Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 125 of 202
Found at i:38682850 original size:55 final size:55
Alignment explanation
Indices: 38682766--38682887 Score: 244
Period size: 55 Copynumber: 2.2 Consensus size: 55
38682756 NNNNNNNNNN
38682766 CTAACCATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGATAATTTTA
1 CTAACCATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGATAATTTTA
38682821 CTAACCATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGATAATTTTA
1 CTAACCATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGATAATTTTA
38682876 CTAACCATTAAC
1 CTAACCATTAAC
38682888 TTAATAATTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 67 1.00
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.42
Consensus pattern (55 bp):
CTAACCATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGATAATTTTA
Found at i:38682872 original size:18 final size:18
Alignment explanation
Indices: 38682849--38682918 Score: 68
Period size: 18 Copynumber: 3.6 Consensus size: 18
38682839 TTTGGACTTA
38682849 ATAATTTTACATAATTTG
1 ATAATTTTACATAATTTG
* *
38682867 ATAATTTTACTAACCATTAACTTA
1 ATAA-TTT--T-A-CA-TAATTTG
38682891 ATAATTTTACATAATTTG
1 ATAATTTTACATAATTTG
38682909 ATAATTTTAC
1 ATAATTTTAC
38682919 TAACCATTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
18 19 0.45
19 5 0.12
20 1 0.02
21 2 0.05
22 1 0.02
23 5 0.12
24 9 0.21
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (18 bp):
ATAATTTTACATAATTTG
Found at i:38682892 original size:42 final size:42
Alignment explanation
Indices: 38682844--38682929 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
38682834 CAATTTTTGG
38682844 ACTTAATAATTTTACATAATTTGATAATTTTACTAACCATTA
1 ACTTAATAATTTTACATAATTTGATAATTTTACTAACCATTA
38682886 ACTTAATAATTTTACATAATTTGATAATTTTACTAACCATTA
1 ACTTAATAATTTTACATAATTTGATAATTTTACTAACCATTA
38682928 AC
1 AC
38682930 ACAATTTTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.41, C:0.13, G:0.02, T:0.44
Consensus pattern (42 bp):
ACTTAATAATTTTACATAATTTGATAATTTTACTAACCATTA
Found at i:38690457 original size:51 final size:51
Alignment explanation
Indices: 38690381--38690483 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 51
38690371 ATTTTTCTTG
38690381 AAATTTTACCAGGGGCAAAACTGTCAAAATTTTACCAGAGGCAAAATTGTCA
1 AAATTTTACCAGGGGCAAAACTGTCAAAATTTTA-CAGAGGCAAAATTGTCA
* * * *
38690433 AAATTTTA-CAGGGGTAAAATTGTCAAAATTTTACAGGGGTAAAATTGTCA
1 AAATTTTACCAGGGGCAAAACTGTCAAAATTTTACAGAGGCAAAATTGTCA
38690483 A
1 A
38690484 TTTTTTGGGG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
50 16 0.34
51 23 0.49
52 8 0.17
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (51 bp):
AAATTTTACCAGGGGCAAAACTGTCAAAATTTTACAGAGGCAAAATTGTCA
Found at i:38690489 original size:25 final size:26
Alignment explanation
Indices: 38690381--38690483 Score: 156
Period size: 25 Copynumber: 4.0 Consensus size: 26
38690371 ATTTTTCTTG
*
38690381 AAATTTTACCAGGGGCAAAACTGTCA
1 AAATTTTACCAGGGGCAAAATTGTCA
*
38690407 AAATTTTACCAGAGGCAAAATTGTCA
1 AAATTTTACCAGGGGCAAAATTGTCA
*
38690433 AAATTTTA-CAGGGGTAAAATTGTCA
1 AAATTTTACCAGGGGCAAAATTGTCA
*
38690458 AAATTTTA-CAGGGGTAAAATTGTCA
1 AAATTTTACCAGGGGCAAAATTGTCA
38690483 A
1 A
38690484 TTTTTTGGGG
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
25 41 0.56
26 32 0.44
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (26 bp):
AAATTTTACCAGGGGCAAAATTGTCA
Found at i:38696483 original size:30 final size:30
Alignment explanation
Indices: 38696449--38696515 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
38696439 ATTAGTAAAG
* *
38696449 ATAAAATTGTACTTTGAGCCCCTAAAAATT
1 ATAAAATTGTAATTTAAGCCCCTAAAAATT
* * **
38696479 ATAAAATTTTAATTTAATCCTTTAAAAATT
1 ATAAAATTGTAATTTAAGCCCCTAAAAATT
38696509 ATAAAAT
1 ATAAAAT
38696516 AGAGGCTATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.39
Consensus pattern (30 bp):
ATAAAATTGTAATTTAAGCCCCTAAAAATT
Found at i:38701179 original size:166 final size:167
Alignment explanation
Indices: 38700979--38701316 Score: 660
Period size: 166 Copynumber: 2.0 Consensus size: 167
38700969 AATTTGTGAC
38700979 TTTGACAAACTTTACAATCCCCTTCTGCCTTCATCCACATCATTCTTCATCATTTCGTATTAGAT
1 TTTGACAAACTTTACAATCCCCTTCTGCCTTCATCCACATCATTCTTCATCATTTCGTATTAGAT
38701044 TTGGGCATTTTGGGTGTTCATGGTTGATTCCTAAACTGATTTCCATTGCAAAACAGCCTATAAGC
66 TTGGGCATTTTGGGTGTTCATGGTTGATTCCTAAACTGATTTCCATTGCAAAACAGCCTATAAGC
38701109 AGTTTTTACCCAGAATGTTTTTC-AAAAAAAAATATT
131 AGTTTTTACCCAGAATGTTTTTCAAAAAAAAAATATT
*
38701145 TTTGACAAACTTTACGATCCCCTTCTGCCTTCATCCACATCATTCTTCATCATTTCGTATTAGAT
1 TTTGACAAACTTTACAATCCCCTTCTGCCTTCATCCACATCATTCTTCATCATTTCGTATTAGAT
38701210 TTGGGCATTTTGGGTGTTCATGGTTGATTCCTAAACTGATTTCCATTGCAAAACAGCCTATAAGC
66 TTGGGCATTTTGGGTGTTCATGGTTGATTCCTAAACTGATTTCCATTGCAAAACAGCCTATAAGC
38701275 AGTTTTTACCCAGAATGTTTTTCAAAAAAAAAATATT
131 AGTTTTTACCCAGAATGTTTTTCAAAAAAAAAATATT
38701312 TTTGA
1 TTTGA
38701317 GTGGGTAAAT
Statistics
Matches: 170, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
166 152 0.89
167 18 0.11
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (167 bp):
TTTGACAAACTTTACAATCCCCTTCTGCCTTCATCCACATCATTCTTCATCATTTCGTATTAGAT
TTGGGCATTTTGGGTGTTCATGGTTGATTCCTAAACTGATTTCCATTGCAAAACAGCCTATAAGC
AGTTTTTACCCAGAATGTTTTTCAAAAAAAAAATATT
Found at i:38703813 original size:30 final size:30
Alignment explanation
Indices: 38703778--38703847 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
38703768 ACGATCGAAA
**
38703778 AAAATCAAGATTCACTTTTTTGTTTTCAAG
1 AAAATCAAGATTCACTTTCGTGTTTTCAAG
38703808 AAAATCAAGATTCACTTTCGTGTTTTCAAG
1 AAAATCAAGATTCACTTTCGTGTTTTCAAG
*
38703838 GAAATCAAGA
1 AAAATCAAGA
38703848 AATCGAATCT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (30 bp):
AAAATCAAGATTCACTTTCGTGTTTTCAAG
Found at i:38711119 original size:29 final size:29
Alignment explanation
Indices: 38711077--38711135 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
38711067 TCACAGTCCC
38711077 TATGGGTACGATAACTCGACATTTACTAG
1 TATGGGTACGATAACTCGACATTTACTAG
* *
38711106 TATGGGTATGATAACTTGACATTTACTAG
1 TATGGGTACGATAACTCGACATTTACTAG
38711135 T
1 T
38711136 CACTTTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.36
Consensus pattern (29 bp):
TATGGGTACGATAACTCGACATTTACTAG
Found at i:38721369 original size:27 final size:29
Alignment explanation
Indices: 38721324--38721393 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 29
38721314 CACAAATTTG
38721324 AAATTTAGTCCATGCAC-TTT-AATTTTA
1 AAATTTAGTCCATGCACTTTTAAATTTTA
* * **
38721351 GAATTTAGTCCCTTTACTTTTTAAATTTTA
1 AAATTTAGTCCATGCAC-TTTTAAATTTTA
38721381 AAATTTAGGTCCA
1 AAATTTA-GTCCA
38721394 ACTATTAACA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 13 0.39
29 3 0.09
30 13 0.39
31 4 0.12
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (29 bp):
AAATTTAGTCCATGCACTTTTAAATTTTA
Found at i:38722903 original size:187 final size:187
Alignment explanation
Indices: 38722587--38722962 Score: 716
Period size: 187 Copynumber: 2.0 Consensus size: 187
38722577 CTCCAGTGGT
38722587 ATTAGAGAATAGAAGTTGTTAGTCAGTTAGTGAGGTTGTTACTCAGTTCAGAAAGTCTATAAATA
1 ATTAGAGAATAGAAGTTGTTAGTCAGTTAGTGAGGTTGTTACTCAGTTCAGAAAGTCTATAAATA
38722652 CTGCACATTAAGAATTAAGAAGTAAGCAAGTTTGAATAAACAAACAAGAAGTTTATTATATTATT
66 CTGCACATTAAGAATTAAGAAGTAAGCAAGTTTGAATAAACAAACAAGAAGTTTATTATATTATT
38722717 TTCTCCATTTTCACTCTCTGTTTGGATAGATATCTCCTTCTTTTATCTAGTTCTTTC
131 TTCTCCATTTTCACTCTCTGTTTGGATAGATATCTCCTTCTTTTATCTAGTTCTTTC
38722774 ATTAGAGAATAGAAGTTGTTAGTCAGTTAGTGAGGTTGTTACTCAGTTCAGAAAGTCTATAAATA
1 ATTAGAGAATAGAAGTTGTTAGTCAGTTAGTGAGGTTGTTACTCAGTTCAGAAAGTCTATAAATA
* * * *
38722839 TTGTACATTAAGAATTAAGAAGTAAGCAAGTTTGAATAAACAAACAAGAATTTTATTCTATTATT
66 CTGCACATTAAGAATTAAGAAGTAAGCAAGTTTGAATAAACAAACAAGAAGTTTATTATATTATT
38722904 TTCTCCATTTTCACTCTCTGTTTGGATAGATATCTCCTTCTTTTATCTAGTTCTTTC
131 TTCTCCATTTTCACTCTCTGTTTGGATAGATATCTCCTTCTTTTATCTAGTTCTTTC
38722961 AT
1 AT
38722963 GGTATCATTC
Statistics
Matches: 185, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
187 185 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.39
Consensus pattern (187 bp):
ATTAGAGAATAGAAGTTGTTAGTCAGTTAGTGAGGTTGTTACTCAGTTCAGAAAGTCTATAAATA
CTGCACATTAAGAATTAAGAAGTAAGCAAGTTTGAATAAACAAACAAGAAGTTTATTATATTATT
TTCTCCATTTTCACTCTCTGTTTGGATAGATATCTCCTTCTTTTATCTAGTTCTTTC
Found at i:38724044 original size:45 final size:45
Alignment explanation
Indices: 38723988--38724084 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 45
38723978 ACAATTTATG
*
38723988 GTCAAAATAGAAATGGTGGTCAAAATTGGAGTAATGGCATGCAAA
1 GTCAGAATAGAAATGGTGGTCAAAATTGGAGTAATGGCATGCAAA
* **
38724033 GTCAGAATAGAAATGGTGGTCAAAATTGGGGTGCTGGCATGCAAA
1 GTCAGAATAGAAATGGTGGTCAAAATTGGAGTAATGGCATGCAAA
*
38724078 GTGAGAA
1 GTCAGAA
38724085 ATTGGCACGT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.38, C:0.09, G:0.31, T:0.22
Consensus pattern (45 bp):
GTCAGAATAGAAATGGTGGTCAAAATTGGAGTAATGGCATGCAAA
Found at i:38727810 original size:17 final size:18
Alignment explanation
Indices: 38727788--38727821 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38727778 CTAAGCCACT
38727788 TTCGTTGTC-GAGTTTTA
1 TTCGTTGTCGGAGTTTTA
*
38727805 TTCGTTTTCGGAGTTTT
1 TTCGTTGTCGGAGTTTT
38727822 CTACGGGTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.09, C:0.12, G:0.24, T:0.56
Consensus pattern (18 bp):
TTCGTTGTCGGAGTTTTA
Found at i:38770181 original size:42 final size:41
Alignment explanation
Indices: 38770122--38770263 Score: 156
Period size: 42 Copynumber: 3.6 Consensus size: 41
38770112 TGATTCCCCC
*
38770122 AAGGGGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGA
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTATCTT-AATGTGA
* *
38770164 AAGGGGTTGCTAAGTGCTGATTCC-CTG-A--TTCAT-TG-
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTATCTTAATGTGA
* *
38770199 --GTGGTTGCTAAGTGCTAATTCCACCGTATCATTGAATGTGA
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTATC-TT-AATGTGA
38770240 AAGGGGTTGCTAAGTGCTGATTCC
1 AAGGGGTTGCTAAGTGCTGATTCC
38770264 CCGAATCATT
Statistics
Matches: 81, Mismatches: 9, Indels: 19
0.74 0.08 0.17
Matches are distributed among these distances:
33 20 0.25
34 2 0.02
35 1 0.01
36 2 0.02
37 2 0.02
38 4 0.05
39 2 0.02
40 3 0.04
41 2 0.02
42 23 0.28
43 20 0.25
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCTGATTCCACCGTATCTTAATGTGA
Found at i:38770210 original size:33 final size:33
Alignment explanation
Indices: 38770168--38770302 Score: 119
Period size: 33 Copynumber: 3.8 Consensus size: 33
38770158 ATGTGAAAGG
*
