Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008719.1 Hibiscus syriacus cultivar Beakdansim tig00111774_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: 4817204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 18
Found at i:4651976 original size:36 final size:34
Alignment explanation
Indices: 4651929--4651997 Score: 111
Period size: 36 Copynumber: 2.0 Consensus size: 34
4651919 AATTTCTTCT
4651929 CAAATAAATTGTGGATGTGTGATATCTGTTAAATTC
1 CAAATAAATTGTGGATGTGTGATAT-T-TTAAATTC
*
4651965 CAAATAAATTGTGGATGTGTGGTATTTTAAATT
1 CAAATAAATTGTGGATGTGTGATATTTTAAATT
4651998 GTTTTAGTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 7 0.22
35 1 0.03
36 24 0.75
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (34 bp):
CAAATAAATTGTGGATGTGTGATATTTTAAATTC
Found at i:4654876 original size:24 final size:24
Alignment explanation
Indices: 4654849--4654896 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
4654839 CGTTCGTGAA
* *
4654849 CGTTCGTTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCATTTATGTT
4654873 CGTTCGGTTATGTTCATTTATGTT
1 CGTTCGGTTATGTTCATTTATGTT
4654897 TAACCCAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.10, C:0.12, G:0.21, T:0.56
Consensus pattern (24 bp):
CGTTCGGTTATGTTCATTTATGTT
Found at i:4654887 original size:10 final size:10
Alignment explanation
Indices: 4654850--4654876 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
4654840 GTTCGTGAAC
4654850 GTTCGTTTAT
1 GTTCGTTTAT
4654860 GTTCGTTTAT
1 GTTCGTTTAT
4654870 GTTCGTT
1 GTTCGTT
4654877 CGGTTATGTT
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:0.07, C:0.11, G:0.22, T:0.59
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:4655972 original size:10 final size:10
Alignment explanation
Indices: 4655957--4656031 Score: 70
Period size: 10 Copynumber: 7.7 Consensus size: 10
4655947 GAGTCTCCAA
4655957 CGTTTATGTT
1 CGTTTATGTT
4655967 CGTTTATGTT
1 CGTTTATGTT
4655977 CGTGTTTAT-TT
1 C--GTTTATGTT
* *
4655988 ATGTTCATGTT
1 -CGTTTATGTT
4655999 CGTTTATGTT
1 CGTTTATGTT
4656009 CG--T-TG-T
1 CGTTTATGTT
4656015 CGTTTATGTT
1 CGTTTATGTT
4656025 CGTTTAT
1 CGTTTAT
4656032 TTATTAAATG
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
6 3 0.06
7 2 0.04
8 2 0.04
9 2 0.04
10 34 0.64
11 4 0.08
12 6 0.11
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:4655988 original size:16 final size:16
Alignment explanation
Indices: 4655963--4656035 Score: 71
Period size: 16 Copynumber: 4.7 Consensus size: 16
4655953 CCAACGTTTA
*
4655963 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
* *
4655979 TGTTTATTTATGTTCA
1 TGTTCATTTATGTTCG
*
4655995 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
*
4656011 T-TGTCGTTTATGTTCG
1 TGT-TCATTTATGTTCG
4656027 T-TT-ATTTAT
1 TGTTCATTTAT
4656036 TAAATGAACG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 42 0.86
ACGTcount: A:0.11, C:0.10, G:0.19, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:4656021 original size:32 final size:32
Alignment explanation
Indices: 4655962--4656025 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
4655952 TCCAACGTTT
*
4655962 ATGTTCGTTTATGTTCGTGTTTATTTATGTTC
1 ATGTTCGTTTATGTTCGTGTTCATTTATGTTC
*
4655994 ATGTTCGTTTATGTTCGT-TGTCGTTTATGTTC
1 ATGTTCGTTTATGTTCGTGT-TCATTTATGTTC
4656026 GTTTATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 1 0.03
32 28 0.97
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.58
Consensus pattern (32 bp):
ATGTTCGTTTATGTTCGTGTTCATTTATGTTC
Found at i:4656120 original size:16 final size:16
Alignment explanation
Indices: 4656099--4656129 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4656089 AAAAATTTTG
4656099 TTCGTTTATGTTCGTA
1 TTCGTTTATGTTCGTA
4656115 TTCGTTTATGTTCGT
1 TTCGTTTATGTTCGT
4656130 TTATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.13, G:0.19, T:0.58
Consensus pattern (16 bp):
TTCGTTTATGTTCGTA
Found at i:4658209 original size:32 final size:31
Alignment explanation
Indices: 4658173--4658249 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
4658163 CGGGGCCGTG
*
4658173 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
4658205 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
4658236 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
4658250 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:4658232 original size:63 final size:63
Alignment explanation
Indices: 4658126--4658249 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
4658116 CCCTAAGGGA
* * ** *
4658126 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
4658189 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
4658250 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:4659142 original size:13 final size:13
Alignment explanation
Indices: 4659124--4659162 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
4659114 AAGAAAGTCA
4659124 ACGGTCAACGGTC
1 ACGGTCAACGGTC
4659137 ACGGTCAACGGTC
1 ACGGTCAACGGTC
4659150 ACGGTCAACGGTC
1 ACGGTCAACGGTC
4659163 GGGTCGGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:4659145 original size:20 final size:20
Alignment explanation
Indices: 4659120--4659162 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
4659110 GTCAAAGAAA
4659120 GTCAACGGTCAACGGTCACG
1 GTCAACGGTCAACGGTCACG
4659140 GTCAACGGTC-ACGGTCAACG
1 GTCAACGGTCAACGGTC-ACG
4659160 GTC
1 GTC
4659163 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.16
Consensus pattern (20 bp):
GTCAACGGTCAACGGTCACG
Found at i:4659174 original size:17 final size:17
Alignment explanation
Indices: 4659152--4659208 Score: 105
Period size: 17 Copynumber: 3.4 Consensus size: 17
4659142 CAACGGTCAC
4659152 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
4659169 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
4659186 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
4659203 GGTCAA
1 GGTCAA
4659209 ACCGGTTCAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.16, C:0.23, G:0.44, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:4659179 original size:7 final size:7
Alignment explanation
Indices: 4659120--4659162 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
4659110 GTCAAAGAAA
4659120 GTCAACG
1 GTCAACG
4659127 GTCAACG
1 GTCAACG
4659134 GTC-ACG
1 GTCAACG
4659140 GTCAACG
1 GTCAACG
4659147 GTC-ACG
1 GTCAACG
4659153 GTCAACG
1 GTCAACG
4659160 GTC
1 GTC
4659163 GGGTCGGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.35
7 22 0.65
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:4659227 original size:19 final size:18
Alignment explanation
Indices: 4659203--4659262 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
4659193 AGTCGGGTCG
*
4659203 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGG-TCAAACC
4659222 GGTCAAACCGGTCAAACC
1 GGTCAAACCGGTCAAACC
* *
4659240 GGTTCAAAACTGGTTAAACC
1 GG-TC-AAACCGGTCAAACC
4659260 GGT
1 GGT
4659263 TTTCCAGCAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 8 0.22
19 14 0.39
20 14 0.39
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.18
Consensus pattern (18 bp):
GGTCAAACCGGTCAAACC
Found at i:4659233 original size:9 final size:9
Alignment explanation
Indices: 4659203--4659262 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
4659193 AGTCGGGTCG
4659203 GGTCAAACC
1 GGTCAAACC
*
4659212 GGTTCAGACC
1 GG-TCAAACC
4659222 GGTCAAACC
1 GGTCAAACC
4659231 GGTCAAACC
1 GGTCAAACC
*
4659240 GGTTCAAAACT
1 GG-TC-AAACC
*
4659251 GGTTAAACC
1 GGTCAAACC
4659260 GGT
1 GGT
4659263 TTTCCAGCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 26 0.60
10 11 0.26
11 6 0.14
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:4660124 original size:2 final size:2
Alignment explanation
Indices: 4660117--4660151 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4660107 ATTTTATTTC
4660117 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4660152 AAAGAATCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4660338 original size:13 final size:13
Alignment explanation
Indices: 4660308--4660340 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
