Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008387.1 Hibiscus syriacus cultivar Beakdansim tig00111151_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: 2491990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 12
Found at i:1083445 original size:12 final size:12
Alignment explanation
Indices: 1083425--1083463 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
1083415 CTTAATTTTA
1083425 TTTATTTTTAATT
1 TTTA-TTTTAATT
*
1083438 TTTATTTTATTT
1 TTTATTTTAATT
1083450 TTTATTTTATATT
1 TTTATTTTA-ATT
1083463 T
1 T
1083464 ACATATTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 16 0.70
13 7 0.30
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTATTTTAATT
Found at i:1083464 original size:18 final size:17
Alignment explanation
Indices: 1083411--1083464 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
1083401 GTTTTTTTAA
*
1083411 TATTCTTAA-TTTTATT
1 TATTTTTAATTTTTATT
1083427 TATTTTTAATTTTTATTT
1 TATTTTTAATTTTTA-TT
*
1083445 TATTTTTTATTTTATATT
1 TATTTTTAATTTT-TATT
1083463 TA
1 TA
1083465 CATATTACAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 8 0.24
17 5 0.15
18 18 0.55
19 2 0.06
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTTTTAATTTTTATT
Found at i:1086250 original size:160 final size:160
Alignment explanation
Indices: 1085890--1086364 Score: 899
Period size: 160 Copynumber: 3.0 Consensus size: 160
1085880 AATTTTAATG
1085890 CCCTCAATTATTTGCTTTAGTGCCATGTCTCTTACTCACACGCACACTATTAATTTTTTATGTCT
1 CCCTCAATTATTTGCTTTAGTGCCATGTCTCTTACTCACACGCACACTATTAATTTTTTATGTCT
1085955 CTT--ACACACACTATCAAGGAATATATTGTTTTTTTATTTTATTTAT-A-A-TA-TTATTTATT
66 CTTACACACACACTATCAAGGAATATATTGTTTTTTTATTTTATTTATAATATTATTTATTTATT
1086014 TATTTGCATTGGTCTGATCCCACATTATGT
131 TATTTGCATTGGTCTGATCCCACATTATGT
1086044 CCCTCAATTATTTGCTTTAGTGCCATGTCTCTTACTCACACGCACACTATTAATTTTTTATGTCT
1 CCCTCAATTATTTGCTTTAGTGCCATGTCTCTTACTCACACGCACACTATTAATTTTTTATGTCT
1086109 CTTACACACACACTATCAAGGAATATATTGTTTTTTTATTTTATTTATAATATTATTTATTTATT
66 CTTACACACACACTATCAAGGAATATATTGTTTTTTTATTTTATTTATAATATTATTTATTTATT
1086174 TATTTGCATTGGTCTGATCCCACATTATGT
131 TATTTGCATTGGTCTGATCCCACATTATGT
1086204 CCCTCAATTATTTGCTTTAGTGCCATGTCTCTTACTCACACGCACACTATTAATTTTTTATGTCT
1 CCCTCAATTATTTGCTTTAGTGCCATGTCTCTTACTCACACGCACACTATTAATTTTTTATGTCT
1086269 CTTACACACACACTATCAAGGAATATATTGTTTTTTTTATTTTATTTATAATATTATTTATTTAT
66 CTTACACACACACTATCAAGGAATATATTG-TTTTTTTATTTTATTTATAATATTATTTATTTAT
1086334 TTATTTGCATTGGTCTGATCCCACATTATGT
130 TTATTTGCATTGGTCTGATCCCACATTATGT
1086365 AACCATGTCT
Statistics
Matches: 314, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
154 68 0.22
156 43 0.14
157 1 0.00
158 1 0.00
159 2 0.01
160 134 0.43
161 65 0.21
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (160 bp):
CCCTCAATTATTTGCTTTAGTGCCATGTCTCTTACTCACACGCACACTATTAATTTTTTATGTCT
CTTACACACACACTATCAAGGAATATATTGTTTTTTTATTTTATTTATAATATTATTTATTTATT
TATTTGCATTGGTCTGATCCCACATTATGT
Found at i:1086481 original size:314 final size:304
Alignment explanation
Indices: 1085890--1086483 Score: 740
Period size: 314 Copynumber: 1.9 Consensus size: 304
1085880 AATTTTAATG
1085890 CCCTCAATTATTTGCTTTAGTGCCATGTCTCTTACTCACACGCACACTATTAATTTTTTATGTCT
1 CCCTCAATTATTTGCTTTAGTGCCATGTCTCTTACTCACACGCACACTATTAATTTTTTATGTCT
1085955 CTTACACACACTATCAAGGAATATATTGTTTTTTTATTTTATTTATAATATTATTTATTTATTTG
66 CTTACACACACTATCAAGGAATATATTGTTTTTTTATTTTATTTATAATATTATTTATTTATTTG
* * *
1086020 CATTGGTCTGATCCCACATTATGTCCCTCAATTATTTGCTTTAGTGCCATGTCTCTTACTCACAC
131 CATTGGTCTGATCCCACATTATGTCCCTCAATTATTTGCTTTA-TGCCACGCCTCTGACTCACAC
* *** * **
1086085 GCACACTATTAATTTTTTATGTCTCTTACACACACACTATCAAGGAATATATTGTTTTTTTATTT
195 GCACACTATCAATCACTTATGTCTCTT--------A-GATCAAGGAATATATTCCTTTTTTATTT
1086150 TATTTATAATATTATTTATTTATTTATTTGCATTGGTCTGATCCCACATTATGT
251 TATTTATAATATTATTTATTTATTTATTTGCATTGGTCTGATCCCACATTATGT
1086204 CCCTCAATTATTTGCTTTAGTGCCATGTCTCTTACTCACACGCACACTATTAATTTTTTATGTCT
1 CCCTCAATTATTTGCTTTAGTGCCATGTCTCTTACTCACACGCACACTATTAATTTTTTATGTCT
1086269 CTTACACACACACTATCAAGGAATATATTGTTTTTTTTATTTTATTTATAATATTATTTATTTAT
66 CTT--ACACACACTATCAAGGAATATATTG-TTTTTTTATTTTATTTAT-A-A-TA-TTATTTAT
**
1086334 TTATTTGCATTGGTCTGATCCCACATTATGTAACCATGTCTATCAATTATTTG-TTT-T-TTACG
124 TTATTTGCATTGGTCTGATCCCACATTATGT--CC----C--TCAATTATTTGCTTTATGCCACG
* * * *
1086396 CCTCTGCCTCTACACGCACAC-A-CCATCACTT-T-T-T-TT-GGTCAAGTAATATATTCCTTTT
181 CCTCTGACTC-ACACGCACACTATCAATCACTTATGTCTCTTAGATCAAGGAATATATTCCTTTT
1086454 TTATTTTATTTATAATATTATTTATTTATT
245 TTATTTTATTTATAATATTATTTATTTATT
1086484 CTTTATATTA
Statistics
Matches: 248, Mismatches: 16, Indels: 36
0.83 0.05 0.12
Matches are distributed among these distances:
310 47 0.19
314 68 0.27
316 25 0.10
317 18 0.07
318 1 0.00
319 1 0.00
320 4 0.02
321 40 0.16
322 1 0.00
323 3 0.01
324 4 0.02
325 10 0.04
326 11 0.04
327 1 0.00
328 3 0.01
329 11 0.04
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.47
Consensus pattern (304 bp):
CCCTCAATTATTTGCTTTAGTGCCATGTCTCTTACTCACACGCACACTATTAATTTTTTATGTCT
CTTACACACACTATCAAGGAATATATTGTTTTTTTATTTTATTTATAATATTATTTATTTATTTG
CATTGGTCTGATCCCACATTATGTCCCTCAATTATTTGCTTTATGCCACGCCTCTGACTCACACG
CACACTATCAATCACTTATGTCTCTTAGATCAAGGAATATATTCCTTTTTTATTTTATTTATAAT
ATTATTTATTTATTTATTTGCATTGGTCTGATCCCACATTATGT
Found at i:1086706 original size:16 final size:16
Alignment explanation
Indices: 1086679--1086723 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
1086669 AGATATGAAA
1086679 AAATTCAATTTAAATTT
1 AAATT-AATTTAAATTT
*
1086696 AAATTAATTTAATTTT
1 AAATTAATTTAAATTT
*
1086712 AAAATAATTTAA
1 AAATTAATTTAA
1086724 TTAATTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 21 0.81
17 5 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTAATTTAAATTT
Found at i:1086724 original size:16 final size:16
Alignment explanation
Indices: 1086685--1086725 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1086675 GAAAAAATTC
* *
1086685 AATTTAAATTTAAATT
1 AATTTAATTTTAAAAT
1086701 AATTTAATTTTAAAAT
1 AATTTAATTTTAAAAT
1086717 AATTTAATT
1 AATTTAATT
1086726 AATTCAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTTAATTTTAAAAT
Found at i:1101300 original size:22 final size:21
Alignment explanation
Indices: 1101268--1101340 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 21
1101258 AACCCATCAG
*
1101268 TAAGTCTTTCGAGCATGATGA
1 TAAGTCCTTCGAGCATGATGA
* *
1101289 TGAAGTCCTTCGGGCCATCA-G-
1 T-AAGTCCTTCGAG-CATGATGA
*
1101310 TAAGTCTTTCGAGCATGATGA
1 TAAGTCCTTCGAGCATGATGA
*
1101331 TTAAATCCTT
1 -TAAGTCCTT
1101341 TGGGTAATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
19 4 0.10
20 11 0.28
21 2 0.05
22 18 0.46
23 4 0.10
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (21 bp):
TAAGTCCTTCGAGCATGATGA
Found at i:1101320 original size:20 final size:20
Alignment explanation
Indices: 1101261--1101323 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
1101251 CTTAGTAAAC
1101261 CCATCAGTAAGTCTTTCGAG
1 CCATCAGTAAGTCTTTCGAG
* * *
1101281 -CATGATGATGAAGTCCTTCGGG
1 CCATCA-G-T-AAGTCTTTCGAG
1101303 CCATCAGTAAGTCTTTCGAG
1 CCATCAGTAAGTCTTTCGAG
1101323 C
1 C
1101324 ATGATGATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 4 0.12
20 12 0.36
21 2 0.06
22 11 0.33
23 4 0.12
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (20 bp):
CCATCAGTAAGTCTTTCGAG
Found at i:1101320 original size:42 final size:42
Alignment explanation
Indices: 1101261--1101466 Score: 149
Period size: 42 Copynumber: 5.0 Consensus size: 42
1101251 CTTAGTAAAC
*
1101261 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* *
1101303 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
** ** * * * * **
1101345 TAATTTGTAAG-CCTTC-ACCGAAGA-GTAGTG-AAGCAAAT----
1 CCATCAGTAAGTCTTTCGAGC-ATGATG-A-TGAAATC-CTTCGGG
*
1101383 CCATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* ** * *
1101425 TCATTTGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
1101467 TAATTTGTAA
Statistics
Matches: 121, Mismatches: 31, Indels: 24
0.69 0.18 0.14
Matches are distributed among these distances:
38 9 0.07
39 11 0.09
40 6 0.05
41 11 0.09
42 84 0.69
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (42 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
Found at i:1101422 original size:22 final size:21
Alignment explanation
Indices: 1101397--1101464 Score: 50
Period size: 22 Copynumber: 3.2 Consensus size: 21
1101387 CAATAAGTCT
*
1101397 TTCGAGCATGATGATGAAATCC
1 TTCGAGCATGATGAT-AAATCA
* * * *
1101419 TTCGGGTCAT-TTG-TAAGTCT
1 TTCGAG-CATGATGATAAATCA
1101439 TTCGAGCATGATGATTAAATCA
1 TTCGAGCATGATGA-TAAATCA
1101461 TTCG
1 TTCG
1101465 GGTAATTTGT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 3 0.09
20 11 0.32
21 1 0.03
22 16 0.47
23 3 0.09
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35
Consensus pattern (21 bp):
TTCGAGCATGATGATAAATCA
Found at i:1101467 original size:42 final size:42
Alignment explanation
Indices: 1101390--1101477 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
1101380 AATCCATCAA
* *
1101390 TAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTTG
1 TAAGTCTTTCGAGCATGATGATGAAATCATTCGGGTAATTTG
*
1101432 TAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTG
1 TAAGTCTTTCGAGCATGATGATGAAATCATTCGGGTAATTTG
1101474 TAAG
1 TAAG
1101478 ACTTCACCGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (42 bp):
TAAGTCTTTCGAGCATGATGATGAAATCATTCGGGTAATTTG
Found at i:1101483 original size:122 final size:122
Alignment explanation
Indices: 1101261--1101557 Score: 486
Period size: 122 Copynumber: 2.4 Consensus size: 122
1101251 CTTAGTAAAC
* * **
1101261 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTTGTAAGTCTTTCGAGCAT
* * *
1101326 GATGATTAAATCCTTTGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
66 GATGATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGTGAAGCAAAT
*
1101383 CCATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTTGTAAGTCTTTCGAGCAT
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTTGTAAGTCTTTCGAGCAT
1101448 GATGATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGTGAAGCAAAT
66 GATGATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGTGAAGCAAAT
* * * *
1101505 CCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTTGTAAG
1101558 CCTTCACGGA
Statistics
Matches: 162, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
122 162 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (122 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTTGTAAGTCTTTCGAGCAT
GATGATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGTGAAGCAAAT
Found at i:1101564 original size:80 final size:80
Alignment explanation
Indices: 1101431--1101751 Score: 490
Period size: 80 Copynumber: 4.1 Consensus size: 80
1101421 CGGGTCATTT
*
1101431 GTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGT
1 GTAAGTCTTTCGAGCATGATAATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGT
1101496 GAAGCAAATCCATCA
66 GAAGCAAATCCATCA
* * * *
1101511 GTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGAGTAGT
1 GTAAGTCTTTCGAGCATGATAATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGT
*
1101576 GAAGCAAACCCATCA
66 GAAGCAAATCCATCA
* *
1101591 GTAAGTCTTTCGAGCATGATGA-T-AATCATTCAGGT-A-TTGTAAGACTTCA-CGAAGAGTAGT
1 GTAAGTCTTTCGAGCATGATAATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGT
1101651 GAAGCAAATCCATCA
66 GAAGCAAATCCATCA
* * * *
1101666 GTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGAGTAGT
1 GTAAGTCTTTCGAGCATGATAATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGT
*
1101731 GAAGCAAATCCGTCA
66 GAAGCAAATCCATCA
1101746 GTAAGT
1 GTAAGT
1101752 GCCATCAATA
Statistics
Matches: 216, Mismatches: 20, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
75 45 0.21
76 12 0.06
77 11 0.05
78 11 0.05
79 12 0.06
80 125 0.58
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (80 bp):
GTAAGTCTTTCGAGCATGATAATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGT
GAAGCAAATCCATCA
Found at i:1101662 original size:155 final size:160
Alignment explanation
Indices: 1101431--1101751 Score: 580
Period size: 155 Copynumber: 2.0 Consensus size: 160
1101421 CGGGTCATTT
*
1101431 GTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGT
1 GTAAGTCTTTCGAGCATGATGATTAAATCATTCAGGTAATTTGTAAGACTTCACCGAAGAGTAGT
1101496 GAAGCAAATCCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCT
66 GAAGCAAATCCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCT
1101561 TCACGGAAGAGTAGTGAAGCAAACCCATCA
131 TCACGGAAGAGTAGTGAAGCAAACCCATCA
1101591 GTAAGTCTTTCGAGCATGATGA-T-AATCATTCAGGT-A-TTGTAAGACTTCA-CGAAGAGTAGT
1 GTAAGTCTTTCGAGCATGATGATTAAATCATTCAGGTAATTTGTAAGACTTCACCGAAGAGTAGT
1101651 GAAGCAAATCCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCT
66 GAAGCAAATCCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCT
* *
1101716 TCACGGAAGAGTAGTGAAGCAAATCCGTCA
131 TCACGGAAGAGTAGTGAAGCAAACCCATCA
1101746 GTAAGT
1 GTAAGT
1101752 GCCATCAATA
Statistics
Matches: 158, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
155 110 0.70
156 13 0.08
157 1 0.01
158 11 0.07
159 1 0.01
160 22 0.14
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (160 bp):
GTAAGTCTTTCGAGCATGATGATTAAATCATTCAGGTAATTTGTAAGACTTCACCGAAGAGTAGT
GAAGCAAATCCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCT
TCACGGAAGAGTAGTGAAGCAAACCCATCA
Found at i:1101813 original size:42 final size:41
Alignment explanation
Indices: 1101754--1101882 Score: 152
Period size: 42 Copynumber: 3.1 Consensus size: 41
1101744 CAGTAAGTGC
*
1101754 CATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGAT-AAATCCTTCGGGT
* *
1101796 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGAT
1 CATCAGTAAGTCTTTCGAGCATGATGA-TAAATCCTTCGGGT
** * * *
1101838 CATTTGTGAGT-TTCTCGAACAAGATGATAAATCCTTCGGGT
1 CATCAGTAAGTCTT-TCGAGCATGATGATAAATCCTTCGGGT
1101879 CATC
1 CATC
1101883 CATAAGACCT
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
41 17 0.23
42 56 0.76
43 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (41 bp):
CATCAGTAAGTCTTTCGAGCATGATGATAAATCCTTCGGGT
Found at i:1101831 original size:22 final size:22
Alignment explanation
Indices: 1101764--1101834 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
1101754 CATCAATAAG
*
1101764 TCTTTCGAGCATGATGATGAAA
1 TCTTTCGAGCATGATGATTAAA
* * * *
1101786 TCCTTCGGGTCATCA-G--TAAG
1 TCTTTCGAG-CATGATGATTAAA
1101806 TCTTTCGAGCATGATGATTAAA
1 TCTTTCGAGCATGATGATTAAA
1101828 TCTTTCG
1 TCTTTCG
1101835 GATCATTTGT
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
19 4 0.11
20 10 0.28
22 18 0.50
23 4 0.11
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.35
Consensus pattern (22 bp):
TCTTTCGAGCATGATGATTAAA
Found at i:1102294 original size:52 final size:53
Alignment explanation
Indices: 1102181--1102282 Score: 179
Period size: 53 Copynumber: 1.9 Consensus size: 53
1102171 AGAATCACAC
*
1102181 CAGAAGATTGCTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGG
*
1102234 CAGAAGATTGTTCGAGTTCTACTCCCTGAA-CAAGAGGGAGCGGACCCAT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCAT
1102283 CATTTGAAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 18 0.38
53 29 0.62
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.19
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGG
Found at i:1105134 original size:5 final size:5
Alignment explanation
Indices: 1105126--1105157 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1105116 ATTATATTAT
1105126 AAATA AAATA AAATA AAATA AAAT- AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAA
1105158 AATCCTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:1105494 original size:10 final size:10
Alignment explanation
Indices: 1105465--1105496 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1105455 TTCAGTAAAT
*
1105465 ATGTTCGTTT
1 ATGTTCGTTC
1105475 ATGTTCGTTC
1 ATGTTCGTTC
1105485 ATGTTCGTTC
1 ATGTTCGTTC
1105495 AT
1 AT
1105497 TTATGTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.12, C:0.16, G:0.19, T:0.53
Consensus pattern (10 bp):
ATGTTCGTTC
Found at i:1105494 original size:14 final size:14
Alignment explanation
Indices: 1105467--1105517 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
1105457 CAGTAAATAT
1105467 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
1105481 GTTC----ATGTTC
1 GTTCGTTTATGTTC
*
1105491 GTTCATTTATGTTC
1 GTTCGTTTATGTTC
*
1105505 ATTCGTTTATGTT
1 GTTCGTTTATGTT
1105518 AGTTTATGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 10 0.32
14 21 0.68
ACGTcount: A:0.12, C:0.14, G:0.18, T:0.57
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:1105511 original size:18 final size:18
Alignment explanation
Indices: 1105488--1105538 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
1105478 TTCGTTCATG
1105488 TTCGTTCATTTATGTTCA
1 TTCGTTCATTTATGTTCA
* *
1105506 TTCGTTTATGTTA-GTTTA
1 TTCGTTCAT-TTATGTTCA
1105524 TGT-GTTCATTTATGT
1 T-TCGTTCATTTATGT
1105539 ATAGCCCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 3 0.11
18 20 0.74
19 4 0.15
ACGTcount: A:0.16, C:0.10, G:0.16, T:0.59
Consensus pattern (18 bp):
TTCGTTCATTTATGTTCA
Found at i:1105715 original size:10 final size:10
Alignment explanation
Indices: 1105700--1105817 Score: 110
Period size: 10 Copynumber: 11.5 Consensus size: 10
1105690 AAGAAAAAAA
*
1105700 ATTTATTTTC
1 ATTTATGTTC
*
1105710 ATTTATTTTC
1 ATTTATGTTC
* *
1105720 GTTTACGTTC
1 ATTTATGTTC
1105730 ATTTATGTTC
1 ATTTATGTTC
* *
1105740 GTTTACGTTC
1 ATTTATGTTC
1105750 ATTTATGTTC
1 ATTTATGTTC
* *
1105760 GTTTACGTTC
1 ATTTATGTTC
1105770 ATTTATGTTC
1 ATTTATGTTC
1105780 ATTTATTGTGCTC
1 ATTTA-TGT--TC
*
1105793 GTTTATGTTC
1 ATTTATGTTC
*
1105803 ATTTGTGTTC
1 ATTTATGTTC
*
1105813 GTTTA
1 ATTTA
1105818 CGTTTGTTTG
Statistics
Matches: 87, Mismatches: 18, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
10 75 0.86
11 3 0.03
12 3 0.03
13 6 0.07
ACGTcount: A:0.15, C:0.13, G:0.14, T:0.58
Consensus pattern (10 bp):
ATTTATGTTC
Found at i:1105730 original size:20 final size:20
Alignment explanation
Indices: 1105707--1105841 Score: 140
Period size: 20 Copynumber: 7.1 Consensus size: 20
1105697 AAAATTTATT
*
1105707 TTCATTTATTTTCGTTTACG
1 TTCATTTATGTTCGTTTACG
1105727 TTCATTTATGTTCGTTTACG
1 TTCATTTATGTTCGTTTACG
1105747 TTCATTTATGTTCGTTTACG
1 TTCATTTATGTTCGTTTACG
1105767 TTCATTTATGTTC----A--
1 TTCATTTATGTTCGTTTACG
* * * *
1105781 TTTA-TTGTGCTCGTTTATG
1 TTCATTTATGTTCGTTTACG
*
1105800 TTCATTTGTGTTCGTTTACG
1 TTCATTTATGTTCGTTTACG
** *
1105820 TTTGTTTGTGTTCGTTTACG
1 TTCATTTATGTTCGTTTACG
1105840 TT
1 TT
1105842 TGTTTATTGT
Statistics
Matches: 99, Mismatches: 9, Indels: 14
0.81 0.07 0.11
Matches are distributed among these distances:
13 6 0.06
14 3 0.03
16 1 0.01
17 1 0.01
19 3 0.03
20 85 0.86
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.58
Consensus pattern (20 bp):
TTCATTTATGTTCGTTTACG
Found at i:1105826 original size:10 final size:10
Alignment explanation
Indices: 1105793--1105874 Score: 65
Period size: 10 Copynumber: 7.9 Consensus size: 10
1105783 TATTGTGCTC
*
1105793 GTTTATGTTC
1 GTTTATGTTT
* * *
1105803 ATTTGTGTTC
1 GTTTATGTTT
*
1105813 GTTTACGTTT
1 GTTTATGTTT
* *
1105823 GTTTGTGTTC
1 GTTTATGTTT
*
1105833 GTTTACGTTT
1 GTTTATGTTT
1105843 GTTTATTGTGTTT
1 GTTTA---TGTTT
1105856 GTTTATGTTT
1 GTTTATGTTT
1105866 GTTTATGTT
1 GTTTATGTT
1105875 CGTTCATTTG
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
10 47 0.84
13 9 0.16
ACGTcount: A:0.09, C:0.06, G:0.22, T:0.63
Consensus pattern (10 bp):
GTTTATGTTT
Found at i:1105832 original size:53 final size:50
Alignment explanation
Indices: 1105721--1105821 Score: 148
Period size: 53 Copynumber: 2.0 Consensus size: 50
1105711 TTTATTTTCG
*
1105721 TTTACGTTCATTTATGTTCGTTTACGTTCATTTATGTTCGTTTACGTTCA
1 TTTATGTTCATTTATGTTCGTTTACGTTCATTTATGTTCGTTTACGTTCA
* *
1105771 TTTATGTTCATTTATTGTGCTCGTTTATGTTCATTTGTGTTCGTTTACGTT
1 TTTATGTTCATTTA-TGT--TCGTTTACGTTCATTTATGTTCGTTTACGTT
1105822 TGTTTGTGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
50 13 0.29
51 3 0.07
53 29 0.64
ACGTcount: A:0.14, C:0.14, G:0.16, T:0.56
Consensus pattern (50 bp):
TTTATGTTCATTTATGTTCGTTTACGTTCATTTATGTTCGTTTACGTTCA
Found at i:1105842 original size:20 final size:20
Alignment explanation
Indices: 1105785--1105878 Score: 98
Period size: 20 Copynumber: 4.5 Consensus size: 20
1105775 TGTTCATTTA
* * **
1105785 TTGTGCTCGTTTATGTTCAT
1 TTGTGTTCGTTTACGTTTGT
1105805 TTGTGTTCGTTTACGTTTGT
1 TTGTGTTCGTTTACGTTTGT
1105825 TTGTGTTCGTTTACGTTTGTTT
1 TTGTGTTCGTTTACGTTTG--T
* *
1105847 ATTGTGTTTGTTTATGTTTGT
1 -TTGTGTTCGTTTACGTTTGT
*
1105868 TTATGTTCGTT
1 TTGTGTTCGTT
1105879 CATTTGTGTT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
20 44 0.70
21 1 0.02
22 1 0.02
23 17 0.27
ACGTcount: A:0.07, C:0.09, G:0.22, T:0.62
Consensus pattern (20 bp):
TTGTGTTCGTTTACGTTTGT
Found at i:1105848 original size:73 final size:70
Alignment explanation
Indices: 1105700--1105841 Score: 203
Period size: 73 Copynumber: 2.0 Consensus size: 70
1105690 AAGAAAAAAA
*
1105700 ATTTATTTTCATTTATTTTCGTTTACGTTCATTTATGTTCGTTTACGTTCATTTATGTTCGTTTA
1 ATTTATGTTCATTTATTTTCGTTTACGTTCATTTATGTTCGTTTACGTTCATTTATGTTCGTTTA
1105765 CGTTC
66 CGTTC
* * ** *
1105770 ATTTATGTTCATTTATTGTGCTCGTTTATGTTCATTTGTGTTCGTTTACGTTTGTTTGTGTTCGT
1 ATTTATGTTCATTTATT-T--TCGTTTACGTTCATTTATGTTCGTTTACGTTCATTTATGTTCGT
1105835 TTACGTT
63 TTACGTT
1105842 TGTTTATTGT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
70 16 0.25
71 1 0.02
73 46 0.73
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.58
Consensus pattern (70 bp):
ATTTATGTTCATTTATTTTCGTTTACGTTCATTTATGTTCGTTTACGTTCATTTATGTTCGTTTA
CGTTC
Found at i:1105870 original size:73 final size:71
Alignment explanation
Indices: 1105711--1105894 Score: 174
Period size: 73 Copynumber: 2.5 Consensus size: 71
1105701 TTTATTTTCA
* *
1105711 TTTAT-TTTCGTTTACGTTCATTTATGTTCGTTTACGTTCATTTATGTTCGTTTACGTTCATTTA
1 TTTATGTTT-GTTTATGTTCATTTGTGTTCGTTTACGTTCATTTATGTTCGTTTACGTTCATTTA
1105775 TGTTCATT
65 TGTT-ATT
* * * ** * **
1105783 TATTGTGCTCGTTTATGTTCATTTGTGTTCGTTTACGTTTGTTTGTGTTCGTTTACGTTTGTTTA
1 T-TTATGTTTGTTTATGTTCATTTGTGTTCGTTTACGTTCATTTATGTTCGTTTACGTTCATTTA
1105848 TTGTGT-TT
65 -TGT-TATT
1105856 GTTTATGTTTGTTTATGTTCGTTCATTTGTGTTCGTTTA
1 -TTTATGTTTGTTTA---T-GTTCATTTGTGTTCGTTTA
1105895 TTATTTAAAT
Statistics
Matches: 90, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
72 1 0.01
73 63 0.70
74 5 0.06
75 1 0.01
76 1 0.01
77 19 0.21
ACGTcount: A:0.11, C:0.11, G:0.18, T:0.60
Consensus pattern (71 bp):
TTTATGTTTGTTTATGTTCATTTGTGTTCGTTTACGTTCATTTATGTTCGTTTACGTTCATTTAT
GTTATT
Found at i:1113945 original size:22 final size:22
Alignment explanation
Indices: 1113920--1113968 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1113910 GTCTGGATTG
1113920 AGTCGTCTTCGATGGAAGAGGC
1 AGTCGTCTTCGATGGAAGAGGC
1113942 AGTCGTCTTCGATGGAAGAGGC
1 AGTCGTCTTCGATGGAAGAGGC
1113964 AGTCG
1 AGTCG
1113969 CCTCCCCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.22
Consensus pattern (22 bp):
AGTCGTCTTCGATGGAAGAGGC
Found at i:1115491 original size:2 final size:2
Alignment explanation
Indices: 1115486--1115513 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1115476 CTATAAAAAA
1115486 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
1115514 TAGCATTTTT
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:1120584 original size:15 final size:15
Alignment explanation
Indices: 1120564--1120593 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1120554 CAAATTATAT
1120564 CTCTAAATTAGGAAA
1 CTCTAAATTAGGAAA
*
1120579 CTCTAAGTTAGGAAA
1 CTCTAAATTAGGAAA
1120594 GATACTAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (15 bp):
