Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007823.1 Hibiscus syriacus cultivar Beakdansim tig00110160_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6287495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 33
Found at i:3228984 original size:13 final size:15
Alignment explanation
Indices: 3228966--3228997 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
3228956 TGAAAATTTT
3228966 ATATCATTT-TCAA-
1 ATATCATTTGTCAAG
3228979 ATATCATTTGTCAAG
1 ATATCATTTGTCAAG
3228994 ATAT
1 ATAT
3228998 TCTTGAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 4 0.24
15 4 0.24
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (15 bp):
ATATCATTTGTCAAG
Found at i:3229678 original size:2 final size:2
Alignment explanation
Indices: 3229617--3229663 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3229607 TATTTTCATC
3229617 TA TA TA 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 TA TA TA
3229659 TA TA T
1 TA TA T
3229664 GAGTCAATGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3229970 original size:23 final size:25
Alignment explanation
Indices: 3229918--3229980 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 25
3229908 TAGATGATTT
3229918 ATATTATGATATATTATCAATAAAATA
1 ATATTAT--TATATTATCAATAAAATA
* *
3229945 ATATTTTTATATTATTAA-AAAA-A
1 ATATTATTATATTATCAATAAAATA
3229968 ATATTATTATATT
1 ATATTATTATATT
3229981 TCAGATCGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 13 0.39
24 4 0.12
25 10 0.30
27 6 0.18
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
ATATTATTATATTATCAATAAAATA
Found at i:3230268 original size:39 final size:40
Alignment explanation
Indices: 3230211--3230294 Score: 118
Period size: 39 Copynumber: 2.1 Consensus size: 40
3230201 CACTCTTGAG
* *
3230211 GTCTT-TTCTATTTGTCTGAAGAATTCATGCAGTCGTGAA
1 GTCTTCTTCTATTTGTCTGAAAAAGTCATGCAGTCGTGAA
* *
3230250 GTCTTCTTC-ATTTTTCTGAAAAAGTCATGCAGTCGTGGA
1 GTCTTCTTCTATTTGTCTGAAAAAGTCATGCAGTCGTGAA
3230289 GTCTTC
1 GTCTTC
3230295 ATATTTAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.93
40 3 0.08
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.40
Consensus pattern (40 bp):
GTCTTCTTCTATTTGTCTGAAAAAGTCATGCAGTCGTGAA
Found at i:3234685 original size:45 final size:45
Alignment explanation
Indices: 3234621--3234710 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
3234611 GTAAGTCAGA
* *
3234621 TTAAGTTTTCTCCCTCAGACTTGTCTTGAATGTCAGAGTGCATAG
1 TTAAGTTTTCTCCCTCAGACTTATCATGAATGTCAGAGTGCATAG
3234666 TTAAGTTTTCTCCCTCAGACTTATCATGAATGTCAGAGTGCATAG
1 TTAAGTTTTCTCCCTCAGACTTATCATGAATGTCAGAGTGCATAG
3234711 CTGTAGACAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (45 bp):
TTAAGTTTTCTCCCTCAGACTTATCATGAATGTCAGAGTGCATAG
Found at i:3234835 original size:22 final size:22
Alignment explanation
Indices: 3234807--3235068 Score: 121
Period size: 22 Copynumber: 11.9 Consensus size: 22
3234797 TGAAAATAAT
**
3234807 ATATAGTTTTTGAAAGTATACA
1 ATATAGTTTTTGAAAACATACA
*
3234829 ATATAGTTTTTGAAAACATATA
1 ATATAGTTTTTGAAAACATACA
* * **
3234851 ATATGGTTTTTAAAAACATATT
1 ATATAGTTTTTGAAAACATACA
* *
3234873 ATATAG-TTTTAAAAACATATAA
1 ATATAGTTTTTGAAAACATA-CA
*
3234895 TATATAATTTTTG--AA-A-AC-
1 -ATATAGTTTTTGAAAACATACA
* **
3234913 --ATGGTTTTTGAAAACATATT
1 ATATAGTTTTTGAAAACATACA
**
3234933 ATATAGTTTTTGAAAACATATT
1 ATATAGTTTTTGAAAACATACA
* * *
3234955 ATATAG-GTTTAAAAACATATAA
1 ATATAGTTTTTGAAAACATA-CA
* * * *
3234977 TATATAGATTTTAAAAATATATA
1 -ATATAGTTTTTGAAAACATACA
* * **
3235000 ATATAATTTTTAAAAACATATT
1 ATATAGTTTTTGAAAACATACA
*
3235022 ATATAG-TTTTAAAAACATATAACATA
1 ATATAGTTTTTGAAAAC--AT-AC--A
3235048 TATATAGTTTTTGAAAACATA
1 -ATATAGTTTTTGAAAACATA
3235069 TGTAACATAT
Statistics
Matches: 189, Mismatches: 31, Indels: 37
0.74 0.12 0.14
Matches are distributed among these distances:
15 8 0.04
17 2 0.01
18 1 0.01
19 1 0.01
20 1 0.01
21 35 0.19
22 93 0.49
23 14 0.07
24 16 0.08
25 1 0.01
26 2 0.01
27 6 0.03
28 9 0.05
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.41
Consensus pattern (22 bp):
ATATAGTTTTTGAAAACATACA
Found at i:3234900 original size:67 final size:64
Alignment explanation
Indices: 3234829--3235043 Score: 210
Period size: 67 Copynumber: 3.3 Consensus size: 64
3234819 AAAGTATACA
*
3234829 ATATAGTTTTTGAAAACATATAATATGGTTTTTAAAAACATATTATATAGTTTTAAAAACATATA
1 ATATAG-TTTTAAAAACATATAATATGGTTTTTAAAAACATATTATATAGTTTTAAAAACATAT-
3234894 AT
64 -T
* * * *
3234896 ATATAATTTTTGAAAAC-------ATGGTTTTTGAAAACATATTATATAGTTTTTGAAAACATAT
1 ATAT-AGTTTTAAAAACATATAATATGGTTTTTAAAAACATATTATATAG-TTTTAAAAACATAT
3234954 T
64 T
* * * * * *
3234955 ATATAGGTTTAAAAACATATAATATATAGATTTTAAAAATATATAATATAATTTTTAAAAACATA
1 ATATAGTTTTAAAAACATAT-A-ATATGGTTTTTAAAAACATATTATAT-AGTTTTAAAAACATA
3235020 TT
63 TT
3235022 ATATAGTTTTAAAAACATATAA
1 ATATAGTTTTAAAAACATATAA
3235044 CATATATATA
Statistics
Matches: 122, Mismatches: 14, Indels: 26
0.75 0.09 0.16
Matches are distributed among these distances:
58 9 0.07
59 5 0.04
60 25 0.20
61 13 0.11
65 1 0.01
66 1 0.01
67 66 0.54
68 2 0.02
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.41
Consensus pattern (64 bp):
ATATAGTTTTAAAAACATATAATATGGTTTTTAAAAACATATTATATAGTTTTAAAAACATATT
Found at i:3234920 original size:82 final size:83
Alignment explanation
Indices: 3234834--3234988 Score: 267
Period size: 82 Copynumber: 1.9 Consensus size: 83
3234824 ATACAATATA
* *
3234834 GTTTTTGAAAACATATAATATGGTTTTTAAAAACATATTATATAGTTTTAAAAACATATAATATA
1 GTTTTTGAAAACATATAATATAGTTTTTAAAAACATATTATATAGGTTTAAAAACATATAATATA
3234899 TA-ATTTTTGAAAACATG
66 TAGATTTTTGAAAACATG
* *
3234916 GTTTTTGAAAACATATTATATAGTTTTTGAAAACATATTATATAGGTTTAAAAACATATAATATA
1 GTTTTTGAAAACATATAATATAGTTTTTAAAAACATATTATATAGGTTTAAAAACATATAATATA
3234981 TAGATTTT
66 TAGATTTT
3234989 AAAAATATAT
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
82 63 0.93
83 5 0.07
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.43
Consensus pattern (83 bp):
GTTTTTGAAAACATATAATATAGTTTTTAAAAACATATTATATAGGTTTAAAAACATATAATATA
TAGATTTTTGAAAACATG
Found at i:3234937 original size:104 final size:103
Alignment explanation
Indices: 3234829--3235018 Score: 287
Period size: 104 Copynumber: 1.8 Consensus size: 103
3234819 AAAGTATACA
3234829 ATATAGTTTTTGAAAACATATAATAT-GGTTTTTAAAAACATAT-TATATAG-TTTTAAAAACAT
1 ATATAGTTTTTGAAAACATATAATATAGG--TTTAAAAACATATATATATAGATTTTAAAAACAT
*
3234891 ATAATATATAATTTTTGAAAACATGGTTTTTGAAAACATATT
64 AT-A-ATATAATTTTTAAAAACATGGTTTTTGAAAACATATT
* *
3234933 ATATAGTTTTTGAAAACATATTATATAGGTTTAAAAACATATAATATATAGATTTTAAAAATATA
1 ATATAGTTTTTGAAAACATATAATATAGGTTTAAAAACATAT-ATATATAGATTTTAAAAACATA
3234998 TAATATAATTTTTAAAAACAT
65 TAATATAATTTTTAAAAACAT
3235019 ATTATATAGT
Statistics
Matches: 79, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
103 13 0.16
104 43 0.54
105 10 0.13
106 13 0.16
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (103 bp):
ATATAGTTTTTGAAAACATATAATATAGGTTTAAAAACATATATATATAGATTTTAAAAACATAT
AATATAATTTTTAAAAACATGGTTTTTGAAAACATATT
Found at i:3234945 original size:37 final size:38
Alignment explanation
Indices: 3234879--3234951 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
3234869 TATTATATAG
3234879 TTTTAAAAACATATAATATATAATTTTTGAAAACATGGT
1 TTTTAAAAACATAT-ATATATAATTTTTGAAAACATGGT
* *
3234918 TTTTGAAAACATAT-TATATAGTTTTTGAAAACAT
1 TTTTAAAAACATATATATATAATTTTTGAAAACAT
3234952 ATTATATAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 19 0.59
39 13 0.41
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (38 bp):
TTTTAAAAACATATATATATAATTTTTGAAAACATGGT
Found at i:3235025 original size:29 final size:28
Alignment explanation
Indices: 3234993--3235122 Score: 87
Period size: 28 Copynumber: 4.8 Consensus size: 28
3234983 GATTTTAAAA
3234993 ATATATAATATAATTTTTAAAAAC-----
1 ATATAT-ATATAATTTTTAAAAACATATT
* *
3235017 ATAT-TATAT-AGTTTTAAAAACATATA
1 ATATATATATAATTTTTAAAAACATATT
* * *
3235043 ACATATATATAGTTTTTGAAAACATATGT
1 ATATATATATAATTTTTAAAAACATAT-T
* * * *
3235072 A-ACATATATAATTTTTGAAAATATAAT
1 ATATATATATAATTTTTAAAAACATATT
3235099 ATATATTATATAATTTTTTAAAAA
1 ATATA-TATATAA-TTTTTAAAAA
3235123 AATAGTAGAC
Statistics
Matches: 83, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
21 11 0.13
22 4 0.05
23 1 0.01
24 4 0.05
26 3 0.04
27 7 0.08
28 36 0.43
29 8 0.10
30 9 0.11
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (28 bp):
ATATATATATAATTTTTAAAAACATATT
Found at i:3235047 original size:28 final size:30
Alignment explanation
Indices: 3235014--3235139 Score: 104
Period size: 28 Copynumber: 4.3 Consensus size: 30
3235004 AATTTTTAAA
3235014 AACATATTATATAG-TTTTAAAAACATA-T
1 AACATATTATATAGTTTTTAAAAACATAGT
*
3235042 AACATA-TATATAGTTTTTGAAAACATATGT
1 AACATATTATATAGTTTTTAAAAACATA-GT
* * *
3235072 AACATA-TATA-A-TTTTTGAAAATATAAT
1 AACATATTATATAGTTTTTAAAAACATAGT
* * *
3235099 -ATATATTATATAATTTTTTAAAAAAATAGT
1 AACATATTATAT-AGTTTTTAAAAACATAGT
*
3235129 AGACTTATTAT
1 A-ACATATTAT
3235140 TATTATTATT
Statistics
Matches: 80, Mismatches: 9, Indels: 14
0.78 0.09 0.14
Matches are distributed among these distances:
26 4 0.05
27 12 0.15
28 31 0.39
29 2 0.03
30 24 0.30
32 7 0.09
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.42
Consensus pattern (30 bp):
AACATATTATATAGTTTTTAAAAACATAGT
Found at i:3235103 original size:22 final size:22
Alignment explanation
Indices: 3234917--3235103 Score: 99
Period size: 22 Copynumber: 8.0 Consensus size: 22
3234907 GAAAACATGG
* * * *
3234917 TTTTTGAAAACATATTATATAG
1 TTTTTAAAAATATAATATATAA
* * * *
3234939 TTTTTGAAAACATATTATATAG
1 TTTTTAAAAATATAATATATAA
* *
3234961 GTTTAAAAACATATAATATATAGA
1 TTTTTAAAA-ATATAATATATA-A
3234985 -TTTTAAAAATAT-ATAATATAA
1 TTTTTAAAAATATAAT-ATATAA
* * *
3235006 TTTTTAAAAACATATTATATAG
1 TTTTTAAAAATATAATATATAA
*
3235028 TTTTAAAAACATATAACATATATATA
1 TTTTTAAAA-ATAT-A-ATATATA-A
3235054 GTTTTTGAAAACATATGTAACATATATAA
1 -TTTTT-AAAA-ATA--T-A-ATATATAA
*
3235083 TTTTTGAAAATATAATATATA
1 TTTTTAAAAATATAATATATA
3235104 TTATATAATT
Statistics
Matches: 136, Mismatches: 16, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
21 3 0.02
22 68 0.50
23 22 0.16
24 2 0.01
25 6 0.04
26 3 0.02
27 7 0.05
28 13 0.10
29 1 0.01
30 11 0.08
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (22 bp):
TTTTTAAAAATATAATATATAA
Found at i:3235136 original size:29 final size:27
Alignment explanation
Indices: 3235028--3235126 Score: 83
