Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 16 of 79
Found at i:5342348 original size:34 final size:34
Alignment explanation
Indices: 5342310--5342379 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
5342300 TTAAGCAACG
5342310 AACAAGTAAAAATAGTAGAAGAAATTGAAAAGTT
1 AACAAGTAAAAATAGTAGAAGAAATTGAAAAGTT
5342344 AACAAGTAAAAATAGTAGAAGAAATTGAAAAGTT
1 AACAAGTAAAAATAGTAGAAGAAATTGAAAAGTT
5342378 AA
1 AA
5342380 ACACACAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (34 bp):
AACAAGTAAAAATAGTAGAAGAAATTGAAAAGTT
Found at i:5342659 original size:24 final size:24
Alignment explanation
Indices: 5342632--5342683 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5342622 TTAGTAAGTC
*
5342632 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
5342656 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
5342680 AAAT
1 AAAT
5342684 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:5347511 original size:20 final size:22
Alignment explanation
Indices: 5347476--5347518 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
5347466 TAGTAAGTAC
5347476 ACATGTGTTTATAATATGATTA
1 ACATGTGTTTATAATATGATTA
*
5347498 ACATGT-TTTA-AATATGCTTA
1 ACATGTGTTTATAATATGATTA
5347518 A
1 A
5347519 AGTTATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (22 bp):
ACATGTGTTTATAATATGATTA
Found at i:5347832 original size:42 final size:42
Alignment explanation
Indices: 5347784--5347865 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
5347774 AAATAAAGAA
* *
5347784 TTTGTTGCGTTATTGCAACTCTTTCCTTAAATAAATCTTAAT
1 TTTGTTGCATTATAGCAACTCTTTCCTTAAATAAATCTTAAT
*** *
5347826 TTTGTTGCATTATAGCTGTTCTTTCCTTGAATAAATCTTA
1 TTTGTTGCATTATAGCAACTCTTTCCTTAAATAAATCTTA
5347866 TCTTGTCTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (42 bp):
TTTGTTGCATTATAGCAACTCTTTCCTTAAATAAATCTTAAT
Found at i:5348340 original size:6 final size:6
Alignment explanation
Indices: 5348329--5348353 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5348319 ATTTTAACCC
5348329 TAAAAT TAAAAT TAAAAT TAAAAT T
1 TAAAAT TAAAAT TAAAAT TAAAAT T
5348354 GATCATTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TAAAAT
Found at i:5348734 original size:11 final size:12
Alignment explanation
Indices: 5348715--5348743 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5348705 TTTAGAGTTA
5348715 AATTTTTTTTAT
1 AATTTTTTTTAT
5348727 AATTTTTTTTAT
1 AATTTTTTTTAT
5348739 AATTT
1 AATTT
5348744 CATATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
AATTTTTTTTAT
Found at i:5350739 original size:57 final size:58
Alignment explanation
Indices: 5350651--5350764 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 58
5350641 ATTCAAATTC
5350651 AATTCGCAACGATAATATTTCTCTTGAGAAGG-TTTTTTTATCAGGTATGGCTCCTTT
1 AATTCGCAACGATAATATTTCTCTTGAGAAGGTTTTTTTTATCAGGTATGGCTCCTTT
5350708 AATTCGCAACGATAATATTTCTCTTGAGAAGGTTTTTTTTTATCAGGTATGGCTCCT
1 AATTCGCAACGATAATATTTCTCTTGAGAAGG-TTTTTTTTATCAGGTATGGCTCCT
5350765 AACTCTATAA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
57 32 0.58
59 23 0.42
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.42
Consensus pattern (58 bp):
AATTCGCAACGATAATATTTCTCTTGAGAAGGTTTTTTTTATCAGGTATGGCTCCTTT
Found at i:5351509 original size:89 final size:89
Alignment explanation
Indices: 5351358--5351536 Score: 322
Period size: 89 Copynumber: 2.0 Consensus size: 89
5351348 TAGAGGCTTA
5351358 AAAGTAGATAACATTATTGCCAAATTGGGTTTTCAATTTTCTCATCGAGTGGAAGTTGTTGGTTT
1 AAAGTAGATAACATTATTGCCAAATTGGGTTTTCAATTTTCTCATCGAGTGGAAGTTGTTGGTTT
*
5351423 TTCCGGAAGAATTTGGGTTGGTTG
66 TTCCAGAAGAATTTGGGTTGGTTG
* * *
5351447 AAAGTGGATAACATTATTGCCAAATTGGGTTTTTAGTTTTCTCATCGAGTGGAAGTTGTTGGTTT
1 AAAGTAGATAACATTATTGCCAAATTGGGTTTTCAATTTTCTCATCGAGTGGAAGTTGTTGGTTT
5351512 TTCCAGAAGAATTTGGGTTGGTTG
66 TTCCAGAAGAATTTGGGTTGGTTG
5351536 A
1 A
5351537 GAATCATGCA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.25, C:0.09, G:0.26, T:0.40
Consensus pattern (89 bp):
AAAGTAGATAACATTATTGCCAAATTGGGTTTTCAATTTTCTCATCGAGTGGAAGTTGTTGGTTT
TTCCAGAAGAATTTGGGTTGGTTG
Found at i:5355251 original size:154 final size:152
Alignment explanation
Indices: 5354980--5355266 Score: 457
Period size: 154 Copynumber: 1.9 Consensus size: 152
5354970 ATTTCGGTCC
*
5354980 TTTGTTCGTATTTTTTCCCAGATTTTATTACTTTTAAAAAATATACTATTTTCTAATTTTATTAT
1 TTTGTTCGTATTTTTTCCCAGATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTATTAT
* * * *
5355045 TTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTAA
66 TTTACATTATTTTAGTACATCATGTTTGAAATGTATTAATTTAATATATTTTTTAAATAAATTAA
5355110 AAAAAAACTCTTATTTCTGCCA
131 AAAAAAACTCTTATTTCTGCCA
* * * *
5355132 TTTGTTCGTATTTTTTCTCGGATTTTATTACTTTCAATAAAAATATATTATTTTTTAATTTTATT
1 TTTGTTCGTATTTTTTCCCAGATTTTATTACTTT-AA-AAAAATATACTATTTTCTAATTTTATT
*
5355197 ATTTTACATTATTTTAGTATATCATGTTTGAAATGTATTAATTTAATATATTTTTTAAATAAATT
64 ATTTTACATTATTTTAGTACATCATGTTTGAAATGTATTAATTTAATATATTTTTTAAATAAATT
*
5355262 TAAAA
129 AAAAA
5355267 CAACCTTAAA
Statistics
Matches: 122, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
152 32 0.26
153 1 0.01
154 89 0.73
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (152 bp):
TTTGTTCGTATTTTTTCCCAGATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTATTAT
TTTACATTATTTTAGTACATCATGTTTGAAATGTATTAATTTAATATATTTTTTAAATAAATTAA
AAAAAAACTCTTATTTCTGCCA
Found at i:5355628 original size:153 final size:152
Alignment explanation
Indices: 5355401--5355782 Score: 511
Period size: 153 Copynumber: 2.5 Consensus size: 152
5355391 TAAAATTAGA
5355401 AAATAAAATTTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTC-AGATTTTATTACT
1 AAAT-AAATTTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCGA-ATTTTATTACT
* *
5355465 TTTAATAAAAATATATTATTTTC-ATATTTTATTATTTTACATTATTTTAATACATTATGTTTGA
64 TTTAATAAAAATATACTATTTTCTA-ATTTTATTATTTTACATTATTTTAATACAGTATGTTTGA
* * *
5355529 AATTTATTAATTAATTGT-TTTTTT
128 AATGTATTAATTAAGTGTGTTTTGT
* *
5355553 AAATAAATTTAGTAAAAAACCCTTATTTCGACCCTTTATTCGTATTTTTTCTCGAATTTTATTAC
1 AAATAAATTTA--AAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTT-TCGAATTTTATTAC
* *
5355618 TTTTTA-AAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACAGTATGTTTGA
63 TTTTAATAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAATACAGTATGTTTGA
* *
5355682 AATGTATTCATTTAGTGTGTTTTGT
128 AATGTATTAATTAAGTGTGTTTTGT
* * * * *
5355707 AAATAAATTTAAAAAAAACCATTATTTTGGCCATTTGTTTGTATTTTTTTCCGGATTTTATTACT
1 AAATAAATTT-AAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTT-CGAATTTTATTACT
*
5355772 TTCAATAAAAA
64 TTTAATAAAAA
5355783 CACACTAAAT
Statistics
Matches: 201, Mismatches: 20, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
151 7 0.03
152 5 0.02
153 149 0.74
154 38 0.19
155 2 0.01
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.51
Consensus pattern (152 bp):
AAATAAATTTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCGAATTTTATTACTTT
TAATAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAATACAGTATGTTTGAAAT
GTATTAATTAAGTGTGTTTTGT
Found at i:5359781 original size:125 final size:124
Alignment explanation
Indices: 5359419--5359786 Score: 515
Period size: 125 Copynumber: 3.0 Consensus size: 124
5359409 TCGGGTTCTG
5359419 AAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTA-CTAGGATGCTT
1 AAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC-AGGATGCTT
* * * * * *
5359483 TATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACACGTTTTTGCTACAATAGGTCCTG
65 TATGAGAAGAATTTATGAAATCGCGCCCACGTGGACGCGCTTTTGCTATAGTAGGTCCTA
* * *
5359543 AAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAATATAAAAAACGCTTCAAGCAGGATG-TG
1 AAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAATCGCTTCTAGCAGGATGCT-
* * * * * * *
5359607 ATCTGAGAAGAATTTCTAAAATCGCGCCCTCATGGACGCGCTTTTGCTATAGTTGGTCCTA
64 TTATGAGAAGAATTTATGAAATCGCGCCCACGTGGACGCGCTTTTGCTATAGTAGGTCCTA
* * *
5359668 AAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATGGCTTCTAGCAGAATGCTT
1 AAA-AAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTT
5359733 TATGAGAAGAATTTATGAAATCGCGCCCACGTGGACGCGCTTTTGCTATAGTAG
65 TATGAGAAGAATTTATGAAATCGCGCCCACGTGGACGCGCTTTTGCTATAGTAG
5359787 CATGTTTGGG
Statistics
Matches: 211, Mismatches: 28, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
124 40 0.19
125 134 0.64
126 37 0.18
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (124 bp):
AAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTTT
ATGAGAAGAATTTATGAAATCGCGCCCACGTGGACGCGCTTTTGCTATAGTAGGTCCTA
Found at i:5362998 original size:14 final size:15
Alignment explanation
Indices: 5362979--5363008 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5362969 TTTTTAAGCC
5362979 TTTATGTT-AGGGTT
1 TTTATGTTAAGGGTT
5362993 TTTATGTTAAGGGTT
1 TTTATGTTAAGGGTT
5363008 T
1 T
5363009 AGGGTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.57
Consensus pattern (15 bp):
TTTATGTTAAGGGTT
Found at i:5363010 original size:22 final size:22
Alignment explanation
Indices: 5362985--5364031 Score: 557
Period size: 22 Copynumber: 47.0 Consensus size: 22
5362975 AGCCTTTATG
*
5362985 TTAGGGTTTTTATGTTAAGGGT
1 TTAGGGTTTTTAGGTTAAGGGT
*
5363007 TTAGGGTTTTTAGGTTGAGGG-
1 TTAGGGTTTTTAGGTTAAGGGT
*
5363028 TTAGGGTTTTTAGGTTTAGGGT
1 TTAGGGTTTTTAGGTTAAGGGT
* *
5363050 TTAGAGTTTTAAGGTTTAA-GG-
1 TTAGGGTTTTTAGG-TTAAGGGT
5363071 TTAGGGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAGGTTAAGGGT
* *
5363093 TTAGGG--TTTATGTTAAGAGT
1 TTAGGGTTTTTAGGTTAAGGGT
* ** *
5363113 TTATGGAATTTAGGTTAATGGT
1 TTAGGGTTTTTAGGTTAAGGGT
*
5363135 TTAGGG-TTTTAGGGTTTAGGGTTT
1 TTAGGGTTTTTA-GGTTAAGGG--T
* *** *
5363159 TTA-GGTTAAGGGTTAGTGTTTTTAGAT
1 TTAGGGTT----TTTAG-G-TTAAGGGT
*
5363186 TAAGGG--TTTAGGGTTTTTAA--GT
1 TTAGGGTTTTTA-GG---TTAAGGGT
* * *
5363208 TTAAGG-TTTAAGGTTTAGGGT
1 TTAGGGTTTTTAGGTTAAGGGT
* *
5363229 TTAAGGTTTTTAGGTTAATGG-
1 TTAGGGTTTTTAGGTTAAGGGT
*
5363250 TTAGGGTTTAT-GGTTAAGGG-
1 TTAGGGTTTTTAGGTTAAGGGT
* ** *
5363270 TTATGGAATTTAAGTTAAGGGT
1 TTAGGGTTTTTAGGTTAAGGGT
* * *
5363292 TTAGTGTTTTTCGGTTGAGGG-
1 TTAGGGTTTTTAGGTTAAGGGT
* * * *
5363313 TTAAGGTTTTTAAGTTTAGAG-
1 TTAGGGTTTTTAGGTTAAGGGT
*
5363334 TTAGGG-GTTTAGGTTAAGGGT
1 TTAGGGTTTTTAGGTTAAGGGT
* *
5363355 TTAAGG-TTTTAGGTTAAGAGT
1 TTAGGGTTTTTAGGTTAAGGGT
* *
5363376 TTAGGG-TTTAAGGTTTAAGGTTT
1 TTAGGGTTTTTAGG-TTAAGG-GT
**
5363399 TTA-GGTTAAT-GGTT-AGGGTTT
1 TTAGGGTTTTTAGGTTAAGGG--T
*
5363420 TTA-GGTTAAGGGTTTAGGATTTTA-GGT
1 TTAGGGTT-----TTTAGG--TTAAGGGT
*
5363447 TAAGGGTTTATGGAATTTAGGTTAAGGGT
1 TTAGGG--T-T----TTTAGGTTAAGGGT
* *
5363476 TTATGG-TTTTATGGTTTAGGG-
1 TTAGGGTTTTTA-GGTTAAGGGT
** *
5363497 TTAGGGTTTTTAAATTAAAGGT
1 TTAGGGTTTTTAGGTTAAGGGT
* *
5363519 TTACGG-TCTTAGGTTAAGGGT
1 TTAGGGTTTTTAGGTTAAGGGT
* **
5363540 TTATGGAGTTTAGGTTAAGGG-
1 TTAGGGTTTTTAGGTTAAGGGT
5363561 TTAGGGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAGGTTAAGGGT
* **
5363583 TTATGGAGTTTAGGTTAAGGG-
1 TTAGGGTTTTTAGGTTAAGGGT
5363604 TTAGGGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAGGTTAAGGGT
* **
5363626 TTATGGAGTTTAGGTTAAGGG-
1 TTAGGGTTTTTAGGTTAAGGGT
5363647 TTAGGGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAGGTTAAGGGT
* **
5363669 TTATGGAGTTTAGGTTAAGGG-
1 TTAGGGTTTTTAGGTTAAGGGT
*
5363690 TTAGGGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAGGTTAAGGGT
* ** * *
5363712 TTATGGAATTTAGGATTTAGAGT
1 TTAGGGTTTTTAGG-TTAAGGGT
5363735 TTAGGGTTTATGTAATTTAGGTTAAGGGT
1 TTAGGG----T-T--TTTAGGTTAAGGGT
* *
5363764 TTAGGGTTTTTAGGTTGAGAG-
1 TTAGGGTTTTTAGGTTAAGGGT
*
5363785 TTAGGGTTTTTAGGTTAAGAGT
1 TTAGGGTTTTTAGGTTAAGGGT
* **
5363807 TTATGGAATTTAGGTTAAGGGT
1 TTAGGGTTTTTAGGTTAAGGGT
*
5363829 TAAGGGTTTTTAGGTTAAGGG-
1 TTAGGGTTTTTAGGTTAAGGGT
5363850 TTAGGGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAGGTTAAGGGT
*
5363872 TTAGGGTTTTTAGGTTGAGGG-
1 TTAGGGTTTTTAGGTTAAGGGT
* * *
5363893 TTAGTGTTTTTTA-GTTTAGTGT
1 TTAG-GGTTTTTAGGTTAAGGGT
* **
5363915 GTAGGGTTTTTAGGTTTGGGGT
1 TTAGGGTTTTTAGGTTAAGGGT
* *
5363937 TTAAAGGTTAGAGTTTTTAGCTTAAGGAT
1 TT--A-G---G-GTTTTTAGGTTAAGGGT
* *
5363966 TTATGGTTTTTAGGTTTAGGGT
1 TTAGGGTTTTTAGGTTAAGGGT
* * ** *
5363988 TTAGTGTTTTAAATTTAAGTG-
1 TTAGGGTTTTTAGGTTAAGGGT
*
5364009 TTAGGGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAGGTTAAGGGT
5364031 T
1 T
5364032 AGGATTAGGG
Statistics
Matches: 783, Mismatches: 167, Indels: 150
0.71 0.15 0.14
Matches are distributed among these distances:
19 3 0.00
20 49 0.06
21 297 0.38
22 314 0.40
23 26 0.03
24 10 0.01
25 3 0.00
26 1 0.00
27 10 0.01
28 12 0.02
29 42 0.05
30 15 0.02
31 1 0.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.45
Consensus pattern (22 bp):
TTAGGGTTTTTAGGTTAAGGGT
Found at i:5363022 original size:15 final size:15
Alignment explanation
Indices: 5363004--5363094 Score: 51
Period size: 15 Copynumber: 5.8 Consensus size: 15
5362994 TTATGTTAAG
5363004 GGTTTAGGGTTTTTA
1 GGTTTAGGGTTTTTA
*
5363019 GGTTGAGGGTTAGGGTTTTTA
1 GGTTTAGGG-T----T-TTTA
**
5363040 GGTTTAGGGTTTAGA
1 GGTTTAGGGTTTTTA
* * *
5363055 GTTTTAAGG-TTTAA
1 GGTTTAGGGTTTTTA
5363069 GG-TTAGGGTTTTTA
1 GGTTTAGGGTTTTTA
*
5363083 GGTTAAGGGTTT
1 GGTTTAGGGTTT
5363095 AGGGTTTATG
Statistics
Matches: 56, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
13 5 0.09
14 10 0.18
15 25 0.45
16 2 0.04
20 2 0.04
21 12 0.21
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.46
Consensus pattern (15 bp):
GGTTTAGGGTTTTTA
Found at i:5363031 original size:21 final size:21
Alignment explanation
Indices: 5362984--5363930 Score: 428
Period size: 21 Copynumber: 43.8 Consensus size: 21
5362974 AAGCCTTTAT
*
5362984 GTTAGGGTTTTTATGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGG
*
5363005 GTTTAGGGTTTTTAGGTTGAGG
1 G-TTAGGGTTTTTAGGTTAAGG
*
5363027 GTTAGGGTTTTTAGGTTTAGG
1 GTTAGGGTTTTTAGGTTAAGG
* *
5363048 GTTTAGAGTTTTAAGGTTTAA-G
1 G-TTAGGGTTTTTAGG-TTAAGG
5363070 GTTAGGGTTTTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGG
*
5363091 GTTTAGGG--TTTATGTTAAGAG
1 G-TTAGGGTTTTTAGGTTAAG-G
* * **
5363112 TTTATGGAATTTAGGTTAATGG
1 GTTAGGGTTTTTAGGTTAA-GG
*
5363134 TTTAGGG-TTTTA-G----GG
1 GTTAGGGTTTTTAGGTTAAGG
*
5363149 TTTAGGGTTTTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGG
* *
5363170 GTTAGTGTTTTTAGATTAAGG
1 GTTAGGGTTTTTAGGTTAAGG
*
5363191 GTTTAGGGTTTTTAAGTTTAAGG
1 G-TTAGGGTTTTT-AGGTTAAGG
* *
5363214 TTTAAGG--TTTAGGGTTTAAGG
1 GTTAGGGTTTTTA-GG-TTAAGG
* **
5363235 TTTTTA-GGTTAAT-GGTT-A--
1 --GTTAGGGTTTTTAGGTTAAGG
*
5363253 ----GGGTTTAT-GGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGG
* ** *
5363269 GTTATGGAATTTAAGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGG
* * *
5363290 GTTTAGTGTTTTTCGGTTGAGG
1 G-TTAGGGTTTTTAGGTTAAGG
* * * *
5363312 GTTAAGGTTTTTAAGTTTAGA
1 GTTAGGGTTTTTAGGTTAAGG
*
5363333 GTTAGGG-GTTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGG
*
5363353 GTTTAAGG-TTTTAGGTTAAGAG
1 G-TTAGGGTTTTTAGGTTAAG-G
* *
5363375 TTTAGGG-TTTAAGGTTTAAGG
1 GTTAGGGTTTTTAGG-TTAAGG
* **
5363396 TTTTTA-GGTTAAT-GGTT-AGG
1 --GTTAGGGTTTTTAGGTTAAGG
*
5363416 GTTTTTA-GGTTAAGGGTTTAGGATTTTA-G
1 G---TTAGGGTT-----TTTAGG--TTAAGG
5363445 GTTAAGGGTTTATGGAATTTAGGTTAAGG
1 GTT-AGGG--T-T----TTTAGGTTAAGG
* * * ***
5363474 GTTTATGG-TTTTATGGTTTAG
1 G-TTAGGGTTTTTAGGTTAAGG
**
5363495 GGTTAGGGTTTTTAAATTAAAGG
1 G-TTAGGGTTTTTAGGTT-AAGG
* * *
5363518 TTTACGG-TCTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGG
* **
5363538 GTTTATGGAGTTTAGGTTAAGG
1 G-TTAGGGTTTTTAGGTTAAGG
5363560 GTTAGGGTTTTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGG
* **
5363581 GTTTATGGAGTTTAGGTTAAGG
1 G-TTAGGGTTTTTAGGTTAAGG
5363603 GTTAGGGTTTTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGG
* **
5363624 GTTTATGGAGTTTAGGTTAAGG
1 G-TTAGGGTTTTTAGGTTAAGG
5363646 GTTAGGGTTTTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGG
* **
5363667 GTTTATGGAGTTTAGGTTAAGG
1 G-TTAGGGTTTTTAGGTTAAGG
*
5363689 GTTAGGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGG
* ** *
5363710 GTTTATGGAATTTAGGATTTAGAG
1 G-TTAGGGTTTTTAGG-TTAAG-G
*
5363734 TTTAGGGTTTATGTAATTTAGGTTAAGG
1 GTTAGGG----T-T--TTTAGGTTAAGG
* *
5363762 GTTTAGGGTTTTTAGGTTGAGA
1 G-TTAGGGTTTTTAGGTTAAGG
5363784 GTTAGGGTTTTTAGGTTAAGAG
1 GTTAGGGTTTTTAGGTTAAG-G
* * **
5363806 TTTATGGAATTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGG
5363827 GTTAAGGGTTTTTAGGTTAAGG
1 GTT-AGGGTTTTTAGGTTAAGG
5363849 GTTAGGGTTTTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGG
*
5363870 GTTTAGGGTTTTTAGGTTGAGG
1 G-TTAGGGTTTTTAGGTTAAGG
* * *
5363892 GTTAGTGTTTTTTA-GTTTAGT
1 GTTAG-GGTTTTTAGGTTAAGG
5363913 GTGTAGGGTTTTTAGGTT
1 GT-TAGGGTTTTTAGGTT
5363931 TGGGGTTTAA
Statistics
Matches: 708, Mismatches: 136, Indels: 163
0.70 0.14 0.16
Matches are distributed among these distances:
13 10 0.01
14 1 0.00
15 9 0.01
16 5 0.01
17 1 0.00
19 1 0.00
20 46 0.06
21 287 0.41
22 263 0.37
23 31 0.04
24 3 0.00
25 2 0.00
26 3 0.00
27 3 0.00
28 6 0.01
29 19 0.03
30 17 0.02
31 1 0.00
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.45
Consensus pattern (21 bp):
GTTAGGGTTTTTAGGTTAAGG
Found at i:5363034 original size:43 final size:43
Alignment explanation
Indices: 5362984--5364031 Score: 768
Period size: 43 Copynumber: 24.6 Consensus size: 43
5362974 AAGCCTTTAT
* *
5362984 GTTAGGGTTTTTATGTTAAGGGTTTAGGGTTTTTAGGTTGAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
* * *
5363027 GTTAGGGTTTTTAGGTTTAGGGTTTAGAGTTTTAAGGTTTAA-G
1 GTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGG-TTAAGG
*
5363070 GTTAGGGTTTTTAGGTTAAGGGTTTAGGG--TTTATGTTAAGAG
1 GTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAG-G
* * ** *
5363112 TTTATGGAATTTAGGTTAATGGTTTAGGG-TTTTA-G----GG
1 GTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
* * *
5363149 TTTAGGGTTTTTAGGTTAAGGG-TTAGTGTTTTTAGATTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
* *
5363191 GTTTAGGGTTTTTAAGTTTAA-GGTTTAAGG--TTTA-G----GG
1 G-TTAGGGTTTTT-AGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
* * * *
5363228 TTTAAGGTTTTTAGGTTAATGG-TTAGGGTTTAT-GGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
* ** * * * *
5363269 GTTATGGAATTTAAGTTAAGGGTTTAGTGTTTTTCGGTTGAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
* * * * *
5363312 GTTAAGGTTTTTAAGTTTAGAG-TTAGGG-GTTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
* *
5363353 GTTTAAGG-TTTTAGGTTAAGAGTTTAGGG----T---TTAAGG
1 G-TTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
* * *
5363389 TTTAAGGTTTTTAGGTTAATGG-TTAGGGTTTTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
* * **
5363431 GTTTA-GGATTTTAGGTTAAGGGTTTATGGAATTTAGGTTAAGG
1 G-TTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
* * **
5363474 GTTTATGG-TTTTATGGTTTAGGG-TTAGGGTTTTTAAATTAAAGG
1 G-TTAGGGTTTTTA-GGTTAAGGGTTTAGGGTTTTTAGGTT-AAGG
* * * * **
5363518 TTTACGG-TCTTAGGTTAAGGGTTTATGGAGTTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
* **
5363560 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAGTTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
* **
5363603 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAGTTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
* **
5363646 GTTAGGGTTTTTAGGTTAAGGGTTTATGGAGTTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
* * ** *
5363689 GTTAGGGTTTTTAAGTTAAGGGTTTATGGAATTTAGGATTTAGAG
1 GTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGG-TTAAG-G
* * *
5363734 TTTAGGGTTTATGTAATTTAGGTTAAGGGTTTAGGGTTTTTAGGTTGAGA
1 GTTAGGG----T-T--TTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
* * **
5363784 GTTAGGGTTTTTAGGTTAAGAGTTTATGGAATTTAGGTTAAGG
1 GTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
5363827 GTTAAGGGTTTTTAGGTTAAGGG-TTAGGGTTTTTAGGTTAAGG
1 GTT-AGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
* * * *
5363870 GTTTAGGGTTTTTAGGTTGAGGG-TTAGTGTTTTTTA-GTTTAGT
1 G-TTAGGGTTTTTAGGTTAAGGGTTTAG-GGTTTTTAGGTTAAGG
** *
5363913 GTGTAGGGTTTTTAGGTTTGGGGTTTAAAGGTTAGAGTTTTTAGCTTAAGG
1 GT-TAGGGTTTTTAGGTTAAGGGTTT--A-G---G-GTTTTTAGGTTAAGG
* * * * * ** *
5363964 ATTTATGGTTTTTAGGTTTAGGGTTTAGTGTTTTAAATTTAAGT
1 -GTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
*
5364008 GTTAGGGTTTTTAAGTTAAGGGTT
1 GTTAGGGTTTTTAGGTTAAGGGTT
5364032 AGGATTAGGG
Statistics
Matches: 822, Mismatches: 121, Indels: 124
0.77 0.11 0.12
Matches are distributed among these distances:
35 23 0.03
36 35 0.04
37 29 0.04
38 1 0.00
39 2 0.00
40 4 0.00
41 45 0.05
42 97 0.12
43 433 0.53
44 71 0.09
45 8 0.01
46 2 0.00
47 1 0.00
48 1 0.00
49 3 0.00
50 13 0.02
51 29 0.04
52 25 0.03
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.45
Consensus pattern (43 bp):
GTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGG
Found at i:5363150 original size:15 final size:14
Alignment explanation
Indices: 5363132--5363237 Score: 63
Period size: 15 Copynumber: 7.4 Consensus size: 14
5363122 TTAGGTTAAT
5363132 GGTTTAGGGTTTTA
1 GGTTTAGGGTTTTA
5363146 GGGTTTAGGGTTTTTA
1 -GGTTTAGGG-TTTTA
*
5363162 GGTTAAGGG--TTA
1 GGTTTAGGGTTTTA
*** * *
5363174 GTGTTTTTAGATTAA
1 G-GTTTAGGGTTTTA
5363189 GGGTTTAGGGTTTTTA
1 -GGTTTAGGG-TTTTA
* * *
5363205 AGTTTAAGGTTTAA
1 GGTTTAGGGTTTTA
*
5363219 GGTTTAGGGTTTAA
1 GGTTTAGGGTTTTA
5363233 GGTTT
1 GGTTT
5363238 TTAGGTTAAT
Statistics
Matches: 69, Mismatches: 16, Indels: 13
0.70 0.16 0.13
Matches are distributed among these distances:
12 4 0.06
13 4 0.06
14 21 0.30
15 31 0.45
16 9 0.13
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (14 bp):
GGTTTAGGGTTTTA
Found at i:5363212 original size:6 final size:7
Alignment explanation
Indices: 5363201--5363398 Score: 64
Period size: 7 Copynumber: 28.4 Consensus size: 7
5363191 GTTTAGGGTT
5363201 TTTAA-G
1 TTTAAGG
5363207 TTTAAGG
1 TTTAAGG
5363214 TTTAAGG
1 TTTAAGG
*
5363221 TTTAGGG
1 TTTAAGG
5363228 TTTAAGG
1 TTTAAGG
*
5363235 TTTTTAGG
1 -TTTAAGG
5363243 -TTAATGG
1 TTTAA-GG
*
5363250 -TTAGGG
1 TTTAAGG
*
5363256 TTTATGG
1 TTTAAGG
5363263 -TTAAGG
1 TTTAAGG
* *
5363269 GTTATGG
1 TTTAAGG
5363276 AATTTAA-G
1 --TTTAAGG
5363284 -TTAAGGG
1 TTTAA-GG
5363291 TTT-AGTG
1 TTTAAG-G
**
5363298 TTTTTCGG
1 -TTTAAGG
*
5363306 -TTGAGG
1 TTTAAGG
*
5363312 GTTAAGG
1 TTTAAGG
5363319 TTTTTAA-G
1 --TTTAAGG
5363327 TTT-AGAG
1 TTTAAG-G
*
5363334 -TTAGGGG
1 TTTA-AGG
5363341 TTT-AGG
1 TTTAAGG
5363347 -TTAAGGG
1 TTTAA-GG
5363354 TTTAAGG
1 TTTAAGG
*
5363361 TTTTAGG
1 TTTAAGG
5363368 -TTAAGAG
1 TTTAAG-G
*
5363375 TTTAGGG
1 TTTAAGG
5363382 TTTAAGG
1 TTTAAGG
5363389 TTTAAGG
1 TTTAAGG
5363396 TTT
1 TTT
5363399 TTAGGTTAAT
Statistics
Matches: 145, Mismatches: 21, Indels: 51
0.67 0.10 0.24
Matches are distributed among these distances:
5 7 0.05
6 32 0.22
7 73 0.50
8 25 0.17
9 8 0.06
ACGTcount: A:0.23, C:0.01, G:0.32, T:0.44
Consensus pattern (7 bp):
TTTAAGG
Found at i:5363424 original size:57 final size:56
Alignment explanation
Indices: 5363341--5363451 Score: 152
Period size: 57 Copynumber: 2.0 Consensus size: 56
5363331 GAGTTAGGGG
*
5363341 TTTAGGTTAAGGGTTTAAGGTTTTAGGTTAAGAGTTTAGGGTTTAAGGTTTAAGGTT
1 TTTAGGTTAAGGGTTTAAGGTTTTAGGTTAAGAGTTTAGGATTTAAGG-TTAAGGTT
* * * *
5363398 TTTAGGTTAATGG-TTAGGGTTTTTAGGTTAAGGGTTTAGGATTTTAGGTTAAGG
1 TTTAGGTTAAGGGTTTAAGG-TTTTAGGTTAAGAGTTTAGGATTTAAGGTTAAGG
5363452 GTTTATGGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
56 11 0.23
57 37 0.77
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.44
Consensus pattern (56 bp):
TTTAGGTTAAGGGTTTAAGGTTTTAGGTTAAGAGTTTAGGATTTAAGGTTAAGGTT
Found at i:5363434 original size:36 final size:36
Alignment explanation
Indices: 5363340--5363419 Score: 107
Period size: 35 Copynumber: 2.3 Consensus size: 36
5363330 AGAGTTAGGG
5363340 GTTTA-GG-TTAAGGGTTTAAGG-TTTTAGGTTAAGA
1 GTTTAGGGTTTAA-GGTTTAAGGTTTTTAGGTTAAGA
5363374 GTTTAGGGTTTAAGGTTTAAGGTTTTTAGGTTAATG-
1 GTTTAGGGTTTAAGGTTTAAGGTTTTTAGGTTAA-GA
5363410 G-TTAGGGTTT
1 GTTTAGGGTTT
5363420 TTAGGTTAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
34 5 0.12
35 20 0.48
36 16 0.38
37 1 0.02
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.45
Consensus pattern (36 bp):
GTTTAGGGTTTAAGGTTTAAGGTTTTTAGGTTAAGA
Found at i:5363741 original size:30 final size:29
Alignment explanation
Indices: 5363698--5363772 Score: 98
Period size: 30 Copynumber: 2.6 Consensus size: 29
5363688 GGTTAGGGTT
*
5363698 TTTA-AGTTAAGGGTTTATGGAATTTAGG
1 TTTAGAGTTTAGGGTTTATGGAATTTAGG
*
5363726 ATTTAGAGTTTAGGGTTTATGTAATTTAGG
1 -TTTAGAGTTTAGGGTTTATGGAATTTAGG
* *
5363756 TTAAGGGTTTAGGGTTT
1 TTTAGAGTTTAGGGTTT
5363773 TTAGGTTGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 19 0.46
30 22 0.54
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.45
Consensus pattern (29 bp):
TTTAGAGTTTAGGGTTTATGGAATTTAGG
Found at i:5363937 original size:65 final size:64
Alignment explanation
Indices: 5363727--5363939 Score: 239
Period size: 65 Copynumber: 3.3 Consensus size: 64
5363717 GAATTTAGGA
* * * *
5363727 TTTAGAGTTTAGGGTTTATGTAATTTAGGTTAAGGGTTTAGGGTTTTTAGGTTGAGAGTTAGGGT
1 TTTAG-GTTAAGGGTTTAGGGAATTTAGGTTAAGGG-TTAGGGTTTTTAGGTTAAGAGTTAGGGT
5363792 T
64 T
* * *
5363793 TTTAGGTTAAGAGTTTATGGAATTTAGGTTAAGGGTTAAGGGTTTTTAGGTTAAGGGTTAGGGTT
1 TTTAGGTTAAGGGTTTAGGGAATTTAGGTTAAGGGTT-AGGGTTTTTAGGTTAAGAGTTAGGGTT
** * * * *
5363858 TTTAGGTTAAGGGTTTAGGGTTTTTAGGTTGAGGGTTAGTGTTTTTTA-GTTTAGTGTGTAGGGT
1 TTTAGGTTAAGGGTTTAGGGAATTTAGGTTAAGGGTTAG-GGTTTTTAGGTTAAGAGT-TAGGGT
5363922 T
64 T
**
5363923 TTTAGGTTTGGGGTTTA
1 TTTAGGTTAAGGGTTTA
5363940 AAGGTTAGAG
Statistics
Matches: 129, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
64 11 0.09
65 113 0.88
66 5 0.04
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (64 bp):
TTTAGGTTAAGGGTTTAGGGAATTTAGGTTAAGGGTTAGGGTTTTTAGGTTAAGAGTTAGGGTT
Found at i:5363962 original size:94 final size:94
Alignment explanation
Indices: 5363843--5364020 Score: 252
Period size: 94 Copynumber: 1.9 Consensus size: 94
5363833 GGTTTTTAGG
* * * * * *
5363843 TTAAGGGTTAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTGAGGG-TTAGTGTTTTTTAG
1 TTAAAGGTTAGAGTTTTTAGCTTAAGGATTTAGGGTTTTTAGGTTGAGGGTTTAGTG-TTTTAAA
5363907 TTT-AGTGTGTAGGGTTTTTAGGTTTGGGGT
65 TTTAAGTGT-TAGGGTTTTTAGGTTTGGGGT
* *
5363937 TTAAAGGTTAGAGTTTTTAGCTTAAGGATTTATGGTTTTTAGGTTTAGGGTTTAGTGTTTTAAAT
1 TTAAAGGTTAGAGTTTTTAGCTTAAGGATTTAGGGTTTTTAGGTTGAGGGTTTAGTGTTTTAAAT
5364002 TTAAGTGTTAGGGTTTTTA
66 TTAAGTGTTAGGGTTTTTA
5364021 AGTTAAGGGT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
94 63 0.85
95 11 0.15
ACGTcount: A:0.19, C:0.01, G:0.31, T:0.49
Consensus pattern (94 bp):
TTAAAGGTTAGAGTTTTTAGCTTAAGGATTTAGGGTTTTTAGGTTGAGGGTTTAGTGTTTTAAAT
TTAAGTGTTAGGGTTTTTAGGTTTGGGGT
Found at i:5364012 original size:21 final size:21
Alignment explanation
Indices: 5363983--5364034 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
5363973 TTTTAGGTTT
* *
5363983 AGGGTTTAGTGTTTTAAATTTA
1 AGGG-TTAGGGTTTTAAAGTTA
* *
5364005 AGTGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTAAAGTTA
5364026 AGGGTTAGG
1 AGGGTTAGG
5364035 ATTAGGGTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (21 bp):
AGGGTTAGGGTTTTAAAGTTA
Found at i:5364641 original size:18 final size:18
Alignment explanation
Indices: 5364618--5364655 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5364608 CTCGGAAACA
* *
5364618 GATACATATAAGGGTTAG
1 GATACATAAAAGGGCTAG
5364636 GATACATAAAAGGGCTAG
1 GATACATAAAAGGGCTAG
5364654 GA
1 GA
5364656 AACACACCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.08, G:0.29, T:0.21
Consensus pattern (18 bp):
GATACATAAAAGGGCTAG
Found at i:5375860 original size:76 final size:75
Alignment explanation
Indices: 5375779--5376133 Score: 258
Period size: 76 Copynumber: 4.9 Consensus size: 75
5375769 GAAATAACGA
* *
5375779 ATAAATG-ACTAAATAAATAGATAAGATAAATATAGATAATATTAAATTTAAGTATTTAAAAAAA
1 ATAAATGTA-TAAATAAATAGATAA-ACAAATATAAATAATATTAAATTTAAGTATTTAAAAAAA
5375843 TTTAAAGGAATG
64 TTTAAAGGAATG
* * ** * *
5375855 ATAAATGTATAAATAAACCAG-TAAAACAAATATAAACAATATTGGATTTAAATATTT---AATA
1 ATAAATGTATAAATAAA-TAGAT-AAACAAATATAAATAATATTAAATTTAAGTATTTAAAAAAA
** *
5375916 GGT-AA--AAGG
64 TTTAAAGGAATG
* * * *
5375925 AT-AATGAACAAATAAATAAATATAACAAATATAAATAGTATTAAATTTAAGTATTTAAAAAAAT
1 ATAAATGTATAAATAAATAGATA-AACAAATATAAATAATATTAAATTTAAGTATTTAAAAAAAT
5375989 TTAAAGGAATG
65 TTAAAGGAATG
* * ** * *
5376000 ATAAATGTATAAATAAACCAG-TAAAACAAATATAAACAATATTGGATTTAAATATTT---AATA
