Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 14 of 31
Found at i:3184063 original size:19 final size:20
Alignment explanation
Indices: 3184039--3184081 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
3184029 TTACGACACA
3184039 TAATTACTA-TAAAAAAATT
1 TAATTACTAGTAAAAAAATT
3184058 TAATTACTAGGTAAAAAAATT
1 TAATTACTA-GTAAAAAAATT
3184079 TAA
1 TAA
3184082 GCCATAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 9 0.41
21 13 0.59
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (20 bp):
TAATTACTAGTAAAAAAATT
Found at i:3186288 original size:15 final size:16
Alignment explanation
Indices: 3186268--3186299 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3186258 ATAATTTTAA
3186268 AAAATTAT-AAATTAT
1 AAAATTATAAAATTAT
3186283 AAAATTATAAAATTAT
1 AAAATTATAAAATTAT
3186299 A
1 A
3186300 TTTATAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATTATAAAATTAT
Found at i:3186289 original size:8 final size:8
Alignment explanation
Indices: 3186268--3186299 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
3186258 ATAATTTTAA
3186268 AAAATTAT
1 AAAATTAT
3186276 -AAATTAT
1 AAAATTAT
3186283 AAAATTAT
1 AAAATTAT
3186291 AAAATTAT
1 AAAATTAT
3186299 A
1 A
3186300 TTTATAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AAAATTAT
Found at i:3188336 original size:16 final size:17
Alignment explanation
Indices: 3188311--3188344 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
3188301 ATAAAAATAT
3188311 ATTTATAAAAAATAGAA
1 ATTTATAAAAAATAGAA
3188328 ATTTA-AAAAAATAGAA
1 ATTTATAAAAAATAGAA
3188344 A
1 A
3188345 AATAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (17 bp):
ATTTATAAAAAATAGAA
Found at i:3188350 original size:16 final size:16
Alignment explanation
Indices: 3188317--3188351 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3188307 ATATATTTAT
**
3188317 AAAAAATAGAAATTTA
1 AAAAAATAGAAAAATA
3188333 AAAAAATAGAAAAATA
1 AAAAAATAGAAAAATA
3188349 AAA
1 AAA
3188352 TATAACTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (16 bp):
AAAAAATAGAAAAATA
Found at i:3206286 original size:20 final size:22
Alignment explanation
Indices: 3206252--3206292 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3206242 GTTATCTCAT
*
3206252 GTTTTATATTTCCAT-TATTTG
1 GTTTTATATTGCCATATATTTG
3206273 GTTTT-TATTGCCATATATTT
1 GTTTTATATTGCCATATATTT
3206293 CTGTTGTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.61
Consensus pattern (22 bp):
GTTTTATATTGCCATATATTTG
Found at i:3213363 original size:3 final size:3
Alignment explanation
Indices: 3213355--3213384 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3213345 GATAGACGGT
3213355 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3213385 ACATTGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3213513 original size:2 final size:2
Alignment explanation
Indices: 3213506--3213548 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
3213496 TTGGATATTC
*
3213506 CT CT CT CT CT C- CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3213547 CT
1 CT
3213549 TATTTACCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:3220024 original size:27 final size:27
Alignment explanation
Indices: 3219970--3220024 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
3219960 TAATAATGTT
*
3219970 TAATAAAATCAAATAAAATAATAAATA
1 TAATAAAATCAAATAAAATAAGAAATA
* * * *
3219997 TAATACAATCAATTTAAATAAGATATA
1 TAATAAAATCAAATAAAATAAGAAATA
3220024 T
1 T
3220025 TTTTTGTATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (27 bp):
TAATAAAATCAAATAAAATAAGAAATA
Found at i:3221182 original size:2 final size:2
Alignment explanation
Indices: 3221175--3221203 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3221165 AAATGATACC
3221175 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3221204 ACAACGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3221500 original size:17 final size:18
Alignment explanation
Indices: 3221480--3221513 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3221470 ATTTAGTTGT
3221480 TAAAAT-TTTTTATATTA
1 TAAAATATTTTTATATTA
3221497 TAAAATATTTTTATATT
1 TAAAATATTTTTATATT
3221514 TATATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TAAAATATTTTTATATTA
Found at i:3221539 original size:17 final size:16
Alignment explanation
Indices: 3221508--3221543 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
3221498 AAAATATTTT
*
3221508 TATATTTATATTTAAA
1 TATATTTAAATTTAAA
3221524 TATATATTAAATTTAAA
1 TATAT-TTAAATTTAAA
3221541 TAT
1 TAT
3221544 TTACGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATTTAAATTTAAA
Found at i:3235105 original size:3 final size:3
Alignment explanation
Indices: 3235097--3235122 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3235087 CTGGTTGCAA
3235097 CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CA
3235123 ACTCTTGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:3236395 original size:31 final size:31
Alignment explanation
Indices: 3236335--3236397 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
3236325 ATTACGATAT
*
3236335 ATAATATTATTTATATTTTAATATTAAAAAA
1 ATAATATTATTTATATTTTAAAATTAAAAAA
*
3236366 ATAAT-TTATTTATTTTTTAAAATTAAAAAA
1 ATAATATTATTTATATTTTAAAATTAAAAAA
3236396 AT
1 AT
3236398 TAAAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
ATAATATTATTTATATTTTAAAATTAAAAAA
Found at i:3236492 original size:21 final size:22
Alignment explanation
Indices: 3236461--3236501 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3236451 AATATAATTA
* *
3236461 TTTTAAATATTTAATTATAACC
1 TTTTAAATATTAAATAATAACC
3236483 TTTT-AATATTAAATAATAA
1 TTTTAAATATTAAATAATAA
3236502 AATATAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTAAATATTAAATAATAACC
Found at i:3236524 original size:15 final size:15
Alignment explanation
Indices: 3236487--3236530 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
3236477 ATAACCTTTT
*
3236487 AATATTAAATAATAA
1 AATATTAATTAATAA
*
3236502 AATA-TAATTAATTA
1 AATATTAATTAATAA
*
3236516 AATATTAATTTATAA
1 AATATTAATTAATAA
3236531 GAAAAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATATTAATTAATAA
Found at i:3236567 original size:3 final size:3
Alignment explanation
Indices: 3236559--3236587 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3236549 CAATTCCTAA
3236559 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3236588 CTTTCAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3245027 original size:17 final size:17
Alignment explanation
Indices: 3245007--3245057 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
3244997 TTATATAATA
3245007 TAAATATATATAAAAAT
1 TAAATATATATAAAAAT
* *