38770168 GGTTGCTAAGTGCTGATTCCCTGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
38770201 GGTTGCTAAGTGCTAATTCCACCG-TATCATTGAATGT
1 GGTTGCTAAGTGCTGATTCC-CCGAT-TCATTG---GT
*
38770238 GAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 ------GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
38770277 GGTTGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
38770303 AATGGATAAC
Statistics
Matches: 83, Mismatches: 6, Indels: 25
0.73 0.05 0.22
Matches are distributed among these distances:
33 39 0.47
34 12 0.14
37 2 0.02
39 2 0.02
42 9 0.11
43 19 0.23
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:38770256 original size:76 final size:75
Alignment explanation
Indices: 38770020--38770300 Score: 396
Period size: 76 Copynumber: 3.8 Consensus size: 75
38770010 TGATTCCCCC
* * * *
38770020 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATC
38770085 TTAAATGTGA
66 TTAAATGTGA
* * * *
38770095 AGGGGGTTGCTAAGTGCTGATTCCCC----CA-AGG-GGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATC
38770154 TTAAATGTGA
66 TTAAATGTGA
* *
38770164 AAGGGGTTGCTAAGTGCTGATTCCCTGATTCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATC
*
38770229 ATTGAATGTGA
66 -TTAAATGTGA
38770240 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAA-TCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCT-AATTCCACCG
38770301 ATAATGGATA
Statistics
Matches: 185, Mismatches: 13, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
69 60 0.32
70 2 0.01
71 2 0.01
73 2 0.01
74 2 0.01
75 50 0.27
76 65 0.35
77 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.32
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATC
TTAAATGTGA
Found at i:38777479 original size:21 final size:21
Alignment explanation
Indices: 38777433--38777480 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
38777423 GTATAATGCA
38777433 TTTAAATAATATAATTAACAT
1 TTTAAATAATATAATTAACAT
* * * *
38777454 ATTAAATAATATATTTTATAT
1 TTTAAATAATATAATTAACAT
38777475 TTTAAA
1 TTTAAA
38777481 ATCACACTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTAAATAATATAATTAACAT
Found at i:38780964 original size:27 final size:27
Alignment explanation
Indices: 38780927--38781270 Score: 310
Period size: 27 Copynumber: 12.8 Consensus size: 27
38780917 TGCGATTCGT
* *
38780927 GGGTAAAATTATCGAAATACCCTCGAT
1 GGGTAAAATTATCGAAATACCCTCAAA
*
38780954 GGGTAAAATTA-CTGAAATACCCTCAAT
1 GGGTAAAATTATC-GAAATACCCTCAAA
* *
38780981 GGGTAAAATTACCGAAATACCCCCGAAA
1 GGGTAAAATTATCGAAATACCCTC-AAA
38781009 -GGTAAAATTATCGAAATACCCT-AAA
1 GGGTAAAATTATCGAAATACCCTCAAA
* * *
38781034 GGGTAAAATCATCGAAATACTCTCGAA
1 GGGTAAAATTATCGAAATACCCTCAAA
* * *
38781061 GAGTAAAATTA-CTAAAATACCCTCAAT
1 GGGTAAAATTATC-GAAATACCCTCAAA
*
38781088 GGGTAAAATTATCGAAATACCCTTGAAA
1 GGGTAAAATTATCGAAATACCC-TCAAA
* * *
38781116 -GATAAAATTA-CTGAAGTACTCTCAAA
1 GGGTAAAATTATC-GAAATACCCTCAAA
* *
38781142 GGGTAAAATTA-CTAAAATACTCTCAATA
1 GGGTAAAATTATC-GAAATACCCTCAA-A
38781170 -GGTAAAATTATCGAAATACCCTCAAA
1 GGGTAAAATTATCGAAATACCCTCAAA
** * **
38781196 GGAAAAAATTATCAAAATACCCTTGAA
1 GGGTAAAATTATCGAAATACCCTCAAA
* * *
38781223 GGGTAAAATTACCGTAATGGCCCT-AAA
1 GGGTAAAATTATCGAAAT-ACCCTCAAA
* *
38781250 GGGTAAAATTTTTGAAATACC
1 GGGTAAAATTATCGAAATACC
38781271 ACTGAGGGGT
Statistics
Matches: 259, Mismatches: 44, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
25 3 0.01
26 30 0.12
27 213 0.82
28 13 0.05
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (27 bp):
GGGTAAAATTATCGAAATACCCTCAAA
Found at i:38780989 original size:54 final size:54
Alignment explanation
Indices: 38780927--38781285 Score: 363
Period size: 54 Copynumber: 6.7 Consensus size: 54
38780917 TGCGATTCGT
* *
38780927 GGGTAAAATTATCGAAATACCCTCGATGGGTAAAATTACTGAAATACCCTCAAT
1 GGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTGAAATACCCTCAAA
* * *
38780981 GGGTAAAATTACCGAAATACCCCCGAAAGGTAAAATTA-TCGAAATACCCT-AAA
1 GGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACT-GAAATACCCTCAAA
* * * * *
38781034 GGGTAAAATCATCGAAATACTCTCGAAGAGTAAAATTACTAAAATACCCTCAAT
1 GGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTGAAATACCCTCAAA
* * * * *
38781088 GGGTAAAATTATCGAAATACCCTTGAAAGATAAAATTACTGAAGTACTCTCAAA
1 GGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTGAAATACCCTCAAA
* * *
38781142 GGGTAAAATTA-CTAAAATACTCTC-AATAGGTAAAATTA-TCGAAATACCCTCAAA
1 GGGTAAAATTATC-GAAATACCCTCGAA-GGGTAAAATTACT-GAAATACCCTCAAA
** * * * * *
38781196 GGAAAAAATTATCAAAATACCCTTGAAGGGTAAAATTACCGTAATGGCCCT-AAA
1 GGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTGAAAT-ACCCTCAAA
* * *
38781250 GGGTAAAATTTTTGAAATACCACT-GAGGGGTAAAAT
1 GGGTAAAATTATCGAAATACC-CTCGAAGGGTAAAAT
38781286 GACCGTTATA
Statistics
Matches: 251, Mismatches: 43, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
53 48 0.19
54 194 0.77
55 9 0.04
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (54 bp):
GGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTGAAATACCCTCAAA
Found at i:38781204 original size:81 final size:81
Alignment explanation
Indices: 38780928--38781234 Score: 354
Period size: 81 Copynumber: 3.8 Consensus size: 81
38780918 GCGATTCGTG
* * * * *
38780928 GGTAAAATTATCGAAATACCCTCGATGGGTAAAATTACTGAAATACCCTCAATGGGTAAAATTAC
1 GGTAAAATTATCGAAATACCCTCAAAGGATAAAATTACTGAAATACTCTCAAAGGGTAAAATTAC
** *
38780993 CGAAATACCCCCGAA-A
66 TAAAATACCCTC-AATA
* * * *
38781009 GGTAAAATTATCGAAATACCCT-AAAGGGTAAAATCA-TCGAAATACTCTCGAAGAGTAAAATTA
1 GGTAAAATTATCGAAATACCCTCAAAGGATAAAATTACT-GAAATACTCTCAAAGGGTAAAATTA
*
38781072 CTAAAATACCCTCAATG
65 CTAAAATACCCTCAATA
* *
38781089 GGTAAAATTATCGAAATACCCTTGAAA-GATAAAATTACTGAAGTACTCTCAAAGGGTAAAATTA
1 GGTAAAATTATCGAAATACCC-TCAAAGGATAAAATTACTGAAATACTCTCAAAGGGTAAAATTA
*
38781153 CTAAAATACTCTCAATA
65 CTAAAATACCCTCAATA
* * * **
38781170 GGTAAAATTATCGAAATACCCTCAAAGGAAAAAATTA-TCAAAATACCCTTGAAGGGTAAAATTA
1 GGTAAAATTATCGAAATACCCTCAAAGGATAAAATTACT-GAAATACTCTCAAAGGGTAAAATTA
38781234 C
65 C
38781235 CGTAATGGCC
Statistics
Matches: 194, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
79 3 0.02
80 68 0.35
81 119 0.61
82 4 0.02
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (81 bp):
GGTAAAATTATCGAAATACCCTCAAAGGATAAAATTACTGAAATACTCTCAAAGGGTAAAATTAC
TAAAATACCCTCAATA
Found at i:38781255 original size:81 final size:81
Alignment explanation
Indices: 38780927--38781270 Score: 344
Period size: 81 Copynumber: 4.3 Consensus size: 81
38780917 TGCGATTCGT
* * *
38780927 GGGTAAAATTATCGAAATACCCTCGATGGGTAAAATTACTGAAATACCCTC-AATGGGTAAAATT
1 GGGTAAAATTATCGAAATACCCTCAAAGGATAAAATTACTGAAATACCCTCGAA-GGGTAAAATT
* *
38780991 ACCGAAATACCCCCGAAA
65 ACCAAAATACCCTC-AAA
* * * *
38781009 -GGTAAAATTATCGAAATACCCT-AAAGGGTAAAATCA-TCGAAATACTCTCGAAGAGTAAAATT
1 GGGTAAAATTATCGAAATACCCTCAAAGGATAAAATTACT-GAAATACCCTCGAAGGGTAAAATT
* *
38781071 ACTAAAATACCCTCAAT
65 ACCAAAATACCCTCAAA
* * * *
38781088 GGGTAAAATTATCGAAATACCCTTGAAA-GATAAAATTACTGAAGTACTCTCAAAGGGTAAAATT
1 GGGTAAAATTATCGAAATACCC-TCAAAGGATAAAATTACTGAAATACCCTCGAAGGGTAAAATT
* *
38781152 ACTAAAATACTCTCAATA
65 ACCAAAATACCCTCAA-A
* * *
38781170 -GGTAAAATTATCGAAATACCCTCAAAGGAAAAAATTA-TCAAAATACCCTTGAAGGGTAAAATT
1 GGGTAAAATTATCGAAATACCCTCAAAGGATAAAATTACT-GAAATACCCTCGAAGGGTAAAATT
** *
38781233 ACCGTAATGGCCCT-AAA
65 ACCAAAAT-ACCCTCAAA
* *
38781250 GGGTAAAATTTTTGAAATACC
1 GGGTAAAATTATCGAAATACC
38781271 ACTGAGGGGT
Statistics
Matches: 221, Mismatches: 30, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
79 3 0.01
80 68 0.31
81 143 0.65
82 7 0.03
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (81 bp):
GGGTAAAATTATCGAAATACCCTCAAAGGATAAAATTACTGAAATACCCTCGAAGGGTAAAATTA
CCAAAATACCCTCAAA
Found at i:38781527 original size:26 final size:26
Alignment explanation
Indices: 38781496--38781563 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
38781486 TTATTGGCAA
*
38781496 CTTTGCTGCGATATTGATACTGATAG
1 CTTTGCTGCGATATTGATACTGACAG
* * *
38781522 CTTTGCTGCGTTACTGATACTGGCAG
1 CTTTGCTGCGATATTGATACTGACAG
*
38781548 CTTTGCTACGATATTG
1 CTTTGCTGCGATATTG
38781564 GTGTGTTGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (26 bp):
CTTTGCTGCGATATTGATACTGACAG
Found at i:38781709 original size:28 final size:29
Alignment explanation
Indices: 38781677--38781752 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
38781667 GATAAGTGTT
*
38781677 TTGGGCTAAGACCCACAC-TGTTACTGTA
1 TTGGGCTAAGACCCACACTTATTACTGTA
*
38781705 TTGGGCTAAGGCCCACACTTTATTACTGTA
1 TTGGGCTAAGACCCACAC-TTATTACTGTA
* *
38781735 TTGGGCTATGCCCCACAC
1 TTGGGCTAAGACCCACAC
38781753 ACTGCTATTG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 17 0.40
30 25 0.60
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (29 bp):
TTGGGCTAAGACCCACACTTATTACTGTA
Found at i:38781765 original size:30 final size:30
Alignment explanation
Indices: 38781677--38781771 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
38781667 GATAAGTGTT
*
38781677 TTGGGCTAAG-ACC-CACACTGTTACTGTA
1 TTGGGCTAAGCCCCACACACTGTTACTGTA
* ** *
38781705 TTGGGCTAAGGCCCACACTTTATTACTGTA
1 TTGGGCTAAGCCCCACACACTGTTACTGTA
* * *
38781735 TTGGGCTATGCCCCACACACTGCTATTGTA
1 TTGGGCTAAGCCCCACACACTGTTACTGTA
*
38781765 TAGGGCT
1 TTGGGCT
38781772 CAGGCCAAGC
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
28 10 0.19
29 2 0.04
30 41 0.77
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (30 bp):
TTGGGCTAAGCCCCACACACTGTTACTGTA
Found at i:38787448 original size:27 final size:27
Alignment explanation
Indices: 38787410--38787755 Score: 257
Period size: 27 Copynumber: 12.8 Consensus size: 27
38787400 GTTTGGTTCG
* *
38787410 TGGGTAAAATTATCGAAATAGCCTCGA
1 TGGGTAAAATTATCGAAATACCCTCAA
*
38787437 TGGGTAAAATTA-CTGAAATACCCTTAA
1 TGGGTAAAATTATC-GAAATACCCTCAA
* *
38787464 TGGGTAAAATTACCAAAATACCC-CTAA
1 TGGGTAAAATTATCGAAATACCCTC-AA
*
38787491 AGGGTAAAATTATCGAAATACCCTCGAA
1 TGGGTAAAATTATCGAAATACCCTC-AA
38787519 -GGGTAAAATTA-CTGAAATACTCC-CGAA
1 TGGGTAAAATTATC-GAAATAC-CCTC-AA
* * *
38787546 -GGGTAAACTTACCGAAATACCTTCAA
1 TGGGTAAAATTATCGAAATACCCTCAA
* *
38787572 TGGGTAAAATTATCGAAACACCCTTGAA
1 TGGGTAAAATTATCGAAATACCC-TCAA
* *
38787600 -GGGTAAAATTACCGAAATACCCTTAA
1 TGGGTAAAATTATCGAAATACCCTCAA
* * *
38787626 TGAGTAAAATTATTGAAATACCCACGAA
1 TGGGTAAAATTATCGAAATACCCTC-AA
* * * *
38787654 T-GATGAAATTACCAAAATACCCTCAA
1 TGGGTAAAATTATCGAAATACCCTCAA
*
38787680 AGGG-AAAATT-TACTGAAATACCCTCGAA
1 TGGGTAAAATTAT-C-GAAATACCCTC-AA
* * *
38787708 -GGGTAAAATTACCGTAATGCTCC-CAA
1 TGGGTAAAATTATCGAAATAC-CCTCAA
* * *
38787734 AGGGTAAATTTATAGAAATACC
