Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6984689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 29
Found at i:3283376 original size:18 final size:18
Alignment explanation
Indices: 3283328--3283379 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
3283318 CGACTCGTTT
* * *
3283328 ACCCAACCCGTTAACCTG
1 ACCCGACCCGTTGACCCG
3283346 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
3283364 ACCCGACCCGTTGACC
1 ACCCGACCCGTTGACC
3283380 GTTGACCCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.21, C:0.48, G:0.17, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:3283379 original size:13 final size:13
Alignment explanation
Indices: 3283344--3283368 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3283334 CCCGTTAACC
3283344 TGACCCGACCCGT
1 TGACCCGACCCGT
3283357 TGACCCGACCCG
1 TGACCCGACCCG
3283369 ACCCGTTGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:3285986 original size:12 final size:12
Alignment explanation
Indices: 3285949--3285987 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3285939 ATCTGATACT
3285949 TGACATGGATTC
1 TGACATGGATTC
*
3285961 TGATAT-GATATC
1 TGACATGGAT-TC
3285973 TGACATGGATTC
1 TGACATGGATTC
3285985 TGA
1 TGA
3285988 TCTGGTACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:3285997 original size:48 final size:48
Alignment explanation
Indices: 3285933--3286027 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
3285923 TTCGATTTGA
3285933 ATTCTGATCTGATACTTGACATGGATTCTGATATGATA-TCTGACATGG
1 ATTCTGATCTGATACTTGACATGGATTCTGATATGATACT-TGACATGG
* * *
3285981 ATTCTGATCTGGTACTTGACTTGGATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATGGATTCTGATATGATACTTGACATG
3286028 AATTATGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 42 0.98
49 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (48 bp):
ATTCTGATCTGATACTTGACATGGATTCTGATATGATACTTGACATGG
Found at i:3286041 original size:24 final size:24
Alignment explanation
Indices: 3285933--3286027 Score: 129
Period size: 24 Copynumber: 4.0 Consensus size: 24
3285923 TTCGATTTGA
*
3285933 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
3285957 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
* * *
3285981 ATTCTGATCTGGTACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
*
3286005 ATTTTGATATGATACTTGACATG
1 ATTCTGATATGATACTTGACATG
3286028 AATTATGTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
23 1 0.02
24 59 0.97
25 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:3286204 original size:43 final size:43
Alignment explanation
Indices: 3286143--3286233 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
3286133 GGGCCTTACT
*
3286143 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
3286186 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
3286229 TGGTG
1 TGGTG
3286234 CGTTCGGTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.16, C:0.11, G:0.37, T:0.35
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
Found at i:3288399 original size:13 final size:13
Alignment explanation
Indices: 3288383--3288423 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
3288373 CGACCCAACT
3288383 CGTTTACCCGACC
1 CGTTTACCCGACC
* *
3288396 CGTTGACCCGACT
1 CGTTTACCCGACC
*
3288409 TGTTTACCCGACC
1 CGTTTACCCGACC
3288422 CG
1 CG
3288424 ACCCGTTAAC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.15, C:0.41, G:0.20, T:0.24
Consensus pattern (13 bp):
CGTTTACCCGACC
Found at i:3288413 original size:26 final size:26
Alignment explanation
Indices: 3288374--3288423 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
3288364 AACCCGACCC
3288374 GACCCAACTCGTTTACCCGACCCGTT
1 GACCCAACTCGTTTACCCGACCCGTT
* *
3288400 GACCCGACTTGTTTACCCGACCCG
1 GACCCAACTCGTTTACCCGACCCG
3288424 ACCCGTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.42, G:0.18, T:0.22
Consensus pattern (26 bp):
GACCCAACTCGTTTACCCGACCCGTT
Found at i:3288423 original size:18 final size:18
Alignment explanation
Indices: 3288400--3288448 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
3288390 CCGACCCGTT
** *
3288400 GACCCGACTTGTTTACCC
1 GACCCGACCCGTTAACCC
3288418 GACCCGACCCGTTAACCC
1 GACCCGACCCGTTAACCC
3288436 GACCCGACCCGTT
1 GACCCGACCCGTT
3288449 GATCGTTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.18, C:0.45, G:0.18, T:0.18
Consensus pattern (18 bp):
GACCCGACCCGTTAACCC
Found at i:3291041 original size:12 final size:12
Alignment explanation
Indices: 3291004--3291042 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3290994 ATCTGATACT
3291004 TGACATGGATTC
1 TGACATGGATTC
*
3291016 TGATAT-GATATC
1 TGACATGGAT-TC
3291028 TGACATGGATTC
1 TGACATGGATTC
3291040 TGA
1 TGA
3291043 TCTGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:3291047 original size:48 final size:48
Alignment explanation
Indices: 3290988--3291082 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
3290978 TTCGATTTGA
3290988 ATTCTGATCTGATACTTGACATGGATTCTGATATGATA-TCTGACATGG
1 ATTCTGATCTGATACTTGACATGGATTCTGATATGATACT-TGACATGG
* *
3291036 ATTCTGATCTGATACTTGACTTGGATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATGGATTCTGATATGATACTTGACATG
3291083 AATTATGTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 43 0.98
49 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (48 bp):
ATTCTGATCTGATACTTGACATGGATTCTGATATGATACTTGACATGG
Found at i:3291096 original size:24 final size:24
Alignment explanation
Indices: 3290988--3291082 Score: 138
Period size: 24 Copynumber: 4.0 Consensus size: 24
3290978 TTCGATTTGA
*
3290988 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
3291012 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
* *
3291036 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
*
3291060 ATTTTGATATGATACTTGACATG
1 ATTCTGATATGATACTTGACATG
3291083 AATTATGTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
23 1 0.02
24 61 0.97
25 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:3291259 original size:43 final size:43
Alignment explanation
Indices: 3291198--3291288 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
3291188 GGGCCTTACT
*
3291198 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
3291241 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
3291284 TGGTG
1 TGGTG
3291289 CGTTCGGTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.16, C:0.11, G:0.37, T:0.35
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
Found at i:3297994 original size:85 final size:87
Alignment explanation
Indices: 3297877--3298083 Score: 215
Period size: 85 Copynumber: 2.4 Consensus size: 87
3297867 CAAAACTTGA
* * * * * * * *
3297877 GCTATAGATTCATTAAGAGTGTAAAACTCAACCTCAATACTCGGTGTATCCATCCAGTC-TGTCT
1 GCTATGGATTTATTAAGAGTGAAAAACTCAACCTCAAAAATCAGAGTATCCATCAAGTCAT-TCT
*
3297941 CACTAAGACCAC-CA-AAATTAG
65 AACTAAGACCACACATAAATTAG
* * *
3297962 GCTATGGATTTGTTAAGAATGAAAAACTCAACCTAAAAAATCAGAGTATCCATCAAGTCATTCTA
1 GCTATGGATTTATTAAGAGTGAAAAACTCAACCTCAAAAATCAGAGTATCCATCAAGTCATTCTA
* ** *
3298027 ACTAGGACCACACATATTTTGG
66 ACTAAGACCACACATAAATTAG
*
3298049 GCTATGGATTTATTATGAGT-ATAAAACTCAACCTC
1 GCTATGGATTTATTAAGAGTGA-AAAACTCAACCTC
3298084 TCAAGTGTAC
Statistics
Matches: 98, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
85 61 0.62
86 4 0.04
87 33 0.34
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (87 bp):
GCTATGGATTTATTAAGAGTGAAAAACTCAACCTCAAAAATCAGAGTATCCATCAAGTCATTCTA
ACTAAGACCACACATAAATTAG
Found at i:3300145 original size:90 final size:90
Alignment explanation
Indices: 3300033--3300200 Score: 282
Period size: 90 Copynumber: 1.9 Consensus size: 90
3300023 TATTTAATTT
* * *
3300033 CAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCATGATATGATTAGGGTAACT
1 CAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCATAATATGATTAGGGTAACT
3300098 TGGATATAAAAGGATTATTAGATTC
66 TGGATATAAAAGGATTATTAGATTC
* *
3300123 CAATTAATTAAATGTAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGATTAGGGTAACT
1 CAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCATAATATGATTAGGGTAACT
*
3300188 TGGCTATAAAAGG
66 TGGATATAAAAGG
3300201 GTGTGTTAGG
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 72 1.00
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (90 bp):
CAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCATAATATGATTAGGGTAACT
TGGATATAAAAGGATTATTAGATTC
Found at i:3301265 original size:130 final size:130
Alignment explanation
Indices: 3300949--3301297 Score: 468
Period size: 131 Copynumber: 2.7 Consensus size: 130
3300939 TAATTCTAAT
* *
3300949 AGAGAGAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAG
1 AGAGAAAAAGATAATATCTAATTATTTCCAATCGAGAATAAATGA-CTCTCATGCCTTAAAGCAG
* * * ** * *
3301014 TTATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCTTCTTAAAATTCAATATTGATTC
65 TCATTTATTACTCCAATCGAAATAAAGAGACATCACTATTTCAACCTAAAATTCAATATTGATCC
3301079 A
130 A
* * * *
3301080 AGAGAAAAAAATAATATCTAATTATTTCCAATCGAGAATAAATTATCTCTTATGCCTTAAACCAG
1 AGAGAAAAAGATAATATCTAATTATTTCCAATCGAGAATAAATGA-CTCTCATGCCTTAAAGCAG
* *
3301145 TCATTTAATACTCCAATCGAAATAAAGAGACATCGCTACTTT-AACCTAAAA-TCAATATTGATC
65 TCATTTATTACTCCAATCGAAATAAAGAGACATCACTA-TTTCAACCTAAAATTCAATATTGATC
*
3301208 CG
129 CA
* *
3301210 AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACATCTCATGCCTTAAAGAAG
1 AGAGAAAAAGATAATATCTAATTATTTCCAATCGAGAATAAATGAC-TCTCATGCCTTAAAGCAG
* *
3301275 TCATTTATTACTCCTACCGAAAT
65 TCATTTATTACTCCAATCGAAAT
3301298 GAAAAGATAT
Statistics
Matches: 190, Mismatches: 26, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
129 1 0.01
130 89 0.47
131 97 0.51
132 3 0.02
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (130 bp):
AGAGAAAAAGATAATATCTAATTATTTCCAATCGAGAATAAATGACTCTCATGCCTTAAAGCAGT
CATTTATTACTCCAATCGAAATAAAGAGACATCACTATTTCAACCTAAAATTCAATATTGATCCA
Found at i:3302301 original size:107 final size:109
Alignment explanation
Indices: 3302118--3302313 Score: 263
Period size: 107 Copynumber: 1.8 Consensus size: 109
3302108 TAAGAGGGTC
* * *
3302118 TAAACAACAAATAACCCTAAAATACATAGCATGCATAAGAAATGAGTAAATAAAAATTTTAGTCC
1 TAAACAACAAATAACCCAAAAATACATAGCATGCATAAGAAATGAGTAAATAAAAAGTTCAGTCC
* * *
3302183 TTATAGGTGACTTACATGCGAAAATACGCTAAACTATGGAAGAG
