Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 17 of 105
Found at i:3549849 original size:18 final size:17
Alignment explanation
Indices: 3549828--3549861 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3549818 ATGCATATCG
*
3549828 TATTATTGATTATAATTT
1 TATTATT-ATAATAATTT
3549846 TATTATTATAATAATT
1 TATTATTATAATAATT
3549862 AATTTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TATTATTATAATAATTT
Found at i:3549864 original size:21 final size:20
Alignment explanation
Indices: 3549840--3549889 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 20
3549830 TTATTGATTA
3549840 TAATTTTATTATTAT-AATAAT
1 TAATTTTATT-TTATCAA-AAT
3549861 TAATTTTAATTTTATCAAAAT
1 TAATTTT-ATTTTATCAAAAT
3549882 TAATTTTA
1 TAATTTTA
3549890 CCATTAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 1 0.04
21 21 0.78
22 5 0.19
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATTTTATTTTATCAAAAT
Found at i:3553095 original size:27 final size:27
Alignment explanation
Indices: 3553065--3553118 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
3553055 TATATAAAAA
3553065 ATAA-TTAACATATTA-ATTAATAAATTT
1 ATAATTTAA-ATATTATATTAA-AAATTT
3553092 ATAATTTAAATATTATATTAAAAATTT
1 ATAATTTAAATATTATATTAAAAATTT
3553119 TTAAAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (27 bp):
ATAATTTAAATATTATATTAAAAATTT
Found at i:3553128 original size:28 final size:27
Alignment explanation
Indices: 3553067--3553129 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
3553057 TATAAAAAAT
3553067 AATTAACATATTAATTAATAAATTTATA
1 AATTAA-ATATTAATTAATAAATTTATA
* *
3553095 ATTTAAATATTATATTAA-AAATTTTTAA
1 AATTAAATATTA-ATTAATAAATTTAT-A
3553123 AATTAAA
1 AATTAAA
3553130 ATATCACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 13 0.43
28 17 0.57
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
AATTAAATATTAATTAATAAATTTATA
Found at i:3553131 original size:29 final size:26
Alignment explanation
Indices: 3553067--3553142 Score: 71
Period size: 29 Copynumber: 2.7 Consensus size: 26
3553057 TATAAAAAAT
* *
3553067 AATTAACATATTAATTAATAAATTTAT
1 AATTAAAATATTAATTAA-AAATTTAA
*
3553094 AATTTAAATATTATATTAAAAATTTTTAA
1 AATTAAAATATTA-ATTAAAAA--TTTAA
*
3553123 AATTAAAATATCACATTAAA
1 AATTAAAATATTA-ATTAAA
3553143 TTTTTACTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 14 0.35
28 5 0.12
29 21 0.52
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (26 bp):
AATTAAAATATTAATTAAAAATTTAA
Found at i:3557152 original size:2 final size:2
Alignment explanation
Indices: 3557145--3557170 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3557135 GGTGTTAAAT
3557145 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
3557171 GATCTGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3558813 original size:38 final size:38
Alignment explanation
Indices: 3558771--3558847 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
3558761 TATATGTTTG
3558771 TTTGTCTATGGTACTAATGATTACATCATGGCATGAAT
1 TTTGTCTATGGTACTAATGATTACATCATGGCATGAAT
* *
3558809 TTTGTCTATGGTTCTAATGATTACATCATGGTATGAAT
1 TTTGTCTATGGTACTAATGATTACATCATGGCATGAAT
3558847 T
1 T
3558848 CCGGTGCTGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (38 bp):
TTTGTCTATGGTACTAATGATTACATCATGGCATGAAT
Found at i:3560765 original size:76 final size:76
Alignment explanation
Indices: 3560634--3560785 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
3560624 TAACAACAAG
3560634 AAGCATTTTGATATAGAGGCCAAGTAAGTAATTCATAAACCGGGGACCCTCTTATCCGTCAATGG
1 AAGCATTTTGATATAGAGGCCAAGTAAGTAATTCATAAACCGGGGACCCTCTTATCCGTCAATGG
3560699 CAAGGTTTTCT
66 CAAGGTTTTCT
*
3560710 AAGCGTTTTGATATAGAGGCCAAGTAAGTAATTCATAAACCGGGGACCCTCTTATCCGTCAATGG
1 AAGCATTTTGATATAGAGGCCAAGTAAGTAATTCATAAACCGGGGACCCTCTTATCCGTCAATGG
3560775 CAAGGTTTTCT
66 CAAGGTTTTCT
3560786 TGGAGGTTTA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (76 bp):
AAGCATTTTGATATAGAGGCCAAGTAAGTAATTCATAAACCGGGGACCCTCTTATCCGTCAATGG
CAAGGTTTTCT
Found at i:3561106 original size:11 final size:11
Alignment explanation
Indices: 3561076--3561115 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
3561066 TAATGACAAG
*
3561076 ATATAAAAATG
1 ATATAAAAATA
*
3561087 ATACAAAAAGTA
1 ATATAAAAA-TA
3561099 ATATAAAAATA
1 ATATAAAAATA
3561110 ATATAA
1 ATATAA
3561116 TTTAAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:3573048 original size:21 final size:21
Alignment explanation
Indices: 3572980--3573053 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 21
3572970 AGCATGAAAA
3572980 AAATTTAGAAAATATTCTAAA-
1 AAATTTA-AAAATATTCTAAAG
*
3573001 AATTCTTTAAAAA-ATTTCTAAAG
1 AA--ATTTAAAAATA-TTCTAAAG
3573024 -AATTTAAAAATATTCTAAAG
1 AAATTTAAAAATATTCTAAAG
3573044 AAATTTAAAA
1 AAATTTAAAA
3573054 TTATAGAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
20 16 0.36
21 13 0.29
22 12 0.27
23 4 0.09
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.35
Consensus pattern (21 bp):
AAATTTAAAAATATTCTAAAG
Found at i:3573074 original size:21 final size:21
Alignment explanation
Indices: 3573050--3573093 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3573040 AAAGAAATTT
*
3573050 AAAATTATAGAAATTCAAAAA
1 AAAATTATAAAAATTCAAAAA
* *
3573071 AAAATTTTAAAAATTCTAAAA
1 AAAATTATAAAAATTCAAAAA
3573092 AA
1 AA
3573094 TTTTAAACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAATTATAAAAATTCAAAAA
Found at i:3573136 original size:20 final size:19
Alignment explanation
Indices: 3572977--3573143 Score: 91
Period size: 19 Copynumber: 7.9 Consensus size: 19
3572967 GTTAGCATGA
3572977 AAAAAATTTAGAAAATATTCT
1 AAAAAATTTA-AAAA-ATTCT
*
3572998 AAAAATTCTTTAAAAAATTTCT
1 AAAAA--ATTTAAAAAA-TTCT
*
3573020 AAAGAATTTAAAAATATTCT
1 AAAAAATTTAAAAA-ATTCT
*
3573040 AAAGAAATTTAAAATTATAGAAATTCAAA
1 AAA-AAATTT---A--A-A-AAATTC--T
*
3573069 AAAAAATTTTAAAAATTCT
1 AAAAAATTTAAAAAATTCT
* ** *
3573088 AAAAAATTTTAAACTTTTT
1 AAAAAATTTAAAAAATTCT
*
3573107 TAAAAATTTAAAAAATTCT
1 AAAAAATTTAAAAAATTCT
*
3573126 AAAATAATTTATAAAATT
1 AAAA-AATTTAAAAAATT
3573144 TTTAGAAAAT
Statistics
Matches: 114, Mismatches: 17, Indels: 31
0.70 0.10 0.19
Matches are distributed among these distances:
19 33 0.29
20 27 0.24
21 18 0.16
22 13 0.11
23 5 0.04
24 1 0.01
26 1 0.01
27 5 0.04
28 8 0.07
29 3 0.03
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAAAATTTAAAAAATTCT
Found at i:3573143 original size:9 final size:9
Alignment explanation
Indices: 3572977--3573144 Score: 63
Period size: 9 Copynumber: 17.0 Consensus size: 9
3572967 GTTAGCATGA
3572977 AAAAAATTT
1 AAAAAATTT
3572986 AGAAAATATTCT
1 A-AAAA-ATT-T
*
3572998 AAAAATTCTTT
1 AAAAA--ATTT
3573009 AAAAAATTTCT
1 AAAAAA-TT-T
*
3573020 AAAGAATTT
1 AAAAAATTT
3573029 AAAAATATTCT
1 AAAAA-ATT-T
3573040 AAAGAAATTT
1 AAA-AAATTT
3573050 --AAAA-TT
1 AAAAAATTT
* *
3573056 ATAGAAATTCAAA
1 A-AAAAATT---T
3573069 AAAAAATTT
1 AAAAAATTT
*
3573078 TAAAAATTCT
1 AAAAAATT-T
3573088 AAAAAATTTT
1 AAAAAA-TTT
***
3573098 AAACTTTTT
1 AAAAAATTT
*
3573107 TAAAAATTT
1 AAAAAATTT
3573116 AAAAAATTCT
1 AAAAAATT-T
3573126 AAAATAATTT
1 AAAA-AATTT
*
3573136 ATAAAATTT
1 AAAAAATTT
3573145 TTAGAAAATC
Statistics
Matches: 120, Mismatches: 19, Indels: 40
0.67 0.11 0.22
Matches are distributed among these distances:
6 2 0.02
7 3 0.03
8 1 0.01
9 36 0.30
10 32 0.27
11 32 0.27
12 13 0.11
13 1 0.01
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (9 bp):
AAAAAATTT
Found at i:3573267 original size:25 final size:24
Alignment explanation
Indices: 3573239--3573290 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
3573229 AAATTCAAAA
3573239 AAATTAAAAAATTCTAAAAACATCT
1 AAATTAAAAAATT-TAAAAACATCT
** * *
3573264 AAATTTTAAAATTTTAAAATATCT
1 AAATTAAAAAATTTAAAAACATCT
3573288 AAA
1 AAA
3573291 AAATTTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATTAAAAAATTTAAAAACATCT
Found at i:3573297 original size:18 final size:18
Alignment explanation
Indices: 3573271--3573374 Score: 79
Period size: 18 Copynumber: 5.7 Consensus size: 18
3573261 TCTAAATTTT
*
3573271 AAAATTTTAAAATATCTA
1 AAAAATTTAAAATATCTA
* * **
3573289 AAAAATTTAAATTTTGAA
1 AAAAATTTAAAATATCTA
3573307 AAAAATTTAAAA-ATCTA
1 AAAAATTTAAAATATCTA
* *
3573324 AAAACTTTTAAAAT-TTTAA
1 AAAA-ATTTAAAATATCT-A
3573343 AAAAATTCTAAAA-ATTCTA
1 AAAAATT-TAAAATA-TCTA
3573362 ACAAAATTTAAAA
1 A-AAAATTTAAAA
3573375 ATTCAATAAC
Statistics
Matches: 66, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
17 6 0.09
18 35 0.53
19 17 0.26
20 8 0.12
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.35
Consensus pattern (18 bp):
AAAAATTTAAAATATCTA
Found at i:3573320 original size:8 final size:8
Alignment explanation
Indices: 3573307--3573377 Score: 52
Period size: 8 Copynumber: 7.9 Consensus size: 8
3573297 AAATTTTGAA
3573307 AAAAATTT
1 AAAAATTT
*
3573315 AAAAATCT
1 AAAAATTT
3573323 AAAAACTTTT
1 AAAAA--TTT
*
3573333 AAAATTTT
1 AAAAATTT
3573341 AAAAAAATTCT
1 --AAAAATT-T
3573352 AAAAATTCT
1 AAAAATT-T
3573361 AACAAAATTT
1 -A-AAAATTT
3573371 AAAAATT
1 AAAAATT
3573378 CAATAACAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
8 21 0.40
9 10 0.19
10 14 0.27
11 7 0.13
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (8 bp):
AAAAATTT
Found at i:3573388 original size:19 final size:20
Alignment explanation
Indices: 3573308--3573378 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
3573298 AATTTTGAAA
3573308 AAAATT-TAAAAA-TCTAA-
1 AAAATTCTAAAAATTCTAAC
* * * *
3573325 AAACTT-TTAAAATTTTAAA
1 AAAATTCTAAAAATTCTAAC
3573344 AAAATTCTAAAAATTCTAAC
1 AAAATTCTAAAAATTCTAAC
3573364 AAAATT-TAAAAATTC
1 AAAATTCTAAAAATTC
3573379 AATAACAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
