Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001838.1 Hibiscus syriacus cultivar Beakdansim tig00003721_pilon, 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: 3924084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 18
Found at i:1934383 original size:17 final size:17
Alignment explanation
Indices: 1934360--1934445 Score: 72
Period size: 17 Copynumber: 5.3 Consensus size: 17
1934350 ACCCGATTAT
1934360 CGGGTACCCGAAAAATC
1 CGGGTACCCGAAAAATC
* **
1934377 TGGGTACCCG-ATTA-C
1 CGGGTACCCGAAAAATC
*
1934392 CGGGTACCCGCAAAATC
1 CGGGTACCCGAAAAATC
**
1934409 CGGGTACCCG-ATTA-C
1 CGGGTACCCGAAAAATC
* *
1934424 CGGGTACCCGTAACATC
1 CGGGTACCCGAAAAATC
1934441 CGGGT
1 CGGGT
1934446 CGGGACACGG
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
15 21 0.38
16 8 0.15
17 26 0.47
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.17
Consensus pattern (17 bp):
CGGGTACCCGAAAAATC
Found at i:1934387 original size:32 final size:32
Alignment explanation
Indices: 1934345--1934445 Score: 157
Period size: 32 Copynumber: 3.2 Consensus size: 32
1934335 AACCGGGTAT
*
1934345 CGGGTACCCGATTATCGGGTACCCGAAAAATC
1 CGGGTACCCGATTACCGGGTACCCGAAAAATC
* *
1934377 TGGGTACCCGATTACCGGGTACCCGCAAAATC
1 CGGGTACCCGATTACCGGGTACCCGAAAAATC
* *
1934409 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCGGGTACCCGAAAAATC
1934441 CGGGT
1 CGGGT
1934446 CGGGACACGG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 63 1.00
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.19
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGAAAAATC
Found at i:1935868 original size:33 final size:34
Alignment explanation
Indices: 1935792--1935869 Score: 81
Period size: 33 Copynumber: 2.3 Consensus size: 34
1935782 ATATGATATT
* **
1935792 AAAATGAAATAAAAATTAAATATTAAATATATTTT
1 AAAAT-AAATAAAAATTAAATATTAAATATAATAC
*
1935827 AAAA-AAATAAATATTAAAATATTAAA-A-AATAC
1 AAAATAAATAAAAATT-AAATATTAAATATAATAC
1935859 AAAATAAATAA
1 AAAATAAATAA
1935870 TTTAAATACT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
32 6 0.16
33 17 0.46
34 10 0.27
35 4 0.11
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (34 bp):
AAAATAAATAAAAATTAAATATTAAATATAATAC
Found at i:1937096 original size:9 final size:8
Alignment explanation
Indices: 1937051--1937186 Score: 51
Period size: 8 Copynumber: 15.5 Consensus size: 8
1937041 GGTCAACAAA
1937051 AAAAATAAT
1 AAAAA-AAT
1937060 AAAATAAATT
1 AAAA-AAA-T
*
1937070 AAATAAAT
1 AAAAAAAT
1937078 AAGAAAAAAT
1 -A-AAAAAAT
1937088 AAAACAAAT
1 AAAA-AAAT
1937097 AAAAAAATTT
1 AAAAAAA--T
1937107 AAAAACAA-
1 AAAAA-AAT
1937115 AAAAGAAAT
1 AAAA-AAAT
1937124 CGAAATAAAAT
1 --AAA-AAAAT
*
1937135 AATAAAAT
1 AAAAAAAT
** *
1937143 TTAAAGA-
1 AAAAAAAT
*
1937150 ACAAAAAT
1 AAAAAAAT
*
1937158 AAAAAGAT
1 AAAAAAAT
*
1937166 AAAAAAAC
1 AAAAAAAT
*
1937174 ACTAAAAAT
1 A-AAAAAAT
1937183 AAAA
1 AAAA
1937187 TAAAAAAGGG
Statistics
Matches: 95, Mismatches: 17, Indels: 31
0.66 0.12 0.22
Matches are distributed among these distances:
7 4 0.04
8 36 0.38
9 28 0.29
10 17 0.18
11 9 0.09
12 1 0.01
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.17
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1937096 original size:19 final size:21
Alignment explanation
Indices: 1937074--1937122 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
1937064 TAAATTAAAT
1937074 AAATAAGAAAAA-AT-AAAAC
1 AAATAAGAAAAATATAAAAAC
*
1937093 AAATAA-AAAAATTTAAAAAC
1 AAATAAGAAAAATATAAAAAC
*
1937113 AAAAAAGAAA
1 AAATAAGAAA
1937123 TCGAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 5 0.20
19 7 0.28
20 10 0.40
21 3 0.12
ACGTcount: A:0.80, C:0.04, G:0.04, T:0.12
Consensus pattern (21 bp):
AAATAAGAAAAATATAAAAAC
Found at i:1937237 original size:21 final size:21
Alignment explanation
Indices: 1937198--1937253 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
1937188 AAAAAAGGGA
1937198 AAATAAAATAAAA-ATAATA-T
1 AAAT-AAATAAAATATAATATT
*
1937218 ATATATAATAAAATATAATATT
1 AAATA-AATAAAATATAATATT
1937240 AAATAAATAAAATA
1 AAATAAATAAAATA
1937254 AAAACTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.03
20 10 0.32
21 15 0.48
22 5 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATAAATAAAATATAATATT
Found at i:1948645 original size:22 final size:22
Alignment explanation
Indices: 1948620--1948661 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1948610 AGTCGAGGGT
*
1948620 TACATAGGTCATTCGGGACATA
1 TACATAGGTCATTCAGGACATA
1948642 TACATAGGTCATTCAGGACA
1 TACATAGGTCATTCAGGACA
1948662 AATTTCACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (22 bp):
TACATAGGTCATTCAGGACATA
Found at i:1952911 original size:20 final size:20
Alignment explanation
Indices: 1952882--1952920 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1952872 ATGGGTACCT
*
1952882 ATACTACTATAGTAGTATCG
1 ATACTACTATAGTAATATCG
*
1952902 ATACTGCTATAGTAATATC
1 ATACTACTATAGTAATATC
1952921 AAGTCCGACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (20 bp):
ATACTACTATAGTAATATCG
Found at i:1952981 original size:21 final size:21
Alignment explanation
Indices: 1952952--1953031 Score: 151
Period size: 21 Copynumber: 3.8 Consensus size: 21
1952942 AAATATTACA
1952952 AAGGTAGTACCGATACTCATTG
1 AAGG-AGTACCGATACTCATTG
1952974 AAGGAGTACCGATACTCATTG
1 AAGGAGTACCGATACTCATTG
1952995 AAGGAGTACCGATACTCATTG
1 AAGGAGTACCGATACTCATTG
1953016 AAGGAGTACCGATACT
1 AAGGAGTACCGATACT
1953032 ACTTGTTCTG
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 54 0.93
22 4 0.07
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (21 bp):
AAGGAGTACCGATACTCATTG
Found at i:1962281 original size:19 final size:19
Alignment explanation
Indices: 1962257--1962296 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1962247 TGAATAATTT
* *
1962257 AATCGAATATATAATTTTA
1 AATCGAATATAAAATCTTA
1962276 AATCGAATATAAAATCTTA
1 AATCGAATATAAAATCTTA
1962295 AA
1 AA
1962297 ATTCAATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (19 bp):
AATCGAATATAAAATCTTA
Found at i:1962419 original size:12 final size:13
Alignment explanation
Indices: 1962397--1962430 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1962387 TAAGATTTTC
1962397 TTTGAAAATCATT
1 TTTGAAAATCATT
1962410 TTTG-AAATCATT
1 TTTGAAAATCATT
*
1962422 TTTTAAAAT
1 TTTGAAAAT
1962431 TACCCCCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (13 bp):
TTTGAAAATCATT
Found at i:1964161 original size:19 final size:20
Alignment explanation
Indices: 1964120--1964161 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
1964110 AGTTTTCATG
*
1964120 AAAACAACATAATTAAATCA
1 AAAACAACATAATTAAAACA
* *
1964140 AAAACAACA-ATTTAAAAGA
1 AAAACAACATAATTAAAACA
1964159 AAA
1 AAA
1964162 TCATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.69, C:0.12, G:0.02, T:0.17
Consensus pattern (20 bp):
AAAACAACATAATTAAAACA
Found at i:1964629 original size:21 final size:23
Alignment explanation
Indices: 1964553--1964630 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 23
1964543 AACCTGACGG
*
1964553 GTGTATCGATACAC--TC-GGGA
1 GTGTATCGATACACATTCAAGGA
*
1964573 GTGTATGGATACACATTCAAGGA
1 GTGTATCGATACACATTCAAGGA
* *
1964596 GTGTATCGGTACACATTC-A-TA
1 GTGTATCGATACACATTCAAGGA
*
1964617 GTGTATCCATACAC
1 GTGTATCGATACAC
1964631 TTTGCAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 13 0.27
21 13 0.27
22 3 0.06
23 19 0.40
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (23 bp):
GTGTATCGATACACATTCAAGGA
Found at i:1968902 original size:18 final size:18
Alignment explanation
Indices: 1968861--1968903 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1968851 AACTCCAACG
*
1968861 TTCTTCTTTTTCTCTGTC
1 TTCTTCTTTATCTCTGTC
*
1968879 TCCTTCTTTATCTC-GTC
1 TTCTTCTTTATCTCTGTC
1968896 TTTCTTCT
1 -TTCTTCT
1968904 CGAGGTCTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.02, C:0.30, G:0.05, T:0.63
Consensus pattern (18 bp):
TTCTTCTTTATCTCTGTC
Found at i:1970666 original size:19 final size:19
Alignment explanation
Indices: 1970642--1970681 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1970632 CGAATAATTT
* *
1970642 AATCGAATATATAATTTTA
1 AATCGAATATAAAATCTTA
1970661 AATCGAATATAAAATCTTA
1 AATCGAATATAAAATCTTA
1970680 AA
1 AA
1970682 ATTCAATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (19 bp):
AATCGAATATAAAATCTTA
Found at i:1980926 original size:29 final size:29
Alignment explanation
Indices: 1980884--1980941 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
1980874 GACTGACTAG
*
1980884 AATAACACTACCATTACCAACTTTAACCT
1 AATAACACTACCATTACCAACTTGAACCT
1980913 AATAACACTACCATTACCAACTTGAACCT
1 AATAACACTACCATTACCAACTTGAACCT
1980942 TACCTGAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.41, C:0.31, G:0.02, T:0.26
Consensus pattern (29 bp):
AATAACACTACCATTACCAACTTGAACCT
Found at i:1990065 original size:215 final size:214
Alignment explanation
Indices: 1989673--1990384 Score: 1053
Period size: 215 Copynumber: 3.3 Consensus size: 214
1989663 ATTTTATGAA
* * *
1989673 AAATACAAATTT-AAGAATTAAATTGAACAAATATGAAATTGCAAATAAAAATTTAAATAAATTA
1 AAATA-AAATTTGAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTA
1989737 AACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACA
65 AACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACA
* ** * *
1989802 AAAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAATATCATTAAGTAAAAA
130 AAAAA-TACTAAATTATACCTATTTAAAAAGTTATGGGCCAATTAAAAATAGAAATAAGTAATAA
* *
1989867 GTATGGATCAATTTCATATGC
194 GTATGGGTCAATTTCAGATGC
* * *
1989888 AAATAAAATTTGAAGGACTAAATTAAAAAAATATGAAATTACAAATAAAAATTTAAATTAATTAA
1 AAATAAAATTTGAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
