Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 14 of 126
Found at i:3249645 original size:2 final size:2
Alignment explanation
Indices: 3249629--3249663 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3249619 ACAAAATTAG
*
3249629 AT AT CT AT A- 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 AT
3249664 GATACAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3249793 original size:25 final size:25
Alignment explanation
Indices: 3249757--3249816 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
3249747 TTTATATTTT
* *
3249757 TAATATTAATATAAATTATGATATA
1 TAATATTAATATAAAATATAATATA
*
3249782 TAATATTGATATAAAATATAATATA
1 TAATATTAATATAAAATATAATATA
3249807 -AATATATAAT
1 TAATAT-TAAT
3249817 TTATTAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 5 0.17
25 25 0.83
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (25 bp):
TAATATTAATATAAAATATAATATA
Found at i:3249811 original size:18 final size:18
Alignment explanation
Indices: 3249758--3249812 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
3249748 TTATATTTTT
*
3249758 AATATTAATATAAATTATGA
1 AATA-TAATATAAA-TATAA
* **
3249778 TATATAATATTGATATAA
1 AATATAATATAAATATAA
3249796 AATATAATATAAATATA
1 AATATAATATAAATATA
3249813 TAATTTATTA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
18 18 0.64
19 7 0.25
20 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
AATATAATATAAATATAA
Found at i:3249813 original size:13 final size:13
Alignment explanation
Indices: 3249758--3249816 Score: 63
Period size: 12 Copynumber: 4.8 Consensus size: 13
3249748 TTATATTTTT
3249758 AATAT-TAATATA
1 AATATATAATATA
*
3249770 AAT-TATGATATA
1 AATATATAATATA
*
3249782 TAATAT-TGATATA
1 -AATATATAATATA
3249795 AA-ATATAATATA
1 AATATATAATATA
3249807 AATATATAAT
1 AATATATAAT
3249817 TTATTAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 3 0.08
12 19 0.47
13 17 0.43
14 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
AATATATAATATA
Found at i:3256981 original size:22 final size:22
Alignment explanation
Indices: 3256942--3256984 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3256932 AAATTAAAAC
***
3256942 CTTAAAAATCACTCCAAAATAT
1 CTTAAAAATCAAAACAAAATAT
3256964 CTTAAAAATCAAAACAAAATA
1 CTTAAAAATCAAAACAAAATA
3256985 ATAAAAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (22 bp):
CTTAAAAATCAAAACAAAATAT
Found at i:3258377 original size:21 final size:22
Alignment explanation
Indices: 3258351--3258399 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
3258341 TGTTAAGTAC
*
3258351 AAAAAATGATAAA-AT-AAATCA
1 AAAAAATGA-AAATATAAAAACA
3258372 AAAAAATGAAAATATAAAAACA
1 AAAAAATGAAAATATAAAAACA
3258394 AAAAAA
1 AAAAAA
3258400 ATTTTATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 3 0.12
21 11 0.44
22 11 0.44
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (22 bp):
AAAAAATGAAAATATAAAAACA
Found at i:3259349 original size:299 final size:306
Alignment explanation
Indices: 3258802--3259486 Score: 889
Period size: 317 Copynumber: 2.2 Consensus size: 306
3258792 TTCAAATTTG
*
3258802 ATATAGGCATGTCTTATGTACCTAGGTTTTTCTACTACCTTATGTA--AGATAATGGGAAGTAAT
1 ATATAGGCATGTCTTATGTACCTAGGTTTTTTTACTACCTTATGTATGAGATAATGGGAAGTAAT
3258865 ATGACCTCTAGGACTTTTATTGATGATGTTTTTGGTGTCTTAGTTAAAAAGAGGTGAGGTGAGGT
66 ATGACCTCTAGGACTTTTATTGATGATGTTTTTGGTGTCTTAGTTAAAAAGAGGTGAGGTGAGGT
* * *
3258930 TAGAGAAAAGATAATCTAAATCTAAAGTTGAAGAATAGAGTTAAAGGGTGTCAGAATTATCATTT
131 TAGAGAAAAGATAATCTAAACCTAAAGTTGAAGAATAGAGTTAAAAGGTGTAAGAATTATCATTT
* * ** *
3258995 TATGGTGTGTTTCGATGTCGCGTTGGGTATGAAAGAAGAAAGGAAGGT-AA-AAG-AA-G-GT-G
196 TAGGGTGTGTTTCAATGTCAAGTTGGATATGAAAGAAGAAAGG-AGGTAAAGAAGAAAGGAGTAG
* *
3259054 AA-G-TGTGAATGAGAAGCTTCAAAGTAAGGAAAGCATAGATGTGAA
260 AAGGATGTGAATGAGAAGCTTCAAAGGAAGGAAAGCATAAATGTGAA
*
3259099 ATATAGGCATGTCTTATGTACCTAGGTTTTTTTACTACCTTATGTATGAGATAACGGGAAGTAAT
1 ATATAGGCATGTCTTATGTACCTAGGTTTTTTTACTACCTTATGTATGAGATAATGGGAAGTAAT
* *
3259164 ATGACCTCTAGGACTTTTATTGATGGTGTTTTTGGTGTCTTAGTTAAAAAGATGTG-GGTGAGGT
66 ATGACCTCTAGGACTTTTATTGATGATGTTTTTGGTGTCTTAGTTAAAAAGAGGTGAGGTGAGGT
* *
3259228 TAGAGGAAAGATAATCTAAACCTACAGTTGAAGAATAGAGTTAAAAGGTGTAAGAATTATCATTT
131 TAGAGAAAAGATAATCTAAACCTAAAGTTGAAGAATAGAGTTAAAAGGTGTAAGAATTATCATTT
** *
3259293 T-GGGTGTGTTTCAATGCTCAAGTTGATGATAT-ATTTG-AGATAAGG-GTATGAAAGAAGAAAG
196 TAGGGTGTGTTTCAATG-TCAAGTTG--GATATGA-AAGAAGA-AAGGAG-GT-AAAGAAGAAAG
*
3259354 GAAGTCAAAAGAAGGTGAAATGTGAATGCGAAGCTTCAAAGGAAGGAAAGCATAAATGTGAA
254 G-AGT----AGAA-G-G--ATGTGAATGAGAAGCTTCAAAGGAAGGAAAGCATAAATGTGAA
* * *
3259416 ATATAGTCATGTTTTATGTACCTA-GTTTTTTCTACTACCTTATGTATGAGATAATGGAAAGTAA
1 ATATAGGCATGTCTTATGTACCTAGGTTTTTT-TACTACCTTATGTATGAGATAATGGGAAGTAA
3259480 TATGACC
65 TATGACC
3259487 ATAACAGTTG
Statistics
Matches: 337, Mismatches: 24, Indels: 34
0.85 0.06 0.09
Matches are distributed among these distances:
297 58 0.17
298 76 0.23
299 75 0.22
300 9 0.03
301 2 0.01
302 3 0.01
303 2 0.01
304 1 0.00
306 2 0.01
311 3 0.01
314 1 0.00
316 7 0.02
317 98 0.29
ACGTcount: A:0.35, C:0.08, G:0.25, T:0.32
Consensus pattern (306 bp):
ATATAGGCATGTCTTATGTACCTAGGTTTTTTTACTACCTTATGTATGAGATAATGGGAAGTAAT
ATGACCTCTAGGACTTTTATTGATGATGTTTTTGGTGTCTTAGTTAAAAAGAGGTGAGGTGAGGT
TAGAGAAAAGATAATCTAAACCTAAAGTTGAAGAATAGAGTTAAAAGGTGTAAGAATTATCATTT
TAGGGTGTGTTTCAATGTCAAGTTGGATATGAAAGAAGAAAGGAGGTAAAGAAGAAAGGAGTAGA
AGGATGTGAATGAGAAGCTTCAAAGGAAGGAAAGCATAAATGTGAA
Found at i:3260206 original size:15 final size:17
Alignment explanation
Indices: 3260186--3260218 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
3260176 AAATTAATCG
3260186 GTGCACTT-TTTC-AAA
1 GTGCACTTATTTCGAAA
3260201 GTGCACTTATTTCGAAA
1 GTGCACTTATTTCGAAA
3260218 G
1 G
3260219 GGTGTGTACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (17 bp):
GTGCACTTATTTCGAAA
Found at i:3260486 original size:21 final size:21
Alignment explanation
Indices: 3260462--3260521 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
3260452 GATTACTGTG
3260462 ATTTAAATTTTAATTATTTAA
1 ATTTAAATTTTAATTATTTAA
3260483 ATTTAAATTTTAATTATTTAA
1 ATTTAAATTTTAATTATTTAA
*
3260504 ATTAAAATTTTAA-TATTT
1 ATTTAAATTTTAATTATTT
3260522 TATCAATAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 5 0.13
21 33 0.87
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTAAATTTTAATTATTTAA
Found at i:3260506 original size:15 final size:15
Alignment explanation
Indices: 3260462--3260491 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3260452 GATTACTGTG
*
3260462 ATTTAAATTTTAATT
1 ATTTAAATTTAAATT
3260477 ATTTAAATTTAAATT
1 ATTTAAATTTAAATT
3260492 TTAATTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTAAATTTAAATT
Found at i:3260841 original size:28 final size:28
Alignment explanation
Indices: 3260809--3260865 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
3260799 TTTATTAAAA
* *
3260809 TCATCTTAAATATATGACTTATAAT-TAT
1 TCATCTTAAAT-TATCACGTATAATATAT
3260837 TCATCTTAAATTATCACGTATAATATAT
1 TCATCTTAAATTATCACGTATAATATAT
3260865 T
1 T
3260866 TTATTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.46
Consensus pattern (28 bp):
TCATCTTAAATTATCACGTATAATATAT
Found at i:3270308 original size:15 final size:16
Alignment explanation
Indices: 3270280--3270309 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3270270 TTTCGGACAG
3270280 AAAGCCAAAGCCTTGA
1 AAAGCCAAAGCCTTGA
3270296 AAAGCCAAA-CCTTG
1 AAAGCCAAAGCCTTG
3270310 CTCACAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.27, G:0.17, T:0.13
Consensus pattern (16 bp):
AAAGCCAAAGCCTTGA
Found at i:3279419 original size:17 final size:16
Alignment explanation
Indices: 3279372--3279431 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
3279362 ATAGGAGGAT
3279372 ATTAATTTTATATTTA
1 ATTAATTTTATATTTA
* *
3279388 ATAAATATTTA-ATTTT
1 ATTAAT-TTTATATTTA
3279404 ATGTAATTTTATATTTA
1 AT-TAATTTTATATTTA
3279421 AGTTGAATTTT
1 A-TT-AATTTT
3279432 TTTATTTACT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 15 0.43
17 13 0.37
18 7 0.20
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (16 bp):
ATTAATTTTATATTTA
Found at i:3285047 original size:25 final size:25
Alignment explanation
Indices: 3285015--3285080 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 25
3285005 TTAATATAAC
3285015 TATTAAAATATTAAAAATAATTTAT
1 TATTAAAATATTAAAAATAATTTAT
** *
3285040 TATTAAAATATATTGAAATTATTTAT
1 TATTAAAATAT-TAAAAATAATTTAT
*
3285066 TATGAAAATTATTAA
1 TATTAAAA-TATTAA
3285081 TATAAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 11 0.33
26 19 0.58
27 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (25 bp):
TATTAAAATATTAAAAATAATTTAT
Found at i:3285058 original size:26 final size:26
Alignment explanation
Indices: 3285015--3285085 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 26
3285005 TTAATATAAC
*
3285015 TATTAAAATAT-TAAAAATAATTTAT
1 TATTAAAATATATTAAAATAATTTAT
* *
3285040 TATTAAAATATATTGAAATTATTTAT
1 TATTAAAATATATTAAAATAATTTAT
* *
3285066 TATGAAAAT-TATTAATATAA
1 TATTAAAATATATTAAAATAA
3285086 AAAAAATTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 19 0.50
26 19 0.50
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (26 bp):
TATTAAAATATATTAAAATAATTTAT
Found at i:3285088 original size:15 final size:16
Alignment explanation
Indices: 3285055--3285163 Score: 64
Period size: 15 Copynumber: 6.6 Consensus size: 16
3285045 AAATATATTG
* *
3285055 AAATTATTTATTATGA
