Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008150.1 Hibiscus syriacus cultivar Beakdansim tig00110716_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: 3012591
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 14
Found at i:1817814 original size:21 final size:20
Alignment explanation
Indices: 1817770--1817825 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
1817760 AATGCAATTA
***
1817770 GTGCATCGATGCATCCTTAT
1 GTGCATCGATGCATCAGGAT
1817790 GTGCATCGATGCATCAAGGAT
1 GTGCATCGATGCATC-AGGAT
1817811 GTGCATCGATGCATC
1 GTGCATCGATGCATC
1817826 CTGTTGTGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCAGGAT
Found at i:1818238 original size:34 final size:32
Alignment explanation
Indices: 1818199--1818268 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
1818189 TTTTGTAAAG
* * *
1818199 GGGAAATGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1818233 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1818265 GGGA
1 GGGA
1818269 GTTGTAAGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1818923 original size:111 final size:111
Alignment explanation
Indices: 1818790--1819260 Score: 620
Period size: 111 Copynumber: 4.2 Consensus size: 111
1818780 ATATTGATCT
* * * * * *
1818790 TTTTTATAAAAAGTATCTATACTTTAAACATATTAAGTAAATTTTACTGGTTTTGTCATAATAAA
1 TTTTTAT-AAAAGGATCGATACTTTCAACATATCAAGTAAATTTTACCGGTTTTGTCATAATGAA
*
1818855 ACTAGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCC
65 ACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCC
* * ** *
1818902 CTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCCTTTTTTTCATAATGAAA
1 TTTTTATAAAAGGATCGATACTTTCAACATATCAAGTAAATTTTACCGGTTTTGTCATAATGAAA
* *
1818967 CTGGTTTTGTCATATTTTTTTACCTGATATATTGTAAAGTATTTATCC
66 CTGGTTTTGTCATA--TTTTTACCTGTTATATTGTAAAGTATCTATCC
* *
1819015 TTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTTTGTCATAATGAAA
1 TTTTTATAAAAGGATCGATACTTTCAACATATCAAGTAAATTTTACCGGTTTTGTCATAATGAAA
* * *
1819080 CTGGGTTTGTCATATTTTTACATGTTATATTGTAAAGTATCTATCA
66 CTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCC
* * *
1819126 TTTTTATAAAAAGATCGATACTTTCAGCATATCAAGTAAATTTTACCAGTTTTGTCATAATGAAA
1 TTTTTATAAAAGGATCGATACTTTCAACATATCAAGTAAATTTTACCGGTTTTGTCATAATGAAA
* ** * * * * *
1819191 TTGGTTTTGTCATATTTTTTTCTATTATATTGTAAAATAGCGATACA
66 CTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTAT-CC
*
1819238 TTTTTAT-AAAGTATCGATACTTT
1 TTTTTATAAAAGGATCGATACTTT
1819261 ATAGGCGCTA
Statistics
Matches: 318, Mismatches: 38, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
111 198 0.62
112 15 0.05
113 105 0.33
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (111 bp):
TTTTTATAAAAGGATCGATACTTTCAACATATCAAGTAAATTTTACCGGTTTTGTCATAATGAAA
CTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCC
Found at i:1819198 original size:224 final size:223
Alignment explanation
Indices: 1818781--1819261 Score: 655
Period size: 224 Copynumber: 2.2 Consensus size: 223
1818771 TTTAAAAAAA
* * * * *
1818781 TATTGATCTTTTTTATAAAAAGTATCTATACTTTAAACATATTAAGTAAATTTTACTGGTTTTGT
1 TATTGATCCTTTTTATAAAAAGGATCGATACTTTAAACATATCAAGTAAATTTTACCGGTTTTGT
* * *
1818846 CATAATAAAACTAGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCCCTTTTATAA
66 CATAATAAAACTAGGTTTGTCATATTTTTACATGTTATATTGTAAAGTATCTATCACTTTTATAA
* * ** *
1818911 AAGGATCGATACTTTCAACATATCAGGTAAATTTTACCCTTTTTTTCATAATGAAACTGGTTTTG
131 AAAGATCGATACTTTCAACATATCAAGTAAATTTTACCAGTTTTGTCATAATGAAACTGGTTTTG
1818976 TCATATTTTTTTACCTGA-TATATTGTAAAG
196 TCATATTTTTTT--CT-ATTATATTGTAAAG
* * * *
1819006 TATTTATCCTTTTTAT-AAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTTTGT
1 TATTGATCCTTTTTATAAAAAGGATCGATACTTTAAACATATCAAGTAAATTTTACCGGTTTTGT
* * *
1819070 CATAATGAAACTGGGTTTGTCATATTTTTACATGTTATATTGTAAAGTATCTATCATTTTTATAA
66 CATAATAAAACTAGGTTTGTCATATTTTTACATGTTATATTGTAAAGTATCTATCACTTTTATAA
* *
1819135 AAAGATCGATACTTTCAGCATATCAAGTAAATTTTACCAGTTTTGTCATAATGAAATTGGTTTTG
131 AAAGATCGATACTTTCAACATATCAAGTAAATTTTACCAGTTTTGTCATAATGAAACTGGTTTTG
*
1819200 TCATATTTTTTTCTATTATATTGTAAAA
196 TCATATTTTTTTCTATTATATTGTAAAG
** * *
1819228 TAGCGATACATTTTTAT--AAAGTATCGATACTTTA
1 TATTGAT-CCTTTTTATAAAAAGGATCGATACTTTA
1819262 TAGGCGCTAT
Statistics
Matches: 225, Mismatches: 29, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
221 1 0.00
222 32 0.14
223 8 0.04
224 170 0.76
225 14 0.06
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (223 bp):
TATTGATCCTTTTTATAAAAAGGATCGATACTTTAAACATATCAAGTAAATTTTACCGGTTTTGT
CATAATAAAACTAGGTTTGTCATATTTTTACATGTTATATTGTAAAGTATCTATCACTTTTATAA
AAAGATCGATACTTTCAACATATCAAGTAAATTTTACCAGTTTTGTCATAATGAAACTGGTTTTG
TCATATTTTTTTCTATTATATTGTAAAG
Found at i:1819537 original size:23 final size:23
Alignment explanation
Indices: 1819507--1819567 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
1819497 AGTAAGTAAT
*
1819507 TACCTATTTTGTTATATAAACGC
1 TACCTATTATGTTATATAAACGC
1819530 TACCTATTACT-TTATATAAACGC
1 TACCTATTA-TGTTATATAAACGC
*
1819553 TACCTAATATGTTAT
1 TACCTATTATGTTAT
1819568 TGTGCTTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
24 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.43
Consensus pattern (23 bp):
TACCTATTATGTTATATAAACGC
Found at i:1819630 original size:23 final size:23
Alignment explanation
Indices: 1819604--1819656 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
1819594 AACATATTTT
*
1819604 ATTATATAAGCGTTACCTATTAC
1 ATTATATAAGCGCTACCTATTAC
1819627 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTATTAC
1819650 ATTATAT
1 ATTATAT
1819657 CAACGGTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.40
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTATTAC
Found at i:1819701 original size:110 final size:110
Alignment explanation
Indices: 1819518--1819748 Score: 356
Period size: 110 Copynumber: 2.1 Consensus size: 110
1819508 ACCTATTTTG
* * *
1819518 TTATATAAACGCTACCTATTACTTTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATGT
1 TTATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTATGCTTGATAATGT
*
1819583 TTTCAGTAATTAACATATTTTATTATATAAGCGTTACCTATTACA
66 TTTCAGTAATTAACATATTTTATTATATAAGCGCTACCTATTACA
* * * *
1819628 TTATATAAGCGCTACCTATTACATTATATCAACGGTATCTAATATGTTATTATGTTTGATAATG-
1 TTATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTATGCTTGATAATGT
* *
1819692 TTTCTAGTAATTAACCTATTTTATTATATAAGCGCTACTTATTACA
66 TTTC-AGTAATTAACATATTTTATTATATAAGCGCTACCTATTACA
1819738 TTATATAAGCG
1 TTATATAAGCG
1819749 GTAAGTAATA
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
109 4 0.04
110 106 0.96
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (110 bp):
TTATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTATGCTTGATAATGT
TTTCAGTAATTAACATATTTTATTATATAAGCGCTACCTATTACA
Found at i:1819774 original size:87 final size:86
Alignment explanation
Indices: 1819618--1819783 Score: 228
Period size: 87 Copynumber: 1.9 Consensus size: 86
1819608 TATAAGCGTT
*
1819618 ACCTATTACATTATATAAGCGCTACCTATTACATTATATCAACGGTATCTAATATGTTATTATGT
1 ACCTATTACATTATATAAGCGCTACCTATTACATTATATCAACGGTAACTAATATGTTA-TATGT
*
1819683 TTGATAATGTTTCTAGTAATTA
65 TTGATAATATTTCTAGTAATTA
** * *
1819705 ACCTATTTTATTATATAAGCGCTACTTATTACATTATAT-AAGCGGTAAGTAATATGTTA-ATGT
1 ACCTATTACATTATATAAGCGCTACCTATTACATTATATCAA-CGGTAACTAATATGTTATATGT
1819768 ACTTGATAATATTTCT
65 --TTGATAATATTTCT
1819784 GATTAAATGA
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
85 4 0.06
86 2 0.03
87 64 0.91
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (86 bp):
ACCTATTACATTATATAAGCGCTACCTATTACATTATATCAACGGTAACTAATATGTTATATGTT
TGATAATATTTCTAGTAATTA
Found at i:1823215 original size:16 final size:16
Alignment explanation
Indices: 1823187--1823221 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1823177 GTTGAGTGTA
1823187 ATAAAAAATATAATTT
1 ATAAAAAATATAATTT
1823203 ATAAATAAA-ATAATTT
1 ATAAA-AAATATAATTT
1823219 ATA
1 ATA
1823222 TTTTTATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAAAAAATATAATTT
Found at i:1824064 original size:25 final size:26
Alignment explanation
Indices: 1824030--1824078 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
1824020 AAAATGAATC
1824030 TTATGATTTTTAT-GATTTTTAGGGA
1 TTATGATTTTTATGGATTTTTAGGGA
*
1824055 TTATGATTTTTTTGGATTTTTAGG
1 TTATGATTTTTATGGATTTTTAGG
1824079 AATTTAGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.59
Consensus pattern (26 bp):
TTATGATTTTTATGGATTTTTAGGGA
Found at i:1824091 original size:28 final size:28
Alignment explanation
Indices: 1824034--1824125 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 28
1824024 TGAATCTTAT
* * *
1824034 GATTTTTAT-GATTTTTAGGGA-TTA-T
1 GATTTTTTTGGATTTTTAGGAATTTAGG
1824059 GATTTTTTTGGATTTTTAGGAATTTAGG
1 GATTTTTTTGGATTTTTAGGAATTTAGG
1824087 GA-TTTTTTGAGATTTTCT-GGAATTTAAGG
1 GATTTTTTTG-GATTTT-TAGGAATTT-AGG
1824116 G-TTTTTTTGG
1 GATTTTTTTGG
1824126 GAATTTTAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
25 8 0.14
26 11 0.19
27 10 0.18
28 16 0.28
29 12 0.21
ACGTcount: A:0.21, C:0.01, G:0.24, T:0.54
Consensus pattern (28 bp):
GATTTTTTTGGATTTTTAGGAATTTAGG
Found at i:1826067 original size:30 final size:30
Alignment explanation
Indices: 1826033--1826094 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1826023 AGAGATTTTA
1826033 TTTTTAGTGAAGGGTGCTCCGATTGGTTGT
1 TTTTTAGTGAAGGGTGCTCCGATTGGTTGT
1826063 TTTTTAGTGAAGGGTGCTCCGATTGGTTGT
1 TTTTTAGTGAAGGGTGCTCCGATTGGTTGT
1826093 TT
1 TT
1826095 ATACAAAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.13, C:0.10, G:0.32, T:0.45
Consensus pattern (30 bp):
TTTTTAGTGAAGGGTGCTCCGATTGGTTGT
Found at i:1829251 original size:115 final size:115
Alignment explanation
Indices: 1829033--1829293 Score: 357
Period size: 115 Copynumber: 2.3 Consensus size: 115
1829023 TTTTGAGTTC
* *
1829033 CAAGTTCTTCTCATTATGAACTTTCACTCTTCTGTTCAGATGAGTTCTTCTCATTATGAACATTT
1 CAAGTTCTTCTCATTATGAAC-TTC-TTCTTCTGTTCAGATGAGTTCTTCTCATTATGAACATTC
*** * *
1829098 CTTTGAAATGTTGATCCACATCCTTCTGTGATGGATTTGAGCAAAGGTCGAA
64 CTTTGAAATGAAAATCCACACCCTTCTATGATGGATTTGAGCAAAGGTCGAA
*
