Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008283.1 Hibiscus syriacus cultivar Beakdansim tig00110945_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: 2862730
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 14
Found at i:218154 original size:79 final size:79
Alignment explanation
Indices: 218019--218252 Score: 337
Period size: 79 Copynumber: 3.0 Consensus size: 79
218009 AAACCAATGA
*
218019 ATAAAAGAATAATGCATATGGGTGCATTAAT-GCATGAAAGGATGCCTTGGCTGATATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCCTTAGCTGATATGTATATG
218083 GGTACATTATCAGC
66 GGTACATTATCAGC
* * * *
218097 ATAACAGAATAATGCATATGGGTGTATTAGTGGCATGAAAGGATGCCTTAGCAGATATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCCTTAGCTGATATGTATATG
218162 GGTACATTATCAGC
66 GGTACATTATCAGC
* * * * * *
218176 ATAAAAGAATAATGCATATTGGTGCATTATTGGCATGACAA-GATGCCATAGTTGAAATGCATAT
1 ATAAAAGAATAATGCATATGGGTGCATTAATGGCATGA-AAGGATGCCTTAGCTGATATGTATAT
*
218240 GGGTGCATTATCA
65 GGGTACATTATCA
218253 ACAGGAAAGT
Statistics
Matches: 139, Mismatches: 15, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
78 28 0.20
79 109 0.78
80 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCCTTAGCTGATATGTATATG
GGTACATTATCAGC
Found at i:218464 original size:45 final size:44
Alignment explanation
Indices: 218225--218463 Score: 255
Period size: 45 Copynumber: 5.3 Consensus size: 44
218215 AAGATGCCAT
* *
218225 AGTTGAAATGCATATGGGTGCATTATCAACAGGAAAGTATACTAG
1 AGTTGAAATGCATATGGGTGCATTATCAACA-GAAAATATACTAA
* *
218270 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATGCTAG
1 AGTTGAAATGCATATGGGTGCATTATCAACAG-AAAATATACTAA
* * ** *
218315 AGTTGAAATGTATATGAGCACATTATCAACAGAAAAGTATACTAT
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAA-TATACTAA
* * * * *
218360 GGTTGAAATGTATATGGGTACATTATCTACATAAAAGTATACTATA
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAA-TATACTA-A
* **
218406 A-TTGAAATGCATAAGGGTGCATTATCAACAGAAAATATGTTAA
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAATATACTAA
*
218449 AGTTTAAAATGCATA
1 AG-TTGAAATGCATA
218464 ATGATGTATT
Statistics
Matches: 166, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
43 2 0.01
44 10 0.06
45 154 0.93
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.29
Consensus pattern (44 bp):
AGTTGAAATGCATATGGGTGCATTATCAACAGAAAATATACTAA
Found at i:219120 original size:2 final size:2
Alignment explanation
Indices: 219113--219139 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
219103 TGAAGGGATG
219113 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 A
219140 ATGTATAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:222981 original size:19 final size:22
Alignment explanation
Indices: 222957--223011 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
222947 ATCTAATTTA
222957 GGTATTGATACCA-AG-AT-GG
1 GGTATTGATACCATAGCATAGG
222976 GGTATT-AGTACCATAGCATAGG
1 GGTATTGA-TACCATAGCATAGG
*
222998 GGTATCGATACCAT
1 GGTATTGATACCAT
223012 GGTGAGGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 1 0.03
19 11 0.37
20 2 0.07
21 2 0.07
22 13 0.43
23 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (22 bp):
GGTATTGATACCATAGCATAGG
Found at i:223572 original size:45 final size:44
Alignment explanation
Indices: 223507--223645 Score: 113
Period size: 45 Copynumber: 3.3 Consensus size: 44
223497 AGAATAATGC
*
223507 ATATGGGTGCATTAATGGCATGAAAGGATGCCTTAACTAATATGT
1 ATATGGGTACATT-ATGGCATGAAAGGATGCCTTAACTAATATGT
*
223552 ATATGGGTACATTATCGGCAT---A--A---C--AA--AATAATGC
1 ATATGGGTACATTAT-GGCATGAAAGGATGCCTTAACTAAT-ATGT
* * *
223586 ATATGGATGCATTAGTGACATGAAAGGATGCCTTAACTAATATGT
1 ATATGGGTACATTA-TGGCATGAAAGGATGCCTTAACTAATATGT
223631 ATATGGGTACATTAT
1 ATATGGGTACATTAT
223646 CAGCATAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 31
0.65 0.07 0.28
Matches are distributed among these distances:
33 3 0.04
34 19 0.27
35 3 0.04
37 2 0.03
39 1 0.01
40 1 0.01
42 2 0.03
44 5 0.07
45 32 0.45
46 3 0.04
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.31
Consensus pattern (44 bp):
ATATGGGTACATTATGGCATGAAAGGATGCCTTAACTAATATGT
Found at i:223630 original size:79 final size:81
Alignment explanation
Indices: 223497--223698 Score: 327
Period size: 79 Copynumber: 2.5 Consensus size: 81
223487 AATGAATAAA
223497 AGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCCTTAACTAATATGTATATGGGTAC
1 AGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCCTTAACTAATATGTATATGGGTAC
* *
223562 ATTATCGGCATAACA-
66 ATTATCAGCATAAAAG
* * *
223577 A-AATAATGCATATGGATGCATTAGTGACATGAAAGGATGCCTTAACTAATATGTATATGGGTAC
1 AGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCCTTAACTAATATGTATATGGGTAC
223641 ATTATCAGCATAAAAG
66 ATTATCAGCATAAAAG
* *
223657 AGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCC
1 AGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCC
223699 ATAGTTGAAA
Statistics
Matches: 111, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
79 73 0.66
80 2 0.02
81 36 0.32
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (81 bp):
AGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCCTTAACTAATATGTATATGGGTAC
ATTATCAGCATAAAAG
Found at i:223726 original size:45 final size:45
Alignment explanation
Indices: 223662--223917 Score: 298
Period size: 45 Copynumber: 5.7 Consensus size: 45
223652 AAAAGAGAAT
*** * * *
223662 AATGCATATGGGTGCATTATTGGCATGAAATG-ATGCCATAGTTGA
1 AATGCATATGGGTGCATTATCAACA-GAAAAGTATACTATAGTTGA
* * * *
223707 AATGCATATGGGTGCATTATAAAAAGGAAAGTATACTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* * * *
223752 AATGCATGTGGGTGCATTATCAACAGAAACGTATGCTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* * *
223797 AATGTATATGGGTACATTATCAACAGAAAAGTATACTATGGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* * ** *
223842 AATGTATATGGGTACATTATCTGCATAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
223887 AATGCATATGGGTGCATTATCAACAGAAAAG
1 AATGCATATGGGTGCATTATCAACAGAAAAG
223918 ATGTTAAAGT
Statistics
Matches: 179, Mismatches: 31, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
44 4 0.02
45 175 0.98
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
Found at i:223951 original size:90 final size:88
Alignment explanation
Indices: 223699--223951 Score: 247
Period size: 90 Copynumber: 2.8 Consensus size: 88
223689 AAATGATGCC
* * * * *
223699 ATAGTTGAAATGCATATGGGTGCATTATAAAAAGGAAAGTATACTAGAGTTGAAATGCATGTGGG
1 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAAAGTTGAAATGCATAT--G
* * *
223764 TGCATTATCAACAGAAACGTATGCT
64 TGTATTATCAACAGAAAAGTATACT
* * * ** * *
223789 AGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATGGG
1 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAAAGTTGAAATGCATATGTG
** *
223854 TACATTATCTGCATAAAAGTATACT
66 T--ATTATCAACAGAAAAGTATACT
** *
223879 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG-ATGTTAAAGTTTAAAATGCATAATG
1 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAAAG-TTGAAATGCAT-ATG
223943 ATGTATTAT
64 -TGTATTAT
223952 AAATATAAAT
Statistics
Matches: 131, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
88 2 0.02
89 5 0.04
90 119 0.91
91 3 0.02
92 2 0.02
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (88 bp):
ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAAAGTTGAAATGCATATGTG
TATTATCAACAGAAAAGTATACT
Found at i:224532 original size:81 final size:81
Alignment explanation
Indices: 224388--224540 Score: 200
Period size: 81 Copynumber: 1.9 Consensus size: 81
224378 ATGCCCTAGA
** *
224388 TGTGCAATTGACAGAAAAGTGTCAAATATGCCAGTTAGATGAACAGTTAAGTATCGTTGAGTAAA
1 TGTGCAATTGACAGAAAAGTGTCAAATATGCCAGTTAGATGAACAGTTAACAATCGTTAAGTAAA
224453 AGAATAATGGTCTAAC
66 AGAATAATGGTCTAAC
* * * * **
224469 TGTGCAATTGGCAGAAATGTGTCAATTATGCTAGTTAGATGAAGGGTTAAACAAT-GTTAAGTAA
1 TGTGCAATTGACAGAAAAGTGTCAAATATGCCAGTTAGATGAACAGTT-AACAATCGTTAAGTAA
*
224533 GAGAATAA
65 AAGAATAA
224541 ATGAATTTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
81 57 0.93
82 4 0.07
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.28
Consensus pattern (81 bp):
TGTGCAATTGACAGAAAAGTGTCAAATATGCCAGTTAGATGAACAGTTAACAATCGTTAAGTAAA
AGAATAATGGTCTAAC
Found at i:224601 original size:2 final size:2
Alignment explanation
Indices: 224594--224624 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
224584 TGAAGGGATG
224594 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
224625 ATGTATAACT
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:232256 original size:13 final size:13
Alignment explanation
Indices: 232238--232269 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
232228 GACCTTTTGT
232238 ATTTGCATTTAGC
1 ATTTGCATTTAGC
232251 ATTTGCA-TTAGC
1 ATTTGCATTTAGC
232263 A-TTGCAT
1 ATTTGCAT
232270 ATATTCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 6 0.33
13 7 0.39
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTTGCATTTAGC
Found at i:237074 original size:37 final size:37
Alignment explanation
Indices: 237023--237404 Score: 276
Period size: 37 Copynumber: 10.1 Consensus size: 37
237013 GTCCTTCGGG
*
237023 CCATCTAAAGCCTTCACAGAAGAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAAT
* * *
237060 CCATCATAACCCTTCACGGAAGAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAAT
* * * ****
237097 CCATCAGTAAGCCTTC-CGAGCATGACG-A-TTAAGTCCTCGGG
1 CCATC-TTAAGCCTTCAC-AG-AAGA-GTAGTGAAG--C-AAAT
* *
237138 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAGT
1 CCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAAT
* * * *
237175 CAATATTAAGCCTTCACCGAAGAGTAGTAAAGCAAAT
1 CCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAAT
*
237212 CAATCTTAAGCCTTCACCA-AAGAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCA-CAGAAGAGTAGTGAAGCAAAT
* * * * * ***
237249 CCATCAGTAAGTCTTC-CAAGCATGA-TAATTAAGTCATCCGGG
1 CCATC-TTAAGCCTTCAC-AG-AAGAGTAGTGAAG-CA---AAT
*
237291 CCATCTTAAGCCTTCACCA-AAAAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCA-CAGAAGAGTAGTGAAGCAAAT
