Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 61 of 325
Found at i:16143190 original size:8 final size:8
Alignment explanation
Indices: 16143179--16143207 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
16143169 CTAAATCTGC
16143179 TAAAAAAA
1 TAAAAAAA
16143187 T-AAAAAA
1 TAAAAAAA
16143194 TAAAAAAA
1 TAAAAAAA
16143202 TAAAAA
1 TAAAAA
16143208 GTGGTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (8 bp):
TAAAAAAA
Found at i:16143199 original size:15 final size:15
Alignment explanation
Indices: 16143179--16143207 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16143169 CTAAATCTGC
16143179 TAAAAAAATAAAAAA
1 TAAAAAAATAAAAAA
16143194 TAAAAAAATAAAAA
1 TAAAAAAATAAAAA
16143208 GTGGTTTAAA
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (15 bp):
TAAAAAAATAAAAAA
Found at i:16148527 original size:14 final size:14
Alignment explanation
Indices: 16148508--16148560 Score: 106
Period size: 14 Copynumber: 3.8 Consensus size: 14
16148498 TCAAAACAAG
16148508 AATTAAGAACACAT
1 AATTAAGAACACAT
16148522 AATTAAGAACACAT
1 AATTAAGAACACAT
16148536 AATTAAGAACACAT
1 AATTAAGAACACAT
16148550 AATTAAGAACA
1 AATTAAGAACA
16148561 AGTTAAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.58, C:0.13, G:0.08, T:0.21
Consensus pattern (14 bp):
AATTAAGAACACAT
Found at i:16155550 original size:128 final size:128
Alignment explanation
Indices: 16155276--16155594 Score: 371
Period size: 128 Copynumber: 2.5 Consensus size: 128
16155266 CGAAAAAACC
* * * *
16155276 GAAACCCAGCACAGTAGGGCACGATTCCTCAAATTTCTAAACATTGAGCATTGCCTTGTTTT-AG
1 GAAACCCAGCACAGTAGGGCACGATTCCTCGAATTTCCAAACATCGAACATTGCCTTGTTTTAAG
* * * *
16155340 AATTTAGAAAACATGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACGGGAAATT
66 AATTTACAAAACAGGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACAGAAAATT
* * *
16155403 GCAACCCAGCACAATAGGGCACGATTCCCCGAATTTCCAAACATCGAACATTGCCTTCGTTTTAA
1 GAAACCCAGCACAGTAGGGCACGATTCCTCGAATTTCCAAACATCGAACATTGCCTT-GTTTTAA
* * * * *
16155468 GGAATTTTCAATGTAC-GGA-TGAAATT-TCAAGGAATATTTGATTA-TTTGGACAAACAGAAAA
65 -GAATTTACAA--AACAGGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACAGAAAA
16155529 TT
127 TT
* * *
16155531 GAAACCCAGCACAGTAGGGCACGATTCCTCGAGTTCCCAAACATC-AATCATTACCTTTGTTTTA
1 GAAACCCAGCACAGTAGGGCACGATTCCTCGAATTTCCAAACATCGAA-CATTGCC-TTGTTTTA
16155595 GTAAATTTTC
Statistics
Matches: 163, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
127 52 0.32
128 73 0.45
129 19 0.12
130 15 0.09
131 2 0.01
132 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (128 bp):
GAAACCCAGCACAGTAGGGCACGATTCCTCGAATTTCCAAACATCGAACATTGCCTTGTTTTAAG
AATTTACAAAACAGGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACAGAAAATT
Found at i:16156156 original size:26 final size:27
Alignment explanation
Indices: 16156106--16156163 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 27
16156096 TGATTATTAA
*
16156106 AATAGATATTATATAGAAATAAATTTGG
1 AATAGATA-TATATAGAAATAAATTTAG
16156134 AATAGATA-ATATACGAAAT-AATTTAG
1 AATAGATATATATA-GAAATAAATTTAG
16156160 AATA
1 AATA
16156164 AAACATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 15 0.54
27 5 0.18
28 8 0.29
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (27 bp):
AATAGATATATATAGAAATAAATTTAG
Found at i:16156171 original size:26 final size:26
Alignment explanation
Indices: 16156116--16156171 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
16156106 AATAGATATT
* *
16156116 ATATAGAAATAAATTTGGAATAGATA
1 ATATAGAAATAAATTTAGAATAGAAA
16156142 ATATACGAAAT-AATTTAGAATA-AAA
1 ATATA-GAAATAAATTTAGAATAGAAA
16156167 CATAT
1 -ATAT
16156172 TAATTTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 2 0.08
26 19 0.73
27 5 0.19
ACGTcount: A:0.55, C:0.04, G:0.11, T:0.30
Consensus pattern (26 bp):
ATATAGAAATAAATTTAGAATAGAAA
Found at i:16162398 original size:23 final size:21
Alignment explanation
Indices: 16162370--16162416 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
16162360 TATTTGAGTA
16162370 TGAATGCATAAATGTATGCGTAT
1 TGAATG-ATAAATG-ATGCGTAT
* *
16162393 TGAATGTTAAATGATGTGTAT
1 TGAATGATAAATGATGCGTAT
16162414 TGA
1 TGA
16162417 TCGGTAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 6 0.27
23 6 0.27
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.38
Consensus pattern (21 bp):
TGAATGATAAATGATGCGTAT
Found at i:16164950 original size:26 final size:26
Alignment explanation
Indices: 16164912--16165047 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
16164902 TGATACAAAT
** *
16164912 TGATAATAAGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
16164938 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
16164964 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
16164990 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
16165016 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
16165042 TGATAA
1 TGATAA
16165048 GAATATGATG
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 103 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:16181350 original size:38 final size:39
Alignment explanation
Indices: 16181237--16181379 Score: 234
Period size: 39 Copynumber: 3.7 Consensus size: 39
16181227 CCGCACAAAG
*
16181237 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCACAATTTGCACAATT
* * *
16181277 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
16181316 GCCTTCGGGCTTAGCCCGG-TATCACAATTTGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
16181354 GCCTTCGGGCTTAGCCCGGATATCAC
1 GCCTTCGGGCTTAGCCCGGATATCAC
16181380 TCGAACATTC
Statistics
Matches: 95, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
38 35 0.37
39 51 0.54
40 9 0.09
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
Found at i:16181358 original size:77 final size:79
Alignment explanation
Indices: 16181197--16181378 Score: 269
Period size: 77 Copynumber: 2.3 Consensus size: 79
16181187 TCGTTCAAAC
* * **
16181197 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
1 GCCTTCGGG-CTTAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
16181262 ACAATTTGCACAATT
65 ACAATTTGCACAATT
* ** *
16181277 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGG-CTTAGCCCGG-TATCA
1 GCCTTCGGGCTTAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCA
16181340 CAATTTGCACAATT
66 CAATTTGCACAATT
16181354 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
16181379 CTCGAACATT
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
77 44 0.47
78 9 0.10
79 32 0.34
80 9 0.10
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (79 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCA
CAATTTGCACAATT
Found at i:16189348 original size:38 final size:39
Alignment explanation
Indices: 16189235--16189377 Score: 234
Period size: 39 Copynumber: 3.7 Consensus size: 39
16189225 CCGCACAAAG
*
16189235 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCACAATTTGCACAATT
* * *
16189275 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
16189314 GCCTTCGGGCTTAGCCCGG-TATCACAATTTGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
16189352 GCCTTCGGGCTTAGCCCGGATATCAC
1 GCCTTCGGGCTTAGCCCGGATATCAC
16189378 TCGAACATTC
Statistics
Matches: 95, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
38 35 0.37
39 51 0.54
40 9 0.09
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
Found at i:16189356 original size:77 final size:79
Alignment explanation
Indices: 16189195--16189376 Score: 269
Period size: 77 Copynumber: 2.3 Consensus size: 79
16189185 TCGTTCAAAC
* * **
16189195 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
1 GCCTTCGGG-CTTAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
16189260 ACAATTTGCACAATT
65 ACAATTTGCACAATT
* ** *
16189275 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGG-CTTAGCCCGG-TATCA
1 GCCTTCGGGCTTAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCA
16189338 CAATTTGCACAATT
66 CAATTTGCACAATT
16189352 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
16189377 CTCGAACATT
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
77 44 0.47
78 9 0.10
79 32 0.34
80 9 0.10
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (79 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCA
CAATTTGCACAATT
Found at i:16196140 original size:29 final size:29
Alignment explanation
Indices: 16196098--16196157 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
16196088 AAAGAGTAGA
16196098 AATGTGCAACAGAGATATTTTGTGACAAC
1 AATGTGCAACAGAGATATTTTGTGACAAC
16196127 AATGTGCAACAGAGATATTTTGTGACAAC
1 AATGTGCAACAGAGATATTTTGTGACAAC
16196156 AA
1 AA
16196158 ATCCACTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (29 bp):
AATGTGCAACAGAGATATTTTGTGACAAC
Found at i:16197906 original size:65 final size:65
Alignment explanation
Indices: 16197836--16198020 Score: 193
Period size: 65 Copynumber: 2.8 Consensus size: 65
16197826 TGTTTTTTTA
* *
16197836 AAATATCTA-TTTTCAATAGTTTATCATGCTCCTATAAGACACTTGTCAACCCCT-TTACC-ATG
1 AAATATCTATTTTTCAATAGTTTATCATACTCCTATAAGACACTTGTCAACCCCTAAT-CCTAT-
16197898 CTT
64 -TT
* * *
16197901 AAATATCTATTTTTTATAAATATTTTA-CTATACTCTTAT-AGTACACTTGTCAACCCCTAATCC
1 AAATATCTA--TTTT-TCAATAGTTTATC-ATACTCCTATAAG-ACACTTGTCAACCCCTAATCC
16197964 TATTT
61 TATTT
*
16197969 AAATATCTATTTTTCAATAGTTTATCATAC-CCATATAGGACACTTGTCAACC
