Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008523.1 Hibiscus syriacus cultivar Beakdansim tig00111392_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: 4657139
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 18
Found at i:3957674 original size:20 final size:21
Alignment explanation
Indices: 3957613--3957688 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
3957603 CGCGTTGCGA
3957613 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
3957634 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
3957654 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
3957675 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
3957689 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:3957810 original size:33 final size:33
Alignment explanation
Indices: 3957768--3957838 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
3957758 AATACTAACT
*
3957768 TGAAAATCGCAACGAGAGAATAACAACGCGAAA
1 TGAAAATCGCAACGACAGAATAACAACGCGAAA
***
3957801 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAACAACGCGAAA
3957834 TGAAA
1 TGAAA
3957839 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAACAACGCGAAA
Found at i:3958070 original size:22 final size:22
Alignment explanation
Indices: 3958018--3958072 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3958008 TGGTTGTGAG
**
3958018 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
3958040 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
3958062 GGATTTCTTCG
1 GGATTTCTTCG
3958073 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3958244 original size:20 final size:20
Alignment explanation
Indices: 3958219--3958372 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
3958209 CTTTAAATAT
3958219 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3958239 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3958261 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3958280 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
3958300 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3958320 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3958340 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3958360 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3958373 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3958346 original size:40 final size:40
Alignment explanation
Indices: 3958218--3958372 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
3958208 GCTTTAAATA
*
3958218 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
3958259 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
3958299 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
3958339 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
3958373 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:3958389 original size:21 final size:21
Alignment explanation
Indices: 3958359--3958441 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
3958349 ATTTTCATAT
*
3958359 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
3958380 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
3958401 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
3958422 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
3958442 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:3958432 original size:42 final size:43
Alignment explanation
Indices: 3958339--3958437 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
3958329 ATTTATGTGT
* *
3958339 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
3958380 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
3958422 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
3958438 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:3959878 original size:237 final size:235
Alignment explanation
Indices: 3959465--3959936 Score: 881
Period size: 237 Copynumber: 2.0 Consensus size: 235
3959455 CTATCACTCT
3959465 CAACAATCAATCGTTCCTTAGAGCACCATTTAGAAGTAGCGAAGAAACATAAACCATTTAATGGC
1 CAACAATCAATCGTTCCTTAGAGCACCATTTAGAAGTAGCGAAGAAACATAAACCATTTAATGGC
** *
3959530 CTTTAATTCCATCAAAGAAGGAGGACCTGGACCAGAAGCTTCTTGAAATGATCCTAGCATTGTGT
66 CTTTAATTCCAAAAAAGAAGGAGGACCTGGACCAGAAGCTTCTTGAAATGATCCTAGCACTGTGT
*
3959595 CAGACTCATCTCTTAAAACTCCACCTAAACCACTAGCCTTCCAATCACTTTTGACAGCAACATCC
131 CAGACTCATCTCTTAAAACTCAACCTAAACCACTAGCCTTCCAATCACTTTTGACAGCAACATCC
3959660 ACGTTCAACTTTAGAAATCCCACAGGGGGAGGGGACCAAG
196 ACGTTCAACTTTAGAAATCCCACAGGGGGAGGGGACCAAG
*
3959700 CAACAATCAATCGTTCCTTAGAGCACCATTTAGAAGTATCGAAGAAACATAAACCATGTTTAATG
1 CAACAATCAATCGTTCCTTAGAGCACCATTTAGAAGTAGCGAAGAAACATAAACCA--TTTAATG
3959765 GCCTTTAATTCCAAAAAAGAAGGAGGACCTGGACCAGAAGCTTCTTGAAATGATCCTAGCACTGT
64 GCCTTTAATTCCAAAAAAGAAGGAGGACCTGGACCAGAAGCTTCTTGAAATGATCCTAGCACTGT
3959830 GTCAGACTCATCTCTTAAAACTCAACCTAAACCACTAGCCTTCCAATCACTTTTGACAGCAACAT
129 GTCAGACTCATCTCTTAAAACTCAACCTAAACCACTAGCCTTCCAATCACTTTTGACAGCAACAT
3959895 CCACGTTCAACTTTAGAAATCCCACAGGGGGAGGGGACCAAG
194 CCACGTTCAACTTTAGAAATCCCACAGGGGGAGGGGACCAAG
3959937 AAATCTGATT
Statistics
Matches: 230, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
235 55 0.24
237 175 0.76
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (235 bp):
CAACAATCAATCGTTCCTTAGAGCACCATTTAGAAGTAGCGAAGAAACATAAACCATTTAATGGC
CTTTAATTCCAAAAAAGAAGGAGGACCTGGACCAGAAGCTTCTTGAAATGATCCTAGCACTGTGT
CAGACTCATCTCTTAAAACTCAACCTAAACCACTAGCCTTCCAATCACTTTTGACAGCAACATCC
ACGTTCAACTTTAGAAATCCCACAGGGGGAGGGGACCAAG
Found at i:3969485 original size:15 final size:16
Alignment explanation
Indices: 3969453--3969485 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3969443 AAAATCTTTC
3969453 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
3969469 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
3969484 TT
1 TT
3969486 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:3970252 original size:16 final size:16
Alignment explanation
Indices: 3970228--3970261 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3970218 TATCGCCGAC
*
3970228 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
3970244 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
3970260 CG
1 CG
3970262 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:3972937 original size:136 final size:136
Alignment explanation
Indices: 3972751--3973450 Score: 831
Period size: 136 Copynumber: 5.1 Consensus size: 136
3972741 CCAAAACAAA
* * * * * *
3972751 ACAAAAATGATAAATT-AGATACTAAACGTGTAGTTTATAGGGATGTTCATTTTTCGGTTTTAGA
1 ACAAAAGTGAT-AATTGAG-TACTAAACGTGTAGTTTAAAGGGGTATTCATTGTTCGGTTTTAAA
* * * *
3972815 TGTATAGTTTAGTACCCAATTATCACTTTTGTTTCGTTTTAGTCATCTAACTTTTTTTTGTCAAA
64 CGTGTAGTTTAGTACCCAATTATCACTTTTGTTTCGTTTTGGTCATCCAACTTTTTTTTGTCAAA
3972880 ATCATAGC
129 ATCATAGC
* * *
3972888 ACAAAAGTGATAATTGAGTATTAAATGTGTAGTTTAAAGGGGTGTTCATTGTTCGGTTTTAAACG
1 ACAAAAGTGATAATTGAGTACTAAACGTGTAGTTTAAAGGGGTATTCATTGTTCGGTTTTAAACG
* * * * *
3972953 CGTAGTTTAGTACCGAATTATCACTTTTATTTCGTTTAGGTCATCCAACTATTTTTT-TCAAAAT
66 TGTAGTTTAGTACCCAATTATCACTTTTGTTTCGTTTTGGTCATCCAACTTTTTTTTGTCAAAAT
3973017 CATAGC
131 CATAGC
* * * * * *
3973023 ACAAAAGTGATAATTTAGGTATTAAAAGTGTAGTTTATAGGGGTATACATTGTTCAGTTTTAAAC
1 ACAAAAGTGATAATTGA-GTACTAAACGTGTAGTTTAAAGGGGTATTCATTGTTCGGTTTTAAAC
*
3973088 GTGTAGTTTAGTACCCAATTATCACTTTTGTTTCATTTTGGTCATCCAACTATTTTTTTTGTCAA
65 GTGTAGTTTAGTACCCAATTATCACTTTTGTTTCGTTTTGGTCATCCAAC--TTTTTTTTGTCAA
3973153 AATCATAGC
128 AATCATAGC
* * * *
3973162 ACAAAAGCGATAATTGGGTACTAAATGTGTAGTTTAAAGGGGTATTCATTGTTCAGTTTTAAACG
1 ACAAAAGTGATAATTGAGTACTAAACGTGTAGTTTAAAGGGGTATTCATTGTTCGGTTTTAAACG
* * * * * * *
3973227 TGTAGTTTAGTATCGAATTATCACTTTTATTTTGTTTTTGGTCATCTAA--ATATTTTGTCAAAA
66 TGTAGTTTAGTACCCAATTATCACTTTTGTTTCG-TTTTGGTCATCCAACTTTTTTTTGTCAAAA
3973290 TCATAGC
130 TCATAGC
* * * * *
3973297 ATAAAAGTGATAATTTAGGTACTAAACATGTAGTTTATAA-GGATATACATTGTTCGGTTTTAAA
1 ACAAAAGTGATAATTGA-GTACTAAACGTGTAGTTTA-AAGGGGTATTCATTGTTCGGTTTTAAA
* * * * * *
3973361 CGTGTAGTTTAGTACCCAATTATCATTTTTGTTTCGGTTTGGACA-CCCACCTATTTTT-TC-AA
64 CGTGTAGTTTAGTACCCAATTATCACTTTTGTTTCGTTTTGGTCATCCAACTTTTTTTTGTCAAA
3973423 ATCATAGC
129 ATCATAGC
* *
3973431 AGAAAAGTAATAATTGAGTA
1 ACAAAAGTGATAATTGAGTA
3973451 GCTTAAGGGG
Statistics
Matches: 486, Mismatches: 67, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
133 3 0.01
134 26 0.05
135 70 0.14
136 253 0.52
137 14 0.03
138 80 0.16
139 40 0.08
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (136 bp):
ACAAAAGTGATAATTGAGTACTAAACGTGTAGTTTAAAGGGGTATTCATTGTTCGGTTTTAAACG
TGTAGTTTAGTACCCAATTATCACTTTTGTTTCGTTTTGGTCATCCAACTTTTTTTTGTCAAAAT
CATAGC
Found at i:3973290 original size:274 final size:271
Alignment explanation
Indices: 3972751--3973518 Score: 994
Period size: 274 Copynumber: 2.9 Consensus size: 271
3972741 CCAAAACAAA
* * * * * * * * *
3972751 ACAAAAATGATAAATTAGATACTAAACGTGTAGTTTATAGGGATGTTCATTTTTCGGTTTTAGAT
1 ACAAAAGTGATAATTTAGGTACTAAAAGTGTAGTTTATAGGGATATACATTGTTCGGTTTTAAAC
* * *
3972816 GTATAGTTTAGTACCCAATTATCACTTTTGTTTCGTTTTAGTCATCTAAC--TTTTTTTTGTCAA
66 GTGTAGTTTAGTACCCAATTATCACTTTTGTTTCGTTTTGGTCATCCAACTATTTTTTTTGTCAA
*
3972879 AATCATAGCACAAAAGTGATAATTGAGTATTAAATGTGTAGTTTAAAGGGGTGTTCATTGTTCGG
131 AATCATAGCACAAAAG-GATAATTG-GTA-TAAATGTGTAGTTTAAAGGGGTGTTCATTGTTCAG
* * *
3972944 TTTTAAACGCGTAGTTTAGTACCGAATTATCACTTTTATTTCGTTTAGGTCATCCAACTATTTTT
193 TTTTAAACGTGTAGTTTAGTATCGAATTATCACTTTTATTTCGTTTAGGTCATCCAAATATTTTT
*
3973009 TTCAAAATCATAGC
258 GTCAAAATCATAGC
* * *
3973023 ACAAAAGTGATAATTTAGGTATTAAAAGTGTAGTTTATAGGGGTATACATTGTTCAGTTTTAAAC