* *
1989953 GCAACACACATTGATGAGGGATCAAATTGAAATAATTTTAAATTGTGATGTTGAAATTAATACAA
66 ACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAA
1990018 AAAATACTAAATTATACCTATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAG
131 AAAATACTAAATTATACCTATTTAAAAAGTTATGGGCCAA-TTAAAAATAGAAATAAGTAATAAG
*
1990083 AATGGGTCAATTTCAGATGC
195 TATGGGTCAATTTCAGATGC
* * *
1990103 AAATAAAATTTGGAGGACTAAATTGAACAAATATAAAATTACAAATAAAAATTTAAATAAACTAA
1 AAATAAAATTTGAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
* *
1990168 ACAACACA-A---A--AGGGATCAAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATACAA
66 ACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAA
** *
1990227 AATGTACTAAATTATA-CTAATTTAAAAATTTATGGGCCAATTAATAAATAGAAATAAGTAATAA
131 AAAATACTAAATTATACCT-ATTTAAAAAGTTATGGGCCAATTAA-AAATAGAAATAAGTAATAA
1990291 GTATGGGTCAATTTCAGATGC
194 GTATGGGTCAATTTCAGATGC
* * * * * *
1990312 AAATAAAATGTGGATGACTAAATTGAATAAACATGAAATTACAAATAACAATTTAAATAAATTAA
1 AAATAAAATTTGAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
1990377 ACAACACA
66 ACAACACA
1990385 AAAGGGATCA
Statistics
Matches: 456, Mismatches: 37, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
208 6 0.01
209 185 0.41
211 1 0.00
214 42 0.09
215 222 0.49
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (214 bp):
AAATAAAATTTGAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
ACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAA
AAAATACTAAATTATACCTATTTAAAAAGTTATGGGCCAATTAAAAATAGAAATAAGTAATAAGT
ATGGGTCAATTTCAGATGC
Found at i:1990473 original size:2 final size:2
Alignment explanation
Indices: 1990468--1990579 Score: 50
Period size: 2 Copynumber: 54.5 Consensus size: 2
1990458 AAAACAACTA
* * * *
1990468 AT AT AT AT AT AT AT AT GT GT A- AT AT AA ACT AT AT AGT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT
* * * *
1990511 AT AA AGT AT AT GT AT -T AT AT AT AT AA ACT AT AT AGT TT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT
* * *
1990553 AT AT GT AT -T AT GT AT AA ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT A
1990580 CAATGTATAA
Statistics
Matches: 81, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
1 3 0.04
2 72 0.89
3 6 0.07
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1990502 original size:20 final size:21
Alignment explanation
Indices: 1990468--1990790 Score: 86
Period size: 20 Copynumber: 16.1 Consensus size: 21
1990458 AAAACAACTA
* *
1990468 ATATATATA-TATATATGTGT
1 ATATATAAACTATATATGTAT
*
1990488 A-ATATAAACTATATA-GTTT
1 ATATATAAACTATATATGTAT
*
1990507 ATATATAAAGTATATGTAT-TAT
1 ATATATAAACTATA--TATGTAT
*
1990529 ATATATAAACTATATA-GTTT
1 ATATATAAACTATATATGTAT
**
1990549 ATATAT-ATGTAT-TATGTAT
1 ATATATAAACTATATATGTAT
* * *
1990568 AAACTATATA-TACA-ATGTAT
1 ATA-TATAAACTATATATGTAT
* * * *
1990588 AAACTGTAATACTATAT-GGTTT
1 ATA-TATAA-ACTATATATGTAT
* *
1990610 ATATATGAAC--TAT-TGAACT
1 ATATATAAACTATATATGTA-T
* * * *
1990629 ATATAGAACCTACATA-GTTT
1 ATATATAAACTATATATGTAT
* *
1990649 ATATATAAATTATATATGAATT
1 ATATATAAACTATATATGTA-T
*
1990671 ATATATAAACTATACAAT-T-T
1 ATATATAAACTATA-TATGTAT
* *
1990691 ATATTTATA-TAT-TATGTAT
1 ATATATAAACTATATATGTAT
*
1990710 A-ATTATAAA-TA-ATATATAT
1 ATA-TATAAACTATATATGTAT
* * *
1990729 -TGTATAAATTATATA-GTTT
1 ATATATAAACTATATATGTAT
*
1990748 ATTAATATAAACTATATA-GTTT
1 A-T-ATATAAACTATATATGTAT
*
1990770 ATATATATA-TATATAT-TAT
1 ATATATAAACTATATATGTAT
1990789 AT
1 AT
1990791 GGTTTAGGGT
Statistics
Matches: 220, Mismatches: 52, Indels: 63
0.66 0.16 0.19
Matches are distributed among these distances:
17 2 0.01
18 14 0.06
19 58 0.26
20 78 0.35
21 10 0.05
22 56 0.25
23 2 0.01
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (21 bp):
ATATATAAACTATATATGTAT
Found at i:1990534 original size:22 final size:22
Alignment explanation
Indices: 1990489--1990556 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
1990479 TATATGTGTA
1990489 ATATAAACTATATAG-TT-TAT
1 ATATAAACTATATAGTTTATAT
*
1990509 ATATAAAGTATAT-GTATTATAT
1 ATATAAACTATATAGT-TTATAT
1990531 ATATAAACTATATAGTTTATAT
1 ATATAAACTATATAGTTTATAT
1990553 ATAT
1 ATAT
1990557 GTATTATGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.02
20 12 0.29
21 2 0.05
22 25 0.60
23 2 0.05
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (22 bp):
ATATAAACTATATAGTTTATAT
Found at i:1990576 original size:42 final size:42
Alignment explanation
Indices: 1990489--1990577 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
1990479 TATATGTGTA
*
1990489 ATATAAACTATATAGTTTATATATAAAGTATATGTATTATAT
1 ATATAAACTATATAGTTTATATATAAAGTATATGTATTAAAT
*
1990531 ATATAAACTATATAGTTTATATAT-ATGTATTATGTA-TAAACT
1 ATATAAACTATATAGTTTATATATAAAGTA-TATGTATTAAA-T
1990573 ATATA
1 ATATA
1990578 TACAATGTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 7 0.16
42 36 0.84
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (42 bp):
ATATAAACTATATAGTTTATATATAAAGTATATGTATTAAAT
Found at i:1990661 original size:11 final size:11
Alignment explanation
Indices: 1990647--1990684 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
1990637 CCTACATAGT
1990647 TTATATATAAA
1 TTATATATAAA
*
1990658 TTATATATGAA
1 TTATATATAAA
1990669 TTATATATAAA
1 TTATATATAAA
*
1990680 CTATA
1 TTATA
1990685 CAATTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (11 bp):
TTATATATAAA
Found at i:1990710 original size:17 final size:17
Alignment explanation
Indices: 1990690--1990743 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
1990680 CTATACAATT
* *
1990690 TATATTTATATATTATG
1 TATATTTATAAATTATA
* *
1990707 TATAATTATAAATAATA
1 TATATTTATAAATTATA
1990724 TATATTGTATAAATTATA
1 TATATT-TATAAATTATA
1990742 TA
1 TA
1990744 GTTTATTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:1990763 original size:22 final size:24
Alignment explanation
Indices: 1990722--1990780 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 24
1990712 TTATAAATAA
* *
1990722 TATATATTGTATAAATTATATAGTT
1 TATATA-TATATAAACTATATAGTT
1990747 TAT-TA-ATATAAACTATATAGTT
1 TATATATATATAAACTATATAGTT
1990769 TATATATATATA
1 TATATATATATA
1990781 TATATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 18 0.60
23 2 0.07
24 7 0.23
25 3 0.10
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (24 bp):
TATATATATATAAACTATATAGTT
Found at i:1990909 original size:12 final size:12
Alignment explanation
Indices: 1990869--1990913 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
1990859 TATAAACTAC
*
1990869 ATACTATAATTT
1 ATACTATATTTT
*
1990881 ATATTTATATTTAT
1 ATA-CTATATTT-T
1990895 ATACTATATTTT
1 ATACTATATTTT
1990907 ATACTAT
1 ATACTAT
1990914 TTATATAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 11 0.39
13 13 0.46
14 4 0.14
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (12 bp):
ATACTATATTTT
Found at i:1990920 original size:25 final size:26
Alignment explanation
Indices: 1990869--1990941 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 26
1990859 TATAAACTAC
*
1990869 ATACTATAATTTATATTTATATTTAT
1 ATACTATAATTTATATCTATATTTAT
*
1990895 ATACTATATTTTATA-CTAT-TTATAT
1 ATACTATAATTTATATCTATATT-TAT
* * *
1990920 AAACTATAGTTTATATTTATAT
1 ATACTATAATTTATATCTATAT
1990942 ACTATATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 2 0.05
25 19 0.49
26 17 0.44
27 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.55
Consensus pattern (26 bp):
ATACTATAATTTATATCTATATTTAT
Found at i:1990948 original size:58 final size:58
Alignment explanation
Indices: 1990853--1990965 Score: 133
Period size: 58 Copynumber: 1.9 Consensus size: 58
1990843 TTAGGGTTTA
* * *
1990853 TATTTATATAAACTACATACTATAATTTATATTTATATTTAT-ATACTATATTTTATAC
1 TATTTATATAAACTACATACTATAATTTATATCTATATATATGA-ACTATAGTTTATAC
* *
1990911 TATTTATATAAACT--ATAGTTTATATTTATATACTATATATATGAACTATAGTTTA
1 TATTTATATAAACTACATACTATA-ATTTATAT-CTATATATATGAACTATAGTTTA
1990966 CATATGAACT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
56 6 0.13
57 8 0.17
58 32 0.68
59 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (58 bp):
TATTTATATAAACTACATACTATAATTTATATCTATATATATGAACTATAGTTTATAC
Found at i:1990952 original size:33 final size:33
Alignment explanation
Indices: 1990899--1991010 Score: 120
Period size: 33 Copynumber: 3.4 Consensus size: 33
1990889 ATTTATATAC
*
1990899 TATATTT-TATACTATTTATATAAACTATAGTT
1 TATATTTATATACTATATATATAAACTATAGTT
*
1990931 TATATTTATATACTATATATATGAACTATAGTT
1 TATATTTATATACTATATATATAAACTATAGTT
** * *
1990964 TACATATGAACTATA-TATATATATATACTAAAGTT
1 T--ATATTTA-TATACTATATATATAAACTATAGTT
*
1990999 GATATTTATATA
1 TATATTTATATA
1991011 TGAACTATAG
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
32 11 0.17
33 29 0.44
35 22 0.33
36 4 0.06
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.47
Consensus pattern (33 bp):
TATATTTATATACTATATATATAAACTATAGTT
Found at i:1990970 original size:18 final size:18
Alignment explanation
Indices: 1990949--1991156 Score: 98
Period size: 18 Copynumber: 10.7 Consensus size: 18
1990939 TATACTATAT
1990949 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
* *
1990967 ATATGAACTATATATATATAT
1 ATATGAACTATA-GT-T-TAC
* * *
1990988 ATACTAAAGTTGATA-TTTAT
1 ATA-TGAA-CT-ATAGTTTAC
*
1991008 ATATGAACTATAGGTTAC
1 ATATGAACTATAGTTTAC
* * *
1991026 ATATAAACTATATAATTTAT
1 ATATGAAC--TATAGTTTAC
1991046 ATACT-AACTATAGTTTAC
1 ATA-TGAACTATAGTTTAC
*
1991064 ATATAAACTATAGTTGATATTTAC
1 ATATGAACTATA---G---TTTAC
1991088 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
* *
1991106 ATATGAATTATA-TATATAT
1 ATATGAACTATAGT-T-TAC
*
1991125 ATATAAACTATATAGTTTAC
1 ATATGAAC--TATAGTTTAC
*
1991145 ATATGACCTATA
