Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 39 of 120
Found at i:10566982 original size:27 final size:27
Alignment explanation
Indices: 10566946--10567030 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
10566936 ATACAGTAGA
* *
10566946 AAAAGAAAGCCTTTGTGGCGATCGATG
1 AAAAGGAAGCCTTTGTGGCGATCTATG
* *
10566973 AAAAGGAAGCCTTTGTAGCGACCTATG
1 AAAAGGAAGCCTTTGTGGCGATCTATG
* * *
10567000 AAAATGAAGTCTTTGTGGCGATTTATG
1 AAAAGGAAGCCTTTGTGGCGATCTATG
10567027 AAAA
1 AAAA
10567031 ATGAAGTCTA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (27 bp):
AAAAGGAAGCCTTTGTGGCGATCTATG
Found at i:10567129 original size:27 final size:27
Alignment explanation
Indices: 10567099--10567158 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
10567089 CTTTACAGCA
10567099 TATTCT-GTAAGAGAAGCCTTTGTGGCG
1 TATTCTAGTAAGA-AAGCCTTTGTGGCG
* *
10567126 TATT-TAGTAATAAAGCCTTTGTGGTG
1 TATTCTAGTAAGAAAGCCTTTGTGGCG
10567152 TATTCTA
1 TATTCTA
10567159 ATAGATTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 18 0.62
27 11 0.38
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (27 bp):
TATTCTAGTAAGAAAGCCTTTGTGGCG
Found at i:10569264 original size:16 final size:18
Alignment explanation
Indices: 10569238--10569270 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
10569228 TTAAATTAGA
10569238 TAAATTAATTTT-TCAAT
1 TAAATTAATTTTCTCAAT
10569255 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
10569271 CCCAAATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:10573063 original size:17 final size:17
Alignment explanation
Indices: 10573040--10573075 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
10573030 AATAAAAAAA
*
10573040 ATAAAAAAATTGATTATT
1 ATAAAAATATT-ATTATT
10573058 ATAAAAATATTATTATT
1 ATAAAAATATTATTATT
10573075 A
1 A
10573076 AATTAAGCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
ATAAAAATATTATTATT
Found at i:10574889 original size:23 final size:25
Alignment explanation
Indices: 10574862--10574910 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
10574852 AATTTAAGTT
10574862 AAATTAAAA-AAT-TTAAAAATATG
1 AAATTAAAATAATGTTAAAAATATG
*
10574885 AAATTAAAATAATGTTTAAAATATG
1 AAATTAAAATAATGTTAAAAATATG
10574910 A
1 A
10574911 TTAATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.39
24 3 0.13
25 11 0.48
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (25 bp):
AAATTAAAATAATGTTAAAAATATG
Found at i:10574913 original size:23 final size:22
Alignment explanation
Indices: 10574863--10574914 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
10574853 ATTTAAGTTA
10574863 AATTAAAAAATTTAAAAATATG
1 AATTAAAAAATTTAAAAATATG
*
10574885 AAATTAAAATAATGTTTAAAATATG
1 -AATTAAAA-AAT-TTAAAAATATG
10574910 -ATTAA
1 AATTAA
10574915 TTTTTAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 13 0.50
24 3 0.12
25 10 0.38
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.35
Consensus pattern (22 bp):
AATTAAAAAATTTAAAAATATG
Found at i:10575934 original size:28 final size:28
Alignment explanation
Indices: 10575902--10575972 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 28
10575892 AAAACAACTT
*
10575902 TATTAAAACTTATTTTTATTTA-ATAAAA
1 TATTAAAACTTATTGTT-TTTATATAAAA
10575930 TATTATAAA--TATTGTTTTTATATAAAA
1 TATTA-AAACTTATTGTTTTTATATAAAA
10575957 T-TTAAATACTTTATTG
1 TATTAAA-AC-TTATTG
10575973 CAACAATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
25 2 0.06
26 8 0.22
27 13 0.36
28 5 0.14
29 8 0.22
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (28 bp):
TATTAAAACTTATTGTTTTTATATAAAA
Found at i:10576988 original size:2 final size:2
Alignment explanation
Indices: 10576981--10577014 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10576971 TGCTTTATTC
10576981 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
10577015 TTGAGTAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10588770 original size:21 final size:21
Alignment explanation
Indices: 10588727--10588771 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
10588717 CTAAAAATTT
* * **
10588727 AAAAATATTATATATATTCTA
1 AAAAATATTAAAAATATGATA
10588748 AAAAATATTAAAAATATGATA
1 AAAAATATTAAAAATATGATA
10588769 AAA
1 AAA
10588772 TCTCATAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAAATATTAAAAATATGATA
Found at i:10590542 original size:2 final size:2
Alignment explanation
Indices: 10590535--10590571 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
10590525 CATATGTTAC
10590535 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10590572 CTCAGTGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10592483 original size:12 final size:12
Alignment explanation
Indices: 10592466--10592491 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10592456 CTTTTCCCTT
10592466 CCATCGGTTCTG
1 CCATCGGTTCTG
10592478 CCATCGGTTCTG
1 CCATCGGTTCTG
10592490 CC
1 CC
10592492 GTCACTTAAT
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:0.08, C:0.38, G:0.23, T:0.31
Consensus pattern (12 bp):
CCATCGGTTCTG
Found at i:10593084 original size:14 final size:14
Alignment explanation
Indices: 10593065--10593096 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
10593055 TGTGAATAAA
10593065 CCTTCATCTAAAGC
1 CCTTCATCTAAAGC
10593079 CCTTCATCTAAAGC
1 CCTTCATCTAAAGC
10593093 CCTT
1 CCTT
10593097 ATCAAATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.38, G:0.06, T:0.31
Consensus pattern (14 bp):
CCTTCATCTAAAGC
Found at i:10595460 original size:18 final size:17
Alignment explanation
Indices: 10595437--10595471 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
10595427 ATATATTATG
10595437 ATTTTAGTAAATTCATAT
1 ATTTTAGTAAATT-ATAT
*
10595455 ATTTTATTAAATTATAT
1 ATTTTAGTAAATTATAT
10595472 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTAGTAAATTATAT
Found at i:10595662 original size:39 final size:42
Alignment explanation
Indices: 10595617--10595717 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 42
10595607 TTTCCTTATG
*
10595617 CTATTACACCTCTATTT-CATTCAACCAAACACAAA-AA-TAC
1 CTATTACGCCTCTATTTCCATTCAACCAAACA-AAAGAATTAC
10595657 C-ATTACGCCTCTATTCCATTCCATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTA-T---TTCCATTCAACCAAACAAAAGAATTAC
10595702 CTATTACGCCTCTATT
1 CTATTACGCCTCTATT
10595718 CTATTACACT
Statistics
Matches: 52, Mismatches: 1, Indels: 14
0.78 0.01 0.21
Matches are distributed among these distances:
39 11 0.21
40 2 0.04
42 1 0.02
43 5 0.10
44 16 0.31
45 5 0.10
46 12 0.23
ACGTcount: A:0.37, C:0.31, G:0.03, T:0.30
Consensus pattern (42 bp):
CTATTACGCCTCTATTTCCATTCAACCAAACAAAAGAATTAC
Found at i:10595723 original size:16 final size:16
Alignment explanation
Indices: 10595702--10595757 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
10595692 AAAGAATTAC
*
10595702 CTATTACGCCTCTATT
1 CTATTACACCTCTATT
*
10595718 CTATTACACTTCTATT
1 CTATTACACCTCTATT
*
10595734 CCATTACACCTCTATT
1 CTATTACACCTCTATT
10595750 CTATTACA
1 CTATTACA
10595758 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.25, C:0.30, G:0.02, T:0.43
Consensus pattern (16 bp):
CTATTACACCTCTATT
Found at i:10596147 original size:17 final size:17
Alignment explanation
Indices: 10596102--10596157 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
10596092 TGAAAAAAAA
*
10596102 TAAAA-ATAAAAATCAAT
1 TAAAATATAAAAAT-TAT
*
10596119 TAAAGTTATAAAAATTAT
1 TAAA-ATATAAAAATTAT
10596137 TAAAATATAAAAA-TAT
1 TAAAATATAAAAATTAT
10596153 TAAAA
1 TAAAA
10596158 ATTAGAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 8 0.24
17 12 0.35
18 6 0.18
19 8 0.24
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
TAAAATATAAAAATTAT
Found at i:10596167 original size:19 final size:20
Alignment explanation
Indices: 10596145--10596236 Score: 77
Period size: 19 Copynumber: 4.8 Consensus size: 20
10596135 ATTAAAATAT
10596145 AAAAATAT-TAAAAATTAG-A
1 AAAAATATATAAAAATT-GTA
*
10596164 AAAAAAATTATAAAAATTGTA
1 AAAAATA-TATAAAAATTGTA
10596185 AAAAAT-TATAAAAATTGT-
1 AAAAATATATAAAAATTGTA
* * * *
10596203 AAAATTTTATAAAAGTAGT-
1 AAAAATATATAAAAATTGTA
*
10596222 AAAAATATAGAAAAA
1 AAAAATATATAAAAA
10596237 AAATTATAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
18 5 0.08
19 39 0.65
20 2 0.03
21 14 0.23
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (20 bp):
AAAAATATATAAAAATTGTA
Found at i:10596171 original size:21 final size:20
Alignment explanation
Indices: 10596145--10596206 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
10596135 ATTAAAATAT
10596145 AAAAATATTAAAAATTAGAAA
1 AAAAATATTAAAAATT-GAAA
*
10596166 AAAAAT-TATAAAAATTGTAA
1 AAAAATAT-TAAAAATTGAAA
*
10596186 AAAATTA-TAAAAATTGTAAA
1 AAAAATATTAAAAATTG-AAA
10596206 A
1 A
10596207 TTTTATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
19 9 0.26
20 12 0.34
21 14 0.40
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (20 bp):
AAAAATATTAAAAATTGAAA
Found at i:10596247 original size:9 final size:9
Alignment explanation
Indices: 10596124--10596216 Score: 73
Period size: 9 Copynumber: 9.9 Consensus size: 9
10596114 TCAATTAAAG
10596124 TTATAAAAA
1 TTATAAAAA
*
10596133 TTATTAAAA
1 TTATAAAAA
10596142 -TATAAAAA
1 TTATAAAAA
10596150 -TATTAAAAA
1 TTA-TAAAAA
*
10596159 TTAGAAAAAAAA
1 TT---ATAAAAA
10596171 TTATAAAAA
1 TTATAAAAA
*
10596180 TTGTAAAAAA
1 TTAT-AAAAA
10596190 TTATAAAAA
1 TTATAAAAA
* *
10596199 TTGTAAAATT
1 TTATAAAA-A
10596209 TTATAAAA
1 TTATAAAA
10596217 GTAGTAAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
8 9 0.13
9 35 0.51
10 16 0.24
12 7 0.10
13 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (9 bp):
TTATAAAAA
Found at i:10596277 original size:41 final size:41
Alignment explanation
Indices: 10596194--10596277 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
10596184 AAAAAATTAT
* *
10596194 AAAAATTGTAAAATTTTATAAAAGTAGTAAAAATATAGAAA
1 AAAAATTATAAAATTTTATAAAAGTAGTAAAAATATAAAAA
* *
10596235 AAAAATTATAAAATTTTAT-AAAGTCGTAAGAAA-ATTAAAA
1 AAAAATTATAAAATTTTATAAAAGTAGTAA-AAATATAAAAA
10596275 AAA
1 AAA
10596278 TGTAAAGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
40 17 0.45
41 21 0.55
ACGTcount: A:0.62, C:0.01, G:0.08, T:0.29
Consensus pattern (41 bp):
AAAAATTATAAAATTTTATAAAAGTAGTAAAAATATAAAAA
Found at i:10596373 original size:16 final size:17
Alignment explanation
Indices: 10596343--10596375 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
10596333 GCAATTTATA
10596343 ATTTTTCTATAATTTTT
1 ATTTTTCTATAATTTTT