1 ACAAAAGTGATAATTTAGGTACTAAAAGTGTAGTTTATAGGGATATACATTGTTCGGTTTTAAAC
*
3973088 GTGTAGTTTAGTACCCAATTATCACTTTTGTTTCATTTTGGTCATCCAACTATTTTTTTTGTCAA
66 GTGTAGTTTAGTACCCAATTATCACTTTTGTTTCGTTTTGGTCATCCAACTATTTTTTTTGTCAA
*
3973153 AATCATAGCACAAAAGCGATAATTGGGTACTAAATGTGTAGTTTAAAGGGGTATTCATTGTTCAG
131 AATCATAGCACAAAAG-GATAATT-GGTA-TAAATGTGTAGTTTAAAGGGGTGTTCATTGTTCAG
* * *
3973218 TTTTAAACGTGTAGTTTAGTATCGAATTATCACTTTTATTTTGTTTTTGGTCATCTAAATA-TTT
193 TTTTAAACGTGTAGTTTAGTATCGAATTATCACTTTTATTTCG-TTTAGGTCATCCAAATATTTT
3973282 TGTCAAAATCATAGC
257 TGTCAAAATCATAGC
* *
3973297 ATAAAAGTGATAATTTAGGTACTAAACA-TGTAGTTTATAAGGATATACATTGTTCGGTTTTAAA
1 ACAAAAGTGATAATTTAGGTACTAAA-AGTGTAGTTTATAGGGATATACATTGTTCGGTTTTAAA
* * * * *
3973361 CGTGTAGTTTAGTACCCAATTATCATTTTTGTTTCGGTTTGGACACCCACCTA---TTTTT-TC-
65 CGTGTAGTTTAGTACCCAATTATCACTTTTGTTTCGTTTTGGTCATCCAACTATTTTTTTTGTCA
* * * * * *
3973421 AAATCATAGCAGAAAA-G-T-A-----ATAATTGAGTAGCTTAAGGGGGTGTTCATTGTTCCGTT
130 AAATCATAGCACAAAAGGATAATTGGTATAAATGTGTAGTTTAAAGGGGTGTTCATTGTTCAGTT
*
3973478 TTAAACATGTAGTTTAGTATCGAATTATCACTTTTATTTCG
195 TTAAACGTGTAGTTTAGTATCGAATTATCACTTTTATTTCG
3973519 ACTGAACATT
Statistics
Matches: 444, Mismatches: 47, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
258 70 0.16
259 1 0.00
265 1 0.00
266 1 0.00
267 1 0.00
269 15 0.03
270 2 0.00
271 5 0.01
272 99 0.22
274 233 0.52
275 16 0.04
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (271 bp):
ACAAAAGTGATAATTTAGGTACTAAAAGTGTAGTTTATAGGGATATACATTGTTCGGTTTTAAAC
GTGTAGTTTAGTACCCAATTATCACTTTTGTTTCGTTTTGGTCATCCAACTATTTTTTTTGTCAA
AATCATAGCACAAAAGGATAATTGGTATAAATGTGTAGTTTAAAGGGGTGTTCATTGTTCAGTTT
TAAACGTGTAGTTTAGTATCGAATTATCACTTTTATTTCGTTTAGGTCATCCAAATATTTTTGTC
AAAATCATAGC
Found at i:3980008 original size:30 final size:30
Alignment explanation
Indices: 3979972--3980030 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
3979962 GAATTTAGAA
* * *
3979972 AAAAAAAATATTTTACACATTTGTTTTGAT
1 AAAAAAAATACTTTAAACATTTATTTTGAT
*
3980002 AAAAAAAATACTTTAAATATTTATTTTGA
1 AAAAAAAATACTTTAAACATTTATTTTGA
3980031 CCAAAACGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (30 bp):
AAAAAAAATACTTTAAACATTTATTTTGAT
Found at i:3980814 original size:35 final size:35
Alignment explanation
Indices: 3980767--3980852 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
3980757 AAAACAGTCA
* * *
3980767 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
3980802 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
3980837 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
3980853 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:3980846 original size:21 final size:21
Alignment explanation
Indices: 3980821--3980863 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3980811 TTCTAAACCC
3980821 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
3980842 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
3980863 T
1 T
3980864 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:3981018 original size:16 final size:18
Alignment explanation
Indices: 3980986--3981019 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
3980976 TATTAATGTA
3980986 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
3981004 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
3981020 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:3981660 original size:130 final size:130
Alignment explanation
Indices: 3981457--3981704 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
3981447 AATTTTCTTC
* * *
3981457 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
3981522 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
3981587 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
3981652 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTATGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
3981705 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:3999612 original size:20 final size:21
Alignment explanation
Indices: 3999587--3999626 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3999577 CTCCGTGCTA
*
3999587 AGGCTAAGGTAA-GCTAAACT
1 AGGCTAAGATAAGGCTAAACT
3999607 AGGCTAAGATAAGGCTAAAC
1 AGGCTAAGATAAGGCTAAAC
3999627 ACTCACTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.17
Consensus pattern (21 bp):
AGGCTAAGATAAGGCTAAACT
Found at i:4006739 original size:10 final size:11
Alignment explanation
Indices: 4006721--4006754 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
4006711 TTTATTTTTT
4006721 AAATGTTTTATA
1 AAAT-TTTTATA
4006733 AAATTTTTATA
1 AAATTTTTATA
4006744 AAA-TTTTATA
1 AAATTTTTATA
4006754 A
1 A
4006755 GTTCTAATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 10 0.45
12 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
AAATTTTTATA
Found at i:4008188 original size:22 final size:22
Alignment explanation
Indices: 4008160--4008206 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
4008150 ACAAATATTA
4008160 TAAATAATACAACT-TTTTAAAT
1 TAAATAATACAA-TGTTTTAAAT
*
4008182 TAAATAATATAATGTTTTAAAT
1 TAAATAATACAATGTTTTAAAT
4008204 TAA
1 TAA
4008207 GAAACGTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAATAATACAATGTTTTAAAT
Found at i:4021810 original size:24 final size:26
Alignment explanation
Indices: 4021765--4021816 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
4021755 CGTTCATAAA
**
4021765 CGTTCGATTATATGTTCGTTTATGTT
1 CGTTCGATTATATGTTAATTTATGTT
4021791 CGTTC-ATT-TATGTTAATTTATGTT
1 CGTTCGATTATATGTTAATTTATGTT
4021815 CG
1 CG
4021817 AACATGAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.67
25 3 0.12
26 5 0.21
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.54
Consensus pattern (26 bp):
CGTTCGATTATATGTTAATTTATGTT
Found at i:4022103 original size:20 final size:20
Alignment explanation
Indices: 4022078--4022118 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
4022068 GTGTTTGTGT
*
4022078 TGTTCGTTTGTGTTCATTTA
1 TGTTCGTTCGTGTTCATTTA
*
4022098 TGTTCGTTCGTGTTCGTTTA
1 TGTTCGTTCGTGTTCATTTA
4022118 T
1 T
4022119 TATTTAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.07, C:0.12, G:0.22, T:0.59
Consensus pattern (20 bp):
TGTTCGTTCGTGTTCATTTA
Found at i:4022111 original size:10 final size:10
Alignment explanation
Indices: 4022065--4022116 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
4022055 TAAGTTTTTT
*
4022065 TTTGTGTTTG
1 TTTGTGTTCG
*
4022075 TGT-TGTTCG
1 TTTGTGTTCG
*
4022084 TTTGTGTTCA
1 TTTGTGTTCG
*
4022094 TTTATGTTCG
1 TTTGTGTTCG
*
4022104 TTCGTGTTCG
1 TTTGTGTTCG
4022114 TTT
1 TTT
4022117 ATTATTTAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
9 7 0.22
10 25 0.78
ACGTcount: A:0.04, C:0.10, G:0.25, T:0.62
Consensus pattern (10 bp):
TTTGTGTTCG
Found at i:4029023 original size:8 final size:8
Alignment explanation
Indices: 4029010--4029050 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
4029000 CTCATTTTCA
4029010 GAGAATTT
1 GAGAATTT
4029018 GAGAATTT
1 GAGAATTT
*
4029026 -AGAGTTT
1 GAGAATTT
*
4029033 GGGAATTT
1 GAGAATTT
4029041 GAGAATTT
1 GAGAATTT
4029049 GA
1 GA
4029051 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:4029346 original size:128 final size:128
Alignment explanation
Indices: 4029118--4030003 Score: 1684
Period size: 128 Copynumber: 6.9 Consensus size: 128
4029108 CTATAATCGG
4029118 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
* *
4029183 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACTTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
4029246 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
4029311 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
4029374 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
* *
4029439 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATAAGTATCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
* *
4029502 TTCACTATTAACATGAAGGCGCGTTCCCGGAGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
4029567 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
4029630 TTCACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
4029694 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
4029757 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
4029822 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
* * *
4029885 TTCACTATTCACATGAAGGTGCGTTCCCGGGGGGGCGCCTTCCATTATTTCGTCAGAGAATACGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
4029950 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGT
4030004 TTGAATAACT
Statistics
Matches: 744, Mismatches: 13, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
127 126 0.17
128 618 0.83
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:4030473 original size:34 final size:34
Alignment explanation
Indices: 4030394--4030492 Score: 130
Period size: 33 Copynumber: 3.0 Consensus size: 34
4030384 AAATTTAATG
*
4030394 TTAAATTTCGAATACTATAATTTATA-TTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
4030427 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
4030460 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
4030493 AACATTTATC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
32 14 0.25
33 21 0.38
34 20 0.36
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:4031078 original size:21 final size:21
Alignment explanation
Indices: 4031011--4031080 Score: 106
Period size: 21 Copynumber: 3.3 Consensus size: 21
4031001 TATGATATAA
*
4031011 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