1829150 CAAGTTCTTCTCATTATGAACTTCTTCTTCT-TT-GGATGAGTTCTTCTCATTATGAACACTTCC
1 CAAGTTCTTCTCATTATGAACTTCTTCTTCTGTTCAGATGAGTTCTTCTCATTATGAACA-TTCC
* *
1829213 TTTGGAAATGAAAATCCATC-CCCTTCTATGATGTATTTGAGCAAAGGTTGAA
65 TTT-GAAATGAAAATCCA-CACCCTTCTATGATGGATTTGAGCAAAGGTCGAA
*
1829265 CAAGTTCTTGTCATTATGAACTTCTTCTT
1 CAAGTTCTTCTCATTATGAACTTCTTCTT
1829294 TCTTCTTCTA
Statistics
Matches: 130, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
113 24 0.18
114 8 0.06
115 73 0.56
116 4 0.03
117 21 0.16
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (115 bp):
CAAGTTCTTCTCATTATGAACTTCTTCTTCTGTTCAGATGAGTTCTTCTCATTATGAACATTCCT
TTGAAATGAAAATCCACACCCTTCTATGATGGATTTGAGCAAAGGTCGAA
Found at i:1829567 original size:115 final size:117
Alignment explanation
Indices: 1829336--1829736 Score: 440
Period size: 115 Copynumber: 3.4 Consensus size: 117
1829326 AACAAGTTAC
* *
1829336 TCTCATTATGAACTTCTTCTCTCTTATCGGATGAGTTCTTCTCATTATATGAACTCT-TCATTGG
1 TCTCATTATGAACTTCTTCTATCTTATAGGATGAGTTCTTCTCA-T-TATGAACTCTCT-ATTGG
* * * * *
1829400 GAATGATGATCCACCTCCTTTTGTGATGGAATCGAACAAAGACTGAACAAGTTCT
63 GAATGATGATCCAACTCATTTTGTGATGGAATCGAACAAAAACTAAAAAAGTTCT
*
1829455 TCTCATTATGAACTTCTTCTATCTTATAGGATGAGTTC-T-TCATTATGAACTCTCTATTTGGAA
1 TCTCATTATGAACTTCTTCTATCTTATAGGATGAGTTCTTCTCATTATGAACTCTCTATTGGGAA
* * *
1829518 TGATGATCCAATTTATTTTGTGATGGAATCGGACAAAAACTAAAAAAGTTCT
66 TGATGATCCAACTCATTTTGTGATGGAATCGAACAAAAACTAAAAAAGTTCT
* *
1829570 TCTCATTATGAACTTATTCTATCTTATCA-GATGAGTTCTTCTCATTATGAACTCTCCA-TGGGA
1 TCTCATTATGAACTTCTTCTATCTTAT-AGGATGAGTTCTTCTCATTATGAACTCTCTATTGGGA
* * * * * * * * * **
1829633 ATGATGATTCACCTTC-TTCTATAATGGAATTGAAGAAATATTGAATCAAGTTCT
65 ATGATGATCCAAC-TCATTTTGTGATGGAATCGAACAAAAACT-AAAAAAGTTCT
* * *
1829687 TCTCATTATGAACTTCTTTCT-T-TCATCGGACGAGTTCTTCTCATTATGAA
1 TCTCATTATGAACTTC-TTCTATCTTATAGGATGAGTTCTTCTCATTATGAA
1829737 GCATTCCATG
Statistics
Matches: 242, Mismatches: 32, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
115 96 0.40
116 60 0.25
117 45 0.19
118 5 0.02
119 36 0.15
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (117 bp):
TCTCATTATGAACTTCTTCTATCTTATAGGATGAGTTCTTCTCATTATGAACTCTCTATTGGGAA
TGATGATCCAACTCATTTTGTGATGGAATCGAACAAAAACTAAAAAAGTTCT
Found at i:1830682 original size:6 final size:6
Alignment explanation
Indices: 1830671--1830736 Score: 59
Period size: 6 Copynumber: 11.2 Consensus size: 6
1830661 GAACCTCTCA
*
1830671 TTTTCT TTTTCTT TTTTCCT TTTT-T TTTT-T TCTTT-T CTTTCT TTTTCT
1 TTTTCT TTTTC-T TTTT-CT TTTTCT TTTTCT T-TTTCT TTTTCT TTTTCT
*
1830719 TTTTCC TTTT-T TTTTCT T
1 TTTTCT TTTTCT TTTTCT T
1830737 AGATGCTGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
5 14 0.27
6 26 0.51
7 10 0.20
8 1 0.02
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:1846753 original size:15 final size:15
Alignment explanation
Indices: 1846733--1846762 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1846723 CTAGGACATT
1846733 TGGTTTAGATAACGA
1 TGGTTTAGATAACGA
1846748 TGGTTTAGATAACGA
1 TGGTTTAGATAACGA
1846763 AAAAGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (15 bp):
TGGTTTAGATAACGA
Found at i:1852582 original size:60 final size:60
Alignment explanation
Indices: 1852501--1852689 Score: 202
Period size: 60 Copynumber: 3.1 Consensus size: 60
1852491 TGCATCATAT
* * * *
1852501 ATCCCCAAATTAT-AATCCTCATTTTACATTGGTCCTTAAACTTTTGAATATTTCAATTTC
1 ATCCCCAAACTATGAAT-CTCATTCTAAATTAGTCCTTAAACTTTTGAATATTTCAATTTC
** * * *
1852561 ATCCCCAAACTATGAATCTCATTCTAAATTAGTCCTTAATTTTTTTAACA-TTCTAAATTC
1 ATCCCCAAACTATGAATCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTTC-AATTTC
* * * ** * *
1852621 ATCCCTAAACTATGACTCTTATTCTAAATTAGTCCCCAAACTTTTGAGTGTTTCAATTTC
1 ATCCCCAAACTATGAATCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTTCAATTTC
1852681 ATCCCCAAA
1 ATCCCCAAA
1852690 TCCATCCAAA
Statistics
Matches: 104, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
59 3 0.03
60 95 0.91
61 6 0.06
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.40
Consensus pattern (60 bp):
ATCCCCAAACTATGAATCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTTCAATTTC
Found at i:1858093 original size:19 final size:19
Alignment explanation
Indices: 1858059--1858095 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1858049 ATGACCAACA
*
1858059 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
1858078 AAATCGCAACGTGATCTC
1 AAATCGCAACGCGATCTC
1858096 CAGTATCGCA
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:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1858204 original size:19 final size:20
Alignment explanation
Indices: 1858160--1858207 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1858150 CGATTCTGAA
* *
1858160 TGCGATAGTCCAAATTCGCGT
1 TGCGATAGTCCAAAATC-CAT
1858181 TGCGATAGTCCAAAAT-CAT
1 TGCGATAGTCCAAAATCCAT
1858200 TGCGATAG
1 TGCGATAG
1858208 CACTGTTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.40
21 15 0.60
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (20 bp):
TGCGATAGTCCAAAATCCAT
Found at i:1858225 original size:21 final size:21
Alignment explanation
Indices: 1858199--1858343 Score: 245
Period size: 21 Copynumber: 6.9 Consensus size: 21
1858189 TCCAAAATCA
1858199 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
1858220 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
1858241 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
1858262 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
* *
1858283 TTGTGATAGCACTGTTCACCA
1 TTGCGATAGCACTGTTCACCG
**
1858304 TTGCGATAATACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
*
1858325 TTGCGATAGCATTGTTCAC
1 TTGCGATAGCACTGTTCAC
1858344 ATTTTATAAT
Statistics
Matches: 115, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 115 1.00
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (21 bp):
TTGCGATAGCACTGTTCACCG
Found at i:1859077 original size:21 final size:21
Alignment explanation
Indices: 1859054--1859134 Score: 126
Period size: 21 Copynumber: 3.9 Consensus size: 21
1859044 TCGCAATGTG
* *
1859054 AACAGTGTTATCGCAACGGTG
1 AACAGTGCTATCGCAACGGTA
1859075 AACAGTGCTATCGCAACGGTA
1 AACAGTGCTATCGCAACGGTA
* *
1859096 AACAGTACTATTGCAACGGTA
1 AACAGTGCTATCGCAACGGTA
1859117 AACAGTGCTATCGCAACG
1 AACAGTGCTATCGCAACG
1859135 CGAATTCGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.21
Consensus pattern (21 bp):
AACAGTGCTATCGCAACGGTA
Found at i:1859148 original size:21 final size:21
Alignment explanation
Indices: 1859124--1859170 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1859114 GTAAACAGTG
1859124 CTATCGCAACGCGAATTCGGA
1 CTATCGCAACGCGAATTCGGA
*
1859145 CTATCGCAACGCGAATTTGGA
1 CTATCGCAACGCGAATTCGGA
1859166 CTATC
1 CTATC
1859171 AGAATCGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
CTATCGCAACGCGAATTCGGA
Found at i:1859148 original size:42 final size:42
Alignment explanation
Indices: 1859062--1859155 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 42
1859052 TGAACAGTGT
* *
1859062 TATCGCAACGGTGAACAGTGCTATCGCAACGGTAAACAGTAC
1 TATCGCAACGGTAAACAGTGCTATCGCAACGGTAAACAGGAC
* *
1859104 TATTGCAACGGTAAACAGTGCTATCGCAACGCG-AATTC-GGAC
1 TATCGCAACGGTAAACAGTGCTATCGCAACG-GTAA-ACAGGAC
1859146 TATCGCAACG
1 TATCGCAACG
1859156 CGAATTTGGA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
42 43 0.96
43 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.20
Consensus pattern (42 bp):
TATCGCAACGGTAAACAGTGCTATCGCAACGGTAAACAGGAC
Found at i:1859244 original size:20 final size:19
Alignment explanation
Indices: 1859221--1859266 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1859211 GAAAATTTAT
* *
1859221 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
1859241 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
1859260 TTGCGAT
1 TTGCGAT
1859267 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:1859256 original size:19 final size:19
Alignment explanation
Indices: 1859232--1859268 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1859222 TGCGATACTG
*
1859232 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
1859251 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
1859269 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:1859844 original size:156 final size:155
Alignment explanation
Indices: 1859552--1859857 Score: 533
Period size: 156 Copynumber: 2.0 Consensus size: 155
1859542 AAAAATTCTT
1859552 AAAGTTTGACTTTCATAAAAAAGAAAACACAAATAAGATTGATATGAAAGGACCTGTGGTAGATG
1 AAAGTTTGACTTTCATAAAAAAGAAAACACAAATAAGATTGATATGAAAGGACCTGTGGTAGATG
* * *
1859617 GTGAAGATGCAGCTTATAATTTGTATAATGATTGTGGTAATGGCATGGTTTCAGTGTTCGAAAAG
66 GTGAAGATGCAACTTATAATTTGTATAACGATTATGGTAATGGCATGGTTTCAGTGTTCGAAAAG
1859682 GAAAAAAAATAGATATCTTTATCTC
131 GAAAAAAAATAGATATCTTTATCTC
* *
1859707 AAAGTTTGACTTTCATAAAAAAGACAAACACAAATAAGGTTGATATGAAAGGACTTGTGGTAGAT
1 AAAGTTTGACTTTCATAAAAAAGA-AAACACAAATAAGATTGATATGAAAGGACCTGTGGTAGAT
1859772 GGTGAAGATGCAACTTATAATTTGTATAACGATTATGGTAATGGCATGGGTTTCAGTGTTCGAAA
65 GGTGAAGATGCAACTTATAATTTGTATAACGATTATGGTAATGGCAT-GGTTTCAGTGTTCGAAA
*
1859837 A-GTAAAAAAATAGATATCTTT
129 AGGAAAAAAAATAGATATCTTT
1859858 CTGGCACTAA
Statistics
Matches: 143, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
155 24 0.17
156 101 0.71
157 18 0.13
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (155 bp):
AAAGTTTGACTTTCATAAAAAAGAAAACACAAATAAGATTGATATGAAAGGACCTGTGGTAGATG
GTGAAGATGCAACTTATAATTTGTATAACGATTATGGTAATGGCATGGTTTCAGTGTTCGAAAAG
GAAAAAAAATAGATATCTTTATCTC
Found at i:1861622 original size:18 final size:19
Alignment explanation
Indices: 1861599--1861638 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
1861589 GTTCAATTAA
1861599 TTTTTTAAAAATA-TATAT
1 TTTTTTAAAAATATTATAT
*
1861617 TTTTTTATAAATATTATAT
1 TTTTTTAAAAATATTATAT
1861636 TTT
1 TTT
1861639 ATAGAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTTAAAAATATTATAT
Found at i:1869045 original size:28 final size:31
Alignment explanation
Indices: 1869010--1869082 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 31
1869000 AATTATCACT
1869010 TTTGTTTCATTTTAATATCTAA-ATTT-TTA
1 TTTGTTTCATTTTAATATCTAATATTTATTA
