Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000422.1 Hibiscus syriacus cultivar Beakdansim tig00000773_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2457469
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 12
Found at i:1661453 original size:17 final size:19
Alignment explanation
Indices: 1661409--1661459 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
1661399 TCCAAAATGA
*
1661409 GTAGTATCGATACTCTACTT
1 GTAGTATCGATACCCTAC-T
1661429 GTAGTATCGATACCCTA-T
1 GTAGTATCGATACCCTACT
*
1661447 G-AGTATCGGTACC
1 GTAGTATCGATACC
1661460 AAAATTGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 11 0.38
18 2 0.07
20 16 0.55
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (19 bp):
GTAGTATCGATACCCTACT
Found at i:1662256 original size:2 final size:2
Alignment explanation
Indices: 1662249--1662307 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1662239 TTTGGGGTGT
1662249 TA TA TA 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
1662291 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1662308 TTAGGAGATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1666016 original size:21 final size:20
Alignment explanation
Indices: 1665984--1666027 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1665974 CCTTATATTA
*
1665984 TAATATTTAAATTTCAAATCT
1 TAATATTTAAATTTAAAAT-T
1666005 TAAT-TTTAAAATTTAAAATT
1 TAATATTT-AAATTTAAAATT
1666025 TAA
1 TAA
1666028 ATCCTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATATTTAAATTTAAAATT
Found at i:1667393 original size:23 final size:23
Alignment explanation
Indices: 1667367--1667417 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1667357 AATAACATAT
* **
1667367 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAACGCTTATATAATAAAA
*
1667390 TAGGCAACGCTTATATAATAAAA
1 TAGGTAACGCTTATATAATAAAA
1667413 TAGGT
1 TAGGT
1667418 TAATTACTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (23 bp):
TAGGTAACGCTTATATAATAAAA
Found at i:1667542 original size:23 final size:23
Alignment explanation
Indices: 1667516--1667565 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1667506 ATCAAGCACA
* *
1667516 ATAACATATTAGGTAGT-GCTTAT
1 ATAACATAATAGGCA-TCGCTTAT
*
1667539 ATAACGTAATAGGCATCGCTTAT
1 ATAACATAATAGGCATCGCTTAT
1667562 ATAA
1 ATAA
1667566 TAAAATAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (23 bp):
ATAACATAATAGGCATCGCTTAT
Found at i:1667633 original size:158 final size:158
Alignment explanation
Indices: 1667345--1667709 Score: 649
Period size: 158 Copynumber: 2.3 Consensus size: 158
1667335 AACCATAAAT
* *
1667345 ATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGCAACGCTTATATAATA
1 ATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGCAACGCTTATATAATA
*
1667410 AAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTACCAAGG
66 AAATAGATTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTACCAAGG
1667475 ATAACATAACCGGTTAATTACCGGAAAC
131 ATAACATAACCGGTTAATTACCGGAAAC
* *
1667503 ATTATCAAGCACAATAACATATTAGGTAGTGCTTATATAACGTAATAGGCATCGCTTATATAATA
1 ATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGCAACGCTTATATAATA
1667568 AAATAGATTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTACCAAGG
66 AAATAGATTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTACCAAGG
* *
1667633 ATAACATAACCTGTTAATTACTGGAAAC
131 ATAACATAACCGGTTAATTACCGGAAAC
* *
1667661 ATTATCAAGCATAATAACATATTAGGTAGCGCTTATGTAACGTAATAGG
1 ATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGG
1667710 TTGCACATTA
Statistics
Matches: 197, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
158 197 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (158 bp):
ATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGCAACGCTTATATAATA
AAATAGATTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTACCAAGG
ATAACATAACCGGTTAATTACCGGAAAC
Found at i:1670206 original size:196 final size:199
Alignment explanation
Indices: 1669568--1670701 Score: 1562
Period size: 196 Copynumber: 5.8 Consensus size: 199
1669558 GCGTAATTTT
* * * * *
1669568 AAAAAATATCGATACAAATTTAAAAAGTGTTGATACATTATGTTGACCTATTTTCTAATTAACCA
1 AAAAAGTATCGACACAAATTTAAATAGTGTCGATACATTATGTTGACCTATTTTCTAATTAACCG
* * *
1669633 GTATATTTCTATCGGTTACATTGTAAATTTACCTATTACATGATAATTATCGGTTTTGATATTTT
66 GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATGATAATTATCGGTTTCGATGTTTT
* * *
1669698 TGGGGTCCATACTTTTAATAAATATATCGACACTTTATGCGTACACCTCGTTTGGGCATTCATTC
131 TGGGGTCGATACTTTTAA-AAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTC
*
1669763 TAGAC
195 TGGAC
* * * *
1669768 AAAAAGTATCAACA-AAATTTAAATAGTATCGATACATTATGTTGACCTATTTTTTAATTAACTG
1 AAAAAGTATCGACACAAATTTAAATAGTGTCGATACATTATGTTGACCTATTTTCTAATTAACCG
* * * * *
1669832 ATATATTTCTACCGGTTACATTGTAAATTTA-CTCATTATATGATAATTATTGATTTTGATGTTT
66 GTATATTTCTACCGGTTACATTGTAAATTTACCT-ATTACATGATAATTATCGGTTTCGATGTTT
*
1669896 TTGGGGTCGATACTTTTAAAATTGTATCGACACTTTATGCGTGCACCTCGTTT-GGCATTCATTC
130 TTGGGGTCGATACTTTTAAAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTC
1669960 TGGAC
195 TGGAC
1669965 AAAAAGTATCGACAC-AATTTAAATAGTGTCGATACATTATGTTGACCTATTTTCTAATTAACCG
1 AAAAAGTATCGACACAAATTTAAATAGTGTCGATACATTATGTTGACCTATTTTCTAATTAACCG
* *
1670029 GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTGT
66 GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATGATAATTATCGGTTTCGATGTTTT
* *
1670094 TGGGGTCGATAC-TTAAAAAATGTATCGACACTTTATGCGTGCACCTCGTTT-GTCATTCATTCT
131 TGGGGTCGATACTTTTAAAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCT
1670157 GGAC
196 GGAC
* * **
1670161 AAAAAGTATCGATAC-AATTTAAATAGTGTCGATACATTTTGTTGACCTATTTTCTAATTAATTG
1 AAAAAGTATCGACACAAATTTAAATAGTGTCGATACATTATGTTGACCTATTTTCTAATTAACCG
* * *
1670225 GTATATTTCTACCGGTTACATTGTAAATTAACCTATTAAATTATAATTATCGGTTTCGAT-TTTT
66 GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATGATAATTATCGGTTTCGATGTTTT
* * *
1670289 TTGGGTCGATACTTTTAAAAATGTATCGACACTTTATGTGTGCACCTCGTTTGGGCATTCATTAT
131 TGGGGTCGATACTTTTAAAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCT
1670354 GGAC
196 GGAC
*
1670358 AAAAAGTATCGACACAAATTTCACA-AGTGTCGATACATTATGTTGACCTATTTTCTAATTAACC
1 AAAAAGTATCGACACAAATTT-AAATAGTGTCGATACATTATGTTGACCTATTTTCTAATTAACC
* *
1670422 GGTATATTTCTACCGGTCACATTGTAAATTTACCTATTACATGATAATTATCGGTTTCAATGTTT
65 GGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATGATAATTATCGGTTTCGATGTTT
*
1670487 TTGGGGTCGACAC-TTT----ATG--T-G--------T--GT--ACCTCGTTTGGGCATTCATTC
130 TTGGGGTCGATACTTTTAAAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTC
*
1670532 TAGAC
195 TGGAC
* *
1670537 AAAAAGTATCGACACAAATTTCACA-AGTGTCGATACATTATGTTAACCTATTTTCTAATTAAAC
1 AAAAAGTATCGACACAAATTT-AAATAGTGTCGATACATTATGTTGACCTATTTTCTAATT-AAC
* *
1670601 CGATATATTTCTACCGGTTACATTGTAAATTTACC---TACATGATAATTATCGGTTTTGAT-TT
64 CGGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATGATAATTATCGGTTTCGATGTT
* *
1670662 TTTGGGGTCGATACTTTTAAAATTGTATAGACACTTTATG
129 TTTGGGGTCGATACTTTTAAAAATGTATCGACACTTTATG
1670702 TTTACCTATT
Statistics
Matches: 841, Mismatches: 67, Indels: 59
0.87 0.07 0.06
Matches are distributed among these distances:
176 15 0.02
177 25 0.03
179 83 0.10
180 36 0.04
181 4 0.00
183 2 0.00
184 1 0.00
191 1 0.00
192 2 0.00
194 3 0.00
195 14 0.02
196 207 0.25
197 169 0.20
198 135 0.16
199 133 0.16
200 11 0.01
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (199 bp):
AAAAAGTATCGACACAAATTTAAATAGTGTCGATACATTATGTTGACCTATTTTCTAATTAACCG
GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATGATAATTATCGGTTTCGATGTTTT
TGGGGTCGATACTTTTAAAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCT
GGAC
Found at i:1670496 original size:394 final size:392
Alignment explanation
Indices: 1669568--1670702 Score: 1600
Period size: 393 Copynumber: 2.9 Consensus size: 392
1669558 GCGTAATTTT
* * * *
1669568 AAAAAATATCGATACAAATTTAAAAAGTGTTGATACATTATGTTGACCTATTTTCTAATTAACCA
1 AAAAAGTATCGACACAAATTT-AAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAACCG
* * *
1669633 GTATATTTCTATCGGTTACATTGTAAATTTACCTATTACATGATAATTATCGGTTTTGATATTTT
65 GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATGATAATTATCGGTTTCGATGTTTT
* * *
1669698 TGGGGTCCATACTTTTAATAAATATATCGACACTTTATGCGTACACCTCGTTTGGGCATTCATTC
130 TGGGGTCGATAC--TTAA-AAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTC
* * * *
1669763 TAGACAAAAAGTATCAACAAAATTTAAATAGTATCGATACATTATGTTGACCTATTTTTTAATTA
192 TAGACAAAAAGTATCGACACAATTTAAATAGTGTCGATACATTATGTTGACCTATTTTCTAATTA
* * *
1669828 ACTGATATATTTCTACCGGTTACATTGTAAATTTA-CTCATTATATGATAATTATTGATTTTGAT
257 ACTGATATATTTCTACCGGTTACATTGTAAATTTACCT-ATTAAATGATAATTATCGGTTTTGAT
*
1669892 GTTTTTGGGGTCGATACTTTTAAAATTGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCA
321 -TTTTTGGGGTCGATACTTTTAAAATTGTATCGACACTTTATGTGTGCACCTCGTTTGGCATTCA
*
1669957 TTCTGGAC
385 TTATGGAC
1669965 AAAAAGTATCGACAC-AATTTAAATAGTGTCGATACATTATGTTGACCTATTTTCTAATTAACCG
1 AAAAAGTATCGACACAAATTTAAA-AGTGTCGATACATTATGTTGACCTATTTTCTAATTAACCG
* *
1670029 GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTGT
65 GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATGATAATTATCGGTTTCGATGTTTT
* *
1670094 TGGGGTCGATACTTAAAAAATGTATCGACACTTTATGCGTGCACCTCGTTT-GTCATTCATTCTG
130 TGGGGTCGATACTT-AAAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCTA
* * *
1670158 GACAAAAAGTATCGATACAATTTAAATAGTGTCGATACATTTTGTTGACCTATTTTCTAATTAAT
194 GACAAAAAGTATCGACACAATTTAAATAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAC
* * * *
1670223 TGGTATATTTCTACCGGTTACATTGTAAATTAACCTATTAAATTATAATTATCGGTTTCGATTTT
