1896489 AAAATTTCTA
1896499 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
1896526 AATGACACTA
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:1898832 original size:12 final size:12
Alignment explanation
Indices: 1898815--1898842 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1898805 TGATCTAATA
1898815 TATACATATGTG
1 TATACATATGTG
1898827 TATACATATGTG
1 TATACATATGTG
1898839 TATA
1 TATA
1898843 TATTATGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (12 bp):
TATACATATGTG
Found at i:1898844 original size:14 final size:14
Alignment explanation
Indices: 1898813--1898844 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
1898803 TCTGATCTAA
1898813 TATATACATATGTG
1 TATATACATATGTG
1898827 --TATACATATGTG
1 TATATACATATGTG
1898839 TATATA
1 TATATA
1898845 TTATGTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 4
0.80 0.00 0.20
Matches are distributed among these distances:
12 12 0.75
14 4 0.25
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (14 bp):
TATATACATATGTG
Found at i:1900149 original size:18 final size:18
Alignment explanation
Indices: 1900126--1900180 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
1900116 TGAGGTAGAA
*
1900126 GTAGAGGCACCAGCGGAG
1 GTAGAGGCACCAGCAGAG
* **
1900144 GTAGAGGCGCCAGCACTG
1 GTAGAGGCACCAGCAGAG
1900162 GTAGAGGCACCAGCAGAG
1 GTAGAGGCACCAGCAGAG
1900180 G
1 G
1900181 AAACTGTTGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.42, T:0.07
Consensus pattern (18 bp):
GTAGAGGCACCAGCAGAG
Found at i:1900523 original size:160 final size:160
Alignment explanation
Indices: 1900253--1901047 Score: 1234
Period size: 160 Copynumber: 5.0 Consensus size: 160
1900243 AATACCGATG
* * *
1900253 AGGAACAACAAAGGCTTCTTTTGAAACAGAAGACAATGGTTG---AACAACAACAACAGTATATT
1 AGGAACAACAAAGGCATCTTTTGGAACAGAAGACAATGGTTGAACAACAACAACAACAATATATT
* * * * *
1900315 CTGGTACTTCGCAGTAATCACCAGTTCTAGTTATAAATTTTCTATCATCTGCCATATGGATGCAG
66 CTGGTAATTTGCAGTAATCACCAGTTCTAGTTATAAATTTTGTATCATCTACCATAGGGATGCAG
* * *
1900380 ATATGAAATAATGCATGTCATTGTGGCTGT
131 ATATGAAGTAGTGCATGTCGTTGTGGCTGT
* * *
1900410 AGGAACAACAAAGGCATCTTTCGGAACAGAAGAAAATGGTTGAACAACAACAACAACAATATCTT
1 AGGAACAACAAAGGCATCTTTTGGAACAGAAGACAATGGTTGAACAACAACAACAACAATATATT
* *
1900475 CTGGTAATTTGCAGTAATCATCAGTTCCAGTTATAAATTTTGTATCATCTACCATAGGGATGCAG
66 CTGGTAATTTGCAGTAATCACCAGTTCTAGTTATAAATTTTGTATCATCTACCATAGGGATGCAG
*
1900540 ATATGAAGTAGTGCATGTTGTTGTGGCTGT
131 ATATGAAGTAGTGCATGTCGTTGTGGCTGT
*
1900570 AGGAACAACAAAAGCATCTTTTGGAACAGAAGACAATGGTTGAACAACAACAACAACAATATATT
1 AGGAACAACAAAGGCATCTTTTGGAACAGAAGACAATGGTTGAACAACAACAACAACAATATATT
* * * *
1900635 -TGGTAATTTGCAGTAATCATCATTTCTAGTTGTAAATTTTGTATCATCTGCCATAGGGATGCAG
66 CTGGTAATTTGCAGTAATCACCAGTTCTAGTTATAAATTTTGTATCATCTACCATAGGGATGCAG
1900699 ATATGAAGTAGTGCATGTC---GTGGCTGT
131 ATATGAAGTAGTGCATGTCGTTGTGGCTGT
* *
1900726 AGGGACAACAAAGGCATCTTTTGGAACAGAAGGCAATGGTTGAACAACAACAACAACAATATATT
1 AGGAACAACAAAGGCATCTTTTGGAACAGAAGACAATGGTTGAACAACAACAACAACAATATATT
* *
1900791 CTGGTAATTTGCAGTAATCACCAGTTCTAGGTATAAATTTTGTATCATCTACCCTAGGGATGCAG
66 CTGGTAATTTGCAGTAATCACCAGTTCTAGTTATAAATTTTGTATCATCTACCATAGGGATGCAG
*
1900856 ATATGAAGTAGTGCATGTCGTTGTGGCTGC
131 ATATGAAGTAGTGCATGTCGTTGTGGCTGT
* *
1900886 AGGAACAACAAAGGCATCTTTTGAAACAGATGACAATGGTTG---AACAACAACAA-AATATATT
1 AGGAACAACAAAGGCATCTTTTGGAACAGAAGACAATGGTTGAACAACAACAACAACAATATATT
* *
1900947 CTGGTAATTTGCAGTAATCACCAGTTCTAGTTATAAGTTTTGTATTATCTACCATAGGGATGCAG
66 CTGGTAATTTGCAGTAATCACCAGTTCTAGTTATAAATTTTGTATCATCTACCATAGGGATGCAG
1901012 ATATGAAGTAGTGCATGTCGTTGTGGCTGT
131 ATATGAAGTAGTGCATGTCGTTGTGGCTGT
1901042 AGGAAC
1 AGGAAC
1901048 TGAAGAATAC
Statistics
Matches: 586, Mismatches: 45, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
156 174 0.30
157 126 0.22
159 78 0.13
160 208 0.35
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (160 bp):
AGGAACAACAAAGGCATCTTTTGGAACAGAAGACAATGGTTGAACAACAACAACAACAATATATT
CTGGTAATTTGCAGTAATCACCAGTTCTAGTTATAAATTTTGTATCATCTACCATAGGGATGCAG
ATATGAAGTAGTGCATGTCGTTGTGGCTGT
Found at i:1900828 original size:316 final size:314
Alignment explanation
Indices: 1900253--1901047 Score: 1243
Period size: 316 Copynumber: 2.5 Consensus size: 314
1900243 AATACCGATG
* *
1900253 AGGAACAACAAAGGCTTCTTTTGAAACAGAAGACAATGGTTGAACAACAACAACAGTATATTCTG
1 AGGAACAACAAAGGCATCTTTTGAAACAGAAGACAATGGTTGAACAACAACAACAATATATTCTG
* * * *
1900318 GTACTTCGCAGTAATCACCAGTTCTAGTTATAAATTTTCTATCATCTGCCATATGGATGCAGATA
66 GTAATTTGCAGTAATCACCAGTTCTAGTTATAAATTTTGTATCATCTGCCATAGGGATGCAGATA
* *
1900383 TGAAATAATGCATGTCATTGTGGCTGTAGGAACAACAAAGGCATCTTTCGGAACAGAAGAAAATG
131 TGAAGTAGTGCATGTC---GTGGCTGTAGGAACAACAAAGGCATCTTTCGGAACAGAAGAAAATG
* * *
1900448 GTTGAACAACAACAACAACAATATCTTCTGGTAATTTGCAGTAATCATCAGTTCCAGTTATAAAT
193 GTTGAACAACAACAACAACAATATATTCTGGTAATTTGCAGTAATCACCAGTTCCAGGTATAAAT
* *
1900513 TTTGTATCATCTACCATAGGGATGCAGATATGAAGTAGTGCATGTTGTTGTGGCTGT
258 TTTGTATCATCTACCATAGGGATGCAGATATGAAGTAGTGCATGTCGTTGTGGCTGC
* *
1900570 AGGAACAACAAAAGCATCTTTTGGAACAGAAGACAATGGTTGAACAACAACAACAACAATATATT
1 AGGAACAACAAAGGCATCTTTTGAAACAGAAGACAATGGTTG---AACAACAACAACAATATATT
* * *
1900635 -TGGTAATTTGCAGTAATCATCATTTCTAGTTGTAAATTTTGTATCATCTGCCATAGGGATGCAG
63 CTGGTAATTTGCAGTAATCACCAGTTCTAGTTATAAATTTTGTATCATCTGCCATAGGGATGCAG
* * **
1900699 ATATGAAGTAGTGCATGTCGTGGCTGTAGGGACAACAAAGGCATCTTTTGGAACAGAAGGCAATG
128 ATATGAAGTAGTGCATGTCGTGGCTGTAGGAACAACAAAGGCATCTTTCGGAACAGAAGAAAATG
*
1900764 GTTGAACAACAACAACAACAATATATTCTGGTAATTTGCAGTAATCACCAGTTCTAGGTATAAAT
193 GTTGAACAACAACAACAACAATATATTCTGGTAATTTGCAGTAATCACCAGTTCCAGGTATAAAT
*
1900829 TTTGTATCATCTACCCTAGGGATGCAGATATGAAGTAGTGCATGTCGTTGTGGCTGC
258 TTTGTATCATCTACCATAGGGATGCAGATATGAAGTAGTGCATGTCGTTGTGGCTGC
*
1900886 AGGAACAACAAAGGCATCTTTTGAAACAGATGACAATGGTTGAACAACAACAA-AATATATTCTG
1 AGGAACAACAAAGGCATCTTTTGAAACAGAAGACAATGGTTGAACAACAACAACAATATATTCTG
* * *
1900950 GTAATTTGCAGTAATCACCAGTTCTAGTTATAAGTTTTGTATTATCTACCATAGGGATGCAGATA
66 GTAATTTGCAGTAATCACCAGTTCTAGTTATAAATTTTGTATCATCTGCCATAGGGATGCAGATA
1901015 TGAAGTAGTGCATGTCGTTGTGGCTGTAGGAAC
131 TGAAGTAGTGCATGTC---GTGGCTGTAGGAAC
1901048 TGAAGAATAC
Statistics
Matches: 437, Mismatches: 34, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
312 8 0.02
313 88 0.20
316 209 0.48
317 39 0.09
319 74 0.17
320 19 0.04
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (314 bp):
AGGAACAACAAAGGCATCTTTTGAAACAGAAGACAATGGTTGAACAACAACAACAATATATTCTG
GTAATTTGCAGTAATCACCAGTTCTAGTTATAAATTTTGTATCATCTGCCATAGGGATGCAGATA
TGAAGTAGTGCATGTCGTGGCTGTAGGAACAACAAAGGCATCTTTCGGAACAGAAGAAAATGGTT
GAACAACAACAACAACAATATATTCTGGTAATTTGCAGTAATCACCAGTTCCAGGTATAAATTTT
GTATCATCTACCATAGGGATGCAGATATGAAGTAGTGCATGTCGTTGTGGCTGC
Found at i:1905812 original size:21 final size:21
Alignment explanation
Indices: 1905788--1905860 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
1905778 TTTTCCCAAT
1905788 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTGGGAAAA
** *
1905809 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTGGGAAAA
**
1905829 TCGCAACACGAATTGGGAAAA
1 TCGCAATGCGAATTGGGAAAA
1905850 TCGCAATGCGA
1 TCGCAATGCGA
1905861 TACTGACTAT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 15 0.37
21 26 0.63
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTGGGAAAA
Found at i:1905874 original size:20 final size:20
Alignment explanation
