Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 193 of 195
Found at i:35322798 original size:5 final size:5
Alignment explanation
Indices: 35322782--35322813 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
35322772 ATAATTGCAG
*
35322782 TTAAA TTGAA TTAAA TTAAA TTAAA TTAAA TT
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TT
35322814 TGCTTTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:35323556 original size:3 final size:3
Alignment explanation
Indices: 35323548--35323572 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35323538 TCCCCCTCCC
35323548 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
35323573 CCTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:35323789 original size:2 final size:2
Alignment explanation
Indices: 35323782--35323809 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35323772 GTTCTCTGTT
35323782 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
35323810 CGTCATCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:35324103 original size:11 final size:11
Alignment explanation
Indices: 35324087--35324112 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35324077 TATTAATTAT
35324087 TTTATTATATA
1 TTTATTATATA
35324098 TTTATTATATA
1 TTTATTATATA
35324109 TTTA
1 TTTA
35324113 AATAAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTATTATATA
Found at i:35324382 original size:5 final size:5
Alignment explanation
Indices: 35324374--35324406 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
35324364 CTTAATTATA
35324374 ATTTT ATTTT ATTTT ATTTT ATTTT AATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT -ATTTT AT
35324407 ATATCAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:35325046 original size:20 final size:20
Alignment explanation
Indices: 35325008--35325048 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
35324998 TACTTGAATC
* *
35325008 ATATATAATATTATATTATA
1 ATATATAAAAATATATTATA
*
35325028 ATATATAAAAATATTTTATA
1 ATATATAAAAATATATTATA
35325048 A
1 A
35325049 GATTTACTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATATAAAAATATATTATA
Found at i:35334763 original size:3 final size:3
Alignment explanation
Indices: 35334755--35334781 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
35334745 GTAAGATTTG
35334755 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
35334782 GTTAATCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:35340950 original size:15 final size:16
Alignment explanation
Indices: 35340930--35340964 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
35340920 ATGGTTTTTA
35340930 TTTATTTTTAAT-AAT
1 TTTATTTTTAATAAAT
*
35340945 TTTATTTTTATTAAAT
1 TTTATTTTTAATAAAT
35340961 TTTA
1 TTTA
35340965 AAACATCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTATTTTTAATAAAT
Found at i:35345082 original size:60 final size:60
Alignment explanation
Indices: 35344985--35345099 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 60
35344975 TCAAGATCCG
* *
35344985 AAACCCATTTCGTTATTACAACGTTGACCCTTCGTGGCTTCTTTGCCATCTCTCCTTCCA
1 AAACCCATTTCCTTATTACAACGTTGACCCTTCGTGGCTTCTTTACCATCTCTCCTTCCA
* * *
35345045 AAACCCATTTCCTTATTAGC-ATGTTGATCCTTTGTGGCTTCTTTACCATCTCTCC
1 AAACCCATTTCCTTATTA-CAACGTTGACCCTTCGTGGCTTCTTTACCATCTCTCC
35345100 GTAATTCTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
60 48 0.98
61 1 0.02
ACGTcount: A:0.18, C:0.31, G:0.11, T:0.39
Consensus pattern (60 bp):
AAACCCATTTCCTTATTACAACGTTGACCCTTCGTGGCTTCTTTACCATCTCTCCTTCCA
Found at i:35345837 original size:26 final size:27
Alignment explanation
Indices: 35345782--35345837 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
35345772 TTTTTTTTAC
* *
35345782 TAAATTTTAAAGTAAAAGTTACAGTCA
1 TAAATTATAAAGTAAAAGTTACAATCA
* *
35345809 TAAATTATAAA-TTAAAGTTACAATTA
1 TAAATTATAAAGTAAAAGTTACAATCA
35345835 TAA
1 TAA
35345838 TCAAATATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (27 bp):
TAAATTATAAAGTAAAAGTTACAATCA
Found at i:35363578 original size:25 final size:25
Alignment explanation
Indices: 35363550--35363600 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
35363540 TCTGACATAT
*
35363550 TGAAAGATGGACTGCTATTTAATAA
1 TGAAAGATGGACAGCTATTTAATAA
35363575 TGAAAGATGGACAGCTATTTAATAA
1 TGAAAGATGGACAGCTATTTAATAA
35363600 T
1 T
35363601 TTATCAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (25 bp):
TGAAAGATGGACAGCTATTTAATAA
Found at i:35376808 original size:21 final size:22
Alignment explanation
Indices: 35376784--35376828 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
35376774 TTATTTATCT
*
35376784 AAATC-TATTTAAAT-ATATTAA
1 AAATCATATTAAAATAATA-TAA
35376805 AAATCATATTAAAATAATATAA
1 AAATCATATTAAAATAATATAA
35376827 AA
1 AA
35376829 TTTAAAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 13 0.62
23 3 0.14
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATCATATTAAAATAATATAA
Found at i:35395477 original size:20 final size:22
Alignment explanation
Indices: 35395452--35395503 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
35395442 ACTTTGATGC
35395452 ATAATTTATAT-ATT-ATTAAT
1 ATAATTTATATCATTGATTAAT
35395472 ATAATTATTATATCATTGATTAAT
1 ATAA-T-TTATATCATTGATTAAT
*
35395496 ATATTTTA
1 ATAATTTA
35395504 AATTTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.15
21 1 0.04
22 9 0.33
23 4 0.15
24 9 0.33
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
ATAATTTATATCATTGATTAAT
Found at i:35395516 original size:17 final size:16
Alignment explanation
Indices: 35395491--35395548 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
35395481 ATATCATTGA
35395491 TTAATATATTTTAAATT
1 TTAA-ATATTTTAAATT
35395508 TTAAA-ATATTTAAA--
1 TTAAATAT-TTTAAATT
*
35395522 ATAAATATTTTTAAATT
1 TTAAATA-TTTTAAATT
35395539 TTAAATATTT
1 TTAAATATTT
35395549 AATTATGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
14 4 0.12
15 9 0.26
16 11 0.32
17 10 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATATTTTAAATT
Found at i:35397160 original size:43 final size:43
Alignment explanation
Indices: 35397099--35397186 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
35397089 TTGATGAAAG
35397099 GTTAATAGGTTTCTAATTTATATATGCTAAGGTGAAATGTTTT
1 GTTAATAGGTTTCTAATTTATATATGCTAAGGTGAAATGTTTT
35397142 GTTAATAGGTTTCTAATTTATATATGCTAAGGTGAAATGTTTT
1 GTTAATAGGTTTCTAATTTATATATGCTAAGGTGAAATGTTTT
35397185 GT
1 GT
35397187 GTCAGATTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.47
Consensus pattern (43 bp):
GTTAATAGGTTTCTAATTTATATATGCTAAGGTGAAATGTTTT
Found at i:35414096 original size:3 final size:3
Alignment explanation
Indices: 35414088--35414112 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35414078 GGATACTCGT
35414088 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
35414113 TGAACAGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:35415322 original size:109 final size:104
Alignment explanation
Indices: 35415075--35415445 Score: 534
Period size: 109 Copynumber: 3.5 Consensus size: 104
35415065 TAAAATAAAT
* *
35415075 AATGAATGTTTTTATTTTTAGAATTGTTGGTGTTTGATAAAATAATTACTTATCAAACTTCTCAG
