Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 94 of 130
Found at i:18420277 original size:54 final size:53
Alignment explanation
Indices: 18420079--18420291 Score: 171
Period size: 53 Copynumber: 4.0 Consensus size: 53
18420069 CAAAGGCTTT
* * * * * * * *
18420079 AAAATTTTTATCTTTAAAAAAGCTCTTTTAAACATAGGCTTAATAACTTTAAA
1 AAAATTCTCATCTTGAAAAAAGCTCATCTAAGCAAAGGCTCAATAACTTTAAA
* * * * * * *
18420132 GAAA-TCTTCATATTG-AAAAAGCTTCCTTTCAGCAGAGG-TTAATAACTTTAAA
1 AAAATTC-TCATCTTGAAAAAAGC-TCATCTAAGCAAAGGCTCAATAACTTTAAA
* * * *
18420184 AAAATTCTCATCTTGAAAAAAGCTCTTCTAAGTAGAGGCTCAATAATTTTAAA
1 AAAATTCTCATCTTGAAAAAAGCTCATCTAAGCAAAGGCTCAATAACTTTAAA
* * * *
18420237 AAAATTTTCATCTTGAAAAAAAGTTCATCTAGGCAAAGGCTCAACAACTTTAAA
1 AAAATTCTCATCTTG-AAAAAAGCTCATCTAAGCAAAGGCTCAATAACTTTAAA
18420291 A
1 A
18420292 TTTTATTTTA
Statistics
Matches: 129, Mismatches: 25, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
52 43 0.33
53 54 0.42
54 32 0.25
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (53 bp):
AAAATTCTCATCTTGAAAAAAGCTCATCTAAGCAAAGGCTCAATAACTTTAAA
Found at i:18431328 original size:19 final size:20
Alignment explanation
Indices: 18431295--18431347 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
18431285 TGTATGAAAA
18431295 TTTTTCTTTTCATTT-TTTGG-
1 TTTTT-TTTT-ATTTGTTTGGC
18431315 TTTGTTTTTTATTTGTTTGGC
1 TTT-TTTTTTATTTGTTTGGC
18431336 TTTTTTTTTATT
1 TTTTTTTTTATT
18431348 AAAAGTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.13
20 21 0.70
21 5 0.17
ACGTcount: A:0.06, C:0.06, G:0.11, T:0.77
Consensus pattern (20 bp):
TTTTTTTTTATTTGTTTGGC
Found at i:18432591 original size:30 final size:30
Alignment explanation
Indices: 18432505--18432592 Score: 74
Period size: 30 Copynumber: 3.0 Consensus size: 30
18432495 CTTACACTTT
* * **
18432505 TTATTAATTTA-TATTATTAGAAAGTTCATTT
1 TTATTTATTTATTATTATT--AAAGTTTATCA
***
18432536 TTATTT-TTTATT-TTATTATTTTTTATCA
1 TTATTTATTTATTATTATTAAAGTTTATCA
18432564 TTATTTATTTATTATTATTAAAGTTTATC
1 TTATTTATTTATTATTATTAAAGTTTATC
18432593 TTAAAATTAA
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
28 11 0.25
29 6 0.14
30 21 0.48
31 6 0.14
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (30 bp):
TTATTTATTTATTATTATTAAAGTTTATCA
Found at i:18433743 original size:20 final size:20
Alignment explanation
Indices: 18433696--18433743 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
18433686 TTTTTTTTTC
18433696 TTTTTTTTTTTTAGTCTTTG
1 TTTTTTTTTTTTAGTCTTTG
*
18433716 TTTGTTTTTTTTT-GTTTTTG
1 TTT-TTTTTTTTTAGTCTTTG
*
18433736 TATTTTTT
1 TTTTTTTT
18433744 ATATTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.20
20 11 0.44
21 9 0.36
ACGTcount: A:0.04, C:0.02, G:0.10, T:0.83
Consensus pattern (20 bp):
TTTTTTTTTTTTAGTCTTTG
Found at i:18435175 original size:3 final size:3
Alignment explanation
Indices: 18435169--18435204 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
18435159 ATAATTATTC
18435169 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18435205 CTTAAGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:18436482 original size:14 final size:15
Alignment explanation
Indices: 18436463--18436493 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
18436453 TAATATTATT
18436463 ATTATT-TTAAAAAA
1 ATTATTATTAAAAAA
18436477 ATTATTATTAAAAAA
1 ATTATTATTAAAAAA
18436492 AT
1 AT
18436494 ATATATCCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTATTATTAAAAAA
Found at i:18438386 original size:6 final size:6
Alignment explanation
Indices: 18438375--18438410 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
18438365 GGCCAGTGAA
*
18438375 ATGCTG ATGCTG CTGCTG ATGCTG ATGCTG ATGCTG
1 ATGCTG ATGCTG ATGCTG ATGCTG ATGCTG ATGCTG
18438411 GACGCATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.14, C:0.19, G:0.33, T:0.33
Consensus pattern (6 bp):
ATGCTG
Found at i:18439663 original size:38 final size:36
Alignment explanation
Indices: 18439594--18439664 Score: 88
Period size: 38 Copynumber: 1.9 Consensus size: 36
18439584 AAAATTTATA
* * * *
18439594 AAATTTTTTAAAAAAATTTTGATATATTTTTTAAAT
1 AAATTTTTTAAAAAAATATTAATAAAATTTTTAAAT
18439630 AAATATTTTTAATAAAAATATTAATAAAATTTTTA
1 AAAT-TTTTTAA-AAAAATATTAATAAAATTTTTA
18439665 TCATTAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 4 0.14
37 7 0.24
38 18 0.62
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (36 bp):
AAATTTTTTAAAAAAATATTAATAAAATTTTTAAAT
Found at i:18439773 original size:12 final size:12
Alignment explanation
Indices: 18439756--18439797 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
18439746 ACTTATTAAT
18439756 TTAAAATTTTTA
1 TTAAAATTTTTA
*
18439768 TTAAAATATTTA
1 TTAAAATTTTTA
*
18439780 TT-AAATTATTA
1 TTAAAATTTTTA
18439791 TTTAAAA
1 -TTAAAA
18439798 AATTTTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 7 0.28
12 15 0.60
13 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAAATTTTTA
Found at i:18440249 original size:24 final size:24
Alignment explanation
Indices: 18440215--18440262 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
18440205 TGATTCAATC
18440215 ATATTTAATAAATTTATAAAAATT
1 ATATTTAATAAATTTATAAAAATT
* * *
18440239 ATATTTTATAATTTTTTAAAAATT
1 ATATTTAATAAATTTATAAAAATT
18440263 TTAAAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATTTAATAAATTTATAAAAATT
Found at i:18444862 original size:69 final size:68
Alignment explanation
Indices: 18444729--18444862 Score: 169
Period size: 69 Copynumber: 2.0 Consensus size: 68
18444719 TGTAAATGTC
* * ** * * * *
18444729 TTTTTTGTTTTTTTTTTTTTGTAGTATGTAGATTAAATGTCTTTTTCATGATGCATATGCAAGTG
1 TTTTTTGTTTTATTTTTTTTATAACATGTAGATCAAATGTCATTTTCATGATACAGATGCAAGTG
18444794 TGA
66 TGA
* *
18444797 TTTTTTGTTGTTATTTTTTTTATAACATGTAGATCAAATGTCATTTTCATGATATAGATGTAAGT
1 TTTTTTGTT-TTATTTTTTTTATAACATGTAGATCAAATGTCATTTTCATGATACAGATGCAAGT
18444862 G
65 G
18444863 ATGTAACTAC
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
68 9 0.16
69 46 0.84
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.54
Consensus pattern (68 bp):
TTTTTTGTTTTATTTTTTTTATAACATGTAGATCAAATGTCATTTTCATGATACAGATGCAAGTG
TGA
Found at i:18445803 original size:22 final size:23
Alignment explanation
Indices: 18445778--18445820 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
18445768 AACTTTGGCA
18445778 TTCTACTTT-CTTGA-ATTCTATC
1 TTCT-CTTTACTTGAGATTCTATC
*
18445800 TTCTTTTTACTTGAGATTCTA
1 TTCTCTTTACTTGAGATTCTA
18445821 GCTAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 3 0.17
22 9 0.50
23 6 0.33
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.56
Consensus pattern (23 bp):
TTCTCTTTACTTGAGATTCTATC
Found at i:18446042 original size:150 final size:152
Alignment explanation
Indices: 18445755--18446097 Score: 371
Period size: 150 Copynumber: 2.3 Consensus size: 152
18445745 TTTTTTTTTG
*
18445755 AACATTTGA-TTTCAACTTTGGCATTCTACTTTCTTGAATTCTATCTTCTTTTTACTTGAGATTC
1 AACATTTGACTTT-AACTTTAGCATTCTACTTTCTTGAATTCTATCTTCTTTTTACTTGAGATTC
* * * ** * *
18445819 TAGCTAATATTTTATTCACTTTTTTACCCTGAACTTTCATCTTCGAGGTGCATGTCTTCTTTTTC
65 TAGCTAATACTTTATTCACTTTTTTACCCTGAACTCTCATATTCGAAATACATGTCTTCTTTCTC
*
18445884 -TTACTTTTTTTTTTTT-GGGGA
130 TTTACTTTTTTTTTTTTACGGGA
*
18445905 AACATTTGACTGTAACTTTAGCATTCTACTTTCTTGAATTCTATCTTCTTTTT-CTT-AGGATTC
1 AACATTTGACTTTAACTTTAGCATTCTACTTTCTTGAATTCTATCTTCTTTTTACTTGA-GATTC
* * * *
18445968 TAGTTGATGCTTTATTTAC-TTTTTACCCT-AGACTCTCATATAT-GAAATACATGTCTTTCTTT
65 TAGCTAATACTTTATTCACTTTTTTACCCTGA-ACTCTCATAT-TCGAAATACATGTC-TTCTTT
* **
18446030 CTCGGTTT-TTTTTTTTTTTTTAACTTGA
127 CTC--TTTACTTTTTTTTTTTT-ACGGGA
** *
18446058 AACATTTGACTTTATTTTTAGCAATCTACTTTCTTGAATT
1 AACATTTGACTTTAACTTTAGCATTCTACTTTCTTGAATT
18446098 TTTAGGATTT
Statistics
Matches: 162, Mismatches: 21, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
147 1 0.01
148 28 0.17
149 31 0.19
150 48 0.30
151 14 0.09
152 2 0.01
153 38 0.23
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (152 bp):
AACATTTGACTTTAACTTTAGCATTCTACTTTCTTGAATTCTATCTTCTTTTTACTTGAGATTCT
AGCTAATACTTTATTCACTTTTTTACCCTGAACTCTCATATTCGAAATACATGTCTTCTTTCTCT
TTACTTTTTTTTTTTTACGGGA
Found at i:18451865 original size:9 final size:9
Alignment explanation
Indices: 18451851--18451890 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
18451841 TTAATCTTGT
*
18451851 TTAATTTTA
1 TTAATTATA
18451860 TTAATTATA
1 TTAATTATA
18451869 TATAATTATA
1 T-TAATTATA
*
18451879 TTAATTGTA
1 TTAATTATA
18451888 TTA
1 TTA
18451891 GTCACATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 19 0.68
10 9 0.32
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
TTAATTATA
Found at i:18452983 original size:3 final size:3
Alignment explanation
Indices: 18452975--18453014 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
18452965 TTGTAGGAAT
18452975 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
18453015 ATTTGATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:18453040 original size:40 final size:45
Alignment explanation
Indices: 18452993--18453084 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 45
18452983 AATAATAATA
18452993 ATAATAATAATAATAATAATAAATT-TG-A-TAAT-TTATATTTTAT
1 ATAAT-ATAA-AATAATAATAAATTATGTATTAATATTATATTTTAT
* * *
18453036 ATAATATAAAATATTAATAATTTATGTATTTATATTATATTTTAT
1 ATAATATAAAATAATAATAAATTATGTATTAATATTATATTTTAT
18453081 ATAA
1 ATAA
18453085 AAAATTATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
41 12 0.29
42 6 0.14
43 6 0.14
44 3 0.07
45 15 0.36
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (45 bp):
ATAATATAAAATAATAATAAATTATGTATTAATATTATATTTTAT
Found at i:18453121 original size:32 final size:32
Alignment explanation
Indices: 18453079--18453140 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
18453069 ATTATATTTT
* *
18453079 ATATAAAAAATTATATAGTA-TAATTTTTATCG
1 ATATAAAAAA-TATAAAATATTAATTTTTATCG
*
18453111 ATATTAAAAATATAAAATATTAATTTTTAT
