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 16 of 126
Found at i:3765828 original size:67 final size:64
Alignment explanation
Indices: 3765713--3765842 Score: 156
Period size: 67 Copynumber: 2.0 Consensus size: 64
3765703 ATTCAAATAT
* * * *
3765713 TTTAAATGGTATAAATATGTATATTATTTATTTTTTTCTTCTTTTTATTGTTTAATCTTTAAACC
1 TTTAAATGGTATAAATATGTATATAATTTATTTTATTATTCTTATTA-T-TTT-ATCTTTAAACC
3765778 AC
63 AC
*
3765780 TTTAAATGGTATAAATCT-TATATAATTTATTAGTTATTATT-TTATTATTTTATCTTTAAACCA
1 TTTAAATGGTATAAATATGTATATAATTTATT--TTATTATTCTTATTATTTTATCTTTAAACCA
3765843 TTATATATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
64 12 0.21
65 3 0.05
66 13 0.23
67 22 0.39
68 6 0.11
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (64 bp):
TTTAAATGGTATAAATATGTATATAATTTATTTTATTATTCTTATTATTTTATCTTTAAACCAC
Found at i:3766067 original size:18 final size:19
Alignment explanation
Indices: 3766025--3766069 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
3766015 AAACTTAGTT
3766025 AAAATATA-ATAAAACTTA
1 AAAATATATATAAAACTTA
* *
3766043 TATATATATATAAAAC-TA
1 AAAATATATATAAAACTTA
3766061 AAAATATAT
1 AAAATATAT
3766070 GATTACTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATATATATAAAACTTA
Found at i:3766333 original size:15 final size:15
Alignment explanation
Indices: 3766309--3766345 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3766299 AATAAAATAA
*
3766309 TTTAATTAATTTAAT
1 TTTAAATAATTTAAT
3766324 TTTAAATAATTTAAT
1 TTTAAATAATTTAAT
*
3766339 TTAAAAT
1 TTTAAAT
3766346 TAATCAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAAATAATTTAAT
Found at i:3775909 original size:8 final size:8
Alignment explanation
Indices: 3775898--3776028 Score: 113
Period size: 8 Copynumber: 16.1 Consensus size: 8
3775888 ACATACATAT
3775898 TATATGTA
1 TATATGTA
3775906 TATATGTA
1 TATATGTA
3775914 TATATGTA
1 TATATGTA
*
3775922 TGTATGTA
1 TATATGTA
3775930 TATATGTA
1 TATATGTA
3775938 TATATGCATAGA
1 TATATG--T--A
3775950 TATATGTA
1 TATATGTA
*
3775958 TGTATGTA
1 TATATGTA
* **
3775966 CATACATA
1 TATATGTA
*
3775974 CATATGTA
1 TATATGTA
*
3775982 GATATGTA
1 TATATGTA
*
3775990 TGTA--TA
1 TATATGTA
*
3775996 TATATATA
1 TATATGTA
*
3776004 TGTATGTA
1 TATATGTA
3776012 TATATGTA
1 TATATGTA
*
3776020 TGTATGTA
1 TATATGTA
3776028 T
1 T
3776029 GTATTATGTC
Statistics
Matches: 100, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
6 5 0.05
8 86 0.86
10 2 0.02
12 7 0.07
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (8 bp):
TATATGTA
Found at i:3775919 original size:16 final size:16
Alignment explanation
Indices: 3775898--3776037 Score: 133
Period size: 16 Copynumber: 8.7 Consensus size: 16
3775888 ACATACATAT
*
3775898 TATATGTATATATGTA
1 TATATGTATGTATGTA
3775914 TATATGTATGTATGTA
1 TATATGTATGTATGTA
*
3775930 TATATGTATATATGCATAGA
1 TATATGTATGTATG--T--A
3775950 TATATGTATGTATGTA
1 TATATGTATGTATGTA
* ** **
3775966 CATACATACATATGTA
1 TATATGTATGTATGTA
*
3775982 GATATGTATGTA--TA
1 TATATGTATGTATGTA
*
3775996 TATATATATGTATGTA
1 TATATGTATGTATGTA
3776012 TATATGTATGTATGTA
1 TATATGTATGTATGTA
*
3776028 TGTAT-TATGT
1 TATATGTATGT
3776038 CAAAACCTTT
Statistics
Matches: 101, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
14 12 0.12
15 5 0.05
16 68 0.67
18 2 0.02
20 14 0.14
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (16 bp):
TATATGTATGTATGTA
Found at i:3775925 original size:4 final size:4
Alignment explanation
Indices: 3775900--3776037 Score: 88
Period size: 4 Copynumber: 35.2 Consensus size: 4
3775890 ATACATATTA
* * * * *
3775900 TATG TATA TATG TATA TATG TATG TATG TATA TATG TATA TATG CATAG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT-G
* ** ** **
3775949 -ATA TATG TATG TATG TACA TACA TACA TATG TA-G ATATG TATG TA--
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG -TATG TATG TATG
* * *
3775994 TATA TATA TATG TATG TATA TATG TATG TATG TATG TAT- TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
3776038 CAAAACCTTT
Statistics
Matches: 109, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
2 2 0.02
3 4 0.04
4 101 0.93
5 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (4 bp):
TATG
Found at i:3786455 original size:14 final size:14
Alignment explanation
Indices: 3786433--3786493 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
3786423 TATTTGTAAT
*
3786433 CTTTCATATTTTAG
1 CTTTAATATTTTAG
* *
3786447 CTTTAATATGTTAT
1 CTTTAATATTTTAG
**
3786461 CTTTCCTATTTTAG
1 CTTTAATATTTTAG
* *
3786475 TTTTAAATATTTTAT
1 CTTT-AATATTTTAG
3786490 CTTT
1 CTTT
3786494 GACTAAAATC
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
14 24 0.71
15 10 0.29
ACGTcount: A:0.23, C:0.11, G:0.05, T:0.61
Consensus pattern (14 bp):
CTTTAATATTTTAG
Found at i:3786462 original size:28 final size:29
Alignment explanation
Indices: 3786431--3786493 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
3786421 ATTATTTGTA
3786431 ATCTTTCATATTTTAGCTTT-AATATGTT
1 ATCTTTCATATTTTAGCTTTAAATATGTT
* * *
3786459 ATCTTTCCTATTTTAGTTTTAAATATTTT
1 ATCTTTCATATTTTAGCTTTAAATATGTT
3786488 ATCTTT
1 ATCTTT
3786494 GACTAAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 18 0.58
29 13 0.42
ACGTcount: A:0.24, C:0.11, G:0.05, T:0.60
Consensus pattern (29 bp):
ATCTTTCATATTTTAGCTTTAAATATGTT
Found at i:3787498 original size:2 final size:2
Alignment explanation
Indices: 3787491--3787515 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3787481 ATGCATTTGA
3787491 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
3787516 CACGCACACA
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:3789604 original size:31 final size:30
Alignment explanation
Indices: 3789567--3789630 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
3789557 TTATTAGATA
3789567 TAAATTAA-AATTTAAAAACCTTATTTAAATG
1 TAAATTAATAA-TTAAAAA-CTTATTTAAATG
* *
3789598 TAAATTAATAATTAATAATTTATTTAAATG
1 TAAATTAATAATTAAAAACTTATTTAAATG
3789628 TAA
1 TAA
3789631 TAAAGTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 14 0.47
31 14 0.47
32 2 0.07
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (30 bp):
TAAATTAATAATTAAAAACTTATTTAAATG
Found at i:3792689 original size:19 final size:18
Alignment explanation
Indices: 3792641--3792690 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
3792631 TTAGATGAGT
*
3792641 AAAATAAAATAAGTAATAA
1 AAAAT-AAATAAGTAAGAA
* *
3792660 AAAAGATATAACGTAAGAA
1 AAAATAAATAA-GTAAGAA
3792679 AAAATAAATAAG
1 AAAATAAATAAG
3792691 ATGACTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.70, C:0.02, G:0.10, T:0.18
Consensus pattern (18 bp):
AAAATAAATAAGTAAGAA
Found at i:3796357 original size:2 final size:2
Alignment explanation
Indices: 3796350--3796383 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3796340 GTATAAGTGG
3796350 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3796384 TAGACCCTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3804104 original size:8 final size:8
Alignment explanation
Indices: 3804091--3804231 Score: 76
Period size: 8 Copynumber: 17.9 Consensus size: 8
3804081 ACATACATAT
3804091 TATATGTA
1 TATATGTA
*
3804099 TGTATGTA
1 TATATGTA
3804107 TATATGTA
1 TATATGTA
*
3804115 TATATATA
1 TATATGTA
3804123 TGCATA-G-A
1 T--ATATGTA
*
3804131 TATATGTC
1 TATATGTA
*
3804139 TGTATGTA
1 TATATGTA
* **
3804147 CATACATA
1 TATATGTA
* **
3804155 CATACATA
1 TATATGTA
3804163 TATA-GATA
1 TATATG-TA
*
3804171 TGTATGTA
1 TATATGTA
*
3804179 TATATATA
1 TATATGTA
3804187 TATATGTA
1 TATATGTA
*
3804195 TGTATGTA
1 TATATGTA
*
3804203 TGTATGTA
1 TATATGTA
*
3804211 TGTATGTA
1 TATATGTA
*
3804219 TGTA-GTA
1 TATATGTA
3804226 T-TATGT
1 TATATGT
3804232 CAAAACCTGT
Statistics
Matches: 108, Mismatches: 18, Indels: 15
0.77 0.13 0.11
Matches are distributed among these distances:
6 5 0.05
7 7 0.06
8 92 0.85
9 1 0.01
10 3 0.03
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (8 bp):
TATATGTA
Found at i:3804114 original size:12 final size:12
Alignment explanation
Indices: 3804097--3804231 Score: 78
Period size: 12 Copynumber: 11.4 Consensus size: 12
3804087 ATATTATATG
3804097 TATGTATGTATA
1 TATGTATGTATA
*
3804109 TATGTATATATA
1 TATGTATGTATA
*
3804121 TATGCATAG-ATA
1 TATGTAT-GTATA
* *
3804133 TATGTCTGTATG
1 TATGTATGTATA
** ** *
3804145 TACATACATACA
1 TATGTATGTATA
** * *
3804157 TACATATATAGA
1 TATGTATGTATA
3804169 TATGTATGTATA
1 TATGTATGTATA
* * *
3804181 TATATATATATG
1 TATGTATGTATA
*
3804193 TATGTATGTATG
1 TATGTATGTATA
*
3804205 TATGTATGTATG
1 TATGTATGTATA
3804217 TATGTA-GTAT-
1 TATGTATGTATA
3804227 TATGT
1 TATGT
3804232 CAAAACCTGT
Statistics
Matches: 97, Mismatches: 24, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
10 5 0.05
11 5 0.05
12 87 0.90
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (12 bp):
TATGTATGTATA
Found at i:3804176 original size:4 final size:4
Alignment explanation
Indices: 3804169--3804231 Score: 85
Period size: 4 Copynumber: 16.2 Consensus size: 4
3804159 CATATATAGA
* * *
3804169 TATG TATG TATA TATA TATA TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
3804217 TATG TA-G TAT- TATG T
1 TATG TATG TATG TATG T
3804232 CAAAACCTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
3 6 0.11
4 49 0.89