Period size: 29 Copynumber: 3.5 Consensus size: 27
3235018 TATTATATAG
*
3235028 TTTTAAAAACATATAACATATATATAGTT
1 TTTTAAAAAAATATAACATATATA-A-TT
* * *
3235057 TTTGAAAACATATGTAACATATATAATT
1 TTTTAAAA-AAATATAACATATATAATT
* *
3235085 TTTGAAAATATAATATATA-TTATATAATT
1 TTTTAAAA-A-AATATA-ACATATATAATT
3235114 TTTTAAAAAAATA
1 TTTTAAAAAAATA
3235127 GTAGACTTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
27 4 0.07
28 12 0.20
29 28 0.47
30 15 0.25
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (27 bp):
TTTTAAAAAAATATAACATATATAATT
Found at i:3243862 original size:3 final size:3
Alignment explanation
Indices: 3243854--3243901 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
3243844 TATATTATAT
3243854 TTA TTA TTA TATA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3243899 TTA
1 TTA
3243902 CTAATATCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3243865 original size:21 final size:21
Alignment explanation
Indices: 3243841--3243920 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 21
3243831 TGGGATTAAA
3243841 ATATATATTATATTTATTA-T
1 ATATATATTATATTTATTATT
3243861 -TATATATTATA-TTATTATT
1 ATATATATTATATTTATTATT
3243880 AT-TATTATTAT-TATTATTATT
1 ATATA-TATTATAT-TTATTATT
*
3243901 ACTAATATCATTTTATTTAT
1 A-T-ATAT-ATTATATTTAT
3243921 ATTTTATGCA
Statistics
Matches: 49, Mismatches: 1, Indels: 16
0.74 0.02 0.24
Matches are distributed among these distances:
18 6 0.12
19 14 0.29
20 7 0.14
21 9 0.18
22 1 0.02
23 1 0.02
24 10 0.20
25 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATATATTATATTTATTATT
Found at i:3245246 original size:21 final size:20
Alignment explanation
Indices: 3245220--3245258 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3245210 ATTTTAGTCC
3245220 TATTATTACATGATATATTAT
1 TATTATTACATGA-ATATTAT
*
3245241 TATTATTATATGAATATT
1 TATTATTACATGAATATT
3245259 TGGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (20 bp):
TATTATTACATGAATATTAT
Found at i:3246654 original size:153 final size:154
Alignment explanation
Indices: 3246375--3246681 Score: 528
Period size: 153 Copynumber: 2.0 Consensus size: 154
3246365 TAACCGACTC
*
3246375 CCGAACCTGTTTTAATTAAATCTTTGGTAAACGCAGACCAACATTTGACTTAAAAAATGATTTGT
1 CCGAACATGTTTTAATTAAATCTTTGGTAAACGCAGACCAACATTTGACTTAAAAAATGATTTGT
* *
3246440 CTTAAAATTATTTTTTAAAGACATTTTTAGGTATTCGACCTACCTAACTCAAAGGTTGATGGCGA
66 CTTAAAATTATTTTTTAAAGACATTTTTAGGTATTCGACATACCTAACTCAAAGGTTGATGGAGA
*
3246505 CTCTTTT-CAATTTAATCCAAATTA
131 CT-TTTTCCAATTTAAACCAAATTA
* * *
3246529 CCGAACATGTTTTAATTAAATCTTTGGTAAACGCAGACCAACATTT-TCTTGAAAAATGATTTTT
1 CCGAACATGTTTTAATTAAATCTTTGGTAAACGCAGACCAACATTTGACTTAAAAAATGATTTGT
3246593 CTTAAAATTATTTTTTAAAGACATTTTTAGGTATTCGACATACCTAACTCAAAGGTTGATGGAGA
66 CTTAAAATTATTTTTTAAAGACATTTTTAGGTATTCGACATACCTAACTCAAAGGTTGATGGAGA
3246658 CTTTTTCCAATTTAAACCAAATTA
131 CTTTTTCCAATTTAAACCAAATTA
3246682 ATTCAAAATC
Statistics
Matches: 145, Mismatches: 7, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
152 4 0.03
153 96 0.66
154 45 0.31
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (154 bp):
CCGAACATGTTTTAATTAAATCTTTGGTAAACGCAGACCAACATTTGACTTAAAAAATGATTTGT
CTTAAAATTATTTTTTAAAGACATTTTTAGGTATTCGACATACCTAACTCAAAGGTTGATGGAGA
CTTTTTCCAATTTAAACCAAATTA
Found at i:3254170 original size:90 final size:90
Alignment explanation
Indices: 3254017--3254218 Score: 332
Period size: 90 Copynumber: 2.2 Consensus size: 90
3254007 CCTTCAGGGG
*
3254017 TTTGTAAGTCCTTTGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGA
1 TTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGA
**
3254082 AACTAAGCCTTTGGGGGTTTCTTGA
66 AACTAAGCCTTCAGGGGTTTCTTGA
*
3254107 TTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCATTGCAGGATGTTTTCAAATGAGATTTTAGA
1 TTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGA
*
3254172 AATTAAGCCTTCAGGGGTTTCTTGA
66 AACTAAGCCTTCAGGGGTTTCTTGA
* * *
3254197 TTTTTAAATCCTTCGGGTCATC
1 TTTGTAAGTCCTTCGGGCCATC
3254219 AGTAAGTCTT
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 104 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (90 bp):
TTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGA
AACTAAGCCTTCAGGGGTTTCTTGA
Found at i:3254266 original size:42 final size:42
Alignment explanation
Indices: 3254194--3254277 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
3254184 AGGGGTTTCT
* * *
3254194 TGATTTTTAAATCCTTCGGGTCATCAGTAAGTCTTTTGAGCA
1 TGATTCTTAAATCCTTCAGGTCATCAGTAAGTCTTTCGAGCA
* *
3254236 TGATTCTTAAATCCTTCAGGTTATCTGTAAGTCTTTCGAGCA
1 TGATTCTTAAATCCTTCAGGTCATCAGTAAGTCTTTCGAGCA
3254278 AGATGATAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (42 bp):
TGATTCTTAAATCCTTCAGGTCATCAGTAAGTCTTTCGAGCA
Found at i:3254570 original size:136 final size:136
Alignment explanation
Indices: 3254326--3254811 Score: 728
Period size: 136 Copynumber: 3.6 Consensus size: 136
3254316 TTCGTTGCTC
* * * * * * *
3254326 GATTCATGACATTTTGAATCAATGACACCTTGCTTGAGGGATT-AGTATTTCCAATGGAGAGTTC
1 GATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAGGGATTGA-CATTTCCAATTGAGAGTTC
*
3254390 ATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCT
65 ATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCT
3254455 ATCACTT
130 ATCACTT
* *
3254462 GATTCACGGTATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTGTGAGTTCA
1 GATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTGAGAGTTCA
*
3254527 TAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTTGACCTA
66 TAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTA
*
3254592 TCACTC
131 TCACTT
* * ** * * *
3254598 GATTCACGGCATTTTGAACCAGTGACACCTCGCTTGAGGGATCAACATTT-CTAGTGAAGAATTC
1 GATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTG-AGAGTTC
*
3254662 ATAATGAGAAGAACTCATCCGACAGAGGGAAAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCT
65 ATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCT
3254727 ATCACTT
130 ATCACTT
* *
3254734 GATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAA--AAGAGTTCA
1 GATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTGAGAGTTCA
3254797 TAATGAGAAGAACTC
66 TAATGAGAAGAACTC
3254812 GTCTTAAAGG
Statistics
Matches: 315, Mismatches: 32, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
134 22 0.07
135 4 0.01
136 286 0.91
137 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (136 bp):
GATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTGAGAGTTCA
TAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTA
TCACTT
Found at i:3255108 original size:3 final size:3
Alignment explanation
Indices: 3255100--3255162 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
3255090 TATATTATAT
* * *
3255100 TTA TTA TTA TATA CTA -TA ATA TTA TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3255145 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
3255163 CTAATATCAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.04
3 50 0.93
4 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3256512 original size:18 final size:17
Alignment explanation
Indices: 3256489--3256524 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
3256479 ATTTTAGTCC
3256489 TATTATTACATGATATAT
1 TATTATTACATGA-ATAT
*
3256507 TATTATTATATGAATAT
1 TATTATTACATGAATAT
3256524 T
1 T
3256525 TGGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.53
Consensus pattern (17 bp):
TATTATTACATGAATAT
Found at i:3258809 original size:20 final size:19
Alignment explanation
Indices: 3258784--3258822 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
3258774 TGTTAGTCAG
3258784 GGGTATCAATACCAACAGGT
1 GGGTATCAATACCAA-AGGT
*
3258804 GGGTATCGATACCAAAGGT
1 GGGTATCAATACCAAAGGT
3258823 TTAGTATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (19 bp):
GGGTATCAATACCAAAGGT
Found at i:3262031 original size:20 final size:20
Alignment explanation
Indices: 3261984--3262036 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
3261974 ACTCAAGGTA
*
3261984 ATATCGATACTACTTGAAAG
1 ATATCGATACTACATGAAAG
* *
3262004 AGTATCGATACTACATGTATG
1 A-TATCGATACTACATGAAAG
3262025 ATATCGATACTA
1 ATATCGATACTA
3262037 AGGGTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (20 bp):
ATATCGATACTACATGAAAG
Found at i:3275723 original size:30 final size:30
Alignment explanation
Indices: 3275689--3275748 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
3275679 AAAATGACTT
3275689 TATTTCGAACTTAAAATCACTTAAAACATA
1 TATTTCGAACTTAAAATCACTTAAAACATA
3275719 TATTTCGAACTTAAAATCACTTAAAACATA
1 TATTTCGAACTTAAAATCACTTAAAACATA
3275749 GCTTTGATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (30 bp):
TATTTCGAACTTAAAATCACTTAAAACATA
Found at i:3277169 original size:54 final size:54
Alignment explanation
Indices: 3277033--3277162 Score: 145
Period size: 54 Copynumber: 2.4 Consensus size: 54
3277023 GATACTTCCC
* * * * *
3277033 TTCAAGGGTATTGATACCCCCTTATGGTACCGATACCAAAATAACATTTGATGT
1 TTCAAGGGTATAGATACCTCCTAAAGGTACCGATACCAAAATAACATTCGATGT
* ** **
3277087 TTCAAGGGTATCGATACCTCCTAAAGGTACCGATACCAATCTGGCATTCGATGT
1 TTCAAGGGTATAGATACCTCCTAAAGGTACCGATACCAAAATAACATTCGATGT
*
3277141 TTTAA-GGTATAGATACCATCCT
1 TTCAAGGGTATAGATACC-TCCT
3277163 TTAGGTATCA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 11 0.17
54 53 0.83
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (54 bp):
TTCAAGGGTATAGATACCTCCTAAAGGTACCGATACCAAAATAACATTCGATGT
Found at i:3293122 original size:28 final size:28
Alignment explanation
Indices: 3293039--3293138 Score: 121
Period size: 30 Copynumber: 3.5 Consensus size: 28
3293029 TTTCATTTAA
*
3293039 GTACCTAAAGTATTTTTTGGTCAAAATAA
1 GTACCT-AAGTATTTTTTGGTCAAAATAG
*
3293068 GTACATAAGTTATCTTTTTGGTCAAAATAG
1 GTACCTAAG-TAT-TTTTTGGTCAAAATAG
*
3293098 GTACCTAGAGTATTTTAT-GTCAAAATAG
1 GTACCTA-AGTATTTTTTGGTCAAAATAG
*
3293126 GTACCTAACTATT
1 GTACCTAAGTATT
3293139 CAAATTTTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
27 5 0.08
28 20 0.32
29 12 0.19
30 24 0.38
31 2 0.03
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (28 bp):
GTACCTAAGTATTTTTTGGTCAAAATAG
Found at i:3293291 original size:31 final size:30
Alignment explanation
Indices: 3293221--3293324 Score: 138
Period size: 30 Copynumber: 3.5 Consensus size: 30
3293211 AAAAAAATTG
*
3293221 AATACTTTAGGTACCTATTTTGACAAAAAA
1 AATACTTTAGGTACCTATTTTGACCAAAAA
* * *
3293251 AATATTTTAGGTGCCTATTTTAACCAAAAA
1 AATACTTTAGGTACCTATTTTGACCAAAAA
* *
3293281 TATAACTTTAGGTACTTATTTTGA-CAAAAA
