Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000388.1 Hibiscus syriacus cultivar Beakdansim tig00000714_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: 69169
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:76 original size:15 final size:15
Alignment explanation
Indices: 56--104 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
46 ATCATTGACT
56 TTTAATTCTTTTTAA
1 TTTAATTCTTTTTAA
* *
71 TTTAATCCCTTTTAA
1 TTTAATTCTTTTTAA
*
86 TTTGAATTTTCTTTTAA
1 TTT-AATTCT-TTTTAA
103 TT
1 TT
105 CTTTTATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 16 0.59
16 3 0.11
17 8 0.30
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.63
Consensus pattern (15 bp):
TTTAATTCTTTTTAA
Found at i:253 original size:18 final size:19
Alignment explanation
Indices: 209--251 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
199 ATTTGAATCG
209 AACTTTTAAA-TTTAATTT
1 AACTTTTAAATTTTAATTT
227 AACTTTTAAATTTTAATTT
1 AACTTTTAAATTTTAATTT
246 AACTTT
1 AACTTT
252 AATTTTCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (19 bp):
AACTTTTAAATTTTAATTT
Found at i:3553 original size:15 final size:15
Alignment explanation
Indices: 3533--3562 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3523 ATTTTTTATC
3533 TCTTAAAATTATTTT
1 TCTTAAAATTATTTT
3548 TCTTAAAATTATTTT
1 TCTTAAAATTATTTT
3563 AAGGTATTTT
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:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (15 bp):
TCTTAAAATTATTTT
Found at i:11228 original size:20 final size:20
Alignment explanation
Indices: 11199--11243 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
11189 CCCAAATTGC
* * *
11199 TAAGTCTTTCGTGCCATCAG
1 TAAGTATTTCGGGCCAACAG
11219 TAAGTATTTCGGGCCAACAG
1 TAAGTATTTCGGGCCAACAG
11239 TAAGT
1 TAAGT
11244 CTTTAGAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (20 bp):
TAAGTATTTCGGGCCAACAG
Found at i:11286 original size:42 final size:41
Alignment explanation
Indices: 11226--11319 Score: 116
Period size: 42 Copynumber: 2.3 Consensus size: 41
11216 CAGTAAGTAT
* * * *
11226 TTCGGGCCAACAGTAAGTCTTTAGAGCATGATGATTAAATCC
1 TTCGGGCCATCTGCAAGTCTTTAGAGCAAGATGA-TAAATCC
* * *
11268 TTCGGGTCATCTGCAAGTCTTTCGAGCAAGATGATAAGTCC
1 TTCGGGCCATCTGCAAGTCTTTAGAGCAAGATGATAAATCC
11309 TTCGGGCCATC
1 TTCGGGCCATC
11320 CGTAAGACCT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 16 0.36
42 28 0.64
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (41 bp):
TTCGGGCCATCTGCAAGTCTTTAGAGCAAGATGATAAATCC
Found at i:11542 original size:42 final size:41
Alignment explanation
Indices: 11480--11584 Score: 138
Period size: 42 Copynumber: 2.5 Consensus size: 41
11470 AATTGGTAAG
** *
11480 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCTGTAAGTCTTTCGAGCAAGATGA-TAAA
* *
11522 TCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAG
1 TCCTTCGGGCCATCTGTAAGTCTTTCGAGCAAGATGATAAA
* *
11563 TCCTTCGAGCCATTTGTAAGTC
1 TCCTTCGGGCCATCTGTAAGTC
11585 CTTCAGGTAG
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 22 0.40
42 33 0.60
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (41 bp):
TCCTTCGGGCCATCTGTAAGTCTTTCGAGCAAGATGATAAA
Found at i:11562 original size:21 final size:21
Alignment explanation
Indices: 11495--11572 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
11485 CGGGCCATCA
* *
11495 ATAAGTCTTTCGAGCATGATG
1 ATAAGTCCTTCGAGCAAGATG
* * **
11516 ATTAAATCCTTCGGGTC-ATCTG
1 A-TAAGTCCTTCGAG-CAAGATG
*
11538 -TAAGTCTTTCGAGCAAGATG
1 ATAAGTCCTTCGAGCAAGATG
11558 ATAAGTCCTTCGAGC
1 ATAAGTCCTTCGAGC
11573 CATTTGTAAG
Statistics
Matches: 41, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
19 1 0.02
20 13 0.32
21 14 0.34
22 12 0.29
23 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (21 bp):
ATAAGTCCTTCGAGCAAGATG
Found at i:11584 original size:20 final size:20
Alignment explanation
Indices: 11475--11588 Score: 70
Period size: 20 Copynumber: 5.5 Consensus size: 20
11465 TCCCAAATTG
*
11475 GTAAGTCCTTCGGGCCATCA-
1 GTAAGTCCTTCGAGCCAT-AT
* *
11495 ATAAGTCTTTCGAG-CATGAT
1 GTAAGTCCTTCGAGCCAT-AT
* * * *
11515 GATTAAATCCTTCGGGTCATCT
1 G--TAAGTCCTTCGAGCCATAT
* * *
11537 GTAAGTCTTTCGAGCAAGAT
1 GTAAGTCCTTCGAGCCATAT
*
11557 GATAAGTCCTTCGAGCCATTT
1 G-TAAGTCCTTCGAGCCATAT
11578 GTAAGTCCTTC
1 GTAAGTCCTTC
11589 AGGTAGGATG
Statistics
Matches: 69, Mismatches: 20, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
19 4 0.06
20 34 0.49
21 16 0.23
22 12 0.17
23 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (20 bp):
GTAAGTCCTTCGAGCCATAT
Found at i:22042 original size:18 final size:18
Alignment explanation
Indices: 22016--22051 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
22006 TCGGAAGGAC
*
22016 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
22034 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
22052 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:33067 original size:20 final size:21
Alignment explanation
Indices: 33033--33071 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
33023 AGACTAAATC
*
33033 GAAATAAATGCAAAATATAAA
1 GAAATAAATGAAAAATATAAA
33054 GAAAT-AATGAAAAATATA
1 GAAATAAATGAAAAATATA
33072 GTAAATTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.67, C:0.03, G:0.10, T:0.21
Consensus pattern (21 bp):
GAAATAAATGAAAAATATAAA
Found at i:33108 original size:2 final size:2
Alignment explanation
Indices: 33103--33180 Score: 90
Period size: 2 Copynumber: 39.5 Consensus size: 2
33093 AATTCAAAAA
*
33103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AGT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* *
33145 AT AT AA AT -T AT AT AT AT AT ACT AT AT TT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A
33181 AACTATATAA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
1 3 0.05
2 60 0.92
3 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33185 original size:18 final size:19
Alignment explanation
Indices: 33152--33188 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
33142 TATATATAAA
*
33152 TTATATATATATACTATAT
1 TTATATATATAAACTATAT
33171 TTATAT-TATAAACTATAT
1 TTATATATATAAACTATAT
33189 AATTATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATATATATAAACTATAT
Found at i:33250 original size:24 final size:23
Alignment explanation
Indices: 33105--33189 Score: 65
Period size: 24 Copynumber: 3.9 Consensus size: 23