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:3804185 original size:20 final size:20
Alignment explanation
Indices: 3804160--3804219 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
3804150 ACATACATAC
3804160 ATATATAGATATGTATGTAT
1 ATATATAGATATGTATGTAT
*
3804180 ATATATATATATGTATGTAT
1 ATATATAGATATGTATGTAT
* *
3804200 GTATGTATG-TATGTATGTAT
1 ATATATA-GATATGTATGTAT
3804220 GTAGTATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (20 bp):
ATATATAGATATGTATGTAT
Found at i:3814654 original size:28 final size:29
Alignment explanation
Indices: 3814623--3814685 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
3814613 ATTATTTGTA
*
3814623 ATCTTTCATATTTTGGCTTT-AATATGTT
1 ATCTTTCATATTTTAGCTTTAAATATGTT
* * *
3814651 ATCTTTCCTATTTTAGTTTTAAATATTTT
1 ATCTTTCATATTTTAGCTTTAAATATGTT
3814680 ATCTTT
1 ATCTTT
3814686 GACTAAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 17 0.57
29 13 0.43
ACGTcount: A:0.22, C:0.11, G:0.06, T:0.60
Consensus pattern (29 bp):
ATCTTTCATATTTTAGCTTTAAATATGTT
Found at i:3815689 original size:2 final size:2
Alignment explanation
Indices: 3815682--3815708 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3815672 ATGCATTTGA
3815682 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 A
3815709 CATGCACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3817820 original size:30 final size:27
Alignment explanation
Indices: 3817722--3817820 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 27
3817712 TGTTAAAGGC
*
3817722 TTATTTAAGTATAAATTCAAGATTAAACAT
1 TTATTTAAATATAAATT-AA-ATTAAA-AT
* *
3817752 TTATTTAGATATAAATTAAAATTTAAAAAC
1 TTATTTAAATATAAATT-AAA-TT-AAAAT
3817782 TTATTTAAATATAAATTGATAATTAATAAT
1 TTATTTAAATATAAATT-A-AATTAA-AAT
3817812 TTATTTAAA
1 TTATTTAAA
3817821 GGTAATGAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
29 3 0.05
30 50 0.86
31 5 0.09
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (27 bp):
TTATTTAAATATAAATTAAATTAAAAT
Found at i:3818264 original size:22 final size:22
Alignment explanation
Indices: 3818239--3818297 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
3818229 TTTGTTTCTA
*
3818239 TTTTTTTTATTTTTCATTTATT
1 TTTTTTTTATTTTTCATATATT
* *
3818261 TTTTTTTAATTTTTTATATATT
1 TTTTTTTTATTTTTCATATATT
3818283 TTATTTTATTATTTT
1 TT-TTTT-TTATTTT
3818298 AATGGGACCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 21 0.68
23 4 0.13
24 6 0.19
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTTTTATTTTTCATATATT
Found at i:3818272 original size:11 final size:10
Alignment explanation
Indices: 3818239--3818297 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
3818229 TTTGTTTCTA
3818239 TTTTTTTTAT
1 TTTTTTTTAT
*
3818249 TTTTCATTTAT
1 TTTT-TTTTAT
3818260 TTTTTTTTAAT
1 TTTTTTTT-AT
*
3818271 TTTTTATATAT
1 TTTTT-TTTAT
*
3818282 TTTATTTTAT
1 TTTTTTTTAT
3818292 TATTTT
1 T-TTTT
3818298 AATGGGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
10 12 0.31
11 25 0.64
12 2 0.05
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:3820889 original size:19 final size:18
Alignment explanation
Indices: 3820841--3820890 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
3820831 TTAGATGAGT
*
3820841 AAAATAAAATAAGTAATAA
1 AAAAT-AAATAAGTAAGAA
* *
3820860 AAAAGATATAACGTAAGAA
1 AAAATAAATAA-GTAAGAA
3820879 AAAATAAATAAG
1 AAAATAAATAAG
3820891 ATGACTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.70, C:0.02, G:0.10, T:0.18
Consensus pattern (18 bp):
AAAATAAATAAGTAAGAA
Found at i:3821576 original size:58 final size:57
Alignment explanation
Indices: 3821438--3821635 Score: 166
Period size: 59 Copynumber: 3.4 Consensus size: 57
3821428 CTATTACAGC
* * *
3821438 AACTACATTTTTTAAAATGGAAACATAGTCATTAATTGAACAAAAAATTTTATTGTATAAA
1 AACTACATTTTTT-AAATGGAAACATAGTCTTTATTTGAA-AAAAAA--TTATTGTACAAA
* * * * * *
3821499 GACT--AGTTTTCAAAGGGAAACATAGCCTTTTTTTGAAAAAAAATTATTGTACAAA
1 AACTACATTTTTTAAATGGAAACATAGTCTTTATTTGAAAAAAAATTATTGTACAAA
* * * *
3821554 AACTACATTTTTTAAATTGGAAATATGGTCTTTAATTTAAAAAAAAAGTATTGTACAAA
1 AACTACATTTTTTAAA-TGGAAACATAGTCTTT-ATTTGAAAAAAAATTATTGTACAAA
* * * *
3821613 GACAACGTTTCTTAAAGTGGAAA
1 AACTACATTTTTTAAA-TGGAAA
3821636 TGTGGTCTTT
Statistics
Matches: 109, Mismatches: 24, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
55 14 0.13
57 14 0.13
58 33 0.30
59 45 0.41
61 3 0.03
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34
Consensus pattern (57 bp):
AACTACATTTTTTAAATGGAAACATAGTCTTTATTTGAAAAAAAATTATTGTACAAA
Found at i:3821606 original size:59 final size:59
Alignment explanation
Indices: 3821534--3821649 Score: 169
Period size: 59 Copynumber: 2.0 Consensus size: 59
3821524 CCTTTTTTTG
* * * *
3821534 AAAAAAAATTATTGTACAAAAACTACATTTTTTAAATTGGAAATATGGTCTTTAATTTA
1 AAAAAAAAGTATTGTACAAAAACAACATTTCTTAAAGTGGAAATATGGTCTTTAATTTA
* * *
3821593 AAAAAAAAGTATTGTACAAAGACAACGTTTCTTAAAGTGGAAATGTGGTCTTTAATT
1 AAAAAAAAGTATTGTACAAAAACAACATTTCTTAAAGTGGAAATATGGTCTTTAATT
3821650 GTACATAGCC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (59 bp):
AAAAAAAAGTATTGTACAAAAACAACATTTCTTAAAGTGGAAATATGGTCTTTAATTTA
Found at i:3826545 original size:28 final size:29
Alignment explanation
Indices: 3826477--3826552 Score: 109
Period size: 28 Copynumber: 2.6 Consensus size: 29
3826467 TATATTTTTA
*
3826477 TTATATCTGAATAAATTTTAAATTTTAAAT
1 TTATATCTAAATAAA-TTTAAATTTTAAAT
*
3826507 TTATATCTAAATAAATTTAACTTTT-AAT
1 TTATATCTAAATAAATTTAAATTTTAAAT
*
3826535 TTATATTTAAATAAATTT
1 TTATATCTAAATAAATTT
3826553 GATATAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 20 0.47
29 9 0.21
30 14 0.33
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (29 bp):
TTATATCTAAATAAATTTAAATTTTAAAT
Found at i:3832910 original size:21 final size:22
Alignment explanation
Indices: 3832880--3832920 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3832870 AACCTAGAAA
3832880 AAAAAGAAAAGAGAAAAAAAGC
1 AAAAAGAAAAGAGAAAAAAAGC
*
3832902 AAAAA-AAAATAGAAAAAAA
1 AAAAAGAAAAGAGAAAAAAA
3832921 TGAGAGAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAGAAAAGAGAAAAAAAGC
Found at i:3840829 original size:13 final size:13
Alignment explanation
Indices: 3840811--3840838 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3840801 AACCCACACT
3840811 TTAATATTGCATA
1 TTAATATTGCATA
3840824 TTAATATTGCATA
1 TTAATATTGCATA
3840837 TT
1 TT
3840839 TTTATGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (13 bp):
TTAATATTGCATA
Found at i:3846567 original size:22 final size:22
Alignment explanation
Indices: 3846542--3846585 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3846532 ATTTAATTCA
3846542 TATATAAATTAAAAA-TAAAAAT
1 TATAT-AATTAAAAATTAAAAAT
*
3846564 TATATATTTAAAAATTAAAAAT
1 TATATAATTAAAAATTAAAAAT
3846586 AAAAACTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TATATAATTAAAAATTAAAAAT
Found at i:3857318 original size:23 final size:23
Alignment explanation
Indices: 3857271--3857427 Score: 85
Period size: 23 Copynumber: 6.8 Consensus size: 23
3857261 CCCAATGAAC
*
3857271 TTTTATTTTTA-TTTTCATACATAT
1 TTTTATTTTTATTTTTTAT-C-TAT
3857295 TTTTATTTTTATTTTTTATCTAT
1 TTTTATTTTTATTTTTTATCTAT
** * **
3857318 TAATATTTTTATTATTTATCTGC
1 TTTTATTTTTATTTTTTATCTAT
*
3857341 TTTTATTTTTCA-TTATTAT-TAT
1 TTTTATTTTT-ATTTTTTATCTAT
*
3857363 TTATCTATTTCTT-TTATTTATCTA-
1 TT-T-TATTT-TTATTTTTTATCTAT
* *
3857387 -ATTATTTTT-TTTGTTATCTAT
1 TTTTATTTTTATTTTTTATCTAT
** *
3857408 TAATATATTTATCTTTTTAT
1 TTTTATTTTTAT-TTTTTAT
3857428 TTTGATTAAT
Statistics
Matches: 102, Mismatches: 20, Indels: 22
0.71 0.14 0.15
Matches are distributed among these distances:
20 11 0.11
21 5 0.05
22 11 0.11
23 36 0.35
24 29 0.28
25 10 0.10
ACGTcount: A:0.23, C:0.07, G:0.01, T:0.69
Consensus pattern (23 bp):
TTTTATTTTTATTTTTTATCTAT
Found at i:3857394 original size:17 final size:17
Alignment explanation
Indices: 3857352--3857394 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
3857342 TTTATTTTTC
3857352 ATTATTATTATTTATCTA
1 ATTATT-TTATTTATCTA
* *
3857370 TTTCTTTTATTTATCTA
1 ATTATTTTATTTATCTA
3857387 ATTATTTT
1 ATTATTTT
3857395 TTTTGTTATC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTATTTTATTTATCTA
Found at i:3857397 original size:20 final size:21
Alignment explanation
Indices: 3857368--3857406 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
3857358 ATTATTTATC
3857368 TATTTCTTTTAT-TTATCTAAT
1 TATTTCTTTT-TGTTATCTAAT
3857389 TATTT-TTTTTGTTATCTA
1 TATTTCTTTTTGTTATCTA
3857407 TTAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.06
20 11 0.65
21 5 0.29
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.69
Consensus pattern (21 bp):
TATTTCTTTTTGTTATCTAAT
Found at i:3857423 original size:47 final size:46
Alignment explanation
Indices: 3857297--3857429 Score: 107
Period size: 45 Copynumber: 2.9 Consensus size: 46
3857287 ATACATATTT
* * * *
3857297 TTATTTTTATTTTTTATCTATTAATATTTTTAT-TATTTATCTGCTT
1 TTATTTTTATTTATTATCTATTAATATATTTATCT-TTTATTTGCTA
* * *
3857343 TTATTTTTCA-TTATTAT-TATTTATCTA-TT-TCTTTTATTTATCTAA
1 TTATTTTT-ATTTATTATCTATTAATATATTTATCTTTTATTT-GCT-A
*
3857388 TTATTTTT-TTTGTTATCTATTAATATATTTATCTTTTTATTT
1 TTATTTTTATTTATTATCTATTAATATATTTATC-TTTTATTT
3857430 TGATTAATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
43 7 0.10
44 11 0.16
45 23 0.34