4660298 AATCCCACCT
4660308 TATAA-ATTACTC
1 TATAATATTACTC
4660320 TCATAATATTACTC
1 T-ATAATATTACTC
4660334 TATAATA
1 TATAATA
4660341 CCCAATCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.05
13 10 0.53
14 8 0.42
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (13 bp):
TATAATATTACTC
Found at i:4680763 original size:160 final size:165
Alignment explanation
Indices: 4680573--4680897 Score: 583
Period size: 161 Copynumber: 2.0 Consensus size: 165
4680563 CTGAAGGCTG
4680573 CAAACTGTCTTATAATCCCCCTTATTTCTTAAACCTAGCCCAGCATAATCTCCC-TTTTACTACT
1 CAAACTGTCTTATAATCCCCCTTATTTCTTAAACCTAGCCCAGCATAATCTCCCTTTTTACTACT
4680637 CCCCAAACTGTGACCTTCTGACACAACTTCATTAATGTCTTTCCCTGCCAAGC-TC-TTTTGAAA
66 CCCCAAACTGTGACCTTCTGACACAACTTCATTAATGTCTTTCCCTGCCAAGCTTCATTTTGAAA
4680700 A-TGA-TTTCTGTCA-CTGCTGCACCAA-CCCGACA
131 ACTGATTTTCT-TCACCTGCTGCACCAACCCCGACA
4680732 CAAACTGTCTTTATAATCCCCCTTATTTCTTAAACCTAGCCCAGCATAATCTCCCTTTTTACTAC
1 CAAACTGTC-TTATAATCCCCCTTATTTCTTAAACCTAGCCCAGCATAATCTCCCTTTTTACTAC
4680797 TCCCCAAACTGTGACCTTCTGACACAACTTCATTAATGTCTTTCCCTGCCAAGCTTCATTTTGAA
65 TCCCCAAACTGTGACCTTCTGACACAACTTCATTAATGTCTTTCCCTGCCAAGCTTCATTTTGAA
4680862 AACTGATTTTCTTCACCTGCTGCACCAACCCCGACA
130 AACTGATTTTCTTCACCTGCTGCACCAACCCCGACA
4680898 GGAAATCCCT
Statistics
Matches: 158, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
159 9 0.06
160 45 0.28
161 63 0.40
162 2 0.01
163 9 0.06
164 6 0.04
165 17 0.11
166 7 0.04
ACGTcount: A:0.26, C:0.33, G:0.09, T:0.33
Consensus pattern (165 bp):
CAAACTGTCTTATAATCCCCCTTATTTCTTAAACCTAGCCCAGCATAATCTCCCTTTTTACTACT
CCCCAAACTGTGACCTTCTGACACAACTTCATTAATGTCTTTCCCTGCCAAGCTTCATTTTGAAA
ACTGATTTTCTTCACCTGCTGCACCAACCCCGACA
Found at i:4693437 original size:8 final size:8
Alignment explanation
Indices: 4693405--4693498 Score: 50
Period size: 8 Copynumber: 11.5 Consensus size: 8
4693395 TAAAACACTA
4693405 TAAAAAAT
1 TAAAAAAT
**
4693413 TAAAATTT
1 TAAAAAAT
4693421 TAAGTAAAAT
1 TAA--AAAAT
4693431 TAAAAAAAT
1 T-AAAAAAT
*
4693440 TATAAAA-
1 TAAAAAAT
**
4693447 TAACCAAT
1 TAAAAAAT
4693455 TAAAGAAAT
1 TAAA-AAAT
*
4693464 TATAAAA-
1 TAAAAAAT
*
4693471 TAATAAAT
1 TAAAAAAT
*
4693479 T-ATAAAT
1 TAAAAAAT
4693486 ATAAAAAAT
1 -TAAAAAAT
4693495 TAAA
1 TAAA
4693499 TTTAAATATA
Statistics
Matches: 64, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
7 15 0.23
8 26 0.41
9 17 0.27
10 4 0.06
11 2 0.03
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (8 bp):
TAAAAAAT
Found at i:4693455 original size:24 final size:24
Alignment explanation
Indices: 4693428--4693473 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
4693418 TTTTAAGTAA
4693428 AATTAAAAAAATTATAAAATAACC
1 AATTAAAAAAATTATAAAATAACC
*
4693452 AATTAAAGAAATTATAAAATAA
1 AATTAAAAAAATTATAAAATAA
4693474 TAAATTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (24 bp):
AATTAAAAAAATTATAAAATAACC
Found at i:4693479 original size:24 final size:24
Alignment explanation
Indices: 4693427--4693480 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
4693417 ATTTTAAGTA
4693427 AAATTAAAAAAATTATAAAATAAC
1 AAATTAAAAAAATTATAAAATAAC
* * *
4693451 CAATTAAAGAAATTATAAAATAAT
1 AAATTAAAAAAATTATAAAATAAC
4693475 AAATTA
1 AAATTA
4693481 TAAATATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (24 bp):
AAATTAAAAAAATTATAAAATAAC
Found at i:4693480 original size:15 final size:16
Alignment explanation
Indices: 4693455--4693496 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
4693445 AATAACCAAT
4693455 TAAAGAAATTATAAA-A
1 TAAA-AAATTATAAATA
*
4693471 TAATAAATTATAAATA
1 TAAAAAATTATAAATA
4693487 TAAAAAATTA
1 TAAAAAATTA
4693497 AATTTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
TAAAAAATTATAAATA
Found at i:4693506 original size:20 final size:21
Alignment explanation
Indices: 4693464--4693508 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
4693454 TTAAAGAAAT
4693464 TATAAAATAATAAATTATAAA
1 TATAAAATAATAAATTATAAA
4693485 TATAAAA-AATTAAATT-TAAA
1 TATAAAATAA-TAAATTATAAA
4693505 TATA
1 TATA
4693509 TTTATAAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TATAAAATAATAAATTATAAA
Found at i:4696265 original size:12 final size:12
Alignment explanation
Indices: 4696248--4696283 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
4696238 TATCATGTTC
4696248 TCATATCACATG
1 TCATATCACATG
*
4696260 TCATATCACATA
1 TCATATCACATG
4696272 TCATATCACATG
1 TCATATCACATG
4696284 AACATATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:4696694 original size:64 final size:62
Alignment explanation
Indices: 4696586--4696810 Score: 236
Period size: 64 Copynumber: 3.5 Consensus size: 62
4696576 TAATGAAGGT
* * ** ** *
4696586 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTATTATTG-TGGG
* *
4696650 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTT-ATTATT-GTGGG
** ***
4696714 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTATT-TTGAAAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATG-TTTATTATTGTGGG
** *
4696776 AGTGCATCGATGCACTACCAATGCATCGATACACC
1 A-TGCATCGATGCACTACTTATGCATCGATGCACC
4696811 TTCAAACAAT
Statistics
Matches: 136, Mismatches: 21, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
62 2 0.01
63 32 0.24
64 99 0.73
65 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (62 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTATTATTGTGGG
Found at i:4697819 original size:2 final size:2
Alignment explanation
Indices: 4697752--4697801 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
4697742 GTTTATTTAT
4697752 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4697794 TA TA TA TA
1 TA TA TA TA
4697802 AAATTTTCCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4698138 original size:24 final size:25
Alignment explanation
Indices: 4698087--4698155 Score: 90
Period size: 23 Copynumber: 2.9 Consensus size: 25
4698077 ATTTGAAGAA
4698087 AAAATCC-GGTATCCGAATACCCGC
1 AAAATCCGGGTATCCGAATACCCGC
*
4698111 -AAATCCGGGTAT-CGGATACCCGC
1 AAAATCCGGGTATCCGAATACCCGC
* *
4698134 AAAATCCGGGTACCCGATTACC
1 AAAATCCGGGTATCCGAATACC
4698156 GGATACCCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 16 0.42
24 16 0.42
25 6 0.16
ACGTcount: A:0.30, C:0.32, G:0.20, T:0.17
Consensus pattern (25 bp):
AAAATCCGGGTATCCGAATACCCGC
Found at i:4698544 original size:11 final size:10
Alignment explanation
Indices: 4698524--4698553 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
4698514 TTAGAGTTAT
4698524 AAAAATTTTA
1 AAAAATTTTA
4698534 AAAAATATTTA
1 AAAAAT-TTTA
4698545 AAAAATTTT
1 AAAAATTTT
4698554 GAAATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AAAAATTTTA
Found at i:4702348 original size:13 final size:11
Alignment explanation
Indices: 4702318--4702342 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4702308 ATTTACATAA
4702318 TTTTTTATATT
1 TTTTTTATATT
4702329 TTTTTTATATT
1 TTTTTTATATT
4702340 TTT
1 TTT
4702343 CTTTTAACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTATATT
Found at i:4703351 original size:2 final size:2
Alignment explanation
Indices: 4703344--4703371 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4703334 ACTTTCTAGG
4703344 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
4703372 TTCTGGACTC
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:4705490 original size:146 final size:146
Alignment explanation
Indices: 4705291--4705583 Score: 543
Period size: 146 Copynumber: 2.0 Consensus size: 146
4705281 AGCAGATTTT
*
4705291 TACAAATGTCTTCGCTTGGTATCTTTCTTAGAACATGGCAATTTCTTTAACTTAATGTCTTTGGT
1 TACAAATGTCTTCGCTTGGTATCTTTCTTAGAACATGACAATTTCTTTAACTTAATGTCTTTGGT
4705356 TTAATTACTACTAAATGAGCAGAGGACATTTGGCCATCTAATCTTGACCTTTAATCATATCATGC
66 TTAATTACTACTAAATGAGCAGAGGACATTTGGCCATCTAATCTTGACCTTTAATCATATCATGC
4705421 CGTA-CCAAGTCTTCG
131 CGTACCCAAGTCTTCG
*
4705436 TACAAATGTCTTCGCTTGTGTATCTTTCTTAGAACATGACGATTTCTTTAACTTAATGTCTTTGG
1 TACAAATGTCTTCGCTTG-GTATCTTTCTTAGAACATGACAATTTCTTTAACTTAATGTCTTTGG
4705501 TTTAATTACTACTAAATGAGCAGAGGACATTTGGCCATCTAATCTTGACCTTTAATCATATCATG