33095 TTCAAAAAAT
* *
33105 ATATATATATATA-TATATATAT
1 ATATATATATAAACTATATATAA
**
33127 ATATATATATAAGTTTATATATAA
1 ATATATATATAA-ACTATATATAA
*
33151 ATTATATATATATACTATAT-T--
1 A-TATATATATAAACTATATATAA
33172 -TATAT-TATAAACTATATA
1 ATATATATATAAACTATATA
33190 ATTATTATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
18 11 0.21
19 5 0.10
22 11 0.21
23 1 0.02
24 14 0.27
25 10 0.19
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (23 bp):
ATATATATATAAACTATATATAA
Found at i:33274 original size:13 final size:13
Alignment explanation
Indices: 33103--33274 Score: 81
Period size: 13 Copynumber: 13.2 Consensus size: 13
33093 AATTCAAAAA
*
33103 ATATATATATA-T
1 ATATATATAAACT
*
33115 ATATATATATA-T
1 ATATATATAAACT
*
33127 ATATATATATAAGT
1 ATATATATA-AACT
* *
33141 TTATATATAAATT
1 ATATATATAAACT
*
33154 ATATATATATACT
1 ATATATATAAACT
* *
33167 ATAT-T-TATATT
1 ATATATATAAACT
*
33178 ATAAACTATATAA-T
1 ATATA-TATA-AACT
**
33192 -TAT-TATAAGTT
1 ATATATATAAACT
*
33203 ATATATATAAATT
1 ATATATATAAACT
*
33216 ATGGTCATATGAAA-T
1 AT-AT-ATAT-AAACT
33231 ATATATATAAACT
1 ATATATATAAACT
**
33244 ATATATGCAAACT
1 ATATATATAAACT
33257 ATATATGTATAAACT
1 ATATA--TATAAACT
33272 ATA
1 ATA
33275 AAAAGTATAT
Statistics
Matches: 127, Mismatches: 18, Indels: 27
0.74 0.10 0.16
Matches are distributed among these distances:
10 1 0.01
11 13 0.10
12 28 0.22
13 51 0.40
14 14 0.11
15 17 0.13
16 3 0.02
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (13 bp):
ATATATATAAACT
Found at i:33463 original size:17 final size:17
Alignment explanation
Indices: 33441--33482 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
33431 TTGGAAAATT
33441 TTGAGATTATAGA-GAAA
1 TTGAGATT-TAGAGGAAA
33458 TTGAGAATTTAGAGGGAAA
1 TTGAG-ATTTAGA-GGAAA
33477 TTGAGA
1 TTGAGA
33483 ATTGAGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 9 0.41
18 4 0.18
19 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (17 bp):
TTGAGATTTAGAGGAAA
Found at i:33735 original size:10 final size:10
Alignment explanation
Indices: 33709--33783 Score: 64
Period size: 10 Copynumber: 7.5 Consensus size: 10
33699 GCGCGCGCGC
33709 GCGTGTGTGT
1 GCGTGTGTGT
33719 GC-T-TGTGT
1 GCGTGTGTGT
33727 GCGTGTGTGCAT
1 GCGTGTGTG--T
* *
33739 GCGCGTGCGT
1 GCGTGTGTGT
* *
33749 GCGCGTGCGT
1 GCGTGTGTGT
*
33759 GCGTGTGCGT
1 GCGTGTGTGT
*
33769 GCGTATGTGT
1 GCGTGTGTGT
33779 GCGTG
1 GCGTG
33784 CGTGCGTGCG
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
8 7 0.13
9 2 0.04
10 38 0.69
12 8 0.15
ACGTcount: A:0.03, C:0.19, G:0.47, T:0.32
Consensus pattern (10 bp):
GCGTGTGTGT
Found at i:33750 original size:4 final size:4
Alignment explanation
Indices: 33741--33809 Score: 69
Period size: 4 Copynumber: 18.2 Consensus size: 4
33731 GTGTGCATGC
*
33741 GCGT GCGT GC-- GCGT GCGT GCGT --GT GCGT GCGTAT GTGT GCGT GCGT
1 GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCG--T GCGT GCGT GCGT
33787 GCGT GCGT GCGT GC-- GCGT GCGT G
1 GCGT GCGT GCGT GCGT GCGT GCGT G
33810 TATAAACTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
2 6 0.11
4 46 0.84
6 3 0.05
ACGTcount: A:0.01, C:0.23, G:0.49, T:0.26
Consensus pattern (4 bp):
GCGT
Found at i:33758 original size:14 final size:14
Alignment explanation
Indices: 33741--33809 Score: 88
Period size: 14 Copynumber: 5.1 Consensus size: 14
33731 GTGTGCATGC
*
33741 GCGTGCGTGCGCGT
1 GCGTGCGTGTGCGT
33755 GCGTGCGTGTGCGT
1 GCGTGCGTGTGCGT
**
33769 GCGTATGTGTGCGT
1 GCGTGCGTGTGCGT
33783 GCGTGC--GTGCGT
1 GCGTGCGTGTGCGT
*
33795 GCGTGCGCGTGCGT
1 GCGTGCGTGTGCGT
33809 G
1 G
33810 TATAAACTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
12 12 0.25
14 36 0.75
ACGTcount: A:0.01, C:0.23, G:0.49, T:0.26
Consensus pattern (14 bp):
GCGTGCGTGTGCGT
Found at i:33806 original size:10 final size:10
Alignment explanation
Indices: 33733--33809 Score: 77
Period size: 10 Copynumber: 7.7 Consensus size: 10
33723 GTGTGCGTGT
*
33733 GTGCATGCGC
1 GTGCGTGCGC
33743 GTGCGTGCGC
1 GTGCGTGCGC
*
33753 GTGCGTGCGT
1 GTGCGTGCGC
33763 GTGCGT--GC
1 GTGCGTGCGC
** *
33771 GTATGTGTGC
1 GTGCGTGCGC
33781 GTGCGTGCGTGC
1 GTGCGTGC--GC
33793 GTGCGTGCGC
1 GTGCGTGCGC
33803 GTGCGTG
1 GTGCGTG
33810 TATAAACTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
8 5 0.09
10 40 0.73
12 10 0.18
ACGTcount: A:0.03, C:0.23, G:0.48, T:0.26
Consensus pattern (10 bp):
GTGCGTGCGC
Found at i:33908 original size:2 final size:2
Alignment explanation
Indices: 33901--33939 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
33891 ATCTATAGAT
33901 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33940 GAAATATTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34033 original size:7 final size:7
Alignment explanation
Indices: 34021--34053 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
34011 CCCTAAATAT
34021 TTAACCC
1 TTAACCC
34028 TTAACCC
1 TTAACCC
34035 TTAACCC
1 TTAACCC
34042 -TAA-CC
1 TTAACCC
34047 TTAACCC
1 TTAACCC
34054 ATGAACTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 2 0.08
6 6 0.25
7 16 0.67
ACGTcount: A:0.30, C:0.42, G:0.00, T:0.27
Consensus pattern (7 bp):
TTAACCC
Found at i:34161 original size:12 final size:12
Alignment explanation
Indices: 34141--34171 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
34131 TATTAATATA
34141 GTATATATGTAT
1 GTATATATGTAT
*
34153 GTATGTATGTAT
1 GTATATATGTAT
34165 GTATATA
1 GTATATA
34172 AACTATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.48
Consensus pattern (12 bp):
GTATATATGTAT
Found at i:34232 original size:76 final size:75
Alignment explanation
Indices: 34092--34236 Score: 247
Period size: 78 Copynumber: 1.9 Consensus size: 75
34082 TGCGTGCGTG
34092 TATAAACTATATAAAATATAGTTTATAAATTATAATTTATATTAATATAGTATATATGTATGTAT
1 TATAAACTATATAAAATATAGTTTATAAATTATAATTTATATTAATATAGTATATA-GTATGTAT
34157 GTATGTATGTA
65 GTATGTATGTA
*
34168 TATAAACTATATAAACTATATAGTTTATAAATTGTAATTTATATTAATATAGTATATA-TATGTA
1 TATAAACTATATAAA--ATATAGTTTATAAATTATAATTTATATTAATATAGTATATAGTATGTA
34232 TGTAT
64 TGTAT
34237 AACTAATATA
Statistics
Matches: 66, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
76 26 0.39
78 40 0.61
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.46
Consensus pattern (75 bp):
TATAAACTATATAAAATATAGTTTATAAATTATAATTTATATTAATATAGTATATAGTATGTATG
TATGTATGTA
Found at i:34268 original size:2 final size:2
Alignment explanation
