Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004117.1 Hibiscus syriacus cultivar Beakdansim tig00009009_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: 2456583
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 7 of 9
Found at i:1755347 original size:30 final size:30
Alignment explanation
Indices: 1755313--1755385 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
1755303 CTCGTAGGAC
*
1755313 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAGAGGTCATAAAGAACCTCGACAA
1755343 CTATCCAGAGGTCATAAAGAACCTCGACAA
1 CTATCCAGAGGTCATAAAGAACCTCGACAA
*
1755373 CTATCCATAGGTC
1 CTATCCAGAGGTC
1755386 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGAACCTCGACAA
Found at i:1755393 original size:30 final size:30
Alignment explanation
Indices: 1755313--1755396 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 30
1755303 CTCGTAGGAC
* *
1755313 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGACAA
*
1755343 CTATCCAGAGGTCATAAAGAACCTCGACAA
1 CTATCCAGAGGTCACAAAGAACCTCGACAA
* * *
1755373 CTATCCATAGGTCCCGAAGAACCT
1 CTATCCAGAGGTCACAAAGAACCT
1755397 AGGTAAACTG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.36, C:0.29, G:0.18, T:0.18
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGACAA
Found at i:1756194 original size:20 final size:20
Alignment explanation
Indices: 1756169--1756206 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1756159 CTTTGAAATA
1756169 TTAATGCATCGATGCACCCC
1 TTAATGCATCGATGCACCCC
1756189 TTAATGCATCGATGCACC
1 TTAATGCATCGATGCACC
1756207 TTCAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (20 bp):
TTAATGCATCGATGCACCCC
Found at i:1756245 original size:21 final size:21
Alignment explanation
Indices: 1756221--1756293 Score: 137
Period size: 21 Copynumber: 3.5 Consensus size: 21
1756211 AAATTTGTCT
1756221 TAGTGCATCGGTACATACTCA
1 TAGTGCATCGGTACATACTCA
1756242 TAGTGCATCGGTACATACTCA
1 TAGTGCATCGGTACATACTCA
1756263 TAGTGCATCGGTACATACTCA
1 TAGTGCATCGGTACATACTCA
*
1756284 TAGTGTATCG
1 TAGTGCATCG
1756294 ATGCACCTGC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (21 bp):
TAGTGCATCGGTACATACTCA
Found at i:1758256 original size:3 final size:3
Alignment explanation
Indices: 1758248--1758315 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
1758238 GTAATAGGTG
*
1758248 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1758296 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
1758316 TTTTTTTAGA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1758851 original size:152 final size:152
Alignment explanation
Indices: 1758575--1758879 Score: 556
Period size: 152 Copynumber: 2.0 Consensus size: 152
1758565 TTGAATATCG
* *
1758575 GGATTGTGTTTGTAAACTAGCCGCAGCTAGTGTTCGTATCATATTTGTATTTTGGTTTGTATTAA
1 GGATTGTGTTTGTAAACTAGCCACAGCTAGTGTTCGTATCATATTTGTATTTTGGTTCGTATTAA
1758640 TAATAGCGTGCGAGTTAAAAAATTACCGAAAGCCCATTCACGCTTCCAACAATAAAAATATAAAA
66 TAATAGCGTGCGAGTTAAAAAATTACCGAAAGCCCATTCACGCTTCCAACAATAAAAATATAAAA
*
1758705 TAAATATCATTTCAACTCAAAT
131 TAAATATCATTTAAACTCAAAT
*
1758727 GGATTGTGTTTGTAAACTAGCCACAGCTAGTGTTCGTATCGTATTTGTATTTTGGTTCGTATTAA
1 GGATTGTGTTTGTAAACTAGCCACAGCTAGTGTTCGTATCATATTTGTATTTTGGTTCGTATTAA
* *
1758792 TAATAGCGTGTGAGTTATAAAATTACCGAAAGCCCATTCACGCTTCCAACAATAAAAATATAAAA
66 TAATAGCGTGCGAGTTAAAAAATTACCGAAAGCCCATTCACGCTTCCAACAATAAAAATATAAAA
1758857 TAAATATCATTTAAACTCAAAT
131 TAAATATCATTTAAACTCAAAT
1758879 G
1 G
1758880 TCTTGCAAGT
Statistics
Matches: 147, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 147 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (152 bp):
GGATTGTGTTTGTAAACTAGCCACAGCTAGTGTTCGTATCATATTTGTATTTTGGTTCGTATTAA
TAATAGCGTGCGAGTTAAAAAATTACCGAAAGCCCATTCACGCTTCCAACAATAAAAATATAAAA
TAAATATCATTTAAACTCAAAT
Found at i:1760041 original size:14 final size:14
Alignment explanation
Indices: 1760022--1760058 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1760012 CATTTAAATG
1760022 ATGAACGAACACAA
1 ATGAACGAACACAA
*
1760036 ATGAACGAACATAA
1 ATGAACGAACACAA
*
1760050 ACGAACGAA
1 ATGAACGAA
1760059 TGTAAATGAA
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:0.57, C:0.19, G:0.16, T:0.08
Consensus pattern (14 bp):
ATGAACGAACACAA
Found at i:1760357 original size:14 final size:14
Alignment explanation
Indices: 1760338--1760405 Score: 65
Period size: 14 Copynumber: 5.1 Consensus size: 14
1760328 GAGATTGAGC
*
1760338 CAAACATAAATGAA
1 CAAACATAAACGAA
1760352 CAAACATAAACGAA
1 CAAACATAAACGAA
*
1760366 CGAAA-GT--A--AA
1 C-AAACATAAACGAA
*
1760376 CAAACATAAATGAA
1 CAAACATAAACGAA
1760390 CAAACATAAACGAA
1 CAAACATAAACGAA
1760404 CA
1 CA
1760406 TATTATCGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
9 3 0.07
10 4 0.09
12 2 0.05
14 32 0.73
15 3 0.07
ACGTcount: A:0.63, C:0.18, G:0.09, T:0.10
Consensus pattern (14 bp):
CAAACATAAACGAA
Found at i:1760382 original size:24 final size:24
Alignment explanation
Indices: 1760350--1760407 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
1760340 AACATAAATG
*
1760350 AACAAACATAAACGAACGAAA-GTA
1 AACAAACATAAACGAAC-AAACATA
*
1760374 AACAAACATAAATGAACAAACATA
1 AACAAACATAAACGAACAAACATA
*
1760398 AACGAACATA
1 AACAAACATA
1760408 TTATCGAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 3 0.10
24 27 0.90
ACGTcount: A:0.64, C:0.17, G:0.09, T:0.10
Consensus pattern (24 bp):
AACAAACATAAACGAACAAACATA
Found at i:1760632 original size:33 final size:33
Alignment explanation
Indices: 1760595--1760663 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1760585 TAATAAGTAA
1760595 CAAATGATACTGATTGATGAATATGTCTAATTC
1 CAAATGATACTGATTGATGAATATGTCTAATTC
1760628 CAAATGATACTGATTGATGAATATGTCTAATTC
1 CAAATGATACTGATTGATGAATATGTCTAATTC
1760661 CAA
1 CAA
1760664 TCAAAATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (33 bp):
CAAATGATACTGATTGATGAATATGTCTAATTC
Found at i:1762236 original size:16 final size:16
Alignment explanation
Indices: 1762215--1762250 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1762205 GAATTTAAGC
*
1762215 ATCATGTTCATGTGTA
1 ATCATGTTCATGTGGA
1762231 ATCATGTTCATGTGGA
1 ATCATGTTCATGTGGA
1762247 ATCA
1 ATCA
1762251 AAGAAGCGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (16 bp):
ATCATGTTCATGTGGA
Found at i:1768324 original size:13 final size:13
Alignment explanation
Indices: 1768306--1768358 Score: 79
Period size: 13 Copynumber: 3.8 Consensus size: 13
1768296 GTAAACGAAC
1768306 ATAAATGAACACA
1 ATAAATGAACACA
1768319 ATAAATGAACACAA
1 ATAAATGAACAC-A
1768333 ATGTAAATGAACACA
1 A--TAAATGAACACA
1768348 ATAAATGAACA
1 ATAAATGAACA
1768359 TAAACGAACG
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
13 22 0.59
14 2 0.05
15 2 0.05
16 11 0.30
ACGTcount: A:0.60, C:0.13, G:0.09, T:0.17
Consensus pattern (13 bp):
ATAAATGAACACA
Found at i:1768406 original size:10 final size:10
Alignment explanation
Indices: 1768348--1768392 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
1768338 AATGAACACA
*
1768348 ATAAATGAAC
1 ATAAACGAAC
1768358 ATAAACGAAC
1 ATAAACGAAC
*
1768368 GTAAACGAAC
1 ATAAACGAAC
*
1768378 ATAAATGAAC
1 ATAAACGAAC
1768388 A-AAAC
1 ATAAAC
1768393 AAACGAACAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 3 0.10
10 27 0.90
ACGTcount: A:0.60, C:0.16, G:0.11, T:0.13
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1768849 original size:33 final size:33
Alignment explanation
Indices: 1768812--1768880 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1768802 TAATAAGTAA
1768812 CAAATGATACTGATTGATGAATATGTCTAATTC
1 CAAATGATACTGATTGATGAATATGTCTAATTC
1768845 CAAATGATACTGATTGATGAATATGTCTAATTC
1 CAAATGATACTGATTGATGAATATGTCTAATTC
1768878 CAA
1 CAA
1768881 TCAAAATTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (33 bp):
CAAATGATACTGATTGATGAATATGTCTAATTC
Found at i:1772807 original size:7 final size:7
