Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 73
Found at i:1015309 original size:27 final size:27
Alignment explanation
Indices: 1015271--1015338 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
1015261 ACACAGAGAG
* * * *
1015271 AAAAAAATAAAATATATAACAAAAG-GA
1 AAAAAAAGAAAAAAGAT-ACAAAAGAAA
*
1015298 AAAAAAAGAAAAAAGATAGAAAAGAAA
1 AAAAAAAGAAAAAAGATACAAAAGAAA
1015325 AAAAAAAGAAAAAA
1 AAAAAAAGAAAAAA
1015339 ATAGAGAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.81, C:0.01, G:0.10, T:0.07
Consensus pattern (27 bp):
AAAAAAAGAAAAAAGATACAAAAGAAA
Found at i:1015319 original size:20 final size:20
Alignment explanation
Indices: 1015296--1015356 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 20
1015286 ATAACAAAAG
1015296 GAAAA-AAAAGAAAAAAGATA
1 GAAAAGAAAA-AAAAAAGATA
*
1015316 GAAAAGAAAAAAAAAAGAAA
1 GAAAAGAAAAAAAAAAGATA
*
1015336 AAAATAGAGAATAAAAAAAGA
1 GAAA-AGA-AA-AAAAAAAGA
1015357 GAAAGAAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 17 0.49
21 7 0.20
22 2 0.06
23 9 0.26
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (20 bp):
GAAAAGAAAAAAAAAAGATA
Found at i:1015320 original size:26 final size:26
Alignment explanation
Indices: 1015291--1015371 Score: 92
Period size: 27 Copynumber: 3.1 Consensus size: 26
1015281 AATATATAAC
*
1015291 AAAAGGAAAAAAAAGAAAAAAGATAG
1 AAAAGAAAAAAAAAGAAAAAAGATAG
1015317 AAAAGAAAAAAAAAAGAAAAAA-ATAG
1 AAAAG-AAAAAAAAAGAAAAAAGATAG
* * * *
1015343 AGAATAAAAAAAGAGAAAGAAAGAAAG
1 AAAAGAAAAAAAAAGAAA-AAAGATAG
1015370 AA
1 AA
1015372 GAATAAACGA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
25 12 0.26
26 15 0.33
27 19 0.41
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (26 bp):
AAAAGAAAAAAAAAGAAAAAAGATAG
Found at i:1015334 original size:16 final size:16
Alignment explanation
Indices: 1015297--1015336 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1015287 TAACAAAAGG
1015297 AAAA-AAAAGAAAAAA
1 AAAAGAAAAGAAAAAA
* *
1015312 GATAGAAAAGAAAAAA
1 AAAAGAAAAGAAAAAA
1015328 AAAAGAAAA
1 AAAAGAAAA
1015337 AAATAGAGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAA
Found at i:1015351 original size:13 final size:12
Alignment explanation
Indices: 1015297--1015370 Score: 62
Period size: 13 Copynumber: 5.8 Consensus size: 12
1015287 TAACAAAAGG
1015297 AAAAAAAAGA-A
1 AAAAAAAAGAGA
*
1015308 AAAAGATAGAAAAGA
1 AAAA-A-A-AAGAGA
1015323 AAAAAAAA-AGA
1 AAAAAAAAGAGA
*
1015334 AAAAAATAGAGA
1 AAAAAAAAGAGA
1015346 ATAAAAAAAGAGA
1 A-AAAAAAAGAGA
1015359 AAGAAAGAAAGA
1 AA-AAA-AAAGA
1015371 AGAATAAACG
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
11 14 0.27
12 8 0.15
13 16 0.31
14 9 0.17
15 5 0.10
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (12 bp):
AAAAAAAAGAGA
Found at i:1015374 original size:28 final size:27
Alignment explanation
Indices: 1015297--1015378 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 27
1015287 TAACAAAAGG
*
1015297 AAAAAAAAGAAAAAAGATAGAA-AAGAA
1 AAAAAAAAGAAAAAAGAGAGAATAA-AA
*
1015324 AAAAAAAAGAAAAAAATAGAGAATAAAA
1 AAAAAAAAG-AAAAAAGAGAGAATAAAA
*
1015352 AAAGAGAAAGAAAGAAAGA-AGAATAAA
1 AAA-AAAAAGAAA-AAAGAGAGAATAAA
1015379 CGATCAAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
27 9 0.19
28 27 0.57
29 11 0.23
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (27 bp):
AAAAAAAAGAAAAAAGAGAGAATAAAA
Found at i:1017325 original size:54 final size:54
Alignment explanation
Indices: 1017261--1017386 Score: 168
Period size: 54 Copynumber: 2.4 Consensus size: 54
1017251 CAGCTAAGGT
* *
1017261 GTTTTTAAAGAAACTAAGTTTGATTTCCAGAAGTTCCTTGATGA-TTTCAAATGA
1 GTTTTTAAAGAAACTAAGTCT-ATTTCCAGAAGTTCCTTGACGATTTTCAAATGA
* * * *
1017315 GTTTTTAAAGAAACTAAGTCTATTTTCAGAAGTTTCTTGACGATTTTTAAATTA
1 GTTTTTAAAGAAACTAAGTCTATTTCCAGAAGTTCCTTGACGATTTTCAAATGA
1017369 --TTTTAAAGAAACTAAGTC
1 GTTTTTAAAGAAACTAAGTC
1017387 CGATTTTTGA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
52 18 0.28
53 19 0.29
54 28 0.43
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.40
Consensus pattern (54 bp):
GTTTTTAAAGAAACTAAGTCTATTTCCAGAAGTTCCTTGACGATTTTCAAATGA
Found at i:1017565 original size:52 final size:51
Alignment explanation
Indices: 1017263--1017569 Score: 215
Period size: 53 Copynumber: 5.8 Consensus size: 51
1017253 GCTAAGGTGT
* * * *
1017263 TTTTAAAGAAACTAAGTTTGATTTCCAGAAGTTCCTTGATGATTTCAAATGA
1 TTTT-AAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGTTTTCAAATGA
* * *
1017315 GTTTTTAAAGAAACTAAGTCT-ATTTTCAGAAGTTTCTTGACGATTTTTAAATTA
1 --TTTT-AAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG-TTTTCAAATGA
* * *
1017369 TTTTAAAGAAACTAAGTCCGATTTT-TGAAAGTTTCTTGATTTTTCTCAAATGA
1 TTTT-AAGAAACTAAGTCTGATTTTCAG-AAGTTTCTTGATGTTT-TCAAATGA
* ** * * **
1017422 TCTTTCAAAGAAATTAAACCTCATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
1 T-TTT--AAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGTTTTCAAATG-A
* * * * * * *
1017477 TTTCAAAGAAATTAAGCCTAATTTTTAG-GGATTTCTTGATGCTTTCAAATGTA
1 TTT-TAAGAAACTAAGTCTGATTTTCAGAAG-TTTCTTGATGTTTTCAAATG-A
* **
1017530 TTTTTAGAAACTAAGTCTGATTTTCAGTGGTTTCTTGATG
1 TTTTAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG
1017570 ATTATCTCTA
Statistics
Matches: 209, Mismatches: 33, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
52 52 0.25
53 87 0.42
54 38 0.18
55 31 0.15
56 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (51 bp):
TTTTAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGTTTTCAAATGA
Found at i:1017789 original size:90 final size:89
Alignment explanation
Indices: 1017633--1018257 Score: 881
Period size: 90 Copynumber: 7.1 Consensus size: 89
1017623 TAGACAACTA
*
1017633 AGAAACTAAGCCTTCAGGGGCTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGT
1 AGAAACTAAGCCTTC-GGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGT
*
1017698 GCAGAATGTTTTCAAATGAGATTTT
65 GCAGGATGTTTTCAAATGAGATTTT
* * * * *
1017723 AGAAAATAAACCTTCGGGGATTTATTGATTTGTAAGTCCTTCGAGCCATCCATAAGACCTTTAGT
1 AGAAACTAAGCCTTCGGGG-TTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGT
*
1017788 GCATGATGTTTTCAAATGAGATTTT
65 GCAGGATGTTTTCAAATGAGATTTT
* *
1017813 AGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCAGGCCATCCATAAGATCTTCAGT
1 AGAAACTAAGCCTTC-GGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGT
*
1017878 GCAGGATGTTTTCAAACGAGATTTT
65 GCAGGATGTTTTCAAATGAGATTTT
* *
1017903 AGAAACTAAGCCTTCGGGGTTTCTTGATTTGTAAGTCCTTTGGGACATCCATAAGACCTTCAGTG
1 AGAAACTAAGCCTTCGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTG
* *
1017968 CATGATATTTTTC--A--A-A---T
66 CAGGAT-GTTTTCAAATGAGATTTT
1017985 -GAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGT
1 AGAAACTAAGCCTTCG-GGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGT
*
1018049 GCAGGATGTTTT----TCA-A---T
65 GCAGGATGTTTTCAAATGAGATTTT
*
1018066 -GAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAATTCCTTCGGGCCATCCATAAGACCTTCAGT
1 AGAAACTAAGCCTTC-GGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGT
*
1018130 GCAGGATGTTTTCAAATTAGATTTT
65 GCAGGATGTTTTCAAATGAGATTTT
*
1018155 AGAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCACAAGACCTTCAGT
1 AGAAACTAAGCCTTCG-GGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGT
*
1018220 GCAGGATGTTTTCAAATGAGTTTTT
65 GCAGGATGTTTTCAAATGAGATTTT
1018245 AGAAACTAAGCCT
1 AGAAACTAAGCCT
1018258 GATTTTCAGG
Statistics
Matches: 485, Mismatches: 33, Indels: 34
0.88 0.06 0.06
Matches are distributed among these distances:
81 95 0.20
82 54 0.11
85 3 0.01
86 2 0.00
88 1 0.00
89 57 0.12
90 269 0.55
91 4 0.01
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (89 bp):
AGAAACTAAGCCTTCGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTG
CAGGATGTTTTCAAATGAGATTTT
Found at i:1018049 original size:171 final size:176
Alignment explanation
Indices: 1017633--1018257 Score: 841
Period size: 171 Copynumber: 3.6 Consensus size: 176
1017623 TAGACAACTA
*
1017633 AGAAACTAAGCCTTC-AGGGGCTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAG
1 AGAAACTAAGCCTTCGA-GGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAG
* * * * * *
1017697 TGCAGAATGTTTTCAAATGAGATTTTAGAAAATAAACCTTCGGGGATTTATTGATTTGTAAGTCC
65 TGCAGGATGTTTTCAAACGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCC
* * * *
1017762 TTCGAGCCATCCATAAGACCTTTAGTGCATGATGTTTTCAAATGAGATTTT
130 TTCGGGACATCCATAAGACCTTCAGTGCAGGATGTTTTC-AAT-AGA--TT
* * *
1017813 AGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCAGGCCATCCATAAGATCTTCAGT
1 AGAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGT
1017878 GCAGGATGTTTTCAAACGAGATTTTAGAAACTAAGCCTTC-GGGGTTTCTTGATTTGTAAGTCCT
66 GCAGGATGTTTTCAAACGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCT
* * *
1017942 TTGGGACATCCATAAGACCTTCAGTGCATGATATTTTTC-A-A-A-T
131 TCGGGACATCCATAAGACCTTCAGTGCAGGAT-GTTTTCAATAGATT
1017985 -GAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGT
1 AGAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGT
* *
1018049 GCAGGATGTTTT---TC-A-A---T-GAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAATTCCT
66 GCAGGATGTTTTCAAACGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCT
*
1018105 TCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATTAGATTTT
131 TCGGGACATCCATAAGACCTTCAGTGCAGGATGTTTTC-AA-TAGA--TT
*
1018155 AGAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCACAAGACCTTCAGT
1 AGAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGT
* *
1018220 GCAGGATGTTTTCAAATGAGTTTTTAGAAACTAAGCCT
66 GCAGGATGTTTTCAAACGAGATTTTAGAAACTAAGCCT
1018258 GATTTTCAGG
Statistics
Matches: 396, Mismatches: 28, Indels: 42
0.85 0.06 0.09
Matches are distributed among these distances:
162 19 0.05
163 53 0.13
164 1 0.00
166 2 0.01
167 2 0.01
168 1 0.00
170 1 0.00
171 148 0.37
172 1 0.00
175 2 0.01
176 1 0.00
178 1 0.00
179 51 0.13
180 113 0.29
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (176 bp):
AGAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGT
GCAGGATGTTTTCAAACGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCT
TCGGGACATCCATAAGACCTTCAGTGCAGGATGTTTTCAATAGATT
Found at i:1018076 original size:81 final size:81
Alignment explanation
Indices: 1017904--1018231 Score: 487
Period size: 81 Copynumber: 3.9 Consensus size: 81
1017894 CGAGATTTTA
* *
1017904 GAAACTAAGCCTTCG-GGGTTTCTTGATTTGTAAGTCCTTTGGGACATCCATAAGACCTTCAGTG
1 GAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTG
* *
1017968 CATGATATTTTTCAAAT
66 CAGGATGTTTTTC-AAT
1017985 GAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTG
1 GAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTG
1018050 CAGGATGTTTTTCAAT
66 CAGGATGTTTTTCAAT
* *
1018066 GAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAATTCCTTCGGGCCATCCATAAGACCTTCAGTG
1 GAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTG
*
1018131 CAGGATGTTTTCAAATTAGATTTT
66 CAGGATGTTTT----TCA-A---T
*
1018155 AGAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCACAAGACCTTCAGT
1 -GAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGT
1018220 GCAGGATGTTTT
65 GCAGGATGTTTT
1018232 CAAATGAGTT
Statistics
Matches: 227, Mismatches: 10, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
81 92 0.41
82 58 0.26
85 2 0.01
86 1 0.00
89 1 0.00
90 73 0.32
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (81 bp):
GAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTG
CAGGATGTTTTTCAAT
Found at i:1018343 original size:37 final size:36
Alignment explanation
Indices: 1018300--1018399 Score: 130
Period size: 36 Copynumber: 2.8 Consensus size: 36
1018290 AAAAAAAGTG
* *
1018300 AATTTTGTCTCACTTGAGACAATTTTTATTCAAAACA
1 AATTTTGTCTCATTTGAGACAATTTTT-CTCAAAACA
* *
1018337 AGTTTTGTCTCTTTTGAGACAATTTTTCTCAAAACA
1 AATTTTGTCTCATTTGAGACAATTTTTCTCAAAACA
* *
1018373 AATTTCGTCTCGTTTGAGAC-ATTTTTC
1 AATTTTGTCTCATTTGAGACAATTTTTC
