Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 150 of 160
Found at i:29363380 original size:20 final size:21
Alignment explanation
Indices: 29363355--29363410 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
29363345 ATAATTATTT
* *
29363355 TATATTCAAATTTAT-TTAAA
1 TATATTAAAAATTATATTAAA
29363375 TATATTAAAAATTATATTAAAA
1 TATATTAAAAATTATATT-AAA
29363397 TAATATTTAAAAAT
1 T-ATA-TTAAAAAT
29363411 AAAAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 13 0.43
21 2 0.07
22 4 0.13
23 3 0.10
24 8 0.27
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TATATTAAAAATTATATTAAA
Found at i:29363396 original size:11 final size:11
Alignment explanation
Indices: 29363354--29363408 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
29363344 AATAATTATT
*
29363354 TTATATTCAAA
1 TTATATTAAAA
*
29363365 TT-TATTTAAA
1 TTATATTAAAA
29363375 -TATATTAAAAA
1 TTATATT-AAAA
29363386 TTATATTAAAA
1 TTATATTAAAA
*
29363397 TAATATTTAAAA
1 TTATA-TTAAAA
29363409 ATAAAAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
9 1 0.03
10 11 0.30
11 13 0.35
12 12 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (11 bp):
TTATATTAAAA
Found at i:29363429 original size:33 final size:33
Alignment explanation
Indices: 29363367--29363429 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
29363357 TATTCAAATT
* *
29363367 TATTTAAATATATTAAAAATTATATTAAAATAA
1 TATTTAAATATATAAAAAATTAAATTAAAATAA
29363400 TATTTAAA-A-ATAAAAAATTTAAATATAAAA
1 TATTTAAATATATAAAAAA-TTAAAT-TAAAA
29363430 ATTTATCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
31 7 0.27
32 6 0.23
33 13 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (33 bp):
TATTTAAATATATAAAAAATTAAATTAAAATAA
Found at i:29363431 original size:14 final size:15
Alignment explanation
Indices: 29363401--29363434 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
29363391 TTAAAATAAT
29363401 ATTTAAAAATAAAAA
1 ATTTAAAAATAAAAA
*
29363416 ATTTAAATAT-AAAA
1 ATTTAAAAATAAAAA
29363430 ATTTA
1 ATTTA
29363435 TCAATCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTTAAAAATAAAAA
Found at i:29367088 original size:2 final size:2
Alignment explanation
Indices: 29367081--29367105 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29367071 ATAAGCATGT
29367081 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
29367106 TTTTTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:29380565 original size:12 final size:12
Alignment explanation
Indices: 29380548--29380572 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29380538 TAATTTTTCA
29380548 AAATTTTTAATT
1 AAATTTTTAATT
29380560 AAATTTTTAATT
1 AAATTTTTAATT
29380572 A
1 A
29380573 TCCAAAATTA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATTTTTAATT
Found at i:29380565 original size:29 final size:29
Alignment explanation
Indices: 29380523--29380581 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
29380513 ATGACCTAAA
* * * *
29380523 TTTTATTTTAATTTTTAATTTTTCAAAAT
1 TTTTAATTAAATTTTTAATTATCCAAAAT
29380552 TTTTAATTAAATTTTTAATTATCCAAAAT
1 TTTTAATTAAATTTTTAATTATCCAAAAT
29380581 T
1 T
29380582 ATTTTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTAATTAAATTTTTAATTATCCAAAAT
Found at i:29380737 original size:30 final size:30
Alignment explanation
Indices: 29380680--29380739 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
29380670 GTGATAAAAA
*
29380680 AAAGATCAAAATAAAATTCTTTAAAAATTT
1 AAAGATCAAAATAAAATTATTTAAAAATTT
* *
29380710 AAAGATCAATGATAAAA-TATTTCAAAATTT
1 AAAGATCAA-AATAAAATTATTTAAAAATTT
29380740 TACATAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (30 bp):
AAAGATCAAAATAAAATTATTTAAAAATTT
Found at i:29381114 original size:22 final size:22
Alignment explanation
Indices: 29381089--29381134 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
29381079 ATTAAAATTT
29381089 TTTTTAATTACAATTACAATAA
1 TTTTTAATTACAATTACAATAA
** *
29381111 TTTTTTTTTTCAATTACAATAA
1 TTTTTAATTACAATTACAATAA
29381133 TT
1 TT
29381135 ACAATAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTTTAATTACAATTACAATAA
Found at i:29381138 original size:31 final size:27
Alignment explanation
Indices: 29381081--29381146 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 27
29381071 AATTTTTCAT
*
29381081 TAAAATTTTTTTTAATTACAATTACAA
1 TAAATTTTTTTTTAATTACAATTACAA
*
29381108 TAATTTTTTTTTTCAATTACAATAATTACAA
1 TAAATTTTTTTTT-AATTAC---AATTACAA
29381139 TAAATTTT
1 TAAATTTT
29381147 ATTACTGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 11 0.34
28 6 0.19
31 15 0.47
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.52
Consensus pattern (27 bp):
TAAATTTTTTTTTAATTACAATTACAA
Found at i:29389331 original size:46 final size:44
Alignment explanation
Indices: 29389252--29389340 Score: 108
Period size: 46 Copynumber: 2.0 Consensus size: 44
29389242 AGATAATAAC
*
29389252 ATTTAAATAAATATAAATATAATTATTTTTTAAATATAAAATTATA
1 ATTTAAATAAATATAAATATAATTATTTATTAAA-AT-AAATTATA
* * *
29389298 ATTTAATTATATATAAATGTAATT-TTCTATTAAAATAAATTAT
1 ATTTAAATAAATATAAATATAATTATT-TATTAAAATAAATTAT
29389341 TAAATAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 7 0.18
45 4 0.11
46 27 0.71
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (44 bp):
ATTTAAATAAATATAAATATAATTATTTATTAAAATAAATTATA
Found at i:29389366 original size:17 final size:16
Alignment explanation
Indices: 29389337--29389369 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
29389327 TTAAAATAAA
29389337 TTATTAAATAATATAT
1 TTATTAAATAATATAT
29389353 TTATTAATATAATATAT
1 TTATTAA-ATAATATAT
29389370 ATAAATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTAAATAATATAT
Found at i:29389377 original size:19 final size:19
Alignment explanation
Indices: 29389332--29389388 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
29389322 TTCTATTAAA
*
29389332 ATAAATTATTAAATAATAT
1 ATAAATTAATAAATAATAT
**
29389351 ATTTATTAATATAAT-ATAT
1 ATAAATTAATA-AATAATAT
29389370 ATAAATTAAGTAAATAATA
1 ATAAATTAA-TAAATAATA
29389389 AAATTTATTC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
19 22 0.73
20 8 0.27
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATAAATTAATAAATAATAT
Found at i:29389596 original size:13 final size:14
Alignment explanation
Indices: 29389573--29389601 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
29389563 TACAAAATTT
29389573 ATTTAATAAATAAA
1 ATTTAATAAATAAA
29389587 ATTTAA-AAATAAA
1 ATTTAATAAATAAA
29389600 AT
1 AT
29389602 GATTTGACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATTTAATAAATAAA
Found at i:29390125 original size:21 final size:21
Alignment explanation
Indices: 29390099--29390143 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
29390089 TTTTTTAATG
*
29390099 AAATTTATTAAATAA-AAAATA
1 AAATTTAATAAA-AATAAAATA
29390120 AAATTTAATAAAAATAAAATA
1 AAATTTAATAAAAATAAAATA
29390141 AAA
1 AAA
29390144 AACGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATTTAATAAAAATAAAATA
Found at i:29399005 original size:23 final size:21
Alignment explanation
Indices: 29398978--29399047 Score: 56
Period size: 23 Copynumber: 3.3 Consensus size: 21
29398968 TATATTAATA
*
29398978 AATAAACAATACTATAGCATATT
1 AATAAA-AATAATATA-CATATT
29399001 AAT--AAATAATATAC-TATT
1 AATAAAAATAATATACATATT
* *
29399019 AATAAATAATATTATAATATATT
1 AATAAA-AATAATAT-ACATATT
29399042 AATAAA
1 AATAAA
29399048 TGATATATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
18 7 0.18
19 1 0.03
20 9 0.23
21 8 0.21
22 1 0.03
23 13 0.33
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.36
Consensus pattern (21 bp):
AATAAAAATAATATACATATT
Found at i:29399020 original size:18 final size:18
Alignment explanation
Indices: 29398996--29399199 Score: 94
Period size: 18 Copynumber: 12.1 Consensus size: 18
29398986 ATACTATAGC
29398996 ATATTAATAAATAATATA
1 ATATTAATAAATAATATA
*
29399014 CTATTAATAAATAATATTATAA
