Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 6 of 130
Found at i:1566176 original size:22 final size:22
Alignment explanation
Indices: 1566151--1566192 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1566141 TCCATAATTT
1566151 AATATACAA-TTATTATTGATTA
1 AATATA-AAGTTATTATTGATTA
*
1566173 AATATAAAGTTATTGTTGAT
1 AATATAAAGTTATTATTGAT
1566193 GTTGTCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (22 bp):
AATATAAAGTTATTATTGATTA
Found at i:1566862 original size:14 final size:14
Alignment explanation
Indices: 1566843--1566873 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1566833 TTTTTAATTA
1566843 TAAAATTTCCTATT
1 TAAAATTTCCTATT
1566857 TAAAATTTCCTATT
1 TAAAATTTCCTATT
1566871 TAA
1 TAA
1566874 TTAAGCGCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAAATTTCCTATT
Found at i:1567425 original size:38 final size:38
Alignment explanation
Indices: 1567374--1567455 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
1567364 ATAAAAGTAC
*
1567374 AAATCATTATTAAATAGATACTTTCACGATAAGAATAT
1 AAATCATTATTAAATAGATACTGTCACGATAAGAATAT
1567412 AAATCATTATTAAATAGATACTGTCACGATAAGAATAT
1 AAATCATTATTAAATAGATACTGTCACGATAAGAATAT
1567450 AAATCA
1 AAATCA
1567456 CTAATCATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.32
Consensus pattern (38 bp):
AAATCATTATTAAATAGATACTGTCACGATAAGAATAT
Found at i:1568219 original size:11 final size:11
Alignment explanation
Indices: 1568203--1568227 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1568193 CGTATTGCTC
1568203 TTTTTGAATAA
1 TTTTTGAATAA
1568214 TTTTTGAATAA
1 TTTTTGAATAA
1568225 TTT
1 TTT
1568228 AATTTATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (11 bp):
TTTTTGAATAA
Found at i:1568649 original size:16 final size:16
Alignment explanation
Indices: 1568603--1568650 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 16
1568593 TTTAATATAG
1568603 TTTAATTTGATATAAAT
1 TTTAA-TTGATATAAAT
1568620 TTT-ATT--TATAAAT
1 TTTAATTGATATAAAT
*
1568633 TTTAATTGATTTAAAT
1 TTTAATTGATATAAAT
1568649 TT
1 TT
1568651 AAATAACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
13 10 0.37
14 3 0.11
15 2 0.07
16 9 0.33
17 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
TTTAATTGATATAAAT
Found at i:1568857 original size:153 final size:152
Alignment explanation
Indices: 1568640--1569091 Score: 602
Period size: 168 Copynumber: 2.8 Consensus size: 152
1568630 AATTTTAATT
* * *
1568640 GATTTAAATTTAAATAACTAACAAATAAAAAGCTATATTTTTAATGACAAATAATCTTTATTAAA
1 GATTTAAATTTAAATAACTAACTAAT-AAAAGCTATATATTTAATGACAAATAATCATTATTAAA
*
1568705 TAAATAAGAAATGCTAGAAATTGAAATA-TAAATTTGTTATTTTTTAAAATTTATAAAGATATTT
65 TAAATAA-AAATGCTAGAAATTTAAA-AGTAAATTTGTTATTTTTTAAAATTTATAAAGATATTT
1568769 ATGTTATTCATTTTTAACACTTTTA
128 ATGTTATTCATTTTTAACACTTTTA
*
1568794 GATTTAAATTTAAATAACTAACTAATAAAAGTTATATATTTAATGACAAATAATCATTATTAAAT
1 GATTTAAATTTAAATAACTAACTAATAAAAGCTATATATTTAATGACAAATAATCATTATTAAAT
* *
1568859 AAATAATTAATGCTA-AAATTTAAAAGTAAATTTATTATTTTTTAAAATTTATAAGGGTATTTAT
66 AAATAA-AAATGCTAGAAATTTAAAAGTAAATTTGTTATTTTTTAAAATTTAT-A----A---A-
*
1568923 GTCGTTCATTATTAATGTTATTCATTTTTAACACTTTTA
121 ---G---A-TATTTATGTTATTCATTTTTAACACTTTTA
1568962 GATTTAAATTTAAATAACTAACTAATAAAAGCTATATATTTAATGACAAATAATCATTATTAAAT
1 GATTTAAATTTAAATAACTAACTAATAAAAGCTATATATTTAATGACAAATAATCATTATTAAAT
* * *
1569027 AAATAAATAATGCTAGAAATTTAAAAGTAAATTTGTTATTTCTTAAAATTTATAAGGGTATTTAT
66 AAATAAA-AATGCTAGAAATTTAAAAGTAAATTTGTTATTTTTTAAAATTTATAAAGATATTTAT
1569092 ATCGTTCACT
Statistics
Matches: 263, Mismatches: 16, Indels: 39
0.83 0.05 0.12
Matches are distributed among these distances:
151 1 0.00
152 33 0.13
153 56 0.21
154 25 0.10
157 2 0.01
160 1 0.00
164 2 0.01
167 1 0.00
168 107 0.41
169 35 0.13
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (152 bp):
GATTTAAATTTAAATAACTAACTAATAAAAGCTATATATTTAATGACAAATAATCATTATTAAAT
AAATAAAAATGCTAGAAATTTAAAAGTAAATTTGTTATTTTTTAAAATTTATAAAGATATTTATG
TTATTCATTTTTAACACTTTTA
Found at i:1569022 original size:87 final size:87
Alignment explanation
Indices: 1568764--1569024 Score: 211
Period size: 87 Copynumber: 3.1 Consensus size: 87
1568754 TTTATAAAGA
*
1568764 TATTTATGTTATTCATTTTTAACACTTTTAGATTTAAATTTAAATAACTAACTAATAAAAGTTAT
1 TATTAATGTTATTCATTTTTAACACTTTTAGATTTAAATTTAAATAACTAACTAATAAAAGTTAT
1568829 ATATTTAATGACAAATAATCAT
66 ATATTTAATGACAAATAATCAT
** ** ** * * ** * * ** ** *
1568851 TATTAA----ATAAATAATTAATGC--TAAAATTTAAAAGTAAATTTATTATTTTTTAAAATTTA
1 TATTAATGTTATTCATTTTTAACACTTTTAGATTTAAATTTAAA-TAACTAACTAATAAAAGTTA
* *
1568910 TAAGGGTATTT-ATGTC--GT--TCAT
65 T-A---TATTTAATGACAAATAATCAT
*
1568932 TATTAATGTTATTCATTTTTAACACTTTTAGATTTAAATTTAAATAACTAACTAATAAAAGCTAT
1 TATTAATGTTATTCATTTTTAACACTTTTAGATTTAAATTTAAATAACTAACTAATAAAAGTTAT
1568997 ATATTTAATGACAAATAATCAT
66 ATATTTAATGACAAATAATCAT
1569019 TATTAA
1 TATTAA
1569025 ATAAATAAAT
Statistics
Matches: 118, Mismatches: 40, Indels: 32
0.62 0.21 0.17
Matches are distributed among these distances:
81 23 0.19
82 19 0.16
83 15 0.13
85 15 0.13
86 18 0.15
87 28 0.24
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (87 bp):
TATTAATGTTATTCATTTTTAACACTTTTAGATTTAAATTTAAATAACTAACTAATAAAAGTTAT
ATATTTAATGACAAATAATCAT
Found at i:1570034 original size:17 final size:17
Alignment explanation
Indices: 1570014--1570062 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
1570004 TTTAATATAG
1570014 TTTAATTTGATATAAAT
1 TTTAATTTGATATAAAT
*
1570031 TTT-ATTT-ATA-AATT
1 TTTAATTTGATATAAAT
*
1570045 TTTAA-TTGATTTAAAT
1 TTTAATTTGATATAAAT
1570061 TT
1 TT
1570063 AAATAACTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
14 8 0.31
15 6 0.23
16 9 0.35
17 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (17 bp):
TTTAATTTGATATAAAT
Found at i:1570282 original size:152 final size:154
Alignment explanation
Indices: 1570052--1570359 Score: 460
Period size: 152 Copynumber: 2.0 Consensus size: 154
1570042 ATTTTTAATT
* *
1570052 GATTTAAATTTAAATAACTAACAAATAAAAAGCTATATTTTTAATGACAAATAATCTTTATTAAA
1 GATTTAAATTTAAATAACTAACAAATAAAAAGCTATATATTTAATGACAAATAATCATTATTAAA
*
1570117 TAAATAAAAAATGCTAGAAATTCAAATA-TAAATTTGTTATTTTTTAAAATTTATAAAGATATTT
66 TAAATAAAAAATGCTAAAAATTCAAA-AGTAAATTTGTTATTTTTTAAAATTTATAAAGATATTT
* *
1570181 AAGTTATTCATTTTTAACACTTTTA
130 AAGTCATTCATTATTAACACTTTTA
* *
1570206 GATTTAAATTTAAATAACTAACTAAT-AAAA-TTATATATTTAATGACAAATAATCATTATTAAA
1 GATTTAAATTTAAATAACTAACAAATAAAAAGCTATATATTTAATGACAAATAATCATTATTAAA
** * *
1570269 TAAATAATTAATGCTAAAAATTTAAAAGTAAATTTGTTATTTTTTAAAATTTATAAGGATATTTA
66 TAAATAAAAAATGCTAAAAATTCAAAAGTAAATTTGTTATTTTTTAAAATTTATAAAGATATTTA
* * *
1570334 TGTCGTTCATTATTAATACTTTTA
131 AGTCATTCATTATTAACACTTTTA
1570358 GA
1 GA
1570360 GTTCACAGTT
Statistics
Matches: 139, Mismatches: 14, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
151 1 0.01
152 109 0.78
153 4 0.03
154 25 0.18
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (154 bp):
GATTTAAATTTAAATAACTAACAAATAAAAAGCTATATATTTAATGACAAATAATCATTATTAAA
TAAATAAAAAATGCTAAAAATTCAAAAGTAAATTTGTTATTTTTTAAAATTTATAAAGATATTTA
AGTCATTCATTATTAACACTTTTA
Found at i:1572843 original size:45 final size:45
Alignment explanation
Indices: 1572794--1572883 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
1572784 AAACTTTACC
1572794 ACATTCCCCACGGAAAAATAAAAAATGGAGATTTGTTATGGTGTT
1 ACATTCCCCACGGAAAAATAAAAAATGGAGATTTGTTATGGTGTT
1572839 ACATTCCCCACGGAAAAATAAAAAATGGAGATTTGTTATGGTGTT
1 ACATTCCCCACGGAAAAATAAAAAATGGAGATTTGTTATGGTGTT
1572884 CCTCAATCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (45 bp):
ACATTCCCCACGGAAAAATAAAAAATGGAGATTTGTTATGGTGTT
Found at i:1575221 original size:2 final size:2
Alignment explanation
Indices: 1575214--1575240 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1575204 AATCACCAAG
1575214 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1575241 TTTGCTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1580145 original size:2 final size:2
Alignment explanation
Indices: 1580138--1580166 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1580128 CAAACTCTTT
1580138 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1580167 GGGGTTTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1594252 original size:52 final size:52
Alignment explanation
Indices: 1594162--1594318 Score: 183
Period size: 52 Copynumber: 3.0 Consensus size: 52
1594152 TATAACCATA
* * * * * * *
1594162 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAAAATTCTTCTCCTGTAAGT
1 CAAACTTACCTATTAAGAATCTCTTTCCTTTTAGAATTCTTCTCCTGCAAGT
* *
1594214 CAAACTTACCTATTAAGAATCTCTTTCCTTTTAGAATTCTTATCTTGCAAGT
1 CAAACTTACCTATTAAGAATCTCTTTCCTTTTAGAATTCTTCTCCTGCAAGT
**
1594266 CAAACTTACCTATTAAGAATACTCTTT-CTTTT-GAAATTCTTCTTTTGCAAGT
1 CAAACTTACCTATTAAGAAT-CTCTTTCCTTTTAG-AATTCTTCTCCTGCAAGT