1018400 CTTTGAAATA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
35 7 0.12
36 25 0.45
37 24 0.43
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (36 bp):
AATTTTGTCTCATTTGAGACAATTTTTCTCAAAACA
Found at i:1018525 original size:21 final size:21
Alignment explanation
Indices: 1018499--1018546 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1018489 TGAGACAATT
1018499 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
1018520 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
1018541 TCCCTT
1 TCCCTT
1018547 AAGATAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.27, G:0.08, T:0.40
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTTGTC
Found at i:1018558 original size:57 final size:57
Alignment explanation
Indices: 1018470--1018584 Score: 149
Period size: 57 Copynumber: 2.0 Consensus size: 57
1018460 TTTTTTCTCA
* *
1018470 AAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCCTTG
1 AAACAAATTTCGTCTCCCTTAAGACAATTTCCCTTGAAACAAATTTTGTCTCCCTTG
* * * ** * *
1018527 AAACAAATTTTGTCTCCCTTAAGATAGTTTCCCTTGAAATGAGTTTTGTCTCTCTTG
1 AAACAAATTTCGTCTCCCTTAAGACAATTTCCCTTGAAACAAATTTTGTCTCCCTTG
1018584 A
1 A
1018585 GACAGTTTCA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (57 bp):
AAACAAATTTCGTCTCCCTTAAGACAATTTCCCTTGAAACAAATTTTGTCTCCCTTG
Found at i:1018704 original size:36 final size:36
Alignment explanation
Indices: 1018523--1018708 Score: 164
Period size: 36 Copynumber: 5.2 Consensus size: 36
1018513 TTTTGTCTCC
* * *
1018523 CTTGAAACAAATTTTGTCTCCCTTAAGATAGTTTCC
1 CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
** * * *
1018559 CTTGAAATGAGTTTTGTCTCTCTTGAGACAGTTTCA
1 CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
*
1018595 CTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCT
1 CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
* ***** * * *
1018631 GTTGAAACAAAAAAAATAT---TTGA-ATATATTTCT
1 CTTGAAACAAATTTTGTCTCCCTTGAGACA-GTTTCT
*
1018664 CTTGAAACAAATTTTATCTCCCTTGAGACAGTTTCT
1 CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
1018700 CTTGAAACA
1 CTTGAAACA
1018709 TAAAATCTTT
Statistics
Matches: 116, Mismatches: 29, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
32 2 0.02
33 22 0.19
36 90 0.78
37 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (36 bp):
CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
Found at i:1018756 original size:67 final size:67
Alignment explanation
Indices: 1018520--1018853 Score: 275
Period size: 67 Copynumber: 4.9 Consensus size: 67
1018510 AAATTTTGTC
* * * * ****
1018520 TCCCTTGAAACAAATTTTGTCTCCCTTAAGATAGTTTCCCTTGAAATGAGTTTTGTCTCTCTTGA
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA-CA---TAAAATCT-TTGA
1018585 GA-CAGTT
61 GATCA-TT
* * * * *
1018592 TCACTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTGTTGAAACAAAAAAAATATTTGA-AT
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC--ATAAAATCTTTGAGAT
*
1018656 ATATT
64 -CATT
* * *
1018661 TCTCTTGAAACAAATTTTATCTCCCTTGAGACAGTTTCTCTTGAAACATAAAATCTTTGAGGTCA
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAATCTTTGAGATCA
1018726 TT
66 TT
* * * ***
1018728 TCCCTTGAAACGAGTTTTGTCTCTCTTGAGACAGTTT-TCCTTGAAACA-CCGATCTTTGAGATC
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCT-CTTGAAACATAAAATCTTTGAGATC
*
1018791 GTT
65 ATT
* * *
1018794 TCCCTTG-AACTGAATTTTGTCTCCCTAT-AGACAATTCCTCTTGAAACATAAAATCTTTGA
1 TCCCTTGAAAC-AAATTTTGTCTCCCT-TGAGACAGTTTCTCTTGAAACATAAAATCTTTGA
1018854 TTGTGTTTTC
Statistics
Matches: 213, Mismatches: 39, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
65 3 0.01
66 50 0.23
67 65 0.31
68 2 0.01
69 49 0.23
70 3 0.01
72 40 0.19
73 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (67 bp):
TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAATCTTTGAGATCA
TT
Found at i:1019463 original size:91 final size:90
Alignment explanation
Indices: 1019245--1019950 Score: 1015
Period size: 91 Copynumber: 7.8 Consensus size: 90
1019235 TTCCATCAAT
* *
1019245 ATTTTCAGTGGATAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGACA-AAGTTCATAAT--
1 ATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGA-AGAAGTTCATAATGA
*
1019307 G-AGAACTTGTTCAACCTTGGTTCAAG
65 GAAGAACTTGTTCAACCTTGGCTC-AG
** * *
1019333 ATTTTTAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGGGAGAAGAAGTTAATAATGAG
1 ATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAG
*
1019398 AAGAACTTGTTCAACTTTGGCTCAG
66 AAGAACTTGTTCAACCTTGGCTCAG
* * ** *
1019423 CATTTCCAATAGAGAGTTCATAATGAGAAGAACTTGTCCAACGAGTGAGAAGAAGTTCATAATGA
1 -ATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA
* *
1019488 GAAGAACTTGTTCAACCTTGGTTTAAG
65 GAAGAACTTGTTCAACCTTGG-CTCAG
*
1019515 ATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAGCGAGGGAGAAGAAGTTCATAATGAG
1 ATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAG
*
1019580 AAGAACTTGTTCAACCTTAGCTCAG
66 AAGAACTTGTTCAACCTTGGCTCAG
* ** * * *
1019605 CATTTCTAACGGAGAGTTCATAATGAGAAGAACTCCTCCAACGAGGGAAAAGAAGTTCCTAATGA
1 -ATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA
*
1019670 GAAGAACTTGTTCAACCTTGGTTCAGG
65 GAAGAACTTGTTCAACCTTGGCTCA-G
** *
1019697 ATTTCCAGTGGAGAGTTCATAATGATCAGAACTCATCCAGCGAGGGAGAAGAAGTTCATAATGAG
1 ATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAG
*
1019762 AAGAACTTGTTCAACCTTAGCTCAG
66 AAGAACTTGTTCAACCTTGGCTCAG
* **
1019787 CATTTCTAACGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA
1 -ATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA
*
1019852 GAAGAACTTGTTCAACTTTGGCTCATG
65 GAAGAACTTGTTCAACCTTGGCTCA-G
*
1019879 ATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCACAATGAG
1 ATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAG
1019944 AAGAACT
66 AAGAACT
1019951 CATCCAACGA
Statistics
Matches: 549, Mismatches: 59, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
87 1 0.00
88 56 0.10
90 7 0.01
91 480 0.87
92 5 0.01
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (90 bp):
ATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAACCTTGGCTCAG
Found at i:1019500 original size:20 final size:20
Alignment explanation
Indices: 1019438--1019501 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
1019428 CCAATAGAGA
1019438 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
*
1019458 GTCCA-ACGAGTGAGAAGAA---
1 GTTCATA--A-TGAGAAGAACTT
1019477 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
1019497 GTTCA
1 GTTCA
1019502 ACCTTGGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
17 9 0.26
18 1 0.03
19 5 0.14
20 10 0.29
21 1 0.03
22 9 0.26
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:1019562 original size:182 final size:182
Alignment explanation
Indices: 1019258--1019950 Score: 1124
Period size: 182 Copynumber: 3.8 Consensus size: 182
1019248 TTCAGTGGAT
1019258 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGACA-AAGTTCATAAT--G-AGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGA-AGAAGTTCATAATGAGAAGAACTTGTTC
** *
1019319 AACCTTGGTTCAAGATTTTTAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGGGAGAAG
65 AACCTTGGTTCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAG
* * * * **
1019384 AAGTTAATAATGAGAAGAACTTGTTCAACTTTGGCTCAGCATTTCCAATAGAG
130 AAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAGCATTTCTAACGGAG
** *
1019437 AGTTCATAATGAGAAGAACTTGTCCAACGAGTGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* *
1019502 ACCTTGGTTTAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAGCGAGGGAGAAGA
66 ACCTTGGTTCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGA
1019567 AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAGCATTTCTAACGGAG
131 AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAGCATTTCTAACGGAG
* * *
1019619 AGTTCATAATGAGAAGAACTCCTCCAACGAGGGAAAAGAAGTTCCTAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* ** *
1019684 ACCTTGGTTCAGGATTTCCAGTGGAGAGTTCATAATGATCAGAACTCATCCAGCGAGGGAGAAGA
66 ACCTTGGTTCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGA
1019749 AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAGCATTTCTAACGGAG
131 AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAGCATTTCTAACGGAG
1019801 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * *
1019866 ACTTTGGCTCATGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGA
66 ACCTTGGTTCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGA
*
1019931 AGTTCACAATGAGAAGAACT
131 AGTTCATAATGAGAAGAACT
1019951 CATCCAACGA
Statistics
Matches: 477, Mismatches: 33, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
178 1 0.00
179 44 0.09
181 1 0.00
182 431 0.90
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (182 bp):
AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTGGTTCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAGCATTTCTAACGGAG
Found at i:1019930 original size:22 final size:22
Alignment explanation
Indices: 1019902--1019970 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 22
1019892 AGTTCATAAT
1019902 GAGAAGAACTCATCCAACGAGG
1 GAGAAGAACTCATCCAACGAGG
* **
1019924 GAGAAGAAGT--T-C-AC-AAT
1 GAGAAGAACTCATCCAACGAGG
1019941 GAGAAGAACTCATCCAACGAGG
1 GAGAAGAACTCATCCAACGAGG
1019963 GAGAAGAA
1 GAGAAGAA
1019971 GTTTATAATG
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
17 10 0.28
18 2 0.06
19 2 0.06
20 2 0.06
21 2 0.06
22 18 0.50
ACGTcount: A:0.45, C:0.17, G:0.28, T:0.10
Consensus pattern (22 bp):
GAGAAGAACTCATCCAACGAGG
Found at i:1019935 original size:39 final size:39
Alignment explanation
Indices: 1019892--1019989 Score: 178
Period size: 39 Copynumber: 2.5 Consensus size: 39
1019882 TCCAGTGGAG
1019892 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGA
*
1019931 AGTTCACAATGAGAAGAACTCATCCAACGAGGGAGAAGA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGA
*
1019970 AGTTTATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
1019990 TGTTCAACCT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.17
Consensus pattern (39 bp):
AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGA
Found at i:1019952 original size:130 final size:130
Alignment explanation
Indices: 1019801--1020080 Score: 488
Period size: 130 Copynumber: 2.2 Consensus size: 130
1019791 TCTAACGGAG
1019801 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * *
1019866 ACTTTGGCTCATGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGA
66 ACCTTGGCTCAAGATTTCCAGTGGAGAGTTAATAATGAGAAGAACTCATCCAACGAAGGAGAAGA
* *
1019931 AGTTCACAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTTATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* *
1019996 ACCTTGGTTCAAGATTTCCAGTGGAGAGTTAATAATGAGAATAACTCATCCAACGAAGGAGAAGA
66 ACCTTGGCTCAAGATTTCCAGTGGAGAGTTAATAATGAGAAGAACTCATCCAACGAAGGAGAAGA
1020061 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
1020081 TGTTCAACCG
Statistics
Matches: 141, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 141 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.23
Consensus pattern (130 bp):
AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTGGCTCAAGATTTCCAGTGGAGAGTTAATAATGAGAAGAACTCATCCAACGAAGGAGAAGA
Found at i:1020104 original size:91 final size:91
Alignment explanation
Indices: 1019938--1020107 Score: 277
Period size: 91 Copynumber: 1.9 Consensus size: 91
1019928 AGAAGTTCAC
* * * *
1019938 AATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTTATAATGAGAAGAACTTGTTCAACCTTGG
1 AATGAGAAGAACTCATCCAACGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCGTAG
* *
1020003 TTCAAGATTTCCAGTGGAGAGTTAAT
66 ATCAACATTTCCAGTGGAGAGTTAAT
*
1020029 AATGAGAATAACTCATCCAACGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCGTAG
1 AATGAGAAGAACTCATCCAACGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCGTAG
1020094 ATCAACATTTCCAG
66 ATCAACATTTCCAG
1020108 AAGAACCCGC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 72 1.00
