Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 42
Found at i:1004181 original size:14 final size:13
Alignment explanation
Indices: 1004157--1004190 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1004147 ATTTTAATAA
*
1004157 ATATAAATATTTT
1 ATATTAATATTTT
1004170 ATAATTAATATTTT
1 AT-ATTAATATTTT
1004184 ATATTAA
1 ATATTAA
1004191 AATAGAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATATTAATATTTT
Found at i:1005641 original size:10 final size:10
Alignment explanation
Indices: 1005626--1005660 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
1005616 CTTTCGTTCT
1005626 TCTTCCTTTC
1 TCTTCCTTTC
1005636 TCTTCCTTTC
1 TCTTCCTTTC
1005646 TCTTCCTTTC
1 TCTTCCTTTC
1005656 TCTTC
1 TCTTC
1005661 AGTCTTCACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (10 bp):
TCTTCCTTTC
Found at i:1009020 original size:12 final size:12
Alignment explanation
Indices: 1008995--1009064 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
1008985 ACGAAGATAT
* *
1008995 CAGAAATCAAAA
1 CAGAATTCAGAA
1009007 CAGAATTCAGAA
1 CAGAATTCAGAA
1009019 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
1009031 CAGAATCCAGAT
1 CAGAATTCAGAA
*
1009043 CAGAAATCAGAA
1 CAGAATTCAGAA
1009055 CAGAATTCAG
1 CAGAATTCAG
1009065 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1009064 original size:48 final size:47
Alignment explanation
Indices: 1008993--1009101 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
1008983 AAACGAAGAT
*
1008993 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
1009040 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
1009088 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
1009102 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:1009099 original size:24 final size:25
Alignment explanation
Indices: 1008993--1009101 Score: 109
Period size: 24 Copynumber: 4.5 Consensus size: 25
1008983 AAACGAAGAT
*
1008993 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
1009017 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
1009041 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
1009065 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
1009090 -TCGGAAATCAGA
1 ATCAGAAATCAGA
1009102 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:1010264 original size:18 final size:18
Alignment explanation
Indices: 1010243--1010277 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1010233 TTCCATCCGG
*
1010243 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1010261 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1010278 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1011595 original size:8 final size:8
Alignment explanation
Indices: 1011565--1011639 Score: 61
Period size: 8 Copynumber: 9.5 Consensus size: 8
1011555 TCAAAGTTTT
1011565 GGTCAACAG
1 GGTCAAC-G
1011574 TGGTCAAC-
1 -GGTCAACG
1011582 GGTCAACG
1 GGTCAACG
1011590 GGTCAAC-
1 GGTCAACG
*
1011597 GGTAAACG
1 GGTCAACG
1011605 GGT---CG
1 GGTCAACG
1011610 GGTCAACG
1 GGTCAACG
*
1011618 GGTCGAGTCG
1 GGTC-A-ACG
1011628 GGTCAACG
1 GGTCAACG
1011636 GGTC
1 GGTC
1011640 GGGTAAACGG
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
5 5 0.09
7 13 0.24
8 22 0.40
9 2 0.04
10 13 0.24
ACGTcount: A:0.23, C:0.23, G:0.39, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:1011595 original size:15 final size:15
Alignment explanation
Indices: 1011565--1011621 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
1011555 TCAAAGTTTT
1011565 GGTCAACAGTGGTCAAC
1 GGTCAAC-G-GGTCAAC
1011582 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
* *
1011597 GGTAAACGGGTC--G
1 GGTCAACGGGTCAAC
1011610 GGTCAACGGGTC
1 GGTCAACGGGTC
1011622 GAGTCGGGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 11 0.30
15 18 0.49
16 1 0.03
17 7 0.19
ACGTcount: A:0.25, C:0.23, G:0.37, T:0.16
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:1011619 original size:13 final size:13
Alignment explanation
Indices: 1011582--1011657 Score: 62
Period size: 13 Copynumber: 5.3 Consensus size: 13
1011572 AGTGGTCAAC
*
1011582 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
*
1011597 GGTAAACGGGTCG
1 GGTCAACGGGTCG
1011610 GGTCAACGGGTCGAGTCG
1 GGTCAAC--G--G-GTCG
1011628 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1011641 GGTAAACGGGTCG
1 GGTCAACGGGTCG
1011654 GGTC
1 GGTC
1011658 GGGTAAACGG
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
13 25 0.49
14 1 0.02
15 12 0.24
16 1 0.02
17 1 0.02
18 11 0.22
ACGTcount: A:0.20, C:0.21, G:0.43, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1011629 original size:18 final size:18
Alignment explanation
Indices: 1011603--1011679 Score: 92
Period size: 18 Copynumber: 4.6 Consensus size: 18
1011593 CAACGGTAAA
*
1011603 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
* *
1011621 CGAGTCGGGTCAAC----
1 CGGGTCGGGTAAACGGGT
1011635 -GGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
1011652 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
1011670 CGGGTCGGGT
1 CGGGTCGGGT
1011680 TATGACCGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
13 11 0.22
18 40 0.78
ACGTcount: A:0.14, C:0.19, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:1011639 original size:31 final size:31
Alignment explanation
Indices: 1011582--1011675 Score: 131
Period size: 31 Copynumber: 3.1 Consensus size: 31
1011572 AGTGGTCAAC
*
1011582 GGTCAACGGGTC-A-AC-GGTAAACGGGTCG
1 GGTCAACGGGTCGAGTCGGGTAAACGGGTCG
*
1011610 GGTCAACGGGTCGAGTCGGGTCAACGGGTCG
1 GGTCAACGGGTCGAGTCGGGTAAACGGGTCG
* *
1011641 GGTAAACGGGTCGGGTCGGGTAAACGGGTCG
1 GGTCAACGGGTCGAGTCGGGTAAACGGGTCG
1011672 GGTC
1 GGTC
1011676 GGGTTATGAC
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 12 0.21
29 1 0.02
30 1 0.02
31 43 0.75
ACGTcount: A:0.19, C:0.20, G:0.45, T:0.16
Consensus pattern (31 bp):
GGTCAACGGGTCGAGTCGGGTAAACGGGTCG
Found at i:1015460 original size:2 final size:2
Alignment explanation
Indices: 1015453--1015514 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1015443 ATATAGAGCC
1015453 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1015495 GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA
1015515 CTGTTGCAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1015916 original size:21 final size:21
Alignment explanation
Indices: 1015866--1015923 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
1015856 AATCAGTTCT
1015866 CAGAATCGCAATGCGATAGTA
1 CAGAATCGCAATGCGATAGTA
* ** *
1015887 CA-AATTCGCATTGCGATTTTC
1 CAGAA-TCGCAATGCGATAGTA
*
1015908 CAGAATCGCAACGCGA
1 CAGAATCGCAATGCGA
1015924 ATATGAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (21 bp):
CAGAATCGCAATGCGATAGTA
Found at i:1015936 original size:20 final size:20
Alignment explanation
Indices: 1015911--1016182 Score: 201
Period size: 20 Copynumber: 13.5 Consensus size: 20
1015901 GATTTTCCAG
** *
1015911 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
**
1015931 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATC-CGTA
* *
1015951 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* * *
1015970 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCCGT-A
* *
1015992 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
1016012 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
* *
1016033 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
1016053 AATCGCAACG-AAGATACGTA
1 AATCGCAACGCGA-ATCCGTA
* *
1016073 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGTA
* *
1016093 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
1016113 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
** *
1016133 AATCGCAATACGAATACGTA
1 AATCGCAACGCGAATCCGTA
** *
1016153 AATCGCAATACGAATCTGTA
1 AATCGCAACGCGAATCCGTA
1016173 AATCGCAACG
1 AATCGCAACG
1016183 AGATTCTGAC
Statistics
Matches: 200, Mismatches: 42, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.00
20 165 0.82
21 33 0.17
22 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:1016017 original size:41 final size:40
Alignment explanation
Indices: 1015911--1016185 Score: 270
Period size: 40 Copynumber: 6.8 Consensus size: 40
1015901 GATTTTCCAG
* ** * * * **
1015911 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * * *
1015951 AATCGCAACGCG-ATTC-TGACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGTATCCGT-A-AATCGCAACGAGAATACGT-A
* *
1015992 AATCGTAACGCGTATCCGTAAATCGCAACGACAATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-A
*
1016033 AATAGCAACGCGTATCCGTAAATCGCAACGA-AGATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGA-ATACGTA
*
1016073 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* *
1016113 AATCGCAATGCGTATCCGTAAATCGCAA-TACGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGA-GAATACGTA
** * *
1016153 AATCGCAATACGAATCTGTAAATCGCAACGAGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGA
1016186 TTCTGACTAT
Statistics
Matches: 199, Mismatches: 27, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
39 4 0.02
40 124 0.62
41 66 0.33
42 4 0.02
43 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
Found at i:1016201 original size:80 final size:80
Alignment explanation
Indices: 1015911--1016185 Score: 263
Period size: 81 Copynumber: 3.4 Consensus size: 80
1015901 GATTTTCCAG
* * * * * ** * * *
1015911 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCG-ATTC-TGACTAT