66 CTATAGGTGACTAACATGCAAAAATACGCTAAACTATGGAAGAG
* * * *
3302227 TAAACAACAAAT-ATCCAAAAATATATATCATGCATAA-AAACT-AGTAAATAACAAGTTCAGTC
1 TAAACAACAAATAACCCAAAAATACATAGCATGCATAAGAAA-TGAGTAAATAAAAAGTTCAGTC
*
3302289 CCTATATGTGACTAACATGCAAAAA
65 CCTATAGGTGACTAACATGCAAAAA
3302314 CATGCGAGAG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
107 41 0.55
108 22 0.29
109 12 0.16
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (109 bp):
TAAACAACAAATAACCCAAAAATACATAGCATGCATAAGAAATGAGTAAATAAAAAGTTCAGTCC
CTATAGGTGACTAACATGCAAAAATACGCTAAACTATGGAAGAG
Found at i:3303301 original size:3 final size:3
Alignment explanation
Indices: 3303293--3303333 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
3303283 CTTGGCTTGC
*
3303293 ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3303334 GTCAGGATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3304476 original size:19 final size:19
Alignment explanation
Indices: 3304454--3304492 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3304444 CTTTTTTGCG
*
3304454 TCATTTTTTCTTTTTC-TTT
1 TCATTTTAT-TTTTTCATTT
3304473 TCATTTTATTTTTTCATTT
1 TCATTTTATTTTTTCATTT
3304492 T
1 T
3304493 TTTCTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (19 bp):
TCATTTTATTTTTTCATTT
Found at i:3332600 original size:20 final size:20
Alignment explanation
Indices: 3332575--3332645 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
3332565 ATACTAATAT
3332575 AAAATTATTAATTAGGTTAA
1 AAAATTATTAATTAGGTTAA
* * **
3332595 AAAATTAATTCAATCA-ATTTT
1 AAAATT-ATT-AATTAGGTTAA
3332616 AAAATTATTAATTAGGTTAA
1 AAAATTATTAATTAGGTTAA
*
3332636 AAATTTATTA
1 AAAATTATTA
3332646 TTATTATTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 4 0.10
20 20 0.51
21 11 0.28
22 4 0.10
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (20 bp):
AAAATTATTAATTAGGTTAA
Found at i:3332648 original size:3 final size:3
Alignment explanation
Indices: 3332640--3332674 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3332630 GGTTAAAAAT
*
3332640 TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3332675 TCTTTTAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3336758 original size:3 final size:3
Alignment explanation
Indices: 3336750--3336812 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
3336740 AATTGTTTAG
3336750 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
3336798 ATA ATA TTA ATA ATA
1 ATA ATA ATA ATA ATA
3336813 CAGTTTTGTA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:3338399 original size:35 final size:36
Alignment explanation
Indices: 3338325--3338423 Score: 119
Period size: 35 Copynumber: 2.8 Consensus size: 36
3338315 GTGCTTGTGG
* * * * *
3338325 ATCCTATCTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTAT
*
3338361 ATCCTATTTTAGGAG-TTGAATCCTAGCATAATTAT
1 ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTAT
*
3338396 ATCCTATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTAG-GAGTTTGAATCCTAG
3338424 TAGGACGAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
35 26 0.48
36 17 0.31
37 11 0.20
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTAT
Found at i:3339181 original size:106 final size:103
Alignment explanation
Indices: 3338879--3339644 Score: 715
Period size: 109 Copynumber: 7.4 Consensus size: 103
3338869 AATATTGTTC
* * * * *
3338879 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGA-A
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAAT-TGAAAAT-TTTGTTGACA
* * * * *
3338943 AGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
63 A-CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * *
3338985 CGAGTCTAATATCCTTCGCTGTGAAGATGAAATTGACTCTG-AA-CG-AAATCTTGTTGACAATC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAATTTTGTTGACAACC
3339047 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
*
3339085 CGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-TTG-AAAAT-TTTGTTGACA
3339150 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
63 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * ** *
3339191 CGAGTGGCACGATATCCTCCG-TCGTGGAGTT-AAAATCGCGGATGAAACTGAAAAGTTGTTCGT
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGC-TCTGAAATTGAAAA-TT-TT-GT
* *
3339254 TGACAACCAGCCGTCCTTTCGTTGTGAAGTTAAACTTGTGTTGTCT
58 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * * * *
3339300 CGGGTAGCACGATATCCTCCG-TCGTGGAGTTAAAATCGGCTCTGGAATTGGGAAATTATTTGTT
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATT--GAAAAT-TTTGTT
*
3339364 GACAACCAGCCGTCCCTTCGCTGTGAAGTTGAAC-T-TGTTGTCT
59 GACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * **
3339407 CGAGTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTCCGAAATTG------TTGTCGACAGTC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAATTTTGTTGACAACC
* * *
3339466 AGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
66 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
3339504 TGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAACTAGGAAAA--TTGTTGACAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-T-TGAAAATTTTGTTGACAA
3339567 CCAG-CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
3339606 TGAGTTCAATATCCTTCGC-GTGAAGTCGAAATTGACTCT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
3339645 AGATAAAATT
Statistics
Matches: 555, Mismatches: 77, Indels: 61
0.80 0.11 0.09
Matches are distributed among these distances:
95 33 0.06
96 1 0.00
97 46 0.08
98 1 0.00
99 1 0.00
100 80 0.14
101 24 0.04
102 51 0.09
103 12 0.02
104 31 0.06
105 7 0.01
106 89 0.16
107 17 0.03
108 14 0.03
109 135 0.24
110 8 0.01
111 5 0.01
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (103 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAATTTTGTTGACAACC
AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:3339530 original size:97 final size:99
Alignment explanation
Indices: 3339359--3339639 Score: 342
Period size: 102 Copynumber: 2.8 Consensus size: 99
3339349 GGGAAATTAT
* * *
3339359 TTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGT-TGTCTCGAGTCCAATATCCTT
1 TTGTCGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTGTCTTGAGTCCAATATCCTT
* *
3339423 CGCTGTGAAGTTGAGATTGGCTCC-GAAA-T-TG-
66 CGCTGTGAAGTTGAAATTGGC-CCTGAAACTAGGA
** * * *
3339454 TTGTCGACAGTCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCT
1 TTGTCGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTCTTGAGTCCAATATCCT
3339519 TCGCTGTGAAGTTGAAATTGGCCCTGAAACTAGGAAAA
65 TCGCTGTGAAGTTGAAATTGGCCCTGAAACTAGG---A
* *
3339557 TTGTTGACAACCAG-CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTTCAATATCCT
1 TTGTCGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTCTTGAGTCCAATATCCT
*
3339621 TCGC-GTGAAGTCGAAATTG
65 TCGCTGTGAAGTTGAAATTG
3339640 ACTCTAGATA
Statistics
Matches: 158, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
95 37 0.23
96 2 0.01
97 43 0.27
98 1 0.01
99 1 0.01
101 14 0.09
102 49 0.31
103 11 0.07
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.33
Consensus pattern (99 bp):
TTGTCGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTGTCTTGAGTCCAATATCCTT
CGCTGTGAAGTTGAAATTGGCCCTGAAACTAGGA
Found at i:3340129 original size:36 final size:36
Alignment explanation
Indices: 3340052--3340237 Score: 127
Period size: 36 Copynumber: 5.3 Consensus size: 36
3340042 AAGATGATGC
* * **
3340052 TTCAAGAGAAAACTATCTCAAGGGAGACAAAAATTTTT
1 TTCAAGAG-AAACTGTCTCAAGAGAGAC-AAAATTCAT
*
3340090 TTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCAT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCAT
* * * *** *
3340126 TTCAAGGGAAA-TGTTTTC-A-A-TG--TTTA-T-GT
1 TTCAAGAGAAACTG-TCTCAAGAGAGACAAAATTCAT
* **
3340155 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCAT
* *
3340191 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCAT
*
3340227 TTCAAGGGAAA
1 TTCAAGAGAAA
3340238 TGTTTTCAAT
Statistics
Matches: 114, Mismatches: 25, Indels: 20
0.72 0.16 0.13
Matches are distributed among these distances:
29 14 0.12
30 4 0.04
31 1 0.01
32 1 0.01
33 1 0.01
34 2 0.02
35 4 0.04
36 62 0.54
37 17 0.15
38 8 0.07
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (36 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCAT
Found at i:3340215 original size:101 final size:101
Alignment explanation
Indices: 3340052--3340435 Score: 580
Period size: 101 Copynumber: 3.8 Consensus size: 101
3340042 AAGATGATGC
* * *
3340052 TTCAAGAGAAAACTATCTCAAGGGAGACAAAAATTTTTTTCAAGAGAAACTGTCTCAAGAGAGAC
1 TTCAAGAG-AAACTGTCTCAAGGGAGAC-AAAATTTTTTTCAAGGGAAACTATCTCAAGAGAGAC
*
3340117 GAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
64 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
3340155 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTTCAAGGGAAACTATCTCAAGAGAGACAA
1 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTTCAAGGGAAACTATCTCAAGAGAGACAA
3340220 AATTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
66 AATTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
* * **
3340256 TTC-AGAGAAATTGTCTCAATGGAGACGGAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACA
1 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT-TTTCAAGGGAAACTATCTCAAGAGAGACA
*
3340320 AAACTC-TTTCAAGGGAAATG-TTTCAATGTTTATGT
65 AAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
* *
3340355 TTCAAGAGAAACTGTCTCAAGGGAG--AAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTTCAAGGGAAACTATCTCAAGAGAGACAA
* **
3340418 AGTTTGTTTCAAGGGAAA
66 AATTCATTTCAAGGGAAA
3340436 CTGTCTCAAG
Statistics
Matches: 260, Mismatches: 18, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
97 31 0.12
98 17 0.07
99 18 0.07
100 60 0.23
101 108 0.42
102 18 0.07
103 8 0.03
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (101 bp):
TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTTCAAGGGAAACTATCTCAAGAGAGACAA
AATTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
Found at i:3340366 original size:63 final size:63
Alignment explanation
Indices: 3340289--3340408 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 63
3340279 GACGGAATTT
* *
3340289 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCTTTCAAGGGAAA-TGTTTCAATGTTTA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGA-AAAACTCTTTCAAGGGAAACTGTCTCAATGTTTA