Indices: 34261--34316 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
34251 ATCTATAGAT
34261 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
34303 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
34317 GAAACATTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34475 original size:11 final size:11
Alignment explanation
Indices: 34437--34492 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
34427 GAACTATATA
34437 TATATATAAAC
1 TATATATAAAC
* *
34448 CATATAT--AG
1 TATATATAAAC
*
34457 TATTTATAAAC
1 TATATATAAAC
34468 TATATAT--A-
1 TATATATAAAC
34476 TATATATAAAC
1 TATATATAAAC
34487 TATATA
1 TATATA
34493 AAGTAAATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
8 7 0.21
9 7 0.21
10 1 0.03
11 19 0.56
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (11 bp):
TATATATAAAC
Found at i:34605 original size:21 final size:21
Alignment explanation
Indices: 34575--34618 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
34565 AGTTTTATAG
34575 AAATCCTAAACCCTAAACACT
1 AAATCCTAAACCCTAAACACT
* * *
34596 AAATCTTAAACCTTAAACCCT
1 AAATCCTAAACCCTAAACACT
34617 AA
1 AA
34619 TATAAATAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATCCTAAACCCTAAACACT
Found at i:35007 original size:524 final size:526
Alignment explanation
Indices: 34468--36470 Score: 2631
Period size: 524 Copynumber: 3.7 Consensus size: 526
34458 ATTTATAAAC
* * * *
34468 TATATATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAATACTTTTCATA
1 TATATATATATATATAAACTATAAAAAGTAAATTACTTATATAGTTTATAGAAACACTATGCATA
* * *
34533 AAATATATAAAGTAATAAAGTAATA-AATGTATAG-T-TTTATAGAAATCCTAAACCCTAAACAC
66 AACTATATAAAGTAATAAAGT-ATACAATTTATAGATATTTATA-AAAACCTAAACCCTAAACAC
* * * ** * *
34595 TAAATCTTAAACCTTAAACCCTAATATAAATAGACTAATACTAATGTATATATATTTATAATAAA
129 TAAATCCTAAACCCTAAACCATAATATAAATAGACTAGCACTAATGCATATATATTTGTAATAAA
** * *
34660 ATTGTGGGCTTATGTATTGGGCCTATGTAAACTAATATAAATGGACTAGCACTAATGCAAATGGA
194 AGAGTGAGCTTATGTATTGGGCCTATGTAAACTAATGTAAATGGACTAGCACTAATGCAAATGGA
* *
34725 CTTATTTTTTGGTTTTATTATTACTTATTCATAACAATAAAATTAATGGGCTATTAATGTGAATT
259 CTTATTTTTTGGTTTTATTATTACTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATT
* * * *
34790 AATCTAACATGCAAATAAAATATTAATTATGCAAATGAAATTAATATGACATGTACTACTATTTA
324 AACCTAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATATGGCATGTACTACTATTTA
* *
34855 TGAATCATATAATATGCAATGTGACATACTAATTATTTAACA-CATAATAAATCATGTTTTATAT
389 TGAACCATATAATATGCAATGTGACATACTAATTATTTAACACCA-AATTAATCATGTTTTATAT
*
34919 AATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATATAATATGTATGTATAACCC
453 AATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATATAATATGTATGTATAAACC
34984 ATGTATAG-
518 ATGTATAGA
*
34992 TATATATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTATGCATA
1 TATATATATATATATAAACTATAAAAAGTAAATTACTTATATAGTTTATAGAAACACTATGCATA
* * * * * * * ** * * **
35057 AACTAAATAAAGAAATAAAGCATATAGTTTATACAAAACTCT-AAACCCTAAACTTTAAAGCA-T
66 AACTATATAAAGTAATAAAGTATACAATTTATAGATATTTATAAAAACCTAAACCCTAAA-CACT
* * *
35120 AAATCCTAAACCCTAAACCCTAATATTAATGGACTAGCACTAATGCATATATATTTGTAATAAAA
130 AAATCCTAAACCCTAAACCATAATATAAATAGACTAGCACTAATGCATATATATTTGTAATAAAA
* * * * *
35185 GAGTGAGCTTATGTATTGGGCCTATATAAACTAATGTAAATGTACCAGCACTATTGCAAATTGAC
195 GAGTGAGCTTATGTATTGGGCCTATGTAAACTAATGTAAATGGACTAGCACTAATGCAAATGGAC
* *
35250 TTATTTTTTTGTTTTATTATTATTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTA
260 TTATTTTTTGGTTTTATTATTACTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTA
35315 ACCTAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATATGGCATGTACTACTATTTAT
325 ACCTAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATATGGCATGTACTACTATTTAT
* * * *
35380 TAACCATATAATATACAATGTGACATACTAATTATTTAATACCAAATTAACCATGTTTTATATAA
390 GAACCATATAATATGCAATGTGACATACTAATTATTTAACACCAAATTAATCATGTTTTATATAA
*
35445 TTTACATTTGAATAATTTTATTAATTTTATTAAATAATTTTATATAATATGTATGTATAAACCAT
455 TTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATATAATATGTATGTATAAACCAT
35510 GTATAGTATATATAAA
520 GTATAG---------A
* *
35526 CTATATATATATATATAAAACTATAAAAAGTAAATTACTTATATAATTTATAGAAATACTATGCA
1 -TATATATATATATAT-AAACTATAAAAAGTAAATTACTTATATAGTTTATAGAAACACTATGCA
* * * *
35591 TAAACTATATAAAGTAATAAAGTATACAGTTTATAGAAATCCTAAATCATAAATCCTAAACCCTA
64 TAAACTATATAAAGTAATAAAGTATACAATTTATAGATAT--T-TAT-A-AAAACCTAAACCCT-
* * * *
35656 AATTTTAAACTATAAACACTAAACCCTAAACCATAATATAAATAAACTAGCACTAATACATATAT
123 AA----ACACTA-AATC-CTAAACCCTAAACCATAATATAAATAGACTAGCACTAATGCATATAT
* * *
35721 ATTTGTAATAAAAGAGTGAGCTTATGTATCGGGCCTATGTAAACTAATGTAAATGAACTAACACT
182 ATTTGTAATAAAAGAGTGAGCTTATGTATTGGGCCTATGTAAACTAATGTAAATGGACTAGCACT
* *
35786 AATACAAATAGACTTATTTTTTGGTTTTATTATTACTTATTCATAACAACAAAATAAATGGGCTA
247 AATGCAAATGGACTTATTTTTTGGTTTTATTATTACTTATTCATAACAACAAAATAAATGGGCTA
35851 TTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATATGGCATG
312 TTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATATGGCATG
*
35916 TACTACTATTTATGAACCATATAATATGCAATTTGACATACTAATTATTTAACACCAAATTAATC
377 TACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAACACCAAATTAATC
* *
35981 ATGTGTTATATAATTTACATTTAAATAATTTTATCAATTTTATTAAATAATTTTATATAATATGT
442 ATGTTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATATAATATGT
*
36046 ATGTATAAATCATGTATAGTATATATAAACTA
507 ATGTATAAACCATGTATAG------------A
36078 TATATATATATATATAAACTATAAAAAGTAAATTACTTATATAG-TTATAGAAACACTATGCATA
1 TATATATATATATATAAACTATAAAAAGTAAATTACTTATATAGTTTATAGAAACACTATGCATA
* *
36142 AACTATATAAAGTAATAAAGTATATAGTTTATAGAAACCCTAAATCATTAACCCTTAACTTTAAA
66 AACTATATAAAGTAATAAAGTATACAATTTATAG--A---T--AT--TT-A----TAA----AAA
** * * *
36207 CCATAAATACTAAACCCTAAA-CCATAAACCATAAACCATAATATAAATGGACTAGCACTAATGC
113 CC-TAAACCCTAAACACTAAATCC-TAAACCCTAAACCATAATATAAATAGACTAGCACTAATGC
36271 ATATATATTTGTAATAAAAGAGTG-GACTTATGTATTGGGCCTATGTAAACTAATGTAAATGGAC
176 ATATATATTTGTAATAAAAGAGTGAG-CTTATGTATTGGGCCTATGTAAACTAATGTAAATGGAC
36335 TAGCACTAATGCAAATGGACTTATTTTTTGGTTTTATTATTACTTATTCATAACAACAAAATAAA
240 TAGCACTAATGCAAATGGACTTATTTTTTGGTTTTATTATTACTTATTCATAACAACAAAATAAA
* * *
36400 TGGGCTATTAATTTGAATTAATCTAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATG
305 TGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATA
36465 TGGCAT
370 TGGCAT
36471 TGTAACCCCC
Statistics
