Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 118 of 235
Found at i:40292328 original size:16 final size:16
Alignment explanation
Indices: 40292303--40292349 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
40292293 AGCTTCAAGC
*
40292303 CCCTCACTCTCTCTCT
1 CCCTCCCTCTCTCTCT
* *
40292319 CCCTCCCTCTCTTTTT
1 CCCTCCCTCTCTCTCT
*
40292335 CTCTCCCTCTCTCTC
1 CCCTCCCTCTCTCTC
40292350 CTTTCCCTCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.02, C:0.55, G:0.00, T:0.43
Consensus pattern (16 bp):
CCCTCCCTCTCTCTCT
Found at i:40292337 original size:20 final size:19
Alignment explanation
Indices: 40292314--40292364 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
40292304 CCTCACTCTC
*
40292314 TCTCTCCCTCCCTCTCTTTT
1 TCTCTCCCTCCCTCTC-CTT
*
40292334 TCTCTCCCTCTCTCTCCTT
1 TCTCTCCCTCCCTCTCCTT
*
40292353 TCCCTCCCTCCC
1 TCTCTCCCTCCC
40292365 CCCCCCACAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (19 bp):
TCTCTCCCTCCCTCTCCTT
Found at i:40292391 original size:2 final size:2
Alignment explanation
Indices: 40292386--40292417 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40292376 CACACACACA
40292386 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
40292418 TTCAGTTTTG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:40294240 original size:10 final size:10
Alignment explanation
Indices: 40294213--40294262 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
40294203 TTAAATTCTA
40294213 AAAGATAAAT
1 AAAGATAAAT
40294223 ACAA-ATAAAT
1 A-AAGATAAAT
* *
40294233 AAATATAATT
1 AAAGATAAAT
*
40294243 GAAGATAAAT
1 AAAGATAAAT
40294253 AAAGATAAAT
1 AAAGATAAAT
40294263 GCTAAAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 29 0.88
11 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:40295260 original size:76 final size:74
Alignment explanation
Indices: 40295134--40295287 Score: 227
Period size: 76 Copynumber: 2.1 Consensus size: 74
40295124 ATCAGAAACA
* * * * *
40295134 TGGTTTCGAAGCCACCAAATTCGGTGAGTAAGTTTGTAAATATTATTATTAGTTGTAACAGCCCT
1 TGGTTTCGAAGCCACCAAATCCAGCGAGTAAGTTCGTAAATATTATTATTAGTCGTAACAGCCCT
40295199 ATTTTTTTCAG
66 A--TTTTTCAG
* *
40295210 TGGTTTCGAGGCCACCAAATCCAGCGAGTAAGTTCGTAAATATTATTATTAGTCGTAACAGTCCT
1 TGGTTTCGAAGCCACCAAATCCAGCGAGTAAGTTCGTAAATATTATTATTAGTCGTAACAGCCCT
40295275 ATTTTTCAG
66 ATTTTTCAG
40295284 TGGT
1 TGGT
40295288 GTCGGAAACA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
74 12 0.17
76 59 0.83
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (74 bp):
TGGTTTCGAAGCCACCAAATCCAGCGAGTAAGTTCGTAAATATTATTATTAGTCGTAACAGCCCT
ATTTTTCAG
Found at i:40296762 original size:21 final size:21
Alignment explanation
Indices: 40296736--40296798 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
40296726 TTGGGTGGAA
*
40296736 CAGCTCTTACAAGCTTCTGTT
1 CAGCTCTTACGAGCTTCTGTT
*
40296757 CAGCTCTTACGAGCTTTTGTT
1 CAGCTCTTACGAGCTTCTGTT
*
40296778 TAGCTCTTACGAGCTTCTGTT
1 CAGCTCTTACGAGCTTCTGTT
40296799 GGCGTATTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.41
Consensus pattern (21 bp):
CAGCTCTTACGAGCTTCTGTT
Found at i:40300807 original size:80 final size:81
Alignment explanation
Indices: 40300723--40300879 Score: 271
Period size: 81 Copynumber: 2.0 Consensus size: 81
40300713 TTGATGTCTC
**
40300723 AAATCTATACCAAAAAAGGGTGAG-AGTTTTTTTTTTGAGTTCCAATGCAATGCCATAAAGAACT
1 AAATCTATACCAAAAAAGGGTGAGAACATTTTTTTTTGAGTTCCAATGCAATGCCATAAAGAACT
40300787 ACTCTTGATAATTTCT
66 ACTCTTGATAATTTCT
* *
40300803 AAATCTATATCAAAAAAGGGTGAGAACATTTTTTTTTGAGTTCTAATGCAATGCCATAAAGAACT
1 AAATCTATACCAAAAAAGGGTGAGAACATTTTTTTTTGAGTTCCAATGCAATGCCATAAAGAACT
40300868 ACTCTTGATAAT
66 ACTCTTGATAAT
40300880 GATGTTTGGA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
80 23 0.32
81 49 0.68
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (81 bp):
AAATCTATACCAAAAAAGGGTGAGAACATTTTTTTTTGAGTTCCAATGCAATGCCATAAAGAACT
ACTCTTGATAATTTCT
Found at i:40301157 original size:16 final size:16
Alignment explanation
Indices: 40301133--40301163 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40301123 TTTAATTTCA
*
40301133 TGTTTTTATTTTTTTG
1 TGTTATTATTTTTTTG
40301149 TGTTATTATTTTTTT
1 TGTTATTATTTTTTT
40301164 TAATTTGTCG
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:0.10, C:0.00, G:0.10, T:0.81
Consensus pattern (16 bp):
TGTTATTATTTTTTTG
Found at i:40301239 original size:39 final size:39
Alignment explanation
Indices: 40301196--40301277 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
40301186 TGCTATAAAT
*
40301196 ATTTTTTTATTATGAAGTAGATGTCTATTAAAATAAGAA
1 ATTTTTTTATTATGAAGTAGATGCCTATTAAAATAAGAA
40301235 ATTTTTTTATTATGAAGTAGATGCCTATTAAAATAAGAA
1 ATTTTTTTATTATGAAGTAGATGCCTATTAAAATAAGAA
40301274 ATTT
1 ATTT
40301278 GATGTATCCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (39 bp):
ATTTTTTTATTATGAAGTAGATGCCTATTAAAATAAGAA
Found at i:40307460 original size:25 final size:25
Alignment explanation
Indices: 40307426--40307476 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
40307416 TTAAAATAAT
*
40307426 TGTGTGAAAAGAAGAGAAAGAAATC
1 TGTGTCAAAAGAAGAGAAAGAAATC
40307451 TGTGTCAAAAGAAGAGAAAGAAATC
1 TGTGTCAAAAGAAGAGAAAGAAATC
40307476 T
1 T
40307477 CACAAATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.51, C:0.06, G:0.25, T:0.18
Consensus pattern (25 bp):
TGTGTCAAAAGAAGAGAAAGAAATC
Found at i:40315412 original size:48 final size:48
Alignment explanation
Indices: 40315341--40315436 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
40315331 AAGAGATGGT
40315341 TGTGATAAAGAAAAGTAGAGTTCACCCTTACGAAATGTTACATCCATA
1 TGTGATAAAGAAAAGTAGAGTTCACCCTTACGAAATGTTACATCCATA
40315389 TGTGATAAAGAAAAGTAGAGTTCACCCTTACGAAATGTTACATCCATA
1 TGTGATAAAGAAAAGTAGAGTTCACCCTTACGAAATGTTACATCCATA
40315437 CTTACAAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (48 bp):
TGTGATAAAGAAAAGTAGAGTTCACCCTTACGAAATGTTACATCCATA
Found at i:40324461 original size:42 final size:42
Alignment explanation
Indices: 40324402--40324486 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
40324392 GAATGATTAC
40324402 AACCATAATCACATTTTCCCTCAAATCAAATTGTGAAGGCAT
1 AACCATAATCACATTTTCCCTCAAATCAAATTGTGAAGGCAT
40324444 AACCATAATCACATTTTCCCTCAAATCAAATTGTGAAGGCAT
1 AACCATAATCACATTTTCCCTCAAATCAAATTGTGAAGGCAT
40324486 A
1 A
40324487 CTTGTAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (42 bp):
AACCATAATCACATTTTCCCTCAAATCAAATTGTGAAGGCAT
Found at i:40330039 original size:73 final size:73
Alignment explanation
Indices: 40329957--40330142 Score: 354
Period size: 73 Copynumber: 2.5 Consensus size: 73
40329947 ACAACTTGAC
40329957 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
40330022 CACTAACA
66 CACTAACA
*
40330030 AACTTAGTTGGAATACAACTAAGTTTTATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
40330095 CACTAACA
66 CACTAACA
*
40330103 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
40330143 AATAATAATA
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 110 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.28
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:40334469 original size:73 final size:73
Alignment explanation
Indices: 40334387--40334572 Score: 354
Period size: 73 Copynumber: 2.5 Consensus size: 73
40334377 ACAACTTGAC
40334387 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
40334452 CACTAACA
66 CACTAACA
*
40334460 AACTTAGTTGGAATACAACTAAGTTTTATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
40334525 CACTAACA
66 CACTAACA
*
40334533 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
40334573 AATAATAATA
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 110 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.28
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:40342618 original size:22 final size:22
Alignment explanation
Indices: 40342593--40342646 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
40342583 TTGTTTTTAA
* *
40342593 AAAATTAT-TTAATTTTAATTAT
1 AAAATTATATAAATATT-ATTAT
*
40342615 AAAAATATATAAATATTATTAT
1 AAAATTATATAAATATTATTAT
*
40342637 AACATTATAT
1 AAAATTATAT
40342647 TTTTTAAACA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAATTATATAAATATTATTAT
Found at i:40346198 original size:55 final size:55
Alignment explanation
Indices: 40346114--40346230 Score: 216
Period size: 55 Copynumber: 2.1 Consensus size: 55
40346104 CTGACTTGGG
*
40346114 TCACACGGCCAACCACACGCCCGTGTGACCAGCCTGTGTGCCATTCGAAATGACC
1 TCACACGGCCAACCACACGCCCGTGTGACCAGCCCGTGTGCCATTCGAAATGACC
*
40346169 TCACACGGCCAACCACACGCCCGTGTGACCAGCCCGTGTGCCATTCGAAATGGCC
1 TCACACGGCCAACCACACGCCCGTGTGACCAGCCCGTGTGCCATTCGAAATGACC
40346224 TCACACG
1 TCACACG
40346231 CCCGTGTGCC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.23, C:0.39, G:0.22, T:0.15
Consensus pattern (55 bp):
TCACACGGCCAACCACACGCCCGTGTGACCAGCCCGTGTGCCATTCGAAATGACC
Found at i:40347141 original size:17 final size:17