1 ATATAAAAAATATAAAATATTAATTTTTAT
18453141 TAAAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 7 0.27
32 19 0.73
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (32 bp):
ATATAAAAAATATAAAATATTAATTTTTATCG
Found at i:18453753 original size:59 final size:59
Alignment explanation
Indices: 18453661--18453779 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
18453651 TCCAAGTGGT
* *
18453661 ACCCAACCACAAGACGGACATATTGTTTATTATTAACAGATTCAATGTTAAGTTTGGAG
1 ACCCAACCACAAGACAGACATATTGTTTATTATTAACAGATTCAATATTAAGTTTGGAG
18453720 ACCCAACCACAAGACAGACATATTGTTTATTATTAACAGATTCAATATTAAGTTTGGAG
1 ACCCAACCACAAGACAGACATATTGTTTATTATTAACAGATTCAATATTAAGTTTGGAG
18453779 A
1 A
18453780 AATTACCGCA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (59 bp):
ACCCAACCACAAGACAGACATATTGTTTATTATTAACAGATTCAATATTAAGTTTGGAG
Found at i:18455004 original size:16 final size:18
Alignment explanation
Indices: 18454972--18455007 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
18454962 TATAATTTAC
18454972 AATACTAAAAGATGATAT
1 AATACTAAAAGATGATAT
18454990 AATA-TAAAA-ATGATAT
1 AATACTAAAAGATGATAT
18455006 AA
1 AA
18455008 AAAAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 5 0.28
18 4 0.22
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (18 bp):
AATACTAAAAGATGATAT
Found at i:18455007 original size:11 final size:11
Alignment explanation
Indices: 18454988--18455025 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
18454978 AAAAGATGAT
18454988 ATAATATAAAA
1 ATAATATAAAA
*
18454999 ATGATATAAAA
1 ATAATATAAAA
18455010 A-AATATAAAA
1 ATAATATAAAA
18455020 ATAATA
1 ATAATA
18455026 CCGATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:18460373 original size:20 final size:20
Alignment explanation
Indices: 18460348--18460389 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
18460338 ATTGCGCACG
18460348 CATCTTTTGCTTTAATTGCA
1 CATCTTTTGCTTTAATTGCA
18460368 CATCTTTTGCTTTAATTGCA
1 CATCTTTTGCTTTAATTGCA
18460388 CA
1 CA
18460390 ATCTGCATAG
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:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (20 bp):
CATCTTTTGCTTTAATTGCA
Found at i:18464824 original size:2 final size:2
Alignment explanation
Indices: 18464817--18464851 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
18464807 TATGGTATGG
18464817 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 A
18464852 GTAAACTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18466552 original size:12 final size:11
Alignment explanation
Indices: 18466526--18466558 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
18466516 TATCCTTTTT
*
18466526 AATATGATTAA
1 AATATAATTAA
18466537 AATATAATTAA
1 AATATAATTAA
18466548 AA-ATAATTAA
1 AATATAATTAA
18466558 A
1 A
18466559 TAATTAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (11 bp):
AATATAATTAA
Found at i:18472973 original size:20 final size:20
Alignment explanation
Indices: 18472944--18472987 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
18472934 TAATTCAAGT
*
18472944 TTTC-GGGTTTAGGTTTGGA
1 TTTCTGGGTTTAGGTTTGAA
18472963 TTTCTGGGTTTAGGTTTGAA
1 TTTCTGGGTTTAGGTTTGAA
18472983 TTTCT
1 TTTCT
18472988 AGGCTTGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.11, C:0.07, G:0.30, T:0.52
Consensus pattern (20 bp):
TTTCTGGGTTTAGGTTTGAA
Found at i:18473298 original size:21 final size:21
Alignment explanation
Indices: 18473274--18473322 Score: 91
Period size: 20 Copynumber: 2.4 Consensus size: 21
18473264 TCAGCCAGCC
18473274 TAGGATCCATGTGAACCCATT
1 TAGGATCCATGTGAACCCATT
18473295 TAGGAT-CATGTGAACCCATT
1 TAGGATCCATGTGAACCCATT
18473315 TAGGATCC
1 TAGGATCC
18473323 GTGAGCCGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (21 bp):
TAGGATCCATGTGAACCCATT
Found at i:18473446 original size:12 final size:12
Alignment explanation
Indices: 18473429--18473473 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
18473419 TTTTTTCTTA
*
18473429 TTTTATTTTTAT
1 TTTTATTTTCAT
18473441 TTTTATTTTCA-
1 TTTTATTTTCAT
18473452 TTTTATTTATCAT
1 TTTTATTT-TCAT
*
18473465 TATTATTTT
1 TTTTATTTT
18473474 ACTAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 8 0.28
12 14 0.48
13 7 0.24
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATTTTCAT
Found at i:18473448 original size:17 final size:18
Alignment explanation
Indices: 18473426--18473473 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
18473416 AGCTTTTTTC
18473426 TTATTTTATTTTTATTT-
1 TTATTTTATTTTTATTTA
18473443 TTATTTTCA-TTTTATTTA
1 TTATTTT-ATTTTTATTTA
*
18473461 TCATTATTATTTT
1 TTATT-TTATTTT
18473474 ACTAATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 15 0.58
18 6 0.23
19 5 0.19
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (18 bp):
TTATTTTATTTTTATTTA
Found at i:18485065 original size:9 final size:9
Alignment explanation
Indices: 18485049--18485084 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
18485039 TGTCTAGTAA
18485049 ACTATTATT
1 ACTATTATT
*
18485058 ATTATTATT
1 ACTATTATT
*
18485067 ACTACTATT
1 ACTATTATT
18485076 ACTATTATT
1 ACTATTATT
18485085 TTCTTTTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (9 bp):
ACTATTATT
Found at i:18485513 original size:20 final size:19
Alignment explanation
Indices: 18485471--18485513 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
18485461 ATAGTTCAAG
* *
18485471 TTTCTAGGTTTAGGTTTGGA
1 TTTCTAGGTTT-GGGTTGAA
18485491 TTTCTAGGTTTGGAGTTGAA
1 TTTCTAGGTTTGG-GTTGAA
18485511 TTT
1 TTT
18485514 TTGAAAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.16, C:0.05, G:0.28, T:0.51
Consensus pattern (19 bp):
TTTCTAGGTTTGGGTTGAA
Found at i:18485877 original size:13 final size:13
Alignment explanation
Indices: 18485850--18485892 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
18485840 GATCGTAGGG
*
18485850 TTTTGTTTTTA-T
1 TTTTATTTTTATT
18485862 TTTTATTTTTATT
1 TTTTATTTTTATT
18485875 TTTTGA-TTTTATT
1 TTTT-ATTTTTATT
18485888 TTTTA
1 TTTTA
18485893 CAATTTTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 11 0.39
13 16 0.57
14 1 0.04
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:18485949 original size:18 final size:17
Alignment explanation
Indices: 18485911--18485951 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
18485901 ATTTTAAGCT
* *
18485911 TTATTTTATTTTCATTT
1 TTATTTAATTTTCATTA
18485928 TTATTTAATTTATCATTA
1 TTATTTAATTT-TCATTA
18485946 TTATTT
1 TTATTT
18485952 TACTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTAATTTTCATTA
Found at i:18486949 original size:45 final size:45
Alignment explanation
Indices: 18486860--18486952 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 45
18486850 TTTCACTATG
* *
18486860 TTTTCTATGTAAAAAAATGTAGTATTTGAATCACAAAATCCATGT
1 TTTTCTATGTAAAAAAATGTAGTATTTGAATAAAAAAATCCATGT
* *
18486905 TTTTTTATGT-AAAAAATGTAGTTTTTGACATAAAAAAGAT-CATGT
1 TTTTCTATGTAAAAAAATGTAGTATTTGA-ATAAAAAA-ATCCATGT
18486950 TTT
1 TTT
18486953 GATAGCTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 17 0.40
45 23 0.55
46 2 0.05
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.42
Consensus pattern (45 bp):
TTTTCTATGTAAAAAAATGTAGTATTTGAATAAAAAAATCCATGT
Found at i:18491205 original size:6 final size:6
Alignment explanation
Indices: 18491194--18491219 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
18491184 CTACCAAAAT
18491194 CCTAAA CCTAAA CCTAAA CCTAAA CC
1 CCTAAA CCTAAA CCTAAA CCTAAA CC
18491220 CACATACTTA
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:0.46, C:0.38, G:0.00, T:0.15
Consensus pattern (6 bp):
CCTAAA
Found at i:18500116 original size:14 final size:13
Alignment explanation
Indices: 18500097--18500201 Score: 61
Period size: 14 Copynumber: 7.5 Consensus size: 13
18500087 TTAAGGTTTC
18500097 GGGTTTTAATTGTA
1 GGGTTTTAATT-TA
18500111 GGGTTTT-ATTTA
1 GGGTTTTAATTTA
**
18500123 GAATTTTAATTTTA
1 GGGTTTTAA-TTTA
18500137 GGGTTTCACTTAAGATTTTA
1 GGG-TT---TT-A-A-TTTA
*
18500157 GGG-TTTCATTTA
1 GGGTTTTAATTTA
18500169 GGGTTTTAACTTTA
1 GGGTTTTAA-TTTA
**
18500183 GGGTTTTGTTTTA
1 GGGTTTTAATTTA
18500196 GGGTTT
1 GGGTTT
18500202 CAAAATTTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 21
0.72 0.08 0.21
Matches are distributed among these distances:
12 14 0.19
13 19 0.26
14 23 0.32
15 4 0.05
18 3 0.04
19 1 0.01
20 9 0.12
ACGTcount: A:0.20, C:0.04, G:0.24, T:0.52
Consensus pattern (13 bp):
GGGTTTTAATTTA
Found at i:18500154 original size:26 final size:26
Alignment explanation
Indices: 18500100--18500156 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
18500090 AGGTTTCGGG
* *
18500100 TTTTAATTGTAGGGTTTTATTTAGAA
1 TTTTAATTGTAGGGTTTCATTAAGAA
*
18500126 TTTTAATTTTAGGGTTTCACTTAAG-A
1 TTTTAATTGTAGGGTTTCA-TTAAGAA
18500152 TTTTA
1 TTTTA
18500157 GGGTTTCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.26, C:0.04, G:0.16, T:0.54
Consensus pattern (26 bp):
TTTTAATTGTAGGGTTTCATTAAGAA
Found at i:18500197 original size:13 final size:13
Alignment explanation
Indices: 18500151--18500201 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
18500141 TTCACTTAAG
*
18500151 ATTTTAGGGTTTC
1 ATTTTAGGGTTTT
18500164 A-TTTAGGGTTTT
1 ATTTTAGGGTTTT
*
18500176 AACTTTAGGGTTTT
1 -ATTTTAGGGTTTT
*
18500190 GTTTTAGGGTTT
1 ATTTTAGGGTTT
18500202 CAAAATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 10 0.30
13 12 0.36
14 11 0.33
ACGTcount: A:0.16, C:0.04, G:0.25, T:0.55
Consensus pattern (13 bp):
ATTTTAGGGTTTT
Found at i:18500340 original size:3 final size:3
Alignment explanation
Indices: 18500332--18500357 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
18500322 CATTAAAACT
18500332 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
18500358 TAACATCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:18501930 original size:22 final size:21
Alignment explanation
Indices: 18501892--18501933 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18501882 TTTTTTTTTT