*
10596360 ATTTTT-TATCATTTTT
1 ATTTTTCTATAATTTTT
10596376 CGCCATAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTTCTATAATTTTT
Found at i:10596490 original size:9 final size:9
Alignment explanation
Indices: 10596476--10596566 Score: 56
Period size: 10 Copynumber: 9.4 Consensus size: 9
10596466 TTTTGATGCA
10596476 TTTTATAAT
1 TTTTATAAT
*
10596485 TTTTATAAAA
1 TTTTAT-AAT
*
10596495 TTATATATAT
1 TTTTATA-AT
**
10596505 TTTTACGAT
1 TTTTATAAT
10596514 TTTTATAATT
1 TTTTATAA-T
*
10596524 TTTTCTAAT
1 TTTTATAAT
* *
10596533 TTCTAATAAAA
1 TT-TTAT-AAT
*
10596544 TTTAATAAT
1 TTTTATAAT
10596553 TTTTATAAAT
1 TTTTAT-AAT
10596563 TTTT
1 TTTT
10596567 GCCACATGTC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
9 25 0.40
10 33 0.53
11 4 0.06
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (9 bp):
TTTTATAAT
Found at i:10598683 original size:33 final size:33
Alignment explanation
Indices: 10598634--10598756 Score: 201
Period size: 33 Copynumber: 3.7 Consensus size: 33
10598624 ATGATCACTT
* *
10598634 GAGCCAATCCATCCATCACACCAATGCTCATAA
1 GAGCTAATCCAACCATCACACCAATGCTCATAA
*
10598667 GAGCTAATCCAACCATCACACCGATGCTCATAA
1 GAGCTAATCCAACCATCACACCAATGCTCATAA
*
10598700 GAGCTAAACCAACCATCACACCAATGCTCATAA
1 GAGCTAATCCAACCATCACACCAATGCTCATAA
*
10598733 GAGCTAATCCAACCAACACACCAA
1 GAGCTAATCCAACCATCACACCAA
10598757 AAAGAGAGTA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 83 1.00
ACGTcount: A:0.40, C:0.35, G:0.10, T:0.15
Consensus pattern (33 bp):
GAGCTAATCCAACCATCACACCAATGCTCATAA
Found at i:10602324 original size:22 final size:19
Alignment explanation
Indices: 10602287--10602330 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 19
10602277 AACCATAAAA
10602287 ACATTAAATTTAACACATT
1 ACATTAAATTTAACACATT
10602306 ACATATAAACTTTAAACACATT
1 ACAT-TAAA-TTT-AACACATT
10602328 ACA
1 ACA
10602331 ATTCCAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.18
20 4 0.18
21 3 0.14
22 11 0.50
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (19 bp):
ACATTAAATTTAACACATT
Found at i:10602901 original size:20 final size:20
Alignment explanation
Indices: 10602876--10602944 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
10602866 CAGAGACATA
10602876 GAAGTGTAAACAAAGGCACC
1 GAAGTGTAAACAAAGGCACC
* *
10602896 GAAGTGCAAACAAAGGCA-A
1 GAAGTGTAAACAAAGGCACC
* * * *
10602915 GATTGTGTAATCAGAGACACC
1 GA-AGTGTAAACAAAGGCACC
10602936 GAAGTGTAA
1 GAAGTGTAA
10602945 GTAGAGGCAC
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
19 2 0.05
20 34 0.89
21 2 0.05
ACGTcount: A:0.43, C:0.16, G:0.26, T:0.14
Consensus pattern (20 bp):
GAAGTGTAAACAAAGGCACC
Found at i:10602953 original size:60 final size:60
Alignment explanation
Indices: 10602849--10602964 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
10602839 ATGCTATAAG
* * * *
10602849 AGGCACGATTATGCAATCAGAGACATAGAAGTGTAAACAAAGGCACCGAAGTGCAAACAA
1 AGGCAAGATTATGCAATCAGAGACACAGAAGTGTAAACAAAGGCACCAAAATGCAAACAA
* * * ** *
10602909 AGGCAAGATTGTGTAATCAGAGACACCGAAGTGTAAGTAGAGGCACCAAAATGCAA
1 AGGCAAGATTATGCAATCAGAGACACAGAAGTGTAAACAAAGGCACCAAAATGCAA
10602965 CCTCGTACAA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.15
Consensus pattern (60 bp):
AGGCAAGATTATGCAATCAGAGACACAGAAGTGTAAACAAAGGCACCAAAATGCAAACAA
Found at i:10614978 original size:16 final size:16
Alignment explanation
Indices: 10614957--10615011 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
10614947 AAATAAATTA
10614957 TGAAGAGTTAGAAATG
1 TGAAGAGTTAGAAATG
*
10614973 TGAAGAAACTT-G-AA-G
1 TGAAG--AGTTAGAAATG
10614988 ATGAAGAGTTAGAAATG
1 -TGAAGAGTTAGAAATG
10615005 TGAAGAG
1 TGAAGAG
10615012 ACTTGAAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
14 3 0.10
15 2 0.06
16 21 0.68
17 2 0.06
18 3 0.10
ACGTcount: A:0.45, C:0.02, G:0.31, T:0.22
Consensus pattern (16 bp):
TGAAGAGTTAGAAATG
Found at i:10614997 original size:32 final size:32
Alignment explanation
Indices: 10614956--10615030 Score: 141
Period size: 32 Copynumber: 2.3 Consensus size: 32
10614946 AAAATAAATT
10614956 ATGAAGAGTTAGAAATGTGAAGAAACTTGAAG
1 ATGAAGAGTTAGAAATGTGAAGAAACTTGAAG
*
10614988 ATGAAGAGTTAGAAATGTGAAGAGACTTGAAG
1 ATGAAGAGTTAGAAATGTGAAGAAACTTGAAG
10615020 ATGAAGAGTTA
1 ATGAAGAGTTA
10615031 CACACATACA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.45, C:0.03, G:0.29, T:0.23
Consensus pattern (32 bp):
ATGAAGAGTTAGAAATGTGAAGAAACTTGAAG
Found at i:10615024 original size:16 final size:16
Alignment explanation
Indices: 10614973--10615027 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
10614963 GTTAGAAATG
*
10614973 TGAAGAAACTTGAAGA
1 TGAAGAGACTTGAAGA
10614989 TGAAGAG--TTAGAA-A
1 TGAAGAGACTT-GAAGA
10615003 TGTGAAGAGACTTGAAGA
1 --TGAAGAGACTTGAAGA
10615021 TGAAGAG
1 TGAAGAG
10615028 TTACACACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
14 3 0.09
15 3 0.09
16 20 0.62
17 3 0.09
18 3 0.09
ACGTcount: A:0.45, C:0.04, G:0.31, T:0.20
Consensus pattern (16 bp):
TGAAGAGACTTGAAGA
Found at i:10615094 original size:39 final size:39
Alignment explanation
Indices: 10615040--10615128 Score: 169
Period size: 39 Copynumber: 2.3 Consensus size: 39
10615030 ACACACATAC
10615040 ATGAATAGTCACAACTCCTATAGCAATTAAGTGATGTAG
1 ATGAATAGTCACAACTCCTATAGCAATTAAGTGATGTAG
*
10615079 ATGAATAGTCACAACTCCTATAGCATTTAAGTGATGTAG
1 ATGAATAGTCACAACTCCTATAGCAATTAAGTGATGTAG
10615118 ATGAATAGTCA
1 ATGAATAGTCA
10615129 TTTACAACTC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (39 bp):
ATGAATAGTCACAACTCCTATAGCAATTAAGTGATGTAG
Found at i:10622743 original size:498 final size:499
Alignment explanation
Indices: 10621743--10623200 Score: 1744
Period size: 498 Copynumber: 2.8 Consensus size: 499
10621733 CTCTATTTTC
* **
10621743 AAATTAAAACAGAATTTGAAGAGATAAACTCAGCTGAGGAAAAATAAAAAAATGTATTGGGCTAA
1 AAATTAAAACAGAATTTGAAGAGATAAACTCTGCTGAGGAAAAATAAAATTATGTATTGGGCTAA
* * * *
10621808 AATATCCGTAAGTCTAGGAAAAATTAATAGTAATGTAAAATATTGATTTAAATAATAGGATAAAA
66 AATATCCGCAGGTCTAGGAAAAATTAATAGTAATGTAAAATATTAATTTAAATAATAGGATCAAA
* * *
10621873 CCAGAAAAATATAGATATATATATATATATAATCTAAAAAACATAAATTGGAAAT-AAAACTGGA
131 CC----------AGA-ACATATATATATATAATCTAAAAAATAGAAATTGGAAATAAAAACTGGA
* * *
10621937 TCGAAATTGTATACTCGTAGGT-AGGCAAAAATTCGATTGGTAGTTGAGGCTTGTTTTCACAGTT
185 TCGAAATTGTATACTCGTAGGTAAGG-AAAAATCCGACTGGTAGTTGAGGCCTGTTTTCACAGTT
** * * * *
10622001 TCTTTAAGGTAGATTTGGCTGCTCCTTTGGTGCTAGAGAAATGTTGGTCGACTATCTCCCAAGAT
249 TCTTTAAGACAGATTAGGCTGCTCCTTTGGTGCTGGAGAAATGTTGGTCGACTGTCTCCCAGGAT
* * * * *
10622066 ACAATAACGATATGAGCACACCAGTAGCACGGCTACAGTGATCAACGAATTGTAGCCTAGCTTTC
314 ACAACAACGAGATGAGCACAGCAGTAACACGGCTGCAGTGATCAACGAATTGTAGCCTAGCTTTC
* * *
10622131 TTCTATCACTGAAAACAT-GTTCAAAATATGAAGGGAAAA-TATGTCGAAACTTTTGCAGAAAAA
379 TTCTATCATTGAAAAC-TGGTTCGAAATATGAAGGGAAAAGT-TCTCGAAACTTTTGCAGAAAAA
* * *
10622194 ATGGGAAAATTTAAGTTTTTTTTTTCCTAAAGATTATTCTTTTTCCTTTTAATTCCAA
442 ATGGGAAAAATGAAGTTTTCTTTTTCCTAAAGATTATTCTTTTTCCTTTTAATTCCAA
* * * *
10622252 AAATTAAAACAGAATTTGAAGAGATAAAATGCTGCTAATGAAAATTAAAATTATGTATTGGGCTA
1 AAATTAAAACAGAATTTGAAGAGATAAACT-CTGCTGAGGAAAAATAAAATTATGTATTGGGCTA
*
10622317 AAATATCCGCAGGTCTAGGAAAAATTAATAGTAATATAAAATATTAATTTAAATAATAGGATCAA
65 AAATATCCGCAGGTCTAGGAAAAATTAATAGTAATGTAAAATATTAATTTAAATAATAGGATCAA
* *
10622382 ACCAGAACA-ATATATATATAATCTAAAAAATAGAAATTGGAAATAAAAACTTGATAGAAATTGT
130 ACCAGAACATATATATATATAATCTAAAAAATAGAAATTGGAAATAAAAACTGGATCGAAATTGT
*
10622446 ATACTCGTAGGTAAGGAAAAATCCGACTGGTAGTTGAGGCCTGTTTTCACAG-TTCCTTAAGACA
195 ATACTCGTAGGTAAGGAAAAATCCGACTGGTAGTTGAGGCCTGTTTTCACAGTTTCTTTAAGACA
* * * *
10622510 GATTAGACTGCTACTTTGGTGTTGGAGAAATATTGGTCGACTGTCTCCCAGGATACAACAACGAG
260 GATTAGGCTGCTCCTTTGGTGCTGGAGAAATGTTGGTCGACTGTCTCCCAGGATACAACAACGAG
* * ** ** * *
10622575 ATGAACACAGTAGTAACACAACTGCAACGATCAACGAACTGTAGCTTAGCTTTCTTCTATCATTG
325 ATGAGCACAGCAGTAACACGGCTGCAGTGATCAACGAATTGTAGCCTAGCTTTCTTCTATCATTG
** * *
10622640 AAAACTGGTTCGAAATATGAAGGGAAAAGTTCTCGAATTTTTTGTAG-GAAAATCGGGAAAAATG
390 AAAACTGGTTCGAAATATGAAGGGAAAAGTTCTCGAAACTTTTGCAGAAAAAAT-GGGAAAAATG
*
10622704 CAGTTTTCTTTTTCCTAAAGATTATTCTTTTTCCTTTTAATTCCAA
454 AAGTTTTCTTTTTCCTAAAGATTATTCTTTTTCCTTTTAATTCCAA
* * *
10622750 AAATTAAAATAGAATTTGAAGAGATAAACTCTGCTGAGGAAAACTAAAATTATGTATTAGGCTAA
1 AAATTAAAACAGAATTTGAAGAGATAAACTCTGCTGAGGAAAAATAAAATTATGTATTGGGCTAA
* * * * *
10622815 AATATCCACAGGTCTAGGAAAATTTAATAGTAATGTAAAATA-TAGATTTCAATCATAGGATCGA
66 AATATCCGCAGGTCTAGGAAAAATTAATAGTAATGTAAAATATTA-ATTTAAATAATAGGATCAA
*
10622879 ACCAGAACAATATATATATATATATATATATATATATATATATATATATAATCTAAAATAGAAAT
130 ACCAGAAC-----------------------ATATATATATATA-ATCTAA---AAAATAGAAAT
* * **
10622944 TGGAAAGAAAAACTGGATCGAAATTGTATAGTCAAAGGTAAGGAAAAATCCGACTGGTAGTTGAG
168 TGGAAATAAAAACTGGATCGAAATTGTATACTCGTAGGTAAGGAAAAATCCGACTGGTAGTTGAG
* * * *
10623009 GCCTGTTTTCACAGTTTCTTTAAGACAAATTCGGCTGCTCCTTTGGTGCTGAAGAAATGTTGGTT
233 GCCTGTTTTCACAGTTTCTTTAAGACAGATTAGGCTGCTCCTTTGGTGCTGGAGAAATGTTGGTC
* * * *
10623074 GACTGTCTCCCAGCATACAACAACAAGATGAGCACAGCAGTATCATGGCTGCAGTGATCAACGAA
298 GACTGTCTCCCAGGATACAACAACGAGATGAGCACAGCAGTAACACGGCTGCAGTGATCAACGAA
* * * *
10623139 TTGTAGCCTAGCTTTCTTCTATCATAGAAAATTGGTTCGAAATATGAAGAGAAAAGATCTCG
363 TTGTAGCCTAGCTTTCTTCTATCATTGAAAACTGGTTCGAAATATGAAGGGAAAAGTTCTCG
10623201 NNNNNNNNNN
Statistics
Matches: 814, Mismatches: 99, Indels: 55
0.84 0.10 0.06
Matches are distributed among these distances:
496 2 0.00
497 100 0.12
498 268 0.33
499 65 0.08
500 6 0.01
509 29 0.04
510 91 0.11
520 1 0.00
521 11 0.01
522 5 0.01
525 84 0.10
526 152 0.19
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (499 bp):
AAATTAAAACAGAATTTGAAGAGATAAACTCTGCTGAGGAAAAATAAAATTATGTATTGGGCTAA
AATATCCGCAGGTCTAGGAAAAATTAATAGTAATGTAAAATATTAATTTAAATAATAGGATCAAA
CCAGAACATATATATATATAATCTAAAAAATAGAAATTGGAAATAAAAACTGGATCGAAATTGTA
TACTCGTAGGTAAGGAAAAATCCGACTGGTAGTTGAGGCCTGTTTTCACAGTTTCTTTAAGACAG
ATTAGGCTGCTCCTTTGGTGCTGGAGAAATGTTGGTCGACTGTCTCCCAGGATACAACAACGAGA
TGAGCACAGCAGTAACACGGCTGCAGTGATCAACGAATTGTAGCCTAGCTTTCTTCTATCATTGA
AAACTGGTTCGAAATATGAAGGGAAAAGTTCTCGAAACTTTTGCAGAAAAAATGGGAAAAATGAA
GTTTTCTTTTTCCTAAAGATTATTCTTTTTCCTTTTAATTCCAA
Found at i:10622895 original size:2 final size:2
Alignment explanation
Indices: 10622888--10622928 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
10622878 AACCAGAACA