1 AATCGCAACACGAATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGT-A-AAT
*
1015974 CGCAACG-AGTATCCGTAA
64 CGCAACGAAG-ATACGT-A
* * * * * * *
1015992 AATCGTAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATAGCAACGCGTATCCGTAAATC
1 AATCGCAACACGAATCTGTAAATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATC
1016057 GCAACGAAGATACGTA
65 GCAACGAAGATACGTA
* *
1016073 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCG
1 AATCGCAACACGAATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCG
1016138 CAATACG-A-ATACGTA
66 C-A-ACGAAGATACGTA
*
1016153 AATCGCAATACGAATCTGTAAATCGCAACGAGA
1 AATCGCAACACGAATCTGTAAATCGCAACGAGA
1016186 TTCTGACTAT
Statistics
Matches: 166, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
80 62 0.37
81 68 0.41
82 29 0.17
83 6 0.04
84 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (80 bp):
AATCGCAACACGAATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCG
CAACGAAGATACGTA
Found at i:1017069 original size:24 final size:24
Alignment explanation
Indices: 1017042--1017095 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1017032 GTATTCGAAA
1017042 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1017066 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1017090 TTTGAT
1 TTTGAT
1017096 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:1019688 original size:20 final size:19
Alignment explanation
Indices: 1019605--1019690 Score: 56
Period size: 20 Copynumber: 4.7 Consensus size: 19
1019595 CAATCATCTT
*
1019605 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
1019625 AATTACTATCGCAA--CGA
1 AATGACTATCGCAACGCGA
* * *
1019642 GA-GA--ATCACAATGCGA
1 AATGACTATCGCAACGCGA
**
1019658 AATGAAAATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
1019678 AATGACTATCGCA
1 AATGACTATCGCA
1019691 TTACGATTCT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
14 6 0.12
16 5 0.10
17 5 0.10
18 1 0.02
19 8 0.16
20 25 0.50
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:1019854 original size:14 final size:14
Alignment explanation
Indices: 1019837--1019873 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1019827 CATCAATTAA
1019837 ACAAATCAAATTTT
1 ACAAATCAAATTTT
**
1019851 ACAAATCATCTTTT
1 ACAAATCAAATTTT
1019865 ACAAATCAA
1 ACAAATCAA
1019874 TTAAACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAAATTTT
Found at i:1021310 original size:42 final size:42
Alignment explanation
Indices: 1021264--1021343 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
1021254 CGATGACAGT
* *
1021264 GGCCTCTTGAACGGTAGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
1021306 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
1021344 CAGGCGAGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:1021875 original size:33 final size:33
Alignment explanation
Indices: 1021838--1021917 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
1021828 GCGATTATAG
* * *
1021838 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGAATTTCA
1021871 TTTCGCGTTGCGATTCTCTCGTTGCGAATTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGAATTTCA
*
1021904 TTTCACGTTGCGAT
1 TTTCGCGTTGCGAT
1021918 AGTCATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGAATTTCA
Found at i:1021881 original size:19 final size:19
Alignment explanation
Indices: 1021857--1021941 Score: 72
Period size: 19 Copynumber: 4.6 Consensus size: 19
1021847 GCGATTTTGT
*
1021857 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCA
*
1021876 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCA
*
1021890 CGTTGCGAATTTCATTTCA
1 CGTTGCGATTTTCATTTCA
**
1021909 CGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCA--TTTCA
1021930 CGTTGCGATTTT
1 CGTTGCGATTTT
1021942 AAGTTTCGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
14 10 0.19
16 3 0.06
17 3 0.06
19 21 0.40
21 15 0.29
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCA
Found at i:1022151 original size:94 final size:94
Alignment explanation
Indices: 1022005--1022384 Score: 638
Period size: 94 Copynumber: 4.1 Consensus size: 94
1021995 ATGGATTGCA
* *
1022005 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1022069 TTAGCAGAATTGACAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1022098 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1022163 TTAGTAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1022192 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
1022257 TTAGTAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
1022286 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATATTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* * *
1022350 TTTAGCAGTACTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
1022380 TTACT
1 TTACT
1022385 AAGCAATCTA
Statistics
Matches: 274, Mismatches: 10, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
93 23 0.08
94 251 0.92
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1024143 original size:19 final size:19
Alignment explanation
Indices: 1024079--1024224 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
1024069 TCTTTTGGTT
*
1024079 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
1024098 GAGAATGAAAATCGTAATGC
1 GA-AATGAAAATCGCAACGC
**
1024118 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
1024138 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
1024155 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAACGC
*
1024171 GAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
1024188 G--A-GAGAATTGCAACGC
1 GAAATGAAAATCGCAACGC
*
1024204 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1024223 GA
1 GA
1024225 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
14 18 0.19
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 38 0.39
20 27 0.28
21 2 0.02
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1024173 original size:33 final size:33
Alignment explanation
Indices: 1024128--1024219 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
1024118 GGAAATGACT
1024128 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
1024161 ATCGCAATGCGAAATTAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
1024194 ATTGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
1024220 TGCGATTTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:1024305 original size:40 final size:40
Alignment explanation
Indices: 1024247--1024338 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
1024237 GTTGCGATTA
**
1024247 TCTCGTTGCGATTTTCA-TTTCGCGTTGCGATTTTCATTT
1 TCTCGTTGCGATAGTCATTTTCGCGTTGCGATTTTCATTT
*
1024286 CTCTCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTT
1 -TCTCGTTGCGATAGTCATTTTCGCGTTGCGATTTTCATTT
*
1024327 TCTTGTTGCGAT
1 TCTCGTTGCGAT
1024339 TTTAAGTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
40 26 0.55
41 21 0.45
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.50
Consensus pattern (40 bp):
TCTCGTTGCGATAGTCATTTTCGCGTTGCGATTTTCATTT
Found at i:1024316 original size:20 final size:20
Alignment explanation
Indices: 1024251--1024341 Score: 114
Period size: 20 Copynumber: 4.5 Consensus size: 20
1024241 CGATTATCTC
*
1024251 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
1024270 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCGT
**
1024290 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCGT
*
1024311 GTTGCGATTTTCATTTTCTT
1 GTTGCGATTTTCATTTTCGT
1024331 GTTGCGATTTT
1 GTTGCGATTTT
1024342 AAGTTTAGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
19 13 0.21
20 32 0.52
21 17 0.27
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.52
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:1025095 original size:20 final size:20
Alignment explanation
Indices: 1024902--1025095 Score: 182
Period size: 20 Copynumber: 9.7 Consensus size: 20
1024892 GCTTTAAAAA
*
1024902 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGTAT
1024922 AT-GCGTTGCGATTTTACGTAT
1 -TCGCGTTGCGA-TTTACGTAT
1024943 T-GTCGTTGCGATTTACGTAT
1 TCG-CGTTGCGATTTACGTAT
*
1024963 TCTCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGTAT
*
1024983 TCTCGTTGCGATTTACAG-AT
1 TCGCGTTGCGATTTAC-GTAT
* *
1025003 ACGCGTTGCGATTTATGTAT
1 TCGCGTTGCGATTTACGTAT
* *
1025023 TCTCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGTAT
* * * *
1025043 ACGTGTTGCGATAGT-CAG-AA
1 TCGCGTTGCGAT-TTAC-GTAT
* *
1025063 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGTAT
1025083 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1025096 CTGGAAAATC
Statistics
Matches: 145, Mismatches: 19, Indels: 19
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.01
20 123 0.85
21 20 0.14
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTACGTAT
Found at i:1025157 original size:21 final size:21
Alignment explanation
Indices: 1025061--1025160 Score: 64
Period size: 21 Copynumber: 4.8 Consensus size: 21
1025051 CGATAGTCAG
*
1025061 AATCGCGTTGCGATT-TTCAT
1 AATCGCATTGCGATTCTTCAT
* * ** *
1025081 ATTCGCGTTGCGATTCTGGAA
1 AATCGCATTGCGATTCTTCAT
*
1025102 AATCGCAATGCGAATT-TGT-ACT
1 AATCGCATTGCG-ATTCT-TCA-T
* *
1025124 -ATCGTATTACGATTCTTCAT
1 AATCGCATTGCGATTCTTCAT
1025144 AATCGCATTGCGATTCT
1 AATCGCATTGCGATTCT
1025161 GGGAACTGAT
Statistics
Matches: 59, Mismatches: 14, Indels: 13
0.69 0.16 0.15
Matches are distributed among these distances:
20 19 0.32
21 37 0.63
22 3 0.05
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (21 bp):