1 AATGAATGTTTTTATTTTTAGAATTGTTGGTGTTTGATAAAAAAATTATTTATCAAACTTCTCAG
35415140 AAAAAATGGTAAGGATGT--AAAAA-AATAATGAATGATTG
66 -AAAAA-GGTAAGGATGTAAAAAAATAATAATGAATGATTG
*
35415178 AATGAATGTTTTTATTTTTATAATTGTTGGTGTTTGATAAAAAAATTATTTATCAAACTTCTCAG
1 AATGAATGTTTTTATTTTTAGAATTGTTGGTGTTTGATAAAAAAATTATTTATCAAACTTCTCAG
*
35415243 AAAAAGGTAAGGATGTAAAAAAGAATAATAATAATGAATAATTG
66 AAAAAGGTAAGGATGT---AAA-AA-AATAATAATGAATGATTG
* * *
35415287 AATGAATGTTTTTATTTTTAGAATTGTTGGTGTTTGATAAAAAAATTATTTATTAAACTTATGAG
1 AATGAATGTTTTTATTTTTAGAATTGTTGGTGTTTGATAAAAAAATTATTTATCAAACTTCTCAG
*
35415352 AAAAAGGTAAGGATGCAAAAAAATAATAATGAATGATTG
66 AAAAAGGTAAGGATGTAAAAAAATAATAATGAATGATTG
* *
35415391 AATGAATGAATTTTT-TTTTTAGCATTGTTGGTGTTTGATAAAAAAAAATATTTAT
1 AATGAATG--TTTTTATTTTTAGAATTGTTGGTGTTTGAT-AAAAAAATTATTTAT
35415446 TACATTTGAG
Statistics
Matches: 245, Mismatches: 12, Indels: 19
0.89 0.04 0.07
Matches are distributed among these distances:
101 11 0.04
102 5 0.02
103 62 0.25
104 25 0.10
105 25 0.10
106 23 0.09
107 2 0.01
108 2 0.01
109 90 0.37
ACGTcount: A:0.42, C:0.03, G:0.16, T:0.39
Consensus pattern (104 bp):
AATGAATGTTTTTATTTTTAGAATTGTTGGTGTTTGATAAAAAAATTATTTATCAAACTTCTCAG
AAAAAGGTAAGGATGTAAAAAAATAATAATGAATGATTG
Found at i:35415552 original size:23 final size:23
Alignment explanation
Indices: 35415526--35415617 Score: 76
Period size: 23 Copynumber: 3.8 Consensus size: 23
35415516 TTTATTCTTA
* *
35415526 AATATTAAATAAACATGTTTATG
1 AATATTAAATAAATATATTTATG
* *
35415549 AATATATATAGATAAATATATTCATA
1 AATAT-TA-A-ATAAATATATTTATG
*
35415575 AATAATAAATAAATATATTTATG
1 AATATTAAATAAATATATTTATG
* * *
35415598 ATTAATAAAAAAATTATATT
1 AATATTAAATAAA-TATATT
35415618 CAAATAAATT
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
23 29 0.52
24 9 0.16
25 3 0.05
26 15 0.27
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.39
Consensus pattern (23 bp):
AATATTAAATAAATATATTTATG
Found at i:35415626 original size:49 final size:49
Alignment explanation
Indices: 35415518--35415619 Score: 120
Period size: 49 Copynumber: 2.1 Consensus size: 49
35415508 TAAACGAATT
* * * * *
35415518 TATTCTTAAATATTAAATAAACATGTTTATGAATATATATAGATAAATA
1 TATTCATAAATAATAAATAAACATATTTATGAATATATATAAAAAAATA
*
35415567 TATTCATAAATAATAAATAAATATATTTATG-AT-TA-ATAAAAAAATTA
1 TATTCATAAATAATAAATAAACATATTTATGAATATATATAAAAAAA-TA
35415614 TATTCA
1 TATTCA
35415620 AATAAATTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
46 7 0.15
47 10 0.22
48 2 0.04
49 27 0.59
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (49 bp):
TATTCATAAATAATAAATAAACATATTTATGAATATATATAAAAAAATA
Found at i:35427506 original size:81 final size:82
Alignment explanation
Indices: 35427362--35427524 Score: 249
Period size: 81 Copynumber: 2.0 Consensus size: 82
35427352 TTGCGTGGAA
* *
35427362 GCCTCCATCGAGAAAATCTAGGCCGTTGGTTTTTGGGCCCACTTTCATTTCAAATTA-TCTTTTT
1 GCCTCCATCAAGAAAACCTAGGCCGTTGGTTTTTGGGCCCACTTTCATTTCAAATTATTCTTTTT
35427426 TACTTTTATTATTTATT
66 TACTTTTATTATTTATT
* * *
35427443 GCCTCCATCAAGAAAACCTAGGCCGTTGG-TTTTGGGCCCACTTTCTTTTCAAATTTTGTTTTTT
1 GCCTCCATCAAGAAAACCTAGGCCGTTGGTTTTTGGGCCCACTTTCATTTCAAATTAT-TCTTTT
*
35427507 TTGCTTTTATTATTTATT
65 TTACTTTTATTATTTATT
35427525 TCTGATTTCG
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
80 25 0.34
81 27 0.36
82 22 0.30
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.47
Consensus pattern (82 bp):
GCCTCCATCAAGAAAACCTAGGCCGTTGGTTTTTGGGCCCACTTTCATTTCAAATTATTCTTTTT
TACTTTTATTATTTATT
Found at i:35429570 original size:114 final size:114
Alignment explanation
Indices: 35429353--35429579 Score: 305
Period size: 114 Copynumber: 2.0 Consensus size: 114
35429343 TTAAATTAGG
** *
35429353 TGTCAACTAAATATTAATTCATATGACATATGGAATAGTTAGATTCATAAAGATTACATGTTAAT
1 TGTCAACTAAATATTAATTCATATGACATACAGAAAAGTTAGATTCATAAAGATTACATGTTAAT
* *
35429418 AATATTTAGACACATAATATTTTATTTACATTATTTAAATAAATAAAGT
66 AATATTTAGACACATAATATTTTATTTACATGACTTAAATAAATAAAGT
* * *
35429467 TGTCAACTAAATATTAATTCATATGACATACATAAAAGTTAGACTT-ATAAAGATTATATGTTCA
1 TGTCAACTAAATATTAATTCATATGACATACAGAAAAGTTAGA-TTCATAAAGATTACATGTTAA
* ** **
35429531 TAATATTTAGTCGTATAATATTCTT-TTTATGTGACTTAAATAAATAAAG
65 TAATATTTAGACACATAATATT-TTATTTACATGACTTAAATAAATAAAG
35429580 ATTTAAGAGT
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
114 94 0.96
115 4 0.04
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (114 bp):
TGTCAACTAAATATTAATTCATATGACATACAGAAAAGTTAGATTCATAAAGATTACATGTTAAT
AATATTTAGACACATAATATTTTATTTACATGACTTAAATAAATAAAGT
Found at i:35443407 original size:2 final size:2
Alignment explanation
Indices: 35443395--35443433 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
35443385 GTAGAGGATG
*
35443395 AT AT TT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35443434 CAAAGAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35447368 original size:17 final size:17
Alignment explanation
Indices: 35447327--35447360 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
35447317 CTAGCAAAAA
35447327 TCCACATCTTGGATAAG
1 TCCACATCTTGGATAAG
35447344 TCCACATCTTGGATAAG
1 TCCACATCTTGGATAAG
35447361 GATCCATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (17 bp):
TCCACATCTTGGATAAG
Found at i:35456835 original size:25 final size:25
Alignment explanation
Indices: 35456801--35456851 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
35456791 AAAGTGTTGA
35456801 ACGTGGAGAGTCTACTTTTAATGAG
1 ACGTGGAGAGTCTACTTTTAATGAG
35456826 ACGTGGAGAGTCTACTTTTAATGAG
1 ACGTGGAGAGTCTACTTTTAATGAG
35456851 A
1 A
35456852 TTAGCTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.31
Consensus pattern (25 bp):
ACGTGGAGAGTCTACTTTTAATGAG
Found at i:35459163 original size:2 final size:2
Alignment explanation
Indices: 35459156--35459183 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35459146 TTCTGCCTAC
35459156 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35459184 CTGCAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35460414 original size:1 final size:1
Alignment explanation
Indices: 35460408--35460432 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
35460398 TAACGATTGT
35460408 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
35460433 AGGATGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:35472404 original size:3 final size:3
Alignment explanation
Indices: 35472396--35472424 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
35472386 AAACACAAAT
35472396 ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35472425 TACCAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:35472416 original size:11 final size:11
Alignment explanation
Indices: 35472396--35472426 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
35472386 AAACACAAAT
35472396 ATAATAATAATA
1 ATAAT-ATAATA
35472408 ATAATATAATA
1 ATAATATAATA
35472419 ATAATATA
1 ATAATATA
35472427 CCAATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATATAATA
Found at i:35477676 original size:2 final size:2
Alignment explanation
Indices: 35477669--35477693 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35477659 ACCAAAGCCG