* * ** *
3340352 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAATTTGTTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGAAAAACTCTTTCAAGGGAAACTGTCTCAA
3340409 GAGAGACAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
62 16 0.33
63 33 0.67
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (63 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGAAAAACTCTTTCAAGGGAAACTGTCTCAATGTTTA
Found at i:3340382 original size:17 final size:17
Alignment explanation
Indices: 3340360--3340414 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 17
3340350 TATGTTTCAA
3340360 GAGAAACTGTCTCAAGG
1 GAGAAACTGTCTCAAGG
* *
3340377 GAGAAAATTTGTTTCAA-G
1 GAG-AAA-CTGTCTCAAGG
*
3340395 G-GAAACTGTCTCAAGA
1 GAGAAACTGTCTCAAGG
3340411 GAGA
1 GAGA
3340415 CAAAGTTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
15 7 0.24
16 4 0.14
17 6 0.21
18 5 0.17
19 7 0.24
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.22
Consensus pattern (17 bp):
GAGAAACTGTCTCAAGG
Found at i:3340431 original size:36 final size:35
Alignment explanation
Indices: 3340352--3340453 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 35
3340342 TCAATGTTTA
* *
3340352 TGTTTCAAGAGAAACTGTCTCAAGGGAGA-AAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATT
3340386 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA-TT
3340422 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
3340454 TGGTGAGCAC
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
34 27 0.42
35 3 0.05
36 34 0.53
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.25
Consensus pattern (35 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATT
Found at i:3341319 original size:22 final size:22
Alignment explanation
Indices: 3341294--3341344 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
3341284 TTGTGTTTGG
3341294 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
3341316 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
3341338 TCAAAGG
1 TCAAAGG
3341345 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:3341980 original size:15 final size:15
Alignment explanation
Indices: 3341960--3342016 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
3341950 CCTTTTTTTA
3341960 TTTTGTTCTTTCTTT
1 TTTTGTTCTTTCTTT
*
3341975 TTTTGTTCTTGTTTTT
1 TTTTGTTCTT-TCTTT
*
3341991 TTTTTTTGC-TTCTTT
1 TTTTGTT-CTTTCTTT
3342006 TCTTT-TTCTTT
1 T-TTTGTTCTTT
3342017 TTGCCCTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 1 0.03
15 19 0.54
16 14 0.40
17 1 0.03
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (15 bp):
TTTTGTTCTTTCTTT
Found at i:3341986 original size:21 final size:20
Alignment explanation
Indices: 3341952--3342019 Score: 79
Period size: 20 Copynumber: 3.4 Consensus size: 20
3341942 TTTTGTCCCC
*
3341952 TTTTTTTATT-TTGTTCTTT
1 TTTTTTTGTTCTTGTTCTTT
3341971 CTTTTTTTGTTCTTGTT-TTT
1 -TTTTTTTGTTCTTGTTCTTT
3341991 TTTTTTTGCTTCTT-TTCTTT
1 TTTTTTTG-TTCTTGTTCTTT
3342011 TTCTTTTTG
1 TT-TTTTTG
3342020 CCCTTTTTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
19 10 0.23
20 22 0.51
21 11 0.26
ACGTcount: A:0.01, C:0.10, G:0.07, T:0.81
Consensus pattern (20 bp):
TTTTTTTGTTCTTGTTCTTT
Found at i:3342025 original size:20 final size:21
Alignment explanation
Indices: 3341987--3342026 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3341977 TTGTTCTTGT
* *
3341987 TTTTTTTTTTTGCTTCTTTTC
1 TTTTTCTTTTTGCTCCTTTTC
3342008 TTTTTCTTTTTGC-CCTTTT
1 TTTTTCTTTTTGCTCCTTTT
3342027 TGTTCTGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTTTCTTTTTGCTCCTTTTC
Found at i:3346152 original size:2 final size:2
Alignment explanation
Indices: 3346147--3346191 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3346137 GTGTGTTGAC
3346147 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
3346189 AT A
1 AT A
3346192 ATTGAAAGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3349628 original size:21 final size:21
Alignment explanation
Indices: 3349598--3349639 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3349588 TTTCTTGGAG
* *
3349598 TGTTTGGTGAGTTTTTTTTTT
1 TGTTTGGTGAGGTTATTTTTT
*
3349619 TGTTTTGTGAGGTTATTTTTT
1 TGTTTGGTGAGGTTATTTTTT
3349640 ATTACTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.00, G:0.24, T:0.69
Consensus pattern (21 bp):
TGTTTGGTGAGGTTATTTTTT
Found at i:3354029 original size:64 final size:64
Alignment explanation
Indices: 3353926--3354082 Score: 147
Period size: 64 Copynumber: 2.5 Consensus size: 64
3353916 TTCAGTGTGT
* ** * * * * *
3353926 ATCGATGCACAGAAAGTACATCAATGCACCCATTAAAAATGGAAATATCGAATGCAATTAATGC
1 ATCGATGCATAGGTAGTGCATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATTAATGC
* ** **
3353990 ATCGATGCATAAGG-AGTGCATCGATGCACCC-TCTTAAAATGAAAACATCGAAGGTGATTTGTG
1 ATCGATGCAT-AGGTAGTGCATCGATGCACCCAT-TAAAAATGAAAACATCGAAGGCAATTAATG
*
3354053 T
64 C
*
3354054 ATCGATGCATTGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGTAGTGCATCGATGCAC
3354083 TTCAAGAGAA
Statistics
Matches: 76, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
63 3 0.04
64 71 0.93
65 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATTAATGC
Found at i:3355277 original size:2 final size:2
Alignment explanation
Indices: 3355270--3355309 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3355260 GAACATGGGA
3355270 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
3355310 GATAAGACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3360087 original size:14 final size:14
Alignment explanation
Indices: 3360068--3360101 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3360058 TGTTTATGAG
3360068 TATGATAGAGGTGA
1 TATGATAGAGGTGA
**
3360082 TATGATCTAGGTGA
1 TATGATAGAGGTGA
3360096 TATGAT
1 TATGAT
3360102 CTAGGTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.35
Consensus pattern (14 bp):
TATGATAGAGGTGA
Found at i:3360102 original size:14 final size:14
Alignment explanation
Indices: 3360076--3360109 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
3360066 AGTATGATAG
3360076 AGGTGATATGATCT
1 AGGTGATATGATCT
3360090 AGGTGATATGATCT
1 AGGTGATATGATCT
3360104 AGGTGA
1 AGGTGA
3360110 ATATCATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.32
Consensus pattern (14 bp):
AGGTGATATGATCT
Found at i:3360346 original size:2 final size:2
Alignment explanation
Indices: 3360334--3360366 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3360324 GAACATGGGA
*
3360334 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3360367 ATAAGACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3360745 original size:23 final size:23
Alignment explanation
Indices: 3360712--3360755 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3360702 AACCTTATAT
*
3360712 GGCACTTCGGTG-AATTTCTACGC
1 GGCACTACGGTGCAA-TTCTACGC
3360735 GGCACTACGGTGCAATTCTAC
1 GGCACTACGGTGCAATTCTAC
3360756 ATGGCAGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:3360761 original size:23 final size:23
Alignment explanation
Indices: 3360710--3360761 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
3360700 ACAACCTTAT
*
3360710 ATGGCACTTCGGTGAATTTCTAC
1 ATGGCACTACGGTGAATTTCTAC
**
3360733 GCGGCACTACGGTGCAA-TTCTAC
1 ATGGCACTACGGTG-AATTTCTAC
3360756 ATGGCA
1 ATGGCA
3360762 GTTCAGTACA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (23 bp):
ATGGCACTACGGTGAATTTCTAC
Found at i:3362049 original size:273 final size:273
Alignment explanation
Indices: 3361562--3362106 Score: 950
Period size: 273 Copynumber: 2.0 Consensus size: 273
3361552 GCTACTATTT
3361562 TCCACCACTTGCCACCCTCAAACGAATGGTCAAACTGATATGGTGAATCGAGTACTTTCCATGTT
1 TCCACCACTTGCCACCCTCAAACGAATGGTCAAACTGATATGGTGAATCGAGTACTTTCCATGTT
* *
3361627 ACTTCTATCTATCATTCGGAAGAATTTGAAAACATGGGAGGAGAGTTTACCACATGTGGAGTTTG
66 ACTTCGATCTATCATTCGAAAGAATTTGAAAACATGGGAGGAGAGTTTACCACATGTGGAGTTTG
*
3361692 CATACAACCGTTCAATCCATACTACTACGGGGCGTACACCTTTCGAAGTGGTGTATGAGTTCAAT
131 CATACAACCGTTCAATCCATACTACTACGGGGCGTACACCTTTCAAAGTGGTGTATGAGTTCAAT
*
3361757 CCATTAACACCAATAGACTTGTTACCATTACCTGCTGATCAAATTATGAATAAAGATGGACTTAA
196 CCATTAACACCAATAGACTTGTTACCATTACCTGCTAATCAAATTATGAATAAAGATGGACTTAA
3361822 CAAAGCTGAGTTC
261 CAAAGCTGAGTTC
* * * *
3361835 TCCACCATTTTCCACCCTCAAACGGATGGTCAAACTGA-AGTGGTGAATCGAGTATTTTCCATGT
1 TCCACCACTTGCCACCCTCAAACGAATGGTCAAACTGATA-TGGTGAATCGAGTACTTTCCATGT
3361899 TACTTCGATCTATCATTCGAAAGAATTTGAGAAA-ATGGGAGGAGAGTTTACCACATGTGGAGTT
65 TACTTCGATCTATCATTCGAAAGAATTTGA-AAACATGGGAGGAGAGTTTACCACATGTGGAGTT
* *
3361963 TGCATACAACCGTTCAATCCATACTACTACGGGGCGTACGCCTTTCAAAGTGGTGTATGGGTTCA
129 TGCATACAACCGTTCAATCCATACTACTACGGGGCGTACACCTTTCAAAGTGGTGTATGAGTTCA
* *
3362028 ATCCATTAACACCGATAGACTTGTTACCATTACCTGCTAATCAAATTGTGAATAAAGATGGACTT
194 ATCCATTAACACCAATAGACTTGTTACCATTACCTGCTAATCAAATTATGAATAAAGATGGACTT
3362093 AACAAAGCTGAGTT
259 AACAAAGCTGAGTT
3362107 TGTTAAGAAG
Statistics
Matches: 258, Mismatches: 12, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
272 1 0.00
273 254 0.98
274 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (273 bp):
TCCACCACTTGCCACCCTCAAACGAATGGTCAAACTGATATGGTGAATCGAGTACTTTCCATGTT
ACTTCGATCTATCATTCGAAAGAATTTGAAAACATGGGAGGAGAGTTTACCACATGTGGAGTTTG
CATACAACCGTTCAATCCATACTACTACGGGGCGTACACCTTTCAAAGTGGTGTATGAGTTCAAT
CCATTAACACCAATAGACTTGTTACCATTACCTGCTAATCAAATTATGAATAAAGATGGACTTAA
CAAAGCTGAGTTC
Found at i:3369643 original size:14 final size:17
Alignment explanation
Indices: 3369610--3369649 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
3369600 ATCCTTTAGC
3369610 ATAGTTTGTTTATAATA
1 ATAGTTTGTTTATAATA
3369627 ATAGTTTGTTTATAATA
1 ATAGTTTGTTTATAATA
3369644 ATAGTT
1 ATAGTT
3369650 ATCAGGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (17 bp):
ATAGTTTGTTTATAATA
Found at i:3371569 original size:26 final size:26
Alignment explanation
Indices: 3371531--3371600 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
3371521 ATGATTTTAT
*
3371531 TTTAGTTATA-TTTATTTTTTTGAAGTA
1 TTTA-TTATATTTTA-TGTTTTGAAGTA
3371558 TTTATTATATTTTCATGTTTTGAAGTA
1 TTTATTATATTTT-ATGTTTTGAAGTA
* *
3371585 GTTATGATATTTTATG
1 TTTATTATATTTTATG
3371601 ATTTATCCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
26 8 0.21
27 29 0.76