1 TGGGTAAAATTATCGAAATACC
38787756 TTCGAGAGGT
Statistics
Matches: 255, Mismatches: 44, Indels: 41
0.75 0.13 0.12
Matches are distributed among these distances:
26 19 0.07
27 212 0.83
28 24 0.09
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (27 bp):
TGGGTAAAATTATCGAAATACCCTCAA
Found at i:38787474 original size:54 final size:54
Alignment explanation
Indices: 38787410--38787775 Score: 336
Period size: 54 Copynumber: 6.8 Consensus size: 54
38787400 GTTTGGTTCG
* * *
38787410 TGGGTAAAATTATCGAAATAGCCTCGATGGGTAAAATTACTGAAATACCCTTAA
1 TGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTTAA
* * * * *
38787464 TGGGTAAAATTACCAAAATACCC-CTAAAGGGTAAAATTATCGAAATACCCTCGAA
1 TGGGTAAAATTATCGAAATACCCTC-GAAGGGTAAAATTACCGAAATACCCT-TAA
*
38787519 -GGGTAAAATTA-CTGAAATACTCC-CGAAGGGTAAACTTACCGAAATA-CCTTCAA
1 TGGGTAAAATTATC-GAAATAC-CCTCGAAGGGTAAAATTACCGAAATACCCTT-AA
* *
38787572 TGGGTAAAATTATCGAAACACCCTTGAAGGGTAAAATTACCGAAATACCCTTAA
1 TGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTTAA
* * * * * * * *
38787626 TGAGTAAAATTATTGAAATACCCACGAATGATGAAATTACCAAAATACCCTCAA
1 TGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTTAA
* * * *
38787680 AGGG-AAAATT-TACTGAAATACCCTCGAAGGGTAAAATTACCGTAATGCTCC-CAA
1 TGGGTAAAATTAT-C-GAAATACCCTCGAAGGGTAAAATTACCGAAATAC-CCTTAA
* * * * *
38787734 AGGGTAAATTTATAGAAATACCTTCG-AGAGGTAAAATGACCG
1 TGGGTAAAATTATCGAAATACCCTCGAAG-GGTAAAATTACCG
38787776 TTATACCCCT
Statistics
Matches: 257, Mismatches: 40, Indels: 30
0.79 0.12 0.09
Matches are distributed among these distances:
52 1 0.00
53 17 0.07
54 221 0.86
55 17 0.07
56 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (54 bp):
TGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTTAA
Found at i:38787550 original size:81 final size:80
Alignment explanation
Indices: 38787411--38787770 Score: 368
Period size: 81 Copynumber: 4.5 Consensus size: 80
38787401 TTTGGTTCGT
* * **
38787411 GGGTAAAATTATCGAAATAGCCTCGATGGGTAAAATTACTGAAATACCCTTAATGGGTAAAATTA
1 GGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTGAAATACCCCGAATGGGTAAAATTA
*
38787476 CCAAAATACCCCTAAA
66 CCGAAATACCCC-AAA
*
38787492 GGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTGAAATACTCCCGAA-GGGTAAACTT
1 GGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTGAAATAC-CCCGAATGGGTAAAATT
* *
38787556 ACCGAAATACCTTCAAT
65 ACCGAAATACC-CCAAA
* * * ** *
38787573 GGGTAAAATTATCGAAACACCCTTGAAGGGTAAAATTACCGAAATACCCTTAATGAGTAAAATTA
1 GGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTGAAATACCCCGAATGGGTAAAATTA
** *
38787638 TTGAAATACCCACGAA
66 CCGAAATACCC-CAAA
* * * * * *
38787654 TGATGAAATTACCAAAATACCCTCAAAGGG-AAAATTTACTGAAATACCCTCGAA-GGGTAAAAT
1 GGGTAAAATTATCGAAATACCCTCGAAGGGTAAAA-TTACTGAAATACCC-CGAATGGGTAAAAT
* *
38787717 TACCGTAATGCTCCCAAA
64 TACCGAAATAC-CCCAAA
* * *
38787735 GGGTAAATTTATAGAAATACCTTCG-AGAGGTAAAAT
1 GGGTAAAATTATCGAAATACCCTCGAAG-GGTAAAAT
38787771 GACCGTTATA
Statistics
Matches: 224, Mismatches: 46, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
80 10 0.04
81 201 0.90
82 13 0.06
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.24
Consensus pattern (80 bp):
GGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTGAAATACCCCGAATGGGTAAAATTA
CCGAAATACCCCAAA
Found at i:38787994 original size:26 final size:26
Alignment explanation
Indices: 38787965--38788071 Score: 101
Period size: 26 Copynumber: 4.1 Consensus size: 26
38787955 TTTGCCACAA
38787965 ATACTGTTACTGGCAGCTTTGC-ACTG
1 ATACTGTTACTGGCAGCTTTGCTAC-G
* * * *
38787991 ATACTGATACTGGTAGCTCTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTACG
*
38788017 ATACTGTTATTGGCAGCTTTGCTAC-
1 ATACTGTTACTGGCAGCTTTGCTACG
** * *
38788042 ATTACTAATACTGGCAGCTTTCCTGCG
1 A-TACTGTTACTGGCAGCTTTGCTACG
38788069 ATA
1 ATA
38788072 TTGGTGTGTT
Statistics
Matches: 64, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
25 1 0.02
26 61 0.95
27 2 0.03
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.35
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGCTACG
Found at i:38788053 original size:52 final size:51
Alignment explanation
Indices: 38787965--38788071 Score: 135
Period size: 52 Copynumber: 2.1 Consensus size: 51
38787955 TTTGCCACAA
* * *
38787965 ATACTGTTACTGGCAGCTTTGCACTGATACTGATACTGGTAGCTCTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCACT-ATACTAATACTGGCAGCTCTCCTGCG
* *
38788017 ATACTGTTATTGGCAGCTTTGCTAC-ATTACTAATACTGGCAGCTTTCCTGCG
1 ATACTGTTACTGGCAGCTTTGC-ACTA-TACTAATACTGGCAGCTCTCCTGCG
38788069 ATA
1 ATA
38788072 TTGGTGTGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
51 1 0.02
52 45 0.94
53 2 0.04
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.35
Consensus pattern (51 bp):
ATACTGTTACTGGCAGCTTTGCACTATACTAATACTGGCAGCTCTCCTGCG
Found at i:38788219 original size:28 final size:28
Alignment explanation
Indices: 38788174--38788253 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
38788164 ACTGCATTTG
*
38788174 TACTGATTACTATTTTGGGCTAAGGCCTA
1 TACTG-TTACTATATTGGGCTAAGGCCTA
38788203 TACTGTTACTATATTGGGCTAAGGCCTA
1 TACTGTTACTATATTGGGCTAAGGCCTA
* *
38788231 CACTTTGTTACTGTATTGGGCTA
1 TAC--TGTTACTATATTGGGCTA
38788254 TAGCCTACAC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 24 0.52
29 5 0.11
30 17 0.37
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (28 bp):
TACTGTTACTATATTGGGCTAAGGCCTA
Found at i:38788242 original size:30 final size:28
Alignment explanation
Indices: 38788175--38788263 Score: 108
Period size: 30 Copynumber: 3.1 Consensus size: 28
38788165 CTGCATTTGT
* *
38788175 ACTGATTACTATTTTGGGCTAAGGCCTAT
1 ACTG-TTACTATATTGGGCTAAGGCCTAC
38788204 ACTGTTACTATATTGGGCTAAGGCCTAC
1 ACTGTTACTATATTGGGCTAAGGCCTAC
*
38788232 ACTTTGTTACTGTATTGGGCTATA-GCCTAC
1 AC--TGTTACTATATTGGGCTA-AGGCCTAC
38788262 AC
1 AC
38788264 ACTACTACTG
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
28 24 0.44
29 4 0.07
30 25 0.46
31 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (28 bp):
ACTGTTACTATATTGGGCTAAGGCCTAC
Found at i:38791089 original size:20 final size:20
Alignment explanation
Indices: 38791066--38791112 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
38791056 AACAAGAACT
38791066 GAAAAGAAA-AAATAAGAAAA
1 GAAAAGAAAGAAAT-AGAAAA
* *
38791086 GAAAGGAAAGAAATGGAAAA
1 GAAAAGAAAGAAATAGAAAA
*
38791106 GATAAGA
1 GAAAAGA
38791113 GTGGCGTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.06
Consensus pattern (20 bp):
GAAAAGAAAGAAATAGAAAA
Found at i:38792363 original size:11 final size:11
Alignment explanation
Indices: 38792347--38792390 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
38792337 ATTATTAAAA
38792347 TTATTAATTTT
1 TTATTAATTTT
38792358 TTATTAATTTT
1 TTATTAATTTT
*
38792369 CTAATTAA-TTT
1 -TTATTAATTTT
38792380 TTATTAATTTT
1 TTATTAATTTT
38792391 AATTTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 6 0.21
11 17 0.59
12 6 0.21
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATTAATTTT
Found at i:38792385 original size:10 final size:10
Alignment explanation
Indices: 38792347--38792400 Score: 63
Period size: 10 Copynumber: 5.1 Consensus size: 10
38792337 ATTATTAAAA
38792347 TTATTAATTTT
1 TTATTAA-TTT
38792358 TTATTAATTT
1 TTATTAATTT
38792368 TCTAATTAATTT
1 T-T-ATTAATTT
38792380 TTATTAATTT
1 TTATTAATTT
* *
38792390 TAATTTATTT
1 TTATTAATTT
38792400 T
1 T
38792401 CGACAGTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
10 21 0.54
11 9 0.23
12 9 0.23
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (10 bp):
TTATTAATTT
Found at i:38796171 original size:19 final size:19
Alignment explanation
Indices: 38796147--38796185 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
38796137 AATATTTTCT
*
38796147 AGTAAATCATTTTACAGAA
1 AGTAAAACATTTTACAGAA
*
38796166 AGTAAAACATTTTCCAGAA
1 AGTAAAACATTTTACAGAA
38796185 A
1 A
38796186 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (19 bp):
AGTAAAACATTTTACAGAA
Found at i:38796188 original size:33 final size:34
Alignment explanation
Indices: 38796135--38796199 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
38796125 CAAACAGCAG
* *
38796135 AAAATATTTTCTAGTAAATCATTTTACAGAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAGT
*
38796169 AAAACATTTTCCAG-AAATCATTTTACGGAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAA
38796200 ACATTTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAGT
Found at i:38796192 original size:14 final size:14
Alignment explanation
Indices: 38796169--38796208 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
38796159 TACAGAAAGT
*
38796169 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
38796183 AAATCATTTTACGG
1 AAAACATTTTACAG
38796197 AAAACATTTTAC
1 AAAACATTTTAC
38796209 TAGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:38799200 original size:46 final size:46
Alignment explanation
Indices: 38799144--38799258 Score: 185
Period size: 46 Copynumber: 2.5 Consensus size: 46
38799134 GACACCGTAG
* * *
38799144 ACAGAACGGCTAAAAGCCATAAGTATCGCAGCAACGCTGCCAGTTA
1 ACAGAACGGCTAAAAGCCATAAGTATCACAACAACGCTGCCACTTA
*
38799190 ACGGAACGGCTAAAAGCCATAAGTATCACAACAACGCTGCCACTTA
1 ACAGAACGGCTAAAAGCCATAAGTATCACAACAACGCTGCCACTTA
*
38799236 ACAGAACGACTAAAAGCCATAAG
1 ACAGAACGGCTAAAAGCCATAAG
38799259 CAAAAAGGCA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.41, C:0.26, G:0.19, T:0.14
Consensus pattern (46 bp):
ACAGAACGGCTAAAAGCCATAAGTATCACAACAACGCTGCCACTTA
Found at i:38799731 original size:27 final size:27
Alignment explanation
Indices: 38799458--38799722 Score: 291
Period size: 27 Copynumber: 9.8 Consensus size: 27
38799448 CTCTTAGATC
* *
38799458 ATTTTACCCTTTG-GAGGTATTTTGATA
1 ATTTTACCCTTCGAG-GGTATTTTGGTA
* * *
38799485 ATTTTACCCTTCGAAGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTTGGTA
*
38799512 ATTTTACCCTTCGAGGGTATTTTAGTA
1 ATTTTACCCTTCGAGGGTATTTTGGTA
*
38799539 ATTTTATCCTTCGAGGGTATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTTGGTA
* *
38799566 ATTTTACCCTTTGAGGGTACTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTTGGTA
* * * *
38799593 ATTTTACCCTTTGGGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTTGGTA
* *
38799620 ATTTTACACTTCGGGGGTATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTTGGTA
* * *
38799647 ATTTTACCCTTTGAAGGTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTTGGTA
* **
38799674 TTTTTACCAC-TCGAGGGTATTTCAGTA
1 ATTTTACC-CTTCGAGGGTATTTTGGTA
**
38799701 ATTTTACCCTTTAAGGGTATTT
1 ATTTTACCCTTCGAGGGTATTT
38799723 AAGTCATTTA
Statistics
