Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002352.1 Hibiscus syriacus cultivar Beakdansim tig00004797_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: 2012169
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1737054 original size:27 final size:27
Alignment explanation
Indices: 1736980--1737068 Score: 81
Period size: 30 Copynumber: 3.1 Consensus size: 27
1736970 ATAATATATT
*
1736980 ATAATAATAATAATAAAAT-ATACAATA
1 ATAATAATAATAAT-AAATGATAAAATA
* *
1737007 ATAATAATAAAGACAAAAAATGATAAAATA
1 ATAATAAT--A-ATAATAAATGATAAAATA
*
1737037 ATAATAATAATAATAAATAGTATAATATA
1 ATAATAATAATAATAAAT-G-ATAAAATA
1737066 ATA
1 ATA
1737069 GTAAGAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
27 15 0.30
28 2 0.04
29 15 0.30
30 18 0.36
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.28
Consensus pattern (27 bp):
ATAATAATAATAATAAATGATAAAATA
Found at i:1737077 original size:23 final size:24
Alignment explanation
Indices: 1737034--1737078 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1737024 AAATGATAAA
*
1737034 ATAATAATAATAATAATAAATAGT
1 ATAATAATAATAATAAGAAATAGT
*
1737058 ATAAT-ATAATAGTAAGAAATA
1 ATAATAATAATAATAAGAAATA
1737079 AAAAACCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (24 bp):
ATAATAATAATAATAAGAAATAGT
Found at i:1737196 original size:5 final size:5
Alignment explanation
Indices: 1737161--1737212 Score: 63
Period size: 5 Copynumber: 10.4 Consensus size: 5
1737151 ATAAGATATT
*
1737161 AAATA AAA-A TAATA AAAGTA AAAGT- AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAA-TA AAA-TA AAATA AAATA AAATA AAATA AAATA
1737211 AA
1 AA
1737213 CAACAAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
4 4 0.10
5 31 0.74
6 7 0.17
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:1738887 original size:84 final size:84
Alignment explanation
Indices: 1738647--1739370 Score: 769
Period size: 84 Copynumber: 8.7 Consensus size: 84
1738637 AATGTAATCG
* * * * * *
1738647 AACTCGAAGGTCTTT-GATGACTA-ATAACCCTTCTTGCCATGAGTTATGCTGCAAATGAAGTGC
1 AACTCGAAGGTCTTTGGTTGAC-AGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
*
1738710 CTTGGAGCTGAGCGTAGTCG
65 CTTGGAGCTGAGCGTAGTCA
* * * * *
1738730 AACTCGAAGGTCTTT-GTTGACAGATAACCCTTTTAGCCTTGAGTTATGCTACAAATGATGTGCC
1 AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-C
* *
1738794 CTCGAAGCTGAGCGTAGTCA
65 CTTGGAGCTGAGCGTAGTCA
* * * * * *
1738814 AACTTGAAGGTCTTCGGTTGGCAGATAACCCTTCTCGAATTAAGCTATGCTGCAAATGATATGCC
1 AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
1738879 TTGGAGCTGAGCGTAGTCA
66 TTGGAGCTGAGCGTAGTCA
* ** * *
1738898 AAATCGAAGGTCTTTGGTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATATGCC
1 AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
*
1738963 TTGGAGATGAGCGTAGTCA
66 TTGGAGCTGAGCGTAGTCA
* * * * *
1738982 AACTCGAAGGTCTTTTGGTT-ACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGC
1 AACTCGAAGGTC-TTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-
*** * *
1739046 CCTCAAAGCTGAGTGTAATCA
64 CCTTGGAGCTGAGCGTAGTCA
* * * *
1739067 AACTCGAGGGTC-TTCG--G-CAGATAGCCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCC
1 AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
* * *
1739128 TTGGAGCTGAGCGGAATCG
66 TTGGAGCTGAGCGTAGTCA
* * * * * *
1739147 AACTCAAAGATCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG-C
1 AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
* * *
1739210 TGTCGAAGCTGAGCGTAATCG
66 T-T-GGAGCTGAGCGTAGTCA
* * *
1739231 AACTCGAGGGTCTTT-G--G-CAGATAGCCCTTCTCGACTTAA-TCTATTCTGCAAATGATGTGC
1 AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGT-TATGCTGCAAATGATGTGC
*
1739291 CTTGGAGCTGAGCGTAGTCG
65 CTTGGAGCTGAGCGTAGTCA
1739311 AACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
1 AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
1739371 CACCTTTGAA
Statistics
Matches: 541, Mismatches: 83, Indels: 34
0.82 0.13 0.05
Matches are distributed among these distances:
80 54 0.10
81 76 0.14
82 8 0.01
83 133 0.25
84 199 0.37
85 71 0.13
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (84 bp):
AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
TTGGAGCTGAGCGTAGTCA
Found at i:1739206 original size:164 final size:163
Alignment explanation
Indices: 1738644--1739409 Score: 816
Period size: 164 Copynumber: 4.6 Consensus size: 163
1738634 TTGAATGTAA
* * * *
1738644 TCGAACTCGAAGGTCTTTGATGACTA-ATAACCCTTCTTGCCATGAGTTATGCTGCAAATGAAGT
1 TCGAACTCGAAGGTCTTTGGTGAC-AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
* * * * * * * *
1738708 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTTTAGCCTTGAG
65 GCCTCGAAGCTGAGCGTAATCAAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTCGACTTAAG
* *
1738773 TTATGCTACAAATGATGTGCCCTCGAAGCTGAGCGTAG
127 TTATGCTACAAATGATGTG-CCTTGGAGCTGAGCGTAG
* * * * * ** * * *
1738811 TCAAACTTGAAGGTCTTCGGTTGGCAGATAACCCTTCTCGAATTAAGCTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
* * * * *
1738876 GCCTTGGAGCTGAGCGTAGTCAAAATCGAAGGTCTTTGGTTGGTAGATAACCCTTCTCGACTTAA
65 GCCTCGAAGCTGAGCGTAATCAAACTCGAAGGTC--T--TTGGCAGATAACCCTTCTCGACTTAA
* *
1738941 GTTATGCTACAAATGATATGCCTTGGAGATGAGCGTAG
126 GTTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAG
* * * *
1738979 TCAAACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
* * * * *
1739044 GCCCTCAAAGCTGAGTGTAATCAAACTCGAGGGTCTTCGGCAGATAGCCCTTCTCGACTTAAGTT
65 G-CCTCGAAGCTGAGCGTAATCAAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTT
** * *
1739109 ATGCTGTAAATGATGTGCCTTGGAGCTGAGCGGAA
129 ATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAG
* * *
1739144 TCGAACTCAAAGATCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG
* * * *
1739209 CTGTCGAAGCTGAGCGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAA-TCT
66 C-CTCGAAGCTGAGCGTAATCAAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGT-T
* *
1739273 ATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
129 ATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAG
* * * **
1739308 TCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGCA
1 TCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG
* * * * *
1739373 CCTTTGAAGTTGAGTGTAATCGAACACGAAGGTCTTT
66 CC-TCGAAGCTGAGCGTAATCAAACTCGAAGGTCTTT
1739410 TGTTGGCAAC
Statistics
Matches: 508, Mismatches: 80, Indels: 25
0.83 0.13 0.04
Matches are distributed among these distances:
163 2 0.00
164 221 0.44
165 67 0.13
167 18 0.04
168 129 0.25
169 66 0.13
170 2 0.00
172 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (163 bp):
TCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG
CCTCGAAGCTGAGCGTAATCAAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTAT
GCTACAAATGATGTGCCTTGGAGCTGAGCGTAG
Found at i:1744782 original size:18 final size:18
Alignment explanation
Indices: 1744761--1744840 Score: 90
Period size: 18 Copynumber: 4.4 Consensus size: 18
1744751 AAAAGTTAGT
*
1744761 AAAAAAAGAAAATAAATA
1 AAAAAAATAAAATAAATA
* *
1744779 AAAATAATAAAAT-GATA
1 AAAAAAATAAAATAAATA
1744796 AAAAAAATTAAAATAAATA
1 AAAAAAA-TAAAATAAATA
* *
1744815 AAGAAAATAAAATGAATA
1 AAAAAAATAAAATAAATA
1744833 AAATAAAA
1 AAA-AAAA
1744841 AAGTAAAAGG
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
17 9 0.18
18 29 0.57
19 13 0.25
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (18 bp):
AAAAAAATAAAATAAATA
Found at i:1744801 original size:36 final size:37
Alignment explanation
Indices: 1744761--1744841 Score: 112
Period size: 36 Copynumber: 2.2 Consensus size: 37
1744751 AAAAGTTAGT
1744761 AAAAAAAGAAAATAAATAAA-AATAATAAAATG-ATAA
1 AAAAAAAGAAAATAAATAAAGAA-AATAAAATGAATAA
**
1744797 AAAAAATTAAAATAAATAAAGAAAATAAAATGAATAA
1 AAAAAAAGAAAATAAATAAAGAAAATAAAATGAATAA
1744834 AATAAAAA
1 AA-AAAAA
1744842 AGTAAAAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
36 27 0.69
37 8 0.21
38 4 0.10
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (37 bp):
AAAAAAAGAAAATAAATAAAGAAAATAAAATGAATAA
Found at i:1744832 original size:22 final size:22
Alignment explanation
Indices: 1744764--1744848 Score: 66
Period size: 23 Copynumber: 3.8 Consensus size: 22
1744754 AGTTAGTAAA
*
1744764 AAAAGAAAATAAATAAAAAT-AAT
1 AAAATAAAA-AAAT-AAAATGAAT
* * * *
1744787 AAAATGATAAAA-AAAATTAAA
1 AAAATAAAAAAATAAAATGAAT
1744808 ATAAATAAAGAAAATAAAATGAAT
1 A-AAATAAA-AAAATAAAATGAAT
*
1744832 AAAATAAAAAAGTAAAA
1 AAAATAAAAAAATAAAA
1744849 GGGTTAGTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
20 5 0.10
21 3 0.06
22 16 0.33
23 17 0.35
24 8 0.16
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (22 bp):
AAAATAAAAAAATAAAATGAAT
Found at i:1744836 original size:9 final size:9
Alignment explanation
Indices: 1744760--1744839 Score: 69
Period size: 9 Copynumber: 9.0 Consensus size: 9
1744750 TAAAAGTTAG
1744760 TAAAA-AAA
1 TAAAATAAA
*
1744768 GAAAATAAA
1 TAAAATAAA
1744777 TAAAA-ATAA
1 TAAAATA-AA
*
1744786 TAAAAT-GA
1 TAAAATAAA
*
1744794 TAAAAAAAA
1 TAAAATAAA
1744803 TTAAAATAAA
1 -TAAAATAAA
1744813 TAAAGA-AAA
1 TAAA-ATAAA
*
1744822 TAAAATGAA
1 TAAAATAAA
1744831 TAAAATAAA
1 TAAAATAAA
1744840 AAAGTAAAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
8 12 0.21
9 36 0.63
10 9 0.16
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (9 bp):
TAAAATAAA
Found at i:1745992 original size:18 final size:18
Alignment explanation
Indices: 1745971--1746049 Score: 88
Period size: 18 Copynumber: 4.4 Consensus size: 18
1745961 AAAAGTTAGT
*
1745971 AAAAAAAGAAAATAAATA
1 AAAAAAATAAAATAAATA
* *
1745989 AAAATAATAAAAT-GATA
1 AAAAAAATAAAATAAATA
*
1746006 AAAAAATTAAAATAAATA
1 AAAAAAATAAAATAAATA
* *
1746024 AAGAAAATAAAATGAATA
1 AAAAAAATAAAATAAATA
1746042 AAATAAAA
1 AAA-AAAA
1746050 AAGTAAAAGG
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
17 14 0.29
18 31 0.63
19 4 0.08
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (18 bp):
AAAAAAATAAAATAAATA
Found at i:1745997 original size:9 final size:9
Alignment explanation
Indices: 1745979--1746044 Score: 50
Period size: 8 Copynumber: 7.3 Consensus size: 9
1745969 GTAAAAAAAG
1745979 AAAATAAATA
1 AAAAT-AATA
1745989 AAAATAAT-
1 AAAATAATA
*
1745997 AAAATGATA
1 AAAATAATA
*
1746006 AAAA-AATT
1 AAAATAATA
1746014 AAAATAAATA
1 AAAAT-AATA
1746024 AAGAA-AAT-
1 AA-AATAATA
1746032 AAAATGAATA
1 AAAAT-AATA
1746042 AAA
1 AAA
1746045 TAAAAAAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
7 2 0.04
8 15 0.33
9 13 0.29
10 13 0.29
11 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (9 bp):
AAAATAATA
Found at i:1746018 original size:35 final size:35
Alignment explanation
Indices: 1745970--1746044 Score: 109
Period size: 35 Copynumber: 2.1 Consensus size: 35
1745960 TAAAAGTTAG
1745970 TAAAAAAAGAAAATAAATAAA-AATAATAAAATG-A
1 TAAAAAAAGAAAATAAATAAAGAA-AATAAAATGAA
*
1746004 TAAAAAAATTAAAATAAATAAAGAAAATAAAATGAA
1 TAAAAAAA-GAAAATAAATAAAGAAAATAAAATGAA
1746040 TAAAA
1 TAAAA
1746045 TAAAAAAGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
34 8 0.22