28 1 0.03
ACGTcount: A:0.26, C:0.01, G:0.13, T:0.60
Consensus pattern (26 bp):
TTTATTATATTTTATGTTTTGAAGTA
Found at i:3375699 original size:12 final size:12
Alignment explanation
Indices: 3375674--3375743 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
3375664 ACGAAGATAT
* *
3375674 CAGAAATCAAAA
1 CAGAATTCAGAA
3375686 CAGAATTCAGAA
1 CAGAATTCAGAA
3375698 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
3375710 CAGAATCCAGAT
1 CAGAATTCAGAA
*
3375722 CAGAAATCAGAA
1 CAGAATTCAGAA
3375734 CAGAATTCAG
1 CAGAATTCAG
3375744 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:3375701 original size:24 final size:24
Alignment explanation
Indices: 3375674--3375766 Score: 105
Period size: 24 Copynumber: 3.9 Consensus size: 24
3375664 ACGAAGATAT
*
3375674 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * *
3375698 CAGATATCAGAACAGAATCCAGAT
1 CAGAAATCAGAACAGAATTCAGAA
**
3375722 CAGAAATCAGAACAGAATTCAGGT
1 CAGAAATCAGAACAGAATTCAGAA
***
3375746 CATTTATCAGAACAGAATTCA
1 CAGAAATCAGAACAGAATTCA
3375767 AGTCGGAAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:3375743 original size:48 final size:48
Alignment explanation
Indices: 3375672--3375763 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
3375662 AAACGAAGAT
3375672 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
* ** **
3375720 ATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAAT
3375764 TCAAGTCGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.18
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
Found at i:3375776 original size:48 final size:48
Alignment explanation
Indices: 3375672--3375776 Score: 131
Period size: 48 Copynumber: 2.2 Consensus size: 48
3375662 AAACGAAGAT
*
3375672 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCAAG
* ** **
3375720 ATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAA-TCAAG
*
3375769 -TCGGAAAT
1 ATCAGAAAT
3375777 ACAATAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
48 45 0.92
49 4 0.08
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCAAG
Found at i:3376943 original size:18 final size:18
Alignment explanation
Indices: 3376922--3376956 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3376912 TTCCATCCGG
*
3376922 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
3376940 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
3376957 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:3378299 original size:13 final size:13
Alignment explanation
Indices: 3378266--3378341 Score: 71
Period size: 13 Copynumber: 5.3 Consensus size: 13
3378256 GGTCAACGCC
*
3378266 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
3378281 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3378294 GGTCAACGGGTCGAG
1 GGTCAACGGGTC--G
3378309 TCAGGTCAACGGGTCG
1 ---GGTCAACGGGTCG
*
3378325 GGTAAACGGGTCG
1 GGTCAACGGGTCG
3378338 GGTC
1 GGTC
3378342 GGGTAAACGG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 27 0.51
15 13 0.25
16 1 0.02
18 12 0.23
ACGTcount: A:0.20, C:0.22, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3378319 original size:31 final size:30
Alignment explanation
Indices: 3378266--3378359 Score: 120
Period size: 31 Copynumber: 3.1 Consensus size: 30
3378256 GGTCAACGCC
*
3378266 GGTCAACGGGTC-A-ACGGTCAACGGGTCG
1 GGTCAACGGGTCGAGTCGGTCAACGGGTCG
3378294 GGTCAACGGGTCGAGTCAGGTCAACGGGTCG
1 GGTCAACGGGTCGAGTC-GGTCAACGGGTCG
* * *
3378325 GGTAAACGGGTCGGGTCGGGTAAACGGGTCG
1 GGTCAACGGGTCGAGTC-GGTCAACGGGTCG
3378356 GGTC
1 GGTC
3378360 GGGTTGTGAC
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 12 0.21
29 1 0.02
30 1 0.02
31 43 0.75
ACGTcount: A:0.19, C:0.21, G:0.44, T:0.16
Consensus pattern (30 bp):
GGTCAACGGGTCGAGTCGGTCAACGGGTCG
Found at i:3378323 original size:8 final size:8
Alignment explanation
Indices: 3378246--3378305 Score: 56
Period size: 8 Copynumber: 7.5 Consensus size: 8
3378236 TCAAAGTTTT
3378246 GGTCAACAG
1 GGTCAAC-G
3378255 TGGTCAACG
1 -GGTCAACG
3378264 CCGGTCAACG
1 --GGTCAACG
3378274 GGTCAAC-
1 GGTCAACG
3378281 GGTCAACG
1 GGTCAACG
3378289 GGT---CG
1 GGTCAACG
3378294 GGTCAACG
1 GGTCAACG
3378302 GGTC
1 GGTC
3378306 GAGTCAGGTC
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
5 5 0.11
7 7 0.16
8 16 0.36
9 1 0.02
10 15 0.34
ACGTcount: A:0.22, C:0.27, G:0.37, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:3378339 original size:18 final size:18
Alignment explanation
Indices: 3378318--3378363 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
3378308 GTCAGGTCAA
3378318 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
3378336 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
3378354 CGGGTCGGGT
1 CGGGTCGGGT
3378364 TGTGACCGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.13, C:0.17, G:0.52, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:3380508 original size:12 final size:12
Alignment explanation
Indices: 3380483--3380552 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
3380473 ACGAAGATAT
* *
3380483 CAGAAATCAAAA
1 CAGAATTCAGAA
3380495 CAGAATTCAGAA
1 CAGAATTCAGAA
3380507 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
3380519 TAGAATCCAGAT
1 CAGAATTCAGAA
*
3380531 CAGAAATCAGAA
1 CAGAATTCAGAA
3380543 CAGAATTCAG
1 CAGAATTCAG
3380553 GTCATTTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.51, C:0.17, G:0.16, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:3380563 original size:48 final size:47
Alignment explanation
Indices: 3380481--3380589 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 47
3380471 AAACGAAGAT
* *
3380481 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAATAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
3380528 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
3380576 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
3380590 TAAAATATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
47 1 0.02
48 51 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.19
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:3380587 original size:24 final size:25
Alignment explanation
Indices: 3380481--3380589 Score: 100
Period size: 24 Copynumber: 4.5 Consensus size: 25
3380471 AAACGAAGAT
*
3380481 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * * *
3380505 AACAGATATCAGAATAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
3380529 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
3380553 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
3380578 -TCGGAAATCAGA
1 ATCAGAAATCAGA
3380590 TAAAATATTT
Statistics
Matches: 67, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
23 2 0.03
24 61 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.19
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:3381751 original size:18 final size:18
Alignment explanation
Indices: 3381730--3381765 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3381720 CTTCCATCCG
*
3381730 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
3381748 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
3381766 GTATTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:3383100 original size:13 final size:13
Alignment explanation
Indices: 3383082--3383142 Score: 68
Period size: 13 Copynumber: 4.3 Consensus size: 13
3383072 GCCGGTCAAC
3383082 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3383095 GGTCAACGGGTCGAGTCG
1 GGTCAAC--G--G-GTCG
3383113 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
3383126 GGTAAACGGGTCG
1 GGTCAACGGGTCG
3383139 GGTC
1 GGTC
3383143 TGGTAAACGG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 26 0.63
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 11 0.27
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3383114 original size:18 final size:18
Alignment explanation
Indices: 3383091--3383125 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3383081 CGGTCAACGG
3383091 GTCGGGTCAACGGGTCGA
1 GTCGGGTCAACGGGTCGA
3383109 GTCGGGTCAACGGGTCG
1 GTCGGGTCAACGGGTCG
3383126 GGTAAACGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.17
Consensus pattern (18 bp):
GTCGGGTCAACGGGTCGA
Found at i:3383120 original size:31 final size:31
Alignment explanation
Indices: 3383082--3383160 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
3383072 GCCGGTCAAC
3383082 GGTCAACGGGTCGGGTCAACGGGTCGAGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGAGTCG
* * *
3383113 GGTCAACGGGTCGGGTAAACGGGTCGGGTCT
1 GGTCAACGGGTCGGGTCAACGGGTCGAGTCG
*
3383144 GGTAAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
3383161 GGGTTGTGAC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.16, C:0.20, G:0.46, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGAGTCG
Found at i:3383140 original size:18 final size:18
Alignment explanation
Indices: 3383119--3383164 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
3383109 GTCGGGTCAA
3383119 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
*
3383137 CGGGTCTGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
3383155 CGGGTCGGGT
1 CGGGTCGGGT
3383165 TGTGACCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.13, C:0.17, G:0.50, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:3389035 original size:48 final size:48
Alignment explanation
Indices: 3388964--3389056 Score: 177
Period size: 48 Copynumber: 1.9 Consensus size: 48
3388954 ATCAACAAGC
3388964 TTTTCAACATATGATAAATTATAGAATTACTAGAGATATTTGAGAGAG
1 TTTTCAACATATGATAAATTATAGAATTACTAGAGATATTTGAGAGAG
*
3389012 TTTTCAATATATGATAAATTATAGAATTACTAGAGATATTTGAGA
1 TTTTCAACATATGATAAATTATAGAATTACTAGAGATATTTGAGA
3389057 AAGAGATGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (48 bp):
TTTTCAACATATGATAAATTATAGAATTACTAGAGATATTTGAGAGAG
Found at i:3396792 original size:2 final size:2
Alignment explanation
Indices: 3396785--3396822 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3396775 CTCAAGAATA
3396785 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
3396823 CTCATATGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3401489 original size:14 final size:14
Alignment explanation
Indices: 3401470--3401499 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3401460 TGCTTTCTTT
