Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_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: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 38
Found at i:3845332 original size:3 final size:3
Alignment explanation
Indices: 3845326--3845402 Score: 81
Period size: 3 Copynumber: 26.7 Consensus size: 3
3845316 GTATTATTTG
* * **
3845326 TAA TAA TAA -ATA TAT TAA -AA T-A TAA TAA TAA TAG TAA TTG TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3845369 T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3845403 TATAGTCTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
2 7 0.11
3 53 0.87
4 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3845670 original size:20 final size:20
Alignment explanation
Indices: 3845642--3845715 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
3845632 AAAACATTCT
*
3845642 ACCCTGAGGTTTTATAGATG
1 ACCCGGAGGTTTTATAGATG
*
3845662 ACCCGGAGGTTTTATAGAGG
1 ACCCGGAGGTTTTATAGATG
* *
3845682 ACCCGGAGGTTTTATAAATC
1 ACCCGGAGGTTTTATAGATG
*
3845702 ACTCGGAGGTTTTA
1 ACCCGGAGGTTTTA
3845716 ATTTTCTTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (20 bp):
ACCCGGAGGTTTTATAGATG
Found at i:3845809 original size:20 final size:20
Alignment explanation
Indices: 3845781--3845834 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
3845771 AAAACATCAT
* * *
3845781 ACCCTGAGGTTTTATAAATG
1 ACCCAGAGGATTTACAAATG
*
3845801 ACCCAGAGGATTTACAAATT
1 ACCCAGAGGATTTACAAATG
*
3845821 ACCCGGAGGATTTA
1 ACCCAGAGGATTTA
3845835 ATTTTCTGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (20 bp):
ACCCAGAGGATTTACAAATG
Found at i:3845825 original size:139 final size:139
Alignment explanation
Indices: 3845566--3845834 Score: 407
Period size: 139 Copynumber: 1.9 Consensus size: 139
3845556 ACAGACGACC
3845566 CGGAGGATTTAATTTTTTAGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATGC
1 CGGAGGATTTAATTTTTTAGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATGC
* * * * * * *
3845631 GAAAACATTCTACCCTGAGGTTTTATAGATGACCCGGAGGTTTTATAGAGGACCCGGAGGTTTTA
66 AAAAACATTCTACCCTGAGGTTTTATAAATGACCCAGAGGATTTACAAAGGACCCGGAGGATTTA
3845696 TAAATCACT
131 TAAATCACT
* *
3845705 CGGAGGTTTTAATTTTCTT-GAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATT
1 CGGAGGATTTAATTTT-TTAGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATG
**
3845769 CAAAAACA-TCATACCCTGAGGTTTTATAAATGACCCAGAGGATTTACAAATTACCCGGAGGATT
65 CAAAAACATTC-TACCCTGAGGTTTTATAAATGACCCAGAGGATTTACAAAGGACCCGGAGGATT
3845833 TA
129 TA
3845835 ATTTTCTGGA
Statistics
Matches: 117, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
138 2 0.02
139 113 0.97
140 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (139 bp):
CGGAGGATTTAATTTTTTAGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATGC
AAAAACATTCTACCCTGAGGTTTTATAAATGACCCAGAGGATTTACAAAGGACCCGGAGGATTTA
TAAATCACT
Found at i:3845878 original size:119 final size:119
Alignment explanation
Indices: 3845662--3845959 Score: 445
Period size: 119 Copynumber: 2.5 Consensus size: 119
3845652 TTTATAGATG
* * * * * * *
3845662 ACCCGGAGGTTTTATAGAGGACCCGGAGGTTTTATAAATCACTCGGAGGTTTTAATTTTCTTGAA
1 ACCCTGAGGTTTTATAGATGACCCGGAGGATTTACAAATCACCCGGAGGATTTAATTTTCTGGAA
**
3845727 CATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCAT-TCAAAAACATCAT
66 CATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGT-AAAAACATCAT
* * *
3845781 ACCCTGAGGTTTTATAAATGACCCAGAGGATTTACAAATTACCCGGAGGATTTAATTTTCTGGAA
1 ACCCTGAGGTTTTATAGATGACCCGGAGGATTTACAAATCACCCGGAGGATTTAATTTTCTGGAA
* *
3845846 CATTAAATGAGAAACTTTGAAAATTGCTTTCTCATTTTCATGTGAAAACATCAT
66 CATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGTAAAAACATCAT
*
3845900 ACCCTGAGGTTTTATAGATGACCTGGAGGATTTACAAATCACCCGGAGGATTTAATTTTC
1 ACCCTGAGGTTTTATAGATGACCCGGAGGATTTACAAATCACCCGGAGGATTTAATTTTC
3845960 ATGAGAAAGC
Statistics
Matches: 160, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
119 159 0.99
120 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (119 bp):
ACCCTGAGGTTTTATAGATGACCCGGAGGATTTACAAATCACCCGGAGGATTTAATTTTCTGGAA
CATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGTAAAAACATCAT
Found at i:3846009 original size:75 final size:75
Alignment explanation
Indices: 3845879--3846034 Score: 240
Period size: 75 Copynumber: 2.1 Consensus size: 75
3845869 TTGCTTTCTC
* * * **
3845879 ATTTTCATGTGAAAACATCATACCCTGAGGTTTTATAGATGACCTGGAGGATTTACAAATCACCC
1 ATTTTCATGAGAAAACATCATACCCTGAGGTTTGACAGATGACCCAGAGGATTTACAAATCACCC
*
3845944 GGAGGATTTA
66 GAAGGATTTA
* *
3845954 ATTTTCATGAGAAAGCATCATACCCTGAGGTTTGACAGATGACCCAGAGGTTTTACAAATCACCC
1 ATTTTCATGAGAAAACATCATACCCTGAGGTTTGACAGATGACCCAGAGGATTTACAAATCACCC
3846019 GAAGGATTTA
66 GAAGGATTTA
3846029 ATTTTC
1 ATTTTC
3846035 TTGAACATTA
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (75 bp):
ATTTTCATGAGAAAACATCATACCCTGAGGTTTGACAGATGACCCAGAGGATTTACAAATCACCC
GAAGGATTTA
Found at i:3846018 original size:20 final size:20
Alignment explanation
Indices: 3845975--3846018 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
3845965 AAAGCATCAT
* * *
3845975 ACCCTGAGGTTTGACAGATG
1 ACCCAGAGGTTTGACAAATC
*
3845995 ACCCAGAGGTTTTACAAATC
1 ACCCAGAGGTTTGACAAATC
3846015 ACCC
1 ACCC
3846019 GAAGGATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (20 bp):
ACCCAGAGGTTTGACAAATC
Found at i:3846089 original size:194 final size:194
Alignment explanation
Indices: 3845775--3846132 Score: 572
Period size: 194 Copynumber: 1.8 Consensus size: 194
3845765 CATTCAAAAA
* * * *
3845775 CATCATACCCTGAGGTTTTATAAATGACCCAGAGGATTTACAAATTACCCGGAGGATTTAATTTT
1 CATCATACCCTGAGGTTTGACAAATGACCCAGAGGATTTACAAATCACCCGAAGGATTTAATTTT
* * * *
3845840 CTGGAACATTAAATGAGAAACTTTGAAAATTGCTTTCTCATTTTCATGTGAAAACATCATACCCT
66 CTGGAACATTAAATGAGAAACTTTGAAAATCGCTATATCATTTTCATGCGAAAACATCATACCCT
*
3845905 GAGGTTTTATAGATGACCTGGAGGATTTACAAATCACCCGGAGGATTTAATTTTCATGAGAAAG
131 GAGGTTTTATAGATGACCCGGAGGATTTACAAATCACCCGGAGGATTTAATTTTCATGAGAAAG
* *
3845969 CATCATACCCTGAGGTTTGACAGATGACCCAGAGGTTTTACAAATCACCCGAAGGATTTAATTTT
1 CATCATACCCTGAGGTTTGACAAATGACCCAGAGGATTTACAAATCACCCGAAGGATTTAATTTT
* *
3846034 CTTGAACATTAAATGAGAAACTTTGAAAATCGCTATATCATTTTCATGCGAAAACATCTTACCCT
66 CTGGAACATTAAATGAGAAACTTTGAAAATCGCTATATCATTTTCATGCGAAAACATCATACCCT
* * *
3846099 GGGGTTTTATAGATGACCCGGCGGTTTTACAAAT
131 GAGGTTTTATAGATGACCCGGAGGATTTACAAAT
3846133 GTGTGGCAAA
Statistics
Matches: 148, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
194 148 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (194 bp):
CATCATACCCTGAGGTTTGACAAATGACCCAGAGGATTTACAAATCACCCGAAGGATTTAATTTT
CTGGAACATTAAATGAGAAACTTTGAAAATCGCTATATCATTTTCATGCGAAAACATCATACCCT
GAGGTTTTATAGATGACCCGGAGGATTTACAAATCACCCGGAGGATTTAATTTTCATGAGAAAG
Found at i:3847728 original size:51 final size:51
Alignment explanation
Indices: 3847625--3847858 Score: 244
Period size: 51 Copynumber: 4.6 Consensus size: 51
3847615 ATATCCCAAC
* ** * * *
3847625 CTTTTT-ATGCTGGTGTGAGCCTTCAAGATGCCTCAAATGGATTACTTTTGT
1 CTTTTTCATGCTGATGTGAGCCTTCAAGACACC-CACATGGATAACTTCTGT
* * *
3847676 CTTTTTCATGCTAATGTGAGCCTTTAAGACACCCACATGGATAACTTATGT
1 CTTTTTCATGCTGATGTGAGCCTTCAAGACACCCACATGGATAACTTCTGT
* * * *
3847727 CTTTTTTATGCTGATGTGAG-CTT-AAGATGC-CCCAGATGGATTACTTCTAT
1 CTTTTTCATGCTGATGTGAGCCTTCAAGA--CACCCACATGGATAACTTCTGT
*
3847777 C-TTTTCATGCTGATGTGAGCCTTCAAGATACCCACATGGATAACTTCTGACT
1 CTTTTTCATGCTGATGTGAGCCTTCAAGACACCCACATGGATAACTTCTG--T
*
3847829 CTTTTTTTATGCTGATGTGAGCCTTCAAGA
1 C-TTTTTCATGCTGATGTGAGCCTTCAAGA
3847859 TGCCCCAGAT
Statistics
Matches: 153, Mismatches: 20, Indels: 17
0.81 0.11 0.09
Matches are distributed among these distances:
49 21 0.14
50 39 0.25
51 44 0.29
52 23 0.15
54 26 0.17
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (51 bp):
CTTTTTCATGCTGATGTGAGCCTTCAAGACACCCACATGGATAACTTCTGT
Found at i:3847810 original size:100 final size:105
Alignment explanation
Indices: 3847626--3847872 Score: 369
Period size: 100 Copynumber: 2.4 Consensus size: 105
3847616 TATCCCAACC
* * * * *
3847626 TTTTTATGCTGGTGTGAGCCTTCAAGATGCCTCAAATGGATTACTTTTGTCTTTTTCATGCTAAT
1 TTTTTATGCTGATGTGAGCCTTCAAGATGCCCCAGATGGATTACTTCTATCTTTTTCATGCTAAT
*
3847691 GTGAGCCTTTAAGACACCCACATGGATAACTTATG-TC-T
66 GTGAGCCTTCAAGACACCCACATGGATAACTTATGATCTT
*
3847729 TTTTTATGCTGATGTGAG-CTT-AAGATGCCCCAGATGGATTACTTCTATC-TTTTCATGCTGAT
1 TTTTTATGCTGATGTGAGCCTTCAAGATGCCCCAGATGGATTACTTCTATCTTTTTCATGCTAAT
* *
3847791 GTGAGCCTTCAAGATACCCACATGGATAACTTCTGACTCTT
66 GTGAGCCTTCAAGACACCCACATGGATAACTTATGA-TCTT
3847832 TTTTTATGCTGATGTGAGCCTTCAAGATGCCCCAGATGGAT
1 TTTTTATGCTGATGTGAGCCTTCAAGATGCCCCAGATGGAT
3847873 AATATGGACC
Statistics
Matches: 130, Mismatches: 9, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
100 44 0.34
101 24 0.18
102 5 0.04
103 36 0.28
104 3 0.02
105 18 0.14
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.37
Consensus pattern (105 bp):
TTTTTATGCTGATGTGAGCCTTCAAGATGCCCCAGATGGATTACTTCTATCTTTTTCATGCTAAT
GTGAGCCTTCAAGACACCCACATGGATAACTTATGATCTT
Found at i:3847816 original size:50 final size:51
Alignment explanation
Indices: 3847626--3847874 Score: 261
Period size: 50 Copynumber: 4.8 Consensus size: 51
3847616 TATCCCAACC
* * * * * *
3847626 TTTTTATGCTGGTGTGAGCCTTCAAGATGCCTCAAATGGATTACTTTTGTCT
1 TTTTTATGCTGATGTGAGCCTTCAAGATACC-CACATGGATAACTTCTATCT
* * * * * *
3847678 TTTTCATGCTAATGTGAGCCTTTAAGACACCCACATGGATAACTTATGTCT
1 TTTTTATGCTGATGTGAGCCTTCAAGATACCCACATGGATAACTTCTATCT
* * *
3847729 TTTTTATGCTGATGTGAG-CTT-AAGATGCCCCAGATGGATTACTTCTATC-
1 TTTTTATGCTGATGTGAGCCTTCAAGAT-ACCCACATGGATAACTTCTATCT
*
3847778 TTTTCATGCTGATGTGAGCCTTCAAGATACCCACATGGATAACTTCTGACTCTT
1 TTTTTATGCTGATGTGAGCCTTCAAGATACCCACATGGATAACTTCT-A-TC-T
* *
3847832 TTTTTATGCTGATGTGAGCCTTCAAGATGCCCCAGATGGATAA
1 TTTTTATGCTGATGTGAGCCTTCAAGAT-ACCCACATGGATAA
3847875 TATGGACCTT
Statistics
Matches: 165, Mismatches: 24, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
49 21 0.13
50 39 0.24
51 39 0.24
52 27 0.16
54 27 0.16
55 12 0.07
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (51 bp):
TTTTTATGCTGATGTGAGCCTTCAAGATACCCACATGGATAACTTCTATCT
Found at i:3849379 original size:19 final size:19
Alignment explanation
Indices: 3849351--3849415 Score: 89
Period size: 18 Copynumber: 3.5 Consensus size: 19
3849341 CTTGATTCAA
*
3849351 TTTCTTTTTTTCTTTTATT
1 TTTCTCTTTTTCTTTTATT
3849370 TTTCTC-TTTTCTTTTATT
1 TTTCTCTTTTTCTTTTATT
*
3849388 TTTCTCTTTTT-TTTTCTTT
1 TTTCTCTTTTTCTTTT-ATT
3849407 TTTCTCTTT
1 TTTCTCTTT
3849416 CATTTCAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
18 22 0.52
19 20 0.48
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTCTCTTTTTCTTTTATT
Found at i:3856589 original size:13 final size:13
Alignment explanation
Indices: 3856551--3856591 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
3856541 CGGTCACTAT
3856551 TCACTA-TCGACGA
1 TCACTATTC-ACGA
*
3856564 TTACTATTC-CGA
1 TCACTATTCACGA
3856576 TCACTATTCACGA
1 TCACTATTCACGA
3856589 TCA
1 TCA
3856592 GAAAAAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 11 0.46
13 11 0.46
14 2 0.08
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (13 bp):
TCACTATTCACGA
Found at i:3860149 original size:31 final size:30
Alignment explanation
Indices: 3860114--3860182 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
3860104 AACCATTCAC
**
3860114 AACTTTTCCAAAATTACCAAATTAGTCCCCT
1 AACTTTTAAAAAATT-CCAAATTAGTCCCCT
* * *
3860145 AACTTTTAAAAAATTTCAAATTGGTCCCCA
1 AACTTTTAAAAAATTCCAAATTAGTCCCCT
*
3860175 AATTTTTA
1 AACTTTTA
