Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000989.1 Hibiscus syriacus cultivar Beakdansim tig00001980_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: 949177
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 1 of 3
Found at i:10293 original size:2 final size:2
Alignment explanation
Indices: 10286--10322 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
10276 TTTTTAAAAC
10286 AT 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 AT A
10323 CCCCCATCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10514 original size:24 final size:24
Alignment explanation
Indices: 10487--10586 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
10477 GATATCAAAA
*
10487 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
10511 ATCATAACAGAATCCAGTTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
10535 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
10559 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
10583 ATCA
1 ATCA
10587 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:10586 original size:48 final size:48
Alignment explanation
Indices: 10480--10588 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
10470 AAACGGAGAT
* * * * *
10480 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
10528 TTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
10576 ATCAGAAATCAGA
1 ATCAGAAATCAGA
10589 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:13085 original size:7 final size:7
Alignment explanation
Indices: 13073--13112 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
13063 TGGTCAACTC
13073 CGGTCAA
1 CGGTCAA
13080 CGGTCAA
1 CGGTCAA
13087 CGGGTCAA
1 C-GGTCAA
13095 CGGTCAA
1 CGGTCAA
13102 CGGGTCAA
1 C-GGTCAA
13110 CGG
1 CGG
13113 GTCGGGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 17 0.55
8 14 0.45
ACGTcount: A:0.25, C:0.28, G:0.35, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:13094 original size:15 final size:15
Alignment explanation
Indices: 13074--13112 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
13064 GGTCAACTCC
13074 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
13089 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
13104 GGTCAACGG
1 GGTCAACGG
13113 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:13133 original size:18 final size:18
Alignment explanation
Indices: 13096--13187 Score: 111
Period size: 18 Copynumber: 5.2 Consensus size: 18
13086 ACGGGTCAAC
13096 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
13117 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
13135 GGTCAAC--G--GGGTCA
1 GGTCAACGGGTCGGGTCG
*
13149 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
13167 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
13185 GGT
1 GGT
13188 TGTGACCGGT
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
14 11 0.17
16 2 0.03
18 39 0.62
21 11 0.17
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.16
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:13144 original size:8 final size:8
Alignment explanation
Indices: 13074--13128 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
13064 GGTCAACTCC
13074 GGTCAAC-
1 GGTCAACG
13081 GGTCAACG
1 GGTCAACG
13089 GGTCAAC-
1 GGTCAACG
13096 GGTCAACG
1 GGTCAACG
13104 GGTCAACG
1 GGTCAACG
13112 GGT---CG
1 GGTCAACG
13117 GGTCAACG
1 GGTCAACG
13125 GGTC
1 GGTC
13129 GGGTCGGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.12
7 14 0.33
8 24 0.56
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:13157 original size:32 final size:32
Alignment explanation
Indices: 13102--13176 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
13092 CAACGGTCAA
* *
13102 CGGGTCAAC-GGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGGTCAGGTAAACGGGTCGGGT
13133 CGGGTCAACGGGGTCAGGTAAACGGGTCGGGT
1 CGGGTCAACGGGGTCAGGTAAACGGGTCGGGT
13165 CGGGTCAACGGG
1 CGGGTCAACGGG
13177 TCGGGTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 9 0.22
32 32 0.78
ACGTcount: A:0.16, C:0.21, G:0.48, T:0.15
Consensus pattern (32 bp):
CGGGTCAACGGGGTCAGGTAAACGGGTCGGGT
Found at i:13183 original size:13 final size:13
Alignment explanation
Indices: 13102--13133 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
13092 CAACGGTCAA
13102 CGGGTCAACGGGT
1 CGGGTCAACGGGT
13115 CGGGTCAACGGGT
1 CGGGTCAACGGGT
13128 CGGGTC
1 CGGGTC
13134 GGGTCAACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:15145 original size:2 final size:2
Alignment explanation
Indices: 15138--15164 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15128 TTTTTAAAAC
15138 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 A
15165 CCCCCATCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15357 original size:24 final size:24
Alignment explanation
Indices: 15330--15429 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
15320 GATATCAAAA
*
15330 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
15354 ATCATAACAGAATCCAGTTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* * *
15378 ATCAGAACAGATTTCATATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
15402 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
15426 ATCA
1 ATCA
15430 GATAAAATTC
Statistics
Matches: 57, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
23 2 0.04
24 53 0.93
25 2 0.04
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.24
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:15429 original size:48 final size:48
Alignment explanation
Indices: 15323--15431 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
15313 AAACGGAGAT
* * * * *
15323 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
15371 TTTAGGAATCAGAACAGATTTCATATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
15419 ATCAGAAATCAGA
1 ATCAGAAATCAGA
15432 TAAAATTCAT
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:17914 original size:7 final size:7
Alignment explanation
Indices: 17902--17933 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
17892 TGGTCAACTC
17902 CGGTCAA
1 CGGTCAA
17909 CGGTCAA
1 CGGTCAA
17916 CGGGTCAA
1 C-GGTCAA
17924 CGGTCAA
1 CGGTCAA
17931 CGG
1 CGG
17934 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:17923 original size:8 final size:8
Alignment explanation
Indices: 17903--17968 Score: 61
Period size: 8 Copynumber: 8.6 Consensus size: 8
17893 GGTCAACTCC
17903 GGTCAAC-
1 GGTCAACG
17910 GGTCAACG
1 GGTCAACG
17918 GGTCAAC-
1 GGTCAACG
17925 GGTCAACG
1 GGTCAACG
17933 GGT---CG
1 GGTCAACG
17938 GGTCAACG
1 GGTCAACG
**
17946 GGTCGGGTCG
1 GGTC--AACG
17956 GGTCAACG
1 GGTCAACG
17964 GGTCA
1 GGTCA
17969 GGTAAACGGG
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
5 5 0.10
7 14 0.29
8 23 0.48
10 6 0.12
ACGTcount: A:0.20, C:0.24, G:0.41, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:17923 original size:15 final size:15
Alignment explanation
Indices: 17903--17949 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
17893 GGTCAACTCC
17903 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
17918 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
17933 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
17946 GGTC
1 GGTC
17950 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:17954 original size:18 final size:18
Alignment explanation
Indices: 17931--18007 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
17921 CAACGGTCAA
17931 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
17949 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
* *
17962 CGGGTCAGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
17980 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
17998 CGGGTCGGGT
1 CGGGTCGGGT
18008 TGTGACCGTC
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
13 11 0.22
18 39 0.78
ACGTcount: A:0.13, C:0.21, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:17963 original size:31 final size:31
Alignment explanation
Indices: 17925--18003 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
17915 ACGGGTCAAC
17925 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
* *
17956 GGTCAACGGGTCAGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
17987 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
