Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 13 of 378
Found at i:3670063 original size:226 final size:225
Alignment explanation
Indices: 3669590--3670263 Score: 1114
Period size: 226 Copynumber: 3.0 Consensus size: 225
3669580 ATAGAATTAA
* * * *
3669590 TGTAAGGTTGCTTATATTAGGCATGATTAAATTAATTAGAGAAGATCACAGTCTAATCAACACAA
1 TGTAAGGTTGCTTATATTTGGCATGATTATATTAATTAGAGAAGATCACAGTGTAATCAACTCAA
*
3669655 TAATACAAAAACATTGAGAAGAAAGGCACATGTATTTATTTTCTCCAGATATCTTCTTAATTATC
66 TAATACAAAAA-ATTGAGAAGAAAGGCACATGTATTTATTTTCTCCAGAGATCTTC-T--TT-TC
* *
3669720 ACTTTATGCATGAAATATATGTAATTTGCTAATTATGGATAGAATTGAGAAGAATATTGCCTTCT
126 ACTTTATGCATGAAATATATGTAATTTGCTAATTATGGATAGATTTGAGAAGAATATTGCCTTGT
*
3669785 TTAGTTTACTGGTGCTATATTAAAACTACTAAGAG
191 TTAGTTTACTGGTGCTTTATTAAAACTACTAAGAG
* *
3669820 TGTAAGGTTGCTTATATTTGGCATGATTATATTAATTAGAGAAGATCAGAGTGTAATCAATTCAA
1 TGTAAGGTTGCTTATATTTGGCATGATTATATTAATTAGAGAAGATCACAGTGTAATCAACTCAA
3669885 TAATACAAAAAATTGAGAAGAAAGGCACATGTATTTATTTTCTCCAGAGATCTTCTTTTCACTTT
66 TAATACAAAAAATTGAGAAGAAAGGCACATGTATTTATTTTCTCCAGAGATCTTCTTTTCACTTT
3669950 ATGCATGAAATATATGTAATTTGCTAATTATGGATAGAGTTTGAGAAGAATATTGCCTTGTTTAG
131 ATGCATGAAATATATGTAATTTGCTAATTATGGATAGA-TTTGAGAAGAATATTGCCTTGTTTAG
*
3670015 TTTACTGGGGCTTTATTAAAACTACTAAGAG
195 TTTACTGGTGCTTTATTAAAACTACTAAGAG
* *
3670046 TGTAAGGTTGGTTATATTTGGCATGATTATATTAATTAGAGAAGATCACAGAGTAATCAACTCAA
1 TGTAAGGTTGCTTATATTTGGCATGATTATATTAATTAGAGAAGATCACAGTGTAATCAACTCAA
* * *
3670111 TAATACAAAAAATTCAGAAGAAAGGCACATGTATTTATTTTCTCGCCAGTGATCTTCTTATCACT
66 TAATACAAAAAATTGAGAAGAAAGGCACATGTATTTATTTTCT--CCAGAGATCTTCTTTTCACT
3670176 TTATGCATGAAATATATGTAATTTGCTAATTATGGATAGAATTTGAGAAGAATATTGCCTTGTTT
129 TTATGCATGAAATATATGTAATTTGCTAATTATGGATAG-ATTTGAGAAGAATATTGCCTTGTTT
*
3670241 AGTTTACTGGTGCTTTGTTAAAA
193 AGTTTACTGGTGCTTTATTAAAA
3670264 GTATGAAGTT
Statistics
Matches: 420, Mismatches: 20, Indels: 10
0.93 0.04 0.02
Matches are distributed among these distances:
225 45 0.11
226 158 0.38
228 103 0.25
229 44 0.10
230 70 0.17
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.36
Consensus pattern (225 bp):
TGTAAGGTTGCTTATATTTGGCATGATTATATTAATTAGAGAAGATCACAGTGTAATCAACTCAA
TAATACAAAAAATTGAGAAGAAAGGCACATGTATTTATTTTCTCCAGAGATCTTCTTTTCACTTT
ATGCATGAAATATATGTAATTTGCTAATTATGGATAGATTTGAGAAGAATATTGCCTTGTTTAGT
TTACTGGTGCTTTATTAAAACTACTAAGAG
Found at i:3670343 original size:31 final size:31
Alignment explanation
Indices: 3670294--3670352 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
3670284 ATGTGCATAT
* *
3670294 ATTTGATTATCAATCTTTTAAAATGAGTCAA
1 ATTTAATTATCAACCTTTTAAAATGAGTCAA
*
3670325 ATTTAATTATTAACCTTTTAAAATGAGT
1 ATTTAATTATCAACCTTTTAAAATGAGT
3670353 TGAATTGCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (31 bp):
ATTTAATTATCAACCTTTTAAAATGAGTCAA
Found at i:3671004 original size:52 final size:52
Alignment explanation
Indices: 3670926--3671029 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
3670916 AAAGCTACAT
*
3670926 TAATAGATTGATAAATTTTAAATAGTGACTAGTATATCATACAATAAATCAA
1 TAATAGATTGATAAATTTTAAATAGTGACTAGTATACCATACAATAAATCAA
3670978 TAATAGATTGATAAATTTTAAATAGTGACTAGTATACCATACAATAAATCAA
1 TAATAGATTGATAAATTTTAAATAGTGACTAGTATACCATACAATAAATCAA
3671030 AAGTTGTTGA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.34
Consensus pattern (52 bp):
TAATAGATTGATAAATTTTAAATAGTGACTAGTATACCATACAATAAATCAA
Found at i:3674265 original size:15 final size:15
Alignment explanation
Indices: 3674247--3674279 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3674237 ATAAAAAATG
3674247 TAAGTTTAAATACGT
1 TAAGTTTAAATACGT
3674262 TAAGTTTAAATACGT
1 TAAGTTTAAATACGT
3674277 TAA
1 TAA
3674280 AATGTACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (15 bp):
TAAGTTTAAATACGT
Found at i:3682344 original size:42 final size:41
Alignment explanation
Indices: 3682281--3682359 Score: 131
Period size: 42 Copynumber: 1.9 Consensus size: 41
3682271 TCAATTTTTT
*
3682281 GAAAATACCAAATTTAATGGAACTAAAATTTTAAAAGTCCA
1 GAAAATACAAAATTTAATGGAACTAAAATTTTAAAAGTCCA
*
3682322 GAAAATAGCAAAATTTAGTGGAACTAAAATTTTAAAAG
1 GAAAATA-CAAAATTTAATGGAACTAAAATTTTAAAAG
3682360 CATATGGACT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 7 0.20
42 28 0.80
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.27
Consensus pattern (41 bp):
GAAAATACAAAATTTAATGGAACTAAAATTTTAAAAGTCCA
Found at i:3684836 original size:33 final size:33
Alignment explanation
Indices: 3684770--3684836 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 33
3684760 ATAAATACTT
*
3684770 ATTTTTTTTATTTTTCAATAAAACGAAAACATGA
1 ATTTTTTCTATTTTTCAATAAAAC-AAAACATGA
* *
3684804 ATTTATTTCTATTTTTCTATAATAC-AAACATGA
1 ATTT-TTTCTATTTTTCAATAAAACAAAACATGA
3684837 GAAAAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 8 0.28
34 4 0.14
35 17 0.59
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.46
Consensus pattern (33 bp):
ATTTTTTCTATTTTTCAATAAAACAAAACATGA
Found at i:3695618 original size:21 final size:21
Alignment explanation
Indices: 3695592--3695640 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3695582 TGACGTTTTG
3695592 GAAGCCACCATAGAAATTGCT
1 GAAGCCACCATAGAAATTGCT
* **
3695613 GAAGCCACCATTGATCTTGCT
1 GAAGCCACCATAGAAATTGCT
3695634 GAAGCCA
1 GAAGCCA
3695641 TTGGTGATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (21 bp):
GAAGCCACCATAGAAATTGCT
Found at i:3697088 original size:24 final size:24
Alignment explanation
Indices: 3697047--3697111 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
3697037 TGTTACTTTC
*
3697047 ACAGTTGGGA-CTTCTTT-GAACTTA
1 ACAGTTGGAACCTT-TTTGGAA-TTA
3697071 ACAGTTGGAACCTTTTTGGAATTA
1 ACAGTTGGAACCTTTTTGGAATTA
* * *
3697095 ATAATTGGAGCCTTTTT
1 ACAGTTGGAACCTTTTT
3697112 TTTAAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
24 29 0.83
25 6 0.17
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (24 bp):
ACAGTTGGAACCTTTTTGGAATTA
Found at i:3698386 original size:5 final size:5
Alignment explanation
Indices: 3698376--3698409 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
3698366 GCATAGTGTG
3698376 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
3698410 AACACATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:3704141 original size:5 final size:5
Alignment explanation
Indices: 3704131--3704171 Score: 64
Period size: 5 Copynumber: 7.8 Consensus size: 5
3704121 CGAATTTGTA
3704131 AAAAT AAAAT AAAAT AAAAT AAAAAGT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT -AAAA-T AAAAT AAAAT AAAA
3704172 CACACAGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 25 0.74
6 8 0.24
7 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:3704160 original size:22 final size:21
Alignment explanation
Indices: 3704129--3704171 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
3704119 TACGAATTTG
3704129 TAAAAATAAAATAAAATAAAA
1 TAAAAATAAAATAAAATAAAA
3704150 TAAAAAGTAAAATAAAATAAAA
1 TAAAAA-TAAAATAAAATAAAA
3704172 CACACAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (21 bp):
TAAAAATAAAATAAAATAAAA
Found at i:3704373 original size:25 final size:25
Alignment explanation
Indices: 3704343--3704393 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
3704333 AGAAAAGAAG
3704343 TGTAATTCTATATGAATTTTACTTT
1 TGTAATTCTATATGAATTTTACTTT
3704368 TGTAATTCTATATGAATTTTACTTT
1 TGTAATTCTATATGAATTTTACTTT
3704393 T
1 T
3704394 ATTTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (25 bp):
TGTAATTCTATATGAATTTTACTTT
Found at i:3707311 original size:12 final size:11
Alignment explanation
Indices: 3707287--3707316 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
3707277 TAGATTTGGT
3707287 AAATAAAATAA
1 AAATAAAATAA
3707298 AAATAAACATAA
1 AAATAAA-ATAA
3707310 AAATAAA
1 AAATAAA
3707317 TATTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:3708999 original size:18 final size:18
Alignment explanation
Indices: 3708967--3709001 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3708957 TTATGTGTAT
* *
3708967 TGTATTTGTACATAAATA
1 TGTATTTGAAAATAAATA
3708985 TGTATTTGAAAATAAAT
1 TGTATTTGAAAATAAAT
3709002 GTTGTTTTGG
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:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (18 bp):
TGTATTTGAAAATAAATA
Found at i:3720599 original size:25 final size:23
Alignment explanation
Indices: 3720559--3720608 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
3720549 ATTTTTATTT
3720559 TTATTTTTAAAATATTTAAA-ATA
1 TTATTTTTAAAATA-TTAAACATA
*
3720582 TTATATTTTAATATTATTAAACATA
1 TTAT-TTTTAA-AATATTAAACATA
3720607 TT
1 TT
3720609 TAATTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 4 0.17
24 11 0.48
25 8 0.35
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TTATTTTTAAAATATTAAACATA
Found at i:3720624 original size:33 final size:29
Alignment explanation
Indices: 3720552--3720624 Score: 76
Period size: 34 Copynumber: 2.3 Consensus size: 29
3720542 TGATAATATT
3720552 TTTATTTTT-ATTTTTAAAATATTTAAAA
1 TTTATTTTTAATTTTTAAAATATTTAAAA
*
3720580 TATTATATTTTAATATTATTAAACATATTTAATTA
1 T-TTAT-TTTTAAT-TT-TTAAA-ATATTTAA-AA
3720615 TTTATTTTTA
1 TTTATTTTTA
3720625 GTAATATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
28 1 0.03
29 4 0.11
30 4 0.11
31 2 0.05
32 2 0.05
33 10 0.27
34 12 0.32
35 2 0.05
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTATTTTTAATTTTTAAAATATTTAAAA
Found at i:3720658 original size:22 final size:22
Alignment explanation
Indices: 3720633--3720676 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3720623 TAGTAATATA
3720633 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
3720655 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
3720677 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:3721248 original size:18 final size:17
Alignment explanation
Indices: 3721225--3721258 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3721215 TTTTGAATTT
3721225 TATTATTTATTTAATATA
1 TATTA-TTATTTAATATA
*
3721243 TATTATTATTTTATAT
1 TATTATTATTTAATAT
3721259 TAAAATTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATTATTTAATATA
Found at i:3721318 original size:10 final size:11
Alignment explanation
Indices: 3721303--3721339 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
3721293 AAATCCATTA
3721303 TATTATATAT-
1 TATTATATATG
3721313 TATTATAT-TG
1 TATTATATATG
*
3721323 TTTTATATATG
1 TATTATATATG
3721334 TATTAT
1 TATTAT
3721340 TTATATTGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
9 1 0.04
10 15 0.65
11 7 0.30
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (11 bp):
TATTATATATG
Found at i:3721330 original size:25 final size:26
Alignment explanation
Indices: 3721299--3721356 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
3721289 TGGAAAATCC
3721299 ATTATATTATATATTA-TTATATTGT
1 ATTATATTATATATTATTTATATTGT
* *
3721324 TTTATA-TATGTATTATTTATATTGT
1 ATTATATTATATATTATTTATATTGT
3721349 ATTA-ATTA
1 ATTATATTA
3721357 AAATATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (26 bp):
ATTATATTATATATTATTTATATTGT
Found at i:3721351 original size:14 final size:15
Alignment explanation
Indices: 3721324--3721352 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3721314 ATTATATTGT
3721324 TTTATATATGTATTA
1 TTTATATATGTATTA
3721339 TTTATAT-TGTATTA
1 TTTATATATGTATTA
3721353 ATTAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (15 bp):
TTTATATATGTATTA
Found at i:3727520 original size:46 final size:46
Alignment explanation
Indices: 3727470--3727642 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
3727460 TGGTTGAGCA
*
3727470 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
3727516 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
3727563 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
3727609 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
3727643 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:3727626 original size:93 final size:93
Alignment explanation
Indices: 3727467--3727637 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
3727457 GGATGGTTGA
* *
3727467 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
3727532 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
3727560 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
3727625 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
3727638 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:3727904 original size:19 final size:20
Alignment explanation
Indices: 3727867--3727904 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
3727857 ATAAGGTGGT
3727867 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
3727887 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
3727905 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:3735196 original size:46 final size:46
Alignment explanation
Indices: 3735032--3735202 Score: 197
Period size: 46 Copynumber: 3.7 Consensus size: 46
3735022 GGTTGAGCAT
*
3735032 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG-
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
* * * * *
3735077 TCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ACGC
* *
3735122 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
*
3735170 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
3735203 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
42 6 0.06
44 4 0.04
45 27 0.26
46 31 0.30
47 27 0.26
48 5 0.05
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
Found at i:3735461 original size:19 final size:20
Alignment explanation
Indices: 3735424--3735461 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
3735414 ATAAGGTGGT
3735424 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
3735444 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
3735462 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:3744923 original size:39 final size:39
Alignment explanation
Indices: 3744878--3744954 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
3744868 ATGTATGGCA
*
3744878 TTATCATACTTAAAACAAACTATCAGATTTACAGTTTTT
1 TTATCATACTTAAAACAAACTATCAGATTCACAGTTTTT
* *
3744917 TTATCATACTTAAAACAGACTATCAGATTCATAGTTTT
1 TTATCATACTTAAAACAAACTATCAGATTCACAGTTTT
3744955 AGGGTTTGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (39 bp):
TTATCATACTTAAAACAAACTATCAGATTCACAGTTTTT
Found at i:3748558 original size:83 final size:86
Alignment explanation
Indices: 3748409--3748654 Score: 347
Period size: 83 Copynumber: 2.9 Consensus size: 86
3748399 TTGTCCGTTT
* *
3748409 TCTTTTCAAATTGATCAATTTTAGTACCTAT-CTTTTAGCATTTTAAATTTTAATCTTGACTGGG
1 TCTTTTCAAATTGATCAATTTTAGTACCTATACTTTTAGAATTTTAAATTTTAATCTTGACTTGG
**
3748473 TAACGGTTAAATTGTCCAATA
66 TAACAATTAAATTGTCCAATA
*
3748494 T-TTTTGAAATTGATCAA-TTTAGT-CCTATACTTTTAGAATTTTAAATTTTAATCTTGACTTGG
1 TCTTTTCAAATTGATCAATTTTAGTACCTATACTTTTAGAATTTTAAATTTTAATCTTGACTTGG
* *
3748556 TAACAATTAAATTGTCCATTT
66 TAACAATTAAATTGTCCAATA
* ** * *
3748577 TCTTTTCAAATTGATCAATTTTAGTCCCTGCATTTTTAGAATTTTAAATTTTAATCTTAACTTGG
1 TCTTTTCAAATTGATCAATTTTAGTACCTATACTTTTAGAATTTTAAATTTTAATCTTGACTTGG
*
3748642 TAACACTTAAATT
66 TAACAATTAAATT
3748655 CGTTTAATTA
Statistics
Matches: 144, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
82 5 0.03
83 55 0.38
84 30 0.21
85 7 0.05
86 47 0.33
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (86 bp):
TCTTTTCAAATTGATCAATTTTAGTACCTATACTTTTAGAATTTTAAATTTTAATCTTGACTTGG
TAACAATTAAATTGTCCAATA
Found at i:3758553 original size:18 final size:18
Alignment explanation
Indices: 3758532--3758582 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
3758522 TTTTCTTCTC
*
3758532 CTCATTATTATTCT-CATT
1 CTCATTATTATTATAC-TT
*
3758550 CTCATCATTATTATACTT
1 CTCATTATTATTATACTT
*
3758568 CTTATTATTATTATA
1 CTCATTATTATTATA
3758583 GTAGAGAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.55
Consensus pattern (18 bp):
CTCATTATTATTATACTT
Found at i:3759587 original size:87 final size:87
Alignment explanation
Indices: 3759436--3759603 Score: 205
Period size: 87 Copynumber: 1.9 Consensus size: 87
3759426 TACTCGATAT
* * * * * * *
3759436 TGCAGATTGCGATATGTGATGTTTTGCTTTGGACTTTGTCTTAATGAAATTGGTATGCATATGGT
1 TGCAGAATGCGATATATGATGTTTTGCTTTGGACTCTGCCTTAACGAAATAGGTATGCAAATGGT
3759501 CTCACTTT-TATATATATCGTAC
66 CTCA-TTTCTATATATATCGTAC
* * *
3759523 TGCAGAATGCGATATATGATGTTTTG-TTTGGAACTCTGCCTTTACGGAATAGGTATGGAAATGG
1 TGCAGAATGCGATATATGATGTTTTGCTTTGG-ACTCTGCCTTAACGAAATAGGTATGCAAATGG
*
3759587 TCTTATTTCTATATATA
65 TCTCATTTCTATATATA
3759604 CCGAAGCATA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
86 8 0.12
87 60 0.88
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (87 bp):
TGCAGAATGCGATATATGATGTTTTGCTTTGGACTCTGCCTTAACGAAATAGGTATGCAAATGGT
CTCATTTCTATATATATCGTAC
Found at i:3767083 original size:18 final size:18
Alignment explanation
Indices: 3767062--3767112 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
3767052 TTTTCTTCTC
*
3767062 CTCATTATTATTCT-CATT
1 CTCATTATTATTATAC-TT
*
3767080 CTCATCATTATTATACTT
1 CTCATTATTATTATACTT
*
3767098 CTTATTATTATTATA
1 CTCATTATTATTATA
3767113 GTAGAGAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.55
Consensus pattern (18 bp):
CTCATTATTATTATACTT
Found at i:3768117 original size:87 final size:87
Alignment explanation
Indices: 3767966--3768133 Score: 205
Period size: 87 Copynumber: 1.9 Consensus size: 87
3767956 TACTCGATAT
* * * * * * *
3767966 TGCAGATTGCGATATGTGATGTTTTGCTTTGGACTTTGTCTTAATGAAATTGGTATGCATATGGT
1 TGCAGAATGCGATATATGATGTTTTGCTTTGGACTCTGCCTTAACGAAATAGGTATGCAAATGGT
3768031 CTCACTTT-TATATATATCGTAC
66 CTCA-TTTCTATATATATCGTAC
* * *
3768053 TGCAGAATGCGATATATGATGTTTTG-TTTGGAACTCTGCCTTTACGGAATAGGTATGGAAATGG
1 TGCAGAATGCGATATATGATGTTTTGCTTTGG-ACTCTGCCTTAACGAAATAGGTATGCAAATGG
*
3768117 TCTTATTTCTATATATA
65 TCTCATTTCTATATATA
3768134 CCGAAGCATA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
86 8 0.12
87 60 0.88
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (87 bp):
TGCAGAATGCGATATATGATGTTTTGCTTTGGACTCTGCCTTAACGAAATAGGTATGCAAATGGT
CTCATTTCTATATATATCGTAC
Found at i:3771340 original size:17 final size:18
Alignment explanation
Indices: 3771304--3771347 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3771294 AAAAAAGTAA
3771304 TTTTATA-ATTTTTATGAT
1 TTTTATATA-TTTTATGAT
*
3771322 TTTTTTATATTTTAT-AT
1 TTTTATATATTTTATGAT
3771339 TTTTATATA
1 TTTTATATA
3771348 AATAGATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 10 0.43
18 12 0.52
19 1 0.04
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTATATATTTTATGAT
Found at i:3771346 original size:8 final size:8
Alignment explanation
Indices: 3771304--3771346 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 8
3771294 AAAAAAGTAA
3771304 TTTTATAAT
1 TTTTAT-AT
3771313 TTTTATGAT
1 TTTTAT-AT
*
3771322 TTTTTTAT
1 TTTTATAT
3771330 ATTTTATAT
1 -TTTTATAT
3771339 TTTTATAT
1 TTTTATAT
3771347 AAATAGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
8 10 0.33
9 20 0.67
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (8 bp):
TTTTATAT
Found at i:3779608 original size:21 final size:20
Alignment explanation
Indices: 3779570--3779615 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
3779560 GGTTAGCCTA
3779570 TTTT-AAATTTATCCATATCAT
1 TTTTAAAATTTATCCATAT--T
*
3779591 TTTTAAAATTTAT-TATATT
1 TTTTAAAATTTATCCATATT
3779610 TTTTAA
1 TTTTAA
3779616 TTTTAATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
21 8 0.35
22 8 0.35
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAAAATTTATCCATATT
Found at i:3783269 original size:28 final size:28
Alignment explanation
Indices: 3783237--3783291 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
3783227 CAAGGCTAAC
3783237 TTTT-ATCT-CTTGATTTCAATTTCAATCT
1 TTTTAATCTACTTG-TTT-AATTTCAATCT
*
3783265 TTTTAATTTACTTGTTTAATTTCAATC
1 TTTTAATCTACTTGTTTAATTTCAATC
3783292 ATTTACTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 14 0.58
29 6 0.25
30 4 0.17
ACGTcount: A:0.24, C:0.15, G:0.04, T:0.58
Consensus pattern (28 bp):
TTTTAATCTACTTGTTTAATTTCAATCT
Found at i:3789673 original size:21 final size:22
Alignment explanation
Indices: 3789647--3789705 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