Alignment explanation
Indices: 40347121--40347176 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
40347111 ATAATAATAT
40347121 ACAACTCATATTAATCC
1 ACAACTCATATTAATCC
** **
40347138 ACAAAC-CTATAACAATAT
1 AC-AACTC-ATATTAATCC
40347156 ACAACTCATATTAATCC
1 ACAACTCATATTAATCC
40347173 ACAA
1 ACAA
40347177 ACCTATCACA
Statistics
Matches: 28, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (17 bp):
ACAACTCATATTAATCC
Found at i:40347149 original size:35 final size:35
Alignment explanation
Indices: 40347110--40347182 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
40347100 AACAATTGAA
*
40347110 TATAATAATATACAACTCATATTAATCCACAAACC
1 TATAACAATATACAACTCATATTAATCCACAAACC
40347145 TATAACAATATACAACTCATATTAATCCACAAACC
1 TATAACAATATACAACTCATATTAATCCACAAACC
40347180 TAT
1 TAT
40347183 CACATGATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (35 bp):
TATAACAATATACAACTCATATTAATCCACAAACC
Found at i:40352522 original size:18 final size:17
Alignment explanation
Indices: 40352481--40352522 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
40352471 AAAAGTTGAG
40352481 TTTT-AATAGCTAAAGA
1 TTTTAAATAGCTAAAGA
* *
40352497 TATTAAATAGCTATAGAA
1 TTTTAAATAGCTAAAG-A
40352515 TTTTAAAT
1 TTTTAAAT
40352523 TGGAGGTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 10 0.48
18 8 0.38
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (17 bp):
TTTTAAATAGCTAAAGA
Found at i:40353546 original size:25 final size:25
Alignment explanation
Indices: 40353518--40353584 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
40353508 GACACACCAC
40353518 AGCTCGTATGAGCTTCCCGTTATAT
1 AGCTCGTATGAGCTTCCCGTTATAT
* * * *
40353543 AGCTCGCATGAGTTTTCCGTTATTT
1 AGCTCGTATGAGCTTCCCGTTATAT
40353568 AGCTCGTATGAGCTTCC
1 AGCTCGTATGAGCTTCC
40353585 TGATATTCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (25 bp):
AGCTCGTATGAGCTTCCCGTTATAT
Found at i:40353827 original size:12 final size:12
Alignment explanation
Indices: 40353810--40353850 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
40353800 ATATGTGTTA
40353810 GATTTTATATGT
1 GATTTTATATGT
*
40353822 GATTTTCAT-T-A
1 GATTTT-ATATGT
40353833 GATTTTATATGT
1 GATTTTATATGT
40353845 GATTTT
1 GATTTT
40353851 CATGGCTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 2 0.08
11 7 0.29
12 13 0.54
13 2 0.08
ACGTcount: A:0.24, C:0.02, G:0.15, T:0.59
Consensus pattern (12 bp):
GATTTTATATGT
Found at i:40353837 original size:23 final size:23
Alignment explanation
Indices: 40353807--40353853 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
40353797 ACCATATGTG
40353807 TTAGATTTTATATGTGATTTTCA
1 TTAGATTTTATATGTGATTTTCA
40353830 TTAGATTTTATATGTGATTTTCA
1 TTAGATTTTATATGTGATTTTCA
40353853 T
1 T
40353854 GGCTAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.13, T:0.57
Consensus pattern (23 bp):
TTAGATTTTATATGTGATTTTCA
Found at i:40362382 original size:25 final size:25
Alignment explanation
Indices: 40362348--40362398 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
40362338 TTCCTTATAA
**
40362348 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
40362373 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
40362398 A
1 A
40362399 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:40362397 original size:12 final size:12
Alignment explanation
Indices: 40362351--40362398 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
40362341 CTTATAAACT
40362351 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
40362363 TTCTATTAGGACT
1 TTAAATTAGGA-A
40362376 TTAAATTAGGAA
1 TTAAATTAGGAA
*
40362388 TTAGATTAGGA
1 TTAAATTAGGA
40362399 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:40366084 original size:25 final size:25
Alignment explanation
Indices: 40366050--40366100 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
40366040 TTCCTTATAA
**
40366050 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
40366075 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
40366100 A
1 A
40366101 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:40366099 original size:12 final size:12
Alignment explanation
Indices: 40366053--40366100 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
40366043 CTTATAAACT
40366053 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
40366065 TTCTATTAGGACT
1 TTAAATTAGGA-A
40366078 TTAAATTAGGAA
1 TTAAATTAGGAA
*
40366090 TTAGATTAGGA
1 TTAAATTAGGA
40366101 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:40380514 original size:24 final size:24
Alignment explanation
Indices: 40380486--40380536 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
40380476 AAATTAATAC
40380486 ATGCAGTGGCTTATATGTCTTTAA
1 ATGCAGTGGCTTATATGTCTTTAA
* *
40380510 ATGCAGTGGCTTATGTGTCTTTTA
1 ATGCAGTGGCTTATATGTCTTTAA
40380534 ATG
1 ATG
40380537 TTAGGGGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.43
Consensus pattern (24 bp):
ATGCAGTGGCTTATATGTCTTTAA
Found at i:40380605 original size:74 final size:74
Alignment explanation
Indices: 40380518--40380808 Score: 582
Period size: 74 Copynumber: 3.9 Consensus size: 74
40380508 AAATGCAGTG
40380518 GCTTATGTGTCTTTTAATGTTAGGGGTAAAGGTTGAAACACTACCACACACACGAGACTCTATTC
1 GCTTATGTGTCTTTTAATGTTAGGGGTAAAGGTTGAAACACTACCACACACACGAGACTCTATTC
40380583 TTTTTAGTA
66 TTTTTAGTA
40380592 GCTTATGTGTCTTTTAATGTTAGGGGTAAAGGTTGAAACACTACCACACACACGAGACTCTATTC
1 GCTTATGTGTCTTTTAATGTTAGGGGTAAAGGTTGAAACACTACCACACACACGAGACTCTATTC
40380657 TTTTTAGTA
66 TTTTTAGTA
40380666 GCTTATGTGTCTTTTAATGTTAGGGGTAAAGGTTGAAACACTACCACACACACGAGACTCTATTC
1 GCTTATGTGTCTTTTAATGTTAGGGGTAAAGGTTGAAACACTACCACACACACGAGACTCTATTC
40380731 TTTTTAGTA
66 TTTTTAGTA
40380740 GCTTATGTGTCTTTTAATGTTAGGGGTAAAGGTTGAAACACTACCACACACACGAGACTCTATTC
1 GCTTATGTGTCTTTTAATGTTAGGGGTAAAGGTTGAAACACTACCACACACACGAGACTCTATTC
40380805 TTTT
66 TTTT
40380809 GGTAGAAGTC
Statistics
Matches: 217, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 217 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (74 bp):
GCTTATGTGTCTTTTAATGTTAGGGGTAAAGGTTGAAACACTACCACACACACGAGACTCTATTC
TTTTTAGTA
Found at i:40382110 original size:7 final size:7
Alignment explanation
Indices: 40382094--40382160 Score: 66
Period size: 7 Copynumber: 9.6 Consensus size: 7
40382084 CTCGATCCTA
40382094 AATTCTC
1 AATTCTC
*
40382101 AATCCTC
1 AATTCTC
*
40382108 AATTTTC
1 AATTCTC
40382115 -ATTCCTC
1 AATT-CTC
*
40382122 AATTTTC
1 AATTCTC
*
40382129 AATTTTC
1 AATTCTC
40382136 AA-TCATC
1 AATTC-TC
40382143 AATTCTC
1 AATTCTC
40382150 AATTCTC
1 AATTCTC
40382157 AATT
1 AATT
40382161 ATTATTTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
6 4 0.08
7 41 0.82
8 5 0.10
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.45
Consensus pattern (7 bp):
AATTCTC
Found at i:40382122 original size:21 final size:21
Alignment explanation
Indices: 40382098--40382159 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
40382088 ATCCTAAATT
* *
40382098 CTCAATCCTCAATTTTCATTC
1 CTCAATTCTCAATTTTCAATC
*
40382119 CTCAATTTTCAATTTTCAATC
1 CTCAATTCTCAATTTTCAATC
* *
40382140 ATCAATTCTCAATTCTCAAT
1 CTCAATTCTCAATTTTCAAT
40382160 TATTATTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44
Consensus pattern (21 bp):
CTCAATTCTCAATTTTCAATC
Found at i:40385703 original size:21 final size:21
Alignment explanation
Indices: 40385643--40385703 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
40385633 AGGCACTTTA
*
40385643 TGTGTCGTATTTCAGGTACCTCG
1 TGTGTCGT-TTT-AGGCACCTCG
*** *
40385666 TGTGTCGTAGCAAGCACCTCG
1 TGTGTCGTTTTAGGCACCTCG
40385687 TGTGTCGTTTTAGGCAC
1 TGTGTCGTTTTAGGCAC
40385704 TTTATGTGTC
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 21 0.72
23 8 0.28
ACGTcount: A:0.15, C:0.23, G:0.28, T:0.34
Consensus pattern (21 bp):
TGTGTCGTTTTAGGCACCTCG
Found at i:40387709 original size:22 final size:21
Alignment explanation
Indices: 40387656--40387717 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
40387646 GGTGGAAGTG
* *
40387656 TGAGCAAATTATCTGCATCGT
1 TGAGCAATTTATCTGCACCGT
***
40387677 TGAGTGGTTTATCTGCACCGTT
1 TGAGCAATTTATCTGCACCG-T
*
40387699 TGAGCAATTTATCTACACC
1 TGAGCAATTTATCTGCACC
40387718 ATTTAGTGGT
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.35
Consensus pattern (21 bp):
TGAGCAATTTATCTGCACCGT
Found at i:40387732 original size:21 final size:22
Alignment explanation
Indices: 40387676--40387732 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
40387666 ATCTGCATCG
* *
40387676 TTGAGTGGTTTATCTGCACCGT
1 TTGAGTGGTTTATCTACACCAT
***
40387698 TTGAGCAATTTATCTACACCAT
1 TTGAGTGGTTTATCTACACCAT
40387720 TT-AGTGGTTTATC
1 TTGAGTGGTTTATC
40387733 CATACCGTAT
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (22 bp):
TTGAGTGGTTTATCTACACCAT
Found at i:40387740 original size:43 final size:43
Alignment explanation
Indices: 40387656--40387740 Score: 98
Period size: 43 Copynumber: 2.0 Consensus size: 43
