Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 117 of 208
Found at i:35545939 original size:27 final size:27
Alignment explanation
Indices: 35545901--35545976 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
35545891 ATAATACGAG
*
35545901 TGGTGCCACCAATGGCATTGGCACCAT
1 TGGTGCCGCCAATGGCATTGGCACCAT
** *
35545928 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGCATTGGCACCAT
**
35545955 TGGTGCCGCCAATTCCATTGGC
1 TGGTGCCGCCAATGGCATTGGC
35545977 GTGACCAGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.16, C:0.29, G:0.28, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAATGGCATTGGCACCAT
Found at i:35546067 original size:24 final size:24
Alignment explanation
Indices: 35546040--35546085 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
35546030 GTTTTTTTTG
35546040 ATATATTTTGGTAAATAAAAAATT
1 ATATATTTTGGTAAATAAAAAATT
35546064 ATATATTTTGGTAAATAAAAAA
1 ATATATTTTGGTAAATAAAAAA
35546086 AAGTAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (24 bp):
ATATATTTTGGTAAATAAAAAATT
Found at i:35546106 original size:24 final size:24
Alignment explanation
Indices: 35546040--35546107 Score: 91
Period size: 24 Copynumber: 2.7 Consensus size: 24
35546030 GTTTTTTTTG
*
35546040 ATATATTTTGGTAAATAAAAAATT
1 ATATATTTTGGTAAATAAAAAATA
35546064 ATATATTTTGGTAAATAAAAAAAAGTA
1 ATATATTTTGGTAAAT--AAAAAA-TA
35546091 ATAATATTTTGGTAAAT
1 AT-ATATTTTGGTAAAT
35546108 TTTTATTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
24 16 0.41
26 6 0.15
27 3 0.08
28 14 0.36
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (24 bp):
ATATATTTTGGTAAATAAAAAATA
Found at i:35546523 original size:5 final size:5
Alignment explanation
Indices: 35546513--35546537 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
35546503 TGTATTTAAA
35546513 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
35546538 TAAACAGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:35567565 original size:11 final size:11
Alignment explanation
Indices: 35567549--35567582 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
35567539 CGGCCCATAA
35567549 TAAATATATAT
1 TAAATATATAT
35567560 TAAATATATA-
1 TAAATATATAT
35567570 TAATATATATAT
1 TAA-ATATATAT
35567582 T
1 T
35567583 TGATTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 17 0.81
12 1 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TAAATATATAT
Found at i:35579096 original size:49 final size:49
Alignment explanation
Indices: 35579039--35579138 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
35579029 AGGGTTAGGG
35579039 GTGTTACATGCAACGTGCTTTAACCTAATAACACAAAAAACAATAAAGT
1 GTGTTACATGCAACGTGCTTTAACCTAATAACACAAAAAACAATAAAGT
35579088 GTGTTACATGCAACGTGCTTTAACCTAATAACACAAAAAACAATAAAGT
1 GTGTTACATGCAACGTGCTTTAACCTAATAACACAAAAAACAATAAAGT
35579137 GT
1 GT
35579139 TAGAATGCGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (49 bp):
GTGTTACATGCAACGTGCTTTAACCTAATAACACAAAAAACAATAAAGT
Found at i:35579752 original size:4 final size:4
Alignment explanation
Indices: 35579743--35579784 Score: 50
Period size: 4 Copynumber: 10.0 Consensus size: 4
35579733 ATCCAAGTCA
35579743 AAAT AAAT AAAT AAAT AAGAT AAAT AAAAT AGAAT -AAT AAAT
1 AAAT AAAT AAAT AAAT AA-AT AAAT -AAAT A-AAT AAAT AAAT
35579785 CAAAGATTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 3 0.09
4 20 0.59
5 11 0.32
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:35579782 original size:17 final size:16
Alignment explanation
Indices: 35579743--35579784 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
35579733 ATCCAAGTCA
35579743 AAATAAATAAATAAAT
1 AAATAAATAAATAAAT
35579759 AAGATAAATAAAATAGAAT
1 AA-ATAAAT-AAATA-AAT
35579778 -AATAAAT
1 AAATAAAT
35579785 CAAAGATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.09
17 12 0.52
18 6 0.26
19 3 0.13
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (16 bp):
AAATAAATAAATAAAT
Found at i:35584927 original size:31 final size:31
Alignment explanation
Indices: 35584771--35584928 Score: 129
Period size: 31 Copynumber: 5.1 Consensus size: 31
35584761 GTATATGTTT
* * * * * *
35584771 TATAAATTGCTGAATTTCAATTGTTTATATA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * * * * *
35584802 TTTACATTGTCGAATTTGATTGGTGTATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
35584833 TATACATAGCCAAATTTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
35584864 TATTCATTACCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * * *
35584894 TATACGTTGCCGAATTTAATTCGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
35584925 TATA
1 TATA
35584929 TATATATTGC
Statistics
Matches: 97, Mismatches: 29, Indels: 2
0.76 0.23 0.02
Matches are distributed among these distances:
30 27 0.28
31 70 0.72
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.44
Consensus pattern (31 bp):
TATACATTGCCGAATTTGATTTGTATATAGA
Found at i:35588636 original size:3 final size:3
Alignment explanation
Indices: 35588628--35588683 Score: 80
Period size: 3 Copynumber: 18.7 Consensus size: 3
35588618 GTGAATTAAA
35588628 TAT TAT TA- TAT TAT TAT ATAT TAT TAT TA- TAT TAT TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT -TAT TAT
35588673 TAT TAT TAT TA
1 TAT TAT TAT TA
35588684 ACTAATATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.08
3 39 0.80
4 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:35588643 original size:18 final size:18
Alignment explanation
Indices: 35588622--35588684 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 18
35588612 ATATTTGTGA
35588622 ATTAAATATTATTATATT
1 ATTAAATATTATTATATT
35588640 ATTATATATTATTATTATATT
1 ATTA-A-A-TATTATTATATT
*
35588661 ATTATATATTATTATTATT
1 ATTAAATATTATTA-TATT
35588680 ATTAA
1 ATTAA
35588685 CTAATATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 12 0.31
19 10 0.26
20 1 0.03
21 16 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTAAATATTATTATATT
Found at i:35588693 original size:24 final size:21
Alignment explanation
Indices: 35588628--35588683 Score: 103
Period size: 21 Copynumber: 2.6 Consensus size: 21
35588618 GTGAATTAAA
35588628 TATTATTATATTATTATATAT
1 TATTATTATATTATTATATAT
35588649 TATTATTATATTATTATATAT
1 TATTATTATATTATTATATAT
35588670 TATTATTATTATTA
1 TATTATTA-TATTA
35588684 ACTAATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 29 0.85
22 5 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTATTATATTATTATATAT
Found at i:35589801 original size:46 final size:42
Alignment explanation
Indices: 35589743--35589846 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 42
35589733 GCTTTGCCGA
* * *
35589743 TCAGGCAATTTATGTGTCGAACATCAGGCACTTTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCG--CATCAGGCACCTCATGTGTCGT-T
* *
35589788 CTCAGGCACTTTATGTGTCGTATCAGGCACCTCGTGTGTCGTT
1 -TCAGGCACTTTATGTGTCGCATCAGGCACCTCATGTGTCGTT
35589831 TCAGGCAC-TTATGTGT
1 TCAGGCACTTTATGTGT
35589847 TGTATACTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
41 8 0.15
42 8 0.15
43 1 0.02
44 18 0.34
46 18 0.34
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (42 bp):
TCAGGCACTTTATGTGTCGCATCAGGCACCTCATGTGTCGTT
Found at i:35589810 original size:23 final size:22
Alignment explanation
Indices: 35589743--35589851 Score: 116
Period size: 23 Copynumber: 5.0 Consensus size: 22
35589733 GCTTTGCCGA
* * *
35589743 TCAGGCAATTTATGTGTCGAACA
1 TCAGGCACTTTATGTGTCGTA-T
35589766 TCAGGCACTTTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
35589788 CTCAGGCACTTTATGTGTCGTA-
1 -TCAGGCACTTTATGTGTCGTAT
* **
35589810 TCAGGCACCTCGTGTGTCGT-T
1 TCAGGCACTTTATGTGTCGTAT
*
35589831 TCAGGCAC-TTATGTGTTGTAT
1 TCAGGCACTTTATGTGTCGTAT
35589852 ACTGATCAGG
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
20 8 0.11
21 26 0.35
23 40 0.54
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (22 bp):
TCAGGCACTTTATGTGTCGTAT
Found at i:35590030 original size:13 final size:13
Alignment explanation
Indices: 35590012--35590055 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
35590002 ATGAGGAAAT
35590012 TTGAAATTGTGGA
1 TTGAAATTGTGGA
35590025 TTGAAATTGTGGA
1 TTGAAATTGTGGA
*
35590038 TTGAAATTG-AGA
1 TTGAAATTGTGGA
35590050 TTGAAA
1 TTGAAA
35590056 ACGAAAGGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 8 0.27
13 22 0.73
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (13 bp):
TTGAAATTGTGGA
Found at i:35593279 original size:62 final size:61
Alignment explanation
Indices: 35593201--35593359 Score: 158
Period size: 61 Copynumber: 2.6 Consensus size: 61
35593191 TGTATGTGTT
* * * ** * *
35593201 TTATATATTGCTGAATTTCAATTT-TTTATAGATATACATTGTTGAATTTGATTTGTATATGG
1 TTATACATTGCCGAATTT-AATTTGTATATAGATATACATTGCCGAA-TTAATTTGTATATAG
* * *
35593263 TTATACATTGCCGAATTTGATTTGTATATGGATATTCATTGCCGAATTAATTTGTATATAG
1 TTATACATTGCCGAATTTAATTTGTATATAGATATACATTGCCGAATTAATTTGTATATAG
* * * * *
35593324 ATATACGTTGCCGAATTTGATTCGTATATGGATATA
1 TTATACATTGCCGAATTTAATTTGTATATAGATATA
35593360 TATATTGCCA
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
61 49 0.60
62 33 0.40
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (61 bp):
TTATACATTGCCGAATTTAATTTGTATATAGATATACATTGCCGAATTAATTTGTATATAG
Found at i:35593318 original size:30 final size:31
Alignment explanation
Indices: 35593231--35593359 Score: 179
Period size: 31 Copynumber: 4.2 Consensus size: 31
35593221 ATTTTTTATA
**
35593231 GATATACATTGTTGAATTTGATTTGTATATG
1 GATATACATTGCCGAATTTGATTTGTATATG
*
35593262 GTTATACATTGCCGAATTTGATTTGTATATG
1 GATATACATTGCCGAATTTGATTTGTATATG
* * *
35593293 GATATTCATTGCCGAA-TTAATTTGTATATA
1 GATATACATTGCCGAATTTGATTTGTATATG
* *
35593323 GATATACGTTGCCGAATTTGATTCGTATATG
1 GATATACATTGCCGAATTTGATTTGTATATG
35593354 GATATA
1 GATATA
35593360 TATATTGCCA
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
30 26 0.31
31 59 0.69
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (31 bp):
GATATACATTGCCGAATTTGATTTGTATATG
Found at i:35595317 original size:17 final size:17
Alignment explanation
Indices: 35595295--35595349 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
35595285 AATTGCCACC
35595295 AATATTCTTTGGTTTGT
1 AATATTCTTTGGTTTGT
* *
35595312 AATATTCCGTTT-ATTTTT
1 AATATT-C-TTTGGTTTGT
*
35595330 AATATTCTTTGGTGTGT
1 AATATTCTTTGGTTTGT
35595347 AAT
1 AAT
35595350 TTCCACTATC
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 3 0.10
17 13 0.43
18 11 0.37
19 3 0.10
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (17 bp):
AATATTCTTTGGTTTGT
Found at i:35596289 original size:32 final size:32
Alignment explanation