Matches: 1304, Mismatches: 122, Indels: 74
0.87 0.08 0.05
Matches are distributed among these distances:
523 3 0.00
524 460 0.35
525 4 0.00
526 2 0.00
535 15 0.01
536 79 0.06
539 1 0.00
542 11 0.01
543 2 0.00
546 1 0.00
547 3 0.00
548 3 0.00
549 419 0.32
550 28 0.02
551 16 0.01
552 2 0.00
555 2 0.00
556 232 0.18
557 2 0.00
558 5 0.00
559 1 0.00
560 1 0.00
562 6 0.00
563 6 0.00
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (526 bp):
TATATATATATATATAAACTATAAAAAGTAAATTACTTATATAGTTTATAGAAACACTATGCATA
AACTATATAAAGTAATAAAGTATACAATTTATAGATATTTATAAAAACCTAAACCCTAAACACTA
AATCCTAAACCCTAAACCATAATATAAATAGACTAGCACTAATGCATATATATTTGTAATAAAAG
AGTGAGCTTATGTATTGGGCCTATGTAAACTAATGTAAATGGACTAGCACTAATGCAAATGGACT
TATTTTTTGGTTTTATTATTACTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAA
CCTAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATATGGCATGTACTACTATTTATG
AACCATATAATATGCAATGTGACATACTAATTATTTAACACCAAATTAATCATGTTTTATATAAT
TTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATATAATATGTATGTATAAACCATG
TATAGA
Found at i:35115 original size:14 final size:14
Alignment explanation
Indices: 35092--35142 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
35082 AGTTTATACA
35092 AAACTCTAAACCCT
1 AAACTCTAAACCCT
* * *
35106 AAACTTTAAAGCAT
1 AAACTCTAAACCCT
35120 AAA-TCCTAAACCCT
1 AAACT-CTAAACCCT
*
35134 AAACCCTAA
1 AAACTCTAA
35143 TATTAATGGA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
13 1 0.04
14 27 0.96
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.22
Consensus pattern (14 bp):
AAACTCTAAACCCT
Found at i:35546 original size:20 final size:20
Alignment explanation
Indices: 35485--35550 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
35475 TAAATAATTT
*
35485 TATATAATATGTATGTATAAAC
1 TATAT-ATA-GTATATATAAAC
* *
35507 CATGTATAGTATATATAAAC
1 TATATATAGTATATATAAAC
35527 TATATATA-TATATATAAAAC
1 TATATATAGTATATAT-AAAC
35547 TATA
1 TATA
35551 AAAAGTAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
19 7 0.18
20 25 0.66
21 3 0.08
22 3 0.08
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (20 bp):
TATATATAGTATATATAAAC
Found at i:36032 original size:549 final size:543
Alignment explanation
Indices: 34432--36470 Score: 2848
Period size: 549 Copynumber: 3.8 Consensus size: 543
34422 CCCATGAACT
* * * * *
34432 ATATATATATATAAACCATATATAGTATTTATAAACTATATATATATATATAAACTATATAAAGT
1 ATATGTATGTATAAACCATGTATAGTATATATAAACTATATATATATATATAAACTATAAAAAGT
* * * * * *
34497 AAATTACTTATATAGTTTATAGAAATACTTTTCATAAAATATATAAAGTAATAAAGTA-ATAAAT
66 AAATTACTTATATAATTTATAGAAACACTATGCATAAACTATATAAAGTAATAAAGTATAT-AGT
* ** * * * * * *
34561 GTATAG-T-TTTATAGAAATCCTAAACCCT-AA----ACACTA-AATCTTAAACCTTAAACCCTA
130 TTATAGATCTAAATATAAATCCTAAACCCTAAATTTTAAACTATAAACCTAAACCCTAAACCATA
** * * ** *
34618 ATATAAATAGACTAATACTAATGTATATATATTTATAATAAAATTGTGGGCTTATGTATTGGGCC
195 ATATAAATAGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTGAGCTTATGTATTGGGCC
*
34683 TATGTAAACTAATATAAATGGACTAGCACTAATGCAAATGGACTTATTTTTTGGTTTTATTATTA
260 TATGTAAACTAATGTAAATGGACTAGCACTAATGCAAATGGACTTATTTTTTGGTTTTATTATTA
* * * * *
34748 CTTATTCATAACAATAAAATTAATGGGCTATTAATGTGAATTAATCTAACATGCAAATAAAATAT
325 CTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATAC
* *
34813 TAATTATGCAAATGAAATTAATATGACATGTACTACTATTTATGAATCATATAATATGCAATGTG
390 TAATTATGCAAATGAAATTAATATGGCATGTACTACTATTTATGAACCATATAATATGCAATGTG
*
34878 ACATACTAATTATTTAACA-CATAATAAATCATGTTTTATATAATTTACATTTAAATAATTTTAT
455 ACATACTAATTATTTAACACCA-AATTAATCATGTTTTATATAATTTACATTTAAATAATTTTAT
34942 TAATTTTATTAAATAATTTTATATA
519 TAATTTTATTAAATAATTTTATATA
* *
34967 ATATGTATGTATAACCCATGTATAG-----------TATATATATATATATAAACTATATAAAGT
1 ATATGTATGTATAAACCATGTATAGTATATATAAACTATATATATATATATAAACTATAAAAAGT
* * * *
35021 AAATTACTTATATAGTTTATAGAAACACTATGCATAAACTAAATAAAGAAATAAAGCATATAGTT
66 AAATTACTTATATAATTTATAGAAACACTATGCATAAACTATATAAAGTAATAAAGTATATAGTT
* * *
35086 TAT--A-C---A-A-AACT-CTAAACCCTAAACTTTAAAGC-ATAAATCCTAAACCCTAAACCCT
131 TATAGATCTAAATATAAATCCTAAACCCTAAATTTTAAA-CTATAAA-CCTAAACCCTAAACCAT
* *
35141 AATATTAATGGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTGAGCTTATGTATTGGGC
194 AATATAAATAGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTGAGCTTATGTATTGGGC
* * * * * *
35206 CTATATAAACTAATGTAAATGTACCAGCACTATTGCAAATTGACTTATTTTTTTGTTTTATTATT
259 CTATGTAAACTAATGTAAATGGACTAGCACTAATGCAAATGGACTTATTTTTTGGTTTTATTATT
*
35271 ATTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATA
324 ACTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATA
* *
35336 CTAATTATGCAAATGAAATTAATATGGCATGTACTACTATTTATTAACCATATAATATACAATGT
389 CTAATTATGCAAATGAAATTAATATGGCATGTACTACTATTTATGAACCATATAATATGCAATGT
* * *
35401 GACATACTAATTATTTAATACCAAATTAACCATGTTTTATATAATTTACATTTGAATAATTTTAT
454 GACATACTAATTATTTAACACCAAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTAT
35466 TAATTTTATTAAATAATTTTATATA
519 TAATTTTATTAAATAATTTTATATA
35491 ATATGTATGTATAAACCATGTATAGTATATATAAACTATATATATATATATAAAACTATAAAAAG
1 ATATGTATGTATAAACCATGTATAGTATATATAAACTATATATATATATAT-AAACTATAAAAAG
* *
35556 TAAATTACTTATATAATTTATAGAAATACTATGCATAAACTATATAAAGTAATAAAGTATACAGT
65 TAAATTACTTATATAATTTATAGAAACACTATGCATAAACTATATAAAGTAATAAAGTATATAGT
35621 TTATAGAAATCCTAAATCATAAATCCTAAACCCTAAATTTTAAACTATAAACACTAAACCCTAAA
130 TTATAG--AT-CTAAAT-ATAAATCCTAAACCCTAAATTTTAAACTATAAAC-CTAAACCCTAAA
* * *
35686 CCATAATATAAATAAACTAGCACTAATACATATATATTTGTAATAAAAGAGTGAGCTTATGTATC
190 CCATAATATAAATAGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTGAGCTTATGTATT
* * * *
35751 GGGCCTATGTAAACTAATGTAAATGAACTAACACTAATACAAATAGACTTATTTTTTGGTTTTAT
255 GGGCCTATGTAAACTAATGTAAATGGACTAGCACTAATGCAAATGGACTTATTTTTTGGTTTTAT
35816 TATTACTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAA
320 TATTACTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAA
35881 AATACTAATTATGCAAATGAAATTAATATGGCATGTACTACTATTTATGAACCATATAATATGCA
385 AATACTAATTATGCAAATGAAATTAATATGGCATGTACTACTATTTATGAACCATATAATATGCA
* *
35946 ATTTGACATACTAATTATTTAACACCAAATTAATCATGTGTTATATAATTTACATTTAAATAATT
450 ATGTGACATACTAATTATTTAACACCAAATTAATCATGTTTTATATAATTTACATTTAAATAATT
*
36011 TTATCAATTTTATTAAATAATTTTATATA
515 TTATTAATTTTATTAAATAATTTTATATA
*
36040 ATATGTATGTATAAATCATGTATAGTATATATAAACTATATATATATATATATAAACTATAAAAA
1 ATATGTATGTATAAACCATGTATAGTATATATAAAC--TATATATATATATATAAACTATAAAAA