17 10 0.23
18 4 0.09
19 14 0.32
20 16 0.36
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATTCTAAAAATTCTAAC
Found at i:3573390 original size:18 final size:19
Alignment explanation
Indices: 3573271--3573378 Score: 91
Period size: 19 Copynumber: 5.8 Consensus size: 19
3573261 TCTAAATTTT
*
3573271 AAAATTTTAAAATATCTAA-
1 AAAATTTAAAAAT-TCTAAC
* *
3573290 AAAATTT--AAATTTTGAAA
1 AAAATTTAAAAATTCT-AAC
3573308 AAAATTTAAAAA-TCTAA-
1 AAAATTTAAAAATTCTAAC
* * * *
3573325 AAACTTTTAAAATTTTAAA
1 AAAATTTAAAAATTCTAAC
3573344 AAAATTCTAAAAATTCTAAC
1 AAAATT-TAAAAATTCTAAC
3573364 AAAATTTAAAAATTC
1 AAAATTTAAAAATTC
3573379 AATAACAATT
Statistics
Matches: 73, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
16 2 0.03
17 16 0.22
18 13 0.18
19 23 0.32
20 19 0.26
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.35
Consensus pattern (19 bp):
AAAATTTAAAAATTCTAAC
Found at i:3573450 original size:20 final size:20
Alignment explanation
Indices: 3573425--3573463 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3573415 TTTTTATAAA
*
3573425 TTTATAGAATTTTATTTTTT
1 TTTATAAAATTTTATTTTTT
3573445 TTTATAAAATTTTATTTTT
1 TTTATAAAATTTTATTTTT
3573464 ATAAATTTTA
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:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTATAAAATTTTATTTTTT
Found at i:3573464 original size:16 final size:15
Alignment explanation
Indices: 3573438--3573478 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
3573428 ATAGAATTTT
3573438 ATTTT-TTTTTATAAA
1 ATTTTATTTTTAT-AA
3573453 ATTTTATTTTTATAA
1 ATTTTATTTTTATAA
3573468 ATTTTAATTTT
1 ATTTT-ATTTT
3573479 GTTGGAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTATTTTTATAA
Found at i:3573472 original size:10 final size:11
Alignment explanation
Indices: 3573400--3573424 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3573390 AGGAAAGTTA
3573400 AAAATTTTTAT
1 AAAATTTTTAT
3573411 AAAATTTTTAT
1 AAAATTTTTAT
3573422 AAA
1 AAA
3573425 TTTATAGAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAAATTTTTAT
Found at i:3573963 original size:9 final size:9
Alignment explanation
Indices: 3573932--3574064 Score: 63
Period size: 9 Copynumber: 13.8 Consensus size: 9
3573922 TTTAAAAAAA
3573932 TTTTAGAATT
1 TTTTA-AATT
*
3573942 GTTTTGAATTT
1 -TTTT-AAATT
3573953 TTTTAAATTT
1 TTTTAAA-TT
* *
3573963 TTTTTAAGT
1 TTTTAAATT
* *
3573972 TTCTAAAAT
1 TTTTAAATT
*
3573981 TTTTAGAAAT
1 TTTTA-AATT
3573991 TTTTACAA-T
1 TTTTA-AATT
*
3574000 TTCTAGAA-T
1 TTTTA-AATT
3574009 TTTTAATATT
1 TTTTAA-ATT
3574019 TTTTACTAATT
1 TTTTA--AATT
*
3574030 TTTAAAATAT
1 TTTTAAAT-T
*
3574040 TTTTAAATA
1 TTTTAAATT
*
3574049 TTTAAAATT
1 TTTTAAATT
3574058 TTTTAAA
1 TTTTAAA
3574065 ATTTCTTTTT
Statistics
Matches: 96, Mismatches: 18, Indels: 18
0.73 0.14 0.14
Matches are distributed among these distances:
8 1 0.01
9 42 0.44
10 37 0.39
11 14 0.15
12 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.58
Consensus pattern (9 bp):
TTTTAAATT
Found at i:3573983 original size:28 final size:27
Alignment explanation
Indices: 3573952--3574047 Score: 93
Period size: 28 Copynumber: 3.3 Consensus size: 27
3573942 GTTTTGAATT
**
3573952 TTTTTAAATTTTTTTTAAGTTTCTAAAA
1 TTTTTAAATTTTTTACAA-TTTCTAAAA
* *
3573980 TTTTTAGAAATTTTTACAATTTCTAGAA
1 TTTTTA-AATTTTTTACAATTTCTAAAA
*
3574008 TTTTTAATATTTTTTACTAATTTTTAAAATA
1 TTTTTAA-ATTTTTTAC-AATTTCT-AAA-A
3574039 TTTTTAAAT
1 TTTTTAAAT
3574048 ATTTAAAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
27 1 0.02
28 28 0.50
29 15 0.27
30 4 0.07
31 8 0.14
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.58
Consensus pattern (27 bp):
TTTTTAAATTTTTTACAATTTCTAAAA
Found at i:3573992 original size:10 final size:9
Alignment explanation
Indices: 3573952--3574068 Score: 81
Period size: 10 Copynumber: 12.3 Consensus size: 9
3573942 GTTTTGAATT
*
3573952 TTTTTAAATT
1 TTTTTAAA-A
* *
3573962 TTTTTTAAG
1 TTTTTAAAA
*
3573971 TTTCTAAAA
1 TTTTTAAAA
3573980 TTTTTAGAAA
1 TTTTTA-AAA
*
3573990 TTTTTACAA
1 TTTTTAAAA
* *
3573999 TTTCTAGAA
1 TTTTTAAAA
*
3574008 TTTTTAATAT
1 TTTTTAA-AA
*
3574018 TTTTTACTAA
1 TTTTTA-AAA
3574028 TTTTTAAAA
1 TTTTTAAAA
*
3574037 TATTTTTAAA
1 T-TTTTAAAA
*
3574047 TATTTAAAA
1 TTTTTAAAA
3574056 TTTTTTAAAA
1 -TTTTTAAAA
3574066 TTT
1 TTT
3574069 CTTTTTATGT
Statistics
Matches: 83, Mismatches: 19, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
9 37 0.45
10 46 0.55
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:3574066 original size:19 final size:19
Alignment explanation
Indices: 3573644--3574068 Score: 104
Period size: 19 Copynumber: 22.0 Consensus size: 19
3573634 TTTTTCGAAA
3573644 TTAAAATTTTTTTATAAA-TT
1 TTAAAA-TTTTTTA-AAATTT
* *
3573664 TTAAAAATTTGTAAAATACTT
1 TTAAAATTTTTTAAAAT--TT
3573685 TT--AATTTTTTCAAAATTT
1 TTAAAATTTTTT-AAAATTT
** *
3573703 TTAAAAAAATTTTAGAATTAT
1 TT-AAAATTTTTTAAAATT-T
** * **
3573724 TTGGAATTTTTTTATGTTT
1 TTAAAATTTTTTAAAATTT
* *
3573743 CTAAAA-TTTTTAGAATTT
1 TTAAAATTTTTTAAAATTT
* * * *
3573761 TAAAAAGTTTTTAGAAGTT
1 TTAAAATTTTTTAAAATTT
*
3573780 TTAAATATTTTTGT-GAATTT
1 TTAAA-ATTTTT-TAAAATTT
* **
3573800 TT--TATTTTTTTCAATTGT
1 TTAAAATTTTTTAAAATT-T
* ** *
3573818 CTAAAAATACTTTAAAAGTTA
1 -TTAAAATTTTTTAAAA-TTT
*
3573839 TTAAAA-TTTTTAGAATTTT
1 TTAAAATTTTTTA-AAATTT
* *
3573858 TTATAATTTTTTGAAA---
1 TTAAAATTTTTTAAAATTT
* * **
3573874 TGAAATTTTTTTTTAATTT
1 TTAAAATTTTTTAAAATTT
** **
3573893 AAAAAATATTTTATAATTTTT
1 TTAAAAT-TTTT-TAAAATTT
** *
3573914 TTCAAAATTTTAAAAAAATT
1 TT-AAAATTTTTTAAAATTT
* **
3573934 TTAGAATTGTTTTGAATTTTT
1 TTAAAATT-TTTT-AAAATTT
* * *
3573955 TTAAATTTTTTTTAAGTTT
1 TTAAAATTTTTTAAAATTT
*
3573974 CTAAAA-TTTTTAGAAATTT
1 TTAAAATTTTTTA-AAATTT
* * *
3573993 TTACAA-TTTCTAGAATTT
1 TTAAAATTTTTTAAAATTT
* *
3574011 TTAATATTTTTTACTAATTT
1 TTAAAATTTTTTA-AAATTT
*
3574031 TTAAAATATTTTT-AAATAT
1 TTAAAAT-TTTTTAAAATTT
3574050 TTAAAATTTTTTAAAATTT
1 TTAAAATTTTTTAAAATTT
3574069 CTTTTTATGT
Statistics
Matches: 282, Mismatches: 91, Indels: 65
0.64 0.21 0.15
Matches are distributed among these distances:
16 12 0.04
17 10 0.04
18 39 0.14
19 96 0.34
20 75 0.27
21 43 0.15
22 7 0.02
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (19 bp):
TTAAAATTTTTTAAAATTT
Found at i:3574520 original size:82 final size:83
Alignment explanation
Indices: 3574361--3574529 Score: 304
Period size: 82 Copynumber: 2.0 Consensus size: 83
3574351 ACTTTTAAAA
* *
3574361 AATATCTATATGGATTGTTATAAGAGATAATATTTCTTTTTTTTTATGATTGACAATTTTTATTT
1 AATATCTATATGGATTGTTATAAGAGATAATATATC-TTCTTTTTATGATTGACAATTTTTATTT
3574426 AAGAAAATTTTTAAATACT
65 AAGAAAATTTTTAAATACT
3574445 AATATCTATATGGATTGTTATAAGAGATAATATATC-TCTTTTTATGATTGACAATTTTTATTTA
1 AATATCTATATGGATTGTTATAAGAGATAATATATCTTCTTTTTATGATTGACAATTTTTATTTA
3574509 AGAAAATTTTTAAATACT
66 AGAAAATTTTTAAATACT
3574527 AAT
1 AAT
3574530 TAAATCATCT
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
82 48 0.58
84 35 0.42
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.48
Consensus pattern (83 bp):
AATATCTATATGGATTGTTATAAGAGATAATATATCTTCTTTTTATGATTGACAATTTTTATTTA
AGAAAATTTTTAAATACT
Found at i:3574724 original size:20 final size:19
Alignment explanation
Indices: 3574683--3574728 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
3574673 AGCTCAGTTA
3574683 TTTATATTTTATTTTTAAAT
1 TTTATATTTTATTTTT-AAT
3574703 TTTATGATTATTATTTTT-AT
1 TTTAT-ATT-TTATTTTTAAT
3574723 TTTATA
1 TTTATA
3574729 CATATTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.04
20 12 0.50
21 3 0.12
22 8 0.33
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTATATTTTATTTTTAAT
Found at i:3574974 original size:31 final size:32
Alignment explanation
Indices: 3574937--3575028 Score: 141
Period size: 31 Copynumber: 2.8 Consensus size: 32
3574927 GGATAAAGCA
3574937 TAGCTTTTGAAGTTAACTTGATATTAAGTTCT
1 TAGCTTTTGAAGTTAACTTGATATTAAGTTCT
3574969 T-GCTTTTGAAGTTAACTTGATATTAAGTTCT
1 TAGCTTTTGAAGTTAACTTGATATTAAGTTCT
* *
3575000 TATCTGTTTGAAATTAACTTTGATATTAA
1 TAGCT-TTTGAAGTTAAC-TTGATATTAA
3575029 ATTCCTGTAG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
31 31 0.56
32 3 0.05
33 11 0.20
34 10 0.18
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48
Consensus pattern (32 bp):
TAGCTTTTGAAGTTAACTTGATATTAAGTTCT
Found at i:3576742 original size:21 final size:20
Alignment explanation
Indices: 3576717--3576765 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
3576707 AAGGTGAACA
*
3576717 ATATAATGGTATCATTATTAT
1 ATATAATGCTATCATTA-TAT
3576738 ATATAATGCTATCATTATAT
1 ATATAATGCTATCATTATAT
*
3576758 ATAAAATG
1 ATATAATG
3576766 TTTGTCTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (20 bp):
ATATAATGCTATCATTATAT
Found at i:3583265 original size:27 final size:28
Alignment explanation
Indices: 3583207--3583275 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
3583197 AGATAATAAC
* *
3583207 GAATCAAATTAAA-AAAAAATTAAATCT
1 GAATCAAATCAAATAAAAAATTAAATAT
*
3583234 AAATCAAATCAAATAAAAAATT-AATAT
1 GAATCAAATCAAATAAAAAATTAAATAT
3583261 GAATCAAATCAAATA
1 GAATCAAATCAAATA
3583276 TTATGATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 29 0.78
28 8 0.22
ACGTcount: A:0.64, C:0.09, G:0.03, T:0.25
Consensus pattern (28 bp):
GAATCAAATCAAATAAAAAATTAAATAT
Found at i:3584458 original size:18 final size:18
Alignment explanation
Indices: 3584435--3584470 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3584425 ATTTTTTAAT
*
3584435 TATTTATTTAATTATATA
1 TATTTATGTAATTATATA
3584453 TATTTATGTAATTATATA
1 TATTTATGTAATTATATA
3584471 ATTATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TATTTATGTAATTATATA
Found at i:3584476 original size:8 final size:8
