Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_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: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 30 of 31
Found at i:5798751 original size:20 final size:20
Alignment explanation
Indices: 5798726--5798771 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
5798716 CAATTTGCGA
5798726 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
5798746 TTTCGCGTTGTGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
5798766 TATCGC
1 TTTCGC
5798772 AACGCTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:5800212 original size:25 final size:25
Alignment explanation
Indices: 5800165--5800212 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5800155 CATTATTTTC
*
5800165 CAAATAATGTACCCATAAAAATGAT
1 CAAATAATGTACCCACAAAAATGAT
* *
5800190 CAAATAATGTAGCCACAACAATG
1 CAAATAATGTACCCACAAAAATG
5800213 TTTAATTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.10, T:0.21
Consensus pattern (25 bp):
CAAATAATGTACCCACAAAAATGAT
Found at i:5800346 original size:20 final size:20
Alignment explanation
Indices: 5800318--5800367 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
5800308 GCAACGCTTA
*
5800318 TTTCGCGTTGTGAATTTTAC
1 TTTCGCGTTGTGAATTTGAC
*
5800338 TTTCACGTTGTGAATTTGAC
1 TTTCGCGTTGTGAATTTGAC
5800358 TTTCGCGTTG
1 TTTCGCGTTG
5800368 ATCGCAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.14, C:0.16, G:0.22, T:0.48
Consensus pattern (20 bp):
TTTCGCGTTGTGAATTTGAC
Found at i:5800676 original size:18 final size:18
Alignment explanation
Indices: 5800653--5800688 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5800643 AAGCCGGTGG
*
5800653 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
5800671 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
5800689 CCTTTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:5802994 original size:23 final size:24
Alignment explanation
Indices: 5802951--5802996 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5802941 ATCATAAAAA
5802951 TCCGAGTATTGACCAAGATCAAAG
1 TCCGAGTATTGACCAAGATCAAAG
*
5802975 TCCGGGTATTGA-CAAGATCAAA
1 TCCGAGTATTGACCAAGATCAAA
5802997 TTTTGAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (24 bp):
TCCGAGTATTGACCAAGATCAAAG
Found at i:5803953 original size:19 final size:20
Alignment explanation
Indices: 5803927--5804001 Score: 91
Period size: 19 Copynumber: 3.8 Consensus size: 20
5803917 GAAACTAAAA
5803927 CATGTTGCGAAATT-AAATT
1 CATGTTGCGAAATTGAAATT
* *
5803946 CGTGTTGCGAATTTGAAATT
1 CATGTTGCGAAATTGAAATT
*
5803966 CA-GTTGCGAATTTGAAATT
1 CATGTTGCGAAATTGAAATT
*
5803985 CCATGTTGCGAATTTGA
1 -CATGTTGCGAAATTGA
5804002 CTTTAGCATT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 29 0.58
20 8 0.16
21 13 0.26
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.37
Consensus pattern (20 bp):
CATGTTGCGAAATTGAAATT
Found at i:5803966 original size:20 final size:20
Alignment explanation
Indices: 5803929--5804061 Score: 110
Period size: 20 Copynumber: 6.7 Consensus size: 20
5803919 AACTAAAACA
*
5803929 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAATTTGAAATTCG
5803948 TGTTGCGAATTTGAAATTC-
1 TGTTGCGAATTTGAAATTCG
* *
5803967 AGTTGCGAATTTGAAATTCCA
1 TGTTGCGAATTTGAAATT-CG
** *
5803988 TGTTGCGAATTTGACTTTAG
1 TGTTGCGAATTTGAAATTCG
** *
5804008 CATTGCGAATTTG-ACTATCG
1 TGTTGCGAATTTGAAAT-TCG
* ** *
5804028 CGTTGCGAATTTGACTTTTG
1 TGTTGCGAATTTGAAATTCG
5804048 TGTTGCGAATTTGA
1 TGTTGCGAATTTGA
5804062 CTATCACATT
Statistics
Matches: 92, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
19 29 0.32
20 47 0.51
21 16 0.17
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.40
Consensus pattern (20 bp):
TGTTGCGAATTTGAAATTCG
Found at i:5804020 original size:60 final size:61
Alignment explanation
Indices: 5803950--5804081 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 61
5803940 TAAATTCGTG
*
5803950 TTGCGAATTTGAAAT-TC-AGTTGCGAATTTGAAATTCCATGTTGCGAATTTGACT-TTAGCA
1 TTGCGAATTTGAAATATCGAGTTGCGAATTTG-AATTCCATGTTGCGAATTTGACTATCA-CA
* * * ***
5804010 TTGCGAATTTG-ACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCACA
1 TTGCGAATTTGAAATATCGAGTTGCGAATTTGAATTCCATGTTGCGAATTTGACTATCACA
*
5804070 TTGTGAATTTGA
1 TTGCGAATTTGA
5804082 CTTCTGTGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
59 2 0.03
60 44 0.73
61 14 0.23
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (61 bp):
TTGCGAATTTGAAATATCGAGTTGCGAATTTGAATTCCATGTTGCGAATTTGACTATCACA
Found at i:5804062 original size:20 final size:20
Alignment explanation
Indices: 5803944--5804120 Score: 121
Period size: 20 Copynumber: 8.8 Consensus size: 20
5803934 CGAAATTAAA
* **
5803944 TTCGTGTTGCGAATTTGAAA
1 TTCGCGTTGCGAATTTGACT
* **
5803964 TTC-AGTTGCGAATTTGAAA
1 TTCGCGTTGCGAATTTGACT
5803983 TTC-CATGTTGCGAATTTGACT
1 TTCGC--GTTGCGAATTTGACT
* *
5804004 TTAGCATTGCGAATTTGACT
1 TTCGCGTTGCGAATTTGACT
*
5804024 ATCGCGTTGCGAATTTGACT
1 TTCGCGTTGCGAATTTGACT
* *
5804044 TTTGTGTTGCGAATTTGACT
1 TTCGCGTTGCGAATTTGACT
* * * *
5804064 ATCACATTGTGAATTTGAC-
1 TTCGCGTTGCGAATTTGACT
* *
5804083 TTCTGTGTTGCG-ATTT-ACAGA
1 TTC-GCGTTGCGAATTTGAC--T
5804104 TTCGCGTTGCGAATTTG
1 TTCGCGTTGCGAATTTG
5804121 GAAAATCGCA
Statistics
Matches: 124, Mismatches: 24, Indels: 16
0.76 0.15 0.10
Matches are distributed among these distances:
18 2 0.02
19 24 0.19
20 75 0.60
21 22 0.18
22 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.41
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTGACT
Found at i:5804113 original size:60 final size:60
Alignment explanation
Indices: 5803968--5804120 Score: 154
Period size: 60 Copynumber: 2.5 Consensus size: 60
5803958 TTGAAATTCA
* *
5803968 GTTGCGAATTTGAAATTC-CATGTTGCGAATTTGACTTTAGCATTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACATTCGC--GTTGCGAATTTGACTTCAGCATTGCGAATTTGACTATCGC
* * * * *
5804029 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCA-CATTGTGAATTTGACT-TCTGT
1 GTTGCGAATTTGACATTCGCGTTGCGAATTTGACT-TCAGCATTGCGAATTTGACTATC-GC
5804089 GTTGCG-ATTT-ACAGATTCGCGTTGCGAATTTG
1 GTTGCGAATTTGAC--ATTCGCGTTGCGAATTTG
5804121 GAAAATCGCA
Statistics
Matches: 77, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
58 2 0.03
59 6 0.08
60 52 0.68
61 17 0.22
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.41
Consensus pattern (60 bp):
GTTGCGAATTTGACATTCGCGTTGCGAATTTGACTTCAGCATTGCGAATTTGACTATCGC
Found at i:5804118 original size:40 final size:40
Alignment explanation
Indices: 5803989--5804120 Score: 144
Period size: 40 Copynumber: 3.3 Consensus size: 40
5803979 GAAATTCCAT
** *
5803989 GTTGCGAATTTGACTT-TAGCATTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTCT-GTGTTGCGAATTTGACGATCGC
* * *
5804029 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCAC
1 GTTGCGAATTTGACTTCTGTGTTGCGAATTTGACGATCGC
* *
5804069 ATTGTGAATTTGACTTCTGTGTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGACTTCTGTGTTGCGAATTTGAC-GA-TCGC
5804109 GTTGCGAATTTG
1 GTTGCGAATTTG
5804121 GAAAATCGCA
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
38 2 0.03
39 5 0.06
40 71 0.90
41 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.41
Consensus pattern (40 bp):
GTTGCGAATTTGACTTCTGTGTTGCGAATTTGACGATCGC
Found at i:5804363 original size:17 final size:18
Alignment explanation
Indices: 5804341--5804374 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5804331 ATGTAAAAAT
*
5804341 AAATATTTAAT-TTTAAA
1 AAATATTAAATATTTAAA
5804358 AAATATTAAATATTTAA
1 AAATATTAAATATTTAA
5804375 TCATGTAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATATTAAATATTTAAA
Found at i:5806537 original size:31 final size:32
Alignment explanation
Indices: 5806499--5806561 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
5806489 AAAATTTTAG
5806499 AAATTATAAAACGATCATTAAATTTT-TTAAA
1 AAATTATAAAACGATCATTAAATTTTATTAAA
* * *
5806530 AAATTATAGAATGTTCATTAAATTTTATTAAA
1 AAATTATAAAACGATCATTAAATTTTATTAAA
5806562 TTATTACAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (32 bp):
AAATTATAAAACGATCATTAAATTTTATTAAA
Found at i:5806565 original size:29 final size:29
Alignment explanation
Indices: 5806490--5806565 Score: 75
Period size: 31 Copynumber: 2.6 Consensus size: 29
5806480 TTTATTACTA
*
5806490 AAATTTTA-GAAATTATAAAACGATCATT
1 AAATTTTATTAAATTATAAAACGATCATT
* * *
5806518 AAATTTT-TTAAAAAATTATAGAATGTTCATT
1 AAATTTTATT---AAATTATAAAACGATCATT
5806549 AAATTTTATTAAATTAT
1 AAATTTTATTAAATTAT
5806566 TACAAAATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
28 7 0.18
29 7 0.18
31 23 0.59
32 2 0.05
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.43
Consensus pattern (29 bp):
AAATTTTATTAAATTATAAAACGATCATT
Found at i:5806582 original size:32 final size:31
Alignment explanation
Indices: 5806499--5806582 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
5806489 AAAATTTTAG
* *
5806499 AAATTATAAAACGATCATTAAATTTTTTAAA
1 AAATTATAAAATGATTATTAAATTTTTTAAA
*
5806530 AAATTATAGAATG-TTCATTAAATTTTATTAAA
1 AAATTATAAAATGATT-ATTAAATTTT-TTAAA