65 TTTAATTACTACTAAATGAGCAGAGGACATTTGGCCATCTAATCTTGACCTTTAATCATATCATG
*
4705566 TCGTACCCAAGTCTTCG
130 CCGTACCCAAGTCTTCG
4705583 T
1 T
4705584 TGCAGCTTGA
Statistics
Matches: 143, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
145 18 0.13
146 113 0.79
147 12 0.08
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (146 bp):
TACAAATGTCTTCGCTTGGTATCTTTCTTAGAACATGACAATTTCTTTAACTTAATGTCTTTGGT
TTAATTACTACTAAATGAGCAGAGGACATTTGGCCATCTAATCTTGACCTTTAATCATATCATGC
CGTACCCAAGTCTTCG
Found at i:4710077 original size:31 final size:31
Alignment explanation
Indices: 4710001--4710074 Score: 123
Period size: 30 Copynumber: 2.4 Consensus size: 31
4709991 AAAATATGCA
* *
4710001 TTTAGTACTTAAACTATCAGTTTTGATTTGT
1 TTTAGTACCTAAACTATCAGTTTTGATCTGT
4710032 TTTAGTACCTAAACTATCAG-TTTGATCTGT
1 TTTAGTACCTAAACTATCAGTTTTGATCTGT
4710062 TTTAGTACCTAAA
1 TTTAGTACCTAAA
4710075 ACTTTCATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 22 0.54
31 19 0.46
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (31 bp):
TTTAGTACCTAAACTATCAGTTTTGATCTGT
Found at i:4714334 original size:20 final size:20
Alignment explanation
Indices: 4714311--4714369 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 20
4714301 TCTTAAGTTC
*
4714311 AATTCAAACTCGAAATAAAA
1 AATTAAAACTCGAAATAAAA
4714331 AATTAAAGCTCGACTCGAAATAAAA
1 AATTAAA-----ACTCGAAATAAAA
4714356 AATTAAAACTCGAA
1 AATTAAAACTCGAA
4714370 TCAAGATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
20 13 0.39
25 20 0.61
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.20
Consensus pattern (20 bp):
AATTAAAACTCGAAATAAAA
Found at i:4714346 original size:25 final size:25
Alignment explanation
Indices: 4714318--4714368 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
4714308 TTCAATTCAA
*
4714318 ACTCGAAATAAAAAATTAAAGCTCG
1 ACTCGAAATAAAAAATTAAAACTCG
4714343 ACTCGAAATAAAAAATTAAAACTCG
1 ACTCGAAATAAAAAATTAAAACTCG
4714368 A
1 A
4714369 ATCAAGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.20
Consensus pattern (25 bp):
ACTCGAAATAAAAAATTAAAACTCG
Found at i:4714378 original size:25 final size:25
Alignment explanation
Indices: 4714320--4714380 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
4714310 CAATTCAAAC
* *
4714320 TCGAAATAAAAAATTAAAGCTCGAC
1 TCGAAATAAAAAATTAAAACTCGAA
4714345 TCGAAATAAAAAATTAAAACTCGAA
1 TCGAAATAAAAAATTAAAACTCGAA
4714370 TC-AAGATAAAA
1 TCGAA-ATAAAA
4714381 CTATTTGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 2 0.06
25 31 0.94
ACGTcount: A:0.57, C:0.13, G:0.10, T:0.20
Consensus pattern (25 bp):
TCGAAATAAAAAATTAAAACTCGAA
Found at i:4718163 original size:30 final size:30
Alignment explanation
Indices: 4718098--4718164 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
4718088 ATGTTTATTT
* *
4718098 CGTGTTCGTGTTAGTTTATTTATTTTTGAA
1 CGTGTTCGTGTTAGTTTATTTATTGTTCAA
* *
4718128 GGTGTTCGTGTTCGTTTATTTATTGTTCAA
1 CGTGTTCGTGTTAGTTTATTTATTGTTCAA
4718158 CGTGTTC
1 CGTGTTC
4718165 ATTTAATACC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.13, C:0.10, G:0.22, T:0.54
Consensus pattern (30 bp):
CGTGTTCGTGTTAGTTTATTTATTGTTCAA
Found at i:4720391 original size:30 final size:29
Alignment explanation
Indices: 4720357--4720413 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
4720347 CAAATATACA
4720357 AAATT-AATTTCAAAACTCAAAATTGAAAAT
1 AAATTGAATTTCAAAA-TCAAAA-TGAAAAT
* *
4720387 AAATTGATTTTGAAAATCAAAATGAAA
1 AAATTGAATTTCAAAATCAAAATGAAA
4720414 TTTTGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.21
30 11 0.46
31 8 0.33
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (29 bp):
AAATTGAATTTCAAAATCAAAATGAAAAT
Found at i:4721595 original size:20 final size:20
Alignment explanation
Indices: 4721553--4721597 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
4721543 ACAATTTGTA
4721553 TTTTTTAACAATTCATATCC
1 TTTTTTAACAATTCATATCC
*
4721573 TTTTGTTAACAATTGATAT-C
1 TTTT-TTAACAATTCATATCC
4721593 TTTTT
1 TTTTT
4721598 CATTAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 9 0.39
21 13 0.57
ACGTcount: A:0.27, C:0.13, G:0.04, T:0.56
Consensus pattern (20 bp):
TTTTTTAACAATTCATATCC
Found at i:4721847 original size:20 final size:20
Alignment explanation
Indices: 4721809--4721860 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
4721799 AAAATGTTTT
*
4721809 TATGAATAGTA-CTGTACTG
1 TATGAATAGTACCAGTACTG
4721828 TATGAATAGTACCAGTACTG
1 TATGAATAGTACCAGTACTG
*
4721848 TATAAATAGTACC
1 TATGAATAGTACC
4721861 GATATTGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (20 bp):
TATGAATAGTACCAGTACTG
Found at i:4726444 original size:112 final size:111
Alignment explanation
Indices: 4726061--4726444 Score: 418
Period size: 111 Copynumber: 3.4 Consensus size: 111
4726051 AACAAGGACA
* * * *
4726061 TGAATAGTTAAGATTTTAC-GTCATTTGAAATTATTATTGTCCTAGATCTGATTTTTCTTTCACT
1 TGAATAGTTAAAATTCT-CTGTCATTTGAAATTATTATTGTCAT-GATATGATTTTTCTTTCACT
* * *
4726125 ATAATGAAAGTTCTGATTTGAGGTGATA-TTT-CGTTGAAAAAAGGATG
64 ATAATTAAAGTTCTGATTTGAGGTGATATTTTAC-TAGAAAAAAGAATG
* * *
4726172 TGAATAGTTAAAATTCTCTTTTATTTGAAATTATTATTGTTATGAGTATGATTTTTC-TTCTACT
1 TGAATAGTTAAAATTCTCTGTCATTTGAAATTATTATTGTCATGA-TATGATTTTTCTTTC-ACT
* * **
4726236 ATAATTAAAGTTCTGATTTGAGGTGATGTTTCACTAGAAAAAA-AACA
64 ATAATTAAAGTTCTGATTTGAGGTGATATTTTACTAGAAAAAAGAATG
* * * * *
4726283 CGAATAGTTAAAATTCTCTGTCATTTAAAATTATTATTGTCCTCAATATGATTTTCCTTTCACTA
1 TGAATAGTTAAAATTCTCTGTCATTTGAAATTATTATTGTCAT-GATATGATTTTTCTTTCACTA
* * * * * *
4726348 TAATTAAAGTTTTAATCTGATGTGACATTTTACTGGAAAAAAGAATG
65 TAATTAAAGTTCTGATTTGAGGTGATATTTTACTAGAAAAAAGAATG
* * *
4726395 TGAATAGTTAAAGTTCTATGCCATTTGAAATTATTATTGTCATGGATATG
1 TGAATAGTTAAAATTCTCTGTCATTTGAAATTATTATTGTCAT-GATATG
4726445 GCTATTGTTA
Statistics
Matches: 225, Mismatches: 40, Indels: 15
0.80 0.14 0.05
Matches are distributed among these distances:
110 6 0.03
111 160 0.71
112 58 0.26
113 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (111 bp):
TGAATAGTTAAAATTCTCTGTCATTTGAAATTATTATTGTCATGATATGATTTTTCTTTCACTAT
AATTAAAGTTCTGATTTGAGGTGATATTTTACTAGAAAAAAGAATG
Found at i:4736269 original size:20 final size:20
Alignment explanation
Indices: 4736244--4736281 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4736234 TAAAACCTGA
4736244 CGAGTGTAGCAATGCACAAC
1 CGAGTGTAGCAATGCACAAC
* *
4736264 CGAGTGTATCGATGCACA
1 CGAGTGTAGCAATGCACA
4736282 TTCAAAGAAT
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:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (20 bp):
CGAGTGTAGCAATGCACAAC
Found at i:4736318 original size:44 final size:44
Alignment explanation
Indices: 4736266--4736369 Score: 156
Period size: 44 Copynumber: 2.4 Consensus size: 44
4736256 TGCACAACCG
* *
4736266 AGTGTATCGATGCACATTCAA-AGAATGCATTGGTGCACATTCAT
1 AGTGTATCGATGCACATTCAAGAG-ATGCATCGGTACACATTCAT
* *
4736310 AGTGTATCGATGCATATTCAAGAGATGCATCGGTACACTTTCAT
1 AGTGTATCGATGCACATTCAAGAGATGCATCGGTACACATTCAT
4736354 AGTGTATCGATGCACA
1 AGTGTATCGATGCACA
4736370 GTGCACAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 52 0.96
45 2 0.04
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (44 bp):
AGTGTATCGATGCACATTCAAGAGATGCATCGGTACACATTCAT
Found at i:4738919 original size:26 final size:26
Alignment explanation
Indices: 4738888--4738943 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
4738878 CACTAAGAAT
4738888 TTTCCAAAAAATTCACTAATTTGTTC
1 TTTCCAAAAAATTCACTAATTTGTTC
**
4738914 TTTCCAACTAATTCACTAATTTGTTC
1 TTTCCAAAAAATTCACTAATTTGTTC
4738940 TTTC
1 TTTC
4738944 TTTTGAGGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.46
Consensus pattern (26 bp):
TTTCCAAAAAATTCACTAATTTGTTC
Found at i:4740603 original size:44 final size:44
Alignment explanation
Indices: 4740530--4740616 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
4740520 TTGTGCAATG
** *
4740530 TGCATTGATACACTATAAAAGTGTGCCGATGCATTCCTTGAATA
1 TGCATTGATACACTATAAAAGTGCACCGATGCATTCATTGAATA
*
4740574 TGCATTGATGCACTAT-AAAGATGCACCGATGCATTCATTGAAT
1 TGCATTGATACACTATAAAAG-TGCACCGATGCATTCATTGAAT