3860183 TAAGCCTTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (30 bp):
AACTTTTAAAAAATTCCAAATTAGTCCCCT
Found at i:3861334 original size:31 final size:31
Alignment explanation
Indices: 3861299--3861366 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
3861289 TTGGTTCCTA
*
3861299 AACTTTTCTAAAGTTTATACTTTAGTCACTT
1 AACTTTTCTAAAGTTCATACTTTAGTCACTT
* *
3861330 AACTTTTTTAAAGTTCATACTTTGGTCACTT
1 AACTTTTCTAAAGTTCATACTTTAGTCACTT
3861361 AACTTT
1 AACTTT
3861367 AAAAAATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (31 bp):
AACTTTTCTAAAGTTCATACTTTAGTCACTT
Found at i:3863589 original size:70 final size:70
Alignment explanation
Indices: 3863476--3863615 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
3863466 AAATACTCGG
3863476 TCTAAAGAATCCTTGATCTAGTAGCTCTTGAAATTGGTTCTTTTTTCTCTTAACTCAATCGCATC
1 TCTAAAGAATCCTTGATCTAGTAGCTCTTGAAATTGGTTCTTTTTTCTCTTAACTCAATCGCATC
3863541 CATTT
66 CATTT
3863546 TCTAAAGAATCCTTGATCTAGTAGCTCTTGAAATTGGTTCTTTTTTCTCTTAACTCAATCGCATC
1 TCTAAAGAATCCTTGATCTAGTAGCTCTTGAAATTGGTTCTTTTTTCTCTTAACTCAATCGCATC
3863611 CATTT
66 CATTT
3863616 GATACGAACT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.43
Consensus pattern (70 bp):
TCTAAAGAATCCTTGATCTAGTAGCTCTTGAAATTGGTTCTTTTTTCTCTTAACTCAATCGCATC
CATTT
Found at i:3866295 original size:24 final size:24
Alignment explanation
Indices: 3866263--3866308 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3866253 TCTTCCTGAG
* *
3866263 GATGTATAAAATATTTATGTACAC
1 GATGTATAAAACATCTATGTACAC
3866287 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
3866309 CGTGTCATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:3866904 original size:30 final size:31
Alignment explanation
Indices: 3866844--3866904 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 31
3866834 CAACCATTCA
* *
3866844 TAACTTTTCCAAAACTATCAAATTGGTCCCC
1 TAACTTTTCCAAAACTATCAAAATGATCCCC
*
3866875 TAACTTTT-CAAAA-TTTACAAAATGATCCCC
1 TAACTTTTCCAAAACTAT-CAAAATGATCCCC
3866905 AAATTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 2 0.08
30 16 0.62
31 8 0.31
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (31 bp):
TAACTTTTCCAAAACTATCAAAATGATCCCC
Found at i:3867774 original size:123 final size:122
Alignment explanation
Indices: 3867548--3867804 Score: 489
Period size: 123 Copynumber: 2.1 Consensus size: 122
3867538 AAATGTTAAA
3867548 TTACCAATTTACCCTTAAAATTAAAATATCTTTCCTAATTTACCCATAATGAACTTGATATTTAC
1 TTACCAATTTACCCTTAAAATTAAAATATCTTTCCTAATTTACCCATAATGAACTTGATATTTAC
3867613 CTTAATACCAAGCCAAAACCTTATCGTCTTCCAAAGTCAAAGATGAACAAAATATTT
66 CTTAATACCAAGCCAAAACCTTATCGTCTTCCAAAGTCAAAGATGAACAAAATATTT
3867670 TTACCAATTTTACCCTTAAAATTAAAATATCTTTCCTAATTTACCCATAATGAACTTGATATTTA
1 TTACCAA-TTTACCCTTAAAATTAAAATATCTTTCCTAATTTACCCATAATGAACTTGATATTTA
3867735 CCTTAATACCAAGCCAAAACCTTATCGTCTTCCAAAGTCAAAGATGAACAAAATATTT
65 CCTTAATACCAAGCCAAAACCTTATCGTCTTCCAAAGTCAAAGATGAACAAAATATTT
*
3867793 TT-CCACTTTACC
1 TTACCAATTTACC
3867805 GTTTTGCCCT
Statistics
Matches: 133, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
121 6 0.05
122 10 0.08
123 117 0.88
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (122 bp):
TTACCAATTTACCCTTAAAATTAAAATATCTTTCCTAATTTACCCATAATGAACTTGATATTTAC
CTTAATACCAAGCCAAAACCTTATCGTCTTCCAAAGTCAAAGATGAACAAAATATTT
Found at i:3868190 original size:32 final size:31
Alignment explanation
Indices: 3868151--3868218 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
3868141 TTAGTCTCTA
* * *
3868151 AACTTTTCCAAAGTTTATACTTTGGTCATTT
1 AACTTTTTCAAAGTTTATACCTTGGTCACTT
3868182 AACTTTTTCAAAGTTTATACCTTGGTCACTT
1 AACTTTTTCAAAGTTTATACCTTGGTCACTT
3868213 AACTTT
1 AACTTT
3868219 AAAAATTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.26, C:0.18, G:0.09, T:0.47
Consensus pattern (31 bp):
AACTTTTTCAAAGTTTATACCTTGGTCACTT
Found at i:3869056 original size:21 final size:21
Alignment explanation
Indices: 3869030--3869159 Score: 89
Period size: 21 Copynumber: 6.1 Consensus size: 21
3869020 ACTCATATTC
*
3869030 TAAACCCTAAATCTTAATTTA
1 TAAACCCTAAATCATAATTTA
*
3869051 TAAACCCTAAATCATAAATTA
1 TAAACCCTAAATCATAATTTA
* * **
3869072 TGAACCCTAAATCCTAATCCA
1 TAAACCCTAAATCATAATTTA
** * * *
3869093 TAAACTATAAAACCCTAAATTA
1 TAAACCCT-AAATCATAATTTA
* * **
3869115 TAAACCCCAAATCCTAAACTA
1 TAAACCCTAAATCATAATTTA
* * *
3869136 TAAACCTTAACTCATAATTCA
1 TAAACCCTAAATCATAATTTA
3869157 TAA
1 TAA
3869160 TCTTTAAATA
Statistics
Matches: 82, Mismatches: 26, Indels: 2
0.75 0.24 0.02
Matches are distributed among these distances:
21 68 0.83
22 14 0.17
ACGTcount: A:0.47, C:0.24, G:0.01, T:0.28
Consensus pattern (21 bp):
TAAACCCTAAATCATAATTTA
Found at i:3869082 original size:28 final size:29
Alignment explanation
Indices: 3869051--3869111 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
3869041 TCTTAATTTA
* *
3869051 TAAACCCTAAAT-CATAAATTAT-GAACCC
1 TAAACCCT-AATCCATAAACTATAAAACCC
*
3869079 TAAATCCTAATCCATAAACTATAAAACCC
1 TAAACCCTAATCCATAAACTATAAAACCC
3869108 TAAA
1 TAAA
3869112 TTATAAACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 3 0.11
28 16 0.57
29 9 0.32
ACGTcount: A:0.49, C:0.25, G:0.02, T:0.25
Consensus pattern (29 bp):
TAAACCCTAATCCATAAACTATAAAACCC
Found at i:3869121 original size:14 final size:14
Alignment explanation
Indices: 3869065--3869126 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
3869055 CCCTAAATCA
*
3869065 TAAATTATGAACCC
1 TAAATTATAAACCC
** * *
3869079 TAAATCCTAATCCA
1 TAAATTATAAACCC
*
3869093 TAAACTATAAAACCC
1 TAAATTAT-AAACCC
3869108 TAAATTATAAACCC
1 TAAATTATAAACCC
*
3869122 CAAAT
1 TAAAT
3869127 CCTAAACTAT
Statistics
Matches: 35, Mismatches: 12, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
14 24 0.69
15 11 0.31
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.26
Consensus pattern (14 bp):
TAAATTATAAACCC
Found at i:3869428 original size:19 final size:20
Alignment explanation
Indices: 3869404--3869454 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
3869394 AATGACCAAT
3869404 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
3869423 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
3869443 AAAATCGCAACG
1 AAAATCGCAACG
3869455 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:3869448 original size:20 final size:20
Alignment explanation
Indices: 3869404--3869701 Score: 186
Period size: 20 Copynumber: 14.6 Consensus size: 20
3869394 AATGACCAAT
* *
3869404 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
3869423 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
3869443 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
***
3869463 AAAATCGCAACG-GACAAAAG
1 AAAATCGCAACGCGA-TTTAG
**
3869483 AAAATCGCAACGCGAGTTTCC
1 AAAATCGCAACGCGA-TTTAG
**
3869504 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
3869527 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
3869547 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
3869567 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
3869587 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
3869610 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
3869630 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
3869650 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
3869670 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
3869690 AAAATCGCAACG
1 AAAATCGCAACG
3869702 TTAAAAAGAA
Statistics
Matches: 230, Mismatches: 40, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
19 18 0.08
20 168 0.73
21 15 0.07
23 29 0.13
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:3869582 original size:40 final size:40
Alignment explanation
Indices: 3869508--3869699 Score: 249
Period size: 40 Copynumber: 4.7 Consensus size: 40
3869498 GTTTCCAAGT
*
3869508 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAA
1 TCGCAACGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* * *
3869551 TCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
*
3869591 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* * *
3869634 TCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
*
3869674 TCGCAACGCGATTTAGAAAATCGCAA
1 TCGCAACGCGATTTAGAGAATCGCAA
3869700 CGTTAAAAAG
Statistics
Matches: 130, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
40 77 0.59
41 2 0.02
42 4 0.03
43 47 0.36
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.20
Consensus pattern (40 bp):
TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
Found at i:3869618 original size:83 final size:83
Alignment explanation
Indices: 3869508--3869691 Score: 314
Period size: 83 Copynumber: 2.2 Consensus size: 83
3869498 GTTTCCAAGT
* * * * *
3869508 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
*
3869573 GCAATGCGATTGAGAGAG
66 GCAATGCGATTGAGAGAA
3869591 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
3869656 GCAATGCGATTGAGAGAA
66 GCAATGCGATTGAGAGAA
3869674 TCGCAACGCGATTTAGAA
1 TCGCAACGCGATTTAGAA
3869692 AATCGCAACG
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 95 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.20
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAATGCGATTGAGAGAA
Found at i:3869711 original size:20 final size:20
Alignment explanation
Indices: 3869688--3869731 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
3869678 AACGCGATTT
*
3869688 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
3869708 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
3869728 AGAA
1 AGAA
3869732 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:3869820 original size:6 final size:6
Alignment explanation
Indices: 3869809--3869858 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
3869799 GACACGTATT
3869809 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3869856 ACC
1 ACC
3869859 CGAGACGGCG
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.11
6 39 0.89
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3870541 original size:5 final size:5
Alignment explanation
Indices: 3870533--3870593 Score: 86
Period size: 5 Copynumber: 11.6 Consensus size: 5
3870523 CCGTCTCGTC
*
3870533 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCTGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG
3870585 TCGTGG TCG
1 TCG-GG TCG
3870594 TGGTAATACG
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
5 36 0.68
6 17 0.32
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.26
Consensus pattern (5 bp):
TCGGG
Found at i:3870727 original size:20 final size:20
Alignment explanation
Indices: 3870702--3870852 Score: 185
Period size: 20 Copynumber: 7.4 Consensus size: 20
3870692 ATTTTCAACG
3870702 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTATAAATCGCA
* * *
3870722 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTATAAATCGCA
* *
3870742 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TATAAATCGCA
* * *
3870765 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTATAAATCGCA
*
3870785 TTGCGATTATATAAATCGCA
1 TTGCGATTCTATAAATCGCA
3870805 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTATAAATCGCA
*
3870825 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATAAATCGCA
3870845 TTGCGATT
1 TTGCGATT
3870853 TTCTTCTAAA
Statistics
Matches: 113, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
20 94 0.83
21 2 0.02
22 3 0.03
23 14 0.12
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTATAAATCGCA
Found at i:3870865 original size:83 final size:81
Alignment explanation
Indices: 3870702--3870873 Score: 204
Period size: 83 Copynumber: 2.1 Consensus size: 81
3870692 ATTTTCAACG
* * * * *
