Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, 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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 36 of 64
Found at i:5551401 original size:127 final size:127
Alignment explanation
Indices: 5550647--5551743 Score: 683
Period size: 125 Copynumber: 8.6 Consensus size: 127
5550637 AAAAAAAAGG
* * * * * * * **
5550647 CCTTCAATAATCTCCTGACAAAAACTTGAAAG-GGATTATTGAAGGC-GTTTTCAGTAAAAAAAT
1 CCTTCAATAATCCCCTGATAAAAAATT-AGAGTGGATTATTGAAAGCATTTTTTACAAAAAAAAT
* * * * * * * * * * * **
5550710 GCCTTCAATAAATTACTTAAAAAAATTTTAAGCGATTATTGAAGGCGTTTATGACTAAAAACG
65 ACCTTCAATAATTTTCTTTAAAATATTTGATGGGATTATTAAAGGCATTTGTGACTAAAAATA
* * * * * * *
5550773 CTTTCAATAATCCCC-AATAAAATATTAAAGGGGATTATTGAAGGCAGTTTTTACAAAAAAAAAA
1 CCTTCAATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAAGCATTTTTTAC--AAAAAAAA
* * * * ** * * * **
5550837 AACAATTTCAATATTTTTCTTTAAAA-ATTTTTAAAGGATTATTGAAGGCGTTTTTAGTTTAAAA
64 TAC--CTTCAATAATTTTCTTTAAAATA-TTTGATGGGATTATTAAAGGCATTTGT-GACTAAAA
**
5550901 ACG
125 ATA
* * *** *
5550904 CATTCAATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAAG--TGTTTTATGCAAAAAATT
1 CCTTCAATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAAGCATTTTTTACAAAAAAAATA
* *
5550967 TCTTCAATAA-TTTCTTTTAAAATATTTGAGGGGATTATTGAAA-GCATTTGTGACTAAAAATA
66 CCTTCAATAATTTTC-TTTAAAATATTTGATGGGATTATT-AAAGGCATTTGTGACTAAAAATA
* * * * * *
5551029 CCTTAAATAATCCCCTGATAAAAAATTAGAGTTGCTTATTGAAGGCATTTTCTACAAAAAAAATG
1 CCTTCAATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAAGCATTTTTTACAAAAAAAATA
* * * * * * * * * *
5551094 CCTTCAATAATTTTCATCACATTTTTTCATGGGTTTATTAAAGGCATTTTTTTGTCTAAAAATG
66 CCTTCAATAATTTTCTTTAAAATATTTGATGGGATTATTAAAGGCA--TTTGTGACTAAAAATA
* * ** *
5551158 CCTTCAATAATCCCCT-ATTAAAAAATTGGAATGGATT-TCT-AAAGGCGATTTCTGCAAAAAAA
1 CCTTCAATAATCCCCTGA-TAAAAAATTAGAGTGGATTAT-TGAAA-GC-ATTT-T-----TTAC
* * * * *
5551220 AAAAAAAATACCTTCAATAATTTCCTTTAAAATATTTAAAGGGATTATTGAAGGCGTTTGTGACT
56 AAAAAAAATACCTTCAATAATTTTCTTTAAAATATTTGATGGGATTATTAAAGGCATTTGTGACT
5551285 AAAAATA
121 AAAAATA
* * * * *
5551292 CCCTCAATAATGCCTTGATAAAAAATTGGAGTGAATTATTGAAAGCATTTTTTACAAAAAAAATA
1 CCTTCAATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAAGCATTTTTTACAAAAAAAATA
* * * * * * *
5551357 CCTTCAATAATTTTCTTTACAATTTTTTATGGGATTGTTAAAGGCATTTTTAGTCTAAAAATG
66 CCTTCAATAATTTTCTTTAAAATATTTGATGGGATTATTAAAGGCATTTGT-GACTAAAAATA
* * **
5551420 CCTT-AATAATCTCCTGATAAAAAATTAGAGTGGATTATTGAAAGTATTTTTT-GTAAAAAAATA
1 CCTTCAATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAAGCATTTTTTACAAAAAAAATA
* * * ** *
5551483 TCTTCAATAA-TTTCATTTAAAATATTTGA-GTGATTATTGAAGGTGTTTGTGACTTAAAATA
66 CCTTCAATAATTTTC-TTTAAAATATTTGATGGGATTATTAAAGGCATTTGTGACTAAAAATA
** *** * * * * *
5551544 TTTTCAATAATCTTTTGATAAAAAATTACAGTTGATTATT-AAAGGTATTTTTTGC-AAAAAAAC
1 CCTTCAATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAA-GCATTTTTTACAAAAAAAAT
* * * ** * * **
5551607 ACCTTCAATAATTTAT-TTTAAAATTTTTG-TGAGATTATTGAAGATATTTTTAGTCTAAAAACG
65 ACCTTCAATAATTT-TCTTTAAAATATTTGATGGGATTATTAAAGGCATTTGT-GACTAAAAATA
* * * **
5551670 CCTTCAATAATCCCCTGTTAAAAAATT-GAAATGGATTATT-AAATGC-GTTTTTA-GTAAAAAA
1 CCTTCAATAATCCCCTGATAAAAAATTAG-AGTGGATTATTGAAA-GCATTTTTTACAAAAAAAA
5551731 TACCTTCAATAAT
64 TACCTTCAATAAT
5551744 GTTAAATGTT
Statistics
Matches: 761, Mismatches: 168, Indels: 85
0.75 0.17 0.08
Matches are distributed among these distances:
124 17 0.02
125 200 0.26
126 126 0.17
127 139 0.18
128 34 0.04
129 47 0.06
130 49 0.06
131 24 0.03
132 25 0.03
133 4 0.01
134 46 0.06
135 5 0.01
136 45 0.06
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (127 bp):
CCTTCAATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAAGCATTTTTTACAAAAAAAATA
CCTTCAATAATTTTCTTTAAAATATTTGATGGGATTATTAAAGGCATTTGTGACTAAAAATA
Found at i:5551504 original size:63 final size:60
Alignment explanation
Indices: 5551437--5551629 Score: 167
Period size: 62 Copynumber: 3.1 Consensus size: 60
5551427 AATCTCCTGA
5551437 TAAAAAATTAGAGTGGATTATTGAAAGTATTTTTTGTAAAAAAATATCTTCAATAATTTCATT
1 TAAAAAATTAGAGT-GATTATTGAAAGTATTTTTTG-AAAAAAATATCTTCAATAATTT-ATT
* * * * * ** *
5551500 TAAAATATTTGAGTGATTATTGAAGGT-GTTTGTGACTTAAAATATTTTCAATAATCTT-TT
1 TAAAAAATTAGAGTGATTATTGAAAGTATTTTTTGA-AAAAAATATCTTCAATAAT-TTATT
* * *
5551560 GATAAAAAATTACAGTTGATTATT-AAAGGTATTTTTTGCAAAAAAACACCTTCAATAATTTATT
1 --TAAAAAATTAGAG-TGATTATTGAAA-GTATTTTTTG-AAAAAAATATCTTCAATAATTTATT
*
5551624 TTAAAA
1 TAAAAA
5551630 TTTTTGTGAG
Statistics
Matches: 101, Mismatches: 20, Indels: 19
0.72 0.14 0.14
Matches are distributed among these distances:
60 3 0.03
61 21 0.21
62 31 0.31
63 24 0.24
64 21 0.21
65 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.41
Consensus pattern (60 bp):
TAAAAAATTAGAGTGATTATTGAAAGTATTTTTTGAAAAAAATATCTTCAATAATTTATT
Found at i:5556447 original size:13 final size:13
Alignment explanation
Indices: 5556429--5556466 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
5556419 CTTCTCAATA
5556429 TCTTTATATATGT
1 TCTTTATATATGT
*
5556442 TCTTTACATATGT
1 TCTTTATATATGT
*
5556455 TTTTTATATATG
1 TCTTTATATATG
5556467 CGCTTTTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.61
Consensus pattern (13 bp):
TCTTTATATATGT
Found at i:5558081 original size:160 final size:159
Alignment explanation
Indices: 5557661--5558372 Score: 630
Period size: 161 Copynumber: 4.4 Consensus size: 159
5557651 AAATTTACAG
** * * *
5557661 TTATTGTTCTATTTTAATGGTTTTGATAGTTTCAAGACATGATATTAAACTTATTC-AAATTATT
1 TTATTGTTCTATTTTAA--CATTTGATAGCTTCAATACATGATATTAAACTT-TTCGAAATGATT
* * * * * *
5557725 GAACTTAGTTTCCAC-GATTGATATATATGAAAAAGTTAATGTTTGCATCTATTTAGGACTTTTT
63 GAACTTGGTTTTCACAG-TTGATATATGTGAAAAAGTTATTGTTTACCTCTATTTAGGACTTTTT
* * * *
5557789 ATGTTATTAATAGGTAATAATACAAATTT-TCTA
127 ATGTTGTTAAAAGGCAAAAATACAAATTTGT-TA
* * * *
5557822 TTATTGTTCTATTTTAATAGTTTGGATAACTCCAATACATGATATTAAACTTATCTG-AATGATT
1 TTATTGTTCTATTTTAACA-TTT-GATAGCTTCAATACATGATATTAAACTTTTC-GAAATGATT
* * * * **
5557886 AAACTTGGTTTTCATAGTTGATATGTGTGAAAAAGTTATCGTTTATGTCTATTTAGGACTATTTT
63 GAACTTGGTTTTCACAGTTGATATATGTGAAAAAGTTATTGTTTACCTCTATTTAGGACT-TTTT
* *
5557951 -TGTTGTTAAAATGCAAAAATACAAATTTGTTG
127 ATGTTGTTAAAAGGCAAAAATACAAATTTGTTA
* * * * *
5557983 TTATTATTCTATTTTAACATTTGTATGGCTTTATTACATGATATTAAACAATTTC-AAATGATTG
1 TTATTGTTCTATTTTAACATTTG-ATAGCTTCAATACATGATATTAAAC-TTTTCGAAATGATTG
** * *
5558047 AACTTGGTTTTTGCAGTTGATATATGTAAAAAAGTTATTGTTTACCTCTGTTTAGGA-TTTTTCA
64 AACTTGGTTTTCACAGTTGATATATGTGAAAAAGTTATTGTTTACCTCTATTTAGGACTTTTT-A
** * * *
5558111 AATCGTTAAAAGGTAAAAATACAAATTTGCTA
128 TGTTGTTAAAAGGCAAAAATACAAATTTGTTA
* * * *
5558143 TTATTGTTTTGTTTTAGCAATTTAGATAGCTTCAATACATTATATTAAACTTTTTCGAAA-GATT
1 TTATTGTTCTATTTTAAC-ATTT-GATAGCTTCAATACATGATATTAAAC-TTTTCGAAATGATT
* * * * * * *
5558207 GAACTTGGTATTCACAATTGATATATGTGACAAAGTTGTTGTTTACCTCTGTTAATGACTTTTTT
63 GAACTTGGTTTTCACAGTTGATATATGTGAAAAAGTTATTGTTTACCTCTATTTAGGAC-TTTTT
* * * *
5558272 TTGCTGTTAAAAGGCAAAAATACAAAGTTATTA
127 ATGTTGTTAAAAGGCAAAAATACAAATTTGTTA
* *** * * *
5558305 TTAGTCACCATGTTTTAACAGTTTAGATAGCTTCAATACATGATATTAAACTTGTCCAAATGATT
1 TTATTGTTC-TATTTTAACA-TTT-GATAGCTTCAATACATGATATTAAACTTTTCGAAATGATT
5558370 GAA
63 GAA
5558373 TTTAATTTCC
Statistics
Matches: 443, Mismatches: 88, Indels: 38
0.78 0.15 0.07
Matches are distributed among these distances:
158 4 0.01
159 2 0.00
160 122 0.28
161 220 0.50
162 46 0.10
163 49 0.11
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (159 bp):
TTATTGTTCTATTTTAACATTTGATAGCTTCAATACATGATATTAAACTTTTCGAAATGATTGAA
CTTGGTTTTCACAGTTGATATATGTGAAAAAGTTATTGTTTACCTCTATTTAGGACTTTTTATGT
TGTTAAAAGGCAAAAATACAAATTTGTTA
Found at i:5558134 original size:321 final size:322
Alignment explanation
Indices: 5557697--5558297 Score: 719
Period size: 321 Copynumber: 1.9 Consensus size: 322
5557687 TAGTTTCAAG
* * *
5557697 ACATGATATTAAACTTATTCAAATTATTGAACTTAGTTTCCACGATTGATATATATGAAAAAGTT
1 ACATGATATTAAACATATTCAAATGATTGAACTTAGTTTCCACGATTGATATATATAAAAAAGTT
* ** * * * *
5557762 AATGTTTGCATCTATTTAGGACTTTTTATGTTATTAATAGGTAATAATACAAATTTTCTATTATT
66 AATGTTTACATCTATTTAGGACTTTTTAAATCATTAAAAGGTAAAAATACAAATTTGCTATTATT
* * * *
5557827 GTTCTATTTTAATAGTTTGGATAACTCCAATACATGATATTAAACTTATCT-GAATGATTAAACT
131 GTTCTATTTTAACAATTTAGATAACTCCAATACATGATATTAAACTT-TCTCGAAAGATTAAACT
* * * * ** * *
5557891 TGGTTTTCATAGTTGATATGTGTGAAAAAGTTATCGTTTATGTCTATTTAGGAC-TATTTTTGTT
195 TGGTATTCACAATTGATATATGTGAAAAAGTTATCGTTTACCTCTATTAAGGACTTATTTTTGCT
*
5557955 GTTAAAATGCAAAAATACAAATTTGTTGTTATTATTCTATTTTAACATTTGTATGGCTTTATT
260 GTTAAAAGGCAAAAATACAAATTTGTTGTTATTATTCTATTTTAACATTTGTATGGCTTTATT
* * *
5558018 ACATGATATTAAACA-ATTTCAAATGATTGAACTTGGTTTTTGCA-G-TTGATATATGTAAAAAA
1 ACATGATATTAAACATA-TTCAAATGATTGAACTTAG--TTTCCACGATTGATATATATAAAAAA
* * * *
5558080 GTTATTGTTTACCTCTGTTTAGGA-TTTTTCAAATCGTTAAAAGGTAAAAATACAAATTTGCTAT
63 GTTAATGTTTACATCTATTTAGGACTTTTT-AAATCATTAAAAGGTAAAAATACAAATTTGCTAT
* * * * * * * *
5558144 TATTGTTTTGTTTTAGCAATTTAGATAGCTTCAATACATTATATTAAACTTTTTCGAAAGATTGA