18004 GGGTTGTGAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.15, C:0.22, G:0.47, T:0.16
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:18003 original size:13 final size:13
Alignment explanation
Indices: 17910--17954 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
17900 TCCGGTCAAC
*
17910 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
17925 GGTCAACGGGTCG
1 GGTCAACGGGTCG
17938 GGTCAACGGGTCG
1 GGTCAACGGGTCG
17951 GGTC
1 GGTC
17955 GGGTCAACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:34616 original size:13 final size:13
Alignment explanation
Indices: 34598--34645 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
34588 ACCGGTCATA
34598 ACCCGACCCGTTT
1 ACCCGACCCGTTT
34611 ACCCGACCCGTTT
1 ACCCGACCCGTTT
* *
34624 ACCCGACCAGTTG
1 ACCCGACCCGTTT
34637 A-CCGACCCG
1 ACCCGACCCG
34646 ACCCGTTGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
12 7 0.22
13 25 0.78
ACGTcount: A:0.19, C:0.46, G:0.19, T:0.17
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:34646 original size:17 final size:17
Alignment explanation
Indices: 34624--34675 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
34614 CGACCCGTTT
34624 ACCCGACCAGTTGACC-G
1 ACCCGACC-GTTGACCTG
34641 ACCCGACCCGTTGACCTG
1 ACCCGA-CCGTTGACCTG
34659 ACCCATGACCGTTGACC
1 ACCC--GACCGTTGACC
34676 CGTTGACCGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 13 0.42
18 7 0.23
19 9 0.29
20 2 0.06
ACGTcount: A:0.21, C:0.42, G:0.21, T:0.15
Consensus pattern (17 bp):
ACCCGACCGTTGACCTG
Found at i:34684 original size:15 final size:15
Alignment explanation
Indices: 34645--34690 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
34635 TGACCGACCC
34645 GACCCGTTGACC--T
1 GACCCGTTGACCGTT
*
34658 GACCC-ATGACCGTT
1 GACCCGTTGACCGTT
34672 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
34687 GACC
1 GACC
34691 GGAGTTGACC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 5 0.18
13 5 0.18
14 6 0.21
15 12 0.43
ACGTcount: A:0.17, C:0.37, G:0.24, T:0.22
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:37249 original size:47 final size:48
Alignment explanation
Indices: 37189--37279 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 48
37179 TCCGACTTGA
* * *
37189 ATTCTGTTATGATACCTGACCTGGATTATGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTATGATATGATACTTGACATGG
* *
37236 ATTCTGATCTGATACATGACCTGGATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTATGATATGATACTTGAC
37280 TTGAATTATG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 33 0.87
48 5 0.13
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTATGATATGATACTTGACATGG
Found at i:37296 original size:24 final size:24
Alignment explanation
Indices: 37189--37279 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
37179 TCCGACTTGA
* *
37189 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* * *
37213 ATTATGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* *
37236 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
37260 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
37280 TTGAATTATG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.36
24 36 0.64
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:39503 original size:13 final size:13
Alignment explanation
Indices: 39444--39492 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
39434 ACCGGTCATA
39444 ACCCGACCCGTTT
1 ACCCGACCCGTTT
39457 ACCCGACCCGTTT
1 ACCCGACCCGTTT
* *
39470 ACCCGACCAGTTG
1 ACCCGACCCGTTT
*
39483 ACACGACCCG
1 ACCCGACCCG
39493 ACCCGTTGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.20, C:0.45, G:0.18, T:0.16
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:39508 original size:13 final size:13
Alignment explanation
Indices: 39487--39531 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
39477 CAGTTGACAC
*
39487 GACCCGACCCGTT
1 GACCTGACCCGTT
*
39500 GACCTGACCCATT
1 GACCTGACCCGTT
39513 GACCGTTGACCCGTT
1 GACC--TGACCCGTT
39528 GACC
1 GACC
39532 GTTGACCGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 15 0.56
15 12 0.44
ACGTcount: A:0.18, C:0.40, G:0.22, T:0.20
Consensus pattern (13 bp):
GACCTGACCCGTT
Found at i:39515 original size:8 final size:8
Alignment explanation
Indices: 39492--39538 Score: 50
Period size: 7 Copynumber: 6.5 Consensus size: 8
39482 GACACGACCC
39492 GACCCGTT
1 GACCCGTT
39500 GA-CC--T
1 GACCCGTT
*
39505 GACCCATT
1 GACCCGTT
39513 GA-CCGTT
1 GACCCGTT
39520 GACCCGTT
1 GACCCGTT
39528 GA-CCGTT
1 GACCCGTT
39535 GACC
1 GACC
39539 GGAGTTGACC
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 15 0.45
8 13 0.39
ACGTcount: A:0.17, C:0.36, G:0.23, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:39524 original size:15 final size:15
Alignment explanation
Indices: 39492--39538 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
39482 GACACGACCC
39492 GACCCGTTGACC--T
1 GACCCGTTGACCGTT
*
39505 GACCCATTGACCGTT
1 GACCCGTTGACCGTT
39520 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
39535 GACC
1 GACC
39539 GGAGTTGACC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 11 0.37
15 19 0.63
ACGTcount: A:0.17, C:0.36, G:0.23, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:42109 original size:47 final size:48
Alignment explanation
Indices: 42049--42139 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 48
42039 TCCGACTTGA
* * *
42049 ATTCTGTTATGATACCTGACCTGGATTATGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTATGATATGATACTTGACATGG
* *
42096 ATTCTGATCTGATACATGACCTGGATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTATGATATGATACTTGAC
42140 TTGAATTATG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 33 0.87
48 5 0.13
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTATGATATGATACTTGACATGG
Found at i:42156 original size:24 final size:24
Alignment explanation
Indices: 42049--42139 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
42039 TCCGACTTGA
* *
42049 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* * *
42073 ATTATGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* *
42096 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
42120 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
42140 TTGAATTATG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.36
24 36 0.64
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:52546 original size:24 final size:24
Alignment explanation
Indices: 52514--52577 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
52504 AGAGTCCATG
* *
52514 TCAAGTATCATATAAAAATTCAGA
1 TCAAATATCATATAAAAATCCAGA
* * *
52538 TCAAATATCATATCAGAATCCAGG
1 TCAAATATCATATAAAAATCCAGA
* *
52562 TCAAAAATCAGATAAA
1 TCAAATATCATATAAA
52578 CTATTTATAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (24 bp):
TCAAATATCATATAAAAATCCAGA
Found at i:53308 original size:29 final size:29
Alignment explanation
Indices: 53276--53401 Score: 85
Period size: 29 Copynumber: 4.3 Consensus size: 29
53266 CATTTTACAC
53276 AAATAGCACCATTTTCGAATTAATTCCCA
1 AAATAGCACCATTTTCGAATTAATTCCCA
****** * * *
53305 AAATATTTTTTTTTTTCGAA-AAATTACTA
1 AAATA-GCACCATTTTCGAATTAATTCCCA
53334 AAATAGCACCCA-TTTCGAATTAATTCCCA
1 AAATAGCA-CCATTTTCGAATTAATTCCCA
* ****
53363 GAATAGCACCAAAACCGAATTAATTCCCA
1 AAATAGCACCATTTTCGAATTAATTCCCA
*
53392 GAATAGCACC
1 AAATAGCACC
53402 GGTCAACGGT
Statistics
Matches: 71, Mismatches: 22, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
28 10 0.14
29 53 0.75
30 8 0.11
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (29 bp):
AAATAGCACCATTTTCGAATTAATTCCCA
Found at i:53441 original size:13 final size:12
Alignment explanation
Indices: 53409--53451 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
53399 ACCGGTCAAC
*
53409 GGTCAACGGTCAAC
1 GGTCAACGGTC--G
53423 GGTCAACGGGTCG
1 GGTCAAC-GGTCG
53436 GGTCAACGGTCG
1 GGTCAACGGTCG
53448 GGTC
1 GGTC
53452 GGGTAAACTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 9 0.33
13 7 0.26
14 7 0.26
15 4 0.15
ACGTcount: A:0.19, C:0.26, G:0.40, T:0.16
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:53446 original size:7 final size:7
Alignment explanation
Indices: 53401--53431 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
53391 AGAATAGCAC
53401 CGGTCAA
1 CGGTCAA
53408 CGGTCAA
1 CGGTCAA
53415 CGGTCAA