46 16 0.24
47 3 0.04
48 8 0.12
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.69
Consensus pattern (46 bp):
TTATTTTTATTTATTATCTATTAATATATTTATCTTTTATTTGCTA
Found at i:3857971 original size:15 final size:17
Alignment explanation
Indices: 3857949--3857992 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
3857939 TTCGCGGTTT
3857949 AGAAAGAAGGCAGAG-G
1 AGAAAGAAGGCAGAGAG
*
3857965 A-AAAGAAGGGAAGAGAG
1 AGAAAGAA-GGCAGAGAG
3857982 AGAAAGAAGGC
1 AGAAAGAAGGC
3857993 TCGATCTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 6 0.26
16 7 0.30
17 4 0.17
18 6 0.26
ACGTcount: A:0.55, C:0.05, G:0.41, T:0.00
Consensus pattern (17 bp):
AGAAAGAAGGCAGAGAG
Found at i:3857987 original size:18 final size:17
Alignment explanation
Indices: 3857949--3857991 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
3857939 TTCGCGGTTT
*
3857949 AGAAAGAA-GGCAGAGG
1 AGAAAGAAGGGAAGAGG
3857965 A-AAAGAAGGGAAGAGAG
1 AGAAAGAAGGGAAGAG-G
3857982 AGAAAGAAGG
1 AGAAAGAAGG
3857992 CTCGATCTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 6 0.26
16 7 0.30
17 2 0.09
18 8 0.35
ACGTcount: A:0.56, C:0.02, G:0.42, T:0.00
Consensus pattern (17 bp):
AGAAAGAAGGGAAGAGG
Found at i:3858252 original size:18 final size:18
Alignment explanation
Indices: 3858240--3858285 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
3858230 TTTTTCATTT
3858240 TTTATTTTATTTTATATA
1 TTTATTTTATTTTATATA
3858258 TTTA-TTTATTTTAT-TA
1 TTTATTTTATTTTATATA
3858274 -TTATTATTATTT
1 TTTATT-TTATTT
3858286 ATTGATTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 3 0.12
16 3 0.12
17 16 0.62
18 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTTATTTTATATA
Found at i:3858252 original size:22 final size:22
Alignment explanation
Indices: 3858236--3858288 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
3858226 TTTTTTTTTC
3858236 ATTT-TTTATTTTATTTTATAT
1 ATTTATTTATTTTATTTTATAT
3858257 ATTTATTTATTTTATTATTAT-T
1 ATTTATTTATTTTATT-TTATAT
3858279 A-TTATTTATT
1 ATTTATTTATT
3858289 GATTAGATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 13 0.43
22 13 0.43
23 4 0.13
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (22 bp):
ATTTATTTATTTTATTTTATAT
Found at i:3858264 original size:25 final size:25
Alignment explanation
Indices: 3858236--3858288 Score: 78
Period size: 22 Copynumber: 2.3 Consensus size: 25
3858226 TTTTTTTTTC
3858236 ATTT-TTTATTTTATT-TTA-TA-T
1 ATTTATTTATTTTATTATTATTATT
3858257 ATTTATTTATTTTATTATTATTATT
1 ATTTATTTATTTTATTATTATTATT
3858282 ATTTATT
1 ATTTATT
3858289 GATTAGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.14
22 11 0.39
23 3 0.11
24 2 0.07
25 8 0.29
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (25 bp):
ATTTATTTATTTTATTATTATTATT
Found at i:3858298 original size:25 final size:25
Alignment explanation
Indices: 3858246--3858298 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
3858236 ATTTTTTATT
* **
3858246 TTATTTTATATATTTATTTATTTTA
1 TTATTTTATATATTTATTGATTAGA
3858271 TTATTATTAT-TATTTATTGATTAGA
1 TTATT-TTATATATTTATTGATTAGA
3858296 TTA
1 TTA
3858299 GAATTGTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (25 bp):
TTATTTTATATATTTATTGATTAGA
Found at i:3858408 original size:59 final size:57
Alignment explanation
Indices: 3858343--3858637 Score: 348
Period size: 58 Copynumber: 5.1 Consensus size: 57
3858333 TATTTTATTA
*
3858343 TTTTCTTTAAAATAAGCTTTCAAAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAAT
1 TTTTCTTGAAAATAAGCTTTC-AAAAA-ATATTTTTGAGAAAAAGTTGAAAGTATCAAT
* ** *
3858402 TTTTCTTAAAAATAAGCTTTCTAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTGAAAATAAGCTTTC-AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAAT
* * *
3858460 TTTCCTTGAAAATAAGCTTTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTACCAAT
1 TTTTCTTGAAAATAAGCTTTC-AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAAT
* * *
3858518 TTTTCTT-AGAAACAAGTTTTC-AAAAGTGAATTTTTGAGGAAAAA-TTGAAAGTATCAAT
1 TTTTCTTGA-AAATAAGCTTTCAAAAAAT--ATTTTTGA-GAAAAAGTTGAAAGTATCAAT
* *
3858576 TTTTCTCGAAATTAAAAG-TTTCAAAAAATA-TTTTGAGAAAAAGTTGAAAGTATCAAT
1 TTTTCTTGAAA--ATAAGCTTTCAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAAT
3858633 TTTTC
1 TTTTC
3858638 CTGTACAAAA
Statistics
Matches: 208, Mismatches: 19, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
56 11 0.05
57 26 0.12
58 127 0.61
59 35 0.17
60 9 0.04
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (57 bp):
TTTTCTTGAAAATAAGCTTTCAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAAT
Found at i:3858491 original size:116 final size:114
Alignment explanation
Indices: 3858342--3858637 Score: 402
Period size: 116 Copynumber: 2.6 Consensus size: 114
3858332 TTATTTTATT
*
3858342 ATTTTCTTTAAAATAAGCTTTCAAAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTC
1 ATTTTCTTGAAAATAAGCTTTC-AAAAA-ATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTC
* *
3858407 TTAAAAATAAGCTTTCTAAAAAG-G-ATTTTTGAGGAAAAGTTGAAAGTATCA
64 TTAAAAACAAG-TTT-TAAAAAGTGAATTTTTGAGGAAAAATTGAAAGTATCA
* *
3858458 ATTTTCCTTGAAAATAAGCTTTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTACCAATTTTTC
1 ATTTT-CTTGAAAATAAGCTTTC-AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTC
* *
3858523 TTAGAAACAAGTTTTCAAAAGTGAATTTTTGAGGAAAAATTGAAAGTATCA
64 TTAAAAACAAGTTTTAAAAAGTGAATTTTTGAGGAAAAATTGAAAGTATCA
* *
3858574 ATTTTTCTCGAAATTAAAAG-TTTCAAAAAATA-TTTTGAGAAAAAGTTGAAAGTATCAATTTTT
1 A-TTTTCTTGAAA--ATAAGCTTTCAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTT
3858637 C
63 C
3858638 CTGTACAAAA
Statistics
Matches: 162, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
114 6 0.04
115 34 0.21
116 89 0.55
117 29 0.18
118 4 0.02
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (114 bp):
ATTTTCTTGAAAATAAGCTTTCAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
AAAAACAAGTTTTAAAAAGTGAATTTTTGAGGAAAAATTGAAAGTATCA
Found at i:3860297 original size:11 final size:11
Alignment explanation
Indices: 3860281--3860305 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3860271 AATGAACTGA
3860281 AAGGAAAAGAT
1 AAGGAAAAGAT
3860292 AAGGAAAAGAT
1 AAGGAAAAGAT
3860303 AAG
1 AAG
3860306 AGTGAAAACT
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:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (11 bp):
AAGGAAAAGAT
Found at i:3862595 original size:15 final size:14
Alignment explanation
Indices: 3862568--3862611 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
3862558 ACAATGGATG
3862568 AAAAATGAGAAAAA
1 AAAAATGAGAAAAA
*
3862582 AAAAGATGATAAAAA
1 AAAA-ATGAGAAAAA
3862597 AAAAA-GAAGAAAAA
1 AAAAATG-AGAAAAA
3862611 A
1 A
3862612 TGAGAAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 1 0.04
14 12 0.46
15 13 0.50
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (14 bp):
AAAAATGAGAAAAA
Found at i:3862611 original size:16 final size:16
Alignment explanation
Indices: 3862577--3862611 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3862567 GAAAAATGAG
* *
3862577 AAAAAAAAAGATGATA
1 AAAAAAAAAGAAGAAA
3862593 AAAAAAAAAGAAGAAA
1 AAAAAAAAAGAAGAAA
3862609 AAA
1 AAA
3862612 TGAGAAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (16 bp):
AAAAAAAAAGAAGAAA
Found at i:3862617 original size:13 final size:12
Alignment explanation
Indices: 3862568--3862619 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
3862558 ACAATGGATG
*
3862568 AAAAATGAGAAA
1 AAAAAAGAGAAA
3862580 AAAAAAGATGATAA
1 AAAAAAGA-GA-AA
*
3862594 AAAAAAAAGAAGA
1 AAAAAAGAGAA-A
*
3862607 AAAAATGAGAAA
1 AAAAAAGAGAAA
3862619 A
1 A
3862620 TGGAAAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 10 0.30
13 14 0.42
14 9 0.27
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAAAAGAGAAA
Found at i:3864390 original size:41 final size:40
Alignment explanation
Indices: 3864313--3864412 Score: 155
Period size: 41 Copynumber: 2.5 Consensus size: 40
3864303 ATTGTCAATG
*
3864313 AGCAATTTACTTTTCAAAATGTGGTGCCTCTGTTTAGAGA
1 AGCAATTTACTTTTCAAAATGTGGTGCCTCTATTTAGAGA
* *
3864353 AGCAATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAGAGG
1 AGCAATTTACTTTTCAAA-ATGTGGTGCCTCTATTTAGAGA
*
3864394 AGCAATTTACTTTCCAAAA
1 AGCAATTTACTTTTCAAAA
3864413 GTTAAGCCTC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 18 0.33
41 36 0.67
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (40 bp):
AGCAATTTACTTTTCAAAATGTGGTGCCTCTATTTAGAGA
Found at i:3864433 original size:39 final size:39
Alignment explanation
Indices: 3864312--3864535 Score: 150
Period size: 41 Copynumber: 5.5 Consensus size: 39
3864302 GATTGTCAAT
*** *
3864312 GAGCAATTTACTTTTCAAAATGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCAAAA-GTTAAGCCTCTGATTAGAG
* **
3864352 AAGCAATTTACTTTTC-AAAGTTGTGGTGCCTCT-ATTTAGAG
1 GAGCAATTTACTTTTCAAAAG-T-T-AAGCCTCTGA-TTAGAG
*
3864393 GAGCAATTTACTTTCCAAAAGTTAAGCCTCTGATTAGAG
1 GAGCAATTTACTTTTCAAAAGTTAAGCCTCTGATTAGAG
* * * *
3864432 GAGCCATTTGCTTTTCAAAGTTGTTAAGCCTATGATTAGAG
1 GAGCAATTTACTTTTCAAA--AGTTAAGCCTCTGATTAGAG
* * * *
3864473 GAGTC-GTTTATTTTTTCAAAGTTGTTGAGCCTCTGATTAGAG
1 GAG-CAATTTA-CTTTTCAAA--AGTTAAGCCTCTGATTAGAG
*
3864515 GAGTC-ATTTATTTTTCCAAAA
1 GAG-CAATTTACTTTT-CAAAA
3864536 TTGTTGAACT
Statistics
Matches: 154, Mismatches: 19, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