127 TATTGTTCTATTTTAACAATTTAGATAACTCCAATACATGATATTAAACTTTCTCGAAAGATTAA
* * * * * *
5558209 ACTTGGTATTCACAATTGATATATGTGACAAAGTTGTTGTTTACCTCTGTTAATGACTTTTTTTT
192 ACTTGGTATTCACAATTGATATATGTGAAAAAGTTATCGTTTACCTCTATTAAGGACTTATTTTT
5558274 GCTGTTAAAAGGCAAAAATACAAA
257 GCTGTTAAAAGGCAAAAATACAAA
5558298 GTTATTATTA
Statistics
Matches: 230, Mismatches: 44, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
320 8 0.03
321 188 0.82
322 29 0.13
323 5 0.02
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (322 bp):
ACATGATATTAAACATATTCAAATGATTGAACTTAGTTTCCACGATTGATATATATAAAAAAGTT
AATGTTTACATCTATTTAGGACTTTTTAAATCATTAAAAGGTAAAAATACAAATTTGCTATTATT
GTTCTATTTTAACAATTTAGATAACTCCAATACATGATATTAAACTTTCTCGAAAGATTAAACTT
GGTATTCACAATTGATATATGTGAAAAAGTTATCGTTTACCTCTATTAAGGACTTATTTTTGCTG
TTAAAAGGCAAAAATACAAATTTGTTGTTATTATTCTATTTTAACATTTGTATGGCTTTATT
Found at i:5563297 original size:8 final size:8
Alignment explanation
Indices: 5563286--5563322 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
5563276 TATTTATTTA
5563286 TATATATT
1 TATATATT
5563294 TATAT-TAT
1 TATATAT-T
5563302 TATATATT
1 TATATATT
5563310 TATATATT
1 TATATATT
5563318 TATAT
1 TATAT
5563323 TTAAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.04
8 25 0.93
9 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATATT
Found at i:5563307 original size:10 final size:9
Alignment explanation
Indices: 5563273--5563322 Score: 54
Period size: 8 Copynumber: 5.9 Consensus size: 9
5563263 AATTATTTTT
*
5563273 TATTATTTA
1 TATTATATA
5563282 T-TTATATA
1 TATTATATA
5563290 TATT-TATA
1 TATTATATA
5563298 TTATTATATA
1 -TATTATATA
5563308 T-TTATATA
1 TATTATATA
5563316 T-TTATAT
1 TATTATAT
5563323 TTAAAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
8 25 0.68
9 8 0.22
10 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
TATTATATA
Found at i:5563309 original size:26 final size:24
Alignment explanation
Indices: 5563273--5563323 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
5563263 AATTATTTTT
5563273 TATTATT-TAT-TTATATATATTTA
1 TATTATTATATATT-TATATATTTA
5563296 TATTATTATATATTTATATATTTA
1 TATTATTATATATTTATATATTTA
5563320 TATT
1 TATT
5563324 TAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 7 0.27
24 17 0.65
25 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TATTATTATATATTTATATATTTA
Found at i:5563340 original size:21 final size:22
Alignment explanation
Indices: 5563311--5563352 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
5563301 TTATATATTT
5563311 ATATATTTATATTTAAAAAATA
1 ATATATTTATATTTAAAAAATA
5563333 ATAT-TTTATATTTAAAAAAT
1 ATATATTTATATTTAAAAAAT
5563353 TTTTAAATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATATTTATATTTAAAAAATA
Found at i:5568588 original size:29 final size:30
Alignment explanation
Indices: 5568548--5568618 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
5568538 GTTAAGTATT
5568548 ATATT-AATTAAAAAATTTTAT-AATTCAA
1 ATATTAAATTAAAAAATTTTATAAATTCAA
* * *
5568576 ATATTAAATTAAAAATTTTTTTAAATTCAT
1 ATATTAAATTAAAAAATTTTATAAATTCAA
* *
5568606 ATAATACATTAAA
1 ATATTAAATTAAA
5568619 TATTTCAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
28 5 0.14
29 14 0.39
30 17 0.47
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (30 bp):
ATATTAAATTAAAAAATTTTATAAATTCAA
Found at i:5570103 original size:19 final size:20
Alignment explanation
Indices: 5570079--5570117 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
5570069 TCAATATCTC
5570079 CATCAATATC-AAACATCAT
1 CATCAATATCAAAACATCAT
5570098 CATCAATATCAAAACATCAT
1 CATCAATATCAAAACATCAT
5570118 TAGATTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (20 bp):
CATCAATATCAAAACATCAT
Found at i:5570134 original size:18 final size:18
Alignment explanation
Indices: 5570111--5570149 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5570101 CAATATCAAA
* *
5570111 ACATCATTAGATTTTCAT
1 ACATCATCAAATTTTCAT
5570129 ACATCATCAAATTTTCAT
1 ACATCATCAAATTTTCAT
5570147 ACA
1 ACA
5570150 ATATTTCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (18 bp):
ACATCATCAAATTTTCAT
Found at i:5578969 original size:129 final size:129
Alignment explanation
Indices: 5578735--5578990 Score: 388
Period size: 129 Copynumber: 2.0 Consensus size: 129
5578725 CCAAGTAGTT
5578735 TCTTGTTGAAATAAAATACAAGATAAATTTCTTGTTATTATCTTTCTAGTTTTTATATTCTACTA
1 TCTTGTTGAAATAAAATACAAGATAAATTTCTTGTTATTATCTTTCTAGTTTTTATATTCTACTA
* *
5578800 AAAAAGTTGATGATTAATAATTCATAAGAGACCTTGAGTCTTATAAAATTTTACTTTTTTTTTG
66 AAAAAGTTGATGATTAATAATTCATAAGAGACCTTAAGTCTTATAAAATTTTACATTTTTTTTG
* * * * * *
5578864 TCTTGTTGAAATAAAATACAAGATAAGTTTCTTGTTATTATTTTTTTGGTTTTTATATTTTATTA
1 TCTTGTTGAAATAAAATACAAGATAAATTTCTTGTTATTATCTTTCTAGTTTTTATATTCTACTA
* ** *
5578929 AAAGAA-TTGATGATTAATCATTCATAAGAGACCTTAAGTCTTATTGAATTTTTCATTTTTTT
66 AAA-AAGTTGATGATTAATAATTCATAAGAGACCTTAAGTCTTATAAAATTTTACATTTTTTT
5578991 ATTGACTTCT
Statistics
Matches: 114, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
129 112 0.98
130 2 0.02
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (129 bp):
TCTTGTTGAAATAAAATACAAGATAAATTTCTTGTTATTATCTTTCTAGTTTTTATATTCTACTA
AAAAAGTTGATGATTAATAATTCATAAGAGACCTTAAGTCTTATAAAATTTTACATTTTTTTTG
Found at i:5580661 original size:44 final size:44
Alignment explanation
Indices: 5580590--5580673 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
5580580 TGTGGGGAAG
5580590 ATGAATTTTTATACTCGCAATAAAGTTTATTATTTAAATGAAAT
1 ATGAATTTTTATACTCGCAATAAAGTTTATTATTTAAATGAAAT
* ** **
5580634 ATGAGTTTTTATACTCTTAATGGAGTTTATTATTTAAATG
1 ATGAATTTTTATACTCGCAATAAAGTTTATTATTTAAATG
5580674 TCTAAAGCAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (44 bp):
ATGAATTTTTATACTCGCAATAAAGTTTATTATTTAAATGAAAT
Found at i:5585267 original size:10 final size:10
Alignment explanation
Indices: 5585249--5585287 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
5585239 AAATATTAAT
5585249 AAAGAAAAGGA
1 AAAG-AAAGGA
*
5585260 AAGGAAAGGA
1 AAAGAAAGGA
*
5585270 AAAGAATGGA
1 AAAGAAAGGA
5585280 AAAGAAAG
1 AAAGAAAG
5585288 TTTTTTAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 21 0.88
11 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.03
Consensus pattern (10 bp):
AAAGAAAGGA
Found at i:5585280 original size:15 final size:16
Alignment explanation
Indices: 5585249--5585286 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5585239 AAATATTAAT
5585249 AAAGAAAAGGAAAGGA
1 AAAGAAAAGGAAAGGA
* *
5585265 AAGGAAAA-GAATGGA
1 AAAGAAAAGGAAAGGA
5585280 AAAGAAA
1 AAAGAAA
5585287 GTTTTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (16 bp):
AAAGAAAAGGAAAGGA
Found at i:5587271 original size:23 final size:23
Alignment explanation
Indices: 5587241--5587293 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
5587231 TTAATATAAC
5587241 TATTAAATATTTAAATT-TATTAT
1 TATTAAATATTTAAATTAT-TTAT
5587264 TATTAAATATTTAAATTATTTAT
1 TATTAAATATTTAAATTATTTAT
5587287 TATTAAA
1 TATTAAA
5587294 ATTATTAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAAATATTTAAATTATTTAT
Found at i:5587281 original size:16 final size:16
Alignment explanation
Indices: 5587262--5587300 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5587252 TAAATTTATT
*
5587262 ATTATTAAATATTTAA
1 ATTATTAAATATTAAA
* *
5587278 ATTATTTATTATTAAA
1 ATTATTAAATATTAAA
5587294 ATTATTA
1 ATTATTA
5587301 GTATTCAAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTATTAAATATTAAA
Found at i:5594531 original size:15 final size:18
Alignment explanation
Indices: 5594490--5594547 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
5594480 AGGATGAATA
*
5594490 ATTATAATTATTTAAA--
1 ATTATAATTATATAAATG
5594506 ATTAT--TTATAT-AA-G
1 ATTATAATTATATAAATG
5594520 -TTATAATTATATAAATG
1 ATTATAATTATATAAATG
5594537 ATTATAATTAT
1 ATTATAATTAT
5594548 TTGAATAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
13 6 0.17
14 5 0.14
15 6 0.17
16 7 0.20
17 1 0.03
18 10 0.29
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
ATTATAATTATATAAATG
Found at i:5597326 original size:10 final size:10
Alignment explanation
Indices: 5597297--5597341 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
5597287 ACATTAAAAG
*
5597297 AAAATTTCTA
1 AAAATTTTTA
*
5597307 AAATATTTTTT
1 AAA-ATTTTTA
5597318 AAAATTTTTA
1 AAAATTTTTA
*
5597328 AAAATTATTA
1 AAAATTTTTA
5597338 AAAA
1 AAAA
5597342 ATAAAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (10 bp):
AAAATTTTTA
Found at i:5597647 original size:20 final size:20
Alignment explanation
Indices: 5597630--5597680 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
5597620 AAAATATATT
5597630 ATTTTTAAAAAATCTATAAA
1 ATTTTTAAAAAATCTATAAA
* *
5597650 ATTTTTTAAAAATTTA-AAA
1 ATTTTTAAAAAATCTATAAA
5597669 CATTTTTAAAAA
1 -ATTTTTAAAAA
5597681 CTTAGAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTTTTAAAAAATCTATAAA
Found at i:5597674 original size:19 final size:18
Alignment explanation
Indices: 5597630--5597697 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 18
5597620 AAAATATATT
5597630 ATTTTTAAAAAATCTATAAAA
1 ATTTTT-AAAAAT-T-TAAAA
*
5597651 TTTTTTAAAAATTTAAAA
1 ATTTTTAAAAATTTAAAA
*
5597669 CATTTTTAAAAACTTAGAAAA