AATCGCATTGCGATTCTTCAT
Found at i:1032078 original size:20 final size:21
Alignment explanation
Indices: 1032053--1032121 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 21
1032043 TTTATTTATT
*
1032053 ATATTATGTATTTTTAAAA-A
1 ATATTATTTATTTTTAAAATA
*
1032073 ATATTATTTATTTTTTAAAATC
1 ATATTATTTA-TTTTTAAAATA
*
1032095 ATATTATTTATTTATTTGAAATA
1 ATATTATTTA-TT-TTTAAAATA
1032118 ATAT
1 ATAT
1032122 CATCTTTAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 9 0.21
21 9 0.21
22 13 0.31
23 11 0.26
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (21 bp):
ATATTATTTATTTTTAAAATA
Found at i:1032333 original size:26 final size:24
Alignment explanation
Indices: 1032284--1032346 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
1032274 AATTTTAAAA
* *
1032284 ATAAATAAATATTTTTATAATATT
1 ATAAATAATTTTTTTTATAATATT
*
1032308 ATAAATATATTTTTTTTGTAATTATT
1 ATAAATA-ATTTTTTTTATAA-TATT
* *
1032334 TTATATAATTTTT
1 ATAAATAATTTTT
1032347 AGAAAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 7 0.22
25 16 0.50
26 9 0.28
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
ATAAATAATTTTTTTTATAATATT
Found at i:1032886 original size:20 final size:20
Alignment explanation
Indices: 1032861--1032898 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1032851 TTAAAATTAA
1032861 ACAAAA-GTGATAATTTATGT
1 ACAAAATGTG-TAATTTATGT
1032881 ACAAAATGTGTAATTTAT
1 ACAAAATGTGTAATTTAT
1032899 TCTTTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (20 bp):
ACAAAATGTGTAATTTATGT
Found at i:1034162 original size:32 final size:32
Alignment explanation
Indices: 1034126--1034191 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
1034116 AAGACAATAA
1034126 TTCTTTTAAGATACAATAAAATTTTATTTTAT
1 TTCTTTTAAGATACAATAAAATTTTATTTTAT
* *
1034158 TTCTTTTAAGATGCAATCAAATTTTATTTTAT
1 TTCTTTTAAGATACAATAAAATTTTATTTTAT
1034190 TT
1 TT
1034192 TCAATCAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.55
Consensus pattern (32 bp):
TTCTTTTAAGATACAATAAAATTTTATTTTAT
Found at i:1040092 original size:21 final size:21
Alignment explanation
Indices: 1040066--1040110 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1040056 GATTTCTGGG
* *
1040066 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1040087 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1040108 CAA
1 CAA
1040111 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1040712 original size:18 final size:18
Alignment explanation
Indices: 1040689--1040723 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1040679 CTAGGAGATT
1040689 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1040707 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1040724 CTAGATGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1040809 original size:21 final size:22
Alignment explanation
Indices: 1040780--1040823 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1040770 GTTGTATGAT
1040780 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
1040801 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
1040823 A
1 A
1040824 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:1041745 original size:149 final size:149
Alignment explanation
Indices: 1041475--1041778 Score: 563
Period size: 149 Copynumber: 2.0 Consensus size: 149
1041465 GAGTCGAGGG
*
1041475 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTTTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
1041540 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
1041605 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
1041624 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1041689 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
1041754 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1041773 TCTACG
1 TCTACG
1041779 GGGCACTTCG
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1041801 original size:23 final size:23
Alignment explanation
Indices: 1041757--1041801 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1041747 ATCATTATAT
*
1041757 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
1041780 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1041802 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:1043515 original size:41 final size:42
Alignment explanation
Indices: 1043417--1043516 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 42
1043407 TCCTTCGGGC
* * * *
1043417 CATCAATAAGCCTTTCGAGCATGATGATTAAATCCTTCAGGT
1 CATCTATAAGTCTTTCGAGCAAGATGATTAAATCATTCAGGT
*
1043459 CATCTATAAGTCTTTCGAGCAAGATGA-TAAGTCATTCA-GT
1 CATCTATAAGTCTTTCGAGCAAGATGATTAAATCATTCAGGT
1043499 CTATCTATAA-TACTTTCG
1 C-ATCTATAAGT-CTTTCG
1043517 TGTAGGATGT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
40 4 0.08
41 23 0.45
42 24 0.47
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (42 bp):
CATCTATAAGTCTTTCGAGCAAGATGATTAAATCATTCAGGT
Found at i:1043690 original size:36 final size:37
Alignment explanation
Indices: 1043635--1043704 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 37
1043625 TTCAATCAAG
*
1043635 ATTTTATCTCACATGAGATT-ATTTTCTTTAAAACAA
1 ATTTTATCTCACATAAGATTGATTTTCTTTAAAACAA
* * *
1043671 ATTTTATCTCACTTAAGATTGTTTTTTTTTAAAA
1 ATTTTATCTCACATAAGATTGATTTTCTTTAAAA
1043705 AAAAATTGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 18 0.62
37 11 0.38
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (37 bp):
ATTTTATCTCACATAAGATTGATTTTCTTTAAAACAA
Found at i:1047214 original size:40 final size:42
Alignment explanation
Indices: 1047136--1047215 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 42
1047126 AAGTTAAAAA
* * *
1047136 ATATTTATATATTTTCATTAAAAAATTTAAATTCATAAAATT
1 ATATATATATATTTTCATTAAAAAATTGAAAATCATAAAATT
* *
1047178 ATATATATATATTTT-TTTACAAAATTGAAAAT-ATAAAA
1 ATATATATATATTTTCATTAAAAAATTGAAAATCATAAAA
1047216 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 6 0.18
41 13 0.39
42 14 0.42
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (42 bp):
ATATATATATATTTTCATTAAAAAATTGAAAATCATAAAATT
Found at i:1048145 original size:22 final size:22
Alignment explanation
Indices: 1048101--1048151 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1048091 CTACGGAGAC
*
1048101 ATCCGTCCCCATCTCAGACGAA
1 ATCCGTCCCCATATCAGACGAA
* **
1048123 ATCCGTCCCCATATCCGGTGAA
1 ATCCGTCCCCATATCAGACGAA
1048145 ATCCGTC
1 ATCCGTC
1048152 TATCTCCACC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.39, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATATCAGACGAA
Found at i:1048542 original size:19 final size:20
Alignment explanation
Indices: 1048520--1048563 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1048510 TCGCAACGCT
*
1048520 ATTTTCA-TTTCGCGTTGCG
1 ATTTTCATTTTCGCGTTACG
*
1048539 ATTTTCATTTTCGTGTTACG
1 ATTTTCATTTTCGCGTTACG
1048559 ATTTT
1 ATTTT
1048564 AAGTTTCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.14, C:0.16, G:0.16, T:0.55
Consensus pattern (20 bp):
ATTTTCATTTTCGCGTTACG
Found at i:1048570 original size:20 final size:20
Alignment explanation
Indices: 1048527--1048570 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1048517 GCTATTTTCA
* * *
1048527 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTACGATTTTAAG
*
1048547 TTTCGTGTTACGATTTTAAG
1 TTTCGCGTTACGATTTTAAG
1048567 TTTC
1 TTTC
1048571 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.16, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGCGTTACGATTTTAAG
Found at i:1050548 original size:21 final size:21
Alignment explanation
Indices: 1050507--1050598 Score: 66
Period size: 21 Copynumber: 4.4 Consensus size: 21
1050497 TGGTGCATGG
**
1050507 CGTGATGAGGT-TCGGTCTTTA
1 CGTGATGAGGTAGAGGT-TTTA
*
1050528 CGTGGTGAGGTAGAGGTTTTA
1 CGTGATGAGGTAGAGGTTTTA
* *
1050549 CGCGATGA--CA-ATGGTACTTTA
1 CGTGATGAGGTAGA-GGT--TTTA
1050570 CGTGATGAGGTAGAGGTTTTA
1 CGTGATGAGGTAGAGGTTTTA
*
1050591 CGCGATGA
1 CGTGATGA
1050599 CAATGGTACT
Statistics
Matches: 55, Mismatches: 9, Indels: 14
0.71 0.12 0.18
Matches are distributed among these distances:
18 1 0.02
19 4 0.07
21 42 0.76
22 3 0.05
23 4 0.07
24 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.35, T:0.32
Consensus pattern (21 bp):
CGTGATGAGGTAGAGGTTTTA
Found at i:1050556 original size:42 final size:42
Alignment explanation
Indices: 1050523--1050623 Score: 193
Period size: 42 Copynumber: 2.4 Consensus size: 42
1050513 GAGGTTCGGT
1050523 CTTTACGTGGTGAGGTAGAGGTTTTACGCGATGACAATGGTA
1 CTTTACGTGGTGAGGTAGAGGTTTTACGCGATGACAATGGTA
*
1050565 CTTTACGTGATGAGGTAGAGGTTTTACGCGATGACAATGGTA
1 CTTTACGTGGTGAGGTAGAGGTTTTACGCGATGACAATGGTA
1050607 CTTTACGTGGTGAGGTA
1 CTTTACGTGGTGAGGTA
1050624 TCTACTTTAC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.24, C:0.12, G:0.33, T:0.32
Consensus pattern (42 bp):
CTTTACGTGGTGAGGTAGAGGTTTTACGCGATGACAATGGTA
Found at i:1050611 original size:21 final size:21
Alignment explanation
Indices: 1050545--1050613 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
1050535 AGGTAGAGGT
1050545 TTTACGCGATGACAATGGTAC
1 TTTACGCGATGACAATGGTAC
* *
1050566 TTTACGTGATGAGGTAGA-GGT--
1 TTTACGCGATGA--CA-ATGGTAC
1050587 TTTACGCGATGACAATGGTAC
1 TTTACGCGATGACAATGGTAC
1050608 TTTACG
1 TTTACG
1050614 TGGTGAGGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
18 1 0.03
19 4 0.11
21 28 0.74
23 4 0.11
24 1 0.03
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (21 bp):
TTTACGCGATGACAATGGTAC