38 1 0.01
39 32 0.21
40 17 0.11
41 58 0.38
42 46 0.30
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (39 bp):
GAGCAATTTACTTTTCAAAAGTTAAGCCTCTGATTAGAG
Found at i:3864468 original size:41 final size:41
Alignment explanation
Indices: 3864312--3864693 Score: 238
Period size: 44 Copynumber: 9.1 Consensus size: 41
3864302 GATTGTCAAT
* * * *
3864312 GAGCAATTTACTTTTCAAAATGTGGT--GCCTCTGTTTAGAG
1 GAGCCATTTACTTTTCAAAGT-TGTTAAGCCTCTGATTAGAG
* * ***
3864352 AAGCAATTTACTTTTCAAAGTTGTGGTGCCTCT-ATTTAGAG
1 GAGCCATTTACTTTTCAAAGTTGTTAAGCCTCTGA-TTAGAG
* * *
3864393 GAGCAATTTACTTTCCAAA--AGTTAAGCCTCTGATTAGAG
1 GAGCCATTTACTTTTCAAAGTTGTTAAGCCTCTGATTAGAG
* *
3864432 GAGCCATTTGCTTTTCAAAGTTGTTAAGCCTATGATTAGAG
1 GAGCCATTTACTTTTCAAAGTTGTTAAGCCTCTGATTAGAG
* * * *
3864473 GAGTCGTTTATTTTTTCAAAGTTGTTGAGCCTCTGATTAGAG
1 GAGCCATTTA-CTTTTCAAAGTTGTTAAGCCTCTGATTAGAG
* * * * *
3864515 GAGTCATTTATTTTTCCAAAATTGTTGAA-CTTCTGATTAGAT
1 GAGCCATTTACTTTT-CAAAGTTGTT-AAGCCTCTGATTAGAG
* * * *
3864557 GAGCCTTGTTGATTTTTCAAAAGTCGTTGAA-CCTCTAATTAGAG
1 GAGCCAT-TT-ACTTTTC-AAAGTTGTT-AAGCCTCTGATTAGAG
* * ** *
3864601 GAGCCTTGTTTATTTTTCAAAAGTCATTGAGCCTCTGATTAGAG
1 GAGCC--ATTTACTTTTC-AAAGTTGTTAAGCCTCTGATTAGAG
** * * *
3864645 GAGCTTTGTTTATGTTTCTCAAAGTTGTTAAGCCTCTGCTTAGAA
1 GAGC--CATTTA-CTTT-TCAAAGTTGTTAAGCCTCTGATTAGAG
3864690 GAGC
1 GAGC
3864694 TTTGATCAAA
Statistics
Matches: 278, Mismatches: 45, Indels: 33
0.78 0.13 0.09
Matches are distributed among these distances:
39 32 0.12
40 20 0.07
41 59 0.21
42 62 0.22
43 5 0.02
44 68 0.24
45 29 0.10
46 3 0.01
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.38
Consensus pattern (41 bp):
GAGCCATTTACTTTTCAAAGTTGTTAAGCCTCTGATTAGAG
Found at i:3864471 original size:80 final size:81
Alignment explanation
Indices: 3864312--3864475 Score: 197
Period size: 80 Copynumber: 2.0 Consensus size: 81
3864302 GATTGTCAAT
* ** *
3864312 GAGCAATTTACTTTTCAAAATGTGGTGCCTCTGTTTAGAGAAGCAATTTACTTTTCAAAGTTGTG
1 GAGCAATTTACTTTCCAAAATGTGAAGCCTCTGATTAGAGAAGCAATTTACTTTTCAAAGTTGTG
** *
3864377 GTGCCTCTATTTAGAG
66 AAGCCTATATTTAGAG
* * * * *
3864393 GAGCAATTTACTTTCCAAAA-GTTAAGCCTCTGATTAGAGGAGCCATTTGCTTTTCAAAGTTGTT
1 GAGCAATTTACTTTCCAAAATGTGAAGCCTCTGATTAGAGAAGCAATTTACTTTTCAAAGTTGTG
3864457 AAGCCTATGA-TTAGAG
66 AAGCCTAT-ATTTAGAG
3864473 GAG
1 GAG
3864476 TCGTTTATTT
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
80 50 0.71
81 20 0.29
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.35
Consensus pattern (81 bp):
GAGCAATTTACTTTCCAAAATGTGAAGCCTCTGATTAGAGAAGCAATTTACTTTTCAAAGTTGTG
AAGCCTATATTTAGAG
Found at i:3864697 original size:45 final size:42
Alignment explanation
Indices: 3864413--3864695 Score: 252
Period size: 44 Copynumber: 6.6 Consensus size: 42
3864403 CTTTCCAAAA
** **
3864413 GTTAAGCCTCTGATTAGAGGAGC-CATTTGCTTTTCAAAGTT
1 GTTAAGCCTCTGATTAGAGGAGCTTGTTTATTTTTCAAAGTT
* *
3864454 GTTAAGCCTATGATTAGAGGAG-TCGTTTATTTTTTCAAAGTT
1 GTTAAGCCTCTGATTAGAGGAGCTTGTTTA-TTTTTCAAAGTT
* ** *
3864496 GTTGAGCCTCTGATTAGAGGAG-TCATTTATTTTTCCAAAATT
1 GTTAAGCCTCTGATTAGAGGAGCTTGTTTATTTTT-CAAAGTT
* * * *
3864538 GTTGAA-CTTCTGATTAGATGAGCCTTGTTGATTTTTCAAAAGTC
1 GTT-AAGCCTCTGATTAGAGGAG-CTTGTTTATTTTTC-AAAGTT
* *
3864582 GTTGAA-CCTCTAATTAGAGGAGCCTTGTTTATTTTTCAAAAGTC
1 GTT-AAGCCTCTGATTAGAGGAG-CTTGTTTATTTTTC-AAAGTT
* *
3864626 ATTGAGCCTCTGATTAGAGGAGCTTTGTTTATGTTTCTCAAAGTT
1 GTTAAGCCTCTGATTAGAGGAGC-TTGTTTAT-TTT-TCAAAGTT
* *
3864671 GTTAAGCCTCTGCTTAGAAGAGCTT
1 GTTAAGCCTCTGATTAGAGGAGCTT
3864696 TGATCAAAAT
Statistics
Matches: 203, Mismatches: 28, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
41 30 0.15
42 60 0.30
43 4 0.02
44 80 0.39
45 27 0.13
46 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (42 bp):
GTTAAGCCTCTGATTAGAGGAGCTTGTTTATTTTTCAAAGTT
Found at i:3864699 original size:130 final size:126
Alignment explanation
Indices: 3864379--3864693 Score: 306
Period size: 130 Copynumber: 2.5 Consensus size: 126
3864369 AAGTTGTGGT
* *
3864379 GCCTCT-ATTTAGAGGAG-CAATTTA-CTTTCCAAAA--GTTAAGCCTCTGATTAGAGGAGCCAT
1 GCCTCTGA-TTAGAGGAGTC-ATTTATGTTTCCAAAATTGTTAAGCCTCTGATTAGAAGAGCCAT
* * * **
3864439 TTG-CTTTTCAAAGTTGTTAAGCCTATGATTAGAGGAGTCGTTTATTTTTTCAAAGTTGTTGA
64 TTGATTTTTCAAAGTCGTTAAGCCTATAATTAGAGGAGTCGTTTATTTTTTCAAAGTCATTGA
* * * *
3864501 GCCTCTGATTAGAGGAGTCATTTATTTTTCCAAAATTGTTGAA-CTTCTGATTAGATGAGCCTTG
1 GCCTCTGATTAGAGGAGTCATTTATGTTTCCAAAATTGTT-AAGCCTCTGATTAGAAGAGCCAT-
* *
3864565 TTGATTTTTCAAAAGTCGTTGAA-CCTCTAATTAGAGGAGCCTTGTTTA-TTTTTCAAAAGTCAT
64 TTGATTTTTC-AAAGTCGTT-AAGCCTATAATTAGAGGAG--TCGTTTATTTTTTC-AAAGTCAT
3864628 TGA
124 TGA
** * *
3864631 GCCTCTGATTAGAGGAGCTTTGTTTATGTTTCTCAAAGTTGTTAAGCCTCTGCTTAGAAGAGC
1 GCCTCTGATTAGAGGAG--TCATTTATGTTTC-CAAAATTGTTAAGCCTCTGATTAGAAGAGC
3864694 TTTGATCAAA
Statistics
Matches: 158, Mismatches: 18, Indels: 23
0.79 0.09 0.12
Matches are distributed among these distances:
122 20 0.13
123 11 0.07
125 20 0.13
126 5 0.03
127 5 0.03
128 22 0.14
129 8 0.05
130 32 0.20
132 12 0.08
133 23 0.15
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.38
Consensus pattern (126 bp):
GCCTCTGATTAGAGGAGTCATTTATGTTTCCAAAATTGTTAAGCCTCTGATTAGAAGAGCCATTT
GATTTTTCAAAGTCGTTAAGCCTATAATTAGAGGAGTCGTTTATTTTTTCAAAGTCATTGA
Found at i:3864975 original size:24 final size:24
Alignment explanation
Indices: 3864927--3865044 Score: 87
Period size: 24 Copynumber: 4.8 Consensus size: 24
3864917 CCCAATGGGC
* ** *
3864927 TTTTATTTTTACTTTCATATATAT
1 TTTTATTTTTATTTTTTTATCTAT
3864951 TTTTATTTTTATTTTTTTATCTAT
1 TTTTATTTTTATTTTTTTATCTAT
** * *
3864975 TAATATTTTTA-TTATTTATCTAC
1 TTTTATTTTTATTTTTTTATCTAT
* *
3864998 TTTTATTATTTATTATATTAT-TAT
1 TTTTATT-TTTATTTTTTTATCTAT
*
3865022 TATTATTTATCTATTTCTTTTAT
1 TTTTATTT-T-TATTT-TTTTAT
3865045 TTATCTAATT
Statistics
Matches: 72, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
23 16 0.22
24 42 0.58
25 9 0.12
26 5 0.07
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTATTTTTATTTTTTTATCTAT
Found at i:3865001 original size:17 final size:16
Alignment explanation
Indices: 3864951--3865092 Score: 69
Period size: 17 Copynumber: 8.4 Consensus size: 16
3864941 TCATATATAT
*
3864951 TTTTATT-TTTAT-TT
1 TTTTATTATTTATCTA
* *
3864965 TTTTATCTATTAATAT-
1 TTTTAT-TATTTATCTA
3864981 TTTTATTATTTATCTA
1 TTTTATTATTTATCTA
*
3864997 CTTTTATTATTTATTATATTA
1 -TTTTATTA--T-TTAT-CTA
3865018 TTATTATTATTTATCTA
1 TT-TTATTATTTATCTA
*
3865035 TTTCTTTTATTTATCTAA
1 TTT-TATTATTTATCT-A
* *
3865053 TTATTTTTTTGTTATCTA
1 TT-TTATTAT-TTATCTA
*
3865071 -TTAATATATTTATCT-
1 TTTTAT-TATTTATCTA
3865086 TTTTATT
1 TTTTATT
3865093 TTGATTAATT
Statistics
Matches: 101, Mismatches: 11, Indels: 31
0.71 0.08 0.22
Matches are distributed among these distances:
14 6 0.06
15 9 0.09
16 23 0.23
17 27 0.27
18 13 0.13
19 9 0.09
20 6 0.06
21 8 0.08
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.69
Consensus pattern (16 bp):
TTTTATTATTTATCTA
Found at i:3865006 original size:3 final size:3
Alignment explanation
Indices: 3864948--3865028 Score: 51
Period size: 3 Copynumber: 26.3 Consensus size: 3
3864938 CTTTCATATA
* * * * *
3864948 TAT TTT TAT TTT TAT T-T TTT TAT CTAT TAA TAT TTT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA-T TAT
3864994 CTACT T-T TAT TATT TAT TA- TAT TAT TAT TAT TAT T
1 -TA-T TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
3865029 TATCTATTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
2 6 0.10
3 42 0.69
4 12 0.20
5 1 0.02
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:3865034 original size:38 final size:36
Alignment explanation
Indices: 3864948--3865072 Score: 127
Period size: 38 Copynumber: 3.5 Consensus size: 36
3864938 CTTTCATATA
* *
3864948 TATTTTTATTT-T-TATTTTTTTATCTATTAA-TAT
1 TATTATTATTTATCTATTTTTTTATTTATTAATTAT
* *
3864981 TTTTATTATTTATCTACTTTTATTATTTATTATATTAT
1 TATTATTATTTATCTA-TTTTTTTATTTATTA-ATTAT
3865019 TATTATTATTTATCTATTTCTTTTATTTATCTAATTAT
1 TATTATTATTTATCTATTT-TTTTATTTAT-TAATTAT
3865057 T-TT-TT-TGTTATCTATT
1 TATTATTAT-TTATCTATT
3865073 AATATATTTA
Statistics
Matches: 78, Mismatches: 6, Indels: 13
0.80 0.06 0.13
Matches are distributed among these distances:
33 9 0.12
34 1 0.01
35 3 0.04
36 24 0.31
37 6 0.08
38 33 0.42
39 2 0.03
ACGTcount: A:0.24, C:0.06, G:0.01, T:0.70
Consensus pattern (36 bp):
TATTATTATTTATCTATTTTTTTATTTATTAATTAT
Found at i:3865404 original size:18 final size:20
Alignment explanation
Indices: 3865362--3865411 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 20
3865352 TAGATTTCGG
* *
3865362 TTGAATTTTTCGGTCAAGTT
1 TTGAATTTTTCGATCAAGCT
3865382 TTGAATTTTT-GATCAA-CT
1 TTGAATTTTTCGATCAAGCT
3865400 TTGAATTTTTCG
1 TTGAATTTTTCG
3865412 GCCAACTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 11 0.41
19 6 0.22
20 10 0.37
ACGTcount: A:0.22, C:0.10, G:0.16, T:0.52
Consensus pattern (20 bp):
TTGAATTTTTCGATCAAGCT
Found at i:3865417 original size:19 final size:19
Alignment explanation
Indices: 3865362--3865420 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
3865352 TAGATTTCGG
*
3865362 TTGAATTTTTCGGTCAAGTT
1 TTGAATTTTTCGGTCAA-CT
*
3865382 TTGAATTTTT-GATCAACT
1 TTGAATTTTTCGGTCAACT
*
3865400 TTGAATTTTTCGGCCAACT
1 TTGAATTTTTCGGTCAACT
3865419 TT