1 AAT-ACTTTAGGTACCTATTTTGACCAAAAA
3293311 AATACTTTAGGTAC
1 AATACTTTAGGTAC
3293325 TTAAATGAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
29 11 0.17
30 36 0.57
31 16 0.25
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (30 bp):
AATACTTTAGGTACCTATTTTGACCAAAAA
Found at i:3293351 original size:60 final size:60
Alignment explanation
Indices: 3293191--3293361 Score: 186
Period size: 60 Copynumber: 2.8 Consensus size: 60
3293181 TTAATTAAAT
* * * *
3293191 AATACTTTAGTTACTTATATAAAAAAATTGAATACTTTAGGTACCTATTTTGACAAAAAA
1 AATACTTTAGGTACTTATATAAAAAAATAGTATACTTTAGGTACTTATTTTGACAAAAAA
* * * *
3293251 AATATTTTAGGTGCCTATTTTAACCAAAAATA-TA-ACTTTAGGTACTTATTTTGAC-AAAAA
1 AATACTTTAGGTACTTA-TATAA--AAAAATAGTATACTTTAGGTACTTATTTTGACAAAAAA
* * *
3293311 AATACTTTAGGTACTTAAATGAAAAAGATAGTATAGTTTAGGTACTTATTT
1 AATACTTTAGGTACTTATAT-AAAAAAATAGTATACTTTAGGTACTTATTT
3293362 GTTATATATA
Statistics
Matches: 90, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
58 6 0.07
59 3 0.03
60 50 0.56
61 24 0.27
62 1 0.01
63 6 0.07
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (60 bp):
AATACTTTAGGTACTTATATAAAAAAATAGTATACTTTAGGTACTTATTTTGACAAAAAA
Found at i:3298457 original size:22 final size:22
Alignment explanation
Indices: 3298410--3298458 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
3298400 ATTAAATAAT
* *
3298410 TATTT-ATTTTTATAAAATTAA
1 TATTTAATTATTATAAAATCAA
3298431 TATTTAATTATTATAAAAATCAA
1 TATTTAATTATTAT-AAAATCAA
3298454 -ATTTA
1 TATTTA
3298459 TAATATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.21
22 12 0.50
23 7 0.29
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TATTTAATTATTATAAAATCAA
Found at i:3300031 original size:20 final size:20
Alignment explanation
Indices: 3300003--3300043 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3299993 CTGATGGTGC
*
3300003 CTTAGACATTCTCATGATAA
1 CTTACACATTCTCATGATAA
3300023 CTTACACATTCTCATGATAA
1 CTTACACATTCTCATGATAA
3300043 C
1 C
3300044 ATAATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.34
Consensus pattern (20 bp):
CTTACACATTCTCATGATAA
Found at i:3300075 original size:2 final size:2
Alignment explanation
Indices: 3300064--3300095 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3300054 ATAGATGAAA
3300064 AT AT -T 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 A
3300096 ATAATTGTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3300553 original size:182 final size:185
Alignment explanation
Indices: 3300111--3300572 Score: 544
Period size: 182 Copynumber: 2.5 Consensus size: 185
3300101 TGTGGTTGCT
* **
3300111 CCCAAGAATGTCATGATTCACTAA-AAATATA--TTGCGATCTGAAATGTTAATATTTTTATTAA
1 CCCAAGAATGTCATGGTTCACTAAGAAAT-TAGGTTGCGATCTGAAACATTAATATTTTTATTAA
* * * * *
3300173 TAAAATGAGTTGCACTTAAAATGTTATCAGAGTTTAAATTGATGGAGCTTTAGATTTTTCCACGA
65 TAAAATGGGTTGCACCTAAAATGTTACCAGAGTTTAAATTAATGGAGCATTAGATTTTTCCAC-A
* *
3300238 TAATAAAAAAAAAGTTAAAAGCTTAAAATGTTATGAATATGTATAGTAAATACGATTGTACC
129 TAATAAAAAAAAAGTTAAAAG----AAATGTTATAAATATGTATAATAAATACGATTGTA-C
* * * * ** *
3300300 CCCAAGAATGTCAAGGTTCACTAAGAAAGTAGGTTACGATATTTAACATTAATATTTTTATTAGT
1 CCCAAGAATGTCATGGTTCACTAAGAAATTAGGTTGCGATCTGAAACATTAATATTTTTATTAAT
* * *
3300365 AAAATGGGTTGCGCCTAAAATGTTACCAGAGTTTAAGTTAATGGAGCATTAGATTTTTCGA-AT-
66 AAAATGGGTTGCACCTAAAATGTTACCAGAGTTTAAATTAATGGAGCATTAGATTTTTCCACATA
* * *
3300428 ATAACAAAATAAGTTAAAAG-AATGTTATAAATATTTATAATAAATAC-AGTTGT-G
131 ATAA-AAAAAAAGTTAAAAGAAATGTTATAAATATGTATAATAAATACGA-TTGTAC
* * *
3300482 CCCAAGAATGTCATGGTTCATTAAGAAATTAGGTTGCAATCTGGAACATTAATATTTTTATTAAT
1 CCCAAGAATGTCATGGTTCACTAAGAAATTAGGTTGCGATCTGAAACATTAATATTTTTATTAAT
*
3300547 AAAATGGGTTGCACCTAAAATATTAC
66 AAAATGGGTTGCACCTAAAATGTTAC
3300573 TTTAGCTTTG
Statistics
Matches: 234, Mismatches: 34, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
182 80 0.34
183 1 0.00
184 28 0.12
188 4 0.02
189 40 0.17
190 3 0.01
191 78 0.33
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (185 bp):
CCCAAGAATGTCATGGTTCACTAAGAAATTAGGTTGCGATCTGAAACATTAATATTTTTATTAAT
AAAATGGGTTGCACCTAAAATGTTACCAGAGTTTAAATTAATGGAGCATTAGATTTTTCCACATA
ATAAAAAAAAAGTTAAAAGAAATGTTATAAATATGTATAATAAATACGATTGTAC
Found at i:3300751 original size:158 final size:158
Alignment explanation
Indices: 3300448--3301123 Score: 865
Period size: 158 Copynumber: 4.3 Consensus size: 158
3300438 AAGTTAAAAG
* * * * * *
3300448 AATGTTATAAATAT-TTATAATAAATACAGTTGTGCCCAAGAATGTCATGGTTCATTAAGAAATT
1 AATGTTATGAATATCTT-TAATAAATCCGGTTGCGCCCAAGAATGTAATGGTTCACTAAGAAATT
* * * *
3300512 AGGTTGCAATCTGGAACATTAATATTTTTATTAATAAAATGGGTTGCACCTAAAATATTACTTTA
65 AGGTTGCGATCTGGAACATTAATATTTTTATTAATAAAATAGGTTGCGCCTAAAATGTTACTTTA
*
3300577 GCTTTGAACAAAATATGGTAAAAACTAAA
130 GCTTTGAACAAAATATGGTAAAAGCTAAA
* * * * * * *
3300606 AATATTATGAATGTCTATAATAAATCCGATTGCACCCAAGAATGTCATGGTTCGCTAAGAAATTA
1 AATGTTATGAATATCTTTAATAAATCCGGTTGCGCCCAAGAATGTAATGGTTCACTAAGAAATTA
* * *
3300671 GGTTGCGATCTTGAACATTAATATTTTTATTAATAAAATAGGTTGTGCCTAAAATGTTACTTTAT
66 GGTTGCGATCTGGAACATTAATATTTTTATTAATAAAATAGGTTGCGCCTAAAATGTTACTTTAG
*
3300736 CTTTGAACAAAATAT-GTTAAAGCTAAA
131 CTTTGAACAAAATATGGTAAAAGCTAAA
* * ** * *
3300763 AATGTTATGAATATATTTAATTAATAAGGTTGTGCCCAAGAATGTAATGATTCACTAAGAAATTA
1 AATGTTATGAATATCTTTAATAAATCCGGTTGCGCCCAAGAATGTAATGGTTCACTAAGAAATTA
* * * *
3300828 GATTGTGATCTGGAACATTAATATATTTATTAATAAAAT-GAGTTGCGCCTAAAATGTTACTATA
66 GGTTGCGATCTGGAACATTAATATTTTTATTAATAAAATAG-GTTGCGCCTAAAATGTTACTTTA
*
3300892 GCTTTGAACAAAATATGTTAAAAGCTAAA
130 GCTTTGAACAAAATATGGTAAAAGCTAAA
*
3300921 AATGTTATGAATATCTTTAATAAATCCGGTTGCGCCCAAGAATGTAATGGTTTACTAA-AATATT
1 AATGTTATGAATATCTTTAATAAATCCGGTTGCGCCCAAGAATGTAATGGTTCACTAAGAA-ATT
* * *
3300985 AGGTTGCGATTTGGAACATTATTATTTTTATTAATAAAATAGGTTTCGCCTAAAATGTTACTTTA
65 AGGTTGCGATCTGGAACATTAATATTTTTATTAATAAAATAGGTTGCGCCTAAAATGTTACTTTA
* * *
3301050 GCTTTGAATAAAATATGTTAAAAGTTAAA
130 GCTTTGAACAAAATATGGTAAAAGCTAAA
* * * * * * * *
3301079 ATTTTTGTAAATATCTATAATAATTCTGGTTGCGCCTAAGAATGT
1 AATGTTATGAATATCTTTAATAAATCCGGTTGCGCCCAAGAATGT
3301124 TATTGATGAA
Statistics
Matches: 447, Mismatches: 66, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
156 1 0.00
157 135 0.30
158 309 0.69
159 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (158 bp):
AATGTTATGAATATCTTTAATAAATCCGGTTGCGCCCAAGAATGTAATGGTTCACTAAGAAATTA
GGTTGCGATCTGGAACATTAATATTTTTATTAATAAAATAGGTTGCGCCTAAAATGTTACTTTAG
CTTTGAACAAAATATGGTAAAAGCTAAA
Found at i:3301020 original size:315 final size:315
Alignment explanation
Indices: 3300448--3301101 Score: 940
Period size: 315 Copynumber: 2.1 Consensus size: 315
3300438 AAGTTAAAAG
* * *
3300448 AATGTTATAAATATTTATAATAAATACAGTTGTGCCCAAGAATGTCATGGTTCATTAAGAAATTA
1 AATGTTATAAATATTTATAATAAATACAGTTGTGCCCAAGAATGTAATGATTCACTAAGAAATTA
* * * *
3300513 GGTTGCAATCTGGAACATTAATATTTTTATTAATAAAATGGGTTGCACCTAAAATATTACTTTAG
66 GATTGCAATCTGGAACATTAATATATTTATTAATAAAATGAGTTGCACCTAAAATATTACTATAG
*
3300578 CTTTGAACAAAATATGGTAAAAACTAAAAATATTATGAATGTCTATAATAAATCCGATTGCACCC
131 CTTTGAACAAAATATGGTAAAAACTAAAAATATTATGAATATCTATAATAAATCCGATTGCACCC
* *
3300643 AAGAATGTCATGGTTCGCTAAGAAATTAGGTTGCGATCTTGAACATTAATATTTTTATTAATAAA
196 AAGAATGTAATGGTTCACTAAGAAATTAGGTTGCGATCTTGAACATTAATATTTTTATTAATAAA
*
3300708 ATAGGTTGT-GCCTAAAATGTTACTTTATCTTTGAACAAAATATGTTAAAGCTAAA
261 ATAGGTT-TCGCCTAAAATGTTACTTTAGCTTTGAACAAAATATGTTAAAGCTAAA
* *
3300763 AATGTTATGAATATATT-TAATTAATA-AGGTTGTGCCCAAGAATGTAATGATTCACTAAGAAAT
1 AATGTTATAAATAT-TTATAATAAATACA-GTTGTGCCCAAGAATGTAATGATTCACTAAGAAAT
** * *
3300826 TAGATTGTGATCTGGAACATTAATATATTTATTAATAAAATGAGTTGCGCCTAAAATGTTACTAT
64 TAGATTGCAATCTGGAACATTAATATATTTATTAATAAAATGAGTTGCACCTAAAATATTACTAT
* * * * * *
3300891 AGCTTTGAACAAAATATGTTAAAAGCTAAAAATGTTATGAATATCTTTAATAAATCCGGTTGCGC
129 AGCTTTGAACAAAATATGGTAAAAACTAAAAATATTATGAATATCTATAATAAATCCGATTGCAC
* *
3300956 CCAAGAATGTAATGGTTTACTAA-AATATTAGGTTGCGAT-TTGGAACATTATTATTTTTATTAA
194 CCAAGAATGTAATGGTTCACTAAGAA-ATTAGGTTGCGATCTT-GAACATTAATATTTTTATTAA
* *
3301019 TAAAATAGGTTTCGCCTAAAATGTTACTTTAGCTTTGAATAAAATATGTTAAAAGTTAAA
257 TAAAATAGGTTTCGCCTAAAATGTTACTTTAGCTTTGAACAAAATATGTT-AAAGCTAAA
* * * *
3301079 ATTTTTGTAAATATCTATAATAA
1 AATGTTATAAATATTTATAATAA
3301102 TTCTGGTTGC
Statistics
Matches: 299, Mismatches: 33, Indels: 13
0.87 0.10 0.04
Matches are distributed among these distances:
314 6 0.02
315 268 0.90
316 25 0.08
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (315 bp):
AATGTTATAAATATTTATAATAAATACAGTTGTGCCCAAGAATGTAATGATTCACTAAGAAATTA
GATTGCAATCTGGAACATTAATATATTTATTAATAAAATGAGTTGCACCTAAAATATTACTATAG
CTTTGAACAAAATATGGTAAAAACTAAAAATATTATGAATATCTATAATAAATCCGATTGCACCC
AAGAATGTAATGGTTCACTAAGAAATTAGGTTGCGATCTTGAACATTAATATTTTTATTAATAAA
ATAGGTTTCGCCTAAAATGTTACTTTAGCTTTGAACAAAATATGTTAAAGCTAAA
Found at i:3307061 original size:12 final size:12
Alignment explanation
Indices: 3307044--3307068 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3307034 TTTGATGCTT
3307044 TCTCTTTGATTC
1 TCTCTTTGATTC
3307056 TCTCTTTGATTC
1 TCTCTTTGATTC
3307068 T
1 T
3307069 AGTTGCTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.08, T:0.60
Consensus pattern (12 bp):
TCTCTTTGATTC
Found at i:3310031 original size:20 final size:20
Alignment explanation
Indices: 3309998--3310035 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3309988 CCCCTTCAAA
3309998 GGGGGAATCAATTCCCTCAT
1 GGGGGAATCAATTCCCTCAT
* *
3310018 GGGGGTATCGATTCCCTC
1 GGGGGAATCAATTCCCTC
3310036 TGCACCAAAA
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:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (20 bp):
GGGGGAATCAATTCCCTCAT
Found at i:3313878 original size:22 final size:21
Alignment explanation
Indices: 3313836--3313875 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3313826 GAGTTTATTT
*
3313836 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3313857 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3313876 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3322245 original size:18 final size:18
Alignment explanation
Indices: 3322219--3322257 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3322209 TAGTTTAAGC
*
3322219 TTTTTAGTTTACTTTGAG
1 TTTTAAGTTTACTTTGAG
* *
3322237 TTTTAAGTTTATTTTTAG
1 TTTTAAGTTTACTTTGAG
3322255 TTT
1 TTT
3322258 ATTTGTTTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.03, G:0.13, T:0.67
Consensus pattern (18 bp):
TTTTAAGTTTACTTTGAG