Found at i:1050629 original size:21 final size:21
Alignment explanation
Indices: 1050605--1050644 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1050595 ATGACAATGG
*
1050605 TACTTTACGTGGTGAGGTATC
1 TACTTTACGTGATGAGGTATC
1050626 TACTTTACGTGATGAGGTA
1 TACTTTACGTGATGAGGTA
1050645 GACGCTCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.38
Consensus pattern (21 bp):
TACTTTACGTGATGAGGTATC
Found at i:1050964 original size:42 final size:42
Alignment explanation
Indices: 1050912--1051020 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 42
1050902 GATTCACCTG
* * * * * *
1050912 TCATCGTTCAAGAGGCCTCTCCTATCGTTGAAGAGGCCCTTA
1 TCATCGTTCAAGAGGCCCCTCCCACCGATCAAGAGGCCATTA
* * *
1050954 TCATCCTTCAATAGGCCCCTCCCACCGATCAAGAGGCCATTG
1 TCATCGTTCAAGAGGCCCCTCCCACCGATCAAGAGGCCATTA
* *
1050996 TCATCGTTCAAGAGGTCCCTACCAC
1 TCATCGTTCAAGAGGCCCCTCCCAC
1051021 TGTTTGAGAG
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCCACCGATCAAGAGGCCATTA
Found at i:1051006 original size:21 final size:21
Alignment explanation
Indices: 1050910--1051015 Score: 79
Period size: 21 Copynumber: 5.0 Consensus size: 21
1050900 CTGATTCACC
1050910 TGTCATCGTTCAAGAGGCCTCT
1 TGTCATCGTTCAAGAGGCC-CT
** *
1050932 CCT-ATCGTTGAAGAGGCCCT
1 TGTCATCGTTCAAGAGGCCCT
* * * *
1050952 TATCATCCTTCAATAGGCCCC
1 TGTCATCGTTCAAGAGGCCCT
** * * *
1050973 TCCCACCGATCAAGAGGCCAT
1 TGTCATCGTTCAAGAGGCCCT
1050994 TGTCATCGTTCAAGAGGTCCCT
1 TGTCATCGTTCAAGAGG-CCCT
1051016 ACCACTGTTT
Statistics
Matches: 60, Mismatches: 22, Indels: 4
0.70 0.26 0.05
Matches are distributed among these distances:
20 3 0.05
21 53 0.88
22 4 0.07
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.26
Consensus pattern (21 bp):
TGTCATCGTTCAAGAGGCCCT
Found at i:1052399 original size:14 final size:14
Alignment explanation
Indices: 1052380--1052406 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1052370 TGATATATTC
1052380 AAAGTTGATTTGTA
1 AAAGTTGATTTGTA
1052394 AAAGTTGATTTGT
1 AAAGTTGATTTGT
1052407 TTAATTGATT
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
AAAGTTGATTTGTA
Found at i:1055921 original size:20 final size:21
Alignment explanation
Indices: 1055875--1055935 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
1055865 TTCCCCTGTG
*
1055875 GGGGGAATCAGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
1055898 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
1055918 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1055936 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 3 0.09
23 12 0.34
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1062200 original size:20 final size:20
Alignment explanation
Indices: 1062162--1062211 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1062152 GTTACGATAG
*
1062162 TCAAATTCGCAACGCGAAAA
1 TCAAATTCGCAAAGCGAAAA
* * *
1062182 TGAAATTCGCAAAGTGAAAG
1 TCAAATTCGCAAAGCGAAAA
1062202 TCAAATTCGC
1 TCAAATTCGC
1062212 GTTGCGATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (20 bp):
TCAAATTCGCAAAGCGAAAA
Found at i:1067926 original size:483 final size:484
Alignment explanation
Indices: 1067019--1067986 Score: 1893
Period size: 483 Copynumber: 2.0 Consensus size: 484
1067009 TGTAATTATG
1067019 TTGCATTTATCTCATGCATAGAGCCTAAGAATATTAAAGAAGCATTAAAAGATGAACATTGGATT
1 TTGCATTTATCTCATGCATAGAGCCTAAGAATATTAAAGAAGCATTAAAAGATGAACATTGGATT
1067084 ATGGCTATGCAAGAAGAGTTAAATCAATTTGAGAGAAGTAAAGTATGAACATTAGTTGAAAGGCC
66 ATGGCTATGCAAGAAGAGTTAAATCAATTTGAGAGAAGTAAAGTATGAACATTAGTTGAAAGGCC
1067149 TAGTAATAAATCTACTGTAGGTACTAGATGGGTGTTTAGGAATAAGCTTGATGAAAATGGTAATA
131 TAGTAATAAATCTACTGTAGGTACTAGATGGGTGTTTAGGAATAAGCTTGATGAAAATGGTAATA
1067214 TAGTGAGAAACAAGGCTAGACTTGTTTCTCAAGGCTATACTCAAGAAGAAGACATAGACTATGAT
196 TAGTGAGAAACAAGGCTAGACTTGTTTCTCAAGGCTATACTCAAGAAGAAGACATAGACTATGAT
*
1067279 GAAACATACGCTCCTGTAGCTAGGATGGAAGCAATTAGAATGTTATTAGCATTTGCATGTTTTCA
261 GAAACATACGCTCATGTAGCTAGGATGGAAGCAATTAGAATGTTATTAGCATTTGCATGTTTTCA
1067344 TGAATTTAAATTATATCAAATGGATGTTAAAAGTGCATTTTTAAATGGTTTTATAAAGGAAGAAG
326 TGAATTTAAATTATATCAAATGGATGTTAAAAGTGCATTTTTAAATGGTTTTATAAAGGAAGAAG
1067409 TGTATGTGGAACAACCTCTAGGTTTTGAAGATTTAAAATTTCCAAATCATATTCTTAAATTAACA
391 TGTATGTGGAACAACCTCTAGGTTTTGAAGATTTAAAATTTCCAAATCATATTCTTAAATTAACA
*
1067474 AAAGCTCTTTATGGTTTAAAATAAGCTCC
456 AAAGCTCTTTATGGTTTAAAACAAGCTCC
1067503 TTGCATTTATCTCATGCATAGAGCCTAAGAATATTAAAGAAGCATTAAAAGATGAACATTGGATT
1 TTGCATTTATCTCATGCATAGAGCCTAAGAATATTAAAGAAGCATTAAAAGATGAACATTGGATT
1067568 ATGGCTATGCAAGAAGAGTTAAATCAATTTGAGAGAAGT-AAGTATGAACATTAGTTGAAAGGCC
66 ATGGCTATGCAAGAAGAGTTAAATCAATTTGAGAGAAGTAAAGTATGAACATTAGTTGAAAGGCC
*
1067632 TAGTAATAAATCTACTGTAGGTACTAGATGGGTGTTTAGGAATAAGCTTGATGAAAGTGGTAATA
131 TAGTAATAAATCTACTGTAGGTACTAGATGGGTGTTTAGGAATAAGCTTGATGAAAATGGTAATA
*
1067697 TAGTGAGAAACAAGGCTAGACTTGTTTCTCAAGGCTATACTCAAGAAGAAGGCATAGACTATGAT
196 TAGTGAGAAACAAGGCTAGACTTGTTTCTCAAGGCTATACTCAAGAAGAAGACATAGACTATGAT
1067762 GAAACATACGCTCATGTAGCTAGGATGGAAGCAATTAGAATGTTATTAGCATTTGCATGTTTTCA
261 GAAACATACGCTCATGTAGCTAGGATGGAAGCAATTAGAATGTTATTAGCATTTGCATGTTTTCA
1067827 TGAATTTAAATTATATCAAATGGATGTTAAAAGTGCATTTTTAAATGGTTTTATAAAGGAAGAAG
326 TGAATTTAAATTATATCAAATGGATGTTAAAAGTGCATTTTTAAATGGTTTTATAAAGGAAGAAG
1067892 TGTATGTGGAACAACCTCTAGGTTTTGAAGATTTAAAATTTCCAAATCATATTCTTAAATTAACA
391 TGTATGTGGAACAACCTCTAGGTTTTGAAGATTTAAAATTTCCAAATCATATTCTTAAATTAACA
1067957 AAAGCTCTTTATGGTTTAAAACAAGCTCC
456 AAAGCTCTTTATGGTTTAAAACAAGCTCC
1067986 T
1 T
1067987 AGAGCTTGGT
Statistics
Matches: 480, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
483 376 0.78
484 104 0.22
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (484 bp):
TTGCATTTATCTCATGCATAGAGCCTAAGAATATTAAAGAAGCATTAAAAGATGAACATTGGATT
ATGGCTATGCAAGAAGAGTTAAATCAATTTGAGAGAAGTAAAGTATGAACATTAGTTGAAAGGCC
TAGTAATAAATCTACTGTAGGTACTAGATGGGTGTTTAGGAATAAGCTTGATGAAAATGGTAATA
TAGTGAGAAACAAGGCTAGACTTGTTTCTCAAGGCTATACTCAAGAAGAAGACATAGACTATGAT
GAAACATACGCTCATGTAGCTAGGATGGAAGCAATTAGAATGTTATTAGCATTTGCATGTTTTCA
TGAATTTAAATTATATCAAATGGATGTTAAAAGTGCATTTTTAAATGGTTTTATAAAGGAAGAAG
TGTATGTGGAACAACCTCTAGGTTTTGAAGATTTAAAATTTCCAAATCATATTCTTAAATTAACA
AAAGCTCTTTATGGTTTAAAACAAGCTCC
Found at i:1070979 original size:21 final size:21
Alignment explanation
Indices: 1070936--1070979 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1070926 ACACCGGGAG
**
1070936 CTAGCTCTTCACGAGCTGTTC
1 CTAGCTCTTCACGAGCTCCTC
* *
1070957 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
1070978 CT
1 CT
1070980 CCTCTTTCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:1071338 original size:14 final size:15
Alignment explanation
Indices: 1071313--1071342 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1071303 TTGATTTTGA
1071313 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
1071328 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
1071342 T
1 T
1071343 AATGTTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.07, C:0.03, G:0.27, T:0.63
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:1071954 original size:28 final size:28
Alignment explanation
Indices: 1071922--1071979 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
1071912 CATCGAATGT
1071922 ATTTCATGCATCGATGCACATACCATGC
1 ATTTCATGCATCGATGCACATACCATGC
1071950 ATTTCATGCATCGATGCACATACCATGC
1 ATTTCATGCATCGATGCACATACCATGC
1071978 AT
1 AT
1071980 CGATGCACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (28 bp):
ATTTCATGCATCGATGCACATACCATGC
Found at i:1072027 original size:65 final size:64
Alignment explanation
Indices: 1071946--1072089 Score: 202
Period size: 65 Copynumber: 2.2 Consensus size: 64
1071936 TGCACATACC
*
1071946 ATGCATTTCATGCATCGATGCA-CATACCATGCATCGATGCACTAAGGAT-TTTATGAAAACATC
1 ATGCATTTGATGCATCGATGCACCA-ACCATGCATCGATGCACTAAGGATATTT-TG-AAACATC
1072009 GA
63 GA
** *
1072011 ATGCATTTGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGCTATTTTGAAACATCGA
1 ATGCATTTGATGCATCGATGCACCAACCATGCATCGATGCACTAAGGATATTTTGAAACATCGA
*
1072075 ATGCACTTGATGCAT
1 ATGCATTTGATGCAT
1072090 TGGTGCACTC
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
64 23 0.32
65 44 0.61
66 5 0.07
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (64 bp):
ATGCATTTGATGCATCGATGCACCAACCATGCATCGATGCACTAAGGATATTTTGAAACATCGA
Found at i:1073284 original size:20 final size:19
Alignment explanation
Indices: 1073256--1073317 Score: 88
Period size: 20 Copynumber: 3.2 Consensus size: 19
1073246 CCGTTAGATA
*
1073256 GGGGGAATCGGTACCCCCT
1 GGGGGAATCTGTACCCCCT
*
1073275 GGGGGAAATCTGTTCCCCCT
1 GGGGG-AATCTGTACCCCCT
1073295 GGGGGGAATCTGTACCCCCT
1 -GGGGGAATCTGTACCCCCT
1073315 GGG
1 GGG
1073318 CAATTTGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 8 0.21
20 25 0.66
21 5 0.13
ACGTcount: A:0.15, C:0.29, G:0.37, T:0.19
Consensus pattern (19 bp):
GGGGGAATCTGTACCCCCT
Found at i:1076702 original size:19 final size:20
Alignment explanation
Indices: 1076678--1076717 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1076668 CGTTAGACAA
* *
1076678 GGGGG-AATCTGTTCCCCCT
1 GGGGGAAATCGGTACCCCCT
1076697 GGGGGAAATCGGTACCCCCT
1 GGGGGAAATCGGTACCCCCT
1076717 G
1 G
1076718 AGTAATCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.15, C:0.30, G:0.35, T:0.20
Consensus pattern (20 bp):
GGGGGAAATCGGTACCCCCT
Found at i:1078254 original size:18 final size:18
Alignment explanation