Indices: 35596253--35596328 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
35596243 TGCAGTTCTA
*
35596253 TGAAATGATAACAAA-TATCAGCTTTC-ATTTTG
1 TGAAATGATAACAAATTA-CAAC-TTCAATTTTG
*
35596285 TGAAAT-AGTAACAAGTTACAACTTCAATTTTG
1 TGAAATGA-TAACAAATTACAACTTCAATTTTG
35596317 TGAAATGATAAC
1 TGAAATGATAAC
35596329 GATGGGAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
31 4 0.11
32 31 0.82
33 3 0.08
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (32 bp):
TGAAATGATAACAAATTACAACTTCAATTTTG
Found at i:35596487 original size:41 final size:42
Alignment explanation
Indices: 35596417--35596497 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 42
35596407 TCCTAATATA
* *
35596417 ACACGGAGAAAAATGCTTCTAGCTAGAAGCATTTTACTGGTG
1 ACACGCAGAAAAACGCTTCTAGCTAGAAGCATTTTACTGGTG
* * *
35596459 ACACGCAG-AAAACGCTTCTAGCTGGAAGCGTTTTTCTGG
1 ACACGCAGAAAAACGCTTCTAGCTAGAAGCATTTTACTGG
35596498 ATCTCCCTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
41 27 0.79
42 7 0.21
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (42 bp):
ACACGCAGAAAAACGCTTCTAGCTAGAAGCATTTTACTGGTG
Found at i:35598836 original size:2 final size:2
Alignment explanation
Indices: 35598829--35598866 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
35598819 TTCTTTAGCA
*
35598829 AT AT AT AT AG 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
35598867 TGTTAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:35604130 original size:18 final size:18
Alignment explanation
Indices: 35604088--35604132 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
35604078 AGACCAAGGT
*
35604088 GAAGACGAAGATGAACAT
1 GAAGACGAAGATGAACAC
* * *
35604106 GATGACGAAGGTGAATAC
1 GAAGACGAAGATGAACAC
35604124 GAAGACGAA
1 GAAGACGAA
35604133 CACAAAGATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.31, T:0.11
Consensus pattern (18 bp):
GAAGACGAAGATGAACAC
Found at i:35604441 original size:74 final size:74
Alignment explanation
Indices: 35604347--35604514 Score: 221
Period size: 74 Copynumber: 2.3 Consensus size: 74
35604337 AGATGACATC
* * *
35604347 AATATAGAAACTACAAATTTTTATTGTAACTCATATTTAT-CTTTGTTACATTCTAACGTAAATT
1 AATA-AGAAACAACAAATTTTCATTGCAACTCATATTTATGC-TTGTTACATTCTAACGTAAATT
35604411 GTACATAAGTG
64 GTACATAAGTG
* * *
35604422 AATAAGAAACCACAAATTTTCATTGCAACTCATATTTGTGCTTGTTACATTCTAAGGTAAATTGT
1 AATAAGAAACAACAAATTTTCATTGCAACTCATATTTATGCTTGTTACATTCTAACGTAAATTGT
* * *
35604487 ACGTTAGTT
66 ACATAAGTG
*
35604496 AATAAGAAATAACAAATTT
1 AATAAGAAACAACAAATTT
35604515 GGTACCCTAA
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
74 77 0.94
75 5 0.06
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (74 bp):
AATAAGAAACAACAAATTTTCATTGCAACTCATATTTATGCTTGTTACATTCTAACGTAAATTGT
ACATAAGTG
Found at i:35604692 original size:161 final size:162
Alignment explanation
Indices: 35604416--35604735 Score: 554
Period size: 161 Copynumber: 2.0 Consensus size: 162
35604406 AAATTGTACA
35604416 TAAGTGAATAAGAAACCACAAATTTTCATTGCAACTCATATTTGTGCTTGTTACATTCTAAGGTA
1 TAAGTGAATAAGAAACCACAAATTTTCATTGCAACTCATATTTGTGCTTGTTACATTCTAAGGTA
* *
35604481 AATTGTACGTTAGTTAATAAGAAATAACAAATTTGGTACCCTAAAATCATGAAGGCATTGTAATG
66 AATTATACGTAAGTTAATAAGAAATAACAAATTTGGTACCCTAAAATCATGAAGGCATTGTAAT-
35604546 AAA-TTTATATCCTCTGAAAGT-AATAAGGTAG
130 AAATTTTATATCCTCTGAAAGTAAATAAGGTAG
* *
35604577 TAAGTTAATAAGAAACCACAAATTTTCATTGCAACTCATATTTGTGTTTGTTACATTCTAAGGTA
1 TAAGTGAATAAGAAACCACAAATTTTCATTGCAACTCATATTTGTGCTTGTTACATTCTAAGGTA
* *
35604642 AATTATACGTAAGTTAATAAGAAATAACAAATTTGGTACCCTAGAATCATGGAGGCATTGTAATA
66 AATTATACGTAAGTTAATAAGAAATAACAAATTTGGTACCCTAAAATCATGAAGGCATTGTAATA
*
35604707 AATTTTATATCCTTTGAAAGTAAATAAGG
131 AATTTTATATCCTCTGAAAGTAAATAAGG
35604736 CTAGCGACAT
Statistics
Matches: 150, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
160 3 0.02
161 140 0.93
162 7 0.05
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (162 bp):
TAAGTGAATAAGAAACCACAAATTTTCATTGCAACTCATATTTGTGCTTGTTACATTCTAAGGTA
AATTATACGTAAGTTAATAAGAAATAACAAATTTGGTACCCTAAAATCATGAAGGCATTGTAATA
AATTTTATATCCTCTGAAAGTAAATAAGGTAG
Found at i:35606636 original size:30 final size:29
Alignment explanation
Indices: 35606576--35606636 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
35606566 TTTTCACCCT
* * *
35606576 TTGTGCAAAATTATCGAAAATAGGTCAAA
1 TTGTGCAAAATTATAGAAAATAAGTAAAA
* *
35606605 TTGTGCAAACTTATTAGAAAATAATTAAAA
1 TTGTGCAAAATTA-TAGAAAATAAGTAAAA
35606635 TT
1 TT
35606637 CAAAATGTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (29 bp):
TTGTGCAAAATTATAGAAAATAAGTAAAA
Found at i:35607781 original size:13 final size:13
Alignment explanation
Indices: 35607763--35607788 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35607753 CACACTTCTT
35607763 ATTTTGCAAATTG
1 ATTTTGCAAATTG
35607776 ATTTTGCAAATTG
1 ATTTTGCAAATTG
35607789 TTCAATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
ATTTTGCAAATTG
Found at i:35609898 original size:7 final size:7
Alignment explanation
Indices: 35609886--35609915 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
35609876 TAATAACAAT
35609886 TAATATA
1 TAATATA
35609893 TAATATA
1 TAATATA
35609900 TAATATAA
1 TAATAT-A
35609908 TAATATA
1 TAATATA
35609915 T
1 T
35609916 TATTTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TAATATA
Found at i:35620886 original size:45 final size:45
Alignment explanation
Indices: 35620822--35620915 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
35620812 AACAGAGACT
* * *
35620822 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
*
35620867 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
35620912 CGGT
1 CGGT
35620916 TCACATAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:35620983 original size:51 final size:50
Alignment explanation
Indices: 35620912--35621107 Score: 223
Period size: 51 Copynumber: 3.9 Consensus size: 50
35620902 CAATGATGTT
* * *
35620912 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATC
* * * * *
35620963 CGATACACGTAGTAGTCTGCACATAGTACTACACACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATC
* * * * * *
35621014 CGGTACGCATAGTAGCCTACACATAGTACTACACATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TC
*
35621064 CGGCACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
35621108 CACTTTCACT
Statistics
Matches: 117, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
49 2 0.02
50 39 0.33
51 74 0.63
52 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCATC
Found at i:35621097 original size:101 final size:101
Alignment explanation
Indices: 35620919--35621103 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
35620909 GTTCGGTTCA
* * * *
35620919 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGTCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCA-TACCATCCGACACACGTAGTAGCCTGCA
35620984 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* *
35621021 CATAGTAGCCTACACATAGTACTACACATGCGACC-TATCATTCCGGCACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCATACCA-TCCGACACACGTAGTAGCCTGCA
35621085 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
35621104 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 4 0.05
101 39 0.51
102 33 0.43
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (101 bp):
CATAGTAGCCTACACATAGTACTACACATGCGACCATACCATCCGACACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:35624494 original size:56 final size:56
Alignment explanation
Indices: 35624371--35624517 Score: 163
Period size: 56 Copynumber: 2.6 Consensus size: 56
35624361 ATTTCTAATT
* * *
35624371 TTTACTTTTTAATTAATGCTTTTAATTAAATTAATTCATGTTGTTTAAAGATTTTTTAT
1 TTTA-TTTTTAATTAATGTTTTTAATT-AA-TAAATCATGTTGTTTAAAGATTTTTTAA
* *
35624430 TTTAATTTTTAATTAATGTTTTTAGTTAATAAAT-ATGTTGTGTTCAAG-TTTTTTAAA
1 TTT-ATTTTTAATTAATGTTTTTAATTAATAAATCATGTTGT-TTAAAGATTTTTT-AA
* *
35624487 TTTATTTTTAATTCATATTTTTAATTAATAA
1 TTTATTTTTAATTAATGTTTTTAATTAATAA
35624518 CTCCTTTATT
Statistics
Matches: 77, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
56 38 0.49
57 13 0.17
58 2 0.03
59 23 0.30
60 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.58
Consensus pattern (56 bp):
TTTATTTTTAATTAATGTTTTTAATTAATAAATCATGTTGTTTAAAGATTTTTTAA
Found at i:35624760 original size:72 final size:72
Alignment explanation
Indices: 35624660--35624825 Score: 203
Period size: 72 Copynumber: 2.3 Consensus size: 72
35624650 TTATATTTTT
* * * * *
35624660 TTATGTCAAATAT-TTATTTTTTCTACCTACATTGTGGATATTGTAAATTCTAATATTATAAAAT
1 TTATTTCAAATATATTATTTTTTCTACCTACATTATGGATATGGAAAATTATAATATTATAAAAT
35624724 -AATACAA
66 CAAT-CAA
* * *
35624731 TTATTTCAAATATCATTGTTTTTTC-ACCTACATTATGGGTATGGAAAATTATAATATTATTAAA
1 TTATTTCAAATAT-ATTATTTTTTCTACCTACATTATGGATATGGAAAATTATAATATTATAAAA
*
35624795 TCAATTAA
65 TCAATCAA
35624803 TTATTTCAAATATTATTATTTTT
1 TTATTTCAAATA-TATTATTTTT
35624826 AGTACATATA
Statistics
Matches: 81, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
71 12 0.15
72 56 0.69
73 13 0.16
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.48
Consensus pattern (72 bp):
TTATTTCAAATATATTATTTTTTCTACCTACATTATGGATATGGAAAATTATAATATTATAAAAT
CAATCAA
Found at i:35625042 original size:17 final size:18
Alignment explanation
Indices: 35625020--35625055 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
35625010 CATAATGATA
*
35625020 TATATAATATAT-TTTAT
1 TATATAATAAATATTTAT
35625037 TATATAATAAATATTTAT
1 TATATAATAAATATTTAT
35625055 T
1 T
35625056 GTTTTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATAATAAATATTTAT
Found at i:35644933 original size:18 final size:18
Alignment explanation
Indices: 35644907--35644941 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35644897 CCTACATAGG
35644907 AAAACAAAACAAACACAC
1 AAAACAAAACAAACACAC
* *
35644925 AAAAGAAAACATACACA
1 AAAACAAAACAAACACA
35644942 AATTAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.23, G:0.03, T:0.03
Consensus pattern (18 bp):
AAAACAAAACAAACACAC
Found at i:35654391 original size:7 final size:7
Alignment explanation
Indices: 35654379--35654404 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
35654369 AGTGCGTTGT
35654379 TTCAACC
1 TTCAACC
35654386 TTCAACC
1 TTCAACC
35654393 TTCAACC
1 TTCAACC
35654400 TTCAA
1 TTCAA
35654405 GTTTTTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (7 bp):
TTCAACC
Found at i:35660975 original size:78 final size:76
Alignment explanation
Indices: 35660891--35661065 Score: 183
Period size: 78 Copynumber: 2.3 Consensus size: 76
35660881 AATCCAATGT
*
35660891 AAAAAAAGGCTGTGAAGAAAAAATAATAATTTTTTAAT-GGTGTCACCGGTCTATCAAGCGACAC