1 ATATGAACTATA
1991157 TATATATACT
Statistics
Matches: 146, Mismatches: 22, Indels: 44
0.69 0.10 0.21
Matches are distributed among these distances:
17 5 0.03
18 62 0.42
19 12 0.08
20 28 0.19
21 14 0.10
22 5 0.03
23 1 0.01
24 19 0.13
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.41
Consensus pattern (18 bp):
ATATGAACTATAGTTTAC
Found at i:1991055 original size:38 final size:38
Alignment explanation
Indices: 1991002--1991158 Score: 165
Period size: 38 Copynumber: 4.0 Consensus size: 38
1990992 TAAAGTTGAT
*
1991002 ATTTATATATGAACTATAGGTTACATATAAACTATATA
1 ATTTATATATGAACTATAGTTTACATATAAACTATATA
1991040 ATTTATATACT-AACTATAGTTTACATATAAACTATAGTTGA
1 ATTTATATA-TGAACTATAGTTTACATATAAACTATA--T-A
* * *
1991081 TATTTACATATGAACTATAGTTTACATATGAATTATAT-
1 -ATTTATATATGAACTATAGTTTACATATAAACTATATA
* * * *
1991119 ATATATATATAAACTATATAGTTTACATATGACCTATATA
1 ATTTATATATGAAC--TATAGTTTACATATAAACTATATA
1991159 TATATACTAT
Statistics
Matches: 101, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
37 11 0.11
38 33 0.33
39 22 0.22
40 2 0.02
41 2 0.02
42 31 0.31
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (38 bp):
ATTTATATATGAACTATAGTTTACATATAAACTATATA
Found at i:1991081 original size:80 final size:80
Alignment explanation
Indices: 1990984--1991148 Score: 226
Period size: 80 Copynumber: 2.0 Consensus size: 80
1990974 CTATATATAT
* * *
1990984 ATATATACTAAAGTTGATATTTATATATGAACTATAGGTTACATATAAACTATATA-ATTTATAT
1 ATATAAACTAAAGTTGATATTTACATATGAACTATAGGTTACATATAAACTATATATATATATAT
1991048 ACTAAC-TATAGTTTAC
66 A--AACATATAGTTTAC
* * * *
1991064 ATATAAACTATAGTTGATATTTACATATGAACTATAGTTTACATATGAATTATATATATATATAT
1 ATATAAACTAAAGTTGATATTTACATATGAACTATAGGTTACATATAAACTATATATATATATAT
1991129 AAACTATATAGTTTAC
66 AAAC-ATATAGTTTAC
1991145 ATAT
1 ATAT
1991149 GACCTATATA
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
79 3 0.04
80 50 0.67
81 22 0.29
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (80 bp):
ATATAAACTAAAGTTGATATTTACATATGAACTATAGGTTACATATAAACTATATATATATATAT
AAACATATAGTTTAC
Found at i:1991199 original size:22 final size:22
Alignment explanation
Indices: 1991157--1991199 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1991147 ATGACCTATA
*
1991157 TATATATACTATAGTTGACATT
1 TATATATACTATAATTGACATT
*
1991179 TATATACTA-TATAATTTACAT
1 TATATA-TACTATAATTGACAT
1991200 ATGACCTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (22 bp):
TATATATACTATAATTGACATT
Found at i:1991213 original size:2 final size:2
Alignment explanation
Indices: 1991206--1991286 Score: 67
Period size: 2 Copynumber: 39.0 Consensus size: 2
1991196 ACATATGACC
* * *
1991206 TA TA TA TA TA TA TA TA CA TA CTA TA GTT TA TA TT TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA
*
1991249 TA TA T- TA TA TA TA TA AA CTA TA TA TA CTA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA
1991287 ATTTTCATAT
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
1 2 0.03
2 54 0.84
3 8 0.12
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1991227 original size:61 final size:62
Alignment explanation
Indices: 1991152--1991281 Score: 174
Period size: 61 Copynumber: 2.1 Consensus size: 62
1991142 TACATATGAC
* * *
1991152 CTATATATATATACTATAGTTGACATTTATATACTATATAATT-TACATATGACCTATATATA
1 CTATATATACATACTATAGTTGACATTTATATACTATAT-ATTATACATATAAACTATATATA
* * * *
1991214 -TATATATACATACTATAGTTTATATTTATATATTATATATTATATATATAAACTATATATA
1 CTATATATACATACTATAGTTGACATTTATATACTATATATTATACATATAAACTATATATA
1991275 CTATATA
1 CTATATA
1991282 GTATAATTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
60 3 0.05
61 50 0.85
62 6 0.10
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.46
Consensus pattern (62 bp):
CTATATATACATACTATAGTTGACATTTATATACTATATATTATACATATAAACTATATATA
Found at i:1991231 original size:92 final size:93
Alignment explanation
Indices: 1991064--1991235 Score: 233
Period size: 92 Copynumber: 1.8 Consensus size: 93
1991054 TATAGTTTAC
* * *
1991064 ATATAAACTATAGTTGATATTTACATATGAACTATAGTTTACATATGAATTATATATATATATAT
1 ATATAAACTATAGTTGACATTTACATAT-AACTATAATTTACATATGAACTATATATATATATAT
1991129 AAACTATATAGTTTACATATGACCTATAT
65 AAACTATATAGTTTACATATGACCTATAT
* * *
1991158 ATATATACTATAGTTGACATTTATATACT-A-TATAATTTACATATGACCTATATATATATATAT
1 ATATAAACTATAGTTGACATTTACATA-TAACTATAATTTACATATGAACTATATATATATATAT
*
1991221 ACA-TACTATAGTTTA
65 AAACTA-TATAGTTTA
1991236 TATTTATATA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
91 2 0.03
92 41 0.59
93 1 0.01
94 24 0.35
95 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (93 bp):
ATATAAACTATAGTTGACATTTACATATAACTATAATTTACATATGAACTATATATATATATATA
AACTATATAGTTTACATATGACCTATAT
Found at i:1991251 original size:92 final size:93
Alignment explanation
Indices: 1991002--1991308 Score: 225
Period size: 92 Copynumber: 3.2 Consensus size: 93
1990992 TAAAGTTGAT
* ** * * * * *
1991002 ATTTATATATGAACTATAGGT-TACATATAAACTATATAATTTATATACTAACTATAGTTTACAT
1 ATTTACATATGAACTATATATATATATATAAACTATATAGTTTACATA-TGAC-ATA---TATAT
* *
1991066 ATAAACTATAGTTGATATTTACATATGAACTATA
61 ATATACTATAGTTGACATTTACATAT-AACTATA
* * *
1991100 GTTTACATATGAATTATATATATATATATAAACTATATAGTTTACATATGACCTATATATATATA
1 ATTTACATATGAACTATATATATATATATAAACTATATAGTTTACATATGACATATATATATATA
*
1991165 CTATAGTTGACATTTATATACT-A-TATA
66 CTATAGTTGACATTTACATA-TAACTATA
* * * * *
1991192 ATTTACATATGACCTATATATATATATATACA-TACTATAGTTTATAT-TTATATATTATATATT
1 ATTTACATATGAACTATATATATATATATAAACTA-TATAGTTTACATATGACATA-TATATA-T
** *
1991255 ATA-TATA-TAAACTATATATAC-TATATAGTATA
63 ATACTATAGTTGAC-AT-T-TACATATA-ACTATA
*
1991287 ATTTTCATATGAACTATATATA
1 ATTTACATATGAACTATATATA
1991309 AAAACCATAT
Statistics
Matches: 171, Mismatches: 27, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
91 9 0.05
92 56 0.33
93 8 0.05
94 29 0.17
95 25 0.15
97 2 0.01
98 19 0.11
99 23 0.13
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (93 bp):
ATTTACATATGAACTATATATATATATATAAACTATATAGTTTACATATGACATATATATATATA
CTATAGTTGACATTTACATATAACTATA
Found at i:1991270 original size:20 final size:20
Alignment explanation
Indices: 1990937--1991415 Score: 80
Period size: 20 Copynumber: 24.6 Consensus size: 20
1990927 AGTTTATATT
* *
1990937 TATATACTATATATATGAAC
1 TATATATTATATATATAAAC
* * *
1990957 TATA-GTT-TACATATGAAC
1 TATATATTATATATATAAAC
*
1990975 TATATATATATATATACTAAAG
1 TATATAT-TATATATA-TAAAC
*
1990997 T-TGATATT-TATATATGAAC
1 TAT-ATATTATATATATAAAC
** *
1991016 TATA-GGT-TACATATAAAC
1 TATATATTATATATATAAAC
1991034 TATATAATT-TATATACT-AAC
1 TATAT-ATTATATATA-TAAAC
* *
1991054 TATA-GTT-TACATATAAAC
1 TATATATTATATATATAAAC
* * *
1991072 TATAGTTGATATTTACATATGAAC
1 TATA--T-AT-TATATATATAAAC
* * * *
1991096 TATA-GTT-TACATATGAAT
1 TATATATTATATATATAAAC
1991114 TATATA-TATATATATAAAC
1 TATATATTATATATATAAAC
* * *
1991133 TATATAGTT-TACATATGACC
1 TATATA-TTATATATATAAAC
*
1991153 TATATA-TATATACTAT--AG
1 TATATATTATATA-TATAAAC
*
1991171 T-TGACA-T-T-TATAT--AC
1 TAT-ATATTATATATATAAAC
* * *
1991186 TATATAATT-TACATATGACC
1 TATAT-ATTATATATATAAAC
1991206 TATATA-TATATATATACATAC
1 TATATATTATATATATA-A-AC
* * *
1991227 TATAGT-TTATATTTATATAT
1 TATA-TATTATATATATAAAC
1991247 TATATATTATATATATAAAC
1 TATATATTATATATATAAAC
* *
1991267 TATATA-TA-CTATAT--AG
1 TATATATTATATATATAAAC
*
1991283 TATA-ATT-T-TCATATGAAC
1 TATATATTATAT-ATATAAAC
* * *
1991301 TATATATAAAAACCATATAAAC
1 TATATAT-TATA-TATATAAAC
* **
1991323 TATATACTATAGT-TGAT-ATT
1 TATATATTATA-TAT-ATAAAC
* * **
1991343 TATATACTATATAAAATAATT
1 TATATATTATAT-ATATAAAC
*
1991364 TAGACTA-TAGTATATATAAAC
1 TATA-TATTA-TATATATAAAC
1991385 TATA-A-TATATATATAAAC
1 TATATATTATATATATAAAC
1991403 TATATATTATATA
1 TATATATTATATA
1991416 GTTCATTAGT
Statistics
Matches: 340, Mismatches: 66, Indels: 106
0.66 0.13 0.21
Matches are distributed among these distances:
15 8 0.02
16 14 0.04
17 5 0.01
18 92 0.27
19 42 0.12
20 93 0.27
21 34 0.10
22 37 0.11
23 1 0.00
24 14 0.04
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (20 bp):
TATATATTATATATATAAAC
Found at i:1991426 original size:51 final size:53
Alignment explanation
Indices: 1991371--1991502 Score: 191
Period size: 51 Copynumber: 2.5 Consensus size: 53
1991361 ATTTAGACTA
*
1991371 TAGTATATATAAACTATAATATATATATAAACTATATA-T-TATATA-GTTCAT
1 TAGTATATATAAACTAT-ATATATATATAAACTATACATTATATATATGTTCAT
* *
1991422 TAGTATATATAAACTATATGGTATATATAAACTATACATTATATATATTTTCAT
1 TAGTATATATAAACTATAT-ATATATATAAACTATACATTATATATATGTTCAT
1991476 TAGTATATATAAACTATATAT-TATATA
1 TAGTATATATAAACTATATATATATATA
1991503 GTTCATTAGT
Statistics
Matches: 73, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
50 2 0.03
51 33 0.45
52 7 0.10
53 7 0.10
54 24 0.33
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (53 bp):
TAGTATATATAAACTATATATATATATAAACTATACATTATATATATGTTCAT
Found at i:1991500 original size:18 final size:18
Alignment explanation
Indices: 1991369--1991552 Score: 130
Period size: 18 Copynumber: 10.2 Consensus size: 18
1991359 TAATTTAGAC
1991369 TATAGTATATATAAACTA
1 TATAGTATATATAAACTA
1991387 TAATA-TATATATAAACTA
1 T-ATAGTATATATAAACTA
**
1991405 TATA-T-TATAT-AGTTCA
1 TATAGTATATATAAACT-A
1991421 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
*
1991438 TATGGTATATATAAACTA
1 TATAGTATATATAAACTA
* * ***
1991456 TACATTATATATATTTTCA
1 TATAGTATATATAAACT-A
1991475 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
* * *
1991492 TATATTATATAGTTCATTAGTA
1 TATAGTATATA--T-A-AACTA
*
1991514 TATA-TAAAGTATAAACTA
1 TATAGTATA-TATAAACTA
*
1991532 TATAGTATATGTAAACTA
1 TATAGTATATATAAACTA
1991550 TAT
1 TAT
1991553 TAGTGTACTA
Statistics