* *
237328 TCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAAT
* *
237365 CAATCTTAAGACTTCACCA-AAGAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCA-CAGAAGAGTAGTGAAGCAAAT
237402 CCA
1 CCA
237405 AGATTTGATA
Statistics
Matches: 268, Mismatches: 53, Indels: 48
0.73 0.14 0.13
Matches are distributed among these distances:
36 2 0.01
37 175 0.65
38 31 0.12
39 13 0.05
40 20 0.07
41 20 0.07
42 6 0.02
43 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (37 bp):
CCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAAT
Found at i:237189 original size:115 final size:116
Alignment explanation
Indices: 236982--237226 Score: 354
Period size: 115 Copynumber: 2.1 Consensus size: 116
236972 TACTTCGAGC
* *
236982 CAAT-AGTAAGCCTTCTGAGCATGAGGATTAAGTCCTTCGGGCCATCTAAAGCCTTCACAGAAGA
1 CAATCAGTAAGCCTTCCGAGCATGACGATTAAGTCCTTCGGGCCATCTAAAGCCTTCACAGAAGA
* * *
237046 GTAGTGAAGCAAATCCATCATAACCCTTCACGGAAGAGTAGTGAAGCAAAT
66 GTAGTGAAGCAAATCAATCATAACCCTTCACCGAAGAGTAGTAAAGCAAAT
* * *
237097 CCATCAGTAAGCCTTCCGAGCATGACGATTAAGTCC-TCGGGCCATCTTAAGCCTTCACCGAAGA
1 CAATCAGTAAGCCTTCCGAGCATGACGATTAAGTCCTTCGGGCCATCTAAAGCCTTCACAGAAGA
* *
237161 GTAGTGAAGCAAGTCAAT-ATTAAGCCTTCACCGAAGAGTAGTAAAGCAAAT
66 GTAGTGAAGCAAATCAATCA-TAACCCTTCACCGAAGAGTAGTAAAGCAAAT
*
237212 CAATC-TTAAGCCTTC
1 CAATCAGTAAGCCTTC
237227 ACCAAAGAGT
Statistics
Matches: 116, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
114 10 0.09
115 77 0.66
116 29 0.25
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (116 bp):
CAATCAGTAAGCCTTCCGAGCATGACGATTAAGTCCTTCGGGCCATCTAAAGCCTTCACAGAAGA
GTAGTGAAGCAAATCAATCATAACCCTTCACCGAAGAGTAGTAAAGCAAAT
Found at i:237308 original size:79 final size:78
Alignment explanation
Indices: 237060--237342 Score: 276
Period size: 78 Copynumber: 3.7 Consensus size: 78
237050 TGAAGCAAAT
* * ** * **
237060 CCATCATAACCCTTCACGGAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTCCGAGCATGACGA
1 CCATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTCCAAGCATGATAA
*
237125 TTAAGTCCTCGGG
66 TTAAGTCATCGGG
* * * *
237138 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAGTCAAT-ATTAAGCCTTCACCGAAG-A-G-
1 CCATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTT--CC-AAGCATGA
* * ***
237199 TAGTAAAG-CA--AAT
63 TAATTAAGTCATCGGG
* *
237212 CAATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCCATCAGTAAGTCTTCCAAGCATGATAA
1 CCATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTCCAAGCATGATAA
237277 TTAAGTCATCCGGG
66 TTAAGTCAT-CGGG
* * *
237291 CCATCTTAAGCCTTCACCAAAAAGTAGTGAAGCAAATTCATC-TTAAGCCTTC
1 CCATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTC
237343 ACCGAAGAGT
Statistics
Matches: 163, Mismatches: 31, Indels: 22
0.75 0.14 0.10
Matches are distributed among these distances:
72 3 0.02
73 3 0.02
74 38 0.23
75 14 0.09
76 3 0.02
77 13 0.08
78 45 0.28
79 42 0.26
80 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (78 bp):
CCATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTCCAAGCATGATAA
TTAAGTCATCGGG
Found at i:237363 original size:153 final size:151
Alignment explanation
Indices: 237024--237404 Score: 573
Period size: 153 Copynumber: 2.5 Consensus size: 151
237014 TCCTTCGGGC
* * * * * **
237024 CATCTAAAGCCTTCACAGAAGAGTAGTGAAGCAAATCCATCATAACCCTTCACGGAAGAGTAGTG
1 CATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCAAAGAGTAGTG
* * *
237089 AAGCAAATCCATCAGTAAGCCTTCCGAGCATGACGATTAAGTCCTCGGGCCATCTTAAGCCTTCA
66 AAGCAAATCCATCAGTAAGCCTTCCAAGCATGACAATTAAGTCATCGGGCCATCTTAAGCCTTCA
* *
237154 CCGAAGAGTAGTGAAGCAAGT
131 CCAAAAAGTAGTGAAGCAAGT
* *
237175 CAATATTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCAATCTTAAGCCTTCACCAAAGAGTAGT
1 C-ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCAAAGAGTAGT
* *
237240 GAAGCAAATCCATCAGTAAGTCTTCCAAGCATGATAATTAAGTCATCCGGGCCATCTTAAGCCTT
65 GAAGCAAATCCATCAGTAAGCCTTCCAAGCATGACAATTAAGTCAT-CGGGCCATCTTAAGCCTT
*
237305 CACCAAAAAGTAGTGAAGCAAATT
129 CACCAAAAAGTAGTGAAGC-AAGT
*
237329 CATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGACTTCACCAAAGAGTAGTG
1 CATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCAAAGAGTAGTG
237394 AAGCAAATCCA
66 AAGCAAATCCA
237405 AGATTTGATA
Statistics
Matches: 207, Mismatches: 20, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
151 1 0.00
152 95 0.46
153 107 0.52
154 4 0.02
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (151 bp):
CATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCAAAGAGTAGTG
AAGCAAATCCATCAGTAAGCCTTCCAAGCATGACAATTAAGTCATCGGGCCATCTTAAGCCTTCA
CCAAAAAGTAGTGAAGCAAGT
Found at i:239566 original size:16 final size:18
Alignment explanation
Indices: 239541--239574 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
239531 TATCCTTTCA
239541 TTTTCGCCAT-CATGTTT
1 TTTTCGCCATGCATGTTT
239558 TTTTC-CCATGCATGTTT
1 TTTTCGCCATGCATGTTT
239575 ATGTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.12, C:0.24, G:0.12, T:0.53
Consensus pattern (18 bp):
TTTTCGCCATGCATGTTT
Found at i:241540 original size:8 final size:8
Alignment explanation
Indices: 241523--241592 Score: 81
Period size: 8 Copynumber: 8.9 Consensus size: 8
241513 GCTTCTTGTC
*
241523 TTCTTGTT
1 TTCTTTTT
241531 TTCTTTTT
1 TTCTTTTT
241539 TTCTTTTT
1 TTCTTTTT
*
241547 CT-TTTTT
1 TTCTTTTT
241554 TTCTTTTT
1 TTCTTTTT
241562 TTCTTTCTT
1 TTCTTT-TT
*
241571 TACTTTTT
1 TTCTTTTT
*
241579 CTCTTTTT
1 TTCTTTTT
241587 TT-TTTT
1 TTCTTTT
241593 CTCTTGGCTT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
7 10 0.19
8 36 0.68
9 7 0.13
ACGTcount: A:0.01, C:0.14, G:0.01, T:0.83
Consensus pattern (8 bp):
TTCTTTTT
Found at i:241559 original size:23 final size:24
Alignment explanation
Indices: 241529--241594 Score: 86
Period size: 23 Copynumber: 2.8 Consensus size: 24
241519 TGTCTTCTTG
241529 TTTTCTTTTTTTCTTTTTCTTT-T
1 TTTTCTTTTTTTCTTTTTCTTTAT
241552 TTTTCTTTTTTTC--TTTCTTTACT
1 TTTTCTTTTTTTCTTTTTCTTTA-T
241575 TTTTCTCTTTTTT-TTTTTCT
1 TTTTCT-TTTTTTCTTTTTCT
241595 CTTGGCTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
21 7 0.18
23 20 0.53
24 6 0.16
25 5 0.13
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTCTTTTTTTCTTTTTCTTTAT
Found at i:241595 original size:14 final size:15
Alignment explanation
Indices: 241529--241597 Score: 88
Period size: 14 Copynumber: 4.6 Consensus size: 15
241519 TGTCTTCTTG
241529 TTTTCT-TTTTTTCT
1 TTTTCTCTTTTTTCT
*
241543 TTTTCTTTTTTTTCT
1 TTTTCTCTTTTTTCT
*
241558 TTTTTTCTTTCTTTACT
1 TTTTCTCTTT-TTT-CT
241575 TTTTCTCTTTTTT-T
1 TTTTCTCTTTTTTCT
241589 TTTTCTCTT
1 TTTTCTCTT
241598 GGCTTTGATT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
14 16 0.33
15 16 0.33
16 6 0.12
17 11 0.22
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCTCTTTTTTCT
Found at i:247822 original size:13 final size:13
Alignment explanation
Indices: 247804--247830 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
247794 ATGTATCACC
247804 ATTGACAAAATTG
1 ATTGACAAAATTG
247817 ATTGACAAAATTG
1 ATTGACAAAATTG
247830 A
1 A
247831 AATACGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (13 bp):
ATTGACAAAATTG
Found at i:252525 original size:13 final size:13
Alignment explanation
Indices: 252507--252532 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
252497 TAATACTAAC
252507 AGGGATTTAAATT
1 AGGGATTTAAATT
252520 AGGGATTTAAATT
1 AGGGATTTAAATT
252533 GTGGTTCAGA
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:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
AGGGATTTAAATT
Found at i:253314 original size:21 final size:22
Alignment explanation
Indices: 253275--253319 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
253265 ATTATATGTG
253275 AAATAAATATAAAAAAAAGTTA
1 AAATAAATATAAAAAAAAGTTA
*
253297 AAATAAATA-AAAATAAAGTTA
1 AAATAAATATAAAAAAAAGTTA
253318 AA
1 AA
253320 TACGACAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (22 bp):
AAATAAATATAAAAAAAAGTTA
Found at i:253357 original size:8 final size:8
Alignment explanation
Indices: 253339--253402 Score: 56
Period size: 8 Copynumber: 7.5 Consensus size: 8
253329 ATTAAAAGCA
253339 AAAAGAAAT
1 AAAA-AAAT
253348 AAAAAAAT
1 AAAAAAAT
253356 AAAATAAAAT
1 -AAA-AAAAT
*
253366 AAGAAAAT
1 AAAAAAAT
**
253374 ATTAAAAT
1 AAAAAAAT
253382 AAAAAAAT
1 AAAAAAAT
*
253390 GAATAAAAT
1 -AAAAAAAT
253399 AAAA
1 AAAA
253403 TAAAAAATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
8 24 0.53
9 16 0.36
10 5 0.11
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (8 bp):
AAAAAAAT
Found at i:253361 original size:5 final size:5
Alignment explanation
Indices: 253351--253407 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
253341 AAGAAATAAA
* *
253351 AAAAT AAAAT AAAAT AAGAA- AATATT AAAAT AAAAA AATGAAT AAAAT
1 AAAAT AAAAT AAAAT AA-AAT AA-AAT AAAAT AAAAT AA--AAT AAAAT
253399 AAAAT AAAA
1 AAAAT AAAA
253408 AATTTAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
5 35 0.81
6 4 0.09
7 4 0.09
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:253366 original size:45 final size:43
Alignment explanation
Indices: 253279--253407 Score: 118
Period size: 45 Copynumber: 2.9 Consensus size: 43
253269 TATGTGAAAT
* * * *
253279 AAATA-TAAAAAAAAGTTAAAATAAATAAAAATAAAGTTAAATACGA
1 AAATATTAAAAAAAA---AAAATGAA-AAAAATAAAATAAAATAAGA
*
253325 CAATATTAAAAGCAAAAAGAAAT-AAAAAAATAAAATAAAATAAGA
1 AAATATTAAAA--AAAAA-AAATGAAAAAAATAAAATAAAATAAGA
* *
253370 AAATATTAAAATAAAAAAATGAATAAAATAAAATAAAA
1 AAATATTAAAAAAAAAAAATGAAAAAAATAAAATAAAA
253408 AATTTAAATT
Statistics
Matches: 71, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
42 4 0.06
43 20 0.28
45 27 0.38
46 7 0.10
47 9 0.13
49 4 0.06
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.19
Consensus pattern (43 bp):
AAATATTAAAAAAAAAAAATGAAAAAAATAAAATAAAATAAGA
Found at i:253381 original size:16 final size:17
Alignment explanation
Indices: 253344--253402 Score: 75
Period size: 16 Copynumber: 3.5 Consensus size: 17