*
36105 GTAAATTACTTATAT-AGTTATAGAAACACTATGCATAAACTATATAAAGTAATAAAGTATATAG
64 GTAAATTACTTATATAATTTATAGAAACACTATGCATAAACTATATAAAGTAATAAAGTATATAG
* * * * ** **
36169 TTTATAGAAACCCTAAATCATTAACCCTTAACTTTAAACCATAAATACTAAACCCTAAACCATAA
129 TTTATAG--A-TCTAAAT-A-TAA-----ATC-CTAAACCCTAAATTTTAAACTATAAACC-TAA
* *
36234 ACCATAAACCATAATATAAATGGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTG-GAC
182 ACCCTAAACCATAATATAAATAGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTGAG-C
36298 TTATGTATTGGGCCTATGTAAACTAATGTAAATGGACTAGCACTAATGCAAATGGACTTATTTTT
246 TTATGTATTGGGCCTATGTAAACTAATGTAAATGGACTAGCACTAATGCAAATGGACTTATTTTT
* *
36363 TGGTTTTATTATTACTTATTCATAACAACAAAATAAATGGGCTATTAATTTGAATTAATCTAACA
311 TGGTTTTATTATTACTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACA
*
36428 TGCAACTAAAATACTAATTATGCAAATGAAATTAATGTGGCAT
376 TGCAACTAAAATACTAATTATGCAAATGAAATTAATATGGCAT
36471 TGTAACCCCC
Statistics
Matches: 1348, Mismatches: 105, Indels: 81
0.88 0.07 0.05
Matches are distributed among these distances:
517 9 0.01
518 5 0.00
519 1 0.00
520 1 0.00
522 3 0.00
523 3 0.00
524 441 0.33
525 4 0.00
535 36 0.03
536 75 0.06
540 1 0.00
542 1 0.00
545 1 0.00
547 1 0.00
548 5 0.00
549 465 0.34
550 30 0.02
551 15 0.01
555 4 0.00
556 247 0.18
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (543 bp):
ATATGTATGTATAAACCATGTATAGTATATATAAACTATATATATATATATAAACTATAAAAAGT
AAATTACTTATATAATTTATAGAAACACTATGCATAAACTATATAAAGTAATAAAGTATATAGTT
TATAGATCTAAATATAAATCCTAAACCCTAAATTTTAAACTATAAACCTAAACCCTAAACCATAA
TATAAATAGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTGAGCTTATGTATTGGGCCT
ATGTAAACTAATGTAAATGGACTAGCACTAATGCAAATGGACTTATTTTTTGGTTTTATTATTAC
TTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACT
AATTATGCAAATGAAATTAATATGGCATGTACTACTATTTATGAACCATATAATATGCAATGTGA
CATACTAATTATTTAACACCAAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTA
ATTTTATTAAATAATTTTATATA
Found at i:36091 original size:21 final size:22
Alignment explanation
Indices: 36060--36100 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
36050 ATAAATCATG
36060 TATAGTATATATAAACTATATA
1 TATAGTATATATAAACTATATA
36082 TATA-TATATATAAACTATA
1 TATAGTATATATAAACTATA
36101 AAAAGTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (22 bp):
TATAGTATATATAAACTATATA
Found at i:36213 original size:7 final size:7
Alignment explanation
Indices: 36203--36247 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
36193 CCCTTAACTT
36203 TAAACCA
1 TAAACCA
*
36210 TAAA-TA
1 TAAACCA
*
36216 CTAAACCC
1 -TAAACCA
36224 TAAACCA
1 TAAACCA
36231 TAAACCA
1 TAAACCA
36238 TAAACCA
1 TAAACCA
36245 TAA
1 TAA
36248 TATAAATGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 1 0.03
7 31 0.97
ACGTcount: A:0.56, C:0.27, G:0.00, T:0.18
Consensus pattern (7 bp):
TAAACCA
Found at i:36241 original size:21 final size:21
Alignment explanation
Indices: 36176--36243 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
36166 TAGTTTATAG
* * *
36176 AAACCCTAAATCATTAACCCT
1 AAACCCTAAACCATAAACCAT
* ** *
36197 TAACTTTAAACCATAAA-TACT
1 AAACCCTAAACCATAAACCA-T
36218 AAACCCTAAACCATAAACCAT
1 AAACCCTAAACCATAAACCAT
36239 AAACC
1 AAACC
36244 ATAATATAAA
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (21 bp):
AAACCCTAAACCATAAACCAT
Found at i:37238 original size:24 final size:24
Alignment explanation
Indices: 37211--37317 Score: 79
Period size: 24 Copynumber: 4.5 Consensus size: 24
37201 AAACGGAGAT
*
37211 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
37235 ATCAGATATCAGAACAGAATCCGG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
37259 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
37283 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
*
37307 ATTAGAAATCA
1 ATCAGAAATCA
37318 GATAAAATAT
Statistics
Matches: 59, Mismatches: 24, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:37317 original size:48 final size:48
Alignment explanation
Indices: 37214--37319 Score: 113
Period size: 48 Copynumber: 2.2 Consensus size: 48
37204 CGGAGATATC
* * * ***
37214 AGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCGGGTT
1 AGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAAATT
* * * * *
37262 AGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAAATT
1 AGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAAATT
37310 AGAAATCAGA
1 AGAAATCAGA
37320 TAAAATATTC
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.22
Consensus pattern (48 bp):
AGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAAATT
Found at i:38481 original size:18 final size:18
Alignment explanation
Indices: 38454--38489 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38444 CGATCTTATT
38454 ATTTAATTCAGTCATTTC
1 ATTTAATTCAGTCATTTC
* *
38472 ATTTACTTCAGTCCTTTC
1 ATTTAATTCAGTCATTTC
38490 GAACAATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTTAATTCAGTCATTTC
Found at i:39805 original size:7 final size:7
Alignment explanation
Indices: 39793--39824 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
39783 TGGTCAACTC
39793 CGGTCAA
1 CGGTCAA
39800 CGGTCAA
1 CGGTCAA
39807 CGGGTCAA
1 C-GGTCAA
39815 CGGTCAA
1 CGGTCAA
39822 CGG
1 CGG
39825 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:39814 original size:8 final size:8
Alignment explanation
Indices: 39794--39840 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
39784 GGTCAACTCC
39794 GGTCAAC-
1 GGTCAACG
39801 GGTCAACG
1 GGTCAACG
39809 GGTCAAC-
1 GGTCAACG
39816 GGTCAACG
1 GGTCAACG
39824 GGT---CG
1 GGTCAACG
39829 GGTCAACG
1 GGTCAACG
39837 GGTC
1 GGTC
39841 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:39814 original size:15 final size:15
Alignment explanation
Indices: 39794--39840 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
39784 GGTCAACTCC
39794 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
39809 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
39824 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
39837 GGTC
1 GGTC
39841 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:39834 original size:13 final size:13
Alignment explanation
Indices: 39801--39845 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
39791 TCCGGTCAAC
*
39801 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
39816 GGTCAACGGGTCG
1 GGTCAACGGGTCG