1 AAATTATTTAATATAA
3285071 AAATTA-TTAATATAA
1 AAATTATTTAATATAA
**
3285086 AAAAAATTATAATTTTATAA
1 AAATTATT-TAA---TATAA
*
3285106 TAA-TATTTAATATTAA
1 AAATTATTTAATA-TAA
3285122 AATATTATATTAATATAA
1 AA-ATTAT-TTAATATAA
* *
3285140 AAA-TACTTAAAAT-A
1 AAATTATTTAATATAA
3285154 AAATTATTTA
1 AAATTATTTA
3285164 TTATTTTATA
Statistics
Matches: 73, Mismatches: 10, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
14 4 0.05
15 24 0.33
16 13 0.18
17 5 0.07
18 11 0.15
19 9 0.12
20 7 0.10
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (16 bp):
AAATTATTTAATATAA
Found at i:3285139 original size:34 final size:33
Alignment explanation
Indices: 3285101--3285166 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 33
3285091 ATTATAATTT
* * *
3285101 TATAATAATATTTAATATTAAAA-TATTATATTAA
1 TATAAAAATACTTAA-AATAAAATTATT-TATTAA
3285135 TATAAAAATACTTAAAATAAAATTATTTATTA
1 TATAAAAATACTTAAAATAAAATTATTTATTA
3285167 TTTTATATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 11 0.39
34 17 0.61
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (33 bp):
TATAAAAATACTTAAAATAAAATTATTTATTAA
Found at i:3285429 original size:13 final size:14
Alignment explanation
Indices: 3285390--3285428 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
3285380 TGAAAATACA
*
3285390 AAAATTATTTTTCT
1 AAAATCATTTTTCT
3285404 AAAATCATTTTTC-
1 AAAATCATTTTTCT
3285417 AAAAGTCATTTT
1 AAAA-TCATTTT
3285429 CTGTGAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (14 bp):
AAAATCATTTTTCT
Found at i:3287007 original size:11 final size:11
Alignment explanation
Indices: 3286991--3287021 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
3286981 TGATAACATA
3286991 ATTACATTAAT
1 ATTACATTAAT
3287002 ATTACA-TAAT
1 ATTACATTAAT
3287012 ATTACATTAA
1 ATTACATTAA
3287022 CAGCTTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (11 bp):
ATTACATTAAT
Found at i:3289394 original size:11 final size:11
Alignment explanation
Indices: 3289378--3289402 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3289368 GTTCATGAGG
3289378 AAATTCATTTA
1 AAATTCATTTA
3289389 AAATTCATTTA
1 AAATTCATTTA
3289400 AAA
1 AAA
3289403 CACATTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATTCATTTA
Found at i:3290014 original size:18 final size:19
Alignment explanation
Indices: 3289975--3290017 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
3289965 AAAAATTGAA
*
3289975 TTATATATTTTTATTAACTT
1 TTATATATTTTTA-TAAATT
3289995 TTATATATTTTTA-AAATT
1 TTATATATTTTTATAAATT
3290013 TTATA
1 TTATA
3290018 AGATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATATATTTTTATAAATT
Found at i:3290087 original size:12 final size:11
Alignment explanation
Indices: 3290053--3290099 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
3290043 AATTTATTTG
3290053 ATAATATTAAA
1 ATAATATTAAA
*
3290064 TATTATATTAAA
1 -ATAATATTAAA
3290076 ATAATATCTAAAA
1 ATAATAT-T-AAA
3290089 ATAA-ATTAAA
1 ATAATATTAAA
3290099 A
1 A
3290100 ATTAATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 4 0.13
11 7 0.23
12 13 0.42
13 7 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATATTAAA
Found at i:3290089 original size:13 final size:12
Alignment explanation
Indices: 3290053--3290106 Score: 58
Period size: 11 Copynumber: 4.5 Consensus size: 12
3290043 AATTTATTTG
*
3290053 ATAATATTAAAT
1 ATAATATTAAAA
*
3290065 ATTATATT-AAA
1 ATAATATTAAAA
3290076 ATAATATCTAAAA
1 ATAATAT-TAAAA
3290089 ATAA-ATTAAAA
1 ATAATATTAAAA
3290100 ATTAATA
1 A-TAATA
3290107 AATCAAACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
11 14 0.40
12 13 0.37
13 8 0.23
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAATATTAAAA
Found at i:3290096 original size:23 final size:23
Alignment explanation
Indices: 3290053--3290099 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3290043 AATTTATTTG
* *
3290053 ATAATATTAAATATTATATTAAA
1 ATAATATTAAATAATAAATTAAA
3290076 ATAATATCTAAA-AATAAATTAAA
1 ATAATAT-TAAATAATAAATTAAA
3290099 A
1 A
3290100 ATTAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
ATAATATTAAATAATAAATTAAA
Found at i:3290154 original size:32 final size:33
Alignment explanation
Indices: 3290117--3290183 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 33
3290107 AATCAAACTT
* * *
3290117 AAAATTTGATTTAAATT-ATATTTAATTATAAA
1 AAAATTTGATTCAAATTCAAATTAAATTATAAA
*
3290149 AAAATTTGATTCAAATTCAAATTAAATTTTAAA
1 AAAATTTGATTCAAATTCAAATTAAATTATAAA
3290182 AA
1 AA
3290184 TTTATAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (33 bp):
AAAATTTGATTCAAATTCAAATTAAATTATAAA
Found at i:3291415 original size:7 final size:7
Alignment explanation
Indices: 3291402--3291458 Score: 96
Period size: 7 Copynumber: 8.1 Consensus size: 7
3291392 ACCTTATTAA
3291402 CACCATC
1 CACCATC
*
3291409 GACCATC
1 CACCATC
*
3291416 GACCATC
1 CACCATC
3291423 CACCATC
1 CACCATC
3291430 CACCATC
1 CACCATC
3291437 CACCATC
1 CACCATC
3291444 CACCATC
1 CACCATC
3291451 CACCATC
1 CACCATC
3291458 C
1 C
3291459 CGAAATTCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.28, C:0.54, G:0.04, T:0.14
Consensus pattern (7 bp):
CACCATC
Found at i:3295055 original size:26 final size:26
Alignment explanation
Indices: 3294999--3295055 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
3294989 TTGGTACAAA
3294999 AATATTATAATAAGATAAAATAAGAT
1 AATATTATAATAAGATAAAATAAGAT
* *
3295025 GATATTATAATAAGATTAAATTAA-AT
1 AATATTATAATAAGA-TAAAATAAGAT
3295051 AATAT
1 AATAT
3295056 CATTTTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 20 0.74
27 7 0.26
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (26 bp):
AATATTATAATAAGATAAAATAAGAT
Found at i:3296808 original size:14 final size:14
Alignment explanation
Indices: 3296785--3296818 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3296775 TTTATTTATA
* *
3296785 AATAATATTATATT
1 AATAAAATTATAAT
3296799 AATAAAATTATAAT
1 AATAAAATTATAAT
3296813 AATAAA
1 AATAAA
3296819 TATTTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAAATTATAAT
Found at i:3296826 original size:26 final size:26
Alignment explanation
Indices: 3296780--3296906 Score: 63
Period size: 26 Copynumber: 5.0 Consensus size: 26
3296770 ATAATTTTAT
* *
3296780 TTATAAATAAT-ATTATATTAATAAAA
1 TTAT-AATAATAAATATTTTAATAAAA
3296806 TTATAATAATAAATATTTTAAT----
1 TTATAATAATAAATATTTTAATAAAA
* * *
3296828 TTA-ATTAATAAATATTATAATAATA
1 TTATAATAATAAATATTTTAATAAAA
* *
3296853 -TATGAATAAATAATATACTATTAATATAA
1 TTAT-AAT-AATAA-ATA-TTTTAATAAAA
* *
3296882 -TATATTAGTAAATATTATTAATAAA
1 TTATAATAATAAATATT-TTAATAAA
3296907 TAATATATTA
Statistics
Matches: 77, Mismatches: 13, Indels: 22
0.69 0.12 0.20
Matches are distributed among these distances:
21 16 0.21
22 3 0.04
24 2 0.03
25 7 0.09
26 25 0.32
27 9 0.12
28 5 0.06
29 10 0.13
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (26 bp):
TTATAATAATAAATATTTTAATAAAA
Found at i:3296836 original size:21 final size:21
Alignment explanation
Indices: 3296804--3296913 Score: 73
Period size: 23 Copynumber: 5.0 Consensus size: 21
3296794 ATATTAATAA
*
3296804 AATTATAATAATAAATATTTT
1 AATTATAATAATAAATATTAT
3296825 AATT-TAATTAATAAATATTAT
1 AATTATAA-TAATAAATATTAT
* *
3296846 AATAATATATGAATAAATAATAT
1 AATTATA-AT-AATAAATATTAT
*
3296869 -ACTATTAAT-ATAATATATTAGT
1 AATTA-TAATAATAA-ATATTA-T
* * *
3296891 AAATATTATTAATAAATAATAT
1 AATTA-TAATAATAAATATTAT
3296913 A
1 A
3296914 TTAATATATT
Statistics
Matches: 71, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
20 7 0.10
21 24 0.34
22 10 0.14
23 26 0.37
24 4 0.06
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.43
Consensus pattern (21 bp):
AATTATAATAATAAATATTAT
Found at i:3296882 original size:31 final size:28
Alignment explanation
Indices: 3296846--3296919 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 28
3296836 TAAATATTAT
* *
3296846 AATAATATATGAATAAATAATATACTATTA
1 AATAATATATTAATAAAT-AT-TACTAATA
* *
3296876 ATATAATATATTAGTAAATATTATTAATA
1 A-ATAATATATTAATAAATATTACTAATA
3296905 AATAATATATTAATA
1 AATAATATATTAATA
3296920 TATTAATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
28 13 0.34
29 7 0.18
30 3 0.08
31 15 0.39
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (28 bp):
AATAATATATTAATAAATATTACTAATA
Found at i:3296912 original size:26 final size:24
Alignment explanation
Indices: 3296862--3296935 Score: 71
Period size: 26 Copynumber: 3.0 Consensus size: 24
3296852 ATATGAATAA
3296862 ATAATATACTATTAATATAAT-ATATT
1 ATAA-ATA-TATTAATA-AATAATATT
3296888 AGTAAATATTATTAATAAATAATA-T
1 A-TAAATA-TATTAATAAATAATATT
* *
3296913 ATTAATATATTAATAAACAATAT
1 ATAAATATATTAATAAATAATAT
3296936 AAAGAATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
23 14 0.33
24 5 0.12
25 5 0.12
26 15 0.36
27 3 0.07
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (24 bp):
ATAAATATATTAATAAATAATATT
Found at i:3296927 original size:44 final size:43
Alignment explanation
Indices: 3296793--3296927 Score: 109
Period size: 44 Copynumber: 3.0 Consensus size: 43
3296783 TAAATAATAT
* *
3296793 TATATTAATAAA-ATTA-TAAT-AATAAATATTTTAATTTAATTAA
1 TATATT-ATAAATATTATTAATAAAT-AATATATTAATAT-ATTAA
* * *
3296836 TAAATATTAT-AATAATATATGAATAAATAATATACTATTA-ATATAA
1 T--ATATTATAAAT-AT-TATTAATAAATAATATATTAATATAT-TAA
3296882 TATATTAGTAAATATTATTAATAAATAATATATTAATATATTAA
1 TATATTA-TAAATATTATTAATAAATAATATATTAATATATTAA
3296926 TA
1 TA
3296928 AACAATATAA
Statistics
Matches: 73, Mismatches: 8, Indels: 21