Indices: 1905849--1905943 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1905839 AATTGGGAAA
*
1905849 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1905869 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1905890 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1905910 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1905930 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1905944 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1905891 original size:41 final size:41
Alignment explanation
Indices: 1905846--1905923 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1905836 ACGAATTGGG
* * *
1905846 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
1905887 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
1905924 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:1906159 original size:22 final size:22
Alignment explanation
Indices: 1906131--1906174 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1906121 CACTCTCTTA
1906131 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1906153 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1906175 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1906458 original size:19 final size:19
Alignment explanation
Indices: 1906408--1906460 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
1906398 AAATCGCAAC
* *
1906408 GCGATTTTAGTTTCGCGTT
1 GCGATTTCATTTTCGCGTT
* *
1906427 GCGATAGTCATTTTCGTGTT
1 GCGAT-TTCATTTTCGCGTT
1906447 GCGATTTCATTTTC
1 GCGATTTCATTTTC
1906461 AGAAACTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.13, C:0.17, G:0.23, T:0.47
Consensus pattern (19 bp):
GCGATTTCATTTTCGCGTT
Found at i:1907798 original size:18 final size:18
Alignment explanation
Indices: 1907777--1907821 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1907767 TCCACTTCGG
*
1907777 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1907795 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1907813 GAGCCATCA
1 GAGCCATCA
1907822 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1908357 original size:19 final size:20
Alignment explanation
Indices: 1908303--1908369 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1908293 TAGTTTACTT
* *
1908303 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1908323 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1908343 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1908362 TCGCAACG
1 TCGCAACG
1908370 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1908377 original size:14 final size:14
Alignment explanation
Indices: 1908358--1908415 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1908348 ATGCGAAATG
1908358 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1908372 AAAATCGCAAAGCGAA
1 AAAATCGC-AA-CGAC
1908388 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1908404 AAAATCGCAACG
1 AAAATCGCAACG
1908416 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 19 0.50
15 2 0.05
16 8 0.21
17 2 0.05
18 7 0.18
ACGTcount: A:0.50, C:0.24, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1908400 original size:32 final size:33
Alignment explanation
Indices: 1908342--1908432 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1908332 GGAAATGGCT
*
1908342 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
1908375 ATCGCAAAGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
*
1908407 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAAAGCGAAATGAAAATCGCAA
1908433 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
Found at i:1908426 original size:19 final size:19
Alignment explanation
Indices: 1908303--1908437 Score: 76
Period size: 19 Copynumber: 7.6 Consensus size: 19
1908293 TAGTTTACTT
* **
1908303 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
1908323 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
1908343 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1908362 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
1908376 TCGCAAAGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
1908394 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1908408 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1908427 TCGCAATGCGA
1 TCGCAACGCGA
1908438 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1908468 original size:14 final size:14
Alignment explanation
Indices: 1908449--1908506 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1908439 TTGTGTTTCG
*
1908449 CGTTGCGATTTTGT
1 CGTTGCGATTTTTT
1908463 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TTT
1908479 CGCGTTGCGATTTTTT
1 --CGTTGCGATTTTTT
1908495 CGTTGCGATTTT
1 CGTTGCGATTTT
1908507 CATTTCGCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 23 0.59
16 5 0.13
18 11 0.28
ACGTcount: A:0.09, C:0.17, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:1908483 original size:32 final size:33
Alignment explanation
Indices: 1908444--1908522 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1908434 GCGATTTGTG
1908444 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1908476 TTTCGCGTTGCGATTTTTTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1908509 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1908523 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1908521 original size:19 final size:19
Alignment explanation
Indices: 1908463--1908580 Score: 104
Period size: 20 Copynumber: 6.4 Consensus size: 19
1908453 GCGATTTTGT
1908463 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1908481 CGTTGCGA-TTT--TTT--
1 CGTTGCGATTTTCATTTCG
1908495 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
1908514 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
1908534 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1908553 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1908573 TGTTGCGA
1 CGTTGCGA
1908581 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 10, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 3 0.04
17 3 0.04
18 11 0.13
19 26 0.31
20 29 0.35
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1909894 original size:42 final size:42
Alignment explanation
Indices: 1909848--1909931 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
1909838 CGATGACAGT
* * *
1909848 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
1909890 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
1909932 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:1911963 original size:20 final size:19
Alignment explanation
Indices: 1911932--1912112 Score: 116
Period size: 20 Copynumber: 9.8 Consensus size: 19
1911922 TCTTTTGGTT
1911932 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1911951 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1911972 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
1911991 G--A-G--AATCGCAAC-A
1 GAAATGAAAATCGCAACGA
**
1912004 CGAAATGACTATCG---CGA
1 -GAAATGAAAATCGCAACGA
** * *
1912021 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
1912038 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
*
1912058 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
1912078 GAAATGAAAATCGCAAC-A
1 GAAATGAAAATCGCAACGA
1912096 CGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
1912113 TGCGATTTTG
Statistics
Matches: 131, Mismatches: 15, Indels: 32
0.74 0.08 0.18
Matches are distributed among these distances:
13 1 0.01
14 16 0.12
15 1 0.01
16 3 0.02
17 5 0.04
18 1 0.01
19 34 0.26
