Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008466.1 Hibiscus syriacus cultivar Beakdansim tig00111280_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: 685270
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:198250 original size:57 final size:57
Alignment explanation
Indices: 198176--198329 Score: 184
Period size: 57 Copynumber: 2.7 Consensus size: 57
198166 AATTTCTTAG
* * ** * *
198176 TTTTTGCAAATAAAGTTCTTATACGAAAATTCATAAACAAATTATGAAATCCTTA-A
1 TTTTTGCACACAAAGTTCCCATACGGAAATTCATAAACAAATTACGAAATCCTTATA
** * * *
198232 CTTTTTGCACACTCAGTTCCCATAAGGAAATTCATAAACAAATTACGAATTTCTTATA
1 -TTTTTGCACACAAAGTTCCCATACGGAAATTCATAAACAAATTACGAAATCCTTATA
*
198290 TTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACAA
1 TTTTTGCACACAAAGTTCCCATACGGAAATTCATAAACAA
198330 TGCCTAACTG
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
57 80 0.99
58 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.32
Consensus pattern (57 bp):
TTTTTGCACACAAAGTTCCCATACGGAAATTCATAAACAAATTACGAAATCCTTATA
Found at i:198439 original size:67 final size:67
Alignment explanation
Indices: 198331--198530 Score: 330
Period size: 67 Copynumber: 3.0 Consensus size: 67
198321 CATAAACAAT
198331 GCCTAACTGTGCATTGACAGAAAGGTGTCAGTTATGCCAGTTAGATGAAAGGCTAAGTCCCTTTG
1 GCCTAACTGTGCATTGACAGAAAGGTGTCAGTTATGCCAGTTAGATGAAAGGCTAAGTCCCTTTG
198396 AG
66 AG
* * * *
198398 GCCTAACTGTGCATTGATAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1 GCCTAACTGTGCATTGACAGAAAGGTGTCAGTTATGCCAGTTAGATGAAAGGCTAAGTCCCTTTG
198463 AG
66 AG
**
198465 ATCTAACTGTGCATTGACAGAAAGGTGTCAGTTATGCCAGTTAGATGAAAGGCTAAG-CGCCTTT
1 GCCTAACTGTGCATTGACAGAAAGGTGTCAGTTATGCCAGTTAGATGAAAGGCTAAGTC-CCTTT
198529 GA
65 GA
198531 CAGAAAGATG
Statistics
Matches: 122, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
67 122 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (67 bp):
GCCTAACTGTGCATTGACAGAAAGGTGTCAGTTATGCCAGTTAGATGAAAGGCTAAGTCCCTTTG
AG
Found at i:198588 original size:49 final size:49
Alignment explanation
Indices: 198478--198579 Score: 150
Period size: 49 Copynumber: 2.1 Consensus size: 49
198468 TAACTGTGCA
* * * *
198478 TTGACAGAAAGGTGTCAGTTATGCCAGTTAGATGAAAGGCTAAGCGCCT
1 TTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGCTAAACACCT
* *
198527 TTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCT
1 TTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGCTAAACACCT
198576 TTGA
1 TTGA
198580 GTAAAAGATT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (49 bp):
TTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGCTAAACACCT
Found at i:198687 original size:81 final size:81
Alignment explanation
Indices: 198526--198688 Score: 195
Period size: 81 Copynumber: 2.0 Consensus size: 81
198516 GCTAAGCGCC
* * * * *
198526 TTTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTA
1 TTTGACAAAAAGATGTCAATCATGCCAGTTAGATAAAAAGTTAAATACCTTTGAGTAAAAGACTA
* *
198591 ATGGCCTAACTATGCA
66 ATGGCATAACAATGCA
* * *
198607 TTTGACAAAAAGGTGTCAATCATGCTA-TATAGATAAAAAGTTAAATGCCTTTGAGTAAAAGACT
1 TTTGACAAAAAGATGTCAATCATGCCAGT-TAGATAAAAAGTTAAATACCTTTGAGTAAAAGACT
*
198671 AGAT-GTATAACAATGCA
65 A-ATGGCATAACAATGCA
198688 T
1 T
198689 AATGTTGTAT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
80 1 0.01
81 66 0.96
82 2 0.03
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (81 bp):
TTTGACAAAAAGATGTCAATCATGCCAGTTAGATAAAAAGTTAAATACCTTTGAGTAAAAGACTA
ATGGCATAACAATGCA
Found at i:198712 original size:20 final size:20
Alignment explanation
Indices: 198674--198712 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
198664 AAAGACTAGA
*
198674 TGTATAACAATGCATAATGT
1 TGTATAACAAGGCATAATGT
198694 TGTATAA-AAGGCATGAATG
1 TGTATAACAAGGCAT-AATG
198713 GATACCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.31
Consensus pattern (20 bp):
TGTATAACAAGGCATAATGT
Found at i:198766 original size:45 final size:45
Alignment explanation
Indices: 198705--199095 Score: 383
Period size: 45 Copynumber: 8.7 Consensus size: 45
198695 GTATAAAAGG
* * * * * *
198705 CATGAATGGATACCATAAATGAAATGTATAAT-AATGTATTATCGT
1 CATGAAAGGATGCCATAATTGAAATGCAT-ATGAATGCATTATCGA
* * * *
198750 CATGAAATGATGCCATAATTAAAATGCATATGAGTGCATTATCGG
1 CATGAAAGGATGCCATAATTGAAATGCATATGAATGCATTATCGA
* *
198795 CATAAAAGGATGCCATAATTGAAATGCATATGTATGCATTATCGA
1 CATGAAAGGATGCCATAATTGAAATGCATATGAATGCATTATCGA
* * ** * *
198840 CATGAAAGGATGCTATAATTTAAATGCATATGGGTACATTATCGG
1 CATGAAAGGATGCCATAATTGAAATGCATATGAATGCATTATCGA
* * ** *
198885 CATGAAAGAATGTCATAATTGAAATGCATATGGGTGCATTATCAA
1 CATGAAAGGATGCCATAATTGAAATGCATATGAATGCATTATCGA
* * * **
198930 CATAAAATGATGACATAATTGAAATGCATATGGGTGCATTATCGA
1 CATGAAAGGATGCCATAATTGAAATGCATATGAATGCATTATCGA
**
198975 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCTG-
1 CATGAAAGGATGCCATAATTGAAATGCATATGAATGCATTATC-GA
* * ** *
199020 CATGAAAGGATGCCATGATTAAAATGCATATGGGTGCATTATTTG-
1 CATGAAAGGATGCCATAATTGAAATGCATATGAATGCATTA-TCGA
** *
199065 CATGAAACAATGCCATAAATGAAAATGCATA
1 CATGAAAGGATGCCATAATTG-AAATGCATA
199096 ATGGTGCATA
Statistics
Matches: 297, Mismatches: 45, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
44 2 0.01
45 284 0.96
46 11 0.04
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (45 bp):
CATGAAAGGATGCCATAATTGAAATGCATATGAATGCATTATCGA
Found at i:198836 original size:90 final size:90
Alignment explanation
Indices: 198742--199104 Score: 478
Period size: 90 Copynumber: 4.0 Consensus size: 90
198732 ATAATAATGT
* * * * *
198742 ATTATCGTCATGAAATGATGCCATAATTAAAATGCATATGAGTGCATTATCGGCATAAAAGGATG
1 ATTATCGACATGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTATCGGCATGAAAGAATG
**
198807 CCATAATTGAAATGCATATGTATGC
66 CCATAATTGAAATGCATATGGGTGC
* * *
198832 ATTATCGACATGAAAGGATGCTATAATTTAAATGCATATGGGTACATTATCGGCATGAAAGAATG
1 ATTATCGACATGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTATCGGCATGAAAGAATG
*
198897 TCATAATTGAAATGCATATGGGTGC
66 CCATAATTGAAATGCATATGGGTGC
* * * * * * *
198922 ATTATCAACATAAAATGATGACATAATTGAAATGCATATGGGTGCATTATCGACATGAAAGGATG
1 ATTATCGACATGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTATCGGCATGAAAGAATG
198987 CCATAATTGAAATGCATATGGGTGC
66 CCATAATTGAAATGCATATGGGTGC
* ** *
199012 ATTATCTG-CATGAAAGGATGCCATGATTAAAATGCATATGGGTGCATTATTTGCATGAAACAAT
1 ATTATC-GACATGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTATCGGCATGAAAGAAT
*
199076 GCCATAAATGAAAATGCATAAT-GGTGC
65 GCCATAATTG-AAATGCAT-ATGGGTGC
199103 AT
1 AT
199105 AATAAGTATG
Statistics
Matches: 237, Mismatches: 33, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
90 220 0.93
91 15 0.06
92 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (90 bp):
ATTATCGACATGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTATCGGCATGAAAGAATG
CCATAATTGAAATGCATATGGGTGC
Found at i:198910 original size:135 final size:134
Alignment explanation
Indices: 198742--199104 Score: 485
Period size: 135 Copynumber: 2.7 Consensus size: 134
198732 ATAATAATGT
* * * *
198742 ATTATCGTCATGAAATGATGCCATAATTAAAATGCATATGAGTGCATTATCGGCATAAAAGGATG
1 ATTATCGGCATGAAA-GATGCCATAATTAAAATGCATATGGGTGCATTATCAGCATAAAACGATG
* * *
198807 CCATAATTGAAATGCATATGTATGCATTATCGACATGAAAGGATGCTATAATTTAAATGCATATG
65 CCATAATTGAAATGCATATGGATGCATTATCGACATGAAAGGATGCCATAATTGAAATGCATATG
198872 GGTAC
130 GGTAC
* * * *
198877 ATTATCGGCATGAAAGAATGTCATAATTGAAATGCATATGGGTGCATTATCAACATAAAATGATG
1 ATTATCGGCATGAAAG-ATGCCATAATTAAAATGCATATGGGTGCATTATCAGCATAAAACGATG
* *
198942 ACATAATTGAAATGCATATGGGTGCATTATCGACATGAAAGGATGCCATAATTGAAATGCATATG
65 CCATAATTGAAATGCATATGGATGCATTATCGACATGAAAGGATGCCATAATTGAAATGCATATG
*
199007 GGTGC
130 GGTAC
* * ** * *
199012 ATTATCTGCATGAAAGGATGCCATGATTAAAATGCATATGGGTGCATTATTTGCATGAAACAATG
1 ATTATCGGCATGAAA-GATGCCATAATTAAAATGCATATGGGTGCATTATCAGCATAAAACGATG
*
199077 CCATAAATGAAAATGCATAATGG-TGCAT
65 CCATAATTG-AAATGCAT-ATGGATGCAT
199105 AATAAGTATG
Statistics
Matches: 199, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
134 1 0.01
135 180 0.90
136 14 0.07
137 4 0.02
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (134 bp):
ATTATCGGCATGAAAGATGCCATAATTAAAATGCATATGGGTGCATTATCAGCATAAAACGATGC
CATAATTGAAATGCATATGGATGCATTATCGACATGAAAGGATGCCATAATTGAAATGCATATGG
GTAC
Found at i:201882 original size:22 final size:20
Alignment explanation
Indices: 201857--201908 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
201847 CCCCTATCAC
201857 GGTATCGATACTACTACACTAT
1 GGTATCGATAC-A-TACACTAT
* *
201879 GGTATCGATA-ATATATTAT
1 GGTATCGATACATACACTAT
201898 GGTATCGATAC
1 GGTATCGATAC
201909 CATTTTTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 16 0.59
20 1 0.04
22 10 0.37
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (20 bp):
GGTATCGATACATACACTAT
Found at i:207221 original size:20 final size:20
Alignment explanation
Indices: 207192--207236 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
207182 AGTAGTACGA
* *
207192 ATACTGCTAAGCCAATACTG
1 ATACTACTAAGCCAATACCG
207212 ATACTACTAAGCCAATACCG
1 ATACTACTAAGCCAATACCG
207232 ATACT
1 ATACT
207237 GTATGCAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (20 bp):
ATACTACTAAGCCAATACCG
Found at i:208132 original size:29 final size:30
Alignment explanation
Indices: 208061--208120 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
208051 CAATTTAAGG
*
208061 CAAAATGGTTTTTTGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
*
208092 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
208121 TTGAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 10 0.37
31 6 0.22
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:208233 original size:20 final size:20
Alignment explanation
Indices: 208210--208286 Score: 92
Period size: 20 Copynumber: 4.1 Consensus size: 20
208200 TTCAAGATTG
* *
208210 CCCAGGGGGTATAGATTCCC
1 CCCAGGGGGTACAGATACCC
208230 CCCAGGGGGTACAGATA--C
1 CCCAGGGGGTACAGATACCC
*
208248 CCC---GGGTACAAATACCC
1 CCCAGGGGGTACAGATACCC
208265 CCCAGGGGGTACAGATACCC
1 CCCAGGGGGTACAGATACCC
208285 CC
1 CC
208287 TGCAGGTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
15 10 0.21
17 4 0.08
18 4 0.08
20 30 0.62
ACGTcount: A:0.25, C:0.35, G:0.27, T:0.13
Consensus pattern (20 bp):
CCCAGGGGGTACAGATACCC
Found at i:208256 original size:15 final size:15
Alignment explanation
Indices: 208236--208265 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
208226 TCCCCCCAGG
*
208236 GGGTACAGATACCCC
1 GGGTACAAATACCCC
208251 GGGTACAAATACCCC
1 GGGTACAAATACCCC