1 ATAAATGTATAAATAAA-TAGAT-AAACAAATATAAATAATATTAAATTTAAGTATTTAAAAAAA
** *
5376061 GGT-AA--AAGG
64 TTTAAAGGAATG
* * * * *
5376070 AT-AATGAACAAATAAATAAATATAACAAATATAAATAGTATTAAATTTAAGTATTTTAAAAAAT
1 ATAAATGTATAAATAAATAGATA-AACAAATATAAATAATATTAAATTTAAGTATTTAAAAAAAT
5376134 AAAGGATAAT
Statistics
Matches: 212, Mismatches: 48, Indels: 42
0.70 0.16 0.14
Matches are distributed among these distances:
68 4 0.02
69 82 0.39
70 10 0.05
72 11 0.05
73 10 0.05
75 5 0.02
76 83 0.39
77 7 0.03
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (75 bp):
ATAAATGTATAAATAAATAGATAAACAAATATAAATAATATTAAATTTAAGTATTTAAAAAAATT
TAAAGGAATG
Found at i:5375938 original size:145 final size:145
Alignment explanation
Indices: 5375789--5376133 Score: 629
Period size: 145 Copynumber: 2.4 Consensus size: 145
5375779 ATAAATGACT
* * * *
5375789 AAATAAATAGATA-AGATAAATATAGATAATATTAAATTTAAGTATTTAAAAAAATTTAAAGGAA
1 AAATAAATAAATATA-ACAAATATAAATAGTATTAAATTTAAGTATTTAAAAAAATTTAAAGGAA
5375853 TGATAAATGTATAAATAAACCAGTAAAACAAATATAAACAATATTGGATTTAAATATTTAATAGG
65 TGATAAATGTATAAATAAACCAGTAAAACAAATATAAACAATATTGGATTTAAATATTTAATAGG
5375918 TAAAAGGATAATGAAC
130 TAAAAGGATAATGAAC
5375934 AAATAAATAAATATAACAAATATAAATAGTATTAAATTTAAGTATTTAAAAAAATTTAAAGGAAT
1 AAATAAATAAATATAACAAATATAAATAGTATTAAATTTAAGTATTTAAAAAAATTTAAAGGAAT
5375999 GATAAATGTATAAATAAACCAGTAAAACAAATATAAACAATATTGGATTTAAATATTTAATAGGT
66 GATAAATGTATAAATAAACCAGTAAAACAAATATAAACAATATTGGATTTAAATATTTAATAGGT
5376064 AAAAGGATAATGAAC
131 AAAAGGATAATGAAC
*
5376079 AAATAAATAAATATAACAAATATAAATAGTATTAAATTTAAGTATTTTAAAAAAT
1 AAATAAATAAATATAACAAATATAAATAGTATTAAATTTAAGTATTTAAAAAAAT
5376134 AAAGGATAAT
Statistics
Matches: 194, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
145 193 0.99
146 1 0.01
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.30
Consensus pattern (145 bp):
AAATAAATAAATATAACAAATATAAATAGTATTAAATTTAAGTATTTAAAAAAATTTAAAGGAAT
GATAAATGTATAAATAAACCAGTAAAACAAATATAAACAATATTGGATTTAAATATTTAATAGGT
AAAAGGATAATGAAC
Found at i:5376155 original size:69 final size:69
Alignment explanation
Indices: 5375782--5376162 Score: 280
Period size: 69 Copynumber: 5.3 Consensus size: 69
5375772 ATAACGAATA
* * * * * *
5375782 AATGACTAAATAAATAGATAAGATAAATATAGATAATATTAAATTTAAGTATTTAAAAAAATTTA
1 AATGAATAAATAAATAAATAAAACAAATATAAATAATATTAAATTTAAGTATTTTAAAAAA--TA
5375847 AAGGAATGAT
64 AA-G---GAT
* ** * * ** * * **
5375857 AAATGTATAAATAAACCAGTAAAACAAATATAAACAATATTGGATTTAAATA-TTTAATAGGTAA
1 -AATGAATAAATAAATAAATAAAACAAATATAAATAATATTAAATTTAAGTATTTTAAAAAAT-A
5375921 AAGGAT
64 AAGGAT
* * * *
5375927 AATGAACAAATAAATAAATATAACAAATATAAATAGTATTAAATTTAAGTATTTAAAAAAATTTA
1 AATGAATAAATAAATAAATAAAACAAATATAAATAATATTAAATTTAAGTATTTTAAAAAA--TA
5375992 AAGGAATGAT
64 AA-G---GAT
* ** * * ** * * **
5376002 AAATGTATAAATAAACCAGTAAAACAAATATAAACAATATTGGATTTAAATA-TTTAATAGGTAA
1 -AATGAATAAATAAATAAATAAAACAAATATAAATAATATTAAATTTAAGTATTTTAAAAAAT-A
5376066 AAGGAT
64 AAGGAT
* * *
5376072 AATGAACAAATAAATAAATATAACAAATATAAATAGTATTAAATTTAAGTATTTTAAAAAATAAA
1 AATGAATAAATAAATAAATAAAACAAATATAAATAATATTAAATTTAAGTATTTTAAAAAATAAA
5376137 GGAT
66 GGAT
*
5376141 AATGAATAAATAAATATATAAA
1 AATGAATAAATAAATAAATAAA
5376163 TAATGAAATT
Statistics
Matches: 230, Mismatches: 64, Indels: 29
0.71 0.20 0.09
Matches are distributed among these distances:
69 106 0.46
70 18 0.08
71 3 0.01
72 2 0.01
73 4 0.02
74 6 0.03
75 13 0.06
76 78 0.34
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.30
Consensus pattern (69 bp):
AATGAATAAATAAATAAATAAAACAAATATAAATAATATTAAATTTAAGTATTTTAAAAAATAAA
GGAT
Found at i:5378411 original size:11 final size:12
Alignment explanation
Indices: 5378391--5378415 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5378381 TAAATTAATT
5378391 AAATATTTTTTA
1 AAATATTTTTTA
5378403 AAATATTTTTTA
1 AAATATTTTTTA
5378415 A
1 A
5378416 TTACATTTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATATTTTTTA
Found at i:5384156 original size:4 final size:4
Alignment explanation
Indices: 5384147--5384187 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
5384137 AATCCAAATA
5384147 TGAG TGAG TGAG TGAG TGAG TGAG TGAG TGAG TGAG TGAG T
1 TGAG TGAG TGAG TGAG TGAG TGAG TGAG TGAG TGAG TGAG T
5384188 TTTGATGCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.49, T:0.27
Consensus pattern (4 bp):
TGAG
Found at i:5385789 original size:2 final size:2
Alignment explanation
Indices: 5385782--5385809 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5385772 TCATTAAAAC
5385782 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5385810 AAATAAAACG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5387062 original size:15 final size:15
Alignment explanation
Indices: 5387040--5387078 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5387030 CACGAAAAAT
*
5387040 TCCCTCTCCTTGTCC
1 TCCCTCTCCTTCTCC
* *
5387055 TTCCTCTCTTTCTCC
1 TCCCTCTCCTTCTCC
5387070 TCCCTCTCC
1 TCCCTCTCC
5387079 CTCATCTCCT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.54, G:0.03, T:0.44
Consensus pattern (15 bp):
TCCCTCTCCTTCTCC
Found at i:5393292 original size:18 final size:19
Alignment explanation
Indices: 5393271--5393317 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
5393261 ACGAAAGGGA
5393271 AAGAAAAACAGAGAGG-AG
1 AAGAAAAACAGAGAGGAAG
5393289 AAG-AAAACGAGAGAGGAAG
1 AAGAAAAAC-AGAGAGGAAG
5393308 AAGAAAAACA
1 AAGAAAAACA
5393318 AAAGCCGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.19
18 10 0.38
19 6 0.23
20 5 0.19
ACGTcount: A:0.64, C:0.06, G:0.30, T:0.00
Consensus pattern (19 bp):
AAGAAAAACAGAGAGGAAG
Found at i:5393311 original size:19 final size:17
Alignment explanation
Indices: 5393275--5393314 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 17
5393265 AAGGGAAAGA
5393275 AAAACAGAGAGGAGAAG
1 AAAACAGAGAGGAGAAG
5393292 AAAACGAGAGAGGAAGAAG
1 AAAAC-AGAGAGG-AGAAG
5393311 AAAA
1 AAAA
5393315 ACAAAAGCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.24
18 7 0.33
19 9 0.43
ACGTcount: A:0.62, C:0.05, G:0.33, T:0.00
Consensus pattern (17 bp):
AAAACAGAGAGGAGAAG
Found at i:5396194 original size:15 final size:15
Alignment explanation
Indices: 5396174--5396207 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5396164 GTTAAAATAA
5396174 ATTTTCTTTCAATTT
1 ATTTTCTTTCAATTT
*
5396189 ATTTTCTTTTAATTT
1 ATTTTCTTTCAATTT
5396204 ATTT
1 ATTT
5396208 CAATTTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTCTTTCAATTT
Found at i:5401750 original size:50 final size:51
Alignment explanation
Indices: 5401648--5401884 Score: 318
Period size: 50 Copynumber: 4.6 Consensus size: 51
5401638 GGTAAAGAAA
5401648 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG-T-ATGAGAGG
*
5401704 TCCCATGTAAGACTATGTCTGGGACATGGCATTGGCACCGAG-ATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGTATGAGAGG
* *
5401754 TCCCATGTAAGACTATGTCTGGGACATGGCGTTGGCACCGAG-ATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGTATGAGAGG
** * * **
5401804 TCCCCCGTAAGACCATGTCTGGTACATGGCATGGGCACCG-GTATGAGAATA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGTATGAG-AGG
5401855 TCCCATGTAAGACCATGTCTGGGACATGGC
1 TCCCATGTAAGACCATGTCTGGGACATGGC
5401885 TTTGACATGT
Statistics
Matches: 166, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
49 1 0.01
50 96 0.58
51 28 0.17
53 3 0.02
55 2 0.01
56 36 0.22
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (51 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGTATGAGAGG
Found at i:5403283 original size:19 final size:20
Alignment explanation
Indices: 5403245--5403283 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
5403235 ATAATGACAT
* *
5403245 GCAAAATATCAAATAAATGA
1 GCAAAATATAAAAAAAATGA
5403265 GCAAAATA-AAAAAAAATGA
1 GCAAAATATAAAAAAAATGA
5403284 AAACATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.67, C:0.08, G:0.10, T:0.15
Consensus pattern (20 bp):
GCAAAATATAAAAAAAATGA
Found at i:5403517 original size:2 final size:2
Alignment explanation
Indices: 5403510--5403534 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5403500 ATACGCATAG
5403510 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
5403535 AAACATTTGC
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:5403761 original size:28 final size:29
Alignment explanation
Indices: 5403730--5403786 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
5403720 CATATATGTA
5403730 TATAATAAA-AAAAATTACA-TATGAAAAT
1 TATAA-AAATAAAAATTACATTATGAAAAT
*
5403758 TATAAAAATAAAAATTACATTATTAAAAT
1 TATAAAAATAAAAATTACATTATGAAAAT
5403787 CATTTAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 3 0.12
28 15 0.58
29 8 0.31
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (29 bp):
TATAAAAATAAAAATTACATTATGAAAAT
Found at i:5408613 original size:7 final size:7
Alignment explanation
Indices: 5408594--5408627 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
5408584 AGTTTGTATG
5408594 GTTAAAT
1 GTTAAAT
5408601 -TTAAAT
1 GTTAAAT
5408607 GTTAAAT
1 GTTAAAT
5408614 GTTAAAT
1 GTTAAAT
*
5408621 TTTAAAT
1 GTTAAAT
5408628 TGATTAATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (7 bp):
GTTAAAT
Found at i:5413653 original size:20 final size:20
Alignment explanation
Indices: 5413624--5413673 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
5413614 ATTTAGCTCT
* *
5413624 TATGAATTTCAATTAACTCC
1 TATGAGTTTCAATTAACTCA
*
5413644 TATGAGTTTCAGTTAACTCA
1 TATGAGTTTCAATTAACTCA
5413664 TATGAGTTTC
1 TATGAGTTTC
5413674 CGTTTAACCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (20 bp):
TATGAGTTTCAATTAACTCA
Found at i:5416058 original size:25 final size:24
Alignment explanation
Indices: 5416012--5416059 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
5416002 ATTTTGTAGG
* *
5416012 GGTTTTTAGCAAAATTTTCCAAAT
1 GGTTTTGAGCAAAATTTCCCAAAT
5416036 GGTTTTGAGCAAAAATTTCCCAAA
1 GGTTTTGAGC-AAAATTTCCCAAA
5416060 GTATCAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (24 bp):
GGTTTTGAGCAAAATTTCCCAAAT
Found at i:5424603 original size:25 final size:26
Alignment explanation
Indices: 5424545--5424596 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
5424535 AAACACATAA
*
5424545 TGGACATTAGCTTGCTGCTGCATTCTTG
1 TGGACATTAGCATGCTGCTGCA-T-TTG
*
5424573 TGGACATTTGCATGCTGCTGCATT
1 TGGACATTAGCATGCTGCTGCATT
5424597 GTTGACAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.05
27 1 0.05
28 20 0.91
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.38
Consensus pattern (26 bp):
TGGACATTAGCATGCTGCTGCATTTG
Found at i:5427660 original size:11 final size:11
Alignment explanation
Indices: 5427645--5427699 Score: 65
Period size: 11 Copynumber: 4.6 Consensus size: 11
5427635 AAAAAATAAA
5427645 AAAAAGTATTTT
1 AAAAA-TATTTT
*
5427657 AAAAATATTTAAA
1 AAAAATATTT--T
5427670 AAAAAGTATTTT
1 AAAAA-TATTTT
5427682 AAAAATATTTT
1 AAAAATATTTT
5427693 AAAAATA
1 AAAAATA
5427700 AAAAATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
11 18 0.47
12 10 0.26
13 5 0.13
14 5 0.13
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:5427661 original size:15 final size:15
Alignment explanation
Indices: 5427641--5427686 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
5427631 TTTTAAAAAA
5427641 TAAAAAAAAGTATTT
1 TAAAAAAAAGTATTT
5427656 T---AAAAA-TA-TT
1 TAAAAAAAAGTATTT
5427666 TAAAAAAAAGTATTT
1 TAAAAAAAAGTATTT
5427681 TAAAAA
1 TAAAAA
5427687 TATTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
10 3 0.12
11 2 0.08
12 5 0.19
13 5 0.19
14 2 0.08
15 9 0.35
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (15 bp):
TAAAAAAAAGTATTT
Found at i:5427675 original size:25 final size:25
Alignment explanation
Indices: 5427641--5427697 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
5427631 TTTTAAAAAA
5427641 TAAAAAAAAGTATTTTAAAAATATT
1 TAAAAAAAAGTATTTTAAAAATATT
5427666 TAAAAAAAAGTATTTTAAAAATATT
1 TAAAAAAAAGTATTTTAAAAATATT
*
5427691 TTAAAAA
1 TAAAAAA
5427698 TAAAAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
TAAAAAAAAGTATTTTAAAAATATT
Found at i:5437133 original size:19 final size:20
Alignment explanation
Indices: 5437096--5437133 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5437086 AAACTATTTA
5437096 ATTAATAAATGTCTTTAAAT
1 ATTAATAAATGTCTTTAAAT
5437116 ATTATATAAA-GT-TTTAAA
1 ATTA-ATAAATGTCTTTAAA
5437134 AATTTCCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTAATAAATGTCTTTAAAT
Found at i:5443164 original size:33 final size:33
Alignment explanation
Indices: 5443124--5443192 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
5443114 AAAACACCAT
5443124 CACCACCCACAAATACTGAACCACAT-ATTGAAC
1 CACCACCCACAAATACTGAACCACATGA-TGAAC
*
5443157 CACCACCCACAAATACTTAACCACATGATGAAC
1 CACCACCCACAAATACTGAACCACATGATGAAC
5443190 CAC
1 CAC
5443193 ATATTGAACC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.42, C:0.38, G:0.06, T:0.14
Consensus pattern (33 bp):
CACCACCCACAAATACTGAACCACATGATGAAC
Found at i:5446543 original size:14 final size:16
Alignment explanation
Indices: 5446524--5446560 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
5446514 TTCATAATAA
5446524 AAATAAAT-AATTA-T
1 AAATAAATCAATTATT
5446538 AAATAAATCCAATTATT
1 AAATAAAT-CAATTATT
5446555 AAATAA
1 AAATAA
5446561 TTTATGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
16 5 0.25
17 7 0.35
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAAATCAATTATT
Found at i:5454667 original size:27 final size:28
Alignment explanation
Indices: 5454637--5454691 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
5454627 TTTAGATTAG
5454637 GACTAAAATT-TCAAATTAAAGTACAAT
1 GACTAAAATTATCAAATTAAAGTACAAT
5454664 GACTAAAATTGATCAAATTAAAGTACAA
1 GACTAAAATT-ATCAAATTAAAGTACAA
5454692 CGGACCAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 10 0.38
29 16 0.62
ACGTcount: A:0.53, C:0.11, G:0.09, T:0.27
Consensus pattern (28 bp):
GACTAAAATTATCAAATTAAAGTACAAT
Found at i:5454702 original size:29 final size:29
Alignment explanation
Indices: 5454635--5454696 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
5454625 TATTTAGATT
5454635 AGGACTAAAATT--TCAAATTAAAGTACA
1 AGGACTAAAATTGATCAAATTAAAGTACA
*
5454662 ATGACTAAAATTGATCAAATTAAAGTACA
1 AGGACTAAAATTGATCAAATTAAAGTACA
5454691 ACGGAC
1 A-GGAC