35477669 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 T
35477694 GAAATTGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35477903 original size:28 final size:28
Alignment explanation
Indices: 35477872--35477955 Score: 102
Period size: 28 Copynumber: 3.0 Consensus size: 28
35477862 TGTCTCAAAT
35477872 TTTTTATTTTTTAAAATAAAAATTTATA
1 TTTTTATTTTTTAAAATAAAAATTTATA
35477900 TTTTTATTATATTT-AAAT-AAAATTT-TA
1 TTTTTATT-T-TTTAAAATAAAAATTTATA
*
35477927 TTTTTATTTTTATATAAATAAATATTTAT
1 TTTTTATTTTT-TA-AAATAAAAATTTAT
35477956 TTAAATAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
25 2 0.04
26 2 0.04
27 10 0.21
28 19 0.40
29 11 0.23
30 4 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTTATTTTTTAAAATAAAAATTTATA
Found at i:35477934 original size:22 final size:22
Alignment explanation
Indices: 35477901--35477966 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
35477891 AAATTTATAT
*
35477901 TTTTA-TTATATTTAAATAAAA
1 TTTTATTTTTATTTAAATAAAA
**
35477922 TTTTATTTTTATTTTTATATAAA
1 TTTTATTTTTATTTAAATA-AAA
** *
35477945 -TAAATATTTATTTAAATAAAA
1 TTTTATTTTTATTTAAATAAAA
35477966 T
1 T
35477967 ATTAATTTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
21 8 0.24
22 23 0.68
23 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTATTTTTATTTAAATAAAA
Found at i:35477960 original size:16 final size:17
Alignment explanation
Indices: 35477935--35477975 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
35477925 TATTTTTATT
*
35477935 TTTATATAAAT-AAATA
1 TTTATTTAAATAAAATA
35477951 TTTATTTAAATAAAATA
1 TTTATTTAAATAAAATA
*
35477968 TTAATTTA
1 TTTATTTA
35477976 TATTGAGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTATTTAAATAAAATA
Found at i:35478021 original size:30 final size:29
Alignment explanation
Indices: 35477985--35478062 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 29
35477975 ATATTGAGAG
*
35477985 TTTATTTAAATATAAATTAAAAGTTA-AGAA
1 TTTATTTAAATA-AAATAAAAAGTTATA-AA
*
35478015 TTTATTTAAATAAAAATAAAAATTTATAAA
1 TTTATTTAAAT-AAAATAAAAAGTTATAAA
35478045 TTTATTTAAATAAAATAA
1 TTTATTTAAATAAAATAA
35478063 TAAAATAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
29 7 0.16
30 35 0.80
31 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (29 bp):
TTTATTTAAATAAAATAAAAAGTTATAAA
Found at i:35486226 original size:2 final size:2
Alignment explanation
Indices: 35486219--35486248 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35486209 CATCATATCG
35486219 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35486249 GAATAATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35492907 original size:5 final size:5
Alignment explanation
Indices: 35492897--35492929 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
35492887 GAGAAGAAAC
35492897 TCTCT TCTCT TCTCT TCTCT TCTC- -CTCT TCTCT
1 TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT
35492930 GCAAACAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 3 0.12
5 23 0.88
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (5 bp):
TCTCT
Found at i:35506266 original size:21 final size:21
Alignment explanation
Indices: 35506237--35506281 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35506227 AATTCTCCTT
* * *
35506237 TTTTTTTTTTTTTTTTTTTAG
1 TTTTCTTTTTTCTTTTCTTAG
35506258 TTTTCTTTTTTCTTTTCTTAG
1 TTTTCTTTTTTCTTTTCTTAG
35506279 TTT
1 TTT
35506282 ACGACGTCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.04, C:0.07, G:0.04, T:0.84
Consensus pattern (21 bp):
TTTTCTTTTTTCTTTTCTTAG
Found at i:35509189 original size:2 final size:2
Alignment explanation
Indices: 35509182--35509206 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35509172 GATGACATGA
35509182 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
35509207 GATTAATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35511777 original size:13 final size:13
Alignment explanation
Indices: 35511759--35511788 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35511749 TTTAAAATTG
*
35511759 AAAAAATAAAAAT
1 AAAAAATAAAAAC
35511772 AAAAAATAAAAAC
1 AAAAAATAAAAAC
35511785 AAAA
1 AAAA
35511789 CATTAGTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (13 bp):
AAAAAATAAAAAC
Found at i:35516140 original size:3 final size:3
Alignment explanation
Indices: 35516132--35516161 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
35516122 TAATTTATGC
*
35516132 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35516162 AAAGCAGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:35517209 original size:2 final size:2
Alignment explanation
Indices: 35517202--35517241 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
35517192 CTACATCTTT
35517202 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35517242 AGTAATGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35517858 original size:24 final size:23
Alignment explanation
Indices: 35517812--35517859 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
35517802 CTTGATAGTT
* *
35517812 TTTTTAAATGAAAATTTATTTTA
1 TTTTTAAATGAAAATTAAATTTA
*
35517835 TTTTTAACATTAAAATTAAATTTA
1 TTTTTAA-ATGAAAATTAAATTTA
35517859 T
1 T
35517860 AAATTAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTTAAATGAAAATTAAATTTA
Found at i:35536450 original size:27 final size:27
Alignment explanation
Indices: 35536420--35536475 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
35536410 TGAAGCACAT
* *
35536420 AATGTATTTCCATAATTAAAAAGTGCC
1 AATGTATTTCCACAATTAAAAAGTACC
*
35536447 AATGTTTTTCCACAATTAAAAAGTACC
1 AATGTATTTCCACAATTAAAAAGTACC
35536474 AA
1 AA
35536476 AAACTGTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (27 bp):
AATGTATTTCCACAATTAAAAAGTACC
Found at i:35545043 original size:59 final size:58
Alignment explanation
Indices: 35544940--35545121 Score: 147
Period size: 59 Copynumber: 3.0 Consensus size: 58
35544930 AAATGTCATA
* * *
35544940 AATAATAA-AAAAATGAAATAAAATTATTTAAGATGTTTTGTGACAAAAAATACATTGAAT
1 AATAATAATAAAAAT-AAATAAGATTA-TTAAGCT-TTTTTTGACAAAAAATACATTGAAT
* * *
35545000 AATAATAATAAAAA-AAATAAGATTATTGAATGCTTTTTTTGACATAAAATACTTTAAAT
1 AATAATAATAAAAATAAATAAGATTATT-AA-GCTTTTTTTGACAAAAAATACATTGAAT
** * *
35545059 AATCTCTTATAAAAATTTAAA-AATGATTATTAAAGAC-TTTTTTGATAAAAAATACATTGAAT
1 AAT-AATAATAAAAA--TAAATAA-GATTATT-AAG-CTTTTTTTGACAAAAAATACATTGAAT
35545121 A
1 A
35545122 GTATAATTCA
Statistics
Matches: 99, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
58 2 0.02
59 36 0.36
60 18 0.18
61 5 0.05
62 25 0.25
63 13 0.13
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.36
Consensus pattern (58 bp):
AATAATAATAAAAATAAATAAGATTATTAAGCTTTTTTTGACAAAAAATACATTGAAT
Found at i:35545537 original size:22 final size:21
Alignment explanation
Indices: 35545498--35545540 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
35545488 ATAAATAAAG
* *
35545498 TAAAAATAATTTATTAATTAT
1 TAAAAATAACTCATTAATTAT
35545519 TAAAAATAACTCATATAATTAT
1 TAAAAATAACTCAT-TAATTAT
35545541 CAAACTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAAATAACTCATTAATTAT
Found at i:35559480 original size:69 final size:69
Alignment explanation
