Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008319.1 Hibiscus syriacus cultivar Beakdansim tig00111022_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4819703
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 21
Found at i:3828443 original size:14 final size:14
Alignment explanation
Indices: 3828424--3828460 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3828414 CATCAATTAA
3828424 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3828438 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3828452 ACAAATCAA
1 ACAAATCAA
3828461 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3830484 original size:94 final size:94
Alignment explanation
Indices: 3830319--3830623 Score: 458
Period size: 94 Copynumber: 3.3 Consensus size: 94
3830309 GAATAGTTTC
* *
3830319 AATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTC
3830384 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
* *
3830413 AATCGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAGAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTC
3830478 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
*
3830507 AATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTT
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA-AAAAGACAAATACTAACTT
* * *
3830571 TATAGTGTT----AATAAACAGTTTAGCAG
65 CACAGTGTTAAAGAATACACAGTTTAGCAG
* * * *
3830597 TATTGGCAGCAATCAAATAAATTTACT
1 AATTGGCAGCAACCGAACAAATTTACT
3830624 AAGCAATCTA
Statistics
Matches: 197, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
90 39 0.20
93 18 0.09
94 140 0.71
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (94 bp):
AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTC
ACAGTGTTAAAGAATACACAGTTTAGCAG
Found at i:3832328 original size:20 final size:20
Alignment explanation
Indices: 3832303--3832398 Score: 91
Period size: 20 Copynumber: 5.2 Consensus size: 20
3832293 TTTTGGTTGA
3832303 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
3832323 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
3832342 AAATGACTATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
3832361 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
3832376 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
3832396 AAT
1 AAT
3832399 CGCAACGCGT
Statistics
Matches: 62, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
14 8 0.13
16 4 0.06
17 2 0.03
18 1 0.02
19 14 0.23
20 33 0.53
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:3832369 original size:14 final size:14
Alignment explanation
Indices: 3832350--3832405 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
3832340 GGAAATGACT
3832350 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
3832364 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
3832383 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
3832397 ATCGCAACG
1 ATCGCAACG
3832406 CGTTGCGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:3832387 original size:33 final size:33
Alignment explanation
Indices: 3832301--3832407 Score: 133
Period size: 33 Copynumber: 3.0 Consensus size: 33
3832291 TCTTTTGGTT
3832301 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
**
3832340 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3832374 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3832407 G
1 G
3832408 TTGCGATTAT
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
33 32 0.51
34 11 0.17
36 1 0.02
37 1 0.02
38 3 0.05
40 15 0.24
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3833027 original size:20 final size:20
Alignment explanation
Indices: 3833004--3833093 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
3832994 AGTCAGATTT
3833004 GCATTGCGATTTACGTATTC
1 GCATTGCGATTTACGTATTC
* *
3833024 GCATTGCGATTTTCCTAATTC
1 GCATTGCGATTTACGT-ATTC
* *
3833045 GCATTGCGATTTACTTAATC
1 GCATTGCGATTTACGTATTC
*
3833065 GCGTTGCGATTTACGTATTC
1 GCATTGCGATTTACGTATTC
3833085 GCATTGCGA
1 GCATTGCGA
3833094 ATTATGAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
20 42 0.70
21 18 0.30
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (20 bp):
GCATTGCGATTTACGTATTC
Found at i:3833056 original size:41 final size:40
Alignment explanation
Indices: 3833004--3833093 Score: 126
Period size: 41 Copynumber: 2.2 Consensus size: 40
3832994 AGTCAGATTT
* *
3833004 GCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTC
1 GCATTGCGATTTACGTAATCGCATTGCGATTTACCT-ATTC
* * *
3833045 GCATTGCGATTTACTTAATCGCGTTGCGATTTACGTATTC
1 GCATTGCGATTTACGTAATCGCATTGCGATTTACCTATTC
3833085 GCATTGCGA
1 GCATTGCGA
3833094 ATTATGAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 13 0.30
41 31 0.70
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (40 bp):
GCATTGCGATTTACGTAATCGCATTGCGATTTACCTATTC
Found at i:3833106 original size:41 final size:42
Alignment explanation
Indices: 3833022--3833231 Score: 157
Period size: 41 Copynumber: 5.1 Consensus size: 42
3833012 ATTTACGTAT
* * * *
3833022 TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACT--TAA
1 TCGCATTGCGATTTACGTAATTCGCATTGCGAATTA-TGAAAA
*
3833063 TCGCGTTGCGATTTACGT-ATTCGCATTGCGAATTATGAAAA
1 TCGCATTGCGATTTACGTAATTCGCATTGCGAATTATGAAAA
** * * * *
3833104 TCGCAACGCGA-ATACGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCATTGCGATTTACGTAATTCGCATTGCGAATTATGAAAA
* * * * * *
3833145 TTGCATTGCGA--TA-GTCAGTATCGCATTGCGATTTTTCAAAT
1 TCGCATTGCGATTTACGT-AAT-TCGCATTGCGAATTATGAAAA
* **
3833186 TTGCATTGCGATTTAC-TAATTCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGATTTACGTAATTCGCATTGCGAATTATGAAAA
3833227 TCGCA
1 TCGCA
3833232 ACGCGAAATT
Statistics
Matches: 131, Mismatches: 30, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
39 3 0.02
40 24 0.18
41 99 0.76
42 2 0.02
43 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (42 bp):
TCGCATTGCGATTTACGTAATTCGCATTGCGAATTATGAAAA
Found at i:3833114 original size:21 final size:21
Alignment explanation
Indices: 3833090--3833145 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
3833080 TATTCGCATT
*
3833090 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
3833111 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
3833131 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
3833146 TGCATTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:3833126 original size:61 final size:61
Alignment explanation
Indices: 3833007--3833127 Score: 138
Period size: 61 Copynumber: 2.0 Consensus size: 61
3832997 CAGATTTGCA
* * * ** * *
3833007 TTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACTTAATCGCG
1 TTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAACGCGATATACTAAATCGCG
*
3833068 TTGCGATTTACGTATTCGCATTGCGAATTAT-GAAAATCGCAACGCGA-ATACGTAAATCGC
1 TTGCGATTTACGTATTCGCATTGCG-ATTATCCAAAATCGCAACGCGATATAC-TAAATCGC
3833128 AATGCGAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 3 0.06
61 43 0.86
62 4 0.08
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (61 bp):
TTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAACGCGATATACTAAATCGCG
Found at i:3833154 original size:21 final size:21
Alignment explanation
Indices: 3833083--3833155 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
3833073 ATTTACGTAT
* *
3833083 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
3833104 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
3833124 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
3833145 TTGCATTGCGA
1 TCGCAATGCGA
3833156 TAGTCAGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:3833211 original size:20 final size:21
Alignment explanation
Indices: 3833165--3833216 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
3833155 ATAGTCAGTA
*
3833165 TCGCATTGCGATTTTTCAAAT
1 TCGCATTGCGATTTTACAAAT
* *
3833186 TTGCATTGCGA-TTTACTAAT
1 TCGCATTGCGATTTTACAAAT
3833206 TCGCATTGCGA
1 TCGCATTGCGA
3833217 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:3833258 original size:21 final size:22
Alignment explanation
Indices: 3833206--3833258 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
3833196 ATTTACTAAT
3833206 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
3833227 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
3833248 TCGCATTGCGA
1 TCGCATTGCGA