20 68 0.52
21 2 0.02
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1912049 original size:19 final size:19
Alignment explanation
Indices: 1912027--1912117 Score: 146
Period size: 20 Copynumber: 4.7 Consensus size: 19
1912017 GCGACCAGAC
1912027 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1912046 AATCGCAACCGCGAAATGAA
1 AATCGCAA-CGCGAAATGAA
1912066 AATCGCAACCGCGAAATGAA
1 AATCGCAA-CGCGAAATGAA
*
1912086 AATCGCAACACGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1912105 AATCGCAATGCGA
1 AATCGCAACGCGA
1912118 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 29 0.43
20 39 0.57
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1912070 original size:39 final size:38
Alignment explanation
Indices: 1911932--1912117 Score: 151
Period size: 33 Copynumber: 5.1 Consensus size: 38
1911922 TCTTTTGGTT
*
1911932 GAAATGAAAATCGCAACGA-GATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAAC-ACGA-AATGAAAATCGCAACGC
** * *
1911971 GGAAATGACTATCGC-A-ACG--A-GAGAATCGCAACAC
1 -GAAATGAAAATCGCAACACGAAATGAAAATCGCAACGC
** * *
1912005 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACACGAAATGAAAATCGCAACGC
*
1912038 GAAATGAAAATCGCAACCGCGAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CACGAAATGAAAATCGCAA-CGC
*
1912078 GAAATGAAAATCGCAACACGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACACGAAATGAAAATCGCAACGC
1912116 GA
1 GA
1912118 TTTTGGTTTC
Statistics
Matches: 125, Mismatches: 11, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
33 40 0.32
34 16 0.13
35 2 0.02
37 1 0.01
38 6 0.05
39 29 0.23
40 31 0.25
ACGTcount: A:0.44, C:0.23, G:0.22, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACACGAAATGAAAATCGCAACGC
Found at i:1912137 original size:19 final size:19
Alignment explanation
Indices: 1912113--1912157 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1912103 AAAATCGCAA
* *
1912113 TGCGATTTTGGTTTCGTGT
1 TGCGATTTTGATTTCGCGT
*
1912132 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
1912151 TGCGATT
1 TGCGATT
1912158 ATCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.13, G:0.27, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:1912735 original size:20 final size:20
Alignment explanation
Indices: 1912710--1912762 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1912700 GCGCTATGTA
1912710 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1912730 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1912750 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1912763 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1912796 original size:20 final size:20
Alignment explanation
Indices: 1912771--1912824 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1912761 GATTTTGTAT
1912771 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1912791 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1912811 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1912825 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1912809 original size:61 final size:61
Alignment explanation
Indices: 1912711--1912827 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1912701 CGCTATGTAA
* * * * *
1912711 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
1912772 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1912828 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1912843 original size:61 final size:61
Alignment explanation
Indices: 1912711--1912845 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
1912701 CGCTATGTAA
* * * * * ** *
1912711 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
1912772 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
1912834 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1912846 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1912935 original size:21 final size:21
Alignment explanation
Indices: 1912895--1912935 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1912885 ATTGTATACC
**
1912895 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1912916 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1912936 GCGAATTTGC
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:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1930769 original size:109 final size:111
Alignment explanation
Indices: 1930585--1930845 Score: 474
Period size: 109 Copynumber: 2.4 Consensus size: 111
1930575 GTTAATTTTT
*
1930585 ACATGCCAAGGTGGATCTCTCAGCGTCTTCACCTGTCGTCTGATGGGAATGCTCGGCGTCTTCAA
1 ACATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTGATGGGAATGCTCGGCGTCTTCAA
*
1930650 GCAATTGGACTGCGGGATCTCTCGGCGTCTTCTGCATGCTACAA-G
66 GCAATTGGACTGCGGGATCTCTCGGCATCTTCTGCATGCTACAAGG
1930695 ACATGCCAAGGTGGATCTCTCGGCGTCTTCACCTG-CGTCTGATGGGAATGCTCGGCGTCTTCAA
1 ACATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTGATGGGAATGCTCGGCGTCTTCAA
1930759 GCAATTGGACTGCGGGATCTCTCGGCATCTTCTGCATGCTACAAGG
66 GCAATTGGACTGCGGGATCTCTCGGCATCTTCTGCATGCTACAAGG
*
1930805 A-ATGCCAATGTGGATCTCTCGGCGTCTTCACCTGTCGTCTG
1 ACATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTG
1930846 GCGGGAATCT
Statistics
Matches: 146, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
109 104 0.71
110 42 0.29
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.28
Consensus pattern (111 bp):
ACATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTGATGGGAATGCTCGGCGTCTTCAA
GCAATTGGACTGCGGGATCTCTCGGCATCTTCTGCATGCTACAAGG
Found at i:1931124 original size:18 final size:18
Alignment explanation
Indices: 1931101--1931141 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1931091 ATGCGTCTGT
1931101 TGAGATTCGTCTGAAGCG
1 TGAGATTCGTCTGAAGCG
1931119 TGAGATTCGTCTGAAGCG
1 TGAGATTCGTCTGAAGCG
1931137 TGAGA
1 TGAGA
1931142 CTAATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.27
Consensus pattern (18 bp):
TGAGATTCGTCTGAAGCG
Found at i:1934627 original size:172 final size:173
Alignment explanation
Indices: 1934334--1934692 Score: 560
Period size: 172 Copynumber: 2.1 Consensus size: 173
1934324 CATAAAATAT
* *
1934334 AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTTGCAATTTAATCACTAAATT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
*
1934399 TATAAATTCTTTCAAATTTAACCAATTAAGCATATTAATACTAAATTCAAGCATAGTATACCAAC
66 TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
* * *
1934464 TTTTTATAATTTACTCTAATTTCTTAAATTCCTCAAATTTTGC
131 TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
* * *
1934507 AAAACGATCCCTAATTACTATTTGGTTCTCAACATTTTCAGAGTTAGCAATTTAATC-CATAAAT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCAC-TAAAT
* * *
1934571 TT-TAAATTCTTTCTAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATAGCAA
65 TTATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAA
* *
1934635 CTTTTAATAATTTACTCTTATTCCTTAAATTCCTTAAATTTTAC
130 CTTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
*
1934679 AAAACGGTCCCTAA
1 AAAACGATCCCTAA
1934693 AACTTTACAA
Statistics
Matches: 170, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
172 111 0.65
173 59 0.35
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (173 bp):
AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
Found at i:1935180 original size:23 final size:23
Alignment explanation
Indices: 1935154--1935197 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1935144 AGTTGCATGC
1935154 CCCCCACATGCAGAAGTGCAGGA
1 CCCCCACATGCAGAAGTGCAGGA
*