Alignment explanation
Indices: 1772791--1772828 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
1772781 GTCAAAGAAA
*
1772791 GTCAATG
1 GTCAACG
1772798 GTCAACG
1 GTCAACG
1772805 GTCAACG
1 GTCAACG
1772812 GTCAACG
1 GTCAACG
1772819 GTCAACG
1 GTCAACG
1772826 GTC
1 GTC
1772829 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:1772835 original size:5 final size:5
Alignment explanation
Indices: 1772825--1772887 Score: 72
Period size: 5 Copynumber: 11.8 Consensus size: 5
1772815 AACGGTCAAC
* *
1772825 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
1772874 GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC
1772888 AACGGTCGAG
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
5 42 0.84
7 8 0.16
ACGTcount: A:0.06, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:1772846 original size:22 final size:22
Alignment explanation
Indices: 1772818--1772904 Score: 165
Period size: 22 Copynumber: 4.0 Consensus size: 22
1772808 AACGGTCAAC
1772818 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1772840 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1772862 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
1772884 GGTCAACGGTCGAGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
1772905 AGACCGGTCA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 64 1.00
ACGTcount: A:0.10, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:1772919 original size:9 final size:9
Alignment explanation
Indices: 1772901--1772999 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
1772891 GGTCGAGTCG
*
1772901 GGTCAGACC
1 GGTCAAACC
1772910 GGTCAAACC
1 GGTCAAACC
* *
1772919 GATTCAGACC
1 G-GTCAAACC
1772929 GGTCAAACC
1 GGTCAAACC
*
1772938 GGTTCGAACC
1 GG-TCAAACC
*
1772948 GGTTGAAACC
1 GG-TCAAACC
1772958 GGTCAAACC
1 GGTCAAACC
1772967 GGTCAGAACC
1 GGTCA-AACC
*
1772977 GGTTGAAAACC
1 GG-T-CAAACC
*
1772988 GGTTAAACC
1 GGTCAAACC
1772997 GGT
1 GGT
1773000 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1772958 original size:29 final size:31
Alignment explanation
Indices: 1772926--1773000 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
1772916 ACCGATTCAG
1772926 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
1772955 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
1772985 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
1773001 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:1772978 original size:19 final size:19
Alignment explanation
Indices: 1772901--1772999 Score: 80
Period size: 19 Copynumber: 5.2 Consensus size: 19
1772891 GGTCGAGTCG
1772901 GGTCAG-ACCGGTCAAACC
1 GGTCAGAACCGGTCAAACC
*
1772919 GATTCAG-ACCGGTCAAACC
1 G-GTCAGAACCGGTCAAACC
*
1772938 GGTTC-GAACCGGTTGAAACC
1 GG-TCAGAACCGG-TCAAACC
1772958 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
* * *
1772977 GGTTGAAAACCGGTTAAACC
1 GG-TCAGAACCGGTCAAACC
1772997 GGT
1 GGT
1773000 TTCCAGCAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.06
19 39 0.58
20 16 0.24
21 8 0.12
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:1780170 original size:7 final size:7
Alignment explanation
Indices: 1780154--1780191 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
1780144 GTCAAAGAAA
*
1780154 GTCAATG
1 GTCAACG
1780161 GTCAACG
1 GTCAACG
1780168 GTCAACG
1 GTCAACG
1780175 GTCAACG
1 GTCAACG
1780182 GTCAACG
1 GTCAACG
1780189 GTC
1 GTC
1780192 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:1780198 original size:5 final size:5
Alignment explanation
Indices: 1780188--1780269 Score: 83
Period size: 5 Copynumber: 15.2 Consensus size: 5
1780178 AACGGTCAAC
* *
1780188 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
1780237 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG G
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG G
1780270 ACCGGTCAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
5 53 0.82
7 12 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.18
Consensus pattern (5 bp):
GGTCG
Found at i:1780209 original size:22 final size:22
Alignment explanation
Indices: 1780181--1780269 Score: 178
Period size: 22 Copynumber: 4.0 Consensus size: 22
1780171 AACGGTCAAC
1780181 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1780203 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1780225 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1780247 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1780269 G
1 G
1780270 ACCGGTCAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 67 1.00
ACGTcount: A:0.09, C:0.22, G:0.51, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:1780213 original size:17 final size:15
Alignment explanation
Indices: 1780187--1780267 Score: 63
Period size: 17 Copynumber: 5.0 Consensus size: 15
1780177 CAACGGTCAA
1780187 CGGTCGGGTCGGGTC
1 CGGTCGGGTCGGGTC
* *
1780202 GGGTCAACGGTCGGGTC
1 CGGTC--GGGTCGGGTC
* *
1780219 GGGTCGGGTCAACGGTC
1 CGGTCGGGTC--GGGTC
*
1780236 GGGTCGGGTCGGGTC
1 CGGTCGGGTCGGGTC
1780251 AACGGTCGGGTCGGGTC
1 --CGGTCGGGTCGGGTC
1780268 GGACCGGTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
15 12 0.22
17 42 0.78
ACGTcount: A:0.07, C:0.23, G:0.51, T:0.19
Consensus pattern (15 bp):
CGGTCGGGTCGGGTC
Found at i:1780304 original size:29 final size:31
Alignment explanation
Indices: 1780270--1780344 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
1780260 GTCGGGTCGG
1780270 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
1780299 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
1780329 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
1780345 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:1780344 original size:9 final size:9
Alignment explanation
Indices: 1780270--1780344 Score: 69
Period size: 9 Copynumber: 7.8 Consensus size: 9
1780260 GTCGGGTCGG
*
1780270 ACCGGTCAA
1 ACCGGTTAA
*
1780279 ACCGGTTCGA
1 ACCGGTT-AA
1780289 ACCGGTTGAA
1 ACCGGTT-AA
*
1780299 ACCGGTCAA
1 ACCGGTTAA
*
1780308 ACCGGTCAGA
1 ACCGGTTA-A
1780318 ACCGGTTGAAA
1 ACCGGTT--AA
1780329 ACCGGTTAA
1 ACCGGTTAA
1780338 ACCGGTT
1 ACCGGTT
1780345 TCCAGCAGCC
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
9 25 0.45
10 22 0.39
11 8 0.14
12 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:1784869 original size:60 final size:60
Alignment explanation
Indices: 1784800--1784927 Score: 175
Period size: 60 Copynumber: 2.1 Consensus size: 60
1784790 ATAGTCAAGT
** * * *
1784800 GACCATTTTGTAACTTTTAATTGTTAGGGGACTCAACAAAGCAATACCCTATAGTTAAGG
1 GACCATTTTGTAACTTTTAATAATCAGGGGACTCAACAAAACAATACCCTATAATTAAGG
* * * *
1784860 GATCATTTTGTAATTTTTAATAATCGGGGGACTCAACAAAACAATACCCTATAATTAGGG
1 GACCATTTTGTAACTTTTAATAATCAGGGGACTCAACAAAACAATACCCTATAATTAAGG
1784920 GACCATTT
1 GACCATTT
1784928 GTGTGTTTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAATCAGGGGACTCAACAAAACAATACCCTATAATTAAGG
Found at i:1787584 original size:24 final size:24
Alignment explanation
Indices: 1787556--1787602 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1787546 GATCAACAAT
*
1787556 AATCAGATCCAGAATCAAGTTCAA
1 AATCAAATCCAGAATCAAGTTCAA
*
1787580 AATCAAATTCAGAATCAAGTTCA
1 AATCAAATCCAGAATCAAGTTCA
1787603 GGCGAATCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.23
Consensus pattern (24 bp):
AATCAAATCCAGAATCAAGTTCAA
Found at i:1787603 original size:12 final size:12
Alignment explanation
Indices: 1787565--1787603 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1787555 TAATCAGATC
1787565 CAGAATCAAGTT
1 CAGAATCAAGTT
* *
1787577 CAAAATCAAATT
1 CAGAATCAAGTT
1787589 CAGAATCAAGTT
1 CAGAATCAAGTT
1787601 CAG
1 CAG
1787604 GCGAATCCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (12 bp):
CAGAATCAAGTT
Found at i:1794914 original size:34 final size:32
Alignment explanation
Indices: 1794875--1794969 Score: 93