1 -ATTTTTAAAAA-TT-TAAAA
5597690 ATTTTTAA
1 ATTTTTAA
5597698 TTTTTTATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 5 0.12
19 11 0.27
20 16 0.39
21 9 0.22
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (18 bp):
ATTTTTAAAAATTTAAAA
Found at i:5597693 original size:20 final size:19
Alignment explanation
Indices: 5597630--5597697 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 19
5597620 AAAATATATT
5597630 ATTTTTAAAAAATCTATAAAA
1 ATTTTTAAAAAAT-TA-AAAA
* * *
5597651 TTTTTTAAAAATTTAAAAC
1 ATTTTTAAAAAATTAAAAA
*
5597670 ATTTTTAAAAACTTAGAAAA
1 ATTTTTAAAAAATTA-AAAA
5597690 ATTTTTAA
1 ATTTTTAA
5597698 TTTTTTATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 16 0.40
20 13 0.32
21 11 0.28
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (19 bp):
ATTTTTAAAAAATTAAAAA
Found at i:5597781 original size:18 final size:16
Alignment explanation
Indices: 5597747--5597794 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 16
5597737 TTTTTTTTGG
*
5597747 ATTTTTATTAAAATTTT
1 ATTTTT-TTAGAATTTT
5597764 ATTTGTTTTCAGAATTTT
1 ATTT-TTTT-AGAATTTT
5597782 ATTTTTTTAGAAT
1 ATTTTTTTAGAAT
5597795 GTTTTAGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 5 0.18
17 10 0.36
18 13 0.46
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.62
Consensus pattern (16 bp):
ATTTTTTTAGAATTTT
Found at i:5597839 original size:11 final size:11
Alignment explanation
Indices: 5597825--5597860 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
5597815 TTTAATTAAT
5597825 AAAAAATTTTA
1 AAAAAATTTTA
5597836 AAAAAATTTTA
1 AAAAAATTTTA
*
5597847 AAAAAAATTTA
1 AAAAAATTTTA
5597858 AAA
1 AAA
5597861 TTTTTTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAAATTTTA
Found at i:5597850 original size:12 final size:12
Alignment explanation
Indices: 5597820--5597860 Score: 59
Period size: 11 Copynumber: 3.5 Consensus size: 12
5597810 AATTATTTAA
5597820 TTAATAAAAAATT
1 TTAA-AAAAAATT
5597833 TT-AAAAAAATT
1 TTAAAAAAAATT
5597844 TTAAAAAAAA-T
1 TTAAAAAAAATT
5597855 TTAAAA
1 TTAAAA
5597861 TTTTTTAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 17 0.63
12 8 0.30
13 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TTAAAAAAAATT
Found at i:5597928 original size:15 final size:15
Alignment explanation
Indices: 5597910--5597957 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
5597900 ATTTAATTTT
5597910 TTTTTATTTTTTAAA
1 TTTTTATTTTTTAAA
* *
5597925 TTTTCATTTTTTAAG
1 TTTTTATTTTTTAAA
5597940 TTTTGTGATTTTTTAAA
1 TTTT-T-ATTTTTTAAA
5597957 T
1 T
5597958 CTTAAGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 17 0.63
17 10 0.37
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (15 bp):
TTTTTATTTTTTAAA
Found at i:5598136 original size:10 final size:9
Alignment explanation
Indices: 5598095--5598227 Score: 72
Period size: 10 Copynumber: 13.3 Consensus size: 9
5598085 TCTTAGTTTA
5598095 TTTACAAATT
1 TTTA-AAATT
5598105 TTAATAAAA-T
1 TT--TAAAATT
*
5598115 TTAAAAAGTT
1 TTTAAAA-TT
5598125 TTTAGAAATT
1 TTTA-AAATT
5598135 TTTAAAATT
1 TTTAAAATT
5598144 TTCTAAAATT
1 TT-TAAAATT
5598154 TCTTAAAACTT
1 T-TTAAAA-TT
5598165 TTTAGAAA-T
1 TTTA-AAATT
*
5598174 TTTAGAATCGT
1 TTTAAAAT--T
*
5598185 TTAAAGAATTT
1 TTTAA-AA-TT
5598196 TTTAAAATT
1 TTTAAAATT
*
5598205 TTAAAAATTAT
1 TTTAAAA-T-T
*
5598216 TTTAGAATT
1 TTTAAAATT
5598225 TTT
1 TTT
5598228 TTTTTATTTT
Statistics
Matches: 98, Mismatches: 9, Indels: 33
0.70 0.06 0.24
Matches are distributed among these distances:
8 6 0.06
9 24 0.24
10 35 0.36
11 28 0.29
12 4 0.04
13 1 0.01
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (9 bp):
TTTAAAATT
Found at i:5600535 original size:20 final size:20
Alignment explanation
Indices: 5600498--5600537 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5600488 TCATATTCTT
*
5600498 AATAATTATTTTTAAACAAA
1 AATAATTATTTATAAACAAA
5600518 AATAATTA-TTATATAACAAA
1 AATAATTATTTATA-AACAAA
5600538 TGGTTATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATTATTTATAAACAAA
Found at i:5601856 original size:9 final size:9
Alignment explanation
Indices: 5601844--5601882 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
5601834 GTTTATGTTA
5601844 TTGATATTG
1 TTGATATTG
5601853 TTGATATTG
1 TTGATATTG
*
5601862 TTGATGTTG
1 TTGATATTG
*
5601871 TTGATGTTG
1 TTGATATTG
5601880 TTG
1 TTG
5601883 TTGATTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.15, C:0.00, G:0.28, T:0.56
Consensus pattern (9 bp):
TTGATATTG
Found at i:5601907 original size:12 final size:12
Alignment explanation
Indices: 5601877--5601914 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5601867 GTTGTTGATG
5601877 TTGTTGTTGATT-
1 TTGTTGTT-ATTA
*
5601889 TTATTGTTATTA
1 TTGTTGTTATTA
5601901 TTGTTGTTATTA
1 TTGTTGTTATTA
5601913 TT
1 TT
5601915 ACAAGAGCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 3 0.13
12 20 0.87
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (12 bp):
TTGTTGTTATTA
Found at i:5605546 original size:3 final size:3
Alignment explanation
Indices: 5605538--5605568 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5605528 AATCATGTTT
5605538 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5605569 TCTACCAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5607493 original size:29 final size:29
Alignment explanation
Indices: 5607442--5607525 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 29
5607432 CACTGTATAT
*
5607442 ATTTTGTTATTTTGTTATATTATATGGTTG
1 ATTTTGTTATTTTTTTAT-TTATATGGTTG
* *
5607472 -TTTTGTTATTTTTATTATTTATTTGTTTG
1 ATTTTGTTATTTTT-TTATTTATATGGTTG
5607501 AATTTT-TTATTTCTTTTATTTATAT
1 -ATTTTGTTATTT-TTTTATTTATAT
5607526 AGTATTTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 21 0.46
30 19 0.41
31 6 0.13
ACGTcount: A:0.19, C:0.01, G:0.10, T:0.70
Consensus pattern (29 bp):
ATTTTGTTATTTTTTTATTTATATGGTTG
Found at i:5609855 original size:3 final size:3
Alignment explanation
Indices: 5609847--5609895 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
5609837 GAAAGCAAAT
* * *
5609847 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA CAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5609895 T
1 T
5609896 TATACCATGC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5616648 original size:11 final size:11
Alignment explanation
Indices: 5616632--5616658 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5616622 CTTGAAGAAG
5616632 AAAAAAATGAA
1 AAAAAAATGAA
5616643 AAAAAAATGAA
1 AAAAAAATGAA
5616654 AAAAA
1 AAAAA
5616659 TAAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAAAATGAA
Found at i:5616696 original size:11 final size:10
Alignment explanation
Indices: 5616632--5616698 Score: 50
Period size: 10 Copynumber: 6.7 Consensus size: 10
5616622 CTTGAAGAAG
5616632 AAAAAAATGAA
1 AAAAAAATG-A
5616643 AAAAAAATG-
1 AAAAAAATGA
*
5616652 AAAAAAATAA
1 AAAAAAATGA
5616662 AAAAATAAT-A
1 AAAAA-AATGA
* *
5616672 AAACAGA-GA
1 AAAAAAATGA
*
5616681 TAAAATAATGA
1 -AAAAAAATGA
5616692 AAAAAAA
1 AAAAAAA
5616699 AAAGAAAAAG
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
9 10 0.23
10 20 0.45
11 14 0.32
ACGTcount: A:0.79, C:0.01, G:0.07, T:0.12
Consensus pattern (10 bp):
AAAAAAATGA
Found at i:5617713 original size:36 final size:36
Alignment explanation
Indices: 5617664--5617755 Score: 98
Period size: 36 Copynumber: 2.6 Consensus size: 36
5617654 CTTGGTTAAT
* ** *
5617664 TTTATTTCCTGACTTACGATTCAATCTTAGTTGTTC
1 TTTATTTCATGACTTACGATTCAATCCCAGTAGTTC
* *
5617700 TTTATTTCTTGACTTGC-AGTTCAATCCCAGTAGTTC
1 TTTATTTCATGACTTACGA-TTCAATCCCAGTAGTTC
*
5617736 TTT-TTTCATGACTTATGATT
1 TTTATTTCATGACTTACGATT
5617756 TCGCCCTTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
35 13 0.28
36 33 0.72
ACGTcount: A:0.20, C:0.18, G:0.12, T:0.50
Consensus pattern (36 bp):
TTTATTTCATGACTTACGATTCAATCCCAGTAGTTC
Found at i:5617869 original size:35 final size:35
Alignment explanation
Indices: 5617823--5617920 Score: 117
Period size: 37 Copynumber: 2.7 Consensus size: 35
5617813 TTTGATTTGT
*
5617823 AATTTAATCTCGATCATTTTTATTTCTCAACTTAC
1 AATTCAATCTCGATCATTTTTATTTCTCAACTTAC
* * *
5617858 AGTTCAGTCTCGATCATTTCTTTATTTTTCAACTTAC
1 AATTCAATCTCGATCA-TT-TTTATTTCTCAACTTAC
*
5617895 AATTCAAT-TCCAATCATTTTTATTTC
1 AATTCAATCT-CGATCATTTTTATTTC
5617921 AGGCTTGTGG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
35 20 0.38
36 5 0.10
37 27 0.52
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.49
Consensus pattern (35 bp):
AATTCAATCTCGATCATTTTTATTTCTCAACTTAC
Found at i:5622226 original size:40 final size:40
Alignment explanation
Indices: 5622169--5622246 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
5622159 GCAAAAAGTT
*
5622169 TCATTAACACCGGCATAAAATAAGAACAATAAATATAATG
1 TCATTAACACCGACATAAAATAAGAACAATAAATATAATG
* *
5622209 TCATTAACACCTACATAAAATAAGAACAGTAAATATAA
1 TCATTAACACCGACATAAAATAAGAACAATAAATATAA
5622247 ACAAAAAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (40 bp):
TCATTAACACCGACATAAAATAAGAACAATAAATATAATG
Found at i:5624426 original size:13 final size:13
Alignment explanation
Indices: 5624405--5624451 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