Matches: 203, Mismatches: 32, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
26 1 0.00
27 201 0.99
28 1 0.00
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.45
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTTGGTA
Found at i:38805276 original size:38 final size:38
Alignment explanation
Indices: 38805225--38805307 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
38805215 CACTAGCACG
* * *
38805225 AAGCCTACTAGGCACAAAGCCTGAATAACACCAGCATA
1 AAGCCTGCTAGGCACAAAGCCTGAATAACACCAACACA
*
38805263 AAGCCTGCTAGGCACAGAGCCTGAATAACACCAACACA
1 AAGCCTGCTAGGCACAAAGCCTGAATAACACCAACACA
38805301 AAGCCTG
1 AAGCCTG
38805308 AATAACACCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.40, C:0.30, G:0.18, T:0.12
Consensus pattern (38 bp):
AAGCCTGCTAGGCACAAAGCCTGAATAACACCAACACA
Found at i:38805305 original size:22 final size:22
Alignment explanation
Indices: 38805275--38805328 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
38805265 GCCTGCTAGG
*
38805275 CACAGAGCCTGAATAACACCAA
1 CACAAAGCCTGAATAACACCAA
38805297 CACAAAGCCTGAATAACACCAA
1 CACAAAGCCTGAATAACACCAA
*
38805319 CATAAAGCCT
1 CACAAAGCCT
38805329 ACTAGGCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.46, C:0.31, G:0.11, T:0.11
Consensus pattern (22 bp):
CACAAAGCCTGAATAACACCAA
Found at i:38805334 original size:60 final size:60
Alignment explanation
Indices: 38805237--38805352 Score: 196
Period size: 60 Copynumber: 1.9 Consensus size: 60
38805227 GCCTACTAGG
* * * *
38805237 CACAAAGCCTGAATAACACCAGCATAAAGCCTGCTAGGCACAGAGCCTGAATAACACCAA
1 CACAAAGCCTGAATAACACCAACATAAAGCCTACTAGGCACAAAGCCTAAATAACACCAA
38805297 CACAAAGCCTGAATAACACCAACATAAAGCCTACTAGGCACAAAGCCTAAATAACA
1 CACAAAGCCTGAATAACACCAACATAAAGCCTACTAGGCACAAAGCCTAAATAACA
38805353 TTATACTTCT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.45, C:0.29, G:0.14, T:0.12
Consensus pattern (60 bp):
CACAAAGCCTGAATAACACCAACATAAAGCCTACTAGGCACAAAGCCTAAATAACACCAA
Found at i:38808292 original size:27 final size:26
Alignment explanation
Indices: 38808262--38808312 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
38808252 ATGAAATTCT
*
38808262 TACAAA-CAACATGATTGATTAACAATA
1 TACAAAGCAA-ATGA-TGAATAACAATA
38808289 TACAAAGCAAATGATGAATAACAA
1 TACAAAGCAAATGATGAATAACAA
38808313 ATTAATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 9 0.41
27 10 0.45
28 3 0.14
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.22
Consensus pattern (26 bp):
TACAAAGCAAATGATGAATAACAATA
Found at i:38808625 original size:23 final size:23
Alignment explanation
Indices: 38808581--38808625 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
38808571 ATAATAAGTT
**
38808581 TAAAAATAATATTAAGCCAATAA
1 TAAAAATAATATTAAAACAATAA
* *
38808604 TAAAAATAATGTTAAAATAATA
1 TAAAAATAATATTAAAACAATA
38808626 TATGAACATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (23 bp):
TAAAAATAATATTAAAACAATAA
Found at i:38810621 original size:44 final size:44
Alignment explanation
Indices: 38810566--38810797 Score: 144
Period size: 44 Copynumber: 5.0 Consensus size: 44
38810556 TTTTAATCCA
* *
38810566 CTCCACTGTAATCTCAGGGAGATAGGATTACTGGTTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
* *
38810610 CTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATGCG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATC---T--G
* * * *** * **
38810659 ATCTACTCTACTGTAA-CTTCAGAGAGATGAGA-TCCTTTATTTTAATCCA
1 --CT-C-C-ACTGTAATC-TCAGGGAGATAAGATTAC-TGGCTTCAATCTG
* * * *
38810708 CTCTACTGTAATCTCAAGGAGATAGGATTACTAGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
* * * * *
38810752 CTCCGCTGTAATCTCAGAGAGATAAGATTTCTGGCTTTAATTTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
38810796 CT
1 CT
38810798 TCATTACACT
Statistics
Matches: 139, Mismatches: 35, Indels: 28
0.69 0.17 0.14
Matches are distributed among these distances:
44 99 0.71
45 3 0.02
46 1 0.01
47 3 0.02
49 1 0.01
51 2 0.01
52 1 0.01
53 4 0.03
54 25 0.18
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (44 bp):
CTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
Found at i:38810765 original size:142 final size:142
Alignment explanation
Indices: 38810509--38810788 Score: 472
Period size: 142 Copynumber: 2.0 Consensus size: 142
38810499 GAGATAAGAC
*
38810509 CTGATGCGATCCTTTCTACAGTAACTTCAGAGAGATGAGATACTTTATTTTAATCCACTCCACTG
1 CTGATGCGATCCTCTCTACAGTAACTTCAGAGAGATGAGATACTTTATTTTAATCCACTCCACTG
* * * *
38810574 TAATCTCAGGGAGATAGGATTACTGGTTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGAGAGATAAGATT
38810639 TCTGGCTTCAAT
131 TCTGGCTTCAAT
* * *
38810651 CTGATGCGAT-CTACTCTACTGTAACTTCAGAGAGATGAGATCCTTTATTTTAATCCACTCTACT
1 CTGATGCGATCCT-CTCTACAGTAACTTCAGAGAGATGAGATACTTTATTTTAATCCACTCCACT
38810715 GTAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGAGAGATAAGAT
65 GTAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGAGAGATAAGAT
38810780 TTCTGGCTT
130 TTCTGGCTT
38810789 TAATTTGCTT
Statistics
Matches: 129, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
141 2 0.02
142 127 0.98
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (142 bp):
CTGATGCGATCCTCTCTACAGTAACTTCAGAGAGATGAGATACTTTATTTTAATCCACTCCACTG
TAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGAGAGATAAGATT
TCTGGCTTCAAT
Found at i:38819462 original size:19 final size:19
Alignment explanation
Indices: 38819422--38819466 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
38819412 ATAATCTTAG
* *
38819422 ATGCATATGATGACATGTA
1 ATGCAGATGATGAAATGTA
38819441 ATGCAGATGCATGAAATG-A
1 ATGCAGATG-ATGAAATGTA
38819460 ATGCAGA
1 ATGCAGA
38819467 AAGGTGCGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.24
Consensus pattern (19 bp):
ATGCAGATGATGAAATGTA
Found at i:38823369 original size:23 final size:23
Alignment explanation
Indices: 38823325--38823369 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
38823315 ATAATAAGTT
**
38823325 TAAAAATAATATTAAGCCAATAA
1 TAAAAATAATATTAAAACAATAA
* *
38823348 TAAAAATAATGTTAAAATAATA
1 TAAAAATAATATTAAAACAATA
38823370 TATGAACATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (23 bp):
TAAAAATAATATTAAAACAATAA
Found at i:38832061 original size:38 final size:37
Alignment explanation
Indices: 38831993--38832141 Score: 201
Period size: 38 Copynumber: 4.0 Consensus size: 37
38831983 TAATACACCG
*
38831993 GCACAAAGTCTACTAGGCACAAAG-TCTGAATAACACT
1 GCACAAAGTCTGCTAGGCACAAAGCT-TGAATAACACT
* * *
38832030 AGCATAAAGCCTGCTAGGCACAGAGCTTGAATAACACT
1 -GCACAAAGTCTGCTAGGCACAAAGCTTGAATAACACT
* *
38832068 GCACAAAATCTGCTAGGCACAGAGCTTGAATAACACT
1 GCACAAAGTCTGCTAGGCACAAAGCTTGAATAACACT
*
38832105 GGCACAAAGTCTGCTAGGCACAAAGCCTGAATAACAC
1 -GCACAAAGTCTGCTAGGCACAAAGCTTGAATAACAC
38832142 CGACACTGAG
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
37 34 0.34
38 64 0.65
39 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.17
Consensus pattern (37 bp):
GCACAAAGTCTGCTAGGCACAAAGCTTGAATAACACT
Found at i:38832119 original size:75 final size:75
Alignment explanation
Indices: 38831993--38832141 Score: 210
Period size: 75 Copynumber: 2.0 Consensus size: 75
38831983 TAATACACCG
* * * *
38831993 GCACAAAGTCTACTAGGCACAAAGTCTGAATAACACTAGCATAAAGCCTGCTAGGCACAGAGCTT
1 GCACAAAATCTACTAGGCACAAAGTCTGAATAACACTAGCACAAAGCCTGCTAGGCACAAAGCCT
38832058 GAATAACACT
66 GAATAACACT
* * * *
38832068 GCACAAAATCTGCTAGGCACAGAG-CTTGAATAACACTGGCACAAAGTCTGCTAGGCACAAAGCC
1 GCACAAAATCTACTAGGCACAAAGTC-TGAATAACACTAGCACAAAGCCTGCTAGGCACAAAGCC
38832132 TGAATAACAC
65 TGAATAACAC
38832142 CGACACTGAG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
74 1 0.02
75 64 0.98
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.17
Consensus pattern (75 bp):
GCACAAAATCTACTAGGCACAAAGTCTGAATAACACTAGCACAAAGCCTGCTAGGCACAAAGCCT
GAATAACACT
Found at i:38837291 original size:22 final size:22
Alignment explanation
Indices: 38837266--38837309 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
38837256 TCTGCATCAT
38837266 TAATAAATGTTTTATCAACAGC
1 TAATAAATGTTTTATCAACAGC
38837288 TAATAAATGTTTTATCAACAGC
1 TAATAAATGTTTTATCAACAGC
38837310 GAAGAGATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (22 bp):
TAATAAATGTTTTATCAACAGC
Found at i:38841937 original size:23 final size:23
Alignment explanation
Indices: 38841911--38841991 Score: 60
Period size: 23 Copynumber: 3.5 Consensus size: 23
38841901 TAATAATTTT
*
38841911 TGGATTGAAGTATAAGTTTAAAA
1 TGGAATGAAGTATAAGTTTAAAA
* **
38841934 TGGAATGAAAATCATAA---TAATTTT
1 TGGAATG-AAGT-ATAAGTTTAA--AA
*
38841958 TGGATTGAAGTATAAGTTTAAAA
1 TGGAATGAAGTATAAGTTTAAAA
38841981 TGGAATGAAGT
1 TGGAATGAAGT
38841992 TAACATTCTT
Statistics
Matches: 42, Mismatches: 9, Indels: 14
0.65 0.14 0.22
Matches are distributed among these distances:
22 7 0.17
23 19 0.45
24 9 0.21
25 7 0.17
ACGTcount: A:0.43, C:0.01, G:0.21, T:0.35
Consensus pattern (23 bp):
TGGAATGAAGTATAAGTTTAAAA
Found at i:38841964 original size:47 final size:47
Alignment explanation
Indices: 38841895--38841989 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
38841885 AGTAATATAT
38841895 AAATCATAATAATTTTTGGATTGAAGTATAAGTTTAAAATGGAATGA
1 AAATCATAATAATTTTTGGATTGAAGTATAAGTTTAAAATGGAATGA
38841942 AAATCATAATAATTTTTGGATTGAAGTATAAGTTTAAAATGGAATGA
1 AAATCATAATAATTTTTGGATTGAAGTATAAGTTTAAAATGGAATGA
38841989 A
1 A
38841990 GTTAACATTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.45, C:0.02, G:0.17, T:0.36
Consensus pattern (47 bp):
AAATCATAATAATTTTTGGATTGAAGTATAAGTTTAAAATGGAATGA
Found at i:38849759 original size:23 final size:22
Alignment explanation
Indices: 38849711--38849763 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
38849701 CATAGTTATT
* * *
38849711 AATAATTATTAAGAAATTATAT
1 AATAAATATTAAGAAATAATAA
*
38849733 AATAAATATTAATTAAATAATAA
1 AATAAATATTAA-GAAATAATAA
38849756 AATAAATA
1 AATAAATA
38849764 ATTACAAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AATAAATATTAAGAAATAATAA
Found at i:38852271 original size:31 final size:31
Alignment explanation
Indices: 38852233--38852301 Score: 138
Period size: 31 Copynumber: 2.2 Consensus size: 31
38852223 AGGTCAAATT
38852233 GAGTTTTGATCCTTCTATTAGGCTCATATTC
1 GAGTTTTGATCCTTCTATTAGGCTCATATTC
38852264 GAGTTTTGATCCTTCTATTAGGCTCATATTC
1 GAGTTTTGATCCTTCTATTAGGCTCATATTC
38852295 GAGTTTT
1 GAGTTTT
38852302 AATCTTTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.46
Consensus pattern (31 bp):
GAGTTTTGATCCTTCTATTAGGCTCATATTC
Found at i:38855632 original size:37 final size:37
Alignment explanation
Indices: 38855581--38855689 Score: 132
Period size: 37 Copynumber: 2.9 Consensus size: 37
