Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007999.1 Hibiscus syriacus cultivar Beakdansim tig00110450_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: 11700749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 50
Found at i:1719385 original size:38 final size:38
Alignment explanation
Indices: 1719310--1719385 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
1719300 AAAAAAGTAT
**
1719310 ATATATATATATATATATATATATATAATATCTAAAAA
1 ATATATATATATATATATATATATATAATATAAAAAAA
* * *
1719348 ATATATGTATATATATATATATATATAGTGTAAAAAAA
1 ATATATATATATATATATATATATATAATATAAAAAAA
1719386 TCAATTGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (38 bp):
ATATATATATATATATATATATATATAATATAAAAAAA
Found at i:1719887 original size:37 final size:37
Alignment explanation
Indices: 1719846--1719950 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
1719836 GTGCTTGTGG
* * *
1719846 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
1719883 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
1719920 ATCATATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1719951 GACGACAGCT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:1721039 original size:212 final size:212
Alignment explanation
Indices: 1720668--1721718 Score: 1565
Period size: 212 Copynumber: 5.0 Consensus size: 212
1720658 GCATTGTTCC
* * * * *
1720668 GAGTCCAATATACTCCG-TCGTGAAGTTGAAATTGGCTATGGAATTGGGAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACA
* *
1720732 ACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGA
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGA
* * * *
1720797 AGTCGAAATTGACTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCAGTCCCTTCGTCGTGAAG
130 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
* * * *
1720862 TCAAACTTTCATTGTCTT
195 TTAAACTTGCGTTGTCTG
* *
1720880 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* * * * * * *
1720945 CCAACGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAACATCATTCGTTGTGAG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
*
1721010 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
1721075 TAAAATTGCGTTGTCTG
196 TAAACTTGCGTTGTCTG
1721092 GAGTCCAATATCCTTCGCTGTGAAGTTGAAA-----T-TG-----G-GAAGTT-TTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* * * *
1721144 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCTAATATCTTTCACTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
* * *
1721209 GTTGAAATTGGCTTTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTTGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
1721274 TGAACTTGCGTTGTCTG
196 TAAACTTGCGTTGTCTG
* *
1721291 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1721356 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
1721421 GTTGAAATTGGCTCTGAAATT-AGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
131 GTTGAAATTGGCTCTGAAATTGA-GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
* *
1721485 TTGAACTTGCGTTGTCTA
195 TTAAACTTGCGTTGTCTG
*
1721503 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1721568 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
* * * *
1721633 GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* * *
1721698 TGAACTTGTGTTGTCTC
196 TAAACTTGCGTTGTCTG
1721715 GAGT
1 GAGT
1721719 GACACGATAT
Statistics
Matches: 763, Mismatches: 60, Indels: 32
0.89 0.07 0.04
Matches are distributed among these distances:
199 172 0.23
200 5 0.01
201 1 0.00
204 1 0.00
205 2 0.00
206 2 0.00
207 1 0.00
210 1 0.00
211 7 0.01
212 570 0.75
213 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (212 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TAAACTTGCGTTGTCTG
Found at i:1721327 original size:106 final size:106
Alignment explanation
Indices: 1720668--1721126 Score: 650
Period size: 106 Copynumber: 4.3 Consensus size: 106
1720658 GCATTGTTCC
* * * * *
1720668 GAGTCCAATATACTCCG-TCGTGAAGTTGAAATTGGCTATGGAATTGGGAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACA
* *
1720732 ACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1720774 GAGTCCAATATCCTTCGCTGTGAAGTCGAAATTGACTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* ** * * *
1720839 CCAGCAGTCCCTTCGTCGTGAAGTCAAACTTTCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1720880 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* * *
1720945 CCAACGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1720986 GAGTCCAACATCATTCGTTGTGAGGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* *
1721051 CCAGCGGTCCCTTCGTCGTGAAGTTAAAATTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1721092 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
1721127 GAAGTTTTTA
Statistics
Matches: 314, Mismatches: 38, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
106 313 1.00
107 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1721333 original size:106 final size:106
Alignment explanation
Indices: 1721118--1721718 Score: 963
Period size: 106 Copynumber: 5.7 Consensus size: 106
1721108 GCTGTGAAGT
* *
1721118 TGAAATTGGGAAGTT-TTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGT
* * * * *
1721182 CTTGAGTCTAATATCTTTCACTGTGAAGTTGAAATTGGCTT
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* * *
1721223 TGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGT
*
1721288 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* *
1721329 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGT
1721394 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
*
1721435 TGAAATT-AGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1 TGAAATTGA-GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTG
* *
1721499 TCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
65 TCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
*
1721541 TGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGT
1721606 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* * * * * *
1721647 TGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGT
*
1721712 CTCGAGT
66 CTGGAGT
1721719 GACACGATAT
Statistics
Matches: 469, Mismatches: 24, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
105 14 0.03
106 454 0.97
107 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
TGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
Found at i:1723357 original size:20 final size:18
Alignment explanation
Indices: 1723322--1723397 Score: 64
Period size: 20 Copynumber: 3.9 Consensus size: 18
1723312 TTTTGTCCCT
**
1723322 TTTTCTTTTTGATTTTTG
1 TTTTCTTTTTTCTTTTTG
1723340 ATCTTTCTTTTTTC-TTTTG
1 -T-TTTCTTTTTTCTTTTTG
*
1723359 TTTCTCTTTTTTCTTTGTTT
1 TTT-TCTTTTTTCTTT-TTG
1723379 TTTTACTTCTTTTCTTTTT
1 TTTT-CTT-TTTTCTTTTT
1723398 TGTTCTCGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
17 2 0.04
18 10 0.21
19 9 0.19
20 19 0.40
21 8 0.17
ACGTcount: A:0.04, C:0.13, G:0.05, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTTTCTTTTTG
Found at i:1723375 original size:17 final size:18
Alignment explanation
Indices: 1723345--1723378 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1723335 TTTTGATCTT
1723345 TCTTTTTTCTTTTGTTTC
1 TCTTTTTTCTTTTGTTTC
1723363 TCTTTTTTC-TTTGTTT
1 TCTTTTTTCTTTTGTTT
1723379 TTTTACTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (18 bp):
TCTTTTTTCTTTTGTTTC
Found at i:1723388 original size:25 final size:26
Alignment explanation
Indices: 1723341--1723401 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
1723331 TGATTTTTGA
**
1723341 TCTTTCTTT-TTTCTTTTGTTTCTCTT
1 TCTTTCTTTGTTTCTTTTACTTCT-TT
1723367 T-TTTCTTTGTTT-TTTTACTTCTTT
1 TCTTTCTTTGTTTCTTTTACTTCTTT
1723391 TCTTT-TTTGTT
1 TCTTTCTTTGTT
1723402 CTCGATTGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
24 9 0.29
25 18 0.58
26 4 0.13
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.79
Consensus pattern (26 bp):
TCTTTCTTTGTTTCTTTTACTTCTTT
Found at i:1723396 original size:16 final size:15
Alignment explanation
Indices: 1723343--1723403 Score: 54
Period size: 16 Copynumber: 4.0 Consensus size: 15
1723333 ATTTTTGATC
*
1723343 TTTCTTTTTTCTTTT
1 TTTCTTTTTTCTTCT
*
1723358 GTTTCTCTTTT-TTCT
1 -TTTCTTTTTTCTTCT
1723373 TTGT-TTTTTTACTTCT
1 TT-TCTTTTTT-CTTCT
*
1723389 TTTCTTTTTTGTTCT
1 TTTCTTTTTTCTTCT
1723404 CGATTGGATC
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
14 7 0.19
15 9 0.24
16 21 0.57
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.79
Consensus pattern (15 bp):
TTTCTTTTTTCTTCT
Found at i:1727563 original size:32 final size:35
Alignment explanation
Indices: 1727518--1727614 Score: 92
Period size: 36 Copynumber: 2.7 Consensus size: 35
1727508 TAATACGCTT
*
1727518 ATAAGTAAAATATATTTAAAAAAA-AGTGTATATAT-
1 ATAA-TAATATATATTTAAAAAAATA-TGTATATATA
*
1727553 AT-ATATATATAATATCTAAAAAATATATGTATATATA
1 ATAATA-ATAT-ATATTTAAAAAA-ATATGTATATATA
*
1727590 ATAATAATATATAGTGTAAAAAAAT
1 ATAATAATATATA-TTTAAAAAAAT
1727615 CAATTGAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
33 2 0.04
34 4 0.08
35 13 0.25
36 15 0.29
37 15 0.29
38 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (35 bp):
ATAATAATATATATTTAAAAAAATATGTATATATA
Found at i:1728116 original size:37 final size:37
Alignment explanation
Indices: 1728075--1728179 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
1728065 GTGCTTGTGG
* * *
1728075 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
1728112 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
1728149 ATCATATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1728180 GACGAAAAGG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:1732412 original size:25 final size:26