1 CGGTCAA
53422 CGGTCAA
1 CGGTCAA
53429 CGG
1 CGG
53432 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:53466 original size:18 final size:17
Alignment explanation
Indices: 53429--53479 Score: 84
Period size: 18 Copynumber: 2.9 Consensus size: 17
53419 CAACGGTCAA
*
53429 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTAAACGGT
53446 CGGGTCGGGTAAACTGGT
1 CGGGTCGGGTAAAC-GGT
53464 CGGGTCGGGTAAACGG
1 CGGGTCGGGTAAACGG
53480 GTAAACGGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 15 0.47
18 17 0.53
ACGTcount: A:0.16, C:0.20, G:0.47, T:0.18
Consensus pattern (17 bp):
CGGGTCGGGTAAACGGT
Found at i:53524 original size:11 final size:10
Alignment explanation
Indices: 53494--53545 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
53484 ACGGGTCGTG
53494 ACCGGTC-AA
1 ACCGGTCAAA
53503 ACCGGTCAAA
1 ACCGGTCAAA
53513 ACCGGTTCAAA
1 ACCGG-TCAAA
*
53524 ACCGGT-TAA
1 ACCGGTCAAA
53533 ACCGGTCAAA
1 ACCGGTCAAA
53543 ACC
1 ACC
53546 AGTTTCCAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 15 0.39
10 13 0.34
11 10 0.26
ACGTcount: A:0.37, C:0.31, G:0.19, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:60591 original size:29 final size:29
Alignment explanation
Indices: 60559--60684 Score: 94
Period size: 29 Copynumber: 4.3 Consensus size: 29
60549 CATTTTACAC
60559 AAATAGCACCATTTTCGAATTAATTCCCA
1 AAATAGCACCATTTTCGAATTAATTCCCA
** *** * * *
60588 AAATATTATTTTTTTTCGAA-AAATTACTA
1 AAATAGCA-CCATTTTCGAATTAATTCCCA
60617 AAATAGCACCCA-TTTCGAATTAATTCCCA
1 AAATAGCA-CCATTTTCGAATTAATTCCCA
* ****
60646 GAATAGCACCAAAACCGAATTAATTCCCA
1 AAATAGCACCATTTTCGAATTAATTCCCA
*
60675 GAATAGCACC
1 AAATAGCACC
60685 GGTCAACGGT
Statistics
Matches: 73, Mismatches: 21, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
28 10 0.14
29 55 0.75
30 8 0.11
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.29
Consensus pattern (29 bp):
AAATAGCACCATTTTCGAATTAATTCCCA
Found at i:60731 original size:13 final size:12
Alignment explanation
Indices: 60685--60741 Score: 51
Period size: 14 Copynumber: 4.3 Consensus size: 12
60675 GAATAGCACC
*
60685 GGTCAACGGTCAAC
1 GGTCAACGGTC--G
*
60699 GGTCAACGGTCAAC
1 GGTCAACGGTC--G
60713 GGTCAACGGGTCG
1 GGTCAAC-GGTCG
60726 GGTCAACGGTCG
1 GGTCAACGGTCG
60738 GGTC
1 GGTC
60742 GGGTAAACTG
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
12 9 0.22
13 7 0.17
14 21 0.51
15 4 0.10
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:60736 original size:7 final size:7
Alignment explanation
Indices: 60684--60721 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
60674 AGAATAGCAC
60684 CGGTCAA
1 CGGTCAA
60691 CGGTCAA
1 CGGTCAA
60698 CGGTCAA
1 CGGTCAA
60705 CGGTCAA
1 CGGTCAA
60712 CGGTCAA
1 CGGTCAA
60719 CGG
1 CGG
60722 GTCGGGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:60756 original size:18 final size:17
Alignment explanation
Indices: 60719--60769 Score: 84
Period size: 18 Copynumber: 2.9 Consensus size: 17
60709 CAACGGTCAA
*
60719 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTAAACGGT
60736 CGGGTCGGGTAAACTGGT
1 CGGGTCGGGTAAAC-GGT
60754 CGGGTCGGGTAAACGG
1 CGGGTCGGGTAAACGG
60770 GTAAACGGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 15 0.47
18 17 0.53
ACGTcount: A:0.16, C:0.20, G:0.47, T:0.18
Consensus pattern (17 bp):
CGGGTCGGGTAAACGGT
Found at i:60814 original size:11 final size:10
Alignment explanation
Indices: 60784--60835 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
60774 ACGGGTCGTG
60784 ACCGGTC-AA
1 ACCGGTCAAA
60793 ACCGGTCAAA
1 ACCGGTCAAA
60803 ACCGGTTCAAA
1 ACCGG-TCAAA
*
60814 ACCGGT-TAA
1 ACCGGTCAAA
60823 ACCGGTCAAA
1 ACCGGTCAAA
60833 ACC
1 ACC
60836 AGTTTCCAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 15 0.39
10 13 0.34
11 10 0.26
ACGTcount: A:0.37, C:0.31, G:0.19, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:86419 original size:18 final size:18
Alignment explanation
Indices: 86398--86433 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
86388 CTTCCATCCG
*
86398 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
86416 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
86434 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:87723 original size:7 final size:7
Alignment explanation
Indices: 87711--87742 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
87701 TGGTCAACTC
87711 CGGTCAA
1 CGGTCAA
87718 CGGTCAA
1 CGGTCAA
87725 CGAGTCAA
1 CG-GTCAA
87733 CGGTCAA
1 CGGTCAA
87740 CGG
1 CGG
87743 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.28, C:0.28, G:0.31, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:87733 original size:15 final size:15
Alignment explanation
Indices: 87713--87741 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
87703 GTCAACTCCG
87713 GTCAACGGTCAACGA
1 GTCAACGGTCAACGA
87728 GTCAACGGTCAACG
1 GTCAACGGTCAACG
87742 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):
GTCAACGGTCAACGA
Found at i:87767 original size:18 final size:18
Alignment explanation
Indices: 87740--87816 Score: 92
Period size: 18 Copynumber: 4.6 Consensus size: 18
87730 CAACGGTCAA
87740 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
87758 CGGGTGGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
* *
87771 CGGGTCGGGTAAATGGGT
1 CGGGTCGGGTCAACGGGT
87789 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
87807 CGGGTCGGGT
1 CGGGTCGGGT
87817 TATGACCGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
13 11 0.22
18 38 0.78
ACGTcount: A:0.12, C:0.18, G:0.52, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:87772 original size:31 final size:31
Alignment explanation
Indices: 87734--87812 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
87724 ACGAGTCAAC
*
87734 GGTCAACGGGTCGGGTCAACGGGTCGGGTGG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
* *
87765 GGTCAACGGGTCGGGTAAATGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
87796 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
87813 GGGTTATGAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.14, C:0.19, G:0.49, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:87776 original size:8 final size:8
Alignment explanation
Indices: 87712--87758 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
87702 GGTCAACTCC
87712 GGTCAAC-
1 GGTCAACG
87719 GGTCAACG
1 GGTCAACG
*
87727 AGTCAAC-
1 GGTCAACG
87734 GGTCAACG
1 GGTCAACG
87742 GGT---CG
1 GGTCAACG
87747 GGTCAACG
1 GGTCAACG
87755 GGTC
1 GGTC
87759 GGGTGGGGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
5 5 0.15
7 13 0.39
8 15 0.45
ACGTcount: A:0.23, C:0.26, G:0.36, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:87812 original size:13 final size:13
Alignment explanation
Indices: 87734--87794 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 13
87724 ACGAGTCAAC
87734 GGTCAACGGGTCG
1 GGTCAACGGGTCG
87747 GGTCAACGGGTCGGGTGG
1 GGTCAACGGGTC-----G
87765 GGTCAACGGGTCG
1 GGTCAACGGGTCG
* *
87778 GGTAAATGGGTCG
1 GGTCAACGGGTCG
87791 GGTC
1 GGTC
87795 GGGTCAACGG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 27 0.68
18 13 0.32
ACGTcount: A:0.15, C:0.18, G:0.49, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:89818 original size:24 final size:24
Alignment explanation
Indices: 89801--89923 Score: 103
Period size: 24 Copynumber: 5.2 Consensus size: 24
89791 ATCAAAATAT
*
89801 AAATCAGGTCAAGTATCATATCAG
1 AAATCAGGTCAAGTATCAAATCAG
* *
89825 AAATCAGGTCAAGTAACAGATCA-
1 AAATCAGGTCAAGTATCAAATCAG
* *
89848 AAATCCAAGTCAAGTATCAGATCAG
1 AAAT-CAGGTCAAGTATCAAATCAG
* *
89873 -AATCCATGTC-AG-ATCAGATCAG
1 AAAT-CAGGTCAAGTATCAAATCAG
** *
89895 -AATCCTGTCAAGTATCAGATCAG
1 AAATCAGGTCAAGTATCAAATCAG
89918 AAATCA
1 AAATCA
89924 AATCGAAAAT
Statistics
Matches: 87, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
21 5 0.06
22 15 0.17
23 16 0.18
24 51 0.59
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (24 bp):
AAATCAGGTCAAGTATCAAATCAG
Found at i:91024 original size:18 final size:18
Alignment explanation
Indices: 91001--91036 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
90991 CCTTCCACCG
*
91001 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
91019 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
