Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, 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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 17 of 127
Found at i:3949396 original size:30 final size:29
Alignment explanation
Indices: 3949310--3949398 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 29
3949300 ATATCCTAAC
* * * * *
3949310 AATAAAAAATAAAAAATTATATTATATTAA
1 AATAATAAAT-AAAAATAAAATAATATTCA
*
3949340 AATAATAAATAAAAATAAAATTATATTCA
1 AATAATAAATAAAAATAAAATAATATTCA
*
3949369 AATAATGAAA-AAATAATAAAGTAATATTCA
1 AATAAT-AAATAAA-AATAAAATAATATTCA
3949399 CACAATTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
29 25 0.49
30 26 0.51
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (29 bp):
AATAATAAATAAAAATAAAATAATATTCA
Found at i:3950191 original size:38 final size:39
Alignment explanation
Indices: 3950149--3950245 Score: 126
Period size: 38 Copynumber: 2.5 Consensus size: 39
3950139 CATGCTGAAA
3950149 GAAACCAGTAGTCTGCTGTAGGAAACCAACAGAC-G-CAG
1 GAAACCAGTAGTCTGCTGTA-GAAACCAACAGACTGACAG
* * *
3950187 GAAACCAGTAGTCTACTGTAGAAACCAGCAGTCTGCTACAG
1 GAAACCAGTAGTCTGCTGTAGAAACCAACAGACTG--ACAG
3950228 GAAACCAGTAGTCTGCTG
1 GAAACCAGTAGTCTGCTG
3950246 CTATCTTTGC
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
37 11 0.22
38 20 0.39
41 20 0.39
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.18
Consensus pattern (39 bp):
GAAACCAGTAGTCTGCTGTAGAAACCAACAGACTGACAG
Found at i:3950212 original size:20 final size:21
Alignment explanation
Indices: 3950184--3950241 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
3950174 CCAACAGACG
*
3950184 CAGGAAACCAGTAGTCTACTG
1 CAGGAAACCAGTAGTCTACTA
* * *
3950205 TA-GAAACCAGCAGTCTGCTA
1 CAGGAAACCAGTAGTCTACTA
3950225 CAGGAAACCAGTAGTCT
1 CAGGAAACCAGTAGTCT
3950242 GCTGCTATCT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.19
Consensus pattern (21 bp):
CAGGAAACCAGTAGTCTACTA
Found at i:3951286 original size:9 final size:9
Alignment explanation
Indices: 3951272--3951296 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3951262 TATTATAAGA
3951272 TCGATTAAT
1 TCGATTAAT
3951281 TCGATTAAT
1 TCGATTAAT
3951290 TCGATTA
1 TCGATTA
3951297 TCAATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (9 bp):
TCGATTAAT
Found at i:3952107 original size:19 final size:19
Alignment explanation
Indices: 3952080--3952126 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
3952070 AGAACATTTT
* *
3952080 TTATTTTTAAATTTTTATA
1 TTATATTTAAATATTTATA
3952099 TTATATTT--ATATTTATA
1 TTATATTTAAATATTTATA
3952116 TTCATATTTAA
1 TT-ATATTTAA
3952127 TGAATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 10 0.43
18 6 0.26
19 7 0.30
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATATTTAAATATTTATA
Found at i:3952116 original size:12 final size:12
Alignment explanation
Indices: 3952093--3952125 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3952083 TTTTTAAATT
3952093 TTTATA-TTATA
1 TTTATATTTATA
3952104 TTTATATTTATA
1 TTTATATTTATA
*
3952116 TTCATATTTA
1 TTTATATTTA
3952126 ATGAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTATATTTATA
Found at i:3954292 original size:28 final size:26
Alignment explanation
Indices: 3954261--3954325 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 26
3954251 ATTAATTAAA
* *
3954261 ATTAATATATTTTTATTGAAAAATATAT
1 ATTAATATATATTTA-TAAAAAAT-TAT
*
3954289 ATTAATAAATATTTATAAAAAATTAT
1 ATTAATATATATTTATAAAAAATTAT
3954315 -TTAAATATATA
1 ATT-AATATATA
3954326 AAATAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 2 0.06
26 10 0.31
27 7 0.22
28 13 0.41
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTAATATATATTTATAAAAAATTAT
Found at i:3954341 original size:13 final size:13
Alignment explanation
Indices: 3954325--3954361 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
3954315 TTAAATATAT
3954325 AAAATAAAAATAA
1 AAAATAAAAATAA
3954338 AAAATAAAAATAA
1 AAAATAAAAATAA
*
3954351 AAAATATAAAT
1 AAAATAAAAAT
3954362 TTGTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:3954342 original size:7 final size:7
Alignment explanation
Indices: 3954325--3954356 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
3954315 TTAAATATAT
3954325 AAAAT-A
1 AAAATAA
3954331 AAAATAA
1 AAAATAA
3954338 AAAAT-A
1 AAAATAA
3954344 AAAATAA
1 AAAATAA
3954351 AAAATA
1 AAAATA
3954357 TAAATTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 11 0.46
7 13 0.54
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAAATAA
Found at i:3962227 original size:13 final size:12
Alignment explanation
Indices: 3962196--3962234 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3962186 AAATTTTATA
3962196 AATAATTTTTTT
1 AATAATTTTTTT
3962208 AATAATTTTTTT
1 AATAATTTTTTT
* *
3962220 ATTAAATTATTTT
1 AAT-AATTTTTTT
3962233 AA
1 AA
3962235 AGAAAATATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
AATAATTTTTTT
Found at i:3962792 original size:24 final size:26
Alignment explanation
Indices: 3962750--3962807 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
3962740 ATACTAAAAA
3962750 AATAAAAATAATATAATTT-AAAATTTT
1 AATAAAAAT-ATATAATTTGAAAA-TTT
*
3962777 AATAAAAAT-TAT-ATTTGTAAATTT
1 AATAAAAATATATAATTTGAAAATTT
3962801 AATAAAA
1 AATAAAA
3962808 GTAAATTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 14 0.48
25 6 0.21
27 9 0.31
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (26 bp):
AATAAAAATATATAATTTGAAAATTT
Found at i:3969384 original size:3 final size:3
Alignment explanation
Indices: 3969376--3969407 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3969366 GGGTACATAC
3969376 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3969408 ATTTAGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3970220 original size:14 final size:13
Alignment explanation
Indices: 3970179--3970207 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3970169 AAAAATGATT
3970179 AAAT-AAAAATTA
1 AAATAAAAAATTA
3970191 AAATAAAAAATTA
1 AAATAAAAAATTA
3970204 AAAT
1 AAAT
3970208 TGATAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAAAAATTA
Found at i:3980389 original size:2 final size:2
Alignment explanation
Indices: 3980382--3980415 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3980372 GTTGCTTAAG
3980382 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3980416 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3980420 original size:2 final size:2
Alignment explanation
Indices: 3980415--3980440 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3980405 TATATATATA
3980415 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
3980441 GTTAAAGAAA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3996234 original size:26 final size:27
Alignment explanation
Indices: 3996194--3996248 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 27
3996184 CATACGCGCC
*
3996194 CACACACACGTATATGAAATAAGTTTTA
1 CACACACACG-ATATGAAATAAGTCTTA
3996222 CACACACAC-ATATGAAATAAGTCTTA
1 CACACACACGATATGAAATAAGTCTTA
3996248 C
1 C
3996249 CGTGAAGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 17 0.65
28 9 0.35
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (27 bp):
CACACACACGATATGAAATAAGTCTTA
Found at i:4001398 original size:22 final size:24
Alignment explanation
Indices: 4001350--4001417 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 24
4001340 AAAATAAAAA
* * * *
4001350 TAAATATTTTATATAAAATCTATT
1 TAAATAATATATAAAAAATTTATT
*
4001374 TAAAT-ATAT-TAAAAATTTTATT
1 TAAATAATATATAAAAAATTTATT
4001396 TAAATAATATATAAAAAATTTA
1 TAAATAATATATAAAAAATTTA
4001418 AAATTTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 15 0.42
23 6 0.17
24 15 0.42
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (24 bp):
TAAATAATATATAAAAAATTTATT
Found at i:4001511 original size:16 final size:15
Alignment explanation
Indices: 4001454--4001512 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
4001444 AATCAAACTG
*
4001454 ATAAAATTTAATTTGA
1 ATAAAA-TTAATTTAA
*
4001470 ATCAAATTAATTTTAA
1 ATAAAATTAA-TTTAA
*
4001486 AAAAATATTAATTTAA
1 ATAAA-ATTAATTTAA
4001502 ATTAAAATTAA
1 A-TAAAATTAA
4001513 AAATTAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 4 0.11
16 23 0.66
17 8 0.23
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (15 bp):
ATAAAATTAATTTAA
Found at i:4007267 original size:26 final size:25
Alignment explanation
Indices: 4007237--4007298 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 25
4007227 TGGTGGGATT
*
4007237 GGGTGGGGTGGCGTGCGTTGGGGGTA
1 GGGTGGGGTGGCGTGAGTT-GGGGTA
* *
4007263 GGGTGGGGGTGGGGTGAGTTTGGGTA