Alignment explanation
Indices: 1732378--1732432 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
1732368 TGATTTACTT
* *
1732378 TTAATCTACACATTTTA-TAAAAAAA
1 TTAATCTACACACTTTACAAAAAAAA
1732403 TTAATCTACACACTTTACAAAAAAAA
1 TTAATCTACACACTTTACAAAAAAAA
1732429 TTAA
1 TTAA
1732433 CTTACTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.33
Consensus pattern (26 bp):
TTAATCTACACACTTTACAAAAAAAA
Found at i:1735687 original size:18 final size:18
Alignment explanation
Indices: 1735666--1735701 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1735656 AAATTTGTTG
*
1735666 TTTTAATTAAAATTAAAA
1 TTTTAATTAAAATGAAAA
*
1735684 TTTTTATTAAAATGAAAA
1 TTTTAATTAAAATGAAAA
1735702 ACATGTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TTTTAATTAAAATGAAAA
Found at i:1739672 original size:109 final size:107
Alignment explanation
Indices: 1739320--1739790 Score: 432
Period size: 109 Copynumber: 4.4 Consensus size: 107
1739310 AACCGAGAAA
** * * * *
1739320 TTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGT-CTA--
1 TTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGC-ACG
* * * * * *
1739382 ATATCCTTCGTTGTGAAGTTGAAATTGACTCTG-AA-T-GAAA-
65 ATATCCTCCGTCGTGGAGTTGAAATCGGC-CTGAAATTAAAAAG
* * * * *
1739422 -T-CTTGTTGACAATCAGTCGTCCCTTCGTTGTGAAGTTTAACTTGTGTTGTCTCGAGT-C-CAA
1 TTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACGA
* * * *
1739483 TATCCTTCG-CTGTGAAGTTTGAAATTGGCTCTGGAATTTGAAAAA-
66 TATCCTCCGTC-GTGGAG-TTGAAATCGGC-CT-GAAATT-AAAAAG
*
1739528 -TATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCACG
1 TTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCACG
* *
1739592 ATATCCTCCGTCGTGGAGTTGAAATCACGG-ATGAAACTAAAAAG
65 ATATCCTCCGTCGTGGAGTTGAAAT--CGGCCTGAAATTAAAAAG
* * *
1739636 TTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTAAACTTGTATTGTCTCGGGTAGCACG
1 TTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCACG
* ***
1739701 ATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAG
65 ATATCCTCCGTCGTGGAGTTGAAATCGGC-CTGAAATTAAAAAG
* *
1739745 TTGTTCGTTGGCAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
1 TTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
1739791 ACTCTGGCTA
Statistics
Matches: 312, Mismatches: 37, Indels: 33
0.82 0.10 0.09
Matches are distributed among these distances:
100 65 0.21
101 14 0.04
102 1 0.00
103 1 0.00
104 1 0.00
106 4 0.01
107 60 0.19
108 4 0.01
109 144 0.46
110 15 0.05
111 3 0.01
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (107 bp):
TTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACGA
TATCCTCCGTCGTGGAGTTGAAATCGGCCTGAAATTAAAAAG
Found at i:1740342 original size:36 final size:33
Alignment explanation
Indices: 1740247--1740350 Score: 131
Period size: 33 Copynumber: 3.1 Consensus size: 33
1740237 TTTTTCGAGG
*
1740247 GAAACAATCTCAAAGG--TTTTGTGTTTCAAGA
1 GAAACAATTTCAAAGGTTTTTTGTGTTTCAAGA
*
1740278 GAAACATTTTCAAAGGTTTTTTGTGTTTCAAGA
1 GAAACAATTTCAAAGGTTTTTTGTGTTTCAAGA
* *
1740311 GAAACAATTTCATAAGTTTCTTTTTGTGTTTCAGGA
1 GAAACAATTTCA-AAG-GT-TTTTTGTGTTTCAAGA
1740347 GAAA
1 GAAA
1740351 ATTTTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
31 14 0.22
33 26 0.41
34 3 0.05
35 1 0.02
36 19 0.30
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (33 bp):
GAAACAATTTCAAAGGTTTTTTGTGTTTCAAGA
Found at i:1740601 original size:99 final size:102
Alignment explanation
Indices: 1740480--1740673 Score: 340
Period size: 99 Copynumber: 1.9 Consensus size: 102
1740470 AACATATTCA
1740480 AAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCA
1 AAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCA
1740545 ACGTTTATG-TT-AAGAGAAACTTTCTCAAGGGAGAC
66 ACGTTTATGTTTCAAGAGAAACTTTCTCAAGGGAGAC
1740580 AAGA-TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCA
1 AAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCA
* * *
1740644 ATGTTTATGTTTCAAGATAAACTTTTTCAA
66 ACGTTTATGTTTCAAGAGAAACTTTCTCAA
1740674 AGGTTTTTTG
Statistics
Matches: 89, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
99 68 0.76
100 6 0.07
101 15 0.17
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (102 bp):
AAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCA
ACGTTTATGTTTCAAGAGAAACTTTCTCAAGGGAGAC
Found at i:1740607 original size:36 final size:36
Alignment explanation
Indices: 1740560--1740635 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
1740550 TATGTTAAGA
* * * **
1740560 GAAACTTTCTCAAGGGAGACAAGATTTGTTTCAAGG
1 GAAACTATCTCAAGAGAGACAAAATTCATTTCAAGG
1740596 GAAACTATCTCAAGAGAGACAAAATTCATTTCAAGG
1 GAAACTATCTCAAGAGAGACAAAATTCATTTCAAGG
1740632 GAAA
1 GAAA
1740636 TGTTTTCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (36 bp):
GAAACTATCTCAAGAGAGACAAAATTCATTTCAAGG
Found at i:1740690 original size:33 final size:33
Alignment explanation
Indices: 1740651--1740715 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1740641 TCAATGTTTA
* **
1740651 TGTTTCAAGATAAACTTTTTCAAAGGTTTTTTG
1 TGTTTCAAGAGAAACGATTTCAAAGGTTTTTTG
1740684 TGTTTCAAGAGAAACGATTTCAAAGGTTTTTT
1 TGTTTCAAGAGAAACGATTTCAAAGGTTTTTT
1740716 CTAAGGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (33 bp):
TGTTTCAAGAGAAACGATTTCAAAGGTTTTTTG
Found at i:1740768 original size:36 final size:37
Alignment explanation
Indices: 1740704--1740779 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 37
1740694 GAAACGATTT
1740704 CAAAGGTTTTTTCTAAGGAAAACTGTCTCAAGAGAGA
1 CAAAGGTTTTTTCTAAGGAAAACTGTCTCAAGAGAGA
*
1740741 CAAA-GTTTGTTTC-AAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTT-TTTCTAAGGAAAACTGTCTCAAGAGAGA
1740777 CAA
1 CAA
1740780 TGGTGAGCAC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
36 29 0.78
37 8 0.22
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.25
Consensus pattern (37 bp):
CAAAGGTTTTTTCTAAGGAAAACTGTCTCAAGAGAGA
Found at i:1741235 original size:17 final size:17
Alignment explanation
Indices: 1741215--1741248 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1741205 GTTGAATCCC
*
1741215 CAAAGATGCCCCAATAT
1 CAAAAATGCCCCAATAT
1741232 CAAAAATGCCCCAATAT
1 CAAAAATGCCCCAATAT
1741249 TTGATGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.29, G:0.09, T:0.18
Consensus pattern (17 bp):
CAAAAATGCCCCAATAT
Found at i:1742332 original size:11 final size:11
Alignment explanation
Indices: 1742316--1742370 Score: 60
Period size: 12 Copynumber: 5.0 Consensus size: 11
1742306 TCTTTTGATC
1742316 TTTGTTCTTTT
1 TTTGTTCTTTT
1742327 TTTGTTC-TTT
1 TTTGTTCTTTT
*
1742337 TTT-TTCCTTT
1 TTTGTTCTTTT
1742347 TTTGTTTCTTTT
1 TTTG-TTCTTTT
*
1742359 CTTTTTTCTTTT
1 -TTTGTTCTTTT
1742371 CTTCTTTCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 3 0.08
10 12 0.32
11 7 0.18
12 13 0.34
13 3 0.08
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (11 bp):
TTTGTTCTTTT
Found at i:1742340 original size:12 final size:11
Alignment explanation
Indices: 1742320--1742384 Score: 60
Period size: 11 Copynumber: 5.7 Consensus size: 11
1742310 TTGATCTTTG
*
1742320 TTCTTTTTTTG
1 TTCTTTTTTTT
1742331 TTC-TTTTTTT
1 TTCTTTTTTTT
* *
1742341 TCCTTTTTTGT
1 TTCTTTTTTTT
1742352 TTCTTTTCTTTT
1 TTCTTTT-TTTT
1742364 TTCTTTTCTTCTT
1 TTCTTTT-TT-TT
*
1742377 TCCTTTTT
1 TTCTTTTT
1742385 CGATTCTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
10 8 0.18
11 15 0.33
12 14 0.31
13 8 0.18
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:1742349 original size:20 final size:22
Alignment explanation
Indices: 1742324--1742363 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1742314 TCTTTGTTCT
1742324 TTTTTTG-TTCTTTT-TTTTCC
1 TTTTTTGTTTCTTTTCTTTTCC
1742344 TTTTTTGTTTCTTTTCTTTT
1 TTTTTTGTTTCTTTTCTTTT
1742364 TTCTTTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.82
Consensus pattern (22 bp):
TTTTTTGTTTCTTTTCTTTTCC
Found at i:1742378 original size:24 final size:25
Alignment explanation
Indices: 1742336--1742383 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1742326 TTTTGTTCTT
*
1742336 TTTTTTCCTTTTTTGTTT-CTTTTC
1 TTTTTTCCTTTTTTCTTTCCTTTTC
1742360 TTTTTT-CTTTTCTTCTTTCCTTTT
1 TTTTTTCCTTTT-TTCTTTCCTTTT
1742384 TCGATTCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (25 bp):
TTTTTTCCTTTTTTCTTTCCTTTTC
Found at i:1742392 original size:36 final size:32
Alignment explanation
Indices: 1742320--1742392 Score: 83
Period size: 36 Copynumber: 2.2 Consensus size: 32
1742310 TTGATCTTTG
* *
1742320 TTCTTTTTTTGTTCTTTTTTTTCCTTTTTTGT
1 TTCTTTTTTTGTTCTTTTTTTTCCTTTTTCGA
*
1742352 TTCTTTTCTTTTTTCTTTTCTTCTTTCCTTTTTCGA
1 TTCTTTT-TTTGTTC-TTT-TT-TTTCCTTTTTCGA
1742388 TTCTT
1 TTCTT
1742393 ATTGAATCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 7 0.21
33 6 0.18
34 3 0.09
35 2 0.06
36 16 0.47
ACGTcount: A:0.01, C:0.18, G:0.04, T:0.77
Consensus pattern (32 bp):
TTCTTTTTTTGTTCTTTTTTTTCCTTTTTCGA
Found at i:1745410 original size:25 final size:28
Alignment explanation
Indices: 1745349--1745410 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 28
1745339 AATTCAAGTG
* *
1745349 TAAGAAAACATAAAATAATAGCTAAAAA
1 TAAGAAAAGATAAAATAATAGCAAAAAA
1745377 TAA-ACAAAGAT-AAA-AAT-GCAAAAAA
1 TAAGA-AAAGATAAAATAATAGCAAAAAA
1745402 TAAGAAAAG
1 TAAGAAAAG
1745411 CAGTACCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 14 0.47
26 4 0.13
27 4 0.13
28 8 0.27
ACGTcount: A:0.69, C:0.06, G:0.10, T:0.15
Consensus pattern (28 bp):
TAAGAAAAGATAAAATAATAGCAAAAAA
Found at i:1747346 original size:2 final size:2
Alignment explanation