253334 AAGCAAAAAG
*
253344 AAATAAAAAAATAAAATA
1 AAATAAAAAAAT-GAATA
* *
253362 AAATAAGAAAAT-ATTA
1 AAATAAAAAAATGAATA
253378 AAATAAAAAAATGAATA
1 AAATAAAAAAATGAATA
253395 AAATAAAA
1 AAATAAAA
253403 TAAAAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
16 14 0.39
17 11 0.31
18 11 0.31
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (17 bp):
AAATAAAAAAATGAATA
Found at i:253450 original size:20 final size:18
Alignment explanation
Indices: 253413--253457 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
253403 TAAAAAATTT
*
253413 AAATTTTAAAAGAGAAAA
1 AAATGTTAAAAGAGAAAA
253431 AAATGTTAAAAGA-AAGAA
1 AAATGTTAAAAGAGAA-AA
253449 AAATGTTAA
1 AAATGTTAA
253458 CAAAAAACGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.22
Consensus pattern (18 bp):
AAATGTTAAAAGAGAAAA
Found at i:254733 original size:34 final size:36
Alignment explanation
Indices: 254655--255047 Score: 198
Period size: 37 Copynumber: 10.4 Consensus size: 36
254645 TTTTAAAAAG
* * * *
254655 TTATATATAAATTTTCGAAAATGTTTTTGAAACTATA
1 TTATATATATATTTTCAAAAACG-TTTTAAAACTATA
254692 TTATATAT-T-TTTTCAAAAACGTTTTAAAACTATA
1 TTATATATATATTTTCAAAAACGTTTTAAAACTATA
** *
254726 -TATTATATATATTTTCAAAAAAATAAAAAATTATATATA-TATA
1 TTA-TATATATATTTTCAAAAACGT------TT-TA-AAACTATA
* *
254769 TATATATATATATATTCAAAAAATGTTTTCAAAACTATA
1 T-TATATATATATTTTC-AAAAACGTTTT-AAAACTATA
*
254808 -TATTATATATATTTTCAAAAAAATGTTTTAAAAACTATA
1 TTA-TATATATATTTTC--AAAAACGTTTT-AAAACTATA
* **
254847 TATATTATATATTTTTTCAAAAAAAATATTTTCAAAACTATATA
1 T-TA-TATATATATTTTC---AAAAACGTTTT-AAAAC--TATA
**
254891 TTATATATATATTTTCAAAAATATTTTCAAAACTATA
1 TTATATATATATTTTCAAAAACGTTTT-AAAACTATA
*
254928 -TACTATATATATTTTCAAAAATGTTTTCAAAACTATA
1 TTA-TATATATATTTTCAAAAACGTTTT-AAAACTATA
* ** *
254965 -TAT-TATATATATTCAAAAA-AATTCAAAACTATA
1 TTATATATATATTTTCAAAAACGTTTTAAAACTATA
* * **
254998 -CATCATATA-AGTTTTTAAAAATATTTTCAAAACTATA
1 TTAT-ATATATA-TTTTCAAAAACGTTTT-AAAACTATA
255035 -TATTATATATATT
1 TTA-TATATATATT
255048 ATGTATATAT
Statistics
Matches: 297, Mismatches: 28, Indels: 62
0.77 0.07 0.16
Matches are distributed among these distances:
33 13 0.04
34 20 0.07
35 38 0.13
36 17 0.06
37 66 0.22
38 17 0.06
39 45 0.15
41 15 0.05
42 31 0.10
43 8 0.03
44 19 0.06
45 8 0.03
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (36 bp):
TTATATATATATTTTCAAAAACGTTTTAAAACTATA
Found at i:254762 original size:2 final size:2
Alignment explanation
Indices: 254757--254783 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
254747 AATAAAAAAT
254757 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 T
254784 TCAAAAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:254829 original size:39 final size:38
Alignment explanation
Indices: 254765--255047 Score: 332
Period size: 37 Copynumber: 7.4 Consensus size: 38
254755 ATTATATATA
* *
254765 TATATATATATATATATATTCAAAAAATGTTTTCAAAAC
1 TATATAT-TATATATATTTTCAAAAAATATTTTCAAAAC
* *
254804 TATATATTATATATATTTTCAAAAAAATGTTTTAAAAAC
1 TATATATTATATATATTTTC-AAAAAATATTTTCAAAAC
*
254843 TATATATATTATATATTTTTTCAAAAAAAATATTTTCAAAAC
1 --TATATATTATATATATTTTC--AAAAAATATTTTCAAAAC
254885 TATATATTATATATATATTTTC-AAAAATATTTTCAAAAC
1 TATATA-T-TATATATATTTTCAAAAAATATTTTCAAAAC
* *
254924 TATATACTATATATATTTTC-AAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTCAAAAAATATTTTCAAAAC
254961 TATATATTATATATA--TTCAAAAAA-A--TTCAAAAC
1 TATATATTATATATATTTTCAAAAAATATTTTCAAAAC
* * *
254994 TATACATCATATA-AGTTTT-TAAAAATATTTTCAAAAC
1 TATATATTATATATA-TTTTCAAAAAATATTTTCAAAAC
255031 TATATATTATATATATT
1 TATATATTATATATATT
255048 ATGTATATAT
Statistics
Matches: 215, Mismatches: 15, Indels: 30
0.83 0.06 0.12
Matches are distributed among these distances:
32 1 0.00
33 19 0.09
34 5 0.02
35 6 0.03
36 5 0.02
37 64 0.30
38 13 0.06
39 47 0.22
40 6 0.03
41 20 0.09
42 29 0.13
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.43
Consensus pattern (38 bp):
TATATATTATATATATTTTCAAAAAATATTTTCAAAAC
Found at i:256146 original size:22 final size:22
Alignment explanation
Indices: 256118--256162 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
256108 GAACCCATTC
256118 TGAATTGGCTCTCGAACCCGAT
1 TGAATTGGCTCTCGAACCCGAT
*
256140 TGAATTGGCTCTCGAACCTGAT
1 TGAATTGGCTCTCGAACCCGAT
256162 T
1 T
256163 TGAAGTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31
Consensus pattern (22 bp):
TGAATTGGCTCTCGAACCCGAT
Found at i:262680 original size:19 final size:20
Alignment explanation
Indices: 262653--262698 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
262643 TTACATCATG
262653 AAATAAATATAAA-AAACAAA
1 AAATAAATA-AAATAAACAAA
*
262673 AAAT-AATAAAATAAA-TAA
1 AAATAAATAAAATAAACAAA
262691 AAATAAAT
1 AAATAAAT
262699 TTAAATACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 9 0.39
19 10 0.43
20 4 0.17
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (20 bp):
AAATAAATAAAATAAACAAA
Found at i:262683 original size:8 final size:8
Alignment explanation
Indices: 262654--262775 Score: 50
Period size: 8 Copynumber: 14.2 Consensus size: 8
262644 TACATCATGA
262654 AATAAATAT
1 AATAAA-AT
*
262663 AA-AAAAC
1 AATAAAAT
262670 AA-AAAAT
1 AATAAAAT
262677 AATAAAAT
1 AATAAAAT
262685 AAATAAAAAT
1 -AAT-AAAAT
*
262695 AAATTTAAAT
1 -AA-TAAAAT
**
262705 ACGAAAAT
1 AATAAAAT
* *
262713 ATTAAAAG
1 AATAAAAT
*
262721 AGAAAAGAAAT
1 A-ATAA--AAT
*
262732 AAAAAAAT
1 AATAAAAT
262740 AAATAAAAT
1 -AATAAAAT
*
262749 ATTAAAAT
1 AATAAAAT
*
262757 AAAAAAAT
1 AATAAAAT
262765 GAATAAAAT
1 -AATAAAAT
262774 AA
1 AA
262776 AATAAAAATG
Statistics
Matches: 87, Mismatches: 17, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
7 9 0.10
8 36 0.41
9 22 0.25
10 16 0.18
11 4 0.05
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (8 bp):
AATAAAAT
Found at i:262743 original size:12 final size:12
Alignment explanation
Indices: 262723--262772 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
262713 ATTAAAAGAG
*
262723 AAAAGAAATAAA
1 AAAATAAATAAA
262735 AAAATAAATAAA
1 AAAATAAATAAA
* *
262747 ATATTAAAATAAA
1 AAAAT-AAATAAA
*
262760 AAAATGAATAAA
1 AAAATAAATAAA
262772 A
1 A
262773 TAAAATAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
12 21 0.68
13 10 0.32
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (12 bp):
AAAATAAATAAA
Found at i:262748 original size:17 final size:16
Alignment explanation
Indices: 262723--262777 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
262713 ATTAAAAGAG
*
262723 AAAAGAAATAAAAAAAT
1 AAAA-AAATAATAAAAT
*
262740 AAATAAAATATTAAAAT
1 AAA-AAAATAATAAAAT
262757 AAAAAAATGAATAAAAT
1 AAAAAAAT-AATAAAAT
262774 AAAA
1 AAAA
262778 TAAAAATGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 5 0.15
17 27 0.82
18 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (16 bp):
AAAAAAATAATAAAAT
Found at i:262784 original size:36 final size:34
Alignment explanation
Indices: 262671--262790 Score: 100
Period size: 36 Copynumber: 3.4 Consensus size: 34
262661 ATAAAAAACA
* * *
262671 AAAAATAATAAAATAAATAAA-AATAAATTTAAAT
1 AAAAATATTAAAATAAAAAAATAATAAA-ATAAAT
* *
262705 ACGAAAATATTAAAAGAGAAAAGAAATAAAAAAATAAAT
1 A--AAAATATT-AAA-ATAAAA-AAATAATAAAATAAAT
262744 -AAAATATTAAAATAAAAAAATGAATAAAATAAAAT
1 AAAAATATTAAAATAAAAAAAT-AATAAAAT-AAAT
*
262779 AAAAATGTTAAA
1 AAAAATATTAAA
262791 TTTTAAAAGA
Statistics
Matches: 69, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
33 4 0.06
34 13 0.19
35 7 0.10
36 25 0.36
37 3 0.04
38 4 0.06
39 8 0.12
40 5 0.07
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.22
Consensus pattern (34 bp):
AAAAATATTAAAATAAAAAAATAATAAAATAAAT
Found at i:263921 original size:24 final size:22
Alignment explanation
Indices: 263885--263928 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
263875 CCTAAAACAA
263885 AAAATAAAAAAATGAAATAAAACC
1 AAAATAAAAAAAT--AATAAAACC
*
263909 AAAATAAATAAATAATAAAA
1 AAAATAAAAAAATAATAAAA
263929 TGTAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
24 12 0.63
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAATAAAAAAATAATAAAACC
Found at i:263929 original size:32 final size:32
Alignment explanation
Indices: 263878--263939 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
263868 TTTTGGACCT
263878 AAAACAAAAAATAAAAAAATG-AAATAAAACC
1 AAAACAAAAAATAAAAAAATGTAAATAAAACC
* *
263909 AAAATAAATAAATAATAAAATGTAAATAAAA
1 AAAACAAA-AAATAAAAAAATGTAAATAAAA
263940 ACCATATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 7 0.26
32 12 0.44
33 8 0.30
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (32 bp):
AAAACAAAAAATAAAAAAATGTAAATAAAACC
Found at i:264589 original size:16 final size:16
Alignment explanation
Indices: 264568--264598 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
264558 AATGGTTCAC
*
264568 CAATTATAGGATGATT
1 CAATTATAGAATGATT
264584 CAATTATAGAATGAT
1 CAATTATAGAATGAT
264599 AATTTATTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.35
Consensus pattern (16 bp):
CAATTATAGAATGATT
Found at i:274850 original size:31 final size:31
Alignment explanation
Indices: 274807--274911 Score: 99
Period size: 31 Copynumber: 3.4 Consensus size: 31
274797 AAAATTAAAG
* *
274807 TTTAGGTGCTAAAACATATCAAAACTAGTAA
1 TTTAGGTACTAAAACATATCAAAACTAATAA
** ** * *
274838 TTTAGGTACT-AAATGTAT-AGTTTACTCA-AG
1 TTTAGGTACTAAAACATATCA--AAACTAATAA
274868 TTTAGGTACTAAAACATATCAAAACTAATAA
1 TTTAGGTACTAAAACATATCAAAACTAATAA
274899 TTTAGGTACTAAA
1 TTTAGGTACTAAA
274912 TGCATAGTTT
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
29 1 0.02
30 21 0.38
31 32 0.58
32 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.33
Consensus pattern (31 bp):
TTTAGGTACTAAAACATATCAAAACTAATAA
Found at i:274874 original size:30 final size:30
Alignment explanation
Indices: 274838--274932 Score: 95
Period size: 30 Copynumber: 3.1 Consensus size: 30
274828 AAACTAGTAA
*
274838 TTTAGGTACTAAATGTATAGTTTACTCAAG
1 TTTAGGTACTAAATGCATAGTTTACTCAAG
* ** * *
274868 TTTAGGTACTAAA-ACATA-TCAAAACTAATAA