4031032 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
4031053 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
4031074 AACCCTG
1 AACCCTG
4031081 TGGAGATGGC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.07
21 39 0.87
22 3 0.07
ACGTcount: A:0.21, C:0.27, G:0.33, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:4031111 original size:21 final size:21
Alignment explanation
Indices: 4031087--4031134 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
4031077 CCTGTGGAGA
*
4031087 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
*
4031108 TGGCATATAAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
4031129 GGGCAT
1 TGGCAT
4031135 GTACCCCTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.38, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:4032896 original size:34 final size:31
Alignment explanation
Indices: 4032853--4032932 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 31
4032843 TTAATAATTC
* *
4032853 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATA-TA--TTAA
*
4032887 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTACATAAATATATTAA
4032918 TATAAAAAATAATAA
1 TA-AAAAAATAATAA
4032933 CTATTTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 6 0.15
32 11 0.27
33 2 0.05
34 22 0.54
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTACATAAATATATTAA
Found at i:4032898 original size:31 final size:33
Alignment explanation
Indices: 4032856--4032930 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
4032846 ATAATTCTAA
* * *
4032856 ATAAATAATAATTATATAAAT-ATTATTTTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
* *
4032888 A-AAAAAATAA-TATTTACATAAATATATTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
4032919 ATAAAAAATAAT
1 ATAAAAAATAAT
4032931 AACTATTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 7 0.20
31 18 0.51
32 10 0.29
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
ATAAAAAATAATTATATAAATAAATATATTAAT
Found at i:4034614 original size:2 final size:2
Alignment explanation
Indices: 4034607--4034643 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4034597 ATTAATATTA
4034607 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 A
4034644 ATAAATTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4034699 original size:15 final size:16
Alignment explanation
Indices: 4034664--4034701 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
4034654 TTTAAATTAA
4034664 AAATATATTTAATATT
1 AAATATATTTAATATT
*
4034680 -TATATATTTAAT-TT
1 AAATATATTTAATATT
4034694 AAATATAT
1 AAATATAT
4034702 ATATATCCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATATATTTAATATT
Found at i:4035279 original size:17 final size:17
Alignment explanation
Indices: 4035257--4035290 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4035247 GGTAAATTAC
*
4035257 ACGTTTGCTACTCTAAT
1 ACGTTTGATACTCTAAT
4035274 ACGTTTGATACTCTAAT
1 ACGTTTGATACTCTAAT
4035291 TATCACTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (17 bp):
ACGTTTGATACTCTAAT
Found at i:4040180 original size:21 final size:21
Alignment explanation
Indices: 4040156--4040229 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 21
4040146 CGATTTCTCA
4040156 ATTCTCAGGTAATTTGAACAC
1 ATTCTCAGGTAATTTGAACAC
* * * *
4040177 ATTCTCATCG-AATATCGATTTCTC
1 ATTCTCA-GGTAAT-TTGA--ACAC
4040201 AATTCTCAGGTAATTTGAACAC
1 -ATTCTCAGGTAATTTGAACAC
4040223 ATTCTCA
1 ATTCTCA
4040230 TATCGTAGGT
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
21 17 0.44
22 6 0.15
24 6 0.15
25 10 0.26
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (21 bp):
ATTCTCAGGTAATTTGAACAC
Found at i:4040201 original size:46 final size:46
Alignment explanation
Indices: 4040134--4040230 Score: 194
Period size: 46 Copynumber: 2.1 Consensus size: 46
4040124 GACGAGAGTA
4040134 CTCATCGAATATCGATTTCTCAATTCTCAGGTAATTTGAACACATT
1 CTCATCGAATATCGATTTCTCAATTCTCAGGTAATTTGAACACATT
4040180 CTCATCGAATATCGATTTCTCAATTCTCAGGTAATTTGAACACATT
1 CTCATCGAATATCGATTTCTCAATTCTCAGGTAATTTGAACACATT
4040226 CTCAT
1 CTCAT
4040231 ATCGTAGGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (46 bp):
CTCATCGAATATCGATTTCTCAATTCTCAGGTAATTTGAACACATT
Found at i:4054904 original size:23 final size:21
Alignment explanation
Indices: 4054852--4054904 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 21
4054842 CCTATTTATC
*
4054852 TTTTAAATTTTGTAAAAAAAA
1 TTTTAAATTTTATAAAAAAAA
*
4054873 TTATATAAATTTTATAAATTTAAAA
1 TT-T-TAAATTTTATAAA--AAAAA
4054898 TTTTAAA
1 TTTTAAA
4054905 AAATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 2 0.08
22 1 0.04
23 16 0.62
24 1 0.04
25 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TTTTAAATTTTATAAAAAAAA
Found at i:4060245 original size:23 final size:23
Alignment explanation
Indices: 4060218--4060269 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
4060208 TTGATTTAAT
4060218 TTAAAA-AAACAAAAGTTTAAG-GA
1 TTAAAATAAA-AAAAGTTT-AGTGA
*
4060241 TTAAAATTAAAAAAGTTTAGTGA
1 TTAAAATAAAAAAAGTTTAGTGA
4060264 TTAAAA
1 TTAAAA
4060270 CATTTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 2 0.08
23 22 0.85
24 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.12, T:0.29
Consensus pattern (23 bp):
TTAAAATAAAAAAAGTTTAGTGA
Found at i:4062679 original size:11 final size:11
Alignment explanation
Indices: 4062663--4062699 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
4062653 TTTTATAAAA
4062663 AAAAATTATAT
1 AAAAATTATAT
4062674 AAAAATTATATT
1 AAAAATTATA-T
*
4062686 AAAAAATATAT
1 AAAAATTATAT
4062697 AAA
1 AAA
4062700 TTTAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAAATTATAT
Found at i:4062688 original size:12 final size:12
Alignment explanation
Indices: 4062663--4062696 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4062653 TTTTATAAAA
4062663 AAAAATTATA-T
1 AAAAATTATATT
4062674 AAAAATTATATT
1 AAAAATTATATT
*
4062686 AAAAAATATAT
1 AAAAATTATAT
4062697 AAATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAAAATTATATT
Found at i:4083560 original size:22 final size:23
Alignment explanation
Indices: 4083528--4083573 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
4083518 TGAAAAAAAA
*
4083528 TAAAATGATAATTAA-ATTAAAT
1 TAAAATAATAATTAAGATTAAAT
4083550 TAAAATAATAATTAATGATTAAAT
1 TAAAATAATAATTAA-GATTAAAT
4083574 ACATAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
24 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (23 bp):
TAAAATAATAATTAAGATTAAAT
Found at i:4088278 original size:23 final size:23
Alignment explanation
Indices: 4088222--4088280 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
4088212 GGGAGAGACA
* *
4088222 AAATAAGATT-AAAAAATAATTT
1 AAATAAAATTAAAAAAATAATTC
*
4088244 AATTTAAAATTAAAAAAATAATTC
1 AA-ATAAAATTAAAAAAATAATTC
*
4088268 AAATAATATTAAA
1 AAATAAAATTAAA
4088281 TCTTTTATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 2 0.07
23 15 0.50
24 13 0.43
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
AAATAAAATTAAAAAAATAATTC
Found at i:4092835 original size:12 final size:12
Alignment explanation
Indices: 4092818--4092844 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4092808 GACAACATAG
4092818 AAAAATAAGAAA
1 AAAAATAAGAAA
4092830 AAAAATAAGAAA
1 AAAAATAAGAAA
4092842 AAA
1 AAA
4092845 CAGCTAAACA
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:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAATAAGAAA
Found at i:4093165 original size:14 final size:14
Alignment explanation
Indices: 4093129--4093172 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
4093119 TTTTGTAATG
4093129 AACCCTAAACCATA
1 AACCCTAAACCATA
* * *
4093143 AATCATAAATCATA
1 AACCCTAAACCATA
*
4093157 AACCCTAAACCCTA
1 AACCCTAAACCATA
4093171 AA
1 AA
4093173 TATAATTATA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.18
Consensus pattern (14 bp):
AACCCTAAACCATA
Found at i:4093172 original size:21 final size:20
Alignment explanation
Indices: 4093134--4093177 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
4093124 TAATGAACCC
*
4093134 TAAACCATAAATCATAAATCA
1 TAAACCATAAACCATAAAT-A
* *
4093155 TAAACCCTAAACCCTAAATA
1 TAAACCATAAACCATAAATA
4093175 TAA
1 TAA
4093178 TTATATGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (20 bp):
TAAACCATAAACCATAAATA
Found at i:4096243 original size:12 final size:12
Alignment explanation
Indices: 4096228--4096271 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
4096218 TTAAAGCTTG
4096228 AATCGAGCTCAA
1 AATCGAGCTCAA
4096240 AATCGAGCTTC--
1 AATCGAGC-TCAA
*
4096251 AATCAAGCTCAA
1 AATCGAGCTCAA
4096263 AATCGAGCT
1 AATCGAGCT
4096272 GCTTAGCTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
10 2 0.07
11 7 0.26
12 16 0.59
13 2 0.07
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (12 bp):
AATCGAGCTCAA
Found at i:4096248 original size:23 final size:23
Alignment explanation
Indices: 4096222--4096271 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
4096212 TTTGAGTTAA
* *
4096222 AGCTTGAATCGAGCTCAAAATCG
1 AGCTTCAATCAAGCTCAAAATCG
4096245 AGCTTCAATCAAGCTCAAAATCG
1 AGCTTCAATCAAGCTCAAAATCG
4096268 AGCT
1 AGCT
4096272 GCTTAGCTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (23 bp):
AGCTTCAATCAAGCTCAAAATCG
Found at i:4097195 original size:2 final size:2
Alignment explanation
Indices: 4097188--4097224 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4097178 AAACTTTTTA
*
4097188 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4097225 AGATAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4103625 original size:41 final size:41