35 21 0.57
36 8 0.22
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (35 bp):
TAAAAAAAGAAAATAAATAAAGAAAATAAAATGAA
Found at i:1746045 original size:9 final size:9
Alignment explanation
Indices: 1745970--1746048 Score: 69
Period size: 9 Copynumber: 9.0 Consensus size: 9
1745960 TAAAAGTTAG
1745970 TAAAA-AAA
1 TAAAATAAA
*
1745978 GAAAATAAA
1 TAAAATAAA
1745987 TAAAA-ATAA
1 TAAAATA-AA
*
1745996 TAAAAT-GA
1 TAAAATAAA
1746004 TAAAA-AAA
1 TAAAATAAA
1746012 TTAAAATAAA
1 -TAAAATAAA
1746022 TAAAGA-AAA
1 TAAA-ATAAA
*
1746031 TAAAATGAA
1 TAAAATAAA
1746040 TAAAATAAA
1 TAAAATAAA
1746049 AAAGTAAAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
8 13 0.23
9 40 0.70
10 4 0.07
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (9 bp):
TAAAATAAA
Found at i:1753316 original size:19 final size:17
Alignment explanation
Indices: 1753281--1753317 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1753271 AATAACTCTT
1753281 AATTATATTAATTATTA
1 AATTATATTAATTATTA
1753298 AATTATATTATATTTATTA
1 AATTATATTA-A-TTATTA
1753317 A
1 A
1753318 TGTTCGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 1 0.06
19 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTATATTAATTATTA
Found at i:1755725 original size:22 final size:22
Alignment explanation
Indices: 1755688--1755738 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1755678 TAATTACTAA
* *
1755688 AATATTTAAAATATAT-TTATT
1 AATATTTTAAATATATAATATT
1755709 AATATTTTAAATAATATAATATT
1 AATATTTTAAAT-ATATAATATT
1755732 -ATATTTT
1 AATATTTT
1755739 TTAATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 11 0.42
22 11 0.42
23 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATATTTTAAATATATAATATT
Found at i:1755729 original size:8 final size:8
Alignment explanation
Indices: 1755708--1755782 Score: 53
Period size: 8 Copynumber: 9.1 Consensus size: 8
1755698 ATATATTTAT
*
1755708 TAATATTT
1 TAATATTA
*
1755716 TAAATAATA
1 T-AATATTA
1755725 TAATATTA
1 TAATATTA
* *
1755733 T-ATTTTT
1 TAATATTA
1755740 TAATATTA
1 TAATATTA
*
1755748 TTATATTA
1 TAATATTA
1755756 TAATAATATA
1 TAAT-AT-TA
*
1755766 TGATATTA
1 TAATATTA
*
1755774 TATTATTA
1 TAATATTA
1755782 T
1 T
1755783 TTTTATAATA
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
7 5 0.10
8 31 0.61
9 10 0.20
10 5 0.10
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (8 bp):
TAATATTA
Found at i:1755739 original size:23 final size:24
Alignment explanation
Indices: 1755689--1755757 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 24
1755679 AATTACTAAA
* *
1755689 ATATTTAAAAT-ATAT-TTATTA-
1 ATATTTTAAATAATATAATATTAT
1755710 ATATTTTAAATAATATAATATTAT
1 ATATTTTAAATAATATAATATTAT
* * *
1755734 AT-TTTTTAATATTATTATATTAT
1 ATATTTTAAATAATATAATATTAT
1755757 A
1 A
1755758 ATAATATATG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 10 0.25
22 4 0.10
23 24 0.60
24 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATATTTTAAATAATATAATATTAT
Found at i:1755766 original size:31 final size:30
Alignment explanation
Indices: 1755689--1755795 Score: 96
Period size: 31 Copynumber: 3.5 Consensus size: 30
1755679 AATTACTAAA
1755689 ATATTTAA-AATATATTTATTAATATT-TT
1 ATATTTAATAATATATTTATTAATATTATT
* * *
1755717 AAATAATATAATATTATATTTTTTAATATTATT
1 --AT-ATTTAATAATATATTTATTAATATTATT
*
1755750 ATATTATAATAATATATGATATT-ATATTATT
1 ATATT-TAATAATATAT-TTATTAATATTATT
*
1755781 AT-TTTTATAATATAT
1 ATATTTAATAATATAT
1755796 GATAAATTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
29 10 0.16
30 6 0.09
31 27 0.42
32 19 0.30
33 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (30 bp):
ATATTTAATAATATATTTATTAATATTATT
Found at i:1755790 original size:29 final size:31
Alignment explanation
Indices: 1755742--1755799 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
1755732 ATATTTTTTA
1755742 ATATTATTATATTATAATAATATATGATATT
1 ATATTATTATATTATAATAATATATGATATT
*
1755773 ATATTATTAT-TT-TTATAATATATGATA
1 ATATTATTATATTATAATAATATATGATA
1755800 AATTATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 14 0.54
30 2 0.08
31 10 0.38
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
ATATTATTATATTATAATAATATATGATATT
Found at i:1755806 original size:29 final size:27
Alignment explanation
Indices: 1755744--1755807 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
1755734 ATTTTTTAAT
1755744 ATTATTATATTATAATAATATATGATA
1 ATTATTATATTATAATAATATATGATA
* * *
1755771 TTATATTATTATTTTTATAATATATGATAA
1 AT-TATTA-TATTATAATAATATATGAT-A
1755801 ATTATTA
1 ATTATTA
1755808 ATAAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 1 0.03
28 5 0.17
29 22 0.73
30 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (27 bp):
ATTATTATATTATAATAATATATGATA
Found at i:1755856 original size:27 final size:26
Alignment explanation
Indices: 1755800--1755879 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 26
1755790 ATATATGATA
*
1755800 AATTATTAATAA-AATTTATATTATTT
1 AATTATTAATAAGAA-TAATATTATTT
*
1755826 -ATTAATTTACTAA-AATAATATTATTT
1 AATT-A-TTAATAAGAATAATATTATTT
1755852 AATTATTAATAATGAATAATATTATTT
1 AATTATTAATAA-GAATAATATTATTT
1755879 A
1 A
1755880 TATATTTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
25 9 0.20
26 12 0.26
27 25 0.54
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (26 bp):
AATTATTAATAAGAATAATATTATTT
Found at i:1755896 original size:27 final size:27
Alignment explanation
Indices: 1755817--1755901 Score: 79
Period size: 27 Copynumber: 3.1 Consensus size: 27
1755807 AATAAAATTT
*
1755817 ATATTATTTAT-TAATTTACTA-AAATA
1 ATATTATTTATAT-ATTTAATATAAATA
*
1755843 ATATTATTTA-AT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
1755870 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
1755899 ATA
1 ATA
1755902 GTCTAATAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
24 1 0.02
25 4 0.08
26 12 0.25
27 15 0.31
28 9 0.19
29 7 0.15
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:1756071 original size:14 final size:14
Alignment explanation
Indices: 1756041--1756091 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1756031 GAATTTATTT
*
1756041 ATAAAATTTTAGAA
1 ATAATATTTTAGAA
1756055 ATAATATTTTA-ATA
1 ATAATATTTTAGA-A
* *
1756069 ATAATATTGATATAA
1 ATAATATT-TTAGAA
1756084 ATAATATT
1 ATAATATT
1756092 ATATAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 1 0.03
14 19 0.59
15 11 0.34
16 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (14 bp):
ATAATATTTTAGAA
Found at i:1756095 original size:14 final size:14
Alignment explanation
Indices: 1756053--1756097 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
1756043 AAAATTTTAG
*
1756053 AAATAATATTTTA-
1 AAATAATATTATAT
1756066 ATAATAATATTGATAT
1 A-AATAATATT-ATAT
1756082 AAATAATATTATAT
1 AAATAATATTATAT
1756096 AA
1 AA
1756098 TTATTATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 1 0.04
14 15 0.54
15 11 0.39
16 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
AAATAATATTATAT
Found at i:1756124 original size:16 final size:16
Alignment explanation
Indices: 1756065--1756126 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
1756055 ATAATATTTT
*
1756065 AATAATAATATTGATATA
1 AATAATAATATT--TAAA
* * *
1756083 AATAATATTATATAAT
1 AATAATAATATTTAAA
* *
1756099 TATTATAATATTTAAA
1 AATAATAATATTTAAA
1756115 AATAATAATATT
1 AATAATAATATT
1756127 AAATTTTTAT
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
16 23 0.70
18 10 0.30
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
AATAATAATATTTAAA
Found at i:1757278 original size:21 final size:21
Alignment explanation
Indices: 1757224--1757333 Score: 116
Period size: 21 Copynumber: 5.3 Consensus size: 21
1757214 CGTTGACCAT
* *
1757224 TACGGTGTTTGACATGACAGTC
1 TACGGTG-CTGACGTGACAGTC
*
1757246 -ACAGTG-TGACGTGACAGTC
1 TACGGTGCTGACGTGACAGTC
* *
1757265 TAAGGTGCTGACGTGATAGTC
1 TACGGTGCTGACGTGACAGTC
*
1757286 TACGGTGCTGACGTGATAGTC
1 TACGGTGCTGACGTGACAGTC
* *
1757307 TACGGTGCTGACGCGACAATC
1 TACGGTGCTGACGTGACAGTC
*
1757328 CACGGT
1 TACGGT
1757334 AATTGATAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.16
20 4 0.05
21 60 0.79
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.25
Consensus pattern (21 bp):
TACGGTGCTGACGTGACAGTC
Found at i:1757912 original size:15 final size:15
Alignment explanation
Indices: 1757877--1757906 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1757867 AAATTCTCCC
*
1757877 GATTATAAGGTACTA
1 GATTATAAGATACTA
1757892 GATTATAAGATACTA
1 GATTATAAGATACTA
1757907 TTTTATTATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (15 bp):
GATTATAAGATACTA
Found at i:1759159 original size:17 final size:14
Alignment explanation
Indices: 1759136--1759186 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
1759126 ATTGTTCTAC
1759136 TTTTCTTTCATCTTCA
1 TTTTCTTTCAT-TT-A
1759152 TCTTTCTTTC-TTTA
1 T-TTTCTTTCATTTA
1759166 TTTTCTTTCA-TTA
1 TTTTCTTTCATTTA
*
1759179 TTATCTTT
1 TTTTCTTT
1759187 TCACAATTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
13 18 0.56
14 2 0.06
15 2 0.06
16 2 0.06
17 8 0.25
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCTTTCATTTA
Found at i:1759835 original size:172 final size:174
Alignment explanation
Indices: 1759548--1759895 Score: 682
Period size: 172 Copynumber: 2.0 Consensus size: 174
1759538 TAAAGTTATT
1759548 CTGGATGTAACAGTGATAGACGTGATTAGACCAACAAAGATTGGATTTTGGAGATATACTTGAAA
1 CTGGATGTAACAGTGATAGACGTGATTAGACCAACAAAGATTGGATTTTGGAGATATACTTGAAA
1759613 ATTTTGATTAACCAGAGAAGAGTTAACTACAGGGGTTGAGCCCTGTTAACTATAAT-GACATACA
66 ATTTTGATTAACCAGAGAAGAGTTAACTACAGGGGTTGAGCCCTGTTAACTATAATCGACATACA
1759677 TCACGAAGGAAAAATTTTATTTCAATGATCAGTCAAAATTTAGG
131 TCACGAAGGAAAAATTTTATTTCAATGATCAGTCAAAATTTAGG
1759721 CTGGATGTAACAGTGAT-GACGTGATTAGACCAACAAAGATTGGATTTTGGAGATATACTTGAAA
1 CTGGATGTAACAGTGATAGACGTGATTAGACCAACAAAGATTGGATTTTGGAGATATACTTGAAA
1759785 ATTTTGATTAACCAGAGAAGAGTTAACTACAGGGGTTGAGCCCTGTTAACTATAATCGACATACA
66 ATTTTGATTAACCAGAGAAGAGTTAACTACAGGGGTTGAGCCCTGTTAACTATAATCGACATACA
1759850 TCACGAAGGAAAAATTTTATTTCAATGATCAGTCAAAATTTAGG
131 TCACGAAGGAAAAATTTTATTTCAATGATCAGTCAAAATTTAGG
1759894 CT
1 CT
1759896 ATAAAAACCT
Statistics
Matches: 174, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
172 103 0.59
173 71 0.41
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (174 bp):
CTGGATGTAACAGTGATAGACGTGATTAGACCAACAAAGATTGGATTTTGGAGATATACTTGAAA
ATTTTGATTAACCAGAGAAGAGTTAACTACAGGGGTTGAGCCCTGTTAACTATAATCGACATACA
TCACGAAGGAAAAATTTTATTTCAATGATCAGTCAAAATTTAGG
Found at i:1760000 original size:21 final size:20
Alignment explanation
Indices: 1759939--1760001 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 20
1759929 TTTTTATACT
*
1759939 TTATTTATTTT-CTC-TTTA
1 TTATTTATTTTATTCATTTA
1759957 TTA-TTATTTTATTCAGTATTTA
1 TTATTTATTTTATTC---ATTTA
1759979 TATATTTATTTTATTCATTTA
1 T-TATTTATTTTATTCATTTA
1760000 TT
1 TT
1760002 TTCATTAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
17 7 0.19
18 5 0.14
20 1 0.03
21 6 0.16