** *
5806562 TTATTACAAAATGATTATTAA
1 AAATTATAAAATGATTATTAA
5806583 GTTTACTAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
30 1 0.02
31 21 0.49
32 19 0.44
33 2 0.05
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (31 bp):
AAATTATAAAATGATTATTAAATTTTTTAAA
Found at i:5809066 original size:7 final size:7
Alignment explanation
Indices: 5809054--5809089 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
5809044 GTCAAAGGAA
5809054 GTCAACG
1 GTCAACG
5809061 GTCAACG
1 GTCAACG
*
5809068 GTC-ACA
1 GTCAACG
5809074 GTCAACG
1 GTCAACG
5809081 GTCAACG
1 GTCAACG
5809088 GT
1 GT
5809090 ATGGTCGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:5809102 original size:17 final size:17
Alignment explanation
Indices: 5809080--5809137 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
5809070 CACAGTCAAC
5809080 GGTCAACGGTAT-GGTCG
1 GGTCAACGGT-TGGGTCG
5809097 GGTCAACGGTTGGGTCG
1 GGTCAACGGTTGGGTCG
* *
5809114 GGTCAGTCGGGTCGGGTCG
1 GGTCA-AC-GGTTGGGTCG
5809133 GGTCA
1 GGTCA
5809138 GACAGATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
16 1 0.03
17 20 0.56
18 1 0.03
19 14 0.39
ACGTcount: A:0.12, C:0.19, G:0.47, T:0.22
Consensus pattern (17 bp):
GGTCAACGGTTGGGTCG
Found at i:5809157 original size:19 final size:19
Alignment explanation
Indices: 5809135--5809174 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5809125 TCGGGTCGGG
5809135 TCAGACAGATCAAACCGGT
1 TCAGACAGATCAAACCGGT
* *
5809154 TCAGACCGGTCAAACCGGT
1 TCAGACAGATCAAACCGGT
5809173 TC
1 TC
5809175 GAACCGGTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.17
Consensus pattern (19 bp):
TCAGACAGATCAAACCGGT
Found at i:5809163 original size:10 final size:10
Alignment explanation
Indices: 5809144--5809202 Score: 70
Period size: 10 Copynumber: 6.1 Consensus size: 10
5809134 GTCAGACAGA
5809144 TCAAACCGGT
1 TCAAACCGGT
*
5809154 TCAGACCGG-
1 TCAAACCGGT
5809163 TCAAACCGGT
1 TCAAACCGGT
*
5809173 TCGAACCGG-
1 TCAAACCGGT
5809182 TCGAAACCGG-
1 TC-AAACCGGT
5809192 TCAAACCGGT
1 TCAAACCGGT
5809202 T
1 T
5809203 TCCAGCCCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
9 17 0.40
10 25 0.60
ACGTcount: A:0.27, C:0.31, G:0.25, T:0.17
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:5809180 original size:19 final size:18
Alignment explanation
Indices: 5809144--5809201 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 18
5809134 GTCAGACAGA
5809144 TCAAACCGGTTCAGACCGG
1 TCAAACCGGTTCA-ACCGG
5809163 TCAAACCGGTTCGAACCGG
1 TCAAACCGGTTC-AACCGG
5809182 TCGAAACCGG-TCAAACCGG
1 TC-AAACCGGTTC-AACCGG
5809201 T
1 T
5809202 TTCCAGCCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 28 0.78
20 8 0.22
ACGTcount: A:0.28, C:0.31, G:0.26, T:0.16
Consensus pattern (18 bp):
TCAAACCGGTTCAACCGG
Found at i:5821578 original size:42 final size:42
Alignment explanation
Indices: 5821517--5821613 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
5821507 ATAATTTAAG
* *
5821517 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATGAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGATGAAA
* * * *
5821559 TCCTTTGGGTCATCTGTAAGTCTTTAGAGCAAGATGAT-AAG
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGATGAAA
*
5821600 TCATTCGGGCCATC
1 TCCTTCGGGCCATC
5821614 CATAAAGCCT
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 13 0.28
42 33 0.72
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (42 bp):
TCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGATGAAA
Found at i:5821795 original size:42 final size:42
Alignment explanation
Indices: 5821733--5821825 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 42
5821723 ACTTAGTAAG
* *
5821733 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
*
5821775 TCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
5821817 TCCTTCAGG
1 TCCTTCAGG
5821826 TAATTTGTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (42 bp):
TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
Found at i:5821882 original size:13 final size:13
Alignment explanation
Indices: 5821864--5821888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5821854 TGAAGCAAAT
5821864 CCATCAGTAAGTG
1 CCATCAGTAAGTG
5821877 CCATCAGTAAGT
1 CCATCAGTAAGT
5821889 CTTTCGAGCA
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:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:5822011 original size:80 final size:80
Alignment explanation
Indices: 5821878--5822159 Score: 451
Period size: 80 Copynumber: 3.5 Consensus size: 80
5821868 CAGTAAGTGC
5821878 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
5821943 GTAGTGAAGCAAATT
66 GTAGTGAAGCAAATT
* * * ** *
5821958 CATCAGTAAGTCTTTCGAGCATGGTAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACCGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
**
5822023 GTAGTGAAGCAAACC
66 GTAGTGAAGCAAATT
5822038 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
5822103 GTAGTGAAGCAAATT
66 GTAGTGAAGCAAATT
*
5822118 CATCAGTAAGTCTTTCGAGCAGGATG-TTGAAA-CCTTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATT-AAATCC-TTCGGGT
5822160 CATCAGTAAG
Statistics
Matches: 183, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
79 4 0.02
80 179 0.98
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (80 bp):
CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
GTAGTGAAGCAAATT
Found at i:5822164 original size:42 final size:41
Alignment explanation
Indices: 5822117--5822229 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 41
5822107 TGAAGCAAAT
5822117 TCATCAGTAAGTCTTTCGAGCAGGATGTTGAAA-CCTTTCGGG
1 TCATCAGTAAGTCTTTCGAGCAGGATGTT-AAATCC-TTCGGG
*
5822159 TCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
1 TCATCAGTAAGTCTTTCGAGCAGGATG-TTAAATCCTTCGGG
* * *
5822201 TCATCCA-TAAGTCCTTCGGGTAGGATGTT
1 TCAT-CAGTAAGTCTTTCGAGCAGGATGTT
5822230 TTCACACCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
41 2 0.03
42 55 0.87
43 6 0.10
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (41 bp):
TCATCAGTAAGTCTTTCGAGCAGGATGTTAAATCCTTCGGG
Found at i:5822705 original size:53 final size:53
Alignment explanation
Indices: 5822642--5822837 Score: 279
Period size: 53 Copynumber: 3.7 Consensus size: 53
5822632 ATCAAACCAT
*
5822642 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACTCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * *
5822695 AAGATTGTTCGAGTTTTACTCCCTGAAACAAGAGGGAGCAAACCCGTAGACAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
5822748 AAGACTGTTTGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGCT-GGTC-G
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGG-CAG
*
5822801 AAGATTGTTCGAGTTCTACTCCCTGAAGCAATAGGGA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGA
5822838 ACAAACCTTT
Statistics
Matches: 125, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 123 0.98
54 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
Found at i:5830325 original size:20 final size:20
Alignment explanation
Indices: 5830289--5830367 Score: 94
Period size: 20 Copynumber: 4.0 Consensus size: 20
5830279 TCGGGTCGGG
5830289 TCAG-ACCGGTCAAACCGGT
1 TCAGAACCGGTCAAACCGGT
*
5830308 TCAG-ACCAGTCGAAACCGGT
1 TCAGAACCGGTC-AAACCGGT
*
5830328 TC-GAACCGGTCGAAACCAG-
1 TCAGAACCGGTC-AAACCGGT
5830347 TCAGAACCGGTCAAACCGGT
1 TCAGAACCGGTCAAACCGGT
5830367 T
1 T
5830368 TCCAGCATTC
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
19 19 0.37
20 33 0.63
ACGTcount: A:0.29, C:0.30, G:0.25, T:0.15
Consensus pattern (20 bp):
TCAGAACCGGTCAAACCGGT
Found at i:5830336 original size:10 final size:9
Alignment explanation
Indices: 5830293--5830366 Score: 51
Period size: 10 Copynumber: 7.7 Consensus size: 9
5830283 GTCGGGTCAG
*
5830293 ACCGGTCAA
1 ACCGGTCGA
5830302 ACCGGTTC-A
1 ACCGG-TCGA
*
5830311 GACCAGTCGAA
1 -ACCGGTCG-A
5830322 ACCGGTTCGA
1 ACCGG-TCGA
5830332 ACCGGTCGAA
1 ACCGGTCG-A
*
5830342 ACCAGTCAGA
1 ACCGGTC-GA
*
5830352 ACCGGTCAA
1 ACCGGTCGA
5830361 ACCGGT
1 ACCGGT
5830367 TTCCAGCATT
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
9 18 0.34
10 30 0.57
11 5 0.09
ACGTcount: A:0.30, C:0.31, G:0.26, T:0.14
Consensus pattern (9 bp):
ACCGGTCGA
Found at i:5830336 original size:39 final size:39
Alignment explanation
Indices: 5830293--5830367 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
5830283 GTCGGGTCAG
*
5830293 ACCGGTC-AAACCGGTTCAG-ACCAGTCGAAACCGGTTCGA
1 ACCGGTCGAAACCAG-TCAGAACCAGTC-AAACCGGTTCGA
*
5830332 ACCGGTCGAAACCAGTCAGAACCGGTCAAACCGGTT
1 ACCGGTCGAAACCAGTCAGAACCAGTCAAACCGGTT
5830368 TCCAGCATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
39 20 0.62
40 12 0.38
ACGTcount: A:0.29, C:0.31, G:0.25, T:0.15
Consensus pattern (39 bp):
ACCGGTCGAAACCAGTCAGAACCAGTCAAACCGGTTCGA
Found at i:5831683 original size:16 final size:16
Alignment explanation
Indices: 5831662--5831692 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5831652 CAAAATAATT
*
5831662 AAATGTTGAATGATTC
1 AAATGTTGAACGATTC
5831678 AAATGTTGAACGATT
1 AAATGTTGAACGATT