259 TGATATATTTCTACCGGTTACATTGTAAATTTACCTATTAAATGATAATTATCGGTTTTGATTTT
* *
1670288 TTTGGGTCGATACTTTTAAAAATGTATCGACACTTTATGTGTGCACCTCGTTTGGGCATTCATTA
324 TTGGGGTCGATACTTTTAAAATTGTATCGACACTTTATGTGTGCACCTCGTTT-GGCATTCATTA
1670353 TGGAC
388 TGGAC
*
1670358 AAAAAGTATCGACACAAATTTCACAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAACCG
1 AAAAAGTATCGACACAAATTT-AAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAACCG
* *
1670423 GTATATTTCTACCGGTCACATTGTAAATTTACCTATTACATGATAATTATCGGTTTCAATGTTTT
65 GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATGATAATTATCGGTTTCGATGTTTT
* *
1670488 T--GG--G------------G--TCGACACTTTATGTGTGTACCTCGTTTGGGCATTCATTCTAG
130 TGGGGTCGATACTTAAAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCTAG
* *
1670535 ACAAAAAGTATCGACACAAATTTCACA-AGTGTCGATACATTATGTTAACCTATTTTCTAATTAA
195 ACAAAAAGTATCGACAC-AATTT-AAATAGTGTCGATACATTATGTTGACCTATTTTCTAATT-A
* *
1670599 ACCGATATATTTCTACCGGTTACATTGTAAATTTACC---TACATGATAATTATCGGTTTTGATT
257 ACTGATATATTTCTACCGGTTACATTGTAAATTTACCTATTAAATGATAATTATCGGTTTTGATT
*
1670661 TTTTGGGGTCGATACTTTTAAAATTGTATAGACACTTTATGT
322 TTTTGGGGTCGATACTTTTAAAATTGTATCGACACTTTATGT
1670703 TTACCTATTC
Statistics
Matches: 673, Mismatches: 55, Indels: 42
0.87 0.07 0.05
Matches are distributed among these distances:
375 86 0.13
376 28 0.04
377 39 0.06
378 36 0.05
390 1 0.00
392 55 0.08
393 151 0.22
394 143 0.21
395 7 0.01
396 114 0.17
397 13 0.02
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (392 bp):
AAAAAGTATCGACACAAATTTAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAACCGG
TATATTTCTACCGGTTACATTGTAAATTTACCTATTACATGATAATTATCGGTTTCGATGTTTTT
GGGGTCGATACTTAAAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCTAGA
CAAAAAGTATCGACACAATTTAAATAGTGTCGATACATTATGTTGACCTATTTTCTAATTAACTG
ATATATTTCTACCGGTTACATTGTAAATTTACCTATTAAATGATAATTATCGGTTTTGATTTTTT
GGGGTCGATACTTTTAAAATTGTATCGACACTTTATGTGTGCACCTCGTTTGGCATTCATTATGG
AC
Found at i:1672590 original size:31 final size:31
Alignment explanation
Indices: 1672552--1672618 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
1672542 ATGAAAATAT
*
1672552 ACACACAATATAATCAAACCATAACACACAC
1 ACACACAATATAATCAAACCAAAACACACAC
* *
1672583 ACACACAATATAATCAAACCAAAACATACAT
1 ACACACAATATAATCAAACCAAAACACACAC
1672614 ACACA
1 ACACA
1672619 ACAAATTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.13
Consensus pattern (31 bp):
ACACACAATATAATCAAACCAAAACACACAC
Found at i:1673645 original size:6 final size:6
Alignment explanation
Indices: 1673635--1673668 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1673625 CTTGTTTGGA
* *
1673635 TCATCA TCATCT TCATCT TCATCG TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
1673669 TGAGCTCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.21, C:0.32, G:0.03, T:0.44
Consensus pattern (6 bp):
TCATCT
Found at i:1675857 original size:200 final size:200
Alignment explanation
Indices: 1675148--1675900 Score: 1054
Period size: 199 Copynumber: 3.8 Consensus size: 200
1675138 CGTAATTTAA
* * * *
1675148 AAAAAGTATCGACATAATTTTAAAAAGTGTCGATACATTATGTAGACTTATTTTCTCATAAAATT
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACT
* * *
1675213 GGTATATATCTACCGGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTT
66 GGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTT
** * * * *
1675278 TTGGGATTAATAAAATTTT-AAATGTATCAACACTTTATGCGTGCACCTAGTTTGGCATGCATTC
131 TTGGGATCGATATAATTTTAAAAAGTATCGACACTTTATGCGTGCACCTAGTTTGTCATGCATTC
*
1675342 TGGAA
196 TGGAC
* * *
1675347 AAAAAGAATCGACACAAATTTTAAAAGTGTCGATACATTATGTAGACCTATTTTCTCAT-AAAGT
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACT
* * *
1675411 CGGTATATTTCTACCGGTTACATTGTAAATTTACCCATTACATTAAAATTATGGGTTTCGAT-TT
66 -GGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTT
** *
1675475 TTTTTGATCG--ATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGT-ATGC
130 TTTGGGATCGATATAATTTTAA-AAA-GTATCGACACTTTATGCGTGCACCTAGTTT-GTCATGC
1675537 ATTCTGGAC
192 ATTCTGGAC
* *
1675546 AAAAAGTATCGACACAAATTTAAAAAAATGTTGATACATTATGTAGACCTATTTTTCTCATAAAA
1 AAAAAGTATCGACACAAATTT-AAAAAGTGTCGATACATTATGTAGACCTA-TTTTCTCATAAAA
*
1675611 CCGGTATA-TTCTTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATG
64 CTGGTATATTTC-TACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATG
* *
1675675 TTTTTGGGATCGATATAATTTTAAAAAATATCGACACTTTATGCGTGCACCTAGTTTGTCATTCA
128 TTTTTGGGATCGATATAATTTTAAAAAGTATCGACACTTTATGCGTGCACCTAGTTTGTCATGCA
*
1675740 TTCTTGAC
193 TTCTGGAC
* * *
1675748 AAAGAGTATCTACACAAATTTAAAAAGTTTCGATACATTATGTAGACCTATTTTCTCATAAAACT
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACT
* * * *
1675813 GGTATATTTATACCGGTTACGTTATAAATTTACCTATTACATTATAATTATTGGTTTTGATGTTT
66 GGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTT
*
1675878 TTGGGATCGATACAA-TTTAAAAA
131 TTGGGATCGATATAATTTTAAAAA
1675901 TTGTTGATAC
Statistics
Matches: 493, Mismatches: 47, Indels: 28
0.87 0.08 0.05
Matches are distributed among these distances:
196 6 0.01
197 1 0.00
198 14 0.03
199 179 0.36
200 116 0.24
201 93 0.19
202 72 0.15
203 3 0.01
204 9 0.02
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (200 bp):
AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACT
GGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTT
TTGGGATCGATATAATTTTAAAAAGTATCGACACTTTATGCGTGCACCTAGTTTGTCATGCATTC
TGGAC
Found at i:1678534 original size:18 final size:18
Alignment explanation
Indices: 1678513--1678547 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1678503 ACATACAAAA
1678513 TTATAAATCATATACAAC
1 TTATAAATCATATACAAC
*
1678531 TTATAAATCGTATACAA
1 TTATAAATCATATACAA
1678548 AATTTCCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (18 bp):
TTATAAATCATATACAAC
Found at i:1680104 original size:18 final size:18
Alignment explanation
Indices: 1680081--1680120 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1680071 TTCCTCCTTA
1680081 CTTCCTCCATCTTTTCTT
1 CTTCCTCCATCTTTTCTT
1680099 CTTCCTCCATCTTTTCTT
1 CTTCCTCCATCTTTTCTT
1680117 CTTC
1 CTTC
1680121 ATATTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.05, C:0.40, G:0.00, T:0.55
Consensus pattern (18 bp):
CTTCCTCCATCTTTTCTT
Found at i:1680368 original size:66 final size:66
Alignment explanation
Indices: 1680228--1680356 Score: 168
Period size: 66 Copynumber: 1.9 Consensus size: 66
1680218 ACTCCCTTTA
* * * *
1680228 CCCCTGTAAGTTCACTCCTCAAATCCATAACTTCCTTCACCACTCCATCAATTTTTTCACCCAGC
1 CCCCT-TAACTTCACCCCTCAAATCCACAACTTCCTTCACCACTCCATCAATTTTTCCACCCAGC
1680293 AC
65 AC
** * * *
1680295 CATCTTAACTTCACCCCTCAACTCCACAACTTCTTTCACCACTCCATCTATTTTTCCACCCA
1 CCCCTTAACTTCACCCCTCAAATCCACAACTTCCTTCACCACTCCATCAATTTTTCCACCCA
1680357 CTTCCCCCTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
66 50 0.94
67 3 0.06
ACGTcount: A:0.25, C:0.42, G:0.02, T:0.31
Consensus pattern (66 bp):
CCCCTTAACTTCACCCCTCAAATCCACAACTTCCTTCACCACTCCATCAATTTTTCCACCCAGCA
C
Found at i:1683118 original size:180 final size:178
Alignment explanation
Indices: 1682814--1683281 Score: 636
Period size: 180 Copynumber: 2.6 Consensus size: 178
1682804 CTTATTAAAA
* * *
1682814 TATCGACACTTTCAACATATCCAGTATCGATTTACCGGTTTTGTCATTTCGAGACCTGTTTTGTC
1 TATCGACACTTTCAACATATCCGGTAGCG-TTTACCGGTTTTGTCATTTCGAGACCGGTTTTGTC
* *
1682879 ATATTTTTACATGTAATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGC
65 ATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGC
* *
1682944 GCTATTACTTATTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATCCAA-G
130 GCTATTACTGATTCTCTTTTAAATTCCAAAAGTGT---TACTTAT-TCCAATC
1682996 TATCGACACTTTCAACATATCCGGTAGCG-TTACCGGTTTTGTCATTTCGAGACCGGTTTTGTCA
1 TATCGACACTTTCAACATATCCGGTAGCGTTTACCGGTTTTGTCATTTCGAGACCGGTTTTGTCA
* *
1683060 TATTTTTACCTGTTATATTGTTATGGAGCGATATATTTTTATAAAGTATCGACACTTTATAGGCG
66 TATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCG
* * *
1683125 CTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTTACTTATTTCAATC
131 CTATTACTGATTCTCTTTTAAATTCCAAAAGTGTTACTTATTCCAATC
* * * ** * ** *
1683173 TAATTGATACTTTTAACATATTTGGTAGCGCTTTACCGATTTTGTCACAAT-GAAACCGGTTTTG
1 T-ATCGACACTTTCAACATATCCGGTAGCG-TTTACCGGTTTTGTCA-TTTCGAGACCGGTTTTG
**
1683237 TCATATTTTTACCTGTTATATTCCTATGGATCGATACATTTTTAT
63 TCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTAT
1683282 TTGTATCGAC
Statistics
Matches: 256, Mismatches: 25, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
176 4 0.02
177 8 0.03
178 23 0.09
180 193 0.75
181 1 0.00
182 27 0.11
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (178 bp):
TATCGACACTTTCAACATATCCGGTAGCGTTTACCGGTTTTGTCATTTCGAGACCGGTTTTGTCA
TATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCG
CTATTACTGATTCTCTTTTAAATTCCAAAAGTGTTACTTATTCCAATC
Found at i:1683553 original size:6 final size:6
Alignment explanation
Indices: 1683542--1683571 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1683532 TTCTTTGATA
1683542 AATTCT AATTCT AATTCT AATTCT AATTCT
1 AATTCT AATTCT AATTCT AATTCT AATTCT
1683572 TTATATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTCT
Found at i:1689938 original size:4 final size:4
Alignment explanation
Indices: 1689929--1689957 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1689919 ATCATCCTTC
1689929 TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
1689958 TTGTTGTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:1690301 original size:2 final size:2
Alignment explanation
Indices: 1690294--1690334 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1690284 TACTTCCAAA