Matches: 128, Mismatches: 24, Indels: 28
0.71 0.13 0.16
Matches are distributed among these distances:
15 4 0.03
16 8 0.06
17 13 0.10
18 79 0.62
19 9 0.07
20 2 0.02
21 4 0.03
22 9 0.07
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (18 bp):
TATAGTATATATAAACTA
Found at i:1991513 original size:33 final size:33
Alignment explanation
Indices: 1991442--1991537 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
1991432 AAACTATATG
* *
1991442 GTATATATAAACTATACATTATATATATTTTCATTA
1 GTATATATAAACTATA-AAT-TATATA-GTTCATTA
*
1991478 GTATATATAAACTATATATTATATAGTTCATTA
1 GTATATATAAACTATAAATTATATAGTTCATTA
* *
1991511 GTATATATAAAGTATAAACTATATAGT
1 GTATATATAAACTATAAATTATATAGT
1991538 ATATGTAAAC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
33 31 0.57
34 6 0.11
35 1 0.02
36 16 0.30
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (33 bp):
GTATATATAAACTATAAATTATATAGTTCATTA
Found at i:1991552 original size:87 final size:87
Alignment explanation
Indices: 1991392--1991552 Score: 234
Period size: 87 Copynumber: 1.9 Consensus size: 87
1991382 AACTATAATA
***
1991392 TATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATATGGTATATATAAACTAT
1 TATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATAAACTATATATAAACTAT
* *
1991457 ACATTATATATATTTTCATTAG
66 AAACTATATATATTTTCATTAG
* * *
1991479 TATATATAAACTATATATTATATAGTTCATTAGTATATATAAAGTATAAACTATATAGTATA-TG
1 TATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATAAACTATATA-TAAACTA
1991543 TAAACTATAT
65 TAAACTATAT
1991553 TAGTGTACTA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
87 62 0.95
88 3 0.05
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (87 bp):
TATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATAAACTATATATAAACTAT
AAACTATATATATTTTCATTAG
Found at i:1991588 original size:21 final size:21
Alignment explanation
Indices: 1991563--1991615 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1991553 TAGTGTACTA
* *
1991563 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAAAC
*
1991584 TATAGTATATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
1991605 TATAGTTTATA
1 TATAGTTTATA
1991616 TTAATGTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.47
Consensus pattern (21 bp):
TATAGTTTATAATTTATAAAC
Found at i:1991628 original size:20 final size:21
Alignment explanation
Indices: 1991548--1991644 Score: 72
Period size: 22 Copynumber: 4.5 Consensus size: 21
1991538 ATATGTAAAC
*
1991548 TATATTAGTGTACTATATAGTT
1 TATATTAATGTAC-ATATAGTT
* * * *
1991570 TATACTTTAT-AACCTATAGTA
1 TATA-TTAATGTACATATAGTT
* **
1991591 TATAATTTATAAAC-TATAGTT
1 TAT-ATTAATGTACATATAGTT
1991612 TATATTAATGTACTATATAGTT
1 TATATTAATGTAC-ATATAGTT
1991634 TATATTAATGT
1 TATATTAATGT
1991645 TAATTATATT
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
20 7 0.11
21 23 0.38
22 28 0.46
23 3 0.05
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.48
Consensus pattern (21 bp):
TATATTAATGTACATATAGTT
Found at i:1991675 original size:14 final size:14
Alignment explanation
Indices: 1991656--1991682 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1991646 AATTATATTA
1991656 ACTATATTTTATAC
1 ACTATATTTTATAC
1991670 ACTATATTTTATA
1 ACTATATTTTATA
1991683 TTAATATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
ACTATATTTTATAC
Found at i:1991698 original size:15 final size:15
Alignment explanation
Indices: 1991678--1991740 Score: 78
Period size: 15 Copynumber: 4.3 Consensus size: 15
1991668 ACACTATATT
1991678 TTATATTAATATTAA
1 TTATATTAATATTAA
1991693 TTATATTAATATTAA
1 TTATATTAATATTAA
*
1991708 TTATAAT-ATA-TAA
1 TTATATTAATATTAA
*
1991721 TTAGT-TTAATATTAG
1 TTA-TATTAATATTAA
1991736 TTATA
1 TTATA
1991741 AATAGTTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
13 7 0.17
14 8 0.20
15 26 0.63
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
TTATATTAATATTAA
Found at i:1991721 original size:28 final size:27
Alignment explanation
Indices: 1991684--1991741 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
1991674 TATTTTATAT
1991684 TAATATTAATTA-TATTAATATTAATTA
1 TAATATTAATTAGT-TTAATATTAATTA
*
1991711 TAATATATAATTAGTTTAATATTAGTTA
1 TAATAT-TAATTAGTTTAATATTAATTA
1991739 TAA
1 TAA
1991742 ATAGTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 6 0.21
28 21 0.75
29 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (27 bp):
TAATATTAATTAGTTTAATATTAATTA
Found at i:1994702 original size:51 final size:48
Alignment explanation
Indices: 1994646--1994755 Score: 168
Period size: 51 Copynumber: 2.2 Consensus size: 48
1994636 AATATAAAAC
*
1994646 TAAATTTTAAAAAGTAATCATATTAATTTAATTATCATAATAATTTATGA
1 TAAATTTTAAAAAGTAACCATATTAATTTAATTATCAT--TAATTTATGA
*
1994696 TAAAATTTTAAAAAGTAACCATATTAATTTAATTATCATTAATTTATTA
1 T-AAATTTTAAAAAGTAACCATATTAATTTAATTATCATTAATTTATGA
1994745 TAAA-TTTAAAA
1 TAAATTTTAAAA
1994756 TAATATAATT
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
47 7 0.12
48 3 0.05
49 10 0.18
50 1 0.02
51 36 0.63
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (48 bp):
TAAATTTTAAAAAGTAACCATATTAATTTAATTATCATTAATTTATGA
Found at i:1994867 original size:16 final size:16
Alignment explanation
Indices: 1994848--1994886 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1994838 TGAGTCAATT
*
1994848 ACAGGTCAGGTTCATA
1 ACAGGTCAGGTTCAAA
*
1994864 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTCAAA
1994880 ACAGGTC
1 ACAGGTC
1994887 GGGTAATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTCAAA
Found at i:1995617 original size:22 final size:22
Alignment explanation
Indices: 1995583--1995645 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
1995573 ATTTGATATT
* *
1995583 TTCATCCTTTTTATTTTTTCTCTT
1 TTCA-CCTCTTTATTTTTTCT-TC
*
1995607 TTC-CCTCTTTA-TTCTTCTTC
1 TTCACCTCTTTATTTTTTCTTC
1995627 TTCATCCTCTTTATTTTTT
1 TTCA-CCTCTTTATTTTTT
1995646 GGTATTTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 4 0.12
21 6 0.19
22 15 0.47
23 4 0.12
24 3 0.09
ACGTcount: A:0.08, C:0.25, G:0.00, T:0.67
Consensus pattern (22 bp):
TTCACCTCTTTATTTTTTCTTC
Found at i:1999660 original size:21 final size:21
Alignment explanation
Indices: 1999635--1999695 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
1999625 AGCCATGGTG
*
1999635 AAGAAGGAAAGAAGGAAAGCC
1 AAGAAGGAAAGAAAGAAAGCC
1999656 AAGAAGGAAAGAAAGAAAGCC
1 AAGAAGGAAAGAAAGAAAGCC
* *
1999677 AAGAAGAAAAGAGAGAAAG
1 AAGAAGGAAAGAAAGAAAG
1999696 AAACTTGCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.62, C:0.07, G:0.31, T:0.00
Consensus pattern (21 bp):
AAGAAGGAAAGAAAGAAAGCC
Found at i:2000310 original size:184 final size:183
Alignment explanation
Indices: 1999992--2000378 Score: 598
Period size: 184 Copynumber: 2.1 Consensus size: 183
1999982 ATTAAATTTT
* * * * *
1999992 AAATTTTAAATATATTATATATAACATATGAGCTCAGTCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
*
2000057 TTTAAGATCTAATAATTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
66 TTTAAGATCTAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
*
2000122 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTAATTAAA
* *
2000176 AAATATTATATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
* * * *
2000241 TTTAAGATAC-AATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATT
66 TTTAAGAT-CTAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATATAAAATT
2000305 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTAATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTAATTAAA
* * *
2000359 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
2000379 AATTAAAAAA
Statistics
Matches: 185, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
182 8 0.04
183 21 0.11
184 155 0.84
185 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGAGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
TTTAAGATCTAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTAATTAAA
Found at i:2002011 original size:14 final size:14
Alignment explanation
Indices: 2001992--2002035 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
2001982 ATTTTTGTTA
2001992 ATTTAATATTATAT
1 ATTTAATATTATAT
2002006 ATTTAATAATTATA-
1 ATTTAAT-ATTATAT
*
2002020 ATTTAATAATATAT
1 ATTTAATATTATAT
2002034 AT
1 AT
2002036 ATATATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 5 0.19
14 16 0.59
15 6 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTAATATTATAT
Found at i:2002122 original size:26 final size:26
Alignment explanation
Indices: 2002087--2002136 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2002077 TTATTATAAT
* *
2002087 TTATTTAATAGGAGTCATTTCTTATA
1 TTATTTAATAAGAATCATTTCTTATA
*
2002113 TTATTTAATAAGAATGATTTCTTA
1 TTATTTAATAAGAATCATTTCTTA
2002137 ATTTAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.50
Consensus pattern (26 bp):
TTATTTAATAAGAATCATTTCTTATA
Found at i:2002287 original size:25 final size:24
Alignment explanation
Indices: 2002256--2002306 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 24
2002246 AATTTATTAT
2002256 ATATATATATATAATT-ATTAATAAA
1 ATATATAT-TAT-ATTAATTAATAAA
2002281 ATATATATTATATTAAATTAATAAA
1 ATATATATTATATT-AATTAATAAA
2002306 A
1 A
2002307 AAATACGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 3 0.12
24 3 0.12
25 18 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATATATTATATTAATTAATAAA
Found at i:2002297 original size:17 final size:19
Alignment explanation
Indices: 2002243--2002291 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
2002233 TCCATTAAGT
*
2002243 TATAATTTATTATATATATATA
1 TATAA-TTATTA-ATA-AAATA
2002265 TATAATTATTAATAAAATA
1 TATAATTATTAATAAAATA
2002284 TAT-ATTAT
1 TATAATTAT