5831693 TAGAGATTCT
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:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (16 bp):
AAATGTTGAACGATTC
Found at i:5831829 original size:38 final size:38
Alignment explanation
Indices: 5831771--5831844 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
5831761 TATATTTCTG
**
5831771 TACTAAATCATTCAGTATTGTTTTACTGAATCAATCGA
1 TACTAAATCATTCAACATTGTTTTACTGAATCAATCGA
* *
5831809 TACTAAATCATTTAACATTGTTTTATTGAATCAATC
1 TACTAAATCATTCAACATTGTTTTACTGAATCAATC
5831845 ATCTCTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (38 bp):
TACTAAATCATTCAACATTGTTTTACTGAATCAATCGA
Found at i:5834021 original size:23 final size:23
Alignment explanation
Indices: 5833995--5834055 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
5833985 ACCGGTCACA
5833995 ACCCGACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGACCCGTTG
* * * *
5834018 ACCCCACCCAACCTGACCCGTTT
1 ACCCGACCCGACCCGACCCGTTG
5834041 ACCCGACCCGACCCG
1 ACCCGACCCGACCCG
5834056 TTGACTCGAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.20, C:0.54, G:0.16, T:0.10
Consensus pattern (23 bp):
ACCCGACCCGACCCGACCCGTTG
Found at i:5834026 original size:18 final size:18
Alignment explanation
Indices: 5833999--5834068 Score: 68
Period size: 18 Copynumber: 3.6 Consensus size: 18
5833989 GTCACAACCC
5833999 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
*
5834017 GACCCCACCCAACCTGACCCGTT
1 GACCCGA--C--CC-GACCCGTT
*
5834040 TACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
*
5834058 GACTCGACCCG
1 GACCCGACCCG
5834069 TTGACCTGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
18 23 0.55
19 2 0.05
20 1 0.02
21 1 0.02
22 2 0.05
23 13 0.31
ACGTcount: A:0.19, C:0.50, G:0.19, T:0.13
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:5834065 original size:13 final size:13
Alignment explanation
Indices: 5834049--5834073 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5834039 TTACCCGACC
5834049 CGACCCGTTGACT
1 CGACCCGTTGACT
5834062 CGACCCGTTGAC
1 CGACCCGTTGAC
5834074 CTGTTGACCG
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:0.40, G:0.24, T:0.20
Consensus pattern (13 bp):
CGACCCGTTGACT
Found at i:5836551 original size:24 final size:24
Alignment explanation
Indices: 5836524--5836615 Score: 150
Period size: 24 Copynumber: 3.8 Consensus size: 24
5836514 TTCGATTTGA
5836524 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
5836548 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
5836572 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
5836596 ATTCTGATCTGATACTTGAC
1 ATTCTGATCTGATACTTGAC
5836616 CTGATTTATG
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
23 1 0.02
24 61 0.97
25 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:5850702 original size:69 final size:69
Alignment explanation
Indices: 5850591--5850719 Score: 197
Period size: 69 Copynumber: 1.9 Consensus size: 69
5850581 TCCATATCCC
* *
5850591 TCCATATATCTAATGCTCAAAAAGCATGAAAATGAAATTCATC-TCATCATACAATTAAGGTGCT
1 TCCATATATATAATGCTCAAAAAGCATGAAAATGAAATTCATCAT-ACCATACAATTAAGGTGCT
5850655 CGACA
65 CGACA
* * *
5850660 TCCATATATATAATGCTCAAAAAGTATGAAAATGTAATTCATCATACCATACAGTTAAGG
1 TCCATATATATAATGCTCAAAAAGCATGAAAATGAAATTCATCATACCATACAATTAAGG
5850720 AAACCTCGAG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
69 53 0.98
70 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.29
Consensus pattern (69 bp):
TCCATATATATAATGCTCAAAAAGCATGAAAATGAAATTCATCATACCATACAATTAAGGTGCTC
GACA
Found at i:5864574 original size:18 final size:18
Alignment explanation
Indices: 5864540--5864574 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5864530 AAATGTGTAC
* *
5864540 ATATGTTATATGTATTGT
1 ATATGTTACATGAATTGT
5864558 ATATGTTACATGAATTG
1 ATATGTTACATGAATTG
5864575 AATGAATATA
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:0.31, C:0.03, G:0.17, T:0.49
Consensus pattern (18 bp):
ATATGTTACATGAATTGT
Found at i:5865924 original size:149 final size:148
Alignment explanation
Indices: 5865611--5865913 Score: 482
Period size: 149 Copynumber: 2.0 Consensus size: 148
5865601 GAGTCGAGGG
* * * * *
5865611 TCTACGCGGTCCTTCGGGACATATGTATATTCTTCGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTTCGGAACATGTATGAAGTCTTTAAGACACATA
* * *
5865676 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATAATGTGTGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTAT
*
5865741 ATGGCACTACGGTGCAAT
131 ATGGAACTACGGTGCAAT
* *
5865759 TCTACGCGGTCCTTCGGGATATATATATATTCTGT-GGAACATGTGTGAAGTCTTGTAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCT-TCGGAACATGTATGAAGTCTT-TAAGACACA
5865823 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
64 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
5865888 ATATGGAACTACGGTGCAAT
129 ATATGGAACTACGGTGCAAT
5865908 TCTACG
1 TCTACG
5865914 TGGCACTTCG
Statistics
Matches: 142, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
148 47 0.33
149 95 0.67
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTTCGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTAT
ATGGAACTACGGTGCAAT
Found at i:5869765 original size:18 final size:18
Alignment explanation
Indices: 5869730--5869765 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5869720 AAAATGGGTA
* *
5869730 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
5869748 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
5869766 AATGAATATA
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:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:5871117 original size:149 final size:148
Alignment explanation
Indices: 5870804--5871106 Score: 491
Period size: 149 Copynumber: 2.0 Consensus size: 148
5870794 GAGTCGAGGG
* * * * *
5870804 TCTACGCGGTCCTTCGGGACATATGTATATTCTTCAGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTTCAGAACATGTATGAAGTCTTTAAGACACATA
* *
5870869 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTAT
5870934 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
* * *
5870952 TCTACGCGGTCCTTCGGGATATATATATATTCTGT-GGAACATGTGTGAAGTCTTGTAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCT-TCAGAACATGTATGAAGTCTT-TAAGACACA
5871016 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
64 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
5871081 ATATGGCACTACGGTGCAAT
129 ATATGGCACTACGGTGCAAT
5871101 TCTACG
1 TCTACG
5871107 TGGCACTTCG
Statistics
Matches: 143, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
148 46 0.32
149 97 0.68
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTTCAGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTAT
ATGGCACTACGGTGCAAT
Found at i:5871118 original size:23 final size:23
Alignment explanation
Indices: 5871084--5871129 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5871074 CATTATTATA
*
5871084 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
*
5871107 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
5871130 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:5874702 original size:19 final size:18
Alignment explanation
Indices: 5874678--5874714 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
5874668 TTTTAATAAA
5874678 TAATAAAATTATTATTAAT
1 TAATAAAATTATT-TTAAT
*
5874697 TAATAATATTATTTTAAT
1 TAATAAAATTATTTTAAT
5874715 ACAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATAAAATTATTTTAAT
Found at i:5884896 original size:85 final size:84
Alignment explanation
Indices: 5884748--5884913 Score: 253
Period size: 85 Copynumber: 2.0 Consensus size: 84
5884738 ATATACTCTT
5884748 TGACACACAATGTGTGGCATCTTCATTTATGACGGGGGCTTCAATGACACCCAATGTAAGTCATA
1 TGACACACAATGTGTGGCATCTTCATTTATGACGGGGGCTTCAATGACACCCAATGTAAGTCATA
*
5884813 AATGTGTGTCATAAATTTA
66 AATGCGTGTCATAAATTTA
* * * * *
5884832 TGACACACAAATGTGTGTCGTCTTCATTTATGACGGGGGCTTCAATGACGCGCAATG-AGCGTCA
1 TGACACAC-AATGTGTGGCATCTTCATTTATGACGGGGGCTTCAATGACACCCAATGTA-AGTCA
5884896 TAAATGCGTGTCATAAAT
64 TAAATGCGTGTCATAAAT
5884914 GTGTGTCATA
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
84 9 0.12
85 65 0.88
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (84 bp):
TGACACACAATGTGTGGCATCTTCATTTATGACGGGGGCTTCAATGACACCCAATGTAAGTCATA
AATGCGTGTCATAAATTTA
Found at i:5884908 original size:13 final size:13
Alignment explanation
Indices: 5884892--5884939 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
5884882 CGCAATGAGC
*
5884892 GTCATAAATGCGT
1 GTCATAAATGTGT
5884905 GTCATAAATGTGT
1 GTCATAAATGTGT
*
5884918 GTCATAAATGTGC
1 GTCATAAATGTGT
5884931 GTCATAAAT
1 GTCATAAAT
5884940 TTATGACGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (13 bp):
GTCATAAATGTGT
Found at i:5884914 original size:26 final size:26
Alignment explanation
Indices: 5884885--5884939 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
5884875 AATGACGCGC
*
5884885 AATGAGCGTCATAAATGCGTGTCATA
1 AATGAGCGTCATAAATGCGCGTCATA
* * *
5884911 AATGTGTGTCATAAATGTGCGTCATA
1 AATGAGCGTCATAAATGCGCGTCATA
5884937 AAT
1 AAT