5624395 TTAGGATATG
*
5624405 AAAAAGAAAGAAA
1 AAAAAGAAAAAAA
*
5624418 AAGAAGAAAAAAA
1 AAAAAGAAAAAAA
*
5624431 AAAAAGAAAAAGA
1 AAAAAGAAAAAAA
*
5624444 GAAAAGAA
1 AAAAAGAA
5624452 GTGTAAATGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:5624436 original size:22 final size:21
Alignment explanation
Indices: 5624405--5624448 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
5624395 TTAGGATATG
*
5624405 AAAAAGAAAGAAAAAGAAGAAA
1 AAAAAAAAAGAAAAAG-AGAAA
5624427 AAAAAAAAAGAAAAAGAGAAA
1 AAAAAAAAAGAAAAAGAGAAA
5624448 A
1 A
5624449 GAAGTGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAGAAAAAGAGAAA
Found at i:5624449 original size:7 final size:6
Alignment explanation
Indices: 5624411--5624451 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
5624401 TATGAAAAAG
*
5624411 AAAGAA AAAGAA GAA-AA AAA-AA AAAGAA AAAGAGA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGA-A AAAGAA
5624452 GTGTAAATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 9 0.29
6 16 0.52
7 6 0.19
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:5624994 original size:126 final size:126
Alignment explanation
Indices: 5624819--5625071 Score: 488
Period size: 126 Copynumber: 2.0 Consensus size: 126
5624809 TAAAGCTCCA
*
5624819 AATCATCCGTTAAATCAGTAATCTAAATGCAACCATTAGTTTTCTGTATCCATCATGAATTTGAT
1 AATCATACGTTAAATCAGTAATCTAAATGCAACCATTAGTTTTCTGTATCCATCATGAATTTGAT
*
5624884 AAGATTTTTAAATGAAAAAATTTATAATATTTAATCAATTATCAGTCTATAGTAGTGTTTT
66 AAGATTTTTAAATAAAAAAATTTATAATATTTAATCAATTATCAGTCTATAGTAGTGTTTT
5624945 AATCATACGTTAAATCAGTAATCTAAATGCAACCATTAGTTTTCTGTATCCATCATGAATTTGAT
1 AATCATACGTTAAATCAGTAATCTAAATGCAACCATTAGTTTTCTGTATCCATCATGAATTTGAT
5625010 AAGATTTTTAAATAAAAAAATTTATAATATTTAATCAATTATCAGTCTATAGTAGTGTTTT
66 AAGATTTTTAAATAAAAAAATTTATAATATTTAATCAATTATCAGTCTATAGTAGTGTTTT
5625071 A
1 A
5625072 TTCTTTTAGC
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 125 1.00
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.40
Consensus pattern (126 bp):
AATCATACGTTAAATCAGTAATCTAAATGCAACCATTAGTTTTCTGTATCCATCATGAATTTGAT
AAGATTTTTAAATAAAAAAATTTATAATATTTAATCAATTATCAGTCTATAGTAGTGTTTT
Found at i:5630525 original size:21 final size:21
Alignment explanation
Indices: 5630499--5630540 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5630489 ATCTTCGTAA
* *
5630499 GAAATCTTTATTATAGTGATG
1 GAAATCTCTATTATAGAGATG
5630520 GAAATCTCTATTATAGAGATG
1 GAAATCTCTATTATAGAGATG
5630541 TTATCAGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (21 bp):
GAAATCTCTATTATAGAGATG
Found at i:5639975 original size:21 final size:21
Alignment explanation
Indices: 5639949--5639998 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
5639939 TTTTGTTTAG
5639949 ATTTTCTTAGCTAGGTCTTGC
1 ATTTTCTTAGCTAGGTCTTGC
5639970 ATTTTCTTAGCTAGGTCTTGC
1 ATTTTCTTAGCTAGGTCTTGC
5639991 ATTTTCTT
1 ATTTTCTT
5639999 GCACTTTTTA
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:0.14, C:0.18, G:0.16, T:0.52
Consensus pattern (21 bp):
ATTTTCTTAGCTAGGTCTTGC
Found at i:5649893 original size:20 final size:20
Alignment explanation
Indices: 5649868--5649917 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
5649858 AAGAAAGATT
5649868 AGTAAATCCTAACAAATCTC
1 AGTAAATCCTAACAAATCTC
5649888 AGTAAATCCTAACAAATCTC
1 AGTAAATCCTAACAAATCTC
*
5649908 GGTAAATCCT
1 AGTAAATCCT
5649918 TTTATCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (20 bp):
AGTAAATCCTAACAAATCTC
Found at i:5651305 original size:17 final size:18
Alignment explanation
Indices: 5651275--5651308 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5651265 AGAAAGTATC
*
5651275 AATTTTTCTTAAAAATAA
1 AATTTTTCTAAAAAATAA
5651293 AATTTTT-TAAAAAATA
1 AATTTTTCTAAAAAATA
5651309 TTTTTTTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTTTCTAAAAAATAA
Found at i:5651305 original size:60 final size:61
Alignment explanation
Indices: 5651240--5651355 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 61
5651230 ATTTTTCACA
* *
5651240 AAAAAAAAAACTTTTAAGGAAAAGTAGAAAGTATCAATTTTTCTTAAAAATAAAATTTTTT
1 AAAAAATAAACTTTTAAGAAAAAGTAGAAAGTATCAATTTTTCTTAAAAATAAAATTTTTT
*** * * *
5651301 AAAAAATATTTTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAGTAAAA
1 AAAAAATAAACTTTTAAGAAAAAGTAGAAAGTATCAATTTTTCTTAAAAATAAAA
5651356 AAAAAAAACT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.35
Consensus pattern (61 bp):
AAAAAATAAACTTTTAAGAAAAAGTAGAAAGTATCAATTTTTCTTAAAAATAAAATTTTTT
Found at i:5651356 original size:67 final size:62
Alignment explanation
Indices: 5651259--5651531 Score: 244
Period size: 59 Copynumber: 4.4 Consensus size: 62
5651249 ACTTTTAAGG
* *
5651259 AAAAGTAGAAAGTATCAATTTTTC-T-TAAAAATAAAATTTTTTAAAAAATATTTTTTTGAGA
1 AAAAGTTGAAAGTATCAATTTTTCTTGTAAAAATAAAA-TTTTCAAAAAATATTTTTTTGAGA
* **
5651320 AAAAGTTGAAAGTATCAATTTTTCTTAAAAGTAAAAAAAAAAAACTTCAAAAAA-ATTATTTTTG
1 AAAAGTTGAAAGTATCAATTTTTCTT----GT-AAAAATAAAATTTTCAAAAAATATT-TTTTTG
*
5651384 AGG
60 AGA
* * **
5651387 AAAAGTTGAAAGTATCAATTTTTCTTG-AAAATTAAAATTTTGAAAAGGTA--TTTTTGAGA
1 AAAAGTTGAAAGTATCAATTTTTCTTGTAAAAATAAAATTTTCAAAAAATATTTTTTTGAGA
* * * * *
5651446 AAAAGTTAAAAGTATCAATTTTTCTCG--AAAAT-AAA-TTTAAAAAAAAAGTATTTTTGGAGA
1 AAAAGTTGAAAGTATCAATTTTTCTTGTAAAAATAAAATTTTCAAAAAATA-T-TTTTTTGAGA
*
5651506 AAAA-TTGAAAGCATCAATTTTTCTTG
1 AAAAGTTGAAAGTATCAATTTTTCTTG
5651532 AAATCAATTT
Statistics
Matches: 174, Mismatches: 25, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
56 8 0.05
57 3 0.02
58 4 0.02
59 52 0.30
60 12 0.07
61 37 0.21
62 2 0.01
63 1 0.01
66 3 0.02
67 43 0.25
68 9 0.05
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.36
Consensus pattern (62 bp):
AAAAGTTGAAAGTATCAATTTTTCTTGTAAAAATAAAATTTTCAAAAAATATTTTTTTGAGA
Found at i:5651491 original size:128 final size:127
Alignment explanation
Indices: 5651251--5651480 Score: 340
Period size: 128 Copynumber: 1.8 Consensus size: 127
5651241 AAAAAAAAAC
*
5651251 TTTTAAGGAAAAGTAGAAAGTATCAATTTTTCTTAAAAATAAAATTTTTTAAAAAATATTTTTTT
1 TTTTAAGGAAAAGTAGAAAGTATCAATTTTTCTTAAAAATAAAATTTTTGAAAAAATA-TTTTTT
* *
5651316 GAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAGTAAAAAAAAAAAACTTCAAAAAAATTAT
65 GAGAAAAAGTTAAAAGTATCAATTTTTCTGAAAAGTAAAAAAAAAAAACTTCAAAAAAATTAT
* * * **
5651379 TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATTAAAA-TTTTGAAAAGGTA-TTTTT
1 TTTTAAGGAAAAGTAGAAAGTATCAATTTTTCTT-AAAAATAAAATTTTTGAAAAAATATTTTTT
5651442 GAGAAAAAGTTAAAAGTATCAATTTTTCTCGAAAA-TAAA
65 GAGAAAAAGTTAAAAGTATCAATTTTTCT-GAAAAGTAAA
5651481 TTTAAAAAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
126 37 0.40
127 4 0.04
128 42 0.46
129 9 0.10
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (127 bp):
TTTTAAGGAAAAGTAGAAAGTATCAATTTTTCTTAAAAATAAAATTTTTGAAAAAATATTTTTTG
AGAAAAAGTTAAAAGTATCAATTTTTCTGAAAAGTAAAAAAAAAAAACTTCAAAAAAATTAT
Found at i:5651552 original size:17 final size:16
Alignment explanation
Indices: 5651518--5651550 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5651508 AATTGAAAGC
5651518 ATCAATTTTTCTTGAA
1 ATCAATTTTTCTTGAA
5651534 ATCAATTTTTCTTGAA
1 ATCAATTTTTCTTGAA
5651550 A
1 A
5651551 ATAAAAACTT
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:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (16 bp):
ATCAATTTTTCTTGAA
Found at i:5655450 original size:13 final size:13
Alignment explanation
Indices: 5655424--5655470 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
5655414 ACAATGGGTG
* *
5655424 AAAAATGATAAAA
1 AAAAAAGATGAAA
5655437 AAAAAAGATGAAA
1 AAAAAAGATGAAA
5655450 AAAAAAGGATGAGAA
1 AAAAAA-GATGA-AA
5655465 AAAAAA
1 AAAAAA
5655471 AAGAAAGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 17 0.57
14 5 0.17
15 8 0.27
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.09
Consensus pattern (13 bp):
AAAAAAGATGAAA
Found at i:5655450 original size:14 final size:14
Alignment explanation
Indices: 5655424--5655471 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
5655414 ACAATGGGTG
*
5655424 AAAAATGAT-AAAA
1 AAAAAAGATGAAAA
5655437 AAAAAAGATGAAAA
1 AAAAAAGATGAAAA
*
5655451 AAAAAGGATGAGAAA
1 AAAAAAGATGA-AAA
5655466 AAAAAA
1 AAAAAA
5655472 AGAAAGGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 8 0.27
14 14 0.47
15 8 0.27
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (14 bp):
AAAAAAGATGAAAA
Found at i:5655452 original size:16 final size:15
Alignment explanation
Indices: 5655424--5655474 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 15
5655414 ACAATGGGTG
5655424 AAAA-ATGATAAAAAA
1 AAAAGATGA-AAAAAA
5655439 AAAAGATG-AAAAAA
1 AAAAGATGAAAAAAA
*
5655453 AAAGGATGAGAAAAAA
1 AAAAGATGA-AAAAAA
5655469 AAAAGA
1 AAAAGA
5655475 AAGGAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 13 0.42
15 4 0.13
16 14 0.45
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (15 bp):
AAAAGATGAAAAAAA
Found at i:5655481 original size:16 final size:17
Alignment explanation
Indices: 5655433--5655504 Score: 78
Period size: 17 Copynumber: 4.4 Consensus size: 17
5655423 GAAAAATGAT
5655433 AAAAAAA-AAAGATG-AA
1 AAAAAAAGAAAGA-GAAA
* *
5655449 AAAAAAAGGATGAGAAA