Alignment explanation
Indices: 3584438--3584485 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
3584428 TTTTAATTAT
*
3584438 TTATTTAA
1 TTATATAA
3584446 TTATATATA
1 TTATATA-A
*
3584455 TTTATGTAA
1 -TTATATAA
3584464 TTATATAA
1 TTATATAA
*
3584472 TTATATAT
1 TTATATAA
3584480 TTATAT
1 TTATAT
3584486 TCAAAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 26 0.76
9 2 0.06
10 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (8 bp):
TTATATAA
Found at i:3584592 original size:76 final size:76
Alignment explanation
Indices: 3584506--3584649 Score: 193
Period size: 77 Copynumber: 1.9 Consensus size: 76
3584496 ATATTTTATT
** *
3584506 AATTTTAAATTAAATCAAATAT-AA-TTTATATAATATCGAATCGAATCAAATCGAATTTAAATA
1 AATTTTAAATTAAATCAAATATAAATTTTATA-AATATAAAATCGAATCAAATCGAATTCAAATA
3584569 TAAAAAAATAAAA
65 -AAAAAAATAAAA
* * **
3584582 AATTTTAAATTAAATCGAATTTAAATTTTATAAATATAAAATCGAATTGAATCGAATTCAAATAA
1 AATTTTAAATTAAATCAAATATAAATTTTATAAATATAAAATCGAATCAAATCGAATTCAAATAA
3584647 AAA
66 AAA
3584650 CTCATTTCAC
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
76 24 0.41
77 29 0.49
78 6 0.10
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (76 bp):
AATTTTAAATTAAATCAAATATAAATTTTATAAATATAAAATCGAATCAAATCGAATTCAAATAA
AAAAAATAAAA
Found at i:3585260 original size:22 final size:23
Alignment explanation
Indices: 3585222--3585265 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
3585212 TTTAATCTAA
*
3585222 ATATATTAATTTTAATAAAAATT
1 ATATATTAAATTTAATAAAAATT
3585245 ATATA-TAAATTTAATAAAAAT
1 ATATATTAAATTTAATAAAAAT
3585266 AAAAAAATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATATTAAATTTAATAAAAATT
Found at i:3592126 original size:24 final size:24
Alignment explanation
Indices: 3592081--3592126 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
3592071 ACGTCATATA
* *
3592081 ATATGCTGATAATATATAAAATTT
1 ATATACTGATAATACATAAAATTT
* *
3592105 ATATACTGATAATGCATCAAAT
1 ATATACTGATAATACATAAAAT
3592127 ATAAACTTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (24 bp):
ATATACTGATAATACATAAAATTT
Found at i:3592720 original size:18 final size:18
Alignment explanation
Indices: 3592699--3592733 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3592689 TAAATGAATT
*
3592699 TTTTTATTATTAGACTTC
1 TTTTTATAATTAGACTTC
3592717 TTTTTATAATTAGACTT
1 TTTTTATAATTAGACTT
3592734 AAAAGTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (18 bp):
TTTTTATAATTAGACTTC
Found at i:3592891 original size:19 final size:21
Alignment explanation
Indices: 3592853--3592892 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
3592843 TTTAAATGAA
*
3592853 TTTTCTTTTTAATTATTAGAC
1 TTTTCTTTTTAATAATTAGAC
3592874 TTTTC-TTTT-ATAATTAGAC
1 TTTTCTTTTTAATAATTAGAC
3592893 CCATTTAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 4 0.22
21 5 0.28
ACGTcount: A:0.25, C:0.10, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTTCTTTTTAATAATTAGAC
Found at i:3594558 original size:10 final size:11
Alignment explanation
Indices: 3594543--3594572 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3594533 TTTTATGAGC
3594543 TTTATTTTA-T
1 TTTATTTTATT
3594553 TTTATTTTATT
1 TTTATTTTATT
3594564 TTTATTTTA
1 TTTATTTTA
3594573 GTTAATGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:3594568 original size:6 final size:5
Alignment explanation
Indices: 3594543--3594572 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
3594533 TTTTATGAGC
3594543 TTTAT TTTAT TTTAT TTTATT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTA-T TTTAT TTTA
3594573 GTTAATGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:3595463 original size:25 final size:26
Alignment explanation
Indices: 3595428--3595491 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
3595418 AATGATTGAA
3595428 TTTATAGAAATTTC-AAATG-GTAAATT
1 TTTATA-AAATTTCTAAATGAG-AAATT
*
3595454 TTTATAAAATTTCTAAGTGAGAAATT
1 TTTATAAAATTTCTAAATGAGAAATT
*
3595480 TCTATAAAATTT
1 TTTATAAAATTT
3595492 TTATTTTCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 7 0.21
26 26 0.76
27 1 0.03
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (26 bp):
TTTATAAAATTTCTAAATGAGAAATT
Found at i:3595531 original size:100 final size:100
Alignment explanation
Indices: 3595426--3595631 Score: 378
Period size: 100 Copynumber: 2.1 Consensus size: 100
3595416 CCAATGATTG
3595426 AATTTATAGAAATTTCAAATGGTAAATTTTTATAAAATTTCTAAGTGAGAAA-TTTCTATAAAAT
1 AATTTATAGAAATTTCAAATGGTAAATTTTTATAAAATTTCTAAGTGA-AAATTTTCTATAAAAT
3595490 TTTTATTTTCTCTAAATTTATCTCAAATGATGGAAT
65 TTTTATTTTCTCTAAATTTATCTCAAATGATGGAAT
*
3595526 AATTTATAGAAATTTCAAATGGTAAATTTTTATAAAATTTTTAAGTGAAAATTTTCTATAAAATT
1 AATTTATAGAAATTTCAAATGGTAAATTTTTATAAAATTTCTAAGTGAAAATTTTCTATAAAATT
*
3595591 TTTATTTTCTCTAAATTTGTCTCAAATGATGGAAT
66 TTTATTTTCTCTAAATTTATCTCAAATGATGGAAT
3595626 AATTTA
1 AATTTA
3595632 GATAAAGTTT
Statistics
Matches: 103, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
99 3 0.03
100 100 0.97
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (100 bp):
AATTTATAGAAATTTCAAATGGTAAATTTTTATAAAATTTCTAAGTGAAAATTTTCTATAAAATT
TTTATTTTCTCTAAATTTATCTCAAATGATGGAAT
Found at i:3595563 original size:25 final size:25
Alignment explanation
Indices: 3595528--3595591 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
3595518 GATGGAATAA
*
3595528 TTTATAGAAATTTCAAA-TGGTAAATT
1 TTTATA-AAATTTCAAAGT-GAAAATT
**
3595554 TTTATAAAATTTTTAAGTGAAAATT
1 TTTATAAAATTTCAAAGTGAAAATT
3595579 TTCTATAAAATTT
1 TT-TATAAAATTT
3595592 TTATTTTCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 16 0.48
26 17 0.52
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (25 bp):
TTTATAAAATTTCAAAGTGAAAATT
Found at i:3595590 original size:12 final size:11
Alignment explanation
Indices: 3595549--3595595 Score: 58
Period size: 11 Copynumber: 3.9 Consensus size: 11
3595539 TTCAAATGGT
3595549 AAATTTTTATA
1 AAATTTTTATA
3595560 AAATTTTTAAGTGA
1 AAATTTTT-A-T-A
3595574 AAATTTTCTATA
1 AAATTTT-TATA
3595586 AAATTTTTAT
1 AAATTTTTAT
3595596 TTTCTCTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 11 0.34
12 9 0.28
13 2 0.06
14 9 0.28
15 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (11 bp):
AAATTTTTATA
Found at i:3596614 original size:5 final size:5
Alignment explanation
Indices: 3596604--3596636 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
3596594 TTTTATGGGC
3596604 TTTAT TTTAT TTTA- TTTAT TTTATT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTT
3596637 TCTTTTCATT
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:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:3596621 original size:14 final size:15
Alignment explanation
Indices: 3596604--3596635 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
3596594 TTTTATGGGC
3596604 TTTATTTTA-TTTTA
1 TTTATTTTATTTTTA
3596618 TTTATTTTATTTTTA
1 TTTATTTTATTTTTA
3596633 TTT
1 TTT
3596636 TTCTTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTATTTTATTTTTA
Found at i:3597189 original size:20 final size:21
Alignment explanation
Indices: 3597159--3597201 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
3597149 TTCTAGAGAA
3597159 AAAATGAGAGAAAAGAAAGGG
1 AAAATGAGAGAAAAGAAAGGG
**
3597180 AAAA-GAGAGAAGGGAAAGGG
1 AAAATGAGAGAAAAGAAAGGG
3597200 AA
1 AA
3597202 GATCTGAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.02
Consensus pattern (21 bp):
AAAATGAGAGAAAAGAAAGGG
Found at i:3597471 original size:24 final size:23
Alignment explanation
Indices: 3597443--3597502 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
3597433 CAACCGAGCT
3597443 GTATTTTTTA-GGGTTTTTGTTTA
1 GTATTTTTTATGGGTTTTT-TTTA
* *
3597466 TTTATTTTTTATGTGTTTTTTTTA
1 -GTATTTTTTATGGGTTTTTTTTA
3597490 GTATTTTTGTATG
1 GTATTTTT-TATG
3597503 ATTAAATTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 7 0.23
24 17 0.55
25 7 0.23
ACGTcount: A:0.13, C:0.00, G:0.17, T:0.70
Consensus pattern (23 bp):
GTATTTTTTATGGGTTTTTTTTA
Found at i:3607055 original size:22 final size:23
Alignment explanation
Indices: 3607029--3607071 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3607019 ATATAGTTTC
*
3607029 TTATCATTATAA-ATGTTATTTA
1 TTATCATTATAATATATTATTTA
3607051 TTATCATTATAATATATTATT
1 TTATCATTATAATATATTATT
3607072 GTAAATTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (23 bp):
TTATCATTATAATATATTATTTA
Found at i:3607243 original size:27 final size:29
Alignment explanation
Indices: 3607213--3607273 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 29
3607203 ATTATAAAAA
3607213 GTTATAAAGAAC-AAAT-ATATTTAATAT
1 GTTATAAAGAACAAAATAATATTTAATAT
3607240 GTTATAAAGAACAAAATAAATATTTAATAT
1 GTTATAAAGAACAAAAT-AATATTTAATAT
3607270 GTTA
1 GTTA
3607274 AGATTTCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 12 0.39
28 4 0.13
30 15 0.48
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.36
Consensus pattern (29 bp):
GTTATAAAGAACAAAATAATATTTAATAT
Found at i:3607674 original size:18 final size:19
Alignment explanation
Indices: 3607651--3607694 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3607641 ATATGAATAA
3607651 AAATAATATAT-ATTTTTT
1 AAATAATATATAATTTTTT
3607669 AAATAATATATAATTTTTT
1 AAATAATATATAATTTTTT
*
3607688 ATATAAT
1 AAATAAT
3607695 TTTTATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AAATAATATATAATTTTTT
Found at i:3608215 original size:13 final size:13
Alignment explanation
Indices: 3608199--3608228 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3608189 AGCCAAACCC
3608199 AAAAAAAAAACAA
1 AAAAAAAAAACAA
*
3608212 AAAAAAAAACCAA
1 AAAAAAAAAACAA
3608225 AAAA
1 AAAA