0.72 0.08 0.21
Matches are distributed among these distances:
43 3 0.04
44 33 0.45
45 14 0.19
46 9 0.12
47 11 0.15
48 3 0.04
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (43 bp):
TATATTATAAATATTATTAATAAATAATATATTAATATATTAA
Found at i:3296934 original size:23 final size:24
Alignment explanation
Indices: 3296892--3296936 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
3296882 TATATTAGTA
*
3296892 AATATTATTAATAAATAATATATT
1 AATATTATTAATAAACAATATATT
3296916 AATA-TATTAATAAACAATATA
1 AATATTATTAATAAACAATATA
3296937 AAGAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
AATATTATTAATAAACAATATATT
Found at i:3297043 original size:15 final size:15
Alignment explanation
Indices: 3297023--3297063 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
3297013 TAGAATTATT
*
3297023 TTTTAATATTAATAA
1 TTTTAATATAAATAA
3297038 TTTTAATAATAAATAA
1 TTTTAAT-ATAAATAA
*
3297054 TTTCAATATA
1 TTTTAATATA
3297064 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:3297070 original size:26 final size:26
Alignment explanation
Indices: 3297033--3297098 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
3297023 TTTTAATATT
3297033 AATA-ATTTTAATAATAAATAATTTC
1 AATATATTTTAATAATAAATAATTTC
*
3297058 AATATATTTTAATAATAAATAATTTT
1 AATATATTTTAATAATAAATAATTTC
*
3297084 TA-ATATTTTAATAAT
1 AATATATTTTAATAAT
3297099 TATATTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 17 0.45
26 21 0.55
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AATATATTTTAATAATAAATAATTTC
Found at i:3297082 original size:16 final size:16
Alignment explanation
Indices: 3297023--3297088 Score: 56
Period size: 15 Copynumber: 4.5 Consensus size: 16
3297013 TAGAATTATT
*
3297023 TTTTAAT-ATTAATAA
1 TTTTAATAATAAATAA
3297038 TTTTAATAATAAATAA
1 TTTTAATAATAAATAA
*
3297054 -TTT--CAAT--AT-A
1 TTTTAATAATAAATAA
3297064 TTTTAATAATAAATAA
1 TTTTAATAATAAATAA
3297080 TTTTTAATA
1 -TTTTAATA
3297089 TTTTAATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
10 1 0.03
11 5 0.12
13 6 0.15
15 12 0.30
16 8 0.20
17 8 0.20
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTAATAATAAATAA
Found at i:3299761 original size:22 final size:24
Alignment explanation
Indices: 3299718--3299766 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
3299708 GAAGAGGAGA
*
3299718 TTATATATTTAAATATTTTTAAAT
1 TTATATATTTAAATATTATTAAAT
* *
3299742 TTATA-ATTTATA-ATTATTAATT
1 TTATATATTTAAATATTATTAAAT
3299764 TTA
1 TTA
3299767 ATAACATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 11 0.50
23 6 0.27
24 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTATATATTTAAATATTATTAAAT
Found at i:3300237 original size:20 final size:19
Alignment explanation
Indices: 3300212--3300268 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
3300202 AAATATTTTT
3300212 AATATTTAATTATTATATTA
1 AATATTT-ATTATTATATTA
*
3300232 AATATTTTATTATAAT-TTA
1 AATA-TTTATTATTATATTA
3300251 ATATAATTTATTATTATA
1 A-AT-ATTTATTATTATA
3300269 AGTCAACCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 4 0.13
20 23 0.74
21 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATTTATTATTATATTA
Found at i:3301066 original size:5 final size:6
Alignment explanation
Indices: 3301050--3301075 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3301040 AAACTCTAAA
3301050 ATTTTT ATTTTT ATTTTT ATTTTT AT
1 ATTTTT ATTTTT ATTTTT ATTTTT AT
3301076 CTATTTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:3301843 original size:17 final size:18
Alignment explanation
Indices: 3301823--3301861 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3301813 AAATAATTAA
3301823 TTATTTTTATTAAT-ATT
1 TTATTTTTATTAATAATT
* *
3301840 TTATTTTTTTTATTAATT
1 TTATTTTTATTAATAATT
3301858 TTAT
1 TTAT
3301862 AATTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTTTTATTAATAATT
Found at i:3301870 original size:20 final size:20
Alignment explanation
Indices: 3301819--3301870 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
3301809 GATCAAATAA
3301819 TTAATTATTTTTATTAATATT
1 TTAATTA-TTTTATTAATATT
* *
3301840 TTATTTTTTTTATTAAT-TT
1 TTAATTATTTTATTAATATT
3301859 TATAATTATTTT
1 T-TAATTATTTT
3301871 TAATTATTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 3 0.12
20 18 0.69
21 5 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTAATTATTTTATTAATATT
Found at i:3302126 original size:60 final size:60
Alignment explanation
Indices: 3302054--3302176 Score: 219
Period size: 60 Copynumber: 2.0 Consensus size: 60
3302044 GGGGGGTTTA
3302054 TTTAGATGAAATAGTACTATAAGAGTTTAATTAGATTATTTCAAATACTAAAAAGTTTTT
1 TTTAGATGAAATAGTACTATAAGAGTTTAATTAGATTATTTCAAATACTAAAAAGTTTTT
* * *
3302114 TTTATATGAAATAGTACTATAAGAGTTTAATTAGATTATTTTAAATATTAAAAAGTTTTT
1 TTTAGATGAAATAGTACTATAAGAGTTTAATTAGATTATTTCAAATACTAAAAAGTTTTT
3302174 TTT
1 TTT
3302177 TTATATTTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.46
Consensus pattern (60 bp):
TTTAGATGAAATAGTACTATAAGAGTTTAATTAGATTATTTCAAATACTAAAAAGTTTTT
Found at i:3302160 original size:34 final size:34
Alignment explanation
Indices: 3302062--3302160 Score: 97
Period size: 30 Copynumber: 3.1 Consensus size: 34
3302052 TATTTAGATG
3302062 AAATAGTACTATAAGAGTTTAATTAGATTA-TTT
1 AAATAGTACTATAAGAGTTTAATTAGATTATTTT
* * * * *
3302095 CAA-A-TACTA-AAAAGTTT--TT--TTTATATG
1 AAATAGTACTATAAGAGTTTAATTAGATTATTTT
3302122 AAATAGTACTATAAGAGTTTAATTAGATTATTTT
1 AAATAGTACTATAAGAGTTTAATTAGATTATTTT
3302156 AAATA
1 AAATA
3302161 TTAAAAAGTT
Statistics
Matches: 48, Mismatches: 10, Indels: 15
0.66 0.14 0.21
Matches are distributed among these distances:
26 3 0.06
27 3 0.06
28 3 0.06
29 5 0.10
30 14 0.29
31 5 0.10
32 3 0.06
33 2 0.04
34 10 0.21
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.42
Consensus pattern (34 bp):
AAATAGTACTATAAGAGTTTAATTAGATTATTTT
Found at i:3307466 original size:20 final size:21
Alignment explanation
Indices: 3307425--3307466 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3307415 AACAATATAA
3307425 TTTCGAATAAATTTTTATTTT
1 TTTCGAATAAATTTTTATTTT
3307446 TTTCGAATAAATTTTTATTTT
1 TTTCGAATAAATTTTTATTTT
3307467 CTCAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTCGAATAAATTTTTATTTT
Found at i:3308702 original size:189 final size:189
Alignment explanation
Indices: 3308377--3308756 Score: 697
Period size: 189 Copynumber: 2.0 Consensus size: 189
3308367 CGAAGCCAGG
*
3308377 TCAGATTCTCTGATATTGGGTTCCACTCTGTCAATCTCCTCCTCTGACGCAGAAACTATCGGAAA
1 TCAGATTCTCTGACATTGGGTTCCACTCTGTCAATCTCCTCCTCTGACGCAGAAACTATCGGAAA
3308442 AGGCTGCAACTCTTCATTTGCACATCTGGTTATATTTCCTTCAACACACTCTGTAACGGAATTTT
66 AGGCTGCAACTCTTCATTTGCACATCTGGTTATATTTCCTTCAACACACTCTGTAACGGAATTTT
3308507 CCTCATCAATTGATTTCCCCATATCCAGGACCGTGTTAGCTGCACTTGCAGAAACCCAT
131 CCTCATCAATTGATTTCCCCATATCCAGGACCGTGTTAGCTGCACTTGCAGAAACCCAT
* * * *
3308566 TCAGGTTCTCTGGCATTGGGTTCCACTCTGTCAATCTTCTCCTCTGATGCAGAAACTATCGGAAA
1 TCAGATTCTCTGACATTGGGTTCCACTCTGTCAATCTCCTCCTCTGACGCAGAAACTATCGGAAA
* *
3308631 AGGCTGCAACTCTTCCTTTTCACATCTGGTTATATTTCCTTCAACACACTCTGTAACGGAATTTT
66 AGGCTGCAACTCTTCATTTGCACATCTGGTTATATTTCCTTCAACACACTCTGTAACGGAATTTT
3308696 CCTCATCAATTGATTTCCCCATATCCAGGACCGTGTTAGCTGCACTTGCAGAAACCCAT
131 CCTCATCAATTGATTTCCCCATATCCAGGACCGTGTTAGCTGCACTTGCAGAAACCCAT
3308755 TC
1 TC
3308757 TTCACCTGTC
Statistics
Matches: 184, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
189 184 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (189 bp):
TCAGATTCTCTGACATTGGGTTCCACTCTGTCAATCTCCTCCTCTGACGCAGAAACTATCGGAAA
AGGCTGCAACTCTTCATTTGCACATCTGGTTATATTTCCTTCAACACACTCTGTAACGGAATTTT
CCTCATCAATTGATTTCCCCATATCCAGGACCGTGTTAGCTGCACTTGCAGAAACCCAT
Found at i:3312878 original size:17 final size:17
Alignment explanation
Indices: 3312856--3312888 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3312846 TATCAGATTT
3312856 TTATA-TATATTATAATA
1 TTATATTATA-TATAATA
3312873 TTATATTATATATAAT
1 TTATATTATATATAAT
3312889 TAACTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATATTATATATAATA
Found at i:3314320 original size:25 final size:26
Alignment explanation
Indices: 3314267--3314321 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
3314257 AGGAGCACAT
* **
3314267 TTAAAAATGTTAAAATATAAAAATTA
1 TTAAAAATGTTAAAATAGAAAAAAAA
*
3314293 TTAAATAT-TTAAAATAGAAAAAAAA
1 TTAAAAATGTTAAAATAGAAAAAAAA
3314318 TTAA
1 TTAA
3314322 GAAAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (26 bp):
TTAAAAATGTTAAAATAGAAAAAAAA
Found at i:3314627 original size:15 final size:16
Alignment explanation
Indices: 3314602--3314631 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3314592 ATATTTGTTA
3314602 AATATATAAAAAAAAT
1 AATATATAAAAAAAAT
3314618 AATA-ATAAAAAAAA
1 AATATATAAAAAAAA
3314632 AAAACCAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
AATATATAAAAAAAAT
Found at i:3315467 original size:20 final size:22
Alignment explanation
Indices: 3315442--3315487 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
3315432 TTAGTAATTT
3315442 TATTAAA-AT-TAATAATTAAA
1 TATTAAATATATAATAATTAAA
3315462 TATTAAATATAATAATAATTAAA
1 TATTAAATAT-ATAATAATTAAA
3315485 TAT
1 TAT
3315488 ATGAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.30
21 2 0.09
23 14 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TATTAAATATATAATAATTAAA
Found at i:3316487 original size:23 final size:21
Alignment explanation
Indices: 3316454--3316501 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 21