3789637 GTTTTAAGAA
*
3789647 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
3789668 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
3789690 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
3789706 GATTTATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.19
21 16 0.50
22 10 0.31
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:3789720 original size:26 final size:24
Alignment explanation
Indices: 3789676--3789725 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
3789666 ATTTGTTTTA
*
3789676 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
3789700 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
3789726 TTTTTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:3807754 original size:21 final size:21
Alignment explanation
Indices: 3807716--3807760 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3807706 TTATGTTAGA
* * *
3807716 AGATAAGTATATGTTTAAAAT
1 AGATAAGCATAGGGTTAAAAT
*
3807737 AGATAAGCATAGGGTTAAGAT
1 AGATAAGCATAGGGTTAAAAT
3807758 AGA
1 AGA
3807761 GTTTGTCACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.29
Consensus pattern (21 bp):
AGATAAGCATAGGGTTAAAAT
Found at i:3808562 original size:17 final size:17
Alignment explanation
Indices: 3808524--3808581 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 17
3808514 TGAGAAAATC
*
3808524 TTTTACTAATTTTTATAT
1 TTTTAATAATTTTTAT-T
*
3808542 TTTTAATAGTTTTTATT
1 TTTTAATAATTTTTATT
3808559 TTTT-ATAATTTTTAATT
1 TTTTAATAATTTTT-ATT
3808576 TTTTAA
1 TTTTAA
3808582 ATATATGCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.23
17 12 0.34
18 15 0.43
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTAATAATTTTTATT
Found at i:3808579 original size:18 final size:17
Alignment explanation
Indices: 3808524--3808580 Score: 62
Period size: 16 Copynumber: 3.3 Consensus size: 17
3808514 TGAGAAAATC
3808524 TTTTACTAATTTTTATATT
1 TTTTA-TAATTTTTAT-TT
* *
3808543 TTTAATAGTTTTTA-TT
1 TTTTATAATTTTTATTT
*
3808559 TTTTATAATTTTTAATT
1 TTTTATAATTTTTATTT
3808576 TTTTA
1 TTTTA
3808581 AATATATGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 14 0.42
17 7 0.21
18 8 0.24
19 4 0.12
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTTATAATTTTTATTT
Found at i:3810399 original size:19 final size:20
Alignment explanation
Indices: 3810360--3810408 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
3810350 TAATATTTAA
3810360 TATTTAATATTTTAAAATTT
1 TATTTAATATTTTAAAATTT
* **
3810380 T-TTTATTATTTTAATTTTT
1 TATTTAATATTTTAAAATTT
3810399 TATTTAATAT
1 TATTTAATAT
3810409 AAAATTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTAATATTTTAAAATTT
Found at i:3811235 original size:17 final size:18
Alignment explanation
Indices: 3811209--3811242 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3811199 TAAAACTAGA
3811209 ATACCAAATAAA-TTATT
1 ATACCAAATAAAGTTATT
*
3811226 ATACCTAATAAAGTTAT
1 ATACCAAATAAAGTTAT
3811243 AATTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (18 bp):
ATACCAAATAAAGTTATT
Found at i:3814738 original size:17 final size:15
Alignment explanation
Indices: 3814711--3814751 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 15
3814701 AACAACTACT
3814711 TTTTTTATTCTTTTATTC
1 TTTTTT-TTC-TTT-TTC
3814729 TTTTTTTTCTTTTTC
1 TTTTTTTTCTTTTTC
3814744 TTTTTTTT
1 TTTTTTTT
3814752 TTGCGACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 11 0.48
16 3 0.13
17 3 0.13
18 6 0.26
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTTTCTTTTTC
Found at i:3814752 original size:17 final size:18
Alignment explanation
Indices: 3814709--3814753 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
3814699 AAAACAACTA
*
3814709 CTTTTTTTATTCTTTTAT
1 CTTTTTTTTTTCTTTTAT
*
3814727 -TCTTTTTTTTCTTTT-T
1 CTTTTTTTTTTCTTTTAT
3814743 CTTTTTTTTTT
1 CTTTTTTTTTT
3814754 GCGACTTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 1 0.04
17 22 0.96
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.84
Consensus pattern (18 bp):
CTTTTTTTTTTCTTTTAT
Found at i:3815144 original size:21 final size:21
Alignment explanation
Indices: 3815118--3815168 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
3815108 AGCGGTGACG
* *
3815118 GTGAGATTAGTTATTGTAACA
1 GTGAGATTAGATAATGTAACA
3815139 GTGAGATTAGATAATGTAACA
1 GTGAGATTAGATAATGTAACA
3815160 GTGAGATTA
1 GTGAGATTA
3815169 AAAACAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.33
Consensus pattern (21 bp):
GTGAGATTAGATAATGTAACA
Found at i:3821923 original size:171 final size:170
Alignment explanation
Indices: 3821623--3821956 Score: 542
Period size: 171 Copynumber: 2.0 Consensus size: 170
3821613 ATCTTTCTCT
*
3821623 TGTACATCATCTGGTTCTCTTCATCAATGGCAATGTCTAGACCCTGCTGAAAAAGGGCATCTAGA
1 TGTACATCATCTGGTTCTCTTAATCAATGGCAATGTCTAGACCCTGCTGAAAAAGGGCATCTAGA
* * * * *
3821688 ACCTTACTTTGCGACATACCAAAATGACCTGTGCCATCAAAGATCTCTACGGCCAATCTTGCATT
66 ACCTCACTTTGCCACATACCAAAATGACCCGTGCCATCAAAGATCTCCACAGCCAATCTTGCATT
*
3821753 TGCAATTGTCAGTCTTGTCCACATGGACGATGTGGTATCA
131 TGCAATTGTCAGTCTTGTCCACATGGACAATGTGGTATCA
*
3821793 TGTACATCATCTGGTTTCTCTTAATCAATGGCAATGTCTAGACTCTGCTGAAAAAGGGCATCTAG
1 TGTACATCATCTGG-TTCTCTTAATCAATGGCAATGTCTAGACCCTGCTGAAAAAGGGCATCTAG
* * *
3821858 AACCTCATTTTGCCACATACCAAAATGACCCGTGCCATCAAAGATCTCCACAGCTAATTTTGCAT
65 AACCTCACTTTGCCACATACCAAAATGACCCGTGCCATCAAAGATCTCCACAGCCAATCTTGCAT
* *
3821923 TTGCAATTGTCGGTCTTGTCCATATGGACAATGT
130 TTGCAATTGTCAGTCTTGTCCACATGGACAATGT
3821957 TGAAGCTCCT
Statistics
Matches: 150, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
170 14 0.09
171 136 0.91
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (170 bp):
TGTACATCATCTGGTTCTCTTAATCAATGGCAATGTCTAGACCCTGCTGAAAAAGGGCATCTAGA
ACCTCACTTTGCCACATACCAAAATGACCCGTGCCATCAAAGATCTCCACAGCCAATCTTGCATT
TGCAATTGTCAGTCTTGTCCACATGGACAATGTGGTATCA
Found at i:3830332 original size:17 final size:17
Alignment explanation
Indices: 3830291--3830333 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
3830281 CAAAACCTAT
*
3830291 AAAAGTTATAAGTAACC
1 AAAAGTTTTAAGTAACC
3830308 AAAAGTTTTAAGTAACC
1 AAAAGTTTTAAGTAACC
3830325 AAAAGTTTT
1 AAAAGTTTT
3830334 GTCAATTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (17 bp):
AAAAGTTTTAAGTAACC
Found at i:3833097 original size:17 final size:17
Alignment explanation
Indices: 3833075--3833108 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3833065 TGAAACCTTC
3833075 ACCAATTTTTCATAAGT
1 ACCAATTTTTCATAAGT
3833092 ACCAATTTTTCATAAGT
1 ACCAATTTTTCATAAGT
3833109 TTATTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (17 bp):
ACCAATTTTTCATAAGT
Found at i:3838431 original size:283 final size:291
Alignment explanation
Indices: 3838073--3838649 Score: 710
Period size: 283 Copynumber: 2.0 Consensus size: 291
3838063 CACTTGAAGA
* * * *
3838073 GGGTTGTAGATTCTTCGTGTTTCCAAGGCTTCTTAGGACTTCTACACGCCACGTTCTATATTTCC
1 GGGTTGTAGATTCTTCATGTATCCAAGGCTTCTTAAGACTTCTACACACCACGTTCTATATTTCC
*
3838138 ATCTATCTTCTTTATTCGCTTCCTTATTATTCTAATC-T-TTGATT-TAT-TA-TT-TTA-TTTT
66 ACCTATCTTCTTTATTCGCTTCCTTATTATTCTAATCGTATTGATTAT-TCTATTTATTATTTTT
** *
3838196 AGTTATTTATTTTAATTGTTTCATCTGACTTGGACTCAATTTCATTTCAGGTTGTGTC-AAAATC
130 AGTTATTTATTTTAATTGTTTCATCCAACTTGGACTCAATTGCATTTCAGGTTGTGTCAAAAATC
* * *
3838260 CAAGTTTCTTT-GAACGTTTAAAG-CCATAAGTCAAA-TCCTCAACTTTGACAAACTTTACGAT-
195 CAAATTTCTTTCGAACGTCTAAAGTCC-TAAGTCAAATTCCTC-ACTTTCACAAACTTTACGATC
*
3838321 TCGCTTCCGCATTCATTCATCTCATTCTTTATCGG
258 T-GCTTCCGCATTCATCCATCTCATTCTTTATCGG
* * * * *
3838356 GGGTTGTGGATTCTTCATGTATCCAAGGTTTCTTAAGACTTCTATATACCACGTTCTATCTTTCC
1 GGGTTGTAGATTCTTCATGTATCCAAGGCTTCTTAAGACTTCTACACACCACGTTCTATATTTCC
** * *
3838421 ACCTATCTTCTTTATTTTCTTCCTTATTTTTCTAATCGTAAATTTATTATTCTATTTTAATTATT
66 ACCTATCTTCTTTATTCGCTTCCTTATTATTCTAATCGT--ATTGATTATTCTA-TTT-ATTATT
* * ** *
3838486 TTTAGTTATTTATTTTAATTGTTTTATCCAACTTGGATTTGATTGCGTTTCAGGTTGTGTCAAAA
127 TTTAGTTATTTATTTTAATTGTTTCATCCAACTTGGACTCAATTGCATTTCAGGTTGTGTCAAAA
* * *
3838551 ATCTAAATTTCTTTCCGAACGTCTAAAGTCCTAAGTTAAATTCGTCACTTTCACAAACTTTACGA
192 ATCCAAATTTCTTT-CGAACGTCTAAAGTCCTAAGTCAAATTCCTCACTTTCACAAACTTTACGA
* *
3838616 TCTGCTTCCGCATTTATCCGTCTCATTCTTTATC
256 TCTGCTTCCGCATTCATCCATCTCATTCTTTATC
3838650 AACTGGCCAC
Statistics
Matches: 246, Mismatches: 31, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
283 89 0.36
284 1 0.00
287 6 0.02
288 3 0.01
290 2 0.01
292 3 0.01
293 54 0.22
294 15 0.06
296 66 0.27
297 7 0.03
ACGTcount: A:0.23, C:0.20, G:0.12, T:0.46
Consensus pattern (291 bp):
GGGTTGTAGATTCTTCATGTATCCAAGGCTTCTTAAGACTTCTACACACCACGTTCTATATTTCC
ACCTATCTTCTTTATTCGCTTCCTTATTATTCTAATCGTATTGATTATTCTATTTATTATTTTTA
GTTATTTATTTTAATTGTTTCATCCAACTTGGACTCAATTGCATTTCAGGTTGTGTCAAAAATCC
AAATTTCTTTCGAACGTCTAAAGTCCTAAGTCAAATTCCTCACTTTCACAAACTTTACGATCTGC
TTCCGCATTCATCCATCTCATTCTTTATCGG
Found at i:3838489 original size:23 final size:23
Alignment explanation
Indices: 3838463--3838510 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3838453 TAATCGTAAA
3838463 TTTA-TTATTCTATTTTAATTATT
1 TTTAGTTATT-TATTTTAATTATT
*
3838486 TTTAGTTATTTATTTTAATTGTT
1 TTTAGTTATTTATTTTAATTATT
3838509 TT
1 TT
3838511 ATCCAACTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTAGTTATTTATTTTAATTATT
Found at i:3849658 original size:22 final size:22
Alignment explanation
Indices: 3849633--3849676 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3849623 AAAGAGTATG
3849633 TAACAATTGCTGCCAGTACAAT
1 TAACAATTGCTGCCAGTACAAT
3849655 TAACAATTGCTGCCAGTACAAT
1 TAACAATTGCTGCCAGTACAAT
3849677 ACTGATACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (22 bp):
TAACAATTGCTGCCAGTACAAT
Found at i:3850459 original size:18 final size:17
Alignment explanation
Indices: 3850438--3850496 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 17
3850428 TTTTTTTTAT
3850438 TTTATCATTTTACTATTA
1 TTTATCATTTTA-TATTA
3850456 TTTAT-ATTATTATTATTA
1 TTTATCATT-TTA-TATTA
* *
3850474 TTTCTCATGTATATATTA
1 TTTATCAT-TTTATATTA
3850492 TTTAT
1 TTTAT
3850497 ATTATTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 3 0.09