1 AAAAAAAGCCTGTGAAGAAAAAA-AAT-A-TTTTTAATGGGTGTCACCGGTCTATCAAGCGACAC
*
35660955 CGATGATGTGTCAGAA
63 AGATGATGTGTC--AA
* * *** * * * * *
35660971 AAAAAAAGCCTATGAATAAAAAAAATATTTTTAATGGGTGTCGTTGGTGTGTCAGGCGACATAGG
1 AAAAAAAGCCTGTGAAGAAAAAAAATATTTTTAATGGGTGTCACCGGTCTATCAAGCGACACAGA
35661036 TGATGTGTC-A
66 TGATGTGTCAA
35661046 AAAAAAAGCCTGTGAAGAAA
1 AAAAAAAGCCTGTGAAGAAA
35661066 TATATATATA
Statistics
Matches: 80, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
75 19 0.24
77 8 0.10
78 30 0.38
79 3 0.04
80 20 0.25
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (76 bp):
AAAAAAAGCCTGTGAAGAAAAAAAATATTTTTAATGGGTGTCACCGGTCTATCAAGCGACACAGA
TGATGTGTCAA
Found at i:35661275 original size:19 final size:19
Alignment explanation
Indices: 35661247--35661322 Score: 100
Period size: 19 Copynumber: 4.1 Consensus size: 19
35661237 TTGGCCAAAA
35661247 TTTT-GTTTCTGTTGAAGT
1 TTTTGGTTTCTGTTGAAGT
*
35661265 TTTTGGTTTCTATTGAAGT
1 TTTTGGTTTCTGTTGAAGT
* * *
35661284 TTTGGGTTTATGTTGAAGC
1 TTTTGGTTTCTGTTGAAGT
*
35661303 TTTTAGTTTCTGTTGAAGT
1 TTTTGGTTTCTGTTGAAGT
35661322 T
1 T
35661323 AAGAAAAAAG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
18 4 0.08
19 44 0.92
ACGTcount: A:0.14, C:0.05, G:0.24, T:0.57
Consensus pattern (19 bp):
TTTTGGTTTCTGTTGAAGT
Found at i:35662521 original size:9 final size:9
Alignment explanation
Indices: 35662504--35662564 Score: 77
Period size: 9 Copynumber: 6.6 Consensus size: 9
35662494 TTCGGTTAAA
35662504 AATTACCCG
1 AATTACCCG
*
35662513 AAATACCCG
1 AATTACCCG
35662522 AATTACCCG
1 AATTACCCG
* *
35662531 ATTTACCTG
1 AATTACCCG
35662540 AAAATTACCCG
1 --AATTACCCG
35662551 AATTACCCG
1 AATTACCCG
35662560 AATTA
1 AATTA
35662565 AATCACTACA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
9 37 0.84
11 7 0.16
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:35662593 original size:17 final size:17
Alignment explanation
Indices: 35662571--35662705 Score: 63
Period size: 17 Copynumber: 7.4 Consensus size: 17
35662561 ATTAAATCAC
35662571 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
35662588 TACATAAATCTTTGAATCAC
1 TACAT-AAT-TAAAAAT-AT
35662608 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
* *** *
35662625 TAAATAAATCTTTGAATCAC
1 TACAT-AAT-TAAAAAT-AT
35662645 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
35662662 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
35662682 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
35662699 TACATAA
1 TACATAA
35662706 GTCTTGAATT
Statistics
Matches: 82, Mismatches: 27, Indels: 18
0.65 0.21 0.14
Matches are distributed among these distances:
17 26 0.32
18 18 0.22
19 19 0.23
20 19 0.23
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.34
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:35662611 original size:37 final size:37
Alignment explanation
Indices: 35662565--35662730 Score: 264
Period size: 37 Copynumber: 4.5 Consensus size: 37
35662555 ACCCGAATTA
35662565 AATCACTACATAATTAAAAATATTACATAAATCTTTG
1 AATCACTACATAATTAAAAATATTACATAAATCTTTG
*
35662602 AATCACTACATAATTAAAAATATTAAATAAATCTTTG
1 AATCACTACATAATTAAAAATATTACATAAATCTTTG
*
35662639 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAATATTACATAAATCTTTG
* *
35662676 AATCACTACATAATTAAAAACATTACATAAGTC-TTG
1 AATCACTACATAATTAAAAATATTACATAAATCTTTG
*
35662712 AATTAAC-ACATAATTAAAA
1 AA-TCACTACATAATTAAAA
35662731 TATAAGTCTT
Statistics
Matches: 123, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
36 17 0.14
37 106 0.86
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (37 bp):
AATCACTACATAATTAAAAATATTACATAAATCTTTG
Found at i:35662613 original size:20 final size:20
Alignment explanation
Indices: 35662588--35662688 Score: 70
Period size: 20 Copynumber: 5.3 Consensus size: 20
35662578 TTAAAAATAT
35662588 TACATAAATCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
*** *
35662608 TACAT-AAT-TAAAAAT-AT
1 TACATAAATCTTTGAATCAC
*
35662625 TAAATAAATCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
*** *
35662645 TACAT-AAT-TAAAAAT-AT
1 TACATAAATCTTTGAATCAC
*
35662662 TACATAAGTCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
35662682 TACATAA
1 TACATAA
35662689 TTAAAAACAT
Statistics
Matches: 56, Mismatches: 19, Indels: 12
0.64 0.22 0.14
Matches are distributed among these distances:
17 11 0.20
18 13 0.23
19 14 0.25
20 18 0.32
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.35
Consensus pattern (20 bp):
TACATAAATCTTTGAATCAC
Found at i:35668457 original size:14 final size:14
Alignment explanation
Indices: 35668433--35668466 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
35668423 TTGTACTTGA
35668433 ATGTT-TGAAATGT
1 ATGTTATGAAATGT
35668446 ATGTTATGAAATGT
1 ATGTTATGAAATGT
*
35668460 GTGTTAT
1 ATGTTAT
35668467 ATTGGTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (14 bp):
ATGTTATGAAATGT
Found at i:35668830 original size:27 final size:27
Alignment explanation
Indices: 35668791--35668985 Score: 189
Period size: 27 Copynumber: 7.2 Consensus size: 27
35668781 ACACGTCAGA
*
35668791 AAAGAATAGCCTTTGTGGCGTATTACG
1 AAAGAATAACCTTTGTGGCGTATTACG
*
35668818 AAATAATAACCTTTGTGGCAAAGT-TTA--
1 AAAGAATAACCTTTGTGGC---GTATTACG
*
35668845 AAAGAATAACATTTGTGGCGTATTACG
1 AAAGAATAACCTTTGTGGCGTATTACG
* *
35668872 AAAGAATAACTTTTGTGGCGTATTATG
1 AAAGAATAACCTTTGTGGCGTATTACG
* * ** * *
35668899 AAAAAACAACCTTTGTGGCAAACTATG
1 AAAGAATAACCTTTGTGGCGTATTACG
*
35668926 AAAGAATAACCTTTGTGGCATATTACG
1 AAAGAATAACCTTTGTGGCGTATTACG
* * * * *
35668953 AAAGAATATCTTTTATGGCGAATTATG
1 AAAGAATAACCTTTGTGGCGTATTACG
35668980 AAAGAA
1 AAAGAA
35668986 AAGCTTCTGT
Statistics
Matches: 139, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
24 2 0.01
25 3 0.02
27 129 0.93
29 3 0.02
30 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (27 bp):
AAAGAATAACCTTTGTGGCGTATTACG
Found at i:35668889 original size:81 final size:81
Alignment explanation
Indices: 35668791--35668982 Score: 267
Period size: 81 Copynumber: 2.4 Consensus size: 81
35668781 ACACGTCAGA
* * * * * * *
35668791 AAAGAATAGCCTTTGTGGCGTATTACGAAATAATAACCTTTGTGGCAAAGTTTAAAAGAATAACA
1 AAAGAATAACTTTTGTGGCGTATTATGAAAAAACAACCTTTGTGGCAAACTATAAAAGAATAACA
*
35668856 TTTGTGGCGTATTACG
66 TTTGTGGCATATTACG
* *
35668872 AAAGAATAACTTTTGTGGCGTATTATGAAAAAACAACCTTTGTGGCAAACTATGAAAGAATAACC
1 AAAGAATAACTTTTGTGGCGTATTATGAAAAAACAACCTTTGTGGCAAACTATAAAAGAATAACA
35668937 TTTGTGGCATATTACG
66 TTTGTGGCATATTACG
* * *
35668953 AAAGAATATCTTTTATGGCGAATTATGAAA
1 AAAGAATAACTTTTGTGGCGTATTATGAAA
35668983 GAAAAGCTTC
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 98 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (81 bp):
AAAGAATAACTTTTGTGGCGTATTATGAAAAAACAACCTTTGTGGCAAACTATAAAAGAATAACA
TTTGTGGCATATTACG
Found at i:35672161 original size:86 final size:85
Alignment explanation
Indices: 35672019--35672223 Score: 262
Period size: 86 Copynumber: 2.4 Consensus size: 85
35672009 TTAAGGGTGT
35672019 AAAAAG-CCCTCAAAC-TTTTAAAAAAACAATTAAGCCTCTTTTTTTTTGCACTCAATT-GAGCA
1 AAAAAGACCCTCAAACTTTTTAAAAAAACAATTAAGCCTCTTTTTTTTTGCACTCAATTGGA-CA
35672081 CTTAAACTTTCAAAATGCATC
65 CTTAAACTTTCAAAATGCATC
** *
35672102 AAAAAGGTCCTCAAACTTTTTAAAAAAACCAATTAAATCC-CTGTTTTTTTT-CACTCAATTGGA
1 AAAAAGACCCTCAAACTTTTTAAAAAAA-CAATT-AAGCCTCT-TTTTTTTTGCACTCAATTGGA
* *
35672165 TACTTGAACTTTCAAAATGCATC
63 CACTTAAACTTTCAAAATGCATC
**
35672188 AAAAAGACCCTCAAA-TTTTTTTAAAAA-AATTAAGCC
1 AAAAAGACCCTCAAACTTTTTAAAAAAACAATTAAGCC
35672224 CCTGCACTTA
Statistics
Matches: 107, Mismatches: 9, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
82 4 0.04
83 10 0.09
84 8 0.07
85 21 0.20
86 50 0.47
87 14 0.13
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (85 bp):
AAAAAGACCCTCAAACTTTTTAAAAAAACAATTAAGCCTCTTTTTTTTTGCACTCAATTGGACAC
TTAAACTTTCAAAATGCATC
Found at i:35673703 original size:44 final size:41
Alignment explanation
Indices: 35673596--35673733 Score: 120
Period size: 44 Copynumber: 3.2 Consensus size: 41
35673586 CTGCTCTTAC
*
35673596 TAAAAATTAGAATTTTTT-T-AAAATTTAAAAATAAA-TTT
1 TAAAAATTAGAATTTTTTATAAAAATTAAAAAATAAATTTT
* * *
35673634 TAGAAATATTATTAAATTTTAATAAAAATATAAAAAATAAATTTAT
1 TA-AAA-ATTA-GAATTTTTTATAAAAAT-TAAAAAATAAATTT-T
35673680 TAAAAATTAGAATTTTTTTATAAAAATCGTAAAAAAATAAAATTTT
1 TAAAAATTAGAA-TTTTTTATAAAAAT--T-AAAAAAT-AAATTTT
*
35673726 TTAAAATT
1 TAAAAATT
35673734 TTATAAAAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
38 2 0.03
39 3 0.04
40 4 0.05
41 6 0.08
42 1 0.01
43 7 0.09
44 26 0.33
45 6 0.08
46 18 0.23
47 6 0.08
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (41 bp):
TAAAAATTAGAATTTTTTATAAAAATTAAAAAATAAATTTT
Found at i:35673978 original size:10 final size:10
Alignment explanation
Indices: 35673965--35674058 Score: 50
Period size: 10 Copynumber: 9.5 Consensus size: 10
35673955 TTTCTATATA
35673965 TTTTATAATT
1 TTTTATAATT
**
35673975 TTTT-CGA-T
1 TTTTATAATT
**
35673983 TTTTATAAAA
1 TTTTATAATT
*
35673993 TTTTACAATT
1 TTTTATAATT
35674003 TTTTATATATT
1 TTTTATA-ATT
*
35674014 TTTT-TACGTT
1 TTTTATA-ATT
* *
35674024 TTTTACATTT
1 TTTTATAATT
*
35674034 TTTTCTAATT
1 TTTTATAATT
* *
35674044 TTTAATAAAT
1 TTTTATAATT
35674054 TTTTA
1 TTTTA
35674059 ATATTTGAAT
Statistics
Matches: 60, Mismatches: 20, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
8 5 0.08
9 2 0.03
10 45 0.75
11 8 0.13
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:35673978 original size:27 final size:28
Alignment explanation
Indices: 35673939--35674010 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 28
35673929 TTCTTATGAG
** *
35673939 TTTATAAAATTTTATATTTCTAT-ATAT
1 TTTATAATTTTTTATATTTCTATAAAAT
** *
35673966 TTTATAATTTTTTCGATTTTTATAAAAT
1 TTTATAATTTTTTATATTTCTATAAAAT
*
35673994 TTTACAATTTTTTATAT
1 TTTATAATTTTTTATAT
35674011 ATTTTTTTAC
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 18 0.51
28 17 0.49
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (28 bp):
TTTATAATTTTTTATATTTCTATAAAAT
Found at i:35674233 original size:90 final size:91
Alignment explanation
Indices: 35674133--35674331 Score: 296
Period size: 89 Copynumber: 2.2 Consensus size: 91
35674123 AATTTTTAAT
35674133 AAAAGCAGGGGCTTAATTGCCTTTTTTGAAAAAGTTTGAGGGTC-TTTTTGATGCATTTTGAAAG
1 AAAAGCAGGGGCTTAATTGCCTTTTTTGAAAAAGTTTGA-GGTCTTTTTTGATGCATTTTGAAAG
* *
35674197 TTCAAGTACCCAATTGAGTG-TAAAAA
65 TTCAAGTACCCAAATGAGTGCAAAAAA
* * * *
35674223 AAAAGTAGGGGATTAATT-TCTTTTTTGAAAAGGTTTGAGGTCTTTTTTGATGCATTTTGAAAGT
