Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 62 of 143
Found at i:19939940 original size:20 final size:20
Alignment explanation
Indices: 19939917--19939955 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19939907 TTGTCCAAAT
*
19939917 TACTGGCAGCTTGTCTGCAA
1 TACTGGCAGCTTATCTGCAA
*
19939937 TACTGGCAGTTTATCTGCA
1 TACTGGCAGCTTATCTGCA
19939956 TTTTTGGTGC
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:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (20 bp):
TACTGGCAGCTTATCTGCAA
Found at i:19954164 original size:7 final size:7
Alignment explanation
Indices: 19954152--19954179 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
19954142 ATTTAAATAT
19954152 TCAACAC
1 TCAACAC
19954159 TCAACAC
1 TCAACAC
19954166 TCAACAC
1 TCAACAC
19954173 TCAACAC
1 TCAACAC
19954180 ATTTGATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14
Consensus pattern (7 bp):
TCAACAC
Found at i:19962782 original size:3 final size:3
Alignment explanation
Indices: 19962774--19962830 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
19962764 GTATTGAGGC
* *
19962774 AGA AGA AGA AGAA AGA A-A AGC AGA AGA AAA AGA AG- AGA AGGA AGA
1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA
*
19962819 AAA AGA AGA AGA
1 AGA AGA AGA AGA
19962831 TGTTGCCCTG
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 4 0.09
3 34 0.77
4 6 0.14
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:19962798 original size:21 final size:23
Alignment explanation
Indices: 19962772--19962830 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
19962762 GGGTATTGAG
19962772 GCAGAAGAAGAAGAA-AGAA-AA
1 GCAGAAGAAGAAGAAGAGAAGAA
*
19962793 GCAGAAGAAAAAGAAGAGAAGGAA
1 GCAGAAGAAGAAGAAGAGAA-GAA
* *
19962817 GAAAAAGAAGAAGA
1 GCAGAAGAAGAAGA
19962831 TGTTGCCCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 14 0.45
22 4 0.13
24 13 0.42
ACGTcount: A:0.66, C:0.03, G:0.31, T:0.00
Consensus pattern (23 bp):
GCAGAAGAAGAAGAAGAGAAGAA
Found at i:19962800 original size:18 final size:17
Alignment explanation
Indices: 19962774--19962830 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
19962764 GTATTGAGGC
19962774 AGAAGAAGAAGAAAGAAA
1 AGAAGAAGAA-AAAGAAA
* *
19962792 AGCAGAAGAAAAAGAAG
1 AGAAGAAGAAAAAGAAA
19962809 AGAAGGAAGAAAAAGAAGA
1 AGAA-GAAGAAAAAGAA-A
19962828 AGA
1 AGA
19962831 TGTTGCCCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 9 0.27
18 21 0.64
19 3 0.09
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (17 bp):
AGAAGAAGAAAAAGAAA
Found at i:19965470 original size:24 final size:24
Alignment explanation
Indices: 19965437--19965483 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
19965427 ATTTATCTTC
*
19965437 TATTAATTTGCCCTGAC-ATTTTA
1 TATTAATTTGCACTGACAATTTTA
19965460 TATTACATTTGCACTGACAATTTT
1 TATTA-ATTTGCACTGACAATTTT
19965484 TACTCTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.47
Consensus pattern (24 bp):
TATTAATTTGCACTGACAATTTTA
Found at i:19972909 original size:24 final size:26
Alignment explanation
Indices: 19972876--19972923 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
19972866 CGACTAGTTA
19972876 GTTGACGAAA-AAT-CCAAAGCAATG
1 GTTGACGAAATAATGCCAAAGCAATG
* *
19972900 GTTGATGAAATCATGCCAAAGCAA
1 GTTGACGAAATAATGCCAAAGCAA
19972924 GCTAACTCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 2 0.10
26 9 0.45
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.19
Consensus pattern (26 bp):
GTTGACGAAATAATGCCAAAGCAATG
Found at i:19989837 original size:37 final size:37
Alignment explanation
Indices: 19989775--19989880 Score: 122
Period size: 37 Copynumber: 2.8 Consensus size: 37
19989765 TTAATCCAGA
* * *
19989775 ATTGCGCCCAAACATGTCGCTGCATGAGCACTTCTAG
1 ATTGCGCCCAAACATGTCGCCGCATGAGCACCTATAG
* * *
19989812 ATTGTGCCCAAACATGTTGCCGCATGAGCACCTATAT
1 ATTGCGCCCAAACATGTCGCCGCATGAGCACCTATAG
* * *
19989849 ATTGCGCCCAAAAACTGTCACCACATGAGCAC
1 ATTGCGCCCAAACA-TGTCGCCGCATGAGCAC
19989881 TTTCAGATTG
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
37 43 0.75
38 14 0.25
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (37 bp):
ATTGCGCCCAAACATGTCGCCGCATGAGCACCTATAG
Found at i:19990008 original size:26 final size:26
Alignment explanation
Indices: 19989972--19990025 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
19989962 CACCCAAGAA
19989972 TGTCGCTGCATGAACATGTACAAAAT
1 TGTCGCTGCATGAACATGTACAAAAT
* *
19989998 TGTCGCTGCATGAACATGTCCAGAAT
1 TGTCGCTGCATGAACATGTACAAAAT
19990024 TG
1 TG
19990026 CGCCTAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (26 bp):
TGTCGCTGCATGAACATGTACAAAAT
Found at i:19999227 original size:18 final size:18
Alignment explanation
Indices: 19999204--19999276 Score: 78
Period size: 18 Copynumber: 4.1 Consensus size: 18
19999194 TTTTATTTAG
19999204 TTGTCATTGCATTTTCAT
1 TTGTCATTGCATTTTCAT
*
19999222 TTGTCACTGCATTTTCAT
1 TTGTCATTGCATTTTCAT
* * * *
19999240 TTGTTAGTACATTTGCA-
1 TTGTCATTGCATTTTCAT
19999257 TTGT-AGTTGCATTTTCAT
1 TTGTCA-TTGCATTTTCAT
19999275 TT
1 TT
19999277 TTATCTGTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
16 1 0.02
17 12 0.27
18 32 0.71
ACGTcount: A:0.18, C:0.15, G:0.14, T:0.53
Consensus pattern (18 bp):
TTGTCATTGCATTTTCAT
Found at i:19999841 original size:10 final size:10
Alignment explanation
Indices: 19999828--19999865 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
19999818 AAAAAATCAC
19999828 AAAAAGAAAG
1 AAAAAGAAAG
19999838 AAAAAGAAAG
1 AAAAAGAAAG
*
19999848 AAGAAAAAAAG
1 AA-AAAGAAAG
19999859 AAAAAGA
1 AAAAAGA
19999866 GAAAAGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:19999853 original size:17 final size:15
Alignment explanation
Indices: 19999828--19999870 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 15
19999818 AAAAAATCAC
19999828 AAAAAGAAAGAAAAAG
1 AAAAAGAAA-AAAAAG
19999844 AAAGAAG-AAAAAAAG
1 AAA-AAGAAAAAAAAG
19999859 AAAAAGAGAAAA
1 AAAAAGA-AAAA
19999871 GAAACATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 3 0.12
15 9 0.38
16 9 0.38
17 3 0.12
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:19999858 original size:21 final size:22
Alignment explanation
Indices: 19999829--19999874 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
19999819 AAAAATCACA
19999829 AAAAGAAAGAAAAAGA-AAGAAG
1 AAAAGAAAGAAAAAGAGAA-AAG
19999851 AAAA-AAAGAAAAAGAGAAAAG
1 AAAAGAAAGAAAAAGAGAAAAG
19999872 AAA
1 AAA
19999875 CATATTGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (22 bp):
AAAAGAAAGAAAAAGAGAAAAG
Found at i:20014205 original size:21 final size:21
Alignment explanation
Indices: 20014181--20014233 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
20014171 TTGTGCTAGC
20014181 TCTATCGATACAAGT-ATG-A
1 TCTATCGATACAAGTCATGCA
*
20014200 TTTCTACCGATACAAGTCATGCA
1 --TCTATCGATACAAGTCATGCA
20014223 TCTATCGATAC
1 TCTATCGATAC
20014234 TAGAAACACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 24 0.86
22 3 0.11
23 1 0.04
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (21 bp):
TCTATCGATACAAGTCATGCA
Found at i:20020468 original size:17 final size:17
Alignment explanation
Indices: 20020443--20020475 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20020433 GGTTGTTCTA
*
20020443 AAGCGTTGTGAAGAAAC
1 AAGCATTGTGAAGAAAC
20020460 AAGCATTGTGAAGAAA
1 AAGCATTGTGAAGAAA
20020476 TAAACTTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.09, G:0.27, T:0.18
Consensus pattern (17 bp):
AAGCATTGTGAAGAAAC
Found at i:20024384 original size:4 final size:4
Alignment explanation
Indices: 20024377--20024416 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
20024367 GTGATATATG
20024377 TGTT TGTT TGTT TGTT TGTT TGTT TGTT TGTT TGTT TGTT
1 TGTT TGTT TGTT TGTT TGTT TGTT TGTT TGTT TGTT TGTT
20024417 CATACTTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.25, T:0.75
Consensus pattern (4 bp):
TGTT
Found at i:20024978 original size:20 final size:20
Alignment explanation
Indices: 20024953--20024990 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20024943 GAATGAGTGC
* *
20024953 TTAAAAAGAAATAAAAATGT
1 TTAAAAAAAAAGAAAAATGT
20024973 TTAAAAAAAAAGAAAAAT
1 TTAAAAAAAAAGAAAAAT
20024991 ATTTTTTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (20 bp):
TTAAAAAAAAAGAAAAATGT
Found at i:20040799 original size:16 final size:16
Alignment explanation
Indices: 20040773--20040807 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
20040763 AAAAAACAAT
20040773 TCACGATCATTTCATGA
1 TCACGATCATTTCAT-A
20040790 TCAC-ATCATTTCATA
1 TCACGATCATTTCATA
20040805 TCA
1 TCA
20040808 ATTACTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 10 0.56
17 4 0.22
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (16 bp):
TCACGATCATTTCATA
Found at i:20041283 original size:20 final size:20
Alignment explanation
Indices: 20041260--20041298 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20041250 ATGAATAATA
*
20041260 GGATTAAGTCATGAACAGTG
1 GGATCAAGTCATGAACAGTG
* *
20041280 GGATCATGTCGTGAACAGT
1 GGATCAAGTCATGAACAGT
20041299 AATAATATAT
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:0.31, C:0.13, G:0.31, T:0.26
Consensus pattern (20 bp):
GGATCAAGTCATGAACAGTG
Found at i:20042276 original size:24 final size:24
Alignment explanation
Indices: 20042215--20042277 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
20042205 TAAAGTAATA
* *
20042215 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
20042239 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
20042263 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
20042278 GATTATTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:20044209 original size:24 final size:24