1 GGGT-GGGGTGGCGTGAGTTGGGGTA
4007289 GGGTGGGGTG
1 GGGTGGGGTG
4007299 CATTAAGGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.19
26 13 0.41
27 13 0.41
ACGTcount: A:0.05, C:0.03, G:0.68, T:0.24
Consensus pattern (25 bp):
GGGTGGGGTGGCGTGAGTTGGGGTA
Found at i:4007582 original size:29 final size:28
Alignment explanation
Indices: 4007538--4007596 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
4007528 AAATTAAATA
** *
4007538 TTATATTTTGATTTTGTTATTTATTAAT
1 TTATATTTTGATTTTGAAATTTAATAAT
4007566 TTATAATTTT-ATATTTGAAATTTAATAAT
1 TTAT-ATTTTGAT-TTTGAAATTTAATAAT
4007595 TT
1 TT
4007597 TTGGTTGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (28 bp):
TTATATTTTGATTTTGAAATTTAATAAT
Found at i:4010469 original size:26 final size:26
Alignment explanation
Indices: 4010433--4010485 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
4010423 CATTTCAGGA
*
4010433 GCTGTTGGATTCTTGGGAGATAGCCG
1 GCTGTTGGATTCTTAGGAGATAGCCG
4010459 GCTGTTGGATTCTTAGGAGATAGCCG
1 GCTGTTGGATTCTTAGGAGATAGCCG
4010485 G
1 G
4010486 TGAATGAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.17, C:0.15, G:0.38, T:0.30
Consensus pattern (26 bp):
GCTGTTGGATTCTTAGGAGATAGCCG
Found at i:4011931 original size:23 final size:22
Alignment explanation
Indices: 4011873--4012193 Score: 80
Period size: 22 Copynumber: 14.4 Consensus size: 22
4011863 AAATTTATTT
* * *
4011873 ATAAATAATATTGTATTACAATTA
1 ATAAATAATA-T-TAATATAATAA
4011897 ATAAATAATATT-ATATGAATAA
1 ATAAATAATATTAATAT-AATAA
*
4011919 ATAATATAATATTAATATAATAT
1 ATAA-ATAATATTAATATAATAA
* * **
4011942 ATTAAT-AGA-TAATAGTAATTT
1 ATAAATAATATTAATA-TAATAA
* * **
4011963 AT-TATATTA-TAATAT-ATTC
1 ATAAATAATATTAATATAATAA
** *
4011982 ATAAATATATTCTAATAT-ATTA
1 ATAAATA-ATATTAATATAATAA
* *
4012004 CTAAATAATAAT-ATATTAATAA
1 ATAAATAATATTAATA-TAATAA
*
4012026 ATAAATCATATT-ATATTAATAA
1 ATAAATAATATTAATA-TAATAA
* *
4012048 AT-CAT-ATTTTAATA-AATAA
1 ATAAATAATATTAATATAATAA
* *
4012067 TATAATAATAAATATTTTTAATTTAATTA
1 -AT-A-AAT-AATA---TTAATATAATAA
* *
4012096 ATAAATATTA-TAATAATATATTA
1 ATAAATAATATTAAT-ATA-ATAA
*
4012119 ATAAATAATA-TATTATTAATAA
1 ATAAATAATATTAATA-TAATAA
* * *
4012141 ATACTATACTATTAATATAATAT
1 ATA-AATAATATTAATATAATAA
*
4012164 ATTAATAAATATT-AT-TAATAA
1 ATAAAT-AATATTAATATAATAA
4012185 ATAATATAA
1 ATAA-ATAA
4012194 AGAATAATAA
Statistics
Matches: 227, Mismatches: 42, Indels: 59
0.69 0.13 0.18
Matches are distributed among these distances:
19 10 0.04
20 20 0.09
21 41 0.18
22 65 0.29
23 53 0.23
24 18 0.08
25 5 0.02
26 3 0.01
27 1 0.00
28 7 0.03
29 4 0.02
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (22 bp):
ATAAATAATATTAATATAATAA
Found at i:4011990 original size:12 final size:11
Alignment explanation
Indices: 4011965--4012002 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
4011955 AGTAATTTAT
4011965 TATATT-ATAA
1 TATATTCATAA
4011975 TATATTCATAAA
1 TATATTCAT-AA
4011987 TATATTC-TAA
1 TATATTCATAA
4011997 TATATT
1 TATATT
4012003 ACTAAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 14 0.54
11 3 0.12
12 9 0.35
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (11 bp):
TATATTCATAA
Found at i:4011992 original size:22 final size:22
Alignment explanation
Indices: 4011893--4012061 Score: 101
Period size: 22 Copynumber: 8.0 Consensus size: 22
4011883 TTGTATTACA
4011893 ATTAATAAATA-A-TAT--TAT
1 ATTAATAAATATATTATAATAT
*
4011911 ATGAATAAATA-A-TAT-A-AT
1 ATTAATAAATATATTATAATAT
4011929 ATTAATATAATATATTAATAGATAAT
1 ATTAATA-AATATATT-ATA-AT-AT
* * *
4011955 AGTAATTTATTATATTATAATAT
1 ATTAA-TAAATATATTATAATAT
* *
4011978 ATTCATAAATATATTCTAATAT
1 ATTAATAAATATATTATAATAT
*
4012000 ATTACT-AA-ATA--ATAATAT
1 ATTAATAAATATATTATAATAT
* * *
4012018 ATTAATAAATAAATCATATTAT
1 ATTAATAAATATATTATAATAT
*
4012040 ATTAATAAATCATATTTTAATA
1 ATTAATAAAT-ATATTATAATA
4012062 AATAATATAA
Statistics
Matches: 116, Mismatches: 20, Indels: 25
0.72 0.12 0.16
Matches are distributed among these distances:
18 33 0.28
19 6 0.05
20 6 0.05
21 3 0.03
22 36 0.31
23 12 0.10
24 3 0.03
25 3 0.03
26 13 0.11
27 1 0.01
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTAATAAATATATTATAATAT
Found at i:4012010 original size:12 final size:10
Alignment explanation
Indices: 4011965--4012007 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
4011955 AGTAATTTAT
*
4011965 TATATTATAA
1 TATATTCTAA
4011975 TATATTCATAAA
1 TATATTC-T-AA
4011987 TATATTCTAA
1 TATATTCTAA
4011997 TATATTACTAA
1 TATATT-CTAA
4012008 ATAATAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 14 0.48
11 6 0.21
12 9 0.31
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (10 bp):
TATATTCTAA
Found at i:4012017 original size:18 final size:18
Alignment explanation
Indices: 4011893--4012162 Score: 127
Period size: 18 Copynumber: 14.6 Consensus size: 18
4011883 TTGTATTACA
*
4011893 ATTAATAAATAATATTAT
1 ATTAATAAATAATAATAT
*
4011911 ATGAATAAATAAT-ATA-
1 ATTAATAAATAATAATAT
*
4011927 A-T-ATTAAT-ATAATAT
1 ATTAATAAATAATAATAT
* *
4011942 ATTAATAGATAATAGTA-
1 ATTAATAAATAATAATAT
* * *
4011959 ATTTATTATATTATAATAT
1 A-TTAATAAATAATAATAT
*
4011978 ATTCATAAATATATTCTAATAT
1 ATTAATAAATA-A---TAATAT
*
4012000 ATTACTAAATAATAATAT
1 ATTAATAAATAATAATAT
4012018 ATTAATAAATAAATCATATTAT
1 ATTAATAAAT-AAT-A-A-TAT
*
4012040 ATTAATAAATCAT-AT-T
1 ATTAATAAATAATAATAT
4012056 -TTAATAAATAAT-ATA-
1 ATTAATAAATAATAATAT
* *
4012071 A-TAATAAATATTTTTAATTT
1 ATTAATAAATA---ATAATAT
4012091 AATTAATAAATATTATAATAATAT
1 -ATTAAT--A-A--ATAATAATAT
4012115 ATTAATAAATAAT-ATATT
1 ATTAATAAATAATAATA-T
*
4012133 ATTAATAAATACT-ATACT
1 ATTAATAAATAATAATA-T
4012151 ATTAATATAATA
1 ATTAATA-AATA
4012163 TATTAATAAA
Statistics
Matches: 195, Mismatches: 26, Indels: 61
0.69 0.09 0.22
Matches are distributed among these distances:
13 2 0.01
14 8 0.04
15 23 0.12
16 3 0.02
17 11 0.06
18 81 0.42
19 11 0.06
20 2 0.01
21 6 0.03
22 32 0.16
23 6 0.03
24 6 0.03
25 1 0.01
27 3 0.02
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (18 bp):
ATTAATAAATAATAATAT
Found at i:4012093 original size:21 final size:22
Alignment explanation
Indices: 4012064--4012125 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 22
4012054 TTTTAATAAA
4012064 TAATATAA-TAATAAATATTTT
1 TAATATAATTAATAAATATTTT
* *
4012085 TAATTTAATTAATAAATA-TTA
1 TAATATAATTAATAAATATTTT
4012106 TAATAATATATTAATAAATA
1 TAAT-ATA-ATTAATAAATA
4012126 ATATATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 13 0.37
22 11 0.31
23 11 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATATAATTAATAAATATTTT
Found at i:4012110 original size:49 final size:47
Alignment explanation
Indices: 4012051--4012182 Score: 114
Period size: 49 Copynumber: 2.8 Consensus size: 47
4012041 TTAATAAATC
*
4012051 ATATTTTAATAAATAATATAATAATAAATATTTTTAATTTAATTAATAA
1 ATATTATAATAAATAATAT-ATAATAAATATTTTTAATTT-ATTAATAA
* *
4012100 ATATTATAAT-AAT-ATAT-TAATAAATA-ATAT-A-TTATTAATAA
1 ATATTATAATAAATAATATATAATAAATATTTTTAATTTATTAATAA
* *
4012141 ATACTATACTATTAATATAATATATTAATAAATATTATTAAT
1 ATA-T-TA-TAATAA-ATAATATA-TAATAAATATTTTTAAT
4012183 AAATAATATA
Statistics
Matches: 65, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
41 11 0.17
42 3 0.05
43 3 0.05
44 5 0.08
45 10 0.15
46 2 0.03
47 8 0.12
48 3 0.05
49 18 0.28
50 1 0.02
51 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (47 bp):
ATATTATAATAAATAATATATAATAAATATTTTTAATTTATTAATAA
Found at i:4012162 original size:41 final size:43
Alignment explanation
Indices: 4012092--4012193 Score: 120
Period size: 41 Copynumber: 2.4 Consensus size: 43
4012082 TTTTAATTTA
*
4012092 ATTAATAAATATTATAATAATATATTAATA-AATAAT-ATATT
1 ATTAATAAATAATATAATAATATATTAATATAATAATAATATT
* * * *
4012133 ATTAATAAATACTATACTATTA-ATATAATATATTAATAAATATT
1 ATTAATAAATAATATAATAATATAT-TAATATAATAAT-AATATT
4012177 ATTAATAAATAATATAA
1 ATTAATAAATAATATAA
4012194 AGAATAATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
40 2 0.04
41 24 0.47
42 5 0.10
44 20 0.39
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (43 bp):
ATTAATAAATAATATAATAATATATTAATATAATAATAATATT
Found at i:4012260 original size:18 final size:17
Alignment explanation
Indices: 4012208--4012260 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
4012198 TAATAAATAG
* *
4012208 TTTATTTTAATTATT-T
1 TTTATATTAAATATTAT
*
4012224 TTTATATTAACATAATAT
1 TTTATATTAA-ATATTAT
4012242 TTTACTATTAAATATTAT
1 TTTA-TATTAAATATTAT
4012260 T
1 T
4012261 GTTAAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 9 0.30
17 3 0.10
18 12 0.40
19 6 0.20
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATATTAAATATTAT
Found at i:4012294 original size:20 final size:20
Alignment explanation
Indices: 4012216--4012295 Score: 55
Period size: 19 Copynumber: 4.2 Consensus size: 20
4012206 AGTTTATTTT
* *
4012216 AATTATTTTTTATATTAACA
1 AATTATTTTTAATATTAATA
*
4012236 TAA-TA-TTTTACTATTAA-A
1 -AATTATTTTTAATATTAATA
* * *
4012254 TATTATTGTTAA-AAT-AT-
1 AATTATTTTTAATATTAATA
4012271 AATTATTTTTAATATTAATA
1 AATTATTTTTAATATTAATA
4012291 AATTA
1 AATTA
4012296 ATAATAAATA
Statistics
Matches: 44, Mismatches: 9, Indels: 13
0.67 0.14 0.20
Matches are distributed among these distances:
17 12 0.27
18 7 0.16
19 16 0.36
20 7 0.16
21 2 0.05
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (20 bp):
AATTATTTTTAATATTAATA
Found at i:4012348 original size:25 final size:26
Alignment explanation
Indices: 4012293--4012349 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
4012283 TATTAATAAA
4012293 TTAATAATAAATAATTTTAATATATT
1 TTAATAATAAATAATTTTAATATATT
*
4012319 TTAATAATAAATAATTTTTA-ATATT
1 TTAATAATAAATAATTTTAATATATT
4012344 TTAATA
1 TTAATA
4012350 GTTATATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 11 0.37
26 19 0.63
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TTAATAATAAATAATTTTAATATATT
Found at i:4013135 original size:19 final size:20
Alignment explanation
Indices: 4013105--4013150 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
4013095 TATATATTTA
*
4013105 TATTATTTAATAA-ATAAAT
1 TATTATTAAATAATATAAAT
*
4013124 TTTTATTAAATAATATAAAT
1 TATTATTAAATAATATAAAT
4013144 TATTATT
1 TATTATT
4013151 TTAGATTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTATTAAATAATATAAAT
Found at i:4013466 original size:12 final size:13
Alignment explanation
Indices: 4013449--4013477 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4013439 TATGCGGAAA
4013449 GAGAAAAA-AGGG
1 GAGAAAAAGAGGG
4013461 GAGAAAAAGAGGG
1 GAGAAAAAGAGGG
4013474 GAGA
1 GAGA
4013478 GTCCAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (13 bp):
GAGAAAAAGAGGG
Found at i:4013631 original size:5 final size:6
Alignment explanation
Indices: 4013614--4013638 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4013604 TCAACTCACC
4013614 TCTTTT TCTTTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT T
4013639 TTAATATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TCTTTT
Found at i:4015458 original size:69 final size:69
Alignment explanation
Indices: 4015377--4015507 Score: 235
Period size: 69 Copynumber: 1.9 Consensus size: 69
4015367 ATAGTTCATG
* *
4015377 AATCTTATCAAATATTTATATTTTAATATATTTTAATTAAAAATTATTATTTTAATTTTATAGCT
1 AATCCTATCAAATATTTATATTTTAATATATTTTAATTAAAAATTATTATTTTAACTTTATAGCT
4015442 TATA
66 TATA
*
4015446 AATCCTATCAAATTTTTATATTTTAATATATTTTAATTAAAAATTATTATTTTAACTTTATA
1 AATCCTATCAAATATTTATATTTTAATATATTTTAATTAAAAATTATTATTTTAACTTTATA
4015508 TATTTGAATT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.53
Consensus pattern (69 bp):
AATCCTATCAAATATTTATATTTTAATATATTTTAATTAAAAATTATTATTTTAACTTTATAGCT
TATA
Found at i:4018177 original size:49 final size:49
Alignment explanation
Indices: 4018105--4018203 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
4018095 AGTGATTTAG
* * *
4018105 ACTTAGCTACTGCTAAGTAGGTATTGATGGCATTAATGAACTTGCCATA
1 ACTTAGCAACTGCTAAGTAGGTATTGAAGGCACTAATGAACTTGCCATA
4018154 ACTTAGCAACTGCTAAGTAGGTATTGAAGGCACTAATGAACTTGCCATA
1 ACTTAGCAACTGCTAAGTAGGTATTGAAGGCACTAATGAACTTGCCATA
4018203 A
1 A
4018204 TTGTGCTACA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (49 bp):
ACTTAGCAACTGCTAAGTAGGTATTGAAGGCACTAATGAACTTGCCATA
Found at i:4019526 original size:13 final size:13
Alignment explanation
Indices: 4019508--4019532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4019498 AGGGCATGTC
4019508 TTAGTAAGTATTT
1 TTAGTAAGTATTT
4019521 TTAGTAAGTATT
1 TTAGTAAGTATT
4019533 CAATTAGCAA
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
TTAGTAAGTATTT
Found at i:4021492 original size:18 final size:18
Alignment explanation
Indices: 4021469--4021504 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4021459 AATTAAAATT
* *
4021469 ACAAAAGTAAAAATAAAA
1 ACAAAAGCAAAAAGAAAA
4021487 ACAAAAGCAAAAAGAAAA
1 ACAAAAGCAAAAAGAAAA
4021505 GATAACTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.78, C:0.08, G:0.08, T:0.06
Consensus pattern (18 bp):
ACAAAAGCAAAAAGAAAA
Found at i:4021979 original size:26 final size:26
Alignment explanation
Indices: 4021930--4021988 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
4021920 TGGTGGGATT
*
4021930 GGGT-GGGGTGGCGTGCGTTGGGGTA
1 GGGTGGGGGTGGCGTGAGTTGGGGTA
* *
4021955 GGGTGGGGGTGGGGTGAGTTTGGGTA
1 GGGTGGGGGTGGCGTGAGTTGGGGTA
4021981 GGGTGGGG
1 GGGTGGGG
4021989 TGCATTAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 4 0.13
26 26 0.87
ACGTcount: A:0.05, C:0.03, G:0.68, T:0.24
Consensus pattern (26 bp):
GGGTGGGGGTGGCGTGAGTTGGGGTA
Found at i:4022272 original size:29 final size:28
Alignment explanation
Indices: 4022228--4022286 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
4022218 AAATTAAATA
** *
4022228 TTATATTTTGATTTTGTTATTTATTAAT
1 TTATATTTTGATTTTGAAATTTAATAAT
4022256 TTATAATTTT-ATATTTGAAATTTAATAAT
1 TTAT-ATTTTGAT-TTTGAAATTTAATAAT
4022285 TT
1 TT
4022287 TTTGGTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (28 bp):
TTATATTTTGATTTTGAAATTTAATAAT
Found at i:4025156 original size:26 final size:26
Alignment explanation
Indices: 4025120--4025172 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
4025110 CATTTCAGGA
*
4025120 GCTGTTGGATTCTTGGGAGATAGCCG
1 GCTGTTGGATTCTTAGGAGATAGCCG
4025146 GCTGTTGGATTCTTAGGAGATAGCCG
1 GCTGTTGGATTCTTAGGAGATAGCCG
4025172 G
1 G
4025173 TGAATGAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.17, C:0.15, G:0.38, T:0.30
Consensus pattern (26 bp):
GCTGTTGGATTCTTAGGAGATAGCCG
Found at i:4026617 original size:23 final size:22
Alignment explanation
Indices: 4026559--4026879 Score: 80
Period size: 22 Copynumber: 14.4 Consensus size: 22
4026549 AAATTTATTT
* * *
4026559 ATAAATAATATTGTATTACAATTA
1 ATAAATAATA-T-TAATATAATAA
4026583 ATAAATAATATT-ATATGAATAA
1 ATAAATAATATTAATAT-AATAA
*
4026605 ATAATATAATATTAATATAATAT
1 ATAA-ATAATATTAATATAATAA
* * **
4026628 ATTAAT-AGA-TAATAGTAATTT
1 ATAAATAATATTAATA-TAATAA
* * **
4026649 AT-TATATTA-TAATAT-ATTC
1 ATAAATAATATTAATATAATAA
** *
4026668 ATAAATATATTCTAATAT-ATTA
1 ATAAATA-ATATTAATATAATAA
* *
4026690 CTAAATAATAAT-ATATTAATAA
1 ATAAATAATATTAATA-TAATAA
*
4026712 ATAAATCATATT-ATATTAATAA
1 ATAAATAATATTAATA-TAATAA
* *
4026734 AT-CAT-ATTTTAATA-AATAA
1 ATAAATAATATTAATATAATAA
* *
4026753 TATAATAATAAATATTTTTAATTTAATTA
1 -AT-A-AAT-AATA---TTAATATAATAA
* *
4026782 ATAAATATTA-TAATAATATATTA
1 ATAAATAATATTAAT-ATA-ATAA
*
4026805 ATAAATAATA-TATTATTAATAA
1 ATAAATAATATTAATA-TAATAA
* * *
4026827 ATACTATACTATTAATATAATAT
1 ATA-AATAATATTAATATAATAA
*
4026850 ATTAATAAATATT-AT-TAATAA
1 ATAAAT-AATATTAATATAATAA
4026871 ATAATATAA
1 ATAA-ATAA
4026880 AGAATAATAA
Statistics
Matches: 227, Mismatches: 42, Indels: 59
0.69 0.13 0.18
Matches are distributed among these distances:
19 10 0.04
20 20 0.09
21 41 0.18
22 65 0.29
23 53 0.23
24 18 0.08
25 5 0.02
26 3 0.01
27 1 0.00
28 7 0.03
29 4 0.02
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (22 bp):
ATAAATAATATTAATATAATAA
Found at i:4026676 original size:12 final size:11
Alignment explanation
Indices: 4026651--4026688 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
4026641 AGTAATTTAT
4026651 TATATT-ATAA
1 TATATTCATAA
4026661 TATATTCATAAA
1 TATATTCAT-AA
4026673 TATATTC-TAA
1 TATATTCATAA
4026683 TATATT
1 TATATT
4026689 ACTAAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 14 0.54
11 3 0.12
12 9 0.35
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (11 bp):
TATATTCATAA
Found at i:4026678 original size:22 final size:22
Alignment explanation
Indices: 4026579--4026747 Score: 101
Period size: 22 Copynumber: 8.0 Consensus size: 22
4026569 TTGTATTACA
4026579 ATTAATAAATA-A-TAT--TAT
1 ATTAATAAATATATTATAATAT
*
4026597 ATGAATAAATA-A-TAT-A-AT
1 ATTAATAAATATATTATAATAT
4026615 ATTAATATAATATATTAATAGATAAT
1 ATTAATA-AATATATT-ATA-AT-AT
* * *
4026641 AGTAATTTATTATATTATAATAT
1 ATTAA-TAAATATATTATAATAT
* *
4026664 ATTCATAAATATATTCTAATAT
1 ATTAATAAATATATTATAATAT
*
4026686 ATTACT-AA-ATA--ATAATAT
1 ATTAATAAATATATTATAATAT
* * *
4026704 ATTAATAAATAAATCATATTAT
1 ATTAATAAATATATTATAATAT
*
4026726 ATTAATAAATCATATTTTAATA
1 ATTAATAAAT-ATATTATAATA
4026748 AATAATATAA
Statistics
Matches: 116, Mismatches: 20, Indels: 25
0.72 0.12 0.16