Indices: 1747339--1747380 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1747329 AGAAGAACAT
1747339 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1747381 GAATGGACTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1754961 original size:24 final size:24
Alignment explanation
Indices: 1754929--1754977 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1754919 CCAACTTTTT
1754929 AATAGTGAAATATGTGATAAATCA
1 AATAGTGAAATATGTGATAAATCA
*
1754953 AATAGTGAAATATTTGATAAATCA
1 AATAGTGAAATATGTGATAAATCA
1754977 A
1 A
1754978 GTACATACAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.14, T:0.31
Consensus pattern (24 bp):
AATAGTGAAATATGTGATAAATCA
Found at i:1757788 original size:24 final size:22
Alignment explanation
Indices: 1757724--1757790 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 22
1757714 TACAAACACT
1757724 TTATAATTTATAAGCTTTAATTAAA
1 TTAT-ATTT-TAA-CTTTAATTAAA
* *
1757749 TTATATTCT--CTCTAATTAAA
1 TTATATTTTAACTTTAATTAAA
1757769 TTCATATTTTAAACTTTAATTA
1 TT-ATATTTT-AACTTTAATTA
1757791 CTTTTAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
20 12 0.35
21 6 0.18
23 1 0.03
24 11 0.32
25 4 0.12
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (22 bp):
TTATATTTTAACTTTAATTAAA
Found at i:1757915 original size:22 final size:23
Alignment explanation
Indices: 1757890--1757933 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1757880 TGGTTACAAA
1757890 TAATTTT-TATAATTTAATCTTT
1 TAATTTTATATAATTTAATCTTT
* *
1757912 TAATTTTATTTAATTTAGTCTT
1 TAATTTTATATAATTTAATCTT
1757934 ATGACTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (23 bp):
TAATTTTATATAATTTAATCTTT
Found at i:1759179 original size:17 final size:16
Alignment explanation
Indices: 1759148--1759181 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1759138 GAGGGCATCG
*
1759148 GTACCATATTATAGTA
1 GTACCATACTATAGTA
1759164 GTACCGATACTATAGTA
1 GTACC-ATACTATAGTA
1759181 G
1 G
1759182 GGGTATCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (16 bp):
GTACCATACTATAGTA
Found at i:1759670 original size:45 final size:45
Alignment explanation
Indices: 1759649--1759854 Score: 274
Period size: 45 Copynumber: 4.6 Consensus size: 45
1759639 GCTACATTTG
1759649 AAATGTATATGGGTACATTATCAACAGAAAAGTATGCAATAGTGT
1 AAATGTATATGGGTACATTATCAACAGAAAAGTATGCAATAGTGT
*
1759694 AAATGTATATGGGTACATTATCAACAGAAAAATATGCAATAGTGT
1 AAATGTATATGGGTACATTATCAACAGAAAAGTATGCAATAGTGT
* *
1759739 AAATGTATATGGGTACATTATCAACA-ATAAAGTATACTATAGT-T
1 AAATGTATATGGGTACATTATCAACAGA-AAAGTATGCAATAGTGT
* * * *
1759783 GAAATGTATATGGGTACATTATCAATAGAAAAATATGCTATGGT-T
1 -AAATGTATATGGGTACATTATCAACAGAAAAGTATGCAATAGTGT
* * *
1759828 GAAATGCATATGGATGCATTATCAACA
1 -AAATGTATATGGGTACATTATCAACA
1759855 TAAATATATA
Statistics
Matches: 146, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
44 2 0.01
45 143 0.98
46 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (45 bp):
AAATGTATATGGGTACATTATCAACAGAAAAGTATGCAATAGTGT
Found at i:1759875 original size:45 final size:44
Alignment explanation
Indices: 1759646--1759884 Score: 150
Period size: 45 Copynumber: 5.3 Consensus size: 44
1759636 GATGCTACAT
* * * *
1759646 TTGAAATGTATATGGGTACATTATCAACAGAAA-AGTATGCAATA-G
1 TTGAAATGCATATGGATACATTATCAACATAAATA-TAT--ATTATG
* * * * *
1759691 -TGTAAATGTATATGGGTACATTATCAACAGAAAAATATGCAATA-G
1 TTG-AAATGCATATGGATACATTATCAACATAAATATAT--ATTATG
* *
1759736 -TGTAAATGTATATGGGTACATTATCAACAATAAAGTATACTA-TA-G
1 TTG-AAATGCATATGGATACATTATCAAC-ATAAA-TATA-TATTATG
* * * * * **
1759781 TTGAAATGTATATGGGTACATTATCAATAGAAAAATATGCTATGG
1 TTGAAATGCATATGGATACATTATCAACATAAATATATATTAT-G
*
1759826 TTGAAATGCATATGGATGCATTATCAACATAAATATATATTATG
1 TTGAAATGCATATGGATACATTATCAACATAAATATATATTATG
1759870 ATTGAAATGCATATG
1 -TTGAAATGCATATG
1759885 AGTGTATTAT
Statistics
Matches: 170, Mismatches: 14, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
42 1 0.01
43 5 0.03
44 7 0.04
45 145 0.85
46 8 0.05
47 3 0.02
48 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (44 bp):
TTGAAATGCATATGGATACATTATCAACATAAATATATATTATG
Found at i:1759875 original size:90 final size:90
Alignment explanation
Indices: 1759649--1759884 Score: 277
Period size: 90 Copynumber: 2.6 Consensus size: 90
1759639 GCTACATTTG
* * * *
1759649 AAATGTATATGGGTACATTATCAACAGA-AAAGTATGCAATAG-TGTAAATGTATATGGGTACAT
1 AAATGCATATGGATACATTATCAACA-ATAAAGTATACTATAGTTG-AAATGTATATGGGTACAT
1759712 TATCAACAGAAAAATATGCAATAGTGT
64 TATCAACAGAAAAATATGCAATAGTGT
* *
1759739 AAATGTATATGGGTACATTATCAACAATAAAGTATACTATAGTTGAAATGTATATGGGTACATTA
1 AAATGCATATGGATACATTATCAACAATAAAGTATACTATAGTTGAAATGTATATGGGTACATTA
* * *
1759804 TCAATAGAAAAATATGCTATGGT-T
66 TCAACAGAAAAATATGCAATAGTGT
* *
1759828 GAAATGCATATGGATGCATTATCAAC-ATAAA-TATA-TATTATGATTGAAATGCATATG
1 -AAATGCATATGGATACATTATCAACAATAAAGTATACTA-TA-G-TTGAAATGTATATG
1759885 AGTGTATTAT
Statistics
Matches: 131, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
87 2 0.02
88 6 0.05
89 8 0.06
90 113 0.86
91 2 0.02
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.32
Consensus pattern (90 bp):
AAATGCATATGGATACATTATCAACAATAAAGTATACTATAGTTGAAATGTATATGGGTACATTA
TCAACAGAAAAATATGCAATAGTGT
Found at i:1759894 original size:45 final size:43
Alignment explanation
Indices: 1759739--1759913 Score: 138
Period size: 45 Copynumber: 3.9 Consensus size: 43
1759729 GCAATAGTGT
* *
1759739 AAATGTATATGGGTACATTATCAACAATAAAGTATACTA-TA-GTTG
1 AAATGCATAT-GGTGCATTATCAAC-ATAAA-TATA-TATTATGTTG
* * * * * **
1759784 AAATGTATATGGGTACATTATCAATAGAAAAATATGCTATGGTTG
1 AAATGCATAT-GGTGCATTATCAACATAAATATATATTAT-GTTG
1759829 AAATGCATATGGATGCATTATCAACATAAATATATATTATGATTG
1 AAATGCATATGG-TGCATTATCAACATAAATATATATTATG-TTG
* * * *
1759874 AAATGCATATGAGTGTATTATTAACATAAAGATATGTTAT
1 AAATGCATATG-GTGCATTATCAACATAAATATATATTAT
1759914 AAATAAAAAT
Statistics
Matches: 109, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
42 1 0.01
43 5 0.05
44 7 0.06
45 95 0.87
46 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (43 bp):
AAATGCATATGGTGCATTATCAACATAAATATATATTATGTTG
Found at i:1759894 original size:135 final size:134
Alignment explanation
Indices: 1759604--1759904 Score: 318
Period size: 135 Copynumber: 2.2 Consensus size: 134
1759594 GAAAAATTAA
* * * * * * * *
1759604 AAATGCATACGGGTGCATTATCAGCATGAAAGGATGCTACATTTGAAATGTATATGGGTACATTA
1 AAATGCATATGAGTACATTATCAACAT-AAAGTATACTATAGTTGAAATGTATATGGGTACATTA
* * * *
1759669 TCAACAGAAAAGTATGCAATAGTGTAAATGTATATGGGTACATTATCAACAGAAAAATATGCAAT
65 TCAACAGAAAAATATGCAATAGTGTAAATGCATATGGATACATTATCAACAGAAAAATATACAAT
1759734 AGTGT
130 AGTGT
* *
1759739 AAATGTATATGGGTACATTATCAACAATAAAGTATACTATAGTTGAAATGTATATGGGTACATTA
1 AAATGCATATGAGTACATTATCAAC-ATAAAGTATACTATAGTTGAAATGTATATGGGTACATTA
* * * * * * **
1759804 TCAATAGAAAAATATGCTATGGT-TGAAATGCATATGGATGCATTATCAACATAAATATATATTA
65 TCAACAGAAAAATATGCAATAGTGT-AAATGCATATGGATACATTATCAACAGAAAAATATACAA
*
1759868 TGATTG-
129 T-AGTGT
** *
1759874 AAATGCATATGAGTGTATTATTAACATAAAG
1 AAATGCATATGAGTACATTATCAACATAAAG
1759905 ATATGTTATA
Statistics
Matches: 137, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
134 7 0.05
135 125 0.91
136 5 0.04
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.31
Consensus pattern (134 bp):
AAATGCATATGAGTACATTATCAACATAAAGTATACTATAGTTGAAATGTATATGGGTACATTAT
CAACAGAAAAATATGCAATAGTGTAAATGCATATGGATACATTATCAACAGAAAAATATACAATA
GTGT
Found at i:1760236 original size:10 final size:10
Alignment explanation
Indices: 1760221--1760254 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
1760211 CTTATATGGC
1760221 ATGTAATTAA
1 ATGTAATTAA
1760231 ATGTAATTAA
1 ATGTAATTAA
*
1760241 ATGTAATAAA
1 ATGTAATTAA
1760251 ATGT
1 ATGT
1760255 TTTGTAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (10 bp):
ATGTAATTAA
Found at i:1765984 original size:21 final size:21
Alignment explanation
Indices: 1765958--1766009 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
1765948 ATTTAATGGA
1765958 TATCGATACCTGGGAAGAGGG
1 TATCGATACCTGGGAAGAGGG
1765979 TATCGATACCTGGGAAGAGGG
1 TATCGATACCTGGGAAGAGGG
1766000 TATCGATACC
1 TATCGATACC
1766010 CTATCATAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.17, G:0.33, T:0.21
Consensus pattern (21 bp):
TATCGATACCTGGGAAGAGGG
Found at i:1766227 original size:17 final size:16
Alignment explanation
Indices: 1766195--1766229 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1766185 AGGGGGTATC
*
1766195 AGTACCATAGTATAGT
1 AGTACCATACTATAGT
1766211 AGTACCGATACTATAGT
1 AGTACC-ATACTATAGT
1766228 AG
1 AG
1766230 GGGTATCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (16 bp):
AGTACCATACTATAGT
Found at i:1766750 original size:44 final size:45
Alignment explanation
Indices: 1766684--1766860 Score: 248
Period size: 45 Copynumber: 4.0 Consensus size: 45
1766674 TATCGTCATG
* * * *
1766684 AAAGGATGCTACAGTTGAAATGTATATGGGTATATTATCAA-AAA
1 AAAGTATGCTATAGTTGAAATGTATATGGGTACATTATCAACAGA
* *
1766728 AAAGTATGCAATAGTTGAAATGTATATGGGTACATTATCAACAGT
1 AAAGTATGCTATAGTTGAAATGTATATGGGTACATTATCAACAGA
* *
1766773 AAAGTATACTATAGTTGAAATGTATATGGGTACACTATCAACAGA
1 AAAGTATGCTATAGTTGAAATGTATATGGGTACATTATCAACAGA
* * *
1766818 AAAGTATGCTATGGTTGAAATGCATATGGGTGCATTATCAACA
1 AAAGTATGCTATAGTTGAAATGTATATGGGTACATTATCAACA
1766861 TAAATATATA
Statistics
Matches: 117, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
44 37 0.32
45 80 0.68
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (45 bp):
AAAGTATGCTATAGTTGAAATGTATATGGGTACATTATCAACAGA
Found at i:1766792 original size:45 final size:44
Alignment explanation
