Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 62
Found at i:1960360 original size:2 final size:2
Alignment explanation
Indices: 1960355--1960399 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1960345 GCACACATAC
1960355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1960396 AT AT
1 AT AT
1960400 TCTGAGCTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1962183 original size:20 final size:20
Alignment explanation
Indices: 1962158--1962197 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1962148 GTCCTTGATA
1962158 ATTGTTTTCTCAAATGTTTT
1 ATTGTTTTCTCAAATGTTTT
* *
1962178 ATTGTTTTCTTAATTGTTTT
1 ATTGTTTTCTCAAATGTTTT
1962198 GATCAGATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.65
Consensus pattern (20 bp):
ATTGTTTTCTCAAATGTTTT
Found at i:1969582 original size:23 final size:23
Alignment explanation
Indices: 1969556--1969603 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1969546 GCCATAGTAG
1969556 TCAAAGATTGTGTCATTTTAGTT
1 TCAAAGATTGTGTCATTTTAGTT
1969579 TCAAAGATTGTGTCATTTTAGTT
1 TCAAAGATTGTGTCATTTTAGTT
1969602 TC
1 TC
1969604 CCTTTTGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (23 bp):
TCAAAGATTGTGTCATTTTAGTT
Found at i:1980849 original size:24 final size:24
Alignment explanation
Indices: 1980817--1980876 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
1980807 GCTCTTGAAC
1980817 TTCGGTTATGTTCATTTATGTTCG
1 TTCGGTTATGTTCATTTATGTTCG
**
1980841 TTCGGTTATGTTTGTTTATGTTCG
1 TTCGGTTATGTTCATTTATGTTCG
**
1980865 TTCATTTATGTT
1 TTCGGTTATGTT
1980877 TAACCCAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.12, C:0.10, G:0.20, T:0.58
Consensus pattern (24 bp):
TTCGGTTATGTTCATTTATGTTCG
Found at i:1981967 original size:10 final size:10
Alignment explanation
Indices: 1981952--1982010 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
1981942 GGGTCTCCAA
1981952 CGTTTATGTT
1 CGTTTATGTT
1981962 CGTTTATGTTT
1 CGTTTATG-TT
*
1981973 GTGTTTAT-TT
1 -CGTTTATGTT
*
1981983 ATGTTCT-TGTT
1 -CGTT-TATGTT
1981994 CGTTTATGTT
1 CGTTTATGTT
1982004 CGTTTAT
1 CGTTTAT
1982011 TTATTAAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
9 1 0.02
10 29 0.71
11 5 0.12
12 6 0.15
ACGTcount: A:0.10, C:0.08, G:0.19, T:0.63
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:1982004 original size:16 final size:17
Alignment explanation
Indices: 1981958--1982004 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
1981948 CCAACGTTTA
1981958 TGTTCGTTTATGTT-TG
1 TGTTCGTTTATGTTCTG
**
1981974 TGTTTATTTATGTTCT-
1 TGTTCGTTTATGTTCTG
1981990 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
1982005 GTTTATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 25 0.96
17 1 0.04
ACGTcount: A:0.09, C:0.09, G:0.19, T:0.64
Consensus pattern (17 bp):
TGTTCGTTTATGTTCTG
Found at i:1982097 original size:16 final size:16
Alignment explanation
Indices: 1982076--1982108 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1982066 AAAAAATTTT
1982076 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1982092 TGTTCGTTTATTTTCG
1 TGTTCGTTTATGTTCG
1982108 T
1 T
1982109 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.21, T:0.61
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1986692 original size:27 final size:28
Alignment explanation
Indices: 1986657--1986732 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
1986647 CAAATTTAAA
* *
1986657 ATATTATTTTT-TAATATTTTCGATTAC
1 ATATAATTTTTATAATATTTTCAATTAC
1986684 ATATAATTTTTATAATATTTTCAATTA-
1 ATATAATTTTTATAATATTTTCAATTAC
* *
1986711 TTATGAAGTTTTTATATTATTT
1 ATAT-AA-TTTTTATAATATTT
1986733 ATAATATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 13 0.31
28 16 0.38
29 13 0.31
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (28 bp):
ATATAATTTTTATAATATTTTCAATTAC
Found at i:1986742 original size:19 final size:19
Alignment explanation
Indices: 1986688--1986744 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
1986678 GATTACATAT
1986688 AATT-TTTATAATATTTTC
1 AATTATTTATAATATTTTC
1986706 AATTA-TTATGAAGT-TTTT-
1 AATTATTTAT-AA-TATTTTC
1986724 ATATTATTTATAATATTTTC
1 A-ATTATTTATAATATTTTC
1986744 A
1 A
1986745 GTTAAAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
18 10 0.31
19 16 0.50
20 6 0.19
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (19 bp):
AATTATTTATAATATTTTC
Found at i:1990046 original size:71 final size:71
Alignment explanation
Indices: 1989883--1990503 Score: 853
Period size: 71 Copynumber: 8.8 Consensus size: 71
1989873 TCTTTAACAC
* * *
1989883 ACCATTTGCGTACTTTA-TCATTTGAATTTATAACAAGGTTTGCACCTCGGGAATTTCTGCCCCT
1 ACCATTTGTGTACTTTATTC-TTTGAATTTATGACAAGGTTTGCACCTCGGGAA-TTATGCCCCT
1989947 CAATCGTA
64 CAATCGTA
*
1989955 GCCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGAATTATGCCCCTCA
1 ACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGAATTATGCCCCTCA
1990020 ATCGTA
66 ATCGTA
* * *
1990026 ACCATTTGTGTATTTTATTCTTTGAATTTATGACAAGGTTTGTACCTCGGGAATTATGTCCCTCA
1 ACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGAATTATGCCCCTCA
1990091 ATCGTA
66 ATCGTA
* * * *
1990097 ATCATTTGTGTACTTTACTT-TTTGAATTTATAACAAGGTTTGAACC-CAGGGAATTTCTGCCCC
1 ACCATTTGTGTACTTTA-TTCTTTGAATTTATGACAAGGTTTGCACCTC-GGGAA-TTATGCCCC
1990160 TCAATCGTA
63 TCAATCGTA
* * * *
1990169 ACCATTTGTGTACTTTACTCTTTGAATTTATAATAAGGTTTGCACCTCGGGAATTATGCCTCTCA
1 ACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGAATTATGCCCCTCA
1990234 ATCGTA
66 ATCGTA
* * * *
1990240 ACCATTTGTGTACTTCATTCTTTGAATTTATGACAAGGTTTGCATCTCGGGAAATATGCCTCTCA
1 ACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGAATTATGCCCCTCA
*
1990305 ATAGTA
66 ATCGTA
* * * * * *
1990311 ACCGTTTGTGTAC----TT-TTTGAATTTATAACAAGGATTGCATCTTGGGAATTTTTGCCCCTC
1 ACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGAA-TTATGCCCCTC
1990371 AATCGTA
65 AATCGTA
* *
1990378 ACTATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGTACCTCGGGAATTATGCCCCTCA
1 ACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGAATTATGCCCCTCA
1990443 ATCGTA
66 ATCGTA
** *
1990449 ACCATTTGTGTACTTTACCCTTTGAATTTATGACAATGTTTGCACCTCGGGAATT
1 ACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGAATT
1990504 CTGTCCCGTA
Statistics
Matches: 489, Mismatches: 48, Indels: 25
0.87 0.09 0.04
Matches are distributed among these distances:
66 30 0.06
67 27 0.06
70 1 0.00
71 290 0.59
72 138 0.28
73 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (71 bp):
ACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGAATTATGCCCCTCA
ATCGTA
Found at i:1990162 original size:143 final size:142
Alignment explanation
Indices: 1989883--1990503 Score: 862
Period size: 143 Copynumber: 4.4 Consensus size: 142
1989873 TCTTTAACAC
* *
1989883 ACCATTTGCGTACTTTA-TCATTTGAATTTATAACAAGGTTTGCACCTCGGGAATTTCTGCCCCT
1 ACCATTTGTGTACTTTACTC-TTTGAATTTATAACAAGGTTTGCACCTCGGGAA-TTATGCCCCT
* *
1989947 CAATCGTAGCCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGAATTAT
64 CAATCGTAACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGAACCTCGGGAATTAT
1990012 GCCCCTCAATCGTA
129 GCCCCTCAATCGTA
* * * * *
1990026 ACCATTTGTGTATTTTATTCTTTGAATTTATGACAAGGTTTGTACCTCGGGAATTATGTCCCTCA
1 ACCATTTGTGTACTTTACTCTTTGAATTTATAACAAGGTTTGCACCTCGGGAATTATGCCCCTCA
* * *
1990091 ATCGTAATCATTTGTGTACTTTACTT-TTTGAATTTATAACAAGGTTTGAACC-CAGGGAATTTC
66 ATCGTAACCATTTGTGTACTTTA-TTCTTTGAATTTATGACAAGGTTTGAACCTC-GGGAA-TTA
1990154 TGCCCCTCAATCGTA
128 TGCCCCTCAATCGTA
* *
1990169 ACCATTTGTGTACTTTACTCTTTGAATTTATAATAAGGTTTGCACCTCGGGAATTATGCCTCTCA
1 ACCATTTGTGTACTTTACTCTTTGAATTTATAACAAGGTTTGCACCTCGGGAATTATGCCCCTCA
* * * *
1990234 ATCGTAACCATTTGTGTACTTCATTCTTTGAATTTATGACAAGGTTTGCATCTCGGGAAATATGC
66 ATCGTAACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGAACCTCGGGAATTATGC
* *
1990299 CTCTCAATAGTA
131 CCCTCAATCGTA
* * * * *
1990311 ACCGTTTGTGTAC--T--T-TTTGAATTTATAACAAGGATTGCATCTTGGGAATTTTTGCCCCTC
1 ACCATTTGTGTACTTTACTCTTTGAATTTATAACAAGGTTTGCACCTCGGGAA-TTATGCCCCTC
* *
1990371 AATCGTAACTATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGTACCTCGGGAATTATG
65 AATCGTAACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGAACCTCGGGAATTATG
1990436 CCCCTCAATCGTA
130 CCCCTCAATCGTA
* * *
1990449 ACCATTTGTGTACTTTACCCTTTGAATTTATGACAATGTTTGCACCTCGGGAATT
1 ACCATTTGTGTACTTTACTCTTTGAATTTATAACAAGGTTTGCACCTCGGGAATT
1990504 CTGTCCCGTA
Statistics
Matches: 418, Mismatches: 48, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
137 29 0.07
138 93 0.22
140 2 0.00
141 1 0.00
142 90 0.22
143 200 0.48
144 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (142 bp):
ACCATTTGTGTACTTTACTCTTTGAATTTATAACAAGGTTTGCACCTCGGGAATTATGCCCCTCA
ATCGTAACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGAACCTCGGGAATTATGC
CCCTCAATCGTA
Found at i:1990262 original size:214 final size:213
Alignment explanation
Indices: 1989883--1990510 Score: 928
Period size: 214 Copynumber: 3.0 Consensus size: 213
1989873 TCTTTAACAC
* *
1989883 ACCATTTGCGTACTTTA-TCATTTGAATTTATAACAAGGTTTGCACCTCGGGAATTTCTGCCCCT
1 ACCATTTGTGTACTTTACT-TTTTGAATTTATAACAAGGTTTGCACC-CGGGAATTTCTGCCCCT
*
1989947 CAATCGTAGCCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGAATTAT
64 CAATCGTAACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGAATTAT
* *
1990012 GCCCCTCAATCGTAACCATTTGTGTATTTTATTCTTTGAATTTATGACAAGGTTTGTACCTCGGG
129 GCCCCTCAATCGTAACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGG
*
1990077 AATTATGTCCCTCAATCGTA