4740617 GTACGTCGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 4 0.11
44 34 0.89
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (44 bp):
TGCATTGATACACTATAAAAGTGCACCGATGCATTCATTGAATA
Found at i:4741131 original size:13 final size:13
Alignment explanation
Indices: 4741113--4741150 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
4741103 TCCATATTTA
4741113 TTTTCAAACATTG
1 TTTTCAAACATTG
*
4741126 TTTTCAAACATAG
1 TTTTCAAACATTG
4741139 TTTTCAAA-ATTG
1 TTTTCAAACATTG
4741151 CCTATTAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 3 0.13
13 20 0.87
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATTG
Found at i:4742562 original size:23 final size:23
Alignment explanation
Indices: 4742532--4742580 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
4742522 TGGTGGTTGG
*
4742532 TTTAATGG-ATGTTTAAACTTTAT
1 TTTAATGGTATATTT-AACTTTAT
*
4742555 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
4742578 TTT
1 TTT
4742581 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:4743076 original size:11 final size:11
Alignment explanation
Indices: 4743060--4743090 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4743050 TTCTTTTCAT
*
4743060 TTTATTTGCTG
1 TTTATTTACTG
4743071 TTTATTTACTG
1 TTTATTTACTG
4743082 TTTATTTAC
1 TTTATTTAC
4743091 CATTTTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.65
Consensus pattern (11 bp):
TTTATTTACTG
Found at i:4749445 original size:20 final size:20
Alignment explanation
Indices: 4749392--4749452 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
4749382 CTCTTAAATA
*
4749392 TTTAACTTTT-TCTTTTCTC
1 TTTAACTTTTATTTTTTCTC
* * *
4749411 TTTCATCCTTAATTTTTTCTC
1 TTT-AACTTTTATTTTTTCTC
4749432 TTTAACTTTTATTTTTTCTC
1 TTTAACTTTTATTTTTTCTC
4749452 T
1 T
4749453 CATTTCTTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
19 3 0.09
20 19 0.58
21 11 0.33
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTAACTTTTATTTTTTCTC
Found at i:4752752 original size:23 final size:23
Alignment explanation
Indices: 4752722--4752770 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
4752712 TGGTGGTTGG
*
4752722 TTTAATGG-ATGTTTAAACTTTAT
1 TTTAATGGTATATTT-AACTTTAT
*
4752745 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
4752768 TTT
1 TTT
4752771 GGTTCCTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:4754727 original size:12 final size:13
Alignment explanation
Indices: 4754701--4754730 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4754691 AGGGGGAGTA
4754701 ATTTTAAAAATTG
1 ATTTTAAAAATTG
4754714 ATTTTAAAAA-TG
1 ATTTTAAAAATTG
4754726 ATTTT
1 ATTTT
4754731 CAAAGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (13 bp):
ATTTTAAAAATTG
Found at i:4755140 original size:18 final size:18
Alignment explanation
Indices: 4755078--4755139 Score: 115
Period size: 18 Copynumber: 3.4 Consensus size: 18
4755068 TTTTTTGTAC
4755078 CGATGCACAACCATGCAT
1 CGATGCACAACCATGCAT
4755096 CGATGCACAACCATGCAT
1 CGATGCACAACCATGCAT
*
4755114 CGATGCACTACCATGCAT
1 CGATGCACAACCATGCAT
4755132 CGATGCAC
1 CGATGCAC
4755140 TCTTGATTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.31, C:0.34, G:0.18, T:0.18
Consensus pattern (18 bp):
CGATGCACAACCATGCAT
Found at i:4757421 original size:20 final size:20
Alignment explanation
Indices: 4757373--4757437 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
4757363 AATTGTATTG
* *
4757373 TACTGTATGAATAGTATCAA
1 TACTATATGAATAGTATCGA
* * *
4757393 CACTGTATGAATATTATCGA
1 TACTATATGAATAGTATCGA
* *
4757413 TACTATATGAACAGTACCGA
1 TACTATATGAATAGTATCGA
4757433 TACTA
1 TACTA
4757438 AAAAACATTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (20 bp):
TACTATATGAATAGTATCGA
Found at i:4758573 original size:130 final size:129
Alignment explanation
Indices: 4758409--4758772 Score: 461
Period size: 130 Copynumber: 2.8 Consensus size: 129
4758399 TCGATATTGA
* * * * *
4758409 GAATAGTAATATCTTTTCATTTT-AGTTTGAGTAATAAATGATTGCTTTAAGGCATGAAAGGTCA
1 GAATAGTGATATCTCTTCATTTTGA-TTGGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCA
* *
4758473 TTTATTCTCGATTAGAAATAATTCA-ATATTAT-GTTTTCTCTCGAATTAATATTGATTTTTAAG
65 TTTATTCTCGATTAGAAATAATT-AGATATTATCGTTTTCTCTCGAA-T-AGATTGAATTTTAAG
4758536 ATG
127 ATG
* * * *
4758539 GAATAGTGATATCTCTTAATTTTGATTGGAGTAATAAATGAGTGCTTTAAGGTATGAGATGTCAA
1 GAATAGTGATATCTCTTCATTTTGATTGGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCAT
* * * *
4758604 TTATTCTCGATTGGAAATCATTAGATATTATCGTTTTCACTCGAATCGATTGAATTTTAAGATG
66 TTATTCTCGATTAGAAATAATTAGATATTATCGTTTTCTCTCGAATAGATTGAATTTTAAGATG
* *
4758668 GAATAGTGATA--TCTTCATTTGGATTGGAGTAATAAATGATTGTTTTAAGGTATGAGAGGTCAT
1 GAATAGTGATATCTCTTCATTTTGATTGGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCAT
* * *
4758731 TTATTCTC-AATCGAAAATAATTAGATATTATCATTTTCTCTC
66 TTATTCTCGATTAG-AAATAATTAGATATTATCGTTTTCTCTC
4758773 TTAAAATTAT
Statistics
Matches: 204, Mismatches: 26, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
126 3 0.01
127 79 0.39
129 27 0.13
130 82 0.40
131 13 0.06
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.41
Consensus pattern (129 bp):
GAATAGTGATATCTCTTCATTTTGATTGGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCAT
TTATTCTCGATTAGAAATAATTAGATATTATCGTTTTCTCTCGAATAGATTGAATTTTAAGATG
Found at i:4758721 original size:127 final size:130
Alignment explanation
Indices: 4758437--4758768 Score: 449
Period size: 127 Copynumber: 2.6 Consensus size: 130
4758427 ATTTTAGTTT
* * *
4758437 GAGTAATAAATGATTGCTTTAAGGCATGAAAGGTCATTTATTCTCGATTAGAAATAATTCA-ATA
1 GAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATT-AGATA
* * * *
4758501 TTAT-GTTTTCTCTCGAATTAATATTGATTTTTAAGATGGAATAGTGATATCTCTTAATTTTGAT
65 TTATCGTTTTCACTCGAATTAAGATTGAATTTTAAGATGGAATAGTGATA-CTCTTAATTTGGAT
4758565 TG
129 TG
* * * *
4758567 GAGTAATAAATGAGTGCTTTAAGGTATGAGATGTCAATTATTCTCGATTGGAAATCATTAGATAT
1 GAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
* *
4758632 TATCGTTTTCACTCGAA-T-CGATTGAATTTTAAGATGGAATAGTGATA-TCTTCATTTGGATTG
66 TATCGTTTTCACTCGAATTAAGATTGAATTTTAAGATGGAATAGTGATACTCTTAATTTGGATTG
* * * *
4758694 GAGTAATAAATGATTGTTTTAAGGTATGAGAGGTCATTTATTCTCAATCGAAAATAATTAGATAT
1 GAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
*
4758759 TATCATTTTC
66 TATCGTTTTC
4758769 TCTCTTAAAA
Statistics
Matches: 178, Mismatches: 22, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
127 79 0.44
129 27 0.15
130 60 0.34
131 12 0.07
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (130 bp):
GAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
TATCGTTTTCACTCGAATTAAGATTGAATTTTAAGATGGAATAGTGATACTCTTAATTTGGATTG
Found at i:4770309 original size:139 final size:138
Alignment explanation
Indices: 4769998--4770340 Score: 386
Period size: 138 Copynumber: 2.5 Consensus size: 138
4769988 CTAGAAAAAA
* * * * *
4769998 GTTGAACAAATTCTTATCATTATAAACTTATTCTTCTTTTTCAGATGAGTTATTCTCATTATAAA
1 GTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATGAGTTCTTCTCATTATAAA
* * * * * * * *
4770063 CTACTTCTGGAAATGTTGATCTTCAAAAGAGGGATTTTTTGATTCAAATCCATATGTGATGAATT
66 CTACCTCTGAAAATATTGATCCTCAAAAGAGGGATTTTTTCATTCAAATCCATAGGAGATGAATC
* *
4770128 AAGGTAAT
131 AAGGCAAG
* * * *
4770136 GTTGAACAAAATT-TTCTTATTATGGACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATTA
1 GTTGAAC-AAATTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATGAGTTCTTCTCATTATAA
* * * * *
4770200 ATTTCCTCTGAAAATATTGATCCTCAAATGA-GGTTCTTCTTTCATTCAATTCCATAGGAGATGA
65 ACTACCTCTGAAAATATTGATCCTCAAAAGAGGGAT-TT-TTTCATTCAAATCCATAGGAGATGA
*
4770264 ATCAATGCAAG
128 ATCAAGGCAAG
* * *
4770275 GTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTC-TCTCATTATGAA
1 GTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATGAGTTCTTCTCATTATAAA
4770339 CT
66 CT
4770341 TCACCTGGAA
Statistics
Matches: 170, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
137 3 0.02
138 91 0.54
139 76 0.45
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (138 bp):
GTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATGAGTTCTTCTCATTATAAA
CTACCTCTGAAAATATTGATCCTCAAAAGAGGGATTTTTTCATTCAAATCCATAGGAGATGAATC
AAGGCAAG
Found at i:4770511 original size:123 final size:123
Alignment explanation
Indices: 4770272--4770711 Score: 473
Period size: 123 Copynumber: 3.7 Consensus size: 123
4770262 GAATCAATGC
* *
4770272 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTC-TCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * * *
4770336 GAAC-TTCACCTGGAAATAGCTCTGCTGCTCTATCTCTTTTTGGAAATGGAGTCAAGCAA
66 GAACTTTC-TCTGGAAATAGCTCTGCTGATCTATCTCCTTATGG-AATAGAGTCAAGCAA
* *
4770395 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTCAAATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * *
4770460 GAACTTTCTCTGGAAA-AGTTGGTGTTGATCTATCTCCTTATGTG-ATAGAGTCATGCAA
66 GAACTTTCTCTGGAAATAGCT-CTGCTGATCTATCTCCTTATG-GAATAGAGTCAAGCAA
* * *
4770518 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTTCTCTTCAGATAAATTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * *** * * * *
4770583 GAACTTTCTCTGG-CA-A---C-GCTGATCCATCGGGTGATGCATTTGAG--AA--AA
66 GAACTTTCTCTGGAAATAGCTCTGCTGATCTATCTCCTTATGGAATAGAGTCAAGCAA
*
4770631 AA-GTTGAACAAGTTCTTCTCATTATGAACTT-TTCCTTCCTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTT-CTTCCTCTTCAGATAAGTTCTTCTCATTA
*
4770694 TGAACTCT-TCTGGAAATA
65 TGAACTTTCTCTGGAAATA
4770712 TTGAAAACAT
Statistics
Matches: 273, Mismatches: 36, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
111 7 0.03
112 62 0.23
113 5 0.02
115 1 0.00
117 17 0.06
122 2 0.01
123 139 0.51
124 36 0.13
125 4 0.01
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACTTTCTCTGGAAATAGCTCTGCTGATCTATCTCCTTATGGAATAGAGTCAAGCAA
Found at i:4770854 original size:73 final size:73
Alignment explanation
Indices: 4770760--4770932 Score: 310
Period size: 73 Copynumber: 2.4 Consensus size: 73
4770750 AAGGTCTTAT
* * *
4770760 CATCTTGCACTGTAGGGCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGAACCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
4770825 TTTGAAAA
66 TTTGAAAA
4770833 CATCATGCACTGTAGGTCTTACAGATGAACCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGAACCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
*
4770898 TTTGAAAG
66 TTTGAAAA
4770906 CATCATGCACTGTAGGTCTTACAGATG
1 CATCATGCACTGTAGGTCTTACAGATG
4770933 TGGGAAATAG
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 96 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (73 bp):
CATCATGCACTGTAGGTCTTACAGATGAACCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
TTTGAAAA
Found at i:4771650 original size:22 final size:22
Alignment explanation
Indices: 4771593--4771650 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
4771583 AATAAAACTT
*
4771593 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* *
4771615 TTATCTTTGGAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
4771637 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
4771651 TGTAGATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:4773023 original size:75 final size:75
Alignment explanation
Indices: 4772899--4773072 Score: 285
Period size: 75 Copynumber: 2.3 Consensus size: 75
4772889 ATGATATGGG
* * *
4772899 TTTCAGCATGTCCCAGCATTGGCTAATACAAACGTTCAAAATGTACCAACATTCTTGATTCTAAT
1 TTTCAGCATGCCCCAGTATTTGCTAATACAAACGTTCAAAATGTACCAACATTCTTGATTCTAAT
4772964 TGAAATAGGC
66 TGAAATAGGC
* *
4772974 TTTCAGCATGCCCCAGTATTTGCTAATACAAACGTTCAAAATGTGCCAACATTCTTGATTCTGAT
1 TTTCAGCATGCCCCAGTATTTGCTAATACAAACGTTCAAAATGTACCAACATTCTTGATTCTAAT
*
4773039 TGAAATGGGC
66 TGAAATAGGC
*
4773049 TTTCAGCATGCCTCAGTATTTGCT
1 TTTCAGCATGCCCCAGTATTTGCT
4773073 GATTATTGTT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 92 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (75 bp):
TTTCAGCATGCCCCAGTATTTGCTAATACAAACGTTCAAAATGTACCAACATTCTTGATTCTAAT
TGAAATAGGC
Found at i:4776408 original size:7 final size:7
Alignment explanation
Indices: 4776394--4776479 Score: 127
Period size: 7 Copynumber: 11.7 Consensus size: 7
4776384 AATTTTTCTT
4776394 TTTTTCC
1 TTTTTCC
*
4776401 TTTCTCC
1 TTTTTCC
4776408 TTTTTCC
1 TTTTTCC
4776415 TTTTTCC
1 TTTTTCC
4776422 TTTTTTCC
1 -TTTTTCC
4776430 TTTTTTCC
1 -TTTTTCC
4776438 TTTTTCC
1 TTTTTCC
4776445 TTTTTTCC
1 -TTTTTCC
4776453 TTTTTCC
1 TTTTTCC
4776460 TTTTTCC
1 TTTTTCC
4776467 TTTTTTCC
1 -TTTTTCC
4776475 TTTTT
1 TTTTT
4776480 ATGAGTATAA
Statistics
Matches: 74, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
7 45 0.61
8 29 0.39
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCC
Found at i:4776411 original size:15 final size:14
Alignment explanation
Indices: 4776394--4776479 Score: 127
Period size: 15 Copynumber: 5.9 Consensus size: 14
4776384 AATTTTTCTT
*
4776394 TTTTTCCTTTCTCC
1 TTTTTCCTTTTTCC
4776408 TTTTTCCTTTTTCC
1 TTTTTCCTTTTTCC
4776422 TTTTTTCCTTTTTTCC
1 -TTTTTCC-TTTTTCC
4776438 TTTTTCCTTTTTTCC
1 TTTTTCC-TTTTTCC
4776453 TTTTTCCTTTTTCC
1 TTTTTCCTTTTTCC
4776467 TTTTTTCCTTTTT
1 -TTTTTCCTTTTT
4776480 ATGAGTATAA
Statistics
Matches: 68, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
14 20 0.29
15 41 0.60
16 7 0.10
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTTCCTTTTTCC
Found at i:4776418 original size:22 final size:22
Alignment explanation
Indices: 4776395--4776479 Score: 120
Period size: 22 Copynumber: 3.8 Consensus size: 22
4776385 ATTTTTCTTT
*
4776395 TTTTCCTTTCTCC-TTTTTCCT
1 TTTTCCTTTTTCCTTTTTTCCT
4776416 TTTTCCTTTTTTCCTTTTTTCCT
1 TTTTCC-TTTTTCCTTTTTTCCT
4776439 TTTTCCTTTTTTCC-TTTTTCCT
1 TTTTCC-TTTTTCCTTTTTTCCT
4776461 TTTTCCTTTTTTCCTTTTT
1 TTTTCC-TTTTTCCTTTTT
4776480 ATGAGTATAA
Statistics
Matches: 60, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
21 6 0.10
22 28 0.47
23 26 0.43
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTCCTTTTTCCTTTTTTCCT
Found at i:4779212 original size:30 final size:30
Alignment explanation
Indices: 4779178--4779241 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
4779168 AGCTTATGGG
*
4779178 CCATATTGCTTGTCTAGACTACAGCTTCTT
1 CCATATTGCTTATCTAGACTACAGCTTCTT
* *
4779208 CCATATTGCTTATCTGGACTGCAGCTTCTT
1 CCATATTGCTTATCTAGACTACAGCTTCTT
4779238 CCAT
1 CCAT
4779242 GACATTCTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.19, C:0.28, G:0.14, T:0.39
Consensus pattern (30 bp):
CCATATTGCTTATCTAGACTACAGCTTCTT
Found at i:4780559 original size:28 final size:26
Alignment explanation
Indices: 4780504--4780578 Score: 75
Period size: 28 Copynumber: 2.9 Consensus size: 26
4780494 AAGCATTAAT
*
4780504 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
4780530 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
*
4780558 AAAAGAA-ATA-AT-TAAAAATTA
1 AAAATAATATACATATAAAAATTA
4780579 AATATATGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
23 8 0.19
24 2 0.05
25 2 0.05
26 9 0.21
27 1 0.02
28 20 0.48
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.32
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:4781299 original size:11 final size:11
Alignment explanation
Indices: 4781264--4781306 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
4781254 CTTTCTTAAT
4781264 ATTTAAAACATA
1 ATTTAAAA-ATA
4781276 A-TT-AAAATA
1 ATTTAAAAATA
4781285 ATTTAAAAATA
1 ATTTAAAAATA
4781296 ATTTATAAAAT
1 ATTTA-AAAAT
4781307 TTATAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 4 0.14
10 5 0.18
11 13 0.46
12 6 0.21
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
ATTTAAAAATA
Found at i:4782220 original size:20 final size:21
Alignment explanation
Indices: 4782182--4782220 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
4782172 ACCTTCGAAG
* *
4782182 TTCGAAGGTTTCCGGTGATGT
1 TTCGAAGGTCTCCGATGATGT
4782203 TTCGAA-GTCTCCGATGAT
1 TTCGAAGGTCTCCGATGAT
4782221 CGAGTAAGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (21 bp):
TTCGAAGGTCTCCGATGATGT
Found at i:4783961 original size:21 final size:21
Alignment explanation
Indices: 4783921--4783961 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4783911 TATGGGCTAG
* *
4783921 GGGAATCGATATCCATTCAAT
1 GGGAATCGATACCCACTCAAT
*
4783942 GGGAATCGATACCCCCTCAA