Indices: 1766696--1766910 Score: 236
Period size: 45 Copynumber: 4.8 Consensus size: 44
1766686 AGGATGCTAC
* * * * *
1766696 AGTTGAAATGTATATGGGTATATTATCAAAAAAAAGTATGCAAT
1 AGTTGAAATGTATATGGGTACATTATCAACATAAAGTATACTAT
1766740 AGTTGAAATGTATATGGGTACATTATCAACAGTAAAGTATACTAT
1 AGTTGAAATGTATATGGGTACATTATCAACA-TAAAGTATACTAT
* * *
1766785 AGTTGAAATGTATATGGGTACACTATCAACAGAAAAGTATGCTAT
1 AGTTGAAATGTATATGGGTACATTATCAACA-TAAAGTATACTAT
* * *
1766830 GGTTGAAATGCATATGGGTGCATTATCAACATAAA-TATA-TATT
1 AGTTGAAATGTATATGGGTACATTATCAACATAAAGTATACTA-T
* * * *
1766873 ATGATTGAAATGCATATGAGTGCATTATTAACATAAAG
1 A-G-TTGAAATGTATATGGGTACATTATCAACATAAAG
1766911 GTATGTTATA
Statistics
Matches: 149, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
42 2 0.01
43 4 0.03
44 33 0.22
45 110 0.74
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (44 bp):
AGTTGAAATGTATATGGGTACATTATCAACATAAAGTATACTAT
Found at i:1766855 original size:90 final size:88
Alignment explanation
Indices: 1766656--1766890 Score: 267
Period size: 89 Copynumber: 2.6 Consensus size: 88
1766646 TGAAAAATTA
* * ** * * * * *
1766656 AAATGCATACGAGTGCATTATCGTCATGAAAGGATGCTACAGTTGAAATGTATATGGGTATATTA
1 AAATGCATATGGGTGCATTATCAACAT-AAAGTATACTATAGTTGAAATGTATATGGGTACACTA
1766721 TCAAAAAAAAGTATGCAATAGTTG
65 TCAAAAAAAAGTATGCAATAGTTG
* *
1766745 AAATGTATATGGGTACATTATCAACAGTAAAGTATACTATAGTTGAAATGTATATGGGTACACTA
1 AAATGCATATGGGTGCATTATCAACA-TAAAGTATACTATAGTTGAAATGTATATGGGTACACTA
* * *
1766810 TCAACAGAAAAGTATGCTATGGTTG
65 TCAA-AAAAAAGTATGCAATAGTTG
*
1766835 AAATGCATATGGGTGCATTATCAACATAAA-TATA-TATTATGATTGAAATGCATATG
1 AAATGCATATGGGTGCATTATCAACATAAAGTATACTA-TA-G-TTGAAATGTATATG
1766891 AGTGCATTAT
Statistics
Matches: 124, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
87 2 0.02
88 6 0.05
89 61 0.49
90 55 0.44
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.31
Consensus pattern (88 bp):
AAATGCATATGGGTGCATTATCAACATAAAGTATACTATAGTTGAAATGTATATGGGTACACTAT
CAAAAAAAAGTATGCAATAGTTG
Found at i:1771018 original size:16 final size:16
Alignment explanation
Indices: 1770997--1771066 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
1770987 ACTCCCTCTT
1770997 TCTCTCTCCCACATTC
1 TCTCTCTCCCACATTC
*
1771013 TCTCTCCCCCACATTC
1 TCTCTCTCCCACATTC
*
1771029 TGTCTCTCCCACATTC
1 TCTCTCTCCCACATTC
*
1771045 TCCCTCTCCC-CTATTC
1 TCTCTCTCCCAC-ATTC
1771061 TCTCTC
1 TCTCTC
1771067 CCTATCTCTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
15 1 0.02
16 46 0.98
ACGTcount: A:0.10, C:0.51, G:0.01, T:0.37
Consensus pattern (16 bp):
TCTCTCTCCCACATTC
Found at i:1771938 original size:20 final size:21
Alignment explanation
Indices: 1771902--1771952 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
1771892 TATTGAAGAG
* *
1771902 GTATCAATA-CTGTAAGGGTA
1 GTATCGATACCTGTAAGGATA
*
1771922 GTATCGATACCTG-AAGGATG
1 GTATCGATACCTGTAAGGATA
*
1771942 GTATTGATACC
1 GTATCGATACC
1771953 CTTAAAACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (21 bp):
GTATCGATACCTGTAAGGATA
Found at i:1772055 original size:19 final size:19
Alignment explanation
Indices: 1772031--1772069 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1772021 TACTATATCA
*
1772031 GTATCGGTA-CCTTGATAAG
1 GTATCGATACCCTTGA-AAG
1772050 GTATCGATACCCTTGAAAG
1 GTATCGATACCCTTGAAAG
1772069 G
1 G
1772070 AAGTATCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (19 bp):
GTATCGATACCCTTGAAAG
Found at i:1772064 original size:54 final size:54
Alignment explanation
Indices: 1771941--1772067 Score: 182
Period size: 54 Copynumber: 2.4 Consensus size: 54
1771931 CCTGAAGGAT
* * * **
1771941 GGTATTGATACCCTTAAAACATCGAATGCTAGATTGGTATCAGTACCTTGAGAA
1 GGTATCGATACCCTTGAAACATCGAATACTAGATCAGTATCAGTACCTTGAGAA
* * *
1771995 GGTATCGATACCCTTGAAACATCGAATACTATATCAGTATCGGTACCTTGATAA
1 GGTATCGATACCCTTGAAACATCGAATACTAGATCAGTATCAGTACCTTGAGAA
1772049 GGTATCGATACCCTTGAAA
1 GGTATCGATACCCTTGAAA
1772068 GGAAGTATCA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (54 bp):
GGTATCGATACCCTTGAAACATCGAATACTAGATCAGTATCAGTACCTTGAGAA
Found at i:1772705 original size:22 final size:23
Alignment explanation
Indices: 1772650--1772697 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
1772640 GATAAATATA
1772650 TGGCACTTCGGTGCAAACTTATG
1 TGGCACTTCGGTGCAAACTTATG
1772673 TGGCACTTCGGTGCAAAC-TATG
1 TGGCACTTCGGTGCAAACTTATG
1772695 TGG
1 TGG
1772698 TCTTTCGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAAACTTATG
Found at i:1777055 original size:2 final size:2
Alignment explanation
Indices: 1777048--1777088 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1777038 CCTTTAATCA
1777048 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1777089 ATTTTTTAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1778235 original size:51 final size:51
Alignment explanation
Indices: 1778145--1778297 Score: 161
Period size: 51 Copynumber: 3.1 Consensus size: 51
1778135 GCAGTAAAGT
* * * *
1778145 GCGCCCCCTGCACCACGCTATACGATGATTTGACGCCACGTGGGGTATAGC
1 GCGCCCCCTGCACCACGCTATACGGTGATCTGGCACCACGTGGGGTATAGC
*
1778196 GCGCCCCCTGCACCACGCTATACGGTGAGCTGGCACCACGT-GGGTATAGC
1 GCGCCCCCTGCACCACGCTATACGGTGATCTGGCACCACGTGGGGTATAGC
* * * * * * *
1778246 ACGGCCCCTGAAGCGCGCTATACTGTATATCT-G-A-CACGTGGGGTATAGC
1 GCGCCCCCTGCACCACGCTATACGGT-GATCTGGCACCACGTGGGGTATAGC
1778295 GCG
1 GCG
1778298 GTGCAGGGGG
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
48 5 0.06
49 12 0.14
50 30 0.35
51 39 0.45
ACGTcount: A:0.20, C:0.32, G:0.29, T:0.19
Consensus pattern (51 bp):
GCGCCCCCTGCACCACGCTATACGGTGATCTGGCACCACGTGGGGTATAGC
Found at i:1778419 original size:12 final size:10
Alignment explanation
Indices: 1778378--1778418 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1778368 TTTATCACAC
1778378 CAAATTCTCT
1 CAAATTCTCT
1778388 CAAATTCTCT
1 CAAATTCTCT
1778398 -AAATTTCTCT
1 CAAA-TTCTCT
*
1778408 CAAATACTCT
1 CAAATTCTCT
1778418 C
1 C
1778419 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1778454 original size:14 final size:14
Alignment explanation
Indices: 1778435--1778461 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1778425 AGGTATATTT
1778435 TATAATATTTTTAG
1 TATAATATTTTTAG
1778449 TATAATATTTTTA
1 TATAATATTTTTA
1778462 CTTTATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
TATAATATTTTTAG
Found at i:1786220 original size:2 final size:2
Alignment explanation
Indices: 1786213--1786252 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1786203 TATGTGTCTA
1786213 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
1786253 TAGTATTACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1787485 original size:21 final size:21
Alignment explanation
Indices: 1787459--1787499 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1787449 AGATGAGTTG
1787459 TAGGATAAATGT-GAACATCCT
1 TAGGATAAATGTAG-ACATCCT
*
1787480 TAGGATGAATGTAGACATCC
1 TAGGATAAATGTAGACATCC
1787500 ATGCGTCCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.27
Consensus pattern (21 bp):
TAGGATAAATGTAGACATCCT
Found at i:1787805 original size:18 final size:18
Alignment explanation
Indices: 1787782--1787829 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
1787772 CCATGAAAAC
* *
1787782 TTAAATAAACTAGTTTAA
1 TTAAATGAACTAATTTAA
*
1787800 TTAAATGAACCAATTTAA
1 TTAAATGAACTAATTTAA
1787818 TTAAATGAACTA
1 TTAAATGAACTA
1787830 CCATTCTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.35
Consensus pattern (18 bp):
TTAAATGAACTAATTTAA
Found at i:1787899 original size:23 final size:23
Alignment explanation
Indices: 1787871--1787914 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1787861 AATTACCACA
*
1787871 CAAAACTAAATGTGTAAATTTAG
1 CAAAACTAAACGTGTAAATTTAG
1787894 CAAAACTAAACGTGTAAATTT
1 CAAAACTAAACGTGTAAATTT
1787915 TTATTCTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (23 bp):
CAAAACTAAACGTGTAAATTTAG
Found at i:1793601 original size:21 final size:21
Alignment explanation
Indices: 1793577--1793619 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1793567 AGGTAGGTTC
*
1793577 TTAGGCCTAATAGG-CCTAAGG
1 TTAGACCTAAT-GGACCTAAGG
*
1793598 TTAGACCTTATGGACCTAAGG
1 TTAGACCTAATGGACCTAAGG
1793619 T
1 T
1793620 ACCCCTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (21 bp):
TTAGACCTAATGGACCTAAGG
Found at i:1800979 original size:10 final size:10
Alignment explanation
Indices: 1800976--1801022 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
1800966 AAAAGAGAAA
* *
1800976 AAAAAAACAA
1 AAAAAAATAG
1800986 AAAAAAATAG
1 AAAAAAATAG
1800996 AAAAAAATAG
1 AAAAAAATAG
*
1801006 AAAAGAAAAAG
1 AAAA-AAATAG
1801017 AAAAAA
1 AAAAAA
1801023 GAAAAAGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
10 24 0.73
11 9 0.27
ACGTcount: A:0.85, C:0.02, G:0.09, T:0.04
Consensus pattern (10 bp):
AAAAAAATAG
Found at i:1800982 original size:13 final size:12
Alignment explanation
Indices: 1800964--1801040 Score: 73
Period size: 13 Copynumber: 5.8 Consensus size: 12
1800954 TATCAATCAG
1800964 AAAAAAGAGAAAA
1 AAAAAAGA-AAAA
*
1800977 AAAAAACAAAAA
1 AAAAAAGAAAAA
*
1800989 AAAATAGAAAAAA
1 AAAAAAG-AAAAA
1801002 ATAGAAAAGAAAAA
1 A-A-AAAAGAAAAA
1801016 GAAAAAAGAAAAAGA
1 -AAAAAAG-AAAA-A
1801031 AAAAAAGAAA
1 AAAAAAGAAA
1801041 TTAAATCAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
12 9 0.17
13 21 0.39
14 18 0.33
15 6 0.11
ACGTcount: A:0.84, C:0.01, G:0.12, T:0.03
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:1800999 original size:7 final size:6
Alignment explanation
Indices: 1800965--1801034 Score: 58
Period size: 6 Copynumber: 11.8 Consensus size: 6
