Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008973.1 Hibiscus syriacus cultivar Beakdansim tig00112319_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: 2070395
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1577119 original size:113 final size:114
Alignment explanation
Indices: 1576966--1577339 Score: 574
Period size: 113 Copynumber: 3.3 Consensus size: 114
1576956 ATTTTCGAAA
* *
1576966 ATATATATAATATATAGTTTTTGAAAATATTTTGAAAATATATATAATATATAGTTTTTGAAAAC
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAG-TTTTGAAAAT
*
1577031 ATTTTGAAAACATATATATAATATATAGTTTTTGA-AACATTTTGAAAAC
65 ATTTTGAAAATATATATATAATATATAGTTTTTGACAACATTTTGAAAAC
*
1577080 ATATATATAATATATAG-TTTTGAAAACATTTTGAAAATATATATAATATATAGATTTGAAAATA
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAATA
* *
1577144 TTTTGAAAATGTATATATAATATTTAGTTTTTGACAACATTTTGAAAAC
66 TTTTGAAAATATATATATAATATATAGTTTTTGACAACATTTTGAAAAC
* * *
1577193 ATATATATAATATATAGTTTTT-AAAAGATTTTTAAAATATATATATAATATATAGTTTTAAAAA
1 ATATATATAATATATAGTTTTTGAAAACA-TTTTGAAA-ATATATATAATATATAGTTTTGAAAA
* * *
1577257 TATTTTGAAATTTTATATACATAATATATAGTTTTTGATAACATTTTGAAAAC
64 TATTTTGAAA--ATATATATATAATATATAGTTTTTGACAACATTTTGAAAAC
1577310 ATATATATAATATATAGTTTTTGAAAACAT
1 ATATATATAATATATAGTTTTTGAAAACAT
1577340 ATATATAATA
Statistics
Matches: 237, Mismatches: 16, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
112 40 0.17
113 71 0.30
114 28 0.12
115 34 0.14
117 59 0.25
118 5 0.02
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.44
Consensus pattern (114 bp):
ATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAATA
TTTTGAAAATATATATATAATATATAGTTTTTGACAACATTTTGAAAAC
Found at i:1577331 original size:28 final size:28
Alignment explanation
Indices: 1577300--1577394 Score: 174
Period size: 28 Copynumber: 3.4 Consensus size: 28
1577290 TTTGATAACA
*
1577300 TTTTGAAAACATATATATAATATATAGT
1 TTTTGAAAACATATATATAATATATTGT
1577328 TTTTGAAAACATATATATAATATATTGT
1 TTTTGAAAACATATATATAATATATTGT
1577356 TTTTGAAAACATATATATAATATATTG-
1 TTTTGAAAACATATATATAATATATTGT
1577383 TTTTGAAAACAT
1 TTTTGAAAACAT
1577395 TTTGAAAATA
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
27 12 0.18
28 54 0.82
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (28 bp):
TTTTGAAAACATATATATAATATATTGT
Found at i:1579963 original size:43 final size:43
Alignment explanation
Indices: 1579896--1579994 Score: 162
Period size: 43 Copynumber: 2.3 Consensus size: 43
1579886 AATCCCTCCA
* *
1579896 ACCAAGCACACCATAATGTGTAGGTTTCCCAGAACCATACATCC
1 ACCAA-CACACCATAATGTGTAGGTTCCCCAGAACCATACACCC
*
1579940 TCCAACACACCATAATGTGTAGGTTCCCCAGAACCATACACCC
1 ACCAACACACCATAATGTGTAGGTTCCCCAGAACCATACACCC
1579983 ACCAACACACCA
1 ACCAACACACCA
1579995 AGTAAGGCCT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 47 0.92
44 4 0.08
ACGTcount: A:0.35, C:0.36, G:0.11, T:0.17
Consensus pattern (43 bp):
ACCAACACACCATAATGTGTAGGTTCCCCAGAACCATACACCC
Found at i:1580140 original size:24 final size:24
Alignment explanation
Indices: 1580110--1580200 Score: 139
Period size: 24 Copynumber: 3.8 Consensus size: 24
1580100 AAACATAATT
1580110 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAAAATC
* *
1580134 CAGGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAAAATC
1580158 CATGTC-AGATATCATATCAAAATC
1 CATGTCAAG-TATCATATCAAAATC
*
1580182 CATGTCAAGTATCAGATCA
1 CATGTCAAGTATCATATCA
1580201 GAATTCAAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
23 2 0.03
24 56 0.93
25 2 0.03
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAAAATC
Found at i:1580181 original size:48 final size:48
Alignment explanation
Indices: 1580110--1580204 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
1580100 AAACATAATT
*
1580110 CATGTCAAGTATCATATCAAAATCCAGGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATC
*
1580158 CATGTC-AGATATCATATCAAAATCCATGTCAAGTATCAGATCAGAAT
1 CATGTCAAG-TATCATATCAAAATCCAGGTCAAGTATCAGATCAGAAT
1580205 TCAAATCGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 2 0.05
48 42 0.95
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (48 bp):
CATGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATC
Found at i:1582822 original size:13 final size:13
Alignment explanation
Indices: 1582806--1582851 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
1582796 GTTAACAGAC
1582806 CGGGTCGGGTTAA
1 CGGGTCGGGTTAA
*
1582819 CGGGTCGGGTAAA
1 CGGGTCGGGTTAA
1582832 CGGGTC-GGTT--
1 CGGGTCGGGTTAA
1582842 CGGGTCGGGT
1 CGGGTCGGGT
1582852 CGGGTTATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 6 0.20
11 3 0.10
12 3 0.10
13 18 0.60
ACGTcount: A:0.11, C:0.17, G:0.50, T:0.22
Consensus pattern (13 bp):
CGGGTCGGGTTAA
Found at i:1585058 original size:40 final size:40
Alignment explanation
Indices: 1585012--1585133 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
1585002 ACCGTAGTGC
1585012 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
1585052 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
1585092 TACACATAAGGTCGTGCCCACCATATACACCGAAATGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1585132 TA
1 TA
1585134 TAAACCTGCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1588125 original size:43 final size:43
Alignment explanation
Indices: 1588064--1588158 Score: 163
Period size: 43 Copynumber: 2.2 Consensus size: 43
1588054 CCTCCAACCG
* * *
1588064 AACACACCATAATGTGTAGGTTTCCCAGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCACAACCAAACACCCACC
1588107 AACACACCATAATGTGTAGGTTCCCCACAACCAAACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCACAACCAAACACCCACC
1588150 AACACACCA
1 AACACACCA
1588159 AGTAGGGCCC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.38, C:0.38, G:0.09, T:0.15
Consensus pattern (43 bp):
AACACACCATAATGTGTAGGTTCCCCACAACCAAACACCCACC
Found at i:1588287 original size:24 final size:24
Alignment explanation
Indices: 1588274--1588368 Score: 147
Period size: 24 Copynumber: 4.0 Consensus size: 24
1588264 AAACATAATT
* *
1588274 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCAGATCAGAATC
*
1588298 CAGGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
1588322 CATGTC-AGATATCAGATCAGAATC
1 CATGTCAAG-TATCAGATCAGAATC
1588346 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCAGATCAGAAT
1588369 TCAAATCGAA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
23 2 0.03
24 61 0.94
25 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (24 bp):
CATGTCAAGTATCAGATCAGAATC
Found at i:1588384 original size:48 final size:48
Alignment explanation
Indices: 1588284--1588391 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 48
1588274 CATGTCAAGT
* ** *
1588284 ATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCATGTCAGAT
1 ATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATCAGAA
* * *
1588332 ATCAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATC-GAAA
1 ATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATCAG-AA
1588380 ATCAGAT-AAAAT
1 ATCAGATCAAAAT
1588392 ATTCATGTGG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
47 5 0.10
48 46 0.90
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.24
Consensus pattern (48 bp):
ATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATCAGAA
Found at i:1590939 original size:13 final size:13
Alignment explanation
Indices: 1590921--1590973 Score: 76
Period size: 13 Copynumber: 4.3 Consensus size: 13
1590911 AACGGTCAAT
1590921 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1590934 GGTCAACAGGTCG
1 GGTCAACGGGTCG
1590947 GGT---CGGGTCG
1 GGTCAACGGGTCG
1590957 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1590970 GGTC
1 GGTC
1590974 GAGTTATGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 9 0.26
13 26 0.74
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1590955 original size:23 final size:23
Alignment explanation
Indices: 1590927--1590974 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
1590917 CAATGGTCAA
1590927 CGGGTCGGGTCAACAGGTCGGGT
1 CGGGTCGGGTCAACAGGTCGGGT
*
1590950 CGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCGGGTCAACAGGTCGGGT
1590973 CG
1 CG
1590975 AGTTATGACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.10, C:0.23, G:0.50, T:0.17
Consensus pattern (23 bp):
CGGGTCGGGTCAACAGGTCGGGT
Found at i:1609992 original size:22 final size:22
Alignment explanation
Indices: 1609966--1610056 Score: 119
Period size: 22 Copynumber: 4.0 Consensus size: 22
1609956 TGATAAATTA
1609966 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
1609988 TTTAAAATAAATCAATCCATACAAC
1 TTTAAAATAAATCAATCCAT---AT
**
1610013 TACAATAATAAATCAATCCATAT
1 TTTAA-AATAAATCAATCCATAT
1610036 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1610057 CTAATAAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
22 36 0.61
23 4 0.07
25 4 0.07
26 15 0.25
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1610062 original size:18 final size:19
Alignment explanation
Indices: 1610018--1610065 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
1610008 ACAACTACAA
*
1610018 TAATAAATCAATCCATATTT
1 TAATAAATCAATCCATA-TC
1610038 TAAAATAAATCAATCCATA-C
1 T--AATAAATCAATCCATATC
1610058 TAATAAAT
1 TAATAAAT
1610066 TATTTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 7 0.28
20 2 0.08
22 16 0.64
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAAATCAATCCATATC
Found at i:1610075 original size:32 final size:31
Alignment explanation
Indices: 1610036--1610277 Score: 181
Period size: 32 Copynumber: 8.7 Consensus size: 31
1610026 CAATCCATAT
1610036 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
1610068 TTTAAAATAAATCAAT---T-C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
1610090 TTTAAAATAAATAAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
1610122 TTTAAAATAAATCAATCCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
1610152 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
1610170 TTTAAAATAAATCAATCCATACTAATAAACTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
1610202 TTTAAAATAAATCAAT---T-C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
1610224 TTTAAAATAAATAAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
1610256 TTTAAAATAAATCAATCCATAC
1 TTTAAAATAAATCAATCCATAC
1610278 AACTACAATA
Statistics
Matches: 169, Mismatches: 5, Indels: 72
0.69 0.02 0.29
Matches are distributed among these distances:
20 1 0.01