1690294 AT AT AT 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 AT AT AT A
1690335 GATAATTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1696110 original size:32 final size:32
Alignment explanation
Indices: 1696074--1696146 Score: 146
Period size: 32 Copynumber: 2.3 Consensus size: 32
1696064 TTTCGTAATC
1696074 CTTAAATTTATTGTAAATAAAACTGAAACATG
1 CTTAAATTTATTGTAAATAAAACTGAAACATG
1696106 CTTAAATTTATTGTAAATAAAACTGAAACATG
1 CTTAAATTTATTGTAAATAAAACTGAAACATG
1696138 CTTAAATTT
1 CTTAAATTT
1696147 CATCTCTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (32 bp):
CTTAAATTTATTGTAAATAAAACTGAAACATG
Found at i:1698086 original size:44 final size:44
Alignment explanation
Indices: 1698021--1698110 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
1698011 TTTCACGCCC
1698021 ATCTCTGTTATATTTTAGTGACACGTGTTTTTACTATCGTCTGT
1 ATCTCTGTTATATTTTAGTGACACGTGTTTTTACTATCGTCTGT
* * *
1698065 ATCTCTGTTATATTTTGGTGACACGTGTTTTTAGTGTCGTCTGT
1 ATCTCTGTTATATTTTAGTGACACGTGTTTTTACTATCGTCTGT
1698109 AT
1 AT
1698111 ATATATATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (44 bp):
ATCTCTGTTATATTTTAGTGACACGTGTTTTTACTATCGTCTGT
Found at i:1699889 original size:27 final size:27
Alignment explanation
Indices: 1699859--1699926 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
1699849 AATTTTAGAT
*
1699859 ATGACCTAATGGGTTAACATTTTTCGC
1 ATGACCTAATGGGCTAACATTTTTCGC
1699886 ATGACCTAATGGGCTAACATTTTTCGC
1 ATGACCTAATGGGCTAACATTTTTCGC
*
1699913 ATGGCCTAATGGGC
1 ATGACCTAATGGGC
1699927 AAAAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (27 bp):
ATGACCTAATGGGCTAACATTTTTCGC
Found at i:1701470 original size:132 final size:135
Alignment explanation
Indices: 1701298--1701626 Score: 366
Period size: 132 Copynumber: 2.4 Consensus size: 135
1701288 AAACCTAGCC
* * * * * * * *
1701298 ATTTGTTGAATCGAATAATTAATTTGGAATCTCGAGCAAAGGCAAGGACCAAATTAAAAATTCTC
1 ATTTATTGAATCAAATAATTAATTTGGAACCTCAAGCAAAGGCGAGGACTAAATTAAAAATCCAC
1701363 CTAAATTAATG-GACTAAGGTGAAATTAAA-CT-T-AAGG-TGATAATATTAAAACCTAATC-AA
66 CTAAATTAA-GAGACTAAGGTGAAATTAAACCTATGAAGGTTG-TAATATTAAAACCTAA-CGAA
1701422 TTTTAACA
128 TTTTAACA
* * *
1701430 ATTTATTGAATCAAATAATTAATTTGGAACCTCTAGCAAAGTCGACGACTAAATTAAAAATCCAC
1 ATTTATTGAATCAAATAATTAATTTGGAACCTCAAGCAAAGGCGAGGACTAAATTAAAAATCCAC
* * * * *
1701495 CTAAATTGAGAGACTGAGGTGAAGTTAAACCTAAAATGTAGGTTGTAATATTAAAACCTAACGGT
66 CTAAATTAAGAGACTAAGGTGAAATTAAACCT---ATGAAGGTTGTAATATTAAAACCTAAC-GA
*
1701560 TTTTTAACA
127 ATTTTAACA
* *
1701569 ATTTATTGAAT-AGAATAATTAATTTAGAACCTCAAGCAAAGGTGAGGACTAAATTAAA
1 ATTTATTGAATCA-AATAATTAATTTGGAACCTCAAGCAAAGGCGAGGACTAAATTAAA
1701627 TATTGATGTA
Statistics
Matches: 165, Mismatches: 21, Indels: 15
0.82 0.10 0.07
Matches are distributed among these distances:
131 1 0.01
132 79 0.48
133 2 0.01
137 2 0.01
138 20 0.12
139 61 0.37
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (135 bp):
ATTTATTGAATCAAATAATTAATTTGGAACCTCAAGCAAAGGCGAGGACTAAATTAAAAATCCAC
CTAAATTAAGAGACTAAGGTGAAATTAAACCTATGAAGGTTGTAATATTAAAACCTAACGAATTT
TAACA
Found at i:1703745 original size:20 final size:21
Alignment explanation
Indices: 1703700--1703745 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
1703690 TATTTTATAA
*
1703700 AACA-AATTATAAAGTATTAT
1 AACATAATTATAAAGTATTAC
*
1703720 AA-ATAATTCTAAA-TATTAC
1 AACATAATTATAAAGTATTAC
1703739 AACATAA
1 AACATAA
1703746 AATTTTACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.33
Consensus pattern (21 bp):
AACATAATTATAAAGTATTAC
Found at i:1706407 original size:18 final size:18
Alignment explanation
Indices: 1706384--1706455 Score: 67
Period size: 18 Copynumber: 3.8 Consensus size: 18
1706374 TGATTTTTAT
1706384 TTATTTATTTACTTT-AAA
1 TTATTTATTTA-TTTAAAA
1706402 TTATTTATTTATTTTGAATAA
1 TTATTTATTTA-TTT-AA-AA
*
1706423 TT-TTTAATTTATTTCAAA
1 TTATTT-ATTTATTTAAAA
*
1706441 TAATTTATTTATTTA
1 TTATTTATTTATTTA
1706456 TTTTGAACTT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
18 25 0.56
19 4 0.09
20 7 0.16
21 9 0.20
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (18 bp):
TTATTTATTTATTTAAAA
Found at i:1706432 original size:21 final size:20
Alignment explanation
Indices: 1706400--1706462 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
1706390 ATTTACTTTA
1706400 AATTATTTATTTATTTTGAAT
1 AATT-TTTATTTATTTTGAAT
**
1706421 AATTTTTAATTTATTTCAAAT
1 AATTTTT-ATTTATTTTGAAT
1706442 AATTTATTTATTTATTTTGAA
1 AA-TT-TTTATTTATTTTGAA
1706463 CTTATTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 3 0.09
21 17 0.49
22 12 0.34
23 3 0.09
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (20 bp):
AATTTTTATTTATTTTGAAT
Found at i:1706936 original size:14 final size:15
Alignment explanation
Indices: 1706917--1706946 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1706907 TAAATCCATG
1706917 TTTATTTATTT-TAA
1 TTTATTTATTTATAA
1706931 TTTATTTATTTATAA
1 TTTATTTATTTATAA
1706946 T
1 T
1706947 ATTTAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATTTATTTATAA
Found at i:1710435 original size:2 final size:2
Alignment explanation
Indices: 1710428--1710457 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1710418 TTCAGAATAC
1710428 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
1710458 TCACAAACCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1718414 original size:191 final size:187
Alignment explanation
Indices: 1718093--1718471 Score: 713
Period size: 191 Copynumber: 2.0 Consensus size: 187
1718083 GCACAATACC
1718093 TTTCTTAGAAATCACACAATCACACATATTTTTCATTTTAAATCAATGGATTTTGTTCGAAACAC
1 TTTCTTAGAAATCACACAATCACACATATTTTTCATTTTAAATCAATGGATTTTGTTCGAAACAC
1718158 AACTCACTCATTGATAAACGACTCCAGACAACTCCATATAACTTCCATTTTAAGATCAACGACTT
66 AACTCACTCATTGATAAACGACTCCAGACAACTCCATATAACTTCCATTTTAAGATCAACGACTT
1718223 TTGTTCGAAATACAACTCACTCAATTGATTCAAAAACATTTTGAAACACACTTACGGA
131 TTGTTCGAAATACAACTCACTC-ATTGATTCAAAAACATTTTGAAACACACTTACGGA
*
1718281 TTTCTTAGAAATCACACAATCACACATATTTTTCATTTTAAGATCAATGGCTTTTGTTCGAAACA
1 TTTCTTAGAAATCACACAATCACACATATTTTTCATTTTAA-ATCAATGGATTTTGTTCGAAACA
1718346 CAACTCACTCATGTGATAAACGGACTCCAGACAACTCCATATAACTTCCATTTTAAGATCAACGA
65 CAACTCACTCAT-TGATAAAC-GACTCCAGACAACTCCATATAACTTCCATTTTAAGATCAACGA
1718411 CTTTTGTTCGAAATACAACTCACTCATTGATTCAAAAACATTTTGAAACACACTTACGGA
128 CTTTTGTTCGAAATACAACTCACTCATTGATTCAAAAACATTTTGAAACACACTTACGGA
1718471 T
1 T
1718472 GATTATCATG
Statistics
Matches: 187, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
188 41 0.22
189 34 0.18
190 44 0.24
191 68 0.36
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.32
Consensus pattern (187 bp):
TTTCTTAGAAATCACACAATCACACATATTTTTCATTTTAAATCAATGGATTTTGTTCGAAACAC
AACTCACTCATTGATAAACGACTCCAGACAACTCCATATAACTTCCATTTTAAGATCAACGACTT
TTGTTCGAAATACAACTCACTCATTGATTCAAAAACATTTTGAAACACACTTACGGA
Found at i:1720032 original size:6 final size:6
Alignment explanation
Indices: 1719992--1720034 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
1719982 TGTAGATGAG
* * * *
1719992 GGTGAT GGTTAT GGTGGT GGTGGT GGTGGT GGTGAT GGTGAT G
1 GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT G
1720035 ATTTTGATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.09, C:0.00, G:0.56, T:0.35
Consensus pattern (6 bp):
GGTGAT
Found at i:1720213 original size:28 final size:28
Alignment explanation
Indices: 1720163--1720223 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
1720153 TTTGTAATTG
*
1720163 TTTTAGTTAATGAAAATCCATTTCTT-TT
1 TTTTAGTTAATCAAAATCCATTT-TTCTT
* **
1720191 TTTTAGTTAATCAAACTTTATTTTTCTT
1 TTTTAGTTAATCAAAATCCATTTTTCTT
1720219 TTTTA
1 TTTTA
1720224 AAGTAATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 2 0.07
28 26 0.93
ACGTcount: A:0.26, C:0.10, G:0.05, T:0.59
Consensus pattern (28 bp):
TTTTAGTTAATCAAAATCCATTTTTCTT
Found at i:1722924 original size:20 final size:18
Alignment explanation
Indices: 1722861--1722926 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 18
1722851 TAACAAATTT
1722861 TTTATTTTTCAATTTAGTCC
1 TTTATTTTTCAATTTA-T-C
*
1722881 TTAATTTTTCATATTT-TC
1 TTTATTTTTCA-ATTTATC
1722899 TTTATTTCTTCAATTTATC
1 TTTATTT-TTCAATTTATC
1722918 ATTTATTTT
1 -TTTATTTT
1722927 AAGTCAATCT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 11 0.28
19 8 0.20
20 17 0.43
21 4 0.10
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTTTTCAATTTATC
Found at i:1723096 original size:158 final size:157
Alignment explanation
Indices: 1722747--1723145 Score: 517
Period size: 158 Copynumber: 2.6 Consensus size: 157
1722737 ATAATTTCAA
* * *
1722747 TATTCCTTCAATTCCTCCTTTATTTTAAGTTCATTT-TTTTACTAAATTTGAACCACA---T-AT
1 TATTTCTTCAATTCATCCTTTATTTTAAGTT--TTTCTTTTACCAAATTTGAACCACATGCTCAT
1722807 AAACTATCGTAGAATACATATGTACATTAAAATCCTCTTTTGAATAACAAATTTTTTATTTTTCA
64 AAACTATCGTAGAATACATATGTACATTAAAATCCTCTTTTGAATAACAAATTTTTTATTTTTCA
* *
1722872 ATTTAGTCCTTAATTTTTCATATTTTCTT
129 ATTTAGTCCTTAATCTTTCATATTTTCCT
* * ***
1722901 TATTTCTTCAATTTATCATTTATTTTAAGTCAATCTTTTACCAAATTTGAACCACATGCTCATAA
1 TATTTCTTCAATTCATCCTTTATTTTAAGTTTTTCTTTTACCAAATTTGAACCACATGCTCATAA
* * * * *
1722966 A-TCATCGTAGAATACATATGTACTTTCAATTTCTCTTTTTG-ATAACAATTTTTTTATTTTTCA
66 ACT-ATCGTAGAATACATATGTACATTAAAATCCTC-TTTTGAATAACAAATTTTTTATTTTTCA
*
1723029 ATTTTGTCCCTTAATCTTTCATATTTTCCT
129 ATTTAGT-CCTTAATCTTTCATATTTTCCT
*
1723059 TATTTCTTCAATTCATCCTTTATTTTAAGTTTTTCTTTTACCAAATTTGAACCACATGCTCATAT
1 TATTTCTTCAATTCATCCTTTATTTTAAGTTTTTCTTTTACCAAATTTGAACCACATGCTCATAA
* *
1723124 ACTA-CAATAGAATACTTATGTA
66 ACTATC-GTAGAATACATATGTA