40387646 GGTGGAAGTG
* * * **
40387656 TGAGCAAATTATCTGCATCGTTGAGTGGTTTATCTGCACCGTT
1 TGAGCAAATTATCTACACCATTGAGTGGTTTATCCACACCGTT
* * *
40387699 TGAGCAATTTATCTACACCATTTAGTGGTTTATCCATACCGT
1 TGAGCAAATTATCTACACCATTGAGTGGTTTATCCACACCGT
40387741 ATAAGCAGTT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.38
Consensus pattern (43 bp):
TGAGCAAATTATCTACACCATTGAGTGGTTTATCCACACCGTT
Found at i:40390860 original size:20 final size:21
Alignment explanation
Indices: 40390822--40390861 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
40390812 AAAAGAACAT
*
40390822 ATTATTATTATTAGGTTTTTA
1 ATTATTATTATTAAGTTTTTA
40390843 ATTA-TATTATTAA-TTTTTA
1 ATTATTATTATTAAGTTTTTA
40390862 TCATATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 8 0.44
21 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
ATTATTATTATTAAGTTTTTA
Found at i:40390867 original size:18 final size:20
Alignment explanation
Indices: 40390827--40390867 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
40390817 AACATATTAT
* *
40390827 TATTATTAGGTTTTTAATTA
1 TATTATTAGATTTTTAATCA
40390847 TATTATTA-ATTTTT-ATCA
1 TATTATTAGATTTTTAATCA
40390865 TAT
1 TAT
40390868 AAAAACAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 6 0.32
19 5 0.26
20 8 0.42
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (20 bp):
TATTATTAGATTTTTAATCA
Found at i:40390956 original size:31 final size:31
Alignment explanation
Indices: 40390914--40390981 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
40390904 ATATGATTTT
**
40390914 ATTAAA-ATTAATGGATAATTAAAAACTAAA
1 ATTAAATATTAATAAATAATTAAAAACTAAA
*
40390944 ATTAAATATTAATAAATAATTAAAAATTAAA
1 ATTAAATATTAATAAATAATTAAAAACTAAA
40390975 A-TAAATA
1 ATTAAATA
40390982 GAAAAATATG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 12 0.35
31 22 0.65
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (31 bp):
ATTAAATATTAATAAATAATTAAAAACTAAA
Found at i:40392496 original size:41 final size:41
Alignment explanation
Indices: 40392451--40392538 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 41
40392441 GAGATCGAGG
* * * *
40392451 TAGCTTCAGTTGTGTAATGCACTTAGTGTGCGAGATTATAA
1 TAGCTTCAGCTATGTAATGCACTTAGTATGCAAGATTATAA
*
40392492 TAGCTTCGGCTATGTAATGCACTTAGTATGCAAGATTATAA
1 TAGCTTCAGCTATGTAATGCACTTAGTATGCAAGATTATAA
40392533 TAGCTT
1 TAGCTT
40392539 TGGCTATGCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (41 bp):
TAGCTTCAGCTATGTAATGCACTTAGTATGCAAGATTATAA
Found at i:40392544 original size:41 final size:41
Alignment explanation
Indices: 40392463--40392563 Score: 141
Period size: 41 Copynumber: 2.4 Consensus size: 41
40392453 GCTTCAGTTG
* *
40392463 TGTAATGCACTTAGTGTGCGAGATTATAATAGCTTCGGCTA
1 TGTAATGCACTTAGTATGCAAGATTATAATAGCTTCGGCTA
*
40392504 TGTAATGCACTTAGTATGCAAGATTATAATAGCTTTGGCTA
1 TGTAATGCACTTAGTATGCAAGATTATAATAGCTTCGGCTA
*
40392545 TGCT-TTGGCACTTAGTATG
1 TG-TAAT-GCACTTAGTATG
40392564 TGAGATATCT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
41 41 0.76
42 13 0.24
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (41 bp):
TGTAATGCACTTAGTATGCAAGATTATAATAGCTTCGGCTA
Found at i:40394478 original size:19 final size:23
Alignment explanation
Indices: 40394454--40394502 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 23
40394444 AAGTTAAATA
40394454 AATAAATAATA-TT-TT-GGTT-
1 AATAAATAATAGTTATTAGGTTG
*
40394473 AATAAAAAATAGTTATTAGGTTG
1 AATAAATAATAGTTATTAGGTTG
40394496 AATAAAT
1 AATAAAT
40394503 TATAAACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.42
20 2 0.08
21 2 0.08
22 4 0.17
23 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (23 bp):
AATAAATAATAGTTATTAGGTTG
Found at i:40399413 original size:13 final size:14
Alignment explanation
Indices: 40399395--40399423 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40399385 TAAAGACTTG
40399395 ATATG-ATTAACCA
1 ATATGAATTAACCA
40399408 ATATGAATTAACCA
1 ATATGAATTAACCA
40399422 AT
1 AT
40399424 GTCACCAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (14 bp):
ATATGAATTAACCA
Found at i:40410964 original size:16 final size:16
Alignment explanation
Indices: 40410943--40410985 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
40410933 TGAGAAACTA
* *
40410943 TTAAAATATATATTTT
1 TTAAAAAATAAATTTT
40410959 TTAAAAAATAAATTTT
1 TTAAAAAATAAATTTT
* *
40410975 ATAATAAATAA
1 TTAAAAAATAA
40410986 TTGTAGTGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAAAATAAATTTT
Found at i:40411808 original size:28 final size:28
Alignment explanation
Indices: 40411776--40411829 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
40411766 CTAAAAAATT
* *
40411776 ATTAATAATATTATTTAAATTATAATAC
1 ATTAATAATAATATTTAAACTATAATAC
*
40411804 ATTAATATTAATATTTAAACTATAAT
1 ATTAATAATAATATTTAAACTATAAT
40411830 GAATTTTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (28 bp):
ATTAATAATAATATTTAAACTATAATAC
Found at i:40421808 original size:32 final size:31
Alignment explanation
Indices: 40421761--40421841 Score: 90
Period size: 32 Copynumber: 2.6 Consensus size: 31
40421751 GAAATTTTAG
*
40421761 TTTGTTGGATTTTGAAATTATCATGTCTTAAA
1 TTTGTTGGATATTGAAATTATCATGT-TTAAA
* * * *
40421793 TTTGTTAGATATTGAATTTATTATGTTTAAG
1 TTTGTTGGATATTGAAATTATCATGTTTAAA
* *
40421824 CTTATTGGATATTGAAAT
1 TTTGTTGGATATTGAAAT
40421842 GATTGACAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 18 0.45
32 22 0.55
ACGTcount: A:0.30, C:0.04, G:0.16, T:0.51
Consensus pattern (31 bp):
TTTGTTGGATATTGAAATTATCATGTTTAAA
Found at i:40422876 original size:25 final size:25
Alignment explanation
Indices: 40422799--40422877 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
40422789 TGTGGTGTAA
* *
40422799 TATTAGTTATGCACTTGGATAATAT
1 TATTAATTATGCATTTGGATAATAT
* * * *
40422824 TGTT-ATTAT-CATGTGG-T-GTAC
1 TATTAATTATGCATTTGGATAATAT
*
40422845 TACTAATTATGCATTTGGATAATAT
1 TATTAATTATGCATTTGGATAATAT
40422870 TATTAATT
1 TATTAATT
40422878 TCTAATATTA
Statistics
Matches: 38, Mismatches: 12, Indels: 8
0.66 0.21 0.14
Matches are distributed among these distances:
21 4 0.11
22 6 0.16
23 11 0.29
24 5 0.13
25 12 0.32
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (25 bp):
TATTAATTATGCATTTGGATAATAT
Found at i:40423199 original size:20 final size:19
Alignment explanation
Indices: 40423155--40423200 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
40423145 CATCCTAACA
*
40423155 CCAGAAAAGTAAATTATTT
1 CCAGAAAAGTAAATCATTT
*
40423174 CTAGAAAAGTAAATCATTTT
1 CCAGAAAAGTAAATCA-TTT
40423194 CCAGAAA
1 CCAGAAA
40423201 TTATTTTTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:40423739 original size:152 final size:153
Alignment explanation
Indices: 40423506--40423815 Score: 550
Period size: 152 Copynumber: 2.0 Consensus size: 153
40423496 AAATTTAAAA
40423506 ATATGCCTTTTCGAAATAATTAGAGATATTATTGTCTCATCGTTTTTTCACTTTCTTCTATTCTA
1 ATATGCCTTTTCGAAATAATTAGAGATATTATTGTCTCATCGTTTTTTCACTTTCTTCTATTCTA
* *
40423571 TGGTTTCTCCATAGTATTTTGACCAATGAAATGTGCTTGTCCCGTAATTATTTTATTTCTTGAGC
66 TGGTTTCTCCATAGTATTTTGACCAATGAAATGTGCTTGTCCCGTAATTATTTTACTTCTTGAAC
40423636 TAATATTACCATTGA-CTTTTTT
131 TAATATTACCATTGATCTTTTTT
*
40423658 ATATGCCTTTTCGAAATAATTAGAGATATTGTTGTCTCATCGTTTTTTCACTTTCTTCTATTCTA
1 ATATGCCTTTTCGAAATAATTAGAGATATTATTGTCTCATCGTTTTTTCACTTTCTTCTATTCTA
* * *
40423723 TGGTTTCTCCATAGTATTTTGACCAATGAAATGTGCTTGTTCCTTAATTCTTTTACTTCTTGAAC
66 TGGTTTCTCCATAGTATTTTGACCAATGAAATGTGCTTGTCCCGTAATTATTTTACTTCTTGAAC
*
40423788 TAATATTACCATTGATTTTTTTT
131 TAATATTACCATTGATCTTTTTT
40423811 ATATG
1 ATATG
40423816 TCAAATCTAG
Statistics
Matches: 150, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
152 139 0.93
153 11 0.07
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.49
Consensus pattern (153 bp):
ATATGCCTTTTCGAAATAATTAGAGATATTATTGTCTCATCGTTTTTTCACTTTCTTCTATTCTA
TGGTTTCTCCATAGTATTTTGACCAATGAAATGTGCTTGTCCCGTAATTATTTTACTTCTTGAAC
TAATATTACCATTGATCTTTTTT
Found at i:40431421 original size:19 final size:20
Alignment explanation
Indices: 40431397--40431437 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
40431387 TTATTATTAA
40431397 AAAATATAT-TTTTAGAAAT
1 AAAATATATATTTTAGAAAT
* *
40431416 AAAATATTTATTTTAGACAT
1 AAAATATATATTTTAGAAAT
40431436 AA
1 AA
40431438 TGTTATAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (20 bp):
AAAATATATATTTTAGAAAT
Found at i:40434890 original size:15 final size:15
Alignment explanation
Indices: 40434872--40434915 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
40434862 CTACTGCTGC
40434872 TGTCCAAACTGTTTT
1 TGTCCAAACTGTTTT
40434887 TGTCCAAACTGTTTT
1 TGTCCAAACTGTTTT
*
40434902 TGTCCAAGCTGTTT
1 TGTCCAAACTGTTT
40434916 ATTACCATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (15 bp):
TGTCCAAACTGTTTT
Found at i:40435029 original size:29 final size:29
Alignment explanation
Indices: 40434987--40435045 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
40434977 TCAATTGAGC
*