5884940 TTATGACGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (26 bp):
AATGAGCGTCATAAATGCGCGTCATA
Found at i:5896814 original size:23 final size:23
Alignment explanation
Indices: 5896739--5896865 Score: 165
Period size: 23 Copynumber: 5.7 Consensus size: 23
5896729 ATTCCCCTAC
* *
5896739 AGGGGGAATTGGTTCCCC-T-AC
1 AGGGGGAATCGGTTCCCCTTCAA
*
5896760 AGGGGGAATCGGTTCCCC-T-AC
1 AGGGGGAATCGGTTCCCCTTCAA
5896781 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
*
5896804 AGAGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
*
5896827 AGGGGGAATCGATTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
*
5896849 AGGGGGAATTGGTTCCC
1 AGGGGGAATCGGTTCCC
5896866 TTCGCACTAA
Statistics
Matches: 97, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
21 38 0.39
22 17 0.18
23 42 0.43
ACGTcount: A:0.21, C:0.25, G:0.31, T:0.22
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:5896868 original size:21 final size:22
Alignment explanation
Indices: 5896720--5896865 Score: 172
Period size: 21 Copynumber: 6.7 Consensus size: 22
5896710 AGAACCCCAT
* * *
5896720 GGGGTATCGATTCCCCTAC-AG
1 GGGGAATCGGTTCCCCTTCAAG
* *
5896741 GGGGAATTGGTTCCCCTAC-AG
1 GGGGAATCGGTTCCCCTTCAAG
*
5896762 GGGGAATCGGTTCCCCTAC-AG
1 GGGGAATCGGTTCCCCTTCAAG
5896783 GGGGAATCGGTTCCCCTTCAAAG
1 GGGGAATCGGTTCCCCTTC-AAG
*
5896806 AGGGAATCGGTTCCCCTTCAAAG
1 GGGGAATCGGTTCCCCTTC-AAG
*
5896829 GGGGAATCGATTCCCCTTCAAG
1 GGGGAATCGGTTCCCCTTCAAG
*
5896851 GGGGAATTGGTTCCC
1 GGGGAATCGGTTCCC
5896866 TTCGCACTAA
Statistics
Matches: 113, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
21 56 0.50
22 16 0.14
23 41 0.36
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.23
Consensus pattern (22 bp):
GGGGAATCGGTTCCCCTTCAAG
Found at i:5898127 original size:18 final size:18
Alignment explanation
Indices: 5898101--5898160 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
5898091 ACCAGTCACA
5898101 ACCCAACCCGACCCGTTG
1 ACCCAACCCGACCCGTTG
*
5898119 ACCCGACCCGACCCGTTG
1 ACCCAACCCGACCCGTTG
*
5898137 ACTCAACCCATTGACCCGTTG
1 ACCCAACCC---GACCCGTTG
5898158 ACC
1 ACC
5898161 GTCGTTGACC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 24 0.69
21 11 0.31
ACGTcount: A:0.22, C:0.47, G:0.17, T:0.15
Consensus pattern (18 bp):
ACCCAACCCGACCCGTTG
Found at i:5900629 original size:24 final size:24
Alignment explanation
Indices: 5900602--5900717 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
5900592 TTCGATTTGA
5900602 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
5900626 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
* *
5900650 ATTTTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
5900674 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
5900698 ATTTTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
5900718 CTGATTTATG
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 80 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:5909930 original size:15 final size:15
Alignment explanation
Indices: 5909884--5909930 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
5909874 TTAGCTAGGT
*
5909884 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
*
5909899 GAGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
5909914 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
5909929 GG
1 GG
5909931 ATGTGGGGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.09, C:0.17, G:0.66, T:0.09
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:5920089 original size:16 final size:16
Alignment explanation
Indices: 5920065--5920098 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5920055 TATCACCGAT
*
5920065 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
5920081 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
5920097 CG
1 CG
5920099 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:5920943 original size:69 final size:69
Alignment explanation
Indices: 5920832--5920960 Score: 197
Period size: 69 Copynumber: 1.9 Consensus size: 69
5920822 TCCATATCCC
* *
5920832 TCCATATATCTAATGCTCAAAAAGCATGAAAATGAAATTCATC-TCATCATACAATTAAGGTGCT
1 TCCATATATATAATGCTCAAAAAGCATGAAAATGAAATTCATCAT-ACCATACAATTAAGGTGCT
5920896 CGACA
65 CGACA
* * *
5920901 TCCATATATATAATGCTCAAAAAGTATGAAAATGTAATTCATCATACCATACAGTTAAGG
1 TCCATATATATAATGCTCAAAAAGCATGAAAATGAAATTCATCATACCATACAATTAAGG
5920961 AAACCTCGAG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
69 53 0.98
70 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.29
Consensus pattern (69 bp):
TCCATATATATAATGCTCAAAAAGCATGAAAATGAAATTCATCATACCATACAATTAAGGTGCTC
GACA
Found at i:5927446 original size:14 final size:14
Alignment explanation
Indices: 5927427--5927453 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5927417 ATCTTGTTTG
5927427 AAATTAAAATATTA
1 AAATTAAAATATTA
5927441 AAATTAAAATATT
1 AAATTAAAATATT
5927454 TTAAAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATTAAAATATTA
Found at i:5930582 original size:20 final size:20
Alignment explanation
Indices: 5930536--5930722 Score: 200
Period size: 20 Copynumber: 9.2 Consensus size: 20
5930526 TTTTCCAAAT
* *
5930536 TCGCATTGCGATTTTCCTAA
1 TCGCATTGCGATTTACGTAA
5930556 TTCGCATTGCGATTTACGTAA
1 -TCGCATTGCGATTTACGTAA
5930577 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
* *
5930597 TCGCATTGCGATTTTCCTAA
1 TCGCATTGCGATTTACGTAA
*
5930617 TTCGCATTACGATTTACGTAA
1 -TCGCATTGCGATTTACGTAA
* * * *
5930638 TCGCAATGTGATTTTCCTAA
1 TCGCATTGCGATTTACGTAA
* *
5930658 TTCGTATTTCGATTTACGTAA
1 -TCGCATTGCGATTTACGTAA
*
5930679 TCGCA-TACGATTTA-GTAAA
1 TCGCATTGCGATTTACGT-AA
5930698 TCGCATTGCGATTTA-GTAAA
1 TCGCATTGCGATTTACGT-AA
5930718 TCGCA
1 TCGCA
5930723 ACGAGATTCT
Statistics
Matches: 141, Mismatches: 21, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
18 2 0.01
19 15 0.11
20 75 0.53
21 49 0.35
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAA
Found at i:5930582 original size:41 final size:41
Alignment explanation
Indices: 5930514--5930722 Score: 219
Period size: 41 Copynumber: 5.1 Consensus size: 41
5930504 GATTCTGACT
* * * * * *
5930514 ATCGTATTGTGATTTTCCAAATTCGCATTGCGATTTTCCTA
1 ATCGCATTGCGATTTACCTAATTCGCATTGCGATTTACGTA
*
5930555 ATTCGCATTGCGATTTACGTAA-TCGCATTGCGATTTACGTA
1 A-TCGCATTGCGATTTACCTAATTCGCATTGCGATTTACGTA
* *
5930596 ATCGCATTGCGATTTTCCTAATTCGCATTACGATTTACGTA
1 ATCGCATTGCGATTTACCTAATTCGCATTGCGATTTACGTA
* * * * *
5930637 ATCGCAATGTGATTTTCCTAATTCGTATTTCGATTTACGTA
1 ATCGCATTGCGATTTACCTAATTCGCATTGCGATTTACGTA
* * *
5930678 ATCGCA-TACGATTTA-GTAAATCGCATTGCGATTTA-GTAA
1 ATCGCATTGCGATTTACCTAATTCGCATTGCGATTTACGT-A
5930717 ATCGCA
1 ATCGCA
5930723 ACGAGATTCT
Statistics
Matches: 144, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
38 2 0.01
39 23 0.16
40 24 0.17
41 80 0.56
42 15 0.10
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (41 bp):
ATCGCATTGCGATTTACCTAATTCGCATTGCGATTTACGTA
Found at i:5930613 original size:61 final size:61
Alignment explanation
Indices: 5930536--5930722 Score: 238
Period size: 61 Copynumber: 3.1 Consensus size: 61
5930526 TTTTCCAAAT
*
5930536 TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTTCCTAATTCGCATTACGATTTACGTAATCGCATTGCGATTTACGTAA
* * * *
5930597 TCGCATTGCGATTTTCCTAATTCGCATTACGATTTACGTAATCGCAATGTGATTTTCCTAA
1 TCGCATTGCGATTTTCCTAATTCGCATTACGATTTACGTAATCGCATTGCGATTTACGTAA
* * * *
5930658 TTCGTATTTCGATTTACGTAA-TCGCA-TACGATTTA-GTAAATCGCATTGCGATTTA-GTAAA
1 -TCGCATTGCGATTTTCCTAATTCGCATTACGATTTACGT-AATCGCATTGCGATTTACGT-AA
5930718 TCGCA
1 TCGCA
5930723 ACGAGATTCT
Statistics
Matches: 109, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
59 7 0.06
60 25 0.23
61 61 0.56
62 16 0.15
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.38
Consensus pattern (61 bp):
TCGCATTGCGATTTTCCTAATTCGCATTACGATTTACGTAATCGCATTGCGATTTACGTAA
Found at i:5930730 original size:20 final size:20
Alignment explanation
Indices: 5930687--5930730 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5930677 AATCGCATAC
** *
5930687 GATTTAGTAAATCGCATTGC
1 GATTTAGTAAATCGCAACGA
5930707 GATTTAGTAAATCGCAACGA
1 GATTTAGTAAATCGCAACGA
5930727 GATT
1 GATT
5930731 CTGACTGTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (20 bp):
GATTTAGTAAATCGCAACGA
Found at i:5931612 original size:24 final size:24
Alignment explanation
Indices: 5931585--5931638 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
5931575 GTATTCGAAA
5931585 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
5931609 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
5931633 TTTGAT
1 TTTGAT
5931639 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:5934172 original size:33 final size:33
Alignment explanation
Indices: 5934135--5934261 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
5934125 GGAAATGACT
* *
5934135 ATCGCAATGTGAAATGAAAATCGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
5934168 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
5934201 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