1 AAATATCTATTTTTCAATAGTTTATCATACTCC-TATAAGACACTTGTCAACC
16198021 TTTAACTCTA
Statistics
Matches: 100, Mismatches: 9, Indels: 22
0.76 0.07 0.17
Matches are distributed among these distances:
64 1 0.01
65 38 0.38
66 6 0.06
68 17 0.17
69 35 0.35
70 3 0.03
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.41
Consensus pattern (65 bp):
AAATATCTATTTTTCAATAGTTTATCATACTCCTATAAGACACTTGTCAACCCCTAATCCTATTT
Found at i:16198463 original size:2 final size:2
Alignment explanation
Indices: 16198456--16198506 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
16198446 AATATTTTTC
* *
16198456 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T TT AT AT A- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
16198495 AT AT AA AT AT AT
1 AT AT AT AT AT AT
16198507 TTTTAATTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16198571 original size:29 final size:26
Alignment explanation
Indices: 16198539--16198602 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 26
16198529 AAATTAATAT
16198539 TTATAAAATATTTTTA-ATTAATTAGTAA
1 TTATAAAAT-TTTTTAGATTAA-T-GTAA
*
16198567 GTTATATAATTTTTTATGATTAATGTAA
1 -TTATAAAATTTTTTA-GATTAATGTAA
16198595 TTATAAAA
1 TTATAAAA
16198603 AAGACACACT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 7 0.23
28 10 0.32
29 9 0.29
30 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (26 bp):
TTATAAAATTTTTTAGATTAATGTAA
Found at i:16202906 original size:10 final size:10
Alignment explanation
Indices: 16202893--16202923 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
16202883 AGTTTAACTT
*
16202893 TTAATTAATC
1 TTAATTAAAC
16202903 TTAATTAAAC
1 TTAATTAAAC
16202913 TTAATTAAAC
1 TTAATTAAAC
16202923 T
1 T
16202924 AACCTTAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (10 bp):
TTAATTAAAC
Found at i:16207609 original size:43 final size:43
Alignment explanation
Indices: 16207546--16207673 Score: 154
Period size: 43 Copynumber: 3.0 Consensus size: 43
16207536 TAGGATTTCT
* *
16207546 AATATGTGTTCTTGTGTAAGACCACATCTGGGACGTTGGCATC
1 AATATGTGTTCTCGTGTAAGACCACGTCTGGGACGTTGGCATC
*
16207589 AATATGTGTTCTCGTATAAGACC-CTGTCTGGGACAG-TGGCATC
1 AATATGTGTTCTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATC
* * *
16207632 GATATGTGATT-ACATGTAAGACCACGTCTGGGACGTTGGCAT
1 AATATGTG-TTCTCGTGTAAGACCACGTCTGGGACGTTGGCAT
16207674 TGTACGATAT
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
42 2 0.03
43 67 0.92
44 4 0.05
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (43 bp):
AATATGTGTTCTCGTGTAAGACCACGTCTGGGACGTTGGCATC
Found at i:16208463 original size:2 final size:2
Alignment explanation
Indices: 16208456--16208494 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
16208446 GGCTATGGCT
*
16208456 TA TA TA TA TA -A GTG 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 TA TA T
16208495 GAATCTTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16211762 original size:14 final size:15
Alignment explanation
Indices: 16211734--16211762 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16211724 TTATAAAAAA
16211734 TTATAAAATATTTAT
1 TTATAAAATATTTAT
16211749 TTATAAAA-ATTTAT
1 TTATAAAATATTTAT
16211763 GACCATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATAAAATATTTAT
Found at i:16225679 original size:34 final size:34
Alignment explanation
Indices: 16225630--16225707 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
16225620 TGATTGCATT
* * *
16225630 ACTGTTACTGTTACTGTATTGGGCTGA-GGCCC-A
1 ACTGATACTGATACTGTAATGGG-TGACGGCCCTA
*
16225663 CACTGATACTGATACTGTAATGGGTTACGGCCCTA
1 -ACTGATACTGATACTGTAATGGGTGACGGCCCTA
16225698 ACTGATACTG
1 ACTGATACTG
16225708 GACTGTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 2 0.05
34 35 0.92
35 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (34 bp):
ACTGATACTGATACTGTAATGGGTGACGGCCCTA
Found at i:16232081 original size:46 final size:46
Alignment explanation
Indices: 16232031--16232206 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
16232021 TGGTTGAGCA
16232031 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
16232077 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
16232122 CATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
16232170 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
16232207 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 63 0.58
47 28 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:16232187 original size:93 final size:93
Alignment explanation
Indices: 16232028--16232198 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
16232018 GGATGGTTGA
* * *
16232028 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
16232093 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
16232121 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
16232186 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
16232199 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:16235243 original size:21 final size:22
Alignment explanation
Indices: 16235219--16235259 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
16235209 GCCACACACT
16235219 CGTGT-GGAAGGGTAACACGCC
1 CGTGTGGGAAGGGTAACACGCC
16235240 CGTGTGGGAAGGGTAACACG
1 CGTGTGGGAAGGGTAACACG
16235260 TTCGTGCCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.24, C:0.20, G:0.41, T:0.15
Consensus pattern (22 bp):
CGTGTGGGAAGGGTAACACGCC
Found at i:16235265 original size:22 final size:21
Alignment explanation
Indices: 16235212--16235265 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
16235202 AAAATAGGCC
*
16235212 ACACACTCGTGTGGAAGGGTA
1 ACACGCTCGTGTGGAAGGGTA
*
16235233 ACACGCCCGTGTGGGAAGGGTA
1 ACACGCTCGTGT-GGAAGGGTA
*
16235255 ACACGTTCGTG
1 ACACGCTCGTG
16235266 CCCCACACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.24, C:0.22, G:0.35, T:0.19
Consensus pattern (21 bp):
ACACGCTCGTGTGGAAGGGTA
Found at i:16236398 original size:47 final size:46
Alignment explanation
Indices: 16236328--16236497 Score: 163
Period size: 47 Copynumber: 3.6 Consensus size: 46
16236318 TTAAGTGCCG
*
16236328 ATGCCATGTCCCAGACATAGTCTTACACTAGCTCATAGCTTCAGTCA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCATA-CTTCAGTCA
* *
16236375 ATGCCATGTCCCAGACATGGTCTTACACTAACT-ATCATCTCTTAG-CA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCAT-A-CT-TCAGTCA
* *
16236422 GATG-CATGTCCCAGACAT-GTCTTACACTAGCCCTCAT-C-TCAATGCTG
1 -ATGCCATGTCCCAGACATGGTCTTACACTAG--CTCATACTTCAGT-C-A
*
16236469 ATGCCATGTCCCAGATATGGTCTTACACT
1 ATGCCATGTCCCAGACATGGTCTTACACT
16236498 GGCTTACACG
Statistics
Matches: 103, Mismatches: 9, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
44 2 0.02
46 18 0.17
47 63 0.61
48 18 0.17
49 2 0.02
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (46 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCATACTTCAGTCA
Found at i:16244154 original size:2 final size:2
Alignment explanation
Indices: 16244147--16244177 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16244137 CTATACATAC
16244147 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16244178 ACATATAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16249779 original size:94 final size:94
Alignment explanation
Indices: 16249583--16249796 Score: 252
Period size: 94 Copynumber: 2.3 Consensus size: 94
16249573 GATATGTGTA
16249583 CTAGTGTAAGACATGTCTGGGACATGCATCAACCACAGTATGAGAGCCAGTGTAAGACATGTCTG
1 CTAGTGTAAGACATGTCTGGGACATGCATCAACCACAGTATGAGAGCCAGTGTAAGACATGTCTG
* * **
16249648 TGACATGCATCATCCTCGAGATATTTAAG
66 GGACATGCATCAACCTCGAGATATACAAG
* * * * * * * *
16249677 CCAATGTAAGACATGTATAGGACATGCATC-AGCATTGAG-ATGAGAGCTAGTGTAGGACATGTC
1 CTAGTGTAAGACATGTCTGGGACATGCATCAACCA--CAGTATGAGAGCCAGTGTAAGACATGTC
* * *
16249740 TGGGACATGCATCAACGTTGCGATATACAAG
64 TGGGACATGCATCAACCTCGAGATATACAAG
*
16249771 CTAGTGTAAGACCTGTCTGGGACATG
1 CTAGTGTAAGACATGTCTGGGACATG
16249797 GTGTCAGCTT
Statistics
Matches: 98, Mismatches: 20, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
93 3 0.03
94 93 0.95
95 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (94 bp):
CTAGTGTAAGACATGTCTGGGACATGCATCAACCACAGTATGAGAGCCAGTGTAAGACATGTCTG
GGACATGCATCAACCTCGAGATATACAAG
Found at i:16249788 original size:48 final size:46
Alignment explanation
Indices: 16249583--16249796 Score: 182
Period size: 46 Copynumber: 4.6 Consensus size: 46
16249573 GATATGTGTA
* *
16249583 CTAGTGTAAGACATGTCTGGGACATGCATCAAC-C-ACAGTATGAGAG
1 CTAGTGTAAGACATGTCTGGGACATGCATCAACTCGAGA-TAT-AAAG
* * * *
16249629 CCAGTGTAAGACATGTCTGTGACATGCATCATCCTCGAGATATTTAAG
1 CTAGTGTAAGACATGTCTGGGACATGCATCA-ACTCGAGATA-TAAAG
* * * * * * * *
16249677 CCAATGTAAGACATGTATAGGACATGCATCAGCATTGAGAT-GAGAG
1 CTAGTGTAAGACATGTCTGGGACATGCATCAAC-TCGAGATATAAAG
* * *
16249723 CTAGTGTAGGACATGTCTGGGACATGCATCAACGTTGCGATATACAAG
1 CTAGTGTAAGACATGTCTGGGACATGCATCAAC-TCGAGATATA-AAG
*
16249771 CTAGTGTAAGACCTGTCTGGGACATG
1 CTAGTGTAAGACATGTCTGGGACATG
16249797 GTGTCAGCTT
Statistics
Matches: 134, Mismatches: 27, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
46 64 0.48
47 3 0.02
48 64 0.48
49 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (46 bp):
CTAGTGTAAGACATGTCTGGGACATGCATCAACTCGAGATATAAAG
Found at i:16249833 original size:21 final size:21
Alignment explanation
