Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009597.1 Hibiscus syriacus cultivar Beakdansim tig00116976_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: 1557931
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 7 of 7
Found at i:1377300 original size:21 final size:21
Alignment explanation
Indices: 1377274--1377385 Score: 109
Period size: 21 Copynumber: 5.3 Consensus size: 21
1377264 GAAGAAGCCC
*
1377274 GATCCACCTACCATTGTTCAG
1 GATCCACCTCCCATTGTTCAG
1377295 GATCCACCTCCCATTGTTCAG
1 GATCCACCTCCCATTGTTCAG
* ** *
1377316 GATTCACCTGTCATTGTTCAA
1 GATCCACCTCCCATTGTTCAG
* * *
1377337 GAGGCC-CCTCCTATCGTTCAG
1 GA-TCCACCTCCCATTGTTCAG
* **
1377358 AATCCACCTCCCACCGTTCAG
1 GATCCACCTCCCATTGTTCAG
1377379 GATCCAC
1 GATCCAC
1377386 ATGGCATACT
Statistics
Matches: 72, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
20 2 0.03
21 69 0.96
22 1 0.01
ACGTcount: A:0.21, C:0.37, G:0.15, T:0.27
Consensus pattern (21 bp):
GATCCACCTCCCATTGTTCAG
Found at i:1379002 original size:12 final size:12
Alignment explanation
Indices: 1378987--1379027 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
1378977 AAAGCTGTTG
*
1378987 TGATTGGGATTT
1 TGATTGCGATTT
*
1378999 TGATTGTGATTT
1 TGATTGCGATTT
1379011 TGATTGCGATTT
1 TGATTGCGATTT
1379023 TGATT
1 TGATT
1379028 TCCTTTTGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.17, C:0.02, G:0.27, T:0.54
Consensus pattern (12 bp):
TGATTGCGATTT
Found at i:1381499 original size:12 final size:12
Alignment explanation
Indices: 1381478--1381511 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1381468 GGTTGTGAGT
*
1381478 TTTGAGATTGTG
1 TTTGATATTGTG
1381490 TTTGATATTGTG
1 TTTGATATTGTG
*
1381502 TTTGGTATTG
1 TTTGATATTG
1381512 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1383301 original size:2 final size:2
Alignment explanation
Indices: 1383294--1383325 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1383284 ATGTCTACAC
1383294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1383326 GCTATCAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1383596 original size:19 final size:19
Alignment explanation
Indices: 1383564--1383603 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1383554 TAAATTATAT
*
1383564 TTTGAGCCTGAAATTCTTAC
1 TTTGAGCCTCAAATTC-TAC
1383584 TTTGA-CCTCAAATTCTAC
1 TTTGAGCCTCAAATTCTAC
1383602 TT
1 TT
1383604 ATTAACCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (19 bp):
TTTGAGCCTCAAATTCTAC
Found at i:1384926 original size:20 final size:20
Alignment explanation
Indices: 1384903--1385048 Score: 82
Period size: 20 Copynumber: 7.2 Consensus size: 20
1384893 GAAACTTGTT
1384903 TTGCGAATTTAAAAATCGCG
1 TTGCGAATTTAAAAATCGCG
* * *
1384923 TTGCTAA--AAAGAAATTCGCC
1 TTGCGAATTTAA-AAA-TCGCG
* * *
1384943 TTGCGAATTCAGAAATCGAG
1 TTGCGAATTTAAAAATCGCG
* * *
1384963 TTGCGAATTTGAAATTCCGTG
1 TTGCGAATTTAAAAAT-CGCG
**
1384984 TTGCGAATTTGGAAA-CTGCG
1 TTGCGAATTTAAAAATC-GCG
* ** **
1385004 TTGCGAAATTGGAGTTCGCG
1 TTGCGAATTTAAAAATCGCG
1385024 TTGCGAATTTAGAAAATCGCG
1 TTGCGAATTTA-AAAATCGCG
1385045 TTGC
1 TTGC
1385049 AAAAAGGAAA
Statistics
Matches: 94, Mismatches: 24, Indels: 15
0.71 0.18 0.11
Matches are distributed among these distances:
18 2 0.02
19 4 0.04
20 57 0.61
21 30 0.32
22 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (20 bp):
TTGCGAATTTAAAAATCGCG
Found at i:1384926 original size:40 final size:40
Alignment explanation
Indices: 1384863--1385091 Score: 117
Period size: 40 Copynumber: 5.7 Consensus size: 40
1384853 ATCGATCATG
** * **
1384863 TTGCGAA-TTAGAAAATCTTGTTGCGAAAAGGAAACTT-GTT
1 TTGCGAATTTA-AAAATCGAGTTGCGAAAAAGAAA-TTCGCC
* *
1384903 TTGCGAATTTAAAAATCGCGTTGCTAAAAAGAAATTCGCC
1 TTGCGAATTTAAAAATCGAGTTGCGAAAAAGAAATTCGCC
* * *** **
1384943 TTGCGAATTCAGAAATCGAGTTGCGAATTTGAAATTCCGTG
1 TTGCGAATTTAAAAATCGAGTTGCGAAAAAGAAATT-CGCC
** * ** * * *
1384984 TTGCGAATTTGGAAA-CTGCGTTGCGAAATTGGAGTTCGCG
1 TTGCGAATTTAAAAATC-GAGTTGCGAAAAAGAAATTCGCC
* **
1385024 TTGCGAATTTAGAAAATCGCGTTGC-AAAAAGGAAATTCGAG
1 TTGCGAATTTA-AAAATCGAGTTGCGAAAAA-GAAATTCGCC
* *
1385065 TTGCAAATTTTAAAA-CTGAGTTGCGAA
1 TTGCGAATTTAAAAATC-GAGTTGCGAA
1385092 TTTGGAAACT
Statistics
Matches: 148, Mismatches: 32, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
39 3 0.02
40 83 0.56
41 61 0.41
42 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.30
Consensus pattern (40 bp):
TTGCGAATTTAAAAATCGAGTTGCGAAAAAGAAATTCGCC
Found at i:1385007 original size:41 final size:40
Alignment explanation
Indices: 1384903--1385091 Score: 132
Period size: 41 Copynumber: 4.7 Consensus size: 40
1384893 GAAACTTGTT
* * ** **
1384903 TTGCGAATTTA-AAAATCGCGTTGCTAAAAAGAAATTCGCC
1 TTGCGAATTTAGAAACT-GCGTTGCGAAATTGAAATTCGAG
* * * *
1384943 TTGCGAATTCAGAAA-TCGAGTTGCGAATTTGAAATTCCGTG
1 TTGCGAATTTAGAAACT-GCGTTGCGAAATTGAAATT-CGAG
* * * *
1384984 TTGCGAATTTGGAAACTGCGTTGCGAAATTGGAGTTCGCG
1 TTGCGAATTTAGAAACTGCGTTGCGAAATTGAAATTCGAG
* * **
1385024 TTGCGAATTTAGAAAATCGCGTTGCAAAAAGGAAATTCGAG
1 TTGCGAATTTAGAAACT-GCGTTGCGAAATTGAAATTCGAG
* *
1385065 TTGCAAATTTTA-AAACTGAGTTGCGAA
1 TTGCGAA-TTTAGAAACTGCGTTGCGAA
1385092 TTTGGAAACT
Statistics
Matches: 117, Mismatches: 27, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
40 52 0.44
41 60 0.51
42 5 0.04
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (40 bp):
TTGCGAATTTAGAAACTGCGTTGCGAAATTGAAATTCGAG
Found at i:1385068 original size:81 final size:80
Alignment explanation
Indices: 1384862--1385098 Score: 219
Period size: 81 Copynumber: 2.9 Consensus size: 80
1384852 AATCGATCAT
** * *
1384862 GTTGCGAA-TTAGAAAATCTTGTTGCGAAAAGGAAACTT-GTTTTGCGAATTTAAAAATCGCGTT
1 GTTGCGAATTTAGAAAATCGAGTTGCGAAAAGGAAA-TTCGTGTTGCGAATTTAAAACT-GCGTT
* ** *
1384925 GCTAAAAAGAAATTCGC
64 GCGAAATTGGAATTCGC
* * *** *
1384942 CTTGCGAATTCAG-AAATCGAGTTGCGAATTTGAAATTCCGTGTTGCGAATTTGGAAACTGCGTT
1 GTTGCGAATTTAGAAAATCGAGTTGCGAAAAGGAAATT-CGTGTTGCGAATTT-AAAACTGCGTT
*
1385006 GCGAAATTGGAGTTCGC
64 GCGAAATTGGAATTCGC
* * * * *
1385023 GTTGCGAATTTAGAAAATCGCGTTGCAAAAAGGAAATTCGAGTTGCAAATTTTAAAACTGAGTTG
1 GTTGCGAATTTAGAAAATCGAGTTGCGAAAAGGAAATTCGTGTTGCGAA-TTTAAAACTGCGTTG