3316444 TTTTGATTTA
*
3316454 ATTTTAATTTTAGTTTTTATC
1 ATTTTAATTTTAGTTATTATC
* *
3316475 ATTTTAAGTTTTTTGTTATTATT
1 ATTTTAA--TTTTAGTTATTATC
3316498 ATTT
1 ATTT
3316502 GTGCATGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 7 0.32
23 15 0.68
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (21 bp):
ATTTTAATTTTAGTTATTATC
Found at i:3317144 original size:15 final size:16
Alignment explanation
Indices: 3317124--3317157 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
3317114 GAAATCCTGA
3317124 AAAACCTCAA-ACCTT
1 AAAACCTCAAGACCTT
3317139 AAAACCTCAAGACCTT
1 AAAACCTCAAGACCTT
3317155 AAA
1 AAA
3317158 TCTTTAAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.50, C:0.29, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAACCTCAAGACCTT
Found at i:3317289 original size:38 final size:38
Alignment explanation
Indices: 3317217--3317343 Score: 105
Period size: 38 Copynumber: 3.3 Consensus size: 38
3317207 TAAACCTCCA
* * **
3317217 AAACCCTCAAAACTATCAAAACCCTAAAAATTTAAATTTG
1 AAACCC-CAAAA-TTTCAAAACCATAAACCTTTAAATTTG
*
3317257 AAACCCCAAAATTTCAAAACCATAAACCTTTAAATTTT
1 AAACCCCAAAATTTCAAAACCATAAACCTTTAAATTTG
* * * * *
3317295 AAACTCTAAAA-TTGAAAA-CTTAAACCTCTAAAACTTTG
1 AAACCCCAAAATTTCAAAACCATAAACCT-TTAAA-TTTG
*
3317333 AAACCTCAAAA
1 AAACCCCAAAA
3317344 CCTTAAAAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
36 8 0.11
37 10 0.14
38 42 0.59
39 5 0.07
40 6 0.08
ACGTcount: A:0.50, C:0.22, G:0.02, T:0.26
Consensus pattern (38 bp):
AAACCCCAAAATTTCAAAACCATAAACCTTTAAATTTG
Found at i:3317385 original size:7 final size:7
Alignment explanation
Indices: 3317333--3317471 Score: 62
Period size: 8 Copynumber: 17.9 Consensus size: 7
3317323 TAAAACTTTG
3317333 AAACCTCA
1 AAACCT-A
3317341 AAACCTTAA
1 AAACC-T-A
3317350 AAATCCTA
1 AAA-CCTA
*
3317358 AACCCTA
1 AAACCTA
*
3317365 AAATCTCA
1 AAACCT-A
*
3317373 ATACCTA
1 AAACCTA
3317380 AAACCTCA
1 AAACCT-A
3317388 AAATCCTA
1 AAA-CCTA
*
3317396 AAACTTCA
1 AAACCT-A
*
3317404 AACGCCTA
1 AA-ACCTA
*
3317412 AAACTTTCA
1 AAAC-CT-A
3317421 AAACTCTA
1 AAAC-CTA
**
3317429 AATTCTA
1 AAACCTA
3317436 AAACCTA
1 AAACCTA
3317443 AAACTCTA
1 AAAC-CTA
3317451 AAACCATA
1 AAACC-TA
* *
3317459 AACCCTG
1 AAACCTA
3317466 AAACCT
1 AAACCT
3317472 CGAATTCTTA
Statistics
Matches: 100, Mismatches: 20, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
7 36 0.36
8 44 0.44
9 18 0.18
10 2 0.02
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.22
Consensus pattern (7 bp):
AAACCTA
Found at i:3317397 original size:16 final size:15
Alignment explanation
Indices: 3317333--3317460 Score: 82
Period size: 15 Copynumber: 8.1 Consensus size: 15
3317323 TAAAACTTTG
3317333 AAACCTCAAAACCTTAA
1 AAACCTCAAAACC-T-A
*
3317350 AAATCCT-AAACCCTA
1 AAA-CCTCAAAACCTA
* *
3317365 AAATCTCAATACCTA
1 AAACCTCAAAACCTA
3317380 AAACCTCAAAATCCTA
1 AAACCTCAAAA-CCTA
* *
3317396 AAACTTCAAACGCCTA
1 AAACCTCAAA-ACCTA
*
3317412 AAACTTTCAAAACTCTA
1 AAAC-CTCAAAAC-CTA
**
3317429 AATTCT-AAAACCTA
1 AAACCTCAAAACCTA
3317443 AAA-CTCTAAAACCATA
1 AAACCTC-AAAACC-TA
3317459 AA
1 AA
3317461 CCCTGAAACC
Statistics
Matches: 89, Mismatches: 13, Indels: 19
0.74 0.11 0.16
Matches are distributed among these distances:
13 2 0.02
14 7 0.08
15 30 0.34
16 28 0.31
17 19 0.21
18 3 0.03
ACGTcount: A:0.50, C:0.27, G:0.01, T:0.22
Consensus pattern (15 bp):
AAACCTCAAAACCTA
Found at i:3317450 original size:15 final size:16
Alignment explanation
Indices: 3317333--3317460 Score: 92
Period size: 16 Copynumber: 8.1 Consensus size: 16
3317323 TAAAACTTTG
3317333 AAAC-CTCAAAACCTTA
1 AAACTCTCAAAACC-TA
* *
3317349 AAAATC-CTAAACCCTA
1 AAACTCTC-AAAACCTA
*
3317365 AAA-TCTCAATACCTA
1 AAACTCTCAAAACCTA
3317380 AAAC-CTCAAAATCCTA
1 AAACTCTCAAAA-CCTA
*
3317396 AAACT-TCAAACGCCTA
1 AAACTCTCAAA-ACCTA
*
3317412 AAACTTTCAAAACTCT-
1 AAACTCTCAAAAC-CTA
*
3317428 AAATTCT-AAAACCTA
1 AAACTCTCAAAACCTA
3317443 AAACTCT-AAAACCATA
1 AAACTCTCAAAACC-TA
3317459 AA
1 AA
3317461 CCCTGAAACC
Statistics
Matches: 91, Mismatches: 10, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
14 2 0.02
15 34 0.37
16 42 0.46
17 13 0.14
ACGTcount: A:0.50, C:0.27, G:0.01, T:0.22
Consensus pattern (16 bp):
AAACTCTCAAAACCTA
Found at i:3317461 original size:15 final size:14
Alignment explanation
Indices: 3317420--3317471 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
3317410 TAAAACTTTC
*
3317420 AAAACTCTAAATTCT
1 AAAAC-CTAAACTCT
3317435 AAAACCTAAAACTCT
1 AAAACCT-AAACTCT
*
3317450 AAAACCATAAACCCT
1 AAAACC-TAAACTCT
*
3317465 GAAACCT
1 AAAACCT
3317472 CGAATTCTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
14 3 0.09
15 28 0.88
16 1 0.03
ACGTcount: A:0.50, C:0.27, G:0.02, T:0.21
Consensus pattern (14 bp):
AAAACCTAAACTCT
Found at i:3317508 original size:24 final size:24
Alignment explanation
Indices: 3317458--3317508 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
3317448 CTAAAACCAT
** * *
3317458 AAACCCTGAAACCTCGAATTCTTA
1 AAACCCTGAAACCTAAAACTCTCA
*
3317482 AAACCTTGAAACCTAAAACTCTCA
1 AAACCCTGAAACCTAAAACTCTCA
3317506 AAA
1 AAA
3317509 TCCTAAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.27, G:0.06, T:0.22
Consensus pattern (24 bp):
AAACCCTGAAACCTAAAACTCTCA
Found at i:3317729 original size:15 final size:16
Alignment explanation
Indices: 3317709--3317742 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
3317699 GAAATCCTGA
3317709 AAAACCTCAA-ACCTT
1 AAAACCTCAATACCTT
3317724 AAAACCTCAATACCTT
1 AAAACCTCAATACCTT
3317740 AAA
1 AAA
3317743 TCTTTAAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAACCTCAATACCTT
Found at i:3317761 original size:585 final size:585
Alignment explanation
Indices: 3317057--3318230 Score: 2251
Period size: 585 Copynumber: 2.0 Consensus size: 585
3317047 CCTAAGATCT
3317057 TAAAATCCAAAACCTTATAAAACCTAAACCTAAAAATTTCAAACCCTCCAAACCTTTGAAATCCT
1 TAAAATCCAAAACCTTATAAAACCTAAACCTAAAAATTTCAAACCCTCCAAACCTTTGAAATCCT
3317122 GAAAAACCTCAAACCTTAAAACCTCAAGACCTTAAATCTTTAAAGCCCTAAACCCCAAAATTTTA
66 GAAAAACCTCAAACCTTAAAACCTCAAGACCTTAAATCTTTAAAGCCCTAAACCCCAAAATTTTA
*
3317187 AAACTCTAAAATCGAAACCCTAAACCTCCAAAACCCTCAAAACTATCAAAACCCTAAAAATTT-A
131 AAACTCTAAAATCAAAACCCTAAACCTCCAAAACCCTCAAAACTATCAAAACCCTAAAAATTTAA
3317251 AATTTGAAACCCCAAAATTTCAAAACCATAAACCTTTAAATTTTAAACTCTAAAATTGAAAACTT
196 AATTTGAAACCCCAAAATTTCAAAACCATAAACCTTTAAATTTTAAACTCTAAAATTGAAAACTT
* * *
3317316 AAACCTCTAAAACTTTGAAACCTCAAAACCTTAAAAATCCTAAACCCTAAAATCTCAATACCTAA
261 AAACCTCTAAAACTTTGAAACCTCAAAACCATAAAAACCCCAAACCCTAAAATCTCAATACCTAA
*
3317381 AACCTCAAAATCCTAAAACTTCAAACGCCTAAAACTTTCAAAACTCTAAATTCTAAAACCTAAAA
326 AACCTCAAAA-CCTAAAACTCCAAACGCCTAAAACTTTCAAAACTCTAAATTCTAAAACCTAAAA
3317446 CTCTAAAACCATAAACCCTGAAACCTCGAATTCTTAAAACCTTGAAACCTAAAACTCTCAAAATC
390 CTCTAAAACCATAAACCCTGAAACCTCGAATTCTTAAAACCTTGAAACCTAAAACTCTCAAAATC
3317511 CTAAAAATCCATCAAGACCTTAAATCTAACCCAAACTTTAAATTCAACACACAACCCTAAAATCA
455 CTAAAAATCCATCAAGACCTTAAATCTAACCCAAACTTTAAATTCAACACACAACCCTAAAATCA
3317576 TCACCCAAAAATTATTCAAACCTTAAAACCTCAACCTAACCCATGCCCAAAACCATTCTAAAATT
520 TCACCCAAAAATTATTCAAACCTTAAAACCTCAACCTAACCCATGCCCAAAACCATTCTAAAATT
3317641 C
585 C
*
3317642 TAAAATCCAAAACCTTATAAAACCTAAACCTAAAAATTTCAAACCCTCTAAACCTTTGAAATCCT
1 TAAAATCCAAAACCTTATAAAACCTAAACCTAAAAATTTCAAACCCTCCAAACCTTTGAAATCCT
*
3317707 GAAAAACCTCAAACCTTAAAACCTCAATACCTTAAATCTTTAAAGCCCTAAACCCCAAAATTTTA
66 GAAAAACCTCAAACCTTAAAACCTCAAGACCTTAAATCTTTAAAGCCCTAAACCCCAAAATTTTA
*
3317772 AAACTCTAAAATCAAAACCCTAAACCTTCAAAACCCTCAAAACTATCAAAACCCTAAAAATTTAA
131 AAACTCTAAAATCAAAACCCTAAACCTCCAAAACCCTCAAAACTATCAAAACCCTAAAAATTTAA
3317837 AATTTGAAACCCCAAAATTTCAAAACCATAAACCTTTAAATTTTAAACTCTAAAATTGAAAACTT
196 AATTTGAAACCCCAAAATTTCAAAACCATAAACCTTTAAATTTTAAACTCTAAAATTGAAAACTT
3317902 AAACCTCTAAAACTTTGAAACCTCAAAACCATAAAAACCCCAAACCCTAAAATCTCAATACCTAA
261 AAACCTCTAAAACTTTGAAACCTCAAAACCATAAAAACCCCAAACCCTAAAATCTCAATACCTAA
3317967 AACCTCAAAACCTAAAACTCCAAACGCCTAAAACTTTCAAAACTCTAAATTCTAAAACCTAAAAC
326 AACCTCAAAACCTAAAACTCCAAACGCCTAAAACTTTCAAAACTCTAAATTCTAAAACCTAAAAC
3318032 TCTAAAACCATAAACCCTGAAACCTCGAATTCTTAAAACCTTGAAACCTAAAACTCTCAAAATCC
391 TCTAAAACCATAAACCCTGAAACCTCGAATTCTTAAAACCTTGAAACCTAAAACTCTCAAAATCC
3318097 TAAAAATCCATCAAGACCTTAAATCTAACCCAAACTTTAAATTCAACACACAACCCTAAAATCAT
456 TAAAAATCCATCAAGACCTTAAATCTAACCCAAACTTTAAATTCAACACACAACCCTAAAATCAT
*
3318162 CACCCAAAAATTATTCAAACCTTAAAACCTCGACCTAACCCATGCCCAAAACCATTCTAAAATTC
521 CACCCAAAAATTATTCAAACCTTAAAACCTCAACCTAACCCATGCCCAAAACCATTCTAAAATTC
3318227 TAAA
1 TAAA
3318231 GATACGTGTG
Statistics
Matches: 579, Mismatches: 9, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
585 441 0.76
586 138 0.24
ACGTcount: A:0.47, C:0.28, G:0.02, T:0.23
Consensus pattern (585 bp):
TAAAATCCAAAACCTTATAAAACCTAAACCTAAAAATTTCAAACCCTCCAAACCTTTGAAATCCT
GAAAAACCTCAAACCTTAAAACCTCAAGACCTTAAATCTTTAAAGCCCTAAACCCCAAAATTTTA
AAACTCTAAAATCAAAACCCTAAACCTCCAAAACCCTCAAAACTATCAAAACCCTAAAAATTTAA
AATTTGAAACCCCAAAATTTCAAAACCATAAACCTTTAAATTTTAAACTCTAAAATTGAAAACTT
AAACCTCTAAAACTTTGAAACCTCAAAACCATAAAAACCCCAAACCCTAAAATCTCAATACCTAA
AACCTCAAAACCTAAAACTCCAAACGCCTAAAACTTTCAAAACTCTAAATTCTAAAACCTAAAAC
TCTAAAACCATAAACCCTGAAACCTCGAATTCTTAAAACCTTGAAACCTAAAACTCTCAAAATCC
TAAAAATCCATCAAGACCTTAAATCTAACCCAAACTTTAAATTCAACACACAACCCTAAAATCAT
CACCCAAAAATTATTCAAACCTTAAAACCTCAACCTAACCCATGCCCAAAACCATTCTAAAATTC
Found at i:3317831 original size:18 final size:17