1 ATATTAATAAAT-A-A-TAT-A
*
29399036 TATATTAATAAATGATATA
1 -ATATTAATAAATAATATA
*
29399055 TTATTAATAAATAATAT-
1 ATATTAATAAATAATATA
* *
29399072 A-A-CAATAAATATTATTA
1 ATATTAATAAATAATA-TA
29399089 AT-TTAAT---TAATA-A
1 ATATTAATAAATAATATA
29399102 ATATT-AT-AAT-A-AT-
1 ATATTAATAAATAATATA
29399115 ATATTAATAAA-AATATA
1 ATATTAATAAATAATATA
*
29399132 CTATTAAT--AT-A-AT-
1 ATATTAATAAATAATATA
29399145 ATATTAATAAAT-ATGATTA
1 ATATTAATAAATAAT-A-TA
*
29399164 ATA--AAT-AATATTATAA
1 ATATTAATAAATAATAT-A
29399180 TATATTAATAAATAATATA
1 -ATATTAATAAATAATATA
29399199 A
1 A
29399200 AGAATAATAA
Statistics
Matches: 141, Mismatches: 14, Indels: 62
0.65 0.06 0.29
Matches are distributed among these distances:
13 18 0.13
14 7 0.05
15 24 0.17
16 9 0.06
17 16 0.11
18 31 0.22
19 9 0.06
20 11 0.08
21 4 0.03
22 1 0.01
23 11 0.08
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (18 bp):
ATATTAATAAATAATATA
Found at i:29399020 original size:45 final size:42
Alignment explanation
Indices: 29398957--29399181 Score: 136
Period size: 41 Copynumber: 5.5 Consensus size: 42
29398947 AATTTTACTT
* *
29398957 ATAAATAATGTTATATTAATAAATAAACAATACTATAGCATATTA
1 ATAAATAAT-ATATATTAATAAAT-AA-AATACTATAACATATTA
* *
29399002 ATAAATAATATACTATTAATAAAT--AATATTATAATATATTA
1 ATAAATAATATA-TATTAATAAATAAAATACTATAACATATTA
* * *
29399043 ATAAATGATATATTATTAATAAATAATATAACAATAA-ATATT-
1 ATAAATAATATA-TATTAATAAATAAAAT-ACTATAACATATTA
* ** *
29399085 AT---TAATTTA-ATTAATAAATATTATA--ATAATATATTA
1 ATAAATAATATATATTAATAAATAAAATACTATAACATATTA
* * * *
29399121 ATAAA-AATATACTATTAATATAATATATTAATA-AATATGATTA
1 ATAAATAATATA-TATTAATA-AATAAAATACTATAACAT-ATTA
29399164 ATAAATAATAT-TA-TAATA
1 ATAAATAATATATATTAATA
29399182 TATTAATAAA
Statistics
Matches: 149, Mismatches: 15, Indels: 36
0.75 0.08 0.18
Matches are distributed among these distances:
34 4 0.03
35 5 0.03
36 3 0.02
37 14 0.09
38 5 0.03
39 5 0.03
40 7 0.05
41 48 0.32
42 9 0.06
43 17 0.11
44 12 0.08
45 20 0.13
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (42 bp):
ATAAATAATATATATTAATAAATAAAATACTATAACATATTA
Found at i:29399069 original size:33 final size:32
Alignment explanation
Indices: 29399032--29399181 Score: 119
Period size: 30 Copynumber: 5.0 Consensus size: 32
29399022 AAATAATATT
29399032 ATAATATATTAATAAATGATATATTATTAATAA
1 ATAATATATTAATAAAT-ATATATTATTAATAA
** *
29399065 ATAATATAACAATAAATAT-TATTAATTTAATTA
1 ATAATATATTAATAAATATATATT-A-TTAATAA
29399098 ATAA-ATATT-AT-AATA-ATA-TATTAATAA
1 ATAATATATTAATAAATATATATTATTAATAA
* *
29399125 A-AATATACT-ATTAATATA-ATATATTAATAA
1 ATAATATATTAATAAATATATAT-TATTAATAA
*
29399155 AT-AT-GATTAATAAATA-ATATTA-TAATA
1 ATAATATATTAATAAATATATATTATTAATA
29399182 TATTAATAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 27
0.72 0.08 0.20
Matches are distributed among these distances:
26 2 0.02
27 13 0.14
28 11 0.11
29 7 0.07
30 26 0.27
31 6 0.06
32 6 0.06
33 25 0.26
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (32 bp):
ATAATATATTAATAAATATATATTATTAATAA
Found at i:29399069 original size:41 final size:40
Alignment explanation
Indices: 29398996--29399198 Score: 190
Period size: 41 Copynumber: 5.1 Consensus size: 40
29398986 ATACTATAGC
* *
29398996 ATATTAATAAATAATATACTATTAATAAATAATATTATAAT
1 ATATTAATAAAT-ATATATTATTAATAAATAATATAATAAT
*
29399037 ATATTAATAAATGATATATTATTAATAAATAATATAACAAT
1 ATATTAATAAAT-ATATATTATTAATAAATAATATAATAAT
* *
29399078 AAATATT-ATTAAT-T-TA--ATTAATAAATATTATAATAAT
1 --ATATTAATAAATATATATTATTAATAAATAATATAATAAT
* *
29399115 ATATTAATAAAAATATACTATTAATATAAT-ATATTAATAAAT
1 ATATTAATAAATATATATTATTAATA-AATAATA-TAAT-AAT
*
29399157 ATGATTAATAAATA-ATATTA-TAATATATTAATA-AATAAT
1 AT-ATTAATAAATATATATTATTAATA-AATAATATAATAAT
29399196 ATA
1 ATA
29399199 AAGAATAATA
Statistics
Matches: 137, Mismatches: 13, Indels: 27
0.77 0.07 0.15
Matches are distributed among these distances:
35 5 0.04
36 4 0.03
37 20 0.15
38 3 0.02
39 7 0.05
40 13 0.09
41 52 0.38
42 18 0.13
43 15 0.11
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (40 bp):
ATATTAATAAATATATATTATTAATAAATAATATAATAAT
Found at i:29399101 original size:22 final size:23
Alignment explanation
Indices: 29399064--29399198 Score: 87
Period size: 25 Copynumber: 5.4 Consensus size: 23
29399054 ATTATTAATA
**
29399064 AATAATATAACAATAAATATTAT
1 AATAATATATTAATAAATATTAT
*
29399087 --TAATTTAATTAATAAATATTAT
1 AATAATAT-ATTAATAAATATTAT
29399109 AATAATATATTAATAAAAATATACTATT
1 AATAATATATTAAT--AAATAT--TA-T
*
29399137 AATATAATATATTAATAAATATGATT
1 -A-ATAATATATTAATAAATATTA-T
29399163 AATAAATAATATT-ATAATATATTAAT
1 AAT-AAT-ATATTAATAA-ATATT-AT
29399189 AAATAATATA
1 -AATAATATA
29399199 AAGAATAATA
Statistics
Matches: 91, Mismatches: 6, Indels: 28
0.73 0.05 0.22
Matches are distributed among these distances:
21 5 0.05
22 13 0.14
23 6 0.07
24 7 0.08
25 17 0.19
26 16 0.18
27 6 0.07
28 7 0.08
29 1 0.01
30 13 0.14
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (23 bp):
AATAATATATTAATAAATATTAT
Found at i:29399155 original size:75 final size:77
Alignment explanation
Indices: 29399016--29399198 Score: 217
Period size: 78 Copynumber: 2.5 Consensus size: 77
29399006 ATAATATACT
* * *
29399016 ATTAATAAATAATATTATAATATATTAATAAATGATATATTATTAATAAATAATATAACAATAAA
1 ATTAATAAATAATATAATAATATATTAATAAATAATATACTATTAAT-AATAATATAACAATAAA
*
29399081 TATTATTAATTTA
65 TATGATTAATTTA
* **
29399094 ATTAATAAATATTATAATAATATATTAATAAA-AATATACTATTAAT-ATAATATATTAATAAAT
1 ATTAATAAATAATATAATAATATATTAATAAATAATATACTATTAATAATAATATAACAATAAAT
29399157 ATGATTAA--T-
66 ATGATTAATTTA
29399166 A--AAT-AAT-AT-T-ATAATATATTAATAAATAATATA
1 ATTAATAAATAATATAATAATATATTAATAAATAATATA
29399199 AAGAATAATA
Statistics
Matches: 96, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
66 16 0.17
67 7 0.07
68 1 0.01
69 3 0.03
70 3 0.03
72 1 0.01
73 1 0.01
75 22 0.23
77 12 0.12
78 30 0.31
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (77 bp):
ATTAATAAATAATATAATAATATATTAATAAATAATATACTATTAATAATAATATAACAATAAAT
ATGATTAATTTA
Found at i:29399212 original size:23 final size:23
Alignment explanation
Indices: 29399154--29399212 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
29399144 TATATTAATA
* * *
29399154 AATATGATTAATAAATAATATTAT
1 AATAT-ATAAATAAATAATATAAG
*
29399178 AATATATTAATAAATAATATAAAG
1 AATATATAAATAAATAATAT-AAG
29399202 AATA-ATAAATA
1 AATATATAAATA
29399213 GTTTTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 21 0.68
24 10 0.32
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (23 bp):
AATATATAAATAAATAATATAAG
Found at i:29399256 original size:19 final size:18
Alignment explanation
Indices: 29399229--29399316 Score: 67
Period size: 19 Copynumber: 4.9 Consensus size: 18
29399219 TTTTAAGTAT
*
29399229 TTTTTATATTAACATAATA
1 TTTTAATATTAA-ATAATA
*
29399248 TTTTAATATTAAATATTA
1 TTTTAATATTAAATAATA
* * *
29399266 TTATTAA-AATATAATTATT
1 TT-TTAATATTA-AATAATA
29399285 TTTTAATATT-AAT-A-A
1 TTTTAATATTAAATAATA
*
29399300 TTTTAATAATAAATAAT
1 TTTTAATATTAAATAAT
29399317 TTCAATATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
15 9 0.17
16 4 0.07
17 4 0.07
18 14 0.26
19 23 0.43
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTTAATATTAAATAATA
Found at i:29399299 original size:20 final size:19
Alignment explanation
Indices: 29399226--29399301 Score: 59
Period size: 18 Copynumber: 4.1 Consensus size: 19
29399216 TTATTTTAAG
*
29399226 TATTTTTT-ATATTAACAT
1 TATTTTTTAATATTAAAAT
* *
29399244 AATATTTTAATATTAAATAT
1 TATTTTTTAATATTAAA-AT
* * *
29399264 TA-TTATTAA-AATATAAT
1 TATTTTTTAATATTAAAAT
29399281 TATTTTTTAATATTAATAAT
1 TATTTTTTAATATTAA-AAT
29399301 T
1 T
29399302 TTAATAATAA
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
17 4 0.10
18 16 0.38
19 15 0.36
20 7 0.17
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTTTTTAATATTAAAAT
Found at i:29399305 original size:15 final size:15
Alignment explanation
Indices: 29399285--29399325 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
29399275 TATAATTATT
*
29399285 TTTTAATATTAATAA
1 TTTTAATATAAATAA
29399300 TTTTAATAATAAATAA
1 TTTTAAT-ATAAATAA
*
29399316 TTTCAATATA
1 TTTTAATATA
29399326 TTTTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTTAATATAAATAA
Found at i:29399328 original size:26 final size:26
Alignment explanation
Indices: 29399295--29399360 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
29399285 TTTTAATATT
29399295 AATA-ATTTTAATAATAAATAATTTC
1 AATATATTTTAATAATAAATAATTTC
* *
29399320 AATATATTTTAATAATAAATAGTTTT
1 AATATATTTTAATAATAAATAATTTC
*
29399346 TA-ATATTTTAATAAT
1 AATATATTTTAATAAT
29399361 TATATTAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 17 0.46
26 20 0.54
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (26 bp):
AATATATTTTAATAATAAATAATTTC
Found at i:29402284 original size:2 final size:2
Alignment explanation
Indices: 29402277--29402309 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29402267 AAGATCTATG
29402277 TA TA TA TA TA TA TA TA 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 TA T
29402310 GTAAAAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29423753 original size:2 final size:2
Alignment explanation
Indices: 29423746--29423782 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
29423736 AGTGCATAAC
29423746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29423783 AGAATGAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29429799 original size:8 final size:8
Alignment explanation
Indices: 29429786--29429810 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29429776 CAGTTTTGAA
29429786 TCAATTTT
1 TCAATTTT
29429794 TCAATTTT
1 TCAATTTT
29429802 TCAATTTT
1 TCAATTTT
29429810 T
1 T
29429811 TTCTCACCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (8 bp):
TCAATTTT
Found at i:29430305 original size:27 final size:27
Alignment explanation
Indices: 29430247--29430305 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
29430237 TAATATATAG
* *
29430247 ATTTGTTATTAAATAATATAAATTATT
1 ATTTTTTATTAAATAAAATAAATTATT
* *
29430274 ATTTTTTATTAATTAAAATTAA-TA-T
1 ATTTTTTATTAAATAAAATAAATTATT
29430299 ATTTTTT
1 ATTTTTT
29430306 GAAAAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 8 0.29
26 2 0.07
27 18 0.64
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (27 bp):
ATTTTTTATTAAATAAAATAAATTATT
Found at i:29430349 original size:25 final size:27
Alignment explanation
Indices: 29430294--29430351 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
29430284 AATTAAAATT
* * *
29430294 AATATATTTTTTGAAAAAATATATATT
1 AATATATATTTTGAAAAAATATACATA
29430321 AATATATATTTT-AAAAAAT-TACATA
1 AATATATATTTTGAAAAAATATACATA
29430346 AATATA
1 AATATA
29430352 CAAGATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 10 0.36
26 7 0.25
27 11 0.39
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (27 bp):
AATATATATTTTGAAAAAATATACATA
Found at i:29431160 original size:23 final size:24
Alignment explanation
Indices: 29431120--29431164 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
29431110 AAAGAATATA
29431120 TTATATTTTATTACTTATTTAATT
1 TTATATTTTATTACTTATTTAATT
29431144 TTATA-TTTATATA-TTATTTAA
1 TTATATTTTAT-TACTTATTTAA
29431165 ATAAAAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (24 bp):
TTATATTTTATTACTTATTTAATT
Found at i:29431207 original size:29 final size:28
Alignment explanation
Indices: 29431144--29431222 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 28
29431134 TTATTTAATT
29431144 TTATATTT-ATATATTATTTAAATAAAA
1 TTATATTTAATATATTATTTAAATAAAA
* *
29431171 GTATTATTTAATATTTTAATTT-AATAAAAA
1 TTA-TATTTAATATATT-ATTTAAAT-AAAA
*
29431201 TTATATTT-ATATA-TAATTAAAT
1 TTATATTTAATATATTATTTAAAT
29431223 TATAATTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
26 3 0.07
27 6 0.14
28 9 0.21
29 14 0.33
30 10 0.24
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (28 bp):
TTATATTTAATATATTATTTAAATAAAA
Found at i:29431217 original size:22 final size:22
Alignment explanation
Indices: 29431191--29431241 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
29431181 ATATTTTAAT
29431191 TTAATAAAAATTAT-ATTTATA
1 TTAATAAAAATTATAATTTATA
*
29431212 TATAAT-TAAATTATAATTTATA
1 T-TAATAAAAATTATAATTTATA
29431234 TTAA-AAAA
1 TTAATAAAA
29431242 TAAATACGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAATAAAAATTATAATTTATA
Found at i:29434250 original size:21 final size:21
Alignment explanation
Indices: 29434224--29434266 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
29434214 AAATGAGGCA
29434224 TATTAGGTATCTCCTTTATAT
1 TATTAGGTATCTCCTTTATAT
29434245 TATTAGGTATCTCCTTTATAT
1 TATTAGGTATCTCCTTTATAT
29434266 T
1 T
29434267 TTTATATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.53
Consensus pattern (21 bp):
TATTAGGTATCTCCTTTATAT
Found at i:29462198 original size:19 final size:19
Alignment explanation
Indices: 29462162--29462204 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
29462152 TTTCCATCAA
*
29462162 TTTTTTAAAATTATTTTAT
1 TTTTTTAAAATCATTTTAT
29462181 TTTTATTAAAATCA-TTTAT
1 TTTT-TTAAAATCATTTTAT
29462200 TTTTT
1 TTTTT
29462205 GTTTTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 13 0.59
20 8 0.36
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTAAAATCATTTTAT
Found at i:29462212 original size:12 final size:12
Alignment explanation
Indices: 29462195--29462228 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
29462185 ATTAAAATCA
*
29462195 TTTATTTTTTGT
1 TTTATTTTTTAT
*
29462207 TTTATTTTTAAT
1 TTTATTTTTTAT
29462219 TTTATTTTTT
1 TTTATTTTTT
29462229 TGTTAGATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (12 bp):
TTTATTTTTTAT
Found at i:29463153 original size:29 final size:27
Alignment explanation
Indices: 29463072--29463153 Score: 69
Period size: 29 Copynumber: 2.9 Consensus size: 27
29463062 TTATTTAATT
* *
29463072 TATATTTATATAT-TATATTAATAAAGA
1 TATATTTATATATAT-TATTTATAAAAA
*
29463099 TATTATTTA-ATATCTTAATTTAATAAAAA
1 TA-TATTTATATATATT-ATTT-ATAAAAA
29463128 TATATTTATATATAATTATGTTATAA
1 TATATTTATATAT-ATTAT-TTATAA
29463154 TTTATATTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
27 7 0.16
28 16 0.36
29 18 0.40
30 4 0.09
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.50
Consensus pattern (27 bp):
TATATTTATATATATTATTTATAAAAA
Found at i:29479443 original size:17 final size:17
Alignment explanation
Indices: 29479422--29479453 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29479412 AATGATTTTT
29479422 TTTTTTC-AAATTTTGA
1 TTTTTTCAAAATTTTGA
29479438 TTTTTTCAAAATTTTG
1 TTTTTTCAAAATTTTG
29479454 CTATCATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTTTTCAAAATTTTGA
Found at i:29486200 original size:20 final size:21
Alignment explanation
Indices: 29486156--29486239 Score: 68
Period size: 19 Copynumber: 4.1 Consensus size: 21
29486146 CATATTTATA
29486156 TTTTAATTTTAAAATAATATG
1 TTTTAATTTTAAAATAATATG
*
29486177 TTTTAATTTATAAGATAAT-T-
1 TTTTAATTT-TAAAATAATATG
* * * *
29486197 TTTTTATTTTCAAGTAAAAT-
1 TTTTAATTTTAAAATAATATG
* *
29486217 TTAT-ATTTTAATATAATATG
1 TTTTAATTTTAAAATAATATG
29486237 TTT
1 TTT
29486240 AAAACATTAA
Statistics
Matches: 48, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
19 16 0.33
20 14 0.29
21 10 0.21
22 8 0.17
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (21 bp):
TTTTAATTTTAAAATAATATG
Found at i:29491969 original size:19 final size:18
Alignment explanation
Indices: 29491926--29491971 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
29491916 AATATTAAAC
29491926 TTACATAATTAATTACTA
1 TTACATAATTAATTACTA
29491944 -TATCATAATTAAATTA-TAA
1 TTA-CATAATT-AATTACT-A
29491963 TTACATAAT
1 TTACATAAT
