Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 42 of 198
Found at i:12594291 original size:50 final size:50
Alignment explanation
Indices: 12594237--12594378 Score: 176
Period size: 50 Copynumber: 2.8 Consensus size: 50
12594227 AGATGTTACA
*
12594237 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
*** * * *
12594287 AGAGGTCCCCCATAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
** * * *
12594337 AGAACTCCCATGTAAGACCATATTTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
12594379 GTACAGAAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 76 1.00
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
Found at i:12597252 original size:40 final size:39
Alignment explanation
Indices: 12597208--12597337 Score: 152
Period size: 40 Copynumber: 3.3 Consensus size: 39
12597198 CAGGCACCGG
* * * *
12597208 AGTGCATTCAGGGGAATGAATGTGCTATCAAGGGCATCGA
1 AGTGCATTCAGGGGCACGAATGTGCTGTCAGGGGCA-CGA
* * *
12597248 AGTGCATTTAGGGGCACAAATGTGCTGTCAGGGGCACCA
1 AGTGCATTCAGGGGCACGAATGTGCTGTCAGGGGCACGA
* *
12597287 TAGTGCATCCAAGGGCACGAATGTGCTGTCAGGGGCACTGA
1 -AGTGCATTCAGGGGCACGAATGTGCTGTCAGGGGCAC-GA
12597328 AGTGCATTCA
1 AGTGCATTCA
12597338 ATAACACCGA
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
39 2 0.03
40 72 0.96
41 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.22
Consensus pattern (39 bp):
AGTGCATTCAGGGGCACGAATGTGCTGTCAGGGGCACGA
Found at i:12597332 original size:20 final size:19
Alignment explanation
Indices: 12597215--12597332 Score: 69
Period size: 20 Copynumber: 5.9 Consensus size: 19
12597205 CGGAGTGCAT
* * *
12597215 TCAGGGGAATGAATGTGCTA
1 TCAGGGGCACGAA-GTGCTG
*
12597235 TCAAGGGCATCGAAGTGCAT-
1 TCAGGGGCA-CGAAGTGC-TG
* *
12597255 TTAGGGGCACAAATGTGCTG
1 TCAGGGGCACGAA-GTGCTG
*
12597275 TCAGGGGCACCATAGTGCAT-
1 TCAGGGGCACGA-AGTGC-TG
* *
12597295 CCAAGGGCACGAATGTGCTG
1 TCAGGGGCACGAA-GTGCTG
12597315 TCAGGGGCACTGAAGTGC
1 TCAGGGGCAC-GAAGTGC
12597333 ATTCAATAAC
Statistics
Matches: 76, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
19 6 0.08
20 61 0.80
21 9 0.12
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.20
Consensus pattern (19 bp):
TCAGGGGCACGAAGTGCTG
Found at i:12599728 original size:31 final size:31
Alignment explanation
Indices: 12599693--12599786 Score: 85
Period size: 24 Copynumber: 3.2 Consensus size: 31
12599683 GAAATAGTAA
12599693 TTTAAGTTCTTGAAGATACAATTAGAATTTT
1 TTTAAGTTCTTGAAGATACAATTAGAATTTT
* **
12599724 TTTAA-----T--AGATACAATCAGAAATAGTAA
1 TTTAAGTTCTTGAAGATACAATTAG-AAT--TTT
12599751 TTTAAGTTCTTGAAGATACAATTAGAATTTT
1 TTTAAGTTCTTGAAGATACAATTAGAATTTT
12599782 TTTAA
1 TTTAA
12599787 TAGATTTTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 20
0.64 0.08 0.27
Matches are distributed among these distances:
24 11 0.23
25 3 0.06
26 1 0.02
27 6 0.13
31 11 0.23
32 1 0.02
33 3 0.06
34 11 0.23
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.41
Consensus pattern (31 bp):
TTTAAGTTCTTGAAGATACAATTAGAATTTT
Found at i:12599747 original size:58 final size:58
Alignment explanation
Indices: 12599677--12599791 Score: 230
Period size: 58 Copynumber: 2.0 Consensus size: 58
12599667 GACAGATGGG
12599677 CAATCAGAAATAGTAATTTAAGTTCTTGAAGATACAATTAGAATTTTTTTAATAGATA
1 CAATCAGAAATAGTAATTTAAGTTCTTGAAGATACAATTAGAATTTTTTTAATAGATA
12599735 CAATCAGAAATAGTAATTTAAGTTCTTGAAGATACAATTAGAATTTTTTTAATAGAT
1 CAATCAGAAATAGTAATTTAAGTTCTTGAAGATACAATTAGAATTTTTTTAATAGAT
12599792 TTTGGAATTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (58 bp):
CAATCAGAAATAGTAATTTAAGTTCTTGAAGATACAATTAGAATTTTTTTAATAGATA
Found at i:12607633 original size:2 final size:2
Alignment explanation
Indices: 12607626--12607658 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12607616 CCCTCCCTTC
12607626 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
12607659 ATTGTTCTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:12610444 original size:31 final size:31
Alignment explanation
Indices: 12610406--12610468 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
12610396 AGGAAAAGGG
12610406 AAAGTTGTTGATTAGTCCGTGAATTTTTACT
1 AAAGTTGTTGATTAGTCCGTGAATTTTTACT
12610437 AAAGTTGTTGATTAGTCCGTGAATTTTTACT
1 AAAGTTGTTGATTAGTCCGTGAATTTTTACT
12610468 A
1 A
12610469 TCTCTATAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (31 bp):
AAAGTTGTTGATTAGTCCGTGAATTTTTACT
Found at i:12613146 original size:18 final size:18
Alignment explanation
Indices: 12613123--12613165 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 18
12613113 ATGCAAGTAG
12613123 TTTGGTTTG-TAATGTGAA
1 TTTGGTTTGATAAT-TGAA
12613141 TTTGGTTTGATAATTGAA
1 TTTGGTTTGATAATTGAA
12613159 TTGTGGT
1 TT-TGGT
12613166 GTCAATGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (18 bp):
TTTGGTTTGATAATTGAA
Found at i:12618545 original size:41 final size:42
Alignment explanation
Indices: 12618485--12618596 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
12618475 CCGAAGGCTG
* ** * *
12618485 AACAGAAGCTTATGAGAGCTAAACGGAAAC-CATACGCGTTA
1 AACAGAAGCTCAAAAGAGCTAAACGAAAACTCATACGCATTA
* *
12618526 AATAGAAGCTCAAAAGAGCTAAACGAAAACTCATATGCATTA
1 AACAGAAGCTCAAAAGAGCTAAACGAAAACTCATACGCATTA
* *
12618568 AACAGAAGCTCATGAA-ACCTAAACGAAAA
1 AACAGAAGCTCA-AAAGAGCTAAACGAAAA
12618597 GTAAACACGA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 25 0.42
42 32 0.54
43 2 0.03
ACGTcount: A:0.48, C:0.19, G:0.17, T:0.16
Consensus pattern (42 bp):
AACAGAAGCTCAAAAGAGCTAAACGAAAACTCATACGCATTA
Found at i:12624547 original size:30 final size:30
Alignment explanation
Indices: 12624511--12624571 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
12624501 GTCTCTGTCT
12624511 CAGATTCAACTATTTCTGAGTCATCAAGTA
1 CAGATTCAACTATTTCTGAGTCATCAAGTA
* *
12624541 CAGATTCGACTCTTTCTGAGTCATCAAGTA
1 CAGATTCAACTATTTCTGAGTCATCAAGTA
12624571 C
1 C
12624572 TTTAGACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (30 bp):
CAGATTCAACTATTTCTGAGTCATCAAGTA
Found at i:12632868 original size:20 final size:22
Alignment explanation
Indices: 12632843--12632883 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12632833 TTTAATCACC
12632843 AAATAG-GGG-AAAAATTAAAA
1 AAATAGAGGGTAAAAATTAAAA
*
12632863 AAATAGAGGGTCAAAATTAAA
1 AAATAGAGGGTAAAAATTAAA
12632884 TTATAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.61, C:0.02, G:0.20, T:0.17
Consensus pattern (22 bp):
AAATAGAGGGTAAAAATTAAAA
Found at i:12633599 original size:18 final size:18
Alignment explanation
Indices: 12633561--12633593 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12633551 AATTTTACTC
12633561 TAATTACATTTCTTAAAA
1 TAATTACATTTCTTAAAA
12633579 TAATTA-ATTT-TTAAA
1 TAATTACATTTCTTAAA
12633594 TTATAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 4 0.27
18 6 0.40
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATTACATTTCTTAAAA
Found at i:12635602 original size:29 final size:30
Alignment explanation
Indices: 12635528--12635602 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
12635518 TCTCAAATCT
*
12635528 ATATATAAATTTTGATTTAATATGTAATTTA
1 ATATATAAATTTTAATTTAATA-GTAATTTA
12635559 ATATATAAATTTTAATTTAATA-T-ATTTA
1 ATATATAAATTTTAATTTAATAGTAATTTA
* *
12635587 TATTTATAAAATTTAA
1 -ATATATAAATTTTAA
12635603 ATGTATACAC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 5 0.12
29 14 0.35
31 21 0.52
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (30 bp):
ATATATAAATTTTAATTTAATAGTAATTTA
Found at i:12639670 original size:20 final size:20
Alignment explanation
Indices: 12639645--12639686 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
12639635 GATAGTTTTG
*
12639645 TTATTTTGGTTATTTTTATT
1 TTATTTTAGTTATTTTTATT
12639665 TTATTTTAGTTATTTTTATT
1 TTATTTTAGTTATTTTTATT
12639685 TT
1 TT
12639687 TCTCTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (20 bp):
TTATTTTAGTTATTTTTATT
Found at i:12640592 original size:19 final size:20
Alignment explanation
Indices: 12640545--12640593 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
12640535 AAAAAAATCA
*
12640545 TTATAAATATTTTATTATAT
1 TTATAAATATTCTATTATAT
*
12640565 TT-TACATATTCTATTAT-T
1 TTATAAATATTCTATTATAT
*
12640583 TTATATATATT
1 TTATAAATATT
12640594 GCACCTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 20 0.80
20 2 0.08
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATAAATATTCTATTATAT
Found at i:12644805 original size:26 final size:26
Alignment explanation
Indices: 12644738--12644810 Score: 103
Period size: 26 Copynumber: 2.8 Consensus size: 26
12644728 TCTCATCCTT
*
12644738 ATTTTACCCTTAGAAAAATTTTGACG
1 ATTTTACCCTTAGTAAAATTTTGACG
*
12644764 ATTTTACCCTTAGTAAAATTTTGATG
1 ATTTTACCCTTAGTAAAATTTTGACG
*
12644790 ATTTTTTCCCTT-GTAAAATTT
1 A-TTTTACCCTTAGTAAAATTT
12644811 CGAGAAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 34 0.79
27 9 0.21
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.47
Consensus pattern (26 bp):
ATTTTACCCTTAGTAAAATTTTGACG
Found at i:12645625 original size:89 final size:89
Alignment explanation
Indices: 12645464--12645635 Score: 281
Period size: 89 Copynumber: 1.9 Consensus size: 89
12645454 TAACTCGTGG
* * *
12645464 CCACATTTATTTTTCATCAACTATGTAATGTCAATGAAAGGATATCATTTACCTATATTTTGGGC
1 CCACATTTACTTTTCATCAACTATGTAATGCCAATGAAAGGATATCATTTACCCATATTTTGGGC
* *
12645529 TATGAATTCTACTGTTGTAGGTTA
66 TATGAATTCCACTATTGTAGGTTA
* *
12645553 CCACGTTTACTTTTCATCAACTATGTAATGCCAATGAGAGGATATCATTTACCCATATTTTGGGC
1 CCACATTTACTTTTCATCAACTATGTAATGCCAATGAAAGGATATCATTTACCCATATTTTGGGC
12645618 TATGAATTCCACTATTGT
66 TATGAATTCCACTATTGT
12645636 GAATGACGCT
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
89 76 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (89 bp):
CCACATTTACTTTTCATCAACTATGTAATGCCAATGAAAGGATATCATTTACCCATATTTTGGGC
TATGAATTCCACTATTGTAGGTTA
Found at i:12648161 original size:16 final size:16
Alignment explanation
Indices: 12648142--12648173 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12648132 GGCACTAAGC
12648142 AACTCAATTACTAATT
1 AACTCAATTACTAATT
12648158 AACTCAATTACTAATT
1 AACTCAATTACTAATT
12648174 GTTTAACCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
AACTCAATTACTAATT
Found at i:12655854 original size:11 final size:10
Alignment explanation
Indices: 12655829--12655859 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
12655819 GAGTAACAAG
12655829 TTAAAAATAT
1 TTAAAAATAT
12655839 TTAAAAATAT
1 TTAAAAATAT
12655849 TATAAAAATAT
1 T-TAAAAATAT