1935177 CCCCCACATGCAGACGTGCAG
1 CCCCCACATGCAGAAGTGCAG
1935198 CCTTGCAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.39, G:0.25, T:0.09
Consensus pattern (23 bp):
CCCCCACATGCAGAAGTGCAGGA
Found at i:1935242 original size:22 final size:22
Alignment explanation
Indices: 1935214--1935267 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
1935204 AGGACCCAGG
1935214 ACCCGTGATTTCTCCTTGCAGA
1 ACCCGTGATTTCTCCTTGCAGA
* *
1935236 ACCCGTGCTCTCTCCTTGCAGA
1 ACCCGTGATTTCTCCTTGCAGA
1935258 ACCCGTGATT
1 ACCCGTGATT
1935268 CTCACGTCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.17, C:0.35, G:0.19, T:0.30
Consensus pattern (22 bp):
ACCCGTGATTTCTCCTTGCAGA
Found at i:1936042 original size:2 final size:2
Alignment explanation
Indices: 1936035--1936059 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1936025 GGTGATTTGC
1936035 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1936060 GTTAGTGGGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1936546 original size:23 final size:21
Alignment explanation
Indices: 1936501--1936546 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1936491 TAGTACGAAT
* *
1936501 ATATATTATTCAAGTACATGA
1 ATATATTATTCAAGAACAGGA
1936522 ATATATTATTCTAAGAATCAGGA
1 ATATATTATTC-AAGAA-CAGGA
1936545 AT
1 AT
1936547 GACAGAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 4 0.19
23 6 0.29
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (21 bp):
ATATATTATTCAAGAACAGGA
Found at i:1936849 original size:20 final size:20
Alignment explanation
Indices: 1936824--1936862 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1936814 CAACATCAAA
1936824 TTCTTGACTCCACTCTTGTT
1 TTCTTGACTCCACTCTTGTT
1936844 TTCTTGACTCCACTCTTGT
1 TTCTTGACTCCACTCTTGT
1936863 ATGTAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.31, G:0.10, T:0.49
Consensus pattern (20 bp):
TTCTTGACTCCACTCTTGTT
Found at i:1941886 original size:3 final size:3
Alignment explanation
Indices: 1941878--1941910 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1941868 TTATCCTTGT
*
1941878 ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1941911 TCAATTCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1944524 original size:2 final size:2
Alignment explanation
Indices: 1944519--1944577 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1944509 TTATTTTTTA
1944519 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
1944561 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1944578 AATTTAAAGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1944824 original size:39 final size:38
Alignment explanation
Indices: 1944720--1944836 Score: 112
Period size: 39 Copynumber: 3.0 Consensus size: 38
1944710 TTTTAAAAAT
* * *
1944720 ATTTAGAATATTA-ATGTGAAATAATTTAAGGAATTAAAA
1 ATTTAGAATGTTATA-GTGAAATAATTTAA-AAATTATAA
* * *
1944759 ATTTAGAATGTTATGGTAGCAA-AATTTAATAAATTATGA
1 ATTTAGAATGTTATAGT-GAAATAATTTAA-AAATTATAA
* *
1944798 ATTTAGGATGTTATAGTGAAATAATTTGAAAATTATAA
1 ATTTAGAATGTTATAGTGAAATAATTTAAAAATTATAA
1944836 A
1 A
1944837 AAAAATAAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
38 12 0.19
39 48 0.76
40 3 0.05
ACGTcount: A:0.47, C:0.01, G:0.15, T:0.38
Consensus pattern (38 bp):
ATTTAGAATGTTATAGTGAAATAATTTAAAAATTATAA
Found at i:1944856 original size:13 final size:13
Alignment explanation
Indices: 1944838--1944862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1944828 AATTATAAAA
1944838 AAAATAAAAAATG
1 AAAATAAAAAATG
1944851 AAAATAAAAAAT
1 AAAATAAAAAAT
1944863 AATATATATA
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:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAATAAAAAATG
Found at i:1944869 original size:2 final size:2
Alignment explanation
Indices: 1944864--1944914 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1944854 ATAAAAAATA
1944864 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
1944906 AT AT AT AT A
1 AT AT AT AT A
1944915 CTAGGTATCG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1947526 original size:21 final size:22
Alignment explanation
Indices: 1947483--1947527 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1947473 ATTTCCATAT
*
1947483 TGTAATAGGGAACCGATTACCC
1 TGTAACAGGGAACCGATTACCC
*
1947505 TGTAACAGGGAATCGA-TACCC
1 TGTAACAGGGAACCGATTACCC
1947526 TG
1 TG
1947528 CTACAATACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (22 bp):
TGTAACAGGGAACCGATTACCC
Found at i:1948044 original size:17 final size:17
Alignment explanation
Indices: 1947999--1948055 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
1947989 TTATCATGAA
*
1947999 CATA-TTTATCAGTAAT
1 CATATTTTATCACTAAT
1948015 CATATTATTATCACTAATT
1 CATATT-TTATCACTAA-T
*
1948034 CAT-TTTTATCATATAAT
1 CATATTTTATCA-CTAAT
1948051 CATAT
1 CATAT
1948056 GTTGAACATT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
16 4 0.12
17 11 0.32
18 15 0.44
19 4 0.12
ACGTcount: A:0.37, C:0.14, G:0.02, T:0.47
Consensus pattern (17 bp):
CATATTTTATCACTAAT
Found at i:1948332 original size:22 final size:22
Alignment explanation
Indices: 1948307--1948367 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
1948297 GGCATATGAA
1948307 ATTTGTCCCGAAGGACCTA-TGT
1 ATTTGTCCCGAAGGACC-ACTGT
* *
1948329 ATTTTTCCCGAATGACCACTGT
1 ATTTGTCCCGAAGGACCACTGT
* *
1948351 ATATGTCCCAAAGGACC
1 ATTTGTCCCGAAGGACC
1948368 GCGTAGACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 1 0.03
22 31 0.97
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCACTGT
Found at i:1948814 original size:2 final size:2
Alignment explanation
Indices: 1948807--1948853 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1948797 ACATATAAGA
1948807 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
1948849 AT AT A
1 AT AT A
1948854 CTAACACACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1953638 original size:22 final size:22
Alignment explanation
Indices: 1953613--1953675 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
1953603 GGCATATGAA
1953613 ATTTGTCCCGAAGGACCTA-TGT
1 ATTTGTCCCGAAGGACC-ACTGT
*
1953635 ATTTGTCCCGATGGACCACTGT
1 ATTTGTCCCGAAGGACCACTGT
* * *
1953657 ATATATCCTGAAGGACCAC
1 ATTTGTCCCGAAGGACCAC
1953676 ATAGACCCTC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCACTGT
Found at i:1957313 original size:13 final size:13
Alignment explanation
Indices: 1957295--1957322 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1957285 GGACAGAATT
1957295 GACACAGATGGAG
1 GACACAGATGGAG
1957308 GACACAGATGGAG
1 GACACAGATGGAG
1957321 GA
1 GA
1957323 TTATTAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.39, T:0.07
Consensus pattern (13 bp):
GACACAGATGGAG
Found at i:1958482 original size:18 final size:17
Alignment explanation
Indices: 1958455--1958488 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1958445 TAGCCCCTAC
1958455 AAAATAGAAAGGATAAT
1 AAAATAGAAAGGATAAT
1958472 AAAATTAGAAAGGATAA
1 AAAA-TAGAAAGGATAA
1958489 AGGAAACTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (17 bp):
AAAATAGAAAGGATAAT
Found at i:1967401 original size:98 final size:98
Alignment explanation
Indices: 1967232--1967433 Score: 325
Period size: 98 Copynumber: 2.1 Consensus size: 98
1967222 TCCCCATATT
* * * *
1967232 TGGAAAGCTGCTCACTTTCCCTGTATTCAGAACAGAAAAATACAATTACACAACAAGGAAGATTT
1 TGGAAAGCTACTCACTTTCCCTGCAATCAGAACAGAAAAATACAATTACACAACAAGGAAGATAT
1967297 CAGGCATTCATAAGGGTTTGGTTTACATTAAAA
66 CAGGCATTCATAAGGGTTTGGTTTACATTAAAA