3833259 TAGTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:3842902 original size:15 final size:15
Alignment explanation
Indices: 3842880--3842914 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3842870 ATTGAAATTC
3842880 AAAA-TATTTAAATA
1 AAAATTATTTAAATA
*
3842894 AAAATTATTTATATA
1 AAAATTATTTAAATA
3842909 AAAATT
1 AAAATT
3842915 CTATTTGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTATTTAAATA
Found at i:3843916 original size:23 final size:23
Alignment explanation
Indices: 3843886--3843996 Score: 141
Period size: 23 Copynumber: 4.8 Consensus size: 23
3843876 CTCGAGACTC
* * *
3843886 AAACTCGACTGAATCTCGATTTT
1 AAACTCGATTCAAGCTCGATTTT
*
3843909 AAACTCGATTCAAGCTCAATTTT
1 AAACTCGATTCAAGCTCGATTTT
*
3843932 AAGCTCGATTCAAGCTCGATTTT
1 AAACTCGATTCAAGCTCGATTTT
* *
3843955 GAGCTCGATTCAAGCTCGATTTT
1 AAACTCGATTCAAGCTCGATTTT
* *
3843978 GAGCTCGATTCAAGCTCGA
1 AAACTCGATTCAAGCTCGA
3843997 CGGGTTTTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 81 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (23 bp):
AAACTCGATTCAAGCTCGATTTT
Found at i:3843917 original size:12 final size:12
Alignment explanation
Indices: 3843900--3843996 Score: 94
Period size: 11 Copynumber: 8.4 Consensus size: 12
3843890 TCGACTGAAT
*
3843900 CTCGATTTTAAA
1 CTCGATTTTAAG
*
3843912 CTCGA-TTCAAG
1 CTCGATTTTAAG
*
3843923 CTCAATTTTAAG
1 CTCGATTTTAAG
*
3843935 CTCGA-TTCAAG
1 CTCGATTTTAAG
*
3843946 CTCGATTTTGAG
1 CTCGATTTTAAG
*
3843958 CTCGA-TTCAAG
1 CTCGATTTTAAG
*
3843969 CTCGATTTTGAG
1 CTCGATTTTAAG
*
3843981 CTCGA-TTCAAG
1 CTCGATTTTAAG
3843992 CTCGA
1 CTCGA
3843997 CGGGTTTTAA
Statistics
Matches: 68, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
11 36 0.53
12 32 0.47
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (12 bp):
CTCGATTTTAAG
Found at i:3843950 original size:46 final size:46
Alignment explanation
Indices: 3843900--3843996 Score: 158
Period size: 46 Copynumber: 2.1 Consensus size: 46
3843890 TCGACTGAAT
3843900 CTCGATTTTAAACTCGATTCAAGCTCAATTTTAAGCTCGATTCAAG
1 CTCGATTTTAAACTCGATTCAAGCTCAATTTTAAGCTCGATTCAAG
* * * *
3843946 CTCGATTTTGAGCTCGATTCAAGCTCGATTTTGAGCTCGATTCAAG
1 CTCGATTTTAAACTCGATTCAAGCTCAATTTTAAGCTCGATTCAAG
3843992 CTCGA
1 CTCGA
3843997 CGGGTTTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (46 bp):
CTCGATTTTAAACTCGATTCAAGCTCAATTTTAAGCTCGATTCAAG
Found at i:3846147 original size:14 final size:14
Alignment explanation
Indices: 3846128--3846166 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
3846118 CATAATCAGA
*
3846128 TTTAGGGTTTATAG
1 TTTAGGGTTTAGAG
*
3846142 TTTAGGATTTAGAG
1 TTTAGGGTTTAGAG
3846156 TTTAGGGTTTA
1 TTTAGGGTTTA
3846167 AGATTCATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTAGAG
Found at i:3846165 original size:21 final size:21
Alignment explanation
Indices: 3846125--3846171 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3846115 TCACATAATC
* *
3846125 AGATTTAGGGTTTATAGTTTA
1 AGATTTAGAGTTTAGAGTTTA
* *
3846146 GGATTTAGAGTTTAGGGTTTA
1 AGATTTAGAGTTTAGAGTTTA
3846167 AGATT
1 AGATT
3846172 CATTACAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (21 bp):
AGATTTAGAGTTTAGAGTTTA
Found at i:3846294 original size:11 final size:11
Alignment explanation
Indices: 3846278--3846340 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
3846268 GTATTATAGA
3846278 ATTTTTAATAT
1 ATTTTTAATAT
3846289 ATTTTTAA-A-
1 ATTTTTAATAT
3846298 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
3846309 ATCAATAATGT
1 ATTTTTAATAT
3846320 ATTTTTAATAT
1 ATTTTTAATAT
3846331 ATTTTTAATA
1 ATTTTTAATA
3846341 ATGTAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:3849146 original size:29 final size:29
Alignment explanation
Indices: 3849111--3849192 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
3849101 AAACTAAATT
*
3849111 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
3849140 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
3849169 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
3849193 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:3853910 original size:29 final size:29
Alignment explanation
Indices: 3853875--3853956 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
3853865 AAACTAAATT
*
3853875 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
3853904 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
3853933 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
3853957 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:3870327 original size:21 final size:22
Alignment explanation
Indices: 3870303--3870343 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3870293 TTGAATTTTA
*
3870303 AAATAATAT-GTTACTAAAACT
1 AAATAATATGGTTAATAAAACT
*
3870324 AAATTATATGGTTAATAAAA
1 AAATAATATGGTTAATAAAA
3870344 TAGTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (22 bp):
AAATAATATGGTTAATAAAACT
Found at i:3879755 original size:23 final size:23
Alignment explanation
Indices: 3879729--3879775 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3879719 GAAAGGAAAG
*
3879729 TTAATATATTATATGATA-AAAAA
1 TTAATATATTAAAT-ATATAAAAA
*
3879752 TTAATCTATTAAATATATAAAAA
1 TTAATATATTAAATATATAAAAA
3879775 T
1 T
3879776 ATACAAAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TTAATATATTAAATATATAAAAA
Found at i:3882554 original size:21 final size:21
Alignment explanation
Indices: 3882528--3882572 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3882518 GATTTCTGGG
* *
3882528 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3882549 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3882570 CAA
1 CAA
3882573 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:3883217 original size:23 final size:24
Alignment explanation
Indices: 3883174--3883220 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
3883164 ATATGGCATG
*
3883174 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
3883198 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
3883221 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:3883436 original size:31 final size:31
Alignment explanation
Indices: 3883398--3883553 Score: 224
Period size: 31 Copynumber: 5.0 Consensus size: 31
3883388 AGGGTCGAGG
*
3883398 GTTTACCTATGTTCTTCTGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3883429 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
3883460 GATTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
3883491 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
3883522 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
3883553 G
1 G
3883554 GTCCTTCGGG
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
31 111 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:3883552 original size:62 final size:62
Alignment explanation
Indices: 3883400--3883553 Score: 249
Period size: 62 Copynumber: 2.5 Consensus size: 62
3883390 GGTCGAGGGT
*
3883400 TTACCTATGTTCTTCTGG-ACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTC-GGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
*
3883462 TTACCTATGTTCTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
*
3883524 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
3883554 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
61 2 0.02
62 83 0.97
63 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (62 bp):
TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
Found at i:3886543 original size:21 final size:21
Alignment explanation
Indices: 3886517--3886561 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3886507 GATTTCTGGG
* *
3886517 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3886538 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3886559 CAA
1 CAA
3886562 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:3887423 original size:31 final size:31
Alignment explanation
Indices: 3887385--3887540 Score: 224
Period size: 31 Copynumber: 5.0 Consensus size: 31
3887375 AGGGTCGAGG
*
3887385 GTTTACCTATGTTCTTCTGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3887416 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
3887447 GATTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
3887478 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