22 44 0.26
23 3 0.02
24 4 0.02
25 3 0.02
26 21 0.12
28 7 0.04
29 2 0.01
30 3 0.02
31 4 0.02
32 77 0.46
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (31 bp):
TTTAAAATAAATCAATCCATACTAATAAATA
Found at i:1610093 original size:102 final size:102
Alignment explanation
Indices: 1609917--1610111 Score: 345
Period size: 102 Copynumber: 1.9 Consensus size: 102
1609907 AATTATTTAA
* * *
1609917 AATAAATCAATCTATATTTTAAAATAAATCATTCCATACTGATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
1609982 CCATATTTTAAAATAAATCAATCCATACAACTACAAT
66 CCATATTTTAAAATAAATAAATCCATACAACTACAAT
1610019 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
1610084 TCATATTTTAAAATAAATAAATCCATAC
66 CCATATTTTAAAATAAATAAATCCATAC
1610112 TAATAAATTA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 88 1.00
ACGTcount: A:0.51, C:0.14, G:0.01, T:0.34
Consensus pattern (102 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATATTTTAAAATAAATAAATCCATACAACTACAAT
Found at i:1610094 original size:22 final size:22
Alignment explanation
Indices: 1610068--1610110 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1610058 TAATAAATTA
* *
1610068 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATAAATCCATAT
1610090 TTTAAAATAAATAAATCCATA
1 TTTAAAATAAATAAATCCATA
1610111 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATAAATCCATAT
Found at i:1610127 original size:134 final size:134
Alignment explanation
Indices: 1609988--1610347 Score: 702
Period size: 134 Copynumber: 2.7 Consensus size: 134
1609978 CAATCCATAT
1609988 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
1610053 CATACTAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATAAATCCATACTAATAA
66 CATACTAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATAAATCCATACTAATAA
1610118 ATTA
131 ATTA
1610122 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
*
1610187 CATACTAATAAACTATTTAAAATAAATCAATTCATATTTTAAAATAAATAAATCCATACTAATAA
66 CATACTAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATAAATCCATACTAATAA
1610252 ATTA
131 ATTA
1610256 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
*
1610321 CATACTAATAAATTATTTTAAATAAAT
66 CATACTAATAAATTATTTAAAATAAAT
1610348 TATTTTAAAA
Statistics
Matches: 223, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 223 1.00
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (134 bp):
TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
CATACTAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATAAATCCATACTAATAA
ATTA
Found at i:1610160 original size:54 final size:54
Alignment explanation
Indices: 1609902--1610142 Score: 370
Period size: 54 Copynumber: 4.6 Consensus size: 54
1609892 ACAACTACAA
* *
1609902 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCATTCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
1609956 TGATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
1610010 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
1610058 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATAAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1610112 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
1610143 CAACTACAAT
Statistics
Matches: 170, Mismatches: 9, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
48 42 0.25
49 2 0.01
50 2 0.01
52 2 0.01
53 1 0.01
54 121 0.71
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:1610186 original size:156 final size:154
Alignment explanation
Indices: 1609902--1610190 Score: 413
Period size: 156 Copynumber: 1.9 Consensus size: 154
1609892 ACAACTACAA
* * *
1609902 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCATTCCATACTGATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATAAATCCATACTAATAAATTAT
* **
1609967 TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCC
66 TTAAAATAAATCAATCCATACTACAAAATAAATCAATCCAT--AACTACAATAATAAATCAATCC
1610032 ATATTTTAAAATAAATCAATCCATAC
129 ATATTTTAAAATAAATCAATCCATAC
1610058 TAATAAATTATTTAAAATAAATCAAT-TCATATTTTAAAATAAATAAATCCATACTAATAAATTA
1 TAATAAATTATTTAAAATAAATCAATCT-ATATTTTAAAATAAATAAATCCATACTAATAAATTA
* **
1610122 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCAT-ATTTTAA-AATAAATCAA
65 TTTAAAATAAATCAATCCAT---ACTACAA-AATAAATCAATCCATAACTACAATAATAAATCAA
1610185 TCCATA
126 TCCATA
1610191 CTAATAAACT
Statistics
Matches: 119, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
155 1 0.01
156 95 0.80
157 4 0.03
159 4 0.03
160 15 0.13
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (154 bp):
TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATAAATCCATACTAATAAATTAT
TTAAAATAAATCAATCCATACTACAAAATAAATCAATCCATAACTACAATAATAAATCAATCCAT
ATTTTAAAATAAATCAATCCATAC
Found at i:1610187 original size:80 final size:79
Alignment explanation
Indices: 1610073--1610240 Score: 246
Period size: 80 Copynumber: 2.1 Consensus size: 79
1610063 AATTATTTAA
*
1610073 AATAAATCAATTCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
1610138 CCATACAACTACAAT
66 CCATACAA-TAAAAT
* *
1610153 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAACTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAAT
* ***
1610218 TCATATTTTAAAAT
66 CCATACAATAAAAT
1610232 AAATAAATC
1 -AATAAATC
1610241 CATACTAATA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
79 5 0.06
80 74 0.94
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (79 bp):
AATAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAATAAAAT
Found at i:1610196 original size:18 final size:19
Alignment explanation
Indices: 1610152--1610198 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 19
1610142 ACAACTACAA
*
1610152 TAATAAATCAATCCATATTT
1 TAATAAATCAATCCATA-TC
1610172 TAAAATAAATCAATCCATA-C
1 T--AATAAATCAATCCATATC
1610192 TAATAAA
1 TAATAAA
1610199 CTATTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 6 0.25
20 2 0.08
22 16 0.67
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (19 bp):
TAATAAATCAATCCATATC
Found at i:1610228 original size:22 final size:22
Alignment explanation
Indices: 1610202--1610244 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1610192 TAATAAACTA
* *
1610202 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATAAATCCATAT
1610224 TTTAAAATAAATAAATCCATA
1 TTTAAAATAAATAAATCCATA
1610245 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATAAATCCATAT
Found at i:1610312 original size:22 final size:22
Alignment explanation
Indices: 1610287--1610382 Score: 84
Period size: 22 Copynumber: 4.2 Consensus size: 22
1610277 CAACTACAAT
1610287 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
**
1610309 AATAAATCAATCCATACTAATAA
1 AATAAATCAATCCATA-TTTTAA
* ** * **
1610332 ATTATTTTAAATAAATTATTTTAA
1 AATA-AATCAATCCA-TATTTTAA
*
1610356 AATAAATCAATCCATATTTTAT
1 AATAAATCAATCCATATTTTAA
1610378 AATAA
1 AATAA
1610383 TTTATTTTAA
Statistics
Matches: 54, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
22 28 0.52
23 12 0.22
24 12 0.22
25 2 0.04
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Found at i:1610347 original size:54 final size:54
Alignment explanation
Indices: 1609902--1610347 Score: 338
Period size: 54 Copynumber: 8.4 Consensus size: 54
1609892 ACAACTACAA
* * *
1609902 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCATTCCATAC
1 TAATAAATTATTTTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
1609956 TGATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
1610010 -AACTACA--A---T-AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * *
1610058 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATAAATCCATAC
1 TAATAAATTATTTTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * **
1610112 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTTAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** ** *
1610169 TTTTAAAATA-AATCAATCCATACTAATAAACTA-TTTAAAATAAATCAATTCATA-
1 TAATAAATTATTTTAAATAAAT-C-AATCCA-TATTTTAAAATAAATCAATCCATAC
** * ** ** **
1610223 TTTTAAAATA-AATAAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTTAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
*
1610278 -AACTACA--A---T-AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1610326 TAATAAATTATTTTAAATAAAT
1 TAATAAATTATTTTAAATAAAT
1610348 TATTTTAAAA
Statistics
Matches: 326, Mismatches: 39, Indels: 54
0.78 0.09 0.13
Matches are distributed among these distances:
48 72 0.22
49 6 0.02
50 7 0.02
51 1 0.00
52 1 0.00
53 4 0.01
54 191 0.59
55 6 0.02
56 6 0.02
57 12 0.04
58 19 0.06
59 1 0.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:1610360 original size:15 final size:15
Alignment explanation
Indices: 1610327--1610474 Score: 181
Period size: 15 Copynumber: 9.5 Consensus size: 15
1610317 AATCCATACT
1610327 AATAAATTATTTT-A
1 AATAAATTATTTTAA
1610341 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1610356 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
1610378 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
1610393 AATAAATTATTTTAT
1 AATAAATTATTTTAA
1610408 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1610423 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
1610438 AATAAATTATTTGAA
1 AATAAATTATTTTAA
1610453 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1610468 AATAAAT
1 AATAAAT
1610475 AAGCTTATTA
Statistics
Matches: 116, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
14 13 0.11
15 86 0.74
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.09
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1610369 original size:69 final size:67
Alignment explanation
Indices: 1610287--1610429 Score: 198
Period size: 67 Copynumber: 2.1 Consensus size: 67
1610277 CAACTACAAT
*
1610287 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTTA-AATAAATTAT
1 AATAAATCAATCCATATTTTAAAAT-AATCAAT-CATA-AAATAAATTATTTTATAATAAATTAT
1610351 TTTAA
63 TTTAA
* ** **
1610356 AATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAATTATTTTATAATAAATTATTTT
1 AATAAATCAATCCATATTTTAAAATAATCAATCATAAAATAAATTATTTTATAATAAATTATTTT
1610421 AA
66 AA
1610423 AATAAAT
1 AATAAAT
1610430 TATTTTATAA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
66 14 0.21
67 24 0.36
68 5 0.07
69 24 0.36
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (67 bp):
AATAAATCAATCCATATTTTAAAATAATCAATCATAAAATAAATTATTTTATAATAAATTATTTT
AA
Found at i:1610857 original size:16 final size:16
Alignment explanation
Indices: 1610836--1610869 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1610826 TCTAACGTCT