3608229 TATGCAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:3608216 original size:12 final size:13
Alignment explanation
Indices: 3608193--3608228 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
3608183 TTTTCCAGCC
*
3608193 AAACCCAAAAAAA
1 AAACCAAAAAAAA
3608206 AAA-CAAAAAAAA
1 AAACCAAAAAAAA
3608218 AAACCAAAAAA
1 AAACCAAAAAA
3608229 TATGCAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (13 bp):
AAACCAAAAAAAA
Found at i:3611922 original size:10 final size:10
Alignment explanation
Indices: 3611893--3611922 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3611883 GCTTCTTTTG
3611893 TAAAAAAAAA
1 TAAAAAAAAA
*
3611903 TAAAATAAAA
1 TAAAAAAAAA
3611913 TAAAAAAAAA
1 TAAAAAAAAA
3611923 GGGCTGCGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:3614422 original size:21 final size:21
Alignment explanation
Indices: 3614388--3614436 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
3614378 AGAATGTTAA
*
3614388 AAAAAATGATATCGTAAATATT
1 AAAAAATGAAATCGTAAAT-TT
3614410 AAAAAAT-AAATCGTAAATTT
1 AAAAAATGAAATCGTAAATTT
*
3614430 ACAAAAT
1 AAAAAAT
3614437 TTAGTGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.32
21 10 0.40
22 7 0.28
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (21 bp):
AAAAAATGAAATCGTAAATTT
Found at i:3614480 original size:29 final size:28
Alignment explanation
Indices: 3614424--3614482 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 28
3614414 AATAAATCGT
3614424 AAATTTACAAAATTTAGTGATTAAAATAA
1 AAATTTACAAAATTTAGTGATT-AAATAA
3614453 AAATTTATCTAAAA-TTAGATGATT-AATAA
1 AAATTTA-C-AAAATTTAG-TGATTAAATAA
3614482 A
1 A
3614483 CATTCCGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
29 13 0.48
30 5 0.19
31 9 0.33
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (28 bp):
AAATTTACAAAATTTAGTGATTAAATAA
Found at i:3616073 original size:20 final size:20
Alignment explanation
Indices: 3616044--3616094 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3616034 TGAGACAGAG
* *
3616044 AAATGAACAGAAATTTTCAT
1 AAATGTACAGAAATTATCAT
* *
3616064 CAATGTACAGATATTATCAT
1 AAATGTACAGAAATTATCAT
3616084 AAATGTACAGA
1 AAATGTACAGA
3616095 GAAATTAACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (20 bp):
AAATGTACAGAAATTATCAT
Found at i:3622596 original size:25 final size:25
Alignment explanation
Indices: 3622559--3622617 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
3622549 AAGGATCTCC
*
3622559 AGCTTTTCCGGTGCTGAAAAGATTA
1 AGCTTTTCTGGTGCTGAAAAGATTA
3622584 AGCTTTTCTGGTGCTGAAAAGATTA
1 AGCTTTTCTGGTGCTGAAAAGATTA
3622609 AGCTTTTCT
1 AGCTTTTCT
3622618 TTCCACATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.37
Consensus pattern (25 bp):
AGCTTTTCTGGTGCTGAAAAGATTA
Found at i:3624484 original size:36 final size:36
Alignment explanation
Indices: 3624441--3624534 Score: 91
Period size: 36 Copynumber: 2.6 Consensus size: 36
3624431 ATCTATTTAA
3624441 TTATGTTTTTTTATTTAAACAAACTTAATCAGATAG
1 TTATGTTTTTTTATTTAAACAAACTTAATCAGATAG
** * * ** **
3624477 TTATGTTTTCCTATTCACACATGCTTTTTCAGATAG
1 TTATGTTTTTTTATTTAAACAAACTTAATCAGATAG
3624513 TCATAT-TTTTTTTATTTAAACA
1 T--TATGTTTTTTTATTTAAACA
3624535 TGTTTACTCA
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
36 29 0.66
37 12 0.27
38 3 0.07
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (36 bp):
TTATGTTTTTTTATTTAAACAAACTTAATCAGATAG
Found at i:3624958 original size:14 final size:14
Alignment explanation
Indices: 3624936--3624968 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3624926 TATCTTTATT
*
3624936 TTTAATTTTTAAAA
1 TTTATTTTTTAAAA
3624950 TTTATTTTTTAAAA
1 TTTATTTTTTAAAA
3624964 TTTAT
1 TTTAT
3624969 AATACCGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTATTTTTTAAAA
Found at i:3634527 original size:16 final size:16
Alignment explanation
Indices: 3634508--3634559 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
3634498 TTTTTAGGAC
*
3634508 TTTGGATTTCAGGGAT
1 TTTGGATTTAAGGGAT
* ** * *
3634524 TTTGAATTTTTGAGAG
1 TTTGGATTTAAGGGAT
3634540 TTTGGATTTAAGGGAT
1 TTTGGATTTAAGGGAT
3634556 TTTG
1 TTTG
3634560 AAAATTAAAA
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:0.21, C:0.02, G:0.29, T:0.48
Consensus pattern (16 bp):
TTTGGATTTAAGGGAT
Found at i:3634533 original size:32 final size:32
Alignment explanation
Indices: 3634497--3634561 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
3634487 TTTCCTTAGG
*
3634497 ATTTTT-AGGACTTTGGATTTCAGGGATTTTGA
1 ATTTTTGA-GACTTTGGATTTAAGGGATTTTGA
*
3634529 ATTTTTGAGAGTTTGGATTTAAGGGATTTTGA
1 ATTTTTGAGACTTTGGATTTAAGGGATTTTGA
3634561 A
1 A
3634562 AATTAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 29 0.97
33 1 0.03
ACGTcount: A:0.25, C:0.03, G:0.26, T:0.46
Consensus pattern (32 bp):
ATTTTTGAGACTTTGGATTTAAGGGATTTTGA
Found at i:3635517 original size:13 final size:13
Alignment explanation
Indices: 3635499--3635523 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3635489 TTCTTCTGTT
3635499 CTTTTTTTTTTTA
1 CTTTTTTTTTTTA
3635512 CTTTTTTTTTTT
1 CTTTTTTTTTTT
3635524 TATAAAATAC
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:0.04, C:0.08, G:0.00, T:0.88
Consensus pattern (13 bp):
CTTTTTTTTTTTA
Found at i:3635661 original size:20 final size:21
Alignment explanation
Indices: 3635623--3635700 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
3635613 TATTTTTTCG
* * *
3635623 TTTTTGTTTCGTTTTGTGT-T
1 TTTTTTTTTCGGTTGGTGTAT
3635643 TTTTTTTTTCGGTTGGTGTAGT
1 TTTTTTTTTCGGTTGGTGTA-T
* *
3635665 TTCTGTTTTCGGTTGGTGTAGT
1 TTTTTTTTTCGGTTGGTGTA-T
* *
3635687 TTCTGTTTTCGGTT
1 TTTTTTTTTCGGTT
3635701 TGGGTGCTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.31
22 35 0.69
ACGTcount: A:0.03, C:0.08, G:0.26, T:0.64
Consensus pattern (21 bp):
TTTTTTTTTCGGTTGGTGTAT
Found at i:3635676 original size:22 final size:22
Alignment explanation
Indices: 3635648--3635700 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
3635638 GTGTTTTTTT
3635648 TTTTCGGTTGGTGTAGTTTCTG
1 TTTTCGGTTGGTGTAGTTTCTG
3635670 TTTTCGGTTGGTGTAGTTTCTG
1 TTTTCGGTTGGTGTAGTTTCTG
3635692 TTTTCGGTT
1 TTTTCGGTT
3635701 TGGGTGCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.04, C:0.09, G:0.30, T:0.57
Consensus pattern (22 bp):
TTTTCGGTTGGTGTAGTTTCTG
Found at i:3635801 original size:23 final size:24
Alignment explanation
Indices: 3635768--3635828 Score: 106
Period size: 24 Copynumber: 2.5 Consensus size: 24
3635758 CTGTCTGGTG
3635768 TTGAACGGGGATTCC-AGAGGGAGA
1 TTGAA-GGGGATTCCGAGAGGGAGA
3635792 TTGAAGGGGATTCCGAGAGGGAGA
1 TTGAAGGGGATTCCGAGAGGGAGA
3635816 TTGAAGGGGATTC
1 TTGAAGGGGATTC
3635829 TAGCCAGCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 9 0.25
24 27 0.75
ACGTcount: A:0.28, C:0.10, G:0.43, T:0.20
Consensus pattern (24 bp):
TTGAAGGGGATTCCGAGAGGGAGA
Found at i:3637782 original size:6 final size:6
Alignment explanation
Indices: 3637767--3637804 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
3637757 GACTGTGTTA
*
3637767 TTTT-T TTTTGT TTTTGT TTTTGT TTTT-T TTTTAT TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTT
3637805 TGGTTGGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 9 0.29
6 22 0.71
ACGTcount: A:0.03, C:0.00, G:0.08, T:0.89
Consensus pattern (6 bp):
TTTTGT
Found at i:3637788 original size:12 final size:11
Alignment explanation
Indices: 3637767--3637805 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
3637757 GACTGTGTTA
3637767 TTTTTTTTTGT
1 TTTTTTTTTGT
3637778 TTTTGTTTTTGT
1 TTTT-TTTTTGT
*
3637790 TTTTTTTTTAT
1 TTTTTTTTTGT
3637801 TTTTT
1 TTTTT
3637806 GGTTGGTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.03, C:0.00, G:0.08, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:3637935 original size:23 final size:22
Alignment explanation
Indices: 3637909--3637952 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
3637899 AGAGATCTGT
**
3637909 TGAAGGGGTTTTCAGAGAGAGCC
1 TGAAGGGGGGTTC-GAGAGAGCC
3637932 TGAAGGGGGGTTCGAGAGAGC
1 TGAAGGGGGGTTCGAGAGAGC
3637953 TTCCTCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.25, C:0.11, G:0.45, T:0.18
Consensus pattern (22 bp):
TGAAGGGGGGTTCGAGAGAGCC
Found at i:3639051 original size:16 final size:16
Alignment explanation
Indices: 3639025--3639104 Score: 65
Period size: 16 Copynumber: 4.9 Consensus size: 16
3639015 TCACACGTGT
3639025 CTTTAGGATTTTTAGGA
1 CTTT-GGATTTTTAGGA
*
3639042 CTTTGGA-TTTCATGGA
1 CTTTGGATTTTTA-GGA
* * *
3639058 TTTTGAATTTTTAGGG
1 CTTTGGATTTTTAGGA
*
3639074 GTTTGGA-TTTTATGGA
1 CTTTGGATTTTTA-GGA
*
3639090 TTTTGGATTTTTAGG
1 CTTTGGATTTTTAGG
3639105 GGTTTTAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
15 9 0.18
16 28 0.56
17 13 0.26
ACGTcount: A:0.19, C:0.04, G:0.26, T:0.51
Consensus pattern (16 bp):
CTTTGGATTTTTAGGA
Found at i:3639105 original size:32 final size:32
Alignment explanation
Indices: 3639030--3639109 Score: 124
Period size: 32 Copynumber: 2.5 Consensus size: 32
3639020 CGTGTCTTTA
**
3639030 GGATTTTTAGGACTTTGGATTTCATGGATTTT
1 GGATTTTTAGGGGTTTGGATTTCATGGATTTT
* *
3639062 GAATTTTTAGGGGTTTGGATTTTATGGATTTT
1 GGATTTTTAGGGGTTTGGATTTCATGGATTTT
3639094 GGATTTTTAGGGGTTT
1 GGATTTTTAGGGGTTT
3639110 TAAAAACTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.17, C:0.03, G:0.29, T:0.51
Consensus pattern (32 bp):
GGATTTTTAGGGGTTTGGATTTCATGGATTTT
Found at i:3641065 original size:22 final size:22
Alignment explanation
Indices: 3641034--3641077 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3641024 ATCGCGAATC
* *
3641034 GAAATTATGCCCTGAGGTCTTA
1 GAAATCATGCCCAGAGGTCTTA
3641056 GAAATCATGCCCAGAGGTCTTA
1 GAAATCATGCCCAGAGGTCTTA
3641078 CAGAATTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (22 bp):