3401470 CTTTTCAATTTTCA
1 CTTTTCAATTTTCA
*
3401484 CTTTTCAGTTTTCA
1 CTTTTCAATTTTCA
3401498 CT
1 CT
3401500 ATATTTGTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.23, G:0.03, T:0.57
Consensus pattern (14 bp):
CTTTTCAATTTTCA
Found at i:3402572 original size:18 final size:18
Alignment explanation
Indices: 3402551--3402597 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
3402541 AATTAATGGA
3402551 GTAAAAAAATAAAAAAAG
1 GTAAAAAAATAAAAAAAG
*
3402569 GTAAAAGAAAT-TAAAAAG
1 GTAAAA-AAATAAAAAAAG
3402587 G-AATAAAAATA
1 GTAA-AAAAATA
3402598 TTAAGTACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 6 0.24
18 15 0.60
19 4 0.16
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (18 bp):
GTAAAAAAATAAAAAAAG
Found at i:3402899 original size:23 final size:23
Alignment explanation
Indices: 3402853--3402917 Score: 51
Period size: 25 Copynumber: 2.7 Consensus size: 23
3402843 AAATTAATAC
* *
3402853 ATATATATATATATATAATGATATA
1 ATATATATA-ATAAAAAAT-ATATA
*
3402878 AGATATATATAATAAAAAATATATA
1 ATATAT--ATAATAAAAAATATATA
*
3402903 ATATAAATAA-AAAAA
1 ATATATATAATAAAAA
3402918 GAGGAATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
22 5 0.15
23 4 0.12
25 14 0.42
26 7 0.21
27 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (23 bp):
ATATATATAATAAAAAATATATA
Found at i:3402901 original size:25 final size:27
Alignment explanation
Indices: 3402853--3402903 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3402843 AAATTAATAC
* *
3402853 ATATATATATATATATAATGATATAAG
1 ATATATATATATAAAAAATGATATAAG
3402880 ATATATATA-ATAAAAAAT-ATATAA
1 ATATATATATATAAAAAATGATATAA
3402904 TATAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 7 0.32
27 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
ATATATATATATAAAAAATGATATAAG
Found at i:3402908 original size:16 final size:17
Alignment explanation
Indices: 3402863--3402909 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
3402853 ATATATATAT
* * *
3402863 ATATATAATGATATAAG
1 ATATATAATAATAAAAA
3402880 ATATAT-ATAATAAAAA
1 ATATATAATAATAAAAA
3402896 ATATATAAT-ATAAA
1 ATATATAATAATAAA
3402910 TAAAAAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 18 0.69
17 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (17 bp):
ATATATAATAATAAAAA
Found at i:3404185 original size:38 final size:36
Alignment explanation
Indices: 3404143--3404231 Score: 135
Period size: 36 Copynumber: 2.4 Consensus size: 36
3404133 TGAGGGTTTG
3404143 GTGTTTCAAGAGAAAC-ATATTCAAAGGTTTTTTTTTTT
1 GTGTTTCAAGAGAAACAAT-TTCAAAGG--TTTTTTTTT
*
3404181 GTGTTTCTAGAGAAACAATTTCAAAGGTTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTT
3404217 GTGTTTCAAGAGAAA
1 GTGTTTCAAGAGAAA
3404232 TTGTATTCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 23 0.48
38 23 0.48
39 2 0.04
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (36 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTT
Found at i:3404219 original size:36 final size:37
Alignment explanation
Indices: 3404143--3404231 Score: 137
Period size: 38 Copynumber: 2.4 Consensus size: 37
3404133 TGAGGGTTTG
3404143 GTGTTTCAAGAGAAACATATTCAAAGGTTTTTTTTTTT
1 GTGTTTCAAGAGAAACATATTCAAAGG-TTTTTTTTTT
*
3404181 GTGTTTCTAGAGAAACA-ATTTCAAAGG-TTTTTTTTT
1 GTGTTTCAAGAGAAACATA-TTCAAAGGTTTTTTTTTT
3404217 GTGTTTCAAGAGAAA
1 GTGTTTCAAGAGAAA
3404232 TTGTATTCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 23 0.48
37 1 0.02
38 24 0.50
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (37 bp):
GTGTTTCAAGAGAAACATATTCAAAGGTTTTTTTTTT
Found at i:3404517 original size:101 final size:101
Alignment explanation
Indices: 3404404--3404783 Score: 426
Period size: 101 Copynumber: 3.8 Consensus size: 101
3404394 AGGGAAATTA
* * *
3404404 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAATG-TTTTCAATGTTTATGTTTCAAGAGAAACT
1 TCTCAAGAGAGACAAAATTTATTTCAA-GGAAAAGATATTCAATGTTT-TGTTTCAAGAGAAACT
* *
3404468 CTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATT
64 GTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATG
* * * * *
3404506 TCT-AAGGGAGACGAAATTTGTTTCAAGGAAAAGATATTCAAATATTTTGTTTCAAGGGAAACTG
1 TCTCAAGAGAGACAAAATTTATTTCAAGGAAAAGATATTC-AATGTTTTGTTTCAAGAGAAACTG
*
3404570 TCTCAAGAGAGACAAAACTT-G--------GAAACTG
65 TCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATG
* * *
3404598 TCTCAAGAGAGACAAAATTAATTTCAAGGGAAATG-TTTTCAATGTTTATGTTTCAAGAGAAACT
1 TCTCAAGAGAGACAAAATTTATTTCAA-GGAAAAGATATTCAATGTTT-TGTTTCAAGAGAAACT
* *
3404662 ATCTCAAGAGAGACGAAACTTAGTTCCAAAAGAAAATG
64 GTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATG
* * * * *
3404700 TCTCAAGGGAGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGATTTTGTTTCAAG-GGAACTG
1 TCTCAAGAGAGACAAAATTTATTTCAAGGAAAAGATATTCAATG-TTTTGTTTCAAGAGAAACTG
3404764 TCTCAAGAGAGACAAAACTT
65 TCTCAAGAGAGACAAAACTT
3404784 GGAAACTGTC
Statistics
Matches: 230, Mismatches: 32, Indels: 33
0.78 0.11 0.11
Matches are distributed among these distances:
92 14 0.06
93 57 0.25
94 7 0.03
100 7 0.03
101 88 0.38
102 54 0.23
103 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (101 bp):
TCTCAAGAGAGACAAAATTTATTTCAAGGAAAAGATATTCAATGTTTTGTTTCAAGAGAAACTGT
CTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATG
Found at i:3404712 original size:102 final size:101
Alignment explanation
Indices: 3404591--3404783 Score: 246
Period size: 102 Copynumber: 1.9 Consensus size: 101
3404581 ACAAAACTTG
* * * *
3404591 GAAACTGTCTCAAGAGAGACAAAATTAATTTCAAGGGAAATG-TTTTCAATG-TTTATGTTTCAA
1 GAAAATGTCTCAAGAGAGACAAAATTAATTTCAA-GGAAAAGATATTCAAAGATTT-TGTTTCAA
*
3404654 GAGAAACTATCTCAAGAGAGACGAAACTTAGTTCCAAAA
64 G-GAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAA
* * **
3404693 GAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGATTTTGTTTCAAGG
1 GAAAATGTCTCAAGAGAGACAAAATTAATTTCAAGGAAAAGATATTCAAAGATTTTGTTTCAAGG
* *
3404758 GAACTGTCTCAAGAGAGACAAAACTT
66 AAACTATCTCAAGAGAGACAAAACTT
3404784 GGAAACTGTC
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
101 30 0.38
102 45 0.58
103 3 0.04
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (101 bp):
GAAAATGTCTCAAGAGAGACAAAATTAATTTCAAGGAAAAGATATTCAAAGATTTTGTTTCAAGG
AAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAA
Found at i:3404765 original size:194 final size:194
Alignment explanation
Indices: 3404404--3404806 Score: 745
Period size: 194 Copynumber: 2.1 Consensus size: 194
3404394 AGGGAAATTA
* *
3404404 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTC
1 TCTCAAGAGAGACAAAATTAATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTA
*
3404469 TCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATTTCTAAGGGAGACGAAATTTGTTTCAAGG
66 TCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTAAGGGAGACGAAATTTGTTTCAAGG
*
3404534 AAAAGATATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTGGAAACTG
131 AAAAGATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTGGAAACTG
3404598 TCTCAAGAGAGACAAAATTAATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTA
1 TCTCAAGAGAGACAAAATTAATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTA
*
3404663 TCTCAAGAGAGACGAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAG
66 TCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCT-AAGGGAGACGAAATTTGTTTCAAG
3404728 GAAAAGATATTCAAAGATTTTGTTTCAAGGG-AACTGTCTCAAGAGAGACAAAACTTGGAAACTG
130 GAAAAGATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTGGAAACTG
3404792 TCTCAAGAGAGACAA
1 TCTCAAGAGAGACAA
3404807 TGATGAGTAT
Statistics
Matches: 203, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
194 149 0.73
195 54 0.27
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (194 bp):
TCTCAAGAGAGACAAAATTAATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTA
TCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTAAGGGAGACGAAATTTGTTTCAAGG
AAAAGATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTGGAAACTG
Found at i:3405124 original size:106 final size:106
Alignment explanation
Indices: 3404931--3405192 Score: 398
Period size: 106 Copynumber: 2.5 Consensus size: 106
3404921 GTATTGTTTT
* * * *
3404931 GAGTCCAATATCCTTCATCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTATGAAACTGGGAAATTATTTGTTGACAA
* *
3404996 CCATCCGTCCCTTCGCTATGAAGTTGAACTTGTGTTGTCTC
66 CCAGCCGTCCCTTCACTATGAAGTTGAACTTGTGTTGTCTC
* *
3405037 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTTTGAAACTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTATGAAACTGGGAAATTATTTGTTGACAA
* * *
3405102 CCAGCTGTCCCTTCACTGTGAAGTTGAACTTGTGTTGTTTC
66 CCAGCCGTCCCTTCACTATGAAGTTGAACTTGTGTTGTCTC
* * *
3405143 GAGTCCAATATTCTTCACTGTGAAGTTGAAATTGGCTATGAAATTGGGAA
1 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTATGAAACTGGGAA
3405193 GCCCCTTCGT
Statistics
Matches: 141, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 141 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTATGAAACTGGGAAATTATTTGTTGACAA
CCAGCCGTCCCTTCACTATGAAGTTGAACTTGTGTTGTCTC
Found at i:3406446 original size:25 final size:27
Alignment explanation
Indices: 3406399--3406448 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
3406389 TTAATACATC
* *
3406399 TATATATATATATATAATGATATAAGA
1 TATATATATATATAAAATAATATAAGA
3406426 TATATATA-ATA-AAAATAATATAA
1 TATATATATATATAAAATAATATAA
3406449 TATAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 3 0.14
27 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (27 bp):
TATATATATATATAAAATAATATAAGA
Found at i:3412125 original size:44 final size:44
Alignment explanation
Indices: 3412054--3412313 Score: 344
Period size: 44 Copynumber: 5.9 Consensus size: 44
3412044 CCATAAGTGG
* * *
3412054 CACCTTTTATGCCAATAATGAACCGTTATGCATTTTCATTTTTGA
1 CACC-TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
* * * *
3412099 CATCTTTCTACCAAAAATGCACCGTTATGCATTTTCATTTATGG
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
*
3412143 CACCTTTCTGCCAATAATGCACTGTTATGCATTTTCATTTATGGA
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT-GA
* *
3412188 -ACCTTT-TACCAATAATGCACCGTTATGAATTTTCATTTATGA
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
* * * *
3412230 CACCTTTTTGCCAATAATGCACTGATATGCATTTTCATTTATGG
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