22 5 0.14
23 2 0.05
24 11 0.30
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (20 bp):
TTATTTATTTTATTCATTTA
Found at i:1762522 original size:10 final size:9
Alignment explanation
Indices: 1762494--1762519 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1762484 ATTTTACTTT
1762494 TTTATTTTA
1 TTTATTTTA
1762503 TTTATTTTA
1 TTTATTTTA
1762512 TTTATTTT
1 TTTATTTT
1762520 TATCTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1764056 original size:18 final size:18
Alignment explanation
Indices: 1764035--1764072 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1764025 TTTATCTCCA
* *
1764035 TCTTTCTTTATTTTTTTT
1 TCTTTCATTATTTTCTTT
1764053 TCTTTCATTATTTTCTTT
1 TCTTTCATTATTTTCTTT
1764071 TC
1 TC
1764073 ACAATGCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (18 bp):
TCTTTCATTATTTTCTTT
Found at i:1764663 original size:15 final size:14
Alignment explanation
Indices: 1764643--1764680 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1764633 TTTATCTACT
1764643 TTATTTATTTTCTCA
1 TTATTTATTTT-TCA
1764658 TTATTT-TTTTTCA
1 TTATTTATTTTTCA
*
1764671 GTATTTATTT
1 TTATTTATTT
1764681 ATTTTATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 8 0.38
14 7 0.33
15 6 0.29
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.71
Consensus pattern (14 bp):
TTATTTATTTTTCA
Found at i:1767373 original size:2 final size:2
Alignment explanation
Indices: 1767366--1767411 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1767356 TTATACCATC
*
1767366 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1767408 AT AT
1 AT AT
1767412 GTACTTAGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1775206 original size:3 final size:3
Alignment explanation
Indices: 1775200--1775264 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
1775190 AATATAAAAC
1775200 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1775248 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
1775265 GTTGAGTTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1778585 original size:20 final size:19
Alignment explanation
Indices: 1778562--1778598 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1778552 AGAACCCCAG
*
1778562 GGGGGTATCGATTCCCCTA
1 GGGGGAATCGATTCCCCTA
*
1778581 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
1778599 TCAAAGGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.27, G:0.35, T:0.24
Consensus pattern (19 bp):
GGGGGAATCGATTCCCCTA
Found at i:1782495 original size:22 final size:21
Alignment explanation
Indices: 1782453--1782492 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1782443 GAGTTTATTT
*
1782453 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1782474 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1782493 ACAATTTCTC
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:1790067 original size:16 final size:18
Alignment explanation
Indices: 1790039--1790073 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1790029 CCTTTATAAG
1790039 AATAAAAATCC-AAAGCA
1 AATAAAAATCCAAAAGCA
1790056 AATAAAAA-CCAAAAGCA
1 AATAAAAATCCAAAAGCA
1790073 A
1 A
1790074 TACATGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.69, C:0.17, G:0.06, T:0.09
Consensus pattern (18 bp):
AATAAAAATCCAAAAGCA
Found at i:1792396 original size:8 final size:8
Alignment explanation
Indices: 1792385--1792625 Score: 198
Period size: 8 Copynumber: 30.4 Consensus size: 8
1792375 TATCTATCTA
*
1792385 TCTGTCTG
1 TCTGCCTG
*
1792393 TCTGTCTG
1 TCTGCCTG
*
1792401 TCTGTCTG
1 TCTGCCTG
*
1792409 TCTGTCTG
1 TCTGCCTG
1792417 TCTG--TG
1 TCTGCCTG
*
1792423 TCTGTCTG
1 TCTGCCTG
*
1792431 TCTGTCTG
1 TCTGCCTG
*
1792439 TCTGTCTG
1 TCTGCCTG
*
1792447 TCTGTCTG
1 TCTGCCTG
*
1792455 TCTGTCTG
1 TCTGCCTG
*
1792463 CCTGCCTG
1 TCTGCCTG
*
1792471 CCTGCCTG
1 TCTGCCTG
*
1792479 CCTGCCTG
1 TCTGCCTG
*
1792487 CCTGCCTG
1 TCTGCCTG
*
1792495 CCTGCCTG
1 TCTGCCTG
*
1792503 CCTGCCTG
1 TCTGCCTG
*
1792511 CCTGCCTG
1 TCTGCCTG
* *
1792519 CCTGCATG
1 TCTGCCTG
*
1792527 CCTGCCTG
1 TCTGCCTG
*
1792535 CCTGCCTG
1 TCTGCCTG
* *
1792543 CCTACCTG
1 TCTGCCTG
*
1792551 CCTGCCTG
1 TCTGCCTG
*
1792559 CCTGCCTG
1 TCTGCCTG
*
1792567 CCTGCCTG
1 TCTGCCTG
*
1792575 CCTGCCTG
1 TCTGCCTG
1792583 TCTGCCTG
1 TCTGCCTG
*
1792591 TCTGTCTG
1 TCTGCCTG
*
1792599 TCTGTCTG
1 TCTGCCTG
*
1792607 TCTGTCTG
1 TCTGCCTG
*
1792615 TCTGTCTG
1 TCTGCCTG
1792623 TCT
1 TCT
1792626 ATCTATCTAT
Statistics
Matches: 223, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
6 6 0.03
8 217 0.97
ACGTcount: A:0.01, C:0.37, G:0.24, T:0.37
Consensus pattern (8 bp):
TCTGCCTG
Found at i:1792459 original size:4 final size:4
Alignment explanation
Indices: 1792460--1792590 Score: 235
Period size: 4 Copynumber: 32.8 Consensus size: 4
1792450 GTCTGTCTGT
1792460 CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC
1 CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC
* *
1792508 CTGC CTGC CTGC CTGC ATGC CTGC CTGC CTGC CTGC CTAC CTGC CTGC
1 CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC
*
1792556 CTGC CTGC CTGC CTGC CTGC CTGC CTGT CTGC CTG
1 CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTG
1792591 TCTGTCTGTC
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 121 1.00
ACGTcount: A:0.02, C:0.48, G:0.24, T:0.26
Consensus pattern (4 bp):
CTGC
Found at i:1792595 original size:4 final size:4
Alignment explanation
Indices: 1792580--1792625 Score: 83
Period size: 4 Copynumber: 11.5 Consensus size: 4
1792570 GCCTGCCTGC
*
1792580 CTGT CTGC CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CT
1 CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CT
1792626 ATCTATCTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.00, C:0.28, G:0.24, T:0.48
Consensus pattern (4 bp):
CTGT
Found at i:1792625 original size:12 final size:12
Alignment explanation
Indices: 1792390--1792622 Score: 202
Period size: 12 Copynumber: 19.6 Consensus size: 12
1792380 ATCTATCTGT
* *
1792390 CTGTCTGTCTGT
1 CTGTCTGCCTGC
* *
1792402 CTGTCTGTCTGT
1 CTGTCTGCCTGC
*
1792414 CTGTCTG--TGT
1 CTGTCTGCCTGC
* *
1792424 CTGTCTGTCTGT
1 CTGTCTGCCTGC
* *
1792436 CTGTCTGTCTGT
1 CTGTCTGCCTGC
* *
1792448 CTGTCTGTCTGT
1 CTGTCTGCCTGC
*
1792460 CTGCCTGCCTGC
1 CTGTCTGCCTGC
*
1792472 CTGCCTGCCTGC
1 CTGTCTGCCTGC
*
1792484 CTGCCTGCCTGC
1 CTGTCTGCCTGC
*
1792496 CTGCCTGCCTGC
1 CTGTCTGCCTGC
*
1792508 CTGCCTGCCTGC
1 CTGTCTGCCTGC
1792520 CTG-CATGCCTGC
1 CTGTC-TGCCTGC
*
1792532 CTGCCTGCCTGC
1 CTGTCTGCCTGC
**
1792544 CTACCTGCCTGC
1 CTGTCTGCCTGC
*
1792556 CTGCCTGCCTGC
1 CTGTCTGCCTGC
*
1792568 CTGCCTGCCTGC
1 CTGTCTGCCTGC
*
1792580 CTGTCTGCCTGT
1 CTGTCTGCCTGC
* *
1792592 CTGTCTGTCTGT
1 CTGTCTGCCTGC
* *
1792604 CTGTCTGTCTGT
1 CTGTCTGCCTGC
1792616 CTGTCTG
1 CTGTCTG
1792623 TCTATCTATC
Statistics
Matches: 209, Mismatches: 8, Indels: 8
0.93 0.04 0.04
Matches are distributed among these distances:
10 10 0.05
11 1 0.00
12 197 0.94
13 1 0.00
ACGTcount: A:0.01, C:0.38, G:0.25, T:0.36
Consensus pattern (12 bp):
CTGTCTGCCTGC
Found at i:1792630 original size:4 final size:4
Alignment explanation
Indices: 1792623--1792647 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1792613 TGTCTGTCTG
1792623 TCTA TCTA TCTA TCTA TCTA TCTA T
1 TCTA TCTA TCTA TCTA TCTA TCTA T
1792648 TCCTAGTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TCTA
Found at i:1794402 original size:4 final size:4
Alignment explanation
Indices: 1794395--1794472 Score: 133
Period size: 4 Copynumber: 20.0 Consensus size: 4
1794385 TATCTATCTA
*
1794395 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG --TG TTTG TCTG TCTG
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
1794441 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
1794473 CCTGCCTGCC
Statistics
Matches: 71, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
2 2 0.03
4 69 0.97
ACGTcount: A:0.00, C:0.23, G:0.26, T:0.51
Consensus pattern (4 bp):
TCTG
Found at i:1794477 original size:4 final size:4
Alignment explanation
Indices: 1794470--1794580 Score: 222
Period size: 4 Copynumber: 27.8 Consensus size: 4
1794460 GTCTGTCTGT
1794470 CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC
1 CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC
1794518 CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC
1 CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC CTGC
1794566 CTGC CTGC CTGC CTG
1 CTGC CTGC CTGC CTG
1794581 TCTGTCTCTA
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 107 1.00
ACGTcount: A:0.00, C:0.50, G:0.25, T:0.25
Consensus pattern (4 bp):
CTGC
Found at i:1794594 original size:4 final size:4
Alignment explanation
Indices: 1794587--1798020 Score: 6705
Period size: 4 Copynumber: 864.0 Consensus size: 4
1794577 CCTGTCTGTC
1794587 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1794635 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1794683 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1794731 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1794779 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1794827 TC-- TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1794873 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1794921 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1794969 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795017 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795065 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795113 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795161 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795209 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795257 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795305 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795353 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795401 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795449 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA --TA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795495 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795543 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795591 TC-- TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795637 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795685 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795733 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795781 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795829 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795877 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795925 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1795973 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796021 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TC-- TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796067 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796115 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796163 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796211 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796259 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796307 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796355 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796403 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796451 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796499 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796547 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796595 TCTA TCTA TCTA TC-- TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796641 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796689 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796737 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796785 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796833 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796881 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796929 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1796977 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797025 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