3245024 TAAAAATAAAATAAAATAT
1 TAAATAT-ATATAAAA-AT
*
3245043 TATATA-ATATAAAAA
1 TAAATATATATAAAAA
3245058 AATACGAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
16 1 0.04
17 13 0.48
18 7 0.26
19 6 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAATATATATAAAAAT
Found at i:3248544 original size:2 final size:2
Alignment explanation
Indices: 3248537--3248567 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3248527 AAACTTTTAC
3248537 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3248568 TACCTGAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3248940 original size:3 final size:3
Alignment explanation
Indices: 3248934--3248958 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3248924 TTTTAATGTT
3248934 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
3248959 TTATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3250013 original size:7 final size:7
Alignment explanation
Indices: 3250005--3250058 Score: 81
Period size: 7 Copynumber: 7.7 Consensus size: 7
3249995 TCCCTTCTTC
*
3250005 CAACTTC
1 CAACTTA
*
3250012 CAACTTC
1 CAACTTA
*
3250019 CAACTTT
1 CAACTTA
3250026 CAACTTA
1 CAACTTA
3250033 CAACTTA
1 CAACTTA
3250040 CAACTTA
1 CAACTTA
3250047 CAACTTA
1 CAACTTA
3250054 CAACT
1 CAACT
3250059 ATAGTGATGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (7 bp):
CAACTTA
Found at i:3250331 original size:2 final size:2
Alignment explanation
Indices: 3250324--3250348 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3250314 ACATTCATAC
3250324 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
3250349 GATTGTTAAT
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:3250425 original size:17 final size:17
Alignment explanation
Indices: 3250398--3250435 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3250388 AAAGTGATAA
*
3250398 AAATGATATATATAATAT
1 AAATGATATATAAAAT-T
3250416 AAAT-ATATATAAAATT
1 AAATGATATATAAAATT
3250432 AAAT
1 AAAT
3250436 TAATTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 10 0.53
18 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
AAATGATATATAAAATT
Found at i:3250784 original size:2 final size:2
Alignment explanation
Indices: 3250777--3250804 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3250767 ATAAATCCTC
3250777 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3250805 ACATATGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3251696 original size:23 final size:23
Alignment explanation
Indices: 3251612--3251697 Score: 57
Period size: 28 Copynumber: 3.4 Consensus size: 23
3251602 AATGTTAGAT
*
3251612 AAAAATATCAAAATATTTGA-TAA
1 AAAAATAT-AAAATATTTAATTAA
** *
3251635 AATTATATTATAAATATTAAATTAAAA
1 AAAAATA-TA-AAATATTTAATT--AA
3251662 TAAAAATTTATAAAATATTTAATTAA
1 -AAAAA--TATAAAATATTTAATTAA
3251688 AAAAATATAA
1 AAAAATATAA
3251698 TTTAAGAACA
Statistics
Matches: 48, Mismatches: 7, Indels: 16
0.68 0.10 0.23
Matches are distributed among these distances:
23 11 0.23
24 9 0.19
25 6 0.12
26 2 0.04
27 2 0.04
28 14 0.29
29 2 0.04
30 2 0.04
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (23 bp):
AAAAATATAAAATATTTAATTAA
Found at i:3256984 original size:2 final size:2
Alignment explanation
Indices: 3256977--3257005 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3256967 TGATTATTCG
3256977 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3257006 GATGAACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3260095 original size:3 final size:3
Alignment explanation
Indices: 3260087--3260121 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3260077 CAATCCAAAC
3260087 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3260122 GAGTTATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3264130 original size:87 final size:88
Alignment explanation
Indices: 3263968--3264218 Score: 335
Period size: 87 Copynumber: 2.9 Consensus size: 88
3263958 ATACTAATTG
* ** * *
3263968 CCAAAATTTTATTACATAGACTGTGTAAACCTTAAAGAGTTATTGCTAATAACAAATATCTATCA
1 CCAAAATTTTATTACATAGCCTGTGTAGCCCTTAAAGAGATATTGCCAATAACAAATATCTATCA
*
3264033 CATAATAAAACCATTTAAACATC
66 CATAACAAAACCATTTAAACATC
* * *
3264056 CCAAAATTTTATTGCATAGCCTATGTAGCCCTTAAA-AGGTA-TGCCAACTAACAAATATCTATC
1 CCAAAATTTTATTACATAGCCTGTGTAGCCCTTAAAGAGATATTGCCAA-TAACAAATATCTATC
3264119 ACATAACAAAACCATTTAAACATC
65 ACATAACAAAACCATTTAAACATC
* * * * * * *
3264143 CCAAAATTTTATTACATAGCCTGTGGAGCCCTCAAAGAGATATTGCAAAAAAGAAATGTTTATCA
1 CCAAAATTTTATTACATAGCCTGTGTAGCCCTTAAAGAGATATTGCCAATAACAAATATCTATCA
3264208 CATAACAAAAC
66 CATAACAAAAC
3264219 AATGAATTAA
Statistics
Matches: 142, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
86 5 0.04
87 74 0.52
88 58 0.41
89 5 0.04
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (88 bp):
CCAAAATTTTATTACATAGCCTGTGTAGCCCTTAAAGAGATATTGCCAATAACAAATATCTATCA
CATAACAAAACCATTTAAACATC
Found at i:3265707 original size:28 final size:29
Alignment explanation
Indices: 3265652--3265717 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
3265642 CCAAATCATT
3265652 ATTTAATAAATAAAAATATTTTTAATTAA
1 ATTTAATAAATAAAAATATTTTTAATTAA
*
3265681 ATTTAAT-TATAAAAATATATTTT-ATTAA
1 ATTTAATAAATAAAAATAT-TTTTAATTAA
*
3265709 GATTGAATA
1 -ATTTAATA
3265718 TTTTTAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 15 0.47
29 17 0.53
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (29 bp):
ATTTAATAAATAAAAATATTTTTAATTAA
Found at i:3267891 original size:33 final size:33
Alignment explanation
Indices: 3267829--3267899 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
3267819 TGCTATTATT
*** *
3267829 AAAACCTATCACTATTTTATTTATCCAAAAAAA
1 AAAACCTATCACTATTTTAAAAAGCCAAAAAAA
* *
3267862 AAAACCTATCACTATTTTAAAAAGGCAAAAACA
1 AAAACCTATCACTATTTTAAAAAGCCAAAAAAA
3267895 AAAAC
1 AAAAC
3267900 AAAAACTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.54, C:0.18, G:0.03, T:0.25
Consensus pattern (33 bp):
AAAACCTATCACTATTTTAAAAAGCCAAAAAAA
Found at i:3271032 original size:22 final size:22
Alignment explanation
Indices: 3271004--3271049 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
3270994 AAAATTGATC
3271004 TGGGCTAAAAATGCCTGAAGTG
1 TGGGCTAAAAATGCCTGAAGTG
3271026 TGGGCTAAAAATGCCTGAAGTG
1 TGGGCTAAAAATGCCTGAAGTG
3271048 TG
1 TG
3271050 CGTGTGTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.13, G:0.33, T:0.24
Consensus pattern (22 bp):
TGGGCTAAAAATGCCTGAAGTG
Found at i:3284455 original size:7 final size:7
Alignment explanation
Indices: 3284424--3284461 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
3284414 TGAAAATCTA
3284424 AAATTTT
1 AAATTTT
3284431 ATAACTTTT
1 A-AA-TTTT
3284440 AAA-TTT
1 AAATTTT
3284446 AAATTTT
1 AAATTTT
3284453 AAATTTT
