Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009596.1 Hibiscus syriacus cultivar Beakdansim tig00116975_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: 1846166
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:192129 original size:5 final size:5
Alignment explanation
Indices: 192119--192156 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
192109 GAGCACGACC
*
192119 CGAGA CGAGA CGAGA CGAGA CGACCA CGAGA CGAGA CG
1 CGAGA CGAGA CGAGA CGAGA CGA-GA CGAGA CGAGA CG
192157 GACAGCGGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.37, C:0.26, G:0.37, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:192136 original size:26 final size:26
Alignment explanation
Indices: 192107--192156 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
192097 ACGTATTACC
192107 ACGAGCACGACC-CGAGACGAGACGAG
1 ACGAG-ACGACCACGAGACGAGACGAG
192133 ACGAGACGACCACGAGACGAGACG
1 ACGAGACGACCACGAGACGAGACG
192157 GACAGCGGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.36, C:0.30, G:0.34, T:0.00
Consensus pattern (26 bp):
ACGAGACGACCACGAGACGAGACGAG
Found at i:192817 original size:20 final size:21
Alignment explanation
Indices: 192776--192833 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
192766 AACTTGGACT
192776 ATCGCAATGCGAATA-T-GTAA
1 ATCGCAATGCG-ATAGTCGTAA
192796 ATCGCAATGCGATAGTCG-AA
1 ATCGCAATGCGATAGTCGTAA
* *
192816 ATTTGCATTGCGATAGTC
1 A-TCGCAATGCGATAGTC
192834 CAAGTTCGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 3 0.09
20 15 0.45
21 15 0.45
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (21 bp):
ATCGCAATGCGATAGTCGTAA
Found at i:192897 original size:21 final size:21
Alignment explanation
Indices: 192869--193218 Score: 293
Period size: 21 Copynumber: 16.9 Consensus size: 21
192859 ATTGCGATTT
* *
192869 AATTCGCATTGCGATAATCGA
1 AATTCGCATTGCGATAGTCCA
*
192890 AGTTCGCATTGCGATAGTCCA
1 AATTCGCATTGCGATAGTCCA
* *
192911 AGTTCGCATTGCGATAGT-CG
1 AATTCGCATTGCGATAGTCCA
* * * *
192931 ACTATCGTATTGCGAT-TTACA
1 AAT-TCGCATTGCGATAGTCCA
* * *
192952 TATTCGCATTGCGATAATCGA
1 AATTCGCATTGCGATAGTCCA
*
192973 AGTTCGCATTGCGATAGTCCA
1 AATTCGCATTGCGATAGTCCA
* * *
192994 AGTTCGCATTGCGAT-TTACA
1 AATTCGCATTGCGATAGTCCA
* * *
193014 TATTCGCATTGCGAT-TTACA
1 AATTCGCATTGCGATAGTCCA
*
193034 TATTCGCATTGCGATAGTCCA
1 AATTCGCATTGCGATAGTCCA
* *
193055 AGTTCGCATTGCGATAGT-CG
1 AATTCGCATTGCGATAGTCCA
* * *
193075 ACTATCGCATTGCGAT-TTACA
1 AAT-TCGCATTGCGATAGTCCA
*
193096 TATTCGCATTGCGATAGTCCA
1 AATTCGCATTGCGATAGTCCA
* *
193117 AGTTCGCATTGCAATAGTCCA
1 AATTCGCATTGCGATAGTCCA
* *
193138 AGTTCGCATTGCGATAGT-CG
1 AATTCGCATTGCGATAGTCCA
* * *
193158 ATTATCGCATTGCGAT-TTACA
1 AAT-TCGCATTGCGATAGTCCA
* *
193179 TATTCGTATTGCGATAGTCCA
1 AATTCGCATTGCGATAGTCCA
*
193200 AGTTCGCATTGCGATAGTC
1 AATTCGCATTGCGATAGTC
193219 GAAGTTTACG
Statistics
Matches: 269, Mismatches: 50, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
20 82 0.30
21 187 0.70
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (21 bp):
AATTCGCATTGCGATAGTCCA
Found at i:192987 original size:83 final size:81
Alignment explanation
Indices: 192797--193224 Score: 516
Period size: 83 Copynumber: 5.3 Consensus size: 81
192787 AATATGTAAA
* * *
192797 TCGCAATGCGATAGTCGAAATTTGCATTGCGATAGTCCAAGTTCGCATTGCGA--TAC-TA-TCG
1 TCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCG
192858 TATTGCGATTT--AAT
66 TATTGCGATTTACAAT
* *
192872 TCGCATTGCGATAATCGAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGT-CGACTA-
1 TCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGAT-TTAC-A-TAT
192935 TCGTATTGCGATTTACATAT
63 TCGTATTGCGATTTACA-AT
*
192955 TCGCATTGCGATAATCGAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCG
1 TCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCG
*
193020 CATTGCGATTTACATAT
66 TATTGCGATTTACA-AT
* * *
193037 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGT-CGACTATCGCATTGCGATTTACATATTC
1 TCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGT-TCGCATTGCGATTTACATATTC
* * *
193101 GCATTGCGATAGTCCAAGT
65 GTATTGCGAT-TTACAA-T
* * * *
193120 TCGCATTGCAATAGTCCAAGTTCGCATTGCGATAGT-CGATTATCGCATTGCGATTTACATATTC
1 TCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGT-TCGCATTGCGATTTACATATTC
* *
193184 GTATTGCGATAGTCCAAGT
65 GTATTGCGAT-TTACAA-T
193203 TCGCATTGCGATAGTCGAAGTT
1 TCGCATTGCGATAGTCGAAGTT
193225 TACGTTGCGA
Statistics
Matches: 322, Mismatches: 17, Indels: 20
0.90 0.05 0.06
Matches are distributed among these distances:
75 49 0.15
77 1 0.00
78 1 0.00
80 16 0.05
81 5 0.02
82 89 0.28
83 161 0.50
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (81 bp):
TCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCG
TATTGCGATTTACAAT
Found at i:193134 original size:62 final size:62
Alignment explanation
Indices: 192797--193152 Score: 268
Period size: 62 Copynumber: 5.9 Consensus size: 62
192787 AATATGTAAA
* * * * *
192797 TCGCAATGCGATAGTCGAAATTTGCATTGCGATAGTCCAAGT-TCGCATTGCGA--TAC-TA-
1 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGT-CAACTATCGCATTGCGATTTACATAT
* * * * * *
192855 TCGTATTGCGAT--T-TAA-TTCGCATTGCGATAATCGAAGT-TCGCATTGCGATAGTCCA-AGT
1 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC-AACTATCGCATTGCGAT-TTACATA-T
* * * * *
192914 TCGCATTGCGATAGT-CGACTATCGTATTGCGAT--T-TACATATTCGCATTGCGA-TAATCGA-
1 TCGCATTGCGATAGTCCAAGT-TCGCATTGCGATAGTCAAC-TA-TCGCATTGCGATTTA-C-AT
192973 AGT
61 A-T
*
192976 TCGCATTGCGATAGTCCAAGTTCGCATTGCGAT--T-TACATATTCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCAAC-TA-TCGCATTGCGATTTACATAT
*
193037 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCAACTATCGCATTGCGATTTACATAT
* *
193099 TCGCATTGCGATAGTCCAAGTTCGCATTGCAATAGTCCAAGT-TCGCATTGCGAT
1 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGT-CAACTATCGCATTGCGAT
193153 AGTCGATTAT
Statistics
Matches: 252, Mismatches: 23, Indels: 42
0.79 0.07 0.13
Matches are distributed among these distances:
53 1 0.00
54 29 0.12
55 2 0.01
56 1 0.00
57 3 0.01
58 10 0.04
59 12 0.05
60 1 0.00
61 39 0.15
62 130 0.52
63 22 0.09
64 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (62 bp):
TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCAACTATCGCATTGCGATTTACATAT
Found at i:193224 original size:21 final size:21
Alignment explanation
Indices: 192797--192851 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
192787 AATATGTAAA
* *
192797 TCGCAATGCGATAGTCGAAAT
1 TCGCATTGCGATAGTCCAAAT
* *
192818 TTGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAAT
192839 TCGCATTGCGATA
1 TCGCATTGCGATA
192852 CTATCGTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAT
Found at i:209643 original size:3 final size:3
Alignment explanation
Indices: 209635--209661 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
209625 TTCGTTGCTG
209635 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
209662 TTATAGACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:213736 original size:14 final size:15
Alignment explanation
Indices: 213716--213765 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 15
213706 TATTGATTAG
213716 ATTAAAAAAT-TAAA
1 ATTAAAAAATATAAA
*
213730 TTTAAAAAATATAAA
1 ATTAAAAAATATAAA
*
213745 ATT-AAAAATAATCAA
1 ATTAAAAAAT-ATAAA
213760 ATTAAA
1 ATTAAA
213766 TTCCGTGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 15 0.50
15 13 0.43
16 2 0.07
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTAAAAAATATAAA
Found at i:213744 original size:15 final size:14
Alignment explanation
Indices: 213716--213752 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
213706 TATTGATTAG
213716 ATTAAAAAATTAAA
1 ATTAAAAAATTAAA
*
213730 TTTAAAAAATATAAA
1 ATTAAAAAAT-TAAA
213745 ATTAAAAA
1 ATTAAAAA
213753 TAATCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATTAAAAAATTAAA
Found at i:220323 original size:97 final size:97
Alignment explanation
Indices: 220157--220352 Score: 392
Period size: 97 Copynumber: 2.0 Consensus size: 97
220147 TAATTATAAT
220157 TAATGTTTTATGTCCCAACCATGATTAGGGATGAGTATTTTATTCAAACATAATAGATTTTAACT
1 TAATGTTTTATGTCCCAACCATGATTAGGGATGAGTATTTTATTCAAACATAATAGATTTTAACT
220222 CGATCTAATAAGGTTAAAATTTTTAAGGGTAA
66 CGATCTAATAAGGTTAAAATTTTTAAGGGTAA
220254 TAATGTTTTATGTCCCAACCATGATTAGGGATGAGTATTTTATTCAAACATAATAGATTTTAACT
1 TAATGTTTTATGTCCCAACCATGATTAGGGATGAGTATTTTATTCAAACATAATAGATTTTAACT
220319 CGATCTAATAAGGTTAAAATTTTTAAGGGTAA
66 CGATCTAATAAGGTTAAAATTTTTAAGGGTAA
220351 TA
1 TA
220353 TAGAGTCGAA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 99 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (97 bp):
TAATGTTTTATGTCCCAACCATGATTAGGGATGAGTATTTTATTCAAACATAATAGATTTTAACT
CGATCTAATAAGGTTAAAATTTTTAAGGGTAA
Found at i:225789 original size:12 final size:12
Alignment explanation
Indices: 225772--225799 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
225762 CAAATAGCGT
225772 TAAATTGAGAAA
1 TAAATTGAGAAA
225784 TAAATTGAGAAA
1 TAAATTGAGAAA
225796 TAAA
1 TAAA
225800 CCTGCATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (12 bp):
TAAATTGAGAAA
Found at i:229951 original size:21 final size:23
Alignment explanation
Indices: 229926--229976 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
229916 AATTCCTTTG
229926 TTGCATTTACA-TTTTGTAT-TT
1 TTGCATTTACATTTTTGTATATT
**
229947 TTGCATTCCCATTTTTGTATATT
1 TTGCATTTACATTTTTGTATATT
229970 TT-CATTT
1 TTGCATTT
229977 GCATGTGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 9 0.36
22 12 0.48
23 4 0.16
ACGTcount: A:0.18, C:0.14, G:0.08, T:0.61
Consensus pattern (23 bp):
TTGCATTTACATTTTTGTATATT
Found at i:231374 original size:25 final size:25
Alignment explanation
Indices: 231336--231425 Score: 76
Period size: 26 Copynumber: 3.4 Consensus size: 25
231326 TAAAAAACAC
231336 AAAAAAAGAA-AGAAAAAATAGAAAGG
1 AAAAAAA-AAGAGAAAAAATAGAAA-G
* *
231362 AAAAAAAAGAGAAACACAGAAAAAGAAAG
1 AAAAAAAA-AGAGA-A-A-AAATAGAAAG
231391 AAAAAAGAAAGAGAAAAAATAG-AAG
1 AAAAAA-AAAGAGAAAAAATAGAAAG
231416 AAAAAGAAAA
1 AAAAA-AAAA
231426 AAAAAAGATT
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
25 12 0.23
26 14 0.26
27 3 0.06
28 2 0.04
29 12 0.23
30 10 0.19
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (25 bp):
AAAAAAAAAGAGAAAAAATAGAAAG
Found at i:231377 original size:43 final size:44
Alignment explanation
Indices: 231330--231433 Score: 135
Period size: 43 Copynumber: 2.4 Consensus size: 44
231320 GATATATAAA
231330 AAACACAAAAAAAGAAAGAAAAAATAGAAAG-GAAAAAAAAG-AG
1 AAACACAAAAAAAGAAAGAAAAAA-AGAAAGAGAAAAAAAAGAAG
* *
231373 AAACACAGAAAAAGAAAG-AAAAAAGAAAGAGAAAAAATAGAAG
1 AAACACAAAAAAAGAAAGAAAAAAAGAAAGAGAAAAAAAAGAAG