91037 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:92265 original size:7 final size:7
Alignment explanation
Indices: 92253--92284 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
92243 TGGTCAACTC
92253 CGGTCAA
1 CGGTCAA
92260 CGGTCAA
1 CGGTCAA
92267 CGAGTCAA
1 CG-GTCAA
92275 CGGTCAA
1 CGGTCAA
92282 CGG
1 CGG
92285 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.28, C:0.28, G:0.31, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:92275 original size:15 final size:15
Alignment explanation
Indices: 92255--92283 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
92245 GTCAACTCCG
92255 GTCAACGGTCAACGA
1 GTCAACGGTCAACGA
92270 GTCAACGGTCAACG
1 GTCAACGGTCAACG
92284 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):
GTCAACGGTCAACGA
Found at i:92309 original size:18 final size:18
Alignment explanation
Indices: 92282--92358 Score: 92
Period size: 18 Copynumber: 4.6 Consensus size: 18
92272 CAACGGTCAA
92282 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
92300 CGGGTGGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
* *
92313 CGGGTCGGGTAAATGGGT
1 CGGGTCGGGTCAACGGGT
92331 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
92349 CGGGTCGGGT
1 CGGGTCGGGT
92359 TATGACCGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
13 11 0.22
18 38 0.78
ACGTcount: A:0.12, C:0.18, G:0.52, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:92314 original size:31 final size:31
Alignment explanation
Indices: 92276--92354 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
92266 ACGAGTCAAC
*
92276 GGTCAACGGGTCGGGTCAACGGGTCGGGTGG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
* *
92307 GGTCAACGGGTCGGGTAAATGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
92338 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
92355 GGGTTATGAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.14, C:0.19, G:0.49, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:92318 original size:8 final size:8
Alignment explanation
Indices: 92254--92300 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
92244 GGTCAACTCC
92254 GGTCAAC-
1 GGTCAACG
92261 GGTCAACG
1 GGTCAACG
*
92269 AGTCAAC-
1 GGTCAACG
92276 GGTCAACG
1 GGTCAACG
92284 GGT---CG
1 GGTCAACG
92289 GGTCAACG
1 GGTCAACG
92297 GGTC
1 GGTC
92301 GGGTGGGGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
5 5 0.15
7 13 0.39
8 15 0.45
ACGTcount: A:0.23, C:0.26, G:0.36, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:92354 original size:13 final size:13
Alignment explanation
Indices: 92276--92336 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 13
92266 ACGAGTCAAC
92276 GGTCAACGGGTCG
1 GGTCAACGGGTCG
92289 GGTCAACGGGTCGGGTGG
1 GGTCAACGGGTC-----G
92307 GGTCAACGGGTCG
1 GGTCAACGGGTCG
* *
92320 GGTAAATGGGTCG
1 GGTCAACGGGTCG
92333 GGTC
1 GGTC
92337 GGGTCAACGG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 27 0.68
18 13 0.32
ACGTcount: A:0.15, C:0.18, G:0.49, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:104175 original size:10 final size:10
Alignment explanation
Indices: 104146--104214 Score: 72
Period size: 10 Copynumber: 7.1 Consensus size: 10
104136 GCTGCTGGAA
104146 AACCGGTTTG
1 AACCGGTTTG
*
104156 -ACCAGTTTTG
1 AACC-GGTTTG
104166 AACCGGTTTG
1 AACCGGTTTG
*
104176 -ACCGGTCTG
1 AACCGGTTTG
104185 AACCGGTTTG
1 AACCGGTTTG
*
104195 -ACCGGTCTG
1 AACCGGTTTG
*
104204 AACCGGGTTG
1 AACCGGTTTG
104214 A
1 A
104215 CCCGACCCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 19 0.40
10 26 0.54
11 3 0.06
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:104188 original size:19 final size:19
Alignment explanation
Indices: 104146--104216 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
104136 GCTGCTGGAA
* *
104146 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
104166 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
104185 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
104204 AACCGGGTTGACC
1 AACCGGTTTGACC
104217 CGACCCGACT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 35 0.73
20 13 0.27
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:104232 original size:17 final size:17
Alignment explanation
Indices: 104210--104267 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
104200 TCTGAACCGG
*
104210 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
104227 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
104244 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
104261 GTTGACC
1 GTTGACC
104268 GTGACCGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:104274 original size:6 final size:7
Alignment explanation
Indices: 104257--104286 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
104247 GACCCGACCC
104257 GACCGTT
1 GACCGTT
104264 GACCG-T
1 GACCGTT
104270 GACCGTT
1 GACCGTT
104277 GACCGTT
1 GACCGTT
104284 GAC
1 GAC
104287 TTTCTTTGAC
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:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:104275 original size:13 final size:13
Alignment explanation
Indices: 104257--104282 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
104247 GACCCGACCC
104257 GACCGTTGACCGT
1 GACCGTTGACCGT
104270 GACCGTTGACCGT
1 GACCGTTGACCGT
104283 TGACTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:105224 original size:63 final size:63
Alignment explanation
Indices: 105156--105279 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
105146 CTAATGTGAC
* * *
105156 TCTTAGGTAGG-CTCTGCGGCCCTGAGATC-ATTCTAGGGTAGGCCCTGC-GGCCCTAAGATGTG
1 TCTTAGGTAGGCCTC-ACGGCCCCGAAATCTA-TCTAGGGTAGGCCCT-CAGGCCCTAAGATGTG
105218 T
63 T
* *
105219 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTAGGGTAGGCCCTCAGGCCCTAAGATGT
105280 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.02
63 48 0.91
64 4 0.08
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTAGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:105239 original size:32 final size:32
Alignment explanation
Indices: 105156--105279 Score: 82
Period size: 31 Copynumber: 4.0 Consensus size: 32
105146 CTAATGTGAC
* * *
105156 TCTTAGGTAGGCTCT-GCGGCCCTGAGAT-CA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
* * *
105186 T-TCTAGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 TCT-TA-GGTAGGCTCTCACGGCCCTAAGATGT-A
* *
105219 TCTTAGGTAGGC-CTCACGGCCCCGAA-ATCTA
1 TCTTAGGTAGGCTCTCACGG-CCCTAAGATGTA
*
105250 TCTTGGGTAGGCTCTCA-GGCCCTAAGATGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT
105280 TCCCTTAGGG
Statistics
Matches: 74, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
29 1 0.01
30 8 0.11
31 39 0.53
32 17 0.23
33 8 0.11
34 1 0.01
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
Found at i:109899 original size:10 final size:10
Alignment explanation
Indices: 109870--109938 Score: 63
Period size: 10 Copynumber: 7.1 Consensus size: 10
109860 GCTGCTGGAA
109870 AACCGGTTTG
1 AACCGGTTTG
*
109880 -ACCAGTTTTG
1 AACC-GGTTTG
109890 AACCGGTTTG
1 AACCGGTTTG
*
109900 -ACCGGTCTG
1 AACCGGTTTG
109909 AACCGGTTTG
1 AACCGGTTTG
* *
109919 -ATCGGTCTG
1 AACCGGTTTG
*
109928 AACCGGGTTG
1 AACCGGTTTG
109938 A
1 A
109939 CCCGACCCGA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 18 0.39
10 25 0.54
11 3 0.07
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:109912 original size:19 final size:19
Alignment explanation
Indices: 109870--109940 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
109860 GCTGCTGGAA
* *
109870 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
109890 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
109909 AACCGGTTTGATCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
109928 AACCGGGTTGACC
1 AACCGGTTTGACC
109941 CGACCCGACT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 33 0.72
20 13 0.28
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:109956 original size:17 final size:17
Alignment explanation
Indices: 109934--109991 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
109924 TCTGAACCGG
*
109934 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
109951 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
109968 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
109985 GTTGACC
1 GTTGACC