1800955 ATCAATCAGA
* * *
1800965 AAAAAG AGAAAAA AAAAAC AAAAA- AAAATAG -AAAA- AAATAG -AAAAG
1 AAAAAG A-AAAAG AAAAAG AAAAAG AAAA-AG AAAAAG AAAAAG AAAAAG
1801011 AAAAAG AAAAAAG AAAAAG AAAAA
1 AAAAAG -AAAAAG AAAAAG AAAAA
1801035 AAGAAATTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
5 12 0.23
6 30 0.57
7 11 0.21
ACGTcount: A:0.84, C:0.01, G:0.11, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:1803992 original size:43 final size:43
Alignment explanation
Indices: 1803930--1804178 Score: 376
Period size: 43 Copynumber: 5.8 Consensus size: 43
1803920 AGAAACTAAT
*
1803930 CTTGAGGGACCATCGTGATATGTAGGGGTTTCTTGATGACAAG
1 CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAG
* * *
1803973 CTTGAGAGACCATCCTGATATGTAGGGGTTCCTTGAAGACAAG
1 CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAG
* *
1804016 CTTGAGGGATCATCGTGATATGTAGGGGATCCTTGATGACAAG
1 CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAG
*
1804059 CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGAAAAG
1 CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAG
*
1804102 CTTAAGGGACCATCGTGATATGTAGGGGTTCCTTGATGA-ACA-
1 CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACA-AG
* * *
1804144 CTCGAGGGACCAACATGATATGTAGGGGTTCCTTG
1 CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTG
1804179 GTGATAACTA
Statistics
Matches: 188, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
42 32 0.17
43 156 0.83
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (43 bp):
CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAG
Found at i:1804278 original size:42 final size:42
Alignment explanation
Indices: 1804219--1804326 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 42
1804209 AAGAGTTTCT
*
1804219 TGATGAGTAAG-TCCTTCGGGCCATC-AGAAAGTCTTTTGAGCA
1 TGATGA-TAAGATCCTTCGGGCCATCTA-AAAGTCTTTCGAGCA
* * *
1804261 TGATGCTTAA-ATCCTTCGGGTCATCTATAAGTCTTTCGAGCA
1 TGATG-ATAAGATCCTTCGGGCCATCTAAAAGTCTTTCGAGCA
1804303 TGATGATAAGA-CCTTCGGGCCATC
1 TGATGATAAGATCCTTCGGGCCATC
1804327 CATAAGACCT
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
41 15 0.27
42 40 0.71
43 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (42 bp):
TGATGATAAGATCCTTCGGGCCATCTAAAAGTCTTTCGAGCA
Found at i:1810558 original size:3 final size:3
Alignment explanation
Indices: 1810552--1810611 Score: 54
Period size: 3 Copynumber: 19.7 Consensus size: 3
1810542 TTATTATTAT
*
1810552 TAA TAA TAA TAA TAA -ATA TAA TAA TAA TAA TAA -ATA TAA T-A TTA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TAA TAA
1810596 TATA TAA TATA TAA TA
1 TA-A TAA TA-A TAA TA
1810612 TTTTTTAAGC
Statistics
Matches: 49, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
2 4 0.08
3 37 0.76
4 8 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1810564 original size:9 final size:10
Alignment explanation
Indices: 1810552--1810611 Score: 76
Period size: 9 Copynumber: 6.5 Consensus size: 10
1810542 TTATTATTAT
1810552 TAATAATA-A
1 TAATAATATA
1810561 TAATAA-ATA
1 TAATAATATA
1810570 TAATAATA-A
1 TAATAATATA
1810579 TAATAA-ATA
1 TAATAATATA
*
1810588 TAATATTATA
1 TAATAATATA
1810598 T-ATAATATA
1 TAATAATATA
1810607 TAATA
1 TAATA
1810612 TTTTTTAAGC
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
8 2 0.05
9 34 0.77
10 8 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAATAATATA
Found at i:1811753 original size:21 final size:21
Alignment explanation
Indices: 1811727--1811777 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1811717 CAATTTGATG
1811727 GTATCGATACTAGGACCTTT-A
1 GTATCGATACT-GGACCTTTCA
*
1811748 GTATCGATA-TTGACCTTTCA
1 GTATCGATACTGGACCTTTCA
1811768 GTATCGATAC
1 GTATCGATAC
1811778 ACAGCCTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 7 0.26
20 11 0.41
21 9 0.33
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (21 bp):
GTATCGATACTGGACCTTTCA
Found at i:1811857 original size:21 final size:21
Alignment explanation
Indices: 1811831--1811897 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
1811821 AAAGCCTTAG
1811831 AGTATCGATACCCTTATATAA
1 AGTATCGATACCCTTATATAA
** *
1811852 AGTATCGATACTTTTCT-TAA
1 AGTATCGATACCCTTATATAA
* *
1811872 GAGTATCGATACCCTTGTATAG
1 -AGTATCGATACCCTTATATAA
1811894 AGTA
1 AGTA
1811898 CCAAAAACCC
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 3 0.08
21 32 0.86
22 2 0.05
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (21 bp):
AGTATCGATACCCTTATATAA
Found at i:1816907 original size:2 final size:2
Alignment explanation
Indices: 1816900--1816924 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1816890 TAATTTAAAC
1816900 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 T
1816925 TAATATTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1817405 original size:21 final size:19
Alignment explanation
Indices: 1817369--1817407 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1817359 CCTAAGATAA
*
1817369 AATTAAAAATTTAATTAAG
1 AATTAAAAATTAAATTAAG
1817388 AATTAAATCAATTAAATTAA
1 AATTAAA--AATTAAATTAA
1817408 ATAAAATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
21 10 0.59
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (19 bp):
AATTAAAAATTAAATTAAG
Found at i:1822719 original size:17 final size:18
Alignment explanation
Indices: 1822685--1822729 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
1822675 AATATGAAAG
*
1822685 AATAAAATAATAAAATAA
1 AATAAATTAATAAAATAA
*
1822703 AATAAATTAA-AACATAA
1 AATAAATTAATAAAATAA
*
1822720 AATAACTTAA
1 AATAAATTAA
1822730 CTTATTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (18 bp):
AATAAATTAATAAAATAA
Found at i:1827923 original size:41 final size:41
Alignment explanation
Indices: 1827763--1827927 Score: 190
Period size: 41 Copynumber: 4.0 Consensus size: 41
1827753 GTGCCATGAT
* * *
1827763 TGAATTGAATTGTGAATTATTGCATGTTGCCATGATCGAA-
1 TGAATCGAATGGTGAATTATTGCATGTTGCCATGATTGAAC
* * * *
1827803 TTATGTCGAATGGTGAATTATTGCATGTTGTCATGATT-ACAT
1 TGA-ATCGAATGGTGAATTATTGCATGTTGCCATGATTGA-AC
*
1827845 TGAGTCGAATGGTGAATTATTGCATGTTGCCATGATTGAAC
1 TGAATCGAATGGTGAATTATTGCATGTTGCCATGATTGAAC
* * * *
1827886 TGAATCGAATTGAGAATTAGTGCATGTTGCCAAGATTGAAC
1 TGAATCGAATGGTGAATTATTGCATGTTGCCATGATTGAAC
1827927 T
1 T
1827928 CGATTGAATT
Statistics
Matches: 107, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
40 3 0.03
41 101 0.94
42 3 0.03
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (41 bp):
TGAATCGAATGGTGAATTATTGCATGTTGCCATGATTGAAC
Found at i:1830857 original size:10 final size:10
Alignment explanation
Indices: 1830839--1830870 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1830829 ATTCACTCGG
*
1830839 TTGAAAGCAA
1 TTGAGAGCAA
1830849 TTGAGAGCAA
1 TTGAGAGCAA
1830859 TTGAGAGCAA
1 TTGAGAGCAA
1830869 TT
1 TT
1830871 TCTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.41, C:0.09, G:0.25, T:0.25
Consensus pattern (10 bp):
TTGAGAGCAA
Found at i:1832486 original size:13 final size:13
Alignment explanation
Indices: 1832468--1832492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1832458 ATTAAAATTT
1832468 ATATATATATATA
1 ATATATATATATA
1832481 ATATATATATAT
1 ATATATATATAT
1832493 TAATTTTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATATATATA
Found at i:1835833 original size:31 final size:30
Alignment explanation
Indices: 1835789--1835847 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
1835779 AAACAACGAG
* *
1835789 ACGAGCTATGAGCATCGAGC-TAACGAGTA
1 ACGAGCTATGAGCAACAAGCTTAACGAGTA
1835818 ACGAGCTTAATGAGCAACAAGCTTAACGAG
1 ACGAGC-T-ATGAGCAACAAGCTTAACGAG
1835848 CAATGAGTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.24
30 1 0.04
31 11 0.44
32 7 0.28
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.17
Consensus pattern (30 bp):
ACGAGCTATGAGCAACAAGCTTAACGAGTA
Found at i:1837654 original size:19 final size:19
Alignment explanation
Indices: 1837630--1837688 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
1837620 GTATATAATA
* *
1837630 TTTTTAAGTCACATCAATT
1 TTTTTAAATCACACCAATT
* *
1837649 TTTTTAAATTATACCAATT
1 TTTTTAAATCACACCAATT
* *
1837668 TTTTTAAATTATACCAATT
1 TTTTTAAATCACACCAATT
1837687 TT
1 TT
1837689 ATTTTTAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTTTAAATCACACCAATT
Found at i:1837670 original size:20 final size:19
Alignment explanation
Indices: 1837644--1837688 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
1837634 TAAGTCACAT
1837644 CAATTTTTTTAAATTATAC
1 CAATTTTTTTAAATTATAC
1837663 CAATTTTTTTAAATTATAC
1 CAATTTTTTTAAATTATAC
1837682 CAATTTT
1 CAATTTT
1837689 ATTTTTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (19 bp):
CAATTTTTTTAAATTATAC
Found at i:1838161 original size:2 final size:2
Alignment explanation
Indices: 1838149--1838207 Score: 59
Period size: 2 Copynumber: 29.5 Consensus size: 2
1838139 TATCAAGTAC
* * *
1838149 AT AT CT AT AT AT A- AT ACT AT A- AT AT AT AT ACT CT AT AT AT AA
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT
1838191 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1838208 GAGAGAGAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
1 2 0.04
2 42 0.89
3 3 0.06
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1838178 original size:21 final size:21
Alignment explanation
Indices: 1838149--1838207 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1838139 TATCAAGTAC
*
1838149 ATATCTATATATAATACTAT-A
1 ATATATATATATAATA-TATAA
*
1838170 ATATATATACTCT-ATATATAA
1 ATATATATA-TATAATATATAA
1838191 ATATATATATAT-ATATA
1 ATATATATATATAATATA