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (91 bp):
AATGAGAAGAACTCATCCAACGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCGTAG
ATCAACATTTCCAGTGGAGAGTTAAT
Found at i:1020107 original size:221 final size:221
Alignment explanation
Indices: 1019710--1020107 Score: 609
Period size: 221 Copynumber: 1.8 Consensus size: 221
1019700 TCCAGTGGAG
* ** *
1019710 AGTTCATAATGATCAGAACTCATCCAGCGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCACAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * *
1019775 ACCTTAGCTCAGCATTTCTAACGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGA
66 ACCTTAGCTCAGCATTTCCAACGGAGAGTTAATAATGAGAAGAACTCATCCAACGAAGGAGAAGA
** * * **
1019840 AGTTCATAATGAGAAGAACTTGTTCAACTTTGGCTCATGATTTCCAGTGGAGAGTTCATAATGAG
131 AGTTCATAATGAGAAGAACTTGTTCAACCGTAGATCAACATTTCCAGTGGAGAGTTCATAATGAG
1019905 AAGAACTCATCCAACGAGGGAGAAGA
196 AAGAACTCATCCAACGAGGGAGAAGA
*
1019931 AGTTCACAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTTATAATGAGAAGAACTTGTTCA
1 AGTTCACAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * ** *
1019996 ACCTTGGTTCAAG-ATTTCCAGTGGAGAGTTAATAATGAGAATAACTCATCCAACGAAGGAGAAG
66 ACCTTAGCTC-AGCATTTCCAACGGAGAGTTAATAATGAGAAGAACTCATCCAACGAAGGAGAAG
1020060 AAGTTCATAATGAGAAGAACTTGTTCAACCGTAGATCAACATTTCCAG
130 AAGTTCATAATGAGAAGAACTTGTTCAACCGTAGATCAACATTTCCAG
1020108 AAGAACCCGC
Statistics
Matches: 157, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
221 155 0.99
222 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (221 bp):
AGTTCACAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTAGCTCAGCATTTCCAACGGAGAGTTAATAATGAGAAGAACTCATCCAACGAAGGAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACCGTAGATCAACATTTCCAGTGGAGAGTTCATAATGAG
AAGAACTCATCCAACGAGGGAGAAGA
Found at i:1024665 original size:69 final size:68
Alignment explanation
Indices: 1024584--1024714 Score: 235
Period size: 69 Copynumber: 1.9 Consensus size: 68
1024574 TGAAAGAGCA
*
1024584 TTGAGCATTGAAACAATAGTGAATTGGTGGGGAAGTAAGGAGGTAATCTTCTTCTTTCTTCTTCT
1 TTGAGCATTGAAACAACAGTGAATTGGTGGGGAAGTAAGGAGGTAATCTTCTTC-TTCTTCTTCT
1024649 TCTC
65 TCTC
*
1024653 TTGAGCATTGAAACAACAGTGAGTTGGTGGGGAAGTAAGGAGGTAATCTTCTTCTTCTTCTT
1 TTGAGCATTGAAACAACAGTGAATTGGTGGGGAAGTAAGGAGGTAATCTTCTTCTTCTTCTT
1024715 TTGGATAAGT
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
68 8 0.13
69 52 0.87
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (68 bp):
TTGAGCATTGAAACAACAGTGAATTGGTGGGGAAGTAAGGAGGTAATCTTCTTCTTCTTCTTCTT
CTC
Found at i:1028667 original size:21 final size:21
Alignment explanation
Indices: 1028643--1028683 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1028633 GTGTCATGCT
*
1028643 TGCATTACATGT-TATGTGATG
1 TGCATT-CATGTCTATATGATG
1028664 TGCATTCATGTCTATATGAT
1 TGCATTCATGTCTATATGAT
1028684 AATGATCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (21 bp):
TGCATTCATGTCTATATGATG
Found at i:1029129 original size:22 final size:22
Alignment explanation
Indices: 1029073--1029131 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
1029063 CCAAGAGTCG
**
1029073 AGTGGTCCTTCGAAACATATAC
1 AGTGGTCCTTCGGGACATATAC
1029095 AGTGGTCCTTCGGGACATATAC
1 AGTGGTCCTTCGGGACATATAC
1029117 AGTGGTCCTTCGGGA
1 AGTGGTCCTTCGGGA
1029132 AAAATTTCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACATATAC
Found at i:1032113 original size:219 final size:219
Alignment explanation
Indices: 1031734--1032175 Score: 821
Period size: 219 Copynumber: 2.0 Consensus size: 219
1031724 GCAAACAAGA
*
1031734 TTCCCATTTCCACAGAACAAGAGGCTTGTTCTGAACGTGCCAGGGACCATTTTCAAGGATCCAGT
1 TTCCCATTTCCACAGAACAAGAGGCTTGTTCTGAACGTGCCAGGGACCATTTTCAAGGATCCAGC
1031799 CCCTCAAATCAAAATTTAAGAATGAGAAACATAAAGGTTAGGGTCAACCAAACTAACGTTCACAT
66 CCCTCAAATCAAAATTTAAGAATGAGAAACATAAAGGTTAGGGTCAACCAAACTAACGTTCACAT
*
1031864 GCGACGATTTCCCCTAAATCAATTCGATGATTCGTTGCATTGAACCAAAGCTTGGAGCCAAACCA
131 GCGACGATTTCCCCCAAATCAATTCGATGATTCGTTGCATTGAACCAAAGCTTGGAGCCAAACCA
1031929 ATAAATTGTCCCACTAGCGCAAAG
196 ATAAATTGTCCCACTAGCGCAAAG
*
1031953 TTCCCATTTCCTCAGAACAAGAGGCTTGTTCTGAACGTGCCAGGGACCATTTTCAAGGATCCAGC
1 TTCCCATTTCCACAGAACAAGAGGCTTGTTCTGAACGTGCCAGGGACCATTTTCAAGGATCCAGC
*
1032018 CCCTCAAATCAGAATTTAAGAATGAGAAACATAAAGGTTAGGGTCAACCAAACTAACGTTCACAT
66 CCCTCAAATCAAAATTTAAGAATGAGAAACATAAAGGTTAGGGTCAACCAAACTAACGTTCACAT
* *
1032083 GCGACGATTTCCCCCAAATCGATTCGATGATTCGTTGCATTGAACCAAAGCTTGGAGCTAAACCA
131 GCGACGATTTCCCCCAAATCAATTCGATGATTCGTTGCATTGAACCAAAGCTTGGAGCCAAACCA
*
1032148 ATAAATTTTCCCACTAGCGCAAAG
196 ATAAATTGTCCCACTAGCGCAAAG
1032172 TTCC
1 TTCC
1032176 ATTCGGCTAA
Statistics
Matches: 216, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
219 216 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (219 bp):
TTCCCATTTCCACAGAACAAGAGGCTTGTTCTGAACGTGCCAGGGACCATTTTCAAGGATCCAGC
CCCTCAAATCAAAATTTAAGAATGAGAAACATAAAGGTTAGGGTCAACCAAACTAACGTTCACAT
GCGACGATTTCCCCCAAATCAATTCGATGATTCGTTGCATTGAACCAAAGCTTGGAGCCAAACCA
ATAAATTGTCCCACTAGCGCAAAG
Found at i:1038625 original size:12 final size:12
Alignment explanation
Indices: 1038610--1038635 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1038600 ACTAACATAA
1038610 GCCTAACAGATT
1 GCCTAACAGATT
1038622 GCCTAACAGATT
1 GCCTAACAGATT
1038634 GC
1 GC
1038636 ACAACTGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (12 bp):
GCCTAACAGATT
Found at i:1038974 original size:36 final size:35
Alignment explanation
Indices: 1038890--1038992 Score: 145
Period size: 35 Copynumber: 2.9 Consensus size: 35
1038880 AAAAGATGAA
* *
1038890 CACTTGAATCGAAAGTG-CGGATGCTTCATTCCGTT
1 CACTTGAATCGAAAGTGTC-GATGCTTCCTTTCGTT
*
1038925 CACTTGAATCGAAAGTGTCGATGCTTCCTTTTGTT
1 CACTTGAATCGAAAGTGTCGATGCTTCCTTTCGTT
*
1038960 CTTCTTGAATCGAAAGTGTCGATGCTTCCTTTC
1 C-ACTTGAATCGAAAGTGTCGATGCTTCCTTTC
1038993 ACTCTTCTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
35 31 0.51
36 30 0.49
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (35 bp):
CACTTGAATCGAAAGTGTCGATGCTTCCTTTCGTT
Found at i:1038999 original size:36 final size:36
Alignment explanation
Indices: 1038892--1039001 Score: 143
Period size: 36 Copynumber: 3.1 Consensus size: 36
1038882 AAGATGAACA
* * *
1038892 CTTGAATCGAAAGTG-CGGATGCTTCATTCCGTTC-A
1 CTTGAATCGAAAGTGTC-GATGCTTCCTTTCGTTCTT
*
1038927 CTTGAATCGAAAGTGTCGATGCTTCCTTTTGTTCTT
1 CTTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTT
**
1038963 CTTGAATCGAAAGTGTCGATGCTTCCTTTCACTCTT
1 CTTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTT
1038999 CTT
1 CTT
1039002 ATTCACCTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
35 29 0.44
36 37 0.56
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (36 bp):
CTTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTT
Found at i:1042070 original size:105 final size:105
Alignment explanation
Indices: 1041887--1042091 Score: 292
Period size: 105 Copynumber: 2.0 Consensus size: 105
1041877 CATTCATTTT
* *
1041887 CCACTTGGGACTTTCCATCTTGACACTCTATTTGGTTATTAGAATTCATATTTTCTTCTAGTTTC
1 CCACTTGGGACTTTCCATCTTGACACTCTATTTGGTTATTAGAATTCACACTTTCTTCTAGTTTC
*
1041952 GAGCTCCGCAAATGTTCCT-CAATCAGTGGTACCTCAGTCA
66 GAGCTCCGCAAATGTT-CTACAACCAGTGGTACCTCAGTCA
*
1041992 CCACTTGTGG-CTTTCCATCTTGACACTCTATTTCGG-TATTAGAATTCACACTTTCTTATTA-T
1 CCACTTG-GGACTTTCCATCTTGACACTCTATTT-GGTTATTAGAATTCACACTTTCTT-CTAGT
* *
1042054 TTCGAGCTCTGTAAATGTTCTACAACCAGTGGTACCTC
63 TTCGAGCTCCGCAAATGTTCTACAACCAGTGGTACCTC
1042092 GGTTTCCACA
Statistics
Matches: 90, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
104 2 0.02
105 82 0.91
106 6 0.07
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.39
Consensus pattern (105 bp):
CCACTTGGGACTTTCCATCTTGACACTCTATTTGGTTATTAGAATTCACACTTTCTTCTAGTTTC
GAGCTCCGCAAATGTTCTACAACCAGTGGTACCTCAGTCA
Found at i:1043193 original size:411 final size:409
Alignment explanation
Indices: 1042319--1043198 Score: 1057
Period size: 411 Copynumber: 2.1 Consensus size: 409
1042309 TCAAGCTTTC
* * *
1042319 GATCTTGACTCTCGATTTGCATGTTGGAATTCACATTCTCTTCTTATTTCAAGCTTTGAAAATGT
1 GATCTTGAC-CTCCATTTGCATGTTGGAATTCACATTCTCTTCTT-TTTCGAGCTCTGAAAATGT
* *
1042384 TGTCCAATCAATGGTACCTAAGGTATCATGGTTTCAACTTCAAGGGCCTGAATAACAGGCTCATC
64 TGTCCAATCAATGGTAACTAAGGTATCATAGTTTCAACTTCAAGGGCCTGAATAACAGGCTCATC
** * * *
1042449 TTCCACCAACATGTCTTTTTCTTCAACAACTCCATAGCCTGAACCATTGGATGAATATGGTTCTA
129 TTCCACCAACATGTCCCTTACTTCAACAACTCCATAGCCTGAACCATTGGATGAACATGGTTCCA
* * * * * *
1042514 CCATCTCCGACTTAATGTTATTATTAACTATATCATCCTTTAGAACAATCTCTATAGTAATTGGT
194 CCATCTCCGACTTAATATTATCATCAACTATATCATCCTCTAGAACAATCTCTATAGTAATTAGC
* * * * * * *
1042579 ATAGGATCAGTAGAAATAGAGTCAGATTTTACTTAAAAACTCGAAATGGGGTTGATTTCATATAC
259 ATAGGACCAGTAGAAACAGAATCAGATTTTACTTAAAAACTCGAAATAGGGCTAATTTCAGATAC
* * * * * *
1042644 CTGATTATTCATAGCATAAGAGCCATACATGTCATCCTCATTCTCTAACTGAGCCTTAGACCCCT
324 ATGATTATTCAAAGCAAAAGAGCCACACATCTCATCCTCATTCTCTAACTGAACCTTAGACCCCT
* ** *
1042709 CGTTAGCAACTTGGGGCGTTG
389 CATTAGCAACTCAGGGCATTG
* * * * * *
1042730 CATCTTGACCTTCCATTTTCATGTTGGAATTCACATTTTCTTGTAGTTTCGAGATCTGAAAATGT
1 GATCTTGACC-TCCATTTGCATGTTGGAATTCACATTCTCTTCT-TTTTCGAGCTCTGAAAATGT
** * * ** *
1042795 TGTCCAATCAATGGTAACTCGGGTATCATAGTTTCAACTTCAATGGTCTGAATAACAGGCTTGTT
64 TGTCCAATCAATGGTAACTAAGGTATCATAGTTTCAACTTCAAGGGCCTGAATAACAGGCTCATC
**
1042860 TTCCACCAACATGTCCCTTACTTTGACAACTCCAT-GACCTGAACCATTGGATGAACATGGTTCC
129 TTCCACCAACATGTCCCTTACTTCAACAACTCCATAG-CCTGAACCATTGGATGAACATGGTTCC
* * * * * * *
1042924 ACCATTTCCGACTTAATATTATCATCAACTATATTATCCTCTAGTACAGT-TGTTTCAGTATTTA
193 ACCATCTCCGACTTAATATTATCATCAACTATATCATCCTCTAGAACAATCTCTAT-AGTAATTA
* *
1042988 GCATAGGACCAGTAGAAACAGAATCAGATTTTACTTGAAATC-CTGAAATAGGGCTAATTTCAGA
257 GCATAGGACCAGTAGAAACAGAATCAGATTTTACTTAAAAACTC-GAAATAGGGCTAATTTCAGA
* * * * *
1043052 TACATGATTGTTCAAAGCAAAAGAGTCACGCATCTCATCCTCGTTCTCTAACTGAACCTTGGGA-
321 TACATGATTATTCAAAGCAAAAGAGCCACACATCTCATCCTCATTCTCTAACTGAACCTT-AGAC
**
1043116 CCCTCATTCTCAACTCAGGGCATTG
385 CCCTCATTAGCAACTCAGGGCATTG
*
1043141 GATCTTCACACTCCATTTGCATGTTGGAATTCACATTCTCTTCATTTTTCGAGCTCTG
1 GATCTTGAC-CTCCATTTGCATGTTGGAATTCACATTCTCTTC-TTTTTCGAGCTCTG
1043199 CATCAATGGC
Statistics
Matches: 390, Mismatches: 71, Indels: 16
0.82 0.15 0.03
Matches are distributed among these distances:
410 6 0.02
411 380 0.97
412 4 0.01
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (409 bp):
GATCTTGACCTCCATTTGCATGTTGGAATTCACATTCTCTTCTTTTTCGAGCTCTGAAAATGTTG
TCCAATCAATGGTAACTAAGGTATCATAGTTTCAACTTCAAGGGCCTGAATAACAGGCTCATCTT
CCACCAACATGTCCCTTACTTCAACAACTCCATAGCCTGAACCATTGGATGAACATGGTTCCACC
ATCTCCGACTTAATATTATCATCAACTATATCATCCTCTAGAACAATCTCTATAGTAATTAGCAT
AGGACCAGTAGAAACAGAATCAGATTTTACTTAAAAACTCGAAATAGGGCTAATTTCAGATACAT
GATTATTCAAAGCAAAAGAGCCACACATCTCATCCTCATTCTCTAACTGAACCTTAGACCCCTCA
TTAGCAACTCAGGGCATTG
Found at i:1044072 original size:408 final size:405
Alignment explanation
Indices: 1043330--1044164 Score: 993
Period size: 408 Copynumber: 2.1 Consensus size: 405
1043320 ATTTCTTCAT
* * * * * *
1043330 CAACTCCTTGTCCTAAAACATTGGATGAATATGGTTCCTCCATCTCTGACTTATCATCAATTATA
1 CAACTCCATGACCTGAACCATTAGATGAATATGGTTCCTCCATCTCTGACTTATCATCAAATATA
* * * *
1043395 TTATCCATTAGTTCAATTTTTTTAGTACTTGACATAGGATCAGTAGAAATAGAATCAGTTTTCAC
66 TTATCCATTACTTCAATCTTTTCAGTACTTGACATAGGATCAGTAGAAATAGAATCAGCTTTCAC
* * * * * * *
1043460 TTGAAACCCTATAATACTGCTTATTTCAGATACATGATTGTTTATAGAAGAAGAGCCATGCATTT
131 TTGAAACCCTAAAATACGGCTAATTACAGATACATGATTGTTCATAGAAGAAGACCCATGCATGT
* * * * *
1043525 AATCCTCATCCTCAAAACTGAGCCTTGGGACTCTTATTCTCAACTTGGGGCATTGGATCCTGACA
196 AATCCTCATCCTCAAAACTGAGCCTTGAGACCCTCATTCTCAACTCGGAGCATTGGATCCTGACA
* * * * * * *
1043590 TTCCATTTCCATGTTGGAATTCATATTCTCTTCTAGTTCAAGCTCTGCAAATTCTGTACAGTCAA
261 TTCAAGTTCCATATTGGAATTCACATTCTCTTCTAGTTCAAGATCTGAAAATTCTATACAGTCAA
* * *
1043655 TGGAACCTCGGGTATCATAGTTTTAACCTCAGTGGCCTGAATAACAATCTC-ATCTTCCACCAAC