10622888 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10622929 ATCTAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10623312 original size:2 final size:2
Alignment explanation
Indices: 10623305--10623341 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
10623295 NNNNNNAATA
10623305 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10623342 AAATTTGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10624175 original size:24 final size:24
Alignment explanation
Indices: 10624143--10624214 Score: 135
Period size: 24 Copynumber: 3.0 Consensus size: 24
10624133 TTTTGCTGGA
*
10624143 AAAATATGAAAAAATTTAGTTTTC
1 AAAATATGAAAAAATTCAGTTTTC
10624167 AAAATATGAAAAAATTCAGTTTTC
1 AAAATATGAAAAAATTCAGTTTTC
10624191 AAAATATGAAAAAATTCAGTTTTC
1 AAAATATGAAAAAATTCAGTTTTC
10624215 TTTTTCCTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.35
Consensus pattern (24 bp):
AAAATATGAAAAAATTCAGTTTTC
Found at i:10624661 original size:549 final size:556
Alignment explanation
Indices: 10623641--10624696 Score: 1391
Period size: 549 Copynumber: 1.9 Consensus size: 556
10623631 AAAAATCAGG
10623641 AAAAATTCAGTTTTCTTTTTCCTAAAGATTATTACTTTTCCTTTTAATTCCAAAAATTAAAACAG
1 AAAAATTCAGTTTTCTTTTTCCTAAAGATTATTACTTTTCCTTTTAATTCCAAAAATTAAAACAG
* * *
10623706 AATTTGAAAAGATAAACTCTGTTGAGGAAAAATAAAATTGTGTATTGGGCTAAAATATCCACAGG
66 AATTTGAAAAGATAAACTATGTTGAGGAAAAATAAAATTATGTATTGGGCTAAAATAGCCACAGG
* *
10623771 TCTAGGAAAAATTAATAGGAGTGTAAAAAATTGATTTAAATCATAGGACCGAACCAGAACAATAT
131 TCTAGGAAAAATTAATAGGAATGTAAAAAATTGATTTAAATCATAGGACCGAACCAAAACAATAT
* * *
10623836 AGATATATATATATATAAAATCTAAAAAATAGAATTTGGAAAGAAAAACTGGATCGAAATTGTAT
196 A-ATATATATATATATAAAA--TAAAAAATAGAATTTAGAAAGAAAAACTAGATCGAAATTATAT
* * * *
10623901 ACTCGTAGGTAGGCAAAAATCTGACTGGTAGTTGAGGCCTGTTGTGATAATTTCCTTAAGACAGA
258 ACTCATAGGTAGGCAAAAATCCGACTGGTAGTTGAGGCCTATTGTGACAATTTCCTTAAGACAGA
* * *
10623966 TTCGATCGCTCATTTGTTGCTGGAGAAATGTTGGCCGACTGTCTCCCAAGATACAACAACGAGAT
323 TTCGATCGCTCATTTGGTGCTAGAGAAATGTTGACCGACTGTCTCCCAAGATACAACAACGAGAT
* * * * * *
10624031 AAACACAGCAATATCACGGCTGCAGTGATTAACGAACTGTAGCCTAGCTTTTTTCTATCATTGAA
388 AAACACAGCAATAGCACAGCTGCAGTGATCAACGAACTGTAGCCTAGCTTTCTTCTATAACTGAA
** ** * *
10624096 AACTTGTTTAAAATATGAAGGGAAAAGATCTTGAAATTTTTGCTGGAAAAATATGAAAAAATTTA
453 AACAAGTTTAAAATATGAACAGAAAAGATCTCGAAATTTTTGCAGGAAAAATATGAAAAAATTTA
10624161 GTTTTCAAAATATGAAAAAATTCAGTTTTCAAAATATGA
518 GTTTTCAAAATATGAAAAAATTCAGTTTTCAAAATATGA
10624200 AAAAATTCAGTTTTCTTTTTCCTAAAGATTATT-CTTTTTTCCTTTTAATTCCAAAAATTAAAAC
1 AAAAATTCAGTTTTCTTTTTCCTAAAGATTATTAC--TTTTCCTTTTAATTCCAAAAATTAAAAC
* * *
10624264 AGAATTTGAAGAGATAAACTATGCTT-A-GAAAATTAAAATTATGTATTGGGCTAAAATAGCCGC
64 AGAATTTGAAAAGATAAACTATG-TTGAGGAAAAATAAAATTATGTATTGGGCTAAAATAGCCAC
* * * * *
10624327 AGGTCTAGGAAATATTAATTGTAATGTAAAATATTGATTTAAATCATAGGATCGAACCAAAAC-A
128 AGGTCTAGGAAAAATTAATAGGAATGTAAAAAATTGATTTAAATCATAGGACCGAACCAAAACAA
* * *
10624391 -AT-ATATATATA-ATCT-GAA-AAAAAA-AGCAA-TTAGAAATAAAAACTAGATCGAAATTATA
193 TATAATATATATATATATAAAATAAAAAATAG-AATTTAGAAAGAAAAACTAGATCGAAATTATA
* * * * *
10624449 TACTTATAGGTAGGGAAAAATCCGAGTGGTAGTTGAGGCCTATTTTGACAGTTTCCTTAAGACAG
257 TACTCATAGGTAGGCAAAAATCCGACTGGTAGTTGAGGCCTATTGTGACAATTTCCTTAAGACAG
* * * * * *
10624514 ATTCGA-CTGTTCCTTTGGTGTTAGAGAAATGTTGATCGACTGTCTCCCAGGATACAACAATGAG
322 ATTCGATC-GCTCATTTGGTGCTAGAGAAATGTTGACCGACTGTCTCCCAAGATACAACAACGAG
* * * * * * * ** *
10624578 ATGAGCACAGCAGTAGCACAGCTGTAGTGATCAATGAACTTTTGTTTGGCTTTCTTCTATAACTG
386 ATAAACACAGCAATAGCACAGCTGCAGTGATCAACGAACTGTAGCCTAGCTTTCTTCTATAACTG
* *
10624643 AAATA-AAGTTTGAAATATGTACAGAAAAGATCTCGAAATTTTTGCAGGAAAAAT
451 AAA-ACAAGTTTAAAATATGAACAGAAAAGATCTCGAAATTTTTGCAGGAAAAAT
10624697 TGGGAAAAAT
Statistics
Matches: 430, Mismatches: 61, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
548 1 0.00
549 229 0.53
550 9 0.02
553 2 0.00
554 3 0.01
555 9 0.02
557 2 0.00
558 2 0.00
559 121 0.28
560 50 0.12
561 2 0.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (556 bp):
AAAAATTCAGTTTTCTTTTTCCTAAAGATTATTACTTTTCCTTTTAATTCCAAAAATTAAAACAG
AATTTGAAAAGATAAACTATGTTGAGGAAAAATAAAATTATGTATTGGGCTAAAATAGCCACAGG
TCTAGGAAAAATTAATAGGAATGTAAAAAATTGATTTAAATCATAGGACCGAACCAAAACAATAT
AATATATATATATATAAAATAAAAAATAGAATTTAGAAAGAAAAACTAGATCGAAATTATATACT
CATAGGTAGGCAAAAATCCGACTGGTAGTTGAGGCCTATTGTGACAATTTCCTTAAGACAGATTC
GATCGCTCATTTGGTGCTAGAGAAATGTTGACCGACTGTCTCCCAAGATACAACAACGAGATAAA
CACAGCAATAGCACAGCTGCAGTGATCAACGAACTGTAGCCTAGCTTTCTTCTATAACTGAAAAC
AAGTTTAAAATATGAACAGAAAAGATCTCGAAATTTTTGCAGGAAAAATATGAAAAAATTTAGTT
TTCAAAATATGAAAAAATTCAGTTTTCAAAATATGA
Found at i:10625170 original size:510 final size:506
Alignment explanation
Indices: 10624191--10625447 Score: 1613
Period size: 510 Copynumber: 2.5 Consensus size: 506
10624181 TTCAGTTTTC
*
10624191 AAAATATGA-AAAAATTCAGTTTTCTTTTTCCTAAAGATTATTCTTTTTTCCTTTTAATTCCAAA
1 AAAAT-TGAGAAAAATTCAGTTTTCTTTTTCCTACAGATTATTC-TTTTTCCTTTTAATTCCAAA
* ** *
10624255 AATTAAAACAGAATTTGAAGAGATAAACTATGCTTA-GAAAATTAAAATTATGTATTGGGCTAAA
64 AATTAAAACAGAATTTGAAGAGATAAACTCTGCCAAGGAAAAATAAAATTATGTATTGGGCTAAA
* * * * * * *
10624319 ATAGCCGCAGGTCTAGGAAATATTAATTGTAATGTAAAATATTGATTTAAATCATAGGATCGAAC
129 ATATCCACATGTTTAGGAAAAATTAATAGTAATGTAAAATATTGATTTAAATCATAGGATCAAAC
* * * * *
10624384 CAAAACAATATATATATAATCT-GAA---AAAAAA-AGCAATTAGAAATAAAAACTAGATCGAAA
194 CAAAACAATATAGATATATTATAAAATCTAAAAAACAGAAATTAGAAATAAAAACTAGATCGAAA
* * * *
10624444 TTATATACTTATAGGTAGGGAAAAATCCGAGTGGTAGTTGAGGCCTATTTTGACAGTTTCCTTAA
259 TTATATACTTATAGGTAGGAAAAAATCCGACTGGTAGTTGAGGCCTATTTTCACAGTTTCATTAA
* * * * * * *
10624509 GACAGATTCGACTGTTCCTTTGGTGTTAGAGAAATGTTGATCGACTGTCTCCCAGGATACAACAA
324 GACAAATTCGACCGCTCCTTTGGTGCTAGAGAAATATTGAGCAACTGTCTCCCAGGATACAACAA
* * * * * * ** *
10624574 TGAGATGAGCACAGCAGTAGCACAGCTGTAGTGATCAATGAACTTTTGTTTGGCTTTCTTCTATA
389 CGAGATGAGCACAGCAATAGCACAGCTGCAGTGATCAACGAACTATAGCCTAGCTTTCTTCTATA
* * **
10624639 ACTGAAATAAAGTTTGAAATATGTACAGAAAAGATCTCGAAATTTTTGCAGGA
454 ACTGAAATAAAGTTCGAAATATGTACAGAAAAGATCTCAAAATTTTTGCAAAA
* * * * *
10624692 AAAATTGGGAAAAATCCTGTTTTCTTTTTCCTACAGGTTATTCTTTTTCCTTTTAATTCCAAGAA
1 AAAATTGAGAAAAATTCAGTTTTCTTTTTCCTACAGATTATTCTTTTTCCTTTTAATTCCAAAAA
* * ** *
10624757 TTAAAAAAGAATTTGAAGAAATAAACTCTGCGGAGGAAAAATAAAATTATGTAGTGGGCTAAAAT
66 TTAAAACAGAATTTGAAGAGATAAACTCTGCCAAGGAAAAATAAAATTATGTATTGGGCTAAAAT
*
10624822 ATCCATATGTTTAGGAAAAATTAATAGTAATGTAAAATATTGATTTAAATCATAGGATCAAACCA
131 ATCCACATGTTTAGGAAAAATTAATAGTAATGTAAAATATTGATTTAAATCATAGGATCAAACCA
* * *
10624887 GAACAATATAGATATCTATGTATAAAAATCTAAAAAACAGAAATTTGAAATAAGAACTAGATCGA
196 AAACAATATAGATA--TAT-TAT-AAAATCTAAAAAACAGAAATTAGAAATAAAAACTAGATCGA
* *
10624952 AATTGTATAC-TAGTAGGTAGGAAAAAATCCGACTGGTAGTTGAGGCCTGTTTTCACAGTTTCAT
257 AATTATATACTTA-TAGGTAGGAAAAAATCCGACTGGTAGTTGAGGCCTATTTTCACAGTTTCAT
* * * *
10625016 TAAGACAAATTCGGCCGCTCCTTTGGTGCTGGAGAAATATTGGGCAACTGTCTCTCAGGATACAA
321 TAAGACAAATTCGACCGCTCCTTTGGTGCTAGAGAAATATTGAGCAACTGTCTCCCAGGATACAA
* * *
10625081 CAACGAGATGAGTACAGCAATAGCACGGCTGCAGTGATCAACGAGCTATAGCCTAGCTTTCTTCT
386 CAACGAGATGAGCACAGCAATAGCACAGCTGCAGTGATCAACGAACTATAGCCTAGCTTTCTTCT
* * *
10625146 ATCACTGAAA-ACATGTTCGAAATATGTAGAGAAAAGATCTCAAAATTTTTGCAAAA
451 ATAACTGAAATA-AAGTTCGAAATATGTACAGAAAAGATCTCAAAATTTTTGCAAAA
*
10625202 AAAATTGAGAAAAATTCAGTTTTCTTTTTCCTACAGATTATTCTTTTTCCTTTTAATTTCAAAAA
1 AAAATTGAGAAAAATTCAGTTTTCTTTTTCCTACAGATTATTCTTTTTCCTTTTAATTCCAAAAA
* * ***
10625267 TTAAAACAGAATTTAAAGAGATAAACTCTACCAAGGAAAAATAAAATTATGTATTAACCTAAAAT
66 TTAAAACAGAATTTGAAGAGATAAACTCTGCCAAGGAAAAATAAAATTATGTATTGGGCTAAAAT
* * *
10625332 ATCTACA-GATCTTA-AAAAAATTAATAGTAATAG-AAAATATTTATTTAAATCATAGGAT-AGA
131 ATCCACATG-T-TTAGGAAAAATTAATAGTAAT-GTAAAATATTGATTTAAATCATAGGATCA-A
*
10625393 ACCAAAACAATATAGATATATATATAAAATCTGAAAAACAGAAATTAGAAATAAA
192 ACCAAAACAATATAGATATAT-TATAAAATCTAAAAAACAGAAATTAGAAATAAA
10625448 CCTATATTGT
Statistics
Matches: 649, Mismatches: 90, Indels: 28
0.85 0.12 0.04
Matches are distributed among these distances:
500 52 0.08
501 132 0.20
503 2 0.00
504 2 0.00
506 2 0.00
507 27 0.04
508 6 0.01
509 11 0.02
510 411 0.63
511 4 0.01
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (506 bp):
AAAATTGAGAAAAATTCAGTTTTCTTTTTCCTACAGATTATTCTTTTTCCTTTTAATTCCAAAAA
TTAAAACAGAATTTGAAGAGATAAACTCTGCCAAGGAAAAATAAAATTATGTATTGGGCTAAAAT
ATCCACATGTTTAGGAAAAATTAATAGTAATGTAAAATATTGATTTAAATCATAGGATCAAACCA
AAACAATATAGATATATTATAAAATCTAAAAAACAGAAATTAGAAATAAAAACTAGATCGAAATT
ATATACTTATAGGTAGGAAAAAATCCGACTGGTAGTTGAGGCCTATTTTCACAGTTTCATTAAGA
CAAATTCGACCGCTCCTTTGGTGCTAGAGAAATATTGAGCAACTGTCTCCCAGGATACAACAACG
AGATGAGCACAGCAATAGCACAGCTGCAGTGATCAACGAACTATAGCCTAGCTTTCTTCTATAAC
TGAAATAAAGTTCGAAATATGTACAGAAAAGATCTCAAAATTTTTGCAAAA
Found at i:10625797 original size:27 final size:27
Alignment explanation
Indices: 10625759--10625823 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
10625749 TCTGTCAGGT
10625759 AGGCGCCAATGAATGTGCCTCATAGAG
1 AGGCGCCAATGAATGTGCCTCATAGAG
*
10625786 AGGCGCCAATGAATGTGCCTCATAGGG
1 AGGCGCCAATGAATGTGCCTCATAGAG
10625813 AGGCGCCAATG
1 AGGCGCCAATG
10625824 GTGGCCTTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.28, C:0.23, G:0.32, T:0.17
Consensus pattern (27 bp):
AGGCGCCAATGAATGTGCCTCATAGAG
Found at i:10626131 original size:21 final size:21
Alignment explanation
Indices: 10626106--10626296 Score: 110
Period size: 21 Copynumber: 9.1 Consensus size: 21
10626096 TGGATTAGTA
*
10626106 TTTTGTATGAATATTCTAATT
1 TTTTGTATGAATATTGTAATT
10626127 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
*
10626146 TTTTGTATGAATCTTGTAATT
1 TTTTGTATGAATATTGTAATT
* * * * *
10626167 ATTTATTTAT-AGTTTTGGATTAGTA
1 -TTT-TGTATGAATATT-G--TAATT
10626192 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
* * *
10626213 ATTTTATAATTAATTTTGT-ATT
1 -TTTTGT-ATGAATATTGTAATT
* * * * *
10626235 TATAGTTTTGGAT-TAGT-A--
1 TTTTG-TATGAATATTGTAATT
*
10626253 TTTTGTATGAATATTGTATTT
1 TTTTGTATGAATATTGTAATT
10626274 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
10626295 TT
1 TT
10626297 GTAATTTTGT
Statistics
Matches: 126, Mismatches: 29, Indels: 30
0.68 0.16 0.16
Matches are distributed among these distances:
17 5 0.04
18 6 0.05
19 18 0.14
20 4 0.03
21 48 0.38
22 16 0.13
23 19 0.15
24 7 0.06
25 3 0.02
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.58
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:10626151 original size:19 final size:19
Alignment explanation