CTCTAAATTAGGAAA
Found at i:1132525 original size:39 final size:39
Alignment explanation
Indices: 1132462--1132541 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 39
1132452 TAGGAGCTTG
* * *
1132462 AGGAGTATTAGGTTCTGATAGGGGAGAGGACGGAGTAGA
1 AGGAGTATTAGGCTCTGATAGGGGAGAAGACGGAATAGA
* *
1132501 AGGAGTATTAGGCTCTTGCT-GGGGAGAAGATGGAATAGA
1 AGGAGTATTAGGCTC-TGATAGGGGAGAAGACGGAATAGA
1132540 AG
1 AG
1132542 CAAGCTGTGC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 32 0.91
40 3 0.09
ACGTcount: A:0.31, C:0.06, G:0.41, T:0.21
Consensus pattern (39 bp):
AGGAGTATTAGGCTCTGATAGGGGAGAAGACGGAATAGA
Found at i:1138087 original size:6 final size:6
Alignment explanation
Indices: 1138076--1138110 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1138066 CTGTAGAACA
*
1138076 TATAGG TATAGG TATAGG TATAGG TATCGG TATAG
1 TATAGG TATAGG TATAGG TATAGG TATAGG TATAG
1138111 ATGTAGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.34
Consensus pattern (6 bp):
TATAGG
Found at i:1145592 original size:102 final size:101
Alignment explanation
Indices: 1145486--1145668 Score: 251
Period size: 102 Copynumber: 1.8 Consensus size: 101
1145476 GATACTAAAA
* ** * * ** *
1145486 GTGTAAGTATGTGTTAAGTGTTACATTTTTTTATTTTA-TTACTTACATCGGTGTAAGTATGTGT
1 GTGT-AGTATGTATTAAGTACTACACTTATTTATTTTATTTACTTACATCAATGTAAGTATGTAT
1145550 TAAGTGTTACACTTTTTTTATTTTATTCACTTACACTC
65 TAAGTGTTACA-TTTTTTTATTTTATTCACTTACACTC
* *
1145588 GTGTAGTATGTATTAAGTACTATACTTATTTATTTTATTTACTTACATCAATGTACGTATGTATT
1 GTGTAGTATGTATTAAGTACTACACTTATTTATTTTATTTACTTACATCAATGTAAGTATGTATT
1145653 AAGTGTTACATTTTTT
66 AAGTGTTACATTTTTT
1145669 ATAATATAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
101 33 0.47
102 37 0.53
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.51
Consensus pattern (101 bp):
GTGTAGTATGTATTAAGTACTACACTTATTTATTTTATTTACTTACATCAATGTAAGTATGTATT
AAGTGTTACATTTTTTTATTTTATTCACTTACACTC
Found at i:1145596 original size:51 final size:50
Alignment explanation
Indices: 1145485--1145668 Score: 228
Period size: 51 Copynumber: 3.6 Consensus size: 50
1145475 AGATACTAAA
*
1145485 AGTGTAAGTATGTGTTAAGTGTTACATTTTTTTATTTTATTACTTACATC
1 AGTGTAAGTATGTATTAAGTGTTACATTTTTTTATTTTATTACTTACATC
* *
1145535 GGTGTAAGTATGTGTTAAGTGTTACACTTTTTTTATTTTATTCACTTACACTC
1 AGTGTAAGTATGTATTAAGTGTTACA-TTTTTTTATTTTATT-ACTTACA-TC
** * * *
1145588 -GTGT-AGTATGTATTAAGTACTATACTTATTTATTTTATTTACTTACATC
1 AGTGTAAGTATGTATTAAGTGTTACATTTTTTTATTTTA-TTACTTACATC
* *
1145637 AATGTACGTATGTATTAAGTGTTACATTTTTT
1 AGTGTAAGTATGTATTAAGTGTTACATTTTTT
1145669 ATAATATAAA
Statistics
Matches: 114, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
49 2 0.02
50 46 0.40
51 53 0.46
52 11 0.10
53 2 0.02
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.51
Consensus pattern (50 bp):
AGTGTAAGTATGTATTAAGTGTTACATTTTTTTATTTTATTACTTACATC
Found at i:1147218 original size:9 final size:10
Alignment explanation
Indices: 1147198--1147252 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
1147188 TGTTATATTA
1147198 AGTATAATAT
1 AGTATAATAT
1147208 AGTATAA-AT
1 AGTATAATAT
*
1147217 AGTATAATAA
1 AGTATAATAT
*
1147227 AGGATATATAT
1 AGTATA-ATAT
1147238 A-TATATATAT
1 AGTATA-ATAT
1147248 A-TATA
1 AGTATA
1147253 TATTAATTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 9 0.23
10 26 0.67
11 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (10 bp):
AGTATAATAT
Found at i:1147237 original size:2 final size:2
Alignment explanation
Indices: 1147230--1147255 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1147220 ATAATAAAGG
1147230 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
1147256 TAATTGTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1151336 original size:130 final size:129
Alignment explanation
Indices: 1151161--1151407 Score: 370
Period size: 130 Copynumber: 1.9 Consensus size: 129
1151151 ATATTTGTAA
*
1151161 TTACATATATAATATTTTTGTTTAAATATAGAAGTAATTTTATTCGAGTTATTATATACTTGTGT
1 TTACATATATAATATTTTTGTTTAAATATAGAAGTAATTTTATTCGAGTTACTATATACTTGTGT
* * *
1151226 AAGCATTGGTGTTGCTAAGTAGCATCGGTACACTAAAAAGTGTGCAACCAATTGATTAATATTG
66 AAGCATTGGTGTTACTAAGCAGCATAGGTACACTAAAAAGTGTGCAACCAATTGATTAATATTG
* * * *
1151290 TTACATATATAATATATTTTTTTTAAATCTAGATG-AAGTTTTATTCGAGTTGCTATATACTTGT
1 TTACATATATAATAT-TTTTGTTTAAATATAGAAGTAA-TTTTATTCGAGTTACTATATACTTGT
* * *
1151354 GTAAGCATTGGTGTTACTGAGCATCATAGGTACACTGAAAAGTGTGCAACCAAT
64 GTAAGCATTGGTGTTACTAAGCAGCATAGGTACACTAAAAAGTGTGCAACCAAT
1151408 GATAATCAAT
Statistics
Matches: 105, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
129 17 0.16
130 88 0.84
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.40
Consensus pattern (129 bp):
TTACATATATAATATTTTTGTTTAAATATAGAAGTAATTTTATTCGAGTTACTATATACTTGTGT
AAGCATTGGTGTTACTAAGCAGCATAGGTACACTAAAAAGTGTGCAACCAATTGATTAATATTG
Found at i:1152402 original size:31 final size:31
Alignment explanation
Indices: 1152367--1152434 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1152357 TCAAAAAATA
*
1152367 TAAGATATGATCACTTTCATTTTTACTTAAT
1 TAAGATAAGATCACTTTCATTTTTACTTAAT
* ** *
1152398 TAAGATAAGGTCACTTTTGTTTTTATTTAAT
1 TAAGATAAGATCACTTTCATTTTTACTTAAT
1152429 TAAGAT
1 TAAGAT
1152435 GTAGTCATCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.49
Consensus pattern (31 bp):
TAAGATAAGATCACTTTCATTTTTACTTAAT
Found at i:1152601 original size:21 final size:20
Alignment explanation
Indices: 1152559--1152613 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
1152549 TTAAAATCAA
*
1152559 TTTTAACATAAAAT-ATATAT
1 TTTTAA-ATAAAATAAAATAT
1152579 TTTTAAATGAAAATAAAATAT
1 TTTTAAAT-AAAATAAAATAT
*
1152600 TTTAAAATAAAATA
1 TTTTAAATAAAATA
1152614 TTTTAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 17 0.55
21 12 0.39
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
TTTTAAATAAAATAAAATAT
Found at i:1152608 original size:15 final size:15
Alignment explanation
Indices: 1152588--1152627 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
1152578 TTTTTAAATG
1152588 AAAATAAAATATTTT
1 AAAATAAAATATTTT
1152603 AAAATAAAATATTTT
1 AAAATAAAATATTTT
*
1152618 AAAATTAAAT
1 AAAATAAAAT
1152628 TAATAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATAAAATATTTT
Found at i:1152626 original size:21 final size:20
Alignment explanation
Indices: 1152558--1152613 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
1152548 TTTAAAATCA
* *
1152558 ATTTTAACATAAAAT-ATAT
1 ATTTTAAAATAAAATAAAAT
*
1152577 ATTTTTAAATGAAAATAAAAT
1 ATTTTAAAAT-AAAATAAAAT
1152598 ATTTTAAAATAAAATA
1 ATTTTAAAATAAAATA
1152614 TTTTAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 8 0.26
20 11 0.35
21 12 0.39
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
ATTTTAAAATAAAATAAAAT
Found at i:1152675 original size:21 final size:23
Alignment explanation
Indices: 1152622--1152680 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 23
1152612 TATTTTAAAA
*
1152622 TTAAA-TTAATAAAAATATATAT
1 TTAAAGTTAATATAAATATATAT
1152644 TTAATAAGTTAATATAAA-A-ATAT
1 TT-A-AAGTTAATATAAATATATAT
1152667 TTAAAGTTAATATA
1 TTAAAGTTAATATA
1152681 TATAAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 11 0.33
22 3 0.09
23 7 0.21
24 3 0.09
25 9 0.27
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (23 bp):
TTAAAGTTAATATAAATATATAT
Found at i:1152731 original size:21 final size:21
Alignment explanation
Indices: 1152707--1152755 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1152697 TTTAAGCATT
1152707 TATACACTAAAATACAAAATA
1 TATACACTAAAATACAAAATA
* *
1152728 TATACACTAAGATGCAAAATA
1 TATACACTAAAATACAAAATA
1152749 TATACAC
1 TATACAC
1152756 CATGTTATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.55, C:0.16, G:0.04, T:0.24
Consensus pattern (21 bp):
TATACACTAAAATACAAAATA
Found at i:1152871 original size:14 final size:14
Alignment explanation
Indices: 1152847--1152884 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1152837 TTTTGCCCCA
*
1152847 ATTTGCTTTCCTTT
1 ATTTTCTTTCCTTT
*
1152861 TTTTTCTTTCCTTT
1 ATTTTCTTTCCTTT
1152875 ATTTTCTTTC
1 ATTTTCTTTC
1152885 AACCAAAGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.71
Consensus pattern (14 bp):
ATTTTCTTTCCTTT
Found at i:1154014 original size:31 final size:31
Alignment explanation
Indices: 1153979--1154042 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
1153969 TAAATACGAC
*
1153979 CACTTTCGTGTTTATTTAATTAAGATATGAT
1 CACTTTCATGTTTATTTAATTAAGATATGAT
* *
1154010 CACTTTCATTTTTATTTAATTAAGATGTGAT
1 CACTTTCATGTTTATTTAATTAAGATATGAT
1154041 CA
1 CA
1154043 TCATTGGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (31 bp):
CACTTTCATGTTTATTTAATTAAGATATGAT
Found at i:1154201 original size:30 final size:27
Alignment explanation
Indices: 1154174--1154232 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
1154164 AACATAAATT
1154174 ATATATTTTAAATAAAAATAAAAATAAA
1 ATAT-TTTTAAATAAAAATAAAAATAAA
* ** *
1154202 ATATTTTTAAATTAAGTTAATAATAAA
1 ATATTTTTAAATAAAAATAAAAATAAA
1154229 ATAT
1 ATAT
1154233 ATTAATAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
ATATTTTTAAATAAAAATAAAAATAAA
Found at i:1154241 original size:24 final size:27
Alignment explanation
Indices: 1154196--1154252 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 27
1154186 TAAAAATAAA
*
1154196 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATTATTAAATTAAGTTAAT
1154223 AATAAAATA-TATT-AA-TAAGTTAAT
1 AATAAAATATTATTAAATTAAGTTAAT
1154247 -ATAAAA
1 AATAAAA
1154253 ATTTTGAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 6 0.21
24 9 0.31
25 2 0.07
26 3 0.10
27 9 0.31
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.39
Consensus pattern (27 bp):
AATAAAATATTATTAAATTAAGTTAAT
Found at i:1154272 original size:24 final size:25
Alignment explanation
Indices: 1154245--1154298 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
1154235 TAATAAGTTA
*
1154245 ATATAAAAATTTTGAAGTTAA-TAT
1 ATATAAAAATTATGAAGTTAAGTAT
* *
1154269 ATATAAATATTATGAATTTAAGTAT
1 ATATAAAAATTATGAAGTTAAGTAT
*
1154294 TTATA
1 ATATA
1154299 CATTAAGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (25 bp):
ATATAAAAATTATGAAGTTAAGTAT
Found at i:1158469 original size:25 final size:25
Alignment explanation
Indices: 1158417--1158500 Score: 95
Period size: 27 Copynumber: 3.4 Consensus size: 25
1158407 TTTAAATAAA
*
1158417 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATATTT-AA-TAAGTTAAT
1158444 AATAAAATATATTTAATAAGTTAAT
1 AATAAAATATATTTAATAAGTTAAT
1158469 -ATAAAA-ATATTT--TAAGTTAAT
1 AATAAAATATATTTAATAAGTTAAT
*
1158490 ATATATAATAT
1 A-ATAAAATAT
1158501 TATGAATATA
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
21 9 0.17
23 11 0.21
24 8 0.15
25 9 0.17
26 2 0.04
27 13 0.25
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
AATAAAATATATTTAATAAGTTAAT
Found at i:1159936 original size:12 final size:12
Alignment explanation
Indices: 1159911--1160002 Score: 71
Period size: 12 Copynumber: 7.8 Consensus size: 12
1159901 ACGGAGATAT
* *
1159911 CAGAAATCAAAA
1 CAGAATTCAGAA
1159923 CAGAATTCAGAA
1 CAGAATTCAGAA
*
1159935 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
1159947 CAGAATCCAGAT
1 CAGAATTCAGAA
*
1159959 CAGAAATCAGAA
1 CAGAATTCAGAA
* **
1159971 CAAAATTCAGGT
1 CAGAATTCAGAA
*
1159983 CAGTA-TCAGAA
1 CAGAATTCAGAA
1159994 CAGAATTCA
1 CAGAATTCA
1160003 AGTCGGAAAT
Statistics
Matches: 59, Mismatches: 18, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
11 10 0.17
12 47 0.80
13 2 0.03
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1159938 original size:24 final size:24
Alignment explanation
Indices: 1159909--1160016 Score: 112
Period size: 24 Copynumber: 4.5 Consensus size: 24
1159899 AAACGGAGAT
*
1159909 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
1159933 AACAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
1159957 ATCAGAAATCAGAACAAAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
1159981 GTCAG-TATCAGAACAGAATTCA-
1 ATCAGAAATCAGAACAGAATTCAG
*
1160003 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
1160017 TAAAATATTT
Statistics
Matches: 67, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
23 18 0.27
24 49 0.73
ACGTcount: A:0.49, C:0.18, G:0.16, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:1160012 original size:47 final size:48
Alignment explanation
Indices: 1159909--1160016 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 48
1159899 AAACGGAGAT
* * * *
1159909 ATCAGAAATCAAAACAGAATTCAGAACAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAAAATTCAGAACAGATATCAGAACAGAATCAAG
**
1159957 ATCAGAAATCAGAACAAAATTCAGGTCAG-TATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAAAATTCAGAACAGATATCAGAACAGAA-TCAAG
*
1160005 -TCGGAAATCAGA
1 ATCAGAAATCAGA
1160017 TAAAATATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
47 23 0.44
48 29 0.56
ACGTcount: A:0.49, C:0.18, G:0.16, T:0.18
Consensus pattern (48 bp):
ATCAGAAATCAGAACAAAATTCAGAACAGATATCAGAACAGAATCAAG
Found at i:1161142 original size:17 final size:18
Alignment explanation
Indices: 1161109--1161142 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1161099 TCAATTTTGT
*
1161109 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
1161127 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
1161143 GACCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:1162349 original size:24 final size:24
Alignment explanation
Indices: 1162322--1162393 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
1162312 AACAATAATA
1162322 AAATATAGATAAATAAAAATAAAT
1 AAATATAGATAAATAAAAATAAAT
* *
1162346 AAATTTAG-TAAAAAGACAAATAAA-
1 AAATATAGATAAATA-A-AAATAAAT
*
1162370 AAATA-AAATAAAT--AAATAAAT
1 AAATATAGATAAATAAAAATAAAT
1162391 AAA
1 AAA
1162394 GAAAAATAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
20 7 0.18
21 3 0.08
23 6 0.15
24 16 0.41
25 7 0.18
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.22
Consensus pattern (24 bp):
AAATATAGATAAATAAAAATAAAT
Found at i:1166112 original size:25 final size:25
Alignment explanation
Indices: 1166084--1166132 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1166074 GTATAAATAA
*
1166084 TTAAATTC-ATAATATTTTTTATATG
1 TTAAATTCAAAAATA-TTTTTATATG
*
1166109 TTAAATTTAAAAATATTTTTATAT
1 TTAAATTCAAAAATATTTTTATAT
1166133 TAACTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
TTAAATTCAAAAATATTTTTATATG
Found at i:1170904 original size:40 final size:40
Alignment explanation
Indices: 1170853--1170928 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
1170843 AAATATGAAA
1170853 TATTGAGTTCATTATTGATTTTTATTTATAATGTTGGACT
1 TATTGAGTTCATTATTGATTTTTATTTATAATGTTGGACT
1170893 TATTGAGTTCATTATTGATTTTTATTTATAATGTTG
1 TATTGAGTTCATTATTGATTTTTATTTATAATGTTG
1170929 TTGGCATTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.25, C:0.04, G:0.14, T:0.57
Consensus pattern (40 bp):
TATTGAGTTCATTATTGATTTTTATTTATAATGTTGGACT
Found at i:1171543 original size:2 final size:2
Alignment explanation
Indices: 1171536--1171573 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1171526 GTTTTGCTTA
1171536 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1171574 GTATGTATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1171578 original size:4 final size:4
Alignment explanation
Indices: 1171571--1171668 Score: 196
Period size: 4 Copynumber: 24.5 Consensus size: 4
1171561 TATATATATA
1171571 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1171619 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1171667 TA
1 TA
1171669 ATCATATAAG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 94 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:1174242 original size:2 final size:2
Alignment explanation
Indices: 1174235--1174274 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1174225 CATTAAGTCA
1174235 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1174275 TCATTCCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1178807 original size:19 final size:20
Alignment explanation
Indices: 1178762--1178811 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1178752 AAAAAATATA
* *
1178762 TTAAATTACACAATTTATTT
1 TTAAATTATACAATATATTT
1178782 TTGAAATTATA-AATATATTT
1 TT-AAATTATACAATATATTT
1178802 TTAAATTATA
1 TTAAATTATA
1178812 TTTAAACTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 8 0.30
20 12 0.44
21 7 0.26
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (20 bp):
TTAAATTATACAATATATTT
Found at i:1180080 original size:22 final size:21
Alignment explanation
Indices: 1180034--1180080 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
1180024 GTTTATAATT
**
1180034 TTTAGGTTTTAAGATTTAGGG
1 TTTAGGTTTTAAGATTTAGAA
1180055 TTTAGGGTTTTAA-ATTTTAGAA
1 TTTA-GGTTTTAAGA-TTTAGAA
1180077 TTTA
1 TTTA
1180081 AAATTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (21 bp):
TTTAGGTTTTAAGATTTAGAA
Found at i:1182764 original size:20 final size:20
Alignment explanation
Indices: 1182739--1182917 Score: 125
Period size: 20 Copynumber: 8.8 Consensus size: 20
1182729 ATGCGAAACA
*
1182739 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* * *
1182759 AAAATCGCAATGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
1182779 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
1182799 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
1182820 AAGAATCGCAATGCGATTCAA-
1 AA-AATCGCAACGCGATT-AAG
* *
1182841 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTAAG
*
1182861 AAAATCGCAACGCGATTCCAG
1 AAAATCGCAACGCGATT-AAG
* * *
1182882 -GAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTAAG
1182901 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
1182918 CCAAGAATCG
Statistics
Matches: 125, Mismatches: 23, Indels: 22
0.74 0.14 0.13
Matches are distributed among these distances:
18 1 0.01
19 3 0.02
20 98 0.78
21 9 0.07
22 14 0.11
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:1182877 original size:40 final size:40
Alignment explanation
Indices: 1182823--1182930 Score: 180
Period size: 40 Copynumber: 2.7 Consensus size: 40
1182813 ATCTTCCAAG
* *
1182823 AATCGCAATGCGATTCAAAGAATCGCAACGCGATTGAGAA
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
* *
1182863 AATCGCAACGCGATTCCAGGAATCGCAATGCGATTGAGAA
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
1182903 AATCGCAACGCGATTCCAAGAATCGCAA
1 AATCGCAACGCGATTCCAAGAATCGCAA
1182931 AACGGCAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (40 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
Found at i:1182909 original size:60 final size:61
Alignment explanation
Indices: 1182797--1182917 Score: 192
Period size: 60 Copynumber: 2.0 Consensus size: 61
1182787 AACGGTCAAA
1182797 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
1 AGAAAATCGCAACGCGA-CTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
* *
1182859 AGAAAATCGCAACGCGA-TTCCAGGAATCGCAATGCGATTGAGAA-AATCGCAACGCGATT
1 AGAAAATCGCAACGCGACTTCCAAGAATCGCAATGCGATTCA-AAGAATCGCAACGCGATT
1182918 CCAAGAATCG
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
60 37 0.66
61 2 0.04
62 17 0.30
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.17
Consensus pattern (61 bp):
AGAAAATCGCAACGCGACTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
Found at i:1182926 original size:20 final size:20
Alignment explanation
Indices: 1182801--1182930 Score: 138
Period size: 20 Copynumber: 6.4 Consensus size: 20
1182791 GTCAAAAGAA
1182801 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAG
* *
1182823 AATCGCAATGCGATTCAAAG
1 AATCGCAACGCGATTCCAAG
* *
1182843 AATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
*
1182863 AATCGCAACGCGATTCCAGG
1 AATCGCAACGCGATTCCAAG
* * *
1182883 AATCGCAATGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
1182903 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
1182923 AATCGCAA
1 AATCGCAA
1182931 AACGGCAAAA
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
19 2 0.02
20 73 0.82
21 2 0.02
22 12 0.13
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGATTCCAAG
Found at i:1183052 original size:6 final size:6
Alignment explanation
Indices: 1183041--1183139 Score: 198
Period size: 6 Copynumber: 16.5 Consensus size: 6
1183031 GACACGTATT
1183041 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1183089 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1183137 ACC
1 ACC
1183140 CGAGACGAGA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 93 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1183899 original size:6 final size:6
Alignment explanation
Indices: 1183888--1183938 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
1183878 TCTCGTCTCG
1183888 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1183936 GGT
1 GGT
1183939 AATACGTGTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1184074 original size:20 final size:20
Alignment explanation
Indices: 1184049--1184325 Score: 298
Period size: 20 Copynumber: 13.8 Consensus size: 20
1184039 TTTTGCCGTT
1184049 TTGCGATTCTTGGAATCGCA
1 TTGCGATTCTTGGAATCGCA
** *
1184069 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCA
*
1184089 TTGCGATTCTTGGAATCGCG
1 TTGCGATTCTTGGAATCGCA
** *
1184109 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCA
* *
1184129 TTGCGATTATTGGAATCGCG
1 TTGCGATTCTTGGAATCGCA
* * *
1184149 TTGCGATTTTCTCG-ATCGCG
1 TTGCGATTCT-TGGAATCGCA
*
1184169 TTGCGATTCTTCGAAGATCGCA
1 TTGCGATTCTT-GGA-ATCGCA
1184191 TTGCGATTCTTGGAATCGCA
1 TTGCGATTCTTGGAATCGCA
*
1184211 TTGCGATTCTTTGG-CTCGCA
1 TTGCGATTC-TTGGAATCGCA
1184231 TTGCGATTCTTTGG-ATCGCA
1 TTGCGATTC-TTGGAATCGCA
1184251 TTGCGATTCTTGGAATCGCA
1 TTGCGATTCTTGGAATCGCA
1184271 TTGCGATTCTTTGG-ATCGCA
1 TTGCGATTC-TTGGAATCGCA
1184291 TTGCGATTCTTTGG-ATCGCA
1 TTGCGATTC-TTGGAATCGCA
1184311 TTGCGATTCTTGGAA
1 TTGCGATTCTTGGAA
1184326 GATCGCGTTG
Statistics
Matches: 227, Mismatches: 18, Indels: 24
0.84 0.07 0.09
Matches are distributed among these distances:
19 13 0.06
20 182 0.80
21 16 0.07
22 16 0.07
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTTGGAATCGCA
Found at i:1184146 original size:60 final size:60
Alignment explanation
Indices: 1184049--1184340 Score: 340
Period size: 60 Copynumber: 4.8 Consensus size: 60
1184039 TTTTGCCGTT
* ** *
1184049 TTGCGATTCTTGGAATCGCATTGCGATT-TTCTCAATCGCGTTGCGATTC-TTGGAATCGCG
1 TTGCGATTCTTTGAATCGCATTGCGATTCTT-GGAATCGCGTTGCGATTCTTTGG-ATCGCA
* * * * *
1184109 TTGCGATT-TTCTCAATCGCGTTGCGATTATTGGAATCGCGTTGCGATT-TTCTCGATCGCG
1 TTGCGATTCTT-TGAATCGCATTGCGATTCTTGGAATCGCGTTGCGATTCTT-TGGATCGCA
* * *
1184169 TTGCGATTCTTCGAAGATCGCATTGCGATTCTTGGAATCGCATTGCGATTCTTTGGCTCGCA
1 TTGCGATTCTTTG-A-ATCGCATTGCGATTCTTGGAATCGCGTTGCGATTCTTTGGATCGCA
* *
1184231 TTGCGATTCTTTGGATCGCATTGCGATTCTTGGAATCGCATTGCGATTCTTTGGATCGCA
1 TTGCGATTCTTTGAATCGCATTGCGATTCTTGGAATCGCGTTGCGATTCTTTGGATCGCA
* *
1184291 TTGCGATTCTTTGGATCGCATTGCGATTCTTGGAAGATCGCGTTGTGATT
1 TTGCGATTCTTTGAATCGCATTGCGATTCTTGG-A-ATCGCGTTGCGATT
1184341 TTCTTTTAAC
Statistics
Matches: 203, Mismatches: 19, Indels: 18
0.85 0.08 0.08
Matches are distributed among these distances:
59 2 0.01
60 130 0.64
61 8 0.04
62 61 0.30
63 2 0.01
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (60 bp):
TTGCGATTCTTTGAATCGCATTGCGATTCTTGGAATCGCGTTGCGATTCTTTGGATCGCA
Found at i:1184360 original size:20 final size:20
Alignment explanation
Indices: 1184331--1184404 Score: 114
Period size: 20 Copynumber: 3.7 Consensus size: 20
1184321 TGGAAGATCG
*
1184331 CGTTGTGATTTTCTTTTAAC
1 CGTTGCGATTTTCTTTTAAC
*
1184351 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTAAC
1184371 CGTTGCGATTTTCTTTTCAA-
1 CGTTGCGATTTTCTTTT-AAC
1184391 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