29491972 AATCAGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 2 0.08
18 8 0.33
19 12 0.50
20 2 0.08
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (18 bp):
TTACATAATTAATTACTA
Found at i:29505632 original size:105 final size:105
Alignment explanation
Indices: 29505497--29505692 Score: 374
Period size: 105 Copynumber: 1.9 Consensus size: 105
29505487 CTGACCAATC
29505497 AGGTACATGTGAAGGTAGTGGTTGTTTGCTAGCCCGGGAAAGATAGACTCTGAACCTCATTTGTT
1 AGGTACATGTGAAGGTAGTGGTTGTTTGCTAGCCCGGGAAAGATAGACTCTGAACCTCATTTGTT
*
29505562 TATGATTATGTTCCACATATACACAATCAGGTACACGTGA
66 TATGATCATGTTCCACATATACACAATCAGGTACACGTGA
*
29505602 AGGTACATGTGAAGGTAGTGGTTGTTTGCTAGCCCGGGAAAGGTAGACTCTGAACCTCATTTGTT
1 AGGTACATGTGAAGGTAGTGGTTGTTTGCTAGCCCGGGAAAGATAGACTCTGAACCTCATTTGTT
29505667 TATGATCATGTTCCACATATACACAA
66 TATGATCATGTTCCACATATACACAA
29505693 AGTTGTTTGA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 89 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (105 bp):
AGGTACATGTGAAGGTAGTGGTTGTTTGCTAGCCCGGGAAAGATAGACTCTGAACCTCATTTGTT
TATGATCATGTTCCACATATACACAATCAGGTACACGTGA
Found at i:29506632 original size:7 final size:7
Alignment explanation
Indices: 29506616--29506649 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
29506606 ATGGAAGGAA
29506616 TTTT-CC
1 TTTTCCC
29506622 TTTTCCC
1 TTTTCCC
29506629 TTTTCCC
1 TTTTCCC
29506636 TTTTCCC
1 TTTTCCC
29506643 TTTTCCC
1 TTTTCCC
29506650 CTTTAATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.15
7 23 0.85
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTCCC
Found at i:29517775 original size:15 final size:13
Alignment explanation
Indices: 29517749--29517788 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 13
29517739 GATATTAAAA
29517749 TTTTAATAAATATT
1 TTTTAA-AAATATT
29517763 TTATTAAATAATATT
1 TT-TTAAA-AATATT
29517778 TTTTAAAAATA
1 TTTTAAAAATA
29517789 ATTGTATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.17
14 8 0.33
15 12 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTTAAAAATATT
Found at i:29517841 original size:20 final size:21
Alignment explanation
Indices: 29517800--29517843 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
29517790 TTGTATGATC
*
29517800 AATTAATTAAATTAAATTTTA
1 AATTAATTAAATTAAATATTA
29517821 AATTAA-TAAATT-AATAATTA
1 AATTAATTAAATTAAAT-ATTA
29517841 AAT
1 AAT
29517844 ATGTTAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 12 0.57
21 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTAATTAAATTAAATATTA
Found at i:29518892 original size:2 final size:2
Alignment explanation
Indices: 29518885--29518911 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29518875 AAATTTCCCA
29518885 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 T
29518912 ATACATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:29519457 original size:2 final size:2
Alignment explanation
Indices: 29519450--29519477 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29519440 TGTGAATTAG
29519450 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
29519478 TAGACTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29519935 original size:34 final size:34
Alignment explanation
Indices: 29519894--29519969 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
29519884 CTTAAATCTA
* * *
29519894 CCAAAAATTCATTTCCAAAAAATATTACAATTAT
1 CCAAAAATGCAATTCCAAAAAACATTACAATTAT
* * * *
29519928 CCGAAAATGCAATTCCGAAAAGCATTGCAATTAT
1 CCAAAAATGCAATTCCAAAAAACATTACAATTAT
29519962 CCAAAAAT
1 CCAAAAAT
29519970 ATATTTTCGA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.26
Consensus pattern (34 bp):
CCAAAAATGCAATTCCAAAAAACATTACAATTAT
Found at i:29520904 original size:12 final size:12
Alignment explanation
Indices: 29520874--29520906 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
29520864 AAATGAGTGA
*
29520874 TTGGGGCTTGAT
1 TTGGGGTTTGAT
29520886 TTGGGGTTTGAT
1 TTGGGGTTTGAT
29520898 TTGGGGTTT
1 TTGGGGTTT
29520907 AATCCCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.03, G:0.42, T:0.48
Consensus pattern (12 bp):
TTGGGGTTTGAT
Found at i:29522067 original size:16 final size:16
Alignment explanation
Indices: 29522046--29522080 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29522036 GCAGCAACGT
*
29522046 ATATATGTATAAATAA
1 ATATATATATAAATAA
*
29522062 ATATATATATATATAA
1 ATATATATATAAATAA
29522078 ATA
1 ATA
29522081 AGTTAAAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
ATATATATATAAATAA
Found at i:29522925 original size:2 final size:2
Alignment explanation
Indices: 29522918--29522952 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
29522908 TCTTTTAATC
*
29522918 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29522953 TTGATTGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29524854 original size:2 final size:2
Alignment explanation
Indices: 29524847--29524896 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
29524837 AATGCCAAGC
* * * *
29524847 AT AT AT AT AC AT AT AC AT AT AT AG AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29524889 AT AT -T AT A
1 AT AT AT AT A
29524897 GTCAGTTATC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:29527495 original size:23 final size:21
Alignment explanation
Indices: 29527469--29527521 Score: 52
Period size: 24 Copynumber: 2.3 Consensus size: 21
29527459 AATAATAATT
*
29527469 ATTATAATTATGATTTTAAAAAA
1 ATTATAATTATGA-ATT-AAAAA
29527492 ATTATTGTAATTATGAATTAAAAA
1 ATTA---TAATTATGAATTAAAAA
29527516 ATTATA
1 ATTATA
29527522 TTAAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
21 2 0.08
23 4 0.15
24 9 0.35
25 2 0.08
26 9 0.35
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (21 bp):
ATTATAATTATGAATTAAAAA
Found at i:29527497 original size:26 final size:25
Alignment explanation
Indices: 29527465--29527530 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 25
29527455 AAATAATAAT
*
29527465 AATTATTATAATTATGATTTTAAAAA
1 AATTATTATAATTATGA-ATTAAAAA
*
29527491 AATTATTGTAATTATGAATTAAAAA
1 AATTATTATAATTATGAATTAAAAA
* *
29527516 ATTATATTAAAATTA
1 AAT-TATTATAATTA
29527531 ATATTTAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 9 0.26
26 25 0.74
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (25 bp):
AATTATTATAATTATGAATTAAAAA
Found at i:29527898 original size:16 final size:17
Alignment explanation
Indices: 29527868--29527899 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29527858 AGTAAAAGCC
29527868 TATTTTTTCTATTAATA
1 TATTTTTTCTATTAATA
29527885 TATTTTTTCT-TTAAT
1 TATTTTTTCTATTAAT
29527900 TTTCAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTTTTCTATTAATA
Found at i:29528355 original size:14 final size:14
Alignment explanation
Indices: 29528338--29528384 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
29528328 AAATAAAATT
29528338 TTTTAAAATATTAA
1 TTTTAAAATATTAA
* * *
29528352 TTTTTATATATTTA
1 TTTTAAAATATTAA
29528366 TTTTAAAAT-TTAA
1 TTTTAAAATATTAA
29528379 TATTTA
1 T-TTTA
29528385 CTCATGAATG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 4 0.15
14 22 0.85
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTAAAATATTAA
Found at i:29535002 original size:9 final size:9
Alignment explanation
Indices: 29534988--29535015 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
29534978 GCGCATATGT
29534988 TTCTTTCAC
1 TTCTTTCAC
29534997 TTCTTTCAC
1 TTCTTTCAC
29535006 TTCTTTCAC
1 TTCTTTCAC
29535015 T
1 T
29535016 CAAAAACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.32, G:0.00, T:0.57
Consensus pattern (9 bp):
TTCTTTCAC
Found at i:29535877 original size:13 final size:12
Alignment explanation
Indices: 29535821--29535882 Score: 51
Period size: 10 Copynumber: 5.2 Consensus size: 12
29535811 ATAATTAATT
29535821 AATTATAATTTAA
1 AATTAT-ATTTAA
*
29535834 AA-T-TATGTAA
1 AATTATATTTAA
29535844 AATT-TA-TTAA
1 AATTATATTTAA
*
29535854 AATTTTATTTAA