Alignment explanation
Indices: 20044181--20044263 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 24
20044171 TAGAGTAATA
*
20044181 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* *
20044205 AGAGTTTAATTGAAACAAATAAA-
1 AGAGTTTAACTCAAACAAATAAAC
* * * *
20044228 TGTAGTTTAATTGAAAAAAATAAAC
1 AG-AGTTTAACTCAAACAAATAAAC
* *
20044253 AAATTTTAACT
1 AGAGTTTAACT
20044264 GAAAGATTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
23 1 0.02
24 47 0.98
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:20044266 original size:24 final size:24
Alignment explanation
Indices: 20044197--20044267 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
20044187 TGACTCAAAC
* *
20044197 AAATAAACAGAGTTTAATTGAAAC
1 AAATAAACAAAGTTTAATTGAAAA
***
20044221 AAATAAATGTAGTTTAATTGAAAA
1 AAATAAACAAAGTTTAATTGAAAA
* *
20044245 AAATAAACAAATTTTAACTGAAA
1 AAATAAACAAAGTTTAATTGAAA
20044268 GATTATTTCT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.56, C:0.06, G:0.10, T:0.28
Consensus pattern (24 bp):
AAATAAACAAAGTTTAATTGAAAA
Found at i:20069782 original size:9 final size:9
Alignment explanation
Indices: 20069768--20069798 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
20069758 GATCGAGTAA
20069768 AATTAAATT
1 AATTAAATT
20069777 AATTAAATT
1 AATTAAATT
20069786 AATTAAAATT
1 AATT-AAATT
20069796 AAT
1 AAT
20069799 ATTTTTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAAATT
Found at i:20069924 original size:37 final size:36
Alignment explanation
Indices: 20069875--20069950 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
20069865 ATTCCAAAAA
20069875 TAATATTATTTTAATAGT-TTAATATTAAATTTAAT-T
1 TAATATTATTTTAATAGTATT-ATATT-AATTTAATAT
*
20069911 TAATACTTATTTTAATAGTATTTTATTAATTTAATAT
1 TAATA-TTATTTTAATAGTATTATATTAATTTAATAT
20069948 TAA
1 TAA
20069951 AGTGAGTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 13 0.36
37 21 0.58
38 2 0.06
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (36 bp):
TAATATTATTTTAATAGTATTATATTAATTTAATAT
Found at i:20069948 original size:11 final size:11
Alignment explanation
Indices: 20069875--20069950 Score: 52
Period size: 12 Copynumber: 6.8 Consensus size: 11
20069865 ATTCCAAAAA
*
20069875 TAATATTATTT
1 TAATATTAATT
20069886 TAATAGTTTAATAT
1 TAATA--TTAAT-T
20069900 TAA-ATTTAATT
1 TAATA-TTAATT
*
20069911 TAATACTTATTT
1 TAATA-TTAATT
*
20069923 TAATAGT-ATT
1 TAATATTAATT
20069933 T--TATTAATT
1 TAATATTAATT
20069942 TAATATTAA
1 TAATATTAA
20069951 AGTGAGTATC
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 3 0.06
11 16 0.31
12 17 0.33
13 5 0.10
14 4 0.08
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:20072733 original size:18 final size:18
Alignment explanation
Indices: 20072710--20072744 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20072700 CTCTCGTTCT
* *
20072710 CTAAGGGGAAGCAGAAAG
1 CTAAGGGAAAGAAGAAAG
20072728 CTAAGGGAAAGAAGAAA
1 CTAAGGGAAAGAAGAAA
20072745 CTGACTAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.09, G:0.34, T:0.06
Consensus pattern (18 bp):
CTAAGGGAAAGAAGAAAG
Found at i:20073690 original size:143 final size:143
Alignment explanation
Indices: 20073432--20073714 Score: 557
Period size: 143 Copynumber: 2.0 Consensus size: 143
20073422 AGATGGTCCC
20073432 TTAAGTATGCTTAAGGAAGTTAGTCTTCTATAATGTGAATCTTGCTTGAAAGGTAAAATGAAGAA
1 TTAAGTATGCTTAAGGAAGTTAGTCTTCTATAATGTGAATCTTGCTTGAAAGGTAAAATGAAGAA
20073497 GAGGTCTTTTAATGCGAAAGGTACAAGGGCCAACCAACCTTTAGAACTTGTGCACACTGATGTAT
66 GAGGTCTTTTAATGCGAAAGGTACAAGGGCCAACCAACCTTTAGAACTTGTGCACACTGATGTAT
20073562 ATGGTCCCATGAG
131 ATGGTCCCATGAG
*
20073575 TTAAGTATGCTTAAGGAAGTTAGTCTTCTATAATGTGAATCTTGCTTGGAAGGTAAAATGAAGAA
1 TTAAGTATGCTTAAGGAAGTTAGTCTTCTATAATGTGAATCTTGCTTGAAAGGTAAAATGAAGAA
20073640 GAGGTCTTTTAATGCGAAAGGTACAAGGGCCAACCAACCTTTAGAACTTGTGCACACTGATGTAT
66 GAGGTCTTTTAATGCGAAAGGTACAAGGGCCAACCAACCTTTAGAACTTGTGCACACTGATGTAT
20073705 ATGGTCCCAT
131 ATGGTCCCAT
20073715 AAGCATTAGT
Statistics
Matches: 139, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 139 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (143 bp):
TTAAGTATGCTTAAGGAAGTTAGTCTTCTATAATGTGAATCTTGCTTGAAAGGTAAAATGAAGAA
GAGGTCTTTTAATGCGAAAGGTACAAGGGCCAACCAACCTTTAGAACTTGTGCACACTGATGTAT
ATGGTCCCATGAG
Found at i:20076277 original size:14 final size:14
Alignment explanation
Indices: 20076249--20076287 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
20076239 TAATTTCACA
*
20076249 TTTCACTATTATGTC
1 TTTCA-TATTTTGTC
*
20076264 TTTTATATTTTGTC
1 TTTCATATTTTGTC
20076278 TTTCATATTT
1 TTTCATATTT
20076288 CGCATGCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.18, C:0.13, G:0.05, T:0.64
Consensus pattern (14 bp):
TTTCATATTTTGTC
Found at i:20077708 original size:18 final size:21
Alignment explanation
Indices: 20077668--20077708 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 21
20077658 AATGTTTATC
*
20077668 TTTTAGATAAACATTTTATTA
1 TTTTAGATAAACATTTTAATA
20077689 TTTTA-ATAAA-A-TTTAATA
1 TTTTAGATAAACATTTTAATA
20077707 TT
1 TT
20077709 AAATTTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 8 0.42
19 1 0.05
20 5 0.26
21 5 0.26
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTTAGATAAACATTTTAATA
Found at i:20077708 original size:21 final size:22
Alignment explanation
Indices: 20077668--20077728 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 22
20077658 AATGTTTATC
20077668 TTTTAGATAAACATTT-TATT-A
1 TTTTA-ATAAACATTTATATTAA
20077689 TTTTAATAAA-ATTTAATATTAA
1 TTTTAATAAACATTT-ATATTAA
* *
20077711 ATTTAATCAAATATTTAT
1 TTTTAAT-AAACATTTAT
20077729 CTTGATAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 4 0.12
20 5 0.15
21 9 0.26
22 7 0.21
23 5 0.15
24 4 0.12
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTAATAAACATTTATATTAA
Found at i:20078915 original size:42 final size:42
Alignment explanation
Indices: 20078869--20079099 Score: 241
Period size: 42 Copynumber: 5.5 Consensus size: 42
20078859 TGCTAGTAAC
* *
20078869 ATGTGGACAAACCACCAGTATTGCAGTCAAGCTACCAGAAAT
1 ATGTGGACAAGCCACCAGTATTGCAGTAAAGCTACCAGAAAT
* * *
20078911 ATGTGGACAATCCACCAGTATTACAGTAAAGCTACCAAAAAT
1 ATGTGGACAAGCCACCAGTATTGCAGTAAAGCTACCAGAAAT
* ** * *
20078953 ATGTAGACAAGCCATTAGTATTGCAGTAAAGCTGCTAGAAAT
1 ATGTGGACAAGCCACCAGTATTGCAGTAAAGCTACCAGAAAT
* * * * *
20078995 ATGTGGACAAGCCACCAATATTGCAGTCAAGCTTCCAGTAAG
1 ATGTGGACAAGCCACCAGTATTGCAGTAAAGCTACCAGAAAT
* * ** * * *
20079037 ATGTGGACAAGCCATCAATATTATAGAAAAACTACCAG-TAT
1 ATGTGGACAAGCCACCAGTATTGCAGTAAAGCTACCAGAAAT
*
20079078 -TGTGGACAAGCCACCAATATTG
1 ATGTGGACAAGCCACCAGTATTG
20079100 TAGATAAACT
Statistics
Matches: 157, Mismatches: 32, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
40 20 0.13
41 1 0.01
42 136 0.87
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.23
Consensus pattern (42 bp):
ATGTGGACAAGCCACCAGTATTGCAGTAAAGCTACCAGAAAT
Found at i:20079093 original size:20 final size:20
Alignment explanation
Indices: 20078992--20079100 Score: 67
Period size: 20 Copynumber: 5.4 Consensus size: 20
20078982 AGCTGCTAGA
20078992 AATA-TGTGGACAAGCCACC
1 AATATTGTGGACAAGCCACC
** * **
20079011 AATATTGCAGTCAAGCTTCC
1 AATATTGTGGACAAGCCACC
* * *
20079031 AGTAAGATGTGGACAAGCCATC
1 AAT-A-TTGTGGACAAGCCACC
* * * * *
20079053 AATATTATAGAAAAACTACC
1 AATATTGTGGACAAGCCACC
*
20079073 AGTATTGTGGACAAGCCACC
1 AATATTGTGGACAAGCCACC
20079093 AATATTGT
1 AATATTGT
20079101 AGATAAACTG
Statistics
Matches: 59, Mismatches: 28, Indels: 5
0.64 0.30 0.05
Matches are distributed among these distances:
19 4 0.07
20 42 0.71
21 2 0.03
22 11 0.19
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (20 bp):
AATATTGTGGACAAGCCACC
Found at i:20079096 original size:40 final size:42
Alignment explanation
Indices: 20078827--20079109 Score: 138
Period size: 42 Copynumber: 6.8 Consensus size: 42
20078817 CACACCAATT
** ** * * * *
20078827 TGTGGACAAGCCATTAATAATTGTAGTTAAGCTGCTAGTAACA
1 TGTGGACAAGCCACCAAT-ATTGTAGAAAAACTACCAGTAAGA
* * * ** * * *
20078870 TGTGGACAAACCACCAGTATTGCAGTCAAGCTACCAGAAATA
1 TGTGGACAAGCCACCAATATTGTAGAAAAACTACCAGTAAGA
* * ** * * ** *
20078912 TGTGGACAATCCACCAGTATTACAGTAAAGCTACCAAAAATA
1 TGTGGACAAGCCACCAATATTGTAGAAAAACTACCAGTAAGA
* ** * * * * * * * *
20078954 TGTAGACAAGCCATTAGTATTGCAGTAAAGCTGCTAGAAATA
1 TGTGGACAAGCCACCAATATTGTAGAAAAACTACCAGTAAGA
* ** * *
20078996 TGTGGACAAGCCACCAATATTGCAGTCAAGCTTCCAGTAAGA
1 TGTGGACAAGCCACCAATATTGTAGAAAAACTACCAGTAAGA
* * *
20079038 TGTGGACAAGCCATCAATATTATAGAAAAACTACCAGT-A-T
1 TGTGGACAAGCCACCAATATTGTAGAAAAACTACCAGTAAGA
*
20079078 TGTGGACAAGCCACCAATATTGTAGATAAACT
1 TGTGGACAAGCCACCAATATTGTAGAAAAACT
20079110 GCTAGTACTT
Statistics
Matches: 198, Mismatches: 42, Indels: 3
0.81 0.17 0.01
Matches are distributed among these distances:
40 29 0.15
41 1 0.01
42 154 0.78
43 14 0.07
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (42 bp):
TGTGGACAAGCCACCAATATTGTAGAAAAACTACCAGTAAGA
Found at i:20080469 original size:51 final size:51
Alignment explanation
Indices: 20080366--20080474 Score: 155
Period size: 51 Copynumber: 2.1 Consensus size: 51
20080356 GAAATTCATG
* * * ** *
20080366 GGCGAGTAGTATATGGAAGCTCGCAAGCGAGAGTTTTTTAATTTTTTGCAA
1 GGCGAGCAGTATATGGAACCTCGCAAGAGAGAGTTTTTTAATTTGGTACAA
20080417 GGCGAGCAGTATATGGAACCTCGCAAGAGAGAGTTTTTTAATTTGGTACAA
1 GGCGAGCAGTATATGGAACCTCGCAAGAGAGAGTTTTTTAATTTGGTACAA
*
20080468 GGTGAGC
1 GGCGAGC
20080475 TATTTGTGGA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.29
Consensus pattern (51 bp):
GGCGAGCAGTATATGGAACCTCGCAAGAGAGAGTTTTTTAATTTGGTACAA
Found at i:20086656 original size:20 final size:20
Alignment explanation
Indices: 20086510--20086660 Score: 108