208266 CCAGGGGGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.23, T:0.13
Consensus pattern (15 bp):
GGGTACAAATACCCC
Found at i:208362 original size:20 final size:21
Alignment explanation
Indices: 208320--208362 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
208310 AACAAAATGT
*
208320 CCAGTGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
*
208341 CCAGGGGGTACTGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
208362 C
1 C
208363 TGTTCAACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.42, G:0.26, T:0.19
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:208424 original size:21 final size:21
Alignment explanation
Indices: 208398--208440 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
208388 ATTTGAATAT
208398 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
208419 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
208440 T
1 T
208441 CTATTCTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (21 bp):
TATGAAGGGGTATCGATTCCC
Found at i:210985 original size:34 final size:30
Alignment explanation
Indices: 210947--211015 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
210937 TTGATATAAC
210947 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
210981 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
211010 AATTTA
1 AATTTA
211016 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:211027 original size:29 final size:30
Alignment explanation
Indices: 210956--211015 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
210946 CAATTTAAGG
210956 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
210987 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
211016 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:211128 original size:20 final size:20
Alignment explanation
Indices: 211105--211145 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
211095 TTCAAGATTG
* *
211105 CCCAGAGGGTATAGATTCCC
1 CCCAGAGGGTACAGATACCC
*
211125 CCCAGGGGGTACAGATACCC
1 CCCAGAGGGTACAGATACCC
211145 C
1 C
211146 GGGTACAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.34, G:0.27, T:0.15
Consensus pattern (20 bp):
CCCAGAGGGTACAGATACCC
Found at i:211151 original size:15 final size:15
Alignment explanation
Indices: 211131--211160 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
211121 TCCCCCCAGG
211131 GGGTACAGATACCCC
1 GGGTACAGATACCCC
211146 GGGTACAGATACCCC
1 GGGTACAGATACCCC
211161 CTGCAGGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:211237 original size:20 final size:21
Alignment explanation
Indices: 211195--211238 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
211185 AACAGAATGT
*
211195 CCAGTGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
211216 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
211237 CC
1 CC
211239 TGTTCAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.45, G:0.25, T:0.16
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:219047 original size:17 final size:17
Alignment explanation
Indices: 219022--219070 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
219012 TGCTCAATCG
*
219022 GTACTGATACTACTTCA
1 GTACCGATACTACTTCA
219039 GTACCGATACTACTTCA
1 GTACCGATACTACTTCA
219056 GTACCGATACTACTT
1 GTACCGATACTACTT
219071 TTCATTGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.33
Consensus pattern (17 bp):
GTACCGATACTACTTCA
Found at i:225021 original size:2 final size:2
Alignment explanation
Indices: 225014--225044 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
225004 TACATACAAA
225014 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
225045 CAAAATACAT
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:225340 original size:103 final size:103
Alignment explanation
Indices: 225220--225408 Score: 378
Period size: 103 Copynumber: 1.8 Consensus size: 103
225210 GAAATGTTAT
225220 AATATTATAAAACTATATATATATATGAAGAAACCATATATATTAACATAACAAAACTATTATAA
1 AATATTATAAAACTATATATATATATGAAGAAACCATATATATTAACATAACAAAACTATTATAA
225285 TTAATATTGTTTTAACATTTTTTTAAAGGTCAACTAAA
66 TTAATATTGTTTTAACATTTTTTTAAAGGTCAACTAAA
225323 AATATTATAAAACTATATATATATATGAAGAAACCATATATATTAACATAACAAAACTATTATAA
1 AATATTATAAAACTATATATATATATGAAGAAACCATATATATTAACATAACAAAACTATTATAA
225388 TTAATATTGTTTTAACATTTT
66 TTAATATTGTTTTAACATTTT
225409 CACTACAATA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 86 1.00
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (103 bp):
AATATTATAAAACTATATATATATATGAAGAAACCATATATATTAACATAACAAAACTATTATAA
TTAATATTGTTTTAACATTTTTTTAAAGGTCAACTAAA
Found at i:225929 original size:22 final size:22
Alignment explanation
Indices: 225903--225945 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
225893 GCTCCCACCC
* *
225903 ACCTCTGTCGCTCGAATCAGAG
1 ACCTCTGCCACTCGAATCAGAG
225925 ACCTCTGCCACTCGAATCAGA
1 ACCTCTGCCACTCGAATCAGA
225946 AGACATATAG
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:0.26, C:0.35, G:0.19, T:0.21
Consensus pattern (22 bp):
ACCTCTGCCACTCGAATCAGAG
Found at i:226676 original size:2 final size:2
Alignment explanation
Indices: 226669--226697 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
226659 TGAATAAAAT
226669 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 T
226698 CCACTTCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:227929 original size:17 final size:17
Alignment explanation
Indices: 227907--227956 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
227897 AAATTCTTCT
227907 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
*
227924 AACA-T--T-GATACTCA
1 AACATTCATAGAAAC-CA
227938 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
227955 AA
1 AA
227957 ACATGAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 4 0.15
14 7 0.27
15 1 0.04
16 1 0.04
17 9 0.35
18 4 0.15
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.20
Consensus pattern (17 bp):
AACATTCATAGAAACCA
Found at i:228320 original size:23 final size:24
Alignment explanation
Indices: 228293--228346 Score: 94
Period size: 23 Copynumber: 2.3 Consensus size: 24
228283 TATGGATGTC
228293 AGGAGATGAGCCTTGAGTT-AAAG
1 AGGAGATGAGCCTTGAGTTGAAAG
228316 AGGAGATGAGCCTTGAGTTGAAAG
1 AGGAGATGAGCCTTGAGTTGAAAG
228340 A-GAGATG
1 AGGAGATG
228347 GCATAGGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 25 0.83
24 5 0.17
ACGTcount: A:0.35, C:0.07, G:0.37, T:0.20
Consensus pattern (24 bp):
AGGAGATGAGCCTTGAGTTGAAAG
Found at i:228945 original size:2 final size:2
Alignment explanation
Indices: 228938--228985 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
228928 CAAGGGATGA
228938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
228980 AT AT AT
1 AT AT AT
228986 GGATGGATAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:232878 original size:20 final size:20
Alignment explanation
Indices: 232855--232905 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
232845 TAACAACATA
232855 AATTTCATCAAAACAGAGC-T
1 AATTTCAT-AAAACAGAGCTT
* *
232875 AATTGCGTAAAACAGAGCTT
1 AATTTCATAAAACAGAGCTT
232895 AATTTCA-AAAA
1 AATTTCATAAAA
232906 ATTTGACTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (20 bp):
AATTTCATAAAACAGAGCTT
Found at i:232991 original size:14 final size:14
Alignment explanation
Indices: 232972--233003 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
232962 AGGCAGCTTG
232972 GCTCGGCTCAAATA
1 GCTCGGCTCAAATA
*
232986 GCTCGGCTCAAATG
1 GCTCGGCTCAAATA
233000 GCTC
1 GCTC
233004 CCCAGGCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.31, G:0.25, T:0.22
Consensus pattern (14 bp):
GCTCGGCTCAAATA
Found at i:234840 original size:25 final size:25
Alignment explanation
Indices: 234812--234865 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
234802 TTTTTTGTTT
234812 TGAAGAAGAATG-AGAAAAGACCACG
1 TGAAGAAGAA-GAAGAAAAGACCACG
*
234837 TGAAGAAGAAGAAGAAAAGAGCACG
1 TGAAGAAGAAGAAGAAAAGACCACG
234862 TGAA
1 TGAA
234866 TTTTTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.54, C:0.09, G:0.30, T:0.07
Consensus pattern (25 bp):
TGAAGAAGAAGAAGAAAAGACCACG
Found at i:236755 original size:23 final size:22
Alignment explanation
Indices: 236729--236771 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
236719 AAAGTTATAA
236729 GTTAGAAGTTAGAAAATTAGCGG
1 GTTAGAAGTTAG-AAATTAGCGG
**
236752 GTTAGCGGTTAGAAATTAGC
1 GTTAGAAGTTAGAAATTAGC
236772 AAAGTTAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (22 bp):
GTTAGAAGTTAGAAATTAGCGG
Found at i:238779 original size:34 final size:33
Alignment explanation
Indices: 238741--238809 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 33
238731 AGATTGTTAC
238741 ATGTTACATAGTTCATTAGGTCA-TTGCATATTAT
1 ATGTTACATAGTTCATTAGGT-AGTTGCATA-TAT
**
238775 ATGTTATGTAGTTCATTAGGTAGTTGCATATAT
1 ATGTTACATAGTTCATTAGGTAGTTGCATATAT
238808 AT
1 AT
238810 TGCGAAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 6 0.19
34 26 0.81
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (33 bp):
ATGTTACATAGTTCATTAGGTAGTTGCATATAT
Found at i:240072 original size:20 final size:21
Alignment explanation
Indices: 240027--240239 Score: 210
Period size: 20 Copynumber: 10.4 Consensus size: 21
240017 GATTCTTACT
*
240027 ATCGCAACGAGTATCCGTAAAA
1 ATCGCAACGCGTATCCGT-AAA
240049 ATCGCAACGCGTATCCGT-AA
1 ATCGCAACGCGTATCCGTAAA
* *
240069 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGTAAA
*
240090 ATCGCAATGCGTATCCGT-AA
1 ATCGCAACGCGTATCCGTAAA
* * *
240110 ATCGCAACGAGAATACGT-AA
1 ATCGCAACGCGTATCCGTAAA
* *
240130 ATCGCAACGCG-ATTC-TGAAT
1 ATCGCAACGCGTATCCGT-AAA
* *
240150 ATCGCAACGAGAATCCGTAAA
1 ATCGCAACGCGTATCCGTAAA
240171 ATCGCAACGCGTATCCGT-AA
1 ATCGCAACGCGTATCCGTAAA
* *
240191 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGTAAA
240212 ATCGCAACGCGTATCCGT-AA
1 ATCGCAACGCGTATCCGTAAA
240232 ATCGCAAC
1 ATCGCAAC
240240 ACGATTTTTA
Statistics
Matches: 159, Mismatches: 22, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
18 1 0.01
19 3 0.02
20 83 0.52
21 54 0.34
22 18 0.11
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGTATCCGTAAA
Found at i:240103 original size:41 final size:41
Alignment explanation
Indices: 240027--240239 Score: 315
Period size: 41 Copynumber: 5.2 Consensus size: 41
240017 GATTCTTACT
* *
240027 ATCGCAACGAGTATCCGTAAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAAATCGCAACGCGTATCCGTAA
* *
240069 ATCGCAACGACAATACGTAAAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
240110 ATCGCAACGAGAATACGT-AAATCGCAACGCG-ATTC-TGAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGT-AA
*