1594318 C
1 C
1594319 TTCTTGTCCA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 1 0.01
52 85 0.92
53 6 0.07
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATCTCTTTCCTTTTAGAATTCTTCTCCTGCAAGT
Found at i:1594438 original size:52 final size:52
Alignment explanation
Indices: 1594358--1594493 Score: 186
Period size: 52 Copynumber: 2.6 Consensus size: 52
1594348 TCTCTTGCCC
* * * * *
1594358 ATTAAGAATCCCTCTCCTCTTAAAATTCTTCTCCTGTAAGTCAAACTTACCT
1 ATTAAGAATCTCTTTCCTTTTAGAATTCTTCTCCTGCAAGTCAAACTTACCT
*
1594410 ATTAAGAATCTCTTTCCTTTTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
1 ATTAAGAATCTCTTTCCTTTTAGAATTCTTCTCCTGCAAGTCAAACTTACCT
1594462 ATTAAGAATTCTCTTT-CTTTT-GAAATTCTTCT
1 ATTAAGAA-TCTCTTTCCTTTTAG-AATTCTTCT
1594494 TTTACAAGTC
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
51 1 0.01
52 68 0.89
53 7 0.09
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.43
Consensus pattern (52 bp):
ATTAAGAATCTCTTTCCTTTTAGAATTCTTCTCCTGCAAGTCAAACTTACCT
Found at i:1594478 original size:185 final size:185
Alignment explanation
Indices: 1594166--1594535 Score: 695
Period size: 185 Copynumber: 2.0 Consensus size: 185
1594156 ACCATACAAA
1594166 CTTGCCCATTAAGAATCCCTCTCCTCTTAAAATTCTTCTCCTGTAAGTCAAACTTACCTATTAAG
1 CTTGCCCATTAAGAATCCCTCTCCTCTTAAAATTCTTCTCCTGTAAGTCAAACTTACCTATTAAG
1594231 AATCTCTTTCCTTTTAGAATTCTTATCTTGCAAGTCAAACTTACCTATTAAGAATACTCTTTCTT
66 AATCTCTTTCCTTTTAGAATTCTTATCTTGCAAGTCAAACTTACCTATTAAGAATACTCTTTCTT
* * *
1594296 TTGAAATTCTTCTTTTGCAAGTCTTCTTGTCCATCAAGCAATATTTGACAAATCT
131 TTGAAATTCTTCTTTTACAAGTCTTCTTGTCCATCAAACAATATCTGACAAATCT
1594351 CTTGCCCATTAAGAATCCCTCTCCTCTTAAAATTCTTCTCCTGTAAGTCAAACTTACCTATTAAG
1 CTTGCCCATTAAGAATCCCTCTCCTCTTAAAATTCTTCTCCTGTAAGTCAAACTTACCTATTAAG
* *
1594416 AATCTCTTTCCTTTTAGAATTCTTCTCTTGCAAGTCAAACTTACCTATTAAGAATTCTCTTTCTT
66 AATCTCTTTCCTTTTAGAATTCTTATCTTGCAAGTCAAACTTACCTATTAAGAATACTCTTTCTT
1594481 TTGAAATTCTTCTTTTACAAGTCTTCTTGTCCATCAAACAATATCTGACAAATCT
131 TTGAAATTCTTCTTTTACAAGTCTTCTTGTCCATCAAACAATATCTGACAAATCT
1594536 AAAAAAATCT
Statistics
Matches: 180, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
185 180 1.00
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.41
Consensus pattern (185 bp):
CTTGCCCATTAAGAATCCCTCTCCTCTTAAAATTCTTCTCCTGTAAGTCAAACTTACCTATTAAG
AATCTCTTTCCTTTTAGAATTCTTATCTTGCAAGTCAAACTTACCTATTAAGAATACTCTTTCTT
TTGAAATTCTTCTTTTACAAGTCTTCTTGTCCATCAAACAATATCTGACAAATCT
Found at i:1595598 original size:52 final size:52
Alignment explanation
Indices: 1595443--1595599 Score: 185
Period size: 52 Copynumber: 3.0 Consensus size: 52
1595433 TATAACCATA
* * * * *
1595443 CAAACTTGCCCATTAAGAATCCT-TCTCCTCTTAGAATTTTTCTCTTGTAAGT
1 CAAACTTACCTATTAAGAATCCTCT-TTCTCTTAGAATTTTTTTCTTGCAAGT
* *
1595495 CAAACTTACCTATTAAGAAT-CTCTTTCTTTTTAGAATTCTTTTCTTGCAAGT
1 CAAACTTACCTATTAAGAATCCTCTTTC-TCTTAGAATTTTTTTCTTGCAAGT
* *
1595547 CAAACTTACCTATTAAGAATCCTCTTTCTCTT-GAAATTTTTTTTTTACAAGT
1 CAAACTTACCTATTAAGAATCCTCTTTCTCTTAG-AATTTTTTTCTTGCAAGT
1595599 C
1 C
1595600 TTCTTGTCCA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
51 5 0.06
52 78 0.87
53 7 0.08
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.44
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATCCTCTTTCTCTTAGAATTTTTTTCTTGCAAGT
Found at i:1600677 original size:33 final size:33
Alignment explanation
Indices: 1600640--1600706 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1600630 TAAGCTCCAG
1600640 AGTAATTTTCAACCAGTTTGAAAATTCCAAACA
1 AGTAATTTTCAACCAGTTTGAAAATTCCAAACA
1600673 AGTAATTTTCAACCAGTTTGAAAATTCCAAACA
1 AGTAATTTTCAACCAGTTTGAAAATTCCAAACA
1600706 A
1 A
1600707 TGAAAGAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (33 bp):
AGTAATTTTCAACCAGTTTGAAAATTCCAAACA
Found at i:1600719 original size:33 final size:33
Alignment explanation
Indices: 1600649--1600719 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
1600639 GAGTAATTTT
****
1600649 CAACCAGTTTGAAAATTCCAAACAAGTAATTTT
1 CAACCAGTTTGAAAATTCCAAACAAGTAAAGAA
1600682 CAACCAGTTTGAAAATTCCAAACAA-TGAAAGAA
1 CAACCAGTTTGAAAATTCCAAACAAGT-AAAGAA
1600715 CAACC
1 CAACC
1600720 TGCCGGACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 1 0.03
33 32 0.97
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (33 bp):
CAACCAGTTTGAAAATTCCAAACAAGTAAAGAA
Found at i:1602649 original size:26 final size:26
Alignment explanation
Indices: 1602620--1602670 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1602610 TGTGTATAAT
1602620 TTTTGTGTTTTAAT-TCTGGTTTTTGG
1 TTTTG-GTTTTAATGTCTGGTTTTTGG
*
1602646 TTTTGGTTTTGATGTCTGGTTTTTG
1 TTTTGGTTTTAATGTCTGGTTTTTG
1602671 TTCAGGGACG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.06, C:0.04, G:0.25, T:0.65
Consensus pattern (26 bp):
TTTTGGTTTTAATGTCTGGTTTTTGG
Found at i:1609774 original size:33 final size:33
Alignment explanation
Indices: 1609732--1609797 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1609722 CAGGAACTAT
1609732 AAGGAAATGTAAACAAATACTACATGAATATCA
1 AAGGAAATGTAAACAAATACTACATGAATATCA
1609765 AAGGAAATGTAAACAAATACTACATGAATATCA
1 AAGGAAATGTAAACAAATACTACATGAATATCA
1609798 TAAAAGCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (33 bp):
AAGGAAATGTAAACAAATACTACATGAATATCA
Found at i:1618401 original size:17 final size:16
Alignment explanation
Indices: 1618361--1618412 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
1618351 TTTATAAATT
*
1618361 ATTTAAAATTAATTTG
1 ATTTAAATTTAATTTG
* *
1618377 AATAAAATTTAAATTTG
1 ATTTAAATTT-AATTTG
*
1618394 ATTTAAATTATTATTTG
1 ATTTAAATT-TAATTTG
1618411 AT
1 AT
1618413 CGAGTTTAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 7 0.25
17 20 0.71
18 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTTAAATTTAATTTG
Found at i:1618515 original size:18 final size:19
Alignment explanation
Indices: 1618492--1618539 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
1618482 TAGTTCATAA
1618492 ATTTAATTAAATTTTTA-T
1 ATTTAATTAAATTTTTATT
* *
1618510 ATTTAAATATATTTTTATT
1 ATTTAATTAAATTTTTATT
1618529 ATTTTAATTAA
1 A-TTTAATTAA
1618540 TAAAATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 15 0.62
19 2 0.08
20 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTAATTAAATTTTTATT
Found at i:1618717 original size:12 final size:12
Alignment explanation
Indices: 1618700--1618747 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
1618690 AAATTAAATC
1618700 AATTTTAAATTA
1 AATTTTAAATTA
1618712 AATTTTAAATCTTA
1 AATTTTAAA--TTA
* *
1618726 AATTTTGAATCA
1 AATTTTAAATTA
1618738 AA-TTTAAATT
1 AATTTTAAATT
1618748 TAATACTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
11 6 0.20
12 13 0.43
14 11 0.37
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (12 bp):
AATTTTAAATTA
Found at i:1618728 original size:14 final size:14
Alignment explanation
Indices: 1618700--1618736 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1618690 AAATTAAATC
1618700 AATTTTAAA--TTA
1 AATTTTAAATCTTA
1618712 AATTTTAAATCTTA
1 AATTTTAAATCTTA
*
1618726 AATTTTGAATC
1 AATTTTAAATC
1618737 AAATTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 9 0.41
14 13 0.59
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (14 bp):
AATTTTAAATCTTA
Found at i:1618740 original size:26 final size:24
Alignment explanation
Indices: 1618700--1618750 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
1618690 AAATTAAATC
*
1618700 AATTTTAAATTAAATTTTAAATCTTA
1 AATTTTAAATCAAA-TTTAAAT-TTA
*
1618726 AATTTTGAATCAAATTTAAATTTA
1 AATTTTAAATCAAATTTAAATTTA
1618750 A
1 A
1618751 TACTTTATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 7 0.30
26 12 0.52
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (24 bp):
AATTTTAAATCAAATTTAAATTTA
Found at i:1622861 original size:28 final size:28
Alignment explanation
Indices: 1622817--1622873 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
1622807 GAAATTTTCG
1622817 AAAGTATCCCTGATTCCATTTCAATATT
1 AAAGTATCCCTGATTCCATTTCAATATT
*
1622845 AAAGTATCCCCTG-TTCCCTTTCAATATT
1 AAAGTAT-CCCTGATTCCATTTCAATATT
1622873 A
1 A
1622874 TATTAGTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (28 bp):
AAAGTATCCCTGATTCCATTTCAATATT
Found at i:1622917 original size:28 final size:29
Alignment explanation
Indices: 1622884--1622941 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
1622874 TATTAGTTTC
* *
1622884 AAAGTATCCCTTCTTTCCTTTC-AATATT
1 AAAGTATCCCTTATTACCTTTCAAATATT
*
1622912 AAAGTATCTCTTATTACCTTTCAAATATT
1 AAAGTATCCCTTATTACCTTTCAAATATT
1622941 A
1 A
1622942 TATTAATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.45
Consensus pattern (29 bp):
AAAGTATCCCTTATTACCTTTCAAATATT
Found at i:1622961 original size:68 final size:67
Alignment explanation
Indices: 1622812--1623095 Score: 385