40434987 TGATTTTTCTCAATTAACTTTTTATTCTA
1 TGATTTTTCTCAATTAACATTTTATTCTA
40435016 TGATTTTTCTCAATTAACATTTTATTCTA
1 TGATTTTTCTCAATTAACATTTTATTCTA
40435045 T
1 T
40435046 CACCTTAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.03, T:0.58
Consensus pattern (29 bp):
TGATTTTTCTCAATTAACATTTTATTCTA
Found at i:40447261 original size:48 final size:46
Alignment explanation
Indices: 40447207--40447326 Score: 122
Period size: 48 Copynumber: 2.6 Consensus size: 46
40447197 TCACAAAGAA
*
40447207 CCATATCGGGAAGCTCACGAAGAGCCTATCGGGAAGCTC-C-GGATAG
1 CCATATCGGGAAGCTCACGAAGAGCCTACCGGGAAGCTCACAGG--AG
* * *
40447253 CCATATATCGGGAAGTTCAAG-CGAGCACTACCGGGAAGCTCACAAGGAG
1 CC--ATATCGGGAAGCTCACGAAGAGC-CTACCGGGAAGCTCAC-AGGAG
40447302 CC-TATCGGGAAGCTCACGAAGAGCC
1 CCATATCGGGAAGCTCACGAAGAGCC
40447327 ATATATCGGG
Statistics
Matches: 60, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
46 17 0.28
47 8 0.13
48 28 0.47
49 5 0.08
51 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.29, T:0.14
Consensus pattern (46 bp):
CCATATCGGGAAGCTCACGAAGAGCCTACCGGGAAGCTCACAGGAG
Found at i:40447267 original size:25 final size:24
Alignment explanation
Indices: 40447197--40447330 Score: 118
Period size: 23 Copynumber: 5.7 Consensus size: 24
40447187 ATCGAGTAGT
* *
40447197 TCACAAAGAACCATATCGGGAAGC
1 TCACGAAGAGCCATATCGGGAAGC
40447221 TCACGAAGAGCC-TATCGGGAAGC
1 TCACGAAGAGCCATATCGGGAAGC
* * *
40447244 TC-CGGATAGCCATATATCGGGAAGT
1 TCACGAAGAGCC--ATATCGGGAAGC
* * *
40447269 TCAAG-CGAG-CACTACCGGGAAGC
1 TCACGAAGAGCCA-TATCGGGAAGC
40447292 TCAC-AAGGAGCC-TATCGGGAAGC
1 TCACGAA-GAGCCATATCGGGAAGC
40447315 TCACGAAGAGCCATAT
1 TCACGAAGAGCCATAT
40447331 ATCGGGACAC
Statistics
Matches: 87, Mismatches: 13, Indels: 20
0.73 0.11 0.17
Matches are distributed among these distances:
22 8 0.09
23 44 0.51
24 19 0.22
25 15 0.17
26 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.15
Consensus pattern (24 bp):
TCACGAAGAGCCATATCGGGAAGC
Found at i:40449489 original size:3 final size:3
Alignment explanation
Indices: 40449475--40449523 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
40449465 TTTTATACTA
*
40449475 AAT AATT AAT AAT AA- AAT AAT AAT GA- AAT AAT AAT AA- AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40449518 AA- AAT A
1 AAT AAT A
40449524 TCTCATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:40449497 original size:11 final size:11
Alignment explanation
Indices: 40449481--40449519 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
40449471 ACTAAATAAT
40449481 TAATAATAAAA
1 TAATAATAAAA
*
40449492 TAATAATGAAA
1 TAATAATAAAA
40449503 TAATAATAAAA
1 TAATAATAAAA
40449514 TAATAA
1 TAATAA
40449520 AATATCTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:40449506 original size:19 final size:19
Alignment explanation
Indices: 40449482--40449523 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
40449472 CTAAATAATT
*
40449482 AATAATAAAATAATAATGA
1 AATAATAAAATAATAATAA
40449501 AATAATAATAA-AATAATAA
1 AATAATAA-AATAATAATAA
40449520 AATA
1 AATA
40449524 TCTCATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AATAATAAAATAATAATAA
Found at i:40449561 original size:18 final size:20
Alignment explanation
Indices: 40449509--40449561 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
40449499 GAAATAATAA
* *
40449509 TAAAATAATAAAATATCTCAT
1 TAAAATAAT-ATATATCTAAT
40449530 TAAAATAATATATATCTAAT
1 TAAAATAATATATATCTAAT
40449550 T-AAATAAT-TATA
1 TAAAATAATATATA
40449562 AAATATTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 4 0.13
19 7 0.23
20 10 0.33
21 9 0.30
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAATAATATATATCTAAT
Found at i:40451458 original size:15 final size:15
Alignment explanation
Indices: 40451438--40451466 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40451428 ATCTGAGAGT
40451438 TGGTTCCCAAGCCAG
1 TGGTTCCCAAGCCAG
40451453 TGGTTCCCAAGCCA
1 TGGTTCCCAAGCCA
40451467 ATCCACTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.34, G:0.24, T:0.21
Consensus pattern (15 bp):
TGGTTCCCAAGCCAG
Found at i:40452808 original size:14 final size:14
Alignment explanation
Indices: 40452770--40452812 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
40452760 TTGCCTTGCA
40452770 AATTTTAAAACATT-
1 AATTTTAAAA-ATTC
*
40452784 ATTTTTCAAAAATTC
1 AATTTT-AAAAATTC
40452799 AATTTTAAAAATTC
1 AATTTTAAAAATTC
40452813 GTAGCGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (14 bp):
AATTTTAAAAATTC
Found at i:40454412 original size:20 final size:21
Alignment explanation
Indices: 40454369--40454413 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
40454359 TATTTATATC
* * *
40454369 AAAAAAAGAGAAGAAATGAGA
1 AAAAAAAAAGAAGAAAAGACA
40454390 AAAAAAAAAG-AGAAAAGACA
1 AAAAAAAAAGAAGAAAAGACA
40454410 AAAA
1 AAAA
40454414 GATTAGATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAGAAGAAAAGACA
Found at i:40454486 original size:12 final size:12
Alignment explanation
Indices: 40454469--40454495 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40454459 GTACAATGTT
40454469 GTTTTCATGGTG
1 GTTTTCATGGTG
40454481 GTTTTCATGGTG
1 GTTTTCATGGTG
40454493 GTT
1 GTT
40454496 ATAGGCGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.33, T:0.52
Consensus pattern (12 bp):
GTTTTCATGGTG
Found at i:40456917 original size:49 final size:48
Alignment explanation
Indices: 40456800--40456932 Score: 173
Period size: 48 Copynumber: 2.8 Consensus size: 48
40456790 ACACAAATAA
* *
40456800 AATATATTACCATCATGGATGGCAT-GACAATGATGGTTCATTCTATTC
1 AATATATTACCATCCTGAATGGC-TCGACAATGATGGTTCATTCTATTC
40456848 AATATATTACCAT-CTCGAATGGCTCGACAATGATGGTTCATTCTATTTC
1 AATATATTACCATCCT-GAATGGCTCGACAATGATGGTTCATTCTA-TTC
* *
40456897 AATAT-TCTACCATCCTGAATGGCCCGACAACGATGG
1 AATATAT-TACCATCCTGAATGGCTCGACAATGATGG
40456933 CTATCATTAT
Statistics
Matches: 76, Mismatches: 4, Indels: 9
0.85 0.04 0.10
Matches are distributed among these distances:
47 2 0.03
48 40 0.53
49 32 0.42
50 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (48 bp):
AATATATTACCATCCTGAATGGCTCGACAATGATGGTTCATTCTATTC
Found at i:40475419 original size:19 final size:19
Alignment explanation
Indices: 40475378--40475420 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
40475368 CAAGCCAAAT
* ** *
40475378 TATTTTATAAAATTATTAT
1 TATTTTAAAAAATTAAAAA
40475397 TATTTTAAAAAATTAAAAA
1 TATTTTAAAAAATTAAAAA
40475416 TATTT
1 TATTT
40475421 AATAGTCATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTTAAAAAATTAAAAA
Found at i:40477293 original size:30 final size:30
Alignment explanation
Indices: 40477258--40477316 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
40477248 AGCAAAAAAC
40477258 TCTCAAATTGCTCCCTAAATTTCTCAAAGT
1 TCTCAAATTGCTCCCTAAATTTCTCAAAGT
* *
40477288 TCTCAAATTTCTCCTTAAATTTCTCAAAG
1 TCTCAAATTGCTCCCTAAATTTCTCAAAG
40477317 CTCTTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (30 bp):
TCTCAAATTGCTCCCTAAATTTCTCAAAGT
Found at i:40479069 original size:18 final size:18
Alignment explanation
Indices: 40479046--40479088 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40479036 TGCTAGGTGC
* *
40479046 GTATCCTAGCCTTTATAT
1 GTATCCTAACCCTTATAT
40479064 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
40479082 GTTTCCT
1 GTATCCT
40479089 TTTCCCAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:40482738 original size:126 final size:125
Alignment explanation
Indices: 40482545--40483065 Score: 670
Period size: 126 Copynumber: 4.1 Consensus size: 125
40482535 AGCCAAACAT
* * * *
40482545 GAACTATTGTAGAAAAAGAGCATCCACGTGAGAGCCTTTTTTCAGTAATTTTGCTGATAGTGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAG-CTTTTTTCA-TAATTTTGCTGACAGTGCAT
* * * * *
40482610 CCTGCTTAAAGCATTATGGGCACTATTTGTTCAGAAAC-GTCTTCTCAAAATTATTTTTTTAG
64 CCTGCTTAAAGCGTTTTTGACACTATTTGTTCAG-AACTGTCTTCTCAAAATTATTTTTTCAG
* * * * *
40482672 TAACTACTATAGAAAAAGAGCGTCTATGTGGGAGCTTTTTTCATCAATTTTGCTGACAGTGTATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAT-AATTTTGCTGACAGTGCATC
* * *
40482737 CTACTTAAAGCGTTTTTTACACTATTTTTTCAGAAAC-GTCTTCTCAAAATTATTTTTTCAG
65 CTGCTTAAAGCGTTTTTGACACTATTTGTTCAG-AACTGTCTTCTCAAAATTATTTTTTCAG
* * *
40482798 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCTTCAATTTTGTTGGCAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAT-AATTTTGCTGACAGTGCATC
* * * * *
40482863 CTGCTTGAAGCGTTTTTGACACTATCTGTTCAGAACTATTTTTTCAAAATTATTTTTT-AG
65 CTGCTTAAAGCGTTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTCAG
* * *
40482923 GAACTACTGTAGAAAACGAGCGTCCATGTGGGAGCTTTTTTCAATAATTTTACTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTC-ATAATTTTGCTGACAGTGCATC
* * * *
40482988 CTGCTTGAAGCGTTTTTGACACTATTTGTTTAGAACTGCCTTTTCAAAATTATTTTTTCAG
65 CTGCTTAAAGCGTTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTCAG
40483049 GAACTACTGTAGAAAAA
1 GAACTACTGTAGAAAAA
40483066 AACCAAGATC
Statistics