*
18501892 TTTTTTGCTGTCAAATGCTTC
1 TTTTTTGCTGCCAAATGCTTC
*
18501913 TTTTTTGCTGCCTGAATGCTT
1 TTTTTTGCTGCC-AAATGCTT
18501934 GTTGCTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.12, C:0.19, G:0.17, T:0.52
Consensus pattern (21 bp):
TTTTTTGCTGCCAAATGCTTC
Found at i:18502816 original size:23 final size:23
Alignment explanation
Indices: 18502790--18502859 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 23
18502780 TCATTTCTTT
18502790 TATTTATTTATTATTTTTATTAC
1 TATTTATTTATTATTTTTATTAC
* * *
18502813 TATTT-TATTATTATATTTACTAT
1 TATTTAT-TTATTATTTTTATTAC
*
18502836 TTTTTATTTTTATATATTTTTATT
1 TATTTA--TTTAT-TATTTTTATT
18502860 TGGTTTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
22 1 0.03
23 22 0.61
25 4 0.11
26 9 0.25
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (23 bp):
TATTTATTTATTATTTTTATTAC
Found at i:18502819 original size:20 final size:20
Alignment explanation
Indices: 18502796--18502848 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
18502786 CTTTTATTTA
18502796 TTTATTATTTTTATTACTAT
1 TTTATTATTTTTATTACTAT
*
18502816 TTTATTA-TTATATTTACTAT
1 TTTATTATTTTTA-TTACTAT
18502836 TTT-TTATTTTTAT
1 TTTATTATTTTTAT
18502849 ATATTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTATTATTTTTATTACTAT
Found at i:18502847 original size:16 final size:16
Alignment explanation
Indices: 18502809--18502860 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 16
18502799 ATTATTTTTA
18502809 TTACTATTTTATTATTATAT
1 TTACTATTTT-TTA-T-T-T
18502829 TTACTATTTTTTATTT
1 TTACTATTTTTTATTT
18502845 TTA-TATATTTTTATTT
1 TTACTAT-TTTTTATTT
18502861 GGTTTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 3 0.10
16 13 0.42
17 1 0.03
18 1 0.03
19 3 0.10
20 10 0.32
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (16 bp):
TTACTATTTTTTATTT
Found at i:18503673 original size:72 final size:72
Alignment explanation
Indices: 18503571--18503720 Score: 185
Period size: 72 Copynumber: 2.1 Consensus size: 72
18503561 AAAAAAAATG
* * * * **
18503571 ATGAATGGGGTTGAGTTGCAAGTTAGAAAATAAGGATGACTAGG-ATTAAAACACAAGTTAAAAA
1 ATGACTGGGGTTGAGTTGCAAGTCAAAAAATAAGAATGACT-GGAATTAAAACACAAGCCAAAAA
18503635 ATAAAGAA
65 ATAAAGAA
* * ** *
18503643 ATGACTGGGGTTGGGTTGCAAGTCAAAAAATAAGAATGACTGGAATTAAACCACTGGCCGAAAAA
1 ATGACTGGGGTTGAGTTGCAAGTCAAAAAATAAGAATGACTGGAATTAAAACACAAGCCAAAAAA
18503708 TAAAGAA
66 TAAAGAA
18503715 ATGACT
1 ATGACT
18503721 ATAACTAAGC
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
71 2 0.03
72 64 0.97
ACGTcount: A:0.45, C:0.09, G:0.24, T:0.21
Consensus pattern (72 bp):
ATGACTGGGGTTGAGTTGCAAGTCAAAAAATAAGAATGACTGGAATTAAAACACAAGCCAAAAAA
TAAAGAA
Found at i:18503774 original size:35 final size:35
Alignment explanation
Indices: 18503733--18503802 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
18503723 AACTAAGCCC
* *
18503733 CAAGTCAAGAAATAA-ATATGATTGAGATTGAACCG
1 CAAGTCAAAAAATAAGA-ATGATTGAGACTGAACCG
*
18503768 CAAGTCAAAAAATAAGAATGATTGGGACTGAACCG
1 CAAGTCAAAAAATAAGAATGATTGAGACTGAACCG
18503803 TAAGCTAGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 30 0.97
36 1 0.03
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.20
Consensus pattern (35 bp):
CAAGTCAAAAAATAAGAATGATTGAGACTGAACCG
Found at i:18504441 original size:20 final size:21
Alignment explanation
Indices: 18504388--18504442 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
18504378 TGTTTAATTT
18504388 TATTAAA-ATTAATAATTAAA
1 TATTAAATATTAATAATTAAA
*
18504408 TATTAAATA-AAATAA-T-AA
1 TATTAAATATTAATAATTAAA
18504426 TAATTAAATATTAATAA
1 T-ATTAAATATTAATAA
18504443 AGAATAAGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 3 0.10
19 9 0.30
20 17 0.57
21 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TATTAAATATTAATAATTAAA
Found at i:18505551 original size:3 final size:3
Alignment explanation
Indices: 18505543--18505580 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
18505533 TATTTTTTAA
18505543 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
18505581 ATGAAAATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:18506001 original size:244 final size:245
Alignment explanation
Indices: 18505741--18506223 Score: 853
Period size: 244 Copynumber: 2.0 Consensus size: 245
18505731 GTAAGAATAT
* *
18505741 TTTTTTTTAAATATTACCATTGTATTAGAGTATTTATAGAAAAA-TTTCAATATGATAAAAATTT
1 TTTTTTTAAAATATTACCATTGTATTAGAGTATTTATA-AAAAATTTTCAATACGATAAAAATTT
*
18505805 CTCTTTTATCAAAAAAATAATAATTAGAAAAAACCAATGAAATTTTTAAAAGAAAAAATAAAATA
65 CTCTTTTATCAAAAAAATAATAATTAGAAAAAACCAATAAAATTTTTAAAAGAAAAAATAAAATA
*
18505870 CATGCATTGATATTTTGTCACTCGCATTGCAAGCATATCCTTATCTTTATGAAAAATAAATATGA
130 CATGCATTGATATTTTGTCACTCGCACTGCAAGCATATCCTTATCTTTATGAAAAATAAATATGA
*
18505935 GCCTTTGAGGATAAGATTCTAAGGTATTCCGA-AAGCGATTCTTACGAAGA
195 GCCTTTGAGGATAAGATTCTAAAGTATTCCGAGAAGCGATTCTTACGAAGA
18505985 TTTTTTTAAAATATTACCATTGTATTAGAGTATTTATAAAAAATTTTCAATACGATAAAAATTTC
1 TTTTTTTAAAATATTACCATTGTATTAGAGTATTTATAAAAAATTTTCAATACGATAAAAATTTC
* *
18506050 TCTTTTATTAAAAAAATAATAATTAGAAAAAACCAATAAAATTTTTAAAGGAAAAAATAAAATAC
66 TCTTTTATCAAAAAAATAATAATTAGAAAAAACCAATAAAATTTTTAAAAGAAAAAATAAAATAC
* *
18506115 GTGCATTGATATTTTGTCACTCGCACTGCAAGCATATCCTTATCTTTATGAAAAATAAATATGAT
131 ATGCATTGATATTTTGTCACTCGCACTGCAAGCATATCCTTATCTTTATGAAAAATAAATATGAG
*
18506180 CCTTTGAGGATAAGATTCTAAAGTATTCTGAGAAGCGATTCTTA
196 CCTTTGAGGATAAGATTCTAAAGTATTCCGAGAAGCGATTCTTA
18506224 TGAAATCTCT
Statistics
Matches: 227, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
243 5 0.02
244 210 0.93
245 12 0.05
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (245 bp):
TTTTTTTAAAATATTACCATTGTATTAGAGTATTTATAAAAAATTTTCAATACGATAAAAATTTC
TCTTTTATCAAAAAAATAATAATTAGAAAAAACCAATAAAATTTTTAAAAGAAAAAATAAAATAC
ATGCATTGATATTTTGTCACTCGCACTGCAAGCATATCCTTATCTTTATGAAAAATAAATATGAG
CCTTTGAGGATAAGATTCTAAAGTATTCCGAGAAGCGATTCTTACGAAGA
Found at i:18508685 original size:34 final size:34
Alignment explanation
Indices: 18508599--18508697 Score: 101
Period size: 34 Copynumber: 2.9 Consensus size: 34
18508589 ACAACGTTTT
* * * * *
18508599 TTTATAAAATGCCACTATTTTAGCGACATTTGTA
1 TTTAAAAAATGTCACTAATTTAGTGGCATTTGTA
* *
18508633 TTTAAAAAACGTCGCTAATTTAGTGGCATTTGTA
1 TTTAAAAAATGTCACTAATTTAGTGGCATTTGTA
* *
18508667 -TTAAAAGAATGTCACTAATATGGTGGCATTT
1 TTTAAAA-AATGTCACTAATTTAGTGGCATTT
18508698 ATATCATAAG
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
33 6 0.11
34 47 0.89
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.38
Consensus pattern (34 bp):
TTTAAAAAATGTCACTAATTTAGTGGCATTTGTA
Found at i:18510602 original size:161 final size:161
Alignment explanation
Indices: 18510295--18510604 Score: 408
Period size: 161 Copynumber: 1.9 Consensus size: 161
18510285 CAAATATACA
* *
18510295 TAAACAATAATTTTTTCACACATATCAACCATAGAAACCAAGTTCAATTATTCGGACAAGTTTAA
1 TAAACAATAACTTTTTCACAAATATCAACCATAGAAACCAAGTTCAATTATTCGGACAAGTTTAA
* * * * **
18510360 TATCATGTATTGAAGCTATCAAAACTGTTAAAATAGAACAATGACAATAATTTTGTATTTTGACC
66 TATCATGTATTGAAACTATCAAAACTATTAAAACAGAACAATAACAATAATTTTACATTTTGACC
18510425 TATTAACAGCACAAAAAGTCCTAAATTGACG
131 TATTAACAGCACAAAAAGTCCTAAATTGACG
* * * * * *
18510456 TAAACAATAACTTTTTCATAAATATCAATCATGGAAACTAAGTTCAA-TACTTTGGATAAGTTTA
1 TAAACAATAACTTTTTCACAAATATCAACCATAGAAACCAAGTTCAATTA-TTCGGACAAGTTTA
** *
18510520 ATATCATGTATTGAAACTATCAAAACTATTAAAACAGAACAATAACTGTTAA-TTTACATTTTTA
65 ATATCATGTATTGAAACTATCAAAACTATTAAAACAGAACAATAAC-AATAATTTTACATTTTGA
* * *
18510584 CCTTTTAACGGTACAAAAAGT
129 CCTATTAACAGCACAAAAAGT
18510605 TCATTCATTC
Statistics
Matches: 127, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
160 2 0.02
161 122 0.96
162 3 0.02
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.33
Consensus pattern (161 bp):
TAAACAATAACTTTTTCACAAATATCAACCATAGAAACCAAGTTCAATTATTCGGACAAGTTTAA
TATCATGTATTGAAACTATCAAAACTATTAAAACAGAACAATAACAATAATTTTACATTTTGACC
TATTAACAGCACAAAAAGTCCTAAATTGACG
Found at i:18517945 original size:28 final size:28
Alignment explanation
Indices: 18517875--18517946 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
18517865 TTAAATATTG
*
18517875 TGGTTTGCTT-AATGATATTGTATGATAT
1 TGGTTTG-TTGAATGGTATTGTATGATAT
*
18517903 TGTTTTGTTGAATGGTATTGTATGATAT
1 TGGTTTGTTGAATGGTATTGTATGATAT
18517931 TGGTTTGTTGAATGGT
1 TGGTTTGTTGAATGGT
18517947 TTGCTGAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 2 0.05
28 38 0.95
ACGTcount: A:0.21, C:0.01, G:0.26, T:0.51
Consensus pattern (28 bp):
TGGTTTGTTGAATGGTATTGTATGATAT
Found at i:18517948 original size:12 final size:12
Alignment explanation
Indices: 18517906--18518006 Score: 62
Period size: 12 Copynumber: 7.9 Consensus size: 12
18517896 ATGATATTGT
18517906 TTTGTTGAATGG
1 TTTGTTGAATGG
18517918 TATTGTATGATATTGG
1 T-TTGT-TGA-A-TGG
18517934 TTTGTTGAATGG
1 TTTGTTGAATGG
*
18517946 TTTGCTGAATAGTG
1 TTTGTTGAAT-G-G
*
18517960 TTT-CTGAATGG
1 TTTGTTGAATGG
** *
18517971 TTTCCTAAATGG
1 TTTGTTGAATGG
18517983 TCTT-TCTGAATGG
1 T-TTGT-TGAATGG
*
18517996 TTTGTTAAATG
1 TTTGTTGAATG
18518007 ATATTTTTTA
Statistics
Matches: 74, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
11 4 0.05
12 29 0.39
13 22 0.30
14 10 0.14
15 5 0.07
16 4 0.05
ACGTcount: A:0.21, C:0.06, G:0.26, T:0.48
Consensus pattern (12 bp):
TTTGTTGAATGG
Found at i:18517996 original size:13 final size:12
Alignment explanation
Indices: 18517939--18517998 Score: 66
Period size: 13 Copynumber: 4.8 Consensus size: 12
18517929 ATTGGTTTGT
*
18517939 TGAATGGTTTGC
1 TGAATGGTTTTC
*
18517951 TGAATAGTGTTTC
1 TGAATGGT-TTTC
*
18517964 TGAATGGTTTCC
1 TGAATGGTTTTC
*
18517976 TAAATGGTCTTTC
1 TGAATGGT-TTTC
18517989 TGAATGGTTT
1 TGAATGGTTT
18517999 GTTAAATGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
12 19 0.49
13 20 0.51
ACGTcount: A:0.20, C:0.10, G:0.25, T:0.45
Consensus pattern (12 bp):
TGAATGGTTTTC