1 TTTAGGTACTAAATGCATAGT--TTACTCA-AG
274899 TTTAGGTACTAAATGCATAGTTTACTCAAG
1 TTTAGGTACTAAATGCATAGTTTACTCAAG
274929 TTTA
1 TTTA
274933 TAATATAAAT
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
28 1 0.02
29 3 0.06
30 22 0.45
31 18 0.37
32 4 0.08
33 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.37
Consensus pattern (30 bp):
TTTAGGTACTAAATGCATAGTTTACTCAAG
Found at i:274874 original size:61 final size:61
Alignment explanation
Indices: 274804--274932 Score: 231
Period size: 61 Copynumber: 2.1 Consensus size: 61
274794 AAAAAAATTA
* * *
274804 AAGTTTAGGTGCTAAAACATATCAAAACTAGTAATTTAGGTACTAAATGTATAGTTTACTC
1 AAGTTTAGGTACTAAAACATATCAAAACTAATAATTTAGGTACTAAATGCATAGTTTACTC
274865 AAGTTTAGGTACTAAAACATATCAAAACTAATAATTTAGGTACTAAATGCATAGTTTACTC
1 AAGTTTAGGTACTAAAACATATCAAAACTAATAATTTAGGTACTAAATGCATAGTTTACTC
274926 AAGTTTA
1 AAGTTTA
274933 TAATATAAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (61 bp):
AAGTTTAGGTACTAAAACATATCAAAACTAATAATTTAGGTACTAAATGCATAGTTTACTC
Found at i:278978 original size:19 final size:20
Alignment explanation
Indices: 278954--278991 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
278944 AATTTAATCG
*
278954 AATATATAAT-TTAAAATTT
1 AATATAAAATCTTAAAATTT
278973 AATATAAAATCTTAAAATT
1 AATATAAAATCTTAAAATT
278992 CATTAACACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTT
Found at i:283882 original size:23 final size:23
Alignment explanation
Indices: 283852--283896 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
283842 ACTACGATGC
283852 AATTCTACGCGGCACTTCGGTGA
1 AATTCTACGCGGCACTTCGGTGA
*
283875 AATTCTACGTGGCACTTCGGTG
1 AATTCTACGCGGCACTTCGGTG
283897 CATTTATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (23 bp):
AATTCTACGCGGCACTTCGGTGA
Found at i:284116 original size:13 final size:14
Alignment explanation
Indices: 284098--284130 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
284088 TTCATGATAG
284098 TATTATGATT-TTA
1 TATTATGATTATTA
284111 TATTAT-ATTATTA
1 TATTATGATTATTA
284124 TATTATG
1 TATTATG
284131 CATCACTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.17
13 15 0.83
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
TATTATGATTATTA
Found at i:290649 original size:23 final size:23
Alignment explanation
Indices: 290616--290672 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
290606 CATTTTATAT
* *
290616 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACAC
290639 GGCACTTCGGTGCAATTCTACAC
1 GGCACTTCGGTGCAATTCTACAC
*
290662 TGCACTTCGGT
1 GGCACTTCGGT
290673 ACATTTATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.19, C:0.30, G:0.25, T:0.26
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACAC
Found at i:293851 original size:15 final size:15
Alignment explanation
Indices: 293830--293873 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
293820 TACCCACCCT
293830 ACATCCGCCCGCCCC
1 ACATCCGCCCGCCCC
*
293845 GCATCCGCCCGCCCC
1 ACATCCGCCCGCCCC
*
293860 ATATCCGCCCGCCC
1 ACATCCGCCCGCCC
293874 AGCTAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.11, C:0.64, G:0.16, T:0.09
Consensus pattern (15 bp):
ACATCCGCCCGCCCC
Found at i:299292 original size:213 final size:214
Alignment explanation
Indices: 298725--299429 Score: 1146
Period size: 213 Copynumber: 3.2 Consensus size: 214
298715 AGGTCTACTG
298725 GAGAGACCTGATCAAAGAGGGACCTTCTCATGCAGGCAACTTGGTTTCTTAGAGCTAATTAGTAA
1 GAGAGACCTGATCAAAGAGGGACCTTCTCATGCAGGCAACTTGGTTTCTTAGAGCT-A--AG---
298790 TTACCTAGAGCTGCTTCCCTTGAATTGGTGCATGTAATCATCCAGTTTATTGAAGTCAATAGGCC
60 -TACCTAGAGCTGCTTCCCTTGAATTGGTGCATGTAATCATCCAGTTTATTGAAGTCAATAGGCC
*
298855 TACTGTTCCTGCATGCATGGATGGATAAAAAAAAGATCGATAGGAATCGCTTGCAACGCCAAGTA
124 TACTGTTCCTGCATGCATGGATGGAT-AAAAAAAGATGGATAGGAATCGCTTGCAACGCCAAGTA
298920 ATTAGAATTCATGTGCGTATATATATAGAGAAA
188 ATTAGAATTCATGTGCG----TATATAGAG--A
*
298953 GAGAGACCTGATCAAAGAGGGACCTTCTCATGCAGGC-ACTTGGTTTCTTAGAGCTAATTAATTA
1 GAGAGACCTGATCAAAGAGGGACCTTCTCATGCAGGCAACTTGGTTTCTTAGAGC----TAAGTA
299017 CCTAGAGCTGCTTCCCTTGAATTGGTGCATGTAATCATCCAGTTTATTGAAGTCAATAGGCCTAC
62 CCTAGAGCTGCTTCCCTTGAATTGGTGCATGTAATCATCCAGTTTATTGAAGTCAATAGGCCTAC
* *
299082 TGTTCCTGCATGCATGGATGGATAGAAAAAACAAGGAT-GGAATCGCTTGCAACGCCAAGTAATT
127 TGTTCCTGCATGCATGGATGGATA-AAAAAAGATGGATAGGAATCGCTTGCAACGCCAAGTAATT
299146 AGAATTCATGTGCGTATATAGAGA
191 AGAATTCATGTGCGTATATAGAGA
299170 GAGAGACCTGATCAAAGAGGGACCTTCTCATGCAGGCAACTTGGTTTCTTAGAGCTAAGTACCTA
1 GAGAGACCTGATCAAAGAGGGACCTTCTCATGCAGGCAACTTGGTTTCTTAGAGCTAAGTACCTA
299235 GAGCTGCTTCCCTTGAATT-GTGCATGTAATCATCCAGTTTATTGAAGTCAATAGGCCTACTGTT
66 GAGCTGCTTCCCTTGAATTGGTGCATGTAATCATCCAGTTTATTGAAGTCAATAGGCCTACTGTT
* *
299299 CCTGCATGCATGGATGGATAAAACAGGATGGATAGGAATCGCTTGCAACGCCAAGTAATTAGAAT
131 CCTGCATGCATGGATGGATAAAAAAAGATGGATAGGAATCGCTTGCAACGCCAAGTAATTAGAAT
299364 TCATGTGCGTGTATATAGAGA
196 TCATGTGC--GTATATAGAGA
299385 GAGAGACCTGATCAAAGAGGGACCTTCTCATGCAGGCAACTTGGT
1 GAGAGACCTGATCAAAGAGGGACCTTCTCATGCAGGCAACTTGGT
299430 GTTGCAAGCG
Statistics
Matches: 459, Mismatches: 9, Indels: 31
0.92 0.02 0.06
Matches are distributed among these distances:
212 9 0.02
213 104 0.23
214 28 0.06
215 56 0.12
217 38 0.08
218 17 0.04
219 9 0.02
223 41 0.09
224 100 0.22
227 17 0.04
228 38 0.08
230 1 0.00
231 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (214 bp):
GAGAGACCTGATCAAAGAGGGACCTTCTCATGCAGGCAACTTGGTTTCTTAGAGCTAAGTACCTA
GAGCTGCTTCCCTTGAATTGGTGCATGTAATCATCCAGTTTATTGAAGTCAATAGGCCTACTGTT
CCTGCATGCATGGATGGATAAAAAAAGATGGATAGGAATCGCTTGCAACGCCAAGTAATTAGAAT
TCATGTGCGTATATAGAGA
Found at i:303849 original size:17 final size:17
Alignment explanation
Indices: 303827--303863 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
303817 AACGGTCAAC
303827 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
303844 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
303861 GGT
1 GGT
303864 TGGTCGGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.22, G:0.49, T:0.19
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:303915 original size:19 final size:19
Alignment explanation
Indices: 303891--303952 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
303881 CGGGTCAGAC
303891 CGGTCAAACCGGTTCGAAT
1 CGGTCAAACCGGTTCGAAT
*
303910 CGGTCAAACC-GTTCAGAAC
1 CGGTCAAACCGGTTC-GAAT
*
303929 CGGTTGAAAACCGGTT-GAAT
1 CGG-T-CAAACCGGTTCGAAT
303949 CGGT
1 CGGT
303953 TTCCAGCAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 4 0.11
19 17 0.47
20 7 0.19
21 5 0.14
22 3 0.08
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.21
Consensus pattern (19 bp):
CGGTCAAACCGGTTCGAAT
Found at i:307310 original size:17 final size:16
Alignment explanation
Indices: 307290--307321 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
307280 AATAAAAAAA
307290 AAAAGAAATATGAAATG
1 AAAAGAAATAT-AAATG
307307 AAAAGAAATATAAAT
1 AAAAGAAATATAAAT
307322 ATAATAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (16 bp):
AAAAGAAATATAAATG
Found at i:309465 original size:3 final size:3
Alignment explanation
Indices: 309452--309501 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
309442 ATGTAAACAA
*
309452 AAT AAT AAAT AAT AAT AAC AAT AAT AAT AAT -AT AAAT AAT AAT -AT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
309497 AAT AA
1 AAT AA
309502 AAAAAATGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 4 0.10
3 32 0.78
4 5 0.12
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:309848 original size:43 final size:40
Alignment explanation
Indices: 309799--309904 Score: 126
Period size: 40 Copynumber: 2.6 Consensus size: 40
309789 ATAACTCGGT
* *
309799 TCCTACGCGATGAGGACGGCTGGTTATCTATGGG-TGACACGGC
1 TCCTACGTGATGAGGACGGCTGG---TC-AGGGGATGACACGGC
*
309842 TCCTACGTGATGAGGA-GGTCTGGTCAGGGGATGACACGGT
1 TCCTACGTGATGAGGACGG-CTGGTCAGGGGATGACACGGC
309882 TCCTACGTGATGAGGACGGCTGG
1 TCCTACGTGATGAGGACGGCTGG
309905 CCATCTTTAG
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
39 4 0.07
40 30 0.53
41 2 0.04
42 2 0.04
43 19 0.33
ACGTcount: A:0.19, C:0.21, G:0.38, T:0.23
Consensus pattern (40 bp):
TCCTACGTGATGAGGACGGCTGGTCAGGGGATGACACGGC
Found at i:309992 original size:28 final size:28
Alignment explanation
Indices: 309923--310004 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
309913 AGTGATTATG
** *
309923 GTTTCAAGGGAAACCGACTCAAAGATTT
1 GTTTCAAGAAAAACAGACTCAAAGATTT
*
309951 GTTT-AAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAGAA-AAACAGACTCAAAGATTT
309979 GTTTCAAGAAAAACA-AGCTCAAAGAT
1 GTTTCAAGAAAAACAGA-CTCAAAGAT
310005 AATGTGTTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
27 3 0.07
28 39 0.85
29 4 0.09
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (28 bp):
GTTTCAAGAAAAACAGACTCAAAGATTT
Found at i:310216 original size:38 final size:38
Alignment explanation
Indices: 310168--310274 Score: 112
Period size: 36 Copynumber: 2.9 Consensus size: 38
310158 TCAAAGATGT
* ***
310168 TTTTATTTCAAGAAAAACATACTCAAAGATTTTGTTTG
1 TTTTGTTTCAAGAAAAACATACTCAAAGATTTTGTAAA
** *
310206 TTTTGTTTCAAGGGAAACATACTCAAAGA--TGGTAAA
1 TTTTGTTTCAAGAAAAACATACTCAAAGATTTTGTAAA
*
310242 TTTTGTTTCAA-AATAAACAGACTCAAAGATTTT
1 TTTTGTTTCAAGAA-AAACATACTCAAAGATTTT
310275 TCTTAAAAGA
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
36 28 0.51
38 27 0.49
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.37
Consensus pattern (38 bp):
TTTTGTTTCAAGAAAAACATACTCAAAGATTTTGTAAA
Found at i:310273 original size:74 final size:70
Alignment explanation
Indices: 310139--310274 Score: 175
Period size: 74 Copynumber: 1.9 Consensus size: 70
310129 CAAAGATCGG
* *
310139 TGTTTCGAGAGAAACAAACTCAAAGATGTTTTTATTTCAAGAAAAACATACTCAAAGATTTTGTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGTTTTTATTTCAAGAAAAACAGACTCAAAGATTTTGTT
310204 TGTTT
66 TGTTT
* * *
310209 TGTTTCAAGGGAAACATACTCAAAGATGGTAAATTTTGTTTCAA-AATAAACAGACTCAAAGATT
1 TGTTTCAAGAGAAACAAACTCAAAGAT-GT---TTTTATTTCAAGAA-AAACAGACTCAAAGATT
310273 TT
61 TT