194 AATTATGTCCCTCAATAGTA
* *
1990097 ATCATTTGTGTACTTTACTTTTTGAATTTATAACAAGGTTTGAACCCAGGGAATTTCTGCCCCTC
1 ACCATTTGTGTACTTTACTTTTTGAATTTATAACAAGGTTTGCACCC-GGGAATTTCTGCCCCTC
* * *
1990162 AATCGTAACCATTTGTGTACTTTACTCTTTGAATTTATAATAAGGTTTGCACCTCGGGAATTATG
65 AATCGTAACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGAATTATG
* * *
1990227 CCTCTCAATCGTAACCATTTGTGTACTTCATTCTTTGAATTTATGACAAGGTTTGCATCTCGGGA
130 CCCCTCAATCGTAACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGA
*
1990292 AATATG-CCTCTCAATAGTA
195 ATTATGTCC-CTCAATAGTA
* * ** *
1990311 ACCGTTTGTG-----TACTTTTTGAATTTATAACAAGGATTGCATCTTGGGAATTTTTGCCCCTC
1 ACCATTTGTGTACTTTACTTTTTGAATTTATAACAAGGTTTGCA-CCCGGGAATTTCTGCCCCTC
* *
1990371 AATCGTAACTATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGTACCTCGGGAATTATG
65 AATCGTAACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGAATTATG
** *
1990436 CCCCTCAATCGTAACCATTTGTGTACTTTACCCTTTGAATTTATGACAATGTTTGCACCTCGGGA
130 CCCCTCAATCGTAACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGA
*
1990501 ATTCTGTCCC
195 ATTATGTCCC
1990511 GTAATCCGTT
Statistics
Matches: 374, Mismatches: 35, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
209 167 0.45
210 3 0.01
213 3 0.01
214 200 0.53
215 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (213 bp):
ACCATTTGTGTACTTTACTTTTTGAATTTATAACAAGGTTTGCACCCGGGAATTTCTGCCCCTCA
ATCGTAACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGAATTATGC
CCCTCAATCGTAACCATTTGTGTACTTTATTCTTTGAATTTATGACAAGGTTTGCACCTCGGGAA
TTATGTCCCTCAATAGTA
Found at i:1995973 original size:26 final size:27
Alignment explanation
Indices: 1995918--1995982 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
1995908 TCGACCTTCA
* **
1995918 AAATAATAATAAAATTATTTTTATACT
1 AAATAATAATAAAATAATTTGCATACT
1995945 AAATAATAATAAAA-AATTTGCA-ACAT
1 AAATAATAATAAAATAATTTGCATAC-T
*
1995971 AAAAAATAATAA
1 AAATAATAATAA
1995983 TAGAATAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 2 0.06
26 17 0.52
27 14 0.42
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (27 bp):
AAATAATAATAAAATAATTTGCATACT
Found at i:1996533 original size:13 final size:13
Alignment explanation
Indices: 1996506--1996541 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
1996496 AAGGAAATTA
1996506 AAATTAATGAAAAT
1 AAATTAAT-AAAAT
1996520 AAATTAATAAAAT
1 AAATTAATAAAAT
*
1996533 AAATAAATA
1 AAATTAATA
1996542 TTGAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (13 bp):
AAATTAATAAAAT
Found at i:2003536 original size:2 final size:2
Alignment explanation
Indices: 2003529--2003554 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2003519 TCATATCACA
2003529 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
2003555 TTGTTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2003682 original size:23 final size:23
Alignment explanation
Indices: 2003656--2003716 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
2003646 CTCGTATAAA
2003656 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
2003679 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
2003702 TGCACTGAAGTGCCA
1 TGCACCGAAGTGCCA
2003717 TATAAAATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:2008335 original size:12 final size:13
Alignment explanation
Indices: 2008309--2008348 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
2008299 CATCAAAACA
2008309 ATATAACAT-TAT
1 ATATAACATATAT
2008321 ATATAACATAT-T
1 ATATAACATATAT
*
2008333 ATAT-ACATATAC
1 ATATAACATATAT
2008345 ATAT
1 ATAT
2008349 TATGCATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 6 0.24
12 18 0.72
13 1 0.04
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATAACATATAT
Found at i:2008670 original size:23 final size:23
Alignment explanation
Indices: 2008652--2008712 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
2008642 CTCGTATAAA
2008652 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
2008675 TGCACTGAAGTTCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
2008698 TACACCGAAGTGCCA
1 TGCACCGAAGTGCCA
2008713 TATAAAATGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:2021308 original size:12 final size:12
Alignment explanation
Indices: 2021291--2021317 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2021281 AATACTATGC
2021291 ATATATAAATAA
1 ATATATAAATAA
2021303 ATATATAAATAA
1 ATATATAAATAA
2021315 ATA
1 ATA
2021318 AATAGTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATATAAATAA
Found at i:2025113 original size:12 final size:12
Alignment explanation
Indices: 2025098--2025127 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2025088 GAAATCAAAT
2025098 AAAATAACAATA
1 AAAATAACAATA
2025110 AAAATAACAATA
1 AAAATAACAATA
2025122 AAAATA
1 AAAATA
2025128 TTTCTATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAATAACAATA
Found at i:2025127 original size:18 final size:17
Alignment explanation
Indices: 2025094--2025127 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2025084 ATATGAAATC
*
2025094 AAATAAAATAACAATAA
1 AAATAAAATAAAAATAA
2025111 AAATAACAATAAAAATA
1 AAATAA-AATAAAAATA
2025128 TTTCTATAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATAAAATAAAAATAA
Found at i:2027082 original size:39 final size:37
Alignment explanation
Indices: 2027009--2027082 Score: 94
Period size: 39 Copynumber: 1.9 Consensus size: 37
2026999 TGGTTATCTA
*
2027009 GGGGTGACACAGCTCTACGCGATGAGGAGATCTGGTC
1 GGGGTGACACAGCTCTACGCGATGAAGAGATCTGGTC
* * *
2027046 GGGGATGACACGGCTCATACGTGATGAAGAGTTCTGG
1 GGGG-TGACACAGCTC-TACGCGATGAAGAGATCTGG
2027083 CCATCTTTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 4 0.13
38 10 0.32
39 17 0.55
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.20
Consensus pattern (37 bp):
GGGGTGACACAGCTCTACGCGATGAAGAGATCTGGTC
Found at i:2027132 original size:129 final size:128
Alignment explanation
Indices: 2026850--2027212 Score: 431
Period size: 129 Copynumber: 2.8 Consensus size: 128
2026840 GACGACATGC
* ** * *
2026850 TCATACGTGATGAAGAGTTCGGGTCGTCTA-GGGTGACACGGTTCTACGTGATGAGGAAATCTGG
1 TCATACGTGATGAGGAGTT--GGTTATCTAGGGGTGACAC-GCTCTACGTGATGAGGAGATCTGG
*
2026914 TCGAGGGATGACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGTGATAACTC
63 TCG-GGGATGACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGCGATAAC-C
*
2026979 GGT
126 AGT
* *
2026982 TC-TAC-TGA-GAGGACGGCTGGTTATCTAGGGGTGACACAGCTCTACGCGATGAGGAGATCTGG
1 TCATACGTGATGAGGA--GTTGGTTATCTAGGGGTGACAC-GCTCTACGTGATGAGGAGATCTGG
*
2027044 TCGGGGATGACACGGCTCATACGTGATGAAGAGTTC-TGGCCATCTTTAGGAAGGGCGATAA-CA
63 TCGGGGATGACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAA-GGCGATAACCA
2027107 GT
127 GT
**
2027109 TCATACGTGATGAGGATGTTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTAA
1 TCATACGTGATGAGGA-GTTGGTTATCTAGGGGTGACACG-CT-CTACGTGATGAGGAGATCTGG
2027174 TCAGGGGATGACA-TG--C-TACGTGATGAAGAGTTCTTGGCC
63 TC-GGGGATGACACTGCTCATACGTGATGAAGAGTTCTTGGCC
2027213 TTTTATAGCG
Statistics
Matches: 203, Mismatches: 17, Indels: 26
0.83 0.07 0.11
Matches are distributed among these distances:
127 22 0.11
128 26 0.13
129 76 0.37
130 62 0.31
131 15 0.07
132 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.26
Consensus pattern (128 bp):
TCATACGTGATGAGGAGTTGGTTATCTAGGGGTGACACGCTCTACGTGATGAGGAGATCTGGTCG
GGGATGACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGCGATAACCAGT
Found at i:2028235 original size:19 final size:19
Alignment explanation
Indices: 2028199--2028234 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2028189 TCCTATTTAT
2028199 TTTTTTTTTTTTCATTTTC
1 TTTTTTTTTTTTCATTTTC
2028218 TTTTTTTTTTTTC-TTTT
1 TTTTTTTTTTTTCATTTT
2028235 TTTCCATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (19 bp):
TTTTTTTTTTTTCATTTTC
Found at i:2028237 original size:13 final size:13
Alignment explanation
Indices: 2028198--2028237 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
2028188 ATCCTATTTA
2028198 TTTTTTT-TTTTT
1 TTTTTTTCTTTTT
**
2028210 TCATTTTCTTTTT
1 TTTTTTTCTTTTT
2028223 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
2028236 TT
1 TT
2028238 CCATCATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTTCTTTTT
Found at i:2031749 original size:20 final size:20
Alignment explanation
Indices: 2031712--2031750 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2031702 CCAAGAGAAT
*
2031712 AATATCAATAAAGAATAAAG
1 AATATCAAGAAAGAATAAAG
2031732 AATACTCAAGAAAG-ATAAA
1 AATA-TCAAGAAAGAATAAA
2031751 ATACTGCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.64, C:0.08, G:0.10, T:0.18
Consensus pattern (20 bp):
AATATCAAGAAAGAATAAAG
Found at i:2045490 original size:20 final size:17
Alignment explanation
Indices: 2045449--2045492 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
2045439 GTTTTTTTGT
*
2045449 ATTTTTAAAGAAATTTA
1 ATTTTTAAACAAATTTA
2045466 ATTTTTAAACATAATATTAA
1 ATTTTTAAACA-AAT-TT-A
2045486 ATTTTTA
1 ATTTTTA
2045493 TTTAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.43
18 3 0.13
19 2 0.09
20 8 0.35
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
ATTTTTAAACAAATTTA
Found at i:2046092 original size:61 final size:60
Alignment explanation
Indices: 2045997--2046115 Score: 220
Period size: 61 Copynumber: 2.0 Consensus size: 60
2045987 AAACTTCAAA
*
2045997 ATTGTCGATTTTTTATTTGATTTCATGAGATTTAAAAGAGTTTTGAGAAAATCTAACTAAT
1 ATTGTCGATTTTATATTTGATTTCATGAGATTTAAAAGAGTTTTGAG-AAATCTAACTAAT
2046058 ATTGTCGATTTTATATTTGATTTCATGAGATTTAAAAGAGTTTTGAGAAATCTAACTA