Found at i:3323834 original size:23 final size:25
Alignment explanation
Indices: 3323787--3323834 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
3323777 AAGTGGATGT
* *
3323787 TTACATTCATTTAATATTTATTAAC
1 TTACATTCATTTAATATATAATAAC
3323812 TTACATT-A-TTAATATATAATAAC
1 TTACATTCATTTAATATATAATAAC
3323835 ATTAACCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.62
24 1 0.05
25 7 0.33
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (25 bp):
TTACATTCATTTAATATATAATAAC
Found at i:3324441 original size:92 final size:92
Alignment explanation
Indices: 3324332--3324518 Score: 349
Period size: 92 Copynumber: 2.0 Consensus size: 92
3324322 TATTTAATAA
3324332 TTAAATCATTGAATATTTATTATACTTTGATCAATTTATCTATAGTTATGTTATTA-GCTTTTTA
1 TTAAATCATTGAATATTTATTATACTTTGATCAATTTATCTATAGTTATGTTATTAGGC-TTTTA
3324396 TCGTATTAAAATTTACACGAATAGATAG
65 TCGTATTAAAATTTACACGAATAGATAG
3324424 TTAAATCATTGAATATTTATTATACTTTGATCAATTTATCTATAGTTATGTTATTAGGCTTTTAT
1 TTAAATCATTGAATATTTATTATACTTTGATCAATTTATCTATAGTTATGTTATTAGGCTTTTAT
*
3324489 CGTATTGAAATTTACACGAATAGATAG
66 CGTATTAAAATTTACACGAATAGATAG
3324516 TTA
1 TTA
3324519 TTAAATAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
92 91 0.98
93 2 0.02
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.47
Consensus pattern (92 bp):
TTAAATCATTGAATATTTATTATACTTTGATCAATTTATCTATAGTTATGTTATTAGGCTTTTAT
CGTATTAAAATTTACACGAATAGATAG
Found at i:3331564 original size:28 final size:27
Alignment explanation
Indices: 3331532--3331589 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
3331522 ACATATTTAA
*
3331532 AAGTAATCAATAAAACAAATATAGTAGC
1 AAGTAAACAATAAAACAAAT-TAGTAGC
* *
3331560 AAGTAAACAATAAAACAGATTATTAGC
1 AAGTAAACAATAAAACAAATTAGTAGC
3331587 AAG
1 AAG
3331590 AAAAGATACA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.21
Consensus pattern (27 bp):
AAGTAAACAATAAAACAAATTAGTAGC
Found at i:3332524 original size:31 final size:31
Alignment explanation
Indices: 3332481--3332542 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
3332471 ATCTATTCCA
* *
3332481 GTTCTAGTTCCAACTAAACTAGTAATGATCT
1 GTTCCAGTTCCAACAAAACTAGTAATGATCT
3332512 GTTCCAGTTCCAACAAAACTAGTAATGATCT
1 GTTCCAGTTCCAACAAAACTAGTAATGATCT
3332543 TTAAAAAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (31 bp):
GTTCCAGTTCCAACAAAACTAGTAATGATCT
Found at i:3333760 original size:2 final size:2
Alignment explanation
Indices: 3333753--3333783 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3333743 TGCTCAAGGT
3333753 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3333784 TAACTAGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3341530 original size:19 final size:20
Alignment explanation
Indices: 3341506--3341544 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3341496 GATTAAACAA
3341506 AATTAAA-AAGAAAAAGTTG
1 AATTAAAGAAGAAAAAGTTG
*
3341525 AATTAAAGAATAAAAAGTTG
1 AATTAAAGAAGAAAAAGTTG
3341545 GATGGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
AATTAAAGAAGAAAAAGTTG
Found at i:3343112 original size:48 final size:50
Alignment explanation
Indices: 3343025--3343119 Score: 142
Period size: 50 Copynumber: 1.9 Consensus size: 50
3343015 TTTTTTAGAT
*
3343025 TATATATATATATATATTATTTTTTATTATCTATTTTATTAATTTATATA
1 TATATATATATATATATTATTTTTTACTATCTATTTTATTAATTTATATA
*
3343075 TATATATATATATATATTA-TTTTTACT-T-TATTATTATTATTTTAT
1 TATATATATATATATATTATTTTTTACTATCTATT-TTATTAATTTAT
3343120 TTATTTGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 4 0.10
48 12 0.29
49 7 0.17
50 19 0.45
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (50 bp):
TATATATATATATATATTATTTTTTACTATCTATTTTATTAATTTATATA
Found at i:3343142 original size:25 final size:25
Alignment explanation
Indices: 3343109--3343165 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
3343099 ACTTTATTAT
*
3343109 TATTATTTTATTTATTTGTTTTATTTA
1 TATT-TTTTATTTATTTCTTTT-TTTA
* *
3343136 TATTTTTTCTTTTTTTCTTTTTTTA
1 TATTTTTTATTTATTTCTTTTTTTA
3343161 TATTT
1 TATTT
3343166 ATTTTACTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 9 0.33
26 14 0.52
27 4 0.15
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.79
Consensus pattern (25 bp):
TATTTTTTATTTATTTCTTTTTTTA
Found at i:3343239 original size:26 final size:26
Alignment explanation
Indices: 3343206--3343255 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
3343196 TTATCTTATC
*
3343206 TTTTATTTAATTTGTTT-TTTCTTCA
1 TTTTATTTAATTTATTTATTTCTTCA
3343231 TTTTAATTTAATTTATTTATTTCTT
1 TTTT-ATTTAATTTATTTATTTCTT
3343256 ATCTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 12 0.55
27 6 0.27
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (26 bp):
TTTTATTTAATTTATTTATTTCTTCA
Found at i:3344670 original size:53 final size:53
Alignment explanation
Indices: 3344607--3344713 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
3344597 GTTACTGACC
3344607 TCGAGAGTCCCTTAAAAAACAACAAGAACAAGATGACAAAACGATAGCTGAAT
1 TCGAGAGTCCCTTAAAAAACAACAAGAACAAGATGACAAAACGATAGCTGAAT
* *
3344660 TCGAGAGTCCCTTCAAAGACAACAAGAACAAGATGACAAAACGATAGCTGAAT
1 TCGAGAGTCCCTTAAAAAACAACAAGAACAAGATGACAAAACGATAGCTGAAT
3344713 T
1 T
3344714 GGAAGCCATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.47, C:0.20, G:0.18, T:0.16
Consensus pattern (53 bp):
TCGAGAGTCCCTTAAAAAACAACAAGAACAAGATGACAAAACGATAGCTGAAT
Found at i:3346356 original size:11 final size:11
Alignment explanation
Indices: 3346340--3346383 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
3346330 AGATTCAATC
3346340 AGAAAAAAAAG
1 AGAAAAAAAAG
*
3346351 AGAAAATAAAG
1 AGAAAAAAAAG
3346362 AGAAAATAAAAAG
1 AG-AAA-AAAAAG
3346375 AGAAAAAAA
1 AGAAAAAAA
3346384 GGAAAATTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:3346374 original size:24 final size:22
Alignment explanation
Indices: 3346345--3346390 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 22
3346335 CAATCAGAAA
3346345 AAAAAGAGAAAATAAAGAGAAAAT
1 AAAAAGAGAAAA-AAAG-GAAAAT
3346369 AAAAAGAGAAAAAAAGGAAAAT
1 AAAAAGAGAAAAAAAGGAAAAT
3346391 TGAAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 6 0.27
23 4 0.18
24 12 0.55
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (22 bp):
AAAAAGAGAAAAAAAGGAAAAT
Found at i:3346388 original size:9 final size:10
Alignment explanation
Indices: 3346343--3346389 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
3346333 TTCAATCAGA
3346343 AAAAAAAGAG
1 AAAAAAAGAG
3346353 AAAATAAAGAG
1 AAAA-AAAGAG
3346364 AAAATAAAAAGAG
1 --AA-AAAAAGAG
3346377 AAAAAAAG-G
1 AAAAAAAGAG
3346386 AAAA
1 AAAA
3346390 TTGAAGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 5 0.15
10 10 0.30
11 8 0.24
13 8 0.24
14 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:3347563 original size:32 final size:32
Alignment explanation
Indices: 3347516--3347605 Score: 117
Period size: 32 Copynumber: 2.8 Consensus size: 32
3347506 TGAGGGAATC
*
3347516 TTTGAAGATTCAACATCAAATTTTGGGACATTT
1 TTTG-AGATTCAACATCAAATATTGGGACATTT
* * * *
3347549 TTTTAGATTTAACATCAAATGTTGGGGCATTT
1 TTTGAGATTCAACATCAAATATTGGGACATTT
*
3347581 TTTGAGATTCAACATCGAATATTGG
1 TTTGAGATTCAACATCAAATATTGG
3347606 TGCATCTTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 46 0.94
33 3 0.06
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATATTGGGACATTT
Found at i:3348338 original size:106 final size:106
Alignment explanation
Indices: 3348148--3348394 Score: 327
Period size: 106 Copynumber: 2.3 Consensus size: 106
3348138 AATTTCAGAG
* *
3348148 CCAATTTCAACTTCACAGCGAAGAATATTGGAATCGAGACAACACAAGTTCAACTTCACTGCGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACTGCGAA
* * *
3348213 GGGACGACTAGTTGCCAACAAACAATTTATCAGTTTCAAAA
66 GGGACGACTAGTTACCAACAAACAATTTACCAGTTCCAAAA
*
3348254 CCAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAT-CGA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCAC-TGCGA
* * * * * * * *
3348318 AGGGATGGCTGGTTATCAACAGACAATTTCCCAGTTCCAGAG
65 AGGGACGACTAGTTACCAACAAACAATTTACCAGTTCCAAAA
*
3348360 CCAATTTCAACTTCA-AGGCGGAGGATATTGGACTC
1 CCAATTTCAACTTCACA-GCGAAGGATATTGGACTC
3348395 AGAACAATAC
Statistics
Matches: 123, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
105 1 0.01
106 121 0.98
107 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (106 bp):
CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACTGCGAA
GGGACGACTAGTTACCAACAAACAATTTACCAGTTCCAAAA
Found at i:3348739 original size:15 final size:15
Alignment explanation
Indices: 3348719--3348753 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3348709 TTTTGTCTCT
*
3348719 CTTGAGATAGTTTCC
1 CTTGAGACAGTTTCC
*
3348734 CTTGAGACAGTTTCT
1 CTTGAGACAGTTTCC
3348749 CTTGA
1 CTTGA
3348754 AGCATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (15 bp):
CTTGAGACAGTTTCC
Found at i:3348944 original size:36 final size:36
Alignment explanation
Indices: 3348898--3348987 Score: 148
Period size: 35 Copynumber: 2.5 Consensus size: 36
3348888 TTGAATACAA
3348898 TTTCTCTTGAAACACAAAAAAAAACCTTTGAA-ATTG
1 TTTCTCTTGAAACACAAAAAAAAACCTTTGAAGA-TG
*
3348934 TTTCTTTTGAAACAC-AAAAAAAACCTTTGAAGATG
1 TTTCTCTTGAAACACAAAAAAAAACCTTTGAAGATG
3348969 TTTCTCTTGAAACACAAAA
1 TTTCTCTTGAAACACAAAA
3348988 CCCTCAAGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
35 32 0.64
36 18 0.36
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (36 bp):
TTTCTCTTGAAACACAAAAAAAAACCTTTGAAGATG
Found at i:3350027 original size:2 final size:2
Alignment explanation
Indices: 3350014--3350083 Score: 83
Period size: 2 Copynumber: 36.5 Consensus size: 2
3350004 TTTATTAATT
*
3350014 TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
3350054 TT TT TA TA TT TA T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3350084 TATTTTTGCT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
1 3 0.05
2 56 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (2 bp):
TA
Found at i:3350138 original size:54 final size:55
Alignment explanation
Indices: 3350066--3350171 Score: 155
Period size: 54 Copynumber: 1.9 Consensus size: 55
3350056 TTTATATTTA
3350066 TTATATATATATATATATTATTT-TTGCTTTTT-TTTATTATTT-TATTTATTTGTT
1 TTATATATATATATATATT-TTTCTT-CTTTTTCTTTATTATTTATATTTATTTGTT
* *
3350120 TTATTTATATATATATATTTTTCTTCTTTTTCTTTATTTTTTATATTTATTT
1 TTATATATATATATATATTTTTCTTCTTTTTCTTTATTATTTATATTTATTT
3350172 ACTTACTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
53 9 0.19
54 29 0.62
55 9 0.19