*
1385088 CGAATTTGGAA
65 CGAAATTGGAA
1385099 ACTGTGTTGT
Statistics
Matches: 123, Mismatches: 28, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
79 2 0.02
80 24 0.20
81 71 0.58
82 26 0.21
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (80 bp):
GTTGCGAATTTAGAAAATCGAGTTGCGAAAAGGAAATTCGTGTTGCGAATTTAAAACTGCGTTGC
GAAATTGGAATTCGC
Found at i:1385100 original size:20 final size:20
Alignment explanation
Indices: 1384960--1385117 Score: 70
Period size: 20 Copynumber: 7.8 Consensus size: 20
1384950 TTCAGAAATC
*
1384960 GAGTTGCGAATTT-GAAATTCC
1 GAGTTGCGAATTTGGAAA--CT
*
1384981 GTGTTGCGAATTTGGAAACT
1 GAGTTGCGAATTTGGAAACT
* * **
1385001 GCGTTGCGAAATTGG-AGTT
1 GAGTTGCGAATTTGGAAACT
* * *
1385020 CGCGTTGCGAATTTAGAAAAT
1 -GAGTTGCGAATTTGGAAACT
* *** *
1385041 CGCGTTGC-AAAAAGGAAATT
1 -GAGTTGCGAATTTGGAAACT
* **
1385061 CGAGTTGCAAATTTTAAAACT
1 -GAGTTGCGAATTTGGAAACT
1385082 GAGTTGCGAATTTGGAAACT
1 GAGTTGCGAATTTGGAAACT
* * *
1385102 GTGTTGTGAAATTGGA
1 GAGTTGCGAATTTGGA
1385118 GTTCGTGTTG
Statistics
Matches: 105, Mismatches: 28, Indels: 9
0.74 0.20 0.06
Matches are distributed among these distances:
19 2 0.02
20 71 0.68
21 28 0.27
22 4 0.04
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.31
Consensus pattern (20 bp):
GAGTTGCGAATTTGGAAACT
Found at i:1389336 original size:11 final size:13
Alignment explanation
Indices: 1389318--1389350 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
1389308 TATATATTTA
1389318 TATTTTATAAT-T
1 TATTTTATAATAT
1389330 T-TTTTATAATAT
1 TATTTTATAATAT
1389342 TATTTTATA
1 TATTTTATA
1389351 TAAGAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.47
12 3 0.16
13 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTTATAATAT
Found at i:1397600 original size:12 final size:12
Alignment explanation
Indices: 1397583--1397633 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
1397573 TTCAAAGAGG
1397583 TTTTATATTTAA
1 TTTTATATTTAA
1397595 TTTTATA-TTATA
1 TTTTATATTTA-A
*
1397607 TTTGAT-TTTAA
1 TTTTATATTTAA
1397618 TTTTA-ATATTAA
1 TTTTATAT-TTAA
1397630 TTTT
1 TTTT
1397634 TAAATAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:1397680 original size:14 final size:12
Alignment explanation
Indices: 1397614--1397811 Score: 75
Period size: 13 Copynumber: 15.5 Consensus size: 12
1397604 ATATTTGATT
*
1397614 TTAATTTTAATA
1 TTAATTATAATA
*
1397626 TTAATTTTTAA-A
1 TTAA-TTATAATA
*
1397638 TAAATTA-AATA
1 TTAATTATAATA
*
1397649 TTAATTTTTTTAATA
1 TTAA---TTATAATA
1397664 TTATATTATATATA
1 TTA-ATTATA-ATA
*
1397678 TTAATTTTAATA
1 TTAATTATAATA
*
1397690 TTAATTTTTTAA-A
1 TTAA--TTATAATA
*
1397703 TAAATTA-AATA
1 TTAATTATAATA
*
1397714 TTAATTTTTAATA
1 TTAA-TTATAATA
*
1397727 TTATATTAAATATA
1 TTA-ATTATA-ATA
*
1397741 TTAATTTTAATA
1 TTAATTATAATA
*
1397753 TTAATTTTTTAA-A
1 TTAA--TTATAATA
*
1397766 TAAATTA-AATA
1 TTAATTATAATA
*
1397777 TTAATTTTTTAATA
1 TTAA--TTATAATA
1397791 TTATATTATAGATA
1 TTA-ATTATA-ATA
1397805 TTTAATT
1 -TTAATT
1397812 TTATATCATA
Statistics
Matches: 143, Mismatches: 19, Indels: 46
0.69 0.09 0.22
Matches are distributed among these distances:
10 6 0.04
11 18 0.13
12 24 0.17
13 43 0.30
14 40 0.28
15 11 0.08
16 1 0.01
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.56
Consensus pattern (12 bp):
TTAATTATAATA
Found at i:1397694 original size:64 final size:64
Alignment explanation
Indices: 1397590--1397814 Score: 355
Period size: 63 Copynumber: 3.5 Consensus size: 64
1397580 AGGTTTTATA
* *
1397590 TTTAATTTTATATTATATTTGATTTTAATTTTAATATTAA-TTTTTAAATAAATTAAATATTAAT
1 TTTAATATTATATTATA--T-ATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAA-
1397654 TTT
62 TTT
1397657 TTTAATATTATATTATATATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAA-TT
1 TTTAATATTATATTATATATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTT
*
1397720 TTTAATATTATATTAAATATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTT
1 TTTAATATTATATTATATATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTT
*
1397784 TTTAATATTATATTATAGATATTTAATTTTA
1 TTTAATATTATATTATATATA-TTAATTTTA
1397815 TATCATATAA
Statistics
Matches: 150, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
63 62 0.41
64 39 0.26
65 33 0.22
67 16 0.11
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (64 bp):
TTTAATATTATATTATATATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTT
Found at i:1397787 original size:38 final size:38
Alignment explanation
Indices: 1397710--1397793 Score: 102
Period size: 38 Copynumber: 2.2 Consensus size: 38
1397700 AAATAAATTA
*
1397710 AATATTAATTTTTAATATTATATTAAATATATTAATTTT
1 AATATTAATTTTTAATATTAAATTAAATATATT-ATTTT
1397749 AATATTAATTTTTTAA-A-TAAATTAAATATTAATT-TTTT
1 AATATTAA-TTTTTAATATTAAATTAAATA-T-ATTATTTT
1397787 AATATTA
1 AATATTA
1397794 TATTATAGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
38 21 0.51
39 10 0.24
40 10 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (38 bp):
AATATTAATTTTTAATATTAAATTAAATATATTATTTT
Found at i:1397833 original size:19 final size:18
Alignment explanation
Indices: 1397809--1397858 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
1397799 TAGATATTTA
1397809 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATAAA-T
*
1397828 ATTTTATATATTATTAAT
1 ATTTTATATATTATAAAT
1397846 ATTTTATAT-TTAT
1 ATTTTATATATTAT
1397859 TTTAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 4 0.14
18 11 0.38
19 14 0.48
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTATATATTATAAAT
Found at i:1397855 original size:127 final size:123
Alignment explanation
Indices: 1397594--1397859 Score: 339
Period size: 127 Copynumber: 2.1 Consensus size: 123
1397584 TTTATATTTA
**
1397594 ATTTTATATTATATTTGATTTTAATTTTAATATTAATTTTTAAATAAATTAAATATTAATTTTTT
1 ATTTTATATTATATTAAATTTTAATTTTAATATTAATTTTTAAATAAATTAAATATTAATTTTTT
*
1397659 TAATATTATATTATATATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAT
66 TAATATTATATTATAGATATTAATTTTAATATTAATTTTTT-AAT-AATTAAATATTAAT
1397719 -TTTTAATATTATATTAAATATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAA-T
1 ATTTT-ATATTATATTAAAT-T-TTAATTTTAATATTAA-TTTTTAAATAAATTAAATATTAATT