Period size: 34 Copynumber: 2.8 Consensus size: 32
1794865 TACTCAAACT
1794875 AAATATCTTTTAATATTCAAATTTAAACAGATA
1 AAATATCTTTTAATATTCAAATTTAAA-AGATA
*
1794908 ATAATATCTTTTAAT-TTGAAATATTCAAAAGATA
1 A-AATATCTTTTAATATTCAAAT-TT-AAAAGATA
* * * *
1794942 AAGTCACCTTTTACTATTCAAACTTAAA
1 AAAT-ATCTTTTAATATTCAAATTTAAA
1794970 TATATATTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
33 12 0.24
34 31 0.61
35 8 0.16
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (32 bp):
AAATATCTTTTAATATTCAAATTTAAAAGATA
Found at i:1800041 original size:35 final size:35
Alignment explanation
Indices: 1799968--1800042 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
1799958 CGTCACGTCC
* **
1799968 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCCAGGAACCGCCA
*
1800003 AGTAAGGCCCTGAGCACACAGCCCAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCCAGGAACCGCCA
1800038 AGTAA
1 AGTAA
1800043 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.31, G:0.27, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCCAGGAACCGCCA
Found at i:1800147 original size:24 final size:24
Alignment explanation
Indices: 1800120--1800210 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
1800110 CATAATTCAA
*
1800120 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAC
* * *
1800144 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAC
1800168 GTCAA-TATCATATCAGAATCCAC
1 GTCAAGTATCATATCAGAATCCAC
* *
1800191 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCATATCAGAAT
1800211 TCAAATTTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 20 0.34
24 38 0.66
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAC
Found at i:1800200 original size:47 final size:48
Alignment explanation
Indices: 1800120--1800210 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
1800110 CATAATTCAA
* * *
1800120 GTCAAGTATCATATCAGAATCCAGGTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCACGTCAGGTATCAGAACAGAATCCAT
*
1800168 GTCAA-TATCATATCAGAATCCACGTCAGGTATCATAACAGAAT
1 GTCAAGTATCATATCAGAATCCACGTCAGGTATCAGAACAGAAT
1800211 TCAAATTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.26
Consensus pattern (48 bp):
GTCAAGTATCATATCAGAATCCACGTCAGGTATCAGAACAGAATCCAT
Found at i:1801807 original size:63 final size:63
Alignment explanation
Indices: 1801708--1801830 Score: 246
Period size: 63 Copynumber: 2.0 Consensus size: 63
1801698 TGCTTTCTTG
1801708 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
1801771 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
1801831 CCTAGGATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (63 bp):
AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
Found at i:1801908 original size:17 final size:18
Alignment explanation
Indices: 1801876--1801912 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1801866 TAAAACTAAC
1801876 ATTTTTATGCACATCAAT
1 ATTTTTATGCACATCAAT
*
1801894 ATTTTTAT-CAGATCAAT
1 ATTTTTATGCACATCAAT
1801911 AT
1 AT
1801913 GTCTGTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (18 bp):
ATTTTTATGCACATCAAT
Found at i:1802763 original size:8 final size:8
Alignment explanation
Indices: 1802740--1802784 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
1802730 GGTCAATAGT
1802740 GGTCAACG
1 GGTCAACG
1802748 CCGGTCAACG
1 --GGTCAACG
1802758 GGTCAAC-
1 GGTCAACG
*
1802765 GATCAACG
1 GGTCAACG
1802773 GGTCAACG
1 GGTCAACG
1802781 GGTC
1 GGTC
1802785 GGGTCAACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 6 0.19
8 18 0.56
10 8 0.25
ACGTcount: A:0.24, C:0.29, G:0.33, T:0.13
Consensus pattern (8 bp):
GGTCAACG
Found at i:1802772 original size:15 final size:15
Alignment explanation
Indices: 1802752--1802780 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1802742 TCAACGCCGG
1802752 TCAACGGGTCAACGA
1 TCAACGGGTCAACGA
1802767 TCAACGGGTCAACG
1 TCAACGGGTCAACG
1802781 GGTCGGGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.14
Consensus pattern (15 bp):
TCAACGGGTCAACGA
Found at i:1802789 original size:13 final size:13
Alignment explanation
Indices: 1802771--1802833 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 13
1802761 CAACGATCAA
1802771 CGGGTCAACGGGT
1 CGGGTCAACGGGT
1802784 CGGGTCAACGGATCGGGT
1 CGGGTC-A---A-CGGGT
*
1802802 CGGGTCAACGAGT
1 CGGGTCAACGGGT
*
1802815 CGGGTAAACGGGT
1 CGGGTCAACGGGT
1802828 CGGGTC
1 CGGGTC
1802834 GGGTTATGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 26 0.63
14 2 0.05
17 2 0.05
18 11 0.27
ACGTcount: A:0.17, C:0.22, G:0.44, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:1802809 original size:31 final size:31
Alignment explanation
Indices: 1802771--1802837 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
1802761 CAACGATCAA
* *
1802771 CGGGTCAACGGGTCGGGTCAACGGATCGGGT
1 CGGGTCAACGAGTCGGGTAAACGGATCGGGT
*
1802802 CGGGTCAACGAGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGAGTCGGGTAAACGGATCGGGT
1802833 CGGGT
1 CGGGT
1802838 TATGACCGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.16
Consensus pattern (31 bp):
CGGGTCAACGAGTCGGGTAAACGGATCGGGT
Found at i:1803745 original size:12 final size:12
Alignment explanation
Indices: 1803728--1803752 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1803718 TGAATTTTAA
1803728 GATTTTACAAAT
1 GATTTTACAAAT
1803740 GATTTTACAAAT
1 GATTTTACAAAT
1803752 G
1 G
1803753 TATATTCGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (12 bp):
GATTTTACAAAT
Found at i:1803949 original size:21 final size:21
Alignment explanation
Indices: 1803923--1803962 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1803913 TTTTTAAAGG
1803923 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
1803944 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
1803963 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:1804051 original size:64 final size:65
Alignment explanation
Indices: 1803924--1804087 Score: 190
Period size: 64 Copynumber: 2.5 Consensus size: 65
1803914 TTTTAAAGGC
*
1803924 ATGCACCGATGCA-TCAATACCATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGCA
1 ATGCACCGATGCACTC--T-CCATGCATCGATGCACTC-ATGAATAAATTAAAACATCGAATGCA
1803987 TTCA
62 TTCA
* * **
1803991 ATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTTG
1 ATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTCA
* ***
1804055 ATGCATCGATGCACAAGCCATGCATCGATGCAC
1 ATGCACCGATGCACTCTCCATGCATCGATGCAC
1804088 CAGGCTATTT
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 53 0.62
65 15 0.17
66 3 0.03
67 13 0.15
68 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (65 bp):
ATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTCA
Found at i:1804105 original size:64 final size:63
Alignment explanation
Indices: 1803973--1804133 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
1803963 GAATAAATTG
* * *** *
1803973 AAACATCGAATGCATTCAATGCACCGATGCACTCTCCATGCATCGATGCACTCTGATTTAATTA
1 AAACATCGAATGCATTTAATGCATCGATGCACAAGCCATGCATCGATGCACGCTGATTT-ATTA
*
1804037 AAACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACCAGGCT-ATTT-TT
1 AAACATCGAATGCATTTAATGCATCGATGCACAAGCCATGCATCGATGCA-C--GCTGATTTATT
*
1804100 C
63 A
*
1804101 AAACATCGAATGCATTTCATGCATCGATGCACA
1 AAACATCGAATGCATTTAATGCATCGATGCACA
1804134 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
64 78 0.92
65 1 0.01
66 4 0.05
67 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (63 bp):
AAACATCGAATGCATTTAATGCATCGATGCACAAGCCATGCATCGATGCACGCTGATTTATTA
Found at i:1809979 original size:24 final size:22
Alignment explanation
Indices: 1809947--1810027 Score: 85
Period size: 24 Copynumber: 3.6 Consensus size: 22
1809937 CATTTAACAA
1809947 TGCATCGATGCATCCCTTTGAAGG
1 TGCATCGATGCATCCC-TTGAA-G
*
1809971 TGCATCGATGCATCCACATG-A-
1 TGCATCGATGCATCC-CTTGAAG
* *
1809992 TGCACCGATGCATGCCTTGAATG