* * *
1967330 TGGAAAGCTACTCATTTTCCCTGCAATCAGAACAGAAAAATACAATTGCACAACTAGGAAGATAT
1 TGGAAAGCTACTCACTTTCCCTGCAATCAGAACAGAAAAATACAATTACACAACAAGGAAGATAT
*
1967395 CAGGCATTCATCAGGGTTTGGTTTACATTAAAA
66 CAGGCATTCATAAGGGTTTGGTTTACATTAAAA
1967428 T-GAAAG
1 TGGAAAG
1967434 TTTTCTCTAA
Statistics
Matches: 96, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
97 5 0.05
98 91 0.95
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (98 bp):
TGGAAAGCTACTCACTTTCCCTGCAATCAGAACAGAAAAATACAATTACACAACAAGGAAGATAT
CAGGCATTCATAAGGGTTTGGTTTACATTAAAA
Found at i:1968943 original size:5 final size:5
Alignment explanation
Indices: 1968933--1968958 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1968923 AGAGAAAAGA
1968933 GGGAG GGGAG GGGAG GGGAG GGGAG G
1 GGGAG GGGAG GGGAG GGGAG GGGAG G
1968959 AGAGAGCGAA
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:0.19, C:0.00, G:0.81, T:0.00
Consensus pattern (5 bp):
GGGAG
Found at i:1972381 original size:3 final size:3
Alignment explanation
Indices: 1972375--1972399 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1972365 TTCTTCTTCT
1972375 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
1972400 ACGAGAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:1973935 original size:22 final size:21
Alignment explanation
Indices: 1973883--1973946 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
1973873 AGTCGAGGGT
1973883 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
* * *
1973904 CTCATAGGTCTTTCAGGACATA
1 TTCATAGGTCCTTCGGGACA-A
*
1973926 TTCACAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
1973947 AATTTCATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:1975748 original size:59 final size:59
Alignment explanation
Indices: 1975633--1975749 Score: 171
Period size: 59 Copynumber: 2.0 Consensus size: 59
1975623 ATATATGTTC
* * * **
1975633 ACACATACATGTGGTATGTGACAGAATAGAAGGAACATGTGATTATAAGATCAATGATT
1 ACACATACATGTGGTATGTGACAGAAAAGAAGAAACATGTGATTAAAAGAGAAATGATT
* *
1975692 ACACGTACATGTGGTATGTGACAGAAAAGAAGAAATATGTGATTAAAAGAGAAATGAT
1 ACACATACATGTGGTATGTGACAGAAAAGAAGAAACATGTGATTAAAAGAGAAATGAT
1975750 ATGAATAAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.25
Consensus pattern (59 bp):
ACACATACATGTGGTATGTGACAGAAAAGAAGAAACATGTGATTAAAAGAGAAATGATT
Found at i:1975905 original size:32 final size:32
Alignment explanation
Indices: 1975869--1975973 Score: 117
Period size: 31 Copynumber: 3.3 Consensus size: 32
1975859 GTTCTACGGA
* *
1975869 ACATATAGACAGAATTACCTATGTCTTTCGAG
1 ACATATGGACACAATTACCTATGTCTTTCGAG
** *
1975901 ACATATGGACATTA-TACCTATGTCTTTTGAG
1 ACATATGGACACAATTACCTATGTCTTTCGAG
*
1975932 ACATAT-GA-ACAATATACATATGTCTTTCGAG
1 ACATATGGACACAAT-TACCTATGTCTTTCGAG
*
1975963 ATATATGGACA
1 ACATATGGACA
1975974 ATATACATAT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
29 2 0.03
30 2 0.03
31 42 0.70
32 13 0.22
33 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (32 bp):
ACATATGGACACAATTACCTATGTCTTTCGAG
Found at i:1975922 original size:31 final size:31
Alignment explanation
Indices: 1975888--1975985 Score: 151
Period size: 31 Copynumber: 3.2 Consensus size: 31
1975878 CAGAATTACC
* *
1975888 TATGTCTTTCGAGACATATGGACATTATACC
1 TATGTCTTTCGAGACATATGGACAATATACA
* *
1975919 TATGTCTTTTGAGACATATGAACAATATACA
1 TATGTCTTTCGAGACATATGGACAATATACA
*
1975950 TATGTCTTTCGAGATATATGGACAATATACA
1 TATGTCTTTCGAGACATATGGACAATATACA
1975981 TATGT
1 TATGT
1975986 TCTAAGGAAC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (31 bp):
TATGTCTTTCGAGACATATGGACAATATACA
Found at i:1975998 original size:62 final size:61
Alignment explanation
Indices: 1975856--1976004 Score: 165
Period size: 62 Copynumber: 2.4 Consensus size: 61
1975846 AGGGTTTACC
* * * * *
1975856 TATGTTCTACGGAACATATAGACAGAATTACCTATGTCTTTCGAGACATATGGACATTATACC
1 TATGTTCTAAGGAACATAT-GA-ACAATTACATATGTCTTTCGAGACATATGGACAATATACA
*** *
1975919 TATG-TCTTTTGAGACATATGAACAATATACATATGTCTTTCGAGATATATGGACAATATACA
1 TATGTTCTAAGGA-ACATATGAACAAT-TACATATGTCTTTCGAGACATATGGACAATATACA
*
1975981 TATGTTCTAAGGAACATATAAACA
1 TATGTTCTAAGGAACATATGAACA
1976005 GTTTACCTAG
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
61 4 0.06
62 52 0.73
63 15 0.21
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (61 bp):
TATGTTCTAAGGAACATATGAACAATTACATATGTCTTTCGAGACATATGGACAATATACA
Found at i:1978158 original size:22 final size:21
Alignment explanation
Indices: 1978110--1978162 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
1978100 ACCGAAATTT
**
1978110 ACTGTAGCAAGGGTATCGGTAC
1 ACTGTAGC-AGGGTATCAATAC
1978132 ACTGTAGCAGGGTATCAATACC
1 ACTGTAGCAGGGTATCAATA-C
*
1978154 CCTGTAGCA
1 ACTGTAGCA
1978163 TTCTGGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (21 bp):
ACTGTAGCAGGGTATCAATAC
Found at i:1978214 original size:22 final size:22
Alignment explanation
Indices: 1978189--1978269 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 22
1978179 CATTCGACAC
*
1978189 TGTTCATAGTACTGTTCACTAT
1 TGTTCATAGTACTATTCACTAT
* * * *
1978211 TGTTTATGGTACTATTTATTAT
1 TGTTCATAGTACTATTCACTAT
* *
1978233 TGTTCAGAGTACTATTCA-TAC
1 TGTTCATAGTACTATTCACTAT
1978254 TG-T-ATAGTACTATTCA
1 TGTTCATAGTACTATTCA
1978270 TAAAAACGTT
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
19 12 0.25
20 1 0.02
21 4 0.08
22 31 0.65
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (22 bp):
TGTTCATAGTACTATTCACTAT
Found at i:1979140 original size:91 final size:94
Alignment explanation
Indices: 1979013--1979198 Score: 297
Period size: 93 Copynumber: 2.0 Consensus size: 94
1979003 AAATGATAAT
*
1979013 ATAAATTAGTTTAAAAAATGATAATATAAATATTTTTATAATTT-ATATA-ATCATACAATTAGG
1 ATAAATTAGTTTAAAAAAT-ATAATATAAATATTTTTATAATTTAATAAATATCATACAATTAGG
1979076 ATCACATAACAATCTACTTAATCATATTTA
65 ATCACATAACAATCTACTTAATCATATTTA
* * *
1979106 ATAAATTAGTTTAACAAAT-TTATATAAATATTTTTATAATTTAATAAATATTATACAATTAGGA
1 ATAAATTAGTTTAAAAAATATAATATAAATATTTTTATAATTTAATAAATATCATACAATTAGGA
*
1979170 TCACATAACAATCTACTTAATCATTTTTA
66 TCACATAACAATCTACTTAATCATATTTA
1979199 TAATTATATA
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
91 22 0.26
92 4 0.05
93 60 0.70
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (94 bp):
ATAAATTAGTTTAAAAAATATAATATAAATATTTTTATAATTTAATAAATATCATACAATTAGGA
TCACATAACAATCTACTTAATCATATTTA
Found at i:1981999 original size:29 final size:29
Alignment explanation
Indices: 1981957--1982016 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1981947 AAGCTTAGTG
1981957 TAATTCTTGTACTAAGTGTCCAAGAAAGT
1 TAATTCTTGTACTAAGTGTCCAAGAAAGT
1981986 TAATTCTTGTACTAAGTGTCCAAGAAAGT
1 TAATTCTTGTACTAAGTGTCCAAGAAAGT
1982015 TA
1 TA
1982017 TGTGTTAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (29 bp):
TAATTCTTGTACTAAGTGTCCAAGAAAGT
Found at i:1983886 original size:43 final size:43
Alignment explanation
Indices: 1983824--1983906 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
1983814 ATTTCTAACT
* *
1983824 TGAAAATCAGTACCACTAAATTTAAAGTAATCCATTAGATACA
1 TGAAAATCAGTACCACTAAACTCAAAGTAATCCATTAGATACA
* ** * *
1983867 TGAAAATCATTACTTCTAAACTCGAAGTAATGCATTAGAT
1 TGAAAATCAGTACCACTAAACTCAAAGTAATCCATTAGAT
1983907 TTTGCTTTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (43 bp):
TGAAAATCAGTACCACTAAACTCAAAGTAATCCATTAGATACA
Found at i:1986513 original size:3 final size:3
Alignment explanation