*** * *
1869039 TTT-TTTCAAAATCATATCTAATATTTATTT
1 TTTGTTTCATTTTAATATCTAATATTTATTA
1869069 TTTGTTTCATTTTA
1 TTTGTTTCATTTTA
1869083 GTACCCTCCA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
28 14 0.44
29 7 0.22
30 5 0.16
31 6 0.19
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (31 bp):
TTTGTTTCATTTTAATATCTAATATTTATTA
Found at i:1872310 original size:21 final size:22
Alignment explanation
Indices: 1872271--1872315 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1872261 ATGTTAGATC
1872271 AAATAAATAAAACTAAATAAAA
1 AAATAAATAAAACTAAATAAAA
1872293 AAATAAA-AAAAC-ATAATAAAA
1 AAATAAATAAAACTA-AATAAAA
1872314 AA
1 AA
1872316 CAAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 1 0.05
21 14 0.64
22 7 0.32
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (22 bp):
AAATAAATAAAACTAAATAAAA
Found at i:1872378 original size:2 final size:2
Alignment explanation
Indices: 1872371--1872439 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
1872361 AAAGAATGAA
1872371 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1872413 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1872440 CATAATAAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1872495 original size:29 final size:30
Alignment explanation
Indices: 1872462--1872524 Score: 74
Period size: 32 Copynumber: 2.1 Consensus size: 30
1872452 TGTTATATTA
1872462 AATAAATAAAA-GAAAAAGAAAAAAATAAT
1 AATAAATAAAACGAAAAAGAAAAAAATAAT
* **
1872491 AATAATTAAAACGTGAGGAAGAAAAAAATAAT
1 AATAAATAAAAC--GAAAAAGAAAAAAATAAT
1872523 AA
1 AA
1872525 AGGACCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 10 0.36
32 18 0.64
ACGTcount: A:0.71, C:0.02, G:0.11, T:0.16
Consensus pattern (30 bp):
AATAAATAAAACGAAAAAGAAAAAAATAAT
Found at i:1875548 original size:21 final size:22
Alignment explanation
Indices: 1875522--1875564 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1875512 ACCCACCTTA
1875522 TTTTC-TTTTCTTTTTCAATTT
1 TTTTCTTTTTCTTTTTCAATTT
*
1875543 TTTTCTTTTTTTTTTTCAATTT
1 TTTTCTTTTTCTTTTTCAATTT
1875565 AGGGCGCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTCTTTTTCTTTTTCAATTT
Found at i:1885381 original size:13 final size:13
Alignment explanation
Indices: 1885365--1885433 Score: 57
Period size: 15 Copynumber: 4.8 Consensus size: 13
1885355 AATTGAATAG
1885365 AGAAATAAAAAAA
1 AGAAATAAAAAAA
1885378 AGAAATGAAAAACAA
1 AGAAAT-AAAAA-AA
*
1885393 AAAAATAAAACAAA
1 AGAAATAAAA-AAA
*
1885407 ACGAAAAAATAAAAA
1 A-GAAATAA-AAAAA
*
1885422 TAAAAATAAAAA
1 -AGAAATAAAAA
1885434 GGAGAATAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
13 6 0.13
14 15 0.33
15 21 0.47
16 3 0.07
ACGTcount: A:0.81, C:0.04, G:0.06, T:0.09
Consensus pattern (13 bp):
AGAAATAAAAAAA
Found at i:1885407 original size:18 final size:18
Alignment explanation
Indices: 1885386--1885420 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1885376 AAAGAAATGA
1885386 AAAACAAAAAAATAAAAC
1 AAAACAAAAAAATAAAAC
*
1885404 AAAACGAAAAAATAAAA
1 AAAACAAAAAAATAAAA
1885421 ATAAAAATAA
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:0.83, C:0.09, G:0.03, T:0.06
Consensus pattern (18 bp):
AAAACAAAAAAATAAAAC
Found at i:1885432 original size:19 final size:18
Alignment explanation
Indices: 1885367--1885433 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 18
1885357 TTGAATAGAG
1885367 AAATAAAAAAAAGAAATGAA
1 AAATAAAAAAAA-AAAT-AA
* *
1885387 AAACAAAAAAATAAAACAA
1 AAATAAAAAAA-AAAATAA
**
1885406 AACGAAAAAATAAAAATAA
1 AAATAAAAAA-AAAAATAA
1885425 AAATAAAAA
1 AAATAAAAA
1885434 GGAGAATAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 23 0.61
20 14 0.37
21 1 0.03
ACGTcount: A:0.82, C:0.04, G:0.04, T:0.09
Consensus pattern (18 bp):
AAATAAAAAAAAAAATAA
Found at i:1885511 original size:92 final size:91
Alignment explanation
Indices: 1885414--1885586 Score: 206
Period size: 92 Copynumber: 1.9 Consensus size: 91
1885404 AAAACGAAAA
* *
1885414 AATAAAAATAAAAATAAAAAGGAGAATAAAATATATAC-ATAGACATAATAAAACATGTTAGATC
1 AATAAAAA-AAAAAGAAAAA-AAGAATAAAATATATACAATAGACATAATAAAACATGTTAGATC
1885478 AAAT-AAATAAACTAAATTTGAAAAACAT
64 AAATAAAATAAA-TAAATTTGAAAAACAT
** * * * * * *
1885506 AATAAAAAAAACCGAAAAAAAGAATGAAATATGTACATATATATATAATTAAACATGTTAGATTA
1 AATAAAAAAAAAAGAAAAAAAGAATAAAATATATACA-ATAGACATAATAAAACATGTTAGATCA
1885571 AATAAAATAAATAAAT
65 AATAAAATAAATAAAT
1885587 AATACTAATA
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
90 14 0.21
91 8 0.12
92 39 0.57
93 7 0.10
ACGTcount: A:0.62, C:0.06, G:0.08, T:0.24
Consensus pattern (91 bp):
AATAAAAAAAAAAGAAAAAAAGAATAAAATATATACAATAGACATAATAAAACATGTTAGATCAA
ATAAAATAAATAAATTTGAAAAACAT
Found at i:1890039 original size:27 final size:25
Alignment explanation
Indices: 1889982--1890073 Score: 96
Period size: 27 Copynumber: 3.6 Consensus size: 25
1889972 TGTCCCAATT
*
1889982 CCAAATGCAACAAATATGTCTCATTA
1 CCAAATGCAACAAATATGTCTCA-AA
* *
1890008 TCAAATGCAACAAAATATGTATCTAAA
1 CCAAATGCAAC-AAATATGTCTC-AAA
*
1890035 CCAAATTCAACAAA-ATGTCTCAATA
1 CCAAATGCAACAAATATGTCTCAA-A
*
1890060 CCAAGTGCAACAAA
1 CCAAATGCAACAAA
1890074 ATAAATAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
24 2 0.04
25 19 0.35
26 13 0.24
27 20 0.36
28 1 0.02
ACGTcount: A:0.48, C:0.22, G:0.08, T:0.23
Consensus pattern (25 bp):
CCAAATGCAACAAATATGTCTCAAA
Found at i:1898109 original size:27 final size:25
Alignment explanation
Indices: 1898053--1898110 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
1898043 AAAATAAAAC
* *
1898053 TAAAAAATAATATATATTAATATAT
1 TAAAAAATAATATATATAAAAATAT
* *
1898078 GAAAATAATAAGTATATATAAAAATTT
1 TAAAA-AATAA-TATATATAAAAATAT
1898105 TAAAAA
1 TAAAAA
1898111 GAATTATAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 4 0.15
26 6 0.23
27 16 0.62
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (25 bp):
TAAAAAATAATATATATAAAAATAT
Found at i:1900345 original size:3 final size:3
Alignment explanation
Indices: 1900335--1900365 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1900325 GTAATAATTT
1900335 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1900366 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1907276 original size:64 final size:64
Alignment explanation
Indices: 1907140--1907277 Score: 172
Period size: 64 Copynumber: 2.2 Consensus size: 64
1907130 GCACTAAGTG
* * ***
1907140 TGCATCGATGCATAAAAGGCATTCGATGTTTTGAATAAGCCTAAGTGCATCGATGCATGATGTG
1 TGCATCGATGCATAAAAGGCATTCGATGTTTTCAATAAACCTAAGTGCATCGATGCATGATAAA
* * *
1907204 TGCATCGATGCATAAAATGCATTCGATGTTTTCATTAAAACCTGAGTGCATCGATGCAT-A-AAA
1 TGCATCGATGCATAAAAGGCATTCGATGTTTTCAAT-AAACCTAAGTGCATCGATGCATGATAAA
1907267 TGCATTCGATG
1 TGCA-TCGATG
1907278 TTCAATTTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
63 4 0.06
64 40 0.62
65 20 0.31
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATAAAAGGCATTCGATGTTTTCAATAAACCTAAGTGCATCGATGCATGATAAA
Found at i:1907674 original size:21 final size:21
Alignment explanation
Indices: 1907645--1907687 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1907635 TCCATTTACA
1907645 TTAAGGTTT-GTGATTTAGGGT
1 TTAAGGTTTAG-GATTTAGGGT
* *
1907666 TTAATGTTTAGGGTTTAGGGT
1 TTAAGGTTTAGGATTTAGGGT
1907687 T
1 T
1907688 ACAATTTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.49
Consensus pattern (21 bp):
TTAAGGTTTAGGATTTAGGGT
Found at i:1908252 original size:2 final size:2
Alignment explanation
Indices: 1908245--1908282 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1908235 TTATGTAGTT
1908245 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1908283 CACTATACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1909286 original size:2 final size:2
Alignment explanation
Indices: 1909279--1909440 Score: 99
Period size: 2 Copynumber: 82.0 Consensus size: 2
1909269 TTCTATAAAC
* *
1909279 TA TA TA TA TA TA TA TA TA -A TC TA TA AA T- TA CT- TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
1909318 CT- TA TA CA TA TA TA TA TA CTA TA T- TA -A TA TA AA T- TA TA -A
1 -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
1909357 TT TA TA AA CTA TA TA GTT TA TA TA GTT TA TA CA TA TA TA GTT TA
1 TA TA TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA
*
1909401 TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1909441 ATTAAATGTA
Statistics
Matches: 122, Mismatches: 22, Indels: 32
0.69 0.12 0.18
Matches are distributed among these distances:
1 9 0.07
2 105 0.86
3 8 0.07
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1909688 original size:19 final size:20
Alignment explanation
Indices: 1909648--1909726 Score: 79
Period size: 20 Copynumber: 3.6 Consensus size: 20
1909638 AAATTTTCTA
1909648 TTCCCTCTAAATTTCCCAAT
1 TTCCCTCTAAATTTCCCAAT
*
1909668 TTCCCTCTAAA-TTCTCAAT
1 TTCCCTCTAAATTTCCCAAT
1909687 TTCCCTATACTCTTAAAATTTCCCAAT
1 TT-CC----CTC-T-AAATTTCCCAAT
1909714 TTCCCTCTAAATT
1 TTCCCTCTAAATT
1909727 CACAAATAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
19 9 0.18
20 18 0.37
21 1 0.02
22 3 0.06
24 3 0.06
25 1 0.02
26 5 0.10
27 9 0.18
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.42
Consensus pattern (20 bp):
TTCCCTCTAAATTTCCCAAT
Found at i:1909811 original size:2 final size:2
Alignment explanation
Indices: 1909804--1909876 Score: 94
Period size: 2 Copynumber: 36.0 Consensus size: 2
1909794 ACTTTGAATA
*
1909804 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1909846 AT AT AGT AT AT AC AT A- ACT TT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT
1909877 GTAATTAAAC
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 59 0.95
3 2 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1910343 original size:17 final size:17
Alignment explanation
Indices: 1910311--1910344 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1910301 GTGAATATTT
*
1910311 TATAGTTTATACATATA
1 TATAGTTTAGACATATA
*
1910328 TATAGTTTAGATATATA
1 TATAGTTTAGACATATA
1910345 GTTTATATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (17 bp):
TATAGTTTAGACATATA
Found at i:1910365 original size:13 final size:13
Alignment explanation
Indices: 1910322--1910366 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