1 GGGAATCGATACCCACTCAA
4783962 ACGAATATGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (21 bp):
GGGAATCGATACCCACTCAAT
Found at i:4784013 original size:19 final size:19
Alignment explanation
Indices: 4783989--4784025 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4783979 GAACGCTAGA
*
4783989 GGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCAG
*
4784008 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
4784026 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.35, G:0.30, T:0.11
Consensus pattern (19 bp):
GGGGAACCGATACCCCCAG
Found at i:4784830 original size:101 final size:101
Alignment explanation
Indices: 4784508--4784822 Score: 535
Period size: 99 Copynumber: 3.1 Consensus size: 101
4784498 GTAGAGGGTC
*
4784508 TATGTGGTCCTTCGGGGTATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTC-GGG-ACATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
4784573 TTGATCCTTGGCATATTTATATGATTCTTAAGGAATGA
64 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* * *
4784611 TATGTGGTCCTTCGGGACATATGTATTCTTTGG-A-ATATGTGAGGTCTGGTGAGACACCTACTT
1 TATGTGGTCCTTCGGGACATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
4784674 GATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 GATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
4784710 TATGTGGTCCTTCGGGACATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TATGTGGTCCTTCGGGACATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
4784775 GATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 GATCCTTGGCATATGTATATGATTCTTAAGGAATGA
4784811 TATGTGGTCCTT
1 TATGTGGTCCTT
4784823 ATGGACATTA
Statistics
Matches: 199, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
99 92 0.46
100 2 0.01
101 89 0.45
102 3 0.02
103 13 0.07
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.37
Consensus pattern (101 bp):
TATGTGGTCCTTCGGGACATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:4784872 original size:23 final size:23
Alignment explanation
Indices: 4784839--4784901 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
4784829 ATTATTATAT
4784839 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
4784862 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
4784885 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
4784902 ATATGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:4786669 original size:10 final size:10
Alignment explanation
Indices: 4786654--4786756 Score: 77
Period size: 10 Copynumber: 10.3 Consensus size: 10
4786644 ATAAAAACTG
4786654 AAAAAGAAAA
1 AAAAAGAAAA
4786664 AAAAAGATAAA
1 AAAAAGA-AAA
* *
4786675 AGAAAGAAAG
1 AAAAAGAAAA
*
4786685 AAAATGAAAA
1 AAAAAGAAAA
4786695 TGAAAAA-AAAA
1 --AAAAAGAAAA
4786706 AAAAA-AAAA
1 AAAAAGAAAA
*
4786715 AATAAG-AAA
1 AAAAAGAAAA
**
4786724 TGAAAGAAAA
1 AAAAAGAAAA
* *
4786734 AGAGAGAAAA
1 AAAAAGAAAA
*
4786744 AAAGAGAAAA
1 AAAAAGAAAA
4786754 AAA
1 AAA
4786757 GGAGAACAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
9 19 0.25
10 39 0.52
11 13 0.17
12 4 0.05
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.05
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:4786688 original size:45 final size:45
Alignment explanation
Indices: 4786633--4786734 Score: 127
Period size: 43 Copynumber: 2.3 Consensus size: 45
4786623 ACTTCGGCCG
* * * *
4786633 AAGAATGAAAAATAAAAACTGAAAAAGAAAAAAAAAGATAA-AAGA
1 AAGAAAGAAAAATAAAAA-TGAAAAAAAAAAAAAAAAAAAATAAGA
*
4786678 AAGAAAG-AAAATGAAAATGAAAAAAAAAAAAAAAAAAAATAAGA
1 AAGAAAGAAAAATAAAAATGAAAAAAAAAAAAAAAAAAAATAAGA
4786722 AATGAAAGAAAAA
1 AA-GAAAGAAAAA
4786735 GAGAGAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
43 19 0.39
44 15 0.31
45 11 0.22
46 4 0.08
ACGTcount: A:0.78, C:0.01, G:0.13, T:0.08
Consensus pattern (45 bp):
AAGAAAGAAAAATAAAAATGAAAAAAAAAAAAAAAAAAAATAAGA
Found at i:4786702 original size:44 final size:45
Alignment explanation
Indices: 4786641--4786733 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 45
4786631 CGAAGAATGA
* *
4786641 AAAATAAAAACTGAAAAAGAAAAAAAAAGATAA-AAGAAA-GAAAG
1 AAAATAAAAACTGAAAAA-AAAAAAAAAAAAAATAAGAAATGAAAG
*
4786685 AAAATGAAAA-TGAAAAAAAAAAAAAAAAAAAATAAGAAATGAAAG
1 AAAATAAAAACTG-AAAAAAAAAAAAAAAAAAATAAGAAATGAAAG
4786730 AAAA
1 AAAA
4786734 AGAGAGAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 14 0.33
44 20 0.47
45 9 0.21
ACGTcount: A:0.80, C:0.01, G:0.12, T:0.08
Consensus pattern (45 bp):
AAAATAAAAACTGAAAAAAAAAAAAAAAAAAATAAGAAATGAAAG
Found at i:4786743 original size:29 final size:29
Alignment explanation
Indices: 4786654--4786753 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 29
4786644 ATAAAAACTG
**
4786654 AAAAAGAAAAAAAAAGATAAAAGAAAGAAA
1 AAAAAGAAAATGAAAGA-AAAAGAAAGAAA
* * * *
4786684 GAAAATGAAAATGAAAAAAAAAAAAAAAAA
1 -AAAAAGAAAATGAAAGAAAAAGAAAGAAA
*
4786714 AAATAAG-AAATGAAAGAAAAAGAGAGAAA
1 AAA-AAGAAAATGAAAGAAAAAGAAAGAAA
4786743 AAAAGAGAAAA
1 AAAA-AGAAAA
4786754 AAAGGAGAAC
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
28 1 0.02
29 26 0.47
30 15 0.27
31 13 0.24
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (29 bp):
AAAAAGAAAATGAAAGAAAAAGAAAGAAA
Found at i:4786744 original size:40 final size:39
Alignment explanation
Indices: 4786657--4786756 Score: 96
Period size: 40 Copynumber: 2.5 Consensus size: 39
4786647 AAAACTGAAA
* * *
4786657 AAGAAAAAAAAAGATAAAAGAAAGAAAGAAAATGAAAATG
1 AAGAAAAAAAAA-AAAAAAAAAAGAAAGAAAATGAAAAAG
*
4786697 AAAAAAAAAAAAAAAAAAAATAAGAAATG-AAA-GAAAAAG
1 AAGAAAAAAAAAAAAAAAAA-AAGAAA-GAAAATGAAAAAG
* *
4786736 AGAGAAAAAAAGAGAAAAAAA
1 A-AGAAAAAAAAAAAAAAAAA
4786757 GGAGAACAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
39 13 0.26
40 36 0.72
41 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (39 bp):
AAGAAAAAAAAAAAAAAAAAAAGAAAGAAAATGAAAAAG
Found at i:4786746 original size:45 final size:42
Alignment explanation
Indices: 4786653--4786756 Score: 111
Period size: 45 Copynumber: 2.4 Consensus size: 42
4786643 AATAAAAACT
* * *
4786653 GAAAAAGAAAAAAAAAGATAAAAGAAAGAAAGAAAATGAAAA
1 GAAAAAGAAAAAAAAAAAAAAAAGAAAGAAAGAAAAAGAAAA
*
4786695 TGAAAAAAAAAAAAAAAAAAAATAAGAAATGAAAGAAAAAGAGAGAA
1 -GAAAAAGAAAAAAAAAAAAAA-AAGAAA-GAAAGAAAAAGA-A-AA
*
4786742 -AAAAAGAGAAAAAAA
1 GAAAAAGAAAAAAAAA
4786757 GGAGAACAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
43 18 0.35
44 6 0.12
45 24 0.47
46 1 0.02
47 2 0.04
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (42 bp):
GAAAAAGAAAAAAAAAAAAAAAAGAAAGAAAGAAAAAGAAAA
Found at i:4786747 original size:12 final size:11
Alignment explanation
Indices: 4786654--4786762 Score: 52
Period size: 11 Copynumber: 9.9 Consensus size: 11
4786644 ATAAAAACTG
4786654 AAAAAGA-AAA
1 AAAAAGAGAAA
*
4786664 AAAAAGATAAA
1 AAAAAGAGAAA
*
4786675 AGAAAGAAAGAAA
1 A-AAA-AGAGAAA
4786688 ATGAAAATGA-AAA
1 A--AAAA-GAGAAA
4786701 AAAAA-A-AAA
1 AAAAAGAGAAA
4786710 AAAAA-A-ATAA
1 AAAAAGAGA-AA
* * *
4786720 GAAATGA-AAG
1 AAAAAGAGAAA
4786730 AAAAAGAGAGAA
1 AAAAAGAGA-AA
4786742 AAAAAGAGAAA
1 AAAAAGAGAAA
*
4786753 AAAAGGAGAA
1 AAAAAGAGAA
4786763 CAAATAAAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
9 11 0.14
10 18 0.22
11 22 0.28
12 13 0.16
13 11 0.14
14 5 0.06
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (11 bp):
AAAAAGAGAAA
Found at i:4786757 original size:10 final size:10
Alignment explanation
Indices: 4786728--4786762 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
4786718 AAGAAATGAA
*
4786728 AGAAAAAGAG
1 AGAAAAAAAG
4786738 AGAAAAAAAG
1 AGAAAAAAAG
4786748 AGAAAAAAAGG
1 AGAAAAAAA-G
4786759 AGAA
1 AGAA
4786763 CAAATAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 18 0.78
11 5 0.22
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAG
Found at i:4792881 original size:23 final size:21
Alignment explanation
Indices: 4792837--4792881 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
4792827 TTTCTGGGCT
*
4792837 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
4792858 AGGGGAATCGGGATACCCCCTCA
1 AGGGGAATC--GATACCCACTCA
4792881 A
1 A
4792882 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