Matches: 345, Mismatches: 45, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
125 116 0.34
126 202 0.59
127 27 0.08
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (125 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATAATTTTGCTGACAGTGCATCC
TGCTTAAAGCGTTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTTCAG
Found at i:40483001 original size:251 final size:253
Alignment explanation
Indices: 40482545--40483065 Score: 705
Period size: 251 Copynumber: 2.1 Consensus size: 253
40482535 AGCCAAACAT
* *
40482545 GAACTATTGTAGAAAAAGAGCATCCACGTGAGAGCCTTTTTTCAGTAATTTTGCTGATAGTGCAT
1 GAACTACTGTAGAAAAAGAGCATCCACGTGAGAGCCTTTTTTCAGTAATTTTGCTGACAGTGCAT
* * * *
40482610 CCTGCTTAAAGCATTATGGGCACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTTAGTAA
66 CCTGCTTAAAGCATTATGGACACTATCTGTTCAGAAACATCTTCTCAAAATTATTTTTTTAGGAA
* * *
40482675 CTACTATAGAAAAAGAGCGTCTATGTGGGAGCTTTTTTCATCAATTTTGCTGACAGTGTATCCTA
131 CTACTATAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTCATCAATTTTACTGACAGTGCATCCTA
* *
40482740 CTTAAAGCGTTTTTTACACTATTT-TTTCAGAAAC-GTCTTCTCAAAATTATTTTTTCAG
196 CTTAAAGCGTTTTTGACACTATTTGTTT-AG-AACTGCCTTCTCAAAATTATTTTTTCAG
* * * * *
40482798 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAG-CTTTTTTC-TTCAATTTTGTTGGCAGTGCA
1 GAACTACTGTAGAAAAAGAGCATCCACGTGAGAGCCTTTTTTCAGT-AATTTTGCTGACAGTGCA
* * * * * *
40482861 TCCTGCTTGAAGCGTTTTTGACACTATCTGTTCAG-AACTATTTTTTCAAAATTA-TTTTTTAGG
65 TCCTGCTTAAAGCATTATGGACACTATCTGTTCAGAAAC-ATCTTCTCAAAATTATTTTTTTAGG
* *
40482924 AACTACTGTAGAAAACGAGCGTCCATGTGGGAGCTTTTTTCAAT-AATTTTACTGACAGTGCATC
129 AACTACTATAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTC-ATCAATTTTACTGACAGTGCATC
* * *
40482988 CTGCTTGAAGCGTTTTTGACACTATTTGTTTAGAACTGCCTTTTCAAAATTATTTTTTCAG
193 CTACTTAAAGCGTTTTTGACACTATTTGTTTAGAACTGCCTTCTCAAAATTATTTTTTCAG
40483049 GAACTACTGTAGAAAAA
1 GAACTACTGTAGAAAAA
40483066 AACCAAGATC
Statistics
Matches: 236, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
250 3 0.01
251 133 0.56
252 69 0.29
253 31 0.13
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (253 bp):
GAACTACTGTAGAAAAAGAGCATCCACGTGAGAGCCTTTTTTCAGTAATTTTGCTGACAGTGCAT
CCTGCTTAAAGCATTATGGACACTATCTGTTCAGAAACATCTTCTCAAAATTATTTTTTTAGGAA
CTACTATAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTCATCAATTTTACTGACAGTGCATCCTA
CTTAAAGCGTTTTTGACACTATTTGTTTAGAACTGCCTTCTCAAAATTATTTTTTCAG
Found at i:40483183 original size:34 final size:33
Alignment explanation
Indices: 40483127--40483268 Score: 119
Period size: 34 Copynumber: 4.2 Consensus size: 33
40483117 CCAATATTAT
* *
40483127 TTTAAAAAAATTAAACCTAAATTTAATTAATTT-
1 TTTAAAAACACTAAACC-AAATTTAATTAATTTA
40483160 TCTTAAAAACACTAAATCCAAATTTAATTAATTTA
1 T-TTAAAAACACTAAA-CCAAATTTAATTAATTTA
* *
40483195 TTT-AAAACCCTTAAACCCTAATTTAATTAATTTA
1 TTTAAAAACAC-TAAA-CCAAATTTAATTAATTTA
*** * * * *
40483229 TTTAACCCCCCGAACCCTAATTTAATTAATTT-
1 TTTAAAAACACTAAACCAAATTTAATTAATTTA
40483261 TTTAAAAA
1 TTTAAAAA
40483269 GAACACTAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
32 5 0.05
33 24 0.26
34 55 0.60
35 7 0.08
ACGTcount: A:0.44, C:0.15, G:0.01, T:0.39
Consensus pattern (33 bp):
TTTAAAAACACTAAACCAAATTTAATTAATTTA
Found at i:40483250 original size:33 final size:33
Alignment explanation
Indices: 40483180--40483266 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 33
40483170 ACTAAATCCA
**
40483180 AATTTAATTAATTTATTTAAAACCCTTAAACCCT
1 AATTTAATTAATTTATTT-AAACCCCCAAACCCT
* *
40483214 AATTTAATTAATTTATTTAACCCCCCGAACCCT
1 AATTTAATTAATTTATTTAAACCCCCAAACCCT
40483247 AATTTAATTAATTT-TTTAAA
1 AATTTAATTAATTTATTTAAA
40483267 AAGAACACTA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 5 0.10
33 25 0.52
34 18 0.38
ACGTcount: A:0.39, C:0.17, G:0.01, T:0.43
Consensus pattern (33 bp):
AATTTAATTAATTTATTTAAACCCCCAAACCCT
Found at i:40483816 original size:50 final size:50
Alignment explanation
Indices: 40483716--40483808 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 50
40483706 AATTTATATT
* * **
40483716 TCTAGTGATTTTAATTGTTATTAATAAATTTATATATCTAATGATTTTTA
1 TCTAGTGATTTTAATTGTTATTAATAAATTTATATATATAATAAAATTTA
*
40483766 TCTAGTGATTTTAATTGTTATTTATAAATTTAT-TA-ATAATAAA
1 TCTAGTGATTTTAATTGTTATTAATAAATTTATATATATAATAAA
40483809 CAATTTATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 5 0.13
49 2 0.05
50 32 0.82
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.53
Consensus pattern (50 bp):
TCTAGTGATTTTAATTGTTATTAATAAATTTATATATATAATAAAATTTA
Found at i:40497666 original size:724 final size:724
Alignment explanation
Indices: 40496280--40497730 Score: 2884
Period size: 724 Copynumber: 2.0 Consensus size: 724
40496270 AAGTAGGCAA
40496280 AAATGGATGATCCAGCATCTTCAAGATCTTCTTCTCCATTTCAGCACGTTGCACTTTATTCTTCA
1 AAATGGATGATCCAGCATCTTCAAGATCTTCTTCTCCATTTCAGCACGTTGCACTTTATTCTTCA
40496345 TGGGCATGGCCAACGCTTCTTTATCCACCACCTTCATCGCATAACAGCATTTTTCATCTGCGTCG
66 TGGGCATGGCCAACGCTTCTTTATCCACCACCTTCATCGCATAACAGCATTTTTCATCTGCGTCG
40496410 GCAAGCTGGCAGAGGTAGACGGTTCCGATGTCGCCGGAACCGATGCGCCGGATGAGCTGGAAATC
131 GCAAGCTGGCAGAGGTAGACGGTTCCGATGTCGCCGGAACCGATGCGCCGGATGAGCTGGAAATC
40496475 ACGGGACGTGAGGCCGGTTTTACGGGCGAAGGTGGCGGAACGGATAGCGGAGTAAGCCAAGTCGG
196 ACGGGACGTGAGGCCGGTTTTACGGGCGAAGGTGGCGGAACGGATAGCGGAGTAAGCCAAGTCGG
*
40496540 AAGATCGGTGGGGTTTGAGATAAAGGTTTTCCGGGGAAGACCGGAGCTCAAAGGAGAGACGGCTG
261 AAGATCGGTGGGGTTTGAGAGAAAGGTTTTCCGGGGAAGACCGGAGCTCAAAGGAGAGACGGCTG
40496605 AAGCTGCTACGGCTTTCACTTGTCATTGAACACTCACTCGATGAACTTAACTCACTTTCTGACTT
326 AAGCTGCTACGGCTTTCACTTGTCATTGAACACTCACTCGATGAACTTAACTCACTTTCTGACTT
40496670 CCGTTCGCACTCCAACATTTTATGTTCTCTCTACTTGTAAGACAGGGAAAATCAACATAAAACTC
391 CCGTTCGCACTCCAACATTTTATGTTCTCTCTACTTGTAAGACAGGGAAAATCAACATAAAACTC
40496735 TTTGATGATCTAAGAAGAAGAAGATGATGATGATGATGATGAAGTCAAAAAAGAAAAAAGTGGGA
456 TTTGATGATCTAAGAAGAAGAAGATGATGATGATGATGATGAAGTCAAAAAAGAAAAAAGTGGGA
40496800 ATCACTTCAGATGACCGAAATTAAAGACGGTGGATAAAAGCAATCAACTTTGAACATTTTGGGTT
521 ATCACTTCAGATGACCGAAATTAAAGACGGTGGATAAAAGCAATCAACTTTGAACATTTTGGGTT
40496865 TTAAGAAGATGATTTGATGATGACTGGAAATCTGGAATCAGATACCCGTAAAGGAGATGAAGGAG
586 TTAAGAAGATGATTTGATGATGACTGGAAATCTGGAATCAGATACCCGTAAAGGAGATGAAGGAG
40496930 AGTCAAATAGTGAAGTAGAAAGAGAGCAGTAAGTTTGAAGGGAAAAAAGGGAGTCAAAAACTATG
651 AGTCAAATAGTGAAGTAGAAAGAGAGCAGTAAGTTTGAAGGGAAAAAAGGGAGTCAAAAACTATG
40496995 GGCAAGCAG
716 GGCAAGCAG
40497004 AAATGGATGATCCAGCATCTTCAAGATCTTCTTCTCCATTTCAGCACGTTGCACTTTATTCTTCA
1 AAATGGATGATCCAGCATCTTCAAGATCTTCTTCTCCATTTCAGCACGTTGCACTTTATTCTTCA
40497069 TGGGCATGGCCAACGCTTCTTTATCCACCACCTTCATCGCATAACAGCATTTTTCATCTGCGTCG
66 TGGGCATGGCCAACGCTTCTTTATCCACCACCTTCATCGCATAACAGCATTTTTCATCTGCGTCG
40497134 GCAAGCTGGCAGAGGTAGACGGTTCCGATGTCGCCGGAACCGATGCGCCGGATGAGCTGGAAATC
131 GCAAGCTGGCAGAGGTAGACGGTTCCGATGTCGCCGGAACCGATGCGCCGGATGAGCTGGAAATC
40497199 ACGGGACGTGAGGCCGGTTTTACGGGCGAAGGTGGCGGAACGGATAGCGGAGTAAGCCAAGTCGG
196 ACGGGACGTGAGGCCGGTTTTACGGGCGAAGGTGGCGGAACGGATAGCGGAGTAAGCCAAGTCGG
40497264 AAGATCGGTGGGGTTTGAGAGAAAGGTTTTCCGGGGAAGACCGGAGCTCAAAGGAGAGACGGCTG
261 AAGATCGGTGGGGTTTGAGAGAAAGGTTTTCCGGGGAAGACCGGAGCTCAAAGGAGAGACGGCTG
*
40497329 GAGCTGCTACGGCTTTCACTTGTCATTGAACACTCACTCGATGAACTTAACTCACTTTCTGACTT
326 AAGCTGCTACGGCTTTCACTTGTCATTGAACACTCACTCGATGAACTTAACTCACTTTCTGACTT
40497394 CCGTTCGCACTCCAACATTTTATGTTCTCTCTACTTGTAAGACAGGGAAAATCAACATAAAACTC
391 CCGTTCGCACTCCAACATTTTATGTTCTCTCTACTTGTAAGACAGGGAAAATCAACATAAAACTC
40497459 TTTGATGATCTAAGAAGAAGAAGATGATGATGATGATGATGAAGTCAAAAAAGAAAAAAGTGGGA
456 TTTGATGATCTAAGAAGAAGAAGATGATGATGATGATGATGAAGTCAAAAAAGAAAAAAGTGGGA
40497524 ATCACTTCAGATGACCGAAATTAAAGACGGTGGATAAAAGCAATCAACTTTGAACATTTTGGGTT
521 ATCACTTCAGATGACCGAAATTAAAGACGGTGGATAAAAGCAATCAACTTTGAACATTTTGGGTT
40497589 TTAAGAAGATGATTTGATGATGACTGGAAATCTGGAATCAGATACCCGTAAAGGAGATGAAGGAG
586 TTAAGAAGATGATTTGATGATGACTGGAAATCTGGAATCAGATACCCGTAAAGGAGATGAAGGAG
40497654 AGTCAAATAGTGAAGTAGAAAGAGAGCAGTAAGTTTGAAGGGAAAAAAGGGAGTCAAAAACTATG
651 AGTCAAATAGTGAAGTAGAAAGAGAGCAGTAAGTTTGAAGGGAAAAAAGGGAGTCAAAAACTATG
40497719 GGCAAGCAG
716 GGCAAGCAG
40497728 AAA
1 AAA
40497731 AGAGAAGAAA
Statistics
Matches: 725, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
724 725 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (724 bp):
AAATGGATGATCCAGCATCTTCAAGATCTTCTTCTCCATTTCAGCACGTTGCACTTTATTCTTCA
TGGGCATGGCCAACGCTTCTTTATCCACCACCTTCATCGCATAACAGCATTTTTCATCTGCGTCG
GCAAGCTGGCAGAGGTAGACGGTTCCGATGTCGCCGGAACCGATGCGCCGGATGAGCTGGAAATC
ACGGGACGTGAGGCCGGTTTTACGGGCGAAGGTGGCGGAACGGATAGCGGAGTAAGCCAAGTCGG
AAGATCGGTGGGGTTTGAGAGAAAGGTTTTCCGGGGAAGACCGGAGCTCAAAGGAGAGACGGCTG
AAGCTGCTACGGCTTTCACTTGTCATTGAACACTCACTCGATGAACTTAACTCACTTTCTGACTT
CCGTTCGCACTCCAACATTTTATGTTCTCTCTACTTGTAAGACAGGGAAAATCAACATAAAACTC
TTTGATGATCTAAGAAGAAGAAGATGATGATGATGATGATGAAGTCAAAAAAGAAAAAAGTGGGA
ATCACTTCAGATGACCGAAATTAAAGACGGTGGATAAAAGCAATCAACTTTGAACATTTTGGGTT