240149 TATCGCAACGAGAATCCGTAAAATCGCAACGCGTATCCGTAA
1 -ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
240191 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
240232 ATCGCAAC
1 ATCGCAAC
240240 ACGATTTTTA
Statistics
Matches: 155, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
38 1 0.01
39 5 0.03
40 29 0.19
41 99 0.64
42 20 0.13
43 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:240169 original size:81 final size:82
Alignment explanation
Indices: 240027--240239 Score: 315
Period size: 81 Copynumber: 2.6 Consensus size: 82
240017 GATTCTTACT
* *
240027 ATCGCAACGAGTATCCGTAAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAAT
1 ATCGCAACGAGAATACGT-AAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAAT
*
240092 CGCAATGCGTATCCGTAA
65 CGCAACGCGTATCCGTAA
* * *
240110 ATCGCAACGAGAATACGT-AAATCGCAACGCG-ATTC-TGAATATCGCAACGAGAATCCGTAAAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGT-AA-ATCGCAACGACAATACGTAAAA
240172 TCGCAACGCGTATCCGTAA
64 TCGCAACGCGTATCCGTAA
*
240191 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAAC
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAAC
240240 ACGATTTTTA
Statistics
Matches: 117, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
79 1 0.01
80 5 0.04
81 68 0.58
82 21 0.18
83 21 0.18
84 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (82 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATC
GCAACGCGTATCCGTAA
Found at i:240224 original size:122 final size:123
Alignment explanation
Indices: 240006--240239 Score: 425
Period size: 122 Copynumber: 1.9 Consensus size: 123
239996 CAGTTTCCAG
* * *
240006 AATCGCAACGCGATTCTTACTATCGCAACGAGTATCCGTAAAAATCGCAACGCGTATCCGTAAAT
1 AATCGCAACGCGATTCTGAATATCGCAACGAGAATCCGTAAAAATCGCAACGCGTATCCGTAAAT
*
240071 CGCAACGACAATACGTAAAATCGCAATGCGTATCCGTAAATCGCAACGAGAATACGTA
66 CGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
240129 AATCGCAACGCGATTCTGAATATCGCAACGAGAATCCGT-AAAATCGCAACGCGTATCCGTAAAT
1 AATCGCAACGCGATTCTGAATATCGCAACGAGAATCCGTAAAAATCGCAACGCGTATCCGTAAAT
240193 CGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAAC
66 CGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAAC
240240 ACGATTTTTA
Statistics
Matches: 107, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
122 71 0.66
123 36 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (123 bp):
AATCGCAACGCGATTCTGAATATCGCAACGAGAATCCGTAAAAATCGCAACGCGTATCCGTAAAT
CGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
Found at i:240800 original size:14 final size:14
Alignment explanation
Indices: 240776--240842 Score: 53
Period size: 14 Copynumber: 4.4 Consensus size: 14
240766 TTCAATCTGC
240776 AGAAGAATCGCAACG
1 AGAA-AATCGCAACG
*
240791 AGATAATCGCAACGCG
1 AGAAAATCGCAA--CG
240807 AAATGAAAATCGCAACG
1 --A-GAAAATCGCAACG
*
240824 AGAGAATCGCAACG
1 AGAAAATCGCAACG
*
240838 CGAAA
1 AGAAA
240843 CCAAAATCGC
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
14 23 0.55
15 4 0.10
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.24
ACGTcount: A:0.46, C:0.21, G:0.24, T:0.09
Consensus pattern (14 bp):
AGAAAATCGCAACG
Found at i:240823 original size:33 final size:33
Alignment explanation
Indices: 240781--240853 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
240771 TCTGCAGAAG
* **
240781 AATCGCAACGAGATAATCGCAACGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAACGCGAAACCAA
240814 AATCGCAACGAGAGAATCGCAACGCGAAACCAA
1 AATCGCAACGAGAGAATCGCAACGCGAAACCAA
240847 AATCGCA
1 AATCGCA
240854 TTGCGATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.45, C:0.25, G:0.21, T:0.10
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAACGCGAAACCAA
Found at i:240912 original size:20 final size:19
Alignment explanation
Indices: 240854--240942 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 19
240844 CAAAATCGCA
240854 TTGCGATTTTCATTT-CGC
1 TTGCGATTTTCATTTCCGC
*
240872 GTTGCGA--TTC-TCT-CG-
1 -TTGCGATTTTCATTTCCGC
240887 TTGCGATTTTCATTTCCGC
1 TTGCGATTTTCATTTCCGC
**
240906 ATTGCGATAGTCATTCTCTCG-
1 -TTGCGATTTTCATT-TC-CGC
240927 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
240943 AACCAAAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 5 0.09
18 2 0.04
19 8 0.14
20 24 0.43
21 2 0.04
22 2 0.04
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCCGC
Found at i:243359 original size:42 final size:42
Alignment explanation
Indices: 243308--243401 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 42
243298 CCACTCCTAT
* * *
243308 CATTGAAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCAC
1 CATTCAAGAGGCCACTATCA-TCATCGAAGAGGT-CCCTCCCAC
* *
243350 CGTTCAAGAGGCCACTATCATCATTGAAGAGGTCCCTCCCAC
1 CATTCAAGAGGCCACTATCATCATCGAAGAGGTCCCTCCCAC
243392 CATTCAAGAG
1 CATTCAAGAG
243402 CCTGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 38 0.86
43 2 0.05
ACGTcount: A:0.26, C:0.35, G:0.18, T:0.21
Consensus pattern (42 bp):
CATTCAAGAGGCCACTATCATCATCGAAGAGGTCCCTCCCAC
Found at i:244774 original size:14 final size:14
Alignment explanation
Indices: 244752--244790 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
244742 TTGATTGTTT
244752 AATTGATTTGTAAA
1 AATTGATTTGTAAA
244766 AGA-TGATTTGTAAA
1 A-ATTGATTTGTAAA
244780 AATTGATTTGT
1 AATTGATTTGT
244791 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:244913 original size:19 final size:19
Alignment explanation
Indices: 244897--244960 Score: 119
Period size: 19 Copynumber: 3.4 Consensus size: 19
244887 AAAAATGACT
244897 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
244916 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
244935 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
244954 ATTGCAA
1 ATCGCAA
244961 CGACAAAATC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.17
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:244974 original size:33 final size:36
Alignment explanation
Indices: 244897--244981 Score: 104
Period size: 38 Copynumber: 2.4 Consensus size: 36
244887 AAAAATGACT
*
244897 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATCAAA
*
244935 ATCGCAATGCGAAATGAAAATTGCAA-CG-A-CAAA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAATCAAA
*
244968 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
244982 CTAAATTCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
33 16 0.36
34 1 0.02
36 2 0.05
38 25 0.57
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATCAAA
Found at i:245009 original size:19 final size:19
Alignment explanation
Indices: 244987--245158 Score: 122
Period size: 19 Copynumber: 9.7 Consensus size: 19
244977 CGAAACTAAA
*
244987 TTCGCGTTGCGATTTTAAT
1 TTCGCGTTGCGATTTTCAT
*
245006 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
245021 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
245039 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
245054 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
245072 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
*
245091 TTCCGCGTTGCGATATTCAT
1 TT-CGCGTTGCGATTTTCAT
245111 ATTCGCGTTGCGATTTTCA-
1 -TTCGCGTTGCGATTTTCAT
245130 --CGC--TGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
245145 TTCGCATTGCGATT
1 TTCGCGTTGCGATT
245159 CTCTCGTTGC
Statistics
Matches: 119, Mismatches: 17, Indels: 34
0.70 0.10 0.20
Matches are distributed among these distances:
14 28 0.24
16 9 0.08
17 8 0.07
19 42 0.35
20 30 0.25
21 2 0.02
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:245033 original size:33 final size:33
Alignment explanation
Indices: 244991--245191 Score: 231
Period size: 33 Copynumber: 5.8 Consensus size: 33
244981 ACTAAATTCG
* *
244991 CGTTGCGATTTTAATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
245024 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
245057 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CT
* * * *
245096 CGTTGCGATATTCATATTCGCGTTGCGATTTTCA
1 CGTTGCGATTTTCAT-TTCGCATTGCGATTCTCT
*
245130 CGCTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* * *
245163 CGTTGCGATTGTAATTTCTGCGTTGCGAT
1 CGTTGCGATTTTCATTTC-GCATTGCGAT
245192 AGTCATTAAG
Statistics
Matches: 144, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
33 89 0.62
34 23 0.16
35 3 0.02
38 2 0.01
39 15 0.10
40 12 0.08
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:245103 original size:20 final size:19
Alignment explanation
Indices: 245024--245157 Score: 99
Period size: 20 Copynumber: 7.5 Consensus size: 19
245014 GCGATTCCCT
*
245024 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
* *
245043 CATTGCG--ATTC---TCT
1 CGTTGCGATATTCATTTCG
*
245057 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
* *
245076 CATTGCGATAGTCATTTCCG
1 CGTTGCGATATTCATTT-CG
245096 CGTTGCGATATTCATATTCG
1 CGTTGCGATATTCAT-TTCG
*
245116 CGTTGCGATTTTCA---CG
1 CGTTGCGATATTCATTTCG
*
245132 C--TGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
*
245149 CATTGCGAT
1 CGTTGCGAT
245158 TCTCTCGTTG
Statistics
Matches: 91, Mismatches: 12, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
14 19 0.21
16 6 0.07
17 6 0.07
19 28 0.31
20 30 0.33
21 2 0.02
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
CGTTGCGATATTCATTTCG
Found at i:245137 original size:106 final size:106
Alignment explanation
Indices: 244989--245198 Score: 314
Period size: 106 Copynumber: 2.0 Consensus size: 106
244979 AAACTAAATT
* * *
244989 CGCGTTGCGATTTTAATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTC
1 CGCGTTGCGATATTAATTTCGCATTGCGATTCCCACGCTGCGATTTTCATTTCGCATTGCGATTC
* *
245054 TCTCGTTGCGATTTTCATTTC-GCATTGCGATAGTCATTTC
66 TCTCGTTGCGATTGTAATTTCTGCATTGCGATAGTCATTTC
* * **
245094 CGCGTTGCGATATTCATATTCGCGTTGCGATTTTCACGCTGCGATTTTCATTTCGCATTGCGATT
1 CGCGTTGCGATATTAAT-TTCGCATTGCGATTCCCACGCTGCGATTTTCATTTCGCATTGCGATT
*
245159 CTCTCGTTGCGATTGTAATTTCTGCGTTGCGATAGTCATT
65 CTCTCGTTGCGATTGTAATTTCTGCATTGCGATAGTCATT
245199 AAGATGATTG
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
105 15 0.16
106 62 0.67
107 16 0.17
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (106 bp):
CGCGTTGCGATATTAATTTCGCATTGCGATTCCCACGCTGCGATTTTCATTTCGCATTGCGATTC
TCTCGTTGCGATTGTAATTTCTGCATTGCGATAGTCATTTC
Found at i:245142 original size:73 final size:66
Alignment explanation
Indices: 244994--245171 Score: 212
Period size: 73 Copynumber: 2.6 Consensus size: 66
244984 AAATTCGCGT
* * * *
244994 TGCGATTTTAATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TGCGATTTTCATTTCGCATTGCGATTCCCGCGTTGCGATATTCATTTCGCATTGCGATTCTCACG
*
245059 T
66 C
*