1 TGCATCGATGCATCCCTTGAA-G
1810015 TGCATCGATGCAT
1 TGCATCGATGCAT
1810028 GAGGCCATGC
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 3 0.06
21 14 0.29
23 13 0.27
24 17 0.35
25 1 0.02
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (22 bp):
TGCATCGATGCATCCCTTGAAG
Found at i:1809982 original size:44 final size:44
Alignment explanation
Indices: 1809927--1810027 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 44
1809917 CTGTGCTTTA
* * *
1809927 TGCACCGATGCATTTAACA-ATGCATCGATGCATCCCTTTGAAGG
1 TGCATCGATGCATTCAACAGATGCACCGATGCATCCC-TTGAAGG
* * *
1809971 TGCATCGATGCA-TCCACATGATGCACCGATGCATGCCTTGAATG
1 TGCATCGATGCATTCAACA-GATGCACCGATGCATCCCTTGAAGG
1810015 TGCATCGATGCAT
1 TGCATCGATGCAT
1810028 GAGGCCATGC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
43 4 0.08
44 29 0.60
45 15 0.31
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (44 bp):
TGCATCGATGCATTCAACAGATGCACCGATGCATCCCTTGAAGG
Found at i:1810770 original size:21 final size:21
Alignment explanation
Indices: 1810730--1810774 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1810720 AAAACCGTCC
*
1810730 TCCCGTTCCTCAACATCCTAA
1 TCCCGTTCCTCAACAACCTAA
**
1810751 TCCCGTTCCTCCCCAACCTAA
1 TCCCGTTCCTCAACAACCTAA
1810772 TCC
1 TCC
1810775 TAATCCTCAT
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:0.20, C:0.49, G:0.04, T:0.27
Consensus pattern (21 bp):
TCCCGTTCCTCAACAACCTAA
Found at i:1812478 original size:12 final size:12
Alignment explanation
Indices: 1812461--1812485 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1812451 TGAATTTTAA
1812461 GATTTTACAAAT
1 GATTTTACAAAT
1812473 GATTTTACAAAT
1 GATTTTACAAAT
1812485 G
1 G
1812486 TATATTCGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (12 bp):
GATTTTACAAAT
Found at i:1812682 original size:21 final size:21
Alignment explanation
Indices: 1812656--1812695 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1812646 TTTTTAAAGG
1812656 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
1812677 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
1812696 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:1812784 original size:64 final size:65
Alignment explanation
Indices: 1812657--1812820 Score: 190
Period size: 64 Copynumber: 2.5 Consensus size: 65
1812647 TTTTAAAGGC
*
1812657 ATGCACCGATGCA-TCAATACCATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGCA
1 ATGCACCGATGCACTC--T-CCATGCATCGATGCACTC-ATGAATAAATTAAAACATCGAATGCA
1812720 TTCA
62 TTCA
* * **
1812724 ATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTTG
1 ATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTCA
* ***
1812788 ATGCATCGATGCACAAGCCATGCATCGATGCAC
1 ATGCACCGATGCACTCTCCATGCATCGATGCAC
1812821 CAGGCTATTT
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 53 0.62
65 15 0.17
66 3 0.03
67 13 0.15
68 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (65 bp):
ATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTCA
Found at i:1812838 original size:64 final size:63
Alignment explanation
Indices: 1812706--1812866 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
1812696 GAATAAATTG
* * *** *
1812706 AAACATCGAATGCATTCAATGCACCGATGCACTCTCCATGCATCGATGCACTCTGATTTAATTA
1 AAACATCGAATGCATTTAATGCATCGATGCACAAGCCATGCATCGATGCACGCTGATTT-ATTA
*
1812770 AAACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACCAGGCT-ATTT-TT
1 AAACATCGAATGCATTTAATGCATCGATGCACAAGCCATGCATCGATGCA-C--GCTGATTTATT
*
1812833 C
63 A
*
1812834 AAACATCGAATGCATTTCATGCATCGATGCACA
1 AAACATCGAATGCATTTAATGCATCGATGCACA
1812867 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
64 78 0.92
65 1 0.01
66 4 0.05
67 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (63 bp):
AAACATCGAATGCATTTAATGCATCGATGCACAAGCCATGCATCGATGCACGCTGATTTATTA
Found at i:1812955 original size:22 final size:22
Alignment explanation
Indices: 1812924--1812981 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
1812914 TTTTACACTG
*
1812924 ATGCACCGATGCATCCTTCATC
1 ATGCATCGATGCATCCTTCATC
1812946 ATGCATCGATGCATCCTTCATC
1 ATGCATCGATGCATCCTTCATC
1812968 ATGCATCGATGCAT
1 ATGCATCGATGCAT
1812982 GAGACGCTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (22 bp):
ATGCATCGATGCATCCTTCATC
Found at i:1814760 original size:35 final size:35
Alignment explanation
Indices: 1814687--1814761 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
1814677 CGTCACATCC
* **
1814687 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCCAGGAACCGCCA
*
1814722 AGTAAGGCCCTGAGCACACAGCCCAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCCAGGAACCGCCA
1814757 AGTAA
1 AGTAA
1814762 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.31, G:0.27, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCCAGGAACCGCCA
Found at i:1814866 original size:24 final size:24
Alignment explanation
Indices: 1814839--1814929 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
1814829 CATAATTCAA
*
1814839 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
1814863 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
1814887 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
1814910 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
1814930 TCAAATTTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.36
24 37 0.64
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:1814909 original size:47 final size:48
Alignment explanation
Indices: 1814839--1814929 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
1814829 CATAATTCAA
* * *
1814839 GTCAAGTATCATATCAGAATCCAGGTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
*
1814887 GTCAA-TATCAGATCAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAAT
1814930 TCAAATTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
Found at i:1816507 original size:63 final size:63
Alignment explanation
Indices: 1816429--1816554 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
1816419 CTTTCTTGAA
*
1816429 CACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCTAG
1 CACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTCCTAG
1816492 CACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTCCTAG
1 CACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTCCTAG
1816555 GATTAAAACC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.25, C:0.29, G:0.11, T:0.34
Consensus pattern (63 bp):
CACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTCCTAG
Found at i:1817504 original size:13 final size:13
Alignment explanation
Indices: 1817486--1817544 Score: 64
Period size: 13 Copynumber: 4.2 Consensus size: 13
1817476 GGGTCAACGA
1817486 TCAACGGGTCGGG
1 TCAACGGGTCGGG
1817499 TCAACGGGTCGGG
1 TCAACGGGTCGGG
*
1817512 TCGGGTTAACGGGTCAGG
1 TC-----AACGGGTCGGG
1817530 TCAACGGGTCGGG
1 TCAACGGGTCGGG
1817543 TC
1 TC
1817545 GGGTCGGGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 27 0.69
18 12 0.31
ACGTcount: A:0.15, C:0.22, G:0.44, T:0.19
Consensus pattern (13 bp):
TCAACGGGTCGGG
Found at i:1817513 original size:18 final size:18
Alignment explanation
Indices: 1817490--1817549 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
1817480 CAACGATCAA
1817490 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
1817508 CGGGTCGGGTTAA-----
1 CGGGTCGGGTCAACGGGT
*
1817521 CGGGTCAGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1817539 CGGGTCGGGTC
1 CGGGTCGGGTC
1817550 GGGTTATGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
13 11 0.33
18 22 0.67
ACGTcount: A:0.12, C:0.22, G:0.48, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1817526 original size:31 final size:31
Alignment explanation
Indices: 1817488--1817548 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
1817478 GTCAACGATC
*
1817488 AACGGGTCGGGTCAACGGGTCGGGTCGGGTT
1 AACGGGTCAGGTCAACGGGTCGGGTCGGGTT