1 TT
3865421 CCAGTTTTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 11 0.32
19 13 0.38
20 10 0.29
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (19 bp):
TTGAATTTTTCGGTCAACT
Found at i:3865836 original size:16 final size:16
Alignment explanation
Indices: 3865796--3865846 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
3865786 TTTTCATTTT
3865796 TTATT-TTATTTA-TA
1 TTATTATTATTTATTA
3865810 -TATATATTTATTTATTA
1 TTAT-TA-TTATTTATTA
3865827 TTATTATTATTTATTGA
1 TTATTATTATTTATT-A
3865844 TTA
1 TTA
3865847 GATTAGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
13 3 0.10
14 1 0.03
16 16 0.52
17 8 0.26
18 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TTATTATTATTTATTA
Found at i:3865878 original size:6 final size:6
Alignment explanation
Indices: 3865867--3865923 Score: 55
Period size: 6 Copynumber: 9.5 Consensus size: 6
3865857 GTTTAATACA
* * *
3865867 TTTTAT TTTTATT TTATTTT TTTTAT TTTTAT TTTCAT TTTCA- TTTTA-
1 TTTTAT TTTTA-T TT-TTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
3865915 TTTTAT TTT
1 TTTTAT TTT
3865924 ATTATTTTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
5 9 0.20
6 27 0.61
7 6 0.14
8 2 0.05
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:3865881 original size:5 final size:5
Alignment explanation
Indices: 3865866--3865926 Score: 79
Period size: 5 Copynumber: 11.6 Consensus size: 5
3865856 TGTTTAATAC
3865866 ATTTT ATTTTT ATTTT ATTTT -TTTT ATTTTT ATTTT CATTTT CATTTT
1 ATTTT A-TTTT ATTTT ATTTT ATTTT A-TTTT ATTTT -ATTTT -ATTTT
3865914 ATTTT ATTTT ATT
1 ATTTT ATTTT ATT
3865927 ATTTTCTTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.08
5 27 0.52
6 21 0.40
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:3866002 original size:60 final size:59
Alignment explanation
Indices: 3865936--3866281 Score: 344
Period size: 58 Copynumber: 5.9 Consensus size: 59
3865926 TATTTTCTTT
* * *
3865936 AAATAAGCTTTCAAAAAAAAATATTTTTGAGGAAAAGTTGAAATTATCAATTTTCCTTGA
1 AAATAAGTTTTC-AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
* * *
3865996 AAATAAGCTTGCTAAAAAAAATATTTTTG-GAGAAAAGTTGAAAGTATCAATTCTCCTTAA
1 AAATAAGTTTTC-AAAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTTAA
** * * * *
3866056 AAATAAGTTTTCAAAAATGA-ATGTTTGAGGAAAAGTTGAAAGTATTAATTTTTCTTAG
1 AAATAAGTTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
* **** * * *
3866114 AAACAAGTTTTCAAAGGTGA-ATTTTTGAGAAAAATTTGAAAGTATCAATTTTTCTTAA
1 AAATAAGTTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
**** * **
3866172 AAATAAGTTTTC-AAAAATGGGTTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTCGA
1 AAATAAGTTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
* **
3866230 AATTAAAGTTTTC-AAAAAAATA-TTTTGAAAAAAAGTTGAAAGTATCAATTTT
1 AAAT-AAGTTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
3866282 TCCTGTACAA
Statistics
Matches: 240, Mismatches: 42, Indels: 10
0.82 0.14 0.03
Matches are distributed among these distances:
57 2 0.01
58 154 0.64
59 21 0.09
60 63 0.26
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.36
Consensus pattern (59 bp):
AAATAAGTTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
Found at i:3866271 original size:174 final size:175
Alignment explanation
Indices: 3865958--3866283 Score: 408
Period size: 174 Copynumber: 1.9 Consensus size: 175
3865948 AAAAAAAAAT
* * * *
3865958 ATTTTTGAGGAAAAGTTGAAATTATCAATTTTCCTTGAAAATAAGCTTGCTAAAAAAAATATTTT
1 ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCTTGCTAAAAAAAAGATTTT
* * **
3866023 TGGAGAAAAGTTGAAAGTATCAATTCTCCTTAAAAATAAGTTTTCAAAAATGAATGTTTGAGGAA
66 TGGAGAAAAATTGAAAGTATCAATTCTCCTCAAAAATAAGTTTTCAAAAA-GAATGTTTGAAAAA
*
3866088 AAGTTGAAAGTATTAATTTTTCTTAGAAACAAGTTTTCAAAGGTGA
130 AAGTTGAAAGTATCAATTTTTCTTAGAAACAAGTTTTCAAAGGTGA
* * * * ** *
3866134 ATTTTTGAGAAAAATTTGAAAGTATCAATTTTTCTTAAAAATAAG-TT-TTCAAAAATGGGTTTT
1 ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCTTGCTAAAAAAAAGATTTT
* * * *
3866197 T-GAGGAAAAATTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTTCAAAAA-AATATTTTGAAA
66 TGGA-GAAAAATTGAAAGTATCAATTCTCCTCAAAAAT-AAGTTTTCAAAAAGAAT-GTTTGAAA
3866260 AAAAGTTGAAAGTATCAATTTTTC
128 AAAAGTTGAAAGTATCAATTTTTC
3866284 CTGTACAAAA
Statistics
Matches: 127, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
173 5 0.04
174 67 0.53
175 15 0.12
176 40 0.31
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (175 bp):
ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCTTGCTAAAAAAAAGATTTT
TGGAGAAAAATTGAAAGTATCAATTCTCCTCAAAAATAAGTTTTCAAAAAGAATGTTTGAAAAAA
AGTTGAAAGTATCAATTTTTCTTAGAAACAAGTTTTCAAAGGTGA
Found at i:3867930 original size:29 final size:30
Alignment explanation
Indices: 3867895--3867953 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
3867885 AAATAAGCTG
*
3867895 GTTGTAATCT-CATCCCTAGAATTAAGTAT
1 GTTGTAATCTACATCCCTAAAATTAAGTAT
*
3867924 GTTGTAATCTATATCCCTAAAATTAAGTAT
1 GTTGTAATCTACATCCCTAAAATTAAGTAT
3867954 TTATATCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (30 bp):
GTTGTAATCTACATCCCTAAAATTAAGTAT
Found at i:3871017 original size:20 final size:20
Alignment explanation
Indices: 3870992--3871041 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
3870982 AAAGCTAAGA
3870992 AGATTGAAGTACTTCCTAGG
1 AGATTGAAGTACTTCCTAGG
*
3871012 AGATTGAAGTACTTTCTAGG
1 AGATTGAAGTACTTCCTAGG
*
3871032 A-ATTAAAGTA
1 AGATTGAAGTA
3871042 GCTCACTCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (20 bp):
AGATTGAAGTACTTCCTAGG
Found at i:3873679 original size:14 final size:14
Alignment explanation
Indices: 3873658--3873695 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3873648 TTTTGAATAG
3873658 AAAACAAA-AGACAA
1 AAAACAAATA-ACAA
*
3873672 ATAACAAATAACAA
1 AAAACAAATAACAA
3873686 AAAACAAATA
1 AAAACAAATA
3873696 TTGTACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 20 0.95
15 1 0.05
ACGTcount: A:0.76, C:0.13, G:0.03, T:0.08
Consensus pattern (14 bp):
AAAACAAATAACAA
Found at i:3875721 original size:14 final size:15
Alignment explanation
Indices: 3875702--3875730 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3875692 AATTATCAAA
3875702 ATTAC-TAAAATATT
1 ATTACTTAAAATATT
3875716 ATTACTTAAAATATT
1 ATTACTTAAAATATT
3875731 TGTCATTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTACTTAAAATATT
Found at i:3880454 original size:18 final size:17
Alignment explanation
Indices: 3880431--3880471 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
3880421 TCGAATCGAA
*
3880431 TTATATATTTTTATTAAT
1 TTATATATATTT-TTAAT
3880449 TTATATATATTTTTAAT
1 TTATATATATTTTTAAT
3880466 TT-TATA
1 TTATATA
3880472 AAATAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.18
17 7 0.32
18 11 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATATATATTTTTAAT
Found at i:3881435 original size:29 final size:30
Alignment explanation
Indices: 3881393--3881449 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
3881383 AATTAATGCA
3881393 GATATGATCAGAATTCTT-TTTTTATTTCG
1 GATATGATCAGAATTCTTATTTTTATTTCG
*
3881422 GATATGATCAGAATTTTTATTTTTATTT
1 GATATGATCAGAATTCTTATTTTTATTT
3881450 TTTTGATAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.26, C:0.07, G:0.12, T:0.54
Consensus pattern (30 bp):
GATATGATCAGAATTCTTATTTTTATTTCG
Found at i:3883791 original size:2 final size:2
Alignment explanation
Indices: 3883784--3883812 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3883774 GATAGAAAAG
3883784 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3883813 CTTACAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3888826 original size:14 final size:15
Alignment explanation
Indices: 3888807--3888836 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3888797 TGAAGAATTT
3888807 AAAAAT-AAAAATAA
1 AAAAATAAAAAATAA
3888821 AAAAATAAAAAATAA
1 AAAAATAAAAAATAA
3888836 A
1 A
3888837 GTCACCACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAATAAAAAATAA
Found at i:3891331 original size:18 final size:17
Alignment explanation
Indices: 3891308--3891352 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
3891298 ACTTAATTTT
3891308 TATTATTTTATTTAATAA
1 TATTATTTTATTTAAT-A
* *
3891326 TATTATTATTATTTTATT
1 TATTATT-TTATTTAATA
3891344 TATTATTTT
1 TATTATTTT
3891353 TTCTATGATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 2 0.08
18 14 0.58
19 8 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTATTTTATTTAATA
Found at i:3891675 original size:49 final size:49
Alignment explanation
Indices: 3891547--3892124 Score: 548
Period size: 49 Copynumber: 11.7 Consensus size: 49
3891537 CCTTTCACTT
* * *
3891547 GAGGCTCAACAATTTTTAAAAATTTAAAATC-TGAAAAAGACTCCTCTCAGCA
1 GAGGCTCAACAA-CTTTAAAAATTT--TATCTTGAAAAAG-CTCCTCTCAACA
* * * * * ** * * *
3891599 AAAGTTTAACAATTTTTGAAATCTTATCTTGAAAAAGCTCTTCTCAGCA
1 GAGGCTCAACAACTTTAAAAATTTTATCTTGAAAAAGCTCCTCTCAACA
*
3891648 GAGGCTTAACAACTTTAAAAATTTTATCTTGAAAAAGGCTCCTCTCAACA
1 GAGGCTCAACAACTTTAAAAATTTTATCTTGAAAAA-GCTCCTCTCAACA
3891698 GAGGCTCAACAACTTTAAAAATTTTATC-TGAAAAAAGCTCCTCTCAACA
1 GAGGCTCAACAACTTTAAAAATTTTATCTTG-AAAAAGCTCCTCTCAACA
* * *
3891747 GAGGTTCAATAACTTT-AAAATTCTTAT-TTGAAAAAGCTCCTCTCAGCA
1 GAGGCTCAACAACTTTAAAAATT-TTATCTTGAAAAAGCTCCTCTCAACA
* * * *
3891795 GAGGCTCAACAACTTTGAAAATTTTCAGCTTGAAAAAGGCTCATCTTAACA