3870702 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTT
1 TTGCGATTATATAAATCGCATTGCGATTCTATAAATCGCATTGCGA-TTTCTTC-AAATCGCATT
*
3870767 GCGACTCTCTCAATCGCA
64 GCGACTCTCTAAATCGCA
3870785 TTGCGATTATATAAATCGCATTGCGATTCTATAAATCGCATTGCGA-TTCTATC-AATCGCATTG
1 TTGCGATTATATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTTCT-TCAAATCGCATTG
* *
3870848 CGATTTTCTTCTAAATCGCG
65 CGA--CTC-TCTAAATCGCA
3870868 TTGCGA
1 TTGCGA
3870874 ACTTGGAAGC
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
80 12 0.16
81 4 0.05
82 4 0.05
83 57 0.74
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (81 bp):
TTGCGATTATATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTTCTTCAAATCGCATTGC
GACTCTCTAAATCGCA
Found at i:3870912 original size:20 final size:20
Alignment explanation
Indices: 3870887--3870938 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
3870877 TGGAAGCTCG
*
3870887 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
3870907 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
3870927 CGTTGCGATTTT
1 CGTTGCGATTTT
3870939 AATCGCGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:3870949 original size:17 final size:18
Alignment explanation
Indices: 3870927--3870976 Score: 84
Period size: 19 Copynumber: 2.8 Consensus size: 18
3870917 TTCTTTTTAA
3870927 CGTTGCGATTTTA-ATCG
1 CGTTGCGATTTTATATCG
3870944 CGTTGCGATTTTGATATCG
1 CGTTGCGATTTT-ATATCG
3870963 CGTTGCGATTTTAT
1 CGTTGCGATTTTAT
3870977 TGGTCATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 12 0.39
18 3 0.10
19 16 0.52
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (18 bp):
CGTTGCGATTTTATATCG
Found at i:3872373 original size:29 final size:29
Alignment explanation
Indices: 3872338--3872419 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
3872328 AAACTAAATT
*
3872338 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
3872367 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
3872396 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
3872420 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:3876805 original size:23 final size:23
Alignment explanation
Indices: 3876778--3876828 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
3876768 ATTGCCTTAG
3876778 CGAAGAATCCAGTATTCCATGAT
1 CGAAGAATCCAGTATTCCATGAT
3876801 CGAAGAATCCAGTATTCCATGAT
1 CGAAGAATCCAGTATTCCATGAT
3876824 CGAAG
1 CGAAG
3876829 CAAGCACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (23 bp):
CGAAGAATCCAGTATTCCATGAT
Found at i:3877101 original size:29 final size:29
Alignment explanation
Indices: 3877066--3877147 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
3877056 AAACTAAATT
*
3877066 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
3877095 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
3877124 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
3877148 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:3879291 original size:14 final size:16
Alignment explanation
Indices: 3879262--3879299 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3879252 TATTTTATGT
3879262 TTTTTTTACTATTTTA
1 TTTTTTTACTATTTTA
3879278 TTTTTTTA-TA-TTTA
1 TTTTTTTACTATTTTA
3879292 TTTGTTTT
1 TTT-TTTT
3879300 TTTAATCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 6 0.29
16 8 0.38
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTTTTACTATTTTA
Found at i:3879293 original size:19 final size:19
Alignment explanation
Indices: 3879250--3879303 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
3879240 TATTTTGTTT
*
3879250 TTTATTTTATGTTTTTTTTA
1 TTTATTTTAT-TTTTTTATA
*
3879270 -CTATTTTATTTTTTTATA
1 TTTATTTTATTTTTTTATA
*
3879288 TTTA-TTTGTTTTTTTA
1 TTTATTTTATTTTTTTA
3879304 ATCATGTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 19 0.66
19 10 0.34
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.78
Consensus pattern (19 bp):
TTTATTTTATTTTTTTATA
Found at i:3879299 original size:18 final size:18
Alignment explanation
Indices: 3879243--3879303 Score: 53
Period size: 18 Copynumber: 3.7 Consensus size: 18
3879233 TTGTACTTAT
3879243 TTTG-TTTTTTAT-TTTA
1 TTTGTTTTTTTATATTTA
*
3879259 --TGTTTTTTT-TA-CTA
1 TTTGTTTTTTTATATTTA
*
3879273 TTTTATTTTTTTATATTTA
1 -TTTGTTTTTTTATATTTA
3879292 TTTGTTTTTTTA
1 TTTGTTTTTTTA
3879304 ATCATGTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
14 5 0.15
15 6 0.18
17 8 0.24
18 13 0.38
19 2 0.06
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.79
Consensus pattern (18 bp):
TTTGTTTTTTTATATTTA
Found at i:3881692 original size:21 final size:21
Alignment explanation
Indices: 3881668--3881720 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
3881658 TTTTCATCTC
*
3881668 GCATTTTGCACTCT-CATTTTT
1 GCATTTTGCA-TATGCATTTTT
*
3881689 GCA-TTTGCATATGTATTTTT
1 GCATTTTGCATATGCATTTTT
3881709 GCATTTTTGCAT
1 GCA-TTTTGCAT
3881721 TAGTATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 2 0.07
20 15 0.56
21 3 0.11
22 7 0.26
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.53
Consensus pattern (21 bp):
GCATTTTGCATATGCATTTTT
Found at i:3882593 original size:8 final size:8
Alignment explanation
Indices: 3882551--3882679 Score: 120
Period size: 8 Copynumber: 15.9 Consensus size: 8
3882541 AAAAATACAT
3882551 AAAAAAAG
1 AAAAAAAG
*
3882559 ATATAAAAG
1 A-AAAAAAG
*
3882568 --AAAGAG
1 AAAAAAAG
* *
3882574 AAGAAAAT
1 AAAAAAAG
3882582 AAAAAAAG
1 AAAAAAAG
3882590 AAAAAAAG
1 AAAAAAAG
*
3882598 AGGAAAAAG
1 A-AAAAAAG
3882607 AAAAAAAGG
1 AAAAAAA-G
*
3882616 AAAAAAGG
1 AAAAAAAG
*
3882624 AAAAAAGG
1 AAAAAAAG
3882632 AAAAAAAG
1 AAAAAAAG
3882640 AGAAAAAAG
1 A-AAAAAAG
3882649 AAAAAAA-
1 AAAAAAAG
*
3882656 AAAGAAAG
1 AAAAAAAG
3882664 AAAAAAAG
1 AAAAAAAG
3882672 AAAGAAAA
1 AAA-AAAA
3882680 AAGAGAGAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
6 4 0.04
7 6 0.06
8 57 0.58
9 32 0.32
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:3882606 original size:17 final size:17
Alignment explanation
Indices: 3882568--3882683 Score: 116
Period size: 17 Copynumber: 6.8 Consensus size: 17
3882558 GATATAAAAG
*
3882568 AAAGAGAAGAAAATAAAA
1 AAAGAGAA-AAAAGAAAA
*
3882586 AAAGA-AAAAAAGAGGAA
1 AAAGAGAAAAAAGA-AAA
*
3882603 AAAGA-AAAAAAGGAAA
1 AAAGAGAAAAAAGAAAA
3882619 AAAG-GAAAAAAGGAAAA
1 AAAGAGAAAAAA-GAAAA
3882636 AAAGAGAAAAAAGAAAA
1 AAAGAGAAAAAAGAAAA
*
3882653 AAA-A-AAGAAAGAAAA
1 AAAGAGAAAAAAGAAAA
3882668 AAAGAAAGAAAAAAGA
1 AAAG--AGAAAAAAGA
3882684 GAGAAAGGAA
Statistics
Matches: 83, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
15 13 0.16
16 18 0.22
17 32 0.39
18 13 0.16
19 7 0.08
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (17 bp):
AAAGAGAAAAAAGAAAA
Found at i:3882680 original size:33 final size:32
Alignment explanation
Indices: 3882564--3882715 Score: 93
Period size: 34 Copynumber: 4.7 Consensus size: 32
3882554 AAAAGATATA
* *
3882564 AAAGAAAG-AGAAG-AAAATAAAAAAAGAAAA
1 AAAGAAAGAAAAAGAAAAAAAAAAAAAGAAAA
*
3882594 AAAG-AGGAAAAAGAAAAAAAGGAAAAAAGGAAAA
1 AAAGAAAGAAAAAGAAAAAAA--AAAAAA-GAAAA
* *
3882628 AAGGAAA-AAAAGAGAAAAAAGAAAAAAA-AAAG
1 AAAGAAAGAAAA-AGAAAAAA-AAAAAAAGAAAA
* *
3882660 AAAG-AA-AAAAAGAAAGAAAAAAGAGAGAAAGGA
1 AAAGAAAGAAAAAGAAA-AAAAAAAAAAGAAA--A
* *
3882693 AAATAAAGAAAGAAGAAAGAAAA
1 AAAGAAAGAAA-AAGAAAAAAAA
3882716 CCGATCAAAT
Statistics
Matches: 95, Mismatches: 12, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
29 2 0.02
30 18 0.19
31 17 0.18
32 6 0.06
33 9 0.09
34 20 0.21
35 16 0.17
36 7 0.07
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.01
Consensus pattern (32 bp):
AAAGAAAGAAAAAGAAAAAAAAAAAAAGAAAA
Found at i:3882688 original size:11 final size:11
Alignment explanation
Indices: 3882564--3882715 Score: 86
Period size: 11 Copynumber: 13.7 Consensus size: 11
3882554 AAAAGATATA
3882564 AAAGAAAGAGAAG
1 AAAGAAA-A-AAG
*
3882577 AAA-ATAAAA-
1 AAAGAAAAAAG
3882586 AAAGAAAAAA-
1 AAAGAAAAAAG
* *
3882596 AGAGGAAAAAG
1 AAAGAAAAAAG
*
3882607 -AA-AAAAAGG
1 AAAGAAAAAAG
3882616 AAA-AAAGGAAA-
1 AAAGAAA--AAAG
3882627 AAAGGAAAAAA-
1 AAA-GAAAAAAG
*
3882638 AGAGAAAAAAG
1 AAAGAAAAAAG
*
3882649 AAAAAAAAAAG
1 AAAGAAAAAAG
3882660 AAAGAAAAAAAG
1 AAAG-AAAAAAG
3882672 AAAGAAAAAAG
1 AAAGAAAAAAG
* *
3882683 AGAGAAAGGAAAAT
1 AAAG-AA--AAAAG
*
3882697 AAAGAAAGAAG
1 AAAGAAAAAAG
3882708 AAAGAAAA
1 AAAGAAAA
3882716 CCGATCAAAT
Statistics
Matches: 109, Mismatches: 18, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
9 8 0.07
10 28 0.26
11 41 0.38
12 17 0.16
13 8 0.07
14 7 0.06
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.01
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:3882701 original size:41 final size:38
Alignment explanation
Indices: 3882551--3882714 Score: 119
Period size: 38 Copynumber: 4.3 Consensus size: 38
3882541 AAAAATACAT
* * *
3882551 AAAAAAAGATATAAAAGAAAGAG-AAGAAAATAAAAAAAG
1 AAAAAAAGAAAGAAAA-AAAGAGAAAGAAAA-AAAGAAAG
* * *
3882590 AAAAAAAG-AGGAAAAAGAA-AAAAAGGAAAAAAGGAAA-
1 AAAAAAAGAAAGAAAAA-AAGAGAAA-GAAAAAAAGAAAG
*
3882627 AAAGGAAAA-AAAGAGAAAAA-AGAAA-AAAAAAAGAAAG
1 AAA--AAAAGAAAGAAAAAAAGAGAAAGAAAAAAAGAAAG
3882664 AAAAAAAGAAAGAAAAAAGAGAGAAAGGAAAATAAAGAAAG
1 AAAAAAAGAAAGAAAAAA-AGAGAAA-GAAAA-AAAGAAAG
*
3882705 -AAGAAAGAAA
1 AAAAAAAGAAA
3882715 ACCGATCAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 25
0.73 0.09 0.18
Matches are distributed among these distances:
35 4 0.04
36 19 0.19
37 9 0.09
38 24 0.24
39 23 0.23
40 13 0.13
41 8 0.08
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (38 bp):
AAAAAAAGAAAGAAAAAAAGAGAAAGAAAAAAAGAAAG
Found at i:3882714 original size:25 final size:22
Alignment explanation
Indices: 3882582--3882710 Score: 104
Period size: 23 Copynumber: 5.6 Consensus size: 22
3882572 AGAAGAAAAT
3882582 AAAAAAAGAA-AAAAAGAGGAAA
1 AAAAAAAGAAGAAAAA-AGGAAA
3882604 AAGAAAAA-AAGGAAAAAAGGAAA
1 AA-AAAAAGAA-GAAAAAAGGAAA
* *
3882627 AAAGGAAAAAAAGAGAAAAAAGAAA
1 AAA--AAAAGAAGA-AAAAAGGAAA
*
3882652 AAAAAAAGAAAGAAAAAAAGAAA
1 AAAAAAAG-AAGAAAAAAGGAAA
* *
3882675 GAAAAAAG-AG-AGAAAGGAAA
1 AAAAAAAGAAGAAAAAAGGAAA
3882695 ATAAAGAAAGAAGAAA
1 A-AAA-AAAGAAGAAA
3882711 GAAAACCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
20 8 0.09
21 5 0.06
22 9 0.10
23 36 0.41
24 16 0.18
25 14 0.16
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (22 bp):
AAAAAAAGAAGAAAAAAGGAAA
Found at i:3884763 original size:60 final size:56
Alignment explanation
Indices: 3884664--3884863 Score: 180
Period size: 60 Copynumber: 3.5 Consensus size: 56
3884654 AAAAGAAAGG
* * *
3884664 TTTTAAAGAAACTAAGCCTGATTTTCAGGGGTTTATTGATGATGATTTCCAAATAATAT
1 TTTTAAAGAAACTAAGCCTAATTTTTA-GGGTTTATTGATGAT-ATTTCCAAATGA-AT
* * *
3884723 TTTTAAAAGAAGCTAAGCCTAATTTTTAGTGATTGT-TTGATG-T-TTT-CAAATGAGT
1 TTTT-AAAGAAACTAAGCCTAATTTTTAG-GGTT-TATTGATGATATTTCCAAATGAAT
* * *
3884778 TTTT--AGAAATTAAGCCTAATTTTCAAGGGTTTCTTGATGATTATTTCCAAA-GAAT
1 TTTTAAAGAAACTAAGCCTAATTTT-TAGGGTTTATTGATGA-TATTTCCAAATGAAT
*
3884833 TTTTAAAGGAAGCTAAGCCTAATTTTTAGGG
1 TTTTAAA-GAAACTAAGCCTAATTTTTAGGG
3884864 GTTCCTTGAT
Statistics
Matches: 115, Mismatches: 14, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
51 1 0.01
52 26 0.23
53 2 0.02
54 1 0.01
55 15 0.13
56 10 0.09
57 8 0.07
58 16 0.14
59 6 0.05
60 29 0.25
61 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.41
Consensus pattern (56 bp):
TTTTAAAGAAACTAAGCCTAATTTTTAGGGTTTATTGATGATATTTCCAAATGAAT
Found at i:3885886 original size:91 final size:91
Alignment explanation
Indices: 3885730--3886171 Score: 595
Period size: 91 Copynumber: 4.9 Consensus size: 91
3885720 AGATAAACCA
* * *