12655860 CGAAAAGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.55
11 9 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TTAAAAATAT
Found at i:12655911 original size:29 final size:26
Alignment explanation
Indices: 12655877--12655948 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 26
12655867 TTCAAATTTT
12655877 ATAAAAATTAAAAATATATAAATTACAAA
1 ATAAAAATTAAAAAT-TATAAA--ACAAA
* *
12655906 ATAAAATTGTAAAAATTATAAAATAAA
1 ATAAAAAT-TAAAAATTATAAAACAAA
12655933 ATAAAAATTACAAAAT
1 ATAAAAATTA-AAAAT
12655949 GTTAAAATAG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
26 2 0.05
27 16 0.42
29 13 0.34
30 7 0.18
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (26 bp):
ATAAAAATTAAAAATTATAAAACAAA
Found at i:12655921 original size:22 final size:19
Alignment explanation
Indices: 12655877--12655948 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 19
12655867 TTCAAATTTT
12655877 ATAAAAATTA-AAAAT---
1 ATAAAAATTACAAAATAAA
*
12655892 ATATAAATTACAAAATAAA
1 ATAAAAATTACAAAATAAA
*
12655911 ATTGTAAAAATTATAAAATAAA
1 A---TAAAAATTACAAAATAAA
12655933 ATAAAAATTACAAAAT
1 ATAAAAATTACAAAAT
12655949 GTTAAAATAG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
15 9 0.20
16 5 0.11
19 15 0.33
22 17 0.37
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (19 bp):
ATAAAAATTACAAAATAAA
Found at i:12656584 original size:13 final size:13
Alignment explanation
Indices: 12656566--12656608 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
12656556 AAAAGCACTT
*
12656566 AGCACTTCTCAAA
1 AGCACTTTTCAAA
* *
12656579 AGCACTTTTCCAC
1 AGCACTTTTCAAA
12656592 AGCACTTTTCAAA
1 AGCACTTTTCAAA
12656605 AGCA
1 AGCA
12656609 ATGAAGAACT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.35, C:0.30, G:0.09, T:0.26
Consensus pattern (13 bp):
AGCACTTTTCAAA
Found at i:12658292 original size:16 final size:16
Alignment explanation
Indices: 12658271--12658306 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
12658261 TCATTCGATT
12658271 GAGTAAATATGCTCTA
1 GAGTAAATATGCTCTA
12658287 GAGTAAATATGCTCTA
1 GAGTAAATATGCTCTA
12658303 GAGT
1 GAGT
12658307 GCATTCCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (16 bp):
GAGTAAATATGCTCTA
Found at i:12661230 original size:25 final size:25
Alignment explanation
Indices: 12661202--12661269 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
12661192 TTTATATGTG
*
12661202 AGCCTGTATGCTAGTATAATATGAA
1 AGCCTATATGCTAGTATAATATGAA
* * **
12661227 AGCCTATATGTTAGTGTAATATGTG
1 AGCCTATATGCTAGTATAATATGAA
* *
12661252 AGCCTATTTGTTAGTATA
1 AGCCTATATGCTAGTATA
12661270 TGCGAGCTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (25 bp):
AGCCTATATGCTAGTATAATATGAA
Found at i:12661289 original size:21 final size:22
Alignment explanation
Indices: 12661227--12661316 Score: 69
Period size: 22 Copynumber: 4.0 Consensus size: 22
12661217 ATAATATGAA
* *
12661227 AGCCTATATGTTAGTGTAATATGTG
1 AGCCTATTTGTTA--GT-ATATGCG
12661252 AGCCTATTTGTTAGTATATGCG
1 AGCCTATTTGTTAGTATATGCG
* *
12661274 AGCTTATTTG-TAGTATATACG
1 AGCCTATTTGTTAGTATATGCG
* *
12661295 AACCCT-TATGTTAG-ATATGCG
1 -AGCCTATTTGTTAGTATATGCG
12661316 A
1 A
12661317 ACCACTTAGA
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
20 1 0.02
21 19 0.35
22 21 0.38
23 2 0.04
25 12 0.22
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (22 bp):
AGCCTATTTGTTAGTATATGCG
Found at i:12663326 original size:13 final size:13
Alignment explanation
Indices: 12663308--12663332 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12663298 CACTCGGTCC
12663308 TGTGTCACGACAA
1 TGTGTCACGACAA
12663321 TGTGTCACGACA
1 TGTGTCACGACA
12663333 TAGTAGTCAG
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:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (13 bp):
TGTGTCACGACAA
Found at i:12669089 original size:21 final size:20
Alignment explanation
Indices: 12669065--12669111 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
12669055 TGAAAGAGGT
*
12669065 TTTATTTTTTTCACTAGTTTA
1 TTTATGTTTTT-ACTAGTTTA
* *
12669086 TTTATGTTTTTGCTTGTTTA
1 TTTATGTTTTTACTAGTTTA
12669106 TTTATG
1 TTTATG
12669112 CTACAAGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.15, C:0.06, G:0.11, T:0.68
Consensus pattern (20 bp):
TTTATGTTTTTACTAGTTTA
Found at i:12670741 original size:17 final size:17
Alignment explanation
Indices: 12670719--12670755 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
12670709 AATAAAAATT
12670719 TATTTTATAATAATAAA
1 TATTTTATAATAATAAA
*
12670736 TATTTTGTAATAATAAA
1 TATTTTATAATAATAAA
12670753 TAT
1 TAT
12670756 CATGTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TATTTTATAATAATAAA
Found at i:12670761 original size:17 final size:17
Alignment explanation
Indices: 12670726--12670761 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12670716 ATTTATTTTA
**
12670726 TAATAATAAATATTTTG
1 TAATAATAAATATCATG
12670743 TAATAATAAATATCATG
1 TAATAATAAATATCATG
12670760 TA
1 TA
12670762 TAAACTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (17 bp):
TAATAATAAATATCATG
Found at i:12679322 original size:15 final size:15
Alignment explanation
Indices: 12679302--12679353 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
12679292 ACTACACAAC
12679302 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
12679317 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
12679336 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
12679351 ATT
1 ATT
12679354 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:12679418 original size:16 final size:16
Alignment explanation
Indices: 12679387--12679423 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
12679377 ATATGAAGAA
12679387 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
12679403 TATT-TTTAAAACTTAT
1 TATTATTTAAAA-TTAT
12679419 TATTA
1 TATTA
12679424 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:12679574 original size:9 final size:9
Alignment explanation
Indices: 12679562--12679587 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12679552 TATTTTATTA
12679562 ATTTTAAAT
1 ATTTTAAAT
12679571 ATTTTAAAT
1 ATTTTAAAT
12679580 ATTTTAAA
1 ATTTTAAA
12679588 AATAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
ATTTTAAAT
Found at i:12680761 original size:3 final size:3
Alignment explanation
Indices: 12680755--12680793 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
12680745 AATAATAATA
12680755 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12680794 AAGAATAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12682476 original size:24 final size:25
Alignment explanation
Indices: 12682449--12682505 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
12682439 ATGTGACACG
12682449 TAATAAAAAA-ATTA-AAATATAATA
1 TAATAAAAAATATTATAAATA-AATA
12682473 TAATATGAAAAATATTATAAATAAATA
1 TAATA--AAAAATATTATAAATAAATA
12682500 T-ATAAA
1 TAATAAA
12682506 TGTTTTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
24 7 0.24
26 8 0.28
27 9 0.31
28 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
TAATAAAAAATATTATAAATAAATA
Found at i:12685949 original size:10 final size:9
Alignment explanation
Indices: 12685922--12685957 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
12685912 TAGAAAGTTA
12685922 ATATATTTT
1 ATATATTTT
12685931 ATA-ATTTT
1 ATATATTTT
12685939 ATAATATTTT
1 AT-ATATTTT
12685949 ATATATTTT
1 ATATATTTT
12685958 TGAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 7 0.28
9 11 0.44
10 7 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
ATATATTTT
Found at i:12688436 original size:3 final size:3
Alignment explanation
Indices: 12688428--12688461 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
12688418 TGTTCTTTGC
* *
12688428 ATT ATT ATT ATT ATT GTT ATT GTT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
12688462 GGGTTTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:12689635 original size:14 final size:16
Alignment explanation
Indices: 12689616--12689655 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
12689606 TTTTTTGTTG
12689616 TCCATAAATTG-A-CA
1 TCCATAAATTGAACCA
12689630 TCCATAAATTGAACCA
1 TCCATAAATTGAACCA
12689646 TCCATCAAAT
1 TCCAT-AAAT
12689656 ACAAACATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.48
15 1 0.04
16 7 0.30
17 4 0.17
ACGTcount: A:0.42, C:0.25, G:0.05, T:0.28
Consensus pattern (16 bp):
TCCATAAATTGAACCA
Found at i:12690667 original size:13 final size:13
Alignment explanation
Indices: 12690649--12690673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12690639 ATAGTGGTAA
12690649 ACATAACATACAC
1 ACATAACATACAC
12690662 ACATAACATACA
1 ACATAACATACA
12690674 TAAACATTAA
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:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (13 bp):
ACATAACATACAC
Found at i:12690753 original size:57 final size:57
Alignment explanation
Indices: 12690667--12690788 Score: 163
Period size: 57 Copynumber: 2.1 Consensus size: 57
12690657 TACACACATA
* * ** *
12690667 ACATACATAAACATTAATAAATAGTCATACACATAACAGTGATATACCACATAATAT
1 ACATACATAAAAATTAATAAACAACCATACACATAACAGTAATATACCACATAATAT
* * * *
12690724 ACATGCATAAAAATTAATAAACAACCATACATATAATAGTAATATGCCACATAATAT
1 ACATACATAAAAATTAATAAACAACCATACACATAACAGTAATATACCACATAATAT
12690781 ACATACAT
1 ACATACAT
12690789 TAAACATGCC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.52, C:0.17, G:0.05, T:0.26
Consensus pattern (57 bp):
ACATACATAAAAATTAATAAACAACCATACACATAACAGTAATATACCACATAATAT
Found at i:12690866 original size:37 final size:36
Alignment explanation
Indices: 12690823--12691073 Score: 179
Period size: 37 Copynumber: 7.1 Consensus size: 36
12690813 AACAAAACAG
*
12690823 TAATATAACACATAACAAACATACAAATATACATACA
1 TAATATAA-ACATAACATACATACAAATATACATACA
* *
12690860 TAATAT--ACATAACATTATATAACACA-A-ACATAACA
1 TAATATAAACATAACA-TACAT-ACAAATATACAT-ACA
* * *
12690895 TTATAT-AACATAATATACATACAAATATACAAACA
1 TAATATAAACATAACATACATACAAATATACATACA
* *
12690930 TAATAGTAAACAT-A-AT--ATACATATATA-ACA-A
1 TAATA-TAAACATAACATACATACAAATATACATACA
*
12690961 T-ACAT-AACATAACATACATACAAATATACA-AGCA
1 TAATATAAACATAACATACATACAAATATACATA-CA
* *
12690995 TAACAGTAAACATAACATACATACAAATATACAAACA
1 TAATA-TAAACATAACATACATACAAATATACATACA
* * *
12691032 TAACATTAAACATAACACACATGCATAATAGTACATAGCA
1 TAATA-TAAACATAACATACATACA-AATA-TACATA-CA
12691072 TA
1 TA
12691074 CATAACATAA
Statistics
Matches: 175, Mismatches: 17, Indels: 41
0.75 0.07 0.18
Matches are distributed among these distances:
28 5 0.03
29 2 0.01
30 4 0.02
31 2 0.01
32 13 0.07
33 11 0.06
34 18 0.10
35 29 0.17
36 17 0.10
37 60 0.34
38 5 0.03
39 5 0.03
40 4 0.02
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (36 bp):
TAATATAAACATAACATACATACAAATATACATACA
Found at i:12690965 original size:14 final size:13
Alignment explanation
Indices: 12690832--12691151 Score: 123
Period size: 12 Copynumber: 24.2 Consensus size: 13
12690822 GTAATATAAC
*
12690832 ACATAACAAACAT
1 ACATAACATACAT
*
12690845 ACA-AATATACAT
1 ACATAACATACAT
*
12690857 ACATAATATACAT
1 ACATAACATACAT
* * *
12690870 AACATTATATAACACAA
1 -ACA-TA-A-CATACAT
*
12690887 ACATAACATTATAT
1 ACATAACA-TACAT
*
12690901 AACATAATATACAT
1 -ACATAACATACAT
* *
12690915 ACA-AATATACAA
1 ACATAACATACAT
*
12690927 ACATAATAGTA-A-
1 ACATAACA-TACAT
*
12690939 ACATAATATACAT
1 ACATAACATACAT
*
12690952 ATATAACAATACAT
1 ACATAAC-ATACAT
12690966 AACATAACATACAT
1 -ACATAACATACAT
*
12690980 ACA-AATATACA-
1 ACATAACATACAT
12690991 AGCATAACAGTA-A-
1 A-CATAACA-TACAT
12691004 ACATAACATACAT
1 ACATAACATACAT
* *
12691017 ACA-AATATACAA
1 ACATAACATACAT
12691029 ACATAACATTA-A-
1 ACATAACA-TACAT
*
12691041 ACATAACACACAT
1 ACATAACATACAT
* *
12691054 GCATAATAGTACAT
1 ACATAACA-TACAT
12691068 AGCAT-ACATAACAT
1 A-CATAACAT-ACAT
*
12691082 AATAGTAAACATAACAT
1 -ACA-T-AACAT-ACAT
*
12691099 ACATAATATACAT
1 ACATAACATACAT
*
12691112 AGCAGTTTA-A-A-A-
1 A-CA--TAACATACAT
12691124 ACATAACATACAT
1 ACATAACATACAT
*
12691137 ACATAACAGACAT
1 ACATAACATACAT
12691150 AC
1 AC
12691152 CTTTCACCCT
Statistics
Matches: 239, Mismatches: 32, Indels: 72
0.70 0.09 0.21
Matches are distributed among these distances:
9 2 0.01
10 1 0.00
11 9 0.04
12 68 0.28
13 68 0.28
14 46 0.19
15 24 0.10
16 8 0.03
17 13 0.05
ACGTcount: A:0.56, C:0.17, G:0.03, T:0.23
Consensus pattern (13 bp):
ACATAACATACAT
Found at i:12690989 original size:65 final size:65
Alignment explanation
Indices: 12690832--12691037 Score: 222
Period size: 65 Copynumber: 3.1 Consensus size: 65
12690822 GTAATATAAC
* * * * *
12690832 ACATAACAAACATACAAATATACATACATAATA-TACATAACATTATATAACACAAACATAACAT
1 ACATAACATACATACAAATATACAAACATAATAGT--A-AACA-TA-AT-ATACATACATAACAA
*
12690896 TATATA
60 TACATA
* *
12690902 ACATAATATACATACAAATATACAAACATAATAGTAAACATAATATACATATATAACAATACATA
1 ACATAACATACATACAAATATACAAACATAATAGTAAACATAATATACATACATAACAATACATA
* * * *
12690967 ACATAACATACATACAAATATACAAGCATAACAGTAAACATAACATACATACA-AA-TATACA-A
1 ACATAACATACATACAAATATACAAACATAATAGTAAACATAATATACATACATAACAATACATA
12691029 ACATAACAT
1 ACATAACAT
12691038 TAAACATAAC
Statistics
Matches: 121, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
62 10 0.08
63 5 0.04
64 2 0.02
65 64 0.53
66 2 0.02
67 2 0.02
68 4 0.03
69 1 0.01
70 30 0.25
71 1 0.01
ACGTcount: A:0.58, C:0.17, G:0.01, T:0.24
Consensus pattern (65 bp):
ACATAACATACATACAAATATACAAACATAATAGTAAACATAATATACATACATAACAATACATA
Found at i:12691077 original size:9 final size:9
Alignment explanation
Indices: 12690832--12691112 Score: 97
Period size: 9 Copynumber: 30.6 Consensus size: 9
12690822 GTAATATAAC
*
12690832 ACATAACAA
1 ACATAACAT
12690841 ACAT-ACA-
1 ACATAACAT
12690848 A-ATATACAT
1 ACATA-ACAT
*
12690857 ACATAATAT
1 ACATAACAT
12690866 ACATAACATT
1 ACATAACA-T
* *
12690876 ATATAACACAA
1 ACAT-A-ACAT
12690887 ACATAACATT
1 ACATAACA-T
*
12690897 ATATAACAT
1 ACATAACAT
12690906 A-ATATACAT
1 ACATA-ACAT
*
12690915 ACA-AATAT
1 ACATAACAT
12690923 ACA-AACAT
1 ACATAACAT
*
12690931 AATAGTAAACAT
1 -ACA-T-AACAT
12690943 A-ATATACAT
1 ACATA-ACAT
*
12690952 ATATAACAAT
1 ACATAAC-AT
12690962 ACATAACAT
1 ACATAACAT
12690971 AACAT-ACAT
1 -ACATAACAT
*
12690980 ACA-AATAT
1 ACATAACAT
*
12690988 ACA-AGCAT
1 ACATAACAT
12690996 AACAGTAAACAT
1 -ACA-T-AACAT
12691008 AACAT-ACAT
1 -ACATAACAT
*
12691017 ACA-AATAT
1 ACATAACAT
12691025 ACA-AACAT
1 ACATAACAT
12691033 AACATTAAACAT
1 -ACA-T-AACAT
*
12691045 AACA-CACAT
1 -ACATAACAT
* *
12691054 GCATAATAGT
1 ACATAACA-T
*
12691064 ACATAGCAT
1 ACATAACAT
12691073 ACATAACAT
1 ACATAACAT
** *
12691082 A-ATAGTAA
1 ACATAACAT
12691090 ACATAACAT
1 ACATAACAT
*
12691099 ACATAATAT
1 ACATAACAT
12691108 ACATA
1 ACATA
12691113 GCAGTTTAAA
Statistics
Matches: 209, Mismatches: 32, Indels: 62
0.69 0.11 0.20
Matches are distributed among these distances:
6 2 0.01
7 1 0.00
8 52 0.25
9 85 0.41
10 38 0.18
11 6 0.03
12 25 0.12
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (9 bp):
ACATAACAT
Found at i:12691102 original size:35 final size:33
Alignment explanation
Indices: 12691063--12691141 Score: 79
Period size: 35 Copynumber: 2.3 Consensus size: 33
12691053 TGCATAATAG
*
12691063 TACATAGCATACATAACA-TAATAGTAAACATAACA
1 TACATA-CATACATAACAGT-ATA-AAAACATAACA
* * *
12691098 TACATAATATACATAGCAGTTTAAAAACATAACA
1 TACAT-ACATACATAACAGTATAAAAACATAACA
12691132 TACATACATA
1 TACATACATA
12691142 ACAGACATAC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
33 4 0.11
34 15 0.41
35 16 0.43
36 2 0.05
ACGTcount: A:0.53, C:0.16, G:0.05, T:0.25
Consensus pattern (33 bp):
TACATACATACATAACAGTATAAAAACATAACA
Found at i:12695052 original size:11 final size:12
Alignment explanation
Indices: 12695036--12695072 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
12695026 ACCTTATAAT
12695036 ATACTATAAA-A
1 ATACTATAAATA
12695047 ATACTATAAATA
1 ATACTATAAATA
*
12695059 ATA-AATAAATA
1 ATACTATAAATA
12695070 ATA
1 ATA
12695073 AAATACTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (12 bp):
ATACTATAAATA
Found at i:12705791 original size:20 final size:20
Alignment explanation
Indices: 12705765--12705873 Score: 76
Period size: 20 Copynumber: 5.2 Consensus size: 20
12705755 TGGTGCATGG
12705765 GTGGCATTCTGCTAGCCTTT
1 GTGGCATTCTGCTAGCCTTT
* *
12705785 ATGGCATAATCTGATCTGGCCTTT
1 GTGGCAT--TCTG--CTAGCCTTT
* * *
12705809 CTGGCATTATGTTAGCCTTT
1 GTGGCATTCTGCTAGCCTTT
* *
12705829 GTGGCA-TCTGATATGGCCTTG
1 GTGGCATTCTGCTA--GCCTTT
* *
12705850 GTGGCATTCTCCTAGCCTTC
1 GTGGCATTCTGCTAGCCTTT
12705870 GTGG
1 GTGG
12705874 TGTAATCTGT
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
19 5 0.07
20 27 0.39
21 11 0.16
22 12 0.17
24 14 0.20
ACGTcount: A:0.14, C:0.23, G:0.26, T:0.38
Consensus pattern (20 bp):
GTGGCATTCTGCTAGCCTTT
Found at i:12705855 original size:41 final size:42
Alignment explanation
Indices: 12705764--12705868 Score: 113
Period size: 41 Copynumber: 2.5 Consensus size: 42
12705754 GTGGTGCATG
* *
12705764 GGTGGCATTCTGCTAGCCTTTATGGCATAATCTGATCTGGCCTT
1 GGTGGCATTATGCTAGCCTTTATGGC--AATCTGATATGGCCTT
** * *
12705808 TCTGGCATTATGTTAGCCTTTGTGGC-ATCTGATATGGCCTT
1 GGTGGCATTATGCTAGCCTTTATGGCAATCTGATATGGCCTT
* *
12705849 GGTGGCATTCTCCTAGCCTT
1 GGTGGCATTATGCTAGCCTT
12705869 CGTGGTGTAA
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
41 29 0.58
44 21 0.42
ACGTcount: A:0.14, C:0.23, G:0.25, T:0.38
Consensus pattern (42 bp):
GGTGGCATTATGCTAGCCTTTATGGCAATCTGATATGGCCTT
Found at i:12706393 original size:28 final size:28
Alignment explanation
Indices: 12706335--12706399 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
12706325 CAATATCAAC
* * * *
12706335 AAGGGTATTCGCCAAAACTATTATTAGT
1 AAGGGTATTCACCAAAACTATGATAAAT
* *
12706363 AAGGGTATTCACCAAAAGTGTGATAAAT
1 AAGGGTATTCACCAAAACTATGATAAAT
12706391 AAGTGGTAT
1 AAG-GGTAT
12706400 CCGCCAAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 25 0.83
29 5 0.17
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (28 bp):
AAGGGTATTCACCAAAACTATGATAAAT
Found at i:12707678 original size:24 final size:24
Alignment explanation
Indices: 12707647--12707701 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
12707637 ATCCAAACAA
12707647 TGAATTTTAATTAATTCAAAATAT
1 TGAATTTTAATTAATTCAAAATAT
12707671 TGAATTTTAATTAATTCAAAATAT
1 TGAATTTTAATTAATTCAAAATAT
12707695 TGAATTT
1 TGAATTT
12707702 GAAATATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (24 bp):
TGAATTTTAATTAATTCAAAATAT
Found at i:12709191 original size:40 final size:39
Alignment explanation
Indices: 12709139--12709214 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 39
12709129 AGTAGCGGCG
* *
12709139 TTTATGAGAAAAACA-CTGCAAAAGGTAAGCAATAGCGACA
1 TTTATGAGAAAAA-AGC-CCAAAAAGTAAGCAATAGCGACA
12709179 TTTATG-GTAAAAAAGCCCAAAAAGTAAGCAATAGCG
1 TTTATGAG-AAAAAAGCCCAAAAAGTAAGCAATAGCG
12709215 GTGTTTGGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
39 20 0.62
40 12 0.38
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.18
Consensus pattern (39 bp):
TTTATGAGAAAAAAGCCCAAAAAGTAAGCAATAGCGACA
Found at i:12709363 original size:48 final size:48
Alignment explanation
Indices: 12709307--12709433 Score: 184
Period size: 48 Copynumber: 2.6 Consensus size: 48
12709297 GCACGAATTA
**
12709307 TTTTCTTTCTCAGTCTTTTCTTTGCTTGAAACCCCAAAATCCTTTCCC
1 TTTTCTTTCTCAGTCTTTTCTTTGCTTGAAACCCCAAAATCCGGTCCC
* *
12709355 TTTTCTTTCCCAGAT-TTCTCTTTGCTTGAAACCCCAAAATCCGGTCCC
1 TTTTCTTTCTCAG-TCTTTTCTTTGCTTGAAACCCCAAAATCCGGTCCC
* *
12709403 TTTTCTTTCTTAGTCTTTTCGTTGCTTGAAA
1 TTTTCTTTCTCAGTCTTTTCTTTGCTTGAAA
12709434 AAAAATACAT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
47 1 0.01
48 67 0.97
49 1 0.01
ACGTcount: A:0.17, C:0.28, G:0.09, T:0.46
Consensus pattern (48 bp):
TTTTCTTTCTCAGTCTTTTCTTTGCTTGAAACCCCAAAATCCGGTCCC
Found at i:12710147 original size:11 final size:11
Alignment explanation
Indices: 12710131--12710156 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12710121 CAAGATTTGA
12710131 TTGATTAATTT
1 TTGATTAATTT
12710142 TTGATTAATTT
1 TTGATTAATTT
12710153 TTGA
1 TTGA
12710157 AAAGTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (11 bp):
TTGATTAATTT
Found at i:12711653 original size:25 final size:26
Alignment explanation
Indices: 12711624--12711675 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
12711614 ATAAAAAATA
*
12711624 AAAAATAAATATCTAAT-TTATTTTTT
1 AAAAAT-AATATCTAATGTAATTTTTT
*
12711650 AAAAATTATATCTAATGTAATTTTTT
1 AAAAATAATATCTAATGTAATTTTTT
12711676 TATTATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (26 bp):
AAAAATAATATCTAATGTAATTTTTT
Found at i:12712872 original size:24 final size:22
Alignment explanation
Indices: 12712845--12712900 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 22
12712835 AATTTCAAAA
12712845 ATAAAACATAATATAATATTTATC
1 ATAAAA-ATAA-ATAATATTTATC
*
12712869 ATAAAAATAAATATTATTTA--
1 ATAAAAATAAATAATATTTATC
*
12712889 ATTAAAATAAAT
1 ATAAAAATAAAT
12712901 TCTTTAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 11 0.37