Indices: 35559341--35559472 Score: 185
Period size: 69 Copynumber: 1.9 Consensus size: 69
35559331 CGATAGTGGT
* * **
35559341 TTTTCACAGCAACCAGATAGGCTCACAAGGTTTGACTCCATAAACAGTGGCAGAAACTTTGGCAG
1 TTTTCACAGCAACCAGAGACGCTCACAAGGTTTGACTCCATAAACAGTACCAGAAACTTTGGCAG
35559406 CGGA
66 CGGA
* * *
35559410 TTTTCACAGCAACCTGAGACGCTCACTAGGTTTGACTCCATAAATAGTACCA-AAGACTTTGGC
1 TTTTCACAGCAACCAGAGACGCTCACAAGGTTTGACTCCATAAACAGTACCAGAA-ACTTTGGC
35559473 CATGGATTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 2 0.04
69 53 0.96
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (69 bp):
TTTTCACAGCAACCAGAGACGCTCACAAGGTTTGACTCCATAAACAGTACCAGAAACTTTGGCAG
CGGA
Found at i:35561863 original size:16 final size:16
Alignment explanation
Indices: 35561839--35561869 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35561829 GTATAGTTTT
*
35561839 AAAATAAGGAAAAAAA
1 AAAAAAAGGAAAAAAA
35561855 AAAAAAAGGAAAAAA
1 AAAAAAAGGAAAAAA
35561870 TGCAAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (16 bp):
AAAAAAAGGAAAAAAA
Found at i:35561971 original size:2 final size:2
Alignment explanation
Indices: 35561964--35561991 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35561954 TCCACACGCC
35561964 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
35561992 TTGGCAGACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:35574422 original size:2 final size:2
Alignment explanation
Indices: 35574415--35574456 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
35574405 TTTATTGCGC
* *
35574415 AT AT AT AT AG AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35574457 TCTTTCTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:35581148 original size:2 final size:2
Alignment explanation
Indices: 35581141--35581189 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
35581131 CTCTTGCAAG
*
35581141 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35581183 TA TA TA T
1 TA TA TA T
35581190 GGTTTAAGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:35590936 original size:2 final size:2
Alignment explanation
Indices: 35590929--35590957 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35590919 ATGTCTCAAT
35590929 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
35590958 ACGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:35590972 original size:2 final size:2
Alignment explanation
Indices: 35590967--35591032 Score: 64
Period size: 2 Copynumber: 33.5 Consensus size: 2
35590957 TACGTGTGTG
* * * *
35590967 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TT TC TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
35591009 TA TA AA T- TA TA TA -A GTA TA TA TA T
1 TA TA TA TA TA TA TA TA -TA TA TA TA T
35591033 TGCCTGAAAG
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
1 2 0.04
2 49 0.94
3 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35592953 original size:2 final size:2
Alignment explanation
Indices: 35592946--35592970 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35592936 ACATACATAC
35592946 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
35592971 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35592975 original size:2 final size:2
Alignment explanation
Indices: 35592970--35593000 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35592960 ATATATATAT
35592970 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
35593001 TAATATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35593935 original size:39 final size:39
Alignment explanation
Indices: 35593880--35593957 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
35593870 AGGAAGAGCC
35593880 AGTGGTAATATGTCAGCAGGTGGCAAGTGAGGATTTTGA
1 AGTGGTAATATGTCAGCAGGTGGCAAGTGAGGATTTTGA
* *
35593919 AGTGGTAATATTTCAGCAGGTGGCAAGTGAGGGTTTTGA
1 AGTGGTAATATGTCAGCAGGTGGCAAGTGAGGATTTTGA
35593958 TTTAAAGCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.27, C:0.08, G:0.36, T:0.29
Consensus pattern (39 bp):
AGTGGTAATATGTCAGCAGGTGGCAAGTGAGGATTTTGA
Found at i:35602388 original size:2 final size:2
Alignment explanation
Indices: 35602381--35602409 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
35602371 GTAATATCTA
35602381 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35602410 TACATGATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:35602568 original size:27 final size:27
Alignment explanation
Indices: 35602531--35602597 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
35602521 CTATTTAATA
35602531 AATTATTTAAATTTAATATGTATAGAT
1 AATTATTTAAATTTAATATGTATAGAT
* * * *
35602558 AATTATATAAATTTAATGTGTTTGGAT
1 AATTATTTAAATTTAATATGTATAGAT
35602585 AATTATTTAAATT
1 AATTATTTAAATT
35602598 CAAATCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (27 bp):
AATTATTTAAATTTAATATGTATAGAT
Found at i:35603911 original size:2 final size:2
Alignment explanation
Indices: 35603906--35603931 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35603896 TGTATATATA
35603906 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
35603932 AGCTTAATAA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:35604697 original size:3 final size:3
Alignment explanation
Indices: 35604689--35604715 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
35604679 TTGTAGTTCA
35604689 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
35604716 TGACATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:35610221 original size:4 final size:4
Alignment explanation
Indices: 35610212--35610238 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
35610202 ACTCTCTGTC
35610212 TCTG TCTG TCTG TCTG TCTG TCTG TCT
1 TCTG TCTG TCTG TCTG TCTG TCTG TCT
35610239 CTCTCTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.22, T:0.52
Consensus pattern (4 bp):
TCTG
Found at i:35615728 original size:2 final size:2
Alignment explanation
Indices: 35615723--35615761 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
35615713 TCTCTCTCTC
* *
35615723 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TG 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
35615762 CAGCCTCTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (2 bp):
TA
Found at i:35620733 original size:26 final size:25
Alignment explanation
Indices: 35620698--35620747 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
35620688 TTAATGGTTA
35620698 TTTCATTTTTTACCTTCTCTTTTACCT
1 TTTCATTTTTT-CCTT-TCTTTTACCT
35620725 TTTCATTTTTT-CTTTCTTTTACC
1 TTTCATTTTTTCCTTTCTTTTACC
35620748 CATATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.39
25 3 0.13
27 11 0.48
ACGTcount: A:0.10, C:0.24, G:0.00, T:0.66
Consensus pattern (25 bp):
TTTCATTTTTTCCTTTCTTTTACCT
Found at i:35631172 original size:2 final size:2
Alignment explanation
Indices: 35631165--35631216 Score: 72
Period size: 2 Copynumber: 26.5 Consensus size: 2
35631155 TGCATGTTGA
*
35631165 AT AT AT AT AT AT AT AT AT AT TT GA- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
35631207 AT AT -T AT AT A
1 AT AT AT AT AT A
35631217 CAGAAATCGG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35631188 original size:24 final size:24