3887509 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
3887540 G
1 G
3887541 GTCCTTCGGG
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
31 111 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:3887539 original size:62 final size:62
Alignment explanation
Indices: 3887387--3887540 Score: 249
Period size: 62 Copynumber: 2.5 Consensus size: 62
3887377 GGTCGAGGGT
*
3887387 TTACCTATGTTCTTCTGG-ACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTC-GGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
*
3887449 TTACCTATGTTCTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
*
3887511 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
3887541 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
61 2 0.02
62 83 0.97
63 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (62 bp):
TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
Found at i:3889078 original size:13 final size:13
Alignment explanation
Indices: 3889040--3889091 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
3889030 GTCATAAATC
*
3889040 TATGACGCACATT
1 TATGACGCGCATT
* * *
3889053 TATAACACACATT
1 TATGACGCGCATT
*
3889066 TATGACTCGCATT
1 TATGACGCGCATT
3889079 TATGACGCGCATT
1 TATGACGCGCATT
3889092 GCGAGTCATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:3891118 original size:22 final size:23
Alignment explanation
Indices: 3891092--3891135 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3891082 TTAGAATTTA
3891092 TATTTTCTTTAATT-GATTTAAG
1 TATTTTCTTTAATTGGATTTAAG
* *
3891114 TATTTTTTTTATTTGGATTTAA
1 TATTTTCTTTAATTGGATTTAA
3891136 AATTAATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64
Consensus pattern (23 bp):
TATTTTCTTTAATTGGATTTAAG
Found at i:3891242 original size:14 final size:14
Alignment explanation
Indices: 3891223--3891252 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3891213 AACATAAGCG
3891223 AACGTAAACAAACA
1 AACGTAAACAAACA
*
3891237 AACGTAAACGAACA
1 AACGTAAACAAACA
3891251 AA
1 AA
3891253 TTACCGAACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.20, G:0.10, T:0.07
Consensus pattern (14 bp):
AACGTAAACAAACA
Found at i:3895071 original size:32 final size:32
Alignment explanation
Indices: 3895035--3895110 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
3895025 CATGTCACGA
* **
3895035 GTACATAAATAACGACATGACATATACTATGT
1 GTACATAAATAACGACATAACATATACTACAT
* * **
3895067 GTACATAAGTGACGATGTAACATATACTACAT
1 GTACATAAATAACGACATAACATATACTACAT
3895099 GTACATAAATAA
1 GTACATAAATAA
3895111 TAATGTGGCA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (32 bp):
GTACATAAATAACGACATAACATATACTACAT
Found at i:3895160 original size:37 final size:35
Alignment explanation
Indices: 3895080--3895178 Score: 96
Period size: 32 Copynumber: 2.9 Consensus size: 35
3895070 CATAAGTGAC
*
3895080 GATGTAACATATACTACATGTACATAAATAATAAT
1 GATGTGACATATACTACATGTACATAAATAATAAT
* *
3895115 G-TG-G-CATATACTATATGTATATAAATGAATAAAT
1 GATGTGACATATACTACATGTACATAAAT-AAT-AAT
** * *
3895149 GATGTGACATATGTTACATATACATTAATA
1 GATGTGACATATACTACATGTACATAAATA
3895179 TATCATATCG
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
32 20 0.40
33 3 0.06
34 6 0.12
35 3 0.06
36 2 0.04
37 16 0.32
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34
Consensus pattern (35 bp):
GATGTGACATATACTACATGTACATAAATAATAAT
Found at i:3897801 original size:63 final size:62
Alignment explanation
Indices: 3897720--3897841 Score: 165
Period size: 63 Copynumber: 2.0 Consensus size: 62
3897710 GTCGAGGGTT
* *
3897720 TACCTATGTTCCACGGAACATATGGACAGAATTACCTATG-TCTTTCGGGACATATGGACAATA
1 TACCTATGTTCCAAGGAACATATGGACAG-ATTACCTAGGTTC-TTCGGGACATATGGACAATA
* * * *
3897783 TACCTATGTTCTAAGGAACATGTGGACAGTTTACCTAGGTTCTTCGGGACCTATGGACA
1 TACCTATGTTCCAAGGAACATATGGACAGATTACCTAGGTTCTTCGGGACATATGGACA
3897842 GTTGTCCAGG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
62 24 0.46
63 28 0.54
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (62 bp):
TACCTATGTTCCAAGGAACATATGGACAGATTACCTAGGTTCTTCGGGACATATGGACAATA
Found at i:3897842 original size:31 final size:31
Alignment explanation
Indices: 3897717--3897844 Score: 123
Period size: 31 Copynumber: 4.1 Consensus size: 31
3897707 AGAGTCGAGG
**
3897717 GTTTACCTATGTTCCACGGAACATATGGACA
1 GTTTACCTATGTTCTTCGGAACATATGGACA
* *
3897748 GAATTACCTATG-TCTTTCGGGACATATGGACA
1 G-TTTACCTATGTTC-TTCGGAACATATGGACA
* * ** *
3897780 ATATACCTATGTTCTAAGGAACATGTGGACA
1 GTTTACCTATGTTCTTCGGAACATATGGACA
* * *
3897811 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTTCGGAACATATGGACA
3897842 GTT
1 GTT
3897845 GTCCAGGTTC
Statistics
Matches: 75, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
31 50 0.67
32 25 0.33
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACA
Found at i:3906258 original size:32 final size:32
Alignment explanation
Indices: 3906198--3906257 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
3906188 TGCTACTAGA
3906198 ATTTCTCGGCGTCTTCTTCAGCATGGGGGTGG
1 ATTTCTCGGCGTCTTCTTCAGCATGGGGGTGG
3906230 ATTTCTCGGCGTCTTCTTCA-CATGGGGG
1 ATTTCTCGGCGTCTTCTTCAGCATGGGGG
3906258 GCGAATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 8 0.29
32 20 0.71
ACGTcount: A:0.10, C:0.23, G:0.32, T:0.35
Consensus pattern (32 bp):
ATTTCTCGGCGTCTTCTTCAGCATGGGGGTGG
Found at i:3908653 original size:24 final size:24
Alignment explanation
Indices: 3908626--3908689 Score: 65
Period size: 27 Copynumber: 2.5 Consensus size: 24
3908616 AGTTTTTTAC
*
3908626 TATTAAATCATTTTTAGTAATAAT
1 TATTAAATCATTTTTAATAATAAT
* *
3908650 TATTATAATTTCATTATTAATAATCAT
1 TATTA-AA--TCATTTTTAATAATAAT
*
3908677 AATTAAATCATTT
1 TATTAAATCATTT
3908690 GTATTAAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
24 10 0.31
25 2 0.06
26 2 0.06
27 18 0.56
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (24 bp):
TATTAAATCATTTTTAATAATAAT
Found at i:3908752 original size:16 final size:16
Alignment explanation
Indices: 3908731--3908762 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3908721 ATTATTAATA
3908731 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
3908747 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
3908763 TAAATATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
ATCATTACTAAATCAT
Found at i:3908753 original size:26 final size:26
Alignment explanation
Indices: 3908719--3908780 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
3908709 TAATAATAAA
*
3908719 ATATTATTAAT-AATCATTACTAA-ATC
1 ATATCATTAATAAATCATTA--AATATC
*
3908745 ATATCATTACTAAATCATTAAATATC
1 ATATCATTAATAAATCATTAAATATC
*
3908771 AAATCATTAA
1 ATATCATTAA
3908781 ATTAATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 2 0.07
26 20 0.67
27 8 0.27
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (26 bp):
ATATCATTAATAAATCATTAAATATC
Found at i:3909225 original size:42 final size:43
Alignment explanation
Indices: 3909178--3909265 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 43
3909168 TTAAAATTTT
* * *
3909178 ATTCATATATTATTCTT-GTTTAAATTAATAGATTAATTG-TTA
1 ATTCATATATTATT-TTCGTATAAATTAATAAATTAATAGATTA
*
3909220 ATTCATATATTATTTTCGTATACATTAATAAATTAATAGATTA
1 ATTCATATATTATTTTCGTATAAATTAATAAATTAATAGATTA
3909263 ATT
1 ATT
3909266 GTTTAAATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 2 0.05
42 32 0.80
43 6 0.15
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (43 bp):
ATTCATATATTATTTTCGTATAAATTAATAAATTAATAGATTA
Found at i:3909412 original size:11 final size:11
Alignment explanation
Indices: 3909404--3909493 Score: 62
Period size: 11 Copynumber: 8.0 Consensus size: 11
3909394 TTATTATTCG
3909404 ATCATTATTAA
1 ATCATTATTAA
3909415 ATCATTATTAA
1 ATCATTATTAA
*
3909426 ATCAAATCATT-A
1 ATC--ATTATTAA
3909438 A--ATTATTAA
1 ATCATTATTAA
3909447 ATCATTATTATTAA
1 ATC---ATTATTAA
*
3909461 ATCATTAAT-A
1 ATCATTATTAA
* *
3909471 ATAAATCATTAA
1 AT-CATTATTAA
3909483 ATCATTATTAA
1 ATCATTATTAA
3909494 TAAATCATAT
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
8 5 0.08
9 2 0.03
10 3 0.05
11 30 0.49
12 5 0.08
13 5 0.08
14 11 0.18
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (11 bp):
ATCATTATTAA
Found at i:3909440 original size:8 final size:8
Alignment explanation