Alignment explanation
Indices: 3317782--3317830 Score: 73
Period size: 16 Copynumber: 2.9 Consensus size: 17
3317772 AAACTCTAAA
*
3317782 ATCAAAACCCTAAACCT
1 ATCAAAACCCTAAAACT
3317799 -TCAAAACCCTCAAAACT
1 ATCAAAACCCT-AAAACT
3317816 ATCAAAACCCTAAAA
1 ATCAAAACCCTAAAA
3317831 ATTTAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 10 0.34
17 9 0.31
18 10 0.34
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.16
Consensus pattern (17 bp):
ATCAAAACCCTAAAACT
Found at i:3317965 original size:15 final size:15
Alignment explanation
Indices: 3317919--3318045 Score: 89
Period size: 15 Copynumber: 8.1 Consensus size: 15
3317909 TAAAACTTTG
3317919 AAACCTCAAAACCATAA
1 AAACCTCAAAACC-T-A
* *
3317936 AAACCCCAAACCCTA
1 AAACCTCAAAACCTA
* *
3317951 AAATCTCAATACCTA
1 AAACCTCAAAACCTA
3317966 AAACCTCAAAACCTA
1 AAACCTCAAAACCTA
*
3317981 AAA-CTCCAAACGCCTA
1 AAACCT-CAAA-ACCTA
*
3317997 AAACTTTCAAAACTCTA
1 AAAC-CTCAAAAC-CTA
**
3318014 AATTCT-AAAACCTA
1 AAACCTCAAAACCTA
3318028 AAA-CTCTAAAACCATA
1 AAACCTC-AAAACC-TA
3318044 AA
1 AA
3318046 CCCTGAAACC
Statistics
Matches: 87, Mismatches: 15, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
13 2 0.02
14 7 0.08
15 43 0.49
16 14 0.16
17 20 0.23
18 1 0.01
ACGTcount: A:0.51, C:0.30, G:0.01, T:0.18
Consensus pattern (15 bp):
AAACCTCAAAACCTA
Found at i:3318038 original size:8 final size:8
Alignment explanation
Indices: 3317963--3318039 Score: 56
Period size: 7 Copynumber: 9.9 Consensus size: 8
3317953 ATCTCAATAC
3317963 CTAAAAC-
1 CTAAAACT
3317970 CTCAAAAC-
1 CT-AAAACT
3317978 CTAAAACT
1 CTAAAACT
* *
3317986 C-CAAACGC
1 CTAAAAC-T
3317994 CTAAAACT
1 CTAAAACT
*
3318002 TTCAAAACT
1 CT-AAAACT
*
3318011 CT-AAATT
1 CTAAAACT
3318018 CTAAAAC-
1 CTAAAACT
3318025 CTAAAACT
1 CTAAAACT
3318033 CTAAAAC
1 CTAAAAC
3318040 CATAAACCCT
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
7 24 0.44
8 20 0.36
9 11 0.20
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.21
Consensus pattern (8 bp):
CTAAAACT
Found at i:3318045 original size:8 final size:7
Alignment explanation
Indices: 3317919--3318056 Score: 60
Period size: 8 Copynumber: 17.9 Consensus size: 7
3317909 TAAAACTTTG
3317919 AAACCTCA
1 AAACCT-A
3317927 AAACCATAA
1 AAACC-T-A
*
3317936 AAACCCCA
1 AAA-CCTA
*
3317944 AACCCTA
1 AAACCTA
*
3317951 AAATCTCA
1 AAACCT-A
*
3317959 ATACCTA
1 AAACCTA
3317966 AAACCTCA
1 AAACCT-A
3317974 AAACCTA
1 AAACCTA
*
3317981 AAACTCCA
1 AAAC-CTA
*
3317989 AACGCCTA
1 AA-ACCTA
*
3317997 AAACTTTCA
1 AAAC-CT-A
3318006 AAACTCTA
1 AAAC-CTA
**
3318014 AATTCTA
1 AAACCTA
3318021 AAACCTA
1 AAACCTA
3318028 AAACTCTA
1 AAAC-CTA
3318036 AAACCATA
1 AAACC-TA
* *
3318044 AACCCTG
1 AAACCTA
3318051 AAACCT
1 AAACCT
3318057 CGAATTCTTA
Statistics
Matches: 98, Mismatches: 22, Indels: 21
0.70 0.16 0.15
Matches are distributed among these distances:
7 38 0.39
8 45 0.46
9 13 0.13
10 2 0.02
ACGTcount: A:0.49, C:0.31, G:0.01, T:0.18
Consensus pattern (7 bp):
AAACCTA
Found at i:3318046 original size:15 final size:14
Alignment explanation
Indices: 3317973--3318056 Score: 51
Period size: 15 Copynumber: 5.5 Consensus size: 14
3317963 CTAAAACCTC
*
3317973 AAAACCTAAAACTCC
1 AAAACCT-AAACTCT
* *
3317988 AAACGCCTAAAACTTT
1 AAA-ACCT-AAACTCT
*
3318004 CAAAACTCTAAATTCT
1 -AAAAC-CTAAACTCT
3318020 AAAACCTAAAACTCT
1 AAAACCT-AAACTCT
*
3318035 AAAACCATAAACCCT
1 AAAACC-TAAACTCT
*
3318050 GAAACCT
1 AAAACCT
3318057 CGAATTCTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
14 3 0.05
15 31 0.56
16 16 0.29
17 5 0.09
ACGTcount: A:0.49, C:0.29, G:0.02, T:0.20
Consensus pattern (14 bp):
AAAACCTAAACTCT
Found at i:3318093 original size:24 final size:24
Alignment explanation
Indices: 3318043--3318093 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
3318033 CTAAAACCAT
** * *
3318043 AAACCCTGAAACCTCGAATTCTTA
1 AAACCCTGAAACCTAAAACTCTCA
*
3318067 AAACCTTGAAACCTAAAACTCTCA
1 AAACCCTGAAACCTAAAACTCTCA
3318091 AAA
1 AAA
3318094 TCCTAAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.27, G:0.06, T:0.22
Consensus pattern (24 bp):
AAACCCTGAAACCTAAAACTCTCA
Found at i:3323758 original size:103 final size:102
Alignment explanation
Indices: 3323576--3323824 Score: 297
Period size: 103 Copynumber: 2.4 Consensus size: 102
3323566 TATTAATAAC
* * * * *
3323576 TGAACAATTACTATATTTTATCAATTACTA-TATTCCATAACAAGAAACATTGTCAATATTGAGA
1 TGAACAATTACTACATTTTATTAATTATTACT-TTTCATAACAAGAAACATTGTCAATATTAAGA
3323640 AATATATTATTTATTTGGGTTTTAACTACATTTTTAGA
65 AATATATTATTTATTTGGGTTTTAACTACATTTTTAGA
* ** *
3323678 T-AAGCAATTACTACATTTTATTAATTATTACGTTTTCATAACAAGAAACATTTTTTATATTAAT
1 TGAA-CAATTACTACATTTTATTAATTATTAC-TTTTCATAACAAGAAACATTGTCAATATTAAG
* *
3323742 AAATATATTATTTATTTGGGTTTTAACTACCTTTTTAGG
64 AAATATATTATTTATTTGGGTTTTAACTACATTTTTAGA
* * * *
3323781 TGAATAATTACCACAATTTATTAATAACTT-CATTTTCATAACAA
1 TGAACAATTACTACATTTTATTAATTA-TTAC-TTTTCATAACAA
3323825 AAAATGTAGT
Statistics
Matches: 126, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
101 2 0.02
102 24 0.19
103 95 0.75
104 5 0.04
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (102 bp):
TGAACAATTACTACATTTTATTAATTATTACTTTTCATAACAAGAAACATTGTCAATATTAAGAA
ATATATTATTTATTTGGGTTTTAACTACATTTTTAGA
Found at i:3325219 original size:34 final size:34
Alignment explanation
Indices: 3325120--3325219 Score: 85
Period size: 34 Copynumber: 2.9 Consensus size: 34
3325110 TTGAAACTTC
* * * * * * *
3325120 ATTTATGAGAATACAATATAATTCTCAGACATGG
1 ATTTTTGAGAATATAATATAATTATTAAAAATGA
* * * *
3325154 ATTTTCGAGAAATATATTAT-ATTTTTGAAAATGA
1 ATTTTTGAG-AATATAATATAATTATTAAAAATGA
3325188 ATTTTTGAGAATATAATATAATTATTAAAAAT
1 ATTTTTGAGAATATAATATAATTATTAAAAAT
3325220 TTATTTTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
33 9 0.18
34 33 0.66
35 8 0.16
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (34 bp):
ATTTTTGAGAATATAATATAATTATTAAAAATGA
Found at i:3328219 original size:17 final size:18
Alignment explanation
Indices: 3328185--3328229 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
3328175 AATTGTTAAC
3328185 AGTTTATATTAATGTTTAT
1 AGTTTATATT-ATGTTTAT
*
3328204 GGTTTATATT-TGTTTAT
1 AGTTTATATTATGTTTAT
3328221 AGTTTATAT
1 AGTTTATAT
3328230 ATTGAACATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.62
19 9 0.38
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (18 bp):
AGTTTATATTATGTTTAT
Found at i:3335497 original size:2 final size:2
Alignment explanation
Indices: 3335492--3335518 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3335482 TATATATATA
3335492 TG 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 TG T
3335519 ATGTATAAAT
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:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3345805 original size:30 final size:29
Alignment explanation
Indices: 3345766--3345874 Score: 137
Period size: 30 Copynumber: 3.7 Consensus size: 29
3345756 TATTTGTATG
*
3345766 AAAATTTATTTAAGTACAAATTAAAAATT
1 AAAATTTATTTAAATACAAATTAAAAATT
* * * * *
3345795 ATATACTTATTTAGATATAAATTAAAATTT
1 A-AAATTTATTTAAATACAAATTAAAAATT
3345825 AAGAATTTATTTAAATACAAATTAAAAATT
1 AA-AATTTATTTAAATACAAATTAAAAATT
3345855 AAAAATTTATTTAAATACAA
1 -AAAATTTATTTAAATACAA
3345875 TAAAAGTATA
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
29 2 0.03
30 62 0.94
31 2 0.03
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAATTTATTTAAATACAAATTAAAAATT
Found at i:3358128 original size:21 final size:21
Alignment explanation
Indices: 3358099--3358138 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3358089 GAATCACCAG
3358099 CCATATGTCACCTGT-TGGGCC
1 CCATATGTCA-CTGTGTGGGCC
*
3358120 CCATGTGTCACTGTGTGGG
1 CCATATGTCACTGTGTGGG
3358139 TTCCAATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.12, C:0.28, G:0.30, T:0.30
Consensus pattern (21 bp):
CCATATGTCACTGTGTGGGCC
Found at i:3360681 original size:30 final size:30
Alignment explanation
Indices: 3360553--3360661 Score: 137
Period size: 30 Copynumber: 3.6 Consensus size: 30
3360543 TATTTGTATG
*
3360553 AAAATTTATTTAAGTACAAATTAAAAATTA
1 AAAATTTATTTAAATACAAATTAAAAATTA
* * * * * *
3360583 TATACTTATTTAGATATAAATTAAAATTTA
1 AAAATTTATTTAAATACAAATTAAAAATTA
* *
3360613 AGAATTCATTTAAATACAAATTAAAAATTA
1 AAAATTTATTTAAATACAAATTAAAAATTA
3360643 AAAATTTATTTAAATACAA
1 AAAATTTATTTAAATACAA
3360662 TAAAAGTATA
Statistics
Matches: 62, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.39
Consensus pattern (30 bp):
AAAATTTATTTAAATACAAATTAAAAATTA
Found at i:3368260 original size:159 final size:158
Alignment explanation
Indices: 3367950--3368244 Score: 403
Period size: 158 Copynumber: 1.9 Consensus size: 158
3367940 AATGTTATTA
* * *
3367950 AAAAAAGAAATAAAATAACAAATAGTATTAATTCATGAATTTGTAATAACAAACAAAATAAATTT
1 AAAAAAGAAATAAAATAACAAAAAGAATCAATTCATGAATTTGTAATAACAAACAAAATAAATTT
* **
3368015 ACGAATTTATTATAAATTTGATGAATCATAAATGCATAATTTTATAGATTCTAAGATGGCATATG
66 ACAAATTTATTATAAATTTGATGAATCATAAATGCATAATTTTATAGATTCTAAGATAACATATG
*
3368080 CATAAACATTTCACAAATCAATTTAAAG
131 AATAAACATTTCACAAATCAATTTAAAG
* * * * *
3368108 AAAAACGAAATAAAATGACAAAAAGAATCAATTTATGAATTTGTAATAATAAATAAAATAAATTT
1 AAAAAAGAAATAAAATAACAAAAAGAATCAATTCATGAATTTGTAATAACAAACAAAATAAATTT
* * * * * *
3368173 ATAAATTCGT-TTATAAATTTGATGAATTATGAATGGATAATTTTGTAGATTCTAAGATAATATA
66 ACAAATT--TATTATAAATTTGATGAATCATAAATGCATAATTTTATAGATTCTAAGATAACATA
3368237 TGAATAAA