Found at i:18518006 original size:25 final size:25
Alignment explanation
Indices: 18517939--18518006 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
18517929 ATTGGTTTGT
* * *
18517939 TGAATGGTTTGCTGAATAGTGTTTC
1 TGAATGGTTTGCTAAATGGTCTTTC
*
18517964 TGAATGGTTTCCTAAATGGTCTTTC
1 TGAATGGTTTGCTAAATGGTCTTTC
*
18517989 TGAATGGTTTGTTAAATG
1 TGAATGGTTTGCTAAATG
18518007 ATATTTTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.22, C:0.09, G:0.25, T:0.44
Consensus pattern (25 bp):
TGAATGGTTTGCTAAATGGTCTTTC
Found at i:18521570 original size:126 final size:129
Alignment explanation
Indices: 18521440--18521669 Score: 292
Period size: 127 Copynumber: 1.8 Consensus size: 129
18521430 AAGCGCATTC
* *
18521440 AAGAATCTG-TTCCAAATTTTTTGCAT-GAATTATT-AAAG-GTATTTTTTACCAAAAATGCCTT
1 AAGAATCTGTTTCAAAATTTTTT-CATAG-ATTATTGAAAGCGT-TTTTTTACCAAAAACGCCTT
* *
18521501 CAGTAATCTTTCAT-AA-AAATTTATTAAATGGATTATTGAAGGCGCTTTCGATAAAAAATGCCT
63 CAATAATCTCTCATGAAGAAATTTATTAAATGGATTATTGAAGGCGCTTTCGATAAAAAATGCCT
18521564 TT
128 TT
* * *
18521566 AAGAATCTGTTTCAAAATTTTTTTATAGATTATTGAAAGCGTTTTTTTGCTAAAAACGCCTTCAA
1 AAGAATCTGTTTCAAAATTTTTTCATAGATTATTGAAAGCGTTTTTTTACCAAAAACGCCTTCAA
* * * *
18521631 TATTCTCTCTTGAAGAGATTTTTTAAATGGATTATTGAA
66 TAATCTCTCATGAAGAAATTTATTAAATGGATTATTGAA
18521670 AGCATTTTGG
Statistics
Matches: 87, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
126 17 0.20
127 44 0.51
128 4 0.05
129 22 0.25
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (129 bp):
AAGAATCTGTTTCAAAATTTTTTCATAGATTATTGAAAGCGTTTTTTTACCAAAAACGCCTTCAA
TAATCTCTCATGAAGAAATTTATTAAATGGATTATTGAAGGCGCTTTCGATAAAAAATGCCTTT
Found at i:18532404 original size:26 final size:26
Alignment explanation
Indices: 18532369--18532432 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
18532359 AGTTTCAGGT
* *
18532369 TTTA-GGTTTTAATTGTAGGGTTTTA
1 TTTAGGGTTTTAATTGTAAGGTTTAA
*
18532394 TTTAGGGTTTTAATTTTAAGGTTTAA
1 TTTAGGGTTTTAATTGTAAGGTTTAA
* *
18532420 CTTAGAGTTTTAA
1 TTTAGGGTTTTAA
18532433 GGTTTCATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 4 0.12
26 29 0.88
ACGTcount: A:0.25, C:0.02, G:0.20, T:0.53
Consensus pattern (26 bp):
TTTAGGGTTTTAATTGTAAGGTTTAA
Found at i:18532411 original size:14 final size:14
Alignment explanation
Indices: 18532368--18532417 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
18532358 GAGTTTCAGG
18532368 TTTTA-GGTTTTAA
1 TTTTAGGGTTTTAA
*
18532381 TTGTAGGGTTTT-A
1 TTTTAGGGTTTTAA
18532394 -TTTAGGGTTTTAA
1 TTTTAGGGTTTTAA
*
18532407 TTTTAAGGTTT
1 TTTTAGGGTTT
18532418 AACTTAGAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 10 0.32
13 6 0.19
14 15 0.48
ACGTcount: A:0.20, C:0.00, G:0.22, T:0.58
Consensus pattern (14 bp):
TTTTAGGGTTTTAA
Found at i:18532450 original size:20 final size:19
Alignment explanation
Indices: 18532406--18532452 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
18532396 TAGGGTTTTA
18532406 ATTTTAAGGTTTAACTTAG
1 ATTTTAAGGTTTAACTTAG
* *
18532425 AGTTTTAAGGTTTCATTTAAG
1 A-TTTTAAGGTTTAACTT-AG
18532446 ATTTTAA
1 ATTTTAA
18532453 CTTTAGGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.49
Consensus pattern (19 bp):
ATTTTAAGGTTTAACTTAG
Found at i:18532475 original size:13 final size:13
Alignment explanation
Indices: 18532427--18532478 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
18532417 TAACTTAGAG
18532427 TTTTAAGGTTTCA
1 TTTTAAGGTTTCA
* *
18532440 -TTTAAGATTTTAA
1 TTTTAAG-GTTTCA
* *
18532453 CTTTAGGGTTTCA
1 TTTTAAGGTTTCA
18532466 TTTTAAGGTTTCA
1 TTTTAAGGTTTCA
18532479 AAATTTTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
12 6 0.20
13 19 0.63
14 5 0.17
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.52
Consensus pattern (13 bp):
TTTTAAGGTTTCA
Found at i:18532614 original size:3 final size:3
Alignment explanation
Indices: 18532606--18532651 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
18532596 TCATTAAAAA
18532606 ATT ATT ATT ATT ATT ATT ATT ATT ATT GA-T ATT -TT ATT ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
18532649 ATT
1 ATT
18532652 TTTAATATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 5 0.13
3 33 0.85
4 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:18533093 original size:17 final size:16
Alignment explanation
Indices: 18533054--18533100 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
18533044 CTACTATTTT
18533054 TTTTTATTATTCTTTA
1 TTTTTATTATTCTTTA
18533070 TTATTTATTTATT-TTTA
1 TT-TTTA-TTATTCTTTA
*
18533087 TATTTTAATATTCT
1 T-TTTTATTATTCT
18533101 ATAATTATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 6 0.23
17 14 0.54
18 6 0.23
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTATTATTCTTTA
Found at i:18535086 original size:7 final size:7
Alignment explanation
Indices: 18535074--18535163 Score: 69
Period size: 7 Copynumber: 12.6 Consensus size: 7
18535064 CCACTTCTTT
18535074 TTTTTTA
1 TTTTTTA
18535081 TTTTTTA
1 TTTTTTA
18535088 -TTTTTA
1 TTTTTTA
*
18535094 TTTTTTT
1 TTTTTTA
18535101 TATTTTTA
1 T-TTTTTA
18535109 -TTTTTA
1 TTTTTTA
**
18535115 -TTACTA
1 TTTTTTA
18535121 TTTTATTA
1 TTTT-TTA
18535129 TTATATTTA
1 TT-T-TTTA
* *
18535138 CTATTTA
1 TTTTTTA
18535145 TTTTTTA
1 TTTTTTA
18535152 TTTTTGTA
1 TTTTT-TA
18535160 TTTT
1 TTTT
18535164 AATAAAATTT
Statistics
Matches: 66, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
6 16 0.24
7 29 0.44
8 15 0.23
9 5 0.08
10 1 0.02
ACGTcount: A:0.19, C:0.02, G:0.01, T:0.78
Consensus pattern (7 bp):
TTTTTTA
Found at i:18535091 original size:6 final size:6
Alignment explanation
Indices: 18535071--18535156 Score: 65
Period size: 6 Copynumber: 14.7 Consensus size: 6
18535061 AACCCACTTC
18535071 TTTT-T TTTTATT TTTTAT TTTTA- -TTT-T TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTA-T TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
** * * *
18535116 TACTA- TTTTAT TATTAT ATTTACT ATTTATT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTA-T TTTTA-T TTTTAT TTTT
18535157 GTATTTTAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
4 3 0.05
5 10 0.15
6 35 0.54
7 17 0.26
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:18535097 original size:11 final size:11
Alignment explanation
Indices: 18535083--18535155 Score: 53
Period size: 11 Copynumber: 6.4 Consensus size: 11
18535073 TTTTTTTATT
18535083 TTTTATTTTTA
1 TTTTATTTTTA
18535094 -TTT-TTTTTA
1 TTTTATTTTTA
18535103 TTTTTATTTTTA
1 -TTTTATTTTTA
*
18535115 TTACTA-TTTTA
1 TT-TTATTTTTA
*
18535126 TTATTATATTTA
1 TT-TTATTTTTA
18535138 CTATTTATTTTTTA
1 -T-TTTA-TTTTTA
18535152 TTTT
1 TTTT
18535156 TGTATTTTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
9 6 0.12
10 3 0.06
11 15 0.30
12 15 0.30
13 5 0.10
14 6 0.12
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:18542208 original size:21 final size:21
Alignment explanation
Indices: 18542166--18542215 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
18542156 AATTTTTATT
*
18542166 TATTTATCAAAATCAGAGATC
1 TATTTATAAAAATCAGAGATC
*
18542187 TATTTATAATAAAT-AGATATC
1 TATTTATAA-AAATCAGAGATC
*
18542208 TCTTTATA
1 TATTTATA
18542216 CATACATAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (21 bp):
TATTTATAAAAATCAGAGATC
Found at i:18550968 original size:29 final size:29
Alignment explanation
Indices: 18550926--18550987 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
18550916 AAACAACCAG
18550926 AAGGATATATCATTCCACGTCAAGAGCAT
1 AAGGATATATCATTCCACGTCAAGAGCAT
18550955 AAGGATATATCATTCCACGTCAAGAGCAT
1 AAGGATATATCATTCCACGTCAAGAGCAT
18550984 AAGG
1 AAGG
18550988 CTTGTAAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (29 bp):
AAGGATATATCATTCCACGTCAAGAGCAT
Found at i:18552800 original size:24 final size:23
Alignment explanation
Indices: 18552732--18552800 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 23
18552722 AAACAGATAA
*
18552732 GTCTATTTAAAATGAACAG-TTTT
1 GTCTATTCAAAAT-AACAGTTTTT
** *
18552755 AACTATTCAAAAATAAATAGTTTTT
1 GTCTATTC-AAAAT-AACAGTTTTT
18552780 GTCTATTCAAAATATACAGTT
1 GTCTATTCAAAATA-ACAGTT
18552801 ATGTTTGTAG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
23 6 0.17
24 19 0.54
25 10 0.29
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.41
Consensus pattern (23 bp):
GTCTATTCAAAATAACAGTTTTT
Found at i:18564747 original size:2 final size:2
Alignment explanation
Indices: 18564742--18564771 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18564732 CCCCCCTCCC
18564742 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
18564772 AAAATTTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:18567711 original size:13 final size:14
Alignment explanation
Indices: 18567681--18567711 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
18567671 TAAAAAAATA
18567681 TTTTTTAAATTTTC
1 TTTTTTAAATTTTC
18567695 TTTTTTAAATTTT-
1 TTTTTTAAATTTTC
18567708 TTTT
1 TTTT
18567712 AAATTGAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTTAAATTTTC
Found at i:18569233 original size:153 final size:154
Alignment explanation
Indices: 18568986--18569299 Score: 470
Period size: 153 Copynumber: 2.0 Consensus size: 154
18568976 TATAAAAGTG
* * * * *
18568986 TAAATTCTAAAAATATTAATAGTGAATGACATAAATATTTTTATAAATTTTAAAAAATAATAAAT
1 TAAA-TCTAAAAATATTAAAAATGAATAACATAAATATCTTTATAAATTTAAAAAAATAATAAAT
* *
18569051 TTATTTTAAAATTTTTAGCATTATTTATTTATTTAATAATGATTATTTATCATTAAATATATAAC
65 TTATTTTAAAATTTTTAGCATTATTTATTTATTTAATAAAGATTATTTATCATTAAAAATATAAC
18569116 -TTTTATTAATTAATTATTTAAATT
130 TTTTTATTAATTAATTATTTAAATT
*
18569140 TAAATCTAAAAGTATTAAAAATGAATAACATAAATATCTTTATAAATTTAAAAAAATAATAAATT
1 TAAATCTAAAAATATTAAAAATGAATAACATAAATATCTTTATAAATTTAAAAAAATAATAAATT
* * *
18569205 TATATTT-CAATTTTTAGCATTTTTTATTTATTTAATAAAGATTATTTGTCATTAAAAATATAAC
66 TAT-TTTAAAATTTTTAGCATTATTTATTTATTTAATAAAGATTATTTATCATTAAAAATATAAC
** *
18569269 TTTTTATTTGTTAGTTATTTAAATT
130 TTTTTATTAATTAATTATTTAAATT
18569294 TAAATC
1 TAAATC