* *
231416 AAAAAGAAAAAAA-AAAGA
1 AAACACAAAAAAAGAAAGA
231434 TTAAAAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
41 6 0.11
42 18 0.34
43 29 0.55
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.02
Consensus pattern (44 bp):
AAACACAAAAAAAGAAAGAAAAAAAGAAAGAGAAAAAAAAGAAG
Found at i:231405 original size:6 final size:6
Alignment explanation
Indices: 231338--231447 Score: 63
Period size: 6 Copynumber: 18.5 Consensus size: 6
231328 AAAAACACAA
* *
231338 AAAAAG AAAGAA- AAAATAG -AAAGG AAAAA- AAAGAG AAACACAG AAAAAG
1 AAAAAG AAA-AAG AAAA-AG AAAAAG AAAAAG AAAAAG AAA-A-AG AAAAAG
* * *
231387 AAAGA- AAAAAG AAAGAG AAAAA- ATAGAAG AAAAAG AAAAA- AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG
*
231433 ATTAAA- AAAAAG AAA
1 A-AAAAG AAAAAG AAA
231448 TAGACAGATC
Statistics
Matches: 79, Mismatches: 12, Indels: 26
0.68 0.10 0.22
Matches are distributed among these distances:
5 19 0.24
6 48 0.61
7 7 0.09
8 5 0.06
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:231405 original size:31 final size:31
Alignment explanation
Indices: 231350--231430 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
231340 AAAGAAAGAA
* *
231350 AAAATAGAAAGGAAAAAAAAGAG-AAACACAG
1 AAAA-AGAAAGAAAAAAAAAGAGAAAAAACAG
*
231381 AAAAAGAAAGAAAAAAGAAAGAGAAAAAATAG
1 AAAAAGAAAGAAAAAA-AAAGAGAAAAAACAG
*
231413 AAGAA-AAAGAAAAAAAAA
1 AAAAAGAAAGAAAAAAAAA
231431 AGATTAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
30 14 0.32
31 20 0.45
32 10 0.23
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (31 bp):
AAAAAGAAAGAAAAAAAAAGAGAAAAAACAG
Found at i:231440 original size:31 final size:29
Alignment explanation
Indices: 231336--231447 Score: 86
Period size: 31 Copynumber: 3.8 Consensus size: 29
231326 TAAAAAACAC
* * * *
231336 AAAAAAAGA-AAGAAAAAATAGAAAG-GA
1 AAAAAAAGAGAAAAAAAAAGAAAAAGAAA
*
231363 AAAAAAAGAGAAACACAGAAAA-AGAAAGAAA
1 AAAAAAAGAGAAA-A-A-AAAAGAAAAAGAAA
*
231394 AAAGAAAGAGAAAAAATAGAAGAAAAAGAAA
1 AAAAAAAGAGAAAAAA-A-AAGAAAAAGAAA
**
231425 AAAAAAAGATTAAAAAAAAGAAA
1 AAAAAAAGAGAAAAAAAAAGAAA
231448 TAGACAGATC
Statistics
Matches: 70, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
27 9 0.13
28 3 0.04
29 9 0.13
30 11 0.16
31 38 0.54
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (29 bp):
AAAAAAAGAGAAAAAAAAAGAAAAAGAAA
Found at i:231445 original size:54 final size:55
Alignment explanation
Indices: 231308--231447 Score: 130
Period size: 54 Copynumber: 2.5 Consensus size: 55
231298 CAACATAGAG
* *
231308 AGAAAAAGAAAAGATATATAAAAAACACAAAAAAAGAAAGAAAAAATAGAAAGGAAAA
1 AGAAAAAAAAAAGAT-TA-AAAAAA-AGAAAAAAAGAAAGAAAAAATAGAAAGGAAAA
* *
231366 A-AAAGAGAAACACAGA--AAAAGAAAG-AAAAAAGAAAGAGAAAAAATAG-AA-GAAAA
1 AGAAA-A-AAA-AAAGATTAAAAAAAAGAAAAAAAG-AA-AGAAAAAATAGAAAGGAAAA
231420 AGAAAAAAAAAAGATTAAAAAAAAGAAA
1 AGAAAAAAAAAAGATTAAAAAAAAGAAA
231448 TAGACAGATC
Statistics
Matches: 67, Mismatches: 6, Indels: 21
0.71 0.06 0.22
Matches are distributed among these distances:
52 4 0.06
53 3 0.04
54 22 0.33
55 10 0.15
56 16 0.24
57 4 0.06
58 2 0.03
59 2 0.03
60 4 0.06
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (55 bp):
AGAAAAAAAAAAGATTAAAAAAAAGAAAAAAAGAAAGAAAAAATAGAAAGGAAAA
Found at i:233458 original size:54 final size:53
Alignment explanation
Indices: 233367--233539 Score: 193
Period size: 54 Copynumber: 3.2 Consensus size: 53
233357 ATTTTCGGAA
**
233367 GTTTCTTGATTTTTCTTAAATGAACATTCAAAGAAATTAAGCCTAATTTTTAGGG
1 GTTTCTTGATTTTT-TTAAATGAATTTTCAAAGAAATTAAGCCT-ATTTTTAGGG
* * *
233422 GTTTCTTGATTTTTTCAAATGAATTTTCAAAGAAATTAAGCCTGGTTTTCAGGG
1 GTTTCTTGATTTTTTTAAATGAATTTTCAAAGAAATTAAGCCT-ATTTTTAGGG
* *** * ** *
233476 GTTTTTTGATTTTTTTTTTTGAATTTTTGAAAGAAGCTAAGCCTACTTTTAGGG
1 GTTTCTTGATTTTTTTAAATGAA-TTTTCAAAGAAATTAAGCCTATTTTTAGGG
233530 GTTTCTTGAT
1 GTTTCTTGAT
233540 AACTGTAAAT
Statistics
Matches: 99, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
54 68 0.69
55 31 0.31
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (53 bp):
GTTTCTTGATTTTTTTAAATGAATTTTCAAAGAAATTAAGCCTATTTTTAGGG
Found at i:234524 original size:139 final size:139
Alignment explanation
Indices: 234272--234904 Score: 920
Period size: 139 Copynumber: 4.6 Consensus size: 139
234262 GGGAAAACCA
* * *
234272 ATCAACACTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTTCAT
*
234337 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTC
66 AATGAGAAGAACTTGTTCAACCTTAACTCGATTCATCACATATGGAGTTGAATCAGCAACACCTC
234402 ACTCGAGGG
131 ACTCGAGGG
* *
234411 AACAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGG-GAAGAAGTTCA
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAT-AAGGGAGAAGAAGTTCA
* * *
234475 TAATGAGAAGAACTTGTTCAACCTTAACTCAATTCGTCACATATGGAGTTGAATCAGTAACACCT
65 TAATGAGAAGAACTTGTTCAACCTTAACTCGATTCATCACATATGGAGTTGAATCAGCAACACCT
234540 CACTCGAGGG
130 CACTCGAGGG
234550 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATA-AGGGAGAAGAAGTTCA
* * * * *****
234615 TAATGAGAAGAGCTTGTTCGA-CTTATCACTCGATTCATGACAT-T----TCGAATCAGTGGTGC
65 TAATGAGAAGAACTTGTTCAACCTTA--ACTCGATTCATCACATATGGAGTTGAATCAGCAACAC
*
234674 TTCACTCGAGGG
128 CTCACTCGAGGG
* *
234686 ATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAACAAGTTCA
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATA-AGGGAGAAGAAGTTCA
* * *
234751 TAATGAGAAGATCTTGTTCAACCTTAGCTCGATTCGTCACATATGGAGTTGAATCAGCAACACCT
65 TAATGAGAAGAACTTGTTCAACCTTAACTCGATTCATCACATATGGAGTTGAATCAGCAACACCT
234816 CACTCGAGGG
130 CACTCGAGGG
* * * *
234826 ATCAACCTTTCCAGTGGAGATTTCATAATGAGAATAACTCATCCGATAAGGGAAAAGAAGTTCAT
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTTCAT
234891 AATGAGAAGAACTT
66 AATGAGAAGAACTT
234905 TAGCTTGCTT
Statistics
Matches: 442, Mismatches: 41, Indels: 22
0.88 0.08 0.04
Matches are distributed among these distances:
135 13 0.03
136 104 0.24
137 4 0.01
138 1 0.00
139 208 0.47
140 99 0.22
141 13 0.03
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (139 bp):
ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTAACTCGATTCATCACATATGGAGTTGAATCAGCAACACCTC
ACTCGAGGG
Found at i:234815 original size:276 final size:276
Alignment explanation
Indices: 234272--234904 Score: 936
Period size: 276 Copynumber: 2.3 Consensus size: 276
234262 GGGAAAACCA
* *
234272 ATCAACACTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAT-GAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCA
* *
234336 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCT
66 TAATGAGAAGAACTTGTTCAACCTTAACTCGATTCATCACATAT---GTCGAATCAGCAACACCT
234401 CACTCGAGGGAACAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGGGA
128 CACTCGAGGGAACAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGGGA
*
234466 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAACTCAATTCGTCACATATGGAGTTGAATCA
193 ACAAGTTCATAATGAGAAGAACTTGTTCAACCTTAACTCAATTCGTCACATATGGAGTTGAATCA
*
234531 GTAACACCTCACTCGAGGG
258 GCAACACCTCACTCGAGGG
234550 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCA
* * * ***** *
234615 TAATGAGAAGAGCTTGTTCGA-CTTATCACTCGATTCATGACAT-T-TCGAATCAGTGGTGCTTC
66 TAATGAGAAGAACTTGTTCAACCTTA--ACTCGATTCATCACATATGTCGAATCAGCAACACCTC
* * *
234677 ACTCGAGGGATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAT-AGAGGGAG
129 ACTCGAGGGAACAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGA-AGGG-G
* * *
234741 AACAAGTTCATAATGAGAAGATCTTGTTCAACCTTAGCTCGATTCGTCACATATGGAGTTGAATC
192 AACAAGTTCATAATGAGAAGAACTTGTTCAACCTTAACTCAATTCGTCACATATGGAGTTGAATC
234806 AGCAACACCTCACTCGAGGG
257 AGCAACACCTCACTCGAGGG
* * * *
234826 ATCAACCTTTCCAGTGGAGATTTCATAATGAGAATAACTCATCCGATA-AGGGAAAAGAAGTTCA
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCA
234890 TAATGAGAAGAACTT
66 TAATGAGAAGAACTT
234905 TAGCTTGCTT
Statistics
Matches: 324, Mismatches: 26, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
274 1 0.00
275 97 0.30
276 126 0.39
278 49 0.15
279 37 0.11
280 14 0.04
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (276 bp):
ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTTAACTCGATTCATCACATATGTCGAATCAGCAACACCTCAC
TCGAGGGAACAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGGGAACA
AGTTCATAATGAGAAGAACTTGTTCAACCTTAACTCAATTCGTCACATATGGAGTTGAATCAGCA
ACACCTCACTCGAGGG
Found at i:235241 original size:240 final size:239
Alignment explanation
Indices: 234823--235382 Score: 818
Period size: 240 Copynumber: 2.4 Consensus size: 239
234813 CCTCACTCGA
* * * * *
234823 GGGATCAACCTTTCCAGTGGAGATTTCATAATGAGAATAACTCATCCGA-TAAGGGAAAAGAAGT
1 GGGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAGGAA-GGAGAAGAAGT
* *
234887 TCATAAT--G-AGAA--G---AACTTTAGCTTGCTTTCATCGTATAAGGAGTTGGAACAACACCG
65 TCATAATGAGAAGAATTGTTCAACTTTAGCTTGCTTTCATCGCATAAGGAATTGGAACAACACCG
*
234944 ACTTTTGCTCGTCCATCACATAAGGAGTTGGATCAGCATAATCATTTAGCTAGTCCCTCACATAA
130 ACTTTTGCTCGTCCATCACATAAGGAGTTGGATCAGCATAATCATTTAGCCAGTCCCTCACATAA
*
235009 GGAGATGGATCAACATTACCTTAGATCAATCATCACAGAAGGAGG
195 GGAGATGGATCAACATCACCTTAGATCAATCATCACAGAAGGAGG
235054 GGGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAGGAAGGAGAAGAAGTT
1 GGGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAGGAAGGAGAAGAAGTT
*
235119 CATAATGAGAAGAATTTGTTCAACTTTAGCTTG-TTTCCATCGCATAAGGAATTGGAACATCACC
66 CATAATGAGAAGAA-TTGTTCAACTTTAGCTTGCTTT-CATCGCATAAGGAATTGGAACAACACC
* *
235183 GACTTTTGCTCGTCCATCACATAGGGAGTTGGATCAGCATAATCATTTCGCCAGTCCCTCACATA
129 GACTTTTGCTCGTCCATCACATAAGGAGTTGGATCAGCATAATCATTTAGCCAGTCCCTCACATA
* * * * *
235248 AGGAGTTGGATTAGCATCACCTTGGCTCAATCATCACAGAAGGAGG
194 AGGAGATGGATCAACATCACCTTAGATCAATCATCACAGAAGGAGG
* * *
235294 TGGATCAACATTTCCAGTTGAGAGTTCATAATGAGAAGAACTCATCCG-GCGAGGGAGAAGAAGT
1 GGGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAG-GAAGGAGAAGAAGT
235358 TCATAATGAGAAGAACTTGTTCAAC
65 TCATAATGAGAAGAA-TTGTTCAAC
235383 CTTGGTGATT
Statistics
Matches: 296, Mismatches: 21, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
231 63 0.21
232 2 0.01
233 1 0.00
234 4 0.01
237 1 0.00
239 4 0.01
240 221 0.75
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (239 bp):
GGGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAGGAAGGAGAAGAAGTT
CATAATGAGAAGAATTGTTCAACTTTAGCTTGCTTTCATCGCATAAGGAATTGGAACAACACCGA
CTTTTGCTCGTCCATCACATAAGGAGTTGGATCAGCATAATCATTTAGCCAGTCCCTCACATAAG
GAGATGGATCAACATCACCTTAGATCAATCATCACAGAAGGAGG
Found at i:238698 original size:21 final size:21
Alignment explanation
Indices: 238655--238694 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
238645 ATTATGTATT
238655 TTTTAATATATATTTTTTTAA
1 TTTTAATATATATTTTTTTAA
238676 TTTTAA-ATA-ATTTTTTTAA
1 TTTTAATATATATTTTTTTAA