1 AAAAGCAGGGGCTTAATTGCCTTTTTTGAAAAAGTTTGAGGTCTTTTTTGATGCATTTTGAAAGT
*
35674287 TTAAGTACCCAAATGAGTGCAAAAAA
66 TCAAGTACCCAAATGAGTGCAAAAAA
*
35674313 AAAAGCATGGGCTTAATTG
1 AAAAGCAGGGGCTTAATTG
35674332 TTTTTTTTTT
Statistics
Matches: 96, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
88 4 0.04
89 56 0.58
90 36 0.38
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.35
Consensus pattern (91 bp):
AAAAGCAGGGGCTTAATTGCCTTTTTTGAAAAAGTTTGAGGTCTTTTTTGATGCATTTTGAAAGT
TCAAGTACCCAAATGAGTGCAAAAAA
Found at i:35674692 original size:21 final size:22
Alignment explanation
Indices: 35674666--35674706 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
35674656 GATAATAGAA
35674666 TATAATAAT-AAAATTTATAAT
1 TATAATAATAAAAATTTATAAT
**
35674687 TATAATTGTAAAAATTTATA
1 TATAATAATAAAAATTTATA
35674707 TAACTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TATAATAATAAAAATTTATAAT
Found at i:35686416 original size:27 final size:27
Alignment explanation
Indices: 35686386--35686456 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
35686376 CGAAATTTCT
* *
35686386 CGTGTTTACAGTCCTAGTGAACTACCC
1 CGTGTTTACAGTCCCAGTGAACCACCC
* *
35686413 CGTGTTTACTGTCCCGGTGAACCACCC
1 CGTGTTTACAGTCCCAGTGAACCACCC
* * *
35686440 TGTGTTTCCTGTCCCAG
1 CGTGTTTACAGTCCCAG
35686457 CAGAGTCTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.15, C:0.32, G:0.21, T:0.31
Consensus pattern (27 bp):
CGTGTTTACAGTCCCAGTGAACCACCC
Found at i:35688446 original size:18 final size:18
Alignment explanation
Indices: 35688420--35688459 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
35688410 GAAAAATAGG
* *
35688420 AAAATGAGAAAGGAAAGA
1 AAAAAGAGAAAAGAAAGA
*
35688438 AAAAAGAGAAAAGAGAGA
1 AAAAAGAGAAAAGAAAGA
35688456 AAAA
1 AAAA
35688460 TGAATGTATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (18 bp):
AAAAAGAGAAAAGAAAGA
Found at i:35693552 original size:13 final size:14
Alignment explanation
Indices: 35693539--35693575 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
35693529 TCTTTAATTT
35693539 ATTATTTTATTTTA
1 ATTATTTTATTTTA
35693553 ATTA-TTTATTTTA
1 ATTATTTTATTTTA
35693566 ATTATTTTAT
1 ATTATTTTAT
35693576 CTGACTTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTATTTTATTTTA
Found at i:35693554 original size:18 final size:18
Alignment explanation
Indices: 35693531--35693565 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
35693521 TATTCTAATC
35693531 TTTAATT-TATTATTTTAT
1 TTTAATTAT-TTATTTTAT
35693549 TTTAATTATTTATTTTA
1 TTTAATTATTTATTTTA
35693566 ATTATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTAATTATTTATTTTAT
Found at i:35695752 original size:25 final size:25
Alignment explanation
Indices: 35695715--35695892 Score: 107
Period size: 25 Copynumber: 7.2 Consensus size: 25
35695705 AAACTCTTCC
* * *
35695715 GAGCCATATAACGGGATGCTCATAT
1 GAGCCATACAACGGGAAGCTCATAA
*
35695740 GAGCCATGCAACGGGAAGCTCATAA
1 GAGCCATACAACGGGAAGCTCATAA
* **
35695765 GAGCCATA-AATTGGGAAGCTCATGC
1 GAGCCATACAA-CGGGAAGCTCATAA
* * * **
35695790 GAGCCA-ATATCGGAAAGCTTC-GGA
1 GAGCCATACAACGGGAAGC-TCATAA
* *
35695814 GAGCCATTA-ATCGGGAAGCTCATGA
1 GAGCCA-TACAACGGGAAGCTCATAA
* *
35695839 GAGCCA-ATTATCGGGAAGCTCA-AGA
1 GAGCCATA-CAACGGGAAGCTCATA-A
* *
35695864 GAGCCATACATCGGGATGCTCATAA
1 GAGCCATACAACGGGAAGCTCATAA
35695889 GAGC
1 GAGC
35695893 TGTGATGAGT
Statistics
Matches: 124, Mismatches: 18, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
23 1 0.01
24 18 0.15
25 102 0.82
26 3 0.02
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (25 bp):
GAGCCATACAACGGGAAGCTCATAA
Found at i:35695794 original size:50 final size:48
Alignment explanation
Indices: 35695751--35695892 Score: 167
Period size: 49 Copynumber: 2.9 Consensus size: 48
35695741 AGCCATGCAA
* *
35695751 CGGGAAGCTCATAAGAGCCATAAATTGGGAAGCTCATGCGAGCCAATAT
1 CGGGAAGCTCA-AAGAGCCATAAATCGGGAAGCTCATGAGAGCCAATAT
* ** *
35695800 CGGAAAGCTTCGGAGAGCCATTAATCGGGAAGCTCATGAGAGCCAATTAT
1 CGGGAAGC-TCAAAGAGCCATAAATCGGGAAGCTCATGAGAGCCAA-TAT
* * *
35695850 CGGGAAGCTCAAGAGAGCCATACATCGGGATGCTCATAAGAGC
1 CGGGAAGCTCAA-AGAGCCATAAATCGGGAAGCTCATGAGAGC
35695893 TGTGATGAGT
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
49 39 0.51
50 38 0.49
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (48 bp):
CGGGAAGCTCAAAGAGCCATAAATCGGGAAGCTCATGAGAGCCAATAT
Found at i:35697200 original size:32 final size:32
Alignment explanation
Indices: 35697146--35697272 Score: 164
Period size: 32 Copynumber: 4.0 Consensus size: 32
35697136 CATAACTACA
* * *
35697146 GTAATATGATTGGCACAAAGCCATCAGTAGCA
1 GTAATATGATCGGCACAAAGCCATCAGTAACG
* * *
35697178 GTGATTTGATCGGCACACAGCCATCAGTAACG
1 GTAATATGATCGGCACAAAGCCATCAGTAACG
* *
35697210 GTAATATGATCGACACAAAGCCATTAGTAACG
1 GTAATATGATCGGCACAAAGCCATCAGTAACG
* *
35697242 GTAATATGGTTGGCACAAAGCCATCAGTAAC
1 GTAATATGATCGGCACAAAGCCATCAGTAAC
35697273 ATCGCAGCAA
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 80 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (32 bp):
GTAATATGATCGGCACAAAGCCATCAGTAACG
Found at i:35697302 original size:26 final size:26
Alignment explanation
Indices: 35697273--35697326 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
35697263 CATCAGTAAC
* *
35697273 ATCGCAGCAAAGTTGCCAGCAATAGT
1 ATCGCAGCAAAGCTGCCAACAATAGT
* *
35697299 ATCGTAGCAAAGCTGCCAATAATAGT
1 ATCGCAGCAAAGCTGCCAACAATAGT
35697325 AT
1 AT
35697327 ATGTGGCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (26 bp):
ATCGCAGCAAAGCTGCCAACAATAGT
Found at i:35699244 original size:27 final size:27
Alignment explanation
Indices: 35699017--35699243 Score: 258
Period size: 27 Copynumber: 8.4 Consensus size: 27
35699007 GGGTAAAATA
* *
35699017 GTCA-TTTACCCTCTAAGGGCATTACG
1 GTCATTTTACCCTATAGGGGCATTACG
*
35699043 GTTATTTTACCCTATAGGGGCATTACG
1 GTCATTTTACCCTATAGGGGCATTACG
* * *
35699070 ATTATTTTACCCTATAGGGGTATTACG
1 GTCATTTTACCCTATAGGGGCATTACG
* * * *
35699097 ATCATTTTACCTTATGGGGGTATTACG
1 GTCATTTTACCCTATAGGGGCATTACG
* * * *
35699124 ATCATTTTACCTTACAAGGGCATTACG
1 GTCATTTTACCCTATAGGGGCATTACG
* *
35699151 GTCATTTTATCCTAAAGGGGCATTACG
1 GTCATTTTACCCTATAGGGGCATTACG
* *
35699178 GTCTTTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTATAGGGGCATTACG
* *
35699205 GTCATTTTACCCAATAGGGGCATTACA
1 GTCATTTTACCCTATAGGGGCATTACG
*
35699232 GTCATTATACCC
1 GTCATTTTACCC
35699244 ATTTTAGGGT
Statistics
Matches: 175, Mismatches: 25, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
26 3 0.02
27 172 0.98
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGCATTACG
Found at i:35710331 original size:36 final size:38
Alignment explanation
Indices: 35710272--35710343 Score: 96
Period size: 36 Copynumber: 1.9 Consensus size: 38
35710262 AAATTACAAA
*
35710272 AAATAATTTTGAAAAATTTAAAATAT-TATTAAAAATGAT
1 AAATAAATTTGAAAAA-TTAAAATATAT-TTAAAAATGAT
35710311 AAATAAATTT-AAAAA-TAAAATATATTTAAAAAT
1 AAATAAATTTGAAAAATTAAAATATATTTAAAAAT
35710344 TTAAGTATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
36 16 0.52
37 1 0.03
38 5 0.16
39 9 0.29
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (38 bp):
AAATAAATTTGAAAAATTAAAATATATTTAAAAATGAT
Found at i:35710352 original size:18 final size:17
Alignment explanation
Indices: 35710290--35710343 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
35710280 TTGAAAAATT
35710290 TAAAATAT-TATTAAAAA
1 TAAAATATAT-TTAAAAA
*
35710307 TGATAAATAAATTTAAAAA
1 T-A-AAATATATTTAAAAA
35710326 TAAAATATATTTAAAAA
1 TAAAATATATTTAAAAA
35710343 T
1 T
35710344 TTAAGTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 16 0.50
18 2 0.06
19 13 0.41
20 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
TAAAATATATTTAAAAA
Found at i:35710664 original size:24 final size:25
Alignment explanation
Indices: 35710636--35710682 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
35710626 AAACAATATT
35710636 TTTTAATAATT-TTT-ACAAATATGC
1 TTTTAA-AATTCTTTAACAAATATGC
*
35710660 TTTTAACATTCTTTAACAAATAT
1 TTTTAAAATTCTTTAACAAATAT
35710683 AATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 3 0.15
24 9 0.45
25 8 0.40
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTTAAAATTCTTTAACAAATATGC
Found at i:35710847 original size:7 final size:7
Alignment explanation
Indices: 35710835--35710878 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
35710825 AATTTTTAAA
35710835 TATTTTT
1 TATTTTT
35710842 TATTTTT
1 TATTTTT
35710849 TATTTTT
1 TATTTTT
*
35710856 CATTTTT
1 TATTTTT
* *
35710863 CATTTTA
1 TATTTTT
*
35710870 TAATTTT
1 TATTTTT
35710877 TA
1 TA
35710879 GTAATGTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (7 bp):
TATTTTT
Found at i:35715365 original size:22 final size:22
Alignment explanation
Indices: 35715335--35715377 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
35715325 ACACCAGAAC
* *
35715335 AGGCTTTTAGCGGCGTTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
35715357 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
35715378 AATGCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:35715575 original size:43 final size:42
Alignment explanation
Indices: 35715469--35715677 Score: 314
Period size: 42 Copynumber: 4.9 Consensus size: 42
35715459 CGCTTACAGA
* *
35715469 AAAAAACGCCACTAAAGATCATGTTCTTTAGCGACGCTTAT-G
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-TGG
35715511 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGG
*
35715553 AAGAAAACGCCGCTAAAAATCATGTTCTTTAGCGGCGCTTTGG
1 AA-AAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGG
*
35715596 AAAAAACGCCGTTAAAGATCATGTTCTTTAGCGGCGCTTTGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGG
* *
35715638 AAGAAAACGCCGCTAAA-AGTAATGTTCTATAGCGGCGCTT
1 AA-AAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTT
35715678 GTTCAAAAAC
Statistics
Matches: 155, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
41 1 0.01
42 81 0.52
43 73 0.47
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGG
Found at i:35715688 original size:85 final size:84
Alignment explanation
Indices: 35715471--35715677 Score: 326
Period size: 85 Copynumber: 2.4 Consensus size: 84
35715461 CTTACAGAAA
* *
35715471 AAAACGCCACT-AAAGATCATGTTCTTTAGCGACGCTTATGAAAAAACGCCGCTAAAGATCATGT
1 AAAACGCCGCTAAAAG-TCATGTTCTTTAGCGGCGCTT-TGAAAAAACGCCGCTAAAGATCATGT
35715535 TCTTTAGCGGCGCTTTGGAAG
64 TCTTTAGCGGCGCTTTGGAAG
* *
35715556 AAAACGCCGCTAAAAATCATGTTCTTTAGCGGCGCTTTGGAAAAAACGCCGTTAAAGATCATGTT
1 AAAACGCCGCTAAAAGTCATGTTCTTTAGCGGCGCTTT-GAAAAAACGCCGCTAAAGATCATGTT
35715621 CTTTAGCGGCGCTTTGGAAG
65 CTTTAGCGGCGCTTTGGAAG
* *