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.72
Consensus pattern (55 bp):
TTATATATATATATATATTTTTCTTCTTTTTCTTTATTATTTATATTTATTTGTT
Found at i:3350156 original size:42 final size:43
Alignment explanation
Indices: 3350105--3350203 Score: 116
Period size: 42 Copynumber: 2.3 Consensus size: 43
3350095 TTTTTTATTA
*
3350105 TTTTATTTATTTGTTT-TATTTATATA-TATA-TATTTT-TCTTCT
1 TTTTCTTTATTT-TTTATATTTATATACT-TACTATTTTATCTT-T
*
3350147 TTTTCTTTATTTTTTATATTTATTTACTTACTATTTTATCTTT
1 TTTTCTTTATTTTTTATATTTATATACTTACTATTTTATCTTT
3350190 TCTTTCTTTATTTT
1 T-TTTCTTTATTTT
3350204 ATTTTATCTT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
41 3 0.06
42 22 0.44
43 9 0.18
44 16 0.32
ACGTcount: A:0.18, C:0.08, G:0.01, T:0.73
Consensus pattern (43 bp):
TTTTCTTTATTTTTTATATTTATATACTTACTATTTTATCTTT
Found at i:3350207 original size:25 final size:26
Alignment explanation
Indices: 3350178--3350248 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 26
3350168 ATTTACTTAC
* *
3350178 TATTTTATCTTTTCTTT-CTTTATTT
1 TATTTTATCTTTTATTTAATTTATTT
3350203 TATTTTATCTTTTATTTAATTTATTT
1 TATTTTATCTTTTATTTAATTTATTT
*
3350229 T-TTTTCAT-TTTAATTTAATT
1 TATTTT-ATCTTTTATTTAATT
3350249 AATTAATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
25 31 0.76
26 10 0.24
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (26 bp):
TATTTTATCTTTTATTTAATTTATTT
Found at i:3351561 original size:20 final size:19
Alignment explanation
Indices: 3351536--3351589 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
3351526 GTGAAATAAA
3351536 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
3351556 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
3351576 AATCGCAACGCGAT
1 AATCGCAACGCGAT
3351590 TATAAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:3351600 original size:21 final size:20
Alignment explanation
Indices: 3351576--3351693 Score: 67
Period size: 21 Copynumber: 5.8 Consensus size: 20
3351566 CAGTTCCCAG
3351576 AATCGCAACGCGATTATAAA
1 AATCGCAACGCGATTATAAA
*
3351596 GAATCGCAATGCGA-TAGTACAA
1 -AATCGCAACGCGATTA-TA-AA
* ** * * *
3351618 ATTCGCATTGCGATTTTTCAG
1 AATCGCAACGCGA-TTATAAA
* * *
3351639 AATTGCAACGCGAATATGAA
1 AATCGCAACGCGATTATAAA
* ** *
3351659 AATTGCAACGCGAACATATA
1 AATCGCAACGCGATTATAAA
3351679 AATCGCAACGCGATT
1 AATCGCAACGCGATT
3351694 CTGACTATTG
Statistics
Matches: 73, Mismatches: 20, Indels: 9
0.72 0.20 0.09
Matches are distributed among these distances:
20 34 0.47
21 35 0.48
22 3 0.04
23 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (20 bp):
AATCGCAACGCGATTATAAA
Found at i:3351664 original size:20 final size:20
Alignment explanation
Indices: 3351639--3351691 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
3351629 GATTTTTCAG
*
3351639 AATTGCAACGCGAATATGA-A
1 AATTGCAACGCGAACAT-ATA
3351659 AATTGCAACGCGAACATATA
1 AATTGCAACGCGAACATATA
*
3351679 AATCGCAACGCGA
1 AATTGCAACGCGA
3351692 TTCTGACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (20 bp):
AATTGCAACGCGAACATATA
Found at i:3351744 original size:20 final size:20
Alignment explanation
Indices: 3351712--3351890 Score: 189
Period size: 20 Copynumber: 8.8 Consensus size: 20
3351702 TGCAACGAGT
*
3351712 ATCCGTAAAATCGCAACGCGT
1 ATCCGT-AAATCGCAACGCGA
**
3351733 ATCCGTAAATCGCAACAAGA
1 ATCCGTAAATCGCAACGCGA
* *
3351753 ATACGTAAAATCGCAACGCGT
1 ATCCGT-AAATCGCAACGCGA
*
3351774 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGCGA
* *
3351794 ATACGTAAATCGCAACGCGT
1 ATCCGTAAATCGCAACGCGA
* * *
3351814 ATCTGTAAATCGCAATGAGA
1 ATCCGTAAATCGCAACGCGA
*
3351834 ATACGTAAATCGCAACGCGA
1 ATCCGTAAATCGCAACGCGA
*
3351854 A-CACGTAAATCGCAATGCGA
1 ATC-CGTAAATCGCAACGCGA
**
3351874 ATCTATAAATCGCAACG
1 ATCCGTAAATCGCAACG
3351891 AGATTCTGAC
Statistics
Matches: 128, Mismatches: 27, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
20 105 0.82
21 23 0.18
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGCGA
Found at i:3351815 original size:40 final size:40
Alignment explanation
Indices: 3351703--3351890 Score: 245
Period size: 40 Copynumber: 4.7 Consensus size: 40
3351693 TCTGACTATT
* *
3351703 GCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATC
1 GCAACGAGAATACGT-AAATCGCAACGCGTATCCGTAAATC
*
3351744 GCAACAAGAATACGTAAAATCGCAACGCGTATCCGTAAATC
1 GCAACGAGAATACGT-AAATCGCAACGCGTATCCGTAAATC
*
3351785 GCAACGAGAATACGTAAATCGCAACGCGTATCTGTAAATC
1 GCAACGAGAATACGTAAATCGCAACGCGTATCCGTAAATC
* *
3351825 GCAATGAGAATACGTAAATCGCAACGCG-AACACGTAAATC
1 GCAACGAGAATACGTAAATCGCAACGCGTATC-CGTAAATC
* * *
3351865 GCAATGCGAAT-CTATAAATCGCAACG
1 GCAACGAGAATAC-GTAAATCGCAACG
3351891 AGATTCTGAC
Statistics
Matches: 135, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 3 0.02
40 80 0.59
41 52 0.39
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (40 bp):
GCAACGAGAATACGTAAATCGCAACGCGTATCCGTAAATC
Found at i:3351908 original size:60 final size:60
Alignment explanation
Indices: 3351643--3351893 Score: 204
Period size: 60 Copynumber: 4.2 Consensus size: 60
3351633 TTTCAGAATT
* * * * * ** * *
3351643 GCAACGCGAATATGAAAATTGCAACGCGAACATATAAATCGCAACGCGATTCTGACT--ATT
1 GCAACGAGAATACGTAAATCGCAACGAGAACACGTAAATCGCAACGCGAATCT-A-TAAATC
* * * * **
3351703 GCAACGAGTATCCGTAAAATCGCAACGCGTATC-CGTAAATCGCAACAAGAATACGTA-AAATC
1 GCAACGAGAATACGT-AAATCGCAACGAG-AACACGTAAATCGCAACGCGAAT-C-TATAAATC
* * * * * *
3351765 GCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTAAATC
1 GCAACGAGAATACGTAAATCGCAACGAGAACACGTAAATCGCAACGCGAATCTATAAATC
* * *
3351825 GCAATGAGAATACGTAAATCGCAACGCGAACACGTAAATCGCAATGCGAATCTATAAATC
1 GCAACGAGAATACGTAAATCGCAACGAGAACACGTAAATCGCAACGCGAATCTATAAATC
3351885 GCAACGAGA
1 GCAACGAGA
3351894 TTCTGACTAT
Statistics
Matches: 152, Mismatches: 31, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
59 1 0.01
60 76 0.50
61 54 0.36
62 20 0.13
63 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (60 bp):
GCAACGAGAATACGTAAATCGCAACGAGAACACGTAAATCGCAACGCGAATCTATAAATC
Found at i:3352783 original size:24 final size:23
Alignment explanation
Indices: 3352751--3352802 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
3352741 AGTATTCGAA
*
3352751 ATTTGATCTTGGTCAATACCCGG
1 ATTTTATCTTGGTCAATACCCGG
*
3352774 ACTTTTATCTTGGTCAATACTCGG
1 A-TTTTATCTTGGTCAATACCCGG
3352798 ATTTT
1 ATTTT
3352803 GATGATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (23 bp):
ATTTTATCTTGGTCAATACCCGG
Found at i:3355484 original size:19 final size:19
Alignment explanation
Indices: 3355355--3355492 Score: 100
Period size: 19 Copynumber: 7.7 Consensus size: 19
3355345 GCAACGAGAG
* *
3355355 AATCACAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
*
3355374 AATCGCAACGCGGAAAT-AA
1 AATCGCAATGC-GAAATGAA
*
3355393 CTATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAA
* *
3355413 AATTGCAA--C--AA-GAG
1 AATCGCAATGCGAAATGAA
3355427 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
**
3355446 AATCGCAA--CG--A-GGG
1 AATCGCAATGCGAAATGAA
3355460 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3355479 AATCGCAACGCGAA
1 AATCGCAATGCGAA
3355493 TTTAGTTTCG
Statistics
Matches: 91, Mismatches: 15, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
14 18 0.20
15 3 0.03
16 3 0.03
17 3 0.03
18 3 0.03
19 46 0.51
20 15 0.16
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3355488 original size:33 final size:33
Alignment explanation
Indices: 3355342--3355488 Score: 177
Period size: 33 Copynumber: 4.3 Consensus size: 33
3355332 AGAAATTACT
* *
3355342 ATCGCAACGAGAGAATCACAATGCAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* *
3355375 ATCGCAACGCGGAAATAACTATCGCAATGCGAAATGAAA
1 ATCGCAA--C-GAGA-GA--ATCGCAATGCGAAATGAAA
* *
3355414 ATTGCAACAAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
*
3355447 ATCGCAACGAGGGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
3355480 ATCGCAACG
1 ATCGCAACG
3355489 CGAATTTAGT
Statistics
Matches: 97, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
33 65 0.67
35 2 0.02
36 5 0.05
37 2 0.02
39 23 0.24
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:3355553 original size:33 final size:33
Alignment explanation
Indices: 3355488--3355574 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
3355478 AAATCGCAAC
* * * * * *
3355488 GCGAATTTAGTTTCGCGTTGCGATTTTGTCGTT
1 GCGATTTTAATTTCGCATTGCAATTATCTCGTT
3355521 GCGATTTTAATTTCGCATTGCAATTATCTCGTT
1 GCGATTTTAATTTCGCATTGCAATTATCTCGTT
*
3355554 GCGATTTTCATTTCGCATTGC
1 GCGATTTTAATTTCGCATTGC
3355575 GATAGTCATT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.45
Consensus pattern (33 bp):
GCGATTTTAATTTCGCATTGCAATTATCTCGTT
Found at i:3355576 original size:19 final size:18
Alignment explanation
Indices: 3355519--3355577 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
3355509 GATTTTGTCG
3355519 TTGCGATTTTAATTTCGCA
1 TTGCGATTTT-ATTTCGCA
* *
3355538 TTGC-A-ATTATCTCG--
1 TTGCGATTTTATTTCGCA
3355552 TTGCGATTTTCATTTCGCA
1 TTGCGATTTT-ATTTCGCA
3355571 TTGCGAT
1 TTGCGAT
3355578 AGTCATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 4 0.13
15 1 0.03
16 7 0.23
17 7 0.23
18 1 0.03
19 11 0.35
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.46
Consensus pattern (18 bp):
TTGCGATTTTATTTCGCA
Found at i:3355703 original size:14 final size:14
Alignment explanation
Indices: 3355684--3355720 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3355674 CATCAATTAA
3355684 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3355698 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3355712 ACAAATCAA
1 ACAAATCAA
3355721 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3357149 original size:42 final size:42
Alignment explanation
Indices: 3357103--3357194 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
3357093 CCTCTTCAAC
* * *
3357103 AATGACAGTGGCCTCTTGAACGGT-GAGAGGGGACTCTCGAGG
1 AATGACAGGGGCCTCTTCAACGATAG-GAGGGGACTCTCGAGG
* * *
3357145 AATGATAGGGGCCTCTTCAACGATAGGAGTGGACTCTTGAGG
1 AATGACAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
*
3357187 GATGACAG
1 AATGACAG
3357195 ACGAGTCAGG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
42 40 0.98
43 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.36, T:0.21
Consensus pattern (42 bp):
AATGACAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
Found at i:3359182 original size:20 final size:20
Alignment explanation
Indices: 3359157--3359218 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