1 GAGGCTCAACAACTTTAAAAATTTT-ATCTTGAAAAA-GCTCCTCTCAACA
* ** *
3891846 GAGTCTCAACAACTTT-AAAA-TCCATCTTGAAAAAGCTCCTCTTAACA
1 GAGGCTCAACAACTTTAAAAATTTTATCTTGAAAAAGCTCCTCTCAACA
*
3891893 GAGG-TCCAACAACTTTAAAAATTTCT-TCTTGGAAAAA-CTCCACTCAACA
1 GAGGCT-CAACAACTTTAAAAATTT-TATCTT-GAAAAAGCTCCTCTCAACA
* * * * *
3891942 GAGGCTCAATAATTTTAAAAATTTCATCTTGGAAAAGCTCCTCTCAGCA
1 GAGGCTCAACAACTTTAAAAATTTTATCTTGAAAAAGCTCCTCTCAACA
* ** * * * * *
3891991 AAGATTTAACAACTTT-AAAATCTCATATTAAAAAAAGCTCCTCTCAACA
1 GAGGCTCAACAACTTTAAAAATTTTATCTT-GAAAAAGCTCCTCTCAACA
* *
3892040 GAGGCTCAACAACTTTTAAAAATTTCATCTTGAAAAAGCTCCTCTCAGCA
1 GAGGCTCAACAAC-TTTAAAAATTTTATCTTGAAAAAGCTCCTCTCAACA
* * * *
3892090 GAAGTTCAACAACTTTAAAAATCTCATC-TGAAAAA
1 GAGGCTCAACAACTTTAAAAATTTTATCTTGAAAAA
3892125 AAGCTCCAAA
Statistics
Matches: 440, Mismatches: 66, Indels: 44
0.80 0.12 0.08
Matches are distributed among these distances:
46 1 0.00
47 25 0.06
48 76 0.17
49 184 0.42
50 101 0.23
51 45 0.10
52 8 0.02
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (49 bp):
GAGGCTCAACAACTTTAAAAATTTTATCTTGAAAAAGCTCCTCTCAACA
Found at i:3892125 original size:99 final size:99
Alignment explanation
Indices: 3891547--3892131 Score: 607
Period size: 99 Copynumber: 5.9 Consensus size: 99
3891537 CCTTTCACTT
* * * *
3891547 GAGGCTCAACAATTTTTAAAAATTTAAAATC-TGAAAAAGACTCCTCTCAGCAAAAGTTTAACAA
1 GAGGCTCAACAA-CTTTAAAAATTT--CATCTTGAAAAAG-CTCCTCTCAGCAGAAGTTCAACAA
* ** * * *
3891611 TTTTTGAAATCTTATCTTG-AAAAAGCTCTTCTCAGCA
62 CTTTAAAAATCTCATCTTGAAAAAAGCTCCTCTCAACA
* * * * *
3891648 GAGGCTTAACAACTTTAAAAATTTTATCTTGAAAAAGGCTCCTCTCAACAGAGGCTCAACAACTT
1 GAGGCTCAACAACTTTAAAAATTTCATCTTGAAAAA-GCTCCTCTCAGCAGAAGTTCAACAACTT
* *
3891713 TAAAAATTTTATC-TGAAAAAAGCTCCTCTCAACA
65 TAAAAATCTCATCTTGAAAAAAGCTCCTCTCAACA
* * * * *
3891747 GAGGTTCAATAACTTT-AAAATTCTTAT-TTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTT
1 GAGGCTCAACAACTTTAAAAATT-TCATCTTGAAAAAGCTCCTCTCAGCAGAAGTTCAACAACTT
* * * * * *
3891810 TGAAAATTTTCAGCTTGAAAAAGGCTCATCTTAACA
65 T-AAAAATCTCATCTTGAAAAAAGCTCCTCTCAACA
* * * * * *
3891846 GAGTCTCAACAACTTT-AAAA-TCCATCTTGAAAAAGCTCCTCTTAACAGAGGTCCAACAACTTT
1 GAGGCTCAACAACTTTAAAAATTTCATCTTGAAAAAGCTCCTCTCAGCAGAAGTTCAACAACTTT
* * * *
3891909 AAAAATTTCTTCTTGGAAAAA-CTCCACTCAACA
66 AAAAATCTCATCTTGAAAAAAGCTCCTCTCAACA
* * * *
3891942 GAGGCTCAATAATTTTAAAAATTTCATCTTGGAAAAGCTCCTCTCAGCA-AAGATTTAACAACTT
1 GAGGCTCAACAACTTTAAAAATTTCATCTTGAAAAAGCTCCTCTCAGCAGAAG-TTCAACAACTT
* *
3892006 T-AAAATCTCATATTAAAAAAAGCTCCTCTCAACA
65 TAAAAATCTCATCTTGAAAAAAGCTCCTCTCAACA
3892040 GAGGCTCAACAACTTTTAAAAATTTCATCTTGAAAAAGCTCCTCTCAGCAGAAGTTCAACAACTT
1 GAGGCTCAACAAC-TTTAAAAATTTCATCTTGAAAAAGCTCCTCTCAGCAGAAGTTCAACAACTT
3892105 TAAAAATCTCATC-TGAAAAAAAGCTCC
65 TAAAAATCTCATCTTG-AAAAAAGCTCC
3892132 AAATCGAGTT
Statistics
Matches: 406, Mismatches: 63, Indels: 31
0.81 0.13 0.06
Matches are distributed among these distances:
96 22 0.05
97 67 0.17
98 117 0.29
99 153 0.38
100 36 0.09
101 11 0.03
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (99 bp):
GAGGCTCAACAACTTTAAAAATTTCATCTTGAAAAAGCTCCTCTCAGCAGAAGTTCAACAACTTT
AAAAATCTCATCTTGAAAAAAGCTCCTCTCAACA
Found at i:3904352 original size:28 final size:29
Alignment explanation
Indices: 3904320--3904374 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
3904310 TTTTTTTATT
3904320 TTTTGTATTATTATTAAA-TTTATTTTTA
1 TTTTGTATTATTATTAAAGTTTATTTTTA
* * *
3904348 TTTTGTTTTGTTTTTAAAGTTTATTTT
1 TTTTGTATTATTATTAAAGTTTATTTT
3904375 AAAAAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (29 bp):
TTTTGTATTATTATTAAAGTTTATTTTTA
Found at i:3904487 original size:11 final size:10
Alignment explanation
Indices: 3904462--3904486 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3904452 AATAATATAT
3904462 AAAAATTCAA
1 AAAAATTCAA
3904472 AAAAATTCAA
1 AAAAATTCAA
3904482 AAAAA
1 AAAAA
3904487 AAATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATTCAA
Found at i:3905484 original size:19 final size:19
Alignment explanation
Indices: 3905443--3905485 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
3905433 CCCTCTTTTT
* *
3905443 TTTTTGTTTTTTTATATAT
1 TTTTTGTATTTTTATATAA
* *
3905462 TTTTTGTATTTTTGTTTAA
1 TTTTTGTATTTTTATATAA
3905481 TTTTT
1 TTTTT
3905486 ATTATTATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (19 bp):
TTTTTGTATTTTTATATAA
Found at i:3906196 original size:34 final size:34
Alignment explanation
Indices: 3906153--3906257 Score: 106
Period size: 43 Copynumber: 2.9 Consensus size: 34
3906143 ATAAAATATG
3906153 AAATTTATTAATATTTTGATCACTAACATTTGTA
1 AAATTTATTAATATTTTGATCACTAACATTTGTA
3906187 AAATTTATTAATATTTTGGCCTCTATTGTCACTAACATTTGTA
1 AAATTTATTAATATTTT-G-----A---TCACTAACATTTGTA
*
3906230 AAATTTATTAATA--TTGATCACAAACATT
1 AAATTTATTAATATTTTGATCACTAACATT
3906258 GAATACTTTT
Statistics
Matches: 61, Mismatches: 1, Indels: 20
0.74 0.01 0.24
Matches are distributed among these distances:
32 10 0.16
34 17 0.28
35 2 0.03
40 2 0.03
41 2 0.03
43 28 0.46
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (34 bp):
AAATTTATTAATATTTTGATCACTAACATTTGTA
Found at i:3906373 original size:14 final size:15
Alignment explanation
Indices: 3906354--3906382 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3906344 AATTATCAAA
3906354 ATTAC-TAAAATATT
1 ATTACTTAAAATATT
3906368 ATTACTTAAAATATT
1 ATTACTTAAAATATT
3906383 TGTCATTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTACTTAAAATATT
Found at i:3914630 original size:2 final size:2
Alignment explanation
Indices: 3914623--3914656 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3914613 AATTGCCAGC
3914623 AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3914657 TGCTTACACT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3916210 original size:16 final size:16
Alignment explanation
Indices: 3916186--3916216 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3916176 TTAAAAATTT
*
3916186 AATTGAAATATAAAAA
1 AATTAAAATATAAAAA
3916202 AATTAAAATATAAAA
1 AATTAAAATATAAAA
3916217 TATAAAATAT
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:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AATTAAAATATAAAAA
Found at i:3916215 original size:7 final size:7
Alignment explanation
Indices: 3916200--3916232 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
3916190 GAAATATAAA
3916200 AAAAT-T
1 AAAATAT
3916206 AAAATAT
1 AAAATAT
3916213 AAAATAT
1 AAAATAT
3916220 AAAATAT
1 AAAATAT
3916227 ATAAAT
1 A-AAAT
3916233 TTACTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 5 0.20
7 16 0.64
8 4 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AAAATAT
Found at i:3916228 original size:16 final size:16
Alignment explanation
Indices: 3916191--3916231 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
3916181 AATTTAATTG
*
3916191 AAATATA-AAAAAATT
1 AAATATATAAAAAATA
*
3916206 AAA-ATATAAAATATA
1 AAATATATAAAAAATA
3916221 AAATATATAAA
1 AAATATATAAA
3916232 TTTACTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 3 0.14
15 12 0.55
16 7 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATATATAAAAAATA
Found at i:3919127 original size:31 final size:31
Alignment explanation
Indices: 3919061--3919120 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
3919051 AATGATAATG
3919061 ATGATTTATGATGATTTTTATAAATTGATCC
1 ATGATTTATGATGATTTTTATAAATTGATCC
* *
3919092 ATGATTTAGTGA-GATTTTTTTATATTGAT
1 ATGATTTA-TGATGATTTTTATAAATTGAT
3919121 TTATGATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.52
Consensus pattern (31 bp):
ATGATTTATGATGATTTTTATAAATTGATCC
Found at i:3928588 original size:14 final size:15
Alignment explanation
Indices: 3928562--3928602 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
3928552 GATCCGAATA
3928562 AAATATATATAATTT
1 AAATATATATAATTT
3928577 AAATAT-TATAATTAT
1 AAATATATATAATT-T
3928592 ATAA-ATATATA
1 A-AATATATATA
3928603 TGTAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 7 0.30
15 10 0.43
16 6 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATATATATAATTT
Found at i:3931744 original size:16 final size:18
Alignment explanation
Indices: 3931704--3931739 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3931694 TGATTTTTTT
*
3931704 TTAATAAAATTACAAGTAA
1 TTAAAAAAATTACAAG-AA
3931723 TTAAAAAAATTACAAGA
1 TTAAAAAAATTACAAGA
3931740 TAAAATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 1 0.06
19 15 0.94
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (18 bp):
TTAAAAAAATTACAAGAA
Found at i:3931989 original size:32 final size:31
Alignment explanation
Indices: 3931890--3932004 Score: 96
Period size: 31 Copynumber: 3.8 Consensus size: 31
3931880 TTAAAATTTT
3931890 AATAAAAATTATA-A-ATAAT-TTTA-ATAA
1 AATAAAAATTATATATATAATATTTATATAA
* * * * *
3931917 AATAAAAATAATATATTTTATATTT-TGTATC
1 AATAAAAATTATATATATAATATTTATATA-A
*
3931948 AATATAAATTATGATATATAATATTTATATAA
1 AATAAAAATTAT-ATATATAATATTTATATAA
* * *
3931980 AATAAAAATTAAATACATAAAATTT
1 AATAAAAATTATATATATAATATTT
3932005 TAATATTTTA
Statistics
Matches: 66, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
27 12 0.18
28 1 0.02
29 3 0.05
30 5 0.08
31 21 0.32
32 21 0.32
33 3 0.05
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (31 bp):