Indices: 16249773--16249838 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
16249763 TATACAAGCT
16249773 AGTGTAAGACCTGTCTGGGAC
1 AGTGTAAGACCTGTCTGGGAC
* * * *
16249794 ATGGTGTCAG-CTTGTTCTGTGTC
1 A--GTGTAAGACCTG-TCTGGGAC
16249817 AGTGTAAGACCTGTCTGGGAC
1 AGTGTAAGACCTGTCTGGGAC
16249838 A
1 A
16249839 TGGCATCGAC
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
21 14 0.42
22 6 0.18
23 13 0.39
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.30
Consensus pattern (21 bp):
AGTGTAAGACCTGTCTGGGAC
Found at i:16249894 original size:49 final size:49
Alignment explanation
Indices: 16249817--16249938 Score: 149
Period size: 49 Copynumber: 2.5 Consensus size: 49
16249807 GTTCTGTGTC
* * *
16249817 AGTGTAAGACCTGTCTGGGACATGGCATC-GACAC-CGATAGATGAGAGCT
1 AGTGTAAGACCTGTCTGGGACATAGCATCAG-C-CTCGATAGATGAAAGCA
* *
16249866 AGTGTAAGACCTGTCTGGGACATAGCATCAGCCTCGCTATATGAAAGCA
1 AGTGTAAGACCTGTCTGGGACATAGCATCAGCCTCGATAGATGAAAGCA
*
16249915 ATTGTAAGACCATGTCTGGGACAT
1 AGTGTAAGACC-TGTCTGGGACAT
16249939 GGCGTCGGTA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
48 1 0.02
49 50 0.78
50 13 0.20
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATAGCATCAGCCTCGATAGATGAAAGCA
Found at i:16251990 original size:27 final size:27
Alignment explanation
Indices: 16251489--16251989 Score: 625
Period size: 27 Copynumber: 18.6 Consensus size: 27
16251479 AAAGTACTCC
16251489 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
16251516 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
16251543 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
16251570 C-AGTTTACAGAATTATTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* * * *
16251597 TGAGTTATAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
16251624 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
16251651 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* **
16251678 -TAGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
16251705 CGATTTATAGAATTACCATTTTACCC-
1 CGATTTACAGAATTACCGTTTTACCCT
* *
16251731 CTAATTTACATAATTACCGTTTTACCC-
1 C-GATTTACAGAATTACCGTTTTACCCT
* *
16251758 CGATTTACATAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
16251785 CGATTTACAGAATTACCGTTTCACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
16251812 CGATTTACAGAATTACCATTTTACCCC
1 CGATTTACAGAATTACCGTTTTACCCT
* *
16251839 CGATTTACATAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
16251866 CTATTTACAGAATTACCGTTTCACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
16251893 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* **
16251920 CGATTTATAGAATTACTATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
16251947 TGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
16251974 CGATTTACAAAATTAC
1 CGATTTACAGAATTAC
16251990 TAAAATACCC
Statistics
Matches: 410, Mismatches: 56, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
26 27 0.07
27 380 0.93
28 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:16253259 original size:25 final size:25
Alignment explanation
Indices: 16253230--16253277 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
16253220 TTATAATATG
* * *
16253230 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
16253255 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
16253278 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:16253346 original size:20 final size:20
Alignment explanation
Indices: 16253321--16253379 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
16253311 TAAATATGGT
16253321 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
16253341 ATGTATGCTATGCACATGAT
1 ATGTATGATATGCACATGAA
16253361 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
16253380 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:16253457 original size:24 final size:24
Alignment explanation
Indices: 16253430--16253572 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
16253420 GAGGAAGTGA
16253430 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
16253454 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
16253478 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
16253501 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
16253525 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
16253549 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
16253573 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:16253523 original size:47 final size:47
Alignment explanation
Indices: 16253430--16253572 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
16253420 GAGGAAGTGA
16253430 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
16253478 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
16253525 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
16253573 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:16253546 original size:71 final size:72
Alignment explanation
Indices: 16253430--16253573 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
16253420 GAGGAAGTGA
*
16253430 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
16253493 CCAGTTAT
65 CCAGTTAT
** * *
16253501 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
16253566 CAGTTAT
66 CAGTTAT
16253573 A
1 A
16253574 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:16253798 original size:31 final size:31
Alignment explanation
Indices: 16253760--16253841 Score: 155
Period size: 31 Copynumber: 2.6 Consensus size: 31
16253750 ATACCGTTTA
16253760 CAGTAATATGAAATATGAAAAGGCTTCGGCC
1 CAGTAATATGAAATATGAAAAGGCTTCGGCC
16253791 CAGTAATATGAAATATGAAAAGGCTTCGGCC
1 CAGTAATATGAAATATGAAAAGGCTTCGGCC
*
16253822 CAGTATTATGAAATATGAAA
1 CAGTAATATGAAATATGAAA
16253842 TATGAAAAGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.24
Consensus pattern (31 bp):
CAGTAATATGAAATATGAAAAGGCTTCGGCC
Found at i:16256017 original size:20 final size:21
Alignment explanation
Indices: 16255979--16256019 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
16255969 CTTGTATAAC
16255979 TATCATCAAACATTCAAAATA
1 TATCATCAAACATTCAAAATA
16256000 TATCATCAAACA-TCAAAATA
1 TATCATCAAACATTCAAAATA
16256020 CTCATGTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.27
Consensus pattern (21 bp):
TATCATCAAACATTCAAAATA
Found at i:16260135 original size:16 final size:16
Alignment explanation
Indices: 16260114--16260150 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
16260104 TAAAAATAGA
16260114 TTCATCAAGGTTCAAT
1 TTCATCAAGGTTCAAT
16260130 TTCATCAAGGTTCAAT
1 TTCATCAAGGTTCAAT
16260146 TTCAT
1 TTCAT
16260151 AATTTATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.41
Consensus pattern (16 bp):
TTCATCAAGGTTCAAT
Found at i:16261048 original size:29 final size:29
Alignment explanation
Indices: 16261014--16261118 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 29
16261004 TACTCGATTT
* * *
16261014 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATACCATTCAAGCC
** * * *
16261043 CGCACACACAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * *
16261072 CGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
*
16261101 TGCACACTTAGTGCCATA
1 CGCACACTTAGTGCCATA
16261119 TATTTCCAGC
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACCATTCAAGCC
Found at i:16261106 original size:58 final size:59
Alignment explanation
Indices: 16261052--16261174 Score: 178
Period size: 58 Copynumber: 2.1 Consensus size: 59
16261042 CCGCACACAC
* *
16261052 AGTGCCATACCCTTCGAGC-TCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
1 AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
* * * *
16261110 AGTGCCATATATTTCCAGCAT-GCACACTCAGTGCCATATTTTTCCAGCATGCACACTT
1 AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
16261168 AGTGCCA
1 AGTGCCA
16261175 ATCTCGTCAC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 57 0.98
59 1 0.02
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.28
Consensus pattern (59 bp):
AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
Found at i:16261119 original size:29 final size:29
Alignment explanation
Indices: 16261073--16261174 Score: 186
Period size: 29 Copynumber: 3.5 Consensus size: 29
16261063 CTTCGAGCTC
16261073 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
16261102 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
* *
16261131 GCACACTCAGTGCCATATTTTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
16261160 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
16261175 ATCTCGTCAC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:16269061 original size:29 final size:29
Alignment explanation
Indices: 16268991--16269095 Score: 88
Period size: 29 Copynumber: 3.7 Consensus size: 29
16268981 ATACTCGATT
* * *
16268991 TCGCACACTTAGTGCCAT-GCGTTTAAGC
1 TCGCACACTTAGTGCCATACCCTTCAAGC
* ** *
16269019 CCGCACACACAGTGCCATACCCTTCGAGC
1 TCGCACACTTAGTGCCATACCCTTCAAGC
*** *
16269048 TCGCACACTTAGTGCCATATATTTCCAGC
1 TCGCACACTTAGTGCCATACCCTTCAAGC
16269077 AT-GCACACTTAGTGCCATA
1 -TCGCACACTTAGTGCCATA
16269096 TATTTCCAGC
Statistics
Matches: 61, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
28 15 0.25
29 45 0.74
30 1 0.02
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (29 bp):
TCGCACACTTAGTGCCATACCCTTCAAGC
Found at i:16269138 original size:28 final size:29