3359147 TTTTGGTTGA
3359157 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
3359177 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
3359196 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
3359216 AAT
1 AAT
3359219 TGTAACGCGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 18 0.46
20 21 0.54
ACGTcount: A:0.50, C:0.16, G:0.23, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:3359201 original size:19 final size:19
Alignment explanation
Indices: 3359155--3359214 Score: 102
Period size: 19 Copynumber: 3.1 Consensus size: 19
3359145 TCTTTTGGTT
3359155 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
3359174 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGA
3359194 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
3359213 GA
1 GA
3359215 GAATTGTAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 20 0.53
20 18 0.47
ACGTcount: A:0.50, C:0.17, G:0.23, T:0.10
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:3359231 original size:33 final size:35
Alignment explanation
Indices: 3359155--3359242 Score: 117
Period size: 39 Copynumber: 2.5 Consensus size: 35
3359145 TCTTTTGGTT
3359155 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAAT----ATCGCAACGC
*
3359194 GAAATGAAAATCGCAACGAGAGAAT-T-GTAACGC
1 GAAATGAAAATCGCAACGAGAGAATATCGCAACGC
3359227 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3359243 TGTGATTTTG
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
33 22 0.46
34 1 0.02
39 25 0.52
ACGTcount: A:0.49, C:0.16, G:0.23, T:0.12
Consensus pattern (35 bp):
GAAATGAAAATCGCAACGAGAGAATATCGCAACGC
Found at i:3359268 original size:19 final size:19
Alignment explanation
Indices: 3359254--3359348 Score: 119
Period size: 19 Copynumber: 5.2 Consensus size: 19
3359244 GTGATTTTGG
3359254 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
3359273 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
3359292 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
* **
3359308 --TCTCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
3359325 TTTCCGCGTTGCGATTTTCA
1 TTT-CGCGTTGCGATTTTCA
3359345 TTTC
1 TTTC
3359349 AACCAAAAGA
Statistics
Matches: 65, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 3 0.05
19 34 0.52
20 16 0.25
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:3359877 original size:20 final size:20
Alignment explanation
Indices: 3359852--3359983 Score: 183
Period size: 20 Copynumber: 6.5 Consensus size: 20
3359842 CTTTAAAAAT
3359852 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3359872 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
3359892 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
3359912 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
3359932 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
3359952 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
3359973 CTCGTTGCGAT
1 CGCGTTGCGAT
3359984 AGTCAGAATC
Statistics
Matches: 96, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 77 0.80
21 19 0.20
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3359912 original size:40 final size:40
Alignment explanation
Indices: 3359854--3360044 Score: 242
Period size: 40 Copynumber: 4.8 Consensus size: 40
3359844 TTAAAAATCG
*
3359854 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
3359894 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
* * *
3359934 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
* ** *
3359975 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATATTCG
1 CGTTGCGAT-TTACAGATA-CGCGTTGCGATTTACGTATTCT
* * *
3360015 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACAGATACGCGTTGCGATT
3360045 ATTGGAAATC
Statistics
Matches: 132, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
39 1 0.01
40 98 0.74
41 32 0.24
42 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (40 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
Found at i:3360006 original size:81 final size:81
Alignment explanation
Indices: 3359851--3360044 Score: 259
Period size: 81 Copynumber: 2.4 Consensus size: 81
3359841 GCTTTAAAAA
* * *
3359851 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACAGATACGC
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATGTACAGATACGC
*
3359915 GTTGCGATTTACGTAT
66 GTTGCGATTTACATAT
*
3359931 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATC
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGAT-GTACAGATA-C
*
3359994 GCGTTGCGATTTATATAT
64 GCGTTGCGATTTACATAT
* ** *
3360012 TCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATT
3360045 ATTGGAAATC
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
80 31 0.31
81 68 0.68
82 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.37
Consensus pattern (81 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATGTACAGATACGC
GTTGCGATTTACATAT
Found at i:3360015 original size:20 final size:20
Alignment explanation
Indices: 3359851--3360128 Score: 143
Period size: 20 Copynumber: 13.8 Consensus size: 20
3359841 GCTTTAAAAA
* **
3359851 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTTCATAT
* * *
3359871 ACGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTTCATAT
* * *
3359891 TCTCGTTGCGATTTACAGAT
1 TCGCGTTGCGATTTTCATAT
* * *
3359911 ACGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTTCATAT
* * **
3359931 TCTCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTTCATAT
* **
3359951 ACGCGTTGCGATTTTACGGAT
1 TCGCGTTGCGATTTT-CATAT
* * ** * *
3359972 ACTCGTTGCGATAGTCAGAA
1 TCGCGTTGCGATTTTCATAT
3359992 TCGCGTTGCGATTTAT-ATAT
1 TCGCGTTGCGATTT-TCATAT
3360012 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
* *
3360032 TCGCGTTGCGATTATTGGA-AA
1 TCGCGTTGCGATT-TT-CATAT
** *
3360053 TCGCAATGCGAATATGT-ACTA-
1 TCGCGTTGCG-AT-TTTCA-TAT
* *
3360074 TCGCATTGCGATTCTTCATAA
1 TCGCGTTGCGATT-TTCATAT
*
3360095 TCGCGTTGCGATTTTTAT-T
1 TCGCGTTGCGATTTTCATAT
*
3360114 TCGCATTGCGATTTT
1 TCGCGTTGCGATTTT
3360129 GTTGGTTATT
Statistics
Matches: 208, Mismatches: 38, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
19 16 0.08
20 135 0.65
21 51 0.25
22 5 0.02
23 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:3360063 original size:81 final size:81
Alignment explanation
Indices: 3359912--3360128 Score: 194
Period size: 81 Copynumber: 2.7 Consensus size: 81
3359902 TTTACAGATA
** * * ** * *
3359912 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCG
1 CGCGTTGCGATTTATATATTCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTA-GGATAATCG
* *
3359977 TTGCG-ATA-GTCAGAAT
65 ATGCGAATATGT-ACAAT
3359993 CGCGTTGCGATTTATATATTCGCGTTGCGATTTTCATATTCGCGTTGCGATTATT-GGA-AATCG
1 CGCGTTGCGATTTATATATTCGCGTTGCGATTTTCATATTCGCGTTGCGATT-TTAGGATAATCG
*
3360056 CAATGCGAATATGTACTAT
65 --ATGCGAATATGTACAAT
* * * *
3360075 CGCATTGCGATTCT-TCATAATCGCGTTGCGATTTTTAT-TTCGCATTGCGATTTT
1 CGCGTTGCGATT-TAT-ATATTCGCGTTGCGATTTTCATATTCGCGTTGCGATTTT
3360129 GTTGGTTATT
Statistics
Matches: 114, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
79 4 0.04
80 3 0.03
81 51 0.45
82 33 0.29
83 23 0.20
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (81 bp):
CGCGTTGCGATTTATATATTCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTAGGATAATCGA
TGCGAATATGTACAAT
Found at i:3371578 original size:25 final size:24
Alignment explanation
Indices: 3371544--3371599 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
3371534 TCAAATTACA
*
3371544 ATTGTGGATTTTGTTGC-GATTGCCG
1 ATTGCGGATTTTGTTGCGGA-TG-CG
3371569 ATTGCGGATTTTGTTGCGGATGCG
1 ATTGCGGATTTTGTTGCGGATGCG
3371593 ATTGCGG
1 ATTGCGG
3371600 TGTCGCGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 9 0.31
25 18 0.62
26 2 0.07
ACGTcount: A:0.12, C:0.12, G:0.36, T:0.39
Consensus pattern (24 bp):
ATTGCGGATTTTGTTGCGGATGCG
Found at i:3372960 original size:6 final size:5
Alignment explanation
Indices: 3372952--3373030 Score: 95
Period size: 5 Copynumber: 15.0 Consensus size: 5
3372942 ATGAGAAAAT
* *
3372952 TTTAA TTTTAA TTTAAA TTTAA ATTAA TTTAA TTTAAA TTTAA ATTAA
1 TTTAA -TTTAA TTT-AA TTTAA TTTAA TTTAA TTT-AA TTTAA TTTAA
*
3373000 TTTAA TTTAAA TTTAA ATTAA TTTAA TTTAA
1 TTTAA TTT-AA TTTAA TTTAA TTTAA TTTAA
3373031 AATAACGTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
5 44 0.69
6 20 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (5 bp):
TTTAA
Found at i:3372980 original size:16 final size:16
Alignment explanation
Indices: 3372959--3373068 Score: 90
Period size: 15 Copynumber: 6.9 Consensus size: 16
3372949 AATTTTAATT
3372959 TTAATTTAAATTTAAA
1 TTAATTTAAATTTAAA
3372975 TTAATTT-AATTT--A
1 TTAATTTAAATTTAAA
*
3372988 --AATTTAAA-TTAAT
1 TTAATTTAAATTTAAA
3373001 TTAATTTAAATTTAAA
1 TTAATTTAAATTTAAA
3373017 TTAATTT-AATTTAAA
1 TTAATTTAAATTTAAA
* *
3373032 ATAACGTTAATAAATAATTTAA
1 TTAA--TT--TAAAT--TTAAA
3373054 TTAATTTAAATTTAA
1 TTAATTTAAATTTAA
3373069 GTAATTAATT
Statistics
Matches: 75, Mismatches: 6, Indels: 26
0.70 0.06 0.24
Matches are distributed among these distances:
11 7 0.09
12 2 0.03
13 1 0.01
15 24 0.32
16 21 0.28
17 2 0.03
18 5 0.07
19 1 0.01
20 5 0.07
22 7 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (16 bp):
TTAATTTAAATTTAAA
Found at i:3373042 original size:21 final size:21
Alignment explanation
Indices: 3372953--3373031 Score: 149
Period size: 21 Copynumber: 3.7 Consensus size: 21
3372943 TGAGAAAATT
3372953 TTAATTTTAATTTAAATTTAAA
1 TTAA-TTTAATTTAAATTTAAA
3372975 TTAATTTAATTTAAATTTAAA
1 TTAATTTAATTTAAATTTAAA
3372996 TTAATTTAATTTAAATTTAAA
1 TTAATTTAATTTAAATTTAAA
3373017 TTAATTTAATTTAAA
1 TTAATTTAATTTAAA
3373032 ATAACGTTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 53 0.93
22 4 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAATTTAATTTAAATTTAAA
Found at i:3373109 original size:12 final size:13
Alignment explanation
Indices: 3373092--3373120 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3373082 AACATAACTA
3373092 TTATGATAT-TAT
1 TTATGATATATAT
3373104 TTATGATATATAT
1 TTATGATATATAT
3373117 TTAT
1 TTAT
3373121 AATCCAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (13 bp):
TTATGATATATAT
Found at i:3374883 original size:22 final size:23
Alignment explanation
Indices: 3374840--3374885 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
3374830 ATGTTCATTT
*
3374840 TACATAACTTAGAAATAAAAAAA
1 TACATAACTTACAAATAAAAAAA
*
3374863 TACATAAC-TACAAATATAAAAA
1 TACATAACTTACAAATAAAAAAA