38855571 AATAAAATGA
* *
38855581 CAAATGCTCTTAAGAGCTAGTCCAACCGAAATCACGC
1 CAAATGCTCATAAGAGCTAGTCCAACCGAAAACACGC
* * *
38855618 CAAAGGCTCATAAGAGCTAATCC-ACCCAATAACACGC
1 CAAATGCTCATAAGAGCTAGTCCAACCGAA-AACACGC
*
38855655 CAATTGCTCCA-AAGAGCTAGTCCAACCGAAAACAC
1 CAAATGCT-CATAAGAGCTAGTCCAACCGAAAACAC
38855690 ATTAAAACAA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
36 5 0.08
37 48 0.80
38 7 0.12
ACGTcount: A:0.39, C:0.31, G:0.15, T:0.16
Consensus pattern (37 bp):
CAAATGCTCATAAGAGCTAGTCCAACCGAAAACACGC
Found at i:38855641 original size:74 final size:74
Alignment explanation
Indices: 38855543--38855685 Score: 205
Period size: 74 Copynumber: 1.9 Consensus size: 74
38855533 CAAAAATACA
* * * * **
38855543 CCAAATGCTCGTAAGAGCTCATCCACCCAATAAAATGACAAATGCTCTTAAGAGCTAGTCCAACC
1 CCAAAGGCTCATAAGAGCTAATCCACCCAATAAAACGACAAATGCTCCAAAGAGCTAGTCCAACC
38855608 GAAATCACG
66 GAAATCACG
* * *
38855617 CCAAAGGCTCATAAGAGCTAATCCACCCAATAACACGCCAATTGCTCCAAAGAGCTAGTCCAACC
1 CCAAAGGCTCATAAGAGCTAATCCACCCAATAAAACGACAAATGCTCCAAAGAGCTAGTCCAACC
38855682 GAAA
66 GAAA
38855686 ACACATTAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.38, C:0.30, G:0.15, T:0.17
Consensus pattern (74 bp):
CCAAAGGCTCATAAGAGCTAATCCACCCAATAAAACGACAAATGCTCCAAAGAGCTAGTCCAACC
GAAATCACG
Found at i:38857543 original size:136 final size:138
Alignment explanation
Indices: 38857237--38857554 Score: 379
Period size: 136 Copynumber: 2.3 Consensus size: 138
38857227 GATATTGAAT
* * * * *
38857237 GTGAGCCCAACTCTAGTTGGGTAAACCAACGATGTTTGCCCCCAGCGCTAGTCGGTTATACCGAT
1 GTGAGCCCAACTCTAGTTGGATAAACCAACGATGTTTGCACCCAACGCTAGTCAGTTATACCGAC
*
38857302 GATTGTGTGCCCAGCACTAGTTAGACAAACTGACAAAAGTTGCGCCTAGCGCTAGTCGAATATAT
66 GATTGTGTGCCCAGCACTAGTT-----AAC-GACAAAAGTTGCGCCCAGCGCTAGTCGAATATAT
38857367 CGAAAAAATCCATA
125 CGAAAAAATCCATA
* * * * * * * *
38857381 GTGAGCCCAACTCTAGCTGGTTAAACCAATGATATTTGCACCCAACGCTATTTAGTTATACTGGC
1 GTGAGCCCAACTCTAGTTGGATAAACCAACGATGTTTGCACCCAACGCTAGTCAGTTATACCGAC
* * * * * *
38857446 GATTGTGTGCCTAGCACTAGTT-A-GACAAAATTTGCTCCCAGTGCTAGTCGAATATATTGACAA
66 GATTGTGTGCCCAGCACTAGTTAACGACAAAAGTTGCGCCCAGCGCTAGTCGAATATATCGAAAA
38857509 AATCCATA
131 AATCCATA
*
38857517 GTGAGCCCAGCTCTAGTTGGATAAACCAACGATGTTTG
1 GTGAGCCCAACTCTAGTTGGATAAACCAACGATGTTTG
38857555 TTTAATTATT
Statistics
Matches: 150, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
136 75 0.50
138 1 0.01
144 74 0.49
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (138 bp):
GTGAGCCCAACTCTAGTTGGATAAACCAACGATGTTTGCACCCAACGCTAGTCAGTTATACCGAC
GATTGTGTGCCCAGCACTAGTTAACGACAAAAGTTGCGCCCAGCGCTAGTCGAATATATCGAAAA
AATCCATA
Found at i:38858600 original size:14 final size:15
Alignment explanation
Indices: 38858581--38858619 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
38858571 ATTTCCTTTA
38858581 CATATTATAATTA-T
1 CATATTATAATTATT
38858595 CATATTATAATTATT
1 CATATTATAATTATT
*
38858610 AATATTATAA
1 CATATTATAA
38858620 CATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
CATATTATAATTATT
Found at i:38859305 original size:19 final size:19
Alignment explanation
Indices: 38859264--38859306 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
38859254 AACCATTTTT
* * *
38859264 ATTTTATTTTTATTTTTAA
1 ATTTTAATTTAATTTTGAA
*
38859283 ATTTTAATTTAATTTTGAG
1 ATTTTAATTTAATTTTGAA
38859302 ATTTT
1 ATTTT
38859307 GATTAGTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (19 bp):
ATTTTAATTTAATTTTGAA
Found at i:38870917 original size:25 final size:24
Alignment explanation
Indices: 38870889--38870977 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 24
38870879 ATGGGCTACA
*
38870889 AACGAGAAGCTCCTCTGAGCTGAAT
1 AACGAGAAGCTCAT-TGAGCTGAAT
*
38870914 AACGGGAAGCTCATGTGAGCTGAAT
1 AACGAGAAGCTCAT-TGAGCTGAAT
* * *
38870939 ATCGAAAAGCTCATTAGAGCTGTAT
1 AACGAGAAGCTCATT-GAGCTGAAT
38870964 AACG-GCAAGCTCAT
1 AACGAG-AAGCTCAT
38870978 AAGAGCTATG
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
24 1 0.02
25 52 0.98
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (24 bp):
AACGAGAAGCTCATTGAGCTGAAT
Found at i:38871177 original size:22 final size:22
Alignment explanation
Indices: 38871126--38871178 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
38871116 TCATGGAAAT
38871126 TGTAC-ATTTAACAAATAATAA
1 TGTACAATTTAACAAATAATAA
*
38871147 T-T-CAATTTAACAGAT-ATGAA
1 TGTACAATTTAACAAATAAT-AA
38871167 TGTACAATTTAA
1 TGTACAATTTAA
38871179 TTACACGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 3 0.11
20 14 0.52
21 2 0.07
22 8 0.30
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (22 bp):
TGTACAATTTAACAAATAATAA
Found at i:38874037 original size:21 final size:21
Alignment explanation
Indices: 38874011--38874059 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
38874001 CAACTCTAAG
38874011 TCATGTGTTAGATAGTTCTTT
1 TCATGTGTTAGATAGTTCTTT
*
38874032 TCATGTGTTGGATAGTTCTTT
1 TCATGTGTTAGATAGTTCTTT
38874053 TCATGTG
1 TCATGTG
38874060 GCTGTAACTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.10, G:0.22, T:0.51
Consensus pattern (21 bp):
TCATGTGTTAGATAGTTCTTT
Found at i:38879227 original size:2 final size:2
Alignment explanation
Indices: 38879220--38879248 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38879210 GGTAAAAACA
38879220 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38879249 CACACACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38879732 original size:43 final size:45
Alignment explanation
Indices: 38879681--38879768 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 45
38879671 CTTGATCAGT
*
38879681 ATACGACACAT-AAGTACCTAAAAT-GACACACGAAGTGCCTGAA
1 ATACGACACATAAAGTACCTAAAATAGACACACAAAGTGCCTGAA
* *
38879724 ATACGACACATAAAGTGCCTAAAATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTACCTAAAATA-GACACACAAAGTGCCTGA
38879769 TCGACAAAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 11 0.28
44 12 0.31
46 16 0.41
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.17
Consensus pattern (45 bp):
ATACGACACATAAAGTACCTAAAATAGACACACAAAGTGCCTGAA
Found at i:38879739 original size:23 final size:23
Alignment explanation
Indices: 38879681--38879768 Score: 110
Period size: 23 Copynumber: 4.0 Consensus size: 23
38879671 CTTGATCAGT
*
38879681 ATACGACACAT-AAGTACCT-AA
1 ATACGACACATAAAGTGCCTGAA
* **
38879702 A-ATGACACACGAAGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
*
38879724 ATACGACACATAAAGTGCCTAAA
1 ATACGACACATAAAGTGCCTGAA
38879747 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
38879769 TCGACAAAGC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
20 7 0.12
21 8 0.14
22 3 0.05
23 38 0.68
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.17
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Found at i:38881096 original size:16 final size:16
Alignment explanation
Indices: 38881060--38881097 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
38881050 TCATAATATG
38881060 ATATTT-ATAATAAAT
1 ATATTTAATAATAAAT
38881075 -TAATTTAATAATAAAT
1 AT-ATTTAATAATAAAT
38881091 ATATTTA
1 ATATTTA
38881098 GTTTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 1 0.05
15 4 0.20
16 14 0.70
17 1 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATTTAATAATAAAT
Found at i:38885444 original size:22 final size:21
Alignment explanation
Indices: 38885419--38885474 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 21
38885409 ATATCAACAC
38885419 AAATATAATCAT-ATACATATCA
1 AAATATAAT-ATCAT-CATATCA
38885441 AAATATGAATATCATCATATCA
1 AAATAT-AATATCATCATATCA
38885463 ATAATTATAATA
1 A-AA-TATAATA
38885475 ATCACAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 16 0.53
23 11 0.37
24 3 0.10
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.34
Consensus pattern (21 bp):
AAATATAATATCATCATATCA
Found at i:38885685 original size:26 final size:26
Alignment explanation
Indices: 38885612--38885689 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
38885602 TCATCCAATA
* *
38885612 ACATACCAT-TTGTGGACAAGCCACC
1 ACATAACATATTGTGGACAAACCACC
* * *
38885637 ACAT-A-A-ATT-TCGATAAACGACC
1 ACATAACATATTGTGGACAAACCACC
38885659 ACATAACATATTGTGGACAAACCACC
1 ACATAACATATTGTGGACAAACCACC
38885685 ACATA
1 ACATA
38885690 TTTGCTGATA
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
22 13 0.32
23 4 0.10
24 1 0.03
25 7 0.17
26 15 0.38
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.21
Consensus pattern (26 bp):
ACATAACATATTGTGGACAAACCACC
Found at i:38885706 original size:47 final size:46
Alignment explanation
Indices: 38885612--38885711 Score: 132
Period size: 47 Copynumber: 2.1 Consensus size: 46
38885602 TCATCCAATA
* *
38885612 ACATACCATTTGTGGACAAGCCACCACATAAATTTCGATAAACGACC
1 ACATAACATTTGTGGACAAACCACCACAT-AATTTCGATAAACGACC
38885659 ACATAACATATTGTGGACAAACCACCACAT-ATTTGCTGAT-AACGACC
1 ACATAACAT-TTGTGGACAAACCACCACATAATTT-C-GATAAACGACC
38885706 ACATAA
1 ACATAA
38885712 TCGCAGATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
46 4 0.08
47 22 0.46
48 22 0.46
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.22
Consensus pattern (46 bp):
ACATAACATTTGTGGACAAACCACCACATAATTTCGATAAACGACC
Found at i:38885720 original size:21 final size:21
Alignment explanation
Indices: 38885682--38885721 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38885672 TGGACAAACC
* * *
38885682 ACCACATATTTGCTGATAACG
1 ACCACATAATCGCAGATAACG
38885703 ACCACATAATCGCAGATAA
1 ACCACATAATCGCAGATAA
38885722 GTTGCCACAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (21 bp):
ACCACATAATCGCAGATAACG
Found at i:38898851 original size:25 final size:25
Alignment explanation
Indices: 38898823--38898876 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
38898813 TTGGCTAATG
**
38898823 TGGCCATGTGTTTTGG-TTGTGGTTT
1 TGGCCATGTGACTTGGCTTGT-GTTT
*
38898848 TGGCCATTTGACTTGGCTTGTGTTT
1 TGGCCATGTGACTTGGCTTGTGTTT
38898873 TGGC
1 TGGC
38898877 ATATTTTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.06, C:0.13, G:0.33, T:0.48
Consensus pattern (25 bp):
TGGCCATGTGACTTGGCTTGTGTTT
Found at i:38905338 original size:25 final size:25
Alignment explanation
Indices: 38905261--38905344 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
38905251 ACAACTCGGG
* * *
38905261 TGAGCATACTGGTTTATAGTTCGTGA
1 TGAGCATACTGATTCACAGTTCGT-A
* * **
38905287 -GAGCATATTGA-TCTACAGCTCAAA
1 TGAGCATACTGATTC-ACAGTTCGTA
38905311 TGAGCATACTGATTCACAGTTCGTA
1 TGAGCATACTGATTCACAGTTCGTA
38905336 TGAGCATAC
1 TGAGCATAC
38905345 ATGTACATGA
Statistics
Matches: 44, Mismatches: 11, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