Period size: 20 Copynumber: 7.6 Consensus size: 20
20086500 TTGTATGGGA
* *
20086510 TTGCAGTTTGGTG-CCTTAGT
1 TTGCACTTTGGTGCCCCT-GT
** *
20086530 TTGCACTACGATGCCCCTGT
1 TTGCACTTTGGTGCCCCTGT
* * *
20086550 TTGCACTTTGATGTCCCTAT
1 TTGCACTTTGGTGCCCCTGT
** *
20086570 TTGCACCATGGTTCCCCTGT
1 TTGCACTTTGGTGCCCCTGT
* * *
20086590 TTGCACTTCGGTGCCTCTAT
1 TTGCACTTTGGTGCCCCTGT
* * **
20086610 TTGAACTATGGTG-CTTTGT
1 TTGCACTTTGGTGCCCCTGT
*
20086629 TTGAACTTTGGTGCCCCTGT
1 TTGCACTTTGGTGCCCCTGT
20086649 TTGCACTTTGGT
1 TTGCACTTTGGT
20086661 ACATTTGTTC
Statistics
Matches: 99, Mismatches: 30, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
19 16 0.16
20 80 0.81
21 3 0.03
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.41
Consensus pattern (20 bp):
TTGCACTTTGGTGCCCCTGT
Found at i:20087699 original size:23 final size:23
Alignment explanation
Indices: 20087650--20087701 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
20087640 TACAATATTC
* * *
20087650 AAATAATATTAATAATGGATGCC
1 AAATAATATTAAAAAGGGATGCA
20087673 AAATAATATTAAAAAGGGCA-GCA
1 AAATAATATTAAAAAGGG-ATGCA
20087696 AAATAA
1 AAATAA
20087702 CATAAACAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.56, C:0.08, G:0.13, T:0.23
Consensus pattern (23 bp):
AAATAATATTAAAAAGGGATGCA
Found at i:20087770 original size:23 final size:22
Alignment explanation
Indices: 20087726--20087794 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 22
20087716 AAACAACAAT
*
20087726 AAAACAACACC-AAAACAT-CC
1 AAAATAACACCGAAAACATACC
*
20087746 AAAATAACATCGAAAACAGTACC
1 AAAATAACACCGAAAACA-TACC
*
20087769 AAAATAGCACCGAAAACAATACC
1 AAAATAACACCGAAAAC-ATACC
20087792 AAA
1 AAA
20087795 GCTGTACCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 9 0.22
21 6 0.15
22 1 0.02
23 24 0.59
24 1 0.02
ACGTcount: A:0.59, C:0.26, G:0.06, T:0.09
Consensus pattern (22 bp):
AAAATAACACCGAAAACATACC
Found at i:20087804 original size:11 final size:11
Alignment explanation
Indices: 20087788--20087828 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
20087778 CCGAAAACAA
20087788 TACCAAAGCTG
1 TACCAAAGCTG
* *
20087799 TACCAAAAACAG
1 TACC-AAAGCTG
20087811 TACCAAAGCTG
1 TACCAAAGCTG
20087822 TACCAAA
1 TACCAAA
20087829 AACAGCATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.46, C:0.27, G:0.12, T:0.15
Consensus pattern (11 bp):
TACCAAAGCTG
Found at i:20087833 original size:23 final size:23
Alignment explanation
Indices: 20087758--20087833 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
20087748 AATAACATCG
* * *
20087758 AAAACAGTACCAAA-ATAGCACCG
1 AAAACAGTACCAAAGCT-GTACCA
*
20087781 AAAACAATACCAAAGCTGTACCA
1 AAAACAGTACCAAAGCTGTACCA
20087804 AAAACAGTACCAAAGCTGTACCA
1 AAAACAGTACCAAAGCTGTACCA
20087827 AAAACAG
1 AAAACAG
20087834 CATCAAATCT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 46 0.98
24 1 0.02
ACGTcount: A:0.53, C:0.25, G:0.12, T:0.11
Consensus pattern (23 bp):
AAAACAGTACCAAAGCTGTACCA
Found at i:20087840 original size:23 final size:23
Alignment explanation
Indices: 20087789--20087855 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
20087779 CGAAAACAAT
*
20087789 ACCAAAGCTGTACCAAAAACAGT
1 ACCAAAGCTGTACCAAAAACAGC
20087812 ACCAAAGCTGTACCAAAAACAGC
1 ACCAAAGCTGTACCAAAAACAGC
* * * *
20087835 ATCAAATCTGCACCAAGAACA
1 ACCAAAGCTGTACCAAAAACA
20087856 ACCTGCAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.48, C:0.28, G:0.12, T:0.12
Consensus pattern (23 bp):
ACCAAAGCTGTACCAAAAACAGC
Found at i:20090132 original size:6 final size:6
Alignment explanation
Indices: 20090123--20090173 Score: 50
Period size: 6 Copynumber: 8.0 Consensus size: 6
20090113 AAAATATAGT
*
20090123 AATTAA AATTAA AATTAA AATTAA TCATTATA AA-TAA AATCTGAA AATTAA
1 AATTAA AATTAA AATTAA AATTAA -AATTA-A AATTAA AAT-T-AA AATTAA
20090174 CAAGAATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
5 3 0.08
6 22 0.58
7 7 0.18
8 6 0.16
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (6 bp):
AATTAA
Found at i:20090169 original size:27 final size:25
Alignment explanation
Indices: 20090124--20090173 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 25
20090114 AAATATAGTA
20090124 ATTAAAATTAAAATTAAAATTAATC
1 ATTAAAATTAAAATTAAAATTAATC
20090149 ATTATAAA-TAAAATCTGAAAATTAA
1 ATTA-AAATTAAAAT-T-AAAATTAA
20090174 CAAGAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 10 0.45
26 4 0.18
27 8 0.36
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (25 bp):
ATTAAAATTAAAATTAAAATTAATC
Found at i:20112034 original size:24 final size:25
Alignment explanation
Indices: 20112005--20112058 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
20111995 TGTGTGCCTA
* *
20112005 CTGTTT-CCTAGCACTTATGTGCTT
1 CTGTTTCCCCAGCACTTATGCGCTT
20112029 CTGTTTCCCCAGCACTTATGCGCTT
1 CTGTTTCCCCAGCACTTATGCGCTT
*
20112054 TTGTT
1 CTGTT
20112059 AAGTACTTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.11, C:0.28, G:0.17, T:0.44
Consensus pattern (25 bp):
CTGTTTCCCCAGCACTTATGCGCTT
Found at i:20112042 original size:25 final size:24
Alignment explanation
Indices: 20111987--20112058 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 24
20111977 GCTTACTGTT
* *
20111987 CAGCACTGTGTGTGCCTACTGTTTCC
1 CAGCACT-TATGTG-CTTCTGTTTCC
*
20112013 TAGCACTTATGTGCTTCTGTTTCCC
1 CAGCACTTATGTGCTTCTGTTT-CC
* *
20112038 CAGCACTTATGCGCTTTTGTT
1 CAGCACTTATGTGCTTCTGTT
20112059 AAGTACTTCG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
24 8 0.21
25 25 0.64
26 6 0.15
ACGTcount: A:0.12, C:0.28, G:0.19, T:0.40
Consensus pattern (24 bp):
CAGCACTTATGTGCTTCTGTTTCC
Found at i:20152445 original size:20 final size:21
Alignment explanation
Indices: 20152409--20152447 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20152399 ATTTTTGTTA
*
20152409 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
20152430 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
20152448 AATTCCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:20162167 original size:2 final size:2
Alignment explanation
Indices: 20162162--20162203 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
20162152 GTGGGTCTTA
20162162 AT AT AT AT 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 AT AT AT AT
20162204 GGGATATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20166864 original size:52 final size:52
Alignment explanation
Indices: 20166779--20166965 Score: 320
Period size: 52 Copynumber: 3.6 Consensus size: 52
20166769 TAAATGCAAA
*
20166779 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
20166831 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
20166883 AGGTCCGATGACTATGTGCCATCGTGAGCATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
20166935 AGGTCCAATGACTATGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
20166966 TAAATGAGAA
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:20170285 original size:58 final size:58
Alignment explanation
Indices: 20170192--20170347 Score: 215
Period size: 58 Copynumber: 2.6 Consensus size: 58
20170182 GTATCTAAAT
* *
20170192 TTGACATTTTTTCTTAATTTGGTACTTAAACTTTTTTTGACCAAATTTGATACTTGAAC
1 TTGACATTTTTTC-TAATTTGGTACCTAAACTTTTTTTGACCAAATTTGATACCTGAAC
* * *
20170251 TTGACGTTTTTTCTAATTTGGTACCTAAA-TTTTTTTGGACCCAATTTTATACCTGAAC
1 TTGACATTTTTTCTAATTTGGTACCTAAACTTTTTTT-GACCAAATTTGATACCTGAAC
*
20170309 TTGACATTTTTTTCCTAATTTGGTACCTAAGCTTTTTTT
1 TTGACA-TTTTTT-CTAATTTGGTACCTAAACTTTTTTT
20170348 AGATTCAATT
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
57 7 0.08
58 38 0.44
59 18 0.21
60 16 0.19
61 7 0.08
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.50
Consensus pattern (58 bp):
TTGACATTTTTTCTAATTTGGTACCTAAACTTTTTTTGACCAAATTTGATACCTGAAC
Found at i:20170630 original size:32 final size:33
Alignment explanation
Indices: 20170586--20170658 Score: 107
Period size: 32 Copynumber: 2.2 Consensus size: 33
20170576 AGTATTAACT
20170586 TAAAAAAATGTCAAGTTT-AGGTACCAAATT-AA
1 TAAAAAAATGTCAAGTTTGA-GTACCAAATTGAA
20170618 -AAAAAAAGTGTCAAGTTTGAGTACCAAATTGAA
1 TAAAAAAA-TGTCAAGTTTGAGTACCAAATTGAA
20170651 TAAAAAAA
1 TAAAAAAA
20170659 AGTTTAGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
31 7 0.19
32 20 0.54
33 3 0.08
34 7 0.19
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.25
Consensus pattern (33 bp):
TAAAAAAATGTCAAGTTTGAGTACCAAATTGAA
Found at i:20170670 original size:28 final size:27
Alignment explanation
Indices: 20170630--20170683 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
20170620 AAAAAGTGTC
*
20170630 AAGTTTGAGTACCAAATTGAATAAAAAA
1 AAGTTTGAGTACCAAATT-AAGAAAAAA
20170658 AAGTTT-AGATACCAAATTAAGAAAAA
1 AAGTTTGAG-TACCAAATTAAGAAAAA
20170684 GTACCAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (27 bp):
AAGTTTGAGTACCAAATTAAGAAAAAA
Found at i:20171299 original size:17 final size:17
Alignment explanation
Indices: 20171247--20171321 Score: 55
Period size: 17 Copynumber: 4.4 Consensus size: 17
20171237 TCCCTTGATT
*
20171247 TTTAACTTTCCATATTC
1 TTTAACCTTCCATATTC
* * *
20171264 CTTAACCTCCCTTGA-TC
1 TTTAACCTTCCAT-ATTC
*
20171281 TTTAACCTTCCATCTTC
1 TTTAACCTTCCATATTC
*
20171298 TTT-ACCTTTTCATATTC
1 TTTAACC-TTCCATATTC
20171315 TTGTAAC
1 TT-TAAC
20171322 TACTTTTTAC
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
16 3 0.07
17 36 0.84
18 2 0.05
19 2 0.05
ACGTcount: A:0.20, C:0.29, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAACCTTCCATATTC
Found at i:20171776 original size:19 final size:20
Alignment explanation
Indices: 20171749--20171787 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
20171739 AACAACTTGA
* *
20171749 ATATTTTTCGTAA-ATATGT
1 ATATCTTTCATAACATATGT
20171768 ATATCTTTCATAACATATGT