109992 GTGACCGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:109991 original size:7 final size:7
Alignment explanation
Indices: 109981--110023 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
109971 GACCCGACCC
109981 GACCGTT
1 GACCGTT
109988 GACCG-T
1 GACCGTT
109994 GACCGTT
1 GACCGTT
*
110001 GACAG-T
1 GACCGTT
110007 GACCGTT
1 GACCGTT
110014 GACCGTT
1 GACCGTT
110021 GAC
1 GAC
110024 TTTCTTTGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 11 0.34
7 21 0.66
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:109999 original size:13 final size:13
Alignment explanation
Indices: 109981--110019 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
109971 GACCCGACCC
109981 GACCGTTGACCGT
1 GACCGTTGACCGT
*
109994 GACCGTTGACAGT
1 GACCGTTGACCGT
110007 GACCGTTGACCGT
1 GACCGTTGACCGT
110020 TGACTTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.18, C:0.28, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:120968 original size:17 final size:17
Alignment explanation
Indices: 120942--120979 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
120932 ACGGTCAACA
* *
120942 GTCAATGGTCGGGTTGG
1 GTCAACGGTCGGGTCGG
120959 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
120976 GTCA
1 GTCA
120980 GTCGGGTCGA
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:0.13, C:0.18, G:0.45, T:0.24
Consensus pattern (17 bp):
GTCAACGGTCGGGTCGG
Found at i:125658 original size:17 final size:17
Alignment explanation
Indices: 125632--125669 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
125622 ACGGTCAACA
* *
125632 GTCAATGGTCGGGTTGG
1 GTCAACGGTCGGGTCGG
125649 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
125666 GTCA
1 GTCA
125670 GTCGGGTCGA
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:0.13, C:0.18, G:0.45, T:0.24
Consensus pattern (17 bp):
GTCAACGGTCGGGTCGG
Found at i:127732 original size:34 final size:34
Alignment explanation
Indices: 127689--127757 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
127679 GTTAAGTATT
127689 CGAAAACAAAAGAAAAAAAATTGTGTAATGAGAA
1 CGAAAACAAAAGAAAAAAAATTGTGTAATGAGAA
127723 CGAAAACAAAAGAAAAAAAATTGTGTAATGAGAA
1 CGAAAACAAAAGAAAAAAAATTGTGTAATGAGAA
127757 C
1 C
127758 AAATAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.61, C:0.07, G:0.17, T:0.14
Consensus pattern (34 bp):
CGAAAACAAAAGAAAAAAAATTGTGTAATGAGAA
Found at i:127758 original size:28 final size:32
Alignment explanation
Indices: 127692--127765 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 32
127682 AAGTATTCGA
127692 AAACAAAAGAAAAAAAATTGTGTAATGAGAACG
1 AAACAAAAGAAAAAAAATTGTGTAAT-AGAACG
127725 AAAACAAAAGAAAAAAAATTGTGTAATGAGAAC-
1 -AAACAAAAGAAAAAAAATTGTGTAAT-AGAACG
*
127758 AAATAAAA
1 AAACAAAA
127766 ATGTCTATGG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 7 0.18
34 32 0.82
ACGTcount: A:0.65, C:0.05, G:0.15, T:0.15
Consensus pattern (32 bp):
AAACAAAAGAAAAAAAATTGTGTAATAGAACG
Found at i:130261 original size:13 final size:13
Alignment explanation
Indices: 130243--130267 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
130233 GGTCAAAGGA
130243 GGTCAACAGTCAC
1 GGTCAACAGTCAC
130256 GGTCAACAGTCA
1 GGTCAACAGTCA
130268 ATGGTCGGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (13 bp):
GGTCAACAGTCAC
Found at i:132048 original size:10 final size:10
Alignment explanation
Indices: 132033--132057 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
132023 TAACCAAAAC
132033 AAATATTTGA
1 AAATATTTGA
132043 AAATATTTGA
1 AAATATTTGA
132053 AAATA
1 AAATA
132058 CCAAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (10 bp):
AAATATTTGA
Found at i:134835 original size:32 final size:32
Alignment explanation
Indices: 134797--134873 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
134787 CGAGATCGTT
* *
134797 GGGCCTACCTAAGAACAT-ATCTTAGGGTCGCA
1 GGGCCTACCTAAGAA-ATGATCTCAGGGCCGCA
**
134829 GGGCCTACCCGAG-AATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAATGATCTCAGGGCCGCA
*
134860 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
134874 GTCACATTAC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
30 2 0.06
31 23 0.64
32 11 0.31
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (32 bp):
GGGCCTACCTAAGAAATGATCTCAGGGCCGCA
Found at i:142033 original size:15 final size:16
Alignment explanation
Indices: 142013--142043 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
142003 GAGCATTGTA
142013 TTAAAAAAC-AAAAAT
1 TTAAAAAACTAAAAAT
142028 TTAAAAAACTAAAAAT
1 TTAAAAAACTAAAAAT
142044 AGATTTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (16 bp):
TTAAAAAACTAAAAAT
Found at i:142421 original size:14 final size:15
Alignment explanation
Indices: 142396--142426 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
142386 TGAAAAGTAA
142396 AATATGTAAAATAAT
1 AATATGTAAAATAAT
142411 AATAT-TAAAATAAT
1 AATATGTAAAATAAT
142425 AA
1 AA
142427 AATTCCCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (15 bp):
AATATGTAAAATAAT
Found at i:143070 original size:15 final size:16
Alignment explanation
Indices: 143050--143080 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
143040 GTGCATTGTA
143050 TTAAAAAAC-AAAAAT
1 TTAAAAAACTAAAAAT
143065 TTAAAAAACTAAAAAT
1 TTAAAAAACTAAAAAT
143081 AGATTTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (16 bp):
TTAAAAAACTAAAAAT
Found at i:143457 original size:14 final size:15
Alignment explanation
Indices: 143432--143462 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
143422 TGAAAAGTAA
143432 AATATGTAAAATAAT
1 AATATGTAAAATAAT
143447 AATAT-TAAAATAAT
1 AATATGTAAAATAAT
143461 AA
1 AA
143463 AATTCCCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (15 bp):
AATATGTAAAATAAT
Found at i:144107 original size:15 final size:16
Alignment explanation
Indices: 144087--144117 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
144077 GTGCATTGTA
144087 TTAAAAAAC-AAAAAT
1 TTAAAAAACTAAAAAT
144102 TTAAAAAACTAAAAAT
1 TTAAAAAACTAAAAAT
144118 AGATTTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (16 bp):
TTAAAAAACTAAAAAT
Found at i:148352 original size:10 final size:10
Alignment explanation
Indices: 148332--148376 Score: 58
Period size: 9 Copynumber: 4.6 Consensus size: 10
148322 ACCGGTTCGG
148332 ACCGGTC-AA
1 ACCGGTCAAA
*
148341 ACCAGTCAAA
1 ACCGGTCAAA
148351 ACCGGTTCAAA
1 ACCGG-TCAAA
148362 ACCGGTC-AA
1 ACCGGTCAAA
148371 ACCGGT
1 ACCGGT
148377 TTTCCAGCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 14 0.44
10 8 0.25
11 10 0.31
ACGTcount: A:0.36, C:0.31, G:0.20, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:148362 original size:11 final size:11
Alignment explanation
Indices: 148346--148377 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
148336 GTCAAACCAG
148346 TCAAAACCGGT
1 TCAAAACCGGT
148357 TCAAAACCGG-
1 TCAAAACCGGT
148367 TC-AAACCGGT
1 TCAAAACCGGT
148377 T
1 T
148378 TTCCAGCTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 7 0.35
10 3 0.15
11 10 0.50
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (11 bp):
TCAAAACCGGT
Found at i:148372 original size:20 final size:21
Alignment explanation
Indices: 148332--148377 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
148322 ACCGGTTCGG
148332 ACCGG-TC-AAACCAGTCAAA
1 ACCGGTTCAAAACCAGTCAAA
*
148351 ACCGGTTCAAAACCGGTC-AA
1 ACCGGTTCAAAACCAGTCAAA
148371 ACCGGTT
1 ACCGGTT
148378 TTCCAGCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 5 0.21
20 11 0.46
21 8 0.33
ACGTcount: A:0.35, C:0.30, G:0.20, T:0.15
Consensus pattern (21 bp):
ACCGGTTCAAAACCAGTCAAA
Found at i:153015 original size:19 final size:19
Alignment explanation
Indices: 152987--153048 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
152977 TGTATTTTAG
*
152987 TTTAAATAGGTTTTAGGAT
1 TTTAATTAGGTTTTAGGAT
* *
153006 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGGAT
* *
153025 ATTATATTA-TTTTTAGGTAT
1 TTTA-ATTAGGTTTTAGG-AT
153045 TTTA
1 TTTA
153049 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
19 24 0.73
20 9 0.27
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGGAT
Found at i:159336 original size:11 final size:11
Alignment explanation
Indices: 159320--159355 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
159310 TTCGTTATAT