5454697 CAAATTCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 11 0.37
29 16 0.53
30 3 0.10
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (29 bp):
AGGACTAAAATTGATCAAATTAAAGTACA
Found at i:5455598 original size:26 final size:26
Alignment explanation
Indices: 5455569--5455663 Score: 68
Period size: 26 Copynumber: 3.4 Consensus size: 26
5455559 TGACAATTTC
5455569 ATTTTTATATTAAATATTATTATATA
1 ATTTTTATATTAAATATTATTATATA
* *
5455595 ATTTATATTTTAAATACTAATAAATTATATTA
1 ATTTTTATATTAAATA-T--T--ATTATA-TA
* *
5455627 ATTTTTTATAAATAAA-ATTATCATATA
1 A-TTTTTAT-ATTAAATATTATTATATA
5455654 ATTTTT-TATT
1 ATTTTTATATT
5455664 TTATCAATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
24 2 0.04
25 1 0.02
26 19 0.35
27 4 0.07
28 5 0.09
29 1 0.02
30 1 0.02
31 6 0.11
32 4 0.07
33 7 0.13
34 4 0.07
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTTTTATATTAAATATTATTATATA
Found at i:5456827 original size:168 final size:169
Alignment explanation
Indices: 5456537--5456844 Score: 474
Period size: 168 Copynumber: 1.8 Consensus size: 169
5456527 TGATGAAAAT
* * * * *
5456537 TAATAATTAACTGTTAATATTAGCAAGTAGTTTTCATTAAATGAGTTTTAAAACTAAAATAGAAT
1 TAATAATTAACTATTAATATTAGCAAATAATTTTCATTAAATCAATTTTAAAACTAAAATAGAAT
* * * *
5456602 CATACTCATTAAACTGTATTTAACAAATTAAGCACAAGATTAAACAATTTCACAATTAACATTAA
66 CATACTCATTAAACTATATTTAACAAATTAAACACAAAATTAAACAATTTCACAATTAAAATTAA
5456667 ATTTATTTTAGTAACAAAATCATAAAAAATTAAATCTAA
131 ATTTATTTTAGTAACAAAATCATAAAAAATTAAATCTAA
*
5456706 TAAT-ATTAACTATTAATATTAGCAAATAATTTTTATTAAATCAATTTTAAAACTAAAATAGAAT
1 TAATAATTAACTATTAATATTAGCAAATAATTTTCATTAAATCAATTTTAAAACTAAAATAGAAT
* * * * *
5456770 TATACTCATTAATCTATATTTAACAAATTAAATACAAAATTAAATAATTTTACAATTAAAATTAA
66 CATACTCATTAAACTATATTTAACAAATTAAACACAAAATTAAACAATTTCACAATTAAAATTAA
5456835 ATTTATTTTA
131 ATTTATTTTA
5456845 ATAATTTATA
Statistics
Matches: 124, Mismatches: 15, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
168 120 0.97
169 4 0.03
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (169 bp):
TAATAATTAACTATTAATATTAGCAAATAATTTTCATTAAATCAATTTTAAAACTAAAATAGAAT
CATACTCATTAAACTATATTTAACAAATTAAACACAAAATTAAACAATTTCACAATTAAAATTAA
ATTTATTTTAGTAACAAAATCATAAAAAATTAAATCTAA
Found at i:5456866 original size:79 final size:81
Alignment explanation
Indices: 5456769--5456928 Score: 306
Period size: 79 Copynumber: 2.0 Consensus size: 81
5456759 TAAAATAGAA
5456769 TTATACTCATTAATCTATATTTAACAAATTAAATACAAAATTAAATAATTTTACAATTAAAATTA
1 TTATACTCATTAATCTATATTTAACAAATTAAATACAAAATTAAATAATTTTACAATTAAAATTA
5456834 AATTTATTTTAATAAT
66 AATTTATTTTAATAAT
5456850 TTATACTCA-T-ATCTATATTTAACAAATTAAATACAAAATTAAATAATTTTACAATTAAAATTA
1 TTATACTCATTAATCTATATTTAACAAATTAAATACAAAATTAAATAATTTTACAATTAAAATTA
5456913 AATTTATTTTAATAAT
66 AATTTATTTTAATAAT
5456929 AAAATCATAA
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
79 69 0.87
80 1 0.01
81 9 0.11
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.43
Consensus pattern (81 bp):
TTATACTCATTAATCTATATTTAACAAATTAAATACAAAATTAAATAATTTTACAATTAAAATTA
AATTTATTTTAATAAT
Found at i:5456931 original size:23 final size:22
Alignment explanation
Indices: 5456884--5456933 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
5456874 AATTAAATAC
*
5456884 AAAATTAAATAATTTTACAATT
1 AAAATTAAATAATTTTACAAAT
*
5456906 AAAATTAAATTTATTTTA-ATAAT
1 AAAATTAAA-TAATTTTACA-AAT
5456929 AAAAT
1 AAAAT
5456934 CATAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAATTAAATAATTTTACAAAT
Found at i:5460801 original size:38 final size:37
Alignment explanation
Indices: 5460759--5460862 Score: 133
Period size: 38 Copynumber: 2.9 Consensus size: 37
5460749 TTAAATCACA
*
5460759 TACTATATAACTTGGGGGTTCGCATACTATGTCATAC
1 TACTATATAACATGGGGGTTCGCATACTATGTCATAC
* *
5460796 GTACTATATAACATAGGGGTTTGCATACTATGTCATAC
1 -TACTATATAACATGGGGGTTCGCATACTATGTCATAC
**
5460834 --C-ATATAACATGATGGTTCGCATACTATGT
1 TACTATATAACATGGGGGTTCGCATACTATGT
5460863 ATTAAGTGAT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
34 24 0.41
35 1 0.02
38 34 0.58
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (37 bp):
TACTATATAACATGGGGGTTCGCATACTATGTCATAC
Found at i:5461248 original size:18 final size:18
Alignment explanation
Indices: 5461225--5461266 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
5461215 TGAAATAGGC
5461225 TTAGGAGTTAG-TTTAAAA
1 TTAGGA-TTAGATTTAAAA
*
5461243 TTAGGATTTGATTTAAAA
1 TTAGGATTAGATTTAAAA
*
5461261 TAAGGA
1 TTAGGA
5461267 CTAAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.38
Consensus pattern (18 bp):
TTAGGATTAGATTTAAAA
Found at i:5466934 original size:156 final size:156
Alignment explanation
Indices: 5466452--5468525 Score: 2610
Period size: 156 Copynumber: 13.2 Consensus size: 156
5466442 TTCTTTTCTT
** * *
5466452 AAAGACGGTGATACTTTCTATAAAA-CTGACAAATCTACTTTTAAAGACATTAGATTTTTCTTTT
1 AAAGACGACGATATTTTCTATAAAATC-GGCAAATCTACTTTTAAAGACATTAGATTTTTCTTTT
* *
5466516 AGAATTTCTCTTATCACTTGGCAAAAGTGAAACACTTTGTAATACATAGTTGCATGCAGTGTAAC
65 GGAATTTCTCTTATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAAC
* *
5466581 ATTAGTGTCTCGTGTTGTTCTTCACTG
130 ATTATTGCCTCGTGTTGTTCTTCACTG
* * * *
5466608 AAAAATC-ACAATATTTTTTATAAAATTGGCAAATCTACTTTTAAAGACATTAGATTTTTCTTTT
1 AAAGA-CGACGATATTTTCTATAAAATCGGCAAATCTACTTTTAAAGACATTAGATTTTTCTTTT
* * *
5466672 GGAATTTCTCTCATCACTTTGGCAAAAGTGAAACACTTTACAATACATAGTTACATGCAGTGTAA
65 GGAATTTCTCTTATCAC-TTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAA
**
5466737 CATTATTGTATCGTGTTGTTCTTCACTG
129 CATTATTGCCTCGTGTTGTTCTTCACTG
* ** ** *
5466765 AAAGATGGTGATATTTTCTATAAAATCAACAAATCTACTTTTAAAG-CTATTAGATCTTTCTTTT
1 AAAGACGACGATATTTTCTATAAAATCGGCAAATCTACTTTTAAAGAC-ATTAGATTTTTCTTTT
*
5466829 GGAATTTCTCTTATCACTTGACAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAAC
65 GGAATTTCTCTTATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAAC
* *
5466894 ATTATTGTCTCCTGTTGTTCTTCACTG
130 ATTATTGCCTCGTGTTGTTCTTCACTG
* *
5466921 AAAAATGACGATATTTTCTATAAAA-CTGGCAAATCTACTTTTAAAGACATTAGATTTTTCTTTT
1 AAAGACGACGATATTTTCTATAAAATC-GGCAAATCTACTTTTAAAGACATTAGATTTTTCTTTT
* *
5466985 AGAATTTCTCTTATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTTAC
65 GGAATTTCTCTTATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAAC
*
5467050 ATTATTGTCTCGTGTTGTTCTTCACTG
130 ATTATTGCCTCGTGTTGTTCTTCACTG
* * *
5467077 AAAAATC-AAGATATTTTCTATAAAATTGGCAAATCTACTTTTAAAGACATTAGATTTTTCTTTT
1 AAAGA-CGACGATATTTTCTATAAAATCGGCAAATCTACTTTTAAAGACATTAGATTTTTCTTTT
* * *
5467141 GAAATTTATCTTATCACTTGGCAAAAGTGAAACACTTTGCAATGCATAGTTGCATGCAGTGTAAC
65 GGAATTTCTCTTATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAAC
*
5467206 ATTA-TGTCATCGTGTTGTTCTTCACTG
130 ATTATTG-CCTCGTGTTGTTCTTCACTG
* * * * * *
5467233 AAAAATGACGATATTTTCTATAAAA-CTGACAAATCTATTTTTAAAGACATTAGAATTTTCTTTC
1 AAAGACGACGATATTTTCTATAAAATC-GGCAAATCTACTTTTAAAGACATTAGATTTTTCTTTT
*
5467297 GGAATTTCTATTATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAAC
65 GGAATTTCTCTTATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAAC
5467362 ATTATTGCCTCGTGTTGTTCTTCACTG
130 ATTATTGCCTCGTGTTGTTCTTCACTG
* * * *
5467389 AAAGACGACGATATTTTCTGTAAAATTGGCGAATCTACTTTTAAAGACATTAGATTATTCTTTTG
1 AAAGACGACGATATTTTCTATAAAATCGGCAAATCTACTTTTAAAGACATTAGATTTTTCTTTTG
* * *
5467454 GAATTTCTCTTATCACTTGGCAAAAGCGAAACACTTTGCAATACATAGTTGCATTCAATGTAACA
66 GAATTTCTCTTATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAACA
5467519 TTATTGCCTCGTGTTGTTCTTCACTG
131 TTATTGCCTCGTGTTGTTCTTCACTG
**
5467545 AAAGACGACGATATTTTCTATAAAATCGGTGAATCTACTTTTAAAGACATTAGATTTTTCTTTTG
1 AAAGACGACGATATTTTCTATAAAATCGGCAAATCTACTTTTAAAGACATTAGATTTTTCTTTTG
* * * * *
5467610 GAATTTCTTTTACCACTTGGCAAAAGTGAAACACTTTGGAATACATAGTTGCATTCAGTGTAGCA
66 GAATTTCTCTTATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAACA
* *
5467675 TTATTGCCTCGTATTGTTCTTCATTG
131 TTATTGCCTCGTGTTGTTCTTCACTG
* * * *
5467701 AAAGACGACGATATTTTCTATAAAATCGGTAAATCTACTTTTAAAGACATTGGA-TCTACTTTTA
1 AAAGACGACGATATTTTCTATAAAATCGGCAAATCTACTTTTAAAGACATTAGATTTTTCTTTT-
* ** * ** *** ** * * *
5467765 AAGACATTAGAT-TTTTCTTTTGG-AATTTCTCTTATCAGTTGGCCAAAGTGAAACACTTTGCAA
65 -GGA-ATT-TCTCTTATCACTTGGCAA-AAGT-GAAACACTTTG-C-AA-T-----A-----C--
* * *
5467828 TACATATTTGCATGCAATGTAACATTATTGCCTCGTGTTCTTCTTCACTG
110 ---ATAGTTGCATGCAGTGTAACATTATTGCCTCGTGTTGTTCTTCACTG
* * * *
5467878 AAAAAC-AGTGATATTTTCTATAAAA-CTGGCGAATCTACTTTTAAAAACATTAGATTTTTCTTT
1 AAAGACGA-CGATATTTTCTATAAAATC-GGCAAATCTACTTTTAAAGACATTAGATTTTTCTTT
* * *
5467941 TGGAATTCCTCTTATCACTTGACAAAAGTGAAACAATTTGCAATACATAGTTGCATGCAGTGTAA
64 TGGAATTTCTCTTATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAA
* * *
5468006 CATTATTGCTTTGTGTTGTTCTTCGCTG
129 CATTATTGCCTCGTGTTGTTCTTCACTG
* * * *
5468034 AAAAACTG-CGATATTTTCTACAAAATTGGCGAATCTACTTTTAAAGACATTAGATTTTTCTTTT
1 AAAGAC-GACGATATTTTCTATAAAATCGGCAAATCTACTTTTAAAGACATTAGATTTTTCTTTT
* * * **
5468098 AGAATTTCTCTTATCACTTGGAAAAAGTGAAACACTTTGCAATGCATAGTTGCATGTTGTGTAAC
65 GGAATTTCTCTTATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAAC
*
5468163 ATTATTGCCTCGTGTTGTTATGT-ACTG
130 ATTATTGCCTCGTGTTGTTCT-TCACTG
* * * * *
5468190 AAAGACGACTATATTTTCTATAAAATTGGCGAATCTACTTTTAAAGACGTTAGATTTTTCGTTTG
1 AAAGACGACGATATTTTCTATAAAATCGGCAAATCTACTTTTAAAGACATTAGATTTTTCTTTTG
**
5468255 GAATTTCTCTTATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGTGGTGTAACA
66 GAATTTCTCTTATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAACA
*
5468320 TTATTGACTCGTGTTGTTCTTCACTG
131 TTATTGCCTCGTGTTGTTCTTCACTG
** ** * * * * * *
5468346 AAAGACGGTGATATTTTCTATAAAATCAACGATTTTAATTTTAAAGACATTAAAATTTTCTTTTG
1 AAAGACGACGATATTTTCTATAAAATCGGCAAATCTACTTTTAAAGACATTAGATTTTTCTTTTG
* *
5468411 GAATATCTCTTATCACTTGGAAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAACA
66 GAATTTCTCTTATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAACA
*
5468476 TTATTGCCTCGTGTTGTTCTGCACTG
131 TTATTGCCTCGTGTTGTTCTTCACTG
*
5468502 AAAGACGGCGATATTTTCTATAAA
1 AAAGACGACGATATTTTCTATAAA
5468526 TTTGGCGAAT
Statistics
Matches: 1677, Mismatches: 192, Indels: 98
0.85 0.10 0.05
Matches are distributed among these distances:
155 12 0.01
156 1375 0.82
157 146 0.09
158 11 0.01
159 7 0.00
161 3 0.00
162 1 0.00
166 1 0.00
167 1 0.00
171 1 0.00
172 3 0.00
173 1 0.00
174 7 0.00
175 11 0.01
176 6 0.00
177 84 0.05
178 7 0.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (156 bp):
AAAGACGACGATATTTTCTATAAAATCGGCAAATCTACTTTTAAAGACATTAGATTTTTCTTTTG
GAATTTCTCTTATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAACA
TTATTGCCTCGTGTTGTTCTTCACTG
Found at i:5467757 original size:21 final size:21
Alignment explanation
Indices: 5467733--5467772 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5467723 AAATCGGTAA
5467733 ATCTACTTTTAAAGACATTGG
1 ATCTACTTTTAAAGACATTGG
5467754 ATCTACTTTTAAAGACATT
1 ATCTACTTTTAAAGACATT
5467773 AGATTTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (21 bp):
ATCTACTTTTAAAGACATTGG
Found at i:5467874 original size:177 final size:177
Alignment explanation
Indices: 5467577--5467928 Score: 519
Period size: 177 Copynumber: 2.0 Consensus size: 177
5467567 AAATCGGTGA
*
5467577 ATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTTTTACCACTTGGCAAAAGTGAAAC
1 ATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTTACCACTTGGCAAAAGTGAAAC
* * * * * * *
5467642 ACTTTGGAATACATAGTTGCATTCAGTGTAGCATTATTGCCTCGTATTGTTCTTCATTGAAAGAC
66 ACTTTGCAATACATAGTTGCATGCAATGTAACATTATTGCCTCGTATTCTTCTTCACTGAAAAAC
* *
5467707 -GACGATATTTTCTATAAAA-TCGGTAAATCTACTTTTAAAGACATTGG
131 AG-CGATATTTTCTATAAAACT-GGCAAATCTACTTTTAAAAACATTGG
* * *
5467754 ATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTTATCAGTTGGCCAAAGTGAAAC
1 ATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTTACCACTTGGCAAAAGTGAAAC
* *
5467819 ACTTTGCAATACATATTTGCATGCAATGTAACATTATTGCCTCGTGTTCTTCTTCACTGAAAAAC
66 ACTTTGCAATACATAGTTGCATGCAATGTAACATTATTGCCTCGTATTCTTCTTCACTGAAAAAC
* *
5467884 AGTGATATTTTCTATAAAACTGGCGAATCTACTTTTAAAAACATT
131 AGCGATATTTTCTATAAAACTGGCAAATCTACTTTTAAAAACATT
5467929 AGATTTTTCT
Statistics
Matches: 156, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
177 154 0.99
178 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (177 bp):
ATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTTACCACTTGGCAAAAGTGAAAC
ACTTTGCAATACATAGTTGCATGCAATGTAACATTATTGCCTCGTATTCTTCTTCACTGAAAAAC
AGCGATATTTTCTATAAAACTGGCAAATCTACTTTTAAAAACATTGG
Found at i:5467992 original size:801 final size:801
Alignment explanation
Indices: 5466953--5468525 Score: 2481
Period size: 801 Copynumber: 2.0 Consensus size: 801
5466943 AAACTGGCAA
5466953 ATCTACTTTTAAAGACATTAGATTTTTCTTTTAGAATTTCTCTTATCACTTGGCAAAAGTGAAAC
1 ATCTACTTTTAAAGACATTAGATTTTTCTTTTAGAATTTCTCTTATCACTTGGCAAAAGTGAAAC
* * * *
5467018 ACTTTGCAATACATAGTTGCATGCAGTGTTACATTATTGTCTCGTGTTGTTCTTCACTGAAAAAT
66 ACTTTGCAATACATAGTTGCATGCAATGTAACATTATTGCCTCGTGTTCTTCTTCACTGAAAAAT
* * *
5467083 CAAGATATTTTCTATAAAATTGGCAAATCTACTTTTAAAGACATTAGATTTTTCTTTTGAAATTT
131 CAAGATATTTTCTATAAAACTGGCAAATCTACTTTTAAAAACATTAGATTTTTCTTTTGAAATTC
* * *
5467148 ATCTTATCACTTGGCAAAAGTGAAACACTTTGCAATGCATAGTTGCATGCAGTGTAACATTA-TG
196 ATCTTATCACTTGACAAAAGTGAAACAATTTGCAATACATAGTTGCATGCAGTGTAACATTATTG
* *
5467212 TCATCGTGTTGTTCTTCACTGAAAAA-TGACGATATTTTCTATAAAACTGACAAATCTATTTTTA
261 -CATCGTGTTGTTCTTCACTGAAAAACTG-CGATATTTTCTACAAAACTGACAAATCTACTTTTA
* *
5467276 AAGACATTAGAATTTTCTTTCGGAATTTCTATTATCACTTGGCAAAAGTGAAACACTTTGCAATA
324 AAGACATTAGAATTTTCTTTCAGAATTTCTATTATCACTTGGAAAAAGTGAAACACTTTGCAATA
*
5467341 CATAGTTGCATGCAGTGTAACATTATTGCCTCGTGTTGTTCT-TCACTGAAAGACGACGATATTT
389 CATAGTTGCATGCAGTGTAACATTATTGCCTCGTGTTGTTATGT-ACTGAAAGACGACGATATTT
* *
5467405 TCTGTAAAATTGGCGAATCTACTTTTAAAGACATTAGATTATTCTTTTGGAATTTCTCTTATCAC
453 TCTATAAAATTGGCGAATCTACTTTTAAAGACATTAGATTATTCGTTTGGAATTTCTCTTATCAC
*
5467470 TTGGCAAAAGCGAAACACTTTGCAATACATAGTTGCAT-TCAATGTAACATTATTGCCTCGTGTT
518 TTGGCAAAAGCGAAACACTTTGCAATACATAGTTGCATGT-AATGTAACATTATTGACTCGTGTT
*** * *
5467534 GTTCTTCACTGAAAGACGACGATATTTTCTATAAAATCGGTGAATCTACTTTTAAAGACATTAGA
582 GTTCTTCACTGAAAGACGACGATATTTTCTATAAAATCAACGAATCTAATTTTAAAGACATTAAA
* * * * *