1 ATATCTTTCATAACATATGT
20171788 CATTAACATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (20 bp):
ATATCTTTCATAACATATGT
Found at i:20176579 original size:17 final size:17
Alignment explanation
Indices: 20176557--20176615 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
20176547 CCCTTGACTT
20176557 TTAACCTTCCATCTTCC
1 TTAACCTTCCATCTTCC
* * *
20176574 TTAACCTCCCTTC-ACC
1 TTAACCTTCCATCTTCC
20176590 TTTAACCTTCCATCTTCC
1 -TTAACCTTCCATCTTCC
20176608 TTAACCTT
1 TTAACCTT
20176616 TCATATTCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 2 0.06
17 30 0.88
18 2 0.06
ACGTcount: A:0.19, C:0.41, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAACCTTCCATCTTCC
Found at i:20176594 original size:34 final size:34
Alignment explanation
Indices: 20176545--20176614 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
20176535 AACCTTTCAT
* *
20176545 CTCCCTTGACTTTTAACCTTCCATCTTCCTTAAC
1 CTCCCTTCACCTTTAACCTTCCATCTTCCTTAAC
20176579 CTCCCTTCACCTTTAACCTTCCATCTTCCTTAAC
1 CTCCCTTCACCTTTAACCTTCCATCTTCCTTAAC
20176613 CT
1 CT
20176615 TTCATATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.17, C:0.41, G:0.01, T:0.40
Consensus pattern (34 bp):
CTCCCTTCACCTTTAACCTTCCATCTTCCTTAAC
Found at i:20177025 original size:21 final size:21
Alignment explanation
Indices: 20177000--20177042 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
20176990 ATTGTTTCTC
*
20177000 AAAAATATTTTTTAGACAAAA
1 AAAAATATTTTTGAGACAAAA
*
20177021 AAAAATATTTTTGAGATAAAA
1 AAAAATATTTTTGAGACAAAA
20177042 A
1 A
20177043 TATTACTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (21 bp):
AAAAATATTTTTGAGACAAAA
Found at i:20177818 original size:24 final size:23
Alignment explanation
Indices: 20177747--20177818 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 23
20177737 ACTGAAGTTT
*
20177747 TCTGTTTGTTTATCGAAAAATAC
1 TCTGTTTGTTTCTCGAAAAATAC
*
20177770 CCTGTTTGTTTCTCTGAAAAATAC
1 TCTGTTTGTTTCTC-GAAAAATAC
20177794 TCTGTTTGTTTCTCGAGAAAATAC
1 TCTGTTTGTTTCTCGA-AAAATAC
20177818 T
1 T
20177819 AGATCCATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
23 14 0.32
24 30 0.68
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (23 bp):
TCTGTTTGTTTCTCGAAAAATAC
Found at i:20178182 original size:20 final size:20
Alignment explanation
Indices: 20178157--20178220 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 20
20178147 ATATGATTTT
20178157 AATAATTTTATATTTTAAAA
1 AATAATTTTATATTTTAAAA
* **
20178177 AATAATTTTAAATTTATTTTAA
1 AATAATTTTATA-TT-TTAAAA
20178199 AATAATTTTAATAATTTTAAAA
1 AATAATTTT-AT-ATTTTAAAA
20178221 TCATTTGCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
20 11 0.32
21 2 0.06
22 17 0.50
23 3 0.09
24 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATAATTTTATATTTTAAAA
Found at i:20178197 original size:11 final size:11
Alignment explanation
Indices: 20178175--20178226 Score: 63
Period size: 11 Copynumber: 4.9 Consensus size: 11
20178165 TATATTTTAA
20178175 AAAATAATTTT
1 AAAATAATTTT
* *
20178186 AAATTTATTTT
1 AAAATAATTTT
20178197 AAAATAATTTT
1 AAAATAATTTT
20178208 --AATAATTTT
1 AAAATAATTTT
*
20178217 AAAATCATTT
1 AAAATAATTT
20178227 GCTGACGTAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 9 0.26
11 25 0.74
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:20178203 original size:22 final size:20
Alignment explanation
Indices: 20178157--20178226 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 20
20178147 ATATGATTTT
20178157 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTT--AA
*
20178177 AATAATTTTAAATTTATTTTAA
1 AATAATTTT-AA-TAATTTTAA
20178199 AATAATTTTAATAATTTTAA
1 AATAATTTTAATAATTTTAA
*
20178219 AATCATTT
1 AATAATTT
20178227 GCTGACGTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 24 0.55
21 2 0.05
22 12 0.27
23 1 0.02
24 5 0.11
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAATTTTAATAATTTTAA
Found at i:20181985 original size:27 final size:27
Alignment explanation
Indices: 20181931--20181986 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
20181921 AAAAAAGTTA
* * ***
20181931 ATTAATTATGTAAATAATTTATTTTTT
1 ATTAAATATGAAAATAATTTAAAATTT
20181958 ATTAAATATGAAAATAATTTAAAATTT
1 ATTAAATATGAAAATAATTTAAAATTT
20181985 AT
1 AT
20181987 AGTAAAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (27 bp):
ATTAAATATGAAAATAATTTAAAATTT
Found at i:20182113 original size:11 final size:10
Alignment explanation
Indices: 20182097--20182131 Score: 54
Period size: 9 Copynumber: 3.5 Consensus size: 10
20182087 TCACTTACAT
20182097 AAATATTATAA
1 AAATATTA-AA
20182108 AAATATTAAA
1 AAATATTAAA
20182118 AAAT-TTAAA
1 AAATATTAAA
20182127 AAATA
1 AAATA
20182132 AAAAAATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.39
10 6 0.26
11 8 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAATATTAAA
Found at i:20182135 original size:17 final size:18
Alignment explanation
Indices: 20182105--20182145 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
20182095 ATAAATATTA
*
20182105 TAAAAATATTAAAAAATT
1 TAAAAATATAAAAAAATT
20182123 TAAAAA-ATAAAAAAATT
1 TAAAAATATAAAAAAATT
20182140 TGAAAA
1 T-AAAA
20182146 CAGTTTTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
TAAAAATATAAAAAAATT
Found at i:20182256 original size:94 final size:86
Alignment explanation
Indices: 20182157--20182363 Score: 209
Period size: 86 Copynumber: 2.3 Consensus size: 86
20182147 AGTTTTACTT
* * *
20182157 TTTTTTGCTGGTGCCATATTAAATGGTACCATCAC-TTCTCAAAATTTGTTAGGTTTTTTTTAAT
1 TTTTTTG-TGGTGTCATATTAAATGGCACCATCACTTTCTCAAAA----TTAAGTTTTTTTTAAT
20182221 GATTTATTATTTATTTTTTAAAATTTAAAA
61 GATTTATTA-TTA-TTTTT-AAA-TTAAAA
* * * * * * * *
20182251 TTTTTTTATGATATCATATTAAATGACACCATCACTTTTTTAAAATTAATTTTTTTTTAATTATT
1 -TTTTTTGTGGTGTCATATTAAATGGCACCATCACTTTCTCAAAATTAAGTTTTTTTTAATGATT
*
20182316 TATTATTATTTTTAAATTAAAT
65 TATTATTATTTTTAAATTAAAA
20182338 TTTTTTGTGGTGTCATATTAAATGGC
1 TTTTTTGTGGTGTCATATTAAATGGC
20182364 GCCACAATTT
Statistics
Matches: 95, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
86 22 0.23
87 5 0.05
88 3 0.03
89 5 0.05
90 3 0.03
91 22 0.23
94 22 0.23
95 13 0.14
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (86 bp):
TTTTTTGTGGTGTCATATTAAATGGCACCATCACTTTCTCAAAATTAAGTTTTTTTTAATGATTT
ATTATTATTTTTAAATTAAAA
Found at i:20182383 original size:86 final size:91
Alignment explanation
Indices: 20182210--20182375 Score: 227
Period size: 86 Copynumber: 1.9 Consensus size: 91
20182200 ATTTGTTAGG
20182210 TTTTTTTTAATGATTTATTATTTATTTTTTAAAATTTAAAATTTTTTTATGATATCATATTAAAT
1 TTTTTTTTAATGATTTATTATTTATTTTTTAAAATTTAAAATTTTTTTATGATATCATATTAAAT
*
20182275 GACACCATCACTTTTTTAAAATTAAT
66 GACACCATCAATTTTTTAAAATTAAT
* * * *
20182301 TTTTTTTTAATTATTTATTA-TTA-TTTTT-AAA-TT-AAATTTTTTTGTGGTGTCATATTAAAT
1 TTTTTTTTAATGATTTATTATTTATTTTTTAAAATTTAAAATTTTTTTATGATATCATATTAAAT
* *
20182361 GGCGCCA-CAATTTTT
66 GACACCATCAATTTTT
20182376 CCTAAATTTC
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
85 7 0.10
86 29 0.43
87 2 0.03
88 3 0.04
89 5 0.07
90 3 0.04
91 19 0.28
ACGTcount: A:0.31, C:0.07, G:0.06, T:0.56
Consensus pattern (91 bp):
TTTTTTTTAATGATTTATTATTTATTTTTTAAAATTTAAAATTTTTTTATGATATCATATTAAAT
GACACCATCAATTTTTTAAAATTAAT
Found at i:20182572 original size:7 final size:7
Alignment explanation
Indices: 20182564--20182595 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
20182554 GGATTAATTT
*
20182564 TTTATTT
1 TTTATTA
20182571 TTTATTA
1 TTTATTA
20182578 TTTATTA
1 TTTATTA
20182585 TTTATTA
1 TTTATTA
20182592 TTTA
1 TTTA
20182596 AATATATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTATTA
Found at i:20182614 original size:18 final size:18
Alignment explanation
Indices: 20182591--20182626 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20182581 ATTATTTATT
20182591 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
* *
20182609 ATTTAAATGTATATTTTA
1 ATTTAAATATATAGTTTA
20182627 TTTTTGGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Found at i:20186586 original size:22 final size:22
Alignment explanation
Indices: 20186561--20186611 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
20186551 ATATATTTAA
*
20186561 TGAAATTATATTACATAACACT
1 TGAAATTATATGACATAACACT
20186583 TGAAATTATATGACATAACACT
1 TGAAATTATATGACATAACACT
*
20186605 TAAAATT
1 TGAAATT
20186612 GGAATGAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (22 bp):
TGAAATTATATGACATAACACT
Found at i:20189638 original size:25 final size:24
Alignment explanation
Indices: 20189583--20189638 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 24
20189573 TATTTTTTTC
* * *
20189583 ATTTATTTTAAAATATATATATTT
1 ATTTATTTAAAAATATATAAAATT
20189607 ATGTTTATTTAAAAATATGATAAAATT
1 A--TTTATTTAAAAATAT-ATAAAATT
20189634 ATTTA
1 ATTTA
20189639 ACGTTTCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
24 1 0.04
25 4 0.15
26 14 0.54
27 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
ATTTATTTAAAAATATATAAAATT
Found at i:20191375 original size:9 final size:9
Alignment explanation
Indices: 20191336--20191382 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 9
20191326 ACTGTTTTAA
20191336 TATTATTTTAT
1 TATTA-TTT-T
20191347 TATTATATTGT
1 TATTAT-TT-T
20191358 TATTATTTT
1 TATTATTTT
20191367 T-TTATTTT
1 TATTATTTT
20191375 TATTATTT
1 TATTATTT
20191383 AAATATTGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 8 0.24
9 8 0.24
10 3 0.09
11 14 0.42
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (9 bp):
TATTATTTT
Found at i:20193362 original size:17 final size:17
Alignment explanation
Indices: 20193342--20193374 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20193332 ATTTGTGTAT