1 AAATTTT
3284460 AA
1 AA
3284462 TCATTGAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.21
7 13 0.46
8 4 0.14
9 5 0.18
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (7 bp):
AAATTTT
Found at i:3284692 original size:6 final size:6
Alignment explanation
Indices: 3284677--3284706 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3284667 GAATGTTTTG
3284677 TTTG-T TTTGAT TTTGAT TTTGAT TTTGAT T
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT T
3284707 ATACCTGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.13, C:0.00, G:0.17, T:0.70
Consensus pattern (6 bp):
TTTGAT
Found at i:3285794 original size:20 final size:20
Alignment explanation
Indices: 3285769--3285811 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3285759 CCTCGAAAGA
3285769 ATGGGGTTGAAATGTCCCCG
1 ATGGGGTTGAAATGTCCCCG
* *
3285789 ATGGGGTTGAAGTGTCCTCG
1 ATGGGGTTGAAATGTCCCCG
3285809 ATG
1 ATG
3285812 AGGACTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.16, G:0.37, T:0.28
Consensus pattern (20 bp):
ATGGGGTTGAAATGTCCCCG
Found at i:3288671 original size:22 final size:22
Alignment explanation
Indices: 3288629--3288672 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3288619 TTTATTTTAT
*
3288629 TATTTAAATATTATTTTATTAA
1 TATTTAAATATTATTTAATTAA
*
3288651 TATTTATATATT-TTTAAATTAA
1 TATTTAAATATTATTT-AATTAA
3288673 AACTTTATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTTAAATATTATTTAATTAA
Found at i:3289144 original size:18 final size:19
Alignment explanation
Indices: 3289112--3289150 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3289102 CTATTTTAGT
**
3289112 AATTTTAAATGTAATA-AA
1 AATTTTAAACATAATATAA
3289130 AATTTTAAACATAATATAA
1 AATTTTAAACATAATATAA
3289149 AA
1 AA
3289151 CATGATATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (19 bp):
AATTTTAAACATAATATAA
Found at i:3289235 original size:12 final size:12
Alignment explanation
Indices: 3289218--3289254 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
3289208 ATTATTAATG
3289218 TATCAAAATATA
1 TATCAAAATATA
3289230 TATCAAAATATA
1 TATCAAAATATA
*
3289242 TGT-AAAATATA
1 TATCAAAATATA
3289253 TA
1 TA
3289255 AAATTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (12 bp):
TATCAAAATATA
Found at i:3289735 original size:13 final size:13
Alignment explanation
Indices: 3289717--3289742 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3289707 ATCAAGCATT
3289717 TAAATTATGATTA
1 TAAATTATGATTA
3289730 TAAATTATGATTA
1 TAAATTATGATTA
3289743 AGGATATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TAAATTATGATTA
Found at i:3295707 original size:26 final size:24
Alignment explanation
Indices: 3295667--3295724 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
3295657 TGGGTGGCTA
* *
3295667 GTCAACAAAAACCACCCTTTGTGTTT
1 GTCAACAAAAACCA-CC-ATATGTTT
*
3295693 GTCAACAAAAGCCACCATATGTTT
1 GTCAACAAAAACCACCATATGTTT
3295717 GTCAACAA
1 GTCAACAA
3295725 TGGTGGTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 14 0.48
25 2 0.07
26 13 0.45
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (24 bp):
GTCAACAAAAACCACCATATGTTT
Found at i:3295757 original size:27 final size:27
Alignment explanation
Indices: 3295714--3295779 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
3295704 CCACCATATG
* *
3295714 TTTGTCAACAATGGTGGTTACTTTGTA
1 TTTGTCAAAAATAGTGGTTACTTTGTA
* * *
3295741 TTTGTCAAAAATAGTGGTTCCTTTTTG
1 TTTGTCAAAAATAGTGGTTACTTTGTA
3295768 TTTGTCAAAAAT
1 TTTGTCAAAAAT
3295780 TATGACTTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (27 bp):
TTTGTCAAAAATAGTGGTTACTTTGTA
Found at i:3295936 original size:48 final size:48
Alignment explanation
Indices: 3295883--3295978 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
3295873 AGTATCCATC
3295883 ATCTCTCTCTTGTATCTCTCTTCAATTCTTTCTCATAATAAAATTGGT
1 ATCTCTCTCTTGTATCTCTCTTCAATTCTTTCTCATAATAAAATTGGT
*
3295931 ATCTCTCTCTTGTATCTCTCTTCAATTCTTTCTCATAATAGAATTGGT
1 ATCTCTCTCTTGTATCTCTCTTCAATTCTTTCTCATAATAAAATTGGT
3295979 GGTGTCCGAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.22, C:0.23, G:0.07, T:0.48
Consensus pattern (48 bp):
ATCTCTCTCTTGTATCTCTCTTCAATTCTTTCTCATAATAAAATTGGT
Found at i:3296655 original size:2 final size:2
Alignment explanation
Indices: 3296650--3296676 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3296640 ATATATATAT
3296650 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
3296677 ACCTTGGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3298135 original size:2 final size:2
Alignment explanation
Indices: 3298128--3298161 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3298118 CCAATATACA
3298128 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3298162 CACCTTATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3299909 original size:2 final size:2
Alignment explanation
Indices: 3299898--3299936 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3299888 TTTAAAATGG
3299898 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3299937 TATCTAGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3302964 original size:35 final size:35
Alignment explanation
Indices: 3302920--3302986 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
3302910 ATGTACTATT
*
3302920 TAAAATATTATATATTT-ATATA-ATTTTTAATATA
1 TAAAATATTATAT-TTTAATAAATATTTTTAATATA
3302954 TAAATATATTATATTTTAATAAATATTTTTAAT
1 TAAA-ATATTATATTTTAATAAATATTTTTAAT
3302987 TCACGATCCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 7 0.24
35 13 0.45
36 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (35 bp):
TAAAATATTATATTTTAATAAATATTTTTAATATA
Found at i:3304088 original size:2 final size:2
Alignment explanation
Indices: 3304083--3304110 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3304073 AAAAATCGAG
3304083 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3304111 TTATTGATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3310037 original size:23 final size:21
Alignment explanation
Indices: 3309983--3310029 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
3309973 TGGACATGTT
3309983 AAAAATGCATGAAACATAATA
1 AAAAATGCATGAAACATAATA
3310004 AAAAATGCATGAAACATAATA
1 AAAAATGCATGAAACATAATA
3310025 AAAAA
1 AAAAA
3310030 AATGCATGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.66, C:0.09, G:0.09, T:0.17
Consensus pattern (21 bp):
AAAAATGCATGAAACATAATA
Found at i:3310995 original size:20 final size:20
Alignment explanation
Indices: 3310948--3311022 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
3310938 AAAAAGACAT
*
3310948 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
3310967 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