1817519 AACGGGTCAGGTCAACGGGTCGGGTCGGGT
1 AACGGGTCAGGTCAACGGGTCGGGTCGGGT
1817549 CGGGTTATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.20, G:0.48, T:0.18
Consensus pattern (31 bp):
AACGGGTCAGGTCAACGGGTCGGGTCGGGTT
Found at i:1819572 original size:35 final size:35
Alignment explanation
Indices: 1819463--1819563 Score: 193
Period size: 35 Copynumber: 2.9 Consensus size: 35
1819453 CGTCACGTCC
*
1819463 AGTAAGGCCCTGAGCACACAGCCGAAGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1819498 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1819533 AGTAAGGCCCTGAGCACACAGCCGAGGAACC
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACC
1819564 TCCAAGTAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.33, C:0.30, G:0.30, T:0.08
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
Found at i:1819678 original size:24 final size:24
Alignment explanation
Indices: 1819651--1819741 Score: 130
Period size: 24 Copynumber: 3.8 Consensus size: 24
1819641 CATAATTCAA
1819651 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* * *
1819675 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAG
1819699 GTCAA-TATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* *
1819722 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCATATCAGAAT
1819742 TCAAATTTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 20 0.34
24 38 0.66
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAG
Found at i:1819721 original size:47 final size:48
Alignment explanation
Indices: 1819651--1819741 Score: 148
Period size: 47 Copynumber: 1.9 Consensus size: 48
1819641 CATAATTCAA
* *
1819651 GTCAAGTATCATATCAGAATCCAGGTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
*
1819699 GTCAA-TATCATATCAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCATATCAGAATCCAGGTCAGGTATCAGAACAGAAT
1819742 TCAAATTTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 35 0.88
48 5 0.12
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.26
Consensus pattern (48 bp):
GTCAAGTATCATATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
Found at i:1821338 original size:63 final size:63
Alignment explanation
Indices: 1821239--1821361 Score: 237
Period size: 63 Copynumber: 2.0 Consensus size: 63
1821229 TGCTTTCTTG
1821239 AACACTCTCTGATCTTGAAACGATTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
1 AACACTCTCTGATCTTGAAACGATTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
*
1821302 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
1 AACACTCTCTGATCTTGAAACGATTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
1821362 CCTAGGATTA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34
Consensus pattern (63 bp):
AACACTCTCTGATCTTGAAACGATTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
Found at i:1822300 original size:15 final size:15
Alignment explanation
Indices: 1822280--1822312 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1822270 TCGTCAACGC
1822280 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
1822295 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
1822310 CGG
1 CGG
1822313 GTCGGGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.36, T:0.12
Consensus pattern (15 bp):
CGGTCAACGGGTCAA
Found at i:1822320 original size:13 final size:13
Alignment explanation
Indices: 1822302--1822364 Score: 72
Period size: 13 Copynumber: 4.5 Consensus size: 13
1822292 CAACGGTCAA
1822302 CGGGTCAACGGGT
1 CGGGTCAACGGGT
1822315 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
1822333 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
1822346 CGGGTAAACGGGT
1 CGGGTCAACGGGT
1822359 CGGGTC
1 CGGGTC
1822365 GGGTCGGGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
13 30 0.70
18 13 0.30
ACGTcount: A:0.14, C:0.22, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:1822340 original size:31 final size:31
Alignment explanation
Indices: 1822302--1822369 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
1822292 CAACGGTCAA
*
1822302 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
1822333 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
1822364 CGGGTC
1 CGGGTC
1822370 GGGTTATGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.13, C:0.22, G:0.49, T:0.16
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
Found at i:1822346 original size:8 final size:8
Alignment explanation
Indices: 1822281--1822328 Score: 68
Period size: 8 Copynumber: 6.5 Consensus size: 8
1822271 CGTCAACGCC
1822281 GGTCAACG
1 GGTCAACG
1822289 GGTCAAC-
1 GGTCAACG
1822296 GGTCAACG
1 GGTCAACG
1822304 GGTCAACG
1 GGTCAACG
1822312 GGT---CG
1 GGTCAACG
1822317 GGTCAACG
1 GGTCAACG
1822325 GGTC
1 GGTC
1822329 GGGTCGGGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.14
7 7 0.19
8 24 0.67
ACGTcount: A:0.21, C:0.25, G:0.40, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1822368 original size:18 final size:18
Alignment explanation
Indices: 1822296--1822350 Score: 83
Period size: 18 Copynumber: 2.9 Consensus size: 18
1822286 ACGGGTCAAC
1822296 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
1822317 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
1822335 GGTCAACGGGTCGGGT
1 GGTCAACGGGTCGGGT
1822351 AAACGGGTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 23 0.68
21 11 0.32
ACGTcount: A:0.15, C:0.22, G:0.47, T:0.16
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:1823618 original size:29 final size:29
Alignment explanation
Indices: 1823576--1823714 Score: 235
Period size: 29 Copynumber: 4.8 Consensus size: 29
1823566 TTTTTTCCAT
1823576 GGTATGCGAAGACTCTTGACGTGGACTTG
1 GGTATGCGAAGACTCTTGACGTGGACTTG
1823605 GGTATGCGAAGACTCTTGACGTGGACTTG
1 GGTATGCGAAGACTCTTGACGTGGACTTG
*
1823634 GGTATGCGAAGACT-TCTGACGCGGACTTG
1 GGTATGCGAAGACTCT-TGACGTGGACTTG
* *
1823663 GGTATGCGAAGACTCCTGACGCGGACTTG
1 GGTATGCGAAGACTCTTGACGTGGACTTG
1823692 GGTATGCGAAGACTCTTGACGTG
1 GGTATGCGAAGACTCTTGACGTG
1823715 TTTCCCCCCC
Statistics
Matches: 104, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
28 1 0.01
29 103 0.99
ACGTcount: A:0.21, C:0.19, G:0.35, T:0.25
Consensus pattern (29 bp):
GGTATGCGAAGACTCTTGACGTGGACTTG
Found at i:1829276 original size:17 final size:17
Alignment explanation
Indices: 1829250--1829288 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1829240 CTGCAAGTGA
*
1829250 AGTTTTCAAGGATTTAG
1 AGTTTCCAAGGATTTAG
1829267 AGTTTCCAAGGATTTAG
1 AGTTTCCAAGGATTTAG
1829284 AGTTT
1 AGTTT
1829289 ACAGAACTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (17 bp):
AGTTTCCAAGGATTTAG
Found at i:1848900 original size:16 final size:16
Alignment explanation
Indices: 1848876--1848909 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1848866 TATCGCCGAC
*
1848876 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
1848892 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
1848908 CG
1 CG
1848910 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:1852608 original size:6 final size:6
Alignment explanation
Indices: 1852597--1852622 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1852587 TCATCTGCTT
1852597 TGGAGC TGGAGC TGGAGC TGGAGC TG
1 TGGAGC TGGAGC TGGAGC TGGAGC TG
1852623 AATCTGGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.50, T:0.19
Consensus pattern (6 bp):
TGGAGC
Found at i:1854910 original size:20 final size:20
Alignment explanation
Indices: 1854882--1854942 Score: 72
Period size: 19 Copynumber: 3.0 Consensus size: 20
1854872 ATAAAAATAA
*
1854882 AAATAATTTTTTAATTTTA-
1 AAATTATTTTTTAATTTTAT
1854901 AAATTTATTTTTT-ATTTTAT
1 AAA-TTATTTTTTAATTTTAT
*
1854921 AAATTATTTTTCTAATTATAT
1 AAATTATTTTT-TAATTTTAT
1854942 A
1 A
1854943 TGTAATCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
19 17 0.47
20 12 0.33
21 7 0.19