35715641 AAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTT
1 AAAACGCCGCTAAAAGTCATGTTCTTTAGCGGCGCTT
35715678 GTTCAAAAAC
Statistics
Matches: 113, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
84 1 0.01
85 109 0.96
86 3 0.03
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (84 bp):
AAAACGCCGCTAAAAGTCATGTTCTTTAGCGGCGCTTTGAAAAAACGCCGCTAAAGATCATGTTC
TTTAGCGGCGCTTTGGAAG
Found at i:35715711 original size:85 final size:85
Alignment explanation
Indices: 35715471--35715719 Score: 299
Period size: 85 Copynumber: 2.9 Consensus size: 85
35715461 CTTACAGAAA
* * * * * *
35715471 AAAACGCCACTAAAGATCATGTTCTTTAGCGACGCTTAT-GAAAAAACGCCGCTAAAGATCATGT
1 AAAACGCCGCTAAAAATAATGTTCTATAGCGGCGCTT-TGGAAAAAACGCCGCGAAAGATCATGT
35715535 TCTTTAGCGGCGCTTTGGAAG
65 TCTTTAGCGGCGCTTTGGAAG
* * **
35715556 AAAACGCCGCTAAAAATCATGTTCTTTAGCGGCGCTTTGGAAAAAACGCCGTTAAAGATCATGTT
1 AAAACGCCGCTAAAAATAATGTTCTATAGCGGCGCTTTGGAAAAAACGCCGCGAAAGATCATGTT
35715621 CTTTAGCGGCGCTTTGGAAG
66 CTTTAGCGGCGCTTTGGAAG
* ** *
35715641 AAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGC-TTGTTCAAAAACGTCGCGAATAG-T-AGT
1 AAAACGCCGCTAAAAATAATGTTCTATAGCGGCGCTTTG-GAAAAAACGCCGCGAA-AGATCA-T
*
35715703 GTTATTTAGCGGCGCTT
63 GTTCTTTAGCGGCGCTT
35715720 ATTTCACAAA
Statistics
Matches: 147, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
84 5 0.03
85 140 0.95
86 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (85 bp):
AAAACGCCGCTAAAAATAATGTTCTATAGCGGCGCTTTGGAAAAAACGCCGCGAAAGATCATGTT
CTTTAGCGGCGCTTTGGAAG
Found at i:35716182 original size:21 final size:21
Alignment explanation
Indices: 35716158--35716206 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
35716148 GCTTCTATCG
* *
35716158 CTGCTTCTCTCGCCGTGGCCT
1 CTGCTTCTCTCGCCGTAGCAT
* *
35716179 CTGCTTCTCTTGCTGTAGCAT
1 CTGCTTCTCTCGCCGTAGCAT
35716200 CTGCTTC
1 CTGCTTC
35716207 CCTCACTGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.04, C:0.37, G:0.20, T:0.39
Consensus pattern (21 bp):
CTGCTTCTCTCGCCGTAGCAT
Found at i:35719009 original size:147 final size:147
Alignment explanation
Indices: 35718810--35719083 Score: 347
Period size: 147 Copynumber: 1.9 Consensus size: 147
35718800 CCTCGTATAG
* * * * *
35718810 ATAAATGTTAAAACATTTTTGCGGCGTTTTAGTTCAAGCCCCACTAACTATAA-ATCAAAACGCA
1 ATAAATGTTAAAACAATGTTGCGGCGTTTTAGTTAAAGCCCCACTAAATATAAGATC-AAACGAA
* * *
35718874 GTCGCTTCAGCAACACTTACCTCAAACCCGTGGCGTTT-TAAAAAAATCGCCACTAATAACATTT
65 GTCGCTTCACCAACACTTAACTCAAACCCGTGGCGTTTCCAAAAAAA-CGCCACTAATAACATTT
35718938 AAAAAACAGCAGCGTTTCT
129 AAAAAACAGCAGCGTTTCT
* *
35718957 ATAAATGTTAGAACAATGTTGCGGCGTTTTAAG-TAAAGCGCCACTAAATATAAGATCAAACGAA
1 ATAAATGTTAAAACAATGTTGCGGCGTTTT-AGTTAAAGCCCCACTAAATATAAGATCAAACGAA
* * * * ** *
35719021 GTCGTTTCCCCAACATTTAACTCAAGCTTGTGGCGTTTCCAAAAAAACGCCACTAATACCATT
65 GTCGCTTCACCAACACTTAACTCAAACCCGTGGCGTTTCCAAAAAAACGCCACTAATAACATT
35719084 GACAAAACGA
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
147 95 0.89
148 12 0.11
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (147 bp):
ATAAATGTTAAAACAATGTTGCGGCGTTTTAGTTAAAGCCCCACTAAATATAAGATCAAACGAAG
TCGCTTCACCAACACTTAACTCAAACCCGTGGCGTTTCCAAAAAAACGCCACTAATAACATTTAA
AAAACAGCAGCGTTTCT
Found at i:35719108 original size:147 final size:147
Alignment explanation
Indices: 35718809--35719134 Score: 338
Period size: 147 Copynumber: 2.2 Consensus size: 147
35718799 GCCTCGTATA
* * * * *
35718809 GATAAATGTTAAAACATTTTTGCGGCGTTTTAGTTCAAGCCCCACTAACTATAAATCAAAACGCA
1 GATAAATGTTAAAACAATGTTGCGGCGTTTTAGTTAAAGCCCCACTAAATATAAATCAAAACGAA
* * * *
35718874 GTCGCTTCAGCAACACTTACCTCAAACCCGTGGCGTTTTAAAAAAATCGCCACTAATAACATTTA
66 GTCGCTTCACCAACACTTAACTCAAACCCGTGGCGTTTCAAAAAAATCGCCACTAATAACATTGA
* *
35718939 AAAAACAGCAGCGTTTC
131 AAAAACAGCAACATTTC
* * *
35718956 TATAAATGTTAGAACAATGTTGCGGCGTTTTAAG-TAAAGCGCCACTAAATATAAGATC-AAACG
1 GATAAATGTTAAAACAATGTTGCGGCGTTTT-AGTTAAAGCCCCACTAAATATAA-ATCAAAACG
* * * * ** *
35719019 AAGTCGTTTCCCCAACATTTAACTCAAGCTTGTGGCGTTTCCAAAAAAA-CGCCACTAATACCAT
64 AAGTCGCTTCACCAACACTTAACTCAAACCCGTGGCGTTT-CAAAAAAATCGCCACTAATAACAT
*
35719083 TGACAAAAC-GACAACATTTC
128 TGAAAAAACAG-CAACATTTC
** * *
35719103 GATAAA-CATAAATACAATTTTGCGGCATTTTA
1 GATAAATGTTAAA-ACAATGTTGCGGCGTTTTA
35719135 TGTAAAACGC
Statistics
Matches: 146, Mismatches: 28, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
146 5 0.03
147 129 0.88
148 12 0.08
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (147 bp):
GATAAATGTTAAAACAATGTTGCGGCGTTTTAGTTAAAGCCCCACTAAATATAAATCAAAACGAA
GTCGCTTCACCAACACTTAACTCAAACCCGTGGCGTTTCAAAAAAATCGCCACTAATAACATTGA
AAAAACAGCAACATTTC
Found at i:35719234 original size:218 final size:218
Alignment explanation
Indices: 35718975--35719440 Score: 833
Period size: 218 Copynumber: 2.1 Consensus size: 218
35718965 TAGAACAATG
*
35718975 TTGCGGCGTTTTAAGTAAAGCGCCACTAAATATAAGATCAAACGAAGTCGTTTCCCCAACATTTA
1 TTGCGGCGTTTTCA--AAAGCGCCACTAAATATAAGATCAAACGAAGTCGTTTCCCCAACATTTA
35719040 ACTCAAGCTTGTGGCGTTTCCAAAAAAACGCCACTAATACCATTGACAAAACGACAACATTTCGA
64 ACTCAAGCTTGTGGCGTTTCCAAAAAAACGCCACTAATACCATTGACAAAACGACAACATTTCGA
*
35719105 TAAACATAAATACAATTTTGCGGCATTTTATGTAAAACGCCAGTAATAGCAACGTAAAAAGGTGC
129 TAAACATAAATACAATTTTGCGGCATTTTATGTAAAACGCCAGTAATAGCAACGTAAAAAGGCGC
35719170 AATTTTATTAACTCCCAATAAAAAT
194 AATTTTATTAACTCCCAATAAAAAT
35719195 TTGCGGCGTTTTCAAAAGCGCCACTAAATATAAGATCAAACGAAGTCGTTTCCCCAACATTTAAC
1 TTGCGGCGTTTTCAAAAGCGCCACTAAATATAAGATCAAACGAAGTCGTTTCCCCAACATTTAAC
* *
35719260 TCAAGCTTGTGGCGTTTTCAAAAAAATGCCACTAATACCATTGACAAAACGACAACATTTCGATA
66 TCAAGCTTGTGGCGTTTCCAAAAAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATA
* * *
35719325 AACATAAATACAATTTTGCGGCATTTTATGTAAAGCGCCAGTAATAGCAACGTAAAACGGCGCAG
131 AACATAAATACAATTTTGCGGCATTTTATGTAAAACGCCAGTAATAGCAACGTAAAAAGGCGCAA
35719390 TTTTATTAACTCCCAATAAAAAT
196 TTTTATTAACTCCCAATAAAAAT
*
35719413 TTGCGGCGTTTTTCAAAAGCACCACTAA
1 TTGCGGCG-TTTTCAAAAGCGCCACTAA
35719441 TGGCGAAGAA
Statistics
Matches: 237, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
218 206 0.87
219 18 0.08
220 13 0.05
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.27
Consensus pattern (218 bp):
TTGCGGCGTTTTCAAAAGCGCCACTAAATATAAGATCAAACGAAGTCGTTTCCCCAACATTTAAC
TCAAGCTTGTGGCGTTTCCAAAAAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATA
AACATAAATACAATTTTGCGGCATTTTATGTAAAACGCCAGTAATAGCAACGTAAAAAGGCGCAA
TTTTATTAACTCCCAATAAAAAT
Found at i:35720041 original size:27 final size:26
Alignment explanation
Indices: 35719994--35720045 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
35719984 TAAACATTAA
35719994 ACCCTAAACTCTAATATAACCTATAAC
1 ACCCTAAACTCTAATATAACC-ATAAC
*
35720021 ACCCTAAACT-TAATTTAAACCATAA
1 ACCCTAAACTCTAATAT-AACCATAA
35720046 ATATATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (26 bp):
ACCCTAAACTCTAATATAACCATAAC
Found at i:35720351 original size:15 final size:16
Alignment explanation
Indices: 35720318--35720355 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
35720308 AAACATTAAA
35720318 CCTTAAACTATAAAACC
1 CCTTAAACTAT-AAACC
*
35720335 CCTTAAACTAT-AGCC
1 CCTTAAACTATAAACC
35720350 CCTTAA
1 CCTTAA
35720356 GCCTCTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
17 11 0.55
ACGTcount: A:0.39, C:0.32, G:0.03, T:0.26
Consensus pattern (16 bp):
CCTTAAACTATAAACC
Found at i:35724393 original size:707 final size:707
Alignment explanation
Indices: 35723049--35724446 Score: 2717
Period size: 707 Copynumber: 2.0 Consensus size: 707
35723039 CATAAAAATT
* *
35723049 AATCATCAACAAAGGCCATCTTCCACAATAGATGTTGTAGTATGGCTAGTAGTTGCGCATACCTC
1 AATCATCAACAAAGCCCATCTTCCACAACAGATGTTGTAGTATGGCTAGTAGTTGCGCATACCTC
35723114 AAAACTTGGAGCAGCTTTTAGAGTAGCATCCCTCGTAGTTTCCTGAACAACAACCATAATGTAGG
66 AAAACTTGGAGCAGCTTTTAGAGTAGCATCCCTCGTAGTTTCCTGAACAACAACCATAATGTAGG
*
35723179 CATTCCCTGCTATTTTAATAGAAGGATTAAACATGTCAAATCCTTCCGACACAAGATGCAAAAGC
131 CATTCCCTACTATTTTAATAGAAGGATTAAACATGTCAAATCCTTCCGACACAAGATGCAAAAGC
*
35723244 TCAAATGGACCTTTGTTGAAATCCACTAGCTCATACTTTAGACATATCTCCAAAAGTGTCCAGGC
196 TCAAATGGACCTTTGTTAAAATCCACTAGCTCATACTTTAGACATATCTCCAAAAGTGTCCAGGC
35723309 ATTGTAGTGTTGGAAAAAATCCAGTTTGAAAATGGTTTTTTTTGCACAATGAAAAATAAAAATTT
261 ATTGTAGTGTTGGAAAAAATCCAGTTTGAAAATGGTTTTTTTTGCACAATGAAAAATAAAAATTT
35723374 TGAAAATCAACTCGATTTGTGATATTTATAGCAATAAACCCTAGACCAAAAATATACCTGTGTTT
326 TGAAAATCAACTCGATTTGTGATATTTATAGCAATAAACCCTAGACCAAAAATATACCTGTGTTT
35723439 TCGGATAGACGGATCCTTGTCGTTTTCAGCTTTCAACTAAACGATCTTCTCCTATATTCTCATGT
391 TCGGATAGACGGATCCTTGTCGTTTTCAGCTTTCAACTAAACGATCTTCTCCTATATTCTCATGT
35723504 TACGAATTGCTTCAAGTGTGGGCTCGAACAAAACGAATCAAACACAGAAACTAGAAATAGTTTTC
456 TACGAATTGCTTCAAGTGTGGGCTCGAACAAAACGAATCAAACACAGAAACTAGAAATAGTTTTC
35723569 TTTTCTTTTGGGTGAAAACGAAAATTCTCTCTTTAAAATAGAAACCAGCAGAATCATTATTTTGA
521 TTTTCTTTTGGGTGAAAACGAAAATTCTCTCTTTAAAATAGAAACCAGCAGAATCATTATTTTGA
35723634 AAAATATATTTAATTCTTAGAGGATAAAAGTCTCTCTATTTTCGGGCAGAATAATAATATCTGAA
586 AAAATATATTTAATTCTTAGAGGATAAAAGTCTCTCTATTTTCGGGCAGAATAATAATATCTGAA
35723699 AGTTGTGTGTAAATAGCCCTGCTAGTGTCATCTATTTATAAAACAACATAAAAGCTC
651 AGTTGTGTGTAAATAGCCCTGCTAGTGTCATCTATTTATAAAACAACATAAAAGCTC
*
35723756 AATCGTCAACAAAGCCCATCTTCCACAACAGATGTTGTAGTATGGCTAGTAGTTGCGCATACCTC
1 AATCATCAACAAAGCCCATCTTCCACAACAGATGTTGTAGTATGGCTAGTAGTTGCGCATACCTC
*
35723821 AAAACTTGG-GCAGCTTTTAGAGTAGCATCCTTCGTAGTTTCCTGAACAACAACCATAATGTAGG
66 AAAACTTGGAGCAGCTTTTAGAGTAGCATCCCTCGTAGTTTCCTGAACAACAACCATAATGTAGG
35723885 CATTCCCTACTATTTTAATAGAAGGATTAAACATGTCAAATCCTTCCGACACAAGATGCAAAAGC
131 CATTCCCTACTATTTTAATAGAAGGATTAAACATGTCAAATCCTTCCGACACAAGATGCAAAAGC
35723950 TCAAATGGACCTTTGTTAAAATCCACTAGCTCATACTTTAGACATATCTCCAAAAGTGTCCAGGC
196 TCAAATGGACCTTTGTTAAAATCCACTAGCTCATACTTTAGACATATCTCCAAAAGTGTCCAGGC
35724015 ATTGTAGTGTTGGAAAAAAATCCAGTTTGAAAATGGTTTTTTTTGCACAATGAAAAATAAAAATT
261 ATTGTAGTGTTGG-AAAAAATCCAGTTTGAAAATGGTTTTTTTTGCACAATGAAAAATAAAAATT
*
35724080 TTGAAAATCAACTCGATTTGTGATATTTATAGCAATAAACCCTATACCAAAAATATACCTGTGTT
325 TTGAAAATCAACTCGATTTGTGATATTTATAGCAATAAACCCTAGACCAAAAATATACCTGTGTT
35724145 TTCGGATAGACGGATCCTTGTCGTTTTCAGCTTTCAACTAAACGATCTTCTCCTATATTCTCATG
390 TTCGGATAGACGGATCCTTGTCGTTTTCAGCTTTCAACTAAACGATCTTCTCCTATATTCTCATG
35724210 TTACGAATTGCTTCAAGTGTGGGCTCGAACAAAACGAATCAAACACAGAAACTAGAAATAGTTTT
455 TTACGAATTGCTTCAAGTGTGGGCTCGAACAAAACGAATCAAACACAGAAACTAGAAATAGTTTT
35724275 CTTTTCTTTTGGGTGAAAACGAAAATTCTCTCTTTAAAATAGAAACCAGCAGAATCATTATTTTG
520 CTTTTCTTTTGGGTGAAAACGAAAATTCTCTCTTTAAAATAGAAACCAGCAGAATCATTATTTTG