159320 TTTTGTTTTTA
1 TTTTGTTTTTA
159331 TTTTGTTTTTA
1 TTTTGTTTTTA
*
159342 TTTT-TTTTAA
1 TTTTGTTTTTA
159352 TTTT
1 TTTT
159356 TTAGCGAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (11 bp):
TTTTGTTTTTA
Found at i:163776 original size:18 final size:18
Alignment explanation
Indices: 163755--163790 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
163745 GGTCAATGCC
*
163755 GGTCAACGGGTCGGGTCG
1 GGTCAACAGGTCGGGTCG
*
163773 GGTCAATAGGTCGGGTCG
1 GGTCAACAGGTCGGGTCG
163791 AGTCGGGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.19, G:0.47, T:0.19
Consensus pattern (18 bp):
GGTCAACAGGTCGGGTCG
Found at i:165299 original size:76 final size:75
Alignment explanation
Indices: 165219--165366 Score: 210
Period size: 76 Copynumber: 2.0 Consensus size: 75
165209 TAAACTCAAA
* *
165219 TTTAGGACAATA-TTTTA-AACATTATATTTTATCTTTGTATTTTAGTTTAAATAGCTTTTTAGT
1 TTTAGGACAATATTTTTATAAC-TTAT-CTTTATCTTTGTATTTTAGTTTAAATAG-GTTTTAGT
165282 ATTTTAATTAAGT
63 ATTTTAATTAAGT
* * *
165295 TTTAGGATATTATTTTTATATCTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
1 TTTAGGACAATATTTTTATAACTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
165360 TTAATTA
66 TTAATTA
165367 GGATTTAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
75 17 0.26
76 37 0.57
77 9 0.14
78 2 0.03
ACGTcount: A:0.29, C:0.05, G:0.09, T:0.57
Consensus pattern (75 bp):
TTTAGGACAATATTTTTATAACTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAGT
Found at i:166053 original size:21 final size:22
Alignment explanation
Indices: 166027--166067 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
166017 CTTTAATTTG
166027 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
166048 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
166068 TATTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:171620 original size:44 final size:44
Alignment explanation
Indices: 171235--171621 Score: 483
Period size: 44 Copynumber: 8.8 Consensus size: 44
171225 AGAGCCTAGA
* * ** * * * *
171235 AAACGGTAAGGTCTTACCCTTGCATATGGGAAAGGAACCTTGAGA
1 AAACTGTAAGG-CTTACCCTTGCACACAGAAAAGGAACCTGGGGG
* ** *
171280 AAACTGTAAGGCTTACCATTGCACACATCAAGGGAACCT-GGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGAAAAGGAACCTGGGGG
* * * * *
171323 AAACTATAAGGCTTACCCTTTCATATAGTAAAGGAACCTGGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGAAAAGGAACCTGGGGG
* *
171367 GAACTGTAAGGCTTACCCTTGCACACAGTAAAGGAACCTGGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGAAAAGGAACCTGGGGG
*
171411 AAACTGTAAGGCTTACCCTTGCACACAGTAAAGGAACCTGGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGAAAAGGAACCTGGGGG
**
171455 AAACTGTAAGGCTTACCCTTGCACACAGCGAAGGAACCTGGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGAAAAGGAACCTGGGGG
*
171499 AAACTCTAAGGCTTACCCTTGCACACA-ACAAAGGAACCTGGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGA-AAAGGAACCTGGGGG
* *
171543 AAACTGTAAGGCTTACCCTTGCACACA-ATAAAGGAACCTAGGGA
1 AAACTGTAAGGCTTACCCTTGCACACAGA-AAAGGAACCTGGGGG
* *
171587 AAACTGTAAGGCATACCCTTGCACATAGAAAAGGA
1 AAACTGTAAGGCTTACCCTTGCACACAGAAAAGGA
171622 GACTGCTATA
Statistics
Matches: 304, Mismatches: 35, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
43 33 0.11
44 260 0.86
45 11 0.04
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (44 bp):
AAACTGTAAGGCTTACCCTTGCACACAGAAAAGGAACCTGGGGG
Found at i:175059 original size:29 final size:29
Alignment explanation
Indices: 174978--175059 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
174968 GCACCCCTTT
* *
174978 TCGAATTAATTCCCATAATAGCAACAAAA
1 TCGAATTAATTCCCAGAATAGCACCAAAA
*
175007 TCGAATTAATTCCTAGAATAGCACCAAAA
1 TCGAATTAATTCCCAGAATAGCACCAAAA
*
175036 TCGAATAAATTCCCAGAATAGCAC
1 TCGAATTAATTCCCAGAATAGCAC
175060 AGGTGAACGA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.23
Consensus pattern (29 bp):
TCGAATTAATTCCCAGAATAGCACCAAAA
Found at i:179088 original size:24 final size:24
Alignment explanation
Indices: 179060--179167 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
179050 AAATATTTTA
*
179060 TCTGATTTCTGACTTGAATTTTGT
1 TCTGATTTCTGACTTGAATTCTGT
* * * *
179084 TCTGATATATGACCTAAATTCTGT
1 TCTGATTTCTGACTTGAATTCTGT
*
179108 TCTGATTTCTGA-TCTGGATTCTGT
1 TCTGATTTCTGACT-TGAATTCTGT
* * *
179132 TCTGATATATG-TTCTGAATTCTGT
1 TCTGATTTCTGACT-TGAATTCTGT
*
179156 TTTGATTTCTGA
1 TCTGATTTCTGA
179168 TATCTCTGTT
Statistics
Matches: 65, Mismatches: 16, Indels: 5
0.76 0.19 0.06
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGACTTGAATTCTGT
Found at i:179112 original size:48 final size:48
Alignment explanation
Indices: 179060--179168 Score: 148
Period size: 48 Copynumber: 2.3 Consensus size: 48
179050 AAATATTTTA
*
179060 TCTGATTTCTGA-CTTGAATTTTGTTCTGATATATGACCTAAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGTTCTGATATATGACCTAAATTCTGT
* ** *
179108 TCTGATTTCTGATCTGGATTCTGTTCTGATATATGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGTTCTGATATATGACCTAAATTCTGT
*
179156 TTTGATTTCTGAT
1 TCTGATTTCTGAT
179169 ATCTCTGTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
48 53 0.98
49 1 0.02
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (48 bp):
TCTGATTTCTGATCTGAATTCTGTTCTGATATATGACCTAAATTCTGT
Found at i:179123 original size:12 final size:12
Alignment explanation
Indices: 179102--179166 Score: 69
Period size: 12 Copynumber: 5.4 Consensus size: 12
179092 ATGACCTAAA
179102 TTCTGTTCTGAT
1 TTCTGTTCTGAT
*
179114 TTCTGATCTGGA-
1 TTCTGTTCT-GAT
179126 TTCTGTTCTGAT
1 TTCTGTTCTGAT
* * *
179138 ATATGTTCTGAA
1 TTCTGTTCTGAT
*
179150 TTCTGTTTTGAT
1 TTCTGTTCTGAT
179162 TTCTG
1 TTCTG
179167 ATATCTCTGT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.54
Consensus pattern (12 bp):
TTCTGTTCTGAT
Found at i:183097 original size:18 final size:18
Alignment explanation
Indices: 183074--183108 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
183064 TTCCATCCGG
*
183074 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
183092 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
183109 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:184283 original size:19 final size:19
Alignment explanation
Indices: 184261--184343 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
184251 CTAGGCGGCT
*
184261 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
184280 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
184299 CGGCTC-G----GCTCAAA
1 CGGCTCGGCTCAGCTCAAA
*
184313 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
184332 CGGCTCGGCTCA
1 CGGCTCGGCTCA
184344 AACGGCTCTC
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.23
15 1 0.02
18 1 0.02
19 42 0.74
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.17
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:184290 original size:14 final size:14
Alignment explanation
Indices: 184285--184351 Score: 80
Period size: 14 Copynumber: 4.4 Consensus size: 14
184275 TCAAACGGCT
*
184285 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
184299 CGGCTCGGCTCAAA
1 CGGCTCGGCTCAAA
184313 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
184331 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
184346 CGGCTC
1 CGGCTC
184352 TCAGGCTTCC
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
14 31 0.66
15 2 0.04
18 2 0.04
19 12 0.26
ACGTcount: A:0.19, C:0.37, G:0.28, T:0.15
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:184310 original size:33 final size:33
Alignment explanation
Indices: 184267--184351 Score: 152
Period size: 33 Copynumber: 2.6 Consensus size: 33
184257 GGCTCGGCTT
*
184267 GGCTCAGCTCAAACGGCTCGGCTCAGCTCAAAC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
*
184300 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAGC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
184333 GGCTCGGCTCAAACGGCTC
1 GGCTCGGCTCAAACGGCTC
184352 TCAGGCTTCC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.15
Consensus pattern (33 bp):
GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
Found at i:188117 original size:18 final size:18
Alignment explanation
Indices: 188094--188128 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
188084 TTCCATCCGG
*
188094 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