AATAAAAATTATATATATAATATTTATATAA
Found at i:3939479 original size:28 final size:28
Alignment explanation
Indices: 3939447--3939502 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3939437 ATTGCTTAGA
3939447 GTAGGGAATGACCCTAATTGCAAAAGTC
1 GTAGGGAATGACCCTAATTGCAAAAGTC
3939475 GTAGGGAATGACCCTAATTGCAAAAGTC
1 GTAGGGAATGACCCTAATTGCAAAAGTC
3939503 AGAATATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (28 bp):
GTAGGGAATGACCCTAATTGCAAAAGTC
Found at i:3943906 original size:3 final size:3
Alignment explanation
Indices: 3943893--3943941 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
3943883 ATTTTACTTG
* *
3943893 TAT TGT TAT TAT TAT TAT TAT T-T T-T TA- TAT TAT TGT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3943938 TAT T
1 TAT T
3943942 TTTGTGGGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 6 0.15
3 34 0.85
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:3946331 original size:2 final size:2
Alignment explanation
Indices: 3946319--3946352 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3946309 CCATGTCAAA
*
3946319 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3946353 TTAACAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3949156 original size:8 final size:8
Alignment explanation
Indices: 3949143--3949172 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
3949133 AATAAATTAA
3949143 AAATAATT
1 AAATAATT
3949151 AAATAATT
1 AAATAATT
3949159 AAATAATT
1 AAATAATT
3949167 AAATAA
1 AAATAA
3949173 AAATAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAATAATT
Found at i:3952929 original size:19 final size:21
Alignment explanation
Indices: 3952905--3952945 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3952895 GGGATTCTTT
3952905 TAATTTA-GTG-TAGTTTCAA
1 TAATTTATGTGATAGTTTCAA
3952924 TAATTTATGTGATAGTTTCAA
1 TAATTTATGTGATAGTTTCAA
3952945 T
1 T
3952946 GCATTGCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
20 3 0.15
21 10 0.50
ACGTcount: A:0.32, C:0.05, G:0.15, T:0.49
Consensus pattern (21 bp):
TAATTTATGTGATAGTTTCAA
Found at i:3953847 original size:18 final size:19
Alignment explanation
Indices: 3953791--3953848 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 19
3953781 TTTTTAAATT
3953791 TAAA-TAAATAACAAATTAAA
1 TAAATTAAATAA-AAA-TAAA
*
3953811 CTAAATTAAA-AATAATAAA
1 -TAAATTAAATAAAAATAAA
3953830 T-AATTAAATAAAAATAAA
1 TAAATTAAATAAAAATAAA
3953848 T
1 T
3953849 TAAGACAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
17 7 0.21
18 10 0.30
19 4 0.12
20 2 0.06
21 6 0.18
22 4 0.12
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAATTAAATAAAAATAAA
Found at i:3959692 original size:31 final size:29
Alignment explanation
Indices: 3959654--3959720 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
3959644 TCTATTTGGT
*
3959654 TTATTTTATAT-TGTTTGCTTTTCTCT-TA
1 TTATTTTTTATCT-TTTGCTTTTCTCTCTA
3959682 TTCATTTTTTATCTTTTGCTTTTCTCTCTA
1 TT-ATTTTTTATCTTTTGCTTTTCTCTCTA
3959712 TTATTTTTT
1 TTATTTTTT
3959721 TAAAATAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
28 2 0.06
29 28 0.80
30 5 0.14
ACGTcount: A:0.12, C:0.13, G:0.04, T:0.70
Consensus pattern (29 bp):
TTATTTTTTATCTTTTGCTTTTCTCTCTA
Found at i:3960073 original size:19 final size:21
Alignment explanation
Indices: 3960029--3960074 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3960019 AGTAATTTTT
*
3960029 GATTAAAATAATTAAAATATA
1 GATTAAAATAATAAAAATATA
*
3960050 TATTAAAAT-ATAAAAAT-TA
1 GATTAAAATAATAAAAATATA
3960069 GATTAA
1 GATTAA
3960075 GTCTATGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 7 0.32
20 7 0.32
21 8 0.36
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
GATTAAAATAATAAAAATATA
Found at i:3962617 original size:19 final size:21
Alignment explanation
Indices: 3962593--3962633 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3962583 GGGATTCTTT
3962593 TAATTTA-GTG-TAGTTTCAA
1 TAATTTATGTGATAGTTTCAA
3962612 TAATTTATGTGATAGTTTCAA
1 TAATTTATGTGATAGTTTCAA
3962633 T
1 T
3962634 GCATTGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
20 3 0.15
21 10 0.50
ACGTcount: A:0.32, C:0.05, G:0.15, T:0.49
Consensus pattern (21 bp):
TAATTTATGTGATAGTTTCAA
Found at i:3964544 original size:2 final size:2
Alignment explanation
Indices: 3964537--3964566 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3964527 TTCCATTTCA
3964537 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3964567 TAAACAACAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3973089 original size:2 final size:2
Alignment explanation
Indices: 3973082--3973107 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3973072 CCATTTCAAA
3973082 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
3973108 TAAACAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3973429 original size:20 final size:20
Alignment explanation
Indices: 3973401--3973439 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3973391 ATATTTTTTA
*
3973401 AATTTTTTTAAAATAAAAAT
1 AATTATTTTAAAATAAAAAT
* *
3973421 AATTATTTTGAAGTAAAAA
1 AATTATTTTAAAATAAAAA
3973440 CCAATTAATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
AATTATTTTAAAATAAAAAT
Found at i:3975873 original size:27 final size:29
Alignment explanation
Indices: 3975842--3975916 Score: 74
Period size: 27 Copynumber: 2.8 Consensus size: 29
3975832 ATTTTTAAAA
3975842 AAAAATAAATATTAAAATAAAAATAAT-T
1 AAAAATAAATATTAAAATAAAAATAATGT
3975870 AAAAATAAA-A-TAAACA-AACAAATAATGT
1 AAAAATAAATATTAAA-ATAA-AAATAATGT
*
3975898 -AAAAT-AAT-TAAAAATAAAA
1 AAAAATAAATATTAAAATAAAA
3975917 TTGACAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
26 11 0.28
27 19 0.47
28 10 0.25
ACGTcount: A:0.73, C:0.03, G:0.01, T:0.23
Consensus pattern (29 bp):
AAAAATAAATATTAAAATAAAAATAATGT
Found at i:3975880 original size:15 final size:15
Alignment explanation
Indices: 3975842--3975882 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3975832 ATTTTTAAAA
3975842 AAAAAT-AAAT-ATT
1 AAAAATAAAATAATT
3975855 -AAAATAAAAATAATT
1 AAAAAT-AAAATAATT
3975870 AAAAATAAAATAA
1 AAAAATAAAATAA
3975883 ACAAACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.21
14 4 0.17
15 10 0.42
16 5 0.21
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATAAAATAATT
Found at i:3980073 original size:21 final size:22
Alignment explanation
Indices: 3980030--3980081 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
3980020 CATATTACGT
*
3980030 AAGTTGATGATACTGATACTC-
1 AAGTTGATGATACTGACACTCA
*
3980051 AAGTTGATGAT-CTTGACATTCA
1 AAGTTGATGATAC-TGACACTCA
3980073 AAG-TGATGA
1 AAGTTGATGA
3980082 AAGGATGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 23 0.85
22 3 0.11
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (22 bp):
AAGTTGATGATACTGACACTCA
Found at i:3982524 original size:58 final size:58
Alignment explanation
Indices: 3982434--3982551 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
3982424 ATCTTTTGGA
*
3982434 GGGGAATGAATGTACTATCAGTTTTAACTTAGTAACTTCTAACCTTTCAACTACTATT
1 GGGGAATGAATGTACTATCAATTTTAACTTAGTAACTTCTAACCTTTCAACTACTATT
3982492 GGGGAATGAATGTACTATCAATTTTAACTTAGTAACTTCTAACCTTTCAACTACTATT
1 GGGGAATGAATGTACTATCAATTTTAACTTAGTAACTTCTAACCTTTCAACTACTATT
3982550 GG
1 GG
3982552 ATTTGGCAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (58 bp):
GGGGAATGAATGTACTATCAATTTTAACTTAGTAACTTCTAACCTTTCAACTACTATT
Found at i:3986820 original size:60 final size:61
Alignment explanation
Indices: 3986754--3986974 Score: 243
Period size: 61 Copynumber: 3.6 Consensus size: 61
3986744 CACTTTTTGT
***
3986754 TCAAAAACGCCTTAAATAATCTCTAATATTTTTTAAAGGATATTATTTAAACCATTTTTAG
1 TCAAAAACGCCTTAAATAATCTCTAATATTTTTTAAAGGATATTATTTAAGGTATTTTTAG
* * *
3986815 T-AAAAAC-CCTTAAATAATACTTTTCA-ATTTTTTGAAGGATATTATTTAAGGTATTTTTTA-
1 TCAAAAACGCCTTAAATAAT-C-TCTAATATTTTTTAAAGGATATTATTTAAGGTA-TTTTTAG
* * ** * *
3986875 TCAAAAATGCTTTAAATAATCTCTAATATTTTTTAAAAAAGATTATTTAAGGTATTTTTGG
1 TCAAAAACGCCTTAAATAATCTCTAATATTTTTTAAAGGATATTATTTAAGGTATTTTTAG
***
3986936 TCAAAAATATCTTAAATAATCTCTAATATTTGTTTAAAG
1 TCAAAAACGCCTTAAATAATCTCTAATATTT-TTTAAAG
3986975 AGGAAAATGC
Statistics
Matches: 133, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
59 11 0.08
60 39 0.29
61 67 0.50
62 16 0.12
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (61 bp):
TCAAAAACGCCTTAAATAATCTCTAATATTTTTTAAAGGATATTATTTAAGGTATTTTTAG
Found at i:3996431 original size:26 final size:25
Alignment explanation
Indices: 3996401--3996501 Score: 91
Period size: 26 Copynumber: 4.0 Consensus size: 25
3996391 TCCTGATTTT
3996401 TAAATTAAAATAAATAACAAATTAAA
1 TAAATTAAAATAAATAA-AAATTAAA
*
3996427 TAAATTAAAATAATTAAATAATTAAA
1 TAAATTAAAATAAATAAA-AATTAAA
* * *
3996453 TAAA-AATAAATAAA-ACAAA-CAAA
1 TAAATTA-AAATAAATAAAAATTAAA
* * *
3996476 TAAAGTAAAATAATTAAAAATAAAA
1 TAAATTAAAATAAATAAAAATTAAA
3996501 T
1 T
3996502 TGAAGAATAA
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
23 13 0.21
24 7 0.11
25 8 0.13
26 33 0.54
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.26
Consensus pattern (25 bp):
TAAATTAAAATAAATAAAAATTAAA
Found at i:3996447 original size:8 final size:8
Alignment explanation
Indices: 3996420--3996455 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
3996410 ATAAATAACA
3996420 AATTAAAT