39829 GGTCAACGGGTCG
1 GGTCAACGGGTCG
39842 GGTC
1 GGTC
39846 GGGTCAATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:39845 original size:18 final size:18
Alignment explanation
Indices: 39822--39929 Score: 119
Period size: 18 Copynumber: 6.6 Consensus size: 18
39812 CAACGGTCAA
39822 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
39840 CGGGTCGGGTCAA----T
1 CGGGTCGGGTCAACGGGT
*
39854 -GGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
39871 CGGGTCGGGTCAA----T
1 CGGGTCGGGTCAACGGGT
*
39885 -GGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
*
39902 CGGGTCGGGTCAATGGGT
1 CGGGTCGGGTCAACGGGT
39920 CGGGTCGGGT
1 CGGGTCGGGT
39930 TGTGACCGGT
Statistics
Matches: 75, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
13 22 0.29
14 2 0.03
17 2 0.03
18 49 0.65
ACGTcount: A:0.13, C:0.18, G:0.50, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:39858 original size:31 final size:31
Alignment explanation
Indices: 39816--39924 Score: 200
Period size: 31 Copynumber: 3.5 Consensus size: 31
39806 ACGGGTCAAC
* *
39816 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAATGGGTCGGGTAAACGGGTCGGGTCG
39847 GGTCAATGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAATGGGTCGGGTAAACGGGTCGGGTCG
39878 GGTCAATGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAATGGGTCGGGTAAACGGGTCGGGTCG
39909 GGTCAATGGGTCGGGT
1 GGTCAATGGGTCGGGT
39925 CGGGTTGTGA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.15, C:0.17, G:0.49, T:0.19
Consensus pattern (31 bp):
GGTCAATGGGTCGGGTAAACGGGTCGGGTCG
Found at i:39925 original size:13 final size:13
Alignment explanation
Indices: 39841--39907 Score: 62
Period size: 13 Copynumber: 4.8 Consensus size: 13
39831 TCAACGGGTC
39841 GGGTCGGGTCAAT
1 GGGTCGGGTCAAT
*
39854 GGGTCGGGTAAACGGGT
1 GGGTCGGGTCAA----T
39871 CGGGTCGGGTCAAT
1 -GGGTCGGGTCAAT
* *
39885 GGGTCGGGTAAAC
1 GGGTCGGGTCAAT
39898 GGGTCGGGTC
1 GGGTCGGGTC
39908 GGGTCAATGG
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
13 31 0.70
14 1 0.02
17 1 0.02
18 11 0.25
ACGTcount: A:0.15, C:0.16, G:0.49, T:0.19
Consensus pattern (13 bp):
GGGTCGGGTCAAT
Found at i:42083 original size:24 final size:24
Alignment explanation
Indices: 42056--42162 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
42046 AAACGGAGAT
*
42056 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
42080 ATCAGATATCAGAACAGAATCCGG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
42104 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
42128 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
42152 ATCAGAAATCA
1 ATCAGAAATCA
42163 GATAAAATAT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:42162 original size:48 final size:48
Alignment explanation
Indices: 42056--42164 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
42046 AAACGGAGAT
* * * **
42056 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCGG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
42104 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
42152 ATCAGAAATCAGA
1 ATCAGAAATCAGA
42165 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:43326 original size:18 final size:18
Alignment explanation
Indices: 43299--43334 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
43289 CGATCTTATT
43299 ATTTAATTCAGTCATTTC
1 ATTTAATTCAGTCATTTC
* *
43317 ATTTACTTCAGTCCTTTC
1 ATTTAATTCAGTCATTTC
43335 GAACAATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTTAATTCAGTCATTTC
Found at i:44659 original size:15 final size:15
Alignment explanation
Indices: 44639--44685 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
44629 GGTCAACTCC
44639 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
44654 GGTCAACGGCCAACG
1 GGTCAACGGTCAACG
*
44669 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
44682 GGTC
1 GGTC
44686 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 11 0.38
15 18 0.62
ACGTcount: A:0.21, C:0.28, G:0.38, T:0.13
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:44682 original size:13 final size:13
Alignment explanation
Indices: 44664--44721 Score: 71
Period size: 13 Copynumber: 4.1 Consensus size: 13
44654 GGTCAACGGC
44664 CAACGGGTCGGGT
1 CAACGGGTCGGGT
44677 CAACGGGTCGGGTCGGGT
1 CAAC--G---GGTCGGGT
44695 CAACGGGTCGGGT
1 CAACGGGTCGGGT
44708 CAACGGGTCGGGT
1 CAACGGGTCGGGT
44721 C
1 C
44722 GGGTCAACGG
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
13 26 0.65
15 1 0.03
16 1 0.03
18 12 0.30
ACGTcount: A:0.14, C:0.24, G:0.47, T:0.16
Consensus pattern (13 bp):
CAACGGGTCGGGT
Found at i:44690 original size:18 final size:18
Alignment explanation
Indices: 44667--44743 Score: 119
Period size: 18 Copynumber: 4.6 Consensus size: 18
44657 CAACGGCCAA
44667 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
44685 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
44698 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
44716 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
44734 CGGGTCGGGT
1 CGGGTCGGGT
44744 TGTGACCGGT
Statistics
Matches: 54, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
13 13 0.24
18 41 0.76
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:44702 original size:31 final size:31
Alignment explanation
Indices: 44664--44739 Score: 152
Period size: 31 Copynumber: 2.5 Consensus size: 31
44654 GGTCAACGGC
44664 CAACGGGTCGGGTCAACGGGTCGGGTCGGGT
1 CAACGGGTCGGGTCAACGGGTCGGGTCGGGT
44695 CAACGGGTCGGGTCAACGGGTCGGGTCGGGT
1 CAACGGGTCGGGTCAACGGGTCGGGTCGGGT
44726 CAACGGGTCGGGTC
1 CAACGGGTCGGGTC
44740 GGGTTGTGAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.13, C:0.24, G:0.47, T:0.16
Consensus pattern (31 bp):
CAACGGGTCGGGTCAACGGGTCGGGTCGGGT
Found at i:44739 original size:13 final size:13
Alignment explanation
Indices: 44685--44721 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
44675 GTCAACGGGT
44685 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
44698 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
44711 CGGGTCGGGTC
1 CGGGTCGGGTC
44722 GGGTCAACGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.11, C:0.24, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:46898 original size:24 final size:24
Alignment explanation
Indices: 46871--46977 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
46861 AAACGGAGAT
*