Alignment explanation
Indices: 16269050--16269150 Score: 186
Period size: 29 Copynumber: 3.5 Consensus size: 29
16269040 CTTCGAGCTC
16269050 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
16269079 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
*
16269108 GCACACTCAGTGCCATAT-TTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
16269136 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
16269151 ATCTCGTCAC
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
28 24 0.34
29 46 0.66
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.29
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:16288735 original size:47 final size:47
Alignment explanation
Indices: 16288666--16288792 Score: 155
Period size: 47 Copynumber: 2.7 Consensus size: 47
16288656 ATAGATAAGT
** * * * *
16288666 ACCTATACCATAACCCATAGCCAAATTAAGGTAACTTATCCCGGAGC
1 ACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCACGGAAC
* * * *
16288713 ACCTATACCATGGCCTATAGCCAAATCAAGGTAACTCCTCACTGAAT
1 ACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCACGGAAC
*
16288760 ACCTATACCATGGCCCGTAGCCAAATCAAGGTA
1 ACCTATACCATGGCCCATAGCCAAATCAAGGTA
16288793 TTATTCGTAC
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 68 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.21
Consensus pattern (47 bp):
ACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCACGGAAC
Found at i:16290997 original size:31 final size:31
Alignment explanation
Indices: 16290936--16290995 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
16290926 CACTTAAGAT
16290936 GTGTGTTTTGATATGTTTTAAGCTCATTTTA
1 GTGTGTTTTGATATGTTTTAAGCTCATTTTA
*
16290967 GTGTGTTTTGATGT-TGTTTAAG-TCATTTT
1 GTGTGTTTTGATATGT-TTTAAGCTCATTTT
16290996 TAAAGTGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.17, C:0.05, G:0.22, T:0.57
Consensus pattern (31 bp):
GTGTGTTTTGATATGTTTTAAGCTCATTTTA
Found at i:16295710 original size:87 final size:87
Alignment explanation
Indices: 16295563--16295738 Score: 325
Period size: 87 Copynumber: 2.0 Consensus size: 87
16295553 GAATAGAAAA
* * *
16295563 TTTATTAAAAGCATATCCATGTGTACAATGATGAAGTTAATGGATGAATCCGGCAGCAATACTTG
1 TTTATTAAAAGCATATCCATGTGTACAATGATGAAGTTAACGGATGAATCCGACAACAATACTTG
16295628 ACATTTTTAAAATGAGATAAAC
66 ACATTTTTAAAATGAGATAAAC
16295650 TTTATTAAAAGCATATCCATGTGTACAATGATGAAGTTAACGGATGAATCCGACAACAATACTTG
1 TTTATTAAAAGCATATCCATGTGTACAATGATGAAGTTAACGGATGAATCCGACAACAATACTTG
16295715 ACATTTTTAAAATGAGATAAAC
66 ACATTTTTAAAATGAGATAAAC
16295737 TT
1 TT
16295739 CTGTGTATTA
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (87 bp):
TTTATTAAAAGCATATCCATGTGTACAATGATGAAGTTAACGGATGAATCCGACAACAATACTTG
ACATTTTTAAAATGAGATAAAC
Found at i:16317368 original size:79 final size:79
Alignment explanation
Indices: 16317280--16317438 Score: 318
Period size: 79 Copynumber: 2.0 Consensus size: 79
16317270 AGTTCTAGAG
16317280 AGAGAAAATGAGAAGCGTTAGATTCATGATAATTTCTAAGTGAGTTTGGATAAGTTTTTGGGCTT
1 AGAGAAAATGAGAAGCGTTAGATTCATGATAATTTCTAAGTGAGTTTGGATAAGTTTTTGGGCTT
16317345 TGGAATATGGTTAA
66 TGGAATATGGTTAA
16317359 AGAGAAAATGAGAAGCGTTAGATTCATGATAATTTCTAAGTGAGTTTGGATAAGTTTTTGGGCTT
1 AGAGAAAATGAGAAGCGTTAGATTCATGATAATTTCTAAGTGAGTTTGGATAAGTTTTTGGGCTT
16317424 TGGAATATGGTTAA
66 TGGAATATGGTTAA
16317438 A
1 A
16317439 TCAATATAAA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (79 bp):
AGAGAAAATGAGAAGCGTTAGATTCATGATAATTTCTAAGTGAGTTTGGATAAGTTTTTGGGCTT
TGGAATATGGTTAA
Found at i:16320150 original size:47 final size:47
Alignment explanation
Indices: 16320097--16320191 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
16320087 TGAAAATTTG
16320097 AAAGTAGGGGTCTAAAACAAGAGAGGCATGTCTCAAGAGATAGCTCT
1 AAAGTAGGGGTCTAAAACAAGAGAGGCATGTCTCAAGAGATAGCTCT
*
16320144 AAAGTAGGGGTCTAAAACAAGATAGGCATGTCTCAAGAGATAGCTCT
1 AAAGTAGGGGTCTAAAACAAGAGAGGCATGTCTCAAGAGATAGCTCT
16320191 A
1 A
16320192 TAGTTGTTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.39, C:0.15, G:0.26, T:0.20
Consensus pattern (47 bp):
AAAGTAGGGGTCTAAAACAAGAGAGGCATGTCTCAAGAGATAGCTCT
Found at i:16344399 original size:10 final size:10
Alignment explanation
Indices: 16344386--16344424 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
16344376 ATATGTGAAT
16344386 ATATCATGGC
1 ATATCATGGC
16344396 ATATCATGTGC
1 ATATCATG-GC
16344407 ATATCATGGC
1 ATATCATGGC
16344417 ATATCATG
1 ATATCATG
16344425 TACAAAAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (10 bp):
ATATCATGGC
Found at i:16344412 original size:21 final size:21
Alignment explanation
Indices: 16344386--16344425 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
16344376 ATATGTGAAT
16344386 ATATCATGGCATATCATGTGC
1 ATATCATGGCATATCATGTGC
16344407 ATATCATGGCATATCATGT
1 ATATCATGGCATATCATGT
16344426 ACAAAAGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (21 bp):
ATATCATGGCATATCATGTGC
Found at i:16354326 original size:33 final size:33
Alignment explanation
Indices: 16354285--16354360 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
16354275 CAAGAGAAAG
16354285 AAAAAATAAGTAATTAAATTAAATTAAATTGCA
1 AAAAAATAAGTAATTAAATTAAATTAAATTGCA
16354318 AAAAAATAAGTAATTAAATTAAATTAAATTGCA
1 AAAAAATAAGTAATTAAATTAAATTAAATTGCA
16354351 AGAAAAATAA
1 A-AAAAATAA
16354361 ATGGCTAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 34 0.81
34 8 0.19
ACGTcount: A:0.63, C:0.03, G:0.07, T:0.28
Consensus pattern (33 bp):
AAAAAATAAGTAATTAAATTAAATTAAATTGCA
Found at i:16356300 original size:19 final size:21
Alignment explanation
Indices: 16356261--16356302 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
16356251 TGTTTCCTCA
16356261 TAGCCTCCTCAGACTCCCATG
1 TAGCCTCCTCAGACTCCCATG
*
16356282 TAGCCTCTTCA-AC-CCCATG
1 TAGCCTCCTCAGACTCCCATG
16356301 TA
1 TA
16356303 TTTTCCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 2 0.10
21 10 0.50
ACGTcount: A:0.21, C:0.40, G:0.12, T:0.26
Consensus pattern (21 bp):
TAGCCTCCTCAGACTCCCATG
Found at i:16361939 original size:44 final size:44
Alignment explanation
Indices: 16361889--16361976 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
16361879 ATTACATGTA
* *
16361889 TCGCATCCATAATGAACTAGGACCAACTCAACGAGCTTGGATGC
1 TCGCATCCATAATGAACTAGGACCAACTCAACAAGCTCGGATGC
*
16361933 TCGCATCCATAATGAACTTGGACCAACTCAACAAGCTCGGATGC
1 TCGCATCCATAATGAACTAGGACCAACTCAACAAGCTCGGATGC
16361977 CTCATACATA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.20
Consensus pattern (44 bp):
TCGCATCCATAATGAACTAGGACCAACTCAACAAGCTCGGATGC
Found at i:16362008 original size:45 final size:44
Alignment explanation
Indices: 16361889--16362008 Score: 118
Period size: 44 Copynumber: 2.7 Consensus size: 44
16361879 ATTACATGTA
* * * *
16361889 TCGCATCCATAATGAA-CTAGGACCAACTCAACGAGCTTGGATGC
1 TCGCATACATAATGAACCCA-GACCAACTCAACAAGCTCGGATGC
* ***
16361933 TCGCATCCATAATGAACTTGGACCAACTCAACAAGCTCGGATGC
1 TCGCATACATAATGAACCCAGACCAACTCAACAAGCTCGGATGC
*
16361977 -CTCATACATATCATGAACCCAGACCAACTCAA
1 TCGCATACATA--ATGAACCCAGACCAACTCAA
16362009 TGAGTCGGAT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
43 8 0.12
44 38 0.59
45 18 0.28
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (44 bp):
TCGCATACATAATGAACCCAGACCAACTCAACAAGCTCGGATGC
Found at i:16366482 original size:101 final size:101
Alignment explanation
Indices: 16366306--16366508 Score: 370
Period size: 101 Copynumber: 2.0 Consensus size: 101
16366296 ATAGTTACAA
*
16366306 AAAGTTTCTCCTTATACTTCGCATACAAGAATGTGCTATCTATCTAGGCACTAGATTTGTAGTGC
1 AAAGTTTCTCCTTATACTTCACATACAAGAATGTGCTATCTATCTAGGCACTAGATTTGTAGTGC
* *
16366371 AGGAAGCCTTCAATAAGTGGCTTAAATGTCTAGAAT
66 AAGAACCCTTCAATAAGTGGCTTAAATGTCTAGAAT
*
16366407 AAAGTTTCTCCTTATACTTCATATACAAGAATGTGCTATCTATCTAGGCACTAGATTTGTAGTGC
1 AAAGTTTCTCCTTATACTTCACATACAAGAATGTGCTATCTATCTAGGCACTAGATTTGTAGTGC
16366472 AAGAACCCTTCAATAAGTGGCTTAAATGTCTAGAAT
66 AAGAACCCTTCAATAAGTGGCTTAAATGTCTAGAAT
16366508 A
1 A
16366509 TATGATGGAA
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 98 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (101 bp):
AAAGTTTCTCCTTATACTTCACATACAAGAATGTGCTATCTATCTAGGCACTAGATTTGTAGTGC
AAGAACCCTTCAATAAGTGGCTTAAATGTCTAGAAT
Found at i:16367464 original size:20 final size:21
Alignment explanation
Indices: 16367439--16367479 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16367429 TTCAGTTTGA
* *
16367439 ATATATT-TTGATGTTAGTTG
1 ATATATTATTAATCTTAGTTG
16367459 ATATATTATTAATCTTAGTTG
1 ATATATTATTAATCTTAGTTG
16367480 TTAAACAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.54
Consensus pattern (21 bp):
ATATATTATTAATCTTAGTTG
Found at i:16370133 original size:48 final size:48
Alignment explanation
Indices: 16370000--16370275 Score: 206
Period size: 48 Copynumber: 5.9 Consensus size: 48
16369990 GGTTATGTGC
* * *
16370000 GATCACATGTAAGACCATGTCTAGGACATGGCTTTGGCATCGATATGT
1 GATCCCATATAAGACCATGTCTAGGACATGGCATTGGCATCGATATGT
* ** * **
16370048 AATTTCGTATAAGACCA----TA-G--ATGGGCTATCAGCATCGATATGT
1 GATCCCATATAAGACCATGTCTAGGACAT-GGC-ATTGGCATCGATATGT
* ** * **
16370091 GATCCCATGTAAGACCATGTCTAGGACATGGCATCAGCATCGATCTAC
1 GATCCCATATAAGACCATGTCTAGGACATGGCATTGGCATCGATATGT
* * * * * **
16370139 AATCCCATATAAGACCATGTCTGGGATATGGCGTTGGCATCGATCTAC
1 GATCCCATATAAGACCATGTCTAGGACATGGCATTGGCATCGATATGT