*
1397782 TTTTTAATATTATATTATAGATATTTAATTTTATATCATATAAATTATTTT-AT-A-T-ATTATT
62 TTTTTAATATTATATTATAGATA-TTAATTTTA-AT-AT-T-AATT-TTTTAATAATTAAATATT
1397843 AAT
121 AAT
1397846 ATTTTATATT-TATT
1 ATTTTATATTATATT
1397860 TTAATTATTT
Statistics
Matches: 126, Mismatches: 4, Indels: 21
0.83 0.03 0.14
Matches are distributed among these distances:
124 4 0.03
125 12 0.10
126 5 0.04
127 52 0.41
128 37 0.29
129 3 0.02
130 2 0.02
131 3 0.02
132 4 0.03
133 4 0.03
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (123 bp):
ATTTTATATTATATTAAATTTTAATTTTAATATTAATTTTTAAATAAATTAAATATTAATTTTTT
TAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAATAATTAAATATTAAT
Found at i:1397875 original size:19 final size:19
Alignment explanation
Indices: 1397824--1397876 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
1397814 ATATCATATA
*
1397824 AATTATTTTATATATTATT
1 AATTATTTTATTTATTATT
1397843 AA-TATTTTATATTTATT-TT
1 AATTA-TTT-TATTTATTATT
1397862 AATTATTTTGATTTA
1 AATTATTTT-ATTTA
1397877 AGTTTAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 3 0.10
19 17 0.59
20 9 0.31
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATTTTATTTATTATT
Found at i:1397877 original size:127 final size:125
Alignment explanation
Indices: 1397591--1397814 Score: 350
Period size: 127 Copynumber: 1.8 Consensus size: 125
1397581 GGTTTTATAT
**
1397591 TTAA-TTTT-ATATTATATTTGAT-T-TTAATTTTAATATTAATTTTTAAATAAATTAAATATTA
1 TTAATTTTTAATATTATATTAAATATATTAATTTTAATATTAATTTTTAAATAAATTAAATATTA
*
1397652 ATTTTTTTAATATTATATTATATATATTAATTTTAATATTAATTTTTTAAATAAATTAAATA
66 ATTTTTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTT-AAT-AATTAAATA
1397714 TTAATTTTTAATATTATATTAAATATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATT
1 TTAATTTTTAATATTATATTAAATATATTAATTTTAATATTAA-TTTTTAAATAAATTAAATATT
1397779 AA-TTTTTTAATATTATATTATAGATATTTAATTTTA
65 AATTTTTTTAATATTATATTATAGATA-TTAATTTTA
1397815 TATCATATAA
Statistics
Matches: 92, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
123 4 0.04
124 4 0.04
125 12 0.13
126 1 0.01
127 39 0.42
128 32 0.35
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (125 bp):
TTAATTTTTAATATTATATTAAATATATTAATTTTAATATTAATTTTTAAATAAATTAAATATTA
ATTTTTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAATAATTAAATA
Found at i:1398373 original size:31 final size:31
Alignment explanation
Indices: 1398332--1398391 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
1398322 TAGTCGTATG
1398332 AATTACTTAAAT-TTCAGTATTGTAAAACTAA
1 AATTACTTAAATCTT-AGTATTGTAAAACTAA
*
1398363 AATTATTTAAATCTTAGTATTGTAAAACT
1 AATTACTTAAATCTTAGTATTGTAAAACT
1398392 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
AATTACTTAAATCTTAGTATTGTAAAACTAA
Found at i:1401293 original size:14 final size:15
Alignment explanation
Indices: 1401274--1401303 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1401264 CTTTGAATTC
1401274 TGGGATT-TTTTGTT
1 TGGGATTCTTTTGTT
1401288 TGGGATTCTTTTGTT
1 TGGGATTCTTTTGTT
1401303 T
1 T
1401304 TATATGGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.07, C:0.03, G:0.27, T:0.63
Consensus pattern (15 bp):
TGGGATTCTTTTGTT
Found at i:1412260 original size:138 final size:138
Alignment explanation
Indices: 1412012--1412279 Score: 509
Period size: 138 Copynumber: 1.9 Consensus size: 138
1412002 ACTAAGCAAA
1412012 TACCATGGGGTCAAAACCAGAGGAAAAACAAAGCAACATGCCCACTGCCCATAGAATTTTTATTA
1 TACCATGGGGTCAAAACCAGAGGAAAAACAAAGCAACATGCCCACTGCCCATAGAATTTTTATTA
*
1412077 ATGAAGAAACAGAGCCTATGTTCAAAGAAAAAGACTTTGATTAATCTGCCAAGTGTTATCAATCA
66 ACGAAGAAACAGAGCCTATGTTCAAAGAAAAAGACTTTGATTAATCTGCCAAGTGTTATCAATCA
1412142 TTCTCAAG
131 TTCTCAAG
**
1412150 TACCATGGGGTCTGAACCAGAGGAAAAACAAAGCAACATGCCCACTGCCCATAGAATTTTTATTA
1 TACCATGGGGTCAAAACCAGAGGAAAAACAAAGCAACATGCCCACTGCCCATAGAATTTTTATTA
1412215 ACGAAGAAACAGAGCCTATGTTCAAAGAAAAAGACTTTGATTAATCTGCCAAGTGTTATCAATCA
66 ACGAAGAAACAGAGCCTATGTTCAAAGAAAAAGACTTTGATTAATCTGCCAAGTGTTATCAATCA
1412280 CCGAACAAGC
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
138 127 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.24
Consensus pattern (138 bp):
TACCATGGGGTCAAAACCAGAGGAAAAACAAAGCAACATGCCCACTGCCCATAGAATTTTTATTA
ACGAAGAAACAGAGCCTATGTTCAAAGAAAAAGACTTTGATTAATCTGCCAAGTGTTATCAATCA
TTCTCAAG
Found at i:1417053 original size:41 final size:41
Alignment explanation
Indices: 1416994--1417091 Score: 178
Period size: 41 Copynumber: 2.4 Consensus size: 41
1416984 AATAGTAGCA
* *
1416994 TAGCTTGTGTAGAAAAAATTTTCACTTTTTTATCTTCTTTT
1 TAGCTTGTGTAGATAAAATTTTCACTTTCTTATCTTCTTTT
1417035 TAGCTTGTGTAGATAAAATTTTCACTTTCTTATCTTCTTTT
1 TAGCTTGTGTAGATAAAATTTTCACTTTCTTATCTTCTTTT
1417076 TAGCTTGTGTAGATAA
1 TAGCTTGTGTAGATAA
1417092 TACTAGGTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.51
Consensus pattern (41 bp):
TAGCTTGTGTAGATAAAATTTTCACTTTCTTATCTTCTTTT
Found at i:1418458 original size:19 final size:20
Alignment explanation
Indices: 1418434--1418489 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
1418424 ATATACGTTT
*
1418434 TATGAACAGT-AAAATATGG
1 TATGAACAGTAAAAATATCG
1418453 TATGAACAGTAAACAATATCG
1 TATGAACAGTAAA-AATATCG
1418474 TATGAACAGTGAAAAA
1 TATGAACAGT-AAAAA
1418490 ATTTGAATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 10 0.30
20 2 0.06
21 18 0.55
22 3 0.09
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.23
Consensus pattern (20 bp):
TATGAACAGTAAAAATATCG
Found at i:1419242 original size:21 final size:20
Alignment explanation
Indices: 1419216--1419271 Score: 94
Period size: 21 Copynumber: 2.8 Consensus size: 20
1419206 CATATGAAAT
1419216 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACT-TA
1419237 TTGTCCCGAAGGACCACTTA
1 TTGTCCCGAAGGACCACTTA
*
1419257 TTATCCCGAAGGACC
1 TTGTCCCGAAGGACC
1419272 TATGAAACCC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.23
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTTA
Found at i:1419263 original size:20 final size:21
Alignment explanation
Indices: 1419219--1419271 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 21
1419209 ATGAAATTTG
*