245060 TGCGATTTTCATTTCGCATTGCGATAGTCATTTCCGCGTTGCGATATTCATATTCGCGTTGCGAT
1 TGCGATTTTCATTTCGCATTGCGAT--TC----CCGCGTTGCGATATTCAT-TTCGCATTGCGAT
*
245125 TTTCACGC
59 TCTCACGC
* *
245133 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGAT
1 TGCGATTTTCATTTCGCATTGCGATTCCCGCGTTGCGAT
245172 TGTAATTTCT
Statistics
Matches: 96, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
66 24 0.25
67 10 0.10
68 2 0.02
71 2 0.02
72 16 0.17
73 42 0.44
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.42
Consensus pattern (66 bp):
TGCGATTTTCATTTCGCATTGCGATTCCCGCGTTGCGATATTCATTTCGCATTGCGATTCTCACG
C
Found at i:247632 original size:24 final size:24
Alignment explanation
Indices: 247598--247651 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
247588 CTGAAACATC
247598 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
247622 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
247646 ATCAAA
1 ATCAAA
247652 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:247665 original size:24 final size:24
Alignment explanation
Indices: 247598--247665 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
247588 CTGAAACATC
* * *
247598 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
247622 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
247646 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
247666 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:247798 original size:12 final size:12
Alignment explanation
Indices: 247777--247810 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
247767 GGTTGTAGGT
*
247777 TTTGAGATTGTG
1 TTTGATATTGTG
247789 TTTGATATTGTG
1 TTTGATATTGTG
*
247801 TTTGGTATTG
1 TTTGATATTG
247811 GGAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:248500 original size:20 final size:19
Alignment explanation
Indices: 248472--248784 Score: 205
Period size: 20 Copynumber: 15.5 Consensus size: 19
248462 AAATTTCAGT
248472 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTAC-GATTCTC
* *
248492 GTTGTGATTTACGGATTATC
1 GTTGCGATTTAC-GATTCTC
*
248512 GTTGCGATTTACGAATTATC
1 GTTGCGATTTACG-ATTCTC
248532 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTAC-GATTCTC
248552 GTTGCGATTTTACGTATTCTC
1 GTTGCGA-TTTACG-ATTCTC
* * * *
248573 GTTACGATTTACGGCTACGC
1 GTTGCGATTTAC-GATTCTC
* *
248593 ATTGCGATTAACGTATTCTC
1 GTTGCGATTTACG-ATTCTC
* *
248613 GTTGCGATATT-CAGAATCGC
1 GTTGCGAT-TTAC-GATTCTC
248633 GTTGCGATTTACGTATTCTC
1 GTTGCGATTTACG-ATTCTC
* * *
248653 ATTGCGATTTACGGATACGC
1 GTTGCGATTTAC-GATTCTC
*
248673 GTTGCGATTTTACGTATTGTC
1 GTTGCGA-TTTACG-ATTCTC
* * *
248694 GTTGTGATTTACAGATACGC
1 GTTGCGATTTAC-GATTCTC
*
248714 GTTGCGATTTTTACGGATACTC
1 GTTGCGA--TTTAC-GATTCTC
* * * *
248736 GTTGCGATAGTAAGAATCGC
1 GTTGCGAT-TTACGATTCTC
* * *
248756 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTAC-GATTCTC
248776 GTTGCGATT
1 GTTGCGATT
248785 CTGGAAAATC
Statistics
Matches: 230, Mismatches: 45, Indels: 36
0.74 0.14 0.12
Matches are distributed among these distances:
19 6 0.03
20 167 0.73
21 39 0.17
22 18 0.08
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (19 bp):
GTTGCGATTTACGATTCTC
Found at i:248534 original size:40 final size:39
Alignment explanation
Indices: 248472--248784 Score: 263
Period size: 40 Copynumber: 7.7 Consensus size: 39
248462 AAATTTCAGT
* * *
248472 GTTGCGATTTACAG-ATTCTCGTTGTGATTTACGGATTATC
1 GTTGCGATTTAC-GTATTCTCGTTGCGATTTACAGA-TAGC
* * **
248512 GTTGCGATTTACGAATTATCGTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGTATTCTCGTTGCGATTTACAGA-TAGC
* * *
248552 GTTGCGATTTTACGTATTCTCGTTACGATTTACGGCTACGC
1 GTTGCGA-TTTACGTATTCTCGTTGCGATTTACAGATA-GC
* * *
248593 ATTGCGATTAACGTATTCTCGTTGCGATATT-CAGAATCGC
1 GTTGCGATTTACGTATTCTCGTTGCGAT-TTACAG-ATAGC
* *
248633 GTTGCGATTTACGTATTCTCATTGCGATTTACGGATACGC
1 GTTGCGATTTACGTATTCTCGTTGCGATTTACAGATA-GC
* *
248673 GTTGCGATTTTACGTATTGTCGTTGTGATTTACAGATACGC
1 GTTGCGA-TTTACGTATTCTCGTTGCGATTTACAGATA-GC
* * * *
248714 GTTGCGATTTTTACGGATACTCGTTGCGATAGTA-AGAATCGC
1 GTTGCGA--TTTACGTATTCTCGTTGCGAT-TTACAG-ATAGC
* * *
248756 GTTGCGATTTTCATATTCGCGTTGCGATT
1 GTTGCGATTTACGTATTCTCGTTGCGATT
248785 CTGGAAAATC
Statistics
Matches: 224, Mismatches: 38, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
39 5 0.02
40 117 0.52
41 69 0.31
42 29 0.13
43 4 0.02
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (39 bp):
GTTGCGATTTACGTATTCTCGTTGCGATTTACAGATAGC
Found at i:248640 original size:121 final size:122
Alignment explanation
Indices: 248511--248765 Score: 341
Period size: 121 Copynumber: 2.1 Consensus size: 122
248501 TACGGATTAT
* * *
248511 CGTTGCGATTTACGAATTATCGTTGCGATTTACAGATTCTCGTTGCGATTTTACGTATTCTCGTT
1 CGTTGCGATTTACGAATTATCATTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTT
* * * * * *
248576 ACGATTTACGGCTACGCATTGCGA-TTAACGTATTCTCGTTGCGATATTCAGAATCG
66 ACGATTTACAGATACGCATTGCGATTTAACGGATACTCGTTGCGATAGTAAGAATCG
* * * *
248632 CGTTGCGATTTACGTATTCTCATTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTT
1 CGTTGCGATTTACGAATTATCATTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTT
** * *
248697 GTGATTTACAGATACGCGTTGCGATTTTTACGGATACTCGTTGCGATAGTAAGAATCG
66 ACGATTTACAGATACGCATTGCGA-TTTAACGGATACTCGTTGCGATAGTAAGAATCG
248755 CGTTGCGATTT
1 CGTTGCGATTT
248766 TCATATTCGC
Statistics
Matches: 115, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
121 77 0.67
123 38 0.33
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (122 bp):
CGTTGCGATTTACGAATTATCATTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTT
ACGATTTACAGATACGCATTGCGATTTAACGGATACTCGTTGCGATAGTAAGAATCG
Found at i:258782 original size:29 final size:29
Alignment explanation
Indices: 258721--258884 Score: 157
Period size: 29 Copynumber: 5.7 Consensus size: 29
258711 ACCGTTGACC
* ** *
258721 GGTGCTATTCTGGGAATTTATTCGATTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
*
258750 GGTGTTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* ** ** **
258779 GGTGCTATTTTGATAATTTTTTCGAAAAA
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* * *
258808 TGTGATATTCTGGGAATTAATTCGAAATT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
258837 GGTGCTATTTTGGGAATTAATTCGAAAAG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
258866 GGTGCTATTTTGGTAATTA
1 GGTGCTATTCTGGGAATTA
258885 TTTTAAAAAG
Statistics
Matches: 107, Mismatches: 28, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 107 1.00
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:258872 original size:87 final size:88
Alignment explanation
Indices: 258726--258888 Score: 256
Period size: 87 Copynumber: 1.9 Consensus size: 88
258716 TGACCGGTGC
* ** * *
258726 TATTCTGGGAATTTATTCGATTTTGGTGTTATTCTGGGAATTAATTCGAAATGGGTGCTATTTTG
1 TATTCTGGGAATTAATTCGAAATTGGTGCTATTCTGGGAATTAATTCGAAAAGGGTGCTATTTTG
258791 ATAATT-TTTTCGAAAAATGTGA
66 ATAATTATTTTCGAAAAATGTGA
*
258813 TATTCTGGGAATTAATTCGAAATTGGTGCTATTTTGGGAATTAATTCGAAAAGGGTGCTATTTTG
1 TATTCTGGGAATTAATTCGAAATTGGTGCTATTCTGGGAATTAATTCGAAAAGGGTGCTATTTTG
*
258878 GTAATTATTTT
66 ATAATTATTTT
258889 AAAAAGGGTC
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
87 64 0.94
88 4 0.06
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (88 bp):
TATTCTGGGAATTAATTCGAAATTGGTGCTATTCTGGGAATTAATTCGAAAAGGGTGCTATTTTG
ATAATTATTTTCGAAAAATGTGA
Found at i:258884 original size:58 final size:58
Alignment explanation
Indices: 258721--258884 Score: 184
Period size: 58 Copynumber: 2.8 Consensus size: 58
258711 ACCGTTGACC
* **** *
258721 GGTGCTATTCTGGGAATTTATTCGATTTTGGTGTTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTTATTCGAAAAAGGTGATATTCTGGGAATTAATTCGAAATG
** * * *
258779 GGTGCTATTTTGATAATTTTTTCGAAAAATGTGATATTCTGGGAATTAATTCGAAATT
1 GGTGCTATTTTGGGAATTTATTCGAAAAAGGTGATATTCTGGGAATTAATTCGAAATG
* * * * *
258837 GGTGCTATTTTGGGAATTAATTCGAAAAGGGTGCTATTTTGGTAATTA
1 GGTGCTATTTTGGGAATTTATTCGAAAAAGGTGATATTCTGGGAATTA
258885 TTTTAAAAAG
Statistics
Matches: 86, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 86 1.00
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.42
Consensus pattern (58 bp):
GGTGCTATTTTGGGAATTTATTCGAAAAAGGTGATATTCTGGGAATTAATTCGAAATG
Found at i:260250 original size:17 final size:19
Alignment explanation
Indices: 260223--260261 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
260213 ATATATGTAT
260223 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
260241 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
260260 TA
1 TA
260262 AGTTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:260745 original size:45 final size:44
Alignment explanation
Indices: 260688--260773 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 44
260678 TCGACCCACC
260688 TTTTTTTTAATTTAAGGCACCCTTTCGGATTTTCACCCTAAATG
1 TTTTTTTTAATTTAAGGCACCCTTTCGGATTTTCACCCTAAATG
* * *
260732 TTTTTTTTCAATTTAAGGCGCTCTTTCGGGTTTTCACCCTAA
1 TTTTTTTT-AATTTAAGGCACCCTTTCGGATTTTCACCCTAA
260774 GCGAAATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 8 0.21
45 30 0.79
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.47
Consensus pattern (44 bp):
TTTTTTTTAATTTAAGGCACCCTTTCGGATTTTCACCCTAAATG
Found at i:270948 original size:17 final size:16
Alignment explanation
Indices: 270926--270993 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 16
270916 ATTTTAAAAG
270926 AAAAATAATAAAATATA
1 AAAAATAATAAAATA-A
*
270943 AAAAATATTAAAATAA
1 AAAAATAATAAAATAA
*
270959 AAAATAAAATAAAATAA
1 AAAA-ATAATAAAATAA
*
270976 TAATAATAAT-AAATAA
1 -AAAAATAATAAAATAA
270992 AA
1 AA
270994 GGGAAATATA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
15 2 0.05
16 11 0.25
17 28 0.64
18 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAATAATAAAATAA
Found at i:270962 original size:32 final size:32
Alignment explanation
Indices: 270907--270974 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 32
270897 AAAAAATGTT
* *
270907 ATATAAAAAATTTTAAAAGAAAAAT-AATAAA
1 ATATAAAAAATATTAAAAAAAAAATAAATAAA
270938 ATATAAAAAATATTAAAATAAAAAATAAAATAAA
1 ATATAAAAAATATTAAAA-AAAAAAT-AAATAAA
270972 ATA
1 ATA
270975 ATAATAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 17 0.53
32 6 0.19
34 9 0.28
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (32 bp):
ATATAAAAAATATTAAAAAAAAAATAAATAAA
Found at i:271017 original size:17 final size:17
Alignment explanation
Indices: 270927--271018 Score: 65
Period size: 16 Copynumber: 5.8 Consensus size: 17
270917 TTTTAAAAGA
270927 AAAATAATAAAATATAA-
1 AAAATAAT-AAATATAAT
*
270944 AAAATATTAAA-ATAA-