Period size: 68 Copynumber: 4.2 Consensus size: 67
1622802 GACACGAAAT
* * * *
1622812 TTTCGAAAGTATCCCTGA-TTCCATTTCAATATTAAAGTATCCCCTGTTCCCTTTCAATATTATA
1 TTTC-AAAGTATCCCTTATTTCC-TTTCAATATTAAAGTATCCCTTATTACCTTTCAATATTATA
1622876 TTAG
64 TTAG
* *
1622880 TTTCAAAGTATCCCTTCTTTCCTTTCAATATTAAAGTATCTCTTATTACCTTTCAAATATTATAT
1 TTTCAAAGTATCCCTTATTTCCTTTCAATATTAAAGTATCCCTTATTACCTTTC-AATATTATAT
*
1622945 TAA
65 TAG
* ** * *
1622948 TTTCAAAGTATCCCTTATTTCCTTTCAATATTAAAATATTTCTTATTCCCTTTCAATA-TAAATT
1 TTTCAAAGTATCCCTTATTTCCTTTCAATATTAAAGTATCCCTTATTACCTTTCAATATTATATT
1623012 AG
66 AG
* * *
1623014 TTCCAAAGTATCCCTTATATCCTTTCAATTTTAAAGTATCCCTTATTACCTTTCAATATTATATT
1 TTTCAAAGTATCCCTTATTTCCTTTCAATATTAAAGTATCCCTTATTACCTTTCAATATTATATT
1623079 AG
66 AG
1623081 TTTCAAAGT-TCCCTT
1 TTTCAAAGTATCCCTT
1623096 TCAATATTAT
Statistics
Matches: 191, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
66 63 0.33
67 58 0.30
68 70 0.37
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (67 bp):
TTTCAAAGTATCCCTTATTTCCTTTCAATATTAAAGTATCCCTTATTACCTTTCAATATTATATT
AG
Found at i:1624430 original size:15 final size:15
Alignment explanation
Indices: 1624407--1624450 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
1624397 TTAAATTTAT
1624407 TTAAATATAAATGTA
1 TTAAATATAAATGTA
*
1624422 TTGAATAT-AAT-TA
1 TTAAATATAAATGTA
1624435 TTAAATTATAAATGTA
1 TTAAA-TATAAATGTA
1624451 AAAAATACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 6 0.25
14 6 0.25
15 10 0.42
16 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
TTAAATATAAATGTA
Found at i:1624678 original size:20 final size:20
Alignment explanation
Indices: 1624653--1624696 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1624643 ATTTTGAAAA
1624653 AAAAATTGATA-AAATTTAAT
1 AAAAATT-ATATAAATTTAAT
*
1624673 AAAAATTATATATATTTAAT
1 AAAAATTATATAAATTTAAT
1624693 AAAA
1 AAAA
1624697 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAATTATATAAATTTAAT
Found at i:1631749 original size:34 final size:30
Alignment explanation
Indices: 1631670--1631756 Score: 104
Period size: 29 Copynumber: 2.8 Consensus size: 30
1631660 CTGCTGGGTG
*
1631670 AAATGAAATATATAAAGCATACATTTATTA
1 AAATGAAATATATAAAGCATACATTAATTA
* *
1631700 ATAT-ATATATATAAAGCATACATTAAACTTA
1 AAATGAAATATATAAAGCATACATT-AA-TTA
1631731 TCAAATGAAATATATAAAGCATACAT
1 --AAATGAAATATATAAAGCATACAT
1631757 AAAAATAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
29 19 0.40
30 4 0.09
31 3 0.06
33 3 0.06
34 18 0.38
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (30 bp):
AAATGAAATATATAAAGCATACATTAATTA
Found at i:1631834 original size:18 final size:19
Alignment explanation
Indices: 1631813--1631855 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1631803 TTATAAATGT
*
1631813 ATTATTAATTTTA-ATAAA
1 ATTATTAATTTGATATAAA
1631831 ATTATT-ATTTGATATAAA
1 ATTATTAATTTGATATAAA
*
1631849 AATATTA
1 ATTATTA
1631856 TAATAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTATTAATTTGATATAAA
Found at i:1632709 original size:19 final size:19
Alignment explanation
Indices: 1632685--1632723 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1632675 AAAAAATATT
* *
1632685 TAAAAAATATTTTTTAAAA
1 TAAAAAATATATCTTAAAA
1632704 TAAAAAATATATCTTAAAA
1 TAAAAAATATATCTTAAAA
1632723 T
1 T
1632724 TTTTTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAAATATATCTTAAAA
Found at i:1634347 original size:4 final size:4
Alignment explanation
Indices: 1634338--1634371 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
1634328 TAACCAAATC
*
1634338 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TATA TC
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TC
1634372 ACCAACCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (4 bp):
TCTA
Found at i:1643907 original size:19 final size:18
Alignment explanation
Indices: 1643883--1643922 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
1643873 GTAAAAAAAA
1643883 AATTATAATATTAATTTTT
1 AATTATAATATT-ATTTTT
*
1643902 AATTATAATATTTTTTTT
1 AATTATAATATTATTTTT
1643920 AAT
1 AAT
1643923 AAAGTAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AATTATAATATTATTTTT
Found at i:1644995 original size:2 final size:2
Alignment explanation
Indices: 1644988--1645032 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1644978 AATAACCAAA
1644988 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1645030 TC T
1 TC T
1645033 ATATATATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1645037 original size:2 final size:2
Alignment explanation
Indices: 1645032--1645064 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1645022 TCTCTCTCTC
1645032 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1645065 CAACAACCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1652534 original size:24 final size:24
Alignment explanation
Indices: 1652491--1652552 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
1652481 AATTAAAATT
*
1652491 ATTAATAATTATTATTATAATTATA
1 ATTAAAAATT-TTATTATAATTATA
* *
1652516 ATTAAAAATTTTATTATAATTTTG
1 ATTAAAAATTTTATTATAATTATA
*
1652540 ATTAAAAAATTTA
1 ATTAAAAATTTTA
1652553 ATTAAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
24 24 0.73
25 9 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTAAAAATTTTATTATAATTATA
Found at i:1652555 original size:37 final size:40
Alignment explanation
Indices: 1652509--1652586 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 40
1652499 TTATTATTAT
1652509 AATTATAATTAAAAATTT-TATT-A-TAATTTTGATTAAAA
1 AATTATAATTAAAAATTTCTATTAATTAATTTT-ATTAAAA
1652547 AATT-TAATTAAAAATTTCTATTAATTTAATTTTATTAAAA
1 AATTATAATTAAAAATTTCTATTAA-TTAATTTTATTAAAA
1652587 TAAATATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
37 13 0.36
38 8 0.22
39 1 0.03
40 7 0.19
41 7 0.19
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (40 bp):
AATTATAATTAAAAATTTCTATTAATTAATTTTATTAAAA
Found at i:1652569 original size:13 final size:12
Alignment explanation
Indices: 1652489--1652586 Score: 65
Period size: 12 Copynumber: 7.8 Consensus size: 12
1652479 GAAATTAAAA
*
1652489 TTATTAATAATT
1 TTATTAAAAATT
*
1652501 ATTATT-ATAATT
1 -TTATTAAAAATT
*
1652513 ATAATTAAAAATT
1 -TTATTAAAAATT
*
1652526 TTATT-ATAATT
1 TTATTAAAAATT
1652537 TTGATTAAAAAATT
1 TT-ATT-AAAAATT
*
1652551 TAATTAAAAATT
1 TTATTAAAAATT
*
1652563 TCTATTAATTTAATT
1 T-TATTAA--AAATT
1652578 TTATTAAAA
1 TTATTAAAA
1652587 TAAATATTTA
Statistics
Matches: 69, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
11 7 0.10
12 27 0.39
13 18 0.26
14 12 0.17
15 5 0.07
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (12 bp):
TTATTAAAAATT
Found at i:1652586 original size:26 final size:25
Alignment explanation
Indices: 1652497--1652587 Score: 69
Period size: 26 Copynumber: 3.6 Consensus size: 25
1652487 AATTATTAAT
* * *
1652497 AATTATTATTATAATTATAATT-AAA
1 AATT-TTATTAAAATTTTGATTAAAA
*
1652522 AATTTTATTATAATTTTGATTAAAA
1 AATTTTATTAAAATTTTGATTAAAA
* **
1652547 AATTTAATTAAAAATTTCT-ATTAATTT
1 AATTTTATT-AAAATTT-TGATTAA-AA
1652574 AATTTTATTAAAAT
1 AATTTTATTAAAAT
1652588 AAATATTTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
24 15 0.27
25 15 0.27
26 16 0.29
27 9 0.16
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (25 bp):
AATTTTATTAAAATTTTGATTAAAA
Found at i:1652594 original size:26 final size:27
Alignment explanation
Indices: 1652565--1652633 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
1652555 TAAAAATTTC
* *
1652565 TATTAATTTAATT-TTATTAAAATAAA
1 TATTAATTTAATTGATAATAAAATAAA
**
1652591 TATTTAAATTTAATTGATAATATGATAAA
1 TA-TT-AATTTAATTGATAATAAAATAAA
1652620 T-TTAATTTAATTGA
1 TATTAATTTAATTGA
1652634 ATCAAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 13 0.36
27 4 0.11
28 9 0.25
29 10 0.28
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (27 bp):
TATTAATTTAATTGATAATAAAATAAA
Found at i:1654193 original size:25 final size:25
Alignment explanation
Indices: 1654165--1654225 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
1654155 AGGACCCCAA
1654165 TTTAATGTTATCTCAACCGGAATTG
1 TTTAATGTTATCTCAACCGGAATTG
1654190 TTTAATGTTATCTCAACCGGAATTG
1 TTTAATGTTATCTCAACCGGAATTG
1654215 TTTAATGTTAT
1 TTTAATGTTAT
1654226 ATAAGTGTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (25 bp):
TTTAATGTTATCTCAACCGGAATTG
Found at i:1654253 original size:37 final size:37
Alignment explanation
Indices: 1654203--1654343 Score: 162
Period size: 37 Copynumber: 3.8 Consensus size: 37
1654193 AATGTTATCT
** *
1654203 CAACCGGAATTGTTTAATGTTATATAAGTGTGGGACC
1 CAACCGGAATTGTTTAATGTTATGCAAGTGTAGGACC
* * *
1654240 CAACCGGAATTGTTGAATGTTATGCAACTGTAGGA-G
1 CAACCGGAATTGTTTAATGTTATGCAAGTGTAGGACC
*
1654276 C--CCGAGAATTGTTTAATGTTATGTAAGTGTAGGACTC
1 CAACCG-GAATTGTTTAATGTTATGCAAGTGTAGGAC-C
* *
1654313 CAGCAGGAATTGTTTAATGTTATGCAAGTGT