3885730 ATCAACATTTCCAGTGG-GAAGTTCATAATGAGAAGAACTTATCCGAA-GAGGAAGACGAAGTTC
1 ATCAACATTTCCAGCGGAG-AGTTCATAATGAGAAGAACTCATCC-AACGAGGAAGAAGAAGTTC
*
3885793 ATAATGAGAAGAACTTGTTTAACCTTGGC
64 ATAATGAGAAGAACTTGTTCAACCTT-GC
* *
3885822 -TCAACAGTTCCAGCGGAGAGTTCATAATGAGAAGAACGCATCCAACGAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCAT
*
3885886 AATGAGAAGAACTTGTTTAACCTTGC
66 AATGAGAAGAACTTGTTCAACCTTGC
* * * * * * *
3885912 ATCACCATATCCAGCGGGGAGTTCATAATGAAAATAACCCATCCAACGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCAT
3885977 AATGAGAAGAACTTGTTCAACCTTGC
66 AATGAGAAGAACTTGTTCAACCTTGC
* * ** * *
3886003 ATCACCATTTCCAGCGGGGAGTTCATAATGAGAAGAACTCATCTGACGAGGGAGAATAAGTTCAT
1 ATCAACATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCAT
* * *
3886068 AATTAGAAGAACTTGTCCAACCTTTC
66 AATGAGAAGAACTTGTTCAACCTTGC
* *
3886094 ATCAACATTTCCAGTGGAGAGTTCATAATGAAAAGAACTCATCCAACGAGGGAA-AAGAAGTTCA
1 ATCAACATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGA-GGAAGAAGAAGTTCA
3886158 TAATGAGAAGAACT
65 TAATGAGAAGAACT
3886172 CATCCAATGA
Statistics
Matches: 313, Mismatches: 33, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
90 4 0.01
91 305 0.97
92 4 0.01
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.23
Consensus pattern (91 bp):
ATCAACATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTGC
Found at i:3886151 original size:22 final size:22
Alignment explanation
Indices: 3886123--3886191 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
3886113 AGTTCATAAT
*
3886123 GAAAAGAACTCATCCAACGAGG
1 GAAAAGAACTCATCCAATGAGG
*
3886145 GAAAAGAAGTTCAT--AATGA--
1 GAAAAGAA-CTCATCCAATGAGG
3886164 G--AAGAACTCATCCAATGAGG
1 GAAAAGAACTCATCCAATGAGG
3886184 GAAAAGAA
1 GAAAAGAA
3886192 GTTCATAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 14
0.69 0.06 0.26
Matches are distributed among these distances:
16 4 0.11
17 5 0.14
18 5 0.14
19 1 0.03
20 1 0.03
21 4 0.11
22 13 0.35
23 4 0.11
ACGTcount: A:0.49, C:0.14, G:0.23, T:0.13
Consensus pattern (22 bp):
GAAAAGAACTCATCCAATGAGG
Found at i:3886156 original size:39 final size:39
Alignment explanation
Indices: 3886113--3886210 Score: 178
Period size: 39 Copynumber: 2.5 Consensus size: 39
3886103 TCCAGTGGAG
*
3886113 AGTTCATAATGAAAAGAACTCATCCAACGAGGGAAAAGA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAAAAGA
*
3886152 AGTTCATAATGAGAAGAACTCATCCAATGAGGGAAAAGA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAAAAGA
3886191 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
3886211 TGTTCAACCT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.18
Consensus pattern (39 bp):
AGTTCATAATGAGAAGAACTCATCCAACGAGGGAAAAGA
Found at i:3886194 original size:130 final size:130
Alignment explanation
Indices: 3886022--3886301 Score: 436
Period size: 130 Copynumber: 2.2 Consensus size: 130
3886012 TCCAGCGGGG
** * * *
3886022 AGTTCATAATGAGAAGAACTCATCTGACGAGGGAGAATAAGTTCATAATTAGAAGAACTTGTCCA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAAAAGAAGTTCATAATGAGAAGAACTTGTCCA
*
3886087 ACCTT-TCATCAACATTTCCAGTGGAGAGTTCATAATGAAAAGAACTCATCCAACGAGGGAAAAG
66 ACCTTGGC-TCAACATTTCCAGTGGAGAGTTCATAATGAAAAGAACTCATCCAACGAGGGAAAAG
3886151 A
130 A
* *
3886152 AGTTCATAATGAGAAGAACTCATCCAATGAGGGAAAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAAAAGAAGTTCATAATGAGAAGAACTTGTCCA
* * * *
3886217 ACCTTGGCTTAGCATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGA
66 ACCTTGGCTCAACATTTCCAGTGGAGAGTTCATAATGAAAAGAACTCATCCAACGAGGGAAAAGA
3886282 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
3886302 TGTTCAACCT
Statistics
Matches: 137, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
130 136 0.99
131 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.23
Consensus pattern (130 bp):
AGTTCATAATGAGAAGAACTCATCCAACGAGGGAAAAGAAGTTCATAATGAGAAGAACTTGTCCA
ACCTTGGCTCAACATTTCCAGTGGAGAGTTCATAATGAAAAGAACTCATCCAACGAGGGAAAAGA
Found at i:3886202 original size:21 final size:21
Alignment explanation
Indices: 3886141--3886203 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
3886131 CTCATCCAAC
3886141 GAGGGAAAAGAAGTTCATAAT
1 GAGGGAAAAGAAGTTCATAAT
*
3886162 GA--G--AAGAA-CTCATCCAAT
1 GAGGGAAAAGAAGTTCAT--AAT
3886180 GAGGGAAAAGAAGTTCATAAT
1 GAGGGAAAAGAAGTTCATAAT
3886201 GAG
1 GAG
3886204 AAGAACTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
16 4 0.12
17 5 0.15
18 5 0.15
19 1 0.03
20 1 0.03
21 8 0.24
22 5 0.15
23 4 0.12
ACGTcount: A:0.46, C:0.10, G:0.27, T:0.17
Consensus pattern (21 bp):
GAGGGAAAAGAAGTTCATAAT
Found at i:3886475 original size:116 final size:116
Alignment explanation
Indices: 3886233--3886447 Score: 292
Period size: 116 Copynumber: 1.9 Consensus size: 116
3886223 GCTTAGCATT
* *
3886233 TCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAG
1 TCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAATTCATAATGAGAAG
* ** * *
3886298 AACTTGTTCAACCTTAGCTCGATTCCATTACAGAATAAACCGATCAACATT
66 AACTTGTTCAACCTTAGCGCGATTCCACGACAGAAGAAACCGATCAACATC
* * * *
3886349 TCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAATTTATAATGAGAAT
1 TCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAATTCATAATGAGAAG
*
3886414 AACTTGTTCGACCTT-G-GCGATTCCACCGA-AGAAG
66 AACTTGTTCAACCTTAGCGCGATTCCA-CGACAGAAG
3886448 GAAGTGGATT
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
114 12 0.14
115 2 0.02
116 73 0.84
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (116 bp):
TCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAATTCATAATGAGAAG
AACTTGTTCAACCTTAGCGCGATTCCACGACAGAAGAAACCGATCAACATC
Found at i:3888317 original size:21 final size:20
Alignment explanation
Indices: 3888284--3888322 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3888274 CTATTTCGGT
3888284 TATTTCTTATCTATAAAAAA
1 TATTTCTTATCTATAAAAAA
*
3888304 TATTCTCTTTTCTATAAAA
1 TATT-TCTTATCTATAAAA
3888323 CGCGAATCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTTCTTATCTATAAAAAA
Found at i:3888615 original size:31 final size:31
Alignment explanation
Indices: 3888577--3888652 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
3888567 GTTACATCGG
3888577 GGACCATATTG-AAA-ATGGACTAAATGTTGGA
1 GGACCATATTGCAAACAT--ACTAAATGTTGGA
*
3888608 GGACCATATTGCAAACATACTAAATGTTGGG
1 GGACCATATTGCAAACATACTAAATGTTGGA
**
3888639 GGACTGTATTGCAA
1 GGACCATATTGCAA
3888653 GTTGTAAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
31 35 0.88
32 3 0.08
33 2 0.05
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (31 bp):
GGACCATATTGCAAACATACTAAATGTTGGA
Found at i:3889710 original size:33 final size:29
Alignment explanation
Indices: 3889660--3889750 Score: 103
Period size: 33 Copynumber: 3.0 Consensus size: 29
3889650 TATCATTCTG
*
3889660 TTTAT-TTTATTTTAATTTAGTCACTATTAT
1 TTTATGTTTA-TTCAATTTAGTCACTATT-T
*
3889690 TATTATGATTTGTTCGAATTTAGTCACTATTT
1 T-TTATG-TTTATTC-AATTTAGTCACTATTT
*
3889722 TTTATGTTTATTCATTTTAGTCACTATTT
1 TTTATGTTTATTCAATTTAGTCACTATTT
3889751 GGATTCTGCT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
29 15 0.28
30 7 0.13
31 9 0.17
32 4 0.08
33 18 0.34
ACGTcount: A:0.24, C:0.09, G:0.08, T:0.59
Consensus pattern (29 bp):
TTTATGTTTATTCAATTTAGTCACTATTT
Found at i:3889741 original size:29 final size:32
Alignment explanation
Indices: 3889673--3889750 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 32
3889663 ATTTTATTTT
*
3889673 AATTTAGTCACTATTATTATTATGATTTGTTCG
1 AATTTAGTCACTATT-TTATTATGATTTATTCG
3889706 AATTTAGTCACTATTTT-TTATG-TTTATTC-
1 AATTTAGTCACTATTTTATTATGATTTATTCG
*
3889735 ATTTTAGTCACTATTT
1 AATTTAGTCACTATTT
3889751 GGATTCTGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 15 0.35
30 6 0.14
31 5 0.12
32 2 0.05
33 15 0.35
ACGTcount: A:0.26, C:0.10, G:0.09, T:0.55
Consensus pattern (32 bp):
AATTTAGTCACTATTTTATTATGATTTATTCG
Found at i:3889919 original size:12 final size:12
Alignment explanation
Indices: 3889902--3889944 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
3889892 GTCCTTGTAG
3889902 TTATTTTATTTT
1 TTATTTTATTTT
*
3889914 TTATTTTATGTT
1 TTATTTTATTTT
*
3889926 TT-TTTAATGTTT
1 TTATTTTAT-TTT
3889938 TTATTTT
1 TTATTTT
3889945 TTATATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
11 5 0.20
12 17 0.68
13 3 0.12
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:3895608 original size:16 final size:16
Alignment explanation
Indices: 3895587--3895619 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3895577 AAAAAAAATT
3895587 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
3895603 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
3895619 T
1 T
3895620 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:3904374 original size:35 final size:35
Alignment explanation
Indices: 3904328--3904402 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
3904318 GTTCATGCAA
3904328 TTGAATATGGAATTAGTAGAATGCGTATGAACGAG
1 TTGAATATGGAATTAGTAGAATGCGTATGAACGAG
3904363 TTGAATATGGAATTAGTAGAATGCGTATGAACGAG
1 TTGAATATGGAATTAGTAGAATGCGTATGAACGAG
3904398 TTGAA
1 TTGAA
3904403 AGCGGATTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.37, C:0.05, G:0.28, T:0.29
Consensus pattern (35 bp):
TTGAATATGGAATTAGTAGAATGCGTATGAACGAG
Found at i:3906941 original size:399 final size:399
Alignment explanation
Indices: 3906197--3907363 Score: 1853
Period size: 399 Copynumber: 2.9 Consensus size: 399
3906187 CGTTATTTAC
*
3906197 AAGTATCGACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACAGGT
1 AAGTATCGACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTCAAAAAACAGGT
* * *
3906262 ACATTTATATCGGTTACATTATAAATTTACCTATTACATTATAATTATCAGTTTCGATATTTTTG
66 ACATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTTG
*
3906327 GGATCGATACTTTTTATAAATGTATCGACACTTTCTGCGTTCACCCTTTTGGGCATTCATTCTGG
131 GGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTCTGG
* *
3906392 AAAAAAGTATCGACACATCATTTAAAAGTGTCGACAA-ATTATGTAGACCTATTCTGACATAAAA
196 AAAAAAGTATCGACACAACA-TTAAAAGTGTCGA-AACATTATGTAGACCTATTCTAACATAAAA
* * * * *
3906456 TCGATATATTTATACCGTTTATATTACAAAATTACCTATTACATTATAATTATGGATTTTGATGT
259 CCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATATTTATGGATTTCGATGT
* *
3906521 TT-TAGGGATCGATACTGTTTAAAAATGTATCGACACTTTATGTGTGCAACCTTTTTGGATTTTC
324 TTCT-GGGATCGATATTGTTTAAAAATGTATCGACACTTTATGGGTGCAACCTTTTTGGATTTTC
3906585 CTTGTGGACCAA
388 CTTGTGGACCAA
* *
3906597 AATTATCGACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTCAAAAAACCGGT
1 AAGTATCGACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTCAAAAAACAGGT
* *
3906662 ACATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTTGATGTTTTTG
66 ACATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTTG
* *
3906727 GGATC-ATACTTTTTATAAATGTATCGACACTTTATGTGTTCACCCATTTGGGCATTCATTCTGG
131 GGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTCTGG
* *
3906791 CAAAAAGTATCGACACAACATTCAAAAGTGTCGAAACATTATGTAGAACTATTCTAACATAAAAC
196 AAAAAAGTATCGACACAACATT-AAAAGTGTCGAAACATTATGTAGACCTATTCTAACATAAAAC
3906856 CGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATATTTATGGATTTCGATGTT
260 CGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATATTTATGGATTTCGATGTT
*
3906921 TCTGGGATCGATATTGTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTTTGGATTTTCCT
325 TCTGGGATCGATATTGTTTAAAAATGTATCGACACTTTATGGGTGCAACCTTTTTGGATTTTCCT
3906986 TGTGGACCAA
390 TGTGGACCAA
* * * * * *
3906996 AAGTATCGATACAAATTCTACAA-GTGTCGATACATTATGTAT-ATCTATTTTATCAAAAAGCTG
1 AAGTATCGACACAAA-TCTAAAACGTGTCGATACATTATGT-TCACCTATTTTCTCAAAAAACAG
** *
3907059 GTTTATTTATACCGGTTACATTGTAAATTTACCTATTATATTATAATTATCAGTTTCGATGTTTT