1 AAAAAAAGAAAGAGAAA
5655466 AAAAAAAGAAAG-GAAA
1 AAAAAAAGAAAGAGAAA
* *
5655482 AAAGAAGGAAAGAGAAA
1 AAAAAAAGAAAGAGAAA
5655499 AAAAAA
1 AAAAAA
5655505 GAGTAAGATG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
16 22 0.48
17 24 0.52
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAAAGAGAAA
Found at i:5655482 original size:32 final size:31
Alignment explanation
Indices: 5655427--5655504 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 31
5655417 ATGGGTGAAA
* *
5655427 AATGATAAAAAAAAAAGATGAAAAAAAAAGG
1 AATGAGAAAAAAAAAAGAGGAAAAAAAAAGG
*
5655458 -ATGAGAAAAAAAAAAGAAAGGAAAAAAGAAGG
1 AATGAGAAAAAAAAAAG--AGGAAAAAAAAAGG
*
5655490 AAAGAGAAAAAAAAA
1 AATGAGAAAAAAAAA
5655505 GAGTAAGATG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
30 15 0.38
32 12 0.30
33 13 0.32
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (31 bp):
AATGAGAAAAAAAAAAGAGGAAAAAAAAAGG
Found at i:5655506 original size:32 final size:32
Alignment explanation
Indices: 5655433--5655504 Score: 94
Period size: 33 Copynumber: 2.3 Consensus size: 32
5655423 GAAAAATGAT
* *
5655433 AAAAAAAAAAG--ATGAAAAAAAAAGGATGAG
1 AAAAAAAAAAGAAAGGAAAAAAAAAGGAAGAG
*
5655463 AAAAAAAAAAGAAAGGAAAAAAGAAGGAAAGAG
1 AAAAAAAAAAGAAAGGAAAAAAAAAGG-AAGAG
5655496 AAAAAAAAA
1 AAAAAAAAA
5655505 GAGTAAGATG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 11 0.31
32 12 0.33
33 13 0.36
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (32 bp):
AAAAAAAAAAGAAAGGAAAAAAAAAGGAAGAG
Found at i:5655519 original size:33 final size:35
Alignment explanation
Indices: 5655460--5655531 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 35
5655450 AAAAAAGGAT
5655460 GAGAAAAAAAAAAGAAAGGAAAAAAGAA-GG-AAA
1 GAGAAAAAAAAAAGAAAGGAAAAAAGAATGGAAAA
* **
5655493 GAGAAAAAAAAAGAGTAA-GATGAAAGAATGGAAAA
1 GAGAAAAAAAAA-AGAAAGGAAAAAAGAATGGAAAA
5655528 GAGA
1 GAGA
5655532 TGGAAATAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 20 0.61
34 6 0.18
35 7 0.21
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.04
Consensus pattern (35 bp):
GAGAAAAAAAAAAGAAAGGAAAAAAGAATGGAAAA
Found at i:5656748 original size:46 final size:46
Alignment explanation
Indices: 5656579--5656991 Score: 515
Period size: 46 Copynumber: 9.0 Consensus size: 46
5656569 ATTTTAAGTT
* * ** * * *
5656579 TTAAAT-AAAATCTTTAAGAAATCCTCACATGAGAATATTTGAGTT
1 TTAAATGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTC
* * ** *
5656624 TTAAATAAGAAATCTTTAAGAAATCCTCAAATGAGAATCTTTGAGTT
1 TTAAATGAG-AATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTC
* *
5656671 TTAAATAAAAAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTC
1 TTAAAT-GAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTC
** *
5656718 TTAAATGAGAATCTTTAAGATGTTTTCAAATGAGAATCTTTGAATC
1 TTAAATGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTC
* *
5656764 TTAAATGAAAATCTTTAAAACATTTTCAAATGAGAATCTTTGAGTC
1 TTAAATGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTC
* * * *
5656810 TTAAATGAAAATCTTTAAGATATTTTCAAATGAAAATCTTTGAAT-
1 TTAAATGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTC
* * *
5656855 TTCAAATGAGAATCTTTAAAACATTTCCAAATGAGAATCTTTGAATC
1 TT-AAATGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTC
*
5656902 TTAAATGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTAAGTC
1 TTAAATGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTC
* * *
5656948 TTAAATTAGAATATTTAAGACGTTTTCAAATGAGAATCTTTGAG
1 TTAAATGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAG
5656992 GTGTGAAACC
Statistics
Matches: 328, Mismatches: 35, Indels: 9
0.88 0.09 0.02
Matches are distributed among these distances:
45 8 0.02
46 236 0.72
47 82 0.25
48 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (46 bp):
TTAAATGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTC
Found at i:5657042 original size:20 final size:20
Alignment explanation
Indices: 5657014--5657065 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
5657004 AAATTTATCG
*
5657014 AATGTGAATCTTCAAAATCA
1 AATGAGAATCTTCAAAATCA
* *
5657034 AATGAGAATCTTCGAATTCA
1 AATGAGAATCTTCAAAATCA
5657054 AATGAGAATCTT
1 AATGAGAATCTT
5657066 TGAGGTGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (20 bp):
AATGAGAATCTTCAAAATCA
Found at i:5657063 original size:78 final size:79
Alignment explanation
Indices: 5656971--5657163 Score: 325
Period size: 78 Copynumber: 2.4 Consensus size: 79
5656961 TTTAAGACGT
5656971 TTTCAAATGAGAATCTTTGAGGTGTGAAACCTAAAATTTATCGAATGTGAATCTTCAAAATCAAA
1 TTTCAAATGAGAATCTTTGAGGTGTGAAACCTAAAATTTATCGAATGTGAATCTTCAAAATCAAA
5657036 TGAGAATCTTCGAA
66 TGAGAATCTTCGAA
* *
5657050 -TTCAAATGAGAATCTTTGAGGTGTGAAACCCAAAATTTATCGAATGTGAATCTTCAAATTCAAA
1 TTTCAAATGAGAATCTTTGAGGTGTGAAACCTAAAATTTATCGAATGTGAATCTTCAAAATCAAA
*
5657114 TGAGAATCTTTGAA
66 TGAGAATCTTCGAA
* *
5657128 TTTTAAATGAGAATCTTTGAGATGTGAAACCCTAAA
1 TTTCAAATGAGAATCTTTGAGGTGTGAAA-CCTAAA
5657164 GTTTGTTAGG
Statistics
Matches: 106, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
78 75 0.71
79 26 0.25
80 5 0.05
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (79 bp):
TTTCAAATGAGAATCTTTGAGGTGTGAAACCTAAAATTTATCGAATGTGAATCTTCAAAATCAAA
TGAGAATCTTCGAA
Found at i:5657120 original size:20 final size:20
Alignment explanation
Indices: 5657092--5657144 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
5657082 AAATTTATCG
*
5657092 AATGTGAATCTTCAAATTCA
1 AATGAGAATCTTCAAATTCA
* * *
5657112 AATGAGAATCTTTGAATTTTA
1 AATGAGAATC-TTCAAATTCA
5657133 AATGAGAATCTT
1 AATGAGAATCTT
5657145 TGAGATGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (20 bp):
AATGAGAATCTTCAAATTCA
Found at i:5657349 original size:114 final size:114
Alignment explanation
Indices: 5657209--5657447 Score: 397
Period size: 114 Copynumber: 2.1 Consensus size: 114
5657199 TTTTGAACTT
*
5657209 TTGGATGTGAATCTCCAAAATTCAAATAAAAAGCTTTGTACTCAACTTTTGGATACGAATCTCTA
1 TTGGATGTGAATCTCCAAAATTCAAATAAAAAGCTTTGAACTCAACTTTTGGATACGAATCTCTA
5657274 AATTTTTGAGTGAGAACCTTTGAACTTAGATGTGAAACTCTAAGATTTC
66 AATTTTTGAGTGAGAACCTTTGAACTTAGATGTGAAACTCTAAGATTTC
* * **
5657323 TTGGATGTGAATCTCTAAAATTCAAATGAAAAGCTTTGAACTCAACTTTTGGATGTGAATCTCTA
1 TTGGATGTGAATCTCCAAAATTCAAATAAAAAGCTTTGAACTCAACTTTTGGATACGAATCTCTA
* *
5657388 AATTTTTTAGTGAGTACCTTTGAACTTAGATGTGAAACTCTAAGATTTC
66 AATTTTTGAGTGAGAACCTTTGAACTTAGATGTGAAACTCTAAGATTTC
**
5657437 TTAAATGTGAA
1 TTGGATGTGAA
5657448 CCTTTTTGAA
Statistics
Matches: 116, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 116 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (114 bp):
TTGGATGTGAATCTCCAAAATTCAAATAAAAAGCTTTGAACTCAACTTTTGGATACGAATCTCTA
AATTTTTGAGTGAGAACCTTTGAACTTAGATGTGAAACTCTAAGATTTC
Found at i:5657804 original size:43 final size:45
Alignment explanation
Indices: 5657755--5657859 Score: 133
Period size: 45 Copynumber: 2.4 Consensus size: 45
5657745 GTGCCCCTGT
* *
5657755 TTAAAGGAGTTTTGTTTATTTTT-TCAAAATCATT-AGCCTCTAA
1 TTAAAGGAGCTTTATTTATTTTTCTCAAAATCATTGAGCCTCTAA
* *
5657798 TTAAAGGAGCTTTATTTATTTTTCTCAAAGTCATTGAGCCTCTAT
1 TTAAAGGAGCTTTATTTATTTTTCTCAAAATCATTGAGCCTCTAA
* * *
5657843 TTAGAGTAACTTTATTT
1 TTAAAGGAGCTTTATTT
5657860 TTAAAAAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
43 21 0.40
44 10 0.19
45 22 0.42
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (45 bp):
TTAAAGGAGCTTTATTTATTTTTCTCAAAATCATTGAGCCTCTAA
Found at i:5658067 original size:12 final size:11
Alignment explanation
Indices: 5658040--5658092 Score: 63
Period size: 12 Copynumber: 4.7 Consensus size: 11
5658030 GATTGTAGGG
*
5658040 ATTTTTA-TTC
1 ATTTTTATTTT
5658050 ATTTTTATTGTT
1 ATTTTTATT-TT
*
5658062 ATTTTTATTTC
1 ATTTTTATTTT
5658073 ATTTTTATTTTT
1 ATTTTTA-TTTT
5658085 ATTTTTAT
1 ATTTTTAT
5658093 GTTCTATCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
10 7 0.19
11 10 0.27
12 20 0.54
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:5658069 original size:6 final size:6
Alignment explanation
Indices: 5658050--5658092 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
5658040 ATTTTTATTC
* *
5658050 ATTTTT ATTGTT ATTTTT A-TTTC ATTTTT ATTTTT ATTTTT AT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT AT
5658093 GTTCTATCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (6 bp):
ATTTTT
Found at i:5658073 original size:23 final size:23
Alignment explanation
Indices: 5658040--5658092 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
5658030 GATTGTAGGG
5658040 ATTTTTA-TTCATTTTTATTGTT
1 ATTTTTATTTCATTTTTATTGTT
*
5658062 ATTTTTATTTCATTTTTATTTTT
1 ATTTTTATTTCATTTTTATTGTT
5658085 ATTTTTAT
1 ATTTTTAT
5658093 GTTCTATCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 7 0.24
23 22 0.76
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (23 bp):
ATTTTTATTTCATTTTTATTGTT
Found at i:5658104 original size:23 final size:23
Alignment explanation
Indices: 5658040--5658106 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
5658030 GATTGTAGGG
* *
5658040 ATTTTTA-TTCATTTTTATTGTT
1 ATTTTTATTTCATATCTATTGTT
* * *
5658062 ATTTTTATTTCATTTTTATTTTT
1 ATTTTTATTTCATATCTATTGTT
5658085 ATTTTTATGTTC-TATCTATTGT
1 ATTTTTAT-TTCATATCTATTGT