*
1797073 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCGA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797121 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797169 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797217 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797265 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797313 TCTA TCTA TCTA TCTA TCTA --TA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797359 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797407 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797455 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797503 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TC-- TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797549 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797597 TC-- TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797643 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797691 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797739 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797787 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797835 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797883 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797931 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TC-- TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1797977 TCTA -CTA TC-A TCTA TCTA TCTA TCTA TCTA TC-A TC-A TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1798021 ATATCTAATT
Statistics
Matches: 3407, Mismatches: 2, Indels: 42
0.99 0.00 0.01
Matches are distributed among these distances:
2 18 0.01
3 12 0.00
4 3377 0.99
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
TCTA
Found at i:1802010 original size:24 final size:25
Alignment explanation
Indices: 1801983--1802032 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
1801973 TTTTCCCTTA
1801983 AAGAAGTTTATTTTTT-ATGAAATG
1 AAGAAGTTTATTTTTTCATGAAATG
* *
1802007 AAGAATTTTTTTTTTTCATGAAATG
1 AAGAAGTTTATTTTTTCATGAAATG
1802032 A
1 A
1802033 CTTGATTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (25 bp):
AAGAAGTTTATTTTTTCATGAAATG
Found at i:1809181 original size:42 final size:41
Alignment explanation
Indices: 1809107--1809199 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 41
1809097 TGCCAAAATT
** * **
1809107 GTATCGATACTGAAAGGGAGTATCGTTACCATAGTATAGTA
1 GTATCGATACTGAAAGAAAGTATCATTACCATAGTATAAAA
*
1809148 GTATCGATACTGAGAGAAAGGTATCATTACCATAGTATAAAA
1 GTATCGATACTGAAAGAAA-GTATCATTACCATAGTATAAAA
1809190 GTATCGATAC
1 GTATCGATAC
1809200 CATGGTAGGG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
41 16 0.36
42 29 0.64
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.28
Consensus pattern (41 bp):
GTATCGATACTGAAAGAAAGTATCATTACCATAGTATAAAA
Found at i:1809597 original size:20 final size:20
Alignment explanation
Indices: 1809572--1809649 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 20
1809562 TATATGAAAT
1809572 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1809592 GCATGAAAGAATGCCATAAATGAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
1809618 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
1809638 GCATGAAAGGAT
1 GCATGAAAGGAT
1809650 ACCATAAATG
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
20 25 0.54
21 3 0.07
22 1 0.02
24 1 0.02
25 3 0.07
26 13 0.28
ACGTcount: A:0.44, C:0.10, G:0.26, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:1809632 original size:46 final size:46
Alignment explanation
Indices: 1809565--1809663 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
1809555 TTATTATTAT
*
1809565 ATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGCCATAA
1 ATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATACCATAA
* *
1809611 ATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATACCATAA
1 ATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATACCATAA
1809657 ATGAAAT
1 ATGAAAT
1809664 TAACAAATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.46, C:0.10, G:0.22, T:0.21
Consensus pattern (46 bp):
ATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATACCATAA
Found at i:1821615 original size:21 final size:21
Alignment explanation
Indices: 1821589--1821672 Score: 64
Period size: 21 Copynumber: 3.9 Consensus size: 21
1821579 TTTTGGTACA
1821589 GAGGGAATCGATCCCCCCCAT
1 GAGGGAATCGATCCCCCCCAT
* * **
1821610 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATCCCCCCCAT
*
1821631 GAATTGGAATCGATTCCCCCCACA-
1 G-A-GGGAATCGA-TCCCCCC-CAT
*
1821655 G-GGGAATCGATACCCCCC
1 GAGGGAATCGATCCCCCCC
1821673 TGGGGTTCTG
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
19 1 0.02
20 6 0.12
21 26 0.54
22 1 0.02
23 7 0.15
24 7 0.15
ACGTcount: A:0.24, C:0.36, G:0.23, T:0.18
Consensus pattern (21 bp):
GAGGGAATCGATCCCCCCCAT
Found at i:1823913 original size:11 final size:11
Alignment explanation
Indices: 1823897--1823926 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1823887 GGAGAAGTAG
1823897 TGTGTTTTAAA
1 TGTGTTTTAAA
*
1823908 TGTGTTTTAAG
1 TGTGTTTTAAA
1823919 TGTGTTTT
1 TGTGTTTT
1823927 TAAAATGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (11 bp):
TGTGTTTTAAA
Found at i:1825917 original size:26 final size:26
Alignment explanation
Indices: 1825881--1826062 Score: 286
Period size: 26 Copynumber: 7.2 Consensus size: 26
1825871 TATTATTATT
1825881 TGAAATGCATGAAAGGATGCCATAAA
1 TGAAATGCATGAAAGGATGCCATAAA
1825907 TGAAATGCATGAAAGGATGCCATAAA
1 TGAAATGCATGAAAGGATGCCATAAA
1825933 TGAAATGCATGAAAGGATGCCATAAA
1 TGAAATGCATGAAAGGATGCCATAAA
1825959 TGAAATGCATGAAAGGATGCCATAAA
1 TGAAATGCATGAAAGGATGCCATAAA
* *
1825985 TGAAATGCATGAAAGAATGTCATAAA
1 TGAAATGCATGAAAGGATGCCATAAA
1826011 TGAAATGCATGAAAGGATG-CAT---
1 TGAAATGCATGAAAGGATGCCATAAA
* *
1826033 T--AAGGCATGAAAGGATGCTATAAA
1 TGAAATGCATGAAAGGATGCCATAAA
1826057 TGAAAT
1 TGAAAT
1826063 TAACAAATAA
Statistics
Matches: 144, Mismatches: 6, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
20 15 0.10
21 2 0.01
22 1 0.01
24 1 0.01
25 3 0.02
26 122 0.85
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (26 bp):
TGAAATGCATGAAAGGATGCCATAAA
Found at i:1842748 original size:3 final size:3
Alignment explanation
Indices: 1842740--1842791 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
1842730 TGTAATTATT
*
1842740 TAA TAA TAA TAA TAA TAGA -AA TAA -AA TAA TAA TAA T-A TACT TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TA-A TAA
1842784 TAA TAA TA
1 TAA TAA TA
1842792 TAAAAAAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
2 5 0.12
3 34 0.81
4 3 0.07
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1843281 original size:112 final size:112
Alignment explanation
Indices: 1843143--1843473 Score: 449
Period size: 109 Copynumber: 3.0 Consensus size: 112
1843133 AGAGTCATGC
* * *
1843143 AAAGGTTGAACAAGCTCTTCTCATTATGAAATTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-AGTTCTTCTCATT
* *
1843207 ATGAACTTTCTCTGGAAAAGTTGATGCATCGAGTGATGAATTCGAGCA
65 ATGAACTTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCGAGCA
* * * *
1843255 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTTAG-TTG-ACTTCTCATTA
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGTTCTTCTCATTA
* **
1843318 TGAACTCTTC-C-GGAAATGTTGATCCATCGAATGATGAATTTAAGCA
66 TGAACT-TTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCGAGCA
*
1843364 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-AGTTCTTCTCATT
* *
1843429 ATGAAC-TTCTTCTGGAACAGTTGATCCATCGAATGATGGATTCGA
65 ATGAACTTTC-TCTGGAAAAGTTGATCCATCGAATGATGAATTCGA
1843474 ATTTTTGCTA
Statistics
Matches: 189, Mismatches: 22, Indels: 15
0.84 0.10 0.07
Matches are distributed among these distances:
109 77 0.41
110 21 0.11
111 5 0.03
112 53 0.28
113 33 0.17
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (112 bp):
AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGTTCTTCTCATTA
TGAACTTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCGAGCA
Found at i:1852408 original size:15 final size:15
Alignment explanation
Indices: 1852388--1852426 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1852378 TGCAATGAAT
1852388 AATGAATGTGTACAA
1 AATGAATGTGTACAA
*
1852403 AATGAATGTGTGCAA
1 AATGAATGTGTACAA
*
1852418 AAAGAATGT
1 AATGAATGT
1852427 ATGCAAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.46, C:0.05, G:0.23, T:0.26
Consensus pattern (15 bp):
AATGAATGTGTACAA
Found at i:1852431 original size:15 final size:15
Alignment explanation
Indices: 1852400--1852434 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1852390 TGAATGTGTA
* *
1852400 CAAAATGAATGTGTG
1 CAAAAAGAATGTATG
1852415 CAAAAAGAATGTATG
1 CAAAAAGAATGTATG
1852430 CAAAA
1 CAAAA
1852435 GGTATTGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.09, G:0.20, T:0.20
Consensus pattern (15 bp):
CAAAAAGAATGTATG
Found at i:1856431 original size:139 final size:142
Alignment explanation
Indices: 1856157--1856438 Score: 321
Period size: 140 Copynumber: 2.0 Consensus size: 142
1856147 TAATTTTATG
* * *
1856157 AAAATATATTAATTTAAATATAAAATAAGATATTTATTTATTTAGAAATATCAGAAAATGTCTTC
1 AAAATATATTAATTT-AATATAAAATAAGATATTTAATTATTTAGAAATATCAGAAAATGACATC
* * * *
1856222 TAGGTGCTTTAAGACAACTCCTTTCTTAATATTAAAATATAAATAAATATTAATAAAACATTTAT
65 CAGGTGCTTTAAGACAACTCATTTCTTAATATTAAAATATAAATAAAAATTAATAAAACATTGAT
1856287 CTTAAAA-TAATT
130 CTTAAAAGTAATT
* *
1856299 AAAATATATATAATTT-ATA-AAAGTAATATATTTAATTATTTA-AAATATCAGAAAATGGACAT
1 AAAATATAT-TAATTTAATATAAAATAAGATATTTAATTATTTAGAAATATCAGAAAAT-GACAT
* * * *
1856361 CCAGTTGCTTTAAGACTAC-CATTTCTTAATATTGAAAA-ATAAATATTAAAATATGATTAAA-A
64 CCAGGTGCTTTAAGACAACTCATTTCTTAATATT-AAAATATAAATA--AAAAT-TAATAAAACA