2002292 ATTAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 5 0.19
19 7 0.27
20 3 0.12
21 6 0.23
22 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATAATTATTAATAAAATA
Found at i:2002309 original size:28 final size:29
Alignment explanation
Indices: 2002253--2002311 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
2002243 TATAATTTAT
* *
2002253 TATATATATATATATAATTATTAATAAAA
1 TATATATATATATATAATTAATAAAAAAA
2002282 TATATAT-TATAT-TAAATTAATAAAAAAA
1 TATATATATATATAT-AATTAATAAAAAAA
2002310 TA
1 TA
2002312 CGAATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 1 0.04
28 19 0.70
29 7 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
TATATATATATATATAATTAATAAAAAAA
Found at i:2002588 original size:25 final size:25
Alignment explanation
Indices: 2002554--2002604 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
2002544 GTATTGGTCC
* * *
2002554 CCGTCCCCGTCTCCGTTTAAAAAAT
1 CCGTACCCGTCCCCGCTTAAAAAAT
2002579 CCGTACCCGTCCCCGCTTAAAAAAT
1 CCGTACCCGTCCCCGCTTAAAAAAT
2002604 C
1 C
2002605 ACTGGGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.39, G:0.12, T:0.24
Consensus pattern (25 bp):
CCGTACCCGTCCCCGCTTAAAAAAT
Found at i:2002745 original size:17 final size:17
Alignment explanation
Indices: 2002723--2002779 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
2002713 CGGGCCAGGT
2002723 ATATATATTTAAATTAA
1 ATATATATTTAAATTAA
* *
2002740 ATATATAAATATTATATATAT
1 ATATAT--AT-TTAAAT-TAA
*
2002761 ATATATATTTAATTTAA
1 ATATATATTTAAATTAA
2002778 AT
1 AT
2002780 TAAATTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
17 10 0.32
18 4 0.13
19 4 0.13
20 5 0.16
21 8 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATATTTAAATTAA
Found at i:2002761 original size:4 final size:4
Alignment explanation
Indices: 2002722--2002812 Score: 52
Period size: 4 Copynumber: 24.5 Consensus size: 4
2002712 TCGGGCCAGG
* * * *
2002722 TATA TATA TTTA AAT- TAAA TATA TAAA TAT- TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * *
2002768 TTTA -ATT TAAA T-TA AATT TAT- TA-A TAT- TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
2002811 TA
1 TA
2002813 ATAATTATTT
Statistics
Matches: 63, Mismatches: 17, Indels: 14
0.67 0.18 0.15
Matches are distributed among these distances:
3 13 0.21
4 50 0.79
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:2002761 original size:6 final size:6
Alignment explanation
Indices: 2002722--2002812 Score: 52
Period size: 6 Copynumber: 16.3 Consensus size: 6
2002712 TCGGGCCAGG
* * * *
2002722 TATATA TATTTA AAT-TA AATATA TAAATA T-TATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * *
2002768 TTTA-A TTTAAA T-TAAA TTTAT- TA-ATA T-TATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
2002811 TA
1 TA
2002813 ATAATTATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
4 2 0.03
5 25 0.36
6 43 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TATATA
Found at i:2002778 original size:43 final size:43
Alignment explanation
Indices: 2002729--2002811 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
2002719 AGGTATATAT
2002729 ATTTAAATTAAATATATAAATATTATATATATATATATATTTA
1 ATTTAAATTAAATATATAAATATTATATATATATATATATTTA
* *
2002772 ATTTAAATTAAATTTATTAATATTATATATATATATATAT
1 ATTTAAATTAAATATATAAATATTATATATATATATATAT
2002812 AATAATTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (43 bp):
ATTTAAATTAAATATATAAATATTATATATATATATATATTTA
Found at i:2002933 original size:42 final size:42
Alignment explanation
Indices: 2002874--2002962 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
2002864 GATTACTAAA
*
2002874 CCCGTCCCCGTCCCCGTTTAACATAAACGATTTTTCCCCTTC
1 CCCGTCCCCGTCCCCGTTTAACATAAACGATTTTTCCCCGTC
* *
2002916 CCCGTCCCCGTCCCCGTTTAGCATAAACGGTTTTTCCCCGTC
1 CCCGTCCCCGTCCCCGTTTAACATAAACGATTTTTCCCCGTC
2002958 CCCGT
1 CCCGT
2002963 TTAATTCGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.13, C:0.44, G:0.13, T:0.29
Consensus pattern (42 bp):
CCCGTCCCCGTCCCCGTTTAACATAAACGATTTTTCCCCGTC
Found at i:2005603 original size:35 final size:33
Alignment explanation
Indices: 2005564--2005722 Score: 96
Period size: 35 Copynumber: 4.6 Consensus size: 33
2005554 ATAAATATTA
2005564 TTTTAATTTGAGATATTAAAAAATATATAATTATC
1 TTTTAATTTGA-ATATTAAAAAATA-ATAATTATC
* * * *
2005599 TTTTAATATTCAA-AGTTAAATAGATAATAAATACC
1 TTTTAAT-TTGAATA-TTAAA-AAATAATAATTATC
* *
2005634 TTTTAATTTGAGATATT-CAAAAGAATAATTATCC
1 TTTTAATTTGA-ATATTAAAAAATAATAATTAT-C
* *
2005668 TTATAATATAT-ATAAATTAAAGAAAT-A-AA-TATC
1 TTTTAAT-T-TGA-ATATTAAA-AAATAATAATTATC
2005701 TTTTAATTTGCAATATTAAAAA
1 TTTTAATTTG-AATATTAAAAA
2005723 GGGATATGAA
Statistics
Matches: 95, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
31 3 0.03
32 8 0.08
33 17 0.18
34 15 0.16
35 38 0.40
36 11 0.12
37 3 0.03
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.41
Consensus pattern (33 bp):
TTTTAATTTGAATATTAAAAAATAATAATTATC
Found at i:2005618 original size:64 final size:64
Alignment explanation
Indices: 2005458--2005620 Score: 170
Period size: 64 Copynumber: 2.5 Consensus size: 64
2005448 TTTACTCAAA
* * *
2005458 ATAGATATA-TTTTAATATTCAAATTTAAACAGATAATTATATATTTTAATTTGAAATATTCAAA
1 ATAGATA-ACTTTTAATATTCAAACTT--A-A-ATAAATATATATTTTAATTTGAAATATTAAAA
2005522 ATAT
61 ATAT
* * *
2005526 ATAGATAACTTTTACTATTTAAACTTAAATAAATAT-TATTTTAATTTGAGATATTAAAAAATAT
1 ATAGATAACTTTTAATATTCAAACTTAAATAAATATATATTTTAATTTGAAATATT-AAAAATAT
* *
2005590 ATA-ATTATCTTTTAATATTCAAAGTTAAATA
1 ATAGA-TAACTTTTAATATTCAAACTTAAATA
2005621 GATAATAAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
63 19 0.23
64 39 0.48
65 1 0.01
66 1 0.01
67 1 0.01
68 21 0.26
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (64 bp):
ATAGATAACTTTTAATATTCAAACTTAAATAAATATATATTTTAATTTGAAATATTAAAAATAT
Found at i:2005688 original size:70 final size:66
Alignment explanation
Indices: 2005564--2005723 Score: 182
Period size: 67 Copynumber: 2.3 Consensus size: 66
2005554 ATAAATATTA
* * *
2005564 TTTTAATTTGAGATATTAAAAAATATATAATTATCTTTTAATATTCAAAGTTAAATAGATAATAA
1 TTTTAATTTGAGATATT-AAAAAGATATAATTATCTTATAATATTCAAAATT-AA-AGA-AATAA
2005629 ATACC
62 ATACC
*
2005634 TTTTAATTTGAGATATTCAAAAGA-ATAATTATCCTTATAATATAT-ATAAATTAAAGAAATAAA
1 TTTTAATTTGAGATATTAAAAAGATATAATTAT-CTTATAATAT-TCA-AAATTAAAGAAATAAA
*
2005697 TATC
63 TACC
2005701 TTTTAATTTGCA-ATATTAAAAAG
1 TTTTAATTTG-AGATATTAAAAAG
2005724 GGATATGAAT
Statistics
Matches: 80, Mismatches: 6, Indels: 11
0.82 0.06 0.11
Matches are distributed among these distances:
67 29 0.36
68 12 0.15
69 17 0.21
70 22 0.28
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (66 bp):
TTTTAATTTGAGATATTAAAAAGATATAATTATCTTATAATATTCAAAATTAAAGAAATAAATAC
C
Found at i:2009017 original size:20 final size:20
Alignment explanation
Indices: 2008982--2009055 Score: 112
Period size: 20 Copynumber: 3.6 Consensus size: 20
2008972 ACGATGGTAC
*
2008982 CGATACTAAGCCCTTTAGTAT
1 CGATACCAA-CCCTTTAGTAT
2009003 CGATACCAACCCTTTAGTAT
1 CGATACCAACCCTTTAGTAT
*
2009023 CGATACCAACACTTTAGTAT
1 CGATACCAACCCTTTAGTAT
*
2009043 CGATACCCACCCT
1 CGATACCAACCCT
2009056 AGGTACCAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 41 0.84
21 8 0.16
ACGTcount: A:0.30, C:0.31, G:0.11, T:0.28
Consensus pattern (20 bp):
CGATACCAACCCTTTAGTAT
Found at i:2010309 original size:12 final size:12
Alignment explanation
Indices: 2010292--2010324 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2010282 GGTATAGATA
*
2010292 TAAATGATAGGT
1 TAAATGACAGGT
2010304 TAAATGACAGGT
1 TAAATGACAGGT
2010316 TAAATGACA
1 TAAATGACA
2010325 TGGACATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.27
Consensus pattern (12 bp):
TAAATGACAGGT
Found at i:2015616 original size:21 final size:21
Alignment explanation
Indices: 2015590--2015629 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2015580 TATCTAGAAC
* *
2015590 AAGGGTATCGGTACCCCTTCA
1 AAGGGTATCGCTACACCTTCA
2015611 AAGGGTATCGCTACACCTT
1 AAGGGTATCGCTACACCTT
2015630 TATTAAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (21 bp):
AAGGGTATCGCTACACCTTCA
Found at i:2016082 original size:20 final size:18
Alignment explanation
Indices: 2016056--2016106 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 18
2016046 ATGTTTAATG
2016056 AAAAAGATACCAATTGTTT
1 AAAAAGATACCAATTG-TT
*
2016075 ACAAAAGAATATCAATTGTT
1 A-AAAAG-ATACCAATTGTT
*
2016095 AAAAACATACCA
1 AAAAAGATACCA
2016107 GTTATTACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 5 0.19
19 5 0.19
20 8 0.30
21 9 0.33
ACGTcount: A:0.53, C:0.14, G:0.08, T:0.25
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:2017294 original size:19 final size:19
Alignment explanation
Indices: 2017270--2017317 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
2017260 TCATTTTGAT
2017270 TTTCAAAATCAACACTAGC
1 TTTCAAAATCAACACTAGC
2017289 TTTCAAAATCAACACTAGC
1 TTTCAAAATCAACACTAGC
2017308 TTTCAAAATC
1 TTTCAAAATC
2017318 GATTTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.29
Consensus pattern (19 bp):
TTTCAAAATCAACACTAGC
Found at i:2018852 original size:33 final size:34
Alignment explanation
Indices: 2018815--2018885 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
2018805 CGTTTACAAC
* *
2018815 TCCCTAG-TTTTTCACGGGATAAACTATAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
* * *
2018848 TCCCTAGCTTTTACACGGGCTTAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
2018882 TCCC
1 TCCC
2018886 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 7 0.22
34 25 0.78
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.34
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
Found at i:2019179 original size:21 final size:21