5934234 ATCACAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
5934262 CGAATGTAGT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:5934264 original size:19 final size:18
Alignment explanation
Indices: 5934115--5934265 Score: 65
Period size: 19 Copynumber: 8.7 Consensus size: 18
5934105 CTTAATGTCT
**
5934115 ATCGCAACGCGGAAATGACT
1 ATCGCAA-GC-GAAATGAAA
*
5934135 ATCGCAATGTGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
* *
5934154 ATCGCAA-TG--A-GAGA
1 ATCGCAAGCGAAATGAAA
5934168 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
* *
5934187 ATTGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
5934201 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
5934220 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
*
5934234 ATCACAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
5934253 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
5934266 TGTAGTTTCG
Statistics
Matches: 98, Mismatches: 17, Indels: 33
0.66 0.11 0.22
Matches are distributed among these distances:
14 25 0.26
15 5 0.05
16 5 0.05
17 6 0.06
18 5 0.05
19 44 0.45
20 8 0.08
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:5934283 original size:19 final size:19
Alignment explanation
Indices: 5934261--5934298 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5934251 AAATCGCAAC
5934261 GCGAATGTAGTTTCGCGTT
1 GCGAATGTAGTTTCGCGTT
* *
5934280 GCGATTTTAGTTTCGCGTT
1 GCGAATGTAGTTTCGCGTT
5934299 ACGATTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.16, G:0.29, T:0.42
Consensus pattern (19 bp):
GCGAATGTAGTTTCGCGTT
Found at i:5934319 original size:33 final size:33
Alignment explanation
Indices: 5934276--5934369 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 33
5934266 TGTAGTTTCG
* *
5934276 CGTTGCGATTTT-AGTTTCGCGTTACGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCGTTACGATTATCT
* *
5934309 TGTTGCGATTTTCATTTCGCGTTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCGTTACGATTATCT
* *
5934342 CGTTGTGATTTTCATTTCGCATTACGAT
1 CGTTGCGATTTTCATTTCGCGTTACGAT
5934370 AGTCATTTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 51 0.98
34 1 0.02
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTACGATTATCT
Found at i:5934334 original size:19 final size:18
Alignment explanation
Indices: 5934271--5934337 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 18
5934261 GCGAATGTAG
5934271 TTTCGCGTTGCGATTTTA
1 TTTCGCGTTGCGATTTTA
*
5934289 GTTTCGCGTTACGATTTT-
1 -TTTCGCGTTGCGATTTTA
*
5934307 GTT---GTTGCGATTTTCA
1 TTTCGCGTTGCGATTTT-A
5934323 TTTCGCGTTGCGATT
1 TTTCGCGTTGCGATT
5934338 ATCTCGTTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 10 0.26
16 2 0.05
17 2 0.05
19 25 0.64
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTTA
Found at i:5934508 original size:13 final size:14
Alignment explanation
Indices: 5934475--5934510 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5934465 CATCAATTAA
5934475 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5934489 ACAAATCATCTTTT
1 ACAAATCAACTTTT
5934503 -CAAATCAA
1 ACAAATCAA
5934511 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5935882 original size:21 final size:20
Alignment explanation
Indices: 5935853--5935932 Score: 54
Period size: 21 Copynumber: 3.9 Consensus size: 20
5935843 GAATGGTGGG
5935853 AGGGACCTCTTCAACGATGAC
1 AGGG-CCTCTTCAACGATGAC
* * **
5935874 AGTGGCCTCTTGAACGGTGGG
1 AG-GGCCTCTTCAACGATGAC
* * *
5935895 AGGGACTC-TCAAGGAATGAT
1 AGGGCCTCTTCAACG-ATGAC
5935915 AGGGGCCTCTTCAACGAT
1 A-GGGCCTCTTCAACGAT
5935933 AGGAGTGGAC
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
19 4 0.09
20 8 0.19
21 24 0.56
22 7 0.16
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (20 bp):
AGGGCCTCTTCAACGATGAC
Found at i:5936393 original size:19 final size:19
Alignment explanation
Indices: 5936353--5936446 Score: 107
Period size: 19 Copynumber: 4.8 Consensus size: 19
5936343 TCTGGAACTT
*
5936353 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAAC--GAGAAATG
** *
5936374 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGAGAAATG
5936393 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGAGA-AATG
* *
5936413 AAAATCGCAACGTGAAATA
1 AAAATCGCAACGAGAAATG
5936432 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
5936447 GAATCGCAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
19 35 0.56
20 18 0.29
21 9 0.15
ACGTcount: A:0.49, C:0.18, G:0.20, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGAGAAATG
Found at i:5936422 original size:39 final size:39
Alignment explanation
Indices: 5936353--5936450 Score: 133
Period size: 39 Copynumber: 2.5 Consensus size: 39
5936343 TCTGGAACTT
* * ** *
5936353 AAAATCGCAACGTGAAAAATGACTATCGCAACGCGAAATG
1 AAAATCGCAACGAG-AGAATGAAAATCGCAACGCGAAATA
*
5936393 AAAATCGCAACGAGAGAATGAAAATCGCAACGTGAAATA
1 AAAATCGCAACGAGAGAATGAAAATCGCAACGCGAAATA
5936432 AAAATCGCAACGAGAGAAT
1 AAAATCGCAACGAGAGAAT
5936451 CGCAATGCGA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 39 0.75
40 13 0.25
ACGTcount: A:0.49, C:0.17, G:0.20, T:0.13
Consensus pattern (39 bp):
AAAATCGCAACGAGAGAATGAAAATCGCAACGCGAAATA
Found at i:5936452 original size:33 final size:36
Alignment explanation
Indices: 5936377--5936476 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 36
5936367 AAAAATGACT
*
5936377 ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATGAAA
1 ATCGCAACGCGAAATAAAAATCGCAAC--GAGAATG-AA
*
5936416 ATCGCAACGTGAAATAAAAATCGCAACGAG-A-G-A
1 ATCGCAACGCGAAATAAAAATCGCAACGAGAATGAA
* *
5936449 ATCGCAATGCGAAATTAAAATCGCAACG
1 ATCGCAACGCGAAATAAAAATCGCAACG
5936477 CGATTATAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
33 26 0.46
35 1 0.02
36 1 0.02
37 3 0.05
39 25 0.45
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (36 bp):
ATCGCAACGCGAAATAAAAATCGCAACGAGAATGAA
Found at i:5936519 original size:39 final size:37
Alignment explanation
Indices: 5936476--5936586 Score: 114
Period size: 39 Copynumber: 2.9 Consensus size: 37
5936466 AAATCGCAAC
*
5936476 GCGATTATAGTTTCGCGCTGCGATTTTTGGTTTCGCGTT
1 GCGATTATA-TTTCGCGCTGCGA-TTTTCGTTTCGCGTT
* *
5936515 GCGATTTTTATTTCGCGTTGCGATTTTCGTTTCGCGTT
1 GCGA-TTATATTTCGCGCTGCGATTTTCGTTTCGCGTT
* * * *
5936553 GCGATTTTCATTCTCTCGTTGCGATTTTCATTTC
1 GCGATTAT-ATT-TCGCGCTGCGATTTTCGTTTC
5936587 AACCAAAAGA
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
37 4 0.06
38 21 0.33
39 35 0.55
40 4 0.06
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.48
Consensus pattern (37 bp):
GCGATTATATTTCGCGCTGCGATTTTCGTTTCGCGTT
Found at i:5936547 original size:58 final size:58
Alignment explanation
Indices: 5936476--5936586 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 58
5936466 AAATCGCAAC
** *
5936476 GCGATTATAGTTTCGCGCTGCGATTTTTGGTT-TCGCGTTGCGATTTTTATTTCGCGTT
1 GCGATTATAGTTTCGCGCTGCGA-TTTTCATTCTCGCGTTGCGATTTTCATTTCGCGTT
* * * *
5936534 GCGATTTTCGTTTCGCGTTGCGATTTTCATTCTCTCGTTGCGATTTTCATTTC
1 GCGATTATAGTTTCGCGCTGCGATTTTCATTCTCGCGTTGCGATTTTCATTTC
5936587 AACCAAAAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
57 6 0.13
58 39 0.87
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.48
Consensus pattern (58 bp):
GCGATTATAGTTTCGCGCTGCGATTTTCATTCTCGCGTTGCGATTTTCATTTCGCGTT
Found at i:5936581 original size:20 final size:19
Alignment explanation
Indices: 5936486--5936586 Score: 130
Period size: 19 Copynumber: 5.2 Consensus size: 19
5936476 GCGATTATAG
* **
5936486 TTTCGCGCTGCGATTTTTGG
1 TTTCGCGTTGCGA-TTTTCA
*
5936506 TTTCGCGTTGCGATTTTTA
1 TTTCGCGTTGCGATTTTCA
*
5936525 TTTCGCGTTGCGATTTTCG
1 TTTCGCGTTGCGATTTTCA
5936544 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
5936563 TTCTCTCGTTGCGATTTTCA
1 TT-TCGCGTTGCGATTTTCA
5936583 TTTC
1 TTTC
5936587 AACCAAAAGA
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
19 43 0.59
20 30 0.41
ACGTcount: A:0.08, C:0.21, G:0.22, T:0.50
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:5936979 original size:92 final size:92
Alignment explanation
Indices: 5936676--5937040 Score: 547
Period size: 91 Copynumber: 4.1 Consensus size: 92
5936666 ATGGATTGCA
* *
5936676 TTACTTCAACCAAAAGACAAAACAAAGACAAATAGTAACTT--CAGTATTAAAGAATACACAG-T
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAG-ATACACAGTT
** *
5936738 TAGCAGAATTGGCAGCAAATG-ACAAAT
65 TAGCAGAATTGGCAGCAACCGAATAAAT
*
5936765 TTACTTTCAACC-AAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGA-ATACAGTT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGATACACAGTT
5936828 TAGCAGAATTGGCAGCAACCGAA-AAAT
65 TAGCAGAATTGGCAGCAACCGAATAAAT
5936855 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGATACACAGTT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGATACACAGTT
5936920 TAGCAGAATTGGCAGCAACCGAATAAAT
65 TAGCAGAATTGGCAGCAACCGAATAAAT
5936948 TTACTTCAACC-AAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT--A-ATA-ACAGTT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGATACACAGTT
*
5937008 TAGCAGTATTGGCAGCAACCGAATAAAT