129 TGAATAAA
3368245 TGTTTTATGG
Statistics
Matches: 117, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
158 62 0.53
159 54 0.46
160 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (158 bp):
AAAAAAGAAATAAAATAACAAAAAGAATCAATTCATGAATTTGTAATAACAAACAAAATAAATTT
ACAAATTTATTATAAATTTGATGAATCATAAATGCATAATTTTATAGATTCTAAGATAACATATG
AATAAACATTTCACAAATCAATTTAAAG
Found at i:3369836 original size:20 final size:20
Alignment explanation
Indices: 3369811--3369852 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3369801 ATGGAAAGTA
3369811 AGATAAAAAATATAAAGAAT
1 AGATAAAAAATATAAAGAAT
3369831 AGATAAAAAATATAAAGAAT
1 AGATAAAAAATATAAAGAAT
3369851 AG
1 AG
3369853 TACAAGAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (20 bp):
AGATAAAAAATATAAAGAAT
Found at i:3373449 original size:37 final size:38
Alignment explanation
Indices: 3373362--3373449 Score: 106
Period size: 37 Copynumber: 2.3 Consensus size: 38
3373352 TAAACTATCA
* * *
3373362 AATATATAAATTATTTCAAAACAAATATAAATCTTAAT
1 AATATATAAATTACTTCAAAACAAAGATAAATATTAAT
** * *
3373400 AATATATAAATTACTTCAAAA-TTAGATAACTATTAGT
1 AATATATAAATTACTTCAAAACAAAGATAAATATTAAT
3373437 AATATATAAATTA
1 AATATATAAATTA
3373450 TAACCTCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 23 0.53
38 20 0.47
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (38 bp):
AATATATAAATTACTTCAAAACAAAGATAAATATTAAT
Found at i:3373677 original size:24 final size:25
Alignment explanation
Indices: 3373644--3373695 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
3373634 CAAAACTTTC
3373644 ACAAATAAAAAATAAAT-A-ACTCA
1 ACAAATAAAAAATAAATAATACTCA
*
3373667 ACAAATAAAAAAATTAATAATACTCA
1 ACAAAT-AAAAAATAAATAATACTCA
3373693 ACA
1 ACA
3373696 TTAATACTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 6 0.24
24 10 0.40
25 1 0.04
26 8 0.32
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.19
Consensus pattern (25 bp):
ACAAATAAAAAATAAATAATACTCA
Found at i:3373702 original size:13 final size:13
Alignment explanation
Indices: 3373684--3373708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3373674 AAAAAATTAA
3373684 TAATACTCAACAT
1 TAATACTCAACAT
3373697 TAATACTCAACA
1 TAATACTCAACA
3373709 AAAAATCTAA
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:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (13 bp):
TAATACTCAACAT
Found at i:3373833 original size:59 final size:59
Alignment explanation
Indices: 3373758--3373901 Score: 186
Period size: 59 Copynumber: 2.4 Consensus size: 59
3373748 AAAATTTAAT
* *
3373758 CAAAA-TCGAAACAAATTTCAACAACTATAA-AACCAACAAAAACTCAATAAATTGGTAAC
1 CAAAACTC-AAACAAATTTCAACAAATA-AATAACCAACAAAAACTCAACAAATTGGTAAC
* * *
3373817 CAAAAC-CTAAATAAATTTCAACAAATAAATAACTAACAAAAACTCAACACATTGGTAAC
1 CAAAACTC-AAACAAATTTCAACAAATAAATAACCAACAAAAACTCAACAAATTGGTAAC
*
3373876 CAAAACTCAAACAAGTTTCAACAAAT
1 CAAAACTCAAACAAATTTCAACAAAT
3373902 TATAACAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
58 2 0.03
59 71 0.96
60 1 0.01
ACGTcount: A:0.56, C:0.21, G:0.04, T:0.19
Consensus pattern (59 bp):
CAAAACTCAAACAAATTTCAACAAATAAATAACCAACAAAAACTCAACAAATTGGTAAC
Found at i:3378101 original size:52 final size:52
Alignment explanation
Indices: 3378012--3378167 Score: 206
Period size: 52 Copynumber: 3.0 Consensus size: 52
3378002 ATAACCATAT
* * * * *
3378012 AAACTTGCCCATTAAGAATGCCTCTCCTCTTAAAATTCTTCTCCTGTAAGTC
1 AAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGTC
* *
3378064 AAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGTC
1 AAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGTC
* **
3378116 AAACTTACCTATTAAGAATCCTCTTT-CTCTTAGAATTCTTCTTTTGCAAGTC
1 AAACTTGCCTATTAAGAATCC-CTTTCCTCTTAGAATTCTTCTCCTGCAAGTC
3378168 TTCTTGTCCA
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
52 89 0.96
53 4 0.04
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.39
Consensus pattern (52 bp):
AAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGTC
Found at i:3378934 original size:16 final size:16
Alignment explanation
Indices: 3378910--3378942 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3378900 GCCATAAACA
3378910 TGGACATCGCAGAGTT
1 TGGACATCGCAGAGTT
*
3378926 TGGATATCGCAGAGTT
1 TGGACATCGCAGAGTT
3378942 T
1 T
3378943 CAAACTAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.30
Consensus pattern (16 bp):
TGGACATCGCAGAGTT
Found at i:3388759 original size:15 final size:15
Alignment explanation
Indices: 3388720--3388768 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
3388710 TGTTTAGGAG
3388720 ATTTATATCGAGATGA
1 ATTTATATCGAGAT-A
*
3388736 ATCTATATCGAGATA
1 ATTTATATCGAGATA
*
3388751 ATTTATATCGATATA
1 ATTTATATCGAGATA
3388766 ATT
1 ATT
3388769 CTGTACTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (15 bp):
ATTTATATCGAGATA
Found at i:3388937 original size:30 final size:32
Alignment explanation
Indices: 3388858--3388937 Score: 83
Period size: 34 Copynumber: 2.4 Consensus size: 32
3388848 TTCACCAACA
*
3388858 TATATGTTTTATTGTTTATTTATATATATTAAAG
1 TATAT-TTTT-TTGTTTATTTATATATATTAAAC
* *
3388892 TATATGTTTTATTGTTTATTTATATATATTCACC
1 TATAT-TTTT-TTGTTTATTTATATATATTAAAC
3388926 T-T-TTTTTTTGTT
1 TATATTTTTTTGTT
3388938 GAAATTTTGG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 5 0.12
31 4 0.09
32 1 0.02
33 1 0.02
34 32 0.74
ACGTcount: A:0.25, C:0.04, G:0.07, T:0.64
Consensus pattern (32 bp):
TATATTTTTTTGTTTATTTATATATATTAAAC
Found at i:3390301 original size:11 final size:9
Alignment explanation
Indices: 3390273--3390308 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
3390263 TTTATTTATT
3390273 AAAAAAATA
1 AAAAAAATA
3390282 AAAAAAATA
1 AAAAAAATA
3390291 AAAACAGAATA
1 AAAA-A-AATA
3390302 AAAAAAA
1 AAAAAAA
3390309 AACGACGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 15 0.60
10 2 0.08
11 8 0.32
ACGTcount: A:0.86, C:0.03, G:0.03, T:0.08
Consensus pattern (9 bp):
AAAAAAATA
Found at i:3397147 original size:30 final size:31
Alignment explanation
Indices: 3397080--3397148 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
3397070 ATGTGAATAT
* * *
3397080 TGAATTTTGCTATGGTACTTTCATTTTTCAT
1 TGAATTTTGCCATGGTAATTTCATTTTTCAA
3397111 TGAATTTTGCCACT-GTAATTTCATTTTT-AA
1 TGAATTTTGCCA-TGGTAATTTCATTTTTCAA
3397141 TGAATTTT
1 TGAATTTT
3397149 AGATTAGAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 9 0.26
31 24 0.71
32 1 0.03
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.54
Consensus pattern (31 bp):
TGAATTTTGCCATGGTAATTTCATTTTTCAA
Found at i:3397319 original size:15 final size:16
Alignment explanation
Indices: 3397290--3397322 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3397280 CTTTTTTATA
3397290 AAATTTTTTGCTAAAAT
1 AAATTTTTT-CTAAAAT
3397307 AAATTTTTT-TAAAAT
1 AAATTTTTTCTAAAAT
3397322 A
1 A
3397323 TTAAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (16 bp):
AAATTTTTTCTAAAAT
Found at i:3403778 original size:2 final size:2
Alignment explanation
Indices: 3403773--3403823 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
3403763 ACACACACAC
* * * *
3403773 AT AT AT AT AC GT AT AT AT GT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3403815 AT AT AT AT A
1 AT AT AT AT A
3403824 CACACATTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3403825 original size:14 final size:14
Alignment explanation
Indices: 3403773--3403825 Score: 79
Period size: 14 Copynumber: 3.8 Consensus size: 14
3403763 ACACACACAC
*
3403773 ATATATATACGTAT
1 ATATATATACATAT
* *
3403787 ATATGTATATATAT
1 ATATATATACATAT
3403801 ATATATATACATAT
1 ATATATATACATAT
3403815 ATATATATACA
1 ATATATATACA
3403826 CACATTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (14 bp):
ATATATATACATAT
Found at i:3405588 original size:27 final size:27
Alignment explanation
Indices: 3405557--3405616 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
3405547 CCTTAATCTA
* *
3405557 TAAATTTATAATACGTTATGATTT-ATT
1 TAAATTTATAATACATTAT-ATTTGAAT
* *
3405584 TAAATTTTTAGTACATTATATTTGAAT
1 TAAATTTATAATACATTATATTTGAAT
3405611 TAAATT
1 TAAATT
3405617 ATATTTGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (27 bp):
TAAATTTATAATACATTATATTTGAAT
Found at i:3407594 original size:2 final size:2
Alignment explanation
Indices: 3407587--3407639 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
3407577 TTGGTTATCT
* *
3407587 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3407629 TA TA TA TA TA T
1 TA TA TA TA TA T
3407640 GAGATCGTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3410289 original size:32 final size:32
Alignment explanation
Indices: 3410248--3410312 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
3410238 GGTAAAATAA
*
3410248 AAGGCGACAATCAATTAAAGTTGCACCAAAAG
1 AAGGCGACAATCAATTAAACTTGCACCAAAAG
* *
3410280 AAGGTGACAATCAATTAAACTTTCACCAAAAG
1 AAGGCGACAATCAATTAAACTTGCACCAAAAG
3410312 A
1 A
3410313 GCAACTTCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (32 bp):
AAGGCGACAATCAATTAAACTTGCACCAAAAG
Found at i:3412131 original size:33 final size:33
Alignment explanation
Indices: 3412089--3412157 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
3412079 GTACTTTGAC
3412089 ATTTGTGCCCTTGGTTTACCCACAAACTTACAA
1 ATTTGTGCCCTTGGTTTACCCACAAACTTACAA
*
3412122 ATTTGTGCCCTTGGTTTACCCACAAACTTGCAA
1 ATTTGTGCCCTTGGTTTACCCACAAACTTACAA
3412155 ATT
1 ATT
3412158 AACTGAGTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (33 bp):