Alignment explanation
Indices: 35631161--35631208 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
35631151 ATCTTGCATG
35631161 TTGAATATATATATATATATATAT
1 TTGAATATATATATATATATATAT
35631185 TTGAATATATATATATATATATAT
1 TTGAATATATATATATATATATAT
35631209 ATTATATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
TTGAATATATATATATATATATAT
Found at i:35634634 original size:2 final size:2
Alignment explanation
Indices: 35634623--35634655 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
35634613 ACACACACAC
*
35634623 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35634656 AAGGCTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:35637202 original size:2 final size:2
Alignment explanation
Indices: 35637195--35637223 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35637185 GGAACGATAT
35637195 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
35637224 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:35637228 original size:2 final size:2
Alignment explanation
Indices: 35637223--35637255 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35637213 TCTCTCTCTC
35637223 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35637256 GTTGCTGTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35644267 original size:18 final size:18
Alignment explanation
Indices: 35644241--35644288 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
35644231 TCTTGGGCTA
*
35644241 TGCTATTGCTATTGATTT
1 TGCTTTTGCTATTGATTT
* *
35644259 TGCTTTTGCTTTTGCTTT
1 TGCTTTTGCTATTGATTT
* *
35644277 TCCTTTTCCTAT
1 TGCTTTTGCTAT
35644289 ACCTATAGCT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.08, C:0.19, G:0.12, T:0.60
Consensus pattern (18 bp):
TGCTTTTGCTATTGATTT
Found at i:35644286 original size:6 final size:6
Alignment explanation
Indices: 35644241--35644283 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
35644231 TCTTGGGCTA
* * * *
35644241 TGCTAT TGCTAT TGATTT TGCTTT TGCTTT TGCTTT TCCTTT T
1 TGCTTT TGCTTT TGCTTT TGCTTT TGCTTT TGCTTT TGCTTT T
35644284 CCTATACCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.07, C:0.16, G:0.14, T:0.63
Consensus pattern (6 bp):
TGCTTT
Found at i:35645023 original size:5 final size:5
Alignment explanation
Indices: 35645001--35645043 Score: 51
Period size: 4 Copynumber: 9.6 Consensus size: 5
35644991 GGTTCGTCTC
35645001 TTTC- TTTC- TTTC- TTTCT TTTCT TTTCT TTTCT TTT-T TTT-T TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
35645044 ATCTGTAGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 20 0.53
5 18 0.47
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTCT
Found at i:35647121 original size:5 final size:5
Alignment explanation
Indices: 35647113--35647159 Score: 67
Period size: 5 Copynumber: 9.4 Consensus size: 5
35647103 TTGAATTGAG
* * *
35647113 GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA GGAAA GGAAA GGAAA GG
1 GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA GG
35647160 AAAATAAAGG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (5 bp):
GGGAA
Found at i:35647160 original size:5 final size:5
Alignment explanation
Indices: 35647116--35647173 Score: 53
Period size: 5 Copynumber: 11.6 Consensus size: 5
35647106 AATTGAGGGG
* * * * * **
35647116 AAGGG AAGGG AAGGG AAGGG AAGGG AAGGA AAGGA AAGGA AAGGA AAATA
1 AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA
35647166 AAGGA AAG
1 AAGGA AAG
35647174 TAGTGGAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.53, C:0.00, G:0.45, T:0.02
Consensus pattern (5 bp):
AAGGA
Found at i:35654916 original size:2 final size:2
Alignment explanation
Indices: 35654911--35654939 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35654901 TATGATTCTT
35654911 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
35654940 TTGTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:35655900 original size:31 final size:32
Alignment explanation
Indices: 35655860--35655919 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
35655850 TTTTTTAACT
*
35655860 TGACTAAATTTATTTTAAAATTAAAAATATGA
1 TGACTAAATTTATTCTAAAATTAAAAATATGA
*
35655892 TGAC-AAATTTGTTCTAAAATTAAAAATA
1 TGACTAAATTTATTCTAAAATTAAAAATA
35655920 AAATGATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (32 bp):
TGACTAAATTTATTCTAAAATTAAAAATATGA
Found at i:35657174 original size:2 final size:2
Alignment explanation
Indices: 35657167--35657199 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35657157 CGTTTTGTTT
35657167 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35657200 GGTTGCCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35659272 original size:5 final size:5
Alignment explanation
Indices: 35659262--35659290 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
35659252 ACTTCCCTAT
35659262 CATAC CATAC CATAC CATAC CATAC CATA
1 CATAC CATAC CATAC CATAC CATAC CATA
35659291 ACAAGATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (5 bp):
CATAC
Found at i:35664408 original size:3 final size:3
Alignment explanation
Indices: 35664400--35664431 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
35664390 AACATACCAA
*
35664400 AAT AAT AAT AAT AAT AAT AAT AAA AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
35664432 AAGGACTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:35668391 original size:2 final size:2
Alignment explanation
Indices: 35668384--35668430 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
35668374 TACGGACCAC
35668384 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
35668426 CT CT C
1 CT CT C
35668431 CCCTCCTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:35668896 original size:4 final size:4
Alignment explanation
Indices: 35668889--35668950 Score: 70
Period size: 4 Copynumber: 15.5 Consensus size: 4
35668879 AAATAAATAA
* * * * *
35668889 ATAT ATAT ATAC ATAC ATAC ATAC ATAT ATAT ATAT ATAT ATAG ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
35668937 AGAT ATAT ATAT AT
1 ATAT ATAT ATAT AT
35668951 TATTTTCAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (4 bp):
ATAT
Found at i:35668924 original size:6 final size:6
Alignment explanation
Indices: 35668889--35668950 Score: 70
Period size: 6 Copynumber: 10.3 Consensus size: 6
35668879 AAATAAATAA
* * * * *
35668889 ATATAT ATATAC ATACAT ACATAC ATATAT ATATAT ATATAT AGATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
35668937 AGATAT ATATAT AT
1 ATATAT ATATAT AT
35668951 TATTTTCAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (6 bp):
ATATAT
Found at i:35674840 original size:15 final size:16
Alignment explanation
Indices: 35674806--35674849 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
35674796 AATGTACTCC
35674806 TATTTTATATTTTAAT
1 TATTTTATATTTTAAT
35674822 TATTTTA-ATTATT-AT
1 TATTTTATATT-TTAAT
*
35674837 TATTTTTTATTTT
1 TATTTTATATTTT
35674850 TTCTTTGACT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTTTATATTTTAAT
Found at i:35674908 original size:11 final size:11
Alignment explanation
Indices: 35674892--35674917 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35674882 TAATTAATTA