Indices: 1078231--1078267 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1078221 CGAAATTTAT
1078231 ATTGAAATTTAAACTCAA
1 ATTGAAATTTAAACTCAA
*
1078249 ATTGAAATTTAAATTCAA
1 ATTGAAATTTAAACTCAA
1078267 A
1 A
1078268 CTCTAATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.35
Consensus pattern (18 bp):
ATTGAAATTTAAACTCAA
Found at i:1078681 original size:25 final size:25
Alignment explanation
Indices: 1078653--1078702 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1078643 TATTATTTTC
* *
1078653 CAAATAATATACCCATAATAATGTT
1 CAAATAATATACCCACAACAATGTT
*
1078678 CAAATAATGTACCCACAACAATGTT
1 CAAATAATATACCCACAACAATGTT
1078703 TAATTGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.28
Consensus pattern (25 bp):
CAAATAATATACCCACAACAATGTT
Found at i:1079035 original size:18 final size:18
Alignment explanation
Indices: 1079012--1079047 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1079002 AAGCCGGTTG
1079012 TGATTGAGATTTTAATTT
1 TGATTGAGATTTTAATTT
* *
1079030 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTAATTT
1079048 CCTTTTGCTT
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:0.22, C:0.03, G:0.19, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTAATTT
Found at i:1081904 original size:21 final size:21
Alignment explanation
Indices: 1081878--1081922 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1081868 GATTTCTGGG
* *
1081878 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1081899 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1081920 CAA
1 CAA
1081923 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1083002 original size:31 final size:31
Alignment explanation
Indices: 1082964--1083028 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1082954 AGAGTCGAGG
*
1082964 GTTTACCTATG-TCTTTCGAGACATATGGAAA
1 GTTTACCTAGGTTC-TTCGAGACATATGGAAA
* *
1082995 GTTTACCTAGGTTCTTCGAGACCTATGGACA
1 GTTTACCTAGGTTCTTCGAGACATATGGAAA
1083026 GTT
1 GTT
1083029 ACCGAGGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGAAA
Found at i:1083048 original size:30 final size:30
Alignment explanation
Indices: 1083014--1083292 Score: 515
Period size: 30 Copynumber: 9.3 Consensus size: 30
1083004 GGTTCTTCGA
*
1083014 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
1083044 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
1083074 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
1083104 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
1083134 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
1083164 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
*
1083194 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
1083224 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* *
1083254 GACCTCTGGACAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
1083283 GACCTCTGGA
1 GACCTCTGGA
1083293 TAGGTCCTTC
Statistics
Matches: 244, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
29 18 0.07
30 226 0.93
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:1083573 original size:2 final size:2
Alignment explanation
Indices: 1083566--1083590 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1083556 GATATGTATG
1083566 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1083591 GAAAGGTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1086656 original size:21 final size:21
Alignment explanation
Indices: 1086630--1086674 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1086620 GATTTCTGGG
* *
1086630 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1086651 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1086672 CAA
1 CAA
1086675 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1087769 original size:31 final size:31
Alignment explanation
Indices: 1087711--1087775 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
1087701 AGAGTCGAGG
*
1087711 GTTTACCTATGTCTTTCGAGACATATGGAAA
1 GTTTACCTAGGTCTTTCGAGACATATGGAAA
* * *
1087742 GTTTACCTAGGT-TCTTCGGGACCTATGGACA
1 GTTTACCTAGGTCT-TTCGAGACATATGGAAA
1087773 GTT
1 GTT
1087776 ACCGAGGATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTCTTTCGAGACATATGGAAA
Found at i:1087822 original size:30 final size:30
Alignment explanation
Indices: 1087761--1088034 Score: 452
Period size: 30 Copynumber: 9.3 Consensus size: 30
1087751 GGTTCTTCGG
*
1087761 GACCTATGGACAGTTACCGAGGATC-TTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* *
1087790 GACCTTTGAACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
1087820 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
1087850 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
1087880 GACCTCTGGACAGTTACCGA-GATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
1087909 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
*
1087939 GACCTCTGGATAGTTACCGA-G--CTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
1087966 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* *
1087996 GACCTCTGGACAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
1088025 GACCTCTGGA
1 GACCTCTGGA
1088035 TAGGTCCTTC
Statistics
Matches: 232, Mismatches: 8, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
27 25 0.11
28 1 0.00
29 71 0.31
30 135 0.58
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:1087830 original size:59 final size:59
Alignment explanation
Indices: 1087761--1088034 Score: 446
Period size: 59 Copynumber: 4.7 Consensus size: 59
1087751 GGTTCTTCGG
* * *
1087761 GACCTATGGACAGTTACCGAGGATC-TTATGACCTTTGAACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGA-GATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTAT
1087820 GACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGA-GATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTAT
1087880 GACCTCTGGACAGTTACCGAGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTAT
*
1087939 GACCTCTGGATAGTTACCGAG--CTTTATGACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
1087996 GACCTCTGGACAGTTACCGGGGTCTTTGTGACCTCTGGA
1 GACCTCTGGACAGTTACCGAGATCTTTATGACCTCTGGA
1088035 TAGGTCCTTC
Statistics
Matches: 205, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
57 55 0.27
59 98 0.48
60 52 0.25
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (59 bp):
GACCTCTGGACAGTTACCGAGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:1087904 original size:89 final size:90
Alignment explanation
Indices: 1087761--1088034 Score: 452
Period size: 89 Copynumber: 3.1 Consensus size: 90
1087751 GGTTCTTCGG
* * *
1087761 GACCTATGGACAGTTACCGAGGATC-TTATGACCTTTGAACAGTTACCGAGGATCTTTATGACCT
1 GACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCT
1087825 CTGGACAGTTACCGAGGATCTTTAT
66 CTGGACAGTTACCGAGGATCTTTAT
1087850 GACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGACAGTTACCGA-GATCTTTATGACCT
1 GACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCT
1087914 CTGGACAGTTACCGAGGATCTTTAT
66 CTGGACAGTTACCGAGGATCTTTAT
*
1087939 GACCTCTGGATAGTTACCGA-G--CTTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCT
1 GACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCT
* *
1088001 CTGGACAGTTACCG-GGGTCTTTGT
66 CTGGACAGTTACCGAGGATCTTTAT
1088025 GACCTCTGGA
1 GACCTCTGGA
1088035 TAGGTCCTTC
Statistics
Matches: 177, Mismatches: 6, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
86 44 0.25
87 28 0.16
88 1 0.01
89 82 0.46
90 22 0.12
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (90 bp):
GACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCT
CTGGACAGTTACCGAGGATCTTTAT
Found at i:1088313 original size:2 final size:2
Alignment explanation
Indices: 1088301--1088330 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1088291 GTATGCATGG
*
1088301 AT AT GT 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
1088331 GAAAGGTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1089744 original size:14 final size:15
Alignment explanation
Indices: 1089708--1089745 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1089698 GAAATCATTG
1089708 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
1089723 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
1089738 AAAAATTA
1 AAAAATTA
1089746 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:1089950 original size:20 final size:20
Alignment explanation
Indices: 1089922--1089992 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
1089912 TAAAATTCGT
*
1089922 GTTGTGAATTCGAAAATCGA
1 GTTGCGAATTCGAAAATCGA
1089942 GTTGCGAATTC-AGAAATCGA
1 GTTGCGAATTCGA-AAATCGA
* * *
1089962 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTCGAAAATC-GA
1089983 GTTGCGAATT
1 GTTGCGAATT
1089993 TGTAAATCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
19 1 0.02
20 31 0.70
21 12 0.27
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTCGAAAATCGA
Found at i:1090036 original size:20 final size:20
Alignment explanation
Indices: 1089935--1090151 Score: 115
Period size: 20 Copynumber: 10.9 Consensus size: 20
1089925 GTGAATTCGA
* **
1089935 AAATCGAGTTGCGAATTCAG
1 AAATCGCGTTGCGAATTTGG
*
1089955 AAATCGAGTTGCGAATTT-G
1 AAATCGCGTTGCGAATTTGG
* *
1089974 AAATTCAGTGTTGCGAATTTGT
1 AAA-TC-GCGTTGCGAATTTGG
** * *
1089996 AAATCGC--AACG-CTTTGT
1 AAATCGCGTTGCGAATTTGG
*
1090013 AAATCACGTTGCGAATTTGG
1 AAATCGCGTTGCGAATTTGG
* *
1090033 AAATCTCGTTACGAATTT-G
1 AAATCGCGTTGCGAATTTGG
** * **
1090052 ACTTCTGTGTTGCG-ATTTAC
1 AAATC-GCGTTGCGAATTTGG
* * *
1090072 AGATTCGCGTTGTGAATTTGA