1910312 ATAGTTTATA
1910322 CATATATATAGTT
1 CATATATATAGTT
* *
1910335 TAGATATATAGTT
1 CATATATATAGTT
*
1910348 TATATATATAGTT
1 CATATATATAGTT
1910361 CATATA
1 CATATA
1910367 AACATTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (13 bp):
CATATATATAGTT
Found at i:1910420 original size:18 final size:18
Alignment explanation
Indices: 1910376--1910434 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
1910366 AAACATTATT
* *
1910376 TATATATATAGCTTATAA
1 TATAAATATAGTTTATAA
*
1910394 TA-ATTATATAGTTTATAA
1 TATA-AATATAGTTTATAA
1910412 TATAAATATAGTTTAT-A
1 TATAAATATAGTTTATAA
1910429 TATAAA
1 TATAAA
1910435 CTTATATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 8 0.22
18 28 0.76
19 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (18 bp):
TATAAATATAGTTTATAA
Found at i:1924694 original size:17 final size:17
Alignment explanation
Indices: 1924672--1924713 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
1924662 CGATGAAAAG
1924672 GGATAGACGCTTGAGTA
1 GGATAGACGCTTGAGTA
*
1924689 GGATAGATGCTTGAGTA
1 GGATAGACGCTTGAGTA
1924706 GGATAGAC
1 GGATAGAC
1924714 AAAGATTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.31, C:0.10, G:0.36, T:0.24
Consensus pattern (17 bp):
GGATAGACGCTTGAGTA
Found at i:1925606 original size:22 final size:22
Alignment explanation
Indices: 1925579--1925620 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1925569 AAACCATTCA
1925579 GGGGGGAATCGGTACCCTCTTG
1 GGGGGGAATCGGTACCCTCTTG
*
1925601 GGGGGGAATCGGTTCCCTCT
1 GGGGGGAATCGGTACCCTCT
1925621 GAGCAATCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (22 bp):
GGGGGGAATCGGTACCCTCTTG
Found at i:1928258 original size:21 final size:21
Alignment explanation
Indices: 1928232--1928312 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
1928222 CAGAACCCCA
*
1928232 GGGGGGTATCGATTCCCCTAT
1 GGGGGGAATCGATTCCCCTAT
* *
1928253 GGGGGGAATCGTTTCCCCTTCAA
1 GGGGGGAATCGATTCCCC-T-AT
* * *
1928276 AGGGGGAATCTATT-CCCTCAA
1 GGGGGGAATCGATTCCCCT-AT
1928297 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGATTCCC
1928313 TCTGCACCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
20 6 0.12
21 27 0.55
22 4 0.08
23 12 0.24
ACGTcount: A:0.19, C:0.25, G:0.32, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTAT
Found at i:1928300 original size:20 final size:20
Alignment explanation
Indices: 1928254--1928314 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
1928244 TTCCCCTATG
*
1928254 GGGGGAATCGTTTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TC-AA
*
1928277 GGGGGAATCTATTCCCTCAA
1 GGGGGAATCGATTCCCTCAA
*
1928297 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
1928315 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 18 0.53
21 2 0.06
22 3 0.09
23 11 0.32
ACGTcount: A:0.20, C:0.26, G:0.30, T:0.25
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAA
Found at i:1931396 original size:13 final size:13
Alignment explanation
Indices: 1931378--1931408 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1931368 AAGGTGATGT
1931378 AACCAACGATATG
1 AACCAACGATATG
*
1931391 AACCAACTATATG
1 AACCAACGATATG
1931404 AACCA
1 AACCA
1931409 GAGAGTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.48, C:0.26, G:0.10, T:0.16
Consensus pattern (13 bp):
AACCAACGATATG
Found at i:1932378 original size:3 final size:3
Alignment explanation
Indices: 1932370--1932407 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
1932360 TTTTTCACTA
*
1932370 TAT TAT TAT TAT TAT TA- TAT ATAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
1932408 AATTAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1932394 original size:21 final size:21
Alignment explanation
Indices: 1932368--1932407 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1932358 AATTTTTCAC
*
1932368 TATATTATTATTATTATTATA
1 TATATTATTAATATTATTATA
1932389 TATATTATTAATATTATTA
1 TATATTATTAATATTATTA
1932408 AATTAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATATTATTAATATTATTATA
Found at i:1932408 original size:9 final size:9
Alignment explanation
Indices: 1932373--1932420 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
1932363 TTCACTATAT
*
1932373 TATTATTAT
1 TATTATTAA
1932382 TATTA-TATA
1 TATTATTA-A
1932391 TATTATTAA
1 TATTATTAA
1932400 TATTATTAA
1 TATTATTAA
1932409 -ATTA--AA
1 TATTATTAA
1932415 TATTAT
1 TATTAT
1932421 AAAACCCTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
6 2 0.06
7 4 0.12
8 6 0.18
9 20 0.59
10 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATTATTAA
Found at i:1934089 original size:17 final size:19
Alignment explanation
Indices: 1934053--1934089 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1934043 CATGAAATAC
1934053 AATATTATAATTTTATAAT
1 AATATTATAATTTTATAAT
*
1934072 AATATT-TATTTTTA-AAT
1 AATATTATAATTTTATAAT
1934089 A
1 A
1934090 TCAAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTATAATTTTATAAT
Found at i:1934957 original size:28 final size:26
Alignment explanation
Indices: 1934926--1934996 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 26
1934916 TAATTCTTTC
1934926 TTTTCAAAATTTTTATATATACTTATT
1 TTTTCAAAATTTTTATATATA-TTATT
*
1934953 ATTTTCATAATATTTATATATATATTATT
1 -TTTTCA-AA-ATTTTTATATATATTATT
*
1934982 TTTT-AATATTTTTAT
1 TTTTCAAAATTTTTAT
1934997 TTTATTTTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
25 7 0.18
26 1 0.03
27 1 0.03
28 10 0.26
29 7 0.18
30 12 0.32
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTCAAAATTTTTATATATATTATT
Found at i:1935034 original size:15 final size:15
Alignment explanation
Indices: 1934994--1935032 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1934984 TTAATATTTT
1934994 TATTTTATTTTCATG
1 TATTTTATTTTCATG
1935009 TATTTTATTTTCAT-
1 TATTTTATTTTCATG
1935023 TA-TTTATTTT
1 TATTTTATTTT
1935033 TTTGTTAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 8 0.33
14 2 0.08
15 14 0.58
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (15 bp):
TATTTTATTTTCATG
Found at i:1935477 original size:16 final size:17
Alignment explanation
Indices: 1935456--1935487 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1935446 AAGTTCTAAC
1935456 TTGTTTTTT-TTTTTTT
1 TTGTTTTTTATTTTTTT
1935472 TTGTTTTTTATTTTTT
1 TTGTTTTTTATTTTTT
1935488 ATGAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.03, C:0.00, G:0.06, T:0.91
Consensus pattern (17 bp):
TTGTTTTTTATTTTTTT
Found at i:1937127 original size:26 final size:27
Alignment explanation
Indices: 1937098--1937167 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 27
1937088 CATTTTACAT
1937098 CTTTGCATTTTTATTTTGTATT-CATA
1 CTTTGCATTTTTATTTTGTATTGCATA
* * *
1937124 CTTT-TATGTTTACTTTTGTCTTGCATA
1 CTTTGCATTTTTA-TTTTGTATTGCATA
* *
1937151 GTTTGCATTCTTATTTT
1 CTTTGCATTTTTATTTT
1937168 TTTATTTATG
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
25 6 0.18
26 12 0.35
27 11 0.32
28 5 0.15
ACGTcount: A:0.16, C:0.13, G:0.10, T:0.61
Consensus pattern (27 bp):
CTTTGCATTTTTATTTTGTATTGCATA
Found at i:1939878 original size:10 final size:9
Alignment explanation
Indices: 1939856--1939921 Score: 63
Period size: 10 Copynumber: 7.7 Consensus size: 9
1939846 TATTATACTT
1939856 AAAAAAAGAG
1 AAAAAAAG-G
1939866 AAAACAAAGG
1 AAAA-AAAGG
1939876 -AAAAAAGG
1 AAAAAAAGG
1939884 AAAAAAAAGG
1 -AAAAAAAGG
1939894 --AAAAAGG
1 AAAAAAAGG
1939901 AAAAAAA-G
1 AAAAAAAGG
1939909 --AAAAAGG
1 AAAAAAAGG
1939916 AAAAAA
1 AAAAAA
1939922 TTGAACCAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 17
0.74 0.00 0.26
Matches are distributed among these distances:
6 5 0.10
7 8 0.17
8 6 0.12
9 12 0.25
10 13 0.27
11 4 0.08
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:1939882 original size:8 final size:8
Alignment explanation
Indices: 1939857--1939921 Score: 62
Period size: 8 Copynumber: 7.8 Consensus size: 8
1939847 ATTATACTTA
1939857 AAAAAAGAG
1 AAAAAAG-G
1939866 AAAACAAAGG
1 -AAA-AAAGG
1939876 AAAAAAGG
1 AAAAAAGG
1939884 AAAAAAAAGG
1 --AAAAAAGG
1939894 -AAAAAGG
1 AAAAAAGG
*
1939901 AAAAAAAG
1 AAAAAAGG
1939909 -AAAAAGG
1 AAAAAAGG
1939916 AAAAAA
1 AAAAAA
1939922 TTGAACCAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
7 13 0.27
8 16 0.33
9 3 0.06
10 12 0.25
11 4 0.08
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:1939897 original size:17 final size:17
Alignment explanation
Indices: 1939858--1939921 Score: 87
Period size: 16 Copynumber: 3.8 Consensus size: 17
1939848 TTATACTTAA
*
1939858 AAAAAGAGAAAACAAAGG
1 AAAAAG-GAAAAAAAAGG
1939876 AAAAAAGGAAAAAAAAGG
1 -AAAAAGGAAAAAAAAGG
1939894 AAAAAGG-AAAAAAA-G
1 AAAAAGGAAAAAAAAGG
1939909 AAAAAGGAAAAAA
1 AAAAAGGAAAAAA
1939922 TTGAACCAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
15 8 0.19
16 12 0.28
17 7 0.16
18 10 0.23
19 6 0.14
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAAAGGAAAAAAAAGG
Found at i:1939906 original size:15 final size:15
Alignment explanation
Indices: 1939871--1939921 Score: 66
Period size: 15 Copynumber: 3.2 Consensus size: 15
1939861 AAGAGAAAAC
1939871 AAAGGAAAAAAGGAAAAA
1 AAAGG-AAAAAGG--AAA
1939889 AAAGGAAAAAGGAAA
1 AAAGGAAAAAGGAAA
*
1939904 AAAAGAAAAAGGAAA
1 AAAGGAAAAAGGAAA
1939919 AAA
1 AAA
1939922 TTGAACCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
15 20 0.62
17 7 0.22
18 5 0.16
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAGGAAAAAGGAAA
Found at i:1939912 original size:6 final size:7
Alignment explanation
Indices: 1939887--1939920 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
1939877 AAAAAGGAAA
1939887 AAAAAGG
1 AAAAAGG
1939894 AAAAAGG
1 AAAAAGG
*
1939901 AAAAAAAG
1 -AAAAAGG
1939909 AAAAAGG
1 AAAAAGG
1939916 AAAAA
1 AAAAA
1939921 ATTGAACCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:1940412 original size:32 final size:32
Alignment explanation
Indices: 1940376--1940437 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
1940366 GTCAGACACA
*
1940376 AGAAGTATCTCTACGAGATGAGCATAACAACG
1 AGAAGTATCTCTACAAGATGAGCATAACAACG
1940408 AGAAGTATCTCTACAAGATGAGCATAACAA
1 AGAAGTATCTCTACAAGATGAGCATAACAA
1940438 TCATTTCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATGAGCATAACAACG
Found at i:1945065 original size:46 final size:45
Alignment explanation
Indices: 1944919--1945599 Score: 1042
Period size: 45 Copynumber: 15.0 Consensus size: 45
1944909 CTATTTCCAA
*
1944919 CATCTGTAAGTCCTTCAGTGCATGAAGTTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTTTC-AAAACCTTCGGGT
1944966 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1945011 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* *
1945057 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
1945103 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAATCCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAA-CCTTCGGGT
*
1945149 CATCTGTAAGTCCTTTAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1945194 CATCTGTAAGTCCTTTAGTGCATGATGTTTTCAAAACCTCCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1945239 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* *
1945285 CATCTGTAAGTCTTTCAGTGCATGATGTTGTCAAAACC-TCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1945329 CATATGTAAG-CCTTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCC-TTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
1945375 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
1945421 CATCTGTAAGTCCTTCAATGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * **
1945466 CATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAATGTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1945511 CATTTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1945556 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAACCTTCGGG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1945600 AGCTTTTTGA
Statistics
Matches: 596, Mismatches: 31, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
43 1 0.00
44 33 0.06
45 277 0.46
46 257 0.43
47 28 0.05
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (45 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:1945280 original size:136 final size:137
Alignment explanation
Indices: 1944919--1945599 Score: 1075
Period size: 136 Copynumber: 5.0 Consensus size: 137
1944909 CTATTTCCAA
* *
1944919 CATCTGTAAGTCCTTCAGTGCATGAAGTTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAG
1 CATCTGTAAGCCCTTCAGTGCATGATG-TTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAG
* * *
1944984 TGCATGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAA
65 TGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAA
1945048 CCTTCGGGT
129 CCTTCGGGT
*
1945057 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT
* *
1945122 GCATGATGTTATCAAAATCCTTCGGGTCATCTGTAAGTCCTTTAGTGCATGATGTTTTCAAAACC
66 GCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACC
1945187 TTCGGGT
131 TTCGGGT
* * * *
1945194 CATCTGTAAGTCCTTTAGTGCATGATGTTTTC-AAAACCTCCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT
* *
1945258 GCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCTTTCAGTGCATGATGTTGTCAAAACC
66 GCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACC
1945323 -TCGGGT
131 TTCGGGT
* * *
1945329 CATATGTAAGCCTTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT
*
1945394 GCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAATGCATGATGTTTTCAAAACC
66 GCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACC
1945459 TTCGGGT
131 TTCGGGT
* ** * *
1945466 CATCTATAAGCCCTTCAGTGCATGATGTTTTC-AAAATGTTCGGGTCATTTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT
* * *
1945530 GCATGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAACC
66 GCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACC
1945594 TTCGGG
131 TTCGGG
1945600 AGCTTTTTGA
Statistics
Matches: 501, Mismatches: 39, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
135 87 0.17
136 223 0.45
137 125 0.25
138 66 0.13
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (137 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT
GCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACC
TTCGGGT
Found at i:1945815 original size:3 final size:3
Alignment explanation
Indices: 1945807--1945844 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
1945797 TTTTTCACTA
*
1945807 TAT TAT TAT TAT TAT TA- TAT ATAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
1945845 AATTAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1945831 original size:21 final size:21
Alignment explanation
Indices: 1945805--1945844 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1945795 AATTTTTCAC
*
1945805 TATATTATTATTATTATTATA
1 TATATTATTAATATTATTATA
1945826 TATATTATTAATATTATTA
1 TATATTATTAATATTATTA
1945845 AATTAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATATTATTAATATTATTATA
Found at i:1945845 original size:9 final size:9
Alignment explanation
Indices: 1945810--1945857 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
1945800 TTCACTATAT
*
1945810 TATTATTAT
1 TATTATTAA
1945819 TATTA-TATA
1 TATTATTA-A
1945828 TATTATTAA
1 TATTATTAA
1945837 TATTATTAA
1 TATTATTAA
1945846 -ATTA--AA
1 TATTATTAA
1945852 TATTAT
1 TATTAT
1945858 AAAACCCTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
6 2 0.06
7 4 0.12
8 6 0.18
9 20 0.59
10 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATTATTAA
Found at i:1957392 original size:54 final size:53
Alignment explanation
Indices: 1957317--1957597 Score: 262
Period size: 54 Copynumber: 5.2 Consensus size: 53
1957307 GATACACATG
* * * *
1957317 TAGTGCCTATACAGTCATTCATAAACATATTATTAATTACGT-GGTTCGCACACA
1 TAGTGCCTATACGGTCGTTCATAAACATATTATGAATT-CGTGGGTT-GCACACT
* * *
1957371 TAGTGCCTATACGGTTGTTCATCAATACAT-GT-TGAATTCTGTGGGTTGCATACT
1 TAGTGCCTATACGGTCGTTCAT-AA-ACATATTATGAATTC-GTGGGTTGCACACT
* * * *
1957425 TAGTGCCTATACGGTCGTTTATCAACCTATGATGAATTTCGTGGGTTGCACACT
1 TAGTGCCTATACGGTCGTTCATAAACATATTATGAA-TTCGTGGGTTGCACACT
* * * * *
1957479 TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTATGGGTTGTACACT
1 TAGTGCCTATACGGTCGTTCATAAACATATTATGAATTC-GTGGGTTGCACACT
* * * * *
1957533 TAGTGCCTATACGCTCGTTCATCATCATATGATGAATTTCGTAGGTTGCACACT
1 TAGTGCCTATACGGTCGTTCATAAACATATTATGAA-TTCGTGGGTTGCACACT
* *
1957587 TAATGTCTATA
1 TAGTGCCTATA
1957598 GTACACATAG
Statistics
Matches: 191, Mismatches: 27, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
52 3 0.02
53 5 0.03
54 166 0.87
55 13 0.07
56 4 0.02
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (53 bp):
TAGTGCCTATACGGTCGTTCATAAACATATTATGAATTCGTGGGTTGCACACT
Found at i:1957515 original size:108 final size:107
Alignment explanation
Indices: 1957317--1957597 Score: 364
Period size: 108 Copynumber: 2.6 Consensus size: 107
1957307 GATACACATG
* * * * * * *
1957317 TAGTGCCTATACAGTCATTCATAAACATATTATTAATTACGTGGTTCGCACACATAGTGCCTATA
1 TAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGTT-GCACACTTAGTGCCTATA
* * * *
1957382 CGGTTGTTCATCAATACATGTTGAATTCTGTGGGTTGCATACT
65 CGGTTGTTCATCAACACATGATGAATTCTATGGGTTGCACACT
* *
1957425 TAGTGCCTATACGGTCGTTTATCAACCTATGATGAATTTCGTGGGTTGCACACTTAGTGCCTATA
1 TAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGT-GGTTGCACACTTAGTGCCTATA
* *
1957490 CGGTTGTTCATCAACATATGATGAATTCTATGGGTTGTACACT
65 CGGTTGTTCATCAACACATGATGAATTCTATGGGTTGCACACT
* * * *
1957533 TAGTGCCTATACGCTCGTTCATCATCATATGATGAATTTCGTAGGTTGCACACTTAATGTCTATA
1 TAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGT-GGTTGCACACTTAGTGCCTATA
1957598 GTACACATAG
Statistics
Matches: 150, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
108 146 0.97
109 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (107 bp):
TAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGTTGCACACTTAGTGCCTATAC
GGTTGTTCATCAACACATGATGAATTCTATGGGTTGCACACT
Found at i:1960168 original size:90 final size:89
Alignment explanation
Indices: 1960062--1960227 Score: 305
Period size: 90 Copynumber: 1.9 Consensus size: 89
1960052 ATTTAATTTC
1960062 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAGGGTAACTT
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAGGGTAACTT
*
1960127 TGATATAAAAGGATTATTAAATTAT
65 GGATATAAAAGGATTATTAAATTAT
1960152 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGTAACTTG
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGTAACTTG
*
1960217 GCTATAAAAGG
66 GATATAAAAGG
1960228 GTGTGTTAGG
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 33 0.45
90 41 0.55
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.37
Consensus pattern (89 bp):
AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGTAACTTG
GATATAAAAGGATTATTAAATTAT
Found at i:1966901 original size:90 final size:89
Alignment explanation
Indices: 1966800--1966965 Score: 305
Period size: 90 Copynumber: 1.9 Consensus size: 89
1966790 ATTTAATTTC
*
1966800 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGATTAGGGTAACTT
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAGGGTAACTT
1966865 GGATATAAAAGGATTATTAAATTAT
65 GGATATAAAAGGATTATTAAATTAT
1966890 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGTAACTTG
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGTAACTTG
*
1966955 GCTATAAAAGG
66 GATATAAAAGG
1966966 GTGTGTTAGG
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 33 0.45
90 41 0.55
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (89 bp):
AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGTAACTTG
GATATAAAAGGATTATTAAATTAT
Found at i:1972579 original size:54 final size:54
Alignment explanation
Indices: 1972478--1972822 Score: 437
Period size: 54 Copynumber: 6.4 Consensus size: 54
1972468 TTTGTTGAGA
* * * * * *
1972478 TGCACACGTAATGCCTATACGGTCATTCATAAACACATATTATGAATTTTGT-GGT
1 TGCACACTTAGTGCCTATACGGTCGTTCAT-CA-ACATATGATGAATTTCGTGGGT
* *
1972533 T-CACATACATAGTGCCTATATGGTCGTTCATCAACATATGATGAATTTCGTGGGT
1 TGCAC--ACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
*
1972588 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATTAATTAT-GTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATT-TCGTGGGT
* * *
1972642 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATTATGAATTACGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
* * * *
1972696 TGCACACTTAGTGCCTATACGATTGTTCATCAATATTTGATGAATTTCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