22 9 0.30
23 4 0.13
24 6 0.20
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAAAAATAAATAATATTTATC
Found at i:12713275 original size:9 final size:9
Alignment explanation
Indices: 12713261--12713368 Score: 80
Period size: 9 Copynumber: 12.2 Consensus size: 9
12713251 AACTTTGGAT
*
12713261 CATAACTTC
1 CATAACTTA
12713270 CATAACTTA
1 CATAACTTA
*
12713279 CATAA-ATA
1 CATAACTTA
* * *
12713287 TATATCATA
1 CATAACTTA
12713296 TCATAACTTA
1 -CATAACTTA
12713306 CATAACTTA
1 CATAACTTA
12713315 CATAA--TA
1 CATAACTTA
*
12713322 CATAA-ATA
1 CATAACTTA
* * *
12713330 TATATCATA
1 CATAACTTA
*
12713339 CCATAACATA
1 -CATAACTTA
12713349 CATAACTTA
1 CATAACTTA
12713358 CATAACTTA
1 CATAACTTA
12713367 CA
1 CA
12713369 CCCATTAGAT
Statistics
Matches: 82, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
7 7 0.09
8 10 0.12
9 52 0.63
10 13 0.16
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.32
Consensus pattern (9 bp):
CATAACTTA
Found at i:12713332 original size:43 final size:44
Alignment explanation
Indices: 12713261--12713364 Score: 165
Period size: 43 Copynumber: 2.4 Consensus size: 44
12713251 AACTTTGGAT
* * *
12713261 CATAACTTCCATAACTTACATAAATATATATCATATCATAACTTA
1 CATAACTTACATAAC-TACATAAATATATATCATACCATAACATA
12713306 CATAACTTACATAA-TACATAAATATATATCATACCATAACATA
1 CATAACTTACATAACTACATAAATATATATCATACCATAACATA
12713349 CATAACTTACATAACT
1 CATAACTTACATAACT
12713365 TACACCCATT
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
43 41 0.75
44 1 0.02
45 13 0.24
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (44 bp):
CATAACTTACATAACTACATAAATATATATCATACCATAACATA
Found at i:12724612 original size:25 final size:25
Alignment explanation
Indices: 12724565--12724613 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
12724555 AATCTCTAAC
*
12724565 TAACTCAGTATAGTTTCAGAAAGTAT
1 TAACTCAGTATA-TTTCAAAAAGTAT
12724591 TAACTACAGTAT-TTTCAAAAAGT
1 TAACT-CAGTATATTTCAAAAAGT
12724614 TCTATCTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 10 0.48
26 5 0.24
27 6 0.29
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (25 bp):
TAACTCAGTATATTTCAAAAAGTAT
Found at i:12731112 original size:28 final size:28
Alignment explanation
Indices: 12731079--12731136 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
12731069 AAACTGGAGA
12731079 TAATCGGAGAAAAGCAAAAGTTGTAGAT
1 TAATCGGAGAAAAGCAAAAGTTGTAGAT
12731107 TAATCGGAGAAAAGCAAAAGTTGTAGAT
1 TAATCGGAGAAAAGCAAAAGTTGTAGAT
12731135 TA
1 TA
12731137 GTCCTTAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.47, C:0.07, G:0.24, T:0.22
Consensus pattern (28 bp):
TAATCGGAGAAAAGCAAAAGTTGTAGAT
Found at i:12731876 original size:11 final size:11
Alignment explanation
Indices: 12731860--12731884 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12731850 ATAGTTTAGC
12731860 TTATTGAATTT
1 TTATTGAATTT
12731871 TTATTGAATTT
1 TTATTGAATTT
12731882 TTA
1 TTA
12731885 AGGTAAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (11 bp):
TTATTGAATTT
Found at i:12736714 original size:20 final size:20
Alignment explanation
Indices: 12736689--12736727 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12736679 TGGCTGAGTT
12736689 TTGACATGCAT-TGTGAATAC
1 TTGACA-GCATGTGTGAATAC
*
12736709 TTGACAGCTTGTGTGAATA
1 TTGACAGCATGTGTGAATA
12736728 GCACCATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGACAGCATGTGTGAATAC
Found at i:12752071 original size:36 final size:36
Alignment explanation
Indices: 12752024--12752110 Score: 115
Period size: 35 Copynumber: 2.4 Consensus size: 36
12752014 TCGAGATTTT
* * *
12752024 CAACCAAAACACACCAGATGCTCATAAGAGCTGGTC
1 CAACCAGAACACACCAGATGCTCATAAGAGATAGTC
12752060 CAACCAGAACACACC-GATGCTCATAAGAGATAGTC
1 CAACCAGAACACACCAGATGCTCATAAGAGATAGTC
*
12752095 TAACC-GAAACACACCA
1 CAACCAG-AACACACCA
12752111 AACAGAAAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
34 1 0.02
35 30 0.67
36 14 0.31
ACGTcount: A:0.41, C:0.31, G:0.15, T:0.13
Consensus pattern (36 bp):
CAACCAGAACACACCAGATGCTCATAAGAGATAGTC
Found at i:12766867 original size:51 final size:51
Alignment explanation
Indices: 12766808--12767101 Score: 301
Period size: 51 Copynumber: 5.8 Consensus size: 51
12766798 TATCGATGAA
* * * *
12766808 CACGTGTGTAGCACTGTGTGAAGTCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGTTGGT
* * * * * * *
12766859 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTA-CTGAGAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATC-GATAA-ATGTTGGT
* * *
12766910 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGTTGGT
* * * * *
12766961 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAA-GCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATG--TTGGT
* ** *
12767012 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAA-CCATAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGTTGGT
*
12767062 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
12767102 ATGATAAAAG
Statistics
Matches: 196, Mismatches: 38, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
49 1 0.01
50 46 0.23
51 147 0.75
52 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGTTGGT
Found at i:12766984 original size:102 final size:102
Alignment explanation
Indices: 12766808--12767089 Score: 440
Period size: 102 Copynumber: 2.8 Consensus size: 102
12766798 TATCGATGAA
* * *
12766808 CACGTGTGTAGCACTGTGTGAAGTCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAC
* *
12766873 TAAGTGAAGGCTACAATGTGTACTGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
12766910 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAC
*
12766975 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
* * *** *
12767012 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAA-CCATAAAACTTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAC
*
12767076 TATGTGAAGGCTAC
66 TAAGTGAAGGCTAC
12767090 TACGTGTATC
Statistics
Matches: 167, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
101 36 0.22
102 131 0.78
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
Found at i:12767124 original size:101 final size:102
Alignment explanation
Indices: 12766815--12767134 Score: 311
Period size: 102 Copynumber: 3.1 Consensus size: 102
12766805 GAACACGTGT
* * * ** *
12766815 GTAGCACTGTGTGAAGTCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGA
1 GTAGTACTGTGTGAAGGCTACTACGTGAATCCATAAAACATGATCACATGTGTAGTACTAAGTGA
* * * * * *** * * *
12766880 AGGCTACAATGTGTACTGAGAAGCTTTGGTCACGTGT
66 AGGCTACTACGTGTACCGAAAAGATAAAGTAACATGG
* **
12766917 GTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTACTAAGTGA
1 GTAGTACTGTGTGAAGGCTACTACGTGAATCCATAAAACATGATCACATGTGTAGTACTAAGTGA
* * *** * * *
12766982 AGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGT
66 AGGCTACTACGTGTACCGAAAAGATAAAGTAACATGG
* * * *
12767019 GTAGTACTATGTGAAGGCTACTACGTGAA-CCATAAAACTTGATCACGTGTGTAGTACTATGTGA
1 GTAGTACTGTGTGAAGGCTACTACGTGAATCCATAAAACATGATCACATGTGTAGTACTAAGTGA
* *
12767083 AGGCTACTACGTGTATCG-AATGATAAAAGTAACATGG
66 AGGCTACTACGTGTACCGAAAAGAT-AAAGTAACATGG
12767120 GTAGTACTGTGTGAA
1 GTAGTACTGTGTGAA
12767135 AAACCCCAAA
Statistics
Matches: 193, Mismatches: 24, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
100 4 0.02
101 65 0.34
102 124 0.64
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (102 bp):
GTAGTACTGTGTGAAGGCTACTACGTGAATCCATAAAACATGATCACATGTGTAGTACTAAGTGA
AGGCTACTACGTGTACCGAAAAGATAAAGTAACATGG
Found at i:12769113 original size:15 final size:14
Alignment explanation
Indices: 12769093--12769137 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
12769083 TAAAACGGGG
12769093 AAGAAAAGAATAAGA
1 AAGAAAAGAA-AAGA
*
12769108 AAGAAACGCAAAAGA
1 AAGAAAAG-AAAAGA
*
12769123 AAGGAAAGAAAAGA
1 AAGAAAAGAAAAGA
12769137 A
1 A
12769138 CATGCCAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 7 0.27
15 17 0.65
16 2 0.08
ACGTcount: A:0.71, C:0.04, G:0.22, T:0.02
Consensus pattern (14 bp):
AAGAAAAGAAAAGA
Found at i:12769354 original size:18 final size:19
Alignment explanation
Indices: 12769310--12769354 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
12769300 TCTTCTTTAA
12769310 CCTT-TAACCTTCCATCTT
1 CCTTATAACCTTCCATCTT
* *
12769328 CCTCA-AACCTTTCATC-T
1 CCTTATAACCTTCCATCTT
12769345 CCTTATAACC
1 CCTTATAACC
12769355 CCTTTTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.22, C:0.40, G:0.00, T:0.38
Consensus pattern (19 bp):
CCTTATAACCTTCCATCTT
Found at i:12775598 original size:17 final size:16
Alignment explanation
Indices: 12775560--12775592 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
12775550 TATACCAATC
12775560 AAAATCATGCATCTAAA
1 AAAATCATGCA-CTAAA
12775577 AAAATCATGCA-TAAA
1 AAAATCATGCACTAAA
12775592 A
1 A
12775593 TGAAATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
17 11 0.69
ACGTcount: A:0.58, C:0.15, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAATCATGCACTAAA
Found at i:12777675 original size:18 final size:18
Alignment explanation
Indices: 12777642--12777680 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12777632 GTATTCTTAT
*
12777642 ATTTCTTTTCAATTCTCA
1 ATTTCTTTTCAATTCTAA
12777660 ATTT-TTTTCAATTTCTAA
1 ATTTCTTTTCAA-TTCTAA
12777678 ATT
1 ATT
12777681 ATCCATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTCTTTTCAATTCTAA
Found at i:12781063 original size:21 final size:20
Alignment explanation
Indices: 12781008--12781062 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
12780998 TAAAATATAT
*
12781008 ATAAATTTGAA-TTTTAAAA
1 ATAATTTTGAATTTTTAAAA
*
12781027 ATAATTTTGAATTTTTGAAA
1 ATAATTTTGAATTTTTAAAA
*
12781047 ATTATTTTGAATTTTT
1 ATAATTTTGAATTTTT
12781063 TTTTGTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 10 0.31
20 22 0.69
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (20 bp):
ATAATTTTGAATTTTTAAAA
Found at i:12781919 original size:16 final size:16
Alignment explanation
Indices: 12781870--12781921 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
12781860 AAGTGAAAAG
* *
12781870 AAAATTAGAAGGATGG
1 AAAATTAGAAAGATGA
* * * *
12781886 AAAATTGGAGACACGA
1 AAAATTAGAAAGATGA
12781902 AAAATTAGAAAGATGA
1 AAAATTAGAAAGATGA
12781918 AAAA
1 AAAA
12781922 CAAAAATTTT
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.58, C:0.04, G:0.23, T:0.15
Consensus pattern (16 bp):
AAAATTAGAAAGATGA
Found at i:12782079 original size:20 final size:20
Alignment explanation
Indices: 12782054--12782092 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12782044 AAATAACATA