5467599 TTTTTCTTTTGGAATTTCTTTTACCACTTGGCAAAAGTGAAACACTTTGGAATACATAGTTGCAT
647 ATTTTCTTTTGGAATATCTCTTACCACTTGGAAAAAGTGAAACACTTTGCAATACATAGTTGCAT
* * * *
5467664 TCAGTGTAGCATTATTGCCTCGTATTGTTCTTCATTGAAAGACGACGATATTTTCTATAAAATCG
712 GCAGTGTAACATTATTGCCTCGTATTGTTCTGCACTGAAAGACGACGATATTTTCTATAAAATCG
5467729 GTAAATCTACTTTTAAAGACATTGG
777 GTAAATCTACTTTTAAAGACATTGG
* * *
5467754 ATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTTATCAGTTGGCCAAAGTGAAAC
1 ATCTACTTTTAAAGACATTAGATTTTTCTTTTAGAATTTCTCTTATCACTTGGCAAAAGTGAAAC
*
5467819 ACTTTGCAATACATATTTGCATGCAATGTAACATTATTGCCTCGTGTTCTTCTTCACTGAAAAA-
66 ACTTTGCAATACATAGTTGCATGCAATGTAACATTATTGCCTCGTGTTCTTCTTCACTGAAAAAT
* * *
5467883 CAGTGATATTTTCTATAAAACTGGCGAATCTACTTTTAAAAACATTAGATTTTTCTTTTGGAATT
131 CA-AGATATTTTCTATAAAACTGGCAAATCTACTTTTAAAAACATTAGATTTTTCTTTTGAAATT
*
5467948 CCTCTTATCACTTGACAAAAGTGAAACAATTTGCAATACATAGTTGCATGCAGTGTAACATTATT
195 CATCTTATCACTTGACAAAAGTGAAACAATTTGCAATACATAGTTGCATGCAGTGTAACATTATT
* * * * * *
5468013 GCTTTGTGTTGTTCTTCGCTGAAAAACTGCGATATTTTCTACAAAATTGGCGAATCTACTTTTAA
260 GCATCGTGTTGTTCTTCACTGAAAAACTGCGATATTTTCTACAAAACTGACAAATCTACTTTTAA
* * * *
5468078 AGACATTAGATTTTTCTTTTAGAATTTCTCTTATCACTTGGAAAAAGTGAAACACTTTGCAATGC
325 AGACATTAGAATTTTCTTTCAGAATTTCTATTATCACTTGGAAAAAGTGAAACACTTTGCAATAC
** *
5468143 ATAGTTGCATGTTGTGTAACATTATTGCCTCGTGTTGTTATGTACTGAAAGACGACTATATTTTC
390 ATAGTTGCATGCAGTGTAACATTATTGCCTCGTGTTGTTATGTACTGAAAGACGACGATATTTTC
* *
5468208 TATAAAATTGGCGAATCTACTTTTAAAGACGTTAGATTTTTCGTTTGGAATTTCTCTTATCACTT
455 TATAAAATTGGCGAATCTACTTTTAAAGACATTAGATTATTCGTTTGGAATTTCTCTTATCACTT
* **
5468273 GGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGTGGTGTAACATTATTGACTCGTGTTGTT
520 GGCAAAAGCGAAACACTTTGCAATACATAGTTGCATGTAATGTAACATTATTGACTCGTGTTGTT
** * *
5468338 CTTCACTGAAAGACGGTGATATTTTCTATAAAATCAACGATTTTAATTTTAAAGACATTAAAATT
585 CTTCACTGAAAGACGACGATATTTTCTATAAAATCAACGAATCTAATTTTAAAGACATTAAAATT
*
5468403 TTCTTTTGGAATATCTCTTATCACTTGGAAAAAGTGAAACACTTTGCAATACATAGTTGCATGCA
650 TTCTTTTGGAATATCTCTTACCACTTGGAAAAAGTGAAACACTTTGCAATACATAGTTGCATGCA
* *
5468468 GTGTAACATTATTGCCTCGTGTTGTTCTGCACTGAAAGACGGCGATATTTTCTATAAA
715 GTGTAACATTATTGCCTCGTATTGTTCTGCACTGAAAGACGACGATATTTTCTATAAA
5468526 TTTGGCGAAT
Statistics
Matches: 702, Mismatches: 65, Indels: 10
0.90 0.08 0.01
Matches are distributed among these distances:
800 2 0.00
801 694 0.99
802 6 0.01
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (801 bp):
ATCTACTTTTAAAGACATTAGATTTTTCTTTTAGAATTTCTCTTATCACTTGGCAAAAGTGAAAC
ACTTTGCAATACATAGTTGCATGCAATGTAACATTATTGCCTCGTGTTCTTCTTCACTGAAAAAT
CAAGATATTTTCTATAAAACTGGCAAATCTACTTTTAAAAACATTAGATTTTTCTTTTGAAATTC
ATCTTATCACTTGACAAAAGTGAAACAATTTGCAATACATAGTTGCATGCAGTGTAACATTATTG
CATCGTGTTGTTCTTCACTGAAAAACTGCGATATTTTCTACAAAACTGACAAATCTACTTTTAAA
GACATTAGAATTTTCTTTCAGAATTTCTATTATCACTTGGAAAAAGTGAAACACTTTGCAATACA
TAGTTGCATGCAGTGTAACATTATTGCCTCGTGTTGTTATGTACTGAAAGACGACGATATTTTCT
ATAAAATTGGCGAATCTACTTTTAAAGACATTAGATTATTCGTTTGGAATTTCTCTTATCACTTG
GCAAAAGCGAAACACTTTGCAATACATAGTTGCATGTAATGTAACATTATTGACTCGTGTTGTTC
TTCACTGAAAGACGACGATATTTTCTATAAAATCAACGAATCTAATTTTAAAGACATTAAAATTT
TCTTTTGGAATATCTCTTACCACTTGGAAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAG
TGTAACATTATTGCCTCGTATTGTTCTGCACTGAAAGACGACGATATTTTCTATAAAATCGGTAA
ATCTACTTTTAAAGACATTGG
Found at i:5469615 original size:7 final size:7
Alignment explanation
Indices: 5469603--5469665 Score: 51
Period size: 7 Copynumber: 9.4 Consensus size: 7
5469593 ATTTTAAAAG
5469603 ATAATAT
1 ATAATAT
5469610 ATAATAT
1 ATAATAT
*
5469617 A-AAAAT
1 ATAATAT
* * *
5469623 TTAAAAG
1 ATAATAT
5469630 ATAATAT
1 ATAATAT
5469637 AT-ATAT
1 ATAATAT
5469643 AT-ATAT
1 ATAATAT
* *
5469649 ATAGTAA
1 ATAATAT
5469656 ATAATAT
1 ATAATAT
5469663 ATA
1 ATA
5469666 TAAAATTTAA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
6 16 0.36
7 28 0.64
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (7 bp):
ATAATAT
Found at i:5469620 original size:27 final size:28
Alignment explanation
Indices: 5469583--5469645 Score: 110
Period size: 27 Copynumber: 2.2 Consensus size: 28
5469573 ATTAAAGATA
5469583 ATATATAAAAATTTTAAAAGATAATATAT
1 ATATATAAAAA-TTTAAAAGATAATATAT
5469612 A-ATATAAAAATTTAAAAGATAATATAT
1 ATATATAAAAATTTAAAAGATAATATAT
5469639 ATATATA
1 ATATATA
5469646 TATATAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 18 0.55
28 14 0.42
29 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (28 bp):
ATATATAAAAATTTAAAAGATAATATAT
Found at i:5470489 original size:10 final size:10
Alignment explanation
Indices: 5470474--5470506 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5470464 CAGAATAGAG
*
5470474 AAAAAAAA-G
1 AAAAAAAATA
5470483 AAAAAAAATA
1 AAAAAAAATA
5470493 AAAAAAAATA
1 AAAAAAAATA
5470503 AAAA
1 AAAA
5470507 CAGATCTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.91, C:0.00, G:0.03, T:0.06
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:5471249 original size:156 final size:156
Alignment explanation
Indices: 5470955--5471366 Score: 583
Period size: 156 Copynumber: 2.6 Consensus size: 156
5470945 GGGTCATTAC
* * *
5470955 ATCTATTTTTAAAGACATTAGATTGTTTTTTTTGGAATTTCTCTTATCACTTGGAAAAAGTGAAA
1 ATCTACTTTTAAAGACATTAGATT-TTTCTTTTGGAATTTCTCTTATCACTTGGCAAAAGTGAAA
* * * *
5471020 CACCTTGCAATACATAGTTCCATGCAGTGTAACATTATTGTCTCGTGTTGTTCTTCACTGAAAAA
65 CACTTTGCAATACATAGTTGCATGCAGTGTAACATTATTGACTCGTGTTGTTCTGCACTGAAAAA
* * * *
5471085 CAATGATATTTTTTGTAAAACCCGCGA
130 CAACGATATTTTCTATAAAACACGCGA
*
5471112 ATCTACTTTTAAAGACATTAGA-TTTTCTTTTGGAATTTCTCTTTATCACTTGGCAAAAGCGAAA
1 ATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTC-TTATCACTTGGCAAAAGTGAAA
* * * *
5471176 CACTTTGCAATATATAGTTGCATGCAGTGTAACATTATTGACTTGTGTTGTTCTGCATTGAAAGA
65 CACTTTGCAATACATAGTTGCATGCAGTGTAACATTATTGACTCGTGTTGTTCTGCACTGAAAAA
** * *
5471241 CGGCGATATTTTCTATAAAATAGGCGA
130 CAACGATATTTTCTATAAAACACGCGA
* *
5471268 ATCTACTTTTAAAGATATTAGATTTTTCTTTTGGAATTTCTCTTATCATTTGGCAAAAGTGAAAC
1 ATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTTATCACTTGGCAAAAGTGAAAC
* *
5471333 ACTTTGCAACACATAGTTGCATGCAATGTAACAT
66 ACTTTGCAATACATAGTTGCATGCAGTGTAACAT
5471367 GTGCAGAAAG
Statistics
Matches: 227, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
155 17 0.07
156 170 0.75
157 40 0.18
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (156 bp):
ATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTTATCACTTGGCAAAAGTGAAAC
ACTTTGCAATACATAGTTGCATGCAGTGTAACATTATTGACTCGTGTTGTTCTGCACTGAAAAAC
AACGATATTTTCTATAAAACACGCGA
Found at i:5471484 original size:137 final size:137
Alignment explanation
Indices: 5471247--5471503 Score: 417
Period size: 137 Copynumber: 1.9 Consensus size: 137
5471237 AAGACGGCGA
5471247 TATTTTCTATAAAATAGGCGAATCTACTTTTAAAGATATTAGATTTTTCTTTTGGAATTTCTCTT
1 TATTTTCTATAAAATAGGCGAATCTACTTTTAAAGATATTAGATTTTTCTTTTGGAATTTCTCTT
* *
5471312 ATCATTTGGCAAAAGTGAAACACTTTGCAACACATAGTTGCATGCAATGTAACATGTGCAGAAAG
66 ATCACTTGGCAAAAGTGAAACACCTTGCAACACATAGTTGCATGCAATGTAACATGTGCAGAAAG
5471377 ATGATGG
131 ATGATGG
* *
5471384 TATTTTCTGTAAAATCA-GCGAATCTACTTTTAAAGATATTAGATTTTTCTTTTGGAATTTCTTT
1 TATTTTCTATAAAAT-AGGCGAATCTACTTTTAAAGATATTAGATTTTTCTTTTGGAATTTCTCT
* * * * *
5471448 TTTCACTTGGCAAAAGTGAAACACCTTGCAATACATAGTTGTATGTAGTGTAACAT
65 TATCACTTGGCAAAAGTGAAACACCTTGCAACACATAGTTGCATGCAATGTAACAT
5471504 TATTACCTCG
Statistics
Matches: 110, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
137 109 0.99
138 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (137 bp):
TATTTTCTATAAAATAGGCGAATCTACTTTTAAAGATATTAGATTTTTCTTTTGGAATTTCTCTT
ATCACTTGGCAAAAGTGAAACACCTTGCAACACATAGTTGCATGCAATGTAACATGTGCAGAAAG
ATGATGG
Found at i:5471588 original size:156 final size:156
Alignment explanation
Indices: 5471384--5472775 Score: 2144
Period size: 156 Copynumber: 8.9 Consensus size: 156
5471374 AAGATGATGG
* ** * *
5471384 TATTTTCTGTAAAATCAGCGAATCTACTTTTAAAGATATTAGATTTTTCTTTTGGAATTTCTTTT
1 TATTTTCTATAAAATTGGCGAATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTT
* * * * *
5471449 TTCACTTGGCAAAAGTGAAACACCTTGCAATACATAGTTGTATGTAGTGTAACATTATTACCTCG
66 ATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAACATTATTGCCTCG
* *
5471514 CGTTGTTCTTCACTGAAAGACAACGA
131 TGTTGTTCTTCACTGAAAGACGACGA
* *
5471540 TATTTTCTATAAAATTGGCAAATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAACTTT-TTT
1 TATTTTCTATAAAATTGGCGAATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAA-TTTCTCT
* *
5471604 TATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTACATGCAATGTAACATTATTGCCTC
65 TATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAACATTATTGCCTC
* * *
5471669 ATGTTGTT-TTACATTGAAAGACGGCGA
130 GTGTTGTTCTT-CACTGAAAGACGACGA
* * * * *
5471696 TATTCTCTATAAAATCGGTGAATCTACTTTTAAATATATTAGATTTTTCTTTTGGAATTTCTCTT
1 TATTTTCTATAAAATTGGCGAATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTT
* * *
5471761 ATCACTTGGCAAAAGTGAAACACTTTGCAATAAATAGTTGCATGTAATGTAACATTATTGCCTCG
66 ATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAACATTATTGCCTCG
* * * *
5471826 TGTTGTTTTTCATTGAAAGACAACAA
131 TGTTGTTCTTCACTGAAAGACGACGA
**
5471852 TATTTTCTATAAAATTGATGAATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTT
1 TATTTTCTATAAAATTGGCGAATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTT
* * ** *
5471917 ATCACTTGGAAAAAGTGAAACACTTTGCAATACATAATTGCATGTTGTGTAACATTATTACCTCG
66 ATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAACATTATTGCCTCG
* *
5471982 TGTTGTTATGT-ACTGAAAGATGACGA
131 TGTTGTTCT-TCACTGAAAGACGACGA
* *
5472008 TATTTTCTATAAAATTGGCGAATCTACTTTTAAAGACATTAGATTTTTCGTTTGGAATTTCTGTT
1 TATTTTCTATAAAATTGGCGAATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTT
*
5472073 ATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCGGTGTAACATTATTGCCTCG
66 ATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAACATTATTGCCTCG
* *
5472138 TGTTGTTATGT-ACTGAAAGACGATGA
131 TGTTGTTCT-TCACTGAAAGACGACGA
* * *
5472164 TATTTTCTATAAAATTGGCGACTCTACTTTTAAAGACATTAGATTTTTCGTTTGGAAATTCTCTT
1 TATTTTCTATAAAATTGGCGAATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTT
* *
5472229 ATCACTTGGAAAAAGTGAAACACTTTGCAATACATAGATGCATGCAGTGTAACATTATTGCCTCG
66 ATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAACATTATTGCCTCG
5472294 TGTTGTTCTTCACTGAAAGACGACGA
131 TGTTGTTCTTCACTGAAAGACGACGA
** * * *
5472320 TATTTTCTATAAAATCAGCGATTCTACTTTTAAAGACATTAGATTTTTCTTTTGAAATATCTCTT
1 TATTTTCTATAAAATTGGCGAATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTT
* *
5472385 ATCACTTGGAAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAGCATTATTGCCTCG
66 ATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAACATTATTGCCTCG
5472450 TGTTGTTCTTCACTGAAAGACGACGA
131 TGTTGTTCTTCACTGAAAGACGACGA
** *
5472476 TATTTTCTATAAAATCAGCGATTCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTT
1 TATTTTCTATAAAATTGGCGAATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTT
* *
5472541 ATCTCTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAATGTAACATTATTGCCTCG
66 ATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAACATTATTGCCTCG
5472606 TGTTGTTCTTCACTGAAAGACGACGA
131 TGTTGTTCTTCACTGAAAGACGACGA
5472632 TATTTTCTATAAAATTGGCGAATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTT
1 TATTTTCTATAAAATTGGCGAATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTT
*
5472697 ATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATTCAGTGTAACATTATTGCCTCG
66 ATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAACATTATTGCCTCG
*
5472762 TGTTATTCTTCACT
131 TGTTGTTCTTCACT
5472776 AAACAAGTAG
Statistics
Matches: 1142, Mismatches: 88, Indels: 12
0.92 0.07 0.01
Matches are distributed among these distances:
155 6 0.01
156 1130 0.99
157 6 0.01
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (156 bp):
TATTTTCTATAAAATTGGCGAATCTACTTTTAAAGACATTAGATTTTTCTTTTGGAATTTCTCTT
ATCACTTGGCAAAAGTGAAACACTTTGCAATACATAGTTGCATGCAGTGTAACATTATTGCCTCG
TGTTGTTCTTCACTGAAAGACGACGA
Found at i:5477315 original size:6 final size:6
Alignment explanation
Indices: 5477306--5477330 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5477296 ATTTTATTTT
5477306 ATATTA ATATTA ATATTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA A
5477331 NNNNNNNNNN
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:5483047 original size:18 final size:18
Alignment explanation
Indices: 5483011--5483055 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5483001 CCCTTAAGCC
5483011 TAATTTTTATATATCTTA
1 TAATTTTTATATATCTTA
* *
5483029 TGATTTTCTATA-ATTTTA
1 TAATTTT-TATATATCTTA
5483047 TAATTTTTA
1 TAATTTTTA
5483056 ATGACTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 2 0.09
18 17 0.74
19 4 0.17
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (18 bp):
TAATTTTTATATATCTTA
Found at i:5483334 original size:13 final size:14
Alignment explanation
Indices: 5483301--5483337 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
5483291 AGATTATTCA
*
5483301 AAATAAAAT-AAAT
1 AAATAAATTAAAAT
5483314 AAATAAATTAAAAT
1 AAATAAATTAAAAT
5483328 AAA-AAATTAA
1 AAATAAATTAA
5483338 TATTATCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAAATTAAAAT
Found at i:5483578 original size:13 final size:14
Alignment explanation
Indices: 5483545--5483581 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
5483535 AAGATTATTC
*
5483545 AAATAAAAT-AAAT
1 AAATAAATTAAAAT
5483558 AAATAAATTAAAAT
1 AAATAAATTAAAAT
5483572 AAA-AAATTAA
1 AAATAAATTAA
5483582 TATTATCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAAATTAAAAT
Found at i:5483730 original size:244 final size:245
Alignment explanation
Indices: 5483290--5483778 Score: 971
Period size: 244 Copynumber: 2.0 Consensus size: 245
5483280 AATTTTATCC
5483290 AAGATTATTCAAAATAAAATAAATAAATAAATTAAAATAAAAAATTAATATTATCAAACAAAATA
1 AAGATTATTCAAAATAAAATAAATAAATAAATTAAAATAAAAAATTAATATTATCAAACAAAATA
5483355 ATTATATTTACCATATCAAATGGTTCTATAATATAAATTGAGTATTTAATTTTGTAGTTTATGAA
66 ATTATATTTACCATATCAAATGGTTCTATAATATAAATTGAGTATTTAATTTTGTAGTTTATGAA
5483420 ACACACACTTACCTAAACAAGGAATAGAATTAATGATTTTTTAGCGTCGGCTGGTGGACTGCTCA
131 ACACACACTTACCTAAACAAGGAATAGAATTAATGATTTTTTAGCGTCGGCTGGTGGACTGCTCA