3310988 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
*
3311008 AATGTATTGATACAT
1 AATGTATCGATACAT
3311023 CAGGGTATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:3311020 original size:40 final size:39
Alignment explanation
Indices: 3310945--3311022 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
3310935 GGTAAAAAGA
* *
3310945 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* * *
3310984 CATACATGTATCGATATATTGAAAAATGTATTGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
3311023 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:3311710 original size:27 final size:27
Alignment explanation
Indices: 3311680--3311734 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
3311670 TTAAACTCAG
3311680 TCAATCACTTCATTAACAATATAAATT
1 TCAATCACTTCATTAACAATATAAATT
*
3311707 TCAATCACTTTATTAACAATATAAATT
1 TCAATCACTTCATTAACAATATAAATT
3311734 T
1 T
3311735 TTATGTCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (27 bp):
TCAATCACTTCATTAACAATATAAATT
Found at i:3312438 original size:29 final size:29
Alignment explanation
Indices: 3312406--3312488 Score: 73
Period size: 29 Copynumber: 2.9 Consensus size: 29
3312396 TTAATTATTT
* *
3312406 TTAATAAATAATATTTCACAAAATTAAAA
1 TTAATAAATAATATTTAACAAAAATAAAA
* * *
3312435 TTAA-AATTATATTTTTAATAAAAATAAAA
1 TTAATAAATA-ATATTTAACAAAAATAAAA
*
3312464 -TAATAAATAAT-TTCTAATAAAAATA
1 TTAATAAATAATATT-TAACAAAAATA
3312489 CACTCAAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
27 2 0.04
28 20 0.44
29 23 0.51
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (29 bp):
TTAATAAATAATATTTAACAAAAATAAAA
Found at i:3329705 original size:15 final size:16
Alignment explanation
Indices: 3329668--3329705 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
3329658 TTAATTATTA
3329668 AATATTAATTTAAATTG
1 AATA-TAATTTAAATTG
3329685 AA-ATAATTTAAATT-
1 AATATAATTTAAATTG
3329699 AATATAA
1 AATATAA
3329706 AATTTTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.10
15 15 0.75
16 1 0.05
17 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
AATATAATTTAAATTG
Found at i:3329739 original size:17 final size:17
Alignment explanation
Indices: 3329717--3329757 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
3329707 ATTTTAAACT
3329717 TTTAATTAAATAAATA-A
1 TTTAATT-AATAAATAGA
*
3329734 TTTAATTTATAAATAGA
1 TTTAATTAATAAATAGA
3329751 TTTAATT
1 TTTAATT
3329758 TATATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TTTAATTAATAAATAGA
Found at i:3329745 original size:16 final size:17
Alignment explanation
Indices: 3329726--3329761 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
3329716 TTTTAATTAA
3329726 ATAAATA-ATTTAATTT
1 ATAAATAGATTTAATTT
3329742 ATAAATAGATTTAATTT
1 ATAAATAGATTTAATTT
3329759 ATA
1 ATA
3329762 TAAAATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATAAATAGATTTAATTT
Found at i:3330218 original size:20 final size:21
Alignment explanation
Indices: 3330183--3330226 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
3330173 TAAATTTATT
*
3330183 TATTTTATTATATTATAATTA
1 TATTTAATTATATTATAATTA
*
3330204 TATTTAATTAT-TTATATTTA
1 TATTTAATTATATTATAATTA
3330224 TAT
1 TAT
3330227 AAATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTAATTATATTATAATTA
Found at i:3330241 original size:34 final size:33
Alignment explanation
Indices: 3330178--3330255 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 33
3330168 ATCGTTAAAT
* *
3330178 TTATTTAT-TTTATTATATTATAATTATATTTAA
1 TTATTTATATTTATTAAATTATAATAATATTT-A
*
3330211 TTATTTATATTTATATAAATTTTAA-AATATTTA
1 TTATTTATATTTAT-TAAATTATAATAATATTTA
3330244 TATATTTATATT
1 T-TATTTATATT
3330256 ATTTTTTCTC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
33 10 0.26
34 21 0.54
35 8 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (33 bp):
TTATTTATATTTATTAAATTATAATAATATTTA
Found at i:3334016 original size:70 final size:70
Alignment explanation
Indices: 3333886--3334071 Score: 315
Period size: 69 Copynumber: 2.7 Consensus size: 70
3333876 GTACTAAAAG
* * *
3333886 TAAAAACAAAGAGTGACCTAAGTTTCAAAC-TTTTAAGTTCATGAATTTAATATTACAAGTCACA
1 TAAAATCAAAGAGCGACCTATGTTTCAAACTTTTTAAGTTCATGAATTTAATATTACAAGTCACA
3333950 TATAC
66 TATAC
3333955 TAAAATCAAAGAGCGACCTATGTTTCAAACTTTTTAAGTTCATGAATTTAATATTACAAGTCACA
1 TAAAATCAAAGAGCGACCTATGTTTCAAACTTTTTAAGTTCATGAATTTAATATTACAAGTCACA
3334020 TATAC
66 TATAC
*
3334025 T-AAATCAAAGAGCGACCTATG-TTCAAACTTTGTAAGTTCATGAATTT
1 TAAAATCAAAGAGCGACCTATGTTTCAAACTTTTTAAGTTCATGAATTT
3334072 GGTATTAAAC
Statistics
Matches: 112, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
68 25 0.22
69 47 0.42
70 40 0.36
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.33
Consensus pattern (70 bp):
TAAAATCAAAGAGCGACCTATGTTTCAAACTTTTTAAGTTCATGAATTTAATATTACAAGTCACA
TATAC
Found at i:3340079 original size:68 final size:67
Alignment explanation
Indices: 3340000--3340133 Score: 196
Period size: 68 Copynumber: 2.0 Consensus size: 67
3339990 AGAAAGCAAT
* * * *
3340000 GCGTTTCCCTTTGCTGAAACTTTAAAATTTGGGTTTGGTTTTTAGTCCATAAGTGTCCAACAATG
1 GCGTTTCCCTTTGCTCAAACTCTAAAATTTGGGCTTGGCTTTTAGTCCA-AAGTGTCCAACAATG
3340065 TAC
65 TAC
* * *
3340068 GCGTTTGCCTTTGCTCAAACTCTAATATTTGGGCTTGGCTTTTAGTCCAAAGTGTCCAACATTGT
1 GCGTTTCCCTTTGCTCAAACTCTAAAATTTGGGCTTGGCTTTTAGTCCAAAGTGTCCAACAATGT
3340133 A
66 A
3340134 GGGTTTAGTT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
67 16 0.27
68 43 0.73
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (67 bp):
GCGTTTCCCTTTGCTCAAACTCTAAAATTTGGGCTTGGCTTTTAGTCCAAAGTGTCCAACAATGT
AC
Found at i:3341353 original size:19 final size:22
Alignment explanation
Indices: 3341331--3341376 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
3341321 ATTGTTTTGG
3341331 TTTACTTTT-AAAT-TT-TTTA
1 TTTACTTTTAAAATGTTATTTA
*
3341350 TTTAAGTTTTAAAATGTTATTTA
1 TTT-ACTTTTAAAATGTTATTTA
3341373 TTTA
1 TTTA
3341377 ATATGATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 3 0.14
20 5 0.23
21 4 0.18
22 3 0.14
23 7 0.32
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.63
Consensus pattern (22 bp):
TTTACTTTTAAAATGTTATTTA
Found at i:3341462 original size:18 final size:19
Alignment explanation
Indices: 3341439--3341476 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3341429 AAATAAATGT
*
3341439 AAAAAA-TAATATTTTAAA
1 AAAAAATTAAAATTTTAAA
3341457 AAAAAATTAAAATTTTAAA
1 AAAAAATTAAAATTTTAAA
3341476 A
1 A
3341477 TGATTGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAAATTAAAATTTTAAA
Found at i:3342360 original size:2 final size:2
Alignment explanation
Indices: 3342348--3342382 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3342338 TTATTCTTAA