238695 AATTACCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 3 0.16
21 6 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTAATATATATTTTTTTAA
Found at i:241006 original size:2 final size:2
Alignment explanation
Indices: 240999--241047 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
240989 GCAATTTTCA
240999 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
241041 AT AT AT A
1 AT AT AT A
241048 GAGAGAGAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:241488 original size:37 final size:37
Alignment explanation
Indices: 241415--241490 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
241405 GTTATAAAAT
* *
241415 ATTTATATATTTTCTTTAAAAATTTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTTGAAAATCATAAA
*
241452 ATTTATATAATTTTTTTTACAAAA-TTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTTGAAAATCATAAA
241489 AT
1 AT
241491 GGTTTAATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 15 0.44
38 15 0.44
39 4 0.12
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAATTTGAAAATCATAAA
Found at i:248647 original size:14 final size:15
Alignment explanation
Indices: 248536--248653 Score: 139
Period size: 15 Copynumber: 7.5 Consensus size: 15
248526 TAATAAGGTT
248536 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
248551 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
248566 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
248581 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
248596 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
248615 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
248633 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
248647 ATTTATT
1 ATTTATT
248654 AGTATGAATT
Statistics
Matches: 90, Mismatches: 6, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
14 12 0.13
15 58 0.64
16 4 0.04
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.07
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:248672 original size:22 final size:22
Alignment explanation
Indices: 248656--248698 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
248646 AATTTATTAG
248656 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
248678 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
248699 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:248672 original size:32 final size:31
Alignment explanation
Indices: 248633--248762 Score: 161
Period size: 32 Copynumber: 4.4 Consensus size: 31
248623 TTTTAAAATA
248633 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATG-ATTG
248665 ATTTATTTT-AA-AA--TA-T-G---GATTG
1 ATTTATTTTAAATAATTTATTAGTATGATTG
*
248687 ATTTATTTTAAATAATTTATTAGTATGTATTA
1 ATTTATTTTAAATAATTTATTAGTATG-ATTG
248719 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTAT-GATTG
248751 ATTTATTTTAAA
1 ATTTATTTTAAA
248763 ATATGGATTG
Statistics
Matches: 85, Mismatches: 2, Indels: 22
0.78 0.02 0.20
Matches are distributed among these distances:
22 13 0.15
23 3 0.04
24 2 0.02
26 3 0.04
27 2 0.02
28 3 0.04
30 2 0.02
31 3 0.04
32 53 0.62
33 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (31 bp):
ATTTATTTTAAATAATTTATTAGTATGATTG
Found at i:248689 original size:69 final size:67
Alignment explanation
Indices: 248551--248765 Score: 237
Period size: 69 Copynumber: 3.2 Consensus size: 67
248541 TTTTAAAATA
248551 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGAT
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGAT
248616 TG
66 TG
* * * * * *
248618 ATTTATTTTAAAATAATTTATT-TTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATG
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATT--T-TAAAATAAATTATTATAAAATATG
248682 GATTG
63 GATTG
* * * *
248687 ATTTATTTT-AAATAATTTATTAGTATGTATTAATTTATTTT-AAAT-AA-T-TTAT-TAGTATG
1 ATTTATTTTAAAATAATTTATTA-TA--AAATAATTTATTTTAAAATAAATTATTATAAAATATG
248746 GATTG
63 GATTG
248751 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
248766 TGGATTGATT
Statistics
Matches: 126, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
64 19 0.15
65 8 0.06
66 14 0.11
67 23 0.18
68 16 0.13
69 34 0.27
70 2 0.02
72 10 0.08
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (67 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGAT
TG
Found at i:248698 original size:54 final size:54
Alignment explanation
Indices: 248633--248874 Score: 256
Period size: 54 Copynumber: 4.4 Consensus size: 54
248623 TTTTAAAATA
248633 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
* * **
248687 ATTTATTTTAAATAATTTATTAGTATGTATTAATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * * ***
248742 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 -ATTTATTTTAAATAATTTATTAGTATGAATTGATTTA-T-TT-TA-AAATATGGATTG
248799 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
248853 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
248875 TTGTAGTTGT
Statistics
Matches: 147, Mismatches: 31, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
53 4 0.03
54 88 0.60
55 13 0.09
56 10 0.07
57 12 0.08
58 19 0.13
59 1 0.01
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
Found at i:248706 original size:14 final size:14
Alignment explanation
Indices: 248687--248739 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
248677 ATATGGATTG
248687 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
248701 ATTTATTAGTATGTATTA
1 ATTTATT--T-T-AAATA
248719 ATTTATTTTAAATA
1 ATTTATTTTAAATA
248733 ATTTATT
1 ATTTATT
248740 AGTATGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 17 0.55
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:248758 original size:22 final size:23
Alignment explanation
Indices: 248733--248806 Score: 71
Period size: 22 Copynumber: 3.2 Consensus size: 23
248723 ATTTTAAATA
248733 ATTTAT-TAGTATGGATTGATTT
1 ATTTATATAGTATGGATTGATTT
* *
248755 ATTT-TAAAATATGGATTGATTT
1 ATTTATATAGTATGGATTGATTT
* *
248777 ATTATTGTAGTTGTATGGATTGATTT
1 A-T-TTATA-TAGTATGGATTGATTT
248803 ATTT
1 ATTT
248807 TAAATAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
21 1 0.02
22 19 0.45
23 1 0.02
24 4 0.10
25 3 0.07
26 14 0.33
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (23 bp):
ATTTATATAGTATGGATTGATTT
Found at i:248847 original size:22 final size:22
Alignment explanation
Indices: 248822--248864 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
248812 AATTTATTAG
248822 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
248844 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
248865 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:248946 original size:31 final size:31
Alignment explanation
Indices: 248889--248947 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
248879 AGTTGTATGG
* **
248889 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTACAAAACTAAA
248920 ATTATTTAAATCTCAGTATTACAAAACT
1 ATTATTTAAATCTCAGTATTACAAAACT
248948 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTACAAAACTAAA
Found at i:251345 original size:50 final size:49
Alignment explanation
Indices: 251277--251388 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 49
251267 TTAGCATGAA
* * * * * *
251277 AGCGCGCCCCTGCACCGCGCTATATGTTGATTTGACGTCACGTGGGTAT
1 AGCGCACCCCTGCACCGCGATATACGATGATCTGACGCCACGTGGGTAT
* *
251326 AGCGCACCCTCTGCCCCGCGATATACGATGATCTGGCGCCACGTGGGTAT
1 AGCGCACCC-CTGCACCGCGATATACGATGATCTGACGCCACGTGGGTAT
*
251376 AACGCACCTCCTG
1 AGCGCACC-CCTG
251389 ATCCGTGCTA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
49 8 0.15
50 43 0.83
51 1 0.02
ACGTcount: A:0.18, C:0.33, G:0.27, T:0.22
Consensus pattern (49 bp):
AGCGCACCCCTGCACCGCGATATACGATGATCTGACGCCACGTGGGTAT
Found at i:251538 original size:10 final size:10
Alignment explanation
Indices: 251523--251557 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
251513 TTTATCACAC
251523 CAAATTCTCT
1 CAAATTCTCT
251533 CAAATTCTCT
1 CAAATTCTCT
251543 -AAATTTCTCT
1 CAAA-TTCTCT
251553 CAAAT
1 CAAAT
251558 ACTATCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 17 0.74
11 3 0.13
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:251881 original size:111 final size:111
Alignment explanation
Indices: 251687--251908 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
251677 TGGAAATCAT
*
251687 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
251752 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAAAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAAAATTAA
* *
251798 ATATCTCGACATTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
251863 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAAAATTAA
251909 TTTTTGTAAT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAAAATTAA
Found at i:253467 original size:18 final size:18
Alignment explanation
Indices: 253414--253469 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
253404 CCAGCAGCTA
* *
253414 CCGCAGCCGTATATGATA
1 CCGCAGCCATATATGATG
*
253432 TCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
253450 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
253468 CC
1 CC
253470 ACCATCGCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:265510 original size:2 final size:2
Alignment explanation
Indices: 265499--265551 Score: 55
Period size: 2 Copynumber: 29.5 Consensus size: 2
265489 AAACCCGAAA
*
265499 AT AT -T AT AT AT AT A- AT -T A- AT AT A- AA AT AT -T 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
265535 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
265552 ATCCGGGCGG
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
1 6 0.14
2 38 0.86
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:267918 original size:3 final size:3
Alignment explanation
Indices: 267910--267960 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
267900 TAAATCACAA
267910 AAT AAT AAT AAT AAT AAT AAT 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 AAT
267958 AAT
1 AAT
267961 TTATGAACAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:289652 original size:60 final size:61
Alignment explanation
Indices: 289588--289787 Score: 196
Period size: 63 Copynumber: 3.3 Consensus size: 61
289578 GTCCTATGAG
* * * *
289588 TATTAAAAGTTATGAAATGGTCC-CTTAACT-ATAGGGTGTTGCTATGTTGAGTCACCCAAT
1 TATTAAAAGTTATAAAATAGTCCTC-TAACTAACAGGATGTTGCTATGTTGAGTCACCCAAT
* * *
289648 TATTAAAAGTTATAAAATAGTCCTCTAACTACAACATGATGTTGCTTTGTTGAGTCACCCGAT
1 TATTAAAAGTTATAAAATAGTCCTCTAACT--AACAGGATGTTGCTATGTTGAGTCACCCAAT
* * * * *
289711 TATTAAAAGTTACAAAATAGTCCTCTAACTGCAACATGATGTT--T-TGTTGAGTCTCTCAAC
1 TATTAAAAGTTATAAAATAGTCCTCTAACT--AACAGGATGTTGCTATGTTGAGTCACCCAAT
*
289771 TATTAAAA-TTACAAAAT
1 TATTAAAAGTTATAAAAT