326 TGAAACCTCGGGTATCAAAGTTTTAACCTCAGTGGCCTGAATAACAAGC-CAATCTTCCACCAAC
1043719 ATGTCCATTCCTTAAA
390 ATGTCCATTCCTTAAA
* **
1043735 CAACTCCATTACCTGAACCATTAGATGAATATGGTTCCTTTATCTCTGACTTAATATCATCAAAT
1 CAACTCCATGACCTGAACCATTAGATGAATATGGTTCCTCCATCTCTGAC-T--TATCATCAAAT
* * * * *
1043800 ATATTATCCTTTAACTT-AGA-CTTTTCGGTGA-TTGACATAGGATCAGTGGAGATTGAATCAGC
63 ATATTATCCATT-ACTTCA-ATCTTTTCAGT-ACTTGACATAGGATCAGTAGAAATAGAATCAGC
** * *
1043862 TTTCACTTGAAACCCTAAAATTGGGCTAATTACATATACCTGATTGTTCATAGCAA-AAGACCCA
125 TTTCACTTGAAACCCTAAAATACGGCTAATTACAGATACATGATTGTTCATAG-AAGAAGACCCA
* * *
1043926 TGCATGTCATCCTCATTCTC-CAACTGAGCCTTGAGACCCTCATTCTCAACTCGGAGCATTGGAT
189 TGCATGTAATCCTCATCCTCAAAACTGAGCCTTGAGACCCTCATTCTCAACTCGGAGCATTGGAT
* *
1043990 -CTCGACTTTCAAGTTCCATATTGGAATTCACATTCTCTTCTTGTTTCAAGATCTGAAAATGT-T
254 CCT-GACATTCAAGTTCCATATTGGAATTCACATTCTCTTCTAG-TTCAAGATCTGAAAAT-TCT
* * * * *
1044053 ATCCATTCAGTGAAACCTCGGGTATCAAAGTTTTAACTTCAGTGGCCTGAATAACAGGCCAATCT
316 ATACAGTCAATGAAACCTCGGGTATCAAAGTTTTAACCTCAGTGGCCTGAATAACAAGCCAATCT
* * * *
1044118 TCCACCAACATGTCCCTTTCTTCAG
381 TCCACCAACATGTCCATTCCTTAAA
1044143 CAACTCCATGACCTGAACCATT
1 CAACTCCATGACCTGAACCATT
1044165 GGATTAATTC
Statistics
Matches: 360, Mismatches: 59, Indels: 19
0.82 0.13 0.04
Matches are distributed among these distances:
405 42 0.12
406 3 0.01
407 73 0.20
408 234 0.65
409 8 0.02
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (405 bp):
CAACTCCATGACCTGAACCATTAGATGAATATGGTTCCTCCATCTCTGACTTATCATCAAATATA
TTATCCATTACTTCAATCTTTTCAGTACTTGACATAGGATCAGTAGAAATAGAATCAGCTTTCAC
TTGAAACCCTAAAATACGGCTAATTACAGATACATGATTGTTCATAGAAGAAGACCCATGCATGT
AATCCTCATCCTCAAAACTGAGCCTTGAGACCCTCATTCTCAACTCGGAGCATTGGATCCTGACA
TTCAAGTTCCATATTGGAATTCACATTCTCTTCTAGTTCAAGATCTGAAAATTCTATACAGTCAA
TGAAACCTCGGGTATCAAAGTTTTAACCTCAGTGGCCTGAATAACAAGCCAATCTTCCACCAACA
TGTCCATTCCTTAAA
Found at i:1050416 original size:3 final size:3
Alignment explanation
Indices: 1050410--1050447 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1050400 AAGTTAACAA
1050410 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1050448 AGAGTTTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1064392 original size:17 final size:17
Alignment explanation
Indices: 1064370--1064402 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1064360 TATGAATCAA
1064370 CCATATAATTTTAAAAC
1 CCATATAATTTTAAAAC
1064387 CCATATAATTTTAAAA
1 CCATATAATTTTAAAA
1064403 AAAAAGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (17 bp):
CCATATAATTTTAAAAC
Found at i:1068273 original size:13 final size:13
Alignment explanation
Indices: 1068255--1068287 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1068245 AAAACACAAC
1068255 ATAAAAATT-AAT
1 ATAAAAATTAAAT
1068267 ATAAAAATTAAAT
1 ATAAAAATTAAAT
1068280 ATAAAAAT
1 ATAAAAAT
1068288 ATAGCATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAAAAATTAAAT
Found at i:1070243 original size:15 final size:16
Alignment explanation
Indices: 1070220--1070256 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
1070210 TCATAATTGA
*
1070220 TAAATATTTAATATAT
1 TAAATATTTAAAATAT
1070236 TAAA-ATTTAAAATAT
1 TAAATATTTAAAATAT
1070251 TAAATA
1 TAAATA
1070257 AAAGATAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATATTTAAAATAT
Found at i:1078243 original size:2 final size:2
Alignment explanation
Indices: 1078236--1078270 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1078226 TTGGTTTTGT
1078236 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1078271 GTGTGTGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1082565 original size:15 final size:15
Alignment explanation
Indices: 1082534--1082609 Score: 71
Period size: 15 Copynumber: 4.8 Consensus size: 15
1082524 AGAATAATTA
*
1082534 TAAAATATTAATATTT
1 TAAAATATT-CTATTT
1082550 TAAAATATTCTATTT
1 TAAAATATTCTATTT
* *
1082565 TTAATTATTCTAATATTT
1 TAAAATATTC---TATTT
1082583 TAAAATATTCTATTT
1 TAAAATATTCTATTT
* *
1082598 TTAATTATTCTA
1 TAAAATATTCTA
1082610 ATATTTTTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
15 28 0.56
16 9 0.18
18 13 0.26
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAAATATTCTATTT
Found at i:1082580 original size:33 final size:33
Alignment explanation
Indices: 1082542--1082616 Score: 150
Period size: 33 Copynumber: 2.3 Consensus size: 33
1082532 TATAAAATAT
1082542 TAATATTTTAAAATATTCTATTTTTAATTATTC
1 TAATATTTTAAAATATTCTATTTTTAATTATTC
1082575 TAATATTTTAAAATATTCTATTTTTAATTATTC
1 TAATATTTTAAAATATTCTATTTTTAATTATTC
1082608 TAATATTTT
1 TAATATTTT
1082617 TTGTCAGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (33 bp):
TAATATTTTAAAATATTCTATTTTTAATTATTC
Found at i:1082583 original size:18 final size:18
Alignment explanation
Indices: 1082560--1082617 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
1082550 TAAAATATTC
1082560 TATTTTTAATTATTCTAA
1 TATTTTTAATTATTCTAA
* *
1082578 TATTTTAAAATATTC---
1 TATTTTTAATTATTCTAA
1082593 TATTTTTAATTATTCTAA
1 TATTTTTAATTATTCTAA
1082611 TATTTTT
1 TATTTTT
1082618 TGTCAGAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 13 0.39
18 20 0.61
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTTTAATTATTCTAA
Found at i:1082601 original size:16 final size:17
Alignment explanation
Indices: 1082534--1082616 Score: 86
Period size: 16 Copynumber: 5.1 Consensus size: 17
1082524 AGAATAATTA
*
1082534 TAAAATATT-AATATTT
1 TAAAATATTCTATATTT
1082550 TAAAATATTCTAT-TTT
1 TAAAATATTCTATATTT
*
1082566 T-AATTATTCTAATATTT
1 TAAAATATTCT-ATATTT
1082583 TAAAATATTCTAT-TTT
1 TAAAATATTCTATATTT
*
1082599 T-AATTATTCTAATATTT
1 TAAAATATTCT-ATATTT
1082616 T
1 T
1082617 TTGTCAGAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
15 16 0.28
16 21 0.37
17 12 0.21
18 8 0.14
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
TAAAATATTCTATATTT
Found at i:1088541 original size:9 final size:9
Alignment explanation
Indices: 1088529--1088580 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
1088519 ATAAACAAGG
*
1088529 TAAAGAAAA
1 TAAATAAAA
*
1088538 TAAATAAGA
1 TAAATAAAA
* *
1088547 TACAAGAGAA
1 TA-AATAAAA
1088557 -AAATAAAA
1 TAAATAAAA
1088565 TAAATAAAA
1 TAAATAAAA
1088574 TAAATAA
1 TAAATAA
1088581 GTAAGATAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
8 5 0.15
9 25 0.74
10 4 0.12
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (9 bp):
TAAATAAAA
Found at i:1088971 original size:2 final size:2
Alignment explanation
Indices: 1088964--1088994 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1088954 AAATAATTTA
*
1088964 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1088995 ATAATAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1090520 original size:106 final size:107
Alignment explanation
Indices: 1090006--1090525 Score: 702
Period size: 105 Copynumber: 5.0 Consensus size: 107
1089996 GCATTGTTCC
* * * * *
1090006 GAGTCCAATAT-CTCCG-TGTGAAGTTGAAATTGGCTCTGGAA-CGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * *
1090068 CCAGTC-GTCCCTTCGTTGTGAAGTTG-ACTT--GTTGTCTC
66 GCAGTCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1090106 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-TGA-AA--T-TTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
1090165 GCA-TCGGTCCCTTTGTCGTGGAGTTGAACTTGCGTTGTCTG
66 GCAGTCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1090206 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1090270 GCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 GCAGTCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1090311 AAGTCCAATATCCTTTGTTGTGAAGTTGAAA-TGGCTCTGAAATTGAGAAGTT-TGTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGT-TTGTTGACA
1090374 AGCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 AGCAGTCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1090416 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * * *
1090481 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 GCAGTCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1090522 GAGT
1 GAGT
1090526 GTCACGATAT
Statistics
Matches: 375, Mismatches: 27, Indels: 30
0.87 0.06 0.07
Matches are distributed among these distances:
96 2 0.01
97 29 0.08
98 5 0.01
100 58 0.15
101 8 0.02
102 23 0.06
103 2 0.01
104 19 0.05
105 157 0.42
106 70 0.19
107 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (107 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
GCAGTCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1090772 original size:36 final size:36
Alignment explanation
Indices: 1090725--1090800 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
1090715 TGTTTGGAGA
* * *
1090725 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
1090761 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
1090797 GAAA
1 GAAA
1090801 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:1090889 original size:39 final size:39
Alignment explanation
Indices: 1090816--1090894 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
1090806 TCAATGTTTA
* *
1090816 TGTTTCAAGAGAAACTATCTCAAAGGAGACAAAATTTTC
1 TGTTTCAAGAGAAACTATCTCAAAGAAGACAAAATCTTC
* * *
1090855 TGTTTCGAGGGAAACTATCTC-AAGCAAGATAAAATCTTC
1 TGTTTCAAGAGAAACTATCTCAAAG-AAGACAAAATCTTC
1090894 T
1 T
1090895 TAAAAAACAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 3 0.09
39 31 0.91
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.29
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAAAGAAGACAAAATCTTC
Found at i:1091023 original size:36 final size:36
Alignment explanation
Indices: 1090910--1091023 Score: 90
Period size: 36 Copynumber: 3.1 Consensus size: 36
1090900 AACAGCCTTG
** *
1090910 AGTGAAATGAAATGCCTTCTTTCGAGTGAAACGGTCTCA
1 AGTGAAAT-AAAT--CTTCTTTCGAGAAAAACAGTCTCA
* * * * **
1090949 AGCGAGA-AAATCTGT-TTT-AAGAAAAACAATCTTG
1 AGTGAAATAAATCT-TCTTTCGAGAAAAACAGTCTCA
1090983 AGTGAAATAAATCTTCTTTCGAGAAAAACAGTCTCA
1 AGTGAAATAAATCTTCTTTCGAGAAAAACAGTCTCA
1091019 AGTGA
1 AGTGA
1091024 GACACAATAT
Statistics
Matches: 56, Mismatches: 15, Indels: 11
0.68 0.18 0.13
Matches are distributed among these distances:
34 15 0.27
35 14 0.25
36 18 0.32
37 4 0.07
39 5 0.09
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (36 bp):
AGTGAAATAAATCTTCTTTCGAGAAAAACAGTCTCA
Found at i:1091056 original size:72 final size:71
Alignment explanation
Indices: 1090897--1091064 Score: 205
Period size: 72 Copynumber: 2.3 Consensus size: 71
1090887 AATCTTCTTA
** ** * *
1090897 AAAAACAGCCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAACGGTCTCAAGCGAGAAAATCT
1 AAAAACAATCTTGAGTGAAAT-AAAT-CCTTCTTTCGAGAAAAACAGTCTCAAGCGAGAAAATAT
1090962 GTTTTAAG
64 GTTTTAAG
*
1090970 AAAAACAATCTTGAGTGAAATAAAT-CTTCTTTCGAGAAAAACAGTCTCAAGTGAGACACAATAT
1 AAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGAAAAACAGTCTCAAGCGAGA-A-AATAT
1091034 GTTTTAAG
64 GTTTTAAG
*
1091042 AAAAACAAAT-TTGAGTGAGATAA
1 AAAAAC-AATCTTGAGTGAAATAA
1091065 TCATCTGCAT
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
70 27 0.32
71 1 0.01
72 34 0.40
73 22 0.26
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (71 bp):
AAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGAAAAACAGTCTCAAGCGAGAAAATATGT
TTTAAG
Found at i:1104220 original size:20 final size:20
Alignment explanation
Indices: 1104197--1104239 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1104187 AATCCACCAC
*
1104197 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGATTCTAA
* *
1104217 ATGCATCTATATGATTCTAA
1 ATGCAACTAAATGATTCTAA
1104237 ATG
1 ATG
1104240 GTCTTTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (20 bp):
ATGCAACTAAATGATTCTAA
Found at i:1108767 original size:24 final size:25
Alignment explanation
Indices: 1108716--1108768 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
1108706 GGTTTTTTTT
*
1108716 TAAAAAAATAATATAATAATAATGAA