GAAATCATGCCCAGAGGTCTTA
Found at i:3641080 original size:109 final size:110
Alignment explanation
Indices: 3640883--3641089 Score: 299
Period size: 109 Copynumber: 1.9 Consensus size: 110
3640873 ATGACGCCGC
* **
3640883 AAGTCAAAAAATAATGAATCGATCAAGATAACATCGCGAATCGATTTTATACCCGGAGGTCTTAC
1 AAGTCAAAAAATAAAGAATCGATCAAGATAACATCGCGAATCGAAATTATACCCGGAGGTCTTAC
***
3640948 AAATCATGCTTGGAGGTCGTACAGAATTGATTGAGATAACACTAT
66 AAATCATGCCCAGAGGTCGTACAGAATTGATTGAGATAACACTAT
** * * *
3640993 AAGTC-AAAAATAAAGAATCGATTGAGATAACATCGCGAATCGAAATTATGCCCTGAGGTCTTAG
1 AAGTCAAAAAATAAAGAATCGATCAAGATAACATCGCGAATCGAAATTATACCCGGAGGTCTTAC
*
3641057 AAATCATGCCCAGAGGTCTTACAGAATTGATTG
66 AAATCATGCCCAGAGGTCGTACAGAATTGATTG
3641090 GAGGTCTTAA
Statistics
Matches: 85, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
109 80 0.94
110 5 0.06
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (110 bp):
AAGTCAAAAAATAAAGAATCGATCAAGATAACATCGCGAATCGAAATTATACCCGGAGGTCTTAC
AAATCATGCCCAGAGGTCGTACAGAATTGATTGAGATAACACTAT
Found at i:3641095 original size:21 final size:22
Alignment explanation
Indices: 3641069--3641129 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
3641059 ATCATGCCCA
*
3641069 GAGGTCTTACAGAATTGAT-TG
1 GAGGTCTTACAGAATTGATCCG
*
3641090 GAGGTCTTA-AAAATCATG-TCCG
1 GAGGTCTTACAGAAT--TGATCCG
3641112 GAGGTCTTACAGAATTGA
1 GAGGTCTTACAGAATTGA
3641130 CTAGGATAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
20 4 0.12
21 12 0.38
22 12 0.38
23 4 0.12
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (22 bp):
GAGGTCTTACAGAATTGATCCG
Found at i:3641116 original size:43 final size:43
Alignment explanation
Indices: 3641047--3641129 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
3641037 ATTATGCCCT
*
3641047 GAGGTCTTAGAAATCATGCCCAGAGGTCTTACAGAATTGATTG
1 GAGGTCTTAAAAATCATGCCCAGAGGTCTTACAGAATTGATTG
* *
3641090 GAGGTCTTAAAAATCATGTCCGGAGGTCTTACAGAATTGA
1 GAGGTCTTAAAAATCATGCCCAGAGGTCTTACAGAATTGA
3641130 CTAGGATAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (43 bp):
GAGGTCTTAAAAATCATGCCCAGAGGTCTTACAGAATTGATTG
Found at i:3641117 original size:22 final size:22
Alignment explanation
Indices: 3641047--3641120 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
3641037 ATTATGCCCT
* * *
3641047 GAGGTCTTAGAAATCATGCCCA
1 GAGGTCTTAAAAATCATGTCCG
* *
3641069 GAGGTCTTACAGAAT--TGAT-TG
1 GAGGTCTTA-AAAATCATG-TCCG
3641090 GAGGTCTTAAAAATCATGTCCG
1 GAGGTCTTAAAAATCATGTCCG
3641112 GAGGTCTTA
1 GAGGTCTTA
3641121 CAGAATTGAC
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
20 4 0.10
21 12 0.30
22 21 0.52
23 3 0.08
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (22 bp):
GAGGTCTTAAAAATCATGTCCG
Found at i:3641213 original size:152 final size:152
Alignment explanation
Indices: 3640937--3641240 Score: 416
Period size: 152 Copynumber: 2.0 Consensus size: 152
3640927 TTTTATACCC
* * * * *
3640937 GGAGGTCTTACAAATCATGCTTGGAGGTCGTACAGAATTGATTGAGATAACACTATAAGTCAAAA
1 GGAGGTCTTAAAAATCATGCTCGGAGGTCGTACAGAATTGATAGAGATAACACCACAAGTCAAAA
* * *
3641002 ATAAAGAATCGATTGAGATAACATCGCGAATCGAAATTATGCCCTGAGGTCTTAGAAATCATGCC
66 ATAAAGAATCGATCGAGATAACACCGCGAATCGAAATTATGCCCGGAGGTCTTAGAAATCATGCC
3641067 CAGAGGTCTTACAGAATTGATT
131 CAGAGGTCTTACAGAATTGATT
* *
3641089 GGAGGTCTTAAAAATCATG-TCCGGAGGTCTTACAGAATTGACTAG-GATAACACCGCAAGTCAA
1 GGAGGTCTTAAAAATCATGCT-CGGAGGTCGTACAGAATTGA-TAGAGATAACACCACAAGTCAA
* * * * *
3641152 AATTATAGAATTGATCGGGATAACACCGCGAATC-AAATTTATGCTCGGAGGTCTTAGAAATCAT
64 AAATAAAGAATCGATCGAGATAACACCGCGAATCGAAA-TTATGCCCGGAGGTCTTAGAAATCAT
*
3641216 GCCCGGAGGTCTTACAGAATTGATT
128 GCCCAGAGGTCTTACAGAATTGATT
3641241 AGAATAACAC
Statistics
Matches: 133, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
151 4 0.03
152 127 0.95
153 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (152 bp):
GGAGGTCTTAAAAATCATGCTCGGAGGTCGTACAGAATTGATAGAGATAACACCACAAGTCAAAA
ATAAAGAATCGATCGAGATAACACCGCGAATCGAAATTATGCCCGGAGGTCTTAGAAATCATGCC
CAGAGGTCTTACAGAATTGATT
Found at i:3641222 original size:109 final size:110
Alignment explanation
Indices: 3641089--3641345 Score: 392
Period size: 110 Copynumber: 2.3 Consensus size: 110
3641079 AGAATTGATT
* * *
3641089 GGAGGTCTTAAAAATCATGTCCGGAGGTCTTACAGAATTGACTAGGATAACACCGCAAGTC-AAA
1 GGAGGTCTTAGAAATCATGTCCGGAGGTCTTACAGAATTGACTAGAATAACACCACAAGTCGAAA
* * *
3641153 -ATTATAGAATTGATCGGGATAACACCGCGAATCAAATTTATGCTC
66 GA-TAAAGAATCGATCGGGATAACACCGCGAATCAAATTTATGCCC
* * *
3641198 GGAGGTCTTAGAAATCATGCCCGGAGGTCTTACAGAATTGATTAGAATAACACTACAAGTCGAAA
1 GGAGGTCTTAGAAATCATGTCCGGAGGTCTTACAGAATTGACTAGAATAACACCACAAGTCGAAA
*
3641263 GATAAAGAATCGATCGGGATAACACCGCGAATCGAATTTATGCCC
66 GATAAAGAATCGATCGGGATAACACCGCGAATCAAATTTATGCCC
*
3641308 GGAGGTCTTAGAAATCATGTTCGGAGGTCTTACAGAAT
1 GGAGGTCTTAGAAATCATGTCCGGAGGTCTTACAGAAT
3641346 CATATCCGGA
Statistics
Matches: 134, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
109 55 0.41
110 78 0.58
111 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (110 bp):
GGAGGTCTTAGAAATCATGTCCGGAGGTCTTACAGAATTGACTAGAATAACACCACAAGTCGAAA
GATAAAGAATCGATCGGGATAACACCGCGAATCAAATTTATGCCC
Found at i:3641344 original size:262 final size:258
Alignment explanation
Indices: 3640869--3641692 Score: 886
Period size: 242 Copynumber: 3.3 Consensus size: 258
3640859 ACAAAACGAT
* * * * ** * * *
3640869 TAGGATGACGCCGCAAGTCAAAA-AATAATGAATCGATCAAGATAACATCGCGAATCGATTTTAT
1 TAGGATAACACCGCAAGTCAAAATTAT-A-GAATTGATCGGGATAACACCGCGAATCAAATTTAT
* * ** * *
3640933 ACCCGGAGGTCTTACAAATCATGCTTGGAGGTCGTACAGAATTGATT-GAGATAACACTATAAGT
64 GCCCGGAGGTCTTAGAAATCATGCCCGGAGGTCTTACAGAATTGATTAGA-ATAACACTACAAGT
* *
3640997 C-AAAAATAAAGAATCGATTGAGATAACATCGCGAATCGAAATTATGCCCTGAGGTCTTAGAAAT
128 CGAAAGATAAAGAATCGATCGAGATAACA-CGCGAATCG-AATTATGCCC-GAGGTCTTAGAAAT
** *
3641061 CATGCCCAGAGGTCTTACAGAATTGATTGGAGGTCTTAAAAATCATGTCCGGAGGTCTTACAGAA
190 CATGTTCGGAGGTCTTACAGAATTGA-TGGAGGTCTTAAAAATCATGTCCGGAGGTCTTACAGAA
3641126 TTGAC
254 TTGAC
3641131 TAGGATAACACCGCAAGTCAAAATTATAGAATTGATCGGGATAACACCGCGAATCAAATTTATGC
1 TAGGATAACACCGCAAGTCAAAATTATAGAATTGATCGGGATAACACCGCGAATCAAATTTATGC
*
3641196 TCGGAGGTCTTAGAAATCATGCCCGGAGGTCTTACAGAATTGATTAGAATAACACTACAAGTCGA
66 CCGGAGGTCTTAGAAATCATGCCCGGAGGTCTTACAGAATTGATTAGAATAACACTACAAGTCGA
*
3641261 AAGATAAAGAATCGATCGGGATAACACCGCGAATCGAATTTATGCCCGGAGGTCTTAGAAATCAT
131 AAGATAAAGAATCGATCGAGATAACA-CGCGAATCGAA-TTATGCCC-GAGGTCTTAGAAATCAT
3641326 GTTCGGAGGTCTTAC---A--GA---A--TC------AT-A--TCCGGAGGTCTTACAGAATTGA
193 GTTCGGAGGTCTTACAGAATTGATGGAGGTCTTAAAAATCATGTCCGGAGGTCTTACAGAATTGA
3641372 C
258 C
* * * *
3641373 TGGAATAACACCGTAAGTCAAAATTATAGAATTGATCGGGATAACACCGCGAATCAATTTTATGC
1 TAGGATAACACCGCAAGTCAAAATTATAGAATTGATCGGGATAACACCGCGAATCAAATTTATGC
*
3641438 CCGGAGGTCTTAGAAATCATGCCC-GAGGTCTTACAGAATTGATTAGAATAACACCACAAGTCGA
66 CCGGAGGTCTTAGAAATCATGCCCGGAGGTCTTACAGAATTGATTAGAATAACACTACAAGTCGA
* *
3641502 AAGATAAAGAATCGATCGAAATAACAC-CG---C-AA--AT---CGA---ATT-----T-ATGTT
131 AAGATAAAGAATCGATCGAGATAACACGCGAATCGAATTATGCCCGAGGTCTTAGAAATCATGTT
* *
3641548 CGGAGATCTTACAGAATTGACTGGAGGTCTTAAAAATCATGCCCGGAGGTCTTACAGAATTGAC
196 CGGAGGTCTTACAGAATTGA-TGGAGGTCTTAAAAATCATGTCCGGAGGTCTTACAGAATTGAC
* * * * * * *
3641612 TGGGATAACACCGTAAGTCAAAAAATAAAAAATTGATCGGGATAACACCGTGAATTAAATTTATG
1 TAGGATAACACCGCAAGTC-AAAATTATAGAATTGATCGGGATAACACCGCGAATCAAATTTATG
**
3641677 CTTGGAGGTCTTAGAA
65 CCCGGAGGTCTTAGAA
3641693 TTCTCAAAAT
Statistics
Matches: 493, Mismatches: 44, Indels: 72
0.81 0.07 0.12
Matches are distributed among these distances:
219 16 0.03
220 1 0.00
222 1 0.00
224 2 0.00
225 2 0.00
228 3 0.01
229 1 0.00
230 2 0.00
232 2 0.00
235 2 0.00
236 3 0.01
237 1 0.00
239 42 0.09
240 54 0.11
241 63 0.13
242 107 0.22
244 1 0.00
245 2 0.00
251 2 0.00
253 1 0.00
257 2 0.00
259 1 0.00
261 86 0.17
262 94 0.19
263 2 0.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (258 bp):
TAGGATAACACCGCAAGTCAAAATTATAGAATTGATCGGGATAACACCGCGAATCAAATTTATGC
CCGGAGGTCTTAGAAATCATGCCCGGAGGTCTTACAGAATTGATTAGAATAACACTACAAGTCGA
AAGATAAAGAATCGATCGAGATAACACGCGAATCGAATTATGCCCGAGGTCTTAGAAATCATGTT
CGGAGGTCTTACAGAATTGATGGAGGTCTTAAAAATCATGTCCGGAGGTCTTACAGAATTGAC
Found at i:3641355 original size:23 final size:23
Alignment explanation
Indices: 3641306--3641368 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
3641296 GAATTTATGC
* *
3641306 CCGGAGGTCTTAGA-AATCATGT
1 CCGGAGGTCTTACAGAATCATAT
*
3641328 TCGGAGGTCTTACAGAATCATAT
1 CCGGAGGTCTTACAGAATCATAT
3641351 CCGGAGGTCTTACAGAAT
1 CCGGAGGTCTTACAGAAT
3641369 TGACTGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 12 0.33
23 24 0.67
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (23 bp):
CCGGAGGTCTTACAGAATCATAT
Found at i:3641435 original size:132 final size:132
Alignment explanation
Indices: 3641196--3641476 Score: 399
Period size: 132 Copynumber: 2.1 Consensus size: 132
3641186 AAATTTATGC
* * * *
3641196 TCGGAGGTCTTAGA-AATCATGCCCGGAGGTCTTACAGAATTGATTAGAATAACACTACAAGTCG
1 TCGGAGGTCTTACAGAATCATACCCGGAGGTCTTACAGAATTGACTAGAATAACACCACAAGTCG
3641260 AAAGATAAAGAATCGATCGGGATAACACCGCGAATCGAATTTATGCCCGGAGGTCTTAGAAATCA
66 AAAGATAAAGAATCGATCGGGATAACACCGCGAATCGAATTTATGCCCGGAGGTCTTAGAAATCA
3641325 TG
131 TG
* * **
3641327 TTCGGAGGTCTTACAGAATCATATCCGGAGGTCTTACAGAATTGACTGGAATAACACCGTAAGTC
1 -TCGGAGGTCTTACAGAATCATACCCGGAGGTCTTACAGAATTGACTAGAATAACACCACAAGTC
* *
3641392 -AAA-ATTATAGAATTGATCGGGATAACACCGCGAATC-AATTTTATGCCCGGAGGTCTTAGAAA
65 GAAAGA-TAAAGAATCGATCGGGATAACACCGCGAATCGAA-TTTATGCCCGGAGGTCTTAGAAA
3641454 TCATG
128 TCATG
* *
3641459 CCCGAGGTCTTACAGAAT
1 TCGGAGGTCTTACAGAAT
3641477 TGATTAGAAT
Statistics