289788 GGTCACCCGA
Statistics
Matches: 123, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
59 9 0.07
60 46 0.37
61 2 0.02
63 66 0.54
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (61 bp):
TATTAAAAGTTATAAAATAGTCCTCTAACTAACAGGATGTTGCTATGTTGAGTCACCCAAT
Found at i:289706 original size:63 final size:63
Alignment explanation
Indices: 289624--289787 Score: 237
Period size: 63 Copynumber: 2.7 Consensus size: 63
289614 AACTATAGGG
* *
289624 TGTTGCTATGTTGAGTCACCCAATTATTAAAAGTTATAAAATAGTCCTCTAACTACAACATGA
1 TGTTGCTTTGTTGAGTCACCCAATTATTAAAAGTTACAAAATAGTCCTCTAACTACAACATGA
* *
289687 TGTTGCTTTGTTGAGTCACCCGATTATTAAAAGTTACAAAATAGTCCTCTAACTGCAACATGA
1 TGTTGCTTTGTTGAGTCACCCAATTATTAAAAGTTACAAAATAGTCCTCTAACTACAACATGA
* * *
289750 TG-T--TTTGTTGAGTCTCTCAACTATTAAAA-TTACAAAAT
1 TGTTGCTTTGTTGAGTCACCCAATTATTAAAAGTTACAAAAT
289788 GGTCACCCGA
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
59 9 0.10
60 22 0.24
62 1 0.01
63 61 0.66
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35
Consensus pattern (63 bp):
TGTTGCTTTGTTGAGTCACCCAATTATTAAAAGTTACAAAATAGTCCTCTAACTACAACATGA
Found at i:290143 original size:60 final size:60
Alignment explanation
Indices: 289997--290121 Score: 171
Period size: 60 Copynumber: 2.1 Consensus size: 60
289987 TAACATATGA
* * * * *
289997 ATAGTCGAGTGACTATTTTATAACTTTTAATAATCAATGGACTCAACAAAGCAATACCCT
1 ATAGTCAAGGGACCATTTCATAACTTTTAATAATCAATGGACTCAACAAAGCAACACCCT
* *
290057 ATAGTCAAGGGACCATTTCATAACTTTTAATACTC-AGGTGACTCAACAAAGCAACACCCT
1 ATAGTCAAGGGACCATTTCATAACTTTTAATAATCAATG-GACTCAACAAAGCAACACCCT
290117 ATAGT
1 ATAGT
290122 TGAAGGATCA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 2 0.04
60 55 0.96
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.29
Consensus pattern (60 bp):
ATAGTCAAGGGACCATTTCATAACTTTTAATAATCAATGGACTCAACAAAGCAACACCCT
Found at i:293001 original size:2 final size:2
Alignment explanation
Indices: 292994--293021 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
292984 AATCCGAGTC
292994 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
293022 GATTCATCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:302109 original size:2 final size:2
Alignment explanation
Indices: 302102--302139 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
302092 TCATTTATTT
302102 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
302140 AAAAAGTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:310833 original size:2 final size:2
Alignment explanation
Indices: 310826--310862 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
310816 ATATTAAAAT
310826 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
310863 GTTTGTGATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:311965 original size:26 final size:26
Alignment explanation
Indices: 311936--311999 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
311926 ATATCATCGG
311936 ATTTAATCTAAATTTAA-AGAAA-TTC
1 ATTTAATCTAAATTTAAGA-AAATTTC
311961 TATTTAATCTAAATTTAAGAAAATTTC
1 -ATTTAATCTAAATTTAAGAAAATTTC
311988 ATTTAATCTAAA
1 ATTTAATCTAAA
312000 ATTTGGCCCG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
26 32 0.89
27 4 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (26 bp):
ATTTAATCTAAATTTAAGAAAATTTC
Found at i:318638 original size:15 final size:16
Alignment explanation
Indices: 318614--318651 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
318604 ACTTTTGTTG
318614 TTTTTTTTTCAT-T-T
1 TTTTTTTTTCATGTCT
318628 TTTTTTCTTTCATGTCT
1 TTTTTT-TTTCATGTCT
318645 TTTTTTT
1 TTTTTTT
318652 CTCTCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.29
15 6 0.29
16 2 0.10
17 7 0.33
ACGTcount: A:0.05, C:0.11, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTCATGTCT
Found at i:329394 original size:27 final size:28
Alignment explanation
Indices: 329337--329395 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
329327 ACTCGATGGG
*
329337 TTAA-TAATAATAATATTTAAAATCAGA
1 TTAATTAAGAATAATATTTAAAATCAGA
*
329364 -TAATTAAGAATAATATTTAAAA-CATA
1 TTAATTAAGAATAATATTTAAAATCAGA
329390 TTAATT
1 TTAATT
329396 GAAATCACTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (28 bp):
TTAATTAAGAATAATATTTAAAATCAGA
Found at i:330832 original size:31 final size:31
Alignment explanation
Indices: 330808--330873 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
330798 TAAAATGTCC
330808 TTAAGATTTATTAAATTATCATAAAATAATCA
1 TTAA-ATTTATTAAATTATCATAAAATAATCA
*
330840 TTAAATTTATTAAATTATTATAAAATAATCA
1 TTAAATTTATTAAATTATCATAAAATAATCA
330871 TTA
1 TTA
330874 TAAGTATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (31 bp):
TTAAATTTATTAAATTATCATAAAATAATCA
Found at i:335112 original size:115 final size:115
Alignment explanation
Indices: 334908--335119 Score: 327
Period size: 115 Copynumber: 1.8 Consensus size: 115
334898 AATTATTACG
* * * *
334908 AAAATAGCACTGTTTCAAAAATATTTACGACAATATCACCTCTTTAAAAATAATTATCAAAATAT
1 AAAATAGCACTGTTTCAAAAATAATTACCAAAATATCACCTCTTTAAAAATAATTACCAAAATAT
334973 CACCGTTTTAAAAATAATTACCAAAATATCACATTTTAAAAATAATTATC
66 CACCGTTTTAAAAATAATTACCAAAATATCACATTTTAAAAATAATTATC
* * * *
335023 AAAATATCACTGTTTTAAAAATAATTACCAAAATATCA-CTGTTTTAAAAATAATTCCCAAAATA
1 AAAATAGCACTGTTTCAAAAATAATTACCAAAATATCACCT-CTTTAAAAATAATTACCAAAATA
*
335087 TCACCGTTTTAAAAATAATTCCCAAAATATCAC
65 TCACCGTTTTAAAAATAATTACCAAAATATCAC
335120 CAGGGTCTGG
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
114 2 0.02
115 85 0.98
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.33
Consensus pattern (115 bp):
AAAATAGCACTGTTTCAAAAATAATTACCAAAATATCACCTCTTTAAAAATAATTACCAAAATAT
CACCGTTTTAAAAATAATTACCAAAATATCACATTTTAAAAATAATTATC
Found at i:335120 original size:29 final size:29
Alignment explanation
Indices: 334902--335120 Score: 289
Period size: 29 Copynumber: 7.6 Consensus size: 29
334892 CACAGCAATT
* * * *
334902 ATTACGAAAATAGCACTGTTTCAAAAATA
1 ATTACCAAAATATCACCGTTTTAAAAATA
* * *
334931 TTTACGACAATATCACC-TCTTTAAAAATA
1 ATTACCAAAATATCACCGT-TTTAAAAATA
*
334960 ATTATCAAAATATCACCGTTTTAAAAATA
1 ATTACCAAAATATCACCGTTTTAAAAATA
*
334989 ATTACCAAAATATCA-CATTTTAAAAATA
1 ATTACCAAAATATCACCGTTTTAAAAATA
* *
335017 ATTATCAAAATATCACTGTTTTAAAAATA
1 ATTACCAAAATATCACCGTTTTAAAAATA
*
335046 ATTACCAAAATATCACTGTTTTAAAAATA
1 ATTACCAAAATATCACCGTTTTAAAAATA
*
335075 ATTCCCAAAATATCACCGTTTTAAAAATA
1 ATTACCAAAATATCACCGTTTTAAAAATA
*
335104 ATTCCCAAAATATCACC
1 ATTACCAAAATATCACC
335121 AGGGTCTGGT
Statistics
Matches: 170, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
28 27 0.16
29 142 0.84
30 1 0.01
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.32
Consensus pattern (29 bp):
ATTACCAAAATATCACCGTTTTAAAAATA
Found at i:339371 original size:21 final size:21
Alignment explanation
Indices: 339345--339389 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
339335 GATTTCTGGG
* *
339345 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
339366 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
339387 CAA
1 CAA
339390 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:340767 original size:32 final size:32
Alignment explanation
Indices: 340725--340825 Score: 111
Period size: 31 Copynumber: 3.2 Consensus size: 32
340715 AGAGTCGAGG
340725 GTTTACCTATGTTCTACGGAACATATGGACAA
1 GTTTACCTATGTTCTACGGAACATATGGACAA
* *
340757 TTTTACCTATG-TCTTTC-GAGACATATGGAC-A
1 GTTTACCTATGTTC-TACGGA-ACATATGGACAA
* * *
340788 GTATACCTATATTCTAAGGAACATATGGAC-A
1 GTTTACCTATGTTCTACGGAACATATGGACAA
340819 GTTTACC
1 GTTTACC
340826 GAGGATCTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
31 31 0.54
32 26 0.46
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (32 bp):
GTTTACCTATGTTCTACGGAACATATGGACAA
Found at i:340857 original size:30 final size:30
Alignment explanation
Indices: 340813--340906 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
340803 AAGGAACATA
340813 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
340844 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
340874 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
340903 TGGA
1 TGGA
340907 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.29
30 35 0.59
31 7 0.12
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:346608 original size:29 final size:29
Alignment explanation
Indices: 346437--346608 Score: 246
Period size: 29 Copynumber: 6.0 Consensus size: 29
346427 AAATAGCATT
*
346437 GTTTTAAAAATATTTA-CAACAATATCACC
1 GTTTTAAAAATAATTACCAA-AATATCACC
*
346466 -TCTTTAAAAATAATTACCAAAATATCATC
1 GT-TTTAAAAATAATTACCAAAATATCACC
346495 GTTTTAAAAATAATTACCAAAATATCACC
1 GTTTTAAAAATAATTACCAAAATATCACC
*
346524 ATTTTAAAAATAATTACCAAAATATCACC
1 GTTTTAAAAATAATTACCAAAATATCACC
346553 GTTTT-AAAATAATT-CTCAAAATATCACC
1 GTTTTAAAAATAATTAC-CAAAATATCACC
346581 GTTTTAAAAATAATT-CTCAAAATATCAC
1 GTTTTAAAAATAATTAC-CAAAATATCAC
346609 TGGATCAGAT
Statistics
Matches: 133, Mismatches: 5, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
27 1 0.01
28 27 0.20
29 101 0.76
30 4 0.03
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.34
Consensus pattern (29 bp):
GTTTTAAAAATAATTACCAAAATATCACC
Found at i:351047 original size:33 final size:33
Alignment explanation
Indices: 351005--351071 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
350995 TGTTGGAGGC
351005 TTGAGAGAATGATTTCCGTTAGTAACATTACTA
1 TTGAGAGAATGATTTCCGTTAGTAACATTACTA
351038 TTGAGAGAATGATTTCCGTTAGTAACATTACTA
1 TTGAGAGAATGATTTCCGTTAGTAACATTACTA
351071 T
1 T
351072 ATCCAGAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (33 bp):
TTGAGAGAATGATTTCCGTTAGTAACATTACTA
Found at i:354575 original size:45 final size:47
Alignment explanation
Indices: 354516--354604 Score: 146
Period size: 45 Copynumber: 1.9 Consensus size: 47
354506 TCGAATAAAT
354516 GCATGCGAACTAGATATCATGCGGTTAGG-TTTATTTTT-TGAACAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
* *
354561 GCATGTGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
354605 TAACAAAGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 27 0.68
46 9 0.22
47 4 0.10
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (47 bp):
GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
Found at i:354631 original size:50 final size:45
Alignment explanation
Indices: 354516--354631 Score: 135
Period size: 45 Copynumber: 2.5 Consensus size: 45
354506 TCGAATAAAT
* *
354516 GCATGCGAACTAGATATCATGCGGTTAGGTTTATTTTTTGAACAA
1 GCATGTGAAGTAGATATCATGCGGTTAGGTTTATTTTTTGAACAA
*
354561 GCATGTGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAATAACAAA
1 GCATGTGAAGTAGATATCATGCGGTTAGG-TTTATTTTT-TG---AAC-AA
*
354612 GCATG-GGAGTAGATATCATG