Matches are distributed among these distances:
18 33 0.28
19 6 0.05
20 6 0.05
21 3 0.03
22 36 0.31
23 12 0.10
24 3 0.03
25 3 0.03
26 13 0.11
27 1 0.01
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTAATAAATATATTATAATAT
Found at i:4026696 original size:12 final size:10
Alignment explanation
Indices: 4026651--4026693 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
4026641 AGTAATTTAT
*
4026651 TATATTATAA
1 TATATTCTAA
4026661 TATATTCATAAA
1 TATATTC-T-AA
4026673 TATATTCTAA
1 TATATTCTAA
4026683 TATATTACTAA
1 TATATT-CTAA
4026694 ATAATAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 14 0.48
11 6 0.21
12 9 0.31
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (10 bp):
TATATTCTAA
Found at i:4026703 original size:18 final size:18
Alignment explanation
Indices: 4026579--4026848 Score: 127
Period size: 18 Copynumber: 14.6 Consensus size: 18
4026569 TTGTATTACA
*
4026579 ATTAATAAATAATATTAT
1 ATTAATAAATAATAATAT
*
4026597 ATGAATAAATAAT-ATA-
1 ATTAATAAATAATAATAT
*
4026613 A-T-ATTAAT-ATAATAT
1 ATTAATAAATAATAATAT
* *
4026628 ATTAATAGATAATAGTA-
1 ATTAATAAATAATAATAT
* * *
4026645 ATTTATTATATTATAATAT
1 A-TTAATAAATAATAATAT
*
4026664 ATTCATAAATATATTCTAATAT
1 ATTAATAAATA-A---TAATAT
*
4026686 ATTACTAAATAATAATAT
1 ATTAATAAATAATAATAT
4026704 ATTAATAAATAAATCATATTAT
1 ATTAATAAAT-AAT-A-A-TAT
*
4026726 ATTAATAAATCAT-AT-T
1 ATTAATAAATAATAATAT
4026742 -TTAATAAATAAT-ATA-
1 ATTAATAAATAATAATAT
* *
4026757 A-TAATAAATATTTTTAATTT
1 ATTAATAAATA---ATAATAT
4026777 AATTAATAAATATTATAATAATAT
1 -ATTAAT--A-A--ATAATAATAT
4026801 ATTAATAAATAAT-ATATT
1 ATTAATAAATAATAATA-T
*
4026819 ATTAATAAATACT-ATACT
1 ATTAATAAATAATAATA-T
4026837 ATTAATATAATA
1 ATTAATA-AATA
4026849 TATTAATAAA
Statistics
Matches: 195, Mismatches: 26, Indels: 61
0.69 0.09 0.22
Matches are distributed among these distances:
13 2 0.01
14 8 0.04
15 23 0.12
16 3 0.02
17 11 0.06
18 81 0.42
19 11 0.06
20 2 0.01
21 6 0.03
22 32 0.16
23 6 0.03
24 6 0.03
25 1 0.01
27 3 0.02
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (18 bp):
ATTAATAAATAATAATAT
Found at i:4026779 original size:21 final size:22
Alignment explanation
Indices: 4026750--4026811 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 22
4026740 TTTTAATAAA
4026750 TAATATAA-TAATAAATATTTT
1 TAATATAATTAATAAATATTTT
* *
4026771 TAATTTAATTAATAAATA-TTA
1 TAATATAATTAATAAATATTTT
4026792 TAATAATATATTAATAAATA
1 TAAT-ATA-ATTAATAAATA
4026812 ATATATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 13 0.37
22 11 0.31
23 11 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATATAATTAATAAATATTTT
Found at i:4026796 original size:49 final size:47
Alignment explanation
Indices: 4026737--4026868 Score: 114
Period size: 49 Copynumber: 2.8 Consensus size: 47
4026727 TTAATAAATC
*
4026737 ATATTTTAATAAATAATATAATAATAAATATTTTTAATTTAATTAATAA
1 ATATTATAATAAATAATAT-ATAATAAATATTTTTAATTT-ATTAATAA
* *
4026786 ATATTATAAT-AAT-ATAT-TAATAAATA-ATAT-A-TTATTAATAA
1 ATATTATAATAAATAATATATAATAAATATTTTTAATTTATTAATAA
* *
4026827 ATACTATACTATTAATATAATATATTAATAAATATTATTAAT
1 ATA-T-TA-TAATAA-ATAATATA-TAATAAATATTTTTAAT
4026869 AAATAATATA
Statistics
Matches: 65, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
41 11 0.17
42 3 0.05
43 3 0.05
44 5 0.08
45 10 0.15
46 2 0.03
47 8 0.12
48 3 0.05
49 18 0.28
50 1 0.02
51 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (47 bp):
ATATTATAATAAATAATATATAATAAATATTTTTAATTTATTAATAA
Found at i:4026848 original size:41 final size:43
Alignment explanation
Indices: 4026778--4026879 Score: 120
Period size: 41 Copynumber: 2.4 Consensus size: 43
4026768 TTTTAATTTA
*
4026778 ATTAATAAATATTATAATAATATATTAATA-AATAAT-ATATT
1 ATTAATAAATAATATAATAATATATTAATATAATAATAATATT
* * * *
4026819 ATTAATAAATACTATACTATTA-ATATAATATATTAATAAATATT
1 ATTAATAAATAATATAATAATATAT-TAATATAATAAT-AATATT
4026863 ATTAATAAATAATATAA
1 ATTAATAAATAATATAA
4026880 AGAATAATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
40 2 0.04
41 24 0.47
42 5 0.10
44 20 0.39
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (43 bp):
ATTAATAAATAATATAATAATATATTAATATAATAATAATATT
Found at i:4026946 original size:18 final size:17
Alignment explanation
Indices: 4026894--4026946 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
4026884 TAATAAATAG
* *
4026894 TTTATTTTAATTATT-T
1 TTTATATTAAATATTAT
*
4026910 TTTATATTAACATAATAT
1 TTTATATTAA-ATATTAT
4026928 TTTACTATTAAATATTAT
1 TTTA-TATTAAATATTAT
4026946 T
1 T
4026947 GTTAAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 9 0.30
17 3 0.10
18 12 0.40
19 6 0.20
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATATTAAATATTAT
Found at i:4026980 original size:20 final size:20
Alignment explanation
Indices: 4026902--4026981 Score: 55
Period size: 19 Copynumber: 4.2 Consensus size: 20
4026892 AGTTTATTTT
* *
4026902 AATTATTTTTTATATTAACA
1 AATTATTTTTAATATTAATA
*
4026922 TAA-TA-TTTTACTATTAA-A
1 -AATTATTTTTAATATTAATA
* * *
4026940 TATTATTGTTAA-AAT-AT-
1 AATTATTTTTAATATTAATA
4026957 AATTATTTTTAATATTAATA
1 AATTATTTTTAATATTAATA
4026977 AATTA
1 AATTA
4026982 ATAATAAATA
Statistics
Matches: 44, Mismatches: 9, Indels: 13
0.67 0.14 0.20
Matches are distributed among these distances:
17 12 0.27
18 7 0.16
19 16 0.36
20 7 0.16
21 2 0.05
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (20 bp):
AATTATTTTTAATATTAATA
Found at i:4027013 original size:25 final size:25
Alignment explanation
Indices: 4026966--4027034 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
4026956 TAATTATTTT
* *
4026966 TAATATTAATA-AATTAATAATAAA
1 TAATTTTAATATATTTAATAATAAA
4026990 TAATTTTAATATATTTAATAATAAA
1 TAATTTTAATATATTTAATAATAAA
4027015 TAATTTTTAATAT-TTTAATA
1 TAA-TTTTAATATATTTAATA
4027035 GTTATATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
24 10 0.24
25 22 0.54
26 9 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TAATTTTAATATATTTAATAATAAA
Found at i:4027020 original size:15 final size:15
Alignment explanation
Indices: 4026964--4027020 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 15
4026954 TATAATTATT
*
4026964 TTTAAT-ATTAATAA
1 TTTAATAATAAATAA
*
4026978 ATTAATAATAAATAA
1 TTTAATAATAAATAA
4026993 TTT--TAAT--AT-A
1 TTTAATAATAAATAA
4027003 TTTAATAATAAATAA
1 TTTAATAATAAATAA
4027018 TTT
1 TTT
4027021 TTAATATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
10 4 0.12
11 2 0.06
12 4 0.12
13 4 0.12
14 7 0.21
15 13 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAATAATAAATAA
Found at i:4027818 original size:19 final size:20
Alignment explanation
Indices: 4027788--4027833 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
4027778 TATATATTTA
*
4027788 TATTATTTAATAA-ATAAAT
1 TATTATTAAATAATATAAAT
*
4027807 TTTTATTAAATAATATAAAT
1 TATTATTAAATAATATAAAT
4027827 TATTATT
1 TATTATT
4027834 TTAGATTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTATTAAATAATATAAAT
Found at i:4028149 original size:12 final size:13
Alignment explanation
Indices: 4028132--4028160 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4028122 TATGCGGAAA
4028132 GAGAAAAA-AGGG
1 GAGAAAAAGAGGG
4028144 GAGAAAAAGAGGG
1 GAGAAAAAGAGGG
4028157 GAGA
1 GAGA
4028161 GTCCAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (13 bp):
GAGAAAAAGAGGG
Found at i:4030128 original size:67 final size:69
Alignment explanation
Indices: 4030042--4030180 Score: 237
Period size: 68 Copynumber: 2.0 Consensus size: 69
4030032 TCTAATTCGA
* *
4030042 ATAGTTTATGAATCTTATCAAATATTT-TATTTTAATATATTTTAATTAAAAATTATTATTTTAA
1 ATAGCTTATGAATCCTATCAAATATTTATATTTTAATATATTTTAATTAAAAATTATTATTTTAA
4030106 -TTT
66 CTTT
*
4030109 ATAGCTTATGAATCCTATCAAATTTTTATATTTTAATATATTTTAATTAAAAATTATTATTTTAA
1 ATAGCTTATGAATCCTATCAAATATTTATATTTTAATATATTTTAATTAAAAATTATTATTTTAA
4030174 CTTT
66 CTTT
4030178 ATA
1 ATA
4030181 TATTGAATTT
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
67 24 0.36
68 37 0.55
69 6 0.09
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (69 bp):
ATAGCTTATGAATCCTATCAAATATTTATATTTTAATATATTTTAATTAAAAATTATTATTTTAA
CTTT
Found at i:4030173 original size:29 final size:29
Alignment explanation
Indices: 4030068--4030173 Score: 86
Period size: 31 Copynumber: 3.3 Consensus size: 29
4030058 ATCAAATATT
4030068 TTATTTTAATATATTTTAATTAAAAATTA
1 TTATTTTAATATATTTTAATTAAAAATTA
* * *
4030097 TTATTTTAATTTATAGCTTATGAATCCTATCAAATTT
1 TTATTTTAA--TATA--TT-TTAAT--TA-AAAATTA
*
4030134 TTATATTTTAATATATTTTAATTAAAAATTA
1 TTAT-TTTA-ATATATTTTAATTAAAAATTA
4030165 TTATTTTAA
1 TTATTTTAA
4030174 CTTTATATAT
Statistics