1 ATTGTCGATTTTATATTTGATTTCATGAGATTTAAAAGAGTTTTGAGAAATCTAACTA
2046116 TAGTGATAGG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
60 11 0.19
61 46 0.81
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (60 bp):
ATTGTCGATTTTATATTTGATTTCATGAGATTTAAAAGAGTTTTGAGAAATCTAACTAAT
Found at i:2050205 original size:27 final size:27
Alignment explanation
Indices: 2050137--2050213 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
2050127 AACTTATCTG
*
2050137 CTTATGACTTCTATCGGTGCTAG---T
1 CTTATGACTTCTATCTGTGCTAGTCTT
2050161 CTTATGAC-TCTATCTGTGCTAGTCTT
1 CTTATGACTTCTATCTGTGCTAGTCTT
2050187 CTTATGACTTCTATCTGTGCTAGTCTT
1 CTTATGACTTCTATCTGTGCTAGTCTT
2050214 ACTTTCATCT
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
23 13 0.27
24 8 0.17
26 9 0.19
27 18 0.38
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (27 bp):
CTTATGACTTCTATCTGTGCTAGTCTT
Found at i:2055687 original size:14 final size:15
Alignment explanation
Indices: 2055661--2055698 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2055651 ATATTTTAAT
2055661 TTAAAAATATAAATA
1 TTAAAAATATAAATA
2055676 TTAAAAAT-TAAATA
1 TTAAAAATATAAATA
*
2055690 -CAAAAATAT
1 TTAAAAATAT
2055699 TATTATTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 6 0.29
14 7 0.33
15 8 0.38
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAAAATATAAATA
Found at i:2055749 original size:21 final size:20
Alignment explanation
Indices: 2055725--2055778 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
2055715 TATTAAATAA
2055725 AAAACAATTA-TATTTAATTTT
1 AAAAC-ATTATTATTT-ATTTT
2055746 AAAACATTATTATTTATTTT
1 AAAACATTATTATTTATTTT
*
2055766 ACAA-ATT-TTATTT
1 AAAACATTATTATTT
2055779 CCAGGCTGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 6 0.19
19 3 0.10
20 12 0.39
21 10 0.32
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.52
Consensus pattern (20 bp):
AAAACATTATTATTTATTTT
Found at i:2055754 original size:20 final size:21
Alignment explanation
Indices: 2055725--2055766 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
2055715 TATTAAATAA
2055725 AAAACAATTA-TATTTAATTTT
1 AAAACAATTATTATTT-ATTTT
2055746 AAAAC-ATTATTATTTATTTT
1 AAAACAATTATTATTTATTTT
2055766 A
1 A
2055767 CAAATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
AAAACAATTATTATTTATTTT
Found at i:2066718 original size:32 final size:32
Alignment explanation
Indices: 2066645--2066849 Score: 173
Period size: 32 Copynumber: 6.2 Consensus size: 32
2066635 GATTACAACT
*
2066645 TAAAACAAGTTCTAACCTAAAATA---GTATC
1 TAAAACAAGTTCCAACCTAAAATATGGGTATC
* *
2066674 CAAAAGCAAGTTCCAACTTAAAATATGGGTATC
1 TAAAA-CAAGTTCCAACCTAAAATATGGGTATC
* * * *
2066707 TAAAACAAGTTCTAACCTACAATATGGTTGCAACC
1 TAAAACAAGTTCCAACCTAAAATATGG--G-TATC
*
2066742 TAAAATCAAGTTCCAACTTAAAATATGGGTATC
1 TAAAA-CAAGTTCCAACCTAAAATATGGGTATC
* * * *
2066775 TAAAATAAGTTTCAACCTAAAATATGGTTGCAACC
1 TAAAACAAGTTCCAACCTAAAATATGG--G-TATC
* * *
2066810 TAAAAACAAGTTCCAACTTAAAATACGAGTATC
1 T-AAAACAAGTTCCAACCTAAAATATGGGTATC
2066843 TAAAACA
1 TAAAACA
2066850 TTCACCTTAA
Statistics
Matches: 138, Mismatches: 26, Indels: 21
0.75 0.14 0.11
Matches are distributed among these distances:
29 4 0.03
30 17 0.12
32 44 0.32
33 19 0.14
34 4 0.03
35 10 0.07
36 40 0.29
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (32 bp):
TAAAACAAGTTCCAACCTAAAATATGGGTATC
Found at i:2066754 original size:36 final size:36
Alignment explanation
Indices: 2066623--2066834 Score: 141
Period size: 32 Copynumber: 6.3 Consensus size: 36
2066613 TTTGATTTTC
* * * *
2066623 AACCTAAAATACGATTACAACTTAAAA-CAAGTTCT
1 AACCTAAAATATGGTTGCAACCTAAAATCAAGTTCT
* * *
2066658 AACCTAAAATA--G-T--ATCC-AAAAGCAAGTTCC
1 AACCTAAAATATGGTTGCAACCTAAAATCAAGTTCT
* * *
2066688 AACTTAAAATATGG--G-TATCTAAAA-CAAGTTCT
1 AACCTAAAATATGGTTGCAACCTAAAATCAAGTTCT
* *
2066720 AACCTACAATATGGTTGCAACCTAAAATCAAGTTCC
1 AACCTAAAATATGGTTGCAACCTAAAATCAAGTTCT
* * *
2066756 AACTTAAAATATGG--G-TATCTAAAAT-AAGTT-T
1 AACCTAAAATATGGTTGCAACCTAAAATCAAGTTCT
* *
2066787 CAACCTAAAATATGGTTGCAACCTAAAAACAAGTTCC
1 -AACCTAAAATATGGTTGCAACCTAAAATCAAGTTCT
*
2066824 AACTTAAAATA
1 AACCTAAAATA
2066835 CGAGTATCTA
Statistics
Matches: 137, Mismatches: 25, Indels: 29
0.72 0.13 0.15
Matches are distributed among these distances:
29 4 0.03
30 19 0.14
32 40 0.29
33 12 0.09
34 3 0.02
35 25 0.18
36 34 0.25
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.26
Consensus pattern (36 bp):
AACCTAAAATATGGTTGCAACCTAAAATCAAGTTCT
Found at i:2066758 original size:18 final size:17
Alignment explanation
Indices: 2066706--2066834 Score: 66
Period size: 18 Copynumber: 7.5 Consensus size: 17
2066696 ATATGGGTAT
* *
2066706 CTAAAACAAGTTCTAAC
1 CTAAAATAAGTTCCAAC
* * *
2066723 CTACAATATGGTTGCAAC
1 CTAAAATA-AGTTCCAAC
2066741 CTAAAATCAAGTTCCAAC
1 CTAAAAT-AAGTTCCAAC
* * * *
2066759 TTAAAATATGGGT---AT
1 CTAAAATA-AGTTCCAAC
*
2066774 CTAAAATAAGTTTCAAC
1 CTAAAATAAGTTCCAAC
* *
2066791 CTAAAATATGGTTGCAAC
1 CTAAAATA-AGTTCCAAC
*
2066809 CTAAAAACAAGTTCCAAC
1 CT-AAAATAAGTTCCAAC
*
2066827 TTAAAATA
1 CTAAAATA
2066835 CGAGTATCTA
Statistics
Matches: 81, Mismatches: 23, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
14 2 0.02
15 8 0.10
17 21 0.26
18 44 0.54
19 6 0.07
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (17 bp):
CTAAAATAAGTTCCAAC
Found at i:2066792 original size:68 final size:68
Alignment explanation
Indices: 2066675--2066849 Score: 280
Period size: 68 Copynumber: 2.6 Consensus size: 68
2066665 AATAGTATCC
* *
2066675 AAAAGCAAGTTCCAACTTAAAATATGGGTATCTAAAACAAGTTCTAACCTACAATATGGTTGCAA
1 AAAAACAAGTTCCAACTTAAAATATGGGTATCTAAAACAAGTTCTAACCTAAAATATGGTTGCAA
2066740 CCT
66 CCT
* *
2066743 AAAATCAAGTTCCAACTTAAAATATGGGTATCTAAAATAAGTT-TCAACCTAAAATATGGTTGCA
1 AAAAACAAGTTCCAACTTAAAATATGGGTATCTAAAACAAGTTCT-AACCTAAAATATGGTTGCA
2066807 ACCT
65 ACCT
* *
2066811 AAAAACAAGTTCCAACTTAAAATACGAGTATCTAAAACA
1 AAAAACAAGTTCCAACTTAAAATATGGGTATCTAAAACA
2066850 TTCACCTTAA
Statistics
Matches: 99, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
67 1 0.01
68 98 0.99
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (68 bp):
AAAAACAAGTTCCAACTTAAAATATGGGTATCTAAAACAAGTTCTAACCTAAAATATGGTTGCAA
CCT
Found at i:2067578 original size:30 final size:28
Alignment explanation
Indices: 2067523--2067578 Score: 67
Period size: 30 Copynumber: 1.9 Consensus size: 28
2067513 TTAATTTAAT
*
2067523 TACCAAAAGTATTTTTTGATTAAAATCG
1 TACCAAAAGTATTTTTTGATCAAAATCG
* *
2067551 TACCTAAAATTATCTTTTTGGTCAAAAT
1 TACC-AAAAGTAT-TTTTTGATCAAAAT
2067579 AAGTACTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 4 0.17
29 7 0.30
30 12 0.52
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (28 bp):
TACCAAAAGTATTTTTTGATCAAAATCG
Found at i:2072317 original size:31 final size:31
Alignment explanation
Indices: 2072279--2072401 Score: 129
Period size: 31 Copynumber: 4.0 Consensus size: 31
2072269 ACATGGTCTC
**
2072279 TAATGTTATCGATTTGTTCGATTATAGTCCA
1 TAATGTTATCGATCCGTTCGATTATAGTCCA
* * * *
2072310 TAATGTTATTGATCTGTTCGATTATAATACA
1 TAATGTTATCGATCCGTTCGATTATAGTCCA
* * *
2072341 TAATGTTATCGATCCGTTTGATTATGGTCCT
1 TAATGTTATCGATCCGTTCGATTATAGTCCA
* * * *
2072372 TAATATTATCGATTCATTCGATTTTAGTCC
1 TAATGTTATCGATCCGTTCGATTATAGTCC
2072402 CTCAGTTGTT
Statistics
Matches: 75, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.46
Consensus pattern (31 bp):
TAATGTTATCGATCCGTTCGATTATAGTCCA
Found at i:2074358 original size:20 final size:20
Alignment explanation
Indices: 2074333--2074374 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2074323 CTAAGAGCCT
*
2074333 ATTTAGGACCATTTAGATGC
1 ATTTAGGACCATATAGATGC
* *
2074353 ATTTAGGAGCATATAGTTGC
1 ATTTAGGACCATATAGATGC
2074373 AT
1 AT
2074375 GTGGTGGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (20 bp):
ATTTAGGACCATATAGATGC
Found at i:2075328 original size:112 final size:112
Alignment explanation
Indices: 2075131--2075354 Score: 439
Period size: 112 Copynumber: 2.0 Consensus size: 112
2075121 TTGTAAGGAA
*
2075131 CGAATGAATCTTGCTTTGTGCTTGTTGATTTTGAGCCCCACCATGAACTAATCCTATTTGGTGGG
1 CGAATGAATCTTGCTTTGTGCTTGTTGATTTCGAGCCCCACCATGAACTAATCCTATTTGGTGGG
2075196 AGTTCGCATGGTTATTTAAGTTGTTATTTTAATGAATGGTTGTTGTT
66 AGTTCGCATGGTTATTTAAGTTGTTATTTTAATGAATGGTTGTTGTT
2075243 CGAATGAATCTTGCTTTGTGCTTGTTGATTTCGAGCCCCACCATGAACTAATCCTATTTGGTGGG
1 CGAATGAATCTTGCTTTGTGCTTGTTGATTTCGAGCCCCACCATGAACTAATCCTATTTGGTGGG
2075308 AGTTCGCATGGTTATTTAAGTTGTTATTTTAATGAATGGTTGTTGTT
66 AGTTCGCATGGTTATTTAAGTTGTTATTTTAATGAATGGTTGTTGTT
2075355 TCATGCTCTA
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 111 1.00
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (112 bp):
CGAATGAATCTTGCTTTGTGCTTGTTGATTTCGAGCCCCACCATGAACTAATCCTATTTGGTGGG
AGTTCGCATGGTTATTTAAGTTGTTATTTTAATGAATGGTTGTTGTT
Found at i:2077068 original size:18 final size:18
Alignment explanation
Indices: 2077033--2077068 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2077023 AAAATGGGTA
* *
2077033 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
2077051 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
2077069 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:2078271 original size:22 final size:18
Alignment explanation
Indices: 2078229--2078298 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 18
2078219 TTAAGGAGTA
*
2078229 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