1610836 GCGCGTCTTCTTCTTG
1 GCGCGTCTTCTTCTTG
1610852 GCGCGTCTTCTTCTTG
1 GCGCGTCTTCTTCTTG
1610868 GC
1 GC
1610870 ACAGACGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.32, G:0.26, T:0.41
Consensus pattern (16 bp):
GCGCGTCTTCTTCTTG
Found at i:1611108 original size:31 final size:30
Alignment explanation
Indices: 1611023--1611110 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 30
1611013 TTTGATAATA
* *
1611023 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
1611054 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
1611085 TAATAAGTATTTTATAATTTTTTAAT
1 TAATAA-TATTTTATAATTTTTTAAT
1611111 CTTTATTGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 41 0.85
32 6 0.12
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:1611232 original size:28 final size:27
Alignment explanation
Indices: 1611180--1611232 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
1611170 GAAAAAATAT
*
1611180 ATTAAACTTAATAAAAAATATTATACA
1 ATTAAACTTAATAAAAAAAATTATACA
*
1611207 ATTAAACTTAGTAAAAAAAAATTATA
1 ATTAAACTTAAT-AAAAAAAATTATA
1611233 TAAAAAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (27 bp):
ATTAAACTTAATAAAAAAAATTATACA
Found at i:1611840 original size:31 final size:29
Alignment explanation
Indices: 1611798--1611883 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 29
1611788 TCAATAAAGT
1611798 TTAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAATTATAAAATA-TTATTAAATTTA
*
1611828 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAA-ATTATAAAA-TATTATTAAATTTA
* *
1611859 TCAAAATACTATAAAATAATTATTA
1 TTAAAA-ATTATAAAAT-ATTATTA
1611884 TATTATCGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
30 7 0.15
31 39 0.81
32 2 0.04
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (29 bp):
TTAAAAATTATAAAATATTATTAAATTTA
Found at i:1611859 original size:20 final size:20
Alignment explanation
Indices: 1611793--1611865 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 20
1611783 TTTCGTCAAT
1611793 AAAG-TTTA-AAAATTA-TA
1 AAAGATTTATAAAATTATTA
* * *
1611810 AAATACTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
1611831 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
1611850 ATAA-ATTTATCAAAAT
1 A-AAGATTTAT-AAAAT
1611866 ACTATAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
17 3 0.07
18 3 0.07
19 12 0.27
20 15 0.34
21 11 0.25
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:1623592 original size:20 final size:20
Alignment explanation
Indices: 1623567--1623621 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1623557 CACCCAGCAC
*
1623567 ATGGATTTAATTATATATGA
1 ATGGATTTAAATATATATGA
*
1623587 ATGGATTTAAATATATATAA
1 ATGGATTTAAATATATATGA
1623607 AT--ATTTAAA-ATATAT
1 ATGGATTTAAATATATAT
1623622 AATAATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 6 0.18
18 7 0.21
20 20 0.61
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (20 bp):
ATGGATTTAAATATATATGA
Found at i:1623621 original size:17 final size:17
Alignment explanation
Indices: 1623591--1623634 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
1623581 ATATGAATGG
1623591 ATTTAAATATATATAA-A
1 ATTTAAA-ATATATAATA
1623608 TATTTAAAATATATAATA
1 -ATTTAAAATATATAATA
1623626 ATTTAAAAT
1 ATTTAAAAT
1623635 TATCAAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTAAAATATATAATA
Found at i:1623714 original size:2 final size:2
Alignment explanation
Indices: 1623707--1623738 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1623697 TATTTATTTA
1623707 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
1623739 TCTATGGATT
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:1625414 original size:37 final size:40
Alignment explanation
Indices: 1625341--1625414 Score: 91
Period size: 37 Copynumber: 1.9 Consensus size: 40
1625331 TGAGTGGTTG
* **
1625341 TATTTATAAGGTATATATATTATCAATTAATCAAGAAAAT
1 TATTTATAAGATATATATATTATCAATTAAAAAAGAAAAT
*
1625381 TATTTATAA-ATAT-TATTTTAT-AATTAAAAAAGAA
1 TATTTATAAGATATATATATTATCAATTAAAAAAGAA
1625415 CTCATAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
37 11 0.37
38 7 0.23
39 3 0.10
40 9 0.30
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (40 bp):
TATTTATAAGATATATATATTATCAATTAAAAAAGAAAAT
Found at i:1628817 original size:20 final size:20
Alignment explanation
Indices: 1628792--1628839 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1628782 TTGACTAATT
*
1628792 GTTGATCGTCTTTGACCATC
1 GTTGATCGTCCTTGACCATC
1628812 GTTGATCGTCCTTGACCATC
1 GTTGATCGTCCTTGACCATC
*
1628832 ATTGATCG
1 GTTGATCG
1628840 ATTGTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.38
Consensus pattern (20 bp):
GTTGATCGTCCTTGACCATC
Found at i:1631624 original size:12 final size:12
Alignment explanation
Indices: 1631604--1631633 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1631594 TATTTTCGGA
1631604 GTTACTGTAGCG
1 GTTACTGTAGCG
*
1631616 GTTATTGTAGCG
1 GTTACTGTAGCG
1631628 GTTACT
1 GTTACT
1631634 ATAACAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.17, C:0.13, G:0.30, T:0.40
Consensus pattern (12 bp):
GTTACTGTAGCG
Found at i:1631967 original size:23 final size:23
Alignment explanation
Indices: 1631937--1631986 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1631927 CATGCTTTAT
*
1631937 GGTACATTTTGGTATTTGGTTAA
1 GGTACATTTTGGTAATTGGTTAA
1631960 GGTACATTTTGGTAATTGGTTAA
1 GGTACATTTTGGTAATTGGTTAA
1631983 GGTA
1 GGTA
1631987 TGAATGAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.04, G:0.28, T:0.44
Consensus pattern (23 bp):
GGTACATTTTGGTAATTGGTTAA
Found at i:1633080 original size:24 final size:24
Alignment explanation
Indices: 1633053--1633119 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 24
1633043 TACTTGAATT
*
1633053 CTAATTGATATAAATATTAAAATC
1 CTAATTGATATAAATAATAAAATC
* ** *
1633077 CTAAGTGATAGCAA-ACTAAAATC
1 CTAATTGATATAAATAATAAAATC
*
1633100 CTAATTAAT-TAAATAATAAA
1 CTAATTGATATAAATAATAAA
1633120 TCTCAAATGT
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
22 2 0.06
23 20 0.61
24 11 0.33
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.31
Consensus pattern (24 bp):
CTAATTGATATAAATAATAAAATC
Found at i:1634222 original size:17 final size:18
Alignment explanation
Indices: 1634189--1634222 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1634179 TCTACGCTTA
1634189 TTTTCAAAATCAAAATAG
1 TTTTCAAAATCAAAATAG
1634207 TTTTCAAAAT-AAAATA
1 TTTTCAAAATCAAAATA
1634223 TTGACTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (18 bp):
TTTTCAAAATCAAAATAG
Found at i:1640208 original size:17 final size:17
Alignment explanation
Indices: 1640186--1640220 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1640176 TTTCTTGGAG
1640186 TGATTTG-TGAAGTTTCT
1 TGATTTGTTGAA-TTTCT
1640203 TGATTTGTTGAATTTCT
1 TGATTTGTTGAATTTCT
1640220 T
1 T
1640221 TCTTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.17, C:0.06, G:0.20, T:0.57
Consensus pattern (17 bp):
TGATTTGTTGAATTTCT
Found at i:1649906 original size:24 final size:24
Alignment explanation
Indices: 1649860--1649914 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1649850 CATAAAATTC
*
1649860 TTTC-TTTTCTTTTCTTTTCAAGT
1 TTTCATTTTCTTTTATTTTCAAGT
1649883 TTTCATTTTCATTTTATTTT-AAGT
1 TTTCATTTTC-TTTTATTTTCAAGT
1649907 TTT-ATTTT
1 TTTCATTTT
1649915 GAAGATGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 9 0.31
24 12 0.41
25 8 0.28
ACGTcount: A:0.15, C:0.11, G:0.04, T:0.71
Consensus pattern (24 bp):
TTTCATTTTCTTTTATTTTCAAGT
Found at i:1652259 original size:21 final size:19
Alignment explanation
Indices: 1652211--1652261 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 19
1652201 TAGATGATTT
1652211 TAAATTATATTTTACTTAA
1 TAAATTATATTTTACTTAA
*
1652230 -AAA-TCTATTTTACTTAAA
1 TAAATTATATTTTACTT-AA
1652248 TAAATTATTATTTT
1 TAAATTA-TATTTT
1652262 TTGAAACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 11 0.42
18 5 0.19
19 3 0.12
20 1 0.04
21 6 0.23
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (19 bp):
TAAATTATATTTTACTTAA
Found at i:1669758 original size:27 final size:27
Alignment explanation
Indices: 1669720--1669774 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1669710 TTCAGCAACA
1669720 TTCTAGATTCATTCTAGAACATTTACT
1 TTCTAGATTCATTCTAGAACATTTACT
1669747 TTCTAGATTCATTCTAGAACATTTACT
1 TTCTAGATTCATTCTAGAACATTTACT
1669774 T
1 T
1669775 CAATATTCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.45
Consensus pattern (27 bp):
TTCTAGATTCATTCTAGAACATTTACT
Found at i:1673430 original size:22 final size:22
Alignment explanation
Indices: 1673400--1673540 Score: 154
Period size: 22 Copynumber: 6.8 Consensus size: 22
1673390 GAGGGTTTAT
1673400 AGTGGTCCTTCGGGACATATCC
1 AGTGGTCCTTCGGGACATATCC
* * *
1673422 AATGGTCCTTTGGGACGTATCC
1 AGTGGTCCTTCGGGACATATCC
*
1673444 AGTGGTCCTTCGGGACGTATCC
1 AGTGGTCCTTCGGGACATATCC
*
1673466 AGTGGTTCTTCGGGACATATCC
1 AGTGGTCCTTCGGGACATATCC
* *
1673488 AGTGGTCTTTCAGGAC--AT--
1 AGTGGTCCTTCGGGACATATCC
*
1673506 AGTGGTCCTTAGGGACATA---
1 AGTGGTCCTTCGGGACATATCC
1673525 A-TGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
1673541 AATATTCACT
Statistics
Matches: 103, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
18 27 0.26
19 1 0.01
20 3 0.03
22 72 0.70
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACATATCC
Found at i:1673511 original size:18 final size:18
Alignment explanation
Indices: 1673488--1673540 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
1673478 GGACATATCC
*
1673488 AGTGGTCTTTCAGGACAT
1 AGTGGTCCTTCAGGACAT
1673506 AGTGGTCCTT-AGGGACAT
1 AGTGGTCCTTCA-GGACAT
* *
1673524 AATGGTCCTTCGGGACA
1 AGTGGTCCTTCAGGACA
1673541 AATATTCACT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 1 0.03
18 29 0.97
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCAGGACAT
Found at i:1680369 original size:22 final size:22
Alignment explanation
Indices: 1680341--1680461 Score: 151
Period size: 22 Copynumber: 5.7 Consensus size: 22
1680331 GAGGGTTTAT
1680341 AGTGGTCCTTCGGGACATATCC
1 AGTGGTCCTTCGGGACATATCC
* *
1680363 AGTGGTCCTTCGGGACGTATCT
1 AGTGGTCCTTCGGGACATATCC
* *
1680385 AGTGGTCCTTTGGGATATATCC
1 AGTGGTCCTTCGGGACATATCC
*
1680407 AGTGGTCCTTCAGG--ATAT--
1 AGTGGTCCTTCGGGACATATCC
1680425 AGTGGTCCTTCGGGACATATCC
1 AGTGGTCCTTCGGGACATATCC
* *
1680447 AATGGTCCTTAGGGA
1 AGTGGTCCTTCGGGA
1680462 TGTAATGGTC
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