Matches: 59, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
29 10 0.17
30 3 0.05
31 13 0.22
32 2 0.03
33 2 0.03
34 8 0.14
35 2 0.03
36 2 0.03
37 13 0.22
38 3 0.05
39 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (29 bp):
TTATTTTAATATATTTTAATTAAAAATTA
Found at i:4030182 original size:34 final size:33
Alignment explanation
Indices: 4030064--4030184 Score: 102
Period size: 34 Copynumber: 3.5 Consensus size: 33
4030054 TCTTATCAAA
*
4030064 TATTTTATTTTAATATATTTTAATTAAAAATTAT
1 TATTTTAATTT-ATATATTTTAATTAAAAATTAT
** * * *
4030098 TATTTTAATTTATAGCTTATGAATCCTATCAAATTTT
1 TATTTTAATTTATATATT-TTAAT--TA-AAAATTAT
* *
4030135 TATATT--TTAATATATTTTAATTAAAAATTAT
1 TATTTTAATTTATATATTTTAATTAAAAATTAT
4030166 TATTTTAACTTTATATATT
1 TATTTTAA-TTTATATATT
4030185 GAATTTGAAT
Statistics
Matches: 65, Mismatches: 15, Indels: 14
0.69 0.16 0.15
Matches are distributed among these distances:
31 11 0.17
32 2 0.03
33 5 0.08
34 27 0.42
35 7 0.11
36 2 0.03
37 11 0.17
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (33 bp):
TATTTTAATTTATATATTTTAATTAAAAATTAT
Found at i:4032862 original size:49 final size:49
Alignment explanation
Indices: 4032790--4032888 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
4032780 TGATTTAGAC
* * *
4032790 TTAGCTACTGCTAAGTAGGTATTGATGGCATTAATGAACTTGCCATAAT
1 TTAGCAACTGCTAAGTAGGTATTGAAGGCACTAATGAACTTGCCATAAT
4032839 TTAGCAACTGCTAAGTAGGTATTGAAGGCACTAATGAACTTGCCATAAT
1 TTAGCAACTGCTAAGTAGGTATTGAAGGCACTAATGAACTTGCCATAAT
4032888 T
1 T
4032889 GTGCTACATC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (49 bp):
TTAGCAACTGCTAAGTAGGTATTGAAGGCACTAATGAACTTGCCATAAT
Found at i:4034207 original size:13 final size:13
Alignment explanation
Indices: 4034189--4034213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4034179 AGGGCATGTC
4034189 TTAGTAAGTATTT
1 TTAGTAAGTATTT
4034202 TTAGTAAGTATT
1 TTAGTAAGTATT
4034214 CAATTAGCAA
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
TTAGTAAGTATTT
Found at i:4036068 original size:52 final size:47
Alignment explanation
Indices: 4036000--4036136 Score: 123
Period size: 48 Copynumber: 2.7 Consensus size: 47
4035990 AAATATATCT
* *
4036000 AATTATTCCACAATTTGAGCTAAATTAGAAATATCTTTTCTTTTTAATTTTTA
1 AATT-TTCCACTATTTGAGCT-AATTAG-AA-A--TTTTCTTTTTAATTTCTA
* *
4036053 AATTTTCCACTATTTGGACCTATTTAGAAATTTTCTTTTTAATTTCTA
1 AATTTTCCACTATTT-GAGCTAATTAGAAATTTTCTTTTTAATTTCTA
* *
4036101 AACTTTT-CACTATTTGAGTTTATTTAGAAAATTTTC
1 AA-TTTTCCACTATTTGAG-CTAATTAG-AAATTTTC
4036137 ATTTCTCTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
47 2 0.03
48 34 0.46
49 12 0.16
50 1 0.01
51 2 0.03
52 15 0.20
53 8 0.11
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (47 bp):
AATTTTCCACTATTTGAGCTAATTAGAAATTTTCTTTTTAATTTCTA
Found at i:4036125 original size:48 final size:49
Alignment explanation
Indices: 4036035--4036136 Score: 138
Period size: 48 Copynumber: 2.1 Consensus size: 49
4036025 TAGAAATATC
*
4036035 TTTTCTTTTTAATTTTTAAATTTTCCACTATTTGGACCTATTTAG-AAA
1 TTTTCTTTTTAATTTCTAAATTTTCCACTATTTGGACCTATTTAGAAAA
**
4036083 TTTTCTTTTTAATTTCTAAACTTTT-CACTATTT-GAGTTTATTTAGAAAA
1 TTTTCTTTTTAATTTCTAAA-TTTTCCACTATTTGGA-CCTATTTAGAAAA
4036132 TTTTC
1 TTTTC
4036137 ATTTCTCTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
47 2 0.04
48 34 0.71
49 12 0.25
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (49 bp):
TTTTCTTTTTAATTTCTAAATTTTCCACTATTTGGACCTATTTAGAAAA
Found at i:4037399 original size:33 final size:33
Alignment explanation
Indices: 4037362--4037428 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
4037352 CAAAAAAAGA
4037362 AAATTTCCAATATGGATGGCCTATACTATTGAC
1 AAATTTCCAATATGGATGGCCTATACTATTGAC
*
4037395 AAATTTCCAATGTGGATGGCCTATACTATTGAC
1 AAATTTCCAATATGGATGGCCTATACTATTGAC
4037428 A
1 A
4037429 TATAGACGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (33 bp):
AAATTTCCAATATGGATGGCCTATACTATTGAC
Found at i:4041472 original size:21 final size:21
Alignment explanation
Indices: 4041428--4041475 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
4041418 CTTGTAATAT
*
4041428 ATTTTGATAATCATTAATACA
1 ATTTTGATAATCATTAATAAA
** *
4041449 ATTTTGATAATTTTTTATAAA
1 ATTTTGATAATCATTAATAAA
4041470 ATTTTG
1 ATTTTG
4041476 GTAACTTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (21 bp):
ATTTTGATAATCATTAATAAA
Found at i:4041766 original size:22 final size:22
Alignment explanation
Indices: 4041738--4041780 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4041728 ATTTGTAATA
*
4041738 TAAAAAATTAGCATGTGTTATG
1 TAAAAAATTAACATGTGTTATG
4041760 TAAAAAATTAACATGTGTTAT
1 TAAAAAATTAACATGTGTTAT
4041781 AATTGCTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
TAAAAAATTAACATGTGTTATG
Found at i:4043497 original size:20 final size:20
Alignment explanation
Indices: 4043474--4043540 Score: 95
Period size: 20 Copynumber: 3.4 Consensus size: 20
4043464 CTATTTCATT
4043474 TTTAGTTTATTTTTTAATGA
1 TTTAGTTTATTTTTTAATGA
4043494 TTTAGTTT-TTCTATTTAAT--
1 TTTAGTTTATT-T-TTTAATGA
4043513 TTTAGTTTATTTTTTAATGA
1 TTTAGTTTATTTTTTAATGA
4043533 TTTAGTTT
1 TTTAGTTT
4043541 CTAATTTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
18 6 0.14
19 11 0.26
20 19 0.45
21 6 0.14
ACGTcount: A:0.22, C:0.01, G:0.09, T:0.67
Consensus pattern (20 bp):
TTTAGTTTATTTTTTAATGA
Found at i:4043527 original size:39 final size:40
Alignment explanation
Indices: 4043453--4043540 Score: 151
Period size: 39 Copynumber: 2.2 Consensus size: 40
4043443 ACTTGCTTTT
* *
4043453 ATTTTGTTTTTCTATTTCATTTTTAGTTTATTTTTTAATG
1 ATTTAGTTTTTCTATTTCAATTTTAGTTTATTTTTTAATG
4043493 ATTTAGTTTTTCTATTT-AATTTTAGTTTATTTTTTAATG
1 ATTTAGTTTTTCTATTTCAATTTTAGTTTATTTTTTAATG
4043532 ATTTAGTTT
1 ATTTAGTTT
4043541 CTAATTTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 30 0.65
40 16 0.35
ACGTcount: A:0.20, C:0.03, G:0.08, T:0.68
Consensus pattern (40 bp):
ATTTAGTTTTTCTATTTCAATTTTAGTTTATTTTTTAATG
Found at i:4043548 original size:21 final size:20
Alignment explanation
Indices: 4043474--4043548 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
4043464 CTATTTCATT
* *
4043474 TTTAGTTTATTTTTTAATGA
1 TTTAGTTTCTATTTTAATGA
4043494 TTTAGTTTTTCTA-TTTAAT--
1 TTTAG--TTTCTATTTTAATGA
* *
4043513 TTTAGTTTATTTTTTAATGA
1 TTTAGTTTCTATTTTAATGA
4043533 TTTAGTTTCTAATTTT
1 TTTAGTTTCT-ATTTT
4043549 TATATGCAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
17 4 0.09
18 6 0.14
19 5 0.12
20 14 0.33
21 10 0.23
22 4 0.09
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTAGTTTCTATTTTAATGA
Found at i:4045337 original size:13 final size:12
Alignment explanation
Indices: 4045318--4045344 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4045308 TGTAATCAAT
4045318 TTATTTTTTAAA
1 TTATTTTTTAAA
4045330 TTATTTTTTAAA
1 TTATTTTTTAAA
4045342 TTA
1 TTA
4045345 AAAATATATC
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):
TTATTTTTTAAA
Found at i:4048617 original size:16 final size:16
Alignment explanation
Indices: 4048596--4048639 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
4048586 TGAGAGGAAT
4048596 AATAATTAAAATAAAC
1 AATAATTAAAATAAAC
* * *
4048612 AATAATTCATATAAAT
1 AATAATTAAAATAAAC
4048628 AATAACTTAAAA
1 AATAA-TTAAAA
4048640 CAAAATTTTC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAATTAAAATAAAC
Found at i:4052374 original size:20 final size:22
Alignment explanation
Indices: 4052332--4052374 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4052322 TGTAACGACC
**
4052332 TTTTTGGTTGGATAAAATTCAA
1 TTTTTGGTTGGATAAAAAACAA
4052354 TTTTTGGTT-GA-AAAAAACAA
1 TTTTTGGTTGGATAAAAAACAA
4052374 T
1 T
4052375 ATTTAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (22 bp):
TTTTTGGTTGGATAAAAAACAA
Found at i:4052438 original size:15 final size:15
Alignment explanation
Indices: 4052407--4052467 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 15
4052397 TTTAATCAAA
*
4052407 TTAATTGAATTTA-TT
1 TTAATT-AATTAATTT
4052422 TTAATTAATTAATTT
1 TTAATTAATTAATTT
* *
4052437 TTAA-AAATAAAATTT
1 TTAATTAAT-TAATTT
4052452 TTAATTTAATTAATTT
1 TTAA-TTAATTAATTT
4052468 ATTTTAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 8 0.22
15 21 0.57
16 5 0.14
17 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TTAATTAATTAATTT
Found at i:4052577 original size:56 final size:57
Alignment explanation
Indices: 4052490--4052603 Score: 212
Period size: 56 Copynumber: 2.0 Consensus size: 57
4052480 ATCGAATCTA
4052490 TAAAATAAATAATACATCGAAATGATCTTCATGACTTCAAAAAAAAGTCGTGTACGC
1 TAAAATAAATAATACATCGAAATGATCTTCATGACTTCAAAAAAAAGTCGTGTACGC
*