1 CAACCGGAATTGTTTAATGTTATGCAAGTGT
1654344 GGGCCCCCAA
Statistics
Matches: 87, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
34 3 0.03
35 26 0.30
36 1 0.01
37 31 0.36
38 24 0.28
39 2 0.02
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.33
Consensus pattern (37 bp):
CAACCGGAATTGTTTAATGTTATGCAAGTGTAGGACC
Found at i:1654294 original size:35 final size:38
Alignment explanation
Indices: 1654208--1654339 Score: 139
Period size: 35 Copynumber: 3.6 Consensus size: 38
1654198 TATCTCAACC
** * * * *
1654208 GGAATTGTTTAATGTTATATAAGTGTGGGAC-CCAACC
1 GGAATTGTTTAATGTTATGCAACTGTAGGACTCCAGCA
*
1654245 GGAATTGTTGAATGTTATGCAACTGTAGGAGC-CC-G-A
1 GGAATTGTTTAATGTTATGCAACTGTAGGA-CTCCAGCA
* *
1654281 -GAATTGTTTAATGTTATGTAAGTGTAGGACTCCAGCA
1 GGAATTGTTTAATGTTATGCAACTGTAGGACTCCAGCA
1654318 GGAATTGTTTAATGTTATGCAA
1 GGAATTGTTTAATGTTATGCAA
1654340 GTGTGGGCCC
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
34 1 0.01
35 28 0.35
36 1 0.01
37 26 0.33
38 23 0.29
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (38 bp):
GGAATTGTTTAATGTTATGCAACTGTAGGACTCCAGCA
Found at i:1654420 original size:38 final size:38
Alignment explanation
Indices: 1654377--1654468 Score: 157
Period size: 38 Copynumber: 2.4 Consensus size: 38
1654367 AAGAACCGAA
*
1654377 GAATTGTTTAATGTTATGTAGGTGTAGGACCCCAACAG
1 GAATTGTTTAATGTTATGTAAGTGTAGGACCCCAACAG
* *
1654415 GAATTGCTTCATGTTATGTAAGTGTAGGACCCCAACAG
1 GAATTGTTTAATGTTATGTAAGTGTAGGACCCCAACAG
1654453 GAATTGTTTAATGTTA
1 GAATTGTTTAATGTTA
1654469 AGCATCCAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (38 bp):
GAATTGTTTAATGTTATGTAAGTGTAGGACCCCAACAG
Found at i:1654752 original size:34 final size:36
Alignment explanation
Indices: 1654714--1654798 Score: 101
Period size: 34 Copynumber: 2.5 Consensus size: 36
1654704 CATATTAACT
*
1654714 ATTTAATTTAAA-ATTAATTGATAATAA-A-TAAAAA
1 ATTTAATTTAAATATAAATTGATAA-AATATTAAAAA
*
1654748 ATTTAATTTAAATATAAATTTATAAAATATTAAAAA
1 ATTTAATTTAAATATAAATTGATAAAATATTAAAAA
1654784 A-TT-A-TTAAATATAAA
1 ATTTAATTTAAATATAAA
1654799 ATAACTCTCT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
33 11 0.24
34 15 0.33
35 13 0.28
36 7 0.15
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (36 bp):
ATTTAATTTAAATATAAATTGATAAAATATTAAAAA
Found at i:1655189 original size:14 final size:13
Alignment explanation
Indices: 1655185--1655217 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1655175 TAATTTATTG
1655185 ATTTTAATTTTCA
1 ATTTTAATTTTCA
1655198 ATTTTAATTTT-A
1 ATTTTAATTTTCA
1655210 A-TTTAATT
1 ATTTTAATT
1655218 ATTTTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.35
12 2 0.10
13 11 0.55
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTAATTTTCA
Found at i:1655206 original size:6 final size:6
Alignment explanation
Indices: 1655185--1655217 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
1655175 TAATTTATTG
1655185 ATTTTA ATTTTCA ATTTTA ATTTTA A-TTTA ATT
1 ATTTTA ATTTT-A ATTTTA ATTTTA ATTTTA ATT
1655218 ATTTTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 14 0.56
7 6 0.24
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTTA
Found at i:1655223 original size:14 final size:15
Alignment explanation
Indices: 1655172--1655226 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 15
1655162 CAATGAAATT
*
1655172 TTTTAATTT-ATTGA
1 TTTTAATTTAATTAA
1655186 TTTTAATTTTCAATTTTAA
1 TTTTAA-TTT-AA--TTAA
1655205 TTTTAATTTAATT-A
1 TTTTAATTTAATTAA
1655219 TTTTAATT
1 TTTTAATT
1655227 AAAAACTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 15 0.43
15 5 0.14
17 3 0.09
18 3 0.09
19 9 0.26
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTTAATTTAATTAA
Found at i:1657585 original size:3 final size:3
Alignment explanation
Indices: 1657577--1657602 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1657567 AAGCTATAAT
1657577 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1657603 TTAAGGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1660883 original size:27 final size:28
Alignment explanation
Indices: 1660854--1660947 Score: 104
Period size: 27 Copynumber: 3.4 Consensus size: 28
1660844 ATATAACATA
*
1660854 AATAAATATGAATAATATGAATATATA-
1 AATAAATATGAATAATACGAATATATAT
*
1660881 AATAAACAT-AATTAATACGAATATATAT
1 AATAAATATGAA-TAATACGAATATATAT
* * *
1660909 AAAAATATATGATTAACACGAATATATAT
1 AATAA-ATATGAATAATACGAATATATAT
1660938 AA-AAATATGA
1 AATAAATATGA
1660948 CGAAAATAAC
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
26 2 0.04
27 28 0.49
28 6 0.11
29 20 0.35
30 1 0.02
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (28 bp):
AATAAATATGAATAATACGAATATATAT
Found at i:1660917 original size:37 final size:38
Alignment explanation
Indices: 1660841--1660917 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 38
1660831 TTAATTTATT
* * *
1660841 TAAATATAACATAAATAAATATGAATAATATGAATATA
1 TAAATATAACATAAATAAATACGAATAATATAAAAATA
*
1660879 TAAATA-AACAT-AATTAATACGAATATATATAAAAATA
1 TAAATATAACATAAATAAATACGAATA-ATATAAAAATA
1660916 TA
1 TA
1660918 TGATTAACAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 12 0.35
37 16 0.47
38 6 0.18
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (38 bp):
TAAATATAACATAAATAAATACGAATAATATAAAAATA
Found at i:1660923 original size:29 final size:29
Alignment explanation
Indices: 1660851--1660945 Score: 108
Period size: 29 Copynumber: 3.3 Consensus size: 29
1660841 TAAATATAAC
* *
1660851 ATAAATAA-ATATGAATAATATGAATATAT
1 ATAAA-AATATATGATTAATACGAATATAT
*
1660880 A-AATAAACATA--ATTAATACGAATATAT
1 ATAA-AAATATATGATTAATACGAATATAT
*
1660907 ATAAAAATATATGATTAACACGAATATAT
1 ATAAAAATATATGATTAATACGAATATAT
1660936 ATAAAAATAT
1 ATAAAAATAT
1660946 GACGAAAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
27 21 0.37
28 6 0.11
29 30 0.53
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.32
Consensus pattern (29 bp):
ATAAAAATATATGATTAATACGAATATAT
Found at i:1661619 original size:2 final size:2
Alignment explanation
Indices: 1661612--1661657 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1661602 GTATCCCATT
1661612 TA TA 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 TA TA
1661654 TA TA
1 TA TA
1661658 AAAGAAAGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1663194 original size:57 final size:56
Alignment explanation
Indices: 1663108--1663216 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 56
1663098 TTCTACATAT
* * **
1663108 TAAGCTTTTATTAGGTAGAAATTTAAATATTATAGC-TTTTTCAATATTATAGATAG
1 TAAGCTTTTATCAGGCAGAAATTTAAATATTATA-CAAGTTTCAATATTATAGATAG
*
1663164 TAAGCTTTTTATCAGGCAGAAATTTCAATATTATACAAGTTTCAATATTATAG
1 TAAGC-TTTTATCAGGCAGAAATTTAAATATTATACAAGTTTCAATATTATAG
1663217 CTTTTTCAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
56 6 0.13
57 40 0.87
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (56 bp):
TAAGCTTTTATCAGGCAGAAATTTAAATATTATACAAGTTTCAATATTATAGATAG
Found at i:1663239 original size:12 final size:12
Alignment explanation
Indices: 1663222--1663267 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
1663212 TATAGCTTTT
*
1663222 TCAATATTAAAG
1 TCAATATTATAG
1663234 TCAATATTATAG
1 TCAATATTATAG
*
1663246 --AATAATATAG
1 TCAATATTATAG
1663256 TCAATATTATAG
1 TCAATATTATAG
1663268 ATACTAAGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 9 0.31
12 20 0.69
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.37
Consensus pattern (12 bp):
TCAATATTATAG
Found at i:1667767 original size:14 final size:16
Alignment explanation
Indices: 1667750--1667782 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1667740 TGACTTAAAA
1667750 TTAATTT-AT-TAATT
1 TTAATTTAATATAATT
1667764 TTAATTTAATATAATT
1 TTAATTTAATATAATT
1667780 TTA
1 TTA
1667783 TAAATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 2 0.12
16 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATTTAATATAATT
Found at i:1667842 original size:18 final size:18
Alignment explanation
Indices: 1667805--1667844 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1667795 TAATTATACA
*
1667805 TAAATATAATATTTTTAT
1 TAAATATAATATTTTAAT
1667823 TAAAT-TAATATTTTAAAT
1 TAAATATAATATTTT-AAT
1667841 TAAA
1 TAAA
1667845 ATATTACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAATATAATATTTTAAT
Found at i:1667857 original size:42 final size:40
Alignment explanation
Indices: 1667774--1667867 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 40
1667764 TTAATTTAAT
* *
1667774 ATAATTTTA-TAAATTATATTTTAATTATACATAAATATA
1 ATAATTTTATTAAATTATATTTTAATTATAAATAAACATA
* *
1667813 ATATTTTTATTAAATTAATATTTTAAATTA-AAATATTACATA
1 ATAATTTTATTAAATT-ATATTTT-AATTATAAATA-AACATA
1667855 ATAATTTTATTAA
1 ATAATTTTATTAA
1667868 TATAATACAT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
39 8 0.17
40 6 0.13
41 11 0.24