*
20193342 TTTTCTTTATTTATTTC
1 TTTTCGTTATTTATTTC
20193359 TTTTCGTTATTTATTT
1 TTTTCGTTATTTATTT
20193375 ATTTATTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTCGTTATTTATTTC
Found at i:20193394 original size:21 final size:21
Alignment explanation
Indices: 20193349--20193395 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
20193339 TATTTTTCTT
* *
20193349 TATTTATTTCTTTTCGTTATT
1 TATTTATTTATTTTCGTTATC
20193370 TATTTATTTATTTTC-TTAATC
1 TATTTATTTATTTTCGTT-ATC
20193391 TATTT
1 TATTT
20193396 TATGGTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (21 bp):
TATTTATTTATTTTCGTTATC
Found at i:20203810 original size:18 final size:18
Alignment explanation
Indices: 20203767--20203801 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20203757 CTTAATGATC
*
20203767 AGATGCAGTCACATGCTA
1 AGATGCAATCACATGCTA
20203785 AGATGCAATCACATGCT
1 AGATGCAATCACATGCT
20203802 CGTATGCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (18 bp):
AGATGCAATCACATGCTA
Found at i:20212306 original size:14 final size:14
Alignment explanation
Indices: 20212287--20212315 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20212277 ATAGATCTTT
20212287 GTCATAGCCTGAAG
1 GTCATAGCCTGAAG
20212301 GTCATAGCCTGAAG
1 GTCATAGCCTGAAG
20212315 G
1 G
20212316 ACAAATCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.21
Consensus pattern (14 bp):
GTCATAGCCTGAAG
Found at i:20217365 original size:12 final size:12
Alignment explanation
Indices: 20217348--20217400 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
20217338 GGGTATCGAG
20217348 GAGGAGAAAGAA
1 GAGGAGAAAGAA
20217360 GAGGAGAAAGAA
1 GAGGAGAAAGAA
*
20217372 GAAGA-AAAGAAA
1 GAGGAGAAAG-AA
*
20217384 GAAGGAGAGA-AA
1 G-AGGAGAAAGAA
20217396 GAGGA
1 GAGGA
20217401 AGTTTTTGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
11 8 0.23
12 22 0.63
13 3 0.09
14 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (12 bp):
GAGGAGAAAGAA
Found at i:20217373 original size:15 final size:15
Alignment explanation
Indices: 20217355--20217394 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
20217345 GAGGAGGAGA
*
20217355 AAGAAGAGGAGAAAG
1 AAGAAGAGAAGAAAG
*
20217370 AAGAAGAAAAGAAAG
1 AAGAAGAGAAGAAAG
*
20217385 AAGGAGAGAA
1 AAGAAGAGAA
20217395 AGAGGAAGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
AAGAAGAGAAGAAAG
Found at i:20231053 original size:16 final size:17
Alignment explanation
Indices: 20231032--20231063 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20231022 AGTTAGCATT
20231032 CTTGCA-TTTTATTGTG
1 CTTGCATTTTTATTGTG
20231048 CTTGCATTTTTATTGT
1 CTTGCATTTTTATTGT
20231064 TACTGCATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.59
Consensus pattern (17 bp):
CTTGCATTTTTATTGTG
Found at i:20233890 original size:12 final size:12
Alignment explanation
Indices: 20233873--20233897 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20233863 GGGTATCGAG
20233873 GAAGAAAAAGAA
1 GAAGAAAAAGAA
20233885 GAAGAAAAAGAA
1 GAAGAAAAAGAA
20233897 G
1 G
20233898 TAGGAGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAAAAGAA
Found at i:20244276 original size:18 final size:17
Alignment explanation
Indices: 20244251--20244284 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
20244241 TATTCCTTTT
20244251 CTAACTTTTATTGATTA
1 CTAACTTTTATTGATTA
*
20244268 CTAATCTTTTGTTGATT
1 CTAA-CTTTTATTGATT
20244285 TTCTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (17 bp):
CTAACTTTTATTGATTA
Found at i:20244499 original size:27 final size:27
Alignment explanation
Indices: 20244461--20244523 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
20244451 CCTCCAATGT
*
20244461 AGCCACAAGGAGTCAACAATATTTCGC
1 AGCCACAAGGAGTCAACAATATATCGC
20244488 AGCCACAAGGAGTCAACAATATATCGC
1 AGCCACAAGGAGTCAACAATATATCGC
*
20244515 TGCCACAAG
1 AGCCACAAG
20244524 AAGAGCAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (27 bp):
AGCCACAAGGAGTCAACAATATATCGC
Found at i:20259410 original size:18 final size:17
Alignment explanation
Indices: 20259385--20259418 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
20259375 TATTCCTTTT
20259385 CTAACTTTTATTGATTA
1 CTAACTTTTATTGATTA
*
20259402 CTAATCTTTTGTTGATT
1 CTAA-CTTTTATTGATT
20259419 TTCTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (17 bp):
CTAACTTTTATTGATTA
Found at i:20259631 original size:27 final size:27
Alignment explanation
Indices: 20259593--20259657 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
20259583 TTCCTCCAAT
* *
20259593 GCAGCCACAAGGGGTCAACAATATTTC
1 GCAGCCACAAGGAGTCAACAATATATC
*
20259620 GCAGGCACAAGGAGTCAACAATATATC
1 GCAGCCACAAGGAGTCAACAATATATC
*
20259647 GCTGCCACAAG
1 GCAGCCACAAG
20259658 AAGAGCAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.15
Consensus pattern (27 bp):
GCAGCCACAAGGAGTCAACAATATATC
Found at i:20275413 original size:17 final size:18
Alignment explanation
Indices: 20275393--20275432 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
20275383 TAAGTTTTAA
20275393 TGCATTTT-TATTATCAC
1 TGCATTTTATATTATCAC
* *
20275410 TGCATTTTATTTTGTCAC
1 TGCATTTTATATTATCAC
20275428 TGCAT
1 TGCAT
20275433 CATTTTGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.53
Consensus pattern (18 bp):
TGCATTTTATATTATCAC
Found at i:20278685 original size:20 final size:21
Alignment explanation
Indices: 20278650--20278688 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
20278640 GGGTGTTGCA
20278650 GAAGAAGAGAAAAGAGAAGTC
1 GAAGAAGAGAAAAGAGAAGTC
*
20278671 GAAGAA-AGGAAAGAGAAG
1 GAAGAAGAGAAAAGAGAAG
20278689 AAAAAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.59, C:0.03, G:0.36, T:0.03
Consensus pattern (21 bp):
GAAGAAGAGAAAAGAGAAGTC
Found at i:20303456 original size:20 final size:21
Alignment explanation
Indices: 20303431--20303469 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20303421 ATCATTTTTA
*
20303431 GCATTTT-TAACTTAGTGACT
1 GCATTTTCTAACTCAGTGACT
20303451 GCATTTTCTAACTCAGTGA
1 GCATTTTCTAACTCAGTGA
20303470 TGCTCAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTGACT
Found at i:20312827 original size:298 final size:298
Alignment explanation
Indices: 20312291--20312882 Score: 1130
Period size: 298 Copynumber: 2.0 Consensus size: 298
20312281 AAATCTAAAC
*
20312291 AAATAGAAAGAGAATTCTTTGAGGAATCGAATAACCGAGCAACCGAGCAAATCGAGATATCATCC
1 AAATAGAAAGAGAATTCTTTGAGGAATCGAATAACCGAGCAACCGAGCAAATCGAGATATCATCA
*
20312356 TTGGAAGGGGAAATGGGTAATTTTGTAAAAATCGAGATTAAGCTCCAATCCAATGATGATGACTC
66 TTGGAAGGGGAAATGGGTAATTTTGTAAAAATCGAGATTAAGCCCCAATCCAATGATGATGACTC
20312421 AATCCCCATAAAGGAAGATGACGATCCCTATATCTTAAATTTAAATCTTCAACTAATTATTGTTA
131 AATCCCCATAAAGGAAGATGACGATCCCTATATCTTAAATTTAAATCTTCAACTAATTATTGTTA
*
20312486 CAAAAACATTGACAGAAGAAATATTAGTTAAAGAGATCATCGATCAAATATTTAATTTCCAATGG
196 CAAAAACATTGACAGAAGAAAAATTAGTTAAAGAGATCATCGATCAAATATTTAATTTCCAATGG
20312551 AAAATAGCAAATATGTATAATACTTTCTTGGTACGAGG
261 AAAATAGCAAATATGTATAATACTTTCTTGGTACGAGG
20312589 AAATAGAAAGAGAATTCTTTGAGGAATCGAATAACCGAGCAACCGAGCAAATCGAGATATCATCA
1 AAATAGAAAGAGAATTCTTTGAGGAATCGAATAACCGAGCAACCGAGCAAATCGAGATATCATCA
20312654 TTGGAAGGGGAAATGGGTAATTTTGTAAAAATCGAGATTAAGCCCCAATCCAATGATGATGACTC
66 TTGGAAGGGGAAATGGGTAATTTTGTAAAAATCGAGATTAAGCCCCAATCCAATGATGATGACTC
20312719 AATCCCCATAAAGGAAGATGACGATCCCTATATCTTAAATTTAAATCTTCAACTAATTATTGTTA
131 AATCCCCATAAAGGAAGATGACGATCCCTATATCTTAAATTTAAATCTTCAACTAATTATTGTTA
* * *
20312784 CAAAACCATTGACAGAAGAAAAATTAGTTGAAGAGATCATCGATCAAATATTTAATTTCCAGTGG
196 CAAAAACATTGACAGAAGAAAAATTAGTTAAAGAGATCATCGATCAAATATTTAATTTCCAATGG
20312849 AAAATAGCAAATATGTATAATACTTTCTTGGTAC
261 AAAATAGCAAATATGTATAATACTTTCTTGGTAC
20312883 AGCAAATCCC
Statistics
Matches: 288, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
298 288 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (298 bp):
AAATAGAAAGAGAATTCTTTGAGGAATCGAATAACCGAGCAACCGAGCAAATCGAGATATCATCA
TTGGAAGGGGAAATGGGTAATTTTGTAAAAATCGAGATTAAGCCCCAATCCAATGATGATGACTC
AATCCCCATAAAGGAAGATGACGATCCCTATATCTTAAATTTAAATCTTCAACTAATTATTGTTA
CAAAAACATTGACAGAAGAAAAATTAGTTAAAGAGATCATCGATCAAATATTTAATTTCCAATGG
AAAATAGCAAATATGTATAATACTTTCTTGGTACGAGG
Found at i:20324134 original size:24 final size:21
Alignment explanation
Indices: 20324092--20324142 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 21
20324082 GTATTGAGAC
20324092 AGAAGAAAGAGAAAGAAAAGA
1 AGAAGAAAGAGAAAGAAAAGA
*
20324113 AGAAGAAGAGAAGGAAGAAAAAGA
1 AGAAGAA-AG-AGAAAG-AAAAGA
20324137 AGAAGA
1 AGAAGA
20324143 TGTTGCCTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 7 0.27
22 2 0.08
23 5 0.19
24 12 0.46
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (21 bp):
AGAAGAAAGAGAAAGAAAAGA
Found at i:20324560 original size:20 final size:20
Alignment explanation
Indices: 20324524--20324572 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
20324514 GTTAGTTGCA
20324524 TGCATTTCTTTTAATTGTCAT-
1 TGCATTT-TTTTAATTGTC-TC
*
20324545 TGCATTTTTTTTATTGTCTC
1 TGCATTTTTTTAATTGTCTC
20324565 TGCATTTT
1 TGCATTTT
20324573 ATTTGTTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 18 0.69
21 7 0.27
ACGTcount: A:0.14, C:0.14, G:0.10, T:0.61
Consensus pattern (20 bp):
TGCATTTTTTTAATTGTCTC
Found at i:20326481 original size:12 final size:12
Alignment explanation
Indices: 20326464--20326488 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20326454 ATTTTATAAC
20326464 ATAAATATTGTT
1 ATAAATATTGTT
20326476 ATAAATATTGTT
1 ATAAATATTGTT
20326488 A
1 A
20326489 ATAGCCTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATAAATATTGTT
Found at i:20327284 original size:12 final size:12
Alignment explanation