*
12782054 CAATATAGAAAGATTGATTC
1 CAATATAGAAAGAGTGATTC
12782074 CAATATAGAAAGAGTGATT
1 CAATATAGAAAGAGTGATT
12782093 TTTATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (20 bp):
CAATATAGAAAGAGTGATTC
Found at i:12784886 original size:18 final size:19
Alignment explanation
Indices: 12784863--12784902 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
12784853 TTCATGTATA
12784863 TATAAAATA-TAGAAAATG
1 TATAAAATATTAGAAAATG
*
12784881 TAT-AAATATTATAAAATG
1 TATAAAATATTAGAAAATG
12784899 TATA
1 TATA
12784903 TGCATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (19 bp):
TATAAAATATTAGAAAATG
Found at i:12785078 original size:3 final size:3
Alignment explanation
Indices: 12785063--12785113 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
12785053 AAAAAACGTG
* * *
12785063 ATA ATA ATT ATA ATA ATA AT- TTA A-A ATA ATA AAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
12785109 GTA AT
1 ATA AT
12785114 GTAAAAAAAC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 3 0.08
3 35 0.92
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:12786833 original size:128 final size:127
Alignment explanation
Indices: 12786594--12786857 Score: 296
Period size: 128 Copynumber: 2.1 Consensus size: 127
12786584 GCAATTTCAA
* * * * * *
12786594 AGATAAGTCTGGATGTGATCTGCTCCCTGTAACTTCAGAGAGGTAAGATCTGTAATTTTAATCCG
1 AGATAAGACTGGATGCGATATGCTCCCTGCAACTTCAGAGAGATAAGATCTATAATTTTAATCCG
* * * * ** * *
12786659 CTCCGCTGCAACTTCAGGGAGATAGGATTGGATTCTTCTGTCTGCTCCACTGTAACTTCAGGG
66 CTCCACTGCAACTTCAGGAAGATAGAATT-GATTCCTCAATCTGCTCCACTGCAACTTAAGGG
* * **
12786722 AGATAAGACTGTATGCGATATGCTCTCTGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCG
1 AGATAAGACTGGATGCGATATGCTCCCTGCAACTTCAGAGAGATAAGATCTATAATTTTAATCCG
* * * *
12786787 CTCCACTGCATCTTCAGGAAGATAGAATT-ATTGGCCTCAATTTGCTCCGCTGCATCTTAAGGG
66 CTCCACTGCAACTTCAGGAAGATAGAATTGATT--CCTCAATCTGCTCCACTGCAACTTAAGGG
12786850 AGATAAGA
1 AGATAAGA
12786858 TTCGACATCT
Statistics
Matches: 112, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
126 3 0.03
128 109 0.97
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (127 bp):
AGATAAGACTGGATGCGATATGCTCCCTGCAACTTCAGAGAGATAAGATCTATAATTTTAATCCG
CTCCACTGCAACTTCAGGAAGATAGAATTGATTCCTCAATCTGCTCCACTGCAACTTAAGGG
Found at i:12786925 original size:50 final size:50
Alignment explanation
Indices: 12786866--12787025 Score: 144
Period size: 50 Copynumber: 3.2 Consensus size: 50
12786856 GATTCGACAT
* *
12786866 CTTCAATCTGTTTAACTGCAATGTCCAGAAAACAAGATCCGCCGTCGTGA
1 CTTCAATCTGTTTAATTGCAATGTCCAGGAAACAAGATCCGCCGTCGTGA
** ** * *** * * *
12786916 CTTCAATCTGTTCCATTGCACCG-CTAGGGAGGTAAGATTCGCCGTTGTGG
1 CTTCAATCTGTTTAATTGCAATGTCCA-GGAAACAAGATCCGCCGTCGTGA
***
12786966 CTTCAATCAT-TTTAATTGCAATGTTGGGGAAACAAGATCCGCCGTCGTGA
1 CTTCAATC-TGTTTAATTGCAATGTCCAGGAAACAAGATCCGCCGTCGTGA
12787016 CTTCAATCTG
1 CTTCAATCTG
12787026 CTCTACTACA
Statistics
Matches: 80, Mismatches: 26, Indels: 8
0.70 0.23 0.07
Matches are distributed among these distances:
49 3 0.04
50 76 0.95
51 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (50 bp):
CTTCAATCTGTTTAATTGCAATGTCCAGGAAACAAGATCCGCCGTCGTGA
Found at i:12787046 original size:50 final size:49
Alignment explanation
Indices: 12786895--12787074 Score: 146
Period size: 50 Copynumber: 3.6 Consensus size: 49
12786885 AATGTCCAGA
*
12786895 AAACAAGATCCGCCGTCGTGACTTCAATCTGTTCCATTGCACCGCTAGGG
1 AAACAAGATCCGCCGTCGTGACTTCAATCTG-TCTATTGCACCGCTAGGG
*** * * * * ** * *
12786945 AGGTAAGATTCGCCGTTGTGGCTTCAATCAT-TTTAATTGCAATGTTGGGG
1 AAACAAGATCCGCCGTCGTGACTTCAATC-TGTCT-ATTGCACCGCTAGGG
* *
12786995 AAACAAGATCCGCCGTCGTGACTTCAATCTGCTCTACTACACCGCTAGGG
1 AAACAAGATCCGCCGTCGTGACTTCAATCTG-TCTATTGCACCGCTAGGG
** * * *
12787045 AAGTAAGATTCGCCGTTGTGGCTTCAATCT
1 AAACAAGATCCGCCGTCGTGACTTCAATCT
12787075 ATTCCACTAT
Statistics
Matches: 96, Mismatches: 30, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
49 2 0.02
50 91 0.95
51 3 0.03
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.28
Consensus pattern (49 bp):
AAACAAGATCCGCCGTCGTGACTTCAATCTGTCTATTGCACCGCTAGGG
Found at i:12787370 original size:88 final size:88
Alignment explanation
Indices: 12787277--12787440 Score: 247
Period size: 88 Copynumber: 1.9 Consensus size: 88
12787267 AGACTGGTGT
* * * * * *
12787277 CTTCGATCTGCTTCGCTGCCAGTATAGGAAGGCAAGATCTTCCATTTTCAACCTACTCCACTGCT
1 CTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCCATTTTCAACCTACTCCACTGCT
* *
12787342 GCTCAGGGAGACAAGACTAGTAC
66 ACTCAAGGAGACAAGACTAGTAC
*
12787365 CTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGCT
1 CTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCCATTTTCAACCTACTCCACTGCT
12787430 ACTCAAGGAGA
66 ACTCAAGGAGA
12787441 TAAGGCTGAA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 67 1.00
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (88 bp):
CTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCCATTTTCAACCTACTCCACTGCT
ACTCAAGGAGACAAGACTAGTAC
Found at i:12787427 original size:45 final size:45
Alignment explanation
Indices: 12787292--12787428 Score: 118
Period size: 45 Copynumber: 3.1 Consensus size: 45
12787282 ATCTGCTTCG
* * * * *
12787292 CTGCCAGTATAGGAAGGCAAGATCTTCCATTTTCAACCTACTCCA
1 CTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCA
*** * ** * * *
12787337 CTGCTGCT-CAGGGAGACAAGA-CTAG-TACCTTCGATCTACTTCA
1 CTGCCAATACAGGAAGACAAGATCT-GCTATTTTCAACCTACTCCA
12787380 CTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCA
1 CTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCA
12787425 CTGC
1 CTGC
12787429 TACTCAAGGA
Statistics
Matches: 66, Mismatches: 22, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
43 19 0.29
44 23 0.35
45 24 0.36
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (45 bp):
CTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCA
Found at i:12792262 original size:26 final size:26
Alignment explanation
Indices: 12792187--12792244 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
12792177 GATTATGAAT
* *
12792187 GAATAAAAGAATGATG--TGGAAAAA
1 GAATAAAAGAATAATGACTCGAAAAA
*
12792211 GAATAAAAGAATAATTACTCGAAAAA
1 GAATAAAAGAATAATGACTCGAAAAA
12792237 GAATAAAA
1 GAATAAAA
12792245 AGACTACTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 14 0.48
26 15 0.52
ACGTcount: A:0.62, C:0.03, G:0.17, T:0.17
Consensus pattern (26 bp):
GAATAAAAGAATAATGACTCGAAAAA
Found at i:12792262 original size:27 final size:27
Alignment explanation
Indices: 12792206--12792269 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
12792196 AATGATGTGG
* *
12792206 AAAAAGAAT-AAAAGAATAATTACTCG
1 AAAAAGAATAAAAAGAATAATGACTCA
* * *
12792232 AAAAAGAATAAAAAGACTACTGGCTCA
1 AAAAAGAATAAAAAGAATAATGACTCA
12792259 AAAAATGAATA
1 AAAAA-GAATA
12792270 CGAAAAGTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 9 0.29
27 17 0.55
28 5 0.16
ACGTcount: A:0.61, C:0.09, G:0.12, T:0.17
Consensus pattern (27 bp):
AAAAAGAATAAAAAGAATAATGACTCA
Found at i:12799550 original size:26 final size:26
Alignment explanation
Indices: 12799507--12799574 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
12799497 AAAAAAATAA
* * * *
12799507 ATGTATACATATATTATAGGAAATGC
1 ATGTATATATAAAATATAGAAAATGC
*
12799533 ATGTATATATAAAATATAGAAAATGT
1 ATGTATATATAAAATATAGAAAATGC
*
12799559 ATATATATTATAAAAT
1 ATGTATA-TATAAAAT
12799575 GTATATGCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
26 27 0.77
27 8 0.23
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.37
Consensus pattern (26 bp):
ATGTATATATAAAATATAGAAAATGC
Found at i:12802931 original size:11 final size:11
Alignment explanation
Indices: 12802910--12802956 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
12802900 GTGTAGTTTG
12802910 TTTATTGTTATT
1 TTTA-TGTTATT
12802922 TTTATGTTATT
1 TTTATGTTATT
12802933 TTTAAT-TTATT
1 TTT-ATGTTATT
* *
12802944 TTAAAGTTATT
1 TTTATGTTATT
12802955 TT
1 TT
12802957 GCTAGTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 1 0.03
11 24 0.77
12 6 0.19
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.70
Consensus pattern (11 bp):
TTTATGTTATT
Found at i:12802954 original size:66 final size:64
Alignment explanation
Indices: 12802880--12803028 Score: 167
Period size: 65 Copynumber: 2.3 Consensus size: 64
12802870 ATGATGAGGA
* * * * * * *
12802880 TAAA-TTATTTTGTTAGTA-TTGTGTAGTTTGTTTATTGTTATTTTTATGTTATTTTTAATTTAT
1 TAAAGTTATTTTGTTAGTATTTGTG-AGGTT-ATGAATGTAATTTTTAT-TAATTTTTAAATTAT
12802943 TT
63 TT
*
12802945 TAAAGTTATTTTGCTAGTAATTTGTGAGGTTATGAATGTAATTTTTATTAATTTTTAAATTATTT
1 TAAAGTTATTTTGTTAGT-ATTTGTGAGGTTATGAATGTAATTTTTATTAATTTTTAAATTATTT
*
12803010 TAACGTTATTTTGTTAGTA
1 TAAAGTTATTTTGTTAGTA
12803029 ATTTTTGTGA
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
64 1 0.01
65 35 0.49
66 25 0.35
67 5 0.07
68 5 0.07
ACGTcount: A:0.26, C:0.01, G:0.13, T:0.59
Consensus pattern (64 bp):
TAAAGTTATTTTGTTAGTATTTGTGAGGTTATGAATGTAATTTTTATTAATTTTTAAATTATTT
Found at i:12807020 original size:32 final size:32
Alignment explanation
Indices: 12806984--12807045 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
12806974 TTATTAAAGA
*
12806984 TTACATCTATTTCTATTGTTAAAAAATAATCC
1 TTACATCTATTTCTATTATTAAAAAATAATCC
12807016 TTACATCTATTTCTATTATTAAAAAATAAT
1 TTACATCTATTTCTATTATTAAAAAATAAT
12807046 TTTTATATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (32 bp):
TTACATCTATTTCTATTATTAAAAAATAATCC
Found at i:12815279 original size:21 final size:21
Alignment explanation
Indices: 12815254--12815295 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12815244 TAGTTGGGGT
* *
12815254 TTAAGGTTTAAGTGTTTAGGG
1 TTAAGGGTTAAGGGTTTAGGG
*
12815275 TTAAGGGTTAGGGGTTTAGGG
1 TTAAGGGTTAAGGGTTTAGGG
12815296 GCTTATAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.38
Consensus pattern (21 bp):
TTAAGGGTTAAGGGTTTAGGG
Found at i:12815534 original size:14 final size:14
Alignment explanation
Indices: 12815515--12815555 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
12815505 GTTTGTGGGT
12815515 TTAAGGTTTAAGGG
1 TTAAGGTTTAAGGG
12815529 TTAAGGGTTT-AGGG
1 TTAA-GGTTTAAGGG
*
12815543 TTAAGGTCTAAGG
1 TTAAGGTTTAAGG
12815556 AATAGAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 4 0.17
14 15 0.62
15 5 0.21
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (14 bp):
TTAAGGTTTAAGGG
Found at i:12818108 original size:67 final size:67
Alignment explanation
Indices: 12817980--12818108 Score: 147