Indices: 1986505--1986557 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
1986495 ATTGATTGAG
*
1986505 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1986553 ATA AT
1 ATA AT
1986558 TTGTTATTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1987400 original size:37 final size:36
Alignment explanation
Indices: 1987350--1987419 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
1987340 TTGATTTTTC
1987350 GAAAAATAAATTACT-GAAATTTGAATTACTGGAACTG
1 GAAAAATAAATTACTAG-AATTTGAATT-CTGGAACTG
*
1987387 GAAAAATGAATTACTAGAATTTGAATTCTGGAA
1 GAAAAATAAATTACTAGAATTTGAATTCTGGAA
1987420 AATGAATTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
36 6 0.19
37 24 0.77
38 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30
Consensus pattern (36 bp):
GAAAAATAAATTACTAGAATTTGAATTCTGGAACTG
Found at i:1987427 original size:14 final size:15
Alignment explanation
Indices: 1987383--1987429 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1987373 AATTACTGGA
1987383 ACTGGAAAAATGAATT
1 ACTGG-AAAATGAATT
* **
1987399 ACTAGAATTTGAATT
1 ACTGGAAAATGAATT
1987414 -CTGGAAAATGAATT
1 ACTGGAAAATGAATT
1987428 AC
1 AC
1987430 ATTTCTGGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
14 11 0.46
15 9 0.38
16 4 0.17
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (15 bp):
ACTGGAAAATGAATT
Found at i:1987675 original size:48 final size:48
Alignment explanation
Indices: 1987565--1987663 Score: 110
Period size: 49 Copynumber: 2.0 Consensus size: 48
1987555 TACAAATATT
*
1987565 AAATATACTAAATAATATTATTTATCATAAAATTTAATATTATTATTTTA
1 AAATATA--AAATAATATTATTTATCATAAAATTTAATATTATAATTTTA
* * * *
1987615 AAATATTAAAATAAT-TTATTTATTATTAAATATTATTTTTATAATTTTA
1 AAATA-TAAAATAATATTATTTATCATAAAAT-TTAATATTATAATTTTA
1987664 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 14 0.33
49 21 0.50
50 5 0.12
51 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (48 bp):
AAATATAAAATAATATTATTTATCATAAAATTTAATATTATAATTTTA
Found at i:1987708 original size:32 final size:30
Alignment explanation
Indices: 1987642--1987710 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
1987632 ATTTATTATT
*
1987642 AAATATT-ATTTTTATAATTTTATTAATAA
1 AAATATTAATTTTTATAATTTTATAAATAA
*
1987671 AAATATTAATTTTTGTATATTTTAGTGAAAT-A
1 AAATATTAATTTTTATA-ATTTTA-T-AAATAA
1987703 AAATATTA
1 AAATATTA
1987711 TAAATTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 7 0.21
30 8 0.24
31 6 0.18
32 10 0.29
33 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (30 bp):
AAATATTAATTTTTATAATTTTATAAATAA
Found at i:1987801 original size:23 final size:23
Alignment explanation
Indices: 1987752--1987814 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
1987742 GTGTTATATT
* **
1987752 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
1987775 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
1987798 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
1987815 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:1987874 original size:25 final size:26
Alignment explanation
Indices: 1987798--1987886 Score: 92
Period size: 28 Copynumber: 3.3 Consensus size: 26
1987788 CTTTATTAAA
1987798 ATATTATTTAAATATATAAATAATATTAT
1 ATATTA-TTAAATATA-AAA-AATATTAT
1987827 -TCATTATTAATATATAAAAAAATATTAT
1 AT-ATTATTAA-ATAT-AAAAAATATTAT
* *
1987855 ATATTATTAAA-ATAAAAAATGTAAT
1 ATATTATTAAATATAAAAAATATTAT
1987880 ATATTAT
1 ATATTAT
1987887 ATTATAATAA
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
25 17 0.31
26 2 0.04
27 1 0.02
28 21 0.39
29 12 0.22
30 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (26 bp):
ATATTATTAAATATAAAAAATATTAT
Found at i:1987950 original size:22 final size:22
Alignment explanation
Indices: 1987919--1987961 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1987909 CTTTATATAA
1987919 TATTAAAAATA-TAATATAATAT
1 TATTAAAAATATTAATA-AATAT
*
1987941 TATTATAAATATTAATAAATA
1 TATTAAAAATATTAATAAATA
1987962 AATAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TATTAAAAATATTAATAAATAT
Found at i:1987976 original size:31 final size:32
Alignment explanation
Indices: 1987807--1987977 Score: 95
Period size: 31 Copynumber: 5.7 Consensus size: 32
1987797 AATATTATTT
*
1987807 AAATAT-ATA-AATAATATTAT-TCATTATT-A
1 AAATATAATATAATAATATTATAT-AATATTAA
* *
1987836 ATATATAA-A-AA-AATATTATATATTATTAA
1 AAATATAATATAATAATATTATATAATATTAA
* * *
1987865 AATAAAAAATGTAAT-ATATTATAT--TA-TAA
1 AA-ATATAATATAATAATATTATATAATATTAA
* * *
1987894 TAATATAAT-TGATTACT-TTATATAATATTAA
1 AAATATAATAT-AATAATATTATATAATATTAA
*
1987925 AAATATAATATAATATTATTATA-AATATTAA
1 AAATATAATATAATAATATTATATAATATTAA
1987956 TAAATA-AATA-AATAAATATTAT
1 -AAATATAATATAAT-AATATTAT
1987978 TTTGATGAAA
Statistics
Matches: 112, Mismatches: 14, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
27 1 0.01
28 27 0.24
29 16 0.14
30 12 0.11
31 34 0.30
32 22 0.20
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (32 bp):
AAATATAATATAATAATATTATATAATATTAA
Found at i:1987989 original size:62 final size:59
Alignment explanation
Indices: 1987923--1988041 Score: 143
Period size: 63 Copynumber: 2.0 Consensus size: 59
1987913 ATATAATATT
*
1987923 AAAAAT-ATAATATAATATTATTATAAATATT-AATAAATAAATAAATAAATATTATTTTGATG
1 AAAAATGATAATAAAATATT-TTATAAATATTAAATAAAT--A-AAATAAA-ATTATTTTGATG
* * *
1987985 AAAAATGATATTAAAATATTTTATTAATATTAAATTAATAAAATAAAATTATTTTGA
1 AAAAATGATAATAAAATATTTTATAAATATTAAATAAATAAAATAAAATTATTTTGA
1988042 GTATTTATTC
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
59 10 0.20
60 7 0.14
61 1 0.02
62 16 0.31
63 17 0.33
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (59 bp):
AAAAATGATAATAAAATATTTTATAAATATTAAATAAATAAAATAAAATTATTTTGATG
Found at i:1988200 original size:42 final size:42
Alignment explanation
Indices: 1988153--1988267 Score: 196
Period size: 41 Copynumber: 2.8 Consensus size: 42
1988143 ATGAATTATA
*
1988153 TTCCGGAAAACCAATTACGTAAAACAAACACGGGAAAACATT
1 TTCCGGAAAACCAATTACGTGAAACAAACACGGGAAAACATT
* *
1988195 TTCCGGAAAACGAATAACGTGAAACAAACAC-GGAAAACATT
1 TTCCGGAAAACCAATTACGTGAAACAAACACGGGAAAACATT
1988236 TTCCGGAAAACCAATTACGTGAAACAAACACG
1 TTCCGGAAAACCAATTACGTGAAACAAACACG
1988268 AGAATTCGGG
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
41 39 0.58
42 28 0.42
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACCAATTACGTGAAACAAACACGGGAAAACATT
Found at i:1988720 original size:5 final size:5
Alignment explanation
Indices: 1988710--1988738 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1988700 GTGAAAAAAT
1988710 CCGAC CCGAC CCGAC CCGAC CCGAC CCGA
1 CCGAC CCGAC CCGAC CCGAC CCGAC CCGA
1988739 AAAATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.59, G:0.21, T:0.00
Consensus pattern (5 bp):
CCGAC
Found at i:1991533 original size:71 final size:71
Alignment explanation
Indices: 1991458--1991599 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
1991448 AGCTGTCTAC
1991458 CCTAAAATTTTATTTGTGATTATCAATATAAATTTTTTTAATAATTAATCACTGTAAAAAATATT
1 CCTAAAATTTTATTTGTGATTATCAATATAAATTTTTTTAATAATTAATCACTGTAAAAAATATT
1991523 TATAGA
66 TATAGA
1991529 CCTAAAATTTTATTTGTGATTATCAATATAAATTTTTTTAATAATTAATCACTGTAAAAAATATT
1 CCTAAAATTTTATTTGTGATTATCAATATAAATTTTTTTAATAATTAATCACTGTAAAAAATATT
1991594 TATAGA
66 TATAGA
1991600 TCGATCACTG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (71 bp):
CCTAAAATTTTATTTGTGATTATCAATATAAATTTTTTTAATAATTAATCACTGTAAAAAATATT
TATAGA
Found at i:2000914 original size:20 final size:20