18 13 0.15
20 8 0.10
22 63 0.75
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACATATCC
Found at i:1680405 original size:44 final size:40
Alignment explanation
Indices: 1680338--1680481 Score: 189
Period size: 40 Copynumber: 3.5 Consensus size: 40
1680328 GTCGAGGGTT
1680338 TATAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGA
1 TATAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGA
* * *
1680378 CGTATCTAGTGGTCCTTTGGGATATATCCAGTGGTCCTTCAGGA
1 --TA--TAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGA
* *
1680422 TATAGTGGTCCTTCGGGACATATCCAATGGTCCTTAGGGA
1 TATAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGA
* *
1680462 TGTAATGGTCCTTCGGGACA
1 TATAGTGGTCCTTCGGGACA
1680482 AATATTCACC
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
40 51 0.57
42 4 0.04
44 35 0.39
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.31
Consensus pattern (40 bp):
TATAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGA
Found at i:1683401 original size:18 final size:18
Alignment explanation
Indices: 1683378--1683412 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1683368 CTGGTAATCT
*
1683378 GGTGTAACAGAATACAAA
1 GGTGTAACAAAATACAAA
1683396 GGTGTAACAAAATACAA
1 GGTGTAACAAAATACAA
1683413 CAAACTAACT
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:0.51, C:0.11, G:0.20, T:0.17
Consensus pattern (18 bp):
GGTGTAACAAAATACAAA
Found at i:1683516 original size:27 final size:27
Alignment explanation
Indices: 1683478--1683532 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1683468 TTCAGCAGCA
1683478 TTCTAGATTCATTCTAGAACATTTACT
1 TTCTAGATTCATTCTAGAACATTTACT
*
1683505 TTCTAGATTCATTCTTGAACATTTACT
1 TTCTAGATTCATTCTAGAACATTTACT
1683532 T
1 T
1683533 CAATAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.47
Consensus pattern (27 bp):
TTCTAGATTCATTCTAGAACATTTACT
Found at i:1689099 original size:29 final size:29
Alignment explanation
Indices: 1688978--1689100 Score: 117
Period size: 29 Copynumber: 4.3 Consensus size: 29
1688968 ATTAAAGGGT
* * *
1688978 AAACTTTTTTATAAATTATAATAAAGGAA
1 AAACCTTTTTGTAAATTATAATAAAGGAC
* * *
1689007 AAACTTTTTTGTAAATTACAATAAA--AT
1 AAACCTTTTTGTAAATTATAATAAAGGAC
* *
1689034 AAACC-TATTGTAAATTAAAATAAAGGAC
1 AAACCTTTTTGTAAATTATAATAAAGGAC
** * *
1689062 AAATATTTTTGCAAATTATAACAAAGGAC
1 AAACCTTTTTGTAAATTATAATAAAGGAC
1689091 AAACCTTTTT
1 AAACCTTTTT
1689101 TATGCATCAT
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
26 17 0.22
27 5 0.07
28 4 0.05
29 50 0.66
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (29 bp):
AAACCTTTTTGTAAATTATAATAAAGGAC
Found at i:1689266 original size:30 final size:31
Alignment explanation
Indices: 1689206--1689268 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
1689196 TCGTCCGTCG
*
1689206 TTATTATATTATATAATATTACAAATTATAT
1 TTATTATATTATATAATATTACAAACTATAT
**
1689237 TTATATATATTATAT-AT-TTACATGCTATAT
1 TTAT-TATATTATATAATATTACAAACTATAT
1689267 TT
1 TT
1689269 TCAGGCCCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 12 0.43
31 6 0.21
32 10 0.36
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.54
Consensus pattern (31 bp):
TTATTATATTATATAATATTACAAACTATAT
Found at i:1690653 original size:13 final size:12
Alignment explanation
Indices: 1690618--1690656 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
1690608 TAAGTTTTAG
1690618 TATTTTTTTATT
1 TATTTTTTTATT
*
1690630 TGATTTGTTTATT
1 T-ATTTTTTTATT
1690643 TATTTATTTTATT
1 TATTT-TTTTATT
1690656 T
1 T
1690657 TTACCTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (12 bp):
TATTTTTTTATT
Found at i:1691608 original size:95 final size:96
Alignment explanation
Indices: 1691401--1691659 Score: 317
Period size: 95 Copynumber: 2.7 Consensus size: 96
1691391 GGCTAACTAG
* * * * *
1691401 ATCCATAAAGCTGGGGCGTTTAACCAATCGTTCTAGAGGGACAGCTCAA--TATCATTGTATAGA
1 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCT-TTATTGTATA-T
* *
1691464 TATTATACACTTTTATCAGGCTACCTGAATATT
64 TATAATACACCTTTATCAGGCTACCTGAATATT
* *
1691497 ATCCATAAAGTTGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
* ** *
1691562 TAAT-CGCCTTTATCAGGCTAGTTGAATCTT
66 TAATACACCTTTATCAGGCTACCTGAATATT
* * * *
1691592 ATCCATAAAGCCGGGGCGTTTAACTAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTGTATAT
1 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-T
1691657 ATA
65 ATA
1691660 TAATTATAAT
Statistics
Matches: 141, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
95 78 0.55
96 53 0.38
97 9 0.06
98 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (96 bp):
ATCCATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATACACCTTTATCAGGCTACCTGAATATT
Found at i:1692368 original size:84 final size:84
Alignment explanation
Indices: 1692211--1692647 Score: 395
Period size: 84 Copynumber: 5.3 Consensus size: 84
1692201 ATTTTATTGA
* * * * * * *
1692211 CAGATAGCCCTTCTTGCCTTGAGCTATGTTGTAAATTTGATTTGCCTCTGAGCTGAGTGTAATTG
1 CAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAA--TGATATGCCTTTGAGCTGAGCGTAGTAG
1692276 AACTCGAAGGTCTTTGGTTGG
64 AACTCGAAGGTCTTTGGTTGG
* * * * * * *
1692297 CAGATAGCCCTTCTTGACTTAAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATATGCCTTTGAGCTGAGCGTAGTAGAA
*
1692362 CTCGAAGGTATTT-GTTGG
66 CTCGAAGGTCTTTGGTTGG
* * ** * * * * *
1692380 TAGATAACCCTTCTAGCCTTGATTTATGTTGCAATTGATATGCCTTGGAGCTGAGCGTAGTATAA
1 CAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATATGCCTTTGAGCTGAGCGTAGTAGAA
*
1692445 CTCGAAGGTCTTTGGTTTG
66 CTCGAAGGTCTTTGGTTGG
* * * * * *
1692464 CAGATAACCCTTCTAGCCTTGAG-T-T-ATGT---TGATGTGCCTGTGAACTAAGCGTAGTAGAA
1 CAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATATGCCTTTGAGCTGAGCGTAGTAGAA
*
1692523 CTCGAAGGTCTTT-TTGTGG
66 CTCGAAGGTCTTTGGT-TGG
* * * * * ** * * *
1692542 TAGATAGCCCTTCTAGCCTTGGGCCATACTGCAAATGATATAACTTAGAGTTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATATGCCTTTGAGCTGAGCGTAGTAGAA
1692607 CTCGAAGGTCTTTGGTTGG
66 CTCGAAGGTCTTTGGTTGG
**
1692626 CAGATAAACCTTCTAGCCTTGA
1 CAGATAGCCCTTCTAGCCTTGA
1692648 AGGGGCGACT
Statistics
Matches: 285, Mismatches: 57, Indels: 20
0.79 0.16 0.06
Matches are distributed among these distances:
77 1 0.00
78 59 0.21
80 1 0.00
81 4 0.01
82 1 0.00
83 67 0.24
84 119 0.42
85 1 0.00
86 32 0.11
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (84 bp):
CAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATATGCCTTTGAGCTGAGCGTAGTAGAA
CTCGAAGGTCTTTGGTTGG
Found at i:1692602 original size:162 final size:165
Alignment explanation
Indices: 1692260--1692647 Score: 433
Period size: 162 Copynumber: 2.4 Consensus size: 165
1692250 ATTTGCCTCT
* * * * * * *
1692260 GAGCTGAGTGTAATTGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTTGACTTAAGCTATG
1 GAGCTGAGCGTAGTAGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGCTATG
* * * * * *
1692325 CTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTGTTGGTAGATAACCC
66 ATGT--ATGATGTGCCTGTGAACTAAGCGTAATAGAACTCGAAGGTATTTGTTGGTAGATAACCC
*** ** * ** *
1692390 TTCTAGCCTTGATTTATGTTGCAATTGATATGCCTTG
129 TTCTAGCCTTGAGCCATACTGCAAATGATATAACTTA
* *
1692427 GAGCTGAGCGTAGTATAACTCGAAGGTCTTTGGTTTGCAGATAACCCTTCTAGCCTTGAG-T-T-
1 GAGCTGAGCGTAGTAGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGCTATG
* * * *
1692489 ATGT-TGATGTGCCTGTGAACTAAGCGTAGTAGAACTCGAAGGTCTTTTTGTGGTAGATAGCCCT
66 ATGTATGATGTGCCTGTGAACTAAGCGTAATAGAACTCGAAGGTATTTGT-TGGTAGATAACCCT
*
1692553 TCTAGCCTTGGGCCATACTGCAAATGATATAACTTA
130 TCTAGCCTTGAGCCATACTGCAAATGATATAACTTA
* * *
1692589 GAGTTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAAACCTTCTAGCCTTGA
1 GAGCTGAGCGTAGTAGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGA
1692648 AGGGGCGACT
Statistics
Matches: 186, Mismatches: 34, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
161 37 0.20
162 93 0.50
164 3 0.02
165 1 0.01
166 1 0.01
167 51 0.27
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (165 bp):
GAGCTGAGCGTAGTAGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGCTATG
ATGTATGATGTGCCTGTGAACTAAGCGTAATAGAACTCGAAGGTATTTGTTGGTAGATAACCCTT
CTAGCCTTGAGCCATACTGCAAATGATATAACTTA
Found at i:1693149 original size:116 final size:116
Alignment explanation
Indices: 1692945--1693508 Score: 781
Period size: 116 Copynumber: 4.9 Consensus size: 116
1692935 TTATCTTTAG
* * * * *
1692945 ATTGGATTTCAACTTCATGACGAAGGATATTCAATTCAAGGCTGAACTTCACAACGTAGGGGCCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGGCCA
* *
1693010 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAATATTC
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTC
* *
1693061 ATTGGATTTCAACTTCATGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATG-AGTGGGTC
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAG-GGGCC
* * *
1693125 ATCCACGGTTTTAACTTCACGACGAAGGGAATCATGCTCACTAGCAACATTC
65 ATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTC
* * * ** *
1693177 ATTGGATTTCCACTTCACGATGAATGATATGTAATTCAAGGCTCAACTTCACAATGAAGGGGTCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGGCCA
* * *
1693242 TCTACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACAAGCAAGATTC
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTC
** * * ** *
1693293 ATTGGATTTCAACTTCAAAACGAATGAAATCCAATTCAAGGCTCAACTTCACAGCGAAGGTGCCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGGCCA
* * * *
1693358 TCCATGGTTTTAACTTCACGACGAAGGGAACCATGCTCACCAGCAACATTC
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTC
* *
1693409 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCCCAACTTCACAATGAAAGGGCCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGGCCA
*
1693474 TCCATGGTTTCAACTTCACGACGAA-GGATATCGTG
66 TCCACGGTTTCAACTTCACGACGAAGGGA-ATCGTG
1693509 TTCATTTACA
Statistics
Matches: 395, Mismatches: 50, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
115 5 0.01
116 388 0.98
117 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (116 bp):
ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGGCCA
TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTC
Found at i:1693660 original size:84 final size:84
Alignment explanation
Indices: 1693510--1694053 Score: 486
Period size: 84 Copynumber: 6.5 Consensus size: 84
1693500 GATATCGTGT
* * * * * * ** * **
1693510 TCATTTACAACATAGCTCAAGGCAAGAAAGGTTATTTTCCAAAAAAAAGGCCTTTAAGTTCGACT
1 TCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCC-AACCAAAGACCTTCGAGTTCGACT
*
1693575 ACGCTCAGCTCTAAGGCACA