35674892 ATTATATTATT
1 ATTATATTATT
35674903 ATTATATTATT
1 ATTATATTATT
35674914 ATTA
1 ATTA
35674918 GAATCTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTATATTATT
Found at i:35687376 original size:190 final size:192
Alignment explanation
Indices: 35687018--35687404 Score: 661
Period size: 190 Copynumber: 2.0 Consensus size: 192
35687008 CTCCAGATAT
* *
35687018 ATTATAACATACATGTTGCCATGTTCATTCAAATTTCCAACTTTGGAGACTTCAATACATGTTGT
1 ATTACAACATACATGTTGCCATGTTCATTCAAATTTCCAACTTGGGAGACTTCAATACATGTTGT
* *
35687083 CCTTCGTTAGCGGAAGAGGGAGAAAGAGAGAGAGAGTAAGCAAAAAAAGAAACCAAACAAATTAA
66 ACTTCGTTAGCGGAAGAGAGAGAAAGAGAGAGAGAGTAAGCAAAAAAAGAAACCAAACAAATTAA
35687148 ATCCCAAAGTTAGAACATATAGTTTTGTTACTGACAATGCCTTAGCAATTAGTATGTCTTTA
131 ATCCCAAAGTTAGAACATATAGTTTTGTTACTGACAATGCCTTAGCAATTAGTATGTCTTTA
*
35687210 ATTACAACATACATGTTGCCATGTTCATTCAAATTTCCAACTTGGGAGACTTCAATACGTGTTGT
1 ATTACAACATACATGTTGCCATGTTCATTCAAATTTCCAACTTGGGAGACTTCAATACATGTTGT
* * * *
35687275 ACTTTGTTAGTGGAAGAGAGAG-AA-AGAGAGAGAGTGAGCAAAAAAAGAAACCGAACAAATTAA
66 ACTTCGTTAGCGGAAGAGAGAGAAAGAGAGAGAGAGTAAGCAAAAAAAGAAACCAAACAAATTAA
* *
35687338 ATCCCGAAGTTAGAACATATTGTTTTGTTACTGACAATGCCTTAGCAATTAGTATGTCTTTA
131 ATCCCAAAGTTAGAACATATAGTTTTGTTACTGACAATGCCTTAGCAATTAGTATGTCTTTA
35687400 ATTAC
1 ATTAC
35687405 TAAAACAAGG
Statistics
Matches: 184, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
190 102 0.55
191 2 0.01
192 80 0.43
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (192 bp):
ATTACAACATACATGTTGCCATGTTCATTCAAATTTCCAACTTGGGAGACTTCAATACATGTTGT
ACTTCGTTAGCGGAAGAGAGAGAAAGAGAGAGAGAGTAAGCAAAAAAAGAAACCAAACAAATTAA
ATCCCAAAGTTAGAACATATAGTTTTGTTACTGACAATGCCTTAGCAATTAGTATGTCTTTA
Found at i:35691169 original size:127 final size:127
Alignment explanation
Indices: 35690943--35691200 Score: 480
Period size: 127 Copynumber: 2.0 Consensus size: 127
35690933 ACATATTTCA
* *
35690943 GCAAGCAACAAATCACAAAAGTTCACAGAAGACACTAGTACTATGATGCTTGAGAGAAGCAGATA
1 GCAAGCAACAAATCACAAAAGCTCACAGAAGACACTACTACTATGATGCTTGAGAGAAGCAGATA
*
35691008 GGTTTCTACAACGCATCTCCCTGTCCCCCGGTGCAGTTCAAAGATAAGCCTTGTTGATATCG
66 GGTTTCTACAACGCATCTCCCTGTCCCCCGGTGCAGTTCAAAGATAAGCCTTGTTGAGATCG
35691070 GCAAGCAACAAATCACAAAAGCTCACAGAAGACACTACTACTATGATGCTTGAGAGAAGCAGATA
1 GCAAGCAACAAATCACAAAAGCTCACAGAAGACACTACTACTATGATGCTTGAGAGAAGCAGATA
*
35691135 GGTTTCTACAACGCATCTCCCTGTCCCCCTGTGCAGTTCAAAGATAAGCCTTGTTGAGATCG
66 GGTTTCTACAACGCATCTCCCTGTCCCCCGGTGCAGTTCAAAGATAAGCCTTGTTGAGATCG
35691197 GCAA
1 GCAA
35691201 AGTAAGGATG
Statistics
Matches: 127, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 127 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (127 bp):
GCAAGCAACAAATCACAAAAGCTCACAGAAGACACTACTACTATGATGCTTGAGAGAAGCAGATA
GGTTTCTACAACGCATCTCCCTGTCCCCCGGTGCAGTTCAAAGATAAGCCTTGTTGAGATCG
Found at i:35692572 original size:3 final size:3
Alignment explanation
Indices: 35692564--35692594 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
35692554 TTACAATTAC
35692564 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
35692595 CCTGACAATA
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:35693697 original size:16 final size:16
Alignment explanation
Indices: 35693656--35693699 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
35693646 TTTTTTTTCC
35693656 TTTATTTTTTATAACTT
1 TTTATTTTTT-TAACTT
* * *
35693673 TTCAATTTTTTAAGTT
1 TTTATTTTTTTAACTT
35693689 TTTATTTTTTT
1 TTTATTTTTTT
35693700 TTAAATTTAG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTATTTTTTTAACTT
Found at i:35694511 original size:13 final size:13
Alignment explanation
Indices: 35694501--35694525 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35694491 TGTTTTTTAT
35694501 TTTTTTATTTTTG
1 TTTTTTATTTTTG
35694514 TTTTTTATTTTT
1 TTTTTTATTTTT
35694526 TTACTTTCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTG
Found at i:35694511 original size:21 final size:21
Alignment explanation
Indices: 35694487--35694528 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
35694477 CATTTTCTCT
35694487 TTTTTGTTTTTTATTTTTTTA
1 TTTTTGTTTTTTATTTTTTTA
35694508 TTTTTGTTTTTTATTTTTTTA
1 TTTTTGTTTTTTATTTTTTTA
35694529 CTTTCCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.05, T:0.86
Consensus pattern (21 bp):
TTTTTGTTTTTTATTTTTTTA
Found at i:35694538 original size:21 final size:21
Alignment explanation
Indices: 35694493--35694545 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
35694483 CTCTTTTTTG
* **
35694493 TTTTTTATTTTTTTATTTTTG
1 TTTTTTATTTTTTTACTTTCC
35694514 TTTTTTATTTTTTTACTTTCC
1 TTTTTTATTTTTTTACTTTCC
*
35694535 TTTTTTGTTTT
1 TTTTTTATTTT
35694546 AATATTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.08, C:0.06, G:0.04, T:0.83
Consensus pattern (21 bp):
TTTTTTATTTTTTTACTTTCC
Found at i:35694879 original size:2 final size:2
Alignment explanation
Indices: 35694838--35694868 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35694828 TCATTTCAAG
35694838 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35694869 AAGGTATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35695716 original size:2 final size:2
Alignment explanation
Indices: 35695709--35695737 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35695699 AATAATAATG
35695709 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
35695738 CACTGTGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35701159 original size:6 final size:6
Alignment explanation
Indices: 35701143--35701178 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
35701133 GATTTCCGAT
*
35701143 TAGCAA AAGCAA TAGCAA TAGCAA TAGCAA TAGCAA
1 TAGCAA TAGCAA TAGCAA TAGCAA TAGCAA TAGCAA
35701179 AGAAGAGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.14
Consensus pattern (6 bp):
TAGCAA
Found at i:35706839 original size:11 final size:11
Alignment explanation
Indices: 35706791--35706869 Score: 52
Period size: 11 Copynumber: 6.6 Consensus size: 11
35706781 GAGAATTTTG
35706791 AATTTAAATTT
1 AATTTAAATTT
35706802 AATTTGAAATTT
1 AATTT-AAATTT
*
35706814 ATTATTAAAAATTT
1 A--ATT-TAAATTT
*
35706828 AATTTGAATTT
1 AATTTAAATTT
*
35706839 AA-TGAAATTTT
1 AATTTAAA-TTT
35706850 AATTTTTAAATTT
1 AA--TTTAAATTT
*
35706863 AAGTTAA
1 AATTTAA
35706870 TTTTTAAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
10 3 0.06
11 21 0.40
12 10 0.19
13 5 0.09
14 14 0.26
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:35714240 original size:10 final size:10
Alignment explanation
Indices: 35714224--35714263 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
35714214 ACTTTGTTAT
35714224 AAGCCGAGCC
1 AAGCCGAGCC
* *
35714234 GAGCCGAACC
1 AAGCCGAGCC
35714244 AAGCCGAGCC
1 AAGCCGAGCC
*
35714254 AAGCCAAGCC
1 AAGCCGAGCC
35714264 CACACAAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.33, C:0.40, G:0.28, T:0.00
Consensus pattern (10 bp):
AAGCCGAGCC
Found at i:35714250 original size:15 final size:15
Alignment explanation
Indices: 35714224--35714263 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
35714214 ACTTTGTTAT
*
35714224 AAGCCGAGCCGAGCC