1419219 TCCCGAAGGACCACTGTATTG
1 TCCCGAAGGACCACTGTATTA
1419240 TCCCGAAGGACCACT-TATTA
1 TCCCGAAGGACCACTGTATTA
1419260 TCCCGAAGGACC
1 TCCCGAAGGACC
1419272 TATGAAACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.21
Consensus pattern (21 bp):
TCCCGAAGGACCACTGTATTA
Found at i:1420670 original size:13 final size:13
Alignment explanation
Indices: 1420652--1420740 Score: 97
Period size: 13 Copynumber: 6.3 Consensus size: 13
1420642 GTCACAACCC
1420652 GACCCGACCCGTT
1 GACCCGACCCGTT
1420665 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1420678 TACCCGACCCGTT
1 GACCCGACCCGTT
1420691 GACCCGACACGACCAGTT
1 GACCCG--AC--CC-GTT
1420709 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1420722 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
1420737 GACC
1 GACC
1420741 GGAGTTGACC
Statistics
Matches: 66, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
13 37 0.56
14 2 0.03
15 14 0.21
16 2 0.03
17 2 0.03
18 9 0.14
ACGTcount: A:0.18, C:0.43, G:0.22, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1420684 original size:26 final size:29
Alignment explanation
Indices: 1420652--1420725 Score: 100
Period size: 31 Copynumber: 2.6 Consensus size: 29
1420642 GTCACAACCC
1420652 GACCCGACCCGTTGACCCG-AC-CC-GTT
1 GACCCGACCCGTTGACCCGAACACCAGTT
*
1420678 TACCCGACCCGTTGACCCGACACGACCAGTT
1 GACCCGACCCGTTGACCCGA-AC-ACCAGTT
1420709 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
1420726 GTTGACCCGT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
26 18 0.44
28 2 0.05
30 2 0.05
31 19 0.46
ACGTcount: A:0.19, C:0.45, G:0.22, T:0.15
Consensus pattern (29 bp):
GACCCGACCCGTTGACCCGAACACCAGTT
Found at i:1420703 original size:18 final size:18
Alignment explanation
Indices: 1420682--1420716 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1420672 CCCGTTTACC
*
1420682 CGACCCGTTGACCCGACA
1 CGACCAGTTGACCCGACA
1420700 CGACCAGTTGACCCGAC
1 CGACCAGTTGACCCGAC
1420717 CCGTTGACCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.43, G:0.23, T:0.11
Consensus pattern (18 bp):
CGACCAGTTGACCCGACA
Found at i:1420711 original size:44 final size:45
Alignment explanation
Indices: 1420648--1420740 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 45
1420638 ACCGGTCACA
* * *
1420648 ACCCGACCCGACCCGTTGACCCGACCCGTTTACC-CGACCCGTTG
1 ACCCGACACGACCAGTTGACCCGACCCGTTGACCGCGACCCGTTG
*
1420692 ACCCGACACGACCAGTTGACCCGACCCGTTGACCGTTGACCCGTTG
1 ACCCGACACGACCAGTTGACCCGACCCGTTGACCG-CGACCCGTTG
1420738 ACC
1 ACC
1420741 GGAGTTGACC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 31 0.72
46 12 0.28
ACGTcount: A:0.18, C:0.44, G:0.22, T:0.16
Consensus pattern (45 bp):
ACCCGACACGACCAGTTGACCCGACCCGTTGACCGCGACCCGTTG
Found at i:1422078 original size:18 final size:18
Alignment explanation
Indices: 1422052--1422087 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1422042 TCGAAAGGAC
*
1422052 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1422070 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1422088 CGGATGGAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1423309 original size:24 final size:24
Alignment explanation
Indices: 1423215--1423321 Score: 90
Period size: 24 Copynumber: 4.5 Consensus size: 24
1423205 ATATTTTATC
* *
1423215 TGATTTCTGATTTGAATTATGTTT
1 TGATATCTGATCTGAATTATGTTT
* * * *
1423239 TGACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTATGTTT
* * * * *
1423263 TGAT-TCCTAACCTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTATGTTT
1423287 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTATGTTT
*
1423311 TGATTTCTGAT
1 TGATATCTGAT
1423322 ATCTCCGTTT
Statistics
Matches: 63, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 61 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (24 bp):
TGATATCTGATCTGAATTATGTTT
Found at i:1425497 original size:18 final size:18
Alignment explanation
Indices: 1425476--1425510 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1425466 CCCGTTTACC
*
1425476 CGACCCGTTGACCCGACA
1 CGACCAGTTGACCCGACA
1425494 CGACCAGTTGACCCGAC
1 CGACCAGTTGACCCGAC
1425511 CCGTTGACCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.43, G:0.23, T:0.11
Consensus pattern (18 bp):
CGACCAGTTGACCCGACA
Found at i:1425510 original size:13 final size:13
Alignment explanation
Indices: 1425446--1425534 Score: 88
Period size: 13 Copynumber: 6.3 Consensus size: 13
1425436 GTCACAACCC
1425446 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1425459 TACCCGACCCGTT
1 GACCCGACCCGTT
*
1425472 TACCCGACCCGTT
1 GACCCGACCCGTT
1425485 GACCCGACACGACCAGTT
1 GACCCG--AC--CC-GTT
1425503 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1425516 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
1425531 GACC
1 GACC
1425535 GGAGTTGACC
Statistics
Matches: 66, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
13 37 0.56
14 2 0.03
15 14 0.21
16 2 0.03
17 2 0.03
18 9 0.14
ACGTcount: A:0.18, C:0.43, G:0.21, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1426873 original size:18 final size:18
Alignment explanation
Indices: 1426847--1426882 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1426837 TCGAAAGGAC
*
1426847 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1426865 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1426883 CGGATGGAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1428103 original size:24 final size:24
Alignment explanation
Indices: 1428009--1428115 Score: 90
Period size: 24 Copynumber: 4.5 Consensus size: 24
1427999 ATATTTTATC
* *
1428009 TGATTTCTGATTTGAATTATGTTT
1 TGATATCTGATCTGAATTATGTTT
* * * *
1428033 TGACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTATGTTT
* * * * *
1428057 TGAT-TCCTAACCTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTATGTTT
1428081 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTATGTTT
*
1428105 TGATTTCTGAT
1 TGATATCTGAT
1428116 ATCTCCGTTT
Statistics
Matches: 63, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 61 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (24 bp):
TGATATCTGATCTGAATTATGTTT
Found at i:1430263 original size:13 final size:13