* *
3342348 AT AT CT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3342383 ACATTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3343232 original size:18 final size:19
Alignment explanation
Indices: 3343205--3343246 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
3343195 TTTTTAAGAA
*
3343205 TTATA-TTTTTATTTAATT
1 TTATAGTTTTTATTAAATT
3343223 TTATAGTTTTTATTAAATT
1 TTATAGTTTTTATTAAATT
3343242 TTATA
1 TTATA
3343247 ATATGAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATAGTTTTTATTAAATT
Found at i:3343861 original size:30 final size:27
Alignment explanation
Indices: 3343805--3343863 Score: 73
Period size: 30 Copynumber: 2.1 Consensus size: 27
3343795 AATATCTTAA
* *
3343805 AATATTTTTAAAATTATTATATATAAT
1 AATATTTTTAAAATTATTAAAAATAAT
3343832 AATATTTTTATAAAATATATTAAAAATAAT
1 AATA-TTTT-TAAAAT-TATTAAAAATAAT
3343862 AA
1 AA
3343864 ATAAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 4 0.15
28 4 0.15
29 6 0.22
30 13 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AATATTTTTAAAATTATTAAAAATAAT
Found at i:3513699 original size:14 final size:14
Alignment explanation
Indices: 3513680--3513706 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3513670 AAATTTCAAG
3513680 CTTTTTTTCTTTTT
1 CTTTTTTTCTTTTT
3513694 CTTTTTTTCTTTT
1 CTTTTTTTCTTTT
3513707 AATTTATTGA
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
CTTTTTTTCTTTTT
Found at i:3517535 original size:2 final size:2
Alignment explanation
Indices: 3517528--3517553 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3517518 AATAACCTGA
3517528 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3517554 TAATTCTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3518939 original size:11 final size:11
Alignment explanation
Indices: 3518923--3518955 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
3518913 GCAAGAAAAA
*
3518923 GCATTTAAATT
1 GCATTTTAATT
3518934 GCATTTTAATT
1 GCATTTTAATT
3518945 GCATTTTAATT
1 GCATTTTAATT
3518956 TAGAATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (11 bp):
GCATTTTAATT
Found at i:3520844 original size:23 final size:22
Alignment explanation
Indices: 3520802--3520846 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
3520792 AAAGTTATTC
*
3520802 AAATTTTTTAATTATTTATTTT
1 AAATTTTTTAATTATATATTTT
3520824 AAATTATTTT-ATTAATATATTTT
1 AAATT-TTTTAATT-ATATATTTT
3520847 GAATATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
AAATTTTTTAATTATATATTTT
Found at i:3520940 original size:13 final size:13
Alignment explanation
Indices: 3520918--3520968 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
3520908 TTTAATATAA
*
3520918 ATATAATTTTAAT
1 ATATATTTTTAAT
3520931 ATATATTTTTTAAT
1 ATATA-TTTTTAAT
*
3520945 TTAATATTTTTAAT
1 AT-ATATTTTTAAT
3520959 GAT-TATTTTT
1 -ATATATTTTT
3520969 TCTTATCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 12 0.38
14 16 0.50
15 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (13 bp):
ATATATTTTTAAT
Found at i:3520951 original size:15 final size:14
Alignment explanation
Indices: 3520924--3520969 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
3520914 ATAAATATAA
3520924 TTTTAATATATATT
1 TTTTAATATATATT
*
3520938 TTTTAATTTA-ATAT
1 TTTTAATATATAT-T
3520952 TTTTAATGAT-TATT
1 TTTTAAT-ATATATT
3520966 TTTT
1 TTTT
3520970 CTTATCAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 2 0.07
14 22 0.81
15 3 0.11
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTTAATATATATT
Found at i:3522336 original size:4 final size:4
Alignment explanation
Indices: 3522329--3522358 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
3522319 AATTAATTAA
3522329 TTAT TTAT TTAT TTAT TTAT TT-T TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
3522359 ATAAATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:3522867 original size:10 final size:10
Alignment explanation
Indices: 3522836--3522898 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
3522826 AAAAAAAGAA
3522836 AAATTTATTT
1 AAATTTATTT
3522846 AAA---ATTT
1 AAATTTATTT
*
3522853 TAATTTATTT
1 AAATTTATTT
3522863 AAATTTATTT
1 AAATTTATTT
3522873 --ATTTAAATTT
1 AAATTT--ATTT
*
3522883 TAATTTATTT
1 AAATTTATTT
3522893 AAATTT
1 AAATTT
3522899 TAATCAAACT
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
7 6 0.14
8 4 0.09
10 29 0.67
12 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
AAATTTATTT
Found at i:3522868 original size:16 final size:16
Alignment explanation
Indices: 3522837--3522902 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
3522827 AAAAAAGAAA
3522837 AATTTATTTAAAATTTT
1 AATTTATTT-AAATTTT
3522854 AATTTATTTAAA-TTT
1 AATTTATTTAAATTTT
3522869 -ATTTATTTAAATTTT
1 AATTTATTTAAATTTT
3522884 AATTTATTTAAATTTT
1 AATTTATTTAAATTTT
3522900 AAT
1 AAT
3522903 CAAACTTCTA
Statistics
Matches: 47, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.23
15 6 0.13
16 21 0.45
17 9 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTTATTTAAATTTT
Found at i:3522883 original size:30 final size:31
Alignment explanation
Indices: 3522838--3522898 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
3522828 AAAAAGAAAA
3522838 ATTTATTTAAAATTTTAATTTATTTAAATTT
1 ATTTATTTAAAATTTTAATTTATTTAAATTT
3522869 ATTTATTT-AAATTTTAATTTATTTAAATTT
1 ATTTATTTAAAATTTTAATTTATTTAAATTT
3522899 TAATCAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
ATTTATTTAAAATTTTAATTTATTTAAATTT
Found at i:3522953 original size:16 final size:16
Alignment explanation
Indices: 3522929--3522959 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3522919 GCATGATCGC
*
3522929 ATTTTAATTTATTTAA
1 ATTTAAATTTATTTAA
3522945 ATTTAAATTTATTTA
1 ATTTAAATTTATTTA
3522960 TTTTTATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTAAATTTATTTAA
Found at i:3523490 original size:94 final size:93
Alignment explanation
Indices: 3523314--3523497 Score: 314
Period size: 94 Copynumber: 2.0 Consensus size: 93
3523304 ATATTATTAA
*
3523314 GCTCCGCGTGAAACACGTGCAAAAATTATTAGGTGAGGTTTGAGAGATTTTCGGTCACAAAAACC
1 GCTCCACGTGAAACACGTGCAAAAATTATTAGGTGAGGTTTGAGAGATTTTCGGTCACAAAAACC
3523379 ATGTTGAAAATACTAAATCTTGTCCTTG
66 ATGTTGAAAATACTAAATCTTGTCCTTG
* *
3523407 GCTCCACGTGAAACACGTGGAATAATTATTAGGTGAGGTTTGAGGAGATTTTCGGTCACAAAAAC
1 GCTCCACGTGAAACACGTGCAAAAATTATTAGGTGAGGTTTGA-GAGATTTTCGGTCACAAAAAC
* *
3523472 CATGTTGAGAATACTAAATGTTGTCC
65 CATGTTGAAAATACTAAATCTTGTCC
3523498 CTTCCGAGTT
Statistics
Matches: 85, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
93 40 0.47
94 45 0.53
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (93 bp):
GCTCCACGTGAAACACGTGCAAAAATTATTAGGTGAGGTTTGAGAGATTTTCGGTCACAAAAACC