1856423 -TGAT-TTAAAAGTAATT
125 TTGATCTTAAAAGTAATT
1856439 TATTTAATTT
Statistics
Matches: 120, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
139 40 0.33
140 51 0.43
141 8 0.07
142 15 0.12
143 6 0.05
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (142 bp):
AAAATATATTAATTTAATATAAAATAAGATATTTAATTATTTAGAAATATCAGAAAATGACATCC
AGGTGCTTTAAGACAACTCATTTCTTAATATTAAAATATAAATAAAAATTAATAAAACATTGATC
TTAAAAGTAATT
Found at i:1858858 original size:16 final size:17
Alignment explanation
Indices: 1858833--1858871 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
1858823 ACTTGAAGAA
1858833 GAAAAAGAAAAAA-AAG
1 GAAAAAGAAAAAATAAG
*
1858849 GAAAAGGAAAAAATAAG
1 GAAAAAGAAAAAATAAG
1858866 GAAAAA
1 GAAAAA
1858872 ATAAGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (17 bp):
GAAAAAGAAAAAATAAG
Found at i:1858868 original size:11 final size:11
Alignment explanation
Indices: 1858852--1858881 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1858842 AAAAAAGGAA
1858852 AAGGAAAAAAT
1 AAGGAAAAAAT
1858863 AAGGAAAAAAT
1 AAGGAAAAAAT
1858874 AA-GAAAAA
1 AAGGAAAAA
1858882 TAAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (11 bp):
AAGGAAAAAAT
Found at i:1859888 original size:139 final size:138
Alignment explanation
Indices: 1859638--1860372 Score: 842
Period size: 139 Copynumber: 5.3 Consensus size: 138
1859628 CATCAACTAT
* ** * *
1859638 GACCAGATCTCCTCAATACATAGGAGTAGTGTCATCCTCAGATAACTAGACTTCCTCATCACGTA
1 GACCAGATCTCCTCAACATGTAGGAGCAGCGTCATCCTCAGATAAC-AGACTTCCTCATCACGTA
* * * * * *
1859703 GGAACCGTGTTCTCTCCAATTTATCCTTAAAGACGGCTAAAAGTCCTCATCATGTAGGAACAATA
65 GGAACCGTGTTGTCTCAAATTTATCCCTAAAGACGGCTAAACGTCCTCATCACGTAGGAACAATG
1859768 TCGTCCACC
130 TCGTCCACC
* * * * * *
1859777 GACCATATCTTCTCAACATATAGGAGCAGCATCATCCTCAGATAATCAGAGTTCGTCATCACGTA
1 GACCAGATCTCCTCAACATGTAGGAGCAGCGTCATCCTCAGATAA-CAGACTTCCTCATCACGTA
* * * *
1859842 GGAACTGTGTTGTCTCAAATTTATCGCTAAAGACGGCTAAACGTCCTCATCAAGTAAGAACAATG
65 GGAACCGTGTTGTCTCAAATTTATCCCTAAAGACGGCTAAACGTCCTCATCACGTAGGAACAATG
1859907 TCGTCCACC
130 TCGTCCACC
* * * * * *
1859916 GACCAGATCTCCTCAACACGTAGGAGCAACATCATCCTCATATAACTAGACTTACTCATCATGTA
1 GACCAGATCTCCTCAACATGTAGGAGCAGCGTCATCCTCAGATAAC-AGACTTCCTCATCACGTA
* * * * * * * *
1859981 GGAACTGTTTTGTCTCCAATTTATCCCTAAAGATGGTTAGACATCCTCATCAGGTAGGAACAATG
65 GGAACCGTGTTGTCTCAAATTTATCCCTAAAGACGGCTAAACGTCCTCATCACGTAGGAACAATG
**
1860046 TCGTCCAAT
130 TCGTCCACC
* * * * * *
1860055 GACCAGATTTCTTCAATATGTAGGAGCAGGGTAATCCTCAGATAACCAAACTTCCTCATCACGTA
1 GACCAGATCTCCTCAACATGTAGGAGCAGCGTCATCCTCAGATAA-CAGACTTCCTCATCACGTA
* * * *
1860120 GGAACCGTGTTGTCTCTAATTTATCCCTAAAGATGACTAAACGTCCTCATCACATAGGAACAATG
65 GGAACCGTGTTGTCTCAAATTTATCCCTAAAGACGGCTAAACGTCCTCATCACGTAGGAACAATG
*
1860185 TTGTCCACC
130 TCGTCCACC
* * *
1860194 GACCAAATCTCCTCAACGTGTAGGAGCAGCGTCATCCTCAGATAATCATACTTCCTCATCACGTA
1 GACCAGATCTCCTCAACATGTAGGAGCAGCGTCATCCTCAGATAA-CAGACTTCCTCATCACGTA
* * * ** * *
1860259 GGAACCGTGTTATCTCCAAA-GTATCCCTAAAGACGACTAAAATTTCTCATCACATAGGAACAAT
65 GGAACCGTGTTGTCT-CAAATTTATCCCTAAAGACGGCTAAACGTCCTCATCACGTAGGAACAAT
* *
1860323 GTTGTCCAAC
129 GTCGTCCACC
* * *
1860333 GACCAGATATCCTCAACACGTATGAGCAGCGTCATCCTCA
1 GACCAGATCTCCTCAACATGTAGGAGCAGCGTCATCCTCA
1860373 TACAGTTAGA
Statistics
Matches: 507, Mismatches: 85, Indels: 8
0.85 0.14 0.01
Matches are distributed among these distances:
138 1 0.00
139 501 0.99
140 5 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (138 bp):
GACCAGATCTCCTCAACATGTAGGAGCAGCGTCATCCTCAGATAACAGACTTCCTCATCACGTAG
GAACCGTGTTGTCTCAAATTTATCCCTAAAGACGGCTAAACGTCCTCATCACGTAGGAACAATGT
CGTCCACC
Found at i:1860604 original size:3 final size:3
Alignment explanation
Indices: 1860596--1860624 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1860586 TGGATTTTAA
1860596 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1860625 ATTTTACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1865839 original size:4 final size:4
Alignment explanation
Indices: 1865830--1865856 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1865820 TTTATTATTA
1865830 GAGG GAGG GAGG GAGG GAGG GAGG GAG
1 GAGG GAGG GAGG GAGG GAGG GAGG GAG
1865857 AGGGAGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.74, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:1866365 original size:15 final size:15
Alignment explanation
Indices: 1866342--1866375 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1866332 TTTTATAATG
1866342 TTAACAAAAAATAAA
1 TTAACAAAAAATAAA
* *
1866357 TTAATAAAAAGTAAA
1 TTAACAAAAAATAAA
1866372 TTAA
1 TTAA
1866376 ATATCTAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (15 bp):
TTAACAAAAAATAAA
Found at i:1867968 original size:14 final size:14
Alignment explanation
Indices: 1867946--1867981 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1867936 CATTTCAAAA
*
1867946 ATAAATTAAATAAT
1 ATAATTTAAATAAT
1867960 ATAATTTAAATAAT
1 ATAATTTAAATAAT
1867974 ATAATTTA
1 ATAATTTA
1867982 TCCTTTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAATTTAAATAAT
Found at i:1868086 original size:31 final size:31
Alignment explanation
Indices: 1868051--1868123 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
1868041 TTATTATATT
* ** *
1868051 TAAAATATATCAATTTAAACTATAATAAAAA
1 TAAAATATATAAATAAAAAATATAATAAAAA
* * *
1868082 TAAAAAATATAAATAAAAAATATAATTATAA
1 TAAAATATATAAATAAAAAATATAATAAAAA
1868113 TAAAAATATAT
1 T-AAAATATAT
1868124 TTTATAATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 25 0.76
32 8 0.24
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (31 bp):
TAAAATATATAAATAAAAAATATAATAAAAA
Found at i:1868095 original size:13 final size:13
Alignment explanation
Indices: 1868074--1868106 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1868064 TTTAAACTAT
*
1868074 AATAAAAATAAAA
1 AATATAAATAAAA
1868087 AATATAAATAAAA
1 AATATAAATAAAA
1868100 AATATAA
1 AATATAA
1868107 TTATAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AATATAAATAAAA
Found at i:1868114 original size:18 final size:17
Alignment explanation
Indices: 1868071--1868133 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 17
1868061 CAATTTAAAC
* *
1868071 TATAATAAAAATAAAAAA
1 TATAATAAAAAT-ATAAT
1868089 TATAAATAAAAAATATAAT
1 TAT-AAT-AAAAATATAAT
*
1868108 TATAATAAAAATATATTT
1 TATAATAAAAATATA-AT
1868126 TATAATAA
1 TATAATAA
1868134 CTCACTATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
17 9 0.23
18 15 0.38
19 9 0.23
20 6 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TATAATAAAAATATAAT
Found at i:1873734 original size:15 final size:15
Alignment explanation
Indices: 1873711--1873744 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1873701 TTTTATAATG
1873711 TTAACAAAAAATAAA
1 TTAACAAAAAATAAA
* *
1873726 TTAATAAAAAGTAAA
1 TTAACAAAAAATAAA
1873741 TTAA
1 TTAA
1873745 ATATCTAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (15 bp):
TTAACAAAAAATAAA
Found at i:1874882 original size:20 final size:22
Alignment explanation
Indices: 1874809--1874883 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 22
1874799 ATATTTATAA
* *
1874809 ATATAATAATAAAATTA-AAAC
1 ATATAATAATAAAATAATAAAG
* *
1874830 CT-TATATAATGAAAATAATAAAT
1 ATATA-ATAAT-AAAATAATAAAG
1874853 ATATAA-AATAAAA-AATAAAG
1 ATATAATAATAAAATAATAAAG
1874873 ATA-AATAATAA
1 ATATAATAATAA
1874884 GACAAGGAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
19 2 0.05
20 16 0.36
21 10 0.23
22 9 0.20
23 5 0.11
24 2 0.05
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (22 bp):
ATATAATAATAAAATAATAAAG
Found at i:1875500 original size:22 final size:22
Alignment explanation
Indices: 1875474--1875516 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1875464 AAAAATGTAT
1875474 ATTATAAATAAATTTAAAATAA
1 ATTATAAATAAATTTAAAATAA
* * *
1875496 ATTATTATTATATTTAAAATA
1 ATTATAAATAAATTTAAAATA
1875517 TATCAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTATAAATAAATTTAAAATAA
Found at i:1875551 original size:15 final size:15
Alignment explanation
Indices: 1875533--1875567 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1875523 TTTAAACTAT
1875533 AATAAAAATAAAAAA
1 AATAAAAATAAAAAA
*
1875548 AATACAAATAAAAAA
1 AATAAAAATAAAAAA
*
1875563 TATAA
1 AATAA
1875568 TTGTAATAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (15 bp):
AATAAAAATAAAAAA
Found at i:1881805 original size:104 final size:105
Alignment explanation
Indices: 1881589--1881811 Score: 261
Period size: 104 Copynumber: 2.1 Consensus size: 105
1881579 ATTTGACAAA
* * * *
1881589 ATTATCAATATAAATTGTGATGATTTTTTTTACACTAAAAATATATTATGTGACAATCAATATTG
1 ATTATCAATATAAATTGTGATAATTTATTTGACACTAAAAATATATTATGTGACAACCAATATTG
* *
1881654 TCACACTGACACTAAGTATTTTTAGTGACCAAATGTTTGATATT
66 T--CAC--ACACTAAGTATTTTTAGTGACCAAATGTTCGATACT
* * * * *
1881698 ATTATCAATATAAATTGTGATAAATTTATTTGACACTGAAAGTATATTTTGTGATAACCAATGTT
1 ATTATCAATATAAATTGTGAT-AATTTATTTGACACTAAAAATATATTATGTGACAACCAATATT
* *
1881763 GT-A-ACAGTAAGTTTTTTTAGTGACCAAATGTTCGATACT
65 GTCACACACTAAGTATTTTTAGTGACCAAATGTTCGATACT
*
1881802 ATTAACAATA
1 ATTATCAATA
1881812 ACTCTATCAC
Statistics
Matches: 99, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
104 41 0.41
107 1 0.01
109 21 0.21
110 36 0.36
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.40
Consensus pattern (105 bp):
ATTATCAATATAAATTGTGATAATTTATTTGACACTAAAAATATATTATGTGACAACCAATATTG
TCACACACTAAGTATTTTTAGTGACCAAATGTTCGATACT
Found at i:1886810 original size:13 final size:13
Alignment explanation
Indices: 1886792--1886816 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1886782 TTGACTTTTT
1886792 GGTCAAAGTCAAA
1 GGTCAAAGTCAAA
1886805 GGTCAAAGTCAA
1 GGTCAAAGTCAA
1886817 CTGGTTGACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (13 bp):
GGTCAAAGTCAAA
Found at i:1886839 original size:14 final size:15
Alignment explanation
Indices: 1886820--1886854 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1886810 AAGTCAACTG
*
1886820 GTTGACTTAGA-CGA
1 GTTGACTCAGACCGA
1886834 GTTGACTCAGACCGA
1 GTTGACTCAGACCGA
1886849 GTTGAC
1 GTTGAC
1886855 ACAGTGGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26
Consensus pattern (15 bp):
GTTGACTCAGACCGA
Found at i:1887825 original size:24 final size:27
Alignment explanation
Indices: 1887777--1887826 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
1887767 TTACTTATTT
1887777 TAATATATATAATATTAATTATTATAA
1 TAATATATATAATATTAATTATTATAA
*
1887804 TAATA-ATTTAAT-TTAATT-TTATA
1 TAATATATATAATATTAATTATTATA
1887827 TTATTTCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 6 0.27
26 6 0.27
27 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TAATATATATAATATTAATTATTATAA
Found at i:1890107 original size:861 final size:861
Alignment explanation
Indices: 1888441--1890170 Score: 3361
Period size: 861 Copynumber: 2.0 Consensus size: 861
1888431 AACTTCAAAA
*
1888441 ATGAGGCTTCTTTCAGTTATTACATATCTTAAAATAGTTTTTACAGAAGTACGGGTCTTTTACTA