2078247 GTCCTACGGGACATATACAGTG
1 GTCCTACGGGAC--AT--AGTG
*
2078269 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
2078287 GTCCTACGGGAC
1 GTCCTACGGGAC
2078299 GAATACTGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 26 0.58
20 4 0.09
22 15 0.33
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.24
Consensus pattern (18 bp):
GTCCTACGGGACATAGTG
Found at i:2087389 original size:20 final size:20
Alignment explanation
Indices: 2087364--2087406 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2087354 TCTAAGATCC
*
2087364 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
2087384 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
2087404 CAT
1 CAT
2087407 GTGGTGGATT
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:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:2088202 original size:70 final size:70
Alignment explanation
Indices: 2088089--2088230 Score: 266
Period size: 70 Copynumber: 2.0 Consensus size: 70
2088079 GAAGGCATTT
2088089 GGCAGTGCACGTCAAAGGCTTTCTCTCCTCCCCTTAGACCTTGCTTTTATATTTTGTTGTTGGGT
1 GGCAGTGCACGTCAAAGGCTTTCTCTCCTCCCCTTAGACCTTGCTTTTATATTTTGTTGTTGGGT
2088154 TGTAA
66 TGTAA
* *
2088159 GGCAGTGCACGTCGAAGGCTTTCTCTCCTCCCCTTAGTCCTTGCTTTTATATTTTGTTGTTGGGT
1 GGCAGTGCACGTCAAAGGCTTTCTCTCCTCCCCTTAGACCTTGCTTTTATATTTTGTTGTTGGGT
2088224 TGTAA
66 TGTAA
2088229 GG
1 GG
2088231 AGCGAATGAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.40
Consensus pattern (70 bp):
GGCAGTGCACGTCAAAGGCTTTCTCTCCTCCCCTTAGACCTTGCTTTTATATTTTGTTGTTGGGT
TGTAA
Found at i:2092187 original size:2 final size:2
Alignment explanation
Indices: 2092180--2092240 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
2092170 GCCCACACTC
2092180 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2092222 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
2092241 AGAACCCGAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2095163 original size:21 final size:21
Alignment explanation
Indices: 2095137--2095184 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2095127 GCAGATCTAC
2095137 GCGCGTTAAGCCGATTACTTG
1 GCGCGTTAAGCCGATTACTTG
*
2095158 GCGCGTTAAGCCGATTACTTT
1 GCGCGTTAAGCCGATTACTTG
2095179 GCGCGT
1 GCGCGT
2095185 AACCGGTCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (21 bp):
GCGCGTTAAGCCGATTACTTG
Found at i:2097756 original size:2 final size:2
Alignment explanation
Indices: 2097749--2097792 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
2097739 TCATTAAATG
*
2097749 TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2097790 TA T
1 TA T
2097793 TGAGAGGGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2108467 original size:19 final size:19
Alignment explanation
Indices: 2108443--2108482 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2108433 AAAAGTAGTC
2108443 AATATCACAGTTTACTATA
1 AATATCACAGTTTACTATA
2108462 AATATCACAGTTTACTATA
1 AATATCACAGTTTACTATA
2108481 AA
1 AA
2108483 AATTAAAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (19 bp):
AATATCACAGTTTACTATA
Found at i:2109732 original size:2 final size:2
Alignment explanation
Indices: 2109725--2109770 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
2109715 TTTTGAAGAA
*
2109725 AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2109766 AT AT A
1 AT AT A
2109771 GTTAATACAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2111122 original size:20 final size:20
Alignment explanation
Indices: 2111097--2111310 Score: 137
Period size: 20 Copynumber: 10.6 Consensus size: 20
2111087 TTCCTAATAT
2111097 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
* *
2111117 GCAATGCGAATTAGGAAAATC
1 GCAATGCGAA-TACGTAAATC
*
2111138 GCAATGC-AATTACGT-ATTC
1 GCAATGCGAA-TACGTAAATC
* * * * * *
2111157 GCATTGCGATTTTCCTAATTT
1 GCAATGCGA-ATACGTAAATC
* * *
2111178 GCATTGCGATTTACGT-ATTC
1 GCAATGCGA-ATACGTAAATC
** * * * *
2111198 GCGTTGCGATTTTCCTAATTC
1 GCAATGCGA-ATACGTAAATC
2111219 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
* * *
2111239 GCAACGCGATTACCTAAATC
1 GCAATGCGAATACGTAAATC
* *
2111259 GCAATGCGAATTAAGAAAATC
1 GCAATGCGAA-TACGTAAATC
*
2111280 GCAATGCGAATACGTAAATA
1 GCAATGCGAATACGTAAATC
2111300 GCAATGCGAAT
1 GCAATGCGAAT
2111311 CTGACTATCG
Statistics
Matches: 155, Mismatches: 33, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
19 9 0.06
20 86 0.55
21 60 0.39
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (20 bp):
GCAATGCGAATACGTAAATC
Found at i:2111125 original size:41 final size:42
Alignment explanation
Indices: 2111080--2111288 Score: 175
Period size: 41 Copynumber: 5.1 Consensus size: 42
2111070 AAATTCGCGT
2111080 TGCGATTTTCCTAATAT-GCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATATCGCAATGCGAATACGTAAATCGCAA
* *** * * *
2111121 TGCGA-ATTAGGAAAATCGCAATGC-AATTACGT-ATTCGCAT
1 TGCGATTTTCCTAATATCGCAATGCGAA-TACGTAAATCGCAA
* * * * **
2111161 TGCGATTTTCCTAAT-TTGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATATCGCAATGCGA-ATACGTAAATCGCAA
2111202 TGCGATTTTCCTAAT-TCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATATCGCAATGCGAATACGTAAATCGCAA
* * * *
2111243 CGCGA-TTACCTAA-ATCGCAATGCGAATTAAGAAAATCGCAA
1 TGCGATTTTCCTAATATCGCAATGCGAA-TACGTAAATCGCAA
2111284 TGCGA
1 TGCGA
2111289 ATACGTAAAT
Statistics
Matches: 133, Mismatches: 27, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
40 50 0.38
41 83 0.62
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (42 bp):
TGCGATTTTCCTAATATCGCAATGCGAATACGTAAATCGCAA
Found at i:2111298 original size:41 final size:41
Alignment explanation
Indices: 2111211--2111310 Score: 130
Period size: 41 Copynumber: 2.5 Consensus size: 41
2111201 TTGCGATTTT
* * * *
2111211 CCTAATTCGCAATGCGAA-TACGTAAATCGCAACGCGATTA
1 CCTAAATCGCAATGCGAATTAAGAAAATCGCAACGCGAATA
*
2111251 CCTAAATCGCAATGCGAATTAAGAAAATCGCAATGCGAATA
1 CCTAAATCGCAATGCGAATTAAGAAAATCGCAACGCGAATA
* *
2111292 CGTAAATAGCAATGCGAAT
1 CCTAAATCGCAATGCGAAT
2111311 CTGACTATCG
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
40 17 0.33
41 35 0.67
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (41 bp):
CCTAAATCGCAATGCGAATTAAGAAAATCGCAACGCGAATA
Found at i:2111911 original size:21 final size:21
Alignment explanation
Indices: 2111851--2111928 Score: 83
Period size: 20 Copynumber: 3.8 Consensus size: 21
2111841 TTCTAAACTT
2111851 AAATCGCAAC-ATGA-AAATGA
1 AAATCGCAACGA-GAGAAATGA
2111871 AAATCGCAAC-ACGA-AAATGA
1 AAATCGCAACGA-GAGAAATGA
** *
2111891 CTATCGCAATGAGAGAAATGA
1 AAATCGCAACGAGAGAAATGA
2111912 AAATCGCAACGAGAGAA
1 AAATCGCAACGAGAGAA
2111929 TCGCAACGCG
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 28 0.57
21 21 0.43
ACGTcount: A:0.51, C:0.17, G:0.19, T:0.13
Consensus pattern (21 bp):
AAATCGCAACGAGAGAAATGA
Found at i:2111932 original size:14 final size:14
Alignment explanation
Indices: 2111910--2111974 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
2111900 TGAGAGAAAT
2111910 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
2111924 GAGAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
2111942 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
2111957 GATAATCGCAACGC
1 GAAAATCGCAACGA
2111971 GAAA
1 GAAA
2111975 CCAAAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 25 0.61
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.24
ACGTcount: A:0.46, C:0.22, G:0.23, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:2111944 original size:33 final size:33
Alignment explanation
Indices: 2111905--2111985 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
2111895 CGCAATGAGA
2111905 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
2111938 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
2111971 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
2111986 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2112055 original size:14 final size:14
Alignment explanation
Indices: 2112003--2112059 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2111993 TTTCATTTCG
2112003 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
2112017 CGTTACGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2112036 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2112050 CGTTGCGATT
1 CGTTGCGATT
2112060 TTTCATTTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2112068 original size:34 final size:33
Alignment explanation
Indices: 2111989--2112113 Score: 196
Period size: 34 Copynumber: 3.7 Consensus size: 33
2111979 AATCGCATTG
2111989 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTA
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTA
*
2112022 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTA
2112055 CGATTTTTCATTTCGCGTTGCGATTCTCTCGTTA
1 CGA-TTTTCATTTCGCGTTGCGATTCTCTCGTTA
** *
2112089 CGATAGTCATTTACACGTTGCGATT
1 CGATTTTCATTT-CGCGTTGCGATT
2112114 TTCATTCTCT
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
33 42 0.49
34 43 0.51
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (33 bp):
CGATTTTCATTTCGCGTTGCGATTCTCTCGTTA
Found at i:2112099 original size:67 final size:67
Alignment explanation
Indices: 2111986--2112141 Score: 215
Period size: 67 Copynumber: 2.2 Consensus size: 67
2111976 CAAAATCGCA
** *
2111986 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTACGATTTTCATTT-CGCGTTGCGATTCTCT
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTACGATAGTCATTTACACGTTGCGATTCTCT
2112050 CG
66 CG
2112052 TTGCGATTTTTCATTTCGCGTTGCGATTCTCTCGTTACGATAGTCATTTACACGTTGCGATTTTC