4052547 TAAAA-AAATAATACATCGAAATGATCTTCATGACTTCAAAAAAAGGTCGTGTACGC
1 TAAAATAAATAATACATCGAAATGATCTTCATGACTTCAAAAAAAAGTCGTGTACGC
4052603 T
1 T
4052604 GAGTCCATGC
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 51 0.91
57 5 0.09
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (57 bp):
TAAAATAAATAATACATCGAAATGATCTTCATGACTTCAAAAAAAAGTCGTGTACGC
Found at i:4053997 original size:17 final size:17
Alignment explanation
Indices: 4053965--4053998 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4053955 TTCTCAAAAA
* *
4053965 ATATTTTATCTTTTTTT
1 ATATTTTATATATTTTT
4053982 ATATTTTATATATTTTT
1 ATATTTTATATATTTTT
4053999 TTAAAATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
ATATTTTATATATTTTT
Found at i:4058798 original size:27 final size:27
Alignment explanation
Indices: 4058763--4058816 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
4058753 CTATAAGTAA
* *
4058763 ATTTTAATAACTTTTGATATAATTTTG
1 ATTTCAATAACTTTTGATAAAATTTTG
4058790 ATTTCAATAACTTTTGATAAAATTTTG
1 ATTTCAATAACTTTTGATAAAATTTTG
4058817 GTAACCTTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.52
Consensus pattern (27 bp):
ATTTCAATAACTTTTGATAAAATTTTG
Found at i:4058821 original size:21 final size:21
Alignment explanation
Indices: 4058797--4058905 Score: 71
Period size: 21 Copynumber: 5.3 Consensus size: 21
4058787 TTGATTTCAA
*
4058797 TAACTTTTGATAAAATTTTGG
1 TAACTTTTAATAAAATTTTGG
* ** *
4058818 TAAC-CTTCGTACAATTTTGG
1 TAACTTTTAATAAAATTTTGG
* * *
4058838 TAACTTGTAAT-ATATTTTGA
1 TAACTTTTAATAAAATTTTGG
* * *
4058858 TAA-TCATTAATACAATTTTGA
1 TAACT-TTTAATAAAATTTTGG
* *
4058879 TAATTTTTTATAAAATTTTGG
1 TAACTTTTAATAAAATTTTGG
4058900 TAACTT
1 TAACTT
4058906 CTTCCTCTCG
Statistics
Matches: 64, Mismatches: 20, Indels: 8
0.70 0.22 0.09
Matches are distributed among these distances:
19 1 0.02
20 29 0.45
21 33 0.52
22 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (21 bp):
TAACTTTTAATAAAATTTTGG
Found at i:4058842 original size:41 final size:41
Alignment explanation
Indices: 4058796--4058903 Score: 110
Period size: 41 Copynumber: 2.6 Consensus size: 41
4058786 TTTGATTTCA
* * **
4058796 ATAACTTTTGATAAAATTTTGGTAACCTTCGTACAATTTTG
1 ATAACTTTTAATAAAATTTTGGTAACATTAATACAATTTTG
* * * *
4058837 GTAACTTGTAAT-ATATTTTGATAATCATTAATACAATTTTG
1 ATAACTTTTAATAAAATTTTGGTAA-CATTAATACAATTTTG
* *
4058878 ATAATTTTTTATAAAATTTTGGTAAC
1 ATAACTTTTAATAAAATTTTGGTAAC
4058904 TTCTTCCTCT
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
40 10 0.20
41 31 0.61
42 10 0.20
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.46
Consensus pattern (41 bp):
ATAACTTTTAATAAAATTTTGGTAACATTAATACAATTTTG
Found at i:4059179 original size:22 final size:22
Alignment explanation
Indices: 4059151--4059193 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4059141 ATTTGTAATA
*
4059151 TAAAAAATTAGCATGTGTTATG
1 TAAAAAATTAACATGTGTTATG
4059173 TAAAAAATTAACATGTGTTAT
1 TAAAAAATTAACATGTGTTAT
4059194 AATTGCTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
TAAAAAATTAACATGTGTTATG
Found at i:4060946 original size:19 final size:19
Alignment explanation
Indices: 4060885--4060950 Score: 82
Period size: 19 Copynumber: 3.4 Consensus size: 19
4060875 CTATTTCATT
4060885 TTTAGTTTATTTTTTAATGA
1 TTTAGTTTA-TTTTTAATGA
*
4060905 TTTAGTTTTTCTATTTAAT--
1 TTTAGTTTAT-T-TTTAATGA
4060924 TTTAGTTTATTTTTAATGA
1 TTTAGTTTATTTTTAATGA
4060943 TTTAGTTT
1 TTTAGTTT
4060951 CTAATTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 6 0.15
18 1 0.03
19 18 0.45
20 9 0.22
21 6 0.15
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTAGTTTATTTTTAATGA
Found at i:4060946 original size:38 final size:40
Alignment explanation
Indices: 4060864--4060950 Score: 142
Period size: 38 Copynumber: 2.2 Consensus size: 40
4060854 ACTTGCTTTT
* *
4060864 ATTTTGTTTTTCTATTTCATTTTTAGTTTATTTTTTAATG
1 ATTTAGTTTTTCTATTTCAATTTTAGTTTATTTTTTAATG
4060904 ATTTAGTTTTTCTATTT-AATTTTAGTTTA-TTTTTAATG
1 ATTTAGTTTTTCTATTTCAATTTTAGTTTATTTTTTAATG
4060942 ATTTAGTTT
1 ATTTAGTTT
4060951 CTAATTTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
38 18 0.40
39 11 0.24
40 16 0.36
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.68
Consensus pattern (40 bp):
ATTTAGTTTTTCTATTTCAATTTTAGTTTATTTTTTAATG
Found at i:4067952 original size:134 final size:134
Alignment explanation
Indices: 4067803--4068070 Score: 464
Period size: 134 Copynumber: 2.0 Consensus size: 134
4067793 CTAATGTTTT
*
4067803 AAAAATATTTCATATTCATAAATTTCATCGACTATCATTAAAATTAATTCGATAAAATCTATCAT
1 AAAAATATTTCATATTCATAAATTTCATCGACTATCATTAAAATTAATTCGATAAAATCTACCAT
*
4067868 CTTAAAACTACATGTATGGCTATGTCTAAGTGACAAAAAAGTAAATCATTTTAACTTTTTATCCT
66 CTTAAAACTACATGTATGGCTATGTCTAAGTGACAAAAAAGTAAATCATTTTAACTTTTTATCAT
4067933 AAAA
131 AAAA
* **
4067937 AAAAATATTTTATATTCATAAATTTTGTCGACTATCATTAAAATTAATTCGATAAAATCTACCAT
1 AAAAATATTTCATATTCATAAATTTCATCGACTATCATTAAAATTAATTCGATAAAATCTACCAT
* * *
4068002 CTTAAAACTATATGTATGGTTATGTCTAAGTGACAAAAAAGTAAATCCTTTTAACTTTTTATCAT
66 CTTAAAACTACATGTATGGCTATGTCTAAGTGACAAAAAAGTAAATCATTTTAACTTTTTATCAT
4068067 AAAA
131 AAAA
4068071 TTTATATCAT
Statistics
Matches: 126, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
134 126 1.00
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (134 bp):
AAAAATATTTCATATTCATAAATTTCATCGACTATCATTAAAATTAATTCGATAAAATCTACCAT
CTTAAAACTACATGTATGGCTATGTCTAAGTGACAAAAAAGTAAATCATTTTAACTTTTTATCAT
AAAA
Found at i:4068080 original size:14 final size:15
Alignment explanation
Indices: 4068061--4068089 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4068051 TTTAACTTTT
4068061 TATCATAAA-ATTTA
1 TATCATAAACATTTA
4068075 TATCATAAACATTTA
1 TATCATAAACATTTA
4068090 CCTTTCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (15 bp):
TATCATAAACATTTA
Found at i:4069439 original size:6 final size:7
Alignment explanation
Indices: 4069422--4069446 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4069412 TTCCTATTTC
4069422 AAAAATT
1 AAAAATT
4069429 AAAAATT
1 AAAAATT
4069436 AAAAATT
1 AAAAATT
4069443 AAAA
1 AAAA
4069447 GCAATGTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAAATT
Found at i:4069937 original size:14 final size:14
Alignment explanation
Indices: 4069918--4069944 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4069908 ATTAATACAA
4069918 TAATTTAATTTAAT
1 TAATTTAATTTAAT
4069932 TAATTTAATTTAA
1 TAATTTAATTTAA
4069945 AATTAATCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATTTAATTTAAT
Found at i:4070911 original size:22 final size:21
Alignment explanation
Indices: 4070886--4070947 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 21
4070876 ATGTTTTATT
*
4070886 TTTTTAACATCTAAAATTTTTA
1 TTTTTAATAT-TAAAATTTTTA
*
4070908 TTTTTTATATTTTAAAATTTTTTA
1 -TTTTTA-ATATTAAAA-TTTTTA
*
4070932 TTTATAATATTAAAAT
1 TTTTTAATATTAAAAT
4070948 CATAAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 1 0.03
22 8 0.24
23 16 0.48
24 8 0.24
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTAATATTAAAATTTTTA
Found at i:4070941 original size:24 final size:23
Alignment explanation
Indices: 4070897--4070942 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
4070887 TTTTAACATC
* *
4070897 TAAAATTTTTATTTTTTATATTT
1 TAAAATTTTTATTTATAATATTT
4070920 TAAAATTTTTTATTTATAATATT
1 TAAAA-TTTTTATTTATAATATT
4070943 AAAATCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TAAAATTTTTATTTATAATATTT
Found at i:4071556 original size:13 final size:14
Alignment explanation
Indices: 4071523--4071554 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4071513 TGATTAAATT
4071523 TTTTTAAATCATAA
1 TTTTTAAATCATAA
*
4071537 TTTTTAAATGATAA
1 TTTTTAAATCATAA
4071551 TTTT
1 TTTT
4071555 AATAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (14 bp):
TTTTTAAATCATAA
Found at i:4084323 original size:49 final size:48
Alignment explanation
Indices: 4084193--4084579 Score: 416
Period size: 48 Copynumber: 8.0 Consensus size: 48
4084183 ATTTCGAGAA
* * *
4084193 AAGATGAGATTTTAAAATTGTAGAGTCTCTGCTGAGAGAAGCTTTTTC
1 AAGATGAGATTTTAAAGTTGTAGAGCCTCTGCTGAGAGGAGCTTTTTC
* * *
4084241 AAGATGAGATTTTAAAGTTATTGAGCTTCTGCTGAGAGGAGCTTTTTC
1 AAGATGAGATTTTAAAGTTGTAGAGCCTCTGCTGAGAGGAGCTTTTTC
* * * * *
4084289 AAAATGAAAACTTTAAAGTTGTTGAGCCTCTGCTGAGATGAGCTTTTTC
1 AAGATG-AGATTTTAAAGTTGTAGAGCCTCTGCTGAGAGGAGCTTTTTC
* * * * *
4084338 AAGATGAGATTTTAAAGTTATAGAACCTCTGGTGAAAAGAGCTTTTTC
1 AAGATGAGATTTTAAAGTTGTAGAGCCTCTGCTGAGAGGAGCTTTTTC
* *
4084386 AAGATTAGATTTTAAAGTTGTAGAGCCTCAGCTGAGAGGAGCTTTTTTC
1 AAGATGAGATTTTAAAGTTGTAGAGCCTCTGCTGAGAGGAGC-TTTTTC
* * *