42 21 0.46
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (40 bp):
ATAATTTTATTAAATTATATTTTAATTATAAATAAACATA
Found at i:1669226 original size:28 final size:28
Alignment explanation
Indices: 1669174--1669239 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
1669164 AAATTCAACC
* *
1669174 TTTTTAATATATTATTTT-ATTTTTTAT
1 TTTTTAATATATTATTTTAAATTTTAAT
1669201 TTTTTAA-ATATTATTAATTAAATTTTAAT
1 TTTTTAATATATTATT--TTAAATTTTAAT
1669230 TTTATTAATA
1 TTT-TTAATA
1669240 AAAATAGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 8 0.25
27 7 0.22
28 2 0.06
29 10 0.31
30 4 0.12
31 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTTTAATATATTATTTTAAATTTTAAT
Found at i:1669244 original size:21 final size:21
Alignment explanation
Indices: 1669202--1669242 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1669192 ATTTTTTATT
*
1669202 TTTTAAATATTATTAATTAAA
1 TTTTAAATATTATTAATAAAA
*
1669223 TTTT-AATTTTATTAATAAAA
1 TTTTAAATATTATTAATAAAA
1669243 ATAGGAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTTAAATATTATTAATAAAA
Found at i:1669844 original size:15 final size:16
Alignment explanation
Indices: 1669826--1669855 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1669816 GAAAAATAAT
1669826 TAAAAAT-AATAAAAA
1 TAAAAATAAATAAAAA
1669841 TAAAAATAAATAAAA
1 TAAAAATAAATAAAA
1669856 TTACCATCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
TAAAAATAAATAAAAA
Found at i:1672564 original size:20 final size:22
Alignment explanation
Indices: 1672535--1672588 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
1672525 ATAATTATTT
*
1672535 TATATCT-AAATC-TATTTAAA
1 TATATCTAAAATCACATTTAAA
*
1672555 TATATTTAAAATCACATTTAAA
1 TATATCTAAAATCACATTTAAA
*
1672577 TAATATATAAAA
1 T-ATATCTAAAA
1672589 AAATAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.21
21 5 0.18
22 8 0.29
23 9 0.32
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (22 bp):
TATATCTAAAATCACATTTAAA
Found at i:1675195 original size:30 final size:30
Alignment explanation
Indices: 1675159--1675215 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1675149 AATAGATAAA
*
1675159 CAGAGCTATAGAAAGCCATAGAAATGGAAT
1 CAGAGCTATAAAAAGCCATAGAAATGGAAT
*
1675189 CAGAGCTATAAAAAGCTATAGAAATGG
1 CAGAGCTATAAAAAGCCATAGAAATGG
1675216 TATCCTCTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.12, G:0.23, T:0.18
Consensus pattern (30 bp):
CAGAGCTATAAAAAGCCATAGAAATGGAAT
Found at i:1675519 original size:28 final size:28
Alignment explanation
Indices: 1675482--1675535 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1675472 CATTTTGATT
*
1675482 AAAAATGATATATTATTATTCACATTTA
1 AAAAATGATATATTAGTATTCACATTTA
1675510 AAAAATGATATATTAGTATTCACATT
1 AAAAATGATATATTAGTATTCACATT
1675536 CTCCTATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (28 bp):
AAAAATGATATATTAGTATTCACATTTA
Found at i:1678346 original size:12 final size:12
Alignment explanation
Indices: 1678331--1678357 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1678321 CCAGGATATC
1678331 ATTATAATCATA
1 ATTATAATCATA
1678343 ATTATAATCATA
1 ATTATAATCATA
1678355 ATT
1 ATT
1678358 TACCAACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTATAATCATA
Found at i:1681922 original size:13 final size:13
Alignment explanation
Indices: 1681901--1681938 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1681891 ATAAATAAAC
*
1681901 TTTTCTTCTTCTT
1 TTTTTTTCTTCTT
1681914 TTTTTTTCTT-TT
1 TTTTTTTCTTCTT
1681926 TCTTTTTTCTTCT
1 T-TTTTTTCTTCT
1681939 CCATTTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 3 0.14
13 18 0.82
14 1 0.05
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTCTTCTT
Found at i:1681922 original size:16 final size:16
Alignment explanation
Indices: 1681901--1681938 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1681891 ATAAATAAAC
1681901 TTTTCTTCTTCTTTTT
1 TTTTCTTCTTCTTTTT
*
1681917 TTTTCTTTTTCTTTTT
1 TTTTCTTCTTCTTTTT
*
1681933 TCTTCT
1 TTTTCT
1681939 CCATTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTTCTTCTTTTT
Found at i:1682384 original size:31 final size:31
Alignment explanation
Indices: 1682346--1682462 Score: 135
Period size: 31 Copynumber: 3.5 Consensus size: 31
1682336 TTCCAACTCA
1682346 TTCTTTGATTTCTGTCTTTGTCATGGGATAG
1 TTCTTTGATTTCTGTCTTTGTCATGGGATAG
*
1682377 TTCTTTGATTTCTGTCTTTGACATGGGATAG
1 TTCTTTGATTTCTGTCTTTGTCATGGGATAG
*
1682408 TCCAACTCATTCTTTGATTTCTTTCTTTGTCATGGGATAG
1 ---------TTCTTTGATTTCTGTCTTTGTCATGGGATAG
1682448 TTCTTTGATTTCTGT
1 TTCTTTGATTTCTGT
1682463 ATAGTTCTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
31 44 0.60
40 29 0.40
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.51
Consensus pattern (31 bp):
TTCTTTGATTTCTGTCTTTGTCATGGGATAG
Found at i:1682423 original size:40 final size:41
Alignment explanation
Indices: 1682377--1682541 Score: 149
Period size: 50 Copynumber: 3.9 Consensus size: 41
1682367 CATGGGATAG
*
1682377 TTCTTTGATTTCTGTCTTTGACATGGGATAG-TCCAACTCA
1 TTCTTTGATTTCTGTCTTTGTCATGGGATAGTTCCAACTCA
* * * *
1682417 TTCTTTGATTTCTTTCTTTGTCATGGGATAGTTCTTTGATTTCTGTATA
1 TTCTTTGATTTCTGTCTTTGTCATGGGATAGTTC---CA--AC--T-CA
1682466 GTTCTTTGATTTCTGTCTTTGTCATGGGATAGTTCCAACTCA
1 -TTCTTTGATTTCTGTCTTTGTCATGGGATAGTTCCAACTCA
* * *
1682508 TTCTTTGATATCT-T-TGTATCAT-GGATAGTTCCAA
1 TTCTTTGATTTCTGTCTTTGTCATGGGATAGTTCCAA
1682542 ATATGGAACT
Statistics
Matches: 103, Mismatches: 12, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
38 12 0.12
39 6 0.06
40 30 0.29
41 14 0.14
42 1 0.01
43 1 0.01
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 33 0.32
ACGTcount: A:0.18, C:0.16, G:0.17, T:0.48
Consensus pattern (41 bp):
TTCTTTGATTTCTGTCTTTGTCATGGGATAGTTCCAACTCA
Found at i:1682444 original size:71 final size:72
Alignment explanation
Indices: 1682327--1682462 Score: 256
Period size: 71 Copynumber: 1.9 Consensus size: 72
1682317 TATAAAATGT
1682327 ATGGGATAGTTCCAACTCATTCTTTGATTTCTGTCTTTGTCATGGGATAGTTCTTTGATTTCTGT
1 ATGGGATAGTTCCAACTCATTCTTTGATTTCTGTCTTTGTCATGGGATAGTTCTTTGATTTCTGT
1682392 CTTTGAC
66 CTTTGAC
*
1682399 ATGGGATAG-TCCAACTCATTCTTTGATTTCTTTCTTTGTCATGGGATAGTTCTTTGATTTCTGT
1 ATGGGATAGTTCCAACTCATTCTTTGATTTCTGTCTTTGTCATGGGATAGTTCTTTGATTTCTGT
1682463 ATAGTTCTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
71 54 0.86
72 9 0.14
ACGTcount: A:0.17, C:0.16, G:0.19, T:0.48
Consensus pattern (72 bp):
ATGGGATAGTTCCAACTCATTCTTTGATTTCTGTCTTTGTCATGGGATAGTTCTTTGATTTCTGT
CTTTGAC
Found at i:1682468 original size:19 final size:19
Alignment explanation
Indices: 1682444--1682481 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1682434 TTGTCATGGG
1682444 ATAGTTCTTTGATTTCTGT
1 ATAGTTCTTTGATTTCTGT
1682463 ATAGTTCTTTGATTTCTGT
1 ATAGTTCTTTGATTTCTGT
1682482 CTTTGTCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.58
Consensus pattern (19 bp):
ATAGTTCTTTGATTTCTGT
Found at i:1688887 original size:29 final size:29
Alignment explanation
Indices: 1688855--1688910 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1688845 TATAAATAGC
**
1688855 ATTAAATTATACATGTAAAAATAATTTAA
1 ATTAAATTATACAAATAAAAATAATTTAA
1688884 ATTAAATTATACAAATAAAAATAATTT
1 ATTAAATTATACAAATAAAAATAATTT
1688911 TTAATAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (29 bp):
ATTAAATTATACAAATAAAAATAATTTAA
Found at i:1690218 original size:14 final size:14
Alignment explanation
Indices: 1690174--1690233 Score: 61
Period size: 14 Copynumber: 4.1 Consensus size: 14
1690164 TTCAATCCTC
1690174 ATTTATGTTATTTTT
1 ATTTAT-TTATTTTT
*
1690189 AATTT-TGTTCTTTTT
1 -ATTTAT-TTATTTTT
1690204 ATTTA-TTATTGTTT
1 ATTTATTTATT-TTT
1690218 ATTTATTTATTTTT
1 ATTTATTTATTTTT
1690232 AT
1 AT
1690234 CAATGTTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
13 4 0.10
14 17 0.44
15 14 0.36
16 4 0.10
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (14 bp):
ATTTATTTATTTTT
Found at i:1690329 original size:21 final size:21
Alignment explanation
Indices: 1690305--1690347 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1690295 AATAAATCAT
*
1690305 ATAAAGTTATCATT-TTTATTA
1 ATAAA-TTATAATTATTTATTA
*
1690326 ATAAATTTTAATTATTTATTA
1 ATAAATTATAATTATTTATTA
1690347 A
1 A
1690348 CTTTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
ATAAATTATAATTATTTATTA
Found at i:1690700 original size:3 final size:3
Alignment explanation
Indices: 1690688--1690731 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
1690678 TACAATTTGG
1690688 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1690732 CAATGAAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1691956 original size:16 final size:17
Alignment explanation
Indices: 1691937--1691984 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
1691927 TTTATTAATA
*
1691937 TAATATATTTTCA-TAT
1 TAATATATTTTAATTAT