1723146 ATTTCAATTC
Statistics
Matches: 211, Mismatches: 24, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
152 1 0.00
153 20 0.09
154 26 0.12
156 2 0.01
157 61 0.29
158 100 0.47
159 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.05, T:0.48
Consensus pattern (157 bp):
TATTTCTTCAATTCATCCTTTATTTTAAGTTTTTCTTTTACCAAATTTGAACCACATGCTCATAA
ACTATCGTAGAATACATATGTACATTAAAATCCTCTTTTGAATAACAAATTTTTTATTTTTCAAT
TTAGTCCTTAATCTTTCATATTTTCCT
Found at i:1723174 original size:158 final size:156
Alignment explanation
Indices: 1722747--1723204 Score: 501
Period size: 158 Copynumber: 2.9 Consensus size: 156
1722737 ATAATTTCAA
* * * *
1722747 TATTCCTTCAATTCCTCCTTTATTTTAAGTTCATTT-TTTTACTAAATTTGAACCACAT-AT-A-
1 TATTTCTTCAATTCATCCTTTATTTTAAGTT--TTTCTTTTACCAAATTTGAACCACATGCTCAT
* * * * *
1722808 AACTATC-GTAGAATACATATGTACA-TTAAAATCCTCTTTTGAATAACAAATTTTTTATTTTTC
64 AACTA-CAGTAGAATACATATGTA-ATTTCAATTCTTCTTTT-TATAACAATTTTTTTATTTTTC
* *
1722871 AATTTAGT-CCTTAATTTTTCATATTTTCTT
126 AATTTAGTCCCTTAATCTTTCATATTTTCCT
* * ***
1722901 TATTTCTTCAATTTATCATTTATTTTAAGTCAATCTTTTACCAAATTTGAACCACATGCTCATAA
1 TATTTCTTCAATTCATCCTTTATTTTAAGTTTTTCTTTTACCAAATTTGAACCACATGCTCATAA
* *
1722966 AT-CATCGTAGAATACATATGTACTTTCAATT-TCTCTTTTTGATAACAATTTTTTTATTTTTCA
66 CTACA--GTAGAATACATATGTAATTTCAATTCT-TCTTTTT-ATAACAATTTTTTTATTTTTCA
*
1723029 ATTTTGTCCCTTAATCTTTCATATTTTCCT
127 ATTTAGTCCCTTAATCTTTCATATTTTCCT
1723059 TATTTCTTCAATTCATCCTTTATTTTAAGTTTTTCTTTTACCAAATTTGAACCACATGCTCATAT
1 TATTTCTTCAATTCATCCTTTATTTTAAGTTTTTCTTTTACCAAATTTGAACCACATGCTCATA-
* * *
1723124 ACTACAATAGAATACTTATGTAATTTCAATTCTTACTTTTTACTAA-AATTTTACTTTCTTTTT-
65 ACTACAGTAGAATACATATGTAATTTCAATTCTT-CTTTTTA-TAACAATTTT--TTTATTTTTC
1723187 -ATTTAGTCCCTTAA-CTTT
126 AATTTAGTCCCTTAATCTTT
1723205 ACATTTTACT
Statistics
Matches: 256, Mismatches: 30, Indels: 33
0.80 0.09 0.10
Matches are distributed among these distances:
152 1 0.00
153 21 0.08
154 28 0.11
155 1 0.00
156 3 0.01
157 58 0.23
158 122 0.48
159 12 0.05
160 10 0.04
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (156 bp):
TATTTCTTCAATTCATCCTTTATTTTAAGTTTTTCTTTTACCAAATTTGAACCACATGCTCATAA
CTACAGTAGAATACATATGTAATTTCAATTCTTCTTTTTATAACAATTTTTTTATTTTTCAATTT
AGTCCCTTAATCTTTCATATTTTCCT
Found at i:1733797 original size:1 final size:1
Alignment explanation
Indices: 1733759--1733785 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1733749 AAATTTTGGC
1733759 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1733786 GCCTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1738186 original size:12 final size:12
Alignment explanation
Indices: 1738169--1738197 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1738159 AGGCTTAATT
1738169 GGACTCCTAAAA
1 GGACTCCTAAAA
1738181 GGACTCCTAAAA
1 GGACTCCTAAAA
1738193 GGACT
1 GGACT
1738198 AGTAGTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (12 bp):
GGACTCCTAAAA
Found at i:1738951 original size:21 final size:20
Alignment explanation
Indices: 1738925--1738986 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
1738915 TTAGTGTTTG
1738925 AGTATCGATACTATGATGAAT
1 AGTATCGATACTA-GATGAAT
* * *
1738946 AGTATCGATATTGGGATGAAC
1 AGTATCGATACT-AGATGAAT
* *
1738967 AGTGTTGATACTAGATGAAT
1 AGTATCGATACTAGATGAAT
1738987 TAGGGTAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 6 0.19
21 26 0.81
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.32
Consensus pattern (20 bp):
AGTATCGATACTAGATGAAT
Found at i:1740595 original size:30 final size:30
Alignment explanation
Indices: 1740535--1740603 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 30
1740525 GTTATATGAG
1740535 CTATGTGA-AAAATGTATGGAAAATTATGT
1 CTATGTGATAAAATGTATGGAAAATTATGT
1740564 CTATGTGATAAAA-GTAT-GAAAATAATATGT
1 CTATGTGATAAAATGTATGGAAAAT--TATGT
*
1740594 CTATGAGATA
1 CTATGTGATA
1740604 CACTATGTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
28 6 0.17
29 12 0.33
30 18 0.50
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.33
Consensus pattern (30 bp):
CTATGTGATAAAATGTATGGAAAATTATGT
Found at i:1740856 original size:25 final size:26
Alignment explanation
Indices: 1740828--1740884 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
1740818 TACGGTGCAA
*
1740828 TTCGGTG-CAAATTTCTACGCGGTC-C
1 TTCGGTGACAAAATTCTACGCGG-CAC
*
1740853 TTCGG-GACAAAATTCTACGTGGCAC
1 TTCGGTGACAAAATTCTACGCGGCAC
1740878 TTCGGTG
1 TTCGGTG
1740885 TAACTTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 2 0.07
25 24 0.89
26 1 0.04
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (26 bp):
TTCGGTGACAAAATTCTACGCGGCAC
Found at i:1741533 original size:22 final size:22
Alignment explanation
Indices: 1741501--1741543 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1741491 GCACTGTAGC
*
1741501 ACTGTTTATGGCACTGTTCATT
1 ACTGTTCATGGCACTGTTCATT
*
1741523 ACTGTTCATGGTACTGTTCAT
1 ACTGTTCATGGCACTGTTCAT
1741544 AAATACGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (22 bp):
ACTGTTCATGGCACTGTTCATT
Found at i:1741537 original size:12 final size:12
Alignment explanation
Indices: 1741501--1741543 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
1741491 GCACTGTAGC
* *
1741501 ACTGTTTATGGC
1 ACTGTTCATGGT
1741513 ACTGTTCAT--T
1 ACTGTTCATGGT
1741523 ACTGTTCATGGT
1 ACTGTTCATGGT
1741535 ACTGTTCAT
1 ACTGTTCAT
1741544 AAATACGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (12 bp):
ACTGTTCATGGT
Found at i:1744223 original size:25 final size:27
Alignment explanation
Indices: 1744195--1744249 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
1744185 CAATTAAAAG
1744195 TTTATAATT-TAAAATTAATTAT-TTT
1 TTTATAATTGTAAAATTAATTATATTT
* *
1744220 TTTATAATTGTAAATTTAGTTATATTT
1 TTTATAATTGTAAAATTAATTATATTT
1744247 TTT
1 TTT
1744250 GGTACAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 9 0.35
26 11 0.42
27 6 0.23
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (27 bp):
TTTATAATTGTAAAATTAATTATATTT
Found at i:1745481 original size:46 final size:45
Alignment explanation
Indices: 1745389--1745481 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 45
1745379 ACACTTTTTA
*
1745389 ATTTTTTAAATTTTTTCACTGAACTTAATATATTAATATTTTAAAT
1 ATTTTTTAAATTTTTTCACTGAACTTAATATATT-ATATTTCAAAT
*
1745435 ATTTTTTTAATTTTTTCACTGAACTTAATATATGT-TATTTGCAAAT
1 ATTTTTTAAATTTTTTCACTGAACTTAATATAT-TATATTT-CAAAT
1745481 A
1 A
1745482 AAAAAGCCCG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
45 5 0.12
46 37 0.86
47 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.54
Consensus pattern (45 bp):
ATTTTTTAAATTTTTTCACTGAACTTAATATATTATATTTCAAAT
Found at i:1746954 original size:2 final size:2
Alignment explanation
Indices: 1746947--1746972 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1746937 AATAATGAAA
1746947 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
1746973 TATTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1747801 original size:9 final size:8
Alignment explanation
Indices: 1747782--1747834 Score: 53
Period size: 8 Copynumber: 7.1 Consensus size: 8
1747772 ATGTTTATTC
1747782 ATTTTTAT
1 ATTTTTAT
1747790 ATTTTTACT
1 ATTTTTA-T
*
1747799 ATTTTTTT
1 ATTTTTAT
1747807 ATTTTT-T
1 ATTTTTAT
1747814 -TTTTT-T
1 ATTTTTAT
1747820 -TTTTTA-
1 ATTTTTAT
1747826 ATTTTTAT
1 ATTTTTAT
1747834 A
1 A
1747835 ACCAAACATG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
6 11 0.28
7 7 0.17
8 15 0.38
9 7 0.17
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (8 bp):
ATTTTTAT
Found at i:1747807 original size:19 final size:19
Alignment explanation
Indices: 1747783--1747832 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
1747773 TGTTTATTCA
1747783 TTTTTATATTTTTACTATT
1 TTTTTATATTTTTACTATT
** *
1747802 TTTTTAT-TTTTTTTTTTT
1 TTTTTATATTTTTACTATT
1747820 TTTTTA-ATTTTTA
1 TTTTTATATTTTTA
1747833 TAACCAAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTATATTTTTACTATT
Found at i:1755595 original size:2 final size:2
Alignment explanation
Indices: 1755588--1755623 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1755578 ACAAAGTAGA
1755588 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
1755624 GATTAAAGCT
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:1756529 original size:168 final size:169
Alignment explanation
Indices: 1756272--1756609 Score: 612
Period size: 168 Copynumber: 2.0 Consensus size: 169
1756262 GGGAACGAGT
1756272 CCCAACTGCAATGAACATCTGCAAACTCAAGACTTAACTTGCTCCAAATCGACATTGACCCGAAT
1 CCCAACTGCAATGAACATCTGCAAACTCAAGACTTAACTTGCTCCAAATCGACATTGACCCGAAT
1756337 ATTTTAGTCTTTTTCGAATGAGTTGAAGGCCAGCTACTACCTC-AACACTCTAAGAATCCTTCTC
66 ATTTTAGTCTTTTTCGAATGAGTTGAAGGCCAGCTACTACCTCAAACACTCTAAGAATCC-T-TC
*
1756401 ACATTCTGCA-CAATTTAAGACCAGTTTCTAAAAATATAAC
129 ACATTCTGCACCAATTTAAGACCAGCTTCTAAAAATATAAC
1756441 CCCAACTGCAATGAACATCTGC-AACTCAAGACTTAACTTGCTCCAAATCGACATTGACCCGAAT
1 CCCAACTGCAATGAACATCTGCAAACTCAAGACTTAACTTGCTCCAAATCGACATTGACCCGAAT
1756505 A-TTTAGTCTTTTTCGAATTGAGTTGAAGGCCAGCTACTACCTCAAACACTCTAAGAATCCTTCA
66 ATTTTAGTCTTTTTCGAA-TGAGTTGAAGGCCAGCTACTACCTCAAACACTCTAAGAATCCTTCA
1756569 CATTCTGCACCAATTTAAGACCAGCTTCTAAAAATATAAC
130 CATTCTGCACCAATTTAAGACCAGCTTCTAAAAATATAAC
1756609 C
1 C
1756610 AGGTCATCTG
Statistics
Matches: 165, Mismatches: 1, Indels: 7
0.95 0.01 0.04
Matches are distributed among these distances:
167 28 0.17
168 99 0.60
169 38 0.23
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.28
Consensus pattern (169 bp):
CCCAACTGCAATGAACATCTGCAAACTCAAGACTTAACTTGCTCCAAATCGACATTGACCCGAAT