ATGTTGAAAATACTAAATCTTGTCCTTG
Found at i:3523709 original size:19 final size:19
Alignment explanation
Indices: 3523666--3523720 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
3523656 TTTTTAATAA
*
3523666 TATAATATATTTAATTTAT
1 TATAATATATTAAATTTAT
3523685 TGATAATATA-TAAATTTAT
1 T-ATAATATATTAAATTTAT
*
3523704 GTATAAATTTATTAAAT
1 -TAT-AATATATTAAAT
3523721 ATAAATTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 11 0.37
20 14 0.47
21 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (19 bp):
TATAATATATTAAATTTAT
Found at i:3523777 original size:2 final size:2
Alignment explanation
Indices: 3523772--3523806 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3523762 TTGTTCTTTG
3523772 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3523807 ATTTGTACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3526461 original size:12 final size:11
Alignment explanation
Indices: 3526416--3526489 Score: 71
Period size: 12 Copynumber: 6.5 Consensus size: 11
3526406 ACAACAATAG
3526416 CTTTTCATTTTT
1 CTTTTC-TTTTT
* *
3526428 ATTTATCTTTAT
1 CTTT-TCTTTTT
*
3526440 CTTTT-TTTTC
1 CTTTTCTTTTT
3526450 CTTTTCTTTTT
1 CTTTTCTTTTT
3526461 CTTTTTCTTTTT
1 C-TTTTCTTTTT
3526473 CTTGTT-TTTTT
1 CTT-TTCTTTTT
3526484 CTTTTC
1 CTTTTC
3526490 CCTTTCTTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
10 10 0.20
11 16 0.31
12 23 0.45
13 2 0.04
ACGTcount: A:0.05, C:0.16, G:0.01, T:0.77
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:3526474 original size:6 final size:6
Alignment explanation
Indices: 3526444--3526488 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
3526434 CTTTATCTTT
* *
3526444 TTTTTC CTTTTC TTTTTC TTTTTC TTTTTC TTGTT- TTTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT
3526489 CCCTTTCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 4 0.12
6 30 0.88
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:3526481 original size:34 final size:33
Alignment explanation
Indices: 3526416--3526498 Score: 94
Period size: 34 Copynumber: 2.5 Consensus size: 33
3526406 ACAACAATAG
*
3526416 CTTTTCATTTTTATTTATCTTTATCTTTTTTTTC
1 CTTTTC-TTTTTCTTTATCTTTATCTTTTTTTTC
* * *
3526450 CTTTTCTTTTTCTTTTTCTTTTTCTTGTTTTTTT
1 CTTTTCTTTTTCTTTATCTTTATCTT-TTTTTTC
**
3526484 CTTTTCCCTTTCTTT
1 CTTTTCTTTTTCTTT
3526499 CTCCCTTCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 17 0.40
34 25 0.60
ACGTcount: A:0.05, C:0.18, G:0.01, T:0.76
Consensus pattern (33 bp):
CTTTTCTTTTTCTTTATCTTTATCTTTTTTTTC
Found at i:3529439 original size:2 final size:2
Alignment explanation
Indices: 3529432--3529460 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3529422 TGTTTTGCTT
3529432 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3529461 GTTTGCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3532391 original size:17 final size:16
Alignment explanation
Indices: 3532371--3532412 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3532361 GTTTAATCGA
*
3532371 TAAATTATTTTAGATTT
1 TAAATTATTTTA-AATT
*
3532388 TAAATTATATTAAATT
1 TAAATTATTTTAAATT
3532404 TAAATTATT
1 TAAATTATT
3532413 AAAAGAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TAAATTATTTTAAATT
Found at i:3533452 original size:21 final size:21
Alignment explanation
Indices: 3533428--3533472 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3533418 AAATTATATC
3533428 AAAATTAT-TATAAATGCTACT
1 AAAATTATCT-TAAATGCTACT
*
3533449 AAAATTATCTTAAATGTTACT
1 AAAATTATCTTAAATGCTACT
3533470 AAA
1 AAA
3533473 GTAATTACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (21 bp):
AAAATTATCTTAAATGCTACT
Found at i:3534019 original size:2 final size:2
Alignment explanation
Indices: 3534012--3534063 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
3534002 GAATAATAAG
3534012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3534054 AT AT AT AT AT
1 AT AT AT AT AT
3534064 GGGACTGAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3536054 original size:10 final size:11
Alignment explanation
Indices: 3536033--3536093 Score: 53
Period size: 10 Copynumber: 5.9 Consensus size: 11
3536023 ATATAATATT
3536033 ATAATATAAAA
1 ATAATATAAAA
3536044 ATAAT-TAAAA
1 ATAATATAAAA
*
3536054 AT-ATA-ATATA
1 ATAATATA-AAA
3536064 A-AATA-AAAA
1 ATAATATAAAA
3536073 ATAATATAAATA
1 ATAATATAAA-A
3536085 A-AATATAAA
1 ATAATATAAA
3536094 TATATGAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 6 0.14
10 18 0.43
11 16 0.38
12 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:3536059 original size:23 final size:23
Alignment explanation
Indices: 3536027--3536112 Score: 79
Period size: 22 Copynumber: 3.7 Consensus size: 23
3536017 TATTAAATAT
* *
3536027 AATATTATAATATAAAAATAATTA
1 AATAATATAATATAAAAATAA-AA
3536051 AA-AATATAATAT-AAAATAAAA
1 AATAATATAATATAAAAATAAAA
3536072 AATAATATAA-ATAAAATATAAATA
1 AATAATATAATATAAAA-ATAAA-A
* *
3536096 TATGAATATATTATAAA
1 AAT-AATATAATATAAA
3536113 TTATTAATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
21 5 0.10
22 17 0.33
23 14 0.27
24 5 0.10
25 6 0.12
26 5 0.10
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (23 bp):
AATAATATAATATAAAAATAAAA
Found at i:3536103 original size:19 final size:16
Alignment explanation
Indices: 3536021--3536097 Score: 68
Period size: 17 Copynumber: 4.8 Consensus size: 16
3536011 CCATAATATT
*
3536021 AAATATAATAT-TATA
1 AAATATAATATAAATA
* * *
3536036 ATATA-AAAATAATTAA
1 AAATATAATATAAAT-A
3536052 AAATATAATATAAAATA
1 AAATATAATAT-AAATA
*
3536069 AAAAATAATATAAATA
1 AAATATAATATAAATA
3536085 AAATATAAATATA
1 AAATAT-AATATA
3536098 TGAATATATT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
14 4 0.08
15 5 0.10
16 15 0.31
17 21 0.44
18 3 0.06
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATATAATATAAATA
Found at i:3536103 original size:28 final size:29
Alignment explanation
Indices: 3536020--3536172 Score: 104
Period size: 28 Copynumber: 5.3 Consensus size: 29
3536010 TCCATAATAT
3536020 TAAATATAATATTATAATATAAAAATAATTA
1 TAAATATAATA-TA-AATATAAAAATAATTA
*
3536051 AAAATATAATATAAA-ATAAAAAATAA-TA
1 TAAATATAATATAAATAT-AAAAATAATTA
* **
3536079 TAAATAAAATATAAATATATGAATATATTA
1 TAAATATAATATAAATATAAAAATA-ATTA
* * **
3536109 TAAAT-T-AT-TAATTTATTAAAATTTTTA
1 TAAATATAATATAA-ATATAAAAATAATTA
* * *
3536136 TAAATATAA-AT-ATTTTAAATATAATTA
1 TAAATATAATATAAATATAAAAATAATTA
3536163 TAATATATAA
1 TAA-ATATAA
3536173 AAATTATATT
Statistics
Matches: 96, Mismatches: 17, Indels: 21
0.72 0.13 0.16
Matches are distributed among these distances:
27 24 0.25
28 38 0.40
29 15 0.16
30 9 0.09
31 10 0.10
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (29 bp):
TAAATATAATATAAATATAAAAATAATTA