* * *
1972750 TGCACACTTAGTGCCTATACGTTCGTTCATCAATATATGATGAATTCCAG-GGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTC-GTGGGT
1972804 TGCACACTTAGTGCCTATA
1 TGCACACTTAGTGCCTATA
1972823 GTACACATAA
Statistics
Matches: 260, Mismatches: 23, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
54 228 0.88
55 8 0.03
56 24 0.09
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (54 bp):
TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
Found at i:1975413 original size:19 final size:19
Alignment explanation
Indices: 1975389--1975438 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
1975379 TACCATATTT
1975389 TAATTTAATAATTTAATAA
1 TAATTTAATAATTTAATAA
* * *
1975408 TAATTTGATAATTTATTAT
1 TAATTTAATAATTTAATAA
1975427 TAATTTAATAAT
1 TAATTTAATAAT
1975439 AAAATTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATTTAATAATTTAATAA
Found at i:1975931 original size:2 final size:2
Alignment explanation
Indices: 1975926--1975960 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1975916 TATATATATA
1975926 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1975961 AAAATCTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1985644 original size:28 final size:29
Alignment explanation
Indices: 1985592--1985656 Score: 123
Period size: 28 Copynumber: 2.3 Consensus size: 29
1985582 ATCTGGCAAC
1985592 CTGATGCGGTAGGGGGTACATAATGCGGT
1 CTGATGCGGTAGGGGGTACATAATGCGGT
1985621 CTGATGCGGTA-GGGGTACATAATGCGGT
1 CTGATGCGGTAGGGGGTACATAATGCGGT
1985649 CTGATGCG
1 CTGATGCG
1985657 ATTATTGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 25 0.69
29 11 0.31
ACGTcount: A:0.20, C:0.15, G:0.40, T:0.25
Consensus pattern (29 bp):
CTGATGCGGTAGGGGGTACATAATGCGGT
Found at i:1988917 original size:19 final size:19
Alignment explanation
Indices: 1988893--1988930 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1988883 AAATGACAAT
1988893 GACGACAGTCATGATTGTG
1 GACGACAGTCATGATTGTG
*
1988912 GACGACGGTCATGATTGTG
1 GACGACAGTCATGATTGTG
1988931 ACCAACAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.26
Consensus pattern (19 bp):
GACGACAGTCATGATTGTG
Found at i:1989006 original size:19 final size:19
Alignment explanation
Indices: 1988971--1989016 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1988961 CTTTTTGTAA
1988971 TTTTTAAAAAAATTAAT-T
1 TTTTTAAAAAAATTAATAT
1988989 TTTTTAAAATATAA-TAATAT
1 TTTTTAAAA-A-AATTAATAT
*
1989009 ATTTTAAA
1 TTTTTAAA
1989017 GTTTTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 9 0.38
19 5 0.21
20 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTTAAAAAAATTAATAT
Found at i:1994866 original size:26 final size:26
Alignment explanation
Indices: 1994837--1994886 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1994827 TAATTATCAA
* *
1994837 GTTAGTAGTTTAGTAACATCAGTATG
1 GTTAGAAGTTTAGTAACATAAGTATG
*
1994863 GTTAGAAGTTTAGTGACATAAGTA
1 GTTAGAAGTTTAGTAACATAAGTA
1994887 ATAATTGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
GTTAGAAGTTTAGTAACATAAGTATG
Found at i:1995235 original size:22 final size:22
Alignment explanation
Indices: 1995210--1995256 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1995200 CAAATGACAC
1995210 ATTAAGAACTTGTTTTAAAATT
1 ATTAAGAACTTGTTTTAAAATT
1995232 ATTAAGAACTTGTTTTAAAATT
1 ATTAAGAACTTGTTTTAAAATT
1995254 ATT
1 ATT
1995257 CTAAGTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (22 bp):
ATTAAGAACTTGTTTTAAAATT
Found at i:2002699 original size:43 final size:42
Alignment explanation
Indices: 2002590--2002735 Score: 168
Period size: 43 Copynumber: 3.4 Consensus size: 42
2002580 AGCGGCGTTT
* * ** *
2002590 AGGTTTGTTATTTAGTGGCATTTTTAGTCAAAACAACTACAAC
1 AGGTTTGTTATTTAGCGGCATTTTTAGGCAAAACGTC-GCAAC
* * *
2002633 ATGTTT-TTATTTAGTGGCGTTTTTAGGCACAAACGTCGCAAC
1 AGGTTTGTTATTTAGCGGCATTTTTAGGCA-AAACGTCGCAAC
*
2002675 AGGTTTGTTATTTAGCGGAATTTTTAGGCAAAACAGTCGCAAC
1 AGGTTTGTTATTTAGCGGCATTTTTAGGCAAAAC-GTCGCAAC
*
2002718 AAGTTTGTTATTTAGCGG
1 AGGTTTGTTATTTAGCGG
2002736 TGTGTTTTCC
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
42 34 0.38
43 55 0.62
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (42 bp):
AGGTTTGTTATTTAGCGGCATTTTTAGGCAAAACGTCGCAAC
Found at i:2002931 original size:41 final size:41
Alignment explanation
Indices: 2002886--2002966 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
2002876 ACCACCTTAA
* *
2002886 ATTTAATTACGATTTGAATTAAGTAATAATATATAAAAACT
1 ATTTAATTACGATTCGAATTAAGTAACAATATATAAAAACT
*
2002927 ATTTATTTACGATTCGAATTAAGTAACAATATATAAAAAC
1 ATTTAATTACGATTCGAATTAAGTAACAATATATAAAAAC
2002967 ATAAATAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (41 bp):
ATTTAATTACGATTCGAATTAAGTAACAATATATAAAAACT
Found at i:2003161 original size:12 final size:12
Alignment explanation
Indices: 2003144--2003187 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
2003134 TTCTGAAATG
2003144 CTGCTTCTCTCT
1 CTGCTTCTCTCT
*
2003156 CTGCTTCTCTCA
1 CTGCTTCTCTCT
2003168 CTG---CTCTCT
1 CTGCTTCTCTCT
2003177 CTGCTTCTCTC
1 CTGCTTCTCTC
2003188 AGACAAAGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
9 8 0.30
12 19 0.70
ACGTcount: A:0.02, C:0.43, G:0.09, T:0.45
Consensus pattern (12 bp):
CTGCTTCTCTCT
Found at i:2003438 original size:13 final size:13
Alignment explanation
Indices: 2003420--2003467 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
2003410 TGCGTCATAA
*
2003420 ATTTATGATGCGC
1 ATTTATGACGCGC
*
2003433 ATTTATGACACGC
1 ATTTATGACGCGC
2003446 ATTTATGACGCGC
1 ATTTATGACGCGC
2003459 ATTTATGAC
1 ATTTATGAC
2003468 TTACATTGCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:2003608 original size:85 final size:84
Alignment explanation
Indices: 2003446--2003606 Score: 261
Period size: 85 Copynumber: 1.9 Consensus size: 84
2003436 TATGACACGC
* *
2003446 ATTTATGACGCGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAGATGA
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
2003511 CACACATTTGTGTATCATAA
66 -ACACATTTGTGTATCATAA
* *
2003531 ATTTATGACACGCATTTATGACTTATATTGCGTGTCATTGAAGCCCCCGTCATAAATGAAAATG-
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
*
2003595 ACACATTCGTGT
66 ACACATTTGTGT
2003607 GTCGTGATTG
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
83 11 0.15
85 60 0.85
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Consensus pattern (84 bp):
ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
ACACATTTGTGTATCATAA
Found at i:2008889 original size:28 final size:28
Alignment explanation
Indices: 2008858--2008916 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
2008848 TCCATGATTG
2008858 TATTATGTATTTCATTTGCCTATACTTA
1 TATTATGTATTTCATTTGCCTATACTTA
* *
2008886 TATTATGTATTTCATTTGCCTCTGCTTA
1 TATTATGTATTTCATTTGCCTATACTTA
2008914 TAT
1 TAT
2008917 GGAATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.22, C:0.15, G:0.08, T:0.54
Consensus pattern (28 bp):
TATTATGTATTTCATTTGCCTATACTTA
Found at i:2017365 original size:90 final size:89
Alignment explanation
Indices: 2017251--2017425 Score: 305
Period size: 90 Copynumber: 2.0 Consensus size: 89
2017241 ATCCGAGTAT
* *
2017251 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGATTAG
2017316 GGTAACTTGGATATAAAAGGATTA
66 GGTAACTTGGATATAAAAGGATTA
*
2017340 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGATTA
*
2017405 GGGTAACTTGGCTATAAAAGG
65 GGGTAACTTGGATATAAAAGG
2017426 GTTTGTTAGG
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 7 0.09
90 74 0.91
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGATTAG
GGTAACTTGGATATAAAAGGATTA
Found at i:2027556 original size:25 final size:26
Alignment explanation
Indices: 2027528--2027576 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2027518 GTCTGATGTG
*
2027528 GTAG-TTTCTAGAAGGTCCAGTCACA
1 GTAGTTTTCTAGAAGATCCAGTCACA
*
2027553 GTAGTTTTCTAGAAGATCTAGTCA
1 GTAGTTTTCTAGAAGATCCAGTCA
2027577 GCGTCTTCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (26 bp):
GTAGTTTTCTAGAAGATCCAGTCACA
Found at i:2035847 original size:11 final size:11
Alignment explanation
Indices: 2035827--2035868 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
2035817 CAACAGTTCG
2035827 AAAA-AGAAAA
1 AAAAGAGAAAA
2035837 AAAAGAGAAAA
1 AAAAGAGAAAA
2035848 AAAAG-GAAAA
1 AAAAGAGAAAA
*
2035858 GAAAATAGAAA
1 -AAAAGAGAAA
2035869 GAGACATGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 9 0.32
11 15 0.54
12 4 0.14
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAGAGAAAA
Found at i:2036693 original size:26 final size:27
Alignment explanation
Indices: 2036663--2036714 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
2036653 GTCCGATGTG
*
2036663 GTAG-TTTCAAGAAGGTCCAGTCAGCA
1 GTAGTTTTCAAGAAGATCCAGTCAGCA
* *
2036689 GTAGTTTTCTAGAAGATCTAGTCAGC
1 GTAGTTTTCAAGAAGATCCAGTCAGC
2036715 GCCTTCTGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (27 bp):
GTAGTTTTCAAGAAGATCCAGTCAGCA
Found at i:2040359 original size:17 final size:18
Alignment explanation
Indices: 2040334--2040377 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
2040324 GTTGTCATTA
* *
2040334 TTTTATAATAAAA-ATAT
1 TTTTTTAATAAAATAGAT
2040351 TTTTTTAATAAAATAGAT
1 TTTTTTAATAAAATAGAT
2040369 TTTATTTAA
1 TTT-TTTAA
2040378 AGTTTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.52
18 6 0.26
19 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTTTTAATAAAATAGAT
Found at i:2042244 original size:39 final size:39
Alignment explanation
Indices: 2042062--2042253 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
2042052 CCTGTACACC
* * * *
2042062 CAGTAAGGGCTTACCCT-ATGCACAAAACAGAGGAGCCTG
1 CAGTAAGGACTTACCCTGA-GCACAAAGCCGAGGAGCCTA
* * * * * *
2042101 CAGTAAGGTCTTATCATGTGCACAAAACAGAGGAGCCTA
1 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTA
2042140 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTA
1 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTA
* *
2042179 TAGTAAGGACTTACCCTGAGCACAAAGCCGATGAGCCTA
1 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTA
*
2042218 CAGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGC
1 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGC
2042254 TTGCGAAAAG
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
39 136 1.00
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.16
Consensus pattern (39 bp):
CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTA
Found at i:2048019 original size:39 final size:39
Alignment explanation
Indices: 2047962--2048075 Score: 129
Period size: 39 Copynumber: 2.9 Consensus size: 39
2047952 CATGTACACC
*
2047962 CAATAAGGGCTTACCATGTGCACAAAGCAGAGGAGCATA
1 CAATAAGGACTTACCATGTGCACAAAGCAGAGGAGCATA
* * * * *
2048001 CAATAAGGTCTTATCATGTGCACAAAGAAGAAGAGCATG
1 CAATAAGGACTTACCATGTGCACAAAGCAGAGGAGCATA
* * * * *
2048040 CAGTAAGGACTTACCCTGAGCATAAAGCTGAGGAGC
1 CAATAAGGACTTACCATGTGCACAAAGCAGAGGAGC
2048076 CTGCGAAAAG
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (39 bp):
CAATAAGGACTTACCATGTGCACAAAGCAGAGGAGCATA
Found at i:2050268 original size:20 final size:19
Alignment explanation
Indices: 2050239--2050312 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
2050229 TGAATCCAAT
*
2050239 GGATCGATCCTTTTACAAGG
1 GGATCAATCCTTTTACAA-G
**
2050259 GGATCAATCCTTTGGCCAAAG
1 GGATCAATCCTTT-TAC-AAG
*
2050280 GGATCAATCTTTTTACTAAG
1 GGATCAATCCTTTTAC-AAG
*
2050300 GGATCGATCCTTT
1 GGATCAATCCTTT
2050313 ATGGAAAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 27 0.63
21 14 0.33
22 2 0.05
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (19 bp):
GGATCAATCCTTTTACAAG
Found at i:2056276 original size:3 final size:3
Alignment explanation
Indices: 2056268--2056299 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2056258 TAGTAAATTG
*
2056268 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2056300 GGGTAAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:2058662 original size:15 final size:15
Alignment explanation
Indices: 2058642--2058685 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2058632 AAATGACAAT
2058642 TTTTATTATTTTTAA
1 TTTTATTATTTTTAA
*
2058657 TTTTA-TATTATGTAA
1 TTTTATTATT-TTTAA
2058672 TTTTATTAATTTTT
1 TTTTATT-ATTTTT
2058686 TATGAATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 4 0.17
15 14 0.58
16 3 0.12
17 3 0.12
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTTATTATTTTTAA
Found at i:2061778 original size:16 final size:17
Alignment explanation
Indices: 2061757--2061808 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
2061747 TTTTTAATTT
2061757 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
2061773 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
2061788 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
2061805 AATT
1 AATT
2061809 TATTTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:2063622 original size:19 final size:19
Alignment explanation
Indices: 2063600--2063642 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2063590 TTAGTTTACA
*
2063600 ATTATGATTGTAAAT-TTTT
1 ATTATAATT-TAAATATTTT
2063619 ATTATAATTTAAATATTTT
1 ATTATAATTTAAATATTTT
*
2063638 TTTAT
1 ATTAT
2063643 TTTTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTATAATTTAAATATTTT
Found at i:2063886 original size:4 final size:4
Alignment explanation
Indices: 2063867--2063907 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
2063857 GTAAAATTCC
* * *
2063867 TTTA ATTA TGTA TTTA TTTA TTTA TTTT TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
2063908 ACACGCATGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:2064259 original size:2 final size:2
Alignment explanation
Indices: 2064248--2064283 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2064238 AAATTTATTA
2064248 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2064284 AAATAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2064379 original size:30 final size:30
Alignment explanation
Indices: 2064343--2064413 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
2064333 ACTAAACCCG
2064343 TCCCCGTTTAACATAAACGGTTTTTCCCCA
1 TCCCCGTTTAACATAAACGGTTTTTCCCCA
* *
2064373 TCCCCGTTTAACATAAACGGTTTTTTCCCG
1 TCCCCGTTTAACATAAACGGTTTTTCCCCA
2064403 TCCCCGTTTAA
1 TCCCCGTTTAA
2064414 TTCGGTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.21, C:0.32, G:0.11, T:0.35
Consensus pattern (30 bp):
TCCCCGTTTAACATAAACGGTTTTTCCCCA
Found at i:2065505 original size:60 final size:60
Alignment explanation
Indices: 2065392--2065506 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 60
2065382 ATAGTCGATT
* * * * * *
2065392 GACCATTTTGTAACTTTGAATAGTCTGATGACTCAATAAAACAGCGTTTTATAATTAAAA
1 GACCATTTTATAACTTTGAATAGTCTAATGACCCAATAAAACAACATTCTATAATTAAAA
* * *
2065452 GACCATTTTATAACTTTTAATAGTCATAAT-ACCCAATAAAATAATATTCTATAAT
1 GACCATTTTATAACTTTGAATAGTC-TAATGACCCAATAAAACAACATTCTATAAT
2065507 CGAGATACCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
60 42 0.93
61 3 0.07
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.37
Consensus pattern (60 bp):
GACCATTTTATAACTTTGAATAGTCTAATGACCCAATAAAACAACATTCTATAATTAAAA
Found at i:2066830 original size:59 final size:59
Alignment explanation
Indices: 2066758--2066874 Score: 200
Period size: 59 Copynumber: 2.0 Consensus size: 59
2066748 GATGGATAAA
2066758 TGTCCTATTGAACCCTCCTAATCGCAATGAAAAGG-CAAACTCGATAATATGGCTCTAAG
1 TGTCCTATTGAACCCTCCTAATCGCAATGAAAAGGAC-AACTCGATAATATGGCTCTAAG
* *
2066817 TGTCCTATTGAACCCTCCTAGTCGTAATGAAAAGGACAACTCGATAATATGGCTCTAA
1 TGTCCTATTGAACCCTCCTAATCGCAATGAAAAGGACAACTCGATAATATGGCTCTAA
2066875 CAAACCCTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
59 54 0.98
60 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.26
Consensus pattern (59 bp):
TGTCCTATTGAACCCTCCTAATCGCAATGAAAAGGACAACTCGATAATATGGCTCTAAG
Found at i:2072932 original size:16 final size:17
Alignment explanation
Indices: 2072903--2072938 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2072893 GAATTTTAGT
2072903 TGTTTTGTAAAAGTAAA
1 TGTTTTGTAAAAGTAAA
*
2072920 TGTTTTG-AAAAGTCAA
1 TGTTTTGTAAAAGTAAA
2072936 TGT
1 TGT
2072939 GACACCTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.42
Consensus pattern (17 bp):
TGTTTTGTAAAAGTAAA
Found at i:2077801 original size:16 final size:17
Alignment explanation
Indices: 2077772--2077807 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
2077762 GAATTTTAGT
2077772 TGTTTTGTAAAAGTCAA
1 TGTTTTGTAAAAGTCAA
2077789 TGTTTTG-AAAAGTCAA
1 TGTTTTGTAAAAGTCAA
2077805 TGT
1 TGT
2077808 GACACCTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (17 bp):
TGTTTTGTAAAAGTCAA
Found at i:2082283 original size:43 final size:43
Alignment explanation
Indices: 2082221--2082450 Score: 381
Period size: 43 Copynumber: 5.4 Consensus size: 43
2082211 TTAATTACCG
*
2082221 TTACAGTTCCCCCATGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
2082264 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
2082307 TTACAGTTCCCTCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *
2082350 TTACAGTTCCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
2082393 TTACAGTT-TCCCAGGTTCCTTTACTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
2082435 TTACAGTTTCCCCAGG
1 TTACAGTTCCCCCAGG
2082451 CTCTTTTTCT
Statistics
Matches: 177, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
42 39 0.22
43 138 0.78
ACGTcount: A:0.17, C:0.28, G:0.24, T:0.31
Consensus pattern (43 bp):
TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:2083432 original size:454 final size:455
Alignment explanation
Indices: 2082585--2083494 Score: 1734
Period size: 454 Copynumber: 2.0 Consensus size: 455
2082575 GGGAACACAC
2082585 TAGATAACCTATTATGATCTCCTGAACCTAAACATTCAAAATATATTGCCCTGGACTAAACGCTT
1 TAGATAACCTATTATGATCTCCTGAACCTAAACATTCAAAATATATTGCCCTGGACTAAACGCTT
2082650 ATTATCTGTTACTACCTGAAATATCCGTAAGATCTCTGCTCAGTATAAAGATCTGTAAATGTCTG
66 ATTATCTGTTACTACCTGAAATATCCGTAAGATCTCTGCTCAGTATAAAGATCTGTAAATGTCTG
* * *
2082715 AACTAATAAGGAAATATATGTTTATCGGTGTCTGCACGTTCTTCAGCATCATTTGGTAGTTCTGT
131 AACTAATAAGGAAATATATGTTTATCGGTATATGCACGTTCTTCAGCATCATCTGGTAGTTCTGT
2082780 ATTACTGAGCTTTTTCGAAGCTCACTCTATTACTCGCCATTGCAGGTTAGAAGAATTAAACCAGT
196 ATTACTGAGCTTTTTCGAAGCTCACTCTATTACTCGCCATTGCAGGTTAGAAGAATTAAACCAGT
2082845 GTATCTATCGACTTCAGTAAAGGAGTTCTTTCGACGTTGTTGCAGAGTATGGTACATGTGATTAG
261 GTATCTATCGACTTCAGTAAAGGAGTTCTTTCGACGTTGTTGCAGAGTATGGTACATGTGATTAG
2082910 GGAGCATGTAATTGTATTTTATTTTAAATACGAGACATAAAATCTATTTTATTTTTGAATATTGA
326 GGAGCATGTAATTGTATTTTATTTTAAATACGAGACATAAAATCTATTTTATTTTTGAATATTGA
2082975 TAAATGATTTTATAAGTTACA-TTTTTAATAAAAGTTTTAAA-TTTTCCTCTATTTTTACAATGG
391 TAAATGATTTTATAAGTTACATTTTTTAATAAAAGTTTTAAATTTTTCCT-TATTTTTACAATGG
2083038 G
455 G
2083039 TAGATAACCTATTATGATCTCCTGAACCTAAACATTCAAAATATATTGCCCTGGACTAAACGCTT
1 TAGATAACCTATTATGATCTCCTGAACCTAAACATTCAAAATATATTGCCCTGGACTAAACGCTT
*
2083104 ATTATCTGTTACTACCTGAAATATCCGTAAGATCTCTGCTCAGTATAAAGATCTGTAGATGTCTG
66 ATTATCTGTTACTACCTGAAATATCCGTAAGATCTCTGCTCAGTATAAAGATCTGTAAATGTCTG
2083169 AACTAATAAGGAAATATATGTTTATCGGTATATGCACGTTCTTCAGCATCATCTGGTAGTTCTGT
131 AACTAATAAGGAAATATATGTTTATCGGTATATGCACGTTCTTCAGCATCATCTGGTAGTTCTGT
2083234 ATTACTGAGCTTTTTCGAAGCTCACTCTATTACTCGCCATTGCAGGTTAGAAGAATTAAACCAGT
196 ATTACTGAGCTTTTTCGAAGCTCACTCTATTACTCGCCATTGCAGGTTAGAAGAATTAAACCAGT
* *
2083299 GTATCTATCGACTTCAGTAAAGGAGTTCTTTCGATGTTGTTGCTGAGTATGGTACATGTGATTAG
261 GTATCTATCGACTTCAGTAAAGGAGTTCTTTCGACGTTGTTGCAGAGTATGGTACATGTGATTAG
2083364 GGAGCATGTAATTGTATTTTATTTTAAATACGAGACATAAAATCTATTTTATTTTTGAATATTGA
326 GGAGCATGTAATTGTATTTTATTTTAAATACGAGACATAAAATCTATTTTATTTTTGAATATTGA
*
2083429 TAAATGATTTTATAAGTTACATTTTTTAATAAAAGTTTTAAATTTTTCGTTATTTTTACAATGGG
391 TAAATGATTTTATAAGTTACATTTTTTAATAAAAGTTTTAAATTTTTCCTTATTTTTACAATGGG
2083494 T
1 T
2083495 CGCTCCAGTG
Statistics
Matches: 447, Mismatches: 7, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
454 405 0.91
455 36 0.08
456 6 0.01
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (455 bp):
TAGATAACCTATTATGATCTCCTGAACCTAAACATTCAAAATATATTGCCCTGGACTAAACGCTT
ATTATCTGTTACTACCTGAAATATCCGTAAGATCTCTGCTCAGTATAAAGATCTGTAAATGTCTG
AACTAATAAGGAAATATATGTTTATCGGTATATGCACGTTCTTCAGCATCATCTGGTAGTTCTGT
ATTACTGAGCTTTTTCGAAGCTCACTCTATTACTCGCCATTGCAGGTTAGAAGAATTAAACCAGT