310275 TCTTAAAAGA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
70 24 0.43
71 2 0.04
73 2 0.04
74 28 0.50
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (70 bp):
TGTTTCAAGAGAAACAAACTCAAAGATGTTTTTATTTCAAGAAAAACAGACTCAAAGATTTTGTT
TGTTT
Found at i:310487 original size:31 final size:31
Alignment explanation
Indices: 310437--310497 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
310427 AAGGGAAACT
310437 ACTCAAAGATGGTTTTATTTCAAAAGAAACAA
1 ACTCAAAGAT-GTTTTATTTCAAAAGAAACAA
* *
310469 ACTCAAAGAT-TTTGTATTTCTAGAGAAAC
1 ACTCAAAGATGTTT-TATTTCAAAAGAAAC
310498 TGCCTCAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 3 0.12
31 13 0.50
32 10 0.38
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (31 bp):
ACTCAAAGATGTTTTATTTCAAAAGAAACAA
Found at i:310846 original size:31 final size:32
Alignment explanation
Indices: 310808--310888 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 32
310798 TTTTTTTCAT
*
310808 TTTGTTTCAAGTGAAACAGAGTCAAAGAT-CC
1 TTTGTTTCAAGTGAAACAGACTCAAAGATACC
** * **
310839 TTTGTTTCAAAAGAAA-TGACTCAAAGATGATG
1 TTTGTTTCAAGTGAAACAGACTCAAAGAT-ACC
310871 TTTGTTTCAAGTGAAACA
1 TTTGTTTCAAGTGAAACA
310889 AATTCGTAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
30 10 0.26
31 14 0.37
32 14 0.37
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (32 bp):
TTTGTTTCAAGTGAAACAGACTCAAAGATACC
Found at i:310951 original size:36 final size:36
Alignment explanation
Indices: 310908--311013 Score: 117
Period size: 36 Copynumber: 3.0 Consensus size: 36
310898 TTTGGAAAAT
*
310908 TGTCTCAAGTGAGACAACATTTGTTTTTAGAGAAAC
1 TGTCTCAAGCGAGACAACATTTGTTTTTAGAGAAAC
* * * * *
310944 TGTCTCAAACGAAACAAAAATTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAACATTTGTTTTTAGAGAAAC
* *
310980 TTTCTCAAGCGAGACAA-AGTTTGATTTT-GAGAAA
1 TGTCTCAAGCGAGACAACA-TTTGTTTTTAGAGAAA
311014 ACGTTCTCAA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
35 7 0.12
36 51 0.88
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAACATTTGTTTTTAGAGAAAC
Found at i:311188 original size:107 final size:106
Alignment explanation
Indices: 311018--311225 Score: 262
Period size: 108 Copynumber: 2.0 Consensus size: 106
311008 GAGAAAACGT
* *
311018 TCTCAAGTGAGATCAACTTTTTTTAATGTGAACAAATTCGAAATTTTTATTCTCAAAGG-AAAAA
1 TCTCAAGTGAGATCAACTTTTTTTAATGTGAACAAATTCGAAATTTGTATTATCAAAGGAAAAAA
**
311082 TGCCTCAAATGAGACGAAATTTGTTTTGAA-AGAAATAACAA
66 TGCCTCAAACAAGACGAAATTTGTTTT-AAGAGAAATAACAA
* *
311123 TCTCAAGTGAGATTAATTTTTGTTTCAA-GTGAATCAAATTCGAAATTTGTA-TATCAAAGGAAA
1 TCTCAAGTGAGATCAACTTTT-TTT-AATGTGAA-CAAATTCGAAATTTGTATTATCAAAGG-AA
* * *
311186 AAAATGTCTCAAGCAAGACGAAGTTTGTTTTAAGAGAAAT
62 AAAATGCCTCAAACAAGACGAAATTTGTTTTAAGAGAAAT
311226 TGTCTTAAAT
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
105 19 0.22
106 16 0.18
107 20 0.23
108 33 0.38
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (106 bp):
TCTCAAGTGAGATCAACTTTTTTTAATGTGAACAAATTCGAAATTTGTATTATCAAAGGAAAAAA
TGCCTCAAACAAGACGAAATTTGTTTTAAGAGAAATAACAA
Found at i:311379 original size:153 final size:154
Alignment explanation
Indices: 311140--311461 Score: 387
Period size: 153 Copynumber: 2.1 Consensus size: 154
311130 TGAGATTAAT
* * * * * *
311140 TTTTGTTTCAAGTGA-ATCAAATTCGAAATTTGTATATCAAAGGAAAAAAATGTCTCAAGCAAGA
1 TTTTGTTTCAAGT-ACAACAAATT-TAAATTTGTATCTTAGA-G-AAAAAATCTCTCAAGCAAGA
* * * * * *
311204 CGAAGTTTGTTTTAAGAGAAATTGTCTTAAATGAGGCAAAATTTGTTTTAAAATTCTCAAAATTT
62 CGAAATTTGCTTTAAGAGAAATTGTCTTAAACGAGACAAAATTAGTTTAAAAATTCTCAAAATTT
*
311269 ATGG-GAAATGTCTCAAGCGAGAAAGAA
127 ATGGAAAAATGTCTCAAGCGAGAAAGAA
* * *
311296 TTTTTTTTCAAGTACAACAAATTTAAATTTGTATCTTAGAGAAAAAATCTCTTAAGCGAGACGAA
1 TTTTGTTTCAAGTACAACAAATTTAAATTTGTATCTTAGAGAAAAAATCTCTCAAGCAAGACGAA
* * * * *
311361 ATTTGCTTTGATAGAAATTGTCTTGAGCGAGACAAAATTAGTTTAAAAATTCTCAAAATTTGTGG
66 ATTTGCTTTAAGAGAAATTGTCTTAAACGAGACAAAATTAGTTTAAAAATTCTCAAAATTTATGG
* *
311426 AAAAATGTTTCAAGCGAGACAGAA
131 AAAAATGTCTCAAGCGAGAAAGAA
311450 TTTTGTTTCAAG
1 TTTTGTTTCAAG
311462 GAAAAAACAC
Statistics
Matches: 140, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
153 75 0.54
154 32 0.23
155 14 0.10
156 19 0.14
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (154 bp):
TTTTGTTTCAAGTACAACAAATTTAAATTTGTATCTTAGAGAAAAAATCTCTCAAGCAAGACGAA
ATTTGCTTTAAGAGAAATTGTCTTAAACGAGACAAAATTAGTTTAAAAATTCTCAAAATTTATGG
AAAAATGTCTCAAGCGAGAAAGAA
Found at i:311954 original size:25 final size:25
Alignment explanation
Indices: 311919--311982 Score: 110
Period size: 25 Copynumber: 2.5 Consensus size: 25
311909 AGATAATTTG
311919 TTTTCCTTGCCCCATCAAAATTTGCC
1 TTTT-CTTGCCCCATCAAAATTTGCC
311945 TTTTCTTGCCCCATCAAAATTTGCC
1 TTTTCTTGCCCCATCAAAATTTGCC
*
311970 TTCTCTTGCCCCA
1 TTTTCTTGCCCCA
311983 ACTTCAATCT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 33 0.89
26 4 0.11
ACGTcount: A:0.17, C:0.36, G:0.08, T:0.39
Consensus pattern (25 bp):
TTTTCTTGCCCCATCAAAATTTGCC
Found at i:313057 original size:45 final size:45
Alignment explanation
Indices: 312981--313109 Score: 133
Period size: 45 Copynumber: 2.8 Consensus size: 45
312971 GAGGGACTCA
* *
312981 TTTTCTATGC-TCTTTGTCATCTTTTTGTTCTTTGCTCTTTTCTTTGT
1 TTTTCTTTGCTTCTTT-TC-TCTTTTTTTTCTTTGCTCTTTTCTTT-T
* *
313028 TTTTGCTTTTCTT-TTTT-TCTTTTTTTTCTTTGCTC-TTTGTTTT
1 TTTT-CTTTGCTTCTTTTCTCTTTTTTTTCTTTGCTCTTTTCTTTT
313071 TTTTCTTTGCTTCTTTTCTCTTTGTTTTTCTGTT-CTCTT
1 TTTTCTTTGCTTCTTTTCTCTTT-TTTTTCT-TTGCTCTT
313110 CGCTTTGATA
Statistics
Matches: 70, Mismatches: 5, Indels: 15
0.78 0.06 0.17
Matches are distributed among these distances:
42 7 0.10
43 9 0.13
44 11 0.16
45 27 0.39
46 3 0.04
47 5 0.07
48 7 0.10
49 1 0.01
ACGTcount: A:0.02, C:0.18, G:0.09, T:0.72
Consensus pattern (45 bp):
TTTTCTTTGCTTCTTTTCTCTTTTTTTTCTTTGCTCTTTTCTTTT
Found at i:313070 original size:20 final size:21
Alignment explanation
Indices: 313002--313086 Score: 75
Period size: 20 Copynumber: 4.0 Consensus size: 21
312992 CTTTGTCATC
* *
313002 TTTTTGTTCTTTGC-TCTTTTC
1 TTTTTTTTCTTTGCTTC-TTTG
* * *
313023 TTTGTTTTTGCTTTTCTTTTTTTC
1 TTT-TTTTT-CTTTGC-TTCTTTG
313047 TTTTTTTTCTTTGC-TCTTTG
1 TTTTTTTTCTTTGCTTCTTTG
313067 TTTTTTTTCTTTGCTTCTTT
1 TTTTTTTTCTTTGCTTCTTT
313087 TCTCTTTGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
20 18 0.34
21 8 0.15
22 9 0.17
23 10 0.19
24 7 0.13
25 1 0.02
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.76
Consensus pattern (21 bp):
TTTTTTTTCTTTGCTTCTTTG
Found at i:313084 original size:28 final size:27
Alignment explanation
Indices: 313018--313099 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 27
313008 TTCTTTGCTC
*
313018 TTTTCTTTGTT-TTTGCT-TTTCTTTT
1 TTTTCTTTGTTCTTTGCTCTTTGTTTT
* *
313043 TTTCTTTTTTTTCTTTGCTCTTTGTTTT
1 TTT-TCTTTGTTCTTTGCTCTTTGTTTT
*
313071 TTTTCTTTGCTTCTTTTCTCTTTGTTTT
1 TTTTCTTTG-TTCTTTGCTCTTTGTTTT
313099 T
1 T
313100 CTGTTCTCTT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
25 3 0.06
26 6 0.13
27 10 0.21
28 28 0.60
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (27 bp):
TTTTCTTTGTTCTTTGCTCTTTGTTTT
Found at i:313101 original size:17 final size:16
Alignment explanation
Indices: 313029--313109 Score: 62
Period size: 17 Copynumber: 5.1 Consensus size: 16
313019 TTTCTTTGTT
*
313029 TTTGCTTTTCTTTTTTTC
1 TTTG-TTTTC-TTTTCTC
* *
313047 TTTTTTTTCTTTGCTC
1 TTTGTTTTCTTTTCTC
313063 TTTG-TTT-TTTT-TC
1 TTTGTTTTCTTTTCTC
*
313076 TTTG-CTTCTTTTCTC
1 TTTGTTTTCTTTTCTC
*
313091 TTTGTTTTTCTGTTCTC
1 TTTG-TTTTCTTTTCTC
313108 TT
1 TT
313110 CGCTTTGATA
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
13 8 0.16
14 7 0.14
15 9 0.18
16 8 0.16
17 16 0.31
18 3 0.06
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.75
Consensus pattern (16 bp):
TTTGTTTTCTTTTCTC
Found at i:314429 original size:14 final size:13
Alignment explanation
Indices: 314384--314426 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
314374 CTTAAAAATG
*
314384 AAATGTAGATGCA
1 AAATGCAGATGCA
314397 AAATGCAAAGATGC-
1 AAATGC--AGATGCA
314411 AAATGCAGATGCA
1 AAATGCAGATGCA
314424 AAA
1 AAA
314427 ATGTTGATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 6 0.23
13 8 0.31
14 6 0.23
15 6 0.23
ACGTcount: A:0.51, C:0.12, G:0.21, T:0.16
Consensus pattern (13 bp):
AAATGCAGATGCA
Found at i:315705 original size:28 final size:28
Alignment explanation
Indices: 315674--315730 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
315664 TCATTGCCTT
315674 ATACCCATACGAGGAATAAATCCCTACG
1 ATACCCATACGAGGAATAAATCCCTACG
315702 ATACCCATACGAGGAATAAATCCCTACG
1 ATACCCATACGAGGAATAAATCCCTACG
315730 A
1 A
315731 AGGTATAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.18
Consensus pattern (28 bp):
ATACCCATACGAGGAATAAATCCCTACG
Found at i:316288 original size:18 final size:20
Alignment explanation
Indices: 316262--316300 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
316252 ACGTCTTTTG
316262 AAATAA-TTTTAAGA-AAAA
1 AAATAATTTTTAAGACAAAA
*
316280 AAATCATTTTTAAGACAAAA
1 AAATAATTTTTAAGACAAAA
316300 A
1 A
316301 TTAGTTTGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 8 0.44
20 5 0.28
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (20 bp):
AAATAATTTTTAAGACAAAA
Found at i:316900 original size:17 final size:16
Alignment explanation
Indices: 316873--316912 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
316863 TAAACAATAA
316873 ATAAATAAAAAGAAAT
1 ATAAATAAAAAGAAAT
*
316889 ATGAAATGAAAAGAAAT
1 AT-AAATAAAAAGAAAT
316906 ATAAATA
1 ATAAATA
316913 TAAATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (16 bp):
ATAAATAAAAAGAAAT
Found at i:318140 original size:2 final size:2
Alignment explanation
Indices: 318133--318162 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
318123 TTTGCACTTA
318133 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
318163 GTGTAATCTA
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:319095 original size:3 final size:3
Alignment explanation
Indices: 319082--319134 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