TTAAGAAGATGATTTGATGATGACTGGAAATCTGGAATCAGATACCCGTAAAGGAGATGAAGGAG
AGTCAAATAGTGAAGTAGAAAGAGAGCAGTAAGTTTGAAGGGAAAAAAGGGAGTCAAAAACTATG
GGCAAGCAG
Found at i:40507647 original size:17 final size:17
Alignment explanation
Indices: 40507627--40507659 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40507617 GTTGAGAAAG
*
40507627 TAATTTAATTAAAATTT
1 TAATTTAAATAAAATTT
40507644 TAATTTAAATAAAATT
1 TAATTTAAATAAAATT
40507660 AAATAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATTTAAATAAAATTT
Found at i:40511926 original size:20 final size:19
Alignment explanation
Indices: 40511903--40511942 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40511893 TTTGTGTGCC
*
40511903 TAAATTAAATTTTTTATAAT
1 TAAA-TAAATATTTTATAAT
*
40511923 TAAATAACTATTTTATAAT
1 TAAATAAATATTTTATAAT
40511942 T
1 T
40511943 TACTCAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TAAATAAATATTTTATAAT
Found at i:40512060 original size:6 final size:6
Alignment explanation
Indices: 40512049--40512100 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
40512039 AAATATATAA
* * *
40512049 AAAAAT AAAAAT AAAAAT AAAAAT --AAAT AAAAAT -TAAAT TAAATT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
40512094 AAAAAT A
1 AAAAAT A
40512101 TAATCTCTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
4 4 0.11
5 4 0.11
6 30 0.79
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (6 bp):
AAAAAT
Found at i:40512076 original size:16 final size:16
Alignment explanation
Indices: 40512039--40512100 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
40512029 TTGTAATTTT
*
40512039 AAATATATAAAAA-AA
1 AAATAAATAAAAATAA
*
40512054 TAA-AAATAAAAATAA
1 AAATAAATAAAAATAA
*
40512069 AAATAAATAAAAATTA
1 AAATAAATAAAAATAA
*
40512085 AATTAAATTAAAAATA
1 AAATAAA-TAAAAATA
40512101 TAATCTCTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
14 8 0.21
15 6 0.16
16 17 0.45
17 7 0.18
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAAATAAAAATAA
Found at i:40512076 original size:22 final size:21
Alignment explanation
Indices: 40512038--40512100 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 21
40512028 GTTGTAATTT
*
40512038 TAAATATATAAAAAAATAAAAA
1 TAAAAATA-AAAAAAATAAAAA
40512060 TAAAAATAAAAATAAATAAAAA
1 TAAAAATAAAAA-AAATAAAAA
* *
40512082 TTAAATTAAATTAAAAATA
1 TAAAAATAAA--AAAAATA
40512101 TAATCTCTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 4 0.11
22 24 0.69
23 5 0.14
24 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAAAATAAAAAAAATAAAAA
Found at i:40513224 original size:14 final size:15
Alignment explanation
Indices: 40513198--40513232 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
40513188 TGCTGTCATG
40513198 GAAGAGTAAGAAGAA
1 GAAGAGTAAGAAGAA
40513213 GAAGAG-AAGAAGAA
1 GAAGAGTAAGAAGAA
40513227 GAAGAG
1 GAAGAG
40513233 GGCAGCAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.03
Consensus pattern (15 bp):
GAAGAGTAAGAAGAA
Found at i:40513257 original size:13 final size:13
Alignment explanation
Indices: 40513239--40513273 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
40513229 AGAGGGCAGC
* *
40513239 AAGAAAGGAAAGA
1 AAGAAAGAAAAAA
40513252 AAGAAAGAAAAAA
1 AAGAAAGAAAAAA
40513265 AAGAAAGAA
1 AAGAAAGAA
40513274 GAGAGACGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAGAAAGAAAAAA
Found at i:40513702 original size:11 final size:11
Alignment explanation
Indices: 40513686--40513715 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
40513676 TAAATTTAAG
*
40513686 AATTAAATTTC
1 AATTAAATTCC
40513697 AATTAAATTCC
1 AATTAAATTCC
40513708 AATTAAAT
1 AATTAAAT
40513716 CAACAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (11 bp):
AATTAAATTCC
Found at i:40514028 original size:27 final size:27
Alignment explanation
Indices: 40513990--40514046 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
40513980 TGGCAGCAGC
40513990 ACCGGTGCCGCCTATAGGGTACCCTCA
1 ACCGGTGCCGCCTATAGGGTACCCTCA
*
40514017 ACCGGTGCCGCCTATGGGGTACCCTCA
1 ACCGGTGCCGCCTATAGGGTACCCTCA
40514044 ACC
1 ACC
40514047 TATATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.18, C:0.39, G:0.26, T:0.18
Consensus pattern (27 bp):
ACCGGTGCCGCCTATAGGGTACCCTCA
Found at i:40516311 original size:20 final size:21
Alignment explanation
Indices: 40516283--40516341 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
40516273 AAAAAAAAAG
*
40516283 AAAAGAAAATAATAAATAAT-
1 AAAATAAAATAATAAATAATA
*
40516303 AAAATAAAAAAATAAA-AATA
1 AAAATAAAATAATAAATAATA
40516323 AAAATAAAAATAA-AAATAA
1 AAAAT-AAAATAATAAATAA
40516342 AGATTGGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 3 0.09
20 22 0.67
21 8 0.24
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (21 bp):
AAAATAAAATAATAAATAATA
Found at i:40516319 original size:6 final size:6
Alignment explanation
Indices: 40516293--40516342 Score: 73
Period size: 6 Copynumber: 8.0 Consensus size: 6
40516283 AAAAGAAAAT
*
40516293 AATAAA TAATAAA ATAAAAA AATAAA AATAAA AATAAA AATAAA AATAAA
1 AATAAA -AATAAA A-ATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
40516343 GATTGGGTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
6 29 0.73
7 11 0.28
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:40522785 original size:26 final size:26
Alignment explanation
Indices: 40522748--40522800 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
40522738 AGTGGTACTT
*
40522748 AAACTATCATTCCGTTACCCGGTTCA
1 AAACTATCATTCCGTTACCCAGTTCA
*
40522774 AAACTATTATTCCGTTACCCAGTTCA
1 AAACTATCATTCCGTTACCCAGTTCA
40522800 A
1 A
40522801 CCTTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.32
Consensus pattern (26 bp):
AAACTATCATTCCGTTACCCAGTTCA
Found at i:40531638 original size:21 final size:21
Alignment explanation
Indices: 40531614--40531653 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40531604 AACCAAATTT
40531614 TATATAAAATATAAAAAATCA
1 TATATAAAATATAAAAAATCA
* *
40531635 TATATAATATATAATAAAT
1 TATATAAAATATAAAAAAT
40531654 TTTAAACAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
TATATAAAATATAAAAAATCA
Found at i:40531644 original size:26 final size:25
Alignment explanation
Indices: 40531589--40531652 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
40531579 AATTTAAAAA
* *
40531589 AATATAAATTAAAAAAACCAAATTT
1 AATATAAAATAAAAAAACCAAATAT
* * *
40531614 TATATAAAATATAAAAAATCATATAT
1 AATATAAAATA-AAAAAACCAAATAT
*
40531640 AATATATAATAAA
1 AATATAAAATAAA
40531653 TTTTAAACAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
25 11 0.35
26 20 0.65
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (25 bp):
AATATAAAATAAAAAAACCAAATAT
Found at i:40531742 original size:46 final size:46
Alignment explanation
Indices: 40531689--40531779 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
40531679 AATATATAAA
* * *
40531689 TATATAAAAAT-CAAATATTATATAAATATTGAAATTTAAAAAAATT
1 TATATAAAAATAAAAAAATTATATAAAAATTGAAA-TTAAAAAAATT
* *
40531735 TATATAAAATTAAAAAAATTATATAAAAATTTAAATTAAAAAAAT
1 TATATAAAAATAAAAAAATTATATAAAAATTGAAATTAAAAAAAT
40531780 CTAAAATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 20 0.51
47 19 0.49
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (46 bp):
TATATAAAAATAAAAAAATTATATAAAAATTGAAATTAAAAAAATT
Found at i:40531744 original size:21 final size:21
Alignment explanation
Indices: 40531720--40531769 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 21
40531710 ATAAATATTG
40531720 AAATTTAAAAAAATT-TATATA
1 AAATTTAAAAAAATTATATA-A
40531741 AAA-TTAAAAAAATTATATAA
1 AAATTTAAAAAAATTATATAA
40531761 AAATTTAAA
1 AAATTTAAA
40531770 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATTTAAAAAAATTATATAA
Found at i:40531765 original size:20 final size:20
Alignment explanation
Indices: 40531724--40531762 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
40531714 ATATTGAAAT
40531724 TTAAAAAAATTTATATAAAA
1 TTAAAAAAATTTATATAAAA
40531744 TTAAAAAAA-TTATATAAAA
1 TTAAAAAAATTTATATAAAA
40531763 ATTTAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAAAAAATTTATATAAAA
Found at i:40531802 original size:16 final size:16
Alignment explanation
Indices: 40531750--40531803 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
40531740 AAAATTAAAA
*
40531750 AAATTATATAAAAATTT
1 AAATTATA-AAAAATAT
*
40531767 AAATTA-AAAAAATCT
1 AAATTATAAAAAATAT
*
40531782 AAAATTATAAAACATAT
1 -AAATTATAAAAAATAT
40531799 AAATT
1 AAATT
40531804 GAAAATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 7 0.22
16 12 0.38
17 13 0.41
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATTATAAAAAATAT
Found at i:40531802 original size:23 final size:21
Alignment explanation
Indices: 40531782--40531823 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
40531772 AAAAAAATCT
40531782 AAAATTATAAAACATATAAATTG
1 AAAATTATAAAA-ATA-AAATTG
*
40531805 AAAATTTTAAAAATAAAAT
1 AAAATTATAAAAATAAAAT
40531824 ATTATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 3 0.17