1838208 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 10 0.30
21 21 0.64
22 2 0.06
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATATATATATAATATATAA
Found at i:1842718 original size:36 final size:36
Alignment explanation
Indices: 1842668--1842736 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
1842658 GCTAGCACAC
* *
1842668 AAAGATCCTGTTAGATTAATACCAAAAGTATTCCAT
1 AAAGATCCTATTAGATTAATACCAAAAGCATTCCAT
*
1842704 AAAGATCCTATTAGATTGATACCAAAAGCATTC
1 AAAGATCCTATTAGATTAATACCAAAAGCATTC
1842737 TACGGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (36 bp):
AAAGATCCTATTAGATTAATACCAAAAGCATTCCAT
Found at i:1843255 original size:43 final size:43
Alignment explanation
Indices: 1843182--1843271 Score: 137
Period size: 43 Copynumber: 2.1 Consensus size: 43
1843172 CTAAATTGTC
*
1843182 TTTGGAGAAGTTAGGAATAAAAGTTTTCCCCTATATGTAAAGT
1 TTTGGAGAAGTTAGGAATAAAAGTTATCCCCTATATGTAAAGT
* *
1843225 TTTGGAGAAGTTAGGAGA-GAAGGTTATCCCCTATATGTAAAGT
1 TTTGGAGAAGTTAGGA-ATAAAAGTTATCCCCTATATGTAAAGT
1843268 TTTG
1 TTTG
1843272 TTTGATGTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.34
Consensus pattern (43 bp):
TTTGGAGAAGTTAGGAATAAAAGTTATCCCCTATATGTAAAGT
Found at i:1849944 original size:77 final size:82
Alignment explanation
Indices: 1849795--1849964 Score: 208
Period size: 77 Copynumber: 2.1 Consensus size: 82
1849785 ATGGCCAAAT
* *
1849795 ATCCTCATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCACGAAGGAATCATATC
1 ATCCTCATCACGAAGGAACAATGTCA-CTACCAATCAGAACTCCTCATCACGAAGGAAGCACATC
* *
1849860 ATCCTTAGACAGCCATAC
65 ATCCTTAGACAACCAGAC
*
1849878 ATCCTCATCAC-AAGGAACAATGTCA-T-CCACTCA-AACT-CTCATCACGAAGG-AGCAACATC
1 ATCCTCATCACGAAGGAACAATGTCACTACCAATCAGAACTCCTCATCACGAAGGAAGC-ACATC
* * *
1849937 ATTCTTAGATAACCAGAT
65 ATCCTTAGACAACCAGAC
1849955 ATCCTCATCA
1 ATCCTCATCA
1849965 TGAAAGAATG
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
76 2 0.03
77 40 0.51
78 4 0.05
79 6 0.08
80 1 0.01
82 14 0.18
83 11 0.14
ACGTcount: A:0.36, C:0.30, G:0.11, T:0.22
Consensus pattern (82 bp):
ATCCTCATCACGAAGGAACAATGTCACTACCAATCAGAACTCCTCATCACGAAGGAAGCACATCA
TCCTTAGACAACCAGAC
Found at i:1850356 original size:136 final size:135
Alignment explanation
Indices: 1849871--1850424 Score: 668
Period size: 127 Copynumber: 4.2 Consensus size: 135
1849861 TCCTTAGACA
*
1849871 GCCATACATCCTCATCAC-AAGGAACAATGTCATCCA-C--TCAAACT-CTCATCACGAAGGAGC
1 GCCAGACATCCTCATCACGAAGGAACAATGTCATCCACCGATCAAACTCCTCATCACGAAGGAGC
* * *
1849931 AACATCATTCTTAGATAACCAGATATCCTCATCATGAAAGAA--TGTTATCTCAAATATCTTTAA
66 AACATCATTCTTAGATAACTAGATGTCCTCATCAAGAAAGAACGTGTTATCTCAAATATCTTTAA
1849994 AGATG
131 AGATG
*
1849999 G-CAGACGT-CTCATCACGAAGGAACAATGTCATCCACCGAT-AAACTCCTCATCAC-AA--AGC
1 GCCAGACATCCTCATCACGAAGGAACAATGTCATCCACCGATCAAACTCCTCATCACGAAGGAGC
*
1850058 AACATCATTCTTAGATAACTAGA--TCCTCATCATGAAAGAACAGTGTTATCT-AAATATCTTTA
66 AACATCATTCTTAGATAACTAGATGTCCTCATCAAGAAAGAAC-GTGTTATCTCAAATATCTTTA
1850120 AAGATG
130 AAGATG
* * *
1850126 GCCAGAC-TACTCATCATGAAGGAACAATGTCATCCACCGATCGAACTCCTCATCACGAA-GAGC
1 GCCAGACATCCTCATCACGAAGGAACAATGTCATCCACCGATCAAACTCCTCATCACGAAGGAGC
* * *
1850189 AACATCATTCTTAGATAGCTAGATGTCCTCATCAAGAAGGAACCGTGTTATCTCAAATATATTTA
66 AACATCATTCTTAGATAACTAGATGTCCTCATCAAGAAAGAA-CGTGTTATCTCAAATATCTTTA
1850254 AAGATG
130 AAGATG
* * *
1850260 GCCAGACATCCTCATCACAAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAGGTAGGAG
1 GCCAGACATCCTCATCACGAAGGAACAATGTCATCCACCGATCA-AACTCCTCATCACGAAGGAG
* * * * * * * *
1850325 CGA-GTCATCCTCAGATAACTAGACGTCCTCATCACA-AAGGAACTTGTTATCTCAAATATCTTC
65 CAACATCATTCTTAGATAACTAGATGTCCTCATCA-AGAAAGAACGTGTTATCTCAAATATCTTT
1850388 AAA-A-G
129 AAAGATG
* * * *
1850393 GTCAGACGTTCTCATCATGAAGG-ACAATGTCA
1 GCCAGACATCCTCATCACGAAGGAACAATGTCA
1850425 AACACAGTTG
Statistics
Matches: 376, Mismatches: 29, Indels: 38
0.85 0.07 0.09
Matches are distributed among these distances:
125 17 0.05
126 8 0.02
127 67 0.18
128 46 0.12
129 20 0.05
130 11 0.03
131 25 0.07
132 9 0.02
133 43 0.11
134 25 0.07
135 53 0.14
136 46 0.12
137 6 0.02
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (135 bp):
GCCAGACATCCTCATCACGAAGGAACAATGTCATCCACCGATCAAACTCCTCATCACGAAGGAGC
AACATCATTCTTAGATAACTAGATGTCCTCATCAAGAAAGAACGTGTTATCTCAAATATCTTTAA
AGATG
Found at i:1857113 original size:22 final size:22
Alignment explanation
Indices: 1857076--1857118 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1857066 AGGATGATGA
*
1857076 TATCATGATATGTAATGGTAAT
1 TATCATGATATATAATGGTAAT
* *
1857098 TATCATGATTTATAATTGTAA
1 TATCATGATATATAATGGTAA
1857119 AATTGTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (22 bp):
TATCATGATATATAATGGTAAT
Found at i:1858624 original size:20 final size:21
Alignment explanation
Indices: 1858585--1858624 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1858575 ATATATTTTA
1858585 TGCACATATATGATATGTTGTT
1 TGCACATATATGA-ATGTTGTT
*
1858607 TGCACGTATATG-ATGTTG
1 TGCACATATATGAATGTTG
1858625 GTATGATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (21 bp):
TGCACATATATGAATGTTGTT
Found at i:1867886 original size:43 final size:43
Alignment explanation
Indices: 1867839--1867993 Score: 136
Period size: 43 Copynumber: 3.6 Consensus size: 43
1867829 GCAAATTTGA
1867839 AAACTCCACAGAAGAGTAGTGGAAGAAATTCAATCATAAATCT
1 AAACTCCACAGAAGAGTAGTGGAAGAAATTCAATCATAAATCT
* ** * **
1867882 AAACTCCACAAAAGAGTAGTGGAACGGATTTTTC-AGCA-AAGTATGA
1 AAACTCCACAGAAGAGTAGTGGAA--GA-AATTCAATCATAA--ATCT
* * * *
1867928 AAATTCCACGGAATAGTAGTGGAAGCAATTCAATCATAAATCT
1 AAACTCCACAGAAGAGTAGTGGAAGAAATTCAATCATAAATCT
* *
1867971 GAACTCCAC-GGAGAGTAGTGGAA
1 AAACTCCACAGAAGAGTAGTGGAA
1867994 CGGATTTTTA
Statistics
Matches: 85, Mismatches: 20, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
42 12 0.14
43 35 0.41
44 6 0.07
45 7 0.08
46 25 0.29
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (43 bp):
AAACTCCACAGAAGAGTAGTGGAAGAAATTCAATCATAAATCT
Found at i:1867946 original size:89 final size:88
Alignment explanation
Indices: 1867799--1868117 Score: 356
Period size: 89 Copynumber: 3.7 Consensus size: 88
1867789 AAAATTCGCT
* * *
1867799 CTCCACGAAA-AGTAGTGGAAC-GATTTTTCAGCAAA-TTTGAAAACTCCACAGAAGAGTAGTGG
1 CTCCACGAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGAAAATTCCACGGAAGAGTAGTGG
1867861 AAGAAATTCAATCATAAATCTAAA
66 AAG-AATTCAATCATAAATCTAAA
* *
1867885 CTCCACAAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGAAAATTCCACGGAATAGTAGTGG
1 CTCCACGAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGAAAATTCCACGGAAGAGTAGTGG
*
1867950 AAGCAATTCAATCATAAATCTGAA
66 AAG-AATTCAATCATAAATCTAAA
* * * * *
1867974 CTCCACG-GAGAGTAGTGGAACGGATTTTT-AGCAAAGTAT-CAAATTTCAGGGAAGAGTAAT-G
1 CTCCACGAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGAAAATTCCACGGAAGAGTAGTGG
* * * **
1868035 AAGCA---AAGCA-AAATTTAGT
66 AAGAATTCAATCATAAATCTAAA
* * *
1868054 TTCCACGAAAGAGTAGTGGAACGGATTTTTCAACAAAGTATG-AAATCTTCACGGAAGAGTAGTG
1 CTCCACGAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGAAAAT-TCCACGGAAGAGTAGTG
1868118 AAGTAATCCA
Statistics
Matches: 200, Mismatches: 25, Indels: 18
0.82 0.10 0.07
Matches are distributed among these distances:
80 11 0.05
81 25 0.12
82 13 0.06
83 14 0.07
84 1 0.00
85 4 0.02
86 25 0.12
87 21 0.10
88 35 0.17
89 51 0.25
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.24
Consensus pattern (88 bp):
CTCCACGAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGAAAATTCCACGGAAGAGTAGTGG
AAGAATTCAATCATAAATCTAAA
Found at i:1868494 original size:13 final size:13
Alignment explanation
Indices: 1868476--1868500 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1868466 AGTGACGATG
1868476 ATTATATATATAC
1 ATTATATATATAC
1868489 ATTATATATATA
1 ATTATATATATA
1868501 ATAAAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTATATATATAC
Found at i:1871578 original size:31 final size:31
Alignment explanation
Indices: 1871542--1871600 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1871532 AACTTAAAAG
*
1871542 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
1871573 AGTTTTACAATACTGTAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
1871601 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1872954 original size:30 final size:29
Alignment explanation
Indices: 1872920--1873090 Score: 174
Period size: 30 Copynumber: 5.9 Consensus size: 29
1872910 TAACTTTAAT
1872920 ACAAACCATATAATATTTCTAACATAGACC
1 ACAAACCATATAATATTTCTAACATA-ACC
* * *
1872950 ACAAACCATATAAT-GTTCTGAA-A-ATCG
1 ACAAACCATATAATATTTCT-AACATAACC
1872977 ACAAACCATATAATATTTCTAACATAAACC
1 ACAAACCATATAATATTTCTAACAT-AACC
* * *
1873007 ATAAACCATATAATGTTT-TGAACAT--CG
1 ACAAACCATATAATATTTCT-AACATAACC
*
1873034 ACAAACCATTTAATATTTCTAACATAGACC
1 ACAAACCATATAATATTTCTAACATA-ACC
* *
1873064 ACAAACCATAAAATATTTCTTACATAA
1 ACAAACCATATAATATTTCTAACATAA
1873091 TCAAAAAGAC
Statistics
Matches: 115, Mismatches: 16, Indels: 21
0.76 0.11 0.14
Matches are distributed among these distances:
27 38 0.33
28 7 0.06
29 7 0.06
30 63 0.55
ACGTcount: A:0.46, C:0.20, G:0.05, T:0.29
Consensus pattern (29 bp):
ACAAACCATATAATATTTCTAACATAACC
Found at i:1872988 original size:27 final size:27
Alignment explanation
Indices: 1872950--1873047 Score: 97
Period size: 27 Copynumber: 3.5 Consensus size: 27
1872940 AACATAGACC
1872950 ACAAACCATATAATGTTCTGAAAATCG
1 ACAAACCATATAATGTTCTGAAAATCG
* * * *
1872977 ACAAACCATATAATATTTCTAACATAAACC
1 ACAAACCATATAAT-GTTCTGA-A-AATCG
* * *
1873007 ATAAACCATATAATGTTTTGAACATCG
1 ACAAACCATATAATGTTCTGAAAATCG
*
1873034 ACAAACCATTTAAT