4084435 AAGATGAGATTTTAAAGCTGTAGAGCCTCTGCTGAGAAGAGCTTTTCC
1 AAGATGAGATTTTAAAGTTGTAGAGCCTCTGCTGAGAGGAGCTTTTTC
* * * * * * **
4084483 AAGATGAAAATTTTAAAATTGTTGAACCTCTGTTAAGAGGAATTTTTTC
1 AAGATG-AGATTTTAAAGTTGTAGAGCCTCTGCTGAGAGGAGCTTTTTC
* * * * *
4084532 AAGATAAAATTTTAAAGTTGTTA-CGCCTCTGCTTATAGGAGCCTTTTT
1 AAGATGAGATTTTAAAGTTG-TAGAGCCTCTGCTGAGAGGAG-CTTTTT
4084580 AAATTTTCAA
Statistics
Matches: 280, Mismatches: 54, Indels: 9
0.82 0.16 0.03
Matches are distributed among these distances:
48 152 0.54
49 128 0.46
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.35
Consensus pattern (48 bp):
AAGATGAGATTTTAAAGTTGTAGAGCCTCTGCTGAGAGGAGCTTTTTC
Found at i:4084380 original size:97 final size:97
Alignment explanation
Indices: 4084193--4084550 Score: 432
Period size: 97 Copynumber: 3.7 Consensus size: 97
4084183 ATTTCGAGAA
* * *
4084193 AAGATG-AGATTTTAAAATTGTAGAGTCTCTGCTGAGAGAAGCTTTTTCAAGATGAGATTTTAAA
1 AAGATGAAAATTTTAAAATTGTAGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATGAGATTTTAAA
* * *
4084257 GTTATTGAGCTTCTGCTGAGAGGAGCTTTTTC
66 GTTATAGAGCCTCTGCTGAGAAGAGCTTTTTC
* * * * *
4084289 AAAATGAAAACTTTAAAGTTGTTGAGCCTCTGCTGAGATGAGCTTTTTCAAGATGAGATTTTAAA
1 AAGATGAAAATTTTAAAATTGTAGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATGAGATTTTAAA
* * *
4084354 GTTATAGAACCTCTGGTGAAAAGAGCTTTTTC
66 GTTATAGAGCCTCTGCTGAGAAGAGCTTTTTC
* * * *
4084386 AAGAT-TAGATTTTAAAGTTGTAGAGCCTCAGCTGAGAGGAGCTTTTTTCAAGATGAGATTTTAA
1 AAGATGAAAATTTTAAAATTGTAGAGCCTCTGCTGAGAGGAGC-TTTTTCAAGATGAGATTTTAA
* * *
4084450 AGCTGTAGAGCCTCTGCTGAGAAGAGCTTTTCC
65 AGTTATAGAGCCTCTGCTGAGAAGAGCTTTTTC
* * * * ** * *
4084483 AAGATGAAAATTTTAAAATTGTTGAACCTCTGTTAAGAGGAATTTTTTCAAGATAAAATTTTAAA
1 AAGATGAAAATTTTAAAATTGTAGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATGAGATTTTAAA
4084548 GTT
66 GTT
4084551 GTTACGCCTC
Statistics
Matches: 219, Mismatches: 40, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
96 36 0.16
97 156 0.71
98 27 0.12
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35
Consensus pattern (97 bp):
AAGATGAAAATTTTAAAATTGTAGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATGAGATTTTAAA
GTTATAGAGCCTCTGCTGAGAAGAGCTTTTTC
Found at i:4084381 original size:145 final size:145
Alignment explanation
Indices: 4084193--4084550 Score: 425
Period size: 145 Copynumber: 2.5 Consensus size: 145
4084183 ATTTCGAGAA
** * * *
4084193 AAGATGAGATTTTAAAATTGTAGAGTCTCTGCTG-AGAGAAGCTTTTTCAAGATGAGATTTTAAA
1 AAGATGAGATTTTAAAATTGTAGAACCTCTGGTGAAAAG-AGCTTTTTCAAGATAAGATTTTAAA
* * * * *
4084257 GTTATTGAGCTTCTGCTGAGAGGAGC-TTTTTCAAAATGAAAACTTTAAAGTTGTTGAGCCTCTG
65 GTTATAGAGCCTCAGCTGAGAGGAGCTTTTTTCAAAATG-AAACTTTAAAGCTGTAGAGCCTCTG
* *
4084321 CTGAGATGAGCTTTTTC
129 CTGAGAAGAGCTTTTCC
* * *
4084338 AAGATGAGATTTTAAAGTTATAGAACCTCTGGTGAAAAGAGCTTTTTCAAGATTAGATTTTAAAG
1 AAGATGAGATTTTAAAATTGTAGAACCTCTGGTGAAAAGAGCTTTTTCAAGATAAGATTTTAAAG
* * * *
4084403 TTGTAGAGCCTCAGCTGAGAGGAGCTTTTTTCAAGATGAGATTTTAAAGCTGTAGAGCCTCTGCT
66 TTATAGAGCCTCAGCTGAGAGGAGCTTTTTTCAAAATGAAACTTTAAAGCTGTAGAGCCTCTGCT
4084468 GAGAAGAGCTTTTCC
131 GAGAAGAGCTTTTCC
* * * * ** *
4084483 AAGATGAAAATTTTAAAATTGTTGAACCTCT-GTTAAGAGGAATTTTTTCAAGATAAAATTTTAA
1 AAGATG-AGATTTTAAAATTGTAGAACCTCTGGTGAA-AAGAGCTTTTTCAAGATAAGATTTTAA
4084547 AGTT
64 AGTT
4084551 GTTACGCCTC
Statistics
Matches: 181, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
145 121 0.67
146 60 0.33
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35
Consensus pattern (145 bp):
AAGATGAGATTTTAAAATTGTAGAACCTCTGGTGAAAAGAGCTTTTTCAAGATAAGATTTTAAAG
TTATAGAGCCTCAGCTGAGAGGAGCTTTTTTCAAAATGAAACTTTAAAGCTGTAGAGCCTCTGCT
GAGAAGAGCTTTTCC
Found at i:4084822 original size:19 final size:18
Alignment explanation
Indices: 4084798--4084837 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
4084788 TCATCATCAT
4084798 TTTTTTTCTCTCTTTTTAC
1 TTTTTTTCTCTCTTTTT-C
*
4084817 TTTTTTTCTTTCTTTTTC
1 TTTTTTTCTCTCTTTTTC
4084835 TTT
1 TTT
4084838 CCTTATCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTTCTCTCTTTTTC
Found at i:4085809 original size:21 final size:22
Alignment explanation
Indices: 4085765--4085810 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
4085755 TTTTAGATTT
* **
4085765 TTTTAATATATTATTTTTGTTA
1 TTTTAATATATTATTCTTCATA
4085787 TTTTAAT-TATTATTCTTCATA
1 TTTTAATATATTATTCTTCATA
4085808 TTT
1 TTT
4085811 ATGCATGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTAATATATTATTCTTCATA
Found at i:4085985 original size:10 final size:10
Alignment explanation
Indices: 4085953--4085996 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
4085943 AAAAAATTTT
4085953 AATTAAATAAA
1 AATT-AATAAA
*
4085964 AA-TAATGCAA
1 AATTAAT-AAA
4085974 AATTAATAAA
1 AATTAATAAA
4085984 AATTAATAAA
1 AATTAATAAA
4085994 AAT
1 AAT
4085997 AAGAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 3 0.10
10 20 0.69
11 6 0.21
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (10 bp):
AATTAATAAA
Found at i:4092171 original size:18 final size:18
Alignment explanation
Indices: 4092148--4092191 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
4092138 TTGTTCCTTA
4092148 ACATCGACCCCCTCTATG
1 ACATCGACCCCCTCTATG
4092166 ACATCGACCCCCTCTATG
1 ACATCGACCCCCTCTATG
4092184 ACATCGAC
1 ACATCGAC
4092192 TTCTAAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.25, C:0.43, G:0.11, T:0.20
Consensus pattern (18 bp):
ACATCGACCCCCTCTATG
Found at i:4095978 original size:2 final size:2
Alignment explanation
Indices: 4095966--4096012 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
4095956 AATTCATGTA
* *
4095966 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4096006 AT AT AT A
1 AT AT AT A
4096013 GAATATAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4096082 original size:25 final size:25
Alignment explanation
Indices: 4096054--4096107 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
4096044 ATTACATATA
4096054 AAATATAAAAATAAATTTTTGTATT
1 AAATATAAAAATAAATTTTTGTATT
* *
4096079 AAATATAAAAATAATTTTTTTTATT
1 AAATATAAAAATAAATTTTTGTATT
4096104 AAAT
1 AAAT
4096108 TTATATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
AAATATAAAAATAAATTTTTGTATT
Found at i:4096106 original size:19 final size:20
Alignment explanation
Indices: 4096084--4096126 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
4096074 GTATTAAATA
4096084 TAAAAATAAT-TTTTTTTAT
1 TAAAAATAATATTTTTTTAT
* *
4096103 T-AAATTTATATTTTTTTAT
1 TAAAAATAATATTTTTTTAT
4096122 TAAAA
1 TAAAA
4096127 TTTTAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 6 0.30
19 11 0.55
20 3 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TAAAAATAATATTTTTTTAT
Found at i:4098653 original size:20 final size:20
Alignment explanation
Indices: 4098628--4098678 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
4098618 GTTTTTAATT
4098628 TCAATTTCGAGCCATACGTG
1 TCAATTTCGAGCCATACGTG
4098648 TCAATTTCGAGCCATACGTG
1 TCAATTTCGAGCCATACGTG
4098668 TCAATTTCGAG
1 TCAATTTCGAG
4098679 TGATTTAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (20 bp):
TCAATTTCGAGCCATACGTG
Found at i:4098857 original size:24 final size:24
Alignment explanation
Indices: 4098830--4098882 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 24
4098820 TAAGTCTTAT
4098830 TTTAAATT-AATAAAAAT-ATAAAAA
1 TTTAAATTAAAT-AAAATGAT-AAAA
*
4098854 TTT-ATTTAAATAAAATGATAAAA
1 TTTAAATTAAATAAAATGATAAAA
4098877 TTTAAA
1 TTTAAA
4098883 ACCTCTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
TTTAAATTAAATAAAATGATAAAA
Found at i:4099011 original size:120 final size:120
Alignment explanation
Indices: 4098868--4099108 Score: 374
Period size: 120 Copynumber: 2.0 Consensus size: 120
4098858 TTTAAATAAA
* * * * *
4098868 ATGATAAAATTTAAAACCTCTTTTAATATTTTAGCCATTAAAAGAAAGTTGTTGTTATGTTACAT
1 ATGACAAAACTTAAAAACTCTTTTAATATTCTAGCCATTAAAAGAAAGTTGTGGTTATGTTACAT
* * *
4098933 CACAATTGAACGAAGAAAGAAAAGAAATTGCAGAAGGGAAACAAAGTTTAATATG
66 CACAATTGAACGAAGAAAGAAAAGAAATTGCAAAAAGGAAAAAAAGTTTAATATG
*
4098988 ATGACAAAACTTAAAAACTCTTTTAATGTTCTAGCCATTAAAAGAAAGTTGTGGTTATGTTACAT
1 ATGACAAAACTTAAAAACTCTTTTAATATTCTAGCCATTAAAAGAAAGTTGTGGTTATGTTACAT
* * *
4099053 CACAATTGAATGAAGAAAGAGATGAAATTGCAAAAAGGAAAAAAAGTTTAATATG
66 CACAATTGAACGAAGAAAGAAAAGAAATTGCAAAAAGGAAAAAAAGTTTAATATG
4099108 A
1 A
4099109 ATTTATTTAC
Statistics
Matches: 109, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
120 109 1.00
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.29
Consensus pattern (120 bp):
ATGACAAAACTTAAAAACTCTTTTAATATTCTAGCCATTAAAAGAAAGTTGTGGTTATGTTACAT