18569300 AATTAAAAAT
Statistics
Matches: 144, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
153 110 0.76
154 34 0.24
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (154 bp):
TAAATCTAAAAATATTAAAAATGAATAACATAAATATCTTTATAAATTTAAAAAAATAATAAATT
TATTTTAAAATTTTTAGCATTATTTATTTATTTAATAAAGATTATTTATCATTAAAAATATAACT
TTTTATTAATTAATTATTTAAATT
Found at i:18569343 original size:15 final size:16
Alignment explanation
Indices: 18569289--18569343 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
18569279 TTAGTTATTT
* *
18569289 AAATTTAAATCAATTA
1 AAATTTATATCAAATA
*
18569305 AAAATT-TA-CAAATA
1 AAATTTATATCAAATA
*
18569319 AAATTTATATCAAATT
1 AAATTTATATCAAATA
18569335 AAA-TTATAT
1 AAATTTATAT
18569344 TAAAATTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 10 0.31
15 9 0.28
16 13 0.41
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTTATATCAAATA
Found at i:18571948 original size:22 final size:22
Alignment explanation
Indices: 18571763--18571949 Score: 89
Period size: 22 Copynumber: 8.5 Consensus size: 22
18571753 AATGACAACG
* **
18571763 TAATAATAAA-TACATAATAAAA
1 TAATAGTAAATTA-ATAATAACT
18571785 TAATAGTAAA-TAATAAATAACT
1 TAATAGTAAATTAAT-AATAACT
* * *
18571807 TAATAGTAAATTATTTAT-ACA
1 TAATAGTAAATTAATAATAACT
*
18571828 TAATTGTAAA-TATATAATAA-T
1 TAATAGTAAATTA-ATAATAACT
* * ** *
18571849 ACAATAGTGAATTAAGGATAATT
1 -TAATAGTAAATTAATAATAACT
* ** *
18571872 TAATA-AAAAAAAAGTGATAACT
1 TAATAGTAAATTAA-TAATAACT
* * *
18571894 TAATAGTAAAGTAATGATGACT
1 TAATAGTAAATTAATAATAACT
* * *
18571916 TAGTTGTAAATTAATAATAATT
1 TAATAGTAAATTAATAATAACT
18571938 TAATAGTAAATT
1 TAATAGTAAATT
18571950 TGATTCAGTT
Statistics
Matches: 122, Mismatches: 34, Indels: 18
0.70 0.20 0.10
Matches are distributed among these distances:
20 2 0.02
21 20 0.16
22 89 0.73
23 11 0.09
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.35
Consensus pattern (22 bp):
TAATAGTAAATTAATAATAACT
Found at i:18572441 original size:22 final size:22
Alignment explanation
Indices: 18572262--18572676 Score: 143
Period size: 22 Copynumber: 18.7 Consensus size: 22
18572252 AATCATAAAG
* *
18572262 AACTTAATAATAAATTAATGAT
1 AACTTAATAGTAAATTAATAAT
* * * *
18572284 AATTTAGTAGTAAA-TAATTTAG
1 AACTTAATAGTAAATTAA-TAAT
*
18572306 AACTTAGTAGT-AATTAATAATT
1 AACTTAATAGTAAATTAATAA-T
* * *
18572328 AAAAATTAAAAGTAAATCAAT-AT
1 --AACTTAATAGTAAATTAATAAT
* * * *
18572351 AACCTAATAAT-AA-TCATCGAT
1 AACTTAATAGTAAATTAAT-AAT
* * * *
18572372 AAATTAATAGTTAATTAGTGAT
1 AACTTAATAGTAAATTAATAAT
* *
18572394 AATTCTGT-ATAGTAAATTAGTGAT
1 AA--CT-TAATAGTAAATTAATAAT
* *
18572418 AACTTAATAATATATTAATAAT
1 AACTTAATAGTAAATTAATAAT
* *
18572440 AATTTAATAGTAAA-TAATTGAT
1 AACTTAATAGTAAATTAA-TAAT
* *
18572462 AACTTAGTAGTAAATCAATAAT
1 AACTTAATAGTAAATTAATAAT
**
18572484 AA-TATAATAGTAAATGCATAAT
1 AACT-TAATAGTAAATTAATAAT
* **
18572506 AACTTAATAGTAAATCAATTGT
1 AACTTAATAGTAAATTAATAAT
* * *
18572528 AACATAATTGTAAATGCAA-AAT
1 AACTTAATAGTAAAT-TAATAAT
* * * * *
18572550 AGCATAGTAGTAAATCAATGAT
1 AACTTAATAGTAAATTAATAAT
** * *
18572572 AACTTAATAAAAAATAAAATGAT
1 AACTTAATAGTAAAT-TAATAAT
* * * *
18572595 AACTTAATAGTTAATCATTGAT
1 AACTTAATAGTAAATTAATAAT
*
18572617 AA-TATAATAGTAAATCAATGAA-
1 AACT-TAATAGTAAATTAAT-AAT
* * * *
18572639 AATTTAGTAATAAATTACAGAA-
1 AACTTAATAGTAAATTA-ATAAT
18572661 AACTTAATAGTAAATT
1 AACTTAATAGTAAATT
18572677 TGTTTTAGTT
Statistics
Matches: 295, Mismatches: 73, Indels: 50
0.71 0.17 0.12
Matches are distributed among these distances:
19 2 0.01
20 2 0.01
21 33 0.11
22 194 0.66
23 30 0.10
24 27 0.09
25 7 0.02
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (22 bp):
AACTTAATAGTAAATTAATAAT
Found at i:18572541 original size:66 final size:66
Alignment explanation
Indices: 18572434--18572894 Score: 265
Period size: 66 Copynumber: 7.0 Consensus size: 66
18572424 ATAATATATT
* *
18572434 AATAATAATTTAATAGTAAATAATTGATAACTTAGTAGTAAATCAATAATAATATAATAGTAAAT
1 AATAATAACTTAATAGTAAATAATTGATAACTTAATAGTAAATCAATAATAATATAATAGTAAAT
18572499 GC
66 -C
* * ** *
18572501 -ATAATAACTTAATAGTAAATCAATTG-TAACATAATTGTAAATGCAA-AATAGCATAGTAGTAA
1 AATAATAACTTAATAGTAAAT-AATTGATAACTTAATAGTAAAT-CAATAATAATATAATAGTAA
18572563 ATC
64 ATC
* ** * * * *
18572566 AATGATAACTTAATAAAAAATAAAATGATAACTTAATAGTTAATCATTGATAATATAATAGTAAA
1 AATAATAACTTAATAGTAAAT-AATTGATAACTTAATAGTAAATCAATAATAATATAATAGTAAA
18572631 TC
65 TC
* * * * ** * *** ** * * *
18572633 AATGAA-AATTTAGTAATAAATTACAGAAAACTTAATAGTAAATTTGTTTTAGTTTAATAGTAAT
1 AAT-AATAACTTAATAGTAAATAATTGATAACTTAATAGTAAATCAATAATAATATAATAGTAAA
18572697 TC
65 TC
* ** * ** * * * * *
18572699 AATTATAAACTTAGCAGTAAATCATAAATAACTTAGA-AATAAATCAATGATAATTTAGTAGTTA
1 AATAAT-AACTTAATAGTAAATAATTGATAACTTA-ATAGTAAATCAATAATAATATAATAGTAA
18572763 ATC
64 ATC
* * * ** * *
18572766 ACTAA-AACTCAATAGTAAATCAA-TGATAACATGGTAGCAAATGC-ATAATAGTAT-ATAGTAA
1 AATAATAACTTAATAGTAAAT-AATTGATAACTTAATAGTAAAT-CAATAATAATATAATAGTAA
18572827 ATC
64 ATC
* * * * * * * * * *
18572830 ATTGATAATTTTATAGTAAATTATTGACAATTTAGTAGTAAATCACTAATAATATTATAGTAAAT
1 AATAATAACTTAATAGTAAATAATTGATAACTTAATAGTAAATCAATAATAATATAATAGTAAAT
18572895 TATTGATAAC
Statistics
Matches: 292, Mismatches: 86, Indels: 33
0.71 0.21 0.08
Matches are distributed among these distances:
64 13 0.04
65 66 0.23
66 116 0.40
67 95 0.33
68 2 0.01
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (66 bp):
AATAATAACTTAATAGTAAATAATTGATAACTTAATAGTAAATCAATAATAATATAATAGTAAAT
C
Found at i:18572846 original size:65 final size:66
Alignment explanation
Indices: 18572777--18572903 Score: 150
Period size: 65 Copynumber: 1.9 Consensus size: 66
18572767 CTAAAACTCA
* * *
18572777 ATAGTAAATCAATGATAACATGGTAGCAAATGCA-TAATAGTA-TATAGTAAATCATTGATAATT
1 ATAGTAAATCAATGACAACATAGTAGCAAAT-CACTAATAATATTATAGTAAATCATTGATAATT
18572840 TT
65 TT
* * ** * *
18572842 ATAGTAAATTATTGACAATTTAGTAGTAAATCACTAATAATATTATAGTAAATTATTGATAA
1 ATAGTAAATCAATGACAACATAGTAGCAAATCACTAATAATATTATAGTAAATCATTGATAA
18572904 CTTGCTGTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
64 2 0.04
65 31 0.61
66 18 0.35
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (66 bp):
ATAGTAAATCAATGACAACATAGTAGCAAATCACTAATAATATTATAGTAAATCATTGATAATTT
T
Found at i:18572847 original size:22 final size:22
Alignment explanation
Indices: 18572819--18572927 Score: 105
Period size: 22 Copynumber: 5.0 Consensus size: 22
18572809 CATAATAGTA
18572819 TATAGTAAATCATTGATAATTT
1 TATAGTAAATCATTGATAATTT
* *
18572841 TATAGTAAATTATTGACAA-TT
1 TATAGTAAATCATTGATAATTT
* * *
18572862 TAGTAGTAAATCACTAATAATAT
1 TA-TAGTAAATCATTGATAATTT
* *
18572885 TATAGTAAATTATTGATAACTT
1 TATAGTAAATCATTGATAATTT
** *
18572907 GCT-GTAAATCAGTGATAATTT
1 TATAGTAAATCATTGATAATTT
18572928 AGTATAAATT
Statistics
Matches: 68, Mismatches: 17, Indels: 5
0.76 0.19 0.06
Matches are distributed among these distances:
21 19 0.28
22 46 0.68
23 3 0.04
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.41
Consensus pattern (22 bp):
TATAGTAAATCATTGATAATTT
Found at i:18572873 original size:44 final size:44
Alignment explanation
Indices: 18572821--18572927 Score: 137
Period size: 44 Copynumber: 2.5 Consensus size: 44
18572811 TAATAGTATA
* *
18572821 TAGTAAATCATTGATAATTTTATAGTAAATTATTGACAATTTAG-
1 TAGTAAATCACTGATAATTTTATAGTAAATTATTGACAACTT-GC
* * *
18572865 TAGTAAATCACTAATAATATTATAGTAAATTATTGATAACTTGC
1 TAGTAAATCACTGATAATTTTATAGTAAATTATTGACAACTTGC
*
18572909 T-GTAAATCAGTGATAATTT
1 TAGTAAATCACTGATAATTT
18572928 AGTATAAATT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
43 16 0.30
44 38 0.70
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (44 bp):
TAGTAAATCACTGATAATTTTATAGTAAATTATTGACAACTTGC
Found at i:18572914 original size:65 final size:67
Alignment explanation
Indices: 18572810--18572936 Score: 161
Period size: 66 Copynumber: 1.9 Consensus size: 67
18572800 TAGCAAATGC
* * * *
18572810 ATAATAGTATATAGTAAATCATTGATAATTTTATAGTAAATTATTGACAATTTAGTAGTAAATCA
1 ATAATAGTATATAGTAAATCATTGATAACTTGATAGTAAATCAGTGACAATTTAGTA-TAAATCA
18572875 CTA
65 CTA
* * *
18572878 ATAATA-T-TATAGTAAATTATTGATAACTTGCT-GTAAATCAGTGATAATTTAGTATAAAT
1 ATAATAGTATATAGTAAATCATTGATAACTTGATAGTAAATCAGTGACAATTTAGTATAAAT
18572937 TAATAATGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
64 5 0.10
65 19 0.37
66 21 0.40
67 1 0.02
68 6 0.12
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (67 bp):
ATAATAGTATATAGTAAATCATTGATAACTTGATAGTAAATCAGTGACAATTTAGTATAAATCAC
TA
Found at i:18573041 original size:10 final size:10
Alignment explanation
Indices: 18572981--18573109 Score: 53
Period size: 11 Copynumber: 11.8 Consensus size: 10
18572971 AACAACTTCT
*
18572981 TAATAAATCA
1 TAATAAATTA
*
18572991 TCAATAACTTTA
1 T-AATAA-ATTA
* *
18573003 TAGTAAGTTA
1 TAATAAATTA
*
18573013 GTAATAATTTTA
1 -TAATAA-ATTA
18573025 TAATAAATTA
1 TAATAAATTA
*
18573035 TAGTAAATTA
1 TAATAAATTA
*
18573045 GTAATAACTTTA
1 -TAATAA-ATTA
18573057 TAATAAAATTA
1 TAAT-AAATTA
*
18573068 TTTAA-AACTTAA
1 --TAATAAATT-A
*
18573080 TAGTAAATTA
1 TAATAAATTA
*
18573090 TCAATAATTTA
1 T-AATAAATTA
18573101 GTAATAAAT
1 -TAATAAAT
18573110 CGTTTACAAC
Statistics
Matches: 89, Mismatches: 17, Indels: 25
0.68 0.13 0.19
Matches are distributed among these distances:
10 20 0.22
11 53 0.60
12 13 0.15
13 3 0.03
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (10 bp):
TAATAAATTA
Found at i:18573046 original size:32 final size:33
Alignment explanation
Indices: 18573000--18573068 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 33
18572990 ATCAATAACT
* *
18573000 TTATAGTAAGTTAGTAATAATTTTATAAT-AAA
1 TTATAGTAAATTAGTAATAACTTTATAATAAAA
18573032 TTATAGTAAATTAGTAATAACTTTATAATAAAA
1 TTATAGTAAATTAGTAATAACTTTATAATAAAA
18573065 TTAT
1 TTAT
18573069 TTAAAACTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 27 0.79
33 7 0.21
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.43