1 ACAAACCATATAAT
1873048 ATTTCTAACA
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
27 28 0.51
28 6 0.11
29 5 0.09
30 16 0.29
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.29
Consensus pattern (27 bp):
ACAAACCATATAATGTTCTGAAAATCG
Found at i:1873013 original size:57 final size:57
Alignment explanation
Indices: 1872920--1873073 Score: 263
Period size: 57 Copynumber: 2.7 Consensus size: 57
1872910 TAACTTTAAT
1872920 ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAATGTTCTGAAAATCG
1 ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAATGTTCTGAAAATCG
* * * *
1872977 ACAAACCATATAATATTTCTAACATAAACCATAAACCATATAATGTTTTGAACATCG
1 ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAATGTTCTGAAAATCG
*
1873034 ACAAACCATTTAATATTTCTAACATAGACCACAAACCATA
1 ACAAACCATATAATATTTCTAACATAGACCACAAACCATA
1873074 AAATATTTCT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 90 1.00
ACGTcount: A:0.46, C:0.21, G:0.05, T:0.27
Consensus pattern (57 bp):
ACAAACCATATAATATTTCTAACATAGACCACAAACCATATAATGTTCTGAAAATCG
Found at i:1874204 original size:22 final size:22
Alignment explanation
Indices: 1874147--1874261 Score: 182
Period size: 22 Copynumber: 5.4 Consensus size: 22
1874137 CACACAAATC
*
1874147 AACATAC--ACAGCAAATACAT
1 AACATACAAACAGCAAATTCAT
*
1874167 AACAT-CAAACAACAAATTCAT
1 AACATACAAACAGCAAATTCAT
1874188 AACATACAAACAGCAAATTCAT
1 AACATACAAACAGCAAATTCAT
*
1874210 AACATACAAACAACAAATTCAT
1 AACATACAAACAGCAAATTCAT
1874232 AACATACAAACAGCAAATTCAT
1 AACATACAAACAGCAAATTCAT
1874254 AACATACA
1 AACATACA
1874262 TACATATACA
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
19 1 0.01
20 5 0.06
21 16 0.18
22 65 0.75
ACGTcount: A:0.57, C:0.23, G:0.03, T:0.17
Consensus pattern (22 bp):
AACATACAAACAGCAAATTCAT
Found at i:1874271 original size:32 final size:32
Alignment explanation
Indices: 1874235--1874301 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
1874225 AATTCATAAC
* *
1874235 ATACAAACAGCAAATTC-ATAACATACATACAT
1 ATACAAACAACAAATACAAT-ACATACATACAT
*
1874267 ATACAAACAACAAATACAATATATACATACAT
1 ATACAAACAACAAATACAATACATACATACAT
1874299 ATA
1 ATA
1874302 TATATATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 29 0.94
33 2 0.06
ACGTcount: A:0.57, C:0.19, G:0.01, T:0.22
Consensus pattern (32 bp):
ATACAAACAACAAATACAATACATACATACAT
Found at i:1874660 original size:29 final size:30
Alignment explanation
Indices: 1874618--1874675 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1874608 GAACACAAGC
* *
1874618 TCTGTAGCAA-GGGGGAATAGCGATCGAGG
1 TCTGCAGCAAGGGGGGAACAGCGATCGAGG
*
1874647 TCTGCAGCGAGGGGGGAACAGCGATCGAG
1 TCTGCAGCAAGGGGGGAACAGCGATCGAG
1874676 TGGGGAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.26, C:0.17, G:0.43, T:0.14
Consensus pattern (30 bp):
TCTGCAGCAAGGGGGGAACAGCGATCGAGG
Found at i:1879541 original size:29 final size:29
Alignment explanation
Indices: 1879499--1879555 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1879489 TAAGATTAGT
* *
1879499 GAAACTTATTACGT-AGAGGTGAGAAGTTG
1 GAAACTTATCACGTGA-AGGTGACAAGTTG
*
1879528 GAAACTTGTCACGTGAAGGTGACAAGTT
1 GAAACTTATCACGTGAAGGTGACAAGTT
1879556 TAATACAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (29 bp):
GAAACTTATCACGTGAAGGTGACAAGTTG
Found at i:1880063 original size:15 final size:15
Alignment explanation
Indices: 1880029--1880074 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
1880019 TTATTATTAT
1880029 TATTTT-ATTTTATAA
1 TATTTTAATTTTA-AA
1880044 TATTTTTAATTTTAAA
1 TA-TTTTAATTTTAAA
1880060 -ATTTTAACTTTTAAA
1 TATTTTAA-TTTTAAA
1880075 CAAAATATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.21
15 10 0.36
16 6 0.21
17 6 0.21
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTTAATTTTAAA
Found at i:1881182 original size:60 final size:61
Alignment explanation
Indices: 1881085--1881207 Score: 162
Period size: 61 Copynumber: 2.0 Consensus size: 61
1881075 TAAGTGATAA
* * *
1881085 TTTTCTAACTTTTAATAGTCAATGGATTTAATAAAAC-ATCGTCCTATAGTTAGAAAATTAT
1 TTTTATAACATTTAATAGTCAATGGATTTAATAAAACAATCGTCCTATA-TTAGAAAATCAT
* *
1881146 TTTTATAACATTTAGTAGTCAA-GGAATTTAA-CAAACAATCGTCCTATATTAGAAAATCAT
1 TTTTATAACATTTAATAGTCAATGG-ATTTAATAAAACAATCGTCCTATATTAGAAAATCAT
1881206 TT
1 TT
1881208 ATAAATTTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
60 19 0.35
61 36 0.65
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (61 bp):
TTTTATAACATTTAATAGTCAATGGATTTAATAAAACAATCGTCCTATATTAGAAAATCAT
Found at i:1888647 original size:32 final size:32
Alignment explanation
Indices: 1888611--1888671 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
1888601 ATCAAACTGC
*
1888611 TTACCACTTAAACTAACCTGTTGATAAACTAT
1 TTACCACTTAAACTAACCTGTTAATAAACTAT
*
1888643 TTACCACTTGAACTAACCTGTTAATAAAC
1 TTACCACTTAAACTAACCTGTTAATAAAC
1888672 AAATACTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.33
Consensus pattern (32 bp):
TTACCACTTAAACTAACCTGTTAATAAACTAT
Found at i:1889029 original size:21 final size:22
Alignment explanation
Indices: 1889003--1889052 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1888993 ACTTGAATTT
* *
1889003 AAAAAAATCAGAAAAA-TATAA
1 AAAAAAATCACAAAAATTACAA
*
1889024 AAAAAAATTACAAAAATTACAA
1 AAAAAAATCACAAAAATTACAA
1889046 AAAAAAA
1 AAAAAAA
1889053 ATTAGTATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (22 bp):
AAAAAAATCACAAAAATTACAA
Found at i:1894905 original size:140 final size:141
Alignment explanation
Indices: 1894645--1894895 Score: 359
Period size: 140 Copynumber: 1.8 Consensus size: 141
1894635 CCCGTTGGTT
*
1894645 AGGCTTCATACACTTTTAGGTGTCTAAACTATACCTCAAATTAACTTTTGGTGCCTAAAGAATTT
1 AGGCTTCATACACTTTTAGGTGTCTAAACTATACCTCAAATTAACTTTTGGTGCCTAAAGAATTG
** * *
1894710 TTTATTAAAAATATGTGCCTAACGTTTTCTTCATTACACTTTTAGGTGTCTACCGTTATAATTTT
66 TTTACGAAAAATAGGTGCCTAACGTTTTCTACATTACACTTTTAGGTGTCTACCGTTATAATTTT
1894775 TTAATTTTTTA
131 TTAATTTTTTA
* *
1894786 AGGCTT-AGTACACTTTTA-GTGTCTAAACTATACCTCAAATTGACTTTTGGTGCTTAAAGAA-T
1 AGGCTTCA-TACACTTTTAGGTGTCTAAACTATACCTCAAATTAACTTTTGGTGCCTAAAGAATT
* * *
1894848 GTTT-CGCAAAATAGGTGCCTAACGTTTT-TAACGTTACATTTTTAGGTG
65 GTTTACGAAAAATAGGTGCCTAACGTTTTCT-ACATTACACTTTTAGGTG
1894896 CATGGACCGT
Statistics
Matches: 98, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
137 1 0.01
138 35 0.36
139 4 0.04
140 42 0.43
141 16 0.16
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (141 bp):
AGGCTTCATACACTTTTAGGTGTCTAAACTATACCTCAAATTAACTTTTGGTGCCTAAAGAATTG
TTTACGAAAAATAGGTGCCTAACGTTTTCTACATTACACTTTTAGGTGTCTACCGTTATAATTTT
TTAATTTTTTA
Found at i:1895828 original size:16 final size:15
Alignment explanation
Indices: 1895803--1895833 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1895793 TTTCTTGTTA
1895803 TCTTTTTGTCTCTTT
1 TCTTTTTGTCTCTTT
1895818 TCTTCTTTGTCTCTTT
1 TCTT-TTTGTCTCTTT
1895834 AACTGACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.00, C:0.23, G:0.06, T:0.71
Consensus pattern (15 bp):
TCTTTTTGTCTCTTT
Found at i:1897137 original size:25 final size:24
Alignment explanation
Indices: 1897108--1897155 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1897098 CAAGATATCG
*
1897108 ATCAGATAAAACATTCATAAATCAA
1 ATCAGAT-AAACAATCATAAATCAA
* *
1897133 ATCAGGTAAACAATCATATATCA
1 ATCAGATAAACAATCATAAATCA
1897156 TAAAAGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.52, C:0.17, G:0.06, T:0.25
Consensus pattern (24 bp):
ATCAGATAAACAATCATAAATCAA
Found at i:1901391 original size:30 final size:29
Alignment explanation
Indices: 1901341--1901409 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 29
1901331 AAAGATAATC
*
1901341 TTATTTTCTAAAATAAAAAATTCTCAAAA
1 TTATTTTCTAAAAGAAAAAATTCTCAAAA
*
1901370 TTATTTTTTATAAAGAAAAAATTCTCAAAA
1 TTATTTTCTA-AAAGAAAAAATTCTCAAAA
1901400 TTATTTTCTA
1 TTATTTTCTA
1901410 CTTTGATGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 9 0.25
30 27 0.75
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.43
Consensus pattern (29 bp):
TTATTTTCTAAAAGAAAAAATTCTCAAAA
Found at i:1901897 original size:15 final size:15
Alignment explanation
Indices: 1901873--1901945 Score: 80
Period size: 15 Copynumber: 4.9 Consensus size: 15
1901863 TTGGTTTTCC
*
1901873 GGAAAATGAATTACT
1 GGAAATTGAATTACT
*
1901888 GGAATTTGAATTACT
1 GGAAATTGAATTACT
1901903 GGAAAATT-AATTACT
1 GG-AAATTGAATTACT
1901918 -GAAATTTGAATT-CT
1 GGAAA-TTGAATTACT
*
1901932 GGAAAATGAATTAC
1 GGAAATTGAATTAC
1901946 ATTTCTGGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
13 3 0.06
14 11 0.22
15 31 0.63
16 4 0.08
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (15 bp):
GGAAATTGAATTACT
Found at i:1901943 original size:29 final size:30
Alignment explanation
Indices: 1901873--1901945 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
1901863 TTGGTTTTCC
*
1901873 GGAAAATGAATTACTGGAATTTGAATTACT
1 GGAAAATGAATTACTGAAATTTGAATTACT
*
1901903 GGAAAATTAATTACTGAAATTTGAATT-CT
1 GGAAAATGAATTACTGAAATTTGAATTACT
1901932 GGAAAATGAATTAC
1 GGAAAATGAATTAC
1901946 ATTTCTGGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 15 0.38
30 25 0.62
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (30 bp):
GGAAAATGAATTACTGAAATTTGAATTACT
Found at i:1902258 original size:90 final size:86
Alignment explanation
Indices: 1902102--1902271 Score: 200
Period size: 88 Copynumber: 1.9 Consensus size: 86
1902092 ATTATTATTT
* * * * *
1902102 TAAAATATTAAAATAATTTATTTATTATTAAATATTATTTTTATAATTTTATTAATAAAAATATT
1 TAAAATATTAAAATAATTTAATTATTATTAAATAATAGTGTTATAATTATATTAATAAAAATATT
*
1902167 AATATTGGTATATTTTAGTGAAA