1 AATTATATTTAA
29535866 AATTCATATTTATA
1 AATT-ATATTTA-A
29535880 AAT
1 AAT
29535883 CATGGACTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
10 14 0.34
11 6 0.15
12 9 0.22
13 8 0.20
14 4 0.10
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (12 bp):
AATTATATTTAA
Found at i:29538755 original size:52 final size:52
Alignment explanation
Indices: 29538669--29538825 Score: 208
Period size: 52 Copynumber: 3.0 Consensus size: 52
29538659 TATAACCATA
* * * *
29538669 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCTTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* *
29538721 CAAACTTGCCTATTAAGAATCCTTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCTTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* * **
29538773 CAAACTTACCTATTAAGAATCCTCTTT-CTCTTGGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCT-TTTCCTCTTAGAATTCTTCTCCTGCAAGT
29538825 C
1 C
29538826 TTCTTGTCCA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
52 91 0.97
53 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.10, T:0.39
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCTTTTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:29539193 original size:25 final size:25
Alignment explanation
Indices: 29539120--29539206 Score: 86
Period size: 25 Copynumber: 3.5 Consensus size: 25
29539110 AAGCTCTTTC
29539120 CATATCTCGAACTGTCAACTCTTAC-
1 CATATCTCGAACTGTCAACTCTT-CT
* ** **
29539145 CATGTCTCGAACCATCGGCTCTTCT
1 CATATCTCGAACTGTCAACTCTTCT
*
29539170 CATATATCGAACTGTCAACTCTTCT
1 CATATCTCGAACTGTCAACTCTTCT
* *
29539195 CATGTTTCGAAC
1 CATATCTCGAAC
29539207 CTTTAGCTCT
Statistics
Matches: 48, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
24 1 0.02
25 47 0.98
ACGTcount: A:0.24, C:0.31, G:0.11, T:0.33
Consensus pattern (25 bp):
CATATCTCGAACTGTCAACTCTTCT
Found at i:29539216 original size:25 final size:25
Alignment explanation
Indices: 29539111--29539241 Score: 70
Period size: 25 Copynumber: 5.2 Consensus size: 25
29539101 TCTCAAACCA
*
29539111 AGCTCTT-TCCATATCTCGAACTGTC
1 AGCTCTTCT-CATATATCGAACTGTC
* * * **
29539136 AACTCTTAC-CATGTCTCGAACCATC
1 AGCTCTT-CTCATATATCGAACTGTC
*
29539161 GGCTCTTCTCATATATCGAACTGTC
1 AGCTCTTCTCATATATCGAACTGTC
* * * *
29539186 AACTCTTCTCATGTTTCGAACCT-TT
1 AGCTCTTCTCATATATCGAA-CTGTC
* * * * *
29539211 AGCTCTTCCCACATTTCAAACTTTC
1 AGCTCTTCTCATATATCGAACTGTC
29539236 AGCTCT
1 AGCTCT
29539242 GATACCACTT
Statistics
Matches: 80, Mismatches: 21, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
24 3 0.04
25 75 0.94
26 2 0.03
ACGTcount: A:0.22, C:0.32, G:0.10, T:0.36
Consensus pattern (25 bp):
AGCTCTTCTCATATATCGAACTGTC
Found at i:29539216 original size:50 final size:51
Alignment explanation
Indices: 29539098--29539218 Score: 144
Period size: 50 Copynumber: 2.5 Consensus size: 51
29539088 ACTTCTTTCT
* *
29539098 ATGTCTCAAACCA--AGCTCTT-TCCATATCTCGAACTGTCAACTCTTACC
1 ATGTCTCGAACCATCAGCTCTTCTCCATATATCGAACTGTCAACTCTTACC
*
29539146 ATGTCTCGAACCATCGGCTCTTCT-CATATATCGAACTGTCAACTCTT-CTC
1 ATGTCTCGAACCATCAGCTCTTCTCCATATATCGAACTGTCAACTCTTAC-C
* * *
29539196 ATGTTTCGAACCTTTAGCTCTTC
1 ATGTCTCGAACCATCAGCTCTTC
29539219 CCACATTTCA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
48 12 0.19
49 1 0.02
50 48 0.77
51 1 0.02
ACGTcount: A:0.23, C:0.31, G:0.11, T:0.35
Consensus pattern (51 bp):
ATGTCTCGAACCATCAGCTCTTCTCCATATATCGAACTGTCAACTCTTACC
Found at i:29539859 original size:52 final size:52
Alignment explanation
Indices: 29539773--29539929 Score: 192
Period size: 52 Copynumber: 3.0 Consensus size: 52
29539763 TATAACCATA
* * * * *
29539773 CAAACTTGCCCATTAAAAATCC-CTCTCATCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTACCTATTAAGAATCCTCTTTC-TCTTAGAATTCTTCTCCTGCAAGT
* *
29539825 CAAACTTACCTATTAAGAATCCT-TTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTACCTATTAAGAATCCTCTTT-CTCTTAGAATTCTTCTCCTGCAAGT
* **
29539877 CAAACTTACCTATTAAGAATCCTCTTTCTCTTGGAATTCTTCTTTTGCAAGT
1 CAAACTTACCTATTAAGAATCCTCTTTCTCTTAGAATTCTTCTCCTGCAAGT
29539929 C
1 C
29539930 TTCTTATCCA
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
52 88 0.96
53 4 0.04
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.39
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATCCTCTTTCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:29539983 original size:11 final size:11
Alignment explanation
Indices: 29539954--29539984 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
29539944 GCAATATCTG
*
29539954 ACAAATCCCAA
1 ACAAATCTCAA
29539965 ACAAATCTCAA
1 ACAAATCTCAA
29539976 ACAAATCTC
1 ACAAATCTC
29539985 TTATGGGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:29540394 original size:2 final size:2
Alignment explanation
Indices: 29540382--29540415 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
29540372 TAATTCTTTA
*
29540382 AT AT GT 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
29540416 TTGTACGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29541307 original size:20 final size:19
Alignment explanation
Indices: 29541268--29541309 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
29541258 ATAGTCAAAA
29541268 TAATATTAAAATATTATTT
1 TAATATTAAAATATTATTT
29541287 TAATATTTATAAATA-TATTT
1 TAATA-TTA-AAATATTATTT
29541307 TAA
1 TAA
29541310 AACCAGCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 11 0.52
21 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATTAAAATATTATTT
Found at i:29549628 original size:56 final size:56
Alignment explanation
Indices: 29549556--29549672 Score: 207
Period size: 56 Copynumber: 2.1 Consensus size: 56
29549546 AAGGTGAGGA
* *
29549556 ATTAATTTATGTCAAGTATTAAAGATATTCACAATGAAAATCAGTCCAGATGATGC
1 ATTAATTTATGGCAAGTATTAAAGATATTCACAATGAAAATCAGTCCAGAAGATGC
29549612 ATTAATTTATGGCAAGTATTAAAGATATTCACAATGAAAATCAGTCCAGAAGATGC
1 ATTAATTTATGGCAAGTATTAAAGATATTCACAATGAAAATCAGTCCAGAAGATGC
*
29549668 GTTAA
1 ATTAA
29549673 GTACAAAAAG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (56 bp):
ATTAATTTATGGCAAGTATTAAAGATATTCACAATGAAAATCAGTCCAGAAGATGC
Found at i:29556000 original size:20 final size:24
Alignment explanation
Indices: 29555975--29556026 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 24
29555965 CTTCGTGATG
29555975 TAATAAAAAAATT-T-TAA-TT-T
1 TAATAAAAAAATTATATAATTTAT
*
29555995 TAATAAAATAATTATATAATTTAT
1 TAATAAAAAAATTATATAATTTAT
29556019 TAATAAAA
1 TAATAAAA
29556027 TATTAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 12 0.44
21 1 0.04
22 3 0.11
23 2 0.07
24 9 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAATAAAAAAATTATATAATTTAT
Found at i:29556040 original size:23 final size:24
Alignment explanation
Indices: 29555994--29556040 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
29555984 AATTTTAATT
*
29555994 TTAATAAAATAATTATATAATTTA
1 TTAATAAAATAATTAAATAATTTA
*
29556018 TTAATAAAAT-ATTAAATATTTTA
1 TTAATAAAATAATTAAATAATTTA
29556041 ATTTTAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTAATAAAATAATTAAATAATTTA
Found at i:29581056 original size:30 final size:30
Alignment explanation
Indices: 29581021--29581088 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
29581011 TTTCTGTAAA
*
29581021 CTTAAATCTTCTGCTGATGGAAGGGGTGGC
1 CTTAAATCTTCTGCTGATGAAAGGGGTGGC
29581051 CTTAAATCTTCTGCTGATGAAAGGGGTGGC
1 CTTAAATCTTCTGCTGATGAAAGGGGTGGC
29581081 CTTAAATC
1 CTTAAATC
29581089 CTTAACCATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (30 bp):
CTTAAATCTTCTGCTGATGAAAGGGGTGGC
Found at i:29582535 original size:13 final size:13
Alignment explanation
Indices: 29582517--29582558 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
29582507 AACTATTGAC
29582517 TTAAATTTTTTAT
1 TTAAATTTTTTAT
29582530 TTAAA-TTTTTA-
1 TTAAATTTTTTAT
*
29582541 TTAAATTATTT-T
1 TTAAATTTTTTAT
29582553 TTAAAT
1 TTAAAT