24 2 0.05
25 40 0.91
26 2 0.05
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (25 bp):
TGAGCATACTGATTCACAGTTCGTA
Found at i:38909011 original size:39 final size:38
Alignment explanation
Indices: 38908967--38909053 Score: 135
Period size: 35 Copynumber: 2.3 Consensus size: 38
38908957 AATTTAATTC
38908967 AATTTATTAATTTAGATAGTAAAAAAATTTATTTTATGT
1 AATTTATT-ATTTAGATAGTAAAAAAATTTATTTTATGT
38909006 AA--T-TTATTTAGATAGTAAAAAAATTTATTTTATGT
1 AATTTATTATTTAGATAGTAAAAAAATTTATTTTATGT
38909041 AATTTATTCATTT
1 AATTTATT-ATTT
38909054 TTGACATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
35 32 0.73
36 2 0.05
37 2 0.05
38 2 0.05
39 6 0.14
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (38 bp):
AATTTATTATTTAGATAGTAAAAAAATTTATTTTATGT
Found at i:38909015 original size:35 final size:35
Alignment explanation
Indices: 38908976--38909048 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
38908966 CAATTTATTA
38908976 ATTTAGATAGTAAAAAAATTTATTTTATGTAATTT
1 ATTTAGATAGTAAAAAAATTTATTTTATGTAATTT
38909011 ATTTAGATAGTAAAAAAATTTATTTTATGTAATTT
1 ATTTAGATAGTAAAAAAATTTATTTTATGTAATTT
38909046 ATT
1 ATT
38909049 CATTTTTGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.49
Consensus pattern (35 bp):
ATTTAGATAGTAAAAAAATTTATTTTATGTAATTT
Found at i:38914534 original size:62 final size:59
Alignment explanation
Indices: 38914444--38914560 Score: 135
Period size: 62 Copynumber: 1.9 Consensus size: 59
38914434 ATTAATTATG
* ** * *
38914444 TTAATATTAAATATAATTTAATTTTTATCCTGTAGATAAAAATTCTATTATTTTAATAAGAT
1 TTAATATTAAATATAATCTAATACTTAT-CT-T-GATAAAAATTATATTAATTTAATAAGAT
* * *
38914506 TTAATATTAGATTTAATCTAATACTTATCTTGATAAATATTATATTAATTTAATA
1 TTAATATTAAATATAATCTAATACTTATCTTGATAAAAATTATATTAATTTAATA
38914561 GTAAAGTGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
59 21 0.45
60 1 0.02
61 2 0.04
62 23 0.49
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (59 bp):
TTAATATTAAATATAATCTAATACTTATCTTGATAAAAATTATATTAATTTAATAAGAT
Found at i:38917576 original size:49 final size:50
Alignment explanation
Indices: 38917512--38917748 Score: 140
Period size: 50 Copynumber: 4.6 Consensus size: 50
38917502 TAATAACATT
* * * *
38917512 CCAAAGCCATGTCCCAGACATGGTCTTATATGAGATGTT-TCCT-GTACTG
1 CCAATGCCATGTCCCAAACATGGTCTTACATGAGA-GTTCTCATAGTACTG
* * * * *
38917561 CCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATTAGTG
1 CCAATGCCATGTCCCAAACATGGTCTTACATGAGAGTTCTCATAGTACTG
* * * * ** * *
38917611 CCCATGCCATGTCCCATACATGGTCTTACAGGGGACCTCTCAT-CT-CGGTA
1 CCAATGCCATGTCCCAAACATGGTCTTACATGAGAGTTCTCATAGTAC--TG
* * * * * * *
38917661 CCAACGCCATGTCCCAGACATGGTCTTATATGAGACCTCTCATAACCTCAATAATG
1 CCAATGCCATGTCCCAAACATGGTCTTACATGAGA-GT-TC-T--CAT-AGTACTG
*
38917717 CCAATGCCATGTCCCAGACATGGTCTTACATG
1 CCAATGCCATGTCCCAAACATGGTCTTACATG
38917749 GGGTCCCATC
Statistics
Matches: 144, Mismatches: 32, Indels: 17
0.75 0.17 0.09
Matches are distributed among these distances:
48 3 0.02
49 33 0.23
50 70 0.49
51 1 0.01
52 2 0.01
53 1 0.01
55 2 0.01
56 31 0.22
57 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (50 bp):
CCAATGCCATGTCCCAAACATGGTCTTACATGAGAGTTCTCATAGTACTG
Found at i:38917652 original size:50 final size:50
Alignment explanation
Indices: 38917559--38917751 Score: 170
Period size: 50 Copynumber: 3.7 Consensus size: 50
38917549 TTTCCTGTAC
* * * * **
38917559 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATTAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATTAG
* * * **
38917609 TGCCCATGCCATGTCCCATACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATTAG
* * * * * *
38917659 TACCAACGCCATGTCCCAGACATGGTCTTATATGAGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCAT-A--T---TAG
38917715 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA-GGGG
38917752 TCCCATCCCC
Statistics
Matches: 110, Mismatches: 26, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
50 78 0.71
53 1 0.01
56 29 0.26
57 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATTAG
Found at i:38917702 original size:100 final size:104
Alignment explanation
Indices: 38917561--38917751 Score: 228
Period size: 100 Copynumber: 1.8 Consensus size: 104
38917551 TCCTGTACTG
* * * ** * *
38917561 CCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCAT-A-T-TAGTGCCCATGCCATGT
1 CCAACGCCATATCCCAAACATGGTCTTACATGAGACCTCTCATAACTATAATGCCAATGCCATGT
*
38917623 CCCATACATGGTCTTACA-GGGGACCTCTCATCTCGGTA
66 CCCAGACATGGTCTTACATGGGGACCTCTCATCTCGGTA
* * *
38917661 CCAACGCCATGTCCCAGACATGGTCTTATATGAGACCTCTCATAACCTCAATAATGCCAATGCCA
1 CCAACGCCATATCCCAAACATGGTCTTACATGAGACCTCTCATAA-CT--ATAATGCCAATGCCA
38917726 TGTCCCAGACATGGTCTTACATGGGG
63 TGTCCCAGACATGGTCTTACATGGGG
38917752 TCCCATCCCC
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
100 35 0.48
101 1 0.01
103 1 0.01
106 32 0.44
107 4 0.05
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.27
Consensus pattern (104 bp):
CCAACGCCATATCCCAAACATGGTCTTACATGAGACCTCTCATAACTATAATGCCAATGCCATGT
CCCAGACATGGTCTTACATGGGGACCTCTCATCTCGGTA
Found at i:38921873 original size:75 final size:76
Alignment explanation
Indices: 38921764--38921951 Score: 211
Period size: 75 Copynumber: 2.5 Consensus size: 76
38921754 TGAAATACCA
* * * ** *
38921764 AATATACTGAATGTTGCTCAATCGAGCAAAATCTA-TTGAACACACTGTGTGATGCTCAATGGAG
1 AATATACCGAATGTTGCTCAATCAAGAAAAATCTACTT-AACACACTGAATGATGCTCAATCGAG
*
38921828 CAA-AACCTACTT
65 -AATAACCTACTG
* * * * *
38921840 AATATACCAAATGTTTCTC-ATCAAGAAAAATCTACTTAATATACTGAATGTTGCTCAATCGAGA
1 AATATACCGAATGTTGCTCAATCAAGAAAAATCTACTTAACACACTGAATGATGCTCAATCGAGA
38921904 ATAACCTACTG
66 ATAACCTACTG
* *
38921915 AATATACCGAATATTGCTCAATCAAGTAAAATCTACT
1 AATATACCGAATGTTGCTCAATCAAGAAAAATCTACT
38921952 AAAATATACT
Statistics
Matches: 93, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
74 2 0.02
75 57 0.61
76 34 0.37
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (76 bp):
AATATACCGAATGTTGCTCAATCAAGAAAAATCTACTTAACACACTGAATGATGCTCAATCGAGA
ATAACCTACTG
Found at i:38921920 original size:38 final size:38
Alignment explanation
Indices: 38921764--38921968 Score: 189
Period size: 38 Copynumber: 5.4 Consensus size: 38
38921754 TGAAATACCA
*
38921764 AATATACTGAATGTTGCTCAATCGAGCAAAATCTATTG
1 AATATACTGAATGTTGCTCAATCGAGCAAAATCTACTG
* * ** * * * *
38921802 AACACACTGTGTGATGCTCAATGGAGCAAAACCTACTT
1 AATATACTGAATGTTGCTCAATCGAGCAAAATCTACTG
** * * * *
38921840 AATATACCAAATGTTTCTC-ATCAAGAAAAATCTACTT
1 AATATACTGAATGTTGCTCAATCGAGCAAAATCTACTG
*
38921877 AATATACTGAATGTTGCTCAATCGAG-AATAACCTACTG
1 AATATACTGAATGTTGCTCAATCGAGCAA-AATCTACTG
* * * * *
38921915 AATATACCGAATATTGCTCAATCAAGTAAAATCTACTAA
1 AATATACTGAATGTTGCTCAATCGAGCAAAATCTACT-G
38921954 AATATACTGAATGTT
1 AATATACTGAATGTT
38921969 CTTCAACCGA
Statistics
Matches: 129, Mismatches: 34, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
37 32 0.25
38 82 0.64
39 15 0.12
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.30
Consensus pattern (38 bp):
AATATACTGAATGTTGCTCAATCGAGCAAAATCTACTG
Found at i:38921980 original size:77 final size:75
Alignment explanation
Indices: 38921831--38921981 Score: 205
Period size: 77 Copynumber: 2.0 Consensus size: 75
38921821 AATGGAGCAA
* * * *
38921831 AACCTACTTAATATACCAAATGTTTCTCATCAAGAAAAATCTACTTAATATACTGAATGTTGCTC
1 AACCTACTGAATATACCAAATATTGCTCATCAAGAAAAATCTACTAAATATACTGAATGTTGCTC
*
38921896 AATCGAGAAT
66 AACCGAGAAT
* *
38921906 AACCTACTGAATATACCGAATATTGCTCAATCAAGTAAAATCTACTAAAATATACTGAATGTT-C
1 AACCTACTGAATATACCAAATATTGCTC-ATCAAGAAAAATCTACT-AAATATACTGAATGTTGC
38921970 TTCAACCGAGAA
64 -TCAACCGAGAA
38921982 AAAAATCACT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
75 24 0.36
76 17 0.26
77 25 0.38
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (75 bp):
AACCTACTGAATATACCAAATATTGCTCATCAAGAAAAATCTACTAAATATACTGAATGTTGCTC
AACCGAGAAT
Found at i:38925748 original size:29 final size:29
Alignment explanation
Indices: 38925714--38925772 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
38925704 CCAAATATAT
* * *
38925714 TGAATGTTGCTCAATGGAGTAAAATCTAC
1 TGAATGTCGCTCAATCGAGCAAAATCTAC
38925743 TGAATGTCGCTCAATCGAGCAAAATCTAC
1 TGAATGTCGCTCAATCGAGCAAAATCTAC
38925772 T
1 T
38925773 AAACACACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (29 bp):
TGAATGTCGCTCAATCGAGCAAAATCTAC
Found at i:38925796 original size:38 final size:38
Alignment explanation
Indices: 38925735--38925994 Score: 204
Period size: 38 Copynumber: 6.8 Consensus size: 38
38925725 CAATGGAGTA
* * * *
38925735 AAATCTACTGAATGTCGCTCAATCGAGCAAAATCTACT
1 AAATATACTAAATGTTGCTCAATCGAGCAAAACCTACT
* *
38925773 AAACACACTAAATGTTGCTCAATCGAGCAAAACCTA-T
1 AAATATACTAAATGTTGCTCAATCGAGCAAAACCTACT
* * *
38925810 AGAATATA-TCGAATGTTGCT-AATCGAACAAAATCTACT
1 A-AATATACT-AAATGTTGCTCAATCGAGCAAAACCTACT
* ** * * * *
38925848 AAATATACTGAATGCCGTTGAATCGAGAAAAATCTACT
1 AAATATACTAAATGTTGCTCAATCGAGCAAAACCTACT
* ** * *
38925886 GAGCACACTAAATGTTGCTCAATCGAGCGAAACCTA-T
1 AAATATACTAAATGTTGCTCAATCGAGCAAAACCTACT
** * *
38925923 CAAATATACCGAATGTTTCTCAATCGAGTAAAACCTACT
1 -AAATATACTAAATGTTGCTCAATCGAGCAAAACCTACT
* * *
38925962 AAAATATATTAAATGTTGTTCAATCAAGCAAAA
1 -AAATATACTAAATGTTGCTCAATCGAGCAAAA
38925995 ATTCACTGAC
Statistics
Matches: 170, Mismatches: 45, Indels: 13
0.75 0.20 0.06
Matches are distributed among these distances:
37 31 0.18
38 113 0.66
39 26 0.15
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (38 bp):
AAATATACTAAATGTTGCTCAATCGAGCAAAACCTACT
Found at i:38925938 original size:113 final size:115
Alignment explanation
Indices: 38925733--38925969 Score: 327
Period size: 113 Copynumber: 2.1 Consensus size: 115
38925723 CTCAATGGAG
* * *
38925733 TAAAATCTACTGAATGTCGCTCAATCGAGCAAAATCTACTAAACACACTAAATGTTGCTCAATCG
1 TAAAATATACTGAATGCCGCTCAATCGAGAAAAATCTACTAAACACACTAAATGTTGCTCAATCG
* *
38925798 AGCAAAACCTATAGAATATATCGAATGTTGCT-AATCGAACAAAATCTAC
66 AGCAAAACCTATAGAATATACCGAATGTTGCTCAATCGAACAAAACCTAC
* * * *
38925847 T-AAATATACTGAATGCCGTTGAATCGAGAAAAATCTACTGAGCACACTAAATGTTGCTCAATCG
1 TAAAATATACTGAATGCCGCTCAATCGAGAAAAATCTACTAAACACACTAAATGTTGCTCAATCG
* * **
38925911 AGCGAAACCTATCA-AATATACCGAATGTTTCTCAATCGAGTAAAACCTAC
66 AGCAAAACCTAT-AGAATATACCGAATGTTGCTCAATCGAACAAAACCTAC
38925961 TAAAATATA
1 TAAAATATA
38925970 TTAAATGTTG
Statistics
Matches: 107, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
113 83 0.78
114 17 0.16
115 7 0.07
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (115 bp):
TAAAATATACTGAATGCCGCTCAATCGAGAAAAATCTACTAAACACACTAAATGTTGCTCAATCG