Alignment explanation
Indices: 1430245--1430332 Score: 88
Period size: 13 Copynumber: 6.3 Consensus size: 13
1430235 GTCACAACCC
1430245 GACCCGACCCGTT
1 GACCCGACCCGTT
1430258 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1430271 TACCCGACCCGTT
1 GACCCGACCCGTT
1430284 GACCCGACACGACCAGTT
1 GACCCG--AC--CC-GTT
1430302 GACCCGACCC-TT
1 GACCCGACCCGTT
*
1430314 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
1430329 GACC
1 GACC
1430333 GGAGTTGACC
Statistics
Matches: 64, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
12 6 0.09
13 30 0.47
14 7 0.11
15 8 0.12
16 2 0.03
17 2 0.03
18 9 0.14
ACGTcount: A:0.18, C:0.43, G:0.22, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1430264 original size:18 final size:18
Alignment explanation
Indices: 1430241--1430326 Score: 57
Period size: 18 Copynumber: 4.3 Consensus size: 18
1430231 ACCGGTCACA
1430241 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1430259 ACCCGACCCGTTTACCCGACCCGTTG
1 ACCCGACCCG---A-----CCCGTTG
* *
1430285 ACCCGACACGACCAGTTG
1 ACCCGACCCGACCCGTTG
1430303 ACCCGACCCTTGA-CCGTTG
1 ACCCGACCC--GACCCGTTG
1430322 ACCCG
1 ACCCG
1430327 TTGACCGGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 19
0.70 0.05 0.25
Matches are distributed among these distances:
18 24 0.44
19 10 0.19
20 2 0.04
21 1 0.02
23 1 0.02
26 16 0.30
ACGTcount: A:0.19, C:0.45, G:0.21, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1430323 original size:19 final size:17
Alignment explanation
Indices: 1430279--1430326 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 17
1430269 TTTACCCGAC
1430279 CCGTTGACCCGACACGA
1 CCGTTGACCCGACACGA
*
1430296 CCAGTTGACCCGACCCTTGA
1 CC-GTTGACCCGACAC--GA
1430316 CCGTTGACCCG
1 CCGTTGACCCG
1430327 TTGACCGGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 2 0.07
18 12 0.44
19 9 0.33
20 4 0.15
ACGTcount: A:0.19, C:0.42, G:0.23, T:0.17
Consensus pattern (17 bp):
CCGTTGACCCGACACGA
Found at i:1431666 original size:18 final size:18
Alignment explanation
Indices: 1431640--1431675 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1431630 TCGAAAGGAC
*
1431640 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1431658 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1431676 CGGATGGAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1432888 original size:24 final size:24
Alignment explanation
Indices: 1432794--1432900 Score: 90
Period size: 24 Copynumber: 4.5 Consensus size: 24
1432784 ATATTTTATC
* *
1432794 TGATTTCTGATTTGAATTATGTTT
1 TGATATCTGATCTGAATTATGTTT
* * * *
1432818 TGACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTATGTTT
* * * * *
1432842 TGAT-TCCTAACCTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTATGTTT
1432866 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTATGTTT
*
1432890 TGATTTCTGAT
1 TGATATCTGAT
1432901 ATCTCCGTTT
Statistics
Matches: 63, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 61 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (24 bp):
TGATATCTGATCTGAATTATGTTT
Found at i:1433770 original size:20 final size:20
Alignment explanation
Indices: 1433745--1433796 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1433735 GAAATTCCCA
*
1433745 TGCATCGATGCCTACCTGTG
1 TGCATCGATGCATACCTGTG
1433765 TGCATCGATGCATACCTGTG
1 TGCATCGATGCATACCTGTG
1433785 TGCATCGATGCA
1 TGCATCGATGCA
1433797 CACTGAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.27, G:0.25, T:0.29
Consensus pattern (20 bp):
TGCATCGATGCATACCTGTG
Found at i:1434977 original size:16 final size:16
Alignment explanation
Indices: 1434944--1434976 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
1434934 GTTTAGTTCC
1434944 TTAAAATATTTTTATT
1 TTAAAATATTTTTATT
1434960 TTAAAA-ATTTTTATT
1 TTAAAATATTTTTATT
1434975 TT
1 TT
1434977 TTATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTAAAATATTTTTATT
Found at i:1436727 original size:60 final size:60
Alignment explanation
Indices: 1436606--1436782 Score: 154
Period size: 60 Copynumber: 2.9 Consensus size: 60
1436596 TGTATTTAAT
* * * *
1436606 CTATAATTTTTATTTTAAA-TAGATCCTTAAACTTTTGAACATT-TCAACTTT-AT-CTTCAAA
1 CTATAACTCTTATTCTAAATTAG-TCCTT-AACTTTTGAACATTAT-AA-TTTCATCCCTCAAA
1436666 CTATAACTCTTATTCTAAATTAGTCCTTAACCTTTTGAACATTATAATTTCATCCCT-AAA
1 CTATAACTCTTATTCTAAATTAGTCCTTAA-CTTTTGAACATTATAATTTCATCCCTCAAA
** *
1436726 CTATGACACTC-T-TTCTAAATTAGTCCCCAGACTTTTGAATATTCA-AATTTCATCCCT
1 CTAT-A-ACTCTTATTCTAAATTAGTCCTTA-ACTTTTGAACATT-ATAATTTCATCCCT
1436783 GAATTCATCC
Statistics
Matches: 101, Mismatches: 7, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
59 5 0.05
60 82 0.81
61 10 0.10
62 4 0.04
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (60 bp):
CTATAACTCTTATTCTAAATTAGTCCTTAACTTTTGAACATTATAATTTCATCCCTCAAA
Found at i:1438056 original size:17 final size:18
Alignment explanation
Indices: 1438036--1438069 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1438026 TTTATAAGGT
1438036 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
*
1438053 ATATTTTGTTAGTATTT
1 ATATTTTATTAGTATTT
1438070 TATTTAATTT
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:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:1438089 original size:21 final size:21
Alignment explanation
Indices: 1438041--1438113 Score: 75
Period size: 16 Copynumber: 3.6 Consensus size: 21
1438031 AAGGTATATT
*
1438041 TTATTATATTTAATATTTTGTTA
1 TTATTTTATTTAAT-TTTTG-TA
*
1438064 GTATTTTATTTAATTTTTG--
1 TTATTTTATTTAATTTTTGTA
1438083 -TA--TTATTTAATTTTTGTA
1 TTATTTTATTTAATTTTTGTA
1438101 TTATTTTATTTAA
1 TTATTTTATTTAA
1438114 ATATTTATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
16 14 0.33
18 2 0.05
19 2 0.05
21 8 0.19
22 5 0.12
23 12 0.28
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
TTATTTTATTTAATTTTTGTA
Found at i:1438108 original size:17 final size:16
Alignment explanation
Indices: 1438069--1438111 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
1438059 TGTTAGTATT
1438069 TTATTTAATTTTTGTA
1 TTATTTAATTTTTGTA
1438085 TTATTTAATTTTTGTA
1 TTATTTAATTTTTGTA
*
1438101 TTATTTTATTT
1 TTATTTAATTT