Alignment explanation
Indices: 2000820--2001188 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
2000810 GATTTTCCAT
* ** *
2000820 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2000840 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
2000860 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2000880 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
2000900 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
2000920 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2000940 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2000960 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2000980 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2001000 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2001020 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2001040 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2001060 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
2001080 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2001100 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2001120 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2001140 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2001160 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2001180 AATCACAAC
1 AATCGCAAC
2001189 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2001909 original size:24 final size:24
Alignment explanation
Indices: 2001870--2001916 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2001860 AAATTTGGTC
2001870 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2001894 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2001917 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:2002108 original size:12 final size:12
Alignment explanation
Indices: 2002091--2002115 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2002081 ATATAATCCT
2002091 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2002103 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2002115 G
1 G
2002116 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:2004480 original size:33 final size:34
Alignment explanation
Indices: 2004393--2004716 Score: 254
Period size: 33 Copynumber: 9.5 Consensus size: 34
2004383 CGGAAAATAC
* *
2004393 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
2004426 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
2004460 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
2004498 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
* *
2004531 AATCGCAATGCGAAATGAAAATCGCAACGA-CAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
2004564 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
2004602 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
2004635 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
2004668 AATCGCAATGCGAAATGAAAATCGCAACGA-GAT
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
2004701 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
2004717 TATAAACGCA
Statistics
Matches: 256, Mismatches: 13, Indels: 44
0.82 0.04 0.14
Matches are distributed among these distances:
33 160 0.62
34 32 0.12
35 12 0.05
36 12 0.05
37 3 0.01
38 37 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:2004508 original size:52 final size:52
Alignment explanation
Indices: 2004421--2004694 Score: 423
Period size: 52 Copynumber: 5.2 Consensus size: 52
2004411 AAATCCCAAC
2004421 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
2004474 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
2004526 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
2004578 ATTAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
2004630 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
2004682 ATGAAAATCGCAA
1 ATGAAAATCGCAA
2004695 CGAGATAATC
Statistics
Matches: 210, Mismatches: 6, Indels: 11
0.93 0.03 0.05
Matches are distributed among these distances:
47 8 0.04
49 3 0.01
50 5 0.02
51 1 0.00
52 177 0.84
53 16 0.08
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:2004676 original size:85 final size:85
Alignment explanation
Indices: 2004479--2004716 Score: 351
Period size: 85 Copynumber: 2.8 Consensus size: 85
2004469 GCGAAATGAA
*
2004479 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAA
*
2004539 TGCGAAATGAAAATCGCAACGACAG
61 TGCGAAATGAAAATCGCAACGAAAG
*
2004564 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
2004629 AATGAAAATCGCAACGAAAG
66 AATGAAAATCGCAACGAAAG
* *
2004649 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
2004714 AAT
66 AAT
2004717 TATAAACGCA
Statistics
Matches: 142, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
85 123 0.87
87 3 0.02
88 5 0.04
89 1 0.01
90 10 0.07
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (85 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAAAATCGCAACGAAAG
Found at i:2004832 original size:19 final size:19
Alignment explanation
Indices: 2004723--2004824 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2004713 AAATTATAAA
2004723 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2004742 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
2004762 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
2004778 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2004795 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2004814 CGCATTGCGAT
1 CGCATTGCGAT
2004825 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:2004950 original size:14 final size:14
Alignment explanation
Indices: 2004931--2004967 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2004921 CATCAATTAC
2004931 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2004945 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2004959 ACAAATCAA
1 ACAAATCAA
2004968 TTAAACAATC
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:2006962 original size:14 final size:14
Alignment explanation
Indices: 2006943--2006999 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2006933 GCGAAATGAA
*
2006943 AATCGCAACGACAG
1 AATCGCAACGAAAG
2006957 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
2006974 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
2006990 AATCGCAACG
1 AATCGCAACG
2007000 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2006970 original size:33 final size:33
Alignment explanation
Indices: 2006924--2007016 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2006914 GCGAAACCAA
*
2006924 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
2006957 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2006990 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2007017 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:2006981 original size:19 final size:19
Alignment explanation
Indices: 2006887--2007021 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
2006877 TAGTTTACTT
* *
2006887 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2006907 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2006926 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2006945 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
2006959 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2006978 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
2006992 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2007011 TCGCAATGCGA
1 TCGCAACGCGA