CACAATTGAACGAAGAAAGAAAAGAAATTGCAAAAAGGAAAAAAAGTTTAATATG
Found at i:4099161 original size:2 final size:2
Alignment explanation
Indices: 4099154--4099212 Score: 79
Period size: 2 Copynumber: 31.0 Consensus size: 2
4099144 AATTCATGTA
*
4099154 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4099194 AT AT AT AT A- AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT
4099213 TATCATATCA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
1 3 0.06
2 48 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4099175 original size:16 final size:16
Alignment explanation
Indices: 4099154--4099225 Score: 80
Period size: 16 Copynumber: 4.6 Consensus size: 16
4099144 AATTCATGTA
*
4099154 ATATATATATATATAT
1 ATATATATAAATATAT
*
4099170 ATATATATATATATAT
1 ATATATATAAATATAT
4099186 AT-TATA-AAATATAT
1 ATATATATAAATATAT
4099200 ATA-ATATAAATAT-T
1 ATATATATAAATATAT
4099214 ATCATATCATAA
1 AT-ATAT-ATAA
4099226 TTTATGATTA
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
14 15 0.30
15 11 0.22
16 20 0.40
17 4 0.08
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATATATAAATATAT
Found at i:4099277 original size:19 final size:18
Alignment explanation
Indices: 4099253--4099298 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 18
4099243 AATATAAAAA
*
4099253 TAAATTTTTTTATTTTTAT
1 TAAATTTTATT-TTTTTAT
4099272 TAAA-TTTATTTTTTTAT
1 TAAATTTTATTTTTTTAT
4099289 TAAAATTTTA
1 T-AAATTTTA
4099299 AATTATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
19 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TAAATTTTATTTTTTTAT
Found at i:4100268 original size:13 final size:13
Alignment explanation
Indices: 4100252--4100276 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4100242 CTTCCTTTAT
4100252 TCTTTTTTTTTTG
1 TCTTTTTTTTTTG
4100265 TCTTTTTTTTTT
1 TCTTTTTTTTTT
4100277 TGGATTTTTC
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:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (13 bp):
TCTTTTTTTTTTG
Found at i:4100335 original size:23 final size:26
Alignment explanation
Indices: 4100296--4100352 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 26
4100286 CAGAATTATG
4100296 TTTTATTTTCTTAACA-TCTAAAA-T
1 TTTTATTTTCTTAACATTCTAAAATT
* *
4100320 TTTTATTTT-TTTACATTTTAAAATT
1 TTTTATTTTCTTAACATTCTAAAATT
4100345 TTTTATTT
1 TTTTATTT
4100353 ATAATATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 5 0.17
24 15 0.52
25 9 0.31
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTTATTTTCTTAACATTCTAAAATT
Found at i:4100909 original size:12 final size:12
Alignment explanation
Indices: 4100892--4100917 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4100882 AAAATTATCC
4100892 TAGAATATGCAT
1 TAGAATATGCAT
4100904 TAGAATATGCAT
1 TAGAATATGCAT
4100916 TA
1 TA
4100918 AAGCTAGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (12 bp):
TAGAATATGCAT
Found at i:4101492 original size:13 final size:14
Alignment explanation
Indices: 4101459--4101490 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4101449 ATTAAATTTT
4101459 TTTTTAAATCATAA
1 TTTTTAAATCATAA
*
4101473 TTTTTAAATGATAA
1 TTTTTAAATCATAA
4101487 TTTT
1 TTTT
4101491 AATAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (14 bp):
TTTTTAAATCATAA
Found at i:4110997 original size:4 final size:4
Alignment explanation
Indices: 4110988--4111026 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
4110978 AATTCCTAAT
*
4110988 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ACAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
4111027 TATATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAC
Found at i:4117801 original size:20 final size:20
Alignment explanation
Indices: 4117764--4117802 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4117754 GACAAACAAA
* *
4117764 ACAAATAAAATAGGAAAAAT
1 ACAAAAAAAAGAGGAAAAAT
*
4117784 ACAAAAAAAAGAGTAAAAA
1 ACAAAAAAAAGAGGAAAAA
4117803 AAAAAGTGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.05, G:0.10, T:0.10
Consensus pattern (20 bp):
ACAAAAAAAAGAGGAAAAAT
Found at i:4117828 original size:25 final size:25
Alignment explanation
Indices: 4117800--4117848 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
4117790 AAAAGAGTAA
4117800 AAAAAAAAGTGAGAATAAAAGAAAG
1 AAAAAAAAGTGAGAATAAAAGAAAG
*
4117825 AAAAATAAGTGAGAATAAAAGAAA
1 AAAAAAAAGTGAGAATAAAAGAAA
4117849 AAACAATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.10
Consensus pattern (25 bp):
AAAAAAAAGTGAGAATAAAAGAAAG
Found at i:4119340 original size:29 final size:30
Alignment explanation
Indices: 4119296--4119354 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
4119286 AATTAATAAA
*
4119296 TTCATAATTTAGATATTATATTAAAGATTT
1 TTCATAATTTAGATATCATATTAAAGATTT
* *
4119326 TTCA-AATTTATATATCATATTAAATATTT
1 TTCATAATTTAGATATCATATTAAAGATTT
4119355 CACTATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (30 bp):
TTCATAATTTAGATATCATATTAAAGATTT
Found at i:4160361 original size:38 final size:33
Alignment explanation
Indices: 4160287--4160349 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
4160277 TTTTGAACAG
*
4160287 TTTGAATTATAAATTAGATGAGAAAAAAAAAAT
1 TTTGAATCATAAATTAGATGAGAAAAAAAAAAT
4160320 TTTGAATCATAAATTAGATGAGAAAAAAAA
1 TTTGAATCATAAATTAGATGAGAAAAAAAA
4160350 TTGAAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.57, C:0.02, G:0.13, T:0.29
Consensus pattern (33 bp):
TTTGAATCATAAATTAGATGAGAAAAAAAAAAT
Found at i:4160779 original size:2 final size:2
Alignment explanation
Indices: 4160768--4160806 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
4160758 AATGTTCATT
*
4160768 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T- TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4160807 TAAAAGCAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:4161120 original size:16 final size:17
Alignment explanation
Indices: 4161096--4161128 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4161086 CTCCTCCTTC
4161096 TTTGCTTTTTTT-TTTT
1 TTTGCTTTTTTTATTTT
*
4161112 TTTGGTTTTTTTATTTT
1 TTTGCTTTTTTTATTTT
4161129 CTTATTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.03, C:0.03, G:0.09, T:0.85
Consensus pattern (17 bp):
TTTGCTTTTTTTATTTT
Found at i:4161386 original size:25 final size:25
Alignment explanation
Indices: 4161352--4161419 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
4161342 GCGGTGAATG
* *
4161352 GATATCGATGGCAAAGAGATAAGCT
1 GATATCGATGGCAAAGAGAGAAGCC
*
4161377 GATATCGATGGCAAACAGAGAAGCC
1 GATATCGATGGCAAAGAGAGAAGCC
*
4161402 GATATCGTTGGCAAAGAG
1 GATATCGATGGCAAAGAG
4161420 TGGTTCACTC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.38, C:0.15, G:0.29, T:0.18
Consensus pattern (25 bp):
GATATCGATGGCAAAGAGAGAAGCC
Found at i:4165065 original size:3 final size:3
Alignment explanation
Indices: 4165050--4165092 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
4165040 CTTTTTGTTA
* * *
4165050 TAT TAT TAA TAT TAT TAT TGT TGT TA- TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4165093 GTATGGTGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:4165070 original size:23 final size:24
Alignment explanation
Indices: 4165043--4165092 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
4165033 ATAAACTCTT
4165043 TTTGTTATATTATTAATATTATTA
1 TTTGTTATATTATTAATATTATTA
*
4165067 TTGTTGTTATATTATTATTATTATTA
1 -T-TTGTTATATTATTAATATTATTA
4165093 GTATGGTGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
TTTGTTATATTATTAATATTATTA
Found at i:4187976 original size:37 final size:39
Alignment explanation
Indices: 4187894--4188004 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 39
4187884 ATTTTTTCAA
* *
4187894 ATTTTCAATAAAGATTATATTTTTATCTTAGAAATATCAT
1 ATTTTCAATAAAGATTGTATCTTTATCTTA-AAATATCAT
* * *
4187934 CTTTTCAACAAAGATTGTATCTTTATC-T-AAATATCTT
1 ATTTTCAATAAAGATTGTATCTTTATCTTAAAATATCAT
4187971 ATTTTCAATAAAGATTGTAAT-TTCTATCTTAAAA
1 ATTTTCAATAAAGATTGT-ATCTT-TATCTTAAAA
4188005 ATGTTATTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
37 26 0.43
38 6 0.10
39 2 0.03
40 26 0.43
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (39 bp):
ATTTTCAATAAAGATTGTATCTTTATCTTAAAATATCAT
Found at i:4188257 original size:25 final size:25
Alignment explanation
Indices: 4188228--4188275 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
4188218 ATAACATATT
*
4188228 ATAACATACGATTATATTTCTAATA
1 ATAACATACAATTATATTTCTAATA
*
4188253 ATAACATATAATTATATTTCTAA
1 ATAACATACAATTATATTTCTAA
4188276 CATAACAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (25 bp):
ATAACATACAATTATATTTCTAATA
Done.