64 GTACATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTT
* *
3907124 TGGGATCGATACTTTTTATAATTGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTAT
129 TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTCT
* *
3907189 -GATAAAAAGTATCGACACAACATTAACAAGTGTCGACACATTATGTAGACCTATTCTCACATAA
194 GGA-AAAAAGTATCGACACAACATTAA-AAGTGTCGAAACATTATGTAGACCTATTCTAACATAA
* *
3907253 AACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATATTTATTGATTTCAAT
257 AACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATATTTATGGATTTCGAT
*
3907318 GTTTCTGGGATCGATACTT-TTTAAAACTGTATCGACACTTTATGGG
322 GTTTCTGGGATCGATA-TTGTTTAAAAATGTATCGACACTTTATGGG
3907364 AAACTTTAAG
Statistics
Matches: 712, Mismatches: 46, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
398 4 0.01
399 358 0.50
400 348 0.49
401 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (399 bp):
AAGTATCGACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTCAAAAAACAGGT
ACATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTTG
GGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTCTGG
AAAAAAGTATCGACACAACATTAAAAGTGTCGAAACATTATGTAGACCTATTCTAACATAAAACC
GGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATATTTATGGATTTCGATGTTT
CTGGGATCGATATTGTTTAAAAATGTATCGACACTTTATGGGTGCAACCTTTTTGGATTTTCCTT
GTGGACCAA
Found at i:3907688 original size:11 final size:11
Alignment explanation
Indices: 3907672--3907696 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3907662 TATAGATAAC
3907672 AATGTTCAAAT
1 AATGTTCAAAT
3907683 AATGTTCAAAT
1 AATGTTCAAAT
3907694 AAT
1 AAT
3907697 TTATACATCA
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:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (11 bp):
AATGTTCAAAT
Found at i:3908720 original size:6 final size:6
Alignment explanation
Indices: 3908702--3908763 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
3908692 ACTTGTTTGG
* * * * * *
3908702 ATCATC ATAATC ATCATC ATCGTC GTCATC ATCTTC ATTATC ATCGTC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
* *
3908750 ATCTTC ATCTTC AT
1 ATCATC ATCATC AT
3908764 TAACCTCATG
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.26, C:0.29, G:0.05, T:0.40
Consensus pattern (6 bp):
ATCATC
Found at i:3908730 original size:12 final size:12
Alignment explanation
Indices: 3908702--3908763 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 12
3908692 ACTTGTTTGG
**
3908702 ATCATCATAATC
1 ATCATCATCGTC
3908714 ATCATCATCGTC
1 ATCATCATCGTC
* *
3908726 GTCATCATCTTC
1 ATCATCATCGTC
*
3908738 ATTATCATCGTC
1 ATCATCATCGTC
* *
3908750 ATCTTCATCTTC
1 ATCATCATCGTC
3908762 AT
1 AT
3908764 TAACCTCATG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.26, C:0.29, G:0.05, T:0.40
Consensus pattern (12 bp):
ATCATCATCGTC
Found at i:3908764 original size:24 final size:24
Alignment explanation
Indices: 3908702--3908765 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
3908692 ACTTGTTTGG
** *
3908702 ATCATCATAATCATCATCATCGTC
1 ATCATCATCTTCATTATCATCGTC
*
3908726 GTCATCATCTTCATTATCATCGTC
1 ATCATCATCTTCATTATCATCGTC
*
3908750 ATCTTCATCTTCATTA
1 ATCATCATCTTCATTA
3908766 ACCTCATGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.27, C:0.28, G:0.05, T:0.41
Consensus pattern (24 bp):
ATCATCATCTTCATTATCATCGTC
Found at i:3910233 original size:160 final size:161
Alignment explanation
Indices: 3910057--3910376 Score: 633
Period size: 160 Copynumber: 2.0 Consensus size: 161
3910047 TGAACCAAGC
3910057 TAGAGCAAAGGCGAGTTTTCTGATTAGTTGGTTATTTGATAAATTAAAGGTTAGGTTTTGATCAT
1 TAGAGCAAAGGCGAGTTTTCTGATTAGTTGGTTATTTGATAAATTAAAGGTTAGGTTTTGATCAT
3910122 TAGATGAAAACTAAGCTTAAGTTGTCTTATAATCAAAACATGAAGAAATTATAAGAGATTAAAGA
66 TAGATGAAAACTAAGCTTAAGTTGTCTTATAATCAAAACATGAAGAAATTATAAGAGATTAAAGA
3910187 AAATAGGTTTTAAAATGAA-TTATGGAAAAA
131 AAATAGGTTTTAAAATGAATTTATGGAAAAA
3910217 TAGAGCAAAGGCGAGTTTTCTGATTAGTTGGTTATTTGATAAATTAAAGGTTAGGTTTTGATCAT
1 TAGAGCAAAGGCGAGTTTTCTGATTAGTTGGTTATTTGATAAATTAAAGGTTAGGTTTTGATCAT
3910282 TAGATGAAAACTAAGCTTAAGTTGTCTTATAATCAAAACATGAAGAAATTATAAGAGATTAAAGA
66 TAGATGAAAACTAAGCTTAAGTTGTCTTATAATCAAAACATGAAGAAATTATAAGAGATTAAAGA
3910347 AAATAGGTTTTAAAATGAATTTATGGAAAA
131 AAATAGGTTTTAAAATGAATTTATGGAAAA
3910377 GAGTTGATAA
Statistics
Matches: 159, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
160 149 0.94
161 10 0.06
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (161 bp):
TAGAGCAAAGGCGAGTTTTCTGATTAGTTGGTTATTTGATAAATTAAAGGTTAGGTTTTGATCAT
TAGATGAAAACTAAGCTTAAGTTGTCTTATAATCAAAACATGAAGAAATTATAAGAGATTAAAGA
AAATAGGTTTTAAAATGAATTTATGGAAAAA
Found at i:3910856 original size:19 final size:19
Alignment explanation
Indices: 3910832--3910881 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
3910822 ATATGATTTA
3910832 TGTATCGATGCATAGATAG
1 TGTATCGATGCATAGATAG
3910851 TGTATCGATGCATAGATAG
1 TGTATCGATGCATAGATAG
3910870 TGTATCGATGCA
1 TGTATCGATGCA
3910882 CCCGTCAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (19 bp):
TGTATCGATGCATAGATAG
Found at i:3919498 original size:64 final size:63
Alignment explanation
Indices: 3919393--3919512 Score: 150
Period size: 64 Copynumber: 1.9 Consensus size: 63
3919383 ATTGTTTAAG
* * * * *
3919393 GTGTATCGATGCACATGAAGTGCATCGATGCGCTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATAGATGCACCCCCTT-AAATAAAAACATCGAATGCCATCA
* * **
3919457 GTGTATCGATGGACAAGTAGTGCATAGATGCACCCCCTTAAATGCAAACATCGAAT
1 GTGTATCGATGCACAAGAAGTGCATAGATGCACCCCCTTAAATAAAAACATCGAAT
3919513 AGGATTTATG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
63 15 0.32
64 32 0.68
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATAGATGCACCCCCTTAAATAAAAACATCGAATGCCATCA
Found at i:3920713 original size:15 final size:15
Alignment explanation
Indices: 3920692--3920762 Score: 81
Period size: 15 Copynumber: 4.5 Consensus size: 15
3920682 CAAATCTAAA
3920692 GTTGAGAAG-CGATTG
1 GTTGAGAAGACG-TTG
* *
3920707 TTTGAGAAGGAGGTTGTG
1 GTTGAGAA-GACG-T-TG
3920725 GTTGAGAAGACGTTG
1 GTTGAGAAGACGTTG
3920740 GTTGAGAAGACGTTG
1 GTTGAGAAGACGTTG
3920755 GTTGAGAA
1 GTTGAGAA
3920763 AGACCGCGCT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
15 32 0.67
16 2 0.04
17 5 0.10
18 9 0.19
ACGTcount: A:0.27, C:0.04, G:0.41, T:0.28
Consensus pattern (15 bp):
GTTGAGAAGACGTTG
Found at i:3921530 original size:199 final size:200
Alignment explanation
Indices: 3921220--3922595 Score: 1470
Period size: 200 Copynumber: 6.9 Consensus size: 200
3921210 TTGGGTTTCC
* * * ** *
3921220 TTATGGAAAAAAAAGTATCGAAACAAATTCCACAAGTGTCGATACATGT-TGTAGACCTATTCTC
1 TTATGG-ACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACAT-TATGTAGACCTATTCT-
* * * ** * * **
3921284 T-CATAAAACTGGTAT-TGTTATACCGGTTACATTGTAAATTTACCTATTACATTATATTTATGG
63 TACATAAAACCGGTATAT-TTATACCAGTTATATTACAAAATTACCTATTACATTATAATTATCT
* * * * *
3921347 GTTTCGATGTTTCTGGTATCGACACATTTTATAAATGTATCAACACTTTATTCGTTTATCATTTT
127 GTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCATTTT
3921412 TTGCATTCA
192 TTGCATTCA
* * *
3921421 TTATGGACAAAAAGTATCGACACAAAAT-AAAAAGTGTTGATATATTATGTAGACCTATTTTTAC
1 TTATGGACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTTAC
* * * *
3921485 ATAAAATCGGTATATTTATACCAATTATATGACAAAATTACCTATTACATTATAATTATTTGTTT
66 ATAAAACCGGTATATTTATACCAGTTATATTACAAAATTACCTATTACATTATAATTATCTGTTT
* * * *
3921550 CGATGTTTTTATAAATGTATCGACA--ATTTAT---TCGT-TC-ATC-CTTT-TT-G-GCATTCA
131 CGATG-TTTT-T---GGGATCGACACTTTTTATAAAT-GTATCGA-CACTTTATTCGTTCA-TCA
*
3921604 --TTTTGGA--CA
188 TTTTTTGCATTCA
** * * *
3921613 --A---A-AAGTA-TCGA-C-ACA-AAAT-AAAAAAGTGTCGATATATTATGTAGTCCTATTCTT
1 TTATGGACAAAAAGT--ATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTT
* *
3921667 ACATAAAACCGGTATATTTATACCTGTTATATTACAAAATTACCTATTACATTATAATTATCCGT
64 ACATAAAACCGGTATATTTATACCAGTTATATTACAAAATTACCTATTACATTATAATTATCTGT
* *
3921732 TTCGATATTTTTGGGATTGACACTTTTTATAAATGTATCGACACTTTTTATAAATGTATCGACAC
129 TTCGATGTTTTTGGGATCGACACTTTTTATAAATGTATCGACAC---TT-T--A--T-TCG----
*
3921797 TTTATTCGTTCATCATTTTTGACATTCA
181 ----TTC-ATCAT--TTTTTG-CATTCA
* *
3921825 TTCTGGAGAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTTAC
1 TTATGGACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTTAC
** * *
3921890 ATAAAATTGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATCTATTT
66 ATAAAACCGGTATATTTATACCAGTTATATTACAAAATTACCTATTACATTATAATTATCTGTTT
* * *
3921955 CGATGTTTTTTGGATCGACGCTTTTTATAAATGTATCAACACTTTATTCGTTCATCATTTTTTGC
131 CGATGTTTTTGGGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCATTTTTTGC
3922020 ATTCA
196 ATTCA
* * * * * * *
3922025 TTATGGACAAAAAGAATCAACATAACATTAAAAAGTGTCGATACATTATGTATACCTATTCTCAC
1 TTATGGACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTTAC
* * * *
3922090 ATAAAACCGGTATATTGATACCAGTTATATTAAAAAATTACCTATTACATTATATTTAT-GGATT
66 ATAAAACCGGTATATTTATACCAGTTATATTACAAAATTACCTATTACATTATAATTATCTG-TT
* *
3922154 TCGATGTTTCTGGGATCGACACTTTTTA-AAATTGTATCGACACTTTATTCATTCATCATTTTTT
130 TCGATGTTTTTGGGATCGACACTTTTTATAAA-TGTATCGACACTTTATTCGTTCATCATTTTTT
3922218 GCATTCA
194 GCATTCA
*
3922225 TTATGGACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCAC
1 TTATGGACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTTAC
* * * *
3922290 ATAAAACCAGTATATTTATACCTGTTATAATACAAAATTACCTATTACATTATAATTATTTGTTT
66 ATAAAACCGGTATATTTATACCAGTTATATTACAAAATTACCTATTACATTATAATTATCTGTTT
* * *
3922355 CGATG-GTTTGGGATCGACACTTTTTATATATGTATCGACACTTTATTCGTTCATCATTTTTGGC
131 CGATGTTTTTGGGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCATTTTTTGC
3922419 ATTCA
196 ATTCA
* * * *
3922424 TTCTAGACAAAAAGCATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTGAC
1 TTATGGACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTTAC
3922489 ATAAAACCGGTATATTTATACC-GATTATATTACAAAATTACCTATTACATTATAATTATCTGTT
66 ATAAAACCGGTATATTTATACCAG-TTATATTACAAAATTACCTATTACATTATAATTATCTGTT
* *
3922553 TCGATGTTTTTGGGATCGACACGTATTATAAATGTATCGACAC
130 TCGATGTTTTTGGGATCGACACTTTTTATAAATGTATCGACAC
3922596 ATATGCTTAC
Statistics
Matches: 994, Mismatches: 114, Indels: 135
0.80 0.09 0.11
Matches are distributed among these distances:
179 7 0.01
181 5 0.01
182 1 0.00
183 6 0.01
184 103 0.10
185 6 0.01
186 4 0.00
187 2 0.00
188 2 0.00
189 1 0.00
190 1 0.00
192 2 0.00
194 7 0.01
195 2 0.00
196 5 0.01
197 2 0.00
198 8 0.01
199 272 0.27
200 358 0.36
201 14 0.01
202 5 0.01
203 4 0.00
204 12 0.01
205 4 0.00
209 5 0.01
210 1 0.00
212 5 0.01
213 1 0.00
215 1 0.00
217 3 0.00
218 6 0.01
219 4 0.00
220 3 0.00
221 132 0.13
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (200 bp):
TTATGGACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTTAC
ATAAAACCGGTATATTTATACCAGTTATATTACAAAATTACCTATTACATTATAATTATCTGTTT
CGATGTTTTTGGGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCATTTTTTGC
ATTCA
Found at i:3921776 original size:21 final size:21
Alignment explanation
Indices: 3921750--3921799 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
3921740 TTTTGGGATT
3921750 GACACTTTTTATAAATGTATC
1 GACACTTTTTATAAATGTATC
3921771 GACACTTTTTATAAATGTATC
1 GACACTTTTTATAAATGTATC
3921792 GACACTTT
1 GACACTTT
3921800 ATTCGTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (21 bp):
GACACTTTTTATAAATGTATC
Found at i:3922570 original size:399 final size:400
Alignment explanation
Indices: 3921768--3922595 Score: 1288
Period size: 399 Copynumber: 2.1 Consensus size: 400
3921758 TTATAAATGT
* * *
3921768 ATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCATTTTTGACATTCATTCTGGAG
1 ATCGACACTTTTTATAAATGTATCGACACTTTATTCATTCATCATTTTTGACATTCATTATGGAC