1 AAAATAATAAATATAAT
*
270959 AAAAT-A-AAATAAAAT
1 AAAATAATAAATATAAT
270974 AATAATAAT-AATA-AAT
1 AA-AATAATAAATATAAT
***
270990 AAAA-GGGAAATATAAT
1 AAAATAATAAATATAAT
271006 AAAATAATAAATA
1 AAAATAATAAATA
271019 ATAGTAGTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
13 3 0.05
14 3 0.05
15 17 0.29
16 18 0.31
17 17 0.29
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAATAATAAATATAAT
Found at i:271084 original size:18 final size:18
Alignment explanation
Indices: 271063--271105 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
271053 GTTGTTTTTA
*
271063 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
271081 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
271099 AAATAAA
1 AAATAAA
271106 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:271978 original size:4 final size:4
Alignment explanation
Indices: 271965--272012 Score: 55
Period size: 4 Copynumber: 12.0 Consensus size: 4
271955 ATTGGACACC
*
271965 TAAA -AAA TAAA T-AA TAAAA TGAA TAAA TAAA TAAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA T-AAA TAAA TAAA TAAA T-AAA TAAA TAAA TAAA
272013 ATAGCATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
3 6 0.16
4 25 0.66
5 7 0.18
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:271993 original size:13 final size:13
Alignment explanation
Indices: 271986--272015 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
271976 TAATAAAATG
271986 AATAAATAAATAA
1 AATAAATAAATAA
271999 AATAAATAAATAA
1 AATAAATAAATAA
272012 AATA
1 AATA
272016 GCATTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAAATAAATAA
Found at i:271999 original size:17 final size:17
Alignment explanation
Indices: 271969--272012 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
271959 GACACCTAAA
271969 AAATAAAT-AATAAAAT
1 AAATAAATAAATAAAAT
*
271985 GAATAAATAAATAAAAT
1 AAATAAATAAATAAAAT
272002 AAATAAATAAA
1 AAATAAATAAA
272013 ATAGCATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (17 bp):
AAATAAATAAATAAAAT
Found at i:272668 original size:2 final size:2
Alignment explanation
Indices: 272613--272657 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
272603 TTTACAACAT
272613 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
272655 TA T
1 TA T
272658 CCTTAATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:272850 original size:18 final size:18
Alignment explanation
Indices: 272813--272848 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
272803 AAATGATTAT
*
272813 ATATGAATTTTATTTAAA
1 ATATGAATTATATTTAAA
272831 ATAT-AATTATATTTAAA
1 ATATGAATTATATTTAAA
272848 A
1 A
272849 ATTATTTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATATGAATTATATTTAAA
Found at i:274479 original size:31 final size:29
Alignment explanation
Indices: 274424--274482 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 29
274414 TAAATTCTAA
*
274424 AAGTAATAAAATAAAATAAAAATAATAAG
1 AAGTAAAAAAATAAAATAAAAATAATAAG
274453 AAGTAAAAAACATAAAATAAAAAATAATAA
1 AAGTAAAAAA-ATAAAAT-AAAAATAATAA
274483 AAAATGCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 9 0.33
30 7 0.26
31 11 0.41
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.19
Consensus pattern (29 bp):
AAGTAAAAAAATAAAATAAAAATAATAAG
Found at i:274485 original size:16 final size:16
Alignment explanation
Indices: 274436--274485 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 16
274426 GTAATAAAAT
274436 AAAAT-AAAAATAATA
1 AAAATAAAAAATAATA
* *
274451 AGAAGTAAAAAA-CAT-
1 A-AAATAAAAAATAATA
274466 AAAATAAAAAATAATA
1 AAAATAAAAAATAATA
274482 AAAA
1 AAAA
274486 ATGCTAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
14 9 0.33
15 4 0.15
16 9 0.33
17 5 0.19
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (16 bp):
AAAATAAAAAATAATA
Found at i:275179 original size:13 final size:13
Alignment explanation
Indices: 275155--275188 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
275145 GCCTAAAAAA
275155 TAATAA-AATAAT
1 TAATAATAATAAT
275167 TAATAATAATAAT
1 TAATAATAATAAT
*
275180 AAATAATAA
1 TAATAATAA
275189 AATATTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAATAATAATAAT
Found at i:275187 original size:7 final size:7
Alignment explanation
Indices: 275152--275189 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
275142 GGGGCCTAAA
275152 AAATAAT
1 AAATAAT
275159 AAAATAAT
1 -AAATAAT
*
275167 TAATAAT
1 AAATAAT
275174 -AATAAT
1 AAATAAT
275180 AAATAAT
1 AAATAAT
275187 AAA
1 AAA
275190 ATATTTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 6 0.21
7 15 0.54
8 7 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAATAAT
Found at i:275192 original size:21 final size:19
Alignment explanation
Indices: 275148--275192 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
275138 GTATGGGGCC
275148 TAAAA-AATAATAAAATAAT
1 TAAAATAATAAT-AAATAAT
275167 TAATAATAATAATAAATAA-
1 TAA-AATAATAATAAATAAT
275186 TAAAATA
1 TAAAATA
275193 TTTTTGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.17
19 6 0.25
20 8 0.33
21 6 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAAATAATAATAAATAAT
Found at i:276357 original size:124 final size:124
Alignment explanation
Indices: 276130--277075 Score: 1437
Period size: 124 Copynumber: 7.6 Consensus size: 124
276120 CAGATGCACA
* * * * * * *
276130 TTCGCTGTGAAGTTGAGCTTTGAATTGGATATTCTTCATTGTGAAATTGAAATCCAATCTAAATA
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGA
* * * * * * * *
276195 TGGATATTGCTGGTGGCCACGATGTCATACGTCATGAAGTTGAAATCGTGGATGACCCC
66 TGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCC
* * *
276254 TTCGTTATGAAGTTGAGCCTTGAATTGGATATCATTCGTCATGAAGTTGAAATCCAATCTAAAGA
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGA
* **
276319 TGAATGTTGCTGGTGGGCACGATATTCTTCGTCGTGAAGTTGAAATCGTGGATGAACCC
66 TGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCC
* * *
276378 TTCGTTGCGAAGTTGAGCCTTGAATTGGATATCCTTCATCATGAAGTTGAAATCCAAAATCTAAA
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCC--AATCTAAA
* *
276443 GATGAATGTTGCTGGTGGGCACGATATCCTTCGTCATGAAGTTGAAATCGTGGATGGCCTC
64 GATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCC
* * *
276504 TTCGTTGTGAAGTTGATCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATTCAATCTAAAGA
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGA
* * * *
276569 TGAATGTTGCTGGTGGGCATGATATCCTTCGTCATGAAGTTGAAATCATGGATGGCCCA
66 TGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCC
*
276628 TTCGTTGTGAAGTTGAGCATTGAATTGGATATCCTTAAC-T-GTGAAGTTGAAATCCAATCTAAA
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTT--CGTCGTGAAGTTGAAATCCAATCTAAA
*
276691 GATGAATGTTGCTGGTGGGCACGATATCCTTCTTCGTGAAGTTGAAATCGTGGATGGCCCC
64 GATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCC
* *
276752 TCCGTTGTGAAGTTAAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGA
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGA
*
276817 TGAATGTTGCTGGTGGGCACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCCCC
66 TGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCC
* * *
276876 TTCGCTGTGAAGTTGAGCCTTGAATTGAATATCATTCGTCGTGAAGTTGAAATCCAATCTAAAGA
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGA
* * *
276941 TTAATGTTGCTGGTGGGCACGATATCCTTCGTTGTGAAGTTGAAATCGTGGATGGCCCA
66 TGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCC
277000 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGA
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGA
*
277065 TAAATGTTGCT
66 TGAATGTTGCT
277076 TCGAGTTCAA
Statistics
Matches: 755, Mismatches: 61, Indels: 12
0.91 0.07 0.01
Matches are distributed among these distances:
122 1 0.00
123 1 0.00
124 636 0.84
125 1 0.00
126 116 0.15
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (124 bp):
TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGA
TGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCC
Found at i:279800 original size:45 final size:45
Alignment explanation
Indices: 279716--280148 Score: 564
Period size: 45 Copynumber: 9.6 Consensus size: 45
279706 CTCTCCAGGT
* * *
279716 CATTACAATCATGGCATCCTTTCATGCCAATAATGCACCCATATG
1 CATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATG
***
279761 CATTTCAATTATTATATCAC-TTCATGCCGATAATGCACCCATATG
1 CATTTCAATTATGGCATC-CTTTCATGCCGATAATGCACCCATATG
* * * *
279806 CATTTTAATTATGACATCCTTTAATGCTGATAATGCACCCATATG
1 CATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATG
* * *
279851 CATTTTAATTATGGCATCCTTTCATGCCGATAATACACCTATATG
1 CATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATG
* * *
279896 CATTTCAATTATGACATCATTTCATGCCCATAATGCACCCATATG
1 CATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATG
*
279941 GATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATG
1 CATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATG
* * * * **
279986 CATTTCAATTATGGCATCATTGCAAGCTGATAATGCACCCATACA
1 CATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATG
* *
280031 CATTTCAATTATGGCATCCTTTTATGCCGATAATACACCCATATG
1 CATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATG
* * * *
280076 CATTTCAATTATGGCATCCTTTCATACCGATAATACA-CTATTATA
1 CATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA-TATG
*
280121 CATTTCATTTATGGCATCCTTTCATGCC
1 CATTTCAATTATGGCATCCTTTCATGCC
280149 TTTTATACAA
Statistics
Matches: 338, Mismatches: 47, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
44 3 0.01
45 334 0.99
46 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (45 bp):
CATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATG
Found at i:280337 original size:81 final size:81
Alignment explanation
Indices: 280183--280337 Score: 206
Period size: 81 Copynumber: 1.9 Consensus size: 81
280173 ATACATCTAG
* * * * * *
280183 TCTTTTACTCAAAGGCATTTAACCTTTCATCTATCTGGCATGATTGACACCTTTTTGTCAAATGA
1 TCTTTTACTCAAAAGCATTTAACCTTTCATCTAACTGGCATAATTGACAACTTTCTATCAAATGA
*
280248 TCAGCTAGGCCATTAA
66 TCAACTAGGCCATTAA
*
280264 TCTTTTACTCAAAAGTATTTAACCTTTCATCTAACTGGCATAATTGGA-AACTTTCTATCAAATG
1 TCTTTTACTCAAAAGCATTTAACCTTTCATCTAACTGGCATAATT-GACAACTTTCTATCAAATG
280328 -TACAACTAGG
65 AT-CAACTAGG
280338 TCTCAAAGGC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
80 1 0.02
81 61 0.95
82 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (81 bp):
TCTTTTACTCAAAAGCATTTAACCTTTCATCTAACTGGCATAATTGACAACTTTCTATCAAATGA
TCAACTAGGCCATTAA
Found at i:280434 original size:67 final size:67
Alignment explanation
Indices: 280286--280605 Score: 462
Period size: 67 Copynumber: 4.8 Consensus size: 67
280276 AAGTATTTAA