1691953 TAATAT-TTTTAATTAT
1 TAATATATTTTAATTAT
*
1691969 AAATATATTATTAATT
1 TAATATATT-TTAATT
1691985 GTAATAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 5 0.19
16 14 0.52
17 2 0.07
18 6 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATATATTTTAATTAT
Found at i:1691996 original size:16 final size:16
Alignment explanation
Indices: 1691969--1692007 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1691959 TTTTAATTAT
1691969 AAATATATTATTAATTG
1 AAATA-ATTATTAATTG
* *
1691986 TAATAATTATTATTTG
1 AAATAATTATTAATTG
1692002 AAATAA
1 AAATAA
1692008 AAATATAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (16 bp):
AAATAATTATTAATTG
Found at i:1693247 original size:19 final size:21
Alignment explanation
Indices: 1693223--1693262 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
1693213 ATAAAAAATT
1693223 ATTTTTAATTA-AT-TATTTA
1 ATTTTTAATTATATATATTTA
*
1693242 ATTTTTCATTATATATATTTA
1 ATTTTTAATTATATATATTTA
1693263 TATAATGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 2 0.11
21 6 0.33
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTAATTATATATATTTA
Found at i:1693308 original size:22 final size:22
Alignment explanation
Indices: 1693279--1693353 Score: 143
Period size: 22 Copynumber: 3.5 Consensus size: 22
1693269 GATATTTTTA
1693279 AATA-TTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
1693300 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
1693322 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
1693344 AATATTTTAT
1 AATATTTTAT
1693354 TAATTTCGGA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 4 0.08
22 49 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:1694226 original size:30 final size:27
Alignment explanation
Indices: 1694181--1694242 Score: 97
Period size: 30 Copynumber: 2.2 Consensus size: 27
1694171 TGCAATTTAC
1694181 ATATATATAAAATTAAAAATAAAAACTA
1 ATATATATAAAATTAAAAATAAAAA-TA
1694209 TATATATATATAAATTAAAAATAAAAATA
1 -ATATATATA-AAATTAAAAATAAAAATA
1694238 ATATA
1 ATATA
1694243 AAAATTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 5 0.16
29 11 0.34
30 16 0.50
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (27 bp):
ATATATATAAAATTAAAAATAAAAATA
Found at i:1694304 original size:25 final size:26
Alignment explanation
Indices: 1694271--1694319 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
1694261 AGTGAATTCA
*
1694271 CACATATATAT-AAATTAAAAAATAT
1 CACATATATATAAAAATAAAAAATAT
1694296 CACATATATATAAAAATAAAAAAT
1 CACATATATATAAAAATAAAAAAT
1694320 TTATGTGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (26 bp):
CACATATATATAAAAATAAAAAATAT
Found at i:1694304 original size:27 final size:26
Alignment explanation
Indices: 1694268--1694319 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
1694258 ATAAGTGAAT
*
1694268 TCACACATATATATAAATTAAAAAATA
1 TCACACATATATA-AAAATAAAAAATA
*
1694295 TCACATATATATAAAAATAAAAAAT
1 TCACACATATATAAAAATAAAAAAT
1694320 TTATGTGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.29
Consensus pattern (26 bp):
TCACACATATATAAAAATAAAAAATA
Found at i:1695232 original size:21 final size:21
Alignment explanation
Indices: 1695208--1695267 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
1695198 TTATTTTTTT
*
1695208 ATATTTTAAAATTTTTAATAA
1 ATATTTTTAAATTTTTAATAA
* *
1695229 ATATTTTTAAA-TTTAAATAT
1 ATATTTTTAAATTTTTAATAA
1695249 ATATTTTTAAATTTTTAAT
1 ATATTTTTAAATTTTTAAT
1695268 TTTTTATGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTTTTAAATTTTTAATAA
Found at i:1696096 original size:16 final size:16
Alignment explanation
Indices: 1696075--1696105 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1696065 TGTCACATGT
1696075 CTTTTTCATGTTTTTC
1 CTTTTTCATGTTTTTC
*
1696091 CTTTTTTATGTTTTT
1 CTTTTTCATGTTTTT
1696106 AATTTTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.13, G:0.06, T:0.74
Consensus pattern (16 bp):
CTTTTTCATGTTTTTC
Found at i:1696664 original size:665 final size:653
Alignment explanation
Indices: 1695378--1697314 Score: 2110
Period size: 656 Copynumber: 3.0 Consensus size: 653
1695368 GTATGACCTA
* * * * *
1695378 CTTGAGTGATGCATGTTCAACAGTATTGATTTCTTAAGTTGTCACATGTCATTTTCATGTTTTTC
1 CTTGAGTGATG--TATTCAACAGAATTGTTTTCTTAAGTTGTCACATATCATTTTCAGGTTTTTC
* * * **
1695443 CCTTTT-TTTTTTGTT-TT-T-AATTTTTCTTCTAAGATA--TTT--AA-T--AAATAT-T-TTT
64 TCTTTTGTTTTTT-TTCTTCTAAAATATT-TAATAA-ATATTTTTAAAATTAGAAATATATATTT
*
1695495 TAAAATATTTTATTTTTTATGTTT-GGATCTACTTATATCAATTTTTTTTTACTTTTCCTTTTTT
126 TAAAATATTTTATTTTTTATGTTTGGGATCTACTTATATCAACTTTTTTTTA----T-C-TTTTT
* * *
1695559 ATTTTTATTTTTTTAATAAAAATATTTAATAAAGA-TTTTTAAATTTTATTTTTTTATAAAATCC
185 ATTTTT-CTTTTTTAATAAAAATATTTAATAAATATTTTTTAGATTTTATTTTTTTATAAAATCC
* * *
1695623 ACTTGATACAAATAGTATGTCACATCTTT-TTTTTATATATATTTAATAAATAAAATTTTATATT
249 ACTTGATACAAATAGTATGTCACATATTTCTTTTTTTATATATTTAATAAATAAATTTTTATATT
* * ** ** * *
1695687 TTATTTTTTGAGACTAACTTAATGT-AAAAAAATATTATGTATTAATTAGTGATTACAACTAGTC
314 TTATTTTTTGAAACTAACTTAATATCAAAAGTATACCATGTATTAAATAGTGATGACAACTAGTC
* * *
1695751 GAATTAAAATAAGTTTTTG-TT-CATCTCGAGTTCAACGC-AATTTCATAAAAATCATATCCAAT
379 GAGTCAAAATAAGTTTTTGCTTAC-T-TCGACTTCAAC-CTAATTTCATAAAAATCATATCCAAT
* * * ** * * *
1695813 TTCAACTTTGACCTGACACAAAAATATTATTTTTTCATACCTGAC-TCAATCCAAACTACAATGT
441 TTCGACTTCGACCTGACACAAAAATATTTTTTTTTCATACCCAACTTGACT-CAAACTGCAATGT
* * * * *
1695877 CT-AAACTACAAGCAACTCAACCT-AAAATTAGTTTAATAATTTTAATTTAGTATAATATTTATA
505 ATAAAAC-GCAAACAACTCGACCTGAAATTTA-TTTAATAATTTTAATTTAGTATAATATTTATA
* ** *
1695940 AAATAATATTTTTAATATGAATTATATTTTAATTATACATAGCTATATTACTG-TTTTCTTATAT
568 AAATATTATTTTTAATATGAATTATATTTTAATTATACATAAATATAATA-TGTTTTTCTTATAT
1696004 TTCATAAATATAATACTAG-TTT
632 TTCATAAATATAATA-TAGTTTT
* * * * * *
1696026 CTTTAGTGATTTATGTTCAACAGAATTGTTTTCTTCAGTTGTCACATGTCTTTTTCATGTTTTTC
1 CTTGAGTGATGTA--TTCAACAGAATTGTTTTCTTAAGTTGTCACATATCATTTTCAGGTTTTT-
*
1696091 CTTTTTTATGTTTTTAATTTTTCTTCTAAAATATTTAATAAATATTTTTTAAAATTA-AAATATA
63 C-TCTTT-TG--TTT--TTTTTCTTCTAAAATATTTAATAAATA-TTTTTAAAATTAGAAATATA
*
1696155 TATAGTTTAAAATATTTTATATTTTATGTTTGGGATCTACTTATATCAACTTTTTTTTA-C-TTT
121 TAT--TTTAAAATATTTTATTTTTTATGTTTGGGATCTACTTATATCAACTTTTTTTTATCTTTT
* *
1696218 T-TTTTTCTTTTTTAATTAAAATAATTAATAAATATTTTTTAGATTTTATTTTTTTTATAAAATC
184 TATTTTTCTTTTTTAATAAAAATATTTAATAAATATTTTTTAGATTTTA-TTTTTTTATAAAATC
1696282 CACTTGATACAAATAGTATGTCACATTATTTTCTTTTTTTATATATTTAATAAATAAATTTTTAT
248 CACTTGATACAAATAGTATGTCACA-TA-TTTCTTTTTTTATATATTTAATAAATAAATTTTTAT
*
1696347 ATTTTATTTTTTGAAACTAACTTAATATCAAAAGTATACCATGTATTAAGTAGTGATGACAA-TA
311 ATTTTATTTTTTGAAACTAACTTAATATCAAAAGTATACCATGTATTAAATAGTGATGACAACTA
* *
1696411 GATCGAGTCAAAACAAGTTTTTGCTTACTTTGACTTCAACCTAATTTCATAAAAATCATATCCAA
376 G-TCGAGTCAAAATAAGTTTTTGCTTACTTCGACTTCAACCTAATTTCATAAAAATCATATCCAA
* * *
1696476 TTTCGACTCCAACCTGACACAAAAATATTTTTTTTTCATACCCAACTTGACTTAAACTGCAATGT
440 TTTCGACTTCGACCTGACACAAAAATATTTTTTTTTCATACCCAACTTGACTCAAACTGCAATGT
1696541 ATAAAACCGCAAACAACTCGACCTGAAATTTATTTAATAATTTTAATTTAGTATAATATTTATAA
505 ATAAAA-CGCAAACAACTCGACCTGAAATTTATTTAATAATTTTAATTTAGTATAATATTTATAA
1696606 AATATTATTTTTAATATGAATTATATTTTAATTATACATAAATATAATATGTTTTTCTTATATTT
569 AATATTATTTTTAATATGAATTATATTTTAATTATACATAAATATAATATGTTTTTCTTATATTT
* *
1696671 CATAAATATAGTATTGTTTT
634 CATAAATATAATATAGTTTT
*
1696691 CTTGAGTGATGTATTCAACAGTATTGTTTTCTTAAGTTGTCACATATCATTTTCAGGTTTTTCTC
1 CTTGAGTGATGTATTCAACAGAATTGTTTTCTTAAGTTGTCACATATCATTTTCAGGTTTTTCTC
*
1696756 TTTTGTTTTTTTTCTTCTAAAATATTTAATAAATATTTTTAAAATTAGAAATGTATATTTTAAAA
66 TTTTGTTTTTTTTCTTCTAAAATATTTAATAAATATTTTTAAAATTAGAAATATATATTTTAAAA
* *
1696821 TATTTTATTTTTTATGTTTGGGAACTACTTGTATCATTTTTTTTTACTTTTACTTTTACTTTCCC
131 TATTTTATTTTTTATGTTTGGGATCTACTTATATCA---------ACTTTT--TTTTA---T--C
1696886 TTTTTTATCTTTTATCTTTTTTAATAAAAATATTTAATAAATATTTTTTAGATTTTATTTTTTTA
180 -TTTTTA--TTTT-TCTTTTTTAATAAAAATATTTAATAAATATTTTTTAGATTTTATTTTTTTA
* * *
1696951 TAAAATCCACTTGATACAAATAATATGTCAC--A--GC--TTTTT-T-T-CTT--T---T---TT
241 TAAAATCCACTTGATACAAATAGTATGTCACATATTTCTTTTTTTATATATTTAATAAATAAATT
* *
1696999 TTTATATTTTATTTTTTAAAACT-ACTTAATATCAAAAGTATACCATATATTAAATAGTGATGAC
306 TTTATATTTTATTTTTTGAAACTAACTTAATATCAAAAGTATACCATGTATTAAATAGTGATGAC
* * * * * * * * *
1697063 AATTAGTCGAGTCCAAATAAGTGTTTGCTCACCTCAACTTCAACTTGATTTCATAAAAGTCATAT
371 AACTAGTCGAGTCAAAATAAGTTTTTGCTTACTTCGACTTCAACCTAATTTCATAAAAATCATAT
* * * *
1697128 CCAATCAT-GACTTCGACTTGACACAAAAATATATTTTTTTTCATATCCTA-TTCGAC-CGAAAC
436 CCAAT-TTCGACTTCGACCTGACACAAAAATAT-TTTTTTTTCATACCCAACTT-GACTC-AAAC
* * * * * *
1697190 CGCAATGTATAAATA-GGAAACAACTTGACTTGAAATTAATTTAATAATTTTAATTTAGTAAAAT
497 TGCAATGTATAAA-ACGCAAACAACTCGACCTGAAATTTATTTAATAATTTTAATTTAGTATAAT
*
1697254 ATTTATAAAATATTATTTTTAATATGAATAATATTTTAATT-TACATAAATATAATAT-TTTT