3374885 T
1 T
3374886 TATATATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.63, C:0.11, G:0.02, T:0.24
Consensus pattern (23 bp):
TACATAACTTACAAATAAAAAAA
Found at i:3375086 original size:16 final size:16
Alignment explanation
Indices: 3375065--3375102 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
3375055 TGCGGCGTTA
3375065 CGTAACGATTTTTGAC
1 CGTAACGATTTTTGAC
3375081 CGTAACGATTTTTGAC
1 CGTAACGATTTTTGAC
3375097 CGTAAC
1 CGTAAC
3375103 AATCGTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (16 bp):
CGTAACGATTTTTGAC
Found at i:3376543 original size:29 final size:29
Alignment explanation
Indices: 3376500--3376611 Score: 188
Period size: 29 Copynumber: 3.8 Consensus size: 29
3376490 CTCACCTAAC
3376500 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
3376530 TAAATGATGTAAGCAATGACATCATTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
3376559 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
**
3376588 TAAATGATGTAAGTGATGACATCA
1 TAAATGATGTAAGCAATGACATCA
3376612 ATTTAGTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 74 0.95
30 4 0.05
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:3379992 original size:15 final size:15
Alignment explanation
Indices: 3379972--3380001 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3379962 CTTTCTCATA
3379972 GTTATTGTTGGAATT
1 GTTATTGTTGGAATT
*
3379987 GTTATTGTTGTAATT
1 GTTATTGTTGGAATT
3380002 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
GTTATTGTTGGAATT
Found at i:3381334 original size:29 final size:29
Alignment explanation
Indices: 3381291--3381402 Score: 188
Period size: 29 Copynumber: 3.8 Consensus size: 29
3381281 CTCACCTAAC
3381291 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
3381321 TAAATGATGTAAGCAATGACATCATTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
3381350 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
**
3381379 TAAATGATGTAAGTGATGACATCA
1 TAAATGATGTAAGCAATGACATCA
3381403 ATTTAGTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 74 0.95
30 4 0.05
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:3381985 original size:29 final size:29
Alignment explanation
Indices: 3381933--3381990 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
3381923 GTATTGGTCG
**
3381933 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCAGCGACCTAC
* *
3381962 TAGGTCGCCATGTCTTCCCAGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCAGCGACCTAC
3381991 AAGAGATTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.36, G:0.26, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCAGCGACCTAC
Found at i:3382105 original size:33 final size:33
Alignment explanation
Indices: 3382031--3382117 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
3382021 CATGCTGGGC
* * * * *
3382031 ATCCGAGGCCATCCGAACGAGCTATGCGAGGGC
1 ATCCGAGGGCAACCGAGCGAGCTATGCAAGGGA
*
3382064 ATCCGAGGGTAACCGAGCGAGCTATGCAAGGGA
1 ATCCGAGGGCAACCGAGCGAGCTATGCAAGGGA
*
3382097 ATCCGAGGGCAGCCGAGCGAG
1 ATCCGAGGGCAACCGAGCGAG
3382118 GGTAGGTCGC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.26, C:0.26, G:0.37, T:0.10
Consensus pattern (33 bp):
ATCCGAGGGCAACCGAGCGAGCTATGCAAGGGA
Found at i:3382154 original size:29 final size:29
Alignment explanation
Indices: 3382121--3382176 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
3382111 GAGCGAGGGT
*
3382121 AGGTCGCCCGAAGTGCATGACGACCTACA
1 AGGTCGCCCGAAGGGCATGACGACCTACA
*
3382150 AGGTCGCCCGGAGGGCATGACGACCTA
1 AGGTCGCCCGAAGGGCATGACGACCTA
3382177 TGTGTTGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.25, C:0.30, G:0.32, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGAAGGGCATGACGACCTACA
Found at i:3385398 original size:3 final size:3
Alignment explanation
Indices: 3385380--3385487 Score: 92
Period size: 3 Copynumber: 35.3 Consensus size: 3
3385370 TTCTTTTAAA
* * * * *
3385380 ATT ATT TTT AATT ATT ATT ATT ATC AAT ATT AAT A-T AGT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * *
3385425 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT AAT ATT ATAC ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT AT-T
*
3385472 CTT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
3385488 AATAATTACA
Statistics
Matches: 83, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
2 2 0.02
3 75 0.90
4 6 0.07
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:3385450 original size:50 final size:50
Alignment explanation
Indices: 3385389--3385489 Score: 150
Period size: 50 Copynumber: 2.0 Consensus size: 50
3385379 AATTATTTTT
*
3385389 AATTATTATTATTATCAATATTAATATAGTAT-TATTATTATTATTATTAA
1 AATTATTATTATTATCAATATT-ATACAGTATATATTATTATTATTATTAA
* * *
3385439 AATTATTATTATTATTAATATTATACATTATATCTTATTATTATTATTAA
1 AATTATTATTATTATCAATATTATACAGTATATATTATTATTATTATTAA
3385489 A
1 A
3385490 TAATTACATT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 7 0.15
50 39 0.85
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (50 bp):
AATTATTATTATTATCAATATTATACAGTATATATTATTATTATTATTAA
Found at i:3386889 original size:36 final size:38
Alignment explanation
Indices: 3386837--3386908 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
3386827 TTTTAATAAG
*
3386837 TTATTTTTTAATCCCTAATTTTAA-TTTATTTATTTTA
1 TTATTTTTTAATCCCTAATTTTAATTTTAGTTATTTTA
* *
3386874 TTATTTTTTTA-CCCTAGTTTTAATTTTAGTTATTT
1 TTATTTTTTAATCCCTAATTTTAATTTTAGTTATTT
3386909 CAGTCATTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 11 0.35
37 20 0.65
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.65
Consensus pattern (38 bp):
TTATTTTTTAATCCCTAATTTTAATTTTAGTTATTTTA
Found at i:3386971 original size:3 final size:3
Alignment explanation
Indices: 3386963--3386989 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3386953 AATATATTTA
3386963 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
3386990 TAGTCATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3389758 original size:35 final size:36
Alignment explanation
Indices: 3389711--3389782 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 36
3389701 TTTAGAGAAG
* *
3389711 TTAGGAGGGAAAGTTA-TCCCTTATATGT-AAAGTTT
1 TTAGGAGGGAAAGCTATTCCC-TACATGTAAAAGTTT
*
3389746 TTAGGAGTGAAAGCTATTCCCTACATGTAAAAGTTT
1 TTAGGAGGGAAAGCTATTCCCTACATGTAAAAGTTT
3389782 T
1 T
3389783 GTTTGATGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 20 0.62
36 12 0.38
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (36 bp):
TTAGGAGGGAAAGCTATTCCCTACATGTAAAAGTTT
Found at i:3392738 original size:9 final size:9
Alignment explanation
Indices: 3392724--3392782 Score: 86
Period size: 9 Copynumber: 6.8 Consensus size: 9
3392714 TATTATACTT
3392724 GAAAAAAAG
1 GAAAAAAAG
3392733 G-AAAAAAG
1 GAAAAAAAG
*
3392741 GAAAAAATG
1 GAAAAAAAG
*
3392750 AAAAAAAAG
1 GAAAAAAAG
3392759 G-AAAAAAG
1 GAAAAAAAG
3392767 GAAAAAAAG
1 GAAAAAAAG
3392776 GAAAAAA
1 GAAAAAA
3392783 GAAAAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
8 16 0.36
9 28 0.64
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (9 bp):
GAAAAAAAG
Found at i:3392739 original size:8 final size:8
Alignment explanation
Indices: 3392726--3392788 Score: 83
Period size: 8 Copynumber: 7.6 Consensus size: 8
3392716 TTATACTTGA
3392726 AAAAAAGG
1 AAAAAAGG
3392734 AAAAAAGG
1 AAAAAAGG
*
3392742 AAAAAATGAA
1 AAAAAA-G-G
3392752 AAAAAAGG
1 AAAAAAGG
3392760 AAAAAAGG
1 AAAAAAGG
3392768 AAAAAAAGG
1 -AAAAAAGG
3392777 AAAAAA-G
1 AAAAAAGG
3392784 AAAAA
1 AAAAA
3392789 GAAAAAATTG
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
7 6 0.12
8 28 0.56
9 10 0.20
10 6 0.12
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (8 bp):
AAAAAAGG
Found at i:3392746 original size:17 final size:17
Alignment explanation
Indices: 3392726--3392788 Score: 94
Period size: 17 Copynumber: 3.8 Consensus size: 17
3392716 TTATACTTGA
3392726 AAAAAAGG-AAAAAAGG
1 AAAAAAGGAAAAAAAGG
*
3392742 AAAAAATGAAAAAAAAGG
1 AAAAAA-GGAAAAAAAGG
3392760 AAAAAAGGAAAAAAAGG
1 AAAAAAGGAAAAAAAGG
3392777 AAAAAA-GAAAAA
1 AAAAAAGGAAAAA
3392789 GAAAAAATTG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.28
17 17 0.40
18 14 0.33
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (17 bp):
AAAAAAGGAAAAAAAGG
Found at i:3392759 original size:26 final size:25
Alignment explanation
Indices: 3392723--3392796 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 25
3392713 ATATTATACT
3392723 TGAAAAAAAGGAAAAAAGGAAAAAA
1 TGAAAAAAAGGAAAAAAGGAAAAAA
3392748 TGAAAAAAAAGGAAAAAAGGAAAAAA
1 TG-AAAAAAAGGAAAAAAGGAAAAAA
* *
3392774 AGGAAAAAA-G-AAAAA-GAAAAAA
1 TGAAAAAAAGGAAAAAAGGAAAAAA
3392796 T
1 T
3392797 TGAACCAAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
22 7 0.16
23 5 0.11
24 1 0.02
25 8 0.18
26 24 0.53
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (25 bp):
TGAAAAAAAGGAAAAAAGGAAAAAA
Found at i:3395612 original size:75 final size:75
Alignment explanation
Indices: 3395467--3395641 Score: 217
Period size: 75 Copynumber: 2.3 Consensus size: 75
3395457 CAAGAAGAAG
* * * *
3395467 ATGTTGGGGCAGGCTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGATGTATTCTGAACGTTT
1 ATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGACGCATTCTGAACGCTT
3395532 ATATTAGCAAA
66 ATATTAGC-AA
* ** * *
3395543 ATGTTGGGGCATGCTGAAAG-CCTTTTTTATCAGAATCAGGAATGTTGACGCATTTTGCACGCTT
1 ATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGACGCATTCTGAACGCTT
* *
3395607 GTATTAGCCA
66 ATATTAGCAA
* *
3395617 ATGTTGGGACATGCTGAAGGCCCAT
1 ATGTTGGGGCATGCTGAAAGCCCAT
3395642 ATTATCCTGT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
74 19 0.23
75 46 0.55
76 19 0.23
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (75 bp):
ATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGACGCATTCTGAACGCTT
ATATTAGCAA
Found at i:3396975 original size:22 final size:22
Alignment explanation
Indices: 3396928--3397026 Score: 121
Period size: 22 Copynumber: 4.6 Consensus size: 22
3396918 ACAATTACCT
* *
3396928 TCTTCAAAGATG--AGATACAC
1 TCTTCAAAGATGATAGATTCTC
*
3396948 TATTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
3396970 TCTTCAAAGATAATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
3396992 TTTTTAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
3397014 TTTTCAAAGATGA
1 TCTTCAAAGATGA
3397027 ATGCTTTATC
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 11 0.16
22 57 0.84
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:3398064 original size:60 final size:60