* * * ** *
280286 CCTTTCATCTAACTGGCATAATTGGA-AACTTTCTATCAAATGTACAACTAGGTCTCAAAGGCAC
1 CCTTTCATCTAACTGGCATAATT-GACACCTTTCTGTC-AATGCACAGTTAGGCCTCAAAGGCAC
280350 TTAG
64 TTAG
*
280354 CCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTT
280419 AG
66 AG
* ** * * *
280421 CCTTTCATCTAACTGGCATAATTGATATTTTTATGTCAATGCATAGTTAGGCCTCAAAGGTACTT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTT
280486 AG
66 AG
* * * *
280488 CATTTCATCTAACTGACATAATTGACACCTTTTTGTCAATGCACAGTTAGGCATCAAAGGCACTT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTT
280553 AG
66 AG
280555 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGG
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGG
280606 ACTTAAATAT
Statistics
Matches: 226, Mismatches: 25, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
67 195 0.86
68 31 0.14
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (67 bp):
CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTT
AG
Found at i:280867 original size:57 final size:57
Alignment explanation
Indices: 280804--280944 Score: 194
Period size: 57 Copynumber: 2.5 Consensus size: 57
280794 TTTTGTAAAT
** *
280804 AAAGTTCTTATACGGAAATTCATAAACAAATTATGAATTCCTTA-ACTTTTTGCACAC
1 AAAGTTCCCATACGGAAATTCATAAACAAATTACGAATTCCTTATA-TTTTTGCACAC
** * *
280861 TCAGTTCCCATAAGGAAATTCATAAACAAATTACGAATTTCTTATATTTTTGCACAC
1 AAAGTTCCCATACGGAAATTCATAAACAAATTACGAATTCCTTATATTTTTGCACAC
*
280918 AAAGTACCCATACGGAAATTCATAAAC
1 AAAGTTCCCATACGGAAATTCATAAAC
280945 CATGCCTAAT
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
57 71 0.99
58 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (57 bp):
AAAGTTCCCATACGGAAATTCATAAACAAATTACGAATTCCTTATATTTTTGCACAC
Found at i:281075 original size:66 final size:67
Alignment explanation
Indices: 280950--281215 Score: 347
Period size: 67 Copynumber: 4.0 Consensus size: 67
280940 TAAACCATGC
* * * *
280950 CTAATTGTGCATTAACAGAAAGATGTCAGTTATGCCAGTTAGATGAAAGGTTAAGTGCCTTTGAG
1 CTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAGTGCCTTTGAG
*
281015 GT
66 AT
* * * *
281017 CTAACTGTGCATTGATAGAAATGTGTCAATTATG-CAGTTAGATGAAAGGATAAGTGCCTTTAAG
1 CTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAGTGCCTTTGAG
281081 AT
66 AT
* * *
281083 CTAACTGTGCATTGACAGAAAGGTGTCAGTTATCCCAGTTAGATGAAAGGCTAAGT-CTCTTTGA
1 CTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAGTGC-CTTTGA
*
281147 GAC
65 GAT
** * *
281150 CTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGA
1 CTAACTGTGCA-TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAGTGCCTTTGA
281215 G
65 G
281216 TAAAAGATTA
Statistics
Matches: 173, Mismatches: 22, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
66 60 0.35
67 64 0.37
68 48 0.28
69 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (67 bp):
CTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAGTGCCTTTGAG
AT
Found at i:281285 original size:81 final size:81
Alignment explanation
Indices: 281149--281303 Score: 222
Period size: 81 Copynumber: 1.9 Consensus size: 81
281139 CTCTTTGAGA
* * * * * *
281149 CCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTG
1 CCTAGCTGTGCATTTGACAAAAAGGGGTCAATCATGCCAGTTAGATAAAAAGTTAAATACCTTTG
281214 AGTAAAAGATTAATGG
66 AGTAAAAGATTAATGG
* *
281230 CCTAGCTGTTCATTTGACAAAAAGGGGTCAATCATGCCA-TATAGATAAAAAGTTAAATGCCTTT
1 CCTAGCTGTGCATTTGACAAAAAGGGGTCAATCATGCCAGT-TAGATAAAAAGTTAAATACCTTT
281294 GAGTAAAAGA
65 GAGTAAAAGA
281304 CTAGATGTAT
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
80 1 0.02
81 64 0.98
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (81 bp):
CCTAGCTGTGCATTTGACAAAAAGGGGTCAATCATGCCAGTTAGATAAAAAGTTAAATACCTTTG
AGTAAAAGATTAATGG
Found at i:281387 original size:45 final size:45
Alignment explanation
Indices: 281338--281784 Score: 538
Period size: 45 Copynumber: 9.9 Consensus size: 45
281328 TTGTATAAAA
* * * *
281338 GGCATGAAAGGATGCCATAAATGAAATGTATAAT-AGTGTATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCAT-ATGGGTGCATTATC
* * *
281383 GGCATGAAAGGATGTCATAATTAAAATGCATATGAGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* *
281428 GACATAAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * *
281473 GGCATGAAATGATGCCATAATTGAAATGTATATGGGTACATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * *
281518 GACATGAAAGAATGTCATAATTGAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * * * * * *
281563 GACATAAAATGATGACATAATTAAAATGCACATGTGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
*
281608 GGCATGAAAGGATGACATAATTGAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * * *
281653 AGCATGAAAGGATGCCAAAATTGAAATACATATGGGTACATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * * * *
281698 GGCTTGAAATGATGCCATGATTAAAATGCATATGGGTGCATTATT
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * *
281743 GGCATGAAAGAATGTCATAAATGAAAATGCATAAT-GGTGCAT
1 GGCATGAAAGGATGCCATAATTG-AAATGCAT-ATGGGTGCAT
281785 AATAAGTATG
Statistics
Matches: 344, Mismatches: 55, Indels: 5
0.85 0.14 0.01
Matches are distributed among these distances:
44 2 0.01
45 325 0.94
46 15 0.04
47 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.28
Consensus pattern (45 bp):
GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
Found at i:281988 original size:2 final size:2
Alignment explanation
Indices: 281981--282011 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
281971 TGACATACTT
281981 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 T
282012 TTCTTTACAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:283512 original size:2 final size:2
Alignment explanation
Indices: 283505--283548 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
283495 ATGTCAAAAG
283505 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
283546 AT A
1 AT A
283549 ACTTTTATGT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:283623 original size:106 final size:106
Alignment explanation
Indices: 283512--283762 Score: 448
Period size: 106 Copynumber: 2.3 Consensus size: 106
283502 AAGATATATA
283512 TATATATATATATATATAATATATATATATATATATAACTTTTATGTTAATGTGATAGATACTCA
1 TATATATATATATATATAATATATATATATATATATAACTTTTATGTTAATGTGATAGATACTCA
283577 AATAATTAAAGTTGTTTGATAATTTCACAAAAATTTGGGAT
66 AATAATTAAAGTTGTTTGATAATTTCACAAAAATTTGGGAT
283618 TATATATATATATATATAATATATATATATATATATAACTTTTATGTTAATGTGATAGATACTCA
1 TATATATATATATATATAATATATATATATATATATAACTTTTATGTTAATGTGATAGATACTCA
283683 AATAATTAAAGTTGTTTGATAATTTCACAAAAATTTGGGAT
66 AATAATTAAAGTTGTTTGATAATTTCACAAAAATTTGGGAT
* * * *
283724 TATATATATGTCAGAAAGATATATATATATATATATATA
1 TATATATATAT-ATATATA-ATATATATATATATATATA
283763 TATATATATA
Statistics
Matches: 139, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
106 116 0.83
107 4 0.03
108 19 0.14
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (106 bp):
TATATATATATATATATAATATATATATATATATATAACTTTTATGTTAATGTGATAGATACTCA
AATAATTAAAGTTGTTTGATAATTTCACAAAAATTTGGGAT
Found at i:283625 original size:2 final size:2
Alignment explanation
Indices: 283618--283654 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
283608 AATTTGGGAT
283618 TA TA TA TA TA TA TA TA TA -A 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
283655 ACTTTTATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:283641 original size:17 final size:17
Alignment explanation
Indices: 283619--283652 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
283609 ATTTGGGATT
283619 ATATATATATATATATA
1 ATATATATATATATATA
283636 ATATATATATATATATA
1 ATATATATATATATATA
283653 TAACTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:283642 original size:19 final size:19
Alignment explanation
Indices: 283618--283655 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
283608 AATTTGGGAT
283618 TATATATATATATATATAA
1 TATATATATATATATATAA
283637 TATATATATATATATATAA
1 TATATATATATATATATAA
283656 CTTTTATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATATATATATATATATAA
Found at i:283747 original size:2 final size:2
Alignment explanation
Indices: 283742--283790 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
283732 TGTCAGAAAG
283742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
283784 AT AT AT A
1 AT AT AT A
283791 ACTTTTATGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:287702 original size:13 final size:13
Alignment explanation
Indices: 287684--287708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
287674 CCTCGATAGG
287684 GTATCGATACCAA
1 GTATCGATACCAA
287697 GTATCGATACCA
1 GTATCGATACCA
287709 TTCAATTTTA
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:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (13 bp):
GTATCGATACCAA
Found at i:290457 original size:18 final size:19
Alignment explanation
Indices: 290434--290473 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
290424 AGTATACTCA
290434 TATAGTACCGATACTAT-G
1 TATAGTACCGATACTATAG
*
290452 TATAGTATCGATACTATAG
1 TATAGTACCGATACTATAG
290471 TAT
1 TAT
290474 GGATACTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TATAGTACCGATACTATAG
Found at i:290471 original size:14 final size:14
Alignment explanation
Indices: 290452--290481 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
290442 CGATACTATG
290452 TATAGTATCGATAC
1 TATAGTATCGATAC
*
290466 TATAGTATGGATAC
1 TATAGTATCGATAC
290480 TA
1 TA
290482 CTTGTCATAG
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:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (14 bp):
TATAGTATCGATAC
Found at i:295801 original size:13 final size:13
Alignment explanation
Indices: 295783--295807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
295773 CCTCGATAGG
295783 GTATCGATACCAA
1 GTATCGATACCAA
295796 GTATCGATACCA
1 GTATCGATACCA
295808 TTCAATTTTA
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:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (13 bp):
GTATCGATACCAA
Found at i:303723 original size:21 final size:20
Alignment explanation
Indices: 303694--303749 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
303684 ATAAATCATA
303694 AAATATTATAATAATGATTCG
1 AAAT-TTATAATAATGATTCG
303715 AAATGTTATAATAATGATTCG
1 AAAT-TTATAATAATGATTCG
* *
303736 TAATTTAAAATAAT
1 AAATTTATAATAAT
303750 ACTAAAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 9 0.28
21 23 0.72
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (20 bp):
AAATTTATAATAATGATTCG
Found at i:311184 original size:19 final size:19
Alignment explanation
Indices: 311160--311204 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