65 TAGCAGAATTGGCAGCAACCGAATAAAT
5937036 TTACT
1 TTACT
5937041 AAGCAATCTA
Statistics
Matches: 260, Mismatches: 7, Indels: 19
0.91 0.02 0.07
Matches are distributed among these distances:
88 38 0.15
89 40 0.15
90 45 0.17
91 65 0.25
92 64 0.25
93 8 0.03
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (92 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGATACACAGTTT
AGCAGAATTGGCAGCAACCGAATAAAT
Found at i:5937010 original size:180 final size:181
Alignment explanation
Indices: 5936676--5937040 Score: 573
Period size: 180 Copynumber: 2.0 Consensus size: 181
5936666 ATGGATTGCA
*
5936676 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATAGTAACTTCAGTATTAAAGAATACACAGTTA
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGTATTAAAGAATACACAGTTA
*
5936740 GCAGAATTGGCAGCAAATGACAAATTTACTTTCAACCAAAGACAAAACAAAGACAAATACTAACT
66 GCAGAATTGGCAGCAAACGACAAATTTACTTTCAACCAAAGACAAAACAAAGACAAATACTAACT
5936805 TCACAGTGTTAAAGAATACAGTTTAGCAGAATTGGCAGCAACCGAA-AAAT
131 TCACAGTGTTAAAGAATACAGTTTAGCAGAATTGGCAGCAACCGAATAAAT
*
5936855 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAG-ATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTT--CAGTATTAAAGAATACACAG-
* *
5936919 TTAGCAGAATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAGACAAAACAAAAGACAAATAC
63 TTAGCAGAATTGGCAGCAAACG-ACAAATTTACTTTCAACCAAAGACAAAAC-AAAGACAAATAC
* *
5936983 TAACTTCACAGTGTT-AA-TA-ACAGTTTAGCAGTATTGGCAGCAACCGAATAAAT
126 TAACTTCACAGTGTTAAAGAATACAGTTTAGCAGAATTGGCAGCAACCGAATAAAT
5937036 TTACT
1 TTACT
5937041 AAGCAATCTA
Statistics
Matches: 172, Mismatches: 7, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
179 4 0.02
180 64 0.37
181 18 0.10
182 50 0.29
183 36 0.21
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (181 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGTATTAAAGAATACACAGTTA
GCAGAATTGGCAGCAAACGACAAATTTACTTTCAACCAAAGACAAAACAAAGACAAATACTAACT
TCACAGTGTTAAAGAATACAGTTTAGCAGAATTGGCAGCAACCGAATAAAT
Found at i:5938730 original size:20 final size:20
Alignment explanation
Indices: 5938705--5938767 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
5938695 TTTTGGTTGA
5938705 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
5938725 AATGAAAATCGCAATGCG-GA-
1 AATGAAAATCGCAA--CGAGAG
**
5938745 AATGACTATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
5938765 AAT
1 AAT
5938768 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 29 0.78
21 2 0.05
22 2 0.05
ACGTcount: A:0.46, C:0.16, G:0.24, T:0.14
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:5938833 original size:19 final size:18
Alignment explanation
Indices: 5938791--5938835 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
5938781 CAAAATCGCA
5938791 ATTCTCGTTGCGATAGTC
1 ATTCTCGTTGCGATAGTC
**
5938809 ATTTCTGCGTTGCGATTTTC
1 A-TTCT-CGTTGCGATAGTC
5938829 ATTCTCG
1 ATTCTCG
5938836 AAACTATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.13
19 8 0.35
20 12 0.52
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.44
Consensus pattern (18 bp):
ATTCTCGTTGCGATAGTC
Found at i:5939425 original size:21 final size:21
Alignment explanation
Indices: 5939401--5939446 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
5939391 TATTCGCATT
5939401 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
5939422 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
5939443 GCGA
1 GCGA
5939447 TCAGAAATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:5970508 original size:22 final size:21
Alignment explanation
Indices: 5970421--5970522 Score: 132
Period size: 21 Copynumber: 4.7 Consensus size: 21
5970411 AGAACCCCAT
5970421 GGGGAATCGGTTCCCCTACAG
1 GGGGAATCGGTTCCCCTACAG
5970442 GGGGAATCGGTTCCCCTACAG
1 GGGGAATCGGTTCCCCTACAG
*
5970463 GGGGAATCGGTTCCCCTTCAAAG
1 GGGGAATCGGTTCCCC-T-ACAG
** *
5970486 GGGGAATCAATTCCCCTTCAAG
1 GGGGAATCGGTTCCCCTAC-AG
*
5970508 GGGGAATTGGTTCCC
1 GGGGAATCGGTTCCC
5970523 TTCGCACTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
21 37 0.53
22 16 0.23
23 17 0.24
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.22
Consensus pattern (21 bp):
GGGGAATCGGTTCCCCTACAG
Found at i:5970524 original size:44 final size:43
Alignment explanation
Indices: 5970421--5970525 Score: 131
Period size: 44 Copynumber: 2.4 Consensus size: 43
5970411 AGAACCCCAT
* * **
5970421 GGGGAATCGGTTCCCCT-ACAGGGGGAATCGGTTCCCCTACAG
1 GGGGAATCGGTTCCCTTCAAAGGGGGAATCAATTCCCCTACAG
*
5970463 GGGGAATCGGTTCCCCTTCAAAGGGGGAATCAATTCCCCTTCAAG
1 GGGGAATCGGTT-CCCTTCAAAGGGGGAATCAATTCCCCTAC-AG
*
5970508 GGGGAATTGGTTCCCTTC
1 GGGGAATCGGTTCCCTTC
5970526 GCACTAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
42 12 0.22
43 4 0.07
44 25 0.46
45 13 0.24
ACGTcount: A:0.20, C:0.27, G:0.30, T:0.23
Consensus pattern (43 bp):
GGGGAATCGGTTCCCTTCAAAGGGGGAATCAATTCCCCTACAG
Found at i:5974363 original size:21 final size:20
Alignment explanation
Indices: 5974329--5974381 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
5974319 GAGTTTATTT
*
5974329 TCATTTTTCA-ATTTTGAAACA
1 TCATTTTT-ATATTTT-AAAAA
5974350 TCATTTTTATATTTTAAAAA
1 TCATTTTTATATTTTAAAAA
*
5974370 TAATTTCTTATA
1 TCATTT-TTATA
5974382 ATCCGAAGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (20 bp):
TCATTTTTATATTTTAAAAA
Found at i:5979041 original size:14 final size:14
Alignment explanation
Indices: 5979019--5979053 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5979009 TATCATTCAA
*
5979019 TTAACCTACAAGTG
1 TTAAGCTACAAGTG
5979033 TTAAGCTACAAGTG
1 TTAAGCTACAAGTG
*
5979047 CTAAGCT
1 TTAAGCT
5979054 TTCTTTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (14 bp):
TTAAGCTACAAGTG
Found at i:5987263 original size:18 final size:18
Alignment explanation
Indices: 5987240--5987331 Score: 98
Period size: 18 Copynumber: 4.9 Consensus size: 18
5987230 CACTGTTATG
5987240 GAGGATAAATTTTATATT
1 GAGGATAAATTTTATATT
5987258 GAGGATAAATTTATAATATAT
1 GAGGATAAATTT-T-ATAT-T
* *
5987279 -A-TATATGATTTTATATT
1 GAGGATA-AATTTTATATT
*
5987296 GATGATAAATTTTATATT
1 GAGGATAAATTTTATATT
5987314 GAGGATAAATTTATATAT
1 GAGGATAAATTT-TATAT
5987332 ATATATATAT
Statistics
Matches: 62, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
17 1 0.02
18 38 0.61
19 13 0.21
20 9 0.15
21 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (18 bp):
GAGGATAAATTTTATATT
Found at i:5996738 original size:59 final size:58
Alignment explanation
Indices: 5996668--5996782 Score: 144
Period size: 59 Copynumber: 1.9 Consensus size: 58
5996658 CCAAATTATG
*
5996668 TCTCATTCTAAATTAG-TCCTCAAACTTTTGAA-ATTCCAATTTCATCTCCAAACTATAAC
1 TCTCATTCTAAATTAGTTCCT--AACTTTTGAATATTCCAATTTCATC-ACAAACTATAAC
* * *
5996727 TCTCATTCTAAATTGGTTTCCTAACTTTTGAATATTTCAATTTTATCACAAACTAT
1 TCTCATTCTAAATTAG-TTCCTAACTTTTGAATATTCCAATTTCATCACAAACTAT
5996783 CGATATGTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
59 33 0.67
60 12 0.24
61 4 0.08
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (58 bp):
TCTCATTCTAAATTAGTTCCTAACTTTTGAATATTCCAATTTCATCACAAACTATAAC
Found at i:6002069 original size:16 final size:17
Alignment explanation
Indices: 6002041--6002074 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
6002031 TCGACTTCTT
*
6002041 TCTTATCAAATAATTAA
1 TCTTATCAAATAAATAA
6002058 TCTTAT-AAATAAATAA
1 TCTTATCAAATAAATAA
6002074 T
1 T
6002075 AAAGATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (17 bp):
TCTTATCAAATAAATAA
Found at i:6002599 original size:25 final size:25
Alignment explanation
Indices: 6002556--6002615 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
6002546 ATTTTAGGAG
*
6002556 AAAAATAATTTATAAAAAAATATA-
1 AAAAAAAATTTATAAAAAAATATAT
*
6002580 AAAATAAAATTT-TAATAAAATTATAT
1 AAAA-AAAATTTATAA-AAAAATATAT
6002606 AAAAAAAATT
1 AAAAAAAATT
6002616 AAAATATATG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 7 0.23
25 20 0.65
26 4 0.13
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (25 bp):
AAAAAAAATTTATAAAAAAATATAT
Found at i:6002621 original size:25 final size:25
Alignment explanation
Indices: 6002571--6002621 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
6002561 TAATTTATAA
**
6002571 AAAAATATAAAAATAAAATTTTAAT
1 AAAAATATAAAAATAAAATTAAAAT
*
6002596 AAAATTATATAAAA-AAAATTAAAAT
1 AAAAATATA-AAAATAAAATTAAAAT
6002621 A
1 A
6002622 TATGATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (25 bp):
AAAAATATAAAAATAAAATTAAAAT
Found at i:6003282 original size:14 final size:14
Alignment explanation
Indices: 6003263--6003290 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6003253 CTGCACCAGA
6003263 CCCAAACACGTGAG
1 CCCAAACACGTGAG
6003277 CCCAAACACGTGAG
1 CCCAAACACGTGAG
6003291 GTTTCCAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.21, T:0.07
Consensus pattern (14 bp):
CCCAAACACGTGAG
Found at i:6004304 original size:16 final size:15
Alignment explanation
Indices: 6004268--6004297 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6004258 AATATTCATA
6004268 TATTTTTTATAGTAT
1 TATTTTTTATAGTAT