35724340 AAAAATATATTTAATTCTTAGAGGATAAAAGTCTCTCTATTTTCGGGCAGAATAATAATATCTGA
585 AAAAATATATTTAATTCTTAGAGGATAAAAGTCTCTCTATTTTCGGGCAGAATAATAATATCTGA
35724405 AAGTTGTGTGTAAATAGCCCTGCTAGTGTCATCTATTTATAA
650 AAGTTGTGTGTAAATAGCCCTGCTAGTGTCATCTATTTATAA
35724447 GGAGAAAATG
Statistics
Matches: 683, Mismatches: 7, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
706 195 0.29
707 488 0.71
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (707 bp):
AATCATCAACAAAGCCCATCTTCCACAACAGATGTTGTAGTATGGCTAGTAGTTGCGCATACCTC
AAAACTTGGAGCAGCTTTTAGAGTAGCATCCCTCGTAGTTTCCTGAACAACAACCATAATGTAGG
CATTCCCTACTATTTTAATAGAAGGATTAAACATGTCAAATCCTTCCGACACAAGATGCAAAAGC
TCAAATGGACCTTTGTTAAAATCCACTAGCTCATACTTTAGACATATCTCCAAAAGTGTCCAGGC
ATTGTAGTGTTGGAAAAAATCCAGTTTGAAAATGGTTTTTTTTGCACAATGAAAAATAAAAATTT
TGAAAATCAACTCGATTTGTGATATTTATAGCAATAAACCCTAGACCAAAAATATACCTGTGTTT
TCGGATAGACGGATCCTTGTCGTTTTCAGCTTTCAACTAAACGATCTTCTCCTATATTCTCATGT
TACGAATTGCTTCAAGTGTGGGCTCGAACAAAACGAATCAAACACAGAAACTAGAAATAGTTTTC
TTTTCTTTTGGGTGAAAACGAAAATTCTCTCTTTAAAATAGAAACCAGCAGAATCATTATTTTGA
AAAATATATTTAATTCTTAGAGGATAAAAGTCTCTCTATTTTCGGGCAGAATAATAATATCTGAA
AGTTGTGTGTAAATAGCCCTGCTAGTGTCATCTATTTATAAAACAACATAAAAGCTC
Found at i:35725912 original size:353 final size:354
Alignment explanation
Indices: 35725264--35725971 Score: 1220
Period size: 353 Copynumber: 2.0 Consensus size: 354
35725254 CGATTAGTGC
35725264 TTGTCCAATGACCTTGTCATAAGTGTGTTACCCTCATAGGATATCCTTAATCTCTTTGGGATAAT
1 TTGTCCAATGACCTTGTCATAAGTGTGTTACCCTCATAGGATATCCTTAATCTCTTTGGGATAAT
* *
35725329 ATTCATTCTCTCAATATGATCTTATTTAATCTCACAGTAACCATTACATATTCTTTCATGAAAAG
66 ATTCATTCTCCCAATATGATCCTATTTAATCTCACAGTAACCATTACATATTCTTTCATGAAAAG
*
35725394 TCAATCACTATCAAATAGTGATCAAGTCATCTATCACAAATACGAACCCATGGTCACGTTTAGTT
131 TCAATCACTATCAAATAATGATCAAGTCATCTATCACAAATACGAACCCATGGTCACGTTTAGTT
* *
35725459 TCCATCACCATGTAATGCCAATGAGAGGATATCATTTTCCCATGTCTCGGGCTATGAATTCCACT
196 TCCATCACCATGTAATGCCAATGAGAGGATATCATTTACCCATGTCTCGGGATATGAATTCCACT
35725524 ATTGTGAATGACACTACATAATGCAAAAGTCGTACA-CAACGCACCAGCTTCCGATTCCTTATCC
261 ATTGTGAATGACACTACATAATGCAAAAGTCGTACACCAACGCACCAGCTTCCGATTCCTTATCC
35725588 ATTCGAACTCAGGCTTTCACTTACATCAA
326 ATTCGAACTCAGGCTTTCACTTACATCAA
* *
35725617 TTGTCCAATGTCCTTGTCATAAGTGTGTTACCCTCATAGGATATCCTTAATCTCTTTTGGATAAT
1 TTGTCCAATGACCTTGTCATAAGTGTGTTACCCTCATAGGATATCCTTAATCTCTTTGGGATAAT
* ** *
35725682 ATTCATTCTCCCAATATGATCCTATTTCATCTCATGGTAACCATTACATATTCTTTCATGAAAAT
66 ATTCATTCTCCCAATATGATCCTATTTAATCTCACAGTAACCATTACATATTCTTTCATGAAAAG
* * * * *
35725747 TTAATCATTATCAAATAATGATCATGTCATTTATCACAAATACGAACCCATGGTCACGTTTCGTT
131 TCAATCACTATCAAATAATGATCAAGTCATCTATCACAAATACGAACCCATGGTCACGTTTAGTT
35725812 TCCATCACCATGTAATGCCAATGAGAGGATATCATTTACCCATGTCTCGGGATATGAATTCCACT
196 TCCATCACCATGTAATGCCAATGAGAGGATATCATTTACCCATGTCTCGGGATATGAATTCCACT
* * *
35725877 ATTGTGAATGACACTACATATTGCAAAATTCGTACACCCAATGCACCAGCTTCCGATTCCTTATC
261 ATTGTGAATGACACTACATAATGCAAAAGTCGTACA-CCAACGCACCAGCTTCCGATTCCTTATC
*
35725942 CATTCGAACTTAGGCTTTCACTTACATCAA
325 CATTCGAACTCAGGCTTTCACTTACATCAA
35725972 AGTATACGAG
Statistics
Matches: 333, Mismatches: 20, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
353 278 0.83
355 55 0.17
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (354 bp):
TTGTCCAATGACCTTGTCATAAGTGTGTTACCCTCATAGGATATCCTTAATCTCTTTGGGATAAT
ATTCATTCTCCCAATATGATCCTATTTAATCTCACAGTAACCATTACATATTCTTTCATGAAAAG
TCAATCACTATCAAATAATGATCAAGTCATCTATCACAAATACGAACCCATGGTCACGTTTAGTT
TCCATCACCATGTAATGCCAATGAGAGGATATCATTTACCCATGTCTCGGGATATGAATTCCACT
ATTGTGAATGACACTACATAATGCAAAAGTCGTACACCAACGCACCAGCTTCCGATTCCTTATCC
ATTCGAACTCAGGCTTTCACTTACATCAA
Found at i:35729320 original size:45 final size:45
Alignment explanation
Indices: 35729256--35729380 Score: 189
Period size: 45 Copynumber: 2.8 Consensus size: 45
35729246 GTTATATTCC
35729256 TAAAATGAGTAAGACCATAGCTGAAAGATGTTATGGCA-TCATAAT
1 TAAAATGAGTAAGACCATAGCTGAAAGATGTTATGGCACT-ATAAT
* * * *
35729301 TAAAATGAGTACGACCATAGTTGAAAGATGATATGGCACTATTAT
1 TAAAATGAGTAAGACCATAGCTGAAAGATGTTATGGCACTATAAT
*
35729346 AAAAATGAGTAAGACCATAGCTGAAAGATGTTATG
1 TAAAATGAGTAAGACCATAGCTGAAAGATGTTATG
35729381 AAATCATATG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 70 0.99
46 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.26
Consensus pattern (45 bp):
TAAAATGAGTAAGACCATAGCTGAAAGATGTTATGGCACTATAAT
Found at i:35733999 original size:16 final size:16
Alignment explanation
Indices: 35733978--35734028 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
35733968 GGTTGGGGTG
35733978 AATGGAATA-AGGTTGT
1 AATGGAATACA-GTTGT
35733994 AATGGAATACAGTTGT
1 AATGGAATACAGTTGT
* *
35734010 AATGGAATAGAGCTGT
1 AATGGAATACAGTTGT
35734026 AAT
1 AAT
35734029 TAGTAATTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 31 0.97
17 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.27, T:0.29
Consensus pattern (16 bp):
AATGGAATACAGTTGT
Found at i:35742406 original size:16 final size:16
Alignment explanation
Indices: 35742385--35742417 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
35742375 CTTTGCTTTG
35742385 GCATTGGGAAAAAGAT
1 GCATTGGGAAAAAGAT
35742401 GCATTGGGAAAAAGAT
1 GCATTGGGAAAAAGAT
35742417 G
1 G
35742418 AACATAAGGC
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:0.42, C:0.06, G:0.33, T:0.18
Consensus pattern (16 bp):
GCATTGGGAAAAAGAT
Found at i:35745370 original size:35 final size:35
Alignment explanation
Indices: 35745311--35745395 Score: 91
Period size: 35 Copynumber: 2.4 Consensus size: 35
35745301 TAGTCTGCTA
** *
35745311 GGACAATAAACACAAAACAAAGTTGAGGTCCACT-G
1 GGACAATAAACATGAAACAAAGTTGAAGTCC-CTCG
* * *
35745346 GGACAATAAACATGGAACAGAGTTGAAGTCCGTCG
1 GGACAATAAACATGAAACAAAGTTGAAGTCCCTCG
*
35745381 GGACAGTAAACATGA
1 GGACAATAAACATGA
35745396 GTAAGACCGT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
34 1 0.02
35 40 0.98
ACGTcount: A:0.42, C:0.18, G:0.25, T:0.15
Consensus pattern (35 bp):
GGACAATAAACATGAAACAAAGTTGAAGTCCCTCG
Found at i:35747408 original size:25 final size:25
Alignment explanation
Indices: 35747378--35747510 Score: 101
Period size: 25 Copynumber: 5.3 Consensus size: 25
35747368 CAAACCAAAC
35747378 AAAGCCTTTGTGGCGAGTTATCT-G
1 AAAGCCTTTGTGGCGAGTTATCTAG
* * * *
35747402 TAAAGCCCTTGTGGCAAATTAT-TCG
1 -AAAGCCTTTGTGGCGAGTTATCTAG
* * *
35747427 AAATGCCTATGTGGCGTA-TTATTTGG
1 AAA-GCCTTTGTGGCG-AGTTATCTAG
* * *
35747453 AGAGCCTTAGTGGCGAAGATATCTAG
1 AAAGCCTTTGTGGCG-AGTTATCTAG
* *
35747479 AAAGCCTTTGAGGCGAGTCATCTAG
1 AAAGCCTTTGTGGCGAGTTATCTAG
35747504 AAAGCCT
1 AAAGCCT
35747511 ATTTGGTGAA
Statistics
Matches: 84, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
24 4 0.05
25 58 0.69
26 22 0.26
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (25 bp):
AAAGCCTTTGTGGCGAGTTATCTAG
Found at i:35754818 original size:22 final size:24
Alignment explanation
Indices: 35754768--35754818 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
35754758 GCCAAGTGAA
35754768 GGTATAT-TTTGAATGATCAATTT
1 GGTATATGTTTGAATGATCAATTT
*
35754791 GG--TATGTTTGAATG-T-GATTT
1 GGTATATGTTTGAATGATCAATTT
35754811 GGTATATG
1 GGTATATG
35754819 GTCAATTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
20 6 0.25
21 4 0.17
22 12 0.50
23 2 0.08
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.47
Consensus pattern (24 bp):
GGTATATGTTTGAATGATCAATTT
Found at i:35756070 original size:31 final size:29
Alignment explanation
Indices: 35756035--35756106 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
35756025 ATTAGAGCCC
35756035 AACCTTTTAAAAGTTGCTCATATAAGGGCCA
1 AACCTTTTAAAA--TGCTCATATAAGGGCCA
* * * *
35756066 AACCTTTCAAAATGCTCATATAATGGTCT
1 AACCTTTTAAAATGCTCATATAAGGGCCA
35756095 AACCTTTATAAA
1 AACCTTT-TAAA
35756107 TATTTGGTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 21 0.60
30 3 0.09
31 11 0.31
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (29 bp):
AACCTTTTAAAATGCTCATATAAGGGCCA
Found at i:35756130 original size:19 final size:19
Alignment explanation
Indices: 35756106--35756149 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
35756096 ACCTTTATAA
35756106 ATATTTGGTGAATTCTAAC
1 ATATTTGGTGAATTCTAAC
35756125 ATATTTGGTGAATTCTAAC
1 ATATTTGGTGAATTCTAAC
*
35756144 GTATTT
1 ATATTT
35756150 AGAATAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (19 bp):
ATATTTGGTGAATTCTAAC
Found at i:35756275 original size:31 final size:29
Alignment explanation
Indices: 35756236--35756315 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
35756226 ACATTTGAGA
*
35756236 AGCTCTTATTTGAGCACTTTCAAAAAGTTTT
1 AGCTCTTATTTGAGCACTTT--AAAAGGTTT
* * *
35756267 GGCTCTTATTTGAGCTCTTTGAAAGGTTT
1 AGCTCTTATTTGAGCACTTTAAAAGGTTT
35756296 AGCT-TTCATTTGAGCACTTT
1 AGCTCTT-ATTTGAGCACTTT
35756316 TGTAAATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
28 2 0.05
29 22 0.52
31 18 0.43
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.44
Consensus pattern (29 bp):
AGCTCTTATTTGAGCACTTTAAAAGGTTT
Found at i:35757813 original size:16 final size:16
Alignment explanation
Indices: 35757792--35757843 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
35757782 TTTGGTTCGC
*
35757792 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
35757808 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
35757824 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
35757840 TGTA
1 TGTA
35757844 ATAGCAAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:35765776 original size:27 final size:28
Alignment explanation
Indices: 35765722--35765786 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 28
35765712 ATAAAAAATA
*
35765722 ACCAAAATGTTATAACTTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTTATTT
35765750 ACCAAAATATTATAA-TTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTTATTT
35765777 ACCAAAATAT
1 ACCAAAATAT
35765787 ACCAAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (28 bp):
ACCAAAATATTATAACTTTTTTTTATTT
Found at i:35765819 original size:17 final size:18
Alignment explanation
Indices: 35765789--35765824 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
35765779 CAAAATATAC
35765789 CAAAAAAACCAAAAACCTG
1 CAAAAAAA-CAAAAACCTG
35765808 CAAAAAAA-AAAAACCTG
1 CAAAAAAACAAAAACCTG
35765825 TGGCGGCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.67, C:0.22, G:0.06, T:0.06
Consensus pattern (18 bp):
CAAAAAAACAAAAACCTG
Found at i:35766109 original size:18 final size:18
Alignment explanation
Indices: 35766088--35766140 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
35766078 AGTAATAACT