* **
3921833 AAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTTACATAAAATT
66 AAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACC
* * *
3921898 GGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATCTATTTCGATGTTT
131 AGTATATTTATACCGGTTATAATACAAAATTACCTATTACATTATAATTATCTATTTCGATGTGT
* * *
3921963 TTTGGATCGACGCTTTTTATAAATGTATCAACACTTTATTCGTTCATCATTTTTTGCATTCATTA
196 TTGGGATCGACACTTTTTATAAATGTATCAACACTTTATTCGTTCATCATTTTTGGCATTCATTA
* * * * *
3922028 TGGACAAAAAGAATCAACATAACATTAAAAAGTGTCGATACATTATGTATACCTATTCTCACATA
261 TAGACAAAAAGAATCAACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATA
*
3922093 AAACCGGTATATTGATACCAGTTATATTAAAAAATTACCTATTACATTATATTTATGGATTTCGA
326 AAACCGGTATATTGATACCAGTTATATTAAAAAATTACCTATTACATTATAATTATGGATTTCGA
3922158 TGTTTCTGGG
391 TGTTTCTGGG
3922168 ATCGACACTTTTTA-AAATTGTATCGACACTTTATTCATTCATCATTTTTTG-CATTCATTATGG
1 ATCGACACTTTTTATAAA-TGTATCGACACTTTATTCATTCATCA-TTTTTGACATTCATTATGG
3922231 ACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAA
64 ACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAA
* * *
3922296 CCAGTATATTTATACCTGTTATAATACAAAATTACCTATTACATTATAATTATTTGTTTCGATG-
129 CCAGTATATTTATACCGGTTATAATACAAAATTACCTATTACATTATAATTATCTATTTCGATGT
* *
3922360 GTTTGGGATCGACACTTTTTATATATGTATCGACACTTTATTCGTTCATCATTTTTGGCATTCAT
194 GTTTGGGATCGACACTTTTTATAAATGTATCAACACTTTATTCGTTCATCATTTTTGGCATTCAT
* * * *
3922425 TCTAGACAAAAAGCATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTGACA
259 TATAGACAAAAAGAATCAACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCACA
* * *
3922490 TAAAACCGGTATATTTATACC-GATTATATTACAAAATTACCTATTACATTATAATTATCTG-TT
324 TAAAACCGGTATATTGATACCAG-TTATATTAAAAAATTACCTATTACATTATAATTAT-GGATT
*
3922553 TCGATGTTTTTGGG
387 TCGATGTTTCTGGG
* *
3922567 ATCGACACGTATTATAAATGTATCGACAC
1 ATCGACACTTTTTATAAATGTATCGACAC
3922596 ATATGCTTAC
Statistics
Matches: 390, Mismatches: 33, Indels: 11
0.90 0.08 0.03
Matches are distributed among these distances:
398 1 0.00
399 209 0.54
400 174 0.45
401 6 0.02
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.38
Consensus pattern (400 bp):
ATCGACACTTTTTATAAATGTATCGACACTTTATTCATTCATCATTTTTGACATTCATTATGGAC
AAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACC
AGTATATTTATACCGGTTATAATACAAAATTACCTATTACATTATAATTATCTATTTCGATGTGT
TTGGGATCGACACTTTTTATAAATGTATCAACACTTTATTCGTTCATCATTTTTGGCATTCATTA
TAGACAAAAAGAATCAACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATA
AAACCGGTATATTGATACCAGTTATATTAAAAAATTACCTATTACATTATAATTATGGATTTCGA
TGTTTCTGGG
Found at i:3922883 original size:19 final size:19
Alignment explanation
Indices: 3922859--3922907 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
3922849 TTACATCCAC
3922859 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
3922878 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
3922897 ATACAAAATTA
1 ATACAAAATTA
3922908 ACTCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:3924479 original size:18 final size:18
Alignment explanation
Indices: 3924456--3924530 Score: 114
Period size: 18 Copynumber: 4.2 Consensus size: 18
3924446 TCCTCCTCAT
*
3924456 TTCCTCCCCCTTTTCTTC
1 TTCCTCCCTCTTTTCTTC
*
3924474 TTCCTCCCTCTTTTTTTC
1 TTCCTCCCTCTTTTCTTC
*
3924492 TTCCTCCCTCTTTTTTTC
1 TTCCTCCCTCTTTTCTTC
*
3924510 TCCCTCCCTCTTTTCTTC
1 TTCCTCCCTCTTTTCTTC
3924528 TTC
1 TTC
3924531 ATATTTTTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCCTCCCTCTTTTCTTC
Found at i:3924829 original size:21 final size:21
Alignment explanation
Indices: 3924805--3924869 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
3924795 CCCATTATGC
* *
3924805 CTCTAAAGTGTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
3924826 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
3924847 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
3924868 CT
1 CT
3924870 TGATTGTCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.15, C:0.32, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:3924971 original size:15 final size:15
Alignment explanation
Indices: 3924953--3924985 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3924943 ACTCTGTTTT
3924953 CCCTCACCATCATCC
1 CCCTCACCATCATCC
*
3924968 CCCTCACCGTCATCC
1 CCCTCACCATCATCC
3924983 CCC
1 CCC
3924986 AATACAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.64, G:0.03, T:0.18
Consensus pattern (15 bp):
CCCTCACCATCATCC
Found at i:3927567 original size:182 final size:181
Alignment explanation
Indices: 3927254--3927855 Score: 839
Period size: 182 Copynumber: 3.3 Consensus size: 181
3927244 TACGCGTACT
* * * *
3927254 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCATTTAGAGACCA
1 TATTAAAGTATCGACACTTGCAATATATCCGGTATCTCTTTACCGGTTTTGTCATTTCGAGACC-
* * * * *
3927319 GGTTTTATCATATTTTTACCTGTTATATCGTTATGGATCGATGCATTTTTATAAAGTATCGACAC
65 GGTTTTATCATATTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACAC
*
3927384 TTTATAGGCGCTAAAACTGATTCTTGTTTAAATTCACAAAGTGTCGATACTTA
130 TTTATAGGCGCTAAAACTGATTCTT-TTTAAATTCACAATGTGTCGATACTTA
* * *
3927437 TATTAAATTATCGACACTTTCAATATATCCGGTAGT-TCTTTACCGGTTTTGTCTTTTCGAGACC
1 TATTAAAGTATCGACACTTGCAATATATCCGGTA-TCTCTTTACCGGTTTTGTCATTTCGAGACC
*
3927501 GGTTTTATCATATTTTTACATGTTATATCGTTGTGGATTGATACATATTTATAAAGAATCGACAC
65 GGTTTTATCATATTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACAC
*
3927566 TTTATAGGCGCTAAAAC-GACTTCTCCTTTAAATTCACAATGTGTCGATACTTA
130 TTTATAGGCGCTAAAACTGA-TTCT-TTTTAAATTCACAATGTGTCGATACTTA
* * ** * **
3927619 TAGTAAAATATCGACACTTGCAATATATTTGGTATCTCTTTACCAGTTTTGTCATTTCCTGACCG
1 TATTAAAGTATCGACACTTGCAATATATCCGGTATCTCTTTACCGGTTTTGTCATTTCGAGACCG
* * * * *
3927684 GTTTTTTCATATTTTTACTTATTATATCATTGTGGATCGATACATATTTATAAAGAATCAACACT
66 GTTTTATCATATTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
*
3927749 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAATGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGATTCT-TTTTAAATTCACAATGTGTCGATACTTA
* * ** *
3927801 TATTAAAGTATTGACACTTGAAATATATCCAATATCTCTTTATCGGTTTTGTCAT
1 TATTAAAGTATCGACACTTGCAATATATCCGGTATCTCTTTACCGGTTTTGTCAT
3927856 ATTTTTACCT
Statistics
Matches: 374, Mismatches: 40, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
181 3 0.01
182 312 0.83
183 59 0.16
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.41
Consensus pattern (181 bp):
TATTAAAGTATCGACACTTGCAATATATCCGGTATCTCTTTACCGGTTTTGTCATTTCGAGACCG
GTTTTATCATATTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
TTATAGGCGCTAAAACTGATTCTTTTTAAATTCACAATGTGTCGATACTTA
Found at i:3927954 original size:162 final size:162
Alignment explanation
Indices: 3927680--3928045 Score: 545
Period size: 162 Copynumber: 2.3 Consensus size: 162
3927670 TCATTTCCTG
* * * *
3927680 ACCGGTTTTTTCATATTTTTACTTATTATATCATTGTGGATCGATACATATTTATAAAGAATCAA
1 ACCGGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCAA
* *
3927745 CACTTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAATGTGTCGATACTTATATTAAAGT
66 CACTTTATAGGCGCTAAAACTACTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTAAAGT
* * * *
3927810 ATTGACACTTGAAATATATCCAATATCTCTTT
131 ATCGACACGTGAAATATATCCAATAGCGCTTT
* *
3927842 ATCGGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGA
1 ACCGGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCAA
* * *
3927907 CACTTTATAGGCTCTACAACTACTTCTCCTTTAAATTCACTATGTGTCGATACTTATATTAAAGT
66 CACTTTATAGGCGCTAAAACTACTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTAAAGT
* **
3927972 ATCGACACGTGCAATATATCCGGTAGCGCTTT
131 ATCGACACGTGAAATATATCCAATAGCGCTTT
* *
3928004 ACCGGTTTTGTCATATTTTT-CCTGTTATATTGATGTGGATCG
1 ACCGGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCG
3928046 TTATAGTTTT
Statistics
Matches: 183, Mismatches: 21, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
161 20 0.11
162 163 0.89
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (162 bp):
ACCGGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCAA
CACTTTATAGGCGCTAAAACTACTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTAAAGT
ATCGACACGTGAAATATATCCAATAGCGCTTT
Found at i:3929716 original size:52 final size:53
Alignment explanation
Indices: 3929632--3929737 Score: 196
Period size: 52 Copynumber: 2.0 Consensus size: 53
3929622 AAATCACCCC
3929632 AAGTCATTAATGCAATTCAACCTTTAATCTTTTAATTTATCAAACATCACCTT
1 AAGTCATTAATGCAATTCAACCTTTAATCTTTTAATTTATCAAACATCACCTT
*
3929685 AAGTCGTTAATGC-ATTCAACCTTTAATCTTTTAATTTATCAAACATCACCTT
1 AAGTCATTAATGCAATTCAACCTTTAATCTTTTAATTTATCAAACATCACCTT
3929737 A
1 A
3929738 GTGAATTCAT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 40 0.77
53 12 0.23
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.40
Consensus pattern (53 bp):
AAGTCATTAATGCAATTCAACCTTTAATCTTTTAATTTATCAAACATCACCTT
Found at i:3935513 original size:26 final size:27
Alignment explanation
Indices: 3935483--3935535 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
3935473 TGAAATTCGG
*
3935483 TTTAAAAT-TTTATATTTT-TAAAAAAC
1 TTTAAAATATTT-TATTTTCGAAAAAAC
3935509 TTTAAAATATTTTATTTTCGAAAAAAC
1 TTTAAAATATTTTATTTTCGAAAAAAC
3935536 ATCCAACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (27 bp):
TTTAAAATATTTTATTTTCGAAAAAAC
Found at i:3935733 original size:16 final size:17
Alignment explanation
Indices: 3935700--3935743 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
3935690 TAATATCATT
3935700 TCAAA-ACCTAAAATTC
1 TCAAATACCTAAAATTC
*
3935716 TCAAATCCCTAAAA-TC
1 TCAAATACCTAAAATTC
3935732 TCAAATACCTAA
1 TCAAATACCTAA
3935744 TCTCTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (17 bp):
TCAAATACCTAAAATTC
Found at i:3939191 original size:70 final size:67
Alignment explanation
Indices: 3939032--3939195 Score: 183
Period size: 65 Copynumber: 2.4 Consensus size: 67
3939022 AATTAAATCC
* * *
3939032 ATATCACTTTTGAATGTTCTAAATTAAAAGATATTTATCTCTTTAATTTAAATATTACTAGTATA
1 ATATCA-TTTTGAATATTTTAAATTAAAAGATATTTATCTCTTTAATTTAAATATTACAAGTATA
3939097 ATT
65 ATT
* * * *
3939100 AT-TC-TTTTAAATATTTTAAATTAAAAGGTATTTATTATTCATTTAACTTTGAATATTA-AACG
1 ATATCATTTTGAATATTTTAAATTAAAAGATATTTA-T-CTC-TTTAA-TTTAAATATTACAA-G
3939162 -ATAATT
61 TATAATT
3939168 ATATCATTTTGAATATTTTAAATTAAAA
1 ATATCATTTTGAATATTTTAAATTAAAA
3939196 TAATATATAT
Statistics
Matches: 81, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
65 26 0.32
66 1 0.01
67 4 0.05
68 16 0.20
69 13 0.16
70 21 0.26
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (67 bp):
ATATCATTTTGAATATTTTAAATTAAAAGATATTTATCTCTTTAATTTAAATATTACAAGTATAA
TT
Found at i:3939193 original size:35 final size:34
Alignment explanation
Indices: 3939094--3939195 Score: 86
Period size: 35 Copynumber: 3.0 Consensus size: 34
3939084 TATTACTAGT
3939094 ATAATTAT-TC-TTTTAAATATTTTAAATTAAAAG
1 ATAATTATATCATTTT-AATATTTTAAATTAAAAG
* * * * *
3939127 GTATTTATTATTCA-TTTAA-CTTTGAATATTAAACG
1 ATAATTA-TA-TCATTTTAATATTTTAA-ATTAAAAG
3939162 ATAATTATATCATTTTGAATATTTTAAATTAAAA
1 ATAATTATATCATTTT-AATATTTTAAATTAAAA
3939196 TAATATATAT
Statistics
Matches: 51, Mismatches: 10, Indels: 14
0.68 0.13 0.19
Matches are distributed among these distances:
33 8 0.16
34 11 0.22
35 22 0.43
36 10 0.20
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (34 bp):
ATAATTATATCATTTTAATATTTTAAATTAAAAG
Found at i:3939215 original size:64 final size:67
Alignment explanation
Indices: 3939051--3939223 Score: 177
Period size: 70 Copynumber: 2.6 Consensus size: 67
3939041 TTGAATGTTC
* *
3939051 TAAATTAAAAG-ATAT-TTATCTC-TTTAA-TTTAAATATTACTA-GTATAATTATTCTTTTAAA