65 ACGCTCAGCTCCAAGGCACA
* * * * *
1693595 TTATTTACAGTATAACTCAAGGCTAGAAGGTTTATCTACCAACCAAAGACCTTCGATTTCGACTA
1 TCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* *
1693660 CGCTCAGCTCTAAGGCATA
66 CGCTCAGCTCCAAGGCACA
* ** * * * * *
1693679 TCATTATTA-A-TATGGCCCAAGGCTAGAAGGGCTATCTACC-ACCAAAAGACCTTCAAGTTTGA
1 TCA-T-TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGA
* *
1693741 CTACGCTCATCTCCCAGGCACA
63 CTACGCTCAGCTCCAAGGCACA
* * **
1693763 TCATTTGCAGCATAACTCAAGGTTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTATACTA
1 TCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
*
1693828 CGCTCAGCTCCAAGGCATA
66 CGCTCAGCTCCAAGGCACA
* * ** * * * *
1693847 TCAATTGCAATATAAATCAAGGCTAGAAGGGTTATCTGCTAA-AAAAGACCTTCGAGTTCGATTA
1 TCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* *
1693911 CACTCAGCTCAAAGGCACA
66 CGCTCAGCTCCAAGGCACA
* * * * * * *
1693930 TCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGATTA
1 TCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* *
1693995 CACTCAGCT-CAGAGGCAAA
66 CGCTCAGCTCCA-AGGCACA
* * *
1694014 TCAAATTTACAGCATAGCTCAAGGCAAGAAGGATTATCTG
1 TC--ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG
1694054 TCAATTAAAT
Statistics
Matches: 375, Mismatches: 74, Indels: 19
0.80 0.16 0.04
Matches are distributed among these distances:
82 2 0.01
83 72 0.19
84 231 0.62
85 36 0.10
86 34 0.09
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (84 bp):
TCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACA
Found at i:1695840 original size:13 final size:14
Alignment explanation
Indices: 1695824--1695865 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 14
1695814 TCCCTTTGAT
1695824 TTTTTATTT-TTTA
1 TTTTTATTTATTTA
1695837 TTTTTATTTATTTA
1 TTTTTATTTATTTA
*
1695851 TTTAATATTTATTTA
1 TTT-TTATTTATTTA
1695866 ATATTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 9 0.35
14 7 0.27
15 10 0.38
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTATTTATTTA
Found at i:1695859 original size:21 final size:20
Alignment explanation
Indices: 1695822--1695860 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1695812 TTTCCCTTTG
**
1695822 ATTTTTTATTTTTTATTTTT
1 ATTTTTTATTTAATATTTTT
1695842 ATTTATTTATTTAATATTT
1 ATTT-TTTATTTAATATTT
1695861 ATTTAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (20 bp):
ATTTTTTATTTAATATTTTT
Found at i:1695861 original size:11 final size:11
Alignment explanation
Indices: 1695845--1695875 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1695835 TATTTTTATT
1695845 TATTTATTTAA
1 TATTTATTTAA
1695856 TATTTATTTAA
1 TATTTATTTAA
1695867 TATTT-TTTA
1 TATTTATTTA
1695876 TCTAACATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:1695875 original size:25 final size:25
Alignment explanation
Indices: 1695833--1695885 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1695823 TTTTTTATTT
* * *
1695833 TTTATTTTTATTTATTTATTTAATA
1 TTTATTTATATTTATTTATCTAACA
1695858 TTTATTTAATATTT-TTTATCTAACA
1 TTTATTT-ATATTTATTTATCTAACA
1695883 TTT
1 TTT
1695886 TCTACTCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTATTTATATTTATTTATCTAACA
Found at i:1697488 original size:26 final size:26
Alignment explanation
Indices: 1697459--1697520 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
1697449 AAACCCTAGC
*
1697459 TGGAACGGTTCGGGTGAAGGCACAAG
1 TGGACCGGTTCGGGTGAAGGCACAAG
* * *
1697485 TGGACCGGCTCGGGTGGAGGCCCAAG
1 TGGACCGGTTCGGGTGAAGGCACAAG
1697511 TGGACCGGTT
1 TGGACCGGTT
1697521 TGGTTCACAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.19, C:0.21, G:0.44, T:0.16
Consensus pattern (26 bp):
TGGACCGGTTCGGGTGAAGGCACAAG
Found at i:1697896 original size:2 final size:2
Alignment explanation
Indices: 1697856--1697880 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1697846 AAATGTAAAA
1697856 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1697881 ATTGTAATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1698883 original size:84 final size:84
Alignment explanation
Indices: 1698406--1698884 Score: 552
Period size: 84 Copynumber: 5.7 Consensus size: 84
1698396 GAGCTGAGTA
* * * * * *
1698406 GAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTT-AATCTATTCTGCAAATAATATG
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGT-TATGCTGCAAATGATATG
* * *
1698470 CCTTTGAGCTGAGTGTAATC
65 CCTTAGAGCTGAGCGTAGTC
* * * * * *
1698490 GTACTCGAAGGTCTTT-GTTGGCATATAACCCTTATAGCCTTGATTTATGCTGCAATTAATATGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGC
*
1698554 CTTTGAGCTGAGCGTAGTC
66 CTTAGAGCTGAGCGTAGTC
* * * * *
1698573 GAACTCGAAGGTCATTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATTATGTGT
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGC
**
1698638 CTGGGAGCTGAGCGTAGTC
66 CTTAGAGCTGAGCGTAGTC
* * * *
1698657 GAACTCGAAGGTCTTTTGG-TGGTAGATAGCCCTTCTAGCCTT-AGGTCATACTGCAAATGATAT
1 GAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGCCTTGA-GTTATGCTGCAAATGATAT
*
1698720 GCCTTAGAGCTGAGCTTAGTC
64 GCCTTAGAGCTGAGCGTAGTC
* *
1698741 GAACTCGAAGGTCTTTGGTTGGCAGATAAACCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGC
1698806 CTTAGAGCTGAGCGTAGTC
66 CTTAGAGCTGAGCGTAGTC
* ** * * * * * *
1698825 GAACTTGAAGGTCTTTTTTTGGCAAATAGCCCTTCTTGCCTTAAGCTATGTTGCAAATGA
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGA
1698885 ACAGGATATT
Statistics
Matches: 337, Mismatches: 52, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
83 74 0.22
84 258 0.77
85 5 0.01
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (84 bp):
GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGC
CTTAGAGCTGAGCGTAGTC
Found at i:1699103 original size:116 final size:116
Alignment explanation
Indices: 1698888--1699383 Score: 717
Period size: 116 Copynumber: 4.3 Consensus size: 116
1698878 CAAATGAACA
* *
1698888 GGATATTCTTCGTCGTGAAGTTGAAATCCAATGAATGTTGCTGGTGAGCACGATTCCCTTCGTCG
1 GGATATCCTTCGTCGTGAAGTTGAAATCCAATGAATGTTGCTGGTGAGCACGATTCCCTTCATCG
* * *
1698953 TGAAGTTGAAACCATGGATGGCCCCTTCGCTGTGAAGTTGAGCCTTGAATT
66 TGAAGTTGAAACCGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGAATT
* * * * * *
1699004 GGATTTCATTCGTTGTTAAGTTGAAATCCAAAGAATGTTGTTGGTGAGCACGATTCCCTTCATCG
1 GGATATCCTTCGTCGTGAAGTTGAAATCCAATGAATGTTGCTGGTGAGCACGATTCCCTTCATCG
* *
1699069 TGAAGTTGAAACCGTAGATGACCCCTTCATTGTGAAGTTGAGCCTTGAATT
66 TGAAGTTGAAACCGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGAATT
* * * * * *
1699120 AGATATCCTTCATCGTGAAGTGGAAATCCAATGAATGTTGCTAGTGAGCATGATTCCCTT-AGCC
1 GGATATCCTTCGTCGTGAAGTTGAAATCCAATGAATGTTGCTGGTGAGCACGATTCCCTTCA-TC
* *
1699184 GTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAACCTTGAATT
65 GTGAAGTTGAAACCGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGAATT
* * * *
1699236 GGATATCCTTCGTCATGAAGTTAAAATCCAATGAATGTTACTGGTGAGCACGATTCCCTTCGTCG
1 GGATATCCTTCGTCGTGAAGTTGAAATCCAATGAATGTTGCTGGTGAGCACGATTCCCTTCATCG
*
1699301 TGAAGTTGAAACCGTGGATGGCCCCTAT-GTTGTGAAGTTGAGCCTTGAATT
66 TGAAGTTGAAACCGTGGATGACCCCT-TCGTTGTGAAGTTGAGCCTTGAATT
*
1699352 GGATATCCTTCGTCATGAAGTTGAAATCCAAT
1 GGATATCCTTCGTCGTGAAGTTGAAATCCAAT
1699384 CTAAAGATAA
Statistics
Matches: 334, Mismatches: 43, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
115 1 0.00
116 332 0.99
117 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (116 bp):
GGATATCCTTCGTCGTGAAGTTGAAATCCAATGAATGTTGCTGGTGAGCACGATTCCCTTCATCG
TGAAGTTGAAACCGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGAATT
Found at i:1700829 original size:95 final size:96
Alignment explanation
Indices: 1700624--1700882 Score: 265
Period size: 95 Copynumber: 2.7 Consensus size: 96
1700614 GGCTAACTGG
* * * * * * * *
1700624 ATCCAT-AAATCTGAGGCGTTTAACCAATTTCTCTAGAGGGACAACTCAA--TATCATTGTATAG
1 ATCCATAAAATC-GGGGAGTTTAACTAATTGCTCTAGAGGGACAACACAAGCT-TTAATGTATAT
* * * *
1700686 ATATTATACACTTTTATCAGGCTACCTGAATATT
64 ATATAAT-CGCCTTTATCAAGCTACCTGAATATT
* * *
1700720 ATCCATAAAGTCGGGGAGTTTAACTAATTGCTCTAGAGGGACAACATAAGCTTTATTGTATAT-T
1 ATCCATAAAATCGGGGAGTTTAACTAATTGCTCTAGAGGGACAACACAAGCTTTAATGTATATAT
* *
1700784 ATAATCGCCTTTATCAAGCTAGCTGAATCTT
66 ATAATCGCCTTTATCAAGCTACCTGAATATT
* * * * *
1700815 ATCCATAAAATCGGGGCGTTTAACTAATTGTTTTAGAGGGACAACCCAAGGTTTAATGTATATAT
1 ATCCATAAAATCGGGGAGTTTAACTAATTGCTCTAGAGGGACAACACAAGCTTTAATGTATATAT
1700880 ATA
66 ATA
1700883 TAATTATAAT
Statistics
Matches: 136, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
95 76 0.56
96 46 0.34
97 13 0.10
98 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (96 bp):
ATCCATAAAATCGGGGAGTTTAACTAATTGCTCTAGAGGGACAACACAAGCTTTAATGTATATAT
ATAATCGCCTTTATCAAGCTACCTGAATATT
Found at i:1701975 original size:116 final size:116
Alignment explanation
Indices: 1701771--1702062 Score: 442
Period size: 116 Copynumber: 2.5 Consensus size: 116
1701761 ATGCAAAAAT
* * * * * *
1701771 GCTCAATTTCACAATGAAGGGGTCATCTACGGTTTCAACTTCATGATGAAGAGAATCGTGCTTAC
1 GCTCAACTTCACAATGAAGGGGTCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCAC
* * *
1701836 CAGCAACATTCATTAGATTTCAACTTCATAATGAATGAAATCCAATTCAAG
66 CAGCAACATTCATTAGATTTCAACTTCACAACGAAGGAAATCCAATTCAAG
* *
1701887 GCTCAACTTCACAGTGAAGGGGTCATCCACGGTTTCAACTTCACGACGAAGGGAATCTTGCTCAC
1 GCTCAACTTCACAATGAAGGGGTCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCAC
* * *
1701952 CAGCAACATTCATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAG
66 CAGCAACATTCATTAGATTTCAACTTCACAACGAAGGAAATCCAATTCAAG
1702003 GCTCAACTTCACAATGAAGGGGTCATCCACGGTTTCAACTTCACGACGAA-GGATATCGTG
1 GCTCAACTTCACAATGAAGGGGTCATCCACGGTTTCAACTTCACGACGAAGGGA-ATCGTG
1702063 TTCATTTGCA
Statistics
Matches: 159, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
115 3 0.02
116 156 0.98
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (116 bp):
GCTCAACTTCACAATGAAGGGGTCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCAC
CAGCAACATTCATTAGATTTCAACTTCACAACGAAGGAAATCCAATTCAAG
Found at i:1702205 original size:84 final size:83
Alignment explanation
Indices: 1702080--1702606 Score: 493
Period size: 84 Copynumber: 6.3 Consensus size: 83
1702070 GCAACATAGA
* * * * * * * *
1702080 TCAAGGCAAGAAGGGCTATTTGCCAAAAAAAGACCTTCAAGTTTGACTACACTCTGCTCTAAGGC
1 TCAAGGCTAGAAGGGTTATCTGCC-AACAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGC
*
1702145 ACATCATTTGCAATATAAC
65 ACATCATTTGCAGTATAAC
* * * * * *
1702164 TCAAGGCTATAAGGTTTATCTTCCAGACAAAGACCTTCAAGTTTGACTACGCTCAACTCTAAGGC