29582559 CATAAATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 5 0.19
12 16 0.62
13 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTAAATTTTTTAT
Found at i:29586347 original size:21 final size:21
Alignment explanation
Indices: 29586321--29586364 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
29586311 ATTTGCGTGG
29586321 ATATAATTCTTCCATTACTTA
1 ATATAATTCTTCCATTACTTA
29586342 ATATAATTCTTCCATTACTTA
1 ATATAATTCTTCCATTACTTA
29586363 AT
1 AT
29586365 CTCAAGAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATAATTCTTCCATTACTTA
Found at i:29593032 original size:4 final size:4
Alignment explanation
Indices: 29593023--29593048 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
29593013 CGGGTAATGT
29593023 TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TT
29593049 TCATTGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:29594167 original size:29 final size:29
Alignment explanation
Indices: 29594122--29594179 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
29594112 TACAAAAAGG
29594122 TGGATTTTTTTCACCTTTACTAATATATT
1 TGGATTTTTTTCACCTTTACTAATATATT
* *
29594151 TGGATTTTTTTCGCCTTTATTAATATATT
1 TGGATTTTTTTCACCTTTACTAATATATT
29594180 AATGTTTGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.12, G:0.09, T:0.57
Consensus pattern (29 bp):
TGGATTTTTTTCACCTTTACTAATATATT
Found at i:29597234 original size:18 final size:17
Alignment explanation
Indices: 29597213--29597246 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
29597203 ATAAATCGAC
29597213 TTCATTAAATTTTGAATT
1 TTCATTAAA-TTTGAATT
*
29597231 TTCATTGAATTTGAAT
1 TTCATTAAATTTGAAT
29597247 ATTTTTGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (17 bp):
TTCATTAAATTTGAATT
Found at i:29599767 original size:20 final size:20
Alignment explanation
Indices: 29599730--29599767 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29599720 CCCATATTAG
*
29599730 TTAAATTTTATTATTTTCTA
1 TTAAATTTTATTAATTTCTA
29599750 TTAAATTCTTA-TAATTTC
1 TTAAATT-TTATTAATTTC
29599768 AGGAAAACGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAAATTTTATTAATTTCTA
Found at i:29612127 original size:24 final size:26
Alignment explanation
Indices: 29612099--29612146 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
29612089 TACGACTCCA
*
29612099 AAAGCAGC-A-AGAGTAAGCAACACT
1 AAAGCAGCGAGAGAGCAAGCAACACT
29612123 AAAGCAGCGAGAGAGCAAGCAACA
1 AAAGCAGCGAGAGAGCAAGCAACA
29612147 GAAAACCACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 1 0.05
26 12 0.57
ACGTcount: A:0.50, C:0.21, G:0.25, T:0.04
Consensus pattern (26 bp):
AAAGCAGCGAGAGAGCAAGCAACACT
Found at i:29615236 original size:14 final size:15
Alignment explanation
Indices: 29615208--29615240 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29615198 TTGCGATTGA
*
29615208 AAAAAATTATAATTT
1 AAAAAAGTATAATTT
29615223 AAAAAAGTAT-ATTT
1 AAAAAAGTATAATTT
29615237 AAAA
1 AAAA
29615241 GTGTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AAAAAAGTATAATTT
Found at i:29616985 original size:2 final size:2
Alignment explanation
Indices: 29616978--29617011 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
29616968 TGCTCGTGCG
29616978 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29617012 ATGAGGCTCT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:29624231 original size:2 final size:2
Alignment explanation
Indices: 29624224--29624251 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29624214 TTTCACGATG
29624224 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
29624252 TTATCCATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29626040 original size:23 final size:23
Alignment explanation
Indices: 29626003--29626058 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
29625993 TTAAAATAAA
* * *
29626003 ATATAAATATAAATATAATATTAT
1 ATATAAATTTTAATA-AAAATTAT
*
29626027 TTA-AAATTTTAATAAAAATTAT
1 ATATAAATTTTAATAAAAATTAT
29626049 ATATAAATTT
1 ATATAAATTT
29626059 GATAAAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 9 0.35
23 15 0.58
24 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATAAATTTTAATAAAAATTAT
Found at i:29626053 original size:34 final size:31
Alignment explanation
Indices: 29625977--29626058 Score: 76
Period size: 34 Copynumber: 2.5 Consensus size: 31
29625967 GTCTTATTTT
* *
29625977 AATTATATTTAATATTTTAAAATAAAATATA
1 AATTATATATAATATTTTAAAATAAAATAAA
* **
29626008 AATATAAATATAATATTATTTAAAATTTTAATAAA
1 AAT-TATATATAATA-T-TTTAAAA-TAAAATAAA
29626043 AATTATATATAA-ATTT
1 AATTATATATAATATTT
29626059 GATAAAATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
31 5 0.12
32 10 0.24
33 2 0.05
34 15 0.37
35 9 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
AATTATATATAATATTTTAAAATAAAATAAA
Found at i:29627392 original size:12 final size:12
Alignment explanation
Indices: 29627377--29627432 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
29627367 ATAAATTATT
29627377 TATTTAATTTTA
1 TATTTAATTTTA
29627389 TATTTAATTTT-
1 TATTTAATTTTA
*
29627400 TA--TAATTATA
1 TATTTAATTTTA
* *
29627410 TATATAAATTTA
1 TATTTAATTTTA
29627422 TATTTATATTT
1 TATTTA-ATTT
29627433 AAAATAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
9 6 0.17
10 2 0.06
11 2 0.06
12 22 0.63
13 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTTAATTTTA
Found at i:29627398 original size:21 final size:23
Alignment explanation
Indices: 29627360--29627422 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 23
29627350 ATAAAAAATA
29627360 TATATATATAAA-TTATTTATTTAAT
1 TATATATATAAATTTA-TTA--TAAT
* *
29627385 TTTATAT-TTAATTT-TTATAAT
1 TATATATATAAATTTATTATAAT
29627406 TATATATATAAATTTAT
1 TATATATATAAATTTAT
29627423 ATTTATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
21 10 0.32
22 6 0.19
23 4 0.13
24 3 0.10
25 8 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATATATATAAATTTATTATAAT
Found at i:29629787 original size:35 final size:35
Alignment explanation
Indices: 29629748--29629825 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 35
29629738 GCCTTTATTC
29629748 TGTTGCTTTTTTGCTTTTCTCTATTGTCTCCTAAG
1 TGTTGCTTTTTTGCTTTTCTCTATTGTCTCCTAAG
29629783 TGTTGCTTTTTTGCTTTTCTCTATTGTCTCCTAAG
1 TGTTGCTTTTTTGCTTTTCTCTATTGTCTCCTAAG
*
29629818 TGCTGCTT
1 TGTTGCTT
29629826 GTTTCTGAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.08, C:0.21, G:0.15, T:0.56
Consensus pattern (35 bp):
TGTTGCTTTTTTGCTTTTCTCTATTGTCTCCTAAG
Found at i:29640209 original size:20 final size:19
Alignment explanation
Indices: 29640181--29640219 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
29640171 TATTCAAATT
* *
29640181 AAAATTTTTTATTTCTTATA
1 AAAACTTTTGATTT-TTATA
29640201 AAAACTTTTGATTTTTATA
1 AAAACTTTTGATTTTTATA
29640220 TATTTATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (19 bp):
AAAACTTTTGATTTTTATA
Found at i:29640819 original size:15 final size:17
Alignment explanation
Indices: 29640791--29640823 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
29640781 TGAAATTTGT
29640791 AATATTATTGAAAGTAA
1 AATATTATTGAAAGTAA
29640808 AATATTA-T-AAAGTAA
1 AATATTATTGAAAGTAA
29640823 A
1 A
29640824 TCAATTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (17 bp):
AATATTATTGAAAGTAA
Found at i:29649641 original size:30 final size:31
Alignment explanation
Indices: 29649607--29649670 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
29649597 TAAATGTTAA
* *
29649607 TATTTATGTAAGTA-TTTTAAAAAATTAATT
1 TATTTATATAAATATTTTTAAAAAATTAATT
29649637 TATTTATATAAATATTTTTAAAAAATTAATT
1 TATTTATATAAATATTTTTAAAAAATTAATT
29649668 TAT
1 TAT
29649671 AGAAACATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (31 bp):
TATTTATATAAATATTTTTAAAAAATTAATT
Found at i:29656829 original size:6 final size:6
Alignment explanation
Indices: 29656820--29656848 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
29656810 ATTTATACGT