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
AAATTATTTTTTAATTTTAT
Found at i:1856059 original size:53 final size:54
Alignment explanation
Indices: 1855938--1856110 Score: 260
Period size: 54 Copynumber: 3.2 Consensus size: 54
1855928 TTGAAGACGC
* * * *
1855938 GCCCACGCCTTAATTGAAGATTTCTTCTGTGATATCTCAGGATGAATAAGCCGT
1 GCCCACGCCTTAACTGAAGACTTCTTCTGCGATAGCTCAGGATGAATAAGCCGT
1855992 GCCCACGCCTTAACTGAAGACTTCTTCTGCGATAGCTCAGGATG-ATAAGCCGT
1 GCCCACGCCTTAACTGAAGACTTCTTCTGCGATAGCTCAGGATGAATAAGCCGT
* * *
1856045 GCCCACGCCTTAACTGATGACTTCTTCTGCGATAGCT-ATGGACGAATAAGTCGT
1 GCCCACGCCTTAACTGAAGACTTCTTCTGCGATAGCTCA-GGATGAATAAGCCGT
1856099 GCCCACGCCTTA
1 GCCCACGCCTTA
1856111 TGCGAGAACC
Statistics
Matches: 110, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
52 1 0.01
53 49 0.45
54 60 0.55
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (54 bp):
GCCCACGCCTTAACTGAAGACTTCTTCTGCGATAGCTCAGGATGAATAAGCCGT
Found at i:1859118 original size:12 final size:12
Alignment explanation
Indices: 1859101--1859126 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1859091 ATGTAACATA
1859101 TAAGAAAATAAT
1 TAAGAAAATAAT
1859113 TAAGAAAATAAT
1 TAAGAAAATAAT
1859125 TA
1 TA
1859127 CATTATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (12 bp):
TAAGAAAATAAT
Found at i:1866659 original size:22 final size:22
Alignment explanation
Indices: 1866620--1866662 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1866610 CCGAAATAAT
*
1866620 AATAAAAATATTATTTTAATTC
1 AATAAAAATATGATTTTAATTC
1866642 AATAAAAATAATGA-TTTAATT
1 AATAAAAAT-ATGATTTTAATT
1866663 AAAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AATAAAAATATGATTTTAATTC
Found at i:1885873 original size:20 final size:18
Alignment explanation
Indices: 1885848--1885886 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1885838 TCTAACATGC
1885848 AAACTATATAGTATATACTA
1 AAACTATATA--ATATACTA
*
1885868 AAACTATGTAATATACTA
1 AAACTATATAATATACTA
1885886 A
1 A
1885887 TGATTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (18 bp):
AAACTATATAATATACTA
Found at i:1885939 original size:17 final size:18
Alignment explanation
Indices: 1885902--1885939 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1885892 TAATATCTAA
1885902 TATAATATGCAATACTATT
1 TATAATATGCAATA-TATT
1885921 TATAATATGCAAT-TATT
1 TATAATATGCAATATATT
1885938 TA
1 TA
1885940 ATATGAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (18 bp):
TATAATATGCAATATATT
Found at i:1886091 original size:16 final size:15
Alignment explanation
Indices: 1886067--1886105 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1886057 TGATTCTCTA
*
1886067 ATATGCATACTATACT
1 ATATACATACTATA-T
1886083 ATATACATACTATAT
1 ATATACATACTATAT
1886098 ATTATACA
1 A-TATACA
1886106 CATATGGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (15 bp):
ATATACATACTATAT
Found at i:1886986 original size:10 final size:10
Alignment explanation
Indices: 1886973--1887019 Score: 53
Period size: 9 Copynumber: 4.9 Consensus size: 10
1886963 TTTGACCAGT
1886973 TTTGAACCGG
1 TTTGAACCGG
1886983 TTTG-ACCGG
1 TTTGAACCGG
* *
1886992 TCTGAACCGA
1 TTTGAACCGG
1887002 TTTG-ACCGG
1 TTTGAACCGG
*
1887011 TCTGAACCG
1 TTTGAACCG
1887020 ACCCGACTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
9 15 0.50
10 15 0.50
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (10 bp):
TTTGAACCGG
Found at i:1886999 original size:19 final size:19
Alignment explanation
Indices: 1886975--1887020 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1886965 TGACCAGTTT
*
1886975 TGAACCGGTTTGACCGGTC
1 TGAACCGATTTGACCGGTC
1886994 TGAACCGATTTGACCGGTC
1 TGAACCGATTTGACCGGTC
1887013 TGAACCGA
1 TGAACCGA
1887021 CCCGACTGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.24
Consensus pattern (19 bp):
TGAACCGATTTGACCGGTC
Found at i:1887055 original size:17 final size:17
Alignment explanation
Indices: 1887033--1887070 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1887023 CGACTGACCC
*
1887033 GACCCGACCCGACTGTT
1 GACCCGACCCGACCGTT
1887050 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1887067 GACC
1 GACC
1887071 GTTGACTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:1893687 original size:10 final size:10
Alignment explanation
Indices: 1893645--1893687 Score: 54
Period size: 9 Copynumber: 4.5 Consensus size: 10
1893635 GCTGCTGGAA
1893645 AACCGGTTTG
1 AACCGGTTTG
*
1893655 -ACCGGTTCG
1 AACCGGTTTG
1893664 AACCGGTTTG
1 AACCGGTTTG
*
1893674 -ACCGGTCTG
1 AACCGGTTTG
1893683 AACCG
1 AACCG
1893688 ACCCGTCTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
9 16 0.57
10 12 0.43
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.23
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:1893695 original size:14 final size:14
Alignment explanation
Indices: 1893673--1893720 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1893663 GAACCGGTTT
*
1893673 GACCGGTCTGAACC
1 GACCCGTCTGAACC
*
1893687 GACCCGTCTGATCC
1 GACCCGTCTGAACC
* *
1893701 GACCCGACTGACCC
1 GACCCGTCTGAACC
1893715 GACCCG
1 GACCCG
1893721 ACCCCACTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.19, C:0.44, G:0.25, T:0.12
Consensus pattern (14 bp):
GACCCGTCTGAACC
Found at i:1897336 original size:14 final size:14
Alignment explanation
Indices: 1897317--1897351 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1897307 CATTTAAATG
1897317 ATGAACGAACACAA
1 ATGAACGAACACAA
*
1897331 ATGAACGAACATAA
1 ATGAACGAACACAA
*
1897345 ACGAACG
1 ATGAACG
1897352 GATGTAAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.54, C:0.20, G:0.17, T:0.09
Consensus pattern (14 bp):
ATGAACGAACACAA
Found at i:1897347 original size:10 final size:10
Alignment explanation
Indices: 1897334--1897451 Score: 55
Period size: 10 Copynumber: 11.3 Consensus size: 10
1897324 AACACAAATG
1897334 AACGAACATA
1 AACGAACATA
1897344 AACGAACGGATGTA
1 AACGAAC--A--TA
1897358 AACGAACATA
1 AACGAACATA
*
1897368 AATGAACACAATA
1 AACG-A-AC-ATA
* *
1897381 AATGAACACA
1 AACGAACATA
* *
1897391 AATCTAA-ATG
1 AA-CGAACATA
1897401 AAC--ACAATA
1 AACGAACA-TA
*
1897410 AATGAACATA
1 AACGAACATA
*
1897420 AACGAACGTA
1 AACGAACATA
1897430 AACGAACATA
1 AACGAACATA
*
1897440 AATGAACA-A
1 AACGAACATA
1897449 AAC
1 AAC
1897452 AAACGAACAT
Statistics
Matches: 83, Mismatches: 13, Indels: 25
0.69 0.11 0.21
Matches are distributed among these distances:
7 1 0.01
8 1 0.01
9 7 0.08
10 45 0.54
11 8 0.10
12 5 0.06
13 7 0.08
14 9 0.11
ACGTcount: A:0.58, C:0.17, G:0.12, T:0.14
Consensus pattern (10 bp):
AACGAACATA
Found at i:1897383 original size:13 final size:13
Alignment explanation
Indices: 1897365--1897417 Score: 79
Period size: 13 Copynumber: 3.8 Consensus size: 13
1897355 GTAAACGAAC
1897365 ATAAATGAACACA
1 ATAAATGAACACA
1897378 ATAAATGAACACAA
1 ATAAATGAACAC-A
1897392 ATCTAAATGAACACA
1 A--TAAATGAACACA
1897407 ATAAATGAACA
1 ATAAATGAACA
1897418 TAAACGAACG
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
13 22 0.59
14 2 0.05
15 2 0.05
16 11 0.30
ACGTcount: A:0.60, C:0.15, G:0.08, T:0.17
Consensus pattern (13 bp):
ATAAATGAACACA
Found at i:1897465 original size:10 final size:10
Alignment explanation
Indices: 1897407--1897451 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
1897397 AATGAACACA
*
1897407 ATAAATGAAC
1 ATAAACGAAC
1897417 ATAAACGAAC
1 ATAAACGAAC
*
1897427 GTAAACGAAC
1 ATAAACGAAC
*
1897437 ATAAATGAAC
1 ATAAACGAAC
1897447 A-AAAC
1 ATAAAC
1897452 AAACGAACAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 3 0.10
10 27 0.90
ACGTcount: A:0.60, C:0.16, G:0.11, T:0.13
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1897932 original size:33 final size:33
Alignment explanation
Indices: 1897895--1897963 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1897885 TAATAAGTAA
1897895 CAAATGATACTGATTGATGAATATGTCTAATTC