* * *
16370187 GATCCCCTATAAGACCATGTCTGGGAAATGGCATTGGCATCGATATGT
1 GATCCCATATAAGACCATGTCTAGGACATGGCATTGGCATCGATATGT
* * * * * *
16370235 GATCCCATGTAAGACCATATCTGGGATATGGTATTGACATC
1 GATCCCATATAAGACCATGTCTAGGACATGGCATTGGCATC
16370276 CTACCATGTG
Statistics
Matches: 183, Mismatches: 36, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
41 2 0.01
42 3 0.02
43 26 0.14
44 2 0.01
47 2 0.01
48 143 0.78
49 3 0.02
50 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (48 bp):
GATCCCATATAAGACCATGTCTAGGACATGGCATTGGCATCGATATGT
Found at i:16370218 original size:96 final size:96
Alignment explanation
Indices: 16370091--16370265 Score: 242
Period size: 96 Copynumber: 1.8 Consensus size: 96
16370081 ATCGATATGT
* * *
16370091 GATCCCATGTAAGACCATGTCTAGGACATGGCATCAGCATCGATCTACAATCCCATATAAGACCA
1 GATCCCATATAAGACCATGTCTAGGAAATGGCATCAGCATCGATATACAATCCCATATAAGACCA
*
16370156 TGTCTGGGATATGGCGTTGGCATCGATCTAC
66 TATCTGGGATATGGCGTTGGCATCGATCTAC
* * ** *** *
16370187 GATCCCCTATAAGACCATGTCTGGGAAATGGCATTGGCATCGATATGTGATCCCATGTAAGACCA
1 GATCCCATATAAGACCATGTCTAGGAAATGGCATCAGCATCGATATACAATCCCATATAAGACCA
16370252 TATCTGGGATATGG
66 TATCTGGGATATGG
16370266 TATTGACATC
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
96 67 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (96 bp):
GATCCCATATAAGACCATGTCTAGGAAATGGCATCAGCATCGATATACAATCCCATATAAGACCA
TATCTGGGATATGGCGTTGGCATCGATCTAC
Found at i:16371542 original size:25 final size:25
Alignment explanation
Indices: 16371504--16371555 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
16371494 CACGGGCGTG
16371504 TGACTTGGCCGTGTGACCCTAATTT
1 TGACTTGGCCGTGTGACCCTAATTT
*
16371529 TGACTTGGCTGTGTGACCCTAATTT
1 TGACTTGGCCGTGTGACCCTAATTT
16371554 TG
1 TG
16371556 TTGATGACGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.38
Consensus pattern (25 bp):
TGACTTGGCCGTGTGACCCTAATTT
Found at i:16378312 original size:24 final size:25
Alignment explanation
Indices: 16378279--16378335 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
16378269 ACTTTAGTCG
*
16378279 TTTTACTTTATTTGC-AATTTAATT
1 TTTTATTTTATTTGCTAATTTAATT
* **
16378303 TTTTATTTTATTTTCTAATTTTCTT
1 TTTTATTTTATTTGCTAATTTAATT
16378328 TTTTATTT
1 TTTTATTT
16378336 GCTTCTGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (25 bp):
TTTTATTTTATTTGCTAATTTAATT
Found at i:16378323 original size:20 final size:20
Alignment explanation
Indices: 16378298--16378335 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16378288 ATTTGCAATT
16378298 TAATTTT-TTATTTTATTTTC
1 TAATTTTCTT-TTTTATTTTC
16378318 TAATTTTCTTTTTTATTT
1 TAATTTTCTTTTTTATTT
16378336 GCTTCTGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (20 bp):
TAATTTTCTTTTTTATTTTC
Found at i:16381600 original size:17 final size:17
Alignment explanation
Indices: 16381578--16381619 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
16381568 CATCGATGAC
16381578 CCAAGCTCCTCTCTCTA
1 CCAAGCTCCTCTCTCTA
16381595 CCAAGCTCCTCTCTCTA
1 CCAAGCTCCTCTCTCTA
16381612 CCAAGCTC
1 CCAAGCTC
16381620 TCGCGTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.19, C:0.48, G:0.07, T:0.26
Consensus pattern (17 bp):
CCAAGCTCCTCTCTCTA
Found at i:16385291 original size:13 final size:13
Alignment explanation
Indices: 16385273--16385299 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16385263 AGCAATCGCA
16385273 CACGGGCGTGTCC
1 CACGGGCGTGTCC
16385286 CACGGGCGTGTCC
1 CACGGGCGTGTCC
16385299 C
1 C
16385300 TGTCGAGCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.41, G:0.37, T:0.15
Consensus pattern (13 bp):
CACGGGCGTGTCC
Found at i:16395819 original size:9 final size:9
Alignment explanation
Indices: 16395781--16395822 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
16395771 ATATTTTTAA
16395781 AAAATT-AT
1 AAAATTCAT
16395789 AAAATATCAT
1 AAAAT-TCAT
* *
16395799 AAAGTTCTT
1 AAAATTCAT
16395808 AAAATTCAT
1 AAAATTCAT
16395817 AAAATT
1 AAAATT
16395823 AATTAATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
8 5 0.18
9 17 0.61
10 6 0.21
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (9 bp):
AAAATTCAT
Found at i:16395828 original size:19 final size:19
Alignment explanation
Indices: 16395781--16395828 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
16395771 ATATTTTTAA
16395781 AAAATTA-TAAAATATCAT
1 AAAATTATTAAAATATCAT
* *
16395799 AAAGTTCTTAAAAT-TCAT
1 AAAATTATTAAAATATCAT
16395817 AAAATTAATTAA
1 AAAATT-ATTAA
16395829 TTATTTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAATTATTAAAATATCAT
Found at i:16395840 original size:19 final size:18
Alignment explanation
Indices: 16395818--16395869 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
16395808 AAAATTCATA
16395818 AAATTAATTAATTATTTTT
1 AAATTAA-TAATTATTTTT
*
16395837 AAATCATAA-AAATATTTTT
1 AAAT--TAATAATTATTTTT
*
16395856 AAATTTATAATTAT
1 AAATTAATAATTAT
16395870 GTAAAAGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
17 2 0.07
18 5 0.19
19 17 0.63
21 3 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATTAATAATTATTTTT
Found at i:16396646 original size:14 final size:14
Alignment explanation
Indices: 16396627--16396653 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16396617 TTATTAAAAA
16396627 TTTTATCTTTCTTT
1 TTTTATCTTTCTTT
16396641 TTTTATCTTTCTT
1 TTTTATCTTTCTT
16396654 AGTTTTCGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATCTTTCTTT
Found at i:16401421 original size:22 final size:24
Alignment explanation
Indices: 16401395--16401439 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
16401385 TATTCGAAAA
*
16401395 TTATT-TTTTAAAA-ATAAAATAT
1 TTATTATTATAAAATATAAAATAT
16401417 TTATTATTATAAAATATAAAATA
1 TTATTATTATAAAATATAAAATA
16401440 ATTGCAACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 7 0.35
24 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTATTATTATAAAATATAAAATAT
Found at i:16405372 original size:25 final size:25
Alignment explanation
Indices: 16405338--16405408 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 25
16405328 AATTTAAATT
* * *
16405338 TTATATTAATATTAAATCATTGTTA
1 TTATATTAATATTAAATAATTATAA
16405363 TTATATTAATATTAAATAATTATAA
1 TTATATTAATATTAAATAATTATAA
16405388 TTATAATT-ATATTAAATAATT
1 TTAT-ATTAATATTAAATAATT
16405409 CCACCGTCCC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
25 39 0.93
26 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (25 bp):
TTATATTAATATTAAATAATTATAA
Found at i:16411572 original size:16 final size:18
Alignment explanation
Indices: 16411540--16411580 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
16411530 ACGAGGAGAA
16411540 AAAAAAAAAACAGAA-TT
1 AAAAAAAAAACAGAATTT
*
16411557 AAAAATAAAACA-AATTT
1 AAAAAAAAAACAGAATTT
16411574 AAAAAAA
1 AAAAAAA
16411581 TTAAAAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.15
Consensus pattern (18 bp):
AAAAAAAAAACAGAATTT
Found at i:16414842 original size:68 final size:67
Alignment explanation
Indices: 16414733--16414921 Score: 229
Period size: 68 Copynumber: 2.8 Consensus size: 67
16414723 CACATGCTAC
* * *
16414733 CATAATCGAGCTATGGTCTTACACAATATA-AAGCTATGTTTAATGTCCTGGCAGACTCCATATG
1 CATAATCGAGCTATGGTCTTACACATTA-AGAAACAATGTTTAATGTCCTGGCAGACTCCATATG
*
16414797 TTTT
65 -TTG
* * *
16414801 CATAATCGAGCTATGGTCTTACATATTAAGAAACCATGTTTAATGTCCTGGCAGACTCTATATGT
1 CATAATCGAGCTATGGTCTTACACATTAAGAAACAATGTTTAATGTCCTGGCAGACTCCATATGT
16414866 TG
66 TG
** * **
16414868 CAATAGCCGAGCTATGGTCTTACACATTATGAATTAATGTTT-ATGTCCTGGCAG
1 C-ATAATCGAGCTATGGTCTTACACATTAAGAAACAATGTTTAATGTCCTGGCAG
16414922 TTTTTCGATT
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
67 16 0.15
68 90 0.85
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (67 bp):
CATAATCGAGCTATGGTCTTACACATTAAGAAACAATGTTTAATGTCCTGGCAGACTCCATATGT
TG
Found at i:16415825 original size:2 final size:2
Alignment explanation
Indices: 16415818--16415861 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
16415808 CGTTCACTTT
*
16415818 CA CA CA CA CA CA CA CA TA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
16415860 CA
1 CA
16415862 TACATACATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:16419989 original size:131 final size:131
Alignment explanation
Indices: 16419745--16420030 Score: 369
Period size: 131 Copynumber: 2.2 Consensus size: 131
16419735 CAATTGTTCA
* **
16419745 TTTAAAAATTCTTTAAAACGAAGGCGATGTTCGATATTTGACAATTCGCGGAATCGTGCCCTAAC
1 TTTAAAAATTCTTTAAAACGAAGGCAATACTCGATATTTGACAATTCGCGGAATCGTGCCCTAAC
* * * * **
16419810 GTGTTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATGTCCCTTTGGAATTTCATTCATGT
66 GTGCTGGGTTGCAATTTCCCGTTCGCTCAAAATAATCGAATATCCCTTTGGAATTTCACCCATGT
*
16419875 T
131 C
* * * * * *
16419876 TTCTAAAAACTCTTTAAAACGAAGGTAATACTCGATGTTTGGCAATTTG-GGAATCGTGCCCTAT
1 TT-TAAAAATTCTTTAAAACGAAGGCAATACTCGATATTTGACAATTCGCGGAATCGTGCCCTAA
* * *
16419940 CGTGCTGGGTTGCGATTTCCCGTTCGTTCAAAATAATCGAATATTCCTTTGGAATTTCACCCATG
65 CGTGCTGGGTTGCAATTTCCCGTTCGCTCAAAATAATCGAATATCCCTTTGGAATTTCACCCATG
16420005 TC
130 TC
*
16420007 TTTAAAAATTCTTT-AAGCGAAGGC
1 TTTAAAAATTCTTTAAAACGAAGGC
16420031 GATGTTTGAT
Statistics
Matches: 132, Mismatches: 22, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
129 8 0.06
130 11 0.08
131 75 0.57
132 38 0.29