1438112 AAATATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (16 bp):
TTATTTAATTTTTGTA
Found at i:1438188 original size:115 final size:114
Alignment explanation
Indices: 1438044--1438385 Score: 620
Period size: 115 Copynumber: 3.0 Consensus size: 114
1438034 GTATATTTTA
*
1438044 TTATATTTAATATTTTGTTAGTATTTTATTTAATTTTTGTATTATTTAATTTTTGTATTATTTTA
1 TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTATTTAATTTTT-TATTATTTTA
*
1438109 TTTAAATATTTATTTTTTTACAGTTATAAAATGGAAAGCGGTCCGCTTCG
65 TTTAAATATTTATTTTTTTACAGTTATAAAATGGAAAGCGGTCTGCTTCG
1438159 TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTATTTAATTTTTTATTATTTTAT
1 TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTATTTAATTTTTTATTATTTTAT
1438224 TTAAATATTTTATTTTTTTACAGTTATAAAATGGAAAGCGGTCTGCTTCG
66 TTAAATA-TTTATTTTTTTACAGTTATAAAATGGAAAGCGGTCTGCTTCG
1438274 TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTATTTAATTTTTTATTATTTTAT
1 TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTATTTAATTTTTTATTATTTTAT
1438339 TT-AA-A--TATTTTTTTACAGTTATAAAATGGAAAGCGGTCTGCTTCG
66 TTAAATATTTATTTTTTTACAGTTATAAAATGGAAAGCGGTCTGCTTCG
1438384 TT
1 TT
1438386 TGGATGAAAA
Statistics
Matches: 224, Mismatches: 2, Indels: 7
0.96 0.01 0.03
Matches are distributed among these distances:
110 42 0.19
113 1 0.00
114 20 0.09
115 161 0.72
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.57
Consensus pattern (114 bp):
TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTATTTAATTTTTTATTATTTTAT
TTAAATATTTATTTTTTTACAGTTATAAAATGGAAAGCGGTCTGCTTCG
Found at i:1438203 original size:16 final size:15
Alignment explanation
Indices: 1438184--1438225 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1438174 TGTTAGTATT
1438184 TTATTTAATTATTGTA
1 TTATTTAATT-TTGTA
*
1438200 TTATTTAATTTTTTA
1 TTATTTAATTTTGTA
*
1438215 TTATTTTATTT
1 TTATTTAATTT
1438226 AAATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTATTTAATTTTGTA
Found at i:1438215 original size:20 final size:21
Alignment explanation
Indices: 1438192--1438237 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1438182 TTTTATTTAA
* *
1438192 TTATTGTATTATTT-AATTTT
1 TTATTATATTATTTAAATATT
*
1438212 TTATTATTTTATTTAAATATT
1 TTATTATATTATTTAAATATT
1438233 TTATT
1 TTATT
1438238 TTTTTACAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
TTATTATATTATTTAAATATT
Found at i:1438241 original size:20 final size:20
Alignment explanation
Indices: 1438200--1438243 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1438190 AATTATTGTA
*
1438200 TTATTTAATTTTTTATTATT
1 TTATTTAATATTTTATTATT
*
1438220 TTATTTAAATATTTTATTTTT
1 TTATTT-AATATTTTATTATT
1438241 TTA
1 TTA
1438244 CAGTTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TTATTTAATATTTTATTATT
Found at i:1438318 original size:16 final size:15
Alignment explanation
Indices: 1438299--1438340 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1438289 TGTTAGTATT
1438299 TTATTTAATTATTGTA
1 TTATTTAATT-TTGTA
*
1438315 TTATTTAATTTTTTA
1 TTATTTAATTTTGTA
*
1438330 TTATTTTATTT
1 TTATTTAATTT
1438341 AAATATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTATTTAATTTTGTA
Found at i:1441813 original size:6 final size:6
Alignment explanation
Indices: 1441802--1441850 Score: 89
Period size: 6 Copynumber: 8.2 Consensus size: 6
1441792 TCTTGTTCCA
*
1441802 ACATAC ACATAC ACATAC ACATAC ACACAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1441850 A
1 A
1441851 TATATGTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.51, C:0.35, G:0.00, T:0.14
Consensus pattern (6 bp):
ACATAC
Found at i:1441860 original size:6 final size:6
Alignment explanation
Indices: 1441851--1441898 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
1441841 TACACATACA
* * * *
1441851 TATATG TATATG CATATG CATATG TATATG TATATA TGTATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1441899 GAGGCAGGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (6 bp):
TATATG
Found at i:1446473 original size:24 final size:24
Alignment explanation
Indices: 1446441--1446495 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
1446431 CTGGATGCAG
1446441 CGTTAATGGACTACAGTGAGCTTC
1 CGTTAATGGACTACAGTGAGCTTC
1446465 CGTTAATGGACTACAGTGAGCTTC
1 CGTTAATGGACTACAGTGAGCTTC
1446489 CGTTAAT
1 CGTTAAT
1446496 AGATCAGTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (24 bp):
CGTTAATGGACTACAGTGAGCTTC
Found at i:1452802 original size:18 final size:19
Alignment explanation
Indices: 1452776--1452811 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1452766 TTAAATTATG
1452776 ATAAAATAAT-ATTTTAAT
1 ATAAAATAATCATTTTAAT
*
1452794 ATAATATAATCATTTTAA
1 ATAAAATAATCATTTTAA
1452812 AAATTATCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAAAATAATCATTTTAAT
Found at i:1463203 original size:21 final size:24
Alignment explanation
Indices: 1463163--1463205 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
1463153 TTTGAGAATG
1463163 AGGAAATAGAGAAGAAATGATTTT
1 AGGAAATAGAGAAGAAATGATTTT
1463187 AGGAAAT-GAG-A-AAATGATT
1 AGGAAATAGAGAAGAAATGATT
1463206 CATTCATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 1 0.05
23 3 0.16
24 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (24 bp):
AGGAAATAGAGAAGAAATGATTTT
Found at i:1467859 original size:17 final size:17
Alignment explanation
Indices: 1467837--1467870 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1467827 CTCAATTTCC
1467837 TAGGATTTATGCTCTTT
1 TAGGATTTATGCTCTTT
1467854 TAGGATTTATGCTCTTT
1 TAGGATTTATGCTCTTT
1467871 CAACAAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.53
Consensus pattern (17 bp):
TAGGATTTATGCTCTTT
Found at i:1474170 original size:27 final size:27
Alignment explanation
Indices: 1474140--1474230 Score: 137
Period size: 27 Copynumber: 3.4 Consensus size: 27
1474130 AACAGTACTA
* *
1474140 AATGATTCAGCATAAAAGTACGTTCTG
1 AATGATTCAGCACAGAAGTACGTTCTG
*
1474167 AATGATTTAGCACAGAAGTACGTTCTG
1 AATGATTCAGCACAGAAGTACGTTCTG
* *
1474194 AATGATTTAGCACAGAAGTACATTCTG
1 AATGATTCAGCACAGAAGTACGTTCTG
1474221 AATGATTCAG
1 AATGATTCAG
1474231 AGCTATTATC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (27 bp):