* *
3412274 CACCTTTTTGCCAATAATGCACAGTTATGCATTTTCATTT
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTT
3412314 TTTTCAGAAA
Statistics
Matches: 190, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
42 2 0.01
43 37 0.19
44 147 0.77
45 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.41
Consensus pattern (44 bp):
CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
Found at i:3412211 original size:131 final size:132
Alignment explanation
Indices: 3412055--3412313 Score: 403
Period size: 131 Copynumber: 2.0 Consensus size: 132
3412045 CATAAGTGGC
* * *
3412055 ACCTTTTATGCCAATAATGAACCGTTATGCATTTTCATTTTTGACATCTTTCTACCAAAAATGCA
1 ACCTTTTA-GCCAATAATGAACCGTTATGAATTTTCATTTATGACACCTTTCTACCAAAAATGCA
* *
3412120 CCGTTATGCATTTTCATTTATGGCACCTTTCTGCCAATAATGCACTGTTATGCATTTTCATTTAT
65 CCGATATGCATTTTCATTTATGGCACCTTTCTGCCAATAATGCACAGTTATGCATTTTCATTTAT
3412185 GGA
130 GGA
* * * *
3412188 ACCTTTTA-CCAATAATGCACCGTTATGAATTTTCATTTATGACACCTTTTTGCCAATAATGCAC
1 ACCTTTTAGCCAATAATGAACCGTTATGAATTTTCATTTATGACACCTTTCTACCAAAAATGCAC
* *
3412252 TGATATGCATTTTCATTTATGGCACCTTTTTGCCAATAATGCACAGTTATGCATTTTCATTT
66 CGATATGCATTTTCATTTATGGCACCTTTCTGCCAATAATGCACAGTTATGCATTTTCATTT
3412314 TTTTCAGAAA
Statistics
Matches: 115, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
131 107 0.93
133 8 0.07
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.41
Consensus pattern (132 bp):
ACCTTTTAGCCAATAATGAACCGTTATGAATTTTCATTTATGACACCTTTCTACCAAAAATGCAC
CGATATGCATTTTCATTTATGGCACCTTTCTGCCAATAATGCACAGTTATGCATTTTCATTTATG
GA
Found at i:3412223 original size:87 final size:87
Alignment explanation
Indices: 3412051--3412313 Score: 366
Period size: 87 Copynumber: 3.0 Consensus size: 87
3412041 ATACCATAAG
* * * * *
3412051 TGGCACCTTTTATGCCAATAATGAACCGTTATGCATTTTCATTT-TTGACATCTTTCTACCAAAA
1 TGGCACC-TTTATGCCAATAATGCACTGTTATGCATTTTCATTTATGGA-ACCTTT-TACCAATA
3412115 ATGCACCGTTATGCATTTTCATTTA
63 ATGCACCGTTATGCATTTTCATTTA
*
3412140 TGGCACCTTTCTGCCAATAATGCACTGTTATGCATTTTCATTTATGGAACCTTTTACCAATAATG
1 TGGCACCTTTATGCCAATAATGCACTGTTATGCATTTTCATTTATGGAACCTTTTACCAATAATG
*
3412205 CACCGTTATGAATTTTCATTTA
66 CACCGTTATGCATTTTCATTTA
* * * * *
3412227 TGACACCTTTTTGCCAATAATGCACTGATATGCATTTTCATTTATGGCACCTTTTTGCCAATAAT
1 TGGCACCTTTATGCCAATAATGCACTGTTATGCATTTTCATTTATGGAACC-TTTTACCAATAAT
*
3412292 GCACAGTTATGCATTTTCATTT
65 GCACCGTTATGCATTTTCATTT
3412314 TTTTCAGAAA
Statistics
Matches: 158, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
87 78 0.49
88 70 0.44
89 10 0.06
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (87 bp):
TGGCACCTTTATGCCAATAATGCACTGTTATGCATTTTCATTTATGGAACCTTTTACCAATAATG
CACCGTTATGCATTTTCATTTA
Found at i:3420005 original size:16 final size:17
Alignment explanation
Indices: 3419984--3420022 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3419974 TCTTTCATTG
3419984 AAAAAAA-ACAAAAGAA
1 AAAAAAAGACAAAAGAA
*
3420000 AAAAAAAGAGAAAAGAA
1 AAAAAAAGACAAAAGAA
3420017 AAAAAA
1 AAAAAA
3420023 GAAAAATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAAAAAGACAAAAGAA
Found at i:3420023 original size:16 final size:16
Alignment explanation
Indices: 3419984--3420028 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
3419974 TCTTTCATTG
*
3419984 AAAAAAAA-CAAAAGA
1 AAAAAAAAGAAAAAGA
3419999 AAAAAAAAGAGAAAAG-
1 AAAAAAAAGA-AAAAGA
3420015 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
3420029 TTGTGCAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 12 0.44
16 10 0.37
17 5 0.19
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAAGA
Found at i:3426482 original size:44 final size:44
Alignment explanation
Indices: 3426420--3426685 Score: 363
Period size: 44 Copynumber: 6.0 Consensus size: 44
3426410 ATACCATAAG
* * *
3426420 TGGCACCTTTTATACCAATAATGC-CCTGTTATGCATTTTCATTTT
1 TGGCACC-TTTCTGCCAATAATGCACC-GTTATGCATTTTCATTTA
* *
3426465 TGGCACCTTTCTGCCAATAATGCACCATTATGAATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
3426509 TGGCACATTTCTTCCAATAATGCACCGTTATGCATTTTTATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
3426553 TGGCACCTTTCTGCCAATAATGCACCGTTACGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
3426597 TGACACATTTCTACCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
** * *
3426641 TGAAACCTTTATGTCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
3426685 T
1 T
3426686 TTTGGTAACA
Statistics
Matches: 197, Mismatches: 23, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
44 188 0.95
45 9 0.05
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:3433777 original size:20 final size:20
Alignment explanation
Indices: 3433752--3433794 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
3433742 TGTAGAGGAA
3433752 TAATAAAAAGGAATTGAAAC
1 TAATAAAAAGGAATTGAAAC
*
3433772 TAATAAGAAGGAATTGAAAC
1 TAATAAAAAGGAATTGAAAC
3433792 TAA
1 TAA
3433795 ACTAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.21
Consensus pattern (20 bp):
TAATAAAAAGGAATTGAAAC
Found at i:3435913 original size:34 final size:35
Alignment explanation
Indices: 3435870--3435938 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
3435860 GAAAACAAGT
3435870 TTGAAAAATTACT-CCCCTTACTCTAACACTTCTC
1 TTGAAAAATTACTCCCCCTTACTCTAACACTTCTC
3435904 TTGAAAAATTACTCCCCCTTACTCTAACACTTCTC
1 TTGAAAAATTACTCCCCCTTACTCTAACACTTCTC
3435939 CCCCTTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 13 0.38
35 21 0.62
ACGTcount: A:0.29, C:0.33, G:0.03, T:0.35
Consensus pattern (35 bp):
TTGAAAAATTACTCCCCCTTACTCTAACACTTCTC
Found at i:3438137 original size:22 final size:22
Alignment explanation
Indices: 3438069--3438151 Score: 96
Period size: 23 Copynumber: 3.8 Consensus size: 22
3438059 CAGAAGCTCC
* *
3438069 AGGGGGTATCGATTCCCCTAC-
1 AGGGGGAATCGATTCCCCTTCA
* *
3438090 AGGGGGAATTGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTTC-A
*
3438113 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
*
3438135 AGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
3438152 TCTGCACCAA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 17 0.32
22 16 0.30
23 20 0.38
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.24
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:3442001 original size:22 final size:21
Alignment explanation
Indices: 3441959--3441998 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3441949 GAGATTATTT
*
3441959 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
3441980 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3441999 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:3446525 original size:30 final size:30
Alignment explanation
Indices: 3446472--3446530 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
3446462 ATTTTAGTTA
* *
3446472 GTGACTAAAATGTAAATTTTG-AAAGTTTG
1 GTGACTAAAATGAAAATTATGAAAAGTTTG
*
3446501 GTGACTAAAGTAGAAAATTATGAAAAGTTT
1 GTGACTAAAAT-GAAAATTATGAAAAGTTT
3446531 AGGGTTCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.40
30 8 0.32
31 7 0.28
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.34
Consensus pattern (30 bp):
GTGACTAAAATGAAAATTATGAAAAGTTTG
Found at i:3449333 original size:61 final size:60
Alignment explanation
Indices: 3449235--3449393 Score: 221
Period size: 61 Copynumber: 2.6 Consensus size: 60
3449225 GTGTTAGGAC
* *
3449235 ACTTAGTGCAGGTGGTGGGCACGACCATATGTATCATATTTGGATCAGCACTAGAGTGT-T
1 ACTTAGTGCAGGTGGTGGG-ACGACCTTATGTATCATATCTGGATCAGCACTAGAGTGTAT
* * *
3449295 AACTTAGTGCAGGTGGTGGGTACAACCTTATGTGTCATATCTGGATTAGCACTAGAGTGTAT
1 -ACTTAGTGCAGGTGGTGGG-ACGACCTTATGTATCATATCTGGATCAGCACTAGAGTGTAT
* *
3449357 ACTTAGTGCAGGTGGTGGGATGACCTTATGTCTCATA
1 ACTTAGTGCAGGTGGTGGGACGACCTTATGTATCATA
3449394 GCACTACGGT
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
60 15 0.17
61 72 0.82
62 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (60 bp):
ACTTAGTGCAGGTGGTGGGACGACCTTATGTATCATATCTGGATCAGCACTAGAGTGTAT
Found at i:3451885 original size:10 final size:9
Alignment explanation
Indices: 3451867--3451914 Score: 60
Period size: 9 Copynumber: 5.1 Consensus size: 9
3451857 TGCTGGAAAT
3451867 CGGTTTGAC
1 CGGTTTGAC
3451876 CGGTTTTGAC
1 CGG-TTTGAC
*
3451886 CGGTCTGAAC
1 CGGTTTG-AC
3451896 CGGTTTGAC
1 CGGTTTGAC
*
3451905 CGGTCTGAC
1 CGGTTTGAC
3451914 C
1 C
3451915 CGACCCGACC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 17 0.50
10 17 0.50
ACGTcount: A:0.12, C:0.27, G:0.31, T:0.29
Consensus pattern (9 bp):
CGGTTTGAC
Found at i:3451902 original size:19 final size:20
Alignment explanation
Indices: 3451874--3451912 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
3451864 AATCGGTTTG
3451874 ACCGGTTTTGACCGGTCTGA
1 ACCGGTTTTGACCGGTCTGA
3451894 ACCGG-TTTGACCGGTCTGA
1 ACCGGTTTTGACCGGTCTGA
3451913 CCCGACCCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.15, C:0.26, G:0.31, T:0.28
Consensus pattern (20 bp):
ACCGGTTTTGACCGGTCTGA
Found at i:3451921 original size:5 final size:5
Alignment explanation
Indices: 3451911--3451957 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
3451901 TGACCGGTCT
* *
3451911 GACCC GACCC GACCC GA-CC AACCC GACCC GA-CC GACCC TACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC
3451958 GTTGACCGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 7 0.19
5 29 0.81
ACGTcount: A:0.23, C:0.57, G:0.17, T:0.02
Consensus pattern (5 bp):
GACCC
Found at i:3451924 original size:19 final size:19
Alignment explanation
Indices: 3451912--3451957 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3451902 GACCGGTCTG
*
3451912 ACCCGACCCGACCCGACCA
1 ACCCGACCCGACCGGACCA
*
3451931 ACCCGACCCGACC-GACCCT
1 ACCCGACCCGACCGGA-CCA
3451950 ACCCGACC
1 ACCCGACC
3451958 GTTGACCGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 2 0.08
19 23 0.92
ACGTcount: A:0.24, C:0.59, G:0.15, T:0.02
Consensus pattern (19 bp):
ACCCGACCCGACCGGACCA
Found at i:3451958 original size:14 final size:14
Alignment explanation
Indices: 3451914--3451958 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
3451904 CCGGTCTGAC
3451914 CCGACCCGACCCGA
1 CCGACCCGACCCGA
*
3451928 CCAACCCGACCCGA
1 CCGACCCGACCCGA
*
3451942 CCGACCCTACCCGA
1 CCGACCCGACCCGA
3451956 CCG
1 CCG
3451959 TTGACCGTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.22, C:0.58, G:0.18, T:0.02