Indices: 3909429--3909489 Score: 67
Period size: 8 Copynumber: 8.1 Consensus size: 8
3909419 TTATTAAATC
3909429 AAATCATT
1 AAATCATT
*
3909437 AAATTATT
1 AAATCATT
3909445 AAATCATT
1 AAATCATT
*
3909453 --ATTATT
1 AAATCATT
3909459 AAATCATT
1 AAATCATT
*
3909467 -AAT-AAT
1 AAATCATT
3909473 AAATCATT
1 AAATCATT
3909481 AAATCATT
1 AAATCATT
3909489 A
1 A
3909490 TTAATAAATC
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
6 7 0.16
7 6 0.14
8 30 0.70
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (8 bp):
AAATCATT
Found at i:3909482 original size:57 final size:57
Alignment explanation
Indices: 3909372--3909486 Score: 135
Period size: 57 Copynumber: 2.0 Consensus size: 57
3909362 AATCATTATT
* ** * * *
3909372 AAATCATTAAATTTCCAATCATTTATTATTCGATCATTATTAAATCATTATTAAATC
1 AAATCATTAAATTTCAAATCATTTATTATTAAATCATTAATAAATAATCATTAAATC
*
3909429 AAATCATTAAATTATTAAATCA-TTATTATTAAATCATTAAT-AATAAATCATTAAATC
1 AAATCATTAAATT-TCAAATCATTTATTATTAAATCATTAATAAAT-AATCATTAAATC
3909486 A
1 A
3909487 TTATTAATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
56 3 0.06
57 40 0.82
58 6 0.12
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.42
Consensus pattern (57 bp):
AAATCATTAAATTTCAAATCATTTATTATTAAATCATTAATAAATAATCATTAAATC
Found at i:3909483 original size:36 final size:36
Alignment explanation
Indices: 3909418--3909502 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 36
3909408 TTATTAAATC
* *
3909418 ATTATTAAATCA-AATCATTAAATTATTAAATCATT
1 ATTATTAAATCATAATCAATAAATCATTAAATCATT
3909453 ATTATTAAATCATTAAT-AATAAATCATTAAATCATT
1 ATTATTAAATCA-TAATCAATAAATCATTAAATCATT
*
3909489 ATTAATAAATCATA
1 ATTATTAAATCATA
3909503 TCATTACACT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
35 14 0.31
36 28 0.62
37 3 0.07
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (36 bp):
ATTATTAAATCATAATCAATAAATCATTAAATCATT
Found at i:3909494 original size:22 final size:23
Alignment explanation
Indices: 3909410--3909501 Score: 102
Period size: 22 Copynumber: 4.1 Consensus size: 23
3909400 TTCGATCATT
3909410 ATTAAATCATTATTAAATCAAATC
1 ATTAAATCATTATT-AATCAAATC
* * *
3909434 ATTAAATTATTA--AATCATTATT
1 ATTAAATCATTATTAATCA-AATC
*
3909456 ATTAAATCATTAATAAT-AAATC
1 ATTAAATCATTATTAATCAAATC
3909478 ATTAAATCATTATTAAT-AAATC
1 ATTAAATCATTATTAATCAAATC
3909500 AT
1 AT
3909502 ATCATTACAC
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
21 5 0.09
22 38 0.66
23 1 0.02
24 14 0.24
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (23 bp):
ATTAAATCATTATTAATCAAATC
Found at i:3909501 original size:14 final size:14
Alignment explanation
Indices: 3909407--3909481 Score: 87
Period size: 14 Copynumber: 5.1 Consensus size: 14
3909397 TTATTCGATC
3909407 ATTATTAAATCATT
1 ATTATTAAATCATT
*
3909421 ATTAAATCAAATCATT
1 ATT--ATTAAATCATT
3909437 AAATTATTAAATCATT
1 --ATTATTAAATCATT
3909453 ATTATTAAATCATT
1 ATTATTAAATCATT
* *
3909467 AATAATAAATCATT
1 ATTATTAAATCATT
3909481 A
1 A
3909482 AATCATTATT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
14 30 0.57
16 20 0.38
18 3 0.06
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:3909785 original size:14 final size:13
Alignment explanation
Indices: 3909745--3909802 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
3909735 TCATTAAAGT
3909745 TCAAATCATTATTA
1 TCAAAT-ATTATTA
*
3909759 GT-AATTATTATTA
1 -TCAAATATTATTA
3909772 TCAAATACTTATTA
1 TCAAATA-TTATTA
*
3909786 --AATTATTATTA
1 TCAAATATTATTA
3909797 TCAAAT
1 TCAAAT
3909803 CATTGTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
11 6 0.17
12 5 0.14
13 14 0.40
14 9 0.26
15 1 0.03
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.47
Consensus pattern (13 bp):
TCAAATATTATTA
Found at i:3909811 original size:25 final size:25
Alignment explanation
Indices: 3909745--3909813 Score: 95
Period size: 25 Copynumber: 2.7 Consensus size: 25
3909735 TCATTAAAGT
3909745 TCAAATCATTATTAGTAATTATTATTA
1 TCAAATCATTATTA--AATTATTATTA
3909772 TCAAAT-ACTTATTAAATTATTATTA
1 TCAAATCA-TTATTAAATTATTATTA
*
3909797 TCAAATCATTGTTAAAT
1 TCAAATCATTATTAAAT
3909814 CAGTAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
25 25 0.64
26 2 0.05
27 12 0.31
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (25 bp):
TCAAATCATTATTAAATTATTATTA
Found at i:3912255 original size:11 final size:11
Alignment explanation
Indices: 3912239--3912270 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
3912229 GTTTAATTGT
3912239 GAAAATTTGGC
1 GAAAATTTGGC
3912250 GAAAATTTGGC
1 GAAAATTTGGC
3912261 GAAAATTTGG
1 GAAAATTTGG
3912271 GGACTGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.28, T:0.28
Consensus pattern (11 bp):
GAAAATTTGGC
Found at i:3912955 original size:10 final size:9
Alignment explanation
Indices: 3912920--3913040 Score: 107
Period size: 10 Copynumber: 12.6 Consensus size: 9
3912910 GCTGCTGGAA
*
3912920 ACCGGTTTA
1 ACCGGTTTG
*
3912929 ACCGGTTTTCA
1 ACCGG-TTT-G
3912940 ACCGGTTCTG
1 ACCGGTT-TG
3912950 ACCGGTTTG
1 ACCGGTTTG
*
3912959 ACCGGTTTCA
1 ACCGGTTT-G
*
3912969 ACCGGTTCG
1 ACCGGTTTG
3912978 AACCGGTTTG
1 -ACCGGTTTG
*
3912988 ACCGGTTTCA
1 ACCGGTTT-G
*
3912998 ACCGGTTCG
1 ACCGGTTTG
3913007 AACCGGTTTG
1 -ACCGGTTTG
*
3913017 ACCGGTCTG
1 ACCGGTTTG
3913026 AACCGGTTTG
1 -ACCGGTTTG
3913036 ACCGG
1 ACCGG
3913041 CCTGACCCGA
Statistics
Matches: 93, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
9 36 0.39
10 50 0.54
11 7 0.08
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:3912964 original size:19 final size:19
Alignment explanation
Indices: 3912940--3913040 Score: 102
Period size: 19 Copynumber: 5.3 Consensus size: 19
3912930 CCGGTTTTCA
3912940 ACCGGTTCTGACCGGTTTG
1 ACCGGTTCTGACCGGTTTG
* *
3912959 ACCGGTT-TCAACCGGTTCG
1 ACCGGTTCT-GACCGGTTTG
*
3912978 AACCGGTT-TGACCGGTTTCA
1 -ACCGGTTCTGACCGGTTT-G
3912998 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTG-ACCGGTTTG
3913017 ACCGG-TCTGAACCGGTTTG
1 ACCGGTTCTG-ACCGGTTTG
3913036 ACCGG
1 ACCGG
3913041 CCTGACCCGA
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
18 3 0.04
19 51 0.73
20 16 0.23
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.27
Consensus pattern (19 bp):
ACCGGTTCTGACCGGTTTG
Found at i:3912982 original size:29 final size:29
Alignment explanation
Indices: 3912919--3913033 Score: 178
Period size: 29 Copynumber: 3.9 Consensus size: 29
3912909 GGCTGCTGGA
*
3912919 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTC-G
3912950 -ACCGGTTTGACCGGTTTCAACCGGTTCG
1 AACCGGTTTGACCGGTTTCAACCGGTTCG
3912978 AACCGGTTTGACCGGTTTCAACCGGTTCG
1 AACCGGTTTGACCGGTTTCAACCGGTTCG
* *
3913007 AACCGGTTTGACCGGTCTGAACCGGTT
1 AACCGGTTTGACCGGTTTCAACCGGTT
3913034 TGACCGGCCT
Statistics
Matches: 80, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
28 1 0.01
29 66 0.82
30 13 0.16
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (29 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:3913045 original size:19 final size:19
Alignment explanation
Indices: 3913006--3913045 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
3912996 CAACCGGTTC
*
3913006 GAACCGGTTTGACCGGTCT
1 GAACCGGTTTGACCGGCCT
3913025 GAACCGGTTTGACCGGCCT
1 GAACCGGTTTGACCGGCCT
3913044 GA
1 GA
3913046 CCCGACCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.23
Consensus pattern (19 bp):
GAACCGGTTTGACCGGCCT
Found at i:3913065 original size:17 final size:17
Alignment explanation
Indices: 3913043--3913098 Score: 103
Period size: 17 Copynumber: 3.3 Consensus size: 17
3913033 TTGACCGGCC
3913043 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
3913060 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
*
3913077 TGACCCGACCCGACCAT
1 TGACCCGACCCGACCGT
3913094 TGACC
1 TGACC
3913099 GTTGACCGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.20, C:0.46, G:0.21, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:3913098 original size:7 final size:7
Alignment explanation
Indices: 3913088--3913118 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3913078 GACCCGACCC
*
3913088 GACCATT
1 GACCGTT
3913095 GACCGTT
1 GACCGTT
3913102 GACCGTT
1 GACCGTT
3913109 GACCGTT
1 GACCGTT
3913116 GAC
1 GAC
3913119 TTTCTTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:3920288 original size:9 final size:9