ATTTTAGTCTTTTTCGAATGAGTTGAAGGCCAGCTACTACCTCAAACACTCTAAGAATCCTTCAC
ATTCTGCACCAATTTAAGACCAGCTTCTAAAAATATAAC
Found at i:1763487 original size:5 final size:5
Alignment explanation
Indices: 1763477--1763506 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1763467 ATACGAGAAA
*
1763477 AATTT AATTT AATTT AAATT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT
1763507 TAAAATAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:1767709 original size:3 final size:3
Alignment explanation
Indices: 1767701--1767756 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
1767691 CAGCGATTGT
1767701 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1767749 TTA TTA TT
1 TTA TTA TT
1767757 TCTCTTTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1769346 original size:17 final size:17
Alignment explanation
Indices: 1769321--1769372 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
1769311 TTTATGAAAT
*
1769321 TATTTAAAATATTAAAA
1 TATTAAAAATATTAAAA
*
1769338 TATTCAAAAATAAT-AAA
1 TATT-AAAAATATTAAAA
1769355 TATTAAAAATAATTAAAA
1 TATTAAAAAT-ATTAAAA
1769373 ATAAAAGCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 6 0.21
17 13 0.45
18 10 0.34
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
TATTAAAAATATTAAAA
Found at i:1769359 original size:25 final size:26
Alignment explanation
Indices: 1769327--1769376 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1769317 AAATTATTTA
1769327 AAATATT-AAAAT-ATTCAAAAATAAT
1 AAATATTAAAAATAATT-AAAAATAAT
1769352 AAATATTAAAAATAATTAAAAATAA
1 AAATATTAAAAATAATTAAAAATAA
1769377 AAGCACTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 7 0.30
26 13 0.57
27 3 0.13
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (26 bp):
AAATATTAAAAATAATTAAAAATAAT
Found at i:1769376 original size:10 final size:9
Alignment explanation
Indices: 1769321--1769375 Score: 53
Period size: 10 Copynumber: 6.2 Consensus size: 9
1769311 TTTATGAAAT
*
1769321 TATTTAAAA
1 TATTAAAAA
1769330 TATT-AAAA
1 TATTAAAAA
1769338 TATTCAAAAA
1 TATT-AAAAA
*
1769348 TA--ATAAA
1 TATTAAAAA
1769355 TATTAAAAA
1 TATTAAAAA
1769364 TAATTAAAAA
1 T-ATTAAAAA
1769374 TA
1 TA
1769376 AAAGCACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 6 0.15
8 8 0.21
9 10 0.26
10 15 0.38
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
TATTAAAAA
Found at i:1769470 original size:24 final size:26
Alignment explanation
Indices: 1769419--1769472 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
1769409 ATAAAAGTTA
*
1769419 TAAAATAATAAATATTATTAAATTAT
1 TAAAATAATAAATATTATTAAATCAT
1769445 TAAAA-AATAAA-ATT-TGTAAATCAT
1 TAAAATAATAAATATTAT-TAAATCAT
1769469 TAAA
1 TAAA
1769473 TCTTTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 1 0.04
24 14 0.54
25 6 0.23
26 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (26 bp):
TAAAATAATAAATATTATTAAATCAT
Found at i:1769473 original size:42 final size:41
Alignment explanation
Indices: 1769404--1769482 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 41
1769394 TAAAAAGTAA
1769404 AAAAAATAAAAGTTATAAAATAATAAATATTATTAAATTATT
1 AAAAAATAAAAGTTATAAAATAATAAATATT-TTAAATTATT
* * * *
1769446 AAAAAATAAAATTTGT-AAATCATTAAATCTTTTAAAT
1 AAAAAATAAAAGTTATAAAAT-AATAAATATTTTAAAT
1769483 ATTTCATTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 10 0.31
42 22 0.69
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (41 bp):
AAAAAATAAAAGTTATAAAATAATAAATATTTTAAATTATT
Found at i:1769860 original size:30 final size:29
Alignment explanation
Indices: 1769815--1769880 Score: 107
Period size: 30 Copynumber: 2.3 Consensus size: 29
1769805 TAGAGTCATA
*
1769815 AATAAAATAATATATATAGTTTTGAAAAT
1 AATATAATAATATATATAGTTTTGAAAAT
1769844 AATATAATATATATATATAGTTTTGAAAAT
1 AATATAATA-ATATATATAGTTTTGAAAAT
1769874 -ATATAAT
1 AATATAAT
1769881 TGTTGAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 15 0.43
30 20 0.57
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (29 bp):
AATATAATAATATATATAGTTTTGAAAAT
Found at i:1769888 original size:17 final size:16
Alignment explanation
Indices: 1769826--1769891 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
1769816 ATAAAATAAT
*
1769826 ATATATAGTTTTGAAA
1 ATATATAATTTTGAAA
* *
1769842 ATAATATAA-TAT--AT
1 AT-ATATAATTTTGAAA
*
1769856 ATATATAGTTTTGAAA
1 ATATATAATTTTGAAA
1769872 ATATATAATTGTTGAAA
1 ATATATAATT-TTGAAA
1769889 ATA
1 ATA
1769892 ACATAAATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
13 5 0.13
14 5 0.13
16 14 0.37
17 14 0.37
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (16 bp):
ATATATAATTTTGAAA
Found at i:1769909 original size:47 final size:47
Alignment explanation
Indices: 1769826--1769920 Score: 122
Period size: 47 Copynumber: 2.0 Consensus size: 47
1769816 ATAAAATAAT
* * *
1769826 ATATATAGTTTTGAAAATAATATAATATATATATATAG-TTTTGAAA
1 ATATATAATTTTGAAAATAACATAATATATAGATATAGCTTTTGAAA
*
1769872 ATATATAATTGTTGAAAATAACATAA-ATATAAGATATAGCTTTTTAAA
1 ATATATAATT-TTGAAAATAACATAATATAT-AGATATAGCTTTTGAAA
1769920 A
1 A
1769921 ATAGTATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
46 13 0.31
47 21 0.50
48 8 0.19
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.40
Consensus pattern (47 bp):
ATATATAATTTTGAAAATAACATAATATATAGATATAGCTTTTGAAA
Found at i:1769953 original size:25 final size:25
Alignment explanation
Indices: 1769905--1769974 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 25
1769895 TAAATATAAG
*
1769905 ATATAGCTTTTTAAAAATAGTATAT
1 ATATAGCTTTTCAAAAATAGTATAT
1769930 ATATAG-TTTTC-AAAATA-TAT-T
1 ATATAGCTTTTCAAAAATAGTATAT
* **
1769951 ATATAGTTTTTTGAAAATAGTATA
1 ATATAGCTTTTCAAAAATAGTATA
1769975 AATGTATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 7 0.18
22 7 0.18
23 12 0.31
24 7 0.18
25 6 0.15
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (25 bp):
ATATAGCTTTTCAAAAATAGTATAT
Found at i:1769997 original size:30 final size:31
Alignment explanation
Indices: 1769942--1770006 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
1769932 ATAGTTTTCA
* *
1769942 AAATATATTATATAGTTTTTTGAAAATAGTAT
1 AAATATATTATATAG-TTCTTGAAAATAATAT
*
1769974 AAATGTATTATATAG-TCTTGAAAATAATAT
1 AAATATATTATATAGTTCTTGAAAATAATAT
1770004 AAA
1 AAA
1770007 GTTATGAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 16 0.53
32 14 0.47
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.42
Consensus pattern (31 bp):
AAATATATTATATAGTTCTTGAAAATAATAT
Found at i:1774568 original size:20 final size:21
Alignment explanation
Indices: 1774523--1774582 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
1774513 TTCCCCTGTG
1774523 GGGGGAATCGGTTCCCTTCAAA
1 GGGGGAATCGGTTCCC-TCAAA
1774545 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
1774565 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1774583 TGTACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 16 0.44
ACGTcount: A:0.18, C:0.25, G:0.35, T:0.22
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1786053 original size:15 final size:14
Alignment explanation
Indices: 1786018--1786054 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
1786008 TAAATATAAT
1786018 TAAAA-TTAAATTG
1 TAAAATTTAAATTG
1786031 TAAAATTTAAATTG
1 TAAAATTTAAATTG
1786045 TAGAAATTTA
1 TA-AAATTTA
1786055 TATTATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.23
14 10 0.45
15 7 0.32
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (14 bp):
TAAAATTTAAATTG
Found at i:1786189 original size:12 final size:13
Alignment explanation
Indices: 1786162--1786194 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1786152 TAATATATCC
*
1786162 TTTAAAATTATAT
1 TTTAAAAATATAT
1786175 TTTAAAAAT-TAT
1 TTTAAAAATATAT
1786187 TTTAAAAA
1 TTTAAAAA
1786195 ATAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAAAAATATAT
Found at i:1790046 original size:19 final size:18
Alignment explanation
Indices: 1790006--1790046 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1789996 ACAATTATTT
1790006 TTATAGTTTAAAAACATA
1 TTATAGTTTAAAAACATA
1790024 -TATAGTTTTCAAAAA-ATA
1 TTATAG-TTT-AAAAACATA
1790042 TTATA
1 TTATA
1790047 TAAAGTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 5 0.25
18 6 0.30
19 9 0.45
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (18 bp):
TTATAGTTTAAAAACATA
Found at i:1793208 original size:13 final size:13
Alignment explanation
Indices: 1793190--1793215 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1793180 TTACAGACGC
1793190 GCATATGAAGATT
1 GCATATGAAGATT
1793203 GCATATGAAGATT
1 GCATATGAAGATT
1793216 TTTCAACTAT
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:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
GCATATGAAGATT
Found at i:1793547 original size:18 final size:18
Alignment explanation
Indices: 1793524--1793571 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1793514 GGGCTAGTTC
1793524 GAAAAGGAAAAATCAAAG
1 GAAAAGGAAAAATCAAAG
1793542 GAAAAGGAAAAATCAAAG
1 GAAAAGGAAAAATCAAAG
*
1793560 AAAAAGGAAAAA
1 GAAAAGGAAAAA
1793572 AAAAGTGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.71, C:0.04, G:0.21, T:0.04
Consensus pattern (18 bp):
GAAAAGGAAAAATCAAAG
Found at i:1795749 original size:5 final size:5
Alignment explanation
Indices: 1795739--1795804 Score: 62
Period size: 5 Copynumber: 13.2 Consensus size: 5
1795729 TATGTTACTT
* * * *
1795739 TTATA TTATA TAATA -TATA TACATA GTATA TTATA ATATA TTATA TTATA
1 TTATA TTATA TTATA TTATA T-TATA TTATA TTATA TTATA TTATA TTATA
* *
1795789 ATATA CTATA TTATA T
1 TTATA TTATA TTATA T
1795805 AGTGGGTATA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