23 11 0.55
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:4792933 original size:19 final size:19
Alignment explanation
Indices: 4792909--4792945 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4792899 GAACGCTAGA
*
4792909 GGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCAG
*
4792928 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
4792946 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.35, G:0.30, T:0.11
Consensus pattern (19 bp):
GGGGAACCGATACCCCCAG
Found at i:4793755 original size:103 final size:103
Alignment explanation
Indices: 4793427--4793743 Score: 580
Period size: 103 Copynumber: 3.1 Consensus size: 103
4793417 GTAGAGGGTC
*
4793427 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
4793492 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
4793530 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACCTAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
4793595 TTGATCCTTGGTATATATATATGATTATTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
4793633 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
4793698 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
4793736 TATGTGGT
1 TATGTGGT
4793744 TCTTATGGAC
Statistics
Matches: 203, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 203 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:4793797 original size:23 final size:23
Alignment explanation
Indices: 4793771--4793831 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
4793761 TATGGAACTA
4793771 CGGTGCAATTCTATGCGGCACTC
1 CGGTGCAATTCTATGCGGCACTC
* * *
4793794 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTATGCGGCACTC
* *
4793817 AGGTGCAATTATATG
1 CGGTGCAATTCTATG
4793832 AGTTGTGGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (23 bp):
CGGTGCAATTCTATGCGGCACTC
Found at i:4795621 original size:10 final size:9
Alignment explanation
Indices: 4795579--4795641 Score: 65
Period size: 9 Copynumber: 6.8 Consensus size: 9
4795569 ATGAAAACTG
4795579 AAAAAAGAA
1 AAAAAAGAA
4795588 AAAAAAGATA
1 AAAAAAGA-A
4795598 AAAGAAAGAA
1 AAA-AAAGAA
*
4795608 AGAAAAAGAG
1 A-AAAAAGAA
*
4795618 AGAAAA-AA
1 AAAAAAGAA
*
4795626 AAAAGAGAA
1 AAAAAAGAA
4795635 AAAAAAG
1 AAAAAAG
4795642 GAGAACAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
8 5 0.11
9 20 0.45
10 12 0.27
11 7 0.16
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:4795626 original size:13 final size:13
Alignment explanation
Indices: 4795597--4795646 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
4795587 AAAAAAAGAT
*
4795597 AAAAGAAAGAAAGA
1 AAAAGAGAGAAA-A
4795611 AAAAGAGAGAAAA
1 AAAAGAGAGAAAA
*
4795624 AAAAAAGAGAAAA
1 AAAAGAGAGAAAA
4795637 AAAAG-GAGAA
1 AAAAGAGAGAA
4795647 CAAATAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 5 0.15
13 17 0.52
14 11 0.33
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAAGAGAGAAAA
Found at i:4795628 original size:15 final size:15
Alignment explanation
Indices: 4795579--4795640 Score: 58
Period size: 14 Copynumber: 4.2 Consensus size: 15
4795569 ATGAAAACTG
*
4795579 AAAAAAGA-AAAAAA
1 AAAAAAGAGAGAAAA
*
4795593 AGATAAAAGAAAG-AAA
1 A-A-AAAAGAGAGAAAA
*
4795609 GAAAAAGAGAGAAAA
1 AAAAAAGAGAGAAAA
4795624 AAAAAAGAGA-AAAA
1 AAAAAAGAGAGAAAA
4795638 AAA
1 AAA
4795641 GGAGAACAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
14 16 0.40
15 14 0.35
16 9 0.22
17 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (15 bp):
AAAAAAGAGAGAAAA
Found at i:4795630 original size:25 final size:25
Alignment explanation
Indices: 4795582--4795655 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 25
4795572 AAAACTGAAA
* * *
4795582 AAAGAAAAA-AAAGATAAAAGAAAG
1 AAAGAAAAAGAGAGAAAAAAAAAAG
4795606 AAAGAAAAAGAGAGAAAAAAAAAAG
1 AAAGAAAAAGAGAGAAAAAAAAAAG
* *
4795631 AGAAAAAAAAG-GAGAACAAATAAAA
1 A-AAGAAAAAGAGAGAA-AAAAAAAA
4795656 TGGGTTTAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 9 0.21
25 18 0.43
26 15 0.36
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (25 bp):
AAAGAAAAAGAGAGAAAAAAAAAAG
Found at i:4795655 original size:27 final size:29
Alignment explanation
Indices: 4795580--4795655 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 29
4795570 TGAAAACTGA
* *
4795580 AAAAAGAAAAAAAAGATAAAAGAAAGAAAG
1 AAAAAGAGAGAAAA-ATAAAAGAAAGAAAG
*
4795610 AAAAAGAGAGAAAAA-AAAA-AGAGAAA-
1 AAAAAGAGAGAAAAATAAAAGAAAGAAAG
4795636 AAAAAG-GAGAACAAATAAAA
1 AAAAAGAGAGAA-AAATAAAA
4795656 TGGGTTTAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
25 5 0.12
26 9 0.22
27 10 0.24
28 4 0.10
29 1 0.02
30 12 0.29
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (29 bp):
AAAAAGAGAGAAAAATAAAAGAAAGAAAG
Found at i:4797080 original size:134 final size:133
Alignment explanation
Indices: 4796848--4797240 Score: 507
Period size: 134 Copynumber: 2.9 Consensus size: 133
4796838 GCGAATCGAA
* * * * *
4796848 CTCGATTCAATCTTCCCTGAAGAACAATTGAATGAATCAACATCCTCATGTATGATTTTCCCCTC
1 CTCGATTCAATCTT-CCTGAAGAACAGTGGAATGAATCAACATCCCCATATCTGATTTT-CCCTC
* * * * * *
4796913 AAGAAGAAGTGGAACAGATCCATATCTTTCAAGATTTGATCTTCCCTTAGTAACAATGTAACAAG
64 AAGAAGAAGCGGAACAAATCAATATCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGTAACAAA
4796978 TCTAC
129 TCTAC
* * * * *
4796983 CTCGATTCAATCTTCACTGAAAAATAGTGGAATGAATCAACGTCCCCATATCTGGTTTTTCCTCA
1 CTCGATTCAATCTTC-CTGAAGAACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCA
* * * *
4797048 AGAAAAAGCGGAACAAATCAATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAAT
65 AGAAGAAGCGGAACAAATCAATATCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGTAACAAAT
*
4797113 CTGC
130 CTAC
* *
4797117 CTCGATTCAATCTTCCATGAAGAACAGTGGAATGAATCAACATCCCCAGATCTTATTTTCCCTCA
1 CTCGATTCAATCTTCC-TGAAGAACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCA
* * * *
4797182 AGAAGAAGCGAAACATATCACTGTCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGTA
65 AGAAGAAGCGGAACAAATCAATATCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGTA
4797241 GATACTCGTT
Statistics
Matches: 221, Mismatches: 35, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
133 1 0.00
134 172 0.78
135 48 0.22
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (133 bp):
CTCGATTCAATCTTCCTGAAGAACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCAA
GAAGAAGCGGAACAAATCAATATCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGTAACAAATC
TAC
Found at i:4800029 original size:12 final size:12
Alignment explanation
Indices: 4800012--4800037 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4800002 TAAATTGTTG
4800012 TTTGCATTTTAA
1 TTTGCATTTTAA
4800024 TTTGCATTTTAA
1 TTTGCATTTTAA
4800036 TT
1 TT
4800038 AACAAATAAA
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:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (12 bp):
TTTGCATTTTAA
Found at i:4800651 original size:16 final size:16
Alignment explanation
Indices: 4800625--4800662 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
4800615 TCTACTAAAG
4800625 CATGATTGGGTAGATAT
1 CATG-TTGGGTAGATAT
4800642 CATGTTGGGTAGATAT
1 CATGTTGGGTAGATAT
4800658 CATGT
1 CATGT
4800663 GAATAAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.37
Consensus pattern (16 bp):
CATGTTGGGTAGATAT
Found at i:4810592 original size:25 final size:24
Alignment explanation
Indices: 4810564--4810638 Score: 82
Period size: 25 Copynumber: 3.1 Consensus size: 24
4810554 AAAAAAGAAG
**
4810564 AAGAAAAAATGAGTGAAAATGAAAA
1 AAGAAAAAATGA-AAAAAATGAAAA
4810589 AAGAAAAAAATGAAAAAAATGAAAA
1 AAG-AAAAAATGAAAAAAATGAAAA
*
4810614 ATG-AAAAATG-AAAAAATGGAAAA
1 AAGAAAAAATGAAAAAAAT-GAAAA
4810637 AA
1 AA
4810639 AGAAGGGTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
22 7 0.16
23 13 0.30
25 15 0.34
26 9 0.20
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (24 bp):
AAGAAAAAATGAAAAAAATGAAAA
Found at i:4810598 original size:16 final size:16
Alignment explanation
Indices: 4810579--4810638 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
4810569 AAAATGAGTG
4810579 AAAATGAAAAAAGAAA