1 A-AATCGCGTTGCGAATTTGG
1090093 AAATCGCGTTGCGAATTTGG
1 AAATCGCGTTGCGAATTTGG
* *
1090113 AAA-CTGAGTTGCGAAATTGG
1 AAATC-GCGTTGCGAATTTGG
**
1090133 AGTTCGCGTTGCGAATTTG
1 AAATCGCGTTGCGAATTTG
1090152 TTGGTCATTT
Statistics
Matches: 151, Mismatches: 34, Indels: 24
0.72 0.16 0.11
Matches are distributed among these distances:
17 11 0.07
18 2 0.01
19 15 0.10
20 97 0.64
21 23 0.15
22 3 0.02
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (20 bp):
AAATCGCGTTGCGAATTTGG
Found at i:1091389 original size:20 final size:22
Alignment explanation
Indices: 1091364--1091403 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1091354 TAATTGCTCC
1091364 TTTG-TTGA-ATTTCATACTAA
1 TTTGTTTGATATTTCATACTAA
*
1091384 TTTGTTTGATATTTGATACT
1 TTTGTTTGATATTTCATACT
1091404 TCTTGTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.25, C:0.07, G:0.12, T:0.55
Consensus pattern (22 bp):
TTTGTTTGATATTTCATACTAA
Found at i:1095377 original size:13 final size:13
Alignment explanation
Indices: 1095359--1095385 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1095349 CAAAAAAATG
1095359 TTTAAGGAATTTT
1 TTTAAGGAATTTT
1095372 TTTAAGGAATTTT
1 TTTAAGGAATTTT
1095385 T
1 T
1095386 ATAAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (13 bp):
TTTAAGGAATTTT
Found at i:1104691 original size:70 final size:70
Alignment explanation
Indices: 1104604--1104734 Score: 235
Period size: 70 Copynumber: 1.9 Consensus size: 70
1104594 AACGGAAGTA
* *
1104604 TGTTTATGTTCGTTCATTTAATAAATAAACAAATATAAATGAACACGAACATAAACGAACAATTT
1 TGTTCATGTTCGTTCATTTAATAAATAAACAAATATAAACGAACACGAACATAAACGAACAATTT
1104669 TTTTT
66 TTTTT
*
1104674 TGTTCATGTTCGTTCATTTAATAAATAAACGAATATAAACGAACACGAACATAAACGAACA
1 TGTTCATGTTCGTTCATTTAATAAATAAACAAATATAAACGAACACGAACATAAACGAACA
1104735 CGAACATAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 58 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (70 bp):
TGTTCATGTTCGTTCATTTAATAAATAAACAAATATAAACGAACACGAACATAAACGAACAATTT
TTTTT
Found at i:1104727 original size:16 final size:16
Alignment explanation
Indices: 1104702--1104766 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
1104692 TAATAAATAA
*
1104702 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
1104718 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1104734 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
1104750 ACGAAAATAAACGAAC
1 ACGAACATAAACGAAC
1104766 A
1 A
1104767 TAAACGTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1105864 original size:24 final size:24
Alignment explanation
Indices: 1105837--1105911 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
1105827 TATTGGGTTA
* *
1105837 AACATAAATGAATGAACATAAACG
1 AACATAAACGAACGAACATAAACG
*
1105861 AACATAACCGAACGAACATAAACG
1 AACATAAACGAACGAACATAAACG
* * *
1105885 AACATAACCGTACGAACATAATCG
1 AACATAAACGAACGAACATAAACG
1105909 AAC
1 AAC
1105912 GTTCACAAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.53, C:0.21, G:0.12, T:0.13
Consensus pattern (24 bp):
AACATAAACGAACGAACATAAACG
Found at i:1105874 original size:14 final size:14
Alignment explanation
Indices: 1105857--1105912 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
1105847 AATGAACATA
1105857 AACGAACATAACCG
1 AACGAACATAACCG
1105871 AACGAACAT-A---
1 AACGAACATAACCG
1105881 AACGAACATAACCG
1 AACGAACATAACCG
* *
1105895 TACGAACATAATCG
1 AACGAACATAACCG
1105909 AACG
1 AACG
1105913 TTCACAAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 24 0.69
ACGTcount: A:0.50, C:0.25, G:0.14, T:0.11
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1118301 original size:32 final size:32
Alignment explanation
Indices: 1118260--1118325 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
1118250 AAATAATATT
*
1118260 TGTGGAGATGCTAGTCATAAGGCTCTCGTTGG
1 TGTGGAGATGCCAGTCATAAGGCTCTCGTTGG
1118292 TGTGGAGATGCCAGTCATAAGGCTCTCGTTGG
1 TGTGGAGATGCCAGTCATAAGGCTCTCGTTGG
1118324 TG
1 TG
1118326 AGTAGAAGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.18, C:0.17, G:0.35, T:0.30
Consensus pattern (32 bp):
TGTGGAGATGCCAGTCATAAGGCTCTCGTTGG
Found at i:1120302 original size:16 final size:16
Alignment explanation
Indices: 1120281--1120311 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1120271 AGAAGACGAG
*
1120281 GTACATTTACATATAC
1 GTACATATACATATAC
1120297 GTACATATACATATA
1 GTACATATACATATA
1120312 TATGTATGGA
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:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (16 bp):
GTACATATACATATAC
Found at i:1127364 original size:24 final size:24
Alignment explanation
Indices: 1127313--1127364 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
1127303 ATTCATACCC
1127313 AAAATCATATAAAAATCATTTAGT
1 AAAATCATATAAAAATCATTTAGT
*
1127337 -AAATCAGTATAACAAT-ATTTTA-T
1 AAAATCA-TATAAAAATCA-TTTAGT
1127360 AAAAT
1 AAAAT
1127365 AATTCAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAAATCATATAAAAATCATTTAGT
Found at i:1130395 original size:65 final size:63
Alignment explanation
Indices: 1130197--1130406 Score: 214
Period size: 65 Copynumber: 3.3 Consensus size: 63
1130187 TGCACTAAGA
* * * *
1130197 GTGCATCGATGCATCAAGTGTATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTT
1130260 G
63 G
*
1130261 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
1130326 -
63 G
* **
1130326 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
1130389 TG
62 TG
*
1130391 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
1130407 CTTTGATAAA
Statistics
Matches: 125, Mismatches: 11, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 48 0.38
65 65 0.52
66 5 0.04
67 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:1132885 original size:19 final size:19
Alignment explanation
Indices: 1132861--1132901 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1132851 ATGTTGTTTT
1132861 GCACGATTTGATGATTAAA
1 GCACGATTTGATGATTAAA
1132880 GCACGATTTGATGATTAAA
1 GCACGATTTGATGATTAAA
1132899 GCA
1 GCA
1132902 GGAGTTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (19 bp):
GCACGATTTGATGATTAAA
Found at i:1132909 original size:19 final size:19
Alignment explanation
Indices: 1132861--1132909 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1132851 ATGTTGTTTT
*
1132861 GCACGATTTGATGATTAAA
1 GCACGAGTTGATGATTAAA
*
1132880 GCACGATTTGATGATTAAA
1 GCACGAGTTGATGATTAAA
*
1132899 GCAGGAGTTGA
1 GCACGAGTTGA
1132910 AAAGCTCGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.29
Consensus pattern (19 bp):
GCACGAGTTGATGATTAAA
Found at i:1136995 original size:22 final size:21
Alignment explanation
Indices: 1136953--1136992 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1136943 GAGTTTATTT
*
1136953 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1136974 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1136993 ACAATTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1139135 original size:65 final size:64
Alignment explanation
Indices: 1138937--1139146 Score: 214
Period size: 65 Copynumber: 3.2 Consensus size: 64
1138927 CTTACTAAGA
* * ** *
1138937 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTTG
* * * *
1139001 GTGCATCGATACAACAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGT
1139064 AT-
63 -TG
* *
1139066 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGG-TT
1139130 G
64 G
*
1139131 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
1139147 CTTTGATAAA
Statistics
Matches: 119, Mismatches: 17, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 49 0.41
65 61 0.51
66 1 0.01
67 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTTG
Found at i:1140753 original size:3 final size:3
Alignment explanation
Indices: 1140745--1140770 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1140735 TAGCATGAAA
1140745 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
1140771 TTTTGAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1144272 original size:11 final size:11
Alignment explanation
Indices: 1144256--1144280 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1144246 AGGTTAAGAA
1144256 ATTAGAGCTCT
1 ATTAGAGCTCT
1144267 ATTAGAGCTCT
1 ATTAGAGCTCT
1144278 ATT
1 ATT
1144281 GGGGAAGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (11 bp):
ATTAGAGCTCT
Found at i:1144705 original size:85 final size:85
Alignment explanation
Indices: 1144582--1144806 Score: 254
Period size: 85 Copynumber: 2.6 Consensus size: 85
1144572 TGACGTGTGC
* * ** * * *
1144582 TTCAATGACATGCAATGTAAGCCATACATGCGTTTCATAAATTTATGACACATAAATTTATGTCA
1 TTCAATGACGTTCAATGTAAGTTATACATGCGTGTCATAAATTTATGACACACAAATGTATGTCA
* *
1144647 AGTAGATTTATGATGGGGGA
66 ACTAGATTTATGACGGGGGA
* *
1144667 TTCAATGACGTTCAATGTAAGTTATACATGCGAGTCATAAATTTATGACACACAAATGTGTGTCA
1 TTCAATGACGTTCAATGTAAGTTATACATGCGTGTCATAAATTTATGACACACAAATGTATGTCA
* ** *
1144732 TCTTTATTTATGACGGGGGC
66 ACTAGATTTATGACGGGGGA
* * * * *
1144752 TTCAATGACGCTCAATG-AACTTTATAAATGTGTGTCATAGATTTATGACACACAA
1 TTCAATGACGTTCAATGTAA-GTTATACATGCGTGTCATAAATTTATGACACACAA
1144807 TTGCGTGTCA
Statistics
Matches: 118, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
84 2 0.02
85 116 0.98
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (85 bp):
TTCAATGACGTTCAATGTAAGTTATACATGCGTGTCATAAATTTATGACACACAAATGTATGTCA
ACTAGATTTATGACGGGGGA
Found at i:1144815 original size:85 final size:85
Alignment explanation