Matches: 134, Mismatches: 12, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
131 19 0.14
132 73 0.54
133 42 0.31
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.25
Consensus pattern (132 bp):
TCGGAGGTCTTACAGAATCATACCCGGAGGTCTTACAGAATTGACTAGAATAACACCACAAGTCG
AAAGATAAAGAATCGATCGGGATAACACCGCGAATCGAATTTATGCCCGGAGGTCTTAGAAATCA
TG
Found at i:3641528 original size:241 final size:240
Alignment explanation
Indices: 3641062--3641692 Score: 894
Period size: 242 Copynumber: 2.6 Consensus size: 240
3641052 CTTAGAAATC
* * * **
3641062 ATGCCCAGAGGTCTTACAGAATTGATTGGAGGTCTTAAAAATCATGTCCGGAGGTCTTACAGAAT
1 ATGCCCGGAGATCTTACAGAATTGACTGGAGGTCTTAAAAATCATACCCGGAGGTCTTACAGAAT
* * * *
3641127 TGACTAGG-ATAACACCGCAAGTC-AAAATTATAGAATTGATCGGGATAACACCGCGAATCAAAT
66 TGACT-GGAATAACACCGTAAGTCAAAAAATAAAAAATTGATCGGGATAACACCGCGAATCAAAT
* *
3641190 TTATGCTCGGAGGTCTTAGAAATCATGCCCGGAGGTCTTACAGAATTGATTAGAATAACACTACA
130 TTATGCCCGGAGGTCTTAGAAATCATGCCC-GAGGTCTTACAGAATTGATTAGAATAACACCACA
** *
3641255 AGTCGAAAGATAAAGAATCGATCGGGATAACACCGCGAATCGAATTT
194 AGTCGAAAGATAAAGAATCGATCGAAATAACACCGCAAATCGAATTT
* * * * *
3641302 ATGCCCGGAGGTCTTAGA-AATCATG-TTCGGAGGTCTTACAGAATCATATCCGGAGGTCTTACA
1 ATGCCCGGAGATCTTACAGAAT--TGACT-GGAGGTCTTA-AAAATCATACCCGGAGGTCTTACA
* * *
3641365 GAATTGACTGGAATAACACCGTAAGTC-AAAATTATAGAATTGATCGGGATAACACCGCGAATCA
62 GAATTGACTGGAATAACACCGTAAGTCAAAAAATAAAAAATTGATCGGGATAACACCGCGAATCA
*
3641429 ATTTTATGCCCGGAGGTCTTAGAAATCATGCCCGAGGTCTTACAGAATTGATTAGAATAACACCA
127 AATTTATGCCCGGAGGTCTTAGAAATCATGCCCGAGGTCTTACAGAATTGATTAGAATAACACCA
3641494 CAAGTCGAAAGATAAAGAATCGATCGAAATAACACCGCAAATCGAATTT
192 CAAGTCGAAAGATAAAGAATCGATCGAAATAACACCGCAAATCGAATTT
** *
3641543 ATGTTCGGAGATCTTACAGAATTGACTGGAGGTCTTAAAAATCATGCCCGGAGGTCTTACAGAAT
1 ATGCCCGGAGATCTTACAGAATTGACTGGAGGTCTTAAAAATCATACCCGGAGGTCTTACAGAAT
* * *
3641608 TGACTGGGATAACACCGTAAGTCAAAAAATAAAAAATTGATCGGGATAACACCGTGAATTAAATT
66 TGACTGGAATAACACCGTAAGTCAAAAAATAAAAAATTGATCGGGATAACACCGCGAATCAAATT
**
3641673 TATGCTTGGAGGTCTTAGAA
131 TATGCCCGGAGGTCTTAGAA
3641693 TTCTCAAAAT
Statistics
Matches: 355, Mismatches: 28, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
239 50 0.14
240 83 0.23
241 106 0.30
242 116 0.33
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (240 bp):
ATGCCCGGAGATCTTACAGAATTGACTGGAGGTCTTAAAAATCATACCCGGAGGTCTTACAGAAT
TGACTGGAATAACACCGTAAGTCAAAAAATAAAAAATTGATCGGGATAACACCGCGAATCAAATT
TATGCCCGGAGGTCTTAGAAATCATGCCCGAGGTCTTACAGAATTGATTAGAATAACACCACAAG
TCGAAAGATAAAGAATCGATCGAAATAACACCGCAAATCGAATTT
Found at i:3641552 original size:109 final size:110
Alignment explanation
Indices: 3641324--3641564 Score: 292
Period size: 109 Copynumber: 2.2 Consensus size: 110
3641314 CTTAGAAATC
* * * **
3641324 ATGTTCGGAGGTCTTACAGAATCATATCCGGAGGTCTTACAGAATTGACTGGAATAACACCGTAA
1 ATGTTCGGAGGTCTTACAGAATCATAGCCCGAGGTCTTACAGAATTGACTAGAATAACACCACAA
* * ** *
3641389 GTCAAAATTATAGAATTGATCGGGATAACACCGCGAATCAATTTT
66 GTCAAAATTAAAGAATCGATCGAAATAACACCGCAAATCAATTTT
** * *
3641434 ATGCCCGGAGGTCTTAGA-AATCAT-GCCCGAGGTCTTACAGAATTGATTAGAATAACACCACAA
1 ATGTTCGGAGGTCTTACAGAATCATAGCCCGAGGTCTTACAGAATTGACTAGAATAACACCACAA
3641497 GTCGAAAGA-TAAAGAATCGATCGAAATAACACCGCAAATCGAA-TTT
66 GTC-AAA-ATTAAAGAATCGATCGAAATAACACCGCAAATC-AATTTT
*
3641543 ATGTTCGGAGATCTTACAGAAT
1 ATGTTCGGAGGTCTTACAGAAT
3641565 TGACTGGAGG
Statistics
Matches: 109, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
108 36 0.33
109 52 0.48
110 21 0.19
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (110 bp):
ATGTTCGGAGGTCTTACAGAATCATAGCCCGAGGTCTTACAGAATTGACTAGAATAACACCACAA
GTCAAAATTAAAGAATCGATCGAAATAACACCGCAAATCAATTTT
Found at i:3641578 original size:21 final size:21
Alignment explanation
Indices: 3641549--3641614 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
3641539 ATTTATGTTC
*
3641549 GGAGATCTTACAGAATTGACT
1 GGAGGTCTTACAGAATTGACT
* * *
3641570 GGAGGTCTTA-AAAATCATGCCC
1 GGAGGTCTTACAGAAT--TGACT
3641592 GGAGGTCTTACAGAATTGACT
1 GGAGGTCTTACAGAATTGACT
3641613 GG
1 GG
3641615 GATAACACCG
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
20 4 0.11
21 14 0.40
22 13 0.37
23 4 0.11
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (21 bp):
GGAGGTCTTACAGAATTGACT
Found at i:3641673 original size:131 final size:130
Alignment explanation
Indices: 3641440--3641689 Score: 322
Period size: 131 Copynumber: 1.9 Consensus size: 130
3641430 TTTTATGCCC
* * * *
3641440 GGAGGTCTTAGAAATCATGCCCGAGGTCTTACAGAATTGATTAGAATAACACCACAAGTCGAAAG
1 GGAGGTCTTAAAAATCATGCCCGAGGTCTTACAGAATTGACTAGAATAACACCACAAGTCAAAAA
* *
3641505 ATAAAGAATCGATCGAAATAACACCGCAAATCGAATTTATG-TTCGGAGATCTTACAGAATTGAC
66 ATAAAAAATCGATCGAAATAACACCGCAAATCAAATTTATGCTT-GGAGATCTTACAGAATTGAC
3641569 T
130 T
* * **
3641570 GGAGGTCTTAAAAATCATGCCCGGAGGTCTTACAGAATTGACTGGGATAACACCGTAAGTCAAAA
1 GGAGGTCTTAAAAATCATGCCC-GAGGTCTTACAGAATTGACTAGAATAACACCACAAGTCAAAA
* ** ** * *
3641635 AATAAAAAATTGATCGGGATAACACCGTGAATTAAATTTATGCTTGGAGGTCTTA
65 AATAAAAAATCGATCGAAATAACACCGCAAATCAAATTTATGCTTGGAGATCTTA
3641690 GAATTCTCAA
Statistics
Matches: 101, Mismatches: 17, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
130 21 0.21
131 78 0.77
132 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (130 bp):
GGAGGTCTTAAAAATCATGCCCGAGGTCTTACAGAATTGACTAGAATAACACCACAAGTCAAAAA
ATAAAAAATCGATCGAAATAACACCGCAAATCAAATTTATGCTTGGAGATCTTACAGAATTGACT
Found at i:3641905 original size:121 final size:121
Alignment explanation
Indices: 3641680--3642000 Score: 466
Period size: 121 Copynumber: 2.7 Consensus size: 121
3641670 ATTTATGCTT
* *
3641680 GGAGGTCTTA-GAATTCTCAAAATCTTTGAATGCTCCTCATAATCAGAGGCAATGAAACTTTAAA
1 GGAGGTCTTACAAATT-TCAAAATCTTTGAATGCTCCTCATAATCAGAGGCGATGAAACTTTAAA
* *
3641744 ATTTAAAAATCTTTTAATCTTAAAATTCGTGCACAAAGGCTTCTAGAGATTATGCCC
65 ATTTAAAAATCTTTTAATCTTAAAAGTCATGCACAAAGGCTTCTAGAGATTATGCCC
* *
3641801 GGAGGTCTTACAAATTTAAAAATCTTTGAATGCTTCTCATAATCAGAGGCGATGAAACTTTAAAA
1 GGAGGTCTTACAAATTTCAAAATCTTTGAATGCTCCTCATAATCAGAGGCGATGAAACTTTAAAA
* * ** * *
3641866 TTTGAAAATCTTTTAATCTTGAAAGTCATGCGTAGAGGCTTTTAGAGATTATGCCC
66 TTTAAAAATCTTTTAATCTTAAAAGTCATGCACAAAGGCTTCTAGAGATTATGCCC
* *
3641922 GGAGGTCTTACAAATCTCAAAATCTTTAAATGCTCCTCATAATC-GAGGCGATGAAACTTTAAAA
1 GGAGGTCTTACAAATTTCAAAATCTTTGAATGCTCCTCATAATCAGAGGCGATGAAACTTT-AAA
* *
3641986 ATCTAAAAATTTTTT
65 ATTTAAAAATCTTTT
3642001 TTTTGAAAAT
Statistics
Matches: 179, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
120 16 0.09
121 159 0.89
122 4 0.02
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (121 bp):
GGAGGTCTTACAAATTTCAAAATCTTTGAATGCTCCTCATAATCAGAGGCGATGAAACTTTAAAA
TTTAAAAATCTTTTAATCTTAAAAGTCATGCACAAAGGCTTCTAGAGATTATGCCC
Found at i:3642614 original size:33 final size:33
Alignment explanation
Indices: 3642510--3643588 Score: 1100
Period size: 33 Copynumber: 32.8 Consensus size: 33
3642500 AAAACTTCTT
* * *
3642510 TTGA-GGCCAAATAAACTTGGCTTAAAT-TTTA
1 TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
* * * * *
3642541 TTAAAGGTCAGCTAAACTGGGCTTAAAT-ATCA
1 TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
*
3642573 TTGATGGCCAGATAACCTGGGCTTAAATCTTCA
1 TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
* * * *
3642606 TTGTTGGCCAGATAAACTGAGTTTAAAACTTCA
1 TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
* * * *
3642639 TTGTTGGCCAGATAAATTGGGCTTAAAACCTCA
1 TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
** *
3642672 TTGATGGCCAGATAAGTTGGGCTTAAAGCTTCA
1 TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
* * * * *
3642705 TTAATGACCAGATAAACTGGGTTTAAAACCTCA
1 TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
* *
3642738 TTAATGGCCAGATAAACTGGGCTTAAAGCTTCA
1 TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
* *
3642771 TTAATAGCCAGATAAACTGGGCTTAAAGTC-TCA
1 TTGATGGCCAGATAAACTGGGCTTAAA-TCTTCA
* *
3642804 TTAATGGACAGATAAACTGGGCTTAAAAT-TTCA
1 TTGATGGCCAGATAAACTGGGCTT-AAATCTTCA
* * * *
3642837 TTAATGGTCAGATAAACTGGGTTTAAAACTTCA
1 TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
* *
3642870 TTAATGGCCAGATAAACTGGGCTTAAATCTTTA
1 TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
* * *
3642903 TTTGA-GGCCAAATAAACTGGGCTTAAAGCCTCA
1 -TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
* * *
3642936 TTGATAGCCAGATAAGCTGGGCTTAAAGCTTCA
1 TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
* *
3642969 TTAATGGCCAGATAAACT-GGCTTAAAGT-ATCA
1 TTGATGGCCAGATAAACTGGGCTTAAA-TCTTCA
* *
3643001 TTGA-GAGCTAGATAAATTGGGCTTAAATCTTCA
1 TTGATG-GCCAGATAAACTGGGCTTAAATCTTCA
* * *
3643034 TTTGA-GGCCAGATAAACTGAGCTTAAAGCCTCA
1 -TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
* *
3643067 TTGATGGCCAGATAAGCTGGGCTTAAAGCTTCA
1 TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
* * *
3643100 TTAATGGCCAAATAAACTGAGCTTAAAGT-TTCA
1 TTGATGGCCAGATAAACTGGGCTTAAA-TCTTCA
* *
3643133 TTGA-GAGCCAGATAAATTGGGCTTAAATTTTCA
1 TTGATG-GCCAGATAAACTGGGCTTAAATCTTCA
* *
3643166 TTTGA-GGCCAGATAAACTGGGCTTAAAGCCTCA
1 -TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
* * *
3643199 TTGATGGTCAAATAAACTGGGCTTAAAGCTTCA
1 TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
*
3643232 TTAATGGCCAGATAAACTGGGCTTAAAGT-TTCA
1 TTGATGGCCAGATAAACTGGGCTTAAA-TCTTCA
* * * *
3643265 TTGA-GAGCCAAATAAATTGGGTTTAAATTTTCA
1 TTGATG-GCCAGATAAACTGGGCTTAAATCTTCA
* *
3643298 TTTGA-GGCCAGATAAACTGGGCTTAAAGCCTCA
1 -TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
* * *
3643331 TTGATGACCAGATAAGCTGGGCTTAAAGCTTCA
1 TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
* * *
3643364 TTAATGGCCAGATAAACTGGACTTAAATTTTCA
1 TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