AGCAAAACCTATAGAATATACCGAATGTTGCTCAATCGAACAAAACCTAC
Found at i:38926682 original size:44 final size:44
Alignment explanation
Indices: 38926609--38926709 Score: 184
Period size: 44 Copynumber: 2.3 Consensus size: 44
38926599 CCTTGACATT
* *
38926609 TTTGAGTGTATTTGAAGATGGTTTTTGTCTTATAAAATTGTGTA
1 TTTGGGTGTTTTTGAAGATGGTTTTTGTCTTATAAAATTGTGTA
38926653 TTTGGGTGTTTTTGAAGATGGTTTTTGTCTTATAAAATTGTGTA
1 TTTGGGTGTTTTTGAAGATGGTTTTTGTCTTATAAAATTGTGTA
38926697 TTTGGGTGTTTTT
1 TTTGGGTGTTTTT
38926710 AGGTACCTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.20, C:0.02, G:0.25, T:0.53
Consensus pattern (44 bp):
TTTGGGTGTTTTTGAAGATGGTTTTTGTCTTATAAAATTGTGTA
Found at i:38926700 original size:21 final size:21
Alignment explanation
Indices: 38926632--38926700 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
38926622 GAAGATGGTT
38926632 TTTGTCTTATAAAATTGTGTA
1 TTTGTCTTATAAAATTGTGTA
* * * *
38926653 TTTGGGTGTTTTTGAAGA-TG-GTT
1 TTT--GT-CTTAT-AAAATTGTGTA
38926676 TTTGTCTTATAAAATTGTGTA
1 TTTGTCTTATAAAATTGTGTA
38926697 TTTG
1 TTTG
38926701 GGTGTTTTTA
Statistics
Matches: 34, Mismatches: 8, Indels: 12
0.63 0.15 0.22
Matches are distributed among these distances:
19 3 0.09
20 5 0.15
21 11 0.32
23 7 0.21
24 5 0.15
25 3 0.09
ACGTcount: A:0.22, C:0.03, G:0.22, T:0.54
Consensus pattern (21 bp):
TTTGTCTTATAAAATTGTGTA
Found at i:38941511 original size:2 final size:2
Alignment explanation
Indices: 38941506--38941530 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38941496 TTTTCATACT
38941506 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 T
38941531 TTATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38941535 original size:4 final size:4
Alignment explanation
Indices: 38941528--38941553 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
38941518 TATATATATA
38941528 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
38941554 AAATTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:38941713 original size:2 final size:2
Alignment explanation
Indices: 38941662--38941705 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
38941652 AATATTCTTT
*
38941662 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38941704 TA
1 TA
38941706 CGTATATACC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38942057 original size:25 final size:25
Alignment explanation
Indices: 38942029--38942078 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
38942019 TAGGTCATTG
*
38942029 TTTA-TTATTATTTATATTAATTTCT
1 TTTATTTACTATTTATATT-ATTTCT
38942054 TTTATTTACTATTTATATTATTTCT
1 TTTATTTACTATTTATATTATTTCT
38942079 ATACAATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTATTTACTATTTATATTATTTCT
Found at i:38952150 original size:15 final size:15
Alignment explanation
Indices: 38952130--38952160 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
38952120 TGAAAAAGAA
38952130 TCAAAAGCAACTAAG
1 TCAAAAGCAACTAAG
38952145 TCAAAAGCAACTAAG
1 TCAAAAGCAACTAAG
38952160 T
1 T
38952161 AAGCTCAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.13, T:0.16
Consensus pattern (15 bp):
TCAAAAGCAACTAAG
Found at i:38957266 original size:11 final size:11
Alignment explanation
Indices: 38957250--38957275 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
38957240 ACTTCTTTCC
38957250 CCTTATAAAGA
1 CCTTATAAAGA
38957261 CCTTATAAAGA
1 CCTTATAAAGA
38957272 CCTT
1 CCTT
38957276 GTTGATCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (11 bp):
CCTTATAAAGA
Found at i:38961527 original size:24 final size:23
Alignment explanation
Indices: 38961477--38961529 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
38961467 TTATTATAAT
* *
38961477 TTTTATTTTTTTTAAAATATGAT
1 TTTTAATTTTTTTAAAATATGAA
* *
38961500 TTTTAATTTTTTTAAATTTATTAA
1 TTTTAATTTTTTTAAA-ATATGAA
38961524 TTTTAA
1 TTTTAA
38961530 AATTTTATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTTAATTTTTTTAAAATATGAA
Found at i:38962497 original size:43 final size:43
Alignment explanation
Indices: 38962432--38962737 Score: 364
Period size: 43 Copynumber: 7.1 Consensus size: 43
38962422 CGCTATTATC
*
38962432 AACGCCGCTATAGATCAGGACCTTTAGCGGCGC-TTTCTCCACA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTC-CCACA
38962475 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACA
* * *
38962518 AACGCCGCTATAGATCAAGACCTTTAGAGGCGCTTTTTCCATA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACA
* * * * * * *
38962561 GACGCAGCTACAGCTCGAGACCTTTAGCGGCGCTTTTTCCATA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACA
* ** * *
38962604 AACGCCGCTATAGCTTGAGACCTTTAGTGACGCTTTTCCCACA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACA
* * *
38962647 AACGCCGCTTTAGCTCGAGACCTTTAGCGGCGCTTTTCCCACA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACA
* * * * * *
38962690 AACGCCGCTATAGAACAA-ACCTTTACCGACACTTTTCGCAAA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACA
38962732 AACGCC
1 AACGCC
38962738 ACTAAAAACT
Statistics
Matches: 231, Mismatches: 31, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
42 25 0.11
43 202 0.87
44 4 0.02
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (43 bp):
AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACA
Found at i:38965211 original size:48 final size:49
Alignment explanation
Indices: 38965153--38965252 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
38965143 GAAAGTGACT
*
38965153 TCAAATTTGATCCTATA-TTCATCATTTGCTATCTCCAAGGCATTGAGG
1 TCAAAATTGATCCTATATTTCATCATTTGCTATCTCCAAGGCATTGAGG
38965201 TCAAAATTGATCCTATATTTCATCATTTGCTATCTCCAAGGCATTGAGG
1 TCAAAATTGATCCTATATTTCATCATTTGCTATCTCCAAGGCATTGAGG
38965250 TCA
1 TCA
38965253 TTTCAATCAT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 16 0.32
49 34 0.68
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (49 bp):
TCAAAATTGATCCTATATTTCATCATTTGCTATCTCCAAGGCATTGAGG
Found at i:38967615 original size:7 final size:7
Alignment explanation
Indices: 38967599--38967660 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
38967589 ACTAATTAAT
*
38967599 CTAAAAC
1 CTAAACC
38967606 CTAAACC
1 CTAAACC
38967613 CTAAACC
1 CTAAACC
*
38967620 CTTAACC
1 CTAAACC
*
38967627 CTTAACC
1 CTAAACC
*
38967634 CTTAACCC
1 C-TAAACC
**
38967642 CTATCCC
1 CTAAACC
*
38967649 CTAACCC
1 CTAAACC
38967656 CTAAA
1 CTAAA
38967661 TTATAAAACA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
7 42 0.89
8 5 0.11
ACGTcount: A:0.35, C:0.44, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:38967633 original size:14 final size:14
Alignment explanation
Indices: 38967609--38967655 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
38967599 CTAAAACCTA
*
38967609 AACCCTAAACCCTT
1 AACCCTTAACCCTT
38967623 AACCCTTAACCCTT
1 AACCCTTAACCCTT
* * *
38967637 AACCCCTATCCCCT
1 AACCCTTAACCCTT
38967651 AACCC
1 AACCC
38967656 CTAAATTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.30, C:0.49, G:0.00, T:0.21
Consensus pattern (14 bp):
AACCCTTAACCCTT
Found at i:38967634 original size:21 final size:21
Alignment explanation
Indices: 38967609--38967660 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
38967599 CTAAAACCTA
* *
38967609 AACCCTAAACCCTTAACCCTT
1 AACCCTAAACCCCTAACCCCT
* *
38967630 AACCCTTAACCCCTATCCCCT
1 AACCCTAAACCCCTAACCCCT
38967651 AACCCCTAAA
1 AA-CCCTAAA
38967661 TTATAAAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.21
Consensus pattern (21 bp):
AACCCTAAACCCCTAACCCCT
Found at i:38968978 original size:41 final size:41
Alignment explanation
Indices: 38968725--38968974 Score: 238
Period size: 41 Copynumber: 6.1 Consensus size: 41
38968715 TAAATTATTT
* * * *
38968725 TAAATCCCTGAGCATTAGTGGCGCTTT-TTAGAAAACGCCGT
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTCA-AAAACGCCGC
* *
38968766 TAAA--ACTAGAGCATTAGCGGCGCTTTCTCAAAAAACGCCGT
1 TAAAGCCCT-GAGCATTAGCGGCGCTTTCTC-AAAAACGCCGC
* * * *
38968807 TAAAGCCTTGAGCATTAGTGGCGCCTCCTCAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
** * * * *
38968848 TAAAGCCCCAAGCATTAGCGACGCCTCCTCAAAAATGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* *
38968889 TATAGCCCCGAGCATTAGCGGCGCTTT-TCCAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCT-CAAAAACGCCGC
* * * *
38968930 TAAATCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
38968971 TAAA
1 TAAA
38968975 TCCCCGAAAC
Statistics
Matches: 176, Mismatches: 26, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
39 2 0.01
40 18 0.10
41 135 0.77
42 20 0.11
43 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (41 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
Found at i:38970816 original size:27 final size:27
Alignment explanation
Indices: 38970786--38970876 Score: 121
Period size: 27 Copynumber: 3.3 Consensus size: 27
38970776 GCCTTAATTC
* *
38970786 AATACAGTAACAACGTGG-GTCTAGCCT
1 AATACAGTAACAATGTGGCCT-TAGCCT
38970813 AATACAGTAACAATGTGGCCTTAGCCT
1 AATACAGTAACAATGTGGCCTTAGCCT
* *
38970840 AATATAGTAACAATGTAGGCCTTAGCCC
1 AATACAGTAACAATGT-GGCCTTAGCCT
38970868 AATACAGTA
1 AATACAGTA
38970877 TCGGTACAGT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
27 38 0.67
28 19 0.33
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (27 bp):
AATACAGTAACAATGTGGCCTTAGCCT
Found at i:38971267 original size:53 final size:53
Alignment explanation
Indices: 38971205--38971364 Score: 198
Period size: 53 Copynumber: 3.0 Consensus size: 53
38971195 CATTTCATCT
*
38971205 CCTA-GGGGTATTTCGGTCATTTTACCCTATTGGGGTATTTCGATCATTTTAC
1 CCTATGGGGTATTTCGGTCATTTTACCCTATTGGGGTATTTCGGTCATTTTAC
* * *
38971257 CCTATGGGGTATTTAGGTCATTCTACCCTA-TGAGGGTATTTCGGTCATTCTAC
1 CCTATGGGGTATTTCGGTCATTTTACCCTATTG-GGGTATTTCGGTCATTTTAC
* * * ** *
38971310 CTTATGGGGGTATTTCGATCATTTTATCCTATAAGGGTATTTTGGTCATTTTAC
1 CCTAT-GGGGTATTTCGGTCATTTTACCCTATTGGGGTATTTCGGTCATTTTAC
38971364 C
1 C
38971365 TATTTTAGGG
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
52 6 0.07
53 45 0.49
54 40 0.44
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (53 bp):
CCTATGGGGTATTTCGGTCATTTTACCCTATTGGGGTATTTCGGTCATTTTAC
Found at i:38971326 original size:80 final size:81
Alignment explanation
Indices: 38971210--38971364 Score: 240
Period size: 80 Copynumber: 1.9 Consensus size: 81
38971200 CATCTCCTAG
* * *
38971210 GGGTATTTCGGTCATTTTACCCTATTGGGGTATTTCGATCATTTTACCCTAT-GGGGTATTTAGG
1 GGGTATTTCGGTCATTCTACCCTATGGGGGTATTTCGATCATTTTACCCTATAAGGGTATTTAGG
38971274 TCATTCTACCCTATGA
66 TCATTCTACCCTATGA
* * *
38971290 GGGTATTTCGGTCATTCTACCTTATGGGGGTATTTCGATCATTTTATCCTATAAGGGTATTTTGG