6004283 TATTTTTTATA-TAT
1 TATTTTTTATAGTAT
6004297 T
1 T
6004298 TTATTTTGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TATTTTTTATAGTAT
Found at i:6004376 original size:2 final size:2
Alignment explanation
Indices: 6004356--6004420 Score: 98
Period size: 2 Copynumber: 33.5 Consensus size: 2
6004346 ATTTATATGT
*
6004356 TA TA T- TA TA T- TA CA 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
*
6004396 TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6004421 GCATTTTATT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
1 2 0.04
2 55 0.96
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6005484 original size:15 final size:15
Alignment explanation
Indices: 6005464--6005501 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
6005454 ATAAAAATAC
6005464 AACTTTATTCATTTA
1 AACTTTATTCATTTA
6005479 AACTTTATTCATTTA
1 AACTTTATTCATTTA
*
6005494 CACTTTAT
1 AACTTTAT
6005502 GTATTACCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.53
Consensus pattern (15 bp):
AACTTTATTCATTTA
Found at i:6007101 original size:28 final size:28
Alignment explanation
Indices: 6007070--6007131 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
6007060 TTGACTCAGA
6007070 TGAGTTAAATCGGACGCA-TTGACTTGGT
1 TGAGTTAAATCGGACG-AGTTGACTTGGT
* * **
6007098 TGAGTTAACTTGGTTGAGTTGACTTGGT
1 TGAGTTAAATCGGACGAGTTGACTTGGT
6007126 TGAGTT
1 TGAGTT
6007132 GACTCAATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 1 0.03
28 28 0.97
ACGTcount: A:0.21, C:0.10, G:0.31, T:0.39
Consensus pattern (28 bp):
TGAGTTAAATCGGACGAGTTGACTTGGT
Found at i:6007132 original size:14 final size:14
Alignment explanation
Indices: 6007088--6007135 Score: 87
Period size: 14 Copynumber: 3.4 Consensus size: 14
6007078 ATCGGACGCA
6007088 TTGACTTGGTTGAG
1 TTGACTTGGTTGAG
*
6007102 TTAACTTGGTTGAG
1 TTGACTTGGTTGAG
6007116 TTGACTTGGTTGAG
1 TTGACTTGGTTGAG
6007130 TTGACT
1 TTGACT
6007136 CAATCTGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.17, C:0.08, G:0.31, T:0.44
Consensus pattern (14 bp):
TTGACTTGGTTGAG
Found at i:6012161 original size:2 final size:2
Alignment explanation
Indices: 6012154--6012203 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
6012144 TACTAATTAC
6012154 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
6012196 TA TA TA TA
1 TA TA TA TA
6012204 CATACATACA
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:6014194 original size:44 final size:42
Alignment explanation
Indices: 6013971--6014195 Score: 132
Period size: 44 Copynumber: 5.1 Consensus size: 42
6013961 TAAGTTTGGT
* * *
6013971 TATATAGCAGCATTTTTAGGCACAAATGCCGTTAAATGTCGTGA
1 TATATAGCAGCATTTTT-GGCACAAACG-CGCTAAATGTCATGA
* *
6014015 TATATAGCAGCATTTTTGGACACAAACACTGCTAAATGTCATAA
1 TATATAGCAGCATTTTTGG-CACAAACGC-GCTAAATGTCATGA
* * ** * * *
6014059 TATATAGCGGCGTTTTTCTCTGCAAACTTCGCTAGATGTCATGA
1 TATATAGCAGCATTTTTGGC-ACAAAC-GCGCTAAATGTCATGA
* * * * * * * *
6014103 AATAAAGC-GACATTTTTTGTACAAACGTTG-GAATAAGT-ATGGT
1 TATATAGCAG-CATTTTTGGCACAAACG-CGCTAA-ATGTCAT-GA
*
6014146 TATATAGCAGCGTTTTTGGGCACAAACGCGACTAAATGTCATGA
1 TATATAGCAGCATTTTT-GGCACAAACGCG-CTAAATGTCATGA
6014190 TATATA
1 TATATA
6014196 TCGGCGTTTT
Statistics
Matches: 133, Mismatches: 35, Indels: 26
0.69 0.18 0.13
Matches are distributed among these distances:
42 3 0.02
43 28 0.21
44 97 0.73
45 5 0.04
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (42 bp):
TATATAGCAGCATTTTTGGCACAAACGCGCTAAATGTCATGA
Found at i:6016124 original size:20 final size:21
Alignment explanation
Indices: 6016099--6016150 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
6016089 TTTTCCCAAT
*
6016099 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
* **
6016119 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGAAAAA
6016140 TCGCAATGCGA
1 TCGCAATGCGA
6016151 TAATGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:6016164 original size:20 final size:20
Alignment explanation
Indices: 6016139--6016252 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
6016129 AATTGGAAAA
*
6016139 ATCGCAATGCGATAATGACT
1 ATCGCAATGCGATACTGACT
*
6016159 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
6016179 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
*
6016200 ATCGCAATGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
6016220 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
6016240 TTCGCAACGCGAT
1 ATCGCAATGCGAT
6016253 TTACATAGCG
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.77
21 14 0.17
22 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:6016183 original size:61 final size:61
Alignment explanation
Indices: 6016136--6016252 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
6016126 GCGAATTGGA
* * * *
6016136 AAAATCGCAATGCGATAATGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAATGAGATAATGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
6016197 AAAATCGCAATGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAATGAGATAATGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
6016253 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAATGAGATAATGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:6016204 original size:41 final size:40
Alignment explanation
Indices: 6016139--6016232 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 40
6016129 AATTGGAAAA
* * *
6016139 ATCGCAATGCGATAATGACTATCGCAATGCGATACTTACT
1 ATCGCAATGCGATAATGACAATCGCAATGAGATACTGACT
6016179 ATCGCAATGCGATAAT-ACAAAATCGCAATGAGATACTGACT
1 ATCGCAATGCGATAATGAC--AATCGCAATGAGATACTGACT
* *
6016220 TTCGCAACGCGAT
1 ATCGCAATGCGAT
6016233 TCTGACTTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
39 2 0.04
40 16 0.34
41 29 0.62
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (40 bp):
ATCGCAATGCGATAATGACAATCGCAATGAGATACTGACT
Found at i:6016856 original size:19 final size:19
Alignment explanation
Indices: 6016812--6016850 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
6016802 AGAGAATCGG
*
6016812 AACGCGAAATAAAAAACGC
1 AACGCGAAACAAAAAACGC
*
6016831 AACGCGAAACAAAAATCGC
1 AACGCGAAACAAAAAACGC
6016850 A
1 A
6016851 TTGCGATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.23, G:0.15, T:0.05
Consensus pattern (19 bp):
AACGCGAAACAAAAAACGC
Found at i:6016868 original size:19 final size:19
Alignment explanation
Indices: 6016846--6017010 Score: 143
Period size: 19 Copynumber: 9.1 Consensus size: 19
6016836 GAAACAAAAA
*
6016846 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
6016865 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
6016884 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
6016903 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
6016917 TCTCGTCGCGATATTCATT
1 TCGCGTTGCGATTTTCATT
6016936 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
6016950 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
6016969 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
* *
6016989 ATCTCGTTGCGATTTTTATT
1 -TCGCGTTGCGATTTTCATT
6017009 TC
1 TC
6017011 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 24
0.75 0.09 0.15
Matches are distributed among these distances:
14 19 0.16
16 5 0.04
17 6 0.05
19 58 0.49
20 30 0.25
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:6016926 original size:38 final size:35
Alignment explanation
Indices: 6016851--6017010 Score: 148
Period size: 33 Copynumber: 4.5 Consensus size: 35
6016841 AAAAATCGCA
* *
6016851 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TTTCTCTC-CG
6016889 TTGCGATTTTCATTTCGCGTTGCGA-TTCTCT-CG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTCTCCG
* *
6016922 TCGCGATATTCATTTCGCGTTGCGA-TTCTCT-CG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTCTCCG
** *
6016955 TTGCGATAGTCATTTCCGCGTTGCGATTCTCATTATCTCG
1 TTGCGATTTTCATTT-CGCGTTGCGATT-TC--TCTC-CG
*
6016995 TTGCGATTTTTATTTC
1 TTGCGATTTTCATTTC
6017011 AACCAAAAGA
Statistics
Matches: 105, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
33 46 0.44
34 10 0.10
35 5 0.05
36 2 0.02
38 27 0.26
39 1 0.01
40 14 0.13
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.46
Consensus pattern (35 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTCTCCG
Found at i:6016934 original size:33 final size:33
Alignment explanation
Indices: 6016891--6016985 Score: 154
Period size: 33 Copynumber: 2.8 Consensus size: 33
6016881 ATTTCGCGTT
*
6016891 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTC
1 GCGATATTCATTTCGCGTTGCGATTCTCTCGTC
*
6016924 GCGATATTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATATTCATTTCGCGTTGCGATTCTCTCGTC
*
6016957 GCGATAGTCATTTCCGCGTTGCGATTCTC
1 GCGATATTCATTT-CGCGTTGCGATTCTC
6016986 ATTATCTCGT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 43 0.74
34 15 0.26
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (33 bp):
GCGATATTCATTTCGCGTTGCGATTCTCTCGTC
Found at i:6019089 original size:21 final size:21
Alignment explanation
Indices: 6019065--6019131 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