1 TTGCGA-TTTTCATTTCGCGTTGCGATTCTCTCGTTACGATAGTCATTTACACGTTGCG------
2112117 ATTCTCTCG
59 ATTCTCTCG
2112126 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2112142 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
66 6 0.08
67 40 0.51
68 8 0.10
73 10 0.13
74 15 0.19
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (67 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTACGATAGTCATTTACACGTTGCGATTCTCT
CG
Found at i:2112118 original size:20 final size:19
Alignment explanation
Indices: 2111986--2112142 Score: 83
Period size: 20 Copynumber: 8.9 Consensus size: 19
2111976 CAAAATCGCA
*
2111986 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCACG
*
2112005 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCACG
* *
2112019 TTACGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCACG
*
2112038 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCACG
*
2112052 TTGCGATTTTTCATTTCGCG
1 TTGCGA-TTTTCATTTCACG
*
2112072 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCACG
* **
2112086 TTACGATAGTCATTTACACG
1 TTGCGATTTTCATTT-CACG
*
2112106 TTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATT-TCACG
2112126 TTGCGATTTTCATTTCA
1 TTGCGATTTTCATTTCA
2112143 ACCAAAAGAC
Statistics
Matches: 105, Mismatches: 15, Indels: 36
0.67 0.10 0.23
Matches are distributed among these distances:
14 28 0.27
16 5 0.05
17 12 0.11
19 18 0.17
20 41 0.39
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCACG
Found at i:2114090 original size:94 final size:94
Alignment explanation
Indices: 2113805--2114173 Score: 556
Period size: 94 Copynumber: 4.0 Consensus size: 94
2113795 TAGATTGCTT
* * *
2113805 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTCAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2113866 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
2113895 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGT---GTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
2113957 ATTTGTCTTTGTTTTGTCTTTTGGATGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
2113986 AGTAAATTTGTTCGGTTACTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2114051 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
2114080 AGTAAATTTGTTCGTTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
2114145 ATTTATCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2114174 GTATGCAATC
Statistics
Matches: 257, Mismatches: 14, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
90 53 0.21
91 67 0.26
92 3 0.01
93 2 0.01
94 132 0.51
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2114113 original size:185 final size:184
Alignment explanation
Indices: 2113805--2114173 Score: 548
Period size: 185 Copynumber: 2.0 Consensus size: 184
2113795 TAGATTGCTT
*
2113805 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTCAAGTTAGTATTT
1 AGTAAATTTATTCGGTTACTGCCAATACTGCTAAACTGTTTATTAACACTGTCAAGTTAGTATTT
* *
2113870 GTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAATTGTG
66 GTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTACCAATTCTGCTAAACTGTG
* *
2113935 TATTCTTT-A-ACACTG-TGTTAGTATTTGTCTTTGTTTTGTCTTTTGGATGAA
131 TATTCTTTAATACACTGAAGTTAGTATTTATCTTTGTTTTGTCTTTTGGATGAA
* * * *
2113986 AGTAAATTTGTTCGGTTACTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTACTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTCAAGTTAGT
* *
2114051 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGTTTGCTACCAATTCTGCTAAA
62 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-AAGTAAATTTATTCGGTTGCTACCAATTCTGCTAAA
* *
2114115 CTGTGTATTCTTTAATACTCTGAAGTTAGTATTTATCTTTGTTTTGTCTTTTGGTTGAA
126 CTGTGTATTCTTTAATACACTGAAGTTAGTATTTATCTTTGTTTTGTCTTTTGGATGAA
2114174 GTATGCAATC
Statistics
Matches: 167, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
181 33 0.20
183 3 0.02
184 22 0.13
185 70 0.42
186 1 0.01
187 5 0.03
188 33 0.20
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.48
Consensus pattern (184 bp):
AGTAAATTTATTCGGTTACTGCCAATACTGCTAAACTGTTTATTAACACTGTCAAGTTAGTATTT
GTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTACCAATTCTGCTAAACTGTG
TATTCTTTAATACACTGAAGTTAGTATTTATCTTTGTTTTGTCTTTTGGATGAA
Found at i:2114294 original size:20 final size:19
Alignment explanation
Indices: 2114267--2114343 Score: 118
Period size: 19 Copynumber: 4.0 Consensus size: 19
2114257 TCTTTTGGTT
2114267 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
2114286 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGA
* *
2114306 GAAACGAAAATCGCAACGT
1 GAAATGAAAATCGCAACGA
2114325 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
2114344 CAAAATCGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
19 34 0.65
20 18 0.35
ACGTcount: A:0.49, C:0.18, G:0.22, T:0.10
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:2114368 original size:20 final size:19
Alignment explanation
Indices: 2114267--2114382 Score: 125
Period size: 20 Copynumber: 6.3 Consensus size: 19
2114257 TCTTTTGGTT
* *
2114267 GAAATGAAAATCGCAACGA
1 GAAACGAAAATCGCAACGC
*
2114286 GAGAATGAAAATCGCAACGC
1 GA-AACGAAAATCGCAACGC
*
2114306 GAAACGAAAATCGCAACGT
1 GAAACGAAAATCGCAACGC
*
2114325 GAAATGAAAATCGCAA--C
1 GAAACGAAAATCGCAACGC
2114342 G--AC-AAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
*
2114358 GAAACCAAAAATCGCAACGC
1 GAAA-CGAAAATCGCAACGC
2114378 GAAAC
1 GAAAC
2114383 TATAATCGCG
Statistics
Matches: 84, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 1 0.01
18 1 0.01
19 34 0.40
20 35 0.42
ACGTcount: A:0.49, C:0.22, G:0.20, T:0.09
Consensus pattern (19 bp):
GAAACGAAAATCGCAACGC
Found at i:2114391 original size:19 final size:19
Alignment explanation
Indices: 2114273--2114391 Score: 108
Period size: 19 Copynumber: 6.4 Consensus size: 19
2114263 GGTTGAAATG
*
2114273 AAAATCGCAACGAGAGAA-T
1 AAAATCGCAACGCGA-AACT
*
2114292 GAAAATCGCAACGCGAAACG
1 -AAAATCGCAACGCGAAACT
*
2114312 AAAATCGCAACGTGAAA-T
1 AAAATCGCAACGCGAAACT
2114330 GAAAATCGCAA--CG--AC-
1 -AAAATCGCAACGCGAAACT
*
2114345 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAA-CT
2114365 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
*
2114384 ATAATCGC
1 AAAATCGC
2114392 GTTGCGATTT
Statistics
Matches: 83, Mismatches: 7, Indels: 19
0.76 0.06 0.17
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 1 0.01
18 1 0.01
19 37 0.45
20 31 0.37
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACT
Found at i:2114458 original size:17 final size:17
Alignment explanation
Indices: 2114391--2114468 Score: 54
Period size: 17 Copynumber: 4.5 Consensus size: 17
2114381 ACTATAATCG
*
2114391 CGTTGCGATTTTAATTT
1 CGTTGCGATTTTCATTT
*
2114408 CGCATTGCGA--TTC-TCT
1 CG--TTGCGATTTTCATTT
* *
2114424 CGTTGAGATTTTTATTT
1 CGTTGCGATTTTCATTT
*
2114441 CGTTGCGATTTTCGTTT
1 CGTTGCGATTTTCATTT
2114458 CACGTTGCGAT
1 --CGTTGCGAT
2114469 AGTCATTTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
14 5 0.11
16 6 0.13
17 20 0.43
19 15 0.33
ACGTcount: A:0.14, C:0.18, G:0.21, T:0.47
Consensus pattern (17 bp):
CGTTGCGATTTTCATTT
Found at i:2114465 original size:19 final size:20
Alignment explanation
Indices: 2114441--2114496 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
2114431 ATTTTTATTT
2114441 CGTTGCGATTTTC-GTTTCA
1 CGTTGCGATTTTCAGTTTCA
** *
2114460 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATTTTCAGTTTCA
* *
2114480 CGTTTCGATTTTAAGTT
1 CGTTGCGATTTTCAGTT
2114497 ACATATATTC
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTCAGTTTCA
Found at i:2116508 original size:19 final size:19
Alignment explanation
Indices: 2116486--2116603 Score: 85
Period size: 19 Copynumber: 6.7 Consensus size: 19
2116476 CGAAACTAAA
2116486 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2116505 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
2116520 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2116538 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
2116553 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
2116571 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
2116590 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
2116604 AGACATTAAG
Statistics
Matches: 74, Mismatches: 14, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 35 0.47
20 10 0.14
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:2116532 original size:33 final size:33
Alignment explanation
Indices: 2116490--2116583 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
2116480 ACTAAATTCG
*
2116490 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
2116523 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
2116556 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2116584 AGTCATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:2116602 original size:20 final size:19
Alignment explanation
Indices: 2116556--2116610 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
2116546 GCGATTCTCT
**
2116556 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
2116575 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
2116595 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
2116611 AAGATGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:2119118 original size:24 final size:24
Alignment explanation
Indices: 2119084--2119137 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2119074 CTGAAAAATC
*