29656820 ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATA
29656849 TGTGTGTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:29659319 original size:29 final size:29
Alignment explanation
Indices: 29659286--29659394 Score: 89
Period size: 30 Copynumber: 3.7 Consensus size: 29
29659276 AAATCAAAAG
*
29659286 TTTAATTGAATTAAAATAAATGT-TTAAGA
1 TTTAATTGAATTAAAATAAATATATTAA-A
* * *
29659315 TTTAATTTG-ATGAAAATAAATATCTAAAAA
1 TTTAA-TTGAATTAAAATAAATATAT-TAAA
* * *
29659345 TTTAATTAAATAAAAATAAAAATATTAAA
1 TTTAATTGAATTAAAATAAATATATTAAA
29659374 TTTTAA-TGAATTTAAAATAAA
1 -TTTAATTGAA-TTAAAATAAA
29659395 AAATTGATGA
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
29 25 0.39
30 37 0.58
31 2 0.03
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.39
Consensus pattern (29 bp):
TTTAATTGAATTAAAATAAATATATTAAA
Found at i:29659361 original size:30 final size:29
Alignment explanation
Indices: 29659281--29659373 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
29659271 TTTTTAAATC
* * * *
29659281 AAAAGTTTAATTGAATTAAAATAAATGTT
1 AAAAATTTAATTAAATAAAAATAAATATT
* * ** *
29659310 TAAGATTTAATTTGATGAAAATAAATATCT
1 AAAAATTTAATTAAATAAAAATAAATAT-T
29659340 AAAAATTTAATTAAATAAAAATAAAAATATT
1 AAAAATTTAATTAAATAAAAAT--AAATATT
29659371 AAA
1 AAA
29659374 TTTTAATGAA
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
29 21 0.43
30 18 0.37
31 4 0.08
32 6 0.12
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.35
Consensus pattern (29 bp):
AAAAATTTAATTAAATAAAAATAAATATT
Found at i:29663270 original size:2 final size:2
Alignment explanation
Indices: 29663263--29663290 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29663253 CAATTGTTTC
29663263 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
29663291 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29669737 original size:30 final size:30
Alignment explanation
Indices: 29669703--29669787 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
29669693 ATTTCTTAGA
*
29669703 TAAAATTTTAATTATA-CATAATTAAACATT
1 TAAAATATTAATTATATC-TAATTAAACATT
* * *
29669733 TAAAATATTATTTTTATCTAATTAAACCTT
1 TAAAATATTAATTATATCTAATTAAACATT
* * * *
29669763 TAAAATACTATTTTTATTTAATTAA
1 TAAAATATTAATTATATCTAATTAA
29669788 GACCTTAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
30 47 0.98
31 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAAATATTAATTATATCTAATTAAACATT
Found at i:29669816 original size:29 final size:30
Alignment explanation
Indices: 29669721--29669806 Score: 120
Period size: 30 Copynumber: 2.9 Consensus size: 30
29669711 TAATTATACA
* * *
29669721 TAATTAAACATTTAAAATATTATTTTTATC
1 TAATTAAACCTTTAAAATACTATTTTTATT
29669751 TAATTAAACCTTTAAAATACTATTTTTATT
1 TAATTAAACCTTTAAAATACTATTTTTATT
*
29669781 TAATTAAGACC-TTAAATTACTATTTT
1 TAATTAA-ACCTTTAAAATACTATTTT
29669807 GTTTTATTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 48 0.94
31 3 0.06
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (30 bp):
TAATTAAACCTTTAAAATACTATTTTTATT
Found at i:29670316 original size:34 final size:35
Alignment explanation
Indices: 29670251--29670325 Score: 109
Period size: 34 Copynumber: 2.2 Consensus size: 35
29670241 AAATAATTTA
* *
29670251 TTAA-ATAAGAATTCATTGTTTTATATAGAAAATT
1 TTAAGATAAGAATTCATCGTTTCATATAGAAAATT
29670285 TTAAGATAAGAATTCATCG-TTCATATAGAAAATT
1 TTAAGATAAGAATTCATCGTTTCATATAGAAAATT
*
29670319 ATAAGAT
1 TTAAGAT
29670326 GTGAATTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 24 0.65
35 13 0.35
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (35 bp):
TTAAGATAAGAATTCATCGTTTCATATAGAAAATT
Found at i:29670776 original size:22 final size:22
Alignment explanation
Indices: 29670751--29670794 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
29670741 CACAAAATTT
* * *
29670751 TATTTTAATTAAATAATTGTAA
1 TATTATAATAAAAAAATTGTAA
*
29670773 TATTATAGTAAAAAAATTGTAA
1 TATTATAATAAAAAAATTGTAA
29670795 GTAATATACT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (22 bp):
TATTATAATAAAAAAATTGTAA
Found at i:29670897 original size:36 final size:36
Alignment explanation
Indices: 29670850--29670925 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
29670840 AAAATCATGT
29670850 ATATTTATAAATAATATTGAAAATATCATACGAGAG
1 ATATTTATAAATAATATTGAAAATATCATACGAGAG
29670886 ATATTTATAAATAATATTGAAAATATCATACGAGAG
1 ATATTTATAAATAATATTGAAAATATCATACGAGAG
29670922 ATAT
1 ATAT
29670926 ACTCCATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (36 bp):
ATATTTATAAATAATATTGAAAATATCATACGAGAG
Found at i:29677444 original size:45 final size:45
Alignment explanation
Indices: 29677380--29677473 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
29677370 GGTTCAAAAT
29677380 TTCAAATCTATCATTTGCAATCCTTTCATGAAAGTTGACATATCA
1 TTCAAATCTATCATTTGCAATCCTTTCATGAAAGTTGACATATCA
29677425 TTCAAATCTATCATTTGCAATCCTTTCATGAAAGTTGACATATCA
1 TTCAAATCTATCATTTGCAATCCTTTCATGAAAGTTGACATATCA
29677470 TTCA
1 TTCA
29677474 GATGGTTCGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (45 bp):
TTCAAATCTATCATTTGCAATCCTTTCATGAAAGTTGACATATCA
Found at i:29682806 original size:38 final size:39
Alignment explanation
Indices: 29682753--29682829 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 39
29682743 TCTAGCAGGT
*
29682753 TTCCAGATAAGAAATGACTGAGACAAACGGACA-GCTGG
1 TTCCAGATAACAAATGACTGAGACAAACGGACAGGCTGG
* * *
29682791 TTCCAGGTAACAAATGACTGAGAGAAACGGTCAGGCTGG
1 TTCCAGATAACAAATGACTGAGACAAACGGACAGGCTGG
29682830 ATAGTTGTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
38 29 0.85
39 5 0.15
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.17
Consensus pattern (39 bp):
TTCCAGATAACAAATGACTGAGACAAACGGACAGGCTGG
Found at i:29686769 original size:2 final size:2
Alignment explanation
Indices: 29686762--29686791 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
29686752 AAAATTATTC
29686762 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29686792 ATTTAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29693939 original size:28 final size:30
Alignment explanation
Indices: 29693899--29694028 Score: 82
Period size: 28 Copynumber: 4.6 Consensus size: 30
29693889 TTAATTTAAT
29693899 AATATAATA-TTTATAAAATATTATTTAT-
1 AATATAATATTTTATAAAATATTATTTATA
* ***
29693927 AATGTAA-ATTTTATCTCA-ATTATTTATA
1 AATATAATATTTTATAAAATATTATTTATA
* * * *
29693955 AATATAATATTTTATTAAATA-AATGTATT
1 AATATAATATTTTATAAAATATTATTTATA
*
29693984 AA-ATAATAATTTTAT-TAATA-TATTATATA
1 AATATAAT-ATTTTATAAAATATTATT-TATA
*
29694013 AATA-AA-ATTATATAAA
1 AATATAATATTTTATAAA
29694029 TAATAAAATA
Statistics
Matches: 77, Mismatches: 17, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
27 16 0.21
28 30 0.39
29 29 0.38
30 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (30 bp):
AATATAATATTTTATAAAATATTATTTATA
Found at i:29693999 original size:16 final size:16
Alignment explanation
Indices: 29693980--29694034 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 16
29693970 TAAATAAATG
*
29693980 TATTAAATAATAATTT
1 TATTAAATAATAATTA
29693996 TATT-AAT-AT-ATTA
1 TATTAAATAATAATTA
29694009 TA-TAAATAA-AATTA
1 TATTAAATAATAATTA
29694023 TA-TAAATAATAA
1 TATTAAATAATAA
29694035 AATATATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
12 1 0.03
13 8 0.24
14 16 0.47
15 5 0.15
16 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TATTAAATAATAATTA
Found at i:29694042 original size:18 final size:19
Alignment explanation
Indices: 29694000--29694043 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
29693990 TAATTTTATT
*
29694000 AATATAT-TATATAAATAA
1 AATATATATAAATAAATAA
29694018 AAT-TATATAAAT-AATAA
1 AATATATATAAATAAATAA
29694035 AATATATAT
1 AATATATAT
29694044 TCTTATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATATATATAAATAAATAA
Found at i:29694952 original size:15 final size:16
Alignment explanation