*
35766088 CTATTTTAATTTAATAAA
1 CTATTCTAATTTAATAAA
*
35766106 CTATTCTCATTTAATAAA
1 CTATTCTAATTTAATAAA
35766124 C---TCTAATTTAATAAA
1 CTATTCTAATTTAATAAA
35766139 CT
1 CT
35766141 CTATTTTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 14 0.45
18 17 0.55
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (18 bp):
CTATTCTAATTTAATAAA
Found at i:35766134 original size:15 final size:15
Alignment explanation
Indices: 35766094--35766143 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
35766084 AACTCTATTT
35766094 TAATTTAATAAACTATTC
1 TAATTTAATAAAC---TC
*
35766112 TCATTTAATAAACTC
1 TAATTTAATAAACTC
35766127 TAATTTAATAAACTC
1 TAATTTAATAAACTC
35766142 TA
1 TA
35766144 TTTTGGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 18 0.60
18 12 0.40
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATTTAATAAACTC
Found at i:35766177 original size:23 final size:23
Alignment explanation
Indices: 35766151--35766222 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
35766141 CTATTTTGGT
35766151 AATTTGATGAGAATAGTTTATTA
1 AATTTGATGAGAATAGTTTATTA
*
35766174 AA-TT-A--A-AATAGAGTTATTAA
1 AATTTGATGAGAATAG-TTTATT-A
35766194 GTAATTTGATGAGAATAGTTTATTA
1 --AATTTGATGAGAATAGTTTATTA
35766219 AATT
1 AATT
35766223 AAAATAGAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 18
0.66 0.03 0.31
Matches are distributed among these distances:
18 5 0.13
19 6 0.16
20 1 0.03
21 1 0.03
22 4 0.11
23 8 0.21
24 1 0.03
25 1 0.03
26 6 0.16
27 5 0.13
ACGTcount: A:0.43, C:0.00, G:0.15, T:0.42
Consensus pattern (23 bp):
AATTTGATGAGAATAGTTTATTA
Found at i:35766213 original size:45 final size:45
Alignment explanation
Indices: 35766149--35766237 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
35766139 CTCTATTTTG
35766149 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTAA
1 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTAA
35766194 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTA
1 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTA
35766238 CTTNNNNNNN
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (45 bp):
GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTAA
Found at i:35775200 original size:3 final size:3
Alignment explanation
Indices: 35775194--35775229 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
35775184 AAGCAAAAAA
35775194 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
35775230 TAAATGTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:35776305 original size:42 final size:43
Alignment explanation
Indices: 35776221--35776306 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 43
35776211 ATGGAGAACG
** *
35776221 GGAAACATTTGGAAATAATTATGGTTTTCTCCAAAATGAAAAT
1 GGAAACATTTAAAAATAATTATGGTTTTCTCCAAAATAAAAAT
**
35776264 GGAAACATTTAAAAATGAATT-T-GTTTTCTCTGAAATAAAAAT
1 GGAAACATTTAAAAAT-AATTATGGTTTTCTCCAAAATAAAAAT
35776306 G
1 G
35776307 ACCTGGAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 18 0.49
43 15 0.41
44 4 0.11
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (43 bp):
GGAAACATTTAAAAATAATTATGGTTTTCTCCAAAATAAAAAT
Found at i:35779271 original size:63 final size:64
Alignment explanation
Indices: 35779197--35779321 Score: 182
Period size: 63 Copynumber: 2.0 Consensus size: 64
35779187 TCTAGGTCAT
* *
35779197 TTTTCATTTTCATTTTTATTTTGGAGAAAACCACATTCATTTCCAAATGA-TTC-CATTTCTCCA
1 TTTTCATTTTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAAT-ATTTCTCATTTCTCCA
* * *
35779260 TTTTCATTTTCATTTTCATTTTTGAGAAAACTATAATCATTTCCAAATATTTCTCATTTCTC
1 TTTTCATTTTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATATTTCTCATTTCTC
35779322 TATATTCACC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
62 1 0.02
63 46 0.84
64 8 0.15
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (64 bp):
TTTTCATTTTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATATTTCTCATTTCTCCA
Found at i:35785228 original size:58 final size:57
Alignment explanation
Indices: 35785138--35785253 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 57
35785128 ATAAAATTAA
* *
35785138 CTCTAATAGTAGGTGTGAGAAAATTACTTAAACACAAAGAACAATTCAGGGAATTTAT
1 CTCTAATAGCAGGTGTGAAAAAATTACTTAAACACAAA-AACAATTCAGGGAATTTAT
* * *
35785196 CTCTAATGGCAGGTGTGAAAAAATTATTTAAACACAAAAATAATTCAGGGAATTTAT
1 CTCTAATAGCAGGTGTGAAAAAATTACTTAAACACAAAAACAATTCAGGGAATTTAT
35785253 C
1 C
35785254 GTATAAACAT
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 19 0.36
58 34 0.64
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.28
Consensus pattern (57 bp):
CTCTAATAGCAGGTGTGAAAAAATTACTTAAACACAAAAACAATTCAGGGAATTTAT
Found at i:35787247 original size:3 final size:3
Alignment explanation
Indices: 35787239--35787311 Score: 51
Period size: 3 Copynumber: 23.7 Consensus size: 3
35787229 CAACTATACA
* * * *
35787239 AAT AAT AAT AAA AAT AGT AAC AGT AAT AAT AA- AAT AACT AAAT AACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T -AAT AA-T
*
35787286 AA- ATAT AAT AAT AAC AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AA
35787312 ACGCGGTGGC
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
2 3 0.06
3 43 0.80
4 6 0.11
5 2 0.04
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:35788182 original size:30 final size:30
Alignment explanation
Indices: 35788146--35788217 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
35788136 CGCCCGTGTG
*
35788146 TTAGGCCGTGTGTCATAGACGACCATGTCT
1 TTAGGCCGTGTATCATAGACGACCATGTCT
** *
35788176 TTAGGCCGTGTATTTTAGACGGCCATGTCT
1 TTAGGCCGTGTATCATAGACGACCATGTCT
35788206 TTAGGCCGTGTA
1 TTAGGCCGTGTA
35788218 ACTCACTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.18, C:0.21, G:0.28, T:0.33
Consensus pattern (30 bp):
TTAGGCCGTGTATCATAGACGACCATGTCT
Found at i:35790700 original size:48 final size:48
Alignment explanation
Indices: 35790581--35790792 Score: 201
Period size: 48 Copynumber: 4.4 Consensus size: 48
35790571 ACTTATCGAA
* * *
35790581 ATAAAAACAGATTTCTCGGTGGCCTGCACACAGTCCGTACCACCTTTGT
1 ATAATAACAGA-TTATCGGTGGCCTGCACACAGTCCGTACCACCCTTGT
* * * * *
35790630 GTAATAGCAGATTCTCGATGGCCTGCACATAGTCCGTACCACCCTTGT
1 ATAATAACAGATTATCGGTGGCCTGCACACAGTCCGTACCACCCTTGT
** * * *
35790678 ATCTTAACA-AGTTATTGGTGGCCTGCACACAGTCTGTGCCACCCTTGT
1 ATAATAACAGA-TTATCGGTGGCCTGCACACAGTCCGTACCACCCTTGT
* * * * * * *
35790726 GTCACAATAGAATATCGGTGGCCTGCACACAGTCCGTGCCACACTTGT
1 ATAATAACAGATTATCGGTGGCCTGCACACAGTCCGTACCACCCTTGT
* *
35790774 GTCATAACAGATTATCGGT
1 ATAATAACAGATTATCGGT
35790793 ACGCATAGTA
Statistics
Matches: 134, Mismatches: 27, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
47 1 0.01
48 124 0.93
49 9 0.07
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (48 bp):
ATAATAACAGATTATCGGTGGCCTGCACACAGTCCGTACCACCCTTGT
Found at i:35790762 original size:96 final size:96
Alignment explanation
Indices: 35790598--35790782 Score: 235
Period size: 96 Copynumber: 1.9 Consensus size: 96
35790588 CAGATTTCTC
* * * * * *
35790598 GGTGGCCTGCACACAGTCCGTACCACCTTTGTGTAATAGCAGATTCTCGATGGCCTGCACATAGT
1 GGTGGCCTGCACACAGTCCGTACCACCCTTGTGTAACAACAGAATATCGATGGCCTGCACACAGT
* *
35790663 CCGTACCACCCTTGTATCTTAACAAGTTATT
66 CCGTACCACACTTGTATCATAACAAGTTATT
* * * * *
35790694 GGTGGCCTGCACACAGTCTGTGCCACCCTTGTGTCACAATAGAATATCGGTGGCCTGCACACAGT
1 GGTGGCCTGCACACAGTCCGTACCACCCTTGTGTAACAACAGAATATCGATGGCCTGCACACAGT
* *
35790759 CCGTGCCACACTTGTGTCATAACA
66 CCGTACCACACTTGTATCATAACA
35790783 GATTATCGGT
Statistics
Matches: 74, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
96 74 1.00
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (96 bp):
GGTGGCCTGCACACAGTCCGTACCACCCTTGTGTAACAACAGAATATCGATGGCCTGCACACAGT
CCGTACCACACTTGTATCATAACAAGTTATT
Found at i:35794673 original size:15 final size:14
Alignment explanation
Indices: 35794637--35794685 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
35794627 ATCAAAAAAG
**
35794637 AAAAATTAAAATGT
1 AAAAATTAAAATAA
35794651 AAAAATTAAAATAA
1 AAAAATTAAAATAA
35794665 AAAATATTAAAATAA
1 AAAA-ATTAAAATAA
35794680 AAAAAT
1 AAAAAT
35794686 AGCTAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 18 0.56
15 14 0.44
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (14 bp):
AAAAATTAAAATAA
Found at i:35796870 original size:21 final size:21
Alignment explanation
Indices: 35796841--35796883 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
35796831 GGACGGCTAG
35796841 GGCTGAAAAATAAAAGAATAAA
1 GGCTGAAAAATAAAAGAA-AAA
35796863 GGCT-AAAAATAAAAGAAAAA
1 GGCTGAAAAATAAAAGAAAAA
35796883 G
1 G
35796884 TAATATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.19
21 13 0.62
22 4 0.19
ACGTcount: A:0.65, C:0.05, G:0.19, T:0.12
Consensus pattern (21 bp):
GGCTGAAAAATAAAAGAAAAA
Found at i:35799520 original size:9 final size:9
Alignment explanation
Indices: 35799477--35799520 Score: 54
Period size: 10 Copynumber: 4.8 Consensus size: 9
35799467 AATTAATTTT
35799477 TAAAAATT-
1 TAAAAATTA
35799485 TAAAAATTCA
1 TAAAAATT-A
*
35799495 AAAAAATTA
1 TAAAAATTA
35799504 TTAAAAATTA
1 -TAAAAATTA
35799514 TAAAAAT
1 TAAAAAT
35799521 ATTTTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 8 0.26
9 8 0.26
10 15 0.48
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (9 bp):
TAAAAATTA
Found at i:35806101 original size:9 final size:9
Alignment explanation
Indices: 35806087--35806112 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
35806077 TATGCACACA
35806087 ATATGTGAT
1 ATATGTGAT
35806096 ATATGTGAT
1 ATATGTGAT
35806105 ATATGTGA
1 ATATGTGA
35806113 ACATGACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (9 bp):
ATATGTGAT
Found at i:35808448 original size:30 final size:28
Alignment explanation
Indices: 35808218--35808469 Score: 165
Period size: 29 Copynumber: 8.7 Consensus size: 28
35808208 TATATAAGTG
*
35808218 AGCCTTTGTGGCTA-CATCTATTATAAGGA
1 AGCCTTTGTGGCTATC-TCTACTA-AAGGA
* ** *
35808247 AGTCTTTGTGGCTATCTCTGTTAAAAGA
1 AGCCTTTGTGGCTATCTCTACTAAAGGA
35808275 ATGCCTTTGTGGCTA-C-CT-CTGAAAGGA
1 A-GCCTTTGTGGCTATCTCTACT-AAAGGA
* ** * *
35808302 ATGCCTTTATGGAAATACTCTA-AAAAGAA
1 A-GCCTTTGTGGCTAT-CTCTACTAAAGGA
* **
35808331 AGCCTTTGTGG-TGAGTACTGAATGTTAAAGGA
1 AGCCTTTGTGGCT-A-T-CT--CTACTAAAGGA
* *
35808363 AGCCTTTGTGGCTACTCTCAATTAAAGGA
1 AGCCTTTGTGGCTA-TCTCTACTAAAGGA
* *
35808392 AGCCTTTGTGGCTATCTTTGCTAAAGGA
1 AGCCTTTGTGGCTATCTCTACTAAAGGA
35808420 TAGCCTTTGTGGCTAATCTCTACTAAAGGAA
1 -AGCCTTTGTGGCT-ATCTCTACTAAAGG-A
*
35808451 AACCTTTGTGGCTATCTCT
1 AGCCTTTGTGGCTATCTCT
35808470 GTGAAAAAAC
Statistics
Matches: 179, Mismatches: 28, Indels: 32