1184405 AAATCGCGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
20 49 0.98
21 1 0.02
ACGTcount: A:0.12, C:0.19, G:0.18, T:0.51
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTAAC
Found at i:1184415 original size:40 final size:38
Alignment explanation
Indices: 1184327--1184422 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 38
1184317 TTCTTGGAAG
*
1184327 ATCGCGTTGTGATTTTCTTTTAACCGTTGCGATTTTCT
1 ATCGCGTTGCGATTTTCTTTTAACCGTTGCGATTTTCT
* *
1184365 TTTGACCGTTGCGATTTTCTTTTCAA-CGTTGCGATTTTCT
1 ATCG--CGTTGCGATTTTCTTTT-AACCGTTGCGATTTTCT
1184405 AAATCGCGTTGCGATTTT
1 --ATCGCGTTGCGATTTT
1184423 GATATCGCGT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
38 2 0.04
40 42 0.88
41 2 0.04
42 2 0.04
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.48
Consensus pattern (38 bp):
ATCGCGTTGCGATTTTCTTTTAACCGTTGCGATTTTCT
Found at i:1184431 original size:19 final size:19
Alignment explanation
Indices: 1184391--1184442 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
1184381 TTCTTTTCAA
*
1184391 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTT-GAAATCG
*
1184411 CGTTGCGATTTTGATATCG
1 CGTTGCGATTTTGAAATCG
1184430 CGTTGCGATTTTG
1 CGTTGCGATTTTG
1184443 TTGGTCATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTGAAATCG
Found at i:1186573 original size:31 final size:31
Alignment explanation
Indices: 1186524--1186643 Score: 186
Period size: 31 Copynumber: 3.9 Consensus size: 31
1186514 AGCATTTACT
**
1186524 AATTGGATTATATCATTTAATGACAAAAATG
1 AATTGGATTGCATCATTTAATGACAAAAATG
* *
1186555 AAATGTATTGCATCATTTAATGACAAAAATG
1 AATTGGATTGCATCATTTAATGACAAAAATG
*
1186586 AATTGGATTGCATCATTTAATGAAAAAAATG
1 AATTGGATTGCATCATTTAATGACAAAAATG
*
1186617 AATTGGATTACATCATTTAATGACAAA
1 AATTGGATTGCATCATTTAATGACAAA
1186644 TTAATTTGAT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 80 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.33
Consensus pattern (31 bp):
AATTGGATTGCATCATTTAATGACAAAAATG
Found at i:1186602 original size:62 final size:62
Alignment explanation
Indices: 1186524--1186664 Score: 187
Period size: 62 Copynumber: 2.3 Consensus size: 62
1186514 AGCATTTACT
* * * *
1186524 AATTGGATTATATCATTTAATGACAAAAATGAAATGTATTGCATCATTTAATGACAAAAATG
1 AATTGGATTACATCATTTAATGAAAAAAATGAAATGGATTACATCATTTAATGACAAAAATG
* * *
1186586 AATTGGATTGCATCATTTAATGAAAAAAATGAATTGGATTACATCATTTAATGAC--AAATT
1 AATTGGATTACATCATTTAATGAAAAAAATGAAATGGATTACATCATTTAATGACAAAAATG
* *
1186646 AATTTGATTATATCATTTA
1 AATTGGATTACATCATTTA
1186665 TTTATTTCGT
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
60 20 0.29
62 49 0.71
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (62 bp):
AATTGGATTACATCATTTAATGAAAAAAATGAAATGGATTACATCATTTAATGACAAAAATG
Found at i:1188123 original size:25 final size:27
Alignment explanation
Indices: 1188066--1188128 Score: 78
Period size: 25 Copynumber: 2.4 Consensus size: 27
1188056 ATGTTTTTTA
*
1188066 ATTTT-TAAAAAATTGAAAATGAAAACT
1 ATTTTCTAAAAAATT-AAAATGAAAAAT
*
1188093 AATTTCTAAAAAATT-AAAT-AAAAAT
1 ATTTTCTAAAAAATTAAAATGAAAAAT
1188118 ATTTTCTAAAA
1 ATTTTCTAAAA
1188129 TAAACAGAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 15 0.47
26 4 0.12
27 4 0.12
28 9 0.28
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (27 bp):
ATTTTCTAAAAAATTAAAATGAAAAAT
Found at i:1189510 original size:12 final size:12
Alignment explanation
Indices: 1189493--1189517 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1189483 GTTGTATTTT
1189493 ATAATTACAAGA
1 ATAATTACAAGA
1189505 ATAATTACAAGA
1 ATAATTACAAGA
1189517 A
1 A
1189518 AATAATATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
ATAATTACAAGA
Found at i:1191654 original size:15 final size:14
Alignment explanation
Indices: 1191625--1191651 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1191615 ACAAATAGAT
1191625 ATAAAAAAATAAAG
1 ATAAAAAAATAAAG
1191639 ATAAAAAAATAAA
1 ATAAAAAAATAAA
1191652 AGAAAATGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (14 bp):
ATAAAAAAATAAAG
Found at i:1194512 original size:123 final size:123
Alignment explanation
Indices: 1194333--1194720 Score: 564
Period size: 123 Copynumber: 3.2 Consensus size: 123
1194323 GAATGTTTTC
*
1194333 AACATTTCTAGAAGGAGTTCGTAATAAG-AGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATA
1 AACATTTCTAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATC
* *
1194397 TGAAGAACTTATTCAACCTTTTGCTCGACTCTATTGCAAAAGGAGATAGAGCAACATT
66 TGAAGAACTTATTCAACCTTTTGCTCGATTCTATTGCAGAAGGAGATAGAGCAACATT
* *
1194455 AACATTTCTAAAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATC
1 AACATTTCTAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATC
* * * * * * *
1194520 TAAAGAACTTATTCAACATTTTGCTTGATTCTATTACAGAAGGAGATAGAGTAGCATC
66 TGAAGAACTTATTCAACCTTTTGCTCGATTCTATTGCAGAAGGAGATAGAGCAACATT
* * *
1194578 AACATTTCCAGAAGGAGTTCATAATAAGAAGAACTCATCAT-AAGAGGAAGAAGAAGTTTATAAT
1 AACATTTCTAGAAGGAGTTCGTAATAAGAAGAACTCATC-TGAAGAGGAAGAAGAAGTTCATAAT
* * *
1194642 CTGAAGAACTTATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAAATAGAGCATCATT
65 CTGAAGAACTTATTCAACCTTTTGCTCGATTCTATTGCAGAAGGAGATAGAGCAACATT
** *
1194701 AGTATTTCTAGAAGAAGTTC
1 AACATTTCTAGAAGGAGTTC
1194721 AATATCTGAA
Statistics
Matches: 234, Mismatches: 30, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
122 27 0.12
123 206 0.88
124 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (123 bp):
AACATTTCTAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATC
TGAAGAACTTATTCAACCTTTTGCTCGATTCTATTGCAGAAGGAGATAGAGCAACATT
Found at i:1194728 original size:84 final size:82
Alignment explanation
Indices: 1194626--1194790 Score: 233
Period size: 82 Copynumber: 2.0 Consensus size: 82
1194616 CATAAGAGGA
* *
1194626 AGAAGAAGTTTATAATCTGAAGAACTTATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAAATA
1 AGAAGAAGTTAATAATCTGAAGAACTTATTCAACC-TTAGCTCGATTC-ATCGCAGAAGGAAATA
* *
1194691 GAGCATCATTAGTATTTCT
64 GAGCAGCATTAATATTTCT
* *
1194710 AGAAGAAGTTCAAT-ATCTGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCAGAAGGAGATAG
1 AGAAGAAGTT-AATAATCTGAAGAACTTATTCAACCTTAGCTCGATTCATCGCAGAAGGAAATAG
*
1194774 ATCAGCATTAATATTTC
65 AGCAGCATTAATATTTC
1194791 CATCTTAATC
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
82 30 0.41
83 11 0.15
84 30 0.41
85 2 0.03
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (82 bp):
AGAAGAAGTTAATAATCTGAAGAACTTATTCAACCTTAGCTCGATTCATCGCAGAAGGAAATAGA
GCAGCATTAATATTTCT
Found at i:1196417 original size:36 final size:37
Alignment explanation
Indices: 1196365--1196435 Score: 135
Period size: 36 Copynumber: 1.9 Consensus size: 37
1196355 TTTAATTACA
1196365 TAAATAATATTTATTTATTTTTTAATATTAAGAAAAT
1 TAAATAATATTTATTTATTTTTTAATATTAAGAAAAT
1196402 TAAAT-ATATTTATTTATTTTTTAATATTAAGAAA
1 TAAATAATATTTATTTATTTTTTAATATTAAGAAA
1196436 GGGGTTGTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 29 0.85
37 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (37 bp):
TAAATAATATTTATTTATTTTTTAATATTAAGAAAAT
Found at i:1202009 original size:63 final size:63
Alignment explanation
Indices: 1201910--1202032 Score: 201
Period size: 63 Copynumber: 2.0 Consensus size: 63
1201900 AAGTTGGACA
* * * *
1201910 GTGCTCGACTCGTGCTTATTAAAAAATTTTGCTGCTCGACTTGACTCGTTGCTCGTTAAAATT
1 GTGCTCGACTCGTGATTATTAAAAAAATTTGCTGCTCAACTTGACTCATTGCTCGTTAAAATT
*
1201973 GTGCTCGACTCGTGATTGTTAAAAAAATTTGCTGCTCAACTTGACTCATTGCTCGTTAAA
1 GTGCTCGACTCGTGATTATTAAAAAAATTTGCTGCTCAACTTGACTCATTGCTCGTTAAA
1202033 CTCGACTCGT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (63 bp):
GTGCTCGACTCGTGATTATTAAAAAAATTTGCTGCTCAACTTGACTCATTGCTCGTTAAAATT
Found at i:1206110 original size:94 final size:90
Alignment explanation
Indices: 1205972--1206160 Score: 220
Period size: 88 Copynumber: 2.1 Consensus size: 90
1205962 CAAGAAGGAC
*
1205972 AAAATCTTTTTTTAAGACAAGAACAATCTCAAGTGAGATAAAATTGTTGAAAAATAAATGATTTT
1 AAAATCTTTTTTTAAGACAAGAACAATCTCAAGCGAGATAAAATTGTT-----A-AAATGATTTT
*
1206037 AAGCTTCGAGGGAAGCTATCTCGAGTGAGAT
60 AAGCTCCGAGGGAAGCTATCTCGAGTGAGAT
* ** ** *
1206068 GAAATCTTTTTTTAAGA-AA-AGTAATCTTGAGCGAGATAAAATTGTTAAAATGATTTTGAGCTC
1 AAAATCTTTTTTTAAGACAAGAACAATCTCAAGCGAGATAAAATTGTTAAAATGATTTTAAGCTC
* *
1206131 CTAGGGAAGTTATCTCGAGTGAGAT
66 CGAGGGAAGCTATCTCGAGTGAGAT
1206156 AAAAT
1 AAAAT
1206161 TGTTGAAATG
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
88 41 0.50
89 1 0.01
94 22 0.27
95 2 0.02
96 16 0.20
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.32
Consensus pattern (90 bp):
AAAATCTTTTTTTAAGACAAGAACAATCTCAAGCGAGATAAAATTGTTAAAATGATTTTAAGCTC
CGAGGGAAGCTATCTCGAGTGAGAT
Found at i:1206176 original size:51 final size:51
Alignment explanation
Indices: 1206086--1206203 Score: 164
Period size: 51 Copynumber: 2.3 Consensus size: 51
1206076 TTTTTAAGAA
* * * *
1206086 AAGTAATCTTGAGCGAGATAAAATTGTTAAAATGATTTTGAGCTCCTAGGG
1 AAGTTATCTCGAGTGAGATAAAATTGTTAAAATGATTTTGAGCTCCGAGGG
* * *
1206137 AAGTTATCTCGAGTGAGATAAAATTGTTGAAATGTTTTTGAGCTTCGAGGG
1 AAGTTATCTCGAGTGAGATAAAATTGTTAAAATGATTTTGAGCTCCGAGGG
*
1206188 AAGATATCTCGAGTGA
1 AAGTTATCTCGAGTGA
1206204 CATGAAACCT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.32
Consensus pattern (51 bp):
AAGTTATCTCGAGTGAGATAAAATTGTTAAAATGATTTTGAGCTCCGAGGG
Found at i:1206258 original size:139 final size:139
Alignment explanation
Indices: 1206027--1206316 Score: 384
Period size: 139 Copynumber: 2.1 Consensus size: 139
1206017 GTTGAAAAAT
* * * * * * **
1206027 AAATGATTTTAAGCTTCGAGGGAAGCTATCTCGAGTGAGATGAAATCTTTTTTTAAGAAAAGTAA
1 AAATGTTTTTGAGCTTCGAGGGAAGATATCTCGAGTGACATGAAACCTTGTTTTAAGAAAAACAA
* * ** * *
1206092 TCTTGAGCGAGATAAAATTGTTAAAATGATTTTGAGCTCCTAGGGAAGTTATCTCGAGTGAGAT-
66 TCTCGAGCGAGATAAAATTGTTAAAATGATTTTGAGATCCTAGGGAAACTACCTCGAGCGAGATA
1206156 AAAATTGTTG
131 AAAATT-TTG
1206166 AAATGTTTTTGAGCTTCGAGGGAAGATATCTCGAGTGACATGAAACCTTGTTTTAAGAAAAACAA
1 AAATGTTTTTGAGCTTCGAGGGAAGATATCTCGAGTGACATGAAACCTTGTTTTAAGAAAAACAA
* * * ** *
1206231 TCTCGAGTGGGATAAAATTGTTGAAATGATTTTGAGATTTTAGGGAAACTACCTTGAGCGAGATA
66 TCTCGAGCGAGATAAAATTGTTAAAATGATTTTGAGATCCTAGGGAAACTACCTCGAGCGAGATA
1206296 AAAATTTTG
131 AAAATTTTG
1206305 AAATGTTTTTGA
1 AAATGTTTTTGA
1206317 AATGATTTTC
Statistics
Matches: 130, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
139 124 0.95
140 6 0.05
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (139 bp):
AAATGTTTTTGAGCTTCGAGGGAAGATATCTCGAGTGACATGAAACCTTGTTTTAAGAAAAACAA
TCTCGAGCGAGATAAAATTGTTAAAATGATTTTGAGATCCTAGGGAAACTACCTCGAGCGAGATA
AAAATTTTG
Found at i:1208189 original size:21 final size:21
Alignment explanation
Indices: 1208165--1208211 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
1208155 TTCTCTTCTC
1208165 TTTTTCTTTTATTTCT-TTTGG
1 TTTTTCTTTTATTT-TGTTTGG
* *
1208186 TTTTT-TTTTGTTTTGTTTTG
1 TTTTTCTTTTATTTTGTTTGG
1208206 TTTTTC
1 TTTTTC
1208212 ATTTCTTCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.05
20 16 0.73
21 5 0.23
ACGTcount: A:0.02, C:0.06, G:0.11, T:0.81
Consensus pattern (21 bp):
TTTTTCTTTTATTTTGTTTGG
Found at i:1208575 original size:182 final size:182
Alignment explanation
Indices: 1208250--1208578 Score: 430
Period size: 182 Copynumber: 1.8 Consensus size: 182
1208240 TACATCGGGG
* * *
1208250 AATTCATCACGTCATAATTAATGTCATGATTTAAATATAACCACTTCATGAAGCTCAGACTTACC
1 AATTCACCACGTCACAATTAATGTCACGATTTAAATATAACCACTTCATGAAGCTCAGACTTACC
*** **
1208315 TCAATAGCTGCTTGAATTTGTTTCCAAGTTATCAGCTTACTGCTTTTAGTGAAGTGACCCCGTTT
66 TCAATAGCTGCTTGAATTACCTTCCAAGTTATCAGCTTACTGCTTTTACAGAAGTGACCCCGTTT
*
1208380 TATTGCACTCACTTATTAACTCTTTCTTCTTGTTTTTTCTCACACATCGAAA
131 TATTACACTCACTTATTAACTCTTTCTTCTTGTTTTTTCTCACACATCGAAA
* * * * *
1208432 AATTCACCGCGTCACAATTAATGTCACGATTTGAATATAACCACTTCATGAATCTTAGACTTACT
1 AATTCACCACGTCACAATTAATGTCACGATTTAAATATAACCACTTCATGAAGCTCAGACTTACC
* * * * *
1208497 TCAATAGCTGTTTGAAATTACCTT-CAATTTATCAGCTTATTG-TTTTCAACAG-AGTGGCCTCG