Indices: 20327267--20327291 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20327257 TGACCCGTTT
20327267 TCCTATAATCTA
1 TCCTATAATCTA
20327279 TCCTATAATCTA
1 TCCTATAATCTA
20327291 T
1 T
20327292 AATATAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (12 bp):
TCCTATAATCTA
Found at i:20330481 original size:18 final size:18
Alignment explanation
Indices: 20330456--20330505 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
20330446 AAGATTGAAC
*
20330456 TTTA-ACTTTTAATTGTT
1 TTTAGACTTTTAATTATT
**
20330473 TTTAGACTTTTCTTTATT
1 TTTAGACTTTTAATTATT
*
20330491 TTTAGACTTGTAATT
1 TTTAGACTTTTAATT
20330506 TTTGGGATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.62
Consensus pattern (18 bp):
TTTAGACTTTTAATTATT
Found at i:20333214 original size:45 final size:46
Alignment explanation
Indices: 20333146--20333232 Score: 158
Period size: 45 Copynumber: 1.9 Consensus size: 46
20333136 ATAAAGCAAA
*
20333146 TATCAAAACTTCCGTGTAGAGTACTATCGGTACTTAAATTCTCAAC
1 TATCAAAACTTCCGTGTAGAGTACTACCGGTACTTAAATTCTCAAC
20333192 TATCAAAACTT-CGTGTAGAGTACTACCGGTACTTAAATTCT
1 TATCAAAACTTCCGTGTAGAGTACTACCGGTACTTAAATTCT
20333233 TACTACCGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
45 29 0.73
46 11 0.28
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (46 bp):
TATCAAAACTTCCGTGTAGAGTACTACCGGTACTTAAATTCTCAAC
Found at i:20334146 original size:40 final size:40
Alignment explanation
Indices: 20334082--20334217 Score: 164
Period size: 40 Copynumber: 3.4 Consensus size: 40
20334072 CAAAAATTTG
* * * * **
20334082 GCTTGAATTTTAACACCAGCTTATAGCCTGCTAAGTTGTA
1 GCTTGAACTTTATCATCGGCTTATAGCCTGCTAAGCCGTA
* * *
20334122 GCTTGAACTTTATCATTGGTTTATAGTCTGCTAAGCCGTA
1 GCTTGAACTTTATCATCGGCTTATAGCCTGCTAAGCCGTA
* * *
20334162 GCTTGAACTGTATCCTCGGCTTATAGCCTGTTAAGCCGTA
1 GCTTGAACTTTATCATCGGCTTATAGCCTGCTAAGCCGTA
20334202 GCTTGAACTTTATCAT
1 GCTTGAACTTTATCAT
20334218 ACATAGCATA
Statistics
Matches: 79, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.37
Consensus pattern (40 bp):
GCTTGAACTTTATCATCGGCTTATAGCCTGCTAAGCCGTA
Found at i:20345079 original size:22 final size:23
Alignment explanation
Indices: 20345054--20345096 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
20345044 TAAAAAAGAG
*
20345054 AAAATTTAGTTTTTTA-AAAATA
1 AAAATCTAGTTTTTTAGAAAATA
*
20345076 AAAATCTGGTTTTTTAGAAAA
1 AAAATCTAGTTTTTTAGAAAA
20345097 GTTTAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (23 bp):
AAAATCTAGTTTTTTAGAAAATA
Found at i:20345451 original size:146 final size:147
Alignment explanation
Indices: 20345091--20345593 Score: 656
Period size: 149 Copynumber: 3.4 Consensus size: 147
20345081 CTGGTTTTTT
* * * *
20345091 AGAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTTAACTATTTTGAAATAAAAGTTTTG
1 AGAAAAATTTAAATTTTTAAACAAAGTTTTGA-TTTTTTTTAACTATTTCGAAATAAAAGTTTAG
** **
20345156 ATTTTTAAG-AAAGTAGTGATTTTCATTAAAAAATGAAAATTTTTATATTTTTTTTAAA-AAAAA
65 ATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAA--AAAAAGTTTATA-TTTTTAAAAATAAAAA
*
20345219 TTTAG-TTTTTAGTTATTTTAA
127 TAT-GTTTTTTAGTTATTTTAA
* * ** * * *
20345240 AGAAAAAAATTAAAATTTTAAATTAAGTTTTAATTTCTTTTAACTATTTTGAAATAAAAGTTTAG
1 AG-AAAAATTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAG
20345305 ATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAAAATAAAGTTTATA-TTTTAAAAATAAAAATA
65 ATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAAAA-AAAGTTTATATTTTTAAAAATAAAAATA
20345369 TGTTTTTTAGTTATTTTAA
129 TGTTTTTTAGTTATTTTAA
*
20345388 AGAAAAATTTAAATTTTTAAACAAAGTTTTGA-TTTTTTTAATTATTTCGAAATAAAAGTTTAGA
1 AGAAAAATTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGA
* * * * *
20345452 TTTTTAAATAAAGTTGTGATTTTCATTAAAAAAAGAAAGTTTAGATTTTTAAAAAATAAAAATCT
66 TTTTTAAGTAAAGTAGTGATTTTCATTAAAAAAAAAAAGTTTATATTTTT-AAAAATAAAAATAT
*
20345517 GTTTTTTAGTGATTTTAA
130 GTTTTTTAGTTATTTTAA
* *
20345535 AGTGAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAATTATTTCGAAATAAA
1 A--GAAAAATTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAA
20345594 GTAGTGATTT
Statistics
Matches: 317, Mismatches: 27, Indels: 19
0.87 0.07 0.05
Matches are distributed among these distances:
145 9 0.03
146 65 0.21
147 64 0.20
148 27 0.09
149 79 0.25
150 73 0.23
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.46
Consensus pattern (147 bp):
AGAAAAATTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGA
TTTTTAAGTAAAGTAGTGATTTTCATTAAAAAAAAAAAGTTTATATTTTTAAAAATAAAAATATG
TTTTTTAGTTATTTTAA
Found at i:20347069 original size:241 final size:237
Alignment explanation
Indices: 20346641--20347122 Score: 714
Period size: 241 Copynumber: 2.0 Consensus size: 237
20346631 AAATCTTTTA
* * *
20346641 AAATCATAATAATGATAAAAGATAAAATAAGTTGTAGATAAATTTTAATATTTCTCTTAATTTAT
1 AAATCAGAATAATGATAAAAGATAAAATAAGTTGTAGATAAATTATAATATTTCTCTTAATTCAT
* * *
20346706 TAGTAATTTTTAGGTTTTTTTAGGATTCTAAAATAAAATTAGTTTTAAGAATTGAAGGTATGTTA
66 TAGTAATTTTTAGGTTTTTTTAGGATTCTAAAATAAAATTAATTTTAAAAATTGAAAGTATGTTA
* *
20346771 CTAGAATTATTTAAGTATCTTTTAGGATTCGCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAA
131 CTAGAATTATTTAAGTATCATTTAGGATTCGCAATAGAAGTAAAAATCTCTAATTTAAGTTTTAA
* *
20346836 ATTAGATAAGTTTGGCGAACACGTTTTAGTCAAGTTACAAGT
196 ATTAGATAAGTTTGGCAAACACGTCTTAGTCAAGTTACAAGT
* ** *
20346878 AAATCAGAGTAATGATAAAAGATCGAATAAGTTGTAGATGAATTATAATATTTCTCTTAATTCAT
1 AAATCAGAATAATGATAAAAGATAAAATAAGTTGTAGATAAATTATAATATTTCTCTTAATTCAT
* *
20346943 TAGTAATTTTTTTTAGGTTTTTTTTAGTATTCTAAAATAGAATTAATTTTAAAAATTGAAAGTAT
66 TAGTAA---TTTTTAGG-TTTTTTTAGGATTCTAAAATAAAATTAATTTTAAAAATTGAAAGTAT
* * ** *
20347008 TTTACTAGAATTATTT-AGATATCATTTAGGGTTCTTAATAGGAGTAAAAATCTCTAATTTAAGT
127 GTTACTAGAATTATTTAAG-TATCATTTAGGATTCGCAATAGAAGTAAAAATCTCTAATTTAAGT
*
20347072 TTTAAATTAGATAAGTTTGGTAAACACGTCTTAGTCAAGTTACAAGT
191 TTTAAATTAGATAAGTTTGGCAAACACGTCTTAGTCAAGTTACAAGT
20347119 AAAT
1 AAAT
20347123 TGGAGGTATT
Statistics
Matches: 218, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
237 64 0.29
240 10 0.05
241 144 0.66
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (237 bp):
AAATCAGAATAATGATAAAAGATAAAATAAGTTGTAGATAAATTATAATATTTCTCTTAATTCAT
TAGTAATTTTTAGGTTTTTTTAGGATTCTAAAATAAAATTAATTTTAAAAATTGAAAGTATGTTA
CTAGAATTATTTAAGTATCATTTAGGATTCGCAATAGAAGTAAAAATCTCTAATTTAAGTTTTAA
ATTAGATAAGTTTGGCAAACACGTCTTAGTCAAGTTACAAGT
Found at i:20350437 original size:4 final size:4
Alignment explanation
Indices: 20350428--20350473 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
20350418 GTGTCGCAAT
* * * *
20350428 TTCA TTCA TTCA CTCA TTCA TTCA TTCA GTCA GTCA TTCA CTCA TT
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TT
20350474 TGCTCGTTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.24, C:0.28, G:0.04, T:0.43
Consensus pattern (4 bp):
TTCA
Found at i:20355853 original size:42 final size:42
Alignment explanation
Indices: 20355582--20355854 Score: 330
Period size: 42 Copynumber: 6.5 Consensus size: 42
20355572 AAGGAAAGCA
* * * *
20355582 TTCATTGCATTTAGAGGCCCAGGTGTGAAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGCCCATTTACTT
** * * *
20355624 TTCATCACATTTAGAGGCCCAAGTGTGGAGGCCCATTTACTA
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGCCCATTTACTT
* * *
20355666 TTCATTACATTTAGAGGCCTAGGTGTGGAGGTCCATTTGCTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGCCCATTTACTT
* *
20355708 TTCATTGCATTTAAAGGCCTAGGTGTGGAGGCCCATTTATTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGCCCATTTACTT
** * *
20355750 TTTGTTGCATTTAGAGGCCCAGGTGTGGAGGCTCATTTACTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGCCCATTTACTT
* ** * *
20355792 TTCGTTGCATTCGGAGGCCTAGGTGTGGAGGCCCATGTAGTT
1 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGCCCATTTACTT
*
20355834 TTCATTGCAATTAGAGGCCTA
1 TTCATTGCATTTAGAGGCCTA
20355855 AGCATAGAGA
Statistics
Matches: 196, Mismatches: 35, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 196 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCTAGGTGTGGAGGCCCATTTACTT
Found at i:20356231 original size:3 final size:3
Alignment explanation
Indices: 20356223--20356279 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
20356213 AAGGGCCCAA
* * * * * *
20356223 ATT ATT ATT ATC ATC ATC ATC ATT ATT ATT ATT ATT ATT ACT CTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20356271 ATT ATT ATT
1 ATT ATT ATT
20356280 TAAATTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:20357045 original size:150 final size:150
Alignment explanation
Indices: 20356841--20357344 Score: 657
Period size: 151 Copynumber: 3.4 Consensus size: 150
20356831 GTTCTTTTAG
* * *
20356841 AAAAATTTAAAATTTTAAACAAAGTTTTGATTTTTTTTAATTATTTCGAAATAAAAGTTTAGATT
1 AAAAATTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
*
20356906 TTTAA-AAAAGTAGTGATTTTCATTAAAAAAAAGGAAAAAGTTTATATTTTTAAATATAAAAATC
66 TTTAAGTAAAGTAGTGATTTTCATT-AAAAAAA-GAAAAAGTTTATATTTTTAAATATAAAAATC
20356970 TATTTTTTAGTTATTTTAAATA
129 TATTTTTTAGTTATTTTAAATA
* *
20356992 AAAAATTTAAATTTGTAAATAAAGTTTTGA-TTTTTTTAACTATTTCGTAATAAAAGTTT-GTAT
1 AAAAATTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAG-AT
* * *
20357055 TTTTAAGTAAAGTAGTAATTTTCATTAAAAAAAGAAATAAATTTTATATTTTTAAAAATAAAAAT
65 TTTTAAGTAAAGTAGTGATTTTCATTAAAAAAAG-AA-AAAGTTTATATTTTTAAATATAAAAAT
* * *
20357120 ATA-TTTTTAGTTATTTTTAAGA
128 CTATTTTTTAGTTATTTTAAATA
* * * *
20357142 AAAAGTTTAAATTTTTAAATAAAGTTTTAATTTTTTTTAATTATTTCGAAATAAAAGTTTAAATT
1 AAAAATTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
* *
20357207 TTTAAGTAAACTAGTGATTTTCATT----AAA-AAAAAGTTTAGATTTTTAAAATATAAAAATCT
66 TTTAAGTAAAGTAGTGATTTTCATTAAAAAAAGAAAAAGTTTATATTTTT-AAATATAAAAATCT
* ** *
20357267 GTTTTTTAGAGATTTTAAAGTG