Indices: 10626105--10626166 Score: 88
Period size: 19 Copynumber: 3.2 Consensus size: 19
10626095 TTGGATTAGT
*
10626105 ATTTTGTATGAATATTCTA
1 ATTTTGTATGAATATTGTA
10626124 ATTTTTTGTATGAATATTGTA
1 A--TTTTGTATGAATATTGTA
*
10626145 ATTTTGTATGAATCTTGTA
1 ATTTTGTATGAATATTGTA
10626164 ATT
1 ATT
10626167 ATTTATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 21 0.54
21 18 0.46
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.55
Consensus pattern (19 bp):
ATTTTGTATGAATATTGTA
Found at i:10626253 original size:61 final size:63
Alignment explanation
Indices: 10626127--10626294 Score: 218
Period size: 61 Copynumber: 2.6 Consensus size: 63
10626117 TATTCTAATT
10626127 TTTTGTATGAATATTGTAATTTTGTATGAATCTTGTAATTATTTATTTATAGTTTTGGATTAGTA
1 TTTTGTATGAATATTGTAATTTTGTATGAA--TTGTAATTATTTATTTATAGTTTTGGATTAGTA
*
10626192 TTTTGTATGAATATTGTAATTATTTTAT-AA-T-TAATT-TTGTATTTATAGTTTTGGATTAGTA
1 TTTTGTATGAATATTGTAATT-TTGTATGAATTGTAATTATT-TATTTATAGTTTTGGATTAGTA
*
10626253 TTTTGTATGAATATTGTATTTTTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTA--ATTTTGTATG-A-ATTGTAATT
10626295 TTGTAATTTT
Statistics
Matches: 91, Mismatches: 3, Indels: 16
0.83 0.03 0.15
Matches are distributed among these distances:
60 2 0.02
61 45 0.49
62 6 0.07
63 2 0.02
64 1 0.01
65 24 0.26
66 6 0.07
67 5 0.05
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.57
Consensus pattern (63 bp):
TTTTGTATGAATATTGTAATTTTGTATGAATTGTAATTATTTATTTATAGTTTTGGATTAGTA
Found at i:10626287 original size:147 final size:137
Alignment explanation
Indices: 10626087--10626366 Score: 389
Period size: 147 Copynumber: 2.0 Consensus size: 137
10626077 ATTTATAGTG
10626087 TTTATAGTTTGGATTAGTATTTTGTATGAATATTCTAATTTTTTGTATGAATATTGTAATTTTGT
1 TTTATAGTTTGGATTAGTATTTTGTATGAATATTCTAATTTTTTGTATGAATATTGTAATTTTG-
* * * * *
10626152 ATGAATCTTGTAATTATTTATTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTAATTATTT
65 -T-AATCTTGT-ATGA-ATATTT-TAATATT-G--TAATATTTTGTATGAATATTGTAATTATTT
10626217 TATAATTAATTTTGTA
122 TATAATTAATTTTGTA
* *
10626233 TTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTATTTTTTTGTATGAATATTGTAATTTTG
1 TTTATAG-TTTGGATTAGTATTTTGTATGAATATTCTAATTTTTTGTATGAATATTGTAATTTTG
* *
10626298 TAATTTTGTATGAATATTTTAATATTGTAATTTTTTGTATGAATATTGTAATTATTTTATAATTA
65 TAATCTTGTATGAATATTTTAATATTGTAATATTTTGTATGAATATTGTAATTATTTTATAATTA
10626363 ATTT
130 ATTT
10626367 GTTAGTAATT
Statistics
Matches: 124, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
138 40 0.32
140 1 0.01
141 5 0.04
142 5 0.04
143 3 0.02
144 7 0.06
145 1 0.01
146 7 0.06
147 55 0.44
ACGTcount: A:0.29, C:0.01, G:0.13, T:0.57
Consensus pattern (137 bp):
TTTATAGTTTGGATTAGTATTTTGTATGAATATTCTAATTTTTTGTATGAATATTGTAATTTTGT
AATCTTGTATGAATATTTTAATATTGTAATATTTTGTATGAATATTGTAATTATTTTATAATTAA
TTTTGTA
Found at i:10626299 original size:29 final size:28
Alignment explanation
Indices: 10626266--10626350 Score: 118
Period size: 29 Copynumber: 3.0 Consensus size: 28
10626256 TGTATGAATA
10626266 TTGTATTTTTTTGTATGAATATTGTAATT
1 TTGTA-TTTTTTGTATGAATATTGTAATT
* * *
10626295 TTGTA-ATTTTGTATGAATATTTTAATA
1 TTGTATTTTTTGTATGAATATTGTAATT
10626322 TTGTAATTTTTTGTATGAATATTGTAATT
1 TTGT-ATTTTTTGTATGAATATTGTAATT
10626351 ATTTTATAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.48
28 1 0.02
29 24 0.50
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (28 bp):
TTGTATTTTTTGTATGAATATTGTAATT
Found at i:10626305 original size:61 final size:61
Alignment explanation
Indices: 10626127--10626350 Score: 207
Period size: 61 Copynumber: 3.7 Consensus size: 61
10626117 TATTCTAATT
*
10626127 TTTTGTATGAATATTGTA--ATTTTGTATGAATCTTGTAATTATTTATTTATAGTTTTGGATTAG
1 TTTTGTATGAATATTGTATTATTTTGTATGAATATTGTAA-T-TTTA--TA-A-TTTTGGATTAG
10626190 TA
60 TA
* * * *
10626192 TTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGT-A-TTTATAGTTTTGGATTAGTA
1 TTTTGTATGAATATTGT-ATTATTTTGT-ATGAATATTGTAATTTTATAATTTTGGATTAGTA
* * * *
10626253 TTTTGTATGAATATTGTATTTTTTTGTATGAATATTGTAATTTTGTAATTTTGTA-T-GAA
1 TTTTGTATGAATATTGTATTATTTTGTATGAATATTGTAATTTTATAATTTTGGATTAGTA
*
10626312 TATT-T-T-AATATTGTAATT-TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGT-ATTATTTTGTATGAATATTGTAATT
10626351 ATTTTATAAT
Statistics
Matches: 139, Mismatches: 13, Indels: 23
0.79 0.07 0.13
Matches are distributed among these distances:
56 29 0.21
57 4 0.03
58 1 0.01
59 14 0.10
60 10 0.07
61 41 0.29
63 2 0.01
65 21 0.15
66 1 0.01
68 7 0.05
69 9 0.06
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (61 bp):
TTTTGTATGAATATTGTATTATTTTGTATGAATATTGTAATTTTATAATTTTGGATTAGTA
Found at i:10626309 original size:27 final size:28
Alignment explanation
Indices: 10626273--10626350 Score: 122
Period size: 27 Copynumber: 2.8 Consensus size: 28
10626263 ATATTGTATT
10626273 TTTTTGTATGAATATTGTAATTTTGTAA
1 TTTTTGTATGAATATTGTAATTTTGTAA
* *
10626301 -TTTTGTATGAATATTTTAATATTGTAA
1 TTTTTGTATGAATATTGTAATTTTGTAA
10626328 TTTTTTGTATGAATATTGTAATT
1 -TTTTTGTATGAATATTGTAATT
10626351 ATTTTATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 25 0.57
29 19 0.43
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (28 bp):
TTTTTGTATGAATATTGTAATTTTGTAA
Found at i:10627794 original size:31 final size:32
Alignment explanation
Indices: 10627735--10627799 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
10627725 GGCAAATTAC
10627735 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
10627767 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
10627798 AA
1 AA
10627800 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:10631307 original size:27 final size:27
Alignment explanation
Indices: 10631277--10631331 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
10631267 CTCAACATGA
* *
10631277 CACCACTAATGGCGCCTCTCAGATAGG
1 CACCACCAATGGCGACTCTCAGATAGG
* *
10631304 CACCACCATTGGCGACTCTGAGATAGG
1 CACCACCAATGGCGACTCTCAGATAGG
10631331 C
1 C
10631332 GTCACTACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.33, G:0.24, T:0.18
Consensus pattern (27 bp):
CACCACCAATGGCGACTCTCAGATAGG
Found at i:10632066 original size:3 final size:3
Alignment explanation
Indices: 10632058--10632099 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
10632048 ACTTCAAAGC
10632058 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
10632100 ACGGTGGACC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:10636068 original size:5 final size:5
Alignment explanation
Indices: 10636058--10636090 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
10636048 CTTAGACTTC
10636058 TCTTT TCTTT TCTTT T-TTT TCTTTT TCTTT TCT
1 TCTTT TCTTT TCTTT TCTTT TC-TTT TCTTT TCT
10636091 AACTCAGGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 17 0.65
6 5 0.19
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TCTTT
Found at i:10639289 original size:45 final size:46
Alignment explanation
Indices: 10639220--10639306 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 46
10639210 GCAAAAAAAA
*
10639220 AAAAACTAAATTATAATAAAAAA-TTATTTATAAATCATAAACACT
1 AAAAACTAAATTATAATAAAAAATTTATTTATAAATAATAAACACT
* *
10639265 AAAAACTAATTTATAATAATAAATTTATTTATAAATAATAAA
1 AAAAACTAAATTATAATAAAAAATTTATTTATAAATAATAAA
10639307 TTCCAAACTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
45 21 0.55
46 17 0.45
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (46 bp):
AAAAACTAAATTATAATAAAAAATTTATTTATAAATAATAAACACT
Found at i:10639296 original size:18 final size:19
Alignment explanation
Indices: 10639273--10639308 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
10639263 CTAAAAACTA
10639273 ATTTAT-AATAATAAATTT
1 ATTTATAAATAATAAATTT
10639291 ATTTATAAATAATAAATT
1 ATTTATAAATAATAAATT
10639309 CCAAACTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTATAAATAATAAATTT
Found at i:10639296 original size:46 final size:45
Alignment explanation
Indices: 10639220--10639306 Score: 138
Period size: 46 Copynumber: 1.9 Consensus size: 45
10639210 GCAAAAAAAA
*
10639220 AAAAACTAAATTATAATAAAAAATTATTTATAAATCATAAACACT
1 AAAAACTAAATTATAATAAAAAATTATTTATAAATAATAAACACT
* *
10639265 AAAAACTAATTTATAATAATAAATTTATTTATAAATAATAAA
1 AAAAACTAAATTATAATAA-AAAATTATTTATAAATAATAAA
10639307 TTCCAAACTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
45 18 0.47
46 20 0.53
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (45 bp):
AAAAACTAAATTATAATAAAAAATTATTTATAAATAATAAACACT
Found at i:10640196 original size:9 final size:9
Alignment explanation
Indices: 10640182--10640219 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
10640172 TTGAATTGAT
10640182 TTTTTATAA
1 TTTTTATAA
10640191 TTTTTATAA
1 TTTTTATAA
*
10640200 ATTTTA-AA
1 TTTTTATAA
10640208 TTTTTATAA
1 TTTTTATAA
10640217 TTT
1 TTT
10640220 ACTTATTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTTATAA
Found at i:10640211 original size:17 final size:18
Alignment explanation
Indices: 10640183--10640216 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
10640173 TGAATTGATT
10640183 TTTTATAATTTTTATAAA
1 TTTTATAATTTTTATAAA
10640201 TTTTA-AATTTTTATAA
1 TTTTATAATTTTTATAA
10640217 TTTACTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATAATTTTTATAAA
Found at i:10640396 original size:9 final size:9
Alignment explanation
Indices: 10640384--10640450 Score: 75
Period size: 9 Copynumber: 7.4 Consensus size: 9
10640374 AAATTTTAGA
10640384 ATTTTTTAT
1 ATTTTTTAT
10640393 ATTTTTTAT
1 ATTTTTTAT
*
10640402 ATTTTTTAA
1 ATTTTTTAT
10640411 ATTTTTT-T
1 ATTTTTTAT
10640419 ATTCTTTT-T
1 ATT-TTTTAT
*
10640428 ATTTTTCAT
1 ATTTTTTAT
*
10640437 AACTTTTTAT
1 -ATTTTTTAT
10640447 ATTT
1 ATTT
10640451 AAAAATTATA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
8 6 0.12
9 36 0.73
10 7 0.14
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:10640417 original size:28 final size:27
Alignment explanation
Indices: 10640377--10640450 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
10640367 TAATATTAAA
10640377 TTTTAGAATTTTTTATATTTTTTATATT
1 TTTTAGAATTTTTTATATTTTTT-TATT
10640405 TTTTA-AATTTTTT-TATTCTTTTTATT
1 TTTTAGAATTTTTTATATT-TTTTTATT
* * *
10640431 TTTCATAACTTTTTATATTT
1 TTTTAGAATTTTTTATATTT
10640451 AAAAATTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 12 0.29
27 20 0.49
28 9 0.22
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (27 bp):
TTTTAGAATTTTTTATATTTTTTTATT
Found at i:10641731 original size:20 final size:20
Alignment explanation