5483485 GGGACTCTAAAGGAAGCTGGTTATCAGGATATAGCAGAAACATAGGAGTT
196 GGGACTCTAAAGGAAGCTGGTTATCAGGATATAGCAGAAACATAGGAGTT
5483535 AAGATTATTC-AAATAAAATAAATAAATAAATTAAAATAAAAAATTAATATTATCAAACAAAATA
1 AAGATTATTCAAAATAAAATAAATAAATAAATTAAAATAAAAAATTAATATTATCAAACAAAATA
5483599 ATTATATTTACCATATCAAATGGTTCTATAATATAAATTGAGTATTTAATTTTGTAGTTTATGAA
66 ATTATATTTACCATATCAAATGGTTCTATAATATAAATTGAGTATTTAATTTTGTAGTTTATGAA
5483664 ACACACACTTACCTAAACAAGGAATAGAATTAATGATTTTTTAGCGTCGGCTGGTGGACTGCTCA
131 ACACACACTTACCTAAACAAGGAATAGAATTAATGATTTTTTAGCGTCGGCTGGTGGACTGCTCA
5483729 GGGACTCTAAAGGAAGCTGGTTATCAGGATATAGCAGAAACATAGGAGTT
196 GGGACTCTAAAGGAAGCTGGTTATCAGGATATAGCAGAAACATAGGAGTT
5483779 TGCTGAGTCC
Statistics
Matches: 244, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
244 234 0.96
245 10 0.04
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (245 bp):
AAGATTATTCAAAATAAAATAAATAAATAAATTAAAATAAAAAATTAATATTATCAAACAAAATA
ATTATATTTACCATATCAAATGGTTCTATAATATAAATTGAGTATTTAATTTTGTAGTTTATGAA
ACACACACTTACCTAAACAAGGAATAGAATTAATGATTTTTTAGCGTCGGCTGGTGGACTGCTCA
GGGACTCTAAAGGAAGCTGGTTATCAGGATATAGCAGAAACATAGGAGTT
Found at i:5485497 original size:3 final size:3
Alignment explanation
Indices: 5485489--5485572 Score: 91
Period size: 3 Copynumber: 28.7 Consensus size: 3
5485479 GTTTTGTTAC
* * * *
5485489 TAT TAT TAT TAT CAT TAT AAT TA- AAT T-T CAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
5485535 TAT TAT TAT TAT TAC TAT TGT TAT TAT TAT TAC TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5485573 CCGCTTTGTA
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
2 2 0.03
3 63 0.97
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:5488108 original size:21 final size:20
Alignment explanation
Indices: 5488062--5488108 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
5488052 ATGGTATCCA
5488062 AGCAAAGACTAAGGAAATGG
1 AGCAAAGACTAAGGAAATGG
* *
5488082 ATCAAAGA-TTAGAGAAATTGG
1 AGCAAAGACTAAG-GAAA-TGG
5488103 AGCAAA
1 AGCAAA
5488109 TGCAAAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.14
20 11 0.50
21 8 0.36
ACGTcount: A:0.51, C:0.09, G:0.26, T:0.15
Consensus pattern (20 bp):
AGCAAAGACTAAGGAAATGG
Found at i:5490595 original size:9 final size:10
Alignment explanation
Indices: 5490578--5490604 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
5490568 CAGATCTAAT
5490578 TCAAAAAAAA
1 TCAAAAAAAA
5490588 TCAAAAAAAA
1 TCAAAAAAAA
5490598 TCAAAAA
1 TCAAAAA
5490605 TAAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (10 bp):
TCAAAAAAAA
Found at i:5491599 original size:7 final size:7
Alignment explanation
Indices: 5491587--5491620 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
5491577 AAAAAAAGGG
5491587 ATGAAAA
1 ATGAAAA
5491594 ATGAAAA
1 ATGAAAA
5491601 ATG-AAA
1 ATGAAAA
5491607 ATGAAAA
1 ATGAAAA
5491614 ATGAAAA
1 ATGAAAA
5491621 GAAATGACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGAAAA
Found at i:5491607 original size:13 final size:13
Alignment explanation
Indices: 5491591--5491624 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
5491581 AAAGGGATGA
5491591 AAAATGAAAAATG
1 AAAATGAAAAATG
5491604 AAAATGAAAAATG
1 AAAATGAAAAATG
5491617 AAAA-GAAA
1 AAAATGAAA
5491625 TGACGGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:5496548 original size:131 final size:131
Alignment explanation
Indices: 5496309--5496892 Score: 927
Period size: 131 Copynumber: 4.5 Consensus size: 131
5496299 ATCAGTGAAT
* * * * * *
5496309 ATTGTAGATCTTATCTCCCTAGGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTCCCC
1 ATTGCAGATCTTGTCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCC
* * *
5496374 AGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAACAGTGGAATAGGTTGGA
66 AAGAGTAGGGAAACAAATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGA
5496439 A
131 A
5496440 ATTGCAGATCTTGTCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCC
1 ATTGCAGATCTTGTCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCC
*
5496505 AAGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGA
66 AAGAGTAGGGAAACAAATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGA
5496570 A
131 A
* * * * *
5496571 ATTGCAAATCTTATCTCCCTAAGCAATAATGGAGCAGATCGAAGACTGTGAATCTTATCTT-CCC
1 ATTGCAGATCTTGTCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCC
*
5496635 AAGGAGTAGGGAAACAAATTTAAGCCACAAGTCCTATGTCCCTGACCAGTAGTGGAATAGGTTGG
66 AA-GAGTAGGGAAACAAATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGG
5496700 AA
130 AA
*
5496702 ATTGCAGATCTTGTCTCCCTAAGCAATAGTGGAGCTGATCGAAGACGGCGAATCTTATCTTCCCC
1 ATTGCAGATCTTGTCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCC
* * *
5496767 AGGAGTAGGGAAACAAATTTAAGCCATAAGTTCTATGTCCCTGACCAGCAGTGGAATAGGTTGGA
66 AAGAGTAGGGAAACAAATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGA
5496832 A
131 A
* * * **
5496833 ATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGAGGGAAAATCTTATCT
1 ATTGCAGATCTTGTCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGAATCTTATCT
5496893 CCCTGAAGTT
Statistics
Matches: 420, Mismatches: 31, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
130 5 0.01
131 411 0.98
132 4 0.01
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (131 bp):
ATTGCAGATCTTGTCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCC
AAGAGTAGGGAAACAAATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGA
A
Found at i:5496936 original size:44 final size:43
Alignment explanation
Indices: 5496883--5497117 Score: 177
Period size: 44 Copynumber: 5.3 Consensus size: 43
5496873 GAAGAGGGAA
*
5496883 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAG-CAAT
* * * * *
5496927 AATCCTATCTCCCTAAAGTTGTAATGGAGCGGATTAAAGTAAT
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCAAT
* * *
5496970 AGGTCTTATCTCCCTGAAGTTGCAACGGAGCAGACTGAGTAAGC-A-
1 A-ATCTTATCTCCCTGAAGTTGCAATGGAGCAGA-TTA--AAGCAAT
** * * * ** * *
5497015 GGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGATCGAAGATAACA
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAG-CAA-T
* * * *
5497060 AATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGTCGAT
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAG-CAAT
*
5497104 AATCCTATCTCCCT
1 AATCTTATCTCCCT
5497118 AAGGTTGTGT
Statistics
Matches: 150, Mismatches: 33, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
41 3 0.02
43 5 0.03
44 102 0.68
45 36 0.24
46 1 0.01
47 3 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCAAT
Found at i:5496978 original size:88 final size:88
Alignment explanation
Indices: 5496882--5497138 Score: 250
Period size: 88 Copynumber: 2.9 Consensus size: 88
5496872 CGAAGAGGGA
5496882 AAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCCGATAATCCTATCTCCCTAAAGTT
1 AAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAG-CGATAATCCTATCTCCCTAAAGTT
* *
5496947 GTAATGGAGCGGATTAAAG-TAAT
65 GTAATGGAGCGGATCAAAGATAAC
** * * ** * * *
5496970 AGGTCTTATCTCCCTGAAGTTGCAACGGAGCAGACTGAGTAAGC-A-GGTCTTATCCCCCTGAAG
1 AAATCTTATCTCCCTGAAGTTGCAATGGAGCAGA-TTA--AAGCGATAATCCTATCTCCCTAAAG
* * * * *
5497033 TTGCAGTGGGGCAGATCGAAGATAAC
63 TTGTAATGGAGCGGATCAAAGATAAC
* * * *
5497059 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGTCGATAATCCTATCTCCCTAAGGTT
1 AAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAG-CGATAATCCTATCTCCCTAAAGTT
**
5497124 GTGTTGGAGCGGATC
65 GTAATGGAGCGGATC
5497139 CTATCTCTCT
Statistics
Matches: 128, Mismatches: 34, Indels: 13
0.73 0.19 0.07
Matches are distributed among these distances:
86 3 0.02
87 1 0.01
88 61 0.48
89 59 0.46
90 1 0.01
91 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (88 bp):
AAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCGATAATCCTATCTCCCTAAAGTTG
TAATGGAGCGGATCAAAGATAAC
Found at i:5500353 original size:14 final size:14
Alignment explanation
Indices: 5500334--5500393 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
5500324 AGGTCAATTT
5500334 AGGGTTAAAGGTTA
1 AGGGTTAAAGGTTA
*
5500348 AGGGTT-TAGTGTTA
1 AGGGTTAAAG-GTTA
* * *
5500362 AGGGCTAATGGTTG
1 AGGGTTAAAGGTTA
*
5500376 AGGGTTTAAGGTTTA
1 AGGGTTAAAGG-TTA
5500391 AGG
1 AGG
5500394 TCTAAAAAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
13 2 0.06
14 26 0.76
15 6 0.18
ACGTcount: A:0.27, C:0.02, G:0.38, T:0.33
Consensus pattern (14 bp):
AGGGTTAAAGGTTA
Found at i:5521713 original size:25 final size:25
Alignment explanation
Indices: 5521685--5521777 Score: 96
Period size: 25 Copynumber: 3.6 Consensus size: 25
5521675 CCAAATATTA
5521685 GGAAGCTCAAAAGAGCCATTAATCG
1 GGAAGCTCAAAAGAGCCATTAATCG
* *
5521710 GGAAGCTCATGAAAAAGCCTTTAATCG
1 GGAAGCTCA--AAAGAGCCATTAATCG
* * * *
5521737 GAAAGCTCTAAAGAGCCATAAATTG
1 GGAAGCTCAAAAGAGCCATTAATCG
* *
5521762 GGACGCTCATAAGAGC
1 GGAAGCTCAAAAGAGC
5521778 TATAGTGTGT
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
25 33 0.61
27 21 0.39
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (25 bp):
GGAAGCTCAAAAGAGCCATTAATCG
Found at i:5529646 original size:20 final size:20
Alignment explanation
Indices: 5529610--5529647 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5529600 CGTGATCCGA
*
5529610 TTAAAACACAAGGATTTTTT
1 TTAAAACACAAGAATTTTTT
*
5529630 TTAAAACACGAGAATTTT
1 TTAAAACACAAGAATTTT
5529648 GAAGCACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAAAACACAAGAATTTTTT
Found at i:5529700 original size:17 final size:17
Alignment explanation
Indices: 5529680--5530113 Score: 117
Period size: 17 Copynumber: 24.3 Consensus size: 17
5529670 AAAACGAAAG
*
5529680 TTTTTAAACACGATAAT
1 TTTTTAAACACGAGAAT
* *
5529697 TTTTGAAAACACTAGAAT
1 TTTT-TAAACACGAGAAT
*
5529715 TTTTAAAACAC-AGAAAT
1 TTTTTAAACACGAG-AAT
** *
5529732 TTTAGAAACACGAAAAT
1 TTTTTAAACACGAGAAT
* *
5529749 TTTTTAAAAACACAACAAT
1 TTTTT--AAACACGAGAAT
*
5529768 TTTTGAAACACGAGAAT
1 TTTTTAAACACGAGAAT
* * * *
5529785 TTTTTAAAAAAACAAAAAAA
1 TTTTT--AAACAC-GAGAAT
* * * *
5529805 ATTTAAAATACGAAAAT
1 TTTTTAAACACGAGAAT
* * *
5529822 TTGTGAAACGCGAGAAT
1 TTTTTAAACACGAGAAT
** *
5529839 TGTTGAAAACACGAAAAT
1 T-TTTTAAACACGAGAAT
* * *
5529857 TTTTGAAAACTCGACAAT
1 TTTT-TAAACACGAGAAT
* * *
5529875 TTTTGAAAACATGAAAAT
1 TTTT-TAAACACGAGAAT
*
5529893 TTTTGAAACACG-GAAAT
1 TTTTTAAACACGAG-AAT
** *
5529910 TTTGGAAAACACTAGAATT
1 TTT-TTAAACACGAGAA-T
*
5529929 GTTTTTAATCACG-GAAATT
1 -TTTTTAAACACGAG-AA-T
*
5529948 TTTTTGGAAAACACGAGGAT
1 TTTTT---AAACACGAGAAT
*
5529968 TTTTTAAACACGAAAAT
1 TTTTTAAACACGAGAAT
* *
5529985 TTTTGGAAACACGA-AAA
1 TTTT-TAAACACGAGAAT
*
5530002 TTTTTAAACACGA-ATTTT
1 TTTTTAAACACGAGA--AT
* *
5530020 TTTTTGAAAACATGA-AAA
1 TTTTT--AAACACGAGAAT
* * *
5530038 CTTTTAGACACGAAAATT
1 TTTTTAAACACGAGAA-T
* *
5530056 TTTTTGAAA-ACAAGAAA
1 TTTTT-AAACACGAGAAT
* * *
5530073 ATTTTAAACCCAAGAAT
1 TTTTTAAACACGAGAAT
5530090 TTTTTGAAAACACGAGAAT
1 TTTTT--AAACACGAGAAT
5530109 TTTTT
1 TTTTT
5530114 GATTTTTTCT
Statistics
Matches: 309, Mismatches: 77, Indels: 60
0.69 0.17 0.13
Matches are distributed among these distances:
16 20 0.06
17 109 0.35
18 102 0.33
19 47 0.15
20 23 0.07
21 7 0.02
22 1 0.00
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (17 bp):
TTTTTAAACACGAGAAT
Found at i:5529706 original size:18 final size:18
Alignment explanation
Indices: 5529662--5530112 Score: 256
Period size: 18 Copynumber: 25.3 Consensus size: 18
5529652 CACAAATTTT
* * *
5529662 TTTTTAAAAAAACGAAAG
1 TTTTTGAAAACACGAAAA
*
5529680 TTTTT--AAACACGATAA
1 TTTTTGAAAACACGAAAA
* *
5529696 TTTTTGAAAACACTAGAA
1 TTTTTGAAAACACGAAAA
5529714 TTTTT-AAAACAC-AGAAA
1 TTTTTGAAAACACGA-AAA
*
5529731 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
5529748 TTTTTTAAAAACAC-AACAA
1 -TTTTTGAAAACACGAA-AA
*
5529767 TTTTTG-AAACACGAGAAT
1 TTTTTGAAAACACGA-AAA
* * *
5529785 TTTTTAAAAAAACAAAAAA
1 TTTTTGAAAACAC-GAAAA
** *
5529804 AATTT-AAAATACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
5529821 TTTGTG-AAACGCGAGAA
1 TTTTTGAAAACACGAAAA
*
5529838 TTGTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
5529856 TTTTTGAAAACTCGACAA
1 TTTTTGAAAACACGAAAA
*
5529874 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
*
5529892 TTTTTG-AAACACGGAAA
1 TTTTTGAAAACACGAAAA
* * *
5529909 TTTTGGAAAACACTAGAA
1 TTTTTGAAAACACGAAAA
** * *
5529927 TTGTTTTTAATCACGGAAATT
1 TT-TTTGAAAACAC-GAAA-A
**
5529948 TTTTTGGAAAACACGAGGA
1 TTTTT-GAAAACACGAAAA
*
5529967 TTTTT-TAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
5529984 TTTTTGGAAACACGAAAA
1 TTTTTGAAAACACGAAAA
**
5530002 TTTTT--AAACACGAATTTT
1 TTTTTGAAAACACGAA--AA
*
5530020 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
* *
5530038 CTTTT--AGACACGAAAA
1 TTTTTGAAAACACGAAAA
*
5530054 TTTTTTTGAAAACAAGAAAA
1 --TTTTTGAAAACACGAAAA
*
5530074 -TTTT--AAAC-CCAAGAA
1 TTTTTGAAAACACGAA-AA
*
5530089 TTTTTTGAAAACACGAGAA
1 -TTTTTGAAAACACGAAAA
5530108 TTTTT
1 TTTTT
5530113 TGATTTTTTC
Statistics
Matches: 326, Mismatches: 73, Indels: 68
0.70 0.16 0.15
Matches are distributed among these distances:
14 2 0.01
15 6 0.02
16 32 0.10
17 82 0.25
18 133 0.41
19 37 0.11
20 27 0.08
21 7 0.02
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.32
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:5530924 original size:20 final size:20
Alignment explanation
Indices: 5530901--5530949 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
5530891 TCCCCCTTTC
5530901 TTTTTTCTTTTTTCCCTTCT
1 TTTTTTCTTTTTTCCCTTCT
* *
5530921 TTTTTTCTTTTTTTCTTTCT
1 TTTTTTCTTTTTTCCCTTCT
5530941 TTTTTTCTT
1 TTTTTTCTT
5530950 CCCCGTTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTCTTTTTTCCCTTCT
Found at i:5530939 original size:12 final size:12
Alignment explanation
Indices: 5530920--5530949 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5530910 TTTTCCCTTC
5530920 TTTT-TTTCTTT
1 TTTTCTTTCTTT
5530931 TTTTCTTTCTTT
1 TTTTCTTTCTTT
5530943 TTTTCTT
1 TTTTCTT
5530950 CCCCGTTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTCTTTCTTT
Found at i:5531051 original size:1 final size:1
Alignment explanation
Indices: 5531045--5531112 Score: 55
Period size: 1 Copynumber: 68.0 Consensus size: 1
5531035 CCATTTCTTC
** * ** ** * *
5531045 TTTTTTTTCCTTTGTTTTTTTTTTCCTTTTTTTTCCTTGTTGTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5531110 TTT