Alignment explanation
Indices: 3920274--3920376 Score: 62
Period size: 9 Copynumber: 10.8 Consensus size: 9
3920264 GGCTGCTGGA
3920274 AACCGGTTT
1 AACCGGTTT
3920283 AACCGGTTTT
1 AACCGG-TTT
3920293 CAACCGGTTCT
1 -AACCGGTT-T
*
3920304 GACCGGTTT
1 AACCGGTTT
* *
3920313 GACCGGTTCG
1 AACCGGTT-T
*
3920323 AACCGATTT
1 AACCGGTTT
* *
3920332 GACCGGTCTA
1 AACCGGT-TT
3920342 AACCGGTTT
1 AACCGGTTT
* *
3920351 GACCGGTCTG
1 AACCGGT-TT
*
3920361 AGCCGGTTT
1 AACCGGTTT
*
3920370 GACCGGT
1 AACCGGT
3920377 CTGACCCGAC
Statistics
Matches: 71, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
9 33 0.46
10 31 0.44
11 7 0.10
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.28
Consensus pattern (9 bp):
AACCGGTTT
Found at i:3920299 original size:20 final size:21
Alignment explanation
Indices: 3920274--3920312 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3920264 GGCTGCTGGA
3920274 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
3920294 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
3920313 GACCGGTTCG
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:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:3920319 original size:19 final size:18
Alignment explanation
Indices: 3920295--3920382 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 18
3920285 CCGGTTTTCA
3920295 ACCGGTTCTGACCGGTTTG
1 ACCGG-TCTGACCGGTTTG
*
3920314 ACCGGT-TCGAACCGATTTG
1 ACCGGTCT-G-ACCGGTTTG
*
3920333 ACCGGTCTAAACCGGTTTG
1 ACCGGTCT-GACCGGTTTG
3920352 ACCGGTCTGAGCCGGTTTG
1 ACCGGTCTGA-CCGGTTTG
3920371 ACCGGTCTGACC
1 ACCGGTCTGACC
3920383 CGACCCGACC
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
17 1 0.02
18 5 0.08
19 53 0.88
20 1 0.02
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.26
Consensus pattern (18 bp):
ACCGGTCTGACCGGTTTG
Found at i:3920381 original size:9 final size:9
Alignment explanation
Indices: 3920295--3920382 Score: 70
Period size: 9 Copynumber: 9.3 Consensus size: 9
3920285 CCGGTTTTCA
3920295 ACCGGTTCTG
1 ACCGG-TCTG
*
3920305 ACCGGTTTG
1 ACCGGTCTG
3920314 ACCGGT-TCG
1 ACCGGTCT-G
* *
3920323 AACCGATTTG
1 -ACCGGTCTG
*
3920333 ACCGGTCTAA
1 ACCGGTCT-G
*
3920343 ACCGGTTTG
1 ACCGGTCTG
3920352 ACCGGTCTG
1 ACCGGTCTG
*
3920361 AGCCGGTTTG
1 A-CCGGTCTG
3920371 ACCGGTCTG
1 ACCGGTCTG
3920380 ACC
1 ACC
3920383 CGACCCGACC
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
8 1 0.02
9 35 0.56
10 26 0.41
11 1 0.02
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.26
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:3920400 original size:17 final size:17
Alignment explanation
Indices: 3920378--3920433 Score: 103
Period size: 17 Copynumber: 3.3 Consensus size: 17
3920368 TTGACCGGTC
3920378 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
*
3920395 TGACCCGACCCGACTGT
1 TGACCCGACCCGACCGT
3920412 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
3920429 TGACC
1 TGACC
3920434 GTTGACCGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:3923403 original size:63 final size:64
Alignment explanation
Indices: 3923294--3923441 Score: 244
Period size: 63 Copynumber: 2.3 Consensus size: 64
3923284 TCCCTTTGCT
*
3923294 TGGAAGACGCCGAGAGATCCATTTTCCCATGCTTAAAGACGCCGAGCATTCCCCCGAGCGTGCA
1 TGGAAGACGCCGAGAGATCCATTTTCCCATGCTTAAAGACGCCGAGCATTCCCCCGAGCATGCA
*
3923358 TGGAAGACGCCGAGAGATCCA-TTTCCCATGCTTGAAGACGCCGAGCATTCCCCCGAGCATGCA
1 TGGAAGACGCCGAGAGATCCATTTTCCCATGCTTAAAGACGCCGAGCATTCCCCCGAGCATGCA
* * *
3923421 TAGAAGACGCCAAGATATCCA
1 TGGAAGACGCCGAGAGATCCA
3923442 AGTTGGCAAG
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
63 58 0.73
64 21 0.27
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (64 bp):
TGGAAGACGCCGAGAGATCCATTTTCCCATGCTTAAAGACGCCGAGCATTCCCCCGAGCATGCA
Found at i:3923419 original size:31 final size:32
Alignment explanation
Indices: 3923321--3923431 Score: 93
Period size: 32 Copynumber: 3.5 Consensus size: 32
3923311 TCCATTTTCC
*
3923321 CATGC-TTAAAGACGCCGAGCATTCCCCCGAG
1 CATGCATTGAAGACGCCGAGCATTCCCCCGAG
* * * ******
3923352 CGTGCATGGAAGACGCCGAG-AGATCCATTTCC
1 CATGCATTGAAGACGCCGAGCA-TTCCCCCGAG
3923384 CATGC-TTGAAGACGCCGAGCATTCCCCCGAG
1 CATGCATTGAAGACGCCGAGCATTCCCCCGAG
*
3923415 CATGCATAGAAGACGCC
1 CATGCATTGAAGACGCC
3923432 AAGATATCCA
Statistics
Matches: 56, Mismatches: 20, Indels: 7
0.67 0.24 0.08
Matches are distributed among these distances:
31 26 0.46
32 30 0.54
ACGTcount: A:0.26, C:0.32, G:0.25, T:0.16
Consensus pattern (32 bp):
CATGCATTGAAGACGCCGAGCATTCCCCCGAG
Found at i:3925994 original size:48 final size:48
Alignment explanation
Indices: 3925923--3926027 Score: 201
Period size: 48 Copynumber: 2.2 Consensus size: 48
3925913 CCGGGGTTAG
3925923 CACTTCAATCAAACGTTACCTTTTTGTTTGAATCATAGTGAAGAAAGA
1 CACTTCAATCAAACGTTACCTTTTTGTTTGAATCATAGTGAAGAAAGA
*
3925971 CACTTCATTCAAACGTTACCTTTTTGTTTGAATCATAGTGAAGAAAGA
1 CACTTCAATCAAACGTTACCTTTTTGTTTGAATCATAGTGAAGAAAGA
3926019 CACTTCAAT
1 CACTTCAAT
3926028 TTTGCATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (48 bp):
CACTTCAATCAAACGTTACCTTTTTGTTTGAATCATAGTGAAGAAAGA
Found at i:3943608 original size:23 final size:23
Alignment explanation
Indices: 3943578--3943622 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
3943568 TAACGCACCC
3943578 GAAAACCAAGATAAGGTAGCATT
1 GAAAACCAAGATAAGGTAGCATT
3943601 GAAAACCAAGATAAGGTAGCAT
1 GAAAACCAAGATAAGGTAGCAT
3943623 AAAGGCAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.13, G:0.22, T:0.16
Consensus pattern (23 bp):
GAAAACCAAGATAAGGTAGCATT
Found at i:3957826 original size:10 final size:10
Alignment explanation
Indices: 3957811--3957837 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3957801 GAGTATTAAG
3957811 TAGCTCGTTT
1 TAGCTCGTTT
3957821 TAGCTCGTTT
1 TAGCTCGTTT
3957831 TAGCTCG
1 TAGCTCG
3957838 ATAAGAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (10 bp):
TAGCTCGTTT
Found at i:3963086 original size:34 final size:35
Alignment explanation
Indices: 3963023--3963089 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
3963013 TTTAATTGAA
*
3963023 TCATTCGGGTATGTATCGGGTTTCTGGTTTAGGAT
1 TCATTCGGGTATGTATCGGGTTTCGGGTTTAGGAT
*
3963058 TCATTCGGGTATGTTTC-GGTTTCGGGTTTAGG
1 TCATTCGGGTATGTATCGGGTTTCGGGTTTAGG
3963090 TTTAAGAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 14 0.47
35 16 0.53
ACGTcount: A:0.12, C:0.12, G:0.33, T:0.43
Consensus pattern (35 bp):
TCATTCGGGTATGTATCGGGTTTCGGGTTTAGGAT
Found at i:3972703 original size:13 final size:14
Alignment explanation
Indices: 3972685--3972731 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
3972675 CATTACACAT
3972685 TCACATA-TTCATA
1 TCACATAGTTCATA
*
3972698 TCACATAGTTC-TT
1 TCACATAGTTCATA
*
3972711 TCACATAGCTCTATA
1 TCACATAGTTC-ATA
3972726 TCACAT
1 TCACAT
3972732 TTCATATGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 18 0.64
14 3 0.11
15 7 0.25
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (14 bp):
TCACATAGTTCATA
Found at i:3973416 original size:20 final size:20
Alignment explanation
Indices: 3973391--3973428 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3973381 TTCCCCTTGA
3973391 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
3973411 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
3973429 TTAACATGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:3976075 original size:64 final size:62
Alignment explanation
Indices: 3975949--3976085 Score: 177
Period size: 64 Copynumber: 2.2 Consensus size: 62
3975939 TTCAGTGTGT
* *
3975949 ATCGATGCACCCCTTAAAATGGAAACATCGAATGCAATTGGTGCATCGATGCATAAGGAGTGC
1 ATCGATGCACCCCTTAAAATGAAAACATCGAAGGCAATTGGTGCATCGATGCAT-AGGAGTGC
* * *
3976012 ATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTAATTTGTGTATCGATGCAT-GGATAGTGC
1 ATCGATGCA-CCCCTTAAAATGAAAACATCGAAGGCAATTGGTGCATCGATGCATAGG--AGTGC
*
3976076 ATCAATGCAC
1 ATCGATGCAC
3976086 ATGTTAAAGA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
62 2 0.03
63 10 0.15
64 53 0.82
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.25
Consensus pattern (62 bp):
ATCGATGCACCCCTTAAAATGAAAACATCGAAGGCAATTGGTGCATCGATGCATAGGAGTGC
Found at i:3976118 original size:20 final size:20
Alignment explanation