Alignment explanation
Indices: 3397966--3398079 Score: 183
Period size: 60 Copynumber: 1.9 Consensus size: 60
3397956 CTATTTCCAA
* *
3397966 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTCAGGGT
1 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTCAGGGT
* * *
3398026 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGTTTTTT
1 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTT
3398080 GATCTTAAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (60 bp):
CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTCAGGGT
Found at i:3398138 original size:73 final size:73
Alignment explanation
Indices: 3398019--3398331 Score: 556
Period size: 73 Copynumber: 4.3 Consensus size: 73
3398009 GGGAGCTTTT
*
3398019 TCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGTTTTTTGATC
1 TCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATC
3398084 TTAAAGCC
66 TTAAAGCC
3398092 TCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATC
1 TCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATC
3398157 TTAAA-CTC
66 TTAAAGC-C
*
3398165 TCAGGGTCATCTGTAAGACCTACAGTGCATGATTTTTTCAAAAAGCCTTCGGGAGCTTTTTGATC
1 TCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATC
3398230 TTAAAGCC
66 TTAAAGCC
* *
3398238 TCAGGGTCATCTGTAAGACCTATAGTGCATAATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATC
1 TCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATC
3398303 TTAAAGCC
66 TTAAAGCC
**
3398311 TCAGGGTCATCCATAAGACCT
1 TCAGGGTCATCTGTAAGACCT
3398332 CTGGGCAGAA
Statistics
Matches: 231, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
72 1 0.00
73 229 0.99
74 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (73 bp):
TCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATC
TTAAAGCC
Found at i:3398498 original size:3 final size:3
Alignment explanation
Indices: 3398480--3398581 Score: 71
Period size: 3 Copynumber: 33.3 Consensus size: 3
3398470 TTCTTTTAAA
* * * * *
3398480 ATT ATT TTT AATT ATT ATT ATT ATC AAT ATT AAT A-T AGT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * * * *
3398525 ATT AAA ATT ATT ATT ATT AAT AAT ATT ATAC ATT ATAT CTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT AT-T ATT ATT ATT
3398572 ATT ATT ATT A
1 ATT ATT ATT A
3398582 AATAATTACA
Statistics
Matches: 77, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
2 2 0.03
3 69 0.90
4 6 0.08
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:3398534 original size:23 final size:22
Alignment explanation
Indices: 3398487--3398543 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 22
3398477 AAAATTATTT
* *
3398487 TTAATTATTATTATTATCAATA
1 TTAATTAGTATTATTATCAAAA
*
3398509 TTAATATAGTATTATTATTAAAA
1 TTAAT-TAGTATTATTATCAAAA
*
3398532 TT-ATTATTATTA
1 TTAATTAGTATTA
3398544 ATAATATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 7 0.23
22 7 0.23
23 16 0.53
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TTAATTAGTATTATTATCAAAA
Found at i:3398536 original size:26 final size:25
Alignment explanation
Indices: 3398475--3398537 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
3398465 TCACTTTCTT
** *
3398475 TTAAAATTATTTTTAATTATTATTA
1 TTAAAATTATTAATAAGTATTATTA
*
3398500 TTATCAA-TATTAATATAGTATTATTA
1 TTA-AAATTATTAATA-AGTATTATTA
3398526 TTAAAATTATTA
1 TTAAAATTATTA
3398538 TTATTAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
25 11 0.37
26 19 0.63
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
TTAAAATTATTAATAAGTATTATTA
Found at i:3398568 original size:41 final size:39
Alignment explanation
Indices: 3398480--3398587 Score: 114
Period size: 41 Copynumber: 2.7 Consensus size: 39
3398470 TTCTTTTAAA
* *
3398480 ATTATTTTTAATTATTATTATT-ATCAATATTAATATAGT
1 ATTATTATTAATTATTATTATTAAT-AATATTAATACAGT
*
3398519 ATTATTATTAAAATTATTATTATTAATAATATT-ATACATT
1 ATTATTATT--AATTATTATTATTAATAATATTAATACAGT
*
3398559 ATATCTTATT-ATTATTATTATTAAATAAT
1 AT-TATTATTAATTATTATTATT-AATAAT
3398588 TACATTACAA
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
38 12 0.20
39 14 0.23
40 7 0.12
41 25 0.42
42 2 0.03
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.55
Consensus pattern (39 bp):
ATTATTATTAATTATTATTATTAATAATATTAATACAGT
Found at i:3400033 original size:3 final size:3
Alignment explanation
Indices: 3400025--3400054 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3400015 AATATATTTA
3400025 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3400055 TAGTCATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3406685 original size:26 final size:25
Alignment explanation
Indices: 3406647--3406699 Score: 97
Period size: 26 Copynumber: 2.1 Consensus size: 25
3406637 CACCACCGGA
3406647 TCGTGGTGGCCAAGTTTGGTTTTGG
1 TCGTGGTGGCCAAGTTTGGTTTTGG
3406672 TCGTGGTTGGCCAAGTTTGGTTTTGG
1 TCGTGG-TGGCCAAGTTTGGTTTTGG
3406698 TC
1 TC
3406700 TTGGCATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.08, C:0.13, G:0.38, T:0.42
Consensus pattern (25 bp):
TCGTGGTGGCCAAGTTTGGTTTTGG
Found at i:3407000 original size:201 final size:202
Alignment explanation
Indices: 3406654--3407056 Score: 799
Period size: 201 Copynumber: 2.0 Consensus size: 202
3406644 GGATCGTGGT
3406654 GGCCAAGTTTGGTTTTGGTCGTGGTTGGCCAAGTTTGGTTTTGGTCTTGGCATTTGTCGCTGTTC
1 GGCCAAGTTTGGTTTTGGTCGTGGTTGGCCAAGTTTGGTTTTGGTCTTGGCATTTGTCGCTGTTC
3406719 GTTGGAGGAGTGAGAGAAAAAACAAACATGGCAACGATATTTTAGGGTTTCACGTTTAATATACT
66 GTTGGAGGAGTGAGAGAAAAAACAAACATGGCAACGATATTTTAGGGTTTCACGTTTAATATACT
3406784 TAAACAGCAAAGAATTAGTCTTAATATCGAAGGTTTTGGGTTAATGTCAATTAGGTTCTCCAACT
131 TAAACAGCAAAGAATTAGTCTTAATATCGAAGGTTTTGGGTTAATGTCAATTAGGTTCTCCAACT
3406849 TTAAGCG
196 TTAAGCG
3406856 GGCCAAGTTTGGTTTTGGTCGTGG-TGGCCAAGTTTGGTTTTGGTCTTGGCATTTGTCGCTGTTC
1 GGCCAAGTTTGGTTTTGGTCGTGGTTGGCCAAGTTTGGTTTTGGTCTTGGCATTTGTCGCTGTTC
3406920 GTTGGAGGAGTGAGAGAAAAAACAAACATGGCAACGATATTTTAGGGTTTCACGTTTAATATACT
66 GTTGGAGGAGTGAGAGAAAAAACAAACATGGCAACGATATTTTAGGGTTTCACGTTTAATATACT
3406985 TAAACAGCAAAGAATTAGTCTTAATATCGAAGGTTTTGGGTTAATGTCAATTAGGTTCTCCAACT
131 TAAACAGCAAAGAATTAGTCTTAATATCGAAGGTTTTGGGTTAATGTCAATTAGGTTCTCCAACT
3407050 TTAAGCG
196 TTAAGCG
3407057 CAAATTTGCA
Statistics
Matches: 201, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
201 177 0.88
202 24 0.12
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.34
Consensus pattern (202 bp):
GGCCAAGTTTGGTTTTGGTCGTGGTTGGCCAAGTTTGGTTTTGGTCTTGGCATTTGTCGCTGTTC
GTTGGAGGAGTGAGAGAAAAAACAAACATGGCAACGATATTTTAGGGTTTCACGTTTAATATACT
TAAACAGCAAAGAATTAGTCTTAATATCGAAGGTTTTGGGTTAATGTCAATTAGGTTCTCCAACT
TTAAGCG
Found at i:3411314 original size:81 final size:82
Alignment explanation
Indices: 3411201--3411396 Score: 252
Period size: 81 Copynumber: 2.4 Consensus size: 82
3411191 CATTTTATAA
* * * *
3411201 CGGCGTTTTCTAAAAAAACACCACTAAGGTACAAGTCTGT-TTCGACGTTTATTTAAAAA-GCCA
1 CGGCGTTTTCT-AAAAAACACCACTAAAGTACAAGTCTGTAGT-GACGTTTATTCAAAAATACCA
*
3411264 CTATATATGAAACTTATTG
64 CTATATATGAAACCTATTG
* * *
3411283 CGGTGTTTTCTAAAAAACACCACTAAAGTACAAGTCTGTAGTGGCGTTTGTTCAAAAATACCACT
1 CGGCGTTTTCTAAAAAACACCACTAAAGTACAAGTCTGTAGTGACGTTTATTCAAAAATACCACT
3411348 ATATATGAAACCTATTG
66 ATATATGAAACCTATTG
* * *
3411365 TGGCGTTTGTGTAAAAAACGCCACTAAAGTAC
1 CGGCGTTT-TCTAAAAAACACCACTAAAGTAC
3411397 CAATTTGTTG
Statistics
Matches: 99, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
81 40 0.40
82 38 0.38
83 21 0.21
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (82 bp):
CGGCGTTTTCTAAAAAACACCACTAAAGTACAAGTCTGTAGTGACGTTTATTCAAAAATACCACT
ATATATGAAACCTATTG
Found at i:3411423 original size:83 final size:82
Alignment explanation
Indices: 3411201--3411448 Score: 254
Period size: 83 Copynumber: 3.0 Consensus size: 82
3411191 CATTTTATAA
* * * * * *
3411201 CGGCGTTTTCTAAAAAAACACCACTAAGGTACAAGTCTGT-TTCGACGTTTATTTAAAAA-GCCA
1 CGGCGTTTTCT-AAAAAACACCACTAAAGTACAAGTCTGTAGT-GGCGTTTGTTCAAAAACACCA
*
3411264 CTATATATGAAACTTATTG
64 CTATATATGAAACCTATTG
* *
3411283 CGGTGTTTTCTAAAAAACACCACTAAAGTACAAGTCTGTAGTGGCGTTTGTTCAAAAATACCACT
1 CGGCGTTTTCTAAAAAACACCACTAAAGTACAAGTCTGTAGTGGCGTTTGTTCAAAAACACCACT
3411348 ATATATGAAACCTATTG
66 ATATATGAAACCTATTG
* * * * *
3411365 TGGCGTTTGTGTAAAAAACGCCACTAAAGTACCAA-TTTGTTGTGGCAG-TTG-TCTAAAAACAC
1 CGGCGTTT-TCTAAAAAACACCACTAAAGTA-CAAGTCTGTAGTGGC-GTTTGTTC-AAAAACAC
* * *
3411427 CACGATATATGTACCCTATTG
62 CACTATATATGAAACCTATTG
3411448 C
1 C
3411449 AGCATTTGTA
Statistics
Matches: 141, Mismatches: 19, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
81 40 0.28
82 40 0.28
83 57 0.40
84 4 0.03
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (82 bp):
CGGCGTTTTCTAAAAAACACCACTAAAGTACAAGTCTGTAGTGGCGTTTGTTCAAAAACACCACT
ATATATGAAACCTATTG
Found at i:3411457 original size:83 final size:82
Alignment explanation
Indices: 3411213--3411478 Score: 195
Period size: 83 Copynumber: 3.2 Consensus size: 82
3411203 GCGTTTTCTA
* * * * * * * *
3411213 AAAAAACACCACTAAGGTA-CAAGTCTGT-TTCGACGTTTATTTAAAAA-GCCACTATATATGAA
1 AAAAAACGCCACTAAAGTACCAAGTCTGTAGT-GGCGTTTGTTCAAAAACACCACGATATATGAA
* * ** *
3411275 ACTTATTGCGGTGTTTTCT
65 ACCTATTGCAG-CATTTGT
* * *
3411294 AAAAAACACCACTAAAGTA-CAAGTCTGTAGTGGCGTTTGTTCAAAAATACCACTATATATGAAA
1 AAAAAACGCCACTAAAGTACCAAGTCTGTAGTGGCGTTTGTTCAAAAACACCACGATATATGAAA
** *
3411358 CCTATTGTGGCGTTTGTGT
66 CCTATTGCAGC-ATT-TGT
* * *
3411377 AAAAAACGCCACTAAAGTACCAA-TTTGTTGTGGCAG-TTG-TCTAAAAACACCACGATATATGT
1 AAAAAACGCCACTAAAGTACCAAGTCTGTAGTGGC-GTTTGTTC-AAAAACACCACGATATATGA
*
3411439 ACCCTATTGCAGCATTTGT
64 AACCTATTGCAGCATTTGT
* *
3411458 AAAATAATGCCTCTAAAGTAC
1 AAAA-AACGCCACTAAAGTAC
3411479 TAGGTTTTAG
Statistics
Matches: 155, Mismatches: 22, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
81 47 0.30
82 45 0.29
83 59 0.38
84 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (82 bp):
AAAAAACGCCACTAAAGTACCAAGTCTGTAGTGGCGTTTGTTCAAAAACACCACGATATATGAAA
CCTATTGCAGCATTTGT
Found at i:3414233 original size:31 final size:31
Alignment explanation
Indices: 3414172--3414233 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
3414162 CTGATATTTC
*
3414172 AATTTATGTGATTCGATTTTCTTGTTTTTTA
1 AATTTATGTGATTCGATTTCCTTGTTTTTTA
**
3414203 AATTTATGTGATTTTATTTCCTT-TTCTTTTA
1 AATTTATGTGATTCGATTTCCTTGTT-TTTTA
3414234 CAAGATGTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.19, C:0.08, G:0.10, T:0.63
Consensus pattern (31 bp):
AATTTATGTGATTCGATTTCCTTGTTTTTTA
Done.