1 CAAATGATACTGATTGATGAATATGTCTAATTC
1897928 CAAATGATACTGATTGATGAATATGTCTAATTC
1 CAAATGATACTGATTGATGAATATGTCTAATTC
1897961 CAA
1 CAA
1897964 TCAAAATTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (33 bp):
CAAATGATACTGATTGATGAATATGTCTAATTC
Found at i:1904819 original size:24 final size:24
Alignment explanation
Indices: 1904792--1904859 Score: 102
Period size: 24 Copynumber: 2.8 Consensus size: 24
1904782 CATAAATCAG
*
1904792 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
1904816 GTC-AGATATCAGATCATAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
1904840 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
1904860 TCCAATCGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
23 2 0.05
24 35 0.90
25 2 0.05
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:1905657 original size:44 final size:44
Alignment explanation
Indices: 1905607--1905712 Score: 167
Period size: 44 Copynumber: 2.4 Consensus size: 44
1905597 TTTATCCCAT
1905607 AAGCTCGTAAGCTTATTTTACCAAAATACTTACCAATATTCCAA
1 AAGCTCGTAAGCTTATTTTACCAAAATACTTACCAATATTCCAA
* * * *
1905651 AAGCTCGTAAGCTTATTTTACCCATATACTTGCCATTATTCCAA
1 AAGCTCGTAAGCTTATTTTACCAAAATACTTACCAATATTCCAA
*
1905695 AAGCTTGTAAGCTTATTT
1 AAGCTCGTAAGCTTATTT
1905713 GTATGCTTAC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (44 bp):
AAGCTCGTAAGCTTATTTTACCAAAATACTTACCAATATTCCAA
Found at i:1905842 original size:40 final size:40
Alignment explanation
Indices: 1905798--1905879 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
1905788 ACCGTAGTGC
1905798 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1905838 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1905878 TA
1 TA
1905880 TAAACATGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1918537 original size:18 final size:19
Alignment explanation
Indices: 1918516--1918553 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1918506 TAAATTAATT
* *
1918516 TTTTAATATTTTTTA-TAA
1 TTTTAAAATTATTTACTAA
1918534 TTTTAAAATTATTTACTAA
1 TTTTAAAATTATTTACTAA
1918553 T
1 T
1918554 ATAACATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTAAAATTATTTACTAA
Found at i:1919176 original size:17 final size:17
Alignment explanation
Indices: 1919154--1919191 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1919144 AGTATTTAAT
**
1919154 CAGGCTTTTAATCAGGC
1 CAGGCTTTTAAAAAGGC
1919171 CAGGCTTTTAAAAAGGC
1 CAGGCTTTTAAAAAGGC
1919188 CAGG
1 CAGG
1919192 TCGAGCCGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (17 bp):
CAGGCTTTTAAAAAGGC
Found at i:1925370 original size:26 final size:27
Alignment explanation
Indices: 1925322--1925374 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
1925312 TAACATCTAC
**
1925322 AAGACACACAGGCAATACTTTTTTTTAG
1 AAGACACACAAACAATAC-TTTTTTTAG
1925350 AAGACACACAAACAATA-TTTTTTTA
1 AAGACACACAAACAATACTTTTTTTA
1925375 AAAATAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
28 15 0.65
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (27 bp):
AAGACACACAAACAATACTTTTTTTAG
Found at i:1925428 original size:16 final size:16
Alignment explanation
Indices: 1925407--1925441 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1925397 ACCAGTATTG
1925407 AATCTCATGTGCATTC
1 AATCTCATGTGCATTC
1925423 AATCTCATGTGCATTC
1 AATCTCATGTGCATTC
1925439 AAT
1 AAT
1925442 TTCTCTCCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (16 bp):
AATCTCATGTGCATTC
Found at i:1925694 original size:7 final size:7
Alignment explanation
Indices: 1925672--1925701 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1925662 TGAACCCCCT
1925672 TTTATTC
1 TTTATTC
1925679 TTT-TTC
1 TTTATTC
1925685 TTTATTC
1 TTTATTC
1925692 TTTATTC
1 TTTATTC
1925699 TTT
1 TTT
1925702 TTTTTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTATTC
Found at i:1925697 original size:20 final size:18
Alignment explanation
Indices: 1925671--1925722 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 18
1925661 TTGAACCCCC
1925671 TTTTATTCTTTTTCTTTAT
1 TTTTATTCTTTTT-TTTAT
*
1925690 TCTTTATTCTTTTTTTTCT
1 T-TTTATTCTTTTTTTTAT
1925709 TTTT-TTCTTTTTTT
1 TTTTATTCTTTTTTT
1925723 ATTCAAACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 10 0.32
18 3 0.10
19 6 0.19
20 12 0.39
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTATTCTTTTTTTTAT
Found at i:1925710 original size:16 final size:17
Alignment explanation
Indices: 1925670--1925722 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
1925660 CTTGAACCCC
1925670 CTTTTATTCTTTTTCTTT
1 CTTTTATTCTTTTT-TTT
*
1925688 ATTCTTTATTCTTTTTTTT
1 -CT-TTTATTCTTTTTTTT
*
1925707 CTTTTTTTCTTTTTTT
1 CTTTTATTCTTTTTTT
1925723 ATTCAAACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 13 0.43
18 1 0.03
19 4 0.13
20 12 0.40
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (17 bp):
CTTTTATTCTTTTTTTT
Found at i:1932196 original size:12 final size:12
Alignment explanation
Indices: 1932171--1932263 Score: 75
Period size: 12 Copynumber: 7.8 Consensus size: 12
1932161 ACGGAGATAT
* *
1932171 CAGAAATCAAAA
1 CAGAATTCAGAA
1932183 CAGAATTCAGAA
1 CAGAATTCAGAA
1932195 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
1932207 CAGAATCCAGAT
1 CAGAATTCAGAA
1932219 CAGAAATT-AGAA
1 CAG-AATTCAGAA
*
1932231 CAGAATTCAGAT
1 CAGAATTCAGAA
*
1932243 CATGTA-TCAGAA
1 CA-GAATTCAGAA
*
1932255 TAGAATTCA
1 CAGAATTCA
1932264 AGTTAGAAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
11 8 0.12
12 49 0.77
13 7 0.11
ACGTcount: A:0.49, C:0.16, G:0.15, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1932198 original size:24 final size:24
Alignment explanation
Indices: 1932171--1932263 Score: 98
Period size: 24 Copynumber: 3.9 Consensus size: 24
1932161 ACGGAGATAT
*
1932171 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * *
1932195 CAGATATCAGAACAGAATCCAGAT
1 CAGAAATCAGAACAGAATTCAGAA
* *
1932219 CAGAAATTAGAACAGAATTCAGAT
1 CAGAAATCAGAACAGAATTCAGAA
* *
1932243 CATG-TATCAGAATAGAATTCA
1 CA-GAAATCAGAACAGAATTCA
1932264 AGTTAGAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 57 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.15, T:0.19
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:1932240 original size:48 final size:48
Alignment explanation
Indices: 1932169--1932260 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
1932159 AAACGGAGAT
1932169 ATCAGAAATCAAAACAGAATTCAGAACA-GATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGAACATG-TATCAGAACAGAATCCAG
* * * *
1932217 ATCAGAAATTAGAACAGAATTCAGATCATGTATCAGAATAGAAT
1 ATCAGAAATCAAAACAGAATTCAGAACATGTATCAGAACAGAAT
1932261 TCAAGTTAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 38 0.97
49 1 0.03
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGAACATGTATCAGAACAGAATCCAG
Found at i:1932272 original size:48 final size:48
Alignment explanation
Indices: 1932169--1932275 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
1932159 AAACGGAGAT
*
1932169 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCAAG
* * * *
1932217 ATCAGAAATTAGAACAGAATTCAGATCATG-TATCAGAATAGAATTCAAG
1 ATCAGAAATCAAAACAGAATTCAGAACA-GATATCAGAACAGAA-TCAAG
*
1932266 -TTAGAAATCA
1 ATCAGAAATCA
1932276 GATAAAATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
48 45 0.90
49 5 0.10
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCAAG
Found at i:1934789 original size:18 final size:18
Alignment explanation
Indices: 1934766--1934805 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1934756 TCGGATCAAT
1934766 GGGTCGAGTCAA-AGGGTC
1 GGGTCGAGTCAACA-GGTC
*
1934784 GGGTCGGGTCAACAGGTC
1 GGGTCGAGTCAACAGGTC
1934802 GGGT
1 GGGT
1934806 AAACGGGTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.17, C:0.17, G:0.47, T:0.17
Consensus pattern (18 bp):
GGGTCGAGTCAACAGGTC
Found at i:1934801 original size:13 final size:13