Consensus pattern (33 bp):
TTATAGTAAATTAGTAATAACTTTATAATAAAA
Found at i:18573057 original size:22 final size:22
Alignment explanation
Indices: 18573032--18573090 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
18573022 TTATAATAAA
18573032 TTATAGTAAATTA-GTAATAACT
1 TTATAGTAAATTATGTAA-AACT
* *
18573054 TTATAATAAAATTATTTAAAACT
1 TTATAGT-AAATTATGTAAAACT
*
18573077 TAATAGTAAATTAT
1 TTATAGTAAATTAT
18573091 CAATAATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 13 0.42
23 15 0.48
24 3 0.10
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.42
Consensus pattern (22 bp):
TTATAGTAAATTATGTAAAACT
Found at i:18573437 original size:22 final size:22
Alignment explanation
Indices: 18573403--18573481 Score: 95
Period size: 22 Copynumber: 3.5 Consensus size: 22
18573393 GTATTTATTG
* *
18573403 ATAAATTAATAGTAAATCATAA
1 ATAACTTAATAGTAAATCATTA
* * *
18573425 ATAACTTAGTAGTAATTCAATTG
1 ATAACTTAATAGTAAATC-ATTA
*
18573448 ATAACTTAATAGTAAATAATTA
1 ATAACTTAATAGTAAATCATTA
18573470 ATAACTTAATAG
1 ATAACTTAATAG
18573482 CTAATTATTA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
22 30 0.64
23 17 0.36
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (22 bp):
ATAACTTAATAGTAAATCATTA
Found at i:18573463 original size:45 final size:46
Alignment explanation
Indices: 18573399--18573487 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 46
18573389 TATTGTATTT
* *
18573399 ATTGATAAATTAATAGTAAATCATAAATAACTTAGTAG-TAATTCA
1 ATTGATAAATTAATAGTAAATAATAAATAACTTAATAGCTAATTCA
* *
18573444 ATTGATAACTTAATAGTAAATAATTAATAACTTAATAGCTAATT
1 ATTGATAAATTAATAGTAAATAATAAATAACTTAATAGCTAATT
18573488 ATTAAAAAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 34 0.87
46 5 0.13
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.37
Consensus pattern (46 bp):
ATTGATAAATTAATAGTAAATAATAAATAACTTAATAGCTAATTCA
Found at i:18573491 original size:22 final size:22
Alignment explanation
Indices: 18573397--18573492 Score: 88
Period size: 22 Copynumber: 4.3 Consensus size: 22
18573387 TATATTGTAT
* *
18573397 TTATTGATAAATTAATAGTAAA
1 TTATTAATAACTTAATAGTAAA
* * *
18573419 TCATAAATAACTTAGTAGT-AA
1 TTATTAATAACTTAATAGTAAA
*
18573440 TTCAATTGATAACTTAATAGTAAA
1 TT--ATTAATAACTTAATAGTAAA
*
18573464 TAATTAATAACTTAATAGCT-AA
1 TTATTAATAACTTAATAG-TAAA
18573486 TTATTAA
1 TTATTAA
18573493 AAAGTTAGTA
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
21 3 0.05
22 37 0.64
23 15 0.26
24 3 0.05
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (22 bp):
TTATTAATAACTTAATAGTAAA
Found at i:18573660 original size:22 final size:22
Alignment explanation
Indices: 18573635--18573784 Score: 81
Period size: 22 Copynumber: 6.8 Consensus size: 22
18573625 AGTAATAAAT
* *
18573635 TAGTTAATCATTGATAATTTTA
1 TAGTAAATCATTGATAACTTTA
*
18573657 TAGTAAATCATTTATAACTTTA
1 TAGTAAATCATTGATAACTTTA
* *
18573679 TAGAAAATTAGTT-ATAACTTTA
1 TAGTAAATCA-TTGATAACTTTA
* * **
18573701 TAATAAATTATCAATAAC-TTA
1 TAGTAAATCATTGATAACTTTA
* * * * *
18573722 GTAATACATTATTCATAACTTAA
1 -TAGTAAATCATTGATAACTTTA
* *
18573745 TAGTAAATTATTAATAA-TTTAA
1 TAGTAAATCATTGATAACTTT-A
* * *
18573767 TAATAAATTATTAATAAC
1 TAGTAAATCATTGATAAC
18573785 ATAATAATAA
Statistics
Matches: 105, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
21 6 0.06
22 95 0.90
23 4 0.04
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.43
Consensus pattern (22 bp):
TAGTAAATCATTGATAACTTTA
Found at i:18573716 original size:11 final size:10
Alignment explanation
Indices: 18573698--18573798 Score: 67
Period size: 11 Copynumber: 9.3 Consensus size: 10
18573688 AGTTATAACT
18573698 TTATAATAAA
1 TTATAATAAA
*
18573708 TTATCAATAAC
1 TTAT-AATAAA
*
18573719 TTAGTAATACA
1 TTA-TAATAAA
* *
18573730 TTATTCATAAC
1 TTA-TAATAAA
*
18573741 TTAATAGTAAA
1 TT-ATAATAAA
*
18573752 TTATTAATAAT
1 TTA-TAATAAA
18573763 TTAATAATAAA
1 TT-ATAATAAA
18573774 TTATTAATAACA
1 TTA-TAATAA-A
*
18573786 TAATAATAAA
1 TTATAATAAA
18573796 TTA
1 TTA
18573799 GTTATAATAA
Statistics
Matches: 69, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
10 9 0.13
11 54 0.78
12 6 0.09
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (10 bp):
TTATAATAAA
Found at i:18573805 original size:22 final size:22
Alignment explanation
Indices: 18573660--18573798 Score: 147
Period size: 22 Copynumber: 6.3 Consensus size: 22
18573650 AATTTTATAG
* * *
18573660 TAAATCATTTATAACTTTATAGA
1 TAAATTATTAATAACTTAATA-A
*
18573683 -AAATTAGTT-ATAACTTTATAA
1 TAAATTA-TTAATAACTTAATAA
* *
18573704 TAAATTATCAATAACTTAGTAA
1 TAAATTATTAATAACTTAATAA
* * *
18573726 TACATTATTCATAACTTAATAG
1 TAAATTATTAATAACTTAATAA
*
18573748 TAAATTATTAATAATTTAATAA
1 TAAATTATTAATAACTTAATAA
*
18573770 TAAATTATTAATAACATAATAA
1 TAAATTATTAATAACTTAATAA
18573792 TAAATTA
1 TAAATTA
18573799 GTTATAATAA
Statistics
Matches: 98, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
21 2 0.02
22 94 0.96
23 2 0.02
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (22 bp):
TAAATTATTAATAACTTAATAA
Found at i:18573866 original size:22 final size:22
Alignment explanation
Indices: 18573839--18573889 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
18573829 TATAATTTAT
18573839 TGATAACTTAA-TGATAAATCGG
1 TGATAACTTAAGTG-TAAATCGG
*
18573861 TTATAA-TTAAGTTGTAAATCGG
1 TGATAACTTAAG-TGTAAATCGG
18573883 TGATAAC
1 TGATAAC
18573890 AATAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 4 0.17
22 18 0.75
23 2 0.08
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (22 bp):
TGATAACTTAAGTGTAAATCGG
Found at i:18574003 original size:24 final size:24
Alignment explanation
Indices: 18573971--18574033 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
18573961 CTATTCATAT
* *
18573971 TTTAATAGTAAATTAGTGAT-ATAA
1 TTTAGTAGTAAATCAGTGATAAT-A
*
18573995 TTTAGTAGTAAATCATTGATAATA
1 TTTAGTAGTAAATCAGTGATAATA
*
18574019 TATAGTAGTAAATCA
1 TTTAGTAGTAAATCA
18574034 TTGCTAACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 32 0.94
25 2 0.06
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.40
Consensus pattern (24 bp):
TTTAGTAGTAAATCAGTGATAATA
Found at i:18580859 original size:18 final size:18
Alignment explanation
Indices: 18580828--18580864 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
18580818 CTTGTGTAAA
*
18580828 CCTTCAAAGTTTCTTTCT
1 CCTTCAAAGCTTCTTTCT
*
18580846 CCTTCGAAGCTTCTTTCT
1 CCTTCAAAGCTTCTTTCT
18580864 C
1 C
18580865 AATTGGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.32, G:0.08, T:0.46
Consensus pattern (18 bp):
CCTTCAAAGCTTCTTTCT
Found at i:18582411 original size:2 final size:2
Alignment explanation
Indices: 18582404--18582434 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18582394 TCCACACCAT
18582404 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 T
18582435 CATGATTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18583366 original size:52 final size:52
Alignment explanation
Indices: 18583211--18583367 Score: 171
Period size: 52 Copynumber: 3.0 Consensus size: 52
18583201 TATAACCATA
** *
18583211 CAAACTTTACC-ATTAAGAATCC-CTATTCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAAC-TTACCTATTAAGAATCCTCT-TTCTCTTAGAATTCTTCTTTTGCAAGT
* * * *
18583263 CAAACTTGCCTATTAAGAATCCAT-TTTCTTTTAGAATT-TTTTTCTTACAAGT
1 CAAACTTACCTATTAAGAATCC-TCTTTCTCTTAGAATTCTTCTT-TTGCAAGT
18583315 CAAACTTACCTATTAAGAATCCTCTTT-TGCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTACCTATTAAGAATCCTCTTTCT-CTTAGAATTCTTCTTTTGCAAGT
18583367 C
1 C
18583368 TTCTTGTCCA
Statistics
Matches: 87, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
51 9 0.10
52 73 0.84
53 5 0.06
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATCCTCTTTCTCTTAGAATTCTTCTTTTGCAAGT
Found at i:18583407 original size:11 final size:11
Alignment explanation
Indices: 18583391--18583422 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
18583381 AGCAATATCT
18583391 AACAAATCTCA
1 AACAAATCTCA
18583402 AACAAATCTCA
1 AACAAATCTCA
18583413 AACAAATCTC
1 AACAAATCTC
18583423 TTATGGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (11 bp):
AACAAATCTCA
Found at i:18585223 original size:14 final size:14
Alignment explanation
Indices: 18585203--18585237 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
18585193 TTATTAACAT
18585203 TTTTTTTATTATTTA
1 TTTTTTTATT-TTTA
18585218 TTTTTTTATTTTTA
1 TTTTTTTATTTTTA
18585232 TTTTTT
1 TTTTTT
18585238 AATTCTCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTTATTTTTA
Found at i:18585423 original size:2 final size:2
Alignment explanation
Indices: 18585412--18585446 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
18585402 TTCATATACT
18585412 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
18585447 GTTTGATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18587435 original size:24 final size:24
Alignment explanation
Indices: 18587407--18587453 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
18587397 TTCATATCAG
*
18587407 ATAAAAATATTTAATTATTAATTA
1 ATAAAAATAATTAATTATTAATTA
* *
18587431 ATAAAATTAATTATTTATTAATT
1 ATAAAAATAATTAATTATTAATT
18587454 TTATTTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATAAAAATAATTAATTATTAATTA
Found at i:18594402 original size:31 final size:31
Alignment explanation
Indices: 18594364--18594426 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
18594354 TGTGAGAAAA
18594364 GTTATAGCATTCCCACAACACCCATCCAAAG
1 GTTATAGCATTCCCACAACACCCATCCAAAG
18594395 GTTATAGCATTCCCACAACACCCATCCAAAG
1 GTTATAGCATTCCCACAACACCCATCCAAAG
18594426 G
1 G
18594427 ATGGTACCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.35, G:0.11, T:0.19
Consensus pattern (31 bp):
GTTATAGCATTCCCACAACACCCATCCAAAG
Found at i:18594807 original size:59 final size:58
Alignment explanation
Indices: 18594685--18595129 Score: 456
Period size: 59 Copynumber: 7.6 Consensus size: 58
18594675 GCTTTTATTC
* * * *