1 TAAAAAAATAAAATAATAATAA-GAA
1108742 TAAAAAAATGAAAATAATAA-AA-AA
1 TAAAAAAAT-AAAATAATAATAAGAA
1108766 TAA
1 TAA
1108769 TATAAAGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 5 0.20
26 11 0.44
27 9 0.36
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (25 bp):
TAAAAAAATAAAATAATAATAAGAA
Found at i:1109057 original size:16 final size:18
Alignment explanation
Indices: 1109025--1109059 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1109015 ATATATACAT
1109025 ATAATAATAACATGAATA
1 ATAATAATAACATGAATA
1109043 ATAA-AATAA-ATGAATA
1 ATAATAATAACATGAATA
1109059 A
1 A
1109060 ATATCTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 5 0.29
18 4 0.24
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.26
Consensus pattern (18 bp):
ATAATAATAACATGAATA
Found at i:1109654 original size:26 final size:27
Alignment explanation
Indices: 1109625--1109682 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
1109615 TGTTCATGTT
* *
1109625 TAAAAGTT-TTAATTAAAAAT-AACATA
1 TAAAA-TTATTAAATAAAAATAAAAATA
1109651 TAAAATTATTAAATAAAAATAAAAATA
1 TAAAATTATTAAATAAAAATAAAAATA
1109678 TAAAA
1 TAAAA
1109683 ATAATATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 16 0.57
27 10 0.36
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (27 bp):
TAAAATTATTAAATAAAAATAAAAATA
Found at i:1109691 original size:19 final size:19
Alignment explanation
Indices: 1109638--1109705 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
1109628 AAGTTTTAAT
*
1109638 TAAAAATAACATATAAAATTA
1 TAAAAAT-A-ATATAAAAATA
1109659 TTAAATAA-AA-ATAAAAATA
1 -TAAA-AATAATATAAAAATA
* *
1109678 TAAAAATAATATAAATATT
1 TAAAAATAATATAAAAATA
1109697 TAAAAATAA
1 TAAAAATAA
1109706 AAATAATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
17 2 0.05
18 6 0.15
19 24 0.60
20 1 0.03
21 1 0.03
22 4 0.10
23 2 0.05
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAAAATAATATAAAAATA
Found at i:1109704 original size:33 final size:35
Alignment explanation
Indices: 1109664--1109732 Score: 106
Period size: 33 Copynumber: 2.0 Consensus size: 35
1109654 AATTATTAAA
1109664 TAAAAATAAAAAT-ATAAAAAT-AATATAAATATT
1 TAAAAATAAAAATAATAAAAATCAATATAAATATT
* *
1109697 TAAAAATAAAAATAATAAAAATCTATCTAAATATT
1 TAAAAATAAAAATAATAAAAATCAATATAAATATT
1109732 T
1 T
1109733 TTTTTATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 13 0.41
34 8 0.25
35 11 0.34
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (35 bp):
TAAAAATAAAAATAATAAAAATCAATATAAATATT
Found at i:1109713 original size:19 final size:20
Alignment explanation
Indices: 1109661--1109711 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1109651 TAAAATTATT
*
1109661 AAATAAAAATAAAAATATAA
1 AAATAAAAATAAATATATAA
* *
1109681 AAAT-AATATAAATATTTAA
1 AAATAAAAATAAATATATAA
1109700 AAATAAAAATAA
1 AAATAAAAATAA
1109712 TAAAAATCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATAAAAATAAATATATAA
Found at i:1109729 original size:25 final size:25
Alignment explanation
Indices: 1109662--1109718 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
1109652 AAAATTATTA
*
1109662 AATAAAAATA-A-AAATATAAAAAT
1 AATAAAAATATATAAAAATAAAAAT
* *
1109685 AATATAAATATTTAAAAATAAAAAT
1 AATAAAAATATATAAAAATAAAAAT
1109710 AATAAAAAT
1 AATAAAAAT
1109719 CTATCTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 9 0.32
25 19 0.68
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (25 bp):
AATAAAAATATATAAAAATAAAAAT
Found at i:1120910 original size:13 final size:13
Alignment explanation
Indices: 1120891--1120950 Score: 57
Period size: 13 Copynumber: 4.2 Consensus size: 13
1120881 GTCATAACCC
*
1120891 GACCCGACCTGTT
1 GACCCGACCCGTT
*
1120904 TACCCGACCCGTT
1 GACCCGACCCGTT
1120917 GACCCGACCCAACCAGTT
1 GACCCGA--C--CC-GTT
1120935 GACCCGACCCGTT
1 GACCCGACCCGTT
1120948 GAC
1 GAC
1120951 TCATTGACTG
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 23 0.59
14 2 0.05
15 1 0.03
16 1 0.03
17 2 0.05
18 10 0.26
ACGTcount: A:0.20, C:0.43, G:0.20, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1120922 original size:31 final size:31
Alignment explanation
Indices: 1120887--1120950 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
1120877 ACCGGTCATA
* * *
1120887 ACCCGACCCGACCTGTTTACCCGACCCGTTG
1 ACCCGACCCAACCAGTTGACCCGACCCGTTG
1120918 ACCCGACCCAACCAGTTGACCCGACCCGTTG
1 ACCCGACCCAACCAGTTGACCCGACCCGTTG
1120949 AC
1 AC
1120951 TCATTGACTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.20, C:0.45, G:0.19, T:0.16
Consensus pattern (31 bp):
ACCCGACCCAACCAGTTGACCCGACCCGTTG
Found at i:1120926 original size:18 final size:18
Alignment explanation
Indices: 1120905--1120945 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1120895 CGACCTGTTT
*
1120905 ACCCGACCCGTTGACCCG
1 ACCCGACCAGTTGACCCG
*
1120923 ACCCAACCAGTTGACCCG
1 ACCCGACCAGTTGACCCG
1120941 ACCCG
1 ACCCG
1120946 TTGACTCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.22, C:0.49, G:0.20, T:0.10
Consensus pattern (18 bp):
ACCCGACCAGTTGACCCG
Found at i:1122427 original size:26 final size:26
Alignment explanation
Indices: 1122404--1122461 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
1122394 AGAATATCAC
1122404 CAAGCTTAGGAATGATTGGATATCCT
1 CAAGCTTAGGAATGATTGGATATCCT
1122430 CAAGCTTAGGAATGATTGGATATCCT
1 CAAGCTTAGGAATGATTGGATATCCT
*
1122456 CGAGCT
1 CAAGCT
1122462 CTGAAATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (26 bp):
CAAGCTTAGGAATGATTGGATATCCT
Found at i:1122469 original size:26 final size:26
Alignment explanation
Indices: 1122404--1122475 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
1122394 AGAATATCAC
*
1122404 CAAGCTTAGGAATGATTGGATATCCT
1 CAAGCTTAGAAATGATTGGATATCCT
*
1122430 CAAGCTTAGGAATGATTGGATATCCT
1 CAAGCTTAGAAATGATTGGATATCCT
* *
1122456 CGAGCTCT-GAAATGAATGGA
1 CAAGCT-TAGAAATGATTGGA
1122476 ATAAAACTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
26 41 0.98
27 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (26 bp):
CAAGCTTAGAAATGATTGGATATCCT
Found at i:1123864 original size:43 final size:42
Alignment explanation
Indices: 1123802--1124254 Score: 645
Period size: 43 Copynumber: 10.8 Consensus size: 42
1123792 TTAATTACCG
* *
1123802 TTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGT-CCTTTGCTGTGTGCAAGGGTAAGCC
* * *
1123845 ATACAGTTCCCCCATGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGT-CCTTTGCTGTGTGCAAGGGTAAGCC
1123888 TTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGG-TCCTTTGCTGTGTGCAAGGGTAAGCC
*
1123931 TTAACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TT-ACAGTTTCCCCAGGT-CCTTTGCTGTGTGCAAGGGTAAGCC
1123975 TTACAGTTTCCCCAGGTTCCTTTGC--TGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGG-TCCTTTGCTGTGTGCAAGGGTAAGCC
1124016 TTACAGTTT-CCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGG-TCCTTTGCTGTGTGCAAGGGTAAGCC
* *
1124058 TTACAGTTT-CCCAGGTTCTTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGG-TCCTTTGCTGTGTGCAAGGGTAAGCC
*
1124100 TTACAGTTTCCCCAGGTTCTTTGCTGTGTGCAA-GGTAAGCC
1 TTACAGTTTCCCCAGGTCCTTTGCTGTGTGCAAGGGTAAGCC
* *
1124141 TTACAGTTT-CCCAGGTTCTTTGTTGTGTGCAAGGGT-AGCC
1 TTACAGTTTCCCCAGGTCCTTTGCTGTGTGCAAGGGTAAGCC
* *
1124181 TTACAGTTTCCCTAGGTCTTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCTTTGCTGTGTGCAAGGGTAAGCC
*
1124223 TT-CAGTTTCCCCAGGTTCTTTG-TGTGTGCAAG
1 TTACAGTTTCCCCAGGTCCTTTGCTGTGTGCAAG
1124255 TATAAGACTT
Statistics
Matches: 379, Mismatches: 21, Indels: 23
0.90 0.05 0.05
Matches are distributed among these distances:
40 60 0.16
41 85 0.22
42 85 0.22
43 107 0.28
44 42 0.11
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (42 bp):
TTACAGTTTCCCCAGGTCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:1125672 original size:2 final size:2
Alignment explanation
Indices: 1125665--1125696 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1125655 TCAATCTACA
1125665 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1125697 ATTTACGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1130316 original size:23 final size:23
Alignment explanation
Indices: 1130290--1130431 Score: 166
Period size: 23 Copynumber: 6.3 Consensus size: 23
1130280 TGAAAGACCA
*
1130290 CACATAGGTTTGTACCAAAGTGC
1 CACATAGGTTTGCACCAAAGTGC
1130313 CACATAGGTTTGCACCAAAGTGC
1 CACATAGGTTTGCACCAAAGTGC
* * *
1130336 CACATA-ATTAT-C-CTGAAAG-AC
1 CACATAGGTT-TGCAC-CAAAGTGC
* *
1130357 CATATAGGTTTGTACCAAAGTGC
1 CACATAGGTTTGCACCAAAGTGC
*
1130380 CACATAGGTTTGCACCGAAGTGC
1 CACATAGGTTTGCACCAAAGTGC
*
1130403 CACATAGGTTTGCACCGAAGTGC
1 CACATAGGTTTGCACCAAAGTGC
1130426 CACATA
1 CACATA
1130432 TTTATCCCGA
Statistics
Matches: 101, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
21 8 0.08
22 13 0.13
23 80 0.79
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (23 bp):
CACATAGGTTTGCACCAAAGTGC
Found at i:1130365 original size:44 final size:44
Alignment explanation
Indices: 1130312--1130452 Score: 160
Period size: 44 Copynumber: 3.2 Consensus size: 44
1130302 TACCAAAGTG
*
1130312 CCACATAGGTTTGCACCAAAGTGCCACATAATTATCCTGAAAGA
1 CCACATAGGTTTGCACCAAAGTGCCACATAATTATCCCGAAAGA
* * * *
1130356 CCATATAGGTTTGTACCAAAGTGCCACATAGGTT-TGCACCG-AAGTG
1 CCACATAGGTTTGCACCAAAGTGCCACATA-ATTAT-C-CCGAAAG-A
* * *
1130402 CCACATAGGTTTGCACCGAAGTGCCACATATTTATCCCGAAGGA
1 CCACATAGGTTTGCACCAAAGTGCCACATAATTATCCCGAAAGA
1130446 CCACATA
1 CCACATA
1130453 AAACTCTCGA
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
44 39 0.49
45 11 0.14
46 30 0.38
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (44 bp):
CCACATAGGTTTGCACCAAAGTGCCACATAATTATCCCGAAAGA
Found at i:1130394 original size:67 final size:69
Alignment explanation
Indices: 1130252--1130408 Score: 273
Period size: 67 Copynumber: 2.3 Consensus size: 69
1130242 CAACTCATAA
*
1130252 TTTGCATCGAAGTGCCACATAATTATCCTGAAAGACCACACATAGGTTTGTACCAAAGTGCCACA
1 TTTGCACCGAAGTGCCACATAATTATCCTGAAAGACCACACATAGGTTTGTACCAAAGTGCCACA
1130317 TAGG
66 TAGG
* *
1130321 TTTGCACCAAAGTGCCACATAATTATCCTGAAAGA-C-CATATAGGTTTGTACCAAAGTGCCACA
1 TTTGCACCGAAGTGCCACATAATTATCCTGAAAGACCACACATAGGTTTGTACCAAAGTGCCACA
1130384 TAGG
66 TAGG
1130388 TTTGCACCGAAGTGCCACATA
1 TTTGCACCGAAGTGCCACATA
1130409 GGTTTGCACC
Statistics
Matches: 84, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
67 50 0.60
68 1 0.01
69 33 0.39
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (69 bp):
TTTGCACCGAAGTGCCACATAATTATCCTGAAAGACCACACATAGGTTTGTACCAAAGTGCCACA
TAGG
Found at i:1131082 original size:55 final size:54
Alignment explanation
Indices: 1131015--1131153 Score: 147
Period size: 55 Copynumber: 2.5 Consensus size: 54
1131005 CCCTTCAAGT
*
1131015 GTATCGATACCTCCTCATGGTACCGATACCAAAAATAACATTCGATGTTTCGAGG
1 GTATCGATACCTCCTCAAGGTACCGATACC-AAAATAACATTCGATGTTTCGAGG
* * * ** *
1131070 GTATCGGTACCTCTTCAAGGTACCGATACCAATATGGCATTCGATGTTT-TAGGG
1 GTATCGATACCTCCTCAAGGTACCGATACCAAAATAACATTCGATGTTTCGA-GG
* *
1131124 GTATCAATACCATCCTACAA-GTATCGATAC
1 GTATCGATACC-TCCT-CAAGGTACCGATAC
1131154 TACCCTTACA
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
53 1 0.01
54 27 0.39
55 39 0.56
56 3 0.04
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (54 bp):
GTATCGATACCTCCTCAAGGTACCGATACCAAAATAACATTCGATGTTTCGAGG
Found at i:1131153 original size:20 final size:20
Alignment explanation
Indices: 1131124--1131174 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1131114 TGTTTTAGGG
* *
1131124 GTATCAATACCATCC-TACAA
1 GTATCGATACCACCCTTAC-A
*
1131144 GTATCGATACTACCCTTACA
1 GTATCGATACCACCCTTACA
1131164 GTATCGATACC
1 GTATCGATACC
1131175 TCTTCAACAG
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:0.33, C:0.29, G:0.10, T:0.27
Consensus pattern (20 bp):
GTATCGATACCACCCTTACA
Found at i:1133744 original size:25 final size:25
Alignment explanation
Indices: 1133715--1133767 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
1133705 TATTTACGCT