1 GCATGTGAAGTAGATATCATG
354632 TTGGGTACGA
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
45 27 0.44
46 9 0.15
47 2 0.03
50 16 0.26
51 7 0.11
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.34
Consensus pattern (45 bp):
GCATGTGAAGTAGATATCATGCGGTTAGGTTTATTTTTTGAACAA
Found at i:361608 original size:1 final size:1
Alignment explanation
Indices: 361602--361632 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
361592 TATTTATACG
*
361602 AAAAAAAAAAAAAAAAAAAGAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
361633 TTGTTTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:364227 original size:25 final size:25
Alignment explanation
Indices: 364190--364316 Score: 58
Period size: 23 Copynumber: 5.2 Consensus size: 25
364180 TTTTGCTTGA
* *
364190 AGAAGAAATAAAAGAGAAAAAAATG
1 AGAAAAAAGAAAAGAGAAAAAAATG
* *
364215 AGAAAAAAGAAAAATGATGGAAAAAACG
1 AGAAAAAAG-AAAA-GA-GAAAAAAATG
*
364243 A-AAAGAAA-AAAAGA-AGAAAAATG
1 AGAAA-AAAGAAAAGAGAAAAAAATG
*
364266 -GAAAAGGAAGAAAA-TG--AAAAATG
1 AGAAAA--AAGAAAAGAGAAAAAAATG
*
364289 A-AAAAAGAGAAAA-TGAAAAAAA-G
1 AGAAAAA-AGAAAAGAGAAAAAAATG
364312 AGAAA
1 AGAAA
364317 TAAAAGGAGG
Statistics
Matches: 80, Mismatches: 8, Indels: 29
0.68 0.07 0.25
Matches are distributed among these distances:
21 1 0.01
22 9 0.11
23 22 0.28
24 10 0.12
25 13 0.16
26 8 0.10
27 5 0.06
28 12 0.15
ACGTcount: A:0.72, C:0.01, G:0.20, T:0.06
Consensus pattern (25 bp):
AGAAAAAAGAAAAGAGAAAAAAATG
Found at i:364228 original size:19 final size:18
Alignment explanation
Indices: 364199--364251 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
364189 AAGAAGAAAT
364199 AAAAGAGAAAAAAATGAGAA
1 AAAAGA-AAAAAAATG-GAA
**
364219 AAAAGAAAAATGATGGAA
1 AAAAGAAAAAAAATGGAA
364237 AAAACGAAAAGAAAA
1 AAAA-GAAAA-AAAA
364252 AAAGAAGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 7 0.26
19 12 0.44
20 8 0.30
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.06
Consensus pattern (18 bp):
AAAAGAAAAAAAATGGAA
Found at i:364229 original size:16 final size:16
Alignment explanation
Indices: 364208--364301 Score: 56
Period size: 16 Copynumber: 5.8 Consensus size: 16
364198 TAAAAGAGAA
364208 AAAAATGAGAAAAAAG
1 AAAAATGAGAAAAAAG
364224 AAAAATGATGGAAAAAACG
1 AAAAATGA--GAAAAAA-G
*
364243 -AAAA-GAAAAAAAGAAG
1 AAAAATG-AGAAAA-AAG
364259 AAAAATG-GAAAAGGAAG
1 AAAAATGAGAAAA--AAG
*
364276 -AAAAT--GAAAAATG
1 AAAAATGAGAAAAAAG
*
364289 AAAAAAGAGAAAA
1 AAAAATGAGAAAA
364302 TGAAAAAAAG
Statistics
Matches: 63, Mismatches: 4, Indels: 22
0.71 0.04 0.25
Matches are distributed among these distances:
13 2 0.03
14 4 0.06
15 5 0.08
16 27 0.43
17 11 0.17
18 13 0.21
19 1 0.02
ACGTcount: A:0.72, C:0.01, G:0.20, T:0.06
Consensus pattern (16 bp):
AAAAATGAGAAAAAAG
Found at i:364291 original size:22 final size:23
Alignment explanation
Indices: 364258--364308 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
364248 AAAAAAAGAA
*
364258 GAAAAATGG-AAAAGGAAGAAAAT
1 GAAAAATGGAAAAAAG-AGAAAAT
364281 GAAAAAT-GAAAAAAGAGAAAAT
1 GAAAAATGGAAAAAAGAGAAAAT
364303 GAAAAA
1 GAAAAA
364309 AAGAGAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.08
Consensus pattern (23 bp):
GAAAAATGGAAAAAAGAGAAAAT
Found at i:364307 original size:14 final size:14
Alignment explanation
Indices: 364209--364321 Score: 65
Period size: 15 Copynumber: 7.7 Consensus size: 14
364199 AAAAGAGAAA
364209 AAAATGAGAAAAAAG
1 AAAATGA-AAAAAAG
364224 AAAAATGATGGAAAAAACG
1 -AAAATGA---AAAAAA-G
364243 AAAA-GAAAAAAAG
1 AAAATGAAAAAAAG
**
364256 --AA-GAAAAATGG
1 AAAATGAAAAAAAG
* *
364267 AAAAGGAAGAAAATG
1 AAAATGAA-AAAAAG
364282 AAAAATGAAAAAAGAG
1 -AAAATGAAAAAA-AG
364298 AAAATGAAAAAAAG
1 AAAATGAAAAAAAG
364312 AGAAAT-AAAA
1 A-AAATGAAAA
364322 GGAGGGTTCA
Statistics
Matches: 81, Mismatches: 6, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
11 9 0.11
13 3 0.04
14 16 0.20
15 24 0.30
16 15 0.19
17 2 0.02
18 11 0.14
19 1 0.01
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.07
Consensus pattern (14 bp):
AAAATGAAAAAAAG
Found at i:364308 original size:16 final size:17
Alignment explanation
Indices: 364243--364316 Score: 68
Period size: 16 Copynumber: 4.6 Consensus size: 17
364233 GGAAAAAACG
* *
364243 AAAAGAAAAAAAGAAGA
1 AAAAGAGAAAATGAAGA
*
364260 AAAATG-GAAAAGGAAGA
1 AAAA-GAGAAAATGAAGA
*
364277 AAATGA-AAAATG-A-A
1 AAAAGAGAAAATGAAGA
364291 AAAAGAGAAAATGAA-A
1 AAAAGAGAAAATGAAGA
364307 AAAAGAGAAA
1 AAAAGAGAAA
364317 TAAAAGGAGG
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
14 6 0.12
15 7 0.15
16 18 0.38
17 16 0.33
18 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.05
Consensus pattern (17 bp):
AAAAGAGAAAATGAAGA
Found at i:365644 original size:37 final size:37
Alignment explanation
Indices: 365587--365669 Score: 132
Period size: 37 Copynumber: 2.2 Consensus size: 37
365577 GTTGGATCTT
* *
365587 TGAAACAAATCAATCTTAAGCCTTCACGGAAGAGTAG
1 TGAAGCAAATCAATCTTAAGCCTTCACGGAAGAATAG
365624 TGAAGCAAATC-ATCTATAAGCCTTCACGGAAGAATAG
1 TGAAGCAAATCAATCT-TAAGCCTTCACGGAAGAATAG
365661 TGAAGCAAA
1 TGAAGCAAA
365670 CCCGTTTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 4 0.09
37 39 0.91
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.20
Consensus pattern (37 bp):
TGAAGCAAATCAATCTTAAGCCTTCACGGAAGAATAG
Found at i:365731 original size:55 final size:55
Alignment explanation
Indices: 365672--366273 Score: 707
Period size: 55 Copynumber: 11.1 Consensus size: 55
365662 GAAGCAAACC
*
365672 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACT
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
*
365727 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGTAGGAATAGAGAGCGGAC-
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
*
365781 CTGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 C-GTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
*
365837 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
* *
365892 CATTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
*
365947 CGTTTTATGAAGATTGTTTGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
* * * * *
366002 TGTTTTTTGAAGATTGTTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
* * * * *
366057 C-CTTTATTGAAGA----TCGAG-TCTTATACTCCCTGAACGAATAGGGAGCAGACA
1 CGTTTTA-TGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACA
* * * *
366108 CGTTTGT-TGAAGA----TCGAG-TCTTATACTCCCTGAACGAATAGGGAGCAGACA
1 CGTTT-TATGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACA
* * * * * *
366159 CGTTTGT-TGAAGATTATTCGAG-TCTTATACTCCCTAAACGAATAGGGAGCAGACA
1 CGTTT-TATGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACA
* * * * * *
366214 TGTTTGT-TGAAGATTGTTTGAG-TCTTATACTCCCTGAATGAATAGGGAGCAGACA
1 CGTTT-TATGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACA
366269 CGTTT
1 CGTTT
366274 GCCAATGATT
Statistics
Matches: 511, Mismatches: 26, Indels: 20
0.92 0.05 0.04
Matches are distributed among these distances:
50 1 0.00
51 89 0.17
52 2 0.00
53 1 0.00
54 4 0.01
55 413 0.81
56 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (55 bp):
CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
Found at i:366097 original size:51 final size:51
Alignment explanation
Indices: 366021--366337 Score: 339
Period size: 55 Copynumber: 6.0 Consensus size: 51
366011 AAGATTGTTT
* * * * *
366021 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACCTTTATTGAAGATC
1 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTATTGAAGATC
*
366072 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATC
1 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTATTGAAGATC
*
366123 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTATTC
1 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTATTGAAG---A-TC
* * * *
366178 GAGTCTTATACTCCCTAAACGAATAGGGAGCAGACATGTTTGTTGAAGATTGTTT
1 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTATTGAAGA----TC
* * * *
366233 GAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGCCAATGATTGTTC
1 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTT---ATTGA-AGATC
* * * *
366288 GAGTCTTATACTCCTTGAAAGAAAAGGGAGCAGACCCG-TTATTTGAAGAT
1 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTA-TTGAAGAT
366338 TTTTCAAGTA
Statistics
Matches: 230, Mismatches: 24, Indels: 24
0.83 0.09 0.09
Matches are distributed among these distances:
51 96 0.42
52 4 0.02
54 3 0.01
55 123 0.53
58 3 0.01
59 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (51 bp):
GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTATTGAAGATC
Found at i:368986 original size:4 final size:4
Alignment explanation
Indices: 368977--369003 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
368967 AATTACATTA
368977 ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATA
369004 TCCATAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:372519 original size:21 final size:20
Alignment explanation
Indices: 372433--372589 Score: 84
Period size: 20 Copynumber: 7.8 Consensus size: 20
372423 AAATGACCAA
**
372433 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
372452 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
372472 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
372492 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
372513 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
372533 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
372553 CCAAAATCGCAACACGAATAT
1 -CAAAATCGCAACGCGATTTT
*
372574 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
372590 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 9
0.72 0.22 0.06
Matches are distributed among these distances:
19 16 0.16
20 55 0.54
21 31 0.30
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:372599 original size:20 final size:20
Alignment explanation
Indices: 372576--372749 Score: 199
Period size: 20 Copynumber: 8.7 Consensus size: 20
372566 ACGAATATGA
* *
372576 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
372596 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
372616 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
372636 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
372656 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
372676 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTATCCGT
* * *
372696 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
372716 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
372737 AAATCGCAACGCG
1 AAATCGCAACGCG
372750 ATATTTAAAG
Statistics
Matches: 128, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
19 1 0.01
20 109 0.85
21 17 0.13