Period size: 67 Copynumber: 1.9 Consensus size: 67
12817970 TAATATGGAC
* ** *
12817980 ATATAACCTATATTCCAATTTTATTAATAATAAATTTTATAATTTATCGAATAAATGTAAATTCG
1 ATATAACCTATATTCCAAATTTATTAATAATAAATTTTATAATTTATAAAATAAATATAAATTCG
12818045 AT
66 AT
* * *
12818047 ATATAACCTATATTTCAAATTTATTAGTAA-ACAATTTT-TAAATTT-TAAAAATAATTATAAAT
1 ATATAACCTATATTCCAAATTTATTAATAATA-AATTTTAT-AATTTAT-AAAATAAATATAAAT
12818109 AAGAAGTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
66 3 0.06
67 49 0.94
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (67 bp):
ATATAACCTATATTCCAAATTTATTAATAATAAATTTTATAATTTATAAAATAAATATAAATTCG
AT
Found at i:12818218 original size:19 final size:19
Alignment explanation
Indices: 12818190--12818229 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12818180 ATAACTTATA
*
12818190 AATATTTATATACATTTTT
1 AATATATATATACATTTTT
*
12818209 AATATATATATATATTTTT
1 AATATATATATACATTTTT
12818228 AA
1 AA
12818230 AATCTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
AATATATATATACATTTTT
Found at i:12818237 original size:19 final size:19
Alignment explanation
Indices: 12818196--12818250 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
12818186 TATAAATATT
* *
12818196 TATATACATTTTTAATATA
1 TATATATATTTTTAAAATA
*
12818215 TATATATATTTTTAAAATC
1 TATATATATTTTTAAAATA
12818234 TATAT-T-TTTTTCAAAAT
1 TATATATATTTTT-AAAAT
12818251 TTATTAATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.16
18 6 0.19
19 21 0.66
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TATATATATTTTTAAAATA
Found at i:12818255 original size:16 final size:17
Alignment explanation
Indices: 12818217--12818250 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12818207 TTAATATATA
*
12818217 TATATATTTTTAAAATC
1 TATATTTTTTTAAAATC
12818234 TATATTTTTTTCAAAAT
1 TATATTTTTTT-AAAAT
12818251 TTATTAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTTTTTTAAAATC
Found at i:12818390 original size:9 final size:9
Alignment explanation
Indices: 12818372--12818898 Score: 577
Period size: 9 Copynumber: 60.2 Consensus size: 9
12818362 CATATATAGA
*
12818372 AACTTGCAT
1 AACTTACAT
12818381 AACTTACAT
1 AACTTACAT
12818390 AACTTACAT
1 AACTTACAT
* *
12818399 AAATTAAAT
1 AACTTACAT
12818408 AACTTACAT
1 AACTTACAT
12818417 AACTTACAT
1 AACTTACAT
12818426 AA-TT--A-
1 AACTTACAT
* *
12818431 AAGTCTAAAT
1 AACT-TACAT
12818441 AACTTACAT
1 AACTTACAT
* *
12818450 AAATTAAAT
1 AACTTACAT
12818459 AACTTACAT
1 AACTTACAT
12818468 AACTTACAT
1 AACTTACAT
* *
12818477 AAATTAAAT
1 AACTTACAT
12818486 AACTTACAT
1 AACTTACAT
12818495 AACTTACAT
1 AACTTACAT
12818504 AACTTACAT
1 AACTTACAT
12818513 AACTTACAT
1 AACTTACAT
* *
12818522 AAATTAAAT
1 AACTTACAT
*
12818531 AACTTACAC
1 AACTTACAT
*
12818540 AAATTACAT
1 AACTTACAT
12818549 AACTTACAT
1 AACTTACAT
12818558 AACTTACAT
1 AACTTACAT
* *
12818567 AAATTAAAT
1 AACTTACAT
*
12818576 AACTTCCAT
1 AACTTACAT
*
12818585 AACTTAAAT
1 AACTTACAT
12818594 AACTTACAT
1 AACTTACAT
12818603 AA--TACAT
1 AACTTACAT
*
12818610 AACCTT-CCT
1 AA-CTTACAT
12818619 AACTTACAT
1 AACTTACAT
*
12818628 AA--TACAC
1 AACTTACAT
*
12818635 AACCTACAT
1 AACTTACAT
*
12818644 AACTCACAT
1 AACTTACAT
*
12818653 AA--TACAC
1 AACTTACAT
12818660 AACTTACAT
1 AACTTACAT
12818669 AACTTACAT
1 AACTTACAT
12818678 AACTTACAT
1 AACTTACAT
* *
12818687 AAATTAAAT
1 AACTTACAT
12818696 AACTTACAT
1 AACTTACAT
12818705 AACTTACAT
1 AACTTACAT
* *
12818714 AAATTAAAT
1 AACTTACAT
*
12818723 AACTTACAC
1 AACTTACAT
*
12818732 AAATTACAT
1 AACTTACAT
12818741 AACTTACAT
1 AACTTACAT
12818750 AACTTACAT
1 AACTTACAT
12818759 AACTTACAT
1 AACTTACAT
12818768 AACTTACAT
1 AACTTACAT
12818777 AACTTACAT
1 AACTTACAT
* *
12818786 AAATTAAAT
1 AACTTACAT
12818795 AACTTACAT
1 AACTTACAT
*
12818804 AACTTAAAT
1 AACTTACAT
12818813 AACTTACAT
1 AACTTACAT
12818822 AA--TACAT
1 AACTTACAT
*
12818829 AACCTT-CTT
1 AA-CTTACAT
12818838 AACTTACAT
1 AACTTACAT
*
12818847 AA--TACAC
1 AACTTACAT
*
12818854 AACCTACAT
1 AACTTACAT
*
12818863 AACTCACAT
1 AACTTACAT
*
12818872 AA--TACAC
1 AACTTACAT
12818879 AACTTACAT
1 AACTTACAT
12818888 AACTTACAT
1 AACTTACAT
12818897 AA
1 AA
12818899 TACATAAAAA
Statistics
Matches: 430, Mismatches: 67, Indels: 42
0.80 0.12 0.08
Matches are distributed among these distances:
5 2 0.00
6 2 0.00
7 37 0.09
8 8 0.02
9 376 0.87
10 5 0.01
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:12818417 original size:27 final size:27
Alignment explanation
Indices: 12818317--12818905 Score: 579
Period size: 27 Copynumber: 22.7 Consensus size: 27
12818307 CTTATATATA
*
12818317 AACTTACATAA--TACATAACTTAAAT
1 AACTTACATAACTTACATAACTTACAT
* *
12818342 AACATAC--AA--TATATAACTTACAT
1 AACTTACATAACTTACATAACTTACAT
* *
12818365 -A-TATAGA-AACTTGCATAACTTACAT
1 AACT-TACATAACTTACATAACTTACAT
* *
12818390 AACTTACATAAATTAAATAACTTACAT
1 AACTTACATAACTTACATAACTTACAT
* *
12818417 AACTTACATAA-TT--A-AAGTCTAAAT
1 AACTTACATAACTTACATAACT-TACAT
* *
12818441 AACTTACATAAATTAAATAACTTACAT
1 AACTTACATAACTTACATAACTTACAT
* *
12818468 AACTTACATAAATTAAATAACTTACAT
1 AACTTACATAACTTACATAACTTACAT
12818495 AACTTACATAACTTACATAACTTACAT
1 AACTTACATAACTTACATAACTTACAT
* * * *
12818522 AAATTAAATAACTTACACAAATTACAT
1 AACTTACATAACTTACATAACTTACAT
* *
12818549 AACTTACATAACTTACATAAATTAAAT
1 AACTTACATAACTTACATAACTTACAT
* *
12818576 AACTTCCATAACTTAAATAACTTACAT
1 AACTTACATAACTTACATAACTTACAT
*
12818603 AA--TACATAACCTT-CCTAACTTACAT
1 AACTTACATAA-CTTACATAACTTACAT
* * *
12818628 AA--TACACAACCTACATAACTCACAT
1 AACTTACATAACTTACATAACTTACAT
*
12818653 AA--TACACAACTTACATAACTTACAT
1 AACTTACATAACTTACATAACTTACAT
* *
12818678 AACTTACATAAATTAAATAACTTACAT
1 AACTTACATAACTTACATAACTTACAT
* * *
12818705 AACTTACATAAATTAAATAACTTACAC
1 AACTTACATAACTTACATAACTTACAT
*
12818732 AAATTACATAACTTACATAACTTACAT
1 AACTTACATAACTTACATAACTTACAT
12818759 AACTTACATAACTTACATAACTTACAT
1 AACTTACATAACTTACATAACTTACAT
* * *
12818786 AAATTAAATAACTTACATAACTTAAAT
1 AACTTACATAACTTACATAACTTACAT
*
12818813 AACTTACATAA--TACATAACCTT-CTT
1 AACTTACATAACTTACATAA-CTTACAT
* *
12818838 AACTTACATAA--TACACAACCTACAT
1 AACTTACATAACTTACATAACTTACAT
* *
12818863 AACTCACATAA--TACACAACTTACAT
1 AACTTACATAACTTACATAACTTACAT
12818888 AACTTACATAA--TACATAA
1 AACTTACATAACTTACATAA
12818906 AAATATATCA
Statistics
Matches: 485, Mismatches: 61, Indels: 36
0.83 0.10 0.06
Matches are distributed among these distances:
22 3 0.01
23 19 0.04
24 20 0.04
25 145 0.30
26 12 0.02
27 283 0.58
28 3 0.01
ACGTcount: A:0.49, C:0.19, G:0.01, T:0.31
Consensus pattern (27 bp):
AACTTACATAACTTACATAACTTACAT
Found at i:12818666 original size:219 final size:219
Alignment explanation
Indices: 12818441--12818906 Score: 774
Period size: 219 Copynumber: 2.1 Consensus size: 219
12818431 AAGTCTAAAT
* * * * * *
12818441 AACTTACATAAATTAAATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAA
1 AACTTACATAACTTACATAACTTACATAAATTAAATAAATTAAATAACTTACATAAATTAAATAA
* *
12818506 CTTACATAACTTACATAAATTAAATAACTTACACAAATTACATAACTTACATAACTTACATAAAT
66 CTTACACAAATTACATAAATTAAATAACTTACACAAATTACATAACTTACATAACTTACATAAAT
*
12818571 TAAATAACTTCCATAACTTAAATAACTTACATAATACATAACCTTCCTAACTTACATAATACACA
131 TAAATAACTTACATAACTTAAATAACTTACATAATACATAACCTTCCTAACTTACATAATACACA
12818636 ACCTACATAACTCACATAATACAC
196 ACCTACATAACTCACATAATACAC
* *
12818660 AACTTACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAAATTAAATAA
1 AACTTACATAACTTACATAACTTACATAAATTAAATAAATTAAATAACTTACATAAATTAAATAA
* * * *
12818725 CTTACACAAATTACATAACTTACATAACTTACATAACTTACATAACTTACATAACTTACATAAAT
66 CTTACACAAATTACATAAATTAAATAACTTACACAAATTACATAACTTACATAACTTACATAAAT
*
12818790 TAAATAACTTACATAACTTAAATAACTTACATAATACATAACCTTCTTAACTTACATAATACACA
131 TAAATAACTTACATAACTTAAATAACTTACATAATACATAACCTTCCTAACTTACATAATACACA
12818855 ACCTACATAACTCACATAATACAC
196 ACCTACATAACTCACATAATACAC
12818879 AACTTACATAACTTACATAA--TACATAAA
1 AACTTACATAACTTACATAACTTACATAAA
12818907 AATATATCAT
Statistics
Matches: 231, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
217 8 0.03
219 223 0.97
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (219 bp):
AACTTACATAACTTACATAACTTACATAAATTAAATAAATTAAATAACTTACATAAATTAAATAA
CTTACACAAATTACATAAATTAAATAACTTACACAAATTACATAACTTACATAACTTACATAAAT
TAAATAACTTACATAACTTAAATAACTTACATAATACATAACCTTCCTAACTTACATAATACACA
ACCTACATAACTCACATAATACAC
Found at i:12824396 original size:21 final size:21
Alignment explanation
Indices: 12824370--12824441 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
12824360 CTACAACTTA
*
12824370 AAGCAGAGGCGGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
*
12824391 AAGCAGAGACTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
*
12824412 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
12824433 AAGCAGAGG
1 AAGCAGAGG
12824442 TTCAAAAGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.38, C:0.18, G:0.42, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:12824908 original size:43 final size:42
Alignment explanation
Indices: 12824857--12824953 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
12824847 TCATGTTCTA
12824857 TAGCGGCGTTTCTGAAGAAAGCG-TCGCTAAAGAAC-ATGATCTT
1 TAGCGGCGTTT-TGAAGAAAGCGCT-GCTAAAGAACAAT-ATCTT
* * ***
12824900 TAGTGGCGTTTTTATTTAAGCGCTGCTAAAGAACAATATCTT
1 TAGCGGCGTTTTGAAGAAAGCGCTGCTAAAGAACAATATCTT
12824942 TAGCGGCGTTTT
1 TAGCGGCGTTTT
12824954 TCTCCATGCG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
42 33 0.72
43 13 0.28
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (42 bp):
TAGCGGCGTTTTGAAGAAAGCGCTGCTAAAGAACAATATCTT
Found at i:12824930 original size:42 final size:41
Alignment explanation
Indices: 12824882--12825116 Score: 213
Period size: 42 Copynumber: 5.5 Consensus size: 41
12824872 AGAAAGCGTC
*
12824882 GCTAAAGAACATGATCTTTAGTGGCGTTTTTATTTAAGCGCT
1 GCTAAAGAACATGATCTTTAGCGGCGTTTTT-TTTAAGCGCT
** * *
12824924 GCTAAAGAACAAT-ATCTTTAGCGGCGTTTTTCTCCATGCGCC
1 GCTAAAGAAC-ATGATCTTTAGCGGCGTTTTT-TTTAAGCGCT
* * *
12824966 GCTAAAGAACATGATCTTTAGCGGTGACTTTTTTTAAAGTG-T
1 GCTAAAGAACATGATCTTTAGCGGCG--TTTTTTTTAAGCGCT
* * * *
12825008 CGCTAAAGAACATGATCATTAGCGGCGCATTTTTCTAAGAGCT
1 -GCTAAAGAACATGATCTTTAGCGGCG-TTTTTTTTAAGCGCT
* *
12825051 GCTAAAGAACATGATCTTTAGCGACGCATTTTTTTTCGAAGCGCC
1 GCTAAAGAACATGATCTTTAGCG--GCGTTTTTTTT--AAGCGCT
* *
12825096 GCTAAAGAACATTACCTTTAG
1 GCTAAAGAACATGATCTTTAG
12825117 GTTCTTTAGC
Statistics
Matches: 157, Mismatches: 26, Indels: 17
0.79 0.13 0.09