1 TTT
5531113 GTTCTTCTTG
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.00, C:0.09, G:0.04, T:0.87
Consensus pattern (1 bp):
T
Found at i:5531066 original size:16 final size:15
Alignment explanation
Indices: 5531045--5531112 Score: 70
Period size: 16 Copynumber: 4.5 Consensus size: 15
5531035 CCATTTCTTC
5531045 TTTTTTTTCCTTTGTT
1 TTTTTTTTCCTTT-TT
5531061 TTTTTTTTCCTTTTT
1 TTTTTTTTCCTTTTT
* *
5531076 TTTCCTTGTT-GTTTTT
1 TTT--TTTTTCCTTTTT
5531092 TTTTTTTT--TTTTT
1 TTTTTTTTCCTTTTT
5531105 TTTTTTTT
1 TTTTTTTT
5531113 GTTCTTCTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
13 13 0.28
14 4 0.09
15 5 0.11
16 21 0.45
17 4 0.09
ACGTcount: A:0.00, C:0.09, G:0.04, T:0.87
Consensus pattern (15 bp):
TTTTTTTTCCTTTTT
Found at i:5531080 original size:26 final size:28
Alignment explanation
Indices: 5531044--5531106 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
5531034 CCCATTTCTT
5531044 CTTTTTTTTCC-T-TTGTTTTTTTTTTC
1 CTTTTTTTTCCTTGTTGTTTTTTTTTTC
*
5531070 CTTTTTTTTCCTTGTTGTTTTTTTTTTT
1 CTTTTTTTTCCTTGTTGTTTTTTTTTTC
*
5531098 TTTTTTTTT
1 CTTTTTTTT
5531107 TTTTTTGTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 11 0.33
27 1 0.03
28 21 0.64
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (28 bp):
CTTTTTTTTCCTTGTTGTTTTTTTTTTC
Found at i:5531115 original size:30 final size:30
Alignment explanation
Indices: 5531044--5531108 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
5531034 CCCATTTCTT
5531044 CTTTTTTTTCC-T-TTG--TTTTTTTTTTC
1 CTTTTTTTTCCTTGTTGTTTTTTTTTTTTC
*
5531070 CTTTTTTTTCCTTGTTGTTTTTTTTTTTTT
1 CTTTTTTTTCCTTGTTGTTTTTTTTTTTTC
*
5531100 TTTTTTTTT
1 CTTTTTTTT
5531109 TTTTGTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 11 0.33
27 1 0.03
28 3 0.09
30 18 0.55
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.85
Consensus pattern (30 bp):
CTTTTTTTTCCTTGTTGTTTTTTTTTTTTC
Found at i:5531574 original size:30 final size:29
Alignment explanation
Indices: 5531504--5531604 Score: 78
Period size: 30 Copynumber: 3.4 Consensus size: 29
5531494 TTAAAGGCCC
* * * * *
5531504 AAATGTAATTTACAAATTATTAGGGGTTA
1 AAATGTAATTTAAAAAATGTTAAGGGTCA
*
5531533 AGATGTAAATTTAGAAAAATGTTAAGGGTCA
1 AAATGT-AATTTA-AAAAATGTTAAGGGTCA
* * *
5531564 AAATGTAATTTTTAAAAA-GTTTAGGGGCTA
1 AAATGTAA-TTTAAAAAATGTTAAGGGTC-A
5531594 AAATGTAATTT
1 AAATGTAATTT
5531605 GTATTTTTTG
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
29 16 0.28
30 22 0.38
31 20 0.34
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.36
Consensus pattern (29 bp):
AAATGTAATTTAAAAAATGTTAAGGGTCA
Found at i:5531882 original size:14 final size:14
Alignment explanation
Indices: 5531863--5531889 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5531853 TCTAAAATTA
5531863 TTATATTTTTTTGT
1 TTATATTTTTTTGT
5531877 TTATATTTTTTTG
1 TTATATTTTTTTG
5531890 AAAGCCTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (14 bp):
TTATATTTTTTTGT
Found at i:5532013 original size:76 final size:73
Alignment explanation
Indices: 5531931--5532138 Score: 231
Period size: 75 Copynumber: 2.8 Consensus size: 73
5531921 GATCCAAAGT
* *
5531931 TCAACTCACTTCTCAAATTATGAGTTGAGCTTTGAAAAATAGAAATTGAAAAATACCTCAGCATA
1 TCAACTCACCTCTCAAATTATGAGTTGA--TTTGAAAAAAAGAAATT-AAAAATACCTCAGCATA
5531996 T-GACCCAAGGC
63 TAG-CCCAAGGC
* * * **
5532007 TCAACTCACCTCTCGCAA-TATAAGTTGATTTTTGAAAAACAGAAATTAAAAATACCTCAGTGTA
1 TCAACTCACCTCTC-AAATTATGAGTTGA--TTTGAAAAAAAGAAATTAAAAATACCTCAGCATA
5532071 TAGCCCAAGGC
63 TAGCCCAAGGC
** *
5532082 TCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAAAAGAAATTAAAAATACCT
1 TCAACTCACCTCTCAAATTATGAGTTGATTT--GAAAAAAAGAAATTAAAAATACCT
5532139 TGGGGTGTAG
Statistics
Matches: 114, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
73 3 0.03
74 1 0.01
75 69 0.61
76 39 0.34
77 2 0.02
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (73 bp):
TCAACTCACCTCTCAAATTATGAGTTGATTTGAAAAAAAGAAATTAAAAATACCTCAGCATATAG
CCCAAGGC
Found at i:5532091 original size:75 final size:75
Alignment explanation
Indices: 5531961--5532138 Score: 250
Period size: 75 Copynumber: 2.4 Consensus size: 75
5531951 TGAGTTGAGC
*
5531961 TTTGAAAAATAGAAATTGAAAAATACCTCAGCATATGACCCAAGGCTCAACTCACCTCTCGCAAT
1 TTTGAAAAAAAGAAATT-AAAAATACCTCAGCATATGACCCAAGGCTCAACTCACCTCTCGCAAT
5532026 ATAAGTTGATT
65 ATAAGTTGATT
* ** *
5532037 TTTGAAAAACAGAAATTAAAAATACCTCAGTGTAT-AGCCCAAGGCTCAACTCACCTCTCGCATT
1 TTTGAAAAAAAGAAATTAAAAATACCTCAGCATATGA-CCCAAGGCTCAACTCACCTCTCGCAAT
*
5532101 ATGAGTTGATT
65 ATAAGTTGATT
***
5532112 TAAAAAAAAAAGAAATTAAAAATACCT
1 TTTGAAAAAAAGAAATTAAAAATACCT
5532139 TGGGGTGTAG
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
74 1 0.01
75 75 0.82
76 16 0.17
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (75 bp):
TTTGAAAAAAAGAAATTAAAAATACCTCAGCATATGACCCAAGGCTCAACTCACCTCTCGCAATA
TAAGTTGATT
Found at i:5532673 original size:30 final size:29
Alignment explanation
Indices: 5532603--5532703 Score: 78
Period size: 30 Copynumber: 3.4 Consensus size: 29
5532593 TTAAAGGCCC
* * * * *
5532603 AAATGTAATTTACAAATTATTAGGGGTTA
1 AAATGTAATTTAAAAAATGTTAAGGGTCA
*
5532632 AGATGTAAATTTAGAAAAATGTTAAGGGTCA
1 AAATGT-AATTTA-AAAAATGTTAAGGGTCA
* * *
5532663 AAATGTAATTTTTAAAAA-GTTTAGGGGCTA
1 AAATGTAA-TTTAAAAAATGTTAAGGGTC-A
5532693 AAATGTAATTT
1 AAATGTAATTT
5532704 GTATTTTTTG
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
29 16 0.28
30 22 0.38
31 20 0.34
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.36
Consensus pattern (29 bp):
AAATGTAATTTAAAAAATGTTAAGGGTCA
Found at i:5532981 original size:14 final size:14
Alignment explanation
Indices: 5532962--5532988 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5532952 TCTAAAATTA
5532962 TTATATTTTTTTGT
1 TTATATTTTTTTGT
5532976 TTATATTTTTTTG
1 TTATATTTTTTTG
5532989 AAAGCCTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (14 bp):
TTATATTTTTTTGT
Found at i:5533190 original size:75 final size:74
Alignment explanation
Indices: 5533060--5533688 Score: 503
Period size: 75 Copynumber: 8.3 Consensus size: 74
5533050 TGAGTTGAGC
* **
5533060 TTTGAAAAATAGAAATTGAAAAATACCTCAG-CATATGACCCAAGGCTCAACTCACCTCTCGCAA
1 TTTGAAAAACAGAAATT-AAAAATACCTCAGTGTTA-G-CCCAAGGCTCAACTCACCTCTCGCAA
5533124 TATAAGTTGATT
63 TATAAGTTGATT
*
5533136 TTTGAAAAACAGAAATTAAAAATACCTCAGTGTATAGCCCAAGGCTCAACTCACCTCTCGCATTA
1 TTTGAAAAACAGAAATTAAAAATACCTCAGTGT-TAGCCCAAGGCTCAACTCACCTCTCGCAATA
*
5533201 TGAGTTGATT
65 TAAGTTGATT
*** * ** **
5533211 TAAAAAAAAAAGAAATTAAAAATACCTTGGTGTGTAGCCTTAGG-T----TCACCTCTCGCAATA
1 TTTGAAAAACAGAAATTAAAAATACCTCAGTGT-TAGCCCAAGGCTCAACTCACCTCTCGCAATA
*
5533271 TGAGTTGATT
65 TAAGTTGATT
* * * *
5533281 TTTGAAAAACATAAATTGAAGAAAAAAAACCTCAGT-TTGTGACCCAAGAG-TCAACTTACCTCT
1 TTTGAAAAACAGAAATT-----AAAAATACCTCAGTGTT-AG-CCCAAG-GCTCAACTCACCTCT
5533344 CGCAATATAAGTTGATTT
58 CGCAATATAAGTTGA-TT
* * * ** *
5533362 TTTGGAAAATAGAAATTAAAATATACCTCAGCATGTGA-CCTGAGGCTCAACTCACTTCTCGCAA
1 TTTGAAAAACAGAAATTAAAA-ATACCTCAG--TGTTAGCCCAAGGCTCAACTCACCTCTCGCAA
*
5533426 TATGAGTTGATTTT
63 TATAAGTTGA--TT
* * * *
5533440 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGA-CCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTTGAAAAACAGAAATTAAAAATACCTCAGTGTTAGCCCAAGGCTCAACTCACCTCTCGCAATAT
*
5533504 GAGTTGATATT
66 AAGTTG--ATT
* * * * ** * * *
5533515 TTTGAAAAGCAGAAATTGAAAATACCTCAGCG-TGGCCTGAGGCTCAACTCACTTCTCGCATTGT
1 TTTGAAAAACAGAAATTAAAAATACCTCAGTGTTAGCCCAAGGCTCAACTCACCTCTCGCAATAT
5533579 AAGTTGATT
66 AAGTTGATT
* *
5533588 TTTGAAAAACAGAAATTGAGAAATACCTTGGCA-TG-T-GCCCAAGGCTCAACTCACCTCTTGCA
1 TTTGAAAAACAGAAATT-AAAAATACC-T--CAGTGTTAGCCCAAGGCTCAACTCACCTCTCGCA
* *
5533650 TTATAATTTGATTT
62 ATATAAGTTGA-TT
***
5533664 TTTTTTAAACAGAAATTGAAAAATA
1 TTTGAAAAACAGAAATT-AAAAATA
5533689 TTTCTTGAAA
Statistics
Matches: 457, Mismatches: 67, Indels: 58
0.79 0.12 0.10
Matches are distributed among these distances:
70 36 0.08
73 20 0.04
74 10 0.02
75 231 0.51
76 49 0.11
77 51 0.11
78 21 0.05
79 1 0.00
80 22 0.05
81 16 0.04
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (74 bp):
TTTGAAAAACAGAAATTAAAAATACCTCAGTGTTAGCCCAAGGCTCAACTCACCTCTCGCAATAT
AAGTTGATT
Found at i:5533663 original size:302 final size:299
Alignment explanation
Indices: 5533060--5533688 Score: 725
Period size: 302 Copynumber: 2.1 Consensus size: 299
5533050 TGAGTTGAGC
5533060 TTTGAAAAATAGAAATTGAAAAATACCTCAGCATATGACCCAAGGCTCAACTCACCTCTCGCAAT
1 TTTGAAAAATAGAAATTGAAAAATACCTCAGCATATGACCCAAGGCTCAACTCACCTCTCGCAAT
* *
5533125 ATAAGTTGATTTTTGAAAAACAGAAATTAAAAATACCTCAGTGTATAGCCCAAGGCTCAACTCAC
66 ATAAGTTGATTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAGAGCCCAAGGCTCAACTCAC
* ** * *
5533190 CTCTCGCATTATGAGTTGATTTAAAAAAAAAAGAAATTAAAAATACCTTGGTGTGTAGCCTTAGG
131 CTCTCGCAATATGAGTTGATTTAAAAAAAAAAGAAATTAAAAATACCTCAGCGTG-AGCCTGAGG
* * **
5533255 TTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAAGAAAAAAAACCTCAGTTTG
195 TTCACCTCTCGCAATATAAGTTGATTTTTGAAAAACAGAAATTGAAG--AAAAAACCTCAGCATG
*
5533320 TGACCCAAGAGTCAACTTACCTCTCGCAATATAAGTTGATTT
258 TGACCCAAGAGTCAACTCACCTCTCGCAATATAAGTTGATTT
* * ** *
5533362 TTTGGAAAATAGAAATT-AAAATATACCTCAGCATGTGACCTGAGGCTCAACTCACTTCTCGCAA
1 TTTGAAAAATAGAAATTGAAAA-ATACCTCAGCATATGACCCAAGGCTCAACTCACCTCTCGCAA
* * *
5533426 TATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT-GA-CCCGAGGCTCAACT
65 TATAAGTTGA--TTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAGAGCCCAAGGCTCAACT
*** ** *
5533489 CACCTCTCGCAATATGAGTTGATATTTTTGAAAAGCAGAAATTGAAAATACCTCAGCGTG-GCCT
128 CACCTCTCGCAATATGAGTTG--ATTTAAAAAAAAAAGAAATTAAAAATACCTCAGCGTGAGCCT
* * * *
5533553 GAGGCTCAACTCACTTCTCGCATTGTAAGTTGATTTTTGAAAAACAGAAATTG-AG-AAATACCT
191 GAGG-T----TCACCTCTCGCAATATAAGTTGATTTTTGAAAAACAGAAATTGAAGAAAAAACCT
** * * *
5533616 TGGCATGTG-CCCAAG-GCTCAACTCACCTCTTGCATTATAATTTGATTT
251 CAGCATGTGACCCAAGAG-TCAACTCACCTCTCGCAATATAAGTTGATTT
*** *
5533664 TTTTTTAAACAGAAATTGAAAAATA
1 TTTGAAAAATAGAAATTGAAAAATA
5533689 TTTCTTGAAA
Statistics
Matches: 276, Mismatches: 39, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
301 5 0.02
302 152 0.55
303 18 0.07
304 61 0.22
306 2 0.01
307 38 0.14
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (299 bp):
TTTGAAAAATAGAAATTGAAAAATACCTCAGCATATGACCCAAGGCTCAACTCACCTCTCGCAAT
ATAAGTTGATTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTAGAGCCCAAGGCTCAACTCAC
CTCTCGCAATATGAGTTGATTTAAAAAAAAAAGAAATTAAAAATACCTCAGCGTGAGCCTGAGGT
TCACCTCTCGCAATATAAGTTGATTTTTGAAAAACAGAAATTGAAGAAAAAACCTCAGCATGTGA
CCCAAGAGTCAACTCACCTCTCGCAATATAAGTTGATTT
Found at i:5533687 original size:150 final size:152
Alignment explanation
Indices: 5533060--5533688 Score: 612
Period size: 150 Copynumber: 4.2 Consensus size: 152
5533050 TGAGTTGAGC
* * **
5533060 TTTGAAAAATAGAAATTGAAAAATACCTCAGCATATGACCCAAGGCTCAACTCACCTCTCGCAAT
1 TTTG-AAAACAGAAATTGAAAAATACCTCAGCA-GTGACCTGAGGCTCAACTCACCTCTCGCAAT
* *
5533125 ATAAGTTGATTTTTGAAAAACAGAAATT-AAAAATACCTCAG--TGTATAGCCCAAGGCTCAACT
64 ATAAGTTGATTTTTGAAAAACAGAAATTGAGAAATACCTCAGCATGT-GA-CCCAAGGCTCAACT
* *
5533187 CACCTCTCGCATTATGAGTTGA-TTT
127 CACCTCTCGCAATATAAGTTGATTTT
**** * * ** *
5533212 AAAAAAAAAAGAAATT-AAAAATACCT-TGGTGTGTAGCCTTAGG-T----TCACCTCTCGCAAT
1 TTTGAAAACAGAAATTGAAAAATACCTCAGCAGTG-A-CCTGAGGCTCAACTCACCTCTCGCAAT
* * * **
5533270 ATGAGTTGATTTTTGAAAAACATAAATTGAAGAAAAAAAACCTCAGTTTGTGACCCAAGAG-TCA
64 ATAAGTTGATTTTTGAAAAACAGAAATTG-AG---AAATACCTCAGCATGTGACCCAAG-GCTCA
*
5533334 ACTTACCTCTCGCAATATAAGTTGATTTT
124 ACTCACCTCTCGCAATATAAGTTGATTTT
* * *
5533363 TTGGAAAATAGAAATT-AAAATATACCTCAGCATGTGACCTGAGGCTCAACTCACTTCTCGCAAT
1 TTTGAAAACAGAAATTGAAAA-ATACCTCAGCA-GTGACCTGAGGCTCAACTCACCTCTCGCAAT
* *
5533427 ATGAGTTGATTTTTTTGAAAAACAGAAATTGA-AAATACCTCAGC--GTGACCCGAGGCTCAACT
64 ATAAGTTGA--TTTTTGAAAAACAGAAATTGAGAAATACCTCAGCATGTGACCCAAGGCTCAACT
* *
5533489 CACCTCTCGCAATATGAGTTGATATT
127 CACCTCTCGCAATATAAGTTGATTTT
* * * *
5533515 TTTGAAAAGCAGAAATTG-AAAATACCTCAGC-GTGGCCTGAGGCTCAACTCACTTCTCGCATTG
1 TTTGAAAA-CAGAAATTGAAAAATACCTCAGCAGTGACCTGAGGCTCAACTCACCTCTCGCAATA
**
5533578 TAAGTTGATTTTTGAAAAACAGAAATTGAGAAATACCTTGGCATGTG-CCCAAGGCTCAACTCAC
65 TAAGTTGATTTTTGAAAAACAGAAATTGAGAAATACCTCAGCATGTGACCCAAGGCTCAACTCAC
* * *
5533642 CTCTTGCATTATAATTTGATTTT
130 CTCTCGCAATATAAGTTGATTTT
**
5533665 TTTTTAAACAGAAATTGAAAAATA
1 TTTGAAAACAGAAATTGAAAAATA
5533689 TTTCTTGAAA
Statistics
Matches: 397, Mismatches: 52, Indels: 58
0.78 0.10 0.11
Matches are distributed among these distances:
145 40 0.10
147 1 0.00
148 23 0.06
149 22 0.06
150 138 0.35
151 35 0.09
152 70 0.18
153 13 0.03
154 13 0.03
157 22 0.06
158 1 0.00
159 19 0.05
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (152 bp):
TTTGAAAACAGAAATTGAAAAATACCTCAGCAGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
AAGTTGATTTTTGAAAAACAGAAATTGAGAAATACCTCAGCATGTGACCCAAGGCTCAACTCACC
TCTCGCAATATAAGTTGATTTT
Found at i:5534558 original size:17 final size:17
Alignment explanation
Indices: 5534536--5534581 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
5534526 CATCTTGCTT
5534536 TTTCTT-TTTCTTTTTTG
1 TTTCTTGTTT-TTTTTTG
5534553 TTTCTTGTTTTTTTTTG
1 TTTCTTGTTTTTTTTTG
5534570 -TT-TTGTTTTTTT
1 TTTCTTGTTTTTTT
5534582 AGGCATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.36
16 2 0.07
17 13 0.46
18 3 0.11
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.85
Consensus pattern (17 bp):
TTTCTTGTTTTTTTTTG
Found at i:5544992 original size:9 final size:9
Alignment explanation
Indices: 5544978--5545002 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5544968 TTTGAACAAG
5544978 AAATTTTGA
1 AAATTTTGA
5544987 AAATTTTGA
1 AAATTTTGA
5544996 AAATTTT
1 AAATTTT
5545003 AACAACATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (9 bp):
AAATTTTGA
Found at i:5545455 original size:20 final size:20
Alignment explanation
Indices: 5545419--5545456 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5545409 CGTGATCCGA
*
5545419 TTAAAACACGATGATTTTTT
1 TTAAAACACGAAGATTTTTT
5545439 TTAAAACAC-AAGAATTTT
1 TTAAAACACGAAG-ATTTT
5545457 GAAGCACGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (20 bp):
TTAAAACACGAAGATTTTTT
Found at i:5545509 original size:18 final size:18