5658107 ACTCTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
22 7 0.18
23 29 0.74
24 3 0.08
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.72
Consensus pattern (23 bp):
ATTTTTATTTCATATCTATTGTT
Found at i:5659762 original size:60 final size:57
Alignment explanation
Indices: 5659682--5659987 Score: 211
Period size: 60 Copynumber: 5.1 Consensus size: 57
5659672 TATTTTTTAC
* ** *
5659682 AAAAAAAATTTTTAAGAAAAAATTGAAAGTACCAATTTTTCTTAAAAATAAAATTTTT
1 AAAAAATATTTTTTTGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAA-TTTT
* *
5659740 AAAAATATATGTTTTTTGAAAAAAAGTTGAAAGTATCAA-TTTTCTTAAAAAAAAAAAAAAACTT
1 AAAAA-ATAT-TTTTTTG-AAAAAA-TTGAAAGTATCAATTTTTCTT-----AAAAATAAAATTT
*
5659804 C
57 T
*
5659805 AAAAAA-ATTATTTTTGAGAAAAAGTTGAAAGTTTCAATTTTTCTTAAAAATTAAAATTTT
1 AAAAAATATT-TTTTTGA-AAAAA-TTGAAAGTATCAATTTTTCTTAAAAA-TAAAATTTT
** ** * * * * **
5659865 GAAAAGGTATTTTTGAGGAAAAGTTGAAAGTACCAATTTTTCTCAAAAATAAAAATTAA
1 -AAAAAATATTTTTTTGAAAAAATTGAAAGTATCAATTTTTCTTAAAAAT-AAAATTTT
* * * * *
5659924 AAAAAAAACTTTTTTGGAGAAAAGTTGAAAGTATCAATTTTTTTTGAAAATAAAAACTTTT
1 AAAAAATA-TTTTTTTGA-AAAAATTGAAAGTATCAATTTTTCTTAAAAAT-AAAA-TTTT
5659985 AAA
1 AAA
5659988 TGCTTTAAGG
Statistics
Matches: 195, Mismatches: 34, Indels: 35
0.74 0.13 0.13
Matches are distributed among these distances:
58 11 0.06
59 43 0.22
60 48 0.25
61 26 0.13
62 17 0.09
63 26 0.13
64 8 0.04
65 7 0.04
66 9 0.05
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.35
Consensus pattern (57 bp):
AAAAAATATTTTTTTGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTTT
Found at i:5659825 original size:125 final size:119
Alignment explanation
Indices: 5659680--5659987 Score: 322
Period size: 125 Copynumber: 2.5 Consensus size: 119
5659670 AATATTTTTT
* * *
5659680 ACAAAAAAA-ATTTTTAAGAAAAAATTGAAAGTACCAATTTTTCTTAAAAATAAAATTTTTAAAA
1 ACAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAA-TTTTAAAA
* * *
5659744 ATATATGTTTTTTGAAAAAAAGTTGAAAGTATCAA-TTTTCTTAAAAA-AAAAAAAAA
65 AGATA---TTTTTGAAAAAAAGTTGAAAGTACCAATTTTTCTCAAAAATAAAAAAAAA
*
5659800 ACTTCAAAAAAATTATTTTTGAGAAAAAGTTGAAAGTTTCAATTTTTCTTAAAAATTAAAATTTT
1 A---CAAAAAAA-TATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAA-TAAAATTTT
* * ** *
5659865 GAAAAGGTATTTTTGAGGAAAAGTTGAAAGTACCAATTTTTCTCAAAAATAAAAATTAAA
61 AAAAAGATATTTTTGAAAAAAAGTTGAAAGTACCAATTTTTCTCAAAAATAAAAA-AAAA
* * *
5659925 A-AAAAAACT-TTTTTG-GAGAAAAGTTGAAAGTATCAATTTTTTTTGAAAATAAAAACTTTTAA
1 ACAAAAAAATATTTTTGAGA-AAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAAA-TTTTAA
5659987 A
63 A
5659988 TGCTTTAAGG
Statistics
Matches: 159, Mismatches: 17, Indels: 24
0.80 0.09 0.12
Matches are distributed among these distances:
118 3 0.02
119 38 0.24
120 8 0.05
121 6 0.04
122 24 0.15
123 19 0.12
124 5 0.03
125 51 0.32
126 5 0.03
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (119 bp):
ACAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTAAAAA
GATATTTTTGAAAAAAAGTTGAAAGTACCAATTTTTCTCAAAAATAAAAAAAAA
Found at i:5668136 original size:12 final size:12
Alignment explanation
Indices: 5668119--5668161 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
5668109 TTTCTGTAAT
5668119 AATAACAACAAC
1 AATAACAACAAC
*
5668131 AATAACAACAAA
1 AATAACAACAAC
* *
5668143 AATAAGATCAAC
1 AATAACAACAAC
*
5668155 AACAACA
1 AATAACA
5668162 TCACTAAATC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.67, C:0.21, G:0.02, T:0.09
Consensus pattern (12 bp):
AATAACAACAAC
Found at i:5668174 original size:20 final size:20
Alignment explanation
Indices: 5668149--5668195 Score: 73
Period size: 17 Copynumber: 2.5 Consensus size: 20
5668139 CAAAAATAAG
5668149 ATCAACAACAACATCACTAA
1 ATCAACAACAACATCACTAA
5668169 AT---CAACAACATCACTAA
1 ATCAACAACAACATCACTAA
5668186 ATCAACAACA
1 ATCAACAACA
5668196 TAAACAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 17 0.71
20 7 0.29
ACGTcount: A:0.55, C:0.30, G:0.00, T:0.15
Consensus pattern (20 bp):
ATCAACAACAACATCACTAA
Found at i:5668176 original size:17 final size:17
Alignment explanation
Indices: 5668154--5668196 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
5668144 ATAAGATCAA
5668154 CAACAACATCACTAAAT
1 CAACAACATCACTAAAT
5668171 CAACAACATCACTAAAT
1 CAACAACATCACTAAAT
5668188 CAACAACAT
1 CAACAACAT
5668197 AAACAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.16
Consensus pattern (17 bp):
CAACAACATCACTAAAT
Found at i:5675329 original size:18 final size:18
Alignment explanation
Indices: 5675303--5675337 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5675293 TTATACGAGT
*
5675303 ACATATTTAATATATTTA
1 ACATATTTAATACATTTA
*
5675321 ACATGTTTAATACATTT
1 ACATATTTAATACATTT
5675338 TTATATTTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.49
Consensus pattern (18 bp):
ACATATTTAATACATTTA
Found at i:5680793 original size:22 final size:22
Alignment explanation
Indices: 5680763--5680808 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
5680753 AAAAGAAAAG
* *
5680763 AACAGACAACAAAATAAAATTA
1 AACAAACAACAAAATAAAAATA
*
5680785 AACAAACAATAAAATAAAAATA
1 AACAAACAACAAAATAAAAATA
5680807 AA
1 AA
5680809 AAATAAAGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.74, C:0.11, G:0.02, T:0.13
Consensus pattern (22 bp):
AACAAACAACAAAATAAAAATA
Found at i:5686338 original size:26 final size:28
Alignment explanation
Indices: 5686309--5686380 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 28
5686299 TTAAATTGTA
5686309 AAATAAATTTGATAATTTAAT-A-TAAT
1 AAATAAATTTGATAATTTAATAATTAAT
*
5686335 AAATAAATCTT-ATTATTTAATACATTAAT
1 AAATAAAT-TTGATAATTTAATA-ATTAAT
5686364 AAAT-AATTTGAATAATT
1 AAATAAATTTG-ATAATT
5686381 ATTAAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
26 17 0.45
27 4 0.11
28 4 0.11
29 13 0.34
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (28 bp):
AAATAAATTTGATAATTTAATAATTAAT
Found at i:5686381 original size:20 final size:20
Alignment explanation
Indices: 5686349--5686394 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
5686339 AAATCTTATT
5686349 ATTTAATACATTAATAAATA
1 ATTTAATACATTAATAAATA
*
5686369 ATTTGAATA-ATTATTAAATA
1 ATTT-AATACATTAATAAATA
5686389 ATTTAA
1 ATTTAA
5686395 AATTATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 18 0.75
21 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTTAATACATTAATAAATA
Found at i:5686551 original size:17 final size:19
Alignment explanation
Indices: 5686529--5686565 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
5686519 ATTAAATAAT
5686529 TTTTTTATC-TA-TCTTTA
1 TTTTTTATCTTACTCTTTA
5686546 TTTTTTATCTTACTCTTTA
1 TTTTTTATCTTACTCTTTA
5686565 T
1 T
5686566 AAATCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 2 0.11
19 7 0.39
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTTATCTTACTCTTTA
Found at i:5687661 original size:2 final size:2
Alignment explanation
Indices: 5687654--5687689 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
5687644 CTTTCAACTC
* *
5687654 GT GT GT GT GT TT GT GT GT GT AT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
5687690 TTCTGTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.44, T:0.53
Consensus pattern (2 bp):
GT
Found at i:5691192 original size:30 final size:32
Alignment explanation
Indices: 5691156--5691225 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 32
5691146 CGAAATTAAT
* * *
5691156 AAAATATTATTTTTTAAATATA-A-ATATTTA
1 AAAATATTATTATATAAATATATATATAATTA
*
5691186 AAAATATCATTATATAAATATATATATAATTA
1 AAAATATTATTATATAAATATATATATAATTA
5691218 AAAA-ATTA
1 AAAATATTA
5691226 AAAAATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 19 0.58
31 4 0.12
32 10 0.30
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (32 bp):
AAAATATTATTATATAAATATATATATAATTA
Found at i:5692694 original size:14 final size:14
Alignment explanation
Indices: 5692671--5692705 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5692661 ATAATTTATT
5692671 AAAT-TAAATAAAC
1 AAATATAAATAAAC
5692684 AAATATAAATAAAC
1 AAATATAAATAAAC
5692698 AAA-ATAAA
1 AAATATAAA
5692706 ATATATTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATATAAATAAAC
Found at i:5699450 original size:20 final size:20
Alignment explanation
Indices: 5699425--5699477 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
5699415 TGATGTGATA
5699425 ATTTAAAATTTATTATAAAT
1 ATTTAAAATTTATTATAAAT
5699445 ATTTAAAATTTATTATAAAT
1 ATTTAAAATTTATTATAAAT
5699465 ATTTAAAATTTAT
1 ATTTAAAATTTAT
5699478 ATACTATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTAAAATTTATTATAAAT
Found at i:5700060 original size:52 final size:53
Alignment explanation
Indices: 5699990--5700091 Score: 163
Period size: 52 Copynumber: 1.9 Consensus size: 53
5699980 AACACTTAAC
* *
5699990 AGATAAATTTATTATACAAAATAGTAAATAAATATATAGTAAATAAAAAATTA
1 AGATAAATTTATTATACAAAATAGAAAATAAATATATAATAAATAAAAAATTA
5700043 AGAT-AATTTAATT-TACAAAATAGAAAATAAATATATAATAAATAAAAAA
1 AGATAAATTT-ATTATACAAAATAGAAAATAAATATATAATAAATAAAAAA
5700092 AATTAAGAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
52 39 0.85
53 7 0.15
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (53 bp):