Alignment explanation
Indices: 2019155--2019194 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2019145 CTAGAACAGG
*
2019155 GGGTATCGATACCCCTTCAAA
1 GGGTATCGATACACCTTCAAA
2019176 GGGTATCGATACACCTTCA
1 GGGTATCGATACACCTTCA
2019195 TTAAATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (21 bp):
GGGTATCGATACACCTTCAAA
Found at i:2019278 original size:15 final size:15
Alignment explanation
Indices: 2019258--2019287 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2019248 TACCCAGGCA
2019258 GGGGTATCGGTACCC
1 GGGGTATCGGTACCC
*
2019273 GGGGTATGGGTACCC
1 GGGGTATCGGTACCC
2019288 ATAGGGGTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.43, T:0.20
Consensus pattern (15 bp):
GGGGTATCGGTACCC
Found at i:2019287 original size:35 final size:33
Alignment explanation
Indices: 2019238--2019305 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
2019228 TTGTAGCTAG
* *
2019238 GGGGTATTGATACCCAGGCAGGGGTATCGGTACCC
1 GGGGTATGGATACCCA--CAGGGGTATCGATACCC
* *
2019273 GGGGTATGGGTACCCATAGGGGTATCGATACCC
1 GGGGTATGGATACCCACAGGGGTATCGATACCC
2019306 TTTTTGCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 15 0.52
35 14 0.48
ACGTcount: A:0.21, C:0.22, G:0.37, T:0.21
Consensus pattern (33 bp):
GGGGTATGGATACCCACAGGGGTATCGATACCC
Found at i:2020447 original size:15 final size:13
Alignment explanation
Indices: 2020404--2020434 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2020394 ATTTATAGTG
2020404 GATTTTCAAGATA
1 GATTTTCAAGATA
2020417 GATTTTCAAGATA
1 GATTTTCAAGATA
2020430 GATTT
1 GATTT
2020435 ACTCAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (13 bp):
GATTTTCAAGATA
Found at i:2020676 original size:20 final size:20
Alignment explanation
Indices: 2020661--2020698 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2020651 ACTAATATTC
2020661 ACATTAAAGAGATAATTTGA
1 ACATTAAAGAGATAATTTGA
*
2020681 ATATTAAAGAGATAATTT
1 ACATTAAAGAGATAATTT
2020699 TTTTAATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.13, T:0.34
Consensus pattern (20 bp):
ACATTAAAGAGATAATTTGA
Found at i:2023353 original size:32 final size:32
Alignment explanation
Indices: 2023309--2023381 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
2023299 CGATCTTCCT
* *
2023309 TTAGTTTTTCTCGAATACTAAAGATCAATAAC
1 TTAGTTTCTCTCGAACACTAAAGATCAATAAC
2023341 TTAGTTTCTCTCGAACACTAAAGATCAATAAC
1 TTAGTTTCTCTCGAACACTAAAGATCAATAAC
2023373 TTAGTTTCT
1 TTAGTTTCT
2023382 TTTGAAAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (32 bp):
TTAGTTTCTCTCGAACACTAAAGATCAATAAC
Found at i:2023393 original size:32 final size:32
Alignment explanation
Indices: 2023309--2023393 Score: 125
Period size: 32 Copynumber: 2.7 Consensus size: 32
2023299 CGATCTTCCT
* *
2023309 TTAGTTTTTCTCGAATACTAAAGATCAATAAC
1 TTAGTTTCTCTCGAAAACTAAAGATCAATAAC
*
2023341 TTAGTTTCTCTCGAACACTAAAGATCAATAAC
1 TTAGTTTCTCTCGAAAACTAAAGATCAATAAC
* *
2023373 TTAGTTTCTTTTGAAAACTAA
1 TTAGTTTCTCTCGAAAACTAA
2023394 GTAGTATACT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (32 bp):
TTAGTTTCTCTCGAAAACTAAAGATCAATAAC
Found at i:2027047 original size:15 final size:15
Alignment explanation
Indices: 2027029--2027059 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2027019 ATAAAATAAA
2027029 AAATTTGAAAAATTG
1 AAATTTGAAAAATTG
*
2027044 AAATTTGAAAAGTTG
1 AAATTTGAAAAATTG
2027059 A
1 A
2027060 CTTTTTCCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (15 bp):
AAATTTGAAAAATTG
Found at i:2039679 original size:81 final size:81
Alignment explanation
Indices: 2039559--2039737 Score: 288
Period size: 81 Copynumber: 2.2 Consensus size: 81
2039549 AGATCCATCG
* *
2039559 TATGGCAGTGTCATAATATAATATGAATATATGATTTAGGGGTGCTCATGTCATAACCCATATCA
1 TATGGTAGTGTCATAATATAATATGAATATATGATTTAGGGGTGAT-ATGTCATAACCCATATCA
2039624 A-GAATTAATTATATTA
65 ACGAATTAATTATATTA
* **
2039640 TATGGTAGTGTCATAATATAATATGAATATATGATTTAGGTGTGATATGTCATAATTCATATCAA
1 TATGGTAGTGTCATAATATAATATGAATATATGATTTAGGGGTGATATGTCATAACCCATATCAA
*
2039705 CGTATTAATTATATTA
66 CGAATTAATTATATTA
2039721 TATGGTAGTGTCATAAT
1 TATGGTAGTGTCATAAT
2039738 CAGATTTAGG
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
80 17 0.19
81 74 0.81
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.39
Consensus pattern (81 bp):
TATGGTAGTGTCATAATATAATATGAATATATGATTTAGGGGTGATATGTCATAACCCATATCAA
CGAATTAATTATATTA
Found at i:2039694 original size:39 final size:39
Alignment explanation
Indices: 2039567--2039695 Score: 104
Period size: 39 Copynumber: 3.2 Consensus size: 39
2039557 CGTATGGCAG
* *
2039567 TGTCATAATATAATATGAATATATGATTTAGGGGTGCTCA
1 TGTCATAATATAATATGAATATATGATTTAGGTGTGAT-A
* * * * *
2039607 TGTCATAACCCAT-ATCAAGAAT-TAATTATATTA--TATGGTA
1 TGTCATAA--TATAAT-ATGAATAT-ATGAT-TTAGGTGTGATA
2039647 GTGTCATAATATAATATGAATATATGATTTAGGTGTGATA
1 -TGTCATAATATAATATGAATATATGATTTAGGTGTGATA
2039687 TGTCATAAT
1 TGTCATAAT
2039696 TCATATCAAC
Statistics
Matches: 68, Mismatches: 11, Indels: 21
0.68 0.11 0.21
Matches are distributed among these distances:
38 3 0.04
39 20 0.29
40 17 0.25
41 14 0.21
42 11 0.16
43 3 0.04
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (39 bp):
TGTCATAATATAATATGAATATATGATTTAGGTGTGATA
Found at i:2039865 original size:22 final size:20
Alignment explanation
Indices: 2039838--2039889 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
2039828 AATTCCGTCC
2039838 AAATTATAATAT-ATATATAT
1 AAATTATAATATAATAT-TAT
*
2039858 ACATATTATTATATAATATTAT
1 A-A-ATTATAATATAATATTAT
2039880 AAATTATAAT
1 AAATTATAAT
2039890 TTTATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 8 0.30
21 2 0.07
22 13 0.48
23 4 0.15
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATTATAATATAATATTAT
Found at i:2040967 original size:2 final size:2
Alignment explanation
Indices: 2040962--2040988 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2040952 TTACGCTTAT
2040962 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 T
2040989 TCACTCTTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2046603 original size:100 final size:100
Alignment explanation
Indices: 2046420--2046779 Score: 335
Period size: 100 Copynumber: 3.4 Consensus size: 100
2046410 GGCTTCCCAA
* * *
2046420 TTTCAGAGCCCATTTCAACTTCACAGCGAAGGATATTTGACTCAAGACAACACAAGCTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCAAGACAACACAAGCTCAACTTC
*
2046485 ACAGCGAAAGGGCAACTGACTGTCAACAAACAACT
66 ACAACGAAAGGGCAACTGACTGTCAACAAACAACT
* *
2046520 TTTCAGAGCCAATTTCAACTTCATATCGAAAGATATTGGACTCAAGACAACACAAGCTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCAAGACAACACAAGCTCAACTTC
* * * *
2046585 ACAATGAAGGGGCGACTGATTGTCAACAAACAACTTTTTAGCT
66 ACAACGAAAGGGCAACTGACTGTCAACAAAC-A------A-CT
* * * * * *
2046628 TCATTCAGAGTCAATTTCAACATCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAAAT
1 T--TTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCAAGACAACACAAGCTCAACT
** * ** * *
2046693 TCACTGCGAAGGGGCAACTGGTTGTCAACAAATAATT
64 TCACAACGAAAGGGCAACTGACTGTCAACAAACAACT
* *
2046730 TCCCAGTTCTAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTCA
1 T-----TTC-AGAGCCAATTTCAACTTCACAG-CGAAAGATATTGGACTCA
2046780 GAGCGATATA
Statistics
Matches: 213, Mismatches: 32, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
100 86 0.40
101 1 0.00
102 2 0.01
103 1 0.00
105 4 0.02
106 33 0.15
107 1 0.00
108 3 0.01
109 1 0.00
110 81 0.38
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (100 bp):
TTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCAAGACAACACAAGCTCAACTTC
ACAACGAAAGGGCAACTGACTGTCAACAAACAACT
Found at i:2046718 original size:110 final size:110
Alignment explanation
Indices: 2046521--2046724 Score: 291
Period size: 110 Copynumber: 1.9 Consensus size: 110
2046511 CAAACAACTT
* * * * *
2046521 TTCAGAGCCAATTTCAACTTCATATCGAAAGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACATCACAGCGAAAGATATTGAACTCAAGACAACACAAGCTCAAATTCA
* *
2046586 CAATGAAGGGGCGACTGATTGTCAACAAACAACTTTTTAGCTTCA
66 CAACGAAGGGGCAACTGATTGTCAACAAACAACTTTTTAGCTTCA
* * *
2046631 TTCAGAGTCAATTTCAACATCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAAATTCA
1 TTCAGAGCCAATTTCAACATCACAGCGAAAGATATTGAACTCAAGACAACACAAGCTCAAATTCA
** *
2046696 CTGCGAAGGGGCAACTGGTTGTCAACAAA
66 CAACGAAGGGGCAACTGATTGTCAACAAA
2046725 TAATTTCCCA
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
110 81 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.23
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACATCACAGCGAAAGATATTGAACTCAAGACAACACAAGCTCAAATTCA
CAACGAAGGGGCAACTGATTGTCAACAAACAACTTTTTAGCTTCA
Found at i:2047067 original size:129 final size:129
Alignment explanation
Indices: 2046885--2047173 Score: 533
Period size: 129 Copynumber: 2.2 Consensus size: 129
2046875 CTATCTCTAG
* * *
2046885 ATTGGATTTTAACTTCATGACGAAGGATATCCAACTCAAAGAATGAGTGTCTGTCAACAAACTTT
1 ATTGGATTTTAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAATGTCTGTCAACAAACTTT
*
2046950 CCAGTTTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGCCTCGAAACAACGCAACTTAC
66 CCAGTTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGCCTCGAAACAACGCAACTTAC
*
2047014 ATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAATGTCTGTCAACAAACTTT
1 ATTGGATTTTAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAATGTCTGTCAACAAACTTT
2047079 CCAGTTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGCCTCGAAACAACGCAACTTAC
66 CCAGTTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGCCTCGAAACAACGCAACTTAC
2047143 ATTGGATTTTAACTTCACGACGAAGGATATC
1 ATTGGATTTTAACTTCACGACGAAGGATATC
2047174 TAATTCTCAA
Statistics
Matches: 154, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