* * *
3643397 TTGA-GAGCCAGATAAATTAGGCTTAAATTTTCA
1 TTGATG-GCCAGATAAACTGGGCTTAAATCTTCA
* * * *
3643430 TTTACGGCCAGATAAACTGGGCTTAAAGCCTCA
1 TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
*
3643463 TTGATGGCCAGATAAACTGGGCTTAAAGCTTCA
1 TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
*
3643496 TTAATGGCCAGATAAACTGGGCTTAAAGT-TTCA
1 TTGATGGCCAGATAAACTGGGCTTAAA-TCTTCA
* *
3643529 TTGA-GAGCCAGATAAATTGGGCTTAAATCTTTA
1 TTGATG-GCCAGATAAACTGGGCTTAAATCTTCA
3643562 TTTGA-GGCCAGATAAACTGGGCTTAAA
1 -TTGATGGCCAGATAAACTGGGCTTAAA
3643589 GCTTTTTTTT
Statistics
Matches: 886, Mismatches: 132, Indels: 58
0.82 0.12 0.05
Matches are distributed among these distances:
31 4 0.00
32 95 0.11
33 759 0.86
34 28 0.03
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (33 bp):
TTGATGGCCAGATAAACTGGGCTTAAATCTTCA
Found at i:3642739 original size:132 final size:132
Alignment explanation
Indices: 3642499--3643590 Score: 1434
Period size: 132 Copynumber: 8.3 Consensus size: 132
3642489 TTTGAAACTC
* * * * ** * * * * * *
3642499 TAAAACTTCTTTTGAGGCCAAATAAACTTGGCTTAAA-TTTTATTAAAGGTCAGCTAAACTGGGC
1 TAAATCTTCATTTGAGGCCAGATAAACTGGGCTTAAAGCCTCATTGATGGCCAGATAAGCTGGGC
* * * *
3642563 TTAAA--TATCATTGATGGCCAGATAACCTGGGCTTAAA-TCTTCATTGTTG-GCCAGATAAACT
66 TTAAAGCT-TCATTAATGGCCAGATAAACTGGGCTTAAAGT-TTCATTG-AGAGCCAGATAAATT
* *
3642624 GAGTT
128 GGGCT
* * * * *
3642629 TAAAACTTCA-TTGTTGGCCAGATAAATTGGGCTTAAAACCTCATTGATGGCCAGATAAGTTGGG
1 TAAATCTTCATTTG-AGGCCAGATAAACTGGGCTTAAAGCCTCATTGATGGCCAGATAAGCTGGG
* * *** * *
3642693 CTTAAAGCTTCATTAATGACCAGATAAACTGGGTTTAAAACCTCATTAATG-GCCAGATAAACTG
65 CTTAAAGCTTCATTAATGGCCAGATAAACTGGGCTTAAAGTTTCATTGA-GAGCCAGATAAATTG
3642757 GGCT
129 GGCT
* * * * *
3642761 TAAAGCTTCATTAAT-A-GCCAGATAAACTGGGCTTAAAGTCTCATTAATGGACAGATAAACTGG
1 TAAATCTTCATT--TGAGGCCAGATAAACTGGGCTTAAAGCCTCATTGATGGCCAGATAAGCTGG
** * * ** * *
3642824 GCTTAAAATTTCATTAATGGTCAGATAAACTGGGTTTAAAACTTCATTAATG-GCCAGATAAACT
64 GCTTAAAGCTTCATTAATGGCCAGATAAACTGGGCTTAAAGTTTCATTGA-GAGCCAGATAAATT
3642888 GGGCT
128 GGGCT
* * *
3642893 TAAATCTTTATTTGAGGCCAAATAAACTGGGCTTAAAGCCTCATTGATAGCCAGATAAGCTGGGC
1 TAAATCTTCATTTGAGGCCAGATAAACTGGGCTTAAAGCCTCATTGATGGCCAGATAAGCTGGGC
* *
3642958 TTAAAGCTTCATTAATGGCCAGATAAACT-GGCTTAAAGTATCATTGAGAGCTAGATAAATTGGG
66 TTAAAGCTTCATTAATGGCCAGATAAACTGGGCTTAAAGTTTCATTGAGAGCCAGATAAATTGGG
3643022 CT
131 CT
*
3643024 TAAATCTTCATTTGAGGCCAGATAAACTGAGCTTAAAGCCTCATTGATGGCCAGATAAGCTGGGC
1 TAAATCTTCATTTGAGGCCAGATAAACTGGGCTTAAAGCCTCATTGATGGCCAGATAAGCTGGGC
* *
3643089 TTAAAGCTTCATTAATGGCCAAATAAACTGAGCTTAAAGTTTCATTGAGAGCCAGATAAATTGGG
66 TTAAAGCTTCATTAATGGCCAGATAAACTGGGCTTAAAGTTTCATTGAGAGCCAGATAAATTGGG
3643154 CT
131 CT
* * * *
3643156 TAAATTTTCATTTGAGGCCAGATAAACTGGGCTTAAAGCCTCATTGATGGTCAAATAAACTGGGC
1 TAAATCTTCATTTGAGGCCAGATAAACTGGGCTTAAAGCCTCATTGATGGCCAGATAAGCTGGGC
*
3643221 TTAAAGCTTCATTAATGGCCAGATAAACTGGGCTTAAAGTTTCATTGAGAGCCAAATAAATTGGG
66 TTAAAGCTTCATTAATGGCCAGATAAACTGGGCTTAAAGTTTCATTGAGAGCCAGATAAATTGGG
*
3643286 TT
131 CT
* *
3643288 TAAATTTTCATTTGAGGCCAGATAAACTGGGCTTAAAGCCTCATTGATGACCAGATAAGCTGGGC
1 TAAATCTTCATTTGAGGCCAGATAAACTGGGCTTAAAGCCTCATTGATGGCCAGATAAGCTGGGC
* * *
3643353 TTAAAGCTTCATTAATGGCCAGATAAACTGGACTTAAATTTTCATTGAGAGCCAGATAAATTAGG
66 TTAAAGCTTCATTAATGGCCAGATAAACTGGGCTTAAAGTTTCATTGAGAGCCAGATAAATTGGG
3643418 CT
131 CT
* *
3643420 TAAATTTTCATTT-ACGGCCAGATAAACTGGGCTTAAAGCCTCATTGATGGCCAGATAAACTGGG
1 TAAATCTTCATTTGA-GGCCAGATAAACTGGGCTTAAAGCCTCATTGATGGCCAGATAAGCTGGG
3643484 CTTAAAGCTTCATTAATGGCCAGATAAACTGGGCTTAAAGTTTCATTGAGAGCCAGATAAATTGG
65 CTTAAAGCTTCATTAATGGCCAGATAAACTGGGCTTAAAGTTTCATTGAGAGCCAGATAAATTGG
3643549 GCT
130 GCT
*
3643552 TAAATCTTTATTTGAGGCCAGATAAACTGGGCTTAAAGC
1 TAAATCTTCATTTGAGGCCAGATAAACTGGGCTTAAAGC
3643591 TTTTTTTTCT
Statistics
Matches: 858, Mismatches: 89, Indels: 28
0.88 0.09 0.03
Matches are distributed among these distances:
129 3 0.00
130 30 0.03
131 142 0.17
132 679 0.79
133 3 0.00
135 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (132 bp):
TAAATCTTCATTTGAGGCCAGATAAACTGGGCTTAAAGCCTCATTGATGGCCAGATAAGCTGGGC
TTAAAGCTTCATTAATGGCCAGATAAACTGGGCTTAAAGTTTCATTGAGAGCCAGATAAATTGGG
CT
Found at i:3645597 original size:13 final size:14
Alignment explanation
Indices: 3645579--3645609 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3645569 CAAAACTTTA
3645579 TTTTTT-CTTTTTT
1 TTTTTTACTTTTTT
3645592 TTTTTTACTTTTTT
1 TTTTTTACTTTTTT
3645606 TTTT
1 TTTT
3645610 CAAGATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.03, C:0.06, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTACTTTTTT
Found at i:3653810 original size:16 final size:17
Alignment explanation
Indices: 3653779--3653821 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
3653769 TTTAATTTTT
*
3653779 ATTTTTAGCAACTTTCC
1 ATTTTTAGTAACTTTCC
*
3653796 ATTTTTAGTAA-TTTCT
1 ATTTTTAGTAACTTTCC
*
3653812 ATATTTAGTA
1 ATTTTTAGTA
3653822 TGCTTTAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.28, C:0.12, G:0.07, T:0.53
Consensus pattern (17 bp):
ATTTTTAGTAACTTTCC
Found at i:3662166 original size:20 final size:20
Alignment explanation
Indices: 3662141--3662178 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3662131 TTGACAAAAA
*
3662141 TTTTTGTTGATAATAATAAT
1 TTTTTGTCGATAATAATAAT
*
3662161 TTTTTGTCGGTAATAATA
1 TTTTTGTCGATAATAATA
3662179 TCATCGACGG
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:0.32, C:0.03, G:0.13, T:0.53
Consensus pattern (20 bp):
TTTTTGTCGATAATAATAAT
Found at i:3684184 original size:18 final size:18
Alignment explanation
Indices: 3684145--3684185 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3684135 ATATGTAATC
* *
3684145 TTAAATTAATTTGACATA
1 TTAAATTAATTTAAAATA
*
3684163 TTAAATTAATTTAAAATT
1 TTAAATTAATTTAAAATA
3684181 TTAAA
1 TTAAA
3684186 ATATTCTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
TTAAATTAATTTAAAATA
Found at i:3685180 original size:21 final size:22
Alignment explanation
Indices: 3685149--3685189 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
3685139 GCCACCAATC
3685149 CACCCTCACACCCAATAGTCTT
1 CACCCTCACACCCAATAGTCTT
3685171 CACCC-CACACCCAATAGTC
1 CACCCTCACACCCAATAGTC
3685190 CATTTTCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.29, C:0.49, G:0.05, T:0.17
Consensus pattern (22 bp):
CACCCTCACACCCAATAGTCTT
Found at i:3686746 original size:18 final size:15
Alignment explanation
Indices: 3686704--3686750 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
3686694 TTTATTTTTC
3686704 TAAATAAAAAATAATA
1 TAAATAAAAAA-AATA
3686720 TAAATAAAAAAAATA
1 TAAATAAAAAAAATA
3686735 TGAAAATGAAAAAAAA
1 T--AAAT-AAAAAAAA
3686751 GAAATCAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.18
16 11 0.39
17 4 0.14
18 8 0.29
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (15 bp):
TAAATAAAAAAAATA
Found at i:3695194 original size:12 final size:12
Alignment explanation
Indices: 3695177--3695204 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3695167 CACATATTTA
3695177 TCATTTTATCAT
1 TCATTTTATCAT
3695189 TCATTTTATCAT
1 TCATTTTATCAT
3695201 TCAT
1 TCAT
3695205 ATAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.18, G:0.00, T:0.57
Consensus pattern (12 bp):
TCATTTTATCAT
Found at i:3701920 original size:49 final size:49
Alignment explanation
Indices: 3701848--3701947 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
3701838 TCGAGGTATT
*
3701848 TTGTTATATCCTAATCATCTTATCAACATTTTGACCGTCAAGTCAACAC
1 TTGTTATATCCTAATCATCTTATCAACATTTTGACCGTCAAGACAACAC
*
3701897 TTGTTATATCTTAATCATCTTATCAACATTTTGACCGTCAAGACAACAC
1 TTGTTATATCCTAATCATCTTATCAACATTTTGACCGTCAAGACAACAC
3701946 TT
1 TT
3701948 ATTGACCACC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (49 bp):
TTGTTATATCCTAATCATCTTATCAACATTTTGACCGTCAAGACAACAC
Found at i:3707280 original size:31 final size:29
Alignment explanation
Indices: 3707242--3707310 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 29
3707232 AATTAAGATC
*
3707242 AAATTTATTATTATATTATAATTTAATATTA
1 AAATTTATTATTACATTATAATTT--TATTA
* *
3707273 AAATTTATCATTACATTTTAATTTTATTA
1 AAATTTATTATTACATTATAATTTTATTA
3707302 AAATTTATT
1 AAATTTATT
3707311 GTTTTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 13 0.38
31 21 0.62
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (29 bp):
AAATTTATTATTACATTATAATTTTATTA
Found at i:3707319 original size:29 final size:29
Alignment explanation
Indices: 3707242--3707330 Score: 106
Period size: 29 Copynumber: 3.0 Consensus size: 29
3707232 AATTAAGATC
*
3707242 AAATTTATTATTATATTATAATTTAATATTA
1 AAATTTATTATTATATTTTAATTT--TATTA
* *
3707273 AAATTTATCATTACATTTTAATTTTATTA
1 AAATTTATTATTATATTTTAATTTTATTA
* * *
3707302 AAATTTATTGTTTTATTTTGATTTTATTA
1 AAATTTATTATTATATTTTAATTTTATTA
3707331 TTTTGAATAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
29 29 0.58
31 21 0.42
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (29 bp):
AAATTTATTATTATATTTTAATTTTATTA
Found at i:3708301 original size:24 final size:23
Alignment explanation
Indices: 3708264--3708344 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 23
3708254 TTTTTTGTTC
* *
3708264 ATTTTTTGAGATATTTCAAATTATAT
1 ATTTTTT-A-ATATTTAAAATT-TTT
*
3708290 ATTTTTTAATATCTAAAATTTTT
1 ATTTTTTAATATTTAAAATTTTT
3708313 ATTATTTT-ATATTTTAAAATTTTTT
1 ATT-TTTTAATA-TTTAAAA-TTTTT
3708338 ATTTTTT
1 ATTTTTT
3708345 TAACAAATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
23 8 0.17
24 24 0.50
25 9 0.19
26 7 0.15
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (23 bp):
ATTTTTTAATATTTAAAATTTTT
Found at i:3709709 original size:14 final size:14