ATTTGTGCCCTTGGTTTACCCACAAACTTACAA
Found at i:3412821 original size:21 final size:21
Alignment explanation
Indices: 3412791--3412830 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3412781 ATATATTTTT
3412791 TAAATATTTTATA-ATAAATGC
1 TAAATATTTT-TACATAAATGC
*
3412812 TAAATCTTTTTACATAAAT
1 TAAATATTTTTACATAAAT
3412831 TTAAAATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (21 bp):
TAAATATTTTTACATAAATGC
Found at i:3414509 original size:19 final size:20
Alignment explanation
Indices: 3414472--3414514 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
3414462 TATTTGATTT
3414472 TTTTAAAATATAATATT-AA
1 TTTTAAAATATAATATTAAA
* * *
3414491 TTTTAATATATTATTTTAAA
1 TTTTAAAATATAATATTAAA
3414511 TTTT
1 TTTT
3414515 TTAATTTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTAAAATATAATATTAAA
Found at i:3414875 original size:15 final size:16
Alignment explanation
Indices: 3414830--3414872 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
3414820 TTTTAATTTT
*
3414830 AAAAAGTAAAAT-ATA
1 AAAAATTAAAATAATA
3414845 AAAAATTAAATTATAATA
1 AAAAATTAAA--ATAATA
3414863 AAAAATTAAA
1 AAAAATTAAA
3414873 TAAATTCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 9 0.38
17 2 0.08
18 13 0.54
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (16 bp):
AAAAATTAAAATAATA
Found at i:3417331 original size:20 final size:19
Alignment explanation
Indices: 3417308--3417360 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
3417298 CACTTACAAT
*
3417308 TTTTATTATTTCAATATTAA
1 TTTTATTATTTCAAAATT-A
3417328 TTTTCATTATTT-AAAATTA
1 TTTT-ATTATTTCAAAATTA
*
3417347 TCTTATTAATTTCA
1 TTTTATT-ATTTCA
3417361 TAATGGATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 3 0.11
19 8 0.29
20 10 0.36
21 7 0.25
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTATTATTTCAAAATTA
Found at i:3426756 original size:357 final size:356
Alignment explanation
Indices: 3426101--3426866 Score: 1016
Period size: 357 Copynumber: 2.1 Consensus size: 356
3426091 TATAACAAAT
*
3426101 TATTGAAGGCGTTTTATAATAAAAGACGTCTTTAATAATCCGAAAAAAATTTTTTTGAAAAATTA
1 TATTGAAGGCG-TTTATAATAAAAGACGCCTTTAATAATCCGAAAAAAATTTTTTTGAAAAATTA
** *
3426166 TTGAAGGCGTTGTTATCTGTAACCACCTTCACTAATTATCTACAAACTGTGATAGAAATTATTAA
65 TTGAAGGCGTTGTTATCTACAACCACCTTCACTAATTATATACAAACTGTGATAGAAATTATTAA
* * * **
3426231 AAACATTTTTCTTGGATATATGCCTTCAATAACCGTATTAAAATTTGTGTGGCAGTATATAGAAA
130 AAACATCTTTCTTGGATATACGCCTTCAATAACCATATTAAAATTTGTGTAACAGTATATAGAAA
* * ** *
3426296 GTATTTTACAATAGAAAACGCCTTTAATAATTCTTAAAATTTTTAGTGGAAAAATTTTGAAGGCA
195 GTATTTTACAATAGAAAACACATTTAATAATTCCCAAAATTTTTAGTGGAAAAATTTTGAAAGCA
* * * * *
3426361 TCTGTTATTAACAAACGCCTTCAGTAATGGATTACTAAGTTTAAAAGTATATTGAAGGCACCTTT
260 TATGTTATTAACAAACGCCTTCAATAATGAATTACTAAGTTTAAAAGTATATTGAAAGCACATTT
* * * *
3426426 TCGAAGAAACGCCTTTCATAACCATTGTGGTA
325 TCAAAGAAACACCTTTCATAACCATCGTGATA
* * * * *
3426458 TATTGAAGGCATGTTATAATAAAAGATGCCTTTAATAATCTG-AAATAATTTTTTTAGAGAAATT
1 TATTGAAGGCGT-TTATAATAAAAGACGCCTTTAATAATCCGAAAAAAATTTTTTT-GAAAAATT
* * *
3426522 ATTGAAGGCGTTGTTATCTACAATCGCCTTCACTAATTATATATAAACTGTGATAGAAATTATTA
64 ATTGAAGGCGTTGTTATCTACAACCACCTTCACTAATTATATACAAACTGTGATAGAAATTATTA
* ** * * * *
3426587 AAGATGTCTTTCTTGGATATACGTCTTCAATAACTATGTTAAAATTTGTGTAACGGTATATAGAA
129 AAAACATCTTTCTTGGATATACGCCTTCAATAACCATATTAAAATTTGTGTAACAGTATATAGAA
* * * *
3426652 CGTATTTTACAGTAGAAGACACATTTAATGATTCCCAAAATTTTTAGT-GAGAAAATTTTGAAAG
194 AGTATTTTACAATAGAAAACACATTTAATAATTCCCAAAATTTTTAGTGGA-AAAATTTTGAAAG
* * * *
3426716 CGTATGTTATTAGCAAACGCCTTCAATAATGAATTACTAAGTTTAAAGGTATATTGAAAGCGCAT
258 CATATGTTATTAACAAACGCCTTCAATAATGAATTACTAAGTTTAAAAGTATATTGAAAGCACAT
* * *
3426781 TTTCAAATAAACATCTTTTATAACCATCGTGATA
323 TTTCAAAGAAACACCTTTCATAACCATCGTGATA
*
3426815 TATTGAAGGCGTTTCATAATAAAAGACGCCTTTAATAATCC-AAAAAACTTTT
1 TATTGAAGGCGTTT-ATAATAAAAGACGCCTTTAATAATCCGAAAAAAATTTT
3426867 GTTAAGCAAA
Statistics
Matches: 350, Mismatches: 54, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
356 17 0.05
357 333 0.95
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (356 bp):
TATTGAAGGCGTTTATAATAAAAGACGCCTTTAATAATCCGAAAAAAATTTTTTTGAAAAATTAT
TGAAGGCGTTGTTATCTACAACCACCTTCACTAATTATATACAAACTGTGATAGAAATTATTAAA
AACATCTTTCTTGGATATACGCCTTCAATAACCATATTAAAATTTGTGTAACAGTATATAGAAAG
TATTTTACAATAGAAAACACATTTAATAATTCCCAAAATTTTTAGTGGAAAAATTTTGAAAGCAT
ATGTTATTAACAAACGCCTTCAATAATGAATTACTAAGTTTAAAAGTATATTGAAAGCACATTTT
CAAAGAAACACCTTTCATAACCATCGTGATA
Found at i:3434206 original size:21 final size:20
Alignment explanation
Indices: 3434167--3434206 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3434157 GCTCTTTACT
**
3434167 AAAAATAAAATTTATTATAA
1 AAAAATAAAAAATATTATAA
3434187 AAAAATAAAAAATATATATA
1 AAAAATAAAAAATAT-TATA
3434207 TTTTTATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAATAAAAAATATTATAA
Found at i:3438350 original size:16 final size:17
Alignment explanation
Indices: 3438313--3438357 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
3438303 AATAAAAATA
*
3438313 AAAATTTATTTATTTTTC
1 AAAA-TTATTTATTTCTC
3438331 AAAATTATTT-TTTCTC
1 AAAATTATTTATTTCTC
3438347 AAAATT-TTTAT
1 AAAATTATTTAT
3438358 AATTTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 3 0.12
16 12 0.48
17 6 0.24
18 4 0.16
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (17 bp):
AAAATTATTTATTTCTC
Found at i:3442381 original size:183 final size:180
Alignment explanation
Indices: 3442039--3442398 Score: 490
Period size: 183 Copynumber: 2.0 Consensus size: 180
3442029 CTCCCCTCAC
*
3442039 GTGTAGGTCCATCAGAATTCACAAGTATGTACCCCAAAAACATAGCAATAAACAAACTAGGCTAT
1 GTGTAGGTCCATCAGAATTCAC-A--ATGTACCCCAAAAACATAGCAACAAACAAACTAGGCTAT
* * * *
3442104 AAAACCATGTTAAGCATCCCAACTAAACCAATTGGCAATAAACGGGCTCAACCTTAATAGAAGGT
63 AAAACCATGTTAAGCATCCCAACTAAACCAATTGGCAACAAACGGGCCCAACCTAAATAGAAGGC
* **
3442169 CAAAACAAACTTCAACCTACCTTGATATGGAAATTCTATCTCATTCAACCCAT
128 CAAAACAAACTTCAAACTACAATGATATGGAAATTCTATCTCATTCAACCCAT
* * * *
3442222 GTGTAGGTCCATCAGAATTCAC-ATGTACCTCGAAAACGTAGCAACAAACAACCTAGTG-TATAA
1 GTGTAGGTCCATCAGAATTCACAATGTACCCCAAAAACATAGCAACAAACAAACTAG-GCTATAA
** * *
3442285 AACTGTGTTAAGCATCCCAACTAAACCAATTGGCAACAATGATGGAAGCCCAACCTAAATGGAAG
65 AACCATGTTAAGCATCCCAACTAAACCAATTGGCAACAA--ACGG--GCCCAACCTAAATAGAAG
3442350 GCCAAAACAAACTTCAAACTACAATGATATGGAAATTCTATCTCATTCA
126 GCCAAAACAAACTTCAAACTACAATGATATGGAAATTCTATCTCATTCA
3442399 CTAGGTTATT
Statistics
Matches: 156, Mismatches: 16, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
179 70 0.45
180 1 0.01
181 3 0.02
183 82 0.53
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (180 bp):
GTGTAGGTCCATCAGAATTCACAATGTACCCCAAAAACATAGCAACAAACAAACTAGGCTATAAA
ACCATGTTAAGCATCCCAACTAAACCAATTGGCAACAAACGGGCCCAACCTAAATAGAAGGCCAA
AACAAACTTCAAACTACAATGATATGGAAATTCTATCTCATTCAACCCAT
Found at i:3449792 original size:2 final size:2
Alignment explanation
Indices: 3449787--3449811 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3449777 TGGAATGAAA
3449787 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 A
3449812 ATAGGCAGAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3450724 original size:18 final size:18
Alignment explanation
Indices: 3450701--3450736 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3450691 GAATCCTTCT
*
3450701 TGAAAGGAAAAAGTGAAA
1 TGAAAGGAAAAAATGAAA
3450719 TGAAAGGAAAAAATGAAA
1 TGAAAGGAAAAAATGAAA
3450737 AAGAGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11
Consensus pattern (18 bp):
TGAAAGGAAAAAATGAAA
Found at i:3452415 original size:33 final size:33
Alignment explanation
Indices: 3452357--3452462 Score: 106
Period size: 33 Copynumber: 3.2 Consensus size: 33
3452347 CTTGGCTCAT
** *
3452357 TCCAATCACTTTTATTTTT-TACCTTAGTTCAA
1 TCCAATCACTTCCATTTTTCGACCTTAGTTCAA
* * *
3452389 TCCATTTACTTCCATTTTTCGACCTTAGTTCAG
1 TCCAATCACTTCCATTTTTCGACCTTAGTTCAA
* ** *
3452422 TCCAATCACTTTCATTTTTTTACCTTAGCTCAA
1 TCCAATCACTTCCATTTTTCGACCTTAGTTCAA
*
3452455 TCCGATCA
1 TCCAATCA
3452463 TTTTTCTTTT
Statistics
Matches: 59, Mismatches: 14, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
32 15 0.25
33 44 0.75
ACGTcount: A:0.23, C:0.26, G:0.06, T:0.45
Consensus pattern (33 bp):
TCCAATCACTTCCATTTTTCGACCTTAGTTCAA
Found at i:3452485 original size:32 final size:32
Alignment explanation
Indices: 3452445--3452568 Score: 108
Period size: 32 Copynumber: 3.9 Consensus size: 32
3452435 ATTTTTTTAC
*
3452445 CTTAGCTCAATCCGATCATTTTTCTTTTCGAT
1 CTTAGCTCAATCCGATCATTTTTATTTTCGAT
* * * * *
3452477 TTTGGCTCAGTCTGATCATTTTTATTTTTGAT
1 CTTAGCTCAATCCGATCATTTTTATTTTCGAT
* * *
3452509 CTTAGCTCAAT-CTAGTCAATTTTATTTTCGAC
1 CTTAGCTCAATCCGA-TCATTTTTATTTTCGAT
* * *
3452541 CTT-GACTCAATCCGGTCACTTTCATTTT
1 CTTAG-CTCAATCCGATCATTTTTATTTT
3452569 TAACCTTAGT
Statistics
Matches: 71, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
31 2 0.03
32 68 0.96
33 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.48
Consensus pattern (32 bp):
CTTAGCTCAATCCGATCATTTTTATTTTCGAT
Found at i:3452596 original size:64 final size:64
Alignment explanation
Indices: 3452341--3452607 Score: 194
Period size: 64 Copynumber: 4.1 Consensus size: 64
3452331 CATCTCCATC
* * * * * * * * **
3452341 TTCGATCTTGGCTCATTCCAATCACTTTTATTTTTTACCTTAGTTCAATCCATTTACTTCCATTT
1 TTCGACCTTGACTCAGTCCGATCACTTTCATTTTTTACCTTAGCTCAATCCAATCACTTTTA-TT
* * * * *