130 ATTTTTTAGTTATTTTAAA-TA
* * *
20357289 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTACTTCAAAATAAAA
1 AAAAATTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAA
20357345 ATTTTAATTT
Statistics
Matches: 310, Mismatches: 34, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
144 13 0.04
145 14 0.05
146 14 0.05
147 55 0.18
149 2 0.01
150 88 0.28
151 124 0.40
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (150 bp):
AAAAATTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
TTTAAGTAAAGTAGTGATTTTCATTAAAAAAAGAAAAAGTTTATATTTTTAAATATAAAAATCTA
TTTTTTAGTTATTTTAAATA
Found at i:20357177 original size:20 final size:20
Alignment explanation
Indices: 20357132--20357176 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
20357122 ATTTTTAGTT
20357132 ATTTTTAAGAAAAAGTTTAA
1 ATTTTTAAGAAAAAGTTTAA
* *
20357152 ATTTTTAA-ATAAAGTTTTA
1 ATTTTTAAGAAAAAGTTTAA
20357171 ATTTTT
1 ATTTTT
20357177 TTTAATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (20 bp):
ATTTTTAAGAAAAAGTTTAA
Found at i:20358813 original size:240 final size:238
Alignment explanation
Indices: 20358392--20358869 Score: 773
Period size: 240 Copynumber: 2.0 Consensus size: 238
20358382 AAAATCATAA
*
20358392 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
1 TAATGATAAAAGATCGAATAAGTTGTAAATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
* *
20358457 TTAAGTTTTTTTTAAGATTCTAAAATAGAATTAATTTTAATAATTGAAGGTATTTTACTAGAATT
66 TTAAGTTTTTTTTAAGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAGAATT
* **
20358522 ATTTAAGTATCTTTTAGGATTCTTGTTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
131 ATTTAAGTATCCTTTAGGATTCTTACTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
*
20358587 AGTTTGGCGAACACGTTTTAGTCAAGTTACAAGTAAATCGGAG
196 AGTTTGGCGAACACGTCTTAGTCAAGTTACAAGTAAATCGGAG
20358630 TAATGATAAAAGATCGAATAAGTTGTAAATGAATTTTAATATTTCTCTTAATTCATTAGT-ACTT
1 TAATGATAAAAGATCGAATAAGTTGTAAATGAATTTTAATATTTCTCTTAATTCATTAGTAAC--
*
20358694 TTTTTTAGGTTTTTTTT-AGTATTCT-AAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTA
64 --TTTTAAGTTTTTTTTAAG-ATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTA
* * *
20358757 GAATTATTTAGGTATCCTTTAGGGTTCTTACTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATT
126 GAATTATTTAAGTATCCTTTAGGATTCTTACTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATT
* *
20358822 AGATAAGTTTGGTGAACACGTCTTAGTCAAGTTACAAGTAAATTGGAG
191 AGATAAGTTTGGCGAACACGTCTTAGTCAAGTTACAAGTAAATCGGAG
20358870 GCGTTTTTTA
Statistics
Matches: 222, Mismatches: 13, Indels: 8
0.91 0.05 0.03
Matches are distributed among these distances:
237 2 0.01
238 59 0.27
240 142 0.64
241 19 0.09
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (238 bp):
TAATGATAAAAGATCGAATAAGTTGTAAATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
TTAAGTTTTTTTTAAGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAGAATT
ATTTAAGTATCCTTTAGGATTCTTACTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
AGTTTGGCGAACACGTCTTAGTCAAGTTACAAGTAAATCGGAG
Found at i:20361370 original size:62 final size:62
Alignment explanation
Indices: 20361294--20361417 Score: 221
Period size: 62 Copynumber: 2.0 Consensus size: 62
20361284 GGTCTATTTA
* *
20361294 TAGCCTTCTGATGGTTGTCATCCTCATCCCTAGGTTAGTTTATATTCTCGGGTTTAATGATG
1 TAGCCTTCTGATGGTCGTCATCCTCATCCCTAGGTTAGTTGATATTCTCGGGTTTAATGATG
*
20361356 TAGCCTTCTGATGGTCGTCATCCTCATCCCTAGGTTAGTTGATGTTCTCGGGTTTAATGATG
1 TAGCCTTCTGATGGTCGTCATCCTCATCCCTAGGTTAGTTGATATTCTCGGGTTTAATGATG
20361418 CATTGTGAAG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (62 bp):
TAGCCTTCTGATGGTCGTCATCCTCATCCCTAGGTTAGTTGATATTCTCGGGTTTAATGATG
Found at i:20368514 original size:73 final size:74
Alignment explanation
Indices: 20368342--20368514 Score: 303
Period size: 74 Copynumber: 2.4 Consensus size: 74
20368332 ATTGATTGAT
*
20368342 ATTGATTTATATTATTTGATTATTTTGATGTTTGATATAACAAAAATGGGAGAAAAAAAGGTAAA
1 ATTGATTGATATTATTTGATTATTTTGATGTTTGATATAACAAAAATGGGAGAAAAAAAGGTAAA
* **
20368407 TTAAGGTGC
66 CTAAGGTAA
20368416 ATTGATTGATATTATTTGATTATTTTGATGTTTGATATAACAAAAATGGGAG-AAAAAAGGTAAA
1 ATTGATTGATATTATTTGATTATTTTGATGTTTGATATAACAAAAATGGGAGAAAAAAAGGTAAA
20368480 CTAAGGTAA
66 CTAAGGTAA
20368489 ATTGATTGATATTATTTGATTATTTT
1 ATTGATTGATATTATTTGATTATTTT
20368515 TTTATGCTAA
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
73 44 0.46
74 51 0.54
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.40
Consensus pattern (74 bp):
ATTGATTGATATTATTTGATTATTTTGATGTTTGATATAACAAAAATGGGAGAAAAAAAGGTAAA
CTAAGGTAA
Found at i:20368893 original size:19 final size:19
Alignment explanation
Indices: 20368860--20368939 Score: 54
Period size: 20 Copynumber: 4.0 Consensus size: 19
20368850 AAATCAAGTT
*
20368860 AAATGATTTTAAACAAGTCA
1 AAATGA-TTTCAACAAGTCA
* *
20368880 AAATGATTTCAACAAACTTA
1 AAATGATTTCAAC-AAGTCA
* *
20368900 AAATCATTTTAACACA-TCA
1 AAATGATTTCAACA-AGTCA
*
20368919 AAATAATTTCCAAACAAGTCA
1 AAATGATTT-C-AACAAGTCA
20368940 GAATTGCTCT
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
19 17 0.36
20 23 0.49
21 7 0.15
ACGTcount: A:0.50, C:0.16, G:0.05, T:0.29
Consensus pattern (19 bp):
AAATGATTTCAACAAGTCA
Found at i:20369399 original size:135 final size:135
Alignment explanation
Indices: 20369209--20369475 Score: 516
Period size: 135 Copynumber: 2.0 Consensus size: 135
20369199 TTTTGTGTGA
*
20369209 TATCAATACTCGTAATTGCAAGTGAAATAAATGCTTTGGTTTTTCACCCCTAACAACTATATTCA
1 TATCAATACTCGTAATTGCAAGTGAAATAAATGCTTTGGTTTTTCACCCCCAACAACTATATTCA
20369274 TTACTCCAACAACCTCAATGTTTGGAAATTAATTAGGGAGTATAAAGGCCAACTTCAAATGACCC
66 TTACTCCAACAACCTCAATGTTTGGAAATTAATTAGGGAGTATAAAGGCCAACTTCAAATGACCC
20369339 TATGG
131 TATGG
20369344 TATCAATACTCGTAATTGCAAGTGAAATAAATGCTTTGGTTTTTCACCCCCAACAACTATATTCA
1 TATCAATACTCGTAATTGCAAGTGAAATAAATGCTTTGGTTTTTCACCCCCAACAACTATATTCA
*
20369409 TTACTCCAACAACCTCAATGTTTGGAAATTAATTAGGGAGTATAAAGGCCAACTTCTAATGACCC
66 TTACTCCAACAACCTCAATGTTTGGAAATTAATTAGGGAGTATAAAGGCCAACTTCAAATGACCC
20369474 TA
131 TA
20369476 CAATAACCTT
Statistics
Matches: 130, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
135 130 1.00
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (135 bp):
TATCAATACTCGTAATTGCAAGTGAAATAAATGCTTTGGTTTTTCACCCCCAACAACTATATTCA
TTACTCCAACAACCTCAATGTTTGGAAATTAATTAGGGAGTATAAAGGCCAACTTCAAATGACCC
TATGG
Found at i:20373289 original size:16 final size:17
Alignment explanation
Indices: 20373251--20373282 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
20373241 AATAAATAAA
20373251 AAATATATAAAATTATT
1 AAATATATAAAATTATT
20373268 AAATAT-TAAAATTAT
1 AAATATATAAAATTAT
20373283 ATAATATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATATAAAATTATT
Found at i:20379505 original size:806 final size:807
Alignment explanation
Indices: 20377953--20379565 Score: 3219
Period size: 806 Copynumber: 2.0 Consensus size: 807
20377943 ATAAGAAAAC
20377953 AATAAAAATGTTTTTCGTGAAACCATTTACAAGCAAACAAACAAAGTCTAATTTTTATCACCTCA
1 AATAAAAATGTTTTTCGTGAAACCATTTACAAGCAAACAAACAAAGTCTAATTTTTATCACCTCA
20378018 TAATTTATTTATTAATATTTTATTTATTGGTTATCTTTTTTGCTTGTTTAATTGCTTCAATTATC
66 TAATTTATTTATTAATATTTTATTTATTGGTTATCTTTTTTGCTTGTTTAATTGCTTCAATTATC
20378083 TTCTGATTCTTGTCACTATGTATTTTGAAATTAAAATTTATATTAAATGTAAAAATATAATTTTT
131 TTCTGATTCTTGTCACTATGTATTTTGAAATTAAAATTTATATTAAATGTAAAAATATAATTTTT
20378148 TAATAAAAGTTATTTTAAAGATAAAATGTGAAATTGACACCAACATATAATTTTAACAATAATAT
196 TAATAAAAGTTATTTTAAAGATAAAATGTGAAATTGACACCAACATATAATTTTAACAATAATAT
20378213 TTTATCGCATCATCAATAATTCAATTTTAACATAAATTTATAAAGATTAAATATGATTAAATAAT
261 TTTATCGCATCATCAATAATTCAATTTTAACATAAATTTATAAAGATTAAATATGATTAAATAAT
20378278 TCAATAACATAAAGAGAACAAAATATACAATTTAATTTAATAATATAAATAGTAGATATAAATAA
326 TCAATAACATAAAGAGAACAAAATATACAATTTAATTTAATAATATAAATAGTAGATATAAATAA
20378343 AATTGTTATTATTTAAATTTAGAATTTTTTTGAATGATTTTGATTTTTGATTTGGTGTAAAGCGT
391 AATTGTTATTATTTAAATTTAGAATTTTTTTGAATGATTTTGATTTTTGATTTGGTGTAAAGCGT
20378408 GAGGAGTAAAAGTTTAGGGAAAAATAAAAAGTTTGAGGGGTTTGGGGAGTAAAATTTTGGAGAAA
456 GAGGAGTAAAAGTTTAGGGAAAAATAAAAAGTTTGAGGGGTTTGGGGAGTAAAATTTTGGAGAAA
20378473 AAATATTTTAAAAAAATTGGGGAGGGGGAATGAGCTTAGGGTAAATAGGGGAGGGGATGGGAGGA
521 AAATATTTTAAAAAAATTGGGGAGGGGGAATGAGCTTAGGGTAAATAGGGGAGGGGATGGGAGGA
20378538 AAGTAAAAGTTTTGGGGGGGAAAGTGGGAGGGAGTAAAAGTTTTGGGATAAAATAAAAAGGCTTG
586 AAGTAAAAGTTTTGGGGGGGAAAGTGGGAGGGAGTAAAAGTTTTGGGATAAAATAAAAAGGCTTG
20378603 GGGGTTTGAAGTAAAAATTTAAAATATTATAGTTTAATATTTGGTTTATTCGAATTATTCAAATT
651 GGGGTTTGAAGTAAAAATTTAAAATATTATAGTTTAATATTTGGTTTATTCGAATTATTCAAATT
20378668 CAAAAATTCAACTCGATTCGAACTCGAAATTC-AAAAAAAATTCAAGTTGACTTGAATAACTCGA
716 CAAAAATTCAACTCGATTCGAACTCGAAATTCAAAAAAAAATTCAAGTTGACTTGAATAACTCGA
20378732 TTTTTTAACTCGAAATTGAATTTTTTT
781 TTTTTTAACTCGAAATTGAATTTTTTT
20378759 AATAAAAATGTTTTTCGTGAAACCATTTACAAGCAAACAAACAAAGTCTAATTTTTATCACCTCA
1 AATAAAAATGTTTTTCGTGAAACCATTTACAAGCAAACAAACAAAGTCTAATTTTTATCACCTCA
20378824 TAATTTATTTATTAATATTTTATTTATTGGTTATCTTTTTTGCTTGTTTAATTGCTTCAATTATC
66 TAATTTATTTATTAATATTTTATTTATTGGTTATCTTTTTTGCTTGTTTAATTGCTTCAATTATC
20378889 TTCTGATTCTTGTCACTATGTATTTTGAAATTAAAATTTATATTAAATGTAAAAATATAATTTTT
131 TTCTGATTCTTGTCACTATGTATTTTGAAATTAAAATTTATATTAAATGTAAAAATATAATTTTT
20378954 TAATAAAAGTTATTTTAAAGATAAAATGTGAAATTGACACCAACATATAATTTTAACAATAATAT
196 TAATAAAAGTTATTTTAAAGATAAAATGTGAAATTGACACCAACATATAATTTTAACAATAATAT
20379019 TTTATCGCATCATCAATAATTCAATTTTAACATAAATTTATAAAGATTAAATATGATTAAATAAT
261 TTTATCGCATCATCAATAATTCAATTTTAACATAAATTTATAAAGATTAAATATGATTAAATAAT
20379084 TCAATAACATAAAGAGAACAAAATATACAATTTAATTTAATAATATAAATAGTAGATATAAATAA
326 TCAATAACATAAAGAGAACAAAATATACAATTTAATTTAATAATATAAATAGTAGATATAAATAA