2119084 ATCAAAATCCGAGTATTGTCCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2119108 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2119132 ATCAAA
1 ATCAAA
2119138 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2124895 original size:14 final size:14
Alignment explanation
Indices: 2124878--2124909 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2124868 GATCGGTTAT
*
2124878 GTTTGTTTATGTTC
1 GTTTGATTATGTTC
2124892 GTTTGATTATGTTC
1 GTTTGATTATGTTC
2124906 GTTT
1 GTTT
2124910 ATGTTCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.06, G:0.22, T:0.62
Consensus pattern (14 bp):
GTTTGATTATGTTC
Found at i:2124925 original size:24 final size:24
Alignment explanation
Indices: 2124874--2124928 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
2124864 GTTTGATCGG
* * *
2124874 TTATGTTTGTTTATGTTCGTTTGA
1 TTATGTTCGTTTATGTTCGATTCA
2124898 TTATGTTCGTTTATGTTC-ATTCA
1 TTATGTTCGTTTATGTTCGATTCA
2124921 TTTATGTT
1 -TTATGTT
2124929 TAACTCAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.15, C:0.07, G:0.16, T:0.62
Consensus pattern (24 bp):
TTATGTTCGTTTATGTTCGATTCA
Found at i:2125668 original size:10 final size:10
Alignment explanation
Indices: 2125653--2125727 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
2125643 GGGTCTCCAA
2125653 CGTTTATGTT
1 CGTTTATGTT
2125663 CGTTTATGTT
1 CGTTTATGTT
2125673 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
2125684 ATGTTCGTGTT
1 -CGTTTATGTT
2125695 CGTTTATGTT
1 CGTTTATGTT
2125705 CG----TGTT
1 CGTTTATGTT
2125711 CGTTTATGTT
1 CGTTTATGTT
2125721 CGTTTAT
1 CGTTTAT
2125728 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:2125684 original size:16 final size:16
Alignment explanation
Indices: 2125659--2125723 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
2125649 CCAACGTTTA
2125659 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
2125675 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
2125691 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2125707 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2125723 T
1 T
2125724 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2125814 original size:16 final size:16
Alignment explanation
Indices: 2125793--2125825 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2125783 AAAAAAAAAT
2125793 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2125809 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2125825 T
1 T
2125826 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2128872 original size:16 final size:16
Alignment explanation
Indices: 2128851--2128885 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2128841 CTTATTCAGG
*
2128851 AAAAATGATATAATTT
1 AAAAATAATATAATTT
2128867 AAAAATAATATAATTT
1 AAAAATAATATAATTT
2128883 AAA
1 AAA
2128886 TACTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
AAAAATAATATAATTT
Found at i:2132219 original size:23 final size:23
Alignment explanation
Indices: 2132187--2132251 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
2132177 TATATTTTTG
*
2132187 TGACATGTTTATCTCTGTCATTA
1 TGACACGTTTATCTCTGTCATTA
* * *
2132210 TGACACGTTTATTTATGTCTTTA
1 TGACACGTTTATCTCTGTCATTA
* *
2132233 TGAGACGTTTTTCTCTGTC
1 TGACACGTTTATCTCTGTC
2132252 TTTTGGTAGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.17, G:0.15, T:0.49
Consensus pattern (23 bp):
TGACACGTTTATCTCTGTCATTA
Found at i:2136216 original size:2 final size:2
Alignment explanation
Indices: 2136209--2136249 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2136199 TTATTCTTTA
2136209 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2136250 ATTTTTCAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2136447 original size:20 final size:20
Alignment explanation
Indices: 2136424--2136475 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2136414 AACGCGATCC
2136424 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
2136444 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
2136464 CCAAAATCGCAA
1 CCAGAATCGCAA
2136476 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:2136492 original size:21 final size:20
Alignment explanation
Indices: 2136465--2136563 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
2136455 AATCAGTTTC
2136465 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
2136486 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2136507 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2136527 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
2136548 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2136564 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2136592 original size:20 final size:20
Alignment explanation
Indices: 2136530--2136723 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
2136520 CGATTTTCCA
* ** *
2136530 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
2136550 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
2136570 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2136590 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
2136610 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
2136630 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2136650 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
2136670 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
2136690 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
2136711 AAATCGCAACGCG
1 AAATCGCAACGCG
2136724 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:2136614 original size:60 final size:60
Alignment explanation
Indices: 2136530--2136723 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
2136520 CGATTTTCCA
* ** * *
2136530 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
2136590 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
2136650 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
2136711 AAATCGCAACGCG
1 AAATCGCAACGCG
2136724 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:2137143 original size:33 final size:33
Alignment explanation
Indices: 2137104--2137174 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2137094 TTCACTTAGA
2137104 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2137137 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2137170 TTTCA
1 TTTCA
2137175 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2137314 original size:14 final size:14
Alignment explanation
Indices: 2137295--2137349 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2137285 AGAATGACTG
2137295 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
2137309 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
2137328 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
2137342 TCGCAACG
1 TCGCAACG
2137350 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:2137362 original size:33 final size:33
Alignment explanation
Indices: 2137295--2137365 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2137285 AGAATGACTG
***
2137295 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2137328 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2137361 TCGCA
1 TCGCA
2137366 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:2137383 original size:19 final size:19
Alignment explanation
Indices: 2137361--2137425 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
2137351 GAAACCAAAA
*
2137361 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2137380 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2137394 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2137413 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2137426 CTCTCGTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 22 0.58
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2137402 original size:14 final size:14
Alignment explanation
Indices: 2137383--2137472 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
2137373 TTTCATTTCG
2137383 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2137397 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2137416 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2137430 CGTTGCGATTGTCATCTCT
1 CGTTGCGA---T--TCTCT
2137449 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2137463 CGTTGCGATT
1 CGTTGCGATT
2137473 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 33 0.52
16 4 0.06
17 4 0.06
19 23 0.36
ACGTcount: A:0.09, C:0.26, G:0.22, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2137408 original size:33 final size:33
Alignment explanation
Indices: 2137366--2137480 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
2137356 CAAAATCGCA
2137366 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2137399 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* * *
2137432 TTGCGATTGTCATCTCTCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2137465 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2137481 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2139579 original size:93 final size:93
Alignment explanation
Indices: 2139174--2139644 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
2139164 TAGATTGCTT
2139174 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2139239 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2139267 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2139331 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2139358 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2139422 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2139450 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2139515 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2139543 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2139608 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2139636 AGTAAATTT