1 AAGCCAAGCCGAGCC
35714239 GAA-CCAAGCCGAGCC
1 -AAGCCAAGCCGAGCC
35714254 AAGCCAAGCC
1 AAGCCAAGCC
35714264 CACACAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.33, C:0.40, G:0.28, T:0.00
Consensus pattern (15 bp):
AAGCCAAGCCGAGCC
Found at i:35723026 original size:2 final size:2
Alignment explanation
Indices: 35723021--35723054 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
35723011 CTTTTTTTAT
*
35723021 TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35723055 GAGAGAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35723059 original size:2 final size:2
Alignment explanation
Indices: 35723054--35723092 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
35723044 ATATATATAT
35723054 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
35723093 AGTTGTGTTT
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35725736 original size:23 final size:23
Alignment explanation
Indices: 35725688--35725736 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
35725678 TTCATTTATT
* *
35725688 TTTTTAATTTTTAATTAGTAACA
1 TTTTTAAATTTTAATCAGTAACA
*
35725711 TTTTTAAATTTTATATCA-TAATA
1 TTTTTAAATTTTA-ATCAGTAACA
35725734 TTT
1 TTT
35725737 ATTTTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTTTAAATTTTAATCAGTAACA
Found at i:35727711 original size:16 final size:16
Alignment explanation
Indices: 35727689--35727724 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
35727679 ATGAAGATAA
*
35727689 AAAAAAAAAAGAATCTT
1 AAAAAAAAAA-AATCAT
35727706 AAAAAAAAAAAATCAT
1 AAAAAAAAAAAATCAT
35727722 AAA
1 AAA
35727725 TAATTACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.78, C:0.06, G:0.03, T:0.14
Consensus pattern (16 bp):
AAAAAAAAAAAATCAT
Found at i:35729621 original size:13 final size:13
Alignment explanation
Indices: 35729603--35729629 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35729593 AATTTCTAGA
35729603 TTTCGATGAAATT
1 TTTCGATGAAATT
35729616 TTTCGATGAAATT
1 TTTCGATGAAATT
35729629 T
1 T
35729630 AAATTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (13 bp):
TTTCGATGAAATT
Found at i:35729835 original size:14 final size:14
Alignment explanation
Indices: 35729816--35729852 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
35729806 AGAGAGAGGG
35729816 AGAGAAAATGGGGA
1 AGAGAAAATGGGGA
35729830 AGAGAAAGA-GGGGA
1 AGAGAAA-ATGGGGA
35729844 AGAGAAAAT
1 AGAGAAAAT
35729853 TTGGTGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 1 0.05
14 19 0.90
15 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.41, T:0.05
Consensus pattern (14 bp):
AGAGAAAATGGGGA
Found at i:35730207 original size:25 final size:25
Alignment explanation
Indices: 35730179--35730226 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
35730169 TTAATTATCC
35730179 AATGATGAAATTTATA-AAAATTTCA
1 AATGAT-AAATTTATATAAAATTTCA
* *
35730204 AATGGTAAATTTCTATAAAATTT
1 AATGATAAATTTATATAAAATTT
35730227 TTGGGTGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (25 bp):
AATGATAAATTTATATAAAATTTCA
Found at i:35731641 original size:17 final size:17
Alignment explanation
Indices: 35731615--35731659 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
35731605 TTGGGAATTA
*
35731615 TTTA-TTTATTT-TATT
1 TTTATTTTATTTATATG
35731630 TTGTATTTTATTTATATG
1 TT-TATTTTATTTATATG
35731648 TTTATTTT-TTTA
1 TTTATTTTATTTA
35731660 AGTATTATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.08
16 6 0.23
17 13 0.50
18 5 0.19
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (17 bp):
TTTATTTTATTTATATG
Found at i:35731774 original size:13 final size:13
Alignment explanation
Indices: 35731747--35731783 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
35731737 GTAGACACCA
*
35731747 TTTTA-TTATTAT
1 TTTTATTTATTTT
35731759 TTTTATTTATTTT
1 TTTTATTTATTTT
35731772 TTTTATTT-TTTT
1 TTTTATTTATTTT
35731784 CATTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTATTTATTTT
Found at i:35731777 original size:22 final size:21
Alignment explanation
Indices: 35731748--35731793 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
35731738 TAGACACCAT
35731748 TTTATTATTATTTTT-ATTTATT
1 TTTATTATT-TTTTTCATTT-TT
*
35731770 TTTTTTATTTTTTTCATTTTT
1 TTTATTATTTTTTTCATTTTT
35731791 TTT
1 TTT
35731794 CTGGCAGTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTATTATTTTTTTCATTTTT
Found at i:35731779 original size:19 final size:18
Alignment explanation
Indices: 35731745--35731793 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
35731735 ATGTAGACAC
35731745 CATTTTATTATTATTTTTATT
1 CATTTT-TT-TTATTTTT-TT
*
35731766 TATTTTTTTTATTTTTTT
1 CATTTTTTTTATTTTTTT
35731784 CATTTTTTTT
1 CATTTTTTTT
35731794 CTGGCAGTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 8 0.31
20 2 0.08
21 5 0.19
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (18 bp):
CATTTTTTTTATTTTTTT
Found at i:35731794 original size:10 final size:9
Alignment explanation
Indices: 35731755--35731793 Score: 60
Period size: 9 Copynumber: 4.2 Consensus size: 9
35731745 CATTTTATTA
35731755 TTATTTTTAT
1 TTATTTTT-T
35731765 TTATTTTTT
1 TTATTTTTT
35731774 TTATTTTTT
1 TTATTTTTT
*
35731783 TCATTTTTT
1 TTATTTTTT
35731792 TT
1 TT
35731794 CTGGCAGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.85
Consensus pattern (9 bp):
TTATTTTTT
Found at i:35732004 original size:25 final size:25
Alignment explanation
Indices: 35731976--35732037 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
35731966 AGACCTTGCC
*
35731976 AAAAAAAAAATCTTTTTTC-GAATCA
1 AAAAAAAAAATCTTCTTTCTGAAT-A
**
35732001 AAAAAAGAAAAT-TTCTTTCTGCCTA
1 AAAAAA-AAAATCTTCTTTCTGAATA
35732026 AAAAAAAAAATC
1 AAAAAAAAAATC
35732038 AAAATAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.16
25 19 0.61
26 7 0.23
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (25 bp):
AAAAAAAAAATCTTCTTTCTGAATA
Found at i:35732719 original size:22 final size:23
Alignment explanation
Indices: 35732684--35732729 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
35732674 AATAAATTTT
* *
35732684 TTTTTTAATTTTTAT-ATATTAA
1 TTTTTGAATATTTATCATATTAA
35732706 TTTTTGAATATTTATGCATATTAA
1 TTTTTGAATATTTAT-CATATTAA
35732730 AATATTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (23 bp):
TTTTTGAATATTTATCATATTAA
Found at i:35733111 original size:16 final size:15
Alignment explanation
Indices: 35733080--35733119 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
35733070 TTGTTTTTTG
35733080 TATTTTATATTTTAT
1 TATTTTATATTTTAT
*
35733095 TATTTT-TATTGTA-
1 TATTTTATATTTTAT
35733108 TATTTTAT-TTTT
1 TATTTTATATTTT
35733120 TTTCCTTCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.41
14 7 0.32
15 6 0.27
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (15 bp):
TATTTTATATTTTAT
Found at i:35733121 original size:21 final size:21
Alignment explanation
Indices: 35733073--35733122 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
35733063 GCCCACTTTG
* *
35733073 TTTTTTGTATTTTATATTTTA
1 TTTTTTTTATTGTATATTTTA
*
35733094 TTATTTTTATTGTATATTTTA
1 TTTTTTTTATTGTATATTTTA
35733115 TTTTTTTT
1 TTTTTTTT
35733123 CCTTCCTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (21 bp):