23 11 0.61
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAATTATAAAAATAAAATTG
Found at i:40531931 original size:33 final size:33
Alignment explanation
Indices: 40531869--40531933 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
40531859 TTTCAAAAAC
* *
40531869 TCTAAATTCTAAAAATTCTAATATATATATATA
1 TCTAAATTCTAAAAATTCAAAAATATATATATA
*
40531902 TCTAAATTTCTAAAAATT-AAAAATTTATATAT
1 TCTAAA-TTCTAAAAATTCAAAAATATATATAT
40531934 GTTTTGGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 17 0.61
34 11 0.39
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (33 bp):
TCTAAATTCTAAAAATTCAAAAATATATATATA
Found at i:40531958 original size:20 final size:20
Alignment explanation
Indices: 40531933--40531981 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
40531923 AATTTATATA
40531933 TGTTTTGGATGAACTTTGTC
1 TGTTTTGGATGAACTTTGTC
*
40531953 TGTTTTGGATGAAGTTTGTC
1 TGTTTTGGATGAACTTTGTC
*
40531973 TATTTTGGA
1 TGTTTTGGA
40531982 AATTTAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.16, C:0.06, G:0.27, T:0.51
Consensus pattern (20 bp):
TGTTTTGGATGAACTTTGTC
Found at i:40536564 original size:16 final size:15
Alignment explanation
Indices: 40536534--40536563 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40536524 TATTCTAAAA
40536534 AAAATTAAATATTTT
1 AAAATTAAATATTTT
40536549 AAAATTAAATATTTT
1 AAAATTAAATATTTT
40536564 TCTAAAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAATTAAATATTTT
Found at i:40542010 original size:25 final size:25
Alignment explanation
Indices: 40541974--40542089 Score: 78
Period size: 25 Copynumber: 4.6 Consensus size: 25
40541964 AATATCAGGT
40541974 AGCTCTAT-AGAGCTATTAATCGGAA
1 AGCTC-ATGAGAGCTATTAATCGGAA
** * *
40541999 AGCTTGTGAGAGCCATATAAT-GGGA
1 AGCTCATGAGAGCTAT-TAATCGGAA
* * *
40542024 TGCTCATGAGAGCTAAATAA-AGGAA
1 AGCTCATGAGAGCT-ATTAATCGGAA
* *
40542049 AGCTCGTGAGAGACTATT-ATCGGGA
1 AGCTCATGAGAG-CTATTAATCGGAA
*
40542074 CGCTCATGAGAGCTAT
1 AGCTCATGAGAGCTAT
40542090 GGTGTTTCTG
Statistics
Matches: 68, Mismatches: 17, Indels: 13
0.69 0.17 0.13
Matches are distributed among these distances:
24 6 0.09
25 55 0.81
26 7 0.10
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.24
Consensus pattern (25 bp):
AGCTCATGAGAGCTATTAATCGGAA
Found at i:40542037 original size:50 final size:49
Alignment explanation
Indices: 40541982--40542089 Score: 128
Period size: 50 Copynumber: 2.2 Consensus size: 49
40541972 GTAGCTCTAT
* * * *
40541982 AGAGCTATTAATCGGAAAGCTTGTGAGAGCCATATAAT-GGGATGCTCATG
1 AGAGCTATTAA-AGGAAAGCTCGTGAGAGAC-TATAATCGGGACGCTCATG
* *
40542032 AGAGCTAAATAAAGGAAAGCTCGTGAGAGACTATTATCGGGACGCTCATG
1 AGAGCT-ATTAAAGGAAAGCTCGTGAGAGACTATAATCGGGACGCTCATG
40542082 AGAGCTAT
1 AGAGCTAT
40542090 GGTGTTTCTG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
49 6 0.12
50 39 0.80
51 4 0.08
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (49 bp):
AGAGCTATTAAAGGAAAGCTCGTGAGAGACTATAATCGGGACGCTCATG
Found at i:40545605 original size:19 final size:19
Alignment explanation
Indices: 40545563--40545619 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
40545553 TACTTCATGC
* *
40545563 AATTTTTTTTAAAATTCTT
1 AATTTTTTTTATAATTTTT
*
40545582 -ATTTTTTTT-GAATTTTT
1 AATTTTTTTTATAATTTTT
40545599 AATTTTTTTTATAATTTTT
1 AATTTTTTTTATAATTTTT
40545618 AA
1 AA
40545620 ATTATGTGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 6 0.18
18 18 0.55
19 9 0.27
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (19 bp):
AATTTTTTTTATAATTTTT
Found at i:40549855 original size:17 final size:15
Alignment explanation
Indices: 40549828--40549866 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
40549818 ATATAAGAAC
*
40549828 ATTTTATTATTAAATT
1 ATTTTAATATT-AATT
40549844 ATATTTAATATTAATT
1 AT-TTTAATATTAATT
40549860 ATTTTAA
1 ATTTTAA
40549867 ATTGTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 8 0.38
17 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTAATATTAATT
Found at i:40550984 original size:13 final size:13
Alignment explanation
Indices: 40550966--40550990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40550956 GAGAAATTAC
40550966 TAAATAAGAATAT
1 TAAATAAGAATAT
40550979 TAAATAAGAATA
1 TAAATAAGAATA
40550991 AATTTTATTT
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:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (13 bp):
TAAATAAGAATAT
Found at i:40561250 original size:55 final size:55
Alignment explanation
Indices: 40561166--40561284 Score: 193
Period size: 55 Copynumber: 2.2 Consensus size: 55
40561156 CAATAGGTCT
* * *
40561166 TCATATAGGGTTCAGGTATGGTTTAAGTTGGAAATGGTGTTTATATTCCTATGAC
1 TCATATAGGGTACAGGTATGGTTCAAGTTGGAAATGGTGCTTATATTCCTATGAC
* *
40561221 TCATATAGGGTACATGTATGGTTCAAGTTGGAAATGGTGCTTATATTCCTATTAC
1 TCATATAGGGTACAGGTATGGTTCAAGTTGGAAATGGTGCTTATATTCCTATGAC
40561276 TCATATAGG
1 TCATATAGG
40561285 CCAATTAGCA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.39
Consensus pattern (55 bp):
TCATATAGGGTACAGGTATGGTTCAAGTTGGAAATGGTGCTTATATTCCTATGAC
Found at i:40566833 original size:24 final size:24
Alignment explanation
Indices: 40566801--40566849 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
40566791 CCAAACTATG
40566801 ACTTTTATATGCAATTATATTGTA
1 ACTTTTATATGCAATTATATTGTA
40566825 ACTTTTATATGCAATTATATTGTA
1 ACTTTTATATGCAATTATATTGTA
40566849 A
1 A
40566850 TTATGGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (24 bp):
ACTTTTATATGCAATTATATTGTA
Found at i:40569422 original size:43 final size:43
Alignment explanation
Indices: 40569358--40569554 Score: 209
Period size: 43 Copynumber: 4.6 Consensus size: 43
40569348 CATAGGATTC
*
40569358 CGATATGTGATTTCGTGTAAGACCACGTTTGGGACGTTGGCAT
1 CGATATGTGATTTCGTGTAAGACCATGTTTGGGACGTTGGCAT
* *
40569401 CGATATGTGATTTCATATAAGACCATGTTTGGGACGTTGGCAT
1 CGATATGTGATTTCGTGTAAGACCATGTTTGGGACGTTGGCAT
* * * **
40569444 CGATTTGTGATTTACGTGTAAGACCATGTCTGGGACATTGGTGT
1 CGATATGTGATTT-CGTGTAAGACCATGTTTGGGACGTTGGCAT
* * * ** *
40569488 TGTATATG-G-TTTCGTGTAAGACCCTGTCTGGGACAATGGCTT
1 CG-ATATGTGATTTCGTGTAAGACCATGTTTGGGACGTTGGCAT
* * *
40569530 CGATATTTGATTACATGTAAGACCA
1 CGATATGTGATTTCGTGTAAGACCA
40569555 CATCCGGGAC
Statistics
Matches: 129, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
41 4 0.03
42 28 0.22
43 67 0.52
44 26 0.20
45 4 0.03
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (43 bp):
CGATATGTGATTTCGTGTAAGACCATGTTTGGGACGTTGGCAT
Found at i:40569520 original size:86 final size:88
Alignment explanation
Indices: 40569358--40569577 Score: 236
Period size: 86 Copynumber: 2.6 Consensus size: 88
40569348 CATAGGATTC
* * * *
40569358 CGATATGTGATTT-CGTGTAAGACCACGTTTGGGACGTTGGCATCG-ATATGTGATTTCATATAA
1 CGATTTGTGATTTACGTGTAAGACCACGTCTGGGACGTTGGCGTTGTATATGTGATTTCATATAA
* **
40569421 GACCATGTTTGGGACGTTGGCAT
66 GACCATGTCTGGGACAATGGCAT
* * * * *
40569444 CGATTTGTGATTTACGTGTAAGACCATGTCTGGGACATTGGTGTTGTATATG-G-TTTCGTGTAA
1 CGATTTGTGATTTACGTGTAAGACCACGTCTGGGACGTTGGCGTTGTATATGTGATTTCATATAA
* *
40569507 GACCCTGTCTGGGACAATGGCTT
66 GACCATGTCTGGGACAATGGCAT
* * *
40569530 CGATATT-TGA-TTACATGTAAGACCACATCCGGGACGTTGGCGTTGTAT
1 CGAT-TTGTGATTTACGTGTAAGACCACGTCTGGGACGTTGGCGTTGTAT
40569578 GAGTTTATGA
Statistics
Matches: 111, Mismatches: 20, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
85 32 0.29
86 45 0.41
87 29 0.26
88 5 0.05
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (88 bp):
CGATTTGTGATTTACGTGTAAGACCACGTCTGGGACGTTGGCGTTGTATATGTGATTTCATATAA
GACCATGTCTGGGACAATGGCAT
Found at i:40583897 original size:18 final size:18
Alignment explanation
Indices: 40583871--40583905 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40583861 TAGTCAAACG
*
40583871 AATCGAATTATTTGAATT
1 AATCAAATTATTTGAATT
40583889 AATCAAATTATTTGAAT
1 AATCAAATTATTTGAAT
40583906 CAACTCGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (18 bp):
AATCAAATTATTTGAATT
Found at i:40584117 original size:21 final size:22
Alignment explanation
Indices: 40584091--40584141 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
40584081 NNNNCCCCCC
40584091 CCCCCAA-TTTTACTATCTCAA
1 CCCCCAAGTTTTACTATCTCAA
*
40584112 CCCCCAATGTTTTACTCTCTCAA
1 CCCCCAA-GTTTTACTATCTCAA
40584135 CCCCCAA
1 CCCCCAA
40584142 AACATTTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 7 0.26
23 20 0.74
ACGTcount: A:0.25, C:0.43, G:0.02, T:0.29
Consensus pattern (22 bp):
CCCCCAAGTTTTACTATCTCAA
Found at i:40584168 original size:19 final size:19
Alignment explanation
Indices: 40584135--40584173 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
40584125 ACTCTCTCAA
40584135 CCCCCAAAACATTTTACTTT
1 CCCCCAAAACATTTTA-TTT
40584155 CCCCCAAAAC-TTTTATTT
1 CCCCCAAAACATTTTATTT
40584173 C
1 C
40584174 TCACCTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 5 0.26
20 10 0.53
ACGTcount: A:0.28, C:0.36, G:0.00, T:0.36
Consensus pattern (19 bp):
CCCCCAAAACATTTTATTT