1 AGTAAATTT
2139645 ATCCATTCAA
Statistics
Matches: 376, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
91 91 0.24
92 91 0.24
93 194 0.52
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2139728 original size:19 final size:19
Alignment explanation
Indices: 2139688--2139815 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
2139678 TAGTTTACTT
* *
2139688 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2139708 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2139727 TCGCAACGCGAAA-TGAAA
1 TCGCAACGCGAAACCAAAA
*
2139745 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
2139759 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2139778 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
2139792 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2139811 TCGCA
1 TCGCA
2139816 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
14 19 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 36 0.41
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2139784 original size:33 final size:32
Alignment explanation
Indices: 2139724--2139815 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
2139714 CGCGAAACCA
**
2139724 AAATCGCAACGCGAAA-TGAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
2139755 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
2139788 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
2139816 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
31 1 0.02
32 16 0.29
33 39 0.70
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:2139833 original size:19 final size:19
Alignment explanation
Indices: 2139811--2139945 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
2139801 GAAACCAAAA
*
2139811 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2139830 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
2139846 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2139863 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2139879 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2139896 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
2139915 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2139935 TCGTGTTGCGA
1 TCGCGTTGCGA
2139946 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2139852 original size:14 final size:14
Alignment explanation
Indices: 2139833--2139889 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2139823 TTTCATTTCG
2139833 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
2139847 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
2139864 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
2139880 CGTTGCGATT
1 CGTTGCGATT
2139890 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2139858 original size:33 final size:33
Alignment explanation
Indices: 2139816--2139908 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2139806 CAAAATCGCA
*
2139816 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
2139849 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
2139882 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2139909 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:2141801 original size:38 final size:38
Alignment explanation
Indices: 2141758--2141830 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
2141748 AATTGATTGT
*
2141758 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
2141796 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
2141831 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:2141817 original size:19 final size:19
Alignment explanation
Indices: 2141753--2141817 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
2141743 AGTTTAATTG
*
2141753 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
2141772 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
2141790 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
2141810 ATTGATTT
1 ATTGATTT
2141818 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:2141831 original size:14 final size:14
Alignment explanation
Indices: 2141812--2141847 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2141802 ATTGTTTAAT
2141812 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2141826 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2141840 TGATTTGT
1 TGATTTGT
2141848 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2142040 original size:20 final size:19
Alignment explanation
Indices: 2141954--2142054 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
2141944 AAAAATGACT
2141954 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
2141972 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2141991 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2142005 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2142024 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2142044 ATCGCAATGCG
1 ATCGCAATGCG
2142055 TTTATAATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 17 0.23
19 23 0.31
20 19 0.26
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2142107 original size:19 final size:19
Alignment explanation
Indices: 2142083--2142389 Score: 358
Period size: 19 Copynumber: 17.4 Consensus size: 19
2142073 GATTATCTCG
2142083 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2142102 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2142121 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
2142135 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2142154 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2142173 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
2142192 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
2142211 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
2142226 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2142244 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2142263 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2142277 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2142296 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2142315 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2142329 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2142349 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2142363 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2142382 TTGCGATT
1 TTGCGATT
2142390 GTATTTTCCG
Statistics
Matches: 249, Mismatches: 13, Indels: 52
0.79 0.04 0.17
Matches are distributed among these distances:
14 32 0.13
15 2 0.01
16 31 0.12
17 28 0.11
18 5 0.02
19 139 0.56
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2142158 original size:71 final size:71
Alignment explanation
Indices: 2142083--2142322 Score: 355
Period size: 71 Copynumber: 3.4 Consensus size: 71
2142073 GATTATCTCG
2142083 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
2142148 TTCGCA
66 TTCGCA
* *
2142154 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
* *
2142217 TT-ATGTCG-G
61 TTCATTTCGCA
*
2142226 TT-CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
2142290 TTCGCA
66 TTCGCA
2142296 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
2142323 CTCTCGTTGC
Statistics
Matches: 150, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
66 6 0.04
68 6 0.04
69 7 0.05
70 2 0.01
71 107 0.71
72 2 0.01
73 7 0.05
74 7 0.05
76 6 0.04
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:2142220 original size:142 final size:137
Alignment explanation
Indices: 2142051--2142389 Score: 513
Period size: 142 Copynumber: 2.4 Consensus size: 137
2142041 AAAATCGCAA
2142051 TGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTT-TAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
*
2142115 TTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
65 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-
*
2142180 TTTCATTTCGTAT
129 -TTC-TCTCG--T
*
2142193 TGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTTTAATTTCGCATTGCGATTATCTC-GTTGCGATTTTCATTTCGCATTGCGATTTTCAT
2142257 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
65 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
2142322 TCTCTCGT
130 TCTCTCGT
* * * *
2142330 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTAATTT-CGCATTGCGATTATC-TCGTTGCGATTTTCATTTCGCATTGCGATT
2142390 GTATTTTCCG
Statistics
Matches: 184, Mismatches: 8, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
137 17 0.09
138 35 0.19
139 5 0.03
140 3 0.02
142 118 0.64
143 6 0.03
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (137 bp):
TGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
CTCTCGT
Found at i:2142328 original size:52 final size:52
Alignment explanation
Indices: 2142083--2142361 Score: 354
Period size: 52 Copynumber: 5.2 Consensus size: 52
2142073 GATTATCTCG
*
2142083 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
2142135 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
2142192 TTGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
2142244 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
2142296 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
2142349 TTGCGATTTTCAT
1 TTGCGATTTTCAT
2142362 GTTGGGATTT
Statistics
Matches: 212, Mismatches: 7, Indels: 15