1 ATGATGCTTCTTTCAGTTATTACATATCTTAAAATAGTTTTTACAGAAGTACGGGTCTTTTACTA
1888506 ATCTTTAACCAGTTGAGTATACATTCTCGCCAAAACTCTCCCTTATTCCCAATAAAAGAATATGA
66 ATCTTTAACCAGTTGAGTATACATTCTCGCCAAAACTCTCCCTTATTCCCAATAAAAGAATATGA
1888571 ACGGAATTATTCTTGTGGAATCAATTCGACCTTAGTTACGAGGTTAGGCTTATAGAGCAATAACA
131 ACGGAATTATTCTTGTGGAATCAATTCGACCTTAGTTACGAGGTTAGGCTTATAGAGCAATAACA
*
1888636 TCTCCCAATTTCATTTATGGAGTCGGGTCAGAATTTCTCGGATAAGTAACTCTCACATTACTCGT
196 TCTCCCAATTTCATTTATGGAGTCGGGTAAGAATTTCTCGGATAAGTAACTCTCACATTACTCGT
*
1888701 GAGATACTTTACAAAATTTGGAAAAATATTATTGATATTCCTTTATGCATAGGTCGATCCCTAAC
261 GAGATACTTTACAAAATTTGGAAAAATATTACTGATATTCCTTTATGCATAGGTCGATCCCTAAC
1888766 GAATAGAAAACTTAGGTTAGCTCGTTTCAGAGAGGGACTCGATCTTGGTGTTTCGACTTAGAGAA
326 GAATAGAAAACTTAGGTTAGCTCGTTTCAGAGAGGGACTCGATCTTGGTGTTTCGACTTAGAGAA
1888831 GTACAGTTACAGTCTAGGGGCATGTACTGACCAAACATCTTTTGACATTCGACCGGTCGGTCTAT
391 GTACAGTTACAGTCTAGGGGCATGTACTGACCAAACATCTTTTGACATTCGACCGGTCGGTCTAT
*
1888896 CTAGAAAAATTTGACTCAACCTAGGCTATGATACCACTAAATGTAAACCCCTCAAACTGATGAGG
456 CTAGAAAAATTTGACTCAACCTAGGCTATGATACCACTAAATGTAAACCCCTCAAACTGATAAGG
*
1888961 GTGGCCCAATCTGATCAAGGGTGTCCCATTAGGGCCACCGGAGTGACCCACCGTAAATATCTTAG
521 GTGGCCCAATCTGATCAAGGGTGTCCCATTAGGGCCACCGAAGTGACCCACCGTAAATATCTTAG
1889026 AAAAATTAAATTTATTATTAAAACATGTAACGTCATAAAATCATTTATAAATACAAAAGTAAATT
586 AAAAATTAAATTTATTATTAAAACATGTAACGTCATAAAATCATTTATAAATACAAAAGTAAATT
*
1889091 TTACTAGTATTCAGAAATAAAACAAATTTCAGACTCACATGTGAAACAAATTAGAACCTATTTGC
651 TTACTAGTATTCAGAAATAAAACAAATTTCAGACTCACATGTGAAACAAATTAGAACATATTTGC
*
1889156 CCCCTAATCACATGCACCGTACTCCTCAAGCAACGCTGATGAAACTCCCTTACTGAAGTCAATAG
716 CCCCTAATCACATGCACCGTACTCCTCAAGCAACGCCGATGAAACTCCCTTACTGAAGTCAATAG
1889221 CTGCACTGGTATGTTTCTTTTAACCTGAAATGGTGAATAACAGAGTGAGCTTTGGGAAGCTCAGT
781 CTGCACTGGTATGTTTCTTTTAACCTGAAATGGTGAATAACAGAGTGAGCTTTGGGAAGCTCAGT
1889286 AATACAATACTATCAG
846 AATACAATACTATCAG
1889302 ATGATGCTTCTTTCAGTTATTACATATCTTAAAATAGTTTTTACAGAAGTACGGGTCTTTTACTA
1 ATGATGCTTCTTTCAGTTATTACATATCTTAAAATAGTTTTTACAGAAGTACGGGTCTTTTACTA
1889367 ATCTTTAACCAGTTGAGTATACATTCTCGCCAAAACTCTCCCTTATTCCCAATAAAAGAATATGA
66 ATCTTTAACCAGTTGAGTATACATTCTCGCCAAAACTCTCCCTTATTCCCAATAAAAGAATATGA
1889432 ACGGAATTATTCTTGTGGAATCAATTCGACCTTAGTTACGAGGTTAGGCTTATAGAGCAATAACA
131 ACGGAATTATTCTTGTGGAATCAATTCGACCTTAGTTACGAGGTTAGGCTTATAGAGCAATAACA
1889497 TCTCCCAATTTCATTTATGGAGTCGGGTAAGAATTTCTCGGATAAGTAACTCTCACATTACTCGT
196 TCTCCCAATTTCATTTATGGAGTCGGGTAAGAATTTCTCGGATAAGTAACTCTCACATTACTCGT
* *
1889562 GAGGTACTTTACAAAATTTGGACAAATATTACTGATATTCCTTTATGCATAGGTCGATCCCTAAC
261 GAGATACTTTACAAAATTTGGAAAAATATTACTGATATTCCTTTATGCATAGGTCGATCCCTAAC
1889627 GAATAGAAAACTTAGGTTAGCTCGTTTCAGAGAGGGACTCGATCTTGGTGTTTCGACTTAGAGAA
326 GAATAGAAAACTTAGGTTAGCTCGTTTCAGAGAGGGACTCGATCTTGGTGTTTCGACTTAGAGAA
1889692 GTACAGTTACAGTCTAGGGGCATGTACTGACCAAACATCTTTTGACATTCGACCGGTCGGTCTAT
391 GTACAGTTACAGTCTAGGGGCATGTACTGACCAAACATCTTTTGACATTCGACCGGTCGGTCTAT
*
1889757 CTAGAAAAATTTGACTCAACCTAGGCTCTGATACCACTAAATGTAAACCCCTCAAACTGATAAGG
456 CTAGAAAAATTTGACTCAACCTAGGCTATGATACCACTAAATGTAAACCCCTCAAACTGATAAGG
*
1889822 GTGGCCCGATCTGATCAAGGGTGTCCCATTAGGGCCACCGAAGTGACCCACCGTAAATATCTTAG
521 GTGGCCCAATCTGATCAAGGGTGTCCCATTAGGGCCACCGAAGTGACCCACCGTAAATATCTTAG
1889887 AAAAATTAAATTTATTATTAAAACATGTAACGTCATAAAATCATTTATAAATACAAAAGTAAATT
586 AAAAATTAAATTTATTATTAAAACATGTAACGTCATAAAATCATTTATAAATACAAAAGTAAATT
1889952 TTACTAGTATTCAGAAATAAAACAAATTTCAGACTCACATGTGAAACAAATTAGAACATATTTGC
651 TTACTAGTATTCAGAAATAAAACAAATTTCAGACTCACATGTGAAACAAATTAGAACATATTTGC
1890017 CCCCTAATCACATGCACCGTACTCCTCAAGCAACGCCGATGAAACTCCCTTACTGAAGTCAATAG
716 CCCCTAATCACATGCACCGTACTCCTCAAGCAACGCCGATGAAACTCCCTTACTGAAGTCAATAG
1890082 CTGCACTGGTATGTTTCTTTTAACCTGAAATGGTGAATAACAGAGTGAGCTTTGGGAAGCTCAGT
781 CTGCACTGGTATGTTTCTTTTAACCTGAAATGGTGAATAACAGAGTGAGCTTTGGGAAGCTCAGT
1890147 AATACAATACTATCAG
846 AATACAATACTATCAG
1890163 ATGATGCT
1 ATGATGCT
1890171 ACAAGACATG
Statistics
Matches: 858, Mismatches: 11, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
861 858 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (861 bp):
ATGATGCTTCTTTCAGTTATTACATATCTTAAAATAGTTTTTACAGAAGTACGGGTCTTTTACTA
ATCTTTAACCAGTTGAGTATACATTCTCGCCAAAACTCTCCCTTATTCCCAATAAAAGAATATGA
ACGGAATTATTCTTGTGGAATCAATTCGACCTTAGTTACGAGGTTAGGCTTATAGAGCAATAACA
TCTCCCAATTTCATTTATGGAGTCGGGTAAGAATTTCTCGGATAAGTAACTCTCACATTACTCGT
GAGATACTTTACAAAATTTGGAAAAATATTACTGATATTCCTTTATGCATAGGTCGATCCCTAAC
GAATAGAAAACTTAGGTTAGCTCGTTTCAGAGAGGGACTCGATCTTGGTGTTTCGACTTAGAGAA
GTACAGTTACAGTCTAGGGGCATGTACTGACCAAACATCTTTTGACATTCGACCGGTCGGTCTAT
CTAGAAAAATTTGACTCAACCTAGGCTATGATACCACTAAATGTAAACCCCTCAAACTGATAAGG
GTGGCCCAATCTGATCAAGGGTGTCCCATTAGGGCCACCGAAGTGACCCACCGTAAATATCTTAG
AAAAATTAAATTTATTATTAAAACATGTAACGTCATAAAATCATTTATAAATACAAAAGTAAATT
TTACTAGTATTCAGAAATAAAACAAATTTCAGACTCACATGTGAAACAAATTAGAACATATTTGC
CCCCTAATCACATGCACCGTACTCCTCAAGCAACGCCGATGAAACTCCCTTACTGAAGTCAATAG
CTGCACTGGTATGTTTCTTTTAACCTGAAATGGTGAATAACAGAGTGAGCTTTGGGAAGCTCAGT
AATACAATACTATCAG
Found at i:1892142 original size:17 final size:17
Alignment explanation
Indices: 1892100--1892155 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
1892090 CTGAGCAGGC
* *
1892100 GGGTCGGGCAGACGGGC
1 GGGTCGGGCAAACGGGA
* * *
1892117 GAGTAGGGCAAATGGGA
1 GGGTCGGGCAAACGGGA
*
1892134 GGGTCGGGCAAACGGGT
1 GGGTCGGGCAAACGGGA
1892151 GGGTC
1 GGGTC
1892156 AAATAGACTT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.20, C:0.16, G:0.54, T:0.11
Consensus pattern (17 bp):
GGGTCGGGCAAACGGGA
Found at i:1893115 original size:33 final size:33
Alignment explanation
Indices: 1893051--1893117 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
1893041 TTTATGGAAG
* *
1893051 ATAAATATAATATAGTTAAATTTATTTTAAAAT
1 ATAAATATAATATAGTTAAATTTAATATAAAAT
1893084 ATAAATATAA-ATA-TTAAGATTTAAATATAAAAT
1 ATAAATATAATATAGTTAA-ATTT-AATATAAAAT
1893117 A
1 A
1893118 ATACCTAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 4 0.13
32 7 0.23
33 19 0.63
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (33 bp):
ATAAATATAATATAGTTAAATTTAATATAAAAT
Found at i:1894756 original size:19 final size:20
Alignment explanation
Indices: 1894732--1894779 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1894722 AATGATTTTC
* * *
1894732 TTTTGAAAGCTAAAATG-GA
1 TTTTGAAAACCAAAATGAAA
1894751 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACCAAAATGAAA
1894771 TTTTGAAAA
1 TTTTGAAAA
1894780 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (20 bp):
TTTTGAAAACCAAAATGAAA
Found at i:1897987 original size:40 final size:42
Alignment explanation
Indices: 1897935--1898090 Score: 264
Period size: 42 Copynumber: 3.8 Consensus size: 42
1897925 ATTATTGTCA
1897935 TCACAAATCACCAACTAAGACTA-ATGACAAAAA-AA-TATCG
1 TCACAAATCACCAACTAAGACTAGA-GACAAAAACAATTATCG
*
1897975 TTACAAATCACCAACTAAGACTAGAGACAAAAACAATTATCG
1 TCACAAATCACCAACTAAGACTAGAGACAAAAACAATTATCG
1898017 TCACAAATCACCAACTAAGACTAGAGACAAAAACAATTATCG
1 TCACAAATCACCAACTAAGACTAGAGACAAAAACAATTATCG
*
1898059 TCACAAATCACCAACTAAGACTAGTGACAAAA
1 TCACAAATCACCAACTAAGACTAGAGACAAAA
1898091 TGTTTTCATC
Statistics
Matches: 110, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
40 30 0.27
41 3 0.03
42 77 0.70
ACGTcount: A:0.51, C:0.23, G:0.09, T:0.17
Consensus pattern (42 bp):
TCACAAATCACCAACTAAGACTAGAGACAAAAACAATTATCG
Found at i:1906196 original size:18 final size:18
Alignment explanation
Indices: 1906175--1906225 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
1906165 TGGGTACTAG
1906175 ATTGAATTTCAGTACTCA
1 ATTGAATTTCAGTACTCA
*
1906193 ATTGAATTTCAGTACTCG
1 ATTGAATTTCAGTACTCA
1906211 ATTGAATTTCAGTAC
1 ATTGAATTTCAGTAC
1906226 GTCATTTCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (18 bp):
ATTGAATTTCAGTACTCA
Found at i:1910610 original size:9 final size:9
Alignment explanation
Indices: 1910596--1910620 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1910586 AGCTATTTTT
1910596 CTTCTTCTC
1 CTTCTTCTC
1910605 CTTCTTCTC
1 CTTCTTCTC
1910614 CTTCTTC
1 CTTCTTC
1910621 CCCGTTGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (9 bp):
CTTCTTCTC
Found at i:1922111 original size:21 final size:22
Alignment explanation
Indices: 1922072--1922115 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1922062 CTTTATAAAA
*
1922072 AAAATAGTTTTTAATCTTTGAG
1 AAAATAGCTTTTAATCTTTGAG
1922094 AAAATAGCTTTT-ATCTTTGAG
1 AAAATAGCTTTTAATCTTTGAG
1922115 A
1 A
1922116 TGTGAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (22 bp):
AAAATAGCTTTTAATCTTTGAG
Found at i:1922818 original size:18 final size:18
Alignment explanation
Indices: 1922804--1922849 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1922794 GTATTTTTAT
*
1922804 TTATTTTTTTATTTTGAA
1 TTATTTATTTATTTTGAA
1922822 TTATTTATTTATTTTGAA
1 TTATTTATTTATTTTGAA
*
1922840 TCATTTATTT
1 TTATTTATTT
1922850 CGAATAAATT
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:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (18 bp):
TTATTTATTTATTTTGAA
Found at i:1929524 original size:20 final size:20
Alignment explanation
Indices: 1929499--1929536 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1929489 AAAATTCAAG
1929499 TTTTTA-GATTTATATTTTTA
1 TTTTTAGGATTTA-ATTTTTA
1929519 TTTTTAGGATTTAATTTT
1 TTTTTAGGATTTAATTTT
1929537 AAACAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (20 bp):
TTTTTAGGATTTAATTTTTA
Found at i:1929669 original size:16 final size:16
Alignment explanation
Indices: 1929648--1929679 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1929638 AATAAAAATT
*
1929648 ATTTTCTTTTATTTTC
1 ATTTTCTTTAATTTTC
1929664 ATTTTCTTTAATTTTC
1 ATTTTCTTTAATTTTC
1929680 TTTCAATCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTCTTTAATTTTC
Found at i:1930278 original size:19 final size:19
Alignment explanation
Indices: 1930254--1930292 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1930244 ATCTTTTTTT
*
1930254 TTTTATTTTTCTTCTTCTA
1 TTTTATTTCTCTTCTTCTA
1930273 TTTTATTTCTCTTCTTCTA
1 TTTTATTTCTCTTCTTCTA
1930292 T
1 T
1930293 AAATCCCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATTTCTCTTCTTCTA
Found at i:1930660 original size:6 final size:6
Alignment explanation
Indices: 1930649--1930725 Score: 57
Period size: 6 Copynumber: 12.2 Consensus size: 6
1930639 GAGGGCATCA
* * *
1930649 TATTTT TATTTT TCGTTTTT TCAATTTT TATTTT TATTTT TATTTT CAATTT
1 TATTTT TATTTT T--ATTTT T--ATTTT TATTTT TATTTT TATTTT TATTTT
* *
1930701 TATGATT TA-TTT TGTTTT TATTTT T
1 TAT-TTT TATTTT TATTTT TATTTT T
1930726 CTTTGAATTT
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
5 3 0.05
6 38 0.68
7 4 0.07
8 11 0.20
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (6 bp):
TATTTT
Found at i:1930709 original size:25 final size:25
Alignment explanation
Indices: 1930666--1930713 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1930656 ATTTTTCGTT
*
1930666 TTTTCAATTTTTATTTTTATTTTTA
1 TTTTCAATTTTTATATTTATTTTTA