Matches are distributed among these distances:
41 2 0.01
42 87 0.55
43 37 0.24
44 7 0.04
45 24 0.15
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (41 bp):
GCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTAAGCGCT
Found at i:12825030 original size:85 final size:83
Alignment explanation
Indices: 12824881--12825106 Score: 226
Period size: 85 Copynumber: 2.7 Consensus size: 83
12824871 AAGAAAGCGT
* * *
12824881 CGCTAAAGAACATGATCTTTAGTGGCGTTTTTATTTAAGCGCTGCTAAAGAACAATATCTTTAGC
1 CGCTAAAGAACATGATCTTTAGCGGCGTTTTTATTAAAGCGCTGCTAAAGAACAATATCATTAGC
* *
12824946 GGCG-TTTTTCTCCATGCGC
66 GGCGATTTTTCT--AAGAGC
* *
12824965 CGCTAAAGAACATGATCTTTAGCGGTGACTTTTT-TTAAAGTG-TCGCTAAAGAAC-ATGATCAT
1 CGCTAAAGAACATGATCTTTAGCGGCG--TTTTTATTAAAGCGCT-GCTAAAGAACAAT-ATCAT
12825027 TAGCGGCGCATTTTTCTAAGAGC
62 TAGCGGCG-ATTTTTCTAAGAGC
* * * * *
12825050 TGCTAAAGAACATGATCTTTAGCGACGCATTTTTTTTCGAAGCGCCGCTAAAGAACA
1 CGCTAAAGAACATGATCTTTAGCG--GCGTTTTTATT-AAAGCGCTGCTAAAGAACA
12825107 TTACCTTTAG
Statistics
Matches: 117, Mismatches: 13, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
84 28 0.24
85 60 0.51
86 7 0.06
87 22 0.19
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (83 bp):
CGCTAAAGAACATGATCTTTAGCGGCGTTTTTATTAAAGCGCTGCTAAAGAACAATATCATTAGC
GGCGATTTTTCTAAGAGC
Found at i:12825052 original size:127 final size:129
Alignment explanation
Indices: 12824874--12825116 Score: 323
Period size: 127 Copynumber: 1.9 Consensus size: 129
12824864 GTTTCTGAAG
* * * * *
12824874 AAAGCGTCGCTAAAGAACATGATCTTTAGTGGCGTTTTTATTTAAGCGCTGCTAAAGAACAAT-A
1 AAAGCGTCGCTAAAGAACATGATCATTAGCGGCGATTTTATCTAAGAGCTGCTAAAGAAC-ATGA
* *
12824938 TCTTTAGCG-GC-GTTTTTCTCCATGCGCCGCTAAAGAACATGATCTTTAGCGGTGACTTTTTTT
65 TCTTTAGCGAGCAGTTTTTCTCCAAGCGCCGCTAAAGAACATGACCTTTAGCGGTGACTTTTTTT
*
12825001 AAAGTGTCGCTAAAGAACATGATCATTAGCGGCGCATTTT-TCTAAGAGCTGCTAAAGAACATGA
1 AAAGCGTCGCTAAAGAACATGATCATTAGCGGCG-ATTTTATCTAAGAGCTGCTAAAGAACATGA
* * * *
12825065 TCTTTAGCGACGCATTTTTTTTCGAAGCGCCGCTAAAGAACATTACCTTTAG
65 TCTTTAGCGA-GCAGTTTTTCTCCAAGCGCCGCTAAAGAACATGACCTTTAG
12825117 GTTCTTTAGC
Statistics
Matches: 99, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
126 2 0.02
127 59 0.60
128 4 0.04
129 2 0.02
130 32 0.32
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (129 bp):
AAAGCGTCGCTAAAGAACATGATCATTAGCGGCGATTTTATCTAAGAGCTGCTAAAGAACATGAT
CTTTAGCGAGCAGTTTTTCTCCAAGCGCCGCTAAAGAACATGACCTTTAGCGGTGACTTTTTTT
Found at i:12825349 original size:72 final size:72
Alignment explanation
Indices: 12825232--12825377 Score: 265
Period size: 72 Copynumber: 2.0 Consensus size: 72
12825222 GGGCGCTAAA
* *
12825232 AAGCGCCACTAAAGGCCTAAAAAATGCCGCTAAAAACCTGTTCTGGTGTAGTGCCTATGTTGAAA
1 AAGCGCCACTAAAGGACTAAAAAACGCCGCTAAAAACCTGTTCTGGTGTAGTGCCTATGTTGAAA
12825297 GTATTAT
66 GTATTAT
*
12825304 AAGCGCCGCTAAAGGACTAAAAAACGCCGCTAAAAACCTGTTCTGGTGTAGTGCCTATGTTGAAA
1 AAGCGCCACTAAAGGACTAAAAAACGCCGCTAAAAACCTGTTCTGGTGTAGTGCCTATGTTGAAA
12825369 GTATTAT
66 GTATTAT
12825376 AA
1 AA
12825378 ATAATAGAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Consensus pattern (72 bp):
AAGCGCCACTAAAGGACTAAAAAACGCCGCTAAAAACCTGTTCTGGTGTAGTGCCTATGTTGAAA
GTATTAT
Found at i:12829160 original size:5 final size:5
Alignment explanation
Indices: 12829128--12829172 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
12829118 TTTCTTTCAT
*
12829128 TTTTA TTTT- TATTA -TTTA -TTTA -TTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
12829173 TCTTTCTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
4 14 0.39
5 22 0.61
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:12829182 original size:15 final size:15
Alignment explanation
Indices: 12829128--12829172 Score: 53
Period size: 13 Copynumber: 3.3 Consensus size: 15
12829118 TTTCTTTCAT
*
12829128 TTTTATTTT-TATTA
1 TTTTATTTTATTTTA
12829142 -TTTA-TTTA-TTTA
1 TTTTATTTTATTTTA
12829154 TTTTATTTTATTTTA
1 TTTTATTTTATTTTA
12829169 TTTT
1 TTTT
12829173 TCTTTCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
12 6 0.23
13 8 0.31
14 4 0.15
15 8 0.31
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTATTTTATTTTA
Found at i:12833672 original size:6 final size:6
Alignment explanation
Indices: 12833653--12833797 Score: 87
Period size: 7 Copynumber: 21.7 Consensus size: 6
12833643 CAGAATCAAA
*
12833653 AAAATC AAAA-- AAAATT AAAATC AAAAAATC AAAAAATC AAAAAATC
1 AAAATC AAAATC AAAATC AAAATC --AAAATC --AAAATC --AAAATC
12833699 AAAAATC AAAAATC AAAAATC AAAAATC AAAAATC AAAAATC AAAAATC
1 -AAAATC -AAAATC -AAAATC -AAAATC -AAAATC -AAAATC -AAAATC
** *
12833748 AAAAATC AAAAATC AAAAATC AAAAATC AAAAAA AAAATC AAAGTC AAAA
1 -AAAATC -AAAATC -AAAATC -AAAATC AAAATC AAAATC AAAATC AAAA
12833798 ATAGGAGAAA
Statistics
Matches: 128, Mismatches: 7, Indels: 8
0.90 0.05 0.06
Matches are distributed among these distances:
4 4 0.03
6 25 0.20
7 77 0.60
8 22 0.17
ACGTcount: A:0.73, C:0.12, G:0.01, T:0.14
Consensus pattern (6 bp):
AAAATC
Found at i:12833672 original size:7 final size:7
Alignment explanation
Indices: 12833669--12833799 Score: 205
Period size: 7 Copynumber: 18.7 Consensus size: 7
12833659 AAAAAAAATT
12833669 AAAATCAA
1 AAAATC-A
12833677 AAAATCAA
1 AAAATC-A
12833685 AAAATCAA
1 AAAATC-A
12833693 AAAATCA
1 AAAATCA
12833700 AAAATCA
1 AAAATCA
12833707 AAAATCA
1 AAAATCA
12833714 AAAATCA
1 AAAATCA
12833721 AAAATCA
1 AAAATCA
12833728 AAAATCA
1 AAAATCA
12833735 AAAATCA
1 AAAATCA
12833742 AAAATCA
1 AAAATCA
12833749 AAAATCA
1 AAAATCA
12833756 AAAATCA
1 AAAATCA
12833763 AAAATCA
1 AAAATCA
12833770 AAAATCA
1 AAAATCA
12833777 AAAA--A
1 AAAATCA
12833782 AAAATC-
1 AAAATCA
*
12833788 AAAGTCA
1 AAAATCA
12833795 AAAAT
1 AAAAT
12833800 AGGAGAAAAA
Statistics
Matches: 118, Mismatches: 2, Indels: 7
0.93 0.02 0.06
Matches are distributed among these distances:
5 5 0.04
6 5 0.04
7 86 0.73
8 22 0.19
ACGTcount: A:0.73, C:0.13, G:0.01, T:0.14
Consensus pattern (7 bp):
AAAATCA
Found at i:12833832 original size:12 final size:14
Alignment explanation
Indices: 12833804--12833836 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
12833794 AAAAATAGGA
12833804 GAAAAAGAAAGAAG
1 GAAAAAGAAAGAAG
12833818 GAAAAAG-AA-AAG
1 GAAAAAGAAAGAAG
12833830 GAAAAAG
1 GAAAAAG
12833837 GAGAGGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 2 0.11
14 7 0.37
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
GAAAAAGAAAGAAG
Found at i:12834688 original size:12 final size:12
Alignment explanation
Indices: 12834673--12834698 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12834663 ACCAAAAAAA
12834673 AATGAAAAAATG
1 AATGAAAAAATG
12834685 AATGAAAAAATG
1 AATGAAAAAATG
12834697 AA
1 AA
12834699 AAAATGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (12 bp):
AATGAAAAAATG
Found at i:12834694 original size:20 final size:18
Alignment explanation
Indices: 12834667--12834719 Score: 88
Period size: 20 Copynumber: 2.8 Consensus size: 18
12834657 AGTCAAACCA
12834667 AAAAAAAATGAAAAAATG
1 AAAAAAAATGAAAAAATG
12834685 AATGAAAAAATGAAAAAATG
1 AA--AAAAAATGAAAAAATG
12834705 AAAAAAAATGAAAAA
1 AAAAAAAATGAAAAA
12834720 TTAAAAATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.45
20 18 0.55
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAAAAAATGAAAAAATG
Found at i:12834719 original size:8 final size:8
Alignment explanation
Indices: 12834669--12834710 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
12834659 TCAAACCAAA
12834669 AAAAAATG
1 AAAAAATG
12834677 AAAAAATG
1 AAAAAATG
12834685 ----AATG
1 AAAAAATG
12834689 AAAAAATG
1 AAAAAATG
12834697 AAAAAATG
1 AAAAAATG
12834705 AAAAAA
1 AAAAAA
12834711 AATGAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
4 4 0.13
8 26 0.87
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:12836048 original size:88 final size:88
Alignment explanation
Indices: 12835899--12836579 Score: 1034
Period size: 88 Copynumber: 7.8 Consensus size: 88
12835889 AACATATCAG
* * * *
12835899 TGAAGACAACAGATCTTGCATTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGAAAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
12835964 TTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
*
12835987 TGAAGACAAAAGATCTTGCCTTCCTGCATTGAAAGCGAAGCAGGTCGAAGACTCAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGAAAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
12836052 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* *
12836075 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAA-TGAAGCAAGTCGAAGACACAAACCTTGCC
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGA-AAGCGAAGCAGGTCGAAGACACAAACCTTGCC
*
12836139 TCTCTCGGTTGTGATAGAGCTGGT
65 TCTCTCGGTTGTGATGGAGCTGGT
12836163 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAA-CGAAGCAGGTCGAAGACACAAACCTTGCC
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGA-AAGCGAAGCAGGTCGAAGACACAAACCTTGCC
12836227 TCTCTCGGTTGTGATGGAGCTGGT
65 TCTCTCGGTTGTGATGGAGCTGGT
* *
12836251 TGAAGACAAAAGATCTTGCCTTCCTGCATTGAAAGCGAAGCAGGTCAAAGACTCAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGAAAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
12836316 CTCTCGGTTGTGATAGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* *
12836339 TGAAGACAAAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGAAAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
12836404 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* *
12836427 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAAACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGAAAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
** *
12836492 C-CATCGGTT-ACAGTGGAGCTAGT
66 CTC-TCGGTTGTGA-TGGAGCTGGT
* ** * * *
12836515 TGAAGATAGCAGATCTTGCCTTCCTGCGTT-AACAACGAAGCAGATCGAA-A-ACAAAGCCTTGC
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGAA-AGCGAAGCAGGTCGAAGACACAAA-CCTTGC
12836577 CTC
64 CTC
12836580 CATTGGTTGC
Statistics
Matches: 554, Mismatches: 33, Indels: 13
0.92 0.05 0.02
Matches are distributed among these distances:
86 5 0.01
87 15 0.03
88 532 0.96
89 2 0.00
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.24
Consensus pattern (88 bp):
TGAAGACAAAAGATCTTGCCTTCCTGCATTGAAAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
CTCTCGGTTGTGATGGAGCTGGT
Found at i:12836806 original size:44 final size:43
Alignment explanation
Indices: 12836738--12837129 Score: 264
Period size: 44 Copynumber: 9.0 Consensus size: 43
12836728 TAGATCGCAT
* *