*
1133715 TATTAATACTATGATATATAAAATA
1 TATTAAAACTATGATATATAAAATA
1133740 TATTAAAACTATGATATATAAAATA
1 TATTAAAACTATGATATATAAAATA
1133765 TAT
1 TAT
1133768 CAGTTAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (25 bp):
TATTAAAACTATGATATATAAAATA
Found at i:1134887 original size:29 final size:29
Alignment explanation
Indices: 1134845--1134918 Score: 121
Period size: 29 Copynumber: 2.6 Consensus size: 29
1134835 ATACATTTCA
* *
1134845 ATAATCTTTTATTCCTTTAACCAAATACT
1 ATAATCTTATATTCCTTTAACCAAACACT
*
1134874 ATAATCTTATATTCCTTTAACTAAACACT
1 ATAATCTTATATTCCTTTAACCAAACACT
1134903 ATAATCTTATATTCCT
1 ATAATCTTATATTCCT
1134919 GCTAAACGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (29 bp):
ATAATCTTATATTCCTTTAACCAAACACT
Found at i:1142337 original size:30 final size:30
Alignment explanation
Indices: 1142228--1142383 Score: 93
Period size: 30 Copynumber: 5.1 Consensus size: 30
1142218 AAATGCAAAT
* *
1142228 CTGACACTACTATGCATTATTTGAATGCAACA
1 CTGACACTATTATGCATTA-TT-AATACAACA
* * * *
1142260 CTGACACTGTTGTTGC-TTATCAAATAC-ACG
1 CTGACACTATT-ATGCATTAT-TAATACAACA
* * * *
1142290 CTAACATTGA-TGTGCATTATTAATACAACC
1 CTGACACT-ATTATGCATTATTAATACAACA
* * *
1142320 CTGACACTATTTTGCATTATAAATGCAACA
1 CTGACACTATTATGCATTATTAATACAACA
* * *
1142350 TTGACACTGTTATGCATTATCTGATACAACA
1 CTGACACTATTATGCATTAT-TAATACAACA
1142381 CTG
1 CTG
1142384 CTAGTATCTG
Statistics
Matches: 92, Mismatches: 25, Indels: 15
0.70 0.19 0.11
Matches are distributed among these distances:
29 9 0.10
30 54 0.59
31 14 0.15
32 12 0.13
33 3 0.03
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (30 bp):
CTGACACTATTATGCATTATTAATACAACA
Found at i:1143997 original size:15 final size:13
Alignment explanation
Indices: 1143970--1143995 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1143960 AATAGCTTCT
1143970 CTCTCTAAGGAGA
1 CTCTCTAAGGAGA
1143983 CTCTCTAAGGAGA
1 CTCTCTAAGGAGA
1143996 GAGAAGCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (13 bp):
CTCTCTAAGGAGA
Found at i:1148971 original size:62 final size:61
Alignment explanation
Indices: 1148862--1149165 Score: 283
Period size: 62 Copynumber: 5.0 Consensus size: 61
1148852 TCTTGTTTCC
* * * * * * * *
1148862 TAGAGTCAATATTGACTCCCTCGTGAAGAGAAGTCAACATTTGTTATTTTTGGCTCTTTAG
1 TAGAGTAAATATTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
* * *
1148923 TAGAGTAAATCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTTTGAATCCTCAG
1 TAGAGTAAAT-ATTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
* * * * * *
1148985 TAGAGTCAATATTTAGC-TCTCTCGTGAAGATAAGTCAACATTTTTTTATTTCTAACT-CTCAG
1 TAGAGTAAATATTGA-CTTC-CTCGTGAAGAGAAGTCAAC-CTTTATTATTTCTGACTCCTCAG
* * * *
1149047 TAGAGT-CATCATTGACTTCCTCATGAAGAGAAGTCAACCTTTATTATTCCTGACTCC-CTG
1 TAGAGTAAAT-ATTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
* ** * * *
1149107 TAGAGTCAAATTTTTTCTTCCTCGTGAAGAGAAATCAAACTTTATGATTTCTGACTCCT
1 TAGAGT-AAATATTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCT
1149166 TAGAGGAACT
Statistics
Matches: 197, Mismatches: 36, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
60 21 0.11
61 74 0.38
62 90 0.46
63 12 0.06
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (61 bp):
TAGAGTAAATATTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
Found at i:1149081 original size:123 final size:122
Alignment explanation
Indices: 1148862--1149144 Score: 345
Period size: 123 Copynumber: 2.3 Consensus size: 122
1148852 TCTTGTTTCC
* * ** *
1148862 TAGAGTCAATATTGACTCCCTCGTGAAGAGAAGTCAACATTTGTTATTTTTGGCTCTTTAGTAGA
1 TAGAGTCAATATTTACTCCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTAACTCTTCAGTAGA
* * **
1148927 GTAAATCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTTTGAATCCTCAG
66 GTAAATCATTGACTTCCTCATGAAGAGAAGTCAACCTTTATTATTCCTGAATCC-CAG
* * *
1148985 TAGAGTCAATATTTAGCTCTCTCGTGAAGATAAGTCAACATTTTTTTATTTCTAACTC-TCAGTA
1 TAGAGTCAATATTTA-CTCCCTCGTGAAGAGAAGTCAACA-TTTGTTATTTCTAACTCTTCAGTA
* * *
1149049 GAGT-CATCATTGACTTCCTCATGAAGAGAAGTCAACCTTTATTATTCCTGACTCCCTG
64 GAGTAAATCATTGACTTCCTCATGAAGAGAAGTCAACCTTTATTATTCCTGAATCCCAG
* * * *
1149107 TAGAGTCAAATTTTTTCTTCCTCGTGAAGAGAAATCAA
1 TAGAGTC-AATATTTACTCCCTCGTGAAGAGAAGTCAA
1149145 ACTTTATGAT
Statistics
Matches: 136, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
122 27 0.20
123 65 0.48
124 31 0.23
125 13 0.10
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (122 bp):
TAGAGTCAATATTTACTCCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTAACTCTTCAGTAGA
GTAAATCATTGACTTCCTCATGAAGAGAAGTCAACCTTTATTATTCCTGAATCCCAG
Found at i:1149337 original size:36 final size:36
Alignment explanation
Indices: 1149297--1149687 Score: 604
Period size: 36 Copynumber: 10.9 Consensus size: 36
1149287 CAACCTCGAG
* * * *
1149297 CTTAGCCTACATGGAAGAGTAGTGAAGTAAAGCCAT
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
* *
1149333 CTTAGCCTCTACAGAAGAGTAGTGAAGCAAAGCAAT
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
*
1149369 CTTATCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
* * * *
1149405 CTTAACCTCGACGGAAGAGTAATGAAGCAAATCAAT
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
1149441 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
*
1149477 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAACAAT
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
*
1149513 CTTAGCCTCCACGAAAGAGTAGTGAAGCAAAGCAAT
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
*
1149549 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAACAAT
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
*
1149585 CTTAGCCTCCACGAAAGAGTAGTGAAGCAAAGCAAT
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
* * *
1149621 CTTAGCCTTCACAGAAGAGTAGTGAAGCAAAGC-AC
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
*
1149656 CTTAGCCTCCACGGAAGAGTAGTGAAGAAAAG
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAG
1149688 GCTAAAGAGT
Statistics
Matches: 324, Mismatches: 31, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 0.09
36 294 0.91
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (36 bp):
CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
Found at i:1149459 original size:108 final size:108
Alignment explanation
Indices: 1149297--1149814 Score: 692
Period size: 108 Copynumber: 4.9 Consensus size: 108
1149287 CAACCTCGAG
* * * * * *
1149297 CTTAGCCTACATGGAAGAGTAGTGAAGTAAAGCCATCTTAGCCTCTACAGAAGAGTAGTGAAGCA
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCA
*
1149362 AAGCAATCTTATCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
66 AAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
* * * *
1149405 CTTAACCTCGACGGAAGAGTAATGAAGCAAATCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCA
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCA
*
1149470 AAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAACAAT
66 AAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
*
1149513 CTTAGCCTCCACGAAAGAGTAGTGAAGCAAAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCA
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCA
* *
1149578 AAACAATCTTAGCCTCCACGAAAGAGTAGTGAAGCAAAGCAAT
66 AAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
* * *
1149621 CTTAGCCTTCACAGAAGAGTAGTGAAGCAAAGC-ACCTTAGCCTCCACGGAAGAGTAGTGAAG--
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCA
* *
1149683 -A--AA----AGGCT--A---AAGAGTAGTGAAGCAAAGCCAT
66 AAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
* * *
1149714 TTTAGCCTCCACGGAAGAGTA-TG-AGACAAAGCCATCTTAGCCTCCACGAAAGAGTAGTGAAGC
1 CTTAGCCTCCACGGAAGAGTAGTGAAG-CAAAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGC
*
1149777 AAAGCCATCTTAGCCTCCACGGAAGAGTAGTGAAGCAA
65 AAAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCAA
1149815 GAACAGATTA
Statistics
Matches: 361, Mismatches: 33, Indels: 33
0.85 0.08 0.08
Matches are distributed among these distances:
91 2 0.01
92 8 0.02
93 66 0.18
96 2 0.01
98 5 0.01
102 6 0.02
104 2 0.01
107 44 0.12
108 226 0.63
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (108 bp):
CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCA
AAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
Found at i:1149746 original size:35 final size:36
Alignment explanation
Indices: 1149692--1149814 Score: 205
Period size: 36 Copynumber: 3.4 Consensus size: 36
1149682 GAAAAGGCTA
*
1149692 AAGAGTAGTGAAGCAAAGCCATTTTAGCCTCCACGG
1 AAGAGTAGTGAAGCAAAGCCATCTTAGCCTCCACGG
*
1149728 AAGAGTA-TG-AGACAAAGCCATCTTAGCCTCCACGA
1 AAGAGTAGTGAAG-CAAAGCCATCTTAGCCTCCACGG
1149763 AAGAGTAGTGAAGCAAAGCCATCTTAGCCTCCACGG
1 AAGAGTAGTGAAGCAAAGCCATCTTAGCCTCCACGG
1149799 AAGAGTAGTGAAGCAA
1 AAGAGTAGTGAAGCAA
1149815 GAACAGATTA
Statistics
Matches: 81, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
34 2 0.02
35 30 0.37
36 47 0.58
37 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (36 bp):
AAGAGTAGTGAAGCAAAGCCATCTTAGCCTCCACGG
Found at i:1149757 original size:93 final size:93
Alignment explanation
Indices: 1149598--1149780 Score: 271
Period size: 93 Copynumber: 2.0 Consensus size: 93
1149588 AGCCTCCACG
*
1149598 AAAGAGTAGTGAAGCAAAGCAATCTTAGCCTTCACAGAAGAGTAGTGAAGCAAAGCACCTTAGCC
1 AAAGAGTAGTGAAGCAAAGCAATCTTAGCCTCCACAGAAGAGTAGTGAAGCAAAGCACCTTAGCC
*
1149663 TCCACGGAAGAGTAGTGAAGAAAAGGCT
66 TCCACGAAAGAGTAGTGAAGAAAAGGCT
* * * *
1149691 AAAGAGTAGTGAAGCAAAGCCATTTTAGCCTCCACGGAAGAGTA-TG-AGACAAAGCCATCTTAG
1 AAAGAGTAGTGAAGCAAAGCAATCTTAGCCTCCACAGAAGAGTAGTGAAG-CAAAG-CACCTTAG
*
1149754 CCTCCACGAAAGAGTAGTGAAGCAAAG
64 CCTCCACGAAAGAGTAGTGAAGAAAAG
1149781 CCATCTTAGC
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
91 2 0.02
92 7 0.09
93 72 0.89
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.16
Consensus pattern (93 bp):
AAAGAGTAGTGAAGCAAAGCAATCTTAGCCTCCACAGAAGAGTAGTGAAGCAAAGCACCTTAGCC
TCCACGAAAGAGTAGTGAAGAAAAGGCT
Found at i:1152585 original size:19 final size:19
Alignment explanation
Indices: 1152561--1152613 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 19
1152551 AAACAAGAGA
*
1152561 GAAGAAAATGAGAAGGA-AT
1 GAAGAAAA-GAGAAGAAGAT
1152580 GAAGAAATGAAGAGAAGAAGAT
1 GAAG-AA--AAGAGAAGAAGAT
1152602 GAAGAAAAGAGA
1 GAAGAAAAGAGA
1152614 TAAAAGGCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
19 10 0.34
20 2 0.07
21 9 0.31
22 8 0.28
ACGTcount: A:0.60, C:0.00, G:0.32, T:0.08
Consensus pattern (19 bp):
GAAGAAAAGAGAAGAAGAT
Found at i:1154070 original size:16 final size:17
Alignment explanation
Indices: 1154049--1154081 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1154039 ACACACTAAA
1154049 TCGGTT-TCGGTTTTTT
1 TCGGTTATCGGTTTTTT
1154065 TCGGTTATCGGTTTTTT
1 TCGGTTATCGGTTTTTT
1154082 AGATCAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.12, G:0.24, T:0.61
Consensus pattern (17 bp):
TCGGTTATCGGTTTTTT
Found at i:1157705 original size:20 final size:20
Alignment explanation
Indices: 1157661--1157708 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1157651 CACATTGAAG
* *
1157661 GGTAGCTCTGAACATGCGAA
1 GGTATCTCTAAACATGCGAA
1157681 GGTATCTCTAAACATGCGAA
1 GGTATCTCTAAACATGCGAA
1157701 GGTATCTC
1 GGTATCTC
1157709 ATTTTGAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (20 bp):
GGTATCTCTAAACATGCGAA
Found at i:1158739 original size:28 final size:28
Alignment explanation
Indices: 1158702--1158756 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
1158692 CTATAATACA
1158702 TGTTAGAATTTGTTATCAAAATTTTATG
1 TGTTAGAATTTGTTATCAAAATTTTATG
*
1158730 TGTTAGAATTTGTTATCAAATTTTTAT
1 TGTTAGAATTTGTTATCAAAATTTTAT
1158757 ATTAATCTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.53
Consensus pattern (28 bp):
TGTTAGAATTTGTTATCAAAATTTTATG
Found at i:1159846 original size:34 final size:33
Alignment explanation
Indices: 1159751--1159860 Score: 118
Period size: 32 Copynumber: 3.4 Consensus size: 33