Indices: 10641697--10641738 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
10641687 AACTATTTAA
** *
10641697 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
10641717 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
10641737 AT
1 AT
10641739 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:10643814 original size:15 final size:16
Alignment explanation
Indices: 10643789--10643822 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
10643779 AATATGAAGC
10643789 GTTTGATAAATTTAAA
1 GTTTGATAAATTTAAA
*
10643805 GTTT-ATAAATTTGAA
1 GTTTGATAAATTTAAA
10643820 GTT
1 GTT
10643823 GAAATTCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (16 bp):
GTTTGATAAATTTAAA
Found at i:10649808 original size:21 final size:21
Alignment explanation
Indices: 10649784--10649839 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
10649774 CGGAACAATT
*
10649784 AAGAAAAAGA-GAAATACAAAA
1 AAGAAAAAGATCAAAT-CAAAA
*
10649805 AAG-AATAGATCAAATCAAAA
1 AAGAAAAAGATCAAATCAAAA
*
10649825 AAGAAATAGAATCAA
1 AAGAAAAAG-ATCAA
10649840 CAATTTGTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 13 0.43
21 12 0.40
22 5 0.17
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.11
Consensus pattern (21 bp):
AAGAAAAAGATCAAATCAAAA
Found at i:10649825 original size:20 final size:23
Alignment explanation
Indices: 10649795--10649839 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
10649785 AGAAAAAGAG
10649795 AAATACAAAAAAG-AATAG-ATC
1 AAATACAAAAAAGAAATAGAATC
10649816 AAAT-CAAAAAAGAAATAGAATC
1 AAATACAAAAAAGAAATAGAATC
10649838 AA
1 AA
10649840 CAATTTGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (23 bp):
AAATACAAAAAAGAAATAGAATC
Found at i:10652702 original size:34 final size:35
Alignment explanation
Indices: 10652654--10652739 Score: 120
Period size: 34 Copynumber: 2.5 Consensus size: 35
10652644 AATGATACCA
10652654 AAAATGATGAGTGAACAGGAGAGATTCCCTGCAA-
1 AAAATGATGAGTGAACAGGAGAGATTCCCTGCAAC
* * *
10652688 GAAATGATGTGTGAACATGAGAGATTCCCTGCAAC
1 AAAATGATGAGTGAACAGGAGAGATTCCCTGCAAC
* *
10652723 AAAATAATGCGTGAACA
1 AAAATGATGAGTGAACA
10652740 TGAAATATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
34 31 0.69
35 14 0.31
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (35 bp):
AAAATGATGAGTGAACAGGAGAGATTCCCTGCAAC
Found at i:10653758 original size:20 final size:20
Alignment explanation
Indices: 10653724--10653765 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
10653714 AACTATTTAA
** *
10653724 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
10653744 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
10653764 AT
1 AT
10653766 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:10655382 original size:32 final size:32
Alignment explanation
Indices: 10655337--10655410 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
10655327 GTAGTCCATC
* *
10655337 ATTAATCACTATAACCATGTGTCTAAACCCAA
1 ATTAATCATTATAACCATGAGTCTAAACCCAA
*
10655369 ATTAATCATTATAACCATGAGTCTAAACCCTA
1 ATTAATCATTATAACCATGAGTCTAAACCCAA
*
10655401 GTTAATCATT
1 ATTAATCATT
10655411 GCAAGGTGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (32 bp):
ATTAATCATTATAACCATGAGTCTAAACCCAA
Found at i:10658771 original size:12 final size:11
Alignment explanation
Indices: 10658750--10658782 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
10658740 AAGTTATAAT
10658750 AAAAATAAAAG
1 AAAAATAAAAG
10658761 AAAATATAAAAG
1 AAAA-ATAAAAG
10658773 AAAAA-AAAAG
1 AAAAATAAAAG
10658783 TATGAAAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.24
11 5 0.24
12 11 0.52
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (11 bp):
AAAAATAAAAG
Found at i:10659468 original size:35 final size:35
Alignment explanation
Indices: 10659415--10659600 Score: 122
Period size: 35 Copynumber: 5.3 Consensus size: 35
10659405 TCACACATAT
* *
10659415 TTGTCGGTTTTAAC-GACCAGCGCAAGGCTCATTTA
1 TTGTCGGTTAT-ACTGACCAGCGCAAGGCACATTTA
* * *
10659450 TTGTCGGTTATACTGACCAGTGCTAGGCACATATA
1 TTGTCGGTTATACTGACCAGCGCAAGGCACATTTA
* * * * * * **
10659485 TTTGTTGATTTTATTGACTAGCGCAGGGTGCATTTA
1 -TTGTCGGTTATACTGACCAGCGCAAGGCACATTTA
* * ** **
10659521 TTGTCGGTTATACCGACCAGTGCTGGGCACACATA
1 TTGTCGGTTATACTGACCAGCGCAAGGCACATTTA
* * * *
10659556 TTTTTCGGTTCTACTAACCAGCGCAGGGCACATTTA
1 -TTGTCGGTTATACTGACCAGCGCAAGGCACATTTA
*
10659592 TTGCCGGTT
1 TTGTCGGTT
10659601 TTATCGGCCA
Statistics
Matches: 110, Mismatches: 38, Indels: 6
0.71 0.25 0.04
Matches are distributed among these distances:
34 2 0.02
35 57 0.52
36 51 0.46
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.34
Consensus pattern (35 bp):
TTGTCGGTTATACTGACCAGCGCAAGGCACATTTA
Found at i:10659579 original size:71 final size:70
Alignment explanation
Indices: 10659406--10659600 Score: 223
Period size: 71 Copynumber: 2.7 Consensus size: 70
10659396 GAAATGATTT
* * *
10659406 CACACATATTTGTCGGTTTTAAC-GACCAGCGCAAGGCTCATTTATTGTCGGTTATACTGACCAG
1 CACACATATTTTTCGGTTTT-ACTGACCAGCGC-AGGGTCATTTATTGTCGGTTATACCGACCAG
10659470 TGCTAGG
64 TGCTAGG
* * * *
10659477 CACATATATTTGTT-GATTTTATTGACTAGCGCAGGGTGCATTTATTGTCGGTTATACCGACCAG
1 CACACATATTT-TTCGGTTTTACTGACCAGCGCAGGGT-CATTTATTGTCGGTTATACCGACCAG
*
10659541 TGCTGGG
64 TGCTAGG
* * * *
10659548 CACACATATTTTTCGGTTCTACTAACCAGCGCAGGGCACATTTATTGCCGGTT
1 CACACATATTTTTCGGTTTTACTGACCAGCGCAGGG-TCATTTATTGTCGGTT
10659601 TTATCGGCCA
Statistics
Matches: 103, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
70 7 0.07
71 95 0.92
72 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (70 bp):
CACACATATTTTTCGGTTTTACTGACCAGCGCAGGGTCATTTATTGTCGGTTATACCGACCAGTG
CTAGG
Found at i:10672232 original size:96 final size:96
Alignment explanation
Indices: 10671940--10672258 Score: 464
Period size: 97 Copynumber: 3.3 Consensus size: 96
10671930 AACAACTAGT
* * *
10671940 TTTATTTGA-TTTTTCCTTAAAAACCCTAAATACTAAACCCCAATCTAATTTTTTTAAAATTTAT
1 TTTATTTAATTTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAA-TTTTTTAAAATTTAT
*
10672004 AATTAATTTACTCAAGTAACTCC-AAGCCCTAA
65 AATTAATTTACTCAAGTAAC-CCTAAACCCTAA
* ** *
10672036 TTTATTTGATTTTTTTTTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTAAAAAATTTAT
1 TTTATTTAATTTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTT-TAAAATTTAT
*
10672101 AATTAATATACTCAAGTAACCCTAAACCCTAA
65 AATTAATTTACTCAAGTAACCCTAAACCCTAA
*
10672133 TTTATTTAATTTTTTCCTTAAAAACCTTAAACACTAAACCCTAATCTAATTTTTTAAAATTTATA
1 TTTATTTAATTTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTAAAATTTATA
* * * *
10672198 ATTAATTTAATTAAGGAACCCTAAACCCTTA
66 ATTAATTTACTCAAGTAACCCTAAACCCTAA
10672229 TTTATTTAATTTTTTCCTT-AAAACCCTAAA
1 TTTATTTAATTTTTTCCTTAAAAACCCTAAA
10672259 ATCTAAAAAT
Statistics
Matches: 202, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
95 10 0.05
96 71 0.35
97 121 0.60
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.41
Consensus pattern (96 bp):
TTTATTTAATTTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTAAAATTTATA
ATTAATTTACTCAAGTAACCCTAAACCCTAA
Found at i:10684318 original size:17 final size:17
Alignment explanation
Indices: 10684297--10684339 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
10684287 ATCGATGAAA
10684297 TTTTAAAATTTACAATTC
1 TTTTAAAATTTA-AATTC
* *
10684315 -TTTAAATTTTAATTTC
1 TTTTAAAATTTAAATTC
10684331 TTTTAAAAT
1 TTTTAAAAT
10684340 ATAGTTGTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAAAATTTAAATTC
Found at i:10689334 original size:23 final size:22
Alignment explanation
Indices: 10689291--10689334 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
10689281 TTCTAAGTTG
10689291 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
10689314 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
10689335 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:10689532 original size:51 final size:51
Alignment explanation
Indices: 10689474--10689662 Score: 213
Period size: 51 Copynumber: 3.7 Consensus size: 51
10689464 ATGTTTGGTT
* *
10689474 CACATAGTAGCCTGCACATAGTACTACACATTTGA-CTATTACCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCCA-TACCATCCGATA
* * * * * *
10689525 CACATAGTAGCTTGCACATAGTACTACACACGTGATCGAAACTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCCATACCATCCGATA
* * * *
10689576 CGCGTAGTAGCCTGCACATAGTACTACACATGCGACCCAT--CATTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCCATACCA-TCCGATA
* *
10689626 CACGTAGTAGCCTGCACATAGTACTACACACGTGACC
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACC
10689663 ATTACTATCA
Statistics
Matches: 117, Mismatches: 19, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
49 1 0.01
50 40 0.34
51 74 0.63
52 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.23
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGACCCATACCATCCGATA
Found at i:10689654 original size:101 final size:101
Alignment explanation
Indices: 10689478--10689660 Score: 271
Period size: 101 Copynumber: 1.8 Consensus size: 101
10689468 TTGGTTCACA
** * *
10689478 TAGTAGCCTGCACATAGTACTACACATTTGACTATTACCATCCGATACACATAGTAGCTTGCACA
1 TAGTAGCCTGCACATAGTACTACACATGCGACCATTA-CATCCGATACACATAGTAGCCTGCACA
10689543 TAGTACTACACACGTGATCGAAACTATCCGATACGCG
65 TAGTACTACACACGTGATCGAAACTATCCGATACGCG
* *
10689580 TAGTAGCCTGCACATAGTACTACACATGCGACCCA-T-CATTCCGGTACACGTAGTAGCCTGCAC
1 TAGTAGCCTGCACATAGTACTACACATGCGA-CCATTACA-TCCGATACACATAGTAGCCTGCAC
10689643 ATAGTACTACACACGTGA
64 ATAGTACTACACACGTGA
10689661 CCATTACTAT
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
100 2 0.03
101 39 0.53
102 30 0.41
103 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (101 bp):
TAGTAGCCTGCACATAGTACTACACATGCGACCATTACATCCGATACACATAGTAGCCTGCACAT
AGTACTACACACGTGATCGAAACTATCCGATACGCG
Found at i:10689692 original size:101 final size:101
Alignment explanation
Indices: 10689472--10689694 Score: 247
Period size: 101 Copynumber: 2.2 Consensus size: 101
10689462 TAATGTTTGG
** * *
10689472 TTCACATAGTAGCCTGCACATAGTACTACACATTTGACTATTACCATCCGATACACATAGTAGCT
1 TTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATTA-CATCCGATACACATAGTAGCC
*
10689537 TGCACATAGTACTACACACGTGATCGAAACTATCCGA
65 TGCACATAGTACTACACACGTGATCCAAACTATCCGA
* * * * *
10689574 TACGCGTAGTAGCCTGCACATAGTACTACACATGCGACCCA-T-CATTCCGGTACACGTAGTAGC
1 TTCACATAGTAGCCTGCACATAGTACTACACATGCGA-CCATTACA-TCCGATACACATAGTAGC
* *
10689637 CTGCACATAGTACTACACACGTGA-CCATTACTATCAC-T