2007022 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2007039 original size:19 final size:19
Alignment explanation
Indices: 2007017--2007145 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2007007 AAAATCGCAA
2007017 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2007036 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2007050 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2007069 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2007083 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2007102 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2007121 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2007141 TGCGA
1 TGCGA
2007146 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2007059 original size:33 final size:33
Alignment explanation
Indices: 2007017--2007108 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2007007 AAAATCGCAA
2007017 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
2007050 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
2007083 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2007109 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2007336 original size:93 final size:93
Alignment explanation
Indices: 2007177--2007643 Score: 918
Period size: 93 Copynumber: 5.0 Consensus size: 93
2007167 GCAAATTGAA
2007177 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
2007242 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
2007270 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
2007335 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
2007363 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
2007428 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
2007456 ACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
2007520 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
2007548 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
2007613 GCAGAATTGGCAGCAACCGAATAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
2007641 ACT
1 ACT
2007644 AAGCAATCTA
Statistics
Matches: 372, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.25
93 280 0.75
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTT
Found at i:2007614 original size:185 final size:186
Alignment explanation
Indices: 2007177--2007643 Score: 918
Period size: 185 Copynumber: 2.5 Consensus size: 186
2007167 GCAAATTGAA
2007177 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
2007242 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
2007307 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
2007363 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
2007428 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
2007492 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
2007548 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
2007613 GCAGAATTGGCAGCAACCGAATAAATTTACT
66 GCAGAATTGGCAGCAACCGAACAAATTTACT
2007644 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
185 154 0.55
186 126 0.45
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
Found at i:2009363 original size:14 final size:14
Alignment explanation
Indices: 2009344--2009432 Score: 79
Period size: 14 Copynumber: 5.7 Consensus size: 14
2009334 TTGAAATGAA
2009344 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2009358 AATCGCAACGAGAATG
1 AATCGCAACGAG-A-G
*
2009374 ACTGTCGCAACGAGAG
1 A--ATCGCAACGAGAG
*
2009390 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2009409 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2009423 AATCGCAACG
1 AATCGCAACG
2009433 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 6 0.10
17 3 0.05
18 11 0.18
19 10 0.16
ACGTcount: A:0.42, C:0.22, G:0.26, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2009414 original size:19 final size:19
Alignment explanation
Indices: 2009390--2009454 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
2009380 GCAACGAGAG
2009390 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2009409 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
2009423 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2009442 AATCGCAATGCGA
1 AATCGCAACGCGA
2009455 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2009415 original size:33 final size:33
Alignment explanation
Indices: 2009336--2009449 Score: 185
Period size: 33 Copynumber: 3.5 Consensus size: 33
2009326 TCTTTTGGTT
*
2009336 GAAATGAAAATCGCAACGAGAGAATCGCAACGA
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
***
2009369 G-AATGACTGTCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2009401 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2009434 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2009450 TGCGATTTTG
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
32 28 0.38
33 45 0.62
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2009485 original size:14 final size:14
Alignment explanation
Indices: 2009466--2009520 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2009456 TTTGGTTTCG
2009466 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2009480 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2009499 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2009513 CGTTGCGA
1 CGTTGCGA
2009521 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2009498 original size:33 final size:33
Alignment explanation
Indices: 2009450--2009520 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2009440 AAAATCGCAA
**
2009450 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2009483 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2009516 TGCGA
1 TGCGA
2009521 CAGTCATTCT
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:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2009528 original size:33 final size:33
Alignment explanation
Indices: 2009461--2009540 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
2009451 GCGATTTTGG
***
2009461 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
2009494 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
2009527 -TTCTCGTTGCGATT
1 TTTCGCGTTGCGATT
2009541 TTCATTTATC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 13 0.30
33 30 0.70
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:2009545 original size:18 final size:18
Alignment explanation
Indices: 2009477--2009546 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 18
2009467 GTTGCGATTC
2009477 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTTTCA-T
*
2009496 TCGCGTTGCGA--TTC--
1 TCTCGTTGCGATTTTCAT
***
2009510 TCTCGTTGCGACAGTCAT
1 TCTCGTTGCGATTTTCAT
2009528 TCTCGTTGCGATTTTCAT
1 TCTCGTTGCGATTTTCAT
2009546 T
1 T
2009547 TATCTCGTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
14 10 0.24
16 2 0.05
17 3 0.07
18 16 0.39
19 10 0.24
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (18 bp):
TCTCGTTGCGATTTTCAT
Found at i:2009681 original size:33 final size:32
Alignment explanation
Indices: 2009639--2009708 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 32
2009629 AATACTAACT
*
2009639 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCG-AA
* *
2009672 TGAAAATCGCAACGACAGAATCGTAACGCGAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAA
2009704 TGAAA
1 TGAAA
2009709 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 7 0.21
33 27 0.79
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (32 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAA
Done.