Indices: 3976093--3976130 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3976083 CACATGTTAA
3976093 AGAATGAATCGATGCACTGT
1 AGAATGAATCGATGCACTGT
* *
3976113 AGAATGCATTGATGCACT
1 AGAATGAATCGATGCACT
3976131 TCAAGGGGAA
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:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (20 bp):
AGAATGAATCGATGCACTGT
Found at i:3976637 original size:13 final size:14
Alignment explanation
Indices: 3976608--3976638 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3976598 AACCATGCAA
3976608 GTGATATGAACTAT
1 GTGATATGAACTAT
3976622 GTGATATGAA-TAT
1 GTGATATGAACTAT
3976635 GTGA
1 GTGA
3976639 AATATGATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (14 bp):
GTGATATGAACTAT
Found at i:3980172 original size:20 final size:20
Alignment explanation
Indices: 3980147--3980184 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3980137 TTCCCCTTGA
3980147 AGTGCATCAATACATTCTAC
1 AGTGCATCAATACATTCTAC
* *
3980167 AGTGCATCGATGCATTCT
1 AGTGCATCAATACATTCT
3980185 TTAACATGTG
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:0.29, C:0.24, G:0.16, T:0.32
Consensus pattern (20 bp):
AGTGCATCAATACATTCTAC
Found at i:3981598 original size:5 final size:5
Alignment explanation
Indices: 3981588--3981616 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
3981578 ACTCATACAC
3981588 ATCAT ATCAT ATCAT ATCAT ATCAT ATCA
1 ATCAT ATCAT ATCAT ATCAT ATCAT ATCA
3981617 CCCAATAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (5 bp):
ATCAT
Found at i:3981828 original size:30 final size:30
Alignment explanation
Indices: 3981788--3981848 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
3981778 GTCCCGAAGG
3981788 ACCTATCCATATGTTCCGAAGAACATAGGT
1 ACCTATCCATATGTTCCGAAGAACATAGGT
*
3981818 ACCTGTCCATATGTTCCGAAGAACATAGGT
1 ACCTATCCATATGTTCCGAAGAACATAGGT
3981848 A
1 A
3981849 ACCCTCGACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (30 bp):
ACCTATCCATATGTTCCGAAGAACATAGGT
Found at i:3997802 original size:2 final size:2
Alignment explanation
Indices: 3997795--3997822 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3997785 TAATAAATGA
3997795 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
3997823 CAATCCAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4004282 original size:16 final size:16
Alignment explanation
Indices: 4004257--4004292 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4004247 CTTCACCAGA
*
4004257 TCCATCGAAAAGTGTC
1 TCCATCGAAAAGGGTC
*
4004273 TCCATTGAAAAGGGTC
1 TCCATCGAAAAGGGTC
4004289 TCCA
1 TCCA
4004293 ATGGGAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (16 bp):
TCCATCGAAAAGGGTC
Found at i:4016753 original size:46 final size:46
Alignment explanation
Indices: 4016700--4016790 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
4016690 GTATCTTAAA
** * *
4016700 TAACTATCTGTAATGTCTTTTAGAAACTCAATTGAGGTTCTTTCCG
1 TAACTATCTCCAAGGTCTTTTAGAAACTCAATTGAGATTCTTTCCG
* * *
4016746 TAACTATCTCCAAGGTCTTTTGGAAACTCATTTGATATTCTTTCC
1 TAACTATCTCCAAGGTCTTTTAGAAACTCAATTGAGATTCTTTCC
4016791 TTTCTGTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (46 bp):
TAACTATCTCCAAGGTCTTTTAGAAACTCAATTGAGATTCTTTCCG
Found at i:4022445 original size:28 final size:31
Alignment explanation
Indices: 4022408--4022468 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 31
4022398 TATGTTTGTT
*
4022408 TTTTCAGTTTAGTGTCTAAT-TTTT-TTTCG
1 TTTTCAGTTTAGTGCCTAATGTTTTATTTCG
*
4022437 TTTT-AGTTTGGTGCCTAATGTTTTATTTCG
1 TTTTCAGTTTAGTGCCTAATGTTTTATTTCG
4022467 TT
1 TT
4022469 ACTTAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 13 0.46
29 8 0.29
30 7 0.25
ACGTcount: A:0.13, C:0.10, G:0.16, T:0.61
Consensus pattern (31 bp):
TTTTCAGTTTAGTGCCTAATGTTTTATTTCG
Found at i:4022960 original size:27 final size:27
Alignment explanation
Indices: 4022922--4022974 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
4022912 ACGGTGGCGA
*
4022922 TCGGCGTGAGTTT-AGGAGTTAAAATGG
1 TCGGCATGAGTTTGAGGA-TTAAAATGG
*
4022949 TCGGCATGAGTTTGAGGATTGAAATG
1 TCGGCATGAGTTTGAGGATTAAAATG
4022975 AAGATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.26, C:0.08, G:0.36, T:0.30
Consensus pattern (27 bp):
TCGGCATGAGTTTGAGGATTAAAATGG
Found at i:4027384 original size:15 final size:15
Alignment explanation
Indices: 4027347--4027384 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
4027337 TTTATTTATT
4027347 TTTTTAATATTTTAA
1 TTTTTAATATTTTAA
* *
4027362 TCTCTAATATTTTAA
1 TTTTTAATATTTTAA
4027377 TTTTTAAT
1 TTTTTAAT
4027385 TAAAATAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTAATATTTTAA
Found at i:4028805 original size:195 final size:196
Alignment explanation
Indices: 4028471--4028834 Score: 631
Period size: 195 Copynumber: 1.9 Consensus size: 196
4028461 TGGCTAGCCC
*
4028471 TTTTTCCCATATATATGGGATAAGGGGAAGGTAAGATAGTAGGCTACCCCCAACATCAGGTTGAG
1 TTTTTCCCATATATATGGGATAAGGGGAAGGTAAGATAGTAGGCTACCCCCAACACCAGGTTGAG
* * * *
4028536 GGCAGTTTCCGTAAGAGACCTCCGAATTATGAAATGCCCTCCATGGGACTCGATCCCACGACTTC
66 AGCAGCTTCCGTAAGAGACCTCCGAATTATGAAATGCCCTCCATGGGACTCAATCCCACGACCTC
4028601 AAAGTTAAGAACCTTGTGCTCTACCAACTGAGCTGGATGATCATTTCTATATAAATGGCTGTTCC
131 AAAGTTAAGAACCTTGTGCTCTACCAACTGAGCTGGATGATCATTTCTATATAAATGGCTGTTCC
4028666 T
196 T
* * *
4028667 TTTTTCCCATATGTATGGGGTAA-GGGAAGGTAAGATAGTAGGCTACCCCCAATACCAGGTTGAG
1 TTTTTCCCATATATATGGGATAAGGGGAAGGTAAGATAGTAGGCTACCCCCAACACCAGGTTGAG
4028731 AGCAGCTTCCGTAAGAGACCTCCGAATTATGAAATGCCCTCCATGGGACTCAATCCCACGACCTC
66 AGCAGCTTCCGTAAGAGACCTCCGAATTATGAAATGCCCTCCATGGGACTCAATCCCACGACCTC
* *
4028796 AAGGTTAAGAATCTTGTGCTCTACCAACTGAGCTGGATG
131 AAAGTTAAGAACCTTGTGCTCTACCAACTGAGCTGGATG
4028835 GTCAAGTGTA
Statistics
Matches: 158, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
195 137 0.87
196 21 0.13
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (196 bp):
TTTTTCCCATATATATGGGATAAGGGGAAGGTAAGATAGTAGGCTACCCCCAACACCAGGTTGAG
AGCAGCTTCCGTAAGAGACCTCCGAATTATGAAATGCCCTCCATGGGACTCAATCCCACGACCTC
AAAGTTAAGAACCTTGTGCTCTACCAACTGAGCTGGATGATCATTTCTATATAAATGGCTGTTCC
T
Found at i:4034711 original size:20 final size:20
Alignment explanation
Indices: 4034686--4034755 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
4034676 GCGAAGTTCG
4034686 CGTTGCGATTCATTCCAAAT
1 CGTTGCGATTCATTCCAAAT
* * *
4034706 CGTTGCGA-T-AGTCGAAGTT
1 CGTTGCGATTCATTCCAA-AT
4034725 CGCGTTGCGATTCATTCCAAAT
1 --CGTTGCGATTCATTCCAAAT
4034747 CGTTGCGAT
1 CGTTGCGAT
4034756 AGGCGAAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 5 0.13
19 2 0.05
20 17 0.44
21 8 0.21
22 2 0.05
23 5 0.13
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (20 bp):
CGTTGCGATTCATTCCAAAT
Found at i:4034722 original size:41 final size:41
Alignment explanation
Indices: 4034627--4034840 Score: 365
Period size: 41 Copynumber: 5.2 Consensus size: 41
4034617 GATTCGCAAC
* *
4034627 GCGATAGTCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
4034669 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
*
4034710 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
*
4034751 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
*
4034792 GCGATAGGCAAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
4034834 GCGATAG
1 GCGATAG
4034841 TCCAAATATT
Statistics
Matches: 164, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
41 118 0.72
42 46 0.28
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.31
Consensus pattern (41 bp):
GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
Found at i:4034940 original size:5 final size:6
Alignment explanation
Indices: 4034891--4034938 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
4034881 ATATAGAATT
4034891 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
4034936 ACC
1 ACC
4034939 CGGGACTGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.36
6 27 0.64
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:4035627 original size:6 final size:6
Alignment explanation
Indices: 4035611--4035642 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
4035601 TCCCGTCCCG
4035611 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
4035643 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:4035905 original size:16 final size:17
Alignment explanation