46871 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
46895 ATCAGATATCAGAACAGAATCCGG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
46919 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
46943 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
46967 ATCAGAAATCA
1 ATCAGAAATCA
46978 GATAAAATAT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:46977 original size:48 final size:48
Alignment explanation
Indices: 46871--46979 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
46861 AAACGGAGAT
* * * **
46871 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCGG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
46919 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
46967 ATCAGAAATCAGA
1 ATCAGAAATCAGA
46980 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:48141 original size:18 final size:18
Alignment explanation
Indices: 48114--48149 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
48104 CGATCTTATT
48114 ATTTAATTCAGTCATTTC
1 ATTTAATTCAGTCATTTC
* *
48132 ATTTACTTCAGTCCTTTC
1 ATTTAATTCAGTCATTTC
48150 GAACAATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTTAATTCAGTCATTTC
Found at i:49467 original size:7 final size:7
Alignment explanation
Indices: 49455--49484 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
49445 GTCAACTCCA
49455 GTCAACG
1 GTCAACG
49462 GTCAACGG
1 GTCAAC-G
49470 GTCAACG
1 GTCAACG
49477 GTCAACG
1 GTCAACG
49484 G
1 G
49485 GTCGGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.27, C:0.27, G:0.33, T:0.13
Consensus pattern (7 bp):
GTCAACG
Found at i:49474 original size:8 final size:8
Alignment explanation
Indices: 49455--49500 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
49445 GTCAACTCCA
49455 GTCAAC-G
1 GTCAACGG
49462 GTCAACGG
1 GTCAACGG
49470 GTCAAC-G
1 GTCAACGG
49477 GTCAACGG
1 GTCAACGG
49485 GT---CGG
1 GTCAACGG
49490 GTCAACGG
1 GTCAACGG
49498 GTC
1 GTC
49501 GGGTCGGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
5 5 0.15
7 13 0.38
8 16 0.47
ACGTcount: A:0.22, C:0.26, G:0.37, T:0.15
Consensus pattern (8 bp):
GTCAACGG
Found at i:49475 original size:15 final size:15
Alignment explanation
Indices: 49455--49500 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
49445 GTCAACTCCA
49455 GTCAACGGTCAACGG
1 GTCAACGGTCAACGG
49470 GTCAACGGTCAACGG
1 GTCAACGGTCAACGG
*
49485 GTC--GGGTCAACGG
1 GTCAACGGTCAACGG
49498 GTC
1 GTC
49501 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.40
15 18 0.60
ACGTcount: A:0.22, C:0.26, G:0.37, T:0.15
Consensus pattern (15 bp):
GTCAACGGTCAACGG
Found at i:49494 original size:13 final size:13
Alignment explanation
Indices: 49461--49558 Score: 103
Period size: 13 Copynumber: 7.3 Consensus size: 13
49451 TCCAGTCAAC
*
49461 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
49476 GGTCAACGGGTCG
1 GGTCAACGGGTCG
49489 GGTCAACGGGTCG
1 GGTCAACGGGTCG
49502 GGT---CGGGTCG
1 GGTCAACGGGTCG
49512 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
49525 GGTAAACGGGTCGGTCG
1 GGTCAAC--G--GGTCG
49542 GGTCAACGGGTCG
1 GGTCAACGGGTCG
49555 GGTC
1 GGTC
49559 GGGTTGTGAC
Statistics
Matches: 73, Mismatches: 3, Indels: 16
0.79 0.03 0.17
Matches are distributed among these distances:
10 10 0.14
13 38 0.52
15 14 0.19
17 11 0.15
ACGTcount: A:0.15, C:0.22, G:0.46, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:49505 original size:18 final size:18
Alignment explanation
Indices: 49482--49562 Score: 98
Period size: 18 Copynumber: 4.6 Consensus size: 18
49472 CAACGGTCAA
49482 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
49500 CGGGTCGGGT---CGGGT
1 CGGGTCGGGTCAACGGGT
*
49515 CAACGGGTCGGGTAAACGGGT
1 ---CGGGTCGGGTCAACGGGT
49536 C-GGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
49553 CGGGTCGGGT
1 CGGGTCGGGT
49563 TGTGACCGGT
Statistics
Matches: 55, Mismatches: 1, Indels: 14
0.79 0.01 0.20
Matches are distributed among these distances:
15 5 0.09
17 16 0.29
18 29 0.53
21 5 0.09
ACGTcount: A:0.11, C:0.21, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:49519 original size:36 final size:35
Alignment explanation
Indices: 49476--49545 Score: 122
Period size: 36 Copynumber: 2.0 Consensus size: 35
49466 ACGGGTCAAC
*
49476 GGTCAACGGGTCGGGTCAACGGGTCGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTC-GGTCGGGTCG
49512 GGTCAACGGGTCGGGTAAACGGGTCGGTCGGGTC
1 GGTCAACGGGTCGGGTAAACGGGTCGGTCGGGTC
49546 AACGGGTCGG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 9 0.27
36 24 0.73
ACGTcount: A:0.13, C:0.21, G:0.49, T:0.17
Consensus pattern (35 bp):
GGTCAACGGGTCGGGTAAACGGGTCGGTCGGGTCG
Found at i:49543 original size:30 final size:31
Alignment explanation
Indices: 49500--49557 Score: 109
Period size: 30 Copynumber: 1.9 Consensus size: 31
49490 GTCAACGGGT
49500 CGGGTCGGGTCGGGTCAACGGGTCGGGTAAA
1 CGGGTCGGGTCGGGTCAACGGGTCGGGTAAA
49531 CGGGTC-GGTCGGGTCAACGGGTCGGGT
1 CGGGTCGGGTCGGGTCAACGGGTCGGGT
49558 CGGGTTGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.12, C:0.21, G:0.50, T:0.17
Consensus pattern (31 bp):
CGGGTCGGGTCGGGTCAACGGGTCGGGTAAA
Found at i:50454 original size:13 final size:13
Alignment explanation
Indices: 50422--50448 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
50412 TAATTTACAT
50422 TTAAATAATTTTA
1 TTAAATAATTTTA
50435 TTAAATAATTTTA
1 TTAAATAATTTTA
50448 T
1 T
50449 ATAATATGTA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:51456 original size:2 final size:2
Alignment explanation
Indices: 51444--51485 Score: 57
Period size: 2 Copynumber: 20.0 Consensus size: 2
51434 ATAAACCATG
*
51444 TA TA GTA TA TA TA AA CTA 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
51486 AACTATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 33 0.92
3 3 0.08
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:51512 original size:29 final size:29
Alignment explanation
Indices: 51444--51502 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
51434 ATAAACCATG
* *
51444 TATAGTATATATAAACTATATATATATATA
1 TATA-TATATATAAACTATAAAAATATATA
51474 TATATATATATAAACTATAAAAAGTATAT
1 TATATATATATAAACTATAAAAA-TATAT
51503 TACTTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (29 bp):
TATATATATATAAACTATAAAAATATATA
Found at i:51585 original size:7 final size:7
Alignment explanation
Indices: 51575--51660 Score: 64
Period size: 7 Copynumber: 12.3 Consensus size: 7