4 3 0.06
5 42 0.88
6 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (5 bp):
TTATA
Found at i:1795783 original size:15 final size:15
Alignment explanation
Indices: 1795765--1795803 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1795755 ATATACATAG
*
1795765 TATATTATAATATAT
1 TATATTATAATATAC
1795780 TATATTATAATATAC
1 TATATTATAATATAC
1795795 TATATTATA
1 TATATTATA
1795804 TAGTGGGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATTATAATATAC
Found at i:1795788 original size:20 final size:20
Alignment explanation
Indices: 1795739--1795804 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
1795729 TATGTTACTT
*
1795739 TTATATTATATAAT-ATATA
1 TTATATTATATTATAATATA
* *
1795758 TACATAGTATATTATAATATA
1 T-TATATTATATTATAATATA
* *
1795779 TTATATTATAATATACTATA
1 TTATATTATATTATAATATA
1795799 TTATAT
1 TTATAT
1795805 AGTGGGTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 1 0.03
20 31 0.82
21 6 0.16
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (20 bp):
TTATATTATATTATAATATA
Found at i:1803226 original size:17 final size:17
Alignment explanation
Indices: 1803204--1803238 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1803194 TTTGGCATCC
1803204 CCATATAT-GCATGTATG
1 CCATATATAGCA-GTATG
1803221 CCATATATAGCAGTATG
1 CCATATATAGCAGTATG
1803238 C
1 C
1803239 TTTCCTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (17 bp):
CCATATATAGCAGTATG
Found at i:1804174 original size:31 final size:29
Alignment explanation
Indices: 1804124--1804193 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
1804114 TATTTTATGA
*
1804124 ATTTTA-T-ATTAATAAAATATTTTAATAT
1 ATTTTATTAATTAATAAAATA-TTTAAAAT
*
1804152 CATTTTATTAATTATTAAAATATTTAAAAT
1 -ATTTTATTAATTAATAAAATATTTAAAAT
1804182 ATATTTATTAAT
1 AT-TTTATTAAT
1804194 ATTTCTAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 8 0.22
30 17 0.47
31 11 0.31
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
ATTTTATTAATTAATAAAATATTTAAAAT
Found at i:1804189 original size:30 final size:31
Alignment explanation
Indices: 1804124--1804193 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
1804114 TATTTTATGA
*
1804124 ATTTTA-T-ATTAATAAAATATTTTAATATC
1 ATTTTATTAATTAATAAAATATTTAAATATC
*
1804153 ATTTTATTAATTATTAAAATATTTAAA-AT-
1 ATTTTATTAATTAATAAAATATTTAAATATC
1804182 ATATTTATTAAT
1 AT-TTTATTAAT
1804194 ATTTCTAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 8 0.22
30 12 0.33
31 16 0.44
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (31 bp):
ATTTTATTAATTAATAAAATATTTAAATATC
Found at i:1804237 original size:31 final size:35
Alignment explanation
Indices: 1804180--1804250 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 35
1804170 AATATTTAAA
*
1804180 ATATATTTATTAATATTTCTAATAAAATAAT-ATT
1 ATATATTTATTAACATTTCTAATAAAATAATAATT
1804214 ATATA-TT-TTAACATTT-TAATAAAATAATCAATT
1 ATATATTTATTAACATTTCTAATAAAATAAT-AATT
1804247 ATAT
1 ATAT
1804251 TATAATAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
31 12 0.35
32 8 0.24
33 9 0.26
34 5 0.15
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (35 bp):
ATATATTTATTAACATTTCTAATAAAATAATAATT
Found at i:1804437 original size:23 final size:23
Alignment explanation
Indices: 1804405--1804456 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
1804395 ATAATCTAAT
*
1804405 AATATTTTAATAAAAATATTTAA
1 AATATATTAATAAAAATATTTAA
* ** *
1804428 AATATATTAATTAATCTTTTTAA
1 AATATATTAATAAAAATATTTAA
1804451 AATATA
1 AATATA
1804457 ATATAATATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
AATATATTAATAAAAATATTTAA
Found at i:1807132 original size:23 final size:23
Alignment explanation
Indices: 1807070--1807144 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
1807060 AAATGAGTTG
* *
1807070 ATAAACAAGTTTCAAATGAGCCA
1 ATAAACAAATTTTAAATGAGCCA
* **
1807093 AGAAA-TGATTTTCAAATGAGCCA
1 ATAAACAAATTTT-AAATGAGCCA
*
1807116 ATAAACAAATTTTAAATGAGTCA
1 ATAAACAAATTTTAAATGAGCCA
1807139 ATAAAC
1 ATAAAC
1807145 GAGCCAAGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
22 3 0.07
23 33 0.80
24 5 0.12
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.25
Consensus pattern (23 bp):
ATAAACAAATTTTAAATGAGCCA
Found at i:1819173 original size:16 final size:17
Alignment explanation
Indices: 1819143--1819179 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
1819133 ATATATTTTG
1819143 AAAACAATTTTAAGA-A
1 AAAACAATTTTAAGACA
1819159 AAAAC-ATTTTAAAGACA
1 AAAACAATTTT-AAGACA
1819176 AAAA
1 AAAA
1819180 ATGGTATGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.26
16 9 0.47
17 5 0.26
ACGTcount: A:0.65, C:0.08, G:0.05, T:0.22
Consensus pattern (17 bp):
AAAACAATTTTAAGACA
Found at i:1826797 original size:18 final size:19
Alignment explanation
Indices: 1826776--1826819 Score: 81
Period size: 18 Copynumber: 2.4 Consensus size: 19
1826766 GTTATTTTTA
1826776 AAATAAAAGATAAA-AATT
1 AAATAAAAGATAAATAATT
1826794 AAATAAAAGATAAATAATT
1 AAATAAAAGATAAATAATT
1826813 AAATAAA
1 AAATAAA
1826820 TAATCTAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (19 bp):
AAATAAAAGATAAATAATT
Found at i:1828004 original size:35 final size:36
Alignment explanation
Indices: 1827960--1828027 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
1827950 TTAAAAAATA
* *
1827960 ATATTATATATAT-TTTAAAAATGTTTTCAAAAACT
1 ATATAATATATATATATAAAAATGTTTTCAAAAACT
* *
1827995 ATATAATATATATATATATATATGTTTTCAAAA
1 ATATAATATATATATATAAAAATGTTTTCAAAA
1828028 TGTTTCCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 12 0.43
36 16 0.57
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (36 bp):
ATATAATATATATATATAAAAATGTTTTCAAAAACT
Found at i:1828052 original size:45 final size:47
Alignment explanation
Indices: 1827960--1828056 Score: 151
Period size: 47 Copynumber: 2.1 Consensus size: 47
1827950 TTAAAAAATA
*
1827960 ATAT-TATATATATTTTAAAAATGTTTTCAAAAACTATATAATATAT
1 ATATATATATATATTTTAAAAATGTTTCCAAAAACTATATAATATAT
* * *
1828006 ATATATATATATGTTTTCAAAATGTTTCCAAAAACTATATATTATAT
1 ATATATATATATATTTTAAAAATGTTTCCAAAAACTATATAATATAT
1828053 ATAT
1 ATAT
1828057 GTTTTCAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
46 4 0.09
47 42 0.91
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (47 bp):
ATATATATATATATTTTAAAAATGTTTCCAAAAACTATATAATATAT
Found at i:1836443 original size:15 final size:15
Alignment explanation
Indices: 1836421--1836455 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 15
1836411 AAAAATGTTA
1836421 AAAGAGAAAATAAAAAT
1 AAAGA-AAAAT-AAAAT
1836438 AAAGAAAAATAAAAT
1 AAAGAAAAATAAAAT
1836453 AAA
1 AAA
1836456 AAAGAAGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 5 0.28
17 5 0.28
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (15 bp):
AAAGAAAAATAAAAT
Found at i:1836628 original size:18 final size:18
Alignment explanation
Indices: 1836607--1836649 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1836597 GTTATTTTTA
1836607 AAATAAAAGATAAG-AATT
1 AAATAAAAGA-AAGTAATT
1836625 AAATAAAAGAAAGTAATT
1 AAATAAAAGAAAGTAATT
1836643 AAATAAA
1 AAATAAA
1836650 TAATCTAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAGTAATT
Found at i:1837762 original size:16 final size:16
Alignment explanation
Indices: 1837751--1837787 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
1837741 AAAAATAACA
1837751 AAATGAATAAATAAAT
1 AAATGAATAAATAAAT
1837767 AAATGAAAATAAATAAAT
1 AAATG--AATAAATAAAT
1837785 AAA
1 AAA
1837788 ATGGCTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
18 14 0.74
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (16 bp):
AAATGAATAAATAAAT
Found at i:1837778 original size:14 final size:13
Alignment explanation
Indices: 1837759--1837789 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
1837749 CAAAATGAAT
1837759 AAATAAATAAATGA
1 AAATAAATAAAT-A
1837773 AAATAAATAAATA
1 AAATAAATAAATA
1837786 AAAT
1 AAAT
1837790 GGCTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
AAATAAATAAATA
Found at i:1839559 original size:32 final size:34
Alignment explanation
Indices: 1839523--1839592 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
1839513 ACCTTACAAC
* *
1839523 TCCCTAG-TTTTTC-CGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
* *
1839555 TCCCTAGCTTTTACATGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
1839589 TCCC
1 TCCC
1839593 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.33
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
Found at i:1839984 original size:21 final size:21
Alignment explanation
Indices: 1839960--1840023 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
1839950 GCAGCCTTGA
*
1839960 TGCATGGATGCATGGATGCAC
1 TGCAGGGATGCATGGATGCAC
*
1839981 TGCAGGGATGCATAGATGCAC
1 TGCAGGGATGCATGGATGCAC
1840002 TGCAGGGATGCATGGATGCAC
1 TGCAGGGATGCATGGATGCAC
1840023 T
1 T
1840024 TTGAAACCCT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.22
Consensus pattern (21 bp):
TGCAGGGATGCATGGATGCAC
Found at i:1840138 original size:30 final size:30
Alignment explanation
Indices: 1840104--1840163 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1840094 AACTTTGAAT
1840104 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
1840134 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
1840164 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:1840298 original size:21 final size:21
Alignment explanation
Indices: 1840274--1840313 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1840264 ATGTTTAATG
*
1840274 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATAAATTGTTAAC
*
1840295 AAAATGATATAAATTGTTA