18 26 0.76
19 4 0.12
20 1 0.03
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTATCATTTTATATTA
Found at i:3850635 original size:12 final size:13
Alignment explanation
Indices: 3850584--3850640 Score: 61
Period size: 12 Copynumber: 4.7 Consensus size: 13
3850574 TTCTGACTAC
3850584 TATTATTATATATG
1 TATTATTAT-TATG
3850598 TA-TA-TA-TATG
1 TATTATTATTATG
*
3850608 TATTATTGTT-TG
1 TATTATTATTATG
3850620 TATTATTATTAT-
1 TATTATTATTATG
3850632 TATTATTAT
1 TATTATTAT
3850641 CACCCCTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 6 0.16
11 2 0.05
12 23 0.62
13 4 0.11
14 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (13 bp):
TATTATTATTATG
Found at i:3850919 original size:124 final size:124
Alignment explanation
Indices: 3850715--3850938 Score: 310
Period size: 124 Copynumber: 1.8 Consensus size: 124
3850705 TTATTTTTGC
* * *
3850715 TATTACTATTATTATTATATATTAGTGTATATTTTTATGTATATATATATATTTATATATAGTAT
1 TATTACTATTATTATTATATAGTAGTGTATATTTTTATATACATATATATATTTATATATAGTAT
* * *
3850780 TGTTTTTTATTACTTTAATTTAATATTTTTATTATATTTGCTTTTTGTATTTCTATATT
66 TGTATTATATTACTTTAATTTAATATTATTATTATATTTGCTTTTTGTATTTCTATATT
* * *
3850839 TATTATTATTATTATTATATAGTAGTGTGTATTTCTATTATATACATATATATATTTTTATATAG
1 TATTACTATTATTATTATATAGTAGTGTATA-TT-T-TTATATACATATATATATTTATATATAG
*
3850904 TA-T-TATTAT-TTACTTTACTTTAATATTATTATTAT
63 TATTGTATTATATTACTTTAATTTAATATTATTATTAT
3850939 TATCATTATA
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
124 52 0.60
125 6 0.07
126 2 0.02
127 27 0.31
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.60
Consensus pattern (124 bp):
TATTACTATTATTATTATATAGTAGTGTATATTTTTATATACATATATATATTTATATATAGTAT
TGTATTATATTACTTTAATTTAATATTATTATTATATTTGCTTTTTGTATTTCTATATT
Found at i:3862941 original size:87 final size:87
Alignment explanation
Indices: 3862542--3863662 Score: 1198
Period size: 86 Copynumber: 13.0 Consensus size: 87
3862532 CTAGAATCAG
* * * * * ** *
3862542 TGAATTTGCAGATCTTATCTCCCTAAGCAGTAGGGAAACAAATCGAGGTTGATGGGCCTTAAACC
1 TGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGACGAAGGGCCTTAAACC
*
3862607 CCTAAGCAGTAGGGTAACAGAC
66 CCTAAGCAGTAGGGTAACAGGC
* *** * * * *
3862629 CGAA-TTACAGATCTTATTTCCCTAAGCAGTAGTGG-AGCAGATCGAAAACAAAGGGTCTTAAAC
1 TGAATTTACAGATCTTAACCCCCTAAGCAGTAG-GGAAACAGATCGAAGACGAAGGGCCTTAAAC
*
3862692 CCCTAAGCAGTAGGGTAACAGAC
65 CCCTAAGCAGTAGGGTAACAGGC
* * * * ** * *
3862715 -CAAATTACAGATCTTATCTCCCTAAGCAGTA-TTAGAGCAGATCGAAGACGAAGGGTCTTAAAC
1 TGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGA-AACAGATCGAAGACGAAGGGCCTTAAAC
*
3862778 CCCTAAGCAGTAGGGTAACAGAC
65 CCCTAAGCAGTAGGGTAACAGGC
* * * * * * * *
3862801 -CAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGG-AGCAGATCAAAGACGAAGGGCATTAAAC
1 TGAATTTACAGATCTTAACCCCCTAAGCAGTAG-GGAAACAGATCGAAGACGAAGGGCCTTAAAC
3862864 CCCTAAGCAGTAGGGTAACAGGC
65 CCCTAAGCAGTAGGGTAACAGGC
* * * *
3862887 TGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCAAAGACGAAGGGTCTTAAACC
1 TGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGACGAAGGGCCTTAAACC
*
3862952 CCTAAGCAGTAGGGTAACAGAC
66 CCTAAGCAGTAGGGTAACAGGC
** * * * * *
3862974 CAAATTGT--AGATCTTATCTCCCTAAGTAGTAGTGG-AGCAGATCGAAGACGAAGGGTCTTAAA
1 TGAATT-TACAGATCTTAACCCCCTAAGCAGTAG-GGAAACAGATCGAAGACGAAGGGCCTTAAA
*
3863036 CCCCTAAACAGTAGGGTAACAGGC
64 CCCCTAAGCAGTAGGGTAACAGGC
* * * *
3863060 TGAATTTACAGATCTTATCCCCCTAAGCAGTAGTGG-AGCA-ATTGAA-AGCG-ATGGCCTT-AA
1 TGAATTTACAGATCTTAACCCCCTAAGCAGTAG-GGAAACAGATCGAAGA-CGAAGGGCCTTAAA
*
3863120 CCCCTAAGCAGTAGGGTAGCAGGC
64 CCCCTAAGCAGTAGGGTAACAGGC
* * **
3863144 TAAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGGTGGGCCTTAAACC
1 TGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGACGAAGGGCCTTAAACC
*
3863209 CCTAAGCAGTAGGGTAACAGGT
66 CCTAAGCAGTAGGGTAACAGGC
*
3863231 TGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGACGATGGGCCTTAAACC
1 TGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGACGAAGGGCCTTAAACC
3863296 CCTAAGCAGTAGGGTAACAGGC
66 CCTAAGCAGTAGGGTAACAGGC
* * * *
3863318 TAAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACATATCAAAGACGATA-AGCCTTAAAC
1 TGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGACGA-AGGGCCTTAAAC
*
3863382 CCCTAAGCAGTAAGGTAACAGGC
65 CCCTAAGCAGTAGGGTAACAGGC
* * ** **
3863405 -AAATTTACAG------A--CCCTAAACAGTAGGGAAACAGATCGAAGGTGACA-AACCTTAAAC
1 TGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGACGA-AGGGCCTTAAAC
3863460 CCCTAAGCAGTAGGGTAACAGGC
65 CCCTAAGCAGTAGGGTAACAGGC
* ** *
3863483 TGAAGATTTACAGATCTTAAACCCCCTAAGTAGTAGGGAAACAGATCGAAGGTGACA-AGCCTT-
1 TG-A-ATTTACAGATCTT-AACCCCCTAAGCAGTAGGGAAACAGATCGAAGACGA-AGGGCCTTA
*
3863546 AACCCCTAAACAGTAGGGTAACAGGC
62 AACCCCTAAGCAGTAGGGTAACAGGC
* * * *
3863572 TAAATTTACAGATCTTAACACCCTAAGTAGTAGGGAAACAGATCGAAGACGATGGGCCTTAAACC
1 TGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGACGAAGGGCCTTAAACC
* * *
3863637 CTTAAGCAGTAGGGTACCAAGC
66 CCTAAGCAGTAGGGTAACAGGC
3863659 TGAA
1 TGAA
3863663 AATTACAACT
Statistics
Matches: 904, Mismatches: 97, Indels: 66
0.85 0.09 0.06
Matches are distributed among these distances:
78 59 0.07
80 2 0.00
81 8 0.01
83 2 0.00
84 58 0.06
85 16 0.02
86 355 0.39
87 338 0.37
88 3 0.00
89 26 0.03
90 37 0.04
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (87 bp):
TGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGACGAAGGGCCTTAAACC
CCTAAGCAGTAGGGTAACAGGC
Found at i:3863217 original size:44 final size:44
Alignment explanation
Indices: 3862562--3863650 Score: 327
Period size: 44 Copynumber: 25.3 Consensus size: 44
3862552 GATCTTATCT
* * * *
3862562 CCCTAAGCAGTAGGGAAACAAATCGAGGTTGATGGGCCTTAAAC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGGCCTTAAAC
* * * * ** ***
3862606 CCCTAAGCAGTAGGGTAACAGACCG-A-ATTACAGATCTTATTT
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGGCCTTAAAC
* ** * *
3862648 CCCTAAGCAGTAGTGG-AGCAGATCGAA-AACAAAGGGTCTTAAAC
1 CCCTAAGCAGTAG-GGAAACAGATCGAAGATGATA-GGCCTTAAAC
* * * * ** *
3862692 CCCTAAGCAGTAGGGTAACAGA-CCAA-ATTACAGATCTT-ATC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGGCCTTAAAC
** * * *
3862733 TCCCTAAGCAGTA-TTAGAGCAGATCGAAGACGA-AGGGTCTTAAAC
1 -CCCTAAGCAGTAGGGA-AACAGATCGAAGATGATA-GGCCTTAAAC
* * * ** *
3862778 CCCTAAGCAGTAGGGTAACAGA-CCAA-ATTG-CAGATCTT-ATC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGA-TGATAGGCCTTAAAC
* * * *
3862819 TCCCTAAGCAGTAGTGG-AGCAGATCAAAGACGA-AGGGCATTAAAC
1 -CCCTAAGCAGTAG-GGAAACAGATCGAAGATGATA-GGCCTTAAAC
* * * *** ** *
3862864 CCCTAAGCAGTAGGGTAACAG-GCTGAA-TTTCCAGATCTTAACC
1 CCCTAAGCAGTAGGGAAACAGATC-GAAGATGATAGGCCTTAAAC
* * * *
3862907 CCCTAAGCAGTAGGGAAATAGATCAAAGACGA-AGGGTCTTAAAC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGATA-GGCCTTAAAC
* * ** *
3862951 CCCTAAGCAGTAGGGTAACAGA-CCAA-ATTG-TAGATCTT-ATC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGA-TGATAGGCCTTAAAC
* * * *
3862992 TCCCTAAGTAGTAGTGG-AGCAGATCGAAGACGA-AGGGTCTTAAAC
1 -CCCTAAGCAGTAG-GGAAACAGATCGAAGATGATA-GGCCTTAAAC
* * * * * * ** **
3863037 CCCTAAACAGTAGGGTAACAG-GCTGAA-TTTACAGATCTTATCC
1 CCCTAAGCAGTAGGGAAACAGATC-GAAGATGATAGGCCTTAAAC
* * *
3863080 CCCTAAGCAGTAGTGG-AGCA-ATTGAA-AGCGAT-GGCCTT-AAC
1 CCCTAAGCAGTAG-GGAAACAGATCGAAGA-TGATAGGCCTTAAAC
* * * * * * ** *
3863121 CCCTAAGCAGTAGGGTAGCAG-GCTAA-ATTTACAGATCTTAACC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGA-TGATAGGCCTTAAAC
* *
3863164 CCCTAAGCAGTAGGGAAACAGATCGAAGATGGTGGGCCTTAAAC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGGCCTTAAAC
* * * * * * ** *
3863208 CCCTAAGCAGTAGGGTAACAGGTTGAA-TTTACAGATCTTAACC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGGCCTTAAAC
* *
3863251 CCCTAAGCAGTAGGGAAACAGATCGAAGACGATGGGCCTTAAAC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGGCCTTAAAC
* * * * * ** *
3863295 CCCTAAGCAGTAGGGTAACAG-GCTAA-ATTTACAGATCTTAACC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGA-TGATAGGCCTTAAAC
* * * *
3863338 CCCTAAGCAGTAGGGAAACATATCAAAGACGATAAGCCTTAAAC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGGCCTTAAAC
* * * * *
3863382 CCCTAAGCAGTAAGGTAACAG-GC-AA-AT-TTA---C--AGA-
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGGCCTTAAAC
* * * **
3863416 CCCTAAACAGTAGGGAAACAGATCGAAGGTGACAAACCTTAAAC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGGCCTTAAAC
* * * * **
3863460 CCCTAAGCAGTAGGGTAACAG-GCTGAAGATTTACAGATCTTAAACC
1 CCCTAAGCAGTAGGGAAACAGATC-GAAGA-TGATAGGCCTTAAA-C
* * * *
3863506 CCCTAAGTAGTAGGGAAACAGATCGAAGGTGACAAGCCTT-AAC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGGCCTTAAAC
* * * * * * **
3863549 CCCTAAACAGTAGGGTAACAG-GCTAA-ATTTACAGATCTT-AAC
1 CCCTAAGCAGTAGGGAAACAGATCGAAGA-TGATAGGCCTTAAAC
* * *
3863591 ACCCTAAGTAGTAGGGAAACAGATCGAAGACGATGGGCCTTAAAC
1 -CCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGGCCTTAAAC
*
3863636 CCTTAAGCAGTAGGG
1 CCCTAAGCAGTAGGG
3863651 TACCAAGCTG
Statistics
Matches: 750, Mismatches: 225, Indels: 140
0.67 0.20 0.13
Matches are distributed among these distances:
34 18 0.02
35 3 0.00
36 2 0.00
37 2 0.00
38 1 0.00
40 4 0.01
41 30 0.04
42 123 0.16
43 224 0.30
44 288 0.38
45 30 0.04
46 24 0.03
47 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (44 bp):
CCCTAAGCAGTAGGGAAACAGATCGAAGATGATAGGCCTTAAAC
Found at i:3863467 original size:78 final size:80
Alignment explanation
Indices: 3863337--3863652 Score: 305
Period size: 78 Copynumber: 3.8 Consensus size: 80
3863327 AGATCTTAAC
* * ** * *
3863337 CCCCTAAGCAGTAGGGAAACATATCAAAGACGATAAGCCTTAAACCCCTAAGCAGTAAGGTAACA
1 CCCCTAAGCAGTAGGGAAACAGATCGAAGGTGACAAGCCTTAAACCCCTAAGCAGTAGGGTAACA
3863402 GGC-AAATTTACAGA
66 GGCTAAATTTACAGA
* *
3863416 -CCCTAAACAGTAGGGAAACAGATCGAAGGTGACAAACCTTAAACCCCTAAGCAGTAGGGTAACA
1 CCCCTAAGCAGTAGGGAAACAGATCGAAGGTGACAAGCCTTAAACCCCTAAGCAGTAGGGTAACA
3863480 GGCTGAAGATTTACAGATCTTAAA
66 GGCT-AA-ATTTACAG-------A
* *
3863504 CCCCCTAAGTAGTAGGGAAACAGATCGAAGGTGACAAGCCTT-AACCCCTAAACAGTAGGGTAAC
1 -CCCCTAAGCAGTAGGGAAACAGATCGAAGGTGACAAGCCTTAAACCCCTAAGCAGTAGGGTAAC
3863568 AGGCTAAATTTACAGATCTTAA
65 AGGCTAAATTTACAG------A
* ** *** *