66 TCAATAGCTGCTTG-AATTACCTTCCAAGTTATCAGCTTACTGCTTTT--ACAGAAGTGACCCCG
*
1208559 TTTTATTACGCTCACTTATT
128 TTTTATTACACTCACTTATT
1208579 GACAATTTTT
Statistics
Matches: 124, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
181 4 0.03
182 112 0.90
183 8 0.06
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.39
Consensus pattern (182 bp):
AATTCACCACGTCACAATTAATGTCACGATTTAAATATAACCACTTCATGAAGCTCAGACTTACC
TCAATAGCTGCTTGAATTACCTTCCAAGTTATCAGCTTACTGCTTTTACAGAAGTGACCCCGTTT
TATTACACTCACTTATTAACTCTTTCTTCTTGTTTTTTCTCACACATCGAAA
Found at i:1216125 original size:20 final size:20
Alignment explanation
Indices: 1216088--1216125 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1216078 CAAAATGGGT
*
1216088 ATCGATACCTCTATAGTAGC
1 ATCGATACCTCTACAGTAGC
1216108 ATCGATA-CTGCTACAGTA
1 ATCGATACCT-CTACAGTA
1216126 AAATCAAGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (20 bp):
ATCGATACCTCTACAGTAGC
Found at i:1218838 original size:20 final size:20
Alignment explanation
Indices: 1218799--1218856 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
1218789 AAACTGTTTT
**
1218799 TATGAATAGTATTG-TACTG
1 TATGAATAGTACCGATACTG
1218818 TATGAATAGTACCGATACTG
1 TATGAATAGTACCGATACTG
1218838 TATGAATAGTACCGATACT
1 TATGAATAGTACCGATACT
1218857 ATGTGAACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 12 0.33
20 24 0.67
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (20 bp):
TATGAATAGTACCGATACTG
Found at i:1218863 original size:20 final size:20
Alignment explanation
Indices: 1218799--1218863 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
1218789 AAACTGTTTT
** *
1218799 TATGAATAGTATTG-TACTG
1 TATGAATAGTACCGATACTA
*
1218818 TATGAATAGTACCGATACTG
1 TATGAATAGTACCGATACTA
1218838 TATGAATAGTACCGATACTA
1 TATGAATAGTACCGATACTA
*
1218858 TGTGAA
1 TATGAA
1218864 CAATAATGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 12 0.29
20 29 0.71
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (20 bp):
TATGAATAGTACCGATACTA
Found at i:1218935 original size:20 final size:20
Alignment explanation
Indices: 1218910--1218950 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
1218900 ATACAAAATG
1218910 AGTATCGATATCT-CTACAGT
1 AGTATCGATA-CTACTACAGT
1218930 AGTATCGATACTACTACAGT
1 AGTATCGATACTACTACAGT
1218950 A
1 A
1218951 AAATCAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (20 bp):
AGTATCGATACTACTACAGT
Found at i:1222675 original size:20 final size:21
Alignment explanation
Indices: 1222645--1222683 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1222635 ATTACAGGTA
1222645 CAAATATGACAAAACCGGTCC
1 CAAATATGACAAAACCGGTCC
*
1222666 CAAA-ATGACAAAATCGGT
1 CAAATATGACAAAACCGGT
1222684 AAAACGCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (21 bp):
CAAATATGACAAAACCGGTCC
Found at i:1223100 original size:182 final size:182
Alignment explanation
Indices: 1222619--1223814 Score: 1625
Period size: 182 Copynumber: 6.6 Consensus size: 182
1222609 TGAAAAATGG
* * * * * * * *
1222619 ATCGCTCCATAGCAATATTACAGGTACAAATATGACAAAACCGGTC-CCAAAATGACAAAATCGG
1 ATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGG
* *
1222683 TAAAACGCTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGAATT
66 -AAAAAGCTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATT
* * * * * *
1222748 T--AATAGAA-AAGTTATAGCACTTATAAAGTGTCGATACTTTA-AAAATATAT
130 TAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAA-ATAT
* *
1222798 ATCGATCCAGAACAATATAACAGGTAAAAATATGATAAAACTGGTCT-AAAAATGACAAAACCGG
1 ATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGG
* * * *
1222862 AAAAAGTTACCGGATATATTGAAAGTGTCGATAATTTAATATTAGTATAGACACTTTCTAAATTT
66 AAAAAGCTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTT
* *
1222927 AAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCAACACTTTATTAAAATAT
131 AAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATAT
* *
1222979 ATCGAT-CATTACCAATATAACAGGTAAAAATATGATAAAACATGTCTCAAAAATGACAAAACCG
1 ATCGATCCA-TAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCG
* * * *
1223043 GAAAAAGTTACCGAATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATT
65 GAAAAAGCTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATT
* * * * *
1223108 TAAAAGAGAAAAAGTTATTGCGCTTATAAAGTGTCGACACTTTATGAAAATGT
130 TAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATAT
* * *
1223161 ATCGATCCATAACAATATAACAGGTACAAATATGATAAAACAGGTCACAAAATTGACAAAACCAG
1 ATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACC-G
* * * * *
1223226 TAAAACGCTACCAGATATATTGAAAGTGTCGATAATTTAATATAAGTATCTAAACTTTCTGAATT
65 GAAAAAGCTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATT
* * ** *
1223291 TAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAAAAT
130 TAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATAT
* *
1223344 ATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACCGGTCTCAAAAATGAAAAAACCGG
1 ATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGG
* * *
1223409 AAAAAGTTGCCGGATATATTGAAAGTGTCGATAATTTAATATTAGTATCGACACTTTCTGAATTT
66 AAAAAGCTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTT
*
1223474 AAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATGT
131 AAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATAT
* *
1223526 ATCGATCCTTACCAATATAACAGGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCG
1 ATCGATCCATAACAATATAACA-GGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCG
* * * * *
1223591 GAAAAAGCTACTGGATATGTTAAAATTGTCGATAATTTAATATAAGTATCGACACTTTCTTAATT
65 GAAAAAGCTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATT
* * * *
1223656 TAAAAGAGAAGAAGTTATAGCACTTAAAAAGTGTTGACACTTTATGAAAATGT
130 TAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATAT
* * *
1223709 ATCGATCCATAACAATATAACAGGTAAAAATATTATAAAACCGGTCTC-AAAATGACAAAACTGG
1 ATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGG
* * * * *
1223773 TAAATAGATATCGGATATGTTGAAAGTGTCGATACTTTAATA
66 -AAAAAGCTACCGGATATATTGAAAGTGTCGATAATTTAATA
1223815 AGTACGCGTA
Statistics
Matches: 899, Mismatches: 107, Indels: 19
0.88 0.10 0.02
Matches are distributed among these distances:
178 59 0.07
179 54 0.06
180 8 0.01
181 87 0.10
182 362 0.40
183 329 0.37
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (182 bp):
ATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGG
AAAAAGCTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTT
AAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATAT
Found at i:1223221 original size:21 final size:20
Alignment explanation
Indices: 1223179--1223222 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1223169 ATAACAATAT
*
1223179 AACAGGTACAAATATGATAA
1 AACAGGTACAAATATGACAA
1223199 AACAGGTCACAAA-ATTGACAA
1 AACAGGT-ACAAATA-TGACAA
1223220 AAC
1 AAC
1223223 CAGTAAAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.55, C:0.16, G:0.14, T:0.16
Consensus pattern (20 bp):
AACAGGTACAAATATGACAA
Found at i:1223313 original size:365 final size:364
Alignment explanation
Indices: 1222619--1223814 Score: 1665
Period size: 365 Copynumber: 3.3 Consensus size: 364
1222609 TGAAAAATGG
* * * * * * *
1222619 ATCGCTCCATAGCAATATTACAGGTACAAATATGACAAAACCGGTC-CCAAAATGACAAAATCGG
1 ATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACCGGTCTCAAAAATGACAAAACCGG
* * *
1222683 TAAAACGCTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGAATT
66 TAAAAAGTTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATT
* * * * * *
1222748 T--AATAG-AAAAGTTATAGCACTTATAAAGTGTCGATACTTTA-AAAATATATATCGATCCAGA
131 TAAAAGAGAAAAAGTTATAGCGCTTATAAAGTGTCGACACTTTATGAAA-ATGTATCGATCCATA
* *
1222809 ACAATATAACAGGTAAAAATATGATAAAACTGGTCTA-AAAATGACAAAACCGGAAAAAGTTACC
195 ACAATATAACAGGTAAAAATATGATAAAACAGGTC-ACAAAATGACAAAACCGGAAAAAGCTACC
* *
1222873 GGATATATTGAAAGTGTCGATAATTTAATATTAGTATAGACACTTTCTAAATTTAAAAGAGAAGA
259 GGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTAAATTTAAAAGAGAAGA
* *
1222938 AGTTATAGCGCCTAAAAAGTGTCAACACTTTATTAAAATAT
324 AGTTATAGCGCCTAAAAAGTGTCGACACTTTATAAAAATAT
* **
1222979 ATCGAT-CATTACCAATATAACAGGTAAAAATATGATAAAACATGTCTCAAAAATGACAAAACCG
1 ATCGATCCA-TAACAATATAACAGGTAAAAATATGATAAAACCGGTCTCAAAAATGACAAAACCG
* * *
1223043 G-AAAAAGTTACCGAATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAAT
65 GTAAAAAGTTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAAT
*
1223107 TTAAAAGAGAAAAAGTTATTGCGCTTATAAAGTGTCGACACTTTATGAAAATGTATCGATCCATA
130 TTAAAAGAGAAAAAGTTATAGCGCTTATAAAGTGTCGACACTTTATGAAAATGTATCGATCCATA
* * *
1223172 ACAATATAACAGGTACAAATATGATAAAACAGGTCACAAAATTGACAAAACCAGTAAAACGCTAC
195 ACAATATAACAGGTAAAAATATGATAAAACAGGTCACAAAA-TGACAAAACC-GGAAAAAGCTAC
* * * *
1223237 CAGATATATTGAAAGTGTCGATAATTTAATATAAGTATCTAAACTTTCTGAATTTAAAAGAGAAG
258 CGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTAAATTTAAAAGAGAAG
* * * *
1223302 AAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAAAAT
323 AAGTTATAGCGCCTAAAAAGTGTCGACACTTTATAAAAATAT
*
1223344 ATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACCGGTCTCAAAAATGAAAAAACCGG
1 ATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACCGGTCTCAAAAATGACAAAACCGG
* *
1223409 -AAAAAGTTGCCGGATATATTGAAAGTGTCGATAATTTAATATTAGTATCGACACTTTCTGAATT
66 TAAAAAGTTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATT
* * * * *
1223473 TAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCTTAC
131 TAAAAGAGAAAAAGTTATAGCGCTTATAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAA
* *
1223538 CAATATAACAGGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGGAAAAAGCTACT
196 CAATATAACA-GGTAAAAATATGATAAAACAGGTCAC-AAAATGACAAAACCGGAAAAAGCTACC
* * * *
1223603 GGATATGTTAAAATTGTCGATAATTTAATATAAGTATCGACACTTTCTTAATTTAAAAGAGAAGA
259 GGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTAAATTTAAAAGAGAAGA
* * * * *
1223668 AGTTATAGCACTTAAAAAGTGTTGACACTTTATGAAAATGT
324 AGTTATAGCGCCTAAAAAGTGTCGACACTTTATAAAAATAT
* *
1223709 ATCGATCCATAACAATATAACAGGTAAAAATATTATAAAACCGGTCTC-AAAATGACAAAACTGG
1 ATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACCGGTCTCAAAAATGACAAAACCGG
* * * * *
1223773 TAAATAGATATCGGATATGTTGAAAGTGTCGATACTTTAATA
66 TAAAAAGTTACCGGATATATTGAAAGTGTCGATAATTTAATA
1223815 AGTACGCGTA
Statistics
Matches: 739, Mismatches: 84, Indels: 21
0.88 0.10 0.02
Matches are distributed among these distances:
359 2 0.00
360 95 0.13
361 16 0.02
362 5 0.01
363 82 0.11
364 27 0.04
365 472 0.64
366 36 0.05
367 4 0.01
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (364 bp):
ATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACCGGTCTCAAAAATGACAAAACCGG
TAAAAAGTTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATT
TAAAAGAGAAAAAGTTATAGCGCTTATAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAA
CAATATAACAGGTAAAAATATGATAAAACAGGTCACAAAATGACAAAACCGGAAAAAGCTACCGG
ATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTAAATTTAAAAGAGAAGAAG
TTATAGCGCCTAAAAAGTGTCGACACTTTATAAAAATAT
Found at i:1224226 original size:18 final size:19
Alignment explanation
Indices: 1224203--1224247 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1224193 TAGTTAATAT
1224203 TTATAGGTA-AAAATGATA
1 TTATAGGTAGAAAATGATA
1224221 TTATAGGTAGAAAATGATA
1 TTATAGGTAGAAAATGATA
*
1224240 TTTTAGGT
1 TTATAGGT
1224248 TGTATAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (19 bp):
TTATAGGTAGAAAATGATA
Found at i:1224533 original size:18 final size:18
Alignment explanation
Indices: 1224498--1224536 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1224488 TTGAAATGGT
1224498 AATTGGATTAAAACTTTA
1 AATTGGATTAAAACTTTA
*
1224516 AATT-GATTACAAATTTTA
1 AATTGGATTA-AAACTTTA
1224534 AAT
1 AAT
1224537 GTTGACAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (18 bp):
AATTGGATTAAAACTTTA
Found at i:1225807 original size:9 final size:9
Alignment explanation
Indices: 1225790--1225837 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