1159741 TTTCTATTTG
* *
1159751 GGTTGCTTTCGGATAGG-GTTAAATTTGATTTA
1 GGTTGCTTTCGGATAGGTGTTAAATTTGGTTCA
* *
1159783 GGTTGCTTTCAGATCGGT-TTAAATTTGGTTCA
1 GGTTGCTTTCGGATAGGTGTTAAATTTGGTTCA
* *
1159815 GGTTTCTTTCGGTTAGGTGTTAAAATTTGGTTC-
1 GGTTGCTTTCGGATAGGTGTT-AAATTTGGTTCA
*
1159848 GAGTTTCTTTCGG
1 G-GTTGCTTTCGG
1159861 TTCAAGTTGC
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
32 41 0.62
33 3 0.05
34 22 0.33
ACGTcount: A:0.17, C:0.10, G:0.27, T:0.45
Consensus pattern (33 bp):
GGTTGCTTTCGGATAGGTGTTAAATTTGGTTCA
Found at i:1159868 original size:16 final size:16
Alignment explanation
Indices: 1159854--1159937 Score: 116
Period size: 16 Copynumber: 5.2 Consensus size: 16
1159844 GTTCGAGTTT
*
1159854 CTTTCGGTTCAAGTTG
1 CTTTCGGTTCAGGTTG
1159870 CTTTCGGTTCAGGTTAG
1 CTTTCGGTTCAGGTT-G
*
1159887 C-TTAGGTTCAGGTTG
1 CTTTCGGTTCAGGTTG
*
1159902 CTTTCAGTTCAGGTTG
1 CTTTCGGTTCAGGTTG
*
1159918 CTTTCGGTTCGGGTTG
1 CTTTCGGTTCAGGTTG
1159934 CTTT
1 CTTT
1159938 TGCTTCGGGT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
15 2 0.03
16 56 0.93
17 2 0.03
ACGTcount: A:0.10, C:0.18, G:0.29, T:0.44
Consensus pattern (16 bp):
CTTTCGGTTCAGGTTG
Found at i:1159944 original size:16 final size:16
Alignment explanation
Indices: 1159866--1159948 Score: 62
Period size: 16 Copynumber: 5.2 Consensus size: 16
1159856 TTCGGTTCAA
* *
1159866 GTTGCTTTCGGTTCAG
1 GTTGCTTTCGCTTCGG
* * *
1159882 GTTAGC-TTAGGTTCAG
1 GTT-GCTTTCGCTTCGG
*
1159898 GTTGCTTTCAG-TTCAG
1 GTTGCTTTC-GCTTCGG
*
1159914 GTTGCTTTCGGTTCGG
1 GTTGCTTTCGCTTCGG
*
1159930 GTTGCTTTTGCTTCGG
1 GTTGCTTTCGCTTCGG
1159946 GTT
1 GTT
1159949 AGTTTCGATT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
15 3 0.05
16 52 0.90
17 3 0.05
ACGTcount: A:0.07, C:0.17, G:0.31, T:0.45
Consensus pattern (16 bp):
GTTGCTTTCGCTTCGG
Found at i:1159955 original size:32 final size:31
Alignment explanation
Indices: 1159855--1159955 Score: 96
Period size: 32 Copynumber: 3.2 Consensus size: 31
1159845 TTCGAGTTTC
* *
1159855 TTTCGGTTCAAGTTGCTTTCGGTTCAGGTTAG
1 TTTCGGTTCAGGTTGCTTT-AGTTCAGGTTAG
* *
1159887 CTTAGGTTCAGGTTGCTTTCAGTTCAGGTT-G
1 TTTCGGTTCAGGTTGCTTT-AGTTCAGGTTAG
* * *
1159918 CTTTCGGTTCGGGTTGCTTTTGCTTCGGGTTAG
1 -TTTCGGTTCAGGTTGCTTTAG-TTCAGGTTAG
1159951 TTTCG
1 TTTCG
1159956 ATTTTGGTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
31 2 0.04
32 54 0.95
33 1 0.02
ACGTcount: A:0.09, C:0.17, G:0.30, T:0.45
Consensus pattern (31 bp):
TTTCGGTTCAGGTTGCTTTAGTTCAGGTTAG
Found at i:1159960 original size:22 final size:22
Alignment explanation
Indices: 1159935--1159976 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1159925 TTCGGGTTGC
*
1159935 TTTTGCTTCGGGTTAGTTTCGA
1 TTTTGCTTCGGGTTAATTTCGA
* *
1159957 TTTTGGTTTGGGTTAATTTC
1 TTTTGCTTCGGGTTAATTTC
1159977 TGTTCGGGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.10, C:0.10, G:0.26, T:0.55
Consensus pattern (22 bp):
TTTTGCTTCGGGTTAATTTCGA
Found at i:1159970 original size:38 final size:39
Alignment explanation
Indices: 1159923--1159998 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 39
1159913 GGTTGCTTTC
** *
1159923 GGTTCGGGTTGCTTT-TGCTTCGGGTTAGTTTC-GATTTT
1 GGTTCGGGTTAATTTCTG-TTCGGGTTACTTTCGGATTTT
*
1159961 GGTTTGGGTTAATTTCTGTTCGGGTTACTTTCGGATTT
1 GGTTCGGGTTAATTTCTGTTCGGGTTACTTTCGGATTT
1159999 GCTAAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 25 0.78
39 7 0.22
ACGTcount: A:0.08, C:0.12, G:0.30, T:0.50
Consensus pattern (39 bp):
GGTTCGGGTTAATTTCTGTTCGGGTTACTTTCGGATTTT
Found at i:1161352 original size:32 final size:32
Alignment explanation
Indices: 1161313--1161375 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1161303 TCTATTGTAC
1161313 TGGATTGATGCAATTATACATGCATAACTGAT
1 TGGATTGATGCAATTATACATGCATAACTGAT
* *
1161345 TGGATTGATGCAATTTTACATGCATAGCTGA
1 TGGATTGATGCAATTATACATGCATAACTGA
1161376 GGGCCCTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.35
Consensus pattern (32 bp):
TGGATTGATGCAATTATACATGCATAACTGAT
Found at i:1162747 original size:54 final size:54
Alignment explanation
Indices: 1162294--1162767 Score: 671
Period size: 54 Copynumber: 8.8 Consensus size: 54
1162284 AATACGGTCG
** * * ** ** *
1162294 TTCATAAACACATTATGAATTCCGTGGGTTGCACACTTAGTGACAATACGAAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* * * *
1162348 TTCATAAACTCATTATGAATTTTTTAAGTTGCACAAACAGTGCCAATACGGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* *
1162402 TTCATAAACTTATTATGAATTTCTTAAGTTGCACATATAGTGCCAATACGAAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* *
1162456 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTTCCAATACAAAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* *
1162510 TTCATAAACTCATTATGAATTTCTTAAGTTTCACACACAGTGCCAATAC-ATAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGA-AAA
* * *
1162564 TTAATAAACTTATTATGAATTTCTTAAGTTGCACACAGAGTGTCAATACGAAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* *
1162618 TTCATAAACTTATTATGAATTTCTTATGTTGCACACACAGTGCCAATACGGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* **
1162672 TTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTATCAATACGAAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* *
1162726 TTCATAAACTTATTATGAATTTCTTAAATTGCACACATAGTG
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
1162768 TCCATTTGGT
Statistics
Matches: 376, Mismatches: 42, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
53 1 0.00
54 374 0.99
55 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (54 bp):
TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
Found at i:1163205 original size:26 final size:26
Alignment explanation
Indices: 1163176--1163285 Score: 211
Period size: 26 Copynumber: 4.2 Consensus size: 26
1163166 TCTGGAATCT
1163176 ATGATATCGATACCTTCCTCATAGTA
1 ATGATATCGATACCTTCCTCATAGTA
1163202 ATGATATCGATACCTTCCTCATAGTA
1 ATGATATCGATACCTTCCTCATAGTA
1163228 ATGATATCGATACCTTCCTCATAGTA
1 ATGATATCGATACCTTCCTCATAGTA
*
1163254 ATGATATTGATACCTTCCTCATAGTA
1 ATGATATCGATACCTTCCTCATAGTA
1163280 ATGATA
1 ATGATA
1163286 CCCACACCAG
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 83 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (26 bp):
ATGATATCGATACCTTCCTCATAGTA
Found at i:1193877 original size:29 final size:28
Alignment explanation
Indices: 1193826--1193882 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
1193816 CAAGTCTTAG
* * * *
1193826 AAAAATTGGGGATCATTTTATAAGTTTT
1 AAAAATTGGAGATCAATTCATAAATTTT
1193854 AAAAAGTTGGAGATCAATTCATAAATTTT
1 AAAAA-TTGGAGATCAATTCATAAATTTT
1193883 GGAAAATAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (28 bp):
AAAAATTGGAGATCAATTCATAAATTTT
Found at i:1212800 original size:45 final size:45
Alignment explanation
Indices: 1212769--1212988 Score: 287
Period size: 45 Copynumber: 4.9 Consensus size: 45
1212759 AACTATAACA
*
1212769 ACTTTTCTGTTGATAATGCACCCATATGCATTTCAATTATAGTAT
1 ACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTAT
* * * * *
1212814 ACTTTTATGTTGATAATGTACCCATATACATCTCAACCATAGTAT
1 ACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTAT
* * * * * **
1212859 ACTTTCCTGTTGAGAATGTACCCATATACATTTCAACTCTAGCGT
1 ACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTAT
*
1212904 ACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTAT
1 ACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTAT
* * *
1212949 ACATTTATGTTGATAATGCACCTATATGCATTTCAACTAT
1 ACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTAT
1212989 GGAATCCTTT
Statistics
Matches: 151, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 151 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (45 bp):
ACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTAT
Found at i:1213020 original size:135 final size:135
Alignment explanation
Indices: 1212769--1213025 Score: 336
Period size: 135 Copynumber: 1.9 Consensus size: 135
1212759 AACTATAACA
* * *
1212769 ACTTTTCTGTTGATAATGCACCCATATGCATTTCAATTATAGTATACTTTTATGTTGATAATGTA
1 ACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACATTTATGTTGATAATGCA
* * ** *
1212834 CCCATATACATCTCAACCATAGTATACTTTCCTGTTGAGAATGTACCCATATACATTTCAACTCT
66 CCCATATACATCTCAACCATAGAATACTTTCATGTCCAGAATGCACCCATATACATTTCAACTCT
1212899 AGCGT
131 AGCGT
*
1212904 ACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATACATTTATGTTGATAATGCA
1 ACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACATTTATGTTGATAATGCA
* * * * * * * * *
1212969 CCTATATGCATTTCAACTATGGAATCCTTTCATG-CCACTAATGCACTCATATGCATT
66 CCCATATACATCTCAACCATAGAATACTTTCATGTCCA-GAATGCACCCATATACATT
1213026 AGTCTTTTAT
Statistics
Matches: 103, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
134 1 0.01
135 102 0.99
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.38
Consensus pattern (135 bp):
ACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACATTTATGTTGATAATGCA
CCCATATACATCTCAACCATAGAATACTTTCATGTCCAGAATGCACCCATATACATTTCAACTCT
AGCGT
Found at i:1213083 original size:79 final size:79
Alignment explanation
Indices: 1212963--1213113 Score: 214
Period size: 79 Copynumber: 1.9 Consensus size: 79
1212953 TTATGTTGAT
* * *
1212963 AATGCACCTATATGCATTTCAACTATGGAATCCTTTCATGCCACTAATGCA-CTCATATGCATTA
1 AATGCACCCATATACATTTCAACTATGGAATCCTTTCATGCCAATAATGCACCT-ATATGCATTA
1213027 GTCTTTTATACTGAC
65 GTCTTTTATACTGAC
* * * * *
1213042 AATGTACCCATATACATTTCATCTATGGCATCCTTTTATGCCAATAATGCACCTATATGCATTAT
1 AATGCACCCATATACATTTCAACTATGGAATCCTTTCATGCCAATAATGCACCTATATGCATTAG
1213107 TCTTTTA
66 TCTTTTA
1213114 GATTTATTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
79 61 0.97
80 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (79 bp):
AATGCACCCATATACATTTCAACTATGGAATCCTTTCATGCCAATAATGCACCTATATGCATTAG
TCTTTTATACTGAC
Found at i:1213542 original size:20 final size:21
Alignment explanation
Indices: 1213517--1213580 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
1213507 GACCCTTCAA
1213517 TATCGATACCCCTA-CTATCG
1 TATCGATACCCCTAGCTATCG
* *
1213537 TATCGATACCACTATGCTATGG
1 TATCGATACCCCTA-GCTATCG
* *
1213559 TACCGATACCCCCTAGATATCG
1 TATCGATA-CCCCTAGCTATCG
1213581 ATACCAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 13 0.37
22 17 0.49
23 5 0.14
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.28
Consensus pattern (21 bp):
TATCGATACCCCTAGCTATCG
Found at i:1214342 original size:2 final size:2
Alignment explanation
Indices: 1214337--1214369 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1214327 TTTATTTATC
1214337 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 T
1214370 CTACCATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1220558 original size:20 final size:20
Alignment explanation
Indices: 1220533--1220583 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1220523 CTATTAAGAT
*
1220533 TATCGATACTCTACCCTCGG
1 TATCGATACTCTACCCTCAG
* *
1220553 TATCGATCCTCTACCTTCAG
1 TATCGATACTCTACCCTCAG
1220573 TATCGATACTC
1 TATCGATACTC
1220584 ACATGTGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.22, C:0.33, G:0.12, T:0.33
Consensus pattern (20 bp):
TATCGATACTCTACCCTCAG
Found at i:1220595 original size:18 final size:18
Alignment explanation
Indices: 1220572--1220617 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
1220562 TCTACCTTCA
*
1220572 GTATCGATACTCACATGT
1 GTATCGATACTCACATGC
1220590 GTATCGATACTCACATGC
1 GTATCGATACTCACATGC
1220608 GTATCGATAC
1 GTATCGATAC
1220618 CAAAATAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (18 bp):
GTATCGATACTCACATGC
Found at i:1224071 original size:43 final size:44
Alignment explanation
Indices: 1223990--1224075 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 44
1223980 TTTTTGAATG
* * * *
1223990 TTATTGAATTGTTTAAAATTTATATTGTTGTTTGTACTGAAATA
1 TTATTAAAATGTTTAAAATTTATATTATTGTTTATACTGAAATA
* *
1224034 TTATTAAAATGTTTACATTTTA-ATTATTGTTTATACTGAAAT