AGATAAATTTATTATACAAAATAGAAAATAAATATATAATAAATAAAAAATTA
Found at i:5702227 original size:11 final size:11
Alignment explanation
Indices: 5702202--5702260 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
5702192 GATTTGCAAT
* *
5702202 AATTTTTATTT
1 AATTTATATTA
*
5702213 AATTTATTTTA
1 AATTTATATTA
5702224 AATTTGAATATTA
1 AATTT--ATATTA
*
5702237 AATATATATTA
1 AATTTATATTA
*
5702248 AATTTAAATTA
1 AATTTATATTA
5702259 AA
1 AA
5702261 AAATAAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 30 0.77
13 9 0.23
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (11 bp):
AATTTATATTA
Found at i:5702398 original size:23 final size:22
Alignment explanation
Indices: 5702372--5702437 Score: 61
Period size: 21 Copynumber: 3.1 Consensus size: 22
5702362 AAAATTATTT
5702372 AAATATATCAAAATTTAATAATA
1 AAATATAT-AAAATTTAATAATA
5702395 AAATAATATATAAA---AATAATA
1 AAAT-ATATA-AAATTTAATAATA
*
5702416 AAAT-T-TAAAATTTAAAAATA
1 AAATATATAAAATTTAATAATA
5702436 AA
1 AA
5702438 TAAATCAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
17 3 0.08
18 2 0.05
19 1 0.03
20 8 0.22
21 11 0.30
23 5 0.14
24 7 0.19
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATATATAAAATTTAATAATA
Found at i:5702420 original size:34 final size:32
Alignment explanation
Indices: 5702342--5702441 Score: 87
Period size: 34 Copynumber: 3.1 Consensus size: 32
5702332 TTATAAAAAT
* * *
5702342 AAAATAAT-AAATTTTATATAAAAATTATTTA
1 AAAATAATAAAATTTAATATAAAAAATATATA
*
5702373 AATAT-ATCAAAATTTAATAATAAAATAATATATA
1 AAAATAAT-AAAATTTAAT-ATAAAA-AATATATA
* * *
5702407 AAAATAATAAAATTTAAAATTTAAAAATAAATA
1 AAAATAATAAAATTTAATA-TAAAAAATATATA
5702440 AA
1 AA
5702442 TCAAAAAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
30 2 0.04
31 4 0.07
32 8 0.15
33 16 0.29
34 23 0.42
35 2 0.04
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (32 bp):
AAAATAATAAAATTTAATATAAAAAATATATA
Found at i:5702448 original size:23 final size:23
Alignment explanation
Indices: 5702388--5702448 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
5702378 ATCAAAATTT
* *
5702388 AATAATAAAAT--AATATATAAA
1 AATAATAAAATCAAAAATTTAAA
**
5702409 AATAATAAAATTTAAAATTTAAA
1 AATAATAAAATCAAAAATTTAAA
5702432 AATAA-ATAAATCAAAAA
1 AATAATA-AAATCAAAAA
5702449 AATTAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 11 0.33
22 1 0.03
23 21 0.64
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (23 bp):
AATAATAAAATCAAAAATTTAAA
Found at i:5702503 original size:26 final size:30
Alignment explanation
Indices: 5702448--5702508 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 30
5702438 TAAATCAAAA
5702448 AAATTAAATTAATAATATCATATTCAATTC
1 AAATTAAATTAATAATATCATATTCAATTC
*
5702478 AAATTAAA-TCATAATAT-AT-TT-AATTC
1 AAATTAAATTAATAATATCATATTCAATTC
5702504 AAATT
1 AAATT
5702509 CTAAATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 10 0.33
27 2 0.07
28 2 0.07
29 8 0.27
30 8 0.27
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (30 bp):
AAATTAAATTAATAATATCATATTCAATTC
Found at i:5703989 original size:29 final size:30
Alignment explanation
Indices: 5703931--5704006 Score: 100
Period size: 29 Copynumber: 2.5 Consensus size: 30
5703921 TAATATTTTG
5703931 ATTTTTAAATTATAATAAAATGCTTAATATA
1 ATTTTTAAATTATAA-AAAATGCTTAATATA
* *
5703962 ATTTTTAAATTTTAAAAAATTC-TAATATA
1 ATTTTTAAATTATAAAAAATGCTTAATATA
* *
5703991 ATATATAAATTATAAA
1 ATTTTTAAATTATAAA
5704007 TCTATTAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 20 0.50
30 6 0.15
31 14 0.35
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (30 bp):
ATTTTTAAATTATAAAAAATGCTTAATATA
Found at i:5704146 original size:29 final size:30
Alignment explanation
Indices: 5704120--5704181 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
5704110 TTCATCAAAT
*
5704120 ATTACATTAAATATTTT-TAAAATTCAATA
1 ATTACATTAAACATTTTATAAAATTCAATA
* *
5704149 ATTATATTAAACATTTTACTAAAATTTAATA
1 ATTACATTAAACATTTTA-TAAAATTCAATA
5704180 AT
1 AT
5704182 CATTTTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.54
31 13 0.46
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (30 bp):
ATTACATTAAACATTTTATAAAATTCAATA
Found at i:5704180 original size:31 final size:29
Alignment explanation
Indices: 5704120--5704195 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 29
5704110 TTCATCAAAT
* *
5704120 ATTACATTAAATATTTTTAAAATTCAATA
1 ATTATATTAAACATTTTTAAAATTCAATA
*
5704149 ATTATATTAAACATTTTACTAAAATTTAATA
1 ATTATATTAAACATTTT--TAAAATTCAATA
* *
5704180 ATCATTTTAAAACATT
1 ATTATATT-AAACATT
5704196 AATCCTAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 15 0.38
31 17 0.44
32 7 0.18
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTATATTAAACATTTTTAAAATTCAATA
Found at i:5705779 original size:17 final size:16
Alignment explanation
Indices: 5705754--5705792 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
5705744 AAGGGCTTAC
*
5705754 ATTGTTTTTTCTTTTTT
1 ATTGATTTTT-TTTTTT
5705771 ATTGATTTTTTTTTTT
1 ATTGATTTTTTTTTTT
5705787 ACTTGA
1 A-TTGA
5705793 ATGATGTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (16 bp):
ATTGATTTTTTTTTTT
Found at i:5714390 original size:2 final size:2
Alignment explanation
Indices: 5714383--5714421 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5714373 ATTTTTGTTT
5714383 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5714422 TCTTGTGATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5717329 original size:2 final size:2
Alignment explanation
Indices: 5717317--5717362 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
5717307 TTATGACATC
* * *
5717317 TA TA AA TA TA TA TA TA CA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5717359 TA TA
1 TA TA
5717363 AAGAGTTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:5717341 original size:16 final size:16
Alignment explanation
Indices: 5717322--5717362 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
5717312 ACATCTATAA
5717322 ATATATATATACATAT
1 ATATATATATACATAT
5717338 ATATATATATACATAT
1 ATATATATATACATAT
5717354 ATATATATA
1 ATATATATA
5717363 AAGAGTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATATATATACATAT
Found at i:5717829 original size:29 final size:29
Alignment explanation
Indices: 5717780--5717844 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
5717770 AATAGATTTT
* * **
5717780 TTAAAAAAATATTAACAAAATTTTTATTA
1 TTAAATAAATATCAACAAAATTTAAATTA
5717809 TTAAATAAATATCAA-ATAAATTTAAATTA
1 TTAAATAAATATCAACA-AAATTTAAATTA
5717838 -TAAATAA
1 TTAAATAA
5717845 TATTTATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 8 0.26
29 23 0.74
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (29 bp):
TTAAATAAATATCAACAAAATTTAAATTA
Found at i:5726713 original size:21 final size:20
Alignment explanation
Indices: 5726681--5726720 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5726671 TTTAAACATC
* *
5726681 ATATTTATTAATTATATGAT
1 ATATATATTAATTAAATGAT
5726701 ATATATATATAATTAAATGA
1 ATATATAT-TAATTAAATGA
5726721 CTTTGTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
ATATATATTAATTAAATGAT
Found at i:5727078 original size:2 final size:2
Alignment explanation
Indices: 5727071--5727108 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
5727061 CATTTGCCTT
*
5727071 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5727109 AAACTTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5733340 original size:9 final size:9
Alignment explanation
Indices: 5733326--5733357 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
5733316 TCGTAAAGTT
5733326 TTTTTTTTA
1 TTTTTTTTA
5733335 TTTTTTTTTA
1 -TTTTTTTTA
5733345 TTTTTTTTA
1 TTTTTTTTA
5733354 TTTT
1 TTTT
5733358 CACTTATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:5733340 original size:10 final size:10
Alignment explanation
Indices: 5733325--5733357 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
5733315 ATCGTAAAGT
5733325 TTTTTTTTTA
1 TTTTTTTTTA
5733335 TTTTTTTTTA
1 TTTTTTTTTA
5733345 -TTTTTTTTA
1 TTTTTTTTTA
5733354 TTTT
1 TTTT
5733358 CACTTATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:5733364 original size:19 final size:19
Alignment explanation
Indices: 5733326--5733365 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5733316 TCGTAAAGTT
***
5733326 TTTTTTTTATTTTTTTTTA
1 TTTTTTTTATTTTCACTTA
5733345 TTTTTTTTATTTTCACTTA
1 TTTTTTTTATTTTCACTTA
5733364 TT
1 TT
5733366 GTCATATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTTATTTTCACTTA
Found at i:5733519 original size:25 final size:25
Alignment explanation
Indices: 5733491--5733577 Score: 68
Period size: 25 Copynumber: 3.4 Consensus size: 25
5733481 CTAAATAAAA
5733491 AAATAAAAAACAAAAAAATCTTTTC
1 AAATAAAAAACAAAAAAATCTTTTC
**** * *
5733516 AAATAAGTTTTC-AAAAAATCTATTA
1 AAATAA-AAAACAAAAAAATCTTTTC
* *
5733541 AAACAAAAAACAAAAAAATCCTTTC
1 AAATAAAAAACAAAAAAATCTTTTC
5733566 AATAATAAAAAA
1 -A-AATAAAAAA
5733578 ATCTTTTTTC
Statistics
Matches: 43, Mismatches: 15, Indels: 6
0.67 0.23 0.09
Matches are distributed among these distances:
24 1 0.02
25 32 0.74
26 2 0.05
27 8 0.19
ACGTcount: A:0.63, C:0.11, G:0.01, T:0.24