3863590 CACCCTAAGTAGTAGGGAAACAGATCGAAGACGATGGGCCTTAAACCCTTAAGCAGTAGGGTA
1 C-CCCTAAGCAGTAGGGAAACAGATCGAAGGTGACAAGCCTTAAACCCCTAAGCAGTAGGGTA
3863653 CCAAGCTGAA
Statistics
Matches: 200, Mismatches: 23, Indels: 20
0.82 0.09 0.08
Matches are distributed among these distances:
78 59 0.29
80 2 0.01
81 8 0.04
85 1 0.00
86 38 0.19
87 26 0.13
88 3 0.01
89 26 0.13
90 37 0.19
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.18
Consensus pattern (80 bp):
CCCCTAAGCAGTAGGGAAACAGATCGAAGGTGACAAGCCTTAAACCCCTAAGCAGTAGGGTAACA
GGCTAAATTTACAGA
Found at i:3863519 original size:46 final size:44
Alignment explanation
Indices: 3863457--3863612 Score: 151
Period size: 43 Copynumber: 3.5 Consensus size: 44
3863447 ACAAACCTTA
*
3863457 AACCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAGATCTT
1 AACCCCTAAGCAGTAGGGAAACAGGCTGAAGATTTACAGATCTT
* * * * *
3863501 AAACCCCCTAAGTAGTAGGGAAACA-GATCGAAG-GTGACA-AGCCTT
1 -AA-CCCCTAAGCAGTAGGGAAACAGGCT-GAAGATTTACAGA-TCTT
* *
3863546 AACCCCTAAACAGTAGGGTAACAGGCT-AA-ATTTACAGATCTT
1 AACCCCTAAGCAGTAGGGAAACAGGCTGAAGATTTACAGATCTT
*
3863588 AACACCCTAAGTAGTAGGGAAACAG
1 AAC-CCCTAAGCAGTAGGGAAACAG
3863613 ATCGAAGACG
Statistics
Matches: 88, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
42 12 0.14
43 37 0.42
44 5 0.06
45 11 0.12
46 23 0.26
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (44 bp):
AACCCCTAAGCAGTAGGGAAACAGGCTGAAGATTTACAGATCTT
Found at i:3864210 original size:30 final size:30
Alignment explanation
Indices: 3864176--3864261 Score: 154
Period size: 30 Copynumber: 2.9 Consensus size: 30
3864166 AAAACCCTAG
3864176 CCACCTTGCCTCCCACTTGCACCTACTCCA
1 CCACCTTGCCTCCCACTTGCACCTACTCCA
3864206 CCACCTTGCCTCCCACTTGCACCTACTCCA
1 CCACCTTGCCTCCCACTTGCACCTACTCCA
* *
3864236 CCACCTTGTCTCCCACTTACACCTAC
1 CCACCTTGCCTCCCACTTGCACCTAC
3864262 ACCATCAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.17, C:0.52, G:0.06, T:0.24
Consensus pattern (30 bp):
CCACCTTGCCTCCCACTTGCACCTACTCCA
Found at i:3864792 original size:3 final size:3
Alignment explanation
Indices: 3864760--3864844 Score: 56
Period size: 3 Copynumber: 28.3 Consensus size: 3
3864750 TTATTTTTTT
* *
3864760 TTA TT- TTA TCA TT- TTA CTA TTA TT- TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
3864803 TT- TCTCA TGTA TATA TTA TTA TT- TATA TTA TTA TTA -TA TTA T
1 TTA T-T-A T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T
3864845 ATATACCCTC
Statistics
Matches: 66, Mismatches: 6, Indels: 20
0.72 0.07 0.22
Matches are distributed among these distances:
2 9 0.14
3 48 0.73
4 7 0.11
5 2 0.03
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3864969 original size:12 final size:13
Alignment explanation
Indices: 3864918--3864974 Score: 61
Period size: 12 Copynumber: 4.7 Consensus size: 13
3864908 TTTCTGCTAC
3864918 TATTATTATATATG
1 TATTATTAT-TATG
3864932 TA-TA-TA-TATG
1 TATTATTATTATG
*
3864942 TATTATTGTT-TG
1 TATTATTATTATG
3864954 TATTATTATTAT-
1 TATTATTATTATG
3864966 TATTATTAT
1 TATTATTAT
3864975 CACCCCTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 6 0.16
11 2 0.05
12 23 0.62
13 4 0.11
14 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (13 bp):
TATTATTATTATG
Found at i:3865237 original size:18 final size:19
Alignment explanation
Indices: 3865214--3865251 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3865204 TATTATATAC
3865214 ATATATA-TATATATT-TTT
1 ATATATAGTAT-TATTGTTT
3865232 ATATATAGTATTATTGTTT
1 ATATATAGTATTATTGTTT
3865251 A
1 A
3865252 CTTTACTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
ATATATAGTATTATTGTTT
Found at i:3870401 original size:15 final size:16
Alignment explanation
Indices: 3870381--3870413 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3870371 ATATATATTT
3870381 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
3870396 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
3870413 T
1 T
3870414 ATAACCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:3870486 original size:21 final size:22
Alignment explanation
Indices: 3870460--3870518 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
3870450 GTTTTAAGAA
*
3870460 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
3870481 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
3870503 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
3870519 GATTTATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.19
21 16 0.50
22 10 0.31
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:3870533 original size:26 final size:24
Alignment explanation
Indices: 3870489--3870537 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
3870479 ATTTGTTTTA
*
3870489 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
3870513 ATATTTGATTTATTATATTTTTAAA
1 ATATTTG-TTT-TTATATTTTTAAA
3870538 AGTTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:3878186 original size:20 final size:20
Alignment explanation
Indices: 3878161--3878200 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3878151 AACGAAAACC
*
3878161 ACAATAGCAAATGACAGCAA
1 ACAATAACAAATGACAGCAA
* *
3878181 ACAATAACAGATTACAGCAA
1 ACAATAACAAATGACAGCAA
3878201 GGATTTTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.12
Consensus pattern (20 bp):
ACAATAACAAATGACAGCAA
Found at i:3879624 original size:2 final size:2
Alignment explanation
Indices: 3879612--3879646 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3879602 AAGATAGTCT
*
3879612 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3879647 TTGTATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3881681 original size:33 final size:33
Alignment explanation
Indices: 3881644--3881710 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
3881634 TGACGGAAGA
3881644 ATGCTGCCAGTTCGTGGAGAAAAACAAGTTTTT
1 ATGCTGCCAGTTCGTGGAGAAAAACAAGTTTTT
3881677 ATGCTGCCAGTTCGTGGAGAAAAACAAGTTTTT
1 ATGCTGCCAGTTCGTGGAGAAAAACAAGTTTTT
3881710 A
1 A
3881711 CTTGAAGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (33 bp):
ATGCTGCCAGTTCGTGGAGAAAAACAAGTTTTT
Found at i:3884324 original size:1 final size:1
Alignment explanation
Indices: 3884314--3884361 Score: 60
Period size: 1 Copynumber: 48.0 Consensus size: 1
3884304 ATCAAATTCC
* * * *
3884314 AAAAACAAAAAAAAAAAAACAAAAACAAAAAAAAACAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3884362 GGTTGCTAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3884337 original size:10 final size:10
Alignment explanation
Indices: 3884314--3884358 Score: 74
Period size: 10 Copynumber: 4.5 Consensus size: 10
3884304 ATCAAATTCC
3884314 AAAAACAAAA
1 AAAAACAAAA
3884324 AAAAA-AAAA
1 AAAAACAAAA
3884333 CAAAAACAAAA
1 -AAAAACAAAA
3884344 AAAAACAAAA
1 AAAAACAAAA
3884354 AAAAA
1 AAAAA
3884359 AAAGGTTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 4 0.12
10 25 0.76
11 4 0.12
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:3886161 original size:15 final size:16
Alignment explanation
Indices: 3886136--3886166 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3886126 AGAAAAAGAA
3886136 AAAAGAAAAGATCATT
1 AAAAGAAAAGATCATT
3886152 AAAA-AAAAGATCATT
1 AAAAGAAAAGATCATT
3886167 TTCATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.19
Consensus pattern (16 bp):
AAAAGAAAAGATCATT
Found at i:3886331 original size:64 final size:64
Alignment explanation
Indices: 3886193--3886382 Score: 283
Period size: 64 Copynumber: 3.0 Consensus size: 64
3886183 ATATATCATT
* * *
3886193 CATCACATCTAATTAGGTGCATTTGATTCATTTTAATCAT-AGATCCTAATTATTTGACATAAG
1 CATCACATCTAGTTAGGTGCATTTGATTCATTTTGATCATAACATCCTAATTATTTGACATAAG
* *
3886256 CATCACATCTAGTTAGGTGCATTTGATTCATTTTGATCATAACATTCTAATTAGTTGACATAAG
1 CATCACATCTAGTTAGGTGCATTTGATTCATTTTGATCATAACATCCTAATTATTTGACATAAG
* * * * *
3886320 TATCACATCTAGTTAGGAGTATTTGATTTATTTTGATCATAACATCCTAATTATTTGGCATAA
1 CATCACATCTAGTTAGGTGCATTTGATTCATTTTGATCATAACATCCTAATTATTTGACATAA
3886383 ACATGATACA
Statistics
Matches: 114, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
63 38 0.33
64 76 0.67
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.41
Consensus pattern (64 bp):
CATCACATCTAGTTAGGTGCATTTGATTCATTTTGATCATAACATCCTAATTATTTGACATAAG
Found at i:3886651 original size:44 final size:44
Alignment explanation
Indices: 3886569--3886667 Score: 105
Period size: 44 Copynumber: 2.2 Consensus size: 44
3886559 AATATACAAG
** *
3886569 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAGAT-TGAAGA
1 TCTTATCTCCCTAAAGCAGCAGCGGAGCAGACTAAAGATGTG-A-A
*
3886614 TCTTATCTCCCT-AAGCAGTAGCGGAGCAGA-TCAAAGATGGTGAA
1 TCTTATCTCCCTAAAGCAGCAGCGGAGCAGACT-AAAGAT-GTGAA
3886658 TCTTATCTCC
1 TCTTATCTCC
3886668 ATGTATCGGC
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 1 0.02
44 31 0.66
45 13 0.28
46 2 0.04
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTAAAGCAGCAGCGGAGCAGACTAAAGATGTGAA
Found at i:3886941 original size:89 final size:89
Alignment explanation
Indices: 3886802--3886965 Score: 210
Period size: 89 Copynumber: 1.8 Consensus size: 89
3886792 GAAAAGACAA
* * *
3886802 ATCTTATCTCTATGTATCGGCAATGGAGCAGATTGACGATAGTAGTCTTATCT-TCCTGAGGTAG
1 ATCTTATCTCCATGTATCGGCAATGGAGCAGATTAACGATAGTAGCCTTATCTCT-CTGAGGTAG
3886866 CAA-AGAAGCAGACTGGAATTTACAG
65 CAAGAG-AGCAGACTGGAATTTACAG
* * *
3886891 ATCTTATCTCCATGTATCGGCAATGGAGTAGATTTTAACTATTG-A-CCTTATCTCTCTGAGGTA
1 ATCTTATCTCCATGTATCGGCAATGGAGCAGA--TTAACGATAGTAGCCTTATCTCTCTGAGGTA
3886954 GCAAGAGAGCAG
64 GCAAGAGAGCAG
3886966 GTTGGCGATT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
89 54 0.83
90 4 0.06
91 7 0.11
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (89 bp):
ATCTTATCTCCATGTATCGGCAATGGAGCAGATTAACGATAGTAGCCTTATCTCTCTGAGGTAGC
AAGAGAGCAGACTGGAATTTACAG
Found at i:3887336 original size:263 final size:262
Alignment explanation
Indices: 3886891--3887540 Score: 800
Period size: 263 Copynumber: 2.5 Consensus size: 262
3886881 GAATTTACAG
* * **
3886891 ATCTTATCTCCATGTATCGGCAATGGAGTAGATTTTAACTATTGACCTTATCTCTCTGAGGTAGC
1 ATCTTATCTCCATGTATCGGCAATGGAGCAGATTTT-ACCA-CCACCTTATCTCTCTGAGGTAGC