Consensus pattern (14 bp):
CCGACCCGACCCGA
Found at i:3459184 original size:10 final size:10
Alignment explanation
Indices: 3459163--3459242 Score: 58
Period size: 10 Copynumber: 8.2 Consensus size: 10
3459153 CGTTTGACCA
3459163 GTTTTCAACCG
1 GTTTT-AACCG
3459174 GTTTTAACCG
1 GTTTTAACCG
* *
3459184 GTTTGAA-CT
1 GTTTTAACCG
*
3459193 GTTTTGACCG
1 GTTTTAACCG
* *
3459203 GTCTGAACC-
1 GTTTTAACCG
*
3459212 GTTTTGACCG
1 GTTTTAACCG
* *
3459222 GTCTGAACCG
1 GTTTTAACCG
3459232 G-TTTAACCG
1 GTTTTAACCG
3459241 GT
1 GT
3459243 CTGACCCGAC
Statistics
Matches: 50, Mismatches: 16, Indels: 7
0.68 0.22 0.10
Matches are distributed among these distances:
9 19 0.38
10 26 0.52
11 5 0.10
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (10 bp):
GTTTTAACCG
Found at i:3459202 original size:19 final size:19
Alignment explanation
Indices: 3459169--3459246 Score: 102
Period size: 19 Copynumber: 4.1 Consensus size: 19
3459159 ACCAGTTTTC
* *
3459169 AACCGGTTTTAACCGGTTTG
1 AACC-GTTTTGACCGGTCTG
*
3459189 AACTGTTTTGACCGGTCTG
1 AACCGTTTTGACCGGTCTG
3459208 AACCGTTTTGACCGGTCTG
1 AACCGTTTTGACCGGTCTG
* *
3459227 AACCGGTTTAACCGGTCTG
1 AACCGTTTTGACCGGTCTG
3459246 A
1 A
3459247 CCCGACCCGA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 49 0.94
20 3 0.06
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (19 bp):
AACCGTTTTGACCGGTCTG
Found at i:3459267 original size:4 final size:5
Alignment explanation
Indices: 3459245--3459277 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
3459235 TAACCGGTCT
*
3459245 GACCC GACCC GACCC GA-CC GACCC AACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACC
3459278 GTTGACTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.24, C:0.58, G:0.18, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:3459267 original size:14 final size:14
Alignment explanation
Indices: 3459248--3459278 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3459238 CCGGTCTGAC
*
3459248 CCGACCCGACCCGA
1 CCGACCCAACCCGA
3459262 CCGACCCAACCCGA
1 CCGACCCAACCCGA
3459276 CCG
1 CCG
3459279 TTGACTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (14 bp):
CCGACCCAACCCGA
Found at i:3461555 original size:14 final size:14
Alignment explanation
Indices: 3461536--3461573 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
3461526 CTACACTTGG
3461536 TGGTTAGATACTGT
1 TGGTTAGATACTGT
3461550 TGGTTAGATACTGT
1 TGGTTAGATACTGT
3461564 TGGTTAGATA
1 TGGTTAGATA
3461574 TCTCGGTTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.24, C:0.05, G:0.29, T:0.42
Consensus pattern (14 bp):
TGGTTAGATACTGT
Found at i:3462953 original size:54 final size:54
Alignment explanation
Indices: 3462864--3463337 Score: 578
Period size: 54 Copynumber: 8.8 Consensus size: 54
3462854 TGGATACTAT
* * * * * * *
3462864 AACTTATTATAAATTCCTTAGTTTTGCACATATAGTGTCGATATAGTAATTCACA
1 AACTAATTATGAATTACTTAG-GTTGCACACATAGTGTCAATACAGTAATTCACA
* *
3462919 AACTCATTATGAATTACGTAGGTTGCACACATAGTGTCAATACAGTAATTCACA
1 AACTAATTATGAATTACTTAGGTTGCACACATAGTGTCAATACAGTAATTCACA
* * * * * * * * *
3462973 AATTCATTATGAATTACGTGGGTTTCATACATAGTGCCAATACGGTAATTCATA
1 AACTAATTATGAATTACTTAGGTTGCACACATAGTGTCAATACAGTAATTCACA
* *
3463027 AACTAATTATGAATTACTTAGGTTGAACACATAGTGTCAATACAATAATTCACA
1 AACTAATTATGAATTACTTAGGTTGCACACATAGTGTCAATACAGTAATTCACA
*
3463081 AACTAATTATGAATTACTTAGGTTGCACACATAGTGTCAATACGGTAATTCACA
1 AACTAATTATGAATTACTTAGGTTGCACACATAGTGTCAATACAGTAATTCACA
* *
3463135 AACTAATTATGAATTATTTAGGTTGCACACATAGT-TCCAATACGGTAATTCACA
1 AACTAATTATGAATTACTTAGGTTGCACACATAGTGT-CAATACAGTAATTCACA
* * *
3463189 AACTCATTATGAATTACGTGGGTTGCACACATAGTG-CAAATAC-GATAATTCACA
1 AACTAATTATGAATTACTTAGGTTGCACACATAGTGTC-AATACAG-TAATTCACA
* * * *
3463243 AACTAATTATAAATTACATAGGTTGCACACA-AGTGCCAATACGGTAATTCACA
1 AACTAATTATGAATTACTTAGGTTGCACACATAGTGTCAATACAGTAATTCACA
* * * *
3463296 AACTAGTTATGAACTACTTAGGTTGCACAGATAGTGCCAATA
1 AACTAATTATGAATTACTTAGGTTGCACACATAGTGTCAATA
3463338 TGGTAATTGT
Statistics
Matches: 369, Mismatches: 43, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
53 47 0.13
54 305 0.83
55 17 0.05
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (54 bp):
AACTAATTATGAATTACTTAGGTTGCACACATAGTGTCAATACAGTAATTCACA
Found at i:3465310 original size:47 final size:45
Alignment explanation
Indices: 3465235--3465360 Score: 139
Period size: 47 Copynumber: 2.8 Consensus size: 45
3465225 TATAAAATCT
*
3465235 CTTACCATTTATCCCATAAGCT-ATTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCA-TAAGCTTATTTTACCAAAATA
* * * *
3465280 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
* **
3465327 CTTGCCA-TTATTCTGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCATAAGCTTATTT
3465361 GCATGGTTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
44 22 0.32
45 10 0.14
46 2 0.03
47 35 0.51
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.41
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
Found at i:3469301 original size:18 final size:17
Alignment explanation
Indices: 3469278--3469366 Score: 83
Period size: 18 Copynumber: 5.0 Consensus size: 17
3469268 TTTAGTCTCG
3469278 CATTTTTTTTTCATTTCT
1 CATTTTTTTTTCATTT-T
*
3469296 CATTTTTTTCTC-TATTT
1 CATTTTTTTTTCAT-TTT
*
3469313 C-TTTTCTTTCTCATTTT
1 CATTTT-TTTTTCATTTT
*
3469330 CATTTTTTTCTTCGTTTT
1 CATTTTTTT-TTCATTTT
3469348 CATTTTCTTTTTCTATTTT
1 CATTTT-TTTTTC-ATTTT
3469367 TTTATAATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
16 4 0.07
17 16 0.27
18 33 0.55
19 7 0.12
ACGTcount: A:0.09, C:0.18, G:0.01, T:0.72
Consensus pattern (17 bp):
CATTTTTTTTTCATTTT
Found at i:3469303 original size:16 final size:15
Alignment explanation
Indices: 3469282--3469329 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
3469272 GTCTCGCATT
3469282 TTTTTTTCATTTCTCA
1 TTTTTTTC-TTTCTCA
3469298 TTTTTTTC--TCT-A
1 TTTTTTTCTTTCTCA
3469310 TTTCTTTTCTTTCTCA
1 TTT-TTTTCTTTCTCA
3469326 TTTT
1 TTTT
3469330 CATTTTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.14
13 8 0.29
15 4 0.14
16 12 0.43
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTTTCTTTCTCA
Found at i:3469303 original size:17 final size:17
Alignment explanation
Indices: 3469281--3469338 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
3469271 AGTCTCGCAT
3469281 TTTTTTTTCATTTCTCA
1 TTTTTTTTCATTTCTCA
3469298 TTTTTTTCTCTATTTCT--
1 TTTTTTT-TC-ATTTCTCA
*
3469315 TTTCTTTCTCATTT-TCA
1 TTT-TTTTTCATTTCTCA
3469332 TTTTTTT
1 TTTTTTT
3469339 CTTCGTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
15 1 0.03
16 7 0.21
17 15 0.44
18 5 0.15
19 6 0.18
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTTTCATTTCTCA
Found at i:3469339 original size:17 final size:17
Alignment explanation
Indices: 3469278--3469353 Score: 84
Period size: 18 Copynumber: 4.4 Consensus size: 17
3469268 TTTAGTCTCG
*
3469278 CATTTTTTTTTCATTTCT
1 CATTTTTTTCTCATTT-T
3469296 CATTTTTTTCTC-TATTT
1 CATTTTTTTCTCAT-TTT
3469313 C-TTTTCTTTCTCATTTT
1 CATTTT-TTTCTCATTTT
*
3469330 CATTTTTTTCTTCGTTTT
1 CATTTTTTTC-TCATTTT
3469348 CATTTT
1 CATTTT
3469354 CTTTTTCTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
16 4 0.08
17 17 0.33
18 30 0.59
ACGTcount: A:0.09, C:0.18, G:0.01, T:0.71
Consensus pattern (17 bp):
CATTTTTTTCTCATTTT
Found at i:3482890 original size:47 final size:44
Alignment explanation
Indices: 3482824--3482949 Score: 153
Period size: 47 Copynumber: 2.8 Consensus size: 44
3482814 TATAAAATCT
*
3482824 CTTACCACTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
3482869 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCA-TT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
3482916 CTTGCCATTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTATTCCATAAGCTCGTAAGCTTATTT
3482950 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 23 0.32
45 9 0.13
46 2 0.03
47 37 0.52
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (44 bp):
CTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:3488380 original size:26 final size:26
Alignment explanation
Indices: 3488351--3488410 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
3488341 AAATGGATAC
3488351 AAATCTATGTAACGACATAACCGGGA
1 AAATCTATGTAACGACATAACCGGGA
3488377 AAATCTATGTAACGACATAACCGGGA
1 AAATCTATGTAACGACATAACCGGGA
3488403 AAATCTAT
1 AAATCTAT
3488411 AACAATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (26 bp):
AAATCTATGTAACGACATAACCGGGA
Found at i:3505330 original size:16 final size:15
Alignment explanation
Indices: 3505309--3505381 Score: 83
Period size: 16 Copynumber: 4.7 Consensus size: 15
3505299 AAGAAAAAAT
*
3505309 AAAAAAGAATAAGAA
1 AAAAAAAAATAAGAA
3505324 AAAAAAAGAATAAGAA
1 AAAAAAA-AATAAGAA
*
3505340 AATAAGAAAATAAGAA
1 AA-AAAAAAATAAGAA
*
3505356 AAAGAAAAATAATGAA
1 AAAAAAAAATAA-GAA
*
3505372 AAAATAAAAT
1 AAAAAAAAAT
3505382 TGAAAAGGGA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
15 14 0.29
16 31 0.63
17 4 0.08
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (15 bp):
AAAAAAAAATAAGAA
Found at i:3505345 original size:8 final size:8
Alignment explanation
Indices: 3505316--3505357 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
3505306 AATAAAAAAG
3505316 AATAAGAA
1 AATAAGAA
*
3505324 AA-AAAAA
1 AATAAGAA
3505331 GAATAAGAA
1 -AATAAGAA
3505340 AATAAGAA
1 AATAAGAA
3505348 AATAAGAA
1 AATAAGAA
3505356 AA
1 AA
3505358 AGAAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 4 0.13
8 22 0.73
9 4 0.13
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (8 bp):
AATAAGAA
Found at i:3505376 original size:34 final size:33
Alignment explanation
Indices: 3505301--3505380 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
3505291 CTCTGTTAAA
3505301 GAAAAAATAAAAAAGAATAAGAAAAAAAAAGAAT
1 GAAAAAAT-AAAAAGAATAAGAAAAAAAAAGAAT
* *
3505335 -AAGAAAATAAGAA-AATAAGAAAAAGAAAAATAAT
1 GAA-AAAATAAAAAGAATAAG-AAAA-AAAAAGAAT
3505369 GAAAAAATAAAA
1 GAAAAAATAAAA
3505381 TTGAAAAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
32 6 0.15
33 10 0.26
34 21 0.54
35 2 0.05
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (33 bp):
GAAAAAATAAAAAGAATAAGAAAAAAAAAGAAT
Found at i:3505380 original size:22 final size:20
Alignment explanation