TTTTTTTTATTGTATATTTTA
Found at i:35733149 original size:4 final size:4
Alignment explanation
Indices: 35733142--35733327 Score: 77
Period size: 4 Copynumber: 46.8 Consensus size: 4
35733132 ATATCCTATG
* * *
35733142 TATT TA-T TATT TATT TGTT T-GT TATT ACTATT TATT AATATA TATT
1 TATT TATT TATT TATT TATT TATT TATT --TATT TATT --TATT TATT
* * * *
35733188 TAGT TATT TATT TATT TATT TGTT TATGT TAATA TATA TATT TA-T TA-T
1 TATT TATT TATT TATT TATT TATT TAT-T T-ATT TATT TATT TATT TATT
* ** * **
35733236 TACT TAAC TATT TATT TA-T TATT ATATA TACA TATT TA-T TA-T TATT
1 TATT TATT TATT TATT TATT TATT -TATT TATT TATT TATT TATT TATT
* * *
35733282 TATC TATT TATA TATT ATAATT TATC TA-T TATT TA-T T-TT TATT TAT
1 TATT TATT TATT TATT -T-ATT TATT TATT TATT TATT TATT TATT TAT
35733328 CTGTTAATGT
Statistics
Matches: 140, Mismatches: 25, Indels: 34
0.70 0.13 0.17
Matches are distributed among these distances:
3 26 0.19
4 94 0.67
5 8 0.06
6 12 0.09
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (4 bp):
TATT
Found at i:35733198 original size:22 final size:21
Alignment explanation
Indices: 35733142--35733327 Score: 102
Period size: 22 Copynumber: 8.7 Consensus size: 21
35733132 ATATCCTATG
** *
35733142 TATTTATTATTTATTTGTTTGT
1 TATTTATTATTTATTAATAT-T
* *
35733164 TA-TTACTATTTATTAATATA
1 TATTTATTATTTATTAATATT
35733184 TATTTAGTTATTTATT--TATT
1 TATTTA-TTATTTATTAATATT
* * *
35733204 TATTTGTTTATGTTAAT-ATATA
1 TATTT-ATTAT-TTATTAATATT
35733226 TATTTATTA-TTACTTAACTATT
1 TATTTATTATTTA-TTAA-TATT
35733248 TATTTATTATTATATATACATATT
1 TATTTATTATT-TAT-TA-ATATT
35733272 TA-TTATTATTTATCT-AT-TT
1 TATTTATTATTTAT-TAATATT
* *
35733291 ATATATTATAATTTATCTATTATT
1 -TAT-TTATTATTTAT-TAATATT
35733315 TATTT-TTATTTAT
1 TATTTATTATTTAT
35733328 CTGTTAATGT
Statistics
Matches: 130, Mismatches: 17, Indels: 35
0.71 0.09 0.19
Matches are distributed among these distances:
19 5 0.04
20 19 0.15
21 31 0.24
22 48 0.37
23 14 0.11
24 12 0.09
25 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (21 bp):
TATTTATTATTTATTAATATT
Found at i:35733225 original size:42 final size:42
Alignment explanation
Indices: 35733179--35733329 Score: 162
Period size: 42 Copynumber: 3.6 Consensus size: 42
35733169 CTATTTATTA
* * *
35733179 ATATATATTTAGTTATTTATTTATTTATTTGTTTA-TGTTA-AT
1 ATATATATTTA-TTA-TTATTTATCTATTTATTTATTATTATAT
* *
35733221 ATATATATTTATTATTACTTAACTATTTATTTATTATTATAT
1 ATATATATTTATTATTATTTATCTATTTATTTATTATTATAT
* * * *
35733263 ATACATATTTATTATTATTTATCTATTTATATATTATAATTT
1 ATATATATTTATTATTATTTATCTATTTATTTATTATTATAT
* *
35733305 ATCTATTATTTATTTTTATTTATCT
1 ATATA-TATTTATTATTATTTATCT
35733330 GTTAATGTTT
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
40 15 0.16
41 7 0.08
42 52 0.57
43 18 0.20
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (42 bp):
ATATATATTTATTATTATTTATCTATTTATTTATTATTATAT
Found at i:35733273 original size:20 final size:18
Alignment explanation
Indices: 35733169--35733327 Score: 81
Period size: 18 Copynumber: 8.4 Consensus size: 18
35733159 TTTGTTATTA
*
35733169 CTATTTATTAATATATAT
1 CTATTTATTATTATATAT
* * *
35733187 TTAGTTATTTATTTATTTAT
1 CTATTTA-TTA-TTATATAT
* * *
35733207 TTGTTTATGT-TAATATAT
1 CTATTTAT-TATTATATAT
*
35733225 ATATTTATTATTACTTAACTAT
1 CTATTTATTATTA--T-A-TAT
*
35733247 TTATTTATTATTATATAT
1 CTATTTATTATTATATAT
*
35733265 ACATATTTATTATTATTTAT
1 -C-TATTTATTATTATATAT
35733285 CTATTTATATATTATA-AT
1 CTATTTAT-TATTATATAT
* * *
35733303 TTATCTATTATT-TATTT
1 CTATTTATTATTATATAT
*
35733320 TTATTTAT
1 CTATTTAT
35733328 CTGTTAATGT
Statistics
Matches: 110, Mismatches: 19, Indels: 25
0.71 0.12 0.16
Matches are distributed among these distances:
16 2 0.02
17 13 0.12
18 37 0.34
19 12 0.11
20 30 0.27
21 1 0.01
22 15 0.14
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (18 bp):
CTATTTATTATTATATAT
Found at i:35733364 original size:42 final size:41
Alignment explanation
Indices: 35733268--35733382 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 41
35733258 TATATATACA
* * * *
35733268 TATTTATTATTATTTATCTATTTATATATTATAATTTATCTAT
1 TATTTATTTTTAATTATCTA-TTA-ATATTTTCATTTATCTAT
* * *
35733311 TATTTATTTTTATTTATCTGTTAATGTTTTCATTTATCTGAT
1 TATTTATTTTTAATTATCTATTAATATTTTCATTTATCT-AT
35733353 TATTT-TCTTTTAATTATCTATTAATATTTT
1 TATTTAT-TTTTAATTATCTATTAATATTTT
35733383 TTATTTGATT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
41 14 0.23
42 30 0.48
43 18 0.29
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (41 bp):
TATTTATTTTTAATTATCTATTAATATTTTCATTTATCTAT
Found at i:35733384 original size:21 final size:20
Alignment explanation
Indices: 35733281--35733385 Score: 68
Period size: 21 Copynumber: 5.0 Consensus size: 20
35733271 TTATTATTAT
* *
35733281 TTATCTATTTATATATTATAA
1 TTATCTA-TTATATTTTTTAA
* *
35733302 TTTATCTATTATTTATTTTTAT
1 -TTATCTATTATAT-TTTTTAA
* * *
35733324 TTATCTGTTA-ATGTTTTCAT
1 TTATCTATTATAT-TTTTTAA
*
35733344 TTATCTGATTATTTTCTTTTAA
1 TTATCT-ATTATATT-TTTTAA
35733366 TTATCTATTAATATTTTTTA
1 TTATCTATT-ATATTTTTTA
35733386 TTTGATTTTT
Statistics
Matches: 65, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
20 13 0.20
21 26 0.40
22 26 0.40
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.64
Consensus pattern (20 bp):
TTATCTATTATATTTTTTAA
Found at i:35734223 original size:13 final size:13
Alignment explanation
Indices: 35734205--35734229 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35734195 CTTTAAGCCG
35734205 AGCCGAGCCGTTA
1 AGCCGAGCCGTTA
35734218 AGCCGAGCCGTT
1 AGCCGAGCCGTT
35734230 CCTAGGTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.16
Consensus pattern (13 bp):
AGCCGAGCCGTTA
Found at i:35734281 original size:19 final size:19
Alignment explanation
Indices: 35734244--35734281 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
35734234 GGTTATTTAT
*
35734244 TTATTTATTATTATTATTA
1 TTATTTATTATTATGATTA
35734263 TTATTTATTGATTA-GATTA
1 TTATTTATT-ATTATGATTA
35734282 GATTTGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TTATTTATTATTATGATTA
Found at i:35734307 original size:6 final size:6
Alignment explanation
Indices: 35734296--35734355 Score: 52
Period size: 6 Copynumber: 9.7 Consensus size: 6
35734286 TGTTTAATAC
* *
35734296 TTTTTA TTTTTA -TTTTA TTTTATT TTCCTTTA TTTTTA -TTTTA TTTTTT
1 TTTTTA TTTTTA TTTTTA TTTT-TA TT--TTTA TTTTTA TTTTTA TTTTTA
35734345 TATTTTA TTTT
1 T-TTTTA TTTT
35734356 CTTTAAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
5 10 0.23
6 21 0.48
7 8 0.18
8 3 0.07
9 2 0.05
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:35734311 original size:5 final size:5
Alignment explanation
Indices: 35734297--35734355 Score: 68
Period size: 5 Copynumber: 11.8 Consensus size: 5
35734287 GTTTAATACT
* *
35734297 TTTTA TTTTTA TTTTA TTTTA TTTTC CTTTA TTTTTA TTTTA -TTT- TTTTA
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA
35734347 TTTTA TTTT
1 TTTTA TTTT
35734356 CTTTAAATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
4 6 0.13
5 31 0.67
6 9 0.20
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Done.