319072 ATGTAAGCAA
*
319082 AAT AAT AAAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
319128 -AT AAT AA
1 AAT AAT AA
319135 AAAAATGACC
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:319595 original size:28 final size:28
Alignment explanation
Indices: 319555--319651 Score: 99
Period size: 28 Copynumber: 3.4 Consensus size: 28
319545 AGTGATTATG
** *
319555 GTTTCAAGGGAAACCGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
319583 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
*
319611 GTTTCGAGAA-AAACA-AGCTCAAAGATAATGT
1 GTTTC-AAAAGAAACAGA-CTCAAAGAT--T-T
319642 GTTTCAAAAG
1 GTTTCAAAAG
319652 CAACTGTTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
27 1 0.02
28 44 0.76
29 3 0.05
30 4 0.07
31 6 0.10
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACTCAAAGATTT
Found at i:319818 original size:32 final size:32
Alignment explanation
Indices: 319771--319907 Score: 116
Period size: 36 Copynumber: 4.0 Consensus size: 32
319761 CAAAGATCAG
*
319771 TGTTTCGAGAGAAACAAACTCAAAGATGTTTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGTTTT
* *
319803 TGTTTCAAGAAAAACATACTCAAAGATTTTGTTTGCTT
1 TGTTTCAAGAGAAACAAACTCAAAGA---TG-TT--TT
*
319841 TGTTTCAAGGGAAACAAACTCAAAGATGGTAAATTT
1 TGTTTCAAGAGAAACAAACTCAAAGAT-GT---TTT
*
319877 TGTTTCCAA-AGAAACAGACTCAAAGAT-TTTT
1 TGTTT-CAAGAGAAACAAACTCAAAGATGTTTT
319908 CTTAAAAGAG
Statistics
Matches: 86, Mismatches: 8, Indels: 23
0.74 0.07 0.20
Matches are distributed among these distances:
31 3 0.03
32 23 0.27
34 1 0.01
35 4 0.05
36 26 0.30
37 3 0.03
38 26 0.30
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (32 bp):
TGTTTCAAGAGAAACAAACTCAAAGATGTTTT
Found at i:319903 original size:74 final size:70
Alignment explanation
Indices: 319771--319906 Score: 184
Period size: 74 Copynumber: 1.9 Consensus size: 70
319761 CAAAGATCAG
* *
319771 TGTTTCGAGAGAAACAAACTCAAAGATGTTTTTGTTTCAAGAAAAACATACTCAAAGATTTTGTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGTTTTTGTTTCAAGAAAAACAGACTCAAAGATTTTGTT
319836 TGCTT
66 TGCTT
* *
319841 TGTTTCAAGGGAAACAAACTCAAAGATGGTAAATTTTGTTTCCAA-AGAAACAGACTCAAAGATT
1 TGTTTCAAGAGAAACAAACTCAAAGAT-GT---TTTTGTTT-CAAGAAAAACAGACTCAAAGATT
319905 TT
61 TT
319907 TCTTAAAAGA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
70 25 0.44
71 2 0.04
74 27 0.47
75 3 0.05
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (70 bp):
TGTTTCAAGAGAAACAAACTCAAAGATGTTTTTGTTTCAAGAAAAACAGACTCAAAGATTTTGTT
TGCTT
Found at i:320031 original size:31 final size:32
Alignment explanation
Indices: 319999--320110 Score: 102
Period size: 32 Copynumber: 3.5 Consensus size: 32
319989 GTTTTCGGAG
*
319999 AACAAACTCAAAGATGATCTTGTTTTAAGAGA
1 AACAAACTCAAAGATGATCTTGTTTCAAGAGA
* * **
320031 AACTATCTCAAGAGTCAAAAT-TTGTTTCAAGAGA
1 AACAAACTCAA-AG--ATGATCTTGTTTCAAGAGA
* * * *
320065 AAC-GACTCAAAGATGGTTTTATTTCAAGAGA
1 AACAAACTCAAAGATGATCTTGTTTCAAGAGA
320096 AACAAACTCAAAGAT
1 AACAAACTCAAAGAT
320111 TTTGTATTTC
Statistics
Matches: 63, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
30 2 0.03
31 15 0.24
32 21 0.33
33 7 0.11
34 15 0.24
35 3 0.05
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (32 bp):
AACAAACTCAAAGATGATCTTGTTTCAAGAGA
Found at i:320107 original size:97 final size:96
Alignment explanation
Indices: 319999--320207 Score: 237
Period size: 97 Copynumber: 2.2 Consensus size: 96
319989 GTTTTCGGAG
* **
319999 AACAAACTCAAAGATGATCTTGT-TTT-AAGAGAAACTATCTCAA-GAGTCAAAATTTGTTTCAA
1 AACAAACTCAAAGAT--T-TTGTATTTCAAGAGAAACTACCTCAAGGAAACAAAATTTGTTTCAA
*
320061 GAGAAACGA-CTCAAAGATGGTTTTATTTCAAGAGA
63 GAGAAACGATCTCAAAGATGG--GTATTTCAAGAGA
* * * *
320096 AACAAACTCAAAGATTTTGTATTTCTAGAGAAACTGCCTCAAGGGAAACAAAATTTGTTTTAATA
1 AACAAACTCAAAGATTTTGTATTTCAAGAGAAACTACCTCAA-GGAAACAAAATTTGTTTCAAGA
* *
320161 GAAACGATCTCAAAGGTGGGTGTTTCAAGAGA
65 GAAACGATCTCAAAGATGGGTATTTCAAGAGA
*
320193 AACTAACTCAAAGAT
1 AACAAACTCAAAGAT
320208 AAGTGTTTCA
Statistics
Matches: 96, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
94 4 0.04
95 4 0.04
96 14 0.15
97 40 0.42
98 24 0.25
99 10 0.10
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (96 bp):
AACAAACTCAAAGATTTTGTATTTCAAGAGAAACTACCTCAAGGAAACAAAATTTGTTTCAAGAG
AAACGATCTCAAAGATGGGTATTTCAAGAGA
Found at i:320137 original size:31 final size:30
Alignment explanation
Indices: 320055--320129 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 30
320045 TCAAAATTTG
320055 TTTCAAGAGAAACGACTCAAAGATGGTTTTA
1 TTTCAAGAGAAACGACTCAAAGAT-GTTTTA
*
320086 TTTCAAGAGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGAGAAAC-GACTCAAAGATGTTT-TA
*
320117 TTTCTAGAGAAAC
1 TTTCAAGAGAAAC
320130 TGCCTCAAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 3 0.08
31 27 0.68
32 10 0.25
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.29
Consensus pattern (30 bp):
TTTCAAGAGAAACGACTCAAAGATGTTTTA
Found at i:320328 original size:33 final size:33
Alignment explanation
Indices: 320272--320334 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
320262 GAGACAAAAT
*
320272 TTTGTTTCAAAAGAAAAATACTCAAAGATGAGC
1 TTTGTTTCAAAAGAAAAAGACTCAAAGATGAGC
** * *
320305 TTTGTTTCAAGGGAAACAGACTCACAGATG
1 TTTGTTTCAAAAGAAAAAGACTCAAAGATG
320335 GTAAATGTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (33 bp):
TTTGTTTCAAAAGAAAAAGACTCAAAGATGAGC
Found at i:320519 original size:32 final size:31
Alignment explanation
Indices: 320440--320498 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
320430 TTTTTTTCAT
* *
320440 TTTGTTTCAACTGAAACAGAGTCAAAGATCC
1 TTTGTTTCAAATGAAACAGACTCAAAGATCC
*
320471 TTTGTTTCAAAAGAAAC-GACTCAAAGAT
1 TTTGTTTCAAATGAAACAGACTCAAAGAT
320499 GATGTTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (31 bp):
TTTGTTTCAAATGAAACAGACTCAAAGATCC
Found at i:320579 original size:36 final size:35
Alignment explanation
Indices: 320536--320645 Score: 132
Period size: 36 Copynumber: 3.1 Consensus size: 35
320526 GTAATTTGCA
* *
320536 AAATTGTCTCAAGTGATACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAAACAA-ATTTGTTTTTAGAG
* *
320572 AAATTGTCTCAAACGAAACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGCGAAAC-AAATTTGTTTTTAGAG
* *
320608 AAATTTTCTCAAGCGAGACAAAGTTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAAACAAA-TTTGTTTTTAGAG
320643 AAA
1 AAA
320646 ACGATCTCAA
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
35 9 0.14
36 53 0.83
37 2 0.03
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (35 bp):
AAATTGTCTCAAGCGAAACAAATTTGTTTTTAGAG
Found at i:320837 original size:108 final size:105
Alignment explanation
Indices: 320649--320857 Score: 244
Period size: 108 Copynumber: 2.0 Consensus size: 105
320639 TGAGAAAACG
* * * *
320649 ATCTCAAGTGAGATCAACTTTTTTTAATGTGAACAAATTTGAATTTTGTATTCTCAAAGGAAAAA
1 ATCTCAAGTGAGATCAACTTTTTTTAATGTGAACAAATTCGAAATTTGTATTATAAAAGGAAAAA
**
320714 TGCCTCAAATGAGACGAAATTTGTTTTGAA-AGAAATAACA
66 TGCCTCAAACAAGACGAAATTTGTTTT-AAGAGAAATAACA
* *
320754 ATCTCAAGTGAGATTAATTTTTGTTTCAA-GTGAATCAAATTCGAAATTTGTA-TATAAAAGGAA
1 ATCTCAAGTGAGATCAACTTTT-TTT-AATGTGAA-CAAATTCGAAATTTGTATTATAAAAGG--
* * *
320817 AAAAATGTCTCAAGCAAGACGAAGTTTGTTTTAAGAGAAAT
61 AAAAATGCCTCAAACAAGACGAAATTTGTTTTAAGAGAAAT
320858 TGTCTCAAAT
Statistics
Matches: 87, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
105 20 0.23
106 15 0.17
107 19 0.22
108 33 0.38
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (105 bp):
ATCTCAAGTGAGATCAACTTTTTTTAATGTGAACAAATTCGAAATTTGTATTATAAAAGGAAAAA
TGCCTCAAACAAGACGAAATTTGTTTTAAGAGAAATAACA
Found at i:325038 original size:55 final size:55
Alignment explanation
Indices: 324975--325543 Score: 579
Period size: 55 Copynumber: 10.6 Consensus size: 55
324965 ATGACAGTCT
* ** *
324975 GCTCCCTATTCTTTCATG-GAGTATAAGACTCGAACAATCTTCAATAAACGTATCT
1 GCTCCCTATTCCTTCA-GAGAGTATAAGACTCGAACAATCTTCAATAAACGGGTCC
* * *
325030 GCTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGGGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGGGTCC
* *
325085 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTC-ATAAAACGGGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAAT-AAACGGGTCC
* *
325140 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTC-ATAAAACAGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAAT-AAACGGGTCC
*
325195 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAATAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAATAAACGGGTCC
* *
325250 GCTCCCTA-TCCGTTCAGGGAGTAT-AGAACCCGAACAATCTTC-ATAAAACGGGTCC
1 GCTCCCTATTCC-TTCAGAGAGTATAAG-ACTCGAACAATCTTCAAT-AAACGGGTCC
* *
325305 GCTCCCTA-TCCGTTCAGGGAGTATAAGACTCG----ATCTTCAATAAACGTGTCC
1 GCTCCCTATTCC-TTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGGGTCC
* * ** **
325356 GCTCCCTATTCCTTCAGAGAGTATATGACTCAAACAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGGGTCC
* ** **
325411 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGGGTCC
* ** ** *
325462 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGGGTCC
* *
325513 ACTCCCTATTCCTTCAGAGAGTATATGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTC
325544 AATCTTCAAC
Statistics
Matches: 476, Mismatches: 24, Indels: 31
0.90 0.05 0.06
Matches are distributed among these distances:
51 139 0.29
52 5 0.01
54 10 0.02
55 318 0.67
56 4 0.01
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGGGTCC
Found at i:325243 original size:165 final size:165
Alignment explanation
Indices: 324975--325537 Score: 646
Period size: 165 Copynumber: 3.5 Consensus size: 165
324965 ATGACAGTCT
* * *
324975 GCTCCCTATTCTTTCATG-GAGTATAAGACTCGAACAATCTTCAATAAACGTATCTGCTCCCTAT
1 GCTCCCTATTCCTTCA-GAGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCCGCTCCCTAT
* * * *
325039 TCATTCAGGGAGTATA-AGACTCGAACAATCTTCAATAAACGGGTCTGCTCTCTATTCCTTCAGA
65 TCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAATAAACGGGTCCGCTCCCTATTCCTTCAGA
*
325103 GAGTATAGAACTCGAACAATCTTCATAAAACGGGTCT