Indices: 3505299--3505380 Score: 65
Period size: 23 Copynumber: 3.6 Consensus size: 20
3505289 ATCTCTGTTA
* *
3505299 AAGAAAAAATAAAAAAGAAT
1 AAGAAAAAAAAAAAAAAAAT
3505319 AAGAAAAAAAAAGAATAAGAAAAT
1 AAG-AAAAAAAA-AA-AA-AAAAT
3505343 AAGAAAATAAGAAAAAGAAAAAT
1 AAGAAAA-AA-AAAAA-AAAAAT
3505366 AATGAAAAAATAAAA
1 AA-GAAAAAA-AAAA
3505381 TTGAAAAGGG
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
20 3 0.06
21 7 0.14
22 2 0.04
23 20 0.39
24 17 0.33
25 2 0.04
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (20 bp):
AAGAAAAAAAAAAAAAAAAT
Found at i:3507008 original size:87 final size:88
Alignment explanation
Indices: 3506889--3507051 Score: 195
Period size: 87 Copynumber: 1.9 Consensus size: 88
3506879 CTTCAACTTT
* *** ***
3506889 TTGCATGATTCTATCACAGAAAGAGATAGATCAGCATTGACATTTTGTTTGATTCTTCAAAGAAG
1 TTGCATGATTCTATCACAGAAAGAGATAGATCAACAACAACATTTCACTTGATTCTTCAAAGAAG
3506954 GAGTTGGATCAACATTTGTTATG
66 GAGTTGGATCAACATTTGTTATG
* * * * *
3506977 TTGCTTGATTCT-TCACA-AAAGGAGTTGGATCAACAACAACCTTTCACTTGATTCTTCACAGAA
1 TTGCATGATTCTATCACAGAAA-GAGATAGATCAACAACAACATTTCACTTGATTCTTCAAAGAA
3507040 GGAGTTGGATCA
65 GGAGTTGGATCA
3507052 GTAAAAATCT
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
86 3 0.05
87 48 0.77
88 11 0.18
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (88 bp):
TTGCATGATTCTATCACAGAAAGAGATAGATCAACAACAACATTTCACTTGATTCTTCAAAGAAG
GAGTTGGATCAACATTTGTTATG
Found at i:3507075 original size:43 final size:43
Alignment explanation
Indices: 3506977--3507129 Score: 155
Period size: 43 Copynumber: 3.6 Consensus size: 43
3506967 ATTTGTTATG
* ** *
3506977 TTGCTTGATTCTTCACAAAAGGAGTTGGATCAACAACAACCTT
1 TTGCTTGATTCTTCACAGAAGGAGTTGGATCAGTAACAATCTT
** *
3507020 TCACTTGATTCTTCACAGAAGGAGTTGGATCAGTAAAAATCTT
1 TTGCTTGATTCTTCACAGAAGGAGTTGGATCAGTAACAATCTT
* * * ** *
3507063 TTGCTTGGTTCTTCACAG-ATGAGTTGAATCAGTGTCAATCTA
1 TTGCTTGATTCTTCACAGAAGGAGTTGGATCAGTAACAATCTT
* * *
3507105 GTGCTTGTTTCTTCACAGAATGAGT
1 TTGCTTGATTCTTCACAGAAGGAGT
3507130 CGAAACAACA
Statistics
Matches: 91, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 34 0.37
43 57 0.63
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (43 bp):
TTGCTTGATTCTTCACAGAAGGAGTTGGATCAGTAACAATCTT
Found at i:3507094 original size:42 final size:43
Alignment explanation
Indices: 3507023--3507129 Score: 126
Period size: 42 Copynumber: 2.5 Consensus size: 43
3507013 CAACCTTTCA
* * **
3507023 CTTGATTCTTCACAGAAGGAGTTGGATCAGTAAAAATCTTTTG
1 CTTGATTCTTCACAGAATGAGTTGAATCAGTAAAAATCTAGTG
* ***
3507066 CTTGGTTCTTCACAG-ATGAGTTGAATCAGTGTCAATCTAGTG
1 CTTGATTCTTCACAGAATGAGTTGAATCAGTAAAAATCTAGTG
*
3507108 CTTGTTTCTTCACAGAATGAGT
1 CTTGATTCTTCACAGAATGAGT
3507130 CGAAACAACA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 34 0.63
43 20 0.37
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (43 bp):
CTTGATTCTTCACAGAATGAGTTGAATCAGTAAAAATCTAGTG
Found at i:3507340 original size:207 final size:209
Alignment explanation
Indices: 3506981--3507508 Score: 577
Period size: 207 Copynumber: 2.5 Consensus size: 209
3506971 GTTATGTTGC
**** * * * * * * *
3506981 TTGATTCTTCACAAAAGGAGTTGGATCAACAACAACCT-TTCACTTGATTCTTCACAGAAGGAGT
1 TTGATTCTTCACAAAAGGAGTTGGATCAACATTTGCATGGT-ACTCGGTCCTTCACAGAAAGATT
* * *** * * * *
3507045 TGGATCAGTAAAAATCTTTTGCTTGGTTCTTCACAG-ATGAGTTGAATCAGTGTCAATCTAGTGC
65 TGGATCAGTAACAACCTTGCACTTGATTCTTCACAGAAGGAGTTAAATCAGCGTCAATCTAGTGC
* *
3507109 TTGTTTCTTCACAGAATGAGTCGAAACAACATCACCATGTTGCTTGATTCTAT-C-AT-ATAGAT
130 TTGTTTATTCACAGAATAAGTCGAAACAACATCACCATGTTGCTTGATTCTATACAATGATAGAT
*
3507171 CAACATTGGCATTT-T
195 CAACATCGGC-TTTAT
* * * *
3507186 TTTATTCTTCACAAAAGGAGTTGGATCAACATTTGTCATGTTACTCGGTCCTTCAGAGAAGGAAT
1 TTGATTCTTCACAAAAGGAGTTGGATCAACATTTG-CATGGTACTCGGTCCTTCACAGAAAG-AT
* *
3507251 TT-GATCAGTAGCAACCTTGCACTTGATTCTTCATAGAAGGAGTTAAATCAGCGTCAATCT-GAT
64 TTGGATCAGTAACAACCTTGCACTTGATTCTTCACAGAAGGAGTTAAATCAGCGTCAATCTAG-T
*
3507314 GCTTGTTTATTCACAGAATAAGTCGAAACAACGTCACCATGTTGCTTGATTCTATCACAGAATGA
128 GCTTGTTTATTCACAGAATAAGTCGAAACAACATCACCATGTTGCTTGATTCTAT-AC--AAT--
3507379 GATAGATCAACATCGGCTTTAT
188 GATAGATCAACATCGGCTTTAT
* * * *
3507401 TTGATTCTTCACAGAAGGAGTTGGATCAACTTTTGCATGGTACTTGGTCCTTCACTGAAAGATTT
1 TTGATTCTTCACAAAAGGAGTTGGATCAACATTTGCATGGTACTCGGTCCTTCACAGAAAGATTT
* * *
3507466 GGATCAGTAACAATCTTTCACTTGATTCTTCACATAAGGAGTT
66 GGATCAGTAACAACCTTGCACTTGATTCTTCACAGAAGGAGTT
3507509 GGATCAGTGA
Statistics
Matches: 269, Mismatches: 39, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
205 30 0.11
206 45 0.17
207 78 0.29
209 1 0.00
212 2 0.01
213 4 0.01
214 61 0.23
215 48 0.18
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (209 bp):
TTGATTCTTCACAAAAGGAGTTGGATCAACATTTGCATGGTACTCGGTCCTTCACAGAAAGATTT
GGATCAGTAACAACCTTGCACTTGATTCTTCACAGAAGGAGTTAAATCAGCGTCAATCTAGTGCT
TGTTTATTCACAGAATAAGTCGAAACAACATCACCATGTTGCTTGATTCTATACAATGATAGATC
AACATCGGCTTTAT
Found at i:3507408 original size:249 final size:250
Alignment explanation
Indices: 3506914--3507392 Score: 536
Period size: 249 Copynumber: 1.9 Consensus size: 250
3506904 ACAGAAAGAG
* *
3506914 ATAGATCAGCATTGACATTTTGTTTGATTCTTCAAAGAAGGAGTTGGATCAACATTTGTTATGTT
1 ATAGATCAACATTGACATTTTGTTTGATTCTTCAAAGAAGGAGTTGGATCAACATTTGTCATGTT
* * * * *
3506979 GCTTGATTCTTCACAAAAGGAGTTGGATCAACAACAACCTTTCACTTGATTCTTCACAGAAGGAG
66 ACTCGATCCTTCACAAAAGGAATTGGATCAACAACAACCTTGCACTTGATTCTTCACAGAAGGAG
** * ** * * * * **
3507044 TTGGATCAGTAAAAATCTTTTGCTTGGTTCTTCACAGATGAGTTGAATCAGTGTCAATCTAGTGC
131 TTAAATCAGCAAAAATCTGATGCTTGGTTATTCACAGATAAGTCGAAACAACGTCAATCTA-TGC
* * *
3507109 TTGTTTCTTCACAGAATGAGTCGAAACAACATCACCATGTTGCTTGATTCTATCAT
195 TTGATTCTTCACAGAATGAGTAGAAACAACATCACCATGTTACTTGATTCTATCAT
*
3507165 ATAGATCAACATTGGCATTTT-TTT-ATTCTTCACAA-AAGGAGTTGGATCAACATTTGTCATGT
1 ATAGATCAACATTGACATTTTGTTTGATTCTTCA-AAGAAGGAGTTGGATCAACATTTGTCATGT
* * * * ** * *
3507227 TACTCGGTCCTTCAGAGAAGGAATTTGATCAGTAGCAACCTTGCACTTGATTCTTCATAGAAGGA
65 TACTCGATCCTTCACAAAAGGAATTGGATCAACAACAACCTTGCACTTGATTCTTCACAGAAGGA
*** * *
3507292 GTTAAATCAGCGTCAATCTGATGCTTGTTTATTCACAGAATAAGTCGAAACAACGTCACCATGT-
130 GTTAAATCAGCAAAAATCTGATGCTTGGTTATTCACAG-ATAAGTCGAAACAACGTCA--ATCTA
*
3507356 TGCTTGATTCTATCACAGAATGAGATAG-ATCAACATC
192 TGCTTGATTCT-TCACAGAATGAG-TAGAAACAACATC
3507393 GGCTTTATTT
Statistics
Matches: 187, Mismatches: 35, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
249 114 0.61
250 29 0.16
251 39 0.21
252 5 0.03
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (250 bp):
ATAGATCAACATTGACATTTTGTTTGATTCTTCAAAGAAGGAGTTGGATCAACATTTGTCATGTT
ACTCGATCCTTCACAAAAGGAATTGGATCAACAACAACCTTGCACTTGATTCTTCACAGAAGGAG
TTAAATCAGCAAAAATCTGATGCTTGGTTATTCACAGATAAGTCGAAACAACGTCAATCTATGCT
TGATTCTTCACAGAATGAGTAGAAACAACATCACCATGTTACTTGATTCTATCAT
Found at i:3507548 original size:43 final size:43
Alignment explanation
Indices: 3507442--3507552 Score: 127
Period size: 43 Copynumber: 2.6 Consensus size: 43
3507432 TTTGCATGGT
* * * *
3507442 ACTTGGTCCTTCACT-GAAAGATTTGGATCAGTAACAATCTTTC
1 ACTTGGTTCTTCA-TAGAAGGAGTTGGATCAGTAACAATATTTC
* * *
3507485 ACTTGATTCTTCACATAAGGAGTTGGATCAGTGAA-AATATTTC
1 ACTTGGTTCTTCATAGAAGGAGTTGGATCAGT-AACAATATTTC
3507528 ACTTGGTTCTTCATAGAAGGAGTTG
1 ACTTGGTTCTTCATAGAAGGAGTTG
3507553 AACCAACGTC
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
43 54 0.96
44 2 0.04
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (43 bp):
ACTTGGTTCTTCATAGAAGGAGTTGGATCAGTAACAATATTTC
Found at i:3507562 original size:214 final size:207
Alignment explanation
Indices: 3507108--3507562 Score: 513
Period size: 214 Copynumber: 2.2 Consensus size: 207
3507098 CAATCTAGTG
*
3507108 CTTGTTTCTTCACAGAATGAGTCGAAACAACATCACCATGTTGCTTGATTCTATCATATAGATCA
1 CTTGTTTCTTCACAGAATGAGTCGAAACAACGTCACCATGTTGCTTGATTCTATCATATAGATCA
* * *
3507173 ACATTGGCATTTTTTTATTCTTCACAAAAGGAGTTGGATCAACATTTGTCATGTTACTCGGTCCT
66 ACATCGGCATTTTTTGATTCTTCACAAAAGGAGTTGGATCAACATTTGTCATGGTACTCGGTCCT
* * * *
3507238 TCAGAGAAGGAATTTGATCAGTAGCAACCTTGCACTTGATTCTTCATAGAAGGAGTTAAATCAGC
131 TCACAGAAAGAATTTGATCAGTAACAACCTTGCACTTGATTCTTCACAGAAGGAGTTAAATCAGC
** * *
3507303 GTCAATCTGATG
196 GAAAATATGATA
* *
3507315 CTTGTTTATTCACAGAATAAGTCGAAACAACGTCACCATGTTGCTTGATTCTATCACAGAATGAG
1 CTTGTTTCTTCACAGAATGAGTCGAAACAACGTCACCATGTTGCTTGATTCTAT--C---AT---
* *
3507380 ATAGATCAACATCGGC-TTTATTTGATTCTTCACAGAAGGAGTTGGATCAACTTTTG-CATGGTA
58 ATAGATCAACATCGGCATTT-TTTGATTCTTCACAAAAGGAGTTGGATCAACATTTGTCATGGTA
* * * * *
3507443 CTTGGTCCTTCACTGAAAG-ATTTGGATCAGTAACAATCTTTCACTTGATTCTTCACATAAGGAG
122 CTCGGTCCTTCACAGAAAGAATTT-GATCAGTAACAACCTTGCACTTGATTCTTCACAGAAGGAG
** * *
3507507 TTGGATCAGTGAAAATAT-TTCA
186 TTAAATCAGCGAAAATATGAT-A
* * * * *
3507529 CTTGGTTCTTCATAGAAGGAGTTGAACCAACGTC
1 CTTGTTTCTTCACAGAATGAGTCGAAACAACGTC
3507563 GATTTGGTGC
Statistics
Matches: 205, Mismatches: 32, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
207 51 0.25
209 1 0.00
212 2 0.01
213 5 0.02
214 98 0.48
215 48 0.23
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (207 bp):
CTTGTTTCTTCACAGAATGAGTCGAAACAACGTCACCATGTTGCTTGATTCTATCATATAGATCA
ACATCGGCATTTTTTGATTCTTCACAAAAGGAGTTGGATCAACATTTGTCATGGTACTCGGTCCT
TCACAGAAAGAATTTGATCAGTAACAACCTTGCACTTGATTCTTCACAGAAGGAGTTAAATCAGC
GAAAATATGATA
Found at i:3509916 original size:21 final size:22
Alignment explanation
Indices: 3509892--3509948 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
3509882 TAACACTAGG
3509892 TACCTAGCTAGCTAT-CTACAC
1 TACCTAGCTAGCTATACTACAC
* *
3509913 TACCTAGGTAGCT-TACTACCC
1 TACCTAGCTAGCTATACTACAC
* *
3509934 TAGCTAGCTACCTAT
1 TACCTAGCTAGCTAT
3509949 GTCACCACCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.03
21 27 0.93
22 1 0.03
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.30
Consensus pattern (22 bp):
TACCTAGCTAGCTATACTACAC
Found at i:3514902 original size:10 final size:10
Alignment explanation
Indices: 3514887--3514916 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3514877 GGACCGGTTG
3514887 AAAACCGGAA
1 AAAACCGGAA
*
3514897 AAAACCGGGA
1 AAAACCGGAA
3514907 AAAACCGGAA
1 AAAACCGGAA
3514917 TTTTTGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.20, G:0.23, T:0.00
Consensus pattern (10 bp):
AAAACCGGAA
Done.