188112 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
188129 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:189302 original size:19 final size:19
Alignment explanation
Indices: 189280--189362 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
189270 CTAGGCGGCT
*
189280 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
189299 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
189318 CGGCTC-G----GCTCAAA
1 CGGCTCGGCTCAGCTCAAA
*
189332 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
189351 CGGCTCGGCTCA
1 CGGCTCGGCTCA
189363 AACGGCTCCT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.23
15 1 0.02
18 1 0.02
19 42 0.74
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.17
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:189309 original size:14 final size:14
Alignment explanation
Indices: 189304--189370 Score: 80
Period size: 14 Copynumber: 4.4 Consensus size: 14
189294 TCAAACGGCT
*
189304 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
189318 CGGCTCGGCTCAAA
1 CGGCTCGGCTCAAA
189332 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
189350 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
189365 CGGCTC
1 CGGCTC
189371 CTCAGGCTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
14 31 0.66
15 2 0.04
18 2 0.04
19 12 0.26
ACGTcount: A:0.19, C:0.37, G:0.28, T:0.15
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:189329 original size:33 final size:33
Alignment explanation
Indices: 189286--189370 Score: 152
Period size: 33 Copynumber: 2.6 Consensus size: 33
189276 GGCTCGGCTT
*
189286 GGCTCAGCTCAAACGGCTCGGCTCAGCTCAAAC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
*
189319 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAGC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
189352 GGCTCGGCTCAAACGGCTC
1 GGCTCGGCTCAAACGGCTC
189371 CTCAGGCTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.15
Consensus pattern (33 bp):
GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
Found at i:190751 original size:31 final size:31
Alignment explanation
Indices: 190713--190784 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
190703 TCATAACCTG
* *
190713 ACCCGACCCGACCCGTTTACCCGACCCGTTC
1 ACCCGACCCGACCCGTTGACCCAACCCGTTC
* *
190744 ACCCGACCCGACCTGTTGACCCAACCCGTTG
1 ACCCGACCCGACCCGTTGACCCAACCCGTTC
190775 ACCCGACCCG
1 ACCCGACCCG
190785 GTGACCGTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.18, C:0.50, G:0.18, T:0.14
Consensus pattern (31 bp):
ACCCGACCCGACCCGTTGACCCAACCCGTTC
Found at i:190752 original size:18 final size:18
Alignment explanation
Indices: 190731--190771 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
190721 CGACCCGTTT
*
190731 ACCCGACCCGTTCACCCG
1 ACCCGACCCGTTCACCCA
* *
190749 ACCCGACCTGTTGACCCA
1 ACCCGACCCGTTCACCCA
190767 ACCCG
1 ACCCG
190772 TTGACCCGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.51, G:0.17, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGTTCACCCA
Found at i:190764 original size:13 final size:13
Alignment explanation
Indices: 190717--190790 Score: 67
Period size: 13 Copynumber: 5.3 Consensus size: 13
190707 AACCTGACCC
190717 GACCCGACCCGTT
1 GACCCGACCCGTT
*
190730 TACCCGACCCGTT
1 GACCCGACCCGTT
*
190743 CACCCGACCCGACCTGTT
1 -----GACCCGACCCGTT
*
190761 GACCCAACCCGTT
1 GACCCGACCCGTT
*
190774 GACCCGACCCGGT
1 GACCCGACCCGTT
190787 GACC
1 GACC
190791 GTTGACCGAC
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
13 38 0.78
18 11 0.22
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:193323 original size:12 final size:12
Alignment explanation
Indices: 193308--193367 Score: 68
Period size: 12 Copynumber: 5.0 Consensus size: 12
193298 GATATATGAC
193308 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
193320 CTGATTTCTGAT
1 CTGAATTCTGTT
*
193332 CTGGATTCTGTT
1 CTGAATTCTGTT
*
193344 CTG-ATATCTTTT
1 CTGAAT-TCTGTT
193356 CTGAATTCTGTT
1 CTGAATTCTGTT
193368 TTGATTTTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 2 0.05
12 35 0.90
13 2 0.05
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.52
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:193346 original size:48 final size:49
Alignment explanation
Indices: 193275--193379 Score: 124
Period size: 48 Copynumber: 2.2 Consensus size: 49
193265 ATTTTATCTA
*
193275 ATTTCTGA-CTTGAATTTTGTTCTGATATATGACCTGAATTCTGTTCTG
1 ATTTCTGATCTTGAATTCTGTTCTGATATATGACCTGAATTCTGTTCTG
* * *** *
193323 ATTTCTGATC-TGGATTCTGTTCTGATATCTTTTCTGAATTCTGTTTTG
1 ATTTCTGATCTTGAATTCTGTTCTGATATATGACCTGAATTCTGTTCTG
*
193371 ATTTTTGAT
1 ATTTCTGAT
193380 ATCTCTGTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 47 0.98
49 1 0.02
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.52
Consensus pattern (49 bp):
ATTTCTGATCTTGAATTCTGTTCTGATATATGACCTGAATTCTGTTCTG
Found at i:193358 original size:24 final size:24
Alignment explanation
Indices: 193285--193372 Score: 104
Period size: 24 Copynumber: 3.7 Consensus size: 24
193275 ATTTCTGACT
* * *
193285 TGAATTTTGTTCTGATATATGACC
1 TGAATTCTGTTCTGATATCTGATC
*
193309 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATCTGATC
* **
193333 TGGATTCTGTTCTGATATCTTTTC
1 TGAATTCTGTTCTGATATCTGATC
*
193357 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
193373 TTTTGATATC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.18, C:0.14, G:0.17, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:216608 original size:164 final size:164
Alignment explanation
Indices: 216337--216664 Score: 656
Period size: 164 Copynumber: 2.0 Consensus size: 164
216327 GATACCGTCC
216337 AGATCCAGATCACATCATTCAGGTTGATGAGGTAGAGCTGAGACCTGATTTGTCATATGAGGAGG
1 AGATCCAGATCACATCATTCAGGTTGATGAGGTAGAGCTGAGACCTGATTTGTCATATGAGGAGG
216402 AGCCTGTTCAGGTTTTAGAGAGGGATGAGCGAGTTCTTCGGAATAGGCGTATTCCAATGGTCAAA
66 AGCCTGTTCAGGTTTTAGAGAGGGATGAGCGAGTTCTTCGGAATAGGCGTATTCCAATGGTCAAA
216467 GTTCAGTGGAGTAATCGTAGCCCCTCAGAAGCTA
131 GTTCAGTGGAGTAATCGTAGCCCCTCAGAAGCTA
216501 AGATCCAGATCACATCATTCAGGTTGATGAGGTAGAGCTGAGACCTGATTTGTCATATGAGGAGG
1 AGATCCAGATCACATCATTCAGGTTGATGAGGTAGAGCTGAGACCTGATTTGTCATATGAGGAGG
216566 AGCCTGTTCAGGTTTTAGAGAGGGATGAGCGAGTTCTTCGGAATAGGCGTATTCCAATGGTCAAA
66 AGCCTGTTCAGGTTTTAGAGAGGGATGAGCGAGTTCTTCGGAATAGGCGTATTCCAATGGTCAAA
216631 GTTCAGTGGAGTAATCGTAGCCCCTCAGAAGCTA
131 GTTCAGTGGAGTAATCGTAGCCCCTCAGAAGCTA
216665 CTTGGGAGAC
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 164 1.00
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.26
Consensus pattern (164 bp):
AGATCCAGATCACATCATTCAGGTTGATGAGGTAGAGCTGAGACCTGATTTGTCATATGAGGAGG
AGCCTGTTCAGGTTTTAGAGAGGGATGAGCGAGTTCTTCGGAATAGGCGTATTCCAATGGTCAAA
GTTCAGTGGAGTAATCGTAGCCCCTCAGAAGCTA
Found at i:217446 original size:13 final size:13
Alignment explanation
Indices: 217428--217452 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
217418 GACCGGTCAT
217428 GACCCGTTGACCC
1 GACCCGTTGACCC
217441 GACCCGTTGACC
1 GACCCGTTGACC
217453 TGACTCGACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.44, G:0.24, T:0.16
Consensus pattern (13 bp):
GACCCGTTGACCC
Found at i:217456 original size:18 final size:17
Alignment explanation
Indices: 217435--217469 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
217425 CATGACCCGT
217435 TGACCCGACCCGTTGACC
1 TGACCCGA-CCGTTGACC
*
217453 TGACTCGACCGTTGACC
1 TGACCCGACCGTTGACC
217470 GTTGACCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.17, C:0.40, G:0.23, T:0.20
Consensus pattern (17 bp):
TGACCCGACCGTTGACC
Found at i:217539 original size:29 final size:30
Alignment explanation
Indices: 217479--217633 Score: 110
Period size: 29 Copynumber: 5.3 Consensus size: 30
217469 CGTTGACCGA
* **
217479 TGCTATTCTGAGAATTAATTC-AGTTTCG-G
1 TGCTATTTTGAGAATTAATTCGAAATT-GAG
*
217508 TGCTATTATGAGAATTAATTCGAAA-TGAG
1 TGCTATTTTGAGAATTAATTCGAAATTGAG
* * *
217537 TGCTATTTTG-GTAATT-TTTCAAAAATTTA-
1 TGCTATTTTGAG-AATTAATTC-GAAATTGAG
* * * *
217566 TGATATTCTGGGAATTAATTTGAAATTG-G
1 TGCTATTTTGAGAATTAATTCGAAATTGAG
* *
217595 TGCTATTTTGAGAATTAATTCGAAA-AGGG
1 TGCTATTTTGAGAATTAATTCGAAATTGAG
217624 TGCTATTTTG
1 TGCTATTTTG
217634 GTAATTATTT
Statistics
Matches: 99, Mismatches: 18, Indels: 18
0.73 0.13 0.13
Matches are distributed among these distances:
28 6 0.06
29 87 0.88
30 6 0.06
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (30 bp):
TGCTATTTTGAGAATTAATTCGAAATTGAG
Found at i:217639 original size:29 final size:28
Alignment explanation
Indices: 217506--217660 Score: 96
Period size: 29 Copynumber: 5.4 Consensus size: 28
217496 ATTCAGTTTC
* *
217506 GGTGCTATTATGAGAATTAATTCGAAATG
1 GGTGCTATTTTG-GAATTAATTCGAAAAG
* * * *
217535 AGTGCTATTTTGGTAATT-TTTCAAAAATT
1 GGTGCTATTTTGG-AATTAATTCGAAAA-G
** * * * **
217564 TATGATATTCTGGGAATTAATTTGAAATT
1 GGTGCTATT-TTGGAATTAATTCGAAAAG
217593 GGTGCTATTTTGAGAATTAATTCGAAAAG
1 GGTGCTATTTTG-GAATTAATTCGAAAAG
* **
217622 GGTGCTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGG-AATTAATTCGAAAAG
*
217651 AGTGCTATTT
1 GGTGCTATTT
217661 GTATAAAATG
Statistics
Matches: 95, Mismatches: 25, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
28 10 0.11
29 77 0.81
30 8 0.08
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42
Consensus pattern (28 bp):
GGTGCTATTTTGGAATTAATTCGAAAAG
Found at i:219927 original size:135 final size:134
Alignment explanation
Indices: 219696--219977 Score: 327
Period size: 135 Copynumber: 2.1 Consensus size: 134
219686 GACGGCTTAC
* ** * * * *
219696 CGGGTTCGAATTTGGCGAATTGGACATGGGATTCGGATTCAGAACGTTGAAAGCATAAAATATGA
1 CGGGTTCGAATTTCGAAAAATGGACATGGGAATCGGATTCAGAACGTCGAAAACATAAAATATGA
* * * ** *
219761 CTTTTCGGAAATTTGGAATTTTCGGTCAAAATCAAAGTCAACGGGTTTGACTGGTAATTTCGAGG
66 CTCTTCGGAAATTTCGAATTTTCGGTCAAAATCAAAGTCAACGAGTTTGACTGACAATTTCGAGA
219826 CCTT
131 CCTT
* *
219830 CGGGTTCGAATTTCGAAAAATGGACA-GTGGAATCGGATTTCAGGACGTCGAAAAACATAAAGTA
1 CGGGTTCGAATTTCGAAAAATGGACATG-GGAATCGGA-TTCAGAACGTCG-AAAACATAAAATA
* * *
219894 TGAC-CTTCTGAAATTTCGAATTCTT-GGTCAAAATTAAAGTCAACGAGTTTGACTGACAATTTG
63 TGACTCTTCGGAAATTTCGAATT-TTCGGTCAAAATCAAAGTCAACGAGTTTGACTGACAATTTC
*
219957 GAGACTTT
127 GAGACCTT
*
219965 CGAGTTCGAATTT
1 CGGGTTCGAATTT
219978 GGTGAAACGG
Statistics
Matches: 124, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
133 1 0.01
134 30 0.24
135 76 0.61
136 17 0.14
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (134 bp):
CGGGTTCGAATTTCGAAAAATGGACATGGGAATCGGATTCAGAACGTCGAAAACATAAAATATGA
CTCTTCGGAAATTTCGAATTTTCGGTCAAAATCAAAGTCAACGAGTTTGACTGACAATTTCGAGA
CCTT
Found at i:220156 original size:29 final size:29
Alignment explanation
Indices: 220113--220268 Score: 93
Period size: 29 Copynumber: 5.4 Consensus size: 29
220103 ACATTTTATA
* *
220113 AAAATAGCACTCTTTTTAAAATAATTAC-C
1 AAAATAGCACCCTTTTCAAAATAATT-CTC
* *
220142 AAAATAGCACCCTTTTCGAATTAATTCTC
1 AAAATAGCACCCTTTTCAAAATAATTCTC
** * *
220171 AAAATAGCACCAATTTCAAATTAATTCCC
1 AAAATAGCACCCTTTTCAAAATAATTCTC
* * *** *
220200 AGAATATCATAAATTTTCGAAAA-AATAC-C
1 AAAATAGCA-CCCTTTTC-AAAATAATTCTC
* * *
220229 AAAATAGCACCCATTTCGAATTAATTCTC
1 AAAATAGCACCCTTTTCAAAATAATTCTC
**
220258 AGGATAGCACC
1 AAAATAGCACC
220269 AAAACTGAAT
Statistics
Matches: 96, Mismatches: 26, Indels: 10
0.73 0.20 0.08
Matches are distributed among these distances:
27 2 0.02
28 9 0.09
29 73 0.76
30 9 0.09
31 3 0.03
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.29
Consensus pattern (29 bp):
AAAATAGCACCCTTTTCAAAATAATTCTC
Found at i:246415 original size:29 final size:30
Alignment explanation
Indices: 246365--246556 Score: 223
Period size: 29 Copynumber: 6.6 Consensus size: 30
246355 CACATTCAAA
*
246365 AATTCCCAAAATGTCACC-TTTTTCAAAAT
1 AATTCCCAGAATGTCACCTTTTTTCAAAAT
**
246394 AATT-CCAGAATGTCACCTTTTTTTGAAAT
1 AATTCCCAGAATGTCACCTTTTTTCAAAAT
* * *
246423 ATTTCCTAGATTGTCACC-TTTTTCAAAAT
1 AATTCCCAGAATGTCACCTTTTTTCAAAAT
* *
246452 AATTCCCAAAATGTCACCTTTTTT-GAAAT
1 AATTCCCAGAATGTCACCTTTTTTCAAAAT
*
246481 ATTTCCCAGAATGTCACCTTTTTTCAAAAT
1 AATTCCCAGAATGTCACCTTTTTTCAAAAT
* * *
246511 AATTACCAAAATATCA-CTTTTTTCAAAAT
1 AATTCCCAGAATGTCACCTTTTTTCAAAAT
* *
246540 ATTTCCCAGAATATCAC
1 AATTCCCAGAATGTCAC
246557 TGGGTCGGGT
Statistics
Matches: 135, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
28 12 0.09
29 91 0.67
30 32 0.24
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.39
Consensus pattern (30 bp):
AATTCCCAGAATGTCACCTTTTTTCAAAAT
Found at i:246446 original size:58 final size:59
Alignment explanation
Indices: 246367--246556 Score: 269
Period size: 59 Copynumber: 3.3 Consensus size: 59
246357 CATTCAAAAA
* *
246367 TTCCCAAAATGTCACCTTTTTCAAAATAATT-CCAGAATGTCACCTTTTTTTGAAATAT
1 TTCCCAGAATGTCACCTTTTTCAAAATAATTACCAAAATGTCACCTTTTTTTGAAATAT
* * *
246425 TTCCTAGATTGTCACCTTTTTCAAAATAATTCCCAAAATGTCACC-TTTTTTGAAATAT
1 TTCCCAGAATGTCACCTTTTTCAAAATAATTACCAAAATGTCACCTTTTTTTGAAATAT
* **
246483 TTCCCAGAATGTCACCTTTTTTCAAAATAATTACCAAAATATCA-CTTTTTTCAAAATAT
1 TTCCCAGAATGTCACC-TTTTTCAAAATAATTACCAAAATGTCACCTTTTTTTGAAATAT
*
246542 TTCCCAGAATATCAC
1 TTCCCAGAATGTCAC
246557 TGGGTCGGGT
Statistics
Matches: 118, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
58 56 0.47
59 62 0.53
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.39
Consensus pattern (59 bp):
TTCCCAGAATGTCACCTTTTTCAAAATAATTACCAAAATGTCACCTTTTTTTGAAATAT
Found at i:246504 original size:59 final size:57
Alignment explanation
Indices: 246367--246556 Score: 265
Period size: 58 Copynumber: 3.3 Consensus size: 57
246357 CATTCAAAAA
* *
246367 TTCCCAAAATGTCACCTTTTTCAAAATAATTCCAGAATGTCACCTTTTTTTGAAATAT
1 TTCCCAGAATGTCACCTTTTTCAAAATAATTCCAAAATGTCACC-TTTTTTGAAATAT
* *
246425 TTCCTAGATTGTCACCTTTTTCAAAATAATTCCCAAAATGTCACCTTTTTTGAAATAT
1 TTCCCAGAATGTCACCTTTTTCAAAATAATT-CCAAAATGTCACCTTTTTTGAAATAT
* *
246483 TTCCCAGAATGTCACCTTTTTTCAAAATAATTACCAAAATATCA-CTTTTTTCAAAATAT
1 TTCCCAGAATGTCACC-TTTTTCAAAATAATT-CCAAAATGTCACCTTTTTT-GAAATAT
*
246542 TTCCCAGAATATCAC
1 TTCCCAGAATGTCAC
246557 TGGGTCGGGT
Statistics
Matches: 119, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
58 62 0.52
59 57 0.48
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.39
Consensus pattern (57 bp):
TTCCCAGAATGTCACCTTTTTCAAAATAATTCCAAAATGTCACCTTTTTTGAAATAT
Found at i:248953 original size:129 final size:130
Alignment explanation
Indices: 248757--248995 Score: 324
Period size: 129 Copynumber: 1.8 Consensus size: 130
248747 TCGATTAGGG
* ** * * *
248757 GCTTTCGAGTCAGAATTTGGCAAAATGGACTTCGGAATCAGATTCAGGATGTCGAAAAACATTAA
1 GCTTTCGAGTCAGAATTTGGAAAAACAGACTTCGGAATCAGACTCAGGACGTCGAAAAACATGAA
248822 ATATGACTTTTCAAAAAATTTT-AC-TTTTTGGTCAAAATCAACGGGTTTGATTGACAATTTCAA
66 ATATGACTTTT-AAAAAATTTTGACTTTTTTGGTCAAAATCAACGGGTTTGATTGACAATTTCAA
248885 A
130 A
* * *
248886 GCTTTCGGGTTCA-AATTTGGAAAAACAGACTTCGGATTCAGACTCAGGACGTCGTAAAGA-ATG
1 GCTTTCGAG-TCAGAATTTGGAAAAACAGACTTCGGAATCAGACTCAGGACGTCG-AAAAACATG
* *
248949 AAATATGACTTTTAGAAAATTTTGACTTTTTTGGTCAAAGTCAACGG
64 AAATATGACTTTTAAAAAATTTTGACTTTTTTGGTCAAAATCAACGG
248996 TCAACGGGTC
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
128 9 0.09
129 60 0.63
130 26 0.27
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (130 bp):
GCTTTCGAGTCAGAATTTGGAAAAACAGACTTCGGAATCAGACTCAGGACGTCGAAAAACATGAA
ATATGACTTTTAAAAAATTTTGACTTTTTTGGTCAAAATCAACGGGTTTGATTGACAATTTCAAA
Found at i:249604 original size:17 final size:17
Alignment explanation
Indices: 249572--249607 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
249562 TTTCTGATTT
**
249572 CAATCAGAAATGAATTG
1 CAATCAGAAACAAATTG
249589 CAATCAGAAACAAATTG
1 CAATCAGAAACAAATTG
249606 CA
1 CA
249608 CGCATATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.19
Consensus pattern (17 bp):
CAATCAGAAACAAATTG
Found at i:257383 original size:16 final size:16
Alignment explanation
Indices: 257362--257392 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
257352 GCGCATTGTA
257362 TTAAAAACGAAAAATT
1 TTAAAAACGAAAAATT
*
257378 TTAAAAACTAAAAAT
1 TTAAAAACGAAAAAT
257393 AAATTTATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (16 bp):
TTAAAAACGAAAAATT
Found at i:263740 original size:11 final size:11
Alignment explanation
Indices: 263724--263773 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
263714 TACTTATTAG
263724 TTTTAATTGAT
1 TTTTAATTGAT
***
263735 TTTTAAAACAT
1 TTTTAATTGAT
**
263746 TTAAAATTGAT
1 TTTTAATTGAT
263757 TTTTAATTGAT
1 TTTTAATTGAT
263768 TTTTAA
1 TTTTAA
263774 AAATGTAAAA
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (11 bp):
TTTTAATTGAT
Done.