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (131 bp):
TTTAAAAATTCTTTAAAACGAAGGCAATACTCGATATTTGACAATTCGCGGAATCGTGCCCTAAC
GTGCTGGGTTGCAATTTCCCGTTCGCTCAAAATAATCGAATATCCCTTTGGAATTTCACCCATGT
C
Found at i:16420104 original size:130 final size:127
Alignment explanation
Indices: 16419745--16420106 Score: 352
Period size: 131 Copynumber: 2.8 Consensus size: 127
16419735 CAATTGTTCA
*
16419745 TTTAAAAATTCTTTAAAACGAAGGCGATGTTCGATATTTGACAATTCGCGGAATCGTGCCCTAAC
1 TTTAAAAATTCTTTAAAACGAAGGCGATGTTCGATATTAGA-AATTCG-GGAATCGTGCCCT-AC
* * * **
16419810 -GTGTTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATGTCCCTTTGGAATTTCATTCATG
63 TGTGTTGGGTTGCGATTTCTCGTTAGCT--AAATAATCGAATATCCCTTTGGAATTTCACCCATG
*
16419874 TT
126 TC
* ** ** * * * *
16419876 TTCTAAAAACTCTTTAAAACGAAGGTAATACTCGATGTTTGGCAATTTGGGAATCGTGCCCTA-T
1 TT-TAAAAATTCTTTAAAACGAAGGCGATGTTCGAT-ATTAGAAATTCGGGAATCGTGCCCTACT
* * * * *
16419940 CGTGCTGGGTTGCGATTTCCCGTTCGTTCAAAATAATCGAATATTCCTTTGGAATTTCACCCATG
64 -GTGTTGGGTTGCGATTTCTCGTTAG--CTAAATAATCGAATATCCCTTTGGAATTTCACCCATG
16420005 TC
126 TC
* * *
16420007 TTTAAAAATTCTTT-AAGCGAAGGCGATGTTTGATATCTAGAAATTCGAGGAGTCGTGCCCTACT
1 TTTAAAAATTCTTTAAAACGAAGGCGATGTTCGATAT-TAGAAATTCG-GGAATCGTGCCCTACT
*
16420071 GTGTTGGGTTTCGATTTTCTCGTTAGACTAAATAAT
64 GTGTTGGGTTGCGA-TTTCTCGTTAG-CTAAATAAT
16420107 TGGGCATCCT
Statistics
Matches: 184, Mismatches: 37, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
128 1 0.01
129 21 0.11
130 45 0.24
131 80 0.43
132 33 0.18
133 4 0.02
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (127 bp):
TTTAAAAATTCTTTAAAACGAAGGCGATGTTCGATATTAGAAATTCGGGAATCGTGCCCTACTGT
GTTGGGTTGCGATTTCTCGTTAGCTAAATAATCGAATATCCCTTTGGAATTTCACCCATGTC
Found at i:16435100 original size:130 final size:130
Alignment explanation
Indices: 16434759--16435101 Score: 395
Period size: 131 Copynumber: 2.6 Consensus size: 130
16434749 CAATTGTTCA
16434759 TTTAAAAATTCTTTAAAACGAAGGCGATGTTCGATATTTGGCAATTCGCGGAATCGTGCCCTAAC
1 TTTAAAAATTCTTTAAAACGAAGGCGATGTTCGATATTTGGCAATTCG-GGAATCGTGCCCT-AC
* * * * * * **
16434824 -GTGTTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATGTCCCTTTGGAATTTCATTCATG
64 TGTGCTGGGTTGCGATTTCCCGTTCGCTCAAAACAATCGAATATCCCTTTGGAATTTCACCCATG
*
16434888 TT
129 TC
* ** ** *
16434890 TTCTAAAAACTCTTTAAAACGAAGGTAATACTCGATGTTTGGCAATTCGGGAATCGTGCCCTA-T
1 TT-TAAAAATTCTTTAAAACGAAGGCGATGTTCGATATTTGGCAATTCGGGAATCGTGCCCTACT
* * *
16434954 CGTGCTGGGTTGCGATTTCCCGTTCGTTCAATACAATCGAATATTCCTTTGGAATTTCACCCATG
65 -GTGCTGGGTTGCGATTTCCCGTTCGCTCAAAACAATCGAATATCCCTTTGGAATTTCACCCATG
16435019 TC
129 TC
* * * * * *
16435021 TTTAAAAATTCTTTAAGA-GAAGGCGATGTTCGATATCTAGAAATCCGAGGAGTCGTGCCCTACT
1 TTTAAAAATTCTTTAAAACGAAGGCGATGTTCGATATTTGGCAATTCG-GGAATCGTGCCCTACT
*
16435085 GTGCTGGGTTTCGATTT
65 GTGCTGGGTTGCGATTT
16435102 TCTCGTTAGA
Statistics
Matches: 176, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
129 20 0.11
130 44 0.25
131 72 0.41
132 40 0.23
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (130 bp):
TTTAAAAATTCTTTAAAACGAAGGCGATGTTCGATATTTGGCAATTCGGGAATCGTGCCCTACTG
TGCTGGGTTGCGATTTCCCGTTCGCTCAAAACAATCGAATATCCCTTTGGAATTTCACCCATGTC
Found at i:16441493 original size:93 final size:93
Alignment explanation
Indices: 16441362--16441532 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
16441352 GCCCATAAGT
* * *
16441362 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
16441427 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
16441455 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
16441520 CGAGTTCGGATGC
66 CGAGCTCGGATGC
16441533 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:16441529 original size:46 final size:46
Alignment explanation
Indices: 16441354--16441529 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
16441344 TGTAACCCGC
* * * *
16441354 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* *
16441400 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCAT
* *
16441450 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
*
16441493 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
16441530 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 1 0.01
43 8 0.07
44 1 0.01
46 64 0.58
47 28 0.25
49 1 0.01
50 6 0.05
51 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
Found at i:16444300 original size:68 final size:68
Alignment explanation
Indices: 16444191--16444463 Score: 332
Period size: 68 Copynumber: 4.0 Consensus size: 68
16444181 TAGTTCACCA
* * * * * * * *
16444191 TCCTAGTGGACTTCACATGCTGCCATAGACGAGCTATGGTCTTACACAATATGAACCCCTATTTA
1 TCCTAGTGGACTCCATATGTTGCCATAGTCAAGCTATGGTCTTACACATTATGAACCCATGTTTA
16444256 ATG
66 ATG
* * *
16444259 TCCTAGTGGACACCATATGTTGTCATAGTCAAACTATGGTCTTACACATTATGAACCCATGTTTA
1 TCCTAGTGGACTCCATATGTTGCCATAGTCAAGCTATGGTCTTACACATTATGAACCCATGTTTA
16444324 ATG
66 ATG
* * *** * * **
16444327 TCTTGGTGGACTTTTTATGTTGCCATAG-CTGAGCTATGGTCTTACATATTATGAACTGATGTTT
1 TCCTAGTGGACTCCATATGTTGCCATAGTC-AAGCTATGGTCTTACACATTATGAACCCATGTTT
16444391 AATG
65 AATG
* *
16444395 TCCTAGCGGACTCCATATGTTGCCATAGTCAAGCTATGGTCATACACATTATGAACCCATGTTTA
1 TCCTAGTGGACTCCATATGTTGCCATAGTCAAGCTATGGTCTTACACATTATGAACCCATGTTTA
16444460 ATG
66 ATG
16444463 T
1 T
16444464 ATTGACGTAC
Statistics
Matches: 169, Mismatches: 34, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
67 1 0.01
68 167 0.99
69 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (68 bp):
TCCTAGTGGACTCCATATGTTGCCATAGTCAAGCTATGGTCTTACACATTATGAACCCATGTTTA
ATG
Found at i:16444441 original size:136 final size:136
Alignment explanation
Indices: 16444211--16444463 Score: 391
Period size: 136 Copynumber: 1.9 Consensus size: 136
16444201 CTTCACATGC
* *
16444211 TGCCATAGACGAGCTATGGTCTTACACAATATGAACCCCTATTTAATGTCCTAGTGGACACCATA
1 TGCCATAGACGAGCTATGGTCTTACACAATATGAACCCATATTTAATGTCCTAGCGGACACCATA
* *
16444276 TGTTGTCATAGTCAAACTATGGTCTTACACATTATGAACCCATGTTTAATGTCTTGGTGGACTTT
66 TGTTGCCATAGTCAAACTATGGTCATACACATTATGAACCCATGTTTAATGTCTTGGTGGACTTT
16444341 TTATGT
131 TTATGT
* * ** * *
16444347 TGCCATAG-CTGAGCTATGGTCTTACATATTATGAACTGATGTTTAATGTCCTAGCGGACTCCAT
1 TGCCATAGAC-GAGCTATGGTCTTACACAATATGAACCCATATTTAATGTCCTAGCGGACACCAT
*
16444411 ATGTTGCCATAGTCAAGCTATGGTCATACACATTATGAACCCATGTTTAATGT
65 ATGTTGCCATAGTCAAACTATGGTCATACACATTATGAACCCATGTTTAATGT
16444464 ATTGACGTAC
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
135 1 0.01
136 104 0.99
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (136 bp):
TGCCATAGACGAGCTATGGTCTTACACAATATGAACCCATATTTAATGTCCTAGCGGACACCATA
TGTTGCCATAGTCAAACTATGGTCATACACATTATGAACCCATGTTTAATGTCTTGGTGGACTTT
TTATGT
Found at i:16448415 original size:25 final size:25
Alignment explanation
Indices: 16448367--16448414 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
16448357 TATTCCTAGA
* *
16448367 ATAGTTAGAGTTTAACTACGAAAAG
1 ATAGTTAGAGTCTAACTAAGAAAAG
16448392 ATAG-TAGAGTCTAACTAAGAAAA
1 ATAGTTAGAGTCTAACTAAGAAAA
16448415 ATAAACTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.48, C:0.08, G:0.19, T:0.25
Consensus pattern (25 bp):
ATAGTTAGAGTCTAACTAAGAAAAG
Found at i:16448887 original size:14 final size:14
Alignment explanation
Indices: 16448865--16448894 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16448855 TTATTCTAAA
*
16448865 AAAATTTTAAAAAT
1 AAAACTTTAAAAAT
16448879 AAAACTTTAAAAAT
1 AAAACTTTAAAAAT
16448893 AA
1 AA
16448895 TATTTCCAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAACTTTAAAAAT
Found at i:16449189 original size:21 final size:21
Alignment explanation
Indices: 16449141--16449185 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
16449131 TAAAGATTCC
*
16449141 AAAATTTTATAAAAGTACATA
1 AAAATTTTATAAAAGTAAATA
16449162 AAAATTTTATAAAA-TAAATA
1 AAAATTTTATAAAAGTAAATA
16449182 AAAA
1 AAAA
16449186 ATTTGCACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAATTTTATAAAAGTAAATA
Found at i:16454071 original size:29 final size:29
Alignment explanation
Indices: 16454031--16454089 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
16454021 GTAATTTAAT
16454031 ATATATAAATTTAATTTTGAT-TTAAATAA
1 ATATATAAATTT-ATTTTGATATTAAATAA
* *
16454060 ATATATAGATTTATTTTTATATTAAATAA
1 ATATATAAATTTATTTTGATATTAAATAA
16454089 A
1 A
16454090 ATACAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
ATATATAAATTTATTTTGATATTAAATAA
Found at i:16455013 original size:15 final size:17
Alignment explanation
Indices: 16454993--16455045 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 17
16454983 CGTCTAATAG
16454993 AAATAT-TAAAATT-TA
1 AAATATATAAAATTATA
16455008 AAATATATAAAATTATAA
1 AAATATATAAAATTAT-A
* *
16455026 AAAGATATATAATTATA
1 AAATATATAAAATTATA
16455043 AAA
1 AAA
16455046 ATTATTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 6 0.18
16 7 0.21
17 5 0.15
18 15 0.45
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAATATATAAAATTATA
Found at i:16455127 original size:24 final size:24
Alignment explanation
Indices: 16455073--16455127 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
16455063 TTTTAATTTC
* * *
16455073 TTTATAATATATAAATTATCTAAA
1 TTTAAAATATATAAAATATATAAA
* *
16455097 ATAAAAATATATAAAATATATAAA
1 TTTAAAATATATAAAATATATAAA
16455121 TTTAAAA
1 TTTAAAA
16455128 AGAATATAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