6019055 TCATTCCTCG
6019065 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
6019086 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
6019107 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
6019128 AGAG
1 AGAG
6019132 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:6019089 original size:42 final size:42
Alignment explanation
Indices: 6019013--6019131 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
6019003 GACTCGCCTT
* * * * * * *
6019013 TCATCCCTCAAGAGTCCACTCCTATCGTTAAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
6019055 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
6019097 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
6019132 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:6020509 original size:14 final size:14
Alignment explanation
Indices: 6020490--6020525 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
6020480 ATTGTTTAAT
6020490 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
6020504 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
6020518 TGATTTGT
1 TGATTTGT
6020526 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:6020707 original size:19 final size:19
Alignment explanation
Indices: 6020632--6020698 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
6020622 AAAAAGTACT
* *
6020632 ATCGCAATGGGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
6020651 ATCGCAA--C--AA-GAGA
1 ATCGCAACGCGAAATGAAA
6020665 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
6020684 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
6020699 TAAATTCGCG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.25
15 2 0.05
16 1 0.03
18 2 0.05
19 25 0.62
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:6020749 original size:33 final size:33
Alignment explanation
Indices: 6020707--6020866 Score: 259
Period size: 33 Copynumber: 4.8 Consensus size: 33
6020697 ATTAAATTCG
* *
6020707 CGTTGCGATTTTCATTTCGCACTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* **
6020740 CGTTGCGATTTTCATTTCGCATTGCGAAAT-TAG
1 CGTTGCGATTTTCATTTCGCATTGCG-ATTCTCT
6020773 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
6020806 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
6020839 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
6020867 AATAATTTCC
Statistics
Matches: 117, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
32 2 0.02
33 113 0.97
34 2 0.02
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:6020813 original size:14 final size:14
Alignment explanation
Indices: 6020794--6020848 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
6020784 TCATTTCGCA
6020794 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
6020808 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
6020825 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
6020841 TTGCGATT
1 TTGCGATT
6020849 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:6023175 original size:12 final size:12
Alignment explanation
Indices: 6023158--6023182 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6023148 TCTTCGGGGA
6023158 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6023170 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6023182 C
1 C
6023183 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:6023391 original size:24 final size:24
Alignment explanation
Indices: 6023357--6023410 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
6023347 CTGAAACATC
* *
6023357 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
6023381 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
6023405 ATCAAA
1 ATCAAA
6023411 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:6024424 original size:20 final size:20
Alignment explanation
Indices: 6024399--6024436 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6024389 ATTCATTTGA
*
6024399 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGAGAAAATGG
6024419 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
6024437 CGCAATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:6024479 original size:14 final size:14
Alignment explanation
Indices: 6024460--6024513 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
6024450 GAAAACCGCA
6024460 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
6024474 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
6024491 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
6024507 TTGCGAT
1 TTGCGAT
6024514 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:6024479 original size:33 final size:33
Alignment explanation
Indices: 6024442--6024512 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
6024432 AAAATCGCAA
6024442 TGCGAAATGAAAACCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAACCGCATTGCGATTTTCTCGT
** ** ***
6024475 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAACCGCATTGCGATTTTCTCGT
6024508 TGCGA
1 TGCGA
6024513 TAGCCATTTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (33 bp):
TGCGAAATGAAAACCGCATTGCGATTTTCTCGT
Found at i:6024513 original size:33 final size:33
Alignment explanation
Indices: 6024456--6024532 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 33
6024446 AAATGAAAAC
***
6024456 CGCATTGCGATTTTCTCGTTGCGATTTTCATTT
1 CGCATTGCGATTTTCTCGTTGCGATAGCCATTT
6024489 CGCATTGCGATTTTCTCGTTGCGATAGCCATTT
1 CGCATTGCGATTTTCTCGTTGCGATAGCCATTT
*
6024522 CGCGTTGCGAT
1 CGCATTGCGAT
6024533 AGTCTGTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
CGCATTGCGATTTTCTCGTTGCGATAGCCATTT
Found at i:6024639 original size:14 final size:14
Alignment explanation
Indices: 6024620--6024670 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
6024610 CATCAATTAA
6024620 ACAAATCAACATTT
1 ACAAATCAACATTT
6024634 ACAAATCAACATTT
1 ACAAATCAACATTT
*
6024648 ACAAATCATA-TTTT
1 ACAAATCA-ACATTT
6024662 ACAAATCAA
1 ACAAATCAA
6024671 TTAAACAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
13 1 0.03
14 33 0.94
15 1 0.03
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:6026561 original size:20 final size:19
Alignment explanation
Indices: 6026537--6026623 Score: 104
Period size: 20 Copynumber: 4.5 Consensus size: 19
6026527 CGAAACTTAA
6026537 AATCGCAACGCGAAAATGAC
1 AATCGCAACGCG-AAATGAC
* *
6026557 TATCGCAACGCGGAAATGGC
1 AATCGCAACGC-GAAATGAC
* * *
6026577 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAC
6026596 AATCGCAACGCGAAATGA-
1 AATCGCAACGCGAAATGAC
6026614 AATCGCAACG
1 AATCGCAACG
6026624 ACAAAATCGC
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
18 10 0.17
19 22 0.37
20 26 0.44
21 1 0.02
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAC
Found at i:6026604 original size:39 final size:39
Alignment explanation
Indices: 6026538--6026612 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
6026528 GAAACTTAAA
**
6026538 ATCGCAACGCGAAAATGACTATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGAAAATCGCAACGC-GAAATGGCT
*
6026578 ATCGCAATGCG-AAATGAAAATCGCAACGCGAAATG
1 ATCGCAACGCGAAAATGAAAATCGCAACGCGAAATG
6026613 AAATCGCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 6 0.19
39 16 0.50
40 10 0.31
ACGTcount: A:0.39, C:0.23, G:0.24, T:0.15
Consensus pattern (39 bp):
ATCGCAACGCGAAAATGAAAATCGCAACGCGAAATGGCT
Found at i:6026690 original size:14 final size:14
Alignment explanation
Indices: 6026671--6026728 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
6026661 TTTCATTTCG
6026671 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
6026685 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
6026701 CGCATTGCAATTTTGT
1 CG--TTGCGATTTTGT
6026717 CGTTGCGATTTT
1 CGTTGCGATTTT
6026729 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:6026701 original size:32 final size:33
Alignment explanation
Indices: 6026654--6026744 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
6026644 ATAAATCGCA
*
6026654 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
6026687 TTGCGA-TTTCATTTCGCATTGCAATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
6026719 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
6026745 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:6026763 original size:20 final size:19
Alignment explanation
Indices: 6026729--6026783 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
6026719 TTGCGATTTT
*
6026729 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
6026748 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
6026768 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
6026784 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:6027285 original size:18 final size:18
Alignment explanation
Indices: 6027259--6027303 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
6027249 GTCGATTAGA
*
6027259 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
6027277 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
6027295 TGATGGCTC
1 TGATGGCTC
6027304 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Done.