129 154 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (129 bp):
ATTGGATTTTAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAATGTCTGTCAACAAACTTT
CCAGTTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGCCTCGAAACAACGCAACTTAC
Found at i:2047609 original size:2 final size:2
Alignment explanation
Indices: 2047598--2047641 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
2047588 CCGTCCAAAT
2047598 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2047637 T- TA TA
1 TA TA TA
2047642 AATTATAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.11
2 34 0.89
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2049179 original size:31 final size:31
Alignment explanation
Indices: 2049141--2049265 Score: 155
Period size: 31 Copynumber: 4.0 Consensus size: 31
2049131 GATCCTTGGC
*
2049141 AACTGTCCATATGTTCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
**
2049172 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
*
2049203 TACTGTCCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* *
2049234 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
2049266 TACCCTCGAC
Statistics
Matches: 80, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
30 3 0.04
31 51 0.64
32 23 0.29
33 3 0.04
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:2049257 original size:63 final size:62
Alignment explanation
Indices: 2049142--2049268 Score: 186
Period size: 63 Copynumber: 2.0 Consensus size: 62
2049132 ATCCTTGGCA
* *
2049142 ACTGTCCATATGTTCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATATGTTCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
*
2049204 ACTGTCCATATG-TCTCGAA-AGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
1 ACTGTCCATATGTTC-CGAAGA-ACATAGGTAA-ACTGTCCATATGTTCCGTAGAACATAGGTAT
2049267 AC
1 AC
2049269 CCTCGACTCT
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
61 3 0.05
62 25 0.42
63 31 0.53
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (62 bp):
ACTGTCCATATGTTCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:2057119 original size:41 final size:41
Alignment explanation
Indices: 2057032--2057156 Score: 164
Period size: 41 Copynumber: 3.1 Consensus size: 41
2057022 AATGCATGGA
* *
2057032 TAGATGTGCTGCATTTAACAGCAAGA-T-AATGCATTGAAT
1 TAGACGTGCTGCATTTAACAGTAAGATTAAATGCATTGAAT
* * * *
2057071 TAGACGTGCTGCTTTTAACAGTAGGATTAAATACATTGAAC
1 TAGACGTGCTGCATTTAACAGTAAGATTAAATGCATTGAAT
* *
2057112 TAGACGTGCTGCATTTAACAATATGATTAAATGCATTGAAT
1 TAGACGTGCTGCATTTAACAGTAAGATTAAATGCATTGAAT
2057153 TAGA
1 TAGA
2057157 TGAGGAACTG
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 22 0.30
40 1 0.01
41 50 0.68
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (41 bp):
TAGACGTGCTGCATTTAACAGTAAGATTAAATGCATTGAAT
Found at i:2062565 original size:19 final size:18
Alignment explanation
Indices: 2062530--2062572 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
2062520 AATAAATAAT
*
2062530 TAATATATAATTATTTTTA
1 TAAT-TATAATAATTTTTA
2062549 TAATTATAATAATTTTTTA
1 TAATTATAATAA-TTTTTA
2062568 TAATT
1 TAATT
2062573 GAAATATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TAATTATAATAATTTTTA
Found at i:2066936 original size:45 final size:46
Alignment explanation
Indices: 2066857--2066944 Score: 126
Period size: 45 Copynumber: 1.9 Consensus size: 46
2066847 AAATAGCTTG
* *
2066857 AGTGCATCGATGCAAGGTCTAGTGCATCGATGCATCAAATGCACTA
1 AGTGCATCGATGCAAGGTATAGTGCATCGATGCATAAAATGCACTA
*
2066903 AGTGCATTGATGCATA-GTATA-TGCATCGATGCATAAAATGCA
1 AGTGCATCGATGCA-AGGTATAGTGCATCGATGCATAAAATGCA
2066945 TTCAATGTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
45 20 0.53
46 17 0.45
47 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (46 bp):
AGTGCATCGATGCAAGGTATAGTGCATCGATGCATAAAATGCACTA
Found at i:2077838 original size:28 final size:29
Alignment explanation
Indices: 2077783--2077842 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
2077773 TTTCAACATT
2077783 TATTCCCAACTTGAGGGGGACGTGTAGGA
1 TATTCCCAACTTGAGGGGGACGTGTAGGA
2077812 TATTCCCAACTTGAGGGGGA-GTGTAGGA
1 TATTCCCAACTTGAGGGGGACGTGTAGGA
2077840 TAT
1 TAT
2077843 GCAGTACATG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 11 0.35
29 20 0.65
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (29 bp):
TATTCCCAACTTGAGGGGGACGTGTAGGA
Found at i:2082036 original size:32 final size:32
Alignment explanation
Indices: 2082000--2082061 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
2081990 CCTTTATAAT
* *
2082000 TTATAAAACAATCATTATATTTTATTAAATTA
1 TTATAAAACAATCATTAAATTTTATGAAATTA
* *
2082032 TTATAAAATAATCGTTAAATTTTATGAAAT
1 TTATAAAACAATCATTAAATTTTATGAAAT
2082062 GTTTATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (32 bp):
TTATAAAACAATCATTAAATTTTATGAAATTA
Found at i:2082068 original size:32 final size:31
Alignment explanation
Indices: 2081999--2082068 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
2081989 ACCTTTATAA
* *
2081999 TTTATAAAACAATCATTATATTTTATTAAAT
1 TTTATAAAACAATCATTAAATTTTATGAAAT
* *
2082030 TATTATAAAATAATCGTTAAATTTTATGAAAT
1 T-TTATAAAACAATCATTAAATTTTATGAAAT
2082062 GTTTATA
1 -TTTATA
2082069 TTTTATAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 1 0.03
32 31 0.94
33 1 0.03
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (31 bp):
TTTATAAAACAATCATTAAATTTTATGAAAT
Found at i:2082397 original size:22 final size:21
Alignment explanation
Indices: 2082354--2082402 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
2082344 TTGAAATATC
* *
2082354 AAATATAAATATATACTCATA
1 AAATATAAATATATAATAATA
*
2082375 AAATGATAAATATTTAATAATA
1 AAAT-ATAAATATATAATAATA
2082397 ATAATA
1 A-AATA
2082403 ATACATTCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 4 0.17
22 16 0.70
23 3 0.13
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (21 bp):
AAATATAAATATATAATAATA
Found at i:2083678 original size:31 final size:29
Alignment explanation
Indices: 2083620--2083685 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 29
2083610 AAATTTTTTG
* *
2083620 TTATTAAATTTTTAAAAGTTATTAAATAA
1 TTATTAAATTTTCAAAAGTTATAAAATAA
*
2083649 TTATTTAATTTATCAAATAGTTATAAAATAA
1 TTATTAAATTT-TCAAA-AGTTATAAAATAA
*
2083680 CTATTA
1 TTATTA
2083686 TATTATAGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 10 0.33
30 4 0.13
31 16 0.53
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (29 bp):
TTATTAAATTTTCAAAAGTTATAAAATAA
Found at i:2084968 original size:19 final size:19
Alignment explanation
Indices: 2084906--2084969 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
2084896 TTAGATAAAC
*
2084906 TTAATTATTTTTATATAATT
1 TTAATTATTTTAATATAA-T
*
2084926 TTAA-TATTTTAATA-ACT
1 TTAATTATTTTAATATAAT
* *
2084943 TAAAATTATTTAAATATAAT
1 T-TAATTATTTTAATATAAT
2084963 TTAATTA
1 TTAATTA
2084970 CCTCTACTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
17 2 0.06
18 3 0.09
19 23 0.66
20 7 0.20
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAATTATTTTAATATAAT
Found at i:2085938 original size:23 final size:22
Alignment explanation
Indices: 2085912--2085969 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
2085902 TCGAGTTAAA
2085912 AATAATTTAATTTTTTAATTTTT
1 AATAATTTAATTTTTT-ATTTTT
*
2085935 AATAATTTAA-TTTATATTTTT
1 AATAATTTAATTTTTTATTTTT
2085956 -AT-ATTTAATTTTTT
1 AATAATTTAATTTTTT
2085970 TGAACACTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 6 0.19
20 6 0.19
21 6 0.19
22 4 0.12
23 10 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
AATAATTTAATTTTTTATTTTT
Found at i:2085963 original size:19 final size:20
Alignment explanation
Indices: 2085925--2085966 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
2085915 AATTTAATTT
2085925 TTTAATTTTTAATAATTTAA
1 TTTAATTTTTAATAATTTAA
2085945 TTTATATTTTT-AT-ATTTAA
1 TTTA-ATTTTTAATAATTTAA
2085964 TTT
1 TTT
2085967 TTTTGAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.43
20 6 0.29
21 6 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTAATTTTTAATAATTTAA
Found at i:2086323 original size:25 final size:25
Alignment explanation
Indices: 2086294--2086369 Score: 143
Period size: 25 Copynumber: 3.0 Consensus size: 25
2086284 AATATATAAT
*
2086294 TTTATACTGGTTTGATATTAAAATA
1 TTTATATTGGTTTGATATTAAAATA
2086319 TTTATATTGGTTTGATATTAAAATA
1 TTTATATTGGTTTGATATTAAAATA
2086344 TTTATATTGGTTTGATATTAAAATA
1 TTTATATTGGTTTGATATTAAAATA
2086369 T
1 T
2086370 AACTGTATGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.51
Consensus pattern (25 bp):
TTTATATTGGTTTGATATTAAAATA
Found at i:2087207 original size:12 final size:12
Alignment explanation
Indices: 2087190--2087217 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2087180 TTGAATGAAA
2087190 TGCTGGATTCCT
1 TGCTGGATTCCT
2087202 TGCTGGATTCCT
1 TGCTGGATTCCT
2087214 TGCT
1 TGCT
2087218 AGATGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.25, G:0.25, T:0.43
Consensus pattern (12 bp):
TGCTGGATTCCT
Found at i:2102556 original size:3 final size:3
Alignment explanation
Indices: 2102548--2102623 Score: 152
Period size: 3 Copynumber: 25.3 Consensus size: 3
2102538 AGTACTCTTC
2102548 TAT TAT TAT TAT 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 TAT TAT TAT TAT
2102596 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2102624 TTCATTTAGA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2102691 original size:17 final size:17
Alignment explanation
Indices: 2102653--2102693 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2102643 TTGGATATAC
**
2102653 GTTTTGATATTATTATT
1 GTTTTGATATTATTAAG
*
2102670 ATTTTGATATTATTAAG
1 GTTTTGATATTATTAAG
2102687 GTTTTGA
1 GTTTTGA