TTTAAAATATATAAAATATATAAA
Found at i:16456805 original size:40 final size:40
Alignment explanation
Indices: 16456731--16456908 Score: 148
Period size: 40 Copynumber: 4.5 Consensus size: 40
16456721 GAATCACGTA
* **
16456731 CCTTCGGGAT-TTAA-CCGGATATAACCACAAGCACAATTG
1 CCTTCGGG-TCTTAACCCGGATATAACAACTCGCACAATTG
* *** *
16456770 CCTTCGGGTCTTAACCCGGATTTGGTAACTTGCACAATTG
1 CCTTCGGGTCTTAACCCGGATATAACAACTCGCACAATTG
* *
16456810 CCTTTGGGTCTTAGCCCGGATATAACAACTCGCACGAA-TG
1 CCTTCGGGTCTTAACCCGGATATAACAACTCGCAC-AATTG
* * * * *
16456850 CCTTCGGGTCTTAGCCCAGATATAATC-ACTAGCATAAATG
1 CCTTCGGGTCTTAACCCGGATATAA-CAACTCGCACAATTG
* *
16456890 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGTCTTAACCCGG
16456909 GTATCATTCA
Statistics
Matches: 114, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
38 1 0.01
39 14 0.12
40 96 0.84
41 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CCTTCGGGTCTTAACCCGGATATAACAACTCGCACAATTG
Found at i:16456892 original size:80 final size:80
Alignment explanation
Indices: 16456731--16456908 Score: 189
Period size: 80 Copynumber: 2.2 Consensus size: 80
16456721 GAATCACGTA
* * * * * **
16456731 CCTTCGGGATTTA-ACCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGATTTGG
1 CCTTCGGGACTTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCAGATATAA
* *
16456795 TAACTTGCACAATTG
66 TAACTAGCACAAATG
* * ** *
16456810 CCTTTGGGTCTTAGCCCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGCCCAGATATA
1 CCTTCGGGACTTAGCCCGGATATAACAACAAGCAC-AATTGCCTTCGGGTCTTAACCCAGATATA
* *
16456874 ATCACTAGCATAAATG
65 ATAACTAGCACAAATG
16456890 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
16456909 GTATCATTCA
Statistics
Matches: 79, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
79 10 0.13
80 67 0.85
81 2 0.03
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCAGATATAA
TAACTAGCACAAATG
Found at i:16461334 original size:2 final size:2
Alignment explanation
Indices: 16461283--16461317 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16461273 AATTAACTGA
16461283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16461318 AACTCATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16467597 original size:2 final size:2
Alignment explanation
Indices: 16467590--16467625 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
16467580 TCACATGAAA
16467590 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
16467626 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16468368 original size:2 final size:2
Alignment explanation
Indices: 16468361--16468398 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
16468351 AATTAACTGA
*
16468361 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16468399 TCATGAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16471144 original size:27 final size:28
Alignment explanation
Indices: 16471114--16471166 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
16471104 CAACGAGTAC
* *
16471114 AGATAAAGG-CAAGGAAAAGCTAGTTAG
1 AGATAAAGGTAAAGGAAAACCTAGTTAG
16471141 AGATAAAGGTAAAGGAAAACCTAGTT
1 AGATAAAGGTAAAGGAAAACCTAGTT
16471167 TAAACTTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.49, C:0.08, G:0.26, T:0.17
Consensus pattern (28 bp):
AGATAAAGGTAAAGGAAAACCTAGTTAG
Found at i:16472608 original size:13 final size:13
Alignment explanation
Indices: 16472592--16472617 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16472582 TATTCTCATA
16472592 AATCATTCAATAC
1 AATCATTCAATAC
16472605 AATCATTCAATAC
1 AATCATTCAATAC
16472618 GACACCAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
AATCATTCAATAC
Found at i:16473999 original size:47 final size:46
Alignment explanation
Indices: 16473940--16474195 Score: 245
Period size: 47 Copynumber: 5.5 Consensus size: 46
16473930 TATGCTAGTA
*
16473940 TAAGACATGTCTGGGACATGCATCGGCCACATTATGAGTGCCAGTG
1 TAAGACATGTCTGGGACATGCATCGGCCACATGATGAGTGCCAGTG
*
16473986 TAAGACCATGTCTGGGACATGCATCGGCCACATTATGAGTGCCAGTG
1 TAAGA-CATGTCTGGGACATGCATCGGCCACATGATGAGTGCCAGTG
* * * ** *
16474033 TAAGACCATATTTGGGACATGGCATTGGTGTAGA-GATGAGTGCCAGTG
1 TAAGA-CATGTCTGGGACAT-GCATCGG-CCACATGATGAGTGCCAGTG
* * * *
16474081 TAAGGCATATCTGGGACATGCATCAGCCTCGATGATGA-TAGCCAGTG
1 TAAGACATGTCTGGGACATGCATCGGCCAC-ATGATGAGT-GCCAGTG
* * * *
16474128 TAAGACGTGTCTGGGACATGCATCGGCTA-A-GA-GTCGTGCTAGTG
1 TAAGACATGTCTGGGACATGCATCGGCCACATGATG-AGTGCCAGTG
*
16474172 TAAGACATATC-GAGGACATGCATC
1 TAAGACATGTCTG-GGACATGCATC
16474196 AGCACGTATA
Statistics
Matches: 176, Mismatches: 25, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
43 2 0.01
44 28 0.16
45 2 0.01
46 12 0.07
47 107 0.61
48 23 0.13
49 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (46 bp):
TAAGACATGTCTGGGACATGCATCGGCCACATGATGAGTGCCAGTG
Found at i:16475148 original size:55 final size:54
Alignment explanation
Indices: 16475032--16475156 Score: 155
Period size: 55 Copynumber: 2.3 Consensus size: 54
16475022 AAGGGTAGGC
**
16475032 CACACGGGCGTGTGTCATGACCGTGTTTTAAAGTCAATGTTGTCCATGGGCAGG
1 CACACGGGCGTGTGTCATGACCGTGTTTTAAAGTCAATGTTGTCCACAGGCAGG
* *
16475086 CCACACGGGCGTGTGTCATGGCCGTGTTTTAAAGTCAGTGTTG-CACACAGGCTAAGG
1 -CACACGGGCGTGTGTCATGACCGTGTTTTAAAGTCAATGTTGTC-CACAGGC--AGG
*
16475143 -GCACGGGCGTGTGT
1 CACACGGGCGTGTGT
16475157 GACCACACGG
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
54 1 0.02
55 58 0.94
57 3 0.05
ACGTcount: A:0.19, C:0.22, G:0.34, T:0.26
Consensus pattern (54 bp):
CACACGGGCGTGTGTCATGACCGTGTTTTAAAGTCAATGTTGTCCACAGGCAGG
Found at i:16476005 original size:17 final size:18
Alignment explanation
Indices: 16475983--16476016 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16475973 AGCTCGTATG
16475983 TAAATAACT-TAAATCAT
1 TAAATAACTATAAATCAT
*
16476000 TAAATAAGTATAAATCA
1 TAAATAACTATAAATCA
16476017 ACCAATTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (18 bp):
TAAATAACTATAAATCAT
Found at i:16476045 original size:21 final size:21
Alignment explanation
Indices: 16476019--16476059 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
16476009 ATAAATCAAC
16476019 CAATTTCACATTAACTACAAG
1 CAATTTCACATTAACTACAAG
16476040 CAATTTCACATTAACTACAA
1 CAATTTCACATTAACTACAA
16476060 ACCTTTCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.24, G:0.02, T:0.29
Consensus pattern (21 bp):
CAATTTCACATTAACTACAAG
Found at i:16481921 original size:30 final size:30
Alignment explanation
Indices: 16481885--16481945 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
16481875 TAGGTTTCAG
16481885 TTAAAATATACTTTTACAAAGCTATTTTAA
1 TTAAAATATACTTTTACAAAGCTATTTTAA
16481915 TTAAAATATACTTTTACAAAGCTATTTTAA
1 TTAAAATATACTTTTACAAAGCTATTTTAA
16481945 T
1 T
16481946 ATTAAAGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (30 bp):
TTAAAATATACTTTTACAAAGCTATTTTAA
Found at i:16491725 original size:20 final size:21
Alignment explanation
Indices: 16491690--16491728 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
16491680 CTATAATCGA
16491690 TTAAATAAACTAATTATCTAG
1 TTAAATAAACTAATTATCTAG
*
16491711 TTAAAT-AATTAATTATCT
1 TTAAATAAACTAATTATCT
16491729 TCGATTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (21 bp):
TTAAATAAACTAATTATCTAG
Found at i:16494174 original size:13 final size:13
Alignment explanation
Indices: 16494156--16494180 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16494146 AGCATCAAAG
16494156 GGGCACACGGCCT
1 GGGCACACGGCCT
16494169 GGGCACACGGCC
1 GGGCACACGGCC
16494181 ATGTGGCTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.40, T:0.04
Consensus pattern (13 bp):
GGGCACACGGCCT
Found at i:16495623 original size:22 final size:23
Alignment explanation
Indices: 16495593--16495641 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
16495583 ATCCCCCAAA
* *
16495593 CCCTATTTTT-CTTTTTTTTTTT
1 CCCTATTTTTCCTTTCTTTCTTT
*
16495615 CCCTTTTTTTCCTTTCTTTCTTT
1 CCCTATTTTTCCTTTCTTTCTTT
16495638 CCCT
1 CCCT
16495642 GTTCTGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (23 bp):
CCCTATTTTTCCTTTCTTTCTTT
Found at i:16502719 original size:24 final size:23
Alignment explanation
Indices: 16502692--16502741 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
16502682 TTCGTCCTTC
16502692 TTTCTTTCCT-TTTTCTTTATTTTA
1 TTTCTTT-CTATTTTCTTTA-TTTA
*
16502716 TTTCTTTTTATTTTCTTTATTTA
1 TTTCTTTCTATTTTCTTTATTTA
16502739 TTT
1 TTT
16502742 TAACTATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTCTTTCTATTTTCTTTATTTA
Found at i:16502724 original size:19 final size:19
Alignment explanation
Indices: 16502689--16502742 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
16502679 TGTTTCGTCC
* *
16502689 TTCTTTCTTTCCTTTTTCTT
1 TTCTTTATTT-CTTTTTATT
16502709 TAT-TTTATTTCTTTTTATT
1 T-TCTTTATTTCTTTTTATT
*
16502728 TTCTTTATTTATTTT
1 TTCTTTATTTCTTTT
16502743 AACTATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 1 0.03
19 20 0.69
20 7 0.24
21 1 0.03
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (19 bp):
TTCTTTATTTCTTTTTATT
Found at i:16509024 original size:42 final size:43
Alignment explanation
Indices: 16508939--16509025 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 43
16508929 ATTACATGTA
* * *
16508939 TCGCATCCATTATGAACTCAGACCAATTCAACGAGTTCGGATGC
1 TCGCATCCATAATGAACTCAGACC-ATTCAACGAGCTCAGATGC
*