0.75 0.12 0.13
Matches are distributed among these distances:
26 1 0.01
27 19 0.11
28 26 0.15
29 83 0.46
30 27 0.15
31 4 0.02
32 18 0.10
33 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.33
Consensus pattern (28 bp):
AGCCTTTGTGGCTATCTCTACTAAAGGA
Found at i:35808485 original size:58 final size:58
Alignment explanation
Indices: 35808363--35808488 Score: 148
Period size: 58 Copynumber: 2.2 Consensus size: 58
35808353 TGTTAAAGGA
* * * * ** *
35808363 AGCCTTTGTGGCTACTCTCAATTAAAGGAAGCCTTTGTGGCTATCTTTGCTAAAGGAT
1 AGCCTTTGTGGCTAATCTCAACTAAAGGAAACCTTTGTGGCTATCTCTGCTAAAAAAC
*
35808421 AGCCTTTGTGGCTAATCTCTACTAAAGGAAAACCTTTGTGGCTATCTCTG-TGAAAAAAC
1 AGCCTTTGTGGCTAATCTCAACTAAAGG-AAACCTTTGTGGCTATCTCTGCT-AAAAAAC
35808480 A-CCTTTGTG
1 AGCCTTTGTG
35808489 ATGAGACTCT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 34 0.59
59 24 0.41
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (58 bp):
AGCCTTTGTGGCTAATCTCAACTAAAGGAAACCTTTGTGGCTATCTCTGCTAAAAAAC
Found at i:35808954 original size:41 final size:41
Alignment explanation
Indices: 35808909--35808997 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
35808899 ATATAGTATC
35808909 TACCAAAGAAGAAAGAAAGGTTAAGAAATACCTCAAGAATG
1 TACCAAAGAAGAAAGAAAGGTTAAGAAATACCTCAAGAATG
35808950 TACCAAAGAAGAAAGAAAGGTTAAGAAATACCTCAAGAATG
1 TACCAAAGAAGAAAGAAAGGTTAAGAAATACCTCAAGAATG
35808991 TA-CAAAG
1 TACCAAAG
35808998 TAACATATGC
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 5 0.10
41 43 0.90
ACGTcount: A:0.54, C:0.12, G:0.19, T:0.15
Consensus pattern (41 bp):
TACCAAAGAAGAAAGAAAGGTTAAGAAATACCTCAAGAATG
Found at i:35812931 original size:19 final size:17
Alignment explanation
Indices: 35812907--35812942 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
35812897 TATTTTATTG
35812907 TTATTGTATAACTTTTGTT
1 TTATTGT-TAA-TTTTGTT
35812926 TTATTGTTAATTTTGTT
1 TTATTGTTAATTTTGTT
35812943 ACTATTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 3 0.18
19 7 0.41
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTATTGTTAATTTTGTT
Found at i:35815995 original size:50 final size:51
Alignment explanation
Indices: 35815935--35816046 Score: 149
Period size: 50 Copynumber: 2.2 Consensus size: 51
35815925 AACCAAACCA
* *
35815935 AGCCTTTGTGGCCA-ATTAACTAAAGAGCCTTTATGGCAAATTATCTAAAG
1 AGCCTTTGTGGCCAGATTAACTAAAGAGCCTTAATGGCAAATGATCTAAAG
* * *
35815985 AGCCTTTGTGG-CAGATTATCTGAAGAGCCTTAATGGCAGATGATCTAAAG
1 AGCCTTTGTGGCCAGATTAACTAAAGAGCCTTAATGGCAAATGATCTAAAG
35816035 AGTCC-TTGTGGC
1 AG-CCTTTGTGGC
35816047 GTATTACTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
49 2 0.04
50 50 0.93
51 2 0.04
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (51 bp):
AGCCTTTGTGGCCAGATTAACTAAAGAGCCTTAATGGCAAATGATCTAAAG
Found at i:35816046 original size:25 final size:25
Alignment explanation
Indices: 35815935--35816041 Score: 126
Period size: 25 Copynumber: 4.2 Consensus size: 25
35815925 AACCAAACCA
* *
35815935 AGCCTTTGTGGCCA-ATTAACTAAAG
1 AGCCTTTATGG-CAGATTATCTAAAG
*
35815960 AGCCTTTATGGCAAATTATCTAAAG
1 AGCCTTTATGGCAGATTATCTAAAG
* *
35815985 AGCCTTTGTGGCAGATTATCTGAAG
1 AGCCTTTATGGCAGATTATCTAAAG
* *
35816010 AGCCTTAATGGCAGATGATCTAAAG
1 AGCCTTTATGGCAGATTATCTAAAG
35816035 AGTCCTT
1 AG-CCTT
35816042 GTGGCGTATT
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
24 2 0.03
25 65 0.92
26 4 0.06
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (25 bp):
AGCCTTTATGGCAGATTATCTAAAG
Found at i:35824795 original size:10 final size:10
Alignment explanation
Indices: 35824782--35824827 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
35824772 CTGTGACTAA
*
35824782 ATGTGATTGT
1 ATGTGATTAT
*
35824792 ATGTAATTAT
1 ATGTGATTAT
*
35824802 ATGTGCTTAT
1 ATGTGATTAT
35824812 ATGTGATTGAT
1 ATGTGATT-AT
35824823 ATGTG
1 ATGTG
35824828 TCGGAATACA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 23 0.77
11 7 0.23
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (10 bp):
ATGTGATTAT
Found at i:35832425 original size:10 final size:10
Alignment explanation
Indices: 35832412--35832457 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
35832402 CTGTGACTAA
*
35832412 ATGTGATTGT
1 ATGTGATTAT
*
35832422 ATGTAATTAT
1 ATGTGATTAT
*
35832432 ATGTGCTTAT
1 ATGTGATTAT
35832442 ATGTGATTGAT
1 ATGTGATT-AT
35832453 ATGTG
1 ATGTG
35832458 TCGGAATATG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 23 0.77
11 7 0.23
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (10 bp):
ATGTGATTAT
Found at i:35839062 original size:21 final size:20
Alignment explanation
Indices: 35839024--35839061 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
35839014 TTTTCCTCCC
*
35839024 AAAACTTTTACTTCCCCCTA
1 AAAAATTTTACTTCCCCCTA
35839044 AAAAATTTTACTTCCCCC
1 AAAAATTTTACTTCCCCC
35839062 CGAACCGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAATTTTACTTCCCCCTA
Found at i:35839112 original size:28 final size:28
Alignment explanation
Indices: 35839075--35839133 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
35839065 ACCGCTAAAA
*
35839075 TTTTTCCCTTTTACTTCCCCCCAAAATT
1 TTTTTCCCTTTTACTTCCCCCCAAAACT
* * **
35839103 TTTTTTCCTTTTGCTTTTCCCCAAAACT
1 TTTTTCCCTTTTACTTCCCCCCAAAACT
35839131 TTT
1 TTT
35839134 ACTTCCTCCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.15, C:0.31, G:0.02, T:0.53
Consensus pattern (28 bp):
TTTTTCCCTTTTACTTCCCCCCAAAACT
Found at i:35839675 original size:10 final size:10
Alignment explanation
Indices: 35839657--35839689 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
35839647 AATTTTTTTC
35839657 ATTCGATTCA
1 ATTCGATTCA
*
35839667 ATTCAATTCA
1 ATTCGATTCA
35839677 ATTCGATTCA
1 ATTCGATTCA
35839687 ATT
1 ATT
35839690 GAGCGCTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (10 bp):
ATTCGATTCA
Found at i:35842206 original size:55 final size:55
Alignment explanation
Indices: 35842141--35842244 Score: 127
Period size: 55 Copynumber: 1.9 Consensus size: 55
35842131 CCCAACATCG
* ** *
35842141 AATACCCACACGGTCGGGCACACGACCTATGACACAACTGTGTGGCCCTTTTTCA
1 AATACCCACACGGGCGAACACACGACCTAAGACACAACTGTGTGGCCCTTTTTCA
* * ** *
35842196 AATACTCACACGGGCGAACACACGAGCTAAGACATGACTGTGTGTCCCT
1 AATACCCACACGGGCGAACACACGACCTAAGACACAACTGTGTGGCCCT
35842245 ACTTCGAATG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 40 1.00
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.20
Consensus pattern (55 bp):
AATACCCACACGGGCGAACACACGACCTAAGACACAACTGTGTGGCCCTTTTTCA
Found at i:35854431 original size:39 final size:39
Alignment explanation
Indices: 35854355--35854587 Score: 156
Period size: 39 Copynumber: 6.1 Consensus size: 39
35854345 AAGCCAGCAT
* ** * * *
35854355 CAACAGCAGCAGCAACAG-ATGCAGCCACTGCTACAACAG
1 CAACAGCAGCAGCAGCAGCA-GCTCCCACAGCTGCAACAA
35854394 CAACAG-ATGCCA-CAGCAGCAGCTCCCACAGCTGCAACAA
1 CAACAGCA-G-CAGCAGCAGCAGCTCCCACAGCTGCAACAA
*
35854433 CAACAGCAGCAGCAGCAGCAGCTTCCACAGCTGCAACAA
1 CAACAGCAGCAGCAGCAGCAGCTCCCACAGCTGCAACAA
* * * ** * * *
35854472 CAGCAGCAGCAACAGCCGCAGCAGCAACAGCCGC-TC--
1 CAACAGCAGCAGCAGCAGCAGCTCCCACAGCTGCAACAA
* *** * * * * *
35854508 CCACATTTGCAACAGCAACAACTCCCTCAGCTGCAACAG
1 CAACAGCAGCAGCAGCAGCAGCTCCCACAGCTGCAACAA
*
35854547 CAACAGCAGCAGCAGCAGCAACTCTCC-CAGCTGCAACAA
1 CAACAGCAGCAGCAGCAGCAGCTC-CCACAGCTGCAACAA
35854586 CA
1 CA
35854588 GCAGATGCCC
Statistics
Matches: 149, Mismatches: 36, Indels: 18
0.73 0.18 0.09
Matches are distributed among these distances:
36 21 0.14
37 1 0.01
38 4 0.03
39 117 0.79
40 6 0.04
ACGTcount: A:0.35, C:0.38, G:0.19, T:0.08
Consensus pattern (39 bp):
CAACAGCAGCAGCAGCAGCAGCTCCCACAGCTGCAACAA
Found at i:35854454 original size:15 final size:15
Alignment explanation
Indices: 35854405--35854502 Score: 63
Period size: 15 Copynumber: 6.3 Consensus size: 15
35854395 AACAGATGCC
** *
35854405 ACAGCAGCAGCTCCC
1 ACAGCAGCAGCAGCA
* * *
35854420 ACAGCTGCAACAACA
1 ACAGCAGCAGCAGCA
35854435 ACAGCAGCAGCAGCA
1 ACAGCAGCAGCAGCA
* *
35854450 GCAGCTTCCA-CAGCTGCA
1 ACAG----CAGCAGCAGCA
*
35854468 ACAACAGCAGCAGCA
1 ACAGCAGCAGCAGCA
*
35854483 ACAGCCGCAGCAGCA
1 ACAGCAGCAGCAGCA
35854498 ACAGC
1 ACAGC
35854503 CGCTCCCACA
Statistics
Matches: 63, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
14 2 0.03
15 50 0.79
18 9 0.14
19 2 0.03
ACGTcount: A:0.36, C:0.38, G:0.21, T:0.05
Consensus pattern (15 bp):
ACAGCAGCAGCAGCA
Found at i:35854475 original size:36 final size:37
Alignment explanation
Indices: 35854406--35854487 Score: 121
Period size: 36 Copynumber: 2.2 Consensus size: 37
35854396 ACAGATGCCA
35854406 CAGCAGCAGCTCCCACAGCTGCAACAACAACAGCAGCAG
1 CAGCAGCAGCTCCCACAGCTG--ACAACAACAGCAGCAG
*
35854445 CAGCAGCAGCTTCCACAGCTG-CAACAACAGCAGCAG
1 CAGCAGCAGCTCCCACAGCTGACAACAACAGCAGCAG
*
35854481 CAACAGC
1 CAGCAGC
35854488 CGCAGCAGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
36 21 0.51
39 20 0.49
ACGTcount: A:0.35, C:0.38, G:0.21, T:0.06
Consensus pattern (37 bp):
CAGCAGCAGCTCCCACAGCTGACAACAACAGCAGCAG
Found at i:35854482 original size:114 final size:112
Alignment explanation
Indices: 35854355--35854591 Score: 280
Period size: 114 Copynumber: 2.1 Consensus size: 112
35854345 AAGCCAGCAT
* * * * *
35854355 CAACAGCAGCAGCAACAGATGCAGCCACTGCTACAACAG-CAACAGATGCCACAGCAGCAGCTCC
1 CAACAGCAGCAGCAACAGACGCAG-CA--GCAACAACAGCCAACAGATGCAACAGCAACAACTCC
*
35854419 CACAGCTGCAACAACAACAGCAGCAGCAGCAGCAGCT-TCCACAGCTGCAA
63 CACAGCTGCAACAACAACAGCAGCAGCAGCAGCAACTCTCC-CAGCTGCAA
* * * * **
35854469 CAACAGCAGCAGCAACAGCCGCAGCAGCAACAGCCGCTCCCACATTTGCAACAGCAACAACTCCC
1 CAACAGCAGCAGCAACAGACGCAGCAGCAACAACAG--CCAACAGATGCAACAGCAACAACTCCC
* *
35854534 TCAGCTGCAACAGCAACAGCAGCAGCAGCAGCAACTCTCCCAGCTGCAA
64 ACAGCTGCAACAACAACAGCAGCAGCAGCAGCAACTCTCCCAGCTGCAA
35854583 CAACAGCAG
1 CAACAGCAG
35854592 ATGCCCCAGT
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
111 7 0.07
113 2 0.02
114 93 0.89
115 3 0.03
ACGTcount: A:0.35, C:0.38, G:0.19, T:0.08
Consensus pattern (112 bp):
CAACAGCAGCAGCAACAGACGCAGCAGCAACAACAGCCAACAGATGCAACAGCAACAACTCCCAC
AGCTGCAACAACAACAGCAGCAGCAGCAGCAACTCTCCCAGCTGCAA
Found at i:35854503 original size:15 final size:15
Alignment explanation
Indices: 35854460--35854505 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
35854450 GCAGCTTCCA
* * *
35854460 CAGCTGCAACAACAG
1 CAGCAGCAACAGCCG
35854475 CAGCAGCAACAGCCG
1 CAGCAGCAACAGCCG
35854490 CAGCAGCAACAGCCG
1 CAGCAGCAACAGCCG
35854505 C
1 C
35854506 TCCCACATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.35, C:0.39, G:0.24, T:0.02
Consensus pattern (15 bp):
CAGCAGCAACAGCCG
Done.