Indices: 29694934--29694968 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
29694924 AAAAAAGTTA
*
29694934 AAAACTAAAAAAAT-G
1 AAAACAAAAAAAATAG
29694949 AAAACAAAAAAAATAG
1 AAAACAAAAAAAATAG
29694965 AAAA
1 AAAA
29694969 AACCAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.80, C:0.06, G:0.06, T:0.09
Consensus pattern (16 bp):
AAAACAAAAAAAATAG
Found at i:29694952 original size:16 final size:16
Alignment explanation
Indices: 29694922--29694969 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
29694912 TTATTTACTT
*
29694922 AAAAAAAAGTTAAAAAC
1 AAAAAAAA-TGAAAAAC
*
29694939 TAAAAAAATG-AAAAC
1 AAAAAAAATGAAAAAC
29694954 AAAAAAAATAGAAAAA
1 AAAAAAAAT-GAAAAA
29694970 ACCAAATGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 13 0.50
16 2 0.08
17 11 0.42
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAAAAAATGAAAAAC
Found at i:29695702 original size:11 final size:12
Alignment explanation
Indices: 29695678--29695706 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
29695668 AATAACATTA
29695678 AATTTAAGATTT
1 AATTTAAGATTT
29695690 AATTTAA-ATTT
1 AATTTAAGATTT
29695701 AATTTA
1 AATTTA
29695707 TTTAAGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (12 bp):
AATTTAAGATTT
Found at i:29699252 original size:12 final size:12
Alignment explanation
Indices: 29699235--29699268 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
29699225 ATCAAAAGTT
29699235 CTAGACAGCCCA
1 CTAGACAGCCCA
29699247 CTAGACAGCCCA
1 CTAGACAGCCCA
29699259 CTAGACAGCC
1 CTAGACAGCC
29699269 TATCAACAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.32, C:0.41, G:0.18, T:0.09
Consensus pattern (12 bp):
CTAGACAGCCCA
Found at i:29704797 original size:32 final size:32
Alignment explanation
Indices: 29704761--29704826 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
29704751 TATCATTTCG
29704761 TTGATTAAAAAAATTAATTAAAAATTA-ATTTA
1 TTGATTAAAAAAATTAA-TAAAAATTATATTTA
** * *
29704793 TTGATTTTAAAAATTTATAAAATTTATATTTA
1 TTGATTAAAAAAATTAATAAAAATTATATTTA
29704825 TT
1 TT
29704827 CACTGATGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 8 0.28
32 21 0.72
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (32 bp):
TTGATTAAAAAAATTAATAAAAATTATATTTA
Found at i:29705390 original size:21 final size:21
Alignment explanation
Indices: 29705366--29705406 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29705356 ATTATATTTA
29705366 AGTTACCGAAA-TTGTTTCAAG
1 AGTTA-CGAAATTTGTTTCAAG
*
29705387 AGTTACTAAATTTGTTTCAA
1 AGTTACGAAATTTGTTTCAA
29705407 ATATTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (21 bp):
AGTTACGAAATTTGTTTCAAG
Found at i:29705447 original size:33 final size:34
Alignment explanation
Indices: 29705405--29705472 Score: 104
Period size: 33 Copynumber: 2.0 Consensus size: 34
29705395 AATTTGTTTC
29705405 AAATATTATCAAAATTA-TATTAAAAATTATCAAA
1 AAATATTATCAAAATTATTA-TAAAAATTATCAAA
*
29705439 AAAT-TTATCAAAATTGTTATAAAAATTATCAAA
1 AAATATTATCAAAATTATTATAAAAATTATCAAA
29705472 A
1 A
29705473 TTTTATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 26 0.81
34 6 0.19
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.35
Consensus pattern (34 bp):
AAATATTATCAAAATTATTATAAAAATTATCAAA
Found at i:29705451 original size:21 final size:21
Alignment explanation
Indices: 29705427--29705503 Score: 72
Period size: 21 Copynumber: 3.7 Consensus size: 21
29705417 AATTATATTA
29705427 AAAATTATCA-AAAAATTTATC
1 AAAATTATCATAAAAA-TTATC
* *
29705448 AAAATTGTTATAAAAATTATC
1 AAAATTATCATAAAAATTATC
*
29705469 AAAATT-TTATAAAAAGTTA-C
1 AAAATTATCATAAAAA-TTATC
29705489 TAAAATTAT-ATAAAA
1 -AAAATTATCATAAAA
29705504 TCTTACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
20 10 0.20
21 34 0.68
22 6 0.12
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (21 bp):
AAAATTATCATAAAAATTATC
Found at i:29705509 original size:21 final size:21
Alignment explanation
Indices: 29705456--29705509 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
29705446 TCAAAATTGT
*
29705456 TATAAAAA-TTA-TCAAAATTT
1 TATAAAAACTTACT-AAAATTA
*
29705476 TATAAAAAGTTACTAAAATTA
1 TATAAAAACTTACTAAAATTA
*
29705497 TATAAAATCTTAC
1 TATAAAAACTTAC
29705510 CAAATTGTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.28
21 20 0.69
22 1 0.03
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (21 bp):
TATAAAAACTTACTAAAATTA
Found at i:29705564 original size:21 final size:21
Alignment explanation
Indices: 29705530--29705578 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
29705520 CAAATATTGT
29705530 CAAAATT-GTTTGAA-AGTTAC
1 CAAAATTAGTTTGAATA-TTAC
* *
29705550 CAAAATTATTTTGAATATTAT
1 CAAAATTAGTTTGAATATTAC
29705571 CAAAATTA
1 CAAAATTA
29705579 AATCAAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.28
21 17 0.68
22 1 0.04
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (21 bp):
CAAAATTAGTTTGAATATTAC
Found at i:29705674 original size:21 final size:22
Alignment explanation
Indices: 29705650--29705725 Score: 77
Period size: 21 Copynumber: 3.6 Consensus size: 22
29705640 TGTAGTGAAA
29705650 TTATCAAAATTATTTCGAAA-G
1 TTATCAAAATTATTTCGAAATG
* * *
29705671 TTATCAAAATAATAT-AAAATG
1 TTATCAAAATTATTTCGAAATG
* * *
29705692 TTACCAAATTTATTTC-AAATT
1 TTATCAAAATTATTTCGAAATG
29705713 TTATCAAAATTAT
1 TTATCAAAATTAT
29705726 ATAAATGTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 3 0.07
21 40 0.93
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTATTTCGAAATG
Found at i:29705718 original size:42 final size:41
Alignment explanation
Indices: 29705654--29705735 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 41
29705644 GTGAAATTAT
29705654 CAAAATTATTTCGAAAGTTATCAAAATAATATAAAATGTTAC
1 CAAAATTATTTCGAAAGTTATCAAAATAATAT-AAATGTTAC
* * *
29705696 CAAATTTATTTC-AAATTTTATCAAAATTATATAAATGTTA
1 CAAAATTATTTCGAAA-GTTATCAAAATAATATAAATGTTA
29705736 TTGAAGTCGT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 11 0.31
42 25 0.69
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.39
Consensus pattern (41 bp):
CAAAATTATTTCGAAAGTTATCAAAATAATATAAATGTTAC
Found at i:29705953 original size:21 final size:21
Alignment explanation
Indices: 29705929--29705969 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
29705919 AAGCTCATCA
*
29705929 AAATCATATCATAAGTTATTT
1 AAATCATATCAAAAGTTATTT
29705950 AAATCATATCAAAAGTTATT
1 AAATCATATCAAAAGTTATT
29705970 AAAAATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (21 bp):
AAATCATATCAAAAGTTATTT
Found at i:29707312 original size:16 final size:16
Alignment explanation
Indices: 29707293--29707334 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
29707283 AAATAATAAT
29707293 TATTATTATTAAAAAA
1 TATTATTATTAAAAAA
*
29707309 TATT-TTAATAAAAAA
1 TATTATTATTAAAAAA
29707324 -ATTATT-TTAAA
1 TATTATTATTAAA
29707335 TAGTTTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 7 0.30
15 12 0.52
16 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATTATTATTAAAAAA
Found at i:29707329 original size:17 final size:17
Alignment explanation
Indices: 29707290--29707333 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
29707280 TAAAAATAAT
*
29707290 AATTATTATT-ATTAAAA
1 AATTATT-TTAATAAAAA
29707307 AA-TATTTTAATAAAAA
1 AATTATTTTAATAAAAA
29707323 AATTATTTTAA
1 AATTATTTTAA
29707334 ATAGTTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 12 0.50
17 10 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTATTTTAATAAAAA
Found at i:29716513 original size:22 final size:23
Alignment explanation
Indices: 29716464--29716515 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
29716454 AAAATCCTCT
* *
29716464 AAATTTAAAAATTCAATTGACTG
1 AAATTTAAAAATTCAATTAACTA
* *
29716487 CAATTTAAAAATT-AATTAATTA
1 AAATTTAAAAATTCAATTAACTA
29716509 AAATTTA
1 AAATTTA
29716516 TCACATAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (23 bp):
AAATTTAAAAATTCAATTAACTA
Done.