Indices: 1144546--1144817 Score: 235
Period size: 85 Copynumber: 3.2 Consensus size: 85
1144536 CAATCACGAT
* * * * * * ** *
1144546 ACACGAATGTGTGTCATCTTT-TTTAATGACGTGTGCTTCAATGAC-ATGCAATGTAAGCCATAC
1 ACACAAATGCGTGTCATCTTTATTT-ATGACGGGGGATTCAATGACGCT-CAATGTAAGTTATAA
**
1144609 ATGCGTTTCATAAATTTATGAC
64 ATGCGAGTCATAAATTTATGAC
* *** ** ** * * *
1144631 ACATAAATTTATGTCAAGTAGATTTATGATGGGGGATTCAATGACGTTCAATGTAAGTTATACAT
1 ACACAAATGCGTGTCATCTTTATTTATGACGGGGGATTCAATGACGCTCAATGTAAGTTATAAAT
1144696 GCGAGTCATAAATTTATGAC
66 GCGAGTCATAAATTTATGAC
* * *
1144716 ACACAAATGTGTGTCATCTTTATTTATGACGGGGGCTTCAATGACGCTCAATG-AACTTTATAAA
1 ACACAAATGCGTGTCATCTTTATTTATGACGGGGGATTCAATGACGCTCAATGTAA-GTTATAAA
* * *
1144780 TGTGTGTCATAGATTTATGAC
65 TGCGAGTCATAAATTTATGAC
*
1144801 ACACAATTGCGTGTCAT
1 ACACAAATGCGTGTCAT
1144818 AAAAAATTCA
Statistics
Matches: 150, Mismatches: 34, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
84 2 0.01
85 144 0.96
86 4 0.03
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (85 bp):
ACACAAATGCGTGTCATCTTTATTTATGACGGGGGATTCAATGACGCTCAATGTAAGTTATAAAT
GCGAGTCATAAATTTATGAC
Found at i:1152401 original size:80 final size:78
Alignment explanation
Indices: 1152264--1152422 Score: 284
Period size: 80 Copynumber: 2.0 Consensus size: 78
1152254 CATTTTTTTC
1152264 TCGAGAAAATTAACGAAGAAAGATTTGAAAACGAGATGGAAAAATCGAATGAACAGTGATGGGGC
1 TCGAGAAAATTAACGAAGAAAGATTTGAAAACGAGATGGAAAAATCGAATGAACA--G-TGGGGC
1152329 ACTGGTTATGAAAAAT
63 ACTGGTTATGAAAAAT
1152345 TCGAGAAAATTAACGAAGAAAGATTTG-AAACGAGATGGAAAAATCGAATGAACAGTGGGGCACT
1 TCGAGAAAATTAACGAAGAAAGATTTGAAAACGAGATGGAAAAATCGAATGAACAGTGGGGCACT
1152409 GGTTATGAAAAAT
66 GGTTATGAAAAAT
1152422 T
1 T
1152423 ATATATAGGT
Statistics
Matches: 78, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
77 23 0.29
78 1 0.01
80 27 0.35
81 27 0.35
ACGTcount: A:0.45, C:0.09, G:0.26, T:0.20
Consensus pattern (78 bp):
TCGAGAAAATTAACGAAGAAAGATTTGAAAACGAGATGGAAAAATCGAATGAACAGTGGGGCACT
GGTTATGAAAAAT
Found at i:1158561 original size:22 final size:23
Alignment explanation
Indices: 1158521--1158568 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1158511 AAAGAATAAA
1158521 AAAAAGGTTAGAAAAAATAAAAT
1 AAAAAGGTTAGAAAAAATAAAAT
* * *
1158544 AAAAATGTTA-AAATAATAACAT
1 AAAAAGGTTAGAAAAAATAAAAT
1158566 AAA
1 AAA
1158569 TAAAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.21
Consensus pattern (23 bp):
AAAAAGGTTAGAAAAAATAAAAT
Found at i:1159615 original size:39 final size:39
Alignment explanation
Indices: 1159562--1159678 Score: 164
Period size: 41 Copynumber: 3.0 Consensus size: 39
1159552 CGAACTCCAA
*
1159562 TTCGCAACAC-ATTTTCCAAATTCGCAATGCGATTTATT
1 TTCGCAACACGATTTTCCAAATTCGCAACGCGATTTATT
1159600 TTCGCAACACGATTTTCCAAATTCGCAACGCGATTTTATTT
1 TTCGCAACACGATTTTCCAAATTCGCAACGCGA-TTTA-TT
* * * *
1159641 TTTGCAACGCGAATTTCCAAATTCGTAACGCGATTTAT
1 TTCGCAACACGATTTTCCAAATTCGCAACGCGATTTAT
1159679 CTGATAAACT
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
38 10 0.14
39 22 0.31
40 8 0.11
41 31 0.44
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (39 bp):
TTCGCAACACGATTTTCCAAATTCGCAACGCGATTTATT
Found at i:1159786 original size:20 final size:21
Alignment explanation
Indices: 1159743--1159787 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1159733 CCCATGTTAT
1159743 TTTCGCAATGCGAACTTAAAG
1 TTTCGCAATGCGAACTTAAAG
1159764 TTTCGCAATGCGAACTT-AAG
1 TTTCGCAATGCGAACTTAAAG
1159784 TTTC
1 TTTC
1159788 ACAAACCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (21 bp):
TTTCGCAATGCGAACTTAAAG
Found at i:1160829 original size:19 final size:20
Alignment explanation
Indices: 1160783--1160837 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
1160773 GTGAATTTGG
1160783 AAATTCGCGTTGCGAAAAAT
1 AAATTCGCGTTGCGAAAAAT
1160803 AAATTCGCGTTGCGAAAAAT
1 AAATTCGCGTTGCGAAAAAT
1160823 AAA-TCGCGTTGCGAA
1 AAATTCGCGTTGCGAA
1160838 TTTGGAAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 12 0.34
20 23 0.66
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (20 bp):
AAATTCGCGTTGCGAAAAAT
Found at i:1161177 original size:21 final size:20
Alignment explanation
Indices: 1161142--1161181 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
1161132 AAAATTAACA
1161142 ATATAATAATAATAAGTAATT
1 ATATAATAATAATAA-TAATT
1161163 ATATAATAA-AGATAATAAT
1 ATATAATAATA-ATAATAAT
1161182 AACAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (20 bp):
ATATAATAATAATAATAATT
Found at i:1161594 original size:111 final size:111
Alignment explanation
Indices: 1161398--1161618 Score: 327
Period size: 111 Copynumber: 2.0 Consensus size: 111
1161388 AAGATGAATA
*
1161398 TTGCTGGTGAGCACAATTCCCTTCGTCGTGAAATTGAAACCGTGGATGACCCCTAAGTCGTGAAG
1 TTGCTGGTGAACACAATTCCCTTCGTCGTGAAATTGAAACCGTGGATGACCCCTAAGTCGTGAAG
*
1161463 TTGAGCCTTGACTTGAATATCCTTCATCGTGAAGTTGAAATCCAAG
66 TTGAGCCTTGAATTGAATATCCTTCATCGTGAAGTTGAAATCCAAG
* * * * * * *
1161509 TTGCTGGTGAACACGATTCCCTTCGTCGTGAAGTTGAAACTGTGGATGGCCCATTCA-TTGTGAA
1 TTGCTGGTGAACACAATTCCCTTCGTCGTGAAATTGAAACCGTGGATGACCC-CTAAGTCGTGAA
* *
1161573 GTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
65 GTTGAGCCTTGAATTGAATATCCTTCATCGTGAAGTTGAAATCCAA
1161619 TGTAAGTTGC
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
111 96 0.98
112 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (111 bp):
TTGCTGGTGAACACAATTCCCTTCGTCGTGAAATTGAAACCGTGGATGACCCCTAAGTCGTGAAG
TTGAGCCTTGAATTGAATATCCTTCATCGTGAAGTTGAAATCCAAG
Found at i:1162100 original size:43 final size:42
Alignment explanation
Indices: 1162052--1162198 Score: 107
Period size: 43 Copynumber: 3.2 Consensus size: 42
1162042 CTCATTCGTC
1162052 GTGAAGTTGAGCTTGTGTTGTCTTTGGTCCAATATCCTTCGCT
1 GTGAAGTTGAGCTTGTGTTGT-TTTGGTCCAATATCCTTCGCT
** * * * * * *
1162095 GTGAAGTTGAAATTGGGAAGTTG-TTTGTTAACAGTCGGTCGCCCCTTCACT
1 GTGAAGTTGAGCTT--G-TGTTGTTTTGGT-CCAAT--AT----CCTTCGCT
1162146 GTGAAGTTGAGCTTGTGTTGTTTTGAGTCCAATATCCTTCGCT
1 GTGAAGTTGAGCTTGTGTTGTTTTG-GTCCAATATCCTTCGCT
1162189 GTGAAGTTGA
1 GTGAAGTTGA
1162199 AATTGGCTCT
Statistics
Matches: 76, Mismatches: 16, Indels: 24
0.66 0.14 0.21
Matches are distributed among these distances:
43 29 0.38
44 5 0.07
45 4 0.05
46 4 0.05
47 2 0.03
48 4 0.05
49 8 0.11
50 1 0.01
51 19 0.25
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.38
Consensus pattern (42 bp):
GTGAAGTTGAGCTTGTGTTGTTTTGGTCCAATATCCTTCGCT
Found at i:1164364 original size:64 final size:62
Alignment explanation
Indices: 1164277--1164448 Score: 185
Period size: 57 Copynumber: 2.8 Consensus size: 62
1164267 TTTTAAAAAA
**
1164277 AAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAT
1 AAACATCGAATGCAATTCATGCATCGATGCAT-AGTAGTGCATCGATGCATCCCAGCAATAAT
**
1164340 GAAACATCGAATGCAATTGGTGCATCGATGC-----A-TGCATCGATGCATCCCAGCAATAAT
1 -AAACATCGAATGCAATTCATGCATCGATGCATAGTAGTGCATCGATGCATCCCAGCAATAAT
* ** * *
1164397 AATACATCGAATACCTTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 AA-ACATCGAATGCAATTCATGCATCGATGCAT-AGTAGTGCATCGATGCAT
1164449 ACCTTCATTA
Statistics
Matches: 90, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
56 2 0.02
57 45 0.50
58 1 0.01
63 1 0.01
64 41 0.46
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (62 bp):
AAACATCGAATGCAATTCATGCATCGATGCATAGTAGTGCATCGATGCATCCCAGCAATAAT
Found at i:1164377 original size:12 final size:12
Alignment explanation
Indices: 1164360--1164384 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1164350 ATGCAATTGG
1164360 TGCATCGATGCA
1 TGCATCGATGCA
1164372 TGCATCGATGCA
1 TGCATCGATGCA
1164384 T
1 T
1164385 CCCAGCAATA
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:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (12 bp):
TGCATCGATGCA
Found at i:1164783 original size:12 final size:12
Alignment explanation
Indices: 1164753--1164797 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
1164743 ATATATGTTC
1164753 ATGTGATATGAT
1 ATGTGATATGAT
1164765 A-GTGATATGAT
1 ATGTGATATGAT
*
1164776 ATGTGATATGAC
1 ATGTGATATGAT
*
1164788 CTGTGATATG
1 ATGTGATATG
1164798 TGTTGAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 11 0.37
12 19 0.63
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (12 bp):
ATGTGATATGAT
Found at i:1167045 original size:21 final size:21
Alignment explanation
Indices: 1167021--1167062 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1167011 TATGAGAAAT
*
1167021 TGTTTTAAAATAT-AAAAATGA
1 TGTTTCAAAAT-TGAAAAATGA
1167042 TGTTTCAAAATTGAAAAATGA
1 TGTTTCAAAATTGAAAAATGA
1167063 AAACAAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (21 bp):
TGTTTCAAAATTGAAAAATGA
Found at i:1170826 original size:21 final size:21
Alignment explanation
Indices: 1170789--1170849 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 21
1170779 TTTTGGTGCA
*
1170789 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
*
1170809 GAGGGAACCGATT-CCCCCTT
1 GAGGGAACCGATTCCCCCCAT
1170829 GAAGGGAACCGATTCCCCCCA
1 G-AGGGAACCGATTCCCCCCA
1170850 CAGTGGAATC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 17 0.49
21 13 0.37
22 5 0.14
ACGTcount: A:0.25, C:0.36, G:0.25, T:0.15
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:1170857 original size:21 final size:20
Alignment explanation
Indices: 1170810--1170869 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
1170800 TCCCCCCATG
*
1170810 AGGGAACCGATTCCCCCTTGA
1 AGGGAACCGATTCCCCC-TCA