Alignment explanation
Indices: 4103568--4103649 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
4103558 GCAGAAGCAG
*
4103568 ATGATTGCAGACGAGGGACAACCGCATGCAAAAATGATCCC
1 ATGATTGCAGACGAGGGACAACCGCATACAAAAATGATCCC
4103609 ATGATTGCAGACGAGGGACAACCGCATACAAAAATGATCCC
1 ATGATTGCAGACGAGGGACAACCGCATACAAAAATGATCCC
4103650 TGCAAAGCTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (41 bp):
ATGATTGCAGACGAGGGACAACCGCATACAAAAATGATCCC
Found at i:4112087 original size:29 final size:27
Alignment explanation
Indices: 4112039--4112092 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
4112029 TTAGGAGTAG
4112039 ATAAATTTATAAAAAAATAAAGAAAAAA
1 ATAAATTTATAAAAAAATAAA-AAAAAA
* *
4112067 ATAAATTT-TAATAAAATATAAAAAAA
1 ATAAATTTATAAAAAAATAAAAAAAAA
4112093 TTTAAATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.25
27 10 0.42
28 8 0.33
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (27 bp):
ATAAATTTATAAAAAAATAAAAAAAAA
Found at i:4112106 original size:28 final size:27
Alignment explanation
Indices: 4112039--4112108 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
4112029 TTAGGAGTAG
*
4112039 ATAAATTTATAAAAAAATAAAGAAAAAA
1 ATAAA-TTATAATAAAATAAAGAAAAAA
* *
4112067 ATAAATTTTAATAAAATATAA-AAAAAT
1 ATAAATTATAATAAAATA-AAGAAAAAA
*
4112094 TTAAATGTATAATAA
1 ATAAAT-TATAATAA
4112109 TTTTAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 21 0.60
28 14 0.40
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (27 bp):
ATAAATTATAATAAAATAAAGAAAAAA
Found at i:4112227 original size:2 final size:2
Alignment explanation
Indices: 4112220--4112247 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4112210 TCTCCTTTGA
4112220 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4112248 GGATTCCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4112455 original size:24 final size:25
Alignment explanation
Indices: 4112422--4112470 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
4112412 ACTATAATAA
*
4112422 AATTATAATATTAATTT-TGTATTTT
1 AATTATAATA-TAATTTATCTATTTT
4112447 AATT-TAATATAATTTATCTATTTT
1 AATTATAATATAATTTATCTATTTT
4112471 TTAATCTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 12 0.55
25 4 0.18
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
AATTATAATATAATTTATCTATTTT
Found at i:4114299 original size:4 final size:4
Alignment explanation
Indices: 4114292--4114566 Score: 550
Period size: 4 Copynumber: 68.8 Consensus size: 4
4114282 GGGTGTGTGT
4114292 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4114340 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4114388 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4114436 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4114484 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4114532 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
4114567 TATATATACG
Statistics
Matches: 271, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 271 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:4123092 original size:28 final size:28
Alignment explanation
Indices: 4123052--4123106 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
4123042 GCCTTAGTTG
4123052 AACTTCTGACATATTCTGACAAGGCACA
1 AACTTCTGACATATTCTGACAAGGCACA
*
4123080 AACTTCTGACATATTTTGACAAGGCAC
1 AACTTCTGACATATTCTGACAAGGCAC
4123107 GAATCGTCAT
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:0.35, C:0.24, G:0.15, T:0.27
Consensus pattern (28 bp):
AACTTCTGACATATTCTGACAAGGCACA
Found at i:4134901 original size:200 final size:196
Alignment explanation
Indices: 4134548--4134946 Score: 469
Period size: 200 Copynumber: 2.0 Consensus size: 196
4134538 TGAAAAGGAG
* * * * *
4134548 GATTCCAATTTAACCCTCCATTACCTTGCCAAGGTGATGCAGAAGACTGAGGAATTCAGAAGTAG
1 GATTCCAATTTAACACTCCATTACCTTGCCAAGGTGATGCAAAAGACAGAAGAATTCAGAAG-AC
* * * * ** * *
4134613 TAACTTTAAGTGCTTGTCCAGAAATCATAAGGCAGGCAGGAAATGATTAAAAATAACAAAATCAG
65 TAACGTCAAGTGATTGTCCAGAAATCATAAGGAAGGCAGGAAACAATTAAAAACAACAAAATCAA
* * * * * * *
4134678 AGTTCAAGGGTTCAGCCAAAAATCAAGGGGATACTATGTGATCATTAACAACGGTAATCATTGAC
130 AGTTCAAGGGTTCAACCAAAAATCAAGGAGATACTACGCGACCATAAACAACGGTAAGCATTGAC
4134743 AT
195 AT
* * *
4134745 GATTCCGATTTAACACTCCATTAGCTTGCCAAGGTGATGCAAAAGACCAGAAGATATTTA-AA-A
1 GATTCCAATTTAACACTCCATTACCTTGCCAAGGTGATGCAAAAGA-CAGAAGA-ATTCAGAAGA
* *
4134808 CTAACAGTCAAGTGATTGTCCAGAAATCATTACAAGGAATGCAGGAAACAATTAAAAACAGCAAA
64 CTAAC-GTCAAGTGATTGTCCAGAAATCA-T--AAGGAAGGCAGGAAACAATTAAAAACAACAAA
* *
4134873 ATCAAAGTTCAAGGGTTCAACCAAAAATCAAGGAGCTACTACGCGACCATAAACAACGTTAAGCA
125 ATCAAAGTTCAAGGGTTCAACCAAAAATCAAGGAGATACTACGCGACCATAAACAACGGTAAGCA
*
4134938 TTGATAT
190 TTGACAT
4134945 GA
1 GA
4134947 AAAAGAGAGA
Statistics
Matches: 168, Mismatches: 28, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
196 5 0.03
197 62 0.37
198 8 0.05
199 4 0.02
200 89 0.53
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (196 bp):
GATTCCAATTTAACACTCCATTACCTTGCCAAGGTGATGCAAAAGACAGAAGAATTCAGAAGACT
AACGTCAAGTGATTGTCCAGAAATCATAAGGAAGGCAGGAAACAATTAAAAACAACAAAATCAAA
GTTCAAGGGTTCAACCAAAAATCAAGGAGATACTACGCGACCATAAACAACGGTAAGCATTGACA
T
Found at i:4139666 original size:69 final size:69
Alignment explanation
Indices: 4139548--4139678 Score: 156
Period size: 69 Copynumber: 1.9 Consensus size: 69
4139538 TCCATGGCTG
* * *** * *
4139548 AAGTCTTTGCTGCTATTTATGGAATCGAACCTAGTGATTGTCTCGGGTTGC-CGTGAAAATCCGC
1 AAGTCTTTGCTACTATCTATGGAATCGAACCTAGTGAGCCTATCAGGTTGCGC-TGAAAATCCGC
4139612 TGCCA
65 TGCCA
* * *
4139617 AAGTCTTTGCTACTGTCTATGGAGTCGAACCTCGTGAGCCTATCAGGTTGCGCTGAAAATCC
1 AAGTCTTTGCTACTATCTATGGAATCGAACCTAGTGAGCCTATCAGGTTGCGCTGAAAATCC
4139679 ACCATCATTC
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
69 50 0.98
70 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (69 bp):
AAGTCTTTGCTACTATCTATGGAATCGAACCTAGTGAGCCTATCAGGTTGCGCTGAAAATCCGCT
GCCA
Found at i:4143647 original size:18 final size:18
Alignment explanation
Indices: 4143620--4143790 Score: 197
Period size: 18 Copynumber: 9.4 Consensus size: 18
4143610 GTGAGTAATC
* *
4143620 GGCTGTGCACCTATCCCT
1 GGCTGGGCACCCATCCCT
* * *
4143638 GGCTGAGCACTCATCCCA
1 GGCTGGGCACCCATCCCT
4143656 GGCTGGGCACCCATCCCT
1 GGCTGGGCACCCATCCCT
* *
4143674 GGCTGAGCACCCATTCCT
1 GGCTGGGCACCCATCCCT
4143692 GGCTGGGCACCCATCCCT
1 GGCTGGGCACCCATCCCT
4143710 GGCTGGGCACCCATTCGCTTCCT
1 GGCTGGGCACCCA-T--C--CCT
4143733 GGCTGGGCA--C--CCCT
1 GGCTGGGCACCCATCCCT
4143747 GGCTGGGCACCCATCCCT
1 GGCTGGGCACCCATCCCT
*
4143765 GGCTGGGCACCCATTCCT
1 GGCTGGGCACCCATCCCT
4143783 GGCTGGGC
1 GGCTGGGC
4143791 CCCCGTTCCA
Statistics
Matches: 132, Mismatches: 12, Indels: 18
0.81 0.07 0.11
Matches are distributed among these distances:
14 12 0.09
16 2 0.02
18 103 0.78
19 1 0.01
21 2 0.02
23 12 0.09
ACGTcount: A:0.12, C:0.40, G:0.28, T:0.20
Consensus pattern (18 bp):
GGCTGGGCACCCATCCCT
Found at i:4143749 original size:14 final size:14
Alignment explanation
Indices: 4143730--4143758 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4143720 CCATTCGCTT
4143730 CCTGGCTGGGCACC
1 CCTGGCTGGGCACC
4143744 CCTGGCTGGGCACC
1 CCTGGCTGGGCACC
4143758 C
1 C
4143759 ATCCCTGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.45, G:0.34, T:0.14
Consensus pattern (14 bp):
CCTGGCTGGGCACC
Found at i:4143762 original size:55 final size:53
Alignment explanation
Indices: 4143634--4143781 Score: 185
Period size: 55 Copynumber: 2.7 Consensus size: 53
4143624 GTGCACCTAT
* * *
4143634 CCCTGGCTGAGCACTCATCCCAGGCTGGGCACCCA-T-CCCTGGCTGAGCACC
1 CCCTGGCTGGGCACCCATCCCTGGCTGGGCACCCATTCCCCTGGCTGAGCACC
*
4143685 CATTCCTGGCTGGGCACCCATCCCTGGCTGGGCACCCATTCGCTTCCTGGCTGGGCA-C
1 C---CCTGGCTGGGCACCCATCCCTGGCTGGGCACCCATTC-C--CCTGGCTGAGCACC
4143743 CCCTGGCTGGGCACCCATCCCTGGCTGGGCACCCATTCC
1 CCCTGGCTGGGCACCCATCCCTGGCTGGGCACCCATTCC
4143782 TGGCTGGGCC
Statistics
Matches: 85, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
51 1 0.01
54 32 0.38
55 38 0.45
57 1 0.01
58 2 0.02
59 11 0.13
ACGTcount: A:0.12, C:0.43, G:0.26, T:0.19
Consensus pattern (53 bp):
CCCTGGCTGGGCACCCATCCCTGGCTGGGCACCCATTCCCCTGGCTGAGCACC
Found at i:4152102 original size:3 final size:3
Alignment explanation
Indices: 4152094--4152126 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
4152084 ATTTAAAAAC
4152094 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4152127 TTGTGATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4164228 original size:37 final size:38
Alignment explanation
Indices: 4164182--4164255 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
4164172 ATTTTTTTTC
4164182 GAGTATGGTCGGG-TTTTTTAAGTGTGATATTCGGGTT
1 GAGTATGGTCGGGTTTTTTTAAGTGTGATATTCGGGTT
*
4164219 GAGTCTGGTCGGGTTTTTTTAAGTGTGATATTCGGGT
1 GAGTATGGTCGGGTTTTTTTAAGTGTGATATTCGGGT
4164256 CGGGTTCGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 12 0.34
38 23 0.66
ACGTcount: A:0.15, C:0.07, G:0.35, T:0.43
Consensus pattern (38 bp):
GAGTATGGTCGGGTTTTTTTAAGTGTGATATTCGGGTT
Found at i:4164487 original size:254 final size:251
Alignment explanation
Indices: 4163961--4164488 Score: 749
Period size: 254 Copynumber: 2.1 Consensus size: 251
4163951 TTTTGTTTGG
* *
4163961 GTCGGATCGGGTTTTTTTAAGTGTGATATTCGGTTTGGGTCGGGTCGGGTTTATGGTGAAAAAAA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTC----TGGGTCGGGTCGGGTTTAGGGTG-AAAAAA
*
4164026 ACCGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAA
61 ACCGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCAGATTAAGTCACTGTTTTTATTAAA
*
4164091 TAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTTGGATTTCTAATTCATATATTCGGGTCG
126 TAAAAATAATTTTTTATTATTTCGGGTCGGGTC--G--GGATTTCTAATTCATATATTCGGGTCG
* * * *
4164156 GGTCGGATGAAACTTTATTTTTTTTCGAGTATGGTCGGGTTTTTTAAGTGTGATATTCGGGTTGA
187 GGTCGGATGAAACTTTATTTTTGTTCGAGTAGGGTCGGGTTTTTTAAGTGTGATATTCAGGTCGA
*
4164221 GTCTGGTCGGGTTTTTTTAAGTGTGATATTC-GGGTCGGGTTCGGGTTTAGGGTG-AAAAAACCG
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCTGGGTCGGG-TCGGGTTTAGGGTGAAAAAAACCG
*
4164284 GACCGACCCGAAAATATATATAATTCGGGTCGGGTCAGATTAAGTCACTGTTTTTATTAAATAAA
65 GACCGACCCGAAAATATATATAATTCAGGTCGGGTCAGATTAAGTCACTGTTTTTATTAAATAAA
*
4164349 CATAATTTTTTATTATTTCGGGTCGGGTC-GGATTTCTAATTCATATATTCGGGTCAGGTCGGGT
130 AATAATTTTTTATTATTTCGGGTCGGGTCGGGATTTCTAATTCATATATTC--G---GGTCGGGT
* * *
4164413 CGGATGAAACTTTA-TTTTGTTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCAGGTCGA
190 CGGATGAAACTTTATTTTTGTTCGAGTAGGGTCGGGTTTTTTAAGTGTGATATTCAGGTCGA
*
4164474 GTGGGGTTCGGGTTT
1 GTCGGG-TCGGGTTT
4164489 AGGGTGAAAA
Statistics
Matches: 245, Mismatches: 16, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
249 21 0.09
251 1 0.00
253 44 0.18
254 129 0.53
255 8 0.03
256 13 0.05
260 29 0.12
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (251 bp):
GTCGGGTCGGGTTTTTTTAAGTGTGATATTCTGGGTCGGGTCGGGTTTAGGGTGAAAAAAACCGG
ACCGACCCGAAAATATATATAATTCAGGTCGGGTCAGATTAAGTCACTGTTTTTATTAAATAAAA
ATAATTTTTTATTATTTCGGGTCGGGTCGGGATTTCTAATTCATATATTCGGGTCGGGTCGGATG
AAACTTTATTTTTGTTCGAGTAGGGTCGGGTTTTTTAAGTGTGATATTCAGGTCGA
Found at i:4165077 original size:16 final size:18
Alignment explanation
Indices: 4165053--4165098 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
4165043 TATGGAATTG
4165053 GATTCCAATT-CTT-ACA
1 GATTCCAATTCCTTCACA
*
4165069 GATTTCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
4165087 GATTCTAATTCC
1 GATTCCAATTCC
4165099 CTCATAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 9 0.36
17 3 0.12
18 13 0.52
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.39
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:4165338 original size:18 final size:16
Alignment explanation
Indices: 4165302--4165347 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
4165292 ATTGGAATTG
4165302 GATTCCAATTCCTACA
1 GATTCCAATTCCTACA
*
4165318 GATTTCAATTCCTTCACA
1 GATTCCAATTCC-T-ACA
*
4165336 GATTCTAATTCC
1 GATTCCAATTCC
4165348 CTCATAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.44
17 1 0.04
18 13 0.52
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.37
Consensus pattern (16 bp):
GATTCCAATTCCTACA
Found at i:4165586 original size:18 final size:16
Alignment explanation
Indices: 4165550--4165595 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
4165540 ATTGGAATTG
4165550 GATTCCAATTCCTACA
1 GATTCCAATTCCTACA
*
4165566 GATTTCAATTCCTTCACA
1 GATTCCAATTCC-T-ACA
*
4165584 GATTCTAATTCC
1 GATTCCAATTCC
4165596 CTCATAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.44
17 1 0.04
18 13 0.52
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.37
Consensus pattern (16 bp):
GATTCCAATTCCTACA
Found at i:4165660 original size:248 final size:249
Alignment explanation
Indices: 4165045--4165784 Score: 1457
Period size: 248 Copynumber: 3.0 Consensus size: 249
4165035 AAACAGAATA
*
4165045 TGGAATTGGATTCCAATTCTTACAGATTTCAATTCCTTCACAGATTCTAATTCCCTCATAAACAT
1 TGGAATTGGATTCCAATTCCTACAGATTTCAATTCCTTCACAGATTCTAATTCCCTCATAAACAT
4165110 TCCAGCGAACCAAACGCCACTTTAGTGTTAATATGGACTATTTGAGTTATTTGTTCATTAAAGTA
66 TCCAGCGAACCAAACGCCACTTTAGTGTTAATATGGACTATTTGAGTTATTTGTTCATTAAAGTA
4165175 TACTTTAGGGGTTTATTAATGATTAACAAAGTGATCTTAGTGGTTAAAGAGATAATTGTTAATTT
131 TACTTTAGGGGTTTATTAATGATTAACAAAGTGATCTTAGTGGTTAAAGAGATAATTGTTAATTT
4165240 TAGACGTAATGGATTAAAATACCAAGGATTACATTAGGGTATTTTAGACGTAAT
196 TAGACGTAATGGATTAAAATACCAAGGATTACATTAGGGTATTTTAGACGTAAT
4165294 TGGAATTGGATTCCAATTCCTACAGATTTCAATTCCTTCACAGATTCTAATTCCCTCATAAACAT
1 TGGAATTGGATTCCAATTCCTACAGATTTCAATTCCTTCACAGATTCTAATTCCCTCATAAACAT
4165359 TCCAGCGAACCAAACGCCACTTTAGTGTTAATATGGACTATTTGAGTTATTTGTTCATTAAAGTA
66 TCCAGCGAACCAAACGCCACTTTAGTGTTAATATGGACTATTTGAGTTATTTGTTCATTAAAGTA
4165424 TACTTTAGGGGTTTATTAATGATTAACAAAGTGATCTTAGTGGTTAAAGAGATAATTGTTAA-TT
131 TACTTTAGGGGTTTATTAATGATTAACAAAGTGATCTTAGTGGTTAAAGAGATAATTGTTAATTT
4165488 TAGACGTAATGGATTAAAATACCAAGGATTACATTAGGGTATTTTAGACGTAAT
196 TAGACGTAATGGATTAAAATACCAAGGATTACATTAGGGTATTTTAGACGTAAT
4165542 TGGAATTGGATTCCAATTCCTACAGATTTCAATTCCTTCACAGATTCTAATTCCCTCATAAACAT
1 TGGAATTGGATTCCAATTCCTACAGATTTCAATTCCTTCACAGATTCTAATTCCCTCATAAACAT
4165607 TCCAGCGAACCAAACGCCACTTTAGTGTTAATATGGACTATTTGAGTTATTTGTTCATTAAAGTA
66 TCCAGCGAACCAAACGCCACTTTAGTGTTAATATGGACTATTTGAGTTATTTGTTCATTAAAGTA
4165672 TACTTTAGGGGTTTATTAATGATTAACAAAGTGATCTTAGTGGTTAAAGAGATAATTGTTAATTT
131 TACTTTAGGGGTTTATTAATGATTAACAAAGTGATCTTAGTGGTTAAAGAGATAATTGTTAATTT
4165737 TAGACGTAATGGATTAAAATACCAAGGATTACATTAGGGTA-TTTAGAC
196 TAGACGTAATGGATTAAAATACCAAGGATTACATTAGGGTATTTTAGAC
4165785 CAAAAGTTTC
Statistics
Matches: 489, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
248 255 0.52
249 234 0.48
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (249 bp):
TGGAATTGGATTCCAATTCCTACAGATTTCAATTCCTTCACAGATTCTAATTCCCTCATAAACAT
TCCAGCGAACCAAACGCCACTTTAGTGTTAATATGGACTATTTGAGTTATTTGTTCATTAAAGTA
TACTTTAGGGGTTTATTAATGATTAACAAAGTGATCTTAGTGGTTAAAGAGATAATTGTTAATTT
TAGACGTAATGGATTAAAATACCAAGGATTACATTAGGGTATTTTAGACGTAAT
Found at i:4170913 original size:22 final size:20
Alignment explanation
Indices: 4170873--4170913 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
4170863 ATCCTTATCC
4170873 TATTTTTTTATTAAAATAAA
1 TATTTTTTTATTAAAATAAA
*
4170893 TATTTTTATTTTTCAAAATAA
1 TATTTTT-TTATT-AAAATAA
4170914 CTCTCATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTTTTTTATTAAAATAAA
Found at i:4171320 original size:15 final size:17
Alignment explanation
Indices: 4171300--4171341 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
4171290 CTACATTTTT
*
4171300 TAAAATTA-AA-ATATA
1 TAAAATTATAAGATAGA
4171315 TAAAATTATAAGATAGA
1 TAAAATTATAAGATAGA
*
4171332 TAAAAATATA
1 TAAAATTATA
4171342 TTTAAATTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 8 0.35
16 2 0.09
17 13 0.57
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (17 bp):
TAAAATTATAAGATAGA
Found at i:4173963 original size:227 final size:227
Alignment explanation
Indices: 4173722--4174145 Score: 636
Period size: 228 Copynumber: 1.9 Consensus size: 227
4173712 AAATATTTTT
* ** * **
4173722 ATCTAAACCTTAAAAAAGACTTTGTAGATATTAA-ACTTGTCATGTTCAATTCAAATAATTTATT
1 ATCTAAACCTTAAAAAAGACTTTGTAAATATTAATACTAATCATGTTCAATCCAAATAATTTACG
4173786 TCACGTTGATTTGAAACTTAAAATCACATAAAGTAAAACATTTCTGACAAAGAAACAGAACAAAA
66 TCACGTTGATTTGAAACTTAAAATCACATAAAGTAAAACATTTCTGACAAAGAAACAGAACAAAA
* *
4173851 AAGACT-TTTGGAAAATGAGTTATGTTTCTTTCCCCCAAAAATTTACAAGAGCCCTAGACTCTGT
131 AAGA-TGTTTGAAAAATGAATTATGTTTCTTTCCCCCAAAAATTTAC-AGAGCCCTAGACTCTGT
4173915 AAATATAGAGAGAGGGGGGGGAGAAAGCGATTTC
194 AAATATAGAGAGAGGGGGGGGAGAAAGCGATTTC
* *
4173949 ATCTAAACCTTAAAAACGACTTTGTAAATATTAATCCTAATCATGTTCAATCCAAATAATTTACG
1 ATCTAAACCTTAAAAAAGACTTTGTAAATATTAATACTAATCATGTTCAATCCAAATAATTTACG
** * * * * *
4174014 TCATTTTGATTTGAAACTTAAAATCACCTAAAGTCAAACATTTGTGATAAAGAAACAGAACATAA
66 TCACGTTGATTTGAAACTTAAAATCACATAAAGTAAAACATTTCTGACAAAGAAACAGAACAAAA
* * *
4174079 AATATGTTTGAAAAATGAATTATGTTTCTTTCCCCTAAAAATTTACAGAGCCCTAGACTTTGTAA
131 AAGATGTTTGAAAAATGAATTATGTTTCTTTCCCCCAAAAATTTACAGAGCCCTAGACTCTGTAA
4174144 AT
196 AT
4174146 GGGGGGAAGA
Statistics
Matches: 175, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
227 53 0.30
228 122 0.70
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (227 bp):
ATCTAAACCTTAAAAAAGACTTTGTAAATATTAATACTAATCATGTTCAATCCAAATAATTTACG
TCACGTTGATTTGAAACTTAAAATCACATAAAGTAAAACATTTCTGACAAAGAAACAGAACAAAA
AAGATGTTTGAAAAATGAATTATGTTTCTTTCCCCCAAAAATTTACAGAGCCCTAGACTCTGTAA
ATATAGAGAGAGGGGGGGGAGAAAGCGATTTC
Found at i:4186613 original size:28 final size:28
Alignment explanation
Indices: 4186580--4186638 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
4186570 AAATTAATGT
* *
4186580 TATTTCAAGTTTTAATTAATAAGAATTA
1 TATTTCAAGTTTTAATTAATAAAAATAA
*
4186608 TATTTCGAGTTTTAATTAATAAAAATAA
1 TATTTCAAGTTTTAATTAATAAAAATAA
4186636 TAT
1 TAT
4186639 ATAGGTGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (28 bp):
TATTTCAAGTTTTAATTAATAAAAATAA
Found at i:4190472 original size:15 final size:14
Alignment explanation
Indices: 4190452--4190514 Score: 58
Period size: 15 Copynumber: 4.4 Consensus size: 14
4190442 CAGATAAAAA
4190452 AATATAATCTTAATT
1 AATATAATCTTAA-T
*
4190467 AATATAAACCTTAAT
1 AATAT-AATCTTAAT
*
4190482 AATA-AATATTAATCT
1 AATATAATCTTAA--T
4190497 AATATAAT-TTAAT
1 AATATAATCTTAAT
4190510 AATAT
1 AATAT
4190515 TGTATAAGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
13 12 0.29
15 19 0.46
16 10 0.24
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATAATCTTAAT
Found at i:4193159 original size:23 final size:22
Alignment explanation
Indices: 4193117--4193197 Score: 108
Period size: 23 Copynumber: 3.6 Consensus size: 22
4193107 ATTCTACCTG
*
4193117 TATGACACATTTTTTCTGTCTT
1 TATGACACATTTTTTTTGTCTT
*
4193139 TATGACATATTTTTCTTTGTCTT
1 TATGACACATTTTT-TTTGTCTT
* *
4193162 TATGACACAATTTTATTTATCTT
1 TATGACAC-ATTTTTTTTGTCTT
4193185 TATGACACATTTT
1 TATGACACATTTT