66 -A-ATTAGTATATTTTAGTGAAA
* *
1902190 TAAAATATTATAAATTATATTAATTATTTATTAAAGTAATAGTGTTAT-ATTATATT-TTAAAAA
1 TAAAATATTA-AAATAAT-TTAATTA-TTATTAAA-TAATAGTGTTATAATTATATTAATAAAAA
1902253 TATTAATTAGTATATTTTA
62 TATTAATTAGTATATTTTA
1902272 AATATCTTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
88 23 0.33
89 7 0.10
90 16 0.23
91 15 0.21
92 9 0.13
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (86 bp):
TAAAATATTAAAATAATTTAATTATTATTAAATAATAGTGTTATAATTATATTAATAAAAATATT
AATTAGTATATTTTAGTGAAA
Found at i:1902375 original size:23 final size:22
Alignment explanation
Indices: 1902331--1902375 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1902321 AGTAAATATA
* *
1902331 TAAAAAAATTATTATATATTAT
1 TAAAAAAAATATAATATATTAT
*
1902353 TAAAATAAAATATAATATCTTAT
1 TAAAA-AAAATATAATATATTAT
1902376 ATTAGTATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAAAAAATATAATATATTAT
Found at i:1902385 original size:52 final size:52
Alignment explanation
Indices: 1902329--1902439 Score: 122
Period size: 52 Copynumber: 2.1 Consensus size: 52
1902319 TTAGTAAATA
1902329 TATAA-AAAAATTATTATATATTAT-TAA-AAT-AAAATATAATATCTTATATTAG
1 TATAATAAAAATTATTAT-T-TTATATAATAATAAAAATATAATA--TTATATTAG
* * * *
1902381 TATAATATAATTTATTATTTTATATAATATTAAAAATATAATATTATATTAT
1 TATAATAAAAATTATTATTTTATATAATAATAAAAATATAATATTATATTAG
1902433 TATAATA
1 TATAATA
1902440 TAATAAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
51 4 0.08
52 24 0.47
53 12 0.24
54 11 0.22
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (52 bp):
TATAATAAAAATTATTATTTTATATAATAATAAAAATATAATATTATATTAG
Found at i:1902387 original size:23 final size:22
Alignment explanation
Indices: 1902361--1902441 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 22
1902351 ATTAAAATAA
*
1902361 AATATAATATCTTATATTAGTAT
1 AATATAATATATTATATTA-TAT
* *
1902384 AATATAATTTATTATTTTATAT
1 AATATAATATATTATATTATAT
* *
1902406 AATATTAAAAATATAATATTATATT
1 AATA-T-AATATATTATATTATA-T
*
1902431 ATTATAATATA
1 AATATAATATA
1902442 ATAAATATAT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
22 7 0.15
23 22 0.48
24 13 0.28
25 4 0.09
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (22 bp):
AATATAATATATTATATTATAT
Found at i:1902700 original size:41 final size:41
Alignment explanation
Indices: 1902649--1902764 Score: 169
Period size: 42 Copynumber: 2.8 Consensus size: 41
1902639 ATGAATTACA
* * *
1902649 TTCCGGAAAACGAATTATGTAAAACAAACACGGAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGAAAACATT
*
1902690 TTCCGAAAAACGAATAACGTGAAACAAACACGAGAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACG-GAAAACATT
* *
1902732 TTCCAAAAAACGAATTACATGAAACAAACACGG
1 TTCCGAAAAACGAATTACGTGAAACAAACACGG
1902765 GATTTCGGGA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 29 0.43
42 38 0.57
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (41 bp):
TTCCGAAAAACGAATTACGTGAAACAAACACGGAAAACATT
Found at i:1902822 original size:24 final size:24
Alignment explanation
Indices: 1902790--1902838 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1902780 CAATTCCGTA
1902790 ATTGATTTTACGTCAAACAAACAC
1 ATTGATTTTACGTCAAACAAACAC
*
1902814 ATTGGTTTTACGTCAAACAAACAC
1 ATTGATTTTACGTCAAACAAACAC
1902838 A
1 A
1902839 CCCTAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (24 bp):
ATTGATTTTACGTCAAACAAACAC
Found at i:1903150 original size:17 final size:18
Alignment explanation
Indices: 1903117--1903150 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1903107 CCACTATTAG
1903117 TGAACCGGTCAGAACCGT
1 TGAACCGGTCAGAACCGT
*
1903135 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
1903151 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGT
Found at i:1903390 original size:16 final size:16
Alignment explanation
Indices: 1903369--1903399 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1903359 TAATATTGAA
1903369 ACTTGAACTCAAAAAG
1 ACTTGAACTCAAAAAG
1903385 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
1903400 AAAATTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:1903472 original size:14 final size:14
Alignment explanation
Indices: 1903453--1903480 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1903443 AAGTGAAAGA
1903453 ATAGTTATATAATT
1 ATAGTTATATAATT
1903467 ATAGTTATATAATT
1 ATAGTTATATAATT
1903481 TTATTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:1906060 original size:24 final size:24
Alignment explanation
Indices: 1906014--1906061 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1906004 CGCCTACTCC
1906014 CACTTTCTTGCCTCCGCCAACAGT
1 CACTTTCTTGCCTCCGCCAACAGT
1906038 CACTTTCTTGCCTCCGCCAACAGT
1 CACTTTCTTGCCTCCGCCAACAGT
1906062 ACCGGAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.42, G:0.12, T:0.29
Consensus pattern (24 bp):
CACTTTCTTGCCTCCGCCAACAGT
Found at i:1911308 original size:25 final size:27
Alignment explanation
Indices: 1911263--1911369 Score: 75
Period size: 27 Copynumber: 4.0 Consensus size: 27
1911253 TAAAATAAAG
1911263 ATAAAATATTTTTAAATTAAGTTAATA
1 ATAAAATATTTTTAAATTAAGTTAATA
1911290 ATAAAAT-TTATTT-AA-TAAGTTAAT-
1 ATAAAATATT-TTTAAATTAAGTTAATA
1911314 ATAAGGAAATATTTTTTAAATTTAA--T-ATA
1 AT-A--AAATA-TTTTTAAA-TTAAGTTAATA
* * *
1911343 TATAAAATATTATGAATTTAAGTTAAT
1 -ATAAAATATTTTTAAATTAAGTTAAT
1911370 TATTTATATA
Statistics
Matches: 63, Mismatches: 3, Indels: 27
0.68 0.03 0.29
Matches are distributed among these distances:
24 2 0.03
25 14 0.22
26 9 0.14
27 20 0.32
28 7 0.11
29 6 0.10
30 2 0.03
31 3 0.05
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.45
Consensus pattern (27 bp):
ATAAAATATTTTTAAATTAAGTTAATA
Found at i:1912261 original size:21 final size:21
Alignment explanation
Indices: 1912237--1912289 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1912227 ACACTTAGGG
1912237 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
1912258 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
1912279 TACCGATTCCC
1 AACCGATTCCC
1912290 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:1912506 original size:13 final size:13
Alignment explanation
Indices: 1912485--1912539 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1912475 AAGTTCGATA
*
1912485 AATTCAAATACTT
1 AATTGAAATACTT
1912498 AATTGAAATACTT
1 AATTGAAATACTT
* *
1912511 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
1912525 AATTGAAATACTT
1 AATTGAAATACTT
1912538 AA
1 AA
1912540 ATACTTTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:1912570 original size:33 final size:33
Alignment explanation
Indices: 1912525--1912623 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
1912515 AACTCAACAT
* *
1912525 AATTGAAATACTTAAATACTTTCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTTGATA
*
1912558 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTTGATA
*
1912591 AATTCAAATACTTAAAAAC-TTCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTTGATA
1912623 A
1 A
1912624 TTGAAACAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 12 0.20
33 49 0.80
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.34
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTTCAAGTTTGATA
Found at i:1914964 original size:23 final size:24
Alignment explanation
Indices: 1914938--1914990 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
1914928 TTAAACCCAG
* *
1914938 ACCGGTTTTTTTTCCGG-ATAAAA
1 ACCGGTTTTTTATCCGGTAAAAAA
1914961 ACCGGTTTTTTATCCGGTAAAAAA
1 ACCGGTTTTTTATCCGGTAAAAAA
1914985 ACCGGT
1 ACCGGT
1914991 CTAGGTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (24 bp):
ACCGGTTTTTTATCCGGTAAAAAA
Found at i:1916603 original size:13 final size:13
Alignment explanation
Indices: 1916585--1916623 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1916575 ATTGAATGTC
1916585 AAAATAGATAAAA
1 AAAATAGATAAAA
* *
1916598 AAAATAGGTAATA
1 AAAATAGATAAAA
*
1916611 AAAATAAATAAAA
1 AAAATAGATAAAA
1916624 TGAAGAAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (13 bp):
AAAATAGATAAAA
Found at i:1916632 original size:9 final size:8
Alignment explanation
Indices: 1916620--1916900 Score: 59
Period size: 9 Copynumber: 35.1 Consensus size: 8
1916610 AAAAATAAAT
1916620 AAAATGAAG
1 AAAAT-AAG
1916629 AAAATAAG
1 AAAATAAG
1916637 ATAAAT---
1 A-AAATAAG
1916643 AAAATAA-
1 AAAATAAG
1916650 AAAATAA-
1 AAAATAAG
1916657 ATGAAATAAAG
1 A--AAAT-AAG
* *
1916668 ATAAAGAAA
1 A-AAATAAG
1916677 AAAATAA-
1 AAAATAAG
*
1916684 AAAATAAAT
1 AAAAT-AAG
1916693 AAAATAAAG
1 AAAAT-AAG
*
1916702 ATAAAAAAG
1 A-AAATAAG
*
1916711 TAATATAAAG
1 -AAAAT-AAG
1916721 AAAATAA-
1 AAAATAAG
1916728 AAAA-AA-
1 AAAATAAG
*
1916734 CAAATAA-
1 AAAATAAG
*
1916741 AATA-AAG
1 AAAATAAG
1916748 AAAATAA-
1 AAAATAAG
1916755 AAAATAAAG
1 AAAAT-AAG
1916764 ATAAAGATAGAG
1 --AAA-ATA-AG
1916776 AAAATAA-
1 AAAATAAG
1916783 ATAAATAA-
1 A-AAATAAG
1916791 ATAAATAAAG
1 A-AAAT-AAG
*
1916801 ATAA-AA-
1 AAAATAAG
1916807 AAAA-AA-
1 AAAATAAG
1916813 AAAATAA-
1 AAAATAAG
* *
1916820 AAAACAAAT
1 AAAA-TAAG
1916829 AAAATAAAG
1 AAAAT-AAG
1916838 AAAATAA-
1 AAAATAAG
* *
1916845 AAAACAAAT
1 AAAA-TAAG
1916854 AAAATAAAG
1 AAAAT-AAG
1916863 AAAATAAG
1 AAAATAAG
**
1916871 -GTA-AAG
1 AAAATAAG
*
1916877 AAAATAAT
1 AAAATAAG
1916885 AAAATAA-
1 AAAATAAG
1916892 AAAATAAG
1 AAAATAAG
1916900 A
1 A
1916901 TAAAAACAAT
Statistics
Matches: 212, Mismatches: 26, Indels: 69
0.69 0.08 0.22
Matches are distributed among these distances:
5 4 0.02
6 20 0.09
7 51 0.24
8 49 0.23
9 63 0.30
10 16 0.08
11 5 0.02
12 4 0.02
ACGTcount: A:0.77, C:0.01, G:0.07, T:0.15
Consensus pattern (8 bp):
AAAATAAG
Done.