1 AATTAAAT
3996428 AAATTAAAAT
1 -AATT-AAAT
3996438 AATTAAAT
1 AATTAAAT
3996446 AATTAAAT
1 AATTAAAT
3996454 AA
1 AA
3996456 AAATAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 14 0.54
9 8 0.31
10 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AATTAAAT
Found at i:3996459 original size:14 final size:14
Alignment explanation
Indices: 3996408--3996499 Score: 53
Period size: 14 Copynumber: 6.2 Consensus size: 14
3996398 TTTTAAATTA
3996408 AAATAAATAACAAATT
1 AAATAAATAA-AAA-T
*
3996424 AAATAAATTAAAAT
1 AAATAAATAAAAAT
*
3996438 AATTAAATAATTAAAT
1 AAATAAATAA--AAAT
*
3996454 AAAAATAAAT-AAAAC
1 --AAATAAATAAAAAT
* *
3996469 AAACAAAT-AAAGT
1 AAATAAATAAAAAT
*
3996482 AAAATAATTAAAAAT
1 -AAATAAATAAAAAT
3996497 AAA
1 AAA
3996500 ATTGAAGAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
13 10 0.17
14 18 0.31
15 10 0.17
16 13 0.22
17 1 0.02
18 7 0.12
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:3999279 original size:28 final size:28
Alignment explanation
Indices: 3999247--3999313 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
3999237 ATAAAACCTA
* *
3999247 AATACTTATAAAACCTGTATTTAAACTT
1 AATACTTATAAAACATATATTTAAACTT
* * *
3999275 AATACTTATAGAAGATATATTTAAAGTT
1 AATACTTATAAAACATATATTTAAACTT
*
3999303 AATGCTTATAA
1 AATACTTATAA
3999314 TCAGATCTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (28 bp):
AATACTTATAAAACATATATTTAAACTT
Found at i:4000425 original size:24 final size:24
Alignment explanation
Indices: 4000393--4000442 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
4000383 CCGAGATTTA
*
4000393 GGCTTCACCTAGATTTCCTTGAAT
1 GGCTTCACCTAGATTGCCTTGAAT
4000417 GGCTTCACCTAGATTGCCTTGAAT
1 GGCTTCACCTAGATTGCCTTGAAT
4000441 GG
1 GG
4000443 TTCTTTTGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (24 bp):
GGCTTCACCTAGATTGCCTTGAAT
Found at i:4001720 original size:201 final size:201
Alignment explanation
Indices: 4001368--4001769 Score: 732
Period size: 201 Copynumber: 2.0 Consensus size: 201
4001358 GGTGACAATG
4001368 GTATTGAAGTTGTAATCGCACAGTTTGAGGCAAGAGGAGGACAAGGACTCATTAGCTTTGCGGCA
1 GTATTGAAGTTGTAATCGCACAGTTTGAGGCAAGAGGAGGACAAGGACTCATTAGCTTTGCGGCA
*
4001433 CTGGGACTCTTCTCCTCTGGAGGGATTTCCTGGGTGGCCTCTTCAAATTCCTCCGCAGGGTTTAC
66 CTGGGACTCTTCTCCTCTGGAGGGATTTCCTGGGTGGCCTCTTCAAATTCCTCCACAGGGTTTAC
* *
4001498 ACAGATATCAACCATTGCTTCTGCATCACCATAATCTAGCATCTTGTGAATTGGGTTATCACCCA
131 ACAGATATCAACCAATGCTTCTGCATCACCATAATCTAGCATCTTGTGAATTGGGATATCACCCA
4001563 CAACAC
196 CAACAC
*
4001569 GTATTGAAGTTGTAATCGCACAGTTTGAGGTAAGAGGAGGACAAGGACTCATTAGCTTTGCGGCA
1 GTATTGAAGTTGTAATCGCACAGTTTGAGGCAAGAGGAGGACAAGGACTCATTAGCTTTGCGGCA
* *
4001634 GTGGGACTCTTCTCCTCTGGAGGGATTTCCTGGGTGGTCTCTTCAAATTCCTCCACAGGGTTTAC
66 CTGGGACTCTTCTCCTCTGGAGGGATTTCCTGGGTGGCCTCTTCAAATTCCTCCACAGGGTTTAC
* *
4001699 ACAGATATCGACCAATGCTTCTGCATCACCATTATCTAGCATCTTGTGAATTGGGATATCACCCA
131 ACAGATATCAACCAATGCTTCTGCATCACCATAATCTAGCATCTTGTGAATTGGGATATCACCCA
4001764 CAACAC
196 CAACAC
4001770 ATCGGGGAGC
Statistics
Matches: 193, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
201 193 1.00
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (201 bp):
GTATTGAAGTTGTAATCGCACAGTTTGAGGCAAGAGGAGGACAAGGACTCATTAGCTTTGCGGCA
CTGGGACTCTTCTCCTCTGGAGGGATTTCCTGGGTGGCCTCTTCAAATTCCTCCACAGGGTTTAC
ACAGATATCAACCAATGCTTCTGCATCACCATAATCTAGCATCTTGTGAATTGGGATATCACCCA
CAACAC
Found at i:4004341 original size:20 final size:20
Alignment explanation
Indices: 4004304--4004346 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
4004294 ATCCCACAAA
** * *
4004304 AATTTTCCGGAAATAAAACT
1 AATTTTCCAAAAAAAAAAAT
4004324 AATTTTCCAAAAAAAAAAAT
1 AATTTTCCAAAAAAAAAAAT
4004344 AAT
1 AAT
4004347 AAATGATACC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.28
Consensus pattern (20 bp):
AATTTTCCAAAAAAAAAAAT
Found at i:4005213 original size:11 final size:12
Alignment explanation
Indices: 4005197--4005225 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
4005187 ATTTGACTTG
4005197 AAATAAATATA-
1 AAATAAATATAT
4005208 AAATAAATATAT
1 AAATAAATATAT
4005220 AAATAA
1 AAATAA
4005226 TTAAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAATAAATATAT
Found at i:4022670 original size:14 final size:14
Alignment explanation
Indices: 4022651--4022695 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
4022641 TTAAATTTAA
*
4022651 ATACATATGTATAT
1 ATACATATATATAT
4022665 ATACATATATATAT
1 ATACATATATATAT
*
4022679 ATACAAATATATAT
1 ATACATATATATAT
4022693 ATA
1 ATA
4022696 TGAAAAAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (14 bp):
ATACATATATATAT
Found at i:4028430 original size:16 final size:17
Alignment explanation
Indices: 4028389--4028430 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
4028379 TAAATTAATT
*
4028389 ATCATTTTATCCTATCT
1 ATCATTTTATCCTATCA
* *
4028406 ATTATTTTATGC-ATCA
1 ATCATTTTATCCTATCA
4028422 ATCATTTTA
1 ATCATTTTA
4028431 GAGCAAATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.52
Consensus pattern (17 bp):
ATCATTTTATCCTATCA
Found at i:4028924 original size:13 final size:13
Alignment explanation
Indices: 4028906--4028954 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
4028896 ACATATATAT
4028906 AAAATTAAAAATA
1 AAAATTAAAAATA
**
4028919 AAAATTATATCTATA
1 AAAATTA-A-AAATA
*
4028934 AAAATTAAAAATT
1 AAAATTAAAAATA
4028947 AAAATTAA
1 AAAATTAA
4028955 GTTAATAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
13 17 0.59
14 2 0.07
15 10 0.34
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAAATA
Found at i:4029266 original size:30 final size:28
Alignment explanation
Indices: 4029231--4029322 Score: 94
Period size: 30 Copynumber: 3.1 Consensus size: 28
4029221 TAAACAGCTC
4029231 TAATACAAATTAAAAGTTAAGAATTTATT
1 TAATACAAATTAAAAGTTAA-AATTTATT
* *
4029260 TGAATACAAATTAGAGGTTAAAATTTTATT
1 T-AATACAAATTAAAAGTTAAAA-TTTATT
** *
4029290 TATATGTAAATTAAAAGCTAAAGATTTATT
1 TA-ATACAAATTAAAAGTTAAA-ATTTATT
4029320 TAA
1 TAA
4029323 ATATAATCAA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
29 5 0.10
30 46 0.88
31 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (28 bp):
TAATACAAATTAAAAGTTAAAATTTATT
Found at i:4030208 original size:23 final size:23
Alignment explanation
Indices: 4030182--4030225 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4030172 ATAATTATTT
4030182 TTAAAAAAATAATATTTAATAAA
1 TTAAAAAAATAATATTTAATAAA
**
4030205 TTAAAAATTTAATATTTAATA
1 TTAAAAAAATAATATTTAATA
4030226 TTTATAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TTAAAAAAATAATATTTAATAAA
Found at i:4032252 original size:19 final size:19
Alignment explanation
Indices: 4032214--4032252 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
4032204 GAAGTTGTTA
4032214 AAAATTAAATTATGATTATT
1 AAAATTAAA-TATGATTATT
4032234 AAAATTAAA-ATGTATTATT
1 AAAATTAAATATG-ATTATT
4032253 TTATCAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 6 0.33
20 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (19 bp):
AAAATTAAATATGATTATT
Found at i:4033820 original size:70 final size:72
Alignment explanation
Indices: 4033701--4033844 Score: 211
Period size: 70 Copynumber: 2.0 Consensus size: 72
4033691 GTCTTTTTTA
*
4033701 TAATTATTTAAATAATTATAATTTTTTTGTTATATAGCTATTATAAACAAATA-TTTTTATTCAA
1 TAATTATTTAAATAATTATAATTTTTTTGTTATATAACTATTATAAACAAATATTTTTTATTCAA
4033765 ACATAAT
66 ACATAAT
* * * * * *
4033772 TAATTATTT-AATAGTTATAATTTTTTTGTTATATAATTATTTTCAACAAATATTTTTTATTTAG
1 TAATTATTTAAATAATTATAATTTTTTTGTTATATAACTATTATAAACAAATATTTTTTATTCAA
4033836 ACATAAT
66 ACATAAT
4033843 TA
1 TA
4033845 TTTAAACTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 38 0.58
71 27 0.42
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (72 bp):
TAATTATTTAAATAATTATAATTTTTTTGTTATATAACTATTATAAACAAATATTTTTTATTCAA
ACATAAT
Found at i:4036453 original size:11 final size:11
Alignment explanation
Indices: 4036438--4036504 Score: 55
Period size: 11 Copynumber: 5.9 Consensus size: 11
4036428 ATTTGATTTG
4036438 AATTTAATATA
1 AATTTAATATA
*
4036449 TATTTAATATTTA
1 AATTTAATA--TA
4036462 AATTTAATATA
1 AATTTAATATA
** *
4036473 AATCAAATAAA
1 AATTTAATATA
4036484 AATTTAA-ATTA
1 AATTTAATA-TA
*
4036495 AATTAAATAT
1 AATTTAATAT
4036505 TATGATTTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
10 1 0.02
11 31 0.72
12 1 0.02
13 10 0.23
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (11 bp):
AATTTAATATA
Found at i:4036486 original size:22 final size:22
Alignment explanation
Indices: 4036461--4036503 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4036451 TTTAATATTT
4036461 AAATTT-AATATAAATCAAATAA
1 AAATTTAAAT-TAAATCAAATAA
*
4036483 AAATTTAAATTAAATTAAATA
1 AAATTTAAATTAAATCAAATA
4036504 TTATGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATTTAAATTAAATCAAATAA
Found at i:4044519 original size:15 final size:17
Alignment explanation
Indices: 4044499--4044535 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
4044489 AAAATAAAAT
4044499 TTAAATT-ATTT-TTAA
1 TTAAATTCATTTATTAA
4044514 TTAAATTCATTTATTAA
1 TTAAATTCATTTATTAA
*
4044531 ATAAA
1 TTAAA
4044536 AAATGAGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 4 0.21
17 8 0.42
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAAATTCATTTATTAA
Done.