Found at i:3537391 original size:30 final size:30
Alignment explanation
Indices: 3537333--3537391 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
3537323 TTTTTTATTT
* * *
3537333 TTAAAAAATTATAATTATTATATTTATAAA
1 TTAAAAAATTATAAATATAATATATATAAA
3537363 TTAAAAAATT-TAAATATCAATATATATAA
1 TTAAAAAATTATAAATAT-AATATATATAA
3537392 TAATTTGTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (30 bp):
TTAAAAAATTATAAATATAATATATATAAA
Found at i:3538079 original size:16 final size:16
Alignment explanation
Indices: 3538060--3538092 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3538050 CATATTTATG
3538060 TTTA-ATAATATTTTAA
1 TTTATATAA-ATTTTAA
3538076 TTTATATAAATTTTAA
1 TTTATATAAATTTTAA
3538092 T
1 T
3538093 ATATCAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTATATAAATTTTAA
Found at i:3538117 original size:32 final size:33
Alignment explanation
Indices: 3538066--3538129 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
3538056 TATGTTTAAT
* *
3538066 AATATTTTAATTTATATAAATTT-TAATATATC
1 AATAATTTAATTTATATAAATTTAAAATATATC
3538098 AATAATTTATATTT-TATAAATTTAAAATATAT
1 AATAATTTA-ATTTATATAAATTTAAAATATAT
3538130 TCGTGTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (33 bp):
AATAATTTAATTTATATAAATTTAAAATATATC
Found at i:3540149 original size:2 final size:2
Alignment explanation
Indices: 3540142--3540171 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3540132 AGAACTGAAA
3540142 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3540172 TAATTGAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3545568 original size:2 final size:2
Alignment explanation
Indices: 3545561--3545588 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3545551 TGACCATGGT
3545561 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3545589 CCCCTCCCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3553607 original size:15 final size:15
Alignment explanation
Indices: 3553583--3553620 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3553573 CAATGACCTC
*
3553583 ATATTTTATATTTAT
1 ATATTATATATTTAT
3553598 ATATTATATATTTAT
1 ATATTATATATTTAT
3553613 ATTATTAT
1 A-TATTAT
3553621 TTTTAGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATATTATATATTTAT
Found at i:3554504 original size:23 final size:23
Alignment explanation
Indices: 3554478--3554523 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3554468 TTTATATTAC
3554478 TATCATAATT-AGAAACGAGAAAG
1 TATCATAATTGAG-AACGAGAAAG
* *
3554501 TATCATGATTGAGAAGGAGAAAG
1 TATCATAATTGAGAACGAGAAAG
3554524 AATTATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.48, C:0.07, G:0.24, T:0.22
Consensus pattern (23 bp):
TATCATAATTGAGAACGAGAAAG
Found at i:3558107 original size:2 final size:2
Alignment explanation
Indices: 3558100--3558128 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3558090 TCTTTTCTTA
3558100 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3558129 AAGATTGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3562012 original size:22 final size:21
Alignment explanation
Indices: 3561987--3562034 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3561977 AATAATTTCA
3561987 AAATATTAAAAAAATTAAATTT
1 AAATATT-AAAAAATTAAATTT
* * *
3562009 AAATATTTAAATATTTAATTT
1 AAATATTAAAAAATTAAATTT
3562030 AAATA
1 AAATA
3562035 ATTTATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATATTAAAAAATTAAATTT
Found at i:3562030 original size:21 final size:21
Alignment explanation
Indices: 3561998--3562059 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
3561988 AATATTAAAA
*
3561998 AAATTAAATTTAAATATTTA-
1 AAATTTAATTTAAATATTTAT
3562018 AATATTTAATTTAAATAATTTAT
1 AA-ATTTAATTTAAAT-ATTTAT
* *
3562041 AAATTTAATTAAAAAATTT
1 AAATTTAATTTAAATATTT
3562060 TAATTAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 2 0.06
21 16 0.44
22 16 0.44
23 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATTTAATTTAAATATTTAT
Found at i:3562239 original size:2 final size:2
Alignment explanation
Indices: 3562232--3562260 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3562222 TCTAAATCCT
3562232 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3562261 TTCACTCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3568365 original size:12 final size:12
Alignment explanation
Indices: 3568350--3568380 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3568340 TCATCCGCAG
3568350 CACCATCCAAGT
1 CACCATCCAAGT
*
3568362 CACCGTCCAAGT
1 CACCATCCAAGT
3568374 CACCATC
1 CACCATC
3568381 TTCTTCTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.29, C:0.45, G:0.10, T:0.16
Consensus pattern (12 bp):
CACCATCCAAGT
Found at i:3569376 original size:14 final size:16
Alignment explanation
Indices: 3569351--3569382 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3569341 ATTCTATCTG
3569351 AATTTAAAATA-TTAA
1 AATTTAAAATATTTAA
3569366 AATTT-AAATATTTAA
1 AATTTAAAATATTTAA
3569381 AA
1 AA
3569383 AATTAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTAAAATATTTAA
Found at i:3571567 original size:13 final size:13
Alignment explanation
Indices: 3571551--3571598 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
3571541 TTACTTCATA
3571551 AATTTAATTTATT
1 AATTTAATTTATT
** *
3571564 AATTCGATTCATT
1 AATTTAATTTATT
* *
3571577 GATTTAATTTATA
1 AATTTAATTTATT
3571590 AATTTAATT
1 AATTTAATT
3571599 CATGAGTTCA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (13 bp):
AATTTAATTTATT
Found at i:3571599 original size:26 final size:26
Alignment explanation
Indices: 3571552--3571601 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3571542 TACTTCATAA
* *
3571552 ATTTAATTTATTAATTCGATTCATTG
1 ATTTAATTTATAAATTCAATTCATTG
*
3571578 ATTTAATTTATAAATTTAATTCAT
1 ATTTAATTTATAAATTCAATTCAT
3571602 GAGTTCAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (26 bp):
ATTTAATTTATAAATTCAATTCATTG
Found at i:3578469 original size:3 final size:3
Alignment explanation
Indices: 3578456--3578499 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
3578446 ACAATGGCAA
*
3578456 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3578500 CAACAACATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3579792 original size:19 final size:19
Alignment explanation
Indices: 3579768--3579807 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3579758 ACAGATTATC
3579768 CAAGTGATCAACAGTGTTT
1 CAAGTGATCAACAGTGTTT
3579787 CAAGTGATCAACAGTGTTT
1 CAAGTGATCAACAGTGTTT
3579806 CA
1 CA
3579808 TAATTCAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (19 bp):
CAAGTGATCAACAGTGTTT
Found at i:3587502 original size:2 final size:2
Alignment explanation