4193198 CGTTCATTTG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
22 18 0.35
23 29 0.56
24 5 0.10
ACGTcount: A:0.23, C:0.15, G:0.07, T:0.54
Consensus pattern (22 bp):
TATGACACATTTTTTTTGTCTT
Found at i:4198900 original size:22 final size:22
Alignment explanation
Indices: 4198874--4198917 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4198864 CCTTGATAAT
*
4198874 TATAGGGTGAAGTATACAAATA
1 TATAGGGTAAAGTATACAAATA
4198896 TATAGGGTAAAGTATACAAATA
1 TATAGGGTAAAGTATACAAATA
4198918 ATCCCTCGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (22 bp):
TATAGGGTAAAGTATACAAATA
Found at i:4217146 original size:18 final size:18
Alignment explanation
Indices: 4217123--4217157 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4217113 GTGATGGCGG
*
4217123 CATCATATATGGCTGCGA
1 CATCATAAATGGCTGCGA
4217141 CATCATAAATGGCTGCG
1 CATCATAAATGGCTGCG
4217158 GTGGCTGCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (18 bp):
CATCATAAATGGCTGCGA
Found at i:4221061 original size:19 final size:18
Alignment explanation
Indices: 4221037--4221085 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
4221027 CTAATATTTG
4221037 ATTAAATTATTATTATATT
1 ATTAAATTATTATTA-ATT
*
4221056 ATTAAAGTATT-TTAATT
1 ATTAAATTATTATTAATT
4221073 -TTAATATT-TTATT
1 ATTAA-ATTATTATT
4221086 TGGGATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 6 0.23
17 7 0.27
18 3 0.12
19 10 0.38
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
ATTAAATTATTATTAATT
Found at i:4227908 original size:2 final size:2
Alignment explanation
Indices: 4227901--4227928 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4227891 ATAGTTCTAC
4227901 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
4227929 GGGTCACTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4229243 original size:17 final size:17
Alignment explanation
Indices: 4229194--4229244 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
4229184 GAAATTTAAA
*
4229194 ATTTCAAAA-TATATTT
1 ATTTCAAAATTATAATT
*
4229210 AATTT-AAAATTCT-ATT
1 -ATTTCAAAATTATAATT
4229226 ATTTCAAAATTATAATT
1 ATTTCAAAATTATAATT
4229243 AT
1 AT
4229245 GAGAAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 4 0.14
16 13 0.46
17 11 0.39
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTCAAAATTATAATT
Found at i:4229293 original size:23 final size:26
Alignment explanation
Indices: 4229250--4229299 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
4229240 ATTATGAGAA
*
4229250 AAAATAATTTATATATATTTATAAAT
1 AAAATAATTTATATATATTTAGAAAT
4229276 AAAAT-ATTTAT-T-TATTTAGAAAT
1 AAAATAATTTATATATATTTAGAAAT
4229299 A
1 A
4229300 TCAGAAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 6 0.26
26 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AAAATAATTTATATATATTTAGAAAT
Found at i:4230527 original size:17 final size:17
Alignment explanation
Indices: 4230502--4230535 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4230492 TTATTTCGAA
4230502 AAAAATAAAATACAAAT
1 AAAAATAAAATACAAAT
*
4230519 AAAAGTAAAATACAAAT
1 AAAAATAAAATACAAAT
4230536 CTGAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAATAAAATACAAAT
Found at i:4231480 original size:24 final size:23
Alignment explanation
Indices: 4231445--4231489 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
4231435 TGAACAAGCT
4231445 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
4231469 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
4231490 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:4231619 original size:112 final size:113
Alignment explanation
Indices: 4231429--4231948 Score: 850
Period size: 112 Copynumber: 4.6 Consensus size: 113
4231419 AGCATCAAAC
* ** * * *
4231429 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATT
1 AAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATT
4231494 ATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAG-GCA
65 ATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGAGCA
4231542 AAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
1 AAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
*
4231607 TGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTC-GAGCA
66 TGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGAGCA
4231654 AAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
1 AAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
* *
4231719 TGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAA-TCCGAGCA
66 TGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGAGCA
* *
4231766 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
1 AAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
** * *
4231831 TGAACTTTCTCTGGAAAAAATAATTCATCAAGTGATGAATTCAG-GGA
66 TGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGAGCA
* *
4231878 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
1 AAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
4231943 TGAACT
66 TGAACT
4231949 CTAACTGGCA
Statistics
Matches: 385, Mismatches: 19, Indels: 7
0.94 0.05 0.02
Matches are distributed among these distances:
111 3 0.01
112 342 0.89
113 40 0.10
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (113 bp):
AAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
TGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGAGCA
Found at i:4231992 original size:224 final size:224
Alignment explanation
Indices: 4231429--4232010 Score: 869
Period size: 224 Copynumber: 2.6 Consensus size: 224
4231419 AGCATCAAAC
** * *
4231429 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATT
* * *
4231494 ATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGGCAAAAGGTTAAACAAATTC
65 ATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCAAGCAAAAGGTTAAACAAGTTC
*
4231559 TTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA
130 TTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA
***
4231624 TGTTAATCCATCAAGTGATGAATTCGAGCA
195 AAATAATCCATCAAGTGATGAATTCGAGCA
* *
4231654 AAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
* *
4231719 TGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATCCGAGCAAAAGGTTAAACAAGTTCT
66 TGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCT
4231784 TCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAA
131 TCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAA
* *
4231849 AATAATTCATCAAGTGATGAATTC-AGGGA
196 AATAATCCATCAAGTGATGAATTCGA-GCA
4231878 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
* ** * * * * * ** * * *
4231943 TGAACTCTAACTGGCACTGCTGATCCACCGGGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCT
66 TGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCT
4232008 TCT
131 TCT
4232011 TCTTCAAATG
Statistics
Matches: 322, Mismatches: 34, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
223 1 0.00
224 284 0.88
225 37 0.11
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (224 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCT
TCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAA
AATAATCCATCAAGTGATGAATTCGAGCA
Found at i:4232016 original size:92 final size:92
Alignment explanation
Indices: 4231912--4232102 Score: 301
Period size: 92 Copynumber: 2.1 Consensus size: 92
4231902 TATGAATTTC
* * * * ***
4231912 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGCACTGCTGATCCACCGGGTG
1 TTCTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTGGCAATGATGATCCACCAAATG
4231977 ATGAATTTAAGCAAAAAGTTGAACAAG
66 ATGAATTTAAGCAAAAAGTTGAACAAG
* *
4232004 TTCTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTGGTAATGATGATCCATCAAATG
1 TTCTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTGGCAATGATGATCCACCAAATG
4232069 ATGAATTTAAGCAAAAAGTTGAACAAG
66 ATGAATTTAAGCAAAAAGTTGAACAAG
4232096 TTCTTCT
1 TTCTTCT
4232103 CATTATGAAC
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (92 bp):
TTCTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTGGCAATGATGATCCACCAAATG
ATGAATTTAAGCAAAAAGTTGAACAAG
Found at i:4232073 original size:204 final size:205
Alignment explanation
Indices: 4231800--4232215 Score: 555
Period size: 204 Copynumber: 2.0 Consensus size: 205
4231790 TATGAACTTC
* * * ** * *
4231800 TTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAATAATTCATCAAGTG
1 TTCTTCTTCTTCAAATAAGTTCTTCTCATTATGAACTCTAACTGGAAAAAATAATCCATCAAATG
* * * *
4231865 ATGAATTCAGGGAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATG
66 ATGAATTCAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * **
4231929 AGTTCTTCTCATTATGAACTCTAACTGGCACTGCTGATCCACCGGGTGATGAATTTAAGCAAAAA
131 AGTTCTTCTCATTATGAACTCTAACTGGAAATGCTGATCCACCGAATGATGAATTTAAGCAAAAA
*
4231994 GTTGAACAAG
196 GTTGAACAAA
* * ** *
4232004 TTCTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTGGTAATGATGATCCATCAAATG
1 TTCTTCTTCTTCAAATAAGTTCTTCTCATTATGAACTCTAACTGGAAAAAATAATCCATCAAATG
* *
4232069 ATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 ATGAATTCAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* ** * * * *
4232134 AGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCGAATGATGGATTTGAGCAAAAG
131 AGTTCTTCTCATTATGAACTCTAACTGGAAATGCTGATCCACCGAATGATGAATTTAAGCAAAAA
4232199 GTTGAACAAA
196 GTTGAACAAA
4232209 TTCTTCT
1 TTCTTCT
4232216 CATTATGAAT
Statistics
Matches: 181, Mismatches: 30, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
204 101 0.56
205 80 0.44
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (205 bp):
TTCTTCTTCTTCAAATAAGTTCTTCTCATTATGAACTCTAACTGGAAAAAATAATCCATCAAATG
ATGAATTCAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