3452406 TTCGACCTT-AGTTCAGTCCAATCACTTTCATTTTTTTACCTTAGCTCAATCCGATCATTTTTCT
1 TTCGACCTTGA-CTCAGTCCGATCACTTTCA-TTTTTTACCTTAGCTCAATCCAATCACTTTTAT
3452470 T
64 T
** * * * * * * * * *
3452471 TTCGATTTTGGCTCAGTCTGATCATTTTTATTTTTGATCTTAGCTCAATCTAGTCAATTTTATT
1 TTCGACCTTGACTCAGTCCGATCACTTTCATTTTTTACCTTAGCTCAATCCAATCACTTTTATT
* * * * * * *
3452535 TTCGACCTTGACTCAATCCGGTCACTTTCATTTTTAACCTTAGTTCAGTCCAATTACTTTTATC
1 TTCGACCTTGACTCAGTCCGATCACTTTCATTTTTTACCTTAGCTCAATCCAATCACTTTTATT
*
3452599 TTCAACCTT
1 TTCGACCTT
3452608 AGTTTAATTA
Statistics
Matches: 153, Mismatches: 46, Indels: 7
0.74 0.22 0.03
Matches are distributed among these distances:
64 82 0.54
65 47 0.31
66 24 0.16
ACGTcount: A:0.21, C:0.24, G:0.09, T:0.47
Consensus pattern (64 bp):
TTCGACCTTGACTCAGTCCGATCACTTTCATTTTTTACCTTAGCTCAATCCAATCACTTTTATT
Found at i:3453214 original size:16 final size:17
Alignment explanation
Indices: 3453193--3453224 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3453183 TTTATCTTTT
3453193 AATTATC-TTTAATTTC
1 AATTATCTTTTAATTTC
3453209 AATTATCTTTTAATTT
1 AATTATCTTTTAATTT
3453225 ATCTGATATT
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:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTATCTTTTAATTTC
Found at i:3454037 original size:32 final size:32
Alignment explanation
Indices: 3454001--3454063 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
3453991 TATGTCATAA
*
3454001 AAACAGAGAATACAAGCGACAAACAATGTAGG
1 AAACAGAGAATACAAGCAACAAACAATGTAGG
* *
3454033 AAACAGAGAATACAAGCAACAAGCGATGTAG
1 AAACAGAGAATACAAGCAACAAACAATGTAG
3454064 AAAAATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.52, C:0.16, G:0.22, T:0.10
Consensus pattern (32 bp):
AAACAGAGAATACAAGCAACAAACAATGTAGG
Found at i:3460510 original size:22 final size:23
Alignment explanation
Indices: 3460476--3460524 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
3460466 AATTTACTTT
*
3460476 TAATTTATCTGAAATTATTAAATA
1 TAATTTA-CTGAAATAATTAAATA
3460500 TAATTTA-TGAAATAATTAAATA
1 TAATTTACTGAAATAATTAAATA
3460522 TAA
1 TAA
3460525 CTCACATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 17 0.71
24 7 0.29
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (23 bp):
TAATTTACTGAAATAATTAAATA
Found at i:3466884 original size:18 final size:18
Alignment explanation
Indices: 3466861--3466896 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3466851 TCTTAGTAGG
3466861 CCTTTT-TTTTATGTTTTT
1 CCTTTTATTTTAT-TTTTT
3466879 CCTTTTATTTTATTTTTT
1 CCTTTTATTTTATTTTTT
3466897 GGTTGCCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.78
Consensus pattern (18 bp):
CCTTTTATTTTATTTTTT
Found at i:3474062 original size:176 final size:169
Alignment explanation
Indices: 3473743--3474081 Score: 457
Period size: 176 Copynumber: 2.0 Consensus size: 169
3473733 AATGCTGTGC
* *
3473743 AGAAGTTATTCTTGCTGTGTTACACAGAATGGATAAAGAAATGACTCAAAAGCTGAAGGGGATGG
1 AGAAGTTAGTCTTGCTGTGTTACACAGAATGGATAAAGAAATGACTCAAAAGCAGAAGGGGATGG
* * * *
3473808 ATAAGGTCACTTAATTCAAAAAGCTAGGTTTCTGAGTAAACATAGATGTTATGTGTCAAGTGGTG
66 ATAAGGTCACTTAATTCAAAAAGCTAGGCTTCTGAGTAAAAATAAATGGTATGTGTCAAGTGGTG
* * *
3473873 CTCTGGCAAAGTAGGACATAAGACGAGA-AGAAATGAAA
131 CTCTGGCAAAGTAGAACACAAGACAAGAGAGAAATGAAA
*
3473911 AGAAGTTAGTCTTGCTGTGTTACACAGAATGGATAACTAGAGATGACTCAAAAGGCAGAAAACAA
1 AGAAGTTAGTCTTGCTGTGTTACACAGAATGGATAA--AGAAATGACTCAAAA-GCAG-----AA
*
3473976 GGGGATGGATAAGGTCACTTAATTCAAACAGCTAGGCTTCTGAGTAAAAATAAATGGTATGTG-C
58 GGGGATGGATAAGGTCACTTAATTCAAAAAGCTAGGCTTCTGAGTAAAAATAAATGGTATGTGTC
* * *
3474040 CAGTAGGTGCTGTGGTAAAGTAGAACACAAGACAAGAGAGAA
123 AAGT-GGTGCTCTGGCAAAGTAGAACACAAGACAAGAGAGAA
3474082 GAAATGGGAG
Statistics
Matches: 147, Mismatches: 14, Indels: 11
0.85 0.08 0.06
Matches are distributed among these distances:
168 35 0.24
170 14 0.10
171 3 0.02
175 4 0.03
176 87 0.59
177 4 0.03
ACGTcount: A:0.39, C:0.12, G:0.26, T:0.23
Consensus pattern (169 bp):
AGAAGTTAGTCTTGCTGTGTTACACAGAATGGATAAAGAAATGACTCAAAAGCAGAAGGGGATGG
ATAAGGTCACTTAATTCAAAAAGCTAGGCTTCTGAGTAAAAATAAATGGTATGTGTCAAGTGGTG
CTCTGGCAAAGTAGAACACAAGACAAGAGAGAAATGAAA
Found at i:3483421 original size:16 final size:17
Alignment explanation
Indices: 3483386--3483423 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3483376 AATATGCATC
*
3483386 TAAAT-TTTTATATTTT
1 TAAATATTTTATATTTA
3483402 TAAATATTTTATA-TTA
1 TAAATATTTTATATTTA
3483418 TAAATA
1 TAAATA
3483424 AAATTTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TAAATATTTTATATTTA
Found at i:3483439 original size:21 final size:23
Alignment explanation
Indices: 3483415--3483461 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
3483405 ATATTTTATA
*
3483415 TTATAAAT-AAAATTTATTCC-T
1 TTATAAATAAAAATTTAATCCAT
3483436 TTATAAATAAAAATTTAATCCAT
1 TTATAAATAAAAATTTAATCCAT
3483459 TTA
1 TTA
3483462 AAAACTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.35
22 11 0.48
23 4 0.17
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.45
Consensus pattern (23 bp):
TTATAAATAAAAATTTAATCCAT
Found at i:3483566 original size:17 final size:16
Alignment explanation
Indices: 3483528--3483566 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
3483518 TATATTAAAA
*
3483528 ATAAATTTATTTATTT
1 ATAAATTTATTAATTT
3483544 ACTAAATTTATTCAATTT
1 A-TAAATTTATT-AATTT
3483562 ATAAA
1 ATAAA
3483567 CAAAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 14 0.70
18 5 0.25
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATAAATTTATTAATTT
Found at i:3483922 original size:21 final size:22
Alignment explanation
Indices: 3483875--3483923 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
3483865 TTTATTTTTT
* *
3483875 TAATTTTTATATTGTTTTAATA
1 TAATTTTTATATTATTTAAATA
3483897 TAATTTTTA-ATATATTTAAATA
1 TAATTTTTATAT-TATTTAAATA
3483919 -AATTT
1 TAATTT
3483924 AGATTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TAATTTTTATATTATTTAAATA
Found at i:3483975 original size:16 final size:16
Alignment explanation
Indices: 3483956--3483994 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
3483946 ATTTTATAAA
3483956 AATTTAAAAAATATAT
1 AATTTAAAAAATATAT
*
3483972 AATTTAAAATATATAT
1 AATTTAAAAAATATAT
3483988 AATTTAA
1 AATTTAA
3483995 TTCGATTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTAAAAAATATAT
Found at i:3485014 original size:16 final size:16
Alignment explanation
Indices: 3484993--3485023 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3484983 AATTTATACT
*
3484993 GAAGTGAATCTGTGTC
1 GAAGTGAATATGTGTC
3485009 GAAGTGAATATGTGT
1 GAAGTGAATATGTGT
3485024 TAAAAGTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.32
Consensus pattern (16 bp):
GAAGTGAATATGTGTC
Found at i:3485583 original size:19 final size:19
Alignment explanation
Indices: 3485559--3485606 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
3485549 AGTCGTGCTA
*
3485559 AGCTTTTTTGACTGAGGTG
1 AGCTTTTTTGACTGAGCTG
* *
3485578 AGCTTTTTTTATTGAGCTG
1 AGCTTTTTTGACTGAGCTG
*
3485597 AGCTCTTTTG
1 AGCTTTTTTG
3485607 GTTAAGTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.15, C:0.12, G:0.25, T:0.48
Consensus pattern (19 bp):
AGCTTTTTTGACTGAGCTG
Found at i:3486368 original size:19 final size:19
Alignment explanation
Indices: 3486314--3486369 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
3486304 AGCTGAGCTA
* *
3486314 AGCTCTTTTGGTCAAGCTG
1 AGCTCTTTTAGTCAAGTTG
* * *
3486333 GGCTTTTTTAATCAAGTTG
1 AGCTCTTTTAGTCAAGTTG
3486352 AGCTCTTTTAGTCAAGTT
1 AGCTCTTTTAGTCAAGTT
3486370 AATCACTTTG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (19 bp):
AGCTCTTTTAGTCAAGTTG
Found at i:3490340 original size:172 final size:174
Alignment explanation
Indices: 3490011--3490340 Score: 459
Period size: 172 Copynumber: 1.9 Consensus size: 174
3490001 ATGCAGTGGA
* * *
3490011 TTATAGCTGAATCTTTTCTTTTGTGATGGTTGAATCAAAAATTATTTTCACTTCCTATTAGTTTT
1 TTATAGCTGAATCTCTTCTCTTGTGATAGTTGAATCAAAAATTATTTTCACTTCCTATTAGTTTT
* *
3490076 GTTGCATATGGTAAATTGTTTTTTTTCTTTGGAGAATAAGGCGGAAAGACATATTTGTTAAAAGA
66 GTTGCATATGGTAAATTGATTTTTTTCTTTGGAGAATAAGGCAGAAAGACATATTTGTTAAAAGA
* * *
3490141 CATGTATCTTTGGCTTTCCGTTTATTATAATTGTAGCTGAATCT
131 CATGGATCTTTGGCTCTCCGCTTATTATAATTGTAGCTGAATCT
* * * *
3490185 TTATAGCTGAATCTCTTCTCTTGTGATAGTTGAAT-AAAGATTATTTTCATTTGCTGTTAGTTTT
1 TTATAGCTGAATCTCTTCTCTTGTGATAGTTGAATCAAAAATTATTTTCACTTCCTATTAGTTTT
* * * *
3490249 GTTGCATATGGTAAATT-ATTTTTTTCTTTGGAGGAA-AATGCATAAATACATGTTTGTTAAAAG
66 GTTGCATATGGTAAATTGATTTTTTTCTTTGGA-GAATAAGGCAGAAAGACATATTTGTTAAAAG
* * *
3490312 GCATGGGTCTTTGGCTCTCTGCTTATTAT
130 ACATGGATCTTTGGCTCTCCGCTTATTAT
3490341 TTGCTTAATT
Statistics
Matches: 136, Mismatches: 19, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
172 59 0.43
173 45 0.33
174 32 0.24
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (174 bp):
TTATAGCTGAATCTCTTCTCTTGTGATAGTTGAATCAAAAATTATTTTCACTTCCTATTAGTTTT
GTTGCATATGGTAAATTGATTTTTTTCTTTGGAGAATAAGGCAGAAAGACATATTTGTTAAAAGA
CATGGATCTTTGGCTCTCCGCTTATTATAATTGTAGCTGAATCT
Found at i:3496198 original size:24 final size:23
Alignment explanation
Indices: 3496170--3496214 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3496160 AGATATTGTG
3496170 GAAAAACTAAGA-AATAAAACTGT
1 GAAAAACTAAGAGAA-AAAACTGT
3496193 GAAAAACTAAGAGAAAAAACTG
1 GAAAAACTAAGAGAAAAAACTG
3496215 AACGTATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.62, C:0.09, G:0.16, T:0.13
Consensus pattern (23 bp):
GAAAAACTAAGAGAAAAAACTGT
Done.