22 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:372603 original size:61 final size:61
Alignment explanation
Indices: 372433--372608 Score: 180
Period size: 61 Copynumber: 2.9 Consensus size: 61
372423 AAATGACCAA
* * * *
372433 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGATCCCCAGAATCGCAAAT-C-AGTTTC
1 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACAAAATCGC-AATGCGAGTTTC
* * * ** * * *
372492 CAAAATCGCAACGCGATTCTTGAAAATCGCAATGCGATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAAT-ATGAAAATCGCAACGCGATACACAAAATCGCAATGCGAGTTTC
*
372554 CAAAATCGCAACACGAATATGAAAATCGCAACGCGA-ACACATAAATCGCAATGCG
1 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACA-AAATCGCAATGCG
372609 TATCCGTAAA
Statistics
Matches: 93, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
59 16 0.17
60 5 0.05
61 51 0.55
62 21 0.23
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (61 bp):
CAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACAAAATCGCAATGCGAGTTTC
Found at i:372642 original size:60 final size:60
Alignment explanation
Indices: 372576--372749 Score: 240
Period size: 60 Copynumber: 2.9 Consensus size: 60
372566 ACGAATATGA
* *
372576 AAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGT
* *** * *
372636 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGT
** *
372696 AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGTAAATCGCAACGCG
372750 ATATTTAAAG
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 66 0.68
61 31 0.32
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGT
Found at i:373172 original size:33 final size:33
Alignment explanation
Indices: 373133--373203 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
373123 TTCACTTAGA
373133 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
373166 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
373199 TTTCA
1 TTTCA
373204 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:373340 original size:19 final size:20
Alignment explanation
Indices: 373283--373357 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
373273 TGCAGAAGAG
* *
373283 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGACAA
**
373304 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGACAA
*
373324 TCGCAACGCGA-AATGACAA
1 TCGCAACGAGAGAATGACAA
373343 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
373358 CGCAACGCGA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
19 16 0.36
20 18 0.40
21 11 0.24
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGACAA
Found at i:373360 original size:14 final size:14
Alignment explanation
Indices: 373341--373397 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
373331 GCGAAATGAC
373341 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
373355 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
373374 AATCGCAACGAGAG
1 AATCGCAACGAGAG
373388 AATCGCAACG
1 AATCGCAACG
373398 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:373366 original size:33 final size:33
Alignment explanation
Indices: 373295--373413 Score: 157
Period size: 33 Copynumber: 3.4 Consensus size: 33
373285 GCAACGAGAT
373295 AAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGCG
1 AAATGAAAATCGCAACGAGAG-A--A---TCGCAACGCG
*
373334 AAATGACAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
373367 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
373400 AAACCAAAATCGCA
1 AAATGAAAATCGCA
373414 TTGCGATTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
33 54 0.71
36 1 0.01
38 1 0.01
39 20 0.26
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.10
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:373379 original size:19 final size:19
Alignment explanation
Indices: 373295--373383 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
373285 GCAACGAGAT
*
373295 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
***
373314 AGAATGACTGTCGCAACGCG
1 A-AATGAAAATCGCAACGCG
*
373334 AAATGACAATCGCAA--CG
1 AAATGAAAATCGCAACGCG
*
373351 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
373367 AAATGAAAATCGCAACG
1 AAATGAAAATCGCAACG
373384 AGAGAATCGC
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 25 0.45
20 15 0.27
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:373450 original size:14 final size:14
Alignment explanation
Indices: 373431--373487 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
373421 TTTTATTTCG
373431 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
373445 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
373464 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
373478 CGTTGCGATT
1 CGTTGCGATT
373488 GTCATTTCGC
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:373456 original size:33 final size:33
Alignment explanation
Indices: 373414--373534 Score: 161
Period size: 33 Copynumber: 3.5 Consensus size: 33
373404 CAAAATCGCA
*
373414 TTGCGATTTTTATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
373447 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
373480 TTGCGATTGTCATTTCGCATTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCG
373519 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
373535 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
33 51 0.65
35 1 0.01
36 1 0.01
37 1 0.01
39 24 0.31
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:373469 original size:19 final size:19
Alignment explanation
Indices: 373409--373534 Score: 83
Period size: 19 Copynumber: 7.1 Consensus size: 19
373399 GAAACCAAAA
* *
373409 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
373428 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
373442 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
373461 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
373475 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
* ***
373494 TCGCATTGCGACAGTCATT
1 TCGCGTTGCGATTTTCATT
*
373513 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
373533 TC
1 TC
373535 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 15, Indels: 22
0.69 0.13 0.19
Matches are distributed among these distances:
14 20 0.25
16 5 0.06
17 5 0.06
19 37 0.46
20 14 0.17
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:375389 original size:93 final size:93
Alignment explanation
Indices: 375230--375698 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
375220 TAGATTGCTT
*
375230 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
375295 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
375323 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
375388 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
375416 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
375481 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
375509 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
375574 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
375602 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTTTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
375667 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
375694 AGTAA
1 AGTAA
375699 TGCAATCCAT
Statistics
Matches: 374, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 368 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:375786 original size:19 final size:19
Alignment explanation
Indices: 375746--375855 Score: 78
Period size: 19 Copynumber: 6.3 Consensus size: 19
375736 TAGTTTACTT
* *
375746 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
375766 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
375785 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
375799 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
375818 TAGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
**
375832 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
375851 TCGCA
1 TCGCA
375856 TTGCGATTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
14 15 0.21
16 11 0.15
17 10 0.14
19 25 0.34
20 12 0.16
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:375810 original size:33 final size:33
Alignment explanation
Indices: 375764--375855 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 33
375754 CGAAACTTAA
*
375764 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
* *
375797 AATCGCAATGCGAAATGAAAATAGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
**
375830 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
375856 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.48, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:375839 original size:14 final size:14
Alignment explanation
Indices: 375783--375839 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
375773 GCGAAATGAA
*
375783 AATCGCAACGACAG
1 AATCGCAACGAAAG
375797 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
375814 AAAATAGCAACGAAAG
1 --AATCGCAACGAAAG
375830 AATCGCAACG
1 AATCGCAACG
375840 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 6 0.17
19 7 0.20
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:375873 original size:19 final size:19
Alignment explanation
Indices: 375851--375985 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
375841 GAAACCAAAA
*
375851 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
375870 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
375886 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
375903 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
375919 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
375936 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
375955 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
375975 TCGTGTTGCGA
1 TCGCGTTGCGA
375986 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:375892 original size:14 final size:14
Alignment explanation
Indices: 375873--375929 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
375863 TTTCATTTCG
375873 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
375887 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
375904 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
375920 CGTTGCGATT
1 CGTTGCGATT
375930 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:375898 original size:33 final size:33
Alignment explanation
Indices: 375856--375948 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
375846 CAAAATCGCA
*
375856 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
375889 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
375922 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
375949 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:377929 original size:14 final size:14