64 CTGCACATAGTACTACACACGTGATCCA-AACTATC-CGA
* *
10689675 TTCACATAGTGGACTGCACA
1 TTCACATAGTAGCCTGCACA
10689695 CAATCCGTGC
Statistics
Matches: 100, Mismatches: 17, Indels: 9
0.79 0.13 0.07
Matches are distributed among these distances:
100 4 0.04
101 60 0.60
102 34 0.34
103 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (101 bp):
TTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATTACATCCGATACACATAGTAGCCT
GCACATAGTACTACACACGTGATCCAAACTATCCGA
Found at i:10691373 original size:30 final size:31
Alignment explanation
Indices: 10691315--10691373 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
10691305 TTGTCTTTAC
*
10691315 TTTTCTTTCATCTTTTTAGCTTTCTAGTTAG
1 TTTTCTTTCATCTTTTTAGCGTTCTAGTTAG
*
10691346 TTTTC-TTCATCTTTTCTAGGGTT-TAGTT
1 TTTTCTTTCATCTTTT-TAGCGTTCTAGTT
10691374 TAGAACTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.12, C:0.15, G:0.12, T:0.61
Consensus pattern (31 bp):
TTTTCTTTCATCTTTTTAGCGTTCTAGTTAG
Found at i:10697193 original size:2 final size:2
Alignment explanation
Indices: 10697186--10697221 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10697176 GTCATGCTTC
10697186 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10697222 GGTGGATTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10699190 original size:19 final size:20
Alignment explanation
Indices: 10699153--10699190 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10699143 AATGAGTCAT
*
10699153 TTAAGAAAGAAATTAATTTC
1 TTAAAAAAGAAATTAATTTC
10699173 TTAAAAAAGAAA-TAATTT
1 TTAAAAAAGAAATTAATTT
10699191 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (20 bp):
TTAAAAAAGAAATTAATTTC
Found at i:10700647 original size:41 final size:39
Alignment explanation
Indices: 10700530--10700651 Score: 124
Period size: 37 Copynumber: 3.1 Consensus size: 39
10700520 TTTGGTACCT
* * *
10700530 AGTGCCTCATCGGATAATTCGAAGTAATAAATTGACACCC
1 AGTGCCTCAT-TGATAATCCGAAGTAGTAAATTGACACCC
* * * *
10700570 AGTGTCTCATTGGCTAAACCG-A--AGTAAATTGGCACCC
1 AGTGCCTCATT-GATAATCCGAAGTAGTAAATTGACACCC
10700607 AGTGCCTCATTGAATTAATCCGAAGTAGTAAATTGACACCC
1 AGTGCCTCATTG-A-TAATCCGAAGTAGTAAATTGACACCC
10700648 AGTG
1 AGTG
10700652 TCTCGTCGAC
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
36 1 0.02
37 23 0.35
38 6 0.09
39 2 0.03
40 15 0.23
41 18 0.28
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (39 bp):
AGTGCCTCATTGATAATCCGAAGTAGTAAATTGACACCC
Found at i:10701651 original size:2 final size:2
Alignment explanation
Indices: 10701644--10701688 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
10701634 TTATTATTAT
10701644 TA TA TA TA -A TA TA TA -A TA TA TA -A TA TA TA -A TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10701681 TA TA TA TA
1 TA TA TA TA
10701689 CTTATAGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
1 5 0.13
2 33 0.87
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:10701657 original size:7 final size:7
Alignment explanation
Indices: 10701645--10701686 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
10701635 TATTATTATT
10701645 ATATATA
1 ATATATA
10701652 ATATATA
1 ATATATA
10701659 ATATATA
1 ATATATA
10701666 ATATATA
1 ATATATA
10701673 ATATATA
1 ATATATA
10701680 ATATATA
1 ATATATA
10701687 TACTTATAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATATATA
Found at i:10704845 original size:7 final size:7
Alignment explanation
Indices: 10704833--10704878 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
10704823 GGCTTAAGGT
10704833 TTAGGGG
1 TTAGGGG
10704840 TTAGGGG
1 TTAGGGG
**
10704847 TTAGACG
1 TTAGGGG
10704854 TTAGGGG
1 TTAGGGG
10704861 TTAGGGG
1 TTAGGGG
10704868 TTTAGGGG
1 -TTAGGGG
10704876 TTA
1 TTA
10704879 TGCTTTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
7 27 0.79
8 7 0.21
ACGTcount: A:0.17, C:0.02, G:0.48, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:10704894 original size:21 final size:21
Alignment explanation
Indices: 10704868--10704913 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
10704858 GGGTTAGGGG
*
10704868 TTTAGGGGTTATGCTTTATGA
1 TTTAGGGGTTAGGCTTTATGA
* * *
10704889 TTTAGGGTTTAGGGTTTATGT
1 TTTAGGGGTTAGGCTTTATGA
10704910 TTTA
1 TTTA
10704914 TAATTTAGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.17, C:0.02, G:0.28, T:0.52
Consensus pattern (21 bp):
TTTAGGGGTTAGGCTTTATGA
Found at i:10704896 original size:28 final size:28
Alignment explanation
Indices: 10704865--10704928 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
10704855 TAGGGGTTAG
*
10704865 GGGTTTAGGGGTTATGCTTTATGATTTA
1 GGGTTTAGGGGTTATGCTTTATAATTTA
* *
10704893 GGGTTTAGGGTTTATGTTTTATAATTTA
1 GGGTTTAGGGGTTATGCTTTATAATTTA
10704921 GGGTTTAG
1 GGGTTTAG
10704929 ATTAATTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.48
Consensus pattern (28 bp):
GGGTTTAGGGGTTATGCTTTATAATTTA
Found at i:10708703 original size:43 final size:44
Alignment explanation
Indices: 10708642--10708729 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 44
10708632 GAGTTCGTTA
* * *
10708642 CAAGATTTCCTTGATTAAGTAAATGTATTATA-TCTTTTATTAC
1 CAAGATTTACTTGATTAAGAAAATGCATTATATTCTTTTATTAC
* *
10708685 CAAGATTTACTTGATTAAGAAAATGCATTGTATTTTTTTATTAC
1 CAAGATTTACTTGATTAAGAAAATGCATTATATTCTTTTATTAC
10708729 C
1 C
10708730 TTGCAATGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 28 0.72
44 11 0.28
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.45
Consensus pattern (44 bp):
CAAGATTTACTTGATTAAGAAAATGCATTATATTCTTTTATTAC
Found at i:10709176 original size:43 final size:43
Alignment explanation
Indices: 10709098--10709304 Score: 238
Period size: 43 Copynumber: 4.8 Consensus size: 43
10709088 TTTTTGCGAG
* * * * *
10709098 AAGCGTCGCTAAAGGT-TTGTTCTATAGCAGAGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTATTGATCTATAGCGGCGTTTGTGGAAA
* * *
10709140 AAGCACCGCTAAAGGTATTGAGCTATAGCGGCGTTTGTGAAAA
1 AAGCGCCGCTAAAGGTATTGATCTATAGCGGCGTTTGTGGAAA
*
10709183 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
1 AAGCGCCGCTAAAGGTATTGATCTATAGCGGCGTTTGTGGAAA
** * * * * *
10709226 AAATGCCGCTAAAGGTCTTGAGCTATAGCAGTGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTATTGATCTATAGCGGCGTTTGTGGAAA
*
10709269 AAGCGTCGCTAAAGGTCA-TGATCTATAGCGGCGTTT
1 AAGCGCCGCTAAAGGT-ATTGATCTATAGCGGCGTTT
10709305 ATTTCTAAAA
Statistics
Matches: 138, Mismatches: 25, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
42 14 0.10
43 124 0.90
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTATTGATCTATAGCGGCGTTTGTGGAAA
Found at i:10709247 original size:86 final size:86
Alignment explanation
Indices: 10709098--10709304 Score: 281
Period size: 86 Copynumber: 2.4 Consensus size: 86
10709088 TTTTTGCGAG
* * * * *
10709098 AAGCGTCGCTAAAGGT-TTGTTCTATAGCAGAGTTTGTGGGAAAAGCACCGCTAAAGGTATTGAG
1 AAGCGTCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAACACCGCTAAAGGTATTGAG
*
10709162 CTATAGCGGCGTTTGTGAAAA
66 CTATAGCAGCGTTTGTGAAAA
* ** *
10709183 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAATGCCGCTAAAGGTCTTGAG
1 AAGCGTCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAACACCGCTAAAGGTATTGAG
* **
10709248 CTATAGCAGTGTTTGTGGGAA
66 CTATAGCAGCGTTTGTGAAAA
*
10709269 AAGCGTCGCTAAAGGTCATGATCTATAGCGGCGTTT
1 AAGCGTCGCTAAAGGTCTTGATCTATAGCGGCGTTT
10709305 ATTTCTAAAA
Statistics
Matches: 106, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
85 15 0.14
86 91 0.86
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (86 bp):
AAGCGTCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAACACCGCTAAAGGTATTGAG
CTATAGCAGCGTTTGTGAAAA
Found at i:10712308 original size:2 final size:2
Alignment explanation
Indices: 10712301--10712325 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10712291 TGTGCATGCG
10712301 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
10712326 TCTAGCAGTT
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:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:10713549 original size:30 final size:33
Alignment explanation
Indices: 10713488--10713549 Score: 76
Period size: 34 Copynumber: 1.9 Consensus size: 33
10713478 ACTATAAAAC
**
10713488 ATTTATTATTAAATATTTATAAATTGTAATATAT
1 ATTTATTATTAAATA-TTATAAATTACAATATAT
10713522 ATTTATTATTAAA-A-TA-AAATTACAATAT
1 ATTTATTATTAAATATTATAAATTACAATAT
10713550 TAAATAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 10 0.38
31 2 0.08
33 1 0.04
34 13 0.50
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (33 bp):
ATTTATTATTAAATATTATAAATTACAATATAT
Found at i:10713596 original size:39 final size:40
Alignment explanation
Indices: 10713514--10713614 Score: 97
Period size: 39 Copynumber: 2.5 Consensus size: 40
10713504 TTATAAATTG
*
10713514 TAATATATATT-TATTATTAAA-ATAAAATTACAATATTAAA
1 TAATAT-TATTATATTATTAAATATAAAATTACAACATT-AA
10713554 TAAT-TTATTATATTATTAAATATAAATAATTA-AACATT-A
1 TAATATTATTATATTATTAAATAT-AA-AATTACAACATTAA
*
10713593 TAATATT-TGATATTATTTAAAT
1 TAATATTATTATATTA-TTAAAT
10713615 TTTAGAAATT
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
38 4 0.08
39 23 0.43
40 14 0.26
41 7 0.13
42 5 0.09
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (40 bp):
TAATATTATTATATTATTAAATATAAAATTACAACATTAA
Found at i:10723199 original size:15 final size:15
Alignment explanation
Indices: 10723179--10723207 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10723169 ATATTTCCTC
10723179 TATTATAATTATAAT
1 TATTATAATTATAAT
10723194 TATTATAATTATAA
1 TATTATAATTATAA
10723208 AAAATTATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTATAATTATAAT
Found at i:10723841 original size:39 final size:39
Alignment explanation
Indices: 10723795--10723890 Score: 147
Period size: 39 Copynumber: 2.5 Consensus size: 39
10723785 GGAGTTGTAA
*
10723795 GTGACTATTCATCTACATCACTTAAGTGCTATAGGAGCT
1 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGCT
* * *
10723834 GTGACTATTTATCTTCATCACTTAAATGCTATAGGAGTT
1 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGCT
*
10723873 ATGACTATTCATCTACAT
1 GTGACTATTCATCTACAT
10723891 GCTTGTGTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (39 bp):
GTGACTATTCATCTACATCACTTAAATGCTATAGGAGCT
Found at i:10724982 original size:12 final size:12
Alignment explanation
Indices: 10724960--10724989 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
10724950 TTATAACCAT
10724960 GAATCTTCCTTGA
1 GAAT-TTCCTTGA
10724973 GAATTTCCTTGA
1 GAATTTCCTTGA
10724985 GAATT
1 GAATT