1 GGGTATTTCGGTCATTCTACCCTATGGGGGTATTTCGATCATTTTACCCTATAAGGGTATTTAGG
*
38971355 TCATTTTACC
66 TCATTCTACC
38971365 TATTTTAGGG
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
80 48 0.72
81 19 0.28
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (81 bp):
GGGTATTTCGGTCATTCTACCCTATGGGGGTATTTCGATCATTTTACCCTATAAGGGTATTTAGG
TCATTCTACCCTATGA
Found at i:38971361 original size:27 final size:27
Alignment explanation
Indices: 38971209--38971364 Score: 197
Period size: 27 Copynumber: 5.8 Consensus size: 27
38971199 TCATCTCCTA
*
38971209 GGGGTATTTCGGTCATTTTACCCTATT
1 GGGGTATTTCGGTCATTTTACCCTATG
*
38971236 GGGGTATTTCGATCATTTTACCCTAT-
1 GGGGTATTTCGGTCATTTTACCCTATG
* *
38971262 GGGGTATTTAGGTCATTCTACCCTATG
1 GGGGTATTTCGGTCATTTTACCCTATG
* * *
38971289 AGGGTATTTCGGTCATTCTACCTTATG
1 GGGGTATTTCGGTCATTTTACCCTATG
* * *
38971316 GGGGTATTTCGATCATTTTATCCTATA
1 GGGGTATTTCGGTCATTTTACCCTATG
* *
38971343 AGGGTATTTTGGTCATTTTACC
1 GGGGTATTTCGGTCATTTTACC
38971365 TATTTTAGGG
Statistics
Matches: 111, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
26 23 0.21
27 88 0.79
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (27 bp):
GGGGTATTTCGGTCATTTTACCCTATG
Found at i:38979470 original size:50 final size:50
Alignment explanation
Indices: 38979402--38979746 Score: 546
Period size: 50 Copynumber: 6.9 Consensus size: 50
38979392 TTTCCTATAC
* * ** *
38979402 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* ** *
38979452 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
38979502 AGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
38979552 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
38979602 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
38979652 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
38979702 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
38979747 AATTTCAATA
Statistics
Matches: 272, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 272 1.00
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:38979624 original size:150 final size:150
Alignment explanation
Indices: 38979354--38979747 Score: 549
Period size: 150 Copynumber: 2.6 Consensus size: 150
38979344 AATATAACAC
* ** * * ** *
38979354 GCCAAAGCTATGTCCCAGACATAATCTTACATGGGATGTTTC--CTATACTGCCAATGCCATATC
1 GCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGA-TGCCAATGCCATGTC
* ** * *
38979417 CCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTA
65 CCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGACATGGTCTTA
* *
38979482 CGGGGGACCTCTTATCTCGGA
130 CAGGGGACCTCTCATCTCGGA
* *
38979503 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGATGCCAACGCCATGTCC
1 GCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGATGCCAATGCCATGTCC
*
38979568 CAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTAC
66 CAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGACATGGTCTTAC
* *
38979633 ATGGGACCTCTCATCTCGGT
131 AGGGGACCTCTCATCTCGGA
* * * *
38979653 GCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCC
1 GCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGATGCCAATGCCATGTCC
38979718 CAGACATGGTCTTACATGGGACCTCTCATA
66 CAGACATGGTCTTACATGGGACCTCTCATA
38979748 ATTTCAATAA
Statistics
Matches: 217, Mismatches: 26, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
149 36 0.17
150 178 0.82
151 3 0.01
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.26
Consensus pattern (150 bp):
GCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGATGCCAATGCCATGTCC
CAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGACATGGTCTTAC
AGGGGACCTCTCATCTCGGA
Found at i:38983618 original size:12 final size:12
Alignment explanation
Indices: 38983601--38983628 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
38983591 AGACTATTGC
38983601 AAAAAAAATTAT
1 AAAAAAAATTAT
38983613 AAAAAAAATTAT
1 AAAAAAAATTAT
38983625 AAAA
1 AAAA
38983629 TGTGAGTGCA
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:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAAAAATTAT
Found at i:38983957 original size:21 final size:21
Alignment explanation
Indices: 38983917--38983957 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
38983907 GATTTATTGA
*
38983917 GGGCTTTGAATAGGGTTGTTG
1 GGGCTTTGAATAGGGGTGTTG
38983938 GGGCTTT-AATAGGAGGTGTT
1 GGGCTTTGAATAGG-GGTGTT
38983958 AGTCGTGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.17, C:0.05, G:0.41, T:0.37
Consensus pattern (21 bp):
GGGCTTTGAATAGGGGTGTTG
Found at i:38993693 original size:63 final size:63
Alignment explanation
Indices: 38993615--38993737 Score: 221
Period size: 63 Copynumber: 2.0 Consensus size: 63
38993605 TGAACATGGG
38993615 TTTAGTAATTCTAAGTTAA-GAAGTGTAATTGAGCTAACATAATTATGTCATCTTGATTAACTA
1 TTTAGTAATTCTAAGTTAAGGAA-TGTAATTGAGCTAACATAATTATGTCATCTTGATTAACTA
*
38993678 TTTAGTAATTCTAAGTTAAGGAATGTAATTGATCTAACATAATTATGTCATCTTGATTAA
1 TTTAGTAATTCTAAGTTAAGGAATGTAATTGAGCTAACATAATTATGTCATCTTGATTAA
38993738 AACTATCTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
63 55 0.95
64 3 0.05
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.41
Consensus pattern (63 bp):
TTTAGTAATTCTAAGTTAAGGAATGTAATTGAGCTAACATAATTATGTCATCTTGATTAACTA
Found at i:38994347 original size:35 final size:35
Alignment explanation
Indices: 38994264--38994339 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 35
38994254 TGGCTGGAAA
* * * *
38994264 AAAAAGATCTATTGGCTCTACAGAGCGACATCATG
1 AAAATGATCTACTAGCTCTACAGAGCGACACCATG
* *
38994299 AAAATGATCTACTAGCTCTACGGAGTGACACCATG
1 AAAATGATCTACTAGCTCTACAGAGCGACACCATG
*
38994334 TAAATG
1 AAAATG
38994340 TTTTACTAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (35 bp):
AAAATGATCTACTAGCTCTACAGAGCGACACCATG
Found at i:38994786 original size:23 final size:22
Alignment explanation
Indices: 38994755--38994798 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
38994745 TTTTAAAAGG
38994755 TTATATATTTATTTTTATTTGTT
1 TTATATATTTA-TTTTATTTGTT
*
38994778 TTATTTATTTATTTTATTTGT
1 TTATATATTTATTTTATTTGT
38994799 ATTTTTGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (22 bp):
TTATATATTTATTTTATTTGTT
Found at i:38994801 original size:19 final size:19
Alignment explanation
Indices: 38994760--38994802 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
38994750 AAAGGTTATA
* *
38994760 TATTTATTTTTATTTGTTT
1 TATTTATTTATATTTATTT
38994779 TATTTATTTAT-TTTATTT
1 TATTTATTTATATTTATTT
38994797 GTATTT
1 -TATTT
38994803 TTGTGGGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (19 bp):
TATTTATTTATATTTATTT
Found at i:38998398 original size:14 final size:15
Alignment explanation
Indices: 38998374--38998402 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38998364 AGGTTAGATA
38998374 TTTATTTTTATTTGT
1 TTTATTTTTATTTGT
38998389 TTTA-TTTTATTTGT
1 TTTATTTTTATTTGT
38998403 ATTTTTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (15 bp):
TTTATTTTTATTTGT
Found at i:38998734 original size:21 final size:20
Alignment explanation
Indices: 38998692--38998739 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
38998682 GTTCATTCAA
*
38998692 TTCTGTGAAATTCGGCTTGT
1 TTCTGTGAAATTCGACTTGT
*
38998712 TTCTGTGAAATTTGACGTTGT
1 TTCTGTGAAATTCGAC-TTGT
*
38998733 TTGTGTG
1 TTCTGTG
38998740 CTTTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.15, C:0.10, G:0.27, T:0.48
Consensus pattern (20 bp):
TTCTGTGAAATTCGACTTGT
Found at i:38999094 original size:91 final size:91
Alignment explanation
Indices: 38998947--38999117 Score: 270
Period size: 91 Copynumber: 1.9 Consensus size: 91
38998937 GACCATGTAC
* ** **
38998947 AGTTGAGAATTAGGGTTTTCGGGCAAATTATGGTGCCACACGGTCGTGTGGCTGACTTGGGGATA
1 AGTTGAGAATTAGGGTTTTCAGGCAAATTATGGTGCCACACGACCAAGTGGCTGACTTGGGGATA
38999012 TTGTTGATTTTCACACTGCCGTGTCT
66 TTGTTGATTTTCACACTGCCGTGTCT
* * *
38999038 AGTTGGGAATTAGGGTTTTCAGGCAAATTATGGTGCCACACGACCAAGTGGTTGACTTGGGGATT
1 AGTTGAGAATTAGGGTTTTCAGGCAAATTATGGTGCCACACGACCAAGTGGCTGACTTGGGGATA
38999103 TTGTTGATTTTCACA
66 TTGTTGATTTTCACA
38999118 AGGGCGTGTG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 72 1.00
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.34
Consensus pattern (91 bp):
AGTTGAGAATTAGGGTTTTCAGGCAAATTATGGTGCCACACGACCAAGTGGCTGACTTGGGGATA
TTGTTGATTTTCACACTGCCGTGTCT
Found at i:39002405 original size:24 final size:24
Alignment explanation
Indices: 39002345--39002405 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
39002335 GCCATATAGT
** *
39002345 AACATACATAATATTCCACAAGGC
1 AACATACATAATACACCACAAGGA
* *
39002369 AACATACAAAATACACCACAATGA
1 AACATACATAATACACCACAAGGA
*
39002393 AACATAGATAATA
1 AACATACATAATA
39002406 ACTTGTTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.54, C:0.21, G:0.07, T:0.18
Consensus pattern (24 bp):
AACATACATAATACACCACAAGGA
Found at i:39006447 original size:39 final size:39
Alignment explanation
Indices: 39006393--39006468 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
39006383 AGTAGACTTC
*
39006393 GATTTTCTTAAGGATATCTCTACTGGTTCTCTGAGCTTT
1 GATTTTCTTAAGGATATCTCTACTGATTCTCTGAGCTTT
*
39006432 GATTTTCTTAAGGATATCTCTATTGATTCTCTGAGCT
1 GATTTTCTTAAGGATATCTCTACTGATTCTCTGAGCT
39006469 CTAATGTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (39 bp):
GATTTTCTTAAGGATATCTCTACTGATTCTCTGAGCTTT
Found at i:39007738 original size:21 final size:22
Alignment explanation
Indices: 39007709--39007749 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
39007699 CATGAAATTC
39007709 AACACATTAC-ATGCCAACTTA
1 AACACATTACAATGCCAACTTA
* *
39007730 AACATATTACAATTCCAACT
1 AACACATTACAATGCCAACT
39007750 AGAACTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.44, C:0.27, G:0.02, T:0.27
Consensus pattern (22 bp):
AACACATTACAATGCCAACTTA
Found at i:39009895 original size:25 final size:25
Alignment explanation
Indices: 39009867--39009917 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
39009857 CTAGCACGAA
*
39009867 ATGATGATGAAAATGCTTAGATTTC
1 ATGATGAAGAAAATGCTTAGATTTC
*
39009892 ATGATGAAGAAAATGTTTAGATTTC
1 ATGATGAAGAAAATGCTTAGATTTC
39009917 A
1 A
39009918 ATTTATGAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (25 bp):
ATGATGAAGAAAATGCTTAGATTTC
Found at i:39011888 original size:12 final size:12
Alignment explanation
Indices: 39011871--39011897 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39011861 CTTGGACAAT
39011871 CCTACCGAAACC
1 CCTACCGAAACC
39011883 CCTACCGAAACC
1 CCTACCGAAACC
39011895 CCT
1 CCT
39011898 GCCAAATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.52, G:0.07, T:0.11
Consensus pattern (12 bp):
CCTACCGAAACC
Done.