Alignment explanation
Indices: 5545419--5545900 Score: 245
Period size: 18 Copynumber: 27.1 Consensus size: 18
5545409 CGTGATCCGA
*
5545419 TTAAAACACGATGATTTTTT
1 TTAAAACACGA-GA-ATTTT
*
5545439 TTAAAACACAAGAA--TT
1 TTAAAACACGAGAATTTT
* * *
5545455 TTGAAGCACG-TAATTTT
1 TTAAAACACGAGAATTTT
*
5545472 TTAAACAAAACGA-AAGTTTT
1 TT-AA-AACACGAGAA-TTTT
5545492 TT-AAACACGAGAATTTT
1 TTAAAACACGAGAATTTT
* *
5545509 TGAAAACACTAGAA-TTT
1 TTAAAACACGAGAATTTT
*
5545526 TTAAAACACGA-AA-ATT
1 TTAAAACACGAGAATTTT
*
5545542 TTAGAAACAGGA-AATTTTT
1 TTA-AAACACGAGAA-TTTT
* *
5545561 TTAAAACATGACAA-TTT
1 TTAAAACACGAGAATTTT
*
5545578 TTGAAACACGAGAATTTT
1 TTAAAACACGAGAATTTT
* * ***
5545596 TTAAAA-AGCAAAAAAAAT
1 TTAAAACA-CGAGAATTTT
* *
5545614 TTAAAATACGA-AAATTT
1 TTAAAACACGAGAATTTT
* * * *
5545631 ATGAAACGCGAGAATTGT
1 TTAAAACACGAGAATTTT
* *
5545649 TGAAAACACGATAATTTT
1 TTAAAACACGAGAATTTT
* *
5545667 TGAAAACACGATAATTTT
1 TTAAAACACGAGAATTTT
* * *
5545685 TGAAAACATGA-AAATTT
1 TTAAAACACGAGAATTTT
*
5545702 TTGAAACACG-GAAATTTT
1 TTAAAACACGAG-AATTTT
**
5545720 GGAAAACACGAGAATTTTT
1 TTAAAACACGAGAA-TTTT
* *
5545739 TTTAATCACG-GAAATTTTT
1 TTAAAACACGAG-AA-TTTT
* *
5545758 TTGGAAAACACTAGGA-TTT
1 TT--AAAACACGAGAATTTT
* *
5545777 TTGAAACACGA-AAATTT
1 TTAAAACACGAGAATTTT
*
5545794 TTATAAACACGA-AAATTT
1 TTA-AAACACGAGAATTTT
*
5545812 TT-AAACACGAAAATTTT
1 TTAAAACACGAGAATTTT
*
5545829 TTAAAAACACGA-AAATTT
1 TT-AAAACACGAGAATTTT
5545847 TT-AAACACGAGAATTTT
1 TTAAAACACGAGAATTTT
*
5545864 TTGAAAACACGA-AAATTT
1 TT-AAAACACGAGAATTTT
*
5545882 TT-AAACATGAGAATTTT
1 TTAAAACACGAGAATTTT
5545899 TT
1 TT
5545901 GATTTTTTCT
Statistics
Matches: 360, Mismatches: 69, Indels: 69
0.72 0.14 0.14
Matches are distributed among these distances:
15 2 0.01
16 40 0.11
17 107 0.30
18 131 0.36
19 57 0.16
20 16 0.04
21 6 0.02
22 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (18 bp):
TTAAAACACGAGAATTTT
Found at i:5545533 original size:35 final size:35
Alignment explanation
Indices: 5545481--5545899 Score: 309
Period size: 35 Copynumber: 11.8 Consensus size: 35
5545471 TTTAAACAAA
* *
5545481 ACGAAAGTTTTTTAAACACGAGAATTTTTGAAAAC
1 ACGAAAATTTTTAAAACACGAGAATTTTTGAAAAC
* * * *
5545516 ACTAGAATTTTTAAAACACGAAAATTTTAG-AAAC
1 ACGAAAATTTTTAAAACACGAGAATTTTTGAAAAC
* * * *
5545550 AGGAAATTTTTTTAAAACATGACAATTTTTG-AAAC
1 ACGAAA-ATTTTTAAAACACGAGAATTTTTGAAAAC
* * * ** *
5545585 ACGAGAATTTTTTAAAA-AGCAAAAAAAATTT-AAAAT
1 ACGA-AAATTTTTAAAACA-C-GAGAATTTTTGAAAAC
* * * *
5545621 ACGAAAATTTATGAAACGCGAGAATTGTTGAAAAC
1 ACGAAAATTTTTAAAACACGAGAATTTTTGAAAAC
* *
5545656 ACGATAATTTTTGAAAACACGATAATTTTTGAAAAC
1 ACGAAAATTTTT-AAAACACGAGAATTTTTGAAAAC
* * *
5545692 ATGAAAATTTTTGAAACACG-GAAATTTTGGAAAAC
1 ACGAAAATTTTTAAAACACGAG-AATTTTTGAAAAC
* * *
5545727 ACGAGAATTTTTTTTAATCACG-GAAATTTTTTTGGAAAAC
1 ACGA-AA-ATTTTTAAAACACGAG-AA--TTTTT-GAAAAC
* ** * *
5545767 ACTAGGATTTTTGAAACACGAAAATTTTT-ATAAAC
1 ACGAAAATTTTTAAAACACGAGAATTTTTGA-AAAC
* *
5545802 ACGAAAATTTTT-AAACACGAAAATTTTTTAAAAAC
1 ACGAAAATTTTTAAAACACGAGAA-TTTTTGAAAAC
5545837 ACGAAAATTTTT-AAACACGAGAATTTTTTGAAAAC
1 ACGAAAATTTTTAAAACACGAGAA-TTTTTGAAAAC
*
5545872 ACGAAAATTTTT-AAACATGAGAATTTTT
1 ACGAAAATTTTTAAAACACGAGAATTTTT
5545900 TGATTTTTTC
Statistics
Matches: 307, Mismatches: 59, Indels: 37
0.76 0.15 0.09
Matches are distributed among these distances:
34 30 0.10
35 184 0.60
36 52 0.17
37 15 0.05
38 13 0.04
39 4 0.01
40 9 0.03
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (35 bp):
ACGAAAATTTTTAAAACACGAGAATTTTTGAAAAC
Found at i:5545576 original size:19 final size:19
Alignment explanation
Indices: 5545540--5545579 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5545530 AACACGAAAA
5545540 TTTTAGAAACAGGAAATTT
1 TTTTAGAAACAGGAAATTT
*
5545559 TTTTA-AAACATGACAATTT
1 TTTTAGAAACAGGA-AATTT
5545578 TT
1 TT
5545580 GAAACACGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (19 bp):
TTTTAGAAACAGGAAATTT
Found at i:5545683 original size:53 final size:52
Alignment explanation
Indices: 5545481--5545899 Score: 291
Period size: 53 Copynumber: 7.9 Consensus size: 52
5545471 TTTAAACAAA
* * * *
5545481 ACGAAAGTTTTT-TAAACACGAGAATTTTTGAAAACACTAGAATTTTTAAAAC
1 ACGAAAATTTTTGAAAACACGA-AATTTTTGAAAACACGAGAATTTTTGAAAC
* * * * *
5545533 ACGAAAATTTTAG-AAACAGGAAATTTTTTTAAAACATGACAATTTTTGAAAC
1 ACGAAAATTTTTGAAAACACGAAA-TTTTTGAAAACACGAGAATTTTTGAAAC
* * ** ** * * *
5545585 ACGAGAATTTTTTAAAAAGCAAAAAAAATTT-AAAATACGAAAATTTATGAAAC
1 ACGA-AAATTTTTGAAAA-CACGAAATTTTTGAAAACACGAGAATTTTTGAAAC
* * * *
5545638 GCGAGAATTGTTGAAAACACGATAATTTTTGAAAACACGATAATTTTTGAAAAC
1 ACGAAAATTTTTGAAAACACGA-AATTTTTGAAAACACGAGAATTTTTG-AAAC
* * * *
5545692 ATGAAAATTTTTG-AAACACGGAAATTTTGGAAAACACGAGAATTTTTTTTAATC
1 ACGAAAATTTTTGAAAACAC-GAAATTTTTGAAAACACGAGAA--TTTTTGAAAC
* * * * *
5545746 ACGGAAATTTTTTTGGAAAACACTAGGATTTTTG-AAACACGAAAATTTTTATAAAC
1 AC-GAAA-ATTTTT-GAAAACACGA-AATTTTTGAAAACACGAGAATTTTT-GAAAC
* *
5545802 ACGAAAATTTTT--AAACACGAAAATTTTTTAAAAACACGAAAATTTTT-AAAC
1 ACGAAAATTTTTGAAAACACG-AAA-TTTTTGAAAACACGAGAATTTTTGAAAC
* *
5545853 ACGAGAATTTTTTGAAAACACGAAAATTTTT--AAACATGAGAATTTTT
1 ACGA-AAATTTTTGAAAACACG-AAATTTTTGAAAACACGAGAATTTTT
5545900 TGATTTTTTC
Statistics
Matches: 291, Mismatches: 53, Indels: 47
0.74 0.14 0.12
Matches are distributed among these distances:
51 34 0.12
52 71 0.24
53 87 0.30
54 41 0.14
55 23 0.08
56 11 0.04
57 12 0.04
58 12 0.04
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (52 bp):
ACGAAAATTTTTGAAAACACGAAATTTTTGAAAACACGAGAATTTTTGAAAC
Found at i:5545900 original size:35 final size:35
Alignment explanation
Indices: 5545422--5545902 Score: 306
Period size: 35 Copynumber: 13.5 Consensus size: 35
5545412 GATCCGATTA
* * *
5545422 AAACACGATGATTTTTTTTAAAACAC-AAGAATTTTG
1 AAACACGA-GAATTTTTTGAAAACACGAA-AATTTTT
* * * * *
5545458 AAGCACG-TAATTTTTTAAACAAAACGAAAGTTTTTT
1 AAACACGAGAATTTTTTGAA-AACACGAAA-ATTTTT
* *
5545494 AAACACGAGAA-TTTTTGAAAACACTAGAATTTTT
1 AAACACGAGAATTTTTTGAAAACACGAAAATTTTT
* * * *
5545528 AAAACACGA-AAATTTTAG-AAACAGGAAATTTTTTT
1 -AAACACGAGAATTTTTTGAAAACACGAAA-ATTTTT
* * *
5545563 AAAACATGACAA-TTTTTG-AAACACGAGAATTTTTT
1 -AAACACGAGAATTTTTTGAAAACACGA-AAATTTTT
* * * *** * *
5545598 AAAAAGCAAAAAAAATTT-AAAATACGAAAATTTATG
1 AAACA-CGAGAATTTTTTGAAAACACGAAAATTT-TT
* * *
5545634 AAACGCGAGAA-TTGTTGAAAACACGATAATTTTT
1 AAACACGAGAATTTTTTGAAAACACGAAAATTTTT
* *
5545668 GAAAACACGATAA-TTTTTGAAAACATGAAAATTTTT
1 --AAACACGAGAATTTTTTGAAAACACGAAAATTTTT
* * *
5545704 GAAACACG-GAAATTTTGGAAAACACGAGAATTTTTTTT
1 -AAACACGAGAATTTTTTGAAAACACGA-AA--ATTTTT
* * **
5545742 AATCACG-GAAATTTTTTTGGAAAACACTAGGATTTTT
1 AAACACGAG-AA-TTTTTT-GAAAACACGAAAATTTTT
*
5545779 GAAACACGA-AAATTTTT-ATAAACACGAAAATTTTT
1 -AAACACGAGAATTTTTTGA-AAACACGAAAATTTTT
* *
5545814 AAACACGAAAATTTTTTAAAAACACGAAAATTTTT
1 AAACACGAGAATTTTTTGAAAACACGAAAATTTTT
5545849 AAACACGAGAATTTTTTGAAAACACGAAAATTTTT
1 AAACACGAGAATTTTTTGAAAACACGAAAATTTTT
*
5545884 AAACATGAGAATTTTTTGA
1 AAACACGAGAATTTTTTGA
5545903 TTTTTTCTTA
Statistics
Matches: 350, Mismatches: 67, Indels: 57
0.74 0.14 0.12
Matches are distributed among these distances:
34 41 0.12
35 187 0.53
36 80 0.23
37 16 0.05
38 13 0.04
39 4 0.01
40 9 0.03
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.32
Consensus pattern (35 bp):
AAACACGAGAATTTTTTGAAAACACGAAAATTTTT
Found at i:5546329 original size:7 final size:7
Alignment explanation
Indices: 5546319--5546351 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
5546309 CTTTTTGTTT
5546319 TTTTTTC
1 TTTTTTC
*
5546326 TTTTCTC
1 TTTTTTC
5546333 -TTTTTC
1 TTTTTTC
5546339 TTTTTTC
1 TTTTTTC
5546346 TTTTTT
1 TTTTTT
5546352 TGTTTCAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTC
Found at i:5546338 original size:13 final size:13
Alignment explanation
Indices: 5546320--5546350 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5546310 TTTTTGTTTT
5546320 TTTTTCTTTTCTC
1 TTTTTCTTTTCTC
*
5546333 TTTTTCTTTTTTC
1 TTTTTCTTTTCTC
5546346 TTTTT
1 TTTTT
5546351 TTGTTTCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTCTTTTCTC
Found at i:5546342 original size:23 final size:23
Alignment explanation
Indices: 5546309--5546352 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5546299 CAATTGGGGC
*
5546309 CTTTTTGTTTTTT-TTTCTTTTCT
1 CTTTTTCTTTTTTCTTT-TTTTCT
5546332 CTTTTTCTTTTTTCTTTTTTT
1 CTTTTTCTTTTTTCTTTTTTT
5546353 GTTTCAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (23 bp):
CTTTTTCTTTTTTCTTTTTTTCT
Found at i:5546674 original size:4 final size:4
Alignment explanation
Indices: 5546643--5546702 Score: 59
Period size: 4 Copynumber: 14.8 Consensus size: 4
5546633 TTTCTTCCCC
* * *
5546643 CTTT CTTT TTTT CTTT -TTT CCCTT CTTT CTTT CTTT CTTTT TTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT C-TTT CTTT CTTT
*
5546692 CCTT CTTT CTT
1 CTTT CTTT CTT
5546703 CCCCGTTCAG
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
3 3 0.07
4 37 0.82
5 5 0.11
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:5546691 original size:21 final size:22
Alignment explanation
Indices: 5546643--5546702 Score: 77
Period size: 24 Copynumber: 2.7 Consensus size: 22
5546633 TTTCTTCCCC
*
5546643 CTTTCTTTTTTTCTTTTTTCCCTT
1 CTTTCTTTCTTTCTTTTTT--CTT
5546667 CTTTCTTTCTTTCTTTTTT-TT
1 CTTTCTTTCTTTCTTTTTTCTT
*
5546688 CTTTCCTTCTTTCTT
1 CTTTCTTTCTTTCTT
5546703 CCCCGTTCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 16 0.47
24 18 0.53
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (22 bp):
CTTTCTTTCTTTCTTTTTTCTT
Found at i:5546828 original size:25 final size:23
Alignment explanation
Indices: 5546795--5546851 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
5546785 CTCTCCTTTC
* *
5546795 TTCTCTTTTTTTCCTTTGTTTTTTT
1 TTCT-TTTTTTTCC-TTGCTGTTTT
5546820 TTC-TTTTTTTCCTTGCTGTTTT
1 TTCTTTTTTTTCCTTGCTGTTTT
5546842 TTCTTTTTTT
1 TTCTTTTTTT
5546852 ACTTCTTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 11 0.38
23 15 0.52
25 3 0.10
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (23 bp):
TTCTTTTTTTTCCTTGCTGTTTT
Found at i:5546841 original size:22 final size:23
Alignment explanation
Indices: 5546798--5546851 Score: 83
Period size: 22 Copynumber: 2.4 Consensus size: 23
5546788 TCCTTTCTTC
* *
5546798 TCTTTTTTTCCTTTGTTTTTTTT
1 TCTTTTTTTCCTTTGCTGTTTTT
5546821 TCTTTTTTTCC-TTGCTGTTTTT
1 TCTTTTTTTCCTTTGCTGTTTTT
5546843 TCTTTTTTT
1 TCTTTTTTT
5546852 ACTTCTTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.80
Consensus pattern (23 bp):
TCTTTTTTTCCTTTGCTGTTTTT
Found at i:5547318 original size:30 final size:29
Alignment explanation
Indices: 5547266--5547348 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 29
5547256 TTTACAAGTT
* *
5547266 ATTAGGGGTTAAGATGTAAATTTATAAAAAA
1 ATTAGGGGTCAAAATGT-AATTT-TAAAAAA
**
5547297 ATTAGGGGTCAAAATGTAATTTTTGAAAA
1 ATTAGGGGTCAAAATGTAATTTTAAAAAA
*
5547326 GTTCAGGGG-CTAAAATGTAATTT
1 ATT-AGGGGTC-AAAATGTAATTT
5547349 GTATCTTTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 8 0.18
30 22 0.49
31 15 0.33
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.34
Consensus pattern (29 bp):
ATTAGGGGTCAAAATGTAATTTTAAAAAA
Found at i:5556610 original size:21 final size:20
Alignment explanation
Indices: 5556569--5556667 Score: 67
Period size: 21 Copynumber: 4.8 Consensus size: 20
5556559 TGAACTTTTA
*
5556569 CTTTTCGTTTAGCTCTCATGAG
1 CTTTT-GTTTAACTCT-ATGAG
5556591 CTTTTGTTTAACTCATATGAG
1 CTTTTGTTTAACTC-TATGAG
* *
5556612 -TTTCCGTTCAACTCTATCGAG
1 CTTT-TGTTTAACTCTAT-GAG
* *
5556633 CTTCTGTTTAACCCTTATGAG
1 CTTTTGTTTAACTC-TATGAG
* *
5556654 -TTTTTTTTAGCTCT
1 CTTTTGTTTAACTCT
5556668 TACAAGCTTC
Statistics
Matches: 61, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
19 1 0.02
20 15 0.25
21 34 0.56
22 11 0.18
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.47
Consensus pattern (20 bp):
CTTTTGTTTAACTCTATGAG
Found at i:5556687 original size:41 final size:42
Alignment explanation
Indices: 5556631--5556709 Score: 117
Period size: 41 Copynumber: 1.9 Consensus size: 42
5556621 AACTCTATCG
* *
5556631 AGCTTCTGTTTAACCCTTAT-GAGTTTTT-TTTAGCTCTTACA
1 AGCTTCCGTTCAACCCTTATAG-GTTTTTGTTTAGCTCTTACA
5556672 AGCTTCCGTTCAACCCTTATAGGTTTTTGTTTAGCTCT
1 AGCTTCCGTTCAACCCTTATAGGTTTTTGTTTAGCTCT
5556710 CATGAGCTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
41 24 0.71
42 10 0.29
ACGTcount: A:0.18, C:0.22, G:0.14, T:0.47
Consensus pattern (42 bp):
AGCTTCCGTTCAACCCTTATAGGTTTTTGTTTAGCTCTTACA
Found at i:5556715 original size:62 final size:63
Alignment explanation
Indices: 5556570--5556723 Score: 150
Period size: 62 Copynumber: 2.5 Consensus size: 63
5556560 GAACTTTTAC
* ** * * *
5556570 TTTTCGTTTAGCTCTCATGAGCTTTTGTTTAACTCATATGAGTTTCCGTTCAACTCTATCGAG
1 TTTTTGTTTAGCTCTCATGAGCTTTTGTTTAACTCATACAAGCTTCCGTTCAACCCTATAGAG
* * * * * * * *
5556633 CTTCTGTTTAACCCTTATGAG-TTTTTTTTAGCTCTTACAAGCTTCCGTTCAACCCTTATAG-G
1 TTTTTGTTTAGCTCTCATGAGCTTTTGTTTAACTCATACAAGCTTCCGTTCAACCC-TATAGAG
*
5556695 TTTTTGTTTAGCTCTCATGAGCTTCTGTT
1 TTTTTGTTTAGCTCTCATGAGCTTTTGTT
5556724 CAGCTTTTGA
Statistics
Matches: 68, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
62 44 0.65
63 24 0.35
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.46
Consensus pattern (63 bp):
TTTTTGTTTAGCTCTCATGAGCTTTTGTTTAACTCATACAAGCTTCCGTTCAACCCTATAGAG
Found at i:5556718 original size:42 final size:41
Alignment explanation
Indices: 5556576--5556725 Score: 124
Period size: 42 Copynumber: 3.6 Consensus size: 41
5556566 TTACTTTTCG
* * * * * **
5556576 TTTAGCTCTCATGAGCTTTTGTTTAACTCATATGAGTTTCCG
1 TTTAGCTCTCACGAGCTTCTGTTCAACCCTTATGAGTTT-TT
* * *
5556618 TTCAACTCT-ATCGAGCTTCTGTTTAACCCTTATGAGTTTTT
1 TTTAGCTCTCA-CGAGCTTCTGTTCAACCCTTATGAGTTTTT
* * *
5556659 TTTAGCTCTTACAAGCTTCCGTTCAACCCTTAT-AGGTTTTT
1 TTTAGCTCTCACGAGCTTCTGTTCAACCCTTATGA-GTTTTT
*
5556700 GTTTAGCTCTCATGAGCTTCTGTTCA
1 -TTTAGCTCTCACGAGCTTCTGTTCA
5556726 GCTTTTGAGC
Statistics
Matches: 87, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
40 1 0.01
41 33 0.38
42 53 0.61
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.45
Consensus pattern (41 bp):
TTTAGCTCTCACGAGCTTCTGTTCAACCCTTATGAGTTTTT
Done.