Consensus pattern (25 bp):
AAATAAAAAACAAAAAAATCTTTTC
Found at i:5737639 original size:11 final size:11
Alignment explanation
Indices: 5737623--5737659 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5737613 GGTGTGCAGA
5737623 AAAAAAAAGAG
1 AAAAAAAAGAG
5737634 AAAAAAAAG-G
1 AAAAAAAAGAG
5737644 TAAAAAAAA-AG
1 -AAAAAAAAGAG
5737655 AAAAA
1 AAAAA
5737660 GAGACAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:5737658 original size:29 final size:27
Alignment explanation
Indices: 5737622--5737677 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 27
5737612 AGGTGTGCAG
5737622 AAAAAAAAAGAGAAAAAAAAGGTAAAAA
1 AAAAAAAAAGAGAAAAAAAAGG-AAAAA
*
5737650 AAAAGAAAAAGAGACAAAAAAGGAAAAA
1 AAAA-AAAAAGAGAAAAAAAAGGAAAAA
5737678 TGAAGACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (27 bp):
AAAAAAAAAGAGAAAAAAAAGGAAAAA
Found at i:5747250 original size:48 final size:48
Alignment explanation
Indices: 5747198--5747290 Score: 152
Period size: 48 Copynumber: 1.9 Consensus size: 48
5747188 ATATTTACTG
5747198 AATATTATCT-TTTAAAAATAATTTAAAAATAATTATATAAATTAACTA
1 AATATTATCTCTTT-AAAATAATTTAAAAATAATTATATAAATTAACTA
* *
5747246 AATATTATCTCTTTAAAATAATTTTAAAATGATTATATAAATTAA
1 AATATTATCTCTTTAAAATAATTTAAAAATAATTATATAAATTAA
5747291 TCGAGGTTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
48 39 0.93
49 3 0.07
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (48 bp):
AATATTATCTCTTTAAAATAATTTAAAAATAATTATATAAATTAACTA
Found at i:5747847 original size:22 final size:22
Alignment explanation
Indices: 5747820--5747865 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
5747810 GTTTCGCCTT
5747820 GTATCCTCTTGCAATAGAAATG
1 GTATCCTCTTGCAATAGAAATG
5747842 GTATCCTCTTGCAATAGAAATG
1 GTATCCTCTTGCAATAGAAATG
5747864 GT
1 GT
5747866 CAGTGGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (22 bp):
GTATCCTCTTGCAATAGAAATG
Found at i:5750541 original size:16 final size:16
Alignment explanation
Indices: 5750503--5750547 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
5750493 TTATGCATTA
* *
5750503 TATTTTTCTTATGTTT
1 TATTATTCTTTTGTTT
5750519 TATTTATTCTTTTGTTT
1 TA-TTATTCTTTTGTTT
5750536 TATTATT-TTTTG
1 TATTATTCTTTTG
5750548 AAAGATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 5 0.19
16 7 0.27
17 14 0.54
ACGTcount: A:0.13, C:0.04, G:0.07, T:0.76
Consensus pattern (16 bp):
TATTATTCTTTTGTTT
Found at i:5750751 original size:110 final size:110
Alignment explanation
Indices: 5750532--5750737 Score: 349
Period size: 110 Copynumber: 1.9 Consensus size: 110
5750522 TTATTCTTTT
* *
5750532 GTTTTATTATTTTTTGAAAGATTTATAAATTAAAATAATTTTAAAAAACTAATAAAATATATAAT
1 GTTTTATTATGTTTTGAAAGATTTATAAATTAAAATAATTTTAAAAAACTAATAAAATATAAAAT
* *
5750597 TTTATTAATTTATATTATATGTTTAAAATTTAAGAAAAAAACATA
66 TTTATCAATTTATATTACATGTTTAAAATTTAAGAAAAAAACATA
* *
5750642 GTTTTATTATGTTTTGAAAGATTTATAAATTAAAATAATTTTAAAAAATTAATCAAATATAAAAT
1 GTTTTATTATGTTTTGAAAGATTTATAAATTAAAATAATTTTAAAAAACTAATAAAATATAAAAT
*
5750707 TTTATCAATTTGTATTACATGTTTAAAATTT
66 TTTATCAATTTATATTACATGTTTAAAATTT
5750738 TAAATACAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 89 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (110 bp):
GTTTTATTATGTTTTGAAAGATTTATAAATTAAAATAATTTTAAAAAACTAATAAAATATAAAAT
TTTATCAATTTATATTACATGTTTAAAATTTAAGAAAAAAACATA
Found at i:5753111 original size:26 final size:25
Alignment explanation
Indices: 5753082--5753137 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
5753072 TCAAATCACT
5753082 AAAAAAT-TATAAAAAATTTTATATTG
1 AAAAAATATATAAAAAA-TTTAT-TTG
**
5753108 -AAAAATATATATGAAATTTATTTG
1 AAAAAATATATAAAAAATTTATTTG
5753132 AAAAAA
1 AAAAAA
5753138 AAATGACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 3 0.12
25 16 0.62
26 7 0.27
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (25 bp):
AAAAAATATATAAAAAATTTATTTG
Found at i:5755111 original size:16 final size:16
Alignment explanation
Indices: 5755090--5755147 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
5755080 GTTTGAATAA
5755090 TTGAATTCAGATCAAT
1 TTGAATTCAGATCAAT
* *
5755106 TTGAATTCAAACCAAT
1 TTGAATTCAGATCAAT
* *
5755122 TTAAATTC-GAATCAAAA
1 TTGAATTCAG-ATC-AAT
5755139 TTGAATTCA
1 TTGAATTCA
5755148 ACGTTAGATT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
16 23 0.72
17 9 0.28
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (16 bp):
TTGAATTCAGATCAAT
Found at i:5757239 original size:2 final size:2
Alignment explanation
Indices: 5757232--5757257 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5757222 TCCAAGAAAT
5757232 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5757258 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5757262 original size:2 final size:2
Alignment explanation
Indices: 5757257--5757294 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5757247 ATATATATAT
* *
5757257 AG AG AG AG AG AG AG AG AG AG AG AG AG AG CG GG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5757295 CAAGGATGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.45, C:0.03, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5762455 original size:48 final size:48
Alignment explanation
Indices: 5762398--5762495 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
5762388 AAAACTCAAA
* *
5762398 TATAAAACTAAAAATACATTAAATAAATAATTTTATTTTAGGAATTGT
1 TATAAAACTAAAAATACATTAAATAAATAATTTTAGTTTAGAAATTGT
*
5762446 TATAAAACTAAAAATACATTAAATAAATCATTTTAGTTTAGAAATTGT
1 TATAAAACTAAAAATACATTAAATAAATAATTTTAGTTTAGAAATTGT
5762494 TA
1 TA
5762496 GAATTTTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.39
Consensus pattern (48 bp):
TATAAAACTAAAAATACATTAAATAAATAATTTTAGTTTAGAAATTGT
Found at i:5764912 original size:21 final size:19
Alignment explanation
Indices: 5764880--5764919 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
5764870 AATTATTTCA
*
5764880 AAATAATTTTAATAATGAT
1 AAATAATTTTAACAATGAT
5764899 AAATACATATTTAACAATGAT
1 AAATA-AT-TTTAACAATGAT
5764920 TTTGATAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 2 0.11
21 11 0.61
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (19 bp):
AAATAATTTTAACAATGAT
Found at i:5767686 original size:13 final size:13
Alignment explanation
Indices: 5767666--5767703 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5767656 ATAATATTTT
5767666 TATTAAATTAATA
1 TATTAAATTAATA
* *
5767679 TTTTAAATTAAGA
1 TATTAAATTAATA
5767692 TATTAAA-TAATA
1 TATTAAATTAATA
5767704 AGTTTATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (13 bp):
TATTAAATTAATA
Found at i:5768124 original size:24 final size:25
Alignment explanation
Indices: 5768092--5768139 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
5768082 AATTAACAAC
*
5768092 AAAAGTTTCTTAGTTTTTT-ATTAA
1 AAAAATTTCTTAGTTTTTTCATTAA
*
5768116 AAAAATTTCTTGGTTTTTTCATTA
1 AAAAATTTCTTAGTTTTTTCATTA
5768140 TTTATCAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.54
Consensus pattern (25 bp):
AAAAATTTCTTAGTTTTTTCATTAA
Found at i:5770808 original size:28 final size:28
Alignment explanation
Indices: 5770742--5770808 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 28
5770732 TCTCTAGAAT
* *
5770742 TTTTTTATATTTCAAATATATTTTATAAA
1 TTTTTTA-ATTTAAAATATATATTATAAA
* * *
5770771 ATATTAAATTTAAAATA-ATATTATAACA
1 TTTTTTAATTTAAAATATATATTATAA-A
5770799 TTTTTTAATT
1 TTTTTTAATT
5770809 ATAATTTTTT
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
27 8 0.28
28 17 0.59
29 4 0.14
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTTTTAATTTAAAATATATATTATAAA
Found at i:5770998 original size:33 final size:31
Alignment explanation
Indices: 5770914--5770998 Score: 75
Period size: 33 Copynumber: 2.7 Consensus size: 31
5770904 TTACATATCA
* *
5770914 TTTTTAAAAAATTAAGT-AAAAATTTTACAT
1 TTTTTTAAAAATTAAGTAAAAAATTATACAT
** *
5770944 TAGTTTAAAAACTTAAATAAAAAACTTCATA-AT
1 TTTTTTAAAAA-TTAAGTAAAAAA-TT-ATACAT
5770977 TTTTTTAAAATATTAAGTAAAA
1 TTTTTTAAAA-ATTAAGTAAAA
5770999 TTTTCAAATC
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
30 8 0.19
31 5 0.12
32 5 0.12
33 21 0.50
34 3 0.07
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.40
Consensus pattern (31 bp):
TTTTTTAAAAATTAAGTAAAAAATTATACAT
Found at i:5771560 original size:14 final size:14
Alignment explanation
Indices: 5771543--5771572 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5771533 TTTTTTTCTT
5771543 TTTTATAAAATATA
1 TTTTATAAAATATA
5771557 TTTTATAAAATATA
1 TTTTATAAAATATA
5771571 TT
1 TT
5771573 ACAAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTATAAAATATA
Found at i:5772428 original size:25 final size:23
Alignment explanation
Indices: 5772387--5772455 Score: 57
Period size: 27 Copynumber: 2.7 Consensus size: 23
5772377 TAATATGATA
*
5772387 TATATATTTTTTGTATTATAAAATT
1 TATATATATTTT-TATTA-AAAATT
*
5772412 TATATACTATTTTTATTAAAATTT
1 TATATA-TATTTTTATTAAAAATT
5772436 TAAATTATATTATTTTTATT
1 T--A-TATA-TATTTTTATT
5772456 TTTTTGGTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
24 6 0.16
25 11 0.30
26 6 0.16
27 14 0.38
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (23 bp):
TATATATATTTTTATTAAAAATT
Done.