Indices: 4035886--4035918 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4035876 ATCAAATAAT
4035886 ATTTAATTCAAT-TTTA
1 ATTTAATTCAATGTTTA
*
4035902 ATTTAGTTCAATGTTTA
1 ATTTAATTCAATGTTTA
4035919 TAAACATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTTAATTCAATGTTTA
Found at i:4040517 original size:16 final size:16
Alignment explanation
Indices: 4040485--4040525 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
4040475 GTTTACTTCA
*
4040485 GAATGATT-AAGTGCT
1 GAATGATTCAAATGCT
4040500 GAATGATTCAAATGCT
1 GAATGATTCAAATGCT
4040516 GAATGATTCA
1 GAATGATTCA
4040526 GAGGCTCTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (16 bp):
GAATGATTCAAATGCT
Found at i:4048744 original size:28 final size:28
Alignment explanation
Indices: 4048704--4048760 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
4048694 TCAGTTCCAG
4048704 AGTATTAAAACAGAAAATGTAACGGTAA
1 AGTATTAAAACAGAAAATGTAACGGTAA
*
4048732 AGTATTAAAACAGAAAATTTAACGGTAA
1 AGTATTAAAACAGAAAATGTAACGGTAA
4048760 A
1 A
4048761 CCATCAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.54, C:0.07, G:0.16, T:0.23
Consensus pattern (28 bp):
AGTATTAAAACAGAAAATGTAACGGTAA
Found at i:4048769 original size:28 final size:28
Alignment explanation
Indices: 4048710--4048769 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
4048700 CCAGAGTATT
** *
4048710 AAAACAGAAAATGTAACGGTAAAGTATT
1 AAAACAGAAAATGTAACGGTAAACCATC
*
4048738 AAAACAGAAAATTTAACGGTAAACCATC
1 AAAACAGAAAATGTAACGGTAAACCATC
4048766 AAAA
1 AAAA
4048770 ACTTTATTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.57, C:0.12, G:0.13, T:0.18
Consensus pattern (28 bp):
AAAACAGAAAATGTAACGGTAAACCATC
Found at i:4053702 original size:20 final size:21
Alignment explanation
Indices: 4053651--4053718 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 21
4053641 AATCTTTAGA
*
4053651 TGTTATTAAATATTATGAAAT
1 TGTTATTAAATATTATCAAAT
* *
4053672 AGTTGTTAAAT-TTATCAAAT
1 TGTTATTAAATATTATCAAAT
* *
4053692 TGTTATAAAATGATTATTAAAT
1 TGTTATTAAAT-ATTATCAAAT
4053714 T-TTAT
1 TGTTAT
4053719 CGAGTTGTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 16 0.42
21 13 0.34
22 9 0.24
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (21 bp):
TGTTATTAAATATTATCAAAT
Found at i:4054457 original size:17 final size:19
Alignment explanation
Indices: 4054421--4054457 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
4054411 GTCATTTAGG
4054421 TATGTCTATATACAATATT
1 TATGTCTATATACAATATT
*
4054440 TATGT-TATA-ACGATATT
1 TATGTCTATATACAATATT
4054457 T
1 T
4054458 TCATTTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 4 0.24
19 5 0.29
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (19 bp):
TATGTCTATATACAATATT
Found at i:4061903 original size:6 final size:6
Alignment explanation
Indices: 4061892--4061928 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
4061882 GACACATATT
4061892 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
4061929 GCCGAGCCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:4061936 original size:5 final size:5
Alignment explanation
Indices: 4061926--4062004 Score: 113
Period size: 5 Copynumber: 15.8 Consensus size: 5
4061916 ACCACGACCA
* * *
4061926 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
* *
4061976 CGAGC CGAGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
4062005 ACGGACGGAC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 71 1.00
ACGTcount: A:0.19, C:0.37, G:0.41, T:0.04
Consensus pattern (5 bp):
CGAGC
Found at i:4063326 original size:22 final size:22
Alignment explanation
Indices: 4063285--4063365 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
4063275 CTCGTATAAA
4063285 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
4063308 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
4063330 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
4063352 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
4063366 ATATAATGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 45 0.79
23 12 0.21
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:4063361 original size:13 final size:13
Alignment explanation
Indices: 4063299--4063361 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
4063289 CCGAAGTGCC
4063299 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
4063312 CC---GAAGTGC-
1 CCGTAGAATTGCA
4063321 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
4063334 CC---GAAGTGC-
1 CCGTAGAATTGCA
4063343 CCGTAGAATTGCA
1 CCGTAGAATTGCA
4063356 CCGTAG
1 CCGTAG
4063362 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:4064022 original size:2 final size:2
Alignment explanation
Indices: 4064015--4064058 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4064005 TCTCTTAAAC
4064015 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
4064057 AT
1 AT
4064059 TCACATGTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4065074 original size:21 final size:21
Alignment explanation
Indices: 4065050--4065094 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4065040 TCTTGTTCGT
* *
4065050 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
4065071 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
4065092 TTG
1 TTG
4065095 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:4068311 original size:22 final size:22
Alignment explanation
Indices: 4068270--4068350 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
4068260 CTCGTATAAA
4068270 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
4068293 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
4068315 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
4068337 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
4068351 ATATAATGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 45 0.79
23 12 0.21
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:4068346 original size:13 final size:13
Alignment explanation
Indices: 4068284--4068346 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
4068274 CCGAAGTGCC
4068284 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
4068297 CC---GAAGTGC-
1 CCGTAGAATTGCA
4068306 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
4068319 CC---GAAGTGC-
1 CCGTAGAATTGCA
4068328 CCGTAGAATTGCA
1 CCGTAGAATTGCA
4068341 CCGTAG
1 CCGTAG
4068347 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:4069008 original size:2 final size:2
Alignment explanation
Indices: 4069001--4069080 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
4068991 TCTCTTAAAC
4069001 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
4069043 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
4069081 CACATGTTTA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4070104 original size:21 final size:21
Alignment explanation
Indices: 4070080--4070124 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4070070 TCTTGTTCGT
* *
4070080 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
4070101 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
4070122 TTG
1 TTG
4070125 CACAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:4077834 original size:14 final size:15
Alignment explanation
Indices: 4077815--4077843 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4077805 AGTTTTCCAG
4077815 TTAATT-TCTATTTT
1 TTAATTGTCTATTTT
4077829 TTAATTGTCTATTTT
1 TTAATTGTCTATTTT
4077844 AATTAAGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.21, C:0.07, G:0.03, T:0.69
Consensus pattern (15 bp):
TTAATTGTCTATTTT
Found at i:4080115 original size:84 final size:84
Alignment explanation
Indices: 4079966--4080221 Score: 377
Period size: 84 Copynumber: 3.0 Consensus size: 84
4079956 ACCTTAGTCC
* * * * * * *
4079966 AAGTAAAGAGGAAAGAAGTTGAAGCTATTGATGGCTCAAATGGGGTCAACGGTGATCAAGATGCG
1 AAGTAAAGGGGAGAGAAGTTGAGGCTATTGATGGCTCGAATGGGGTAAACGGCGATCAAGCTGCG
4080031 GAATCTGAGAATCGATGTG
66 GAATCTGAGAATCGATGTG
* * * * *
4080050 AAGTAAAGGGGAGAGAAGTTGAGGCTATTGATGTCTTGAATGGGGTAAACTGCGTTCGAGCTGCG
1 AAGTAAAGGGGAGAGAAGTTGAGGCTATTGATGGCTCGAATGGGGTAAACGGCGATCAAGCTGCG
4080115 GAATCTGAGAATCGATGTG
66 GAATCTGAGAATCGATGTG
* *
4080134 ACGTAAAGGGGAGAGAAGTTGAGGCTAATGATGGCTCGAATGGGGTAAACGGCGATCAAGCTGCG
1 AAGTAAAGGGGAGAGAAGTTGAGGCTATTGATGGCTCGAATGGGGTAAACGGCGATCAAGCTGCG