1 TCAAGGCTAGAAGGGTTATCTGCCA-ACAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGC
* * * **
1702229 ATAACATTTGCTGTATGGC
65 ACATCATTTGCAGTATAAC
* * * *
1702248 CCAAGGCTAGAAGGGCTATCTACCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCT-AGG
1 TCAAGGCTAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTACGCTCAGCT-CTAAGG
* *
1702312 CACATCATTTGTAGCATAAC
64 CACATCATTTGCAGTATAAC
* *
1702332 TCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGC
1 TCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGC
* * *
1702397 ATATCAATTGCAGTATAAA
65 ACATCATTTGCAGTATAAC
* *
1702416 TCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCT-TAAAGGC
1 TCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCT-AAGGC
* *
1702480 ACATCATTTGCAGCATAGC
65 ACATCATTTGCAGTATAAC
* * * * * * * *
1702499 TTAAGTCTAGAAGAGCTATCTGCCAACCAAAGATCTTCAAGTTCGATTACACTCAGCTC-AGAGG
1 TCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTCTA-AGG
* * ** *
1702563 CAAATCAAATTTACAACATATC
64 CACATC--ATTTGCAGTATAAC
* *
1702585 TCAAGGCAAGAAGGGCTATCTG
1 TCAAGGCTAGAAGGGTTATCTG
1702607 TCAAAAAATT
Statistics
Matches: 366, Mismatches: 66, Indels: 20
0.81 0.15 0.04
Matches are distributed among these distances:
83 73 0.20
84 261 0.71
85 3 0.01
86 29 0.08
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (83 bp):
TCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCA
CATCATTTGCAGTATAAC
Found at i:1702511 original size:167 final size:166
Alignment explanation
Indices: 1702079--1702606 Score: 549
Period size: 168 Copynumber: 3.1 Consensus size: 166
1702069 TGCAACATAG
* * * * * *
1702079 ATCAAGGCAAGAAGGGCTATTTGCCAAAAAAAGACCTTCAAGTTTGACTACACTCTGCTCTAAGG
1 ATCAAGGCTAGAAGGGCTATCTGCC-AACAAAGACCTTCGAGTTCGACTACACTCAGCT-TAAGG
** * * * *
1702144 CACATCATTTGCAATATAACTCAAGGCTATAAGGTTTATCTTCCAGA-CAAAGACCTTCAAGTTT
64 CACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCA-ACCAAAGACCTTCAAGTTC
* * * * * **
1702208 GACTACGCTCAACTCTAAGGCATAACATTTGCTGTATGG
128 GACTACGCTCAGCTCCAAGGCATATCAATTGCAGTATAA
** * * *
1702247 CCCAAGGCTAGAAGGGCTATCTACCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCT-AG
1 ATCAAGGCTAGAAGGGCTATCTGCCAAC-AAAGACCTTCGAGTTCGACTACACTCAGCT--TAAG
* *
1702311 GCACATCATTTGTAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTC
63 GCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTC
*
1702376 GACTATGCTCAGCTCCAAGGCATATCAATTGCAGTATAA
128 GACTACGCTCAGCTCCAAGGCATATCAATTGCAGTATAA
* *
1702415 ATCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCTTAAAGGC
1 ATCAAGGCTAGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGACTACACTCAGCTT-AAGGC
* * * * * *
1702480 ACATCATTTGCAGCATAGCTTAAGTCTAGAAGAGCTATCTGCCAACCAAAGATCTTCAAGTTCGA
65 ACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGA
* * * * ** *
1702545 TTACACTCAGCT-CAGAGGCAAATCAAATTTACAACATAT
130 CTACGCTCAGCTCCA-AGGCATATC-AA-TTGCAGTATAA
* *
1702584 CTCAAGGCAAGAAGGGCTATCTG
1 ATCAAGGCTAGAAGGGCTATCTG
1702607 TCAAAAAATT
Statistics
Matches: 299, Mismatches: 53, Indels: 15
0.81 0.14 0.04
Matches are distributed among these distances:
165 1 0.00
166 2 0.01
167 108 0.36
168 159 0.53
169 29 0.10
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (166 bp):
ATCAAGGCTAGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGACTACACTCAGCTTAAGGCA
CATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGAC
TACGCTCAGCTCCAAGGCATATCAATTGCAGTATAA
Found at i:1703191 original size:19 final size:21
Alignment explanation
Indices: 1703144--1703195 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
1703134 CGTCCATCGT
1703144 TATTATATTATATAATATTACA
1 TATTATATT-TATAATATTACA
* *
1703166 AATTATATTTAT-ATA-TATA
1 TATTATATTTATAATATTACA
1703185 TATTATATTTA
1 TATTATATTTA
1703196 CATTTATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 13 0.48
20 3 0.11
21 3 0.11
22 8 0.30
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTATATTTATAATATTACA
Found at i:1703402 original size:26 final size:26
Alignment explanation
Indices: 1703363--1703425 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
1703353 TTGAGCTCAT
*
1703363 GAACCGATCCACTTGGGCCTCCACCC
1 GAACCGGTCCACTTGGGCCTCCACCC
* * *
1703389 GAACCGGTCTACTTGTGCCTCCACCT
1 GAACCGGTCCACTTGGGCCTCCACCC
1703415 GAACCGGTCCA
1 GAACCGGTCCA
1703426 GCTAGGGATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.19, C:0.41, G:0.21, T:0.19
Consensus pattern (26 bp):
GAACCGGTCCACTTGGGCCTCCACCC
Found at i:1704651 original size:23 final size:23
Alignment explanation
Indices: 1704625--1704688 Score: 56
Period size: 26 Copynumber: 2.6 Consensus size: 23
1704615 TTTCCCTTTG
*
1704625 ATTTATTATTTTTTTTAATTTTT
1 ATTTATTATTTTTTTTAATATTT
*
1704648 ATTTTCACTTTTTTTTATTTAATATTT
1 A-TTT-A-TTATTTTT-TTTAATATTT
* *
1704675 ATTTAATAATTTTT
1 ATTTATTATTTTTT
1704689 ATCTAACATT
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
23 2 0.06
24 8 0.25
25 2 0.06
26 10 0.31
27 10 0.31
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (23 bp):
ATTTATTATTTTTTTTAATATTT
Found at i:1704652 original size:42 final size:46
Alignment explanation
Indices: 1704568--1704660 Score: 115
Period size: 43 Copynumber: 2.1 Consensus size: 46
1704558 AGTTTCAGTA
* * *
1704568 TTTTTTCCTTGATTTGTTTATTTATTATTTTATTTTTAATTTT-AC
1 TTTTTCCCTTGATTTGATTATTTATTATTTAATTTTTAATTTTCAC
1704613 TTTTTCCCTTTGATTT-ATTATTT-TT-TTTAATTTTT-ATTTTCAC
1 TTTTTCCC-TTGATTTGATTATTTATTATTTAATTTTTAATTTTCAC
1704656 TTTTT
1 TTTTT
1704661 TTTATTTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
42 5 0.12
43 16 0.37
44 2 0.05
45 13 0.30
46 7 0.16
ACGTcount: A:0.16, C:0.09, G:0.03, T:0.72
Consensus pattern (46 bp):
TTTTTCCCTTGATTTGATTATTTATTATTTAATTTTTAATTTTCAC
Found at i:1704666 original size:35 final size:37
Alignment explanation
Indices: 1704587--1704658 Score: 96
Period size: 35 Copynumber: 2.0 Consensus size: 37
1704577 TGATTTGTTT
*
1704587 ATTTATTATTTTATTTTTAATTTTACTTTTTCCCTTTG
1 ATTTATTATTTTATTTTTAATTTTAC-TTTTCACTTTG
1704625 ATTTATTA-TTT-TTTTTAATTTTTA-TTTTCACTTT
1 ATTTATTATTTTATTTTTAA-TTTTACTTTTCACTTT
1704659 TTTTTATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
35 9 0.28
36 7 0.22
37 8 0.25
38 8 0.25
ACGTcount: A:0.19, C:0.08, G:0.01, T:0.71
Consensus pattern (37 bp):
ATTTATTATTTTATTTTTAATTTTACTTTTCACTTTG
Found at i:1710541 original size:13 final size:13
Alignment explanation
Indices: 1710523--1710552 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1710513 AAATGGCAAA
*
1710523 ATATATATATATT
1 ATATATATATAAT
1710536 ATATATATATAAT
1 ATATATATATAAT
1710549 ATAT
1 ATAT
1710553 CATTCCTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATATATATATAAT
Found at i:1710765 original size:16 final size:16
Alignment explanation
Indices: 1710744--1710777 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1710734 TAATTTATGA
1710744 ATTATAACAT-AAAATT
1 ATTATAA-ATAAAAATT
1710760 ATTATAAATAAAAATT
1 ATTATAAATAAAAATT
1710776 AT
1 AT
1710778 AGGTTCGACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTATAAATAAAAATT
Found at i:1711780 original size:7 final size:8
Alignment explanation
Indices: 1711764--1711789 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1711754 ATTTTTGAAG
1711764 AAAATAAA
1 AAAATAAA
1711772 AAAATAAA
1 AAAATAAA
1711780 AAAATAAA
1 AAAATAAA
1711788 AA
1 AA
1711790 TTTTTGCCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAATAAA
Found at i:1712266 original size:2 final size:2
Alignment explanation
Indices: 1712259--1712284 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1712249 AACCTTATTA
1712259 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
1712285 TCCTAATTAT
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:1712503 original size:33 final size:31
Alignment explanation
Indices: 1712466--1712527 Score: 72
Period size: 33 Copynumber: 1.9 Consensus size: 31
1712456 TATTATTATA
1712466 CTTGCCTAT-ATTTGATTTATTTCATTTTTTTCT
1 CTTG-CTATCATTTGATTT-TTT-ATTTTTTTCT
* *
1712499 CTTGCTTTCATTTTATTTTTTATTTTTTT
1 CTTGCTATCATTTGATTTTTTATTTTTTT
1712528 TACTTTGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
31 8 0.31
32 6 0.23
33 12 0.46
ACGTcount: A:0.13, C:0.13, G:0.05, T:0.69
Consensus pattern (31 bp):
CTTGCTATCATTTGATTTTTTATTTTTTTCT
Found at i:1722881 original size:6 final size:6
Alignment explanation
Indices: 1722866--1722924 Score: 57
Period size: 6 Copynumber: 9.0 Consensus size: 6
1722856 GCCCTAAATT
1722866 GAAAAA -AAAAA GAAAAAAGA GAAAAA GAACAGAA GAAAAAA GAAAAA
1 GAAAAA GAAAAA G--AAAA-A GAAAAA GAA-A-AA G-AAAAA GAAAAA
1722913 GAAAAA GAAAAA
1 GAAAAA GAAAAA
1722925 TAAGGTAGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.11
6 21 0.46
7 8 0.17
8 8 0.17
9 4 0.09
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:1722905 original size:23 final size:20
Alignment explanation
Indices: 1722866--1722924 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 20
1722856 GCCCTAAATT
1722866 GAAAAA-AAAAAGAAAAAAGA
1 GAAAAAGAAAAAGAAAAAA-A
1722886 GAAAAAGAACAGAAG-AAAAAA
1 GAAAAAGAA-A-AAGAAAAAAA
1722907 GAAAAAGAAAAAGAAAAA
1 GAAAAAGAAAAAGAAAAA
1722925 TAAGGTAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
19 3 0.09
20 11 0.31
21 12 0.34
22 6 0.17
23 3 0.09
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (20 bp):
GAAAAAGAAAAAGAAAAAAA
Found at i:1724219 original size:100 final size:105
Alignment explanation
Indices: 1724058--1724287 Score: 276
Period size: 100 Copynumber: 2.2 Consensus size: 105
1724048 CAGAGCTAAA
* *
1724058 TTCAACTTCAC-AGCGAAGGATATTGGACCCAAGACAACACAAGCTCAATTTCAAGACGAAGGGG
1 TTCAACTTCACGA-CGAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCAAGACGAAGGGG
* * **
1724122 CGGCTGATTGTCAACACA-AA-TT-CA-TT-CAGAGTCAAT
65 CGGCTGAATGTCAACAAATAATTTCCAGTTCCAGAACCAAT
* * **
1724158 TTCAACTTCACGACGAAGGATATTAGACTCGAGACGGCACAAGCTCAACTTCACAG-CGAAGGGG
1 TTCAACTTCACGACGAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCA-AGACGAAGGGG
1724222 CGGCTGAATGTCAACAAATAATTTCCCAGTTCCAGAACCAAT
65 CGGCTGAATGTCAACAAATAATTT-CCAGTTCCAGAACCAAT
* *
1724264 TTCAACTTCACGGCGGAGGATATT
1 TTCAACTTCACGACGAAGGATATT
1724288 GGATTCGGAA
Statistics
Matches: 110, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
100 69 0.63
101 5 0.05
102 2 0.02
104 2 0.02
105 2 0.02
106 30 0.27
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (105 bp):
TTCAACTTCACGACGAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCAAGACGAAGGGGC
GGCTGAATGTCAACAAATAATTTCCAGTTCCAGAACCAAT