129 GAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
* *
325140 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTC-ATAAAACAG-GTCCGCTCTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAAT-AAAC-GTGTCCGCTCCCT
325202 ATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGGGTCCGCTCCCTA-TCCGTTCA
63 ATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGGGTCCGCTCCCTATTCC-TTCA
* *
325266 GGGAGTATAGAACCCGAACAATCTTCATAAAACGGGTCC
127 GAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
*
325305 GCTCCCTA-TCCGTTCAGGGAGTATAAGACTCG----ATCTTCAATAAACGTGTCCGCTCCCTAT
1 GCTCCCTATTCC-TTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCCGCTCCCTAT
* ** **
325365 TCCTTCAGAGAGTATATG-ACTCAAACAATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGA
65 TCCTTCAGAGAGTATA-GAACTCGAACAATCTTCAATAAACGGGTCCGCTCCCTATTCCTTCAGA
* * **
325429 GAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
129 GAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCC
* ** * **
325462 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCTACTCCCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCCGCTCCCTATT
325523 CCTTCAGAGAGTATA
66 CCTTCAGAGAGTATA
325538 TGACTCAATC
Statistics
Matches: 349, Mismatches: 33, Indels: 40
0.83 0.08 0.09
Matches are distributed among these distances:
156 1 0.00
157 79 0.23
158 3 0.01
160 1 0.00
161 84 0.24
162 6 0.02
164 11 0.03
165 160 0.46
166 4 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (165 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCCGCTCCCTATT
CCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGGGTCCGCTCCCTATTCCTTCAGAGA
GTATAGAACTCGAACAATCTTCATAAAACGGGTCC
Found at i:326994 original size:19 final size:19
Alignment explanation
Indices: 326962--327016 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
326952 TTATATTTTT
326962 CATTTTT-A-TTTTTTCAC
1 CATTTTTCATTTTTTTCAC
*
326979 CATTTTTCATTTTTTTTC-T
1 CATTTTTCA-TTTTTTTCAC
326998 CATTTTTCATTTTCTTTCA
1 CATTTTTCATTTT-TTTCA
327017 TTTTTCCTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
17 7 0.22
18 5 0.16
19 13 0.41
20 7 0.22
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (19 bp):
CATTTTTCATTTTTTTCAC
Found at i:326995 original size:20 final size:20
Alignment explanation
Indices: 326970--327016 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
326960 TTCATTTTTA
326970 TTTTTTCACCATTTTTCATT
1 TTTTTTCACCATTTTTCATT
*
326990 TTTTTTC-TCATTTTTCATT
1 TTTTTTCACCATTTTTCATT
*
327009 TTCTTTCA
1 TTTTTTCA
327017 TTTTTCCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.13, C:0.19, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTTCACCATTTTTCATT
Found at i:327000 original size:12 final size:11
Alignment explanation
Indices: 326981--327069 Score: 51
Period size: 11 Copynumber: 7.9 Consensus size: 11
326971 TTTTTCACCA
326981 TTTTTCATTTT
1 TTTTTCATTTT
326992 TTTTCTCATTTT
1 TTTT-TCATTTT
*
327004 TCATTTTC-TTTCA
1 T--TTTTCATTT-T
* **
327017 TTTTTCCTCCT
1 TTTTTCATTTT
327028 TTTTTC-TTTT
1 TTTTTCATTTT
327038 TTTTTC-TTTT
1 TTTTTCATTTT
327048 TTCTTTC-TCTTT
1 TT-TTTCAT-TTT
*
327060 TTTTTAATTT
1 TTTTTCATTT
327070 CTTCTTCAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
10 14 0.22
11 25 0.40
12 18 0.29
13 3 0.05
14 3 0.05
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTCATTTT
Found at i:327010 original size:17 final size:16
Alignment explanation
Indices: 326957--327022 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 16
326947 ACGTTTTATA
326957 TTTTTCATTTTT-ATT
1 TTTTTCATTTTTCATT
*
326972 TTTTCACCATTTTTCATTTT
1 TTTT--TCATTTTTCA--TT
326992 TTTTCTCATTTTTCATT
1 TTTT-TCATTTTTCATT
327009 TTCTTTCATTTTTC
1 TT-TTTCATTTTTC
327023 CTCCTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
15 4 0.10
17 20 0.48
18 3 0.07
19 9 0.21
20 6 0.14
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTCATTTTTCATT
Found at i:327020 original size:27 final size:27
Alignment explanation
Indices: 326982--327051 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
326972 TTTTCACCAT
*
326982 TTTTCATT-TTTTTTCT-CATTTTTCA
1 TTTTCTTTCTTTTTTCTCCATTTTTCA
* * *
327007 TTTTCTTTCATTTTTCCTCCTTTTTTCT
1 TTTTCTTTC-TTTTTTCTCCATTTTTCA
*
327035 TTTTTTTTCTTTTTTCT
1 TTTTCTTTCTTTTTTCT
327052 TTCTCTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
25 7 0.19
27 14 0.39
28 15 0.42
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.76
Consensus pattern (27 bp):
TTTTCTTTCTTTTTTCTCCATTTTTCA
Found at i:327060 original size:13 final size:11
Alignment explanation
Indices: 326981--327064 Score: 53
Period size: 12 Copynumber: 7.3 Consensus size: 11
326971 TTTTTCACCA
326981 TTTTTCATTTTT
1 TTTTTC-TTTTT
*
326993 TTTCTCATTTTT
1 TTTTTC-TTTTT
* **
327005 CATTTTCTTTCA
1 -TTTTTCTTTTT
* **
327017 TTTTTCCTCCT
1 TTTTTCTTTTT
327028 TTTTTC-TTTT
1 TTTTTCTTTTT
327038 TTTTTCTTTTT
1 TTTTTCTTTTT
327049 TCTTTCTCTTTTT
1 T-TTT-TCTTTTT
327062 TTT
1 TTT
327065 AATTTCTTCT
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
10 8 0.14
11 18 0.32
12 19 0.33
13 12 0.21
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:327064 original size:17 final size:17
Alignment explanation
Indices: 327026--327064 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
327016 ATTTTTCCTC
*
327026 CTTTTTTCTTTTTTTTT
1 CTTTTTTCTTTTCTTTT
327043 CTTTTTTCTTTCTCTTTT
1 CTTTTTTCTTT-TCTTTT
327061 -TTTT
1 CTTTT
327065 AATTTCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
CTTTTTTCTTTTCTTTT
Found at i:327074 original size:23 final size:23
Alignment explanation
Indices: 327032--327075 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
327022 CCTCCTTTTT
** *
327032 TCTTTTTTTTTCTTTTTTCTTTC
1 TCTTTTTTTTAATTTCTTCTTTC
327055 TCTTTTTTTTAATTTCTTCTT
1 TCTTTTTTTTAATTTCTTCTT
327076 CAAGCGAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (23 bp):
TCTTTTTTTTAATTTCTTCTTTC
Found at i:336789 original size:45 final size:47
Alignment explanation
Indices: 336717--336805 Score: 137
Period size: 45 Copynumber: 1.9 Consensus size: 47
336707 TGCTTTGTTA
*
336717 TTCACAAAAATAAATCCTAACTACATGATATCTAATTCGCATGCTTG
1 TTCACAAAAATAAATCCTAACCACATGATATCTAATTCGCATGCTTG
* *
336764 TTCA-AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGC
1 TTCACAAAAATAAATCCTAACCACATGATATCTAATTCGCATGC
336806 ATTTATTCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 26 0.67
46 9 0.23
47 4 0.10
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.29
Consensus pattern (47 bp):
TTCACAAAAATAAATCCTAACCACATGATATCTAATTCGCATGCTTG
Found at i:341250 original size:2 final size:2
Alignment explanation
Indices: 341245--341273 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
341235 AATTTTTTAA
341245 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 A
341274 ACTCAATTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:346424 original size:17 final size:17
Alignment explanation
Indices: 346402--346470 Score: 72
Period size: 17 Copynumber: 4.1 Consensus size: 17
346392 ATTAACATTG
346402 TTAAATCATCATTATTA
1 TTAAATCATCATTATTA
*
346419 TTAAAT--T-ATTGTTA
1 TTAAATCATCATTATTA
346433 TTAAATCATCATCATTATTA
1 TT-AA--ATCATCATTATTA
*
346453 TTAAATCATTATTATTA
1 TTAAATCATCATTATTA
346470 T
1 T
346471 ACCATTAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.19
15 3 0.07
17 21 0.49
19 3 0.07
20 8 0.19
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (17 bp):
TTAAATCATCATTATTA
Found at i:346460 original size:14 final size:14
Alignment explanation
Indices: 346443--346469 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
346433 TTAAATCATC
346443 ATCATTATTATTAA
1 ATCATTATTATTAA
346457 ATCATTATTATTA
1 ATCATTATTATTA
346470 TACCATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
ATCATTATTATTAA
Found at i:346469 original size:20 final size:20
Alignment explanation
Indices: 346423--346470 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
346413 TTATTATTAA
*
346423 ATTATTGTTATTAAATCATC
1 ATTATTATTATTAAATCATC
* *
346443 ATCATTATTATTAAATCATT
1 ATTATTATTATTAAATCATC
346463 ATTATTAT
1 ATTATTAT
346471 ACCATTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTATTATTATTAAATCATC
Found at i:349220 original size:2 final size:2
Alignment explanation
Indices: 349213--349263 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
349203 TACATATGAA
349213 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
349255 AT AT AT AT A
1 AT AT AT AT A
349264 GAACAAAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:350471 original size:60 final size:60
Alignment explanation
Indices: 350391--350554 Score: 170
Period size: 60 Copynumber: 2.7 Consensus size: 60
350381 CTTAAAGTTT
* * * ** * *
350391 TATGATCTTTATT-TCAAATTAGTCCTTAAAGTTTTAAACATTTCAATTTTATCCTTAAAT
1 TATGATCTTCATTCT-AAATTAGTCCTCAAACTTTTAAACATTTCAATTCCATCCCTAAAC
* * * *
350451 TATGAGT-TTCATTCTAAATTAATCCTCAAACTTTTAAGCATTTTAATTCCATCCCTGAAC
1 TATGA-TCTTCATTCTAAATTAGTCCTCAAACTTTTAAACATTTCAATTCCATCCCTAAAC
* *
350511 TATGATCTTCATTCTAAATTAGTCCCCAAACTTTTTTAACATTT
1 TATGATCTTCATTCTAAATTAGTCCTCAAAC-TTTTAAACATTT
350555 TATTTTCATC
Statistics
Matches: 85, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
59 1 0.01
60 72 0.85
61 12 0.14
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (60 bp):
TATGATCTTCATTCTAAATTAGTCCTCAAACTTTTAAACATTTCAATTCCATCCCTAAAC
Found at i:354153 original size:32 final size:32
Alignment explanation
Indices: 354097--354158 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
354087 TCCTAAAGTG
354097 TTTTTTTGTCAAAATAAATACCTAAATGTATAT
1 TTTTTTTGTCAAAATAAATACCTAAA-GTATAT
*
354130 TTTTTTTGTCAAAATAAGT-CCTAAAGTAT
1 TTTTTTTGTCAAAATAAATACCTAAAGTAT
354159 TTTATGTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 4 0.14
32 6 0.21
33 18 0.64
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (32 bp):
TTTTTTTGTCAAAATAAATACCTAAAGTATAT
Found at i:354310 original size:26 final size:26
Alignment explanation
Indices: 354272--354321 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