51565 TATATAAATA
51575 CTAAACC
1 CTAAACC
51582 CTAAACC
1 CTAAACC
*
51589 CTAAACT
1 CTAAACC
* *
51596 TTAAATC
1 CTAAACC
* *
51603 ATAAACA
1 CTAAACC
*
51610 CTAAACA
1 CTAAACC
*
51617 CTAAACT
1 CTAAACC
*
51624 TTAAACC
1 CTAAACC
* *
51631 ATAAACA
1 CTAAACC
*
51638 CTAAACA
1 CTAAACC
51645 CTAAACC
1 CTAAACC
*
51652 ATAAACC
1 CTAAACC
51659 CT
1 CT
51661 CATGTAAATG
Statistics
Matches: 62, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 62 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:51593 original size:21 final size:21
Alignment explanation
Indices: 51568--51657 Score: 83
Period size: 21 Copynumber: 4.3 Consensus size: 21
51558 TATAGTTTAT
*
51568 ATAAATACTAAACCCTAAACC
1 ATAAACACTAAACCCTAAACC
* ** * *
51589 CTAAACTTTAAATCATAAA-C
1 ATAAACACTAAACCCTAAACC
**
51609 ACTAAACACTAAACTTTAAACC
1 A-TAAACACTAAACCCTAAACC
*
51631 ATAAACACTAAACACTAAACC
1 ATAAACACTAAACCCTAAACC
51652 ATAAAC
1 ATAAAC
51658 CCTCATGTAA
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 50 0.94
22 2 0.04
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (21 bp):
ATAAACACTAAACCCTAAACC
Found at i:51658 original size:28 final size:28
Alignment explanation
Indices: 51576--51650 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 28
51566 ATATAAATAC
* * *
51576 TAAACCCTAAACCCTAAACTTTAAATCA
1 TAAACACTAAACACTAAACTTTAAACCA
51604 TAAACACTAAACACTAAACTTTAAACCA
1 TAAACACTAAACACTAAACTTTAAACCA
51632 TAAACACTAAACACTAAAC
1 TAAACACTAAACACTAAAC
51651 CATAAACCCT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (28 bp):
TAAACACTAAACACTAAACTTTAAACCA
Found at i:52154 original size:7 final size:7
Alignment explanation
Indices: 52144--52181 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
52134 CCCTAAACTT
52144 TAAACCA
1 TAAACCA
*
52151 TAAACAA
1 TAAACCA
52158 T-AACCA
1 TAAACCA
52164 CTAAACCA
1 -TAAACCA
52172 TAAACCA
1 TAAACCA
52179 TAA
1 TAA
52182 TGTAAATGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 4 0.15
7 18 0.67
8 5 0.19
ACGTcount: A:0.58, C:0.26, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACCA
Found at i:52434 original size:21 final size:21
Alignment explanation
Indices: 52410--52465 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
52400 TAATTTACAT
52410 TTAAATAATTTTATTATTTTA
1 TTAAATAATTTTATTATTTTA
52431 TTAAATAATTTTATTATTTTA
1 TTAAATAATTTTATTATTTTA
52452 TTAAATAATTTTAT
1 TTAAATAATTTTAT
52466 ATAATAGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTAAATAATTTTATTATTTTA
Found at i:52681 original size:15 final size:16
Alignment explanation
Indices: 52661--52698 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
52651 CGGATCATTT
*
52661 ACAGGTCAGGTTG-AA
1 ACAGGTCAGATTGAAA
*
52676 ACAGGTCATATTGAAA
1 ACAGGTCAGATTGAAA
52692 ACAGGTC
1 ACAGGTC
52699 GGGTAATACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGATTGAAA
Found at i:56765 original size:21 final size:19
Alignment explanation
Indices: 56739--56779 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
56729 TACTAAGTTT
56739 AACAAAAACATTCAACATAAA
1 AACAAAAACATT-AA-ATAAA
56760 AACAAAAACATTAAATAAA
1 AACAAAAACATTAAATAAA
56779 A
1 A
56780 TCACTGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 12 0.60
ACGTcount: A:0.71, C:0.15, G:0.00, T:0.15
Consensus pattern (19 bp):
AACAAAAACATTAAATAAA
Found at i:60719 original size:63 final size:64
Alignment explanation
Indices: 60624--60743 Score: 179
Period size: 63 Copynumber: 1.9 Consensus size: 64
60614 TGTATCAGTC
* *
60624 TGTCTTTAATCCAAAGAACGTATATGATCAAAAGAAACACAAAATATTACTTACCTATGAATTG
1 TGTCTTTAATCCAAAGAACGTATATGACCAAAAGAAACACAAAAAATTACTTACCTATGAATTG
* * * *
60688 TGTCTTTAGTGCAAAGAA-GTGTATGACCAAAAGAAACCCAAAAAATTACTTACCTA
1 TGTCTTTAATCCAAAGAACGTATATGACCAAAAGAAACACAAAAAATTACTTACCTA
60744 GGAGTTGTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
63 34 0.68
64 16 0.32
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (64 bp):
TGTCTTTAATCCAAAGAACGTATATGACCAAAAGAAACACAAAAAATTACTTACCTATGAATTG
Found at i:63527 original size:20 final size:21
Alignment explanation
Indices: 63499--63570 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 21
63489 ATTATGTTTT
*
63499 GGATTGATCCCTTCA-AAAAA
1 GGATCGATCCCTTCACAAAAA
* **
63519 GGATCGATCCCTTGAGGAAAA
1 GGATCGATCCCTTCACAAAAA
* *
63540 GGATCGATCCTTTCACCAAAA
1 GGATCGATCCCTTCACAAAAA
63561 GGATCGATCC
1 GGATCGATCC
63571 ATCGATGAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 13 0.30
21 31 0.70
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (21 bp):
GGATCGATCCCTTCACAAAAA
Found at i:63541 original size:21 final size:21
Alignment explanation
Indices: 63515--63594 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
63505 ATCCCTTCAA
*
63515 AAAAGGATCGATCCCTTGAGG
1 AAAAGGATCGATCCCTTGACG
* * *
63536 AAAAGGATCGATCCTTTCACC
1 AAAAGGATCGATCCCTTGACG
* * *
63557 AAAAGGATCGATCCATCGATG
1 AAAAGGATCGATCCCTTGACG
*
63578 AAAAGGATCAATCCCTT
1 AAAAGGATCGATCCCTT
63595 TTCCTAAAGG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (21 bp):
AAAAGGATCGATCCCTTGACG
Found at i:63562 original size:42 final size:42
Alignment explanation
Indices: 63515--63615 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
63505 ATCCCTTCAA
*
63515 AAAAGGATCGATCCCTTGAGGAAAAGGATCGAT-CCTTTCACC
1 AAAAGGATCGATCCCTTGAGGAAAAGGATCAATCCCTTT-ACC
* * * *
63557 AAAAGGATCGATCCATCGATGAAAAGGATCAATCCCTTTTCC
1 AAAAGGATCGATCCCTTGAGGAAAAGGATCAATCCCTTTACC
* *
63599 TAAAGGATCGATTCCTT
1 AAAAGGATCGATCCCTT
63616 TATTGCAACA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 44 0.90
43 5 0.10
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (42 bp):
AAAAGGATCGATCCCTTGAGGAAAAGGATCAATCCCTTTACC
Found at i:66402 original size:47 final size:48
Alignment explanation
Indices: 66301--66409 Score: 143
Period size: 48 Copynumber: 2.3 Consensus size: 48
66291 TGAATAAATT
* * *
66301 AATAGTAAACTAAAGATAATATTTTGATTTTATCTCAATTCCTAATAA
1 AATAATAAACTAAAGATAATATTTTAATTGTATCTCAATTCCTAATAA
66349 AATAATAAACTAAAGATAATA-TTTAACTCTGTAT-T-AATTCCTAATAA
1 AATAATAAACTAAAGATAATATTTTAA-T-TGTATCTCAATTCCTAATAA
66396 AATAATAAATCTAA
1 AATAATAAA-CTAA
66410 TCCTAAAAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
47 25 0.45
48 26 0.47
49 4 0.07
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.37
Consensus pattern (48 bp):
AATAATAAACTAAAGATAATATTTTAATTGTATCTCAATTCCTAATAA
Done.