AATGATTCAGCACAGAAGTACGTTCTG
Found at i:1477151 original size:34 final size:34
Alignment explanation
Indices: 1477108--1477176 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1477098 GATATTTATG
1477108 TTATTAATCGGTTAAGAAAATTCTAGACATAAAC
1 TTATTAATCGGTTAAGAAAATTCTAGACATAAAC
1477142 TTATTAATCGGTTAAGAAAATTCTAGACATAAAC
1 TTATTAATCGGTTAAGAAAATTCTAGACATAAAC
1477176 T
1 T
1477177 ATCTTTTAAT
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:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (34 bp):
TTATTAATCGGTTAAGAAAATTCTAGACATAAAC
Found at i:1481813 original size:35 final size:35
Alignment explanation
Indices: 1481740--1481814 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
1481730 CGTCACTAAC
**
1481740 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
1481775 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
1481810 AGTAA
1 AGTAA
1481815 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:1481954 original size:23 final size:23
Alignment explanation
Indices: 1481892--1481981 Score: 108
Period size: 23 Copynumber: 3.8 Consensus size: 23
1481882 CATAATTCAA
1481892 GTCAAGTATCATATCAGAATCCAG
1 GTCAA-TATCATATCAGAATCCAG
* * *
1481916 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCATATCAGAATCCAG
1481940 GTCAATATCATATCAGAATCCAG
1 GTCAATATCATATCAGAATCCAG
** *
1481963 GTCAGGATCATAACAGAAT
1 GTCAATATCATATCAGAAT
1481982 TCAAGTCGGA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
23 32 0.57
24 24 0.43
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (23 bp):
GTCAATATCATATCAGAATCCAG
Found at i:1484486 original size:18 final size:18
Alignment explanation
Indices: 1484463--1484508 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
1484453 CAATGGTCAA
1484463 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1484481 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1484499 CGGGTCGGGT
1 CGGGTCGGGT
1484509 TGTGACCGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.09, C:0.22, G:0.52, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1484504 original size:13 final size:13
Alignment explanation
Indices: 1484442--1484486 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
1484432 GGTCAACTCC
*
1484442 GGTCAACGGGTCAAT
1 GGTCAACGGGTC--G
1484457 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1484470 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1484483 GGTC
1 GGTC
1484487 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:0.22, G:0.42, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1486593 original size:35 final size:35
Alignment explanation
Indices: 1486520--1486594 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
1486510 CGTCACTAAC
**
1486520 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
1486555 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
1486590 AGTAA
1 AGTAA
1486595 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:1486734 original size:23 final size:23
Alignment explanation
Indices: 1486672--1486761 Score: 108
Period size: 23 Copynumber: 3.8 Consensus size: 23
1486662 CATAATTCAA
1486672 GTCAAGTATCATATCAGAATCCAG
1 GTCAA-TATCATATCAGAATCCAG
* * *
1486696 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCATATCAGAATCCAG
1486720 GTCAATATCATATCAGAATCCAG
1 GTCAATATCATATCAGAATCCAG
** *
1486743 GTCAGGATCATAACAGAAT
1 GTCAATATCATATCAGAAT
1486762 TCAAGTCGGA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
23 32 0.57
24 24 0.43
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (23 bp):
GTCAATATCATATCAGAATCCAG
Found at i:1489262 original size:18 final size:18
Alignment explanation
Indices: 1489239--1489284 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
1489229 CAATGGTCAA
1489239 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1489257 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1489275 CGGGTCGGGT
1 CGGGTCGGGT
1489285 TGTGACCGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.09, C:0.22, G:0.52, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1489280 original size:13 final size:13
Alignment explanation
Indices: 1489218--1489262 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
1489208 GGTCAACTCC
*
1489218 GGTCAACGGGTCAAT
1 GGTCAACGGGTC--G
1489233 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1489246 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1489259 GGTC
1 GGTC
1489263 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:0.22, G:0.42, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1490835 original size:15 final size:16
Alignment explanation
Indices: 1490815--1490875 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 16
1490805 GGTCAGGTAT
1490815 ATATATTTAA-ATTAA
1 ATATATTTAATATTAA
*
1490830 ATATA-TTAATATTAT
1 ATATATTTAATATTAA
* *
1490845 ATATATATATATAATAA
1 ATATATTTA-ATATTAA
* *
1490862 TTATTTTTAATATT
1 ATATATTTAATATT
1490876 TATCGGGGCG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
14 4 0.11
15 14 0.40
16 6 0.17
17 11 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATATTTAATATTAA
Found at i:1490922 original size:6 final size:6
Alignment explanation
Indices: 1490911--1490939 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1490901 GATTACTAAA
1490911 CCCGTC CCCGTC CCCGTC CCCGTC CCCGT
1 CCCGTC CCCGTC CCCGTC CCCGTC CCCGT
1490940 TTAACATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.66, G:0.17, T:0.17
Consensus pattern (6 bp):
CCCGTC
Found at i:1490963 original size:30 final size:30
Alignment explanation
Indices: 1490927--1491003 Score: 127
Period size: 30 Copynumber: 2.6 Consensus size: 30
1490917 CCCGTCCCCG
1490927 TCCCCGTCCCCGTTTAACATAAACGATTTT
1 TCCCCGTCCCCGTTTAACATAAACGATTTT
* *
1490957 TCCCCGTCCCCGTCTAGCATAAACGATTTT
1 TCCCCGTCCCCGTTTAACATAAACGATTTT
*
1490987 TCCCCATCCCCGTTTAA
1 TCCCCGTCCCCGTTTAA
1491004 TTTTGTTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.21, C:0.38, G:0.10, T:0.31
Consensus pattern (30 bp):
TCCCCGTCCCCGTTTAACATAAACGATTTT
Found at i:1491632 original size:20 final size:20
Alignment explanation