Found at i:40586070 original size:19 final size:18
Alignment explanation
Indices: 40586046--40586084 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
40586036 CCTAGTGGTC
*
40586046 CTTGGAGACAGTGTTCGCA
1 CTTGGAG-CAGTGTTCACA
*
40586065 CTTGGAGGAGTGTTCACA
1 CTTGGAGCAGTGTTCACA
40586083 CT
1 CT
40586085 AAGAAGCGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.28
Consensus pattern (18 bp):
CTTGGAGCAGTGTTCACA
Found at i:40591267 original size:18 final size:19
Alignment explanation
Indices: 40591220--40591273 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 19
40591210 GATAATTCAT
40591220 AACAAATTTTAAAAAAAATAC
1 AACAAATTTT--AAAAAATAC
40591241 AA-AATATTTTAAAAAAT-C
1 AACAA-ATTTTAAAAAATAC
40591259 AACAAA-TTTAAAAAA
1 AACAAATTTTAAAAAA
40591274 AGTTTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 9 0.29
18 4 0.13
19 9 0.29
20 2 0.06
21 7 0.23
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (19 bp):
AACAAATTTTAAAAAATAC
Found at i:40591274 original size:18 final size:19
Alignment explanation
Indices: 40591220--40591274 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 19
40591210 GATAATTCAT
40591220 AACAAATTTTAAAAAAAATAC
1 AACAAA-TTT-AAAAAAATAC
*
40591241 AA-AATATTTTAAAAAAT-C
1 AACAA-ATTTAAAAAAATAC
40591259 AACAAATTTAAAAAAA
1 AACAAATTTAAAAAAA
40591275 GTTTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 13 0.43
19 9 0.30
20 5 0.17
21 3 0.10
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.25
Consensus pattern (19 bp):
AACAAATTTAAAAAAATAC
Found at i:40592871 original size:29 final size:28
Alignment explanation
Indices: 40592799--40592953 Score: 148
Period size: 29 Copynumber: 5.3 Consensus size: 28
40592789 GGTGTATTAG
*
40592799 CGACCATCGAATATGAAAAGGGATGGTTT
1 CGACCATC-AATATGAAAAGGGATGGTTA
* ** * *
40592828 TGAATATCTATTATGAAAAGGGATGGTGA
1 CGACCATC-AATATGAAAAGGGATGGTTA
*
40592857 CGACCATCAACTATGAAAAGGGATGGTGA
1 CGACCATCAA-TATGAAAAGGGATGGTTA
* * *
40592886 CGACCATCGATTAATGAAAATGGATGGTTT
1 CGACCATC-AAT-ATGAAAAGGGATGGTTA
**
40592916 CGACCATCGAATATGAAAAGGGACAGTTA
1 CGACCATC-AATATGAAAAGGGATGGTTA
40592945 CGACCATCA
1 CGACCATCA
40592954 TTTAGCACAC
Statistics
Matches: 103, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
28 2 0.02
29 75 0.73
30 26 0.25
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (28 bp):
CGACCATCAATATGAAAAGGGATGGTTA
Found at i:40592922 original size:59 final size:58
Alignment explanation
Indices: 40592799--40592952 Score: 184
Period size: 59 Copynumber: 2.6 Consensus size: 58
40592789 GGTGTATTAG
** ** *
40592799 CGACCATCGAATATGAAAAGGGATGGTTTTGAATATCTATTATGAAAAGGGATGGTGA
1 CGACCATCGAATATGAAAAGGGATGGTTACGACCATCGATTATGAAAAGGGATGGTGA
* * **
40592857 CGACCATC-AACTATGAAAAGGGATGGTGACGACCATCGATTAATGAAAATGGATGGTTT
1 CGACCATCGAA-TATGAAAAGGGATGGTTACGACCATCGATT-ATGAAAAGGGATGGTGA
**
40592916 CGACCATCGAATATGAAAAGGGACAGTTACGACCATC
1 CGACCATCGAATATGAAAAGGGATGGTTACGACCATC
40592953 ATTTAGCACA
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
57 2 0.02
58 32 0.40
59 45 0.56
60 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.23
Consensus pattern (58 bp):
CGACCATCGAATATGAAAAGGGATGGTTACGACCATCGATTATGAAAAGGGATGGTGA
Found at i:40595203 original size:25 final size:26
Alignment explanation
Indices: 40595165--40595272 Score: 91
Period size: 25 Copynumber: 4.3 Consensus size: 26
40595155 CATGTAAACT
**
40595165 GGAAGCTCTTTCGAGCCATATAA-CG
1 GGAAGCTCAATCGAGCCATATAATCG
***
40595190 GGAAGCTCAATCGAGTTGTAT-ATCG
1 GGAAGCTCAATCGAGCCATATAATCG
*
40595215 AGAAGCTC-ATGCGAGCCATA-AATCG
1 GGAAGCTCAAT-CGAGCCATATAATCG
** *
40595240 GGAAGCTCAAGAGAGTCAT-TAATCG
1 GGAAGCTCAATCGAGCCATATAATCG
40595265 GGAAGCTC
1 GGAAGCTC
40595273 GTGAGAGCCA
Statistics
Matches: 65, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
24 3 0.05
25 61 0.94
26 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.21
Consensus pattern (26 bp):
GGAAGCTCAATCGAGCCATATAATCG
Found at i:40595270 original size:50 final size:50
Alignment explanation
Indices: 40595165--40595282 Score: 125
Period size: 50 Copynumber: 2.4 Consensus size: 50
40595155 CATGTAAACT
* * **
40595165 GGAAGCTCTTTCGAGCCATATAACGGGAAGCTCAATCGAGTTGTATATCG
1 GGAAGCTCATGCGAGCCATATAACGGGAAGCTCAAGAGAGTTGTATATCG
*
40595215 AGAAGCTCATGCGAGCCATA-AATCGGGAAGCTCAAGAGAGTCAT-TA-ATCG
1 GGAAGCTCATGCGAGCCATATAA-CGGGAAGCTCAAGAGAGT--TGTATATCG
* *
40595265 GGAAGCTCGTGAGAGCCA
1 GGAAGCTCATGCGAGCCA
40595283 AATATTGGGA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
49 2 0.04
50 52 0.91
51 2 0.04
52 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.20
Consensus pattern (50 bp):
GGAAGCTCATGCGAGCCATATAACGGGAAGCTCAAGAGAGTTGTATATCG
Found at i:40595278 original size:25 final size:25
Alignment explanation
Indices: 40595211--40595299 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 25
40595201 CGAGTTGTAT
* *
40595211 ATCGAGAAGCTCATGCGAGCCATAA
1 ATCGGGAAGCTCATGAGAGCCATAA
* * *
40595236 ATCGGGAAGCTCAAGAGAGTCATTA
1 ATCGGGAAGCTCATGAGAGCCATAA
*
40595261 ATCGGGAAGCTCGTGAGAGCCA-AA
1 ATCGGGAAGCTCATGAGAGCCATAA
* *
40595285 TATTGGGATGCTCAT
1 -ATCGGGAAGCTCAT
40595300 AAATGATGTG
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
24 1 0.02
25 50 0.98
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20
Consensus pattern (25 bp):
ATCGGGAAGCTCATGAGAGCCATAA
Found at i:40596824 original size:27 final size:27
Alignment explanation
Indices: 40596767--40596826 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
40596757 TTTGCCTTTT
* *
40596767 TTATATTATTTATTATTGTATTTGTCG
1 TTATATTATTTATTATTGTATGTGTCA
* *
40596794 TTATATTA-TTATTATTATTATGTGTTA
1 TTATATTATTTATTATT-GTATGTGTCA
40596821 TTATAT
1 TTATAT
40596827 ATATCTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (27 bp):
TTATATTATTTATTATTGTATGTGTCA
Found at i:40597044 original size:9 final size:9
Alignment explanation
Indices: 40597030--40597055 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
40597020 TATAATATAG
40597030 GTATATATT
1 GTATATATT
40597039 GTATATATT
1 GTATATATT
40597048 GTATATAT
1 GTATATAT
40597056 ATTATGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (9 bp):
GTATATATT
Found at i:40597379 original size:23 final size:21
Alignment explanation
Indices: 40597342--40597383 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
40597332 TATTACTATA
40597342 ACTATTATTTATTAGTATTTT
1 ACTATTATTTATTAGTATTTT
40597363 ACTATTACTATTATTAGTATT
1 ACTATTA-T-TTATTAGTATT
40597384 ATTTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 1 0.05
23 11 0.58
ACGTcount: A:0.31, C:0.07, G:0.05, T:0.57
Consensus pattern (21 bp):
ACTATTATTTATTAGTATTTT
Found at i:40597389 original size:27 final size:25
Alignment explanation
Indices: 40597328--40597389 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 25
40597318 TTATACGTTC
*
40597328 TTATTATTACTATAACTATTATTTA
1 TTATTTTTACTATAACTATTATTTA
*
40597353 TTAGTATTTTACTATTACTATTATTAGTA
1 TTA-T-TTTTACTATAACTATTATT--TA
40597382 TTATTTTT
1 TTATTTTT
40597390 TTTAAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 3 0.10
26 1 0.03
27 21 0.68
28 1 0.03
29 5 0.16
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (25 bp):
TTATTTTTACTATAACTATTATTTA
Found at i:40597513 original size:26 final size:26
Alignment explanation
Indices: 40597459--40597518 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
40597449 ATATGTATGG
*
40597459 TGTATATTCTTAATATTATATATTGTA
1 TGTATATTCTTAATA-TATATATTATA
*
40597486 TGTATTTTCTTAATA-ACTATATTATA
1 TGTATATTCTTAATATA-TATATTATA
40597512 TGTATAT
1 TGTATAT
40597519 ATAGTATGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 1 0.03
26 14 0.48
27 14 0.48
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (26 bp):
TGTATATTCTTAATATATATATTATA
Found at i:40597558 original size:20 final size:20
Alignment explanation
Indices: 40597533--40597572 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
40597523 TATGTACATA
40597533 TTTTTAATAT-TATTATGTAT
1 TTTTTAATATATA-TATGTAT
40597553 TTTTTAATATATATATGTAT
1 TTTTTAATATATATATGTAT
40597573 ATGTGTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTTAATATATATATGTAT
Found at i:40597873 original size:27 final size:27
Alignment explanation
Indices: 40597843--40597895 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
40597833 ATATTATATA
*
40597843 TATTTTTAATACTA-TGTATATATTTTT
1 TATTCTTAATACTACT-TATATATTTTT
* *
40597870 TATTCTTATTATTACTTATATATTTT
1 TATTCTTAATACTACTTATATATTTT
40597896 AATACATACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (27 bp):
TATTCTTAATACTACTTATATATTTTT
Found at i:40597939 original size:3 final size:3
Alignment explanation
Indices: 40597931--40597956 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40597921 TTATCATTGT
40597931 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
40597957 GCTTTCAATA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.