1 TTATTAAAATGTTTAAAATTTATATTATTGTTTATACTGAAAT
1224076 GTTAAGATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 18 0.50
44 18 0.50
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.52
Consensus pattern (44 bp):
TTATTAAAATGTTTAAAATTTATATTATTGTTTATACTGAAATA
Found at i:1227370 original size:20 final size:21
Alignment explanation
Indices: 1227335--1227374 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
1227325 GGGTAGGTAA
1227335 TATCGATATTTTATTCATAGGG
1 TATCGATA-TTTATTCATAGGG
1227357 TATCGATA-TTATTCATAG
1 TATCGATATTTATTCATAG
1227375 AGTAATACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (21 bp):
TATCGATATTTATTCATAGGG
Found at i:1229161 original size:37 final size:37
Alignment explanation
Indices: 1229120--1229235 Score: 187
Period size: 37 Copynumber: 3.1 Consensus size: 37
1229110 TAACAATTTA
* ** *
1229120 TGCACAAACAAATTCTACACTAAACAGTAAACGATTC
1 TGCACTAACAAATTCTGTACTAAACAATAAACGATTC
1229157 TGCACTAACAAATTCTGTACTAAACAATAAACGATTC
1 TGCACTAACAAATTCTGTACTAAACAATAAACGATTC
*
1229194 TGCACTAACAAATTCTGTACTAAACAATAAACGATTA
1 TGCACTAACAAATTCTGTACTAAACAATAAACGATTC
1229231 TGCAC
1 TGCAC
1229236 CAACTTTTCT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 74 1.00
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (37 bp):
TGCACTAACAAATTCTGTACTAAACAATAAACGATTC
Found at i:1229173 original size:15 final size:15
Alignment explanation
Indices: 1229101--1229216 Score: 52
Period size: 15 Copynumber: 6.8 Consensus size: 15
1229091 ACAGTAAACG
1229101 ATTCTGCACTAACAA
1 ATTCTGCACTAACAA
* * *
1229116 TTTATGCACAAACAA
1 ATTCTGCACTAACAA
*
1229131 ATTCTACACTAAACAGTAAA
1 ATTCTGCACT-AAC----AA
1229151 CGATTCTGCACTAACAA
1 --ATTCTGCACTAACAA
*
1229168 ATTCTGTACTAAACAATAAA
1 ATTCTGCACT-AAC----AA
1229188 CGATTCTGCACTAACAA
1 --ATTCTGCACTAACAA
*
1229205 ATTCTGTACTAA
1 ATTCTGCACTAA
1229217 ACAATAAACG
Statistics
Matches: 76, Mismatches: 11, Indels: 28
0.66 0.10 0.24
Matches are distributed among these distances:
15 38 0.50
16 6 0.08
17 4 0.05
20 4 0.05
21 6 0.08
22 18 0.24
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (15 bp):
ATTCTGCACTAACAA
Found at i:1229200 original size:22 final size:22
Alignment explanation
Indices: 1229168--1229235 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 22
1229158 GCACTAACAA
*
1229168 ATTCTGTACTAAACAATAAACG
1 ATTCTGCACTAAACAATAAACG
1229190 ATTCTGCACT-AAC----AA--
1 ATTCTGCACTAAACAATAAACG
*
1229205 ATTCTGTACTAAACAATAAACG
1 ATTCTGCACTAAACAATAAACG
*
1229227 ATTATGCAC
1 ATTCTGCAC
1229236 CAACTTTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
15 9 0.26
16 3 0.09
17 2 0.06
20 2 0.06
21 3 0.09
22 16 0.46
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (22 bp):
ATTCTGCACTAAACAATAAACG
Found at i:1231514 original size:55 final size:55
Alignment explanation
Indices: 1231447--1231942 Score: 672
Period size: 55 Copynumber: 8.9 Consensus size: 55
1231437 TGCACTATCA
* * *
1231447 ATACGGAAATTCATATACTTATTATGAATTTCTTAATTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* * * *
1231502 ATACGAAAATTCATAAACTCATTATGAATTTCTTAGCTTTGAACACAAAGTTCCC
1 ATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* *
1231557 ATAGGGAAATTCATAAACTCATTATGAATTTCTTAGCTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* *
1231612 ATACGGAAATTCATAAACTCATTATGAAATTCTTAGTTTTTTGCACACACAGTGCCC
1 ATACGGAAATTCATAAACTCATTATGAATTTCTTAG--TTTTGCACACAAAGTGCCC
* *
1231669 ATACAGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCTC
1 ATACGGAAATTCATAAACTCATTATGAATTTCTTAG-TTTTGCACACAAAGTGCCC
* * * *
1231725 AGACTGAAATTCTTAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCTC
1 ATACGGAAATTCATAAACTCATTATGAATTTCTTAG-TTTTGCACACAAAGTGCCC
* * * * *
1231781 ATATGGAAATTCATAAACTCAATATGAATTTCTTAGCTTTGAACACAAAGTACCC
1 ATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* * *
1231836 ATATGGAAATTCAT-AACTCATTTTGAATATCTTAGTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* * *
1231890 ATAC-GAAGATTCATAAACTCATCACGAATTTCTTAGCTTTTGCACACACAGTG
1 ATACGGAA-ATTCATAAACTCATTATGAATTTCTTAG-TTTTGCACACAAAGTG
1231943 TCATTTGGTA
Statistics
Matches: 393, Mismatches: 43, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
53 3 0.01
54 43 0.11
55 179 0.46
56 117 0.30
57 51 0.13
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (55 bp):
ATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
Found at i:1235996 original size:13 final size:13
Alignment explanation
Indices: 1235978--1236004 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1235968 ATTAGGAATT
1235978 TTAAAATTAAAAA
1 TTAAAATTAAAAA
1235991 TTAAAATTAAAAA
1 TTAAAATTAAAAA
1236004 T
1 T
1236005 ATATAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TTAAAATTAAAAA
Found at i:1236825 original size:36 final size:36
Alignment explanation
Indices: 1236778--1237037 Score: 359
Period size: 36 Copynumber: 7.2 Consensus size: 36
1236768 AAAGATGAAC
*
1236778 ACTTGAATCGGAAGTGCCAATGCTTCCTCCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTCCCGTTCG
*
1236814 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTC-
1 ACTTGAATCGGAAGTGCCGATGCTTCCTCCCGTTCG
* *
1236849 ACTTGAATCGGAAGTGCCGATGCTTCATTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTCCCGTTCG
*
1236885 ATTTGAATCGGAAGTGCCGATGCTTTCCT-CCGTTCG
1 ACTTGAATCGGAAGTGCCGATGC-TTCCTCCCGTTCG
* *
1236921 ATTTGAATCGGAACTGCCGATGCTTCC-CTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTC-CCGTTCG
*
1236957 ACTTGAATCGGAACTGCCGATGCTTCC-CTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTC-CCGTTCG
* *
1236993 AATTGAATCGGAACTGCCGATGCTTCC-CTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTC-CCGTTCG
1237029 ACTTGAATC
1 ACTTGAATC
1237038 AACGCAAACT
Statistics
Matches: 211, Mismatches: 9, Indels: 8
0.93 0.04 0.04
Matches are distributed among these distances:
35 38 0.18
36 169 0.80
37 4 0.02
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.30
Consensus pattern (36 bp):
ACTTGAATCGGAAGTGCCGATGCTTCCTCCCGTTCG
Found at i:1236999 original size:108 final size:107
Alignment explanation
Indices: 1236780--1237037 Score: 401
Period size: 108 Copynumber: 2.4 Consensus size: 107
1236770 AGATGAACAC
* * *
1236780 TTGAATCGGAAGTGCCAATGC-TTCCTCCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCCTTC
1 TTGAATCGGAAGTGCCGATGCTTTCCT-CCGTTCGACTTGAATCGGAACTGCCGATGCTTCCCTC
* * *
1236844 CGTTCACTTGAATCGGAAGTGCCGATGCTTCATTCCGTTCGAT
65 CGTTCACTTGAATCGGAACTGCCGATGCTTCACTCCGTTCGAA
*
1236887 TTGAATCGGAAGTGCCGATGCTTTCCTCCGTTCGATTTGAATCGGAACTGCCGATGCTTCCCTCC
1 TTGAATCGGAAGTGCCGATGCTTTCCTCCGTTCGACTTGAATCGGAACTGCCGATGCTTCCCTCC
*
1236952 GTTCGACTTGAATCGGAACTGCCGATGCTTCCCTCCGTTCGAA
66 GTTC-ACTTGAATCGGAACTGCCGATGCTTCACTCCGTTCGAA
* *
1236995 TTGAATCGGAACTGCCGATGCTTCCCTCCGTTCGACTTGAATC
1 TTGAATCGGAAGTGCCGATGCTTTCCTCCGTTCGACTTGAATC
1237038 AACGCAAACT
Statistics
Matches: 138, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
107 59 0.43
108 79 0.57
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.30
Consensus pattern (107 bp):
TTGAATCGGAAGTGCCGATGCTTTCCTCCGTTCGACTTGAATCGGAACTGCCGATGCTTCCCTCC
GTTCACTTGAATCGGAACTGCCGATGCTTCACTCCGTTCGAA
Found at i:1239485 original size:2 final size:2
Alignment explanation
Indices: 1239478--1239517 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1239468 TTGATTCATA
1239478 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
1239518 TCGATCTGAC
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:1241673 original size:22 final size:23
Alignment explanation
Indices: 1241637--1241686 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
1241627 TCTTACTAGA
1241637 GTTGACTATTGACCAGTCAGACC
1 GTTGACTATTGACCAGTCAGACC
*
1241660 GTTGACT-TTGACCAGTTAGACC
1 GTTGACTATTGACCAGTCAGACC
1241682 GTTGA
1 GTTGA
1241687 TCGTTGACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (23 bp):
GTTGACTATTGACCAGTCAGACC
Found at i:1243734 original size:19 final size:19
Alignment explanation
Indices: 1243686--1243739 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
1243676 TCCTGAACTT
*
1243686 TGATATCTATTATGATCTC
1 TGATCTCTATTATGATCTC
* * *
1243705 TGATTTATATTTTGATCTC
1 TGATCTCTATTATGATCTC
* *
1243724 TTATCTCTATTCTGAT
1 TGATCTCTATTATGAT
1243740 TTATGATATA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.09, T:0.54
Consensus pattern (19 bp):
TGATCTCTATTATGATCTC
Found at i:1256768 original size:23 final size:22
Alignment explanation
Indices: 1256721--1256770 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
1256711 CATGCAAAGT
*
1256721 TATATGTGATGATATAAGATCA
1 TATATGTGATGATATAAAATCA
1256743 TATATGTTGATGATATATAAAT-A
1 TATATG-TGATGATATA-AAATCA
1256766 TATAT
1 TATAT
1256771 AAACATAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 6 0.24
23 16 0.64
24 3 0.12
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (22 bp):
TATATGTGATGATATAAAATCA
Found at i:1256982 original size:21 final size:22
Alignment explanation
Indices: 1256958--1257006 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1256948 TTCTACGTGG
1256958 TCCTTCGAG-ACATATATGTGA
1 TCCTTCGAGAACATATATGTGA
* *
1256979 TCCTT-GGGAACTTATATGTGA
1 TCCTTCGAGAACATATATGTGA
1257000 TCCTTCG
1 TCCTTCG
1257007 GGATATATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 21 0.88
22 1 0.04
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (22 bp):
TCCTTCGAGAACATATATGTGA
Found at i:1257015 original size:19 final size:19
Alignment explanation
Indices: 1256969--1257015 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
1256959 CCTTCGAGAC
1256969 ATATATGTGATCCTTGGGA
1 ATATATGTGATCCTTGGGA
1256988 ACTTATATGTGATCCTTCGGG-
1 A--TATATGTGATCCTT-GGGA
1257009 ATATATG
1 ATATATG
1257016 GTTGGTCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 7 0.28
21 15 0.60
22 3 0.12
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (19 bp):
ATATATGTGATCCTTGGGA
Found at i:1257082 original size:22 final size:22
Alignment explanation
Indices: 1257018--1257086 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 22
1257008 GATATATGGT
* *
1257018 TGGTCCTTTGGAACA-TATATG
1 TGGTCCTTTGGGACATTCTATG
* ** *
1257039 TAGTCCTACGGGATAATTCTATG
1 TGGTCCTTTGGGA-CATTCTATG
1257062 TGGTCCTTTGGGACATTCTATG
1 TGGTCCTTTGGGACATTCTATG
1257084 TGG
1 TGG
1257087 GACTTCGATG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
21 9 0.25
22 12 0.33
23 15 0.42
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.38
Consensus pattern (22 bp):
TGGTCCTTTGGGACATTCTATG
Found at i:1263467 original size:20 final size:18
Alignment explanation
Indices: 1263440--1263485 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
1263430 TGCATAAGTT
1263440 ATATATATGCTGATATGAG
1 ATATATATGCTG-TATGAG
* *
1263459 ATCATATATGTTGTATGAT
1 AT-ATATATGCTGTATGAG
1263478 ATATATAT
1 ATATATAT
1263486 AAACATAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 6 0.25
19 9 0.38
20 9 0.38
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.43
Consensus pattern (18 bp):
ATATATATGCTGTATGAG
Found at i:1263486 original size:20 final size:21
Alignment explanation
Indices: 1263439--1263486 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
1263429 ATGCATAAGT
1263439 TATATATATGCTGATATGAGA
1 TATATATATGCTGATATGAGA
* * *
1263460 T-CATATATGTTG-TATGATA
1 TATATATATGCTGATATGAGA
1263479 TATATATA
1 TATATATA
1263487 AACATAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 7 0.32
20 14 0.64
21 1 0.05
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.44
Consensus pattern (21 bp):
TATATATATGCTGATATGAGA
Found at i:1263983 original size:3 final size:3
Alignment explanation
Indices: 1263975--1264011 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1263965 ATTTGCATAT
1263975 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1264012 ATATGCCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.