354262 ATTGAATATT
* *
354272 TTAAATATTTATTTTGATAAAAAAAA
1 TTAAATATCTATTTGGATAAAAAAAA
354298 TTAAATATCTATTTGGATAAAAAA
1 TTAAATATCTATTTGGATAAAAAA
354322 GGTAACTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (26 bp):
TTAAATATCTATTTGGATAAAAAAAA
Found at i:355814 original size:20 final size:21
Alignment explanation
Indices: 355789--355840 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
355779 TTTTCCCAAT
*
355789 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
355809 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
355830 TCGCAATGCGA
1 TCGCAATGCGA
355841 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:355853 original size:41 final size:41
Alignment explanation
Indices: 355826--355953 Score: 125
Period size: 41 Copynumber: 3.1 Consensus size: 41
355816 GCGAATTGGG
* * *
355826 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
* * *
355867 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAAT-AC
** * * *
355909 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
*
355948 ATAATC
1 AAAATC
355954 ACAATGCGAT
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
39 2 0.03
40 31 0.44
41 35 0.50
42 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
Found at i:355854 original size:20 final size:20
Alignment explanation
Indices: 355829--355943 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
355819 AATTGGGAAA
*
355829 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
355849 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
355870 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
355890 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
355910 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
355930 TTCGCAACGCGATA
1 ATCGCAACGCGATA
355944 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:356159 original size:22 final size:22
Alignment explanation
Indices: 356131--356174 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
356121 CACTCTCTCA
356131 CCCATCTCCGAAGAAATCCGTC
1 CCCATCTCCGAAGAAATCCGTC
**
356153 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGAAGAAATCCGTC
356175 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.43, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGAAGAAATCCGTC
Found at i:357837 original size:18 final size:18
Alignment explanation
Indices: 357816--357860 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
357806 TCCACTTCGG
*
357816 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
357834 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
357852 GAGCCATCA
1 GAGCCATCA
357861 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:358396 original size:19 final size:20
Alignment explanation
Indices: 358343--358397 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
358333 AGTTTACTTT
* *
358343 CGCAACACGAAAATGACTAC
1 CGCAACGCGGAAATGACTAC
* *
358363 CGCAACGCGGAAATGGCTAT
1 CGCAACGCGGAAATGACTAC
*
358383 CGCAATGC-GAAATGA
1 CGCAACGCGGAAATGA
358398 AAATCGCAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.38, C:0.25, G:0.24, T:0.13
Consensus pattern (20 bp):
CGCAACGCGGAAATGACTAC
Found at i:358416 original size:14 final size:14
Alignment explanation
Indices: 358397--358448 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 14
358387 ATGCGAAATG
358397 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
358411 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
358427 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
358443 AAAATC
1 AAAATC
358449 ACAAAGCGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 15 0.47
16 8 0.25
18 9 0.28
ACGTcount: A:0.50, C:0.23, G:0.15, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:358439 original size:32 final size:33
Alignment explanation
Indices: 358381--358471 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
358371 GGAAATGGCT
358381 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
358414 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
358446 ATCACAAAGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
358472 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:358507 original size:14 final size:14
Alignment explanation
Indices: 358488--358545 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
358478 TTGTGTTTCG
*
358488 CGTTGCGATTTTAT
1 CGTTGCGATTTTTT
358502 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TTT
358518 CGTGTTGCGATTTTTT
1 C--GTTGCGATTTTTT
358534 CGTTGCGATTTT
1 CGTTGCGATTTT
358546 CATTTCGCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 22 0.56
16 7 0.18
18 10 0.26
ACGTcount: A:0.10, C:0.16, G:0.22, T:0.52
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:358525 original size:32 final size:33
Alignment explanation
Indices: 358483--358561 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
358473 GCGATTTGTG
358483 TTTCGCGTTGCGATTTTATCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTATCGTTGCGATTTTCA
* *
358515 TTTCGTGTTGCGATTTTTTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTATCGTTGCGATTTTCA
*
358548 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
358562 AGCCATTTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 25 0.60
33 17 0.40
ACGTcount: A:0.11, C:0.18, G:0.22, T:0.49
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTATCGTTGCGATTTTCA
Found at i:358580 original size:20 final size:19
Alignment explanation
Indices: 358546--358601 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
358536 TTGCGATTTT
*
358546 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
358565 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
358585 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
358602 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:360491 original size:14 final size:14
Alignment explanation
Indices: 360472--360508 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
360462 GATTGTTTAA
360472 TTGATTTGTAAATG
1 TTGATTTGTAAATG
360486 TTGATTTGTAAATG
1 TTGATTTGTAAATG
360500 TTGATTTGT
1 TTGATTTGT
360509 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (14 bp):
TTGATTTGTAAATG
Found at i:360661 original size:14 final size:14
Alignment explanation
Indices: 360618--360668 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 14
360608 AATGGCTATT
360618 GCAACGAGAAAATC
1 GCAACGAGAAAATC
360632 GCAATACGAAATGAAAATC
1 GC-A-ACG--A-GAAAATC
360651 GCAACGAGAAAATC
1 GCAACGAGAAAATC
360665 GCAA
1 GCAA
360669 TGCGATTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 13 0.41
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 9 0.28
ACGTcount: A:0.51, C:0.20, G:0.20, T:0.10
Consensus pattern (14 bp):
GCAACGAGAAAATC
Found at i:360717 original size:20 final size:20
Alignment explanation
Indices: 360692--360749 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
360682 TCGCATTGCA
*
360692 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
360712 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
360732 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
360750 TCAAATTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:361833 original size:24 final size:24
Alignment explanation
Indices: 361806--361859 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
361796 GTATTCGAAA
* *
361806 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
361830 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
361854 TTTGAT
1 TTTGAT
361860 GATGTTTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:363393 original size:19 final size:19
Alignment explanation
Indices: 363369--363461 Score: 71
Period size: 19 Copynumber: 5.4 Consensus size: 19
363359 ATTACGAGAG
363369 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
363388 AATCGCAA--CG--CT-AA
1 AATCGCAATGCGAAATGAA
**
363402 TTTCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
**
363421 AATCGCAA--CG--A-GGG
1 AATCGCAATGCGAAATGAA
363435 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
363454 AATCGCAA
1 AATCGCAA
363462 CATGAATTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 20
0.64 0.12 0.24
Matches are distributed among these distances:
14 17 0.31
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 25 0.46
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:363413 original size:33 final size:32
Alignment explanation
Indices: 363368--363463 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 32
363358 AATTACGAGA
363368 GAATCGCAATGCGAAATGAAAATCGCAAC-GC
1 GAATCGCAATGCGAAATGAAAATCGCAACAGC
* *
363399 TAATTTCGCAATGCGAAATGAAAATCGCAACGAGG
1 GAA--TCGCAATGCGAAATGAAAATCGCAAC-AGC
363434 GAATCGCAATGCGAAATGAAAATCGCAACA
1 GAATCGCAATGCGAAATGAAAATCGCAACA
363464 TGAATTTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
31 2 0.03
32 1 0.02
33 52 0.90
35 3 0.05
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.16
Consensus pattern (32 bp):
GAATCGCAATGCGAAATGAAAATCGCAACAGC
Found at i:363497 original size:14 final size:14
Alignment explanation
Indices: 363478--363534 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
363468 TTTAATTTCG
363478 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
363492 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
363511 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
363525 CGTTGCGATT
1 CGTTGCGATT
363535 TTCATTTCGT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:363514 original size:33 final size:33
Alignment explanation
Indices: 363472--363552 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
363462 CATGAATTTA
363472 ATTTCGCGTTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTCTCTCGTTGCGATTTTC
363505 ATTTCGCGTTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTCTCTCGTTGCGATTTTC
**
363538 ATTTCGTATTGCGAT
1 ATTTCGCGTTGCGAT
363553 AGTACTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.46
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTCTCGTTGCGATTTTC
Done.