1 TAAATTAAAAGTATATATTAT-TCATTTAACTTTGAATATTA-AACG-ATAATTATTCTTTTAAA
3939111 TATTT
63 TATTT
* *
3939116 TAAATTAAAAGGTATTTATTATTCATTTAACTTTGAATATTAAACGATAATTATATCATTTTGAA
1 TAAATTAAAA-GTATATATTATTCATTTAACTTTGAATATTAAACGATAATTAT-TC-TTTTAAA
3939181 TATTT
63 TATTT
*
3939186 TAAATTAAAA-TA-ATA-TA-T-ATTTAAGTTTGAATATTAAA
1 TAAATTAAAAGTATATATTATTCATTTAACTTTGAATATTAAA
3939224 AGTTATCTAT
Statistics
Matches: 94, Mismatches: 6, Indels: 17
0.80 0.05 0.15
Matches are distributed among these distances:
64 19 0.20
65 11 0.12
66 3 0.03
67 7 0.07
68 20 0.21
69 13 0.14
70 21 0.22
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (67 bp):
TAAATTAAAAGTATATATTATTCATTTAACTTTGAATATTAAACGATAATTATTCTTTTAAATAT
TT
Found at i:3939235 original size:64 final size:69
Alignment explanation
Indices: 3939032--3939225 Score: 185
Period size: 68 Copynumber: 2.9 Consensus size: 69
3939022 AATTAAATCC
* * * * **
3939032 ATATCACTTTTGAATGTTCTAAATTAAAAG-ATAT-TTATCTC-TTTAA-TTTAAATATTACTAG
1 ATATCA-TTTTAAATATTTTAAATTAAAAGTATATATTAT-TCATTTAACTTTGAATATTAAAAG
3939093 TATAATT
64 -ATAATT
* *
3939100 AT-TC-TTTTAAATATTTTAAATTAAAAGGTATTTATTATTCATTTAACTTTGAATATTAAACGA
1 ATATCATTTTAAATATTTTAAATTAAAA-GTATATATTATTCATTTAACTTTGAATATTAAAAGA
3939163 TAATT
65 TAATT
* *
3939168 ATATCATTTTGAATATTTTAAATTAAAA-TA-ATA-TA-T-ATTTAAGTTTGAATATTAAAAG
1 ATATCATTTTAAATATTTTAAATTAAAAGTATATATTATTCATTTAACTTTGAATATTAAAAG
3939226 TTATCTATAT
Statistics
Matches: 107, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
64 20 0.19
65 20 0.19
66 3 0.03
67 9 0.08
68 21 0.20
69 13 0.12
70 21 0.20
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (69 bp):
ATATCATTTTAAATATTTTAAATTAAAAGTATATATTATTCATTTAACTTTGAATATTAAAAGAT
AATT
Found at i:3950886 original size:26 final size:26
Alignment explanation
Indices: 3950842--3950903 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
3950832 TCTAAAGATC
* * *
3950842 GACGATGGTCGATGGTGACGAGAAGG
1 GACGGTGGTCAATGATGACGAGAAGG
3950868 GACGGTGGTCAATGATGACGAGAAGG
1 GACGGTGGTCAATGATGACGAGAAGG
*
3950894 GGCGGTGGTC
1 GACGGTGGTC
3950904 GTCAGTGAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.24, C:0.13, G:0.47, T:0.16
Consensus pattern (26 bp):
GACGGTGGTCAATGATGACGAGAAGG
Found at i:3955491 original size:13 final size:12
Alignment explanation
Indices: 3955458--3955500 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
3955448 AGTACAAAAT
*
3955458 AAAAAAAACAAA
1 AAAAAAAAGAAA
*
3955470 TAAAAAAAGAAA
1 AAAAAAAAGAAA
3955482 AAAAAGAAAGAAA
1 AAAAA-AAAGAAA
3955495 GAAAAA
1 -AAAAA
3955501 GTTTAAAGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 14 0.54
13 7 0.27
14 5 0.19
ACGTcount: A:0.86, C:0.02, G:0.09, T:0.02
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:3955495 original size:17 final size:18
Alignment explanation
Indices: 3955461--3955500 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
3955451 ACAAAATAAA
*
3955461 AAAAACAAATAAAAAAAG
1 AAAAACAAAGAAAAAAAG
*
3955479 AAAAA-AAAGAAAGAAAG
1 AAAAACAAAGAAAAAAAG
3955496 AAAAA
1 AAAAA
3955501 GTTTAAAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (18 bp):
AAAAACAAAGAAAAAAAG
Found at i:3955833 original size:14 final size:15
Alignment explanation
Indices: 3955814--3955842 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3955804 GGAGTGTTTG
3955814 GTGAGGTT-TTTTTT
1 GTGAGGTTATTTTTT
3955828 GTGAGGTTATTTTTT
1 GTGAGGTTATTTTTT
3955843 TTACTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.10, C:0.00, G:0.28, T:0.62
Consensus pattern (15 bp):
GTGAGGTTATTTTTT
Found at i:3961526 original size:15 final size:16
Alignment explanation
Indices: 3961506--3961561 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 16
3961496 CTTTAACCTT
3961506 ACAACAC-TTACCACG
1 ACAACACATTACCACG
3961521 ACAACACCATTTACCACG
1 ACAACA-CA-TTACCACG
*
3961539 ACAACACCATTTGCCACG
1 ACAACA-CA-TTACCACG
3961557 ACAAC
1 ACAAC
3961562 GCCATTCACA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
15 6 0.16
16 1 0.03
18 30 0.81
ACGTcount: A:0.39, C:0.39, G:0.07, T:0.14
Consensus pattern (16 bp):
ACAACACATTACCACG
Found at i:3961536 original size:18 final size:18
Alignment explanation
Indices: 3961513--3961567 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
3961503 CTTACAACAC
3961513 TTACCACGACAACACCAT
1 TTACCACGACAACACCAT
3961531 TTACCACGACAACACCAT
1 TTACCACGACAACACCAT
* *
3961549 TTGCCACGACAACGCCAT
1 TTACCACGACAACACCAT
3961567 T
1 T
3961568 CACATTTCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.35, C:0.38, G:0.09, T:0.18
Consensus pattern (18 bp):
TTACCACGACAACACCAT
Found at i:3967746 original size:35 final size:35
Alignment explanation
Indices: 3967700--3967774 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
3967690 TTCATGTTCA
*
3967700 AAATTCCAAAATACTTCAATTACATTCTAAACCCC
1 AAATTCAAAAATACTTCAATTACATTCTAAACCCC
* *
3967735 AAATTCAAAAATACTTCAATTATATTCTAAACCCT
1 AAATTCAAAAATACTTCAATTACATTCTAAACCCC
3967770 AAATT
1 AAATT
3967775 GAAATATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (35 bp):
AAATTCAAAAATACTTCAATTACATTCTAAACCCC
Found at i:3967810 original size:35 final size:35
Alignment explanation
Indices: 3967770--3967847 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
3967760 TCTAAACCCT
*
3967770 AAATTGAAATATTTTAGAATTTGGGGTTTAAAATG
1 AAATTGAAATATTTTAGAATTTGGGATTTAAAATG
* * * *
3967805 TAATTGAATTATTTTGGAATTTGGGATTTAGAATG
1 AAATTGAAATATTTTAGAATTTGGGATTTAAAATG
3967840 AAATTGAA
1 AAATTGAA
3967848 GACTGTGTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (35 bp):
AAATTGAAATATTTTAGAATTTGGGATTTAAAATG
Found at i:3969565 original size:50 final size:50
Alignment explanation
Indices: 3969488--3969582 Score: 172
Period size: 50 Copynumber: 1.9 Consensus size: 50
3969478 CTCCCCCTCT
*
3969488 TCTATGTGGTTACATGATTATCAAATATTTGGAATATACATTGAAGTTCA
1 TCTATGTGGTTACATGATTATCAAATATTGGGAATATACATTGAAGTTCA
*
3969538 TCTATGTGGTTACATGATTATCGAATATTGGGAATATACATTGAA
1 TCTATGTGGTTACATGATTATCAAATATTGGGAATATACATTGAA
3969583 TTTCTTAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (50 bp):
TCTATGTGGTTACATGATTATCAAATATTGGGAATATACATTGAAGTTCA
Found at i:3970087 original size:40 final size:41
Alignment explanation
Indices: 3970042--3970223 Score: 149
Period size: 41 Copynumber: 4.5 Consensus size: 41
3970032 TACTTTAACA
*
3970042 GTGTTTTTATATAAACGCCGCTAAATACT-GTACTTTAGTG
1 GTGTTTTTATACAAACGCCGCTAAATACTAGTACTTTAGTG
* * * *
3970082 GTGTTTTTGTACAAACACCACT-AATGACTCGTACTTTAGTG
1 GTGTTTTTATACAAACGCCGCTAAAT-ACTAGTACTTTAGTG
* * * ** * *
3970123 GCGTTTTTGTATAAAC-ATGACTAAATA-TTGTATTTTAGT-
1 GTGTTTTTATACAAACGCCG-CTAAATACTAGTACTTTAGTG
* * *
3970162 GTCGTTTTAAGCACAATCGCCGCTAAATACTAGTACTTTAGTG
1 GT-GTTTTTA-TACAAACGCCGCTAAATACTAGTACTTTAGTG
*
3970205 GTATTTTTATACAAACGCC
1 GTGTTTTTATACAAACGCC
3970224 ACAATTTATT
Statistics
Matches: 108, Mismatches: 25, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
39 4 0.04
40 36 0.33
41 47 0.44
42 19 0.18
43 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (41 bp):
GTGTTTTTATACAAACGCCGCTAAATACTAGTACTTTAGTG
Found at i:3970353 original size:19 final size:20
Alignment explanation
Indices: 3970321--3970358 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
3970311 CCCGCGCGCT
* *
3970321 TTGAATTTTTTTAA-ATATG
1 TTGAAATTTATTAATATATG
3970340 TTGAAATTTATTAATATAT
1 TTGAAATTTATTAATATAT
3970359 ACTACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (20 bp):
TTGAAATTTATTAATATATG
Found at i:3972281 original size:20 final size:20
Alignment explanation
Indices: 3972256--3972295 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3972246 AAGGGTAAGC
3972256 GACGAATATAGAAATGGAGT
1 GACGAATATAGAAATGGAGT
3972276 GACGAATATAGAAATGGAGT
1 GACGAATATAGAAATGGAGT
3972296 CAAAACTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.30, T:0.20
Consensus pattern (20 bp):
GACGAATATAGAAATGGAGT
Found at i:3972524 original size:21 final size:21
Alignment explanation
Indices: 3972498--3972556 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
3972488 TGATTTATTA
3972498 TTATGGATTTCAAGTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
*
3972519 TTATGGATTTCAAATTTCTTG
1 TTATGGATTTCAAGTTTCTTG
*
3972540 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
3972557 ATTGGATACT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.22, C:0.08, G:0.19, T:0.51
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:3977432 original size:2 final size:2
Alignment explanation
Indices: 3977425--3977451 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3977415 TTGAGTGGTT
3977425 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
3977452 TGTGGACGTT
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:3985228 original size:18 final size:18
Alignment explanation
Indices: 3985171--3985231 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
3985161 TCACTTAAAC
3985171 TATAATAAAAATATATTT
1 TATAATAAAAATATATTT
** *
3985189 TA-AGATAACTCAT-TA-AT
1 TATA-ATAA-AAATATATTT
3985206 TATAATAAAAATATATTT
1 TATAATAAAAATATATTT
3985224 TATAATAA
1 TATAATAA
3985232 CTCACTATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
16 2 0.06
17 10 0.31
18 18 0.56
19 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (18 bp):
TATAATAAAAATATATTT
Found at i:3986134 original size:11 final size:11
Alignment explanation
Indices: 3986120--3986152 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3986110 TGATTTTTAT
3986120 TTAATTTATAA
1 TTAATTTATAA
3986131 TTAATTT-TAA
1 TTAATTTATAA
*
3986141 TTATTTTATAA
1 TTAATTTATAA
3986152 T
1 T
3986153 ATAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTAATTTATAA
Found at i:3988980 original size:10 final size:10
Alignment explanation
Indices: 3988967--3989016 Score: 64
Period size: 10 Copynumber: 4.8 Consensus size: 10
3988957 TAAAAGTTAG
3988967 TAAAAAAAAA
1 TAAAAAAAAA
*
3988977 TAAACAAAAA
1 TAAAAAAAAA
*
3988987 CAATAAAAAAA
1 TAA-AAAAAAA
3988998 TTAAAAAAAAA
1 -TAAAAAAAAA
3989009 TAAAAAAA
1 TAAAAAAA
3989017 TAAAAGAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
10 19 0.56
11 13 0.38
12 2 0.06
ACGTcount: A:0.84, C:0.04, G:0.00, T:0.12
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:3989004 original size:19 final size:18
Alignment explanation
Indices: 3988970--3989021 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 18
3988960 AAGTTAGTAA
3988970 AAAAAAATAAACAAAAACAAT
1 AAAAAAAT-AA-AAAAA-AAT
3988991 AAAAAAATTAAAAAAAAAT
1 AAAAAAA-TAAAAAAAAAT
3989010 AAAAAAATAAAA
1 AAAAAAATAAAA
3989022 GAAAGTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.17
19 10 0.33
20 5 0.17
21 9 0.30
22 1 0.03
ACGTcount: A:0.85, C:0.04, G:0.00, T:0.12
Consensus pattern (18 bp):
AAAAAAATAAAAAAAAAT
Found at i:3990133 original size:14 final size:14
Alignment explanation
Indices: 3990114--3990151 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
3990104 AATAAATGAA
3990114 AATATATATTATGT
1 AATATATATTATGT
*
3990128 AATATA-ATAATGT
1 AATATATATTATGT
3990141 AAT-TATATTAT
1 AATATATATTAT
3990152 ATGAAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 2 0.10
13 13 0.62
14 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (14 bp):
AATATATATTATGT
Found at i:3990842 original size:36 final size:37
Alignment explanation
Indices: 3990795--3990883 Score: 162
Period size: 36 Copynumber: 2.4 Consensus size: 37
3990785 CGAGGATCTG
*
3990795 TGTGTTTCAAGAGAAACATTTTCAAAGG-TTTTTTTT
1 TGTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTT
3990831 TGTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTT
1 TGTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTT
3990868 TGTGTTTCAAGAGAAA
1 TGTGTTTCAAGAGAAA
3990884 ATTGTCTCCA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 27 0.53
37 24 0.47
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (37 bp):
TGTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTT
Found at i:3990944 original size:37 final size:38
Alignment explanation
Indices: 3990870--3990953 Score: 98
Period size: 37 Copynumber: 2.2 Consensus size: 38
3990860 TTTTTTTTTG
* * * * *
3990870 TGTTTCAAGAGAAAATTGTCTCCAGGGAGGCAGAATTT
1 TGTTTCAAGAGAAAACTGTCTCAAGAGAGACAAAATTT
3990908 TGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAATTT
1 TGTTTCAAGAGAAAACTGTCTCAAGAGAGACAAAATTT
**
3990945 CATTTCAAG
1 TGTTTCAAG
3990954 GGAGACAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
37 28 0.72
38 11 0.28
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (38 bp):
TGTTTCAAGAGAAAACTGTCTCAAGAGAGACAAAATTT
Found at i:3990973 original size:21 final size:22
Alignment explanation
Indices: 3990927--3990977 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
3990917 AGAAACTGTC
3990927 TCAAGAGAGACAAAATTTCATT
1 TCAAGAGAGACAAAATTTCATT
* *
3990949 TCAAGGGAGACAAAATTT-GTT
1 TCAAGAGAGACAAAATTTCATT
3990970 TCAAGAGA
1 TCAAGAGA
3990978 AACTATCTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (22 bp):
TCAAGAGAGACAAAATTTCATT
Found at i:3990996 original size:36 final size:36
Alignment explanation
Indices: 3990949--3991263 Score: 310
Period size: 36 Copynumber: 8.9 Consensus size: 36
3990939 AAATTTCATT
* *
3990949 TCAAGGGAGACAAAATTTGTTTCAAGAGAAACTATC
1 TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTC
* *
3990985 TCAAGAGAGACAAAACTTAG-TTCTAAAAGAAACTGTC
1 TCAAGAGAGACAAAA-TTTGTTTC-AAGAGAAACTGTC
* *
3991022 TCAAGGGAGACAAAATTTGTTTCAAG-GAAAACATAT-
1 TCAAGAGAGACAAAATTTGTTTCAAGAG-AAAC-TGTC
* *
3991058 TC-A-A-AG----ATTTTGTTTCAAGGGAAACTGTC
1 TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTC
* * *
3991087 TCAAGAGAGACAAAATTTGTTTCAAGGGAAATTGTA
1 TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTC
* *
3991123 TCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTC
1 TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTC
* *
3991159 TCAAGATAGACAAAATTTGTTTCAAGAGAAACTATC
1 TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTC
* * *
3991195 TCAAGGGAGACAAAATTTGTTTCAAAAAAGAAACCGTC
1 TCAAGAGAGACAAAATTTGTTTC--AAGAGAAACTGTC
* * *
3991233 TCAAG-GGGATAAAATTTGTTTCGAGAGAAAC
1 TCAAGAGAGACAAAATTTGTTTCAAGAGAAAC
3991264 AATCTCAAAG
Statistics
Matches: 233, Mismatches: 30, Indels: 33
0.79 0.10 0.11
Matches are distributed among these distances:
28 2 0.01
29 18 0.08
30 2 0.01
31 1 0.00
32 2 0.01
33 2 0.01
35 9 0.04
36 134 0.58
37 48 0.21
38 15 0.06
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (36 bp):
TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTC
Found at i:3991148 original size:21 final size:21
Alignment explanation
Indices: 3991087--3991148 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
3991077 GGAAACTGTC
*
3991087 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTATT
3991108 TCAAG-G-G---AAATTGTA--
1 TCAAGAGAGACAAAATT-TATT
3991123 TCAAGAGAGACAAAATTTATT
1 TCAAGAGAGACAAAATTTATT
3991144 TCAAG
1 TCAAG
3991149 GGAAACTGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 16
0.65 0.02 0.33
Matches are distributed among these distances:
15 5 0.16
16 6 0.19
17 2 0.06
19 3 0.09
20 6 0.19
21 10 0.31
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTATT
Found at i:3992719 original size:95 final size:95
Alignment explanation
Indices: 3992596--3992889 Score: 509
Period size: 95 Copynumber: 3.1 Consensus size: 95
3992586 CATTGTATAA
* * * *
3992596 ATATTATAATCAACTTTATAAGGTTAGCTGAATA-TTATCCATAAAGCCAGGGCGTTTAACCAAT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAA-ACTTATCCATAAAGCCGGGGCGTTTAACCAAT
3992660 TGCTTTAGAGAGACAACTCAAGCTTTATTGT
65 TGCTTTAGAGAGACAACTCAAGCTTTATTGT
3992691 ATATTATAATCACCTTTATCAGGCTAGCTGAAACTTATCCATAAAGCCGGGGCGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAAACTTATCCATAAAGCCGGGGCGTTTAACCAATT
*
3992756 GCTTTAGAGAGACAACTCAAACTTTATTGT
66 GCTTTAGAGAGACAACTCAAGCTTTATTGT
3992786 ATATTATAATCACCTTTATCAGGCTAGCTGAAACTTATCCATAAAGCCGGGGCGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAAACTTATCCATAAAGCCGGGGCGTTTAACCAATT
*
3992851 GCTATAGAGAGACAACTCAAGCTTTATTGT
66 GCTTTAGAGAGACAACTCAAGCTTTATTGT
3992881 ATATATATA
1 ATAT-TATA
3992890 TAATTATAAT
Statistics
Matches: 190, Mismatches: 7, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
94 1 0.01
95 185 0.97
96 4 0.02
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (95 bp):
ATATTATAATCACCTTTATCAGGCTAGCTGAAACTTATCCATAAAGCCGGGGCGTTTAACCAATT
GCTTTAGAGAGACAACTCAAGCTTTATTGT
Found at i:3995836 original size:23 final size:23
Alignment explanation
Indices: 3995809--3995875 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
3995799 TATCTACCCC
3995809 ACATGCTTATTATTCTTACCCGG
1 ACATGCTTATTATTCTTACCCGG
*
3995832 ACATG---A-T-CTC-TATCCC--
1 ACATGCTTATTATTCTTA-CCCGG
3995848 ACATGCTTATTATTCTTACCCGG
1 ACATGCTTATTATTCTTACCCGG
3995871 ACATG
1 ACATG
3995876 ATCTCTATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 18
0.62 0.04 0.34
Matches are distributed among these distances:
16 5 0.15
17 2 0.06
18 5 0.15
19 2 0.06
20 2 0.06
21 5 0.15
22 2 0.06
23 10 0.30
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (23 bp):
ACATGCTTATTATTCTTACCCGG
Found at i:3995849 original size:39 final size:39
Alignment explanation
Indices: 3995793--3995893 Score: 175
Period size: 39 Copynumber: 2.6 Consensus size: 39
3995783 GTCCTAACGC
* *
3995793 ACATGATATCTACCCCACATGCTTATTATTCTTACCCGG
1 ACATGATCTCTATCCCACATGCTTATTATTCTTACCCGG
3995832 ACATGATCTCTATCCCACATGCTTATTATTCTTACCCGG
1 ACATGATCTCTATCCCACATGCTTATTATTCTTACCCGG
*
3995871 ACATGATCTCTATCCCGCATGCT
1 ACATGATCTCTATCCCACATGCT
3995894 AATTTCAAAC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.24, C:0.32, G:0.11, T:0.34
Consensus pattern (39 bp):
ACATGATCTCTATCCCACATGCTTATTATTCTTACCCGG
Found at i:3997026 original size:12 final size:11
Alignment explanation
Indices: 3996995--3997033 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
3996985 TTAGTTTTAA
3996995 AAAAATAAAAT
1 AAAAATAAAAT
*
3997006 AAGAATAAAAT
1 AAAAATAAAAT
3997017 AATAAATAAAAT
1 AA-AAATAAAAT
3997029 AAAAA
1 AAAAA
3997034 AATATTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:3999139 original size:12 final size:12
Alignment explanation
Indices: 3999122--3999146 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3999112 ATTTAAACAA
3999122 ATATATTTATAT
1 ATATATTTATAT
3999134 ATATATTTATAT
1 ATATATTTATAT
3999146 A
1 A
3999147 AAATAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATATTTATAT
Found at i:4000850 original size:123 final size:123
Alignment explanation
Indices: 4000722--4001301 Score: 910
Period size: 123 Copynumber: 4.7 Consensus size: 123
4000712 GAATTAAGGC
* * * *
4000722 AAGGTTGAATAAGTTCTTCTCATTATGAAATTCTTTTTCCTCATCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* ** * * * *
4000787 GAACTCTAACTGGAAATGTTGATGTTGATCTATCTCTTTCTGCGATAGTGTCAAGCAA
66 GAACTTTCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCATGCAA
*
4000845 AAGGTTGAACAATTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* *
4000910 GAACTTTCTCTGGAAATGTT-AGTGCTGATCTATCTCCTTCTGGGATAGACTCATGCAA
66 GAACTTTCTCTGGAAATGTTGA-TGCTGATCTATCTCCTTCTGCGATAGAGTCATGCAA
* * * *
4000968 AAGGTTGAACAAGTTATTCTCATTATGAACTTTTTCTTCCTCTTCAGATGGGTTCTTCTTATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * *
4001033 GAACTTTCTTTGGAAATGTTGGTGCTGATCTATCTCCTTCTACGATAGAGTCATGCAA
66 GAACTTTCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCATGCAA
*
4001091 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* *
4001156 GAACTTTCTCTGGAAATATTGGTGCTGATCTATCTCCTTCTGCGATAGAGTCATGCAA
66 GAACTTTCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCATGCAA
* *
4001214 AAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCTTCCTCTTAAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
4001279 GAACTTTCTCTGGAAATGTTGAT
66 GAACTTTCTCTGGAAATGTTGAT
4001302 CCATCGAGTG
Statistics
Matches: 418, Mismatches: 37, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
122 1 0.00
123 417 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTTTCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCATGCAA
Found at i:4001362 original size:36 final size:37
Alignment explanation
Indices: 4001316--4001466 Score: 94
Period size: 36 Copynumber: 4.1 Consensus size: 37
4001306 CGAGTGATGG
* *
4001316 AAATTTTTGTTTCTAGTGAAACCGTCTCAAGTGAGAC
1 AAATTCTTGTTTCTAGTGAAACAGTCTCAAGTGAGAC
* ** * *
4001353 GAA-TCTTGTTT-TAAGAAAAACAATCTCAAGTGAGAT
1 AAATTCTTGTTTCT-AGTGAAACAGTCTCAAGTGAGAC
* * * * *
4001389 AAATTGTTGTTTCGAGTGAAACTGTATCGAGTGAGAC
1 AAATTCTTGTTTCTAGTGAAACAGTCTCAAGTGAGAC
* * ** * *
4001426 ACAGT-TTGTTT-TAAGAAAAACAATCTCAAGTGAGAT
1 AAATTCTTGTTTCT-AGTGAAACAGTCTCAAGTGAGAC
4001462 AAATT
1 AAATT
4001467 ACTATTTGAA
Statistics
Matches: 81, Mismatches: 29, Indels: 9
0.68 0.24 0.08
Matches are distributed among these distances:
35 1 0.01
36 52 0.64
37 28 0.35
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (37 bp):
AAATTCTTGTTTCTAGTGAAACAGTCTCAAGTGAGAC
Found at i:4001399 original size:73 final size:73
Alignment explanation
Indices: 4001316--4001466 Score: 225
Period size: 73 Copynumber: 2.1 Consensus size: 73
4001306 CGAGTGATGG
* * *
4001316 AAATTTTTGTTTCTAGTGAAACCGTCTCAAGTGAGACGA-A-TCTTGTTTTAAGAAAAACAATCT
1 AAATTGTTGTTTCGAGTGAAACCGTATCAAGTGAGAC-ACAGT-TTGTTTTAAGAAAAACAATCT
4001379 CAAGTGAGAT
64 CAAGTGAGAT
* *
4001389 AAATTGTTGTTTCGAGTGAAACTGTATCGAGTGAGACACAGTTTGTTTTAAGAAAAACAATCTCA
1 AAATTGTTGTTTCGAGTGAAACCGTATCAAGTGAGACACAGTTTGTTTTAAGAAAAACAATCTCA
4001454 AGTGAGAT
66 AGTGAGAT
4001462 AAATT
1 AAATT
4001467 ACTATTTGAA
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
72 1 0.01
73 69 0.97
74 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (73 bp):
AAATTGTTGTTTCGAGTGAAACCGTATCAAGTGAGACACAGTTTGTTTTAAGAAAAACAATCTCA
AGTGAGAT
Found at i:4003675 original size:75 final size:74
Alignment explanation
Indices: 4003515--4003745 Score: 286
Period size: 75 Copynumber: 3.1 Consensus size: 74
4003505 ATGCCCTAAC
* * * * *
4003515 ATTTGCTGATACAGACGTTCAAAATGCACCGACATTCCTGATTCTGATT-AAAAGGGCTTTCAGC
1 ATTTGCTGATACAAACGTTCAAAATGCATCAATATT-CTGATTCTGATTGAAATGGGCTTTCAGC
*
4003579 ATGCCCCATT
65 ATGCCCCAGT
*
4003589 ATTTGCTGATACAAATGTTCAAAATG-AGTCAATATTCTTGATTCTGATTGAAATGGGCTTTCAG
1 ATTTGCTGATACAAACGTTCAAAATGCA-TCAATATTC-TGATTCTGATTGAAATGGGCTTTCAG
4003653 CATGCCCCAGT
64 CATGCCCCAGT
* ** * *
4003664 ATTTGCTGATACAAACGTTCAAAATGCATTAATATTCCAACTTCTGATTGAAATGGGTTTTCAAC
1 ATTTGCTGATACAAACGTTCAAAATGCATCAATATTCTGA-TTCTGATTGAAATGGGCTTTCAGC
* *
4003729 ATGCTCCAGC
65 ATGCCCCAGT
4003739 ATTTGCT
1 ATTTGCT
4003746 TCTTGTTGAT
Statistics
Matches: 137, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
73 2 0.01
74 41 0.30
75 93 0.68
76 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (74 bp):
ATTTGCTGATACAAACGTTCAAAATGCATCAATATTCTGATTCTGATTGAAATGGGCTTTCAGCA
TGCCCCAGT
Found at i:4010077 original size:12 final size:12
Alignment explanation
Indices: 4010060--4010084 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4010050 AGATGCAAAG
4010060 ATGCAAATACAA
1 ATGCAAATACAA
4010072 ATGCAAATACAA
1 ATGCAAATACAA
4010084 A
1 A
4010085 GATGTGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
ATGCAAATACAA
Done.