AGTTCTTCTCATTATGAACTCTAACTGGAAATGCTGATCCACCGAATGATGAATTTAAGCAAAAA
GTTGAACAAA
Found at i:4232135 original size:113 final size:113
Alignment explanation
Indices: 4232004--4232417 Score: 668
Period size: 113 Copynumber: 3.7 Consensus size: 113
4231994 GTTGAACAAG
* * ** * * *
4232004 TTCTT-CTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTGGTAATGATGATCCATCAAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAAT
* * * * *
4232068 GATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
66 GATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
* * *
4232116 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCGAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAAT
4232181 GATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
66 GATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
*
4232229 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAAT
4232294 GATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
66 GATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
*
4232342 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCATAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAAT
4232407 GATGGATTTGA
66 GATGGATTTGA
4232418 ATCTTTGCTA
Statistics
Matches: 284, Mismatches: 17, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
112 5 0.02
113 279 0.98
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (113 bp):
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAAT
GATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
Found at i:4232844 original size:22 final size:22
Alignment explanation
Indices: 4232819--4232871 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
4232809 TAAAGTTTTA
**
4232819 ATCTTTGAAAAGAGAATCTGTC
1 ATCTTTGAAAAGAGAATCTACC
*
4232841 ATCTTTAAAAAGAGAATCTACC
1 ATCTTTGAAAAGAGAATCTACC
4232863 ATCTTTGAA
1 ATCTTTGAA
4232872 GAGTGTAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (22 bp):
ATCTTTGAAAAGAGAATCTACC
Found at i:4235579 original size:83 final size:83
Alignment explanation
Indices: 4235439--4235703 Score: 460
Period size: 83 Copynumber: 3.2 Consensus size: 83
4235429 CTTATTTCTA
* *
4235439 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTATGTCC-AACCAGATTAGATAACTCAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTG-CCAAACCAGATCAGATAACTCAA
4235503 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* *
4235522 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
4235587 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
4235605 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
4235670 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
4235688 CTATGAGCACATTCAT
1 CTATGAGCAAATTCAT
4235704 TTGTTCCATT
Statistics
Matches: 174, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
82 2 0.01
83 172 0.99
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:4237947 original size:7 final size:7
Alignment explanation
Indices: 4237931--4237971 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
4237921 CTTTATTCGA
*
4237931 TTTTCCT
1 TTTTCTT
4237938 TTTTCTT
1 TTTTCTT
4237945 TTTTCTT
1 TTTTCTT
4237952 TTTT-TT
1 TTTTCTT
4237958 TTCTT-TT
1 TT-TTCTT
4237965 TTTTCTT
1 TTTTCTT
4237972 CTTCTTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTCTT
Found at i:4237959 original size:11 final size:11
Alignment explanation
Indices: 4237938--4237974 Score: 56
Period size: 11 Copynumber: 3.2 Consensus size: 11
4237928 CGATTTTCCT
4237938 TTTTCTTTTTTC
1 TTTT-TTTTTTC
4237950 TTTTTTTTTTC
1 TTTTTTTTTTC
4237961 TTTTTTTTCTTC
1 TTTTTTTT-TTC
4237973 TT
1 TT
4237975 CTTTCTTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:4237959 original size:19 final size:19
Alignment explanation
Indices: 4237931--4237982 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
4237921 CTTTATTCGA
*
4237931 TTTTCCTTTTTCTTTTTTC
1 TTTTCTTTTTTCTTTTTTC
4237950 TTTT-TTTTTTCTTTTTT-
1 TTTTCTTTTTTCTTTTTTC
*
4237967 TTCTTCTTCTTTCTTT
1 TT-TTCTTTTTTCTTT
4237983 GCTGGATGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 2 0.07
18 14 0.48
19 13 0.45
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTCTTTTTTCTTTTTTC
Found at i:4241283 original size:14 final size:14
Alignment explanation
Indices: 4241249--4241302 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
4241239 TTGTGCAATA
* *
4241249 CAAATGCAAAGATG
1 CAAATGTAAATATG
4241263 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
4241278 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
4241292 TAAATGTAAAT
1 CAAATGTAAAT
4241303 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:4242883 original size:18 final size:17
Alignment explanation
Indices: 4242855--4242913 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 17
4242845 TAACAGATAA
*
4242855 ATAAAATTAATACCTGAAT
1 ATAAAAATAATA--TGAAT
*
4242874 A-AAAAATAATATTAAT
1 ATAAAAATAATATGAAT
4242890 ATAAAAATAATA--AAT
1 ATAAAAATAATATGAAT
4242905 AATAAAAAT
1 -ATAAAAAT
4242914 TTGAAAGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
15 3 0.08
16 13 0.36
17 10 0.28
18 9 0.25
19 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (17 bp):
ATAAAAATAATATGAAT
Found at i:4243396 original size:17 final size:17
Alignment explanation
Indices: 4243347--4243397 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
4243337 GAAATTTAAA
*
4243347 ATTTCAAAA-TATATTT
1 ATTTCAAAATTATAATT
*
4243363 AATTT-AAAATTCT-ATT
1 -ATTTCAAAATTATAATT
4243379 ATTTCAAAATTATAATT
1 ATTTCAAAATTATAATT
4243396 AT
1 AT
4243398 GAGAAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 4 0.14
16 13 0.46
17 11 0.39
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTCAAAATTATAATT
Found at i:4243441 original size:22 final size:23
Alignment explanation
Indices: 4243399--4243449 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
4243389 TATAATTATG
4243399 AGAAA-AAATAATTTATATATTT
1 AGAAATAAATAATTTATATATTT
* *
4243421 ATAAATAAAT-ATTTATTTATTT
1 AGAAATAAATAATTTATATATTT
4243443 AGAAATA
1 AGAAATA
4243450 TCAGAAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
AGAAATAAATAATTTATATATTT
Found at i:4244664 original size:17 final size:17
Alignment explanation
Indices: 4244639--4244672 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4244629 TATTTCGAAA
4244639 AAAAATAAAATACAAAT
1 AAAAATAAAATACAAAT
*
4244656 AAAAGTAAAATACAAAT
1 AAAAATAAAATACAAAT
4244673 CTGAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAATAAAATACAAAT
Found at i:4245409 original size:17 final size:17
Alignment explanation
Indices: 4245387--4245425 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
4245377 TGAATCAAAT
4245387 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
4245404 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
4245421 -AATTA
1 TAATTA
4245426 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:4246356 original size:20 final size:21
Alignment explanation
Indices: 4246331--4246382 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
4246321 TTTTCCCAAT
*
4246331 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
4246351 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
4246372 TCGCAATGCGA
1 TCGCAATGCGA
4246383 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:4246396 original size:20 final size:20
Alignment explanation
Indices: 4246371--4246484 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
4246361 AATTGGGAAA
*
4246371 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
4246391 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
4246411 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
4246432 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
4246452 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
4246472 TTCGCAACGCGAT
1 ATCGCAACGCGAT
4246485 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:4246415 original size:61 final size:61
Alignment explanation
Indices: 4246368--4246484 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
4246358 GCGAATTGGG
* * * * *
4246368 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
4246429 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
4246485 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:4247036 original size:19 final size:19
Alignment explanation
Indices: 4246998--4247064 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
4246988 TTCGAGAATG
4246998 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
4247018 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* *
4247037 AAAAACGCAACGCGAAACA
1 AAAATCGCAACGCGAAATA
4247056 AAAATCGCA
1 AAAATCGCA
4247065 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.51, C:0.24, G:0.16, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:4247082 original size:19 final size:19
Alignment explanation
Indices: 4247060--4247211 Score: 170
Period size: 19 Copynumber: 8.1 Consensus size: 19
4247050 GAAACAAAAA
* *
4247060 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
4247079 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
4247098 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
4247117 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
4247137 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
4247151 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
4247170 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
4247190 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
4247210 TC
1 TC
4247212 AACCAAAAGA
Statistics