** * *
3886956 AAGAGAGCAGGTTGGCGATTGTAGTCTTGTCTTCCTGAGGTAGCAAGGAAGCAGACTAAAGATTG
64 AAGAGAGCAGGTTGAAGAATG-AGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAGA-TG
* * * * *
3887021 AAGATTTTATTTCCCTGAACAGAAGCGGGGTAGATCGAAAGAGGCAAATCTTATCTCCATATATC
127 AAGATCTTATTTCCCTCAACAGAAGCAGAGTAGATCGAAAAAGGCAAATCTTATCTCCATATATC
** * * * * * * * *
3887086 GGTAATGGAGCAGGTTTAAGCCCCAAGATCTTATCTCCCT-AAGCAGTAGCGGAGCAGATCAAAG
192 GCCAATAGAACAGATTTAAGCCCCAAGAT-TCATCTCCCTGAAGCAGCAGCAGAACAAATCAAAG
3887150 ATGGTGA
256 ATGGTGA
* *
3887157 ATCTTATCTCCATGTATCGGCAATGGAGCAGATTTTACCACCAACTTATCTCTTTGAGGTAGCAA
1 ATCTTATCTCCATGTATCGGCAATGGAGCAGATTTTACCACCACCTTATCTCTCTGAGGTAGCAA
* * *
3887222 GAGGGCAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGAAAGTAGACTAAATG-TGAAA
66 GAGAGCAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAA-GATG-AA
* * ** * *
3887286 GATCTTATTTCTCTCAACAGAAGTAGAGTAGATCGAAAAAGGTGAATCTTATCTTCATGTATCGC
129 GATCTTATTTCCCTCAACAGAAGCAGAGTAGATCGAAAAAGGCAAATCTTATCTCCATATATCGC
* * * ** * *
3887351 CAATAGAATAGATTTAAGCCCCAAGATTCATTTTCCTGAAGTTGCAGCAGAACAAATTACAGATG
194 CAATAGAACAGATTTAAGCCCCAAGATTCATCTCCCTGAAGCAGCAGCAGAACAAATCAAAGATG
3887416 GTGA
259 GTGA
* * * *
3887420 ATTTTATCTCCATGTATCGGCAATGGGGCAGAGTTTAGCCACCAGCCTTATCTCTCTGAAGTAGC
1 ATCTTATCTCCATGTATCGGCAATGGAGCAGATTTTA-CCACCA-CCTTATCTCTCTGAGGTAGC
3887485 AAGAGAGCAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACT
64 AAGAGAGCAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACT
3887541 GAGAATTGAA
Statistics
Matches: 329, Mismatches: 50, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
262 9 0.03
263 169 0.51
264 43 0.13
265 73 0.22
266 35 0.11
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (262 bp):
ATCTTATCTCCATGTATCGGCAATGGAGCAGATTTTACCACCACCTTATCTCTCTGAGGTAGCAA
GAGAGCAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAGATGAAGA
TCTTATTTCCCTCAACAGAAGCAGAGTAGATCGAAAAAGGCAAATCTTATCTCCATATATCGCCA
ATAGAACAGATTTAAGCCCCAAGATTCATCTCCCTGAAGCAGCAGCAGAACAAATCAAAGATGGT
GA
Found at i:3887870 original size:148 final size:142
Alignment explanation
Indices: 3887603--3887877 Score: 370
Period size: 148 Copynumber: 1.9 Consensus size: 142
3887593 ATGGTGAATC
* * * * * *
3887603 TTATCTCCATGTATTGGCGATGGAGCAGATTTTAGCCACTGACTTTATCTCTCTGAGATAGCAAA
1 TTATCACCATGTACTGGCAATGGAGCAGATTTAAGCCACAGACCTTATCTCTCTGAGATAGCAAA
* *
3887668 AGAGCAGCGATTGTAGTCTTATCTTCTTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGATTGA
66 AGAGCAGCGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAGATTGAAGATTGA
3887733 AGGACGTAAATA
131 AGGACGTAAATA
* * *
3887745 TTATCACCATGTACTGGTAATGGAGCAGATTTAAGCCTCAAGACCTTATCTCTCTGAGGTAGCAA
1 TTATCACCATGTACTGGCAATGGAGCAGATTTAAGCCAC-AGACCTTATCTCTCTGAGATAGCAA
* * *
3887810 GAGAGCAGGTTGAAAATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGATTAAAGATTGAA
65 AAGAGCA-G-CG---ATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAGATTGAA
3887875 GAT
125 GAT
3887878 CTATTTCCAT
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
142 33 0.29
143 28 0.25
144 1 0.01
145 1 0.01
148 50 0.44
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (142 bp):
TTATCACCATGTACTGGCAATGGAGCAGATTTAAGCCACAGACCTTATCTCTCTGAGATAGCAAA
AGAGCAGCGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAGATTGAAGATTGA
AGGACGTAAATA
Found at i:3888410 original size:20 final size:20
Alignment explanation
Indices: 3888385--3888424 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3888375 AACGAAAACC
*
3888385 ACAATAGCAAATGACAGCAA
1 ACAATAACAAATGACAGCAA
* *
3888405 ACAATAACAGATTACAGCAA
1 ACAATAACAAATGACAGCAA
3888425 GGATTTTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.12
Consensus pattern (20 bp):
ACAATAACAAATGACAGCAA
Found at i:3889846 original size:2 final size:2
Alignment explanation
Indices: 3889834--3889876 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3889824 AAGATAGTCT
*
3889834 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3889876 T
1 T
3889877 TTGTATAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3892792 original size:18 final size:19
Alignment explanation
Indices: 3892755--3892794 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
3892745 ATTCTCATTT
* *
3892755 TTATTTGTTACTGTTTATA
1 TTATTTGTTAATGTTAATA
3892774 TTATTTG-TAATGTTAATA
1 TTATTTGTTAATGTTAATA
3892792 TTA
1 TTA
3892795 ATGGTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.60
Consensus pattern (19 bp):
TTATTTGTTAATGTTAATA
Found at i:3893393 original size:17 final size:17
Alignment explanation
Indices: 3893371--3893406 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3893361 TTAAATGATA
3893371 TTTTGACATATAATTAT
1 TTTTGACATATAATTAT
3893388 TTTTGACATATAATTAT
1 TTTTGACATATAATTAT
3893405 TT
1 TT
3893407 CTAACATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTTGACATATAATTAT
Found at i:3893413 original size:17 final size:17
Alignment explanation
Indices: 3893376--3893413 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3893366 TGATATTTTG
* *
3893376 ACATATAATTATTTTTG
1 ACATATAATTATTTCTA
3893393 ACATATAATTATTTCTA
1 ACATATAATTATTTCTA
3893410 ACAT
1 ACAT
3893414 TTTTTTCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (17 bp):
ACATATAATTATTTCTA
Found at i:3906039 original size:64 final size:64
Alignment explanation
Indices: 3905929--3906054 Score: 207
Period size: 64 Copynumber: 2.0 Consensus size: 64
3905919 CTACATGTAT
* * *
3905929 CATTTAGTTAGGAGTATTTGATTCATTTCGATCATAGCACCCTAATTATTTGACATAAGCATCA
1 CATTTAGTTAGGAGCATTTGATTCATTTCGATCATAACACCATAATTATTTGACATAAGCATCA
* *
3905993 CATTTAGTTAGGAGCATTTGATTCATTTCGATCATAACATCATAATTATTTGGCATAAGCAT
1 CATTTAGTTAGGAGCATTTGATTCATTTCGATCATAACACCATAATTATTTGACATAAGCAT
3906055 GTGCATATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (64 bp):
CATTTAGTTAGGAGCATTTGATTCATTTCGATCATAACACCATAATTATTTGACATAAGCATCA
Found at i:3906565 original size:178 final size:180
Alignment explanation
Indices: 3906119--3906703 Score: 686
Period size: 178 Copynumber: 3.3 Consensus size: 180
3906109 ATTGGTAAAG
* * * *
3906119 ATTGAAGATTTTATCTCCCTGAAGTTGCAGTGGAGTAGATCTTTGCAGATGGTGAATCTTATCTC
1 ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCGCAGATGGCGAATCTTATCTC
* * * * * *
3906184 CATGTATCGGCAATAGAGTAGATTTAAGC-CTTAAGCATTACCTCTCTGAGGTAGCAAGAGAGCA
66 CATGTATCGGCAATGGAGCAGATTTTAGCTATTAA-CCTTATCTCTCTGAGGTAGCAAGAGAGCA
* *
3906248 GGTTGAAGATTGAAGTCTTATCTTCTTGAGGTAGCAAGGAAGTAGACTGA-A
130 GGTTGAAGATTG-AGTCTTATCTTCCTGAGGTAGCAAGGAAGTAGATTGAGA
* * ** * *
3906299 GACTGAAGATCTTATCTCCCT-AAGCAGTAGCGAAGCAGA---TCG-AGGATGGCGAATCTTATC
1 -ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCGCA-GATGGCGAATCTTATC
* *
3906359 TCCATGTATCGGTAATGGAGCAGATTTTAGCTATTGACCTTATCTCTCTGAGGTAGCAAGAGAGC
64 TCCATGTATCGGCAATGGAGCAGATTTTAGCTATTAACCTTATCTCTCTGAGGTAGCAAGAGAGC
** * * *
3906424 AGGTTGGCGATTGAGTCTTATCTGCCTGAAGTAGCAAGGAAGCAGATTGAGA
129 AGGTTGAAGATTGAGTCTTATCTTCCTGAGGTAGCAAGGAAGTAGATTGAGA
* * * *
3906476 ATTGAAGATTTTATCTCCTTGAAGTTGTAGTGGAGCAAATCTTCGCAGAT-G-GAATCTTATCTC
1 ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCGCAGATGGCGAATCTTATCTC
* * * *
3906539 CATGTATCGACAATGGAGCAGATTTTA-CTATTAAACCTTATCTCTCTAAAGTAGCAAGAGAGTA
66 CATGTATCGGCAATGGAGCAGATTTTAGCTATT-AACCTTATCTCTCTGAGGTAGCAAGAGAGCA
* * *
3906603 GGTTAAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGTAGATTGGGA
130 GGTTGAAGATTGAGTCTTATCTTCCTGAGGTAGCAAGGAAGTAGATTGAGA
* * * * *
3906654 ATTAAAGATTTGATCTCTCTGAAGTTACAGCGGAGCGGATCTTCGCAGAT
1 ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCGCAGAT
3906704 CTCCATGTAT
Statistics
Matches: 339, Mismatches: 56, Indels: 21
0.81 0.13 0.05
Matches are distributed among these distances:
176 50 0.15
177 100 0.29
178 151 0.45
179 1 0.00
180 18 0.05
181 19 0.06
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (180 bp):
ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCGCAGATGGCGAATCTTATCTC
CATGTATCGGCAATGGAGCAGATTTTAGCTATTAACCTTATCTCTCTGAGGTAGCAAGAGAGCAG
GTTGAAGATTGAGTCTTATCTTCCTGAGGTAGCAAGGAAGTAGATTGAGA
Found at i:3913117 original size:35 final size:35
Alignment explanation
Indices: 3912998--3913128 Score: 102
Period size: 35 Copynumber: 3.6 Consensus size: 35
3912988 GCTAATTGAA
* * * *
3912998 ATACCATACCTACATTTTACAACTCGGCATGGGA-A
1 ATACCATACCTACATTTCACAACTCAGTAT-GGATG
** * **
3913033 ATGTCATACCTACGTTTCTTAACTCAGTATGGATTTG
1 ATACCATACCTACATTTCACAACTCAGTATGGA--TG
*
3913070 ATAATATCATACCTACATTTCACAACTCAGTATGGATG
1 ---ATACCATACCTACATTTCACAACTCAGTATGGATG
*
3913108 ATACCATACCAACATTTCACA
1 ATACCATACCTACATTTCACA
3913129 CTTTGCCATG
Statistics
Matches: 75, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
34 3 0.04
35 41 0.55
38 2 0.03
40 29 0.39
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (35 bp):
ATACCATACCTACATTTCACAACTCAGTATGGATG
Found at i:3915042 original size:17 final size:17
Alignment explanation
Indices: 3915012--3915044 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3915002 AGTGGAAACA
3915012 TTTGCAACTCTGTTAAC
1 TTTGCAACTCTGTTAAC
3915029 TTTGCTAACT-TGTTAA
1 TTTGC-AACTCTGTTAA
3915045 AACAATATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (17 bp):
TTTGCAACTCTGTTAAC
Found at i:3915417 original size:19 final size:19
Alignment explanation
Indices: 3915393--3915432 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3915383 ATTTTTTTTA
3915393 TTAAACTCGTTATATCTTT
1 TTAAACTCGTTATATCTTT
3915412 TTAAACTCGTTATATCTTT
1 TTAAACTCGTTATATCTTT
3915431 TT
1 TT
3915433 TTTTTTACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.05, T:0.55
Consensus pattern (19 bp):
TTAAACTCGTTATATCTTT
Found at i:3930083 original size:5 final size:5
Alignment explanation
Indices: 3930073--3930104 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
3930063 TTGTGTATTC
3930073 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
3930105 TCACAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:3930087 original size:9 final size:9
Alignment explanation
Indices: 3930073--3930103 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
3930063 TTGTGTATTC