1 AAAAAGATATAAATTGTTA
1840314 CCAATTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGATATAAATTGTTAAC
Found at i:1841496 original size:19 final size:20
Alignment explanation
Indices: 1841453--1841500 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1841443 TCTAAATCCT
*
1841453 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1841473 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1841492 TTTTCAAAA
1 TTTTCAAAA
1841501 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1842839 original size:21 final size:21
Alignment explanation
Indices: 1842795--1842891 Score: 151
Period size: 21 Copynumber: 4.7 Consensus size: 21
1842785 TTGGAGCCTT
* *
1842795 GATGCATGGATGCATGAC-AG
1 GATGCATCGATGCATGGCAAG
*
1842815 GATGTATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
1842836 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
*
1842857 GATGCATTGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
1842878 GATGCATCGATGCA
1 GATGCATCGATGCA
1842892 CTAATTGCAT
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
20 15 0.21
21 55 0.79
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.22
Consensus pattern (21 bp):
GATGCATCGATGCATGGCAAG
Found at i:1843105 original size:30 final size:31
Alignment explanation
Indices: 1843071--1843131 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
1843061 AACTTTGAAT
*
1843071 AAATTCAATTCAAATC-CAAAAACATTTTGC
1 AAATTCAATTCAAATCAAAAAAACATTTTGC
*
1843101 AAATTCAATTCAAGTCAAAAAAACATTTTGC
1 AAATTCAATTCAAATCAAAAAAACATTTTGC
1843132 CTTAAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.30
Consensus pattern (31 bp):
AAATTCAATTCAAATCAAAAAAACATTTTGC
Found at i:1847035 original size:22 final size:22
Alignment explanation
Indices: 1847010--1847080 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 22
1847000 CCACAACTCG
1847010 TAATTTGCACCGAAGTGCCACA
1 TAATTTGCACCGAAGTGCCACA
*
1847032 TAA-TTGC-CCTGAAG-GAC-CA
1 TAATTTGCACC-GAAGTGCCACA
*
1847051 TAGAGTTTGTACCGAAGTGCCACA
1 TA-A-TTTGCACCGAAGTGCCACA
1847075 T-ATTTG
1 TAATTTG
1847081 TCCCGGAGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 15
0.68 0.05 0.26
Matches are distributed among these distances:
19 4 0.10
20 5 0.13
21 12 0.31
22 11 0.28
23 4 0.10
24 3 0.08
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.27
Consensus pattern (22 bp):
TAATTTGCACCGAAGTGCCACA
Found at i:1847094 original size:21 final size:21
Alignment explanation
Indices: 1847062--1847118 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1847052 AGAGTTTGTA
* *
1847062 CCGAAGTG-CCACATATTTGTC
1 CCGAAG-GACCACATAATTATC
*
1847083 CCGGAGGACCACATAATTATC
1 CCGAAGGACCACATAATTATC
*
1847104 TCGAAGGACCACATA
1 CCGAAGGACCACATA
1847119 GACTCTCGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (21 bp):
CCGAAGGACCACATAATTATC
Found at i:1853679 original size:22 final size:22
Alignment explanation
Indices: 1853654--1853724 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 22
1853644 TCACAACTCG
1853654 TAATTTGCATCGAAGTGACACA
1 TAATTTGCATCGAAGTGACACA
*
1853676 TAA-TTGC-CCTGAAG-GACCACA
1 TAATTTGCATC-GAAGTGA-CACA
* * *
1853697 TAGTTTGCATCAAAGTGCCACA
1 TAATTTGCATCGAAGTGACACA
1853719 T-ATTTG
1 TAATTTG
1853725 TCCTGGAGGA
Statistics
Matches: 38, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
20 3 0.08
21 18 0.47
22 15 0.39
23 2 0.05
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.28
Consensus pattern (22 bp):
TAATTTGCATCGAAGTGACACA
Found at i:1853719 original size:43 final size:43
Alignment explanation
Indices: 1853657--1853741 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
1853647 CAACTCGTAA
*
1853657 TTTGCATCGAAGTGACACATAATTGCCCTGAAGGACCACATAG
1 TTTGCATCAAAGTGACACATAATTGCCCTGAAGGACCACATAG
* * * *
1853700 TTTGCATCAAAGTGCCACATATTTGTCCTGGAGGACCACATA
1 TTTGCATCAAAGTGACACATAATTGCCCTGAAGGACCACATA
1853742 ATTGTCTCGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.26
Consensus pattern (43 bp):
TTTGCATCAAAGTGACACATAATTGCCCTGAAGGACCACATAG
Found at i:1853925 original size:21 final size:21
Alignment explanation
Indices: 1853896--1853945 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1853886 ATAGAGTATA
* *
1853896 TTCACATTCAC-TGATTCTAAG
1 TTCATATTCACATG-TTCAAAG
1853917 TTCATATTCACATGTTCAAAG
1 TTCATATTCACATGTTCAAAG
1853938 TTCATATT
1 TTCATATT
1853946 TTCATAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (21 bp):
TTCATATTCACATGTTCAAAG
Found at i:1857324 original size:22 final size:22
Alignment explanation
Indices: 1857299--1857389 Score: 75
Period size: 21 Copynumber: 4.2 Consensus size: 22
1857289 CCACAACTCG
*
1857299 TAATTTGCACCGAAGTGCCACA
1 TAATTTGCACCGAAGTACCACA
1857321 TAA-TTGC-CCTGAAAG-ACCACA
1 TAATTTGCACC-G-AAGTACCACA
* *
1857342 TAGTTTGCACCAAAGTACCACA
1 TAATTTGCACCGAAGTACCACA
* *
1857364 TATTTTTC-CCAGAAG-ACCACA
1 TAATTTGCACC-GAAGTACCACA
1857385 TAATT
1 TAATT
1857390 ATCTCGAAGG
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
20 2 0.04
21 27 0.48
22 25 0.45
23 2 0.04
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.25
Consensus pattern (22 bp):
TAATTTGCACCGAAGTACCACA
Found at i:1857380 original size:43 final size:43
Alignment explanation
Indices: 1857302--1857386 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
1857292 CAACTCGTAA
* * *
1857302 TTTGCACCGAAGTGCCACATAATTGCCCTGAAAGACCACATAG
1 TTTGCACCAAAGTACCACATAATTGCCCAGAAAGACCACATAG
* *
1857345 TTTGCACCAAAGTACCACATATTTTTCCCAG-AAGACCACATA
1 TTTGCACCAAAGTACCACATA-ATTGCCCAGAAAGACCACATA
1857387 ATTATCTCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 30 0.83
44 6 0.17
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (43 bp):
TTTGCACCAAAGTACCACATAATTGCCCAGAAAGACCACATAG
Found at i:1857402 original size:21 final size:21
Alignment explanation
Indices: 1857378--1857429 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1857368 TTTCCCAGAA
1857378 GACCACATAATTATCTCGAAG
1 GACCACATAATTATCTCGAAG
* *
1857399 GACCATATAATTGTCTCGAAG
1 GACCACATAATTATCTCGAAG
1857420 GACCACATAA
1 GACCACATAA
1857430 ACCCTCGACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (21 bp):
GACCACATAATTATCTCGAAG
Found at i:1857612 original size:29 final size:27
Alignment explanation
Indices: 1857559--1857619 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 27
1857549 GTCATAGAGT
*
1857559 ATATTCACATTCACTGATTCTAAGTTC
1 ATATTCACATTCACTGATTCAAAGTTC
1857586 ATATTCACATATTCACATG-TTCAAAGTTC
1 ATATTCAC--ATTCAC-TGATTCAAAGTTC
1857615 ATATT
1 ATATT
1857620 TTCATAACAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 8 0.27
29 20 0.67
30 2 0.07
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.41
Consensus pattern (27 bp):
ATATTCACATTCACTGATTCAAAGTTC
Found at i:1884825 original size:17 final size:17
Alignment explanation
Indices: 1884805--1884843 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1884795 AATTAGGGTG
1884805 TATAAAAAATA-ATCAAA
1 TATAAAAAATATAT-AAA
*
1884822 TATAAAAACTATATAAA
1 TATAAAAAATATATAAA
1884839 TATAA
1 TATAA
1884844 TAGTATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (17 bp):
TATAAAAAATATATAAA
Found at i:1888943 original size:14 final size:14
Alignment explanation
Indices: 1888924--1888956 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1888914 AAGATATCCA
1888924 TTTTCCTGGTCCCC
1 TTTTCCTGGTCCCC
*
1888938 TTTTCCTGGTCCTC
1 TTTTCCTGGTCCCC
1888952 TTTTC
1 TTTTC
1888957 AATTTGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.36, G:0.12, T:0.52
Consensus pattern (14 bp):
TTTTCCTGGTCCCC
Found at i:1891042 original size:34 final size:35
Alignment explanation
Indices: 1890982--1891049 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 35
1890972 TATAAGACCT
*
1890982 ATACATTCATTAACAATTAAATTTAATGTTTTTTA
1 ATACATTCATTAACAATTAAACTTAATGTTTTTTA
1891017 ATACATTCATTAA-AATTAAACTTAATGTTTTTT
1 ATACATTCATTAACAATTAAACTTAATGTTTTTT
1891050 GACTTCTGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 19 0.59
35 13 0.41
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.49
Consensus pattern (35 bp):
ATACATTCATTAACAATTAAACTTAATGTTTTTTA
Found at i:1894819 original size:29 final size:29
Alignment explanation
Indices: 1894711--1894846 Score: 114
Period size: 29 Copynumber: 4.7 Consensus size: 29
1894701 GTAATAATAC
* * * * *
1894711 ACATTATGATAGTTAAGGTACCATATTTG
1 ACATTTTGAAAGTAAAGGTACCACATTCG
* * *
1894740 ACATTTTGACAAACTATAGGTACCGCA-TCAG
1 ACATTTTG--AAAGTAAAGGTACCACATTC-G
1894771 ACATTTT-AAAGTAAAGGTACCACATTCG
1 ACATTTTGAAAGTAAAGGTACCACATTCG
* * * *
1894799 ACATGTTGAAAGTATAGGTACCATATTGG
1 ACATTTTGAAAGTAAAGGTACCACATTCG
*
1894828 ACATTTTAAAAGTAAAGGT
1 ACATTTTGAAAGTAAAGGT
1894847 GTCACGTTGG
Statistics
Matches: 84, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
28 21 0.25
29 43 0.51
30 1 0.01
31 19 0.23
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (29 bp):
ACATTTTGAAAGTAAAGGTACCACATTCG
Found at i:1894831 original size:57 final size:59
Alignment explanation
Indices: 1894725--1894846 Score: 149
Period size: 57 Copynumber: 2.1 Consensus size: 59
1894715 TATGATAGTT
* * * *
1894725 AAGGTACCATATTTGACATTTTGACAAACTATAGGTACCGCATCAGACATTTT-AAAGTA
1 AAGGTACCACATTCGACATGTTGA-AAACTATAGGTACCACATCAGACATTTTAAAAGTA
* * **
1894784 AAGGTACCACATTCGACATGTTG-AAAGTATAGGTACCATATTGGACATTTTAAAAGTA
1 AAGGTACCACATTCGACATGTTGAAAACTATAGGTACCACATCAGACATTTTAAAAGTA
1894842 AAGGT
1 AAGGT
1894847 GTCACGTTGG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
57 23 0.43
58 11 0.20
59 20 0.37
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (59 bp):