Found at i:1725009 original size:2 final size:2
Alignment explanation
Indices: 1725002--1725079 Score: 94
Period size: 2 Copynumber: 41.0 Consensus size: 2
1724992 TAATACATAC
* *
1725002 AT AT AT AT AT A- AT AT CAT AT A- AT GT -T AT AA AT -T AT A- AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
1725040 AT AT AT AT 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 AT AT AT AT
1725080 GGTTTATTTA
Statistics
Matches: 67, Mismatches: 3, Indels: 12
0.82 0.04 0.15
Matches are distributed among these distances:
1 5 0.07
2 60 0.90
3 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1726558 original size:21 final size:21
Alignment explanation
Indices: 1726511--1726559 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1726501 TTATATATAC
1726511 ATTA-TATTTTTTTCTTTCAT
1 ATTATTATTTTTTTCTTTCAT
*
1726531 ATAATTATTTTTTTCTTT-ACT
1 ATTATTATTTTTTTCTTTCA-T
1726552 ATTATTAT
1 ATTATTAT
1726560 ACTTGCCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTATTATTTTTTTCTTTCAT
Found at i:1727064 original size:19 final size:18
Alignment explanation
Indices: 1727022--1727065 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
1727012 CAGAGAATGA
* *
1727022 ATTATTATTTTATTTAAG
1 ATTAATATTTTATCTAAG
1727040 ATTTAATATTTTATCTACAG
1 A-TTAATATTTTATCTA-AG
1727060 ATTAAT
1 ATTAAT
1727066 CTAGAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 18 0.82
20 3 0.14
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (18 bp):
ATTAATATTTTATCTAAG
Found at i:1734669 original size:18 final size:18
Alignment explanation
Indices: 1734646--1734691 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1734636 GACTGGTCAC
*
1734646 AACCCGACCCAACCTGTT
1 AACCCGACCCAACCCGTT
1734664 AACCCGACCCAACCCGTT
1 AACCCGACCCAACCCGTT
*
1734682 TACCCGACCC
1 AACCCGACCC
1734692 GTTGACCCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.26, C:0.50, G:0.11, T:0.13
Consensus pattern (18 bp):
AACCCGACCCAACCCGTT
Found at i:1734704 original size:18 final size:18
Alignment explanation
Indices: 1734683--1734718 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1734673 CAACCCGTTT
1734683 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
1734701 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
1734719 TTGACCGTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.50, G:0.22, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:1734718 original size:13 final size:13
Alignment explanation
Indices: 1734669--1734705 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1734659 CTGTTAACCC
*
1734669 GACCCAACCCGTT
1 GACCCGACCCGTT
*
1734682 TACCCGACCCGTT
1 GACCCGACCCGTT
1734695 GACCCGACCCG
1 GACCCGACCCG
1734706 ACCCGTTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.19, C:0.49, G:0.19, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1736029 original size:18 final size:18
Alignment explanation
Indices: 1736003--1736037 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1735993 TCGAAAGGAC
*
1736003 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1736021 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
1736038 CCGGATGGAA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1745839 original size:2 final size:2
Alignment explanation
Indices: 1745832--1745864 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1745822 TTTTAAAAAC
1745832 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1745865 CCCCCATCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1746002 original size:35 final size:35
Alignment explanation
Indices: 1745930--1746003 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
1745920 AACACATCAT
*
1745930 GTAAGGCCCTGAGCACAAAGCCGAGGAACCGATAA
1 GTAAGGCCCTGAGCACAAAGCCGAGGAACCGACAA
* * **
1745965 GTAAGGCTCTGAGCACACAGCCGAGGAACCTCCAA
1 GTAAGGCCCTGAGCACAAAGCCGAGGAACCGACAA
1746000 GTAA
1 GTAA
1746004 TCTTCCTCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.35, C:0.27, G:0.27, T:0.11
Consensus pattern (35 bp):
GTAAGGCCCTGAGCACAAAGCCGAGGAACCGACAA
Found at i:1746109 original size:24 final size:24
Alignment explanation
Indices: 1746082--1746165 Score: 116
Period size: 24 Copynumber: 3.5 Consensus size: 24
1746072 CATAATTCAA
1746082 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* * * *
1746106 GTCATGTATCAGATTAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAG
1746130 GTCAA-TATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
*
1746153 GTCAGGTATCATA
1 GTCAAGTATCATA
1746166 ACATAATTCA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 19 0.38
24 31 0.62
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAG
Found at i:1751635 original size:19 final size:18
Alignment explanation
Indices: 1751602--1751649 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1751592 ATGGGTTTAT
* *
1751602 TTTTTTTTTCTTTTTGTAA
1 TTTTTTTTT-ATTTTATAA
*
1751621 CTTTTTTTTTATTTTATTA
1 -TTTTTTTTTATTTTATAA
1751640 TTTTTTTTTA
1 TTTTTTTTTA
1751650 ATTTCCCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.40
19 6 0.24
20 9 0.36
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTTTTTTATTTTATAA
Found at i:1754865 original size:25 final size:23
Alignment explanation
Indices: 1754820--1754867 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1754810 AATCAAGAAC
*
1754820 AAAAGGAGAAAATAAAAGAAAAT
1 AAAAGGAGAAAAAAAAAGAAAAT
1754843 AAAAGGAGAAAAAACAAAGGAAAAT
1 AAAAGGAGAAAAAA-AAA-GAAAAT
1754868 TGAAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.59
24 3 0.14
25 6 0.27
ACGTcount: A:0.73, C:0.02, G:0.19, T:0.06
Consensus pattern (23 bp):
AAAAGGAGAAAAAAAAAGAAAAT
Found at i:1756021 original size:32 final size:31
Alignment explanation
Indices: 1755936--1756025 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 31
1755926 GCATCTTTAA
* *
1755936 AGATTCAACATCAA-ATGCTAGGGCATTTTTTG
1 AGATTCAACATCAATAT--TGGGGCATTTGTTG
* *
1755968 AGATTTAACATCAATTTTTGGGGCATTTGTTG
1 AGATTCAACATCAA-TATTGGGGCATTTGTTG
1756000 AGATTCAACATCGAATATTGGGGCAT
1 AGATTCAACATC-AATATTGGGGCAT
1756026 CTTTGGGAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
32 46 0.94
33 2 0.04
34 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (31 bp):
AGATTCAACATCAATATTGGGGCATTTGTTG
Found at i:1757229 original size:37 final size:37
Alignment explanation
Indices: 1757179--1757290 Score: 172
Period size: 37 Copynumber: 3.1 Consensus size: 37
1757169 TTTCCAAGTT
*
1757179 TTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
*
1757216 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
* * *
1757252 TTATCTCTCTTGAGACAGTTTTCCTTAAAACAAAATC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
1757289 TT
1 TT
1757291 TGAATATCTT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 32 0.47
37 36 0.53
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
Found at i:1757266 original size:36 final size:36
Alignment explanation
Indices: 1757177--1757285 Score: 164
Period size: 36 Copynumber: 3.0 Consensus size: 36
1757167 AGTTTCCAAG
*
1757177 TTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
1757214 TCTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
1757250 TTTTATCTCTCTTGAGACAGTTTTCCTTAAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1757286 ATCTTTGAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
36 35 0.53
37 31 0.47
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:1758255 original size:13 final size:13
Alignment explanation
Indices: 1758237--1758273 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1758227 GTCACAACCC
*
1758237 GACCCGACCCGTT
1 GACCCGACCCATT
1758250 GACCCGACCCATT
1 GACCCGACCCATT
*
1758263 GACCTGACCCA
1 GACCCGACCCA
1758274 ACCCGTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.22, C:0.46, G:0.19, T:0.14
Consensus pattern (13 bp):
GACCCGACCCATT
Found at i:1758270 original size:18 final size:18
Alignment explanation
Indices: 1758249--1758290 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1758239 CCCGACCCGT
1758249 TGACCCGACCCATTGACC
1 TGACCCGACCCATTGACC
* *
1758267 TGACCCAACCCGTTGACC
1 TGACCCGACCCATTGACC
1758285 T-ACCCG
1 TGACCCG
1758291 TTTATCGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.21, C:0.45, G:0.17, T:0.17
Consensus pattern (18 bp):
TGACCCGACCCATTGACC
Found at i:1763746 original size:14 final size:14
Alignment explanation
Indices: 1763729--1763759 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1763719 CGGCGATTAC
1763729 GATAAACCGATGAA
1 GATAAACCGATGAA
*
1763743 GATAAATCGATGAA
1 GATAAACCGATGAA
1763757 GAT
1 GAT
1763760 CACCGAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.10, G:0.23, T:0.19
Consensus pattern (14 bp):
GATAAACCGATGAA
Found at i:1766284 original size:27 final size:27
Alignment explanation
Indices: 1766242--1766313 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
1766232 ATTTATATCA
*
1766242 TATTATATA-T-ATATATATATACACG
1 TATTATATATTAAAATATATATACACG
* **
1766267 TATTATATATTAAAATATATTTAGTCG
1 TATTATATATTAAAATATATATACACG
1766294 TATTATATATTAAAATATAT
1 TATTATATATTAAAATATAT
1766314 TTAGTCATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 9 0.22
26 1 0.02
27 31 0.76
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (27 bp):
TATTATATATTAAAATATATATACACG
Found at i:1766314 original size:27 final size:27
Alignment explanation
Indices: 1766265--1766319 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1766255 TATATATACA
1766265 CGTATTATATATTAAAATATATTTAGT
1 CGTATTATATATTAAAATATATTTAGT
1766292 CGTATTATATATTAAAATATATTTAGT
1 CGTATTATATATTAAAATATATTTAGT
1766319 C
1 C
1766320 ATAAAACTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (27 bp):
CGTATTATATATTAAAATATATTTAGT
Found at i:1766407 original size:21 final size:21
Alignment explanation
Indices: 1766358--1766434 Score: 84
Period size: 21 Copynumber: 3.5 Consensus size: 21
1766348 ATATATATAT
*
1766358 ATATATATATATAGTTTAGAAATA
1 ATATAT-TATATATTTTA-AAA-A
1766382 TATATATTATATATTTTAAAAA
1 -ATATATTATATATTTTAAAAA
* *
1766404 ATATATCATATATTTTGAAAA
1 ATATATTATATATTTTAAAAA
1766425 A-ATATTATAT
1 ATATATTATAT
1766435 TATTATTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
20 8 0.17
21 20 0.42
22 1 0.02
23 3 0.06
24 10 0.21
25 6 0.12
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (21 bp):
ATATATTATATATTTTAAAAA
Found at i:1766409 original size:2 final size:2
Alignment explanation
Indices: 1766338--1766395 Score: 73