Indices: 1491609--1491659 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1491599 CACGGAATGT
*
1491609 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGAAATAA
1491629 AAGATTACCAGTGGAAATAA
1 AAGATTACCAGTGGAAATAA
1491649 AAGATTACCAG
1 AAGATTACCAG
1491660 AGAATAGGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.20
Consensus pattern (20 bp):
AAGATTACCAGTGGAAATAA
Found at i:1492300 original size:2 final size:2
Alignment explanation
Indices: 1492295--1492320 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1492285 TATCAATTTA
1492295 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1492321 CATTTAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1515413 original size:10 final size:9
Alignment explanation
Indices: 1515392--1515433 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
1515382 AAAAAGAATA
*
1515392 ATATACAAT
1 ATATATAAT
1515401 ATATATAATT
1 ATATATAA-T
1515411 ATATATAAT
1 ATATATAAT
*
1515420 ACATATAA-
1 ATATATAAT
1515428 ATATAT
1 ATATAT
1515434 TTTGGTCGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
8 5 0.17
9 15 0.52
10 9 0.31
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (9 bp):
ATATATAAT
Found at i:1515420 original size:19 final size:19
Alignment explanation
Indices: 1515392--1515433 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1515382 AAAAAGAATA
* *
1515392 ATATACAATATATATAATT
1 ATATACAATACATATAAAT
*
1515411 ATATATAATACATATAAAT
1 ATATACAATACATATAAAT
1515430 ATAT
1 ATAT
1515434 TTTGGTCGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATACAATACATATAAAT
Found at i:1516066 original size:65 final size:65
Alignment explanation
Indices: 1515974--1516356 Score: 626
Period size: 65 Copynumber: 5.9 Consensus size: 65
1515964 TCTGAAATTG
* * ** * *
1515974 GGGAAGTTGTTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCCGTCTTAAAC
1 GGGAAATT-TTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGACAC
1516039 T
65 T
*
1516040 GGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGATACT
1 GGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGACACT
* * *
1516105 GGGAAATTTTTGTCGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTTTGACACT
1 GGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGACACT
*
1516170 GGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGACATT
1 GGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGACACT
*
1516235 GGGAAA-TTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGACACT
1 GGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGACACT
*
1516299 GGGAAA-TTTTGTTGACAACCAGCGGCCCTTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1 GGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1516357 TGAGTGACAC
Statistics
Matches: 299, Mismatches: 18, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
64 112 0.37
65 180 0.60
66 7 0.02
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.35
Consensus pattern (65 bp):
GGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGACACT
Found at i:1526941 original size:4 final size:4
Alignment explanation
Indices: 1526932--1526963 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
1526922 AATGTTAGTA
1526932 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1526964 GACGAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:1527392 original size:13 final size:13
Alignment explanation
Indices: 1527374--1527399 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1527364 TGAAATCATG
1527374 AGACAACTGGAAA
1 AGACAACTGGAAA
1527387 AGACAACTGGAAA
1 AGACAACTGGAAA
1527400 TTACCTTAGC
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:0.54, C:0.15, G:0.23, T:0.08
Consensus pattern (13 bp):
AGACAACTGGAAA
Found at i:1529391 original size:10 final size:9
Alignment explanation
Indices: 1529370--1529411 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
1529360 AAAAAGAATA
*
1529370 ATATACAAT
1 ATATATAAT
1529379 ATATATAATT
1 ATATATAA-T
1529389 ATATATAAT
1 ATATATAAT
*
1529398 ACATATAA-
1 ATATATAAT
1529406 ATATAT
1 ATATAT
1529412 GTTGGTCGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
8 5 0.17
9 15 0.52
10 9 0.31
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (9 bp):
ATATATAAT
Found at i:1529398 original size:19 final size:19
Alignment explanation
Indices: 1529370--1529411 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1529360 AAAAAGAATA
* *
1529370 ATATACAATATATATAATT
1 ATATACAATACATATAAAT
*
1529389 ATATATAATACATATAAAT
1 ATATACAATACATATAAAT
1529408 ATAT
1 ATAT
1529412 GTTGGTCGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATACAATACATATAAAT
Found at i:1533960 original size:21 final size:22
Alignment explanation
Indices: 1533922--1534002 Score: 100
Period size: 21 Copynumber: 3.9 Consensus size: 22
1533912 CAGAATGTTT
1533922 AGGGGGTACAGATTCCCCCCTC
1 AGGGGGTACAGATTCCCCCCTC
*
1533944 AGGGGGTACCGA--CCCCCC-C
1 AGGGGGTACAGATTCCCCCCTC
*
1533963 AGGGGGTACATATTCCCCCCT-
1 AGGGGGTACAGATTCCCCCCTC
1533984 AGGGGGTACCA-ATTCCCCC
1 AGGGGGTA-CAGATTCCCCC
1534003 TGTTTAACGG
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
19 11 0.21
20 6 0.12
21 22 0.42
22 13 0.25
ACGTcount: A:0.19, C:0.38, G:0.27, T:0.16
Consensus pattern (22 bp):
AGGGGGTACAGATTCCCCCCTC
Found at i:1534296 original size:21 final size:21
Alignment explanation
Indices: 1534267--1534315 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1534257 TCAATACTCA
1534267 TTGTGCTTTCAAGAACACCAT
1 TTGTGCTTTCAAGAACACCAT
*
1534288 TTGTTCTTTCAAGAACACCAT
1 TTGTGCTTTCAAGAACACCAT
1534309 TTGTGCT
1 TTGTGCT
1534316 CTATTGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.39
Consensus pattern (21 bp):
TTGTGCTTTCAAGAACACCAT
Found at i:1541564 original size:21 final size:22
Alignment explanation
Indices: 1541538--1541588 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
1541528 ACAGAATGTC
1541538 CAGGGGGTATAGATTCCCCC-T
1 CAGGGGGTATAGATTCCCCCAT
* *
1541559 CAGGGGATATCGATTCCCCCAT
1 CAGGGGGTATAGATTCCCCCAT
1541581 -AGGGGGTA
1 CAGGGGGTA
1541589 CAAATCCCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.22, C:0.25, G:0.31, T:0.22
Consensus pattern (22 bp):
CAGGGGGTATAGATTCCCCCAT
Done.