10724990 CTTTCAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (12 bp):
GAATTTCCTTGA
Found at i:10728292 original size:43 final size:42
Alignment explanation
Indices: 10728244--10728353 Score: 151
Period size: 39 Copynumber: 2.7 Consensus size: 42
10728234 TAACTCTTTA
*
10728244 TATAGGAGTTGTAAGTGACTATTCATCTACATCACTTAAGTGC
1 TATAGGAGTTGT-AGTGACTATTCATCTACATCACTTAAATGC
*
10728287 TATAGGAGTTGTA---ACTATTCATCTTCATCACTTAAATGC
1 TATAGGAGTTGTAGTGACTATTCATCTACATCACTTAAATGC
10728326 TATAGGAG-T-T-GTGACTATTCATCTACAT
1 TATAGGAGTTGTAGTGACTATTCATCTACAT
10728354 GCATGTGTGT
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
37 1 0.02
38 1 0.02
39 46 0.75
42 1 0.02
43 12 0.20
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (42 bp):
TATAGGAGTTGTAGTGACTATTCATCTACATCACTTAAATGC
Found at i:10728316 original size:39 final size:39
Alignment explanation
Indices: 10728261--10728353 Score: 159
Period size: 39 Copynumber: 2.4 Consensus size: 39
10728251 GTTGTAAGTG
*
10728261 ACTATTCATCTACATCACTTAAGTGCTATAGGAGTTGTA
1 ACTATTCATCTACATCACTTAAATGCTATAGGAGTTGTA
* *
10728300 ACTATTCATCTTCATCACTTAAATGCTATAGGAGTTGTG
1 ACTATTCATCTACATCACTTAAATGCTATAGGAGTTGTA
10728339 ACTATTCATCTACAT
1 ACTATTCATCTACAT
10728354 GCATGTGTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (39 bp):
ACTATTCATCTACATCACTTAAATGCTATAGGAGTTGTA
Found at i:10728387 original size:16 final size:16
Alignment explanation
Indices: 10728366--10728418 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
10728356 ATGTGTGTAG
10728366 CTCTTCATCTTCAAGT
1 CTCTTCATCTTCAAGT
10728382 CTCTTCA-CATTTCTAA--
1 CTCTTCATC--TTC-AAGT
10728398 CTCTTCATCTTCAAGT
1 CTCTTCATCTTCAAGT
10728414 CTCTT
1 CTCTT
10728419 TACATACCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
14 2 0.06
15 4 0.13
16 19 0.61
17 4 0.13
18 2 0.06
ACGTcount: A:0.19, C:0.32, G:0.04, T:0.45
Consensus pattern (16 bp):
CTCTTCATCTTCAAGT
Found at i:10734778 original size:37 final size:36
Alignment explanation
Indices: 10734675--10735142 Score: 436
Period size: 37 Copynumber: 12.6 Consensus size: 36
10734665 TAAGATAAGA
* * * **
10734675 TCTATCCCAAGCTTTTT-AAGTTTGGCTTAGATGGG
1 TCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAGG
*
10734710 TCTA-CCCTAACCTTTTT-TAGGTTGCCTTAGAC-GTG
1 TCTATCCC-AACCTTTTTAAAGGTTGCCTTAGACAG-G
* *
10734745 TCTATCCCAACCATTTTTAAAGATTGCCTTAGACAAG
1 TCTATCCCAACC-TTTTTAAAGGTTGCCTTAGACAGG
10734782 TCTATCCCAACCTTTTTTAAAGGTTG-CTTGAGACAAGG
1 TCTATCCCAACC-TTTTTAAAGGTTGCCTT-AGAC-AGG
* *
10734820 TCTATCCTAACC-TTTT-AAGGTTGCCTTCA-ACGGG
1 TCTATCCCAACCTTTTTAAAGGTTGCCTT-AGACAGG
* * *
10734854 TCTATCCTAACCTTTTTTATAGGATGCCTTAGACAAGG
1 TCTATCCCAACC-TTTTTAAAGGTTGCCTTAGAC-AGG
*
10734892 TCTATTCCAACCTTTTTTTAAAGGTTGCCTTAGACAAGG
1 TCTATCCCAACC--TTTTTAAAGGTTGCCTTAGAC-AGG
*
10734931 TCTATCCCAACCTTTTTAAAGGTTGCTTTAGACAAGG
1 TCTATCCCAACCTTTTTAAAGGTTGCCTTAGAC-AGG
* *
10734968 TCTATCCTAACCTTTTT-AAGGTTTCCTTAGACAAGG
1 TCTATCCCAACCTTTTTAAAGGTTGCCTTAGAC-AGG
*
10735004 TCTA-CCCAACCTTTTTTAAAGGTTGCCTTAGATAAGAAGG
1 TCTATCCCAACC-TTTTTAAAGGTTGCCTTAG---A-CAGG
* * *
10735044 TCTATCCCAACCTTTTT-AAGGTTTCCTTAGATAGC
1 TCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAGG
* *
10735079 TCTATCCTAACCGTTTTTTAAAAGGTTTCCTTAGACAAGG
1 TCTATCCCAACC--TTTTT-AAAGGTTGCCTTAGAC-AGG
10735119 TCTATCCCAACCTTTTTTAAAGGT
1 TCTATCCCAACC-TTTTTAAAGGT
10735143 CGACCTCGAC
Statistics
Matches: 370, Mismatches: 36, Indels: 51
0.81 0.08 0.11
Matches are distributed among these distances:
34 18 0.05
35 60 0.16
36 51 0.14
37 110 0.30
38 31 0.08
39 67 0.18
40 26 0.07
41 7 0.02
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (36 bp):
TCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAGG
Found at i:10734929 original size:148 final size:145
Alignment explanation
Indices: 10734688--10735134 Score: 518
Period size: 148 Copynumber: 3.0 Consensus size: 145
10734678 ATCCCAAGCT
* * *
10734688 TTTTAAGTTTGGCTTAGA-TGGGTCTACCCTAACC-TTTTT-TAGGTTGCCTTAGAC--GTGTCT
1 TTTTAAGGTTGCCTTAGACAGGGTCTA-CCTAACCTTTTTTATAGGTTGCCTTAGACAAG-GTCT
*
10734748 ATCCCAACCATTTTTAAAGATTGCCTTAGACAAGTCTATCCCAACCTTTTTTAAAGGTTGCTTGA
64 ATCCCAACC-TTTTTAAAGGTTGCCTTAGACAAGTCTATCCCAACCTTTTTTAAAGGTTGCTT-A
10734813 GACAAGGTCTATCCTAACC
127 GACAAGGTCTATCCTAACC
*
10734832 TTTTAAGGTTGCCTTCA-AC-GGGTCTATCCTAACCTTTTTTATAGGATGCCTTAGACAAGGTCT
1 TTTTAAGGTTGCCTT-AGACAGGGTCTA-CCTAACCTTTTTTATAGGTTGCCTTAGACAAGGTCT
*
10734895 ATTCCAACCTTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACC-TTTTTAAAGGTTGCTT
64 ATCCCAACC--TTTTTAAAGGTTGCCTTAGACAA-GTCTATCCCAACCTTTTTTAAAGGTTGC-T
10734959 TAGACAAGGTCTATCCTAACC
125 TAGACAAGGTCTATCCTAACC
* * * * *
10734980 TTTTTAAGGTTTCCTTAGACAAGGTCTACCCAACCTTTTTTAAAGGTTGCCTTAGATAAGAAGGT
1 -TTTTAAGGTTGCCTTAGACAGGGTCTACCTAACCTTTTTTATAGGTTGCCTTAG---ACAAGGT
* * * *
10735045 CTATCCCAACCTTTTT-AAGGTTTCCTTAGA-TAGCTCTATCCTAACCGTTTTTTAAAAGGTTTC
62 CTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAG-TCTATCCCAACC-TTTTTT-AAAGG-TTG
*
10735108 CTTAGACAAGGTCTATCCCAACC
123 CTTAGACAAGGTCTATCCTAACC
10735131 TTTT
1 TTTT
10735135 TTAAAGGTCG
Statistics
Matches: 264, Mismatches: 19, Indels: 34
0.83 0.06 0.11
Matches are distributed among these distances:
144 28 0.11
145 6 0.02
146 14 0.05
147 13 0.05
148 70 0.27
149 68 0.26
150 20 0.08
151 26 0.10
152 19 0.07
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (145 bp):
TTTTAAGGTTGCCTTAGACAGGGTCTACCTAACCTTTTTTATAGGTTGCCTTAGACAAGGTCTAT
CCCAACCTTTTTAAAGGTTGCCTTAGACAAGTCTATCCCAACCTTTTTTAAAGGTTGCTTAGACA
AGGTCTATCCTAACC
Found at i:10735138 original size:76 final size:74
Alignment explanation
Indices: 10734675--10735135 Score: 509
Period size: 72 Copynumber: 6.2 Consensus size: 74
10734665 TAAGATAAGA
* * * **
10734675 TCTATCCCAAGCTTTTTAAGTTTGGCTTAGA-TGGGTCTA-CCCTAACCTTTTTT--AGGTTGCC
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCC-AACCTTTTTTAAAGGTTGCC
10734736 TTAGAC--GTG
65 TTAGACAAG-G
*
10734745 TCTATCCCAACCATTTTTAAAGATTGCCTTAGACAA-GTCTATCCCAACCTTTTTTAAAGGTTG-
1 TCTATCCCAACC-TTTTT-AAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTTAAAGGTTGC
10734808 CTTGAGACAAGG
64 CTT-AGACAAGG
* * * * *
10734820 TCTATCCTAACC-TTTTAAGGTTGCCTTCA-AC-GGGTCTATCCTAACCTTTTTTATAGGATGCC
1 TCTATCCCAACCTTTTTAAGGTTGCCTT-AGACAAGGTCTATCCCAACCTTTTTTAAAGGTTGCC
10734882 TTAGACAAGG
65 TTAGACAAGG
*
10734892 TCTATTCCAACCTTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACC-TTTTTAAAGGTTG
1 TCTATCCCAACC--TTTTT-AAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTTAAAGGTTG
*
10734956 CTTTAGACAAGG
63 CCTTAGACAAGG
* *
10734968 TCTATCCTAACCTTTTTAAGGTTTCCTTAGACAAGGTCTA-CCCAACCTTTTTTAAAGGTTGCCT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTTAAAGGTTGCCT
*
10735032 TAGATAAGAAGG
66 TAG---ACAAGG
* * * * *
10735044 TCTATCCCAACCTTTTTAAGGTTTCCTTAGA-TAGCTCTATCCTAACCGTTTTTTAAAAGGTTTC
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACC-TTTTTT-AAAGGTTGC
10735108 CTTAGACAAGG
64 CTTAGACAAGG
10735119 TCTATCCCAACCTTTTT
1 TCTATCCCAACCTTTTT
10735136 TAAAGGTCGA
Statistics
Matches: 337, Mismatches: 29, Indels: 45
0.82 0.07 0.11
Matches are distributed among these distances:
70 11 0.03
71 5 0.01
72 88 0.26
73 54 0.16
74 15 0.04
75 45 0.13
76 87 0.26
77 19 0.06
78 13 0.04
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (74 bp):
TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTTAAAGGTTGCCT
TAGACAAGG
Found at i:10736592 original size:22 final size:22
Alignment explanation
Indices: 10736567--10736611 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
10736557 AAGTATGGAA
*
10736567 CAGTATGAATAAAGAACGTACC
1 CAGTATGAATAAAGAACGCACC
10736589 CAGTATGAATAAAGAACGCACC
1 CAGTATGAATAAAGAACGCACC
10736611 C
1 C
10736612 GCTACAACGT
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:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (22 bp):
CAGTATGAATAAAGAACGCACC
Found at i:10740986 original size:44 final size:44
Alignment explanation
Indices: 10740923--10741013 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
10740913 AACTCTATTT
* *
10740923 TTAGTTTTCCACTTAAACTCTGATTAGTGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTGATTAGTGTAGGTTACTTTAATA
10740967 TTAGTTTCCCACTTAAACTCTGATTAGTGTAGGTTACTTTAATA
1 TTAGTTTCCCACTTAAACTCTGATTAGTGTAGGTTACTTTAATA
10741011 TTA
1 TTA
10741014 TTAGACCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46
Consensus pattern (44 bp):
TTAGTTTCCCACTTAAACTCTGATTAGTGTAGGTTACTTTAATA
Found at i:10743462 original size:114 final size:115
Alignment explanation
Indices: 10743193--10743463 Score: 365
Period size: 115 Copynumber: 2.4 Consensus size: 115
10743183 ATATTGTATT
10743193 ATTTATATTTT-TTAAATGAAATAATATAGAAATATTCAAAATATTGCCTTATTTTAAAAAATTC
1 ATTT-TATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGCCTTATTTTAAAAAATTC
** * ** *
10743257 TATTTTATTAAAAATATTAAAGTAAATTACAATTACTTTATTCAAAACAAC
65 TATTTTATTAAAAATACAAAAGTAAATTACAATGAAATAATTCAAAACAAC
*
10743308 ATTTTATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGTCTTA-TTTAAAAGAATTT
1 ATTTTATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGCCTTATTTTAAAA-AA-TT
*
10743372 CTATTTTATTAAAAATACAAAAGTAAATTAC-ATGAAATAATAT-AAAA-GA-
64 CTATTTTATTAAAAATACAAAAGTAAATTACAATGAAATAAT-TCAAAACAAC
* *
10743421 ATTTCTATTTTATTACATGAAATAATATAAAAATATTCAAAAT
1 ATTT-TATTTTATTAAATGAAATAATATAGAAATATTCAAAAT
10743464 GTTTGTACAA
Statistics
Matches: 141, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
113 4 0.03
114 50 0.35
115 55 0.39
116 32 0.23
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (115 bp):
ATTTTATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGCCTTATTTTAAAAAATTCT
ATTTTATTAAAAATACAAAAGTAAATTACAATGAAATAATTCAAAACAAC
Found at i:10743900 original size:18 final size:18
Alignment explanation
Indices: 10743859--10743901 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
10743849 GACTAGAAAA
* *
10743859 AGGAAACATAAAAGAGTT
1 AGGATACATAAAAGAGCT
*
10743877 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGAGCT
*
10743895 ATGATAC
1 AGGATAC
10743902 GCACCTGGCG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.09, G:0.23, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGAGCT
Found at i:10743996 original size:30 final size:30
Alignment explanation
Indices: 10743962--10744018 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
10743952 TGTTGGGTCG
* *
10743962 GGTGACTGTGTCGGTGCTGTTGCTGGGCCT