561 ATTTATAAAATATTATTTTTAATATGAATTATATTTTAATTATACATAAATATAATATGTTTT
1697315 ATTAAGTTAA
Statistics
Matches: 1116, Mismatches: 102, Indels: 136
0.82 0.08 0.10
Matches are distributed among these distances:
646 1 0.00
648 54 0.05
649 1 0.00
650 3 0.00
651 1 0.00
654 47 0.04
655 30 0.03
656 246 0.22
657 67 0.06
658 33 0.03
659 20 0.02
660 47 0.04
661 7 0.01
662 6 0.01
663 117 0.10
664 133 0.12
665 147 0.13
666 9 0.01
667 26 0.02
668 31 0.03
670 1 0.00
671 1 0.00
673 5 0.00
676 42 0.04
677 41 0.04
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (653 bp):
CTTGAGTGATGTATTCAACAGAATTGTTTTCTTAAGTTGTCACATATCATTTTCAGGTTTTTCTC
TTTTGTTTTTTTTCTTCTAAAATATTTAATAAATATTTTTAAAATTAGAAATATATATTTTAAAA
TATTTTATTTTTTATGTTTGGGATCTACTTATATCAACTTTTTTTTATCTTTTTATTTTTCTTTT
TTAATAAAAATATTTAATAAATATTTTTTAGATTTTATTTTTTTATAAAATCCACTTGATACAAA
TAGTATGTCACATATTTCTTTTTTTATATATTTAATAAATAAATTTTTATATTTTATTTTTTGAA
ACTAACTTAATATCAAAAGTATACCATGTATTAAATAGTGATGACAACTAGTCGAGTCAAAATAA
GTTTTTGCTTACTTCGACTTCAACCTAATTTCATAAAAATCATATCCAATTTCGACTTCGACCTG
ACACAAAAATATTTTTTTTTCATACCCAACTTGACTCAAACTGCAATGTATAAAACGCAAACAAC
TCGACCTGAAATTTATTTAATAATTTTAATTTAGTATAATATTTATAAAATATTATTTTTAATAT
GAATTATATTTTAATTATACATAAATATAATATGTTTTTCTTATATTTCATAAATATAATATAGT
TTT
Found at i:1696667 original size:26 final size:28
Alignment explanation
Indices: 1696637--1696690 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
1696627 TATATTTTAA
1696637 TTATA-CATAAATATAATA-TGTTTTTC
1 TTATATCATAAATATAATATTGTTTTTC
*
1696663 TTATATTTCATAAATATAGTATTGTTTT
1 TTATA--TCATAAATATAATATTGTTTT
1696691 CTTGAGTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 5 0.22
29 12 0.52
30 6 0.26
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.54
Consensus pattern (28 bp):
TTATATCATAAATATAATATTGTTTTTC
Found at i:1700241 original size:2 final size:2
Alignment explanation
Indices: 1700206--1700233 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1700196 TTCTTCATTT
1700206 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1700234 CACTCTCTTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1700640 original size:20 final size:20
Alignment explanation
Indices: 1700615--1700653 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1700605 TCATCTACAA
* *
1700615 TAAAAGCATAGACATACTCC
1 TAAAAGCACAGACACACTCC
1700635 TAAAAGCACAGACACACTC
1 TAAAAGCACAGACACACTC
1700654 TCCAAAGCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.28, G:0.10, T:0.15
Consensus pattern (20 bp):
TAAAAGCACAGACACACTCC
Found at i:1703361 original size:20 final size:19
Alignment explanation
Indices: 1703338--1703392 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 19
1703328 CTCTTTTTTT
*
1703338 TTTTTATTTTTGATTCAAAA
1 TTTTTATTTTTAATT-AAAA
*
1703358 TTTTAATTTTTAATTAAAA
1 TTTTTATTTTTAATTAAAA
*
1703377 TTTTT-TTATTAATTAA
1 TTTTTATTTTTAATTAA
1703393 TTTTTTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 10 0.32
19 8 0.26
20 13 0.42
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTTATTTTTAATTAAAA
Found at i:1703390 original size:18 final size:18
Alignment explanation
Indices: 1703354--1703401 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
1703344 TTTTTGATTC
1703354 AAAATTTTAATTT-TTAATT
1 AAAATTTT--TTTATTAATT
1703373 AAAATTTTTTTATTAATT
1 AAAATTTTTTTATTAATT
*
1703391 -AATTTTTTTTA
1 AAAATTTTTTTA
1703402 ATCATAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 13 0.48
18 6 0.22
19 8 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AAAATTTTTTTATTAATT
Found at i:1704165 original size:20 final size:20
Alignment explanation
Indices: 1704140--1704177 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1704130 AAAATATTTA
*
1704140 AAAATATATGTTTTAAAACT
1 AAAATATATATTTTAAAACT
1704160 AAAATATATATTTTAAAA
1 AAAATATATATTTTAAAA
1704178 TTTTAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (20 bp):
AAAATATATATTTTAAAACT
Found at i:1704901 original size:25 final size:25
Alignment explanation
Indices: 1704867--1704916 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1704857 TTTTTTAATT
1704867 AACACTGCTCTTAACTCTCGAGGCC
1 AACACTGCTCTTAACTCTCGAGGCC
* *
1704892 AACACTGCTCTTGACTCTTGAGGCC
1 AACACTGCTCTTAACTCTCGAGGCC
1704917 TACTTTATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.22, C:0.34, G:0.18, T:0.26
Consensus pattern (25 bp):
AACACTGCTCTTAACTCTCGAGGCC
Found at i:1707440 original size:23 final size:23
Alignment explanation
Indices: 1707414--1707460 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1707404 AATAGTGATA
1707414 GAGATAAAATTAATTACTGTAAT
1 GAGATAAAATTAATTACTGTAAT
1707437 GAGATAAAATTAATTACTGTAAT
1 GAGATAAAATTAATTACTGTAAT
1707460 G
1 G
1707461 GTAAGATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.34
Consensus pattern (23 bp):
GAGATAAAATTAATTACTGTAAT
Found at i:1709035 original size:18 final size:17
Alignment explanation
Indices: 1709008--1709050 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1708998 TTTTATATTA
*
1709008 ATATTTTTAATTGTAAAT
1 ATATTATTAATTGT-AAT
1709026 ATATTATTAATTGTAAT
1 ATATTATTAATTGTAAT
1709043 A-ATTATTA
1 ATATTATTA
1709051 TTTGATACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 7 0.29
17 4 0.17
18 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
ATATTATTAATTGTAAT
Found at i:1710651 original size:25 final size:25
Alignment explanation
Indices: 1710621--1710685 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 25
1710611 AATTCACGTG
* *
1710621 TATATAAAATTTAAAATAAAAGTTA
1 TATATAAAATTAAAAATAAAAATTA
*
1710646 TATATAAAAAAATAAAAATAAAAATTA
1 TATAT--AAAATTAAAAATAAAAATTA
1710673 TATATAAAATTAA
1 TATATAAAATTAA
1710686 TTTATAGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 12 0.35
27 22 0.65
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
TATATAAAATTAAAAATAAAAATTA
Found at i:1711490 original size:12 final size:11
Alignment explanation
Indices: 1711455--1711513 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
1711445 AATTATTATC
1711455 AAAATAAATTA
1 AAAATAAATTA
1711466 AAAGATTAAATTA
1 AAA-A-TAAATTA
1711479 AAAATAAAATTA
1 AAAAT-AAATTA
* *
1711491 ATAGTAAATTA
1 AAAATAAATTA
* *
1711502 ATAATTAATTA
1 AAAATAAATTA
1711513 A
1 A
1711514 CATATCTTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
11 20 0.49
12 11 0.27
13 10 0.24
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (11 bp):
AAAATAAATTA
Found at i:1711498 original size:23 final size:23
Alignment explanation
Indices: 1711455--1711513 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
1711445 AATTATTATC
1711455 AAAATAAATTAAAAGATTAAATTA
1 AAAATAAATTAAAAGA-TAAATTA
*
1711479 AAAATAAAATTAATAG-TAAATTA
1 AAAAT-AAATTAAAAGATAAATTA
* *
1711502 ATAATTAATTAA
1 AAAATAAATTAA
1711514 CATATCTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 6 0.19
23 11 0.35
24 5 0.16
25 9 0.29
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (23 bp):
AAAATAAATTAAAAGATAAATTA
Found at i:1720816 original size:17 final size:18
Alignment explanation
Indices: 1720788--1720821 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1720778 GAGGAAGAAG
1720788 AAGAAGAAAGAAAAGGGA
1 AAGAAGAAAGAAAAGGGA
*
1720806 AAGAA-AAAGAAGAGGG
1 AAGAAGAAAGAAAAGGG
1720822 TAAAATTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (18 bp):
AAGAAGAAAGAAAAGGGA
Found at i:1721212 original size:19 final size:19
Alignment explanation
Indices: 1721190--1721236 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
1721180 ACCACCACCA
*
1721190 TTATAGTGATAGTAGATTG
1 TTATAGTGATAGTAAATTG
1721209 TTATAGTGATAGTAAATTG
1 TTATAGTGATAGTAAATTG
*
1721228 CTATAGTGA
1 TTATAGTGA
1721237 GCTCAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.40
Consensus pattern (19 bp):
TTATAGTGATAGTAAATTG
Found at i:1729021 original size:7 final size:7
Alignment explanation
Indices: 1729001--1729039 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
1728991 CAAACATCTC
1729001 ACTTTGA
1 ACTTTGA
1729008 A-TATTGA
1 ACT-TTGA
1729015 ACTTTGA
1 ACTTTGA
1729022 ACTTTGA
1 ACTTTGA
1729029 ACTTTGA
1 ACTTTGA
1729036 ACTT
1 ACTT
1729040 GTTTAGTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 1 0.03
7 28 0.93
8 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (7 bp):
ACTTTGA
Found at i:1733397 original size:11 final size:10
Alignment explanation
Indices: 1733383--1733407 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1733373 TTTTTGAAAA
1733383 TTTTTCTTTT
1 TTTTTCTTTT
1733393 TTTTTCTTTT
1 TTTTTCTTTT
1733403 TTTTT
1 TTTTT
1733408 GGTGTGATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:1738645 original size:15 final size:15
Alignment explanation
Indices: 1738621--1738651 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1738611 TTCTTTAAAT
1738621 ATAATAAAAAAATAA
1 ATAATAAAAAAATAA