1170831 AGGGAACCGATTCCCCC-CA
1 AGGGAACCGATTCCCCCTCA
* *
1170850 CAGTGGAATCGATACCCCCT
1 -AG-GGAACCGATTCCCCCT
1170870 GGGGTTCTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 1 0.03
20 2 0.06
21 30 0.91
ACGTcount: A:0.25, C:0.37, G:0.22, T:0.17
Consensus pattern (20 bp):
AGGGAACCGATTCCCCCTCA
Found at i:1170868 original size:42 final size:41
Alignment explanation
Indices: 1170790--1170869 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 41
1170780 TTTGGTGCAG
* * *
1170790 AGGGAATCGATCCCCCCATGAGGGAACCGATTCCCCCTTGA
1 AGGGAACCGATCCCCCCATCAGGGAACCGATACCCCCTTGA
*
1170831 AGGGAACCGATTCCCCCCA-CAGTGGAATCGATACCCCCT
1 AGGGAACCGA-TCCCCCCATCAG-GGAACCGATACCCCCT
1170870 GGGGTTCTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 11 0.33
42 22 0.67
ACGTcount: A:0.25, C:0.36, G:0.23, T:0.16
Consensus pattern (41 bp):
AGGGAACCGATCCCCCCATCAGGGAACCGATACCCCCTTGA
Found at i:1180563 original size:64 final size:64
Alignment explanation
Indices: 1180494--1180702 Score: 224
Period size: 64 Copynumber: 3.3 Consensus size: 64
1180484 CGATGCATTG
** **
1180494 GTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTCATGCATCGATGTATA
1 GTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATGCATCGATACATA
1180557 A
64 A
* **
1180558 GTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGCATCGATACATAA
1 GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCGATACATAA
* ** * * ** * * * *
1180622 GGAGTGCATCGATGCATCCCAGCAATAATAATACATCGAATACCTTTTATGCACCGATGCATCA
1 GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCGATACATAA
1180686 GTAGTGCATCGATGCAT
1 GTAGTGCATCGATGCAT
1180703 ACCTTCATTA
Statistics
Matches: 122, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
64 118 0.97
65 4 0.03
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (64 bp):
GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCGATACATAA
Found at i:1184662 original size:6 final size:6
Alignment explanation
Indices: 1184621--1184678 Score: 50
Period size: 6 Copynumber: 9.5 Consensus size: 6
1184611 AAAAGGTTAG
*
1184621 AAAATA AAAA-A AATAAT- AAAGTA AAAATGTTA AAAATA AAAATA AAAAT-
1 AAAATA AAAATA AA-AATA AAAATA AAAA---TA AAAATA AAAATA AAAATA
1184670 AAAATA AAA
1 AAAATA AAA
1184679 TAACATGAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
5 10 0.23
6 27 0.63
9 6 0.14
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:1184662 original size:32 final size:33
Alignment explanation
Indices: 1184610--1184678 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 33
1184600 AAAAGAATAA
*
1184610 AAAAAGGTTAGAAAATAAAAA-AAATAATAAAGT
1 AAAAAGGTTAGAAAATAAAAATAAA-AATAAAAT
*
1184643 AAAAATGTTA-AAAATAAAAATAAAAATAAAAT
1 AAAAAGGTTAGAAAATAAAAATAAAAATAAAAT
1184675 AAAA
1 AAAA
1184679 TAACATGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 21 0.64
33 12 0.36
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (33 bp):
AAAAAGGTTAGAAAATAAAAATAAAAATAAAAT
Found at i:1184700 original size:30 final size:30
Alignment explanation
Indices: 1184658--1184722 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
1184648 TGTTAAAAAT
1184658 AAAAATAAAAATAAA-ATAAAATAACATGAA
1 AAAAATAAAAATAAATAT-AAATAACATGAA
* * * *
1184688 GAAAATATAAATATATATATATAACATGAA
1 AAAAATAAAAATAAATATAAATAACATGAA
1184718 AAAAA
1 AAAAA
1184723 AGGTTTTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.22
Consensus pattern (30 bp):
AAAAATAAAAATAAATATAAATAACATGAA
Found at i:1186133 original size:20 final size:20
Alignment explanation
Indices: 1186096--1186156 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
1186086 GTATCGATCC
*
1186096 AAAATGAT-ATACCAGGTAAA
1 AAAATGATAAAACC-GGTAAA
**
1186116 AAAATGATAAAACCGGTATC
1 AAAATGATAAAACCGGTAAA
1186136 AAAATGATAAAACCGGTAAA
1 AAAATGATAAAACCGGTAAA
1186156 A
1 A
1186157 CGTTACCGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 31 0.89
21 4 0.11
ACGTcount: A:0.56, C:0.11, G:0.15, T:0.18
Consensus pattern (20 bp):
AAAATGATAAAACCGGTAAA
Found at i:1186196 original size:181 final size:182
Alignment explanation
Indices: 1185899--1186370 Score: 705
Period size: 181 Copynumber: 2.6 Consensus size: 182
1185889 GATCCAAATT
* * * * *
1185899 AAAAATGTGTCGATCCAAAATGATATAACAGGTAAAACTATGACAAAACCGATATTAAAATGATA
1 AAAAATGTATCGATCCAAAATGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * *
1185964 AAACCGGTAAAGCGCTACCGGATACATT-TAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* * *
1186028 GTGAATTTAAAAGATAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
131 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* *
1186080 AAAAATGTATCGATCCAAAATGATATACCAGGTAAAAAAATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAATGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
1186145 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
1186209 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* * * * *
1186261 AAAAATATATCAATCCACAACGATATAACAGGTAAAAATATGATAAAATCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAATGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1186326 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
1186371 TGTAAGTACG
Statistics
Matches: 263, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
181 249 0.95
182 14 0.05
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAATGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:1186314 original size:20 final size:19
Alignment explanation
Indices: 1186291--1186337 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1186281 CGATATAACA
*
1186291 GGTAAAAATATGATAAAATC
1 GGTAAAAA-ATGATAAAACC
*
1186311 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1186331 GGTAAAA
1 GGTAAAA
1186338 CGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1188581 original size:21 final size:21
Alignment explanation
Indices: 1188555--1188619 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1188545 AAGACAATCA
*
1188555 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
1188576 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
1188597 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1188618 AG
1 AG
1188620 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1188708 original size:33 final size:33
Alignment explanation
Indices: 1188653--1188718 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1188643 AAATAGATGG
*
1188653 AGTGGTGAAAGAAGTGGAGGTGTTGAGGAGTGA
1 AGTGGTGAAAGAAGTGGAGGTGTTAAGGAGTGA
* *
1188686 AGTGGTGAAAGAAGTTTG-GGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAG-TGGAGGTGTTAAGGAGTGA
1188719 TATTAAGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.47, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTGGAGGTGTTAAGGAGTGA
Found at i:1190538 original size:19 final size:19
Alignment explanation
Indices: 1190514--1190562 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1190504 AATGTAGGGT
1190514 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1190533 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1190552 TAATTTTGTAT
1 TAATTTTGTAT
1190563 GTGATATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1191159 original size:199 final size:200
Alignment explanation
Indices: 1190799--1191521 Score: 1241
Period size: 200 Copynumber: 3.6 Consensus size: 200
1190789 TATAATATGG
*
1190799 CAAACAGGGTGCAACCATAAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGA
1 CAAACAGGGTGCAACAAT-AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGA
* * *
1190864 AACCCAAAAGTATAATGTAATACGTAATTTTTCAATCTAATCGGTACAAGTATACCAGTTTTATG
65 AACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATG
1190929 AGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAAT
130 AGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAAT
1190994 GAATGT
195 GAATGT
* *
1191000 CAAACAGGGTGCAACAATAAAGTGTCGATCAATATAT-AAAAGTGTCGATCCGATAAACATCGAA
1 CAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAA
* *
1191064 ACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGA
66 ACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
* * *
1191129 GAGAATAAGTCTAACTAATGTATCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATG
131 GAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATG
*
1191194 AATGG
196 AATGT
1191199 CAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAA
1 CAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAA
* *
1191264 ACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGATACAAGTATACCGGTTTTATGA
66 ACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
*
1191329 GAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATG
131 GAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATG
1191394 AATGT
196 AATGT
* * *
1191399 CAAACAGGGTGCAACCATAAAGTGTCAATCCATATATAAAAAGTGCCGATCCCATAAACATCGAA
1 CAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAA
* * *
1191464 ACCCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTATAAGTATATCGGT
66 ACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGT
1191522 AATGAATGTG
Statistics
Matches: 492, Mismatches: 29, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
199 188 0.38
200 287 0.58
201 17 0.03
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (200 bp):
CAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAA
ACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
GAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATG
AATGT
Done.