1 AAAATGAAAAAAGAAA
*
4810595 AAAATGAAAAAA-ATGA
1 AAAATGAAAAAAGA-AA
*
4810611 AAAATGAAAAATG-AA
1 AAAATGAAAAAAGAAA
4810626 AAAATGGAAAAAA
1 AAAAT-GAAAAAA
4810639 AGAAGGGTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
15 7 0.19
16 30 0.81
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (16 bp):
AAAATGAAAAAAGAAA
Found at i:4810615 original size:32 final size:32
Alignment explanation
Indices: 4810579--4810639 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
4810569 AAAATGAGTG
4810579 AAAATGAAAAAAGAAAAAAAT-GAAAAAAATGA
1 AAAATGAAAAAAG-AAAAAATGGAAAAAAATGA
*
4810611 AAAATGAAAAATGAAAAAATGGAAAAAAA
1 AAAATGAAAAAAGAAAAAATGGAAAAAAA
4810640 GAAGGGTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (32 bp):
AAAATGAAAAAAGAAAAAATGGAAAAAAATGA
Found at i:4810636 original size:7 final size:7
Alignment explanation
Indices: 4810579--4810628 Score: 55
Period size: 7 Copynumber: 6.6 Consensus size: 7
4810569 AAAATGAGTG
4810579 AAAATGA
1 AAAATGA
*
4810586 AAAAAGAAA
1 AAAATG--A
4810595 AAAATGAAA
1 AAAATG--A
4810604 AAAATGA
1 AAAATGA
4810611 AAAATGA
1 AAAATGA
4810618 AAAATGA
1 AAAATGA
4810625 AAAA
1 AAAA
4810629 ATGGAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
7 24 0.62
9 15 0.38
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (7 bp):
AAAATGA
Found at i:4811645 original size:52 final size:53
Alignment explanation
Indices: 4811565--4812157 Score: 745
Period size: 52 Copynumber: 11.2 Consensus size: 53
4811555 CAACAATTAT
* * *
4811565 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAAACGCAATTGA
1 TGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
*
4811620 TGAAGATTGT-GGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGA
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
* * * * *
4811672 TG-AGATTGTGGGTCTTATACTCTCTGAAGATATAGGGGGCAGACACAATCGT
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
* * *
4811724 TGAAGATCGTTCGAGTCTTATACTCTCTGAAGAAATA-GG-G-AGACGCGATTGA
1 TGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
* * *
4811776 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
* *
4811829 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
1 TGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
4811884 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGG-GCAGACGCAATTGA
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
* * *
4811936 TGAAGATTGTGGGTCTTATACTCTCTGAAGATATAGGGGGCAGACACAATTGAA
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTG-A
* ** *
4811990 GTTGAAGATCGTTCGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG--ATTGA
1 --TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
* * *
4812043 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
* * * *
4812096 TGAAGATTGTTCGAGTCTCATACTCTCTGAAG-AATAGGGAGCAGACACAATTGT
1 TGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
4812150 TGAAGATT
1 TGAAGATT
4812158 CGAGTTCTAT
Statistics
Matches: 479, Mismatches: 42, Indels: 35
0.86 0.08 0.06
Matches are distributed among these distances:
50 24 0.05
51 51 0.11
52 148 0.31
53 77 0.16
54 41 0.09
55 97 0.20
56 41 0.09
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (53 bp):
TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
Found at i:4812154 original size:107 final size:106
Alignment explanation
Indices: 4811565--4812157 Score: 745
Period size: 105 Copynumber: 5.6 Consensus size: 106
4811555 CAACAATTAT
* * * *
4811565 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAAACGCAATTGATGAAGATTGT
1 TGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACAATTGATGAAGATTGT
*
4811630 -GGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGA
64 GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
* * * * *
4811672 TG-AGATTGTGGGTCTTATACTCTCTGAAGATATAGGGGGCAGACACAATCGTTGAAGATCGTTC
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACAATTGATGAAGATTG-T-
* *
4811736 GAGTCTTATACTCTCTGAAGAAATA-GG-G-AGACGCGATTGA
64 GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
* *
4811776 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTC
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACAATTGATGAAGATTG-T-
* *
4811841 GAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
64 GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
*
4811884 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGG-GCAGACGCAATTGATGAAGATTGTGG
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACAATTGATGAAGATTGTGG
* * *
4811948 GTCTTATACTCTCTGAAGATATAGGGGGCAGACACAATTGAA
66 GTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTG-A
* ** * *
4811990 GTTGAAGATCGTTCGTCTTATACTCTCTGAAGAAATAGGGGGCAG--ACGATTGATGAAGATTGT
1 --TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACAATTGATGAAGATTGT
* * *
4812053 GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
64 GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
* * *
4812096 TGAAGATTGTTCGAGTCTCATACTCTCTGAAG-AATAGGGAGCAGACACAATTGTTGAAGATT
1 TGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACAATTGATGAAGATT
4812158 CGAGTTCTAT
Statistics
Matches: 429, Mismatches: 42, Indels: 30
0.86 0.08 0.06
Matches are distributed among these distances:
104 64 0.15
105 133 0.31
106 29 0.07
107 115 0.27
108 84 0.20
109 4 0.01
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (106 bp):
TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACAATTGATGAAGATTGTGG
GTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA
Found at i:4815479 original size:3 final size:3
Alignment explanation
Indices: 4815473--4815592 Score: 96
Period size: 3 Copynumber: 38.0 Consensus size: 3
4815463 TTATACTAAG
* * * *
4815473 TAT TAT TAT TAT TAA TAT TAT TAAG TAG TAT TAT TAT TAGT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TA-T TAT TAT
* * * * * *
4815520 TAC TAT TAT TAT AAAT AAA TAT GCCAA TAT GTAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT --TAT TAT -TAT TAT TAT TAT TAT TAT
4815569 TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
4815593 ACAGATCAAA
Statistics
Matches: 95, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
3 85 0.89
4 9 0.09
5 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:4815481 original size:18 final size:15
Alignment explanation
Indices: 4815457--4815591 Score: 91
Period size: 15 Copynumber: 9.0 Consensus size: 15
4815447 TCTGGAGATC
*
4815457 ATATTATTA-TACTA
1 ATATTATTATTATTA
4815471 AGTATTATTATTATTA
1 A-TATTATTATTATTA
*
4815487 ATATTATTA--AGTA
1 ATATTATTATTATTA
* *
4815500 GTATTATTATTAGTA
1 ATATTATTATTATTA
*
4815515 ATTATTACTATTATT-
1 A-TATTATTATTATTA
* * * *
4815530 ATA-AATAAATATGCCA
1 ATATTATTATTAT--TA
4815546 ATATGTATTATTATTA
1 ATAT-TATTATTATTA
*
4815562 TTATTATTATTATTA
1 ATATTATTATTATTA
*
4815577 TTATTATTATTATTA
1 ATATTATTATTATTA
4815592 TACAGATCAA
Statistics
Matches: 95, Mismatches: 16, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
13 16 0.17
14 3 0.03
15 47 0.49
16 23 0.24
18 6 0.06
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.53
Consensus pattern (15 bp):
ATATTATTATTATTA
Found at i:4815510 original size:19 final size:19
Alignment explanation
Indices: 4815482--4815531 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
4815472 GTATTATTAT
*
4815482 TATTAATATTATTAAGTAG
1 TATTATTATTATTAAGTAG
* * *
4815501 TATTATTATTAGTAATTAT
1 TATTATTATTATTAAGTAG
*
4815520 TACTATTATTAT
1 TATTATTATTAT
4815532 AAATAAATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (19 bp):
TATTATTATTATTAAGTAG
Found at i:4815511 original size:28 final size:30
Alignment explanation
Indices: 4815457--4815521 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 30
4815447 TCTGGAGATC
*
4815457 ATATTATTATACTAAGTATTATTATTATTA
1 ATATTATTATACTAAGTATTATTATTAGTA
*
4815487 ATATTATTA-AGT-AGTATTATTATTAGTA
1 ATATTATTATACTAAGTATTATTATTAGTA
4815515 ATTATTA
1 A-TATTA
4815522 CTATTATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 16 0.50
29 7 0.22
30 9 0.28
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (30 bp):
ATATTATTATACTAAGTATTATTATTAGTA
Done.