18594685 AAGGAAACTTGATACTTTCAATTTTTTCTT-AAAAATATTTCTTGAAATTTTCATTTTC
1 AAGGAAAATTGATACTTTCAATTTTTCCTTAAAAAATATTT-TTAAAATTTTCATTTTT
*
18594743 AAGGAAAATTGATACTTTAAATTTTTCCTTGAAAAAATATTTTTAAAATTTTCATTTTT
1 AAGGAAAATTGATACTTTCAATTTTTCCTT-AAAAAATATTTTTAAAATTTTCATTTTT
* * * * *
18594802 AAGGAAAATTGACATTTTCAATTTTTTC-TCAAAAATCATTTTTTAAAAATTTCA-TTTT
1 AAGGAAAATTGATACTTTCAATTTTTCCTTAAAAAAT-A-TTTTTAAAATTTTCATTTTT
* * * *
18594860 GA-GAAATTTTGATACTTTCAACTTTT-CTTCAAGAAATATTTTTAAAATTTTCATTTTT
1 AAGGAAA-ATTGATACTTTCAATTTTTCCTT-AAAAAATATTTTTAAAATTTTCATTTTT
* * * * * * *
18594918 AAGGAAAAGTTGACATTTTCAATGTTTCCTCAAAATCATTTTTTTGAAATTTTCATTTTT
1 AAGGAAAA-TTGATACTTTCAATTTTTCCTTAAAA-AATATTTTTAAAATTTTCATTTTT
* * * * *
18594978 AAGAAAAATTGATACTTTCAATTTTTTCTCAAGAAACAT-TTTTTGAAATTTTCATTTTC
1 AAGGAAAATTGATACTTTCAATTTTTCCTTAA-AAA-ATATTTTTAAAATTTTCATTTTT
*
18595037 AAGAAAAATTGATACTTTCAACTTTTT-CTTAAAAAATATTTTTCAAAATTTTCATTTTT
1 AAGGAAAATTGATACTTTCAA-TTTTTCCTTAAAAAATATTTTT-AAAATTTTCATTTTT
* *
18595096 AAGGAAAATTAATACTTTTAATGTTTT-CTTAAAA
1 AAGGAAAATTGATACTTTCAAT-TTTTCCTTAAAA
18595130 CATTTTTCTT
Statistics
Matches: 326, Mismatches: 43, Indels: 35
0.81 0.11 0.09
Matches are distributed among these distances:
57 27 0.08
58 65 0.20
59 185 0.57
60 49 0.15
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (58 bp):
AAGGAAAATTGATACTTTCAATTTTTCCTTAAAAAATATTTTTAAAATTTTCATTTTT
Found at i:18595055 original size:25 final size:25
Alignment explanation
Indices: 18594968--18595056 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
18594958 TTTTTGAAAT
*
18594968 TTTCATTTTTAAGAAAAATTGATAC
1 TTTCATTTTCAAGAAAAATTGATAC
* * *
18594993 TTTCAATTTTTTCTCAAGAAACATTTTTTGAAAT
1 TTTC-A---TTT-TCAAGAAA-A---ATTGATAC
18595027 TTTCATTTTCAAGAAAAATTGATAC
1 TTTCATTTTCAAGAAAAATTGATAC
18595052 TTTCA
1 TTTCA
18595057 ACTTTTTCTT
Statistics
Matches: 48, Mismatches: 7, Indels: 18
0.66 0.10 0.25
Matches are distributed among these distances:
25 14 0.29
26 1 0.02
28 1 0.02
29 11 0.23
30 10 0.21
31 1 0.02
33 1 0.02
34 9 0.19
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (25 bp):
TTTCATTTTCAAGAAAAATTGATAC
Found at i:18597402 original size:66 final size:66
Alignment explanation
Indices: 18597291--18597416 Score: 155
Period size: 66 Copynumber: 1.9 Consensus size: 66
18597281 ACATAAGTCG
* * * * * *
18597291 AAATCCAAAATAAAATAACCTAGATTGAATCAAAATGTAACATGAATAACTTGGATTAAGAAATC
1 AAATCCAAAACAAAATAACCTAGACTGAACCAAAATCTAACATGAAGAACTTGGACTAAGAAATC
18597356 A
66 A
* * *
18597357 AAATCCAAAACAAAATGACTTAGACTGAACCAAAATCTGAA-ATGAAGAATTTGGACTAAG
1 AAATCCAAAACAAAATAACCTAGACTGAACCAAAATCT-AACATGAAGAACTTGGACTAAG
18597417 CCGAAGAAGG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
66 48 0.96
67 2 0.04
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.22
Consensus pattern (66 bp):
AAATCCAAAACAAAATAACCTAGACTGAACCAAAATCTAACATGAAGAACTTGGACTAAGAAATC
A
Found at i:18597459 original size:85 final size:85
Alignment explanation
Indices: 18597354--18597991 Score: 769
Period size: 85 Copynumber: 7.5 Consensus size: 85
18597344 GATTAAGAAA
* * * * *
18597354 TCAAAATCCAAAACAAAATGACTTAGACTGAACCAAAATCTGAAATGAAGAATTTGGACTAAGCC
1 TCAAAATCCAAAACAAAATGACCTAGACTGAACCGAAGTCTGAAATGAATAATTTGGACTAAGTC
18597419 GAAGAAGGATTTGACATAAG
66 GAAGAAGGATTTGACATAAG
* * * *
18597439 TTC-AAATCCAAATCAAAATGACCTGGACTGAACTGAAGTCTGAAATGAATAATTTGGATTAAGT
1 -TCAAAATCCAAAACAAAATGACCTAGACTGAACCGAAGTCTGAAATGAATAATTTGGACTAAGT
* *
18597503 TGAAGAAAGATTTGACATAAG
65 CGAAGAAGGATTTGACATAAG
* * * * * *
18597524 TCGAAATTCAAAACAAAATGACCTAGACTGAATCGAGGTCTGAAATGAATAACTTGGACTAAGTT
1 TCAAAATCCAAAACAAAATGACCTAGACTGAACCGAAGTCTGAAATGAATAATTTGGACTAAGTC
* *
18597589 GAATAAGGATTTGACAAAAG
66 GAAGAAGGATTTGACATAAG
* * * *
18597609 TCAAAATCCAAAACAAAATGACCTAGACTGAACTGAGGTCTAAAATGAATAATTTGGACTAAGCC
1 TCAAAATCCAAAACAAAATGACCTAGACTGAACCGAAGTCTGAAATGAATAATTTGGACTAAGTC
18597674 GAAGAAGGATTTGACATAAG
66 GAAGAAGGATTTGACATAAG
** * * * *
18597694 TTGAAATCTAAAACAAAATGACCT-GAATTGAATCGAAGTCTGAAATGAATATTTTGGACTAAGT
1 TCAAAATCCAAAACAAAATGACCTAG-ACTGAACCGAAGTCTGAAATGAATAATTTGGACTAAGT
**
18597758 CGAAGAAGGATTTGACCGAAG
65 CGAAGAAGGATTTGACATAAG
* * * **
18597779 TCAAAATCCAAAACAAAATGACCTGGACTGAATC-AAGGTCTGAAATGAATAACTTGGACTAAAC
1 TCAAAATCCAAAACAAAATGACCTAGACTGAACCGAA-GTCTGAAATGAATAATTTGGACTAAGT
* *
18597843 CAAAGAAAGATTTGACATAAG
65 CGAAGAAGGATTTGACATAAG
* * * *
18597864 TCAAAATCCAAAACAAAATGACTTTGACTGAACTGAAGTCTGGAATGAATAATTTGGACTAAGTC
1 TCAAAATCCAAAACAAAATGACCTAGACTGAACCGAAGTCTGAAATGAATAATTTGGACTAAGTC
* *
18597929 GAAGAAGGATTTGGCATAGG
66 GAAGAAGGATTTGACATAAG
* * * * * * *
18597949 CCAAAATCTAAAACAAAGTGACTTGGACTGAATCGAAGCCTGA
1 TCAAAATCCAAAACAAAATGACCTAGACTGAACCGAAGTCTGA
18597992 CTTCAATTAC
Statistics
Matches: 471, Mismatches: 76, Indels: 11
0.84 0.14 0.02
Matches are distributed among these distances:
84 5 0.01
85 461 0.98
86 5 0.01
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (85 bp):
TCAAAATCCAAAACAAAATGACCTAGACTGAACCGAAGTCTGAAATGAATAATTTGGACTAAGTC
GAAGAAGGATTTGACATAAG
Found at i:18597793 original size:255 final size:255
Alignment explanation
Indices: 18597354--18597991 Score: 900
Period size: 255 Copynumber: 2.5 Consensus size: 255
18597344 GATTAAGAAA
** * *
18597354 TCAAAATCCAAAACAAAATGACTTAGACTGAACCAAAATCTGAAATGAAGAATTTGGACTAAGCC
1 TCAAAATCCAAAACAAAATGACTTAGACTGAACTGAAGTCTGAAATGAATAATTTGGACTAAGCC
* * *
18597419 GAAGAAGGATTTGACATAAGTTCAAATCCAAATCAAAATGACCTGGACTGAA-CTGAAGTCTGAA
66 GAAGAAGGATTTGACATAAGTTAAAATCTAAAACAAAATGACCTGGACTGAATC-GAAGTCTGAA
* * * * *
18597483 ATGAATAATTTGGATTAAGTTGAAGAAAGATTTGACATAAGTCGAAATTCAAAACAAAATGACCT
130 ATGAATAATTTGGACTAAGTCGAAGAAAGATTTGACAGAAGTCAAAATCCAAAACAAAATGACCT
* **** * *
18597548 AGACTGAATCGAGGTCTGAAATGAATAACTTGGACTAAGTTGAATAAGGATTTGACAAAAG
195 AGACTGAATCAAGGTCTGAAATGAATAACTTGGACTAAACCAAAGAAAGATTTGACAAAAG
* * *
18597609 TCAAAATCCAAAACAAAATGACCTAGACTGAACTGAGGTCTAAAATGAATAATTTGGACTAAGCC
1 TCAAAATCCAAAACAAAATGACTTAGACTGAACTGAAGTCTGAAATGAATAATTTGGACTAAGCC
* * *
18597674 GAAGAAGGATTTGACATAAGTTGAAATCTAAAACAAAATGACCTGAATTGAATCGAAGTCTGAAA
66 GAAGAAGGATTTGACATAAGTTAAAATCTAAAACAAAATGACCTGGACTGAATCGAAGTCTGAAA
* * * *
18597739 TGAATATTTTGGACTAAGTCGAAGAAGGATTTGACCGAAGTCAAAATCCAAAACAAAATGACCTG
131 TGAATAATTTGGACTAAGTCGAAGAAAGATTTGACAGAAGTCAAAATCCAAAACAAAATGACCTA
*
18597804 GACTGAATCAAGGTCTGAAATGAATAACTTGGACTAAACCAAAGAAAGATTTGACATAAG
196 GACTGAATCAAGGTCTGAAATGAATAACTTGGACTAAACCAAAGAAAGATTTGACAAAAG
* * *
18597864 TCAAAATCCAAAACAAAATGACTTTGACTGAACTGAAGTCTGGAATGAATAATTTGGACTAAGTC
1 TCAAAATCCAAAACAAAATGACTTAGACTGAACTGAAGTCTGAAATGAATAATTTGGACTAAGCC
* * ** * * *
18597929 GAAGAAGGATTTGGCATAGGCCAAAATCTAAAACAAAGTGACTTGGACTGAATCGAAGCCTGA
66 GAAGAAGGATTTGACATAAGTTAAAATCTAAAACAAAATGACCTGGACTGAATCGAAGTCTGA
18597992 CTTCAATTAC
Statistics
Matches: 337, Mismatches: 45, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
255 336 1.00
256 1 0.00
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (255 bp):
TCAAAATCCAAAACAAAATGACTTAGACTGAACTGAAGTCTGAAATGAATAATTTGGACTAAGCC
GAAGAAGGATTTGACATAAGTTAAAATCTAAAACAAAATGACCTGGACTGAATCGAAGTCTGAAA
TGAATAATTTGGACTAAGTCGAAGAAAGATTTGACAGAAGTCAAAATCCAAAACAAAATGACCTA
GACTGAATCAAGGTCTGAAATGAATAACTTGGACTAAACCAAAGAAAGATTTGACAAAAG
Found at i:18599484 original size:8 final size:8
Alignment explanation
Indices: 18599471--18599496 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
18599461 ATGAAGCATG
18599471 ATTCTATC
1 ATTCTATC
18599479 ATTCTATC
1 ATTCTATC
18599487 ATTCTATC
1 ATTCTATC
18599495 AT
1 AT
18599497 GAGCATGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTCTATC
Found at i:18603319 original size:58 final size:56
Alignment explanation
Indices: 18603254--18603710 Score: 318
Period size: 58 Copynumber: 7.8 Consensus size: 56
18603244 AATGCTTTTA
* * * *
18603254 TTTAAGGAAAATTGATACTTTCAACTTTTTTTAAAAAATATTTCTTGAATTTTTTAT
1 TTTAAGAAAAATTGATACTTTCAACTTTTTTTAAAAAATATTT-TTAAAATTTTCAT
* * ** *
18603311 TTTCAAGGAAAATTGATACTTTTAACTTTTCCTCGAACAAATATTTTTAAAATTTTCATT
1 TTT-AAGAAAAATTGATACTTTCAACTTTT--TTTAAAAAATATTTTTAAAATTTTCA-T
* * * * * * *
18603371 TTTAAGGAAAATTGACA-TTTTAAATTTTTTCTCAAAAATTATTTTTTGAAATTTTCAA
1 TTTAAGAAAAATTGATACTTTCAACTTTTTT-T-AAAAAATA-TTTTTAAAATTTTCAT
* * *
18603429 TTCAAGAAAAATTGATACTTTCAA-TTTTTCCTCAAGAAATATTTTTAAAA-TTTCAT
1 TTTAAGAAAAATTGATACTTTCAACTTTTT--TTAAAAAATATTTTTAAAATTTTCAT
* * * * * *
18603485 TTGTAACGAAAAGTTGACATTTTCAA-TTTTTCCTCAAAAATTATTTTTAAACATTTT-TT
1 TT-TAA-GAAAAATTGATACTTTCAACTTTTT--TTAAAAAATATTTTTAAA-ATTTTCAT
* * *
18603544 TTTAAGAAAAATTGATATTTTCAACTTTTCTTCAAGAAACAT-TTTTTGAAATTTTCAT
1 TTTAAGAAAAATTGATACTTTCAACTTTT-TTTAA-AAA-ATATTTTTAAAATTTTCAT
* **
18603602 TTTCAAGAAAAATTGATACTTTTAACTTTCCTTAAAAAATATTTTTTAAAATTTTCATTTTCAT
1 TTT-AAGAAAAATTGATACTTTCAACTTTTTTTAAAAAATA-TTTTT-AAA-----ATTTTCAT
*
18603666 TTTAAAAAAAAATTGATACTTTCAACTTTTTCTT--AAAATATTTTT
1 TTT-AAGAAAAATTGATACTTTCAACTTTTT-TTAAAAAATATTTTT
18603711 CTTTTACTTT
Statistics
Matches: 324, Mismatches: 47, Indels: 53
0.76 0.11 0.12
Matches are distributed among these distances:
56 10 0.03
57 42 0.13
58 134 0.41
59 72 0.22
60 19 0.06
62 5 0.02
63 6 0.02
64 34 0.10
65 2 0.01
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (56 bp):
TTTAAGAAAAATTGATACTTTCAACTTTTTTTAAAAAATATTTTTAAAATTTTCAT
Found at i:18603417 original size:59 final size:58
Alignment explanation
Indices: 18603254--18603662 Score: 372
Period size: 58 Copynumber: 7.0 Consensus size: 58
18603244 AATGCTTTTA
* * * * * * *
18603254 TTTAAGGAAAATTGATACTTTCAACTTTTT-TTAAAAAATATTTCTTGAATTTTTTATT
1 TTTAAGGAAAATTGATATTTTCAA-TTTTTCCTCAAAAATATTTTTTAAAATTTTCATT
* *
18603312 TTCAAGGAAAATTGATACTTTT-AACTTTTCCTCGAACAAATA-TTTTTAAAATTTTCATT
1 TTTAAGGAAAATTGATA-TTTTCAATTTTTCCTC-AA-AAATATTTTTTAAAATTTTCATT
* * * * *
18603371 TTTAAGGAAAATTGACATTTTAAATTTTTTCTCAAAAATTATTTTTTGAAATTTTCA-A