0.91 0.03 0.06
Matches are distributed among these distances:
51 3 0.01
52 152 0.72
53 19 0.09
54 6 0.03
55 8 0.04
57 24 0.11
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:2144707 original size:12 final size:12
Alignment explanation
Indices: 2144690--2144714 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2144680 TCTTCGGGGA
2144690 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2144702 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2144714 C
1 C
2144715 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2144923 original size:24 final size:24
Alignment explanation
Indices: 2144889--2144935 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2144879 CTGAAACATC
2144889 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2144913 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2144936 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2145636 original size:20 final size:20
Alignment explanation
Indices: 2145608--2145976 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
2145598 AAATTTCAGT
* * * *
2145608 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2145628 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2145648 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2145668 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2145688 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2145708 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2145728 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2145748 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2145768 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2145788 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
2145808 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2145828 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2145848 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
2145868 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
2145888 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2145908 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2145928 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
2145948 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
2145968 GTTGCGATT
1 GTTGCGATT
2145977 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:2147057 original size:17 final size:16
Alignment explanation
Indices: 2147023--2147053 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2147013 TCACACCTTA
2147023 ATAAATTTTTATAAAT
1 ATAAATTTTTATAAAT
2147039 ATAAATTTTTATAAA
1 ATAAATTTTTATAAA
2147054 ATATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAAATTTTTATAAAT
Found at i:2154308 original size:18 final size:18
Alignment explanation
Indices: 2154285--2154332 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
2154275 AGTCACTAAT
*
2154285 TGATCCTAGTTT-GCAACC
1 TGATCCTA-TTTCACAACC
2154303 TGATCCTATTTCACAACC
1 TGATCCTATTTCACAACC
2154321 TGA-CCTTATTTC
1 TGATCC-TATTTC
2154333 TCAATCTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.23, C:0.29, G:0.10, T:0.38
Consensus pattern (18 bp):
TGATCCTATTTCACAACC
Found at i:2156060 original size:16 final size:16
Alignment explanation
Indices: 2156039--2156070 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2156029 ATTATTTACT
*
2156039 TGAATAGTGAATTTTG
1 TGAATAGTGAAATTTG
2156055 TGAATAGTGAAATTTG
1 TGAATAGTGAAATTTG
2156071 GTCGGCGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (16 bp):
TGAATAGTGAAATTTG
Found at i:2158468 original size:65 final size:63
Alignment explanation
Indices: 2158399--2158558 Score: 187
Period size: 65 Copynumber: 2.5 Consensus size: 63
2158389 GAATAAATTG
* * * **
2158399 AACATCGAATGCATTTTATACATCGATGCACATAACATGCATCGATGCACTTAGGGT-TTTATGA
1 AACATCGAATGCATTTTATGCATCGATGCACA-AACATGCATCGATGCAATCAGACTATTT-TG-
2158463 A
63 A
* * * **
2158464 AACATCGAATACACTTGATGCATCGATGCACCAGCCATGCATCGATGCAATCAGACTATTTTGA
1 AACATCGAATGCATTTTATGCATCGATGCA-CAAACATGCATCGATGCAATCAGACTATTTTGA
2158528 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
2158559 TCTTAGTGCA
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 1 0.01
64 28 0.35
65 46 0.57
66 5 0.06
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTTATGCATCGATGCACAAACATGCATCGATGCAATCAGACTATTTTGA
Found at i:2165659 original size:25 final size:24
Alignment explanation
Indices: 2165602--2165678 Score: 84
Period size: 25 Copynumber: 3.1 Consensus size: 24
2165592 AATTTCTATA
*
2165602 TGGTCCTTCGGGACAAATTCTACG
1 TGGTCCTTCGAGACAAATTCTACG
*
2165626 CGGTCCTTCGAGACAAATTCCTACG
1 TGGTCCTTCGAGACAAATT-CTACG
* *
2165651 TGGTACTTCG-GTGCAAAATTCTACG
1 TGGTCCTTCGAG-AC-AAATTCTACG
2165676 TGG
1 TGG
2165679 CACTACGGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
24 18 0.40
25 22 0.49
26 5 0.11
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.29
Consensus pattern (24 bp):
TGGTCCTTCGAGACAAATTCTACG
Found at i:2165687 original size:25 final size:26
Alignment explanation
Indices: 2165640--2165691 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
2165630 CCTTCGAGAC
* *
2165640 AAATTCCTACGTGGTACTTCGGTGCA
1 AAATTCCTACGTGGCACTACGGTGCA
2165666 AAATT-CTACGTGGCACTACGGTGCA
1 AAATTCCTACGTGGCACTACGGTGCA
2165691 A
1 A
2165692 TTTATACGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (26 bp):
AAATTCCTACGTGGCACTACGGTGCA
Found at i:2166489 original size:21 final size:21
Alignment explanation
Indices: 2166463--2166507 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2166453 GATTTCTGGG
* *
2166463 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2166484 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2166505 CAA
1 CAA
2166508 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2168248 original size:23 final size:22
Alignment explanation
Indices: 2168185--2168251 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
2168175 TATGGACATC
*
2168185 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
2168207 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
*
2168229 ATTCTACGGGGAACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
2168252 TTTATACGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
22 28 0.67
23 14 0.33
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:2175516 original size:2 final size:2
Alignment explanation
Indices: 2175459--2175507 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2175449 TTGATTGTTC
2175459 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2175501 AT AT AT A
1 AT AT AT A
2175508 CACATATATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2178395 original size:3 final size:3
Alignment explanation
Indices: 2178387--2178447 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
2178377 CATCTTAATG
2178387 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2178435 TAA TAA TAA TAA T
1 TAA TAA TAA TAA T
2178448 TTTTATTTGC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2178717 original size:19 final size:18
Alignment explanation
Indices: 2178695--2178743 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
2178685 TTTTGTTTTG
2178695 TTTATAATAATTTAATATA
1 TTTATAAT-ATTTAATATA
* *
2178714 TTTATAATTTTTATTATA
1 TTTATAATATTTAATATA
2178732 TTT-TAATGATTT
1 TTTATAAT-ATTT
2178744 TTTGGATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 14 0.54
19 8 0.31
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTATAATATTTAATATA
Found at i:2179950 original size:2 final size:2
Alignment explanation
Indices: 2179945--2179976 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2179935 AAAAAACTTG
2179945 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
2179977 ACATGAGTTG
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:2192405 original size:37 final size:39
Alignment explanation
Indices: 2192338--2192410 Score: 132
Period size: 37 Copynumber: 1.9 Consensus size: 39
2192328 ATGTTAGAAA
2192338 TGATAAATTTAACGAATATATATTTAAATTTATAAAATT
1 TGATAAATTTAACGAATATATATTTAAATTTATAAAATT
2192377 TGATAAATTTAACG-A-ATATATTTAAATTTATAAA
1 TGATAAATTTAACGAATATATATTTAAATTTATAAA
2192411 GTTTTAAGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
37 19 0.56
38 1 0.03
39 14 0.41
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.42
Consensus pattern (39 bp):
TGATAAATTTAACGAATATATATTTAAATTTATAAAATT
Found at i:2197937 original size:3 final size:3
Alignment explanation
Indices: 2197929--2197957 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2197919 CGTAATATTT
2197929 ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2197958 TGTTAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2206133 original size:76 final size:77
Alignment explanation
Indices: 2205975--2206182 Score: 282
Period size: 76 Copynumber: 2.8 Consensus size: 77
2205965 CAAAGCCAAA
* * * **
2205975 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGA-TCCCCCCTAAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
2206039 TTTGGCCCTGAG
66 TTTGGCCCTGAG
*
2206051 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
2206116 TTT-GCTCC-GAG
66 TTTGGC-CCTGAG
* * * *
2206127 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AAG-GGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
2206183 TGTACAACGG
Statistics
Matches: 119, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
74 16 0.13
75 2 0.02
76 83 0.70
77 18 0.15
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCTGAG
Done.