Alignment explanation
Indices: 3709690--3709728 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
3709680 TTTTATTATA
3709690 ATAATTAAAAAATT
1 ATAATTAAAAAATT
3709704 ATAATTAAAAAATT
1 ATAATTAAAAAATT
* *
3709718 GTAAATAAAAA
1 ATAATTAAAAA
3709729 TGCATTCTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
ATAATTAAAAAATT
Found at i:3718704 original size:22 final size:24
Alignment explanation
Indices: 3718679--3718731 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
3718669 ACGATTTAAA
*
3718679 ATTTTATAAAAATC-ATAAA-TAT
1 ATTTTATAAAAATCAAAAAATTAT
*
3718701 ATTTAAT-AAAATCAAAAAATTAT
1 ATTTTATAAAAATCAAAAAATTAT
3718724 ATTTTATA
1 ATTTTATA
3718732 TTTTTATGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 6 0.24
22 10 0.40
23 9 0.36
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
ATTTTATAAAAATCAAAAAATTAT
Found at i:3726378 original size:4 final size:4
Alignment explanation
Indices: 3726369--3726417 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
3726359 AAGGGCATAA
* * * * *
3726369 ATAT ATAT ATAT ATAT ATAT ATGT ATAT ATGT ATGT ATGT ATGT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
3726417 A
1 A
3726418 AACAACAGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:3736901 original size:37 final size:37
Alignment explanation
Indices: 3736860--3736932 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
3736850 AACATGAGAT
3736860 TTATAATTCCTCTTTAAGATCATGACACCAAGCTAGA
1 TTATAATTCCTCTTTAAGATCATGACACCAAGCTAGA
* *
3736897 TTATAATTCCTCTTTAGGGTCATGACACCAAGCTAG
1 TTATAATTCCTCTTTAAGATCATGACACCAAGCTAG
3736933 TGTCACAGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.33
Consensus pattern (37 bp):
TTATAATTCCTCTTTAAGATCATGACACCAAGCTAGA
Found at i:3740862 original size:22 final size:23
Alignment explanation
Indices: 3740811--3740854 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 23
3740801 GAGCACAACT
3740811 TATTAAATAACCATTTTTTAAAA
1 TATTAAATAACCATTTTTTAAAA
3740834 TATTAAATAA-C-TTTTTTAAAA
1 TATTAAATAACCATTTTTTAAAA
3740855 GTGATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.48
22 1 0.05
23 10 0.48
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTAAATAACCATTTTTTAAAA
Found at i:3740864 original size:23 final size:23
Alignment explanation
Indices: 3740815--3740865 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
3740805 ACAACTTATT
*
3740815 AAATAACCATTTTTTAAAATATT
1 AAATAACCATTTTTTAAAATATA
3740838 AAATAA-C-TTTTTTAAAAGTGATA
1 AAATAACCATTTTTTAAAA-T-ATA
3740861 AAATA
1 AAATA
3740866 GTATATTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 10 0.40
22 2 0.08
23 13 0.52
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (23 bp):
AAATAACCATTTTTTAAAATATA
Found at i:3740960 original size:22 final size:20
Alignment explanation
Indices: 3740926--3740968 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 20
3740916 ATAAAAATTA
3740926 TAAGATATTAAATTCTTGATTT
1 TAAGATATTAAATT-TT-ATTT
3740948 TAAGA-ATTAAAATTTTATTT
1 TAAGATATT-AAATTTTATTT
3740968 T
1 T
3740969 TAATATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.25
21 5 0.25
22 10 0.50
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (20 bp):
TAAGATATTAAATTTTATTT
Found at i:3742177 original size:18 final size:20
Alignment explanation
Indices: 3742131--3742177 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
3742121 TAATTTGAGC
3742131 TAAATTTTAAATCTCAAACTT
1 TAAA-TTTAAATCTCAAACTT
*
3742152 TAAA-TTAAAT-TTAAAC-T
1 TAAATTTAAATCTCAAACTT
3742169 TAAATTTAA
1 TAAATTTAA
3742178 TACTATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 5 0.21
18 9 0.38
19 6 0.25
21 4 0.17
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATTTAAATCTCAAACTT
Found at i:3742515 original size:26 final size:25
Alignment explanation
Indices: 3742480--3742540 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
3742470 TGATTTGATC
* *
3742480 TAAAT-TAATATAATATTATTTT-TA
1 TAAATATAAAATATTATT-TTTTATA
3742504 -AAATATAAAATATTATTTTTTAATA
1 TAAATATAAAATATTATTTTTT-ATA
3742529 TAAATATAAAAT
1 TAAATATAAAAT
3742541 TAAATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 8 0.26
24 10 0.32
25 2 0.06
26 11 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TAAATATAAAATATTATTTTTTATA
Found at i:3742535 original size:19 final size:19
Alignment explanation
Indices: 3742484--3742535 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 19
3742474 TTGATCTAAA
3742484 TTAATAT-AATATTATTTT
1 TTAATATAAATATTATTTT
*
3742502 TAAAATATAAAATATTATTTT
1 T-TAATAT-AAATATTATTTT
3742523 TTAATATAAATAT
1 TTAATATAAATAT
3742536 AAAATTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 1 0.03
19 11 0.38
20 5 0.17
21 12 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTAATATAAATATTATTTT
Found at i:3742564 original size:23 final size:22
Alignment explanation
Indices: 3742526--3742569 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
3742516 TTATTTTTTA
3742526 ATATAAATATAAAATTAAATAT
1 ATATAAATATAAAATTAAATAT
*
3742548 ATATAATATATATAATTAAATA
1 ATATAA-ATATAAAATTAAATA
3742570 ATTAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATAAATATAAAATTAAATAT
Found at i:3743431 original size:17 final size:17
Alignment explanation
Indices: 3743411--3743460 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
3743401 TATAAGTTAT
3743411 TTATTTATATATATAAA-
1 TTATTTATATAT-TAAAC
* *
3743428 TTATATATAAATTAAAC
1 TTATTTATATATTAAAC
*
3743445 TTAATTATATATTAAA
1 TTATTTATATATTAAA
3743461 AATAAAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 4 0.15
17 23 0.85
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATTTATATATTAAAC
Found at i:3748178 original size:20 final size:21
Alignment explanation
Indices: 3748142--3748185 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
3748132 ATCAGGAAAG
3748142 TAAGTTCTCAAATTTAGACAC
1 TAAGTTCTCAAATTTAGACAC
*
3748163 TAAGTTCTC-GATTTAGACAC
1 TAAGTTCTCAAATTTAGACAC
3748183 TAA
1 TAA
3748186 ATACATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (21 bp):
TAAGTTCTCAAATTTAGACAC
Found at i:3752907 original size:25 final size:27
Alignment explanation
Indices: 3752852--3752911 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
3752842 AATTAAAATT
* *
3752852 AATATATTTTTATTAAAAAAATATATT
1 AATATATATTTATTAAAAAAATATATA
* *
3752879 AATATATATTTA-T-AAAAATTATCTA
1 AATATATATTTATTAAAAAAATATATA
3752904 AATATATA
1 AATATATA
3752912 AAATAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 17 0.59
26 1 0.03
27 11 0.38
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
AATATATATTTATTAAAAAAATATATA
Found at i:3762338 original size:11 final size:12
Alignment explanation
Indices: 3762317--3762343 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3762307 TAATTGAAAG
3762317 TTAAAATTTTTT
1 TTAAAATTTTTT
3762329 TTAAAATTTTTT
1 TTAAAATTTTTT
3762341 TTA
1 TTA
3762344 TGATCGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTAAAATTTTTT
Found at i:3767566 original size:2 final size:2
Alignment explanation
Indices: 3767559--3767585 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3767549 GCATTATTTT
3767559 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
3767586 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3771419 original size:3 final size:3
Alignment explanation
Indices: 3771405--3771453 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
3771395 TGCTGTTCTC
*
3771405 AAG AAG AGG AAG AAG AAG AAG AAG AAG AAG AAG AAAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG
3771451 AAG
1 AAG
3771454 TAGTTGAGCC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3779308 original size:22 final size:25
Alignment explanation
Indices: 3779283--3779330 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
3779273 ATTTATATTG
*
3779283 ATTT-AATTTTATTAAA-AT-TAAT
1 ATTTAAATTTAATTAAATATATAAT
3779305 ATTTAAATTTAATTAAATATATAAT
1 ATTTAAATTTAATTAAATATATAAT
3779330 A
1 A
3779331 AATTTAGACG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.18
23 11 0.50
24 2 0.09
25 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTTAAATTTAATTAAATATATAAT
Found at i:3779930 original size:16 final size:16
Alignment explanation
Indices: 3779897--3779927 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3779887 TTTTAAAATT
3779897 TAAATTTAATTGTAAA
1 TAAATTTAATTGTAAA
3779913 TAAATTTAATT-TAAA
1 TAAATTTAATTGTAAA
3779928 ATATCTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TAAATTTAATTGTAAA
Found at i:3780682 original size:31 final size:30
Alignment explanation
Indices: 3780635--3780692 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
3780625 ATAAAATAAT
3780635 AAAATAAATTTAAATTTAAAATATTATTAG
1 AAAATAAATTTAAATTTAAAATATTATTAG
* * *
3780665 AAAATTAAATTTCAATTTTATATATTAT
1 AAAA-TAAATTTAAATTTAAAATATTAT
3780693 CTTTATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (30 bp):
AAAATAAATTTAAATTTAAAATATTATTAG
Found at i:3781289 original size:14 final size:13
Alignment explanation
Indices: 3781272--3781301 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
3781262 TTTTAATATA
3781272 TAAAAATTAAAAAT
1 TAAAAATT-AAAAT
3781286 TAAAAATTAAAAT
1 TAAAAATTAAAAT
3781299 TAA
1 TAA
3781302 TTTTAACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAAAATTAAAAT
Found at i:3781290 original size:6 final size:7
Alignment explanation
Indices: 3781272--3781301 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3781262 TTTTAATATA
3781272 TAAAAAT
1 TAAAAAT
3781279 TAAAAAT
1 TAAAAAT
3781286 TAAAAAT
1 TAAAAAT
3781293 T-AAAAT
1 TAAAAAT
3781299 TAA
1 TAA
3781302 TTTTAACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TAAAAAT
Done.