1 TTTAAGGAAAATTGATATTTTCAATTTTTCCTCAAAAA-TATTTTTTAAAATTTTCATT
* * *
18603429 TTCAAGAAAAATTGATACTTTCAATTTTTCCTCAAGAAATA-TTTTTAAAA-TTTCATT
1 TTTAAGGAAAATTGATATTTTCAATTTTTCCTCAA-AAATATTTTTTAAAATTTTCATT
* * *
18603486 TGTAACGAAAAGTTGACATTTTCAATTTTTCCTCAAAAAT-TATTTTTAAACATTTT--TT
1 TTTAAGGAAAA-TTGATATTTTCAATTTTTCCTCAAAAATAT-TTTTTAAA-ATTTTCATT
* * * * *
18603544 TTTAAGAAAAATTGATATTTTCAACTTTTCTTCAAGAAACATTTTTTGAAATTTTCATT
1 TTTAAGGAAAATTGATATTTTCAATTTTTCCTCAA-AAATATTTTTTAAAATTTTCATT
* * * *
18603603 TTCAAGAAAAATTGATACTTTT-AA-CTTTCCTTAAAAAATATTTTTTAAAATTTTCATT
1 TTTAAGGAAAATTGATA-TTTTCAATTTTTCC-TCAAAAATATTTTTTAAAATTTTCATT
18603661 TT
1 TT
18603663 CATTTTAAAA
Statistics
Matches: 288, Mismatches: 43, Indels: 40
0.78 0.12 0.11
Matches are distributed among these distances:
56 5 0.02
57 52 0.18
58 135 0.47
59 84 0.29
60 12 0.04
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.47
Consensus pattern (58 bp):
TTTAAGGAAAATTGATATTTTCAATTTTTCCTCAAAAATATTTTTTAAAATTTTCATT
Found at i:18606268 original size:3 final size:3
Alignment explanation
Indices: 18606252--18606292 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
18606242 AATAAAACTT
* *
18606252 ATA A-A ATA AT- ATA ATA ATA ATA GTA ATA ATA ACA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
18606293 AGATGAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:18606898 original size:118 final size:119
Alignment explanation
Indices: 18606759--18606994 Score: 384
Period size: 119 Copynumber: 2.0 Consensus size: 119
18606749 TAAAAAAATA
*
18606759 ATAAAATAAAAAAGACCAATAAAATTTTTAAAG-AAAAAATAAAATGTGTGCATCAACATATTGC
1 ATAAAATAAAAAAGACCAATAAAATTTCTAAAGAAAAAAATAAAATGTGTGCATCAACATATTGC
**
18606823 CATTCGTATTGCATGCATATTTTTACAAAAAATAAATCCAGGCCTCTGAGGATG
66 CATTCACATTGCATGCATATTTTTACAAAAAATAAATCCAGGCCTCTGAGGATG
* *
18606877 ATAAAATAAAAATGACGAATAAAATTTCTAAAGAAAAAAATAAAATGTGTGCATCAACATATTGC
1 ATAAAATAAAAAAGACCAATAAAATTTCTAAAGAAAAAAATAAAATGTGTGCATCAACATATTGC
* * **
18606942 CATTCACATTGCTTGCATATTTTTACGAAAAATAAATCTGGGCCTCTGAGGAT
66 CATTCACATTGCATGCATATTTTTACAAAAAATAAATCCAGGCCTCTGAGGAT
18606995 AAGGTTTTAA
Statistics
Matches: 108, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
118 30 0.28
119 78 0.72
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (119 bp):
ATAAAATAAAAAAGACCAATAAAATTTCTAAAGAAAAAAATAAAATGTGTGCATCAACATATTGC
CATTCACATTGCATGCATATTTTTACAAAAAATAAATCCAGGCCTCTGAGGATG
Found at i:18607157 original size:3 final size:3
Alignment explanation
Indices: 18607151--18607182 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
18607141 CAACAACAAC
18607151 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
18607183 AGGAAAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:18610654 original size:15 final size:15
Alignment explanation
Indices: 18610636--18610684 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
18610626 AATGATATTA
*
18610636 AATAAAATATTAAAT
1 AATAAAACATTAAAT
* *
18610651 AATAATACATTAATT
1 AATAAAACATTAAAT
* *
18610666 AATTAAACATTAAAA
1 AATAAAACATTAAAT
18610681 AATA
1 AATA
18610685 CAAAAAATAG
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAAAACATTAAAT
Found at i:18627964 original size:24 final size:24
Alignment explanation
Indices: 18627932--18627984 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
18627922 CAATTTCTTA
18627932 ATAGCACAACTGAGACAGTCATCT
1 ATAGCACAACTGAGACAGTCATCT
18627956 ATAGCACAACTGAGACAGTCATCT
1 ATAGCACAACTGAGACAGTCATCT
*
18627980 GTAGC
1 ATAGC
18627985 TCTAAATAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (24 bp):
ATAGCACAACTGAGACAGTCATCT
Found at i:18635158 original size:19 final size:19
Alignment explanation
Indices: 18635117--18635155 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
18635107 TATTGCTTGA
18635117 TTAGTTAACTTTGTTTATT
1 TTAGTTAACTTTGTTTATT
*
18635136 TTAGTTAAGTTT-TTTATT
1 TTAGTTAACTTTGTTTATT
18635154 TT
1 TT
18635156 TAGAATAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.21, C:0.03, G:0.10, T:0.67
Consensus pattern (19 bp):
TTAGTTAACTTTGTTTATT
Found at i:18637253 original size:16 final size:15
Alignment explanation
Indices: 18637224--18637262 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
18637214 ATTAAACCAA
*
18637224 AAATAAAATCAAATC
1 AAATTAAATCAAATC
18637239 AAATTAAATCAAAATC
1 AAATTAAATC-AAATC
18637255 AAATTAAA
1 AAATTAAA
18637263 AAATTTTGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATTAAATCAAATC
Found at i:18637488 original size:22 final size:22
Alignment explanation
Indices: 18637458--18637502 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
18637448 CCAGAAAAAG
** *
18637458 TAAAAATTTTTAATTTGATATT
1 TAAAAATTTACAATTTGAAATT
*
18637480 TAAAGATTTACAATTTGAAATT
1 TAAAAATTTACAATTTGAAATT
18637502 T
1 T
18637503 TAAGGGTTAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (22 bp):
TAAAAATTTACAATTTGAAATT
Found at i:18637644 original size:18 final size:18
Alignment explanation
Indices: 18637600--18637638 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
18637590 AAGATTTGCA
18637600 AAAGATTCAAAAATTCAC
1 AAAGATTCAAAAATTCAC
*
18637618 AAAGATTCAAGAATT-AC
1 AAAGATTCAAAAATTCAC
18637635 AAAG
1 AAAG
18637639 GTTTCAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.56, C:0.13, G:0.10, T:0.21
Consensus pattern (18 bp):
AAAGATTCAAAAATTCAC
Found at i:18637737 original size:18 final size:18
Alignment explanation
Indices: 18637696--18637740 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
18637686 TCATAAATGA
*
18637696 TTCAAGATTCTTAAGGAT
1 TTCAAGATTCATAAGGAT
*
18637714 TCCAAGATTCATATAGG-T
1 TTCAAGATTCATA-AGGAT
18637732 TTCAAGATT
1 TTCAAGATT
18637741 TGCAAAGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (18 bp):
TTCAAGATTCATAAGGAT
Found at i:18637891 original size:18 final size:18
Alignment explanation
Indices: 18637857--18637891 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18637847 TCTTATATGA
* *
18637857 TTCAAGATTCTCTAAGAT
1 TTCAAGATTCACAAAGAT
18637875 TTCAAGATTCACAAAGA
1 TTCAAGATTCACAAAGA
18637892 GTTGCAAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (18 bp):
TTCAAGATTCACAAAGAT
Found at i:18637935 original size:18 final size:18
Alignment explanation
Indices: 18637912--18637983 Score: 76
Period size: 18 Copynumber: 4.0 Consensus size: 18
18637902 TTCAAAAATT
*
18637912 TAAGATTCTTAAAGATTC
1 TAAGATTCATAAAGATTC
*
18637930 TAAGATACGCA-AAAG-TTC
1 TAAGAT--TCATAAAGATTC
*
18637948 TCAGATTCATAAAGATTC
1 TAAGATTCATAAAGATTC
*
18637966 TAAGTTTCATAAAGATTC
1 TAAGATTCATAAAGATTC
18637984 CCAAATTCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
16 2 0.05
17 4 0.09
18 33 0.75
19 4 0.09
20 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (18 bp):
TAAGATTCATAAAGATTC
Found at i:18637992 original size:18 final size:18
Alignment explanation
Indices: 18637870--18637984 Score: 53
Period size: 18 Copynumber: 6.4 Consensus size: 18
18637860 AAGATTCTCT
* *
18637870 AAGATTTCAAGATTCACA
1 AAGATTCCAAGATTCATA
* *
18637888 AAGAGTTGCAAAAGTTCA-A
1 AAGA-TTCCAAGA-TTCATA
* *
18637907 AA-ATT-TAAGATTCTTA
1 AAGATTCCAAGATTCATA
* *
18637923 AAGATTCTAAGATACGCA-A
1 AAGATTCCAAGAT--TCATA
18637942 AAG-TTCTC-AGATTCATA
1 AAGATTC-CAAGATTCATA
* *
18637959 AAGATTCTAAGTTTCATA
1 AAGATTCCAAGATTCATA
18637977 AAGATTCC
1 AAGATTCC
18637985 CAAATTCAAG
Statistics
Matches: 74, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
15 3 0.04
16 8 0.11
17 9 0.12
18 36 0.49
19 13 0.18
20 5 0.07
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (18 bp):
AAGATTCCAAGATTCATA
Found at i:18638001 original size:25 final size:25
Alignment explanation
Indices: 18637962--18638017 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
18637952 ATTCATAAAG
*
18637962 ATTCTAAGTTTCATAAAGATTCCCAA
1 ATTC-AAGATTCATAAAGATTCCCAA
* *
18637988 ATTCAAGATTCATAAAGATTCTCAT
1 ATTCAAGATTCATAAAGATTCCCAA
18638013 ATTCA
1 ATTCA
18638018 CAAAAGTCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (25 bp):
ATTCAAGATTCATAAAGATTCCCAA
Found at i:18638091 original size:18 final size:18
Alignment explanation
Indices: 18638031--18638093 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 18
18638021 AAGTCCCTAG
* *
18638031 ATTTACAAAGA-TTCTAA
1 ATTTGCAAAGACTTCAAA
* *
18638048 CTTTGCAAAGACTTGAAA
1 ATTTGCAAAGACTTCAAA
* * *
18638066 AATCGCAAAGACTTCAAG
1 ATTTGCAAAGACTTCAAA
18638084 ATTTGCAAAG
1 ATTTGCAAAG
18638094 GTTCACAATT
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
17 9 0.26
18 25 0.74
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (18 bp):
ATTTGCAAAGACTTCAAA
Found at i:18638154 original size:47 final size:47
Alignment explanation
Indices: 18638071--18638180 Score: 107
Period size: 47 Copynumber: 2.3 Consensus size: 47
18638061 TGAAAAATCG
* * * *
18638071 CAAAGACTTCAAGATTTGCAAAGGTTCACAATTTTTGTAAAGATTTA
1 CAAACACTTCAAGATTCGCAAAGGTTCACAAATTTTGCAAAGATTTA
* * * *
18638118 CAAACACTTTAAGATTCGCAAAGTTTC-CTAAATTTTGCAAATATTTG
1 CAAACACTTCAAGATTCGCAAAGGTTCAC-AAATTTTGCAAAGATTTA
*
18638165 CGAAA-ACTCCAAGATT
1 C-AAACACTTCAAGATT
18638181 TGTAATGATC
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
46 1 0.02
47 47 0.92
48 3 0.06
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (47 bp):
CAAACACTTCAAGATTCGCAAAGGTTCACAAATTTTGCAAAGATTTA
Found at i:18638277 original size:17 final size:17
Alignment explanation
Indices: 18638231--18638295 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 17
18638221 ATATATCAAT
* *
18638231 TTCGAAAGAATTTTTAGA
1 TTCGTAAGAA-TTTTATA
* * * *
18638249 TTCGCAAAAATTTTGTG
1 TTCGTAAGAATTTTATA
*
18638266 TTTGTAAGAATTTTATA
1 TTCGTAAGAATTTTATA
18638283 TTCGTAAGAATTT
1 TTCGTAAGAATTT
18638296 CAAGTTTGCA
Statistics
Matches: 36, Mismatches: 11, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
17 28 0.78
18 8 0.22
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.45
Consensus pattern (17 bp):
TTCGTAAGAATTTTATA
Done.