1225780 TATTGTCAAT
*
1225790 GAGGTAGAG
1 GAGGCAGAG
1225799 GAGGCAGAG
1 GAGGCAGAG
* *
1225808 GAGGTAGAT
1 GAGGCAGAG
1225817 GAGGCAGAG
1 GAGGCAGAG
*
1225826 GAGGCAGTG
1 GAGGCAGAG
1225835 GAG
1 GAG
1225838 AATGAATAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.54, T:0.08
Consensus pattern (9 bp):
GAGGCAGAG
Found at i:1225813 original size:18 final size:18
Alignment explanation
Indices: 1225790--1225829 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1225780 TATTGTCAAT
1225790 GAGGTAGAGGAGGCAGAG
1 GAGGTAGAGGAGGCAGAG
*
1225808 GAGGTAGATGAGGCAGAG
1 GAGGTAGAGGAGGCAGAG
1225826 GAGG
1 GAGG
1225830 CAGTGGAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.55, T:0.07
Consensus pattern (18 bp):
GAGGTAGAGGAGGCAGAG
Found at i:1226296 original size:22 final size:18
Alignment explanation
Indices: 1226247--1226285 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1226237 GAAAAAATTT
*
1226247 GAAGAAGAGAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1226265 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1226283 GAA
1 GAA
1226286 ATGAGGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.41, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:1227779 original size:19 final size:19
Alignment explanation
Indices: 1227753--1227801 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
1227743 AAATGCATGG
1227753 TTAA-TTTGTATAAGATTT
1 TTAATTTTGTATAAGATTT
*
1227771 TTAATTTTGTATACGATTT
1 TTAATTTTGTATAAGATTT
*
1227790 ATAATTTTGTAT
1 TTAATTTTGTAT
1227802 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TTAATTTTGTATAAGATTT
Found at i:1228490 original size:199 final size:199
Alignment explanation
Indices: 1228147--1229445 Score: 2161
Period size: 199 Copynumber: 6.5 Consensus size: 199
1228137 GTAAACTTAT
* * * *
1228147 GTGTCGATACATTTATAACAAGTGTCCATCCCAAAAATATCGAAAACCATAATTATAATGTCATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
* *
1228212 GGTAAATTAGCATTATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAATA
66 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTA
* *
1228277 TCGACACGAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAAACAAGTACCCTA
131 TCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAAACAAGTGCCCTA
1228342 AAAA
196 AAAA
* *
1228346 GTGTCGATACATTTGTAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
1228411 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTA
66 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTA
*
1228476 TCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCATAATGTATTTCAAAAACAAGTGCCCTA
131 TCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAAACAAGTGCCCTA
1228541 AAAA
196 AAAA
*
1228545 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATGTAATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
* * * * * *
1228610 GGTAAATTATTC-ATGTAAACAGTCTAAATATACCGGTTTTTGATAAAAACAGGTGTACAAAAAG
66 GGTAAATTA-GCAATATAACCGGTCTAAATATACCGGTTTTTGA-GAAAACAGGTGTAAAAAAAG
*
1228674 TATCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAAACAAGTACCC
129 TATCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAAACAAGTGCCC
1228739 TAAAAA
194 TAAAAA
1228745 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
* ** *
1228810 GGTAAATTAACAATATAACCGGTCTAAATATACCAATTTTTGAGAAAACAGGTGTACAAACAA-T
66 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTA-AAAAAAGT
*
1228874 ATCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCCCT
130 ATCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAAACAAGTGCCCT
1228939 AAAAA
195 AAAAA
1228944 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
* * *
1229009 GGTAAATTAGCAATATAACCGGTCTAAATATACCGATTTTTGAGAAAACAGGTGTACAAACAGTA
66 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTA
* * * *
1229074 TCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAGAACCAAGTGCACTA
131 TCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAAACAAGTGCCCTA
1229139 AAAA
196 AAAA
* *
1229143 GTGTCGATACATTTGTAACAAGTATCGATCCTAAAAACATCGAAAACCATAATTATAATGTAATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
* * *
1229208 GGTAAATTAGCAATATAACCGGTCTAAATATACTGGTTTTTGAGAAAACAGGTGTACAAATAGTA
66 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTA
* * * *
1229273 TCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAGAACCAAGTGCACTA
131 TCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAAACAAGTGCCCTA
1229338 AAAA
196 AAAA
* *
1229342 GTGTCGATACATTTGTAACAAGTGTCGATCCCAGAAATATCGAAAACCATAATTATAATGTAATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
* *
1229407 GGTAAATTAGAAATATAACCGGTCTAAATATACTGGTTT
66 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTT
1229446 AAATTGAAAA
Statistics
Matches: 1045, Mismatches: 50, Indels: 10
0.95 0.05 0.01
Matches are distributed among these distances:
198 3 0.00
199 851 0.81
200 191 0.18
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.27
Consensus pattern (199 bp):
GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTA
TCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAAACAAGTGCCCTA
AAAA
Found at i:1229458 original size:598 final size:597
Alignment explanation
Indices: 1228147--1229445 Score: 2181
Period size: 598 Copynumber: 2.2 Consensus size: 597
1228137 GTAAACTTAT
* * *
1228147 GTGTCGATACATTTATAACAAGTGTCCATCCCAAAAATATCGAAAACCATAATTATAATGTCATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAATATCGAAAACCATAATTATAATGTAATA
* *
1228212 GGTAAATTAGCATTATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAATA
66 GGTAAATTAGAAATATAACCGGTCTAAATATACCGGTTTTT-AGAAAACAGGTGTAAAAAAAATA
*
1228277 TCGACACGAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAAACAAGTACCCTA
130 TCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAAACAAGTACCCTA
*
1228342 AAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGT
195 AAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATGT
*
1228407 AATAGGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAA
260 AATAGGTAAATTAGCAATATAACCGGTCTAAATATACCGATTTTTGAGAAAACAGGTGTAAAAAA
* *
1228472 AGTATCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCATAATGTATTTCAAAAACAAGTGC
325 AGTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAAACAAGTGC
* *
1228537 CCTAAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATA
390 ACTAAAAAGTGTCGATACATTTGTAACAAGTATCGATCCCAAAAACATCGAAAAACATAATTATA
* *
1228602 ATGTAATAGGTAAATTATTCATGTAAACAGTCTAAATATACCGGTTTTTGATAAAAACAGGTGTA
455 ATGTAATAGGTAAATTATGCATATAAACAGTCTAAATATACCGGTTTTTGATAAAAACAGGTGTA
*
1228667 CAAAAAGTATCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAAACA
520 CAAAAAGTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAAACA
*
1228732 AGTACCCTAAAAA
585 AGTACACTAAAAA
*
1228745 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAATATCGAAAACCATAATTATAATGTAATA
** * *
1228810 GGTAAATTA-ACAATATAACCGGTCTAAATATACCAATTTTTGAGAAAACAGGTGTACAAACAAT
66 GGTAAATTAGA-AATATAACCGGTCTAAATATACCGGTTTTT-AGAAAACAGGTGTAAAAAAAAT
* *
1228874 ATCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCCCT
129 ATCGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAAACAAGTACCCT
*
1228939 AAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATG
194 AAAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATG
*
1229004 TAATAGGTAAATTAGCAATATAACCGGTCTAAATATACCGATTTTTGAGAAAACAGGTGTACAAA
259 TAATAGGTAAATTAGCAATATAACCGGTCTAAATATACCGATTTTTGAGAAAACAGGTGTAAAAA
* * *
1229069 CAGTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAGAACCAAGTG
324 AAGTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAAACAAGTG
* *
1229134 CACTAAAAAGTGTCGATACATTTGTAACAAGTATCGATCCTAAAAACATCGAAAACCATAATTAT
389 CACTAAAAAGTGTCGATACATTTGTAACAAGTATCGATCCCAAAAACATCGAAAAACATAATTAT
* * * *
1229199 AATGTAATAGGTAAATTA-GCAATATAACCGGTCTAAATATACTGGTTTTTGA-GAAAACAGGTG
454 AATGTAATAGGTAAATTATGC-ATATAAACAGTCTAAATATACCGGTTTTTGATAAAAACAGGTG
* * *
1229262 TACAAATAGTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAGAAC
518 TACAAAAAGTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAAA
*
1229327 CAAGTGCACTAAAAA
583 CAAGTACACTAAAAA
*
1229342 GTGTCGATACATTTGTAACAAGTGTCGATCCCAGAAATATCGAAAACCATAATTATAATGTAATA
1 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAATATCGAAAACCATAATTATAATGTAATA
*
1229407 GGTAAATTAGAAATATAACCGGTCTAAATATACTGGTTT
66 GGTAAATTAGAAATATAACCGGTCTAAATATACCGGTTT
1229446 AAATTGAAAA
Statistics
Matches: 655, Mismatches: 43, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
597 182 0.28
598 473 0.72
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.27
Consensus pattern (597 bp):
GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAATATCGAAAACCATAATTATAATGTAATA
GGTAAATTAGAAATATAACCGGTCTAAATATACCGGTTTTTAGAAAACAGGTGTAAAAAAAATAT
CGACACAAATAGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAAACAAGTACCCTAA
AAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAAACATAATTATAATGTA
ATAGGTAAATTAGCAATATAACCGGTCTAAATATACCGATTTTTGAGAAAACAGGTGTAAAAAAA
GTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAAACAAGTGCA
CTAAAAAGTGTCGATACATTTGTAACAAGTATCGATCCCAAAAACATCGAAAAACATAATTATAA
TGTAATAGGTAAATTATGCATATAAACAGTCTAAATATACCGGTTTTTGATAAAAACAGGTGTAC
AAAAAGTATCGACACAAATAGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAAACAA
GTACACTAAAAA
Found at i:1229816 original size:15 final size:15
Alignment explanation
Indices: 1229796--1229853 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
1229786 TTTCTTAAAT
1229796 CTCTTCTCAACCCAC
1 CTCTTCTCAACCCAC
* *
1229811 CTCTTCCCAACCCAG
1 CTCTTCTCAACCCAC
1229826 CTCTTCTCAACCACAAC
1 CTCTTCTCAACC-C-AC
1229843 CTCCTTCTCAA
1 CT-CTTCTCAA
1229854 ACAATCGCCC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 24 0.67
16 1 0.03
17 3 0.08
18 8 0.22
ACGTcount: A:0.22, C:0.50, G:0.02, T:0.26
Consensus pattern (15 bp):
CTCTTCTCAACCCAC
Found at i:1232743 original size:300 final size:300
Alignment explanation
Indices: 1232195--1232786 Score: 1085
Period size: 300 Copynumber: 2.0 Consensus size: 300
1232185 TCCTAAATCA
* *
1232195 AAATTTCATCCATCCTAAAAACAACTTACTCAATGGATGCATCGGGAGAAAACATCAAATTACAT
1 AAATTCCATCCATCCTAAAAACAACTTACTCAATGGATGCATCGAGAGAAAACATCAAATTACAT
1232260 TTCTAAGGTAACAACATACCTTTTTCAAATATCAACATTAGTGATAATGCGCATAATGAATTTGT
66 TTCTAAGGTAACAACATACCTTTTTCAAATATCAACATTAGTGATAATGCGCATAATGAATTTGT
1232325 ACATAATGTATTTCTAAGGTAACACTTACATTTTTCAAATATACGGGTTTTTGAGAAAACAAGTG
131 ACATAATGTATTTCTAAGGTAACACTTACATTTTTCAAATATACGGGTTTTTGAGAAAACAAGTG
* *
1232390 TACAAAATGTATCGACACAAATAAAACAAGTGTCGATCTCGAAAACATCGAAAAACATAATTATA
196 TACAAAATGTATCGACAAAAATAAAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATA
1232455 ATGTAATAGGTAAATTATTCATGTAAAAGGTCCGAAACCG
261 ATGTAATAGGTAAATTATTCATGTAAAAGGTCCGAAACCG
*
1232495 AAATTCCATCCATCCTAAAAACAACTTACTCAATGGATGCATCGAGAGAAAACATCAAATTCCAT
1 AAATTCCATCCATCCTAAAAACAACTTACTCAATGGATGCATCGAGAGAAAACATCAAATTACAT
* *
1232560 TTCTAAGGTAACAACTTACCTTTTTCAAATATCAACATTAGTGATAATGTGCATAATGAATTTGT
66 TTCTAAGGTAACAACATACCTTTTTCAAATATCAACATTAGTGATAATGCGCATAATGAATTTGT
* *
1232625 CCATAATGTATTTCTAAGGTAACACTTACCTTTTTCAAATATACGGGTTTTTGAGAAAACAAGTG
131 ACATAATGTATTTCTAAGGTAACACTTACATTTTTCAAATATACGGGTTTTTGAGAAAACAAGTG
1232690 TACAAAATGTATCGACAAAAATAAAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATA
196 TACAAAATGTATCGACAAAAATAAAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATA
* *
1232755 ATGTAATAGGTAAATTGTTCATGTAAACGGTC
261 ATGTAATAGGTAAATTATTCATGTAAAAGGTC
1232787 TAAATGTACC
Statistics
Matches: 281, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
300 281 1.00
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.29
Consensus pattern (300 bp):
AAATTCCATCCATCCTAAAAACAACTTACTCAATGGATGCATCGAGAGAAAACATCAAATTACAT
TTCTAAGGTAACAACATACCTTTTTCAAATATCAACATTAGTGATAATGCGCATAATGAATTTGT
ACATAATGTATTTCTAAGGTAACACTTACATTTTTCAAATATACGGGTTTTTGAGAAAACAAGTG
TACAAAATGTATCGACAAAAATAAAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATA
ATGTAATAGGTAAATTATTCATGTAAAAGGTCCGAAACCG
Found at i:1233054 original size:199 final size:200
Alignment explanation
Indices: 1232714--1233614 Score: 1406
Period size: 199 Copynumber: 4.5 Consensus size: 200
1232704 ACAAAAATAA
* *
1232714 AACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATT-GTTC-AT
1 AACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAG--CAAT
* * * * * *
1232777 GTAAACGGTCTAAATGTACCGATTTTTGAGAAAACATGTGTA-AAAAAAGTATCGACACAAATCA
64 ATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAACAAGTATCGACACAAAT-A
* *
1232841 -AACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGAT
128 GAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAAACAAGTGCACTAAAAAGTGTCGAT
*
1232905 ACATTTAT
193 ACATTTGT
*
1232913 AACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATAGGTAAATTAGCAATAT
1 AACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAGCAATAT
**
1232978 AACCGGTCTAAATATACCAATTTTTGAGAAAACAGGTGTACAAACAA-TATCGACACAAATAGAA
66 AACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAACAAGTATCGACACAAATAGAA
* *
1233042 CAAGTGTCGATACTTTTTTGTCCAGAATGTATTTCAAAAACAAGTGCCCT-AAAAGTGTCGATAC
131 CAAGTGTCGATAC-TTTTGGTCCAGAATGTATTTCAAAAACAAGTGCACTAAAAAGTGTCGATAC
1233106 ATTTGT
195 ATTTGT
*
1233112 AACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAGAAATAT
1 AACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAGCAATAT
* *
1233177 AACCGGTCTAAATATATCGGTTTTTGAGAAAACAGGTGTACAAAC-AGTATCAACACAAATAGAA
66 AACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAACAAGTATCGACACAAATAGAA
* * *
1233241 CAAGTGTCGATATTTTTGGTCCAGAATGTATTTCAGAACCAAGTGCACTAAAAAGTGTCGATACA
131 CAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAAACAAGTGCACTAAAAAGTGTCGATACA
1233306 TTTGT
196 TTTGT
* * *
1233311 AACAAGTGTCGATCCTAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTATTC-ATG
1 AACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTA-GCAATA
* *
1233375 TAAACGGTCTAAATATACCGGTTTTTGATAAAACAGGTGTACAAA-AAGTATCGACACAAATAGA
65 TAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAACAAGTATCGACACAAATAGA
* *
1233439 ACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAAACAAGTGCCCTAAAAAGTGTCGATAC
130 ACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAAACAAGTGCACTAAAAAGTGTCGATAC
1233504 ATTTGT
195 ATTTGT
*
1233510 AACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAACAATAT
1 AACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAGCAATAT
* *
1233575 AACCGGTCTAAATGTACCGGTTTTTGAGAAAACATGTGTA
66 AACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTA
1233615 ACACCCCCAA
Statistics
Matches: 647, Mismatches: 45, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
198 36 0.06
199 573 0.89
200 38 0.06
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.28
Consensus pattern (200 bp):
AACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAGCAATAT
AACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAACAAGTATCGACACAAATAGAA
CAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAAACAAGTGCACTAAAAAGTGTCGATACA
TTTGT
Found at i:1234210 original size:22 final size:22
Alignment explanation
Indices: 1234193--1234259 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
1234183 CTCGTATAAA
1234193 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1234215 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1234237 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1234259 T
1 T
1234260 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1234518 original size:30 final size:31
Alignment explanation
Indices: 1234477--1234536 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
1234467 TAGACATAGT
*
1234477 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
1234507 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
1234537 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:1234593 original size:29 final size:29
Alignment explanation
Indices: 1234551--1234622 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
1234541 TTTTCTGCAT
**
1234551 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
1234580 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
1234609 ATTCATGTCATGTA
1 ATTCATGTCATGTA
1234623 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:1235075 original size:67 final size:69
Alignment explanation
Indices: 1234925--1235077 Score: 213
Period size: 68 Copynumber: 2.2 Consensus size: 69
1234915 TTTTTCTCAT
* * *
1234925 GGGGGAATCGGTTCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACG
1 GGGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACG
1234990 ATGA
66 ATGA
* * * *
1234994 GGGGGTATCGGTTCCCCCCC-TGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTC-
1 GGGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACG
1235056 ATTGA
66 A-TGA
1235061 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
1235078 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
66 1 0.01
67 22 0.29
68 34 0.45
69 19 0.25
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (69 bp):
GGGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACG
ATGA
Found at i:1235089 original size:67 final size:67
Alignment explanation
Indices: 1234925--1235099 Score: 194
Period size: 67 Copynumber: 2.6 Consensus size: 67
1234915 TTTTTCTCAT
* * * *
1234925 GGGGGAATCGGTTCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACG
1 GGGGGTATCGGTT-CCCCCC-TGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACG
1234990 ATGA
64 ATGA
* * *
1234994 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTC-A
1 GGGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
1235057 TTGA
65 -TGA
* *
1235061 GGGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
1235100 AACCCAGAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
65 6 0.06
66 1 0.01
67 34 0.36
68 34 0.36
69 19 0.20
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:1241148 original size:22 final size:22
Alignment explanation
Indices: 1241123--1241173 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1241113 CACCACAGCT
*
1241123 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
1241145 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1241167 CGTAGAA
1 CGTAGAA
1241174 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:1241174 original size:22 final size:22
Alignment explanation
Indices: 1241131--1241175 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1241121 CTCGTATAAA
1241131 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1241153 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1241175 T
1 T
1241176 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1241436 original size:30 final size:31
Alignment explanation
Indices: 1241395--1241454 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
1241385 TAGACATAGT
*
1241395 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
1241425 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
1241455 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:1241528 original size:29 final size:29
Alignment explanation
Indices: 1241469--1241539 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
1241459 TTTTCTGCAT
**
1241469 ATTCATGTCATGT-ATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
1241497 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
1241526 ATTCATGTCATGTA
1 ATTCATGTCATGTA
1241540 TCATAATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 13 0.33
29 26 0.67
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:1241992 original size:67 final size:69
Alignment explanation
Indices: 1241842--1241993 Score: 211
Period size: 68 Copynumber: 2.2 Consensus size: 69
1241832 TTTTTCTCAT
* * *
1241842 GGGGGAATCGGTTCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACG
1 GGGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACG
1241907 ATGA
66 ATGA
* * * *
1241911 GGGGGTATCGGTTCCCCCCC-TGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTC-
1 GGGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACG
1241973 ATTGA
66 A-TGA
1241978 GGGGGTATCGGTTCCC
1 GGGGGTATCGGTTCCC
1241994 TTTGAATGGG
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
66 1 0.01
67 21 0.28
68 34 0.45
69 19 0.25
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (69 bp):
GGGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACG
ATGA
Found at i:1246012 original size:182 final size:182
Alignment explanation
Indices: 1245690--1246139 Score: 711
Period size: 182 Copynumber: 2.5 Consensus size: 182
1245680 GTTGATAGTT
* * * * *
1245690 TCGATACTTTATAAAAATCTATCAATCCATAACAATAAAACAGGTAAAAAAATGACAAAACCGGC
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGT
** * * * *
1245755 CTATAAATGACAAAACAGGTAAAGCGCTATCGGATATGTTGATAGTGTCGATACTTTATTATACG
66 CTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATTATAAG
* * *
1245820 TATCGACACTTTTGGAATTTAAAAGAGAATAAGTTATAGCGCTAATAAAGTG
131 TATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAGTG
*
1245872 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAACCGGT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGT
* *
1245937 CTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTTGATACTTTATTGTAAG
66 CTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATTATAAG
* *
1246002 TATTGACACTTTTGGAATTTAAAAGAAAAGATGTTATAGCGCCAATAAAGTG
131 TATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAGTG
* *
1246054 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGAT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGT
1246119 CTCGAAATGACAAAACCGGTA
66 CTCGAAATGACAAAACCGGTA
1246140 GTAAAAAAGT
Statistics
Matches: 246, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
182 246 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGT
CTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATTATAAG
TATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAGTG
Found at i:1246788 original size:23 final size:23
Alignment explanation
Indices: 1246759--1246806 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1246749 AAATAGGTCA
*
1246759 ATATAAGCGCTACCTATTATATT
1 ATATAAGCGCTACCTAATATATT
* * *
1246782 ATATAAGTGTTATCTAATATATT
1 ATATAAGCGCTACCTAATATATT
1246805 AT
1 AT
1246807 TGTACTTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATATATT
Found at i:1251899 original size:127 final size:130
Alignment explanation
Indices: 1251670--1251921 Score: 429
Period size: 127 Copynumber: 2.0 Consensus size: 130
1251660 TCTGTCTTGT
1251670 GTCTCATAGTGTTTAAAATTCCATGTTTTCATGTAAAAATTGTTGGCCAAATGTGTCTGTGTTTT
1 GTCTCATAGTGTTTAAAATTCCATGTTTTCATGTAAAAATTGTTGGCCAAATGTGTCTGTGTTTT
* *
1251735 GTGTAAAAGATGTGGGTTTTATTGTGGTATTTTAGCTGTGCTTGTGTTCGAGTAATAAATATGGA
66 GTGTAAAAGATGTGGGTTTTATTGTGGTATTATAGCTGTGCCTGTGTTCGAGTAATAAATATGGA
* * *
1251800 GTCTCATAGTTTTTAAAATTCCATGTTTTCCTGT-AAAATTGTTGGTCAAATGT-T-TGTGTTTT
1 GTCTCATAGTGTTTAAAATTCCATGTTTTCATGTAAAAATTGTTGGCCAAATGTGTCTGTGTTTT
*
1251862 GTGTAAAAGATGTGGGTTTTATTGTGGTATTATAGCTGTGCCTGTGTTTGAGTAATAAAT
66 GTGTAAAAGATGTGGGTTTTATTGTGGTATTATAGCTGTGCCTGTGTTCGAGTAATAAAT
1251922 TTGATGGCTT
Statistics
Matches: 116, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
127 65 0.56
128 1 0.01
129 18 0.16
130 32 0.28
ACGTcount: A:0.24, C:0.08, G:0.23, T:0.44
Consensus pattern (130 bp):
GTCTCATAGTGTTTAAAATTCCATGTTTTCATGTAAAAATTGTTGGCCAAATGTGTCTGTGTTTT
GTGTAAAAGATGTGGGTTTTATTGTGGTATTATAGCTGTGCCTGTGTTCGAGTAATAAATATGGA
Found at i:1252705 original size:2 final size:2
Alignment explanation
Indices: 1252700--1252731 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1252690 ATACCATTGT
1252700 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1252732 GATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.