20379149 AATTGTTATTATTTAAATTTAGAATTTTTTTGAATGATTTTGATTTTTGATTTGGTGTAAAGCGT
391 AATTGTTATTATTTAAATTTAGAATTTTTTTGAATGATTTTGATTTTTGATTTGGTGTAAAGCGT
20379214 GAGGAGTAAAAGTTTAGGGAAAAATAAAAAGTTTGAGGGGTTTGGGGAGTAAAATTTTGGAGAAA
456 GAGGAGTAAAAGTTTAGGGAAAAATAAAAAGTTTGAGGGGTTTGGGGAGTAAAATTTTGGAGAAA
20379279 AAATATTTTAAAAAAATTGGGGAGGGGGAATGAGCTTAGGGTAAATAGGGGAGGGGATGGGAGGA
521 AAATATTTTAAAAAAATTGGGGAGGGGGAATGAGCTTAGGGTAAATAGGGGAGGGGATGGGAGGA
20379344 AAGTAAAAGTTTTGGGGGGGAAAGTGGGAGGGAGTAAAAGTTTTGGGATAAAATAAAAAGGCTTG
586 AAGTAAAAGTTTTGGGGGGGAAAGTGGGAGGGAGTAAAAGTTTTGGGATAAAATAAAAAGGCTTG
20379409 GGGGTTTGAAGTAAAAATTTAAAATATTATAGTTTAATATTTGGTTTATTCGAATTATTCAAATT
651 GGGGTTTGAAGTAAAAATTTAAAATATTATAGTTTAATATTTGGTTTATTCGAATTATTCAAATT
20379474 CAAAAATTCAACTCGATTCGAACTCGAAATTCAAAAAAAAATTCAAGTTGACTTGAATAACTCGA
716 CAAAAATTCAACTCGATTCGAACTCGAAATTCAAAAAAAAATTCAAGTTGACTTGAATAACTCGA
20379539 TTTTTTAACTCGAAATTGAATTTTTTT
781 TTTTTTAACTCGAAATTGAATTTTTTT
20379566 TTCGATTTTT
Statistics
Matches: 806, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
806 747 0.93
807 59 0.07
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (807 bp):
AATAAAAATGTTTTTCGTGAAACCATTTACAAGCAAACAAACAAAGTCTAATTTTTATCACCTCA
TAATTTATTTATTAATATTTTATTTATTGGTTATCTTTTTTGCTTGTTTAATTGCTTCAATTATC
TTCTGATTCTTGTCACTATGTATTTTGAAATTAAAATTTATATTAAATGTAAAAATATAATTTTT
TAATAAAAGTTATTTTAAAGATAAAATGTGAAATTGACACCAACATATAATTTTAACAATAATAT
TTTATCGCATCATCAATAATTCAATTTTAACATAAATTTATAAAGATTAAATATGATTAAATAAT
TCAATAACATAAAGAGAACAAAATATACAATTTAATTTAATAATATAAATAGTAGATATAAATAA
AATTGTTATTATTTAAATTTAGAATTTTTTTGAATGATTTTGATTTTTGATTTGGTGTAAAGCGT
GAGGAGTAAAAGTTTAGGGAAAAATAAAAAGTTTGAGGGGTTTGGGGAGTAAAATTTTGGAGAAA
AAATATTTTAAAAAAATTGGGGAGGGGGAATGAGCTTAGGGTAAATAGGGGAGGGGATGGGAGGA
AAGTAAAAGTTTTGGGGGGGAAAGTGGGAGGGAGTAAAAGTTTTGGGATAAAATAAAAAGGCTTG
GGGGTTTGAAGTAAAAATTTAAAATATTATAGTTTAATATTTGGTTTATTCGAATTATTCAAATT
CAAAAATTCAACTCGATTCGAACTCGAAATTCAAAAAAAAATTCAAGTTGACTTGAATAACTCGA
TTTTTTAACTCGAAATTGAATTTTTTT
Found at i:20380282 original size:29 final size:29
Alignment explanation
Indices: 20380249--20380344 Score: 156
Period size: 29 Copynumber: 3.3 Consensus size: 29
20380239 GAAGAATATG
* * *
20380249 GAATAATTTAATCAATTTAAATTCAAACA
1 GAATAATTTATTCAATTTAAAATCAATCA
*
20380278 GAATAATTTATTCAATTTAAAATCAATTA
1 GAATAATTTATTCAATTTAAAATCAATCA
20380307 GAATAATTTATTCAATTTAAAATCAATCA
1 GAATAATTTATTCAATTTAAAATCAATCA
20380336 GAATAATTT
1 GAATAATTT
20380345 TAGGTATTGA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (29 bp):
GAATAATTTATTCAATTTAAAATCAATCA
Found at i:20385585 original size:31 final size:31
Alignment explanation
Indices: 20385548--20385609 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
20385538 AATTCGAAAG
20385548 GGAAAAAGCATTTTCCGTTGAACAAAACAAT
1 GGAAAAAGCATTTTCCGTTGAACAAAACAAT
20385579 GGAAAAAGCATTTTCCGTTGAACAAAACAAT
1 GGAAAAAGCATTTTCCGTTGAACAAAACAAT
20385610 CTTTGTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (31 bp):
GGAAAAAGCATTTTCCGTTGAACAAAACAAT
Found at i:20385810 original size:29 final size:29
Alignment explanation
Indices: 20385766--20385910 Score: 148
Period size: 29 Copynumber: 5.3 Consensus size: 29
20385756 TAGAATATGA
* * *
20385766 AATAATTTATTAAATTT-AAATTCAAACGG
1 AATAATTTATTCAATTTAAAATT-AATCAG
*
20385795 AATAATTTATTCAATTTAAAATTAATTAG
1 AATAATTTATTCAATTTAAAATTAATCAG
20385824 AATAATTTATTCAATTTAAAATTAATCTA-
1 AATAATTTATTCAATTTAAAATTAATC-AG
*
20385853 AATAATTTATTC-------AATCAATCAG
1 AATAATTTATTCAATTTAAAATTAATCAG
*
20385875 AATAATTTATTCAATTT-AAATAAATCAG
1 AATAATTTATTCAATTTAAAATTAATCAG
20385903 AATAATTT
1 AATAATTT
20385911 TAGGGTTGAC
Statistics
Matches: 100, Mismatches: 7, Indels: 19
0.79 0.06 0.15
Matches are distributed among these distances:
21 1 0.01
22 19 0.19
28 17 0.17
29 57 0.57
30 6 0.06
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (29 bp):
AATAATTTATTCAATTTAAAATTAATCAG
Found at i:20386534 original size:25 final size:23
Alignment explanation
Indices: 20386491--20386536 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
20386481 CCAACTAGGA
20386491 AATTATTGTTTAGATTTAATTCT
1 AATTATTGTTTAGATTTAATTCT
*
20386514 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
20386537 TGGATCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCT
Found at i:20395431 original size:33 final size:33
Alignment explanation
Indices: 20395373--20395440 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 33
20395363 ATTTGTCGCG
*
20395373 ACACCCTTATGCTGTGTCACGACATAAAAGACA
1 ACACCCTTATGCTGTGTCACAACATAAAAGACA
* * * * *
20395406 ACACCTTTATGTTGTGTCGCAACATAGAATACA
1 ACACCCTTATGCTGTGTCACAACATAAAAGACA
20395439 AC
1 AC
20395441 TTCAGGATTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (33 bp):
ACACCCTTATGCTGTGTCACAACATAAAAGACA
Found at i:20397439 original size:26 final size:25
Alignment explanation
Indices: 20397353--20397444 Score: 73
Period size: 26 Copynumber: 3.7 Consensus size: 25
20397343 ACATGAGGAG
* *
20397353 AGCCTTTGTGGCG-AGTTATCTAAA
1 AGCCTTTGTGGCGAAGTTATTTGAA
* * *
20397377 AACCTTATGTGGAGTA-TTATTTGAGA
1 AGCCTT-TGTGGCGAAGTTATTTGA-A
* *
20397403 AGACTTAGTGGCGAAGTTATTTGGAA
1 AGCCTTTGTGGCGAAGTTATTT-GAA
20397429 AGCCTTTGTGGC-AAGT
1 AGCCTTTGTGGCGAAGT
20397445 CATCTAGAAA
Statistics
Matches: 52, Mismatches: 11, Indels: 9
0.72 0.15 0.12
Matches are distributed among these distances:
24 5 0.10
25 22 0.42
26 23 0.44
27 2 0.04
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (25 bp):
AGCCTTTGTGGCGAAGTTATTTGAA
Found at i:20401979 original size:23 final size:23
Alignment explanation
Indices: 20401949--20402002 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
20401939 TATACTTGTT
20401949 TGGTGTGTTAGGTTGGATGGAGA
1 TGGTGTGTTAGGTTGGATGGAGA
20401972 TGGTGTGTTAGGTTGGATGGAGA
1 TGGTGTGTTAGGTTGGATGGAGA
20401995 TGGTGTGT
1 TGGTGTGT
20402003 AGCGGATGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.15, C:0.00, G:0.48, T:0.37
Consensus pattern (23 bp):
TGGTGTGTTAGGTTGGATGGAGA
Found at i:20405300 original size:29 final size:28
Alignment explanation
Indices: 20405230--20405374 Score: 130
Period size: 29 Copynumber: 5.0 Consensus size: 28
20405220 CCTTATTTTA
** * *
20405230 TTTAAAAATGGTGTTTTGACCCCCTAACTT
1 TTTAAAAATTATGTTTTGA-CCCTTAA-AT
*
20405260 TTTAAAAATTATGTTTTAACCCTTAAAT
1 TTTAAAAATTATGTTTTGACCCTTAAAT
* *
20405288 TTTAAAAAATTATATTTTGACCCCTAAACT
1 TTT-AAAAATTATGTTTTGACCCTTAAA-T
20405318 TTCTAAAAATTATGTTTTGA-CCTTAAATT
1 TT-TAAAAATTATGTTTTGACCCTTAAA-T
* * *
20405347 TTCTAGAAATTATATTTTGACCCCTAAA
1 TT-TAAAAATTATGTTTTGACCCTTAAA
20405375 CTTTCCAAAA
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
28 4 0.04
29 52 0.54
30 40 0.41
31 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (28 bp):
TTTAAAAATTATGTTTTGACCCTTAAAT
Found at i:20405306 original size:59 final size:59
Alignment explanation
Indices: 20405243--20405387 Score: 213
Period size: 59 Copynumber: 2.5 Consensus size: 59
20405233 AAAAATGGTG
*
20405243 TTTTGACCCCCT-AACTTTTTAAAAATTATGTTTTAACCCTTAAATTTT-AAAAAATTATA
1 TTTTGA-CCCCTAAACTTTCTAAAAATTATGTTTTAA-CCTTAAATTTTCAAAAAATTATA
* * *
20405302 TTTTGACCCCTAAACTTTCTAAAAATTATGTTTTGACCTTAAATTTTCTAGAAATTATA
1 TTTTGACCCCTAAACTTTCTAAAAATTATGTTTTAACCTTAAATTTTCAAAAAATTATA
*
20405361 TTTTGACCCCTAAACTTTCCAAAAATT
1 TTTTGACCCCTAAACTTTCTAAAAATT
20405388 TAGATTTGGC
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
58 16 0.20
59 63 0.80
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (59 bp):
TTTTGACCCCTAAACTTTCTAAAAATTATGTTTTAACCTTAAATTTTCAAAAAATTATA
Found at i:20405406 original size:30 final size:30
Alignment explanation
Indices: 20405362--20405428 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
20405352 GAAATTATAT
* *
20405362 TTTGACCCCTAAACTTTCCAAAAATTTAGA
1 TTTGGCCCCCAAACTTTCCAAAAATTTAGA
*
20405392 TTTGGCCCCCAAACTTTCCAAAAATTTGGA
1 TTTGGCCCCCAAACTTTCCAAAAATTTAGA
20405422 TTTGGCC
1 TTTGGCC
20405429 TCGTTTTCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (30 bp):
TTTGGCCCCCAAACTTTCCAAAAATTTAGA
Found at i:20406632 original size:21 final size:21
Alignment explanation
Indices: 20406606--20406669 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
20406596 TGTCATATCA
*
20406606 AAATTTTTGGGGCGTTATAGT
1 AAATTTTTGGGGCTTTATAGT
**
20406627 AAA--TTT--GTATTTATA-T
1 AAATTTTTGGGGCTTTATAGT
20406643 AAATTTTTGGGGCTTTATAGT
1 AAATTTTTGGGGCTTTATAGT
20406664 AAATTT
1 AAATTT
20406670 GTTTGAACTG
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
16 4 0.12
17 6 0.18
18 3 0.09
19 3 0.09
20 7 0.21
21 10 0.30
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.48
Consensus pattern (21 bp):
AAATTTTTGGGGCTTTATAGT
Found at i:20408797 original size:8 final size:8
Alignment explanation
Indices: 20408784--20408811 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
20408774 TACAACTGCT
20408784 ATTTGTTA
1 ATTTGTTA
20408792 ATTTGTTA
1 ATTTGTTA
20408800 ATTTGTTA
1 ATTTGTTA
20408808 ATTT
1 ATTT
20408812 CTTACTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (8 bp):
ATTTGTTA
Found at i:20409184 original size:24 final size:24
Alignment explanation
Indices: 20409166--20409240 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
20409156 AGTTTGACTC
20409166 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
*
20409190 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
* * *
20409214 AAATAATTAAACAAAGTTTAACTG
1 AAACAAATAAACAAAGTTTAATTG
20409238 AAA
1 AAA
20409241 GTTACTTCTC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.57, C:0.08, G:0.09, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAAAGTTTAATTG
Done.