1930691 TTTTCAA-TTTTATGATTTATTTT
1 TTTTCAATTTTTAT-ATTTATTTT
1930714 GTTTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (25 bp):
TTTTCAATTTTTATATTTATTTTTA
Found at i:1930719 original size:25 final size:24
Alignment explanation
Indices: 1930664--1930719 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
1930654 TTATTTTTCG
*
1930664 TTTTTTCAATTTTTATTTTTATTT
1 TTTTTTCAATTTTTATATTTATTT
1930688 TTATTTTCAA-TTTTATGATTTATTT
1 TT-TTTTCAATTTTTAT-ATTTATTT
1930713 TGTTTTT
1 T-TTTTT
1930720 ATTTTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 8 0.29
25 19 0.68
26 1 0.04
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (24 bp):
TTTTTTCAATTTTTATATTTATTT
Found at i:1932094 original size:16 final size:15
Alignment explanation
Indices: 1932075--1932104 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1932065 ATAAAAAAGG
1932075 AAAAAAGGGAAAAAAT
1 AAAAAA-GGAAAAAAT
1932091 AAAAAAGGAAAAAA
1 AAAAAAGGAAAAAA
1932105 ACAGACCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (15 bp):
AAAAAAGGAAAAAAT
Found at i:1932105 original size:9 final size:8
Alignment explanation
Indices: 1932067--1932104 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
1932057 TTCGAACAAT
1932067 AAAAAAGG
1 AAAAAAGG
1932075 AAAAAAGGG
1 AAAAAA-GG
*
1932084 AAAAAA-T
1 AAAAAAGG
1932091 AAAAAAGG
1 AAAAAAGG
1932099 AAAAAA
1 AAAAAA
1932105 ACAGACCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 6 0.23
8 12 0.46
9 8 0.31
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (8 bp):
AAAAAAGG
Found at i:1938510 original size:58 final size:58
Alignment explanation
Indices: 1937995--1938502 Score: 790
Period size: 58 Copynumber: 8.8 Consensus size: 58
1937985 TTTCCTATAT
* * * **
1937995 GGAAATTCATACACTTAGTATGAATCTCTTAA-TGGTT-TGAACACAAAGTGCAAAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACT--TTATGCACACGAAGTGCCCAATAC
* * *
1938053 AGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTTGCACACGAAGTGCCCAATAT
1 GGAAATTCATACACTTAGTATGAATTTCTTAAC-TTTATGCACACGAAGTGCCCAATAC
* *
1938112 AGAAATTCATACACTTAGTATGAATTTCTTAACGTTT-TGCACACGAAGTGCCCAGTAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAAC-TTTATGCACACGAAGTGCCCAATAC
* *
1938170 GGAAATTCGTACACTAAGTATGAA-TTCTTAACTTTATGCACACGAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACTTTATGCACACGAAGTGCCCAATAC
*
1938227 GGAAATTCATGCACTTAGTATGAATTTCTTAACTTTATGCACACGAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACTTTATGCACACGAAGTGCCCAATAC
* *
1938285 GGAAATTCATACAGTTAGTATGAATTTCATAACTTTATGCACACGAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACTTTATGCACACGAAGTGCCCAATAC
*
1938343 GGAAATTCATACACTTAGTACGAATTTCTTAACTTTATGCACACGAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACTTTATGCACACGAAGTGCCCAATAC
1938401 GGAAATTCATACACTTAGTATGAATTTCTTAACTTTATGCACACGAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACTTTATGCACACGAAGTGCCCAATAC
* *
1938459 GGAAATTCATACACTTAGTATGAATTTATTAACTTTAAGCACAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACTTTATGCACAC
1938503 TTAGTGCCAA
Statistics
Matches: 419, Mismatches: 26, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
56 3 0.01
57 49 0.12
58 314 0.75
59 52 0.12
60 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.31
Consensus pattern (58 bp):
GGAAATTCATACACTTAGTATGAATTTCTTAACTTTATGCACACGAAGTGCCCAATAC
Found at i:1938951 original size:20 final size:20
Alignment explanation
Indices: 1938926--1938977 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1938916 GTTTTGAAAT
1938926 GGTATCGATA-TCCTCCCTTC
1 GGTATCGATACTCC-CCCTTC
1938946 GGTATCGATACTCCCCCTTC
1 GGTATCGATACTCCCCCTTC
1938966 GGTATCGATACT
1 GGTATCGATACT
1938978 GATTGAATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (20 bp):
GGTATCGATACTCCCCCTTC
Found at i:1943499 original size:21 final size:21
Alignment explanation
Indices: 1943473--1943517 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1943463 ATACTCGAGC
*
1943473 TAGATTCGATGCAATGGATGA
1 TAGATTCAATGCAATGGATGA
*
1943494 TAGATTCAATGCAGTGGATGA
1 TAGATTCAATGCAATGGATGA
1943515 TAG
1 TAG
1943518 GCTCGACGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (21 bp):
TAGATTCAATGCAATGGATGA
Found at i:1944283 original size:18 final size:18
Alignment explanation
Indices: 1944260--1944294 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1944250 TAACCTCAAA
1944260 ATGGTAACGATACCATGC
1 ATGGTAACGATACCATGC
*
1944278 ATGGTATCGATACCATG
1 ATGGTAACGATACCATG
1944295 TTAATATAGT
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:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (18 bp):
ATGGTAACGATACCATGC
Found at i:1966178 original size:8 final size:8
Alignment explanation
Indices: 1966165--1966207 Score: 68
Period size: 8 Copynumber: 5.2 Consensus size: 8
1966155 TAAATTAATA
1966165 TATATTTT
1 TATATTTT
1966173 TATATTTT
1 TATATTTT
1966181 TATATTTT
1 TATATTTT
*
1966189 AGATATTTT
1 -TATATTTT
1966198 TATATTTT
1 TATATTTT
1966206 TA
1 TA
1966208 ATTAATAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
8 25 0.78
9 7 0.22
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (8 bp):
TATATTTT
Found at i:1966180 original size:25 final size:25
Alignment explanation
Indices: 1966151--1966224 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
1966141 TTTTTTGAAA
1966151 ATTTTAAATTAATATATATTTTTAT
1 ATTTTAAATTAATATATATTTTTAT
* * *
1966176 ATTTTTATATT-TTAGATATTTTTAT
1 A-TTTTAAATTAATATATATTTTTAT
* *
1966201 ATTTTTAATTAATAATTTATTTTT
1 ATTTTAAATTAAT-ATATATTTTT
1966225 GTTTTATAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
24 7 0.18
25 15 0.39
26 16 0.42
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (25 bp):
ATTTTAAATTAATATATATTTTTAT
Found at i:1966196 original size:17 final size:16
Alignment explanation
Indices: 1966165--1966205 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
1966155 TAAATTAATA
*
1966165 TATATTTTTATATTTT
1 TATATTTTGATATTTT
1966181 TATATTTTAGATATTTT
1 TATATTTT-GATATTTT
1966198 TATATTTT
1 TATATTTT
1966206 TAATTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (16 bp):
TATATTTTGATATTTT
Found at i:1968956 original size:14 final size:14
Alignment explanation
Indices: 1968933--1968979 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1968923 ATATTATATA
1968933 AATAAA-AAATAAT
1 AATAAAGAAATAAT
*
1968946 AATAATGAAAT-AT
1 AATAAAGAAATAAT
*
1968959 AATTAAAGCAATAAT
1 AA-TAAAGAAATAAT
1968974 AATAAA
1 AATAAA
1968980 ATAATATTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 9 0.32
14 15 0.54
15 4 0.14
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (14 bp):
AATAAAGAAATAAT
Found at i:1969349 original size:113 final size:113
Alignment explanation
Indices: 1969128--1971048 Score: 3379
Period size: 113 Copynumber: 17.0 Consensus size: 113
1969118 GGACTAAATT
1969128 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAA---CTTCTTCCTTCTTCAGA
1 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* * * * *
1969190 TGAGTTCTTCTCATTATGAACTC-TCTCTGGAAAAGTTAATCCATCGAG
66 TGAGTTCTTCTCATTATGAACTCGAC-CTGGTAATGTTGATCCATCGAA
* * * *
1969238 TGAAGAATTCGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGA
1 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* *
1969303 TGAGTTCTTCTCATTATGAACTCG-CCTTGGCAATGTTGATCTATCGAA
66 TGAGTTCTTCTCATTATGAACTCGACC-TGGTAATGTTGATCCATCGAA
*
1969351 TGATAAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
1969416 TGAGTTCTTCTCATTATGAACTCGACCTGGCAATGTTGATCCATCGAA
66 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
* * *
1969464 TGATGAATTCAGGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGA
1 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* *
1969529 TGAGTTCTTCTTATTATGAACTCGACCTGGTAATGATGATCCATCGAA
66 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
1969577 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
1969642 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAA
66 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
1969690 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1969755 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
66 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
*
1969803 TGATGAATTCAAGTGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1969868 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
66 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
1969916 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* * *
1969981 TGAGTTCTCCTCATTATGAACTTGACCTGGTAATGCTGATCCATCGAA
66 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
1970029 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
1970094 TGAGTTCTTCTCATTATGAGCTCGACCTGGTAATGTTGATCCATCGAA
66 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
1970142 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
1970207 TGAGTTCTTCTCATTATGAACTCGACCTGCTAATGTTGATCCATCGAA
66 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
1970255 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* *
1970320 TGAGTTCTTCTCATTATAAACTCGACCTGGTAATGCTGATCCATCGAA
66 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
*
1970368 TGATGAATTCAAGCGAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1970433 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
66 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
1970481 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
1970546 TGAGTTCTTCTCATTATGAACTTGACCTGGTAATG-TGATCCATCGAA
66 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
1970593 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
1970658 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAA
66 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
* *
1970706 TGATGAATTCAAGTGAAAAGTTGAACAGGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* *
1970771 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCAAA
66 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
1970819 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* *
1970884 TGAGTTCTTCTCATTATAAACTCGACCTGGTAATGCTGATCCATCGAA
66 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
* *
1970932 TGATGAATTCAAGTGAAAAGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* ** * * *
1970997 TGGGTTCTTCTCATTATGAACTCTTCC-AGAAATGTTGATCCATTGAA
66 TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
1971044 TGATG
1 TGATG
1971049 GATTTGAACT
Statistics
Matches: 1739, Mismatches: 65, Indels: 12
0.96 0.04 0.01
Matches are distributed among these distances:
110 42 0.02
112 133 0.08
113 1562 0.90
114 2 0.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (113 bp):
TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
TGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAA
Found at i:1971480 original size:22 final size:23
Alignment explanation
Indices: 1971455--1971509 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
1971445 GATAAAGCTT
*
1971455 TCATCTTTGAAAAA-AGAATCTG
1 TCATCTTTGAAAAAGAGAATCTA