1 GGTGACTGTGTCGGCGCTGTTGATGGGCCT
* *
10743992 GGTGATTGTGTGGGCGCTGTTGATGGG
1 GGTGACTGTGTCGGCGCTGTTGATGGG
10744019 ATTGCATCGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.05, C:0.14, G:0.47, T:0.33
Consensus pattern (30 bp):
GGTGACTGTGTCGGCGCTGTTGATGGGCCT
Found at i:10748773 original size:23 final size:22
Alignment explanation
Indices: 10748731--10748785 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
10748721 CAGCACAAAG
10748731 AAACAACA-AAAAGAAAGAAACAA
1 AAACAACAGAAAAGAAAG-AA-AA
*
10748754 AAACAACAGAAAAG-AGGAAAA
1 AAACAACAGAAAAGAAAGAAAA
*
10748775 AAAGAACAGAA
1 AAACAACAGAA
10748786 TAGGGGAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 12 0.41
22 2 0.07
23 10 0.34
24 5 0.17
ACGTcount: A:0.75, C:0.11, G:0.15, T:0.00
Consensus pattern (22 bp):
AAACAACAGAAAAGAAAGAAAA
Found at i:10748782 original size:24 final size:24
Alignment explanation
Indices: 10748727--10748782 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
10748717 AACACAGCAC
*
10748727 AAAGAAACAACAAAAAGAAAGAAAC
1 AAAG-AACAACAAAAAGAAAGAAAA
*
10748752 AAA-AACAACAGAAAAG-AGGAAAA
1 AAAGAACAACA-AAAAGAAAGAAAA
10748775 AAAGAACA
1 AAAGAACA
10748783 GAATAGGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 15 0.56
24 9 0.33
25 3 0.11
ACGTcount: A:0.75, C:0.11, G:0.14, T:0.00
Consensus pattern (24 bp):
AAAGAACAACAAAAAGAAAGAAAA
Found at i:10749604 original size:3 final size:3
Alignment explanation
Indices: 10749596--10749629 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
10749586 TACTATGATT
10749596 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
10749630 ATACATACGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:10754401 original size:22 final size:22
Alignment explanation
Indices: 10754362--10754403 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
10754352 ACCAATCCAT
*
10754362 TTTAACATATTTTCAAGATAGA
1 TTTAACATATTATCAAGATAGA
10754384 TTTAACATATTCAT-AAGATA
1 TTTAACATATT-ATCAAGATA
10754404 ACCTCATCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (22 bp):
TTTAACATATTATCAAGATAGA
Found at i:10758333 original size:31 final size:31
Alignment explanation
Indices: 10758295--10758366 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
10758285 ACCAATAATT
* *
10758295 ACTCAACTTTGATCTCAATGATAAAACGGTC
1 ACTCAACTTTGATCTCAATGACAAAACAGTC
*
10758326 ACTCAACTTTGGTCTCAATGACAAAACAGTC
1 ACTCAACTTTGATCTCAATGACAAAACAGTC
*
10758357 ACTCGACTTT
1 ACTCAACTTT
10758367 CAATTCAGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.29
Consensus pattern (31 bp):
ACTCAACTTTGATCTCAATGACAAAACAGTC
Found at i:10758377 original size:20 final size:20
Alignment explanation
Indices: 10758352--10758389 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
10758342 AATGACAAAA
*
10758352 CAGTCACTCGACTTTCAATT
1 CAGTCACTCAACTTTCAATT
10758372 CAGTCACTCAACTTTCAA
1 CAGTCACTCAACTTTCAA
10758390 AAAATAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.32, G:0.08, T:0.32
Consensus pattern (20 bp):
CAGTCACTCAACTTTCAATT
Found at i:10759332 original size:29 final size:31
Alignment explanation
Indices: 10759268--10759324 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 31
10759258 GATGAAGAAG
* *
10759268 AAAAAGTATAAACATATTGGGTCATTTACAC
1 AAAAAGTATAAAAATATTGGGCCATTTACAC
10759299 AAAAAGTA-AAAAATATT-GGCCATTTA
1 AAAAAGTATAAAAATATTGGGCCATTTA
10759325 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 8 0.33
31 8 0.33
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (31 bp):
AAAAAGTATAAAAATATTGGGCCATTTACAC
Found at i:10759333 original size:30 final size:31
Alignment explanation
Indices: 10759268--10759333 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
10759258 GATGAAGAAG
* * *
10759268 AAAAAGTATAAACATATTGGGTCATTTACAC
1 AAAAAGTATAAAAATATTGGGCCATTTACAA
*
10759299 AAAAAGTA-AAAAATATT-GGCCATTTATTAA
1 AAAAAGTATAAAAATATTGGGCCATTTA-CAA
10759329 AAAAA
1 AAAAA
10759334 TAGAAAAGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 8 0.27
30 14 0.47
31 8 0.27
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.27
Consensus pattern (31 bp):
AAAAAGTATAAAAATATTGGGCCATTTACAA
Found at i:10760037 original size:12 final size:11
Alignment explanation
Indices: 10760016--10760040 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10760006 TTATTTCAAT
10760016 ATTGAAAAAAA
1 ATTGAAAAAAA
10760027 ATTGAAAAAAA
1 ATTGAAAAAAA
10760038 ATT
1 ATT
10760041 AGAATTTTCA
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (11 bp):
ATTGAAAAAAA
Found at i:10760663 original size:19 final size:20
Alignment explanation
Indices: 10760619--10760663 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
10760609 GAAAAAATCC
*
10760619 TAAAAATTAAGTGATAAAAT
1 TAAAAATTAAGTGACAAAAT
* *
10760639 TGAAAA-TAAGTGACCAAAT
1 TAAAAATTAAGTGACAAAAT
10760658 TAAAAA
1 TAAAAA
10760664 AACTTTTAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.60, C:0.04, G:0.11, T:0.24
Consensus pattern (20 bp):
TAAAAATTAAGTGACAAAAT
Found at i:10769507 original size:17 final size:18
Alignment explanation
Indices: 10769482--10769525 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
10769472 TAATAACATG
*
10769482 AATAATAAATAAATT-TA
1 AATATTAAATAAATTGTA
10769499 AATATTAAA-AAATTGTA
1 AATATTAAATAAATTGTA
*
10769516 AATATAAAAT
1 AATATTAAAT
10769526 TAAGGTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
AATATTAAATAAATTGTA
Found at i:10769511 original size:16 final size:16
Alignment explanation
Indices: 10769486--10769524 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
10769476 AACATGAATA
10769486 ATAAATAAATT-TAAAT
1 ATAAA-AAATTGTAAAT
10769502 ATTAAAAAATTGTAAAT
1 A-TAAAAAATTGTAAAT
10769519 ATAAAA
1 ATAAAA
10769525 TTAAGGTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
ATAAAAAATTGTAAAT
Found at i:10779239 original size:14 final size:15
Alignment explanation
Indices: 10779220--10779257 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
10779210 TTAAAATAAA
10779220 TTTAAAATACTT-TT
1 TTTAAAATACTTATT
**
10779234 TTTAAAATTTTTATT
1 TTTAAAATACTTATT
10779249 TTTAAAATA
1 TTTAAAATA
10779258 AATTTTTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAAAATACTTATT
Found at i:10783678 original size:18 final size:19
Alignment explanation
Indices: 10783655--10783710 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
10783645 TTTTATTACT
10783655 AGTGGTTTATCCACAACA-
1 AGTGGTTTATCCACAACAG
* *
10783673 AGTGGTTCATCCACAATGATG
1 AGTGGTTTATCCACAA-CA-G
10783694 AGTGGTTTATCCACAAC
1 AGTGGTTTATCCACAAC
10783711 GTGGTGTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 15 0.48
19 1 0.03
21 15 0.48
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (19 bp):
AGTGGTTTATCCACAACAG
Found at i:10793427 original size:34 final size:35
Alignment explanation
Indices: 10793371--10793437 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 35
10793361 CTGTCACTGT
*
10793371 ACTGAATATTGATACTATAATGGGCTAAGGCCCTA
1 ACTGAATATTGAAACTATAATGGGCTAAGGCCCTA
*
10793406 ACTGAA-ATTGAAACTGA-AATGGGCTTAGGCCC
1 ACTGAATATTGAAACT-ATAATGGGCTAAGGCCC
10793438 AGACTATGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 22 0.76
35 7 0.24
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.25
Consensus pattern (35 bp):
ACTGAATATTGAAACTATAATGGGCTAAGGCCCTA
Found at i:10799198 original size:95 final size:95
Alignment explanation
Indices: 10799031--10799218 Score: 304
Period size: 95 Copynumber: 2.0 Consensus size: 95
10799021 TCCACAATTT
* * *
10799031 CAAATTTTTTCCTAAAATCATTTCAACACTCCCCCATCCAAATCTCCTTAATTATCTCCAACAAC
1 CAAATTTTCTCCTAAAATCACTCCAACACTCCCCCATCCAAATCTCCTTAATTATCTCCAACAAC
*
10799096 CTTTCCACTATCCGAATTTTAGTCCAACCC
66 CTCTCCACTATCCGAATTTTAGTCCAACCC
* * *
10799126 CAAATTTTCTCCTAAAATCACTCCAACACTCCTCCATCCAAATCTCCTTAATTATCTCTATCAAC
1 CAAATTTTCTCCTAAAATCACTCCAACACTCCCCCATCCAAATCTCCTTAATTATCTCCAACAAC
*
10799191 CTCTCCACTATCGGAATTTTAGTCCAAC
66 CTCTCCACTATCCGAATTTTAGTCCAAC
10799219 TCAAACTCAC
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
95 85 1.00
ACGTcount: A:0.30, C:0.35, G:0.03, T:0.32
Consensus pattern (95 bp):
CAAATTTTCTCCTAAAATCACTCCAACACTCCCCCATCCAAATCTCCTTAATTATCTCCAACAAC
CTCTCCACTATCCGAATTTTAGTCCAACCC
Found at i:10805867 original size:95 final size:94
Alignment explanation
Indices: 10805705--10805893 Score: 306
Period size: 95 Copynumber: 2.0 Consensus size: 94
10805695 ACTCCACAAT
* * *
10805705 CCCAAATTTTCTCCTAAAATCACTCCAACACTCGCCATCCAAATCTCTTTAATTATCTCCAACAA
1 CCCAAATTTTCTCCTAAAATCACTCCAAAACTCCCCATCCAAATCTCCTTAATTATCTCCAACAA
* *
10805770 CCTCTCTACTATCCGAATTTTAGTCCAAC
66 CCTCTCCACTATCAGAATTTTAGTCCAAC
*
10805799 CCCAAATTTTCTCCTAAAATCACTCCAAAACTCCCCCATCCAAATCTCCTTAATTATCTCCATCA
1 CCCAAATTTTCTCCTAAAATCACTCCAAAACT-CCCCATCCAAATCTCCTTAATTATCTCCAACA
*
10805864 ACCTCTCCACTATTAGAATTTTAGTCCAAC
65 ACCTCTCCACTATCAGAATTTTAGTCCAAC
10805894 ACAAACTCGC
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
94 31 0.36
95 56 0.64
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.31
Consensus pattern (94 bp):
CCCAAATTTTCTCCTAAAATCACTCCAAAACTCCCCATCCAAATCTCCTTAATTATCTCCAACAA
CCTCTCCACTATCAGAATTTTAGTCCAAC
Found at i:10806981 original size:20 final size:20
Alignment explanation
Indices: 10806944--10806981 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10806934 GCTGTGTGAG
*
10806944 GGTCTACACGCCCTTGTGGT
1 GGTCTACACGCCCATGTGGT
*
10806964 GGTCTACACGCTCATGTG
1 GGTCTACACGCCCATGTG
10806982 TAAGCTGCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.29, G:0.29, T:0.29
Consensus pattern (20 bp):
GGTCTACACGCCCATGTGGT
Found at i:10809530 original size:20 final size:20
Alignment explanation
Indices: 10809505--10809545 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
10809495 TCCTACTGAG
10809505 TAAGCTTATGTTATATTGTT
1 TAAGCTTATGTTATATTGTT
10809525 TAAGCTTATGTTATATTGTT
1 TAAGCTTATGTTATATTGTT
10809545 T
1 T
10809546 GTAAACTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.15, T:0.56
Consensus pattern (20 bp):
TAAGCTTATGTTATATTGTT
Found at i:10819495 original size:19 final size:18
Alignment explanation
Indices: 10819465--10819501 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
10819455 CTCCAATTAT
*
10819465 AATAAACATAATATAATA
1 AATAAACATAATAAAATA
10819483 AATAAATCATAATAAAATA
1 AATAAA-CATAATAAAATA
10819502 TATTTGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (18 bp):
AATAAACATAATAAAATA
Done.