Matches: 114, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
14 10 0.09
16 2 0.02
17 3 0.03
19 49 0.43
20 49 0.43
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:4247137 original size:39 final size:38
Alignment explanation
Indices: 4247060--4247211 Score: 170
Period size: 39 Copynumber: 4.1 Consensus size: 38
4247050 GAAACAAAAA
*
4247060 TCGCATTGCGATTTTTATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
4247098 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGC-GTTGCGATTTTCATT
* * **
4247137 TCGCGTTGCGA----T-TCTCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
* * *
4247170 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTTATT-TCGCGTTGCGATTTTCATT
4247210 TC
1 TC
4247212 AACCAAAAGA
Statistics
Matches: 97, Mismatches: 9, Indels: 15
0.80 0.07 0.12
Matches are distributed among these distances:
33 14 0.14
34 14 0.14
35 1 0.01
38 22 0.23
39 28 0.29
40 18 0.19
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
Found at i:4247169 original size:33 final size:34
Alignment explanation
Indices: 4247122--4247186 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
4247112 TTATTTCGCG
**
4247122 GTTGCGATTTTCATTT-CGCGTTGCGATTCTCTC
1 GTTGCGATAGTCATTTCCGCGTTGCGATTCTCTC
4247155 GTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 GTTGCGATAGTCATTTCCGCGTTGCGATTCTC
4247187 ATTATCTCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 14 0.48
34 15 0.52
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (34 bp):
GTTGCGATAGTCATTTCCGCGTTGCGATTCTCTC
Found at i:4247179 original size:20 final size:19
Alignment explanation
Indices: 4247154--4247211 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
4247144 GCGATTCTCT
**
4247154 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTT-CG
* *
4247174 CGTTGCGATTCTCATTATCT
1 CGTTGCGATTTTCATT-TCG
4247194 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
4247212 AACCAAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.91
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:4249257 original size:42 final size:42
Alignment explanation
Indices: 4249197--4249319 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
4249187 GCCCGACTCG
* * *
4249197 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
4249239 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
4249281 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
4249320 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:4249277 original size:21 final size:21
Alignment explanation
Indices: 4249253--4249319 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
4249243 TCATTCCTCG
4249253 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
4249274 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
4249295 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
4249316 AGAG
1 AGAG
4249320 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:4250698 original size:14 final size:14
Alignment explanation
Indices: 4250679--4250714 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4250669 ATTGTTTAAT
*
4250679 TGATTTGTAAAAGG
1 TGATTTGTAAAACG
*
4250693 TGATTTGTAAAACT
1 TGATTTGTAAAACG
4250707 TGATTTGT
1 TGATTTGT
4250715 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAACG
Found at i:4250915 original size:19 final size:19
Alignment explanation
Indices: 4250893--4251043 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
4250883 CGAAATTAAA
4250893 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
4250912 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
4250927 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
4250945 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
4250959 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
4250978 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
4250993 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
4251011 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
4251030 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
4251044 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:4250939 original size:33 final size:32
Alignment explanation
Indices: 4250897--4251023 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
4250887 ATTAAATTCG
4250897 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
4250930 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
4250963 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
4250996 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
4251024 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:4250986 original size:66 final size:66
Alignment explanation
Indices: 4250890--4251022 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
4250880 ACGCGAAATT
*
4250890 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
4250955 G
66 G
*
4250956 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
4251021 G
66 G
4251022 A
1 A
4251023 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:4253346 original size:20 final size:19
Alignment explanation
Indices: 4253311--4253376 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
4253301 GAAACTTAAA
4253311 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
4253330 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
4253350 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
4253369 ATCGCAAC
1 ATCGCAAC
4253377 AACAAAATCG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:4253408 original size:32 final size:33
Alignment explanation
Indices: 4253350--4253423 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 33
4253340 GGAAATGGCT
*
4253350 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAACAAA
*
4253383 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAACAAA
*
4253415 ATTGCAACG
1 ATCGCAACG
4253424 ACAAAATCGC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
32 23 0.61
33 15 0.39
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACAACAAA
Found at i:4253437 original size:14 final size:14
Alignment explanation
Indices: 4253366--4253437 Score: 81
Period size: 14 Copynumber: 4.9 Consensus size: 14
4253356 ATGCGAAATG
*
4253366 AAAATCGCAACAAC
1 AAAATCGCAACGAC
*
4253380 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
4253396 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
4253412 AAAATTGCAACGAC
1 AAAATCGCAACGAC
4253426 AAAATCGCAACG
1 AAAATCGCAACG
4253438 CGAAACACAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
14 33 0.67
16 7 0.14
18 9 0.18
ACGTcount: A:0.50, C:0.25, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:4253490 original size:14 final size:14
Alignment explanation
Indices: 4253471--4253528 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
4253461 TTTCATTTCG
4253471 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
4253485 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
4253501 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
4253517 CGTTGCGATTTT
1 CGTTGCGATTTT
4253529 TATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:4253539 original size:33 final size:33
Alignment explanation
Indices: 4253454--4253544 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
4253444 ACAAATCGCA
*
4253454 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
4253487 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
4253519 TTGCGATTTTTATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
4253545 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:4253552 original size:19 final size:20
Alignment explanation
Indices: 4253530--4253572 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4253520 TGCGATTTTT
4253530 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
4253549 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
4253569 ATTT
1 ATTT
4253573 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:4253563 original size:20 final size:20
Alignment explanation
Indices: 4253538--4253583 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
4253528 TTATTTCGCA
4253538 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
4253558 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
4253578 TTGCGA
1 TTGCGA
4253584 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:4254083 original size:18 final size:18
Alignment explanation
Indices: 4254057--4254101 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
4254047 GTCGATCAGA
*
4254057 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
4254075 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
4254093 TGATGGCTC
1 TGATGGCTC
4254102 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:4255445 original size:20 final size:20
Alignment explanation
Indices: 4255420--4255462 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
4255410 ATAGTTTTCT
4255420 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
4255440 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
4255460 GAA
1 GAA
4255463 TTCGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:4255978 original size:20 final size:20
Alignment explanation
Indices: 4255952--4256024 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
4255942 GATTATGTAT
4255952 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
4255972 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
4255992 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
4256012 TATCTCGTTGCGA
1 TATCGCGTTGCGA
4256025 TTTTTTATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Done.