Period size: 2 Copynumber: 29.0 Consensus size: 2
1766328 AGTTTTTAAG
* * *
1766338 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT TT AG AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
1766381 AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT
1766396 TTTAAAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
1 1 0.02
2 47 0.96
3 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1766425 original size:23 final size:23
Alignment explanation
Indices: 1766358--1766443 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 23
1766348 ATATATATAT
* * *
1766358 ATATATATATATAGTTTAGAAATAT
1 ATATAT-TATATA-TTTTGAAAAAA
1766383 ATATATTATATATTTT--AAAAA
1 ATATATTATATATTTTGAAAAAA
*
1766404 ATATATCATATATTTTGAAAAAA
1 ATATATTATATATTTTGAAAAAA
1766427 TATTATATTAT-TATTTT
1 -A-TATATTATATATTTT
1766444 ATTTATTTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
21 18 0.35
23 8 0.15
24 13 0.25
25 13 0.25
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (23 bp):
ATATATTATATATTTTGAAAAAA
Found at i:1767589 original size:20 final size:21
Alignment explanation
Indices: 1767552--1767590 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1767542 AATTATTTAT
1767552 TTTTTTATTTGGTACATTAAC
1 TTTTTTATTTGGTACATTAAC
1767573 TTTTTT-TTT-GTAGCATTA
1 TTTTTTATTTGGTA-CATTA
1767591 TTTAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 8 0.47
21 6 0.35
ACGTcount: A:0.21, C:0.08, G:0.10, T:0.62
Consensus pattern (21 bp):
TTTTTTATTTGGTACATTAAC
Found at i:1770514 original size:31 final size:31
Alignment explanation
Indices: 1770472--1770530 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1770462 AAACTTTATG
* *
1770472 CATTAGAGGATAGTTTCAGTTATGCATCCAA
1 CATTAGAGGATAGTATCAATTATGCATCCAA
*
1770503 CATTAGGGGATAGTATCAATTATGCATC
1 CATTAGAGGATAGTATCAATTATGCATC
1770531 TAGAATTGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (31 bp):
CATTAGAGGATAGTATCAATTATGCATCCAA
Found at i:1771830 original size:28 final size:28
Alignment explanation
Indices: 1771790--1771848 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
1771780 TAGTTTTCTG
** *
1771790 TTTCTGAAAATCCTTCGATTTATATCTA
1 TTTCTGAAAATCCACCGATTTATATCCA
*
1771818 TTTCTGAAAATCCACCTATTTATATCCA
1 TTTCTGAAAATCCACCGATTTATATCCA
1771846 TTT
1 TTT
1771849 TATTACTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (28 bp):
TTTCTGAAAATCCACCGATTTATATCCA
Found at i:1773678 original size:155 final size:158
Alignment explanation
Indices: 1773502--1773819 Score: 597
Period size: 155 Copynumber: 2.0 Consensus size: 158
1773492 ATATATTATC
1773502 AACAGATAGAATTTTTATATAAATAATTTTTAATTAAATATTTAGAATATCACTTGTTAAAAAAT
1 AACAGATAGAATTTTTATATAAATAATTTTTAATTAAATATTTAGAATATCACTTGTTAAAAAAT
1773567 ATAAACCAAGAACAATTTGGTAAAA-ATACATTGCAGTAA-TATTATTCCTTC-ACCAAACACTA
66 ATAAACCAAGAACAATTTGGTAAAATATACATTGCAGTAACTATTATTCCTTCAACCAAACACTA
1773629 TAATCTTACATTCATACCAAACCAACCA
131 TAATCTTACATTCATACCAAACCAACCA
1773657 AACAGATAGAATTTTTATATAAATAATTTTTAATTAAATATTTAGAATATCACTTGTTAAAAAAT
1 AACAGATAGAATTTTTATATAAATAATTTTTAATTAAATATTTAGAATATCACTTGTTAAAAAAT
*
1773722 ATAAACCAAGAACAATTTGGTAAAATATACATTGCAGTAATCTTTTATTCCTTCAACCAAACACT
66 ATAAACCAAGAACAATTTGGTAAAATATACATTGCAGTAA-CTATTATTCCTTCAACCAAACACT
1773787 ATAATCTTACATTCATACCAAACCAACCA
130 ATAATCTTACATTCATACCAAACCAACCA
1773816 AACA
1 AACA
1773820 CAGTAATGTA
Statistics
Matches: 158, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
155 90 0.57
156 14 0.09
158 11 0.07
159 43 0.27
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.33
Consensus pattern (158 bp):
AACAGATAGAATTTTTATATAAATAATTTTTAATTAAATATTTAGAATATCACTTGTTAAAAAAT
ATAAACCAAGAACAATTTGGTAAAATATACATTGCAGTAACTATTATTCCTTCAACCAAACACTA
TAATCTTACATTCATACCAAACCAACCA
Found at i:1775572 original size:14 final size:16
Alignment explanation
Indices: 1775545--1775577 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
1775535 TACATTACAT
1775545 ATTTATATAGTTTATA
1 ATTTATATAGTTTATA
1775561 ATTTATA-A-TTTATA
1 ATTTATATAGTTTATA
1775575 ATT
1 ATT
1775578 ACAAAGTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 1 0.06
16 7 0.41
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
ATTTATATAGTTTATA
Found at i:1777607 original size:55 final size:55
Alignment explanation
Indices: 1777499--1777608 Score: 166
Period size: 55 Copynumber: 2.0 Consensus size: 55
1777489 GATATTCAAA
*
1777499 CGATCCATGAAGAAAGACATCCGATGAATGAAGAAATTTAAAACTGATTGAAGAC
1 CGATCCATGAAGAAAGACATCCGATGAATGAAGAAATTTAAAACTGATCGAAGAC
* * * **
1777554 CGATCCATGAAGAAAGACATTCGATGAATGAAGAAGTTTGAAGTTGATCGAAGAC
1 CGATCCATGAAGAAAGACATCCGATGAATGAAGAAATTTAAAACTGATCGAAGAC
1777609 TTCTTTCAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.21
Consensus pattern (55 bp):
CGATCCATGAAGAAAGACATCCGATGAATGAAGAAATTTAAAACTGATCGAAGAC
Found at i:1782240 original size:17 final size:17
Alignment explanation
Indices: 1782218--1782279 Score: 115
Period size: 17 Copynumber: 3.6 Consensus size: 17
1782208 TTTGAAGAAG
1782218 AAAAGGGAAAATGATGA
1 AAAAGGGAAAATGATGA
*
1782235 AAAAGGGAAAATGATAA
1 AAAAGGGAAAATGATGA
1782252 AAAAGGGAAAATGATGA
1 AAAAGGGAAAATGATGA
1782269 AAAAGGGAAAA
1 AAAAGGGAAAA
1782280 AAAAGAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.63, C:0.00, G:0.27, T:0.10
Consensus pattern (17 bp):
AAAAGGGAAAATGATGA
Found at i:1782287 original size:17 final size:17
Alignment explanation
Indices: 1782218--1782412 Score: 70
Period size: 17 Copynumber: 11.8 Consensus size: 17
1782208 TTTGAAGAAG
** *
1782218 AAAAGGGAAAATGATGA
1 AAAAGGGAAAAAAAAGA
* *
1782235 AAAAGGGAAAATGATA-A
1 AAAAGGGAAAA-AAAAGA
** *
1782252 AAAAGGGAAAATGATGA
1 AAAAGGGAAAAAAAAGA
1782269 AAAAGGGAAAAAAAAGA
1 AAAAGGGAAAAAAAAGA
* **
1782286 AAAAAGGAAAAAGGA-A
1 AAAAGGGAAAAAAAAGA
*
1782302 AAAAGGAGAAAGAGAAAAAA
1 AAAAGG-GAAA-A-AAAAGA
*** *
1782322 AAAAAAAAAAAAAAAAA
1 AAAAGGGAAAAAAAAGA
* *
1782339 AAAAAGAAAAAGAAAAGA
1 AAAAGGGAAAA-AAAAGA
1782357 AAAA---AAGAAAAAAGA
1 AAAAGGGAA-AAAAAAGA
*
1782372 AAAA---AGAAAAAAGA
1 AAAAGGGAAAAAAAAGA
*
1782386 AAAA---AGAAAAAAGA
1 AAAAGGGAAAAAAAAGA
*
1782400 AAAAAGGAAAAAA
1 AAAAGGGAAAAAA
1782413 GAGAGAGAAA
Statistics
Matches: 143, Mismatches: 24, Indels: 22
0.76 0.13 0.12
Matches are distributed among these distances:
14 26 0.18
15 13 0.09
16 8 0.06
17 75 0.52
18 11 0.08
19 5 0.03
20 5 0.03
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (17 bp):
AAAAGGGAAAAAAAAGA
Found at i:1782288 original size:7 final size:7
Alignment explanation
Indices: 1782278--1782414 Score: 169
Period size: 7 Copynumber: 20.1 Consensus size: 7
1782268 AAAAAGGGAA
1782278 AAAAAAG
1 AAAAAAG
1782285 AAAAAAGG
1 AAAAAA-G
*
1782293 AAAAAGG
1 AAAAAAG
1782300 AAAAAAG
1 AAAAAAG
* *
1782307 GAGAAAG
1 AAAAAAG
*
1782314 AGAAAA-
1 AAAAAAG
1782320 AAAAAA-
1 AAAAAAG
1782326 AAAAAA-
1 AAAAAAG
1782332 AAAAAA-
1 AAAAAAG
1782338 AAAAAAG
1 AAAAAAG
1782345 -AAAAAG
1 AAAAAAG
*
1782351 AAAAGA-
1 AAAAAAG
1782357 AAAAAAG
1 AAAAAAG
1782364 AAAAAAG
1 AAAAAAG
1782371 AAAAAAG
1 AAAAAAG
1782378 AAAAAAG
1 AAAAAAG
1782385 AAAAAAG
1 AAAAAAG
1782392 AAAAAAG
1 AAAAAAG
1782399 AAAAAAGG
1 AAAAAA-G
1782407 AAAAAAG
1 AAAAAAG
1782414 A
1 A
1782415 GAGAGAAAAC
Statistics
Matches: 115, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
6 34 0.30
7 68 0.59
8 13 0.11
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1782289 original size:34 final size:34
Alignment explanation
Indices: 1782218--1782324 Score: 119
Period size: 34 Copynumber: 3.1 Consensus size: 34
1782208 TTTGAAGAAG
* *
1782218 AAAAGGGAAAATGATGAAAAAGGGAAAATGATAA
1 AAAAGGGAAAATGATGAAAAAGGGAAAATAAAAA
*
1782252 AAAAGGGAAAATGATGAAAAAGGGAAAAAAAAGAA
1 AAAAGGGAAAATGATGAAAAAGGGAAAATAAA-AA
* * *
1782287 AAAAGGAAAAAGGA--AAAAAGGAGAAAGAGAAAAA
1 AAAAGGGAAAATGATGAAAAAGG-GAAA-ATAAAAA
1782321 AAAA
1 AAAA
1782325 AAAAAAAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
33 7 0.11
34 39 0.61
35 18 0.28
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (34 bp):
AAAAGGGAAAATGATGAAAAAGGGAAAATAAAAA
Found at i:1782409 original size:8 final size:8
Alignment explanation
Indices: 1782267--1782413 Score: 105
Period size: 8 Copynumber: 19.0 Consensus size: 8
1782257 GGAAAATGAT
*
1782267 GAAAAAGG
1 GAAAAAAG
*
1782275 GAAAAAAAA
1 G-AAAAAAG
1782284 GAAAAAAG
1 GAAAAAAG
1782292 G-AAAAAG
1 GAAAAAAG
1782299 GAAAAAAG
1 GAAAAAAG
*
1782307 G-AGAAAG
1 GAAAAAAG
1782314 AGAAAAAA-
1 -GAAAAAAG
*
1782322 -AAAAAAA
1 GAAAAAAG
* *
1782329 AAAAAAAA
1 GAAAAAAG
*
1782337 AAAAAAAG
1 GAAAAAAG
* *
1782345 AAAAAGAAAA
1 -GAAA-AAAG
*
1782355 GAAAAAAA
1 GAAAAAAG
1782363 GAAAAAA-
1 GAAAAAAG
1782370 GAAAAAA-
1 GAAAAAAG
1782377 GAAAAAA-
1 GAAAAAAG
1782384 GAAAAAA-
1 GAAAAAAG
1782391 GAAAAAA-
1 GAAAAAAG
1782398 GAAAAAAG
1 GAAAAAAG
1782406 GAAAAAAG
1 GAAAAAAG
1782414 AGAGAGAAAA
Statistics
Matches: 122, Mismatches: 8, Indels: 18
0.82 0.05 0.12
Matches are distributed among these distances:
6 6 0.05
7 47 0.39
8 49 0.40
9 17 0.14
10 3 0.02
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (8 bp):
GAAAAAAG
Found at i:1782412 original size:1 final size:1
Alignment explanation
Indices: 1782316--1782404 Score: 97
Period size: 1 Copynumber: 89.0 Consensus size: 1
1782306 GGAGAAAGAG
* * * * * *
1782316 AAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAGAAAAGAAAAAAAGAAAAAAGAAAAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
1782381 AAAGAAAAAAGAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAA
1782405 GGAAAAAAGA
Statistics
Matches: 70, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (1 bp):
A
Found at i:1782421 original size:21 final size:22
Alignment explanation
Indices: 1782279--1782414 Score: 158
Period size: 22 Copynumber: 6.3 Consensus size: 22
1782269 AAAAGGGAAA
* *
1782279 AAAAAGAAAAAAGGAAAAAGGA
1 AAAAAGAAAAAAGAAAAAAAGA
* *
1782301 AAAAAGGAGAAAGAGAAAAAA-A
1 AAAAAGAAAAAAGA-AAAAAAGA
1782323 AAAAA-AAAAAA-AAAAAAA-A
1 AAAAAGAAAAAAGAAAAAAAGA
1782342 AAGAAA-AAGAAAAGAAAAAAAGA
1 AA-AAAGAA-AAAAGAAAAAAAGA
1782365 AAAAAGAAAAAAG-AAAAAAGA
1 AAAAAGAAAAAAGAAAAAAAGA
*
1782386 AAAAAGAAAAAAGAAAAAAGGA
1 AAAAAGAAAAAAGAAAAAAAGA
1782408 AAAAAGA
1 AAAAAGA
1782415 GAGAGAAAAC
Statistics
Matches: 100, Mismatches: 7, Indels: 14
0.83 0.06 0.12
Matches are distributed among these distances:
19 9 0.09
20 6 0.06
21 29 0.29
22 46 0.46
23 10 0.10
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAGAAAAAAAGA
Done.