311150 TGTTCCAGTA
311160 GTTCTTCATCTCATTGTCC
1 GTTCTTCATCTCATTGTCC
311179 GTTCTTCATCTCATTGTCC
1 GTTCTTCATCTCATTGTCC
311198 GTTCTTC
1 GTTCTTC
311205 CCGGCAACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.09, C:0.31, G:0.11, T:0.49
Consensus pattern (19 bp):
GTTCTTCATCTCATTGTCC
Found at i:314268 original size:15 final size:15
Alignment explanation
Indices: 314248--314287 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
314238 CTTTCAACGC
*
314248 TGGCCACTATTATGG
1 TGGCCACTACTATGG
314263 TGGCCACTACTATGG
1 TGGCCACTACTATGG
314278 TGGCCACTAC
1 TGGCCACTAC
314288 CCTCTGACCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.28
Consensus pattern (15 bp):
TGGCCACTACTATGG
Found at i:315722 original size:34 final size:33
Alignment explanation
Indices: 315684--315752 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 33
315674 AGATTGTTAC
315684 ATGTTACATAGTTCATTAGGTCA-TTGCATATTAT
1 ATGTTACATAGTTCATTAGGT-AGTTGCATA-TAT
**
315718 ATGTTATGTAGTTCATTAGGTAGTTGCATATAT
1 ATGTTACATAGTTCATTAGGTAGTTGCATATAT
315751 AT
1 AT
315753 TGCATATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 6 0.19
34 26 0.81
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (33 bp):
ATGTTACATAGTTCATTAGGTAGTTGCATATAT
Found at i:315768 original size:38 final size:34
Alignment explanation
Indices: 315691--315768 Score: 86
Period size: 34 Copynumber: 2.2 Consensus size: 34
315681 TACATGTTAC
*
315691 ATAGTTCATTAGGTCATTGCATATTATATGTTAT
1 ATAGTTCATTAGGTCATTGCATATTATATATTAT
*
315725 GTAGTTCATTAGGT-AGTTGCATATATATTGCATATTAT
1 ATAGTTCATTAGGTCA-TTGCATAT-TA-T--ATATTAT
315763 ATAGTT
1 ATAGTT
315769 TTGTTAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
33 1 0.03
34 21 0.58
35 2 0.06
36 1 0.03
38 11 0.31
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (34 bp):
ATAGTTCATTAGGTCATTGCATATTATATATTAT
Found at i:316371 original size:34 final size:34
Alignment explanation
Indices: 316328--316401 Score: 148
Period size: 34 Copynumber: 2.2 Consensus size: 34
316318 AGGATTACCA
316328 AAAATAAAGATCAATGCTGCAACTTAAAATAGAG
1 AAAATAAAGATCAATGCTGCAACTTAAAATAGAG
316362 AAAATAAAGATCAATGCTGCAACTTAAAATAGAG
1 AAAATAAAGATCAATGCTGCAACTTAAAATAGAG
316396 AAAATA
1 AAAATA
316402 TTTTAGCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.55, C:0.11, G:0.14, T:0.20
Consensus pattern (34 bp):
AAAATAAAGATCAATGCTGCAACTTAAAATAGAG
Found at i:327596 original size:48 final size:48
Alignment explanation
Indices: 327525--327620 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
327515 GGTAGACTTG
327525 TTATTGAGTGTGATAGTCTTGTTATGGTTAATTGGATTAAGAATTTGA
1 TTATTGAGTGTGATAGTCTTGTTATGGTTAATTGGATTAAGAATTTGA
327573 TTATTGAGTGTGATAGTCTTGTTATGGTTAATTGGATTAAGAATTTGA
1 TTATTGAGTGTGATAGTCTTGTTATGGTTAATTGGATTAAGAATTTGA
327621 GGGTTGTCCG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.46
Consensus pattern (48 bp):
TTATTGAGTGTGATAGTCTTGTTATGGTTAATTGGATTAAGAATTTGA
Found at i:330911 original size:53 final size:53
Alignment explanation
Indices: 330827--331043 Score: 298
Period size: 53 Copynumber: 4.2 Consensus size: 53
330817 TTTCTAGGTA
* * * *
330827 CTAAGATATTGAGAGATGTACATACTTACACCAGTATAAATATGCGTTAATTG
1 CTAAGATATTGAGAGATGTACATACTTACACCGGTGTAAGTATGTGTTAATTG
* *
330880 CTACGATATTGAGAGATGTACATACTTACACCGGTGTAAGTATGTGTTGATTG
1 CTAAGATATTGAGAGATGTACATACTTACACCGGTGTAAGTATGTGTTAATTG
* * * * *
330933 CTAAGGTATTGCGAAATGTACATACTTACACCGGTGCAAGTATATGTTAATTG
1 CTAAGATATTGAGAGATGTACATACTTACACCGGTGTAAGTATGTGTTAATTG
*
330986 CTAAGATATTGAGAGATGTACATAC--AC-CAGG-GTAAGTATGTGTTAATTG
1 CTAAGATATTGAGAGATGTACATACTTACACCGGTGTAAGTATGTGTTAATTG
331035 CTAAGATAT
1 CTAAGATAT
331044 GATAATCGTT
Statistics
Matches: 145, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
49 25 0.17
50 3 0.02
51 2 0.01
53 115 0.79
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (53 bp):
CTAAGATATTGAGAGATGTACATACTTACACCGGTGTAAGTATGTGTTAATTG
Found at i:335252 original size:32 final size:32
Alignment explanation
Indices: 335206--335273 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 32
335196 TATGTGAGTG
*
335206 AAGACTCTGCTTAACCTATGGACAAAAATTTA
1 AAGACTCTGCTTAACCTATGAACAAAAATTTA
*
335238 AAGACTCT-CGTTAACCTATGAACAACAATTTA
1 AAGACTCTGC-TTAACCTATGAACAAAAATTTA
335270 AAGA
1 AAGA
335274 GACCATTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 1 0.03
32 32 0.97
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (32 bp):
AAGACTCTGCTTAACCTATGAACAAAAATTTA
Found at i:335929 original size:17 final size:18
Alignment explanation
Indices: 335890--335938 Score: 82
Period size: 17 Copynumber: 2.8 Consensus size: 18
335880 TATTTCTGAG
335890 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
335908 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
335925 GGAATTGGAATCTG
1 GGAATTGGAATCTG
335939 AATCTGAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 15 0.50
18 15 0.50
ACGTcount: A:0.31, C:0.08, G:0.33, T:0.29
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:344009 original size:1 final size:1
Alignment explanation
Indices: 343999--344159 Score: 142
Period size: 1 Copynumber: 161.0 Consensus size: 1
343989 CCATCAGGGG
* * * * * * *
343999 AAAAAGAAAAAGAAAAGAAAAAAGAAAAAAAAGAAAAAAAAGAAAAAAAAGAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * ** *
344064 AAAAAAAAGAAAAAAAGAAAAAAAGAAAAAAAGAAAAAAAGAAAAAAAAAGGAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * * *
344129 AAGGAAAAAAAAAGAAATAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
344160 GAAATTGAAT
Statistics
Matches: 124, Mismatches: 36, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
1 124 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.01
Consensus pattern (1 bp):
A
Found at i:344029 original size:8 final size:8
Alignment explanation
Indices: 343999--344159 Score: 175
Period size: 8 Copynumber: 19.2 Consensus size: 8
343989 CCATCAGGGG
343999 AAAAAGAA
1 AAAAAGAA
*
344007 AAAGAAAAGA
1 AAA-AAGA-A
344017 AAAAAGAAA
1 AAAAAG-AA
344026 AAAAAGAAA
1 AAAAAG-AA
344035 AAAAAGAAA
1 AAAAAG-AA
344044 AAAAAGAA
1 AAAAAGAA
344052 AAAAA-AA
1 AAAAAGAA
*
344059 AAAAAAAA
1 AAAAAGAA
344067 AAAAAGAA
1 AAAAAGAA
344075 AAAAAGAA
1 AAAAAGAA
344083 AAAAAGAA
1 AAAAAGAA
344091 AAAAAGAA
1 AAAAAGAA
344099 AAAAAGAAAA
1 AAAAAG--AA
*
344109 AAAAAGGA
1 AAAAAGAA
344117 AAAAAGAAA
1 AAAAAG-AA
344126 AAAAAGGAA
1 AAAAA-GAA
344135 AAAAA-AA
1 AAAAAGAA
*
344142 GAAATA-AA
1 -AAAAAGAA
344150 AAAAAGAA
1 AAAAAGAA
344158 AA
1 AA
344160 GAAATTGAAT
Statistics
Matches: 136, Mismatches: 7, Indels: 20
0.83 0.04 0.12
Matches are distributed among these distances:
7 13 0.10
8 66 0.49
9 43 0.32
10 14 0.10
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.01
Consensus pattern (8 bp):
AAAAAGAA
Found at i:344030 original size:9 final size:9
Alignment explanation
Indices: 343999--344163 Score: 181
Period size: 9 Copynumber: 19.0 Consensus size: 9
343989 CCATCAGGGG
343999 AAAAAGAAA
1 AAAAAGAAA
*
344008 AAGAAA-AGA
1 AA-AAAGAAA
344017 AAAAAGAAA
1 AAAAAGAAA
344026 AAAAAGAAA
1 AAAAAGAAA
344035 AAAAAGAAA
1 AAAAAGAAA
344044 AAAAAG--A
1 AAAAAGAAA
344051 AAAAA-AAA
1 AAAAAGAAA
344059 AAAAA-AAA
1 AAAAAGAAA
344067 AAAAAG-AA
1 AAAAAGAAA
344075 AAAAAG-AA
1 AAAAAGAAA
344083 AAAAAG-AA
1 AAAAAGAAA
344091 AAAAAG-AA
1 AAAAAGAAA
344099 AAAAAGAAA
1 AAAAAGAAA
*
344108 AAAAA-AGGA
1 AAAAAGA-AA
344117 AAAAAGAAA
1 AAAAAGAAA
344126 AAAAAGGAAAA
1 AAAAA-G-AAA
344137 AAAAAGAAA
1 AAAAAGAAA
344146 TAAAAA-AAA
1 -AAAAAGAAA
*
344155 GAAAAGAAA
1 AAAAAGAAA
344164 TTGAATTAAG
Statistics
Matches: 139, Mismatches: 5, Indels: 24
0.83 0.03 0.14
Matches are distributed among these distances:
7 6 0.04
8 54 0.39
9 60 0.43
10 11 0.08
11 8 0.06
ACGTcount: A:0.87, C:0.00, G:0.12, T:0.01
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:346177 original size:29 final size:29
Alignment explanation
Indices: 346144--346302 Score: 81
Period size: 29 Copynumber: 5.2 Consensus size: 29
346134 TCCTCAGTAG
346144 AGTCAATATTTGACTCCCTCGTGAAGAGA
1 AGTCAATATTTGACTCCCTCGTGAAGAGA
* ** * * *
346173 AGTCAACATTTGTTATTTCTGGCTCCTCAATAG-
1 AGTCAATATTTG--A---CTCCCTCGTGAAGAGA
*
346206 AGTCAATATTTGACTCCCTCGTGAAAAGA
1 AGTCAATATTTGACTCCCTCGTGAAGAGA
* * * * *
346235 AGTCAACATTTATTATTCCCGACTCCT-CAGTAG-
1 AGTCAATA-TT-TGACT-CC--CTCGTGAAG-AGA
*
346268 AGTCAATATTTGACTTCCTCGTGAAGAGA
1 AGTCAATATTTGACTCCCTCGTGAAGAGA
346297 AGTCAA
1 AGTCAA
346303 CCTTTATTAT
Statistics
Matches: 92, Mismatches: 24, Indels: 28
0.64 0.17 0.19
Matches are distributed among these distances:
28 16 0.17
29 26 0.28
30 3 0.03
31 8 0.09
32 4 0.04
33 19 0.21
34 16 0.17
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (29 bp):
AGTCAATATTTGACTCCCTCGTGAAGAGA
Found at i:346450 original size:62 final size:62
Alignment explanation
Indices: 346017--346440 Score: 607
Period size: 62 Copynumber: 6.8 Consensus size: 62
346007 TCTTGTTTCC
* * *
346017 TAGAATCAATTTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTTAG
1 TAGAGTCAATATTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
* * *
346079 TAGAATCAATTTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGAATCCTCAG
1 TAGAGTCAATATTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
* * * * *
346141 TAGAGTCAATATTTGACTCCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGGCTCCTCAA
1 TAGAGTCAATATTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
* * * * *
346203 TAGAGTCAATATTTGACTCCCTCGTGAAAAGAAGTCAACATTTATTATTCCCGACTCCTCAG
1 TAGAGTCAATATTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
346265 TAGAGTCAATATTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
1 TAGAGTCAATATTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
** * * * *
346327 TAGAGTCAATATTTGACTTCCTAATGAAGATAAGTCAACATTTATTATTCCTGACTCCCCAG
1 TAGAGTCAATATTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
* * *
346389 TAGAGTCAA-ATTTTGACTTCATCGTGAAGATAAGTTAACCTTTATTATTTCT
1 TAGAGTCAATA-TTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCT
346441 TATTCCCCAG
Statistics
Matches: 328, Mismatches: 33, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
61 1 0.00
62 327 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (62 bp):
TAGAGTCAATATTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
Found at i:346676 original size:36 final size:36
Alignment explanation
Indices: 346625--347177 Score: 881
Period size: 36 Copynumber: 15.4 Consensus size: 36
346615 TCTTATTTCA
346625 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