*
1971477 TCATCTTT-AAAAAGGGAATCTA
1 TCATCTTTGAAAAAGAGAATCTA
1971499 TCATCTTTGAA
1 TCATCTTTGAA
1971510 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 5 0.17
22 22 0.76
23 2 0.07
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (23 bp):
TCATCTTTGAAAAAGAGAATCTA
Found at i:1973875 original size:31 final size:32
Alignment explanation
Indices: 1973840--1973903 Score: 121
Period size: 31 Copynumber: 2.0 Consensus size: 32
1973830 AGATGTGGTC
1973840 TGAATTCATCAATTGCAGAG-TTGACAGATTT
1 TGAATTCATCAATTGCAGAGTTTGACAGATTT
1973871 TGAATTCATCAATTGCAGAGTTTGACAGATTT
1 TGAATTCATCAATTGCAGAGTTTGACAGATTT
1973903 T
1 T
1973904 ATATGTGCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 20 0.62
32 12 0.38
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (32 bp):
TGAATTCATCAATTGCAGAGTTTGACAGATTT
Found at i:1976403 original size:8 final size:8
Alignment explanation
Indices: 1976390--1976489 Score: 78
Period size: 8 Copynumber: 12.2 Consensus size: 8
1976380 CTTGATTTAA
1976390 TTTTTTCT
1 TTTTTTCT
1976398 TTTTTTCT
1 TTTTTTCT
1976406 TTTTTTC-
1 TTTTTTCT
* *
1976413 CTTTTTGT
1 TTTTTTCT
*
1976421 TTTTTCCT
1 TTTTTTCT
*
1976429 TTTTAT-T
1 TTTTTTCT
* *
1976436 TCTTTCCT
1 TTTTTTCT
1976444 TTTTTTCCTTT
1 TTTTTT-C--T
1976455 TTTTTTCT
1 TTTTTTCT
*
1976463 TTTTTCCT
1 TTTTTTCT
1976471 CTTTTTTCT
1 -TTTTTTCT
*
1976480 TTTTTCCT
1 TTTTTTCT
1976488 TT
1 TT
1976490 CTTTGCTGGA
Statistics
Matches: 71, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
7 9 0.13
8 46 0.65
9 8 0.11
10 1 0.01
11 7 0.10
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.80
Consensus pattern (8 bp):
TTTTTTCT
Found at i:1976409 original size:9 final size:9
Alignment explanation
Indices: 1976390--1976484 Score: 70
Period size: 9 Copynumber: 10.4 Consensus size: 9
1976380 CTTGATTTAA
1976390 TTTTTTC-T
1 TTTTTTCTT
1976398 TTTTTTCTT
1 TTTTTTCTT
*
1976407 TTTTTCCTT
1 TTTTTTCTT
1976416 TTTGTTT-TT
1 TTT-TTTCTT
*
1976425 TCCTTTTTATT
1 T--TTTTTCTT
* *
1976436 TCTTTCCTT
1 TTTTTTCTT
*
1976445 TTTTTCCTT
1 TTTTTTCTT
1976454 TTTTTT-TCT
1 TTTTTTCT-T
* *
1976463 TTTTTCCTC
1 TTTTTTCTT
1976472 TTTTTTCTT
1 TTTTTTCTT
1976481 TTTT
1 TTTT
1976485 CCTTTCTTTG
Statistics
Matches: 69, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
8 8 0.12
9 50 0.72
10 6 0.09
11 5 0.07
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.81
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:1976410 original size:10 final size:10
Alignment explanation
Indices: 1976397--1976477 Score: 56
Period size: 10 Copynumber: 7.4 Consensus size: 10
1976387 TAATTTTTTC
1976397 TTTTTTTCTT
1 TTTTTTTCTT
1976407 TTTTTCCTT-TT
1 TTTTT--TTCTT
1976418 TGTTTTTTCCTT
1 T-TTTTTT-CTT
*
1976430 TTTATTTCTTT
1 TTTTTTTC-TT
1976441 CCTTTTTTTCCTT
1 --TTTTTTT-CTT
1976454 TTTTTTTCTT
1 TTTTTTTCTT
**
1976464 TTTTCCTCTT
1 TTTTTTTCTT
1976474 TTTT
1 TTTT
1976478 CTTTTTTCCT
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
10 23 0.40
11 17 0.29
12 9 0.16
13 8 0.14
14 1 0.02
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.80
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:1976417 original size:24 final size:24
Alignment explanation
Indices: 1976390--1976489 Score: 82
Period size: 23 Copynumber: 4.1 Consensus size: 24
1976380 CTTGATTTAA
1976390 TTTTTTCTTTTTTTCTTTTTTTCC
1 TTTTTTCTTTTTTTCTTTTTTTCC
* *
1976414 -TTTTTGTTTTTTCCTTTTTATT--
1 TTTTTTCTTTTTTTCTTTTT-TTCC
* * *
1976436 TCTTTCCTTTTTTTCCTTTTTTTTTC
1 TTTTTTCTTTTTTT-C-TTTTTTTCC
1976462 TTTTTTCCTCTTTTTTC-TTTTTTCC
1 TTTTTT-CT-TTTTTTCTTTTTTTCC
1976487 TTT
1 TTT
1976490 CTTTGCTGGA
Statistics
Matches: 59, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
23 26 0.44
24 5 0.08
25 15 0.25
26 4 0.07
27 3 0.05
28 6 0.10
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.80
Consensus pattern (24 bp):
TTTTTTCTTTTTTTCTTTTTTTCC
Found at i:1976441 original size:29 final size:30
Alignment explanation
Indices: 1976390--1976447 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
1976380 CTTGATTTAA
* * *
1976390 TTTTTTCTTTTTTTCTTTTTTTCCTTTTTG
1 TTTTTTCTCTTTTTATTTCTTTCCTTTTTG
1976420 TTTTTTC-CTTTTTATTTCTTTCCTTTTT
1 TTTTTTCTCTTTTTATTTCTTTCCTTTTT
1976448 TTCCTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (30 bp):
TTTTTTCTCTTTTTATTTCTTTCCTTTTTG
Found at i:1976490 original size:29 final size:29
Alignment explanation
Indices: 1976401--1976493 Score: 88
Period size: 27 Copynumber: 3.2 Consensus size: 29
1976391 TTTTTCTTTT
* *
1976401 TTTCTTTTTT--TCCTTTTTGTTTTTTCC
1 TTTCTTTTTTCCTCTTTTTTCTTTTTTCC
*
1976428 TTTTTATTTCTTTCCT-TTTTTTCCTTTTTT--
1 --TTTCTTT-TTTCCTCTTTTTT-CTTTTTTCC
1976458 TTTCTTTTTTCCTCTTTTTTCTTTTTTCC
1 TTTCTTTTTTCCTCTTTTTTCTTTTTTCC
1976487 TTTCTTT
1 TTTCTTT
1976494 GCTGGATTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
27 13 0.25
28 12 0.23
29 13 0.25
30 3 0.06
31 5 0.09
32 7 0.13
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (29 bp):
TTTCTTTTTTCCTCTTTTTTCTTTTTTCC
Found at i:1976503 original size:27 final size:25
Alignment explanation
Indices: 1976473--1976525 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 25
1976463 TTTTTCCTCT
1976473 TTTTTCTTTTTTCCTTTCTTTGCTGGA
1 TTTTTC-TTTTT-CTTTCTTTGCTGGA
*
1976500 TTTTTCTTTTTCTTTCTTTGTTGGA
1 TTTTTCTTTTTCTTTCTTTGCTGGA
1976525 T
1 T
1976526 GAGTATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 14 0.56
26 5 0.20
27 6 0.24
ACGTcount: A:0.04, C:0.15, G:0.11, T:0.70
Consensus pattern (25 bp):
TTTTTCTTTTTCTTTCTTTGCTGGA
Found at i:1982111 original size:3 final size:3
Alignment explanation
Indices: 1982096--1982154 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
1982086 TATTTATATA
* * **
1982096 AAT AAT AAA AAT AAT AAT AAT GA- AAT AAT AATT AA- AGC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
1982140 AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT A
1982155 TTGCAAATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1982163 original size:26 final size:28
Alignment explanation
Indices: 1982104--1982165 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
1982094 TAAATAATAA
*
1982104 AAATAATAATAATGAAATAATAATTAAAGC
1 AAATAATAATAATAAAATAATAATT--AGC
1982134 -AATAATAATAATAAAATAAT-ATT-GC
1 AAATAATAATAATAAAATAATAATTAGC
1982159 AAATAAT
1 AAATAAT
1982166 GATTAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 2 0.07
26 6 0.20
28 3 0.10
29 19 0.63
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (28 bp):
AAATAATAATAATAAAATAATAATTAGC
Found at i:1982231 original size:29 final size:29
Alignment explanation
Indices: 1982182--1982243 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
1982172 AATAAAAGGA
* *
1982182 ATTAAAAATATAGTGT-TAAAATGTAAAAT
1 ATTAAAAATATAATGTCAAAAATG-AAAAT
1982211 ATTAAAAATA-AATAGTCAAAAATGAAAAT
1 ATTAAAAATATAAT-GTCAAAAATGAAAAT
1982240 -TTAA
1 ATTAA
1982244 TGATTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
28 6 0.21
29 17 0.59
30 6 0.21
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.31
Consensus pattern (29 bp):
ATTAAAAATATAATGTCAAAAATGAAAAT
Found at i:1983593 original size:6 final size:6
Alignment explanation
Indices: 1983578--1983666 Score: 78
Period size: 6 Copynumber: 15.0 Consensus size: 6
1983568 GTTGTATCTG
* * *
1983578 TAATAA -AATAA TAATAT TAATAA TAATAA TAATAT TAATAA TAAAAA
1 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA
* *
1983625 TAA-ATA TAATAG TAATAA AAATAA -ATATAA TAA-ATA TAATAA
1 TAATA-A TAATAA TAATAA TAATAA TA-ATAA TAATA-A TAATAA
1983667 AAAAACCAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
5 8 0.12
6 57 0.84
7 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (6 bp):
TAATAA
Found at i:1983600 original size:9 final size:9
Alignment explanation
Indices: 1983586--1983620 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
1983576 TGTAATAAAA
1983586 TAATAATAT
1 TAATAATAT
*
1983595 TAATAATAA
1 TAATAATAT
1983604 TAATAATAT
1 TAATAATAT
1983613 TAATAATA
1 TAATAATA
1983621 AAAATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TAATAATAT
Found at i:1983626 original size:9 final size:9
Alignment explanation
Indices: 1983578--1983669 Score: 55
Period size: 9 Copynumber: 10.0 Consensus size: 9
1983568 GTTGTATCTG
1983578 TAAT-AAAA
1 TAATAAAAA
1983586 TAATAATATTAA
1 TAATAA-A--AA
*
1983598 TAATAATAA
1 TAATAAAAA
**
1983607 TAATATTAA
1 TAATAAAAA
1983616 TAATAAAAA
1 TAATAAAAA
*
1983625 TAA-ATATAA
1 TAATA-AAAA
*
1983634 TAGTAATAAA
1 TAATAA-AAA
*
1983644 -AATAAATA
1 TAATAAAAA
*
1983652 TAATAAATA
1 TAATAAAAA
1983661 TAATAAAAA
1 TAATAAAAA
1983670 AACCAAATGT
Statistics
Matches: 66, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
8 7 0.11
9 47 0.71
10 4 0.06
12 8 0.12
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (9 bp):
TAATAAAAA
Found at i:1983633 original size:15 final size:15
Alignment explanation
Indices: 1983615--1983669 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
1983605 AATAATATTA
1983615 ATAATAAAAATAAAT
1 ATAATAAAAATAAAT
** *
1983630 ATAATAGTAATAAAA
1 ATAATAAAAATAAAT
*
1983645 ATAA-ATATAATAAAT
1 ATAATA-AAAATAAAT
1983660 ATAATAAAAA
1 ATAATAAAAA
1983670 AACCAAATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
14 1 0.03
15 30 0.94
16 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (15 bp):
ATAATAAAAATAAAT
Found at i:1983663 original size:21 final size:21
Alignment explanation
Indices: 1983583--1983657 Score: 89
Period size: 21 Copynumber: 3.5 Consensus size: 21
1983573 ATCTGTAATA
* *
1983583 AAATAATAATATTAATAATAAT
1 AAAT-ATAATAATAATAAAAAT
*
1983605 -AATAATATTAATAATAAAAAT
1 AAAT-ATAATAATAATAAAAAT
*
1983626 AAATATAATAGTAATAAAAAT
1 AAATATAATAATAATAAAAAT
1983647 AAATATAATAA
1 AAATATAATAA
1983658 ATATAATAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 43 0.93
22 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (21 bp):
AAATATAATAATAATAAAAAT
Found at i:1985366 original size:122 final size:122
Alignment explanation
Indices: 1985141--1985383 Score: 434
Period size: 122 Copynumber: 2.0 Consensus size: 122
1985131 CTACACCGCA
*
1985141 CCTTACGCCACGTGGGGTAAAGCGCCCCTTGCAACACGTCTTTTTTAATTGTGTAAAAAATTCGG
1 CCTTACGCCACGTGGGGTAAAGCGCCCCTTGCAACACGCCTTTTTTAATTGTGTAAAAAATTCGG
1985206 GTGCTAGTTTTATAAATATTTTTAAAATAATGCATAATATGTAATTAATTTCTTTTG
66 GTGCTAGTTTTATAAATATTTTTAAAATAATGCATAATATGTAATTAATTTCTTTTG
1985263 CCTTACGCCACGTGGGGTAAAGCGCCCCTTGCAACACGCCTTTTTTAATTGTGTAAAAAATAT-G
1 CCTTACGCCACGTGGGGTAAAGCGCCCCTTGCAACACGCCTTTTTTAATTGTGTAAAAAAT-TCG
* * *
1985327 GGTGTTAGTTTTATAAATATTTTTAAAATAGTGCCTAATATGTAATTAATTTCTTTT
65 GGTGCTAGTTTTATAAATATTTTTAAAATAATGCATAATATGTAATTAATTTCTTTT
1985384 AGGGTGATAT
Statistics
Matches: 116, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
122 115 0.99
123 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (122 bp):
CCTTACGCCACGTGGGGTAAAGCGCCCCTTGCAACACGCCTTTTTTAATTGTGTAAAAAATTCGG
GTGCTAGTTTTATAAATATTTTTAAAATAATGCATAATATGTAATTAATTTCTTTTG
Done.