2102694 AATTTATATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.59
Consensus pattern (17 bp):
GTTTTGATATTATTAAG
Found at i:2104654 original size:23 final size:23
Alignment explanation
Indices: 2104625--2104671 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2104615 CGACCACCGG
**
2104625 CCGACCACCGACCGGTCACTATT
1 CCGACCACCGACCAATCACTATT
*
2104648 CCGACCACCGGCCAATCACTATT
1 CCGACCACCGACCAATCACTATT
2104671 C
1 C
2104672 ACGTCGTCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.45, G:0.15, T:0.17
Consensus pattern (23 bp):
CCGACCACCGACCAATCACTATT
Found at i:2105213 original size:3 final size:3
Alignment explanation
Indices: 2105207--2105247 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
2105197 TATTATTTAT
* *
2105207 TAA TAA TAA TTA TTA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2105248 TAAAAAAGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2105660 original size:137 final size:137
Alignment explanation
Indices: 2105409--2106204 Score: 1069
Period size: 137 Copynumber: 5.8 Consensus size: 137
2105399 ATATCCAACT
* * * *
2105409 GGTGTATGACATTGTTCCTTCATGATGAGGACGTCTGACCATCTTTGAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* ** * * * * * * * *
2105474 -AGGTTTCTTTGTGATGAGGACGTATAGTTATCTGAGGATGACTCG--GCTCCTACGTGATGAGA
66 CA-GTTCCTTCATGATGAGGACATCTGGCTATCTAAGAATGA-T-GTTGCTCCTTCGTGATGAGG
2105536 AGTTCTGATC
128 AGTTCTGATC
* *
2105546 GGTGGATGACATTGTTCCTTCGTGATGAGGATGTCTGGCCATCTTTAAATATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* * *
2105611 CACTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCATGATGAGGAGT
66 CAGTTCCTTCATGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
2105676 TCTGATC
131 TCTGATC
* *
2105683 GATGGATGACATTGTTCCTTCGTGATGAGGATGTCTGGCCATCTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* * * *
2105748 CTGTTCTTTCATGATGAGGATATCTGGTTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
66 CAGTTCCTTCATGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
2105813 TCTGATC
131 TCTGATC
* * * *
2105820 GGTAGATGACATTATTCCTTCGTGATGAGGATGTCTGGCAATCTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
** * * * * *
2105885 TTGTTCTTTCATGATGAGGATATCTGGTTATCCAAGAATGATGTTGCTCTTTCGTGATGAGGAGT
66 CAGTTCCTTCATGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
2105950 TCTGATC
131 TCTGATC
*
2105957 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTGAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
** * * * *
2106022 CAGTTCCTTTGTGATGAGGACGTCTGGCTGTCTAAGGATGAT-ATGACTCCTTCGTGATGAGGAG
66 CAGTTCCTTCATGATGAGGACATCTGGCTATCTAAGAATGATGTTG-CTCCTTCGTGATGAGGAG
*
2106086 TTCTGATT
130 TTCTGATC
* * *
2106094 GGTAGATGACATTGTTTCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* * *
2106159 CGGTTCCTTCATGATGAGGACGTCTGGCTATCTAAGGATGATGTTG
66 CAGTTCCTTCATGATGAGGACATCTGGCTATCTAAGAATGATGTTG
2106205 ATGGACATGA
Statistics
Matches: 592, Mismatches: 62, Indels: 9
0.89 0.09 0.01
Matches are distributed among these distances:
135 1 0.00
136 3 0.01
137 585 0.99
138 3 0.01
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (137 bp):
GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
CAGTTCCTTCATGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
TCTGATC
Found at i:2112186 original size:45 final size:45
Alignment explanation
Indices: 2112122--2112261 Score: 226
Period size: 45 Copynumber: 3.1 Consensus size: 45
2112112 AAAAACATAA
2112122 AAAGAAATAAATAATGTACAACACACAAATATAATCTTTAAATCT
1 AAAGAAATAAATAATGTACAACACACAAATATAATCTTTAAATCT
2112167 AAAGAAATAAATAATGTACAACACACAAATATAATCTTTAAATCT
1 AAAGAAATAAATAATGTACAACACACAAATATAATCTTTAAATCT
* * * * * *
2112212 AAAGAAACAAATAATGTACAACAAACAAATTTATTCTTTCAATAT
1 AAAGAAATAAATAATGTACAACACACAAATATAATCTTTAAATCT
2112257 AAAGA
1 AAAGA
2112262 CATATAATTA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 89 1.00
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (45 bp):
AAAGAAATAAATAATGTACAACACACAAATATAATCTTTAAATCT
Found at i:2113870 original size:23 final size:23
Alignment explanation
Indices: 2113843--2113889 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2113833 TGACTATCGG
* **
2113843 CCGACCACTGGCTGGTCACTATT
1 CCGACCACCGGCCAGTCACTATT
2113866 CCGACCACCGGCCAGTCACTATT
1 CCGACCACCGGCCAGTCACTATT
2113889 C
1 C
2113890 ACGTCGTCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.19, C:0.40, G:0.19, T:0.21
Consensus pattern (23 bp):
CCGACCACCGGCCAGTCACTATT
Found at i:2114431 original size:3 final size:3
Alignment explanation
Indices: 2114425--2114456 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2114415 TATTATTTAT
*
2114425 TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2114457 TAAAAAGGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2116057 original size:17 final size:17
Alignment explanation
Indices: 2116037--2116078 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
2116027 AAGCTTGTAA
*
2116037 TTCATTTAGGGAAGTAG
1 TTCATTCAGGGAAGTAG
2116054 TTCATTCAGGGAAGTAG
1 TTCATTCAGGGAAGTAG
2116071 TTCATTCA
1 TTCATTCA
2116079 TGCATTTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (17 bp):
TTCATTCAGGGAAGTAG
Found at i:2116142 original size:18 final size:17
Alignment explanation
Indices: 2116116--2116171 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
2116106 TAACTCAGCA
* *
2116116 AGTTAATTGAATAAAGTT
1 AGTTCATTGAATAAA-CT
*
2116134 AGTTCATTGATTAAACT
1 AGTTCATTGAATAAACT
2116151 AGTTCATT-AATCAAACT
1 AGTTCATTGAAT-AAACT
2116168 AGTT
1 AGTT
2116172 TATAATTGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 2 0.06
17 18 0.55
18 13 0.39
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (17 bp):
AGTTCATTGAATAAACT
Found at i:2119309 original size:29 final size:29
Alignment explanation
Indices: 2119276--2119360 Score: 116
Period size: 29 Copynumber: 2.9 Consensus size: 29
2119266 GAGCAAGGGT
* *
2119276 AGGTCGCCCGGAGTGCATGGCAACCTACA
1 AGGTCGCCCGGAGAGCATGGCGACCTACA
** *
2119305 AGGTCGCTTGGAGAGCATAGCGACCTACA
1 AGGTCGCCCGGAGAGCATGGCGACCTACA
*
2119334 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGAGCATGGCGACCTA
2119361 TGTGTTGGGA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGAGCATGGCGACCTACA
Found at i:2120674 original size:21 final size:22
Alignment explanation
Indices: 2120641--2120682 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2120631 TATTATATTT
2120641 ATTAAACAGTTATAAAATAATC
1 ATTAAACAGTTATAAAATAATC
*
2120663 ATTATACA-TTATAAAATAAT
1 ATTAAACAGTTATAAAATAAT
2120683 AATAGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (22 bp):
ATTAAACAGTTATAAAATAATC
Found at i:2122360 original size:14 final size:14
Alignment explanation
Indices: 2122341--2122404 Score: 92
Period size: 14 Copynumber: 4.6 Consensus size: 14
2122331 ACTTCAACAG
2122341 GTTGACTCGGATGA
1 GTTGACTCGGATGA
* *
2122355 GTTGACTCAGAGGA
1 GTTGACTCGGATGA
* *
2122369 CTTGACTCGAATGA
1 GTTGACTCGGATGA
2122383 GTTGACTCGGATGA
1 GTTGACTCGGATGA
2122397 GTTGACTC
1 GTTGACTC
2122405 AATCTTGGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.28
Consensus pattern (14 bp):
GTTGACTCGGATGA
Found at i:2122462 original size:20 final size:20
Alignment explanation
Indices: 2122439--2122484 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
2122429 CAAACAAACC
*
2122439 CGGTTCAGACCGTGTTAGGT
1 CGGTTCAGACCGGGTTAGGT
2122459 CGGTTCAGACCGGGTTAGGT
1 CGGTTCAGACCGGGTTAGGT
2122479 CGGTTC
1 CGGTTC
2122485 GGCTTTAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.22, G:0.37, T:0.28
Consensus pattern (20 bp):
CGGTTCAGACCGGGTTAGGT
Found at i:2126304 original size:23 final size:23
Alignment explanation
Indices: 2126234--2126304 Score: 60
Period size: 23 Copynumber: 3.1 Consensus size: 23
2126224 TCTGCTATCA
*
2126234 TTTATTTCTTATAAAGATGAGAT
1 TTTATTTCTTATAAAAATGAGAT
**
2126257 TTT-TGGCTATATTAATAAA-G-G-T
1 TTTATTTCT-TA-TAA-AAATGAGAT
2126279 TTTATTTCTTATAAAAATGAGAT
1 TTTATTTCTTATAAAAATGAGAT
2126302 TTT
1 TTT
2126305 TCCACTACAA
Statistics
Matches: 36, Mismatches: 5, Indels: 14
0.65 0.09 0.25
Matches are distributed among these distances:
20 3 0.08
21 4 0.11
22 10 0.28
23 13 0.36
24 4 0.11
25 2 0.06
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (23 bp):
TTTATTTCTTATAAAAATGAGAT
Found at i:2126822 original size:14 final size:15
Alignment explanation
Indices: 2126781--2126826 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 15
2126771 AATAGTAATT
*
2126781 AAAATTTATTATTTA
1 AAAATTTATAATTTA
2126796 AAAATTTACTAATTTA
1 AAAATTTA-TAATTTA
*
2126812 AATATTT-TAATTTA
1 AAAATTTATAATTTA
2126826 A
1 A
2126827 TAATATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 8 0.29
15 8 0.29
16 12 0.43
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
AAAATTTATAATTTA
Found at i:2127991 original size:14 final size:15
Alignment explanation
Indices: 2127972--2128001 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2127962 AAGATGAGTT
2127972 TATGTTTTTGA-CAA
1 TATGTTTTTGAGCAA
2127986 TATGTTTTTGAGCAA
1 TATGTTTTTGAGCAA
2128001 T
1 T
2128002 TCTCTACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.50
Consensus pattern (15 bp):
TATGTTTTTGAGCAA
Found at i:2130119 original size:19 final size:19
Alignment explanation
Indices: 2130097--2130147 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
2130087 TTGCTATATT
*
2130097 CTGTCAGTTTTTTTATTTA
1 CTGTCAATTTTTTTATTTA
*
2130116 CTGTGAATTTTTTTTATTTA
1 CTGTCAA-TTTTTTTATTTA
*
2130136 TTGTCAATTTTT
1 CTGTCAATTTTT
2130148 GCTTCATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.18, C:0.08, G:0.10, T:0.65
Consensus pattern (19 bp):
CTGTCAATTTTTTTATTTA
Done.