AAGGTACCACATTCGACATGTTGAAAACTATAGGTACCACATCAGACATTTTAAAAGTA
Found at i:1894856 original size:29 final size:28
Alignment explanation
Indices: 1894725--1894893 Score: 106
Period size: 29 Copynumber: 5.8 Consensus size: 28
1894715 TATGATAGTT
* * *
1894725 AAGGTACCATATTTGACATTTTGACAAACTA
1 AAGGTACCACATTGGACATTTT---AAAGTA
* * **
1894756 TAGGTACCGCATCAGACATTTTAAAGTA
1 AAGGTACCACATTGGACATTTTAAAGTA
* *
1894784 AAGGTACCACATTCGACATGTTGAAAGTA
1 AAGGTACCACATTGGACAT-TTTAAAGTA
* *
1894813 TAGGTACCATATTGGACATTTTAAAAGTA
1 AAGGTACCACATTGGACATTTT-AAAGTA
** * * *
1894842 AAGGTGTCACGTTGGATATTTTTTCATAGTA
1 AAGGTACCACATTGGACA--TTTT-AAAGTA
*
1894873 AAAGTACCACATTGG-CATTTT
1 AAGGTACCACATTGGACATTTT
1894894 GTCGAAGTAT
Statistics
Matches: 106, Mismatches: 28, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
28 26 0.25
29 42 0.40
30 1 0.01
31 37 0.35
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (28 bp):
AAGGTACCACATTGGACATTTTAAAGTA
Found at i:1900140 original size:16 final size:16
Alignment explanation
Indices: 1900121--1900165 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1900111 CCATTTTCTT
1900121 AGTTTGAGAGTTT-CAA
1 AGTTTGAGAGTTTAC-A
*
1900137 AGTTTGAAAGTTTACA
1 AGTTTGAGAGTTTACA
*
1900153 CGTTTGAGAGTTT
1 AGTTTGAGAGTTT
1900166 GAGATTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (16 bp):
AGTTTGAGAGTTTACA
Found at i:1900461 original size:82 final size:83
Alignment explanation
Indices: 1900277--1900556 Score: 351
Period size: 82 Copynumber: 3.5 Consensus size: 83
1900267 ATAGAACATG
* *
1900277 CACCTTTCATTTC-GATGGAAT-GAACACTATGACATGACAGAGATTCTATGAATAATAATGGAA
1 CACCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTATGAATAATAATGGAA
**
1900340 AACGCTTCCATTGGAACA
66 AACGCTTCCCCTGGAACA
*
1900358 CACCTTTCATTTCGGAT-GGATGGAACACTATGACATGGCAGAGATTCTCTGAAT-ATAATGGAA
1 CACCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTATGAATAATAATGGAA
*
1900421 AACGCTTCCCCTAGAACA
66 AACGCTTCCCCTGGAACA
* * * * *
1900439 CATCTTTCATTTCAGATGGGATGTAACAATATGACATGGCAGAGA---TATGAATAATAGTGGAA
1 CACCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTATGAATAATAATGGAA
**
1900501 AACGCTTCCCC-GGAATG
66 AACGCTTCCCCTGGAACA
** * *
1900518 TGCCTTTCATTTTGGATGGGATGAAACACTATGACATGG
1 CACCTTTCATTTCGGATGGGATGGAACACTATGACATGG
1900557 TGGAGATTAT
Statistics
Matches: 173, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
79 41 0.24
80 19 0.11
81 55 0.32
82 58 0.34
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (83 bp):
CACCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTATGAATAATAATGGAA
AACGCTTCCCCTGGAACA
Found at i:1901660 original size:31 final size:32
Alignment explanation
Indices: 1901616--1901675 Score: 113
Period size: 31 Copynumber: 1.9 Consensus size: 32
1901606 CCTTAAACAA
1901616 TAAATAAAAGCATACACATACACCTAAAATAG
1 TAAATAAAAGCATACACATACACCTAAAATAG
1901648 TAAAT-AAAGCATACACATACACCTAAAA
1 TAAATAAAAGCATACACATACACCTAAAA
1901676 CAAATTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.57, C:0.20, G:0.05, T:0.18
Consensus pattern (32 bp):
TAAATAAAAGCATACACATACACCTAAAATAG
Found at i:1904249 original size:17 final size:16
Alignment explanation
Indices: 1904215--1904257 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1904205 AGACCTCGAG
1904215 AAAAAGAACGAGACAA
1 AAAAAGAACGAGACAA
1904231 AAAAAGAGACGAAGA-AA
1 AAAAAGA-ACG-AGACAA
*
1904248 AAGAAGAACG
1 AAAAAGAACG
1904258 TTGGAGTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 10 0.42
17 11 0.46
18 3 0.12
ACGTcount: A:0.67, C:0.09, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAAAGAACGAGACAA
Found at i:1904780 original size:23 final size:24
Alignment explanation
Indices: 1904745--1904799 Score: 94
Period size: 23 Copynumber: 2.3 Consensus size: 24
1904735 AAAAAACAAA
1904745 AATGATCTCATATCCAAGACCAAC
1 AATGATCTCATATCCAAGACCAAC
*
1904769 AATGAT-TCATATCTAAGACCAAC
1 AATGATCTCATATCCAAGACCAAC
1904792 AATGATCT
1 AATGATCT
1904800 TGAAGGTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 22 0.76
24 7 0.24
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.25
Consensus pattern (24 bp):
AATGATCTCATATCCAAGACCAAC
Found at i:1906861 original size:14 final size:14
Alignment explanation
Indices: 1906842--1906870 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1906832 GTTTCAATGA
1906842 ATTTAAATTATATC
1 ATTTAAATTATATC
1906856 ATTTAAATTATATC
1 ATTTAAATTATATC
1906870 A
1 A
1906871 AATGGATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTAAATTATATC
Found at i:1908333 original size:21 final size:21
Alignment explanation
Indices: 1908303--1908372 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
1908293 TTTGTACAAA
*
1908303 GTGCATCGATACACTTTGAAG
1 GTGCACCGATACACTTTGAAG
* * *
1908324 GTGTACCGATGCATCCTTGAAG
1 GTGCACCGATACA-CTTTGAAG
* * *
1908346 GTGCATCGATACACTATGAAA
1 GTGCACCGATACACTTTGAAG
1908367 GTGCAC
1 GTGCAC
1908373 TGATGCATTC
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
21 20 0.54
22 17 0.46
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (21 bp):
GTGCACCGATACACTTTGAAG
Found at i:1908355 original size:22 final size:21
Alignment explanation
Indices: 1908303--1908359 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
1908293 TTTGTACAAA
*
1908303 GTGCATCGATACACTTTGAAG
1 GTGCATCGATACACCTTGAAG
* * *
1908324 GTGTACCGATGCATCCTTGAAG
1 GTGCATCGATACA-CCTTGAAG
1908346 GTGCATCGATACAC
1 GTGCATCGATACAC
1908360 TATGAAAGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (21 bp):
GTGCATCGATACACCTTGAAG
Found at i:1908378 original size:43 final size:44
Alignment explanation
Indices: 1908303--1908404 Score: 134
Period size: 43 Copynumber: 2.3 Consensus size: 44
1908293 TTTGTACAAA
* * *
1908303 GTGCATCGATACACTTTGAAGGTGTACCGATGCA-TCCTTGAAG
1 GTGCATCGATACACTATGAAAGTGCACCGATGCATTCCTTGAAG
* *
1908346 GTGCATCGATACACTATGAAAGTGCACTGATGCATTCCTTGAAT
1 GTGCATCGATACACTATGAAAGTGCACCGATGCATTCCTTGAAG
* *
1908390 GTGTATCAATACACT
1 GTGCATCGATACACT
1908405 CAAGAGTGTA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 30 0.59
44 21 0.41
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (44 bp):
GTGCATCGATACACTATGAAAGTGCACCGATGCATTCCTTGAAG
Found at i:1908589 original size:21 final size:21
Alignment explanation
Indices: 1908559--1908629 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
1908549 TTTGTACAAA
*
1908559 GTGCATCGATACACTTTGAAG
1 GTGCACCGATACACTTTGAAG
* * *
1908580 GTGTACCGATGCATTCCTTGAAG
1 GTGCACCGATACA--CTTTGAAG
* * *
1908603 GTGCATCGATACACTATGAAA
1 GTGCACCGATACACTTTGAAG
1908624 GTGCAC
1 GTGCAC
1908630 TGATGCATTC
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
21 20 0.54
23 17 0.46
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (21 bp):
GTGCACCGATACACTTTGAAG
Found at i:1908612 original size:23 final size:22
Alignment explanation
Indices: 1908574--1908645 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
1908564 TCGATACACT
*
1908574 TTGAAGGTGTACCGATGCATTCC
1 TTGAAGGTGCA-CGATGCATTCC
*
1908597 TTGAAGGTGCATCGATACA---C
1 TTGAAGGTGCA-CGATGCATTCC
*
1908617 TATGAAAGTGCACTGATGCATTCC
1 T-TGAAGGTGCAC-GATGCATTCC
1908641 TTGAA
1 TTGAA
1908646 TGTGTATCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
20 3 0.08
21 14 0.36
23 20 0.51
24 2 0.05
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (22 bp):
TTGAAGGTGCACGATGCATTCC
Found at i:1908635 original size:44 final size:44
Alignment explanation
Indices: 1908559--1908661 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 44
1908549 TTTGTACAAA
* * *
1908559 GTGCATCGATACACTTTGAAGGTGTACCGATGCATTCCTTGAAG
1 GTGCATCGATACACTATGAAAGTGCACCGATGCATTCCTTGAAG
* *
1908603 GTGCATCGATACACTATGAAAGTGCACTGATGCATTCCTTGAAT
1 GTGCATCGATACACTATGAAAGTGCACCGATGCATTCCTTGAAG
* *
1908647 GTGTATCAATACACT
1 GTGCATCGATACACT
1908662 CAAGAGTGTA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (44 bp):
GTGCATCGATACACTATGAAAGTGCACCGATGCATTCCTTGAAG
Found at i:1910614 original size:14 final size:15
Alignment explanation
Indices: 1910587--1910615 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1910577 TTTTGGATGT
1910587 TTTTGGATTGATATG
1 TTTTGGATTGATATG
1910602 TTTTGGA-TGATATG
1 TTTTGGATTGATATG
1910616 AATGTTTGAA
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:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (15 bp):
TTTTGGATTGATATG
Found at i:1910643 original size:2 final size:2
Alignment explanation
Indices: 1910636--1910672 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1910626 CCTAAATGTT
1910636 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1910673 TGGTTTTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1912187 original size:27 final size:27
Alignment explanation
Indices: 1912127--1912194 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
1912117 CGTTGTCCCT
* *
1912127 ATCATCGTCATCCTCATCCTCATTGTC
1 ATCATCGTCATCATCATCCTCATTCTC
* * *
1912154 ATTATCGTCTTCATCATCCTCCTTCTC
1 ATCATCGTCATCATCATCCTCATTCTC
* *
1912181 CTCATCGTTATCAT
1 ATCATCGTCATCAT
1912195 AACTCTCAAC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.18, C:0.35, G:0.06, T:0.41
Consensus pattern (27 bp):
ATCATCGTCATCATCATCCTCATTCTC
Found at i:1914180 original size:14 final size:14
Alignment explanation
Indices: 1914161--1914191 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1914151 CAAAATTATT
1914161 TAAATAAATTCAAA
1 TAAATAAATTCAAA
*
1914175 TAAATAAATTCTAA
1 TAAATAAATTCAAA
1914189 TAA
1 TAA
1914192 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATAAATTCAAA
Done.