Alignment explanation
Indices: 377910--377945 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
377900 ATTGTTTAAT
377910 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
377924 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
377938 TGATTTGT
1 TGATTTGT
377946 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:378067 original size:19 final size:19
Alignment explanation
Indices: 378051--378152 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
378041 CAAAATGACT
378051 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
378070 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
378089 ATCGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
378103 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
378122 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
378142 ATCGCAATGCG
1 ATCGCAATGCG
378153 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 11 0.15
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 41 0.55
20 19 0.25
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:378120 original size:52 final size:53
Alignment explanation
Indices: 378051--378150 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 53
378041 CAAAATGACT
378051 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGAGAGA
378103 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATG
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATG
378151 CGTTTATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.62
53 18 0.38
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.16
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGAGAGA
Found at i:378201 original size:33 final size:33
Alignment explanation
Indices: 378159--378481 Score: 323
Period size: 33 Copynumber: 9.4 Consensus size: 33
378149 TGCGTTTATA
378159 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
378192 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
378225 ATTTCGCATTGCGATTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTC-TCTCG--TTGCGATTTTC
*
378262 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
*
378300 ATTTCGCATTGCGATTCTGTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
378333 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
378373 GTTGCG-ATTTTC-ATT-TCGCATTGCGA-TTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
378403 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
378436 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
*
378470 ATTTCGCGTTGC
1 ATTTCGCATTGC
378482 AATTGTAATT
Statistics
Matches: 254, Mismatches: 17, Indels: 38
0.82 0.06 0.12
Matches are distributed among these distances:
30 9 0.04
31 5 0.02
32 10 0.04
33 92 0.36
34 32 0.13
35 15 0.06
36 7 0.03
37 27 0.11
38 45 0.18
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:378205 original size:19 final size:19
Alignment explanation
Indices: 378181--378457 Score: 364
Period size: 19 Copynumber: 15.7 Consensus size: 19
378171 GATTCTCTCG
378181 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
378200 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
378214 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
378233 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
378251 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
378270 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
378289 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
378308 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
378322 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
378341 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
378360 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
378374 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
378393 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
378411 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
378425 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
378445 TTGCGATTTTCAT
1 TTGCGATTTTCAT
378458 GTTGGGATTT
Statistics
Matches: 230, Mismatches: 6, Indels: 43
0.82 0.02 0.15
Matches are distributed among these distances:
14 24 0.10
16 29 0.13
17 27 0.12
18 38 0.17
19 99 0.43
20 13 0.06
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:378237 original size:52 final size:52
Alignment explanation
Indices: 378181--378457 Score: 459
Period size: 52 Copynumber: 5.2 Consensus size: 52
378171 GATTCTCTCG
*
378181 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
*
378233 TTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
*
378289 TTGCGATTTTCATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
378341 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
378393 TTGCGA-TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
378445 TTGCGATTTTCAT
1 TTGCGATTTTCAT
378458 GTTGGGATTT
Statistics
Matches: 215, Mismatches: 2, Indels: 15
0.93 0.01 0.06
Matches are distributed among these distances:
51 59 0.27
52 92 0.43
53 9 0.04
54 9 0.04
55 3 0.01
56 25 0.12
57 18 0.08
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:380781 original size:12 final size:12
Alignment explanation
Indices: 380764--380788 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
380754 TCTTCGGGGA
380764 CTTTTTCTTCTT
1 CTTTTTCTTCTT
380776 CTTTTTCTTCTT
1 CTTTTTCTTCTT
380788 C
1 C
380789 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:380996 original size:24 final size:24
Alignment explanation
Indices: 380962--381008 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
380952 CTGAAACATC
380962 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
380986 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
381009 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:381717 original size:20 final size:20
Alignment explanation
Indices: 381689--381898 Score: 215
Period size: 20 Copynumber: 10.5 Consensus size: 20
381679 AAATTTCAGT
* * *
381689 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
381709 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
381729 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
381749 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
381769 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
381789 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
* *
381809 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
381829 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
381849 ATTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
381869 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
381889 GTTGCGATTT
1 GTTGCGATTT
381899 TGGAAAATCG
Statistics
Matches: 164, Mismatches: 24, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
20 163 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:381915 original size:21 final size:20
Alignment explanation
Indices: 381865--381962 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
381855 ATTTATGTGT
* * * *
381865 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
381885 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
381906 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
381926 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
381947 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
381963 GACACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:381957 original size:41 final size:41
Alignment explanation
Indices: 381865--382021 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
381855 ATTTATGTGT
* * *
381865 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
381906 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
381947 TCGCGTTGCGATTTTGGACACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
381987 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
382022 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:384084 original size:20 final size:20
Alignment explanation
Indices: 384037--384134 Score: 108
Period size: 20 Copynumber: 4.9 Consensus size: 20
384027 GCGATTTTCC
*
384037 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
384057 GTA-AATCGCAATACGATTAT
1 G-ACTATCGCAATGCGATTAT
* *
384077 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTAT
* *
384097 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTAT
*
384117 GACTATCGCAATGTGATT
1 GACTATCGCAATGCGATT
384135 TTCAAAGCGC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.01
20 65 0.97
21 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:384331 original size:22 final size:22
Alignment explanation
Indices: 384306--384349 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
384296 ACATCCGTCC
384306 CCATCTCCGACGAAATCAGTCT
1 CCATCTCCGACGAAATCAGTCT
* *
384328 CCATCTCCGGCGAAATCCGTCT
1 CCATCTCCGACGAAATCAGTCT
384350 ATCTCCATCT
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:0.39, G:0.16, T:0.23
Consensus pattern (22 bp):
CCATCTCCGACGAAATCAGTCT
Found at i:384800 original size:20 final size:20
Alignment explanation
Indices: 384730--384817 Score: 70
Period size: 20 Copynumber: 4.5 Consensus size: 20
384720 AGAATCGCAA
*
384730 TGCGATTTT-AGTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
* ** ** *
384749 TACGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGTGT
**
384769 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
*
384789 TGCGATTTTCATTTTTGTGT
1 TGCGATTTTCATTTTCGTGT
*
384809 TGTGATTTT
1 TGCGATTTT
384818 AAGTTTCAGA
Statistics
Matches: 54, Mismatches: 14, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
19 6 0.11
20 48 0.89
ACGTcount: A:0.16, C:0.12, G:0.23, T:0.49
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGTGT
Found at i:386508 original size:17 final size:18
Alignment explanation
Indices: 386486--386534 Score: 91
Period size: 17 Copynumber: 2.8 Consensus size: 18
386476 TTTACTCGTA
386486 ATTTCACTTAGATTAA-C
1 ATTTCACTTAGATTAACC
386503 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
386521 ATTTCACTTAGATT
1 ATTTCACTTAGATT
386535 GCTTAGTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:386706 original size:20 final size:20
Alignment explanation
Indices: 386681--386768 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
386671 TAGTTTACTT
386681 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
386701 TCGCAACGTGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
386721 TCGCAACGTGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* **
386741 TCGCAATGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
*
386761 TCACAACG
1 TCGCAACG
386769 AAAGAATCGC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:387407 original size:21 final size:21
Alignment explanation