Indices: 3587495--3587529 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3587485 GTATTTTTCA
3587495 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3587530 TTCTTCCTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3589591 original size:17 final size:17
Alignment explanation
Indices: 3589564--3589603 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3589554 AAATACTCAT
* *
3589564 ATATAATATTTATATTTA
1 ATAT-ATATTTAAATTAA
3589582 ATATATATTTAAATTAA
1 ATATATATTTAAATTAA
3589599 ATATA
1 ATATA
3589604 AAAATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATATTTAAATTAA
Found at i:3589671 original size:19 final size:17
Alignment explanation
Indices: 3589634--3589672 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3589624 AAAATTAAAT
*
3589634 ATATAAAAATTATTTAA
1 ATATAAAAATTATTCAA
3589651 ATATAAAAATATATATCAA
1 ATATAAAAAT-TAT-TCAA
3589670 ATA
1 ATA
3589673 CTCACGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 3 0.16
19 6 0.32
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
ATATAAAAATTATTCAA
Found at i:3592092 original size:45 final size:45
Alignment explanation
Indices: 3592038--3592133 Score: 183
Period size: 45 Copynumber: 2.1 Consensus size: 45
3592028 AAGAACCCCT
3592038 ATTCTCTCTTTTTATTGATAACCAAGAAGATGACGTTAAAGGCCA
1 ATTCTCTCTTTTTATTGATAACCAAGAAGATGACGTTAAAGGCCA
3592083 ATTCTCTCTTTTTATTGATAACCAAGAAGATGACGTTAAAGGCCA
1 ATTCTCTCTTTTTATTGATAACCAAGAAGATGACGTTAAAGGCCA
3592128 AGTTCT
1 A-TTCT
3592134 GGTCGCTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 46 0.92
46 4 0.08
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (45 bp):
ATTCTCTCTTTTTATTGATAACCAAGAAGATGACGTTAAAGGCCA
Found at i:3593901 original size:40 final size:40
Alignment explanation
Indices: 3593846--3593927 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
3593836 TAATTAGAAG
*
3593846 TTAAACATTCTTAAGTTCTAAGATGAGTTTGGATGCTAAA
1 TTAAAAATTCTTAAGTTCTAAGATGAGTTTGGATGCTAAA
3593886 TTAAAAATTCTTAAGTTCTAAGATGAGTTTGGATGCTAAA
1 TTAAAAATTCTTAAGTTCTAAGATGAGTTTGGATGCTAAA
3593926 TT
1 TT
3593928 TGCAGTTGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (40 bp):
TTAAAAATTCTTAAGTTCTAAGATGAGTTTGGATGCTAAA
Found at i:3594441 original size:2 final size:2
Alignment explanation
Indices: 3594434--3594465 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3594424 CTTTAAAAAC
3594434 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3594466 GATAATTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3596826 original size:29 final size:30
Alignment explanation
Indices: 3596794--3596861 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 30
3596784 AACTTTAATT
*
3596794 ATTAATTTTACTAATT-TTTTTATA-ATAAA
1 ATTAATTTTAC-AATTCATTTTATATATAAA
* *
3596823 ATT-ATTTAACAATTCATTTTATATATTAA
1 ATTAATTTTACAATTCATTTTATATATAAA
3596852 ATTAATTTTA
1 ATTAATTTTA
3596862 TATCATTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
27 4 0.12
28 13 0.41
29 10 0.31
30 5 0.16
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (30 bp):
ATTAATTTTACAATTCATTTTATATATAAA
Found at i:3597177 original size:22 final size:21
Alignment explanation
Indices: 3597154--3597207 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
3597144 TAAGTTTTAA
3597154 TTTTTTTTATTAATTAAATAAAT
1 TTTTTTTTA-TAATT-AATAAAT
*
3597177 TTATTTTTTATCATTAATAAAT
1 TT-TTTTTTATAATTAATAAAT
3597199 TATTTTTTT
1 T-TTTTTTT
3597208 GAAAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 14 0.50
23 7 0.25
24 7 0.25
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTTTTATAATTAATAAAT
Found at i:3597203 original size:21 final size:23
Alignment explanation
Indices: 3597152--3597206 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
3597142 TGTAAGTTTT
3597152 AATT-TTTTTTATTAATTAAATA
1 AATTATTTTTTATTAATTAAATA
*
3597174 AATTTATTTTTTA-TCATT-AATA
1 AA-TTATTTTTTATTAATTAAATA
3597196 AATTATTTTTT
1 AATTATTTTTT
3597207 TGAAAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 9 0.30
22 8 0.27
23 6 0.20
24 7 0.23
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
AATTATTTTTTATTAATTAAATA
Found at i:3597834 original size:16 final size:16
Alignment explanation
Indices: 3597793--3597839 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3597783 AAATAGTAAG
*
3597793 ATTAA-TTTATAATAT
1 ATTAATTTTATAATAA
*
3597808 ATCATATTTTTATAATAA
1 AT--TAATTTTATAATAA
3597826 ATTAATTTTATAAT
1 ATTAATTTTATAAT
3597840 TTTTATGCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 2 0.08
16 11 0.42
17 2 0.08
18 11 0.42
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTAATTTTATAATAA
Found at i:3599401 original size:33 final size:32
Alignment explanation
Indices: 3599328--3599401 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 32
3599318 ATTTAATAAA
*
3599328 AATAATTTATTAATTATTTTTTTAACATCATT
1 AATAATTAATTAATTATTTTTTTAACATCATT
* *
3599360 AA-ACATTAATTAATATATTTTTTTCAC-TTATTT
1 AATA-ATTAATTAAT-TATTTTTTTAACATCA-TT
3599393 AATAATTAA
1 AATAATTAA
3599402 ATTCTACTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
31 1 0.03
32 13 0.37
33 20 0.57
34 1 0.03
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.53
Consensus pattern (32 bp):
AATAATTAATTAATTATTTTTTTAACATCATT
Found at i:3599916 original size:18 final size:17
Alignment explanation
Indices: 3599873--3599916 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
3599863 ATAATTATAT
3599873 AAATTAAG-TAAATTTA
1 AAATTAAGTTAAATTTA
* *
3599889 ATATTGAGTTAAAGTTTA
1 AAATTAAGTTAAA-TTTA
3599907 AAATTAAGTT
1 AAATTAAGTT
3599917 TAGTTATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 6 0.27
17 4 0.18
18 12 0.55
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
AAATTAAGTTAAATTTA
Found at i:3600107 original size:14 final size:14
Alignment explanation
Indices: 3600072--3600107 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3600062 GTAAGAACAC
*
3600072 AATAAGAATAAAAA
1 AATAAAAATAAAAA
*
3600086 AATTAAAATAAAAA
1 AATAAAAATAAAAA
3600100 AATAAAAA
1 AATAAAAA
3600108 CATATAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (14 bp):
AATAAAAATAAAAA
Found at i:3604534 original size:2 final size:2
Alignment explanation
Indices: 3604527--3604554 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3604517 AGAGTGTTTA
3604527 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3604555 CCTGTTTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3608287 original size:2 final size:2
Alignment explanation
Indices: 3608280--3608308 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3608270 TGTTTTGCAT
3608280 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3608309 TGTCTGTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.