Alignment explanation
Indices: 1934785--1934819 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1934775 CAAAGGGTCG
1934785 GGTCGGGTCAACA
1 GGTCGGGTCAACA
* *
1934798 GGTCGGGTAAACG
1 GGTCGGGTCAACA
1934811 GGTCGGGTC
1 GGTCGGGTC
1934820 GGGTCGGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.46, T:0.17
Consensus pattern (13 bp):
GGTCGGGTCAACA
Found at i:1934822 original size:31 final size:31
Alignment explanation
Indices: 1934752--1934824 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
1934742 CAACGGTCAA
* **
1934752 CGGGTCGGATCAATGGGTCGAGTCAAAGGGT
1 CGGGTCGGGTCAACAGGTCGAGTCAAAGGGT
*
1934783 CGGGTCGGGTCAACAGGTCGGGT-AAACGGGT
1 CGGGTCGGGTCAACAGGTCGAGTCAAA-GGGT
1934814 CGGGTCGGGTC
1 CGGGTCGGGTC
1934825 GGGTTATGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 3 0.08
31 34 0.92
ACGTcount: A:0.18, C:0.19, G:0.45, T:0.18
Consensus pattern (31 bp):
CGGGTCGGGTCAACAGGTCGAGTCAAAGGGT
Found at i:1946603 original size:25 final size:26
Alignment explanation
Indices: 1946557--1946609 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
1946547 TTTTTTAGTT
*
1946557 AAAATATATTAAATTATAAGATAGATA
1 AAAATATATTAAA-TATAAGATAAATA
*
1946584 AAAATATATTAAA-ATTAGATAAATA
1 AAAATATATTAAATATAAGATAAATA
1946609 A
1 A
1946610 TCATACTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 11 0.46
27 13 0.54
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (26 bp):
AAAATATATTAAATATAAGATAAATA
Found at i:1947459 original size:41 final size:41
Alignment explanation
Indices: 1947397--1947480 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
1947387 AAATTAAAAA
* *
1947397 TAAATACAATAACCTTTAATTTAAAAGTTTTTATAATCCCG
1 TAAATAAAATAACCTTCAATTTAAAAGTTTTTATAATCCCG
1947438 TAAATAAAATAACCTTCAATTTAAAAGTTTTTATAATCCCG
1 TAAATAAAATAACCTTCAATTTAAAAGTTTTTATAATCCCG
1947479 TA
1 TA
1947481 GAACGCAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (41 bp):
TAAATAAAATAACCTTCAATTTAAAAGTTTTTATAATCCCG
Found at i:1948016 original size:62 final size:62
Alignment explanation
Indices: 1947947--1948071 Score: 196
Period size: 62 Copynumber: 2.0 Consensus size: 62
1947937 TAAATAACTC
* ** **
1947947 TATTACATTTAAGTACATTATTAAAGCGTGATGAGTCATTAAGTTTACCTGAGAAGTTGTTT
1 TATTACATTTAAATACATTATTAAAGCACGATGAGTCATTAAGCATACCTGAGAAGTTGTTT
*
1948009 TATTACATTTAAATACATTATTAAAGCACGATGAGTCATTAAGCATGCCTGAGAAGTTGTTT
1 TATTACATTTAAATACATTATTAAAGCACGATGAGTCATTAAGCATACCTGAGAAGTTGTTT
1948071 T
1 T
1948072 CTCCGACGGT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (62 bp):
TATTACATTTAAATACATTATTAAAGCACGATGAGTCATTAAGCATACCTGAGAAGTTGTTT
Found at i:1949600 original size:4 final size:4
Alignment explanation
Indices: 1949586--1949625 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
1949576 AAACACAAAT
1949586 ATAA A-AA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1949626 AAGGTTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.09
4 32 0.91
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:1950352 original size:2 final size:2
Alignment explanation
Indices: 1950345--1950376 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1950335 TTCTAGTGAA
1950345 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
1950377 TTATCAAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1951870 original size:13 final size:12
Alignment explanation
Indices: 1951845--1951869 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1951835 CTGGCCTGAT
1951845 AGCCTTTTTAAA
1 AGCCTTTTTAAA
1951857 AGCCTTTTTAAA
1 AGCCTTTTTAAA
1951869 A
1 A
1951870 AATAACACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
AGCCTTTTTAAA
Found at i:1959973 original size:15 final size:16
Alignment explanation
Indices: 1959941--1959973 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1959931 AAAATCTTTC
1959941 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
1959957 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
1959972 TT
1 TT
1959974 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:1963421 original size:29 final size:29
Alignment explanation
Indices: 1963379--1963435 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1963369 TTTTCACCTA
1963379 ACTAAATTAATGTAAGCAATGACATCAAT
1 ACTAAATTAATGTAAGCAATGACATCAAT
*
1963408 ACTAAATTGATGTAAGCAATGACATCAA
1 ACTAAATTAATGTAAGCAATGACATCAA
1963436 ATTAATTTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.26
Consensus pattern (29 bp):
ACTAAATTAATGTAAGCAATGACATCAAT
Found at i:1966305 original size:29 final size:29
Alignment explanation
Indices: 1966263--1966319 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
1966253 TTTTCACCTA
1966263 ACTAAATTGATGTAAGCAATGACATCAAT
1 ACTAAATTGATGTAAGCAATGACATCAAT
1966292 ACTAAATTGATGTAAGCAATGACATCAA
1 ACTAAATTGATGTAAGCAATGACATCAA
1966320 ATTAATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (29 bp):
ACTAAATTGATGTAAGCAATGACATCAAT
Found at i:1967657 original size:3 final size:3
Alignment explanation
Indices: 1967649--1967674 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1967639 CTAGAATTTT
1967649 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
1967675 TAAGAGAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1971036 original size:19 final size:18
Alignment explanation
Indices: 1971003--1971042 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1970993 CCGACCAGAA
*
1971003 CCGTTGACATGACCCGAC
1 CCGTTGACATGACCCAAC
*
1971021 CCGTTGACTTTGACCCAAC
1 CCGTTGAC-ATGACCCAAC
1971040 CCG
1 CCG
1971043 ACCCGAACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (18 bp):
CCGTTGACATGACCCAAC
Found at i:1971071 original size:43 final size:44
Alignment explanation
Indices: 1970984--1971079 Score: 122
Period size: 43 Copynumber: 2.1 Consensus size: 44
1970974 CCGGTCCAGC
*
1970984 TGACCCAACCCGACCAGAACCGTTGACATGACCCGACCCGTTGACTT
1 TGACCCAACCCGACCAGAACCGTT---ATGACCCGACCCATTGACTT
* * *
1971031 TGACCCAACCCGACCCGAACTGTT-TGACCCGACCTATTGACTT
1 TGACCCAACCCGACCAGAACCGTTATGACCCGACCCATTGACTT
1971074 TGACCC
1 TGACCC
1971080 GAAAAAGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
43 23 0.51
47 22 0.49
ACGTcount: A:0.24, C:0.39, G:0.18, T:0.20
Consensus pattern (44 bp):
TGACCCAACCCGACCAGAACCGTTATGACCCGACCCATTGACTT
Found at i:1972328 original size:21 final size:22
Alignment explanation
Indices: 1972304--1972347 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1972294 ATTTCTGAAG
* *
1972304 TACTTATTTTTTTA-TGATATT
1 TACTGATTTTTCTACTGATATT
*
1972325 TACTGCTTTTTCTACTGATATT
1 TACTGATTTTTCTACTGATATT
1972347 T
1 T
1972348 GATTTATTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.61
Consensus pattern (22 bp):
TACTGATTTTTCTACTGATATT
Found at i:1973240 original size:11 final size:11
Alignment explanation
Indices: 1973224--1973279 Score: 61
Period size: 11 Copynumber: 5.6 Consensus size: 11
1973214 ATGGATTCAA
1973224 ATAGCGGCCAT
1 ATAGCGGCCAT
1973235 ATAGCGG--A-
1 ATAGCGGCCAT
*
1973243 ATAGAGGCCAT
1 ATAGCGGCCAT
1973254 ATAGCGG--A-
1 ATAGCGGCCAT
1973262 ATAGCGGCCAT
1 ATAGCGGCCAT
1973273 ATAGCGG
1 ATAGCGG
1973280 AATAGCGGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
8 13 0.35
9 2 0.05
10 2 0.05
11 20 0.54
ACGTcount: A:0.32, C:0.20, G:0.32, T:0.16
Consensus pattern (11 bp):
ATAGCGGCCAT
Found at i:1973251 original size:19 final size:19
Alignment explanation
Indices: 1973223--1973287 Score: 121
Period size: 19 Copynumber: 3.4 Consensus size: 19
1973213 CATGGATTCA
1973223 AATAGCGGCCATATAGCGG
1 AATAGCGGCCATATAGCGG
*
1973242 AATAGAGGCCATATAGCGG
1 AATAGCGGCCATATAGCGG
1973261 AATAGCGGCCATATAGCGG
1 AATAGCGGCCATATAGCGG
1973280 AATAGCGG
1 AATAGCGG
1973288 GCTGCTATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.34, C:0.18, G:0.32, T:0.15
Consensus pattern (19 bp):
AATAGCGGCCATATAGCGG
Done.