12836738 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCTAG-AATCTTATCTCCCTGAGATTACAGTGGAG
* *
12836782 CAAATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAG-AATCTTATCTCCCTGAGATTACAGTGGAG
* * * * * *
12836826 C-GAATTAAAACCAAGGATCTTATCTCTCTGA-AGTTACAGTAGAG
1 CAG-ATT-GAAGCTAGAATCTTATCTCCCTGAGA-TTACAGTGGAG
* * * * * * * *
12836870 TAGATCGCA-CCAG-GTCTTATTTCCCTGAGATTACGGTGGAA
1 CAGATTGAAGCTAGAATCTTATCTCCCTGAGATTACAGTGGAG
* * *
12836911 CAGACTGAAGAATTTCAG-ATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAG---CT-AGAATCTTATCTCCCTGAGATTACAGTGGAG
*
12836957 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAG-AATCTTATCTCCCTGAGATTACAGTGGAG
* ** * * *
12837001 CGGATT-AAAATAAAGGATCTTATCTCTCTGA-AGTTACAGTAGAG
1 CAGATTGAAGCT--AGAATCTTATCTCCCTGAGA-TTACAGTGGAG
* * * **
12837045 TAGATCG-TG-TCAG-ATCTTATCTCCCTGAGATTACAACGGAG
1 CAGATTGAAGCT-AGAATCTTATCTCCCTGAGATTACAGTGGAG
* *
12837086 CAGATTGAAGTTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAG-AATCTTATCTCCCTGAGATTACAGTGGAG
12837130 TGGATTAAAA
Statistics
Matches: 265, Mismatches: 62, Indels: 42
0.72 0.17 0.11
Matches are distributed among these distances:
41 52 0.20
42 12 0.05
43 9 0.03
44 150 0.57
45 8 0.03
46 34 0.13
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (43 bp):
CAGATTGAAGCTAGAATCTTATCTCCCTGAGATTACAGTGGAG
Found at i:12836870 original size:142 final size:141
Alignment explanation
Indices: 12836597--12836878 Score: 390
Period size: 142 Copynumber: 2.0 Consensus size: 141
12836587 TGCAATGGAG
* *
12836597 CAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTATCCTA
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAAATCAAAGACACTATCCTA
* * *
12836662 TCTCCCTAAAGTTATACTGGAGCAGATTGAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGA
66 TCTCCCTAAAGTTACACTGGAGCAGATTAAAACAAAAGATCTTATCTCTCTGAAGTTACAGCAGA
12836727 GTAGATCGCAT
131 GTAGATCGCAT
** *
12836738 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAG-CTAGTAATCC
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAAATCAAAGAC-ACT-ATCC
* * * *
12836802 TATCTCCCT-GAGATTACAGTGGAGC-GAATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAG
64 TATCTCCCTAAAG-TTACACTGGAGCAG-ATTAAAACAAAAGATCTTATCTCTCTGAAGTTACAG
*
12836865 TAGAGTAGATCGCA
127 CAGAGTAGATCGCA
12836879 CCAGGTCTTA
Statistics
Matches: 124, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
140 1 0.01
141 55 0.44
142 68 0.55
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (141 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAAATCAAAGACACTATCCTA
TCTCCCTAAAGTTACACTGGAGCAGATTAAAACAAAAGATCTTATCTCTCTGAAGTTACAGCAGA
GTAGATCGCAT
Found at i:12837045 original size:175 final size:175
Alignment explanation
Indices: 12836754--12837078 Score: 569
Period size: 175 Copynumber: 1.9 Consensus size: 175
12836744 GAAGCCAGAA
12836754 ATCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
* *
12836819 AGTGGAGCGAATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGG
66 AGTGGAGCGAATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGA
*
12836884 TCTTATTTCCCTGAGATTACGGTGGAACAGACTGAAGAATTTCAG
131 TCTTATCTCCCTGAGATTACGGTGGAACAGACTGAAGAATTTCAG
*
12836929 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
* * ***
12836994 AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTGTCAGA
66 AGTGGAGCGAATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGA
12837059 TCTTATCTCCCTGAGATTAC
131 TCTTATCTCCCTGAGATTAC
12837079 AACGGAGCAG
Statistics
Matches: 141, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
175 141 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (175 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
AGTGGAGCGAATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGA
TCTTATCTCCCTGAGATTACGGTGGAACAGACTGAAGAATTTCAG
Found at i:12837111 original size:304 final size:307
Alignment explanation
Indices: 12836611--12837242 Score: 900
Period size: 304 Copynumber: 2.0 Consensus size: 307
12836601 TTGAAGCCAG
12836611 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTATCCTATCTCCCTAAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTATCCTATCTCCCTAAAGTTA
* *
12836676 TACTGGAGCAGATTGAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAG
66 CACTGGAGCAGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCG-AT-AG
*
12836741 ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGCTAGTAATCCTATC
129 A-T--A--CAG-AATCTTATCTCCCTGAGATTACAACGGAGCAAATTGAAGCTAGTAATCCTATC
*
12836806 TCCCTGAGATTACAGTGGAGCGAATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAGTAGAGT
188 TCCCTGAGATTACAGTGGAGCGAATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAGCAGAGT
*
12836871 AGATCGCACCAGGTCTTATTTCCCTGAGATTACGGTGGAACAGACTGAAGAATTTC
253 AGATCGCACCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAA-AATTTC
** * *
12836927 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-CTAGTAATCCTATCTCCCT-GAGA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAC-ACT-ATCCTATCTCCCTAAAG-
* * * *
12836990 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG-T-
63 TTACACTGGAGCAGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGATA
* *
12837053 G-T-CAG-ATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGTTAGTAATCCTATCTCCCT
128 GATACAGAATCTTATCTCCCTGAGATTACAACGGAGCAAATTGAAGCTAGTAATCCTATCTCCCT
* * **
12837115 GAGATTACAGTGGAGTGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATC
193 GAGATTACAGTGGAGCGAATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATC
** * *
12837180 GCGTCAGGTCTTATTTCCCTGAGATTACAGTGGAATAGATTGAAAATTTC
258 GCACCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAAATTTC
12837230 AGATCTTATCTCC
1 AGATCTTATCTCC
12837243 TAAGGTGGAG
Statistics
Matches: 290, Mismatches: 23, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
303 19 0.07
304 153 0.53
306 3 0.01
311 1 0.00
313 1 0.00
315 2 0.01
316 42 0.14
317 69 0.24
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (307 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTATCCTATCTCCCTAAAGTTA
CACTGGAGCAGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGATAGAT
ACAGAATCTTATCTCCCTGAGATTACAACGGAGCAAATTGAAGCTAGTAATCCTATCTCCCTGAG
ATTACAGTGGAGCGAATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCA
CCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAAATTTC
Found at i:12837220 original size:129 final size:129
Alignment explanation
Indices: 12836925--12837223 Score: 499
Period size: 129 Copynumber: 2.3 Consensus size: 129
12836915 CTGAAGAATT
12836925 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* *
12836990 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTG
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCG
* *
12837054 TCAGATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGA
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* *
12837119 TTACAGTGGAGTGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCG
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCG
* * * **
12837183 TCAGGTCTTATTTCCCTGAGATTACAGTGGAATAGATTGAA
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAA
12837224 AATTTCAGAT
Statistics
Matches: 158, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 158 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (129 bp):
TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCG
Found at i:12838921 original size:5 final size:5
Alignment explanation
Indices: 12838889--12838933 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
12838879 TTTCTTTCAT
*
12838889 TTTTA TTTT- TATTA -TTTA -TTTA -TTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
12838934 TCTTTCTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
4 14 0.39
5 22 0.61
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:12838943 original size:15 final size:15
Alignment explanation
Indices: 12838889--12838933 Score: 53
Period size: 13 Copynumber: 3.3 Consensus size: 15
12838879 TTTCTTTCAT
*
12838889 TTTTATTTT-TATTA
1 TTTTATTTTATTTTA
12838903 -TTTA-TTTA-TTTA
1 TTTTATTTTATTTTA
12838915 TTTTATTTTATTTTA
1 TTTTATTTTATTTTA
12838930 TTTT
1 TTTT
12838934 TCTTTCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
12 6 0.23
13 8 0.31
14 4 0.15
15 8 0.31
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTATTTTATTTTA
Found at i:12845356 original size:17 final size:17
Alignment explanation
Indices: 12845330--12845364 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12845320 CCTCCTCGCA
* *
12845330 CGTGTTGCGCCTGCGCG
1 CGTGTAGCGCCTCCGCG
12845347 CGTGTAGCGCCTCCGCG
1 CGTGTAGCGCCTCCGCG
12845364 C
1 C
12845365 CAAATTCACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.40, G:0.37, T:0.20
Consensus pattern (17 bp):
CGTGTAGCGCCTCCGCG
Found at i:12857495 original size:28 final size:28
Alignment explanation
Indices: 12857453--12857506 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
12857443 ATTTTTTTTA
12857453 GGTAAACTATAACGG-CACGTTTGGTAG
1 GGTAAACTATAACGGCCACGTTTGGTAG
12857480 GGTAAACTTATAACGGCCACGTTTGGT
1 GGTAAAC-TATAACGGCCACGTTTGGT
12857507 TTTGCTTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 7 0.28
28 8 0.32
29 10 0.40
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (28 bp):
GGTAAACTATAACGGCCACGTTTGGTAG
Found at i:12857554 original size:17 final size:17
Alignment explanation
Indices: 12857514--12857555 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
12857504 GGTTTTGCTT
12857514 GTAATGGGAATAGAGGCC
1 GTAATGGGAATAGAGG-C
12857532 GTAATGGGAATAGGAGG-
1 GTAATGGGAATA-GAGGC
12857549 GTAATGG
1 GTAATGG
12857556 ATTTAGAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.33, C:0.05, G:0.43, T:0.19
Consensus pattern (17 bp):
GTAATGGGAATAGAGGC
Found at i:12858490 original size:16 final size:16
Alignment explanation
Indices: 12858453--12858494 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
12858443 TTAATCATAT
*
12858453 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
12858469 TT-AAATATATTATAA
1 TTAAAATATATTATAA
12858484 TTAAAATATAT
1 TTAAAATATAT
12858495 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:12858501 original size:14 final size:15
Alignment explanation
Indices: 12858462--12858503 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12858452 TTTAAACATA
*
12858462 ATTATTATTAAATAT
1 ATTATAATTAAATAT
12858477 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
12858491 A-TATAATTTAATA
1 ATTATAATTAAATA
12858504 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Done.