*
1738636 ATAATTAAAAAATAA
1 ATAATAAAAAAATAA
1738651 A
1 A
1738652 ATATATGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
ATAATAAAAAAATAA
Found at i:1740820 original size:14 final size:17
Alignment explanation
Indices: 1740773--1740811 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
1740763 TTATATATAT
1740773 TTAAAATTATTAAA-AA
1 TTAAAATTATTAAATAA
1740789 TT-AAATT-TT-AATAA
1 TTAAAATTATTAAATAA
1740803 TTAAAATTA
1 TTAAAATTA
1740812 AAATTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
13 2 0.10
14 6 0.30
15 10 0.50
16 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAAATTATTAAATAA
Found at i:1742093 original size:2 final size:2
Alignment explanation
Indices: 1742047--1742079 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1742037 CAAGGGAAAA
1742047 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1742080 AAATGATGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1747691 original size:16 final size:17
Alignment explanation
Indices: 1747658--1747692 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1747648 TCCTCCACTC
*
1747658 CCCTCAACTCTCCTCCT
1 CCCTCAAATCTCCTCCT
1747675 CCCTCAAATCT-CTCCT
1 CCCTCAAATCTCCTCCT
1747691 CC
1 CC
1747693 TTTCCCTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.14, C:0.57, G:0.00, T:0.29
Consensus pattern (17 bp):
CCCTCAAATCTCCTCCT
Found at i:1748514 original size:66 final size:65
Alignment explanation
Indices: 1748394--1748525 Score: 212
Period size: 66 Copynumber: 2.0 Consensus size: 65
1748384 CTTTCTACAT
*
1748394 CCAAATACATGTTAATTATGGTTTTTAATGCATTTGAGTTGATAGTTGAAGGGTTTTGTTGTGAA
1 CCAAATACATGTTAATTATGGTTTTTAATGCATTTGAGTTGATAGTTGAAGGGTTTTGTTATGAA
* *
1748459 CCAAATACATTTTAATTATGGTTTTGTAGTGCATTTGAGTTGATAGCTT-AAGGGTTTTGTTATG
1 CCAAATACATGTTAATTATGGTTTT-TAATGCATTTGAGTTGATAG-TTGAAGGGTTTTGTTATG
1748523 AA
64 AA
1748525 C
1 C
1748526 TTTGTGGATT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
65 24 0.39
66 36 0.58
67 2 0.03
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (65 bp):
CCAAATACATGTTAATTATGGTTTTTAATGCATTTGAGTTGATAGTTGAAGGGTTTTGTTATGAA
Found at i:1754512 original size:183 final size:183
Alignment explanation
Indices: 1754200--1754567 Score: 691
Period size: 183 Copynumber: 2.0 Consensus size: 183
1754190 ATTTCATTAT
*
1754200 TGTAAATTTTAAAGTTGTTGAGTAAGCTTATTTGATTTGTGTAGGTGAAGCTCAAGTGCATGTCA
1 TGTAAATTTTAAAGTTGTTGAGTAAGCTTAGTTGATTTGTGTAGGTGAAGCTCAAGTGCATGTCA
*
1754265 GTTTCAAGTTTTAGTAAACCTAACCATAGTTTTTCTTTTTCTTTAATCGGTGACAGCAGAGAAAA
66 GTTTCAAGTTTTAGTAAACCTAACCATAGTTTTTCTTTTTCTTTAATCAGTGACAGCAGAGAAAA
*
1754330 AAGCTTGACATAGTTTTAGTTGTGTTATTTTTGAATAGTACATTTTTGGTTGC
131 AAGCTTGACATAGTTTTAGTTGTGTTATTTTTGAATAGTACATTTTTGATTGC
1754383 TGTAAATTTTAAAGTTGTTGAGTAAGCTTAGTTGATTTGTGTAGGTGAAGCTCAAGTGCATGTCA
1 TGTAAATTTTAAAGTTGTTGAGTAAGCTTAGTTGATTTGTGTAGGTGAAGCTCAAGTGCATGTCA
*
1754448 GTTTCAAGTTTTAGTAAACCTAACCATAGTTTTTCTTTTTCTTTAATCAGTGACAGCGGAGAAAA
66 GTTTCAAGTTTTAGTAAACCTAACCATAGTTTTTCTTTTTCTTTAATCAGTGACAGCAGAGAAAA
*
1754513 AAGCTTGACATGGTTTTAGTTGTGTTATTTTTGAATAGTACATTTTTGATTGC
131 AAGCTTGACATAGTTTTAGTTGTGTTATTTTTGAATAGTACATTTTTGATTGC
1754566 TG
1 TG
1754568 ATTATCTATA
Statistics
Matches: 180, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 180 1.00
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (183 bp):
TGTAAATTTTAAAGTTGTTGAGTAAGCTTAGTTGATTTGTGTAGGTGAAGCTCAAGTGCATGTCA
GTTTCAAGTTTTAGTAAACCTAACCATAGTTTTTCTTTTTCTTTAATCAGTGACAGCAGAGAAAA
AAGCTTGACATAGTTTTAGTTGTGTTATTTTTGAATAGTACATTTTTGATTGC
Found at i:1760840 original size:30 final size:30
Alignment explanation
Indices: 1760799--1760855 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1760789 TTTTTTATTT
* * *
1760799 ATATATATATTTATATAATGATATTTTTAA
1 ATATATATATTTAAAAAATAATATTTTTAA
*
1760829 ATATTTATATTTAAAAAATAATATTTT
1 ATATATATATTTAAAAAATAATATTTT
1760856 ATTAATTTCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
ATATATATATTTAAAAAATAATATTTTTAA
Found at i:1762100 original size:29 final size:27
Alignment explanation
Indices: 1762040--1762101 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
1762030 TCAAATCAAA
* *
1762040 TATTGAACAAACTCAACACAAAATATT
1 TATTGAACAAACACAAAACAAAATATT
1762067 T-TTGACACAAACACAAAACATATAA-ATT
1 TATTGA-ACAAACACAAAACA-A-AATATT
1762095 TATTGAA
1 TATTGAA
1762102 TCACACTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
26 4 0.14
27 13 0.45
28 6 0.21
29 6 0.21
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (27 bp):
TATTGAACAAACACAAAACAAAATATT
Found at i:1786849 original size:6 final size:6
Alignment explanation
Indices: 1786840--1786870 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1786830 TACATATATG
1786840 TATGTA TATGTA TATGTA TATGTA TATGTA T
1 TATGTA TATGTA TATGTA TATGTA TATGTA T
1786871 TTTCTATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TATGTA
Found at i:1789119 original size:24 final size:24
Alignment explanation
Indices: 1789092--1789139 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1789082 GCCGTGAAAA
1789092 AATGATGTAGTGGTGAATAGCAGT
1 AATGATGTAGTGGTGAATAGCAGT
1789116 AATGATGTAGTGGTGAATAGCAGT
1 AATGATGTAGTGGTGAATAGCAGT
1789140 CTTAACGGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.33, T:0.29
Consensus pattern (24 bp):
AATGATGTAGTGGTGAATAGCAGT
Found at i:1789844 original size:22 final size:22
Alignment explanation
Indices: 1789816--1789859 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1789806 CTAAATCTTC
1789816 CTTAATTCTAG-GAATACAAATA
1 CTTAATTCTAGAG-ATACAAATA
1789838 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
1789860 TAAATATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:1793565 original size:23 final size:25
Alignment explanation
Indices: 1793510--1793568 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
1793500 AAAGGGTTCG
* * *
1793510 GCAATGAAGGCCTAAACAGGATTCG
1 GCAATGAAGGCCTAAACAGAAATCA
1793535 GCAATGAAGGCCTAAA-A-AAATCA
1 GCAATGAAGGCCTAAACAGAAATCA
1793558 GCAATGAAGGC
1 GCAATGAAGGC
1793569 TGAAAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 14 0.45
24 1 0.03
25 16 0.52
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.14
Consensus pattern (25 bp):
GCAATGAAGGCCTAAACAGAAATCA
Found at i:1793799 original size:22 final size:22
Alignment explanation
Indices: 1793758--1793800 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1793748 TAAATCTTCT
*
1793758 TTAATTCTAGGGATACAAATAC
1 TTAATTCTAGAGATACAAATAC
* *
1793780 TTAATTCTAGATATATAAATA
1 TTAATTCTAGAGATACAAATA
1793801 TAAATATACA
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:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (22 bp):
TTAATTCTAGAGATACAAATAC
Found at i:1794030 original size:18 final size:18
Alignment explanation
Indices: 1794009--1794045 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1793999 TGTTCATGTG
* *
1794009 AAATTTTTTTTTTAGGAA
1 AAATTTTGTTTATAGGAA
1794027 AAATTTTGTTTATAGGAA
1 AAATTTTGTTTATAGGAA
1794045 A
1 A
1794046 TTTTAAAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.49
Consensus pattern (18 bp):
AAATTTTGTTTATAGGAA
Found at i:1794103 original size:17 final size:17
Alignment explanation
Indices: 1794076--1794108 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1794066 GGTAGGAAAG
1794076 TTTAAAATTAA-ATAAA
1 TTTAAAATTAATATAAA
1794092 TTTAAGAATTAATATAA
1 TTTAA-AATTAATATAA
1794109 GATAGATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
TTTAAAATTAATATAAA
Found at i:1824198 original size:61 final size:61
Alignment explanation
Indices: 1824128--1824249 Score: 228
Period size: 61 Copynumber: 2.0 Consensus size: 61
1824118 AAAAAATTAA
1824128 TTAGTTGACATGATTGTTAATGTTATTTATT-TTTGTTGGACTGTTGTTATAATTCAAATCC
1 TTAGTTGACATGATTGTTAATGTTATTTATTCTTTGTT-GACTGTTGTTATAATTCAAATCC
1824189 TTAGTTGACATGATTGTTAATGTTATTTATTCTTTGTTGACTGTTGTTATAATTCAAATCC
1 TTAGTTGACATGATTGTTAATGTTATTTATTCTTTGTTGACTGTTGTTATAATTCAAATCC
1824250 AAAACCATGT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
61 54 0.90
62 6 0.10
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.51
Consensus pattern (61 bp):
TTAGTTGACATGATTGTTAATGTTATTTATTCTTTGTTGACTGTTGTTATAATTCAAATCC
Found at i:1825036 original size:53 final size:53
Alignment explanation
Indices: 1824956--1825061 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 53
1824946 CTACCAAATG
* *
1824956 ATGGCTTTTGGGTGGGTTATTGCAGTTGTTTCTAAACTAGCGCCTTTCTCTTC
1 ATGGCTTTTGGGTGGGTTATTGCAGTTGTTACTAAACTAACGCCTTTCTCTTC
*
1825009 ATGGCTTTTGGGTGGGTTATTGCAGTTGTTACTAAACTAACGCTTTTCTCTTC
1 ATGGCTTTTGGGTGGGTTATTGCAGTTGTTACTAAACTAACGCCTTTCTCTTC
1825062 TGAGTCGGTC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.43
Consensus pattern (53 bp):
ATGGCTTTTGGGTGGGTTATTGCAGTTGTTACTAAACTAACGCCTTTCTCTTC
Done.