3930073 TTTATTTTA
1 TTTATTTTA
3930082 TTTATTTTA
1 TTTATTTTA
3930091 TTTTATTTTA
1 -TTTATTTTA
3930101 TTT
1 TTT
3930104 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:3934524 original size:5 final size:5
Alignment explanation
Indices: 3934514--3934550 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
3934504 TTGTGTGTTC
3934514 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
3934551 TCACGTACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:3935398 original size:15 final size:16
Alignment explanation
Indices: 3935363--3935400 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3935353 CTATAATGAT
*
3935363 AAAAAAATAAAGTGTA
1 AAAAAAATAAAGTATA
*
3935379 CAAAAAATAAAG-ATA
1 AAAAAAATAAAGTATA
3935394 AAAAAAA
1 AAAAAAA
3935401 CCTCGAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.13
Consensus pattern (16 bp):
AAAAAAATAAAGTATA
Found at i:3935541 original size:49 final size:49
Alignment explanation
Indices: 3935462--3935559 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 49
3935452 TTATAGTTCT
* *
3935462 AATCTTTTATACCTTAAAATATACATTCATTAACAAATTAGAACCCATA
1 AATCTTTTATACCTTAAAAAATACACTCATTAACAAATTAGAACCCATA
* *
3935511 AATCTTTTATACCTTAAAAAATATACTCATTAACAAATTAGAACTCATA
1 AATCTTTTATACCTTAAAAAATACACTCATTAACAAATTAGAACCCATA
3935560 TATAATACTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.35
Consensus pattern (49 bp):
AATCTTTTATACCTTAAAAAATACACTCATTAACAAATTAGAACCCATA
Found at i:3936642 original size:15 final size:15
Alignment explanation
Indices: 3936618--3936652 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3936608 TTAATCCTTT
*
3936618 ATAAATTATAAAAAA
1 ATAAACTATAAAAAA
3936633 ATAAACTATAAAAAA
1 ATAAACTATAAAAAA
*
3936648 TTAAA
1 ATAAA
3936653 ATTTTATCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAAACTATAAAAAA
Found at i:3936900 original size:29 final size:30
Alignment explanation
Indices: 3936837--3936900 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
3936827 CAATATAATC
3936837 TTTATATATATATATTTAAAATAATAAAAA
1 TTTATATATATATATTTAAAATAATAAAAA
* * *
3936867 ATTATA-ATATAT-TTTAAAAATAATATACA
1 TTTATATATATATATTT-AAAATAATAAAAA
3936896 TTTAT
1 TTTAT
3936901 TCTTTATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 3 0.10
29 21 0.72
30 5 0.17
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (30 bp):
TTTATATATATATATTTAAAATAATAAAAA
Found at i:3937518 original size:35 final size:36
Alignment explanation
Indices: 3937479--3937546 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
3937469 AATTAAATAT
*
3937479 AATACACAAGATAAACTT-CAAATATATAAATTTAA
1 AATACACAAGATAAACTTAAAAATATATAAATTTAA
3937514 AATACACAAGATAAACTTAAAAATATATAAATT
1 AATACACAAGATAAACTTAAAAATATATAAATT
3937547 AACAAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 18 0.58
36 13 0.42
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (36 bp):
AATACACAAGATAAACTTAAAAATATATAAATTTAA
Found at i:3937553 original size:16 final size:16
Alignment explanation
Indices: 3937524--3937557 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3937514 AATACACAAG
3937524 ATAAACTTAAAAATAT
1 ATAAACTTAAAAATAT
3937540 ATAAA-TTAACAAATAT
1 ATAAACTTAA-AAATAT
3937556 AT
1 AT
3937558 TGTAATCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAAACTTAAAAATAT
Found at i:3937718 original size:24 final size:23
Alignment explanation
Indices: 3937660--3937712 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
3937650 CAGTAAATTT
*
3937660 AAAACATTTGTTTATTTTTAAAAG
1 AAAAC-TTAGTTTATTTTTAAAAG
3937684 AAAACTTAGTTTATTTTT-AAA-
1 AAAACTTAGTTTATTTTTAAAAG
3937705 AAAACTTA
1 AAAACTTA
3937713 CAAGTTATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 8 0.29
22 3 0.11
23 12 0.43
24 5 0.18
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (23 bp):
AAAACTTAGTTTATTTTTAAAAG
Found at i:3939274 original size:6 final size:6
Alignment explanation
Indices: 3939263--3939306 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
3939253 ATCTATTTAA
** *
3939263 TTAAAT TTAAAT TCCAAT TTAAAAT CTAAAT TTAAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TT-AAAT TTAAAT TTAAAT TTAAAT T
3939307 AATTATCTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (6 bp):
TTAAAT
Found at i:3939292 original size:19 final size:19
Alignment explanation
Indices: 3939265--3939304 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3939255 CTATTTAATT
* *
3939265 AAATTTAAATTCCAATTTA
1 AAATCTAAATTCAAATTTA
*
3939284 AAATCTAAATTTAAATTTA
1 AAATCTAAATTCAAATTTA
3939303 AA
1 AA
3939305 TTAATTATCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATCTAAATTCAAATTTA
Found at i:3941266 original size:25 final size:23
Alignment explanation
Indices: 3941224--3941276 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
3941214 AAATTTATTT
*
3941224 TTATTATTAATTCTATTATTACTA
1 TTATTATTAATTCCATTATT-CTA
3941248 CTTATTATT-ATTGCCATTATTCTA
1 -TTATTATTAATT-CCATTATTCTA
3941272 TTATT
1 TTATT
3941277 TCTTATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 6 0.23
25 15 0.58
ACGTcount: A:0.28, C:0.11, G:0.02, T:0.58
Consensus pattern (23 bp):
TTATTATTAATTCCATTATTCTA
Found at i:3941368 original size:17 final size:17
Alignment explanation
Indices: 3941341--3941382 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3941331 AGTTATAATC
*
3941341 ATTATTATTCTTTATT-T
1 ATTATTGTTC-TTATTCT
*
3941358 GTTATTGTTCTTATTCT
1 ATTATTGTTCTTATTCT
3941375 ATTATTGT
1 ATTATTGT
3941383 CGTTATTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.67
Consensus pattern (17 bp):
ATTATTGTTCTTATTCT
Found at i:3943011 original size:16 final size:16
Alignment explanation
Indices: 3942990--3943023 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3942980 GGGTGCTAAT
3942990 CCTTCCTCGTACGTAA
1 CCTTCCTCGTACGTAA
3943006 CCTTCCTCGTACGTAA
1 CCTTCCTCGTACGTAA
3943022 CC
1 CC
3943024 GACTCCCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.41, G:0.12, T:0.29
Consensus pattern (16 bp):
CCTTCCTCGTACGTAA
Found at i:3949444 original size:17 final size:18
Alignment explanation
Indices: 3949419--3949454 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3949409 CTCAAAACTA
3949419 TATTCTAAAAA-TTAAAT
1 TATTCTAAAAACTTAAAT
*
3949436 TATTTTAAAAACTTAAAT
1 TATTCTAAAAACTTAAAT
3949454 T
1 T
3949455 TGAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
TATTCTAAAAACTTAAAT
Found at i:3951291 original size:2 final size:2
Alignment explanation
Indices: 3951286--3951327 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3951276 TAAGATACAA
3951286 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
3951328 GCAAAATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3955037 original size:3 final size:3
Alignment explanation
Indices: 3955031--3955353 Score: 111
Period size: 3 Copynumber: 107.7 Consensus size: 3
3955021 AAAAATAGTA
* * * *
3955031 AAT AAT AAT -AT ATT AAT AAG AAT TAT AAT AAT ATAT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* * ** *
3955076 AACA AAT AAT AA- AA- AAT AAC AAT GGGTT AAT AA- AAT AAT AGT AAT
1 AA-T AAT AAT AAT AAT AAT AAT AAT --AAT AAT AAT AAT AAT AAT AAT
* * * * *
3955121 AAT AGA- AGT AAA AAC AAT AAT AAT AAT AA- ATAT AAT AAT AGT GAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
* * * * *
3955166 AGT GAT AAT AGT ACAA AAT -AT AAT AAT AACA AAT AAAT AAGT -AT AGA-
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AA-T AAT -AAT AA-T AAT A-AT
* * *
3955213 AAG GA- AAT -GT AAT AAT AAT AAT AAT AAT ATAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
* * * * *
3955257 AAT AAT AA- AAG AAGT AAT AAA AAT AAA AAT AAC AAT AAT AGT AA-
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
3955301 AAT -AT AAT AAAT AAT AGT AAA AAA AAT AAT AA- AATT AACT AAT -TT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AA-T AA-T AAT AAT
3955346 AAT AAT AA
1 AAT AAT AA
3955354 AGTAGCTAAA
Statistics
Matches: 233, Mismatches: 57, Indels: 60
0.67 0.16 0.17
Matches are distributed among these distances:
2 24 0.10
3 180 0.77
4 28 0.12
5 1 0.00
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:3955083 original size:23 final size:24
Alignment explanation
Indices: 3955030--3955086 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
3955020 AAAAAATAGT
*
3955030 AAATAATAATATATTAATAAGAATT
1 AAATAAT-ATATATTAATAAGAATC
*
3955055 ATAATAATATATATTAATAATAA-C
1 A-AATAATATATATTAATAAGAATC
3955079 AAATAATA
1 AAATAATA
3955087 AAAAATAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 7 0.24
24 1 0.03
25 15 0.52
26 6 0.21
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATAATATATATTAATAAGAATC
Found at i:3955352 original size:56 final size:55
Alignment explanation
Indices: 3955223--3955334 Score: 145
Period size: 56 Copynumber: 2.0 Consensus size: 55
3955213 AAGGAAATGT
* * * *
3955223 AATAATAATAATAATAATATATAATAATAATAATAATAATAAAAGAAGTAATAAA
1 AATAAAAATAATAATAATATAAAATAATAATAATAATAATAAAAAAAATAATAAA
* *
3955278 AATAAAAATAACAATAATAGTAAAAT-ATAATAAATAATAGTAAAAAAAATAATAAA
1 AATAAAAATAATAATAATA-TAAAATAATAAT-AATAATAATAAAAAAAATAATAAA
3955334 A
1 A
3955335 TTAACTAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
55 22 0.45
56 27 0.55
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.26
Consensus pattern (55 bp):
AATAAAAATAATAATAATATAAAATAATAATAATAATAATAAAAAAAATAATAAA
Found at i:3955448 original size:28 final size:28
Alignment explanation
Indices: 3955391--3955474 Score: 138
Period size: 28 Copynumber: 3.1 Consensus size: 28
3955381 GTAGATTCAA
3955391 AAAGAAAAAGAAAATAAATAAA-AA-A-T
1 AAAGAAAAAGAAAA-AAATAAATAACAGT
3955417 AAAGAAAAAGAAAAAAATAAATAACAGT
1 AAAGAAAAAGAAAAAAATAAATAACAGT
3955445 AAAGAAAAAGAAAAAAATAAATAACAGT
1 AAAGAAAAAGAAAAAAATAAATAACAGT
3955473 AA
1 AA
3955475 CCTTTGCCCT
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
25 7 0.13
26 16 0.29
27 1 0.02
28 31 0.56
ACGTcount: A:0.77, C:0.02, G:0.10, T:0.11
Consensus pattern (28 bp):
AAAGAAAAAGAAAAAAATAAATAACAGT
Found at i:3957952 original size:39 final size:39
Alignment explanation