*
4080199 GAATCTGAGAACCGATGTG
66 GAATCTGAGAATCGATGTG
4080218 AAGT
1 AAGT
4080222 TGAAAGACTT
Statistics
Matches: 151, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 151 1.00
ACGTcount: A:0.32, C:0.12, G:0.35, T:0.21
Consensus pattern (84 bp):
AAGTAAAGGGGAGAGAAGTTGAGGCTATTGATGGCTCGAATGGGGTAAACGGCGATCAAGCTGCG
GAATCTGAGAATCGATGTG
Found at i:4081521 original size:37 final size:38
Alignment explanation
Indices: 4081476--4081554 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 38
4081466 AATTGATTAT
4081476 TTCCTGTC-AAAAAATATTATTTTCATTGAGATAACCA
1 TTCCTGTCAAAAAAATATTATTTTCATTGAGATAACCA
4081513 TTCCTGTCAAAAAAAATATTATTTTCATTGAGATAACCA
1 TTCCTGTC-AAAAAAATATTATTTTCATTGAGATAACCA
4081552 TTC
1 TTC
4081555 AGTATCCCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 8 0.20
39 32 0.80
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (38 bp):
TTCCTGTCAAAAAAATATTATTTTCATTGAGATAACCA
Found at i:4082751 original size:282 final size:282
Alignment explanation
Indices: 4082234--4082787 Score: 822
Period size: 282 Copynumber: 2.0 Consensus size: 282
4082224 AATCGAGGGA
* * *
4082234 GTCAGGGGAGATCCTTTTAAGGCAACTTGAGCGTTCTACTCCTACAAAGCCTAGAAGTATTCGGG
1 GTCAGGGGAGATCCTTTTAAGGAAACTTAAGCGTTCTACTCCTACAAAGCCTAGAAGCATTCGGG
* * *
4082299 GGAATACATCCAAGAGGTTTACTCAAAGTGAGCCAAAACCAGATGGTATGTCCAAAGACCTAGAA
66 AGAATACATCCAAAAGGTTTACACAAAGTGAGCCAAAACCAGATGGTATGTCCAAAGACCTAGAA
* * * *
4082364 CTCGAGAAGCAAGAACAGAAGCTTCGAGAACCCGAAAAGCTCCCAGAATATGAATTAAAGGCCAA
131 CTCGAGAAGCAAGAAAAGAAGCTTCGAGAACCCGAAAAGCTCCCAAAATATGAAGTAAAGACCAA
** *
4082429 GAAAGCAAATTTTGGCGGTGAAAAGGCTGCTGTTTCCCCATCAATTAAAGTGAAAACCTCAATGA
196 GAAAGCAAATTTTGGCGGTGAAAAGGCAACTGTATCCCCATCAATTAAAGTGAAAACCTCAATGA
*
4082494 ATCAAGGGCACCAAGCGGGTTT
261 ATCAAGGACACCAAGCGGGTTT
* * * *
4082516 GTCAGGGGAGGTCCTTTTAAGGAAACTTAAGCGTTCTACTCCTACAAAGCCTAGAGGCCTTTGGG
1 GTCAGGGGAGATCCTTTTAAGGAAACTTAAGCGTTCTACTCCTACAAAGCCTAGAAGCATTCGGG
* * *
4082581 AGAATACATCTAAAAGGTTTACACAAAGTGAGCCAAAACCAGATGGTATTTCCAAAGATCTAGAA
66 AGAATACATCCAAAAGGTTTACACAAAGTGAGCCAAAACCAGATGGTATGTCCAAAGACCTAGAA
* *
4082646 CTCGAGAAGCAAGAAAAGCAGTTTCGAGAACCCGAAAAGC-CCCAAAAATATGAAGTAAAGACCA
131 CTCGAGAAGCAAGAAAAGAAGCTTCGAGAACCCGAAAAGCTCCC-AAAATATGAAGTAAAGACCA
* * * * **
4082710 AGCAAGGAAATTTTGGTGGTGATAAGGCAACTGTATCCCCATCAATTAAAGTGAAAGTCTCAATG
195 AGAAAGCAAATTTTGGCGGTGAAAAGGCAACTGTATCCCCATCAATTAAAGTGAAAACCTCAATG
*
4082775 GATCAAGGACACC
260 AATCAAGGACACC
4082788 GAATGGGCTT
Statistics
Matches: 241, Mismatches: 30, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
281 3 0.01
282 238 0.99
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (282 bp):
GTCAGGGGAGATCCTTTTAAGGAAACTTAAGCGTTCTACTCCTACAAAGCCTAGAAGCATTCGGG
AGAATACATCCAAAAGGTTTACACAAAGTGAGCCAAAACCAGATGGTATGTCCAAAGACCTAGAA
CTCGAGAAGCAAGAAAAGAAGCTTCGAGAACCCGAAAAGCTCCCAAAATATGAAGTAAAGACCAA
GAAAGCAAATTTTGGCGGTGAAAAGGCAACTGTATCCCCATCAATTAAAGTGAAAACCTCAATGA
ATCAAGGACACCAAGCGGGTTT
Found at i:4084185 original size:29 final size:29
Alignment explanation
Indices: 4084151--4084207 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
4084141 GGTGACTGAG
*
4084151 TTTAAATAATTTTTAACATATGGTGATAA
1 TTTAAATAATTTTTAACATATGATGATAA
* *
4084180 TTTAAATAGTTTTTAACATGTGATGATA
1 TTTAAATAATTTTTAACATATGATGATA
4084208 TGCATATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.46
Consensus pattern (29 bp):
TTTAAATAATTTTTAACATATGATGATAA
Found at i:4086479 original size:20 final size:20
Alignment explanation
Indices: 4086454--4086504 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
4086444 TCTGGTATGC
4086454 TGGGCCACTTGCTTTGTTCT
1 TGGGCCACTTGCTTTGTTCT
4086474 TGGGCCACTTGCTTTGTTCT
1 TGGGCCACTTGCTTTGTTCT
4086494 TGGGCCACTTG
1 TGGGCCACTTG
4086505 AAAAATGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.06, C:0.25, G:0.27, T:0.41
Consensus pattern (20 bp):
TGGGCCACTTGCTTTGTTCT
Found at i:4087516 original size:16 final size:16
Alignment explanation
Indices: 4087492--4087533 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
4087482 GATGTGAAGT
*
4087492 TGAAATTGACTCTGAA
1 TGAATTTGACTCTGAA
4087508 TGAATTTGACTCTGAA
1 TGAATTTGACTCTGAA
4087524 TGAATTTGAC
1 TGAATTTGAC
4087534 AATCAGTCGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (16 bp):
TGAATTTGACTCTGAA
Found at i:4088110 original size:14 final size:14
Alignment explanation
Indices: 4088091--4088117 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4088081 CGGTTGCATG
4088091 TCTGGAATCTTGAT
1 TCTGGAATCTTGAT
4088105 TCTGGAATCTTGA
1 TCTGGAATCTTGA
4088118 AATTCCAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (14 bp):
TCTGGAATCTTGAT
Found at i:4088736 original size:6 final size:6
Alignment explanation
Indices: 4088721--4088773 Score: 56
Period size: 6 Copynumber: 8.8 Consensus size: 6
4088711 ACCTACCTTA
* *
4088721 TTTTTC -TTTTC TTTTTC TTTTGTTC TTTTTC TCTTT- TTTCTC TTTTTC
1 TTTTTC TTTTTC TTTTTC -TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC
4088769 TTTTT
1 TTTTT
4088774 TTCCAATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 8 0.21
6 22 0.56
7 6 0.15
8 3 0.08
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:4088748 original size:8 final size:7
Alignment explanation
Indices: 4088727--4088774 Score: 62
Period size: 8 Copynumber: 6.6 Consensus size: 7
4088717 CTTATTTTTC
4088727 TTTTC-T
1 TTTTCTT
4088733 TTTTCTT
1 TTTTCTT
4088740 TTGTTCTT
1 TT-TTCTT
4088748 TTTCTCTT
1 TTT-TCTT
4088756 TTTTCTCT
1 TTTTCT-T
4088764 TTTTCTT
1 TTTTCTT
4088771 TTTT
1 TTTT
4088775 TCCAATTTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
6 5 0.13
7 12 0.32
8 21 0.55
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (7 bp):
TTTTCTT
Found at i:4088761 original size:15 final size:15
Alignment explanation
Indices: 4088727--4088774 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
4088717 CTTATTTTTC
4088727 TTTTCTTTTTCT-TT
1 TTTTCTTTTTCTCTT
*
4088741 TGTTCTTTTTCTCTT
1 TTTTCTTTTTCTCTT
4088756 TTTTCTCTTTT-TCTT
1 TTTTCT-TTTTCTCTT
4088771 TTTT
1 TTTT
4088775 TCCAATTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 11 0.37
15 15 0.50
16 4 0.13
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (15 bp):
TTTTCTTTTTCTCTT
Found at i:4088774 original size:25 final size:25
Alignment explanation
Indices: 4088721--4088773 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
4088711 ACCTACCTTA
*
4088721 TTTTTCTTTTCTTTTTCTTTTGTTC
1 TTTTTCTTTTCTTTCTCTTTTGTTC
4088746 TTTTTCTCTTT-TTTCTC-TTT-TTC
1 TTTTTCT-TTTCTTTCTCTTTTGTTC
4088769 TTTTT
1 TTTTT
4088774 TTCCAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 8 0.31
24 3 0.12
25 12 0.46
26 3 0.12
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (25 bp):
TTTTTCTTTTCTTTCTCTTTTGTTC
Found at i:4105353 original size:13 final size:16
Alignment explanation
Indices: 4105311--4105351 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
4105301 GATTGAGATA
4105311 TAATAATATCATATTT
1 TAATAATATCATATTT
4105327 TAATAATATCATATTT
1 TAATAATATCATATTT
4105343 TAATAATAT
1 TAATAATAT
4105352 ATAGTGACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATAATATCATATTT
Found at i:4124143 original size:12 final size:12
Alignment explanation
Indices: 4124126--4124155 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
4124116 TAAATTAATT
4124126 TAAATCTTATTA
1 TAAATCTTATTA
4124138 TAAATCTTATTA
1 TAAATCTTATTA
4124150 TAAATC
1 TAAATC
4124156 AATAGTCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (12 bp):
TAAATCTTATTA
Found at i:4125633 original size:3 final size:3
Alignment explanation
Indices: 4125625--4125669 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
4125615 TTGTTTAAAG
4125625 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4125670 TAAAGAGATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4128141 original size:15 final size:14
Alignment explanation
Indices: 4128122--4128148 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4128112 AACAAACACA
4128122 AAAAAAAAGAAACG
1 AAAAAAAAGAAACG
4128136 AAAAAAAAGAAAC
1 AAAAAAAAGAAAC
4128149 TTGACATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.07, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAACG
Done.