Indices: 387316--387420 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
387306 GACTCACCTG
* *
387316 TCATCATTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
387338 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
387358 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
387379 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
387400 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
387421 CCAACATTCT
Statistics
Matches: 62, Mismatches: 20, Indels: 3
0.73 0.24 0.04
Matches are distributed among these distances:
20 3 0.05
21 58 0.94
22 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:387413 original size:42 final size:42
Alignment explanation
Indices: 387341--387423 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
387331 CCTCCCCTAT
*
387341 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
387383 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
387424 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:388844 original size:14 final size:14
Alignment explanation
Indices: 388821--388872 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
388811 TGATTTATTA
388821 TAAAAATTGATTTG
1 TAAAAATTGATTTG
*
388835 TAAAAGTTGATTTG
1 TAAAAATTGATTTG
* * *
388849 TTTAATATTGATGTG
1 -TAAAAATTGATTTG
388864 TAAATAATT
1 TAAA-AATT
388873 CTTATTTGTT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
14 16 0.55
15 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (14 bp):
TAAAAATTGATTTG
Found at i:389024 original size:20 final size:20
Alignment explanation
Indices: 388971--389024 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
388961 AGGTACACTT
* **
388971 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGACAAAA
*
388991 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
389011 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
389025 TCAATTCGCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:389092 original size:20 final size:20
Alignment explanation
Indices: 389067--389325 Score: 160
Period size: 20 Copynumber: 13.8 Consensus size: 20
389057 GCGATTTTCT
* * *
389067 CGTTGCGATTGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
* *
389087 CGTTGCAATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
389107 CGTTGCGATACTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
389127 CATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
389147 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
* *
389161 CATTGCGATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
* *
389180 CCGTTGAGATAATCAAATTCG
1 -CGTTGCGATAGTCAAATTCG
** *
389201 TATTGCGATAGACAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
389221 CGTTGCG---GT---TTTTG
1 CGTTGCGATAGTCAAATTCG
389235 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
389255 CATTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
389269 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
389289 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
* *
389309 CATTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
389326 GCATGTGTAA
Statistics
Matches: 179, Mismatches: 40, Indels: 40
0.69 0.15 0.15
Matches are distributed among these distances:
14 31 0.17
16 2 0.01
17 3 0.02
18 2 0.01
19 1 0.01
20 138 0.77
21 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:389170 original size:34 final size:33
Alignment explanation
Indices: 389127--389297 Score: 155
Period size: 34 Copynumber: 4.9 Consensus size: 33
389117 CTCAAATTCG
389127 CATTGCGATAGTCAAATTCGCGTTGCGATTTTCT
1 CATTGCGATAGTCAAATTCGCGTTGCGATTTT-T
* * *
389161 CATTGCGATAGTCAAA-TAGCCGTTGAGATAATCAAATT
1 CATTGCGATAGTCAAATTCG-CGTTGCGAT--T---TTT
* *
389199 CGTATTGCGATAGACAAATTCGCGTTGCGGTTTTT
1 C--ATTGCGATAGTCAAATTCGCGTTGCGATTTTT
* *
389234 GCGTTGCGATAGTCAAATTCGCATTGCGATTTTT
1 -CATTGCGATAGTCAAATTCGCGTTGCGATTTTT
* *
389268 GAGTTGCGATAATCAAATTCGCGTTGCGAT
1 CA-TTGCGATAGTCAAATTCGCGTTGCGAT
389298 AGTCAAATTC
Statistics
Matches: 110, Mismatches: 16, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
33 2 0.02
34 77 0.70
35 2 0.02
36 2 0.02
38 3 0.03
39 1 0.01
40 21 0.19
41 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (33 bp):
CATTGCGATAGTCAAATTCGCGTTGCGATTTTT
Found at i:389176 original size:74 final size:74
Alignment explanation
Indices: 389089--389263 Score: 228
Period size: 74 Copynumber: 2.4 Consensus size: 74
389079 CAAATACCCG
* * * *
389089 TTGCAATAATCAAATTCGCGTTGCGATACTCAAATTCGCATTGCGATAGTCAAATTCGCGTTGCG
1 TTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCATTGCGATAGACAAATTCGCGTTGCG
389154 ATTTTCT-CA
66 ATTTT-TGCA
* * *
389163 TTGCGATAGTCAAA-TAGCCGTTGAGATAATCAAATTCGTATTGCGATAGACAAATTCGCGTTGC
1 TTGCGATAGTCAAATTCG-CGTTGCGATAATCAAATTCGCATTGCGATAGACAAATTCGCGTTGC
* *
389227 GGTTTTTGCG
65 GATTTTTGCA
*
389237 TTGCGATAGTCAAATTCGCATTGCGAT
1 TTGCGATAGTCAAATTCGCGTTGCGAT
389264 TTTTGAGTTG
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
73 3 0.03
74 81 0.94
75 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (74 bp):
TTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCATTGCGATAGACAAATTCGCGTTGCG
ATTTTTGCA
Found at i:389192 original size:94 final size:94
Alignment explanation
Indices: 389027--389227 Score: 287
Period size: 94 Copynumber: 2.1 Consensus size: 94
389017 CGCGAAAGTC
* * * *
389027 AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATTGTCAAATACCCGTTG
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTCTCATTGCGATAGTCAAATACCCGTTG
* *
389092 CAATAATCAAATTCGCGTTGCGATACTCA
66 CAATAATCAAATTCGCATTGCGATACACA
* * *
389121 AATTCGCATTGCGATAGTCAAATTCGCGTTGCGATTTTCTCATTGCGATAGTCAAATAGCCGTTG
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTCTCATTGCGATAGTCAAATACCCGTTG
* *
389186 -AGATAATCAAATTCGTATTGCGATAGACA
66 CA-ATAATCAAATTCGCATTGCGATACACA
389215 AATTCGCGTTGCG
1 AATTCGCGTTGCG
389228 GTTTTTGCGT
Statistics
Matches: 94, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
93 1 0.01
94 93 0.99
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (94 bp):
AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTCTCATTGCGATAGTCAAATACCCGTTG
CAATAATCAAATTCGCATTGCGATACACA
Found at i:389225 original size:40 final size:39
Alignment explanation
Indices: 389089--389325 Score: 152
Period size: 34 Copynumber: 6.4 Consensus size: 39
389079 CAAATACCCG
* * *
389089 TTGCAATAATCAAATTCGCGTTGCGATACTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCGTTGCGATA-TCAAATTCGTA
389129 TTGCGATAGTCAAATTCGCGTTGCGAT-T----TTC-TCA
1 TTGCGATAGTCAAATTCGCGTTGCGATATCAAATTCGT-A
* *
389163 TTGCGATAGTCAAA-TAGCCGTTGAGATAATCAAATTCGTA
1 TTGCGATAGTCAAATTCG-CGTTGCGAT-ATCAAATTCGTA
* * *
389203 TTGCGATAGACAAATTCGCGTTGCGGT-T---TTTGCG--
1 TTGCGATAGTCAAATTCGCGTTGCGATATCAAATT-CGTA
* *
389237 TTGCGATAGTCAAATTCGCATTGCGAT-T----TTTG-A
1 TTGCGATAGTCAAATTCGCGTTGCGATATCAAATTCGTA
* **
389270 GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCACA
1 -TTGCGATAGTCAAATTCGCGTTGCGATA-TCAAATTCGTA
*
389311 TTGCGATATTCAAAT
1 TTGCGATAGTCAAAT
389326 GCATGTGTAA
Statistics
Matches: 158, Mismatches: 19, Indels: 40
0.73 0.09 0.18
Matches are distributed among these distances:
32 1 0.01
33 4 0.03
34 76 0.48
35 2 0.01
36 4 0.03
38 2 0.01
40 65 0.41
41 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (39 bp):
TTGCGATAGTCAAATTCGCGTTGCGATATCAAATTCGTA
Found at i:389292 original size:54 final size:53
Alignment explanation
Indices: 389108--389317 Score: 158
Period size: 54 Copynumber: 3.9 Consensus size: 53
389098 TCAAATTCGC
* * *
389108 GTTGCGATACTCAAATTCGCATTGCGATAGTCAAATTCGCGTTGCGATTTTCTCA
1 GTTGCGATA-TCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTT-TAA
* * * * ****
389163 -TTGCGATAGTCAAA-TAGCCGTTGAGATAATCAAATTCGTATTGCGATAGACAA
1 GTTGCGATA-TCAAATTCG-CGTTGCGATAGTCAAATTCGCATTGCGATTTTTAA
* *** * *
389216 ATTCGCG-T-TGCGGTTTTTGCGTTGCGATAGTCAAATTCGCATTGCGATTTTTGA
1 GTT-GCGATAT-C-AAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTTAA
*
389270 GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCACATTGCGAT
1 GTTGCGAT-ATCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGAT
389318 ATTCAAATGC
Statistics
Matches: 116, Mismatches: 30, Indels: 19
0.70 0.18 0.12
Matches are distributed among these distances:
52 1 0.01
53 7 0.06
54 101 0.87
55 6 0.05
56 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (53 bp):
GTTGCGATATCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTTAA
Found at i:389548 original size:140 final size:140
Alignment explanation
Indices: 389296--389565 Score: 477
Period size: 140 Copynumber: 1.9 Consensus size: 140
389286 TCGCGTTGCG
* * * *
389296 ATAGTCAAATTCACATTGCGATATTCAAATGCATGTGTAATAAGTGATATCAACTGAACATATCA
1 ATAGTCAAATTCACATTGCGATATTCAAATGAATGTATAATAAGTGATAACAACTGAACAGATCA
389361 TAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
389426 AACACACATA
131 AACACACATA
* *
389436 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTATAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCACATTGCGATATTCAAATGAATGTATAATAAGTGATAACAACTGAACAGATCA
*
389501 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
389566 TACAACGTTT
Statistics
Matches: 123, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 123 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCACATTGCGATATTCAAATGAATGTATAATAAGTGATAACAACTGAACAGATCA
TAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AACACACATA
Found at i:389648 original size:18 final size:18
Alignment explanation
Indices: 389625--389659 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
389615 AAGCCGGTTG
*
389625 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
389643 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
389660 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:391942 original size:24 final size:24
Alignment explanation
Indices: 391908--391961 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
391898 CTGAAACATC
391908 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
391932 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
391956 ATCAAA
1 ATCAAA
391962 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:392821 original size:20 final size:20
Alignment explanation
Indices: 392775--392845 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
392765 AAATTCAGTG
* * *
392775 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCATAATCGCA
392795 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
* *
392815 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
392835 TTGCGATAGTC
1 TTGCGATAGTC
392846 GAAAAATCGT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Done.