Indices: 3957898--3957978 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
3957888 TTTTGAATAT
3957898 TATCTTGATTGGTATGGTATTACTGTTAATGCAAGAGGA
1 TATCTTGATTGGTATGGTATTACTGTTAATGCAAGAGGA
3957937 TATCTTGATTGGTATGGTATTACTGTTAATGCAAGAGGA
1 TATCTTGATTGGTATGGTATTACTGTTAATGCAAGAGGA
3957976 TAT
1 TAT
3957979 GGGTTTAAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.40
Consensus pattern (39 bp):
TATCTTGATTGGTATGGTATTACTGTTAATGCAAGAGGA
Found at i:3958671 original size:23 final size:23
Alignment explanation
Indices: 3958644--3958704 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
3958634 CTTATTCAAA
3958644 ATAATAAAATATTTAAAATATTTT
1 ATAAT-AAATATTTAAAATATTTT
* * *
3958668 -TAATTAATATTTTATATATTTT
1 ATAATAAATATTTAAAATATTTT
*
3958690 ATAATTAA-ATTTAAA
1 ATAATAAATATTTAAA
3958705 TTTAAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 20 0.65
23 11 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATAATAAATATTTAAAATATTTT
Found at i:3958676 original size:22 final size:23
Alignment explanation
Indices: 3958651--3958704 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
3958641 AAAATAATAA
3958651 AATATTTAAAATATTTT-TAATT
1 AATATTTAAAATATTTTATAATT
* *
3958673 AATATTTTATATATTTTATAATT
1 AATATTTAAAATATTTTATAATT
3958696 AA-ATTTAAA
1 AATATTTAAA
3958705 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATATTTAAAATATTTTATAATT
Found at i:3966310 original size:2 final size:2
Alignment explanation
Indices: 3966303--3966336 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3966293 ACAATAATAC
* *
3966303 TA TA TA TA AA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3966337 ATAGAAATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3966452 original size:12 final size:12
Alignment explanation
Indices: 3966430--3966474 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
3966420 AATAAAAAAC
3966430 AATACTATATATA
1 AATA-TATATATA
3966443 AATATATATATA
1 AATATATATATA
* *
3966455 TATATATACATA
1 AATATATATATA
*
3966467 AAAATATA
1 AATATATA
3966475 CACTAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 24 0.86
13 4 0.14
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATATATATA
Found at i:3966475 original size:12 final size:12
Alignment explanation
Indices: 3966430--3966486 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
3966420 AATAAAAAAC
*
3966430 AATACTATATATA
1 AATA-TATACATA
*
3966443 AATATATATATA
1 AATATATACATA
*
3966455 TATATATACATA
1 AATATATACATA
*
3966467 AAAATATACACT-
1 AATATATACA-TA
3966479 AATATATA
1 AATATATA
3966487 ATAGTAATAG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
12 33 0.87
13 5 0.13
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (12 bp):
AATATATACATA
Found at i:3966583 original size:3 final size:3
Alignment explanation
Indices: 3966575--3966782 Score: 74
Period size: 3 Copynumber: 66.3 Consensus size: 3
3966565 AATAGGGGTG
3966575 ATA ATA ATA ATA ATA ATA CA-A ATA ATA ATA CATA TATA TATA ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA -ATA -ATA -ATA ATA ATA
* * * * * * * *
3966623 GTA GTTA AAA ATA AAA GATA ATA GA-A GTA ACA ATA ATG ATA GTA ATA
1 ATA -ATA ATA ATA ATA -ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* **
3966670 AT- ATAA ATA A-A TATA GAGA GGA CATA TATA AT- ATA ATA ATA AT-
1 ATA AT-A ATA ATA -ATA -ATA ATA -ATA -ATA ATA ATA ATA ATA ATA
3966713 ATAA ATA ATA ATA TATA CATGA GA-A ATA ATA ATA ATA AT- ATAA ATA
1 AT-A ATA ATA ATA -ATA -AT-A -ATA ATA ATA ATA ATA ATA AT-A ATA
* *
3966759 ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3966783 AACAAAGCTC
Statistics
Matches: 156, Mismatches: 28, Indels: 42
0.69 0.12 0.19
Matches are distributed among these distances:
2 13 0.08
3 107 0.69
4 34 0.22
5 2 0.01
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:3967137 original size:22 final size:22
Alignment explanation
Indices: 3967112--3967199 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 22
3967102 CCTTCTTTTC
3967112 CAAAAAAACACCTCCAAAAAAA
1 CAAAAAAACACCTCCAAAAAAA
*
3967134 CAAAAAAACCTCCTCCAAAATAAA
1 CAAAAAAA-CACCTCCAAAA-AAA
* * ** * *
3967158 GAACAATCCTCCTCCAAAAAAC
1 CAAAAAAACACCTCCAAAAAAA
** *
3967180 CAAAAACCCACCTTCAAAAA
1 CAAAAAAACACCTCCAAAAA
3967200 CAAAGTCTTG
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
22 25 0.47
23 21 0.40
24 7 0.13
ACGTcount: A:0.57, C:0.32, G:0.01, T:0.10
Consensus pattern (22 bp):
CAAAAAAACACCTCCAAAAAAA
Found at i:3967148 original size:23 final size:23
Alignment explanation
Indices: 3967112--3967185 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
3967102 CCTTCTTTTC
*
3967112 CAAAAAAA-CACCTCCAAAAAAA
1 CAAAAAAACCTCCTCCAAAAAAA
3967134 CAAAAAAACCTCCTCCAAAATAAA
1 CAAAAAAACCTCCTCCAAAA-AAA
* * * *
3967158 -GAACAATCCTCCTCCAAAAAAC
1 CAAAAAAACCTCCTCCAAAAAAA
3967180 CAAAAA
1 CAAAAA
3967186 CCCACCTTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
22 10 0.24
23 29 0.69
24 3 0.07
ACGTcount: A:0.59, C:0.30, G:0.01, T:0.09
Consensus pattern (23 bp):
CAAAAAAACCTCCTCCAAAAAAA
Found at i:3967732 original size:44 final size:44
Alignment explanation
Indices: 3967630--3968199 Score: 454
Period size: 44 Copynumber: 13.0 Consensus size: 44
3967620 TGTTTTCAAC
* *
3967630 TTGTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTTGAT
1 TTGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATCTTCGAT
* * * * * * * *
3967673 CTGCTTCACTGTAAGCACAAGAATGTCAGATCTGCTATCTTCGAT
1 TTG-TTCCCTATAAGCACAGGGATGCCAAATCTGATATCTTCGAT
* * * * * *
3967718 TTGCTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAAC
1 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATCTTCGAT
* * * *
3967762 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAAC
1 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATCTTCGAT
* *
3967806 TTGTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTTGAT
1 TTGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATCTTCGAT
* * * * * * * *
3967849 CTGCTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTTGAT
1 TTG-TTCCCTATAAGCACAGGGATGCCAAATCTGATATCTTCGAT
* * * * * *
3967894 TTGTTCCCTAAAAGCACAAGGATGCCAAATCTGATGTTTTCAAC
1 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATCTTCGAT
* * * *
3967938 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAAC
1 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATCTTCGAT
* *
3967982 TTGTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTTGAT
1 TTGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATCTTCGAT
* * * * * * *
3968025 CTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGAT
1 TTG-TTCCCTATAAGCACAGGGATGCCAAATCTGATATCTTCGAT
* * * * *
3968070 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAAC
1 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATCTTCGAT
*
3968114 TTGTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTCGAT
1 TTGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATCTTCGAT
* * * * * * *
3968157 CTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
1 TTG-TTCCCTATAAGCACAGGGATGCCAAATCTGATATCTTCG
3968200 GTCTGCTCCT
Statistics
Matches: 423, Mismatches: 89, Indels: 28
0.78 0.16 0.05
Matches are distributed among these distances:
42 6 0.01
43 32 0.08
44 327 0.77
45 50 0.12
46 8 0.02
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (44 bp):
TTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATCTTCGAT
Found at i:3967919 original size:176 final size:176
Alignment explanation
Indices: 3967619--3968140 Score: 981
Period size: 176 Copynumber: 3.0 Consensus size: 176
3967609 CTTCACTTCA
3967619 ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
1 ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
* *
3967684 TAAGCACAAGAATGTCAGATCTGCTATCTTCGATTTGCTCCCTATAAGCACAGGGATGCCAAATC
66 TAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATC
3967749 TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTG
131 TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTG
3967795 ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
1 ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
* * * *
3967860 TAAGCACAGGAATGTCAGATCTGTTATCTTTGATTTGTTCCCTAAAAGCACAAGGATGCCAAATC
66 TAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATC
*
3967925 TGATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTG
131 TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTG
3967971 ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
1 ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
3968036 TAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATC
66 TAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATC
3968101 TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCA
131 TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCA
3968141 TGCTGAAATC
Statistics
Matches: 334, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
176 334 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (176 bp):
ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
TAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATC
TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTG
Found at i:3968142 original size:132 final size:132
Alignment explanation
Indices: 3967938--3968199 Score: 506
Period size: 132 Copynumber: 2.0 Consensus size: 132
3967928 TGTTTTCAAC
3967938 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGG
1 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGG
*
3968003 ATGCCATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
66 ATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
3968068 AT
131 AT
*
3968070 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGG
1 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGG
3968135 ATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
66 ATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
3968200 GTCTGCTCCT
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 128 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (132 bp):
TTGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGG
ATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
AT
Done.