GTATCTATCGACTTCAGTAAAGGAGTTCTTTCGACGTTGTTGCAGAGTATGGTACATGTGATTAG
GGAGCATGTAATTGTATTTTATTTTAAATACGAGACATAAAATCTATTTTATTTTTGAATATTGA
TAAATGATTTTATAAGTTACATTTTTTAATAAAAGTTTTAAATTTTTCCTTATTTTTACAATGGG
Found at i:2088251 original size:43 final size:43
Alignment explanation
Indices: 2088189--2088417 Score: 377
Period size: 43 Copynumber: 5.3 Consensus size: 43
2088179 TTAATTACCG
*
2088189 TTACAGTTCCCCCATGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *
2088232 TTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAACC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
2088275 TTACAGTTCCCCCAGGTCCCCTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *
2088318 TTACTGTTCCCCCAGGTCCCTTTCCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *
2088361 TTACAATTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
2088404 TTACAGTTTCCCCA
1 TTACAGTTCCCCCA
2088418 TGCTCTTTTT
Statistics
Matches: 171, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 171 1.00
ACGTcount: A:0.17, C:0.31, G:0.23, T:0.30
Consensus pattern (43 bp):
TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:2095059 original size:22 final size:22
Alignment explanation
Indices: 2095031--2095075 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2095021 AATTTGGGGC
2095031 ACATGGGTCCCTTATCATCTCA
1 ACATGGGTCCCTTATCATCTCA
2095053 ACATGGGTCCCTTATCATCTCA
1 ACATGGGTCCCTTATCATCTCA
2095075 A
1 A
2095076 TCAATGCGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.31
Consensus pattern (22 bp):
ACATGGGTCCCTTATCATCTCA
Found at i:2097055 original size:2 final size:2
Alignment explanation
Indices: 2097048--2097077 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2097038 AAATTCATTA
2097048 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2097078 TATGAATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2097272 original size:29 final size:29
Alignment explanation
Indices: 2097239--2097298 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
2097229 TTAAATTGCT
* * *
2097239 TACCATTTTAATCAACTTCTTTAATAACA
1 TACCACTTTAACCAACTTCGTTAATAACA
2097268 TACCACTTTAACCAACTTCGTTAATAACA
1 TACCACTTTAACCAACTTCGTTAATAACA
2097297 TA
1 TA
2097299 TTATGAATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (29 bp):
TACCACTTTAACCAACTTCGTTAATAACA
Found at i:2097373 original size:27 final size:27
Alignment explanation
Indices: 2097338--2097389 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
2097328 GAATTTTTTA
* *
2097338 AAAAATCAATTAACGTAATTTTATATT
1 AAAAATCAATAAACATAATTTTATATT
*
2097365 AAAATTCAATAAACATAATTTTATA
1 AAAAATCAATAAACATAATTTTATA
2097390 AAGTAGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (27 bp):
AAAAATCAATAAACATAATTTTATATT
Found at i:2100416 original size:2 final size:2
Alignment explanation
Indices: 2100409--2100436 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2100399 CATATCATAG
2100409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2100437 TTATTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2100814 original size:53 final size:53
Alignment explanation
Indices: 2100773--2101491 Score: 1009
Period size: 53 Copynumber: 13.5 Consensus size: 53
2100763 TCACTTCCTC
* ** * *
2100773 TTTCTTCAGGGAGTAGAACTCGAACATTCTTCTTCCTACGGGCTCGCTCTCTCT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTTCGCTCTCT-A
* *
2100827 TTTCTTCAGGGAGTAGAACTCGAACAATCATCTTCCTACGGG-TCTGCTCTCTC
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTTC-GCTCTCTA
* * * * * *
2100880 TTCCTTTAAGGAGTAGAACTCGAACAATCATCTTCCTACGGGTCCGCTCTCTC
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTTCGCTCTCTA
*
2100933 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTTCGCTCTCTA
* * * *
2100986 TTTCTTCAGGGAGTAGAACTCAAACAATAATCTTTCTACGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTTCGCTCTCTA
* *
2101039 TTTATTCAGGGAGTAAGAACTCGAACAATAATCTTACTACGGGTTCGCTCTCTA
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTTCGCTCTCTA
*
2101093 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGG-TCTGCTCTCTT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTTC-GCTCTCTA
*
2101146 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTTCGCTCTCTA
* * * * *
2101200 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCATACTGGTCCTCTCTCTT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTTCGCTCTCTA
* *
2101253 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTTCGCTCTCTA
*
2101307 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGCTCGCTCTCTA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTTCGCTCTCTA
* *
2101360 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGG-TC-CACCCTA
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTTCGCTCTCTA
* * *
2101412 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTTCTATGGGTCCGC-C-CTA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTTCGCTCTCTA
2101463 TTTTCTTCAGGGAGTAGAACTCGAACAAT
1 -TTTCTTCAGGGAGTAGAACTCGAACAAT
2101492 CTTCTGTTGC
Statistics
Matches: 614, Mismatches: 40, Indels: 24
0.91 0.06 0.04
Matches are distributed among these distances:
51 29 0.05
52 51 0.08
53 310 0.50
54 223 0.36
55 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (53 bp):
TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTTCGCTCTCTA
Found at i:2100914 original size:107 final size:106
Alignment explanation
Indices: 2100773--2101491 Score: 1092
Period size: 107 Copynumber: 6.8 Consensus size: 106
2100763 TCACTTCCTC
* **
2100773 TTTCTTCAGGGAGTAGAACTCGAACATTCTTCTTCCTACGGGCTCGCTCTCTCTTTTCTTCAGGG
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGG-TCGCTCTCT-TTTTCTTCAGGG
* * *
2100838 AGT-AGAACTCGAACAATCATCTTCCTACGGGTCTGCTCTCTC
64 AGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
* * * * *
2100880 TTCCTTTAAGGAGTAGAACTCGAACAATCATCTTCCTACGGGTCCGCTCTCTCTTTCTTCAGGGA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGT-CGCTCTCTTTTTCTTCAGGGA
2100945 GT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
65 GTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
* * *
2100986 TTTCTTCAGGGAGTAGAACTCAAACAATAATCTTTCTACGGGTCCGCTCTCTTTTTATTCAGGGA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGT-CGCTCTCTTTTTCTTCAGGGA
* *
2101051 GTAAGAACTCGAACAATAATCTTACTACGGGTTCGCTCTCTA
65 GTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
2101093 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCTTTTTCTTCAGGGA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC-GCTCTCTTTTTCTTCAGGGA
2101158 GTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
65 GTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
* * *
2101200 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCATACTGGTCCTCTCTCTTTTTCTTCAGGGA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGT-CGCTCTCTTTTTCTTCAGGGA
*
2101265 GTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
65 GTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
*
2101307 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGCTCGCTCTCTATTTCTTCAGGGA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGG-TCGCTCTCTTTTTCTTCAGGGA
*
2101372 GTAAGAACTCGAACAATAATCTTCCTACGGGTCCAC-C-CTA
65 GTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
* *
2101412 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTTCTATGGGTCCGC-C-CTATTTTCTTCAGGG
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGT-CGCTCTCT-TTTTCTTCAGGG
2101475 AGT-AGAACTCGAACAAT
64 AGTAAGAACTCGAACAAT
2101492 CTTCTGTTGC
Statistics
Matches: 568, Mismatches: 37, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
103 16 0.03
104 16 0.03
105 45 0.08
106 112 0.20
107 377 0.66
108 2 0.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (106 bp):
TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCGCTCTCTTTTTCTTCAGGGAG
TAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
Found at i:2101060 original size:160 final size:159
Alignment explanation
Indices: 2100773--2101491 Score: 1090
Period size: 160 Copynumber: 4.5 Consensus size: 159
2100763 TCACTTCCTC
* **
2100773 TTTCTTCAGGGAGTAGAACTCGAACATTCTTCTTCCTACGGG-CTCGCTCTCTCTTTTCTTCAGG
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC-CGCTCTCT-TTTTCTTCAGG
* * * * * *
2100837 GAGTAGAACTCGAACAATCATCTTCCTACGGGTCTGCTCTCTCTTCCTTTAAGGAGTAGAACTCG
64 GAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAGAACTCG
* *
2100902 AACAATCATCTTCCTACGGGTCCGCTCTCTC
129 AACAATAATCTTCCTACGGGTCCGCTCTCTA
*
2100933 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGGA
* * * *
2100998 GTAGAACTCAAACAATAATCTTTCTACGGGTCCGCTCTCTTTTTATTCAGGGAGTAAGAACTCGA
66 GTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGT-AGAACTCGA
* *
2101063 ACAATAATCTTACTACGGGTTCGCTCTCTA
130 ACAATAATCTTCCTACGGGTCCGCTCTCTA
*
2101093 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCTTTTTCTTCAGGGA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGGA
2101158 GTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAGAACTCGA
66 GT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAGAACTCGA
* * * *
2101223 ACAATAATCTTCATACTGGTCCTCTCTCTT
130 ACAATAATCTTCCTACGGGTCCGCTCTCTA
2101253 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGG
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGG
2101318 AGTAGAACTCGAACAATAATCTTCCTACGGG-CTCGCTCTCTATTTCTTCAGGGAGTAAGAACTC
65 AGTAGAACTCGAACAATAATCTTCCTACGGGTC-CGCTCTCTATTTCTTCAGGGAGT-AGAACTC
*
2101382 GAACAATAATCTTCCTACGGGTCCAC-C-CTA
128 GAACAATAATCTTCCTACGGGTCCGCTCTCTA
* *
2101412 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTTCTATGGGTCCGC-C-CTATTTTCTTCAGGG
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCT-TTTTCTTCAGGG
2101475 AGTAGAACTCGAACAAT
65 AGTAGAACTCGAACAAT
2101492 CTTCTGTTGC
Statistics
Matches: 516, Mismatches: 36, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
156 2 0.00
157 30 0.06
158 31 0.06
159 75 0.15
160 246 0.48
161 132 0.26
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (159 bp):
TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGGA
GTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAGAACTCGAA
CAATAATCTTCCTACGGGTCCGCTCTCTA
Done.