1 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
*
346661 ATCTTAGCCTTCACGGAAGAGTAGTGAAGCAAAGCC
1 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
* * *
346697 ATCTTAGCCTTCACGGAAGAGTACTGAAGCAAAGCA
1 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
* *
346733 ATCTTAGCCTCCACGGAAGAGTACTGAAGCAAAGCA
1 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
346769 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
1 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
* *
346805 ATCTTAGCCTTCACGGAAGTGTAGTGAAGCAAAGCC
1 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
*
346841 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCA
1 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
*
346877 ATCTTAGCCTCCATGGAAGAGTAGTGAAGCAAAGCC
1 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
* *
346913 ATCTTAGCCTTCACGGAAGAGTAATGAAGCAAAGCC
1 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
*
346949 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCA
1 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
*
346985 ATCTTAGCCTCCACGAAAGAGTAGTGAAGCAAAGCC
1 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
* *
347021 ATCTTACCCTTCACGGAAGAGTAGTGAAGCAAAGCC
1 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
*
347057 ATCTTAGCCTCCATGGAAGAGTAGTGAAGCAAAGCC
1 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
* *
347093 ATCATAGCCTCCACAGAAGAGTAGTGAAGCAAAGCC
1 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
* * ** *
347129 ATCCTAGGCTCCACATAAGAGTAGTGAAGCAAAGCA
1 ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
*
347165 ATCTTAGCATCCA
1 ATCTTAGCCTCCA
347178 TAAGAGAGGA
Statistics
Matches: 480, Mismatches: 37, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 480 1.00
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (36 bp):
ATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCC
Found at i:347336 original size:19 final size:19
Alignment explanation
Indices: 347308--347353 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
347298 TATGTTATCT
*
347308 CAGATATCTTAAAGATGGC
1 CAGATGTCTTAAAGATGGC
347327 CAGATGTCTTAAAGATGGC
1 CAGATGTCTTAAAGATGGC
347346 CAGATGTC
1 CAGATGTC
347354 CTCATCACGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (19 bp):
CAGATGTCTTAAAGATGGC
Found at i:347586 original size:137 final size:137
Alignment explanation
Indices: 347335--348062 Score: 1093
Period size: 137 Copynumber: 5.3 Consensus size: 137
347325 GCCAGATGTC
* *
347335 TTAAAGATGGCCAGATGTCCTCATCACGAAGGAACAATGTCATCTACCAATCAGAACTCTTCATC
1 TTAAAGATGGACAGATGTCCTCATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATC
*
347400 ACGAAGGAGTCGAT-TCATCCTTAGATAACCAGACATCCTCATCATGAAGGAACTATGTTATCTC
66 ACGAAGGAGTCG-TGTCATCCTTAGATAACCAGACATCCTCATCACGAAGGAACTATGTTATCTC
*
347464 AAATATAT
130 AAATATCT
*
347472 TTAAAGATGGACAGATATCCTCATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATC
1 TTAAAGATGGACAGATGTCCTCATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATC
* *
347537 ACGAAGGAGTTGTGTCATCCTTAAATAACCAGACATCCTCATCACGAAGGAACTATGTTATCTCA
66 ACGAAGGAGTCGTGTCATCCTTAGATAACCAGACATCCTCATCACGAAGGAACTATGTTATCTCA
347602 AATATCT
131 AATATCT
* * * * *
347609 TTAAAGAT-GACCATACGTCCTCATCACGAAGGAACAAAGTCATCTACCAATCAAAACTCTTCAT
1 TTAAAGATGGA-CAGATGTCCTCATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCAT
**
347673 CACTTAGGAGTCGTGTCATCCTTAGATAACCAGACATCCTCATCACGAAGGAACTATGTTATCTC
65 CACGAAGGAGTCGTGTCATCCTTAGATAACCAGACATCCTCATCACGAAGGAACTATGTTATCTC
*
347738 AAATATAT
130 AAATATCT
*
347746 TTAAAGATGGTCAGATGTCCTCATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATC
1 TTAAAGATGGACAGATGTCCTCATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATC
347811 ACGAAGGAGTCGTGTCATCCTTAGATAACCAGACATCCTCATCACGAAGGAACTATGTTATCTCA
66 ACGAAGGAGTCGTGTCATCCTTAGATAACCAGACATCCTCATCACGAAGGAACTATGTTATCTCA
347876 AATATCT
131 AATATCT
* *
347883 TTAAAGAT-GACCAGATGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCAT
1 TTAAAGATGGA-CAGATGTCCTCATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCAT
* * * * ** * ** **
347947 CACGTAGGAGCCGAGTTATTATTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTC
65 CACGAAGGAGTCGTGTCATCCTTAGATAACCAGACATCCTCATCACGAAGGAACTATGTTATCTC
348012 AAATATCT
130 AAATATCT
* * * * * *
348020 TCAAATATGGCCAGACGTCCTCATCATGAAGGAATAATGTCAT
1 TTAAAGATGGACAGATGTCCTCATCACGAAGGAACAATGTCAT
348063 ACACCAGTTG
Statistics
Matches: 539, Mismatches: 47, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
136 4 0.01
137 533 0.99
138 2 0.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (137 bp):
TTAAAGATGGACAGATGTCCTCATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATC
ACGAAGGAGTCGTGTCATCCTTAGATAACCAGACATCCTCATCACGAAGGAACTATGTTATCTCA
AATATCT
Found at i:349509 original size:20 final size:20
Alignment explanation
Indices: 349467--349514 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
349457 TTCTTAAAAT
*
349467 AAAATAAT-ATAATGAATAG
1 AAAATAATAATAATGAACAG
*
349486 AAAAATAATAATAAT-AACAT
1 -AAAATAATAATAATGAACAG
349506 AAAATAATA
1 AAAATAATA
349515 TCATTATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.36
20 11 0.44
21 5 0.20
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (20 bp):
AAAATAATAATAATGAACAG
Found at i:350985 original size:20 final size:20
Alignment explanation
Indices: 350960--351047 Score: 59
Period size: 20 Copynumber: 4.0 Consensus size: 20
350950 AATAAAGTTA
350960 AAATAATTTAATTTTTAATT
1 AAATAATTTAATTTTTAATT
** * *
350980 AAATAATTTGGTTTATAATG
1 AAATAATTTAATTTTTAATT
*
351000 AAAAACATTTTATATTTTTAAATAATT
1 AAATA-A-TTTA-A-TTTT---TAATT
*
351027 TAATAATTTAATTTTTAATT
1 AAATAATTTAATTTTTAATT
351047 A
1 A
351048 TACAATATAT
Statistics
Matches: 49, Mismatches: 12, Indels: 14
0.65 0.16 0.19
Matches are distributed among these distances:
20 25 0.51
21 1 0.02
22 3 0.06
23 4 0.08
24 4 0.08
25 4 0.08
26 1 0.02
27 7 0.14
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (20 bp):
AAATAATTTAATTTTTAATT
Found at i:353688 original size:45 final size:43
Alignment explanation
Indices: 353632--353753 Score: 111
Period size: 45 Copynumber: 2.7 Consensus size: 43
353622 GCTAAAGTTC
* *
353632 GCGGTGTTTG-TTAACAAAAAACGTCGCAATAGGTAAAGATATATA
1 GCGGCGTTTGTTTAA-AAAAAAC--CGCAATAAGTAAAGATATATA
* ** *
353677 GCGGCGTTTGTTTAAAAAACACCGCAATAAGTATTGATATTTA
1 GCGGCGTTTGTTTAAAAAAAACCGCAATAAGTAAAGATATATA
* **
353720 GCGGCGTTTTTTTTAAACAAACGCCGCAATAAGT
1 GCGGCG-TTTGTTTAAA-AAAAACCGCAATAAGT
353754 TCTGATAGGC
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
43 23 0.35
44 9 0.14
45 30 0.45
46 4 0.06
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (43 bp):
GCGGCGTTTGTTTAAAAAAAACCGCAATAAGTAAAGATATATA
Found at i:353696 original size:43 final size:44
Alignment explanation
Indices: 353647--353753 Score: 135
Period size: 43 Copynumber: 2.4 Consensus size: 44
353637 GTTTGTTAAC
* *
353647 AAAAAACGTCGCAATAGGTAAAGATATATAGCGGCG-TTTGTTT
1 AAAAAACGCCGCAATAAGTAAAGATATATAGCGGCGTTTTGTTT
* ** * *
353690 AAAAAACACCGCAATAAGTATTGATATTTAGCGGCGTTTTTTTT
1 AAAAAACGCCGCAATAAGTAAAGATATATAGCGGCGTTTTGTTT
353734 AAACAAACGCCGCAATAAGT
1 AAA-AAACGCCGCAATAAGT
353754 TCTGATAGGC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
43 30 0.56
44 9 0.17
45 15 0.28
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (44 bp):
AAAAAACGCCGCAATAAGTAAAGATATATAGCGGCGTTTTGTTT
Found at i:353760 original size:45 final size:43
Alignment explanation
Indices: 353669--353753 Score: 125
Period size: 45 Copynumber: 1.9 Consensus size: 43
353659 AATAGGTAAA
353669 GATATATAGCGGCGTTTGTTTAAAAAACACCGCAATAAGTATT
1 GATATATAGCGGCGTTTGTTTAAAAAACACCGCAATAAGTATT
* * *
353712 GATATTTAGCGGCGTTTTTTTTAAACAAACGCCGCAATAAGT
1 GATATATAGCGGCG-TTTGTTTAAA-AAACACCGCAATAAGT
353754 TCTGATAGGC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 13 0.35
44 9 0.24
45 15 0.41
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (43 bp):
GATATATAGCGGCGTTTGTTTAAAAAACACCGCAATAAGTATT
Found at i:353801 original size:82 final size:80
Alignment explanation
Indices: 353679--353840 Score: 191
Period size: 82 Copynumber: 2.0 Consensus size: 80
353669 GATATATAGC
* * *
353679 GGCGTTTGTTTAAAAAACACCGCAATAAGTATTGATATTTAGCGGCGTTTTTTTTAAACAAACGC
1 GGCGTTTGTTTAAAAAACACCGCAATAAGTATTGAGATTTAGCGGC-CTTTTTAT-AACAAACGC
*
353744 CGCAATAAGTTCTGATA
64 AGCAATAAGTTCTGATA
* * * * * *
353761 GGCGTTTGTCTT-AAAAACGCCTCAATAGGTGTTGAGATTTAGTGGCCTTTTTATCACAAACGCA
1 GGCGTTTGT-TTAAAAAACACCGCAATAAGTATTGAGATTTAGCGGCCTTTTTATAACAAACGCA
*
353825 GCAATAAGTTTTGATA
65 GCAATAAGTTCTGATA
353841 TTTAGTGGCG
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
80 23 0.34
81 6 0.09
82 37 0.54
83 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (80 bp):
GGCGTTTGTTTAAAAAACACCGCAATAAGTATTGAGATTTAGCGGCCTTTTTATAACAAACGCAG
CAATAAGTTCTGATA
Found at i:354373 original size:21 final size:21
Alignment explanation
Indices: 354348--354397 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
354338 ATTCTTCACA
354348 TCTCTGCTGATAT-GTTGCTTC
1 TCTCTG-TGATATCGTTGCTTC
* *
354369 TCTCTGTGTTGTCGTTGCTTC
1 TCTCTGTGATATCGTTGCTTC
354390 TCTCTGTG
1 TCTCTGTG
354398 CTGCTGTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.04, C:0.24, G:0.22, T:0.50
Consensus pattern (21 bp):
TCTCTGTGATATCGTTGCTTC
Found at i:354406 original size:21 final size:20
Alignment explanation
Indices: 354360--354406 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
354350 TCTGCTGATA
*
354360 TGTTGCTTCTCTCTGTGTTG
1 TGTTGCTTCTCTCTGTGCTG
354380 TCGTTGCTTCTCTCTGTGCTG
1 T-GTTGCTTCTCTCTGTGCTG
354401 CTGTTG
1 -TGTTG
354407 TTTCCCTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.00, C:0.23, G:0.26, T:0.51
Consensus pattern (20 bp):
TGTTGCTTCTCTCTGTGCTG
Found at i:361193 original size:42 final size:42
Alignment explanation
Indices: 361158--361281 Score: 169
Period size: 42 Copynumber: 2.9 Consensus size: 42
361148 GCGTTTTACA
*
361158 TATAAACGCCTCTAATTTACCATTCTATTACGGCGTTTGTGG
1 TATAAACGCCTCTAATTTACCACTCTATTACGGCGTTTGTGG
* *
361200 TATAAACG-CTGCTAATTTACCACTATATTGCGGCGTTTGTGG
1 TATAAACGCCT-CTAATTTACCACTCTATTACGGCGTTTGTGG
* * *
361242 TATAAACGCCGCTACTTTAACACTCTATTACGGCGCTTTG
1 TATAAACGCCTCTAATTTACCACTCTATTACGGCG-TTTG
361282 GCTAAAACGT
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
41 2 0.03
42 64 0.90
43 5 0.07
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (42 bp):
TATAAACGCCTCTAATTTACCACTCTATTACGGCGTTTGTGG
Done.