16508983 TCGCATCCATAATGAACTCGGACC-TTCAACGAGCTCAGATGC
1 TCGCATCCATAATGAACTCAGACCATTCAACGAGCTCAGATGC
16509025 T
1 T
16509026 TCATATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 17 0.44
44 22 0.56
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (43 bp):
TCGCATCCATAATGAACTCAGACCATTCAACGAGCTCAGATGC
Found at i:16509379 original size:2 final size:2
Alignment explanation
Indices: 16509372--16509416 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
16509362 AACTTTTCCA
*
16509372 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AA AT CAT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
16509413 AT AT
1 AT AT
16509417 GCAACATAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 2 0.05
2 34 0.89
3 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16509578 original size:105 final size:105
Alignment explanation
Indices: 16509449--16509659 Score: 422
Period size: 105 Copynumber: 2.0 Consensus size: 105
16509439 TTCAAACATA
16509449 GCATTGCACTATTATTATCATACGAACTTACCTCGAATGTAAATTTCGACCAATTACTCCATTTT
1 GCATTGCACTATTATTATCATACGAACTTACCTCGAATGTAAATTTCGACCAATTACTCCATTTT
16509514 AATCCATAATCTCGTACTTTTCGATTTAAGCCCAAATCTC
66 AATCCATAATCTCGTACTTTTCGATTTAAGCCCAAATCTC
16509554 GCATTGCACTATTATTATCATACGAACTTACCTCGAATGTAAATTTCGACCAATTACTCCATTTT
1 GCATTGCACTATTATTATCATACGAACTTACCTCGAATGTAAATTTCGACCAATTACTCCATTTT
16509619 AATCCATAATCTCGTACTTTTCGATTTAAGCCCAAATCTC
66 AATCCATAATCTCGTACTTTTCGATTTAAGCCCAAATCTC
16509659 G
1 G
16509660 ATTTCCTTGA
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 106 1.00
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (105 bp):
GCATTGCACTATTATTATCATACGAACTTACCTCGAATGTAAATTTCGACCAATTACTCCATTTT
AATCCATAATCTCGTACTTTTCGATTTAAGCCCAAATCTC
Found at i:16510715 original size:21 final size:21
Alignment explanation
Indices: 16510688--16510758 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
16510678 ATTGAAAAAT
16510688 ATAATATTTTATATTAATATA
1 ATAATATTTTATATTAATATA
* * *
16510709 TTAATATTTT-TAATAATAAAA
1 ATAATATTTTATATTAAT-ATA
*
16510730 ATAA-ATTTTATTATCAATATA
1 ATAATATTTTA-TATTAATATA
16510751 ATAATATT
1 ATAATATT
16510759 AAGCTTGATT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
20 11 0.28
21 20 0.51
22 8 0.21
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAATATTTTATATTAATATA
Found at i:16512680 original size:15 final size:16
Alignment explanation
Indices: 16512660--16512692 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
16512650 TTGTCAATTG
*
16512660 TAAAAAAT-TAAAAAA
1 TAAAAAATCCAAAAAA
16512675 TAAAAAATCCAAAAAA
1 TAAAAAATCCAAAAAA
16512691 TA
1 TA
16512693 GATAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (16 bp):
TAAAAAATCCAAAAAA
Found at i:16519244 original size:3 final size:3
Alignment explanation
Indices: 16519238--16519281 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
16519228 AAGAGCTAGA
16519238 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16519282 CAGAAACTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16521912 original size:17 final size:18
Alignment explanation
Indices: 16521884--16521919 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
16521874 ATTATTTCAG
16521884 TAAAAGAAAAATAACAAA
1 TAAAAGAAAAATAACAAA
16521902 TAAAA-AAAAATAACAAA
1 TAAAAGAAAAATAACAAA
16521919 T
1 T
16521920 TTACCTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.78, C:0.06, G:0.03, T:0.14
Consensus pattern (18 bp):
TAAAAGAAAAATAACAAA
Found at i:16524868 original size:43 final size:43
Alignment explanation
Indices: 16524820--16524905 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
16524810 GAACAAGATA
16524820 GTATCTGTAGAAGTATTTTATAACTAAATGTTAATAAAACATT
1 GTATCTGTAGAAGTATTTTATAACTAAATGTTAATAAAACATT
16524863 GTATCTGTAGAAGTATTTTATAACTAAATGTTAATAAAACATT
1 GTATCTGTAGAAGTATTTTATAACTAAATGTTAATAAAACATT
16524906 TACAGCATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.40
Consensus pattern (43 bp):
GTATCTGTAGAAGTATTTTATAACTAAATGTTAATAAAACATT
Found at i:16525896 original size:20 final size:20
Alignment explanation
Indices: 16525871--16525909 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
16525861 TTCTTTGTCC
*
16525871 TTTTTCGTTTTTTTA-TTTTG
1 TTTTTC-TTTATTTACTTTTG
16525891 TTTTTCTTTATTTACTTTT
1 TTTTTCTTTATTTACTTTT
16525910 TCAATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.08, C:0.08, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTATTTACTTTTG
Found at i:16525948 original size:24 final size:24
Alignment explanation
Indices: 16525921--16525968 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
16525911 CAATATTTTC
*
16525921 TTATTTGTCTT-TTATTTGTTTTAT
1 TTATTTGT-TTATTATTAGTTTTAT
16525945 TTATTTGTTTATTATTAGTTTTAT
1 TTATTTGTTTATTATTAGTTTTAT
16525969 AATATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.17, C:0.02, G:0.08, T:0.73
Consensus pattern (24 bp):
TTATTTGTTTATTATTAGTTTTAT
Found at i:16525949 original size:13 final size:13
Alignment explanation
Indices: 16525931--16525968 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
16525921 TTATTTGTCT
16525931 TTTATTTGTTTTA
1 TTTATTTGTTTTA
16525944 TTTATTTG-TTTA
1 TTTATTTGTTTTA
*
16525956 -TTATTAGTTTTA
1 TTTATTTGTTTTA
16525968 T
1 T
16525969 AATATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 6 0.27
12 8 0.36
13 8 0.36
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (13 bp):
TTTATTTGTTTTA
Found at i:16525967 original size:12 final size:12
Alignment explanation
Indices: 16525916--16525968 Score: 56
Period size: 11 Copynumber: 4.5 Consensus size: 12
16525906 TTTTTCAATA
*
16525916 TTTTCTTATTTG
1 TTTTATTATTTG
*
16525928 TCTT-TTATTTG
1 TTTTATTATTTG
16525939 TTTTATTTATTTG
1 TTTTA-TTATTTG
*
16525952 -TTTATTATTAG
1 TTTTATTATTTG
16525963 TTTTAT
1 TTTTAT
16525969 AATATTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
11 16 0.46
12 12 0.34
13 7 0.20
ACGTcount: A:0.15, C:0.04, G:0.08, T:0.74
Consensus pattern (12 bp):
TTTTATTATTTG
Found at i:16525998 original size:22 final size:22
Alignment explanation
Indices: 16525963--16526231 Score: 126
Period size: 22 Copynumber: 12.0 Consensus size: 22
16525953 TTATTATTAG
*
16525963 TTTTATAATATTTTAAATGTATA
1 TTTTA-AATATTTTAAATATATA
*
16525986 TTTTAAATTTTTTATAATAT-TA
1 TTTTAAATATTTTA-AATATATA
*
16526008 TTTTAAAAATTTTAAATATAT-
1 TTTTAAATATTTTAAATATATA
* *
16526029 TTTTAAAAAATTTAAATAT-TA
1 TTTTAAATATTTTAAATATATA
*
16526050 TTTTTGAA-ATTTTAAATAT-TA
1 -TTTTAAATATTTTAAATATATA
* * * *
16526071 TTTTTTAATATTATAAAACATTTA
1 -TTTTAAATATT-TTAAATATATA
*** * *
16526095 AAATACATTATTTTTAAAGATATGA
1 TTTTA-AATA-TTTTAAATATAT-A
* * * *
16526120 CCTTTCAA-A-TTT-ATTATTTA
1 -TTTTAAATATTTTAAATATATA
*
16526140 TTTTATAATATTTTAGAA-GTATA
1 TTTTA-AATATTTTA-AATATATA
*
16526163 TTTTAAATATTTTAAATATTATT
1 TTTTAAATATTTTAAATA-TATA
*
16526186 TTTTAAA-ATTTTAAATATTATT
1 TTTTAAATATTTTAAATA-TATA
16526208 TTTTAAAATTATTTTTAAATATAT
1 TTTT-AAA-TA-TTTTAAATATAT
16526232 TCAAACTCTT
Statistics
Matches: 191, Mismatches: 33, Indels: 42
0.72 0.12 0.16
Matches are distributed among these distances:
19 3 0.02
20 4 0.02
21 49 0.26
22 66 0.35
23 37 0.19
24 14 0.07
25 8 0.04
26 10 0.05
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTTAAATATTTTAAATATATA
Found at i:16526029 original size:42 final size:42
Alignment explanation
Indices: 16525957--16526075 Score: 130
Period size: 42 Copynumber: 2.7 Consensus size: 42
16525947 ATTTGTTTAT
* * ***
16525957 TATTAGTTTTATAATATTTTAAATGTATATTTTAAATTTTTTATAA
1 TATTA-TTTTA-AAAATTTTAAATATAT-TTTTAAAAAATTTA-AA
16526003 TATTATTTTAAAAATTTTAAATATATTTTTAAAAAATTTAAA
1 TATTATTTTAAAAATTTTAAATATATTTTTAAAAAATTTAAA
**
16526045 TATTATTTTTGAAATTTTAAATATTATTTTT
1 TATTATTTTAAAAATTTTAAATA-TATTTTT
16526076 TAATATTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
42 23 0.35
43 18 0.28
44 14 0.22
45 5 0.08
46 5 0.08
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (42 bp):
TATTATTTTAAAAATTTTAAATATATTTTTAAAAAATTTAAA
Found at i:16526032 original size:21 final size:21
Alignment explanation
Indices: 16525963--16526075 Score: 104
Period size: 21 Copynumber: 5.2 Consensus size: 21
16525953 TTATTATTAG
* *
16525963 TTTTATAATATTTTAAATGTAT
1 TTTTA-AAAATTTTAAATATAT
**
16525985 ATTTTAAATTTTTTATAATAT-T
1 -TTTTAAAAATTTTA-AATATAT
16526007 ATTTTAAAAATTTTAAATATAT
1 -TTTTAAAAATTTTAAATATAT
*
16526029 TTTTAAAAAATTTAAATATTAT
1 TTTTAAAAATTTTAAATA-TAT
*
16526051 TTTT-GAAATTTTAAATATTAT
1 TTTTAAAAATTTTAAATA-TAT
16526072 TTTT
1 TTTT
16526076 TAATATTATA
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
21 41 0.51
22 30 0.38
23 9 0.11
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTAAAAATTTTAAATATAT
Found at i:16526218 original size:13 final size:14
Alignment explanation
Indices: 16526172--16526229 Score: 60
Period size: 14 Copynumber: 4.7 Consensus size: 14
16526162 ATTTTAAATA
16526172 TTTTAAATATTATT
1 TTTTAAATATTATT
16526186 TTTT-AA-A--A--
1 TTTTAAATATTATT
16526194 TTTTAAATATTATT
1 TTTTAAATATTATT
16526208 TTTTAAA-ATTA-T
1 TTTTAAATATTATT
16526220 TTTTAAATAT
1 TTTTAAATAT
16526230 ATTCAAACTC
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
8 4 0.11
9 2 0.05
10 2 0.05
12 10 0.27
13 8 0.22
14 11 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTAAATATTATT
Done.